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Gene

SLC9A3

solute carrier family 9 member A3

Summary

Cytogenetic location
5p15.33
Coordinates
Chromosome 5: 470,456–524,449 (GRCh38)
Exons
17 exons across 54 kb
Protein
834 amino acids
Also known as
NHE-3
Previous symbols
NHE3
MANE Select transcript
ENST00000264938.8NM_004174.4
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

  • Congenital Diarrhoeas & Enteropathies

    • Congenital diarrhoea

      Inherited conditions, including congenital chloride diarrhoea (SLC26A3), microvillus inclusion disease (MYO5B), tufting enteropathy (EPCAM) and congenital sodium diarrhoea (SPINT2, SLC9A3), that cause chronic diarrhoea from early infancy.

      • 2 GenCC submitters rate it definitive or strong
      What knowing changes

      A specific diagnosis directs treatment such as electrolyte replacement for chloride diarrhoea, or early planning for parenteral nutrition or intestinal transplant in microvillus inclusion disease and tufting enteropathy.

How SLC9A3 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 SLC9A3 sits. SLC9A3 and 15 genes near it on chromosome 5, from 1 to 997,452.Chromosome 55p15.33p15.33p15.32p15.31p15.2p15.1p14.3p14.2p14.1p13.3p13.2p13.1p12p11q11.1q11.2q12.1q12.2q12.3q13.1q13.2q13.3q14.1q14.2q14.3q15q21.1q21.2q21.3q22.1q22.2q22.3q23.1q23.2q23.3q31.1q31.2q31.3q32q33.1q33.2q33.3q34q35.1q35.2q35.30.2 Mb0.4 Mb0.6 Mb0.8 MbPLEKHG4B: 92,001–189,972, forward strandPLEKHG4BLRRC14B: 191,451–196,334, forward strandLRRC14BCCDC127: 196,868–218,162, reverse strandCCDC127SDHA: 218,206–257,084, forward strandSDHA: 218,298–314,955, forward strandPDCD6: 271,452–314,978, forward strandPDCD6PDCD6-AHRR: 271,670–438,291, forward strandPDCD6-AHRRAHRR: 320,682–438,307, forward strandAHRREXOC3: 442,522–471,939, forward strandEXOC3SLC9A3: 470,456–524,449, reverse strandSLC9A3CEP72: 612,305–667,703, forward strandCEP72TPPP: 658,850–693,997, reverse strandTPPPZDHHC11B: 710,355–784,729, reverse strandZDHHC11BZDHHC11: 795,605–858,973, reverse strandZDHHC11BRD9: 850,291–892,838, reverse strandBRD9TRIP13: 892,849–919,357, forward strandTRIP13Diagram of SLC9A3: 17 exons on the reverse strand of chromosome 5Exon 11: 1 known disease-causing siteExon 7: 1 known disease-causing siteExon 6: 3 known disease-causing sitesExon 5: 1 known disease-causing siteExon 3: 1 known disease-causing siteExon 17: 470,456–473,382, 2,927 basesExon 16: 474,883–475,132, 250 basesExon 15: 475,561–475,671, 111 basesExon 14: 476,020–476,092, 73 basesExon 13: 476,202–476,378, 177 basesExon 12: 476,543–476,672, 130 basesExon 11: 477,332–477,444, 113 basesExon 10: 479,836–479,965, 130 basesExon 9: 481,565–481,635, 71 basesExon 8: 482,068–482,157, 90 basesExon 7: 482,548–482,750, 203 basesExon 6: 483,262–483,482, 221 basesExon 5: 484,520–484,697, 178 basesExon 4: 485,153–485,231, 79 basesExon 3: 488,316–488,476, 161 basesExon 2: 491,769–492,071, 303 basesExon 1: 524,112–524,449, 338 bases171510515′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 5.6 kb of the gene's 54 kb; 2,505 of those bases code for the protein.

How a genome test reads SLC9A3

9

positions in SLC9A3 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 54 kb of SLC9A3, introns included, not only the 5.6 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.). SLC9A3 gene: solute carrier family 9 member A3. Retrieved 16 October 2026, from https://dantelabs.com/genes/slc9a3

Vancouver

Dante Labs. SLC9A3 gene: solute carrier family 9 member A3 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/slc9a3

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