High-throughput discovery of SLC6A1 variants affecting GABA transport in neurological disorders

SLC6A1 encodes the neuronal GABA transporter GAT-1. Pathogenic variants in SLC6A1 lead to haploinsufficiency and are associated with epilepsy, autism and schizophrenia. Most variants observed in patients are rare missense mutations whose functional impact and pathogenicity remain unknown. We quantified GABA uptake of 182 SLC6A1 variants using plasmid expression constructs in SLC6A1-deficient HEK293T cells. Cells were incubated with deuterated GABA, then analyzed by mass spectrometry to assess transporter activity. Of the 102 variants with partial or complete loss of transporter function compared to wildtype, only 24 (23.5%) had previously been classified as Pathogenic or Likely pathogenic in the ClinVar database. This suggests an increase in the number of SLC6A1 variants that are likely pathogenic, implying a 40% increased diagnostic yield for SLC6A1 haploinsufficiency. SLC6A1 variants associated with Schizophrenia did not lead to complete loss of function, suggesting either an association between hypomorphic variants and Schizophrenia or an alternative mechanism of pathogenesis.