MPZ p.Lys201Ter
c.601A>T · rs2526234318 · VCV2016722
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
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. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function |
|---|---|---|
| NMD | escapes | premature termination codon within the last 50 nt of the penultimate exon (5 of 6, 44 nt from its 3' end) — the truncated protein is likely expressed. PVS1 input, not an applied code |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 2.3 | GERP 1.4, phastCons 0.88 |
| Overall | ||
| CADD | 39.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
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
- MPZ
- Protein
- p.Lys201Ter
- Coding
- c.601A>T
- MANE Select
- NM_000530
- dbSNP
- rs2526234318
- Type
- single nucleotide variant
- Location
- chr1:161306152 (GRCh38)
- Gene constraint
- LOEUF 0.708 · pLI 0.11 · ClinGen HI 2/3 (gnomAD)
- Structure
- AlphaFold pLDDT 82.38 · 2 PDB
Similar variants
- 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
- MPZ c.68-2A>C 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-lys201ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown