CXCL13

protein-coding

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

Gene summary

B lymphocyte chemoattractant, independently cloned and named Angie, is an antimicrobial peptide and CXC chemokine strongly expressed in the follicles of the spleen, lymph nodes, and Peyer's patches. It preferentially promotes the migration of B lymphocytes (compared to T cells and macrophages), apparently by stimulating calcium influx into, and chemotaxis of, cells expressing Burkitt's lymphoma receptor 1 (BLR-1). It may therefore function in the homing of B lymphocytes to follicles. [provided by RefSeq, Oct 2014]

Previous symbols:

SCYB13

MANE transcript

NM_001371558.1

Inheritance

—

ClinVar variants

U:10B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr4:77,511,753-77,611,834

External References & Databases

Ensembl (ENSG00000156234)

Transcript & Mutation Effects

hg38 • Region Span ~100.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CXCL13 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 9

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001371558.1. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			9 clinvar	1 clinvar		10
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	10	1	0	11

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 6 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001371558.1	RefSeq	NP_001358487.1	4	MANE Select
ENST00000682537.1	Ensembl	ENSP00000507688.1	4	MANE Select
NM_006419.3	RefSeq	NP_006410.1	4	Standard
ENST00000286758.4	Ensembl	ENSP00000286758.4	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Chemokine signaling pathway - Homo sapiens (human)
Cytokine-cytokine receptor interaction - Homo sapiens (human)
Allograft Rejection
Chemokine signaling pathway
Signaling by GPCR

Biological Process

germinal center formation
lymphocyte chemotaxis across high endothelial venule
chronic inflammatory response
regulation of humoral immune response
inflammatory response

Molecular Function

chemokine activity
heparin binding
fibroblast growth factor binding
CXCR5 chemokine receptor binding
CCR10 chemokine receptor binding

Cellular Component

extracellular region
extracellular space
cell

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000286758
Coding exons: 4
Length: 100082
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.582	46	58.5	0.786	0.00000297	703
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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.;

Recessive Scores

pRec: 0.367

Intolerance Scores

RVIS EVS: 0.21
RVIS percentile EVS: 67.72

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.539

Gene Damage Prediction

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