MRPS2 p.Pro31=
c.93C>T · rs757108896 · VCV2958337
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0494%, mid)
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 -5.6 | GERP -4.6 |
| Overall | ||
| CADD | 1.333 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0494%
Middle Eastern · 3/6,072 alleles
Filtering AF
0.0134%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00717%
Overall
0.00112%
18/1,610,874 alleles · ultra-rare
exomes 13/1,458,704 · genomes 5/152,170 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0494% | 2,024 |
| Admixed American | 0.01% | 9,984 |
| Remaining individualsnot grpmax-eligible | 0.00161% | 62,270 |
| European (non-Finnish) | 0.000678% | 147,402 |
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
- MRPS2
- Protein
- p.Pro31=
- Coding
- c.93C>T
- MANE Select
- NM_016034
- dbSNP
- rs757108896
- Type
- single nucleotide variant
- Location
- chr9:135501047 (GRCh38)
- Gene constraint
- LOEUF 1.166 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.27 · 86 PDB
Similar variants
- MRPS2 p.Pro31Thr Uncertain significance ★ ⚠ same residue
- MRPS2 p.Arg88Gln Uncertain significance ★★ ⚠ same type
- MRPS2 p.Gly24Asp Uncertain significance ★★ ⚠ same type
- MRPS2 p.His134Tyr Uncertain significance ★★ same type
- MRPS2 p.Pro243Leu Uncertain significance ★★ ⚠ same type
- MRPS2 p.Ser5Leu Uncertain significance ★★ ⚠ same type
- MRPS2 p.Trp22Ter Uncertain significance ★★ same type
- MRPS2 c.44-8C>A 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/mrps2-p-pro31 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown