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Gene

SLC6A1

solute carrier family 6 member 1

Summary

Cytogenetic location
3p25.3
Coordinates
Chromosome 3: 10,992,748–11,039,247 (GRCh38)
Exons
16 exons across 46.5 kb
Protein
599 amino acids
Also known as
GAT1, GABATR, GABATHG, GAT-1, hGAT-1
MANE Select transcript
ENST00000287766.10NM_003042.4
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated report relevant to this gene

    • Epilepsy (Full Panel)

      • Epilepsy

        One of 171 genes linked to it

        A brain disorder characterized by episodes of abnormally increased neuronal discharge resulting in transient episodes of sensory or motor neurological dysfunction, or psychic dysfunction. These episodes may or may not be associated with loss of consciousness or convulsions.

        • 5 GenCC submitters rate it definitive or strong

    How SLC6A1 is laid out

    • Coding sequence
    • Untranslated region
    • Intron
    • Direction of transcription
    • Known disease-causing sites
    • Stretches short reads find hard
    Chromosome 3, with a bracket where SLC6A1 sits. SLC6A1 and 4 genes near it on chromosome 3, from 10,515,998 to 11,515,997.Chromosome 33p25.3p26.3p26.2p26.1p25.3p25.2p25.1p24.3p24.2p24.1p23p22.3p22.2p22.1p21.33p21.32p21.31p21.2p21.1p14.3p14.2p14.1p13p12.3p12.2p12.1p11.2p11.1q11.1q11.2q12.1q12.2q12.3q13.11q13.12q13.13q13.2q13.31q13.32q13.33q21.1q21.2q21.3q22.1q22.2q22.3q23q24q25.1q25.2q25.31q25.32q25.33q26.1q26.2q26.31q26.32q26.33q27.1q27.2q27.3q28q2910.6 Mb10.8 Mb11 Mb11.2 Mb11.4 MbATP2B2: 10,324,023–10,708,060, reverse strandATP2B2SLC6A11: 10,816,201–10,940,728, forward strandSLC6A11SLC6A1: 10,992,748–11,039,247, forward strandSLC6A1HRH1: 11,137,093–11,263,731, forward strandHRH1ATG7: 11,272,309–11,557,665, forward strandATG7Diagram of SLC6A1: 16 exons on the forward strand of chromosome 3Exon 3: 13 known disease-causing sitesExon 4: 12 known disease-causing sitesExon 5: 5 known disease-causing sitesExon 6: 5 known disease-causing sitesExon 7: 5 known disease-causing sitesExon 8: 9 known disease-causing sitesExon 9: 10 known disease-causing sitesExon 10: 7 known disease-causing sitesExon 11: 7 known disease-causing sitesExon 12: 7 known disease-causing sitesExon 13: 5 known disease-causing sitesExon 14: 8 known disease-causing sitesExon 15: 8 known disease-causing sitesExon 16: 1 known disease-causing siteExon 1: 10,992,748–10,992,929, 182 basesExon 2: 11,015,672–11,015,733, 62 basesExon 3: 11,017,059–11,017,449, 391 basesExon 4: 11,017,843–11,017,974, 132 basesExon 5: 11,018,598–11,018,698, 101 basesExon 6: 11,020,213–11,020,322, 110 basesExon 7: 11,022,336–11,022,468, 133 basesExon 8: 11,025,449–11,025,583, 135 basesExon 9: 11,025,773–11,025,876, 104 basesExon 10: 11,026,235–11,026,359, 125 basesExon 11: 11,028,735–11,028,847, 113 basesExon 12: 11,029,221–11,029,352, 132 basesExon 13: 11,031,177–11,031,279, 103 basesExon 14: 11,033,639–11,033,739, 101 basesExon 15: 11,034,531–11,034,698, 168 basesExon 16: 11,036,862–11,039,247, 2,386 bases151015165′3′

    Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

    Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

    Nearby genes from Ensembl release 116, on GRCh38.

    Exons make up 4.5 kb of the gene's 46.5 kb; 1,800 of those bases code for the protein.

    How a genome test reads SLC6A1

    121

    positions in SLC6A1 where ClinVar classes a change as pathogenic or likely pathogenic

    None of them falls in a region short reads find hard.

    A whole genome covers all 46.5 kb of SLC6A1, introns included, not only the 4.5 kb of exons.

    Where this comes from

    • HGNC: the gene's symbol, name, other symbols and location.
    • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
    • GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
    • The ACMG secondary findings list, SF v3.2.
    • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
    • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
    • Data release 2026.10.16-c6eea6bf.

    Cite this page

    APA

    Dante Labs. (n.d.). SLC6A1 gene: solute carrier family 6 member 1. Retrieved 16 October 2026, from https://dantelabs.com/genes/slc6a1

    Vancouver

    Dante Labs. SLC6A1 gene: solute carrier family 6 member 1 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/slc6a1

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