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

  • Am J Hum Genet. 2021 Aug 5;108(8):1450-1465. doi: 10.1016/j.ajhg.2021.06.003.
Anna R Duncan  1 ,  Maya M Polovitskaya  2 ,  Héctor Gaitán-Peñas  3 ,  Sara Bertelli  4 ,  Grace E VanNoy  5 ,  Patricia E Grant  6 ,  Anne O'Donnell-Luria  7 ,  Zaheer Valivullah  8 ,  Alysia Kern Lovgren  8 ,  Elaina M England  9 ,  Emanuele Agolini  10 ,  Jill A Madden  11 ,  Klaus Schmitz-Abe  12 ,  Amy Kritzer  13 ,  Pamela Hawley  13 ,  Antonio Novelli  10 ,  Paolo Alfieri  14 ,  Giovanna Stefania Colafati  15 ,  Dagmar Wieczorek  16 ,  Konrad Platzer  17 ,  Johannes Luppe  17 ,  Margarete Koch-Hogrebe  18 ,  Rami Abou Jamra  17 ,  Juanita Neira-Fresneda  19 ,  Anna Lehman  20 ,  Cornelius F Boerkoel  20 ,  Kimberly Seath  20 ,  Lorne Clarke  20 ,  CAUSES Study  20 ,  Yvette van Ierland  21 ,  Emanuela Argilli  22 ,  Elliott H Sherr  22 ,  Andrea Maiorana  23 ,  Thilo Diel  24 ,  Maja Hempel  25 ,  Tatjana Bierhals  25 ,  Raúl Estévez  3 ,  Thomas J Jentsch  26 ,  Michael Pusch  27 ,  Pankaj B Agrawal  28
Affiliations
  • 1. Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA.
  • 2. Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; Max-Delbrück-Centrum für Molekulare Medizin (MDC), 13125 Berlin, Germany.
  • 3. Unitat de Fisiologia, Departament de Ciències Fisiològiques, IDIBELL-Institute of Neurosciences, Universitat de Barcelona-CIBERER, L'Hospitalet de Llobregat, 08907 Barcelona, Spain.
  • 4. Istituto di Biofisica, 16149 Genova, Italy; Scuola Internazionale Superiore di Studi Avanzati (SISSA), 34136 Trieste, Italy.
  • 5. Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA.
  • 6. Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Radiology, Boston Children's Hospital, Boston, MA 02115, USA.
  • 7. Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Division of Genetics & Genomics, Department of Pediatrics, Boston Children's Hospital, MA 02115, USA; Analytic and Translational Genomics Unit, Massachusetts General Hospital, Boston, MA 02114, USA.
  • 8. Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
  • 9. Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics & Genomics, Department of Pediatrics, Boston Children's Hospital, MA 02115, USA.
  • 10. Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy.
  • 11. The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Division of Genetics & Genomics, Department of Pediatrics, Boston Children's Hospital, MA 02115, USA.
  • 12. Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA.
  • 13. Division of Genetics & Genomics, Department of Pediatrics, Boston Children's Hospital, MA 02115, USA.
  • 14. Child and Adolescent Neuropsychiatry Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
  • 15. Oncological Neuroradiology Unit, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy.
  • 16. Institute of Human Genetics, Medical Faculty, Heinrich-Heine University, 40225 Düsseldorf, Germany.
  • 17. Institute of Human Genetics, University of Leipzig Medical Center, 04103 Leipzig, Germany.
  • 18. Vestische Kinder-und Jugendklinik Datteln, Universität Witten-Herdecke, 45711 Datteln, Germany.
  • 19. Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA.
  • 20. Provincial Medical Genetics Program, University of British Columbia, Department of Medical Genetics, Children's and Women's Health Center of British Columbia, Vancouver, BC V6H 3N1, Canada.
  • 21. Erasmus University Medical Center, Department of Clinical Genetics, 3000 CA Rotterdam, the Netherlands.
  • 22. Brain Development Research Program, Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA.
  • 23. Neonatology, Ospedale San Giovanni Calibita Fatebenefratelli, 00186 Roma, Italy.
  • 24. Division of Neonatology and Pediatric Critical Care Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany.
  • 25. Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany.
  • 26. Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; Max-Delbrück-Centrum für Molekulare Medizin (MDC), 13125 Berlin, Germany; NeuroCure Cluster of Excellence, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany. Electronic address: [email protected].
  • 27. Istituto di Biofisica, 16149 Genova, Italy.
  • 28. Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Division of Genetics & Genomics, Department of Pediatrics, Boston Children's Hospital, MA 02115, USA. Electronic address: [email protected].
PMID: 34186028 DOI: 10.1016/j.ajhg.2021.06.003
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; acidification; gain of function; hippocampus; intellectual disability; neurodevelopmental delay; pH sensitivity; voltage gated chloride channel.