CCL20

Chr 2

C-C motif chemokine ligand 20

Also known as: CKb4, Exodus, LARC, MIP-3-alpha, MIP-3a, MIP3A, SCYA20, ST38

NCBI Gene: 6364 ENSG00000115009 UniProt: P78556

The protein CCL20 is a chemokine that binds to receptor CCR6 to attract immune cells including dendritic cells, T-cells, and B-cells to sites of inflammation and mucosal surfaces, and also exhibits antimicrobial activity against bacteria. This gene is not highly constrained against loss-of-function mutations (pLI = 0.0002, LOEUF = 1.875) and is not currently associated with established Mendelian disease phenotypes in pediatric patients.

Summary from RefSeq, UniProt

P/LP submissions

P/LP missense

1.88

LOEUF

Mechanism· predicted

Clinical Summary— CCL20

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Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

24 unique Pathogenic / Likely Pathogenic· 10 VUS of 44 total submissions

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Clinical Trials

3 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

1.88LOEUF

pLI 0.000

Z-score -0.31

OE 1.16 (0.58–1.88)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint

0.59Z-score

OE missense 0.78 (0.61–1.00)

43 obs / 55.3 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios

LoF OE1.16 (0.58–1.88)

0≤0.351.4

Missense OE0.78 (0.61–1.00)

0≤0.61.4

Synonymous OE0.83

0≤1.21.6

LoF obs/exp: 5 / 4.3Missense obs/exp: 43 / 55.3Syn Z: 0.57

0.76top 25%

GOF

0.5269th %ile

LOF

0.1993th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction 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

44 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic23

Likely Pathogenic1

VUS10

Likely Benign4

Benign1

Pathogenic

Likely Pathogenic

VUS

Likely Benign

Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	0	23	0	23
Likely Pathogenic	0	1	0	1
VUS	6	4	0	10
Likely Benign	4	0	0	4
Benign	0	0	1	1
Total	10	28	1	39

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

View in ClinVar →

Protein Context — Lollipop Plot

CCL20 · protein map & ClinVar variants

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

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

Pneumonia

Phase I Single-blind Clinical Trial to Evaluate the Safety and Local Immune Activation of a Toll-like Receptor 5 Agonist (FLAMOD) Administered by Aerosol

RECRUITING

NCT06681402Phase PHASE1Institut National de la Santé Et de la Recherche Médicale, FranceStarted 2025-04-14

FLAMODPlacebo

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

Knee Osteoarthritis

Dietary Supplementation With Blueberry in OA

ACTIVE NOT RECRUITING

NCT05784545Phase NAUniversity of ExeterStarted 2023-05-22