Deleterious Rare Variants Reveal Risk for Loss of GABAA Receptor Function in Patients with Genetic Epilepsy and in the General Population

Abstract

Genetic epilepsies (GEs) account for approximately 50% of all seizure disorders, and familial forms include mutations in single GABAA receptor subunit genes (GABRs). In 144 sporadic GE cases (GECs), exome sequencing of 237 ion channel genes identified 520 GABR variants. Among these variants, 33 rare variants in 11 GABR genes were present in 24 GECs. To assess functional risk of variants in GECs, we selected 8 variants found in GABRA, 3 in GABRB, and 3 in GABRG and compared them to 18 variants found in the general population for GABRA1 (n = 9), GABRB3 (n = 7), and GABRG2 (n = 2). To identify deleterious variants and gain insight into structure-function relationships, we studied the gating properties, surface expression and structural perturbations of the 32 variants. Significant reduction of GABAA receptor function was strongly associated with variants scored as deleterious and mapped within the N-terminal and transmembrane domains. In addition, 12 out of 17 variants mapped along the β+/α- GABA binding interface, were associated with reduction in channel gating and were predicted to cause structural rearrangements of the receptor by in silico simulations. Missense or nonsense mutations of GABRA1, GABRB3 and GABRG2 primarily impair subunit biogenesis. In contrast, GABR variants affected receptor function by impairing gating, suggesting that different mechanisms are operating in GABR epilepsy susceptibility variants and disease-causing mutations. The functional impact of single GABR variants found in individuals with sporadic GEs warrants the use of molecular diagnosis and will ultimately improve the treatment of genetic epilepsies by using a personalized approach.

GABA A Receptor Coupling Junction and Pore GABRB3 Mutations are Linked to Early-Onset Epileptic Encephalopathy

“…This is a distinctive difference between missense mutant residues associated with moderate epilepsies, which are more prone to cause trafficking/assembling impairment and ER retention of the unfolded mutants 44 – 48 . Thus, it appears that missense mutant residues in “structural cassettes” of the receptor that are not directly coupled to activation tend to cause more trafficking defects, than those in domains coupled directly to the activation of the channel, and so the kinetic defects predominate 11 , 49 . This is an interesting concept because in mild epilepsies associated with missense mutant residues the main mechanism shaping the final phenotype appears to be the result of secondary effects caused by deficient protein quality control of unassembled mutant subunits.…”

Gabra2is a genetic modifier of Dravet syndrome in mice

“…This study also highlights the importance of continued efforts in identifying modifier genes in mouse models. Several epilepsy modifier genes, including CACNA1G and GABRA2, were first identified in the Scn1a +/mouse model of Dravet syndrome and later confirmed as epilepsy risk genes in humans (14,23,(33)(34)(35)(36)(37)(38)(39)(40)(41)(42)(43)(44). Identifying modifier genes can provide refined insights into the molecular basis of genetic disease.…”

2017 WONOEP appraisal: Studying epilepsy as a network disease using systems biology approaches

“…These approaches hold great promise for accelerating genetic stratification of patients for predicting outcomes and response to therapy. 10,11 Variants in ion channels 12 and γ-aminobutyric acid receptors 13 are also pleiotropic and arise in complex profiles in the epilepsy and general populations. 7,8 However, because of these efforts, the genetic complexity of the epilepsies has also become clear.…”

“…For example, mutations in mTOR-pathway genes have been associated with pediatric brain tumors, brain malformations, intractable epilepsy, autism, learning disability, and mental retardation, 9 but not all carriers of these mutations manifest all of these phenotypes to the same degree. 10,11 Variants in ion channels 12 and γ-aminobutyric acid receptors 13 are also pleiotropic and arise in complex profiles in the epilepsy and general populations. This phenotypic spectrum arises partially from the time point in development when the mutation occurs as well as the target cellular population.…”