Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.86%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Overall | ||
| CADD | 7.641 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.86%
African / African-American · 1,394/74,966 alleles
Filtering AF
1.78%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.75%
Overall
0.108%
1,744/1,612,700 alleles · low-frequency
exomes 924/1,460,574 · genomes 820/152,126 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.86% | 54 |
| South Asian | 0.181% | 552 |
| Admixed American | 0.14% | 714 |
| Remaining individualsnot grpmax-eligible | 0.126% | 791 |
| Middle Eastern | 0.033% | 3,031 |
| European (non-Finnish) | 0.0017% | 58,990 |
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
- MPG
- Protein
- p.Asp31=
- Coding
- c.93C>T
- MANE Select
- NM_001015052
- dbSNP
- rs2266605
- Type
- single nucleotide variant
- Location
- chr16:79493 (GRCh38)
- Gene constraint
- LOEUF 1.468 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.08 · 9 PDB
- Residue 31
- the 'disordered' region
Similar variants
- MPG p.Val280Ile Uncertain significance ★★ ⚠ same type
- MPG p.Ala200Thr Uncertain significance ★ ⚠ same type
- MPG p.Ala21Pro Uncertain significance ★ ⚠ same type
- MPG p.Ala221Ser Uncertain significance ★ ⚠ same type
- MPG p.Ala255Val Uncertain significance ★ ⚠ same type
- MPG p.Ala96Glu Uncertain significance ★ ⚠ same type
- MPG p.Arg104Gln Uncertain significance ★ ⚠ same type
- MPG p.Arg105Gln 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/mpg-p-asp31 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown