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    GCNT1 glucosaminyl (N-acetyl) transferase 1 [ Homo sapiens (human) ]

    Gene ID: 2650, updated on 27-Nov-2024

    Summary

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    Official Symbol
    GCNT1provided by HGNC
    Official Full Name
    glucosaminyl (N-acetyl) transferase 1provided by HGNC
    Primary source
    HGNC:HGNC:4203
    See related
    Ensembl:ENSG00000187210 MIM:600391; AllianceGenome:HGNC:4203
    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
    G6NT; C2GNT; C2GNT1; NACGT2; NAGCT2; C2GNT-L; C2GlcNAcT
    Summary
    This gene is a member of the beta-1,6-N-acetylglucosaminyltransferase gene family. It is essential to the formation of Gal beta 1-3(GlcNAc beta 1-6)GalNAc structures and the core 2 O-glycan branch. The gene coding this enzyme was originally mapped to 9q21, but was later localized to 9q13. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Jul 2008]
    Expression
    Biased expression in duodenum (RPKM 20.0), stomach (RPKM 13.9) and 13 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See GCNT1 in Genome Data Viewer
    Location:
    9q21.13
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (76393869..76507416)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (88550440..88663979)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (79008785..79122332)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene proprotein convertase subtilisin/kexin type 5 Neighboring gene uncharacterized LOC124902183 Neighboring gene RNA binding motif protein 22 pseudogene 5 Neighboring gene Sharpr-MPRA regulatory region 15008 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:78992236-78992496 Neighboring gene Sharpr-MPRA regulatory region 15545 Neighboring gene Sharpr-MPRA regulatory region 10 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28471 Neighboring gene Sharpr-MPRA regulatory region 2310 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28472 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:79032201-79032782 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28473 Neighboring gene ribosomal protein SA pseudogene 9 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19960 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28474 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19961 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19962 Neighboring gene riboflavin kinase Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr9:79085403-79086064 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28476 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28477 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28478 Neighboring gene H3 histone pseudogene 32 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:79126066-79126566 Neighboring gene uncharacterized LOC124902184 Neighboring gene peptidylprolyl isomerase A pseudogene 87

    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. Expression cloning of a cDNA encoding UDP-GlcNAc:Gal beta 1-3-GalNAc-R (GlcNAc to GalNAc) beta 1-6GlcNAc transferase by gene transfer into CHO cells expressing polyoma large tumor antigen. Bierhuizen MF, et al. Proc Natl Acad Sci U S A, 1992 Oct 1. PMID 1329093, Free PMC Article
    2. The high affinity selectin glycan ligand C2-O-sLex and mRNA transcripts of the core 2 beta-1,6-N-acetylglucosaminyltransferase (C2GnT1) gene are highly expressed in human colorectal adenocarcinomas. St Hill CA, et al. BMC Cancer, 2009 Mar 6. PMID 19267921, Free PMC Article
    3. The role of GCNT1 mediated O-glycosylation in aggressive prostate cancer. Hodgson K, et al. Sci Rep, 2023 Oct 9. PMID 37813880, Free PMC Article
    4. Core 2 N-acetylglucosaminyltransferase-1 expression induces aggressive potential of testicular germ cell tumor. Hatakeyama S, et al. Int J Cancer, 2010 Sep 1. PMID 20017138, Free PMC Article
    5. Haploinsufficiency of C2GnT-I glycosyltransferase renders T lymphoma cells resistant to cell death. Cabrera PV, et al. Blood, 2006 Oct 1. PMID 16778138, Free PMC Article

    See all (48) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The role of GCNT1 mediated O-glycosylation in aggressive prostate cancer.
      Title: The role of GCNT1 mediated O-glycosylation in aggressive prostate cancer.
    2. GCNT1 expression in prostate biopsy specimen is a significant and independent predictor of recurrence after radical prostatectomy, which can be used in pre-treatment decision making for the patient.
      Title: Core 2 β-1, 6-N-acetylglucosaminyltransferase-1 expression in prostate biopsy specimen is an indicator of prostate cancer aggressiveness.
    3. GCNT1 expression in prostate cancer positively correlates with cancer progression and prostate-specific antigen recurrence.
      Title: Detection of Core2 β-1,6-N-Acetylglucosaminyltransferase in Post-Digital Rectal Examination Urine Is a Reliable Indicator for Extracapsular Extension of Prostate Cancer.
    4. Results show that ST3Gal1 uses GM130-GRASP65 and giantin, whereas C2GnT-L uses only giantin for Golgi targeting and defective giantin dimerization in PC-3 and DU145 prostate cancer cells causes fragmentation of the Golgi and prevents its targeting.
      Title: Restoration of compact Golgi morphology in advanced prostate cancer enhances susceptibility to galectin-1-induced apoptosis by modifying mucin O-glycan synthesis.
    5. NMIIA is the master regulator of Golgi fragmentation induced by heat shock or inhibition/depletion of HSP70/90 through interaction with gylosyltransferases.
      Title: Golgi fragmentation induced by heat shock or inhibition of heat shock proteins is mediated by non-muscle myosin IIA via its interaction with glycosyltransferases.
    6. GCNT1 is over-expressed in prostate cancer and is associated with higher levels of core 2 O-sLe(x) in PSA, PAP and MUC1 proteins.
      Title: Increased expression of GCNT1 is associated with altered O-glycosylation of PSA, PAP, and MUC1 in human prostate cancers.
    7. Immunohistochemical expression of core 2 beta1,6-N-acetylglucosaminyl transferase 1 (C2GnT1) in endometrioid-type endometrial carcinoma may be a novel potential prognostic factor.
      Title: Immunohistochemical expression of core 2 β1,6-N-acetylglucosaminyl transferase 1 (C2GnT1) in endometrioid-type endometrial carcinoma: a novel potential prognostic factor.
    8. C2GnT-expressing prostate cancer cells evade NK cell immunity and survive longer in the host blood circulation, thereby resulting in the promotion of prostate cancer metastasis.
      Title: Core2 O-glycan-expressing prostate cancer cells are resistant to NK cell immunity.
    9. GOLPH3 can regulate cell-cell interaction by controlling Golgi retention of C2GnT1.
      Title: Golgi phosphoprotein 3 determines cell binding properties under dynamic flow by controlling Golgi localization of core 2 N-acetylglucosaminyltransferase 1.
    10. Down-regulation of C2GnT1 is correlated with breast cancer
      Title: MUC1 in human and murine mammary carcinoma cells decreases the expression of core 2 β1,6-N-acetylglucosaminyltransferase and β-galactoside α2,3-sialyltransferase.
    Submit: New GeneRIF Correction See all GeneRIFs (31)

    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

    EBI GWAS Catalog

    Description
    Genome-wide association scan for survival on dialysis in African-Americans with type 2 diabetes.
    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)

    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

    • MGC126335, MGC126336

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity TAS
    Traceable Author Statement
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in O-glycan processing TAS
    Traceable Author Statement
    more info
    		  
    involved_in cell adhesion molecule production IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in core 2 O-glycan biosynthetic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in glycoprotein biosynthetic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in kidney morphogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in leukocyte tethering or rolling IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of leukocyte tethering or rolling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in response to insulin IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in tissue morphogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi cisterna IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in Golgi membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in extracellular space IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in membrane TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in trans-Golgi network IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase
    Names
    beta-1,6-N-acetylglucosaminyltransferase
    core 2 GnT
    core 2 beta-1,6-N-acetylglucosaminyltransferase I
    core 2 beta1,6 N-acetylglucosaminyltransferase-I
    core 2 branching enzyme
    core2-GlcNAc-transferase
    glucosaminyl (N-acetyl) transferase 1, core 2 (beta-1,6-N-acetylglucosaminyltransferase)
    leukocyte type core 2 beta-1,6-N-acetylglucosaminyltransferase
    NP_001091102.1
    NP_001091103.1
    NP_001091104.1
    NP_001091105.1
    NP_001394110.1
    NP_001394111.1
    NP_001394112.1
    NP_001394113.1
    NP_001481.2
    XP_047279183.1
    XP_047279184.1
    XP_047279185.1
    XP_054218707.1
    XP_054218708.1
    XP_054218709.1

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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.

    mRNA and Protein(s)

    1. NM_001097633.2 → NP_001091102.1  beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase

      See identical proteins and their annotated locations for NP_001091102.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1, and uses the P2 promoter.
      Source sequence(s)
      AI445628, AL161626, AL832647, BC109101, DA479942
      Consensus CDS
      CCDS6653.1
      UniProtKB/Swiss-Prot
      Q02742, Q6DJZ4
      UniProtKB/TrEMBL
      Q86T81
      Related
      ENSP00000390703.2, ENST00000444201.6
      Conserved Domains (1) summary
      pfam02485
      Location:123 → 391
      Branch; Core-2/I-Branching enzyme

    2. NM_001097634.1 → NP_001091103.1  beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase

      See identical proteins and their annotated locations for NP_001091103.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript, and uses the P1 promoter.
      Source sequence(s)
      AI445628, AL161626, AL832647, AY196293, BC109101
      Consensus CDS
      CCDS6653.1
      UniProtKB/Swiss-Prot
      Q02742, Q6DJZ4
      UniProtKB/TrEMBL
      Q86T81
      Related
      ENSP00000415454.1, ENST00000442371.5
      Conserved Domains (1) summary
      pfam02485
      Location:123 → 391
      Branch; Core-2/I-Branching enzyme

    3. NM_001097635.2 → NP_001091104.1  beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase

      See identical proteins and their annotated locations for NP_001091104.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 1, and uses the P3 promoter.
      Source sequence(s)
      AI445628, AL161626, AL832647, AY196296, BC109101
      Consensus CDS
      CCDS6653.1
      UniProtKB/Swiss-Prot
      Q02742, Q6DJZ4
      UniProtKB/TrEMBL
      Q86T81
      Conserved Domains (1) summary
      pfam02485
      Location:123 → 391
      Branch; Core-2/I-Branching enzyme

    4. NM_001097636.2 → NP_001091105.1  beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase

      See identical proteins and their annotated locations for NP_001091105.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR compared to variant 1, and uses the P4 promoter.
      Source sequence(s)
      AI445628, AL161626, AL832647, AY196297, BC109101
      Consensus CDS
      CCDS6653.1
      UniProtKB/Swiss-Prot
      Q02742, Q6DJZ4
      UniProtKB/TrEMBL
      Q86T81
      Conserved Domains (1) summary
      pfam02485
      Location:123 → 391
      Branch; Core-2/I-Branching enzyme

    5. NM_001407181.1 → NP_001394110.1  beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase

      Status: REVIEWED

      Source sequence(s)
      AL161626, AL391868, AL590664
      UniProtKB/Swiss-Prot
      Q02742, Q6DJZ4

    6. NM_001407182.1 → NP_001394111.1  beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase

      Status: REVIEWED

      Source sequence(s)
      AL161626, AL391868
      UniProtKB/Swiss-Prot
      Q02742, Q6DJZ4

    7. NM_001407183.1 → NP_001394112.1  beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase

      Status: REVIEWED

      Source sequence(s)
      AL161626, AL391868
      UniProtKB/Swiss-Prot
      Q02742, Q6DJZ4

    8. NM_001407184.1 → NP_001394113.1  beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase

      Status: REVIEWED

      Source sequence(s)
      AL161626, AL391868
      UniProtKB/Swiss-Prot
      Q02742, Q6DJZ4

    9. NM_001490.5 → NP_001481.2  beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase

      See identical proteins and their annotated locations for NP_001481.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1, and uses the P2 promoter.
      Source sequence(s)
      AI445628, AL161626, AL832647, BC109101, BP359964
      Consensus CDS
      CCDS6653.1
      UniProtKB/Swiss-Prot
      Q02742, Q6DJZ4
      UniProtKB/TrEMBL
      Q86T81
      Related
      ENSP00000365920.4, ENST00000376730.5
      Conserved Domains (1) summary
      pfam02485
      Location:123 → 391
      Branch; Core-2/I-Branching enzyme

    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_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      76393869..76507416
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047423227.1 → XP_047279183.1  beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase isoform X1

      UniProtKB/Swiss-Prot
      Q02742, Q6DJZ4

    2. XM_047423228.1 → XP_047279184.1  beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase isoform X1

      UniProtKB/Swiss-Prot
      Q02742, Q6DJZ4

    3. XM_047423229.1 → XP_047279185.1  beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase isoform X1

      UniProtKB/Swiss-Prot
      Q02742, Q6DJZ4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      88550440..88663979
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054362732.1 → XP_054218707.1  beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase isoform X1

      UniProtKB/Swiss-Prot
      Q02742, Q6DJZ4

    2. XM_054362733.1 → XP_054218708.1  beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase isoform X1

      UniProtKB/Swiss-Prot
      Q02742, Q6DJZ4

    3. XM_054362734.1 → XP_054218709.1  beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase isoform X1

      UniProtKB/Swiss-Prot
      Q02742, Q6DJZ4
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q02742.2 GenPept UniProtKB/Swiss-Prot:Q02742

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