Rare GABRA3 variants are associated with epileptic seizures, encephalopathy and dysmorphic features.

Authors

Niturad CE1, Lev D2,3,4, Kalscheuer VM5,6, Charzewska A7, Schubert J1,8, Lerman-Sagie T3,4,9, Kroes HY10, Oegema R10, Traverso M11, Specchio N12, Lassota M13, Chelly J14, Bennett-Back O15, Carmi N3,4,10, Koffler-Brill T16, Iacomino M11, Trivisano M12, Capovilla G17, Striano P18, Nawara M7, Rzonca S7, Fischer U5,6, Bienek M5, Jensen C5, Hu H5, Thiele H19, Altmüller J19,20, Krause R8, May P8, Becker F1; EuroEPINOMICS Consortium, Balling R8, Biskup S21, Haas SA22, Nürnberg P19, van Gassen KLI10, Lerche H1, Zara F11, Maljevic S1, Leshinsky-Silver E2,3,16
  1. Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.
  2. Institute of Medical Genetics, Wolfson Medical Center, Holon, Israel.
  3. Metabolic-Neurogenetic Clinic, Wolfson Medical Center, Holon, Israel.
  4. Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel.
  5. Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany.
  6. Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany.
  7. Institute of Mother and Child, Department of Medical Genetics, Kasprzaka 17A, 01-211 Warsaw, Poland.
  8. Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Luxembourg.
  9. Pediatric Neurology Unit, Wolfson Medical Center, Holon, Israel.
  10. Department of Genetics, University Medical Center Utrecht, 3508 AB, The Netherlands.
  11. Laboratory of Neurogenetics and Neuroscience, Institute G. Gaslini, Genova, Italy.
  12. Neurology Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy.
  13. Genetic Clinic, Hetmanska 21, 35-045 Rzeszów, Poland.
  14. IGBMC, Strasbourg, France.
  15. Pediatric Neurology Unit, Hadassah Medical Center, Jerusalem.
  16. Molecular Genetics Laboratory, Wolfson Medical Center, Holon, Israel.
  17. Epilepsy Center, Department of Child Neuropsychiatry, C. Poma Hospital, Mantova, Italy.
  18. Pediatric Neurology and Muscular Diseases Unit, Department of Neurosciences, Rehabilitation, Ophtalmology, Genetics, Maternal and Child Health, Institute G. Gaslini, Genoa, Italy.
  19. Cologne Center for Genomics, Universität zu Köln, Köln, Germany.
  20. Institute of Human Genetics Universitätsklinik, Köln, Germany.
  21. CeGaT GmbH, Tübingen, Germany.
  22. Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany.

Abstract

Genetic epilepsies are caused by mutations in a range of different genes, many of them encoding ion channels, receptors or transporters. While the number of detected variants and genes increased dramatically in the recent years, pleiotropic effects have also been recognized, revealing that clinical syndromes with various degrees of severity arise from a single gene, a single mutation, or from different mutations showing similar functional defects. Accordingly, several genes coding for GABAA receptor subunits have been linked to a spectrum of benign to severe epileptic disorders and it was shown that a loss of function presents the major correlated pathomechanism. Here, we identified six variants in GABRA3 encoding the α3-subunit of the GABAA receptor. This gene is located on chromosome Xq28 and has not been previously associated with human disease. Five missense variants and one microduplication were detected in four families and two sporadic cases presenting with a range of epileptic seizure types, a varying degree of intellectual disability and developmental delay, sometimes with dysmorphic features or nystagmus. The variants co-segregated mostly but not completely with the phenotype in the families, indicating in some cases incomplete penetrance, involvement of other genes, or presence of phenocopies. Overall, males were more severely affected and there were three asymptomatic female mutation carriers compared to only one male without a clinical phenotype. X-chromosome inactivation studies could not explain the phenotypic variability in females. Three detected missense variants are localized in the extracellular GABA-binding NH2-terminus, one in the M2-M3 linker and one in the M4 transmembrane segment of the α3-subunit. Functional studies in Xenopus laevis oocytes revealed a variable but significant reduction of GABA-evoked anion currents for all mutants compared to wild-type receptors. The degree of current reduction correlated partially with the phenotype. The microduplication disrupted GABRA3 expression in fibroblasts of the affected patient. In summary, our results reveal that rare loss-of-function variants in GABRA3 increase the risk for a varying combination of epilepsy, intellectual disability/developmental delay and dysmorphic features, presenting in some pedigrees with an X-linked inheritance pattern.