IL1R2

interleukin 1 receptor type 2, the group of Immunoglobulin like domain containing|CD molecules|Interleukin receptors

Basic information

Region (hg38): 2:101991959-102028544

Previous symbols: [ "IL1RB" ]

Links

ENSG00000115590 ∙ NCBI:7850 ∙ OMIM:147811 ∙ HGNC:5994 ∙ Uniprot:P27930 ∙ 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 IL1R2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IL1R2 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			19	3	1	23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding				1		1
Total	0	0	19	6	2

Variants in IL1R2

This is a list of pathogenic ClinVar variants found in the IL1R2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-102008532-C-A			Likely benign (Jan 01, 2023)
2-102008591-G-A		not specified	Likely benign (Dec 20, 2023)
2-102008640-C-G		not specified	Uncertain significance (May 31, 2023)
2-102009592-G-A		not specified	Likely benign (Nov 08, 2021)
2-102009673-C-T		not specified	Uncertain significance (Jun 05, 2023)
2-102009680-C-G			Likely benign (Jun 09, 2018)
2-102009746-A-G			Benign (Jul 31, 2018)
2-102009757-C-A		not specified	Uncertain significance (Jun 22, 2021)
2-102009765-G-A		not specified	Uncertain significance (Dec 05, 2022)
2-102009793-A-G		not specified	Likely benign (Jun 07, 2024)
2-102009812-C-T			Likely benign (Aug 01, 2022)
2-102015897-C-G		not specified	Uncertain significance (Oct 02, 2023)
2-102015939-C-T		not specified	Uncertain significance (Jan 10, 2023)
2-102015953-C-T		not specified	Uncertain significance (Jun 07, 2024)
2-102015954-C-T		not specified	Uncertain significance (Apr 07, 2022)
2-102016017-G-A		not specified	Uncertain significance (Dec 01, 2022)
2-102019665-G-A			Benign (Dec 31, 2019)
2-102019740-C-T		not specified	Uncertain significance (Nov 13, 2023)
2-102019756-T-C		not specified	Uncertain significance (May 15, 2024)
2-102019761-C-T		not specified	Uncertain significance (May 05, 2023)
2-102019762-A-G		not specified	Uncertain significance (Jun 10, 2024)
2-102019804-G-A		not specified	Uncertain significance (Apr 17, 2024)
2-102022183-T-G			Benign (Apr 24, 2018)
2-102022236-A-G		not specified	Uncertain significance (Feb 06, 2023)
2-102024560-T-G		not specified	Uncertain significance (Sep 01, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IL1R2	protein_coding	protein_coding	ENST00000332549	8	36701

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.54e-15	0.00427	125643	0	105	125748	0.000418

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.111	242	237	1.02	0.0000139	2576
Missense in Polyphen		71	67.738	1.0482		787
Synonymous	0.353	87	91.3	0.953	0.00000530	796
Loss of Function	-0.676	20	17.0	1.18	7.20e-7	214

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000460	0.000459
Ashkenazi Jewish	0.0000997	0.0000992
East Asian	0.000220	0.000217
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000734	0.000730
Middle Eastern	0.000220	0.000217
South Asian	0.000163	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Non-signaling receptor for IL1A, IL1B and IL1RN. Reduces IL1B activities. Serves as a decoy receptor by competetive binding to IL1B and preventing its binding to IL1R1. Also modulates cellular response through non-signaling association with IL1RAP after binding to IL1B. IL1R2 (membrane and secreted forms) preferentially binds IL1B and poorly IL1A and IL1RN. The secreted IL1R2 recruits secreted IL1RAP with high affinity; this complex formation may be the dominant mechanism for neutralization of IL1B by secreted/soluble receptors. {ECO:0000269|PubMed:10975853, ECO:0000269|PubMed:12530978, ECO:0000269|PubMed:7989776, ECO:0000269|PubMed:9862719}.
• Pathway: HTLV-I infection - Homo sapiens (human);Amoebiasis - Homo sapiens (human);Prostate cancer - Homo sapiens (human);Fluid shear stress and atherosclerosis - Homo sapiens (human);Transcriptional misregulation in cancer - Homo sapiens (human);Hematopoietic cell lineage - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Apoptosis Modulation and Signaling;MAPK Signaling Pathway;Interleukin-10 signaling;Signaling by Interleukins;Cytokine Signaling in Immune system;JAK STAT MolecularVariation 1;Interleukin-1 signaling;Immune System;IL1;JAK STAT MolecularVariation 2;JAK STAT pathway and regulation;IL1-mediated signaling events;Interleukin-1 family signaling (Consensus)

Recessive Scores

• pRec: 0.270

Intolerance Scores

• loftool: 0.892
• rvis_EVS: -0.71
• rvis_percentile_EVS: 14.57

Haploinsufficiency Scores

• pHI: 0.701
• hipred: N
• hipred_score: 0.211
• ghis: 0.520

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.889

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Il1r2
• Phenotype: hearing/vestibular/ear phenotype

Gene ontology

• Biological process: immune response;negative regulation of protein processing;cytokine-mediated signaling pathway;negative regulation of interleukin-1 alpha secretion;interleukin-1-mediated signaling pathway;negative regulation of cytokine production involved in inflammatory response;negative regulation of interleukin-1-mediated signaling pathway
• Cellular component: extracellular region;cytoplasm;plasma membrane;integral component of membrane
• Molecular function: interleukin-1 receptor activity;interleukin-1, type II, blocking receptor activity;protein binding;interleukin-1 binding