CD47
protein-codingCD47 molecule, the group of Immunoglobulin like domain containing|CD molecules|Ig-like cell adhesion molecule family
Gene summary
This gene encodes a membrane protein, which is involved in the increase in intracellular calcium concentration that occurs upon cell adhesion to extracellular matrix. The encoded protein is also a receptor for the C-terminal cell binding domain of thrombospondin, and it may play a role in membrane transport and signal transduction. This gene has broad tissue distribution, and is reduced in expression on Rh erythrocytes. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2010]
- MER6
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~48.8 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 CD47 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001777.4. 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 | 4 | 4 | ||||
| missense | 25 | 25 | ||||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 0 | 0 | 34 | 0 | 0 | 34 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001768.1 | 11 | MANE Select | |
| Ensembl | ENSP00000355361.5 | 11 | MANE Select | |
| RefSeq | NP_001369235.1 | 10 | Standard | |
| RefSeq | NP_942088.1 | 9 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- ECM-receptor interaction - Homo sapiens (human)
- Spinal Cord Injury
- Neutrophil degranulation
- Integrin cell surface interactions
- Extracellular matrix organization
Biological Process
- integrin-mediated signaling pathway
- opsonization
- positive regulation of cell population proliferation
- response to bacterium
- cell migration
Molecular Function
- protein binding
- thrombospondin receptor activity
- protein binding involved in heterotypic cell-cell adhesion
- cell-cell adhesion mediator activity
Cellular Component
- plasma membrane
- integral component of plasma membrane
- cell surface
- specific granule membrane
- extracellular exosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000361309
- Coding exons
- 11
- Length
- 47728
- Individuals with no LoFs
- 122508
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 2
- Defined
- 122510
- p
- 0.00000816
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.43 | 108 | 159 | 0.680 | 0.00000779 | 2055 |
| Missense (PolyPhen) | 35 | 71.656 | 0.48844 | 911 | ||
| Synonymous | -0.178 | 59 | 57.3 | 1.03 | 0.00000306 | 623 |
| Loss of Function | 3.36 | 2 | 16.9 | 0.119 | 7.09e-7 | 243 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000019 | 0.000018 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Has a role in both cell adhesion by acting as an adhesion receptor for THBS1 on platelets, and in the modulation of integrins. Plays an important role in memory formation and synaptic plasticity in the hippocampus (By similarity). Receptor for SIRPA, binding to which prevents maturation of immature dendritic cells and inhibits cytokine production by mature dendritic cells. Interaction with SIRPG mediates cell-cell adhesion, enhances superantigen-dependent T-cell-mediated proliferation and costimulates T-cell activation. May play a role in membrane transport and/or integrin dependent signal transduction. May prevent premature elimination of red blood cells. May be involved in membrane permeability changes induced following virus infection. {ECO:0000250, ECO:0000269|PubMed:11509594, ECO:0000269|PubMed:15383453, ECO:0000269|PubMed:7691831}.;
Recessive Scores
- pRec
- 0.474
Intolerance Scores
- LoFtool
- 0.0507
- RVIS EVS
- -0.23
- RVIS percentile EVS
- 36.86
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.388
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |