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GeneBe

CCL1

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

Basic information

Region (hg38): 17:34360327-34363233

Previous symbols: [ "SCYA1" ]

Links

ENSG00000108702NCBI:6346OMIM:182281HGNC:10609Uniprot:P22362AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CCL1 gene.

  • Inborn genetic diseases (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCL1 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
2
clinvar
2
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 2 0 0

Variants in CCL1

This is a list of pathogenic ClinVar variants found in the CCL1 region.

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

Position Type Phenotype Significance ClinVar
17-34360569-T-C Inborn genetic diseases Uncertain significance (May 26, 2023)2511354
17-34360656-T-C Inborn genetic diseases Uncertain significance (Jun 29, 2022)2230021

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CCL1protein_codingprotein_codingENST00000225842 32904
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.007970.573125646031256490.0000119
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.2514651.00.9010.00000245623
Missense in Polyphen1215.4120.7786188
Synonymous-0.1522221.11.040.00000115179
Loss of Function0.17633.350.8961.41e-740

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.000.00
European (Non-Finnish)0.00001760.0000176
Middle Eastern0.00005440.0000544
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Cytokine that is chemotactic for monocytes but not for neutrophils. Binds to CCR8. {ECO:0000269|PubMed:1557400}.;
Pathway
Chemokine signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Aryl Hydrocarbon Receptor;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;G alpha (i) signalling events;GPCR downstream signalling (Consensus)

Intolerance Scores

loftool
0.447
rvis_EVS
0.13
rvis_percentile_EVS
62.74

Haploinsufficiency Scores

pHI
0.00673
hipred
N
hipred_score
0.123
ghis

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.407

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Ccl1
Phenotype
hematopoietic system phenotype; immune system phenotype;

Gene ontology

Biological process
monocyte chemotaxis;cellular calcium ion homeostasis;chemotaxis;inflammatory response;signal transduction;G protein-coupled receptor signaling pathway;positive regulation of cytosolic calcium ion concentration;regulation of signaling receptor activity;viral process;neutrophil chemotaxis;positive regulation of GTPase activity;eosinophil chemotaxis;lymphocyte chemotaxis;positive regulation of inflammatory response;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;positive regulation of monocyte chemotaxis;positive regulation of interleukin-17 secretion
Cellular component
extracellular region;extracellular space;cell
Molecular function
chemokine activity;CCR chemokine receptor binding