IL1RAPL2

protein-coding

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

Gene summary

The protein encoded by this gene is a member of the interleukin 1 receptor family. This protein is similar to the interleukin 1 accessory proteins, and is most closely related to interleukin 1 receptor accessory protein-like 1 (IL1RAPL1). This gene and IL1RAPL1 are located at a region on chromosome X that is associated with X-linked non-syndromic cognitive disability. [provided by RefSeq, Jul 2008]

MANE transcript

NM_017416.2

Inheritance

—

ClinVar variants

U:108B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.09

Max pathogenic AF

—

Genomic locus

chrX:104,566,199-105,767,829

External References & Databases

Ensembl (ENSG00000189108)

Transcript & Mutation Effects

hg38 • Region Span ~1,201.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to IL1RAPL2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 92

not providedTotal: 12

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017416.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			10 clinvar	1 clinvar		11
missense			81 clinvar	3 clinvar		84
nonsense			5 clinvar			5
start loss			1 clinvar			1
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)			9 clinvar			9
Total	0	0	108	4	0	112

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_017416.2	RefSeq	NP_059112.1	10	MANE Select
ENST00000372582.6	Ensembl	ENSP00000361663.1	10	MANE Select
ENST00001135166.1	Ensembl	ENSP00000810065.1	10	Standard
XM_011530905.3	RefSeq	XP_011529207.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Neuronal System
Receptor-type tyrosine-protein phosphatases
Protein-protein interactions at synapses

Biological Process

central nervous system development
cytokine-mediated signaling pathway
regulation of presynapse assembly

Molecular Function

interleukin-1 receptor activity
interleukin-1, type II, blocking receptor activity

Cellular Component

plasma membrane
integral component of membrane
glutamatergic synapse

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000372582
Coding exons: 10
Length: 1200827
Individuals with no LoFs: 125685
Homozygous LoFs: 2
Heterozygous LoFs: 2
Defined: 125689
p: 0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.00	157	245	0.641	0.0000175	4516
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000078	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000025	0.000018	rare
South Asian	0.000064	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.123

Intolerance Scores

LoFtool: 0.280
RVIS EVS: -0.34
RVIS percentile EVS: 30.37

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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