RPS29 p.Phe52=
c.156C>T · rs372043433 · VCV2885455
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00263%, 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 4.5 | GERP 0.85, phastCons 1 |
| Overall | ||
| CADD | 12.74 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00263%
European (non-Finnish) · 31/1,179,310 alleles
Filtering AF
0.00188%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00164%
Overall
0.00198%
32/1,613,044 alleles · very rare
exomes 29/1,460,830 · genomes 3/152,214 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00263% | 38,042 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,438 |
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
- RPS29
- Protein
- p.Phe52=
- Coding
- c.156C>T
- MANE Select
- NM_001032
- dbSNP
- rs372043433
- Type
- single nucleotide variant
- Location
- chr14:49585956 (GRCh38)
- Gene constraint
- LOEUF 0.308 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 93.68 · 195 PDB
Similar variants
- RPS29 p.Ile50Thr Likely pathogenic ★★ same type
- RPS29 c.63-6T>G Uncertain significance ★★ same type
- RPS29 p.Gln41Arg Uncertain significance ★★ ⚠ same type
- RPS29 c.163-57G>A Benign ★★ same type
- RPS29 c.54-496G>C Likely benign ★★ same type
- RPS29 c.62+14T>C Likely benign ★★ same type
- RPS29 c.63-14C>G Likely benign ★★ same type
- RPS29 c.*138A>G 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/rps29-p-phe52 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown