CXCL6
Basic information
Region (hg38): 4:73836640-73849064
Previous symbols: [ "SCYB6" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | |||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 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) | ||
4-73837035-A-G | not specified | Uncertain significance (Jun 11, 2024) | ||
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) | ||
4-73837636-A-G | not specified | Uncertain significance (May 06, 2024) |
GnomAD
Source:
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:
- 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
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