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

    Gene ID: 55624, updated on 2-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
    mouse all
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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 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. FAM3B/PANDER-Like Carbohydrate-Binding Domain in a Glycosyltransferase, POMGNT1. Manya H, et al. Methods Mol Biol, 2020. PMID 32306360
    2. POMGNT1 Is Glycosylated by Mucin-Type O-Glycans. Xin X, et al. Biol Pharm Bull, 2015. PMID 26328495
    3. Clinical, radiological, and genetic survey of patients with muscle-eye-brain disease caused by mutations in POMGNT1. Yiş U, et al. Pediatr Neurol, 2014 May. PMID 24731844
    4. Promoter alteration causes transcriptional repression of the POMGNT1 gene in limb-girdle muscular dystrophy type 2O. Raducu M, et al. Eur J Hum Genet, 2012 Sep. PMID 22419172, Free PMC Article
    5. Worldwide distribution and broader clinical spectrum of muscle-eye-brain disease. Taniguchi K, et al. Hum Mol Genet, 2003 Mar 1. PMID 12588800

    See all (67) 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 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

    • 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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    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.

    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

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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