CCR1

C-C motif chemokine receptor 1, the group of CD molecules|C-C motif chemokine receptors

Basic information

Region (hg38): 3:46201711-46208313

Previous symbols: [ "SCYAR1", "CMKBR1" ]

Links

ENSG00000163823 ∙ NCBI:1230 ∙ OMIM:601159 ∙ HGNC:1602 ∙ Uniprot:P32246 ∙ 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 CCR1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCR1 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				6	3	9
missense			14	3	1	18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	9	4

Variants in CCR1

This is a list of pathogenic ClinVar variants found in the CCR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-46203247-C-T			Benign (Jul 29, 2018)
3-46203295-C-A		not specified	Uncertain significance (Jan 10, 2023)
3-46203300-C-T			Benign (Apr 24, 2018)
3-46203318-G-A			Likely benign (Apr 09, 2018)
3-46203359-G-C		not specified	Uncertain significance (May 23, 2023)
3-46203376-C-T		not specified	Uncertain significance (Oct 06, 2021)
3-46203411-G-A			Benign/Likely benign (May 01, 2024)
3-46203443-A-G			Benign (Jul 29, 2018)
3-46203446-C-T			Likely benign (Dec 31, 2019)
3-46203456-C-T			Likely benign (Oct 01, 2022)
3-46203474-G-T		not specified	Uncertain significance (Nov 14, 2023)
3-46203572-A-C		not specified	Uncertain significance (Nov 12, 2021)
3-46203640-A-G		not specified	Uncertain significance (Mar 28, 2023)
3-46203761-G-A		not specified	Uncertain significance (Dec 05, 2022)
3-46203770-T-A		not specified	Likely benign (Jun 13, 2023)
3-46203838-G-A			Likely benign (Jun 01, 2024)
3-46203839-C-A		not specified	Uncertain significance (Dec 27, 2023)
3-46203876-G-A			Likely benign (Jul 20, 2018)
3-46203933-C-T			Benign (Aug 21, 2018)
3-46204015-A-G		not specified	Uncertain significance (Oct 04, 2022)
3-46204057-G-A		not specified	Uncertain significance (Sep 27, 2022)
3-46204142-C-T		not specified	Uncertain significance (Dec 17, 2023)
3-46204152-C-G			Benign/Likely benign (Oct 01, 2022)
3-46204205-G-T		not specified	Uncertain significance (Jul 13, 2021)
3-46204209-T-G		not specified	Uncertain significance (Nov 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCR1	protein_coding	protein_coding	ENST00000296140	1	6688

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.388	0.603	125724	0	6	125730	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.17	156	203	0.769	0.0000113	2320
Missense in Polyphen		39	68.87	0.56628		888
Synonymous	-0.636	97	89.4	1.09	0.00000526	738
Loss of Function	2.20	2	9.19	0.218	5.98e-7	101

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for a C-C type chemokine. Binds to MIP-1-alpha, MIP-1-delta, RANTES, and MCP-3 and, less efficiently, to MIP-1- beta or MCP-1 and subsequently transduces a signal by increasing the intracellular calcium ions level. Responsible for affecting stem cell proliferation.
• Pathway: Kaposi,s sarcoma-associated herpesvirus infection - Homo sapiens (human);Chemokine signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Peptide GPCRs;Chemokine signaling pathway;Interleukin-10 signaling;GPCRs, Class A Rhodopsin-like;Signaling by GPCR;Signal Transduction;Chemokine receptors bind chemokines;Peptide ligand-binding receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;G alpha (i) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.297

Intolerance Scores

• loftool: 0.124
• rvis_EVS: 0.55
• rvis_percentile_EVS: 81.48

Haploinsufficiency Scores

• pHI: 0.249
• hipred: N
• hipred_score: 0.380
• ghis: 0.406

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.843

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Ccr1
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; digestive/alimentary phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); 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; liver/biliary system phenotype; respiratory system phenotype; renal/urinary system phenotype; immune system phenotype

Gene ontology

• Biological process: dendritic cell chemotaxis;calcium ion transport;cellular calcium ion homeostasis;exocytosis;chemotaxis;inflammatory response;immune response;cell adhesion;cell surface receptor signaling pathway;G protein-coupled receptor signaling pathway;G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger;positive regulation of cytosolic calcium ion concentration;cell-cell signaling;response to wounding;negative regulation of gene expression;cytokine-mediated signaling pathway;calcium-mediated signaling;positive regulation of cell migration;negative regulation of bone mineralization;positive regulation of osteoclast differentiation;positive regulation of calcium ion transport;cell chemotaxis;chemokine-mediated signaling pathway;positive regulation of ERK1 and ERK2 cascade;positive regulation of monocyte chemotaxis
• Cellular component: cytoplasm;plasma membrane;integral component of plasma membrane;external side of plasma membrane
• Molecular function: phosphatidylinositol phospholipase C activity;chemokine receptor activity;protein binding;C-C chemokine receptor activity;chemokine binding;C-C chemokine binding;chemokine (C-C motif) ligand 7 binding;chemokine (C-C motif) ligand 5 binding