MPZ p.Leu202=
c.606G>A · rs2526234286 · VCV2717976
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00446%, eas)
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 · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.48 | GERP 0.32, phastCons 0.99 |
| Overall | ||
| CADD | 13.01 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00446%
East Asian · 2/44,878 alleles
Filtering AF
0.000739%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000276%
Overall
0.000124%
2/1,614,224 alleles · very rare
exomes 2/1,461,890 · genomes 0/152,334 · 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.Leu202=
- Coding
- c.606G>A
- MANE Select
- NM_000530
- dbSNP
- rs2526234286
- Type
- single nucleotide variant
- Location
- chr1:161306147 (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-leu202 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown