GABRA1 frameshift variants impair GABAA receptor proteostasis

The gamma-aminobutyric acid type A receptor (GABAAR) is the most common inhibitory neurotransmitter-gated ion channel in the central nervous system. Pathogenic variants in genes encoding GABAAR subunits can cause receptor dysfunction and lead to genetic epilepsy. Frameshift variants in these genes can result in a premature termination codon, producing truncated receptor subunit variants. However, the pathogenic molecular mechanism as well as functional implications of these frameshift variants remains inadequately characterized. This study focused on four clinical frameshift variants of the 1 subunit of GABAAR (encoded by the GABRA1 gene): K401fs (c.1200del), S326fs (c.975del), V290fs (c.869_888del), and F272fs (c.813del). These variants result in the loss of one to three transmembrane helices, whereas wild type 1 has four transmembrane helices. Therefore, these variants serve as valuable models to evaluate membrane protein biogenesis and proteostasis deficiencies of GABAARs. In HEK293T cells, all four frameshift variants exhibit significantly reduced trafficking to the cell surface, resulting in essentially non-functional ion channels. However, the severity of proteostasis deficiency varied among these four frameshift variants, presumably due to their specific transmembrane domain deletions. The variant 1subunits exhibited endoplasmic reticulum (ER) retention and activated the unfolded protein response (UPR) to varying extents. Our findings revealed that these frameshift variants of GABRA1 utilize overlapping yet distinct molecular mechanisms to impair proteostasis, providing insights into the pathogenesis of GABAAR-associated epilepsy.