IL1A
interleukin 1 alpha, the group of Interleukins
Basic information
Region (hg38): 2:112773925-112784493
Previous symbols: [ "IL1" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (30 variants)
- not_provided (4 variants)
- IL1A-related_disorder (3 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the IL1A gene is commonly pathogenic or not. These statistics are base on transcript: NM_000000575.5. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | |||||
| missense | 29 | 35 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 29 | 6 | 2 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| IL1A | protein_coding | protein_coding | ENST00000263339 | 6 | 10676 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000160 | 0.694 | 125718 | 0 | 25 | 125743 | 0.0000994 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.541 | 125 | 143 | 0.873 | 0.00000697 | 1805 |
| Missense in Polyphen | 28 | 36.925 | 0.7583 | 488 | ||
| Synonymous | 0.829 | 48 | 55.9 | 0.859 | 0.00000307 | 499 |
| Loss of Function | 0.886 | 7 | 10.0 | 0.698 | 4.90e-7 | 129 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000431 | 0.000431 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000829 | 0.000816 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.0000176 | 0.0000176 |
| Middle Eastern | 0.000829 | 0.000816 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Produced by activated macrophages, IL-1 stimulates thymocyte proliferation by inducing IL-2 release, B-cell maturation and proliferation, and fibroblast growth factor activity. IL-1 proteins are involved in the inflammatory response, being identified as endogenous pyrogens, and are reported to stimulate the release of prostaglandin and collagenase from synovial cells.;
- Pathway
- Prion diseases - Homo sapiens (human);Type I diabetes mellitus - Homo sapiens (human);Pertussis - Homo sapiens (human);Salmonella infection - 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);Necroptosis - Homo sapiens (human);Fluid shear stress and atherosclerosis - Homo sapiens (human);Tuberculosis - Homo sapiens (human);MAPK signaling pathway - Homo sapiens (human);Leishmaniasis - Homo sapiens (human);Measles - Homo sapiens (human);Rheumatoid arthritis - Homo sapiens (human);Osteoclast differentiation - Homo sapiens (human);Hematopoietic cell lineage - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Cellular senescence - Homo sapiens (human);JAK-STAT-Core;IL-1 signaling pathway;Allograft Rejection;Spinal Cord Injury;Structural Pathway of Interleukin 1 (IL-1);Hematopoietic Stem Cell Differentiation;Fas Ligand (FasL) pathway and Stress induction of Heat Shock Proteins (HSP) regulation;Senescence-Associated Secretory Phenotype (SASP);Photodynamic therapy-induced NF-kB survival signaling;Interleukin-1 Induced Activation of NF-kappa-B;MAPK Signaling Pathway;Simplified Depiction of MYD88 Distinct Input-Output Pathway;Protein alkylation leading to liver fibrosis;Interleukin-10 signaling;Interleukin-4 and 13 signaling;Hypertrophy Model;Cytokines and Inflammatory Response;Senescence and Autophagy in Cancer;T-Cell antigen Receptor (TCR) Signaling Pathway;Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways;TLR NFkB;Signaling by Interleukins;gata3 participate in activating the th2 cytokine genes expression;il-10 anti-inflammatory signaling pathway;signal transduction through il1r;nf-kb signaling pathway;stress induction of hsp regulation;Cytokine Signaling in Immune system;JAK STAT MolecularVariation 1;Senescence-Associated Secretory Phenotype (SASP);Cellular Senescence;Cellular responses to stress;GPCR signaling-G alpha q;Interleukin-1 signaling;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;Immune System;IL-1 NFkB;IL-1 p38;IL-1 JNK;GPCR signaling-G alpha s Epac and ERK;IL1;Cellular responses to external stimuli;GPCR signaling-G alpha s PKA and ERK;JAK STAT pathway and regulation;a6b1 and a6b4 Integrin signaling;TLR ECSIT MEKK1 JNK;GPCR signaling-G alpha i;Validated transcriptional targets of deltaNp63 isoforms;Interleukin-1 processing;IL1-mediated signaling events;Interleukin-1 family signaling
(Consensus)
Recessive Scores
- pRec
- 0.954
Intolerance Scores
- loftool
- 0.807
- rvis_EVS
- 0.62
- rvis_percentile_EVS
- 83.25
Haploinsufficiency Scores
- pHI
- 0.0448
- hipred
- N
- hipred_score
- 0.123
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.961
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Il1a
- Phenotype
- immune system 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; neoplasm; homeostasis/metabolism 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);
Gene ontology
- Biological process
- fever generation;connective tissue replacement involved in inflammatory response wound healing;apoptotic process;inflammatory response;immune response;cell population proliferation;negative regulation of cell population proliferation;regulation of signaling receptor activity;positive regulation of vascular endothelial growth factor production;positive regulation of gene expression;cytokine-mediated signaling pathway;cellular response to heat;ectopic germ cell programmed cell death;positive regulation of interleukin-2 biosynthetic process;positive regulation of angiogenesis;positive regulation of mitotic nuclear division;positive regulation of transcription by RNA polymerase II;response to copper ion;positive regulation of protein secretion;positive regulation of cytokine secretion;positive regulation of cell division;interleukin-1-mediated signaling pathway;extrinsic apoptotic signaling pathway in absence of ligand;negative regulation of extrinsic apoptotic signaling pathway in absence of ligand
- Cellular component
- extracellular region;extracellular space;cytosol
- Molecular function
- cytokine activity;interleukin-1 receptor binding;copper ion binding;protein binding