Is SLC19A3 p.Ile207Met (c.621A>G) pathogenic?

SLC19A3 p.Ile207Met (c.621A>G) is classified Conflicting classifications of pathogenicity in SLC19A3 (ClinVar, Conflicting submitters, 11 submitters; last evaluated 2026-02-02). AlphaMissense: likely benign (0.0558); Rare (popmax 0.379%, nfe); Associated with biotin-responsive basal ganglia disease.

What condition is associated with SLC19A3 p.Ile207Met (c.621A>G)?

SLC19A3 p.Ile207Met (c.621A>G) is associated with biotin-responsive basal ganglia disease (ClinVar).

How common is SLC19A3 p.Ile207Met (c.621A>G) in the general population?

SLC19A3 p.Ile207Met (c.621A>G) is rare (popmax 0.379%, nfe) (gnomAD).

How is Thiamine-responsive encephalopathy inherited?

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

What do computational predictors say about SLC19A3 p.Ile207Met (c.621A>G)?

AlphaMissense predicts likely benign (score 0.0558) — an in-silico prediction, not a clinical call.

SLC19A3 p.Ile207Met

c.621A>G · rs145804755 · VCV215152

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 11 submitters

AlphaMissense

likely benign

0.0558 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.379%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

biotin-responsive basal ganglia disease

Computational evidence

Protein change
AlphaMissense	0.0558	likely benign
REVEL	0.146	moderately benign-leaning
SaProt	LLR -6.62	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.2	GERP -3.1
Regional constraint	o/e 0.99	unconstrained · MANE · 15 kb · p 0.85 · regional, not allelic
Overall
CADD	4.58	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.379% European (non-Finnish) · 4,477/1,180,052 alleles

Filtering AF 0.37% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.366%

Overall 0.291% 4,700/1,614,128 alleles · rare exomes 4,486/1,461,886 · genomes 214/152,242 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.379%	264
Remaining individualsnot grpmax-eligible	0.232%	431
African / African-American	0.0467%	2,141
Admixed American	0.0467%	2,143
Finnishnot grpmax-eligible	0.0219%	4,574
Middle Eastern	0.0164%	6,084

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.Ile207Met
Coding: c.621A>G
MANE Select: NM_025243
dbSNP: rs145804755
Type: single nucleotide variant
Location: chr2:227699094 (GRCh38)
Gene constraint: LOEUF 0.968 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.96 · 19 PDB

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-ile207met (accessed [today's date]).

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