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GeneBe

CXCL13

C-X-C motif chemokine ligand 13, the group of Chemokine ligands

Basic information

Region (hg38): 4:77511752-77611834

Previous symbols: [ "SCYB13" ]

Links

ENSG00000156234NCBI:10563OMIM:605149HGNC:10639Uniprot:O43927AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CXCL13 gene.

  • Inborn genetic diseases (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CXCL13 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
1
clinvar
1
clinvar
2
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 1 1 0

Variants in CXCL13

This is a list of pathogenic ClinVar variants found in the CXCL13 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
4-77607805-G-A Inborn genetic diseases Uncertain significance (Jun 24, 2022)2409330
4-77611029-A-G Inborn genetic diseases Likely benign (Jan 06, 2023)2467537

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CXCL13protein_codingprotein_codingENST00000286758 4100082
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.8260.17100000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.5824658.50.7860.00000297703
Missense in Polyphen1217.1160.70111196
Synonymous0.1841819.00.9468.79e-7207
Loss of Function2.2205.760.003.09e-767

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
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: Chemotactic for B-lymphocytes but not for T-lymphocytes, monocytes and neutrophils. Does not induce calcium release in B- lymphocytes. Binds to BLR1/CXCR5.;
Pathway
Chemokine 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;CXCR3-mediated signaling events (Consensus)

Recessive Scores

pRec
0.367

Intolerance Scores

loftool
rvis_EVS
0.21
rvis_percentile_EVS
67.72

Haploinsufficiency Scores

pHI
0.410
hipred
N
hipred_score
0.295
ghis

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

AllRecessiveDominant
MendelianLowLowLow
Primary ImmunodeficiencyMediumLowMedium
CancerLowLowLow

Mouse Genome Informatics

Gene name
Cxcl13
Phenotype
cellular phenotype; hematopoietic system phenotype; immune system phenotype;

Gene ontology

Biological process
germinal center formation;lymphocyte chemotaxis across high endothelial venule;chronic inflammatory response;regulation of humoral immune response;inflammatory response;immune response;cell surface receptor signaling pathway;G protein-coupled receptor signaling pathway;positive regulation of cytosolic calcium ion concentration;cell-cell signaling;regulation of signaling receptor activity;positive regulation of T cell chemotaxis;neutrophil chemotaxis;leukocyte chemotaxis;positive regulation of integrin activation;positive regulation of cell-cell adhesion mediated by integrin;B cell chemotaxis;endothelial cell chemotaxis to fibroblast growth factor;defense response to bacterium;regulation of angiogenesis;antimicrobial humoral immune response mediated by antimicrobial peptide;chemokine-mediated signaling pathway;cellular response to lipopolysaccharide;activation of GTPase activity;negative regulation of endothelial cell chemotaxis to fibroblast growth factor
Cellular component
extracellular region;extracellular space;cell
Molecular function
chemokine activity;heparin binding;fibroblast growth factor binding;CXCR5 chemokine receptor binding;CCR10 chemokine receptor binding;protein heterodimerization activity;receptor ligand activity;CXCR3 chemokine receptor binding