MVD p.Phe252=
c.756C>T · VCV4931745
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00535%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.259 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -2.8 | GERP -3.6 |
| Overall | ||
| CADD | 0.709 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00535%
African / African-American · 4/74,730 alleles
Filtering AF
0.00175%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00104%
Overall
0.00106%
17/1,602,260 alleles · very rare
exomes 13/1,450,010 · genomes 4/152,250 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00535% | 18,683 |
| East Asian | 0.00226% | 44,268 |
| South Asian | 0.00225% | 44,508 |
| Remaining individualsnot grpmax-eligible | 0.00161% | 62,008 |
| European (non-Finnish) | 0.000766% | 130,547 |
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.Phe252=
- Coding
- c.756C>T
- MANE Select
- NM_002461
- Type
- single nucleotide variant
- Location
- chr16:88655340 (GRCh38)
- Gene constraint
- LOEUF 1.706 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.52 · 1 PDB
- Residue 252
- 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 p.Pro77= 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
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-phe252 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown