CXCR6
C-X-C motif chemokine receptor 6, the group of C-X-C motif chemokine receptors|CD molecules
Basic information
Region (hg38): 3:45940933-45948351
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 CXCR6 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 | 3 | |||||
| missense | 8 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 8 | 1 | 2 |
Variants in CXCR6
This is a list of pathogenic ClinVar variants found in the CXCR6 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 3-45946566-T-A | not specified | Uncertain significance (Jun 17, 2024) | ||
| 3-45946582-T-C | not specified | Uncertain significance (Sep 04, 2024) | ||
| 3-45946678-C-T | not specified | Uncertain significance (Oct 20, 2021) | ||
| 3-45946712-C-T | Likely benign (Aug 02, 2018) | |||
| 3-45946720-T-C | not specified | Uncertain significance (Aug 29, 2024) | ||
| 3-45946762-A-G | not specified | Uncertain significance (Jan 17, 2024) | ||
| 3-45946801-G-A | not specified | Uncertain significance (Oct 06, 2022) | ||
| 3-45947019-T-C | not specified | Uncertain significance (Oct 16, 2024) | ||
| 3-45947033-C-T | Benign (Dec 31, 2019) | |||
| 3-45947106-G-A | not specified | Uncertain significance (Jan 16, 2024) | ||
| 3-45947183-C-T | Benign (Aug 09, 2018) | |||
| 3-45947241-C-T | not specified | Uncertain significance (Aug 19, 2023) | ||
| 3-45947328-C-T | not specified | Uncertain significance (Oct 27, 2022) | ||
| 3-45947419-G-A | not specified | Uncertain significance (Dec 21, 2023) | ||
| 3-45947450-C-A | not specified | Uncertain significance (Nov 19, 2024) | ||
| 3-45947490-A-C | not specified | Uncertain significance (Oct 26, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CXCR6 | protein_coding | protein_coding | ENST00000458629 | 1 | 7421 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0000572 | 0.473 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.28 | 130 | 178 | 0.730 | 0.00000870 | 2271 |
| Missense in Polyphen | 39 | 58.638 | 0.66509 | 757 | ||
| Synonymous | -0.759 | 80 | 71.8 | 1.11 | 0.00000352 | 677 |
| Loss of Function | 0.418 | 7 | 8.30 | 0.843 | 4.29e-7 | 96 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Receptor for the C-X-C chemokine CXCL16. Used as a coreceptor by SIVs and by strains of HIV-2 and m-tropic HIV-1.;
- Pathway
- Chemokine signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Peptide GPCRs;Chemokine signaling pathway;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
- 0.177
Intolerance Scores
- loftool
- 0.606
- rvis_EVS
- -0.27
- rvis_percentile_EVS
- 34.32
Haploinsufficiency Scores
- pHI
- 0.0421
- hipred
- N
- hipred_score
- 0.180
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.0565
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cxcr6
- Phenotype
- normal phenotype; neoplasm; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan);
Gene ontology
- Biological process
- chemotaxis;inflammatory response;immune response;G protein-coupled receptor signaling pathway;positive regulation of cytosolic calcium ion concentration;viral genome replication;calcium-mediated signaling;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;coreceptor activity;C-C chemokine receptor activity;C-X-C chemokine receptor activity;chemokine binding;C-C chemokine binding;C-X-C chemokine binding