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XCR1 X-C motif chemokine receptor 1 [ Homo sapiens (human) ]

Gene ID: 2829, updated on 5-Mar-2024

Summary

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Official Symbol
XCR1provided by HGNC
Official Full Name
X-C motif chemokine receptor 1provided by HGNC
Primary source
HGNC:HGNC:1625
See related
Ensembl:ENSG00000173578 MIM:600552; AllianceGenome:HGNC:1625
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
GPR5; CCXCR1
Summary
The protein encoded by this gene is a chemokine receptor belonging to the G protein-coupled receptor superfamily. The family members are characterized by the presence of 7 transmembrane domains. The encoded protein transduces a signal by increasing the intracellular calcium ion level. The viral macrophage inflammatory protein-II is an antagonist of this receptor and blocks signaling. Some studies have implicated a cluster of genes at 3p21.31, including this gene, as associated with COVID-19 risk. The encoded protein may also play a role in cell proliferation and migration in several types of cancer. [provided by RefSeq, Jan 2023]
Annotation information
Note: This gene has been reviewed for its involvement in coronavirus biology, and is locus in the vicinity of disease-associated variant(s).
Expression
Biased expression in lymph node (RPKM 2.0), spleen (RPKM 1.4) and 12 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
3p21.31
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (46017007..46085844, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (46032885..46101714, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (46058499..46127336, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene FYVE and coiled-coil domain autophagy adaptor 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:45989039-45989208 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19787 Neighboring gene C-X-C motif chemokine receptor 6 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:46009167-46009806 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:46009807-46010446 Neighboring gene Sharpr-MPRA regulatory region 2695 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:46029541-46030041 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:46034569-46035069 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:46037115-46037614 Neighboring gene uncharacterized LOC105377063 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14287 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:46072313-46072813 Neighboring gene nuclear receptor binding factor 2 pseudogene 2 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_70191 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19790 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19791 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19792 Neighboring gene Sharpr-MPRA regulatory region 1914 Neighboring gene uncharacterized LOC105377067 Neighboring gene FLT1 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:46211627-46212128 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:46212129-46212628 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19794

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Unraveling Risk Genes of COVID-19 by Multi-Omics Integrative Analyses. Baranova A, et al. Front Med (Lausanne), 2021. PMID 34557504, Free PMC Article
  2. An integrative multiomics analysis identifies putative causal genes for COVID-19 severity. Wu L, et al. Genet Med, 2021 Nov. PMID 34183789, Free PMC Article
  3. Genetics Insight for COVID-19 Susceptibility and Severity: A Review. Fricke-Galindo I, et al. Front Immunol, 2021. PMID 33868239, Free PMC Article
  4. Overexpression of chemokine receptor lymphotactin receptor 1 has prognostic value in clear cell renal cell carcinoma. Chang X, et al. Mol Genet Genomic Med, 2021 Jan. PMID 33377624, Free PMC Article
  5. The chemokine lymphotactin and its recombinant variants in oral cancer cell regulation. Abdullah Zubir AZ, et al. Oral Dis, 2020 Nov. PMID 32562323

