CXCR3
C-X-C motif chemokine receptor 3, the group of CD molecules|C-X-C motif chemokine receptors
Basic information
Region (hg38): X:71615916-71618511
Previous symbols: [ "GPR9" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
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 CXCR3 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 | 4 | |||||
| missense | 17 | 21 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 17 | 7 | 1 |
Variants in CXCR3
This is a list of pathogenic ClinVar variants found in the CXCR3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| X-71616482-C-A | not specified | Conflicting classifications of pathogenicity (Feb 01, 2024) | ||
| X-71616500-C-G | not specified | Uncertain significance (Mar 08, 2024) | ||
| X-71616547-T-G | not specified | Uncertain significance (Oct 10, 2023) | ||
| X-71616597-C-T | Likely benign (Mar 01, 2023) | |||
| X-71616612-G-T | not specified | Uncertain significance (May 12, 2024) | ||
| X-71616723-C-T | not specified | Uncertain significance (Mar 19, 2024) | ||
| X-71616761-G-A | Likely benign (Jul 02, 2018) | |||
| X-71616810-A-G | not specified | Uncertain significance (May 20, 2024) | ||
| X-71616834-G-A | not specified | Uncertain significance (May 29, 2024) | ||
| X-71616870-G-A | not specified | Uncertain significance (Dec 21, 2022) | ||
| X-71616899-C-T | Likely benign (May 01, 2022) | |||
| X-71616970-C-T | not specified | Uncertain significance (Dec 05, 2024) | ||
| X-71616988-G-C | not specified | Uncertain significance (Jul 09, 2021) | ||
| X-71616993-T-G | not specified | Uncertain significance (Oct 20, 2021) | ||
| X-71617105-G-A | not specified | Uncertain significance (Nov 07, 2022) | ||
| X-71617131-G-T | not specified | Uncertain significance (Sep 24, 2024) | ||
| X-71617174-T-C | not specified | Likely benign (Jul 20, 2021) | ||
| X-71617218-A-G | not specified | Uncertain significance (Apr 29, 2024) | ||
| X-71617220-G-A | Likely benign (Aug 01, 2022) | |||
| X-71617243-C-T | not specified | Uncertain significance (Sep 10, 2024) | ||
| X-71617255-C-T | not specified | Uncertain significance (Nov 11, 2024) | ||
| X-71617400-G-T | not specified | Uncertain significance (Dec 28, 2022) | ||
| X-71617426-C-A | not specified | Likely benign (Mar 15, 2024) | ||
| X-71617490-T-A | Benign (Aug 29, 2018) | |||
| X-71617534-T-C | not specified | Uncertain significance (Feb 28, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CXCR3 | protein_coding | protein_coding | ENST00000373691 | 1 | 2602 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.181 | 0.771 | 125583 | 2 | 2 | 125587 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.74 | 111 | 176 | 0.630 | 0.0000162 | 2599 |
| Missense in Polyphen | 20 | 54.007 | 0.37032 | 823 | ||
| Synonymous | 0.948 | 76 | 87.3 | 0.871 | 0.00000827 | 962 |
| Loss of Function | 1.63 | 2 | 6.50 | 0.308 | 4.86e-7 | 106 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000812 | 0.0000616 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000719 | 0.0000462 |
| European (Non-Finnish) | 0.0000281 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Isoform 1: Receptor for the C-X-C chemokine CXCL9, CXCL10 and CXCL11 and mediates the proliferation, survival and angiogenic activity of human mesangial cells (HMC) through a heterotrimeric G-protein signaling pathway (PubMed:12782716). Binds to CCL21. Probably promotes cell chemotaxis response. {ECO:0000269|PubMed:12782716}.; FUNCTION: Isoform 3: Mediates the activity of CXCL11.;
- Pathway
- Chemokine signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);GPCRs, Other;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;CXCR3-mediated signaling events
(Consensus)
Recessive Scores
- pRec
- 0.384
Intolerance Scores
- loftool
- 0.509
- rvis_EVS
- -0.1
- rvis_percentile_EVS
- 46.49
Haploinsufficiency Scores
- pHI
- 0.0730
- hipred
- N
- hipred_score
- 0.272
- ghis
- 0.559
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.903
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Low |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cxcr3
- Phenotype
- respiratory system phenotype; neoplasm; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; renal/urinary system phenotype; cellular phenotype; homeostasis/metabolism phenotype; immune system phenotype;
Zebrafish Information Network
- Gene name
- cxcr3.2
- Affected structure
- trunk
- Phenotype tag
- abnormal
- Phenotype quality
- decreased cellular motility
Gene ontology
- Biological process
- angiogenesis;regulation of leukocyte migration;apoptotic process;chemotaxis;inflammatory response;immune response;cell adhesion;cell surface receptor signaling pathway;G protein-coupled receptor signaling pathway;positive regulation of cytosolic calcium ion concentration;T cell chemotaxis;calcium-mediated signaling;cell chemotaxis;chemokine-mediated signaling pathway
- Cellular component
- cytoplasm;plasma membrane;integral component of plasma membrane;external side of plasma membrane
- Molecular function
- chemokine receptor activity;C-C chemokine receptor activity;C-X-C chemokine receptor activity;chemokine binding;C-C chemokine binding