IL1A

interleukin 1 alpha, the group of Interleukins

Basic information

Region (hg38): 2:112773924-112784493

Previous symbols: [ "IL1" ]

Links

ENSG00000115008 ∙ NCBI:3552 ∙ OMIM:147760 ∙ HGNC:5991 ∙ Uniprot:P01583 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the IL1A gene.

• not provided (5 variants)
• Inborn genetic diseases (5 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.

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	1	2
missense			4	2	1	7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	4	3	3

Variants in IL1A

This is a list of pathogenic ClinVar variants found in the IL1A region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
2-112774138-T-TTGAA			Benign (Apr 19, 2019)
2-112775057-G-A		IL1A-related disorder	Likely benign (Apr 30, 2019)
2-112775149-G-T		not specified	Uncertain significance (Dec 08, 2023)
2-112775252-G-A		not specified	Uncertain significance (Dec 14, 2023)
2-112778063-A-T		not specified	Uncertain significance (Sep 20, 2023)
2-112778085-A-C		not specified	Uncertain significance (Jul 11, 2022)
2-112779527-C-T			Likely benign (May 08, 2018)
2-112779528-G-A		not specified	Likely benign (Mar 29, 2022)
2-112779564-T-C		not specified	Uncertain significance (Aug 22, 2022)
2-112779574-C-T			Benign (Aug 16, 2018)
2-112779589-C-G		not specified	Likely benign (Dec 20, 2023)
2-112779589-C-T		not specified	Uncertain significance (Nov 29, 2023)
2-112779613-T-C			Likely benign (Jul 10, 2017)
2-112779643-G-T		not specified	Uncertain significance (Dec 26, 2023)
2-112779646-C-A		IL1A-related disorder	Benign (Oct 22, 2019)
2-112779661-T-C		IL1A-related disorder	Uncertain significance (Nov 06, 2023)
2-112781615-T-A		not specified	Uncertain significance (Dec 06, 2022)
2-112781642-T-A		not specified	Uncertain significance (Oct 13, 2023)
2-112781647-G-A			Benign (Aug 24, 2018)
2-112781655-G-T		IL1A-related disorder	Likely benign (Nov 08, 2019)
2-112781661-A-C		not specified	Uncertain significance (Dec 16, 2023)
2-112781739-T-C		not specified	Uncertain significance (Feb 05, 2024)
2-112781781-T-C		IL1A-related disorder	Likely benign (Sep 20, 2022)
2-112781810-A-C		not specified	Uncertain significance (Oct 24, 2023)
2-112782758-A-T		not specified	Uncertain significance (Aug 21, 2023)

GnomAD

Source: gnomAD

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: dbNSFP

• 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

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