IL13RA2

protein-coding

interleukin 13 receptor subunit alpha 2, the group of CD molecules|Interleukin receptors

Gene summary

The protein encoded by this gene is closely related to Il13RA1, a subuint of the interleukin 13 receptor complex. This protein binds IL13 with high affinity, but lacks cytoplasmic domain, and does not appear to function as a signal mediator. It is reported to play a role in the internalization of IL13. [provided by RefSeq, Jul 2008]

MANE transcript

NM_000640.3

Inheritance

—

ClinVar variants

U:59B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.73

Max pathogenic AF

—

Genomic locus

chrX:115,003,975-115,019,977

External References & Databases

Ensembl (ENSG00000123496)

Transcript & Mutation Effects

hg38 • Region Span ~16.0 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 IL13RA2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 27

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_000640.3. 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			9 clinvar			9
missense			41 clinvar	6 clinvar		47
nonsense			5 clinvar			5
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	59	6	0	65

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 6 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_000640.3	RefSeq	NP_000631.1	9	MANE Select
ENST00000243213.2	Ensembl	ENSP00000243213.1	9	MANE Select
ENST00000371936.5	Ensembl	ENSP00000361004.1	9	Standard
ENST00000958003.1	Ensembl	ENSP00000628062.1	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Jak-STAT signaling pathway - Homo sapiens (human)
JAK-STAT-Core
Interleukin-4 and 13 signaling
Signaling by Interleukins
Cytokine Signaling in Immune system

Biological Process

negative regulation of immunoglobulin production
immunoglobulin mediated immune response
cytokine-mediated signaling pathway
negative regulation of mast cell degranulation

Molecular Function

cytokine receptor activity
protein binding
cytokine binding

Cellular Component

extracellular region
extracellular space
external side of plasma membrane
integral component of membrane
receptor complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000371936
Coding exons: 9
Length: 16003
Individuals with no LoFs: 125642
Homozygous LoFs: 1
Heterozygous LoFs: 10
Defined: 125653
p: 0.0000438

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.760	109	134	0.815	0.00000988	2479
Missense (PolyPhen)		27	34.688	0.77836		674
Synonymous	1.14	40	50.3	0.795	0.00000396	676
Loss of Function	1.02	12	16.4	0.730	0.00000119	300

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00011	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000072	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000074	0.000053	rare
South Asian	0.000053	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Binds as a monomer with high affinity to interleukin-13 (IL13), but not to interleukin-4 (IL4). {ECO:0000269|PubMed:20223216}.;

Recessive Scores

pRec: 0.232

Intolerance Scores

LoFtool: 0.487
RVIS EVS: 0.13
RVIS percentile EVS: 63

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.0682

Gene Damage Prediction

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