OSMR

oncostatin M receptor, the group of Fibronectin type III domain containing

Basic information

Region (hg38): 5:38845858-38945596

Links

ENSG00000145623 ∙ NCBI:9180 ∙ OMIM:601743 ∙ HGNC:8507 ∙ Uniprot:Q99650 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• amyloidosis, primary localized cutaneous, 1 (Strong), mode of inheritance: AD
• amyloidosis, primary localized cutaneous, 1 (Strong), mode of inheritance: AD
• amyloidosis, primary localized cutaneous, 1 (Moderate), mode of inheritance: Semidominant
• familial primary localized cutaneous amyloidosis (Supportive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Amyloidosis, primary localized cutaneous, 1	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Dermatologic	18179886; 19690585

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the OSMR gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OSMR 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				7	4	11
missense		1	49	10	6	66
nonsense			1			1
start loss						0
frameshift			2			2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1	2	1	4
non coding				1	1	2
Total	0	1	52	18	11

Variants in OSMR

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

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

Position	Type	Phenotype	Significance	ClinVar
5-38869048-G-T		Inborn genetic diseases	Uncertain significance (Aug 01, 2022)
5-38869072-A-G		Inborn genetic diseases	Uncertain significance (Mar 02, 2023)
5-38876206-G-A		Inborn genetic diseases	Uncertain significance (Mar 02, 2023)
5-38876212-C-T		Inborn genetic diseases	Uncertain significance (May 26, 2023)
5-38876213-G-A		Inborn genetic diseases	Uncertain significance (Mar 29, 2022)
5-38876259-G-A		OSMR-related disorder	Benign (Dec 31, 2019)
5-38876261-G-A		Inborn genetic diseases	Likely benign (Aug 26, 2022)
5-38876287-G-A		Inborn genetic diseases	Uncertain significance (Nov 16, 2021)
5-38876316-GAAAA-T			Uncertain significance (Feb 25, 2022)
5-38881738-A-G		Inborn genetic diseases	Uncertain significance (Feb 06, 2023)
5-38883810-A-AT		OSMR-related disorder	Likely benign (Dec 23, 2019)
5-38883823-G-T			Likely benign (Sep 01, 2017)
5-38883859-G-A		Inborn genetic diseases	Likely benign (Aug 21, 2023)
5-38883869-A-C		Inborn genetic diseases • OSMR-related disorder	Uncertain significance (Feb 02, 2022)
5-38883902-C-T		Inborn genetic diseases	Uncertain significance (Aug 09, 2021)
5-38883908-G-T		Inborn genetic diseases	Uncertain significance (Dec 07, 2023)
5-38883913-G-A		Inborn genetic diseases	Benign/Likely benign (Mar 29, 2022)
5-38883919-A-G		Inborn genetic diseases	Uncertain significance (Jul 12, 2023)
5-38883969-T-G		OSMR-related disorder	Benign (Nov 15, 2019)
5-38884012-A-T			Benign (Oct 25, 2017)
5-38884090-G-C		Inborn genetic diseases	Uncertain significance (Nov 10, 2022)
5-38884097-T-C		Inborn genetic diseases	Uncertain significance (Dec 19, 2022)
5-38885349-A-C		Inborn genetic diseases	Uncertain significance (Apr 19, 2023)
5-38885400-C-G		Inborn genetic diseases	Uncertain significance (Dec 06, 2022)
5-38886102-C-T			Benign (Mar 29, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OSMR	protein_coding	protein_coding	ENST00000274276	17	99739

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.21e-18	0.598	125583	1	164	125748	0.000656

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.113	495	502	0.986	0.0000250	6489
Missense in Polyphen		112	107.46	1.0423		1524
Synonymous	0.281	182	187	0.974	0.0000100	1811
Loss of Function	1.87	34	48.0	0.709	0.00000247	561

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00139	0.00139
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000381	0.000381
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000563	0.000554
Middle Eastern	0.000381	0.000381
South Asian	0.00140	0.00141
Other	0.00131	0.00130

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Associates with IL31RA to form the IL31 receptor. Binds IL31 to activate STAT3 and possibly STAT1 and STAT5. Capable of transducing OSM-specific signaling events. {ECO:0000269|PubMed:15184896, ECO:0000269|PubMed:8999038}.
• Disease: DISEASE: Amyloidosis, primary localized cutaneous, 1 (PLCA1) [MIM:105250]: A primary amyloidosis characterized by localized cutaneous amyloid deposition. This condition usually presents with itching (especially on the lower legs) and visible changes of skin hyperpigmentation and thickening that may be exacerbated by chronic scratching and rubbing. Primary localized cutaneous amyloidosis is often divided into macular and lichen subtypes although many affected individuals often show both variants coexisting. Lichen amyloidosis characteristically presents as a pruritic eruption of grouped hyperkeratotic papules with a predilection for the shins, calves, ankles and dorsa of feet and thighs. Papules may coalesce to form hyperkeratotic plaques that can resemble lichen planus, lichen simplex or nodular prurigo. Macular amyloidosis is characterized by small pigmented macules that may merge to produce macular hyperpigmentation, sometimes with a reticulate or rippled pattern. In macular and lichen amyloidosis, amyloid is deposited in the papillary dermis in association with grouped colloid bodies, thought to represent degenerate basal keratinocytes. The amyloid deposits probably reflect a combination of degenerate keratin filaments, serum amyloid P component, and deposition of immunoglobulins. {ECO:0000269|PubMed:18179886, ECO:0000269|PubMed:19690585}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• 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;Oncostatin M Signaling Pathway;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;PI3K-Akt Signaling Pathway;Signaling by Interleukins;IL-6-type cytokine receptor ligand interactions;Cytokine Signaling in Immune system;JAK STAT MolecularVariation 1;Oncostatin_M;Immune System;JAK STAT MolecularVariation 2;JAK STAT pathway and regulation;Interleukin-6 family signaling (Consensus)

Recessive Scores

• pRec: 0.0866

Intolerance Scores

• loftool: 0.958
• rvis_EVS: 1.59
• rvis_percentile_EVS: 95.81

Haploinsufficiency Scores

• pHI: 0.167
• hipred: N
• hipred_score: 0.388
• ghis: 0.459

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.984

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Osmr
• Phenotype: hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; immune system phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype; growth/size/body region 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); homeostasis/metabolism phenotype

Gene ontology

• Biological process: positive regulation of acute inflammatory response;positive regulation of cell population proliferation;cytokine-mediated signaling pathway;response to cytokine;oncostatin-M-mediated signaling pathway
• Cellular component: plasma membrane;oncostatin-M receptor complex;external side of plasma membrane;apical plasma membrane;receptor complex
• Molecular function: cytokine receptor activity;oncostatin-M receptor activity;protein binding;growth factor binding;cytokine binding