SLC19A2 p.Ile466=
c.1398C>T · rs370262388 · VCV1582995
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0174%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.32 · evaluated, not missing |
|---|---|---|
| Pangolin | Δ0.35 | loss · gain 0.00 · SpliceAI below 0.2 · independent |
| Constraint at this position | ||
| Conservation | phyloP -0.44 | GERP -4, phastCons 0.004 |
| Overall | ||
| CADD | 2.687 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0174%
African / African-American · 13/74,906 alleles
Filtering AF
0.0103%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00813%
Overall
0.00421%
68/1,613,906 alleles · ultra-rare
exomes 50/1,461,764 · genomes 18/152,142 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0174% | 5,762 |
| Middle Eastern | 0.0164% | 6,084 |
| European (non-Finnish) | 0.00432% | 23,136 |
| Admixed American | 0.00333% | 29,998 |
| South Asian | 0.0011% | 91,086 |
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
- SLC19A2
- Protein
- p.Ile466=
- Coding
- c.1398C>T
- MANE Select
- NM_006996
- dbSNP
- rs370262388
- Type
- single nucleotide variant
- Location
- chr1:169465945 (GRCh38)
- Gene constraint
- LOEUF 0.852 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.99 · 2 PDB
- Residue 466
- an α-helix
Similar variants
- SLC19A2 c.1223+1G>A Pathogenic ★★ same type
- SLC19A2 c.807+2T>G Likely pathogenic ★★ same type
- SLC19A2 p.Arg162Ter Pathogenic ★★ same type
- SLC19A2 p.Arg397Ter Pathogenic/Likely pathogenic ★★ same type
- SLC19A2 p.Gln233Ter Pathogenic ★★ same type
- SLC19A2 p.Glu66Ter Pathogenic ★★ same type
- SLC19A2 p.Gly105Glu Pathogenic/Likely pathogenic ★★ same type
- SLC19A2 p.Gly172Asp Pathogenic/Likely pathogenic ★★ 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/slc19a2-p-ile466 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown