CXCL5
Basic information
Region (hg38): 4:73995642-73998677
Previous symbols: [ "SCYB5" ]
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 CXCL5 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 | 8 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 7 | 1 | 0 |
Variants in CXCL5
This is a list of pathogenic ClinVar variants found in the CXCL5 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 4-73997644-T-C | not specified | Uncertain significance (Jan 03, 2024) | ||
| 4-73998034-C-T | not specified | Likely benign (Jun 09, 2022) | ||
| 4-73998035-T-A | not specified | Uncertain significance (Apr 25, 2022) | ||
| 4-73998224-C-T | not specified | Uncertain significance (Feb 28, 2024) | ||
| 4-73998240-C-T | not specified | Uncertain significance (Jul 25, 2023) | ||
| 4-73998547-G-C | not specified | Uncertain significance (Oct 10, 2023) | ||
| 4-73998559-G-A | not specified | Uncertain significance (Aug 20, 2023) | ||
| 4-73998577-C-T | not specified | Uncertain significance (Dec 16, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CXCL5 | protein_coding | protein_coding | ENST00000296027 | 4 | 3138 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00000504 | 0.138 | 125717 | 0 | 30 | 125747 | 0.000119 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.125 | 65 | 62.2 | 1.04 | 0.00000292 | 714 |
| Missense in Polyphen | 20 | 16.824 | 1.1888 | 223 | ||
| Synonymous | -0.622 | 31 | 26.9 | 1.15 | 0.00000137 | 239 |
| Loss of Function | -0.782 | 7 | 5.09 | 1.37 | 2.16e-7 | 60 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000687 | 0.000684 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.0000441 | 0.0000439 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000132 | 0.000131 |
| Other | 0.000164 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in neutrophil activation. In vitro, ENA-78(8- 78) and ENA-78(9-78) show a threefold higher chemotactic activity for neutrophil granulocytes. {ECO:0000269|PubMed:10095777}.;
- Pathway
- Pertussis - Homo sapiens (human);TNF signaling pathway - 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);Chemokine signaling pathway;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
- 0.203
Intolerance Scores
- loftool
- 0.441
- rvis_EVS
- 0.21
- rvis_percentile_EVS
- 67.72
Haploinsufficiency Scores
- pHI
- 0.285
- hipred
- N
- hipred_score
- 0.112
- ghis
- 0.389
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.242
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Gene ontology
- Biological process
- chemotaxis;inflammatory response;immune response;signal transduction;G protein-coupled receptor signaling pathway;cell-cell signaling;positive regulation of cell population proliferation;regulation of signaling receptor activity;neutrophil chemotaxis;leukocyte chemotaxis;antimicrobial humoral immune response mediated by antimicrobial peptide;chemokine-mediated signaling pathway;cellular response to lipopolysaccharide
- Cellular component
- extracellular region;extracellular space
- Molecular function
- chemokine activity;identical protein binding