CDHR5
protein-codingcadherin related family member 5, the group of Cadherin related
Gene summary
This gene is a novel mucin-like gene that is a member of the cadherin superfamily. While encoding nonpolymorphic tandem repeats rich in proline, serine and threonine similar to mucin proteins, the gene also contains sequence encoding calcium-binding motifs found in all cadherins. The role of the hybrid extracellular region and the specific function of this protein have not yet been determined. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jan 2010]
- MUCDHL
- MUPCDH
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~9.5 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 CDHR5 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_021924.5. 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 | 6 | 2 | 1 | 9 | ||
| missense | 186 | 14 | 1 | 201 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 195 | 16 | 2 | 213 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_068743.3 | 15 | MANE Select | |
| Ensembl | ENSP00000380676.2 | 15 | MANE Select | |
| RefSeq | NP_001165439.2 | 15 | Standard | |
| RefSeq | NP_112554.3 | 14 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- cell adhesion
- homophilic cell adhesion via plasma membrane adhesion molecules
- cell differentiation
- regulation of microvillus length
- intermicrovillar adhesion
Molecular Function
- calcium ion binding
- protein binding
- beta-catenin binding
- cell adhesion molecule binding
Cellular Component
- clathrin-coated pit
- apical plasma membrane
- brush border membrane
- microvillus membrane
- spanning component of plasma membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000358353
- Coding exons
- 15
- Length
- 9514
- Individuals with no LoFs
- 125632
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 109
- Defined
- 125742
- p
- 0.000438
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -1.20 | 621 | 542 | 1.15 | 0.0000354 | 5322 |
| Missense (PolyPhen) | 244 | 230.23 | 1.0598 | 2275 | ||
| Synonymous | -4.12 | 333 | 250 | 1.33 | 0.0000191 | 1871 |
| Loss of Function | 0.329 | 29 | 31.0 | 0.936 | 0.00000147 | 332 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0011 | 0.0011 | notable |
| Latino/Admixed American | 0.00036 | 0.00035 | rare |
| Ashkenazi Jewish | 0.00010 | 0.000099 | rare |
| East Asian | 0.00033 | 0.00033 | rare |
| Finnish | 0.000065 | 0.000046 | rare |
| European (Non-Finnish) | 0.00054 | 0.00052 | rare |
| South Asian | 0.00047 | 0.00042 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Intermicrovillar adhesion molecule that forms, via its extracellular domain, calcium-dependent heterophilic complexes with CDHR2 on adjacent microvilli. Thereby, controls the packing of microvilli at the apical membrane of epithelial cells. Through its cytoplasmic domain, interacts with microvillus cytoplasmic proteins to form the intermicrovillar adhesion complex/IMAC. This complex plays a central role in microvilli and epithelial brush border differentiation. {ECO:0000269|PubMed:24725409}.;
Recessive Scores
- pRec
- 0.115
Intolerance Scores
- LoFtool
- 0.811
- RVIS EVS
- 0.39
- RVIS percentile EVS
- 76.06
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |