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Gene

SLC6A3

solute carrier family 6 member 3

Summary

Cytogenetic location
5p15.33
Coordinates
Chromosome 5: 1,392,794–1,445,440 (GRCh38)
Exons
15 exons across 52.6 kb
Protein
620 amino acids
Also known as
DAT
Previous symbols
DAT1
MANE Select transcript
ENST00000270349.12NM_001044.5
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

  • Dystonia, Myotonia, Paroxysmal Dyskinesia

    • Inherited Dystonia

      Umbrella term covering inherited dystonias, including DYT-TOR1A early-onset generalized dystonia, DYT-THAP1, myoclonus-dystonia (SGCE) and KMT2B-related dystonia.

      • 3 GenCC submitters rate it definitive or strong

How SLC6A3 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 5, with a bracket where SLC6A3 sits. SLC6A3 and 11 genes near it on chromosome 5, from 919,117 to 1,919,116.Chromosome 55p15.33p15.33p15.32p15.31p15.2p15.1p14.3p14.2p14.1p13.3p13.2p13.1p12p11q11.1q11.2q12.1q12.2q12.3q13.1q13.2q13.3q14.1q14.2q14.3q15q21.1q21.2q21.3q22.1q22.2q22.3q23.1q23.2q23.3q31.1q31.2q31.3q32q33.1q33.2q33.3q34q35.1q35.2q35.31 Mb1.2 Mb1.4 Mb1.6 Mb1.8 MbTRIP13: 892,849–919,357, forward strandTRIP13NKD2: 1,008,021–1,040,630, forward strandNKD2SLC12A7: 1,050,384–1,156,237, reverse strandSLC12A7SLC6A19: 1,201,595–1,225,111, forward strandSLC6A19SLC6A18: 1,225,381–1,246,189, forward strandSLC6A18TERT: 1,253,147–1,295,086, reverse strandTERTCLPTM1L: 1,316,821–1,345,100, reverse strandCLPTM1LSLC6A3: 1,392,794–1,445,440, reverse strandSLC6A3LPCAT1: 1,456,480–1,524,282, reverse strandLPCAT1MRPL36: 1,793,019–1,802,029, reverse strandMRPL36NDUFS6: 1,801,363–1,816,051, forward strandNDUFS6IRX4: 1,877,413–1,887,381, reverse strandIRX4Diagram of SLC6A3: 15 exons on the reverse strand of chromosome 5Exon 13: 2 known disease-causing sitesExon 12: 2 known disease-causing sitesExon 8: 1 known disease-causing siteExon 6: 1 known disease-causing siteExon 3: 1 known disease-causing siteExon 2: 1 known disease-causing siteExon 15: 1,392,794–1,394,758, 1,965 basesExon 14: 1,400,915–1,400,986, 72 basesExon 13: 1,402,922–1,403,089, 168 basesExon 12: 1,406,188–1,406,288, 101 basesExon 11: 1,409,026–1,409,125, 100 basesExon 10: 1,409,721–1,409,849, 129 basesExon 9: 1,411,243–1,411,355, 113 basesExon 8: 1,414,691–1,414,815, 125 basesExon 7: 1,416,098–1,416,201, 104 basesExon 6: 1,420,569–1,420,703, 135 basesExon 5: 1,421,876–1,422,014, 139 basesExon 4: 1,432,464–1,432,698, 235 basesExon 3: 1,441,359–1,441,490, 132 basesExon 2: 1,442,912–1,443,242, 331 basesExon 1: 1,445,348–1,445,440, 93 bases15141210864215′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 3.9 kb of the gene's 52.6 kb; 1,863 of those bases code for the protein.

How a genome test reads SLC6A3

13

positions in SLC6A3 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 52.6 kb of SLC6A3, introns included, not only the 3.9 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.). SLC6A3 gene: solute carrier family 6 member 3. Retrieved 17 October 2026, from https://dantelabs.com/genes/slc6a3

Vancouver

Dante Labs. SLC6A3 gene: solute carrier family 6 member 3 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/slc6a3

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