STT3B

protein-coding

STT3 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

NM_178862.3

Inheritance

AR

ClinVar variants

P:1U:108B:58

Top phenotype

Congenital disorder of glycosylation, type Ix

gnomAD constraint

pLI —, LoF o/e 0.12

Max pathogenic AF

—

Genomic locus

chr3:31,532,638-31,638,548

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~105.9 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

STT3B-congenital disorder of glycosylationLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0014271

Submitter: G2P

STT3B-congenital disorder of glycosylationLIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0014271

Submitter: Labcorp Genetics (formerly Invitae)

STT3B-congenital disorder of glycosylationSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0014271

Submitter: Orphanet

STT3B-congenital disorder of glycosylationLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0014271

Submitter: PanelApp Australia

STT3B-congenital disorder of glycosylationLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0014271

Submitter: Ambry Genetics

congenital disorder of glycosylationLIMITED

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)

Congenital disorder of glycosylation, type IxAR

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

Refs: 23842455Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to STT3B variants in ClinVar

4 Conditions Cataloged
STT3B-congenital disorder of glycosylationTotal: 107
not specifiedTotal: 96
not providedTotal: 39
STT3B-related disorderTotal: 3

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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
52
clinvar
2
clinvar
56
missense
1
clinvar
99
clinvar
3
clinvar
1
clinvar
104
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
7
clinvar
7
Total10108553167

Highest pathogenic variant AF is 0.000006572375

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 53 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_178862.3RefSeqNP_849193.116MANE Select
ENST00000295770.4EnsemblENSP00000295770.216MANE Select
ENST00000462235.6EnsemblENSP00000520729.114Standard
ENST00000462235.7EnsemblENSP00000520729.114Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense3.762054220.4860.00002015409
Missense (PolyPhen)59201.280.293122492
Synonymous-0.1841491461.020.000007031528
Loss of Function5.29542.00.1190.00000220508

Population LoF Frequency

PopulationCAFp-valueStatus
African0.0000620.000062rare
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish0.0000930.000092rare
European (Non-Finnish)0.0000360.000035rare
South Asian0.0000330.000033rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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