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    MGAT5B alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase B [ Homo sapiens (human) ]

    Gene ID: 146664, updated on 3-Apr-2024

    Summary

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    Official Symbol
    MGAT5Bprovided by HGNC
    Official Full Name
    alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase Bprovided by HGNC
    Primary source
    HGNC:HGNC:24140
    See related
    Ensembl:ENSG00000167889 MIM:612441; AllianceGenome:HGNC:24140
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    GnT-IX; GnT-VB
    Summary
    Enables alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity and manganese ion binding activity. Involved in protein O-linked glycosylation via serine. Predicted to be located in Golgi membrane. Predicted to be integral component of membrane. Predicted to be active in Golgi apparatus. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in brain (RPKM 5.4) and testis (RPKM 0.7) See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    17q25.2
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (76868404..76950393)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (77760422..77843205)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (74864486..74946475)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985089 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:74822016-74822832 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:74834234-74834958 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12815 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:74835690-74835885 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12816 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12817 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:74837373-74837889 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:74840421-74841249 Neighboring gene Sharpr-MPRA regulatory region 12785 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9029 Neighboring gene long intergenic non-protein coding RNA 868 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:74881066-74881940 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:74901567-74902178 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:74902179-74902790 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:74912167-74912666 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:74933764-74934306 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:74936614-74937172 Neighboring gene uncharacterized LOC105371899 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:74953917-74954830 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9030 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:74965460-74966084 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:74978799-74979337 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:74979338-74979875 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:74991281-74991822 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:74993993-74994533 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12819 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:75048917-75049660 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:75052409-75052622 Neighboring gene Sharpr-MPRA regulatory region 11385 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr17:75084131-75085330 Neighboring gene small Cajal body-specific RNA 16 Neighboring gene SEC14 like lipid binding 1 Neighboring gene microRNA 6516 Neighboring gene small nucleolar RNA host gene 20

    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. Hepatic aberrant glycosylation by N-acetylglucosaminyltransferase V accelerates HDL assembly. Kamada Y, et al. Am J Physiol Gastrointest Liver Physiol, 2016 Nov 1. PMID 27659420
    2. N-acetylglucosaminyltranferase VB expression enhances beta1 integrin- dependent PC12 neurite outgrowth on laminin and collagen. Lee I, et al. J Neurochem, 2006 May. PMID 16606368
    3. A novel beta(1,6)-N-acetylglucosaminyltransferase V (GnT-VB)(1). Kaneko M, et al. FEBS Lett, 2003 Nov 20. PMID 14623122
    4. N-Acetylglucosaminyltransferase IX acts on the GlcNAc beta 1,2-Man alpha 1-Ser/Thr moiety, forming a 2,6-branched structure in brain O-mannosyl glycan. Inamori K, et al. J Biol Chem, 2004 Jan 23. PMID 14617637
    5. Molecular cloning and characterization of human GnT-IX, a novel beta1,6-N-acetylglucosaminyltransferase that is specifically expressed in the brain. Inamori K, et al. J Biol Chem, 2003 Oct 31. PMID 12941944

    See all (40) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Brain-specific glycosylation enzyme GnT-IX maintains levels of protein tyrosine phosphatase receptor PTPRZ, thereby mediating glioma growth.
      Title: Brain-specific glycosylation enzyme GnT-IX maintains levels of protein tyrosine phosphatase receptor PTPRZ, thereby mediating glioma growth.
    2. we found a strong correlation between serum GnT-V activity and HDL-C concentration in human subjects
      Title: Hepatic aberrant glycosylation by N-acetylglucosaminyltransferase V accelerates HDL assembly.
    3. ENPP3 is a regulator of N-acetylglucosaminyltransferase GnT-IX (GnT-Vb)
      Title: Identification of ectonucleotide pyrophosphatase/phosphodiesterase 3 (ENPP3) as a regulator of N-acetylglucosaminyltransferase GnT-IX (GnT-Vb).
    4. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    5. Observational study of gene-disease association. (HuGE Navigator)
      Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
    6. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    7. The activity of GnT-Vb was stimulated over 4-fold in the presence of 10 mM Mn(++), and pH optimum for GnT-Vb was 8.0.
      Title: Comparison of the substrate specificities and catalytic properties of the sister N-acetylglucosaminyltransferases, GnT-V and GnT-Vb (IX).
    8. GnT-Vb-mediated glycosylation of RPTPbeta promotes galectin-1 binding and RPTPbeta levels of retention on the cell surface.
      Title: Receptor tyrosine phosphatase beta (RPTPbeta) activity and signaling are attenuated by glycosylation and subsequent cell surface galectin-1 binding.
    9. GnT-IX is responsible for the synthesis of a unique oligosaccharide structure in the brain
      Title: Molecular cloning and characterization of human GnT-IX, a novel beta1,6-N-acetylglucosaminyltransferase that is specifically expressed in the brain.
    10. These results demonstrate that GnT-VB expression can modulate the rate of neurite outgrowth by affecting beta1 integrin-ECM interaction.
      Title: N-acetylglucosaminyltranferase VB expression enhances beta1 integrin- dependent PC12 neurite outgrowth on laminin and collagen.
    Submit: New GeneRIF Correction See all GeneRIFs (13)

    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
    A meta-analysis of genome-wide association studies of the electrocardiographic early repolarization pattern.
    EBI GWAS Catalog
    Genome-wide study of percent emphysema on computed tomography in the general population. The Multi-Ethnic Study of Atherosclerosis Lung/SNP Health Association Resource Study.
    EBI GWAS Catalog
    The genetic aetiology of cannabis use initiation: a meta-analysis of genome-wide association studies and a SNP-based heritability estimation.
    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

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp160, precursor env Oligosaccharide side-chains of HIV-1 gp160 are processed by glycosidase I and II, mannosidase I and II, acetylglucosaminyl transferase I and II, and fucosyl, galactosyl and sialyl transferases in both the endoplasmic reticulum and golgi apparatus PubMed
    Envelope transmembrane glycoprotein gp41 env Mannose-containing, N-linked oligosaccharide side-chains of HIV-1 gp41 are involved in the initial stage of infection by HIV-1; glycosylation inhibitors block virus-cell and cell-cell fusion and release of the virions PubMed

    Go to the HIV-1, Human Interaction Database

    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

    • FLJ25132, KIAA2008

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables manganese ion binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in protein N-linked glycosylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein O-linked glycosylation via serine IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in Golgi apparatus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in Golgi membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase B
    Names
    N-acetylglucosaminyl-transferase Vb
    N-acetylglucosaminyltransferase IX
    alpha-mannoside beta-1,6-N-acetylglucosaminyltransferase B
    beta(1,6)-N-acetylglucosaminyltransferase V
    glcNAc-T Vb
    hGnTVb
    mannoside acetylglucosaminyltransferase 5B
    mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isoenzyme B
    mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isozyme B
    NP_001186101.1
    NP_653278.2
    NP_945193.1
    XP_006721770.1
    XP_011522654.1
    XP_011522656.1
    XP_047291339.1
    XP_054171076.1
    XP_054171077.1
    XP_054171078.1
    XP_054171079.1
    XP_054171080.1

    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_001199172.2 → NP_001186101.1  alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase B isoform 3

      See identical proteins and their annotated locations for NP_001186101.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence and contains an alternate in-frame exon compared to variant 2. The resulting isoform (3) has a shorter and distinct N-terminus and lacks an internal 2 aa segment compared to isoform 2.
      Source sequence(s)
      AB235153, AC016168, AW191036, BC063862
      Consensus CDS
      CCDS59299.1
      UniProtKB/Swiss-Prot
      Q3V5L5, Q6P3S8, Q6P6B3, Q766X5, Q76D04, Q96LS2
      Related
      ENSP00000456037.2, ENST00000569840.7
      Conserved Domains (1) summary
      pfam15024
      Location:184 → 777
      Glyco_transf_18; Glycosyltransferase family 18

    2. NM_144677.3 → NP_653278.2  alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase B isoform 1

      See identical proteins and their annotated locations for NP_653278.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) differs in the 5' UTR and coding sequence compared to variant 2. The resulting isoform (1) has a shorter and distinct N-terminus compared to isoform 2.
      Source sequence(s)
      AB109185, AB114297, AC016168, AW191036, BC036948, BC041577
      Consensus CDS
      CCDS11751.1
      UniProtKB/Swiss-Prot
      Q3V5L5
      Related
      ENSP00000301618.4, ENST00000301618.8
      Conserved Domains (1) summary
      pfam15024
      Location:184 → 775
      Glyco_transf_18; Glycosyltransferase family 18

    3. NM_198955.1 → NP_945193.1  alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase B isoform 2

      See identical proteins and their annotated locations for NP_945193.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) encodes the longest isoform (2).
      Source sequence(s)
      AB109185, AB114297, AW191036, BC036948
      Consensus CDS
      CCDS45788.1
      UniProtKB/Swiss-Prot
      Q3V5L5
      Related
      ENSP00000391227.2, ENST00000428789.6
      Conserved Domains (1) summary
      pfam15024
      Location:195 → 786
      Glyco_transf_18; Glycosyltransferase family 18

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      76868404..76950393
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006721707.4 → XP_006721770.1  alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase B isoform X1

      Conserved Domains (1) summary
      pfam15024
      Location:121 → 714
      Glyco_transf_18; Glycosyltransferase family 18

    2. XM_011524352.3 → XP_011522654.1  alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase B isoform X2

      Conserved Domains (1) summary
      pfam15024
      Location:184 → 616
      Glyco_transf_18; Glycosyltransferase family 18

    3. XM_047435383.1 → XP_047291339.1  alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase B isoform X3

      Related
      ENSP00000455631.1, ENST00000565043.5

    4. XM_011524354.4 → XP_011522656.1  alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase B isoform X4

      Conserved Domains (1) summary
      pfam15024
      Location:184 → 342
      Glyco_transf_18; Glycosyltransferase family 18

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      77760422..77843205
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054315102.1 → XP_054171077.1  alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase B isoform X1

    2. XM_054315103.1 → XP_054171078.1  alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase B isoform X2

    3. XM_054315104.1 → XP_054171079.1  alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase B isoform X3

    4. XM_054315105.1 → XP_054171080.1  alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase B isoform X4

    5. XM_054315101.1 → XP_054171076.1  alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase B isoform X5

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q3V5L5.2 GenPept UniProtKB/Swiss-Prot:Q3V5L5

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