PMP2 p.Ile84=
c.252C>T · rs149339630 · VCV1619091
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0111%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.002 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.69 | GERP -4.7 |
| Overall | ||
| CADD | 2.75 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0111%
East Asian · 5/44,862 alleles
Filtering AF
0.00435%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00276%
Overall
0.00118%
19/1,611,400 alleles · ultra-rare
exomes 15/1,459,142 · genomes 4/152,258 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0111% | 8,972 |
| African / African-American | 0.004% | 24,983 |
| South Asian | 0.00332% | 30,144 |
| European (non-Finnish) | 0.000679% | 147,326 |
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.Ile84=
- Coding
- c.252C>T
- MANE Select
- NM_002677
- dbSNP
- rs149339630
- Type
- single nucleotide variant
- Location
- chr8:81444596 (GRCh38)
- Gene constraint
- LOEUF 1.511 · pLI 0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 96.49 · 30 PDB
- Residue 84
- a β-strand
Similar variants
- PMP2 p.Ile84Met 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-ile84 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown