Is SLC19A1 p.Ala469Ser (c.1405G>T) pathogenic?

SLC19A1 p.Ala469Ser (c.1405G>T) is classified Uncertain significance in SLC19A1 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2023-11-27). AlphaMissense: likely benign (0.0831); Rare (popmax 0.1%, mid).

How common is SLC19A1 p.Ala469Ser (c.1405G>T) in the general population?

SLC19A1 p.Ala469Ser (c.1405G>T) is rare (popmax 0.1%, mid) (gnomAD).

What do computational predictors say about SLC19A1 p.Ala469Ser (c.1405G>T)?

AlphaMissense predicts likely benign (score 0.0831) — an in-silico prediction, not a clinical call.

SLC19A1 p.Ala469Ser

c.1405G>T · rs560827689 · VCV1405819

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.0831 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.1%, mid)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0831	likely benign
REVEL	0.075	moderately benign-leaning
SaProt	LLR -6.33	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 0.37	GERP 1.4, phastCons 0.036
Regional constraint	o/e 1.00	unconstrained · MANE · 22 kb · p 0.89 · regional, not allelic
Overall
CADD	9.249	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — 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 0.1% Middle Eastern · 6/5,998 alleles

Filtering AF 0.0652% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0593%

Overall 0.00919% 145/1,578,472 alleles · rare exomes 109/1,426,168 · genomes 36/152,304 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.1%	1,000
African / African-American	0.0816%	1,225
Remaining individualsnot grpmax-eligible	0.0375%	2,665
Admixed American	0.0245%	4,078
European (non-Finnish)	0.00352%	28,378
South Asian	0.00115%	86,806

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.Ala469Ser
Coding: c.1405G>T
MANE Select: NM_194255
dbSNP: rs560827689
Type: single nucleotide variant
Location: chr21:45516029 (GRCh38)
Gene constraint: LOEUF 1.585 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 73.30 · 19 PDB

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

Similar variants

SLC19A1 p.Ala469Val Benign ★★ same residue
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

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-ala469ser (accessed [today's date]).

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