CCR6 C-C motif chemokine receptor 6 [Homo sapiens (human)] - Gene

Summary

Official Symbol: CCR6provided by HGNC
Official Full Name: C-C motif chemokine receptor 6provided by HGNC
Primary source: HGNC:HGNC:1607
See related: Ensembl:ENSG00000112486 MIM:601835; AllianceGenome:HGNC:1607
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: BN-1; DCR2; DRY6; CCR-6; CD196; CKRL3; GPR29; CKR-L3; CMKBR6; GPRCY4; STRL22; CC-CKR-6; C-C CKR-6
Summary: This gene encodes a member of the beta chemokine receptor family, which is predicted to be a seven transmembrane protein similar to G protein-coupled receptors. The gene is preferentially expressed by immature dendritic cells and memory T cells. The ligand of this receptor is macrophage inflammatory protein 3 alpha (MIP-3 alpha). This receptor has been shown to be important for B-lineage maturation and antigen-driven B-cell differentiation, and it may regulate the migration and recruitment of dentritic and T cells during inflammatory and immunological responses. Alternatively spliced transcript variants that encode the same protein have been described for this gene. [provided by RefSeq, Jul 2008]
Expression: Biased expression in lymph node (RPKM 8.0), appendix (RPKM 6.0) and 13 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 6q27

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (167111795..167139141)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (168494454..168521816)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (167525283..167552629)

Chromosome 6 - NC_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

CCL18 aggravates atherosclerosis by inducing CCR6-dependent T-cell influx and polarization.
Title: CCL18 aggravates atherosclerosis by inducing CCR6-dependent T-cell influx and polarization.
Pro-Fibrotic Effects of CCL18 on Human Lung Fibroblasts Are Mediated via CCR6.
Title: Pro-Fibrotic Effects of CCL18 on Human Lung Fibroblasts Are Mediated via CCR6.
Role of the CCL20/CCR6 axis in tubular epithelial cell injury: Kidney-specific translational insights from acute kidney injury to chronic kidney disease.
Title: Role of the CCL20/CCR6 axis in tubular epithelial cell injury: Kidney-specific translational insights from acute kidney injury to chronic kidney disease.
Increased gene expression of CCR6 and RORgammat in peripheral blood cells of rheumatoid arthritis patients and their correlation with anti-cyclic citrullinated peptide and disease activity.
Title: Increased gene expression of CCR6 and RORγt in peripheral blood cells of rheumatoid arthritis patients and their correlation with anti-cyclic citrullinated peptide and disease activity.
Clinical Significance of the Pre-Transplant CXCR3 and CCR6 Expression on T Cells In Kidney Graft Recipients.
Title: Clinical Significance of the Pre-Transplant CXCR3 and CCR6 Expression on T Cells In Kidney Graft Recipients.
SMAD4 Suppresses Colitis-associated Carcinoma Through Inhibition of CCL20/CCR6-mediated Inflammation.
Title: SMAD4 Suppresses Colitis-associated Carcinoma Through Inhibition of CCL20/CCR6-mediated Inflammation.
CCR6 activation links innate immune responses to mucosa-associated lymphoid tissue lymphoma development.
Title: CCR6 activation links innate immune responses to mucosa-associated lymphoid tissue lymphoma development.
rs9459874 and rs1012656 in CCR6/FGFR1OP confer susceptibility to primary biliary cholangitis.
Title: rs9459874 and rs1012656 in CCR6/FGFR1OP confer susceptibility to primary biliary cholangitis.
Glycogen synthase kinase 3beta/CCR6-positive bone marrow cells correlate with disease activity in multicentric Castleman disease-TAFRO.
Title: Glycogen synthase kinase 3β/CCR6-positive bone marrow cells correlate with disease activity in multicentric Castleman disease-TAFRO.
Human prostate cancer bone metastases have an actionable immunosuppressive microenvironment.
Title: Human prostate cancer bone metastases have an actionable immunosuppressive microenvironment.

Submit: New GeneRIF Correction See all GeneRIFs (166)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A regulatory variant in CCR6 is associated with rheumatoid arthritis susceptibility. EBI GWAS Catalog EBI GWAS CatalogPubMed
Amerindian-specific regions under positive selection harbour new lipid variants in Latinos. EBI GWAS Catalog EBI GWAS CatalogPubMed
Fucosyltransferase 2 (FUT2) non-secretor status is associated with Crohn's disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genetics of rheumatoid arthritis contributes to biology and drug discovery. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study for vitiligo identifies susceptibility loci at 6q27 and the MHC. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of autistic-like traits in a general population study of young adults. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of Crohn's disease in Koreans revealed three new susceptibility loci and common attributes of genetic susceptibility across ethnic populations. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Novel risk loci for rheumatoid arthritis in Han Chinese and congruence with risk variants in Europeans. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp120	env	HIV-1 gp120 upregulates the expression of chemokine (C-C motif) receptor 6 (CCR6) in human B cells	PubMed
	env	HIV-1 gp120 interactions with CXCR4 and CCR5 lead to the cross-desensitization of CCR6 and CCR7; this gp120-induced inhibition is strictly dependent on CXCR4 or CCR5 and lipid rafts but not on CD4 or V(H)3-expressing BCR	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH70644 (e-PCR)
- UniSTS:50194

D8S2279 (e-PCR)
- UniSTS:473907

CCR6_1762 (e-PCR)
- UniSTS:277065

STS-U68030 (e-PCR)
- UniSTS:41552

RH46835 (e-PCR)
- UniSTS:1916

PMC135988P8 (e-PCR)
- UniSTS:270794

SHGC-105352 (e-PCR)
- UniSTS:183250

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 binding	IDA Inferred from Direct Assay more info	PubMed
enables C-C chemokine binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables C-C chemokine receptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables C-C chemokine receptor activity	IDA Inferred from Direct Assay more info	PubMed
enables C-C chemokine receptor activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables chemokine receptor activity	TAS Traceable Author Statement more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables signaling receptor activity	TAS Traceable Author Statement more info	PubMed

Process	Evidence Code	Pubs
involved_in DN2 thymocyte differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in DN3 thymocyte differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in T cell migration	ISS Inferred from Sequence or Structural Similarity more info
involved_in calcium-mediated signaling	IBA Inferred from Biological aspect of Ancestor more info
involved_in calcium-mediated signaling	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cell chemotaxis	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell chemotaxis	IDA Inferred from Direct Assay more info	PubMed
involved_in cellular defense response	TAS Traceable Author Statement more info	PubMed
involved_in chemokine-mediated signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in chemotaxis	IDA Inferred from Direct Assay more info	PubMed
involved_in chemotaxis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in dendritic cell chemotaxis	TAS Traceable Author Statement more info	PubMed
involved_in humoral immune response	TAS Traceable Author Statement more info	PubMed
involved_in immune response	IBA Inferred from Biological aspect of Ancestor more info
involved_in isotype switching to IgA isotypes	ISS Inferred from Sequence or Structural Similarity more info
involved_in leukocyte migration involved in inflammatory response	ISS Inferred from Sequence or Structural Similarity more info
involved_in lymphocyte migration	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of cytosolic calcium ion concentration	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of dendritic cell chemotaxis	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of flagellated sperm motility involved in capacitation	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of T cell migration	ISS Inferred from Sequence or Structural Similarity more info
involved_in signal transduction	TAS Traceable Author Statement more info	PubMed
involved_in thymocyte migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in thymocyte migration	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in cell surface	IDA Inferred from Direct Assay more info	PubMed
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
located_in sperm flagellum	IDA Inferred from Direct Assay more info	PubMed
located_in sperm midpiece	IDA Inferred from Direct Assay more info	PubMed
located_in sperm plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in sperm principal piece	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: C-C chemokine receptor type 6

Names: G protein-coupled receptor 29; LARC receptor; chemokine (C-C motif) receptor 6; chemokine (C-C) receptor 6; chemokine receptor-like 3; seven-transmembrane receptor, lymphocyte, 22

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)

NM_001394582.1 → NP_001381511.1 C-C chemokine receptor type 6

Status: REVIEWED

Source sequence(s)

AL121935

Consensus CDS

CCDS5298.1

UniProtKB/Swiss-Prot

E1P5C6, P51684, P78553, Q92846

UniProtKB/TrEMBL

A8KAF0

Related

ENSP00000339393.4, ENST00000349984.6

Conserved Domains (1) summary

cd15172
Location:47 → 327

7tmA_CCR6; CC chemokine receptor type 6, member of the class A family of seven-transmembrane G protein-coupled receptors
NM_004367.6 → NP_004358.2 C-C chemokine receptor type 6

See identical proteins and their annotated locations for NP_004358.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) differs in the 5' UTR compared to variant 2. Variants 1 and 2 encode the same protein.

Source sequence(s)

AL121935, CD692892, DN996219

Consensus CDS

CCDS5298.1

UniProtKB/Swiss-Prot

E1P5C6, P51684, P78553, Q92846

UniProtKB/TrEMBL

A8KAF0

Related

ENSP00000383715.2, ENST00000400926.5

Conserved Domains (1) summary

cd15172
Location:47 → 327

7tmA_CCR6; CC chemokine receptor type 6, member of the class A family of seven-transmembrane G protein-coupled receptors
NM_031409.4 → NP_113597.2 C-C chemokine receptor type 6

See identical proteins and their annotated locations for NP_113597.2

Status: REVIEWED

Description

Transcript Variant: This variant (2) is the longer transcript. Variants 1 and 2 encode the same protein.

Source sequence(s)

AL121935, BC037960, DA645096

Consensus CDS

CCDS5298.1

UniProtKB/Swiss-Prot

E1P5C6, P51684, P78553, Q92846

UniProtKB/TrEMBL

A8KAF0

Related

ENSP00000343952.5, ENST00000341935.10

Conserved Domains (1) summary

cd15172
Location:47 → 327

7tmA_CCR6; CC chemokine receptor type 6, member of the class A family of seven-transmembrane G protein-coupled receptors