Is SLC19A3 p.Val103= (c.309G>A) pathogenic?

SLC19A3 p.Val103= (c.309G>A) is classified Benign/Likely benign in SLC19A3 (ClinVar, Multiple submitters, 11 submitters; last evaluated 2026-05-01). Rare (popmax 0.814%, nfe); Associated with biotin-responsive basal ganglia disease.

What condition is associated with SLC19A3 p.Val103= (c.309G>A)?

SLC19A3 p.Val103= (c.309G>A) is associated with biotin-responsive basal ganglia disease (ClinVar).

How common is SLC19A3 p.Val103= (c.309G>A) in the general population?

SLC19A3 p.Val103= (c.309G>A) is rare (popmax 0.814%, nfe) (gnomAD).

How is Thiamine-responsive encephalopathy inherited?

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

SLC19A3 p.Val103=

c.309G>A · rs142837989 · VCV130321

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 11 submitters

gnomAD v4.1

Rare

rare (popmax 0.814%, nfe)

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 0.063	GERP -2.6, phastCons 0.002
Overall
CADD	5.528	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.814% European (non-Finnish) · 9,601/1,180,040 alleles

Filtering AF 0.8% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.794%

Overall 0.755% 12,189/1,614,170 alleles · rare exomes 11,288/1,461,886 · genomes 901/152,284 · joint denominator

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	2.73%	37
European (non-Finnish)grpmax	0.814%	123
Remaining individualsnot grpmax-eligible	0.61%	164
Admixed American	0.485%	206
Ashkenazi Jewishnot grpmax-eligible	0.287%	348
African / African-American	0.112%	893
South Asian	0.0022%	45,540

Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Val103=
Coding: c.309G>A
MANE Select: NM_025243
dbSNP: rs142837989
Type: single nucleotide variant
Location: chr2:227699406 (GRCh38)
Gene constraint: LOEUF 0.968 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.96 · 19 PDB
Residue 103: 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 p.Val103fs Pathogenic ★★ same residue
SLC19A3 p.Val103Met Uncertain significance ★ ⚠ same residue
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

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-val103 (accessed [today's date]).

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