IL1RAPL2

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

Basic information

Region (hg38): X:104566198-105767829

Links

ENSG00000189108 ∙ NCBI:26280 ∙ OMIM:300277 ∙ HGNC:5997 ∙ Uniprot:Q9NP60 ∙ 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 IL1RAPL2 gene.

• Inborn genetic diseases (20 variants)
• not provided (10 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IL1RAPL2 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			12	2		14
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			5	6		11
Total	0	0	18	9	1

Variants in IL1RAPL2

This is a list of pathogenic ClinVar variants found in the IL1RAPL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-104658929-C-T		not specified	Conflicting classifications of pathogenicity (Oct 01, 2022)
X-104658963-C-G		not specified	Uncertain significance (Mar 22, 2023)
X-104658978-T-C		not specified	Uncertain significance (Nov 01, 2022)
X-105195709-C-T			Likely benign (Dec 31, 2019)
X-105219025-A-G		not specified	Uncertain significance (May 18, 2023)
X-105219034-G-A		not specified	Uncertain significance (Sep 29, 2023)
X-105219086-T-C		not specified	Uncertain significance (Nov 09, 2023)
X-105219144-G-T		not specified	Likely benign (Sep 06, 2022)
X-105219260-A-G		not specified	Likely benign (Sep 20, 2023)
X-105219278-TTGAGTA-T			Likely benign (Nov 01, 2022)
X-105219331-G-A		not specified	Uncertain significance (Dec 22, 2023)
X-105219384-G-C			Likely benign (Jul 01, 2022)
X-105219507-C-G			Likely benign (Dec 01, 2022)
X-105219688-C-T		not specified	Uncertain significance (Aug 08, 2022)
X-105219698-C-T		not specified	Uncertain significance (Dec 31, 2023)
X-105219701-C-A		not specified	Uncertain significance (Jun 29, 2023)
X-105219712-C-T		not specified	Uncertain significance (May 18, 2023)
X-105220042-T-C		not specified	Uncertain significance (Oct 13, 2023)
X-105220061-T-G		not specified	Uncertain significance (Feb 05, 2024)
X-105220168-C-T		not specified	Uncertain significance (Sep 25, 2023)
X-105220239-T-G			Likely benign (Feb 01, 2023)
X-105220376-G-T		not specified	Uncertain significance (Dec 27, 2022)
X-105220384-G-C		not specified	Uncertain significance (Feb 13, 2024)
X-105267405-G-A		not specified	Uncertain significance (Oct 04, 2022)
X-105267429-A-C		not specified	Uncertain significance (Sep 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IL1RAPL2	protein_coding	protein_coding	ENST00000372582	10	1200827

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.984	0.0158	125685	2	2	125689	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.00	157	245	0.641	0.0000175	4516
Missense in Polyphen		50	104.96	0.47636		1976
Synonymous	0.0796	88	89.0	0.989	0.00000633	1270
Loss of Function	3.89	2	21.4	0.0934	0.00000157	426

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000780	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000247	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000642	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Neuronal System;Receptor-type tyrosine-protein phosphatases;Protein-protein interactions at synapses (Consensus)

Recessive Scores

• pRec: 0.123

Intolerance Scores

• loftool: 0.280
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.37

Haploinsufficiency Scores

• pHI: 0.301
• hipred: Y
• hipred_score: 0.809
• ghis: 0.397

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Il1rapl2

Gene ontology

• Biological process: central nervous system development;cytokine-mediated signaling pathway;regulation of presynapse assembly
• Cellular component: plasma membrane;integral component of membrane;glutamatergic synapse
• Molecular function: interleukin-1 receptor activity;interleukin-1, type II, blocking receptor activity