OSTC

oligosaccharyltransferase complex non-catalytic subunit, the group of Oligosaccharyltransferase complex subunits

Basic information

Region (hg38): 4:108650585-108667820

Links

ENSG00000198856 ∙ NCBI:58505 ∙ OMIM:619023 ∙ HGNC:24448 ∙ Uniprot:Q9NRP0 ∙ 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 OSTC gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OSTC 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			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	0	0

Variants in OSTC

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

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

Position	Type	Phenotype	Significance	ClinVar
4-108650662-A-G		not specified	Uncertain significance (Aug 01, 2022)
4-108650662-A-T		not specified	Uncertain significance (Nov 12, 2021)
4-108650737-C-T		not specified	Uncertain significance (Mar 11, 2024)
4-108650764-G-A		not specified	Uncertain significance (Aug 05, 2024)
4-108655631-G-C		not specified	Uncertain significance (Jul 10, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OSTC	protein_coding	protein_coding	ENST00000512478	5	17237

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0184	0.904	125725	0	21	125746	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.998	68	95.4	0.713	0.00000483	1106
Missense in Polyphen		8	19.409	0.41218		267
Synonymous	0.424	34	37.3	0.912	0.00000195	340
Loss of Function	1.49	4	8.77	0.456	5.51e-7	98

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000120
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000124	0.000123
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000661	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as substrate-specific component of the N- oligosaccharyl transferase (OST) complex which catalyzes the transfer of a high mannose oligosaccharide from a lipid-linked oligosaccharide donor to an asparagine residue within an Asn-X- Ser/Thr consensus motif in nascent polypeptide chains. May be involved in N-glycosylation of APP (amyloid-beta precursor protein). Can modulate gamma-secretase cleavage of APP by enhancing endoprotelysis of PSEN1. {ECO:0000269|PubMed:21768116, ECO:0000305}.

Intolerance Scores

• loftool: 0.474
• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.63

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.490
• ghis: 0.641

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: H
• 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: Ostc

Gene ontology

• Biological process: protein N-linked glycosylation via asparagine
• Cellular component: oligosaccharyltransferase complex;integral component of membrane
• Molecular function: dolichyl-diphosphooligosaccharide-protein glycotransferase activity;protein binding