CCR5
C-C motif chemokine receptor 5, the group of CD molecules|C-C motif chemokine receptors
Basic information
Region (hg38): 3:46370946-46376206
Previous symbols: [ "CMKBR5" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (23 variants)
- CCR5-related_disorder (6 variants)
- not_provided (4 variants)
- Susceptibility_to_HIV_infection (3 variants)
- West_Nile_virus,_susceptibility_to (1 variants)
- CCR5_POLYMORPHISM,_AFRICAN-AMERICAN (1 variants)
- CCR5_POLYMORPHISM,_ORIENTAL_1 (1 variants)
- CCR5_POLYMORPHISM,_ORIENTAL_2 (1 variants)
- Hepatitis_C_virus,_susceptibility_to (1 variants)
- Type_1_diabetes_mellitus_22 (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCR5 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001394783.1. 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 | 3 | |||||
| missense | 27 | 30 | ||||
| nonsense | 1 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 28 | 4 | 3 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CCR5 | protein_coding | protein_coding | ENST00000343801 | 1 | 6065 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 4.31e-10 | 0.0155 | 107830 | 970 | 16943 | 125743 | 0.0740 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -1.46 | 242 | 186 | 1.30 | 0.00000990 | 2313 |
| Missense in Polyphen | 74 | 53.581 | 1.3811 | 728 | ||
| Synonymous | -1.20 | 92 | 78.4 | 1.17 | 0.00000456 | 711 |
| Loss of Function | -1.33 | 12 | 7.94 | 1.51 | 4.10e-7 | 96 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0508 | 0.0507 |
| Ashkenazi Jewish | 0.133 | 0.132 |
| East Asian | 0.000163 | 0.000163 |
| Finnish | 0.134 | 0.133 |
| European (Non-Finnish) | 0.109 | 0.109 |
| Middle Eastern | 0.000163 | 0.000163 |
| South Asian | 0.0164 | 0.0163 |
| Other | 0.0754 | 0.0734 |
dbNSFP
Source:
- Function
- FUNCTION: Receptor for a number of inflammatory CC-chemokines including CCL3/MIP-1-alpha, CCL4/MIP-1-beta and RANTES and subsequently transduces a signal by increasing the intracellular calcium ion level. May play a role in the control of granulocytic lineage proliferation or differentiation. {ECO:0000269|PubMed:10383387, ECO:0000269|PubMed:11323418, ECO:0000269|PubMed:8639485, ECO:0000269|PubMed:8663314, ECO:0000269|PubMed:8699119}.;
- Disease
- DISEASE: Diabetes mellitus, insulin-dependent, 22 (IDDM22) [MIM:612522]: A multifactorial disorder of glucose homeostasis that is characterized by susceptibility to ketoacidosis in the absence of insulin therapy. Clinical features are polydipsia, polyphagia and polyuria which result from hyperglycemia-induced osmotic diuresis and secondary thirst. These derangements result in long-term complications that affect the eyes, kidneys, nerves, and blood vessels. {ECO:0000269|PubMed:19073967}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.;
- Pathway
- Kaposi,s sarcoma-associated herpesvirus infection - Homo sapiens (human);Endocytosis - Homo sapiens (human);Chemokine signaling pathway - Homo sapiens (human);Toxoplasmosis - Homo sapiens (human);Viral carcinogenesis - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);GPCRs, Other;Peptide GPCRs;Interleukin-10 signaling;GPCRs, Class A Rhodopsin-like;T-Cell antigen Receptor (TCR) Signaling Pathway;Signaling by GPCR;Disease;Signal Transduction;pertussis toxin-insensitive ccr5 signaling in macrophage;il12 and stat4 dependent signaling pathway in th1 development;ion channels and their functional role in vascular endothelium;activation of csk by camp-dependent protein kinase inhibits signaling through the t cell receptor;chrebp regulation by carbohydrates and camp;role of -arrestins in the activation and targeting of map kinases;activation of camp-dependent protein kinase pka;HIV Life Cycle;HIV Infection;Infectious disease;Binding and entry of HIV virion;Chemokine receptors bind chemokines;Peptide ligand-binding receptors;Class A/1 (Rhodopsin-like receptors);roles of arrestin dependent recruitment of src kinases in gpcr signaling;GPCR ligand binding;-arrestins in gpcr desensitization;G alpha (i) signalling events;GPCR downstream signalling;IL12-mediated signaling events;Early Phase of HIV Life Cycle
(Consensus)
Intolerance Scores
- loftool
- 0.807
- rvis_EVS
- 0.49
- rvis_percentile_EVS
- 79.52
Haploinsufficiency Scores
- pHI
- 0.121
- hipred
- N
- hipred_score
- 0.327
- ghis
- 0.427
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- 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
- Ccr5
- 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); hematopoietic system phenotype; neoplasm; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; immune system 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); digestive/alimentary phenotype; vision/eye phenotype; cellular phenotype; homeostasis/metabolism phenotype; muscle phenotype;
Gene ontology
- Biological process
- MAPK cascade;dendritic cell chemotaxis;calcium ion transport;chemotaxis;inflammatory response;immune response;cellular defense response;cell surface receptor signaling pathway;G protein-coupled receptor signaling pathway;positive regulation of cytosolic calcium ion concentration;cell-cell signaling;release of sequestered calcium ion into cytosol by sarcoplasmic reticulum;fusion of virus membrane with host plasma membrane;cytokine-mediated signaling pathway;calcium-mediated signaling;signaling;entry into host cell;cell chemotaxis;chemokine-mediated signaling pathway;response to cholesterol;cellular response to lipopolysaccharide;negative regulation of macrophage apoptotic process
- Cellular component
- cytoplasm;endosome;plasma membrane;integral component of plasma membrane;external side of plasma membrane;cell surface
- Molecular function
- virus receptor activity;actin binding;phosphatidylinositol phospholipase C activity;chemokine receptor activity;protein binding;coreceptor activity;C-C chemokine receptor activity;chemokine binding;C-C chemokine binding;chemokine (C-C motif) ligand 5 binding