IL3RA

interleukin 3 receptor subunit alpha, the group of Pseudoautosomal region 1|CD molecules|Interleukin receptors

Basic information

Region (hg38): Y:1336616-1382689

Links

∙ NCBI:3563 ∙ OMIM:308385, 430000 ∙ HGNC:6012 ∙ Uniprot:P26951 ∙ 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 IL3RA gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IL3RA 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					4 clinvar	4
missense				4 clinvar		4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	4	4

Variants in IL3RA

This is a list of pathogenic ClinVar variants found in the IL3RA region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Significance	ClinVar
Y-1348504-C-T	Likely benign (Jul 07, 2018)	747176
Y-1352169-G-C	Likely benign (Jul 16, 2018)	770823
Y-1352209-C-T	Benign (Jul 16, 2018)	734034
Y-1382426-G-A	Benign (Dec 29, 2017)	730638

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IL3RA	protein_coding	protein_coding	ENST00000331035	11	46070

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.99e-27	0.00000222	124769	13	810	125592	0.00328

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.50	310	244	1.27	0.0000163	2484
Missense in Polyphen		71	43.597	1.6286		557
Synonymous	-4.26	154	99.8	1.54	0.00000742	715
Loss of Function	-2.13	34	23.0	1.48	0.00000113	242

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00196	0.00195
Ashkenazi Jewish	0.0398	0.0396
East Asian	0.00103	0.00103
Finnish	0.000139	0.000139
European (Non-Finnish)	0.00258	0.00258
Middle Eastern	0.00103	0.00103
South Asian	0.00119	0.00108
Other	0.00507	0.00507

dbNSFP

Source: dbNSFP

Function: FUNCTION: This is a receptor for interleukin-3.;
Pathway: PI3K-Akt signaling pathway - Homo sapiens (human);Jak-STAT signaling pathway - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Hematopoietic cell lineage - Homo sapiens (human);Apoptosis - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);JAK-STAT-Core;IL-3 Signaling Pathway;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;PI3K-Akt Signaling Pathway;Signaling by GPCR;IL-3 signaling;Signal Transduction;Signaling by Interleukins;regulation of bad phosphorylation;Cytokine Signaling in Immune system;JAK STAT MolecularVariation 1;il 3 signaling pathway;Immune System;Interleukin receptor SHC signaling;Interleukin-2 family signaling;JAK STAT MolecularVariation 2;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades;JAK STAT pathway and regulation;IL3;G beta:gamma signalling through PI3Kgamma;G-protein beta:gamma signalling;GPCR downstream signalling;IL3-mediated signaling events;Interleukin-3, 5 and GM-CSF signaling (Consensus)

Intolerance Scores

loftool: 0.480
rvis_EVS: -0.09
rvis_percentile_EVS: 47.12

Haploinsufficiency Scores

pHI: 0.127
hipred: N
hipred_score: 0.398
ghis: 0.469

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.914

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Il3ra
Phenotype: immune system phenotype; hematopoietic system phenotype;

Gene ontology

Biological process: MAPK cascade;peptidyl-tyrosine phosphorylation;cytokine-mediated signaling pathway;cellular response to interleukin-3;interleukin-3-mediated signaling pathway
Cellular component: plasma membrane;external side of plasma membrane;integral component of membrane;receptor complex
Molecular function: protein tyrosine kinase activity;cytokine receptor activity;interleukin-3 receptor activity;Ras guanyl-nucleotide exchange factor activity;cytokine binding