MTMR2 p.Ala15=
c.45G>A · rs1178277093 · VCV2196947
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00382%, amr)
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 · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.2 | GERP -2.5, phastCons 0.001 |
| Overall | ||
| CADD | 10.49 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00382%
Admixed American · 2/52,368 alleles
Filtering AF
0.000633%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000237%
Overall
0.000142%
2/1,407,336 alleles · very rare
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.Ala15=
- Coding
- c.45G>A
- MANE Select
- NM_016156
- dbSNP
- rs1178277093
- Type
- single nucleotide variant
- Location
- chr11:95923910 (GRCh38)
- Gene constraint
- LOEUF 0.9 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.44 · 5 PDB
- Residue 15
- the 'disordered' region
Similar variants
- MTMR2 c.804+2T>G Likely pathogenic ★★ same condition
- MTMR2 p.Arg162Ter Pathogenic ★★ same condition
- MTMR2 p.Arg364Ter Pathogenic ★★ same condition
- MTMR2 p.Glu531Ter Pathogenic ★★ same condition
- MTMR2 p.Glu574Ter Pathogenic/Likely pathogenic ★★ same condition
- MTMR2 c.262+4C>T Uncertain significance ★★ same condition
- MTMR2 p.Ala397Gly Uncertain significance ★★ ⚠ same condition
- MTMR2 p.Ala497Thr Uncertain significance ★★ ⚠ 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-ala15 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown