CD5
Basic information
Region (hg38): 11:61102489-61127852
Previous symbols: [ "LEU1" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (51 variants)
- not_provided (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD5 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000014207.4. 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 | 52 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 50 | 3 | 0 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
CD5 | protein_coding | protein_coding | ENST00000347785 | 10 | 25458 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
2.31e-10 | 0.673 | 125703 | 1 | 44 | 125748 | 0.000179 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.962 | 241 | 287 | 0.840 | 0.0000170 | 3199 |
Missense in Polyphen | 75 | 92.402 | 0.81167 | 1025 | ||
Synonymous | 0.315 | 117 | 121 | 0.964 | 0.00000752 | 992 |
Loss of Function | 1.44 | 19 | 27.1 | 0.702 | 0.00000139 | 287 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000126 | 0.000124 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000218 | 0.000217 |
Finnish | 0.0000953 | 0.0000924 |
European (Non-Finnish) | 0.000213 | 0.000211 |
Middle Eastern | 0.000218 | 0.000217 |
South Asian | 0.000395 | 0.000359 |
Other | 0.000164 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: May act as a receptor in regulating T-cell proliferation.;
- Pathway
- Hematopoietic cell lineage - Homo sapiens (human);TCR;BCR
(Consensus)
Recessive Scores
- pRec
- 0.467
Intolerance Scores
- loftool
- 0.701
- rvis_EVS
- 0.8
- rvis_percentile_EVS
- 87.66
Haploinsufficiency Scores
- pHI
- 0.177
- hipred
- N
- hipred_score
- 0.406
- ghis
- 0.402
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.667
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cd5
- 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); immune system phenotype; hematopoietic system phenotype; normal 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);
Gene ontology
- Biological process
- receptor-mediated endocytosis;cell recognition;cell population proliferation;T cell costimulation;apoptotic signaling pathway
- Cellular component
- plasma membrane;integral component of plasma membrane;external side of plasma membrane
- Molecular function
- transmembrane signaling receptor activity;scavenger receptor activity;protein binding;signaling receptor activity