MPEG1 p.Cys577=
c.1731C>T · VCV4911743
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.362%, 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 -5.3 | GERP -3.4 |
| Overall | ||
| CADD | 0.122 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.362%
African / African-American · 272/75,042 alleles
Filtering AF
0.327%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.313%
Overall
0.129%
2,087/1,614,178 alleles · rare
exomes 1,793/1,461,882 · genomes 294/152,296 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.362% | 276 |
| Admixed American | 0.137% | 732 |
| European (non-Finnish) | 0.136% | 735 |
| Ashkenazi Jewishnot grpmax-eligible | 0.125% | 800 |
| Remaining individualsnot grpmax-eligible | 0.0992% | 1,008 |
| Middle Eastern | 0.033% | 3,031 |
| South Asian | 0.0176% | 5,693 |
| Finnishnot grpmax-eligible | 0.0141% | 7,114 |
| East Asian | 0.00223% | 44,880 |
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
- MPEG1
- Protein
- p.Cys577=
- Coding
- c.1731C>T
- MANE Select
- NM_001039396
- Type
- single nucleotide variant
- Location
- chr11:59211135 (GRCh38)
- Gene constraint
- LOEUF 1.941 · pLI 0.02 (gnomAD)
- Structure
- AlphaFold pLDDT 83.22 · 5 PDB
- Residue 577
- a disulfide bond; a UniProt-annotated variant site (in imd77; decreased defense response to bacterium); a β-strand; the 'p2' region
Similar variants
- MPEG1 p.Ala525Val Uncertain significance ★★ ⚠ same type
- MPEG1 p.Gln259Glu Uncertain significance ★★ ⚠ same type
- MPEG1 p.Gln713Arg Uncertain significance ★★ ⚠ same type
- MPEG1 p.His420Tyr Uncertain significance ★★ ⚠ same type
- MPEG1 p.Ala467= Benign ★★ same type
- MPEG1 p.Thr73Ala Likely benign ★★ same type
- MPEG1 p.Ala238Thr Uncertain significance ★ ⚠ same type
- MPEG1 p.Ala238Val 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/mpeg1-p-cys577 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown