CPE p.Pro387=
c.1161A>C · VCV3772284
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.47e-05%, 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 |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -2.9 | GERP -4.1 |
| Overall | ||
| CADD | 1.656 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.47e-05%
European (non-Finnish) · 1/1,179,984 alleles
Overall
6.84e-05%
1/1,461,822 alleles · very rare
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
- CPE
- Protein
- p.Pro387=
- Coding
- c.1161A>C
- MANE Select
- NM_001873
- Type
- single nucleotide variant
- Location
- chr4:165493218 (GRCh38)
- Gene constraint
- LOEUF 0.565 · pLI 0.83 (gnomAD)
- Structure
- AlphaFold pLDDT 90.83
- Residue 387
- a UniProt-annotated variant site (in bdvs)
Similar variants
- CPE p.Arg121Ter Pathogenic ★★ same type
- CPE p.Arg262Trp Uncertain significance ★★ ⚠ same type
- CPE p.Arg297Trp Uncertain significance ★★ ⚠ same type
- CPE p.Asp251Gly Uncertain significance ★★ ⚠ same type
- CPE p.Asp304Ala Uncertain significance ★★ ⚠ same type
- CPE p.Trp21Cys Uncertain significance ★★ ⚠ same type
- CPE c.307+13C>T Likely benign ★★ same type
- CPE c.672+11C>T Likely benign ★★ 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/cpe-p-pro387 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown