Is MPZ p.Phe64del (c.190_192del) pathogenic?

MPZ p.Phe64del (c.190192del) is classified Likely pathogenic in MPZ (ClinVar, Single submitter, 2 submitters; last evaluated 2023-01-17). No gnomAD frequency available for this variant; Associated with Charcot-Marie-Tooth disease type 1B.

What condition is associated with MPZ p.Phe64del (c.190_192del)?

MPZ p.Phe64del (c.190_192del) is associated with Charcot-Marie-Tooth disease type 1B, Charcot-Marie-Tooth disease type 3 (ClinVar).

How common is MPZ p.Phe64del (c.190_192del) in the general population?

MPZ p.Phe64del (c.190_192del) is no gnomAD frequency available for this variant (gnomAD).

How is Charcot-Marie-Tooth disease type 1B inherited?

Typically Autosomal dominant (Orphanet). A genetic counselor can assess individual risk for a family.

MPZ p.Phe64del

c.190_192del · rs1571819975 · VCV637327

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Charcot-Marie-Tooth disease type 1B

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.9	GERP 1.8, phastCons 1

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: MPZ
Protein: p.Phe64del
Coding: c.190_192del
MANE Select: NM_000530
dbSNP: rs1571819975
Type: Deletion
Location: chr1:161307300 (GRCh38)
Gene constraint: LOEUF 0.708 · pLI 0.11 · ClinGen HI 2/3 (gnomAD)
Structure: AlphaFold pLDDT 82.38 · 2 PDB
Residue 64: a β-strand; a UniProt-annotated variant site (in cmt1b and dss); the ig-like v-type domain

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

Disease context

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

Also linked: Charcot-Marie-Tooth disease type 3

For Charcot-Marie-Tooth disease type 1B (Orphanet):

Inheritance: Autosomal dominant
Onset: Adolescent, Adult, Childhood, Infancy
Prevalence: 1-9 / 100 000 (Worldwide)

Similar variants

MPZ p.Arg186fs Pathogenic ★★ same condition
MPZ p.Asp104fs Pathogenic/Likely pathogenic ★★ same condition
MPZ p.Ser44fs Pathogenic/Likely pathogenic ★★ same condition
MPZ p.Ser63del Pathogenic ★★ same condition
MPZ p.Tyr145fs Pathogenic/Likely pathogenic ★★ same condition
MPZ p.Ala188fs Likely pathogenic ★ same condition
MPZ p.Ser11fs Pathogenic ★ same condition
MPZ c.646-10_650del Conflicting classifications of pathogenicity ★ 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-phe64del (accessed [today's date]).

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