CDH17
protein-codingcadherin 17, the group of 7D cadherins
Gene summary
This gene is a member of the cadherin superfamily, genes encoding calcium-dependent, membrane-associated glycoproteins. The encoded protein is cadherin-like, consisting of an extracellular region, containing 7 cadherin domains, and a transmembrane region but lacking the conserved cytoplasmic domain. The protein is a component of the gastrointestinal tract and pancreatic ducts, acting as an intestinal proton-dependent peptide transporter in the first step in oral absorption of many medically important peptide-based drugs. The protein may also play a role in the morphological organization of liver and intestine. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2009]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~90.1 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 CDH17 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_004063.4. 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 | 2 | 2 | 2 | 6 | ||
| missense | 130 | 7 | 2 | 139 | ||
| nonsense | 2 | 2 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 0 | 0 | 138 | 9 | 4 | 151 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_004054.3 | 17 | MANE Select | |
| Ensembl | ENSP00000027335.3 | 17 | MANE Select | |
| RefSeq | NP_001138135.1 | 17 | Standard | |
| RefSeq | NP_001400880.1 | 17 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Gastric cancer - Homo sapiens (human)
- Cell-cell junction organization
- Adherens junctions interactions
- Cell junction organization
- Cell-Cell communication
Biological Process
- cell morphogenesis
- germinal center B cell differentiation
- marginal zone B cell differentiation
- oligopeptide transport
- cell-cell junction assembly
Molecular Function
- integrin binding
- transporter activity
- proton-dependent oligopeptide secondary active transmembrane transporter activity
- calcium ion binding
- cytoskeletal protein binding
Cellular Component
- nucleus
- plasma membrane
- cell-cell adherens junction
- cell surface
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000027335
- Coding exons
- 17
- Length
- 90133
- Individuals with no LoFs
- 125582
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 164
- Defined
- 125746
- p
- 0.000652
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.351 | 438 | 459 | 0.954 | 0.0000238 | 5469 |
| Missense (PolyPhen) | 120 | 140.91 | 0.85158 | 1813 | ||
| Synonymous | -0.801 | 185 | 172 | 1.08 | 0.00000950 | 1620 |
| Loss of Function | 1.74 | 27 | 38.7 | 0.698 | 0.00000197 | 464 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0020 | 0.0020 | notable |
| Latino/Admixed American | 0.00059 | 0.00058 | rare |
| Ashkenazi Jewish | 0.00070 | 0.00069 | rare |
| East Asian | 0.00066 | 0.00065 | rare |
| Finnish | 0.000093 | 0.000092 | rare |
| European (Non-Finnish) | 0.00034 | 0.00033 | rare |
| South Asian | 0.0017 | 0.0017 | notable |
| Other | 0.00033 | 0.00033 | rare |
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. LI-cadherin may have a role in the morphological organization of liver and intestine. Involved in intestinal peptide transport. {ECO:0000269|PubMed:8153632}.;
Recessive Scores
- pRec
- 0.149
Intolerance Scores
- LoFtool
- 0.895
- RVIS EVS
- -0.3
- RVIS percentile EVS
- 32.25
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.386
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |