CCL19
C-C motif chemokine ligand 19, the group of Chemokine ligands
Basic information
Region (hg38): 9:34689569-34691276
Previous symbols: [ "SCYA19" ]
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 CCL19 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 | 0 | |||||
| missense | 6 | |||||
| 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 | 0 | 0 |
Variants in CCL19
This is a list of pathogenic ClinVar variants found in the CCL19 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 9-34689965-G-A | not specified | Uncertain significance (Feb 06, 2023) | ||
| 9-34690235-C-G | not specified | Uncertain significance (Nov 22, 2023) | ||
| 9-34690270-T-G | not specified | Uncertain significance (Oct 20, 2023) | ||
| 9-34690280-T-C | not specified | Uncertain significance (Feb 05, 2024) | ||
| 9-34691094-G-C | not specified | Uncertain significance (Jul 05, 2023) | ||
| 9-34691127-G-C | not specified | Uncertain significance (Apr 25, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CCL19 | protein_coding | protein_coding | ENST00000311925 | 4 | 1711 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.317 | 0.620 | 124332 | 0 | 2 | 124334 | 0.00000804 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.15 | 33 | 57.4 | 0.575 | 0.00000324 | 625 |
| Missense in Polyphen | 11 | 23.652 | 0.46507 | 266 | ||
| Synonymous | 1.95 | 10 | 21.5 | 0.465 | 9.91e-7 | 207 |
| Loss of Function | 1.44 | 1 | 4.16 | 0.240 | 1.77e-7 | 48 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000129 | 0.000126 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: May play a role not only in inflammatory and immunological responses but also in normal lymphocyte recirculation and homing. May play an important role in trafficking of T-cells in thymus, and T-cell and B-cell migration to secondary lymphoid organs. Binds to chemokine receptor CCR7. Recombinant CCL19 shows potent chemotactic activity for T-cells and B-cells but not for granulocytes and monocytes. Binds to atypical chemokine receptor ACKR4 and mediates the recruitment of beta-arrestin (ARRB1/2) to ACKR4. {ECO:0000269|PubMed:9498785}.;
- 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;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
- 0.225
Intolerance Scores
- loftool
- 0.353
- rvis_EVS
- 0.06
- rvis_percentile_EVS
- 58
Haploinsufficiency Scores
- pHI
- 0.0400
- hipred
- N
- hipred_score
- 0.146
- ghis
- 0.444
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.335
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Low |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Low | Medium |
Mouse Genome Informatics
- Gene name
- Ccl19
- Phenotype
- hematopoietic system phenotype; immune system phenotype;
Zebrafish Information Network
- Gene name
- ccl19a.1
- Affected structure
- whole organism
- Phenotype tag
- abnormal
- Phenotype quality
- wholly dorsalized
Gene ontology
- Biological process
- establishment of T cell polarity;immunological synapse formation;dendritic cell chemotaxis;myeloid dendritic cell chemotaxis;monocyte chemotaxis;positive regulation of dendritic cell antigen processing and presentation;cellular calcium ion homeostasis;inflammatory response;immune response;cell communication;G protein-coupled receptor signaling pathway;activation of JUN kinase activity;response to virus;regulation of signaling receptor activity;positive regulation of glycoprotein biosynthetic process;cytokine-mediated signaling pathway;neutrophil chemotaxis;T cell costimulation;positive regulation of interleukin-12 production;positive regulation of tumor necrosis factor production;response to prostaglandin E;positive regulation of T cell proliferation;positive regulation of I-kappaB kinase/NF-kappaB signaling;positive regulation of GTPase activity;positive regulation of phosphatidylinositol 3-kinase activity;positive regulation of T-helper 1 cell differentiation;positive regulation of endocytosis;positive regulation of protein kinase activity;positive regulation of JNK cascade;lymphocyte chemotaxis;positive regulation of receptor-mediated endocytosis;cell maturation;positive regulation of interleukin-1 beta secretion;positive regulation of chemotaxis;release of sequestered calcium ion into cytosol;positive regulation of protein kinase B signaling;regulation of cell projection assembly;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;response to nitric oxide;interleukin-12 secretion;positive regulation of neutrophil chemotaxis;mature conventional dendritic cell differentiation;cellular response to virus;positive regulation of NIK/NF-kappaB signaling;positive regulation of cell motility;positive regulation of dendritic cell dendrite assembly;negative regulation of dendritic cell apoptotic process
- Cellular component
- extracellular region;extracellular space;cell
- Molecular function
- chemokine activity;CCR7 chemokine receptor binding;CCR10 chemokine receptor binding;chemokine receptor binding;CCR chemokine receptor binding