Pathogenic ultra-rare variants in SLC6A1, SLC6A11, GAD1 and GAD2 are new & recurrent GABAergic loci for GGE syndromes

There is a wealth of biological evidence that supports the concept that GABAergic inhibition is causal to some genetic generalized epilepsy (GGE) syndromes. Much is known about postsynaptic GABAAR channelopathies, however, the presynaptic determinants are less well-defined such as the role of GABA transporters ( SLC6A1 / GAT1; SLC6A11 / GAT3), and GABA biosynthesis biology ( GAD1 / GAD67; GAD2 / GAD65). In response, our study screened four presynaptic GABAergic genes in an international cohort of 708 adults and children with epilepsy, predominantly with GGE syndromes, diagnosed within tertiary epilepsy centers. We identified 15 novel / ultra-rare heterozygous SLC6A1 , SLC6A11 , GAD2 , GAD1 variants in 31 unrelated people with epilepsy, of whom 28 had GGE syndromes. A range of missense, nonsense and splice-site variants were discovered in addition to one digenic case with SLC6A1 & GAD2 variants. SLC6A1 genotypes identified in this study show reduced GAT1 activity, quantitatively linked to epilepsy severity and intellectual disability (ID). Functionally validated SLC6A11 and GAD2 variants are a novel GGE finding, where reduced activity of GAT3 uptake or GAD65 enzyme activity is linked to epilepsy severity. Recessive GAD1 loss-of-function variants have recently been described as the cause of developmental and epileptic encephalopathy cases. Here we present the first two gain-of-function GAD1 variants as a novel GAD67 mechanism in epileptogenesis. This further contributes to the association of GABA proteome with GGE and links subtle quantal GABA sensitivities to the genesis of cortico-thalamic absence seizures.