Is SLC19A1 p.Ala340Val (c.1019C>T) pathogenic?

SLC19A1 p.Ala340Val (c.1019C>T) is classified Uncertain significance in SLC19A1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-08-31). AlphaMissense: likely pathogenic (0.5644); Very rare (popmax 0.00523%, eas).

How common is SLC19A1 p.Ala340Val (c.1019C>T) in the general population?

SLC19A1 p.Ala340Val (c.1019C>T) is very rare (popmax 0.00523%, eas) (gnomAD).

What do computational predictors say about SLC19A1 p.Ala340Val (c.1019C>T)?

AlphaMissense predicts likely pathogenic (score 0.5644) — an in-silico prediction, not a clinical call.

SLC19A1 p.Ala340Val

c.1019C>T · rs1355489726 · VCV2716880

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.5644 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00523%, eas)

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Computational evidence

Protein change
AlphaMissense	0.5644	likely pathogenic
REVEL	0.49	indeterminate
SaProt	LLR -10.30	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.2	GERP -0.9, phastCons 0.99
Regional constraint	o/e 1.00	unconstrained · MANE · 22 kb · p 0.89 · regional, not allelic
Overall
CADD	20.4	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00523% East Asian · 2/38,254 alleles

Filtering AF 0.000866% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000324%

Overall 0.000473% 7/1,479,306 alleles · very rare exomes 6/1,327,780 · genomes 1/151,526 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00523%	19,127
Admixed American	0.00249%	40,184
Finnishnot grpmax-eligible	0.00174%	57,508
European (non-Finnish)	0.000268%	372,485

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: SLC19A1
Protein: p.Ala340Val
Coding: c.1019C>T
MANE Select: NM_194255
dbSNP: rs1355489726
Type: single nucleotide variant
Location: chr21:45530902 (GRCh38)
Gene constraint: LOEUF 1.585 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 73.30 · 19 PDB
Residue 340: an α-helix

Full SLC19A1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

COL18A1 p.Arg1081Ter Pathogenic/Likely pathogenic ★★ same type
COL18A1 p.Arg915Ter Pathogenic/Likely pathogenic ★★ same type
RFC1 p.Arg383Ter Pathogenic/Likely pathogenic ★★ same type
COL18A1 c.*30G>A Uncertain significance ★★ same type
COL18A1 p.Ala1089Thr Uncertain significance ★★ ⚠ same type
COL18A1 p.Ala1254Val Uncertain significance ★★ ⚠ same type
COL18A1 p.Arg1081Gln Uncertain significance ★★ ⚠ same type
COL18A1 p.Arg1183His Uncertain significance ★★ same type

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/slc19a1-p-ala340val (accessed [today's date]).

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