OS9

OS9 endoplasmic reticulum lectin, the group of MRH domain containing

Basic information

Region (hg38): 12:57693841-57728342

Links

ENSG00000135506 ∙ NCBI:10956 ∙ OMIM:609677 ∙ HGNC:16994 ∙ Uniprot:Q13438 ∙ 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 OS9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OS9 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				2	2	4
missense			46	2	1	49
nonsense						0
start loss						0
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding			14	2		16
Total	0	0	61	6	3

Variants in OS9

This is a list of pathogenic ClinVar variants found in the OS9 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-57694204-C-G			Uncertain significance (Oct 01, 2023)
12-57694302-G-A			Benign (Nov 20, 2018)
12-57694805-G-A		not specified	Uncertain significance (Jan 30, 2024)
12-57694846-G-A		not specified	Uncertain significance (Apr 09, 2024)
12-57694873-C-A		not specified	Uncertain significance (Jan 02, 2024)
12-57694895-G-C			Uncertain significance (Oct 01, 2023)
12-57694910-C-T		not specified	Uncertain significance (Dec 09, 2023)
12-57695813-G-A		not specified	Uncertain significance (Sep 20, 2023)
12-57695989-A-G		not specified	Uncertain significance (Jun 27, 2022)
12-57696268-T-C			Benign (Nov 20, 2018)
12-57696334-G-C		not specified	Uncertain significance (Sep 29, 2022)
12-57696354-C-T		not specified	Uncertain significance (Dec 03, 2021)
12-57715776-G-A		not specified	Uncertain significance (Nov 07, 2023)
12-57715778-G-A		not specified	Uncertain significance (Nov 01, 2022)
12-57715782-G-T		not specified	Uncertain significance (Aug 17, 2021)
12-57715785-T-C		not specified	Uncertain significance (Sep 09, 2021)
12-57715801-C-T			Likely benign (Oct 01, 2022)
12-57715808-G-A		not specified	Uncertain significance (Apr 24, 2024)
12-57715847-C-T		not specified	Uncertain significance (May 09, 2023)
12-57715853-C-A		not specified	Uncertain significance (Aug 14, 2023)
12-57715857-G-A		not specified	Uncertain significance (Apr 07, 2023)
12-57715924-T-G			Likely benign (Oct 01, 2022)
12-57715933-G-C		not specified	Uncertain significance (Jul 25, 2023)
12-57716136-C-G		not specified	Uncertain significance (Jan 05, 2022)
12-57716414-G-T		not specified	Uncertain significance (Dec 31, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OS9	protein_coding	protein_coding	ENST00000315970	15	27603

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.86e-9	0.995	125709	0	39	125748	0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.05	343	402	0.853	0.0000238	4339
Missense in Polyphen		88	119.54	0.73613		1236
Synonymous	1.51	128	152	0.844	0.00000846	1292
Loss of Function	2.61	20	37.1	0.538	0.00000180	439

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000449	0.000449
Ashkenazi Jewish	0.00	0.00
East Asian	0.000326	0.000326
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000160	0.000158
Middle Eastern	0.000326	0.000326
South Asian	0.0000680	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Lectin which functions in endoplasmic reticulum (ER) quality control and ER-associated degradation (ERAD). May bind terminally misfolded non-glycosylated proteins as well as improperly folded glycoproteins, retain them in the ER, and possibly transfer them to the ubiquitination machinery and promote their degradation. Possible targets include TRPV4. {ECO:0000269|PubMed:17932042, ECO:0000269|PubMed:18264092, ECO:0000269|PubMed:18417469, ECO:0000269|PubMed:19084021, ECO:0000269|PubMed:19346256, ECO:0000269|PubMed:21172656}.
• Pathway: Protein processing in endoplasmic reticulum - Homo sapiens (human);Disorders of transmembrane transporters;Disease;Signal Transduction;Defective CFTR causes cystic fibrosis;ER Quality Control Compartment (ERQC);Calnexin/calreticulin cycle;Post-translational protein modification;Metabolism of proteins;Hypoxic and oxygen homeostasis regulation of HIF-1-alpha;Transport of small molecules;Hedgehog ligand biogenesis;Signaling by Hedgehog;Asparagine N-linked glycosylation;ABC-family proteins mediated transport;N-glycan trimming in the ER and Calnexin/Calreticulin cycle;Hh mutants that don,t undergo autocatalytic processing are degraded by ERAD;Hh mutants abrogate ligand secretion;ABC transporter disorders;Diseases of signal transduction (Consensus)

Intolerance Scores

• loftool: 0.971
• rvis_EVS: -0.82
• rvis_percentile_EVS: 11.88

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.606
• ghis: 0.580

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.700

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Os9
• Phenotype: skeleton phenotype

Gene ontology

• Biological process: ubiquitin-dependent protein catabolic process;protein targeting;protein retention in ER lumen;protein ubiquitination;ubiquitin-dependent ERAD pathway;retrograde protein transport, ER to cytosol;response to endoplasmic reticulum stress;transmembrane transport;negative regulation of retrograde protein transport, ER to cytosol;endoplasmic reticulum mannose trimming
• Cellular component: Hrd1p ubiquitin ligase complex;endoplasmic reticulum;endoplasmic reticulum lumen;endoplasmic reticulum membrane;endoplasmic reticulum quality control compartment
• Molecular function: protease binding;protein binding;carbohydrate binding