CD63
CD63 molecule, the group of Tetraspanins|CD molecules
Basic information
Region (hg38): 12:55725323-55729707
Previous symbols: [ "MLA1" ]
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 CD63 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 | 1 | |||||
| missense | 6 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 1 | |||||
| Total | 0 | 0 | 6 | 0 | 2 |
Variants in CD63
This is a list of pathogenic ClinVar variants found in the CD63 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 12-55726123-C-T | not specified | Uncertain significance (Oct 05, 2023) | ||
| 12-55726197-C-T | not specified | Uncertain significance (Jun 22, 2024) | ||
| 12-55726202-C-T | Uncertain significance (-) | |||
| 12-55726691-C-G | Benign (Nov 20, 2018) | |||
| 12-55726738-T-G | not specified | Uncertain significance (Nov 09, 2023) | ||
| 12-55726739-G-A | Benign (Nov 20, 2018) | |||
| 12-55726760-C-G | not specified | Uncertain significance (Sep 16, 2021) | ||
| 12-55726791-A-G | not specified | Uncertain significance (Jun 24, 2022) | ||
| 12-55727198-C-T | not specified | Uncertain significance (Nov 14, 2024) | ||
| 12-55727222-C-T | not specified | Uncertain significance (Dec 10, 2024) | ||
| 12-55727261-G-A | not specified | Uncertain significance (Jan 04, 2024) | ||
| 12-55727297-G-C | not specified | Uncertain significance (Jan 09, 2024) | ||
| 12-55727312-C-T | not specified | Uncertain significance (Aug 27, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CD63 | protein_coding | protein_coding | ENST00000549117 | 7 | 4385 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0174 | 0.963 | 125705 | 0 | 43 | 125748 | 0.000171 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.767 | 113 | 138 | 0.817 | 0.00000723 | 1561 |
| Missense in Polyphen | 25 | 30.723 | 0.81373 | 375 | ||
| Synonymous | 0.410 | 51 | 54.9 | 0.930 | 0.00000335 | 462 |
| Loss of Function | 2.03 | 5 | 12.9 | 0.388 | 6.39e-7 | 140 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000904 | 0.0000904 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00103 | 0.00103 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000177 | 0.000176 |
| Middle Eastern | 0.00103 | 0.00103 |
| South Asian | 0.0000668 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Functions as cell surface receptor for TIMP1 and plays a role in the activation of cellular signaling cascades. Plays a role in the activation of ITGB1 and integrin signaling, leading to the activation of AKT, FAK/PTK2 and MAP kinases. Promotes cell survival, reorganization of the actin cytoskeleton, cell adhesion, spreading and migration, via its role in the activation of AKT and FAK/PTK2. Plays a role in VEGFA signaling via its role in regulating the internalization of KDR/VEGFR2. Plays a role in intracellular vesicular transport processes, and is required for normal trafficking of the PMEL luminal domain that is essential for the development and maturation of melanocytes. Plays a role in the adhesion of leukocytes onto endothelial cells via its role in the regulation of SELP trafficking. May play a role in mast cell degranulation in response to Ms4a2/FceRI stimulation, but not in mast cell degranulation in response to other stimuli. {ECO:0000269|PubMed:16917503, ECO:0000269|PubMed:21803846, ECO:0000269|PubMed:21962903, ECO:0000269|PubMed:23632027, ECO:0000269|PubMed:24635319}.;
- Pathway
- Lysosome - Homo sapiens (human);Proteoglycans in cancer - Homo sapiens (human);Neutrophil degranulation;Innate Immune System;Immune System;Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;Hemostasis
(Consensus)
Recessive Scores
- pRec
- 0.750
Intolerance Scores
- loftool
- 0.559
- rvis_EVS
- -0.25
- rvis_percentile_EVS
- 35.42
Haploinsufficiency Scores
- pHI
- 0.459
- hipred
- Y
- hipred_score
- 0.707
- ghis
- 0.581
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.869
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cd63
- Phenotype
- renal/urinary system phenotype; digestive/alimentary phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype;
Zebrafish Information Network
- Gene name
- cd63
- Affected structure
- hatching gland cell
- Phenotype tag
- abnormal
- Phenotype quality
- mislocalised
Gene ontology
- Biological process
- positive regulation of receptor internalization;platelet degranulation;cell-matrix adhesion;cell surface receptor signaling pathway;protein transport;cell migration;cellular protein localization;endosome to melanosome transport;neutrophil degranulation;positive regulation of endocytosis;pigment granule maturation;regulation of vascular endothelial growth factor signaling pathway;regulation of potassium ion transmembrane transport;positive regulation of integrin-mediated signaling pathway
- Cellular component
- extracellular space;lysosomal membrane;plasma membrane;integral component of plasma membrane;cell surface;endosome membrane;platelet dense granule membrane;intrinsic component of plasma membrane;late endosome membrane;endosome lumen;multivesicular body membrane;azurophil granule membrane;melanosome;extracellular exosome;multivesicular body, internal vesicle
- Molecular function
- protein binding