CDH13
protein-codingcadherin 13, the group of Major cadherins|MicroRNA protein coding host genes
Gene summary
This gene encodes a member of the cadherin superfamily. The encoded protein is localized to the surface of the cell membrane and is anchored by a GPI moiety, rather than by a transmembrane domain. The protein lacks the cytoplasmic domain characteristic of other cadherins, and so is not thought to be a cell-cell adhesion glycoprotein. This protein acts as a negative regulator of axon growth during neural differentiation. It also protects vascular endothelial cells from apoptosis due to oxidative stress, and is associated with resistance to atherosclerosis. The gene is hypermethylated in many types of cancer. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, May 2011]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~1,173.7 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 CDH13 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001257.5. 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 | 1 | 19 | 5 | 25 | ||
| missense | 124 | 9 | 1 | 134 | ||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 128 | 28 | 6 | 162 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001248.1 | 14 | MANE Select | |
| Ensembl | ENSP00000479395.1 | 14 | MANE Select | |
| RefSeq | NP_001207417.1 | 15 | Standard | |
| RefSeq | NP_001207418.1 | 13 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Pathways in clear cell renal cell carcinoma
- Cell-cell junction organization
- Adherens junctions interactions
- Cell junction organization
- Cell-Cell communication
Biological Process
- mitotic cell cycle
- cell morphogenesis
- positive regulation of endothelial cell proliferation
- positive regulation of cell-matrix adhesion
- sprouting angiogenesis
Molecular Function
- calcium ion binding
- cytoskeletal protein binding
- low-density lipoprotein particle binding
- protein homodimerization activity
- cadherin binding
Cellular Component
- extracellular region
- extracellular space
- cytoplasm
- plasma membrane
- caveola
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000268613
- Coding exons
- 15
- Length
- 1169797
- Individuals with no LoFs
- 124641
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 13
- Defined
- 124654
- p
- 0.0000521
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.533 | 480 | 448 | 1.07 | 0.0000253 | 4971 |
| Missense (PolyPhen) | 125 | 177.7 | 0.70344 | 1989 | ||
| Synonymous | -5.05 | 268 | 181 | 1.48 | 0.0000114 | 1525 |
| Loss of Function | 3.29 | 11 | 30.7 | 0.359 | 0.00000148 | 371 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000069 | 0.000065 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.00010 | 0.000097 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
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. May act as a negative regulator of neural cell growth. {ECO:0000269|PubMed:10737605}.;
Recessive Scores
- pRec
- 0.403
Intolerance Scores
- LoFtool
- 0.493
- RVIS EVS
- 0.31
- RVIS percentile EVS
- 72.23
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0882
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |