CPE p.Gln69=
c.207G>A · rs770785440 · VCV2742048
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0278%, 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 1.9 | GERP -0.17, phastCons 1 |
| Overall | ||
| CADD | 10.41 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0278%
European (non-Finnish) · 328/1,178,946 alleles
Filtering AF
0.0253%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0243%
Overall
0.0217%
350/1,610,232 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0278% | 3,594 |
| Finnishnot grpmax-eligible | 0.0112% | 8,922 |
| South Asian | 0.00883% | 11,324 |
| Remaining individualsnot grpmax-eligible | 0.00803% | 12,450 |
| Admixed American | 0.00167% | 59,868 |
| African / African-American | 0.00134% | 74,892 |
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.Gln69=
- Coding
- c.207G>A
- MANE Select
- NM_001873
- dbSNP
- rs770785440
- Type
- single nucleotide variant
- Location
- chr4:165379428 (GRCh38)
- Gene constraint
- LOEUF 0.565 · pLI 0.83 (gnomAD)
- Structure
- AlphaFold pLDDT 90.83
- Residue 69
- the peptidase m14 domain
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-gln69 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown