CXCL16

C-X-C motif chemokine ligand 16, the group of Chemokine ligands|Scavenger receptors

Basic information

Region (hg38): 17:4733533-4739928

Links

ENSG00000161921 ∙ NCBI:58191 ∙ OMIM:605398 ∙ HGNC:16642 ∙ Uniprot:Q9H2A7 ∙ 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 CXCL16 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CXCL16 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			9	2	1	12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1		1	2
Total	0	0	10	2	2

Variants in CXCL16

This is a list of pathogenic ClinVar variants found in the CXCL16 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-4735106-G-A		not specified	Likely benign (Dec 03, 2024)
17-4735148-G-A		not specified	Likely benign (Jul 22, 2022)
17-4735191-G-T		not specified	Uncertain significance (Sep 22, 2023)
17-4735196-G-A		not specified	Likely benign (Aug 28, 2024)
17-4735200-C-T		not specified	Uncertain significance (Jan 17, 2023)
17-4735235-G-A			Benign (Feb 01, 2018)
17-4735382-G-C		not specified	Uncertain significance (Oct 26, 2022)
17-4735389-G-A		not specified	Uncertain significance (Oct 26, 2021)
17-4735422-C-T		not specified	Uncertain significance (Jun 02, 2023)
17-4735490-G-A		not specified	Likely benign (Dec 15, 2023)
17-4738417-C-G		not specified	Uncertain significance (Apr 20, 2024)
17-4738447-G-C		not specified	Uncertain significance (Oct 08, 2024)
17-4738902-C-T		not specified	Uncertain significance (Mar 01, 2024)
17-4739323-C-A		not specified	Uncertain significance (May 02, 2023)
17-4739335-C-T		not specified	Uncertain significance (Jul 15, 2021)
17-4739365-G-C		not specified	Uncertain significance (Dec 03, 2024)
17-4739368-G-A		not specified	Uncertain significance (Jan 18, 2022)
17-4739388-C-T			Benign (Feb 01, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CXCL16	protein_coding	protein_coding	ENST00000293778	5	6397

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000345	0.602	125740	0	8	125748	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.346	140	152	0.921	0.00000752	1731
Missense in Polyphen		30	37.974	0.79002		426
Synonymous	0.985	55	65.1	0.845	0.00000341	591
Loss of Function	0.768	8	10.7	0.747	4.53e-7	135

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000580	0.0000580
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.000109	0.000109
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a scavenger receptor on macrophages, which specifically binds to OxLDL (oxidized low density lipoprotein), suggesting that it may be involved in pathophysiology such as atherogenesis (By similarity). Induces a strong chemotactic response. Induces calcium mobilization. Binds to CXCR6/Bonzo. {ECO:0000250}.
• Pathway: Chemokine signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Chemokine signaling pathway;TYROBP Causal Network;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: 0.0345

Intolerance Scores

• loftool: 0.606
• rvis_EVS: 0.6
• rvis_percentile_EVS: 82.66

Haploinsufficiency Scores

• pHI: 0.0144
• hipred: N
• hipred_score: 0.123
• ghis: 0.399

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.000625

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cxcl16
• Phenotype: hematopoietic system phenotype; neoplasm; immune system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: receptor-mediated endocytosis;chemotaxis;G protein-coupled receptor signaling pathway;regulation of signaling receptor activity;T cell chemotaxis;positive regulation of cell growth;positive regulation of cell migration;response to cytokine;response to interferon-gamma;response to tumor necrosis factor
• Cellular component: extracellular region;extracellular space;plasma membrane;membrane;integral component of membrane
• Molecular function: low-density lipoprotein particle receptor activity;scavenger receptor activity;chemokine activity