SLC2A3 p.Ser422=
c.1266C>T · rs201655602 · VCV759975
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.63%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -7.6 | GERP -3.1 |
| Overall | ||
| CADD | 2.663 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.63%
South Asian · 574/91,062 alleles
Filtering AF
0.588%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.571%
Overall
0.0457%
738/1,613,964 alleles · rare
exomes 698/1,461,690 · genomes 40/152,274 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.63% | 159 |
| Middle Eastern | 0.066% | 1,514 |
| East Asian | 0.0446% | 2,244 |
| Remaining individualsnot grpmax-eligible | 0.0336% | 2,976 |
| Admixed American | 0.0167% | 6,000 |
| African / African-American | 0.00933% | 10,720 |
| European (non-Finnish) | 0.00864% | 11,567 |
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
- SLC2A3
- Protein
- p.Ser422=
- Coding
- c.1266C>T
- MANE Select
- NM_006931
- dbSNP
- rs201655602
- Type
- single nucleotide variant
- Location
- chr12:7922827 (GRCh38)
- Gene constraint
- LOEUF 0.65 · pLI 0.07 (gnomAD)
- Structure
- AlphaFold pLDDT 90.44 · 7 PDB
- Residue 422
- an α-helix
Similar variants
- SLC2A3 c.1068+4G>A Benign ★★ same type
- SLC2A3 p.Ala149Pro Uncertain significance ★ ⚠ same type
- SLC2A3 p.Ala401Gly Uncertain significance ★ ⚠ same type
- SLC2A3 p.Ala423Thr Uncertain significance ★ ⚠ same type
- SLC2A3 p.Ala429Gly Uncertain significance ★ ⚠ same type
- SLC2A3 p.Ala464Val Uncertain significance ★ ⚠ same type
- SLC2A3 p.Ala52Val Uncertain significance ★ ⚠ same type
- SLC2A3 p.Arg267Gln 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/slc2a3-p-ser422 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown