VARS2 p.Ser355=
c.1065G>A · rs151183326 · VCV382790
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.693%, afr)
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 -2.3 | GERP -0.13 |
| Overall | ||
| CADD | 5.399 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.693%
African / African-American · 520/75,010 alleles
Filtering AF
0.644%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.624%
Overall
0.037%
597/1,612,802 alleles · rare
exomes 234/1,460,546 · genomes 363/152,256 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.693% | 144 |
| Admixed American | 0.075% | 1,334 |
| Remaining individualsnot grpmax-eligible | 0.04% | 2,499 |
| Middle Eastern | 0.0338% | 2,959 |
| European (non-Finnish) | 0.000424% | 236,001 |
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
- VARS2
- Protein
- p.Ser355=
- Coding
- c.1065G>A
- MANE Select
- NM_020442
- dbSNP
- rs151183326
- Type
- single nucleotide variant
- Location
- chr6:30918906 (GRCh38)
- Structure
- AlphaFold pLDDT 88.12
Similar variants
- VARS2 p.Ser355Leu Uncertain significance ★ ⚠ same residue
- VARS2 p.Ser355Pro Uncertain significance ★ ⚠ same residue
- VARS1 p.Arg1058Gln Likely pathogenic ★★ ⚠ same type
- VARS1 p.Arg1119Cys Pathogenic/Likely pathogenic ★★ same type
- VARS1 p.Arg1208Ter Pathogenic/Likely pathogenic ★★ same type
- VARS1 p.Gln1039Ter Likely pathogenic ★★ same type
- VARS1 p.Trp790Ter Pathogenic/Likely pathogenic ★★ same type
- VARS2 c.1480-2A>G 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/vars2-p-ser355 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown