IL1R1

interleukin 1 receptor type 1, the group of CD molecules|Interleukin receptors|TIR domain containing|I-set domain containing

Basic information

Region (hg38): 2:102064543-102179874

Previous symbols: [ "IL1R", "IL1RA" ]

Links

ENSG00000115594 ∙ NCBI:3554 ∙ OMIM:147810 ∙ HGNC:5993 ∙ Uniprot:P14778 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Chronic recurrent multifocal osteomyelitis 3	AD	Allergy/Immunology/Infectious	The condition can manifest with early-onset sterile osteomyelitis and medical management (eg, with monoclonal antibody against IL1B) has been reported as beneficial	Allergy/Immunology/Infectious	37315560

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the IL1R1 gene.

• Inborn genetic diseases (13 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IL1R1 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				2	1	3
missense			11	2		13
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	4	2

Variants in IL1R1

This is a list of pathogenic ClinVar variants found in the IL1R1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-102157782-G-A		not specified	Uncertain significance (Sep 15, 2021)
2-102159742-C-T		Ascending aortic dissection	association (Feb 01, 2021)
2-102160058-G-A		Ascending aortic dissection	association (Feb 01, 2021)
2-102164793-A-C		not specified	Uncertain significance (Jan 24, 2023)
2-102164870-G-A		not specified	Uncertain significance (Dec 14, 2021)
2-102164896-A-G		not specified	Uncertain significance (Aug 08, 2022)
2-102165209-A-G		Chronic multifocal osteomyelitis	Pathogenic (Aug 02, 2023)
2-102166249-C-T		not specified	Uncertain significance (Aug 22, 2023)
2-102168373-A-G		Ascending aortic dissection	association (Feb 01, 2021)
2-102168604-A-G		not specified	Uncertain significance (Nov 07, 2022)
2-102168616-G-A		not specified	Uncertain significance (Aug 02, 2021)
2-102171841-G-A			Likely benign (May 31, 2018)
2-102171877-A-G			Benign (Jun 15, 2018)
2-102172706-A-G		not specified	Uncertain significance (Nov 09, 2023)
2-102172805-A-G		not specified	Uncertain significance (Jun 06, 2022)
2-102174611-T-C		not specified	Uncertain significance (Oct 10, 2023)
2-102174629-T-C		not specified	Uncertain significance (Jan 03, 2024)
2-102175500-C-T			Benign/Likely benign (Aug 01, 2022)
2-102175549-T-A		not specified	Likely benign (Feb 28, 2023)
2-102176491-A-C		not specified	Uncertain significance (Dec 15, 2022)
2-102176589-C-T		not specified	Uncertain significance (Feb 22, 2023)
2-102176590-G-T		not specified	Uncertain significance (Oct 06, 2023)
2-102176674-G-A		not specified	Uncertain significance (Aug 26, 2022)
2-102176677-G-A		not specified	Likely benign (Jun 06, 2023)
2-102176688-T-C		not specified	Uncertain significance (Dec 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IL1R1	protein_coding	protein_coding	ENST00000410023	10	115331

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.151	0.849	125724	0	9	125733	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.92	205	298	0.687	0.0000147	3744
Missense in Polyphen		49	102.51	0.47799		1346
Synonymous	-0.263	113	110	1.03	0.00000591	1044
Loss of Function	3.33	6	23.4	0.256	9.80e-7	337

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000904	0.0000904
Ashkenazi Jewish	0.000130	0.0000992
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000265	0.0000264
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000655	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for IL1A, IL1B and IL1RN. After binding to interleukin-1 associates with the coreceptor IL1RAP to form the high affinity interleukin-1 receptor complex which mediates interleukin-1-dependent activation of NF-kappa-B, MAPK and other pathways. Signaling involves the recruitment of adapter molecules such as TOLLIP, MYD88, and IRAK1 or IRAK2 via the respective TIR domains of the receptor/coreceptor subunits. Binds ligands with comparable affinity and binding of antagonist IL1RN prevents association with IL1RAP to form a signaling complex. Involved in IL1B-mediated costimulation of IFNG production from T-helper 1 (Th1) cells (PubMed:10653850). {ECO:0000269|PubMed:10653850, ECO:0000269|PubMed:10671496}.
• Pathway: Inflammatory mediator regulation of TRP channels - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);Amoebiasis - Homo sapiens (human);Fluid shear stress and atherosclerosis - Homo sapiens (human);Th17 cell differentiation - Homo sapiens (human);MAPK signaling pathway - 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);JAK-STAT-Core;Serotonin Transporter Activity;Apoptosis Modulation and Signaling;IL-1 signaling pathway;Spinal Cord Injury;Structural Pathway of Interleukin 1 (IL-1);IL1 and megakaryocytes in obesity;MAPK Signaling Pathway;Interleukin-10 signaling;Hypertrophy Model;Monoamine Transport;TLR NFkB;Signaling by Interleukins;signal transduction through il1r;nf-kb signaling pathway;Cytokine Signaling in Immune system;JAK STAT MolecularVariation 1;Interleukin-1 signaling;Immune System;IL-1 NFkB;IL-1 p38;IL-1 JNK;IL1;JAK STAT MolecularVariation 2;JAK STAT pathway and regulation;TLR ECSIT MEKK1 JNK;IL1-mediated signaling events;IL12-mediated signaling events;Interleukin-1 family signaling (Consensus)

Recessive Scores

• pRec: 0.601

Intolerance Scores

• loftool: 0.685
• rvis_EVS: 0.09
• rvis_percentile_EVS: 60.47

Haploinsufficiency Scores

• pHI: 0.190
• hipred: N
• hipred_score: 0.214
• ghis: 0.469

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.960

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Il1r1
• Phenotype: adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland 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); homeostasis/metabolism phenotype; cellular phenotype; craniofacial phenotype; muscle 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; 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); normal 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); 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; skeleton phenotype; renal/urinary system phenotype; immune system phenotype; vision/eye phenotype

Gene ontology

• Biological process: inflammatory response;immune response;cell surface receptor signaling pathway;cytokine-mediated signaling pathway;positive regulation of interferon-gamma production;regulation of inflammatory response;interleukin-1-mediated signaling pathway;response to interleukin-1;positive regulation of neutrophil extravasation;positive regulation of T-helper 1 cell cytokine production;positive regulation of interleukin-1-mediated signaling pathway
• Cellular component: extracellular region;plasma membrane;integral component of plasma membrane;external side of plasma membrane;membrane
• Molecular function: protease binding;transmembrane signaling receptor activity;interleukin-1 receptor activity;interleukin-1, type I, activating receptor activity;platelet-derived growth factor receptor binding;protein binding;interleukin-1 binding