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

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]

OMIM ResearchGenerating clinical summary…

Active trials

223

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.04

LOEUF

Multiple*

Mechanism· predicted

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 OE?0.50 (0.26–1.04)

0≤0.351.4

Missense OE?0.59 (0.51–0.69)

0≤0.61.4

Synonymous OE?1.08

0≤1.21.6

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

Background carrier burden — how many people carry a rare variant somewhere in CCR6?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 180

348 rare PASS variants

Rare truncating (LoF)

1 in 11,000

26 rare PASS variants

Rare synonymous (reference)

1 in 360

201 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for CCR6. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 180	1 in 11,000
South Asian	~43k	1 in 110	≈ 1 in 8,600
Remaining (unassigned)	~30k	1 in 160	≈ 1 in 30,000
European (Finnish)	~27k	1 in 1,500	≈ 1 in 27,000
Admixed American	~22k	1 in 230	none seen
African / African American	~21k	1 in 340	≈ 1 in 4,400
East Asian	~20k	1 in 180	≈ 1 in 6,600
Ashkenazi Jewish	~13k	1 in 750	none seen
Middle Eastern	~2,884	1 in 120	≈ 1 in 2,900

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): All 2 coding exons well covered in gnomAD exomes and genomes.? see exons ↓