CX3CR1

C-X3-C motif chemokine receptor 1, the group of C-X-3-C motif chemokine receptors

Basic information

Region (hg38): 3:39263494-39281735

Previous symbols: [ "GPR13", "CMKBRL1" ]

Links

ENSG00000168329 ∙ NCBI:1524 ∙ OMIM:601470 ∙ HGNC:2558 ∙ Uniprot:P49238 ∙ 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 CX3CR1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CX3CR1 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				5	2	7
missense			16	4	1	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	16	9	3

Variants in CX3CR1

This is a list of pathogenic ClinVar variants found in the CX3CR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-39265456-A-G			Benign (Jul 16, 2018)
3-39265530-G-A		not specified	Uncertain significance (Oct 03, 2022)
3-39265531-A-T		not specified	Uncertain significance (Aug 13, 2021)
3-39265558-G-A		not specified	Uncertain significance (Dec 16, 2022)
3-39265660-T-C		not specified	Uncertain significance (Oct 06, 2022)
3-39265671-G-A		-	no classification for the single variant (-)
3-39265678-T-C		not specified	Uncertain significance (Jul 30, 2023)
3-39265685-G-A			Likely benign (Aug 30, 2018)
3-39265725-A-G			not provided (-)
3-39265738-G-A		not specified	Uncertain significance (Mar 14, 2023)
3-39265745-C-T			Benign/Likely benign (Apr 01, 2023)
3-39265765-C-T		-	no classification for the single variant (-)
3-39265776-G-A		not specified	Uncertain significance (Apr 07, 2023)
3-39265778-C-G		not specified	Uncertain significance (Nov 07, 2022)
3-39265853-A-G		CX3CR1-related disorder	Likely benign (Jul 31, 2019)
3-39265934-A-G			Likely benign (May 25, 2018)
3-39265939-G-A		CX3CR1-related disorder	Likely benign (Mar 21, 2022)
3-39265945-C-T		not specified	Uncertain significance (Aug 17, 2021)
3-39265963-G-A		not specified	Uncertain significance (Dec 20, 2021)
3-39265981-C-T		not specified	Uncertain significance (Jan 30, 2024)
3-39266025-G-A		not specified	Uncertain significance (Aug 14, 2023)
3-39266025-G-C		not specified	Uncertain significance (Oct 25, 2023)
3-39266054-G-A			Benign (Jul 04, 2018)
3-39266134-C-A		not specified	Uncertain significance (Nov 03, 2023)
3-39266154-A-G		not specified	Uncertain significance (Dec 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CX3CR1	protein_coding	protein_coding	ENST00000358309	2	18242

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0614	0.876	124787	0	7	124794	0.0000280

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.08	162	206	0.788	0.0000115	2563
Missense in Polyphen		47	68.084	0.69032		917
Synonymous	-0.944	101	89.6	1.13	0.00000579	764
Loss of Function	1.56	3	7.67	0.391	3.30e-7	108

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000557	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.0000265	0.0000265
Middle Eastern	0.0000557	0.0000556
South Asian	0.0000654	0.0000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for the CX3C chemokine fractalkine (CX3CL1); binds to CX3CL1 and mediates both its adhesive and migratory functions (PubMed:9390561, PubMed:23125415). Acts as coreceptor with CD4 for HIV-1 virus envelope protein (in vitro) (PubMed:9726990). Isoform 2 and isoform 3 seem to be more potent HIV-1 coreceptors than isoform 1 (PubMed:14607932). {ECO:0000269|PubMed:14607932, ECO:0000269|PubMed:23125415, ECO:0000269|PubMed:9390561, ECO:0000269|PubMed:9726990}.
• Disease: DISEASE: Macular degeneration, age-related, 12 (ARMD12) [MIM:613784]: A form of age-related macular degeneration, a multifactorial eye disease and the most common cause of irreversible vision loss in the developed world. In most patients, the disease is manifest as ophthalmoscopically visible yellowish accumulations of protein and lipid that lie beneath the retinal pigment epithelium and within an elastin-containing structure known as Bruch membrane. {ECO:0000269|PubMed:15208270}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.
• Pathway: Chemokine signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);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 (Consensus)

Recessive Scores

• pRec: 0.366

Intolerance Scores

• loftool: 0.397
• rvis_EVS: 0.93
• rvis_percentile_EVS: 89.79

Haploinsufficiency Scores

• pHI: 0.337
• hipred: N
• hipred_score: 0.170

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00346

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cx3cr1
• Phenotype: renal/urinary system phenotype; immune system phenotype; vision/eye phenotype; digestive/alimentary 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); pigmentation 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; 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); reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; cellular phenotype; muscle phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Gene ontology

• Biological process: positive regulation of neuroblast proliferation;response to ischemia;chemotaxis;immune response;cellular defense response;cell adhesion;G protein-coupled receptor signaling pathway;phospholipase C-activating G protein-coupled receptor signaling pathway;positive regulation of cytosolic calcium ion concentration;cell-cell signaling;memory;response to wounding;viral process;negative regulation of angiogenesis;calcium-mediated signaling;negative regulation of cell migration;negative regulation of interleukin-1 beta production;social behavior;autocrine signaling;regulation of tumor necrosis factor biosynthetic process;innate immune response;regulation of nitric oxide biosynthetic process;positive regulation of angiogenesis;regulation of synaptic plasticity;regulation of neurogenesis;positive regulation of neurogenesis;leukocyte tethering or rolling;positive regulation of NF-kappaB transcription factor activity;positive regulation of protein kinase B signaling;cell chemotaxis;chemokine-mediated signaling pathway;cellular response to lipopolysaccharide;cellular response to transforming growth factor beta stimulus;negative regulation of hippocampal neuron apoptotic process;multiple spine synapse organization, single dendrite;negative regulation of long-term synaptic potentiation;positive regulation of I-kappaB phosphorylation;regulation of microglial cell migration;negative regulation of apoptotic signaling pathway
• Cellular component: nucleus;nucleoplasm;plasma membrane;integral component of plasma membrane;external side of plasma membrane;cell surface;neuronal cell body membrane;neuron projection;perinuclear region of cytoplasm;dendritic tree
• Molecular function: G protein-coupled receptor activity;chemokine receptor activity;protein binding;G protein-coupled peptide receptor activity;C-C chemokine receptor activity;C-X3-C chemokine receptor activity;chemokine binding;C-C chemokine binding;C-X3-C chemokine binding