CD47
CD47 molecule, the group of Immunoglobulin like domain containing|CD molecules|Ig-like cell adhesion molecule family
Basic information
Region (hg38): 3:108043091-108091862
Previous symbols: [ "MER6" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD47 gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 16 | 16 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 16 | 0 | 0 |
Variants in CD47
This is a list of pathogenic ClinVar variants found in the CD47 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 3-108049630-A-C | not specified | Uncertain significance (Mar 22, 2023) | ||
| 3-108049631-T-C | not specified | Uncertain significance (Nov 15, 2024) | ||
| 3-108049639-G-A | not specified | Uncertain significance (Mar 20, 2023) | ||
| 3-108057549-G-C | not specified | Uncertain significance (Dec 22, 2023) | ||
| 3-108058351-C-T | not specified | Uncertain significance (May 09, 2023) | ||
| 3-108058375-T-C | not specified | Uncertain significance (Oct 12, 2024) | ||
| 3-108058409-C-T | not specified | Uncertain significance (Nov 13, 2023) | ||
| 3-108060760-T-G | not specified | Uncertain significance (Jul 25, 2023) | ||
| 3-108060810-G-C | not specified | Uncertain significance (Oct 29, 2021) | ||
| 3-108071126-T-C | not specified | Uncertain significance (Aug 28, 2024) | ||
| 3-108071135-T-C | not specified | Uncertain significance (Mar 29, 2024) | ||
| 3-108080009-C-T | not specified | Uncertain significance (Apr 13, 2023) | ||
| 3-108080012-T-G | not specified | Uncertain significance (Jan 10, 2025) | ||
| 3-108080081-C-T | not specified | Uncertain significance (Jan 05, 2022) | ||
| 3-108080128-A-G | not specified | Uncertain significance (May 16, 2023) | ||
| 3-108080136-T-A | not specified | Uncertain significance (Jul 25, 2024) | ||
| 3-108080299-G-A | not specified | Uncertain significance (Oct 21, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CD47 | protein_coding | protein_coding | ENST00000361309 | 11 | 47728 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.919 | 0.0807 | 122508 | 0 | 2 | 122510 | 0.00000816 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.43 | 108 | 159 | 0.680 | 0.00000779 | 2055 |
| Missense in 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 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000192 | 0.0000178 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
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}.;
- Pathway
- ECM-receptor interaction - Homo sapiens (human);Spinal Cord Injury;Neutrophil degranulation;Integrin cell surface interactions;Extracellular matrix organization;Innate Immune System;Immune System;Beta3 integrin cell surface interactions;Cell surface interactions at the vascular wall;Hemostasis;Signal regulatory protein family interactions;Cell-Cell communication
(Consensus)
Recessive Scores
- pRec
- 0.474
Intolerance Scores
- loftool
- 0.0507
- rvis_EVS
- -0.23
- rvis_percentile_EVS
- 36.86
Haploinsufficiency Scores
- pHI
- 0.0833
- hipred
- Y
- hipred_score
- 0.594
- ghis
- 0.623
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.388
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cd47
- Phenotype
- homeostasis/metabolism phenotype; cellular phenotype; muscle phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; immune system phenotype; skeleton phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); neoplasm;
Gene ontology
- Biological process
- integrin-mediated signaling pathway;opsonization;positive regulation of cell population proliferation;response to bacterium;cell migration;positive regulation of cell-cell adhesion;extracellular matrix organization;regulation of interferon-gamma production;regulation of interleukin-10 production;regulation of interleukin-12 production;regulation of interleukin-6 production;regulation of tumor necrosis factor production;heterotypic cell-cell adhesion;monocyte extravasation;neutrophil degranulation;regulation of nitric oxide biosynthetic process;positive regulation of inflammatory response;positive regulation of phagocytosis;positive regulation of T cell activation;leukocyte migration;positive regulation of stress fiber assembly;cellular response to interferon-gamma;cellular response to interleukin-1;cellular response to interleukin-12;negative regulation of Fc-gamma receptor signaling pathway involved in phagocytosis
- Cellular component
- plasma membrane;integral component of plasma membrane;cell surface;specific granule membrane;extracellular exosome;tertiary granule membrane
- Molecular function
- protein binding;thrombospondin receptor activity;protein binding involved in heterotypic cell-cell adhesion;cell-cell adhesion mediator activity