The protein encoded by this gene is a beta-1,3-N-acetylglucosaminyltransferase that adds an N-acetylglucosamine moiety to N-acetylgalactosamine-modified serine or threonine. The encoded enzyme is responsible for creating the core 3 structure of O-glycans, which are important components of mucin-type glycoproteins. [provided by RefSeq, Dec 2016] See more...

Aliases for B3GNT6 Gene

Aliases for B3GNT6 Gene

  • UDP-GlcNAc:BetaGal Beta-1,3-N-Acetylglucosaminyltransferase 6 2 3 4 5
  • Core 3 Synthase 2 3 4
  • Acetylgalactosaminyl-O-Glycosyl-Glycoprotein Beta-1,3-N-Acetylglucosaminyltransferase 3 4
  • Beta-1,3-N-Acetylglucosaminyltransferase 6 3 4
  • Beta-1,3-Gn-T6 3 4
  • Beta3Gn-T6 3 4
  • B3Gn-T6 2 3
  • BGnT-6 3 4
  • Beta-1,3-N-Acetylglucosaminyltransferase Protein 3
  • EC 2.4.1.147 4
  • B3GNT6 5

External Ids for B3GNT6 Gene

Previous GeneCards Identifiers for B3GNT6 Gene

  • GC11M068646
  • GC11M067794
  • GC11M066362
  • GC11M065889
  • GC11M065890
  • GC11M065869
  • GC11P076425
  • GC11P076745
  • GC11P073043

Summaries for B3GNT6 Gene

Entrez Gene Summary for B3GNT6 Gene

  • The protein encoded by this gene is a beta-1,3-N-acetylglucosaminyltransferase that adds an N-acetylglucosamine moiety to N-acetylgalactosamine-modified serine or threonine. The encoded enzyme is responsible for creating the core 3 structure of O-glycans, which are important components of mucin-type glycoproteins. [provided by RefSeq, Dec 2016]

GeneCards Summary for B3GNT6 Gene

B3GNT6 (UDP-GlcNAc:BetaGal Beta-1,3-N-Acetylglucosaminyltransferase 6) is a Protein Coding gene. Diseases associated with B3GNT6 include Childhood-Onset Schizophrenia and Schizophrenia. Among its related pathways are O-linked glycosylation and Metabolism of proteins. Gene Ontology (GO) annotations related to this gene include galactosyltransferase activity and beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity. An important paralog of this gene is B3GNT3.

UniProtKB/Swiss-Prot Summary for B3GNT6 Gene

  • Beta-1,3-N-acetylglucosaminyltransferase that synthesizes the core 3 structure of the O-glycan, an important precursor in the biosynthesis of mucin-type glycoproteins. Plays an important role in the synthesis of mucin-type O-glycans in digestive organs.

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for B3GNT6 Gene

Genomics for B3GNT6 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for B3GNT6 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
GH11J077034 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE dbSUPER 250.7 +1.4 1370 3.2 ATF2 CEBPA NFIC CHD4 CEBPB FOXA1 ZFP64 ZNF217 THAP11 FOXA2 B3GNT6 OMP MYO7A ACER3 CAPN5 ENSG00000254988 HSALNG0085887
GH11J077019 Enhancer 1.1 Ensembl ENCODE dbSUPER 8.1 -13.7 -13697 2.6 NFIC ZNF217 EP300 MBD2 ELF1 FOXA2 CTBP1 CUX1 ETV4 STAT3 MYO7A ENSG00000254632 GDPD4 B3GNT6 ENSG00000254988 ACER3 HSALNG0085891
GH11J077015 Enhancer 1 Ensembl ENCODE 8.1 -18.6 -18607 0.9 NCOR1 JUND ATF3 HOMEZ CTBP1 SMAD4 RARA FOSL2 SMARCA4 HDAC2 HSALNG0085891 B3GNT6 HSALNG0085890 ENSG00000254988 ACER3
GH11J076806 Promoter/Enhancer 1.3 Ensembl ENCODE dbSUPER 5.8 -226.8 -226826 1.1 ZNF654 MYC IKZF1 ZNF592 ZIC2 YY1 CTCF REST RAD21 SMC3 ACER3 TSKU-AS1 TSKU LINC02757 EMSY B3GNT6 HSALNG0085883-001 HSALNG0085882 MK280269-012
GH11J076823 Enhancer 1.3 FANTOM5 ENCODE dbSUPER 5.2 -209.6 -209608 3.1 MYC NCOR1 IKZF1 ZNF600 ZNF592 JUND ZIC2 CEBPB DEK HES1 lnc-LRRC32-7 EMSY ACER3 B3GNT6 GDPD4 HSALNG0085883-002 piR-31210-009 TSKU MK280269-012
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around B3GNT6 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for B3GNT6

