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GeneBe

CCL13

C-C motif chemokine ligand 13, the group of Chemokine ligands

Basic information

Region (hg38): 17:34356479-34358610

Previous symbols: [ "SCYA13" ]

Links

ENSG00000181374NCBI:6357OMIM:601391HGNC:10611Uniprot:Q99616AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CCL13 gene.

  • Inborn genetic diseases (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCL13 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
0
missense
3
clinvar
3
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 3 0 0

Variants in CCL13

This is a list of pathogenic ClinVar variants found in the CCL13 region.

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

Position Type Phenotype Significance ClinVar
17-34356545-C-T Inborn genetic diseases Uncertain significance (Feb 14, 2023)2483754
17-34357535-A-G Inborn genetic diseases Uncertain significance (Aug 10, 2023)2617757
17-34358073-A-T Inborn genetic diseases Uncertain significance (Aug 30, 2021)2388806

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CCL13protein_codingprotein_codingENST00000225844 32159
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.04100.6701252920131253050.0000519
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.09954951.00.9610.00000243636
Missense in Polyphen812.3340.6486170
Synonymous-0.5422319.91.159.61e-7190
Loss of Function0.48922.900.6901.22e-735

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00002910.0000291
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.0001060.000106
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Chemotactic factor that attracts monocytes, lymphocytes, basophils and eosinophils, but not neutrophils. Signals through CCR2B and CCR3 receptors. Plays a role in the accumulation of leukocytes at both sides of allergic and non-allergic inflammation. May be involved in the recruitment of monocytes into the arterial wall during the disease process of atherosclerosis. May play a role in the monocyte attraction in tissues chronically exposed to exogenous pathogens.;
Pathway
Chemokine signaling pathway - Homo sapiens (human);NF-kappa B signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Signaling by GPCR;Signal Transduction;Chemokine receptors bind chemokines;Peptide ligand-binding receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;G alpha (i) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

pRec
0.276

Intolerance Scores

loftool
0.551
rvis_EVS
0.37
rvis_percentile_EVS
74.95

Haploinsufficiency Scores

pHI
0.0224
hipred
N
hipred_score
0.112
ghis
0.413

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.731

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Scyl1
Phenotype
muscle 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; growth/size/body region 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); hematopoietic system phenotype; vision/eye 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); skeleton phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);

Gene ontology

Biological process
monocyte chemotaxis;cellular calcium ion homeostasis;chemotaxis;inflammatory response;cytoskeleton organization;signal transduction;G protein-coupled receptor signaling pathway;cell-cell signaling;regulation of cell shape;regulation of signaling receptor activity;neutrophil chemotaxis;killing of cells of other organism;positive regulation of GTPase activity;eosinophil chemotaxis;lymphocyte chemotaxis;antimicrobial humoral immune response mediated by antimicrobial peptide;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
Cellular component
extracellular region;extracellular space;cell
Molecular function
signaling receptor binding;protein binding;chemokine activity;CCR chemokine receptor binding