CXCL3
Basic information
Region (hg38): 4:74036589-74038807
Previous symbols: [ "GRO3" ]
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 CXCL3 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 | 9 | |||||
| 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 | 1 | 0 |
Variants in CXCL3
This is a list of pathogenic ClinVar variants found in the CXCL3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 4-74038151-C-A | not specified | Uncertain significance (Oct 12, 2024) | ||
| 4-74038157-T-G | not specified | Likely benign (Feb 08, 2025) | ||
| 4-74038323-G-A | not specified | Uncertain significance (Jul 02, 2024) | ||
| 4-74038326-C-T | not specified | Likely benign (Jul 12, 2023) | ||
| 4-74038341-T-C | not specified | Uncertain significance (Mar 01, 2024) | ||
| 4-74038389-C-T | not specified | Uncertain significance (May 29, 2024) | ||
| 4-74038408-A-G | not specified | Likely benign (Jan 01, 2025) | ||
| 4-74038517-G-A | not specified | Uncertain significance (Feb 15, 2023) | ||
| 4-74038518-C-A | not specified | Uncertain significance (Feb 15, 2023) | ||
| 4-74038562-C-A | not specified | Uncertain significance (Jan 26, 2025) | ||
| 4-74038601-G-C | not specified | Uncertain significance (Jan 26, 2022) | ||
| 4-74038607-G-C | not specified | Uncertain significance (Sep 16, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CXCL3 | protein_coding | protein_coding | ENST00000296026 | 4 | 2219 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000302 | 0.366 | 125735 | 0 | 10 | 125745 | 0.0000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.723 | 66 | 51.4 | 1.28 | 0.00000228 | 667 |
| Missense in Polyphen | 23 | 18.404 | 1.2497 | 240 | ||
| Synonymous | -1.13 | 29 | 22.2 | 1.30 | 0.00000105 | 232 |
| Loss of Function | -0.166 | 5 | 4.62 | 1.08 | 1.96e-7 | 55 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000868 | 0.0000868 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000264 | 0.0000264 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000131 | 0.000131 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Ligand for CXCR2 (By similarity). Has chemotactic activity for neutrophils. May play a role in inflammation and exert its effects on endothelial cells in an autocrine fashion. In vitro, the processed form GRO-gamma(5-73) shows a fivefold higher chemotactic activity for neutrophilic granulocytes. {ECO:0000250, 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);NOD-like receptor signaling pathway - Homo sapiens (human);IL-17 signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Chemokine signaling pathway;Fibrin Complement Receptor 3 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
- 0.165
Intolerance Scores
- loftool
- 0.615
- rvis_EVS
- -0.03
- rvis_percentile_EVS
- 51.04
Haploinsufficiency Scores
- pHI
- 0.0404
- hipred
- N
- hipred_score
- 0.148
- ghis
- 0.391
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.164
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cxcl2
- Phenotype
Gene ontology
- Biological process
- inflammatory response;immune response;G protein-coupled receptor signaling pathway;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