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Gene

SLC19A3

solute carrier family 19 member 3

Summary

Cytogenetic location
2q36.3
Coordinates
Chromosome 2: 227,683,763–227,718,028 (GRCh38)
Exons
6 exons across 34.3 kb
Protein
496 amino acids
Inheritance
Autosomal recessive
Also known as
THTR2, thTr-2, hTHTR2
MANE Select transcript
ENST00000644224.2NM_025243.4
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 reports relevant to this gene

  • Thiamine Transporter and Metabolism Disorders

    • Disorders of Thiamine Transport and MetabolismAutosomal recessive

      Inherited defects in thiamine transporters or thiamine activation, caused by genes such as SLC19A2, SLC19A3, TPK1 and SLC25A19, which can cause anaemia, diabetes and hearing loss or episodes of severe brain dysfunction.

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

      Knowing allows early treatment with high-dose thiamine, and biotin where appropriate, which can prevent or reduce serious complications in several of these disorders.

Broader groupings

  • Leigh Syndrome

    • One of 69 genes linked to it

      A progressive neurological disease defined by specific neuropathological features associating brainstem and basal ganglia lesions.

      • ClinGen rates the link definitive
      • 1 GenCC submitter rates 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 SLC19A3 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 2, with a bracket where SLC19A3 sits. SLC19A3 and 16 genes near it on chromosome 2, from 227,200,896 to 228,200,895.Chromosome 22q36.3p25.3p25.2p25.1p24.3p24.2p24.1p23.3p23.2p23.1p22.3p22.2p22.1p21p16.3p16.2p16.1p15p14p13.3p13.2p13.1p12p11.2p11.1q11.1q11.2q12.1q12.2q12.3q13q14.1q14.2q14.3q21.1q21.2q21.3q22.1q22.2q22.3q23.1q23.2q23.3q24.1q24.2q24.3q31.1q31.2q31.3q32.1q32.2q32.3q33.1q33.2q33.3q34q35q36.1q36.2q36.3q37.1q37.2q37.3227.4 Mb227.6 Mb227.8 Mb228 Mb228.2 MbCOL4A3: 227,164,509–227,314,792, forward strandCOL4A3MFF: 227,325,151–227,361,188, forward strandMFFTM4SF20: 227,362,038–227,381,995, reverse strandTM4SF20SCYGR1: 227,387,683–227,387,949, reverse strandSCYGR1AGFG1: 227,472,134–227,561,411, forward strandAGFG1SCYGR2: 227,598,893–227,599,255, forward strandSCYGR2SCYGR10: 227,608,784–227,609,101, forward strandSCYGR10SCYGR3: 227,614,538–227,614,840, reverse strandSCYGR3SCYGR4: 227,617,498–227,617,815, forward strandSCYGR4SCYGR5: 227,666,804–227,667,061, forward strandSCYGR5SLC19A3: 227,683,763–227,718,028, reverse strandSLC19A3SCYGR6: 227,724,440–227,724,757, reverse strandSCYGR6SCYGR7: 227,728,335–227,728,625, forward strandSCYGR7SCYGR8: 227,745,894–227,746,220, forward strandSCYGR8CCL20: 227,805,739–227,817,564, forward strandCCL20DAW1: 227,870,931–227,924,344, forward strandDAW1SPHKAP: 227,979,866–228,182,020, reverse strandSPHKAPDiagram of SLC19A3: 6 exons on the reverse strand of chromosome 2Exon 6: 2 known disease-causing sitesExon 5: 4 known disease-causing sitesExon 4: 4 known disease-causing sitesExon 3: 44 known disease-causing sitesExon 2: 12 known disease-causing sitesExon 6: 227,683,763–227,687,573, 3,811 basesExon 5: 227,688,166–227,688,307, 142 basesExon 4: 227,695,889–227,696,081, 193 basesExon 3: 227,698,736–227,699,564, 829 basesExon 2: 227,702,169–227,702,320, 152 basesExon 1: 227,717,943–227,718,028, 86 bases6543215′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 5.2 kb of the gene's 34.3 kb; 1,491 of those bases code for the protein.

How a genome test reads SLC19A3

74

positions in SLC19A3 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 SLC19A3, introns included, not only the 5.2 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.). SLC19A3 gene: solute carrier family 19 member 3. Retrieved 17 October 2026, from https://dantelabs.com/genes/slc19a3

Vancouver

Dante Labs. SLC19A3 gene: solute carrier family 19 member 3 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/slc19a3

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