IL1B
interleukin 1 beta, the group of Interleukins
Basic information
Region (hg38): 2:112829750-112836816
Links
Phenotypes
GenCC
Source:
- hereditary diffuse gastric adenocarcinoma (No Known Disease Relationship), mode of inheritance: Unknown
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (7 variants)
- not provided (5 variants)
- Coronary heart disease, susceptibility to, 2 (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the IL1B 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 | 4 | |||||
| missense | 7 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region ? | 0 | |||||
| non coding ? | 1 | |||||
| Total | 0 | 0 | 7 | 3 | 2 |
Variants in IL1B
This is a list of pathogenic ClinVar variants found in the IL1B region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 2-112830503-T-C | not specified | Uncertain significance (Dec 09, 2023) | ||
| 2-112830541-C-T | Likely benign (Mar 01, 2020) | |||
| 2-112831327-C-T | not specified | Uncertain significance (Dec 03, 2021) | ||
| 2-112832705-T-G | not specified | Uncertain significance (Dec 30, 2023) | ||
| 2-112832764-G-C | not specified | Uncertain significance (Feb 28, 2024) | ||
| 2-112832813-G-A | Antisynthetase syndrome • Endometriosis • Cholangiocarcinoma • IL1B-related disorder | Benign (Nov 19, 2019) | ||
| 2-112832819-G-T | Likely benign (May 01, 2022) | |||
| 2-112832825-T-A | not specified | Uncertain significance (Dec 17, 2021) | ||
| 2-112833437-G-A | not specified | Uncertain significance (Apr 05, 2023) | ||
| 2-112833504-G-A | Benign/Likely benign (May 01, 2022) | |||
| 2-112833515-C-T | not specified | Uncertain significance (Jun 07, 2023) | ||
| 2-112833530-G-T | not specified | Uncertain significance (Dec 20, 2021) | ||
| 2-112833537-G-A | Benign (Jun 21, 2017) | |||
| 2-112833561-G-T | not specified | Uncertain significance (Nov 05, 2021) | ||
| 2-112833580-G-A | IL1B-related disorder | Likely benign (Feb 28, 2019) | ||
| 2-112833585-G-A | Benign (Aug 14, 2018) | |||
| 2-112835183-C-G | Coronary heart disease, susceptibility to, 2 | not provided (-) | ||
| 2-112835573-T-C | not specified | Uncertain significance (Nov 12, 2021) | ||
| 2-112836202-C-T | Uncertain significance (-) | |||
| 2-112836810-G-A | Gastric cancer susceptibility after h. pylori infection | risk factor (Nov 04, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| IL1B | protein_coding | protein_coding | ENST00000263341 | 6 | 7153 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.130 | 0.866 | 125744 | 0 | 4 | 125748 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.15 | 102 | 140 | 0.728 | 0.00000769 | 1810 |
| Missense in Polyphen | 29 | 44.28 | 0.65492 | 630 | ||
| Synonymous | -0.394 | 59 | 55.3 | 1.07 | 0.00000343 | 478 |
| Loss of Function | 2.50 | 4 | 14.1 | 0.283 | 9.12e-7 | 145 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000905 | 0.0000904 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000880 | 0.00000879 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Potent proinflammatory cytokine. Initially discovered as the major endogenous pyrogen, induces prostaglandin synthesis, neutrophil influx and activation, T-cell activation and cytokine production, B-cell activation and antibody production, and fibroblast proliferation and collagen production. Promotes Th17 differentiation of T-cells. Synergizes with IL12/interleukin-12 to induce IFNG synthesis from T-helper 1 (Th1) cells (PubMed:10653850). {ECO:0000269|PubMed:10653850, ECO:0000269|PubMed:3920526}.;
- Pathway
- Prion diseases - Homo sapiens (human);Inflammatory mediator regulation of TRP channels - Homo sapiens (human);Type I diabetes mellitus - Homo sapiens (human);Pertussis - Homo sapiens (human);Salmonella infection - Homo sapiens (human);Legionellosis - Homo sapiens (human);Graft-versus-host disease - Homo sapiens (human);Non-alcoholic fatty liver disease (NAFLD) - Homo sapiens (human);AGE-RAGE signaling pathway in diabetic complications - Homo sapiens (human);Influenza A - Homo sapiens (human);Inflammatory bowel disease (IBD) - Homo sapiens (human);Alzheimer,s disease - Homo sapiens (human);African trypanosomiasis - Homo sapiens (human);TNF signaling pathway - Homo sapiens (human);Amoebiasis - Homo sapiens (human);Malaria - Homo sapiens (human);Cytosolic DNA-sensing pathway - Homo sapiens (human);Chagas disease (American trypanosomiasis) - Homo sapiens (human);Necroptosis - Homo sapiens (human);Toll-like receptor signaling pathway - Homo sapiens (human);NOD-like receptor signaling pathway - Homo sapiens (human);Fluid shear stress and atherosclerosis - Homo sapiens (human);C-type lectin receptor signaling pathway - Homo sapiens (human);Tuberculosis - Homo sapiens (human);Th17 cell differentiation - Homo sapiens (human);MAPK signaling pathway - Homo sapiens (human);Leishmaniasis - Homo sapiens (human);IL-17 signaling pathway - Homo sapiens (human);Measles - Homo sapiens (human);Rheumatoid arthritis - Homo sapiens (human);Osteoclast differentiation - Homo sapiens (human);Hematopoietic cell lineage - Homo sapiens (human);NF-kappa B signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Herpes simplex infection - Homo sapiens (human);JAK-STAT-Core;Nucleotide-binding Oligomerization Domain (NOD) pathway;Regulation of toll-like receptor signaling pathway;Serotonin Transporter Activity;Selenium Micronutrient Network;Vitamin B12 Metabolism;Folate Metabolism;IL-1 signaling pathway;Leptin signaling pathway;Alzheimers Disease;Allograft Rejection;Spinal Cord Injury;JAK-STAT;Hematopoietic Stem Cell Differentiation;IL1 and megakaryocytes in obesity;Aryl Hydrocarbon Receptor Pathway;Nuclear Receptors Meta-Pathway;Myometrial Relaxation and Contraction Pathways;C-type lectin receptors (CLRs);Photodynamic therapy-induced NF-kB survival signaling;Lung fibrosis;MAPK Signaling Pathway;Nanomaterial induced inflammasome activation;Development and heterogeneity of the ILC family;NO-cGMP-PKG mediated Neuroprotection;Interleukin-10 signaling;Interleukin-4 and 13 signaling;Cytokines and Inflammatory Response;Senescence and Autophagy in Cancer;Type II interferon signaling (IFNG);T-Cell antigen Receptor (TCR) Signaling Pathway;Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways;Monoamine Transport;Toll-like Receptor Signaling Pathway;TLR NFkB;Signaling by Interleukins;signal transduction through il1r;nfkb activation by nontypeable hemophilus influenzae;Cytokine Signaling in Immune system;JAK STAT MolecularVariation 1;GPCR signaling-G alpha q;Interleukin-1 signaling;GPCR signaling-cholera toxin;CLEC7A/inflammasome pathway;CLEC7A (Dectin-1) signaling;GPCR signaling-pertussis toxin;C-type lectin receptors (CLRs);Innate Immune System;Immune System;IL-1 NFkB;IL-1 p38;IL-1 JNK;GPCR signaling-G alpha s Epac and ERK;IL1;GPCR signaling-G alpha s PKA and ERK;JAK STAT pathway and regulation;IFN-gamma pathway;TLR ECSIT MEKK1 JNK;GPCR signaling-G alpha i;IL23-mediated signaling events;IL27-mediated signaling events;Interleukin-1 processing;IL1-mediated signaling events;IL12-mediated signaling events;Cellular roles of Anthrax toxin;Interleukin-1 family signaling
(Consensus)
Recessive Scores
- pRec
- 0.992
Intolerance Scores
- loftool
- 0.252
- rvis_EVS
- -0.38
- rvis_percentile_EVS
- 27.42
Haploinsufficiency Scores
- pHI
- 0.0699
- hipred
- N
- hipred_score
- 0.455
- ghis
- 0.540
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 1.00
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Il1b
- Phenotype
- craniofacial phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); neoplasm; 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); immune system phenotype; skeleton 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); 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);
Zebrafish Information Network
- Gene name
- il1b
- Affected structure
- macrophage chemotaxis
- Phenotype tag
- abnormal
- Phenotype quality
- decreased occurrence
Gene ontology
- Biological process
- MAPK cascade;activation of MAPK activity;fever generation;positive regulation of protein phosphorylation;positive regulation of T cell mediated immunity;apoptotic process;inflammatory response;immune response;signal transduction;cell-cell signaling;embryo implantation;positive regulation of cell population proliferation;negative regulation of cell population proliferation;response to carbohydrate;regulation of signaling receptor activity;positive regulation of vascular endothelial growth factor production;positive regulation of gene expression;positive regulation of epithelial to mesenchymal transition;negative regulation of glucose transmembrane transport;smooth muscle adaptation;cytokine-mediated signaling pathway;hyaluronan biosynthetic process;positive regulation of cell migration;neutrophil chemotaxis;sequestering of triglyceride;positive regulation of vascular endothelial growth factor receptor signaling pathway;positive regulation of fever generation;lipopolysaccharide-mediated signaling pathway;positive regulation of prostaglandin secretion;interleukin-1 beta production;interleukin-6 production;positive regulation of granulocyte macrophage colony-stimulating factor production;positive regulation of interferon-gamma production;positive regulation of interleukin-6 production;positive regulation of interleukin-8 production;positive regulation of histone phosphorylation;response to ATP;positive regulation of heterotypic cell-cell adhesion;positive regulation of histone acetylation;ectopic germ cell programmed cell death;positive regulation of myosin light chain kinase activity;cellular response to drug;positive regulation of T cell proliferation;regulation of I-kappaB kinase/NF-kappaB signaling;positive regulation of I-kappaB kinase/NF-kappaB signaling;negative regulation of MAP kinase activity;protein kinase B signaling;positive regulation of chemokine biosynthetic process;positive regulation of interleukin-2 biosynthetic process;positive regulation of interleukin-6 biosynthetic process;positive regulation of nitric oxide biosynthetic process;positive regulation of angiogenesis;negative regulation of lipid metabolic process;positive regulation of mitotic nuclear division;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;positive regulation of JNK cascade;negative regulation of insulin receptor signaling pathway;positive regulation of protein export from nucleus;regulation of defense response to virus by host;positive regulation of phagocytosis;regulation of neurogenesis;negative regulation of neurogenesis;regulation of insulin secretion;negative regulation of synaptic transmission;negative regulation of lipid catabolic process;positive regulation of lipid catabolic process;regulation of nitric-oxide synthase activity;positive regulation of membrane protein ectodomain proteolysis;positive regulation of DNA-binding transcription factor activity;positive regulation of NF-kappaB transcription factor activity;positive regulation of cell division;positive regulation of glial cell proliferation;positive regulation of cell adhesion molecule production;positive regulation of calcidiol 1-monooxygenase activity;negative regulation of adiponectin secretion;regulation of ERK1 and ERK2 cascade;monocyte aggregation;interleukin-1-mediated signaling pathway;cellular response to lipopolysaccharide;cellular response to mechanical stimulus;cellular response to organic substance;cellular response to organic cyclic compound;positive regulation of monocyte chemotactic protein-1 production;extrinsic apoptotic signaling pathway in absence of ligand;positive regulation of neuroinflammatory response;positive regulation of p38MAPK cascade;positive regulation of NIK/NF-kappaB signaling;regulation of establishment of endothelial barrier;positive regulation of T-helper 1 cell cytokine production;positive regulation of interleukin-6 secretion;negative regulation of extrinsic apoptotic signaling pathway in absence of ligand
- Cellular component
- extracellular region;extracellular space;lysosome;cytosol;secretory granule;extracellular exosome
- Molecular function
- cytokine activity;interleukin-1 receptor binding;integrin binding;protein binding;protein domain specific binding