RPSA p.Val76=
c.228T>C · rs577387094 · VCV1600254
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.194%, 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 -0.014 | GERP -4.9, phastCons 0.79 |
| Overall | ||
| CADD | 11.27 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.194%
South Asian · 176/90,824 alleles
Filtering AF
0.17%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.161%
Overall
0.0157%
251/1,601,304 alleles · rare
exomes 240/1,448,976 · genomes 11/152,328 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.194% | 516 |
| Remaining individualsnot grpmax-eligible | 0.0371% | 2,699 |
| European (non-Finnish) | 0.00437% | 22,907 |
| Finnishnot grpmax-eligible | 0.00156% | 64,006 |
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
- RPSA
- Protein
- p.Val76=
- Coding
- c.228T>C
- MANE Select
- NM_002295
- dbSNP
- rs577387094
- Type
- single nucleotide variant
- Location
- chr3:39408700 (GRCh38)
- Gene constraint
- LOEUF 0.144 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 79.45 · 204 PDB
- Residue 76
- a β-strand; the 'interaction with ppp1r16b' region
Similar variants
- RPSA p.Arg191Cys Uncertain significance ★★ ⚠ same type
- RPSA p.Ile145Val Uncertain significance ★★ ⚠ same type
- RPSA c.134-14C>T Likely benign ★★ same type
- RPSA c.134-32C>T Benign ★★ same type
- RPSA c.252+17T>C Benign/Likely benign ★★ same type
- RPSA c.627+10T>C Likely benign ★★ same type
- RPSA c.628-17T>C Likely benign ★★ same type
- RPSA c.-8T>C Benign/Likely benign ★★ 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/rpsa-p-val76 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown