CCL1

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

Basic information

Region (hg38): 17:34360328-34363233

Previous symbols: [ "SCYA1" ]

Links

ENSG00000108702

∙ NCBI:6346 ∙ OMIM:182281 ∙ HGNC:10609 ∙ Uniprot:P22362 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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		not specified	Uncertain significance (May 26, 2023)	2511354
17-34360656-T-C		not specified	Uncertain significance (Jun 29, 2022)	2230021

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCL1	protein_coding	protein_coding	ENST00000225842	3	2904

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00797	0.573	125646	0	3	125649	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.251	46	51.0	0.901	0.00000245	623
Missense in Polyphen		12	15.412	0.7786		188
Synonymous	-0.152	22	21.1	1.04	0.00000115	179
Loss of Function	0.176	3	3.35	0.896	1.41e-7	40

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

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