MPG p.Val259=
c.777C>T · VCV4872041
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0169%, mid)
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 -4 | |
| Overall | ||
| CADD | 0.693 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0169%
Middle Eastern · 1/5,932 alleles
Filtering AF
0.0093%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00729%
Overall
0.00558%
88/1,577,780 alleles · ultra-rare
exomes 76/1,425,556 · genomes 12/152,224 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0169% | 5,932 |
| African / African-American | 0.0162% | 6,178 |
| European (non-Finnish) | 0.00587% | 17,032 |
| Admixed American | 0.00352% | 28,415 |
| Remaining individualsnot grpmax-eligible | 0.0033% | 30,346 |
| South Asian | 0.00229% | 43,599 |
| East Asian | 0.00226% | 44,282 |
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.Val259=
- Coding
- c.777C>T
- MANE Select
- NM_001015052
- Type
- single nucleotide variant
- Location
- chr16:85672 (GRCh38)
- Gene constraint
- LOEUF 1.468 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.08 · 9 PDB
- Residue 259
- a β-strand
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-val259 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown