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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
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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

Associated conditions

Description Tests
Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8
MedGen: C3553813 OMIM: 614830 GeneReviews: Not available
not available
Muscular dystrophy-dystroglycanopathy (limb-girdle), type C, 8
MedGen: C4748320 OMIM: 618135 GeneReviews: Not available
not available

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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