PMPCB p.Ala256=
c.768A>G · VCV3712563
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.1%, eas)
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 -2.1 | GERP -3.4 |
| Overall | ||
| CADD | 1.537 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.1%
East Asian · 493/44,862 alleles
Filtering AF
1.02%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.987%
Overall
0.0309%
498/1,613,022 alleles · low-frequency
exomes 475/1,460,660 · genomes 23/152,362 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 1.1% | 91 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,492 |
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.Ala256=
- Coding
- c.768A>G
- MANE Select
- NM_004279
- Type
- single nucleotide variant
- Location
- chr7:103307627 (GRCh38)
- Gene constraint
- LOEUF 1.085 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.48
Similar variants
- 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
- PMPCB p.Ile221Val 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-ala256 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown