CCR6

C-C motif chemokine receptor 6, the group of C-C motif chemokine receptors|CD molecules

Basic information

Region (hg38): 6:167111806-167139141

Previous symbols: [ "STRL22" ]

Links

ENSG00000112486 ∙ NCBI:1235 ∙ OMIM:601835 ∙ HGNC:1607 ∙ Uniprot:P51684 ∙ 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 CCR6 gene.

• Inborn genetic diseases (9 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCR6 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				1	1	2
missense			9		1	10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	1	2

Variants in CCR6

This is a list of pathogenic ClinVar variants found in the CCR6 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-167136141-G-A		not specified	Uncertain significance (May 03, 2023)
6-167136364-C-T		not specified	Uncertain significance (Aug 02, 2021)
6-167136379-C-T		not specified	Uncertain significance (Feb 16, 2023)
6-167136380-G-A			Likely benign (Jul 31, 2018)
6-167136510-C-T		not specified	Uncertain significance (Aug 03, 2022)
6-167136559-C-T		not specified	Uncertain significance (May 06, 2022)
6-167136700-G-A		not specified	Uncertain significance (Feb 05, 2024)
6-167136707-A-G			Benign (Jul 20, 2018)
6-167136717-C-A		not specified	Uncertain significance (May 23, 2023)
6-167137077-A-G		not specified	Uncertain significance (May 24, 2023)
6-167137266-T-C		not specified	Uncertain significance (Oct 26, 2022)
6-167137336-C-T			Benign (Jul 02, 2018)
6-167137350-A-G		not specified	Uncertain significance (Jun 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCR6	protein_coding	protein_coding	ENST00000341935	2	27890

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00579	0.910	125736	0	12	125748	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.13	127	215	0.591	0.0000120	2459
Missense in Polyphen		21	52.824	0.39755		664
Synonymous	-0.582	100	92.9	1.08	0.00000602	749
Loss of Function	1.48	5	10.1	0.496	5.98e-7	117

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000247	0.000246
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000443	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for the C-C type chemokine CCL20 (PubMed:9169459). Binds to CCL20 and subsequently transduces a signal by increasing the intracellular calcium ion levels (PubMed:20068036). Although CCL20 is its major ligand it can also act as a receptor for non-chemokine ligands such as beta-defensins (PubMed:25585877). Binds to defensin DEFB1 leading to increase in intracellular calcium ions and cAMP levels. Its binding to DEFB1 is essential for the function of DEFB1 in regulating sperm motility and bactericidal activity (PubMed:25122636). Binds to defensins DEFB4 and DEFB4A/B and mediates their chemotactic effects (PubMed:20068036). The ligand-receptor pair CCL20-CCR6 is responsible for the chemotaxis of dendritic cells (DC), effector/ memory T-cells and B-cells and plays an important role at skin and mucosal surfaces under homeostatic and inflammatory conditions, as well as in pathology, including cancer and various autoimmune diseases. CCR6-mediated signals are essential for immune responses to microbes in the intestinal mucosa and in the modulation of inflammatory responses initiated by tissue insult and trauma (PubMed:21376174). CCR6 is essential for the recruitment of both the proinflammatory IL17 producing helper T-cells (Th17) and the regulatory T-cells (Treg) to sites of inflammation. Required for the normal migration of Th17 cells in Peyers-patches and other related tissue sites of the intestine and plays a role in regulating effector T-cell balance and distribution in inflamed intestine. Plays an important role in the coordination of early thymocyte precursor migration events important for normal subsequent thymocyte precursor development, but is not required for the formation of normal thymic natural regulatory T-cells (nTregs). Required for optimal differentiation of DN2 and DN3 thymocyte precursors. Essential for B-cell localization in the subepithelial dome of Peyers-patches and for efficient B-cell isotype switching to IgA in the Peyers-patches. Essential for appropriate anatomical distribution of memory B-cells in the spleen and for the secondary recall response of memory B-cells (By similarity). Positively regulates sperm motility and chemotaxis via its binding to CCL20 (PubMed:23765988). {ECO:0000250|UniProtKB:O54689, ECO:0000269|PubMed:20068036, ECO:0000269|PubMed:23765988, ECO:0000269|PubMed:25122636, ECO:0000269|PubMed:9169459, ECO:0000303|PubMed:21376174, ECO:0000303|PubMed:25585877}.
• Pathway: Chemokine signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Peptide GPCRs;Chemokine signaling pathway;GPCRs, Class A Rhodopsin-like;Signaling by GPCR;Signal Transduction;Antimicrobial peptides;Innate Immune System;Immune System;Chemokine receptors bind chemokines;Peptide ligand-binding receptors;Beta defensins;Class A/1 (Rhodopsin-like receptors);Defensins;GPCR ligand binding;G alpha (i) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.0938

Intolerance Scores

• loftool: 0.479
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.35

Haploinsufficiency Scores

• pHI: 0.343
• hipred: N
• hipred_score: 0.483
• ghis: 0.540

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.834

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccr6
• Phenotype: homeostasis/metabolism phenotype; immune system phenotype; normal phenotype; hematopoietic 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)

Gene ontology

• Biological process: dendritic cell chemotaxis;leukocyte migration involved in inflammatory response;chemotaxis;immune response;humoral immune response;cellular defense response;signal transduction;G protein-coupled receptor signaling pathway;positive regulation of cytosolic calcium ion concentration;positive regulation of epithelial cell migration;calcium-mediated signaling;isotype switching to IgA isotypes;cell chemotaxis;positive regulation of flagellated sperm motility involved in capacitation;chemokine-mediated signaling pathway;lymphocyte migration;T cell migration;thymocyte migration;DN2 thymocyte differentiation;DN3 thymocyte differentiation;regulation of T cell migration;positive regulation of dendritic cell chemotaxis
• Cellular component: plasma membrane;integral component of plasma membrane;external side of plasma membrane;cell surface;sperm flagellum;sperm midpiece;sperm principal piece;sperm plasma membrane
• Molecular function: chemokine receptor activity;protein binding;C-C chemokine receptor activity;chemokine binding;C-C chemokine binding;signaling receptor activity