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: 1235 ENSG00000112486 UniProt: O00421 OMIM: 601835

This gene encodes a G protein-coupled chemokine receptor that binds CCL19 and chemerin, functioning in immune cell migration and the development of Th2 immune responses. The gene shows low constraint to loss-of-function variation (pLI 0.006), and no established Mendelian diseases have been associated with CCR6 mutations in pediatric populations based on the provided data.

OMIM ResearchSummary from RefSeq, UniProt

MultiplemechanismLOEUF 1.04

Clinical Summary— CCR6

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Population Constraint (gnomAD)

Low constraint (pLI 0.01) — loss-of-function variants are relatively tolerated in the population.

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Clinical Trials

4 active or recruiting trials — potential therapeutic options may be available

Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint

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

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

LoF OE0.50 (0.26–1.04)

0≤0.351.4

Missense OE0.59 (0.51–0.69)

0≤0.61.4

Synonymous OE1.08

0≤1.21.6

LoF obs/exp: 5 / 10.1Missense obs/exp: 127 / 214.8Syn Z: -0.58

0.85top 5%

GOF

0.76top 25%

LOF

0.1894th %ile

This gene has evidence for multiple mechanisms of pathogenicity (dominant-negative and gain-of-function). Both the Badonyi & Marsh prediction and the broader genomic evidence point to dominant-negative as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

DNprediction above median

GOFprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

0 submitted variants in ClinVar

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.

3D Protein StructureAlphaFold

External Resources

Links to major genomics databases and tools

Franklin by Genoox

AI-powered variant curation and clinical analysis

DECIPHER

Genomic variants and phenotypes in rare disease patients

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

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

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

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

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