MIA3 p.Pro181=
c.543A>G · VCV4823389
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.48e-05%, 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 -1.8 | GERP -3.7 |
| Overall | ||
| CADD | 3.422 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.48e-05%
European (non-Finnish) · 1/1,179,768 alleles
Overall
6.2e-05%
1/1,613,090 alleles · very rare
exomes 1/1,460,758 · genomes 0/152,332 · 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
- MIA3
- Protein
- p.Pro181=
- Coding
- c.543A>G
- MANE Select
- NM_198551
- Type
- single nucleotide variant
- Location
- chr1:222627763 (GRCh38)
- Gene constraint
- LOEUF 0.551 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 52.49 · 4 PDB
- Residue 181
- the 'disordered' region
Similar variants
- MIA3 p.Pro181Ala Uncertain significance ★ ⚠ same residue
- MIA3 p.Arg1696Gln Uncertain significance ★★ ⚠ same type
- MIA3 p.Arg1809His Uncertain significance ★★ ⚠ same type
- MIA3 p.Thr791Arg Uncertain significance ★★ ⚠ same type
- MIA3 p.Thr910Ala Uncertain significance ★★ ⚠ same type
- MIA3 p.Val648Ala Uncertain significance ★★ ⚠ same type
- MIA3 p.Leu1580= Likely benign ★★ same type
- MIA3 p.Ser903= 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/mia3-p-pro181 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown