OSM

oncostatin M, the group of Interleukin 6 type cytokine family

Basic information

Region (hg38): 22:30262829-30266851

Links

ENSG00000099985 ∙ NCBI:5008 ∙ OMIM:165095 ∙ HGNC:8506 ∙ Uniprot:P13725 ∙ 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 OSM gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OSM 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						0
missense			27	6		33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	6	0

Variants in OSM

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

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

Position	Type	Phenotype	Significance	ClinVar
22-30263906-T-G		not specified	Likely benign (Aug 22, 2023)
22-30263945-G-A		not specified	Uncertain significance (Aug 14, 2023)
22-30263948-C-T		not specified	Uncertain significance (Aug 30, 2022)
22-30263951-C-T		not specified	Uncertain significance (Oct 06, 2021)
22-30264023-G-A		not specified	Uncertain significance (Dec 28, 2023)
22-30264038-T-C		not specified	Uncertain significance (Jul 25, 2023)
22-30264067-C-T		not specified	Uncertain significance (Apr 22, 2024)
22-30264083-G-A		not specified	Uncertain significance (Jun 07, 2024)
22-30264106-G-C		not specified	Uncertain significance (Apr 29, 2024)
22-30264118-G-T		not specified	Uncertain significance (Oct 10, 2023)
22-30264128-C-T		not specified	Likely benign (Jun 18, 2021)
22-30264133-C-T		not specified	Uncertain significance (Oct 24, 2023)
22-30264136-C-A		not specified	Uncertain significance (Feb 15, 2023)
22-30264149-G-A		not specified	Uncertain significance (Jun 16, 2024)
22-30264157-G-A		not specified	Likely benign (Nov 01, 2022)
22-30264163-G-A		not specified	Uncertain significance (May 16, 2024)
22-30264164-A-C		not specified	Uncertain significance (Sep 22, 2023)
22-30264206-G-A		not specified	Likely benign (Mar 20, 2023)
22-30264220-G-A		not specified	Uncertain significance (Nov 22, 2023)
22-30264220-G-C		not specified	Uncertain significance (Dec 20, 2023)
22-30264251-C-T		not specified	Uncertain significance (Jun 06, 2023)
22-30264262-C-T		not specified	Uncertain significance (Jul 12, 2022)
22-30264283-G-A		not specified	Uncertain significance (Jun 29, 2023)
22-30264308-C-T		not specified	Uncertain significance (Aug 08, 2022)
22-30264340-G-T		not specified	Uncertain significance (Jan 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OSM	protein_coding	protein_coding	ENST00000215781	3	4012

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.589	0.374	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.294	152	163	0.935	0.0000104	1625
Missense in Polyphen		33	41.545	0.79431		463
Synonymous	0.781	60	68.2	0.880	0.00000404	533
Loss of Function	1.54	0	2.77	0.00	1.17e-7	32

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Growth regulator. Inhibits the proliferation of a number of tumor cell lines. Stimulates proliferation of AIDS-KS cells. It regulates cytokine production, including IL-6, G-CSF and GM-CSF from endothelial cells. Uses both type I OSM receptor (heterodimers composed of LIPR and IL6ST) and type II OSM receptor (heterodimers composed of OSMR and IL6ST). Involved in the maturation of fetal hepatocytes, thereby promoting liver development and regeneration (By similarity). {ECO:0000250, ECO:0000269|PubMed:1542792, ECO:0000269|PubMed:1542793}.
• Pathway: PI3K-Akt signaling pathway - Homo sapiens (human);Jak-STAT signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);JAK-STAT-Core;Adipogenesis;Oncostatin M Signaling Pathway;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;Interleukin-4 and 13 signaling;PI3K-Akt Signaling Pathway;Signaling by Interleukins;IL-6-type cytokine receptor ligand interactions;Cytokine Signaling in Immune system;Oncostatin_M;Immune System;GMCSF-mediated signaling events;Interleukin-6 family signaling;IL3-mediated signaling events (Consensus)

Recessive Scores

• pRec: 0.717

Intolerance Scores

• loftool: 0.557
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.75

Haploinsufficiency Scores

• pHI: 0.178
• hipred: N
• hipred_score: 0.315
• ghis: 0.468

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.944

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Osm
• Phenotype: homeostasis/metabolism phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); hematopoietic system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: positive regulation of acute inflammatory response;immune response;multicellular organism development;cell population proliferation;positive regulation of cell population proliferation;negative regulation of cell population proliferation;regulation of signaling receptor activity;positive regulation of phosphatidylinositol 3-kinase signaling;cytokine-mediated signaling pathway;positive regulation of peptidyl-serine phosphorylation;oncostatin-M-mediated signaling pathway;regulation of growth;positive regulation of tyrosine phosphorylation of STAT protein;positive regulation of MAPK cascade;positive regulation of transcription by RNA polymerase II;negative regulation of hormone secretion;positive regulation of inflammatory response;positive regulation of peptidyl-tyrosine phosphorylation;positive regulation of cell division;positive regulation of protein kinase B signaling;positive regulation of interleukin-17 secretion
• Cellular component: extracellular region;extracellular space
• Molecular function: cytokine activity;oncostatin-M receptor binding;growth factor activity