IL13RA1

protein-coding

interleukin 13 receptor subunit alpha 1, the group of CD molecules|Interleukin receptors

Gene summary

The protein encoded by this gene is a subunit of the interleukin 13 receptor. This subunit forms a receptor complex with IL4 receptor alpha, a subunit shared by IL13 and IL4 receptors. This subunit serves as a primary IL13-binding subunit of the IL13 receptor, and may also be a component of IL4 receptors. This protein has been shown to bind tyrosine kinase TYK2, and thus may mediate the signaling processes that lead to the activation of JAK1, STAT3 and STAT6 induced by IL13 and IL4. [provided by RefSeq, Jul 2008]

MANE transcript

NM_001560.3

Inheritance

—

ClinVar variants

U:131B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.07

Max pathogenic AF

—

Genomic locus

chrX:118,727,133-118,794,535

External References & Databases

Ensembl (ENSG00000131724)

Transcript & Mutation Effects

hg38 • Region Span ~67.4 kb

Loading mutation effect viewer...

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 IL13RA1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 40

not providedTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001560.3. 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			17 clinvar	1 clinvar	1 clinvar	19
missense			84 clinvar	3 clinvar		87
nonsense			7 clinvar			7
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			23 clinvar			23
Total	0	0	131	4	1	136

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 32 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001560.3	RefSeq	NP_001551.1	11	MANE Select
ENST00000371666.8	Ensembl	ENSP00000360730.3	11	MANE Select
ENST00000371642.1	Ensembl	ENSP00000360705.1	6	Standard
ENST00000371642.2	Ensembl	ENSP00000360705.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Jak-STAT signaling pathway - Homo sapiens (human)
Pathways in cancer - Homo sapiens (human)
Cytokine-cytokine receptor interaction - Homo sapiens (human)
JAK-STAT-Core
TYROBP Causal Network

Biological Process

cell surface receptor signaling pathway
cytokine-mediated signaling pathway
interleukin-13-mediated signaling pathway

Molecular Function

cytokine receptor activity
protein binding
interleukin-13 receptor activity
cytokine binding

Cellular Component

plasma membrane
interleukin-13 receptor complex
external side of plasma membrane
receptor complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000371666
Coding exons: 11
Length: 66968
Individuals with no LoFs: 116139
Homozygous LoFs: 1
Heterozygous LoFs: 1
Defined: 116141
p: 0.00000861

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.522	122	139	0.876	0.00000991	2847
Missense (PolyPhen)		16	37.37	0.42816		772
Synonymous	0.454	44	48.0	0.917	0.00000355	753
Loss of Function	3.31	1	14.7	0.0680	9.98e-7	284

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000040	0.000033	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000013	0.0000092	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Binds with low affinity to interleukin-13 (IL13). Together with IL4RA can form a functional receptor for IL13. Also serves as an alternate accessory protein to the common cytokine receptor gamma chain for interleukin-4 (IL4) signaling, but cannot replace the function of IL2RG in allowing enhanced interleukin-2 (IL2) binding activity.;

Intolerance Scores

LoFtool: 0.163
RVIS EVS: -0.41
RVIS percentile EVS: 26.23

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.896

Gene Damage Prediction

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