See all (42) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Systematic Pan-Cancer Analysis Reveals X-C Motif Chemokine Receptor 1 as a Prognostic and Immunological Biomarker.
    Title: Systematic Pan-Cancer Analysis Reveals X-C Motif Chemokine Receptor 1 as a Prognostic and Immunological Biomarker.
  2. Overexpression of chemokine receptor lymphotactin receptor 1 has prognostic value in clear cell renal cell carcinoma.
    Title: Overexpression of chemokine receptor lymphotactin receptor 1 has prognostic value in clear cell renal cell carcinoma.
  3. Structure-function guided modeling of chemokine-GPCR specificity for the chemokine XCL1 and its receptor XCR1.
    Title: Structure-function guided modeling of chemokine-GPCR specificity for the chemokine XCL1 and its receptor XCR1.
  4. XCL1-XCR1 chemokine pathway promotes trophoblast invasion by increasing matrix metalloproteinase activity in human first-trimester placenta
    Title: XCL1-XCR1 pathway promotes trophoblast invasion at maternal-fetal interface by inducing MMP-2/MMP-9 activity.
  5. Our study provides the basis for further investigation of the molecular mechanism by which down-regulation of XCR1 promotes the development and progression of HCC.
    Title: Transcriptomic analyses of chemokines reveal that down-regulation of XCR1 is associated with advanced hepatocellular carcinoma.
  6. Demonstrate equivalence between human and mouse XCR1(+) dendritic cells and human and mouse Langerhans cells.
    Title: Comparative genomics analysis of mononuclear phagocyte subsets confirms homology between lymphoid tissue-resident and dermal XCR1(+) DCs in mouse and human and distinguishes them from Langerhans cells.
  7. results indicate that XCR1 is a new potential therapeutic target for the treatment of lung cancer bone metastasis
    Title: XCR1 promotes cell growth and migration and is correlated with bone metastasis in non-small cell lung cancer.
  8. Induction of potent CD8 T cell cytotoxicity by specific targeting of antigen to cross-presenting dendritic cells in vivo via murine or human XCR1.
    Title: Induction of potent CD8 T cell cytotoxicity by specific targeting of antigen to cross-presenting dendritic cells in vivo via murine or human XCR1.
  9. XCR1 is expressed early during the course of tumorigenic transformation and contributes towards increased cell migration and proliferation, which can facilitate the prometastatic behavior of epithelial ovarian cancer cells.
    Title: The lymphotactin receptor is expressed in epithelial ovarian carcinoma and contributes to cell migration and proliferation.
  10. CD8alpha-positive dendritic cells (DCs) and CD103-positive DCs belong to a common DC subset which is unequivocally identified by XCR1 transgene expression despite their different anatomical locations.
    Title: Cutting edge: expression of XCR1 defines mouse lymphoid-tissue resident and migratory dendritic cells of the CD8α+ type.
Submit: New GeneRIF Correction See all GeneRIFs (18)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables C-C chemokine binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables C-C chemokine receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables chemokine receptor activity TAS
Traceable Author Statement
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in G protein-coupled receptor signaling pathway TAS
Traceable Author Statement
more info
 PubMed 
involved_in G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger TAS
Traceable Author Statement
more info
 PubMed 
involved_in calcium-mediated signaling IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cell chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in chemokine-mediated signaling pathway IEA
Inferred from Electronic Annotation
more info
  
involved_in chemotaxis TAS
Traceable Author Statement
more info
 PubMed 
involved_in immune response IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in inflammatory response TAS
Traceable Author Statement
more info
 PubMed 
involved_in positive regulation of cytosolic calcium ion concentration IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in release of sequestered calcium ion into cytosol IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in external side of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
chemokine XC receptor 1
Names
G protein-coupled receptor 5
XC chemokine receptor 1
chemokine (C motif) XC receptor 1
chemokine (C motif) receptor 1
lymphotactin receptor

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001024644.2 → NP_001019815.1  chemokine XC receptor 1

    See identical proteins and their annotated locations for NP_001019815.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 3. All three variants encode the same protein.
    Source sequence(s)
    AB189435, AC099782, BC069075, BC095533
    Consensus CDS
    CCDS2736.1
    UniProtKB/Swiss-Prot
    P46094
    UniProtKB/TrEMBL
    B2RAP0, Q502V0
    Related
    ENSP00000310405.3, ENST00000309285.4
    Conserved Domains (1) summary
    cd15182
    Location:32 → 298
    7tmA_XCR1; XC chemokine receptor 1, member of the class A family of seven-transmembrane G protein-coupled receptors

  2. NM_001381860.1 → NP_001368789.1  chemokine XC receptor 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) represents the longest transcript. All three variants encode the same protein.
    Source sequence(s)
    AC099782, AC104439, AC133140
    Consensus CDS
    CCDS2736.1
    UniProtKB/Swiss-Prot
    P46094
    UniProtKB/TrEMBL
    B2RAP0, Q502V0
    Related
    ENSP00000507745.1, ENST00000683768.1
    Conserved Domains (1) summary
    cd15182
    Location:32 → 298
    7tmA_XCR1; XC chemokine receptor 1, member of the class A family of seven-transmembrane G protein-coupled receptors

  3. NM_005283.3 → NP_005274.1  chemokine XC receptor 1

    See identical proteins and their annotated locations for NP_005274.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) differs in the 5' UTR compared to variant 3. All three variants encode the same protein.
    Source sequence(s)
    AB189434, AC099782, BC069075, BC095533
    Consensus CDS
    CCDS2736.1
    UniProtKB/Swiss-Prot
    P46094
    UniProtKB/TrEMBL
    B2RAP0, Q502V0
    Related
    ENSP00000379277.3, ENST00000395946.3
    Conserved Domains (1) summary
    cd15182
    Location:32 → 298
    7tmA_XCR1; XC chemokine receptor 1, member of the class A family of seven-transmembrane G protein-coupled receptors

RNA

  1. NR_170111.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC104439, AC133140

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    46017007..46085844 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    46032885..46101714 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P46094.1 GenPept UniProtKB/Swiss-Prot:P46094

Gene LinkOut

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