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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

ENSG00000160683NCBI:643OMIM:601613HGNC:1060Uniprot:P32302AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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
clinvar
1
clinvar
2
missense
12
clinvar
2
clinvar
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 Inborn genetic diseases Uncertain significance (Sep 06, 2022)2346940
11-118893589-C-G Benign (Jun 29, 2018)789043
11-118893622-C-G Inborn genetic diseases Uncertain significance (Jun 16, 2023)2604483
11-118893704-G-A Inborn genetic diseases Likely benign (May 15, 2023)2546232
11-118893704-G-T Inborn genetic diseases Uncertain significance (Feb 10, 2022)2370535
11-118893740-G-A Inborn genetic diseases Likely benign (Oct 06, 2021)2299919
11-118893866-G-A Inborn genetic diseases Uncertain significance (Jul 09, 2021)2378280
11-118893922-T-G Inborn genetic diseases Uncertain significance (Dec 01, 2022)2330784
11-118894004-G-A Inborn genetic diseases Uncertain significance (Dec 15, 2022)2335517
11-118894372-C-T Benign (Jun 29, 2018)784217
11-118894376-G-A Inborn genetic diseases Uncertain significance (Mar 02, 2023)2472287
11-118894412-G-A Inborn genetic diseases Uncertain significance (Nov 17, 2022)2326454
11-118894418-A-G Inborn genetic diseases Uncertain significance (Mar 01, 2023)2493002
11-118894448-G-A Inborn genetic diseases Uncertain significance (May 23, 2023)2551984
11-118894456-C-T Likely benign (May 13, 2018)745773
11-118894548-G-A Inborn genetic diseases Uncertain significance (Jun 09, 2022)2300139
11-118894565-G-T Inborn genetic diseases Uncertain significance (May 30, 2023)2515498

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CXCR5protein_codingprotein_codingENST00000292174 214034
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.7290.269125743041257470.0000159
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.151492430.6130.00001602403
Missense in Polyphen3992.2230.42289929
Synonymous0.4611041100.9440.00000736809
Loss of Function2.4118.630.1163.67e-796

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00002890.0000289
Ashkenazi Jewish0.00009930.0000992
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00001820.0000176
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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