RPSA p.Ser43=
c.129T>C · VCV3619427
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.48e-05%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · T>G here scores Δ0.31 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3.9 | GERP -2.5 |
| Overall | ||
| CADD | 11.37 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.48e-05%
European (non-Finnish) · 1/1,179,518 alleles
Overall
6.26e-05%
1/1,598,084 alleles · very rare
exomes 1/1,445,776 · genomes 0/152,308 · joint denominator
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.Ser43=
- Coding
- c.129T>C
- MANE Select
- NM_002295
- Type
- single nucleotide variant
- Location
- chr3:39407782 (GRCh38)
- Gene constraint
- LOEUF 0.144 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 79.45 · 204 PDB
- Residue 43
- a modified residue (phosphoserine); an α-helix
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-ser43 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown