CCL16

C-C motif chemokine ligand 16, the group of Chemokine ligands

Basic information

Region (hg38): 17:35976492-35981497

Previous symbols: [ "SCYA16" ]

Links

ENSG00000275152 ∙ NCBI:6360 ∙ OMIM:601394 ∙ HGNC:10614 ∙ Uniprot:O15467 ∙ 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 CCL16 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCL16 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			4	2		6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	2	0

Variants in CCL16

This is a list of pathogenic ClinVar variants found in the CCL16 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-35977594-C-A		not specified	Uncertain significance (Nov 08, 2022)
17-35977636-G-C		not specified	Likely benign (Dec 27, 2023)
17-35977661-C-T		not specified	Likely benign (May 15, 2024)
17-35977690-T-C		not specified	Likely benign (Apr 09, 2024)
17-35977720-T-A		not specified	Uncertain significance (Aug 04, 2023)
17-35977727-C-T		not specified	Likely benign (Dec 19, 2023)
17-35978263-T-C		not specified	Uncertain significance (Mar 28, 2023)
17-35981408-C-T		not specified	Uncertain significance (Apr 11, 2023)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Shows chemotactic activity for lymphocytes and monocytes but not neutrophils. Also shows potent myelosuppressive activity, suppresses proliferation of myeloid progenitor cells. Recombinant SCYA16 shows chemotactic activity for monocytes and THP-1 monocytes, but not for resting lymphocytes and neutrophils. Induces a calcium flux in THP-1 cells that were desensitized by prior expression to RANTES.
• Pathway: Chemokine 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)

Intolerance Scores

• loftool: 0.432
• rvis_EVS: 0.35
• rvis_percentile_EVS: 73.97

Haploinsufficiency Scores

• pHI: 0.129
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.816

Gene Damage Prediction

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

Gene ontology

• Biological process: monocyte chemotaxis;chemotaxis;inflammatory response;cell communication;G protein-coupled receptor signaling pathway;cell-cell signaling;regulation of signaling receptor activity;neutrophil chemotaxis;positive regulation of GTPase activity;eosinophil chemotaxis;lymphocyte chemotaxis;positive 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 region;extracellular space
• Molecular function: protein binding;chemokine activity;chemoattractant activity;CCR chemokine receptor binding