CXCR6

C-X-C motif chemokine receptor 6, the group of C-X-C motif chemokine receptors|CD molecules

Basic information

Region (hg38): 3:45940932-45948351

Links

ENSG00000172215 ∙ NCBI:10663 ∙ OMIM:605163 ∙ HGNC:16647 ∙ Uniprot:O00574 ∙ 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 CXCR6 gene.

• Inborn genetic diseases (5 variants)
• not provided (3 variants)

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				1	2	3
missense			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	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
3-45946678-C-T		not specified	Uncertain significance (Oct 20, 2021)
3-45946712-C-T			Likely benign (Aug 02, 2018)
3-45946762-A-G		not specified	Uncertain significance (Jan 17, 2024)
3-45946801-G-A		not specified	Uncertain significance (Oct 06, 2022)
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)
3-45947490-A-C		not specified	Uncertain significance (Oct 26, 2022)

GnomAD

Source: gnomAD

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: dbNSFP

• 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

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