CCR5

C-C motif chemokine receptor 5, the group of CD molecules|C-C motif chemokine receptors

Basic information

Region (hg38): 3:46370945-46376206

Previous symbols: [ "CMKBR5" ]

Links

ENSG00000160791 ∙ NCBI:1234 ∙ OMIM:601373 ∙ HGNC:1606 ∙ Uniprot:P51681 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CCR5 gene.

• Inborn genetic diseases (10 variants)
• CCR5-related condition (2 variants)
• Multiple sclerosis modifier of disease progression (1 variants)
• not provided (1 variants)
• Susceptibility to HIV infection (1 variants)
• West Nile virus, susceptibility to (1 variants)
• Resistance to hepatitis C virus (1 variants)
• Hepatitis C virus, susceptibility to;Susceptibility to HIV infection;West Nile virus, susceptibility to;Type 1 diabetes mellitus 22 (1 variants)
• West Nile virus, susceptibility to;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.

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						0
missense			13			13
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	0	1

Variants in CCR5

This is a list of pathogenic ClinVar variants found in the CCR5 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-46372971-C-A		CCR5-related disorder	Likely benign (Mar 27, 2019)
3-46372976-T-A		CCR5-related disorder	Uncertain significance (Jan 04, 2023)
3-46372994-G-A		not specified	Uncertain significance (Jul 21, 2021)
3-46373018-T-G		not specified	Uncertain significance (Dec 01, 2022)
3-46373082-G-T		Susceptibility to HIV infection	protective (Jun 01, 2001)
3-46373089-A-T		West Nile virus, susceptibility to;Type 1 diabetes mellitus 22 • Hepatitis C virus, susceptibility to;Susceptibility to HIV infection;West Nile virus, susceptibility to;Type 1 diabetes mellitus 22	Uncertain significance (Mar 30, 2021)
3-46373174-C-T		not specified	Uncertain significance (Dec 16, 2022)
3-46373176-G-A		not specified	Uncertain significance (Apr 25, 2022)
3-46373197-A-T		not specified	Uncertain significance (Dec 06, 2022)
3-46373205-T-A		Susceptibility to HIV infection	protective (Jan 03, 1998)
3-46373218-G-A		CCR5-related disorder	Likely benign (Jun 12, 2019)
3-46373224-T-C		not specified	Uncertain significance (Dec 23, 2023)
3-46373325-G-A		CCR5-related disorder	Likely benign (Oct 22, 2019)
3-46373394-C-G			Uncertain significance (-)
3-46373404-A-G		not specified	Uncertain significance (Dec 20, 2022)
3-46373419-G-T		not specified	Uncertain significance (Apr 10, 2023)
3-46373452-TACAGTCAGTATCAATTCTGGAAGAATTTCCAG-T		Multiple sclerosis modifier of disease progression • Susceptibility to HIV infection • Resistance to hepatitis C virus • West Nile virus, susceptibility to • CCR5-related disorder	Benign (Nov 22, 2019)
3-46373543-A-G		not specified	Uncertain significance (Dec 14, 2023)
3-46373570-G-A		CCR5 POLYMORPHISM, ORIENTAL 2	Benign (Jul 01, 1997)
3-46373617-A-G		CCR5-related disorder	Uncertain significance (Nov 04, 2022)
3-46373643-C-T		CCR5-related disorder	Likely benign (Apr 01, 2019)
3-46373716-T-C		not specified	Uncertain significance (Jun 07, 2023)
3-46373794-GC-G		CCR5 POLYMORPHISM, ORIENTAL 1	Benign (Jul 01, 1997)
3-46373795-C-A		not specified	Uncertain significance (Jul 06, 2021)
3-46373882-T-C		not specified	Uncertain significance (Jan 04, 2024)

GnomAD

Source: gnomAD

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: dbNSFP

• 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
• 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