MRPL12 p.Ser80=
c.240A>C · VCV3771111
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000424%, 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 -1.7 | GERP -3.1 |
| Overall | ||
| CADD | 5.935 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000424%
European (non-Finnish) · 5/1,179,252 alleles
Filtering AF
0.000124%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 9e-05%
Overall
0.00031%
5/1,612,498 alleles · very rare
exomes 5/1,460,284 · genomes 0/152,214 · 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
- MRPL12
- Protein
- p.Ser80=
- Coding
- c.240A>C
- MANE Select
- NM_002949
- Type
- single nucleotide variant
- Location
- chr17:81704409 (GRCh38)
- Gene constraint
- LOEUF 1.048 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 67.55 · 46 PDB
- Residue 80
- an α-helix
Similar variants
- MRPL12 p.Ala124Pro Uncertain significance ★★ ⚠ same type
- MRPL12 p.Ala124Val Uncertain significance ★★ ⚠ same type
- MRPL12 p.Ala33Thr Uncertain significance ★★ ⚠ same type
- MRPL12 p.Arg127Trp Uncertain significance ★★ ⚠ same type
- MRPL12 p.Arg133His Uncertain significance ★★ ⚠ same type
- MRPL12 p.Ile149Val Uncertain significance ★★ ⚠ same type
- MRPL12 p.Leu76Pro Uncertain significance ★★ ⚠ same type
- MRPL12 p.Pro12Arg Uncertain significance ★★ ⚠ 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/mrpl12-p-ser80 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown