CXCR2

C-X-C motif chemokine receptor 2, the group of C-X-C motif chemokine receptors|CD molecules|Interleukin receptors

Basic information

Region (hg38): 2:218125288-218137251

Previous symbols: [ "IL8RB" ]

Links

ENSG00000180871 ∙ NCBI:3579 ∙ OMIM:146928 ∙ HGNC:6027 ∙ Uniprot:P25025 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autosomal recessive severe congenital neutropenia due to CXCR2 deficiency (Supportive), mode of inheritance: AR
• WHIM syndrome 2 (Strong), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CXCR2 gene.

• not provided (142 variants)
• Inborn genetic diseases (15 variants)
• not specified (2 variants)
• CXCR2-related condition (1 variants)
• WHIM syndrome 2 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CXCR2 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	51	8	60
missense		1	77	7	2	87
nonsense	1	1				2
start loss						0
frameshift			2			2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					2	2
Total	1	2	80	58	12

Highest pathogenic variant AF is 0.0000131

Variants in CXCR2

This is a list of pathogenic ClinVar variants found in the CXCR2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-218134532-G-A			Benign (Jun 18, 2021)
2-218134818-T-G			Likely benign (Jan 02, 2024)
2-218134819-G-A			Uncertain significance (Sep 30, 2022)
2-218134828-C-T			Uncertain significance (Dec 31, 2022)
2-218134833-T-C			Uncertain significance (Mar 26, 2022)
2-218134838-G-C			Uncertain significance (Apr 19, 2022)
2-218134844-T-C			Uncertain significance (May 19, 2022)
2-218134862-A-C			Uncertain significance (Aug 04, 2023)
2-218134868-T-G			Uncertain significance (May 29, 2022)
2-218134876-C-T			Likely benign (Sep 08, 2023)
2-218134879-C-T			Likely benign (Nov 27, 2023)
2-218134885-C-T			Likely benign (Nov 04, 2021)
2-218134888-G-T		CXCR2-related disorder	Likely benign (Jan 09, 2024)
2-218134891-C-G		CXCR2-related disorder	Likely benign (Jan 17, 2024)
2-218134891-C-T			Benign (Jan 29, 2024)
2-218134893-C-A			Uncertain significance (Jun 27, 2022)
2-218134895-T-G			Uncertain significance (May 10, 2022)
2-218134909-C-T			Likely benign (Aug 28, 2023)
2-218134910-G-A			Uncertain significance (Nov 03, 2022)
2-218134913-C-T			Uncertain significance (Aug 22, 2022)
2-218134915-A-G			Likely benign (Jul 21, 2023)
2-218134920-A-G			Uncertain significance (Jan 04, 2023)
2-218134941-A-G			Uncertain significance (Dec 12, 2022)
2-218134942-C-T			Likely benign (Oct 28, 2023)
2-218134947-A-G			Uncertain significance (Aug 05, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CXCR2	protein_coding	protein_coding	ENST00000318507	1	11965

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0137	0.877	125731	0	17	125748	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.182	192	199	0.964	0.0000124	2328
Missense in Polyphen		69	85.077	0.81103		1024
Synonymous	-1.55	106	87.6	1.21	0.00000508	781
Loss of Function	1.33	4	8.08	0.495	4.39e-7	97

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000383	0.000383
Ashkenazi Jewish	0.00	0.00
East Asian	0.000217	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.00000879	0.00000879
Middle Eastern	0.000217	0.000217
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for interleukin-8 which is a powerful neutrophil chemotactic factor. Binding of IL-8 to the receptor causes activation of neutrophils. This response is mediated via a G-protein that activates a phosphatidylinositol-calcium second messenger system. Binds to IL-8 with high affinity. Also binds with high affinity to CXCL3, GRO/MGSA and NAP-2.
• Pathway: Endocytosis - Homo sapiens (human);Chemokine signaling pathway - Homo sapiens (human);Epithelial cell signaling in Helicobacter pylori infection - Homo sapiens (human);Phospholipase D 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;Neutrophil degranulation;Signal Transduction;JAK STAT MolecularVariation 1;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;Innate Immune System;Immune System;Chemokine receptors bind chemokines;Peptide ligand-binding receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;GPCR signaling-G alpha s Epac and ERK;GPCR signaling-G alpha s PKA and ERK;JAK STAT MolecularVariation 2;JAK STAT pathway and regulation;G alpha (i) signalling events;GPCR signaling-G alpha i;GPCR downstream signalling;IL8- and CXCR2-mediated signaling events (Consensus)

Recessive Scores

• pRec: 0.325

Intolerance Scores

• loftool: 0.475
• rvis_EVS: 0.6
• rvis_percentile_EVS: 82.74

Haploinsufficiency Scores

• pHI: 0.217
• hipred: N
• hipred_score: 0.273
• ghis: 0.392

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cxcr2
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; renal/urinary system phenotype; skeleton phenotype; immune system phenotype; vision/eye phenotype; 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); neoplasm; reproductive system phenotype; 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); hematopoietic system 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); liver/biliary system phenotype; respiratory system phenotype

Zebrafish Information Network

• Gene name: cxcr2
• Affected structure: vasculature
• Phenotype tag: abnormal
• Phenotype quality: has fewer parts of type

Gene ontology

• Biological process: dendritic cell chemotaxis;acute inflammatory response to antigenic stimulus;chemotaxis;inflammatory response;immune response;cellular defense response;signal transduction;cell surface receptor signaling pathway;G protein-coupled receptor signaling pathway;phospholipase C-activating G protein-coupled receptor signaling pathway;positive regulation of cytosolic calcium ion concentration;positive regulation of cell population proliferation;positive regulation of cardiac muscle cell apoptotic process;calcium-mediated signaling;neutrophil chemotaxis;midbrain development;receptor internalization;negative regulation of neutrophil apoptotic process;interleukin-8-mediated signaling pathway;neutrophil activation;positive regulation of vascular permeability;neutrophil degranulation;positive regulation of angiogenesis;cell chemotaxis;chemokine-mediated signaling pathway;metanephric tubule morphogenesis;positive regulation of neutrophil chemotaxis
• Cellular component: plasma membrane;integral component of plasma membrane;external side of plasma membrane;cell surface;membrane;secretory granule membrane;mast cell granule
• Molecular function: interleukin-8 receptor activity;G protein-coupled receptor activity;protein binding;C-C chemokine receptor activity;C-X-C chemokine receptor activity;chemokine binding;C-C chemokine binding;interleukin-8 binding