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GeneBe

CXCL6

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

Basic information

Region (hg38): 4:73836639-73849064

Previous symbols: [ "SCYB6" ]

Links

ENSG00000124875NCBI:6372OMIM:138965HGNC:10643Uniprot:P80162AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CXCL6 gene.

  • Inborn genetic diseases (5 variants)
  • not provided (1 variants)

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
5
clinvar
5
nonsense
0
start loss
0
frameshift
1
clinvar
1
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 5 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 Inborn genetic diseases Uncertain significance (Sep 28, 2021)2252680
4-73836812-T-A Inborn genetic diseases Uncertain significance (Sep 09, 2021)2248884
4-73837036-A-G Inborn genetic diseases Uncertain significance (Dec 19, 2022)2217943
4-73837092-G-GT Benign (Aug 02, 2018)710320
4-73837093-T-G Inborn genetic diseases Uncertain significance (Jun 06, 2023)2558188
4-73837255-C-G Inborn genetic diseases Uncertain significance (Mar 28, 2022)2231198

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CXCL6protein_codingprotein_codingENST00000226317 412568
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
2.71e-90.0124124408613311257450.00533
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.6818165.51.240.00000303708
Missense in Polyphen2121.3370.98423252
Synonymous-1.033931.61.230.00000154258
Loss of Function-2.30104.652.151.96e-756

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.004140.00414
Ashkenazi Jewish0.000.00
East Asian0.0001090.000109
Finnish0.01080.0106
European (Non-Finnish)0.007780.00776
Middle Eastern0.0001090.000109
South Asian0.003190.00314
Other0.004940.00490

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
ghis

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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