PMP2 p.Val123=
c.369G>A · VCV3677720
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00239%, nfe)
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 |
|---|---|---|
| Pangolin | Δ0.26 | loss · gain 0.00 · not in the SpliceAI release · independent |
| Constraint at this position | ||
| Conservation | phyloP 1.3 | GERP -2.5, phastCons 0.97 |
| Overall | ||
| CADD | 8.014 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00239%
European (non-Finnish) · 28/1,172,794 alleles
Filtering AF
0.00166%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00143%
Overall
0.00175%
28/1,600,062 alleles · very rare
exomes 28/1,447,956 · genomes 0/152,106 · 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
- PMP2
- Protein
- p.Val123=
- Coding
- c.369G>A
- MANE Select
- NM_002677
- Type
- single nucleotide variant
- Location
- chr8:81443428 (GRCh38)
- Gene constraint
- LOEUF 1.511 · pLI 0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 96.49 · 30 PDB
- Residue 123
- a β-strand
Similar variants
- PMP2 p.Val123Met Uncertain significance ★ ⚠ same residue
- PMP2 p.Ile43Asn Pathogenic/Likely pathogenic ★★ same type
- PMP2 p.Ile52Thr Pathogenic/Likely pathogenic ★★ same type
- PMP2 p.Ala116= Uncertain significance ★★ same type
- PMP2 p.Arg53Gln Uncertain significance ★★ ⚠ same type
- PMP2 p.Asn60Thr Uncertain significance ★★ ⚠ same type
- PMP2 p.Asp19Asn Uncertain significance ★★ ⚠ same type
- PMP2 p.Asp48Asn Uncertain significance ★★ ⚠ same type
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/pmp2-p-val123 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown