CPE p.Thr261=
c.783G>A · rs80117208 · VCV721258
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 3.56%, 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 -20 | GERP -3.7 |
| Overall | ||
| CADD | 0.005 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.56%
East Asian · 1,594/44,794 alleles
Filtering AF
3.41%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.35%
Overall
0.127%
2,034/1,605,834 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 3.56% | 28 |
| Remaining individualsnot grpmax-eligible | 0.259% | 386 |
| Admixed American | 0.182% | 550 |
| South Asian | 0.145% | 688 |
| Middle Eastern | 0.0661% | 1,512 |
| African / African-American | 0.0107% | 9,356 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,550 |
| European (non-Finnish) | 0.00213% | 46,906 |
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.Thr261=
- Coding
- c.783G>A
- MANE Select
- NM_001873
- dbSNP
- rs80117208
- Type
- single nucleotide variant
- Location
- chr4:165482352 (GRCh38)
- Gene constraint
- LOEUF 0.565 · pLI 0.83 (gnomAD)
- Structure
- AlphaFold pLDDT 90.83
- Residue 261
- a UniProt-annotated variant site (in bdvs); the peptidase m14 domain
Similar variants
- CPE p.Thr261Met Uncertain significance ⚠ same residue
- 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
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-thr261 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown