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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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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

Gene LinkOut

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