IL13RA1

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

Basic information

Region (hg38): X:118727132-118794535

Links

ENSG00000131724 ∙ NCBI:3597 ∙ OMIM:300119 ∙ HGNC:5974 ∙ Uniprot:P78552 ∙ 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 IL13RA1 gene.

• Inborn genetic diseases (8 variants)
• not provided (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IL13RA1 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			8	2		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding				2		2
Total	0	0	8	5	1

Variants in IL13RA1

This is a list of pathogenic ClinVar variants found in the IL13RA1 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-118727706-G-A		not specified	Uncertain significance (Jan 10, 2023)
X-118741045-T-A		not specified	Uncertain significance (Jan 27, 2022)
X-118741045-T-C			Likely benign (Apr 01, 2023)
X-118741134-A-T		not specified	Uncertain significance (Aug 02, 2022)
X-118746983-A-G		not specified	Uncertain significance (Feb 16, 2023)
X-118749717-A-G		not specified	Uncertain significance (Apr 26, 2023)
X-118749744-A-G		not specified	Uncertain significance (Sep 22, 2022)
X-118749753-G-A		not specified	Uncertain significance (May 27, 2022)
X-118758117-G-A			Likely benign (Jun 13, 2018)
X-118758225-T-C		not specified	Uncertain significance (Nov 09, 2023)
X-118758239-C-A		not specified	Uncertain significance (Apr 11, 2023)
X-118766536-G-A		not specified	Uncertain significance (Sep 14, 2023)
X-118766859-A-G			Likely benign (Dec 01, 2022)
X-118770125-C-T			Likely benign (Nov 01, 2022)
X-118770345-C-T			Likely benign (Nov 01, 2022)
X-118773934-C-T			Benign (Jun 21, 2018)
X-118776442-A-G		not specified	Uncertain significance (Feb 28, 2024)
X-118776447-C-G		not specified	Uncertain significance (Jan 09, 2024)
X-118776495-A-G		not specified	Uncertain significance (Dec 15, 2023)
X-118776517-A-G			Benign (Jun 26, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IL13RA1	protein_coding	protein_coding	ENST00000371666	11	66968

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.963	0.0367	116139	1	1	116141	0.00000861

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.522	122	139	0.876	0.00000991	2847
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000403	0.0000403
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000131	0.00000924
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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

Intolerance Scores

• loftool: 0.163
• rvis_EVS: -0.41
• rvis_percentile_EVS: 26.23

Haploinsufficiency Scores

• pHI: 0.467
• hipred: Y
• hipred_score: 0.508
• ghis: 0.549

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.896

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Il13ra1
• Phenotype: respiratory system phenotype; hematopoietic system phenotype; immune system phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: cell surface receptor signaling pathway;cytokine-mediated signaling pathway;interleukin-13-mediated signaling pathway
• Cellular component: plasma membrane;interleukin-13 receptor complex;external side of plasma membrane;receptor complex
• Molecular function: cytokine receptor activity;protein binding;interleukin-13 receptor activity;cytokine binding