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    STT3A STT3 oligosaccharyltransferase complex catalytic subunit A [ Homo sapiens (human) ]

    Gene ID: 3703, updated on 10-Dec-2024

    Summary

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    Official Symbol
    STT3Aprovided by HGNC
    Official Full Name
    STT3 oligosaccharyltransferase complex catalytic subunit Aprovided by HGNC
    Primary source
    HGNC:HGNC:6172
    See related
    Ensembl:ENSG00000134910 MIM:601134; AllianceGenome:HGNC:6172
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    TMC; ITM1; STT3-A; CDG1WAD; CDG1WAR
    Summary
    The protein encoded by this gene is a catalytic subunit of the N-oligosaccharyltransferase (OST) complex, which functions in the endoplasmic reticulum to transfer glycan chains to asparagine residues of target proteins. A separate complex containing a similar catalytic subunit with an overlapping function also exists. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2015]
    Expression
    Ubiquitous expression in thyroid (RPKM 41.7), endometrium (RPKM 25.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See STT3A in Genome Data Viewer
    Location:
    11q24.2
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (125591769..125623091)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (125621493..125651713)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (125462747..125492986)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene fasciculation and elongation protein zeta 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:125365219-125365722 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:125365723-125366224 Neighboring gene putative uncharacterized protein MGC39545 Neighboring gene CRISPRi-validated cis-regulatory element chr11.5907 Neighboring gene Sharpr-MPRA regulatory region 4861 Neighboring gene CRISPRi-validated cis-regulatory element chr11.5909 Neighboring gene CRISPRi-validated cis-regulatory element chr11.5910 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:125439037-125439538 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5698 Neighboring gene STT3A antisense RNA 1 Neighboring gene RNA, U6 small nuclear 1156, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5699 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:125462019-125462613 Neighboring gene EI24 autophagy associated transmembrane protein Neighboring gene uncharacterized LOC118567325 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5700 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:125496550-125497093 Neighboring gene checkpoint kinase 1 Neighboring gene RNA, U2 small nuclear 35, pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Assignment of the human integral transmembrane protein 1 gene (ITM1) to human chromosome band 11q23.3 by in situ hybridization and YAC mapping. Van Hul W, et al. Cytogenet Cell Genet, 1996. PMID 8941377
    2. Phenotypic Heterogeneity in a Congenital Disorder of Glycosylation Caused by Mutations in STT3A. Ghosh A, et al. J Child Neurol, 2017 May. PMID 28424003
    3. Active site variants in STT3A cause a dominant type I congenital disorder of glycosylation with neuromusculoskeletal findings. Wilson MP, et al. Am J Hum Genet, 2021 Nov 4. PMID 34653363, Free PMC Article
    4. STT3A-mediated viral N-glycosylation underlies the tumor selectivity of oncolytic virus M1. Song D, et al. Oncogene, 2023 Nov. PMID 37864032
    5. Evidence for schizophrenia susceptibility alleles in the Indian population: An association of neurodevelopmental genes in case-control and familial samples. Jajodia A, et al. Schizophr Res, 2015 Mar. PMID 25579050

    See all (155) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. STT3A-mediated viral N-glycosylation underlies the tumor selectivity of oncolytic virus M1.
      Title: STT3A-mediated viral N-glycosylation underlies the tumor selectivity of oncolytic virus M1.
    2. Proteome and Glycoproteome Analyses Reveal the Protein N-Linked Glycosylation Specificity of STT3A and STT3B.
      Title: Proteome and Glycoproteome Analyses Reveal the Protein N-Linked Glycosylation Specificity of STT3A and STT3B.
    3. Active site variants in STT3A cause a dominant type I congenital disorder of glycosylation with neuromusculoskeletal findings.
      Title: Active site variants in STT3A cause a dominant type I congenital disorder of glycosylation with neuromusculoskeletal findings.
    4. Analysis of site occupancy data disclosed several new classes of STT3A-dependent acceptor sites including those with suboptimal flanking sequences and sites located within cysteine-rich protein domains.
      Title: Quantitative glycoproteomics reveals new classes of STT3A- and STT3B-dependent N-glycosylation sites.
    5. Study reports that STT3B-oligosaccharyltransferase, but not STT3A-oligosaccharyltransferase, is a lipid-linked oligosaccharide hydrolase.
      Title: Mammalian STT3A/B oligosaccharyltransferases segregate N-glycosylation at the translocon from lipid-linked oligosaccharide hydrolysis.
    6. DC2 and KCP2 mediate the interaction between the oligosaccharyltransferase STT3A and the endoplasmic reticulum translocon.
      Title: DC2 and KCP2 mediate the interaction between the oligosaccharyltransferase and the ER translocon.
    7. This study showed that Congenital Disorder of Glycosylation Caused by Mutations in STT3A.
      Title: Phenotypic Heterogeneity in a Congenital Disorder of Glycosylation Caused by Mutations in STT3A.
    8. Consensus sites containing large hydrophobic and negatively charged middle residues are frequently skipped by STT3A during protein translation.
      Title: The middle X residue influences cotranslational N-glycosylation consensus site skipping.
    9. Results show homozygous mutation in STT3A and in STT3B causes congenital disorders of glycosylation.
      Title: Mutations in STT3A and STT3B cause two congenital disorders of glycosylation.
    10. DDIT3, STT3A, ARG2 and FAM129A immunohistochemistry does not appear to be useful in the diagnosis of thyroid follicular neoplasias, as they do not reliably distinguish follicular thyroid carcinoma from follicular thyroid adenoma.
      Title: The new molecular markers DDIT3, STT3A, ARG2 and FAM129A are not useful in diagnosing thyroid follicular tumors.
    Submit: New GeneRIF Correction See all GeneRIFs (12)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Congenital disorder of glycosylation, type Iw, autosomal dominant
    MedGen: C5562068 OMIM: 619714 GeneReviews: Not available
    		Compare labs
    STT3A-congenital disorder of glycosylation
    MedGen: C5561935 OMIM: 615596 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Genome-wide association study identifies five new schizophrenia loci.
    EBI GWAS Catalog
    Identification of risk loci with shared effects on five major psychiatric disorders: a genome-wide analysis.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of STT3, subunit of the oligosaccharyltransferase complex, homolog A (STT3A) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC9042, FLJ27038

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables dolichyl-diphosphooligosaccharide-protein glycotransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables dolichyl-diphosphooligosaccharide-protein glycotransferase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables dolichyl-diphosphooligosaccharide-protein glycotransferase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in co-translational protein modification IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in post-translational protein modification IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein N-linked glycosylation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein N-linked glycosylation NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in protein N-linked glycosylation via asparagine IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein N-linked glycosylation via asparagine IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein N-linked glycosylation via asparagine ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in endoplasmic reticulum membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in membrane HDA PubMed 
    part_of oligosaccharyltransferase complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of oligosaccharyltransferase complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    part_of oligosaccharyltransferase complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    part_of oligosaccharyltransferase complex TAS
    Traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A
    Names
    B5
    STT3, subunit of the oligosaccharyltransferase complex, homolog A
    STT3A, catalytic subunit of the oligosaccharyltransferase complex
    STT3A, subunit of the oligosaccharyltransferase complex (catalytic)
    dolichyl-diphosphooligosaccharide protein glycotransferase
    integral membrane protein 1
    integral transmembrane protein 1
    oligosaccharyl transferase subunit STT3A
    transmembrane conserved
    transmembrane protein TMC
    NP_001265432.1
    NP_001265433.1
    NP_689926.1
    XP_011541109.1
    XP_047282851.1
    XP_047282852.1
    XP_047282853.1
    XP_047282854.1
    XP_054224667.1
    XP_054224668.1
    XP_054224669.1
    XP_054224670.1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_042806.1 RefSeqGene

      Range
      5058..35297
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001278503.2 → NP_001265432.1  dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A isoform a

      See identical proteins and their annotated locations for NP_001265432.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a). Variants 1 and 2 both encode the same isoform (a).
      Source sequence(s)
      AP001132, AP001494, BC020965, BE503634, BM667548, BX649102, DA577274
      Consensus CDS
      CCDS8458.1
      UniProtKB/Swiss-Prot
      B4DJ24, E9PNQ1, P46977, Q86XU9, Q8TE35, Q8WUB4
      Related
      ENSP00000436962.1, ENST00000529196.5
      Conserved Domains (1) summary
      pfam02516
      Location:17 → 484
      STT3; Oligosaccharyl transferase STT3 subunit

    2. NM_001278504.2 → NP_001265433.1  dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A isoform b

      See identical proteins and their annotated locations for NP_001265433.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and lacks the exon containing the translation start codon compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (b) with a shorter N-terminus, compared to isoform a.
      Source sequence(s)
      AK295892, AP001132, BC020965, BE503634, BM667548, DA577274
      Consensus CDS
      CCDS60998.1
      Related
      ENSP00000432820.1, ENST00000531491.5
      Conserved Domains (1) summary
      pfam02516
      Location:1 → 392
      STT3; Oligosaccharyl transferase STT3 subunit

    3. NM_152713.5 → NP_689926.1  dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A isoform a

      See identical proteins and their annotated locations for NP_689926.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same isoform (a).
      Source sequence(s)
      AP001132, BC020965, BE503634, BM667548, DA577274
      Consensus CDS
      CCDS8458.1
      UniProtKB/Swiss-Prot
      B4DJ24, E9PNQ1, P46977, Q86XU9, Q8TE35, Q8WUB4
      Related
      ENSP00000376472.3, ENST00000392708.9
      Conserved Domains (1) summary
      pfam02516
      Location:17 → 484
      STT3; Oligosaccharyl transferase STT3 subunit

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      125591769..125623091
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047426897.1 → XP_047282853.1  dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A isoform X1

      UniProtKB/Swiss-Prot
      B4DJ24, E9PNQ1, P46977, Q86XU9, Q8TE35, Q8WUB4

    2. XM_047426895.1 → XP_047282851.1  dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A isoform X1

      UniProtKB/Swiss-Prot
      B4DJ24, E9PNQ1, P46977, Q86XU9, Q8TE35, Q8WUB4

    3. XM_047426896.1 → XP_047282852.1  dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A isoform X1

      UniProtKB/Swiss-Prot
      B4DJ24, E9PNQ1, P46977, Q86XU9, Q8TE35, Q8WUB4

    4. XM_011542807.4 → XP_011541109.1  dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A isoform X1

      See identical proteins and their annotated locations for XP_011541109.1

      UniProtKB/Swiss-Prot
      B4DJ24, E9PNQ1, P46977, Q86XU9, Q8TE35, Q8WUB4
      Conserved Domains (1) summary
      pfam02516
      Location:17 → 484
      STT3; Oligosaccharyl transferase STT3 subunit

    5. XM_047426898.1 → XP_047282854.1  dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A isoform X2

      Related
      ENST00000534472.5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      125621493..125651713
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054368692.1 → XP_054224667.1  dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A isoform X1

      UniProtKB/Swiss-Prot
      B4DJ24, E9PNQ1, P46977, Q86XU9, Q8TE35, Q8WUB4

    2. XM_054368694.1 → XP_054224669.1  dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A isoform X1

      UniProtKB/Swiss-Prot
      B4DJ24, E9PNQ1, P46977, Q86XU9, Q8TE35, Q8WUB4

    3. XM_054368693.1 → XP_054224668.1  dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A isoform X1

      UniProtKB/Swiss-Prot
      B4DJ24, E9PNQ1, P46977, Q86XU9, Q8TE35, Q8WUB4

    4. XM_054368695.1 → XP_054224670.1  dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P46977.2 GenPept UniProtKB/Swiss-Prot:P46977

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