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1. LARP1 haploinsufficiency is associated with an autosomal dominant neurodevelopmental disorder

Author

James Chettle, Raymond J. Louie, Olivia Larner, Robert Best, Kevin Chen, Josephine Morris, Zinaida Dedeic, Anna Childers, R. Curtis Rogers, Barbara R. DuPont, Cindy Skinner, Sébastien Küry, Kevin Uguen, Marc Planes, Danielle Monteil, Megan Li, Aviva Eliyahu, Lior Greenbaum, Nofar Mor, Thomas Besnard, Bertrand Isidor, Benjamin Cogné, Alyssa Blesson, Anne Comi, Ingrid M. Wentzensen, Blake Vuocolo, Seema R. Lalani, Roberta Sierra, Lori Berry, Kent Carter, Stephan J. Sanders, and Sarah P. Blagden

Subjects
LARP1, autism, ASD, NDD, neurodevelopmental, metabolism, Genetics, QH426-470
Abstract

Summary: Autism spectrum disorder (ASD) is a neurodevelopmental disorder (NDD) that affects approximately 4% of males and 1% of females in the United States. While causes of ASD are multi-factorial, single rare genetic variants contribute to around 20% of cases. Here, we report a case series of seven unrelated probands (6 males, 1 female) with ASD or another variable NDD phenotype attributed to de novo heterozygous loss of function or missense variants in the gene LARP1 (La ribonucleoprotein 1). LARP1 encodes an RNA-binding protein that post-transcriptionally regulates the stability and translation of thousands of mRNAs, including those regulating cellular metabolism and metabolic plasticity. Using lymphocytes collected and immortalized from an index proband who carries a truncating variant in one allele of LARP1, we demonstrated that lower cellular levels of LARP1 protein cause reduced rates of aerobic respiration and glycolysis. As expression of LARP1 increases during neurodevelopment, with higher levels in neurons and astrocytes, we propose that LARP1 haploinsufficiency contributes to ASD or related NDDs through attenuated metabolic activity in the developing fetal brain.

Published
2024
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2. Pathological variants in TOP3A cause distinct disorders of mitochondrial and nuclear genome stability

Author

Direnis Erdinc, Alejandro Rodríguez‐Luis, Mahmoud R Fassad, Sarah Mackenzie, Christopher M Watson, Sebastian Valenzuela, Xie Xie, Katja E Menger, Kate Sergeant, Kate Craig, Sila Hopton, Gavin Falkous, Genomics England Research Consortium, Joanna Poulton, Hector Garcia‐Moreno, Paola Giunti, Carlos A de Moura Aschoff, Jonas A Morales Saute, Amelia J Kirby, Camilo Toro, Lynne Wolfe, Danica Novacic, Lior Greenbaum, Aviva Eliyahu, Ortal Barel, Yair Anikster, Robert McFarland, Gráinne S Gorman, Andrew M Schaefer, Claes M Gustafsson, Robert W Taylor, Maria Falkenberg, and Thomas J Nicholls

Subjects
Bloom syndrome, mitochondrial disease, mtDNA, TOP3A, Medicine (General), R5-920, Genetics, QH426-470
Abstract

Abstract Topoisomerase 3α (TOP3A) is an enzyme that removes torsional strain and interlinks between DNA molecules. TOP3A localises to both the nucleus and mitochondria, with the two isoforms playing specialised roles in DNA recombination and replication respectively. Pathogenic variants in TOP3A can cause a disorder similar to Bloom syndrome, which results from bi‐allelic pathogenic variants in BLM, encoding a nuclear‐binding partner of TOP3A. In this work, we describe 11 individuals from 9 families with an adult‐onset mitochondrial disease resulting from bi‐allelic TOP3A gene variants. The majority of patients have a consistent clinical phenotype characterised by bilateral ptosis, ophthalmoplegia, myopathy and axonal sensory‐motor neuropathy. We present a comprehensive characterisation of the effect of TOP3A variants, from individuals with mitochondrial disease and Bloom‐like syndrome, upon mtDNA maintenance and different aspects of enzyme function. Based on these results, we suggest a model whereby the overall severity of the TOP3A catalytic defect determines the clinical outcome, with milder variants causing adult‐onset mitochondrial disease and more severe variants causing a Bloom‐like syndrome with mitochondrial dysfunction in childhood.

Published
2023
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3. Clinical impact of exome sequencing in the setting of a general pediatric ward for hospitalized children with suspected genetic disorders

Author

Maayan Kagan, Rotem Semo-Oz, Yishay Ben Moshe, Danit Atias-Varon, Irit Tirosh, Michal Stern-Zimmer, Aviva Eliyahu, Annick Raas-Rothschild, Maayan Bivas, Omer Shlomovitz, Odelia Chorin, Rachel Rock, Michal Tzadok, Bruria Ben-Zeev, Gali Heimer, Yoav Bolkier, Noah Gruber, Adi Dagan, Bat El Bar Aluma, Itai M. Pessach, Gideon Rechavi, Ortal Barel, Ben Pode-Shakked, Yair Anikster, and Asaf Vivante

Subjects
exome sequencing (ES), general pediatrics, monogenic, hospitalized, inpatient, Genetics, QH426-470
Abstract

Background: Genetic conditions contribute a significant portion of disease etiologies in children admitted to general pediatric wards worldwide. While exome sequencing (ES) has improved clinical diagnosis and management over a variety of pediatric subspecialties, it is not yet routinely used by general pediatric hospitalists. We aim to investigate the impact of exome sequencing in sequencing-naive children suspected of having monogenic disorders while receiving inpatient care.Methods: We prospectively employed exome sequencing in children admitted to the general pediatric inpatient service at a large tertiary medical center in Israel. Genetic analysis was triggered by general and/or subspecialist pediatricians who were part of the primary inpatient team. We determined the diagnostic yield among children who were referred for exome sequencing and observed the effects of genetic diagnosis on medical care.Results: A total of fifty probands were evaluated and exome sequenced during the study period. The most common phenotypes included were neurodevelopmental (56%), gastrointestinal (34%), and congenital cardiac anomalies (24%). A molecular diagnosis was reached in 38% of patients. Among seven patients (37%), the molecular genetic diagnosis influenced subsequent clinical management already during admission or shortly following discharge.Conclusion: We identified a significant fraction of genetic etiologies among undiagnosed children admitted to the general pediatric ward. Our results support that early application of exome sequencing may be maximized by pediatric hospitalists’ high index of suspicion for an underlying genetic etiology, prompting an in-house genetic evaluation. This framework should include a multidisciplinary co-management approach of the primary care team working alongside with subspecialties, geneticists and bioinformaticians.

Published
2023
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4. A single center experience with publicly funded clinical exome sequencing for neurodevelopmental disorders or multiple congenital anomalies

Author

Ben Pode-Shakked, Ortal Barel, Amihood Singer, Miriam Regev, Hana Poran, Aviva Eliyahu, Yael Finezilber, Meirav Segev, Michal Berkenstadt, Hagith Yonath, Haike Reznik-Wolf, Yael Gazit, Odelia Chorin, Gali Heimer, Lidia V. Gabis, Michal Tzadok, Andreea Nissenkorn, Omer Bar-Yosef, Efrat Zohar-Dayan, Bruria Ben-Zeev, Nofar Mor, Nitzan Kol, Omri Nayshool, Noam Shimshoviz, Ifat Bar-Joseph, Dina Marek-Yagel, Elisheva Javasky, Reviva Einy, Moran Gal, Julia Grinshpun-Cohen, Mordechai Shohat, Dan Dominissini, Annick Raas-Rothschild, Gideon Rechavi, Elon Pras, and Lior Greenbaum

Subjects
Medicine, Science
Abstract

Abstract Exome sequencing (ES) is an important diagnostic tool for individuals with neurodevelopmental disorders (NDD) and/or multiple congenital anomalies (MCA). However, the cost of ES limits the test's accessibility for many patients. We evaluated the yield of publicly funded clinical ES, performed at a tertiary center in Israel, over a 3-year period (2018–2020). Probands presented with (1) moderate-to-profound global developmental delay (GDD)/intellectual disability (ID); or (2) mild GDD/ID with epilepsy or congenital anomaly; and/or (3) MCA. Subjects with normal chromosomal microarray analysis who met inclusion criteria were included, totaling 280 consecutive cases. Trio ES (proband and parents) was the default option. In 252 cases (90.0%), indication of NDD was noted. Most probands were males (62.9%), and their mean age at ES submission was 9.3 years (range 1 month to 51 years). Molecular diagnosis was reached in 109 probands (38.9%), mainly due to de novo variants (91/109, 83.5%). Disease-causing variants were identified in 92 genes, 15 of which were implicated in more than a single case. Male sex, families with multiple-affected members and premature birth were significantly associated with lower ES yield (p

Published
2021
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5. Refining the Phenotypic Spectrum of KMT5B-Associated Developmental Delay

Author

Aviva Eliyahu, Ortal Barel, Lior Greenbaum, Gal Zaks Hoffer, Yael Goldberg, Annick Raas-Rothschild, Amihood Singer, Ifat Bar-Joseph, Vered Kunik, Elisheva Javasky, Orna Staretz-Chacham, Naomi Pode-Shakked, Lily Bazak, Noa Ruhrman-Shahar, Elon Pras, Moshe Frydman, Mordechai Shohat, and Ben Pode-Shakked

Subjects
KMT5B, intellectual disability, developmental delay, de novo, macrocephaly, Pediatrics, RJ1-570
Abstract

The role of lysine methyltransferases (KMTs) and demethylases (KDMs) in the regulation of chromatin modification is well-established. Recently, deleterious heterozygous variants in KMT5B were implicated in individuals with intellectual disability (ID) and/or autism spectrum disorder. We describe three unrelated patients with global developmental delay (GDD) or ID, macrocephaly and additional features. Using whole exome sequencing, each of the probands was found to harbor a distinct de novo heterozygous disease-causing variant in KMT5B: c.541C > G (p.His181Asp); c.833A > T (p.Asn278Ile); or c.391_394delAAAG (p.Lys131GlufsTer6). We discuss herein their clinical presentations, and compare them to those of previously reported patients. Furthermore, using a three-dimensional computational model of the KMT5B protein, we demonstrate the predicted structural effects of the two missense variants. Our findings support the role of de novo missense and nonsense variants in KMT5B-associated GDD/ID, and suggest that this gene should be considered in the differential diagnosis of neurodevelopmental disorders accompanied by macrocephaly and/or overgrowth.

Published
2022
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6. Progressive Pseudorheumatoid Dysplasia resolved by whole exome sequencing: a novel mutation in WISP3 and review of the literature

Author

Ben Pode-Shakked, Asaf Vivante, Ortal Barel, Shai Padeh, Dina Marek-Yagel, Alvit Veber, Shachar Abudi, Aviva Eliyahu, Irit Tirosh, Shiri Shpilman, Shirlee Shril, Friedhelm Hildebrandt, Mordechai Shohat, and Yair Anikster

Subjects
WISP3, CCN6, Progressive pseudorheumatoid dysplasia, PPRD, Pseudorheumatoid arthritis of childhood, Internal medicine, RC31-1245, Genetics, QH426-470
Abstract

Abstract Background Progressive pseudorheumatoid dysplasia (PPRD) is a rare autosomal-recessive, non-inflammatory arthropathy, shown to be caused by mutations in the WNT1-inducible signaling pathway protein 3 (WISP3) gene. Although several hundred cases were reported worldwide, the diagnosis remains challenging. Subsequently, the syndrome is often unrecognized and misdiagnosed (for instance, as Juvenile Idiopathic Arthritis), leading to unnecessary procedures and treatments. The objective of the current study was to identify the molecular basis in a family with PPRD and describe their phenotype and course of illness. Patients and methods We present here a multiply affected consanguineous family of Iraqi-Jewish descent with PPRD. The proband, a 6.5 years old girl, presented with bilateral symmetric bony enlargements of the 1st interphalangeal joints of the hands, without signs of synovitis. Molecular analysis of the family was pursued using Whole Exome Sequencing (WES) and homozygosity mapping. Results WES analysis brought to the identification of a novel homozygous missense mutation (c.257G > T, p.C86F) in the WISP3 gene. Following this diagnosis, an additional 53 years old affected family member was found to harbor the mutation. Two other individuals in the family were reported to have had similar involvement however both had died of unrelated causes. Conclusion The reported family underscores the importance of recognition of this unique skeletal dysplasia by clinicians, and especially by pediatric rheumatologists and orthopedic surgeons.

Published
2019
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7. BRPF1‐associated intellectual disability, ptosis, and facial dysmorphism in a multiplex family

Author

Naomi Pode‐Shakked, Ortal Barel, Ben Pode‐Shakked, Aviva Eliyahu, Amihood Singer, Omri Nayshool, Nitzan Kol, Annick Raas‐Rothschild, Elon Pras, and Mordechai Shohat

Subjects
blepharophimosis, BRPF1, intellectual disability, ptosis, Genetics, QH426-470
Abstract

Abstract Background Over 500 epigenetic regulators have been identified throughout the human genome. Of these, approximately 30 chromatin modifiers have been implicated thus far in human disease. Recently, variants in BRPF1, encoding a chromatin reader, have been associated with a previously unrecognized autosomal dominant syndrome manifesting with intellectual disability (ID), hypotonia, dysmorphic facial features, ptosis, and/or blepharophimosis in 22 individuals. Patients and Methods We report a multiply affected nonconsanguineous family of mixed Jewish descent who presented due to ID in three male siblings. Molecular analysis of the family was pursued using whole exome sequencing (WES) and subsequent Sanger sequencing. Results Whole exome sequencing analysis brought to the identification of a novel heterozygous truncating mutation (c.556C>T, p.Q186*) in the BRPF1 gene in the affected siblings and their mother. The four affected individuals showed varying degrees of intellectual disability, distinct facial features including downslanted palpebral fissures, ptosis, and/or blepharophimosis. Their clinical characteristics are discussed in the context of previously reported patients with the BRPF1‐related phenotype. Conclusion The reported family contributes to the current knowledge regarding this unique and newly recognized genetic disorder, and further implicates the role of BRPF1 in human brain development.

Published
2019
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9. Deep intronic variant in the <scp> ARSB </scp> gene as the genetic cause for Maroteaux–Lamy syndrome ( <scp>MPS VI</scp> )

Author

Dina Marek-Yagel, Alvit Veber, Ben Pode-Shakked, Aviva Eliyahu, Elisheva Javasky, Amit Mary Philosoph, Orna Staretz-Chacham, Ortal Barel, Neta Loewenthal, Yair Anikster, and Nechama Shalva

Subjects
Male, Arylsulfatase B, N-Acetylgalactosamine-4-Sulfatase, Genetic counseling, Mutation, Missense, Genetic Counseling, Biology, Deep sequencing, Genetics, medicine, Humans, Missense mutation, Genetic Predisposition to Disease, Gene, Genetics (clinical), Whole genome sequencing, Mucopolysaccharidosis VI, Infant, Exons, Enzyme replacement therapy, medicine.disease, Introns, Arabs, Maroteaux–Lamy syndrome, Child, Preschool, Female
Abstract

Maroteaux-Lamy syndrome (MPS-VI) is a rare autosomal-recessive disorder with a wide spectrum of clinical manifestations, ranging from an attenuated to a rapidly progressive disease. It is caused by variants in ARSB, which encodes the lysosomal arylsulfatase B (ARSB) enzyme, part of the degradation process of glycosaminoglycans in lysosomes. Over 220 variants have been reported so far, with a majority of missense variants. We hereby report two siblings of Bedouin origin with a diagnosis of MPS-VI. Western blots in patient fibroblasts revealed total absence of ARSB protein production. Complete sequencing of the coding region of ARSB did not identify a candidate disease-associated variant. However, deep sequencing of the noncoding region of ARSB by whole genome sequencing (WGS) revealed a c.1142+581A to G variant. The variant is located within intron 5 and fully segregated with the disease in the family. Determination of the genetic cause for these patients enabled targeted treatment by enzyme replacement therapy, along with appropriate genetic counseling and prenatal diagnosis for the family. These results highlight the advantage of WGS as a powerful tool, for improving the diagnostic rate of rare disease-causing variants, and emphasize the importance of studying deep intronic sequence variation as a cause of monogenic disorders.

Published
2021

10. Whole-exome sequencing reveals a monogenic cause in 56% of individuals with laterality disorders and associated congenital heart defects

Author

Yarden Sarouf, Amir Vardi, Ben Pode-Shakked, Yishay Ben Moshe, Alvit Veber, Gideon Rechavi, Yair Anikster, Dina Marek-Yagel, Odelia Chorin, Annick Raas-Rothschild, Shrikant Mane, Yoav Bolkier, Yishay Salem, Danit Atias-Varon, Omer Shlomovitz, Elisheva Javasky, Tal Tirosh-Wagner, Uriel Katz, Jeffrey M. Jacobson, Orna Staretz-Chacham, Nechama Shalva, Ortal Barel, David Mishali, Maayan Kagan, Asaf Vivante, and Aviva Eliyahu

Subjects
Heart Defects, Congenital, Proband, Heart malformation, C21orf59, Heterotaxy Syndrome, Cohort Studies, symbols.namesake, Exome Sequencing, Genetics, Humans, Medicine, Disease-causing Mutation, Genetics (clinical), Exome sequencing, Primary ciliary dyskinesia, Sanger sequencing, biology, business.industry, Homozygote, Membrane Proteins, medicine.disease, Mutation, symbols, biology.protein, Intercellular Signaling Peptides and Proteins, business, Heterotaxy
Abstract

BackgroundThe molecular basis of heterotaxy and congenital heart malformations associated with disruption of left–right asymmetry is broad and heterogenous, with over 25 genes implicated in its pathogenesis thus far.ObjectiveWe sought to elucidate the molecular basis of laterality disorders and associated congenital heart defects in a cohort of 30 unrelated probands of Arab–Muslim descent, using next-generation sequencing techniques.MethodsDetailed clinical phenotyping followed by whole-exome sequencing (WES) was pursued for each of the probands and their parents (when available). Sanger sequencing was used for segregation analysis of disease-causing mutations in the families.ResultsUsing WES, we reached a molecular diagnosis for 17 of the 30 probands (56.7%). Genes known to be associated with heterotaxy and/or primary ciliary dyskinesia, in which homozygous pathogenic or likely pathogenic variants were detected, included CFAP53 (CCDC11), CFAP298 (C21orf59), CFAP300, LRRC6, GDF1, DNAAF1, DNAH5, CCDC39, CCDC40, PKD1L1 and TTC25. Additionally, we detected a homozygous disease causing mutation in DAND5, as a novel recessive monogenic cause for heterotaxy in humans. Three additional probands were found to harbour variants of uncertain significance. These included variants in DNAH6, HYDIN, CELSR1 and CFAP46.ConclusionsOur findings contribute to the current knowledge regarding monogenic causes of heterotaxy and its associated congenital heart defects and underscore the role of next-generation sequencing techniques in the diagnostic workup of such patients, and especially among consanguineous families.

Published
2021

11. MO046: Exome sequencing of Israeli Druze individuals on dialysis reveals common as well as population- specific monogenic etiologies in ∼30%

Author

Omer Shlomovitz, Dina Yagel, Ortal Barel, Danit Atias-Varon, Aviva Eliyahu, Younes Bathish, Victor Frajewicki, Daniel Kushnir, Rinat Zaid, Suheir Assady, Marina Tchirkov, Kamal Hassan, Khaled Khazim, Ronit Geroמ, Anaam Hanut, Farid Nakhoul, Yael Kenig, Refael Gery, Etty Kruzel-Davila, Marcel Leiba, Shimon Storch, Maayan Kagan, Benjamin Dekel, Gidi Rechavi, Rachel Shukrun, Yishay Ben Moshe, Karin Weiss, and Asaf Vivante

Subjects
Transplantation, Nephrology
Abstract

BACKGROUND AND AIMS Genetic etiologies are estimated to affect ∼10% of adults with advanced CKD. However, significant population disparities in genetic kidney disease exist and population-based screening are lacking especially among minority groups. The Druze population is a middle-eastern minority with high rates of end-stage renal disease (ESRD) and consanguinity, which suggests high rates of population-specific monogenic CKD etiologies. We therefore hypothesized that by exome sequencing we will identify a unique distribution of monogenic ESRD causes as compared with prior studies and that important ramifications for clinical practice may ensue. METHOD We initiated a national multicenter study of all Israeli dialysis units in order to provide comprehensive evidence for ESRD's genetic basis (Israeli ESRD Genetic Consortium Cohort). Specifically, during 2020, we recruited 97% (n = 94) of Israeli Druze individuals on dialysis from 12 different hospitals and community-based units. We conducted exome sequencing and diagnostic analysis for all patients. We assessed the diagnostic yield of genetic analysis and its relation to baseline clinical phenotypes. RESULTS Overall, the cohort consists of 94 individuals from 91 different families with first-degree consanguinity rate of 28%. Participants mean age was 62 years (ranging from 18 to 88 years). Most common primary clinical diagnoses were diabetic kidney disease, nephropathy of unknown origin, glomerular or cystic kidney disease, together encompassing 90% of all cases. None had previous molecular diagnosis. Using exome sequencing, we identified a genetic etiology in 27 out of 94 (28.7%) participants. We identified WDR19 (NPHP13) homozygous mutation c.878G > A (p.C293Y) as the most common genetic diagnosis (5.3%). Follow-up clinical characterization revealed that all affected individuals exhibited non-syndromic adulthood-onset ESRD, supporting a profound mutation-dependent phenotypic heterogeneity and weak pre-exome phenotypic specificity. Other prevalent genetic diagnoses included type IV collagen, PKD1, PKD2 and UMOD mutations as well as monogenic forms of diabetes and hyperlipidemia. Molecular diagnosis corresponded to the pre-exome clinical diagnosis in only one-third of the participants. CONCLUSION Exome sequencing in Druze with ESRD yields a genetic diagnosis in just

Published
2022

12. The Genetic Landscape and Epidemiology of Phenylketonuria

Author

Roeland A F Evers, Mariusz Ołtarzewski, Georg F. Hoffmann, Vincenzo Leuzzi, Emil Polak, Youngguo Yu, Maria Gizewska, Belén Pérez, Ana Chiesa, Marianne Rohrbach, Alexander V. Polyakov, Lena Fajkusova, Maja Stojiljkovic, Carla Carducci, Beat Thöny, Farès Namour, Jerry Vockley, Andrea Paras, Francjan J. van Spronsen, François Feillet, Sabine Scholl-Bürgi, Francesco Porta, Amaya Belanger-Quintana, Anastasia Skouma, Barbara K. Burton, Pedro E. Bonfim-Freitas, Sergey I. Kutsev, Johannes Zschocke, Uta Lichter-Konecki, Luiz Carlos Santana da Silva, Katya Kneller, Lourdes R. Desviat, Sven F. Garbade, Aviva Eliyahu, Alicia Hillert, Vera Stoppioni, Nenad Blau, Polina Gundorova, Norma Specola, Yair Anikster, John Christodoulou, Alberto Burlina, Maja Đorđević, Daniela Karall, Harvey L. Levy, Nan Shen, Friedrich K. Trefz, Ania C. Muntau, and Center for Liver, Digestive and Metabolic Diseases (CLDM)

Subjects
0301 basic medicine, PAH DEFICIENCY, BH4, PAH deficiency, PKU, hyperphenylalaninemia, phenylalanine, tetrahydrobiopterin, Compound heterozygosity, PHENYLALANINE-HYDROXYLASE DEFICIENCY, TETRAHYDROBIOPTERIN, 0302 clinical medicine, Genotype-phenotype distinction, Hyperphenylalaninemia, Gene Frequency, Phenylketonurias, Genotype, MOLECULAR CHARACTERIZATION, Genetics (clinical), GENOTYPE-PHENOTYPE CORRELATIONS, Genetics, biology, PHENYLALANINE, Homozygote, Phenylalanine Hydroxylase, Phenotype, STATE, 3. Good health, Europe, symbols, purl.org/becyt/ford/3 [https], HYPERPHENYLALANINEMIA, Phenylalanine hydroxylase, Phenylalanine, DIAGNOSIS, PATIENT, Article, purl.org/becyt/ford/3.3 [https], 03 medical and health sciences, symbols.namesake, medicine, Humans, Genetic Predisposition to Disease, Allele, Alleles, Genetic Association Studies, PAH GENE, MUTATIONS, medicine.disease, Biopterin, 030104 developmental biology, ORIGINS, Mutation, Mendelian inheritance, biology.protein, 030217 neurology & neurosurgery
Abstract

Phenylketonuria (PKU), caused by variants in the phenylalanine hydroxylase (PAH) gene, is the most common autosomal-recessive Mendelian phenotype of amino acid metabolism. We estimated that globally 0.45 million individuals have PKU, with global prevalence 1:23,930 live births (range 1:4,500 [Italy]–1:125,000 [Japan]). Comparing genotypes and metabolic phenotypes from 16,092 affected subjects revealed differences in disease severity in 51 countries from 17 world regions, with the global phenotype distribution of 62% classic PKU, 22% mild PKU, and 16% mild hyperphenylalaninemia. A gradient in genotype and phenotype distribution exists across Europe, from classic PKU in the east to mild PKU in the southwest and mild hyperphenylalaninemia in the south. The c.1241A>G (p.Tyr414Cys)-associated genotype can be traced from Northern to Western Europe, from Sweden via Norway, to Denmark, to the Netherlands. The frequency of classic PKU increases from Europe (56%) via Middle East (71%) to Australia (80%). Of 758 PAH variants, c.1222C>T (p.Arg408Trp) (22.2%), c.1066−11G>A (IVS10−11G>A) (6.4%), and c.782G>A (p.Arg261Gln) (5.5%) were most common and responsible for two prevalent genotypes: p.[Arg408Trp];[Arg408Trp] (11.4%) and c.[1066−11G>A];[1066−11G>A] (2.6%). Most genotypes (73%) were compound heterozygous, 27% were homozygous, and 55% of 3,659 different genotypes occurred in only a single individual. PAH variants were scored using an allelic phenotype value and correlated with pre-treatment blood phenylalanine concentrations (n = 6,115) and tetrahydrobiopterin loading test results (n = 4,381), enabling prediction of both a genotype-based phenotype (88%) and tetrahydrobiopterin responsiveness (83%). This study shows that large genotype databases enable accurate phenotype prediction, allowing appropriate targeting of therapies to optimize clinical outcome. Fil: Hillert, Alicia. No especifíca; Fil: Anikster, Yair. No especifíca; Fil: Belanger Quintana, Amaya. No especifíca; Fil: Burlina, Alberto. No especifíca; Fil: Burton, Barbara K.. No especifíca; Fil: Carducci, Carla. No especifíca; Fil: Chiesa, Ana Elena. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Centro de Investigaciones Endocrinológicas "Dr. César Bergada". Gobierno de la Ciudad de Buenos Aires. Centro de Investigaciones Endocrinológicas "Dr. César Bergada". Fundación de Endocrinología Infantil. Centro de Investigaciones Endocrinológicas "Dr. César Bergada"; Argentina Fil: Christodoulou, John. No especifíca; Fil: Dordevic, Maja. No especifíca; Fil: Desviat, Lourdes R.. No especifíca; Fil: Eliyahu, Aviva. No especifíca; Fil: Evers, Roeland A.F.. No especifíca; Fil: Fajkusova, Lena. No especifíca; Fil: Feillet, Francois. No especifíca; Fil: Bonfim Freitas, Pedro E.. No especifíca; Fil: Gizewska, María. No especifíca; Fil: Gundorova, Polina. No especifíca; Fil: Karall, Daniela. No especifíca; Fil: Kneller, Katya. No especifíca; Fil: Kutsev, Sergey I.. No especifíca; Fil: Leuzzi, Vincenzo. No especifíca; Fil: Levy, Harvey L.. No especifíca; Fil: Lichter Koneck, Uta. No especifíca; Fil: Muntau, Ania C.. No especifíca; Fil: Namour, Fares. No especifíca; Fil: Oltarzewsk, Mariusz. No especifíca; Fil: Paras, Andrea. No especifíca; Fil: Perez, Belén. No especifíca; Fil: Polak, Emil. No especifíca; Fil: Polyakov, Alexander V.. No especifíca; Fil: Porta, Francesco. No especifíca; Fil: Rohrbach, Marianne. No especifíca; Fil: Scholl Bürgi, Sabine. No especifíca; Fil: Spécola, Norma. No especifíca; Fil: Stojiljkovic, Maja. No especifíca; Fil: Shen, Nan. No especifíca; Fil: Santana da Silva, Luiz C.. No especifíca; Fil: Skouma, Anastasia. No especifíca; Fil: van Spronsen, Francjan. No especifíca; Fil: Stoppioni, Vera. No especifíca; Fil: Thöny, Beat. No especifíca; Fil: Trefz, Friedrich K.. No especifíca; Fil: Vockley, Jerry. No especifíca; Fil: Yu, Youngguo. No especifíca; Fil: Zschocke, Johannes. No especifíca; Fil: Hoffmann, Georg F.. No especifíca; Fil: Garbade, Sven F.. No especifíca; Fil: Blau, Nenad. No especifíca

Published
2020

13. Refining the Phenotypic Spectrum of

Author

Aviva, Eliyahu, Ortal, Barel, Lior, Greenbaum, Gal, Zaks Hoffer, Yael, Goldberg, Annick, Raas-Rothschild, Amihood, Singer, Ifat, Bar-Joseph, Vered, Kunik, Elisheva, Javasky, Orna, Staretz-Chacham, Naomi, Pode-Shakked, Lily, Bazak, Noa, Ruhrman-Shahar, Elon, Pras, Moshe, Frydman, Mordechai, Shohat, and Ben, Pode-Shakked

Abstract

The role of lysine methyltransferases (KMTs) and demethylases (KDMs) in the regulation of chromatin modification is well-established. Recently, deleterious heterozygous variants in

Published
2021

14. [THE GENETIC BASIS OF CHRONIC KIDNEY DISEASE IN CHILDREN AND YOUNG ADULTS]

Author

Maayan, Kagan, Aviva, Eliyahu, Yishay, Ben Moshe, and Asaf, Vivante

Subjects
Adult, Young Adult, High-Throughput Nucleotide Sequencing, Humans, Genetic Testing, Renal Insufficiency, Chronic, Kidney
Abstract

Chronic kidney disease (CKD) in children arises from heterogeneous disease etiologies. A large portion is caused by monogenic diseases, which are also known as single-gene disorders or Mendelian diseases. Understanding the genetic underpinnings of childhood and young adulthood, CKD has increased significantly over the last decade due to increased availability of genetic testing as well as clinician's awareness. This led to the discovery of numerous genes that, if mutated, may lead to early onset CKD. So far, hundreds of CKD-causing genes have been reported, explaining ~30% of cases among children and ~10% in adults. Nonetheless, the genetic diagnostic yield varies markedly across different study cohorts, depending on clinical presentation, geographic region and ethnicity. In clinical practice, the diagnosis of genetic kidney diseases may be challenging due to variable expressivity, incomplete penetrance, low index of suspicion, lack of overt symptoms at early disease stages and insufficient availability of next generation sequencing methods. Detection of monogenic causes of CKD provides definitive diagnosis that might end a long distressing odyssey. It enables personalized surveillance and treatments, spares unnecessary diagnostic procedures such as kidney biopsies, prevents the use of inappropriate therapies, and might also prevent incompatible transplantation from an affected relative. Additionally, it allows family genetic consulting and early diagnosis of asymptomatic family members. The notable progress in the field of genetics in addition to the diagnostic challenges of genetic kidney disease led to the emergence of nephrogenetics - a rapidly evolving subspecialty of nephrology and genetics. Preferably, the management of patients with genetic kidney disease should be multi-disciplinary and include collaboration between nephrologists, geneticists and additional consultants as needed. We anticipate that a routine use of genetic testing for CKD patients, as well as additional advancements in genetic discoveries, will further lead to understanding of genetic CKD patho-mechanisms and to the development of novel gene-based therapies. In this review, we will discuss the genetic basis of CKD in children and young adults. We will also discuss the clinical approach to patients with suspected genetic kidney disease.

Published
2021

15. A single center experience with publicly funded clinical exome sequencing for neurodevelopmental disorders or multiple congenital anomalies

Author

Odelia Chorin, Amihood Singer, Aviva Eliyahu, Mordechai Shohat, Dan Dominissini, Annick Raas-Rothschild, Moran Gal, Gideon Rechavi, Andreea Nissenkorn, Hana Poran, Julia Grinshpun-Cohen, Michal Berkenstadt, Yael Gazit, Lidia V. Gabis, Yael Finezilber, Bruria Ben-Zeev, Noam Shimshoviz, Hagith Yonath, Omri Nayshool, Elon Pras, Nofar Mor, Reviva Einy, Efrat Zohar-Dayan, Miriam Regev, Michal Tzadok, Haike Reznik-Wolf, Ben Pode-Shakked, Elisheva Javasky, Ortal Barel, Lior Greenbaum, Dina Marek-Yagel, Ifat Bar-Joseph, Meirav Segev, Nitzan Kol, Gali Heimer, and Omer Bar-Yosef

Subjects
Proband, Adult, Male, Pediatrics, medicine.medical_specialty, Microcephaly, Financing, Government, Adolescent, Science, Cost-Benefit Analysis, Genetic Counseling, Article, Paternal Age, Tertiary Care Centers, Epilepsy, Young Adult, Pregnancy, Prenatal Diagnosis, Intellectual disability, Exome Sequencing, medicine, Humans, Abnormalities, Multiple, Global developmental delay, Genetic Testing, Israel, Child, Exome sequencing, Retrospective Studies, Multidisciplinary, Molecular medicine, business.industry, Medical genetics, Neurodevelopmental disorders, Infant, Newborn, Infant, medicine.disease, Autism spectrum disorder, Premature birth, Child, Preschool, Medicine, Feasibility Studies, Female, business, Maternal Age, Program Evaluation
Abstract

Exome sequencing (ES) is an important diagnostic tool for individuals with neurodevelopmental disorders (NDD) and/or multiple congenital anomalies (MCA). However, the cost of ES limits the test's accessibility for many patients. We evaluated the yield of publicly funded clinical ES, performed at a tertiary center in Israel, over a 3-year period (2018–2020). Probands presented with (1) moderate-to-profound global developmental delay (GDD)/intellectual disability (ID); or (2) mild GDD/ID with epilepsy or congenital anomaly; and/or (3) MCA. Subjects with normal chromosomal microarray analysis who met inclusion criteria were included, totaling 280 consecutive cases. Trio ES (proband and parents) was the default option. In 252 cases (90.0%), indication of NDD was noted. Most probands were males (62.9%), and their mean age at ES submission was 9.3 years (range 1 month to 51 years). Molecular diagnosis was reached in 109 probands (38.9%), mainly due to de novo variants (91/109, 83.5%). Disease-causing variants were identified in 92 genes, 15 of which were implicated in more than a single case. Male sex, families with multiple-affected members and premature birth were significantly associated with lower ES yield (p

Published
2021

16. A multidisciplinary nephrogenetic referral clinic for children and adults-diagnostic achievements and insights

Author

Ben Pode-Shakked, Yishay Ben-Moshe, Ortal Barel, Lilach C. Regev, Maayan Kagan, Aviva Eliyahu, Dina Marek-Yagel, Danit Atias-Varon, Einat Lahav, Naomi Issler, Omer Shlomovitz, Rotem Semo Oz, Nitzan Kol, Nofar Mor, Ifat Bar-Joseph, Yulia Khavkin, Elisheva Javasky, Pazit Beckerman, Meidad Greenberg, Oded Volovelsky, Yael Borovitz, Miriam Davidovits, Orly Haskin, Hadas Alfandary, Shely Levi, Maital Kaidar, Ze’ev Katzir, Avital Angel-Korman, Rachel Becker-Cohen, Efrat Ben-Shalom, Adi Leiba, Eytan Mor, Amit Dagan, Itai M. Pessach, Danny Lotan, Moshe Shashar, Yair Anikster, Annick Raas-Rothschild, Gideon Rechavi, Benjamin Dekel, and Asaf Vivante

Subjects
Phenotype, Nephrology, Pediatrics, Perinatology and Child Health, Exome Sequencing, Humans, Kidney Diseases, Genetic Testing, Child, Referral and Consultation
Abstract

Genetic kidney diseases contribute a significant portion of kidney diseases in children and young adults. Nephrogenetics is a rapidly evolving subspecialty; however, in the clinical setting, increased use of genetic testing poses implementation challenges. Consequently, we established a national nephrogenetics clinic to apply a multidisciplinary model.Patients were referred from different pediatric or adult nephrology units across the country if their primary nephrologist suspected an undiagnosed genetic kidney disease. We determined the diagnostic rate and observed the effect of diagnosis on medical care. We also discuss the requirements of a nephrogenetics clinic in terms of logistics, recommended indications for referral, and building a multidisciplinary team.Over 24 months, genetic evaluation was completed for a total of 74 unrelated probands, with an age range of 10 days to 72 years. The most common phenotypes included congenital anomalies of the kidneys and urinary tract, nephrotic syndrome or unexplained proteinuria, nephrocalcinosis/nephrolithiasis, tubulopathies, and unexplained kidney failure. Over 80% of patients were referred due to clinical suspicion of an undetermined underlying genetic diagnosis. A molecular diagnosis was reached in 42/74 probands, yielding a diagnostic rate of 57%. Of these, over 71% of diagnoses were made via next generation sequencing (gene panel or exome sequencing).We identified a substantial fraction of genetic kidney etiologies among previously undiagnosed individuals which influenced subsequent clinical management. Our results support that nephrogenetics, a rapidly evolving field, may benefit from well-defined multidisciplinary co-management administered by a designated team of nephrologist, geneticist, and bioinformatician. A higher resolution version of the Graphical abstract is available as Supplementary information.

Published
2021

17. Phenotypic expansion of CACNA1C-associated disorders to include isolated neurological manifestations

Author

Lance H. Rodan, Rebecca C. Spillmann, Harley T. Kurata, Shawn M. Lamothe, Jasmine Maghera, Rami Abou Jamra, Anna Alkelai, Stylianos E. Antonarakis, Isis Atallah, Omer Bar-Yosef, Frédéric Bilan, Kathrine Bjorgo, Xavier Blanc, Patrick Van Bogaert, Yoav Bolkier, Lindsay C. Burrage, Björn U. Christ, Jorge L. Granadillo, Patricia Dickson, Kirsten A. Donald, Christèle Dubourg, Aviva Eliyahu, Lisa Emrick, Kendra Engleman, Michaela Veronika Gonfiantini, Jean-Marc Good, Judith Kalser, Chiara Kloeckner, Guus Lachmeijer, Marina Macchiaiolo, Francesco Nicita, Sylvie Odent, Emily O’Heir, Xilma Ortiz-Gonzalez, Marta Pacio-Miguez, María Palomares-Bralo, Loren Pena, Konrad Platzer, Mathieu Quinodoz, Emmanuelle Ranza, Jill A. Rosenfeld, Eliane Roulet-Perez, Avni Santani, Fernando Santos-Simarro, Ben Pode-Shakked, Cara Skraban, Rachel Slaugh, Andrea Superti-Furga, Isabelle Thiffault, Richard H. van Jaabrsveld, Marie Vincent, Hong-Gang Wang, Pia Zacher, Mercedes E. Alejandro, Mahshid S. Azamian, Carlos A. Bacino, Ashok Balasubramanyam, 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, 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, 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, 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, Ellen F. Macnamara, Valerie V. Maduro, Thomas C. Markello, Avi Nath, Donna Novacic, Barbara N. Pusey, Camilo Toro, Colleen E. Wahl, Eva Baker, Elizabeth A. Burke, David R. Adams, William A. Gahl, 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, null 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, Elly Brokamp, Laura Duncan, Rizwan Hamid, Jennifer Kennedy, Mary Kozuira, John H. Newman, John A. PhillipsIII, 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, Eric Rush, Geoffrey S. Pitt, Ping Yee Billie Au, Boston Children's Hospital, University of Alberta, Universität Leipzig [Leipzig], Geneva University Hospital (HUG), Tel Aviv University [Tel Aviv], Service Génétique Médicale [CHU Poitiers], Centre hospitalier universitaire de Poitiers (CHU Poitiers), Cibles moléculaires et thérapeutiques de la maladie d'Alzheimer (CIMoTHeMA), Université de Poitiers, Laboratoire Jacques-Louis Lions (LJLL (UMR_7598)), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Baylor College of Medicine (BCM), Baylor University, Washington University School of Medicine in St. Louis, Washington University in Saint Louis (WUSTL), CHU Pontchaillou [Rennes], 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), Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS), Lausanne University Hospital, Centre de référence Maladies Rares CLAD-Ouest [Rennes], Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], Children’s Hospital of Philadelphia (CHOP ), Hospital Universitario La Paz, unité de recherche de l'institut du thorax UMR1087 UMR6291 (ITX), 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), Centre hospitalier universitaire de Nantes (CHU Nantes), Duke University [Durham], University of Kansas Medical Center [Lawrence], University of Missouri System, Children's Mercy Hospital [Kansas City], Weill Cornell Medicine [New York], University of Calgary, Research reported in this paper was supported by the NIH Common Fund, through the Office of Strategic Coordination/Office of the NIH Director under award number(s) (U01HG007709 [Baylor College of Medicine] and U01HG007672 [Duke University to V.S.]). Additional funding for this project was under award number 1RO1HD090132-01A1 (Cornell University to G.P.). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. Additional funding was provided by a Canadian Institutes of Health Research Grant (MOP-97988 to H.T.K.), and a Rowland and Muriel Haryett Fellowship (University of Alberta, to S.M.L.) and a fellowship from the Ministry of Education and Research of the Community of Madrid to M.P.M. (B2017/BMD-3721), and microgrant from the Rare Disease Foundation (P.Y.B.A. and H.T.K.). Sequencing and analysis was supported by the National Human Genome Research Institute grants UM1 HG008900 and R01 HG009141. K.A.D., B.C., and E.O. were supported the National Institute of Mental Health U01 MH119689., Universität Leipzig, Columbia University Medical Center (CUMC), Columbia University [New York], Tel Aviv University (TAU), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), 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 ), Unité de recherche de l'institut du thorax (ITX-lab), University of Kansas Medical Center [Kansas City, KS, USA], Weill Cornell Medicine [Cornell University], and Cornell University [New York]

Subjects
Ataxia, Calcium Channels, L-Type, Long QT syndrome, Timothy syndrome, Bioinformatics, Article, 03 medical and health sciences, Epilepsy, 0302 clinical medicine, Intellectual disability, medicine, Missense mutation, Humans, Autistic Disorder, Genetics (clinical), 030304 developmental biology, 0303 health sciences, [SDV.GEN]Life Sciences [q-bio]/Genetics, business.industry, medicine.disease, Hypotonia, Long QT Syndrome, Phenotype, Autism, Syndactyly, medicine.symptom, business, 030217 neurology & neurosurgery
Abstract

International audience; Purpose:CACNA1C encodes the alpha-1-subunit of a voltage-dependent L-type calcium channel expressed in human heart and brain. Heterozygous variants in CACNA1C have previously been reported in association with Timothy syndrome and long QT syndrome. Several case reports have suggested that CACNA1C variation may also be associated with a primarily neurological phenotype.Methods:We describe 25 individuals from 22 families with heterozygous variants in CACNA1C, who present with predominantly neurological manifestations.Results:Fourteen individuals have de novo, nontruncating variants and present variably with developmental delays, intellectual disability, autism, hypotonia, ataxia, and epilepsy. Functional studies of a subgroup of missense variants via patch clamp experiments demonstrated differential effects on channel function in vitro, including loss of function (p.Leu1408Val), neutral effect (p.Leu614Arg), and gain of function (p.Leu657Phe, p.Leu614Pro). The remaining 11 individuals from eight families have truncating variants in CACNA1C. The majority of these individuals have expressive language deficits, and half have autism.Conclusion:We expand the phenotype associated with CACNA1C variants to include neurodevelopmental abnormalities and epilepsy, in the absence of classic features of Timothy syndrome or long QT syndrome.

Published
2020

18. Correction: Phenotypic expansion of CACNA1C-associated disorders to include isolated neurological manifestations

Author

Lance H. Rodan, Rebecca C. Spillmann, Harley T. Kurata, Shawn M. Lamothe, Jasmine Maghera, Rami Abou Jamra, Anna Alkelai, Stylianos E. Antonarakis, Isis Atallah, Omer Bar-Yosef, Frédéric Bilan, Kathrine Bjorgo, Xavier Blanc, Patrick Van Bogaert, Yoav Bolkier, Lindsay C. Burrage, Björn U. Christ, Jorge L. Granadillo, Patricia Dickson, Kirsten A. Donald, Christèle Dubourg, Aviva Eliyahu, Lisa Emrick, Kendra Engleman, Michaela Veronika Gonfiantini, Jean-Marc Good, Judith Kalser, Chiara Kloeckner, Guus Lachmeijer, Marina Macchiaiolo, Francesco Nicita, Sylvie Odent, Emily O’Heir, Xilma Ortiz-Gonzalez, Marta Pacio-Miguez, María Palomares-Bralo, Loren Pena, Konrad Platzer, Mathieu Quinodoz, Emmanuelle Ranza, Jill A. Rosenfeld, Eliane Roulet-Perez, Avni Santani, Fernando Santos-Simarro, Ben Pode-Shakked, Cara Skraban, Rachel Slaugh, Andrea Superti-Furga, Isabelle Thiffault, Richard H. van Jaabrsveld, Marie Vincent, Hong-Gang Wang, Pia Zacher, Mercedes E. Alejandro, Mahshid S. Azamian, Carlos A. Bacino, Ashok Balasubramanyam, 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, 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, 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, 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, Ellen F. Macnamara, Valerie V. Maduro, Thomas C. Markello, Avi Nath, Donna Novacic, Barbara N. Pusey, Camilo Toro, Colleen E. Wahl, Eva Baker, Elizabeth A. Burke, David R. Adams, William A. Gahl, 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, null 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, Elly Brokamp, Laura Duncan, Rizwan Hamid, Jennifer Kennedy, Mary Kozuira, John H. Newman, John A. PhillipsIII, 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, Eric Rush, Geoffrey S. Pitt, and Ping Yee Billie Au

Subjects
Genetics (clinical)
Published
2021

19. BRPF1-associated intellectual disability, ptosis, and facial dysmorphism in a multiplex family

Author

Ben Pode-Shakked, Aviva Eliyahu, Nitzan Kol, Mordechai Shohat, Annick Raas-Rothschild, Elon Pras, Naomi Pode-Shakked, Amihood Singer, Ortal Barel, and Omri Nayshool

Subjects
0301 basic medicine, Adult, Male, lcsh:QH426-470, Context (language use), 030105 genetics & heredity, Blepharophimosis, 03 medical and health sciences, symbols.namesake, Ptosis, Intellectual disability, Exome Sequencing, Genetics, medicine, ptosis, Blepharoptosis, Humans, Exome, Family, Molecular Biology, Genetics (clinical), Exome sequencing, Adaptor Proteins, Signal Transducing, Sanger sequencing, business.industry, Genetic disorder, Nuclear Proteins, Original Articles, medicine.disease, Hypotonia, Musculoskeletal Abnormalities, Pedigree, DNA-Binding Proteins, lcsh:Genetics, 030104 developmental biology, BRPF1, intellectual disability, Mutation, symbols, Muscle Hypotonia, Female, Original Article, medicine.symptom, business
Abstract

Background Over 500 epigenetic regulators have been identified throughout the human genome. Of these, approximately 30 chromatin modifiers have been implicated thus far in human disease. Recently, variants in BRPF1, encoding a chromatin reader, have been associated with a previously unrecognized autosomal dominant syndrome manifesting with intellectual disability (ID), hypotonia, dysmorphic facial features, ptosis, and/or blepharophimosis in 22 individuals. Patients and Methods We report a multiply affected nonconsanguineous family of mixed Jewish descent who presented due to ID in three male siblings. Molecular analysis of the family was pursued using whole exome sequencing (WES) and subsequent Sanger sequencing. Results Whole exome sequencing analysis brought to the identification of a novel heterozygous truncating mutation (c.556C>T, p.Q186*) in the BRPF1 gene in the affected siblings and their mother. The four affected individuals showed varying degrees of intellectual disability, distinct facial features including downslanted palpebral fissures, ptosis, and/or blepharophimosis. Their clinical characteristics are discussed in the context of previously reported patients with the BRPF1‐related phenotype. Conclusion The reported family contributes to the current knowledge regarding this unique and newly recognized genetic disorder, and further implicates the role of BRPF1 in human brain development.

Published
2018

20. A novel inborn error of the coenzyme Q10 biosynthesis pathway: cerebellar ataxia and static encephalomyopathy due to COQ5 C-methyltransferase deficiency

Author

Yair Anikster, Sravan Kakani, Settara C. Chandrasekharappa, Hadass Pri-Chen, Carlos Ferreira, John E. Niederhuber, Jennifer Guo, Thierry Vilboux, Robert W. Taylor, John F. Deeken, Langping He, Tal Yardeni, May Christine V. Malicdan, Camilo Toro, Ben Pode-Shakked, Aviva Eliyahu, Amir Dori, Douglas C. Wallace, Bruria Ben-Zeev, Natalia Shelestovich, Dina Marek-Yagel, Ilan Blatt, and William A. Gahl

Subjects
0301 basic medicine, Proband, medicine.medical_specialty, Methyltransferase, Cerebellar Ataxia, DNA Copy Number Variations, Ubiquinone, Mitochondrial disease, Biopsy, Encephalopathy, Biology, Polymorphism, Single Nucleotide, Article, Electron Transport, Mitochondrial Proteins, 03 medical and health sciences, chemistry.chemical_compound, Oxygen Consumption, Mitochondrial Encephalomyopathies, Internal medicine, Genetics, medicine, Leukocytes, Humans, Genetics (clinical), Loss function, Genetic Association Studies, Coenzyme Q10, Cerebellar ataxia, Muscles, Siblings, High-Throughput Nucleotide Sequencing, Methyltransferases, Fibroblasts, medicine.disease, Phenotype, 3. Good health, Biosynthetic Pathways, Pedigree, 030104 developmental biology, Endocrinology, chemistry, Biochemistry, Dietary Supplements, Female, medicine.symptom
Abstract

Primary coenzyme Q10 (CoQ10 ; MIM# 607426) deficiencies are an emerging group of inherited mitochondrial disorders with heterogonous clinical phenotypes. Over a dozen genes are involved in the biosynthesis of CoQ10 , and mutations in several of these are associated with human disease. However, mutations in COQ5 (MIM# 616359), catalyzing the only C-methylation in the CoQ10 synthetic pathway, have not been implicated in human disease. Here, we report three female siblings of Iraqi-Jewish descent, who had varying degrees of cerebellar ataxia, encephalopathy, generalized tonic-clonic seizures, and cognitive disability. Whole-exome and subsequent whole-genome sequencing identified biallelic duplications in the COQ5 gene, leading to reduced levels of CoQ10 in peripheral white blood cells of all affected individuals and reduced CoQ10 levels in the only muscle tissue available from one affected proband. CoQ10 supplementation led to clinical improvement and increased the concentrations of CoQ10 in blood. This is the first report of primary CoQ10 deficiency caused by loss of function of COQ5, with delineation of the clinical, laboratory, histological, and molecular features, and insights regarding targeted treatment with CoQ10 supplementation.

Published
2017

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