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1. Loss of function mutations in GEMIN5 cause a neurodevelopmental disorder

Author

Sukhleen Kour, Deepa S. Rajan, Tyler R. Fortuna, Eric N. Anderson, Caroline Ward, Youngha Lee, Sangmoon Lee, Yong Beom Shin, Jong-Hee Chae, Murim Choi, Karine Siquier, Vincent Cantagrel, Jeanne Amiel, Elliot S. Stolerman, Sarah S. Barnett, Margot A. Cousin, Diana Castro, Kimberly McDonald, Brian Kirmse, Andrea H. Nemeth, Dhivyaa Rajasundaram, A. Micheil Innes, Danielle Lynch, Patrick Frosk, Abigail Collins, Melissa Gibbons, Michele Yang, Isabelle Desguerre, Nathalie Boddaert, Cyril Gitiaux, Siri Lynne Rydning, Kaja K. Selmer, Roser Urreizti, Alberto Garcia-Oguiza, Andrés Nascimento Osorio, Edgard Verdura, Aurora Pujol, Hannah R. McCurry, John E. Landers, Sameer Agnihotri, E. Corina Andriescu, Shade B. Moody, Chanika Phornphutkul, Maria J. Guillen Sacoto, Amber Begtrup, Henry Houlden, Janbernd Kirschner, David Schorling, Sabine Rudnik-Schöneborn, Tim M. Strom, Steffen Leiz, Kali Juliette, Randal Richardson, Ying Yang, Yuehua Zhang, Minghui Wang, Jia Wang, Xiaodong Wang, Konrad Platzer, Sandra Donkervoort, Carsten G. Bönnemann, Matias Wagner, Mahmoud Y. Issa, Hasnaa M. Elbendary, Valentina Stanley, Reza Maroofian, Joseph G. Gleeson, Maha S. Zaki, Jan Senderek, and Udai Bhan Pandey

Subjects
Science
Abstract

GEMIN5, an RNA-binding protein, is required for formation of small nuclear ribonucleoproteins. Here, the authors identify loss of function mutations in GEMIN5 that are associated with a human neurodevelopmental disorder.

Published
2021
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2. Loss-of-function mutations in UDP-Glucose 6-Dehydrogenase cause recessive developmental epileptic encephalopathy

Author

Holger Hengel, Célia Bosso-Lefèvre, George Grady, Emmanuelle Szenker-Ravi, Hankun Li, Sarah Pierce, Élise Lebigot, Thong-Teck Tan, Michelle Y. Eio, Gunaseelan Narayanan, Kagistia Hana Utami, Monica Yau, Nader Handal, Werner Deigendesch, Reinhard Keimer, Hiyam M. Marzouqa, Meral Gunay-Aygun, Michael J. Muriello, Helene Verhelst, Sarah Weckhuysen, Sonal Mahida, Sakkubai Naidu, Terrence G. Thomas, Jiin Ying Lim, Ee Shien Tan, Damien Haye, Michèl A. A. P. Willemsen, Renske Oegema, Wendy G. Mitchell, Tyler Mark Pierson, Marisa V. Andrews, Marcia C. Willing, Lance H. Rodan, Tahsin Stefan Barakat, Marjon van Slegtenhorst, Ralitza H. Gavrilova, Diego Martinelli, Tal Gilboa, Abdullah M. Tamim, Mais O. Hashem, Moeenaldeen D. AlSayed, Maha M. Abdulrahim, Mohammed Al-Owain, Ali Awaji, Adel A. H. Mahmoud, Eissa A. Faqeih, Ali Al Asmari, Sulwan M. Algain, Lamyaa A. Jad, Hesham M. Aldhalaan, Ingo Helbig, David A. Koolen, Angelika Riess, Ingeborg Kraegeloh-Mann, Peter Bauer, Suleyman Gulsuner, Hannah Stamberger, Alvin Yu Jin Ng, Sha Tang, Sumanty Tohari, Boris Keren, Laura E. Schultz-Rogers, Eric W. Klee, Sabina Barresi, Marco Tartaglia, Hagar Mor-Shaked, Sateesh Maddirevula, Amber Begtrup, Aida Telegrafi, Rolph Pfundt, Rebecca Schüle, Brian Ciruna, Carine Bonnard, Mahmoud A. Pouladi, James C. Stewart, Adam Claridge-Chang, Dirk J. Lefeber, Fowzan S. Alkuraya, Ajay S. Mathuru, Byrappa Venkatesh, Joseph J. Barycki, Melanie A. Simpson, Saumya S. Jamuar, Ludger Schöls, and Bruno Reversade

Subjects
Science
Abstract

UDP-glucuronic acid is a component of the extracellular matrix. Here, the authors report biallelic variants in the gene encoding UDP-Glucose 6-Dehydrogenase (UGDH) in individuals affected by developmental epileptic encephalopathies that impair UGDH stability, oligomerization, or enzymatic activity in vitro.

Published
2020
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3. Deep-Phenotyping the Less Severe Spectrum of PIGT Deficiency and Linking the Gene to Myoclonic Atonic Seizures

Author

Allan Bayat, Manuela Pendziwiat, Ewa Obersztyn, Paula Goldenberg, Pia Zacher, Jan Henje Döring, Steffen Syrbe, Amber Begtrup, Artem Borovikov, Artem Sharkov, Aneta Karasińska, Maria Giżewska, Wendy Mitchell, Eva Morava, Rikke S. Møller, and Guido Rubboli

Subjects
myoclonic-atonic seizures, generalized seizures, disease severity, developmental delay, glycosylphosphatidylinositol biosynthesis defects, inherited glycosylphosphatidylinositol-anchored protein (GPI-AP) deficiency, Genetics, QH426-470
Abstract

The two aims of this study were (i) to describe and expand the phenotypic spectrum of PIGT deficiency in affected individuals harboring the c.1582G>A; p.Val528Met or the c.1580A > G; p.Asn527Ser variant in either homozygous or compound heterozygous state, and (ii) to identify potential genotype-phenotype correlations and any differences in disease severity among individuals with and without the PIGT variants. The existing literature was searched to identify individuals with and without the two variants. A detailed phenotypic assessment was performed of 25 individuals (both novel and previously published) with the two PIGT variants. We compared severity of disease between individuals with and without these PIGT variants. Twenty-four individuals carried the PIGT variant Val528Met in either homozygous or compound heterozygous state, and one individual displayed the Asn527Ser variant in a compound heterozygous state. Disease severity in the individual with the Asn527Ser variant was compatible with that in the individuals harboring the Val528Met variant. While individuals without the Asn527Ser or Val528Met variant had focal epilepsy, profound developmental delay (DD), and risk of premature death, those with either of the two variants had moderate to severe DD and later onset of epilepsy with both focal and generalized seizures. Individuals homozygous for the Val528Met variant generally became seizure-free on monotherapy with antiepileptic drugs, compared to other PIGT individuals who were pharmaco-resistant. Two patients were diagnosed with myoclonic-atonic seizures, and a single patient was diagnosed with eyelid myoclonia. Our comprehensive analysis of this large cohort of previously published and novel individuals with PIGT variants broadens the phenotypical spectrum and shows that both Asn527Ser and Val528Met are associated with a milder phenotype and less severe outcome. Our data show that PIGT is a new candidate gene for myoclonic atonic epilepsy. Our genotype-phenotype correlation will be useful for future genetic counseling. Natural history studies of this mild spectrum of PIGT-related disorder may shed light on hitherto unknown aspects of this rare disorder.

Published
2021
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4. Activating de novo mutations in NFE2L2 encoding NRF2 cause a multisystem disorder

Author

Peter Huppke, Susann Weissbach, Joseph A. Church, Rhonda Schnur, Martina Krusen, Steffi Dreha-Kulaczewski, W. Nikolaus Kühn-Velten, Annika Wolf, Brenda Huppke, Francisca Millan, Amber Begtrup, Fatima Almusafri, Holger Thiele, Janine Altmüller, Peter Nürnberg, Michael Müller, and Jutta Gärtner

Subjects
Science
Abstract

The NRF2 transcription factor regulates the response to stress in mammalian cells. Here, the authors show that activating mutations in NRF2, commonly found in cancer cells, are found in four patients with a multisystem disorder characterized by immunodeficiency and neurological symptoms.

Published
2017
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5. Genetic and phenotypic spectrum in the <scp> NONO </scp> ‐associated syndromic disorder

Author

Franziska Roessler, Anita E. Beck, Ball Susie, Bartolomaeus Tobias, Amber Begtrup, Saskia Biskup, Oana Caluseriu, Norman Delanty, Christine Fröhlich, Marie T. Greally, Maike Karnstedt, Chiara Klöckner, Joanne Kurtzberg, Susanna Schubert, Martin Schulze, Michael Weidenbach, Dominik S. Westphal, Maire White, Cordula M. Wolf, Jacob Zyskind, Bernt Popp, and Vincent Strehlow

Subjects
Genetics, Genetics (clinical)
Abstract

The non-POU domain-containing octamer-binding (NONO) protein is involved in multiple steps of gene regulation such as RNA metabolism and DNA repair. Hemizygous pathogenic variants in the NONO gene were confirmed to cause a rare X-linked syndromic disorder. Through our in-house diagnostics and subsequent matchmaking, we identified six unrelated male individuals with pathogenic or likely pathogenic NONO variants. For a detailed comparison, we reviewed all published characterizations of the NONO-associated disorder. The combined cohort consists of 16 live-born males showing developmental delay, corpus callosum anomalies, non-compaction cardiomyopathy and relative macrocephaly as leading symptoms. Seven prenatal literature cases were characterized by cardiac malformations. In this study, we extend the phenotypic spectrum through two more cases with epilepsy as well as two more cases with hematologic anomalies. By RNA expression analysis and structural modeling of a new in-frame splice deletion, we reinforce loss-of-function as the pathomechanism for the NONO-associated syndromic disorder.

Published
2022

6. Heterozygous variants in PRPF8 are associated with neurodevelopmental disorders

Author

Lauren O'Grady, Samantha A. Schrier Vergano, Trevor L. Hoffman, Dean Sarco, Sara Cherny, Emily Bryant, Laura Schultz‐Rogers, Wendy K. Chung, Stephanie Sacharow, Ladonna L. Immken, Susan Holder, Rebecca R. Blackwell, Catherine Buchanan, Roman Yusupov, François Lecoquierre, Anne‐Marie Guerrot, Lance Rodan, Bert B. A. de Vries, Erik Jan Kamsteeg, Fernando Santos Simarro, Maria Palomares‐Bralo, Natasha Brown, Lynn Pais, Alejandro Ferrer, Eric W. Klee, Dusica Babovic‐Vuksanovic, Lindsay Rhodes, Richard Person, Amber Begtrup, Jennifer Keller‐Ramey, Teresa Santiago‐Sim, Rhonda E. Schnur, David A. Sweetser, and Nina B. Gold

Subjects
Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], Genetics, Sensory disorders Donders Center for Medical Neuroscience [Radboudumc 12], Genetics (clinical)
Abstract

Contains fulltext : 282684.pdf (Publisher’s version ) (Closed access) The pre-mRNA-processing factor 8, encoded by PRPF8, is a scaffolding component of a spliceosome complex involved in the removal of introns from mRNA precursors. Previously, heterozygous pathogenic variants in PRPF8 have been associated with autosomal dominant retinitis pigmentosa. More recently, PRPF8 was suggested as a candidate gene for autism spectrum disorder due to the enrichment of sequence variants in this gene in individuals with neurodevelopmental disorders. We report 14 individuals with various forms of neurodevelopmental conditions, found to have heterozygous, predominantly de novo, missense, and loss-of-function variants in PRPF8. These individuals have clinical features that may represent a new neurodevelopmental syndrome.

Published
2022

7. Heterozygous variants in CTR9, which encodes a major component of the PAF1 complex, are associated with a neurodevelopmental disorder

Author

Marije Meuwissen, Aline Verstraeten, Emmanuelle Ranza, Justyna Iwaszkiewicz, Maaike Bastiaansen, Ligia Mateiu, Merlijn Nemegeer, Josephina A.N. Meester, Alexandra Afenjar, Michelle Amaral, Diana Ballhausen, Sarah Barnett, Magalie Barth, Bob Asselbergh, Katrien Spaas, Bavo Heeman, Jennifer Bassetti, Patrick Blackburn, Marie Schaer, Xavier Blanc, Vincent Zoete, Kari Casas, Thomas Courtin, Diane Doummar, Frédéric Guerry, Boris Keren, John Pappas, Rachel Rabin, Amber Begtrup, Marwan Shinawi, Anneke T. Vulto-van Silfhout, Tjitske Kleefstra, Matias Wagner, Alban Ziegler, Elise Schaefer, Benedicte Gerard, Charlotte I. De Bie, Sjoerd J.B. Holwerda, Mary Alice Abbot, Stylianos E. Antonarakis, and Bart Loeys

Subjects
Heterozygote, All institutes and research themes of the Radboud University Medical Center, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], Gene Expression Regulation, Autism Spectrum Disorder, Neurodevelopmental Disorders, Intellectual Disability, Humans, Human medicine, Phosphoproteins, Genetics (clinical), Transcription Factors
Abstract

PURPOSE CTR9 is a subunit of the PAF1 complex (PAF1C) that plays a crucial role in transcription regulation by binding CTR9 to RNA polymerase II. It is involved in transcription-coupled histone modification through promoting H3K4 and H3K36 methylation. We describe the clinical and molecular studies in 13 probands, harboring likely pathogenic CTR9 missense variants, collected through GeneMatcher. METHODS Exome sequencing was performed in all individuals. CTR9 variants were assessed through 3-dimensional modeling of the activated human transcription complex Pol II-DSIF-PAF-SPT6 and the PAF1/CTR9 complex. H3K4/H3K36 methylation analysis, mitophagy assessment based on tetramethylrhodamine ethyl ester perchlorate immunofluorescence, and RNA-sequencing in skin fibroblasts from 4 patients was performed. RESULTS Common clinical findings were variable degrees of intellectual disability, hypotonia, joint hyperlaxity, speech delay, coordination problems, tremor, and autism spectrum disorder. Mild dysmorphism and cardiac anomalies were less frequent. For 11 CTR9 variants, de novo occurrence was shown. Three-dimensional modeling predicted a likely disruptive effect of the variants on local CTR9 structure and protein interaction. Additional studies in fibroblasts did not unveil the downstream functional consequences of the identified variants. CONCLUSION We describe a neurodevelopmental disorder caused by (mainly) de novo variants in CTR9, likely affecting PAF1C function.

Published
2022

8. Gain-of-function mutations in KCNK3 cause a developmental disorder with sleep apnea

Author

Janina Sörmann, Marcus Schewe, Peter Proks, Thibault Jouen-Tachoire, Shanlin Rao, Elena B. Riel, Katherine E. Agre, Amber Begtrup, John Dean, Maria Descartes, Jan Fischer, Alice Gardham, Carrie Lahner, Paul R. Mark, Srikanth Muppidi, Pavel N. Pichurin, Joseph Porrmann, Jens Schallner, Kirstin Smith, Volker Straub, Pradeep Vasudevan, Rebecca Willaert, Elisabeth P. Carpenter, Karin E. J. Rödström, Michael G. Hahn, Thomas Müller, Thomas Baukrowitz, Matthew E. Hurles, Caroline F. Wright, and Stephen J. Tucker

Subjects
Genetics
Abstract

Sleep apnea is a common disorder that represents a global public health burden. KCNK3 encodes TASK-1, a K+ channel implicated in the control of breathing, but its link with sleep apnea remains poorly understood. Here we describe a new developmental disorder with associated sleep apnea (developmental delay with sleep apnea, or DDSA) caused by rare de novo gain-of-function mutations in KCNK3. The mutations cluster around the ‘X-gate’, a gating motif that controls channel opening, and produce overactive channels that no longer respond to inhibition by G-protein-coupled receptor pathways. However, despite their defective X-gating, these mutant channels can still be inhibited by a range of known TASK channel inhibitors. These results not only highlight an important new role for TASK-1 K+ channels and their link with sleep apnea but also identify possible therapeutic strategies.

Published
2023

9. Rare EIF4A2 variants are associated with a neurodevelopmental disorder characterized by intellectual disability, hypotonia, and epilepsy

Author

Maimuna S. Paul, Anna R. Duncan, Casie A. Genetti, Hongling Pan, Adam Jackson, Patricia E. Grant, Jiahai Shi, Michele Pinelli, Nicola Brunetti-Pierri, Alexandra Garza-Flores, Dave Shahani, Russell P. Saneto, Giuseppe Zampino, Chiara Leoni, Emanuele Agolini, Antonio Novelli, Ulrike Blümlein, Tobias B. Haack, Wolfram Heinritz, Eva Matzker, Bader Alhaddad, Rami Abou Jamra, Tobias Bartolomaeus, Saber AlHamdan, Raphael Carapito, Bertrand Isidor, Seiamak Bahram, Alyssa Ritter, Kosuke Izumi, Ben Pode Shakked, Ortal Barel, Bruria Ben Zeev, Amber Begtrup, Deanna Alexis Carere, Sureni V. Mullegama, Timothy Blake Palculict, Daniel G. Calame, Katharina Schwan, Alicia R.P. Aycinena, Rasa Traberg, Sofia Douzgou, Harrison Pirt, Naila Ismayilova, Siddharth Banka, Hsiao-Tuan Chao, Pankaj B. Agrawal, Paul, Maimuna S, Duncan, Anna R, Genetti, Casie A, Pan, Hongling, Jackson, Adam, Grant, Patricia E, Shi, Jiahai, Pinelli, Michele, Brunetti-Pierri, Nicola, Garza-Flores, Alexandra, Shahani, Dave, Saneto, Russell P, Zampino, Giuseppe, Leoni, Chiara, Agolini, Emanuele, Novelli, Antonio, Blümlein, Ulrike, Haack, Tobias B, Heinritz, Wolfram, Matzker, Eva, Alhaddad, Bader, Abou Jamra, Rami, Bartolomaeus, Tobia, Alhamdan, Saber, Carapito, Raphael, Isidor, Bertrand, Bahram, Seiamak, Ritter, Alyssa, Izumi, Kosuke, Shakked, Ben Pode, Barel, Ortal, Ben Zeev, Bruria, Begtrup, Amber, Carere, Deanna Alexi, Mullegama, Sureni V, Palculict, Timothy Blake, Calame, Daniel G, Schwan, Katharina, Aycinena, Alicia R P, Traberg, Rasa, Douzgou, Sofia, Pirt, Harrison, Ismayilova, Naila, Banka, Siddharth, Chao, Hsiao-Tuan, and Agrawal, Pankaj B

Subjects
Genetics, epilepsy, Drosophila, DEAD-box protein, neurodevelopmental disorder, Genetics (clinical), Article, transcription factor
Abstract

Eukaryotic initiation factor-4A2 (EIF4A2) is an ATP-dependent RNA helicase and a member of the DEAD-box protein family that recognizes the 5' cap structure of mRNAs, allows mRNA to bind to the ribosome, and plays an important role in microRNA-regulated gene repression. Here, we report on 15 individuals from 14 families presenting with global developmental delay, intellectual disability, hypotonia, epilepsy, and structural brain anomalies, all of whom have extremely rare de novo mono-allelic or inherited bi-allelic variants in EIF4A2. Neurodegeneration was predominantly reported in individuals with bi-allelic variants. Molecular modeling predicts these variants would perturb structural interactions in key protein domains. To determine the pathogenicity of the EIF4A2 variants in vivo, we examined the mono-allelic variants in Drosophila melanogaster (fruit fly) and identified variant-specific behavioral and developmental defects. The fruit fly homolog of EIF4A2 is eIF4A, a negative regulator of decapentaplegic (dpp) signaling that regulates embryo patterning, eye and wing morphogenesis, and stem cell identity determination. Our loss-of-function (LOF) rescue assay demonstrated a pupal lethality phenotype induced by loss of eIF4A, which was fully rescued with human EIF4A2 wild-type (WT) cDNA expression. In comparison, the EIF4A2 variant cDNAs failed or incompletely rescued the lethality. Overall, our findings reveal that EIF4A2 variants cause a genetic neurodevelopmental syndrome with both LOF and gain of function as underlying mechanisms.

Published
2023

10. Biallelic PRMT7 pathogenic variants are associated with a recognizable syndromic neurodevelopmental disorder with short stature, obesity, and craniofacial and digital abnormalities

Author

Elisa Cali, Mohnish Suri, Marcello Scala, Matteo P. Ferla, Shahryar Alavi, Eissa Ali Faqeih, Emilia K. Bijlsma, Kristen M. Wigby, Diana Baralle, Mohammad Y.V. Mehrjardi, Jennifer Schwab, Konrad Platzer, Katharina Steindl, Mais Hashem, Marilyn Jones, Dmitriy M. Niyazov, Jennifer Jacober, Rebecca Okashah Littlejohn, Denisa Weis, Neda Zadeh, Lance Rodan, Alice Goldenberg, François Lecoquierre, Marina Dutra-Clarke, Gabriella Horvath, Dana Young, Naama Orenstein, Shahad Bawazeer, Anneke T. Vulto-van Silfhout, Yvan Herenger, Mohammadreza Dehghani, Seyed Mohammad Seyedhassani, Amir Bahreini, Mahya E. Nasab, A. Gulhan Ercan-Sencicek, Zahra Firoozfar, Mojtaba Movahedinia, Stephanie Efthymiou, Pasquale Striano, Ehsan Ghayoor Karimiani, Vincenzo Salpietro, Jenny C. Taylor, Melody Redman, Alexander P.A. Stegmann, Andreas Laner, Ghada Abdel-Salam, Megan Li, Mario Bengala, Amelie Johanna Müller, Maria C. Digilio, Anita Rauch, Murat Gunel, Hannah Titheradge, Daniela N. Schweitzer, Alison Kraus, Irene Valenzuela, Scott D. McLean, Chanika Phornphutkul, Mustafa Salih, Amber Begtrup, Rhonda E. Schnur, Erin Torti, Tobias B. Haack, Carlos E. Prada, Fowzan S. Alkuraya, Henry Houlden, Reza Maroofian, MUMC+: DA KG Lab Specialisten (9), RS: FHML non-thematic output, Institut Català de la Salut, [Cali E] Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom. [Suri M] Nottingham Clinical Genetics Service, Nottingham University Hospitals NHS Trust, City Hospital Campus, Nottingham, United Kingdom. [Scala M] Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, Genoa, Italy. Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy. [Ferla MP] Genomic Medicine theme, Oxford Biomedical Research Centre, NIHR, Oxford, Oxfordshire, United Kingdom. Wellcome Centre for Human Genetics, Oxford University, Oxford, Oxfordshire, United Kingdom. [Alavi S] Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom. Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran. Palindrome, Isfahan, Iran. [Faqeih EA] Section of Medical Genetics, Children’s Specialist Hospital, King Fahad Medical, City, Riyadh, Saudi Arabia. [Valenzuela I] Àrea de Genètica Clínica i Molecular, Vall d'Hebron Hospital Universitari, Barcelona, Spain. Grup de Recerca de Medicina Genètica, Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain, and Vall d'Hebron Barcelona Hospital Campus

Subjects
Neurobiologia del desenvolupament, Discapacitat intel·lectual - Aspectes genètics, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], Otros calificadores::Otros calificadores::/genética [Otros calificadores], enfermedades y anomalías neonatales congénitas y hereditarias::enfermedades genéticas congénitas::enanismo [ENFERMEDADES], trastornos mentales::trastornos del desarrollo neurológico [PSIQUIATRÍA Y PSICOLOGÍA], Nanisme, Nervous System Diseases::Neurologic Manifestations::Neurobehavioral Manifestations::Intellectual Disability [DISEASES], All institutes and research themes of the Radboud University Medical Center, Other subheadings::Other subheadings::/genetics [Other subheadings], Congenital, Hereditary, and Neonatal Diseases and Abnormalities::Genetic Diseases, Inborn::Dwarfism [DISEASES], enfermedades del sistema nervioso::manifestaciones neurológicas::manifestaciones neuroconductuales::discapacidad intelectual [ENFERMEDADES], Genetics (clinical), Mental Disorders::Neurodevelopmental Disorders [PSYCHIATRY AND PSYCHOLOGY]
Abstract

Chromatinopathy; Syndromic neurodevelopmental disorder; Syndromic obesity Cromatinopatia; Trastorn sindròmic del neurodesenvolupament; Obesitat sindròmica Cromatinopatía; Trastorno sindrómico del neurodesarrollo; Obesidad sindrómica Purpose Protein arginine methyltransferase 7 (PRMT7) is a member of a family of enzymes that catalyzes the methylation of arginine residues on several protein substrates. Biallelic pathogenic PRMT7 variants have previously been associated with a syndromic neurodevelopmental disorder characterized by short stature, brachydactyly, intellectual developmental disability, and seizures. To our knowledge, no comprehensive study describes the detailed clinical characteristics of this syndrome. Thus, we aim to delineate the phenotypic spectrum of PRMT7-related disorder. Methods We assembled a cohort of 51 affected individuals from 39 different families, gathering clinical information from 36 newly described affected individuals and reviewing data of 15 individuals from the literature. Results The main clinical characteristics of the PRMT7-related syndrome are short stature, mild to severe developmental delay/intellectual disability, hypotonia, brachydactyly, and distinct facial morphology, including bifrontal narrowing, prominent supraorbital ridges, sparse eyebrows, short nose with full/broad nasal tip, thin upper lip, full and everted lower lip, and a prominent or squared-off jaw. Additional variable findings include seizures, obesity, nonspecific magnetic resonance imaging abnormalities, eye abnormalities (i.e., strabismus or nystagmus), and hearing loss. Conclusion This study further delineates and expands the molecular, phenotypic spectrum and natural history of PRMT7-related syndrome characterized by a neurodevelopmental disorder with skeletal, growth, and endocrine abnormalities. The authors thank all patients and families for participation in this study. Part of this research was possible thanks to the Deciphering Developmental Disorders study. The Deciphering Developmental Disorders study presents independent research commissioned by the Health Innovation Challenge Fund (grant number HICF-1009-003). This study makes use of DECIPHER (http://www.deciphergenomics.org), which is funded by Wellcome. See www.ddduk.org/access.html for full acknowledgment. This study was also supported by the Wellcome Trust (WT093205MA and WT104033AIA to H.H. and 203141/Z/16/Z to M.P.F. and J.C.T.), Medical Research Council (H.H.), European Community’s Seventh Framework Programme (FP7/2007-2013, under grant agreement No. 2012-305121 to H.H.), the National Institute for Health Research (NIHR), University College London Hospitals, Biomedical Research Centre, and Fidelity Foundation. The Yale Center for Mendelian Genomics (UM1HG006504) is funded by the National Human Genome Research Institute. D.B. is supported by NIHR Research Professorship (RP-2016-07-011). F.L. and A.G. received funding from European Union and Région Normandie in the context of Recherche Innovation Normandie 2018. Europe gets involved in Normandie with the European Regional Development Fund. The authors thank the families and KFMC Research Centre for the partial support (Intramural Research Fund; Demography of Recessive Diseases in KSA; Grant No. 019-052). This work was also supported by King Salman Center for Disability research through Research Group RG-2022-010.

Published
2023

11. TNPO2 variants associate with human developmental delays, neurologic deficits, and dysmorphic features and alter TNPO2 activity in Drosophila

Author

David A. Koolen, Yue Si, Benjamin Cogné, Pamela Trapane, Eric W. Klee, Manju A. Kurian, Miel Theunis, Eva Morava, Shekeeb S. Mohammad, Oguz Kanca, Matthew J. Moulton, Paulien A Terhal, Peggy Kulch, Queenie K.-G. Tan, An-Chi Tien, Shenzhao Lu, Erica L. Macke, Hugo J. Bellen, Katy Barwick, Bryan E. Hainline, Russell C. Dale, Lindsey D. Goodman, Katherine Sapp, Hermine E. Veenstra-Knol, Eric Legius, Amber Begtrup, Dora Steel, D. Dutta, Victoria H. Klee, Christopher J. Spencer, Bethany Robinette, Ellen van Binsbergen, Michael F. Wangler, Laurence E. Walsh, Shinya Yamamoto, Thomas A. Ravenscroft, Brian Kirmse, Bertrand Isidor, Marijke R. Wevers, Zelha Nil, Heidi Cope, Theresa A. Grebe, Melissa Jones, Wu Lin Charng, Rolph Pfundt, Jolien S. Klein Wassink-Ruiter, and Charlotte A. Haaxma

Subjects
Male, Developmental Disabilities, Gene Dosage, DE-NOVO, medicine.disease_cause, NUCLEAR-IMPORT, Drosophila Proteins, Global developmental delay, RNA, Small Interfering, Genetics (clinical), Neurons, Genetics, Mutation, Gene Expression Regulation, Developmental, Eye Diseases, Hereditary, GAL4 SYSTEM, Disorders of movement Donders Center for Medical Neuroscience [Radboudumc 3], beta Karyopherins, Phenotype, Drosophila melanogaster, Essential gene, Female, Beta Karyopherins, Drosophila Protein, Rare cancers Radboud Institute for Health Sciences [Radboudumc 9], EXPRESSION, C-FOS, PROTEINS, Karyopherins, Biology, Article, All institutes and research themes of the Radboud University Medical Center, Intellectual Disability, medicine, Animals, Humans, Amino Acid Sequence, Alleles, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], COMPLEX, Sequence Homology, Amino Acid, Whole Genome Sequencing, Genome, Human, MUTATIONS, Infant, Newborn, Infant, biology.organism_classification, MUSHROOM BODY, TRANSPORTIN, Musculoskeletal Abnormalities, ran GTP-Binding Protein, Ectopic expression, Sequence Alignment
Abstract

Transportin-2 (TNPO2) mediates multiple pathways including non-classical nucleocytoplasmic shuttling of >60 cargoes, such as developmental and neuronal proteins. We identified 15 individuals carrying de novo coding variants in TNPO2 who presented with global developmental delay (GDD), dysmorphic features, ophthalmologic abnormalities, and neurological features. To assess the nature of these variants, functional studies were performed in Drosophila. We found that fly dTnpo (orthologous to TNPO2) is expressed in a subset of neurons. dTnpo is critical for neuronal maintenance and function as downregulating dTnpo in mature neurons using RNAi disrupts neuronal activity and survival. Altering the activity and expression of dTnpo using mutant alleles or RNAi causes developmental defects, including eye and wing deformities and lethality. These effects are dosage dependent as more severe phenotypes are associated with stronger dTnpo loss. Interestingly, similar phenotypes are observed with dTnpo upregulation and ectopic expression of TNPO2, showing that loss and gain of Transportin activity causes developmental defects. Further, proband-associated variants can cause more or less severe developmental abnormalities compared to wild-type TNPO2 when ectopically expressed. The impact of the variants tested seems to correlate with their position within the protein. Specifically, those that fall within the RAN binding domain cause more severe toxicity and those in the acidic loop are less toxic. Variants within the cargo binding domain show tissue-dependent effects. In summary, dTnpo is an essential gene in flies during development and in neurons. Further, proband-associated de novo variants within TNPO2 disrupt the function of the encoded protein. Hence, TNPO2 variants are causative for neurodevelopmental abnormalities.

Published
2021

13. A human importin-β-related disorder: Syndromic thoracic aortic aneurysm caused by bi-allelic loss-of-function variants in IPO8

Author

Abdulrahman Almesned, Dorien Schepers, Mehran Beiraghi Toosi, Zuhair N. Al-Hassnan, Jill A. Rosenfeld, Erin M. Miller, Hassan Mottaghi Moghaddam Shahri, Maaike Alaerts, Melanie Perik, Desiderio Rodrigues, Aline Verstraeten, Reza Maroofian, Silke Peeters, Cédric H. G. Neutel, Ilse Luyckx, Nicole Revencu, Jenny C. Taylor, Jarl Bastianen, Isabel Pintelon, Henry Houlden, Matteo P. Ferla, Erik Fransen, Kayal Vijayakumar, Lut Van Laer, Anthony R. Dallosso, Mandy Vermont, Isabelle Maystadt, Lotte Van Den Heuvel, Thierry Sluysmans, David Murphy, K. Nicole Weaver, Paria Najarzadeh Torbati, Jotte Rodrigues Bento, Amber Begtrup, Maggie Williams, Ilse Van Gucht, Maaike Bastiaansen, Ashish Chikermane, Gangadhara Bharmappanavara, Alistair T. Pagnamenta, Bart Loeys, Joe Davis Velchev, Julie Evans, Josephina A.N. Meester, Narges Hashemi, Julie Vogt, Pieter-Jan Guns, and Genomics England Res Consortium

Subjects
Adult, Male, 0301 basic medicine, MMP2, Loss of Heterozygosity, Importin, 030204 cardiovascular system & hematology, Biology, Importin 8, Loeys–Dietz syndrome, Thoracic aortic aneurysm, Mice, Young Adult, 03 medical and health sciences, All institutes and research themes of the Radboud University Medical Center, 0302 clinical medicine, Loss of Function Mutation, Transforming Growth Factor beta, Report, TGF beta signaling pathway, Genetics, medicine, Animals, Humans, Child, Genetics (clinical), Mice, Knockout, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], Aortic Aneurysm, Thoracic, Syndrome, beta Karyopherins, medicine.disease, Pedigree, Cell biology, Mice, Inbred C57BL, CTGF, Phenotype, 030104 developmental biology, Child, Preschool, Knockout mouse, Female, Human medicine, Signal Transduction
Abstract

Importin 8, encoded by IPO8, is a ubiquitously expressed member of the importin-beta protein family that translocates cargo molecules such as proteins, RNAs, and ribonucleoprotein complexes into the nucleus in a RanGTP-dependent manner. Current knowledge of the cargoes of importin 8 is limited, but TGF-beta signaling components such as SMAD1-4 have been suggested to be among them. Here, we report that bi-allelic loss-of-function variants in IPO8 cause a syndromic form of thoracic aortic aneurysm(TAA) with clinical overlap with Loeys-Dietz and Shprintzen-Goldberg syndromes. Seven individuals from six unrelated families showed a consistent phenotype with early-onset TAA, motor developmental delay, connective tissue findings, and craniofacial dysmorphic features. A C57BL/6N Ipo8 knockout mouse model recapitulates TAA development from 8-12 weeks onward in both sexes but most prominently shows ascending aorta dilatation with a propensity for dissection in males. Compliance assays suggest augmented passive stiffness of the ascending aorta in male Ipo8(-/-) mice throughout life. Immunohistological investigation of mutant aortic walls reveals elastic fiber disorganization and fragmentation along with a signature of increased TGF-beta signaling, as evidenced by nuclear pSmad2 accumulation. RT-qPCR assays of the aortic wall in male Ipo8(-/-) mice demonstrate decreased Smad6/7 and increased Mmp2 and Ccn2 (Ctgf) expression, reinforcing a role for dysregulation of the TGF-beta signaling pathway in TAA development. Because importin 8 is the most downstream TGF-beta-related effector implicated in TAA pathogenesis so far, it offers opportunities for future mechanistic studies and represents a candidate drug target for TAA.

Published
2021

14. Truncating mutations in YIF1B cause a progressive encephalopathy with various degrees of mixed movement disorder, microcephaly, and epilepsy

Author

Amber Begtrup, Aljouhra AlHargan, Stefan T. Arold, Anoud Abdulmalik Albader, Peter I. Karachunski, Rawan Almass, Laila AlQuait, Tahsin Stefan Barakat, Ibrahim H. Kaya, Aida M. Bertoli-Avella, Eva Medico Salsench, Dilek Colak, Namik Kaya, Monica Segura Castell, Jude Howaidi, Aziza Chedrawi, Jacie Ihinger, Peter Bauer, Jumanah Al-Sufayan, Mohammed A. AlMuhaizea, and Clinical Genetics

Subjects
Male, 0301 basic medicine, Vesicular Transport Proteins, Library science, Genetics department, Pathology and Forensic Medicine, 03 medical and health sciences, Cellular and Molecular Neuroscience, 0302 clinical medicine, Human disease, Political science, Humans, Progressive encephalopathy, Child, Erasmus+, Disability research, Brain Diseases, Epilepsy, Movement Disorders, Pedigree, 030104 developmental biology, Research centre, Child, Preschool, Mutation, Microcephaly, Female, Neurology (clinical), 030217 neurology & neurosurgery, Sequencing Core
Abstract

We are grateful to the patient families for their participation. This research was conducted through intramural funds (RAC# 2120022, 2180004, 2110006) provided by King Faisal Specialist Hospital and Research Centre (KFSHRC). We would like to thank National Plan for Science, Technology and Innovation program under King Abdulaziz City for Science and Technology (NSTIP/KACST) for supporting NK and DC. We thank the King Salman Center for Disability Research for generous funds for NK. We thank the KFSHRC Genotyping and Sequencing Core Facilities at Genetics Department, Research Advisory Council Committees, Saudi Human Genome Program and Purchasing Department (Mr. Faisal Al Otaibi) for facilitating and expediting our requests. The research by STA was supported by funding from King Abdullah University of Science and Technology (KAUST) through the Award No. FCC1/1976-25 form the Office of Sponsored Research. TSB is supported by the Netherlands Organization for Scientific Research (ZonMW Veni, Grant 91617021), a Brain & Behavior Research Foundation NARSAD Young Investigator Grant, an Erasmus MC Fellowship 2017 and Erasmus MC Human Disease Model Award 2018.

Published
2020

15. Missense variants in TAF1 and developmental phenotypes: Challenges of determining pathogenicity

Author

Emma Wakeling, Quan Li, Laurence E. Walsh, Maria J. Guillen Sacoto, Julie Vogt, Jeff L. Waugh, James R. Lupski, Elizabeth E. Palmer, Alan F. Rope, Robert Kleyner, Amalia Mallawaarachchi, Sebastian Lunke, Jennifer E. Posey, Pankaj B. Agrawal, Sebastien Moutton, Laurence Faivre, Zornitza Stark, Prosper Lukusa, Emily Fassi, Gareth Baynam, Gabriela Soares, Antonie D. Kline, Sonja A. de Munnik, Sarah A. Sandaradura, Chunhua Weng, Lucinda Murray, Lisa Ewans, Ganka Douglas, Eyby Leon, Shehla Mohammed, Marcia C. Willing, Elaine Marchi, Nora Alexander, Paul R. Mark, Joris Vermeesch, Lauren Dreyer, Aimé Lumaka, Koenraad Devriendt, Gholson J. Lyon, Helena Ahlfors, Katelyn Payne, Piatek G. Stefan, Jullianne Diaz, Lesley C. Adès, Simona Capponi, Jean-Baptiste Rivière, Michael F. Buckley, Amber Begtrup, H. T. Marc Timmers, Tony Roscioli, Mengge Zhao, Ana R. Gonçalves, Hanyin Cheng, Lisa Worgan, Kai Wang, and Jorge Oliveira

Subjects
Genetics, 0303 health sciences, Heart malformation, 030305 genetics & heredity, Biology, medicine.disease, Article, Hypotonia, 03 medical and health sciences, Autism spectrum disorder, Human Phenotype Ontology, Intellectual disability, medicine, Copy-number variation, Allele, medicine.symptom, Genetics (clinical), Exome sequencing, 030304 developmental biology
Abstract

We recently described a new neurodevelopmental syndrome (TAF1/MRXS33 intellectual disability syndrome) (MIM# 300966) caused by pathogenic variants involving the X-linked gene TAF1, which participates in RNA polymerase II transcription. The initial study reported eleven families, and the syndrome was defined as presenting early in life with hypotonia, facial dysmorphia, and developmental delay that evolved into intellectual disability (ID) and/or autism spectrum disorder (ASD). We have now identified an additional 27 families through a genotype-first approach. Familial segregation analysis, clinical phenotyping, and bioinformatics were capitalized on to assess potential variant pathogenicity, and molecular modelling was performed for those variants falling within structurally characterized domains of TAF1. A novel phenotypic clustering approach was also applied, in which the phenotypes of affected individuals were classified using 51 standardized Human Phenotype Ontology (HPO) terms. Phenotypes associated with TAF1 variants show considerable pleiotropy and clinical variability, but prominent among previously unreported effects were brain morphological abnormalities, seizures, hearing loss, and heart malformations. Our allelic series broadens the phenotypic spectrum of TAF1/MRXS33 intellectual disability syndrome and the range of TAF1 molecular defects in humans. It also illustrates the challenges for determining the pathogenicity of inherited missense variants, particularly for genes mapping to chromosome X. This article is protected by copyright. All rights reserved.

Published
2019

16. Expanding the mutational landscape and clinical phenotype of the YIF1B related brain disorder

Author

Ibrahim H. Kaya, Mehran Beiraghi Toosi, Peter Bauer, Farah Ashrafzadeh, Najmeh Ahangari, Stefan T. Arold, Aida M. Bertoli-Avella, Antonina Wojcik, Mohammad A. Al-Muhaizea, Kelly J. Cardona-Londoño, Meisam Babaei, Amber Begtrup, Nouriya Al-Sannaa, Dilek Colak, Elisa Cali, Ehsan Ghayoor Karimiani, Marian Y. Girgis, Obdulia Sanchez‐Lijarcio, Namik Kaya, Chin-To Fong, Marcelo Vargas, Shima Imannezhad, Tahsin Stefan Barakat, David Murphy, Audrey Schroeder, Paria Najarzadeh Torbati, Henry Houlden, Anita Nikoncuk, Kristina Lanko, Belén Pérez, Salvador Ibáñez-Mico, Reza Maroofian, Mohammad Doosti, Tainá Regina Damaceno Silveira, Ruizhi Deng, Eva Medico Salsench, and Clinical Genetics

Subjects
Male, Mice, Knockout, AcademicSubjects/SCI01870, Vesicular Transport Proteins, Library science, Golgi Apparatus, Scholarship, Mice, Human disease, Neurodevelopmental Disorders, Political science, Mutation, Animals, Humans, AcademicSubjects/MED00310, Female, Neurology (clinical), Cilia, Clinical phenotype, Erasmus+, Letter to the Editor, Disability research, Cells, Cultured
Abstract

Human post-natal neurodevelopmental delay is often associated with cerebral alterations that can lead, by themselves or associated with peripheral deficits, to premature death. Here, we report the clinical features of 10 patients from six independent families with mutations in the autosomal YIF1B gene encoding a ubiquitous protein involved in anterograde traffic from the endoplasmic reticulum to the cell membrane, and in Golgi apparatus morphology. The patients displayed global developmental delay, motor delay, visual deficits with brain MRI evidence of ventricle enlargement, myelination alterations and cerebellar atrophy. A similar profile was observed in the Yif1b knockout (KO) mouse model developed to identify the cellular alterations involved in the clinical defects. In the CNS, mice lacking Yif1b displayed neuronal reduction, altered myelination of the motor cortex, cerebellar atrophy, enlargement of the ventricles, and subcellular alterations of endoplasmic reticulum and Golgi apparatus compartments. Remarkably, although YIF1B was not detected in primary cilia, biallelic YIF1B mutations caused primary cilia abnormalities in skin fibroblasts from both patients and Yif1b-KO mice, and in ciliary architectural components in the Yif1b-KO brain. Consequently, our findings identify YIF1B as an essential gene in early post-natal development in human, and provide a new genetic target that should be tested in patients developing a neurodevelopmental delay during the first year of life. Thus, our work is the first description of a functional deficit linking Golgipathies and ciliopathies, diseases so far associated exclusively to mutations in genes coding for proteins expressed within the primary cilium or related ultrastructures. We therefore propose that these pathologies should be considered as belonging to a larger class of neurodevelopmental diseases depending on proteins involved in the trafficking of proteins towards specific cell membrane compartments.

Published
2021

17. Defective X-gating caused byde novogain-of-function mutations inKCNK3underlies a developmental disorder with sleep apnea

Author

Matthew E. Hurles, Srikanth Muppidi, Jan Fischer, Volker Straub, Pradeep C. Vasudevan, Janina Sörmann, Maria Descartes, Joseph Porrmann, Thomas Baukrowitz, Paul R. Mark, Carrie A. Lahner, Michael G. Hahn, Pavel N. Pichurin, Alice Gardham, Marcus Schewe, Thibault R. H. Jouen-Tachoire, Caroline F. Wright, John R. Dean, Amber Begtrup, Jens Schallner, Stephen J. Tucker, Elena B. Riel, Shanlin Rao, Rebecca Willaert, Thomas Müller, Kirstin Smith, Karin E. J. Rödström, Katherine Agre, Elisabeth P. Carpenter, and Peter Proks

Subjects
Developmental disorder, Gain of function, business.industry, medicine, Sleep apnea, Gating, medicine.disease, business, Receptor, Neuroscience
Abstract

Sleep apnea is a common disorder that represents a global public health burden.KCNK3encodes TASK-1, a K+channel implicated in the control of breathing, but its link with sleep apnea remains poorly understood. Here we describe a novel developmental disorder with sleep apnea caused by rarede novogain-of-function mutations inKCNK3. The mutations cluster around the ‘X-gate’, a gating motif which controls channel opening, and produce overactive channels that no longer respond to inhibition by G-protein coupled receptor pathways, but which can be inhibited by several clinically relevant drugs. These findings demonstrate a clear role for TASK-1 in sleep apnea and identify possible therapeutic strategies.

Published
2021

18. Hematologically important mutations: The autosomal forms of chronic granulomatous disease (third update)

Author

Amber Begtrup, Mohammad Shahrooei, Deniz Cagdas, Douglas B. Kuhns, Juan Luis Valdivieso Shephard, Nezihe Köker, Joachim Roesler, Amy P. Hsu, Marie José Stasia, Antonio Condino-Neto, Harry L. Malech, Jacinta Bustamante, Esmaeil Mortaz, Ilhan Tezcan, Pandiarajan Vignesh, Baruch Wolach, Dirk Roos, María Bravo García-Morato, Marianne Antonius Jakobsen, Steven M. Holland, Roya Sherkat, Rhonda Brandon, Hirokazu Kanegane, Mauno Vihinen, Faris G. Bakri, Lizbeth Blancas-Galicia, Abbas Fayezi, Amit Rawat, Karin van Leeuwen, John I. Gallin, Toshinao Kawai, M. Yavuz Köker, Christa S. Zerbe, Martin de Boer, Manesha Madkaikar, Debra A. Long Priel, Sanquin Research, University of Amsterdam [Amsterdam] (UvA), Laboratory of Clinical Infectious Diseases, NIAID, NIH, Bethesda, Maryland, Neutrophil Monitoring Laboratory, Frederick National Laboratory for Cancer Research (FNLCR), GeneDx [Gaithersburg, MD, USA], Postgraduate Institute of Medical Education and Research, Indian Council of Medical Research [New Dehli] (ICMR), Institut de biologie structurale (IBS - UMR 5075), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), The University of Jordan (JU), University Hospital Carl Gustav Carus [Dresden, Germany], Technische Universität Dresden = Dresden University of Technology (TU Dresden), Erciyes University, Odense University Hospital [Odense, Denmark], Department of Pediatrics, Division of Pediatric Immunology, Faculty of Medicine, Erciyes University, Kayseri, Turkey, and Landsteiner Laboratory

Subjects
Autosomal recessive, medicine.disease_cause, Granulomatous Disease, Chronic, Microbiology, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Chronic granulomatous disease, medicine, Humans, Polymorphism, Molecular Biology, Gene, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, Mutation, Reactive oxygen species, NADPH oxidase, biology, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Superoxide, HERANÇA GENÉTICA, NADPH Oxidases, Cell Biology, Hematology, medicine.disease, 3. Good health, Enzyme, chemistry, biology.protein, Molecular Medicine, P22phox, 030215 immunology
Abstract

Chronic granulomatous disease (CGD) is an immunodeficiency disorder affecting about 1 in 250,000 individuals. CGD patients suffer from severe, recurrent bacterial and fungal infections. The disease is caused by mutations in the genes encoding the components of the leukocyte NADPH oxidase. This enzyme produces superoxide, which is subsequently metabolized to hydrogen peroxide and other reactive oxygen species (ROS). These products are essential for intracellular killing of pathogens by phagocytic leukocytes (neutrophils, eosinophils, monocytes and macrophages). The leukocyte NADPH oxidase is composed of five subunits, four of which are encoded by autosomal genes. These are CYBA, encoding p22phox, NCF1, encoding p47phox, NCF2, encoding p67phox and NCF4, encoding p40phox. This article lists all mutations identified in these genes in CGD patients. In addition, cytochrome b558 chaperone-1 (CYBC1), recently recognized as an essential chaperone protein for the expression of the X-linked NADPH oxidase component gp91phox (also called Nox2), is encoded by the autosomal gene CYBC1. Mutations in this gene also lead to CGD. Finally, RAC2, a small GTPase of the Rho family, is needed for activation of the NADPH oxidase, and mutations in the RAC2 gene therefore also induce CGD-like symptoms. Mutations in these last two genes are also listed in this article.

Published
2021

19. Bi-allelic loss-of-function variants in BCAS3 cause a syndromic neurodevelopmental disorder

Author

Angelika Rieß, Shabab B. Hannan, Hessa S. Alsaif, Tadahiro Mitani, Ghassan Balousha, Siddharth Banka, Kendall C. Parks, Reza Azizi Malamiri, Henry Houlden, James R. Lupski, Elliott H. Sherr, Emanuela Argilli, Joseph J. Gleeson, Osama Balousha, Jakob Admard, Thomas Nägele, Adam Jackson, Zaid Ghanim, Alistair T. Pagnamenta, Ana Velic, Sarah Dyack, Reza Maroofian, Holger Hengel, Hamad Al-Zaidan, Stefanie Schuster, Amber Begtrup, Neda Mazaheri, Helen Kingston, Stephan Ossowski, Davut Pehlivan, Ludger Schöls, Mohammad Yahya Vahidi Mehrjardi, Stefan Hauser, Tobias B. Haack, Sara MacKay, Gholamreza Shariati, Hamid Galehdari, Mathew Osmond, Nicolas Casadei, Martin Fleger, Sevcan Tug Bozdogan, Andreas Kurringer, Ulrich A. Schatz, Boris Macek, Fowzan S. Alkuraya, and Mohammadreza Dehghani

Subjects
Proband, Male, Microcephaly, metabolism [Neurodevelopmental Disorders], Care4Rare Canada Consortium, Proteome, Loss of Heterozygosity, Medical and Health Sciences, Germline, Mice, transcriptomics, Neurodevelopmental disorder, Neoplasm Proteins/genetics, Cell Movement, Loss of Function Mutation, thin corpus callosum, BCAS3, 2.1 Biological and endogenous factors, Global developmental delay, microcephaly, Aetiology, Child, analysis [Proteome], Genetics (clinical), Fibroblasts/metabolism, Genetics, Mice, Knockout, Pediatric, Genetics & Heredity, 0303 health sciences, 030305 genetics & heredity, BCAS3 protein, human, Biological Sciences, ddc, Neoplasm Proteins, Pedigree, Child, Preschool, metabolism [Neoplasm Proteins], Knockout mouse, Drosophila, Female, UAS-Gal4, medicine.symptom, pathology [Fibroblasts], metabolism [Fibroblasts], Adult, Adolescent, pyramidal tract involvement, Knockout, global developmental delay, Biology, Short stature, Article, 03 medical and health sciences, Young Adult, proteomics, ddc:570, etiology [Neurodevelopmental Disorders], fibroblasts, Proteome/analysis, medicine, pathology [Neurodevelopmental Disorders], Neurodevelopmental Disorders/etiology, Animals, Humans, Allele, Preschool, 030304 developmental biology, genetics [Neoplasm Proteins], Human Genome, Infant, medicine.disease, neurodevelopmental disorder, Brain Disorders, Genomics England Research Consortium, Neurodevelopmental Disorders, Congenital Structural Anomalies
Abstract

Summary BCAS3 microtubule-associated cell migration factor (BCAS3) is a large, highly conserved cytoskeletal protein previously proposed to be critical in angiogenesis and implicated in human embryogenesis and tumorigenesis. Here, we established BCAS3 loss-of-function variants as causative for a neurodevelopmental disorder. We report 15 individuals from eight unrelated families with germline bi-allelic loss-of-function variants in BCAS3. All probands share a global developmental delay accompanied by pyramidal tract involvement, microcephaly, short stature, strabismus, dysmorphic facial features, and seizures. The human phenotype is less severe compared with the Bcas3 knockout mouse model and cannot be explained by angiogenic defects alone. Consistent with being loss-of-function alleles, we observed absence of BCAS3 in probands’ primary fibroblasts. By comparing the transcriptomic and proteomic data based on probands’ fibroblasts with those of the knockout mouse model, we identified similar dysregulated pathways resulting from over-representation analysis, while the dysregulation of some proposed key interactors could not be confirmed. Together with the results from a tissue-specific Drosophila loss-of-function model, we demonstrate a vital role for BCAS3 in neural tissue development.

Published
2021

20. Loss of function mutations in GEMIN5 cause a neurodevelopmental disorder

Author

Danielle C. Lynch, Jia Wang, Aurora Pujol, Henry Houlden, Diana Castro, Xiaodong Wang, Jan Senderek, Shade B. Moody, Melissa Gibbons, Tim M. Strom, Abigail Collins, Jong Hee Chae, John Landers, Udai Bhan Pandey, Tyler R. Fortuna, Reza Maroofian, Hannah R. McCurry, Andrea H. Németh, Yuehua Zhang, Nathalie Boddaert, Carsten G. Bönnemann, Sabine Rudnik-Schöneborn, Vincent Cantagrel, Kali Juliette, Jeanne Amiel, Amber Begtrup, Sangmoon Lee, David Schorling, Chanika Phornphutkul, Konrad Platzer, E. Corina Andriescu, Roser Urreizti, Eric N. Anderson, Cyril Gitiaux, Randal Richardson, Maha S. Zaki, Matias Wagner, Hasnaa M. Elbendary, Dhivyaa Rajasundaram, Brian Kirmse, Murim Choi, Sandra Donkervoort, Joseph G. Gleeson, Steffen Leiz, Mahmoud Y. Issa, Valentina Stanley, Patrick Frosk, Siri Lynne Rydning, Karine Siquier, Janbernd Kirschner, Sameer Agnihotri, Sarah S. Barnett, Isabelle Desguerre, Michele Yang, Yong Beom Shin, Deepa S. Rajan, Margot A. Cousin, Andrés Nascimento Osorio, A. Micheil Innes, Ying Yang, Elliot S. Stolerman, Youngha Lee, Kimberly McDonald, Alberto Garcia-Oguiza, Edgard Verdura, Caroline Ward, Maria J. Guillen Sacoto, Minghui Wang, Sukhleen Kour, and Kaja Kristine Selmer

Subjects
Male, 0301 basic medicine, Developmental Disabilities, General Physics and Astronomy, 0302 clinical medicine, Neurodevelopmental disorder, Loss of Function Mutation, RNA-Seq, Neurons, Regulation of gene expression, Myoclonic Cerebellar Dyssynergia, Multidisciplinary, Neurodevelopmental disorders, Developmental disorders, Rigor Mortis, Gene Expression Regulation, Developmental, SMN Complex Proteins, Ribonucleoproteins, Small Nuclear, Hypotonia, Pedigree, Cell biology, medicine.anatomical_structure, Child, Preschool, Gene Knockdown Techniques, Muscle Hypotonia, Drosophila, Female, medicine.symptom, Ataxia, Science, Induced Pluripotent Stem Cells, Biology, Polymorphism, Single Nucleotide, Article, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, medicine, Animals, Humans, snRNP, Amino Acid Sequence, Alleles, Loss function, Cerebellar ataxia, General Chemistry, Motor neuron, medicine.disease, Gene Ontology, HEK293 Cells, 030104 developmental biology, 030217 neurology & neurosurgery
Abstract

GEMIN5, an RNA-binding protein is essential for assembly of the survival motor neuron (SMN) protein complex and facilitates the formation of small nuclear ribonucleoproteins (snRNPs), the building blocks of spliceosomes. Here, we have identified 30 affected individuals from 22 unrelated families presenting with developmental delay, hypotonia, and cerebellar ataxia harboring biallelic variants in the GEMIN5 gene. Mutations in GEMIN5 perturb the subcellular distribution, stability, and expression of GEMIN5 protein and its interacting partners in patient iPSC-derived neurons, suggesting a potential loss-of-function mechanism. GEMIN5 mutations result in disruption of snRNP complex assembly formation in patient iPSC neurons. Furthermore, knock down of rigor mortis, the fly homolog of human GEMIN5, leads to developmental defects, motor dysfunction, and a reduced lifespan. Interestingly, we observed that GEMIN5 variants disrupt a distinct set of transcripts and pathways as compared to SMA patient neurons, suggesting different molecular pathomechanisms. These findings collectively provide evidence that pathogenic variants in GEMIN5 perturb physiological functions and result in a neurodevelopmental delay and ataxia syndrome., GEMIN5, an RNA-binding protein, is required for formation of small nuclear ribonucleoproteins. Here, the authors identify loss of function mutations in GEMIN5 that are associated with a human neurodevelopmental disorder.

Published
2021

21. Missense Variants in the Histone Acetyltransferase Complex Component Gene TRRAP Cause Autism and Syndromic Intellectual Disability

Author

Philippe M. Campeau, Katherine Agre, Vernon R. Sutton, Kirsty McWalter, Bertrand Isidor, Øystein L. Holla, Anna Lehman, Megha Desai, Jonathan Berg, Stéphane Bézieau, Rolph Pfundt, Jennifer Tarpinian, Jennifer B. Humberson, Holly A.F. Stessman, Madeleine R. Geisheker, Emma Bedoukian, Shalini N. Jhangiani, Marine I. Murphree, Annapurna Poduri, Anne-Sophie Denommé-Pichon, Christian Gilissen, Yaping Yang, Eliane Beauregard-Lacroix, Claude Férec, Francesca Filippini, Anne Guimier, Daryl A. Scott, Stephen Sanders, Julie C. Sapp, Ralitza H. Gavrilova, Slavé Petrovski, Ann Nordgren, Sylvia Redon, Ernie M.H.F. Bongers, Shelagh Joss, Jill A. Rosenfeld, Wallid Deb, Ingrid M. Wentzensen, Usha Kini, Vandana Shashi, Mindy H. Li, Stanislas Lyonnet, Thomas Garcia, Øyvind L. Busk, Christoffer Nellåker, Amber Begtrup, Brigitte Gilbert-Dussardier, Thomas Besnard, Francois V. Bolduc, Patrick R. Blackburn, Justine Rousseau, Frédéric Bilan, Eric W. Klee, Christopher T. Gordon, Pavel N. Pichurin, Peggy Kulch, Kevin P. Lally, Laurie Robak, Arnaud Picard, Kristian Tveten, Meredith Park, Sébastien Küry, Jaya Punetha, Moira Blyth, Asbjørg Stray-Pedersen, Jacqueline Harris, Erin L. Heinzen, Nicholas Stong, Cara M. Skraban, Julie S. Cohen, Aida Telegrafi, Xenia Latypova, Zeynep Coban Akdemir, Jacob Zyskind, Caitlin Troyer, Xiang-Jiao Yang, Tuula Rinne, Leslie G. Biesecker, Jennifer E. Posey, Kyle Retterer, Jeanne Amiel, Rui Xiao, Magnus Nordenskjöld, Tammie Dewan, Jennifer A. Sullivan, Charlotte von der Lippe, Evan E. Eichler, Anna Lindstrand, Dominique Bonneau, Yuri A. Zarate, Elaine H. Zackai, Fayth M. Kalb, Daniel H. Lowenstein, Shiri Avni, Benjamin Cogné, Jennifer J. Johnston, Kerri H. Whitlock, Catherine Shain, Séverine Audebert-Bellanger, Malin Kvarnung, Oana Caluseriu, David Goldstein, Annick Toutain, Andres Hernandez-Garcia, Brina Daniels, Sophie Ehresmann, James R. Lupski, Julie McGaughran, Ashley H Ebanks, Kévin Uguen, Marine Legendre, Sylvie Odent, Richard Redon, Erica H. Gerkes, Xiaofei Song, unité de recherche de l'institut du thorax UMR1087 UMR6291 (ITX), Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre hospitalier universitaire de Nantes (CHU Nantes), CHU Sainte Justine [Montréal], Université du Québec à Montréal = University of Québec in Montréal (UQAM), University of Oxford [Oxford], GeneDx [Gaithersburg, MD, USA], Mayo Clinic [Rochester], University of California [San Francisco] (UCSF), University of California, Génétique, génomique fonctionnelle et biotechnologies (UMR 1078) (GGB), Institut Brestois Santé Agro Matière (IBSAM), Université de Brest (UBO)-Université de Brest (UBO)-EFS-Institut National de la Santé et de la Recherche Médicale (INSERM), Etablissement Français du Sang Bretagne, EFS, Hôpital de la Cavale Blanche - CHRU Brest (CHU - BREST ), Johns Hopkins University School of Medicine [Baltimore], Kennedy Krieger Institute [Baltimore], Chapel Allerton Hospital, University of British Columbia (UBC), University of Dundee, Rush University Medical Center [Chicago], Oxford University Hospitals NHS Trust, Queen Elizabeth University Hospital (Glasgow), Trondheim University, Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), University of Virginia [Charlottesville], Texas Children's Hospital [Houston, USA], Baylor College of Medicine (BCM), Baylor University, University of Pennsylvania [Philadelphia], National Human Genome Research Institute (NHGRI), Harvard Medical School [Boston] (HMS), Karolinska University Hospital [Stockholm], Duke University Medical Center, University of Groningen [Groningen], University of Arkansas for Medical Sciences (UAMS), McGovern Medical School [Houston, Texas], The University of Texas Health Science Center at Houston (UTHealth), Phoenix Children's Hospital, Columbia University [New York], University of Southern Queensland (USQ), Telemark Hospital Trust [Skien, Norway], University of Washington [Seattle], Oslo University Hospital [Oslo], Children’s Hospital of Philadelphia (CHOP ), CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Radboud University Medical Center [Nijmegen], Ann & Robert H. Lurie Children's Hospital of Chicago, Imagerie et cerveau (iBrain - Inserm U1253 - UNIV Tours ), Université de Tours-Institut National de la Santé et de la Recherche Médicale (INSERM), CHU Trousseau [Tours], Centre Hospitalier Régional Universitaire de Tours (CHRU Tours), Institut de Génétique et Développement de Rennes (IGDR), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), CHU Pontchaillou [Rennes], Centre de référence Maladies Rares CLAD-Ouest [Rennes], Physiopathologie Cardiovasculaire et Mitochondriale (MITOVASC), Université d'Angers (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre Hospitalier Universitaire d'Angers (CHU Angers), PRES Université Nantes Angers Le Mans (UNAM), Centre Hospitalier Régional Universitaire de Brest (CHRU Brest), Centre hospitalier universitaire de Poitiers (CHU Poitiers), University of Alberta, Boston Children's Hospital, McGill University Health Center [Montreal] (MUHC), Hôpital Morvan - CHRU de Brest (CHU - BREST ), Creighton University Medical School [Omaha, NE, USA], Howard Hughes Medical Institute [Boston] (HHMI), Howard Hughes Medical Institute (HHMI)-Harvard Medical School [Boston] (HMS), National Institute of Neurological Disorders and Stroke, K08 HG008986, National Human Genome Research Institute, BC Children’s Hospital Foundation, Genome British Columbia, Fonds de Recherche du Québec - Santé, Canadian Institutes of Health Research, Center for Individualized Medicine, Mayo Clinic, Health Regional Agency from Poitou-Charentes, French Ministry of Health, RC14_0107, HUGODIMS, NS053998, The Epilepsy Phenome/Genome Project, NS077303, Epi4K, Duke Genome Sequencing Clinic, NINDS R35 NS105078, National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health and Human Development, HG200328 12, intramural research program of the NHGRI, Dart NeuroScience, Kids Brain Health Network, Mining for Miracles, UM1 HG006542, National Heart, Lung, and Blood Institute, CIM Investigative and Functional Genomics Program, R01MH101221, National Institute of Mental Health, Unité de recherche de l'institut du thorax (ITX-lab), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN), University of Oxford, University of California [San Francisco] (UC San Francisco), University of California (UC), EFS-Université de Brest (UBO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Brestois Santé Agro Matière (IBSAM), Université de Brest (UBO), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), University of Virginia, University of Pennsylvania, Université de Tours (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), MitoVasc - Physiopathologie Cardiovasculaire et Mitochondriale (MITOVASC), CCSD, Accord Elsevier, Faculteit Medische Wetenschappen/UMCG, Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )

Subjects
CHROMATIN, Male, 0301 basic medicine, Autism, Sequence Homology, [SDV.GEN] Life Sciences [q-bio]/Genetics, Medical and Health Sciences, 0302 clinical medicine, SCHIZOPHRENIA, Gene expression, 2.1 Biological and endogenous factors, Missense mutation, Aetiology, Child, de novo variants, Genetics (clinical), Pediatric, Genetics & Heredity, Genetics, biology, neurodevelopmental disorders, histone acetylation, Adaptor Proteins, Nuclear Proteins, Metabolic Disorders Radboud Institute for Molecular Life Sciences [Radboudumc 6], Syndrome, Biological Sciences, Prognosis, Phenotype, Chromatin, Mental Health, Histone, intellectual disability, Child, Preschool, Female, REGULATOR, congenital malformations, Rare cancers Radboud Institute for Health Sciences [Radboudumc 9], BRAIN-DEVELOPMENT, Adult, Adolescent, Histone acetyltransferase complex, Intellectual and Developmental Disabilities (IDD), Mutation, Missense, Deciphering Developmental Disorders study, autism spectrum disorder, KAT6B, RNAI SCREEN, Young Adult, 03 medical and health sciences, CAUSES Study, Rare Diseases, Intellectual Disability, Report, COFACTOR, medicine, RUBINSTEIN-TAYBI-SYNDROME, Humans, Amino Acid Sequence, Autistic Disorder, Preschool, Gene, Genetic Association Studies, Adaptor Proteins, Signal Transducing, [SDV.GEN]Life Sciences [q-bio]/Genetics, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], Rubinstein–Taybi syndrome, Signal Transducing, Neurosciences, Infant, medicine.disease, TRRAP, Brain Disorders, SELF-RENEWAL, 030104 developmental biology, DE-NOVO MUTATIONS, Mutation, biology.protein, Missense, 030217 neurology & neurosurgery
Abstract

Contains fulltext : 202928.pdf (Publisher’s version ) (Open Access) Acetylation of the lysine residues in histones and other DNA-binding proteins plays a major role in regulation of eukaryotic gene expression. This process is controlled by histone acetyltransferases (HATs/KATs) found in multiprotein complexes that are recruited to chromatin by the scaffolding subunit transformation/transcription domain-associated protein (TRRAP). TRRAP is evolutionarily conserved and is among the top five genes intolerant to missense variation. Through an international collaboration, 17 distinct de novo or apparently de novo variants were identified in TRRAP in 24 individuals. A strong genotype-phenotype correlation was observed with two distinct clinical spectra. The first is a complex, multi-systemic syndrome associated with various malformations of the brain, heart, kidneys, and genitourinary system and characterized by a wide range of intellectual functioning; a number of affected individuals have intellectual disability (ID) and markedly impaired basic life functions. Individuals with this phenotype had missense variants clustering around the c.3127G>A p.(Ala1043Thr) variant identified in five individuals. The second spectrum manifested with autism spectrum disorder (ASD) and/or ID and epilepsy. Facial dysmorphism was seen in both groups and included upslanted palpebral fissures, epicanthus, telecanthus, a wide nasal bridge and ridge, a broad and smooth philtrum, and a thin upper lip. RNA sequencing analysis of skin fibroblasts derived from affected individuals skin fibroblasts showed significant changes in the expression of several genes implicated in neuronal function and ion transport. Thus, we describe here the clinical spectrum associated with TRRAP pathogenic missense variants, and we suggest a genotype-phenotype correlation useful for clinical evaluation of the pathogenicity of the variants.

Published
2019

22. An autosomal dominant neurological disorder caused by de novo variants in FAR1 resulting in uncontrolled synthesis of ether lipids

Author

Sacha Ferdinandusse, Kirsty McWalter, Heleen te Brinke, Lodewijk IJlst, Petra M. Mooijer, Jos P.N. Ruiter, Alida E.M. van Lint, Mia Pras-Raves, Eric Wever, Francisca Millan, Maria J. Guillen Sacoto, Amber Begtrup, Mark Tarnopolsky, Lauren Brady, Roger L. Ladda, Susan L. Sell, Catherine B. Nowak, Jessica Douglas, Cuixia Tian, Elizabeth Ulm, Seth Perlman, Arlene V. Drack, Karen Chong, Nicole Martin, Jennifer Brault, Elly Brokamp, Camilo Toro, William A. Gahl, Ellen F. Macnamara, Lynne Wolfe, Mercedes E. Alejandro, Mahshid S. Azamian, Carlos A. Bacino, Ashok Balasubramanyam, Lindsay C. Burrage, Hsiao-Tuan Chao, Gary D. Clark, William J. Craigen, Hongzheng Dai, Shweta U. Dhar, Lisa T. Emrick, Alica M. Goldman, Neil A. Hanchard, Fariha Jamal, Lefkothea Karaviti, Seema R. Lalani, Brendan H. Lee, Richard A. Lewis, Ronit Marom, Paolo M. Moretti, David R. Murdock, Sarah K. Nicholas, James P. Orengo, Jennifer E. Posey, Lorraine Potocki, Jill A. Rosenfeld, Susan L. Samson, Daryl A. Scott, Alyssa A. Tran, Tiphanie P. Vogel, Michael F. Wangler, Shinya Yamamoto, Christine M. Eng, Pengfei Liu, Patricia A. Ward, Edward Behrens, Matthew Deardorff, Marni Falk, Kelly Hassey, Kathleen Sullivan, Adeline Vanderver, David B. Goldstein, Heidi Cope, Allyn McConkie-Rosell, Kelly Schoch, Vandana Shashi, Edward C. Smith, Rebecca C. Spillmann, Jennifer A. Sullivan, Queenie K.-G. Tan, Nicole M. Walley, Pankaj B. Agrawal, Alan H. Beggs, Gerard T. Berry, Lauren C. Briere, Laurel A. Cobban, Matthew Coggins, Cynthia M. Cooper, Elizabeth L. Fieg, Frances High, Ingrid A. Holm, Susan Korrick, Joel B. Krier, Sharyn A. Lincoln, Joseph Loscalzo, Richard L. Maas, Calum A. MacRae, J. Carl Pallais, Deepak A. Rao, Lance H. Rodan, Edwin K. Silverman, Joan M. Stoler, David A. Sweetser, Melissa Walker, Chris A. Walsh, Cecilia Esteves, Emily G. Kelley, Isaac S. Kohane, Kimberly LeBlanc, Alexa T. McCray, Anna Nagy, Surendra Dasari, Brendan C. Lanpher, Ian R. Lanza, Eva Morava, Devin Oglesbee, Guney Bademci, Deborah Barbouth, Stephanie Bivona, Olveen Carrasquillo, Ta Chen Peter Chang, Irman Forghani, Alana Grajewski, Rosario Isasi, Byron Lam, Roy Levitt, Xue Zhong Liu, Jacob McCauley, Ralph Sacco, Mario Saporta, Judy Schaechter, Mustafa Tekin, Fred Telischi, Willa Thorson, Stephan Zuchner, Heather A. Colley, Jyoti G. Dayal, David J. Eckstein, Laurie C. Findley, Donna M. Krasnewich, Laura A. Mamounas, Teri A. Manolio, John J. Mulvihill, Grace L. LaMoure, Madison P. Goldrich, Tiina K. Urv, Argenia L. Doss, Maria T. Acosta, Carsten Bonnenmann, Precilla D’Souza, David D. Draper, Carlos Ferreira, Rena A. Godfrey, Catherine A. Groden, Valerie V. Maduro, Thomas C. Markello, Avi Nath, Donna Novacic, Barbara N. Pusey, Colleen E. Wahl, Eva Baker, Elizabeth A. Burke, David R. Adams, May Christine V. Malicdan, Cynthia J. Tifft, Lynne A. Wolfe, John Yang, Bradley Power, Bernadette Gochuico, Laryssa Huryn, Lea Latham, Joie Davis, Deborah Mosbrook-Davis, Francis Rossignol, Ben Solomon, John MacDowall, Audrey Thurm, Wadih Zein, Muhammad Yousef, Margaret Adam, Laura Amendola, Michael Bamshad, Anita Beck, Jimmy Bennett, Beverly Berg-Rood, Elizabeth Blue, Brenna Boyd, Peter Byers, Sirisak Chanprasert, Michael Cunningham, Katrina Dipple, Daniel Doherty, Dawn Earl, Ian Glass, Katie Golden-Grant, Sihoun Hahn, Anne Hing, Fuki M. Hisama, Martha Horike-Pyne, Gail P. Jarvik, Jeffrey Jarvik, Suman Jayadev, Christina Lam, Kenneth Maravilla, Heather Mefford, J. Lawrence Merritt, Ghayda Mirzaa, Deborah Nickerson, Wendy Raskind, Natalie Rosenwasser, C. Ron Scott, Angela Sun, Virginia Sybert, Stephanie Wallace, Mark Wener, Tara Wenger, Euan A. Ashley, Gill Bejerano, Jonathan A. Bernstein, Devon Bonner, Terra R. Coakley, Liliana Fernandez, Paul G. Fisher, Laure Fresard, Jason Hom, Yong Huang, Jennefer N. Kohler, Elijah Kravets, Marta M. Majcherska, Beth A. Martin, Shruti Marwaha, Colleen E. McCormack, Archana N. Raja, Chloe M. Reuter, Maura Ruzhnikov, Jacinda B. Sampson, Kevin S. Smith, Shirley Sutton, Holly K. Tabor, Brianna M. Tucker, Matthew T. Wheeler, Diane B. Zastrow, Chunli Zhao, William E. Byrd, Andrew B. Crouse, Matthew Might, Mariko Nakano-Okuno, Jordan Whitlock, Gabrielle Brown, Manish J. Butte, Esteban C. Dell’Angelica, Naghmeh Dorrani, Emilie D. Douine, Brent L. Fogel, Irma Gutierrez, Alden Huang, Deborah Krakow, Hane Lee, Sandra K. Loo, Bryan C. Mak, Martin G. Martin, Julian A. Martínez-Agosto, Elisabeth McGee, Stanley F. Nelson, Shirley Nieves-Rodriguez, Christina G.S. Palmer, Jeanette C. Papp, Neil H. Parker, Genecee Renteria, Rebecca H. Signer, Janet S. Sinsheimer, Jijun Wan, Lee-kai Wang, Katherine Wesseling Perry, Jeremy D. Woods, Justin Alvey, Ashley Andrews, Jim Bale, John Bohnsack, Lorenzo Botto, John Carey, Laura Pace, Nicola Longo, Gabor Marth, Paolo Moretti, Aaron Quinlan, Matt Velinder, Dave Viskochil, Pinar Bayrak-Toydemir, Rong Mao, Monte Westerfield, Anna Bican, Laura Duncan, Rizwan Hamid, Jennifer Kennedy, Mary Kozuira, John H. Newman, John A. Phillips, Lynette Rives, Amy K. Robertson, Emily Solem, Joy D. Cogan, F. Sessions Cole, Nichole Hayes, Dana Kiley, Kathy Sisco, Jennifer Wambach, Daniel Wegner, Dustin Baldridge, Stephen Pak, Timothy Schedl, Jimann Shin, Lilianna Solnica-Krezel, Quinten Waisfisz, Petra J.G. Zwijnenburg, Alban Ziegler, Magalie Barth, Rosemarie Smith, Sara Ellingwood, Deborah Gaebler-Spira, Somayeh Bakhtiari, Michael C. Kruer, Antoine H.C. van Kampen, Ronald J.A. Wanders, Hans R. Waterham, David Cassiman, Frédéric M. Vaz, Laboratory Genetic Metabolic Diseases, AGEM - Amsterdam Gastroenterology Endocrinology Metabolism, APH - Methodology, Epidemiology and Data Science, APH - Personalized Medicine, Laboratory for General Clinical Chemistry, ARD - Amsterdam Reproduction and Development, Human genetics, ACS - Atherosclerosis & ischemic syndromes, and Amsterdam Reproduction & Development (AR&D)

Subjects
Candidate gene, Hereditary spastic paraplegia, Undiagnosed Diseases Network, Neurological disorder, Biology, medicine.disease, Molecular biology, Article, Biochemical phenotype, Bilateral Cataracts, Gene panel, medicine, Ether lipid synthesis, In patient, Genetics (clinical)
Abstract

Author(s): Ferdinandusse, Sacha; McWalter, Kirsty; Te Brinke, Heleen; IJlst, Lodewijk; Mooijer, Petra M; Ruiter, Jos PN; van Lint, Alida EM; Pras-Raves, Mia; Wever, Eric; Millan, Francisca; Guillen Sacoto, Maria J; Begtrup, Amber; Tarnopolsky, Mark; Brady, Lauren; Ladda, Roger L; Sell, Susan L; Nowak, Catherine B; Douglas, Jessica; Tian, Cuixia; Ulm, Elizabeth; Perlman, Seth; Drack, Arlene V; Chong, Karen; Martin, Nicole; Brault, Jennifer; Brokamp, Elly; Toro, Camilo; Gahl, William A; Macnamara, Ellen F; Wolfe, Lynne; Undiagnosed Diseases Network; Waisfisz, Quinten; Zwijnenburg, Petra JG; Ziegler, Alban; Barth, Magalie; Smith, Rosemarie; Ellingwood, Sara; Gaebler-Spira, Deborah; Bakhtiari, Somayeh; Kruer, Michael C; van Kampen, Antoine HC; Wanders, Ronald JA; Waterham, Hans R; Cassiman, David; Vaz, Frederic M | Abstract: PurposeIn this study we investigate the disease etiology in 12 patients with de novo variants in FAR1 all resulting in an amino acid change at position 480 (p.Arg480Cys/His/Leu).MethodsFollowing next-generation sequencing and clinical phenotyping, functional characterization was performed in patients' fibroblasts using FAR1 enzyme analysis, FAR1 immunoblotting/immunofluorescence, and lipidomics.ResultsAll patients had spastic paraparesis and bilateral congenital/juvenile cataracts, in most combined with speech and gross motor developmental delay and truncal hypotonia. FAR1 deficiency caused by biallelic variants results in defective ether lipid synthesis and plasmalogen deficiency. In contrast, patients' fibroblasts with the de novo FAR1 variants showed elevated plasmalogen levels. Further functional studies in fibroblasts showed that these variants cause a disruption of the plasmalogen-dependent feedback regulation of FAR1 protein levels leading to uncontrolled ether lipid production.ConclusionHeterozygous de novo variants affecting the Arg480 residue of FAR1 lead to an autosomal dominant disorder with a different disease mechanism than that of recessive FAR1 deficiency and a diametrically opposed biochemical phenotype. Our findings show that for patients with spastic paraparesis and bilateral cataracts, FAR1 should be considered as a candidate gene and added to gene panels for hereditary spastic paraplegia, cerebral palsy, and juvenile cataracts.

Published
2021

23. Defining the genotypic and phenotypic spectrum of X-linked MSL3-related disorder

Author

Nicole Fleischer, Grace M. Anbouba, Vandana Shashi, Thomas Meitinger, Damara Ortiz, Sumedha Ghate, Caleb Bupp, Maria J. Guillen Sacoto, Tiana M. Scott, Juliane Winkelmann, Felix Distelmaier, Sarah R Green, Dirk Klee, Carolyn R Serbinski, Lea Velsher, Michael T. Zimmermann, Meriel McEntagart, Gretchen Parsons, Patrick Yap, Evan H. Baugh, David S. Wargowski, Juan C Del Rey Jimenez, Anne K Olsen, Amy Armstrong-Javors, Victoria Mok Siu, Andrew Green, Nikita R. Dsouza, Elisabeth Graf, Sumit Punj, Matias Wagner, Anna Cereda, Naomi Meeks, Barbro Stadheim, Kirsty McWalter, Ingrid M. Wentzensen, Bert Callewaert, Rhonda E. Schnur, Emily Lancaster, Laurie A. Demmer, G. Bradley Schaefer, Kristin Lindstrom, Maria Iascone, Gonzalo Alonso Ramos-Rivera, Loren D M Pena, Amber Begtrup, Richard E. Person, Harrison Moore, Ameni Kdissa, Eric W. Klee, Dana Mittag, Jana Švantnerová, Ingrid Bader, Theresa Brunet, Johannes A. Mayr, Michael Zech, Jennifer A. Sullivan, Margot A. Cousin, Katharina Mayerhanser, Dagmar Wieczorek, Ralitza H. Gavrilova, and Daryl A. Scott

Subjects
Male, Genotype, ACETYLATION, Autism Spectrum Disorder, Chromosomal Proteins, Non-Histone, autism, Biology, Pediatrics, Whole Exome Sequencing, Article, Frameshift mutation, Autism, Developmental Delay, Histone Acetylation, Msl3, X-linked, DOMAIN, Genes, X-Linked, MSL COMPLEX, Intellectual Disability, Intellectual disability, Exome Sequencing, medicine, Medicine and Health Sciences, Missense mutation, Humans, Exome, Genetics (clinical), Exome sequencing, MOF, Genetics, MSL3, MUTATIONS, TRANSCRIPTIONAL REGULATION, Macrocephaly, histone acetylation, Non-Histone, medicine.disease, ddc, Chromosomal Proteins, DNA-Binding Proteins, developmental delay, Phenotype, Genes, Autism spectrum disorder, Female, medicine.symptom, DECAY, DOSAGE COMPENSATION
Abstract

PURPOSE: We sought to delineate the genotypic and phenotypic spectrum of female and male individuals with X-linked, MSL3-related disorder (Basilicata-Akhtar syndrome). METHODS: Twenty-five individuals (15 males, 10 females) with causative variants in MSL3 were ascertained through exome or genome sequencing at ten different sequencing centers. RESULTS: We identified multiple variant types in MSL3 (ten nonsense, six frameshift, four splice site, three missense, one in-frame-deletion, one multi-exon deletion), most proven to be de novo, and clustering in the terminal eight exons suggesting that truncating variants in the first five exons might be compensated by an alternative MSL3 transcript. Three-dimensional modeling of missense and splice variants indicated that these have a deleterious effect. The main clinical findings comprised developmental delay and intellectual disability ranging from mild to severe. Autism spectrum disorder, muscle tone abnormalities, and macrocephaly were common as well as hearing impairment and gastrointestinal problems. Hypoplasia of the cerebellar vermis emerged as a consistent magnetic resonance image (MRI) finding. Females and males were equally affected. Using facial analysis technology, a recognizable facial gestalt was determined. CONCLUSION: Our aggregated data illustrate the genotypic and phenotypic spectrum of X-linked, MSL3-related disorder (Basilicata-Akhtar syndrome). Our cohort improves the understanding of disease related morbidity and allows us to propose detailed surveillance guidelines for affected individuals.

Published
2021

24. Hematologically important mutations: X-linked chronic granulomatous disease (fourth update)

Author

Dirk Roos, Karin van Leeuwen, Amy P. Hsu, Debra Long Priel, Amber Begtrup, Rhonda Brandon, Marie José Stasia, Faris Ghalib Bakri, Nezihe Köker, M. Yavuz Köker, Manisha Madkaika, Martin de Boer, Maria Bravo Garcia-Morato, Juan Luis Valdivieso Shephard, Joachim Roesler, Hirokazu Kanegane, Toshinao Kawai, Gigliola Di Matteo, Mohammad Shahrooei, Jacinta Bustamante, Amit Rawat, Pandiarajan Vignesh, Esmaeil Mortaz, Abbas Fayezi, Deniz Cagdas, Ilhan Tezcan, Maleewan Kitcharoensakkul, Mary C. Dinauer, Isabelle Meyts, Baruch Wolach, Antonio Condino-Neto, Christa S. Zerbe, Steven M. Holland, Harry L. Malech, John I. Gallin, Douglas B. Kuhns, Sanquin Research, University of Amsterdam [Amsterdam] (UvA), Laboratory of Clinical Infectious Diseases, NIAID, NIH, Bethesda, Maryland, GeneDx [Gaithersburg, MD, USA], Institut de biologie structurale (IBS - UMR 5075), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), Division of Infectious Diseases, Department of Medicine, Jordan University Hospital, Neutrophil Monitoring Laboratory, Frederick National Laboratory for Cancer Research (FNLCR), Centre Diagnostic et Recherche sur la Granulomatose septique Chronique (CDiReC), CHUGA, and Landsteiner Laboratory

Subjects
gp91(phox), congenital, hereditary, and neonatal diseases and abnormalities, gp91, Granulomatous Disease, Chronic, CYBB, 03 medical and health sciences, 0302 clinical medicine, X-linked disease, hemic and lymphatic diseases, Humans, Molecular Biology, 030304 developmental biology, Chromosomes, Human, X, 0303 health sciences, NADPH oxidase, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Cell Biology, Hematology, ENZIMAS, 3. Good health, NADPH Oxidase 2, Mutation, Chronic granulomatous disease, Molecular Medicine, 030215 immunology, G6PD
Abstract

International audience; Chronic granulomatous disease (CGD) is an immunodeficiency disorder affecting about 1 in 250,000 individuals. CGD patients suffer from severe bacterial and fungal infections. The disease is caused by a lack of superoxide production by the leukocyte enzyme NADPH oxidase. Superoxide and subsequently formed other reactive oxygen species (ROS) are instrumental in killing phagocytosed micro-organisms in neutrophils, eosinophils, monocytes and macrophages. The leukocyte NADPH oxidase is composed of five subunits, of which the enzymatic component is gp91phox, also called Nox2. This protein is encoded by the CYBB gene on the X chromosome. Mutations in this gene are found in about 70% of all CGD patients in Europe and in about 20% in countries with a high ratio of parental consanguinity. This article lists all mutations identified in CYBB and should therefore help in genetic counseling of X-CGD patients' families. Moreover, apparently benign polymorphisms in CYBB are also given, which should facilitate the recognition of disease-causing mutations. In addition, we also include some mutations in G6PD, the gene on the X chromosome that encodes glucose-6-phosphate dehydrogenase, because inactivity of this enzyme may lead to shortage of NADPH and thus to insufficient activity of NADPH oxidase. Severe G6PD deficiency can induce CGD-like symptoms.

Published
2021

25. Bi-allelic variants in SPATA5L1 lead to intellectual disability, spastic-dystonic cerebral palsy, epilepsy, and hearing loss

Author

Serdal Güngör, Benita Grossmann, Bethany Y. Norton, Zubair M. Ahmed, Wendy K. Chung, John Neidhardt, Julie S. Cohen, Elodie Richard, Yoel Hirsch, Jiankang Li, Jozef Gecz, Ralf A. Husain, Saima Riazuddin, Maria J. Guillen Sacoto, Claudia Steen, Andreas Ziegler, G. Christoph Korenke, Dominic Lenz, Mahim Jain, Urania Kotzaeridou, Henry Houlden, Theresa Brunet, Yavuz Oktay, Semra Hiz, Patricia Cornejo, Sheetal Shetty, Alastair H. MacLennan, Nazira Zharkinbekova, Bader Alhaddad, Dani L. Webber, Mary Alice Abbott, Hanns Lochmüller, Rauan Kaiyrzhanov, Melissa Yelton, Cecilia Mancini, Hakon Hakonarson, Amy Crunk, Simona Amenta, Yiran Guo, Jan Kaslin, Clare L. van Eyk, Richard Webster, Arianna Tucci, Alex M. Pagnozzi, Robert B. Hufnagel, Kirsty McWalter, Sandra M. Nordlie, Kaya Bilguvar, Pasquale Striano, Matias Wagner, Florian Kreuder, Lisa Worgan, Ashley P.L. Marsh, Anna Chassevent, Warren A. Marks, James Liu, Brandon S. Guida, Maria Margherita Mancardi, Kelly Harper, Lance H. Rodan, Rhonda E. Schnur, Dianela Judith Claps Sepulveda, Tzvi Weiden, Michele Pinelli, Marion Rapp, Helen Magee, Jesia G. Berry, Aboulfazl Rad, Michael C. Kruer, Mark A. Corbett, Rita Horvath, Constance Smith-Hicks, Joseph Ekstein, Marta Owczarek-Lipska, Somayeh Bakhtiari, Heinrich Sticht, Thomas Meitinger, Anne M. Comi, Alyssa Blesson, Iris Marquardt, Francesca Clementina Radio, Sergio Padilla-Lopez, Giuseppe Marangi, Christine Makowski, Mona Grimmel, Marco Tartaglia, Sheng Chih Jin, Federico Zara, Andreas Hahn, Shrikant Mane, Michael C Fahey, Marcella Zollino, Barbara Vona, Peter D. Turnpenny, Manuela Morleo, Ute Grasshoff, Amber Begtrup, Richard E. Person, Annalaura Torella, Alexander Münchau, Vincenzo Nigro, Reza Maroofian, John Christodoulou, Tobias B. Haack, Vincenzo Salpietro, Richard, E. M., Bakhtiari, S., Marsh, A. P. L., Kaiyrzhanov, R., Wagner, M., Shetty, S., Pagnozzi, A., Nordlie, S. M., Guida, B. S., Cornejo, P., Magee, H., Liu, J., Norton, B. Y., Webster, R. I., Worgan, L., Hakonarson, H., Li, J., Guo, Y., Jain, M., Blesson, A., Rodan, L. H., Abbott, M. -A., Comi, A., Cohen, J. S., Alhaddad, B., Meitinger, T., Lenz, D., Ziegler, A., Kotzaeridou, U., Brunet, T., Chassevent, A., Smith-Hicks, C., Ekstein, J., Weiden, T., Hahn, A., Zharkinbekova, N., Turnpenny, P., Tucci, A., Yelton, M., Horvath, R., Gungor, S., Hiz, S., Oktay, Y., Lochmuller, H., Zollino, M., Morleo, M., Marangi, G., Nigro, V., Torella, A., Pinelli, M., Amenta, S., Husain, R. A., Grossmann, B., Rapp, M., Steen, C., Marquardt, I., Grimmel, M., Grasshoff, U., Korenke, G. C., Owczarek-Lipska, M., Neidhardt, J., Radio, F. C., Mancini, C., Claps Sepulveda, D. J., Mcwalter, K., Begtrup, A., Crunk, A., Guillen Sacoto, M. J., Person, R., Schnur, R. E., Mancardi, M. M., Kreuder, F., Striano, P., Zara, F., Chung, W. K., Marks, W. A., van Eyk, C. L., Webber, D. L., Corbett, M. A., Harper, K., Berry, J. G., Maclennan, A. H., Gecz, J., Tartaglia, M., Salpietro, V., Christodoulou, J., Kaslin, J., Padilla-Lopez, S., Bilguvar, K., Munchau, A., Ahmed, Z. M., Hufnagel, R. B., Fahey, M. C., Maroofian, R., Houlden, H., Sticht, H., Mane, S. M., Rad, A., Vona, B., Jin, S. C., Haack, T. B., Makowski, C., Hirsch, Y., Riazuddin, S., and Kruer, M. C.

Subjects
Male, Microcephaly, Pathology, Settore MED/03 - GENETICA MEDICA, sensorineural hearing loss, Epilepsy, Neurodevelopmental disorder, sensorineural hearing lo, Genetics (clinical), Allele, ATPases Associated with Diverse Cellular Activitie, medicine.anatomical_structure, Muscle Spasticity, Child, Preschool, Sensorineural hearing loss, Female, movement disorder, medicine.symptom, AAA+ superfamily, Human, Adult, medicine.medical_specialty, Adolescent, Hearing loss, Aaa+ Superfamily, Atpase, Spata5l1, Cerebral Palsy, Intellectual Disability, Movement Disorder, Neurodevelopmental Disorder, Sensorineural Hearing Loss, Biology, Cerebral palsy, White matter, Young Adult, Report, Genetics, medicine, Animals, Humans, ATPase, Genetic Predisposition to Disease, Hearing Loss, SPATA5L1, Hearing Lo, Alleles, cerebral palsy, Periventricular leukomalacia, Animal, Infant, Newborn, Infant, Genetic Variation, medicine.disease, neurodevelopmental disorder, Rats, ATPases Associated with Diverse Cellular Activities, Rat
Abstract

Spermatogenesis-associated 5 like 1 (SPATA5L1) represents an orphan gene encoding a protein of unknown function. We report 28 bi-allelic variants in SPATA5L1 associated with sensorineural hearing loss in 47 individuals from 28 (26 unrelated) families. In addition, 25/47 affected individuals (53%) presented with microcephaly, developmental delay/intellectual disability, cerebral palsy, and/or epilepsy. Modeling indicated damaging effect of variants on the protein, largely via destabilizing effects on protein domains. Brain imaging revealed diminished cerebral volume, thin corpus callosum, and periventricular leukomalacia, and quantitative volumetry demonstrated significantly diminished white matter volumes in several individuals. Immunofluorescent imaging in rat hippocampal neurons revealed localization of Spata511 in neuronal and glial cell nuclei and more prominent expression in neurons. In the rodent inner ear, Spata511 is expressed in the neurosensory hair cells and inner ear supporting cells. Transcriptomic analysis performed with fibroblasts from affected individuals was able to distinguish affected from controls by principal components. Analysis of differentially expressed genes and networks suggested a role for SPATA5L1 in cell surface adhesion receptor function, intracellular focal adhesions, and DNA replication and mitosis. Collectively, our results indicate that bi-allelic SPATA5L1 variants lead to a human disease characterized by sensorineural hearing loss (SNHL) with or without a nonprogressive mixed neurodevelopmental phenotype.

Published
2021

26. Loss-of-function mutations in UDP-Glucose 6-Dehydrogenase cause recessive developmental epileptic encephalopathy

Author

Ali Al Asmari, Emmanuelle Szenker-Ravi, Carine Bonnard, Bruno Reversade, Laura Schultz-Rogers, I. Kraegeloh-Mann, Maha Abdulrahim, Hesham Aldhalaan, Byrappa Venkatesh, Célia Bosso-Lefèvre, Aida Telegrafi, Hiyam M. Marzouqa, Gunaseelan Narayanan, Sha Tang, Sonal Mahida, Melanie A. Simpson, Fowzan S. Alkuraya, Michelle Eio, Eissa Faqeih, Renske Oegema, Sarah Weckhuysen, George Grady, Joseph J. Barycki, Mohammed Al-Owain, Lamyaa A. Jad, David A. Koolen, Marjon van Slegtenhorst, Tyler Mark Pierson, Marisa V. Andrews, Rebecca Schüle, Reinhard Keimer, Amber Begtrup, Sateesh Maddirevula, Michael Muriello, Sakkubai Naidu, Damien Haye, Adel A H Mahmoud, Brian Ciruna, Abdullah Tamim, Thong Teck Tan, Rolph Pfundt, Peter Bauer, Jiin Ying Lim, Ali Awaji, Marco Tartaglia, Meral Gunay-Aygun, Eric W. Klee, Marcia C. Willing, Monica Yau, Angelika Riess, Diego Martinelli, Sabina Barresi, Sumanty Tohari, Werner Deigendesch, Dirk Lefeber, Saumya Shekhar Jamuar, Ludger Schöls, Ralitza H. Gavrilova, Alvin Yu Jin Ng, Hannah Stamberger, Suleyman Gulsuner, Adam Claridge-Chang, Élise Lebigot, Moeenaldeen Al-Sayed, Ee Shien Tan, Kagistia Hana Utami, Sarah B. Pierce, Helene Verhelst, Hankun Li, James C. Stewart, Ingo Helbig, Tal Gilboa, Mahmoud A. Pouladi, Hagar Mor-Shaked, Boris Keren, Ajay S. Mathuru, Holger Hengel, Michèl A.A.P. Willemsen, Nader Handal, Tahsin Stefan Barakat, Sulwan M. Algain, Terrence Thomas, Lance H. Rodan, Mais Hashem, Wendy G. Mitchell, Center for Reproductive Medicine, ARD - Amsterdam Reproduction and Development, ACS - Diabetes & metabolism, Clinical Genetics, Reversade, Bruno, Hengel, H., Bosso-Lefèvre, C., Grady, G., Szenker-Ravi, E., Li, H., Pierce, S., Lebigot, É., Tan, T.-T., Eio, M.Y., Narayanan, G., Utami, K.H., Yau, M., Handal, N., Deigendesch, W., Keimer, R., Marzouqa, H.M., Gunay-Aygun, M., Muriello, M.J., Verhelst, H., Weckhuysen, S., Mahida, S., Naidu, S., Thomas, T.G., Lim, J.Y., Tan, E.S., Haye, D., Willemsen, M.A.A.P., Oegema, R., Mitchell, W.G., Pierson, T.M., Andrews, M.V., Willing, M.C., Rodan, L.H., Barakat, T.S., van Slegtenhorst, M., Gavrilova, R.H., Martinelli, D., Gilboa, T., Tamim, A.M., Hashem, M.O., AlSayed, M.D., Abdulrahim, M.M., Al-Owain, M., Awaji, A., Mahmoud, A.A.H., Faqeih, E.A., Asmari, A.A., Algain, S.M., Jad, L.A., Aldhalaan, H.M., Helbig, I., Koolen, D.A., Riess, A., Kraegeloh-Mann, I., Bauer, P., Gulsuner, S., Stamberger, H., Ng, A.Y.J., Tang, S., Tohari, S., Keren, B., Schultz-Rogers, L.E., Klee, E.W., Barresi, S., Tartaglia, M., Mor-Shaked, H., Maddirevula, S., Begtrup, A., Telegrafi, A., Pfundt, R., Schüle, R., Ciruna, B., Bonnard, C., Pouladi, M.A., Stewart, J.C., Claridge-Chang, A., Lefeber, D.J., Alkuraya, F.S., Mathuru, A.S., Venkatesh, B., Barycki, J.J., Simpson, M.A., Jamuar, S.S., Schöls, L, and School of Medicine

Subjects
0301 basic medicine, Male, Glycobiology, General Physics and Astronomy, VARIANTS, Encephalopathy, Neurodegenerative, Germline, 0302 clinical medicine, UDP-GLUCOSE DEHYDROGENASE, Loss of Function Mutation, Medicine and Health Sciences, EMBRYOGENESIS, 2.1 Biological and endogenous factors, UGDH protein, human, Aetiology, Child, lcsh:Science, Zebrafish, UTILITY, Genetics, pathology [Organoids], Multidisciplinary, Uridine diphosphate glucose dehydrogenase, Uridine diphosphate, DP-glucuronic acid, Syndrome, Disorders of movement Donders Center for Medical Neuroscience [Radboudumc 3], Hypotonia, 3. Good health, Pedigree, DEFICIENCY, genetics [Loss of Function Mutation], Organoids, genetics [Uridine Diphosphate Glucose Dehydrogenase], Child, Preschool, Neurological, Medicine, Female, ddc:500, medicine.symptom, Oxidoreductases, Engineering sciences. Technology, Rare cancers Radboud Institute for Health Sciences [Radboudumc 9], ENZYME, Adolescent, CONGENITAL DISORDER, Science, Intellectual and Developmental Disabilities (IDD), genetics [Epilepsy], chemistry [Oxidoreductases], Genetics and Molecular Biology, Genes, Recessive, Biology, Uridine Diphosphate Glucose Dehydrogenase, Article, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Protein Domains, medicine, Animals, Humans, Recessive, Clinical genetics, Allele, Preschool, Gene, Loss function, Alleles, HEPARAN-SULFATE, Phenocopy, genetics [Oxidoreductases], Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], Epilepsy, GLYCOSYLATION, Neurosciences, Infant, General Chemistry, biology.organism_classification, medicine.disease, Brain Disorders, carbohydrates (lipids), Kinetics, 030104 developmental biology, Genes, General Biochemistry, Neuronal development, lcsh:Q, Human medicine, 030217 neurology & neurosurgery, Congenital disorder
Abstract

Developmental epileptic encephalopathies are devastating disorders characterized by intractable epileptic seizures and developmental delay. Here, we report an allelic series of germline recessive mutations in UGDH in 36 cases from 25 families presenting with epileptic encephalopathy with developmental delay and hypotonia. UGDH encodes an oxidoreductase that converts UDP-glucose to UDP-glucuronic acid, a key component of specific proteoglycans and glycolipids. Consistent with being loss-of-function alleles, we show using patients’ primary fibroblasts and biochemical assays, that these mutations either impair UGDH stability, oligomerization, or enzymatic activity. In vitro, patient-derived cerebral organoids are smaller with a reduced number of proliferating neuronal progenitors while mutant ugdh zebrafish do not phenocopy the human disease. Our study defines UGDH as a key player for the production of extracellular matrix components that are essential for human brain development. Based on the incidence of variants observed, UGDH mutations are likely to be a frequent cause of recessive epileptic encephalopathy., German Research Foundation (DFG); European Union (European Union); NEUROMICS Network; International Coordination Action (ICA); Fund for Scientific Research Flanders (FWO); Netherlands Organization for Scientific Research (ZONMW VIDI); National Medical Research Council, Singapore; A Strategic Positioning Fund on Genetic Orphan Diseases (GODAFIT); Industry Alignment Fund on Singapore Childhood Undiagnosed Diseases Program (SUREKids); Biomedical Research Council, A*STAR; Diana and Steve Marienhoff Fashion Industries Guild Endowed Fellowship in Pediatric Neuromuscular Diseases; Fondazione Bambino Gesù (Vite Coraggiose); Canadian Institutes of Health Research; Natural Sciences and Engineering Research Council of Canada; Eurocores Program EuroEPINOMICS; University of Antwerp Research Fund; FRAXA Foundation; Brain & Behavior Research Foundation, NARSAD Young Investigator Grant

Published
2020

27. NCKAP1 Disruptive Variants Lead to a Neurodevelopmental Disorder with Core Features of Autism

Author

Kun Xia, Samantha Ayres, Amber Begtrup, Danielle Karlowicz, Raphael Bernier, Ahood Alsulaiman, Frédéric Bilan, Rebecca Hernan, Elena Savva, Fowzan S. Alkuraya, Ingrid M. Wentzensen, Mohammad A. Al-Muhaizea, Audrey Labalme, Sumit Punj, Jenny Meylan Merlini, Evan E. Eichler, Lucile Letienne-Cejudo, Alexia Boizot, Natasha J Brown, Emily Bryant, Senwei Tan, Wendy K. Chung, Bin Yu, Inken Dreyer, Maria J. Guillen Sacoto, Jieqiong Tan, Hilde Peeters, Xiangbin Jia, Inge Lore Ruiz-Arana, Brina Daniels, Elizabeth A. Sellars, Linda Pons, Jianjun Ou, Rujia Dai, Guodong Chen, Gaetan Lesca, Lindsay Rhodes, Anne chun-hui Tsai, Chao Chen, Marie T. McDonald, Linda Laux, Kendra Hoekzema, Hui Guo, Christina Fagerberg, Bradley Schaefer, Huidan Wu, Rhonda E. Schnur, Qiumeng Zhang, Federico Santoni, Qian Pan, Rose B. McGee, Lucia Bartoloni, Brigitte Gilbert-Dussardier, Zhengmao Hu, Charlotte Brasch-Andersen, Dhamidhu Eratne, Valerie Slegesky, and Lori A. Carpenter

Subjects
Male, Autism Spectrum Disorder, Gene Expression, Variable Expression, Mice, 0302 clinical medicine, Neurodevelopmental disorder, Genotype-phenotype distinction, Pregnancy, Intellectual disability, Protein Isoforms, RNA, Small Interfering, Child, de novo variants, Genetics (clinical), Cerebral Cortex, Mice, Knockout, Neurons, 0303 health sciences, Learning Disabilities, Phenotype, Pedigree, Autism spectrum disorder, Female, Neuroglia, Adolescent, Genotype, autism spectrum disorder, genotype-phenotype correlation, Biology, Article, 03 medical and health sciences, Young Adult, Intellectual Disability, Genetics, medicine, Animals, Humans, Loss function, 030304 developmental biology, Adaptor Proteins, Signal Transducing, disruptive variant, medicine.disease, neurodevelopmental disorder, NCKAP1, HEK293 Cells, Mutation, Autism, Transcriptome, Neuroscience, 030217 neurology & neurosurgery
Abstract

NCKAP1/NAP1 regulates neuronal cytoskeletal dynamics and is essential for neuronal differentiation in the developing brain. Deleterious variants in NCKAP1 have been identified in individuals with autism spectrum disorder (ASD) and intellectual disability; however, its clinical significance remains unclear. To determine its significance, we assemble genotype and phenotype data for 21 affected individuals from 20 unrelated families with predicted deleterious variants in NCKAP1. This includes 16 individuals with de novo (n = 8), transmitted (n = 6), or inheritance unknown (n = 2) truncating variants, two individuals with structural variants, and three with potentially disruptive de novo missense variants. We report a de novo and ultra-rare deleterious variant burden of NCKAP1 in individuals with neurodevelopmental disorders which needs further replication. ASD or autistic features, language and motor delay, and variable expression of intellectual or learning disability are common clinical features. Among inherited cases, there is evidence of deleterious variants segregating with neuropsychiatric disorders. Based on available human brain transcriptomic data, we show that NCKAP1 is broadly and highly expressed in both prenatal and postnatal periods and demostrate enriched expression in excitatory neurons and radial glias but depleted expression in inhibitory neurons. Mouse in utero electroporation experiments reveal that Nckap1 loss of function promotes neuronal migration during early cortical development. Combined, these data support a role for disruptive NCKAP1 variants in neurodevelopmental delay/autism, possibly by interfering with neuronal migration early in cortical development.

Published
2020

28. New insights into the clinical and molecular spectrum of the novel CYFIP2-related neurodevelopmental disorder and impairment of the WRC-mediated actin dynamics

Author

Katharina Steindl, Alain Verloes, Cornelia Kraus, Rachel Fisher, Katrin Õunap, Amber Begtrup, Steffen Syrbe, Theresa Brunet, Antonio Vitobello, Laurence Faivre, Reza Asadollahi, Jessica Becker, Maja Hempel, Dave A Dyment, Christiane Zweier, John H McDermott, Bernt Popp, Elaine Suk-Ying Goh, Lynette G. Sadleir, Anaïs Begemann, Siddharth Banka, Gwenaël Le Guyader, Elisabeth Schuler, Anne-Sophie Denommé-Pichon, Kathleen Brown, Gaetan Lesca, Frédéric Tran Mau-Them, Lucia Ribeiro Machado Haertel, Maryline Carneiro, Amelie Theresa Van der Ven, Markus Zweier, Hartmut Engels, Heinrich Sticht, Theresia Herget, Jessika Johannsen, Bader Alhaddad, Nadine N. Hauer, Robert C. Day, Tiia Reimand, M. J. Hajianpour, Manuel Schiff, Kirsty McWalter, Margarita Saenz, Tatjana Bierhals, Pierre Meyer, Ange-Line Bruel, Martina Russo, Korbinian M. Riedhammer, Kirsten Cremer, Anita Rauch, Marjolaine Willems, Equipe GAD (LNC - U1231), Lipides - Nutrition - Cancer [Dijon - U1231] (LNC), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Santé et de la Recherche Médicale (INSERM), FHU TRANSLAD (CHU de Dijon), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Centre hospitalier universitaire de Poitiers (CHU Poitiers), Centre de recherche en neurosciences de Lyon (CRNL), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet [Saint-Étienne] (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Physiologie & médecine expérimentale du Cœur et des Muscles [U 1046] (PhyMedExp), Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Maladies neurodéveloppementales et neurovasculaires (NeuroDiderot (UMR_S_1141 / U1141)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), and Hôpital Robert Debré

Subjects
0301 basic medicine, [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, WAVEregulatory complex (WRC), 030105 genetics & heredity, Biology, Article, Intellectual disability, Epilepsy, CYFIP2, WAVE-regulatory complex (WRC), WASF, 03 medical and health sciences, Neurodevelopmental disorder, Seizures, medicine, Missense mutation, Humans, Genetics(clinical), Gene, Genetics (clinical), Actin, Adaptor Proteins, Signal Transducing, Genetics, medicine.disease, Actin cytoskeleton, Phenotype, Hypotonia, Actins, 3. Good health, ddc, 030104 developmental biology, [SDV.BDD.EO]Life Sciences [q-bio]/Development Biology/Embryology and Organogenesis, Neurodevelopmental Disorders, intellectual disability, epilepsy, medicine.symptom
Abstract

International audience; Purpose: A few de novo missense variants in the cytoplasmic FMRP-interacting protein 2 (CYFIP2) gene have recently been described as a novel cause of severe intellectual disability, seizures, and hypotonia in 18 individuals, with p.Arg87 substitutions in the majority.Methods: We assembled data from 19 newly identified and all 18 previously published individuals with CYFIP2 variants. By structural modeling and investigation of WAVE-regulatory complex (WRC)-mediated actin polymerization in six patient fibroblast lines we assessed the impact of CYFIP2 variants on the WRC.Results: Sixteen of 19 individuals harbor two previously described and 11 novel (likely) disease-associated missense variants. We report p.Asp724 as second mutational hotspot (4/19 cases). Genotype–phenotype correlation confirms a consistently severe phenotype in p.Arg87 patients but a more variable phenotype in p.Asp724 and other substitutions. Three individuals with milder phenotypes carry putative loss-of-function variants, which remain of unclear pathogenicity. Structural modeling predicted missense variants to disturb interactions within the WRC or impair CYFIP2 stability. Consistent with its role in WRC-mediated actin polymerization we substantiate aberrant regulation of the actin cytoskeleton in patient fibroblasts.Conclusion: Our study expands the clinical and molecular spectrum of CYFIP2-related neurodevelopmental disorder and provides evidence for aberrant WRC-mediated actin dynamics as contributing cellular pathomechanism.

Published
2020

29. De novo SOX6 variants cause a neurodevelopmental syndrome associated with ADHD, craniosynostosis, and osteochondromas

Author

M. Zarowiecki, A. Devereau, S.M. Wood, J. M. Boissiere, G. Elgar, Cara Forster, Liesbeth Keldermans, A. Sieghart, Allyn McConkie-Rosell, Augusto Rendon, S. R. Thompson, D. Polychronopoulos, Alexandre Arkader, Julien Thevenon, D. Kasperaviciute, Alma Kuechler, Bryan L. Krock, Dominique Martin-Coignard, Damian Smedley, T. Rahim, Barbara Mikat, Amber Begtrup, Priya Prasad, Lindsay B. Henderson, A. Stuckey, Mathilde Nizon, Tim Hubbard, I. U. S. Leong, M. Bleda, L. Lahnstein, C. E. H. Craig, Bertrand Isidor, Sarah Leigh, Joanne Mason, L. Moutsianas, T. Fowler, A. Siddiq, J. Pullinger, Marco Angelozzi, J. Ambrose, S. A. Watters, Saadet Mercimek-Andrews, K. Lawson, Claudia A. L. Ruivenkamp, Ian D. Krantz, J. E. Holman, Solveig Heide, Christel Depienne, Elizabeth T. DeChene, L. C. Daugherty, Alvaro Serrano Russi, Arianna Tucci, Mark J. Caulfield, Marie T. McDonald, Boris Keren, A. C. Need, Damara Ortiz, Nicola Foulds, William Spooner, Dara Tolchin, Eduardo Calpena, C. R. Boustred, Abdul Haseeb, Rudolf Gorazd, Charles Coutton, Alona Sosinsky, D. Perez-Gil, Sarah Stewart, J. M. Hackett, Giada Melistaccio, Andrew O.M. Wilkie, Radka Stoeva, Cédric Le Caignec, Pauline Le Tanno, Benjamin Cogné, Martina Mueller, Naghmeh Dorrani, Pedro Furió-Tarí, Gijs W. E. Santen, Hermann-Josef Lüdecke, Jessica P. Yeager, Julian A. Martinez-Agosto, Damien Haye, Kieran B. Pechter, Mohnish Suri, Livija Medne, M. J. Welland, Patrick Reed, K. Savage, G. C. Chan, Anne C.H. Tsai, F. Maleady-Crowe, A. de Burca, Ellen M. McDonagh, T. Rogers, F. Boardman-Pretty, Emily Lancaster, Katherine R. Smith, Christopher A. Odhams, Véronique Lefebvre, M. Ryten, Olivier Pichon, D. Halai, Aleš Maver, Christine Patch, R. E. Foulger, Frédéric Bilan, Helen Stevens, Hilde Van Esch, Eleanor Williams, Brigitte Gilbert-Dussardier, C. Tregidgo, K. Witkowska, F. J. Lopez, Gwenaël Le Guyader, Richard H Scott, M. Kayikci, Ellen Thomas, and E. Walsh

Subjects
0301 basic medicine, Male, Osteochondroma, Adolescent, Transcription, Genetic, media_common.quotation_subject, Nonsense, Medizin, Active Transport, Cell Nucleus, Mutation, Missense, Biology, Cell fate determination, Translocation, Genetic, Article, Craniosynostosis, 03 medical and health sciences, Craniosynostoses, 0302 clinical medicine, Intellectual disability, Genetics, medicine, Missense mutation, Humans, Computer Simulation, Amino Acid Sequence, RNA-Seq, Child, Gene, Genetics (clinical), media_common, Base Sequence, Brain, Infant, Syndrome, medicine.disease, 030104 developmental biology, Attention Deficit Disorder with Hyperactivity, Neurodevelopmental Disorders, Child, Preschool, Genomic Structural Variation, Autism, Female, Haploinsufficiency, Transcriptome, SOXD Transcription Factors, 030217 neurology & neurosurgery
Abstract

SOX6 belongs to a family of 20 SRY-related HMG-box-containing (SOX) genes that encode transcription factors controlling cell fate and differentiation in many developmental and adult processes. For SOX6, these processes include, but are not limited to, neurogenesis and skeletogenesis. Variants in half of the SOX genes have been shown to cause severe developmental and adult syndromes, referred to as SOXopathies. We here provide evidence that SOX6 variants also cause a SOXopathy. Using clinical and genetic data, we identify 19 individuals harboring various types of SOX6 alterations and exhibiting developmental delay and/or intellectual disability; the individuals are from 17 unrelated families. Additional, inconstant features include attention-deficit/hyperactivity disorder (ADHD), autism, mild facial dysmorphism, craniosynostosis, and multiple osteochondromas. All variants are heterozygous. Fourteen are de novo, one is inherited from a mosaic father, and four offspring from two families have a paternally inherited variant. Intragenic microdeletions, balanced structural rearrangements, frameshifts, and nonsense variants are predicted to inactivate the SOX6 variant allele. Four missense variants occur in residues and protein regions highly conserved evolutionarily. These variants are not detected in the gnomAD control cohort, and the amino acid substitutions are predicted to be damaging. Two of these variants are located in the HMG domain and abolish SOX6 transcriptional activity in vitro. No clear genotype-phenotype correlations are found. Taken together, these findings concur that SOX6 haploinsufficiency leads to a neurodevelopmental SOXopathy that often includes ADHD and abnormal skeletal and other features.

Published
2020

30. De Novo Variants in CNOT1, a Central Component of the CCR4-NOT Complex Involved in Gene Expression and RNA and Protein Stability, Cause Neurodevelopmental Delay

Author

Paul Kruszka, Sreehari Kalvakuri, Austin Larson, Dong Li, Inge van Outersterp, Florence Demurger, Ian Hayes, F. Lucy Raymond, Lauren J. Massingham, Claudia A. L. Ruivenkamp, Ian D. Krantz, Kendra Brunet, Nicole Revencu, Maaike Vreeburg, Donatella Milani, Tjitske Kleefstra, Lisenka E.L.M. Vissers, Maximilian Muenke, Sinje Geuer, Candace Gamble, Rolf Bodmer, Hanka Venselaar, Elke de Boer, Sarina G. Kant, Dilys Weijers, Arjan P.M. de Brouwer, Machteld M. Oud, Maria Iascone, Christopher C. Griffith, Frédéric Tran Mau-Them, Karin Weiss, Megan T. Cho, Ayesha Ahmad, James A. Bartley, Nina Powell Hamilton, Lenika De Simone, George E. Hoganson, Lucie Evenepoel, Simone Kersten, Daniel L. Polla, Himanshu Goel, Antonio Vitobello, Rachel Fisher, Arthur Sorlin, Sébastien Moutton, Myrthe van den Born, Hilary J. Vernon, Michael Kwint, Kaitlyn Burns, Anna Ruiz, Kirsty McWalter, Jenny Morton, Jennifer Schwab, Elizabeth J. Bhoj, Philippe Christophe, Hans van Bokhoven, Elisabeth Gabau, Kimberly M. Nugent, Jill R. Murrell, Thierry Billette de Villemeur, Kathleen Wood, Alexandra Afenjar, Amber Begtrup, Chanika Phornphutkul, Sarah E. Raible, Melde Witmond, Perrine Charles, Claudia Soler-Alfonso, D. Isum Ward, Marjolaine Willems, Boris Keren, Julian Delanne, UCL - SSS/IREC/SLUC - Pôle St.-Luc, UCL - (SLuc) Centre de génétique médicale UCL, Clinical Genetics, Klinische Genetica, RS: GROW - R4 - Reproductive and Perinatal Medicine, and MUMC+: DA KG Polikliniek (9)

Subjects
Male, DYRK1A, Developmental Disabilities, lnfectious Diseases and Global Health Radboud Institute for Molecular Life Sciences [Radboudumc 4], Gene Expression, de novo mutations, Haploinsufficiency, 0302 clinical medicine, Gene expression, Nuclear Receptor Subfamily 4, Group A, Member 2, Genetics (clinical), Genetics, 0303 health sciences, Gene knockdown, repressor, neurodevelopment, Protein Stability, CCR4-NOT complex, Phenotype, developmental delay, intellectual disability, Drosophila, deadenylase complex, Female, regulators, Heterozygote, Receptors, CCR4, Biology, Nervous System Malformations, 03 medical and health sciences, Report, genomics, Humans, Gene, Alleles, 030304 developmental biology, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], Genetic Variation, Protein ubiquitination, Renal disorders Radboud Institute for Molecular Life Sciences [Radboudumc 11], Neurodevelopmental Disorders, SUBUNIT, RNA, CNOT1, Nanomedicine Radboud Institute for Molecular Life Sciences [Radboudumc 19], exome sequencing, 030217 neurology & neurosurgery, Transcription Factors
Abstract

Contains fulltext : 220423.pdf (Publisher’s version ) (Closed access) CNOT1 is a member of the CCR4-NOT complex, which is a master regulator, orchestrating gene expression, RNA deadenylation, and protein ubiquitination. We report on 39 individuals with heterozygous de novo CNOT1 variants, including missense, splice site, and nonsense variants, who present with a clinical spectrum of intellectual disability, motor delay, speech delay, seizures, hypotonia, and behavioral problems. To link CNOT1 dysfunction to the neurodevelopmental phenotype observed, we generated variant-specific Drosophila models, which showed learning and memory defects upon CNOT1 knockdown. Introduction of human wild-type CNOT1 was able to rescue this phenotype, whereas mutants could not or only partially, supporting our hypothesis that CNOT1 impairment results in neurodevelopmental delay. Furthermore, the genetic interaction with autism-spectrum genes, such as ASH1L, DYRK1A, MED13, and SHANK3, was impaired in our Drosophila models. Molecular characterization of CNOT1 variants revealed normal CNOT1 expression levels, with both mutant and wild-type alleles expressed at similar levels. Analysis of protein-protein interactions with other members indicated that the CCR4-NOT complex remained intact. An integrated omics approach of patient-derived genomics and transcriptomics data suggested only minimal effects on endonucleolytic nonsense-mediated mRNA decay components, suggesting that de novo CNOT1 variants are likely haploinsufficient hypomorph or neomorph, rather than dominant negative. In summary, we provide strong evidence that de novo CNOT1 variants cause neurodevelopmental delay with a wide range of additional co-morbidities. Whereas the underlying pathophysiological mechanism warrants further analysis, our data demonstrate an essential and central role of the CCR4-NOT complex in human brain development.

Published
2020

31. Loss of UGP2 in brain leads to a severe epileptic encephalopathy, emphasizing that bi-allelic isoform-specific start-loss mutations of essential genes can cause genetic diseases

Author

Nuzhat Rana, Edwin H. Jacobs, Ehsan Ghayoor Karimiani, Amber Begtrup, Jozef Hertecant, Evita Medici-van den Herik, Mohammad Doosti, Gouri Rao Passi, Mohammadreza Dehghani, Tjakko J. van Ham, Mariya Kozenko, Laila AlQuait, Mohammad Yahya Vahidi Mehrjardi, Dilek Colak, Herma C. van der Linde, Henry Houlden, Eleonora Aronica, Huma Arshad Cheema, Jennefer N. Kohler, Namik Kaya, Krishna Kumar Kandaswamy, Salem Alwadaee, Maysoon Alsagob, Woutje M. Berdowski, Zaynab Khazaei, Renjith Mani, Faisal Al Azri, Amna Al Futaisi, Stephanie Efthymiou, Majid Mojarrad, Aida M. Bertoli-Avella, Murat Gunel, Tahsin Stefan Barakat, Wilfred F. J. van IJcken, Kristin G. Monaghan, Rebecca I. Torene, Atieh Eslahi, Fathiya Al Murshedi, Khalid Awartani, Peter Bauer, Muddathir H. Hamad, Kyle Retterer, Reza Maroofian, Rawan Almass, Erik-Jan Kamsteeg, Serdar Coskun, Jonathan A. Bernstein, Elena Perenthaler, Anita Nikoncuk, Mohammed A. AlMuhaizea, Jana Vandrovcova, Anas M. Dababo, Soheil Yousefi, Fateme Massinaei Darmiyan, Mustafa A. Salih, Lauren Brick, A. Gulhan Ercan-Sencicek, Futwan Al-Mohanna, Ivan Čapo, Faisal Zafar, Khaled O. Alahmadi, Marjon van Slegtenhorst, Walter G. de Valk, Mazhor Al-Dosary, Wafa Qubbaj, Alice S. Brooks, Mehrnaz Ghazvini, Paul van den Berg, Darija Putar, Clinical Genetics, Cell biology, Neurology, Pathology, ANS - Cellular & Molecular Mechanisms, APH - Aging & Later Life, and APH - Mental Health

Subjects
Gene isoform, Protein isoform, Male, Microcephaly, Recurrent mutation, UTP-Glucose-1-Phosphate Uridylyltransferase, UGP2, medicine.disease_cause, Sensory disorders Donders Center for Medical Neuroscience [Radboudumc 12], Pathology and Forensic Medicine, 03 medical and health sciences, Cellular and Molecular Neuroscience, 0302 clinical medicine, epileptic encephalopathy, ATG mutations, start-loss mutation, genetics, whole exome sequencing, microcephaly, recurrent mutation, founder mutation, essential gene, medicine, Genetics, Missense mutation, Animals, Humans, Allele, Founder mutation, Zebrafish, Exome sequencing, 030304 developmental biology, 0303 health sciences, Mutation, Original Paper, Brain Diseases, Genes, Essential, biology, Epileptic encephalopathy, Whole exome sequencing, Infant, biology.organism_classification, medicine.disease, 3. Good health, Pedigree, Start-loss mutation, Essential gene, Child, Preschool, Female, Neurology (clinical), Epileptic Syndromes, 030217 neurology & neurosurgery
Abstract

Developmental and/or epileptic encephalopathies (DEEs) are a group of devastating genetic disorders, resulting in early-onset, therapy-resistant seizures and developmental delay. Here we report on 22 individuals from 15 families presenting with a severe form of intractable epilepsy, severe developmental delay, progressive microcephaly, visual disturbance and similar minor dysmorphisms. Whole exome sequencing identified a recurrent, homozygous variant (chr2:64083454A > G) in the essential UDP-glucose pyrophosphorylase (UGP2) gene in all probands. This rare variant results in a tolerable Met12Val missense change of the longer UGP2 protein isoform but causes a disruption of the start codon of the shorter isoform, which is predominant in brain. We show that the absence of the shorter isoform leads to a reduction of functional UGP2 enzyme in neural stem cells, leading to altered glycogen metabolism, upregulated unfolded protein response and premature neuronal differentiation, as modeled during pluripotent stem cell differentiation in vitro. In contrast, the complete lack of all UGP2 isoforms leads to differentiation defects in multiple lineages in human cells. Reduced expression of Ugp2a/Ugp2b in vivo in zebrafish mimics visual disturbance and mutant animals show a behavioral phenotype. Our study identifies a recurrent start codon mutation in UGP2 as a cause of a novel autosomal recessive DEE syndrome. Importantly, it also shows that isoform-specific start-loss mutations causing expression loss of a tissue-relevant isoform of an essential protein can cause a genetic disease, even when an organism-wide protein absence is incompatible with life. We provide additional examples where a similar disease mechanism applies. Electronic supplementary material The online version of this article (10.1007/s00401-019-02109-6) contains supplementary material, which is available to authorized users.

Published
2020

32. De Novo Variants in SPOP Cause Two Clinically Distinct Neurodevelopmental Disorders

Author

Hanka Venselaar, Jennifer Keller-Ramey, Arjan P.M. de Brouwer, Tiziano Bernasocchi, Amber Begtrup, Michael Parker, Margot I. Van Allen, Koen L.I. van Gassen, Christian Gilissen, Maria J. Nabais Sá, Lisenka E.L.M. Vissers, Ellen R. Elias, Daniela del Gaudio, Sarah L. Sawyer, Bert B.A. de Vries, Farah Kanani, Jean-Philippe Theurillat, Klaas J. Wierenga, Marie-José H. van den Boogaard, Gabriela Purcarin, Rolph Pfundt, Laurens Wiel, and Geniver El Tekle

Subjects
Male, Microcephaly, Adolescent, Mutation, Missense, SPOP, Biology, 03 medical and health sciences, Young Adult, All institutes and research themes of the Radboud University Medical Center, 0302 clinical medicine, Germline mutation, Neurodevelopmental disorder, Report, Intellectual Disability, Genetics, medicine, Missense mutation, Humans, Hypertelorism, Child, Genetics (clinical), Exome sequencing, 030304 developmental biology, 0303 health sciences, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], Skull, Macrocephaly, Facies, Infant, Nuclear Proteins, Metabolic Disorders Radboud Institute for Molecular Life Sciences [Radboudumc 6], medicine.disease, Repressor Proteins, Neurodevelopmental Disorders, Child, Preschool, Female, medicine.symptom, Nanomedicine Radboud Institute for Molecular Life Sciences [Radboudumc 19], 030217 neurology & neurosurgery
Abstract

Recurrent somatic variants in SPOP are cancer specific; endometrial and prostate cancers result from gain-of-function and dominant-negative effects toward BET proteins, respectively. By using clinical exome sequencing, we identified six de novo pathogenic missense variants in SPOP in seven individuals with developmental delay and/or intellectual disability, facial dysmorphisms, and congenital anomalies. Two individuals shared craniofacial dysmorphisms, including congenital microcephaly, that were strikingly different from those of the other five individuals, who had (relative) macrocephaly and hypertelorism. We measured the effect of SPOP variants on BET protein amounts in human Ishikawa endometrial cancer cells and patient-derived cell lines because we hypothesized that variants would lead to functional divergent effects on BET proteins. The de novo variants c.362G>A (p.Arg121Gln) and c. 430G>A (p.Asp144Asn), identified in the first two individuals, resulted in a gain of function, and conversely, the c.73A>G (p.Thr25Ala), c.248A>G (p.Tyr83Cys), c.395G>T (p.Gly132Val), and c.412C>T (p.Arg138Cys) variants resulted in a dominant-negative effect. Our findings suggest that these opposite functional effects caused by the variants in SPOP result in two distinct and clinically recognizable syndromic forms of intellectual disability with contrasting craniofacial dysmorphisms.

Published
2020

33. TANGO2: expanding the clinical phenotype and spectrum of pathogenic variants

Author

Alison M. Muir, Dianne Laboy Cintrón, Katherine H. Kim, Amber Begtrup, Peter I. Karachunski, Almuth Caliebe, Heather C Mefford, Amy Lacroix, J. Lawrence Merritt, Kirsty McWalter, Angela Sun, Sharon F. Suchy, Barbara K. Burton, Ingo Helbig, René Santer, Joline C. Dalton, Dmitriy Niyazov, Rachel Westman, Ganka Douglas, Leah Fleming, Hiltrud Muhle, Kristin G. Monaghan, Alice Basinger, Katherine L. Helbig, Jenny Thies, Kolja Becker, Manuela Pendziwiat, Can Ficicioglu, Megan T. Cho, Jennifer N. Dines, Francisca Millan, and Katie Golden-Grant

Subjects
Male, 0301 basic medicine, Adolescent, DNA Copy Number Variations, Genotype, Developmental Disabilities, Encephalopathy, developmental delay DNA copy-number variation, 030105 genetics & heredity, Compound heterozygosity, Bioinformatics, Article, 03 medical and health sciences, Epilepsy, Genotype-phenotype distinction, Seizures, Intellectual Disability, Intellectual disability, medicine, Humans, Exome, Family, intragenic deletion, Child, Genetics (clinical), Exome sequencing, Brain Diseases, business.industry, Aryl Hydrocarbon Receptor Nuclear Translocator, Correction, medicine.disease, Phenotype, Pedigree, 3. Good health, 030104 developmental biology, Child, Preschool, epilepsy, Female, business, exome sequencing
Abstract

Purpose TANGO2-related disorders were first described in 2016 and prior to this publication, only 15 individuals with TANGO2-related disorder were described in the literature. Primary features include metabolic crisis with rhabdomyolysis, encephalopathy, intellectual disability, seizures, and cardiac arrhythmias. We assess whether genotype and phenotype of TANGO2-related disorder has expanded since the initial discovery and determine the efficacy of exome sequencing (ES) as a diagnostic tool for detecting variants. Methods We present a series of 14 individuals from 11 unrelated families with complex medical and developmental histories, in whom ES or microarray identified compound heterozygous or homozygous variants in TANGO2. Results The initial presentation of patients with TANGO2-related disorders can be variable, including primarily neurological presentations. We expand the phenotype and genotype for TANGO2, highlighting the variability of the disorder. Conclusion TANGO2-related disorders can have a more diverse clinical presentation than previously anticipated. We illustrate the utility of routine ES data reanalysis whereby discovery of novel disease genes can lead to a diagnosis in previously unsolved cases and the need for additional copy-number variation analysis when ES is performed.

Published
2018

34. Correction to: An autosomal dominant neurological disorder caused by de novo variants in FAR1 resulting in uncontrolled synthesis of ether lipids

Author

Sacha Ferdinandusse, Kirsty McWalter, Heleen te Brinke, Lodewijk IJlst, Petra M. Mooijer, Jos P.N. Ruiter, Alida E.M. van Lint, Mia Pras-Raves, Eric Wever, Francisca Millan, Maria J. Guillen Sacoto, Amber Begtrup, Mark Tarnopolsky, Lauren Brady, Roger L. Ladda, Susan L. Sell, Catherine B. Nowak, Jessica Douglas, Cuixia Tian, Elizabeth Ulm, Seth Perlman, Arlene V. Drack, Karen Chong, Nicole Martin, Jennifer Brault, Elly Brokamp, Camilo Toro, William A. Gahl, Ellen F. Macnamara, Lynne Wolfe, Mercedes E. Alejandro, Mahshid S. Azamian, Carlos A. Bacino, Ashok Balasubramanyam, Lindsay C. Burrage, Hsiao-Tuan Chao, Gary D. Clark, William J. Craigen, Hongzheng Dai, Shweta U. Dhar, Lisa T. Emrick, Alica M. Goldman, Neil A. Hanchard, Fariha Jamal, Lefkothea Karaviti, Seema R. Lalani, Brendan H. Lee, Richard A. Lewis, Ronit Marom, Paolo M. Moretti, David R. Murdock, Sarah K. Nicholas, James P. Orengo, Jennifer E. Posey, Lorraine Potocki, Jill A. Rosenfeld, Susan L. Samson, Daryl A. Scott, Alyssa A. Tran, Tiphanie P. Vogel, Michael F. Wangler, Shinya Yamamoto, Christine M. Eng, Pengfei Liu, Patricia A. Ward, Edward Behrens, Matthew Deardorff, Marni Falk, Kelly Hassey, Kathleen Sullivan, Adeline Vanderver, David B. Goldstein, Heidi Cope, Allyn McConkie-Rosell, Kelly Schoch, Vandana Shashi, Edward C. Smith, Rebecca C. Spillmann, Jennifer A. Sullivan, Queenie K.-G. Tan, Nicole M. Walley, Pankaj B. Agrawal, Alan H. Beggs, Gerard T. Berry, Lauren C. Briere, Laurel A. Cobban, Matthew Coggins, Cynthia M. Cooper, Elizabeth L. Fieg, Frances High, Ingrid A. Holm, Susan Korrick, Joel B. Krier, Sharyn A. Lincoln, Joseph Loscalzo, Richard L. Maas, Calum A. MacRae, J. Carl Pallais, Deepak A. Rao, Lance H. Rodan, Edwin K. Silverman, Joan M. Stoler, David A. Sweetser, Melissa Walker, Chris A. Walsh, Cecilia Esteves, Emily G. Kelley, Isaac S. Kohane, Kimberly LeBlanc, Alexa T. McCray, Anna Nagy, Surendra Dasari, Brendan C. Lanpher, Ian R. Lanza, Eva Morava, Devin Oglesbee, Guney Bademci, Deborah Barbouth, Stephanie Bivona, Olveen Carrasquillo, Ta Chen Peter Chang, Irman Forghani, Alana Grajewski, Rosario Isasi, Byron Lam, Roy Levitt, Xue Zhong Liu, Jacob McCauley, Ralph Sacco, Mario Saporta, Judy Schaechter, Mustafa Tekin, Fred Telischi, Willa Thorson, Stephan Zuchner, Heather A. Colley, Jyoti G. Dayal, David J. Eckstein, Laurie C. Findley, Donna M. Krasnewich, Laura A. Mamounas, Teri A. Manolio, John J. Mulvihill, Grace L. LaMoure, Madison P. Goldrich, Tiina K. Urv, Argenia L. Doss, Maria T. Acosta, Carsten Bonnenmann, Precilla D’Souza, David D. Draper, Carlos Ferreira, Rena A. Godfrey, Catherine A. Groden, Valerie V. Maduro, Thomas C. Markello, Avi Nath, Donna Novacic, Barbara N. Pusey, Colleen E. Wahl, Eva Baker, Elizabeth A. Burke, David R. Adams, May Christine V. Malicdan, Cynthia J. Tifft, Lynne A. Wolfe, John Yang, Bradley Power, Bernadette Gochuico, Laryssa Huryn, Lea Latham, Joie Davis, Deborah Mosbrook-Davis, Francis Rossignol, Ben Solomon, John MacDowall, Audrey Thurm, Wadih Zein, Muhammad Yousef, Margaret Adam, Laura Amendola, Michael Bamshad, Anita Beck, Jimmy Bennett, Beverly Berg-Rood, Elizabeth Blue, Brenna Boyd, Peter Byers, Sirisak Chanprasert, Michael Cunningham, Katrina Dipple, Daniel Doherty, Dawn Earl, Ian Glass, Katie Golden-Grant, Sihoun Hahn, Anne Hing, Fuki M. Hisama, Martha Horike-Pyne, Gail P. Jarvik, Jeffrey Jarvik, Suman Jayadev, Christina Lam, Kenneth Maravilla, Heather Mefford, J. Lawrence Merritt, Ghayda Mirzaa, Deborah Nickerson, Wendy Raskind, Natalie Rosenwasser, C. Ron Scott, Angela Sun, Virginia Sybert, Stephanie Wallace, Mark Wener, Tara Wenger, Euan A. Ashley, Gill Bejerano, Jonathan A. Bernstein, Devon Bonner, Terra R. Coakley, Liliana Fernandez, Paul G. Fisher, Laure Fresard, Jason Hom, Yong Huang, Jennefer N. Kohler, Elijah Kravets, Marta M. Majcherska, Beth A. Martin, Shruti Marwaha, Colleen E. McCormack, Archana N. Raja, Chloe M. Reuter, Maura Ruzhnikov, Jacinda B. Sampson, Kevin S. Smith, Shirley Sutton, Holly K. Tabor, Brianna M. Tucker, Matthew T. Wheeler, Diane B. Zastrow, Chunli Zhao, William E. Byrd, Andrew B. Crouse, Matthew Might, Mariko Nakano-Okuno, Jordan Whitlock, Gabrielle Brown, Manish J. Butte, Esteban C. Dell’Angelica, Naghmeh Dorrani, Emilie D. Douine, Brent L. Fogel, Irma Gutierrez, Alden Huang, Deborah Krakow, Hane Lee, Sandra K. Loo, Bryan C. Mak, Martin G. Martin, Julian A. Martínez-Agosto, Elisabeth McGee, Stanley F. Nelson, Shirley Nieves-Rodriguez, Christina G.S. Palmer, Jeanette C. Papp, Neil H. Parker, Genecee Renteria, Rebecca H. Signer, Janet S. Sinsheimer, Jijun Wan, Lee-kai Wang, Katherine Wesseling Perry, Jeremy D. Woods, Justin Alvey, Ashley Andrews, Jim Bale, John Bohnsack, Lorenzo Botto, John Carey, Laura Pace, Nicola Longo, Gabor Marth, Paolo Moretti, Aaron Quinlan, Matt Velinder, Dave Viskochil, Pinar Bayrak-Toydemir, Rong Mao, Monte Westerfield, Anna Bican, Laura Duncan, Rizwan Hamid, Jennifer Kennedy, Mary Kozuira, John H. Newman, John A. Phillips, Lynette Rives, Amy K. Robertson, Emily Solem, Joy D. Cogan, F. Sessions Cole, Nichole Hayes, Dana Kiley, Kathy Sisco, Jennifer Wambach, Daniel Wegner, Dustin Baldridge, Stephen Pak, Timothy Schedl, Jimann Shin, Lilianna Solnica-Krezel, Quinten Waisfisz, Petra J.G. Zwijnenburg, Alban Ziegler, Magalie Barth, Rosemarie Smith, Sara Ellingwood, Deborah Gaebler-Spira, Somayeh Bakhtiari, Michael C. Kruer, Antoine H.C. van Kampen, Ronald J.A. Wanders, Hans R. Waterham, David Cassiman, and Frédéric M. Vaz

Subjects
Phenotype, Spastic Paraplegia, Hereditary, Correction, Humans, Aldehyde Oxidoreductases, Lipids, Genetics (clinical), Ethers
Abstract

In this study we investigate the disease etiology in 12 patients with de novo variants in FAR1 all resulting in an amino acid change at position 480 (p.Arg480Cys/His/Leu).Following next-generation sequencing and clinical phenotyping, functional characterization was performed in patients' fibroblasts using FAR1 enzyme analysis, FAR1 immunoblotting/immunofluorescence, and lipidomics.All patients had spastic paraparesis and bilateral congenital/juvenile cataracts, in most combined with speech and gross motor developmental delay and truncal hypotonia. FAR1 deficiency caused by biallelic variants results in defective ether lipid synthesis and plasmalogen deficiency. In contrast, patients' fibroblasts with the de novo FAR1 variants showed elevated plasmalogen levels. Further functional studies in fibroblasts showed that these variants cause a disruption of the plasmalogen-dependent feedback regulation of FAR1 protein levels leading to uncontrolled ether lipid production.Heterozygous de novo variants affecting the Arg480 residue of FAR1 lead to an autosomal dominant disorder with a different disease mechanism than that of recessive FAR1 deficiency and a diametrically opposed biochemical phenotype. Our findings show that for patients with spastic paraparesis and bilateral cataracts, FAR1 should be considered as a candidate gene and added to gene panels for hereditary spastic paraplegia, cerebral palsy, and juvenile cataracts.

Published
2021

35. WDR26 Haploinsufficiency Causes a Recognizable Syndrome of Intellectual Disability, Seizures, Abnormal Gait, and Distinctive Facial Features

Author

Dagmar Wieczorek, Stephen P. Robertson, Lynne M. Bird, Megan T. Cho, Avni Santani, Amber Begtrup, Cara M. Skraban, Marlies Kempers, Richard E. Person, Tjitske Kleefstra, Martina M. Owens, Koen L.I. van Gassen, Kristin McDonald Gibson, Alice Goldenberg, Preetha Markose, Evelien Zonneveld-Huijssoon, Katelyn Payne, Arjan P.M. de Brouwer, Taylor C. Warner, Jane Juusola, Matthew A. Deardorff, Kajia Cao, John A. Bernat, Claire L. S. Turner, Addie I. Nesbitt, Esther Kinning, Amber Stocco, Patricia G. Wheeler, Nienke E. Verbeek, Alisha Wilkens, David Markie, Ganka Douglas, A. Micheil Innes, Elizabeth Denenberg, P.Y. Billie Au, Katheryn Grand, Rolph Pfundt, Constance F. Wells, and Laurence E. Walsh

Subjects
Male, 0301 basic medicine, RNA Stability, Haploinsufficiency, Biology, medicine.disease_cause, 03 medical and health sciences, 0302 clinical medicine, Seizures, Report, Intellectual Disability, Intellectual disability, Journal Article, Genetics, Spastic, medicine, Humans, Missense mutation, Genetics(clinical), Amino Acid Sequence, Child, Preschool, Gait, Exome, Genetics (clinical), Adaptor Proteins, Signal Transducing, 1q41q42 microdeletion syndrome, Mutation, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], Base Sequence, Facies, Proteins, Syndrome, medicine.disease, Phenotype, 030104 developmental biology, Child, Preschool, Female, Growth and Development, Chromosome Deletion, 030217 neurology & neurosurgery, Rare cancers Radboud Institute for Health Sciences [Radboudumc 9]
Abstract

Contains fulltext : 177285.pdf (Publisher’s version ) (Closed access) We report 15 individuals with de novo pathogenic variants in WDR26. Eleven of the individuals carry loss-of-function mutations, and four harbor missense substitutions. These 15 individuals comprise ten females and five males, and all have intellectual disability with delayed speech, a history of febrile and/or non-febrile seizures, and a wide-based, spastic, and/or stiff-legged gait. These subjects share a set of common facial features that include a prominent maxilla and upper lip that readily reveal the upper gingiva, widely spaced teeth, and a broad nasal tip. Together, these features comprise a recognizable facial phenotype. We compared these features with those of chromosome 1q41q42 microdeletion syndrome, which typically contains WDR26, and noted that clinical features are consistent between the two subsets, suggesting that haploinsufficiency of WDR26 contributes to the pathology of 1q41q42 microdeletion syndrome. Consistent with this, WDR26 loss-of-function single-nucleotide mutations identified in these subjects lead to nonsense-mediated decay with subsequent reduction of RNA expression and protein levels. We derived a structural model of WDR26 and note that missense variants identified in these individuals localize to highly conserved residues of this WD-40-repeat-containing protein. Given that WDR26 mutations have been identified in approximately 1 in 2,000 of subjects in our clinical cohorts and that WDR26 might be poorly annotated in exome variant-interpretation pipelines, we would anticipate that this disorder could be more common than currently appreciated.

Published
2017

36. STAG1 mutations cause a novel cohesinopathy characterised by unspecific syndromic intellectual disability

Author

Julien Thevenon, Christiane Zweier, Hilde Olivié, Nicole Revencu, Aurélia Jacquette, Megan T. Cho, Anne-Laure Mosca-Boidron, Marjolein H. Willemsen, Laurence Faivre, Yannis Duffourd, Odile Boute-Benejean, Elaine H. Zackai, Carey McDougall, Amber Begtrup, Anita Rauch, Christel Thauvin-Robinet, Perrine Charles, Koen L.I. van Gassen, Thomas Smol, Laurence Duplomb-Jego, Daphné Lehalle, Amanda Clarkson, Orrin Devinsky, Catherine Vincent-Delorme, Paul Kuentz, Bénédicte Gérard, Patrick Callier, Karol Rubin, Jean-Baptiste Rivière, Sébastien Moutton, Deborah J. Shears, Ana Lisa Taylor Tavares, Ingrid Simonic, Paulien A. Terhal, Soo-Mi Park, Alice Masurel-Paulet, and Golder N. Wilson

Subjects
0301 basic medicine, Genetics, Mutation, Cohesin complex, Point mutation, Biology, medicine.disease, medicine.disease_cause, Bioinformatics, Frameshift mutation, 03 medical and health sciences, 030104 developmental biology, 0302 clinical medicine, Intellectual disability, medicine, Journal Article, Missense mutation, Gene, 030217 neurology & neurosurgery, Genetics (clinical), Exome sequencing, Rare cancers Radboud Institute for Health Sciences [Radboudumc 9]
Abstract

Item does not contain fulltext BACKGROUND: Cohesinopathies are rare neurodevelopmental disorders arising from a dysfunction in the cohesin pathway, which enables chromosome segregation and regulates gene transcription. So far, eight genes from this pathway have been reported in human disease. STAG1 belongs to the STAG subunit of the core cohesin complex, along with five other subunits. This work aimed to identify the phenotype ascribed to STAG1 mutations. METHODS: Among patients referred for intellectual disability (ID) in genetics departments worldwide, array-comparative genomic hybridisation (CGH), gene panel, whole-exome sequencing or whole-genome sequencing were performed following the local diagnostic standards. RESULTS: A mutation in STAG1 was identified in 17 individuals from 16 families, 9 males and 8 females aged 2-33 years. Four individuals harboured a small microdeletion encompassing STAG1; three individuals from two families had an intragenic STAG1 deletion. Six deletions were identified by array-CGH, one by whole-exome sequencing. Whole-exome sequencing found de novo heterozygous missense or frameshift STAG1 variants in eight patients, a panel of genes involved in ID identified a missense and a frameshift variant in two individuals. The 17 patients shared common facial features, with wide mouth and deep-set eyes. Four individuals had mild microcephaly, seven had epilepsy. CONCLUSIONS: We report an international series of 17 individuals from 16 families presenting with syndromic unspecific ID that could be attributed to a STAG1 deletion or point mutation. This first series reporting the phenotype ascribed to mutation in STAG1 highlights the importance of data sharing in the field of rare disorders.

Published
2017

37. Loss of UGP2 in brain leads to a severe epileptic encephalopathy, emphasizing that bi-allelic isoform specific start-loss mutations of essential genes can cause genetic diseases

Author

Henry Houlden, Aida M. Bertoli-Avella, Marjon van Slegtenhorst, Edwin H. Jacobs, Ehsan Ghayoor Karimiani, Eleonora Aronica, Peter Bauer, Atieh Eslahi, Amna Al Futaisi, Tjakko J. van Ham, Jennefer N. Kohler, Stephanie Efthymiou, Reza Maroofian, Darija Putar, Mariya Kozenko, Jana Vandrovcova, Walter G. de Valk, Jonathan A. Bernstein, Amber Begtrup, Kyle Retterer, Renjith Mani, Jozef Hertecant, Evita Medici-van den Herik, Alice S. Brooks, Elena Perenthaler, Rebecca I. Torene, Woutje M. Berdowski, Wilfred F. J. van IJcken, Kristin G. Monaghan, Majid Mojarrad, Nuzhat Rana, Anita Nikoncuk, Faisal Zafar, Tahsin Stefan Barakat, Paul van den Berg, Soheil Yousefi, Krishna Kumar Kandaswamy, Ivan Čapo, Fathiya Al Murshedi, Fateme Massinaei Darmiyan, Faisal Al Azri, Lauren Brick, Erik-Jan Kamsteeg, Mehrnaz Ghazvini, Herma C. van der Linde, Mohammad Doosti, and Zaynab Khazaei

Subjects
Gene isoform, Protein isoform, Genetics, 0303 health sciences, Mutation, Biology, medicine.disease_cause, biology.organism_classification, 3. Good health, 03 medical and health sciences, 0302 clinical medicine, medicine, Missense mutation, Allele, Gene, Zebrafish, 030217 neurology & neurosurgery, Exome sequencing, 030304 developmental biology
Abstract

Developmental and/or epileptic encephalopathies (DEEs) are a group of devastating genetic disorders, resulting in early onset, therapy resistant seizures and developmental delay. Here we report on 12 individuals from 10 families presenting with a severe form of intractable epilepsy, severe developmental delay, progressive microcephaly and visual disturbance. Whole exome sequencing identified a recurrent, homozygous variant (chr2:64083454A>G) in the essentialUDP-glucose pyrophosphorylase(UGP2) gene in all probands. This rare variant results in a tolerable Met12Val missense change of the longer UGP2 protein isoform but causes a disruption of the start codon of the shorter isoform. We show that the absence of the shorter isoform leads to a reduction of functional UGP2 enzyme in brain cell types, leading to altered glycogen metabolism, upregulated unfolded protein response and premature neuronal differentiation, as modelled during pluripotent stem cell differentiationin vitro. In contrast, the complete lack of all UGP2 isoforms leads to differentiation defects in multiple lineages in human cells. Reduced expression of Ugp2a/Ugp2bin vivoin zebrafish mimics visual disturbance and mutant animals show a behavioral phenotype. Our study identifies a recurrent start codon mutation inUGP2as a cause of a novel autosomal recessive DEE. Importantly, it also shows that isoform specific start-loss mutations causing expression loss of a tissue relevant isoform of an essential protein can cause a genetic disease, even when an organism-wide protein absence is incompatible with life. We provide additional examples where a similar disease mechanism applies.

Published
2019

38. De Novo Pathogenic Variants in N-cadherin Cause a Syndromic Neurodevelopmental Disorder with Corpus Callosum, Axon, Cardiac, Ocular, and Genital Defects

Author

Andrea Accogli, Sara Calabretta, Judith St-Onge, Nassima Boudrahem-Addour, Alexandre Dionne-Laporte, Pascal Joset, Silvia Azzarello-Burri, Anita Rauch, Joel Krier, Elizabeth Fieg, Juan C. Pallais, Allyn McConkie-Rosell, Marie McDonald, Sharon F. Freedman, Jean-Baptiste Rivière, Joël Lafond-Lapalme, Brittany N. Simpson, Robert J. Hopkin, Aurélien Trimouille, Julien Van-Gils, Amber Begtrup, Kirsty McWalter, Heron Delphine, Boris Keren, David Genevieve, Emanuela Argilli, Elliott H. Sherr, Mariasavina Severino, Guy A. Rouleau, Patricia T. Yam, Frédéric Charron, Myriam Srour, Maria T. Acosta, David R. Adams, Pankaj Agrawal, Mercedes E. Alejandro, Patrick Allard, Justin Alvey, Ashley Andrews, Euan A. Ashley, Mahshid S. Azamian, Carlos A. Bacino, Guney Bademci, Eva Baker, Ashok Balasubramanyam, Dustin Baldridge, Jim Bale, Deborah Barbouth, Gabriel F. Batzli, Pinar Bayrak-Toydemir, Alan H. Beggs, Gill Bejerano, Hugo J. Bellen, Jonathan A. Bernstein, Gerard T. Berry, Anna Bican, David P. Bick, Camille L. Birch, Stephanie Bivona, John Bohnsack, Carsten Bonnenmann, Devon Bonner, Braden E. Boone, Bret L. Bostwick, Lorenzo Botto, Lauren C. Briere, Elly Brokamp, Donna M. Brown, Matthew Brush, Elizabeth A. Burke, Lindsay C. Burrage, Manish J. Butte, John Carey, Olveen Carrasquillo, Ta Chen Peter Chang, Hsiao-Tuan Chao, Gary D. Clark, Terra R. Coakley, Laurel A. Cobban, Joy D. Cogan, F. Sessions Cole, Heather A. Colley, Cynthia M. Cooper, Heidi Cope, William J. Craigen, Precilla D’Souza, Surendra Dasari, Mariska Davids, Jyoti G. Dayal, Esteban C. Dell’Angelica, Shweta U. Dhar, Naghmeh Dorrani, Daniel C. Dorset, Emilie D. Douine, David D. Draper, Laura Duncan, David J. Eckstein, Lisa T. Emrick, Christine M. Eng, Cecilia Esteves, Tyra Estwick, Liliana Fernandez, Carlos Ferreira, Elizabeth L. Fieg, Paul G. Fisher, Brent L. Fogel, Irman Forghani, Laure Fresard, William A. Gahl, Rena A. Godfrey, Alica M. Goldman, David B. Goldstein, Jean-Philippe F. Gourdine, Alana Grajewski, Catherine A. Groden, Andrea L. Gropman, Melissa Haendel, Rizwan Hamid, Neil A. Hanchard, Nichole Hayes, Frances High, Ingrid A. Holm, Jason Hom, Alden Huang, Yong Huang, Rosario Isasi, Fariha Jamal, Yong-hui Jiang, Jean M. Johnston, Angela L. Jones, Lefkothea Karaviti, Emily G. Kelley, Dana Kiley, David M. Koeller, Isaac S. Kohane, Jennefer N. Kohler, Deborah Krakow, Donna M. Krasnewich, Susan Korrick, Mary Koziura, Joel B. Krier, Jennifer E. Kyle, Seema R. Lalani, Byron Lam, Brendan C. Lanpher, Ian R. Lanza, C. Christopher Lau, Jozef Lazar, Kimberly LeBlanc, Brendan H. Lee, Hane Lee, Roy Levitt, Shawn E. Levy, Richard A. Lewis, Sharyn A. Lincoln, Pengfei Liu, Xue Zhong Liu, Nicola Longo, Sandra K. Loo, Joseph Loscalzo, Richard L. Maas, Ellen F. Macnamara, Calum A. MacRae, Valerie V. Maduro, Marta M. Majcherska, May Christine V. Malicdan, Laura A. Mamounas, Teri A. Manolio, Rong Mao, Thomas C. Markello, Ronit Marom, Gabor Marth, Beth A. Martin, Martin G. Martin, Julian A. Martínez-Agosto, Shruti Marwaha, Thomas May, Jacob McCauley, Colleen E. McCormack, Alexa T. McCray, Thomas O. Metz, Matthew Might, Eva Morava-Kozicz, Paolo M. Moretti, Marie Morimoto, John J. Mulvihill, David R. Murdock, Avi Nath, Stan F. Nelson, J. Scott Newberry, John H. Newman, Sarah K. Nicholas, Donna Novacic, Devin Oglesbee, James P. Orengo, Laura Pace, Stephen Pak, J. Carl Pallais, Christina G.S. Palmer, Jeanette C. Papp, Neil H. Parker, John A. Phillips, Jennifer E. Posey, John H. Postlethwait, Lorraine Potocki, Barbara N. Pusey, Aaron Quinlan, Archana N. Raja, Genecee Renteria, Chloe M. Reuter, Lynette Rives, Amy K. Robertson, Lance H. Rodan, Jill A. Rosenfeld, Robb K. Rowley, Maura Ruzhnikov, Ralph Sacco, Jacinda B. Sampson, Susan L. Samson, Mario Saporta, Judy Schaechter, Timothy Schedl, Kelly Schoch, Daryl A. Scott, Lisa Shakachite, Prashant Sharma, Vandana Shashi, Kathleen Shields, Jimann Shin, Rebecca Signer, Catherine H. Sillari, Edwin K. Silverman, Janet S. Sinsheimer, Kathy Sisco, Kevin S. Smith, Lilianna Solnica-Krezel, Rebecca C. Spillmann, Joan M. Stoler, Nicholas Stong, Jennifer A. Sullivan, Shirley Sutton, David A. Sweetser, Holly K. Tabor, Cecelia P. Tamburro, Queenie K.-G. Tan, Mustafa Tekin, Fred Telischi, Willa Thorson, Cynthia J. Tifft, Camilo Toro, Alyssa A. Tran, Tiina K. Urv, Matt Velinder, Dave Viskochil, Tiphanie P. Vogel, Colleen E. Wahl, Nicole M. Walley, Chris A. Walsh, Melissa Walker, Jennifer Wambach, Jijun Wan, Lee-kai Wang, Michael F. Wangler, Patricia A. Ward, Katrina M. Waters, Bobbie-Jo M. Webb-Robertson, Daniel Wegner, Monte Westerfield, Matthew T. Wheeler, Anastasia L. Wise, Lynne A. Wolfe, Jeremy D. Woods, Elizabeth A. Worthey, Shinya Yamamoto, John Yang, Amanda J. Yoon, Guoyun Yu, Diane B. Zastrow, Chunli Zhao, Stephan Zuchner, McGill University Health Center [Montreal] (MUHC), Istituto di ricovero e cura a carattere scientifico Azienda Ospedaliera Universitaria 'San Martino' (IRCCS AOU San Martino), Institut de Recherches Cliniques de Montréal (IRCM), Université de Montréal (UdeM), Montreal Neurological Institute and Hospital, McGill University = Université McGill [Montréal, Canada], University hospital of Zurich [Zurich], Universität Zürich [Zürich] = University of Zurich (UZH), Brigham & Women’s Hospital [Boston] (BWH), Harvard Medical School [Boston] (HMS), Duke University [Durham], Duke University Medical Center, Génétique des Anomalies du Développement (GAD), IFR100 - Structure fédérative de recherche Santé-STIC-Université de Bourgogne (UB), University of Cincinnati (UC), Cincinnati Children's Hospital Medical Center, Laboratoire Maladies Rares: Génétique et Métabolisme (Bordeaux) (U1211 INSERM/MRGM), Université de Bordeaux (UB)-Groupe hospitalier Pellegrin-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Bordeaux (UB), GeneDx [Gaithersburg, MD, USA], Service de Génétique Cytogénétique et Embryologie [CHU Pitié-Salpêtrière], CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Cellules Souches, Plasticité Cellulaire, Médecine Régénératrice et Immunothérapies (IRMB), Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), University of California [San Francisco] (UCSF), University of California, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Fondazione 'Istituto Neurologico Nazionale C. Mondino', Hôpital Bicêtre, Université Paris-Sud - Paris 11 (UP11)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Bicêtre, Institute of Physics, Saink School Post, Institut de Physique du Globe de Paris (IPGP), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-IPG PARIS-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Centre National de la Recherche Scientifique (CNRS), Genomics Program and Division of Genetics, Harvard Medical School [Boston] (HMS)-Boston Children's Hospital-The Manton Center for Orphan Disease Research, Représentations musicales (Repmus), Sciences et Technologies de la Musique et du Son (STMS), Institut de Recherche et Coordination Acoustique/Musique (IRCAM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche et Coordination Acoustique/Musique (IRCAM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Drapper, HudsonAlpha Institute for Biotechnology [Huntsville, AL], Queen Mary University of London (QMUL), Institute of Child Health, Department of Molecular and Human Genetics (Baylor College of Medicine), Baylor College of Medecine, Division of Biomedical Statistics and Informatics, Mayo Clinic, Facultat de Fisica, Departament Universitari d'Optica, Universitat de València (UV), Department of Pathology, University of Alabama at Birmingham [ Birmingham] (UAB), Center for Neuroscience Research (CNMC), Center for Neuroscience Research, Oregon Health and Science University [Portland] (OHSU), Baylor College of Medicine (BCM), Baylor University, Stanford University School of Medicine [CA, USA], Department of Molecular Cellular and Developmental Biology, University of California [Los Angeles] (UCLA), University of California-University of California-Howard Hughes Medical Institute (HHMI), Human Genetics, Department of Mathematics [Sussex], University of Sussex, Genomics Program and Division of Genetics [Boston, USA], Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Bioinformatics Research Center, North Carolina State University [Raleigh] (NC State), University of North Carolina System (UNC)-University of North Carolina System (UNC), Biological Sciences Division, Pacific Northwest National Laboratory (PNNL), Departament de Fisica i Enginyeria Nuclear (DEPARTAMENT DI FISICA), Universitat Politècnica de Catalunya [Barcelona] (UPC), Institute of Human Genetics, Rheinische Friedrich-Wilhelms-Universität Bonn, National University of Singapore (NUS), Institute of Neuroscience [Eugene, OR, États-Unis], University of Oregon [Eugene], Boston Children's Hospital, Department of Molecular and Human Genetics [Houston, USA], Metacohorts Consortium, Department of Biological Sciences [Nashville], Vanderbilt University [Nashville], Columbia University Medical Center (CUMC), Columbia University [New York], School of Irish, Celtic Studies, Irish Folklore and Linguistics, University College Dublin [Dublin] (UCD), Stanford School of Medicine [Stanford], Stanford Medicine, Stanford University-Stanford University, Institute for Human Genomics, University of Miami [Coral Gables], ZFIN, Graduate School of Information Systems, University of Electro-Communications [Tokyo] (UEC), John P. Hussman Institute for Human Genomics, University of Miami Leonard M. Miller School of Medicine (UMMSM), Université de Bourgogne (UB)-IFR100 - Structure fédérative de recherche Santé-STIC, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), and Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Heart Defects, Congenital, Heterozygote, [SDV]Life Sciences [q-bio], [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biology, CDH2, Eye, Frameshift mutation, genital defects, corpus callosum, 03 medical and health sciences, 0302 clinical medicine, Report, Genetics, medicine, Missense mutation, Humans, Genitalia, Axon, Frameshift Mutation, Genetics (clinical), N-cadherin, Corpus Callosum Agenesis, Cadherin, eye defects, Cadherins, Molecular biology, Axons, cardiac defects, 030104 developmental biology, medicine.anatomical_structure, ACOG, Neurodevelopmental Disorders, cell-cell adhesion, intellectual disability, Axon guidance, Neural development, 030217 neurology & neurosurgery, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract

International audience; Cadherins constitute a family of transmembrane proteins that mediate calcium-dependent cell-cell adhesion. The extracellular domain of cadherins consists of extracellular cadherin (EC) domains, separated by calcium binding sites. The EC interacts with other cadherin molecules in cis and in trans to mechanically hold apposing cell surfaces together. CDH2 encodes N-cadherin, whose essential roles in neural development include neuronal migration and axon pathfinding. However, CDH2 has not yet been linked to a Mendelian neurodevelopmental disorder. Here, we report de novo heterozygous pathogenic variants (seven missense, two frameshift) in CDH2 in nine individuals with a syndromic neurodevelopmental disorder characterized by global developmental delay and/or intellectual disability, variable axon pathfinding defects (corpus callosum agenesis or hypoplasia, mirror movements, Duane anomaly), and ocular, cardiac, and genital anomalies. All seven missense variants (c.1057G>A [p.Asp353Asn]; c.1789G>A [p.Asp597Asn]; c.1789G>T [p.Asp597Tyr]; c.1802A>C [p.Asn601Thr]; c.1839C>G [p.Cys613Trp]; c.1880A>G [p.Asp627Gly]; c.2027A>G [p.Tyr676Cys]) result in substitution of highly conserved residues, and six of seven cluster within EC domains 4 and 5. Four of the substitutions affect the calcium-binding site in the EC4-EC5 interdomain. We show that cells expressing these variants in the EC4-EC5 domains have a defect in cell-cell adhesion; this defect includes impaired binding in trans with N-cadherin-WT expressed on apposing cells. The two frameshift variants (c.2563_2564delCT [p.Leu855Valfs∗4]; c.2564_2567dupTGTT [p.Leu856Phefs∗5]) are predicted to lead to a truncated cytoplasmic domain. Our study demonstrates that de novo heterozygous variants in CDH2 impair the adhesive activity of N-cadherin, resulting in a multisystemic developmental disorder, that could be named ACOG syndrome (agenesis of corpus callosum, axon pathfinding, cardiac, ocular, and genital defects).

Published
2019

39. Pathogenic WDFY3 variants cause neurodevelopmental disorders and opposing effects on brain size

Author

Meron Azage, David B. Everman, Brooke T. Smith, Steffen Syrbe, Stephen W. Scherer, Jennifer Keller-Ramey, Gregory M. Cooper, Verónica Martínez-Cerdeño, Susan M. Hiatt, Mathew J Wallis, Dmitriy Niyazov, Benjamin Büttner, Rami Abou Jamra, Ryan K. C. Yuen, Johannes R. Lemke, Natasha J Brown, Amber Begtrup, Richard E. Person, Barbara Kellam, Chloé Quélin, Heinrich Sticht, Laurence J. Walsh, Angelo Harlan De Crescenzo, Konstantinos Zarbalis, Jonathan B. Strober, Susan Walker, Alexios A Panoutsopoulos, Shuxi Liu, Diana Le Duc, Urania Kotzaeridou, Michael S. Hildebrand, Michael C. Pride, Eleonora Napoli, Jacqueline N. Crawley, Francis Jeshira Reynoso Santos, Katelyn Payne, Renee Bend, Sandra Yang, Megan T. Cho, Evdokia Anagnostou, Cecilia R Giulivi, Rhonda E. Schnur, Lori Orosco, Andreas Ziegler, Jan H Doering, Christèle Dubourg, Jill L. Silverman, Universität Leipzig [Leipzig], University of California [Davis] (UC Davis), University of California, GeneDx [Gaithersburg, MD, USA], Institut de Génétique et Développement de Rennes (IGDR), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Service de génétique clinique [Rennes], Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-CHU Pontchaillou [Rennes]-hôpital Sud, Shriners Hospitals for Children, U54 HD079125, National Institute of Child Health and Human Development, R21MH115347, National Institute of Mental Health, 286567, Simons Foundation, Nancy Lurie Marks Family Foundation, UM1HG007301, National Human Genome Research Institute, Clinician Scientist Programm, Medizinische Fakultät der Universität Leipzig, Shriners Hospitals for Children Postdoctoral Fellowship, The MIND Institute IDDRC, Universität Leipzig, University of California (UC), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), and Université de Rennes (UR)-CHU Pontchaillou [Rennes]-hôpital Sud

Subjects
0301 basic medicine, Proband, Male, Microcephaly, Secondary, [SDV]Life Sciences [q-bio], Autophagy-Related Proteins, Medical and Health Sciences, Transgenic, Mice, 0302 clinical medicine, Intellectual disability, 2.1 Biological and endogenous factors, Aetiology, Child, Exome, ComputingMilieux_MISCELLANEOUS, Pediatric, Brain, Adaptor Proteins, Organ Size, Mental Health, WDFY3, Autism spectrum disorder, intellectual disability, brain size, Neurological, Female, medicine.symptom, Haploinsufficiency, Biotechnology, Protein Structure, Adolescent, Intellectual and Developmental Disabilities (IDD), Biology, neurodevelopmental delay, 03 medical and health sciences, Clinical Research, medicine, Genetics, Animals, Humans, Preschool, Neurology & Neurosurgery, Psychology and Cognitive Sciences, Macrocephaly, Signal Transducing, Neurosciences, Genetic Variation, medicine.disease, Stem Cell Research, Associative learning, Brain Disorders, 030104 developmental biology, Neurodevelopmental Disorders, Neurology (clinical), Neuroscience, 030217 neurology & neurosurgery
Abstract

The underpinnings of mild to moderate neurodevelopmental delay remain elusive, often leading to late diagnosis and interventions. Here, we present data on exome and genome sequencing as well as array analysis of 13 individuals that point to pathogenic, heterozygous, mostly de novo variants in WDFY3 (significant de novo enrichment P = 0.003) as a monogenic cause of mild and non-specific neurodevelopmental delay. Nine variants were protein-truncating and four missense. Overlapping symptoms included neurodevelopmental delay, intellectual disability, macrocephaly, and psychiatric disorders (autism spectrum disorders/attention deficit hyperactivity disorder). One proband presented with an opposing phenotype of microcephaly and the only missense-variant located in the PH-domain of WDFY3. Findings of this case are supported by previously published data, demonstrating that pathogenic PH-domain variants can lead to microcephaly via canonical Wnt-pathway upregulation. In a separate study, we reported that the autophagy scaffolding protein WDFY3 is required for cerebral cortical size regulation in mice, by controlling proper division of neural progenitors. Here, we show that proliferating cortical neural progenitors of human embryonic brains highly express WDFY3, further supporting a role for this molecule in the regulation of prenatal neurogenesis. We present data on Wnt-pathway dysregulation in Wdfy3-haploinsufficient mice, which display macrocephaly and deficits in motor coordination and associative learning, recapitulating the human phenotype. Consequently, we propose that in humans WDFY3 loss-of-function variants lead to macrocephaly via downregulation of the Wnt pathway. In summary, we present WDFY3 as a novel gene linked to mild to moderate neurodevelopmental delay and intellectual disability and conclude that variants putatively causing haploinsufficiency lead to macrocephaly, while an opposing pathomechanism due to variants in the PH-domain of WDFY3 leads to microcephaly.

Published
2019

40. De Novo Variants Disrupting the HX Repeat Motif of ATN1 Cause a Recognizable Non-Progressive Neurocognitive Syndrome

Author

Tejaswi Kandula, Maria J. Guillen Sacoto, Mais Hashem, Saima Kayani, André E. Minoche, Edwin P. Kirk, Łukasz Jaremko, Heba M. Jalal Ahmed, Marwan Shinawi, Elizabeth E. Palmer, Christel Thauvin, Molly Snyder, Mark J. Cowley, Muddathir H Hamad, Maria Mercedes Villanueva, Seungbeom Hong, Fatema Al Zahrani, Laurence Faivre, Suliat F. Yakubu, Ann M. E. Bye, Velimir Gayevskiy, Megan T. Cho, Jasmeen S. Merzaban, Marisa V. Andrews, Alexander P. Drew, Ruth E. Bristol, Jill A. Rosenfeld, Stefan T. Arold, Lindsay B. Henderson, Antonio Vitobello, Tony Roscioli, Clare Puttick, Mariusz Jaremko, Rui Xiao, Fajr A. Aleisa, Amber Begtrup, Marilyn C. Jones, Fowzan S. Alkuraya, Rebecca Macintosh, Marcel E. Dinger, Kristin Lindstrom, Rani Sachdev, and Angeles Schteinschnaider

Subjects
0301 basic medicine, Male, allelic disorders, Amino Acid Motifs, Neurodegenerative, Medical and Health Sciences, Repetitive Sequences, Epilepsy, Motif (narrative), 0302 clinical medicine, Missense mutation, 2.1 Biological and endogenous factors, Aetiology, Child, Genetics (clinical), Genetics, Pediatric, Genetics & Heredity, Neurodegeneration, Syndrome, Biological Sciences, Prognosis, Phenotype, Hypotonia, developmental delay, intellectual disability, Child, Preschool, symbols, Female, dysmorphic, medicine.symptom, Neurocognitive Disorders, Nerve Tissue Proteins, Biology, 03 medical and health sciences, symbols.namesake, Atrophy, Rare Diseases, Report, medicine, Humans, Preschool, Repetitive Sequences, Nucleic Acid, Nucleic Acid, business.industry, Neurosciences, Correction, Infant, Genetic Variation, medicine.disease, Human genetics, HX repeat, Brain Disorders, 030104 developmental biology, Mendelian inheritance, Human genome, business, Neurocognitive, 030217 neurology & neurosurgery
Abstract

Polyglutamine expansions in the transcriptional co-repressor Atrophin-1, encoded by ATN1, cause the neurodegenerative condition dentatorubral-pallidoluysian atrophy (DRPLA) via a proposed novel toxic gain of function. We present detailed phenotypic information on eight unrelated individuals who have de novo missense and insertion variants within a conserved 16-amino-acid "HX repeat" motif of ATN1. Each of the affected individuals has severe cognitive impairment and hypotonia, a recognizable facial gestalt, and variable congenital anomalies. However, they lack the progressive symptoms typical of DRPLA neurodegeneration. To distinguish this subset of affected individuals from the DRPLA diagnosis, we suggest using the term CHEDDA (congenital hypotonia, epilepsy, developmental delay, digit abnormalities) to classify the condition. CHEDDA-related variants alter the particular structural features of the HX repeat motif, suggesting that CHEDDA results from perturbation of the structural and functional integrity of the HX repeat. We found several non-homologous human genes containing similar motifs of eight to 10 HX repeat sequences, including RERE, where disruptive variants in this motif have also been linked to a separate condition that causes neurocognitive and congenital anomalies. These findings suggest that perturbation of the HX motif might explain other Mendelian human conditions.

Published
2019

41. Aberrant function of the C-terminal tail of HIST1H1E Aacelerates cellular senescence and causes premature aging

Author

Giuseppe Matullo, Brett H. Graham, Elisa Coluzzi, Karit Reinson, Antonella Sgura, Monica H. Wojcik, Luca Pannone, Melissa P. Wasserstein, Lucia Pedace, Seema R. Lalani, Elena Carcarino, Daniela Q.C.M. Barge-Schaapveld, Anke Van Dijck, Austin Larson, Giovanna Carpentieri, Alessandro Bruselles, Simona Petrucci, Simone Pizzi, Elisabetta Flex, Cornelia Di Gaetano, Francesca Clementina Radio, Bruno Dallapiccola, Serena Cecchetti, Clara Viberti, Enrico Bertini, Chieko Chijiwa, Emilia K. Bijlsma, Elisabetta Ferretti, William J. Craigen, Cristina Andreoli, Brian G. Skotko, Daan J. Kamphuis, Alessandro De Luca, J. Louw Roos, Giuseppina Catanzaro, Sandra Kenis, Mariëtte J.V. Hoffer, Katrin Õunap, Maria Karayiorgou, Gijs W. E. Santen, Annette P.M. van den Elzen, Kathleen Brown, Haley Streff, M. E. Suzanne Lewis, Claudia A. L. Ruivenkamp, Xiaoyan Ge, Andrea Ciolfi, Nathalie Van der Aa, Marco Tartaglia, Rossella Rota, Amber Begtrup, Richard E. Person, Simone Martinelli, Koen L.I. van Gassen, R. Frank Kooy, Marije Meuwissen, Magdalena Walkiewicz, Evelina Miele, Marije Koopmans, Sander Pajusalu, Flex, E., Martinelli, S., Van Dijck, A., Ciolfi, A., Cecchetti, S., Coluzzi, E., Pannone, L., Andreoli, C., Radio, F. C., Pizzi, S., Carpentieri, G., Bruselles, A., Catanzaro, G., Pedace, L., Miele, E., Carcarino, E., Ge, X., Chijiwa, C., Lewis, M. E. S., Meuwissen, M., Kenis, S., Van der Aa, N., Larson, A., Brown, K., Wasserstein, M. P., Skotko, B. G., Begtrup, A., Person, R., Karayiorgou, M., Roos, J. L., Van Gassen, K. L., Koopmans, M., Bijlsma, E. K., Santen, G. W. E., Barge-Schaapveld, D. Q. C. M., Ruivenkamp, C. A. L., Hoffer, M. J. V., Lalani, S. R., Streff, H., Craigen, W. J., Graham, B. H., van den Elzen, A. P. M., Kamphuis, D. J., Ounap, K., Reinson, K., Pajusalu, S., Wojcik, M. H., Viberti, C., Di Gaetano, C., Bertini, E., Petrucci, S., De Luca, A., Rota, R., Ferretti, E., Matullo, G., Dallapiccola, B., Sgura, A., Walkiewicz, M., Kooy, R. F., and Tartaglia, M.

Subjects
0301 basic medicine, Premature aging, Senescence, Male, Cell division, methylation profiling, Article, Chromatin remodeling, chromatin remodeling, Histones, 03 medical and health sciences, chemistry.chemical_compound, replicative senescence, 0302 clinical medicine, HIST1H1E, chromatin dynamic, Genetics, accelerated aging, cellular senescence, Humans, Genetics(clinical), Child, Biology, Genetics (clinical), chromatin compaction, chromatin dynamics, linker histone, linker histone H1.4, Aneuploidy, Cell Nucleolus, Cellular Senescence, Chromatin, DNA Methylation, Female, Infant, Middle Aged, biology, DNA replication, Cell biology, 030104 developmental biology, Histone, chemistry, biology.protein, Human medicine, 030217 neurology & neurosurgery, DNA
Abstract

Histones mediate dynamic packaging of nuclear DNA in chromatin, a process that is precisely controlled to guarantee efficient compaction of the genome and proper chromosomal segregation during cell division and to accomplish DNA replication, transcription, and repair. Due to the important structural and regulatory roles played by histones, it is not surprising that histone functional dysregulation or aberrant levels of histones can have severe consequences for multiple cellular processes and ultimately might affect development or contribute to cell transformation. Recently, germline frameshift mutations involving the C-terminal tail of HIST1H1E, which is a widely expressed member of the linker histone family and facilitates higher-order chromatin folding, have been causally linked to an as-yet poorly defined syndrome that includes intellectual disability. We report that these mutations result in stable proteins that reside in the nucleus, bind to chromatin, disrupt proper compaction of DNA, and are associated with a specific methylation pattern. Cells expressing these mutant proteins have a dramatically reduced proliferation rate and competence, hardly enter into the S phase, and undergo accelerated senescence. Remarkably, clinical assessment of a relatively large cohort of subjects sharing these mutations revealed a premature aging phenotype as a previously unrecognized feature of the disorder. Our findings identify a direct link between aberrant chromatin remodeling, cellular senescence, and accelerated aging.

Published
2019

42. De novoloss of function mutations inKIAA2022are associated with epilepsy and neurodevelopmental delay in females

Author

Catherine Nowak, Megan T. Cho, Francisca Millan, Gerald V. Raymond, Aurora Pujol, Kyle Retterer, Amber Begtrup, Rachel Webster, Jessica Douglas, Orrin Devinsky, Wendy K. Chung, Dianalee McKnight, Ayesha Ahmad, and Maria R. Johnson

Subjects
0301 basic medicine, Genetics, education.field_of_study, Population, Biology, medicine.disease, Phenotype, 03 medical and health sciences, Epilepsy, 030104 developmental biology, 0302 clinical medicine, Intellectual disability, medicine, Autism, education, 030217 neurology & neurosurgery, Genetics (clinical), Exome sequencing, Loss function, X chromosome
Abstract

Intellectual disability (ID) affects about 3% of the population and has a male gender bias. Of at least 700 genes currently linked to ID, more than 100 have been identified on the X chromosome, including KIAA2022. KIAA2022 is located on Xq13.3 and is expressed in the developing brain. The protein product of KIAA2022, X‐linked Intellectual Disability Protein Related to Neurite Extension (XPN), is developmentally regulated and is involved in neuronal migration and cell adhesion. The clinical manifestations of loss‐of‐function KIAA2022 mutations have been described previously in 15 males, born from unaffected carrier mothers, but few females. Using whole‐exome sequencing, we identified a cohort of five unrelated female patients with de novo probably gene damaging variants in KIAA2022 and core phenotypic features of ID, developmental delay, epilepsy refractory to treatment, and impaired language, of similar severity as reported for male counterparts. This study supports KIAA2022 as a novel cause of X‐linked dominant ID, and broadens the phenotype for KIAA2022 mutations.

Published
2016

43. De Novo Mutations in SON Disrupt RNA Splicing of Genes Essential for Brain Development and Metabolism, Causing an Intellectual-Disability Syndrome

Author

Ssang-Taek Lim, Helger G. Yntema, Tara Funari, Alexander P.A. Stegmann, Daniel G. MacArthur, Jung-Hyun Kim, Bert B.A. de Vries, Alyson Krokosky, Joost Nicolai, Sha Tang, Serge Romana, Megan T. Cho, Joris A. Veltman, Berivan Baskin, Vandana Shashi, Clesson Turner, Deepali N. Shinde, Maja Hempel, Franco Laccone, Lisenka E.L.M. Vissers, Richard M. Myers, Grazia M.S. Mancini, Daniëlle G.M. Bosch, Eun-Young Erin Ahn, Tamison Jewett, Ganka Douglas, Margot R.F. Reijnders, Eun Young Park, Axel Neu, Dong-Er Zhang, Joshua K. Stone, Davor Lessel, Connie T.R.M. Stumpel, Helga Rehder, Christopher T. Gordon, Luis Rohena, Laurie B. Owen, Dima El-Khechen, Jana Behunova, Tim M. Strom, Julie Vogt, Andrea H. Seeley, Kirsty McWalter, Nuria C. Bramswig, Margje Sinnema, Marlène Rio, Natalie Hauser, Rebecca L. Belmonte, Servi J. C. Stevens, Kristin Lindstrom, Han G. Brunner, Fanny Kortüm, Kelly Schoch, Amber Begtrup, Kristine K. Bachman, Paula A. Bubulya, Stephanie L. Santoro, Jos M. T. Draaisma, Dagmar Wieczorek, Xu Yao, David L. Stachura, Slavé Petrovski, Gregory R. Wilson, David Traver, Clinical Genetics, Genetica & Celbiologie, MUMC+: DA KG Polikliniek (9), RS: GROW - R4 - Reproductive and Perinatal Medicine, Klinische Genetica, Klinische Neurowetenschappen, MUMC+: MA Med Staf Spec Neurologie (9), MUMC+: DA KG Lab Centraal Lab (9), MUMC+: DA Pat Cytologie (9), and MUMC+: DA Klinische Genetica (5)

Subjects
0301 basic medicine, Male, Developmental Disabilities, Medizin, Haploinsufficiency, Bioinformatics, Sensory disorders Donders Center for Medical Neuroscience [Radboudumc 12], 0302 clinical medicine, Intellectual disability, FLNA, Genetics(clinical), Eye Abnormalities, Zebrafish, Genetics (clinical), Genetics, Gene knockdown, Genes, Essential, biology, Brain, Syndrome, Disorders of movement Donders Center for Medical Neuroscience [Radboudumc 3], Pedigree, DNA-Binding Proteins, RNA splicing, Female, Heterozygote, RNA Splicing, Healthcare improvement science Radboud Institute for Health Sciences [Radboudumc 18], Minor Histocompatibility Antigens, 03 medical and health sciences, Metabolic Diseases, Intellectual Disability, Report, medicine, Animals, Humans, RNA, Messenger, Gene, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], RNA, medicine.disease, biology.organism_classification, Spine, 030104 developmental biology, Mutation, Head, 030217 neurology & neurosurgery
Abstract

Contains fulltext : 167701.pdf (Publisher’s version ) (Open Access) The overall understanding of the molecular etiologies of intellectual disability (ID) and developmental delay (DD) is increasing as next-generation sequencing technologies identify genetic variants in individuals with such disorders. However, detailed analyses conclusively confirming these variants, as well as the underlying molecular mechanisms explaining the diseases, are often lacking. Here, we report on an ID syndrome caused by de novo heterozygous loss-of-function (LoF) mutations in SON. The syndrome is characterized by ID and/or DD, malformations of the cerebral cortex, epilepsy, vision problems, musculoskeletal abnormalities, and congenital malformations. Knockdown of son in zebrafish resulted in severe malformation of the spine, brain, and eyes. Importantly, analyses of RNA from affected individuals revealed that genes critical for neuronal migration and cortex organization (TUBG1, FLNA, PNKP, WDR62, PSMD3, and HDAC6) and metabolism (PCK2, PFKL, IDH2, ACY1, and ADA) are significantly downregulated because of the accumulation of mis-spliced transcripts resulting from erroneous SON-mediated RNA splicing. Our data highlight SON as a master regulator governing neurodevelopment and demonstrate the importance of SON-mediated RNA splicing in human development.

Published
2016

44. Mutations in TKT Are the Cause of a Syndrome Including Short Stature, Developmental Delay, and Congenital Heart Defects

Author

Nancy Kramer, Melissa Andrew, Birthe Roos, Vivian Hwa, Mirjam M.C. Wamelink, Kristin G. Monaghan, Jessica Douglas, Lia Boyle, Sulagna C. Saitta, Amber Begtrup, Andrew Dauber, Wendy K. Chung, Julia Wynn, Gajja S. Salomons, Ana Pop, Megan T. Cho, Murray Feingold, Kyle Retterer, Laboratory Medicine, and Amsterdam Neuroscience - Cellular & Molecular Mechanisms

Subjects
0301 basic medicine, Adult, Heart Defects, Congenital, Male, neurodevelopmental disability, Developmental Disabilities, pentose phosphate pathway, Dwarfism, 030204 cardiovascular system & hematology, Biology, Transketolase, Compound heterozygosity, medicine.disease_cause, Short stature, 03 medical and health sciences, Young Adult, 0302 clinical medicine, Cataracts, Report, medicine, Genetics, Missense mutation, Humans, Genetics(clinical), Child, Genetics (clinical), Mutation, Syndrome, transketolase deficiency, medicine.disease, Glutathione, congenital heart disease, Pedigree, TKT, 030104 developmental biology, Child, Preschool, Transketolase activity, Female, medicine.symptom, NADP
Abstract

Whole-exome sequencing (WES) is increasingly being utilized to diagnose individuals with undiagnosed disorders. Developmental delay and short stature are common clinical indications for WES. We performed WES in three families, using proband-parent trios and two additional affected siblings. We identified a syndrome due to an autosomal-recessively inherited deficiency of transketolase, encoded by TKT, on chromosome 3p21. Our series includes three families with a total of five affected individuals, ranging in age from 4 to 25 years. Two families of Ashkenazi Jewish ancestry were homozygous for an 18 base pair in-frame insertion in TKT. The third family was compound heterozygous for nonsense and missense variants in TKT. All affected individuals had short stature and were developmentally delayed. Congenital heart defects were noted in four of the five affected individuals, and there was a history of chronic diarrhea and cataracts in the older individuals with the homozygous 18 base pair insertion. Enzymatic testing confirmed significantly reduced transketolase activity. Elevated urinary excretion of erythritol, arabitol, ribitol, and pent(ul)ose-5-phosphates was detected, as well as elevated amounts of erythritol, arabitol, and ribitol in the plasma of affected individuals. Transketolase deficiency reduces NADPH synthesis and nucleic acid synthesis and cell division and could explain the problems with growth. NADPH is also critical for maintaining cerebral glutathione, which might contribute to the neurodevelopmental delays. Transketolase deficiency is one of a growing list of inborn errors of metabolism in the non-oxidative part of the pentose phosphate pathway.

Published
2016
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45. A recurrent de novo CTBP1 mutation is associated with developmental delay, hypotonia, ataxia, and tooth enamel defects

Author

Sara Halbach, Mark C. Hannibal, David B. Beck, Amber Begtrup, Bridget C. O’Connor, Darrel Waggoner, Carin Yates, Yufeng Shen, Marwan Shinawi, Brad Angle, Kyle Retterer, Wendy K. Chung, Victoria R. Sanders, Renkui Bai, Anne M. Connolly, Megan T. Cho, and Francisca Millan

Subjects
Adult, Male, 0301 basic medicine, Ataxia, Developmental Disabilities, Mutation, Missense, Biology, medicine.disease_cause, Bioinformatics, Young Adult, 03 medical and health sciences, Cellular and Molecular Neuroscience, Intellectual Disability, Exome Sequencing, Intellectual disability, Genetics, medicine, Humans, Missense mutation, Child, Dental Enamel, Genetics (clinical), Exome sequencing, Mutation, medicine.disease, Human genetics, Hypotonia, DNA-Binding Proteins, Alcohol Oxidoreductases, 030104 developmental biology, Failure to thrive, Muscle Hypotonia, Female, medicine.symptom
Abstract

Exome sequencing is an effective way to identify genetic causes of etiologically heterogeneous conditions such as developmental delay and intellectual disabilities. Using exome sequencing, we have identified four patients with similar phenotypes of developmental delay, intellectual disability, failure to thrive, hypotonia, ataxia, and tooth enamel defects who all have the same de novo R331W missense variant in C-terminal binding protein 1 (CTBP1). CTBP1 is a transcriptional regulator critical for development by coordinating different regulatory pathways. The R331W variant found in these patients is within the C-terminal portion of the PLDLS (Pro-Leu-Asp-Leu-Ser) binding cleft, which is the domain through which CTBP1, interacts with chromatin-modifying enzymes and mediates chromatin-dependent gene repression pathways. This is the first report of mutations within CTBP1 in association with any human disease.

Published
2016

46. Additional de novo missense genetic variants in NALCN associated with CLIFAHDD syndrome

Author

Katelyn Payne, K. Mason, S. Debrosse, Megan T. Cho, Wendy K. Chung, Ingrid M. Wentzensen, Jane Juusola, Amber Begtrup, M. Vivero, Yuri A. Zarate, G B Schaefer, Kyle Retterer, K. Bosanko, L. Pollack, S. Deward, and Larry Walsh

Subjects
0301 basic medicine, Genetics, 03 medical and health sciences, 030104 developmental biology, Neurodevelopmental disorder, medicine, Genetic variants, Missense mutation, Biology, medicine.disease, Genetics (clinical), Exome sequencing
Published
2017

47. Missense variants in TAF1 and developmental phenotypes: Challenges of determining pathogenicity

Author

Paul R. Mark, Helena Ahlfors, Lisa Ewans, Ganka Douglas, Zornitza Stark, Lucinda Murray, Sebastian Lunke, Emily Fassi, Lauren Dreyer, Aimé Lumaka, Jullianne Diaz, Koenraad Devriendt, Lisa Worgan, Hanyin Cheng, Pankaj B. Agrawal, Laurence Faivre, H. T. Marc Timmers, Julie Vogt, Elizabeth E. Palmer, Kai Wang, Nora Alexander, Michael F. Buckley, Tony Roscioli, Chunhua Weng, Gabriela Soares, Simona Capponi, Antonie D. Kline, Jorge Oliveira, Amali Mallawaarachchi, Ana R. Gonçalves, Gareth Baynam, Eyby Leon, Marcia C. Willing, Shehla Mohammed, Sarah A. Sandaradura, Elaine Marchi, Katelyn Payne, Amber Begtrup, Piatek G. Stefan, Lesley C. Adès, Mengge Zhao, Emma Wakeling, Jean-Baptiste Rivière, Sébastien Moutton, Quan Li, Maria J. Guillen Sacoto, Jeff L. Waugh, Jennifer E. Posey, Robert Kleyner, Alan F. Rope, Prosper Lukusa, James R. Lupski, Laurence E. Walsh, Joris Vermeesch, Gholson J. Lyon, and Sonja A. de Munnik

Subjects
Genetics, TAF1, Missense mutation, Biology, Pathogenicity, Phenotype, Genetics (clinical)
Published
2020

48. FV 241. Mutations in NFE2L2 Lead to a Novel Treatable Neurological Disorder with Leukoencephalopathy

Author

Peter Huppke, Fatima Almusafri, Martina Krusen, Susann Weissbach, Amber Begtrup, Janine Altmüller, Holger Thiele, Joseph A. Church, Annika Wolf, Peter Nürnberg, Francisca Millan, Nikolaus Kühn-Velten, Steffi Dreha-Kulaczewski, Jutta Gärtner, Rhonda E. Schnur, Michael Müller, and Brenda Huppke

Subjects
Leukoencephalopathy, Pediatrics, medicine.medical_specialty, business.industry, medicine, Neurological disorder, medicine.disease, business, NFE2L2
Published
2018

49. Mutations in TOP3A Cause a Bloom Syndrome-like Disorder

Author

Grainne S. Gorman, William P. Allen, Carol Anne Martin, Rebekah Jobling, Karen E. Heath, Amber Begtrup, Bernd Wollnik, N.S. Ali, Janine Altmüller, Hywel Williams, David A. Parry, Kei Murayama, J. Cruz-Rojo, Nursel Elcioglu, Anna H. Bizard, Yasushi Okazaki, Miriam Aza-Carmona, Fowzan S. Alkuraya, Massimo Bogliolo, Ian D. Hickson, Kata Sarlós, Clare V. Logan, Andrea Leitch, Gökhan Yigit, I Kesterton, Akira Ohtake, Anya Revah-Politi, Masaru Shimura, Roshan Singh Thakur, Jordi Surrallés, A.J. Malallah, Masakazu Kohda, Alejandro Iglesias, Yoshihito Kishita, Roser Pujol, Lesley Turner, Al-Owain, L. Zahavich, Robert W. Taylor, Peter Nürnberg, H.A.M. Dhahrabi, Megan T. Cho, Jimena Barraza-García, Andrew P. Jackson, María José Ramírez, Carolyn Wilson, B.A.Y. Barakat, P. Stevens, P. Le Quesne Stabej, Louise Cleal, and Mehul T. Dattani

Subjects
0301 basic medicine, Genetics, Correction, Biology, medicine.disease, TOP3A, topoisomerase III, genomic instability, RecQ helicases, Article, 03 medical and health sciences, 030104 developmental biology, medicine, Bloom syndrome, Genetics (clinical), BLM, double Holliday junction dissolution
Abstract

Bloom syndrome, caused by biallelic mutations in BLM, is characterized by prenatal-onset growth deficiency, short stature, an erythematous photosensitive malar rash, and increased cancer predisposition. Diagnostically, a hallmark feature is the presence of increased sister chromatid exchanges (SCEs) on cytogenetic testing. Here, we describe biallelic mutations in TOP3A in ten individuals with prenatal-onset growth restriction and microcephaly. TOP3A encodes topoisomerase III alpha (TopIIIα), which binds to BLM as part of the BTRR complex, and promotes dissolution of double Holliday junctions arising during homologous recombination. We also identify a homozygous truncating variant in RMI1, which encodes another component of the BTRR complex, in two individuals with microcephalic dwarfism. The TOP3A mutations substantially reduce cellular levels of TopIIIα, and consequently subjects’ cells demonstrate elevated rates of SCE. Unresolved DNA recombination and/or replication intermediates persist into mitosis, leading to chromosome segregation defects and genome instability that most likely explain the growth restriction seen in these subjects and in Bloom syndrome. Clinical features of mitochondrial dysfunction are evident in several individuals with biallelic TOP3A mutations, consistent with the recently reported additional function of TopIIIα in mitochondrial DNA decatenation. In summary, our findings establish TOP3A mutations as an additional cause of prenatal-onset short stature with increased cytogenetic SCEs and implicate the decatenation activity of the BTRR complex in their pathogenesis.

Published
2018

50. Novel fibronectin mutations and expansion of the phenotype in spondylometaphyseal dysplasia with 'corner fractures'

Author

Jiani Chen, Philippe M. Campeau, Chong Ae Kim, Débora Romeo Bertola, Kirsty McWalter, Outi Mäkitie, Elizabeth A. Fanning, Klaas J. Wierenga, Rebecca Willaert, Jessica J. Alm, Nissan V. Baratang, Luis F. Escobar, Alice Costantini, Guilherme L. Yamamoto, Heather M. McLaughlin, Helena Valta, Amber Begtrup, Patrick Yap, Dieter P. Reinhardt, Children's Hospital, University of Helsinki, Clinicum, University Management, Lastentautien yksikkö, and HUS Children and Adolescents

Subjects
0301 basic medicine, Male, Pathology, Physiology, Endocrinology, Diabetes and Metabolism, Extracellular matrix component, PROTEIN, medicine.disease_cause, Polymerase Chain Reaction, 0302 clinical medicine, Bone Density, RESORPTION, Missense mutation, Child, Mutation, High-Throughput Nucleotide Sequencing, medicine.anatomical_structure, Phenotype, Skeletal dysplasia, Female, medicine.symptom, BONE, Adult, medicine.medical_specialty, Histology, Adolescent, Coxa vara, Corner-fracture, 030209 endocrinology & metabolism, Biology, Osteochondrodysplasias, OSTEOBLAST DIFFERENTIATION, 03 medical and health sciences, Young Adult, Skeletal disorder, medicine, Humans, Fibronectin, Bone Diseases, Developmental, FN1, Ossification, Cartilage, Fibronectins, 030104 developmental biology, GLOMERULOPATHY, 3111 Biomedicine, Ovoid vertebral bodies, MATRIX
Abstract

Heterozygous pathogenic variants in the FN1 gene, encoding fibronectin (FN), have recently been shown to be associated with a skeletal disorder in some individuals affected by spondylometaphyseal dysplasia with “corner fractures” (SMD-CF). The most striking feature characterizing SMD-CF is irregularly shaped metaphyses giving the appearance of “corner fractures”. An array of secondary features, including developmental coxa vara, ovoid vertebral bodies and severe scoliosis, may also be present. FN is an important extra cellular matrix component for bone and cartilage development. Here we report five patients affected by this subtype of SMD-CF caused by five novel FN1 missense mutations: p.Cys123Tyr, p.Cys169Tyr, p.Cys213Tyr, p.Cys231Trp and p.Cys258Tyr. All individuals shared a substitution of a cysteine residue, disrupting disulfide bonds in the FN type-I assembly domains located in the N-terminal assembly region. The abnormal metaphyseal ossification and “corner fracture” appearances were the most remarkable clinical feature in these patients. In addition, generalized skeletal fragility with low-trauma bilateral femoral fractures was identified in one patient. Interestingly, the distal femoral changes in this patient healed with skeletal maturation. Our report expands the phenotypic and genetic spectrum of the FN1-related SMD-CF and emphasizes the importance of FN in bone formation and possibly also in the maintenance of bone strength.

Published
2018

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