IL9R

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

Basic information

Region (hg38): Y:57184216-57199537

Links

ENSG00000292373 ∙ NCBI:3581 ∙ OMIM:300007 ∙ HGNC:6030 ∙ Uniprot:Q01113 ∙ 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 IL9R gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IL9R 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					2	2
missense					4	4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					2	2
Total	0	0	0	0	8

Variants in IL9R

This is a list of pathogenic ClinVar variants found in the IL9R region.

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

Position	Type	Phenotype	Significance	ClinVar
Y-57190090-G-A			Benign (Jun 29, 2018)
Y-57191079-C-T			Benign (Jun 13, 2018)
Y-57196354-G-A			Benign (Jul 31, 2017)
Y-57196457-G-A			Benign (May 24, 2017)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IL9R	protein_coding	protein_coding	ENST00000244174	9	13237

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.68e-22	0.0000360	125217	2	370	125589	0.00148

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.27	374	269	1.39	0.0000142	3343
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00176	0.00176
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.000370	0.000323
European (Non-Finnish)	0.00109	0.00109
Middle Eastern	0.000272	0.000272
South Asian	0.00599	0.00596
Other	0.00163	0.00147

dbNSFP

Source: dbNSFP

• Function: FUNCTION: This is a receptor for interleukin-9.
• Pathway: 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;Signaling by Interleukins;Cytokine Signaling in Immune system;JAK STAT MolecularVariation 1;Interleukin-9 signaling;Immune System;Interleukin-2 family signaling;JAK STAT MolecularVariation 2;JAK STAT pathway and regulation;IL9 (Consensus)

Recessive Scores

• pRec: 0.151

Intolerance Scores

• loftool: 0.748
• rvis_EVS: 0.82
• rvis_percentile_EVS: 88.07

Haploinsufficiency Scores

• pHI: 0.118
• hipred: N
• hipred_score: 0.159
• ghis: 0.401

Essentials

• essential_gene_CRISPR: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.560

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Il9r
• Phenotype: hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: signal transduction;cell population proliferation;interleukin-9-mediated signaling pathway
• Cellular component: extracellular space;plasma membrane;integral component of plasma membrane
• Molecular function: interleukin-9 receptor activity