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GeneBe

CCL19

C-C motif chemokine ligand 19, the group of Chemokine ligands

Basic information

Region (hg38): 9:34689569-34691276

Previous symbols: [ "SCYA19" ]

Links

ENSG00000172724NCBI:6363OMIM:602227HGNC:10617Uniprot:Q99731AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CCL19 gene.

  • Inborn genetic diseases (3 variants)

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
3
clinvar
3
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 3 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 Inborn genetic diseases Uncertain significance (Feb 06, 2023)2473438
9-34691094-G-C Inborn genetic diseases Uncertain significance (Jul 05, 2023)2600019
9-34691127-G-C Inborn genetic diseases Uncertain significance (Apr 25, 2023)2569703

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CCL19protein_codingprotein_codingENST00000311925 41711
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.3170.620124332021243340.00000804
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.153357.40.5750.00000324625
Missense in Polyphen1123.6520.46507266
Synonymous1.951021.50.4659.91e-7207
Loss of Function1.4414.160.2401.77e-748

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001290.000126
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumLowLow
Primary ImmunodeficiencyMediumLowMedium
CancerMediumLowMedium

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