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B3GNT6 (UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 6 (core 3 synthase))

Written2009-05Neeru M Sharma, Prakash Radhakrishnan, Shuhua Tan, Pi-Wan Cheng
Department of Biochemistry, Molecular Biology, College of Medicine, University of Nebraska Medical Center, 985870 Nebraska Medical Center, Omaha, NE 68198-5870, USA

(Note : for Links provided by Atlas : click)


Other namesB3Gn-T6
Core 3 synthase
HGNC (Hugo) B3GNT6
LocusID (NCBI) 192134
Atlas_Id 44427
Location 11q13.5  [Link to chromosome band 11q13]
Location_base_pair Starts at 76745385 and ends at 76753005 bp from pter ( according to hg19-Feb_2009)  [Mapping B3GNT6.png]
Local_order -NA-
Note B3GNT6 is a single-pass type II membrane protein belonging to the glycosyltransferase 31 family.


Note Human B3GNT6 is located on chromosome 11 in the region of q13.4.
  The schematic representation of human B3GNT6 gene and its transcript (ATG, translation start codon; TGA, translation stop codon; UTR, Untranslated region; ORF, Open reading frame).
Description Human B3GNT6 gene is 7,111 bp in length, composed of 2 exons and 1 intron, and located at chromosome 11q13.4.
Transcription B3GNT6 transcript contains two exons. Exon 1 is 121 bp and exon 2 is 1,917 bp. The exon 2 contains 1,155 bp ORF and 762 bp 3'UTR.
Pseudogene -NA-


Note Human UDP-GlcNAc:GalNAca1-Ser/Thr beta-1,3-N-acetylglucosaminyltransferase 6 (core 3 synthase) has 384 amino acids and 43 KDa molecular weight.
  The predicted B3GNT6 structure contains a short N-terminal cytoplasmic tail (CT) (12 aa), a transmembrane domain (TM) (19 aa), a long stem region and catalytic domain (353 aa) at the C-terminal region.
Description B3GNT6/C3S is single-pass type II membrane protein belonging to the glycosyltransferase 31 family.
Expression B3GNT6/C3S gene expression is restricted to mucus-secretory tissues. The level of beta3GnT6 transcript expressed in various human tissues as measured by the real time PCR revealed that the expression level was highest in the stomach, followed by the colon and small intestine. Skeletal muscle and testis expressed the beta3GnT6 transcript at a moderate level. The expression levels in the remaining tissues were very low or not detectable. Its expression was markedly down-regulated in gastric and colorectal carcinomas, which include both tumor tissues and cell lines-derived from these carcinomas.
Localisation Golgi Membrane.
Function B3GNT6/C3S enzyme catalyzes the transfer of GlcNAc from UDP-GlcNAc to GalNAcalpha1-Ser/Thr (Tn antigen) to form the core 3 structure (GlcNAcbeta1-3GalNAcalpha1-Ser/Thr). Core 3 can be extended by the addition of galactose and then other sugars to generate biologically important epitopes or serves as the precursor for the formation of core 4, which in turn can be further elaborated to form more complex structure. Core 3-containing O-glycans are found in the secreted mucins produced in the mucus-secretory tissues. Loss of core 3 synthase results in the loss of not only core 3 glycans but also core 4 glycans. Loss of core 3 could lead to the production of secreted mucins with compromised mucus protection function. As a result, mucus would be more dehydrated, bacteria would be inefficiently cleared from the system, and chronic inflammation would be developed, which eventually would result in development of cancer. A mouse model devoid of core 3 synthase gene has been shown to develop colon cancer. Because the loss of this gene leads to development of colon cancer, B3GNT6/C3S gene is a tumor suppressor gene.
Homology An alignment of the amino acid sequences of five B3GnTs made using ClustalW showed 41, 54, 42, and 35% sequence identity between B3GnT6 and B3GnT2, B3GnT3, B3GnT4, and B3GnT5, respectively, and this sequence similarity was limited to the putative catalytic domains. Five cysteine residues were conserved among these five B3GnTs. However, only B3GNT6/C3S exhibits significant core 3 synthase activity.

Implicated in

Entity Gastric and Colorectal carcinomas
Note Colorectal cancer, which is also called colon cancer or large bowel cancer, includes cancerous growths in the colon, rectum and appendix. Loss of function of the mucus layer is one major cause of this cancer. Globally, cancer of the colon and rectum is the third leading cause of cancer in males and the fourth leading cause of cancer in females. The frequency of colorectal cancer varies around the world. It is common in the Western world and is rare in Asia and Africa. In countries where the people have adopted western diets, the incidence of colorectal cancer is increasing. Colorectal cancer can take many years to develop and early detection of colorectal cancer greatly improves the chances of a cure. Therefore, screening for the disease is recommended in individuals who are at increased risks. Prevention and early detection are key factors in controlling and curing colorectal cancer. Indeed, colorectal cancer is the second most preventable cancer, after lung cancer.
Prognosis B3GNT6/C3S is down-regulated in gastric and colorectal carcinomas, suggesting that it may be used as a marker for distinguishing between benign adenomas and premalignant lesions.
Oncogenesis O-linked oligosaccharides (O-glycans) are the primary components of the intestinal mucus layer that covers the gastrointestinal epithelium. This layer is a dense, carbohydrate-rich matrix that consists primarily of mucins containing multiple serine and threonine residues, which have been modified by O-glycans and account for 80-90% of the mucin mass. The mucus layer and epithelial cells comprise an intestinal barrier that protects epithelial and intestinal mucosal immune cells from potentially harmful luminal microflora and food components. Among all mucin glycan core structures, Core 3 and core 4 are unique to secreted mucins, which may play important roles in protecting the molecular integrity of these mucins and enable them to perform their functions under extreme harsh conditions, such as gastric and colonic environment. Loss of these functions resulted from the loss of core 3 synthase is thought to initiate oncogenesis in the gastrointestinal tract.


Increased susceptibility to colitis and colorectal tumors in mice lacking core 3-derived O-glycans.
An G, Wei B, Xia B, McDaniel JM, Ju T, Cummings RD, Braun J, Xia L.
J Exp Med. 2007 Jun 11;204(6):1417-29. Epub 2007 May 21.
PMID 17517967
Mucin-type O-glycans in human colon and breast cancer: glycodynamics and functions.
Brockhausen I.
EMBO Rep. 2006 Jun;7(6):599-604. (REVIEW)
PMID 16741504
Molecular cloning and characterization of a novel UDP-GlcNAc:GalNAc-peptide beta1,3-N-acetylglucosaminyltransferase (beta 3Gn-T6), an enzyme synthesizing the core 3 structure of O-glycans.
Iwai T, Inaba N, Naundorf A, Zhang Y, Gotoh M, Iwasaki H, Kudo T, Togayachi A, Ishizuka Y, Nakanishi H, Narimatsu H.
J Biol Chem. 2002 Apr 12;277(15):12802-9. Epub 2002 Jan 30.
PMID 11821425
Core 3 synthase is down-regulated in colon carcinoma and profoundly suppresses the metastatic potential of carcinoma cells.
Iwai T, Kudo T, Kawamoto R, Kubota T, Togayachi A, Hiruma T, Okada T, Kawamoto T, Morozumi K, Narimatsu H.
Proc Natl Acad Sci U S A. 2005 Mar 22;102(12):4572-7. Epub 2005 Mar 8.
PMID 15755813


This paper should be referenced as such :
Sharma, NM ; Radhakrishnan, P ; Tan, S ; Cheng, PW
B3GNT6 (UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 6 (core 3 synthase))
Atlas Genet Cytogenet Oncol Haematol. 2010;14(4):353-355.
Free journal version : [ pdf ]   [ DOI ]
On line version :

External links

HGNC (Hugo)B3GNT6   24141
Entrez_Gene (NCBI)B3GNT6  192134  UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 6
AliasesB3Gn-T6; BGnT-6; beta-1,3-Gn-T6; beta3Gn-T6
GeneCards (Weizmann)B3GNT6
Ensembl hg19 (Hinxton)ENSG00000198488 [Gene_View]  chr11:76745385-76753005 [Contig_View]  B3GNT6 [Vega]
Ensembl hg38 (Hinxton)ENSG00000198488 [Gene_View]  chr11:76745385-76753005 [Contig_View]  B3GNT6 [Vega]
ICGC DataPortalENSG00000198488
TCGA cBioPortalB3GNT6
AceView (NCBI)B3GNT6
Genatlas (Paris)B3GNT6
SOURCE (Princeton)B3GNT6
Genetics Home Reference (NIH)B3GNT6
Genomic and cartography
GoldenPath hg19 (UCSC)B3GNT6  -     chr11:76745385-76753005 +  11q13.4   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)B3GNT6  -     11q13.4   [Description]    (hg38-Dec_2013)
EnsemblB3GNT6 - 11q13.4 [CytoView hg19]  B3GNT6 - 11q13.4 [CytoView hg38]
Mapping of homologs : NCBIB3GNT6 [Mapview hg19]  B3GNT6 [Mapview hg38]
Gene and transcription
Genbank (Entrez)AB073740 AK127544 AK172863 AK292773 AK313682
RefSeq transcript (Entrez)NM_138706
RefSeq genomic (Entrez)NC_000011 NC_018922 NT_167190 NW_004929380
Consensus coding sequences : CCDS (NCBI)B3GNT6
Cluster EST : UnigeneHs.352622 [ NCBI ]
CGAP (NCI)Hs.352622
Alternative Splicing GalleryENSG00000198488
Gene ExpressionB3GNT6 [ NCBI-GEO ]   B3GNT6 [ EBI - ARRAY_EXPRESS ]   B3GNT6 [ SEEK ]   B3GNT6 [ MEM ]
Gene Expression Viewer (FireBrowse)B3GNT6 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)192134
GTEX Portal (Tissue expression)B3GNT6
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ6ZMB0 (Uniprot)
NextProtQ6ZMB0  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ6ZMB0
Splice isoforms : SwissVarQ6ZMB0 (Swissvar)
Domains : Interpro (EBI)Glyco_trans_31   
Domain families : Pfam (Sanger)Galactosyl_T (PF01762)   
Domain families : Pfam (NCBI)pfam01762   
DMDM Disease mutations192134
Blocks (Seattle)B3GNT6
Human Protein AtlasENSG00000198488
Peptide AtlasQ6ZMB0
IPIIPI00847164   IPI00977839   IPI00977159   
Protein Interaction databases
IntAct (EBI)Q6ZMB0
Ontologies - Pathways
Ontology : AmiGOGolgi membrane  galactosyltransferase activity  UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity  glycoprotein biosynthetic process  membrane  integral component of membrane  O-glycan processing  O-glycan processing, core 3  beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity  acetylgalactosaminyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity  
Ontology : EGO-EBIGolgi membrane  galactosyltransferase activity  UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity  glycoprotein biosynthetic process  membrane  integral component of membrane  O-glycan processing  O-glycan processing, core 3  beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity  acetylgalactosaminyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity  
Pathways : KEGGMucin type O-Glycan biosynthesis   
REACTOMEQ6ZMB0 [protein]
REACTOME PathwaysR-HSA-913709 O-linked glycosylation of mucins [pathway]
NDEx NetworkB3GNT6
Atlas of Cancer Signalling NetworkB3GNT6
Wikipedia pathwaysB3GNT6
Orthology - Evolution
GeneTree (enSembl)ENSG00000198488
Phylogenetic Trees/Animal Genes : TreeFamB3GNT6
Homologs : HomoloGeneB3GNT6
Homology/Alignments : Family Browser (UCSC)B3GNT6
Gene fusions - Rearrangements
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerB3GNT6 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)B3GNT6
Exome Variant ServerB3GNT6
ExAC (Exome Aggregation Consortium)B3GNT6 (select the gene name)
Genetic variants : HAPMAP192134
Genomic Variants (DGV)B3GNT6 [DGVbeta]
DECIPHER (Syndromes)11:76745385-76753005  ENSG00000198488
CONAN: Copy Number AnalysisB3GNT6 
ICGC Data PortalB3GNT6 
TCGA Data PortalB3GNT6 
Broad Tumor PortalB3GNT6
OASIS PortalB3GNT6 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICB3GNT6 
Mutations and Diseases : HGMDB3GNT6
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch B3GNT6
DgiDB (Drug Gene Interaction Database)B3GNT6
DoCM (Curated mutations)B3GNT6 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)B3GNT6 (select a term)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Genetic Testing Registry B3GNT6
NextProtQ6ZMB0 [Medical]
Huge Navigator B3GNT6 [HugePedia]
snp3D : Map Gene to Disease192134
BioCentury BCIQB3GNT6
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD192134
Chemical/Pharm GKB GenePA164741288
Clinical trialB3GNT6
canSAR (ICR)B3GNT6 (select the gene name)
PubMed6 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Mon Oct 10 11:38:42 CEST 2016

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