CD2
Basic information
Region (hg38): 1:116754430-116769229
Previous symbols: [ "SRBC" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (56 variants)
- not_provided (1 variants)
- Prostate_cancer (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000001767.5. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 50 | 57 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 50 | 7 | 1 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CD2 | protein_coding | protein_coding | ENST00000369478 | 5 | 14844 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.471 | 0.524 | 125538 | 0 | 1 | 125539 | 0.00000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.0669 | 191 | 194 | 0.986 | 0.00000993 | 2312 |
| Missense in Polyphen | 37 | 52.759 | 0.7013 | 648 | ||
| Synonymous | -0.720 | 79 | 71.3 | 1.11 | 0.00000380 | 678 |
| Loss of Function | 2.36 | 2 | 10.1 | 0.198 | 4.20e-7 | 144 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: CD2 interacts with lymphocyte function-associated antigen CD58 (LFA-3) and CD48/BCM1 to mediate adhesion between T- cells and other cell types. CD2 is implicated in the triggering of T-cells, the cytoplasmic domain is implicated in the signaling function.;
- Pathway
- Cell adhesion molecules (CAMs) - Homo sapiens (human);Hematopoietic cell lineage - Homo sapiens (human);stathmin and breast cancer resistance to antimicrotubule agents;ras-independent pathway in nk cell-mediated cytotoxicity;TCR;Cell surface interactions at the vascular wall;Hemostasis
(Consensus)
Recessive Scores
- pRec
- 0.265
Intolerance Scores
- loftool
- 0.142
- rvis_EVS
- 0.4
- rvis_percentile_EVS
- 76.15
Haploinsufficiency Scores
- pHI
- 0.300
- hipred
- Y
- hipred_score
- 0.504
- ghis
- 0.433
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.815
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cd2
- Phenotype
- normal phenotype;
Gene ontology
- Biological process
- membrane raft polarization;apoptotic process;cell surface receptor signaling pathway;natural killer cell activation;positive regulation of myeloid dendritic cell activation;positive regulation of tumor necrosis factor production;heterotypic cell-cell adhesion;T cell activation;regulation of T cell differentiation;leukocyte migration;cell-cell adhesion;positive regulation of interferon-gamma secretion;positive regulation of interleukin-8 secretion
- Cellular component
- plasma membrane;integral component of plasma membrane;external side of plasma membrane;cell surface
- Molecular function
- signaling receptor binding;protein binding;signaling receptor activity