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Küry S, Zhang J, Besnard T, Caro-Llopis A, Zeng X, Robert SM, Josiah SS, Kiziltug E, Denommé-Pichon AS, Cogné B, Kundishora AJ, Hao LT, Li H, Stevenson RE, Louie RJ, Deb W, Torti E, Vignard V, McWalter K, Raymond FL, Rajabi F, Ranza E, Grozeva D, Coury SA, Blanc X, Brischoux-Boucher E, Keren B, Õunap K, Reinson K, Ilves P, Wentzensen IM, Barr EE, Guihard SH, Charles P, Seaby EG, Monaghan KG, Rio M, van Bever Y, van Slegtenhorst M, Chung WK, Wilson A, Quinquis D, Bréhéret F, Retterer K, Lindenbaum P, Scalais E, Rhodes L, Stouffs K, Pereira EM, Berger SM, Milla SS, Jaykumar AB, Cobb MH, Panchagnula S, Duy PQ, Vincent M, Mercier S, Gilbert-Dussardier B, Le Guillou X, Audebert-Bellanger S, Odent S, Schmitt S, Boisseau P, Bonneau D, Toutain A, Colin E, Pasquier L, Redon R, Bouman A, Rosenfeld JA, Friez MJ, Pérez-Peña H, Akhtar Rizvi SR, Haider S, Antonarakis SE, Schwartz CE, Martínez F, Bézieau S, Kahle KT, Isidor B. Rare pathogenic variants in WNK3 cause X-linked intellectual disability. Genet Med 2022; 24:1941-1951. [PMID: 35678782 DOI: 10.1016/j.gim.2022.05.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 02/08/2023] Open
Abstract
PURPOSE WNK3 kinase (PRKWNK3) has been implicated in the development and function of the brain via its regulation of the cation-chloride cotransporters, but the role of WNK3 in human development is unknown. METHOD We ascertained exome or genome sequences of individuals with rare familial or sporadic forms of intellectual disability (ID). RESULTS We identified a total of 6 different maternally-inherited, hemizygous, 3 loss-of-function or 3 pathogenic missense variants (p.Pro204Arg, p.Leu300Ser, p.Glu607Val) in WNK3 in 14 male individuals from 6 unrelated families. Affected individuals had ID with variable presence of epilepsy and structural brain defects. WNK3 variants cosegregated with the disease in 3 different families with multiple affected individuals. This included 1 large family previously diagnosed with X-linked Prieto syndrome. WNK3 pathogenic missense variants localize to the catalytic domain and impede the inhibitory phosphorylation of the neuronal-specific chloride cotransporter KCC2 at threonine 1007, a site critically regulated during the development of synaptic inhibition. CONCLUSION Pathogenic WNK3 variants cause a rare form of human X-linked ID with variable epilepsy and structural brain abnormalities and implicate impaired phospho-regulation of KCC2 as a pathogenic mechanism.
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Affiliation(s)
- Sébastien Küry
- Nantes Université, CHU Nantes, Service de Génétique Médicale, Nantes, France; Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France.
| | - Jinwei Zhang
- Hatherly Laboratories, The Institute of Biomedical and Clinical Sciences, College of Medicine and Health, University of Exeter, Exeter, United Kingdom; Department of Neurosurgery, Yale School of Medicine, Yale University, New Haven, CT; State Key Laboratory of Bio-Organic and Natural Products Chemistry, Research Center of Chemical Kinomics, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Thomas Besnard
- Nantes Université, CHU Nantes, Service de Génétique Médicale, Nantes, France; Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France
| | - Alfonso Caro-Llopis
- Unidad de Genética, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Xue Zeng
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT
| | - Stephanie M Robert
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT
| | - Sunday S Josiah
- Hatherly Laboratories, The Institute of Biomedical and Clinical Sciences, College of Medicine and Health, University of Exeter, Exeter, United Kingdom
| | - Emre Kiziltug
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT
| | - Anne-Sophie Denommé-Pichon
- Département de Biochimie et Génétique, Centre Hospitalier Universitaire Angers, Angers, France; UMR CNRS 6214, INSERM 1083, Université d'Angers, Angers, France
| | - Benjamin Cogné
- Nantes Université, CHU Nantes, Service de Génétique Médicale, Nantes, France; Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France
| | - Adam J Kundishora
- Department of Neurosurgery, Yale School of Medicine, Yale University, New Haven, CT
| | - Le T Hao
- Department of Neurosurgery, Yale School of Medicine, Yale University, New Haven, CT
| | - Hong Li
- Departments of Human Genetics and Pediatrics, School of Medicine, Emory University, Atlanta, GA
| | | | | | - Wallid Deb
- Nantes Université, CHU Nantes, Service de Génétique Médicale, Nantes, France; Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France
| | | | - Virginie Vignard
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France
| | | | - F Lucy Raymond
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Biomedical Campus Cambridge, Cambridge, United Kingdom
| | - Farrah Rajabi
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA
| | - Emmanuelle Ranza
- Medigenome, Swiss Institute of Genomic Medicine, Geneva, Switzerland
| | - Detelina Grozeva
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Biomedical Campus Cambridge, Cambridge, United Kingdom; Centre for Trials Research, Cardiff University, Cardiff, United Kingdom
| | - Stephanie A Coury
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA
| | - Xavier Blanc
- Medigenome, Swiss Institute of Genomic Medicine, Geneva, Switzerland
| | - Elise Brischoux-Boucher
- Centre de Génétique Humaine, CHU de Besançon, Université de Bourgogne Franche-Comté, Besançon, France
| | - Boris Keren
- Department of Genetics, Centre de Référence Déficiences Intellectuelles de Causes Rares, Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Katrin Õunap
- Department of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia; Department of Clinical Genetics, Institute of Clinical Medicine, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Karit Reinson
- Department of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia; Department of Clinical Genetics, Institute of Clinical Medicine, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Pilvi Ilves
- Department of Clinical Genetics, Institute of Clinical Medicine, Faculty of Medicine, University of Tartu, Tartu, Estonia; Department of Radiology, Tartu University Hospital, Tartu, Estonia
| | | | - Eileen E Barr
- Departments of Human Genetics and Pediatrics, School of Medicine, Emory University, Atlanta, GA
| | - Solveig Heide Guihard
- Department of Genetics, Centre de Référence Déficiences Intellectuelles de Causes Rares, Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France; Groupe de Recherche Clinique, Déficience Intellectuelle et Autisme, Sorbonne University, Paris, France
| | - Perrine Charles
- Department of Genetics, Centre de Référence Déficiences Intellectuelles de Causes Rares, Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Eleanor G Seaby
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Genomic Informatics Group, University of Southampton, Southampton, United Kingdom
| | | | - Marlène Rio
- Developmental Brain Disorders laboratory, INSERM UMR 1163, Imagine Institute, University of Paris, Paris, France; Department of Genetics, Centre de Référence Déficiences Intellectuelles de Causes Rares, Necker Enfants Malades Hospital, APHP, Paris, France
| | - Yolande van Bever
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Marjon van Slegtenhorst
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University Irving Medical Center, Columbia University New York, NY
| | - Ashley Wilson
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons and New York-Presbyterian Morgan Stanley Children's Hospital, New York, NY
| | - Delphine Quinquis
- Nantes Université, CHU Nantes, Service de Génétique Médicale, Nantes, France
| | - Flora Bréhéret
- Nantes Université, CHU Nantes, Service de Génétique Médicale, Nantes, France
| | | | - Pierre Lindenbaum
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France
| | - Emmanuel Scalais
- Division of Pediatric Neurology, Department of Pediatrics, Centre Hospitalier de Luxembourg, Luxembourg City, Luxembourg
| | | | - Katrien Stouffs
- Neurogenetics Research Group, Reproduction and Genetics, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan, Brussels, Belgium
| | - Elaine M Pereira
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons and New York-Presbyterian Morgan Stanley Children's Hospital, New York, NY
| | - Sara M Berger
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons and New York-Presbyterian Morgan Stanley Children's Hospital, New York, NY
| | - Sarah S Milla
- Department of Radiology and Imaging Sciences, School of Medicine, Emory University, Atlanta, GA
| | - Ankita B Jaykumar
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX
| | - Melanie H Cobb
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX
| | - Shreyas Panchagnula
- Unidad de Genética, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Phan Q Duy
- Department of Neurosurgery, Yale School of Medicine, Yale University, New Haven, CT
| | - Marie Vincent
- Nantes Université, CHU Nantes, Service de Génétique Médicale, Nantes, France; Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France
| | - Sandra Mercier
- Nantes Université, CHU Nantes, Service de Génétique Médicale, Nantes, France; Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France
| | | | | | | | - Sylvie Odent
- Service de Génétique Clinique, ERN ITHACA, CHU Rennes, Rennes, France; Institut de Génétique et Développement de Rennes, IGDR UMR 6290 CNRS, INSERM, IGDR Univ Rennes, Rennes, France
| | - Sébastien Schmitt
- Nantes Université, CHU Nantes, Service de Génétique Médicale, Nantes, France
| | - Pierre Boisseau
- Nantes Université, CHU Nantes, Service de Génétique Médicale, Nantes, France
| | - Dominique Bonneau
- Département de Biochimie et Génétique, Centre Hospitalier Universitaire Angers, Angers, France; UMR CNRS 6214, INSERM 1083, Université d'Angers, Angers, France
| | - Annick Toutain
- Unité de Génétique Médicale, Centre Hospitalier Régional Universitaire de Tours, France; Unité Mixte de Recherche 1253, iBrain, Université de Tours, Institut National de la Santé et de la Recherche Médicale, Tours, France
| | - Estelle Colin
- Département de Biochimie et Génétique, Centre Hospitalier Universitaire Angers, Angers, France; UMR CNRS 6214, INSERM 1083, Université d'Angers, Angers, France
| | - Laurent Pasquier
- Service de Génétique Clinique, ERN ITHACA, CHU Rennes, Rennes, France; Institut de Génétique et Développement de Rennes, IGDR UMR 6290 CNRS, INSERM, IGDR Univ Rennes, Rennes, France
| | - Richard Redon
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France
| | - Arjan Bouman
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | | | - Helena Pérez-Peña
- Department of Pharmaceutical and Biological Chemistry, UCL School of Pharmacy, University College London, London, United Kingdom
| | - Syed Raza Akhtar Rizvi
- Department of Pharmaceutical and Biological Chemistry, UCL School of Pharmacy, University College London, London, United Kingdom
| | - Shozeb Haider
- Department of Pharmaceutical and Biological Chemistry, UCL School of Pharmacy, University College London, London, United Kingdom; Centre for Advanced Research Computing, University College London, London, United Kingdom
| | - Stylianos E Antonarakis
- Medigenome, Swiss Institute of Genomic Medicine, Geneva, Switzerland; Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland; iGE3, Institute of Genetics and Genomics of Geneva, University of Geneva, Geneva, Switzerland
| | | | - Francisco Martínez
- Unidad de Genética, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Stéphane Bézieau
- Nantes Université, CHU Nantes, Service de Génétique Médicale, Nantes, France; Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France
| | - Kristopher T Kahle
- Department of Neurosurgery, Yale School of Medicine, Yale University, New Haven, CT; Department of Cellular and Molecular Physiology, Yale School of Medicine, Yale University, New Haven, CT; NIH-Yale Centers for Mendelian Genomics, Yale School of Medicine, Yale University, New Haven, CT; Yale Stem Cell Center, Yale School of Medicine, Yale University, New Haven, CT.
| | - Bertrand Isidor
- Nantes Université, CHU Nantes, Service de Génétique Médicale, Nantes, France; Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France
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