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GeneBe

CCL20

C-C motif chemokine ligand 20, the group of Chemokine ligands

Basic information

Region (hg38): 2:227805738-227817564

Previous symbols: [ "SCYA20" ]

Links

ENSG00000115009NCBI:6364OMIM:601960HGNC:10619Uniprot:P78556AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CCL20 gene.

  • Inborn genetic diseases (2 variants)
  • not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCL20 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
clinvar
1
missense
1
clinvar
1
clinvar
2
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 1 1 1

Variants in CCL20

This is a list of pathogenic ClinVar variants found in the CCL20 region.

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

Position Type Phenotype Significance ClinVar
2-227815529-G-A Inborn genetic diseases Likely benign (Aug 01, 2022)2376820
2-227815559-A-G Inborn genetic diseases Uncertain significance (Mar 14, 2023)2460715
2-227816337-C-T Benign (Dec 28, 2017)733334

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CCL20protein_codingprotein_codingENST00000358813 43715
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.0002420.329125727081257350.0000318
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.5874355.30.7780.00000312626
Missense in Polyphen1016.4620.60748210
Synonymous0.5751518.10.8289.45e-7172
Loss of Function-0.30854.311.161.81e-756

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.00009460.0000924
European (Non-Finnish)0.00003600.0000352
Middle Eastern0.000.00
South Asian0.00003300.0000327
Other0.0001640.000163

dbNSFP

Source: dbNSFP

Function
FUNCTION: Acts as a ligand for C-C chemokine receptor CCR6. Signals through binding and activation of CCR6 and induces a strong chemotactic response and mobilization of intracellular calcium ions (PubMed:11352563, PubMed:11035086, 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 (PubMed:21376174). CCL20 acts as a chemotactic factor that attracts lymphocytes and, slightly, neutrophils, but not monocytes (PubMed:9038201, PubMed:11352563). Involved in the recruitment of both the proinflammatory IL17 producing helper T-cells (Th17) and the regulatory T-cells (Treg) to sites of inflammation. Required for optimal migration of thymic natural regulatory T cells (nTregs) and DN1 early thymocyte progenitor cells (By similarity). C-terminal processed forms have been shown to be equally chemotactically active for leukocytes (PubMed:11035086). Positively regulates sperm motility and chemotaxis via its binding to CCR6 which triggers Ca2+ mobilization in the sperm which is important for its motility (PubMed:23765988, PubMed:25122636). Inhibits proliferation of myeloid progenitors in colony formation assays (PubMed:9129037). May be involved in formation and function of the mucosal lymphoid tissues by attracting lymphocytes and dendritic cells towards epithelial cells (By similarity). Possesses antibacterial activity towards E.coli ATCC 25922 and S.aureus ATCC 29213 (PubMed:12149255). {ECO:0000250|UniProtKB:O89093, ECO:0000269|PubMed:11035086, ECO:0000269|PubMed:11352563, ECO:0000269|PubMed:12149255, ECO:0000269|PubMed:20068036, ECO:0000269|PubMed:23765988, ECO:0000269|PubMed:25122636, ECO:0000269|PubMed:9038201, ECO:0000269|PubMed:9129037, ECO:0000303|PubMed:21376174}.;
Pathway
TNF signaling pathway - Homo sapiens (human);Chemokine signaling pathway - Homo sapiens (human);IL-17 signaling pathway - Homo sapiens (human);Rheumatoid arthritis - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);EBV LMP1 signaling;Glucocorticoid Receptor Pathway;Nuclear Receptors Meta-Pathway;Chemokine signaling pathway;Interleukin-10 signaling;Signaling by GPCR;Signal Transduction;Chemokine receptors bind chemokines;Peptide ligand-binding receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;G alpha (i) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

pRec
0.207

Intolerance Scores

loftool
0.479
rvis_EVS
0.3
rvis_percentile_EVS
71.81

Haploinsufficiency Scores

pHI
0.282
hipred
N
hipred_score
0.412
ghis

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.995

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Ccl20
Phenotype

Gene ontology

Biological process
monocyte chemotaxis;chemotaxis;inflammatory response;immune response;signal transduction;G protein-coupled receptor signaling pathway;cell-cell signaling;regulation of signaling receptor activity;cytokine-mediated signaling pathway;neutrophil chemotaxis;calcium-mediated signaling using intracellular calcium source;defense response to bacterium;positive regulation of GTPase activity;lymphocyte chemotaxis;cell chemotaxis;chemokine-mediated signaling pathway;positive regulation of ERK1 and ERK2 cascade;cellular response to interferon-gamma;cellular response to interleukin-1;cellular response to tumor necrosis factor;T cell migration;thymocyte migration;positive regulation of T cell migration
Cellular component
extracellular region;extracellular space
Molecular function
protein binding;chemokine activity;CCR6 chemokine receptor binding;CCR chemokine receptor binding