Functional consequence of pathogenic GABRA3 variants determines whether X-linked inheritance is dominant or recessive

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Abstract

Disorders of GABRA3, the only epilepsy-associated GABAA receptor subunit gene on the X chromosome, have eluded clinical clarity due to ambiguous inheritance patterns and variable phenotypes. The long-standing assumption that all pathogenic variants cause loss of function further obscured genotype–phenotype relationships and hindered progress. Here, we curated a cohort of individuals with a GABRA3 variant, integrating deep phenotyping, genotyping, family history, and electrophysiology with a targeted mouse model. Among 43 individuals with 19 GABRA3 variants, functional analyses revealed gain- and loss-of-function effects, each linked to distinct clinical profiles. Gain-of-function variants were associated with severe, treatment-resistant epilepsy and profound intellectual disability, disproportionately affecting males, who were often nonambulant and had cortical visual impairment. Loss-of-function variants produced milder phenotypes, with epilepsy rarely observed; affected males showed behavioral issues and language delay, while females were unaffected carriers. Our gain-of-function (Gabra3Q242L/+) mouse model mirrored these sex-specific differences, showing increased seizure susceptibility, early death, and marked cortical hyperexcitability. These insights resolve longstanding uncertainties surrounding GABRA3 and redefine how X-linked disorders are interpreted. They demonstrate that it is the functional impact of a variant, not its mere presence, that determines whether a condition manifests dominantly or recessively. This distinction carries important implications for genetic counseling, precision medicine, and the broader interpretation of X-linked neurodevelopmental disorders.

Authors

Katrine M. Johannesen, Khaing Phyu Aung, Vivian W.Y. Liao, Nathan Absalom, Han C. Chua, Xue N. Gan, Miaomiao Mao, Chaseley E. McKenzie, Hian M. Lee, Sebastian Ortiz, Rebecca C. Spillmann, Vandana Shashi, Rodney A. Radtke, Ghayda M. Mirzaa, P. Anne Weisner, Josue Flores Daboub, Caroline Hagedorn, Pinar Bayrak-Toydemir, Desiree DeMille, Jian Zhao, Nandita Bajaj, Yline Capri, Boris Keren, Miriam Schmidts, Ingrid M.B.H. van de Laar, Marjon A. van Slegtenhorst, Rafal Ploski, Marta Bogotko, Danielle K. Bourque, Ebba Alkhunaizi, Lauren Chad, Nada Quercia, Houda Elloumi, Ingrid M. Wentzensen, Michael C. Kruer, Pritha Bisarad, Carolina I. Galaz-Montoya, Violeta Rusu, Dominique Braun, Katie Angione, Jessica C. Win, Camilo Espinosa-Jovel, Pia Zacher, Konrad Platzer, Samuel F. Berkovic, Ingrid E. Scheffer, Mary Chebib, Guido Rubboli, Rikke S. Møller, Christopher A. Reid, Philip K. Ahring