IL1RL2

interleukin 1 receptor like 2, the group of TIR domain containing|Immunoglobulin like domain containing|Interleukin receptors

Basic information

Region (hg38): 2:102187005-102240002

Links

ENSG00000115598 ∙ NCBI:8808 ∙ OMIM:604512 ∙ HGNC:5999 ∙ Uniprot:Q9HB29 ∙ 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 IL1RL2 gene.

• Inborn genetic diseases (23 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IL1RL2 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		2
missense			20	3	2	25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	5	2

Variants in IL1RL2

This is a list of pathogenic ClinVar variants found in the IL1RL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-102187575-C-A		Ascending aortic dissection	association (Feb 01, 2021)
2-102189103-A-T		not specified	Uncertain significance (Feb 16, 2023)
2-102189142-G-A		not specified	Uncertain significance (Oct 26, 2022)
2-102189270-A-G		not specified	Uncertain significance (Jun 16, 2023)
2-102189274-A-T		not specified	Uncertain significance (May 17, 2023)
2-102189285-T-A		not specified	Uncertain significance (Oct 13, 2023)
2-102191996-T-C		not specified	Uncertain significance (May 03, 2023)
2-102192068-G-T		not specified	Uncertain significance (Jul 14, 2023)
2-102192104-C-A		not specified	Uncertain significance (Feb 17, 2024)
2-102212160-T-C			Benign (Jul 13, 2018)
2-102219021-G-T		not specified	Uncertain significance (Feb 28, 2024)
2-102219028-A-G		not specified	Uncertain significance (Aug 14, 2023)
2-102219074-A-C		not specified	Uncertain significance (Nov 23, 2021)
2-102219897-C-T		not specified	Uncertain significance (Jul 12, 2023)
2-102219907-A-G		not specified	Uncertain significance (Dec 12, 2023)
2-102219930-T-C		not specified	Uncertain significance (Nov 03, 2022)
2-102219945-A-T		not specified	Uncertain significance (Sep 16, 2021)
2-102219947-G-T		not specified	Uncertain significance (Mar 29, 2022)
2-102220003-T-C		not specified	Uncertain significance (Oct 30, 2023)
2-102225901-C-T		not specified	Uncertain significance (Dec 21, 2022)
2-102225927-G-A		not specified	Uncertain significance (Dec 01, 2022)
2-102225936-G-A		not specified	Uncertain significance (Nov 18, 2023)
2-102225960-G-A			Benign (Jul 13, 2018)
2-102225961-T-C		not specified	Uncertain significance (Dec 18, 2023)
2-102225975-A-C		not specified	Uncertain significance (Jun 23, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IL1RL2	protein_coding	protein_coding	ENST00000264257	11	53030

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.54e-11	0.746	125580	2	166	125748	0.000668

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.436	303	325	0.932	0.0000174	3759
Missense in Polyphen		82	84.176	0.97415		1016
Synonymous	-1.71	154	129	1.19	0.00000791	1086
Loss of Function	1.61	21	30.6	0.687	0.00000162	360

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00103	0.00103
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.0000929	0.0000924
European (Non-Finnish)	0.000292	0.000290
Middle Eastern	0.000164	0.000163
South Asian	0.00354	0.00344
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for interleukin-36 (IL36A, IL36B and IL36G). After binding to interleukin-36 associates with the coreceptor IL1RAP to form the interleukin-36 receptor complex which mediates interleukin-36-dependent activation of NF-kappa-B, MAPK and other pathways (By similarity). The IL-36 signaling system is thought to be present in epithelial barriers and to take part in local inflammatory response; it is similar to the IL-1 system. Seems to be involved in skin inflammatory response by induction of the IL- 23/IL-17/IL-22 pathway. {ECO:0000250|UniProtKB:Q9ERS7, ECO:0000269|PubMed:11466363}.
• Pathway: Signaling by Interleukins;Cytokine Signaling in Immune system;Immune System;Interleukin-36 pathway;Interleukin-38 signaling;Interleukin-1 family signaling (Consensus)

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.900
• rvis_EVS: -0.17
• rvis_percentile_EVS: 40.6

Haploinsufficiency Scores

• pHI: 0.0909
• hipred: N
• hipred_score: 0.132
• ghis: 0.492

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0684

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Il1rl2
• Phenotype: normal phenotype; hematopoietic system phenotype; immune system 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

Gene ontology

• Biological process: inflammatory response;cellular defense response;signal transduction;cytokine-mediated signaling pathway;positive regulation of interleukin-6 production;innate immune response;positive regulation of T cell differentiation;regulation of inflammatory response;interleukin-1-mediated signaling pathway;cellular response to cytokine stimulus
• Cellular component: plasma membrane;integral component of plasma membrane
• Molecular function: interleukin-1 receptor activity;interleukin-1, type I, activating receptor activity