SLC19A3

Chr 2AR

solute carrier family 19 member 3

Also known as: BBGD, THMD2, THTR2, hTHTR2, thTr-2

This gene encodes a ubiquitously expressed transmembrane thiamine transporter that lacks folate transport activity. Mutations in this gene cause biotin-responsive basal ganglia disease (BBGD); a recessive disorder manifested in childhood that progresses to chronic encephalopathy, dystonia, quadriparesis, and death if untreated. Patients with BBGD have bilateral necrosis in the head of the caudate nucleus and in the putamen. Administration of high doses of biotin in the early progression of the disorder eliminates pathological symptoms while delayed treatment results in residual paraparesis, mild cognitive disability, or dystonia. Administration of thiamine is ineffective in the treatment of this disorder. Experiments have failed to show that this protein can transport biotin. Mutations in this gene also cause a Wernicke's-like encephalopathy.[provided by RefSeq, Jan 2010]

GeneReviewsOMIMResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

Thiamine metabolism dysfunction syndrome 2 (biotin/thiamine-responsive basal ganglia disease type)MIM #607483
AR

Clinical highlights

Gene-disease validity (ClinGen)
Leigh syndrome · ARDefinitivesufficient evidence for diagnostic panels
Interpreting a novel variant
Loss of function is the curated mechanism (Gene2Phenotype) and the gene is intolerant of it in the population — truncating, frameshift and canonical splice variants carry more prior weight here than missense.Curated gene-level mechanism — a prior for triage, not a per-variant call.
0
Active trials
14
Pubs (1 yr)
P/LP submissions
P/LP missense
0.59
LOEUF
LOF
Mechanism· G2P
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GeneReview available — SLC19A3
Authoritative clinical overview · Recommended first read
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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Moderate LoF intolerance
LoF Constraint?
0.59LOEUF
pLI 0.104
Z-score 2.82
OE 0.28 (0.140.59)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?
-0.37Z-score
OE missense 1.06 (0.961.17)
283 obs / 266.2 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios?
LoF OE?0.28 (0.140.59)
00.351.4
Missense OE?1.06 (0.961.17)
00.61.4
Synonymous OE?0.82
01.21.6
LoF obs/exp: 5 / 17.8Missense obs/exp: 283 / 266.2Syn Z: 1.52

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

SLC19A3 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

VCEP specificationsMitochondrial DiseaseReleased
Specifications ↗Panel ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

No active trials found for this gene.

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