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Gene

SLC52A3

solute carrier family 52 member 3

Summary

Cytogenetic location
20p13
Coordinates
Chromosome 20: 760,080–768,500 (GRCh38)
Exons
5 exons across 8.4 kb
Protein
469 amino acids
Inheritance
Autosomal recessive
Also known as
bA371L19.1, hRFT2, RFVT3, RFT2
Previous symbols
C20orf54
MANE Select transcript
ENST00000645534.1NM_033409.4
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

  • Riboflavin Transporter Deficiency

    • Autosomal recessive

      A neuronopathy caused by biallelic variants in SLC52A2 or SLC52A3, with sensorineural hearing loss, bulbar palsy, optic atrophy and respiratory weakness.

      • ClinGen rates the link definitive
      • 6 GenCC submitters rate it definitive or strong
      What knowing changes

      High-dose oral riboflavin can improve outcomes, especially when started early.

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 SLC52A3 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 SLC52A3 sits. SLC52A3 and 19 genes near it on chromosome 20, from 264,290 to 1,264,289.Chromosome 2020p13p13p12.3p12.2p12.1p11.23p11.22p11.21p11.1q11.1q11.21q11.22q11.23q12q13.11q13.12q13.13q13.2q13.31q13.32q13.330.4 Mb0.6 Mb0.8 Mb1 Mb1.2 MbC20orf96: 270,863–290,778, reverse strandC20orf96ZCCHC3: 297,570–300,321, forward strandZCCHC3SOX12: 325,552–330,224, forward strandSOX12NRSN2: 346,695–359,706, forward strandNRSN2TRIB3: 362,835–398,964, forward strandTRIB3RBCK1: 407,393–432,139, forward strandRBCK1TBC1D20: 423,596–462,566, reverse strandTBC1D20CSNK2A1: 472,498–543,835, reverse strandCSNK2A1TCF15: 603,801–610,316, reverse strandTCF15SRXN1: 646,614–653,404, reverse strandSRXN1: 646,626–675,800, reverse strandSCRT2: 661,596–675,802, reverse strandSCRT2SLC52A3: 760,080–768,500, reverse strandSLC52A3FAM110A: 833,707–857,463, forward strandFAM110AANGPT4: 869,900–916,335, reverse strandANGPT4RSPO4: 958,452–1,002,510, reverse strandRSPO4PSMF1: 1,113,240–1,192,353, forward strandPSMF1TMEM74B: 1,178,989–1,186,842, reverse strandTMEM74BC20orf202: 1,203,454–1,209,076, forward strandC20orf202RAD21L1: 1,226,027–1,296,421, forward strandRAD21L1Diagram of SLC52A3: 5 exons on the reverse strand of chromosome 20Exon 5: 1 known disease-causing siteExon 3: 11 known disease-causing sitesExon 2: 10 known disease-causing sitesExon 5: 760,080–761,238, 1,159 basesExon 4: 761,701–761,824, 124 basesExon 3: 763,498–764,003, 506 basesExon 2: 765,208–765,825, 618 basesExon 1: 768,297–768,500, 204 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 2.6 kb of the gene's 8.4 kb; 1,410 of those bases code for the protein.

How a genome test reads SLC52A3

22

positions in SLC52A3 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 8.4 kb of SLC52A3, introns included, not only the 2.6 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.). SLC52A3 gene: solute carrier family 52 member 3. Retrieved 17 October 2026, from https://dantelabs.com/genes/slc52a3

Vancouver

Dante Labs. SLC52A3 gene: solute carrier family 52 member 3 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/slc52a3

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