CXCL6
protein-codingC-X-C motif chemokine ligand 6, the group of Chemokine ligands
Gene summary
The protein encoded by this gene is a member CXC chemokine family. The encoded protein is a chemotactic for neutrophil granulocytes and has antibacterial action against gram-negative and gram-positive bacteria. This gene and other members of the CXC chemokine gene family form a gene cluster in a region of chromosome 4q. [provided by RefSeq, Jun 2020]
- SCYB6
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~12.4 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CXCL6 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_002993.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 21 | 21 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 21 | 0 | 1 | 22 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_002984.1 | 4 | MANE Select | |
| Ensembl | ENSP00000226317.5 | 4 | MANE Select | |
| Ensembl | ENSP00000424819.1 | 3 | Standard | |
| Ensembl | ENSP00000424819.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- 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)
Biological Process
- leukocyte homeostasis
- chemotaxis
- inflammatory response
- immune response
- signal transduction
Molecular Function
- protein binding
- chemokine activity
- heparin binding
Cellular Component
- extracellular region
- extracellular space
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000226317
- Coding exons
- 4
- Length
- 12568
- Individuals with no LoFs
- 124408
- Homozygous LoFs
- 6
- Heterozygous LoFs
- 1331
- Defined
- 125745
- p
- 0.00533
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.681 | 81 | 65.5 | 1.24 | 0.00000303 | 708 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0022 | 0.0022 | notable |
| Latino/Admixed American | 0.0020 | 0.0019 | notable |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0.011 | 0.011 | notable |
| European (Non-Finnish) | 0.0078 | 0.0078 | notable |
| South Asian | 0.0032 | 0.0031 | notable |
| Other | 0.0049 | 0.0049 | notable |
dbNSFP Gene Annotations
Source:
- 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}.;
Recessive Scores
- pRec
- 0.173
Intolerance Scores
- LoFtool
- 0.722
- RVIS EVS
- 0.01
- RVIS percentile EVS
- 54.95
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.539
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |