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Gene

SLC12A5

solute carrier family 12 member 5

Summary

Cytogenetic location
20q13.12
Coordinates
Chromosome 20: 46,029,215–46,060,150 (GRCh38)
Exons
26 exons across 30.9 kb
Protein
1,116 amino acids
Also known as
KIAA1176, KCC2, hKCC2
MANE Select transcript
ENST00000243964.7NM_020708.5
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

    • 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.

        • 3 GenCC submitters rate it definitive or strong

    How SLC12A5 is laid out

    • Coding sequence
    • Untranslated region
    • Intron
    • Direction of transcription
    • Known disease-causing sites
    • Stretches short reads find hard
    Chromosome 20, with a bracket where SLC12A5 sits. SLC12A5 and 32 genes near it on chromosome 20, from 45,544,683 to 46,544,682.Chromosome 2020q13.12p13p12.3p12.2p12.1p11.23p11.22p11.21p11.1q11.1q11.21q11.22q11.23q12q13.11q13.12q13.13q13.2q13.31q13.32q13.3345.6 Mb45.8 Mb46 Mb46.2 Mb46.4 MbEPPIN-WFDC6: 45,534,196–45,547,662, reverse strandEPPIN-WFDC6EPPIN: 45,540,626–45,547,786, reverse strandEPPINWFDC8: 45,551,153–45,579,326, reverse strandWFDC8WFDC9: 45,607,939–45,631,284, reverse strandWFDC9WFDC10A: 45,629,733–45,631,196, forward strandWFDC10AWFDC11: 45,648,563–45,670,270, reverse strandWFDC11WFDC10B: 45,684,651–45,705,019, reverse strandWFDC10BWFDC13: 45,702,038–45,708,817, forward strandWFDC13SPINT4: 45,722,347–45,725,830, forward strandSPINT4WFDC3: 45,747,944–45,791,932, reverse strandWFDC3DNTTIP1: 45,791,937–45,811,427, forward strandUBE2C: 45,812,561–45,816,965, forward strandUBE2CTNNC2: 45,823,214–45,833,745, reverse strandTNNC2SNX21: 45,833,633–45,843,276, forward strandSNX21ACOT8: 45,841,709–45,857,435, reverse strandACOT8ZSWIM3: 45,857,591–45,879,131, forward strandZSWIM1: 45,881,201–45,885,266, forward strandSPATA25: 45,886,491–45,887,626, reverse strandNEURL2: 45,888,002–45,891,220, reverse strandNEURL2CTSA: 45,890,144–45,898,949, forward strandCTSAPLTP: 45,897,535–45,912,235, reverse strandPLTPPCIF1: 45,934,673–45,948,023, forward strandPCIF1ZNF335: 45,948,653–45,972,358, reverse strandZNF335MMP9: 46,008,869–46,016,561, forward strandMMP9SLC12A5: 46,029,215–46,060,150, forward strandSLC12A5NCOA5: 46,060,984–46,089,973, reverse strandNCOA5CD40: 46,118,240–46,130,378, forward strandCD40CDH22: 46,173,737–46,309,009, reverse strandCDH22SLC35H1: 46,345,980–46,364,460, reverse strandSLC35H1ELMO2: 46,366,045–46,432,985, reverse strandELMO2ZNF840P: 46,459,441–46,495,558, forward strandZNF840PZNF334: 46,499,630–46,513,596, reverse strandZNF334OCSTAMP: 46,540,946–46,550,654, reverse strandOCSTAMPDiagram of SLC12A5: 26 exons on the forward strand of chromosome 20Exon 1: 2 known disease-causing sitesExon 2: 1 known disease-causing siteExon 3: 1 known disease-causing siteExon 6: 2 known disease-causing sitesExon 7: 3 known disease-causing sitesExon 8: 4 known disease-causing sitesExon 9: 1 known disease-causing siteExon 10: 1 known disease-causing siteExon 12: 1 known disease-causing siteExon 13: 1 known disease-causing siteExon 14: 1 known disease-causing siteExon 15: 2 known disease-causing sitesExon 16: 2 known disease-causing sitesExon 17: 2 known disease-causing sitesExon 18: 3 known disease-causing sitesExon 19: 2 known disease-causing sitesExon 20: 1 known disease-causing siteExon 21: 1 known disease-causing siteExon 22: 2 known disease-causing sitesExon 23: 1 known disease-causing siteExon 25: 1 known disease-causing siteExon 26: 1 known disease-causing siteExon 1: 46,029,215–46,029,396, 182 basesExon 2: 46,034,948–46,035,042, 95 basesExon 3: 46,035,404–46,035,535, 132 basesExon 4: 46,035,777–46,035,923, 147 basesExon 5: 46,036,741–46,036,795, 55 basesExon 6: 46,037,255–46,037,385, 131 basesExon 7: 46,040,373–46,040,614, 242 basesExon 8: 46,041,329–46,041,540, 212 basesExon 9: 46,043,153–46,043,323, 171 basesExon 10: 46,043,633–46,043,731, 99 basesExon 11: 46,043,876–46,043,933, 58 basesExon 12: 46,044,966–46,045,140, 175 basesExon 13: 46,045,878–46,045,996, 119 basesExon 14: 46,046,338–46,046,436, 99 basesExon 15: 46,047,454–46,047,573, 120 basesExon 16: 46,047,981–46,048,085, 105 basesExon 17: 46,049,622–46,049,790, 169 basesExon 18: 46,051,675–46,051,870, 196 basesExon 19: 46,052,957–46,053,126, 170 basesExon 20: 46,053,578–46,053,709, 132 basesExon 21: 46,054,916–46,055,023, 108 basesExon 22: 46,056,150–46,056,272, 123 basesExon 23: 46,056,365–46,056,564, 200 basesExon 24: 46,056,897–46,056,911, 15 basesExon 25: 46,057,170–46,057,303, 134 basesExon 26: 46,057,514–46,060,150, 2,637 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 6 kb of the gene's 30.9 kb; 3,351 of those bases code for the protein.

    How a genome test reads SLC12A5

    44

    positions in SLC12A5 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 30.9 kb of SLC12A5, introns included, not only the 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.). SLC12A5 gene: solute carrier family 12 member 5. Retrieved 17 October 2026, from https://dantelabs.com/genes/slc12a5

    Vancouver

    Dante Labs. SLC12A5 gene: solute carrier family 12 member 5 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/slc12a5

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