MFN2 p.Val69=
c.207T>C · rs759973329 · VCV2116193
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
Charcot-Marie-Tooth disease type 2
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 -4.3 | GERP -5.5 |
| Overall | ||
| CADD | 1.471 | 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
- MFN2
- Protein
- p.Val69=
- Coding
- c.207T>C
- MANE Select
- NM_014874
- dbSNP
- rs759973329
- Type
- single nucleotide variant
- Location
- chr1:11992586 (GRCh38)
- Gene constraint
- LOEUF 0.602 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 81.94 · 3 PDB
- Residue 69
- a UniProt-annotated variant site (in cmt2a2a; uncertain significance); the 'part of a helix bundle domain, formed by helices from n-terminal and c-terminal regions' region
Similar variants
- MFN2 p.Val69Ile Conflicting classifications of pathogenicity ★ ⚠ same residue
- MFN2 p.Val69Phe Pathogenic ⚠ same residue
- MFN2 c.1160+1G>A Likely pathogenic ★★ same condition
- MFN2 c.475-1G>C Pathogenic ★★ same condition
- MFN2 p.Ala166Val Pathogenic/Likely pathogenic ★★ ⚠ same condition
- MFN2 p.Ala220Thr Pathogenic/Likely pathogenic ★★ same condition
- MFN2 p.Ala383Val Pathogenic/Likely pathogenic ★★ ⚠ same condition
- MFN2 p.Ala738Val Pathogenic/Likely pathogenic ★★ ⚠ same condition
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/mfn2-p-val69 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown