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1. Gain and loss of function variants in EZH1 disrupt neurogenesis and cause dominant and recessive neurodevelopmental disorders

Author

Carolina Gracia-Diaz, Yijing Zhou, Qian Yang, Reza Maroofian, Paula Espana-Bonilla, Chul-Hwan Lee, Shuo Zhang, Natàlia Padilla, Raquel Fueyo, Elisa A. Waxman, Sunyimeng Lei, Garrett Otrimski, Dong Li, Sarah E. Sheppard, Paul Mark, Margaret H. Harr, Hakon Hakonarson, Lance Rodan, Adam Jackson, Pradeep Vasudevan, Corrina Powel, Shehla Mohammed, Sateesh Maddirevula, Hamad Alzaidan, Eissa A. Faqeih, Stephanie Efthymiou, Valentina Turchetti, Fatima Rahman, Shazia Maqbool, Vincenzo Salpietro, Shahnaz H. Ibrahim, Gabriella di Rosa, Henry Houlden, Maha Nasser Alharbi, Nouriya Abbas Al-Sannaa, Peter Bauer, Giovanni Zifarelli, Conchi Estaras, Anna C. E. Hurst, Michelle L. Thompson, Anna Chassevent, Constance L. Smith-Hicks, Xavier de la Cruz, Alexander M. Holtz, Houda Zghal Elloumi, M J Hajianpour, Claudine Rieubland, Dominique Braun, Siddharth Banka, Genomic England Research Consortium, Deborah L. French, Elizabeth A. Heller, Murielle Saade, Hongjun Song, Guo-li Ming, Fowzan S. Alkuraya, Pankaj B. Agrawal, Danny Reinberg, Elizabeth J. Bhoj, Marian A. Martínez-Balbás, and Naiara Akizu

Subjects
Science
Abstract

Abstract Genetic variants in chromatin regulators are frequently found in neurodevelopmental disorders, but their effect in disease etiology is rarely determined. Here, we uncover and functionally define pathogenic variants in the chromatin modifier EZH1 as the cause of dominant and recessive neurodevelopmental disorders in 19 individuals. EZH1 encodes one of the two alternative histone H3 lysine 27 methyltransferases of the PRC2 complex. Unlike the other PRC2 subunits, which are involved in cancers and developmental syndromes, the implication of EZH1 in human development and disease is largely unknown. Using cellular and biochemical studies, we demonstrate that recessive variants impair EZH1 expression causing loss of function effects, while dominant variants are missense mutations that affect evolutionarily conserved aminoacids, likely impacting EZH1 structure or function. Accordingly, we found increased methyltransferase activity leading to gain of function of two EZH1 missense variants. Furthermore, we show that EZH1 is necessary and sufficient for differentiation of neural progenitor cells in the developing chick embryo neural tube. Finally, using human pluripotent stem cell-derived neural cultures and forebrain organoids, we demonstrate that EZH1 variants perturb cortical neuron differentiation. Overall, our work reveals a critical role of EZH1 in neurogenesis regulation and provides molecular diagnosis for previously undefined neurodevelopmental disorders.

Published
2023
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2. The different clinical facets of SYN1-related neurodevelopmental disorders

Author

Ilaria Parenti, Elsa Leitão, Alma Kuechler, Laurent Villard, Cyril Goizet, Cécile Courdier, Allan Bayat, Alessandra Rossi, Sophie Julia, Ange-Line Bruel, Frédéric Tran Mau-Them, Sophie Nambot, Daphné Lehalle, Marjolaine Willems, James Lespinasse, Jamal Ghoumid, Roseline Caumes, Thomas Smol, Salima El Chehadeh, Elise Schaefer, Marie-Thérèse Abi-Warde, Boris Keren, Alexandra Afenjar, Anne-Claude Tabet, Jonathan Levy, Anna Maruani, Ángel Aledo-Serrano, Waltraud Garming, Clara Milleret-Pignot, Anna Chassevent, Marije Koopmans, Nienke E. Verbeek, Richard Person, Rebecca Belles, Gary Bellus, Bonnie A. Salbert, Frank J. Kaiser, Laure Mazzola, Philippe Convers, Laurine Perrin, Amélie Piton, Gert Wiegand, Andrea Accogli, Francesco Brancati, Fabio Benfenati, Nicolas Chatron, David Lewis-Smith, Rhys H. Thomas, Federico Zara, Pasquale Striano, Gaetan Lesca, and Christel Depienne

Subjects
SYN1, synapsins, reflex epilepsy, genotype-phenotype correlation, neurodevelopmental disorders, autism spectrum disorders, Biology (General), QH301-705.5
Abstract

Synapsin-I (SYN1) is a presynaptic phosphoprotein crucial for synaptogenesis and synaptic plasticity. Pathogenic SYN1 variants are associated with variable X-linked neurodevelopmental disorders mainly affecting males. In this study, we expand on the clinical and molecular spectrum of the SYN1-related neurodevelopmental disorders by describing 31 novel individuals harboring 22 different SYN1 variants. We analyzed newly identified as well as previously reported individuals in order to define the frequency of key features associated with these disorders. Specifically, behavioral disturbances such as autism spectrum disorder or attention deficit hyperactivity disorder are observed in 91% of the individuals, epilepsy in 82%, intellectual disability in 77%, and developmental delay in 70%. Seizure types mainly include tonic-clonic or focal seizures with impaired awareness. The presence of reflex seizures is one of the most representative clinical manifestations related to SYN1. In more than half of the cases, seizures are triggered by contact with water, but other triggers are also frequently reported, including rubbing with a towel, fever, toothbrushing, fingernail clipping, falling asleep, and watching others showering or bathing. We additionally describe hyperpnea, emotion, lighting, using a stroboscope, digestive troubles, and defecation as possible triggers in individuals with SYN1 variants. The molecular spectrum of SYN1 variants is broad and encompasses truncating variants (frameshift, nonsense, splicing and start-loss variants) as well as non-truncating variants (missense substitutions and in-frame duplications). Genotype-phenotype correlation revealed that epileptic phenotypes are enriched in individuals with truncating variants. Furthermore, we could show for the first time that individuals with early seizures onset tend to present with severe-to-profound intellectual disability, hence highlighting the existence of an association between early seizure onset and more severe impairment of cognitive functions. Altogether, we present a detailed clinical description of the largest series of individuals with SYN1 variants reported so far and provide the first genotype-phenotype correlations for this gene. A timely molecular diagnosis and genetic counseling are cardinal for appropriate patient management and treatment.

Published
2022
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3. Mutations in the KIF21B kinesin gene cause neurodevelopmental disorders through imbalanced canonical motor activity

Author

Laure Asselin, José Rivera Alvarez, Solveig Heide, Camille S. Bonnet, Peggy Tilly, Hélène Vitet, Chantal Weber, Carlos A. Bacino, Kristin Baranaño, Anna Chassevent, Amy Dameron, Laurence Faivre, Neil A. Hanchard, Sonal Mahida, Kirsty McWalter, Cyril Mignot, Caroline Nava, Agnès Rastetter, Haley Streff, Christel Thauvin-Robinet, Marjan M. Weiss, Gladys Zapata, Petra J. G. Zwijnenburg, Frédéric Saudou, Christel Depienne, Christelle Golzio, Delphine Héron, and Juliette D. Godin

Subjects
Science
Abstract

Kinesins regulate intracellular transport and microtubule dynamics. Here, the authors show that KIF21B variants in humans associate with corpus callosum agenesis and microcephaly. Using mice and zebrafish, they showed the cellular mechanisms altered by the missense KIF21B variants.

Published
2020
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4. Variants in CLDN5 cause a syndrome characterized by seizures, microcephaly and brain calcifications

Author

Ashish R Deshwar, Cheryl Cytrynbaum, Harsha Murthy, Jessica Zon, David Chitayat, Jonathan Volpatti, Ruth Newbury-Ecob, Sian Ellard, Hana Lango Allen, Emily P Yu, Ramil Noche, Suzi Walker, Stephen W Scherer, Sonal Mahida, Christopher M Elitt, Gaël Nicolas, Alice Goldenberg, Pascale Saugier-Veber, Francois Lecoquierre, Ivana Dabaj, Hannah Meddaugh, Michael Marble, Kim M Keppler-Noreuil, Lucy Drayson, Kristin W Barañano, Anna Chassevent, Katie Agre, Pascaline Létard, Frederic Bilan, Gwenaël Le Guyader, Annie Laquerrière, Keri Ramsey, Lindsay Henderson, Lauren Brady, Mark Tarnopolsky, Matthew Bainbridge, Jennifer Friedman, Yline Capri, Larissa Athayde, Fernando Kok, Juliana Gurgel-Giannetti, Luiza L P Ramos, Susan Blaser, James J Dowling, Rosanna Weksberg, Deshwar, Ashish R [0000-0002-9239-3846], Scherer, Stephen W [0000-0002-8326-1999], Nicolas, Gaël [0000-0001-9391-7800], Dabaj, Ivana [0000-0002-2324-1208], Dowling, James J [0000-0002-3984-4169], and Apollo - University of Cambridge Repository

Subjects
brain calcifications, CLDN5, blood brain barrier, Neurology (clinical)
Abstract

The blood–brain barrier ensures CNS homeostasis and protection from injury. Claudin-5 (CLDN5), an important component of tight junctions, is critical for the integrity of the blood–brain barrier. We have identified de novo heterozygous missense variants in CLDN5 in 15 unrelated patients who presented with a shared constellation of features including developmental delay, seizures (primarily infantile onset focal epilepsy), microcephaly and a recognizable pattern of pontine atrophy and brain calcifications. All variants clustered in one subregion/domain of the CLDN5 gene and the recurrent variants demonstrate genotype–phenotype correlations. We modelled both patient variants and loss of function alleles in the zebrafish to show that the variants analogous to those in patients probably result in a novel aberrant function in CLDN5. In total, human patient and zebrafish data provide parallel evidence that pathogenic sequence variants in CLDN5 cause a novel neurodevelopmental disorder involving disruption of the blood–brain barrier and impaired neuronal function.

Published
2023

5. TAOK1 is associated with neurodevelopmental disorder and essential for neuronal maturation and cortical development

Author

Mari Rossi, Melissa K. Gabriel, Rolph Pfundt, Ange Line Bruel, Sonal Mahida, Daniel Groepper, Kristin W. Barañano, Tjitske Kleefstra, Saskia Brulleman, Charlotte de Konink, Angelika Erwin, Aida Telegrafi, Kristin Lindstrom, Amy Blevins, Marjon van Slegtenhorst, Katherine G. Langley, David A. Koolen, Geeske M. van Woerden, Anna Chassevent, Louisa Kalsner, A. Micheil Innes, Ype Elgersma, David R. FitzPatrick, Kristin G. Monaghan, Allison Goodwin, Ben Distel, Karen W. Gripp, Alice S. Brooks, Natasha Shur, Fatima Rehman, Rossella Avagliano Trezza, Amanda Noyes, Melanie Bos, Jane Juusola, Gwynna de Geus, Jennifer B. Humberson, Andrew O.M. Wilkie, Jessica Hoffman, Marleen Simon, David Johnson, Róisín McCormack, Sumit Punj, Maria J. Guillen Sacoto, Julie Fleischer, Eduardo Calpena, Arthur Sorlin, Allison Schreiber, Clinical Genetics, Neurosciences, Medical Biochemistry, and AGEM - Amsterdam Gastroenterology Endocrinology Metabolism

Subjects
MAP Kinase Signaling System, Biology, Mice, 03 medical and health sciences, Neurodevelopmental disorder, Intellectual Disability, Intellectual disability, Genetics, medicine, Animals, Humans, Missense mutation, cortical development, Amino Acids, Protein kinase A, Research Articles, Genetics (clinical), Loss function, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], MAP kinase kinase kinase, Muscular hypotonia, neurodevelopmental disorders, 030305 genetics & heredity, medicine.disease, in utero electroporation, TAOK1, Muscle Hypotonia, Neuroscience, functional genomics, Function (biology), Research Article
Abstract

Thousand and one amino‐acid kinase 1 (TAOK1) is a MAP3K protein kinase, regulating different mitogen‐activated protein kinase pathways, thereby modulating a multitude of processes in the cell. Given the recent finding of TAOK1 involvement in neurodevelopmental disorders (NDDs), we investigated the role of TAOK1 in neuronal function and collected a cohort of 23 individuals with mostly de novo variants in TAOK1 to further define the associated NDD. Here, we provide evidence for an important role for TAOK1 in neuronal function, showing that altered TAOK1 expression levels in the embryonic mouse brain affect neural migration in vivo, as well as neuronal maturation in vitro. The molecular spectrum of the identified TAOK1 variants comprises largely truncating and nonsense variants, but also missense variants, for which we provide evidence that they can have a loss of function or dominant‐negative effect on TAOK1, expanding the potential underlying causative mechanisms resulting in NDD. Taken together, our data indicate that TAOK1 activity needs to be properly controlled for normal neuronal function and that TAOK1 dysregulation leads to a neurodevelopmental disorder mainly comprising similar facial features, developmental delay/intellectual disability and/or variable learning or behavioral problems, muscular hypotonia, infant feeding difficulties, and growth problems., In this study we expand the cohort of individuals with a neurodevelopmental disorder, carrying a de novo variant in TAOK1 (a), thereby further defining the neurodevelopmental disorder caused by TAOK1 malfunctioning. Using both in vivo (b) and in vitro (c) functional assays, we provide evidence that increased as well as decreased levels of TAOK1 cause disruption of neuronal development, showing that TAOK1 plays an important role in neuronal function. Additionally, our data suggests that both gain of function as well as loss of function mutations are potentially causative for the TAOK1‐related neurodevelopmental disorder.

Published
2021

6. Heterozygous NOTCH1 Variants Cause CNS Immune Activation and Microangiopathy

Author

Guy Helman, Parand Zarekiani, Samantha A.M. Tromp, Ashley Andrews, Lorenzo D. Botto, Joshua L. Bonkowsky, Anna Chassevent, Elisa Giorgio, Tommaso Pippucci, Shen Wei, Constance Smith‐Hicks, Giovanna Vaula, Michèl A.A.P Willemsen, Mareike Schimmel, Kurt Vollert, Fumitaka Shimizu, Takashi Kanda, Matthew Lynch, Tony Roscioli, Ryan J. Taft, Cas Simons, Marianna Bugiani, Taco W. Kuijpers, Marjo S. van der Knaap, Pathology, Amsterdam Neuroscience - Cellular & Molecular Mechanisms, Amsterdam Neuroscience - Complex Trait Genetics, Pediatrics, Integrative Neurophysiology, Paediatric Infectious Diseases / Rheumatology / Immunology, AII - Inflammatory diseases, and ARD - Amsterdam Reproduction and Development

Subjects
Chemokine CXCL10, Central Nervous System, Neurology, SDG 3 - Good Health and Well-being, Ectodermal Dysplasia, Leukoencephalopathies, Humans, Neurology (clinical), Receptor, Notch1, Disorders of movement Donders Center for Medical Neuroscience [Radboudumc 3]
Abstract

Item does not contain fulltext NOTCH1 belongs to the NOTCH family of proteins that regulate cell fate and inflammatory responses. Somatic and germline NOTCH1 variants have been implicated in cancer, Adams-Oliver syndrome, and cardiovascular defects. We describe 7 unrelated patients grouped by the presence of leukoencephalopathy with calcifications and heterozygous de novo gain-of-function variants in NOTCH1. Immunologic profiling showed upregulated CSF IP-10, a cytokine secreted downstream of NOTCH1 signaling. Autopsy revealed extensive leukoencephalopathy and microangiopathy with vascular calcifications. This evidence implicates that heterozygous gain-of-function variants in NOTCH1 lead to a chronic central nervous system (CNS) inflammatory response resulting in a calcifying microangiopathy with leukoencephalopathy. ANN NEUROL 2022;92:895-901.

Published
2022

7. ATP8A2-related disorders as recessive cerebellar ataxia

Author

Ibrahim Oncel, Haluk Topaloglu, Kristin Baraῆano, Robert S. Molday, Mireille Claustres, Lise Larrieu, Patrick Calvas, Maria Iascone, Romano Tenconi, Anna Chassevent, Michel Koenig, Mehdi Benkirane, Nesibe Eroglu-Ertugrul, Elif Acar Arslan, Alexander N Harrison, Claire Guissart, Salvy-Córdoba, Nathalie, Laboratoire de génétique des maladies rares. Pathologie moleculaire, etudes fonctionnelles et banque de données génétiques (LGMR), Université Montpellier 1 (UM1)-IFR3, Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), University of British Columbia (UBC), Faculty of Medicine [Hacettepe University], Hacettepe University = Hacettepe Üniversitesi, Karadeniz Technical University (KTU), Kennedy Krieger Institute [Baltimore], ASST Papa Giovanni XXIII [Bergamo, Italy], Università degli Studi di Padova = University of Padua (Unipd), Centre Hospitalier Universitaire de Toulouse (CHU Toulouse), IFR3, Université Montpellier 1 (UM1)-Université Montpellier 1 (UM1)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Universita degli Studi di Padova, Hôpital Purpan [Toulouse], and CHU Toulouse [Toulouse]

Subjects
Male, [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, P4-ATPase, Psychomotor delay, Consanguinity, 0302 clinical medicine, MESH: Child, Missense mutation, 030212 general & internal medicine, Phospholipid Transfer Proteins, Child, Adenosine Triphosphatases, MESH: Phospholipid Transfer Proteins, MESH: Infant, Hypotonia, Pedigree, MESH: Cerebellar Ataxia, 3. Good health, Phenotype, Neurology, Child, Preschool, Female, Cerebellar atrophy, medicine.symptom, Adult, medicine.medical_specialty, Ataxia, Cerebellar Ataxia, MESH: Pedigree, Encephalopathy, Mutation, Missense, Genes, Recessive, [SDV.GEN.GH] Life Sciences [q-bio]/Genetics/Human genetics, MESH: Phenotype, 03 medical and health sciences, [SDV.MHEP.PED] Life Sciences [q-bio]/Human health and pathology/Pediatrics, Atrophy, Internal medicine, MESH: Adenosine Triphosphatases, medicine, Humans, Point Mutation, MESH: Genes, Recessive, MESH: Point Mutation, MESH: Consanguinity, MESH: Mutation, Missense, [SDV.MHEP.PED]Life Sciences [q-bio]/Human health and pathology/Pediatrics, MESH: Humans, Cerebellar ataxia, business.industry, MESH: Child, Preschool, [SDV.NEU.NB] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, Infant, MESH: Adult, Chorea, medicine.disease, MESH: Male, ATP8A2, Endocrinology, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, CAMRQ, Neurology (clinical), business, MESH: Female, 030217 neurology & neurosurgery
Abstract

International audience; ATP8A2-related disorders are autosomal recessive conditions that associate encephalopathy with or without hypotonia, psychomotor delay, abnormal movements, chorea, tremor, optic atrophy and cerebellar atrophy (CARMQ4). Through a multi-centric collaboration, we identified six point mutations (one splice site and five missense mutations) involving ATP8A2 in six individuals from five families. Two patients from one family with the homozygous p.Gly585Val mutation had a milder presentation without encephalopathy. Expression and functional studies of the missense mutations demonstrated that protein levels of four of the five missense variants were very low and lacked phosphatidylserine-activated ATPase activity. One variant p.Ile215Leu, however, expressed at normal levels and displayed phospholipid-activated ATPase activity similar to the non-mutated protein. We therefore expand for the first time the phenotype related to ATP8A2 mutations to less severe forms characterized by cerebellar ataxia without encephalopathy and suggest that ATP8A2 should be analyzed for all cases of syndromic or non-syndromic recessive or sporadic ataxia.

Published
2019

8. BCL11A intellectual developmental disorder: defining the clinical spectrum and genotype-phenotype correlations

Author

Øyvind L. Busk, Kimberley Bradbury, Arjan Bouman, Philippe M. Campeau, Lynne M. Bird, Cornelia Kraus, Colleen Carlston, Rong Mao, Juliette Piard, Laurence Faivre, Amanda Openshaw, Catherine Ward Melver, Mohnish Suri, Christiane Zweier, François Guillemot, Rolph Pfundt, Janice C. Palumbos, Parthiv Haldipur, Jane A. Hurst, Kimberly McDonald, Margaux Serey-Gaut, Luitgard Graul-Neumann, Karen J. Low, Jenny Carmichael, Patrick Ferrerira, Birgit Elisabeth Kristiansen, Ange-Line Bruel, Constance Motter, Andrea Accogli, Darrah N. Haffner, Suhair Hanna, Ruta Marcinkute, Angela Peron, Marcella Zollino, Sofia Maia, James Lespinasse, Claire E. Turner, Sally Ann Lynch, Richard E. Person, Valeria Capra, Kimberly A. Aldinger, Constance Smith-Hicks, Gyri Aasland Gradek, Ingrid M. Wentzensen, Megha Desai, Manuela Morleo, Aditi Shah Parikh, Marcello Scala, Cristina Dias, Gunnar Houge, Telethon Undiagnosed Disease Program, Anne Slavotinek, Roberta Battini, Mary J. Green, Anna Chassevent, Tara Montgomery, David Viskochil, Tatiana Tvrdik, Dawn L. Earl, Karin Weiss, Felice D'Arco, William B. Dobyns, Ping Yee Billie Au, Daniah Beleford, Erica F. Andersen, Bert B.A. de Vries, Jill Clayton-Smith, Christophe Philippe, and Michael J. Bamshad

Subjects
business.industry, Postnatal microcephaly, Microdeletion syndrome, medicine.disease, Bioinformatics, Hypotonia, Developmental disorder, Autism spectrum disorder, Intellectual disability, Fetal hemoglobin, medicine, Missense mutation, medicine.symptom, business
Abstract

PurposeHeterozygous variants in BCL11A underlie an intellectual developmental disorder with persistence of fetal hemoglobin (BCL11A-IDD, a.k.a. Dias-Logan syndrome). We sought to delineate the genotypic and phenotypic spectrum of BCL11A-IDD.MethodsWe performed an in-depth analysis of 42 patients with BCL11A-IDD ascertained through a collaborative network of clinical and research colleagues. We also reviewed 33 additional affected individuals previously reported in the literature or available through public repositories with clinical information.ResultsMolecular and clinical data analysis of 75 patients with BCL11A-IDD identified 60 unique variants (30 frameshift, 7 missense, 6 splice-site, 17 stop-gain) and 8 unique CNVs (microdeletions involving BCL11A only). We redefined the most frequent manifestations of the condition: intellectual disability, hypotonia, behavioral abnormalities, postnatal microcephaly and autism spectrum disorder. Two thirds of patients have brain MRI abnormalities, and we identified a recurrent posterior fossa phenotype of vermian hypoplasia and/or small brainstem. Truncating BCL11A variants, particularly those affecting the long (BCL11A-L) and extra-long (-XL) isoforms, sparing the short (-S) isoform, were associated with increased severity.ConclusionsWe expand the clinical delineation of BCL11A-IDD and identify a potential isoform-specific genotype-phenotype correlation. We show that BCL11A-IDD is associated with posterior fossa anomalies and highlight the differences between BCL11A-IDD and 2p16.1p15 microdeletion syndrome.

Published
2021

9. Delineating the genotypic and phenotypic spectrum of HECW2-related neurodevelopmental disorders

Author

Ingrid M. Wentzensen, Patrick Dunn, Caleb Heid, Esperanza Font-Montgomery, Anna Chassevent, Solveig Heide, Vinod K. Misra, Leandra Folk, Wendy K. Chung, Alexandra Afenjar, Sandra Whalen, Suzanne M. Leal, Thomas Smol, Erin Torti, Kathleen Brown, Isabelle Schrauwen, Anushree Acharya, Magali Barth, Mayada Helal, Mélanie Rama, Thomas Courtin, Irma Järvelä, Maura R.Z. Ruzhnikov, Farouq Thabet, Boris Keren, Haluk Kavus, Kara Withrow, J. Austin Hamm, Elizabeth A. Normand, Mitch Cunningham, Constance Smith-Hicks, Camille Fallot, Fanggeng Zou, Abdul Nasir, Donald R. Love, Alban Ziegler, Columbia University Medical Center (CUMC), Columbia University [New York], The George Washington University (GW), University of Agriculture Faisalabad - UAF (PAKISTAN), GeneDx [Gaithersburg, MD, USA], Stanford University, CHU Lille, Maladies RAres du DEveloppement embryonnaire et du MEtabolisme : du Phénotype au Génotype et à la Fonction - ULR 7364 (RADEME), Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Institut de génétique médicale, University of Colorado Anschutz [Aurora], CHU Trousseau [APHP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Sorbonne Université (SU), Centre Hospitalier Universitaire d'Angers (CHU Angers), PRES Université Nantes Angers Le Mans (UNAM), Kennedy Krieger Institute [Baltimore], Johns Hopkins University School of Medicine [Baltimore], CHU Pitié-Salpêtrière [AP-HP], University of Missouri [Columbia] (Mizzou), University of Missouri System, Sidra Medicine [Doha, Qatar], Children's Hospital of Michigan, Central Michigan University (CMU), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Irma Järvelä / Principal Investigator, Medicum, and Department of Medical and Clinical Genetics

Subjects
0301 basic medicine, INTELLECTUAL DISABILITY, GENES, GENETICS, phenotype, [SDV]Life Sciences [q-bio], human genetics, Biology, VARIANTS, UBIQUITIN LIGASE, 03 medical and health sciences, 0302 clinical medicine, Genotype-phenotype distinction, Neurodevelopmental disorder, Intellectual disability, medicine, Missense mutation, Genetics (clinical), Genetics, Massive parallel sequencing, MUTATIONS, neurology, 1184 Genetics, developmental biology, physiology, medicine.disease, Penetrance, Human genetics, Hypotonia, 030104 developmental biology, NEDL2, genetic variation, 3111 Biomedicine, medicine.symptom, HECW2, 030217 neurology & neurosurgery
Abstract

BackgroundVariants in HECW2 have recently been reported to cause a neurodevelopmental disorder with hypotonia, seizures and impaired language; however, only six variants have been reported and the clinical characteristics have only broadly been defined.MethodsMolecular and clinical data were collected from clinical and research cohorts. Massive parallel sequencing was performed and identified individuals with a HECW2-related neurodevelopmental disorder.ResultsWe identified 13 novel missense variants in HECW2 in 22 unpublished cases, of which 18 were confirmed to have a de novo variant. In addition, we reviewed the genotypes and phenotypes of previously reported and new cases with HECW2 variants (n=35 cases). All variants identified are missense, and the majority of likely pathogenic and pathogenic variants are located in or near the C-terminal HECT domain (88.2%). We identified several clustered variants and four recurrent variants (p.(Arg1191Gln);p.(Asn1199Lys);p.(Phe1327Ser);p.(Arg1330Trp)). Two variants, (p.(Arg1191Gln);p.(Arg1330Trp)), accounted for 22.9% and 20% of cases, respectively. Clinical characterisation suggests complete penetrance for hypotonia with or without spasticity (100%), developmental delay/intellectual disability (100%) and developmental language disorder (100%). Other common features are behavioural problems (88.9%), vision problems (83.9%), motor coordination/movement (75%) and gastrointestinal issues (70%). Seizures were present in 61.3% of individuals. Genotype-phenotype analysis shows that HECT domain variants are more frequently associated with cortical visual impairment and gastrointestinal issues. Seizures were only observed in individuals with variants in or near the HECT domain.ConclusionWe provide a comprehensive review and expansion of the genotypic and phenotypic spectrum of HECW2 disorders, aiding future molecular and clinical diagnosis and management.

Published
2021

10. Delineating the genotypic and phenotypic spectrum of

Author

Anushree, Acharya, Haluk, Kavus, Patrick, Dunn, Abdul, Nasir, Leandra, Folk, Kara, Withrow, Ingrid M, Wentzensen, Maura R Z, Ruzhnikov, Camille, Fallot, Thomas, Smol, Mélanie, Rama, Kathleen, Brown, Sandra, Whalen, Alban, Ziegler, Magali, Barth, Anna, Chassevent, Constance, Smith-Hicks, Alexandra, Afenjar, Thomas, Courtin, Solveig, Heide, Esperanza, Font-Montgomery, Caleb, Heid, J Austin, Hamm, Donald R, Love, Farouq, Thabet, Vinod K, Misra, Mitch, Cunningham, Suzanne M, Leal, Irma, Jarvela, Elizabeth A, Normand, Fanggeng, Zou, Mayada, Helal, Boris, Keren, Erin, Torti, Wendy K, Chung, and Isabelle, Schrauwen

Subjects
Phenotype, Genotype, Neurodevelopmental Disorders, Seizures, Intellectual Disability, Ubiquitin-Protein Ligases, Humans, Muscle Hypotonia
Abstract

Variants inMolecular and clinical data were collected from clinical and research cohorts. Massive parallel sequencing was performed and identified individuals with aWe identified 13 novel missense variants inWe provide a comprehensive review and expansion of the genotypic and phenotypic spectrum of

Published
2021

11. Truncating variants in the SHANK1 gene are associated with a spectrum of neurodevelopmental disorders

Author

Chong Ae Kim, Marwan Shinawi, Naomichi Matsumoto, Anya Revah-Politi, Julia Baptista, Halie J. May, Julie S. Cohen, Julia Rankin, Samantha Toy, Kwame Anyane-Yeboa, Michelle Primiano, Evan H. Baugh, David Goldstein, Richard E. Person, Constance Smith-Hicks, Louise Bier, Katherine W. Roche, Anna Chassevent, Yuri Uchiyama, Michel Guipponi, Joel Victor Fluss, Charles Conlon, Armand Bottani, Jaehoon Jeong, Vimla Aggarwal, Maria resa Te Carminho A. Rodrigues, and Aida Telegrafi

Subjects
Genetics, Neurons, Dendritic spine, HEK 293 cells, HOMER1, Nerve Tissue Proteins, Biology, Phenotype, Article, HEK293 Cells, Cell culture, Neurodevelopmental Disorders, Complementary DNA, Exome Sequencing, Humans, Gene, Genetics (clinical), Exome sequencing
Abstract

Purpose In this study, we aimed to characterize the clinical phenotype of a SHANK1-related disorder and define the functional consequences of SHANK1 truncating variants. Methods Exome sequencing (ES) was performed for six individuals who presented with neurodevelopmental disorders. Individuals were ascertained with the use of GeneMatcher and Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources (DECIPHER). We evaluated potential nonsense-mediated decay (NMD) of two variants by making knock-in cell lines of endogenous truncated SHANK1, and expressed the truncated SHANK1 complementary DNA (cDNA) in HEK293 cells and cultured hippocampal neurons to examine the proteins. Results ES detected de novo truncating variants in SHANK1 in six individuals. Evaluation of NMD resulted in stable transcripts, and the truncated SHANK1 completely lost binding with Homer1, a linker protein that binds to the C-terminus of SHANK1. These variants may disrupt protein–protein networks in dendritic spines. Dispersed localization of the truncated SHANK1 variants within the spine and dendritic shaft was also observed when expressed in neurons, indicating impaired synaptic localization of truncated SHANK1. Conclusion This report expands the clinical spectrum of individuals with truncating SHANK1 variants and describes the impact these variants may have on the pathophysiology of neurodevelopmental disorders.

Published
2021

12. Determining the pathogenicity of variants of uncertain significance and identification of a founder variant in the epilepsy-associated gene, SZT2

Author

Issam Ben-Sahra, Mona Grimmel, Marcello Scala, Nina Ekhilevich, Valeria Capra, Hannah C Happ, Gemma L. Carvill, John Millichap, Lynne M. Bird, Anna Chassevent, Meredith Hiller, Eva M. C. Schwaibold, Tova Hershkovitz, Miriam C. Aziz, Najma Mohamed, Constance Smith-Hicks, Irena Bellinski, Elizabeth E. Gerard, Andrea Accogli, Kristy Zeng, Colleen Gleason, Jonathan Gunti, Lisa Kinsley, Pasquale Striano, Emily Bryant, Karin Weiss, Jeffrey D. Calhoun, Divakar S. Mithal, and Annalaura Torella

Subjects
Genetics, Haplotype, Macrocephaly, epilepsy, mTOR, SZT2, variant, genetics, Biology, medicine.disease, DEPDC5, Phenotype, medicine.anatomical_structure, Neurodevelopmental disorder, variant, medicine, mTOR, SZT2, Missense mutation, epilepsy, genetics, TSC1, medicine.symptom, Gene
Abstract

Biallelic pathogenic variants in SZT2 result in a neurodevelopmental disorder with shared features, including early-onset epilepsy, developmental delay, macrocephaly, and corpus callosum abnormalities. SZT2 is as a critical scaffolding protein in the amino acid sensing arm of the mTOR signaling pathway. Due to its large size (3432 amino acids), lack of crystal structure, and absence of functional domains, it is difficult to determine the pathogenicity of SZT2 missense and in-frame deletions. We report a cohort of twelve individuals with biallelic SZT2 variants and phenotypes consistent with SZT2-related neurodevelopmental disorder. The majority of this cohort contained one or more SZT2 variants of uncertain significance (VUS). We developed a novel individualized platform to functionally characterize SZT2 VUSs. We identified a recurrent in-frame deletion (SZT2 p.Val1984del) which was determined to be a loss-of-function variant and therefore likely pathogenic. Haplotype analysis determined this single in-frame deletion is a founder variant in those of Ashkenazi Jewish ancestry. Overall, we present a FACS-based rapid assay to distinguish pathogenic variants from VUSs in SZT2, using an approach that is widely applicable to other mTORopathies including the most common causes of the focal genetic epilepsies, DEPDC5, TSC1/2, MTOR and NPRL2/3.

Published
2021

13. 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

14. Mutations in the KIF21B kinesin gene cause neurodevelopmental disorders through imbalanced canonical motor activity

Author

Petra J. G. Zwijnenburg, Kirsty McWalter, Sonal Mahida, Delphine Héron, Frédéric Saudou, Hélène Vitet, Anna Chassevent, José Rivera Alvarez, Carlos A. Bacino, Juliette D. Godin, Christel Thauvin-Robinet, Chantal Weber, Laure Asselin, Caroline Nava, Christelle Golzio, Neil A. Hanchard, Christel Depienne, Peggy Tilly, Camille S. Bonnet, Cyril Mignot, Gladys Zapata, Amy Dameron, Marjan M. Weiss, Solveig Heide, Laurence Faivre, Haley Streff, Agnès Rastetter, Kristin W. Barañano, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Groupe de Recherche Clinique : Déficience Intellectuelle et Autisme (GRC), Université Pierre et Marie Curie - Paris 6 (UPMC), Centre de Référence des Déficiences Intellectuelles de Causes Rares, [GIN] Grenoble Institut des Neurosciences (GIN), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes (UGA), Centre Hospitalier Universitaire [Grenoble] (CHU), Baylor College of Medicine (BCM), Baylor University, Texas Children's Hospital [Houston, USA], Kennedy Krieger Institute [Baltimore], GeneDx [Gaithersburg, MD, USA], Centre de génétique - Centre de référence des maladies rares, anomalies du développement et syndromes malformatifs (CHU de Dijon), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), FHU TRANSLAD (CHU de Dijon), Université de Bourgogne (UB), 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), Boston Children's Hospital, Institut du Cerveau et de la Moëlle Epinière = Brain and Spine Institute (ICM), Institut National de la Santé et de la Recherche Médicale (INSERM)-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)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Vrije Universiteit Amsterdam [Amsterdam] (VU), and University of Duisburg-Essen

Subjects
Male, 0301 basic medicine, Microcephaly, Organogenesis, [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, Medizin, Kinesins, General Physics and Astronomy, medicine.disease_cause, Mice, 0302 clinical medicine, Neurodevelopmental disorder, Cell Movement, Gene duplication, Tumours of the digestive tract Radboud Institute for Molecular Life Sciences [Radboudumc 14], Missense mutation, lcsh:Science, Zebrafish, Cerebral Cortex, Neurons, Mutation, Multidisciplinary, Neurodevelopmental disorders, Gene Expression Regulation, Developmental, Organ Size, Pedigree, 3. Good health, Kinesin, Female, Haploinsufficiency, Science, Mutation, Missense, Motor Activity, Biology, Article, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, medicine, Animals, Humans, RNA, Messenger, Cell Proliferation, Corpus Callosum Agenesis, General Chemistry, medicine.disease, Axons, HEK293 Cells, 030104 developmental biology, [SDV.BDD.EO]Life Sciences [q-bio]/Development Biology/Embryology and Organogenesis, Neuronal development, lcsh:Q, Nerve Net, Neuroscience, 030217 neurology & neurosurgery
Abstract

KIF21B is a kinesin protein that promotes intracellular transport and controls microtubule dynamics. We report three missense variants and one duplication in KIF21B in individuals with neurodevelopmental disorders associated with brain malformations, including corpus callosum agenesis (ACC) and microcephaly. We demonstrate, in vivo, that the expression of KIF21B missense variants specifically recapitulates patients’ neurodevelopmental abnormalities, including microcephaly and reduced intra- and inter-hemispheric connectivity. We establish that missense KIF21B variants impede neuronal migration through attenuation of kinesin autoinhibition leading to aberrant KIF21B motility activity. We also show that the ACC-related KIF21B variant independently perturbs axonal growth and ipsilateral axon branching through two distinct mechanisms, both leading to deregulation of canonical kinesin motor activity. The duplication introduces a premature termination codon leading to nonsense-mediated mRNA decay. Although we demonstrate that Kif21b haploinsufficiency leads to an impaired neuronal positioning, the duplication variant might not be pathogenic. Altogether, our data indicate that impaired KIF21B autoregulation and function play a critical role in the pathogenicity of human neurodevelopmental disorder., Kinesins regulate intracellular transport and microtubule dynamics. Here, the authors show that KIF21B variants in humans associate with corpus callosum agenesis and microcephaly. Using mice and zebrafish, they showed the cellular mechanisms altered by the missense KIF21B variants.

Published
2020

15. Author response for 'Heterozygous de novo variants in <scp> CSNK1G1 </scp> are associated with syndromic developmental delay and autism spectrum disorder'

Author

Edward Blair, Elizabeth J. Bhoj, Frank J. Kaiser, Tim M. Strom, Ilaria Parenti, Nina B. Gold, Feliciano J. Ramos, Lance H. Rodan, Juan Pié, Dong Li, Reem Saadeh-Haddad, Beatriz Puisac, Constance Smith-Hicks, Hong Cui, Kirsty McWalter, Anna Chassevent, and Maria J. Guillen Sacoto

Subjects
Genetics, Autism spectrum disorder, business.industry, medicine, medicine.disease, business
Published
2020

16. Heterozygous de novo variants in CSNK1G1 are associated with syndromic developmental delay and autism spectrum disorder

Author

Tim M. Strom, Nina B. Gold, Anna Chassevent, Edward Blair, Lance H. Rodan, Juan Pié, Constance Smith-Hicks, Ilaria Parenti, Feliciano J. Ramos, Maria J. Guillen Sacoto, Kirsty McWalter, Reem Saadeh-Haddad, Elizabeth J. Bhoj, Dong Li, Beatriz Puisac, Frank J. Kaiser, and Hong Cui

Subjects
0301 basic medicine, Adult, Male, Heterozygote, Microarray, Adolescent, Autism Spectrum Disorder, Developmental Disabilities, Morphogenesis, Medizin, 030105 genetics & heredity, Biology, DNA sequencing, 03 medical and health sciences, Epilepsy, Young Adult, Genetics, medicine, Humans, Genetic Predisposition to Disease, Casein Kinase II, Child, Exome, Genetics (clinical), Comparative Genomic Hybridization, Whole Genome Sequencing, medicine.disease, 030104 developmental biology, Autism spectrum disorder, Child, Preschool, Autism, Female, Comparative genomic hybridization
Abstract

The gamma-1 isoform of casein kinase 1, the protein encoded by CSNK1G1, is involved in the growth and morphogenesis of cells. This protein is expressed ubiquitously among many tissue types, including the brain, where it regulates the phosphorylation of N-methyl-D-aspartate receptors and plays a role in synaptic transmission. One prior individual with a de novo variant in CSNK1G presenting with severe developmental delay and early-onset epilepsy has been reported. Here we report an updated clinical history of this previously published case, as well as four additional individuals with de novo variants in CSNK1G1 identified via microarray-based comparative genomic hybridization, exome, or genome sequencing. All individuals (n = 5) had developmental delay. At least three individuals had diagnoses of autism spectrum disorder. All participants were noted to have dysmorphic facial features, although the reported findings varied widely and therefore may not clearly be recognizable. None of the participants had additional major malformations. Taken together, our data suggest that CSNK1G1 may be a cause of syndromic developmental delay and possibly autism spectrum disorder.

Published
2020

17. The broad phenotypic spectrum of PPP2R1A -related neurodevelopmental disorders correlates with the degree of biochemical dysfunction

Author

Amy McTague, Siddharth Srivastava, Tamison Jewett, Ali Al-Beshri, Constance Smith-Hicks, Shelagh Joss, Jennifer A. Sullivan, Sarju G. Mehta, Koenraad Devriendt, Pascal Joset, Laurence Faivre, Emma Kivuva, William G. Wilson, Gunnar Houge, Naama Orenstein, Yana Hoorne, Vickie L. Hannig, Malou Heijligers, Bart Loeys, Vandana Shashi, Katrina Prescott, Iris Verbinnen, Annick Toutain, Lauren M. Baldwin, Stephen P. Fulton, Katharina Steindl, Anne Marie Childs, Anna Chassevent, Shelley Towner, Cornelia Daumer-Haas, Oded Wechsberg, Alison Male, Hannah F. Johnson, Wendy K. Chung, Anita Rauch, Anna Ruiz, Isabelle Maystadt, Sara Reynhout, Sébastien Moutton, Yvette van Ierland, Veerle Janssens, Frédéric Laumonnier, Martina Baethmann, Lisa Lenaerts, Vani Jain, Vinod Varghese, Suzanne M. Koudijs, Elisabeth Gabau, Frédérique Bonnet-Brilhault, Rizwan Hamid, Susan E. Holder, Barbara Plecko, MUMC+: MA Med Staf Spec Neurologie (9), Klinische Genetica, RS: GROW - R4 - Reproductive and Perinatal Medicine, MUMC+: DA KG Polikliniek (9), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Imagerie et cerveau (iBrain - Inserm U1253 - UNIV Tours ), Université de Tours (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM), Service de génétique [Tours], Hôpital Bretonneau-Centre Hospitalier Régional Universitaire de Tours (CHRU Tours), Centre Hospitalier Régional Universitaire de Tours (CHRU Tours), Queen Elizabeth University Hospital (Glasgow), Kennedy Krieger Institute [Baltimore], University of Antwerp (UA), Universität Zürich [Zürich] = University of Zurich (UZH), Addenbrooke’s Hospital [Cambridge, UK], Columbia University Medical Center (CUMC), Columbia University [New York], North West Thames Regional Genetics Service [London, UK] (Harrow), North West Thames Regional Genetics Service, Northwick Park Hospital, Harrow-Northwick Park Hospital [Harrow, UK] (NPH), Wake Forest University, University of Virginia [Charlottesville], Boston Children's Hospital, Prenatal Medicine Munich [Munich, Germany] (PMM), Klinikum Dritter Orden [Munich], Universitat Autònoma de Barcelona (UAB), University Hospital of Wales [Cardiff, UK], University of Alabama at Birmingham [ Birmingham] (UAB), Le Bonheur Children's Hospital [Memphis, TN, USA] (LBCH), Schneider Children’s Medical Center of Israel [Petah Tikva], Sackler Faculty of Medicine, Tel Aviv University [Tel Aviv], Leeds Teaching Hospitals NHS Trust, 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), Maison de Santé Protestante de Bordeaux-Bagatelle (MSPB), Duke University Medical Center, Maastricht University Medical Centre (MUMC), Maastricht University [Maastricht], Royal Devon and Exeter NHS Foundation Trust [UK], Great Ormond Street Institute of Child Health [London, UK] (UCL), University College of London [London] (UCL), Erasmus University Medical Center [Rotterdam] (Erasmus MC), Medical University Graz, Institut de Pathologie et Génétique [Gosselies] (I.P.G.), Vanderbilt University Medical Center [Nashville], Vanderbilt University [Nashville], Haukeland University Hospital, University of Bergen (UiB), Leuven Brain Institute [Leuven, Belgium] (LBI), Université de Tours-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Régional Universitaire de Tours (CHRU Tours)-Hôpital Bretonneau, Centre Hospitalier Régional Universitaire de Tours (CHRU TOURS), Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Clinical Genetics, University of Virginia, University Hospital of Wales (UHW), Tel Aviv University (TAU), Great Ormond Street Institute of Child Health (UCL), and Laumonnier, Frédéric

Subjects
0301 basic medicine, Microcephaly, [SDV]Life Sciences [q-bio], Intellectual disability, 030105 genetics & heredity, Bioinformatics, Epilepsy, Neurodevelopmental disorder, CORE, Protein Phosphatase 2, SPECIFICITY, Genetics (clinical), PROTEIN PHOSPHATASE 2A, Phenotype, Hypotonia, FAMILY, 3. Good health, PP2A, [SDV] Life Sciences [q-bio], PPP2R1A, PPP2R5D, INSIGHTS, intellectual disability, Muscle Hypotonia, medicine.symptom, Language delay, [SDV.GEN.GH] Life Sciences [q-bio]/Genetics/Human genetics, Article, 03 medical and health sciences, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, medicine, Humans, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, business.industry, Macrocephaly, DEPHOSPHORYLATION, medicine.disease, neurodevelopmental disorder, 030104 developmental biology, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Neurodevelopmental Disorders, SUBUNIT, epilepsy, Human medicine, TAU, business, Transcription Factors
Abstract

PURPOSE: Neurodevelopmental disorders (NDD) caused by protein phosphatase 2A (PP2A) dysfunction have mainly been associated with de novo variants in PPP2R5D and PPP2CA, and more rarely in PPP2R1A. Here, we aimed to better understand the latter by characterizing 30 individuals with de novo and often recurrent variants in this PP2A scaffolding Aα subunit. METHODS: Most cases were identified through routine clinical diagnostics. Variants were biochemically characterized for phosphatase activity and interaction with other PP2A subunits. RESULTS: We describe 30 individuals with 16 different variants in PPP2R1A, 21 of whom had variants not previously reported. The severity of developmental delay ranged from mild learning problems to severe intellectual disability (ID) with or without epilepsy. Common features were language delay, hypotonia, and hypermobile joints. Macrocephaly was only seen in individuals without B55α subunit-binding deficit, and these patients had less severe ID and no seizures. Biochemically more disruptive variants with impaired B55α but increased striatin binding were associated with profound ID, epilepsy, corpus callosum hypoplasia, and sometimes microcephaly. CONCLUSION: We significantly expand the phenotypic spectrum of PPP2R1A-related NDD, revealing a broader clinical presentation of the patients and that the functional consequences of the variants are more diverse than previously reported. ispartof: Genetics In Medicine vol:23 issue:2 ispartof: location:United States status: Published online

Published
2020

18. De Novo Missense Variants in FBXW11 Cause Diverse Developmental Phenotypes Including Brain, Eye, and Digit Anomalies

Author

Alaa Afif Mohammed, Yong-hui Jiang, Thalia Antoniadi, Cynthia J. Curry, Celia Zazo Seco, Dorine Bax, Slavé Petrovski, Samuel J.H. Clokie, Vandana Shashi, Stephen W. Wilson, Dianne Gerrelli, Nicola K. Ragge, Marco Tartaglia, Nicolas Chassaing, Andrea Ciolfi, Marleen Simon, Bruce D. Gelb, Helle Andersen, Zöe Powis, Patrick Calvas, Jennifer A. Sullivan, Fabiola Ceroni, Constance Smith-Hicks, Emanuele Bellacchio, Kristina Pilekær Sørensen, Rodrigo M. Young, Christina Fagerberg, Alessandro De Luca, Ellen van Binsbergen, Luigi Memo, William B. Dobyns, Anna Chassevent, Berta Crespo, Richard J. Holt, Holt R.J., Young R.M., Crespo B., Ceroni F., Curry C.J., Bellacchio E., Bax D.A., Ciolfi A., Simon M., Fagerberg C.R., van Binsbergen E., De Luca A., Memo L., Dobyns W.B., Mohammed A.A., Clokie S.J.H., Zazo Seco C., Jiang Y.-H., Sorensen K.P., Andersen H., Sullivan J., Powis Z., Chassevent A., Smith-Hicks C., Petrovski S., Antoniadi T., Shashi V., Gelb B.D., Wilson S.W., Gerrelli D., Tartaglia M., Chassaing N., Calvas P., and Ragge N.K.

Subjects
Adult, Male, Adolescent, hedgehog, Ubiquitin-Protein Ligases, brain, Mutation, Missense, Biology, Fingers, 03 medical and health sciences, Wnt, FBXW11, Report, Genetics, medicine, Humans, Noonan syndrome, Eye Abnormalities, Child, Exome, Zebrafish, development, Genetics (clinical), 030304 developmental biology, 0303 health sciences, neurodevelopment, digit, 030305 genetics & heredity, Wnt signaling pathway, WD40, medicine.disease, biology.organism_classification, beta-Transducin Repeat-Containing Proteins, Phenotype, eye, human development, Ubiquitin ligase complex, Child, Preschool, Eye development, Female
Abstract

The identification of genetic variants implicated in human developmental disorders has been revolutionized by second-generation sequencing combined with international pooling of cases. Here, we describe seven individuals who have diverse yet overlapping developmental anomalies, and who all have de novo missense FBXW11 variants identified by whole exome or whole genome sequencing and not reported in the gnomAD database. Their phenotypes include striking neurodevelopmental, digital, jaw, and eye anomalies, and in one individual, features resembling Noonan syndrome, a condition caused by dysregulated RAS signaling. FBXW11 encodes an F-box protein, part of the Skp1-cullin-F-box (SCF) ubiquitin ligase complex, involved in ubiquitination and proteasomal degradation and thus fundamental to many protein regulatory processes. FBXW11 targets include β-catenin and GLI transcription factors, key mediators of Wnt and Hh signaling, respectively, critical to digital, neurological, and eye development. Structural analyses indicate affected residues cluster at the surface of the loops of the substrate-binding domain of FBXW11, and the variants are predicted to destabilize the protein and/or its interactions. In situ hybridization studies on human and zebrafish embryonic tissues demonstrate FBXW11 is expressed in the developing eye, brain, mandibular processes, and limb buds or pectoral fins. Knockdown of the zebrafish FBXW11 orthologs fbxw11a and fbxw11b resulted in embryos with smaller, misshapen, and underdeveloped eyes and abnormal jaw and pectoral fin development. Our findings support the role of FBXW11 in multiple developmental processes, including those involving the brain, eye, digits, and jaw.

Published
2019

19. A genome-wide DNA methylation signature for SETD1B-related syndrome

Author

Saskia M. Maas, Irene Madrigal, David A. Sweetser, I. M. Krzyzewska, Hyung-Goo Kim, Anna Chassevent, Hirotomo Saitsu, Peter Henneman, E. Rajcan-Separovic, Erfan Aref-Eshghi, Marielle Alders, Sonal Mahida, Audrey Labalme, T. Fukuda, Marie-Line Jacquemont, Karin van der Lip, Raquel Rabionet, Bekim Sadikovic, Suzanne M E Lewis, Marcel M.A.M. Mannens, Andrea Venema, A. J. van Essen, Gaetan Lesca, H. Ikeda, Naomichi Matsumoto, Ying Qiao, Kristin W. Barañano, ARD - Amsterdam Reproduction and Development, Human Genetics, ACS - Pulmonary hypertension & thrombosis, and AGEM - Amsterdam Gastroenterology Endocrinology Metabolism

Subjects
Male, Jumonji Domain-Containing Histone Demethylases, INTELLECTUAL DISABILITY, Autism Spectrum Disorder, Diseases, Anxiety, VARIANTS, Epigenesis, Genetic, SETD1B, 0302 clinical medicine, Loss of Function Mutation, Histone methyltransferase complex, Child, Genetics (clinical), Genetics, 0303 health sciences, Chromatin, LINKING, Child, Preschool, DNA methylation, Female, Adult, Genetic Markers, Adolescent, Biology, DIAGNOSIS, 12Q24.31, 03 medical and health sciences, Histone H3, BECKWITH-WIEDEMANN SYNDROME, Humans, MICRODELETION, Epigenetics, Molecular Biology, Gene, Loss function, 030304 developmental biology, Epilepsy, Research, F-Box Proteins, Infant, Newborn, Histone-Lysine N-Methyltransferase, DNA Methylation, Expressió gènica, Human genetics, Malalties, CpG Islands, Gene expression, 030217 neurology & neurosurgery, Developmental Biology
Abstract

SETD1B is a component of a histone methyltransferase complex that specifically methylates Lys-4 of histone H3 (H3K4) and is responsible for the epigenetic control of chromatin structure and gene expression. De novo microdeletions encompassing this gene as well as de novo missense mutations were previously linked to syndromic intellectual disability (ID). Here, we identify a specific hypermethylation signature associated with loss of function mutations in theSETD1Bgene which may be used as an epigenetic marker supporting the diagnosis of syndromicSETD1B-related diseases. We demonstrate the clinical utility of this unique epi-signature by reclassifying previously identifiedSETD1BVUS (variant of uncertain significance) in two patients.

Published
2019

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