RPS2 p.Ser85=
c.255C>T · rs61741761 · VCV781179
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.11%, 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 -3.7 | GERP -3.8 |
| Overall | ||
| CADD | 0.412 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.11%
African / African-American · 2,333/74,996 alleles
Filtering AF
3.01%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.96%
Overall
0.163%
2,621/1,612,134 alleles · low-frequency
exomes 1,298/1,459,792 · genomes 1,323/152,342 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.11% | 32 |
| Remaining individualsnot grpmax-eligible | 0.175% | 573 |
| Admixed American | 0.158% | 632 |
| Middle Eastern | 0.0338% | 2,958 |
| South Asian | 0.00659% | 15,171 |
| European (non-Finnish) | 0.00645% | 15,509 |
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
- RPS2
- Protein
- p.Ser85=
- Coding
- c.255C>T
- MANE Select
- NM_002952
- dbSNP
- rs61741761
- Type
- single nucleotide variant
- Location
- chr16:1964288 (GRCh38)
- Gene constraint
- LOEUF 0.493 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 82.10 · 204 PDB
Similar variants
- RPS2 p.Arg46= Benign ★★ same type
- RPS2 p.Ala198Ser Uncertain significance ★ ⚠ same type
- RPS2 p.Ala291Thr Uncertain significance ★ ⚠ same type
- RPS2 p.Ala5Gly Uncertain significance ★ ⚠ same type
- RPS2 p.Ala8Pro Uncertain significance ★ ⚠ same type
- RPS2 p.Ala8Val Uncertain significance ★ ⚠ same type
- RPS2 p.Arg167Gly Uncertain significance ★ ⚠ same type
- RPS2 p.Arg187His 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/rps2-p-ser85 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown