SLC6A1 (P30531) variants and mutations

SLC6A1 (also known as P30531) is a human protein-coding gene encoding a sodium- and chloride-dependent GABA transporter 1 protein. It clears GABA from extracellular space into neurons and glial cells, regulating the duration and spatial spread of inhibitory neurotransmission. Haploinsufficiency or dysfunctional variants cause SLC6A1-related neurodevelopmental disorder, commonly with myoclonic-atonic epilepsy, developmental delay, and autism-related features. This analysis covers 1,016 SLC6A1 variants and mutations. Of these, 64% have computational variant effect predictions. Disease context includes epilepsy with myoclonic atonic seizures, Seizure, and hereditary disease. Example SLC6A1 variants include A2E, A2T, and A2V.

Variant analysis overview

Gene: SLC6A1
Protein: P30531
UniProt accession: P30531
Organism: Homo sapiens
Variants analyzed: 1016
Variant scope: all variants
Completed: 2026-08-21

Variant and mutation evidence

Variant composition: 832 unspecified-consequence records; 85 synonymous variants; 76 missense variants; 7 frameshift variants; 3 splice-region variants; 5 stop-gained variants; 1 in-frame deletions; 1 stop retained variant; 2 stop lost; 7 substitution
Prediction scores: 652 variants have prediction scores (64% of the analyzed set).

Clinical, disease, and population context

Disease context: 25 disease associations are represented. Top associations: epilepsy with myoclonic atonic seizures, Seizure, hereditary disease, Intellectual disability, epilepsy, Neurodevelopmental delay, neurodevelopmental disorder, generalized anxiety disorder, autosomal dominant non-syndromic intellectual disability, developmental and epileptic encephalopathy 94, Abnormality of refraction, Global developmental delay.

Protein structure and variant hotspots

Protein features: 12 transmembrane segments; 9 binding sites; 5 post-translational modification sites.
Structural context: 343 variants have structural context.
PTM context: 10 variants overlap post-translational modification sites.

Data sources

Evidence in this analysis draws on EBI Proteins Variation, UniProt, gnomAD v4, EuropePMC, 3D Hotspot Analysis, Interaction Network Analysis, Protein Data Bank, AlphaFold DB, gnomAD constraint, Open Targets, ClinGen, MaveDB, LitVar.

Notable SLC6A1 variants

Examples include A2E, A2T, A2V, A2A, T3T, N4N, G5D, G5R. Listed records include available protein-change notation, database identifiers, clinical classifications, computational predictions, population evidence, experimental measurements, and disease context.

SLC6A1 analysis run — SLC6A1 (1,016 variants) — completed 2026-08-21