SLC19A1 p.Ala279=
c.837C>T · rs577753141 · VCV1670438
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.345%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.007 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -7.8 | GERP -3.4 |
| Overall | ||
| CADD | 2.937 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.345%
East Asian · 155/44,872 alleles
Filtering AF
0.301%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.284%
Overall
0.0119%
192/1,612,754 alleles · rare
exomes 170/1,460,512 · genomes 22/152,242 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.345% | 289 |
| South Asian | 0.0231% | 4,337 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,941 |
| African / African-American | 0.00667% | 14,999 |
| European (non-Finnish) | 0.00017% | 589,897 |
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.Ala279=
- Coding
- c.837C>T
- MANE Select
- NM_194255
- dbSNP
- rs577753141
- Type
- single nucleotide variant
- Location
- chr21:45531501 (GRCh38)
- Gene constraint
- LOEUF 1.585 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.30 · 19 PDB
- Residue 279
- an α-helix
Similar variants
- SLC19A1 p.Ala279Thr Uncertain significance ★ ⚠ same residue
- SLC19A1 p.Ala279Val Uncertain significance ★ 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
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-ala279 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown