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Gene

SLC12A3

solute carrier family 12 member 3

Summary

Cytogenetic location
16q13
Coordinates
Chromosome 16: 56,865,207–56,915,850 (GRCh38)
Exons
26 exons across 50.6 kb
Protein
1,021 amino acids
Inheritance
Autosomal recessive
Also known as
NCCT, NCC, TSC
MANE Select transcript
ENST00000563236.6NM_001126108.2
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

  • Gitelman Syndrome

    • Autosomal recessive

      Gitelman syndrome (GS), also referred to as familial hypokalemia-hypomagnesemia, is characterized by hypokalemic metabolic alkalosis in combination with significant hypomagnesemia and low urinary calcium excretion.

      • 3 GenCC submitters rate it definitive or strong

Inheritance

Autosomal recessive
It takes a changed copy from each parent. With one, you are a carrier and usually unaffected; when both parents are carriers, each child has a one-in-four chance of inheriting two.

How SLC12A3 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 16, with a bracket where SLC12A3 sits. SLC12A3 and 27 genes near it on chromosome 16, from 56,390,529 to 57,390,528.Chromosome 1616q13p13.3p13.2p13.13p13.12p13.11p12.3p12.2p12.1p11.2p11.1q11.1q11.2q12.1q12.2q13q21q22.1q22.2q22.3q23.1q23.2q23.3q24.1q24.2q24.356.4 Mb56.6 Mb56.8 Mb57 Mb57.2 MbAMFR: 56,361,449–56,425,598, reverse strandAMFRNUDT21: 56,428,473–56,452,199, reverse strandNUDT21: 56,430,556–56,501,497, reverse strandOGFOD1: 56,451,508–56,479,122, forward strandOGFOD1BBS2: 56,465,640–56,582,667, reverse strandBBS2MT4: 56,565,073–56,569,108, forward strandMT4MT3: 56,589,074–56,591,093, forward strandMT3MT2A: 56,608,130–56,609,503, forward strandMT2AMT1E: 56,625,475–56,627,112, forward strandMT1EMT1M: 56,632,485–56,633,986, forward strandMT1A: 56,638,202–56,640,087, forward strandMT1B: 56,651,885–56,653,204, forward strandMT1F: 56,657,640–56,660,698, forward strandMT1FMT1G: 56,666,730–56,668,072, reverse strandMT1GMT1H: 56,669,660–56,671,135, forward strandMT1HMT1X: 56,682,058–56,686,110, forward strandMT1XNUP93: 56,730,095–56,850,286, forward strandNUP93SLC12A3: 56,865,207–56,915,850, forward strandSLC12A3HERPUD1: 56,930,815–56,946,491, forward strandHERPUD1CETP: 56,961,922–56,983,845, forward strandCETPNLRC5: 56,989,485–57,084,238, forward strandNLRC5CPNE2: 57,092,517–57,148,369, forward strandCPNE2PSME3IP1: 57,152,466–57,186,175, reverse strandPSME3IP1RSPRY1: 57,186,137–57,242,505, forward strandRSPRY1ARL2BP: 57,245,098–57,259,830, forward strandARL2BPPLLP: 57,248,547–57,284,683, reverse strandPLLPCCL22: 57,357,925–57,366,191, forward strandCCL22CX3CL1: 57,372,457–57,385,044, forward strandCX3CL1Diagram of SLC12A3: 26 exons on the forward strand of chromosome 16Exon 1: 25 known disease-causing sitesExon 2: 13 known disease-causing sitesExon 3: 11 known disease-causing sitesExon 4: 10 known disease-causing sitesExon 5: 15 known disease-causing sitesExon 6: 8 known disease-causing sitesExon 7: 8 known disease-causing sitesExon 8: 17 known disease-causing sitesExon 9: 6 known disease-causing sitesExon 10: 17 known disease-causing sitesExon 11: 9 known disease-causing sitesExon 12: 10 known disease-causing sitesExon 13: 7 known disease-causing sitesExon 14: 15 known disease-causing sitesExon 15: 8 known disease-causing sitesExon 16: 7 known disease-causing sitesExon 17: 7 known disease-causing sitesExon 18: 7 known disease-causing sitesExon 19: 3 known disease-causing sitesExon 21: 7 known disease-causing sitesExon 22: 8 known disease-causing sitesExon 23: 6 known disease-causing sitesExon 24: 8 known disease-causing sitesExon 25: 8 known disease-causing sitesExon 26: 11 known disease-causing sitesExon 1: 56,865,207–56,865,517, 311 basesExon 2: 56,867,070–56,867,216, 147 basesExon 3: 56,868,297–56,868,372, 76 basesExon 4: 56,869,729–56,869,824, 96 basesExon 5: 56,870,096–56,870,235, 140 basesExon 6: 56,870,626–56,870,736, 111 basesExon 7: 56,872,351–56,872,462, 112 basesExon 8: 56,872,656–56,872,786, 131 basesExon 9: 56,878,077–56,878,161, 85 basesExon 10: 56,879,073–56,879,227, 155 basesExon 11: 56,879,542–56,879,649, 108 basesExon 12: 56,880,130–56,880,253, 124 basesExon 13: 56,882,396–56,882,497, 102 basesExon 14: 56,884,049–56,884,204, 156 basesExon 15: 56,885,265–56,885,364, 100 basesExon 16: 56,886,364–56,886,475, 112 basesExon 17: 56,886,953–56,887,093, 141 basesExon 18: 56,887,925–56,888,031, 107 basesExon 19: 56,890,274–56,890,356, 83 basesExon 20: 56,892,083–56,892,133, 51 basesExon 21: 56,892,953–56,893,054, 102 basesExon 22: 56,894,531–56,894,642, 112 basesExon 23: 56,899,530–56,899,616, 87 basesExon 24: 56,902,373–56,902,508, 136 basesExon 25: 56,904,395–56,904,462, 68 basesExon 26: 56,913,264–56,915,850, 2,587 bases1510152025265′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 5.5 kb of the gene's 50.6 kb; 3,066 of those bases code for the protein.

How a genome test reads SLC12A3

310

positions in SLC12A3 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 50.6 kb of SLC12A3, introns included, not only the 5.5 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.). SLC12A3 gene: solute carrier family 12 member 3. Retrieved 17 October 2026, from https://dantelabs.com/genes/slc12a3

Vancouver

Dante Labs. SLC12A3 gene: solute carrier family 12 member 3 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/slc12a3

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