IL9

interleukin 9, the group of Interleukins

Basic information

Region (hg38): 5:135892246-135895841

Links

ENSG00000145839 ∙ NCBI:3578 ∙ OMIM:146931 ∙ HGNC:6029 ∙ Uniprot:P15248 ∙ 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 IL9 gene.

• not_specified (18 variants)
• not_provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IL9 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000000590.2. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			17	1		18
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	17	2	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IL9	protein_coding	protein_coding	ENST00000274520	5	3582

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.11e-7	0.0926	125530	0	213	125743	0.000847

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.253	70	76.2	0.918	0.00000363	944
Missense in Polyphen		26	23.704	1.0969		289
Synonymous	-0.224	32	30.4	1.05	0.00000169	273
Loss of Function	-0.898	8	5.69	1.41	2.39e-7	71

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000183	0.000181
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.00881	0.00885
Finnish	0.00	0.00
European (Non-Finnish)	0.000159	0.000158
Middle Eastern	0.00881	0.00885
South Asian	0.000823	0.000817
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Supports IL-2 independent and IL-4 independent growth of helper T-cells.
• Pathway: Jak-STAT signaling pathway - Homo sapiens (human);Asthma - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);JAK-STAT-Core;IL-9 Signaling Pathway;Development and heterogeneity of the ILC family;T-Cell antigen Receptor (TCR) Signaling Pathway;Signaling by Interleukins;Cytokine Signaling in Immune system;JAK STAT MolecularVariation 1;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;Interleukin-9 signaling;Immune System;Interleukin-2 family signaling;GPCR signaling-G alpha s Epac and ERK;GPCR signaling-G alpha s PKA and ERK;JAK STAT pathway and regulation;GPCR signaling-G alpha i (Consensus)

Recessive Scores

• pRec: 0.280

Intolerance Scores

• loftool: 0.732
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.11

Haploinsufficiency Scores

• pHI: 0.0555
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.631

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Il9
• Phenotype: homeostasis/metabolism phenotype; immune system phenotype; digestive/alimentary phenotype; normal phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: inflammatory response;immune response;positive regulation of cell population proliferation;regulation of signaling receptor activity;positive regulation of cell growth;interleukin-9-mediated signaling pathway;positive regulation of interleukin-5 biosynthetic process
• Cellular component: extracellular region;extracellular space
• Molecular function: cytokine activity;interleukin-9 receptor binding;growth factor activity