CXCR5

C-X-C motif chemokine receptor 5, the group of CD molecules|C-X-C motif chemokine receptors

Basic information

Region (hg38): 11:118883891-118897787

Previous symbols: [ "BLR1" ]

Links

ENSG00000160683 ∙ NCBI:643 ∙ OMIM:601613 ∙ HGNC:1060 ∙ Uniprot:P32302 ∙ 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 CXCR5 gene.

• Inborn genetic diseases (14 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CXCR5 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				1	1	2
missense			12	2		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	12	3	1

Variants in CXCR5

This is a list of pathogenic ClinVar variants found in the CXCR5 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-118883969-G-A		not specified	Uncertain significance (Sep 06, 2022)
11-118893589-C-G			Benign (Jun 29, 2018)
11-118893622-C-G		not specified	Uncertain significance (Jun 16, 2023)
11-118893704-G-A		not specified	Likely benign (May 15, 2023)
11-118893704-G-T		not specified	Uncertain significance (Feb 10, 2022)
11-118893740-G-A		not specified	Likely benign (Oct 06, 2021)
11-118893827-G-A		not specified	Uncertain significance (Mar 16, 2022)
11-118893866-G-A		not specified	Uncertain significance (Jul 09, 2021)
11-118893899-A-G		not specified	Uncertain significance (Dec 12, 2023)
11-118893922-T-G		not specified	Uncertain significance (Dec 01, 2022)
11-118894004-G-A		not specified	Uncertain significance (Dec 15, 2022)
11-118894125-A-T		not specified	Uncertain significance (Jan 30, 2024)
11-118894372-C-T			Benign (Jun 29, 2018)
11-118894376-G-A		not specified	Uncertain significance (Mar 02, 2023)
11-118894412-G-A		not specified	Uncertain significance (Nov 17, 2022)
11-118894418-A-G		not specified	Uncertain significance (Mar 01, 2023)
11-118894448-G-A		not specified	Uncertain significance (May 23, 2023)
11-118894456-C-T			Likely benign (May 13, 2018)
11-118894462-G-A		not specified	Uncertain significance (Jan 03, 2024)
11-118894487-T-A		not specified	Uncertain significance (Oct 25, 2023)
11-118894523-G-A		not specified	Uncertain significance (May 06, 2022)
11-118894548-G-A		not specified	Uncertain significance (Jun 09, 2022)
11-118894565-G-T		not specified	Uncertain significance (May 30, 2023)
11-118894611-G-T		not specified	Uncertain significance (Dec 08, 2023)
11-118894622-C-T		not specified	Uncertain significance (Dec 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CXCR5	protein_coding	protein_coding	ENST00000292174	2	14034

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.729	0.269	125743	0	4	125747	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.15	149	243	0.613	0.0000160	2403
Missense in Polyphen		39	92.223	0.42289		929
Synonymous	0.461	104	110	0.944	0.00000736	809
Loss of Function	2.41	1	8.63	0.116	3.67e-7	96

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000182	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cytokine receptor that binds to B-lymphocyte chemoattractant (BLC). Involved in B-cell migration into B-cell follicles of spleen and Peyer patches but not into those of mesenteric or peripheral lymph nodes. May have a regulatory function in Burkitt lymphoma (BL) lymphomagenesis and/or B-cell differentiation.
• Pathway: Chemokine signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Allograft Rejection;Peptide GPCRs;Chemokine signaling pathway;GPCRs, Class A Rhodopsin-like;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: 0.295

Intolerance Scores

• loftool: 0.276
• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.73

Haploinsufficiency Scores

• pHI: 0.315
• hipred: N
• hipred_score: 0.294
• ghis: 0.455

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.189

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cxcr5
• Phenotype: immune system phenotype; hematopoietic system phenotype; normal phenotype; cellular phenotype

Gene ontology

• Biological process: chemotaxis;immune response;G protein-coupled receptor signaling pathway;positive regulation of cytosolic calcium ion concentration;calcium-mediated signaling;leukocyte chemotaxis;positive regulation of cytokinesis;B cell activation;lymph node development;cell chemotaxis;chemokine-mediated signaling pathway
• Cellular component: plasma membrane;integral component of plasma membrane;external side of plasma membrane
• Molecular function: G protein-coupled receptor activity;protein binding;C-C chemokine receptor activity;C-X-C chemokine receptor activity;chemokine binding;C-C chemokine binding