CCL2
C-C motif chemokine ligand 2, the group of Chemokine ligands
Basic information
Region (hg38): 17:34255274-34257208
Previous symbols: [ "SCYA2" ]
Links
Phenotypes
GenCC
Source:
- neural tube defects, susceptibility to (No Known Disease Relationship), mode of inheritance: AD
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCL2 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 | 2 | |||||
| missense | 1 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 1 | 1 | 1 |
Variants in CCL2
This is a list of pathogenic ClinVar variants found in the CCL2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 17-34256113-G-G | Susceptibility to HIV infection | protective (Nov 07, 2003) | ||
| 17-34256250-T-C | CCL2-related disorder | Benign (Oct 17, 2019) | ||
| 17-34256289-C-T | CCL2-related disorder | Likely benign (Jul 31, 2019) | ||
| 17-34256291-C-T | not specified | Uncertain significance (Jan 10, 2023) | ||
| 17-34256308-A-T | not specified | Uncertain significance (Apr 20, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CCL2 | protein_coding | protein_coding | ENST00000225831 | 3 | 1919 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.608 | 0.360 | 125671 | 0 | 2 | 125673 | 0.00000796 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.19 | 29 | 53.5 | 0.542 | 0.00000257 | 648 |
| Missense in Polyphen | 3 | 11.899 | 0.25212 | 165 | ||
| Synonymous | -0.212 | 23 | 21.7 | 1.06 | 0.00000118 | 187 |
| Loss of Function | 1.59 | 0 | 2.95 | 0.00 | 1.25e-7 | 36 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000615 | 0.0000615 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000881 | 0.00000880 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Chemotactic factor that attracts monocytes and basophils but not neutrophils or eosinophils. Augments monocyte anti-tumor activity. Has been implicated in the pathogenesis of diseases characterized by monocytic infiltrates, like psoriasis, rheumatoid arthritis or atherosclerosis. May be involved in the recruitment of monocytes into the arterial wall during the disease process of atherosclerosis.;
- Pathway
- AGE-RAGE signaling pathway in diabetic complications - Homo sapiens (human);Influenza A - Homo sapiens (human);TNF signaling pathway - Homo sapiens (human);Chemokine signaling pathway - Homo sapiens (human);Malaria - Homo sapiens (human);Chagas disease (American trypanosomiasis) - Homo sapiens (human);NOD-like receptor signaling pathway - Homo sapiens (human);Fluid shear stress and atherosclerosis - Homo sapiens (human);IL-17 signaling pathway - Homo sapiens (human);Rheumatoid arthritis - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Herpes simplex infection - Homo sapiens (human);Selenium Micronutrient Network;Vitamin B12 Metabolism;Folate Metabolism;IL-1 signaling pathway;ATF4 activates genes;TNF related weak inducer of apoptosis (TWEAK) Signaling Pathway;TNF alpha Signaling Pathway;Oncostatin M Signaling Pathway;Spinal Cord Injury;Ectoderm Differentiation;IL1 and megakaryocytes in obesity;Glucocorticoid Receptor Pathway;Nuclear Receptors Meta-Pathway;Lung fibrosis;VEGFA-VEGFR2 Signaling Pathway;Protein alkylation leading to liver fibrosis;Interleukin-10 signaling;Interleukin-4 and 13 signaling;Fibrin Complement Receptor 3 Signaling Pathway;pertussis toxin-insensitive ccr5 signaling in macrophage;IL23-mediated signaling events;GMCSF-mediated signaling events;AP-1 transcription factor network;Validated transcriptional targets of AP1 family members Fra1 and Fra2
(Consensus)
Recessive Scores
- pRec
- 0.886
Intolerance Scores
- loftool
- rvis_EVS
- -0.1
- rvis_percentile_EVS
- 46.2
Haploinsufficiency Scores
- pHI
- 0.461
- hipred
- N
- hipred_score
- 0.299
- ghis
- 0.533
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.902
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Low |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Low | Low | Low |
Mouse Genome Informatics
- Gene name
- Ccl2
- 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); digestive/alimentary phenotype; vision/eye phenotype; immune system phenotype; skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; normal 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; 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); adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); neoplasm; pigmentation phenotype; muscle phenotype; craniofacial phenotype; cellular phenotype; homeostasis/metabolism 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); growth/size/body region phenotype;
Gene ontology
- Biological process
- MAPK cascade;angiogenesis;monocyte chemotaxis;protein phosphorylation;chemotaxis;inflammatory response;humoral immune response;cytoskeleton organization;cell adhesion;signal transduction;cell surface receptor signaling pathway;G protein-coupled receptor signaling pathway;G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger;JAK-STAT cascade;regulation of cell shape;response to bacterium;animal organ morphogenesis;regulation of signaling receptor activity;viral genome replication;cytokine-mediated signaling pathway;cellular homeostasis;neutrophil chemotaxis;lipopolysaccharide-mediated signaling pathway;negative regulation of glial cell apoptotic process;helper T cell extravasation;PERK-mediated unfolded protein response;protein kinase B signaling;negative regulation of neuron apoptotic process;positive regulation of GTPase activity;astrocyte cell migration;cellular response to fibroblast growth factor stimulus;eosinophil chemotaxis;macrophage chemotaxis;lymphocyte chemotaxis;positive regulation of T cell activation;positive regulation of nitric-oxide synthase biosynthetic process;chemokine-mediated signaling pathway;positive regulation of ERK1 and ERK2 cascade;cellular response to lipopolysaccharide;cellular response to interferon-gamma;cellular response to interleukin-1;cellular response to tumor necrosis factor;cellular response to organic cyclic compound;positive regulation of calcium ion import;negative regulation of vascular endothelial cell proliferation;negative regulation of G1/S transition of mitotic cell cycle;positive regulation of endothelial cell apoptotic process;positive regulation of apoptotic cell clearance;negative regulation of natural killer cell chemotaxis
- Cellular component
- extracellular region;extracellular space;cell
- Molecular function
- protein kinase activity;signaling receptor binding;protein binding;chemokine activity;CCR2 chemokine receptor binding;CCR chemokine receptor binding