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. ... See more...

Aliases for GCNT1 Gene

Aliases for GCNT1 Gene

  • Glucosaminyl (N-Acetyl) Transferase 1 2 3 5
  • Glucosaminyl (N-Acetyl) Transferase 1, Core 2 (Beta-1,6-N-Acetylglucosaminyltransferase) 2 3
  • Beta-1,3-Galactosyl-O-Glycosyl-Glycoprotein Beta-1,6-N-Acetylglucosaminyltransferase 3 4
  • Core 2 Beta1,6 N-Acetylglucosaminyltransferase-I 2 3
  • Core2-GlcNAc-Transferase 3 4
  • NACGT2 3 4
  • C2GNT 3 4
  • Beta-1,3-Galactosyl-O-Glycosyl-Glycoprotein Beta-1,6-N--Acetylglucosaminyltransferase 2
  • Core 2 Beta-1,6-N-Acetylglucosaminyltransferase I 3
  • Glucosaminyl (N-Acetyl) Transferase 1, Core 2 2
  • Beta-1,6-N-Acetylglucosaminyltransferase 3
  • Core 2 Branching Enzyme 3
  • Core 2-Branching Enzyme 4
  • EC 2.4.1.102 4
  • Core 2 GnT 3
  • Core 2 GNT 4
  • C2GNT-L 3
  • C2GNT1 3
  • NAGCT2 3
  • G6NT 3

External Ids for GCNT1 Gene

Previous HGNC Symbols for GCNT1 Gene

  • NACGT2

Previous GeneCards Identifiers for GCNT1 Gene

  • GC09P070160
  • GC09P070930
  • GC09P072644
  • GC09P074531
  • GC09P076303
  • GC09P078263
  • GC09P079035
  • GC09P048885
  • GC09P079036

Summaries for GCNT1 Gene

Entrez Gene Summary for GCNT1 Gene

  • 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]

GeneCards Summary for GCNT1 Gene

GCNT1 (Glucosaminyl (N-Acetyl) Transferase 1) is a Protein Coding gene. Among its related pathways are Metabolism of proteins and Globo Sphingolipid Metabolism. Gene Ontology (GO) annotations related to this gene include acetylglucosaminyltransferase activity and beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity. An important paralog of this gene is GCNT3.

UniProtKB/Swiss-Prot Summary for GCNT1 Gene

  • Glycosyltransferase that catalyzes the transfer of an N-acetylglucosamine moiety onto mucin-type core 1 O-glycan to form the branched mucin-type core 2 O-glycan. Mucin-type core 2 O-glycans play an important role in leukocyte extravasation as they serve as scaffolds for the display of the selectin ligand sialyl Lewis X by leukocytes.

Gene Wiki entry for GCNT1 Gene

Additional gene information for GCNT1 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for GCNT1 Gene

Genomics for GCNT1 Gene

GeneHancer (GH) Regulatory Elements for GCNT1 Gene

Promoters and enhancers for GCNT1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH09J076458 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE CraniofacialAtlas 506.5 +40.8 40758 4.1 CTCF NRF1 ZIC2 POLR2A ZBTB10 ZNF423 ZBTB26 KLF4 KLF7 TGIF2 GCNT1 piR-33804-154 RFK piR-54987-147
GH09J076419 Enhancer 0.5 Ensembl 500.7 +0.1 107 0.3 CTCF TRIM22 TCF12 RAD21 GATA3 ELF3 ZNF143 SMC3 ENSG00000233814 GCNT1 lnc-PCSK5-2 piR-47675-120
GH09J076607 Promoter/Enhancer 1.4 Ensembl ENCODE dbSUPER 15.2 +194.7 194672 14.6 ZNF623 MYC ATF2 MYNN MAFF CEBPG MAX CEBPB POLR2A ZBTB11 lnc-RFK-5 GCNT1 PRUNE2 LOC105376095
GH09J076392 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas 8.3 -25.7 -25655 4 EP300 FOXK2 ZBTB40 CTCF SIN3A NRF1 POLR2G USF1 SP1 PHF8 RFK lnc-GCNT1-7 lnc-RFK-1 GCNT1 lnc-RFK-2
GH09J076470 Enhancer 1.2 Ensembl ENCODE CraniofacialAtlas 9.2 +54.1 54050 8.2 USF1 SP1 EP300 RELA MEF2C RCOR1 TRIM22 EZH2 OSR2 BCL11A GCNT1 RFK piR-56186-080 piR-39891-084
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around GCNT1 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for GCNT1

Top Transcription factor binding sites by QIAGEN in the GCNT1 gene promoter:
  • AML1a
  • Arnt
  • FOXF2
  • GCNF
  • GCNF-1
  • HOXA5
  • Ik-1
  • Pbx1a
  • RSRFC4

Genomic Locations for GCNT1 Gene

Genomic Locations for GCNT1 Gene
chr9:76,419,850-76,651,203
(GRCh38/hg38)
Size:
231,354 bases
Orientation:
Plus strand
chr9:79,034,752-79,122,332
(GRCh37/hg19)
Size:
87,581 bases
Orientation:
Plus strand

Genomic View for GCNT1 Gene

Genes around GCNT1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
GCNT1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for GCNT1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for GCNT1 Gene

Proteins for GCNT1 Gene

  • Protein details for GCNT1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q02742-GCNT1_HUMAN
    Recommended name:
    Beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase
    Protein Accession:
    Q02742
    Secondary Accessions:
    • Q6DJZ4

    Protein attributes for GCNT1 Gene

    Size:
    428 amino acids
    Molecular mass:
    49799 Da
    Quaternary structure:
    • Interacts with GOLPH3; may control GCNT1 retention in the Golgi.

neXtProt entry for GCNT1 Gene

Post-translational modifications for GCNT1 Gene

  • Glycosylation at Asn58 and Asn95
  • Modification sites at PhosphoSitePlus

Other Protein References for GCNT1 Gene

No data available for DME Specific Peptides for GCNT1 Gene

Domains & Families for GCNT1 Gene

Gene Families for GCNT1 Gene

Protein Domains for GCNT1 Gene

Blocks:
  • Glycosyl transferase, family 14
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for GCNT1 Gene

GenScript: Design optimal peptide antigens:
  • Core2-GlcNAc-transferase (GCNT1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q02742

UniProtKB/Swiss-Prot:

GCNT1_HUMAN :
  • Belongs to the glycosyltransferase 14 family.
Family:
  • Belongs to the glycosyltransferase 14 family.
genes like me logo Genes that share domains with GCNT1: view

Function for GCNT1 Gene

Molecular function for GCNT1 Gene

UniProtKB/Swiss-Prot Function:
Glycosyltransferase that catalyzes the transfer of an N-acetylglucosamine moiety onto mucin-type core 1 O-glycan to form the branched mucin-type core 2 O-glycan. Mucin-type core 2 O-glycans play an important role in leukocyte extravasation as they serve as scaffolds for the display of the selectin ligand sialyl Lewis X by leukocytes.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=O(3)-[beta-D-galactosyl-(1->3)-N-acetyl-alpha-D-galactosaminyl]-L-seryl-[protein] + UDP-N-acetyl-alpha-D-glucosamine = 3-O-{beta-D-galactosyl-(1->3)-[N-acetyl-beta-D-glucosaminyl-(1->6)]-N-acetyl-alpha-D-galactosaminyl}-L-seryl-[protein] + H(+) + UDP; Xref=Rhea:RHEA:56212, Rhea:RHEA-COMP:13922, Rhea:RHEA-COMP:14419, ChEBI:CHEBI:15378, ChEBI:CHEBI:57705, ChEBI:CHEBI:58223, ChEBI:CHEBI:137949, ChEBI:CHEBI:139605; EC=2.4.1.102;.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=O(3)-[beta-D-galactosyl-(1->3)-N-acetyl-alpha-D-galactosaminyl]-L-threonyl-[protein] + UDP-N-acetyl-alpha-D-glucosamine = 3-O-{beta-D-galactosyl-(1->3)-[N-acetyl-beta-D-glucosaminyl-(1->6)]-N-acetyl-alpha-D-galactosaminyl}-L-threonyl-[protein] + H(+) + UDP; Xref=Rhea:RHEA:56216, Rhea:RHEA-COMP:13923, Rhea:RHEA-COMP:14420, ChEBI:CHEBI:15378, ChEBI:CHEBI:57705, ChEBI:CHEBI:58223, ChEBI:CHEBI:137950, ChEBI:CHEBI:139607; EC=2.4.1.102;.
GENATLAS Biochemistry:
beta-1,6-N-acetyl-glucosaminyl transferase 1,leukocyte type core 2 branching enzyme in O-glycans,widely expressed,including lymph node and bone marrow

Enzyme Numbers (IUBMB) for GCNT1 Gene

Phenotypes From GWAS Catalog for GCNT1 Gene

Gene Ontology (GO) - Molecular Function for GCNT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003829 beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity TAS,IEA --
GO:0005515 protein binding IPI 23027862
GO:0008375 acetylglucosaminyltransferase activity IEA --
GO:0016740 transferase activity IEA --
GO:0016757 transferase activity, transferring glycosyl groups IEA --
genes like me logo Genes that share ontologies with GCNT1: view
genes like me logo Genes that share phenotypes with GCNT1: view

Animal Models for GCNT1 Gene

MGI Knock Outs for GCNT1:

Animal Model Products

  • Taconic Biosciences Mouse Models for GCNT1

CRISPR Products

Clone Products

  • Addgene plasmids for GCNT1

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for GCNT1 Gene

Localization for GCNT1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for GCNT1 Gene

Golgi apparatus membrane; Single-pass type II membrane protein. Note=Also detected in the trans-Golgi network.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for GCNT1 gene
Compartment Confidence
golgi apparatus 5
plasma membrane 3
extracellular 3
endoplasmic reticulum 2
cytoskeleton 1
mitochondrion 1
nucleus 1
endosome 1
cytosol 1
lysosome 1
peroxisome 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear speckles (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for GCNT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane TAS --
GO:0005615 extracellular space IEA --
GO:0005794 Golgi apparatus IEA --
GO:0005802 trans-Golgi network IDA 23027862
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with GCNT1: view

Pathways & Interactions for GCNT1 Gene

genes like me logo Genes that share pathways with GCNT1: view

Pathways by source for GCNT1 Gene

2 KEGG pathways for GCNT1 Gene
1 GeneGo (Thomson Reuters) pathway for GCNT1 Gene
  • Immune response_IL-12 signaling pathway

UniProtKB/Swiss-Prot Q02742-GCNT1_HUMAN

  • Pathway: Protein modification; protein glycosylation.

Gene Ontology (GO) - Biological Process for GCNT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006486 protein glycosylation IEA --
GO:0009101 glycoprotein biosynthetic process IMP 23027862
GO:0016266 O-glycan processing TAS --
GO:0032868 response to insulin IEA --
GO:0048729 tissue morphogenesis IEA --
genes like me logo Genes that share ontologies with GCNT1: view

No data available for SIGNOR curated interactions for GCNT1 Gene

Drugs & Compounds for GCNT1 Gene

(2) Drugs for GCNT1 Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Uridine 5'-diphosphate Experimental Pharma 0

(5) Additional Compounds for GCNT1 Gene - From: HMDB and Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Uridine diphosphate-N-acetylglucosamine
  • (2R,3R,4R,5S,6R)-3-(acetylamino)-4,5-Dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)
  • UDP-GlcNAc
  • UDP-N-Acetyl-D-glucosamine
  • UDP-N-Acetylglucosamine
  • URIDINE-diphosphATE-N-acetylglucosamine
528-04-1
genes like me logo Genes that share compounds with GCNT1: view

Transcripts for GCNT1 Gene

mRNA/cDNA for GCNT1 Gene

5 REFSEQ mRNAs :
16 NCBI additional mRNA sequence :
6 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

  • Addgene plasmids for GCNT1

Alternative Splicing Database (ASD) splice patterns (SP) for GCNT1 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7a · 7b · 7c · 7d · 7e
SP1: - - - -
SP2: - - - -
SP3: -
SP4: - - - - -
SP5:
SP6:

Relevant External Links for GCNT1 Gene

GeneLoc Exon Structure for
GCNT1

Expression for GCNT1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for GCNT1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for GCNT1 Gene

This gene is overexpressed in Stomach (x4.3).

Protein differential expression in normal tissues from HIPED for GCNT1 Gene

This gene is overexpressed in Stomach (64.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for GCNT1 Gene



Protein tissue co-expression partners for GCNT1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for GCNT1

SOURCE GeneReport for Unigene cluster for GCNT1 Gene:

Hs.521568

mRNA Expression by UniProt/SwissProt for GCNT1 Gene:

Q02742-GCNT1_HUMAN
Tissue specificity: Highly expressed in activated T-lymphocytes and myeloid cells.

Evidence on tissue expression from TISSUES for GCNT1 Gene

  • Lung(4.3)
  • Stomach(2)
genes like me logo Genes that share expression patterns with GCNT1: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for GCNT1 Gene

Orthologs for GCNT1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for GCNT1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia GCNT1 31 30
  • 98.99 (n)
OneToOne
dog
(Canis familiaris)
Mammalia GCNT1 31 30
  • 85.57 (n)
OneToOne
cow
(Bos Taurus)
Mammalia GCNT1 31 30
  • 84.27 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Gcnt1 30
  • 83.85 (n)
mouse
(Mus musculus)
Mammalia Gcnt1 17 31 30
  • 83.49 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia GCNT1 31
  • 72 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia GCNT1 31
  • 72 (a)
OneToOne
chicken
(Gallus gallus)
Aves GCNT1 31 30
  • 71.85 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia GCNT1 31
  • 70 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia gcnt1 30
  • 67.41 (n)
African clawed frog
(Xenopus laevis)
Amphibia gcnt1-prov 30
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 45 (a)
OneToMany
Species where no ortholog for GCNT1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for GCNT1 Gene

ENSEMBL:
Gene Tree for GCNT1 (if available)
TreeFam:
Gene Tree for GCNT1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for GCNT1: view image

Paralogs for GCNT1 Gene

Paralogs for GCNT1 Gene

(8) SIMAP similar genes for GCNT1 Gene using alignment to 2 proteins:

  • GCNT1_HUMAN
  • L8E8T5_HUMAN
genes like me logo Genes that share paralogs with GCNT1: view

Variants for GCNT1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for GCNT1 Gene

SNP ID Clinical significance and condition Chr 09 pos Variation AA Info Type
733713 Benign: not provided 76,503,084(+) T/C SYNONYMOUS_VARIANT
rs11546569 - p.Ser158Cys
rs2282683 - p.Ile152Val

Additional dbSNP identifiers (rs#s) for GCNT1 Gene

Structural Variations from Database of Genomic Variants (DGV) for GCNT1 Gene

Variant ID Type Subtype PubMed ID
esv2304624 CNV deletion 18987734
esv2738598 CNV deletion 23290073
nsv1132207 CNV deletion 24896259
nsv437089 CNV loss 16327808
nsv515152 CNV loss 21397061
nsv520423 CNV loss 19592680

Variation tolerance for GCNT1 Gene

Residual Variation Intolerance Score: 22.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.10; 80.50% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for GCNT1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
GCNT1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for GCNT1 Gene

Disorders for GCNT1 Gene

Additional Disease Information for GCNT1

No disorders were found for GCNT1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for GCNT1 Gene

Publications for GCNT1 Gene

  1. Molecular cloning and expression of a novel beta-1, 6-N-acetylglucosaminyltransferase that forms core 2, core 4, and I branches. (PMID: 9915862) Yeh JC … Fukuda M (The Journal of biological chemistry 1999) 2 3 23 54
  2. Genomic organization of core 2 and I branching beta-1,6-N-acetylglucosaminyltransferases. Implication for evolution of the beta-1,6-N-acetylglucosaminyltransferase gene family. (PMID: 7579796) Bierhuizen MF … Fukuda M (Glycobiology 1995) 3 4 23 54
  3. Golgi phosphoprotein 3 determines cell binding properties under dynamic flow by controlling Golgi localization of core 2 N-acetylglucosaminyltransferase 1. (PMID: 23027862) Ali MF … Cheng PW (The Journal of biological chemistry 2012) 3 4 54
  4. Site directed processing: role of amino acid sequences and glycosylation of acceptor glycopeptides in the assembly of extended mucin type O-glycan core 2. (PMID: 19524017) Brockhausen I … Paulsen H (Biochimica et biophysica acta 2009) 3 23 54
  5. 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. (PMID: 19267921) St Hill CA … Walcheck B (BMC cancer 2009) 3 23 54

Products for GCNT1 Gene

Sources for GCNT1 Gene