Top Transcription factor binding sites by QIAGEN in the B3GNT6 gene promoter:
  • AP-4
  • ATF6
  • CUTL1
  • E2F
  • E2F-1
  • NF-1
  • NF-1/L
  • PPAR-gamma1
  • PPAR-gamma2
  • XBP-1

Genomic Locations for B3GNT6 Gene

Latest Assembly
chr11:77,034,398-77,041,973
(GRCh38/hg38)
Size:
7,576 bases
Orientation:
Plus strand

Previous Assembly
chr11:76,745,442-76,753,020
(GRCh37/hg19 by Entrez Gene)
Size:
7,579 bases
Orientation:
Plus strand

chr11:76,745,385-76,753,096
(GRCh37/hg19 by Ensembl)
Size:
7,712 bases
Orientation:
Plus strand

Genomic View for B3GNT6 Gene

Genes around B3GNT6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
B3GNT6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for B3GNT6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for B3GNT6 Gene

Proteins for B3GNT6 Gene

  • Protein details for B3GNT6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6ZMB0-B3GN6_HUMAN
    Recommended name:
    Acetylgalactosaminyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase
    Protein Accession:
    Q6ZMB0
    Secondary Accessions:
    • E9PKS1
    • Q6ZSC5
    • Q8TAZ4
    • Q8TDX1

    Protein attributes for B3GNT6 Gene

    Size:
    384 amino acids
    Molecular mass:
    42748 Da
    Quaternary structure:
    No Data Available
    Miscellaneous:
    • Injection into nude mice significantly suppress lung metastasis, indicating that the core structures of O-glycans are profoundly involved in the metastatic capacity of cancer cells.

    Alternative splice isoforms for B3GNT6 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for B3GNT6 Gene

Post-translational modifications for B3GNT6 Gene

  • Glycosylation at Asn73, Asn77, and Asn196
  • Modification sites at PhosphoSitePlus

Other Protein References for B3GNT6 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for B3GNT6 Gene

Domains & Families for B3GNT6 Gene

Gene Families for B3GNT6 Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Protein Domains for B3GNT6 Gene

InterPro:
Blocks:
  • Glycosyl transferase, family 31

Suggested Antigen Peptide Sequences for B3GNT6 Gene

GenScript: Design optimal peptide antigens:
  • Core 3 synthase (B3GN6_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q6ZMB0

UniProtKB/Swiss-Prot:

B3GN6_HUMAN :
  • Belongs to the glycosyltransferase 31 family.
Family:
  • Belongs to the glycosyltransferase 31 family.
genes like me logo Genes that share domains with B3GNT6: view

Function for B3GNT6 Gene

Molecular function for B3GNT6 Gene

UniProtKB/Swiss-Prot Function:
Beta-1,3-N-acetylglucosaminyltransferase that synthesizes the core 3 structure of the O-glycan, an important precursor in the biosynthesis of mucin-type glycoproteins. Plays an important role in the synthesis of mucin-type O-glycans in digestive organs.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=3-O-[N-acetyl-alpha-D-galactosaminyl]-L-threonyl-[protein] + UDP-N-acetyl-alpha-D-glucosamine = 3-O-[N-acetyl-beta-D-glucosaminyl-(1->3)-N-acetyl-alpha-D-galactosaminyl]-L-threonyl-[protein] + H(+) + UDP; Xref=Rhea:RHEA:46880, Rhea:RHEA-COMP:11689, Rhea:RHEA-COMP:11692, ChEBI:CHEBI:15378, ChEBI:CHEBI:57705, ChEBI:CHEBI:58223, ChEBI:CHEBI:87075, ChEBI:CHEBI:87080; EC=2.4.1.147; Evidence={ECO:0000269|PubMed:7655172};.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=3-O-[N-acetyl-alpha-D-galactosaminyl]-L-seryl-[protein] + UDP-N-acetyl-alpha-D-glucosamine = 3-O-[N-acetyl-beta-D-glucosaminyl-(1->3)-N-acetyl-alpha-D-galactosaminyl]-L-seryl-[protein] + H(+) + UDP; Xref=Rhea:RHEA:46884, Rhea:RHEA-COMP:11691, Rhea:RHEA-COMP:12788, ChEBI:CHEBI:15378, ChEBI:CHEBI:53604, ChEBI:CHEBI:57705, ChEBI:CHEBI:58223, ChEBI:CHEBI:87079; EC=2.4.1.147; Evidence={ECO:0000269|PubMed:7655172};.
UniProtKB/Swiss-Prot Induction:
Down-regulated in gastric and colorectal carcinomas, suggesting that it may be used as a marker for distinguishing between benign adenomas and premalignant lesions (at protein level).
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=3.3 mM for GalNAc-alpha-Bn {ECO:0000269|PubMed:7655172}; Vmax=4.5 nmol/h/mg enzyme with GalNAc-alpha-Bn as substrate {ECO:0000269|PubMed:7655172};

Enzyme Numbers (IUBMB) for B3GNT6 Gene

Phenotypes From GWAS Catalog for B3GNT6 Gene

Gene Ontology (GO) - Molecular Function for B3GNT6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008375 acetylglucosaminyltransferase activity IBA 21873635
GO:0008376 acetylgalactosaminyltransferase activity IBA 21873635
GO:0008378 galactosyltransferase activity IDA 11821425
GO:0008532 N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity IBA 21873635
GO:0016740 transferase activity IEA --
genes like me logo Genes that share ontologies with B3GNT6: view
genes like me logo Genes that share phenotypes with B3GNT6: view

Animal Models for B3GNT6 Gene

MGI Knock Outs for B3GNT6:

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for B3GNT6

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for B3GNT6 Gene

Localization for B3GNT6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for B3GNT6 Gene

Golgi apparatus membrane. Single-pass type II membrane protein.

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 B3GNT6 gene
Compartment Confidence
golgi apparatus 5
extracellular 2
plasma membrane 1
endoplasmic reticulum 1
peroxisome 0
lysosome 0

Gene Ontology (GO) - Cellular Components for B3GNT6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane TAS --
GO:0005794 Golgi apparatus IBA 21873635
GO:0016020 membrane NAS 11821425
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with B3GNT6: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for B3GNT6 Gene

Pathways & Interactions for B3GNT6 Gene

genes like me logo Genes that share pathways with B3GNT6: view

Pathways by source for B3GNT6 Gene

UniProtKB/Swiss-Prot Q6ZMB0-B3GN6_HUMAN

  • Pathway: Protein modification; protein glycosylation.

Gene Ontology (GO) - Biological Process for B3GNT6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006486 protein glycosylation IBA 21873635
GO:0009101 glycoprotein biosynthetic process NAS 11821425
GO:0016266 O-glycan processing TAS --
GO:0016269 O-glycan processing, core 3 NAS 11821425
GO:0018215 protein phosphopantetheinylation IEA --
genes like me logo Genes that share ontologies with B3GNT6: view

No data available for SIGNOR curated interactions for B3GNT6 Gene

Drugs & Compounds for B3GNT6 Gene

No Compound Related Data Available

Transcripts for B3GNT6 Gene

mRNA/cDNA for B3GNT6 Gene

1 REFSEQ mRNAs :
12 NCBI additional mRNA sequence :
2 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for B3GNT6

Alternative Splicing Database (ASD) splice patterns (SP) for B3GNT6 Gene

No ASD Table

Relevant External Links for B3GNT6 Gene

GeneLoc Exon Structure for
B3GNT6

Expression for B3GNT6 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for B3GNT6 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for B3GNT6 Gene

This gene is overexpressed in Colon - Transverse (x22.1), Stomach (x11.4), Small Intestine - Terminal Ileum (x7.0), and Esophagus - Mucosa (x6.8).

Protein differential expression in normal tissues from HIPED for B3GNT6 Gene

This gene is overexpressed in Colon (50.4) and Testis (18.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for B3GNT6 Gene



Protein tissue co-expression partners for B3GNT6 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for B3GNT6

SOURCE GeneReport for Unigene cluster for B3GNT6 Gene:

Hs.352622

mRNA Expression by UniProt/SwissProt for B3GNT6 Gene:

Q6ZMB0-B3GN6_HUMAN
Tissue specificity: Present in stomach and colon (at protein level). Restricted in the stomach, colon and small intestine, where core 3 structure is present.

Evidence on tissue expression from TISSUES for B3GNT6 Gene

  • Intestine(4.3)
  • Pancreas(4.2)
  • Nervous system(2.4)
  • Stomach(2)
genes like me logo Genes that share expression patterns with B3GNT6: view

Primer products for research

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for B3GNT6 Gene

Orthologs for B3GNT6 Gene

This gene was present in the common ancestor of animals.

Orthologs for B3GNT6 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia B3GNT6 29 30
  • 98.96 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia B3GNT6 29 30
  • 86.39 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia B3GNT6 29 30
  • 85.22 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia B3gnt6 29
  • 78.8 (n)
Mouse
(Mus musculus)
Mammalia B3gnt6 29 16 30
  • 78.41 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia -- 30
  • 37 (a)
ManyToMany
Chicken
(Gallus gallus)
Aves B3GNT6 29
  • 63.58 (n)
-- 30
  • 47 (a)
OneToMany
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia b3gnt3 29
  • 51.42 (n)
Zebrafish
(Danio rerio)
Actinopterygii b3gnt3 30
  • 39 (a)
ManyToMany
zgc:86586 30
  • 38 (a)
ManyToMany
si:ch211-126g16.11 30
  • 38 (a)
ManyToMany
si:ch211-126g16.10 30
  • 38 (a)
ManyToMany
Fruit Fly
(Drosophila melanogaster)
Insecta BEST:GH04269 31
  • 31 (a)
Species where no ortholog for B3GNT6 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Lizard (Anolis carolinensis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Platypus (Ornithorhynchus anatinus)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • 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)

Evolution for B3GNT6 Gene

ENSEMBL:
Gene Tree for B3GNT6 (if available)
TreeFam:
Gene Tree for B3GNT6 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for B3GNT6: view image
Alliance of Genome Resources:
Additional Orthologs for B3GNT6

Paralogs for B3GNT6 Gene

(9) SIMAP similar genes for B3GNT6 Gene using alignment to 3 proteins:

  • B3GN6_HUMAN
  • C9JDU9_HUMAN
  • E9PJ79_HUMAN
genes like me logo Genes that share paralogs with B3GNT6: view

Variants for B3GNT6 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for B3GNT6 Gene

SNP ID Clinical significance and condition Chr 11 pos Variation AA Info Type
rs781821239 Likely Pathogenic: Childhood-Onset Schizophrenia 77,040,103(+) C/G
NM_138706.5(B3GNT6):c.552C>G (p.Asp184Glu)
MISSENSE

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for B3GNT6 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for B3GNT6 Gene

Variant ID Type Subtype PubMed ID
nsv1040996 CNV gain 25217958
nsv1138053 CNV deletion 24896259
nsv397 CNV insertion 18451855

Variation tolerance for B3GNT6 Gene

Residual Variation Intolerance Score: 93.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 11.05; 92.15% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for B3GNT6 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
B3GNT6
Leiden Open Variation Database (LOVD)
B3GNT6

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for B3GNT6 Gene

Disorders for B3GNT6 Gene

MalaCards: The human disease database

(2) MalaCards diseases for B3GNT6 Gene - From: CVR and GCD

Disorder Aliases PubMed IDs
childhood-onset schizophrenia
  • childhood schizophrenia
schizophrenia
  • sczd
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for B3GNT6

genes like me logo Genes that share disorders with B3GNT6: view

No data available for UniProtKB/Swiss-Prot and Genatlas for B3GNT6 Gene

Publications for B3GNT6 Gene

  1. 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. (PMID: 11821425) Iwai T … Narimatsu H (The Journal of biological chemistry 2002) 2 3 4
  2. Core 3 synthase is down-regulated in colon carcinoma and profoundly suppresses the metastatic potential of carcinoma cells. (PMID: 15755813) Iwai T … Narimatsu H (Proceedings of the National Academy of Sciences of the United States of America 2005) 3 4
  3. Clinicopathological significance of core 3 O-glycan synthetic enzyme, β1,3-N-acetylglucosaminyltransferase 6 in pancreatic ductal adenocarcinoma. (PMID: 33253272) Doi N … Hiraoka N (PloS one 2020) 3
  4. De novo variants in sporadic cases of childhood onset schizophrenia. (PMID: 26508570) Ambalavanan A … Rouleau GA (European journal of human genetics : EJHG 2016) 72
  5. A Panel of Recombinant Mucins Carrying a Repertoire of Sialylated O-Glycans Based on Different Core Chains for Studies of Glycan Binding Proteins. (PMID: 26274979) Cherian RM … Holgersson J (Biomolecules 2015) 3

Products for B3GNT6 Gene

Sources for B3GNT6 Gene