MPV17 p.Arg41=
c.123G>C · rs1679519053 · VCV1636015
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.177 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP 0.14 | GERP -0.37, phastCons 0.94 |
| Overall | ||
| CADD | 13.69 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- MPV17
- Protein
- p.Arg41=
- Coding
- c.123G>C
- MANE Select
- NM_002437
- dbSNP
- rs1679519053
- Type
- single nucleotide variant
- Location
- chr2:27313057 (GRCh38)
- Gene constraint
- LOEUF 1.368 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.23
- Residue 41
- a UniProt-annotated variant site (in cmt2ee); a UniProt-annotated variant site (in mtdps6)
Similar variants
- MPV17 p.Arg41Gln Pathogenic/Likely pathogenic ★★ ⚠ same residue
- MPV17 p.Arg41Trp Conflicting classifications of pathogenicity ★ ⚠ same residue
- MPV17 p.Arg41fs Pathogenic same residue
- 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
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-arg41 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown