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Gene

SLC7A9

solute carrier family 7 member 9

Summary

Cytogenetic location
19q13.11
Coordinates
Chromosome 19: 32,830,511–32,869,767 (GRCh38)
Exons
13 exons across 39.3 kb
Protein
487 amino acids
Also known as
BAT1
Previous symbols
CSNU3
MANE Select transcript
ENST00000023064.9NM_014270.5
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

  • Cystinuria

    • Cystinuria is a renal tubular amino acid transport disorder characterized by recurrent formation of kidneys cystine stones.

      • ClinGen rates the link definitive
      • 5 GenCC submitters rate it definitive or strong

How SLC7A9 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 19, with a bracket where SLC7A9 sits. SLC7A9 and 15 genes near it on chromosome 19, from 32,350,139 to 33,350,138.Chromosome 1919q13.11p13.3p13.2p13.13p13.12p13.11p12p11q11q12q13.11q13.12q13.13q13.2q13.31q13.32q13.33q13.41q13.42q13.4332.4 Mb32.6 Mb32.8 Mb33 Mb33.2 MbZNF507: 32,345,594–32,387,667, forward strandZNF507DPY19L3: 32,405,543–32,485,895, forward strandDPY19L3PDCD5: 32,581,062–32,587,453, forward strandPDCD5ANKRD27: 32,597,000–32,676,597, reverse strandANKRD27RGS9BP: 32,675,848–32,678,300, forward strandRGS9BPNUDT19: 32,691,786–32,714,101, forward strandNUDT19TDRD12: 32,719,735–32,829,580, forward strandTDRD12SLC7A9: 32,830,511–32,869,767, reverse strandSLC7A9CEP89: 32,875,925–32,972,015, reverse strandCEP89FAAP24: 32,972,209–32,978,721, forward strandFAAP24RHPN2: 32,978,592–33,064,888, reverse strandRHPN2GPATCH1: 33,080,899–33,130,956, forward strandGPATCH1WDR88: 33,132,092–33,175,799, forward strandWDR88LRP3: 33,177,603–33,209,922, forward strandLRP3SLC7A10: 33,208,656–33,225,853, reverse strandSLC7A10CEBPA: 33,299,934–33,302,534, reverse strandCEBPADiagram of SLC7A9: 13 exons on the reverse strand of chromosome 19Exon 13: 1 known disease-causing siteExon 12: 8 known disease-causing sitesExon 11: 2 known disease-causing sitesExon 10: 5 known disease-causing sitesExon 8: 1 known disease-causing siteExon 7: 3 known disease-causing sitesExon 6: 1 known disease-causing siteExon 5: 9 known disease-causing sitesExon 4: 11 known disease-causing sitesExon 3: 5 known disease-causing sitesExon 2: 1 known disease-causing siteExon 13: 32,830,511–32,830,684, 174 basesExon 12: 32,833,149–32,833,323, 175 basesExon 11: 32,842,168–32,842,317, 150 basesExon 10: 32,843,855–32,843,951, 97 basesExon 9: 32,858,440–32,858,543, 104 basesExon 8: 32,859,841–32,859,964, 124 basesExon 7: 32,860,606–32,860,650, 45 basesExon 6: 32,862,118–32,862,217, 100 basesExon 5: 32,862,461–32,862,586, 126 basesExon 4: 32,864,096–32,864,338, 243 basesExon 3: 32,864,629–32,864,776, 148 basesExon 2: 32,868,448–32,868,645, 198 basesExon 1: 32,869,686–32,869,767, 82 bases131210864215′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 1.8 kb of the gene's 39.3 kb; 1,464 of those bases code for the protein.

How a genome test reads SLC7A9

58

positions in SLC7A9 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 39.3 kb of SLC7A9, introns included, not only the 1.8 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.). SLC7A9 gene: solute carrier family 7 member 9. Retrieved 17 October 2026, from https://dantelabs.com/genes/slc7a9

Vancouver

Dante Labs. SLC7A9 gene: solute carrier family 7 member 9 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/slc7a9

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