STT3B
protein-codingSTT3 oligosaccharyltransferase complex catalytic subunit B, the group of Oligosaccharyltransferase complex subunits|STT3 oligosaccharyltransferase catalytic subunits
Gene summary
The protein encoded by this gene is a catalytic subunit of a protein complex that transfers oligosaccharides onto asparagine residues. Defects in this gene are a cause of congenital disorder of glycosylation Ix (CDG1X). [provided by RefSeq, Jun 2014]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~105.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0014271
Submitter: G2P
Inheritance Pattern: Unknown
Disease ID:MONDO:0014271
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0014271
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0014271
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0014271
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0015286
Submitter: ClinGen
*STT3B* was first reported in relation to autosomal recessive congenital disorder of glycosylation in 2013 (Shrimal et al., PMID: 23842455). Two variants (splice, missense) that have been reported in two probands in two publications are included in this curation. This gene-disease relationship is also supported by rescue in patient cells (Shrimal et al., PMID: 23842455) and protein interaction with *STT3A* (which is definitively associated with CDG) (Wen et al., PMID: 36139350). In summary, there is limited evidence to support this gene-disease relationship. Although more evidence is needed to support a causal role, no convincing evidence has emerged that contradicts the gene-disease relationship. This classification was approved by the ClinGen Congenital Disorders of Glycosylation GCEP on the meeting date April 6, 2026 (SOP Version 12).
Clinical Genomic Database (CGD)
Manifestation: Biochemical; Gastrointestinal; Genitourinary; Hematologic; Neurologic; Ophthalmologic
Intervention: Hematologic
Rationale: Awareness of coagulopathies may be beneficial in terms of medical management, especially in situations such as surgery
Comments: Hepatic-metabolized agents should be avoided
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to STT3B variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_178862.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 52 | 2 | 56 | ||
| missense | 1 | 99 | 3 | 1 | 104 | |
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 7 | 7 | ||||
| Total | 1 | 0 | 108 | 55 | 3 | 167 |
Highest pathogenic variant AF is 0.000006572375
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_849193.1 | 16 | MANE Select | |
| Ensembl | ENSP00000295770.2 | 16 | MANE Select | |
| Ensembl | ENSP00000520729.1 | 14 | Standard | |
| Ensembl | ENSP00000520729.1 | 14 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Protein processing in endoplasmic reticulum - Homo sapiens (human)
- N-Glycan biosynthesis - Homo sapiens (human)
- N-Glycan biosynthesis
Biological Process
- glycoprotein catabolic process
- response to unfolded protein
- protein N-linked glycosylation via asparagine
- ubiquitin-dependent ERAD pathway
- co-translational protein modification
Molecular Function
- dolichyl-diphosphooligosaccharide-protein glycotransferase activity
- metal ion binding
Cellular Component
- endoplasmic reticulum
- oligosaccharyltransferase complex
- membrane
- integral component of membrane
- protein-containing complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000295770
- Coding exons
- 16
- Length
- 104983
- Individuals with no LoFs
- 125717
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 8
- Defined
- 125725
- p
- 0.0000318
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 3.76 | 205 | 422 | 0.486 | 0.0000201 | 5409 |
| Missense (PolyPhen) | 59 | 201.28 | 0.29312 | 2492 | ||
| Synonymous | -0.184 | 149 | 146 | 1.02 | 0.00000703 | 1528 |
| Loss of Function | 5.29 | 5 | 42.0 | 0.119 | 0.00000220 | 508 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.000093 | 0.000092 | rare |
| European (Non-Finnish) | 0.000036 | 0.000035 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Catalytic subunit of the oligosaccharyl transferase (OST) complex that catalyzes the initial transfer of a defined glycan (Glc(3)Man(9)GlcNAc(2) in eukaryotes) from the lipid carrier dolichol-pyrophosphate to an asparagine residue within an Asn-X-Ser/Thr consensus motif in nascent polypeptide chains, the first step in protein N-glycosylation. N-glycosylation occurs cotranslationally and the complex associates with the Sec61 complex at the channel-forming translocon complex that mediates protein translocation across the endoplasmic reticulum (ER). All subunits are required for a maximal enzyme activity. This subunit contains the active site and the acceptor peptide and donor lipid- linked oligosaccharide (LLO) binding pockets (By similarity). STT3B is present in a small subset of OST complexes and mediates both cotranslational and post-translational N-glycosylation of target proteins: STT3B-containing complexes are required for efficient post-translational glycosylation and while they are less competent than STT3A-containing complexes for cotranslational glycosylation, they have the ability to mediate glycosylation of some nascent sites that are not accessible for STT3A. STT3B- containing complexes also act post-translationally and mediate modification of skipped glycosylation sites in unfolded proteins. Plays a role in ER-associated degradation (ERAD) pathway that mediates ubiquitin-dependent degradation of misfolded endoplasmic reticulum proteins by mediating N-glycosylation of unfolded proteins, which are then recognized by the ERAD pathway and targeted for degradation. Mediates glycosylation of the disease variant AMYL-TTR 'Asp-38' of TTR at 'Asn-118', leading to its degradation (PubMed:19167329, PubMed:22607976). {ECO:0000250|UniProtKB:P39007, ECO:0000269|PubMed:19167329, ECO:0000269|PubMed:22607976}.;
- Disease
- DISEASE: Congenital disorder of glycosylation 1X (CDG1X) [MIM:615597]: A form of congenital disorder of glycosylation, a multisystem disorder caused by a defect in glycoprotein biosynthesis and characterized by under-glycosylated serum glycoproteins. Congenital disorders of glycosylation result in a wide variety of clinical features, such as defects in the nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency. The broad spectrum of features reflects the critical role of N-glycoproteins during embryonic development, differentiation, and maintenance of cell functions. {ECO:0000269|PubMed:23842455}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.168
Intolerance Scores
- LoFtool
- 0.0734
- RVIS EVS
- -0.76
- RVIS percentile EVS
- 13.33
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- H
- Indispensability pred.
- N
- Indispensability score
- 0.319
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |