CXCR5
Basic information
Region (hg38): 11:118883892-118897787
Previous symbols: [ "BLR1" ]
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 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 | 2 | |||||
missense | 20 | 22 | ||||
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 | 20 | 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) | ||
11-118893660-C-A | not specified | Uncertain significance (Apr 12, 2024) | ||
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) | ||
11-118894183-T-A | not specified | Uncertain significance (May 26, 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 (Jun 07, 2024) | ||
11-118894533-G-A | not specified | Uncertain significance (Mar 20, 2024) | ||
11-118894548-G-A | not specified | Uncertain significance (Jun 09, 2022) |
GnomAD
Source:
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:
- 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