Functional and clinical studies reveal pathophysiological complexity of CLCN4-related neurodevelopmental condition
Authors: Palmer Elizabeth E. , Pusch Michael , Picollo Alessandra , Forwood Caitlin , Nguyen Matthew H. , Suckow Vanessa , Gibbons Jessica , Hoff Alva , Sigfrid Lisa , Megarbane Andre , Nizon Mathilde , Cogné Benjamin , Beneteau Claire , Alkuraya Fowzan S. , Chedrawi Aziza , Hashem Mais O. , Stamberger Hannah , Weckhuysen Sarah , Vanlander Arnaud , Ceulemans Berten , Rajagopalan Sulekha , Nunn Kenneth , Arpin Stéphanie , Raynaud Martine , Motter Constance S. , Ward-Melver Catherine , Janssens Katrien , Meuwissen Marije , Beysen Diane , Dikow Nicola , Grimmel Mona , Haack Tobias B. , Clement Emma , McTague Amy , Hunt David , Townshend Sharron , Ward Michelle , Richards Linda J. , Simons Cas , Costain Gregory , Dupuis Lucie , Mendoza-Londono Roberto , Dudding-Byth Tracy , Boyle Jackie , Saunders Carol , Fleming Emily , El Chehadeh Salima , Spitz Marie-Aude , Piton Amelie , Gerard Bénédicte , Abi Warde Marie-Thérèse , Rea Gillian , McKenna Caoimhe , Douzgou Sofia , Banka Siddharth , Akman Cigdem , Bain Jennifer M. , Sands Tristan T. , Wilson Golder N. , Silvertooth Erin J. , Miller Lauren , Lederer Damien , Sachdev Rani , Macintosh Rebecca , Monestier Olivier , Karadurmus Deniz , Collins Felicity , Carter Melissa , Rohena Luis , Willemsen Marjolein H. , Ockeloen Charlotte W. , Pfundt Rolph , Kroft Sanne D. , Field Michael , Laranjeira Francisco E. R. , Fortuna Ana M. , Soares Ana R. , Michaud Vincent , Naudion Sophie , Golla Sailaja , Weaver David D. , Bird Lynne M. , Friedman Jennifer , Clowes Virginia , Joss Shelagh , Pölsler Laura , Campeau Philippe M. , Blazo Maria , Bijlsma Emilia K. , Rosenfeld Jill A. , Beetz Christian , Powis Zöe , McWalter Kirsty , Brandt Tracy , Torti Erin , Mathot Mikaël , Mohammad Shekeeb S. , Armstrong Ruth , Kalscheuer Vera M. 
Published: November 2022

AbstractMissense and truncating variants in the X-chromosome-linked CLCN4 gene, resulting in reduced or complete loss-of-function (LOF) of the encoded chloride/proton exchanger ClC-4, were recently demonstrated to cause a neurocognitive phenotype in both males and females. Through international clinical matchmaking and interrogation of public variant databases we assembled a database of 90 rare CLCN4 missense variants in 90 families: 41 unique and 18 recurrent variants in 49 families. For 43 families, including 22 males and 33 females, we collated detailed clinical and segregation data. To confirm causality of variants and to obtain insight into disease mechanisms, we investigated the effect on electrophysiological properties of 59 of the variants in Xenopus oocytes using extended voltage and pH ranges. Detailed analyses revealed new pathophysiological mechanisms: 25% (15/59) of variants demonstrated LOF, characterized by a “shift” of the voltage-dependent activation to more positive voltages, and nine variants resulted in a toxic gain-of-function, associated with a disrupted gate allowing inward transport at negative voltages. Functional results were not always in line with in silico pathogenicity scores, highlighting the complexity of pathogenicity assessment for accurate genetic counselling. The complex neurocognitive and psychiatric manifestations of this condition, and hitherto under-recognized impacts on growth, gastrointestinal function, and motor control are discussed. Including published cases, we summarize features in 122 individuals from 67 families with CLCN4-related neurodevelopmental condition and suggest future research directions with the aim of improving the integrated care for individuals with this diagnosis.