CCL2

C-C motif chemokine ligand 2, the group of Chemokine ligands

Basic information

Region (hg38): 17:34255274-34257208

Previous symbols: [ "SCYA2" ]

Links

ENSG00000108691 ∙ NCBI:6347 ∙ OMIM:158105 ∙ HGNC:10618 ∙ Uniprot:P13500 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• neural tube defects, susceptibility to (No Known Disease Relationship), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CCL2 gene.

• not_specified (6 variants)
• CCL2-related_disorder (1 variants)

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. These statistics are base on transcript: NM_000002982.4. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			7			7
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	7	1	0

GnomAD

Source: gnomAD

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
		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: dbNSFP

• 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

• rvis_EVS: -0.1
• rvis_percentile_EVS: 46.2

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

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