CDH1 p.Pro3Phe
c.7_8delinsTT · VCV4868397
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
Conditions
1
hereditary neoplastic syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.14 | GERP -2.5, phastCons 0.17 |
| Regional constraint | o/e 1.05 | unconstrained · MANE · 71 kb · p 0.52 · regional, not allelic |
Variant & gene context
- Gene
- CDH1
- Protein
- p.Pro3Phe
- Coding
- c.7_8delinsTT
- MANE Select
- NM_004360
- Type
- Indel
- Location
- chr16:68737422 (GRCh38)
- Gene constraint
- LOEUF 0.514 · pLI 0.86 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 79.13 · 22 PDB
Similar variants
- CDH1 p.Pro3Ser Uncertain significance ★★★ ⚠ same residue
- CDH1 p.Pro3Arg Likely benign ★★★ same residue
- CDH1 p.Pro3Thr Uncertain significance ★★ ⚠ same residue
- CDH1 p.Pro3= Likely benign ★ same residue
- CDH1 p.Pro42fs Pathogenic ★★★ same condition
- CDH1 p.Ala137Arg Uncertain significance ★★ same condition
- CDH1 p.Asp805Ser Uncertain significance ★★ same condition
- CDH1 p.Gly693Asp Uncertain significance ★★ same condition
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/cdh1-p-pro3phe (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown