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POMGNT1 protein O-linked mannose N-acetylglucosaminyltransferase 1 (beta 1,2-) [ Homo sapiens (human) ]

Gene ID: 55624, updated on 3-Nov-2024

Summary

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Official Symbol
POMGNT1provided by HGNC
Official Full Name
protein O-linked mannose N-acetylglucosaminyltransferase 1 (beta 1,2-)provided by HGNC
Primary source
HGNC:HGNC:19139
See related
Ensembl:ENSG00000085998 MIM:606822; AllianceGenome:HGNC:19139
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
MEB; RP76; GNTI.2; LGMD2O; GnT I.2; LGMDR15; MGAT1.2; gnT-I.2
Summary
This gene encodes a type II transmembrane protein that resides in the Golgi apparatus. It participates in O-mannosyl glycosylation and is specific for alpha linked terminal mannose. Mutations in this gene may be associated with muscle-eye-brain disease and several congenital muscular dystrophies. Alternatively spliced transcript variants that encode different protein isoforms have been described. [provided by RefSeq, Feb 2014]
Expression
Ubiquitous expression in heart (RPKM 23.4), thyroid (RPKM 21.0) and 25 other tissues See more
Orthologs
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Genomic context

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See POMGNT1 in Genome Data Viewer
Location:
1p34.1
Exon count:
25
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (46188683..46220305, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (46065903..46097522, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (46654355..46685977, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene P3R3URF-PIK3R3 readthrough Neighboring gene phosphoinositide-3-kinase regulatory subunit 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 992 Neighboring gene uncharacterized LOC101929626 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 993 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 994 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 995 Neighboring gene PIK3R3 upstream open reading frame Neighboring gene tetraspanin 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 837 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 838 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:46683827-46684328 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:46685102-46685602 Neighboring gene leucine rich adaptor protein 1 Neighboring gene MPRA-validated peak204 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 839 Neighboring gene RAD54 like Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:46750956-46751580 Neighboring gene NANOG hESC enhancer GRCh37_chr1:46764257-46764758 Neighboring gene leucine rich repeat containing 41 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:46766628-46767210 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:46767211-46767793 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 841 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 842 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 843 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 844 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:46768959-46769542 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:46769543-46770124 Neighboring gene ubiquinol-cytochrome c reductase hinge protein

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. Worldwide distribution and broader clinical spectrum of muscle-eye-brain disease. Taniguchi K, et al. Hum Mol Genet, 2003 Mar 1. PMID 12588800
  2. POMGnT1 mutation and phenotypic spectrum in muscle-eye-brain disease. Diesen C, et al. J Med Genet, 2004 Oct. PMID 15466003, Free PMC Article
  3. Severe muscle-eye-brain disease is associated with a homozygous mutation in the POMGnT1 gene. Teber S, et al. Eur J Paediatr Neurol, 2008 Mar. PMID 17881266
  4. Novel POMGnT1 mutations define broader phenotypic spectrum of muscle-eye-brain disease. Hehr U, et al. Neurogenetics, 2007 Nov. PMID 17906881
  5. Effects of length and amino acid sequence of O-mannosyl peptides on substrate specificity of protein O-linked mannose β1,2-N-acetylglucosaminyltransferase 1 (POMGnT1). Akasaka-Manya K, et al. Biochem Biophys Res Commun, 2011 Jul 8. PMID 21684258

See all (69) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Compound variants of FKTN, POMGNT1, and LAMB1 gene identified by prenatal whole-exome sequencing in three fetuses with congenital hydrocephalus.
    Title: Compound variants of FKTN, POMGNT1, and LAMB1 gene identified by prenatal whole-exome sequencing in three fetuses with congenital hydrocephalus.
  2. Identification of a novel missense c.386G > A variant in a boy with the POMGNT1-related muscular dystrophy-dystroglycanopathy.
    Title: Identification of a novel missense c.386G > A variant in a boy with the POMGNT1-related muscular dystrophy-dystroglycanopathy.
  3. Glycosyltransferase POMGNT1 deficiency strengthens N-cadherin-mediated cell-cell adhesion.
    Title: Glycosyltransferase POMGNT1 deficiency strengthens N-cadherin-mediated cell-cell adhesion.
  4. FAM3B/PANDER-Like Carbohydrate-Binding Domain in a Glycosyltransferase, POMGNT1.
    Title: FAM3B/PANDER-Like Carbohydrate-Binding Domain in a Glycosyltransferase, POMGNT1.
  5. Genetic testing revealed two known heterozygous mutations in the POMGnT1 gene confirming muscular dystrophy-dystroglycanopathy type A (MDDGA3), one of a group of diseases collectively known as congenital muscular dystrophies, is an alpha-dystroglycanopathy with characteristic brain and ocular abnormalities.
    Title: Congenital muscular dystrophy-dystroglycanopathy, type A, featuring bilateral retinal dysplasia and vertical angle kappa.
  6. Next-generation sequencing data analysis revealed that all three muscle-eye-brain disease patients had the same novel copy number variations (CNV) g.6668-8257del, which was homozygous in patient 1 and heterozygous in patients 2 and 3.
    Title: Novel copy number variation of POMGNT1 associated with muscle-eye-brain disease detected by next-generation sequencing.
  7. These findings demonstrate that PomGnT1 might be a new focus of glioblastoma (GBM)research for treatment of recurrent Temozolomide -resistant GBM
    Title: PomGnT1 enhances temozolomide resistance by activating epithelial-mesenchymal transition signaling in glioblastoma.
  8. The authors have identified a novel mutation in POMGNT1 that causes nonsyndromic autosomal recessive retinitis pigmentosa, adding to the genetic heterogeneity of this retinal disease.
    Title: Homozygosity Mapping and Whole-Genome Sequencing Links a Missense Mutation in POMGNT1 to Autosomal Recessive Retinitis Pigmentosa.
  9. Study identified recessive POMGNT1 mutations in three unrelated non-syndromic retinitis pigmentosa families showing significant impaired POMGNT1 enzymatic activity.
    Title: Mutations in POMGNT1 cause non-syndromic retinitis pigmentosa.
  10. When association tests were applied to data from the Diabetes Heart Study, it found exome variants of POMGNT1 and JAK1 genes were associated with type 2 diabetes.
    Title: Generalization of Rare Variant Association Tests for Longitudinal Family Studies.
Submit: New GeneRIF Correction See all GeneRIFs (30)

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

Variation

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See Variation Viewer (GRCh37.p13)

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

  • FLJ20277, DKFZp761B182

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables acetylglucosaminyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables acetylglucosaminyltransferase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity TAS
Traceable Author Statement
more info
  
enables carbohydrate binding IEA
Inferred from Electronic Annotation
more info
  
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 O-glycan processing IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in O-glycan processing IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in basement membrane organization IEA
Inferred from Electronic Annotation
more info
  
involved_in dentate gyrus development IEA
Inferred from Electronic Annotation
more info
  
involved_in gene expression IEA
Inferred from Electronic Annotation
more info
  
involved_in localization of cell IEA
Inferred from Electronic Annotation
more info
  
involved_in myelination IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within 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 IEA
Inferred from Electronic Annotation
more info
  
involved_in reactive gliosis IEA
Inferred from Electronic Annotation
more info
  
involved_in sensory perception of sound IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in Golgi membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in Golgi membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in Golgi membrane TAS
Traceable Author Statement
more info
  
located_in membrane IMP
Inferred from Mutant Phenotype
more info
 PubMed 

General protein information

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Preferred Names
protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1
Names
UDP-GlcNAc:alpha-D-mannoside beta-1,2-N-acetylglucosaminyltransferase I.2
NP_001230695.2
NP_001277058.2
NP_001277059.2
NP_001397712.1
NP_060209.4
XP_005271067.1
XP_006710818.1
XP_006710819.1
XP_011540062.1
XP_016857179.1
XP_047280467.1
XP_054193511.1
XP_054193512.1
XP_054193513.1

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_009205.3 RefSeqGene

    Range
    5001..36623
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_701

mRNA and Protein(s)

  1. NM_001243766.2 → NP_001230695.2  protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' and 3' UTRs and uses an alternate splice site in the coding region, compared to variant 1. The encoded isoform (2) is longer and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AL672043
    Consensus CDS
    CCDS57995.1
    UniProtKB/TrEMBL
    A0A8I5KVA5
    Related
    ENSP00000361060.1, ENST00000371992.1
    Conserved Domains (2) summary
    cd02514
    Location:301 → 623
    GT13_GLCNAC-TI; GT13_GLCNAC-TI is involved in an essential step in the synthesis of complex or hybrid-type N-linked oligosaccharides
    cd13937
    Location:99 → 246
    PANDER_GnT-1_2_like; PANDER-like domain of N-acetylglucosaminyltransferases

  2. NM_001290129.2 → NP_001277058.2  protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' and 3' UTRs, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon compared to variant 1. The resulting protein (isoform 3) is shorter and has a distinct N-terminus compared to isoform 1.
    Source sequence(s)
    AL672043
    UniProtKB/TrEMBL
    B7ZAT4
    Conserved Domains (2) summary
    cd02514
    Location:279 → 606
    GT13_GLCNAC-TI; GT13_GLCNAC-TI is involved in an essential step in the synthesis of complex or hybrid-type N-linked oligosaccharides
    cd13937
    Location:77 → 224
    PANDER_GnT-1_2_like; PANDER-like domain of N-acetylglucosaminyltransferases

  3. NM_001290130.2 → NP_001277059.2  protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1 isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' and 3' UTRs, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon compared to variant 1. The resulting protein (isoform 4) is shorter and has a distinct N-terminus compared to isoform 1.
    Source sequence(s)
    AL672043
    UniProtKB/TrEMBL
    B7Z7F2
    Conserved Domains (2) summary
    cd02514
    Location:158 → 485
    GT13_GLCNAC-TI; GT13_GLCNAC-TI is involved in an essential step in the synthesis of complex or hybrid-type N-linked oligosaccharides
    cl19122
    Location:1 → 103
    PANDER_like; Domains similar to the Pancreatic-derived factor

  4. NM_001410783.1 → NP_001397712.1  protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1 isoform 5

    Status: REVIEWED

    Source sequence(s)
    AL672043
    Consensus CDS
    CCDS90941.1
    UniProtKB/TrEMBL
    A0A8I5KNB7

  5. NM_017739.4 → NP_060209.4  protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1 isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the predominant transcript and encodes isoform 1.
    Source sequence(s)
    AB057356, AL672043, BC001471, BQ448444, DA187331
    Consensus CDS
    CCDS531.1
    UniProtKB/Swiss-Prot
    D3DQ16, Q5VST2, Q5VST3, Q8WZA1, Q9BV55, Q9H9L8, Q9NXF9, Q9NYF7
    UniProtKB/TrEMBL
    A0A8I5KVA5
    Related
    ENSP00000361052.3, ENST00000371984.8
    Conserved Domains (2) summary
    cd02514
    Location:301 → 628
    GT13_GLCNAC-TI; GT13_GLCNAC-TI is involved in an essential step in the synthesis of complex or hybrid-type N-linked oligosaccharides
    cd13937
    Location:99 → 246
    PANDER_GnT-1_2_like; PANDER-like domain of N-acetylglucosaminyltransferases

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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    46188683..46220305 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006710756.2 → XP_006710819.1  protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1 isoform X3

    UniProtKB/TrEMBL
    A0A8I5KVA5
    Related
    ENST00000690377.1
    Conserved Domains (2) summary
    cd02514
    Location:301 → 623
    GT13_GLCNAC-TI; GT13_GLCNAC-TI is involved in an essential step in the synthesis of complex or hybrid-type N-linked oligosaccharides
    cd13937
    Location:99 → 246
    PANDER_GnT-1_2_like; PANDER-like domain of N-acetylglucosaminyltransferases

  2. XM_005271010.2 → XP_005271067.1  protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1 isoform X1

    See identical proteins and their annotated locations for XP_005271067.1

    UniProtKB/TrEMBL
    A0A8I5KNB7, A0A8I5KVA5
    Related
    ENSP00000508453.1, ENST00000692369.1
    Conserved Domains (2) summary
    cd02514
    Location:301 → 628
    GT13_GLCNAC-TI; GT13_GLCNAC-TI is involved in an essential step in the synthesis of complex or hybrid-type N-linked oligosaccharides
    cd13937
    Location:99 → 246
    PANDER_GnT-1_2_like; PANDER-like domain of N-acetylglucosaminyltransferases

  3. XM_006710755.2 → XP_006710818.1  protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1 isoform X1

    See identical proteins and their annotated locations for XP_006710818.1

    UniProtKB/TrEMBL
    A0A8I5KNB7, A0A8I5KVA5
    Conserved Domains (2) summary
    cd02514
    Location:301 → 628
    GT13_GLCNAC-TI; GT13_GLCNAC-TI is involved in an essential step in the synthesis of complex or hybrid-type N-linked oligosaccharides
    cd13937
    Location:99 → 246
    PANDER_GnT-1_2_like; PANDER-like domain of N-acetylglucosaminyltransferases

  4. XM_017001690.2 → XP_016857179.1  protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1 isoform X2

    UniProtKB/Swiss-Prot
    D3DQ16, Q5VST2, Q5VST3, Q8WZA1, Q9BV55, Q9H9L8, Q9NXF9, Q9NYF7
    UniProtKB/TrEMBL
    A0A8I5KVA5
    Related
    ENSP00000508736.1, ENST00000686737.1
    Conserved Domains (2) summary
    cd02514
    Location:301 → 628
    GT13_GLCNAC-TI; GT13_GLCNAC-TI is involved in an essential step in the synthesis of complex or hybrid-type N-linked oligosaccharides
    cd13937
    Location:99 → 246
    PANDER_GnT-1_2_like; PANDER-like domain of N-acetylglucosaminyltransferases

  5. XM_047424511.1 → XP_047280467.1  protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1 isoform X2

    UniProtKB/Swiss-Prot
    D3DQ16, Q5VST2, Q5VST3, Q8WZA1, Q9BV55, Q9H9L8, Q9NXF9, Q9NYF7
    Related
    ENSP00000379698.4, ENST00000396420.8

  6. XM_011541760.4 → XP_011540062.1  protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1 isoform X4

    UniProtKB/TrEMBL
    B7ZAT4
    Conserved Domains (2) summary
    cd02514
    Location:279 → 606
    GT13_GLCNAC-TI; GT13_GLCNAC-TI is involved in an essential step in the synthesis of complex or hybrid-type N-linked oligosaccharides
    cd13937
    Location:77 → 224
    PANDER_GnT-1_2_like; PANDER-like domain of N-acetylglucosaminyltransferases

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    46065903..46097522 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054337537.1 → XP_054193512.1  protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1 isoform X3

  2. XM_054337536.1 → XP_054193511.1  protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1 isoform X1

  3. XM_054337538.1 → XP_054193513.1  protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1 isoform X4

    UniProtKB/TrEMBL
    B7Z7Q4
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8WZA1.2 GenPept UniProtKB/Swiss-Prot:Q8WZA1

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