RPSA p.Ser78=
c.234C>T · rs546066905 · VCV1616134
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0519%, 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 -6.9 | GERP -4.9 |
| Overall | ||
| CADD | 4.742 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0519%
South Asian · 47/90,574 alleles
Filtering AF
0.0401%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0359%
Overall
0.00397%
63/1,587,226 alleles · ultra-rare
exomes 60/1,434,944 · genomes 3/152,282 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0519% | 1,927 |
| Middle Eastern | 0.0166% | 6,010 |
| African / African-American | 0.0094% | 10,641 |
| Admixed American | 0.00667% | 14,997 |
| Remaining individualsnot grpmax-eligible | 0.00487% | 20,529 |
| European (non-Finnish) | 8.65e-05% | 1,155,450 |
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.Ser78=
- Coding
- c.234C>T
- MANE Select
- NM_002295
- dbSNP
- rs546066905
- Type
- single nucleotide variant
- Location
- chr3:39408706 (GRCh38)
- Gene constraint
- LOEUF 0.144 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 79.45 · 204 PDB
- Residue 78
- the 'interaction with ppp1r16b' region
Similar variants
- RPSA p.Ser78Tyr Uncertain significance ⚠ same residue
- 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
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-ser78 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown