SLC6A1

Chr 3

solute carrier family 6 member 1

Also known as: GABATHG, GABATR, GAT1, MAE, hGAT-1

NCBI Gene: 6529ENSG00000157103UniProt: P30531

The protein encoded by this gene is a gamma-aminobutyric acid (GABA) transporter that localizes to the plasma membrane. The encoded protein removes GABA from the synaptic cleft, restoring it to presynaptic terminals. [provided by RefSeq, Jan 2017]

GeneReviewsResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

UniProtMyoclonic-atonic epilepsy

Clinical highlights

Interpreting a novel variant
Loss of function is the curated mechanism (Gene2Phenotype) and the gene is intolerant of it in the population — truncating, frameshift and canonical splice variants carry more prior weight here than missense.Curated gene-level mechanism — a prior for triage, not a per-variant call.
3
Active trials
46
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.15
LOEUF· LoF intol.
LOF*
Mechanism· G2P
📖
GeneReview available — SLC6A1
Authoritative clinical overview · Recommended first read
Open GeneReview ↗
Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Dual constrained — LoF & missense intolerant
LoF Constraint?
0.15LOEUF
pLI 1.000
Z-score 5.05
OE 0.03 (0.01–0.15)
Highly constrained

Among the most LoF-intolerant genes (~top 3%)

Missense Constraint?
4.18Z-score
OE missense 0.39 (0.34–0.45)
144 obs / 370.1 exp
Constrained

Highly missense-constrained (top ~0.1%)

Observed / Expected Ratios?
LoF OE?0.03 (0.01–0.15)
0≤0.351.4
Missense OE?0.39 (0.34–0.45)
0≤0.61.4
Synonymous OE?1.10
0≤1.21.6
LoF obs/exp: 1 / 31.7Missense obs/exp: 144 / 370.1Syn Z: -0.96

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

SLC6A1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients