OGN

osteoglycin, the group of Small leucine rich repeat proteoglycans

Basic information

Region (hg38): 9:92383267-92404696

Links

ENSG00000106809 ∙ NCBI:4969 ∙ OMIM:602383 ∙ HGNC:8126 ∙ Uniprot:P20774 ∙ 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 OGN gene.

• Inborn genetic diseases (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OGN 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			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	0

Variants in OGN

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

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

Position	Type	Phenotype	Significance	ClinVar
9-92385727-G-A		not specified	Uncertain significance (Nov 13, 2023)
9-92386262-T-C		not specified	Uncertain significance (Sep 14, 2023)
9-92393116-T-G		not specified	Uncertain significance (Jan 16, 2024)
9-92393149-C-T		not specified	Uncertain significance (Mar 16, 2022)
9-92393161-G-C		not specified	Uncertain significance (Feb 12, 2024)
9-92401118-G-A		not specified	Uncertain significance (Aug 01, 2022)
9-92401127-G-A		not specified	Uncertain significance (Feb 28, 2024)
9-92401159-A-T		not specified	Uncertain significance (Sep 20, 2023)
9-92403325-C-T		not specified	Uncertain significance (Mar 30, 2022)
9-92403329-A-T		not specified	Uncertain significance (May 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OGN	protein_coding	protein_coding	ENST00000262551	6	20730

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000741	0.930	125684	0	58	125742	0.000231

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.14	118	158	0.746	0.00000829	1947
Missense in Polyphen		50	61.142	0.81777		730
Synonymous	0.0926	58	58.9	0.985	0.00000301	573
Loss of Function	1.61	7	13.3	0.525	7.46e-7	179

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00217	0.00212
Ashkenazi Jewish	0.000499	0.000496
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000706	0.0000703
Middle Eastern	0.000109	0.000109
South Asian	0.000166	0.000163
Other	0.000338	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Induces bone formation in conjunction with TGF-beta-1 or TGF-beta-2.
• Pathway: Metabolism of carbohydrates;Keratan sulfate biosynthesis;Keratan sulfate/keratin metabolism;Glycosaminoglycan metabolism;TCR;Metabolism (Consensus)

Intolerance Scores

• loftool: 0.565
• rvis_EVS: -0.43
• rvis_percentile_EVS: 25.15

Haploinsufficiency Scores

• pHI: 0.479
• hipred: N
• hipred_score: 0.445
• ghis: 0.551

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ogn
• 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; vision/eye phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: regulation of signaling receptor activity;keratan sulfate biosynthetic process;keratan sulfate catabolic process;negative regulation of smooth muscle cell proliferation
• Cellular component: extracellular region;extracellular space;Golgi lumen;lysosomal lumen;collagen-containing extracellular matrix;extracellular exosome;extracellular vesicle
• Molecular function: protein binding;growth factor activity;extracellular matrix structural constituent conferring compression resistance