IL3RA
protein-codinginterleukin 3 receptor subunit alpha, the group of Pseudoautosomal region 1|CD molecules|Interleukin receptors
Gene summary
The protein encoded by this gene is an interleukin 3 specific subunit of a heterodimeric cytokine receptor. The receptor is comprised of a ligand specific alpha subunit and a signal transducing beta subunit shared by the receptors for interleukin 3 (IL3), colony stimulating factor 2 (CSF2/GM-CSF), and interleukin 5 (IL5). The binding of this protein to IL3 depends on the beta subunit. The beta subunit is activated by the ligand binding, and is required for the biological activities of IL3. This gene and the gene encoding the colony stimulating factor 2 receptor alpha chain (CSF2RA) form a cytokine receptor gene cluster in a X-Y pseudoautosomal region on chromosomes X or Y. Alternatively spliced transcript variants encoding distinct isoforms have been found. [provided by RefSeq, Jun 2012]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~46.1 kbGenCC 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 IL3RA variants in ClinVar
No annotated ClinVar phenotypes.
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript . 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 | 4 | 4 | ||||
| missense | 4 | 4 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 0 | 4 | 4 | 8 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| Ensembl | ENSP00000327890.4 | 11 | MANE Select | |
| RefSeq | NP_001254642.1 | 18 | Standard | |
| RefSeq | NP_002174.1 | 22 | Standard | |
| Ensembl | ENSP00000370878.2 | 9 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- 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)
Biological Process
- MAPK cascade
- peptidyl-tyrosine phosphorylation
- cytokine-mediated signaling pathway
- cellular response to interleukin-3
- interleukin-3-mediated signaling pathway
Molecular Function
- protein tyrosine kinase activity
- cytokine receptor activity
- interleukin-3 receptor activity
- Ras guanyl-nucleotide exchange factor activity
- cytokine binding
Cellular Component
- plasma membrane
- external side of plasma membrane
- integral component of membrane
- receptor complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000331035
- Coding exons
- 11
- Length
- 46070
- Individuals with no LoFs
- 124769
- Homozygous LoFs
- 13
- Heterozygous LoFs
- 810
- Defined
- 125592
- p
- 0.00328
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -1.50 | 310 | 244 | 1.27 | 0.0000163 | 2484 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00074 | 0.00074 | rare |
| Latino/Admixed American | 0.0012 | 0.0012 | notable |
| Ashkenazi Jewish | 0.040 | 0.040 | notable |
| East Asian | 0.0010 | 0.0010 | notable |
| Finnish | 0.00014 | 0.00014 | rare |
| European (Non-Finnish) | 0.0026 | 0.0026 | notable |
| South Asian | 0.0012 | 0.0011 | notable |
| Other | 0.0051 | 0.0051 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: This is a receptor for interleukin-3.;
Intolerance Scores
- LoFtool
- 0.480
- RVIS EVS
- -0.09
- RVIS percentile EVS
- 47.12
Essentials
- Essential (CRISPR)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.914
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |