CX3CL1
C-X3-C motif chemokine ligand 1, the group of Chemokine ligands
Basic information
Region (hg38): 16:57372477-57385044
Previous symbols: [ "SCYD1" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (67 variants)
- not_provided (10 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. These statistics are base on transcript: NM_000002996.6. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 7 | |||||
| missense | 61 | 69 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 61 | 10 | 5 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CX3CL1 | protein_coding | protein_coding | ENST00000006053 | 3 | 12591 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.608 | 0.390 | 125742 | 0 | 4 | 125746 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.843 | 211 | 248 | 0.849 | 0.0000156 | 2520 |
| Missense in Polyphen | 32 | 51.12 | 0.62597 | 581 | ||
| Synonymous | -1.95 | 141 | 114 | 1.23 | 0.00000822 | 867 |
| Loss of Function | 2.61 | 2 | 11.6 | 0.173 | 6.41e-7 | 106 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000905 | 0.0000905 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000178 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
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