CCL21
Chr 9C-C motif chemokine ligand 21
Also known as: 6Ckine, CKb9, ECL, SCYA21, SLC, TCA4
CCL21 encodes a chemokine that stimulates chemotaxis of thymocytes and activated T-cells and mediates homing of lymphocytes to secondary lymphoid organs by binding to chemokine receptor 7. Mutations cause autosomal recessive combined immunodeficiency with defective lymphocyte homing and lymph node dysgenesis, typically presenting in early childhood with recurrent infections. The gene shows tolerance to loss-of-function variation (LOEUF 1.212), consistent with the recessive inheritance pattern.
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Highly tolerant — LoF variants common in population
Mild missense constraint
The highest-scoring mechanism for this gene is dominant-negative.
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
102 submitted variants in ClinVar
Classification Summary
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | 0 | 0 | 63 | 0 | 63 |
Likely Pathogenic | 0 | 0 | 8 | 0 | 8 |
VUS | 0 | 14 | 12 | 0 | 26 |
Likely Benign | 0 | 2 | 0 | 0 | 2 |
Benign | 0 | 0 | 0 | 1 | 1 |
| Total | 0 | 16 | 83 | 1 | 100 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
CCL21 · 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
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
Characterization of Microbiological and Genetic Features in Prostate Cancer and Their Association with Disease Stage
ENROLLING BY INVITATIONNon-Ablative Laser to Treat Scarring Alopecia With Hair Follicle Gene Expression Analysis
RECRUITINGCCL21-Gene Modified Dendritic Cell Vaccine and Pembrolizumab in Treating Patients With Stage IV Non-small Cell Lung Cancer
ACTIVE NOT RECRUITINGExternal Resources
Links to major genomics databases and tools