CCL16

Chr 17

C-C motif chemokine ligand 16

Also known as: CKb12, HCC-4, ILINCK, LCC-1, LEC, LMC, Mtn-1, NCC-4

NCBI Gene: 6360ENSG00000275152UniProt: O15467

This gene is one of several cytokine genes clustered on the q-arm of chromosome 17. Cytokines are a family of secreted proteins involved in immunoregulatory and inflammatory processes. The CC cytokines are proteins characterized by two adjacent cysteines. The cytokine encoded by this gene displays chemotactic activity for lymphocytes and monocytes but not for neutrophils. This cytokine also shows a potent myelosuppressive activity and suppresses proliferation of myeloid progenitor cells. The expression of this gene is upregulated by IL-10. [provided by RefSeq, Jul 2008]

0
Active trials
6
Pathogenic / LP
32
ClinVar variants
4
Pubs (1 yr)
0.1
Missense Z
1.44
LOEUF
Clinical Summary— CCL16
⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.32) despite low pLI — interpret in context.
📋
ClinVar Variants
6 Pathogenic / Likely Pathogenic· 20 VUS of 32 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.44LOEUF
pLI 0.225
Z-score 1.10
OE 0.32 (0.11–1.44)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
0.12Z-score
OE missense 0.96 (0.78–1.18)
62 obs / 64.8 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.32 (0.11–1.44)
0≤0.351.4
Missense OE0.96 (0.78–1.18)
0≤0.61.4
Synonymous OE0.95
0≤1.21.6
LoF obs/exp: 1 / 3.1Missense obs/exp: 62 / 64.8Syn Z: 0.21
DN
DN
0.74top 25%
GOF
0.4875th %ile
LOF
0.2387th %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

32 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic6
VUS20
Likely Benign6
6
Pathogenic
20
VUS
6
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
6
0
6
Likely Pathogenic
0
0
0
0
0
VUS
0
16
4
0
20
Likely Benign
0
6
0
0
6
Benign
0
0
0
0
0
Total02210032

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

View in ClinVar →

CCL16 · protein map & ClinVar variants

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

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Landmark / reviewRecent case evidence
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 4 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
CCL2 is a key regulator and therapeutic target for periodontitis.
Jiang W et al.·J Clin Periodontol
2023
CCL16 maintains stem cell-like properties in breast cancer by activating CCR2/GSK3β/β-catenin/OCT4 axis.
Shen W et al.·Theranostics
2021
CC Chemokine Family Members' Modulation as a Novel Approach for Treating Central Nervous System and Peripheral Nervous System Injury-A Review of Clinical and Experimental Findings.
Ciechanowska A et al.·Int J Mol Sci
2024Review
Characterizing ligand-receptor interactions and unveiling the pro-tumorigenic role of CCL16-CCR1 axis in the microenvironment of hepatocellular carcinoma.
Dai Z et al.·Front Immunol
2024
Childhood obesity and insulin resistance is correlated with gut microbiome serum protein: an integrated metagenomic and proteomic analysis.
Liu L et al.·Sci Rep
2025Clinical trial
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

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