CDH26
protein-codingcadherin 26, the group of Major cadherins
Gene summary
This gene encodes a member of the cadherin protein family. Cadherins are a family of calcium-dependent adhesion molecules that mediate cell-cell adhesion in all solid tissues and modulate a wide variety of processes, including cell polarization, migration and differentiation. Cadherin domains occur as repeats in the extracellular region and are thought to contribute to the sorting of heterogeneous cell types and the maintenance of orderly structures such as epithelium. This protein is expressed in gastrointestinal epithelial cells and may be upregulated during allergic inflammation. This protein interacts with alpha integrins and may also be involved in leukocyte migration and adhesion. [provided by RefSeq, Jan 2017]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~75.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CDH26 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_177980.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 153 | 10 | 163 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 154 | 10 | 0 | 164 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_817089.1 | 18 | MANE Select | |
| Ensembl | ENSP00000339390.4 | 18 | MANE Select | |
| RefSeq | NP_001335133.1 | 4 | Standard | |
| RefSeq | NP_068582.2 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- cell morphogenesis
- cell-cell junction assembly
- homophilic cell adhesion via plasma membrane adhesion molecules
- calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules
- adherens junction organization
Molecular Function
- integrin binding
- calcium ion binding
- protein binding
- beta-catenin binding
- cytoskeletal protein binding
Cellular Component
- plasma membrane
- cell-cell adherens junction
- cell surface
- integral component of membrane
- catenin complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000348616
- Coding exons
- 18
- Length
- 75596
- Individuals with no LoFs
- 125293
- Homozygous LoFs
- 3
- Heterozygous LoFs
- 452
- Defined
- 125748
- p
- 0.00181
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.282 | 460 | 477 | 0.964 | 0.0000263 | 5425 |
| Missense (PolyPhen) | 124 | 129.09 | 0.96057 | 1650 | ||
| Synonymous | 0.204 | 188 | 192 | 0.981 | 0.0000116 | 1666 |
| Loss of Function | 0.297 | 40 | 42.1 | 0.951 | 0.00000245 | 451 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0016 | 0.0016 | notable |
| Latino/Admixed American | 0.0021 | 0.0021 | notable |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.0022 | 0.0022 | notable |
| Finnish | 0.00023 | 0.00023 | rare |
| European (Non-Finnish) | 0.0013 | 0.0013 | notable |
| South Asian | 0.0048 | 0.0047 | notable |
| Other | 0.0028 | 0.0026 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Cadherins are calcium-dependent cell adhesion proteins. They preferentially interact with themselves in a homophilic manner in connecting cells; cadherins may thus contribute to the sorting of heterogeneous cell types. Ligand for integrins alpha- E/beta-7, ITGAE:ITGAB7, alpha-4/beta-7, ITGA4:ITGAB7 and alpha- 4/beta-1, ITGA4:ITGAB1 through which modulates CD4(+) T cells activation (PubMed:28051089). {ECO:0000269|PubMed:28051089}.;
Recessive Scores
- pRec
- 0.0683
Intolerance Scores
- LoFtool
- 0.981
- RVIS EVS
- 0.92
- RVIS percentile EVS
- 89.58
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.173
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |