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    POMGNT2 protein O-linked mannose N-acetylglucosaminyltransferase 2 (beta 1,4-) [ Homo sapiens (human) ]

    Gene ID: 84892, updated on 2-Nov-2024

    Summary

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    Official Symbol
    POMGNT2provided by HGNC
    Official Full Name
    protein O-linked mannose N-acetylglucosaminyltransferase 2 (beta 1,4-)provided by HGNC
    Primary source
    HGNC:HGNC:25902
    See related
    Ensembl:ENSG00000144647 MIM:614828; AllianceGenome:HGNC:25902
    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
    AGO61; GTDC2; MDDGA8; MDDGC8; C3orf39
    Summary
    This gene encodes a protein with glycosyltransferase activity although its function is not currently known. [provided by RefSeq, Sep 2012]
    Expression
    Ubiquitous expression in endometrium (RPKM 11.1), brain (RPKM 9.1) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See POMGNT2 in Genome Data Viewer
    Location:
    3p22.1
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (43079234..43106079, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (43094564..43121424, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (43120726..43147571, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene KRBOX1 antisense RNA 1 Neighboring gene KRAB box domain containing 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:43025326-43025826 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:43025827-43026327 Neighboring gene golgi associated kinase 1A Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:43104067-43104586 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:43121119-43121620 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:43121621-43122120 Neighboring gene uncharacterized LOC107986079 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:43138968-43139468 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:43139469-43139969 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14253 Neighboring gene uncharacterized LOC105377051 Neighboring gene Sharpr-MPRA regulatory regions 3209 and 6245 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19751 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19752 Neighboring gene uncharacterized LOC105377052

    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 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. The structure of POMGNT2 provides new insights into the mechanism to determine the functional O-mannosylation site on α-dystroglycan. Imae R, et al. Genes Cells, 2021 Jul. PMID 33893702, Free PMC Article
    2. Protein O-Linked Mannose β-1,4-N-Acetylglucosaminyl-transferase 2 (POMGNT2) Is a Gatekeeper Enzyme for Functional Glycosylation of α-Dystroglycan. Halmo SM, et al. J Biol Chem, 2017 Feb 10. PMID 27932460, Free PMC Article
    3. GTDC2 modifies O-mannosylated α-dystroglycan in the endoplasmic reticulum to generate N-acetyl glucosamine epitopes reactive with CTD110.6 antibody. Ogawa M, et al. Biochem Biophys Res Commun, 2013 Oct 11. PMID 24041696
    4. Milder forms of muscular dystrophy associated with POMGNT2 mutations. Endo Y, et al. Neurol Genet, 2015 Dec. PMID 27066570, Free PMC Article
    5. Exome sequencing and functional validation in zebrafish identify GTDC2 mutations as a cause of Walker-Warburg syndrome. Manzini MC, et al. Am J Hum Genet, 2012 Sep 7. PMID 22958903, Free PMC Article

    See all (26) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The structure of POMGNT2 provides new insights into the mechanism to determine the functional O-mannosylation site on alpha-dystroglycan.
      Title: The structure of POMGNT2 provides new insights into the mechanism to determine the functional O-mannosylation site on α-dystroglycan.
    2. POMGNT2 when two of the conserved amino acids are replaced. These findings begin to define the selectivity of POMGNT2 and suggest that this enzyme functions as a gatekeeper enzyme to prevent the vast majority of O-mannosylated sites on proteins from becoming modified with glycan structures functional for binding laminin globular domain-containing proteins
      Title: Protein O-Linked Mannose β-1,4-N-Acetylglucosaminyl-transferase 2 (POMGNT2) Is a Gatekeeper Enzyme for Functional Glycosylation of α-Dystroglycan.
    3. GTDC2 generates CTD110.6 antibody-reactive N-acetylglucosamine epitopes on the O-mannosylated alpha-dystroglycan.
      Title: GTDC2 modifies O-mannosylated α-dystroglycan in the endoplasmic reticulum to generate N-acetyl glucosamine epitopes reactive with CTD110.6 antibody.
    4. Using WES in consanguineous WWS-affected families, we found multiple deleterious mutations in GTDC2 (also known as AGO61). .
      Title: Exome sequencing and functional validation in zebrafish identify GTDC2 mutations as a cause of Walker-Warburg syndrome.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    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

    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

    • FLJ14566

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables acetylglucosaminyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables acetylglucosaminyltransferase activity TAS
    Traceable Author Statement
    more info
    		  
    enables protein O-acetylglucosaminyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein O-acetylglucosaminyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein O-acetylglucosaminyltransferase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in neuron migration ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein O-linked glycosylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein O-linked glycosylation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein O-linked glycosylation TAS
    Traceable Author Statement
    more info
    		  
    involved_in protein O-linked mannosylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein O-linked mannosylation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    is_active_in endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
    Names
    glycosyltransferase-like domain containing 2
    glycosyltransferase-like domain-containing protein 2
    protein O-mannose beta-1,4-N-acetylglucosaminyltransferase 2
    NP_116195.2
    XP_005265572.1
    XP_011532465.1
    XP_016862842.1
    XP_054204124.1
    XP_054204125.1
    XP_054204126.1

    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.

    Genomic

    1. NG_032930.1 RefSeqGene

      Range
      5005..31850
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_706

    mRNA and Protein(s)

    1. NM_032806.6 → NP_116195.2  protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2

      See identical proteins and their annotated locations for NP_116195.2

      Status: VALIDATED

      Source sequence(s)
      AC092042, BC060861
      Consensus CDS
      CCDS2709.1
      UniProtKB/Swiss-Prot
      B3KWC3, Q8NAT1, Q96SY3
      Related
      ENSP00000344125.2, ENST00000344697.3
      Conserved Domains (2) summary
      cd00063
      Location:493 → 580
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      pfam04577
      Location:264 → 395
      DUF563; Protein of unknown function (DUF563)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      43079234..43106079 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011534163.3 → XP_011532465.1  protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2 isoform X1

      See identical proteins and their annotated locations for XP_011532465.1

      UniProtKB/Swiss-Prot
      B3KWC3, Q8NAT1, Q96SY3
      Related
      ENSP00000509610.1, ENST00000687440.1
      Conserved Domains (2) summary
      cd00063
      Location:493 → 580
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      pfam04577
      Location:264 → 395
      DUF563; Protein of unknown function (DUF563)

    2. XM_005265515.4 → XP_005265572.1  protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2 isoform X1

      See identical proteins and their annotated locations for XP_005265572.1

      UniProtKB/Swiss-Prot
      B3KWC3, Q8NAT1, Q96SY3
      Related
      ENSP00000408992.1, ENST00000441964.1
      Conserved Domains (2) summary
      cd00063
      Location:493 → 580
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      pfam04577
      Location:264 → 395
      DUF563; Protein of unknown function (DUF563)

    3. XM_017007353.2 → XP_016862842.1  protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2 isoform X1

      UniProtKB/Swiss-Prot
      B3KWC3, Q8NAT1, Q96SY3
      Related
      ENSP00000509123.1, ENST00000686643.1
      Conserved Domains (2) summary
      cd00063
      Location:493 → 580
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      pfam04577
      Location:264 → 395
      DUF563; Protein of unknown function (DUF563)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      43094564..43121424 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054348150.1 → XP_054204125.1  protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2 isoform X1

      UniProtKB/Swiss-Prot
      B3KWC3, Q8NAT1, Q96SY3

    2. XM_054348149.1 → XP_054204124.1  protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2 isoform X1

      UniProtKB/Swiss-Prot
      B3KWC3, Q8NAT1, Q96SY3

    3. XM_054348151.1 → XP_054204126.1  protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2 isoform X1

      UniProtKB/Swiss-Prot
      B3KWC3, Q8NAT1, Q96SY3
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8NAT1.1 GenPept UniProtKB/Swiss-Prot:Q8NAT1

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