CXCL13
Basic information
Region (hg38): 4:77511752-77611834
Previous symbols: [ "SCYB13" ]
Links
Phenotypes
GenCC
Source:
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 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 | 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 | not specified | Uncertain significance (Jun 24, 2022) | ||
4-77610992-A-T | not specified | Uncertain significance (Jun 22, 2024) | ||
4-77611029-A-G | not specified | Likely benign (Jan 06, 2023) |
GnomAD
Source:
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:
- 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