CCR6

Chr 6

C-C motif chemokine receptor 6

Also known as: BN-1, C-C CKR-6, CC-CKR-6, CCR-6, CD196, CKR-L3, CKRL3, CMKBR6

NCBI Gene: 1235ENSG00000112486UniProt: O00421

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]

92
ClinVar variants
53
Pathogenic / LP
0.01
pLI score
4
Active trials
Clinical Summary— CCR6
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.01) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
53 Pathogenic / Likely Pathogenic· 31 VUS of 92 total submissions
💊
Clinical Trials
4 active or recruiting trials — potential therapeutic options may be available

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
1.04LOEUF
pLI 0.006
Z-score 1.48
OE 0.50 (0.26–1.04)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
2.13Z-score
OE missense 0.59 (0.51–0.69)
127 obs / 214.8 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.50 (0.26–1.04)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.59 (0.51–0.69)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.08
0≤1.21.6
LoF obs/exp: 5 / 10.1Missense obs/exp: 127 / 214.8Syn Z: -0.58

ClinVar Variant Classifications

92 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic50
Likely Pathogenic3
VUS31
Likely Benign7
Benign1
50
Pathogenic
3
Likely Pathogenic
31
VUS
7
Likely Benign
1
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
50
0
50
Likely Pathogenic
0
0
3
0
3
VUS
0
27
4
0
31
Likely Benign
0
6
0
1
7
Benign
0
0
0
1
1
Total03357292

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

CCR6 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Antigen dominance hierarchies shape TCF1(+) progenitor CD8 T cell phenotypes in tumors.
Burger ML et al.·Cell
2021
OMIP-099: 31-color spectral flow cytometry panel to investigate the steady-state phenotype of human T cells.
Zacharias ZR et al.·Cytometry A
2024
Lipid droplet accumulation mediates macrophage survival and Treg recruitment via the CCL20/CCR6 axis in human hepatocellular carcinoma.
Wang Y et al.·Cell Mol Immunol
2024
Interleukin-17A and Keratinocytes in Psoriasis.
Furue M et al.·Int J Mol Sci
2020Review
Epidermal Th22 and Tc17 cells form a localized disease memory in clinically healed psoriasis.
Cheuk S et al.·J Immunol
2014
Mucosal signatures of pathogenic T cells in HLA-B*27+ anterior uveitis and axial spondyloarthritis.
Paley MA et al.·JCI Insight
2024
Pathogenic conversion of Foxp3+ T cells into TH17 cells in autoimmune arthritis.
Komatsu N et al.·Nat Med
2014
Contribution of germline and somatic mutations to risk of neuromyelitis optica spectrum disorder.
Yata T et al.·Cell Genom
2025Meta-analysis
Human LY9 governs CD4(+) T cell IFN-γ immunity to Mycobacterium tuberculosis.
Ogishi M et al.·Sci Immunol
2025
The chemokine CCL20 promotes hepatocyte cholesterol deposition during metabolic dysfunction-associated steatohepatitis by regulating OLR1 expression.
Yin M et al.·Metabolism
2025
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov
Anorexia Nervosa

The Fecal Microbiome Transplant (FMT) Study for Anorexia Nervosa

RECRUITING
NCT07143981London Health Sciences Centre Research Institute OR Lawson Research Institute of St. Joseph'sStarted 2026-01-15
Rhematoid Arthritis

Evaluation of CCR6 Gene Expression and Circulating CCL20 Levels as Potential Biomarkers in Rheumatoid Arthritis

NOT YET RECRUITING
NCT07397741Sohag UniversityStarted 2026-03-01
Gene expression by quantitative Real Time PCR
Type1diabetes

Crosstalk Between Mucosal-Associated Invariant T (MAIT) Cells and the Gut Microbiota and Mucosa in the Development of Type 1 Diabetes in Children

RECRUITING
NCT05054361Institut National de la Santé Et de la Recherche Médicale, FranceStarted 2022-01-01
MAIT cells analysisMAIT cytokines production analysisLactulose/Mannitol Test
Spondyloarthritis

The Role of IL-23 in Chronic Inflammatory Disease: Exploring the Cellular and Molecular Targets of IL-23 Signaling in Peripheral and Axial Spondyloarthritis

RECRUITING
NCT05290363Phase NAInstitut PasteurStarted 2022-10-06
Blood samplingsynovial aspiration

External Resources

Links to major genomics databases and tools