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Gene

SLC24A1

solute carrier family 24 member 1

Summary

Cytogenetic location
15q22.31
Coordinates
Chromosome 15: 65,621,938–65,656,260 (GRCh38)
Exons
10 exons across 34.3 kb
Protein
1,099 amino acids
Also known as
NCKX1, NCKX, RODX, KIAA0702, HsT17412, CSNB1D
MANE Select transcript
ENST00000261892.11NM_004727.3
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 Stationary Night Blindness

    • A group of mostly non-progressive retinal conditions, including Oguchi disease, caused by changes in genes such as NYX, CACNA1F, TRPM1, GRM6, GPR179 and SAG, often with nystagmus or short-sightedness.

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

      A genetic diagnosis explains the symptoms, helps distinguish the condition from progressive retinal diseases and informs family counselling.

How SLC24A1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 15, with a bracket where SLC24A1 sits. SLC24A1 and 11 genes near it on chromosome 15, from 65,139,099 to 66,139,098.Chromosome 1515q22.31p13p12p11.2p11.1q11.1q11.2q12q13.1q13.2q13.3q14q15.1q15.2q15.3q21.1q21.2q21.3q22.1q22.2q22.31q22.32q22.33q23q24.1q24.2q24.3q25.1q25.2q25.3q26.1q26.2q26.365.2 Mb65.4 Mb65.6 Mb65.8 Mb66 MbCLPX: 65,148,219–65,185,643, reverse strandCLPXCILP: 65,194,760–65,211,491, reverse strandCILPPARP16: 65,231,398–65,300,618, reverse strandPARP16IGDCC3: 65,327,127–65,378,087, reverse strandIGDCC3IGDCC4: 65,381,479–65,423,083, reverse strandIGDCC4DPP8: 65,442,463–65,517,757, reverse strandDPP8HACD3: 65,530,418–65,578,353, forward strandHACD3INTS14: 65,578,753–65,611,615, reverse strandINTS14SLC24A1: 65,621,938–65,656,260, forward strandSLC24A1DENND4A: 65,658,046–65,792,307, reverse strandDENND4ARAB11A: 65,726,054–65,894,232, forward strandRAB11AMEGF11: 65,895,079–66,253,811, reverse strandMEGF11Diagram of SLC24A1: 10 exons on the forward strand of chromosome 15Exon 2: 5 known disease-causing sitesExon 4: 3 known disease-causing sitesExon 8: 1 known disease-causing siteExon 9: 1 known disease-causing siteExon 10: 1 known disease-causing siteExon 1: 65,621,938–65,622,092, 155 basesExon 2: 65,623,955–65,625,970, 2,016 basesExon 3: 65,638,128–65,638,181, 54 basesExon 4: 65,639,595–65,639,703, 109 basesExon 5: 65,644,427–65,644,513, 87 basesExon 6: 65,645,612–65,645,703, 92 basesExon 7: 65,650,382–65,650,942, 561 basesExon 8: 65,651,670–65,651,759, 90 basesExon 9: 65,652,642–65,652,808, 167 basesExon 10: 65,653,830–65,656,260, 2,431 bases123456789105′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 5.8 kb of the gene's 34.3 kb; 3,300 of those bases code for the protein.

How a genome test reads SLC24A1

12

positions in SLC24A1 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 34.3 kb of SLC24A1, introns included, not only the 5.8 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.). SLC24A1 gene: solute carrier family 24 member 1. Retrieved 17 October 2026, from https://dantelabs.com/genes/slc24a1

Vancouver

Dante Labs. SLC24A1 gene: solute carrier family 24 member 1 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/slc24a1

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