MTMR2 p.Val124del
c.370_372del · rs2135475047 · VCV1347794
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.48e-05%, nfe)
Conditions
1
Charcot-Marie-Tooth disease type 4
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 3.6 | GERP -0.84, phastCons 1 |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.48e-05%
European (non-Finnish) · 1/1,179,724 alleles
Overall
6.2e-05%
1/1,613,738 alleles · very rare
exomes 1/1,461,410 · genomes 0/152,328 · 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
- MTMR2
- Protein
- p.Val124del
- Coding
- c.370_372del
- MANE Select
- NM_016156
- dbSNP
- rs2135475047
- Type
- Deletion
- Location
- chr11:95862088 (GRCh38)
- Gene constraint
- LOEUF 0.9 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.44 · 5 PDB
- Residue 124
- the gram domain; a β-strand
Similar variants
- MTMR2 p.Lys256fs Pathogenic/Likely pathogenic ★★ same condition
- MTMR2 p.Ser455fs Pathogenic/Likely pathogenic ★★ same condition
- MTMR2 p.Val639fs Uncertain significance ★★ same condition
- MTMR2 c.1770+7_1770+12del Benign/Likely benign ★★ same condition
- MTMR2 p.Arg62del Benign/Likely benign ★★ same condition
- MTMR2 c.1479+1_1479+2del Likely pathogenic ★ same condition
- MTMR2 p.Asn345fs Pathogenic ★ same condition
- MTMR2 p.Asp485fs 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/mtmr2-p-val124del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown