CDH2 p.Pro642fs
c.1925_1928del · VCV3349134
Uncertain significance
No assertion criteria
Classification
Uncertain significance
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
CDH2-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function in a LoF-intolerant gene |
|---|---|---|
| NMD | predicted | premature termination codon in exon 12 of 16 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 0.86 | GERP -2.6, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- CDH2
- Protein
- p.Pro642fs
- Coding
- c.1925_1928del
- MANE Select
- NM_001792
- Type
- Deletion
- Location
- chr18:27985575 (GRCh38)
- Gene constraint
- LOEUF 0.336 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 79.68
- Residue 642
- the cadherin 5 domain
Disease context
CDH2-related disorder
Similar variants
- CDH2 p.Pro642Ser Uncertain significance ★★ ⚠ same residue
- CDH2 p.Pro642Ala Uncertain significance ★ ⚠ same residue
- CDH2 p.Tyr676Cys Pathogenic ★★ same condition
- CDH2 p.Ala673Gly Uncertain significance ★ ⚠ same condition
- CDH2 p.Asp407Asn Conflicting classifications of pathogenicity ★ ⚠ same condition
- CDH2 p.Gly199Val Uncertain significance ★ ⚠ same condition
- CDH2 p.Lys669Asn Uncertain significance ★ ⚠ same condition
- CDH2 p.Asn601Thr Pathogenic 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/cdh2-p-pro642fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown