OSM
oncostatin M, the group of Interleukin 6 type cytokine family
Basic information
Region (hg38): 22:30262829-30266851
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (53 variants)
- Autosomal_dominant_intellectual_disability-craniofacial_anomalies-cardiac_defects_syndrome (1 variants)
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. These statistics are base on transcript: NM_000020530.6. 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 | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 46 | 53 | ||||
| nonsense | 1 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 1 | 46 | 7 | 0 |
Loading clinvar variants...
GnomAD
Source:
| 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:
- 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