PMP2 p.Asp19=
c.57T>C · rs756762402 · VCV2960965
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00187%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.2 | GERP -4.8, phastCons 0.53 |
| Overall | ||
| CADD | 3.791 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00187%
European (non-Finnish) · 22/1,179,506 alleles
Filtering AF
0.00122%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00104%
Overall
0.00136%
22/1,613,612 alleles · very rare
exomes 22/1,461,284 · genomes 0/152,328 · 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.Asp19=
- Coding
- c.57T>C
- MANE Select
- NM_002677
- dbSNP
- rs756762402
- Type
- single nucleotide variant
- Location
- chr8:81447330 (GRCh38)
- Gene constraint
- LOEUF 1.511 · pLI 0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 96.49 · 30 PDB
- Residue 19
- an α-helix
Similar variants
- PMP2 p.Asp19Asn 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.Asp48Asn Uncertain significance ★★ ⚠ same type
- PMP2 p.Glu130Lys 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-asp19 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown