MPZ p.Thr139del
c.415_417del · rs2526237721 · VCV2841808
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no gnomAD frequency available for this variant
Conditions
1
Charcot-Marie-Tooth disease type 1
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 9.3 | GERP -0.69, 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.Thr139del
- Coding
- c.415_417del
- MANE Select
- NM_000530
- dbSNP
- rs2526237721
- Type
- Deletion
- Location
- chr1:161306739 (GRCh38)
- Gene constraint
- LOEUF 0.708 · pLI 0.11 · ClinGen HI 2/3 (gnomAD)
- Structure
- AlphaFold pLDDT 82.38 · 2 PDB
- Residue 139
- a β-strand; the ig-like v-type domain; a UniProt-annotated variant site (in cmt1b)
Similar variants
- MPZ p.Asp104fs Pathogenic/Likely pathogenic ★★ same condition
- MPZ p.Ile162fs Pathogenic/Likely pathogenic ★★ same condition
- MPZ p.Leu144fs Pathogenic ★★ same condition
- MPZ p.Pro26fs 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.Gly213fs 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-thr139del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown