IL1RL1

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

Basic information

Region (hg38): 2:102311502-102352037

Links

ENSG00000115602 ∙ NCBI:9173 ∙ OMIM:601203 ∙ HGNC:5998 ∙ Uniprot:Q01638 ∙ 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 IL1RL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IL1RL1 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				4	3	7
missense			30	6	3	39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	10	6

Variants in IL1RL1

This is a list of pathogenic ClinVar variants found in the IL1RL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-102314488-A-G		Ascending aortic dissection	association (Feb 01, 2021)
2-102338283-G-T			Likely benign (Jun 22, 2018)
2-102338317-C-G		not specified	Uncertain significance (Jun 16, 2024)
2-102338909-C-A		not specified	Uncertain significance (May 24, 2023)
2-102338916-T-C			Likely benign (Dec 01, 2023)
2-102338965-C-T		not specified	Uncertain significance (Sep 17, 2021)
2-102339020-C-G		not specified	Uncertain significance (Dec 27, 2022)
2-102340123-G-A		not specified	Uncertain significance (Apr 13, 2023)
2-102340192-T-A		not specified	Uncertain significance (Oct 13, 2023)
2-102340194-T-C			Benign (Jun 18, 2018)
2-102340228-A-G		not specified	Uncertain significance (Oct 26, 2022)
2-102340676-C-T			Benign (Dec 31, 2019)
2-102340704-C-A		not specified	Uncertain significance (Jul 09, 2021)
2-102340744-G-A			Benign (Feb 05, 2021)
2-102340747-G-A		not specified	Uncertain significance (May 18, 2023)
2-102340784-G-T		not specified	Uncertain significance (Dec 07, 2021)
2-102340802-C-T		not specified	Uncertain significance (Mar 02, 2023)
2-102340819-A-G		not specified	Uncertain significance (Feb 01, 2023)
2-102340821-G-T			Likely benign (Jun 29, 2018)
2-102340826-A-G		not specified	Uncertain significance (Aug 21, 2023)
2-102342236-T-G		not specified	Uncertain significance (Feb 22, 2023)
2-102342258-G-A			Benign/Likely benign (Jan 01, 2023)
2-102343044-G-A		not specified	Likely benign (Dec 27, 2023)
2-102343108-A-T		not specified	Uncertain significance (May 23, 2024)
2-102343174-A-G		not specified	Uncertain significance (May 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IL1RL1	protein_coding	protein_coding	ENST00000233954	10	40536

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.44e-12	0.183	125696	0	51	125747	0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.19	352	295	1.19	0.0000147	3649
Missense in Polyphen		116	98.08	1.1827		1245
Synonymous	0.238	108	111	0.971	0.00000626	1036
Loss of Function	0.874	21	25.8	0.814	0.00000119	325

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000495	0.000485
Ashkenazi Jewish	0.00	0.00
East Asian	0.00139	0.00136
Finnish	0.00	0.00
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.00139	0.00136
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for interleukin-33 (IL-33); signaling requires association of the coreceptor IL1RAP. Its stimulation recruits MYD88, IRAK1, IRAK4, and TRAF6, followed by phosphorylation of MAPK3/ERK1 and/or MAPK1/ERK2, MAPK14, and MAPK8. Possibly involved in helper T-cell function. {ECO:0000269|PubMed:16286016, ECO:0000305|PubMed:19836339}.
• Pathway: Vitamin D Receptor Pathway;Signal Transduction;Signaling by Interleukins;Cytokine Signaling in Immune system;Immune System;PIP3 activates AKT signaling;PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling;Negative regulation of the PI3K/AKT network;Intracellular signaling by second messengers;Interleukin-33 signaling;Interleukin-1 family signaling (Consensus)

Recessive Scores

• pRec: 0.210

Intolerance Scores

• loftool: 0.962
• rvis_EVS: 2.78
• rvis_percentile_EVS: 99.03

Haploinsufficiency Scores

• pHI: 0.131
• hipred: N
• hipred_score: 0.147

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.683

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Il1rl1
• Phenotype: endocrine/exocrine gland phenotype; immune system phenotype; normal phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: negative regulation of T-helper 1 type immune response;immune response;signal transduction;negative regulation of interferon-gamma production;positive regulation of interleukin-5 production;interleukin-33-mediated signaling pathway;positive regulation of macrophage activation;positive regulation of inflammatory response;positive regulation of chemokine secretion
• Cellular component: extracellular region;plasma membrane;external side of plasma membrane;integral component of membrane
• Molecular function: cytokine receptor activity;interleukin-1 receptor activity;protein binding