MVD p.Pro77=
c.231G>A · rs116232108 · VCV790170
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.94%, 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 -15 | GERP -3.8 |
| Overall | ||
| CADD | 0.595 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.94%
African / African-American · 2,209/75,064 alleles
Filtering AF
2.84%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.8%
Overall
0.177%
2,851/1,613,740 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.94% | 34 |
| Middle Eastern | 0.448% | 223 |
| Admixed American | 0.383% | 261 |
| Remaining individualsnot grpmax-eligible | 0.28% | 357 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0439% | 2,278 |
| European (non-Finnish) | 0.0157% | 6,378 |
| South Asian | 0.011% | 9,109 |
| East Asian | 0.00446% | 22,442 |
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
- MVD
- Protein
- p.Pro77=
- Coding
- c.231G>A
- MANE Select
- NM_002461
- dbSNP
- rs116232108
- Type
- single nucleotide variant
- Location
- chr16:88657940 (GRCh38)
- Gene constraint
- LOEUF 1.706 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.52 · 1 PDB
- Residue 77
- an α-helix
Similar variants
- MVD p.Phe249Ser Pathogenic ★★ same type
- MVD p.Thr120Met Uncertain significance ★★ ⚠ same type
- MVD p.Arg78= Benign ★★ same type
- MVD p.Lys368= Benign/Likely benign ★★ same type
- MVD c.1013+1G>T Pathogenic ★ same type
- MVD c.1014-1G>T Likely pathogenic ★ same type
- MVD p.Asn292Ser Pathogenic ★ ⚠ same type
- MVD c.1013+5G>T 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/mvd-p-pro77 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown