XCR1

X-C motif chemokine receptor 1, the group of X-C motif chemokine receptors

Basic information

Region (hg38): 3:46016990-46085825

Previous symbols: [ "GPR5", "CCXCR1" ]

Links

ENSG00000173578 ∙ NCBI:2829 ∙ OMIM:600552 ∙ HGNC:1625 ∙ Uniprot:P46094 ∙ 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 XCR1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the XCR1 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						0
missense			25	2		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	2	0

Variants in XCR1

This is a list of pathogenic ClinVar variants found in the XCR1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-46020998-G-A		not specified	Uncertain significance (Mar 22, 2023)
3-46021023-G-A		not specified	Uncertain significance (May 17, 2023)
3-46021040-C-T		not specified	Likely benign (Aug 30, 2021)
3-46021064-C-T		not specified	Uncertain significance (May 28, 2024)
3-46021076-C-T		not specified	Uncertain significance (Dec 20, 2023)
3-46021137-T-A		not specified	Uncertain significance (Mar 22, 2023)
3-46021140-G-A		not specified	Uncertain significance (Dec 22, 2023)
3-46021146-C-T		not specified	Uncertain significance (Mar 30, 2024)
3-46021161-G-C		not specified	Uncertain significance (Sep 22, 2023)
3-46021290-G-A		not specified	Uncertain significance (Apr 23, 2024)
3-46021292-C-T		not specified	Uncertain significance (Mar 22, 2023)
3-46021332-C-A		not specified	Uncertain significance (Jan 10, 2023)
3-46021442-T-G		not specified	Uncertain significance (May 09, 2023)
3-46021447-G-C		not specified	Uncertain significance (Oct 25, 2023)
3-46021482-C-T		not specified	Uncertain significance (Oct 06, 2022)
3-46021494-C-T		not specified	Uncertain significance (May 24, 2023)
3-46021518-G-A		not specified	Uncertain significance (Feb 12, 2024)
3-46021599-T-A		not specified	Uncertain significance (Jan 30, 2024)
3-46021627-C-A		not specified	Uncertain significance (Jan 03, 2024)
3-46021673-T-C		not specified	Uncertain significance (Jan 18, 2022)
3-46021707-C-G		not specified	Uncertain significance (Jun 21, 2023)
3-46021707-C-T		not specified	Uncertain significance (Jan 19, 2024)
3-46021727-C-T		not specified	Uncertain significance (Feb 28, 2024)
3-46021842-C-G		not specified	Uncertain significance (Aug 05, 2023)
3-46021880-T-A		not specified	Uncertain significance (Jun 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
XCR1	protein_coding	protein_coding	ENST00000309285	1	10719

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0160	0.892	125678	1	67	125746	0.000270

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.12	158	203	0.779	0.0000131	2145
Missense in Polyphen		60	72.388	0.82886		805
Synonymous	0.319	89	92.9	0.958	0.00000590	719
Loss of Function	1.42	4	8.44	0.474	3.66e-7	90

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000489	0.000489
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.000816	0.000816
Finnish	0.00	0.00
European (Non-Finnish)	0.000318	0.000316
Middle Eastern	0.000816	0.000816
South Asian	0.000196	0.000163
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for chemokines SCYC1 and SCYC2. Subsequently transduces a signal by increasing the intracellular calcium ions level. Receptor for XCL1/Lymphotactin. {ECO:0000305}.
• Pathway: Chemokine signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);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 (q) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.121

Intolerance Scores

• loftool: 0.449
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.66

Haploinsufficiency Scores

• pHI: 0.0926
• hipred: N
• hipred_score: 0.244
• ghis: 0.486

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.293

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Xcr1
• Phenotype: immune system phenotype; normal phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: chemotaxis;inflammatory response;immune response;G protein-coupled receptor signaling pathway;G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger;positive regulation of cytosolic calcium ion concentration;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: chemokine receptor activity;C-C chemokine receptor activity;chemokine binding;C-C chemokine binding