Is MPZ p.Val136Gly (c.407T>G) pathogenic?

MPZ p.Val136Gly (c.407T>G) is classified Uncertain significance in MPZ (ClinVar, Single submitter, 1 submitter; last evaluated 2021-12-14). AlphaMissense: ambiguous (0.5609); Very rare (popmax 8.47e-05%, nfe); Associated with Charcot-Marie-Tooth disease type 1.

What condition is associated with MPZ p.Val136Gly (c.407T>G)?

MPZ p.Val136Gly (c.407T>G) is associated with Charcot-Marie-Tooth disease type 1 (ClinVar).

How common is MPZ p.Val136Gly (c.407T>G) in the general population?

MPZ p.Val136Gly (c.407T>G) is very rare (popmax 8.47e-05%, nfe) (gnomAD).

What do computational predictors say about MPZ p.Val136Gly (c.407T>G)?

AlphaMissense predicts ambiguous (score 0.5609) — an in-silico prediction, not a clinical call.

MPZ p.Val136Gly

c.407T>G · rs1571818744 · VCV963646

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.5609 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 8.47e-05%, nfe)

Conditions

Charcot-Marie-Tooth disease type 1

Computational evidence

Protein change
AlphaMissense	0.5609	ambiguous
REVEL	0.514	indeterminate
SaProt	LLR -5.66	tolerated
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 1.8, phastCons 1
Regional constraint	o/e 0.69	unconstrained · MANE · 3,519 bp · p 4.1e-06 · regional, not allelic
Overall
CADD	25.9	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

Grpmax group 8.47e-05% European (non-Finnish) · 1/1,180,002 alleles

Overall 6.2e-05% 1/1,613,908 alleles · very rare exomes 1/1,461,884 · genomes 0/152,024 · 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: MPZ
Protein: p.Val136Gly
Coding: c.407T>G
MANE Select: NM_000530
dbSNP: rs1571818744
Type: single nucleotide variant
Location: chr1:161306749 (GRCh38)
Gene constraint: LOEUF 0.708 · pLI 0.11 · ClinGen HI 2/3 (gnomAD)
Structure: AlphaFold pLDDT 82.38 · 2 PDB
Residue 136: the ig-like v-type domain; a UniProt-annotated variant site (in dss)

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

Disease context

Charcot-Marie-Tooth disease type 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

MPZ p.Val136Glu Uncertain significance ★ ⚠ same residue
MPZ c.235-1G>T Pathogenic/Likely pathogenic ★★ same condition
MPZ c.448+1G>A Pathogenic/Likely pathogenic ★★ same condition
MPZ c.448+1G>T Likely pathogenic ★★ same condition
MPZ c.448+2T>G Likely pathogenic ★★ same condition
MPZ c.584+2T>G Pathogenic ★★ same condition
MPZ c.68-1G>A Pathogenic/Likely pathogenic ★★ same condition
MPZ c.68-1G>C Pathogenic/Likely 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/mpz-p-val136gly (accessed [today's date]).

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