MTMR2 p.Lys89Thr
c.266A>C · VCV4805179
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
AlphaMissense
ambiguous
0.5343 · ACMG-weighted
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
Charcot-Marie-Tooth disease type 4
Computational evidence
| Protein change | ||
| AlphaMissense | 0.5343 | ambiguous |
|---|---|---|
| REVEL | 0.403 | indeterminate |
| SaProt | LLR -7.58 | tolerated |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 7.9 | GERP 2.2, phastCons 1 |
| Regional constraint | o/e 0.74 | unconstrained · MANE · 47 kb · p 1.3e-09 · regional, not allelic |
| Overall | ||
| CADD | 26.8 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
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
- MTMR2
- Protein
- p.Lys89Thr
- Coding
- c.266A>C
- MANE Select
- NM_016156
- Type
- single nucleotide variant
- Location
- chr11:95862363 (GRCh38)
- Gene constraint
- LOEUF 0.9 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.44 · 5 PDB
- Residue 89
- the gram domain; a β-strand
Similar variants
- MTMR2 p.Lys89Glu 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-lys89thr (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown