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

Gene ID: 2650, updated on 28-Oct-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
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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 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)

Genotypes

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 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 O-glycan processing, core 2 IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in cell adhesion molecule production IMP
Inferred from Mutant Phenotype
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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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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