CX3CR1 Gene

HGNC Family	G protein-coupled receptors
Name	chemokine (C-X3-C motif) receptor 1
Description	Fractalkine is a transmembrane protein and chemokine involved in the adhesion and migration of leukocytes. The protein encoded by this gene is a receptor for fractalkine. The encoded protein also is a coreceptor for HIV-1, and some variations in this gene lead to increased susceptibility to HIV-1 infection and rapid progression to AIDS. Four transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Jan 2010]
Summary	{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\n The chemokine receptor CX3CR1 plays a pivotal role in coordinating diverse immune and homeostatic functions across multiple tissues. In the central nervous system, CX3CR1 is predominantly expressed by microglia and is instrumental in mediating neuron–microglia interactions that support synaptic plasticity and normal cognitive functions. Its signaling facilitates the release of key neurotrophic factors such as brain‐derived neurotrophic factor, and disruption of this pathway has been associated with deficits in learning and memory as well as with enhanced tau hyperphosphorylation and aggregation that contribute to neurodegeneration."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "1", "end_ref": "4"}]}, {"type": "t", "text": "\n "}]}, {"type": "t", "text": "\n "}, {"type": "p", "children": [{"type": "t", "text": "\n Within the intestinal mucosa, CX3CR1 expression on certain dendritic cell populations underlies the formation of transepithelial dendrites that sample luminal antigens and clear entero‐invasive pathogens, thereby contributing to mucosal immune surveillance and regulation of inflammation."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "5"}]}, {"type": "t", "text": "\n "}]}, {"type": "t", "text": "\n "}, {"type": "p", "children": [{"type": "t", "text": "\n In the cardiovascular system, CX3CR1 is critical for the survival of specialized monocyte subsets and facilitates their recruitment into atherosclerotic plaques. Its activity has been linked to the maintenance of proinflammatory cell populations in the vessel wall, and genetic deficiency or lower expression of CX3CR1 correlates with reduced plaque formation and a decreased risk of coronary artery disease."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "6", "end_ref": "8"}]}, {"type": "t", "text": "\n "}]}, {"type": "t", "text": "\n "}, {"type": "p", "children": [{"type": "t", "text": "\n Collectively, these findings highlight the multifaceted role of CX3CR1 in modulating immune cell behavior—from facilitating neuron–glia communication and sustaining cognitive function in the brain, to orchestrating antigen sampling in the gut and promoting monocyte survival and recruitment in atherogenesis—thus underscoring its potential as a therapeutic target for neurodegenerative, inflammatory, and cardiovascular diseases.\n "}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Christopher N Parkhurst, Guang Yang, Ipe Ninan, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Microglia promote learning-dependent synapse formation through brain-derived neurotrophic factor."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Cell (2013)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.cell.2013.11.030"}], "href": "https://doi.org/10.1016/j.cell.2013.11.030"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "24360280"}], "href": "https://pubmed.ncbi.nlm.nih.gov/24360280"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Kiran Bhaskar, Megan Konerth, Olga N Kokiko-Cochran, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Regulation of tau pathology by the microglial fractalkine receptor."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Neuron (2010)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.neuron.2010.08.023"}], "href": "https://doi.org/10.1016/j.neuron.2010.08.023"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "20920788"}], "href": "https://pubmed.ncbi.nlm.nih.gov/20920788"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Justin T Rogers, Josh M Morganti, Adam D Bachstetter, et al. "}, {"type": "b", "children": [{"type": "t", "text": "CX3CR1 deficiency leads to impairment of hippocampal cognitive function and synaptic plasticity."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Neurosci (2011)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1523/JNEUROSCI.3667-11.2011"}], "href": "https://doi.org/10.1523/JNEUROSCI.3667-11.2011"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "22072675"}], "href": "https://pubmed.ncbi.nlm.nih.gov/22072675"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Sungho Lee, Nicholas H Varvel, Megan E Konerth, et al. "}, {"type": "b", "children": [{"type": "t", "text": "CX3CR1 deficiency alters microglial activation and reduces beta-amyloid deposition in two Alzheimer's disease mouse models."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Am J Pathol (2010)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.2353/ajpath.2010.100265"}], "href": "https://doi.org/10.2353/ajpath.2010.100265"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "20864679"}], "href": "https://pubmed.ncbi.nlm.nih.gov/20864679"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Jan Hendrik Niess, Stephan Brand, Xiubin Gu, et al. "}, {"type": "b", "children": [{"type": "t", "text": "CX3CR1-mediated dendritic cell access to the intestinal lumen and bacterial clearance."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Science (2005)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1126/science.1102901"}], "href": "https://doi.org/10.1126/science.1102901"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "15653504"}], "href": "https://pubmed.ncbi.nlm.nih.gov/15653504"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "Frank Tacke, David Alvarez, Theodore J Kaplan, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Monocyte subsets differentially employ CCR2, CCR5, and CX3CR1 to accumulate within atherosclerotic plaques."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Clin Invest (2007)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1172/JCI28549"}], "href": "https://doi.org/10.1172/JCI28549"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "17200718"}], "href": "https://pubmed.ncbi.nlm.nih.gov/17200718"}]}, {"type": "r", "ref": 7, "children": [{"type": "t", "text": "Christophe Combadière, Stéphane Potteaux, Ji-Liang Gao, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Decreased atherosclerotic lesion formation in CX3CR1/apolipoprotein E double knockout mice."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Circulation (2003)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1161/01.cir.0000057548.68243.42"}], "href": "https://doi.org/10.1161/01.cir.0000057548.68243.42"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "12600915"}], "href": "https://pubmed.ncbi.nlm.nih.gov/12600915"}]}, {"type": "r", "ref": 8, "children": [{"type": "t", "text": "Limor Landsman, Liat Bar-On, Alma Zernecke, et al. "}, {"type": "b", "children": [{"type": "t", "text": "CX3CR1 is required for monocyte homeostasis and atherogenesis by promoting cell survival."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Blood (2009)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1182/blood-2008-07-170787"}], "href": "https://doi.org/10.1182/blood-2008-07-170787"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "18971423"}], "href": "https://pubmed.ncbi.nlm.nih.gov/18971423"}]}]}]}
Synonyms	GPR13, V28, CCRL1, CMKBRL1, CMKDR1, GPRV28
Proteins	CX3C1_HUMAN
NCBI Gene ID	1524
API
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Predicted Functions
Co-expressed Genes
Expression in Tissues and Cell Lines

Functional Associations

CX3CR1 has 11,090 functional associations with biological entities spanning 8 categories (molecular profile, organism, chemical, functional term, phrase or reference, disease, phenotype or trait, structural feature, cell line, cell type or tissue, gene, protein or microRNA) extracted from 113 datasets.

Click the + buttons to view associations for CX3CR1 from the datasets below.

If available, associations are ranked by standardized value

Harmonizome 3.0

CX3CR1 Gene

Functional Associations

Please acknowledge the Harmonizome in your publications by citing the following reference(s):

	Dataset	Summary
	Achilles Cell Line Gene Essentiality Profiles	cell lines with fitness changed by CX3CR1 gene knockdown relative to other cell lines from the Achilles Cell Line Gene Essentiality Profiles dataset.
	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of CX3CR1 gene relative to other tissues from the Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray	tissue samples with high or low expression of CX3CR1 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	tissue samples with high or low expression of CX3CR1 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq dataset.
	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of CX3CR1 gene relative to other tissues from the Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles dataset.
	BioGPS Cell Line Gene Expression Profiles	cell lines with high or low expression of CX3CR1 gene relative to other cell lines from the BioGPS Cell Line Gene Expression Profiles dataset.
	BioGPS Human Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of CX3CR1 gene relative to other cell types and tissues from the BioGPS Human Cell Type and Tissue Gene Expression Profiles dataset.
	BioGPS Mouse Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of CX3CR1 gene relative to other cell types and tissues from the BioGPS Mouse Cell Type and Tissue Gene Expression Profiles dataset.
	CCLE Cell Line Gene CNV Profiles	cell lines with high or low copy number of CX3CR1 gene relative to other cell lines from the CCLE Cell Line Gene CNV Profiles dataset.
	CCLE Cell Line Gene Expression Profiles	cell lines with high or low expression of CX3CR1 gene relative to other cell lines from the CCLE Cell Line Gene Expression Profiles dataset.
	CellMarker Gene-Cell Type Associations	cell types associated with CX3CR1 gene from the CellMarker Gene-Cell Type Associations dataset.
	ChEA Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of CX3CR1 gene from the CHEA Transcription Factor Binding Site Profiles dataset.
	ChEA Transcription Factor Targets	transcription factors binding the promoter of CX3CR1 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets dataset.
	ChEA Transcription Factor Targets 2022	transcription factors binding the promoter of CX3CR1 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets 2022 dataset.
	CMAP Signatures of Differentially Expressed Genes for Small Molecules	small molecule perturbations changing expression of CX3CR1 gene from the CMAP Signatures of Differentially Expressed Genes for Small Molecules dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores	cellular components containing CX3CR1 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores 2025	cellular components containing CX3CR1 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores 2025 dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores	cellular components co-occuring with CX3CR1 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	cellular components co-occuring with CX3CR1 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset.
	COSMIC Cell Line Gene CNV Profiles	cell lines with high or low copy number of CX3CR1 gene relative to other cell lines from the COSMIC Cell Line Gene CNV Profiles dataset.
	COSMIC Cell Line Gene Mutation Profiles	cell lines with CX3CR1 gene mutations from the COSMIC Cell Line Gene Mutation Profiles dataset.
	CTD Gene-Chemical Interactions	chemicals interacting with CX3CR1 gene/protein from the curated CTD Gene-Chemical Interactions dataset.
	CTD Gene-Disease Associations	diseases associated with CX3CR1 gene/protein from the curated CTD Gene-Disease Associations dataset.
	dbGAP Gene-Trait Associations	traits associated with CX3CR1 gene in GWAS and other genetic association datasets from the dbGAP Gene-Trait Associations dataset.
	DepMap CRISPR Gene Dependency	cell lines with fitness changed by CX3CR1 gene knockdown relative to other cell lines from the DepMap CRISPR Gene Dependency dataset.
	DISEASES Curated Gene-Disease Association Evidence Scores	diseases involving CX3CR1 gene from the DISEASES Curated Gene-Disease Assocation Evidence Scores dataset.
	DISEASES Curated Gene-Disease Association Evidence Scores 2025	diseases involving CX3CR1 gene from the DISEASES Curated Gene-Disease Association Evidence Scores 2025 dataset.
	DISEASES Experimental Gene-Disease Association Evidence Scores 2025	diseases associated with CX3CR1 gene in GWAS datasets from the DISEASES Experimental Gene-Disease Assocation Evidence Scores 2025 dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores	diseases co-occuring with CX3CR1 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	diseases co-occuring with CX3CR1 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores 2025 dataset.
	DisGeNET Gene-Disease Associations	diseases associated with CX3CR1 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Disease Associations dataset.
	DisGeNET Gene-Phenotype Associations	phenotypes associated with CX3CR1 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Phenoptype Associations dataset.
	ENCODE Histone Modification Site Profiles	histone modification site profiles with high histone modification abundance at CX3CR1 gene from the ENCODE Histone Modification Site Profiles dataset.
	ENCODE Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of CX3CR1 gene from the ENCODE Transcription Factor Binding Site Profiles dataset.
	ENCODE Transcription Factor Targets	transcription factors binding the promoter of CX3CR1 gene in ChIP-seq datasets from the ENCODE Transcription Factor Targets dataset.
	GAD Gene-Disease Associations	diseases associated with CX3CR1 gene in GWAS and other genetic association datasets from the GAD Gene-Disease Associations dataset.
	GAD High Level Gene-Disease Associations	diseases associated with CX3CR1 gene in GWAS and other genetic association datasets from the GAD High Level Gene-Disease Associations dataset.
	GDSC Cell Line Gene Expression Profiles	cell lines with high or low expression of CX3CR1 gene relative to other cell lines from the GDSC Cell Line Gene Expression Profiles dataset.
	GeneRIF Biological Term Annotations	biological terms co-occuring with CX3CR1 gene in literature-supported statements describing functions of genes from the GeneRIF Biological Term Annotations dataset.
	GeneSigDB Published Gene Signatures	PubMedIDs of publications reporting gene signatures containing CX3CR1 from the GeneSigDB Published Gene Signatures dataset.