CXCL6

C-X-C motif chemokine ligand 6, the group of Chemokine ligands

Basic information

Region (hg38): 4:73836639-73849064

Previous symbols: [ "SCYB6" ]

Links

ENSG00000124875 ∙ NCBI:6372 ∙ OMIM:138965 ∙ HGNC:10643 ∙ Uniprot:P80162 ∙ 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 CXCL6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CXCL6 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			7			7
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	1

Variants in CXCL6

This is a list of pathogenic ClinVar variants found in the CXCL6 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-73836782-T-C		not specified	Uncertain significance (Sep 28, 2021)
4-73836812-T-A		not specified	Uncertain significance (Sep 09, 2021)
4-73836836-C-T		not specified	Uncertain significance (Dec 12, 2023)
4-73837036-A-G		not specified	Uncertain significance (Dec 19, 2022)
4-73837077-T-C		not specified	Uncertain significance (Feb 06, 2024)
4-73837092-G-GT			Benign (Aug 02, 2018)
4-73837093-T-G		not specified	Uncertain significance (Jun 06, 2023)
4-73837255-C-G		not specified	Uncertain significance (Mar 28, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CXCL6	protein_coding	protein_coding	ENST00000226317	4	12568

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.71e-9	0.0124	124408	6	1331	125745	0.00533

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.681	81	65.5	1.24	0.00000303	708
Missense in Polyphen		21	21.337	0.98423		252
Synonymous	-1.03	39	31.6	1.23	0.00000154	258
Loss of Function	-2.30	10	4.65	2.15	1.96e-7	56

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00414	0.00414
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0108	0.0106
European (Non-Finnish)	0.00778	0.00776
Middle Eastern	0.000109	0.000109
South Asian	0.00319	0.00314
Other	0.00494	0.00490

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Chemotactic for neutrophil granulocytes. Signals through binding and activation of its receptors (CXCR1 and CXCR2). In addition to its chemotactic and angiogenic properties, it has strong antibacterial activity against Gram-positive and Gram- negative bacteria (90-fold-higher when compared to CXCL5 and CXCL7). {ECO:0000269|PubMed:18443119, ECO:0000269|PubMed:8399143, ECO:0000269|PubMed:8423327, ECO:0000269|PubMed:9057843}.
• Pathway: Pertussis - Homo sapiens (human);Chemokine signaling pathway - Homo sapiens (human);IL-17 signaling pathway - Homo sapiens (human);Rheumatoid arthritis - 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)

Recessive Scores

• pRec: 0.173

Intolerance Scores

• loftool: 0.722
• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.95

Haploinsufficiency Scores

• pHI: 0.0817
• hipred: N
• hipred_score: 0.139

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cxcl5
• Phenotype: immune system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: leukocyte homeostasis;chemotaxis;inflammatory response;immune response;signal transduction;G protein-coupled receptor signaling pathway;cell-cell signaling;regulation of signaling receptor activity;neutrophil chemotaxis;leukocyte chemotaxis;regulation of chemokine production;neutrophil activation;defense response to bacterium;antimicrobial humoral immune response mediated by antimicrobial peptide;chemokine-mediated signaling pathway;regulation of neutrophil mediated killing of gram-negative bacterium;cellular response to lipopolysaccharide
• Cellular component: extracellular region;extracellular space
• Molecular function: protein binding;chemokine activity;heparin binding