IL2
interleukin 2, the group of Interleukins
Basic information
Region (hg38): 4:122451470-122456725
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 IL2 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 | 1 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 0 | 1 | 0 |
Variants in IL2
This is a list of pathogenic ClinVar variants found in the IL2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 4-122451780-CA-C | Breast neoplasm | Pathogenic (-) | ||
| 4-122456306-CA-C | Breast neoplasm | Pathogenic (-) | ||
| 4-122456312-C-A | IL2-related disorder | Likely benign (Oct 31, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| IL2 | protein_coding | protein_coding | ENST00000226730 | 4 | 5256 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.480 | 0.500 | 123887 | 0 | 1 | 123888 | 0.00000404 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.43 | 38 | 72.2 | 0.526 | 0.00000312 | 1002 |
| Missense in Polyphen | 11 | 18.771 | 0.586 | 271 | ||
| Synonymous | -1.14 | 34 | 26.6 | 1.28 | 0.00000121 | 286 |
| Loss of Function | 1.86 | 1 | 5.85 | 0.171 | 2.46e-7 | 79 |
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 | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000329 | 0.0000329 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Produced by T-cells in response to antigenic or mitogenic stimulation, this protein is required for T-cell proliferation and other activities crucial to regulation of the immune response. Can stimulate B-cells, monocytes, lymphokine- activated killer cells, natural killer cells, and glioma cells.;
- Disease
- DISEASE: Note=A chromosomal aberration involving IL2 is found in a form of T-cell acute lymphoblastic leukemia (T-ALL). Translocation t(4;16)(q26;p13) with involves TNFRSF17. {ECO:0000269|PubMed:1396583}.;
- Pathway
- PI3K-Akt signaling pathway - Homo sapiens (human);Type I diabetes mellitus - Homo sapiens (human);T cell receptor signaling pathway - Homo sapiens (human);Allograft rejection - Homo sapiens (human);Graft-versus-host disease - Homo sapiens (human);Jak-STAT signaling pathway - Homo sapiens (human);Autoimmune thyroid disease - Homo sapiens (human);Inflammatory bowel disease (IBD) - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);Chagas disease (American trypanosomiasis) - Homo sapiens (human);C-type lectin receptor signaling pathway - Homo sapiens (human);Th17 cell differentiation - Homo sapiens (human);Th1 and Th2 cell differentiation - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Measles - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Intestinal immune network for IgA production - Homo sapiens (human);Tacrolimus/Cyclosporine Pathway, Pharmacodynamics;JAK-STAT-Core;IL-5 Signaling Pathway;Folate Metabolism;Allograft Rejection;Corticotropin-releasing hormone signaling pathway;Spinal Cord Injury;T-Cell Receptor and Co-stimulatory Signaling;Aryl Hydrocarbon Receptor Pathway;Nuclear Receptors Meta-Pathway;Photodynamic therapy-induced AP-1 survival signaling.;Photodynamic therapy-induced NF-kB survival signaling;T-Cell antigen Receptor (TCR) pathway during Staphylococcus aureus infection;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs);PI3K-Akt Signaling Pathway;Inflammatory Response Pathway;IL-2 Signaling Pathway;Cytokines and Inflammatory Response;Signaling by GPCR;Signal Transduction;Gene expression (Transcription);Signaling by Interleukins;il 2 signaling pathway;il-2 receptor beta chain in t cell activation;the 41bb-dependent immune response;Generic Transcription Pathway;Cytokine Signaling in Immune system;IL12 signaling mediated by STAT4;RNA Polymerase II Transcription;Immune System;Interleukin receptor SHC signaling;Interleukin-2 family signaling;SHP2 signaling;Glucocorticoid receptor regulatory network;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades;IL2;IL2-mediated signaling events;Gastrin;Interleukin-2 signaling;RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs);G beta:gamma signalling through PI3Kgamma;G-protein beta:gamma signalling;GPCR downstream signalling;IL23-mediated signaling events;Transcriptional regulation by RUNX1;IL2 signaling events mediated by STAT5;IL27-mediated signaling events;Downstream signaling in naïve CD8+ T cells;Calcineurin-regulated NFAT-dependent transcription in lymphocytes;Regulation of Telomerase;AP-1 transcription factor network;IL2 signaling events mediated by PI3K;IL12-mediated signaling events;Calcium signaling in the CD4+ TCR pathway;Interleukin-3, 5 and GM-CSF signaling
(Consensus)
Recessive Scores
- pRec
- 0.956
Intolerance Scores
- loftool
- rvis_EVS
- 0.3
- rvis_percentile_EVS
- 71.81
Haploinsufficiency Scores
- pHI
- 0.424
- hipred
- N
- hipred_score
- 0.477
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.833
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Il2
- Phenotype
- endocrine/exocrine gland phenotype; growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; respiratory system phenotype; neoplasm; 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); 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); hematopoietic system phenotype; vision/eye phenotype; digestive/alimentary phenotype;
Gene ontology
- Biological process
- MAPK cascade;negative regulation of protein phosphorylation;adaptive immune response;leukocyte activation involved in immune response;negative regulation of B cell apoptotic process;immune response;cell adhesion;positive regulation of cytosolic calcium ion concentration;protein kinase C-activating G protein-coupled receptor signaling pathway;cell-cell signaling;positive regulation of cell population proliferation;regulation of signaling receptor activity;cytokine-mediated signaling pathway;natural killer cell activation;T cell differentiation;positive regulation of cell growth;positive regulation of B cell proliferation;positive regulation of interferon-gamma production;positive regulation of interleukin-17 production;positive regulation of kinase activity;positive regulation of tissue remodeling;interleukin-2-mediated signaling pathway;positive regulation of activated T cell proliferation;positive regulation of tyrosine phosphorylation of STAT protein;negative regulation of apoptotic process;response to ethanol;regulation of regulatory T cell differentiation;positive regulation of regulatory T cell differentiation;negative regulation of heart contraction;positive regulation of transcription by RNA polymerase II;regulation of T cell homeostatic proliferation;positive regulation of isotype switching to IgG isotypes;negative regulation of lymphocyte proliferation;negative regulation of inflammatory response;positive regulation of inflammatory response;positive regulation of immunoglobulin secretion;positive regulation of dendritic spine development;extrinsic apoptotic signaling pathway in absence of ligand;negative regulation of T-helper 17 cell differentiation
- Cellular component
- extracellular region;extracellular space;cell
- Molecular function
- Ras guanyl-nucleotide exchange factor activity;cytokine activity;interleukin-2 receptor binding;protein binding;growth factor activity;kinase activator activity;carbohydrate binding;kappa-type opioid receptor binding;glycosphingolipid binding