Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.8%, afr)
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 -0.8 | |
| Overall | ||
| CADD | 2.279 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.8%
African / African-American · 1,346/74,960 alleles
Filtering AF
1.72%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.68%
Overall
0.0938%
1,510/1,610,426 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.8% | 56 |
| Admixed American | 0.135% | 743 |
| Remaining individualsnot grpmax-eligible | 0.106% | 945 |
| Middle Eastern | 0.033% | 3,029 |
| European (non-Finnish) | 0.00127% | 78,576 |
| South Asian | 0.0011% | 90,822 |
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.Pro63=
- Coding
- c.189G>A
- MANE Select
- NM_001015052
- dbSNP
- rs2266606
- Type
- single nucleotide variant
- Location
- chr16:79589 (GRCh38)
- Gene constraint
- LOEUF 1.468 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.08 · 9 PDB
- Residue 63
- 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-pro63 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown