MRPS2 p.Ser80=
c.240C>T · VCV4701100
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0011%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -9.9 | GERP -3.1 |
| Overall | ||
| CADD | 7.437 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0011%
South Asian · 1/91,086 alleles
Filtering AF
6.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.9e-05%
Overall
0.000248%
4/1,613,852 alleles · very rare
exomes 4/1,461,516 · genomes 0/152,336 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0011% | 91,086 |
| European (non-Finnish) | 0.000254% | 393,332 |
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.Ser80=
- Coding
- c.240C>T
- MANE Select
- NM_016034
- Type
- single nucleotide variant
- Location
- chr9:135501914 (GRCh38)
- Gene constraint
- LOEUF 1.166 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.27 · 86 PDB
Similar variants
- 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
- MRPS2 p.His294Arg 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-ser80 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown