CXCL13

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

Basic information

Region (hg38): 4:77511753-77611834

Previous symbols: [ "SCYB13" ]

Links

ENSG00000156234

∙ NCBI:10563 ∙ OMIM:605149 ∙ HGNC:10639 ∙ Uniprot:O43927 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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	Phenotype	Significance	ClinVar
4-77607805-G-A	not specified	Uncertain significance (Jun 24, 2022)	2409330
4-77610992-A-T	not specified	Uncertain significance (Jun 22, 2024)	3270402
4-77611029-A-G	not specified	Likely benign (Jan 06, 2023)	2467537

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CXCL13	protein_coding	protein_coding	ENST00000286758	4	100082

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.826	0.171	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.582	46	58.5	0.786	0.00000297	703
Missense in Polyphen		12	17.116	0.70111		196
Synonymous	0.184	18	19.0	0.946	8.79e-7	207
Loss of Function	2.22	0	5.76	0.00	3.09e-7	67

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
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: 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

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Medium	Low	Medium
Cancer	Low	Low	Low

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