IL13RA2

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

Basic information

Region (hg38): X:115003974-115019977

Links

ENSG00000123496 ∙ NCBI:3598 ∙ OMIM:300130 ∙ HGNC:5975 ∙ Uniprot:Q14627 ∙ 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 IL13RA2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IL13RA2 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						0
missense			6	1		7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	1	0

Variants in IL13RA2

This is a list of pathogenic ClinVar variants found in the IL13RA2 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-115005222-C-T		not specified	Uncertain significance (Feb 15, 2023)
X-115005229-G-A		not specified	Uncertain significance (Nov 30, 2021)
X-115005258-A-G		not specified	Likely benign (Nov 06, 2023)
X-115009528-G-A		not specified	Uncertain significance (May 11, 2022)
X-115015702-T-G		not specified	Uncertain significance (Apr 15, 2024)
X-115015749-G-A		not specified	Uncertain significance (Aug 28, 2023)
X-115015770-A-T		not specified	Uncertain significance (Nov 12, 2021)
X-115015778-T-A		not specified	Uncertain significance (Jul 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IL13RA2	protein_coding	protein_coding	ENST00000371936	9	16003

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.02e-7	0.602	125642	1	10	125653	0.0000438

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.760	109	134	0.815	0.00000988	2479
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000110	0.000110
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000725	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000744	0.0000528
Middle Eastern	0.0000725	0.0000544
South Asian	0.0000530	0.0000327
Other	0.00	0.00

dbNSFP

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}.
• Pathway: Jak-STAT signaling pathway - Homo sapiens (human);JAK-STAT-Core;Interleukin-4 and 13 signaling;Signaling by Interleukins;Cytokine Signaling in Immune system;JAK STAT MolecularVariation 1;Immune System;JAK STAT MolecularVariation 2;JAK STAT pathway and regulation;IL4-mediated signaling events;IL-13 signaling (Consensus)

Recessive Scores

• pRec: 0.232

Intolerance Scores

• loftool: 0.487
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63

Haploinsufficiency Scores

• pHI: 0.0527
• hipred: N
• hipred_score: 0.112
• ghis: 0.414

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0682

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Il13ra2
• Phenotype: hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); respiratory system phenotype; immune system phenotype; homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: negative regulation of immunoglobulin production;immunoglobulin mediated immune response;cytokine-mediated signaling pathway;negative regulation of mast cell degranulation
• Cellular component: extracellular region;extracellular space;external side of plasma membrane;integral component of membrane;receptor complex
• Molecular function: cytokine receptor activity;protein binding;cytokine binding