CXCL1
Basic information
Region (hg38): 4:73869393-73871308
Previous symbols: [ "MGSA", "GRO1", "FSP" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (20 variants)
- not_provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CXCL1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000001511.4. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 17 | 21 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 17 | 3 | 1 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CXCL1 | protein_coding | protein_coding | ENST00000395761 | 4 | 1850 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.118 | 0.788 | 125734 | 0 | 6 | 125740 | 0.0000239 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.0153 | 61 | 61.3 | 0.995 | 0.00000294 | 663 |
| Missense in Polyphen | 9 | 16.558 | 0.54354 | 203 | ||
| Synonymous | -2.67 | 45 | 27.3 | 1.65 | 0.00000130 | 235 |
| Loss of Function | 1.33 | 2 | 5.30 | 0.377 | 2.26e-7 | 56 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.0000440 | 0.0000439 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Has chemotactic activity for neutrophils. May play a role in inflammation and exerts its effects on endothelial cells in an autocrine fashion. In vitro, the processed forms GRO- alpha(4-73), GRO-alpha(5-73) and GRO-alpha(6-73) show a 30-fold higher chemotactic activity. {ECO:0000269|PubMed:10095777}.;
- Pathway
- Kaposi,s sarcoma-associated herpesvirus infection - Homo sapiens (human);Salmonella infection - Homo sapiens (human);Legionellosis - Homo sapiens (human);TNF signaling pathway - Homo sapiens (human);Chemokine signaling pathway - Homo sapiens (human);Amoebiasis - Homo sapiens (human);Epithelial cell signaling in Helicobacter pylori infection - Homo sapiens (human);NOD-like receptor signaling pathway - Homo sapiens (human);IL-17 signaling pathway - Homo sapiens (human);Rheumatoid arthritis - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Spinal Cord Injury;Interleukin-10 signaling;Cytokines and Inflammatory Response;Senescence and Autophagy in Cancer;Signaling by GPCR;Neutrophil degranulation;Signal Transduction;Innate Immune System;Immune System;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;IL23-mediated signaling events
(Consensus)
Recessive Scores
- pRec
- 0.575
Intolerance Scores
- loftool
- 0.601
- rvis_EVS
- 0.44
- rvis_percentile_EVS
- 77.45
Haploinsufficiency Scores
- pHI
- 0.266
- hipred
- N
- hipred_score
- 0.112
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.753
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;nervous system development;cell population proliferation;negative regulation of cell population proliferation;regulation of signaling receptor activity;cytokine-mediated signaling pathway;actin cytoskeleton organization;neutrophil chemotaxis;leukocyte chemotaxis;intracellular signal transduction;positive regulation of catalytic activity;neutrophil degranulation;antimicrobial humoral immune response mediated by antimicrobial peptide;chemokine-mediated signaling pathway;cellular response to lipopolysaccharide
- Cellular component
- extracellular region;extracellular space;specific granule lumen;tertiary granule lumen
- Molecular function
- signaling receptor binding;chemokine activity;enzyme activator activity;growth factor activity