IL9R

protein-coding

interleukin 9 receptor, the group of Pseudoautosomal region 2|CD molecules|Interleukin receptors

Gene summary

The protein encoded by this gene is a cytokine receptor that specifically mediates the biological effects of interleukin 9 (IL9). The functional IL9 receptor complex requires this protein as well as the interleukin 2 receptor, gamma (IL2RG), a common gamma subunit shared by the receptors of many different cytokines. The ligand binding of this receptor leads to the activation of various JAK kinases and STAT proteins, which connect to different biologic responses. This gene is located at the pseudoautosomal regions of X and Y chromosomes. Genetic studies suggested an association of this gene with the development of asthma. Multiple pseudogenes on chromosome 9, 10, 16, and 18 have been described. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2008]

MANE transcript

N/A

Inheritance

—

ClinVar variants

B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.43

Max pathogenic AF

—

Genomic locus

chrY:57,184,216-57,199,537

External References & Databases

Ensembl (ENSG00000292373)

Transcript & Mutation Effects

hg38 • Region Span ~15.3 kb

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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 IL9R variants in ClinVar

0 Conditions Cataloged

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					2 clinvar	2
missense					4 clinvar	4
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	0	0	6	6

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 42 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
ENST00000244174.11	Ensembl	ENSP00000244174.5	9	MANE Select
NM_002186.3	RefSeq	NP_002177.2	18	Standard
NM_176786.2	RefSeq	NP_789743.2	18	Standard
ENST00000369423.7	Ensembl	ENSP00000358431.2	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Jak-STAT signaling pathway - Homo sapiens (human)
Hematopoietic cell lineage - Homo sapiens (human)
Cytokine-cytokine receptor interaction - Homo sapiens (human)
JAK-STAT-Core
IL-9 Signaling Pathway

Biological Process

signal transduction
cell population proliferation
interleukin-9-mediated signaling pathway

Molecular Function

interleukin-9 receptor activity

Cellular Component

extracellular space
plasma membrane
integral component of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000244174
Coding exons: 9
Length: 13237
Individuals with no LoFs: 125217
Homozygous LoFs: 2
Heterozygous LoFs: 370
Defined: 125589
p: 0.00148

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-2.27	374	269	1.39	0.0000142	3343
Missense (PolyPhen)		76	54.237	1.4012		742
Synonymous	-2.40	143	111	1.29	0.00000616	1032
Loss of Function	-1.77	28	19.6	1.43	9.28e-7	199

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00087	0.00086	rare
Latino/Admixed American	0.00090	0.00090	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00027	0.00027	rare
Finnish	0.00037	0.00032	rare
European (Non-Finnish)	0.0011	0.0011	notable
South Asian	0.0060	0.0060	notable
Other	0.0016	0.0015	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: This is a receptor for interleukin-9.;

Recessive Scores

pRec: 0.151

Intolerance Scores

LoFtool: 0.748
RVIS EVS: 0.82
RVIS percentile EVS: 88.07

Essentials

Essential (CRISPR): E
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.560

Gene Damage Prediction

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