MRPL12 p.Pro109=
c.327T>C · VCV4701809
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00334%, amr)
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 -2 | GERP -0.99 |
| Overall | ||
| CADD | 5.84 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00334%
Admixed American · 2/59,958 alleles
Filtering AF
0.000553%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000207%
Overall
0.000186%
3/1,613,362 alleles · very rare
exomes 2/1,461,164 · genomes 1/152,198 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00334% | 29,979 |
| European (non-Finnish) | 8.48e-05% | 1,179,697 |
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.Pro109=
- Coding
- c.327T>C
- MANE Select
- NM_002949
- Type
- single nucleotide variant
- Location
- chr17:81704698 (GRCh38)
- Gene constraint
- LOEUF 1.048 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 67.55 · 46 PDB
Similar variants
- MRPL12 p.Pro109Leu Uncertain significance ★ ⚠ same residue
- 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
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-pro109 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown