CXCL2
Basic information
Region (hg38): 4:74097040-74099196
Previous symbols: [ "GRO2" ]
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 CXCL2 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 | 10 | |||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 8 | 2 | 0 |
Variants in CXCL2
This is a list of pathogenic ClinVar variants found in the CXCL2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
4-74098622-A-C | not specified | Uncertain significance (Aug 05, 2024) | ||
4-74098643-G-A | not specified | Uncertain significance (Aug 01, 2024) | ||
4-74098683-C-T | not specified | Uncertain significance (Apr 09, 2024) | ||
4-74098874-T-C | not specified | Uncertain significance (Apr 17, 2024) | ||
4-74099033-G-A | not specified | Uncertain significance (Dec 01, 2022) | ||
4-74099033-G-C | not specified | Uncertain significance (Mar 28, 2023) | ||
4-74099036-T-C | not specified | Likely benign (Nov 20, 2024) | ||
4-74099071-C-G | not specified | Uncertain significance (Jan 09, 2024) | ||
4-74099081-G-C | not specified | Uncertain significance (Mar 07, 2025) | ||
4-74099099-C-T | not specified | Likely benign (Jan 29, 2024) | ||
4-74099101-G-T | not specified | Uncertain significance (Dec 25, 2024) | ||
4-74099114-G-C | not specified | Uncertain significance (Nov 15, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
CXCL2 | protein_coding | protein_coding | ENST00000508487 | 4 | 2259 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
3.61e-7 | 0.0583 | 125742 | 0 | 6 | 125748 | 0.0000239 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.0992 | 53 | 51.0 | 1.04 | 0.00000240 | 663 |
Missense in Polyphen | 16 | 16.818 | 0.95138 | 219 | ||
Synonymous | -1.30 | 31 | 23.0 | 1.35 | 0.00000120 | 231 |
Loss of Function | -1.38 | 8 | 4.76 | 1.68 | 2.02e-7 | 57 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000615 | 0.0000615 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000176 | 0.0000176 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.0000654 | 0.0000653 |
Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Produced by activated monocytes and neutrophils and expressed at sites of inflammation. Hematoregulatory chemokine, which, in vitro, suppresses hematopoietic progenitor cell proliferation. GRO-beta(5-73) shows a highly enhanced hematopoietic activity. {ECO:0000269|PubMed:10725737}.;
- 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);NOD-like receptor signaling pathway - Homo sapiens (human);IL-17 signaling pathway - Homo sapiens (human);NF-kappa B signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Spinal Cord Injury;Photodynamic therapy-induced NF-kB survival signaling;Lung fibrosis;Interleukin-10 signaling;Cytokines and Inflammatory Response;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
- 0.533
Haploinsufficiency Scores
- pHI
- 0.0701
- hipred
- N
- hipred_score
- 0.112
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.101
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cxcl1
- Phenotype
- cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan);
Gene ontology
- Biological process
- response to molecule of bacterial origin;chemotaxis;inflammatory response;immune response;G protein-coupled receptor signaling pathway;regulation of signaling receptor activity;cytokine-mediated signaling pathway;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
- protein binding;chemokine activity