CCL17

C-C motif chemokine ligand 17, the group of Chemokine ligands

Basic information

Region (hg38): 16:57404766-57416063

Previous symbols: [ "SCYA17" ]

Links

ENSG00000102970 ∙ NCBI:6361 ∙ OMIM:601520 ∙ HGNC:10615 ∙ Uniprot:Q92583 ∙ 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 CCL17 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCL17 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					1	1
missense			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	1

Variants in CCL17

This is a list of pathogenic ClinVar variants found in the CCL17 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-57413978-G-A		not specified	Uncertain significance (Feb 13, 2024)
16-57415094-T-C			Benign (Apr 23, 2018)
16-57415102-G-A		not specified	Uncertain significance (May 18, 2022)
16-57415129-G-A		not specified	Uncertain significance (Nov 30, 2021)
16-57415131-G-A		not specified	Uncertain significance (Jun 29, 2023)
16-57415781-G-A		not specified	Uncertain significance (Oct 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCL17	protein_coding	protein_coding	ENST00000219244	3	11296

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000139	0.249	125728	0	17	125745	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.476	42	51.6	0.814	0.00000279	595
Missense in Polyphen		14	16.837	0.8315		188
Synonymous	1.12	15	21.6	0.694	0.00000121	190
Loss of Function	-0.697	5	3.58	1.40	2.18e-7	37

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000148	0.000148
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.00	0.00
Finnish	0.0000484	0.0000462
European (Non-Finnish)	0.0000443	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.000196	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Chemotactic factor for T-lymphocytes but not monocytes or granulocytes. May play a role in T-cell development in thymus and in trafficking and activation of mature T-cells. Binds to CCR4. {ECO:0000269|PubMed:10540332}.
• Pathway: Chemokine signaling pathway - Homo sapiens (human);C-type lectin receptor signaling pathway - Homo sapiens (human);IL-17 signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);C-type lectin receptors (CLRs);Chemokine signaling pathway;IL4-mediated signaling events (Consensus)

Recessive Scores

• pRec: 0.239

Intolerance Scores

• loftool: 0.651
• rvis_EVS: 0.44
• rvis_percentile_EVS: 77.45

Haploinsufficiency Scores

• pHI: 0.0800
• hipred: N
• hipred_score: 0.146
• ghis: 0.390

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.871

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccl17
• Phenotype: hematopoietic system phenotype; immune system phenotype; cellular phenotype

Gene ontology

• Biological process: monocyte chemotaxis;chemotaxis;inflammatory response;G protein-coupled receptor signaling pathway;cell-cell signaling;multicellular organism development;regulation of signaling receptor activity;neutrophil chemotaxis;positive regulation of GTPase activity;negative regulation of myoblast differentiation;lymphocyte chemotaxis;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 space
• Molecular function: signaling receptor binding;protein binding;chemokine activity;CCR4 chemokine receptor binding;CCR chemokine receptor binding