RPSA p.Pro234=
c.702C>T · VCV3344854
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00881%, nfe)
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 -6.7 | GERP -4.7 |
| Overall | ||
| CADD | 4.105 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00881%
European (non-Finnish) · 104/1,179,908 alleles
Filtering AF
0.00741%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00692%
Overall
0.00699%
112/1,601,280 alleles · very rare
exomes 108/1,449,138 · genomes 4/152,142 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00881% | 11,345 |
| Remaining individualsnot grpmax-eligible | 0.00641% | 15,598 |
| East Asian | 0.00445% | 22,447 |
| South Asian | 0.0022% | 45,540 |
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.Pro234=
- Coding
- c.702C>T
- MANE Select
- NM_002295
- Type
- single nucleotide variant
- Location
- chr3:39411970 (GRCh38)
- Gene constraint
- LOEUF 0.144 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 79.45 · 204 PDB
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-pro234 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown