CCL21
C-C motif chemokine ligand 21, the group of Chemokine ligands
Basic information
Region (hg38): 9:34709005-34710136
Previous symbols: [ "SCYA21" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCL21 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 | |||||
| missense | 7 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 6 | 1 | 1 |
Variants in CCL21
This is a list of pathogenic ClinVar variants found in the CCL21 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 9-34709419-C-T | not specified | Likely benign (Nov 12, 2021) | ||
| 9-34709423-C-T | not specified | Uncertain significance (Aug 25, 2024) | ||
| 9-34709509-C-A | not specified | Uncertain significance (Dec 09, 2023) | ||
| 9-34709534-C-G | not specified | Uncertain significance (Apr 18, 2024) | ||
| 9-34709542-G-A | not specified | Uncertain significance (Aug 26, 2024) | ||
| 9-34709583-T-C | Benign (Apr 28, 2018) | |||
| 9-34709587-G-T | not specified | Uncertain significance (Jan 03, 2024) | ||
| 9-34709594-T-C | not specified | Uncertain significance (Jan 31, 2024) | ||
| 9-34709674-G-T | not specified | Uncertain significance (Dec 14, 2022) | ||
| 9-34709841-C-A | not specified | Uncertain significance (Mar 21, 2022) | ||
| 9-34710059-T-C | not specified | Uncertain significance (Jul 02, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CCL21 | protein_coding | protein_coding | ENST00000259607 | 4 | 1120 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0362 | 0.842 | 125739 | 0 | 3 | 125742 | 0.0000119 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.118 | 73 | 75.9 | 0.962 | 0.00000419 | 855 |
| Missense in Polyphen | 22 | 28.847 | 0.76263 | 332 | ||
| Synonymous | 0.0625 | 28 | 28.4 | 0.985 | 0.00000131 | 271 |
| Loss of Function | 1.24 | 3 | 6.37 | 0.471 | 2.70e-7 | 74 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000615 | 0.0000615 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000176 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Inhibits hemopoiesis and stimulates chemotaxis. Chemotactic in vitro for thymocytes and activated T-cells, but not for B-cells, macrophages, or neutrophils. Shows preferential activity towards naive T-cells. May play a role in mediating homing of lymphocytes to secondary lymphoid organs. Binds to atypical chemokine receptor ACKR4 and mediates the recruitment of beta-arrestin (ARRB1/2) to ACKR4.;
- Pathway
- Chemokine signaling pathway - Homo sapiens (human);NF-kappa B signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Allograft Rejection;Chemokine signaling pathway;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
- 0.598
Intolerance Scores
- loftool
- 0.442
- rvis_EVS
- -0.08
- rvis_percentile_EVS
- 47.79
Haploinsufficiency Scores
- pHI
- 0.0448
- hipred
- N
- hipred_score
- 0.146
- ghis
- 0.552
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.539
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Low |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Gm21541
- Phenotype
Gene ontology
- Biological process
- establishment of T cell polarity;immunological synapse formation;positive regulation of cell-matrix adhesion;dendritic cell chemotaxis;monocyte chemotaxis;positive regulation of dendritic cell antigen processing and presentation;inflammatory response;immune response;G protein-coupled receptor signaling pathway;cell-cell signaling;regulation of signaling receptor activity;positive regulation of glycoprotein biosynthetic process;positive regulation of T cell chemotaxis;neutrophil chemotaxis;positive regulation of actin filament polymerization;positive regulation of pseudopodium assembly;T cell costimulation;ruffle organization;positive regulation of cell adhesion mediated by integrin;response to prostaglandin E;mesangial cell-matrix adhesion;chemokine (C-C motif) ligand 21 signaling pathway;positive regulation of I-kappaB kinase/NF-kappaB signaling;positive regulation of GTPase activity;positive regulation of phosphatidylinositol 3-kinase activity;positive regulation of protein kinase activity;positive regulation of JNK cascade;lymphocyte chemotaxis;positive regulation of receptor-mediated endocytosis;cell maturation;positive regulation of chemotaxis;release of sequestered calcium ion into cytosol;positive regulation of filopodium assembly;positive regulation of protein kinase B signaling;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;positive regulation of neutrophil chemotaxis;activation of GTPase activity;dendritic cell dendrite assembly;negative regulation of leukocyte tethering or rolling;cellular response to chemokine;positive regulation of cell motility;positive regulation of T cell migration;positive regulation of myeloid dendritic cell chemotaxis;negative regulation of dendritic cell dendrite assembly;negative regulation of dendritic cell apoptotic process
- Cellular component
- extracellular region;extracellular space;cell
- Molecular function
- protein binding;chemokine activity;CCR7 chemokine receptor binding;chemokine receptor binding;CCR chemokine receptor binding