RPSA p.Pro105=
c.315T>C · rs529221890 · VCV797181
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.232%, 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 -4.5 | GERP -4.9 |
| Overall | ||
| CADD | 7.791 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.232%
South Asian · 211/91,060 alleles
Filtering AF
0.206%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.196%
Overall
0.0138%
223/1,610,342 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.232% | 432 |
| Remaining individualsnot grpmax-eligible | 0.00801% | 12,489 |
| East Asian | 0.00223% | 44,884 |
| African / African-American | 0.00133% | 75,032 |
| European (non-Finnish) | 0.000424% | 235,836 |
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.Pro105=
- Coding
- c.315T>C
- MANE Select
- NM_002295
- dbSNP
- rs529221890
- Type
- single nucleotide variant
- Location
- chr3:39410816 (GRCh38)
- Gene constraint
- LOEUF 0.144 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 79.45 · 204 PDB
- Residue 105
- a turn; 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-pro105 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown