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CX3CL1

C-X3-C motif chemokine ligand 1, the group of Chemokine ligands

Basic information

Region (hg38): 16:57372476-57385044

Previous symbols: [ "SCYD1" ]

Links

ENSG00000006210NCBI:6376OMIM:601880HGNC:10647Uniprot:P78423AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CX3CL1 gene.

  • Inborn genetic diseases (24 variants)
  • not provided (11 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CX3CL1 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
3
clinvar
4
clinvar
7
missense
22
clinvar
3
clinvar
1
clinvar
26
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
2
clinvar
2
Total 0 0 22 6 7

Variants in CX3CL1

This is a list of pathogenic ClinVar variants found in the CX3CL1 region.

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

Position Type Phenotype Significance ClinVar
16-57372600-G-T Inborn genetic diseases Uncertain significance (Apr 07, 2022)2281502
16-57372636-C-A Inborn genetic diseases Uncertain significance (Feb 28, 2023)2490288
16-57376022-T-G Benign (Jul 15, 2020)1259556
16-57379748-C-T Benign (Aug 29, 2018)771016
16-57379763-T-C Benign (Jul 09, 2018)774923
16-57382055-T-C Inborn genetic diseases Uncertain significance (May 30, 2023)2552706
16-57382091-G-A Inborn genetic diseases Uncertain significance (Jan 05, 2022)2270305
16-57382093-G-A Benign (Dec 31, 2019)716483
16-57382139-G-A Inborn genetic diseases Uncertain significance (Aug 02, 2021)2371735
16-57382163-G-A Inborn genetic diseases Uncertain significance (Oct 06, 2021)2253403
16-57382188-C-T Inborn genetic diseases Uncertain significance (Apr 28, 2022)2286632
16-57382189-C-T Likely benign (May 15, 2018)744529
16-57382192-C-T Benign (Feb 17, 2018)734681
16-57382193-G-A Inborn genetic diseases Likely benign (Jul 09, 2021)2383853
16-57382315-G-A Likely benign (Mar 06, 2018)735956
16-57382344-T-C Inborn genetic diseases Uncertain significance (Nov 08, 2022)2324459
16-57382353-C-T Inborn genetic diseases Uncertain significance (Jun 29, 2022)2350548
16-57382375-G-T Likely benign (Apr 01, 2023)2646556
16-57382386-C-T Inborn genetic diseases Uncertain significance (Jan 26, 2022)2273918
16-57382398-G-A Inborn genetic diseases Uncertain significance (Aug 12, 2021)2244135
16-57382414-C-T Benign (Jun 18, 2018)711165
16-57382421-G-A Inborn genetic diseases Likely benign (Jul 09, 2021)2384089
16-57382433-A-G Inborn genetic diseases Uncertain significance (Aug 30, 2022)2407689
16-57382484-T-A Inborn genetic diseases Uncertain significance (Aug 02, 2023)2615181
16-57382494-C-G Inborn genetic diseases Uncertain significance (Oct 26, 2022)2319758

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CX3CL1protein_codingprotein_codingENST00000006053 312591
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.6080.390125742041257460.0000159
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.8432112480.8490.00001562520
Missense in Polyphen3251.120.62597581
Synonymous-1.951411141.230.00000822867
Loss of Function2.61211.60.1736.41e-7106

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00009050.0000905
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00001780.0000176
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Acts as a ligand for both CX3CR1 and integrins. Binds to CX3CR1 (PubMed:23125415, PubMed:9931005, PubMed:21829356). Binds to integrins ITGAV:ITGB3 and ITGA4:ITGB1. Can activate integrins in both a CX3CR1-dependent and CX3CR1-independent manner. In the presence of CX3CR1, activates integrins by binding to the classical ligand-binding site (site 1) in integrins. In the absence of CX3CR1, binds to a second site (site 2) in integrins which is distinct from site 1 and enhances the binding of other integrin ligands to site 1 (PubMed:23125415, PubMed:24789099). The soluble form is chemotactic for T-cells and monocytes and not for neutrophils. The membrane-bound form promotes adhesion of those leukocytes to endothelial cells. May play a role in regulating leukocyte adhesion and migration processes at the endothelium (PubMed:9024663, PubMed:9177350). {ECO:0000269|PubMed:21829356, ECO:0000269|PubMed:23125415, ECO:0000269|PubMed:24789099, ECO:0000269|PubMed:9024663, ECO:0000269|PubMed:9177350, ECO:0000269|PubMed:9931005}.;
Pathway
TNF signaling pathway - Homo sapiens (human);Chemokine signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);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;Direct p53 effectors;G alpha (i) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

pRec
0.319

Intolerance Scores

loftool
0.227
rvis_EVS
-0.51
rvis_percentile_EVS
21.65

Haploinsufficiency Scores

pHI
0.133
hipred
N
hipred_score
0.326
ghis
0.492

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.815

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Cx3cl1
Phenotype
cellular phenotype; homeostasis/metabolism phenotype; immune system 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); 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);

Gene ontology

Biological process
microglial cell activation;positive regulation of cell-matrix adhesion;positive regulation of neuroblast proliferation;leukocyte migration involved in inflammatory response;monocyte chemotaxis;response to ischemia;chemotaxis;defense response;inflammatory response;immune response;cell adhesion;G protein-coupled receptor signaling pathway;cell-cell signaling;aging;regulation of signaling receptor activity;negative regulation of cell-substrate adhesion;positive regulation of neuron projection development;neuron remodeling;cytokine-mediated signaling pathway;negative regulation of cell migration;neutrophil chemotaxis;leukocyte chemotaxis;regulation of lipopolysaccharide-mediated signaling pathway;positive regulation of actin filament bundle assembly;negative regulation of interleukin-1 alpha production;negative regulation of interleukin-1 beta production;negative regulation of interleukin-6 production;negative regulation of tumor necrosis factor production;positive regulation of transforming growth factor beta1 production;integrin activation;autocrine signaling;positive regulation of I-kappaB kinase/NF-kappaB signaling;positive regulation of MAPK cascade;positive regulation of GTPase activity;positive regulation of angiogenesis;positive regulation of transcription by RNA polymerase II;regulation of synaptic plasticity;eosinophil chemotaxis;macrophage chemotaxis;lymphocyte chemotaxis;positive regulation of smooth muscle cell proliferation;positive regulation of inflammatory response;regulation of neurogenesis;leukocyte adhesive activation;positive chemotaxis;positive regulation of calcium-independent cell-cell adhesion;positive regulation of NF-kappaB transcription factor activity;positive regulation of release of sequestered calcium ion into cytosol;positive regulation of protein kinase B signaling;angiogenesis involved in wound healing;microglial cell proliferation;neuron cellular homeostasis;chemokine-mediated signaling pathway;positive regulation of ERK1 and ERK2 cascade;cellular response to interferon-gamma;cellular response to interleukin-1;cellular response to tumor necrosis factor;cell-cell adhesion;synapse pruning;negative regulation of hippocampal neuron apoptotic process;negative regulation of glutamate receptor signaling pathway;positive regulation of I-kappaB phosphorylation;negative regulation of microglial cell activation;negative regulation of tumor necrosis factor secretion;negative regulation of neuron migration;negative regulation of apoptotic signaling pathway;negative regulation of extrinsic apoptotic signaling pathway in absence of ligand
Cellular component
extracellular region;extracellular space;plasma membrane;cell surface;membrane;integral component of membrane;cell projection;neuron projection;neuronal cell body;perinuclear region of cytoplasm
Molecular function
signaling receptor binding;integrin binding;protein binding;chemokine activity;CX3C chemokine receptor binding;chemoattractant activity;CXCR1 chemokine receptor binding;CCR chemokine receptor binding