CXADR
protein-codingCXADR Ig-like cell adhesion molecule, the group of V-set domain containing|IgCAM CXADR-related subfamily
Gene summary
The protein encoded by this gene is a type I membrane receptor for group B coxsackieviruses and subgroup C adenoviruses. Several transcript variants encoding different isoforms have been found for this gene. Pseudogenes of this gene are found on chromosomes 15, 18, and 21. [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 ~80.5 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 CXADR variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001338.5. 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 | 7 | 1 | 9 | ||
| missense | 51 | 2 | 53 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 56 | 9 | 1 | 66 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001329.1 | 7 | MANE Select | |
| Ensembl | ENSP00000284878.7 | 7 | MANE Select | |
| RefSeq | NP_001193992.1 | 5 | Standard | |
| RefSeq | NP_001193993.1 | 4 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| cxadr | Danio rerio | Structure: podocyte Quality: morphology abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Viral myocarditis - Homo sapiens (human)
- Immune System
- Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
- Adaptive Immune System
- Cell surface interactions at the vascular wall
Biological Process
- mitochondrion organization
- heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules
- heart development
- germ cell migration
- epithelial structure maintenance
Molecular Function
- virus receptor activity
- integrin binding
- protein binding
- beta-catenin binding
- PDZ domain binding
Cellular Component
- acrosomal vesicle
- extracellular region
- nucleoplasm
- cytoplasm
- plasma membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000284878
- Coding exons
- 7
- Length
- 81198
- Individuals with no LoFs
- 125736
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 11
- Defined
- 125747
- p
- 0.0000437
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.979 | 163 | 202 | 0.806 | 0.0000110 | 2356 |
| Missense (PolyPhen) | 38 | 64.707 | 0.58726 | 790 | ||
| Synonymous | -0.234 | 77 | 74.4 | 1.03 | 0.00000447 | 713 |
| Loss of Function | 3.02 | 4 | 17.8 | 0.225 | 9.95e-7 | 224 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.000058 | 0.000058 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000054 | 0.000053 | rare |
| South Asian | 0.000065 | 0.000065 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Component of the epithelial apical junction complex that may function as a homophilic cell adhesion molecule and is essential for tight junction integrity. Also involved in transepithelial migration of leukocytes through adhesive interactions with JAML a transmembrane protein of the plasma membrane of leukocytes. The interaction between both receptors also mediates the activation of gamma-delta T-cells, a subpopulation of T-cells residing in epithelia and involved in tissue homeostasis and repair. Upon epithelial CXADR-binding, JAML induces downstream cell signaling events in gamma-delta T-cells through PI3-kinase and MAP kinases. It results in proliferation and production of cytokines and growth factors by T-cells that in turn stimulate epithelial tissues repair. {ECO:0000269|PubMed:11734628, ECO:0000269|PubMed:12297051, ECO:0000269|PubMed:15800062, ECO:0000269|PubMed:19064666, ECO:0000269|PubMed:9096397}.; FUNCTION: (Microbial infection) Acts as a receptor for Coxsackievirus B1 to B6. {ECO:0000269|PubMed:10814575, ECO:0000269|PubMed:14978041}.;
Recessive Scores
- pRec
- 0.228
Intolerance Scores
- LoFtool
- 0.319
- RVIS EVS
- -0.01
- RVIS percentile EVS
- 53.51
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.945
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |