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Unique variants in CLCN3, encoding an endosomal anion/proton exchanger, underlie a spectrum of neurodevelopmental disorders

Item Type:Article
Title:Unique variants in CLCN3, encoding an endosomal anion/proton exchanger, underlie a spectrum of neurodevelopmental disorders
Creators Name:Duncan, A.R. and Polovitskaya, M.M. and Gaitán-Peñas, H. and Bertelli, S. and VanNoy, G.E. and Grant, P.E. and O'Donnell-Luria, A. and Valivullah, Z. and Lovgren, A.K. and England, E.M. and Agolini, E. and Madden, J.A. and Schmitz-Abe, K. and Kritzer, A. and Hawley, P. and Novelli, A. and Alfieri, P. and Colafati, G.S. and Wieczorek, D. and Platzer, K. and Luppe, J. and Koch-Hogrebe, M. and Abou Jamra, R. and Neira-Fresneda, J. and Lehman, A. and Boerkoel, C.F. and Seath, K. and Clarke, L. and van Ierland, Y. and Argilli, E. and Sherr, E.H. and Maiorana, A. and Diel, T. and Hempel, M. and Bierhals, T. and Estévez, R. and Jentsch, T.J. and Pusch, M. and Agrawal, P.B.
Abstract:The genetic causes of global developmental delay (GDD) and intellectual disability (ID) are diverse and include variants in numerous ion channels and transporters. Loss-of-function variants in all five endosomal/lysosomal members of the CLC family of Cl(−) channels and Cl(−)/H(+) exchangers lead to pathology in mice, humans, or both. We have identified nine variants in CLCN3, the gene encoding CIC-3, in 11 individuals with GDD/ID and neurodevelopmental disorders of varying severity. In addition to a homozygous frameshift variant in two siblings, we identified eight different heterozygous de novo missense variants. All have GDD/ID, mood or behavioral disorders, and dysmorphic features; 9/11 have structural brain abnormalities; and 6/11 have seizures. The homozygous variants are predicted to cause loss of ClC-3 function, resulting in severe neurological disease similar to the phenotype observed in Clcn3(−/−) mice. Their MRIs show possible neurodegeneration with thin corpora callosa and decreased white matter volumes. Individuals with heterozygous variants had a range of neurodevelopmental anomalies including agenesis of the corpus callosum, pons hypoplasia, and increased gyral folding. To characterize the altered function of the exchanger, electrophysiological analyses were performed in Xenopus oocytes and mammalian cells. Two variants, p.Ile607Thr and p.Thr570Ile, had increased currents at negative cytoplasmic voltages and loss of inhibition by luminal acidic pH. In contrast, two other variants showed no significant difference in the current properties. Overall, our work establishes a role for CLCN3 in human neurodevelopment and shows that both homozygous loss of ClC-3 and heterozygous variants can lead to GDD/ID and neuroanatomical abnormalities.
Keywords:CLCN, Neurodevelopmental Delay, Intellectual Disability, Voltage Gated Chloride Channel, Gain of Function, Hippocampus, pH Sensitivity, Acidification, Animals, Xenopus, Xenopus laevis
Source:American Journal of Human Genetics
ISSN:0002-9297
Publisher:University of Chicago Press
Date:28 June 2021
Official Publication:https://doi.org/10.1016/j.ajhg.2021.06.003
PubMed:View item in PubMed

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