IL3
interleukin 3, the group of Interleukins
Basic information
Region (hg38): 5:132060655-132063204
Links
Phenotypes
GenCC
Source:
No genCC data.
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 IL3 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 | 1 | |||||
| missense | 12 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 1 | |||||
| Total | 0 | 0 | 8 | 3 | 3 |
Variants in IL3
This is a list of pathogenic ClinVar variants found in the IL3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-132060713-C-T | Benign (Jul 16, 2018) | |||
| 5-132060722-G-A | not specified | Likely benign (Jul 19, 2023) | ||
| 5-132060783-C-T | not specified | Uncertain significance (Mar 25, 2024) | ||
| 5-132060865-G-T | not specified | Uncertain significance (Aug 11, 2022) | ||
| 5-132060983-A-G | Likely benign (Jul 31, 2018) | |||
| 5-132060986-G-A | not specified | Likely benign (Aug 30, 2022) | ||
| 5-132060993-C-T | Benign (Jul 06, 2018) | |||
| 5-132062410-A-T | Benign (Jul 06, 2018) | |||
| 5-132062566-C-T | not specified | Uncertain significance (Mar 11, 2022) | ||
| 5-132062684-A-G | not specified | Uncertain significance (Oct 06, 2022) | ||
| 5-132062701-G-C | not specified | Uncertain significance (Oct 12, 2021) | ||
| 5-132062711-C-T | not specified | Uncertain significance (Jan 04, 2024) | ||
| 5-132062712-G-T | not specified | Uncertain significance (Nov 05, 2021) | ||
| 5-132062718-A-G | not specified | Uncertain significance (Jan 03, 2024) | ||
| 5-132062781-C-T | not specified | Uncertain significance (Aug 12, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| IL3 | protein_coding | protein_coding | ENST00000296870 | 5 | 2676 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 2.59e-9 | 0.0231 | 125735 | 0 | 13 | 125748 | 0.0000517 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.232 | 86 | 92.3 | 0.932 | 0.00000566 | 990 |
| Missense in Polyphen | 15 | 12.057 | 1.2441 | 126 | ||
| Synonymous | 0.202 | 39 | 40.6 | 0.960 | 0.00000286 | 302 |
| Loss of Function | -1.28 | 11 | 7.26 | 1.51 | 3.75e-7 | 76 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000578 | 0.0000578 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000352 | 0.0000352 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000229 | 0.000229 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Granulocyte/macrophage colony-stimulating factors are cytokines that act in hematopoiesis by controlling the production, differentiation, and function of 2 related white cell populations of the blood, the granulocytes and the monocytes-macrophages.;
- Pathway
- PI3K-Akt signaling pathway - Homo sapiens (human);Fc epsilon RI signaling pathway - Homo sapiens (human);Jak-STAT signaling pathway - Homo sapiens (human);Acute myeloid leukemia - Homo sapiens (human);Asthma - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Transcriptional misregulation in cancer - Homo sapiens (human);Hematopoietic cell lineage - Homo sapiens (human);Apoptosis - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Fc Epsilon Receptor I Signaling in Mast Cells;JAK-STAT-Core;Differentiation Pathway;Hematopoietic Stem Cell Differentiation;IL-3 Signaling Pathway;Transcriptional regulation by RUNX1;PI3K-Akt Signaling Pathway;Cytokines and Inflammatory Response;Senescence and Autophagy in Cancer;Signaling by GPCR;IL-3 signaling;Signal Transduction;Gene expression (Transcription);Signaling by Interleukins;regulation of bad phosphorylation;Generic Transcription Pathway;Cytokine Signaling in Immune system;JAK STAT MolecularVariation 1;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;RNA Polymerase II Transcription;il 3 signaling pathway;Immune System;Interleukin receptor SHC signaling;Interleukin-2 family signaling;GPCR signaling-G alpha s Epac and ERK;GPCR signaling-G alpha s PKA and ERK;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades;JAK STAT pathway and regulation;IL3;GPCR signaling-G alpha i;RUNX1 regulates transcription of genes involved in interleukin signaling;G beta:gamma signalling through PI3Kgamma;G-protein beta:gamma signalling;GPCR downstream signalling;Transcriptional regulation by RUNX1;Calcineurin-regulated NFAT-dependent transcription in lymphocytes;IL3-mediated signaling events;Calcium signaling in the CD4+ TCR pathway;Interleukin-3, 5 and GM-CSF signaling
(Consensus)
Recessive Scores
- pRec
- 0.0319
Intolerance Scores
- loftool
- 0.781
- rvis_EVS
- 0.53
- rvis_percentile_EVS
- 80.58
Haploinsufficiency Scores
- pHI
- 0.0194
- hipred
- N
- hipred_score
- 0.228
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.0754
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Il3
- Phenotype
- renal/urinary system phenotype; immune system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); neoplasm; hematopoietic 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); respiratory system phenotype; homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype;
Gene ontology
- Biological process
- MAPK cascade;regulation of cytokine-mediated signaling pathway;immune response;cell-cell signaling;nervous system development;positive regulation of cell population proliferation;regulation of signaling receptor activity;peptidyl-tyrosine phosphorylation;cytokine-mediated signaling pathway;embryonic hemopoiesis;positive regulation of tyrosine phosphorylation of STAT protein;positive regulation of peptidyl-tyrosine phosphorylation
- Cellular component
- extracellular region;extracellular space
- Molecular function
- protein tyrosine kinase activity;Ras guanyl-nucleotide exchange factor activity;cytokine activity;interleukin-3 receptor binding;growth factor activity