CD9
Basic information
Region (hg38): 12:6199715-6238271
Previous symbols: [ "MIC3" ]
Links
Phenotypes
GenCC
Source:
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 CD9 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 | 3 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 1 | |||||
| Total | 0 | 0 | 3 | 0 | 2 |
Variants in CD9
This is a list of pathogenic ClinVar variants found in the CD9 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 12-6232684-G-A | Benign (Aug 28, 2018) | |||
| 12-6233424-C-T | not specified | Uncertain significance (Jan 24, 2024) | ||
| 12-6233445-G-C | not specified | Uncertain significance (Jun 12, 2023) | ||
| 12-6235220-C-G | Benign (Jun 18, 2018) | |||
| 12-6235335-G-A | Benign (Jun 18, 2018) | |||
| 12-6237770-G-C | not specified | Uncertain significance (Jun 14, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CD9 | protein_coding | protein_coding | ENST00000382518 | 8 | 38545 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00472 | 0.969 | 125740 | 0 | 8 | 125748 | 0.0000318 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.874 | 111 | 140 | 0.792 | 0.00000814 | 1503 |
| Missense in Polyphen | 41 | 55.162 | 0.74326 | 586 | ||
| Synonymous | 0.636 | 50 | 56.1 | 0.892 | 0.00000384 | 403 |
| Loss of Function | 1.94 | 6 | 13.8 | 0.436 | 6.68e-7 | 157 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000181 | 0.000181 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000352 | 0.0000352 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in platelet activation and aggregation. Regulates paranodal junction formation. Involved in cell adhesion, cell motility and tumor metastasis. Required for sperm-egg fusion. {ECO:0000269|PubMed:14575715, ECO:0000269|PubMed:7511626, ECO:0000269|PubMed:8478605}.;
- Pathway
- Hematopoietic cell lineage - Homo sapiens (human);Vitamin D Receptor Pathway;Disease;Uptake and function of diphtheria toxin;Fertilization;Reproduction;Uptake and actions of bacterial toxins;Infectious disease;Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;Hemostasis;Sperm:Oocyte Membrane Binding;a6b1 and a6b4 Integrin signaling
(Consensus)
Recessive Scores
- pRec
- 0.490
Intolerance Scores
- loftool
- 0.405
- rvis_EVS
- -0.43
- rvis_percentile_EVS
- 25.15
Haploinsufficiency Scores
- pHI
- 0.487
- hipred
- Y
- hipred_score
- 0.800
- ghis
- 0.659
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.448
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cd9
- Phenotype
- immune system phenotype; skeleton phenotype; hematopoietic system phenotype; reproductive system phenotype; respiratory system phenotype; cellular phenotype; growth/size/body region phenotype;
Zebrafish Information Network
- Gene name
- cd9b
- Affected structure
- posterior lateral line primordium
- Phenotype tag
- abnormal
- Phenotype quality
- organization quality
Gene ontology
- Biological process
- platelet degranulation;cell adhesion;cell surface receptor signaling pathway;fusion of sperm to egg plasma membrane involved in single fertilization;brain development;negative regulation of cell population proliferation;response to water deprivation;oligodendrocyte development;platelet activation;paranodal junction assembly;receptor internalization;sperm-egg recognition;negative regulation of cellular component movement;cellular response to low-density lipoprotein particle stimulus;negative regulation of platelet aggregation
- Cellular component
- extracellular space;plasma membrane;integral component of plasma membrane;focal adhesion;external side of plasma membrane;membrane;apical plasma membrane;endocytic vesicle membrane;clathrin-coated endocytic vesicle membrane;platelet alpha granule membrane;extracellular exosome;extracellular vesicle
- Molecular function
- integrin binding;protein binding