CDH20
Chr 18cadherin 20
Also known as: CDH7L3, Cdh7
CDH20 encodes cadherin-20, a calcium-dependent cell adhesion glycoprotein that establishes and maintains specific neuronal connections in the brain through cell-cell adhesion mediated by five extracellular cadherin repeats. Mutations cause neurodevelopmental disorders with intellectual disability and seizures, inherited in an autosomal dominant pattern. The gene shows significant constraint against loss-of-function variants (LOEUF 0.411), indicating that complete loss of protein function is likely deleterious.
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
More LoF-intolerant than ~75% of genes
Mild missense constraint
This gene has evidence for multiple mechanisms of pathogenicity (dominant-negative and gain-of-function). Both the Badonyi & Marsh prediction and the broader genomic evidence point to dominant-negative as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.
Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.
Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.
ClinVar Variant Classifications
194 submitted variants in ClinVar
Classification Summary
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | 0 | 0 | 74 | 0 | 74 |
Likely Pathogenic | 0 | 0 | 5 | 0 | 5 |
VUS | 0 | 105 | 2 | 0 | 107 |
Likely Benign | 0 | 0 | 0 | 3 | 3 |
Benign | 0 | 0 | 0 | 1 | 1 |
| Total | 0 | 105 | 81 | 4 | 190 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
CDH20 · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
External Resources
Links to major genomics databases and tools
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
No active trials found for this gene.
Search ClinicalTrials.gov →External Resources
Links to major genomics databases and tools