Is SLC19A3 p.Tyr14= (c.42C>T) pathogenic?

SLC19A3 p.Tyr14= (c.42C>T) is classified Benign/Likely benign in SLC19A3 (ClinVar, Multiple submitters, 11 submitters; last evaluated 2026-02-03). Common (popmax 5.32%, afr) — too common for a highly-penetrant pathogenic allele; Associated with biotin-responsive basal ganglia disease.

What condition is associated with SLC19A3 p.Tyr14= (c.42C>T)?

SLC19A3 p.Tyr14= (c.42C>T) is associated with biotin-responsive basal ganglia disease (ClinVar).

How is Thiamine-responsive encephalopathy inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

SLC19A3 p.Tyr14=

Q: How common is SLC19A3 p.Tyr14= (c.42C>T) in the general population?

SLC19A3 p.Tyr14= (c.42C>T) is common (popmax 5.32%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.42C>T · rs34080459 · VCV130322

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 11 submitters

gnomAD v4.1

Common

common (popmax 5.32%, afr) — too common for a highly-penetrant pathogenic allele

Conditions

biotin-responsive basal ganglia disease

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.098	GERP -3.5, phastCons 0.088
Overall
CADD	3.554	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 5.32% African / African-American · 3,988/75,014 alleles

Filtering AF 5.18% ClinGen BA1/BS1 input FAF95, joint · FAF99 5.12%

Overall 0.281% 4,533/1,614,048 alleles · common exomes 2,207/1,461,758 · genomes 2,326/152,290 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	5.32%	19
Remaining individualsnot grpmax-eligible	0.379%	264
Admixed American	0.317%	316
Middle Eastern	0.198%	505
South Asian	0.00988%	10,120
European (non-Finnish)	0.00822%	12,164

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: SLC19A3
Protein: p.Tyr14=
Coding: c.42C>T
MANE Select: NM_025243
dbSNP: rs34080459
Type: single nucleotide variant
Location: chr2:227702277 (GRCh38)
Gene constraint: LOEUF 0.968 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.96 · 19 PDB
Residue 14: an α-helix

Full SLC19A3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

biotin-responsive basal ganglia disease — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Thiamine-responsive encephalopathy (Orphanet):

Inheritance: Autosomal recessive
Onset: Adolescent

Similar variants

SLC19A3 c.1172+1G>A Pathogenic/Likely pathogenic ★★ same condition
SLC19A3 c.1172+2T>G Pathogenic ★★ same condition
SLC19A3 c.1173-1G>A Pathogenic/Likely pathogenic ★★ same condition
SLC19A3 c.151-1G>C Likely pathogenic ★★ same condition
SLC19A3 c.980-14A>G Pathogenic/Likely pathogenic ★★ same condition
SLC19A3 p.Gly23Val Pathogenic/Likely pathogenic ★★ same condition
SLC19A3 p.Met1Leu Likely pathogenic ★★ same condition
SLC19A3 p.Ser181Pro Pathogenic ★★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/slc19a3-p-tyr14 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown