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Gene

SLC46A1

solute carrier family 46 member 1

Summary

Cytogenetic location
17q11.2
Coordinates
Chromosome 17: 28,394,642–28,406,212 (GRCh38)
Exons
5 exons across 11.6 kb
Protein
459 amino acids
Inheritance
Autosomal recessive
Also known as
HCP1, MGC9564, PCFT, HsPCFT, hPCFT
MANE Select transcript
ENST00000612814.5NM_080669.6
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

  • Hereditary Folate Malabsorption

    • Autosomal recessive
      • ClinGen rates the link definitive
      • 5 GenCC submitters rate it definitive or strong
      What knowing changes

      High-dose intramuscular (parenteral) folinic acid or levofolinic acid to bypass intestinal absorption blocks

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 SLC46A1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
Chromosome 17, with a bracket where SLC46A1 sits. SLC46A1 and 31 genes near it on chromosome 17, from 27,900,427 to 28,900,426.Chromosome 1717q11.2p13.3p13.2p13.1p12p11.2p11.1q11.1q11.2q12q21.1q21.2q21.31q21.32q21.33q22q23.1q23.2q23.3q24.1q24.2q24.3q25.1q25.2q25.328 Mb28.2 Mb28.4 Mb28.6 Mb28.8 MbNLK: 28,041,709–28,196,381, forward strandNLKTMEM97: 28,319,097–28,332,671, forward strandIFT20: 28,328,319–28,335,489, reverse strandTNFAIP1: 28,335,572–28,349,943, forward strandPOLDIP2: 28,343,133–28,357,623, reverse strandVMA12: 28,357,636–28,363,683, forward strandSEBOX: 28,363,506–28,365,199, reverse strand: 28,364,288–28,368,012, reverse strandSARM1: 28,364,356–28,404,049, forward strandSARM1VTN: 28,366,414–28,373,091, reverse strandVTNSLC46A1: 28,394,642–28,406,212, reverse strandSLC46A1RSKR: 28,455,752–28,614,210, reverse strandRSKRSLC13A2: 28,473,275–28,497,782, forward strandSLC13A2FOXN1: 28,506,243–28,538,900, forward strandFOXN1UNC119: 28,546,705–28,552,655, reverse strandUNC119PIGS: 28,553,383–28,571,794, reverse strandPIGSALDOC: 28,573,115–28,576,948, reverse strandALDOCSPAG5: 28,577,565–28,599,052, reverse strand: 28,580,012–28,614,185, reverse strandBLTP2: 28,614,440–28,645,454, reverse strandBLTP2SDF2: 28,648,346–28,662,189, reverse strandSDF2SUPT6H: 28,661,920–28,702,682, forward strandSUPT6HPROCA1: 28,703,196–28,712,313, reverse strandPROCA1RAB34: 28,713,545–28,719,594, reverse strandRAB34RPL23A: 28,719,940–28,724,365, forward strandRPL23ATLCD1: 28,723,435–28,727,935, reverse strandNEK8: 28,725,897–28,743,455, forward strandTRAF4: 28,743,978–28,772,894, forward strandFAM222B: 28,755,966–28,855,232, reverse strandFAM222BERAL1: 28,854,983–28,861,067, forward strandERAL1FLOT2: 28,879,335–28,897,741, reverse strandFLOT2DHRS13: 28,897,781–28,903,087, reverse strandDHRS13Diagram of SLC46A1: 5 exons on the reverse strand of chromosome 17Exon 4: 2 known disease-causing sitesExon 3: 1 known disease-causing siteExon 2: 4 known disease-causing sitesExon 1: 2 known disease-causing sitesExon 5: 28,394,642–28,399,713, 5,072 basesExon 4: 28,400,610–28,400,766, 157 basesExon 3: 28,402,238–28,402,321, 84 basesExon 2: 28,404,616–28,405,468, 853 basesExon 1: 28,405,887–28,406,212, 326 bases543215′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 6.5 kb of the gene's 11.6 kb; 1,380 of those bases code for the protein.

How a genome test reads SLC46A1

10

positions in SLC46A1 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 11.6 kb of SLC46A1, introns included, not only the 6.5 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.). SLC46A1 gene: solute carrier family 46 member 1. Retrieved 17 October 2026, from https://dantelabs.com/genes/slc46a1

Vancouver

Dante Labs. SLC46A1 gene: solute carrier family 46 member 1 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/slc46a1

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