MPV17 p.Val149=
c.447C>T · rs769048578 · VCV1554914
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000254%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.083 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.22 | GERP -2.4, phastCons 0.84 |
| Overall | ||
| CADD | 6.572 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000254%
European (non-Finnish) · 3/1,179,978 alleles
Filtering AF
6.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.9e-05%
Overall
0.000186%
3/1,613,746 alleles · very rare
exomes 3/1,461,542 · genomes 0/152,204 · joint denominator
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
- MPV17
- Protein
- p.Val149=
- Coding
- c.447C>T
- MANE Select
- NM_002437
- dbSNP
- rs769048578
- Type
- single nucleotide variant
- Location
- chr2:27311913 (GRCh38)
- Gene constraint
- LOEUF 1.368 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.23
- Residue 149
- a UniProt-annotated variant site (in mtdps6)
Similar variants
- MPV17 c.186+2T>C Pathogenic/Likely pathogenic ★★ same type
- MPV17 c.279+1G>T Pathogenic ★★ same type
- MPV17 c.375+1G>A Likely pathogenic ★★ same type
- MPV17 c.375+1G>T Likely pathogenic ★★ same type
- MPV17 c.375+2T>C Likely pathogenic ★★ same type
- MPV17 c.376-1G>A Pathogenic/Likely pathogenic ★★ same type
- MPV17 c.376-2A>C Pathogenic/Likely pathogenic ★★ same type
- MPV17 c.408+1G>A Pathogenic/Likely 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/mpv17-p-val149 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown