Pathogenic variants of human GABRA1 gene associated with epilepsy: A computational approach

Ayla Arslan

doi:10.1016/j.heliyon.2023.e20218

Pathogenic variants of human GABRA1 gene associated with epilepsy: A computational approach

Heliyon. 2023 Sep 15;9(9):e20218. doi: 10.1016/j.heliyon.2023.e20218. eCollection 2023 Sep.

Author

Ayla Arslan¹

Affiliation

¹ Department of Molecular Biology and Genetics, Faculty of Engineering and Natural Sciences, Üsküdar University, Istanbul, Turkey.

Abstract

Critical for brain development, neurodevelopmental and network disorders, the GABRA1 gene encodes for the α1 subunit, an abundantly and developmentally expressed subunit of heteropentameric gamma-aminobutyric acid A receptors (GABA_ARs) mediating primary inhibition in the brain. Mutations of the GABA_AR subunit genes including GABRA1 gene are associated with epilepsy, a group of syndromes, characterized by unprovoked seizures and diagnosed by integrative approach, that involves genetic testing. Despite the diagnostic use of genetic testing, a large fraction of the GABA_AR subunit gene variants including the variants of GABRA1 gene is not known in terms of their molecular consequence, a challenge for precision and personalized medicine. Addressing this, one hundred thirty-seven GABRA1 gene variants of unknown clinical significance have been extracted from the ClinVar database and computationally analyzed for pathogenicity. Eight variants (L49H, P59L, W97R, D99G, G152S, V270G, T294R, P305L) are predicted as pathogenic and mapped to the α1 subunit's extracellular domain (ECD), transmembrane domains (TMDs) and extracellular linker. This is followed by the integration with relevant data for cellular pathology and severity of the epilepsy syndromes retrieved from the literature. Our results suggest that the pathogenic variants in the ECD of GABRA1 (L49H, P59L, W97R, D99G, G152S) will probably manifest decreased surface expression and reduced current with mild epilepsy phenotypes while V270G, T294R in the TMDs and P305L in the linker between the second and the third TMDs will likely cause reduced cell current with severe epilepsy phenotypes. The results presented in this study provides insights for clinical genetics and wet lab experimentation.

Keywords: Alpha 1 subunit; ClinVar; Computational prediction tools; Epilepsy; GABA (A) receptors; GABRA1; Genetic testing; In silico; Non-synonymous; Personalized medicine; SNP; Single nucleotide polymorphism; VUS; Variants of unknown significance; Variation.