PMPCB p.Asp228=
c.684T>C · rs143187508 · VCV2904016
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00134%, afr)
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 -0.37 | GERP -3.7, phastCons 0.16 |
| Overall | ||
| CADD | 7.311 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00134%
African / African-American · 1/74,754 alleles
Overall
6.23e-05%
1/1,604,558 alleles · very rare
exomes 0/1,452,384 · genomes 1/152,174 · 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
- PMPCB
- Protein
- p.Asp228=
- Coding
- c.684T>C
- MANE Select
- NM_004279
- dbSNP
- rs143187508
- Type
- single nucleotide variant
- Location
- chr7:103304438 (GRCh38)
- Gene constraint
- LOEUF 1.085 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.48
Similar variants
- PMPCB p.Asp228Asn Uncertain significance ★ ⚠ same residue
- PMPCB p.Arg175Cys Likely pathogenic ★★ same type
- PMPCB p.Arg209Gln Uncertain significance ★★ ⚠ same type
- PMPCB p.Arg325Cys Uncertain significance ★★ ⚠ same type
- PMPCB p.Arg451Ter Uncertain significance ★★ same type
- PMPCB p.Asn97Ser Uncertain significance ★★ ⚠ same type
- PMPCB p.Gln46Lys Uncertain significance ★★ ⚠ same type
- PMPCB p.Ile160Thr 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/pmpcb-p-asp228 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown