Is MTMR2 p.Val414fs (c.1239_1240del) pathogenic?

MTMR2 p.Val414fs (c.12391240del) is classified Pathogenic in MTMR2 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-11-03). No gnomAD frequency available for this variant; Associated with Charcot-Marie-Tooth disease type 4.

What condition is associated with MTMR2 p.Val414fs (c.1239_1240del)?

MTMR2 p.Val414fs (c.1239_1240del) is associated with Charcot-Marie-Tooth disease type 4 (ClinVar).

How common is MTMR2 p.Val414fs (c.1239_1240del) in the general population?

MTMR2 p.Val414fs (c.1239_1240del) is no gnomAD frequency available for this variant (gnomAD).

MTMR2 p.Val414fs

c.1239_1240del · rs1863723947 · VCV962824

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Charcot-Marie-Tooth disease type 4

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 11 of 15
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 11	GERP 2.8, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: MTMR2
Protein: p.Val414fs
Coding: c.1239_1240del
MANE Select: NM_016156
dbSNP: rs1863723947
Type: Deletion
Location: chr11:95845099 (GRCh38)
Gene constraint: LOEUF 0.9 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 89.44 · 5 PDB
Residue 414: the myotubularin phosphatase domain; a β-strand

Full MTMR2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Charcot-Marie-Tooth disease type 4 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

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-val414fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown