MTMR2 p.Leu25=
c.75G>A · rs1376231939 · VCV543440
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.000261%, nfe)
Conditions
2
Inborn genetic diseases
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 1.9 | GERP -1.3, phastCons 1 |
| Overall | ||
| CADD | 13.93 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000261%
European (non-Finnish) · 3/1,148,972 alleles
Filtering AF
7e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.9e-05%
Overall
0.000214%
3/1,402,070 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.Leu25=
- Coding
- c.75G>A
- MANE Select
- NM_016156
- dbSNP
- rs1376231939
- Type
- single nucleotide variant
- Location
- chr11:95923880 (GRCh38)
- Gene constraint
- LOEUF 0.9 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.44 · 5 PDB
- Residue 25
- the 'disordered' region
Similar variants
- MTMR2 p.Leu25Phe Uncertain significance ★ ⚠ same residue
- 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
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-leu25 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown