VARS2 p.Ser887=
c.2661C>T · rs141162034 · VCV2428261
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0176%, mid)
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 -0.65 | GERP -3.6, phastCons 0.024 |
| Overall | ||
| CADD | 2.753 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0176%
Middle Eastern · 1/5,676 alleles
Filtering AF
0.00355%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00278%
Overall
0.00372%
57/1,530,942 alleles · ultra-rare
exomes 47/1,378,616 · genomes 10/152,326 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0176% | 5,676 |
| African / African-American | 0.00822% | 12,163 |
| European (non-Finnish) | 0.00406% | 24,623 |
| Remaining individualsnot grpmax-eligible | 0.00338% | 29,574 |
| South Asian | 0.00248% | 40,341 |
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.Ser887=
- Coding
- c.2661C>T
- MANE Select
- NM_020442
- dbSNP
- rs141162034
- Type
- single nucleotide variant
- Location
- chr6:30924548 (GRCh38)
- Structure
- AlphaFold pLDDT 88.12
Similar variants
- 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
- VARS2 c.2467-2A>G Pathogenic/Likely pathogenic ★★ same type
- VARS2 p.Arg1002Ter 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-ser887 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown