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    POMT2 protein O-mannosyltransferase 2 [ Homo sapiens (human) ]

    Gene ID: 29954, updated on 2-Nov-2024

    Summary

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    Official Symbol
    POMT2provided by HGNC
    Official Full Name
    protein O-mannosyltransferase 2provided by HGNC
    Primary source
    HGNC:HGNC:19743
    See related
    Ensembl:ENSG00000009830 MIM:607439; AllianceGenome:HGNC:19743
    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
    LGMD2N; MDDGA2; MDDGB2; MDDGC2; LGMDR14
    Summary
    The protein encoded by this gene is an O-mannosyltransferase that requires interaction with the product of the POMT1 gene for enzymatic function. The encoded protein is found in the membrane of the endoplasmic reticulum. Defects in this gene are a cause of Walker-Warburg syndrome (WWS).[provided by RefSeq, Oct 2008]
    Expression
    Broad expression in testis (RPKM 9.9), thyroid (RPKM 4.1) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See POMT2 in Genome Data Viewer
    Location:
    14q24.3
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (77274956..77320883, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (71484305..71530246, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (77741299..77787226, complement)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903351 Neighboring gene microRNA 1260a Neighboring gene neuroglobin Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5968 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:77769341-77769842 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:77769843-77770342 Neighboring gene Sharpr-MPRA regulatory region 2495 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5969 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5970 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:77787600-77788461 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr14:77795945-77797144 Neighboring gene glutathione S-transferase zeta 1 Neighboring gene transmembrane p24 trafficking protein family member 8 Neighboring gene ATP binding cassette subfamily G member 2 (JR blood group) pseudogene

    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. Clinical exome sequencing identifies novel compound heterozygous mutations of the POMT2 gene in patients with limb-girdle muscular dystrophy. Zhao X, et al. Int J Dev Neurosci, 2023 Feb. PMID 36217604
    2. POMT2 intragenic deletions and splicing abnormalities causing congenital muscular dystrophy with mental retardation. Yanagisawa A, et al. Eur J Med Genet, 2009 Jul-Aug. PMID 19138766
    3. Novel cardiovascular findings in association with a POMT2 mutation: three siblings with α-dystroglycanopathy. Martinez HR, et al. Eur J Hum Genet, 2014 Apr. PMID 24002165, Free PMC Article
    4. A novel POMT2 mutation causes mild congenital muscular dystrophy with normal brain MRI. Murakami T, et al. Brain Dev, 2009 Jun. PMID 18804929, Free PMC Article
    5. Cystic kidneys in fetal Walker-Warburg syndrome with POMT2 mutation: Intrafamilial phenotypic variability in four siblings and review of literature. Nabhan MM, et al. Am J Med Genet A, 2017 Oct. PMID 28815891, Free PMC Article

    See all (47) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Clinical exome sequencing identifies novel compound heterozygous mutations of the POMT2 gene in patients with limb-girdle muscular dystrophy.
      Title: Clinical exome sequencing identifies novel compound heterozygous mutations of the POMT2 gene in patients with limb-girdle muscular dystrophy.
    2. POMT1 and POMT2 gene mutations result in 2 cases of alpha-dystroglycanopathy.", trans "POMT1POMT22alpha-.
      Title: POMT1 and POMT2 gene mutations result in 2 cases of alpha-dystroglycanopathy.
    3. The study expands the mutational spectrum for Limb-girdle Muscular Dystrophy type2N, with the description of 11 novel POMT2 mutations in the association with LGMD2N.
      Title: Limb girdle muscular dystrophy due to mutations in POMT2.
    4. Muscle biopsy revealed absent alpha-dystroglycan on immunostaining and genetic testing confirmed the diagnosis with two previously described POMT2 mutations. This is the first reported case of WWS syndrome associated with noncompaction cardiomyopathy
      Title: Noncompaction cardiomyopathy in an infant with Walker-Warburg syndrome.
    5. POMT2 missense mutation is associated with Cystic kidneys in fetal Walker-Warburg syndrome.
      Title: Cystic kidneys in fetal Walker-Warburg syndrome with POMT2 mutation: Intrafamilial phenotypic variability in four siblings and review of literature.
    6. O-mannosylation of cadherins and protocadherins does not require POMT1 and/or POMT2 in contrast to alpha-dystroglycan, and moreover, the O-Man glycans on cadherins are not elongated.
      Title: Mammalian O-mannosylation of cadherins and plexins is independent of protein O-mannosyltransferases 1 and 2.
    7. Our report is the first to document an association between POMT2 mutations and aortopathy with concomitant depressed left ventricular systolic function.
      Title: Novel cardiovascular findings in association with a POMT2 mutation: three siblings with α-dystroglycanopathy.
    8. the effects of replacing Arg(64), Glu(78) and Arg(138)residues in human POMT1 and POMT2 with Ala on complex formation and enzymatic activity were studied.
      Title: Different roles of the two components of human protein O-mannosyltransferase, POMT1 and POMT2.
    9. the function of the gene products is only known for POMT1, POMT2, and POMGnT1, all responsible for the O-mannosylglycan biosynthesis
      Title: POMGnT1, POMT1, and POMT2 mutations in congenital muscular dystrophies.
    10. the N-glycosylation of POMT1 and POMT2 is required for maintaining the conformation as well as the activity of the POMT1-POMT2 complex.
      Title: Role of N-glycans in maintaining the activity of protein O-mannosyltransferases POMT1 and POMT2.
    Submit: New GeneRIF Correction See all GeneRIFs (23)

    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

    Associated conditions

    Description Tests
    Autosomal recessive limb-girdle muscular dystrophy type 2N
    MedGen: C3150418 OMIM: 613158 GeneReviews: Not available
    		not available
    Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1
    MedGen: C4284790 OMIM: 236670 GeneReviews: Not available
    		not available
    Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2
    MedGen: C3150411 OMIM: 613150 GeneReviews: Not available
    		not available
    Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B2
    MedGen: C3150416 OMIM: 613156 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

    • FLJ22309, DKFZp686G10254

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables dolichyl-phosphate-mannose-protein mannosyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables mannosyltransferase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    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 positive regulation of protein O-linked glycosylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein O-linked mannosylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein O-linked mannosylation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in reactive gliosis IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    protein O-mannosyl-transferase 2
    Names
    dolichyl-phosphate-mannose--protein mannosyltransferase 2
    NP_037514.2
    XP_011534977.1
    XP_011534979.1
    XP_047287268.1
    XP_047287269.1
    XP_047287270.1
    XP_047287271.1
    XP_047287272.1
    XP_047287273.1
    XP_047287274.1
    XP_047287275.1
    XP_047287276.1
    XP_054231897.1
    XP_054231898.1
    XP_054231899.1
    XP_054231900.1
    XP_054231901.1
    XP_054231902.1
    XP_054231903.1
    XP_054231904.1
    XP_054231905.1
    XP_054231906.1
    XP_054231907.1

    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_008897.1 RefSeqGene

      Range
      5001..50927
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_844

    mRNA and Protein(s)

    1. NM_013382.7 → NP_037514.2  protein O-mannosyl-transferase 2

      See identical proteins and their annotated locations for NP_037514.2

      Status: REVIEWED

      Source sequence(s)
      AC007375, AC007954
      Consensus CDS
      CCDS9857.1
      UniProtKB/Swiss-Prot
      Q9NSG6, Q9P1W0, Q9P1W2, Q9UKY4
      UniProtKB/TrEMBL
      A0A804HJN3
      Related
      ENSP00000261534.4, ENST00000261534.9
      Conserved Domains (4) summary
      smart00472
      Location:404 → 459
      MIR; Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases
      COG1928
      Location:50 → 750
      PMT1; Dolichyl-phosphate-mannose--protein O-mannosyl transferase [Posttranslational modification, protein turnover, chaperones]
      pfam02366
      Location:62 → 306
      PMT; Dolichyl-phosphate-mannose-protein mannosyltransferase
      pfam16192
      Location:538 → 748
      PMT_4TMC; C-terminal four TMM region of protein-O-mannosyltransferase

    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_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      77274956..77320883 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047431314.1 → XP_047287270.1  protein O-mannosyl-transferase 2 isoform X4

    2. XM_047431318.1 → XP_047287274.1  protein O-mannosyl-transferase 2 isoform X9

      Related
      ENSP00000451967.2, ENST00000556394.2

    3. XM_011536677.4 → XP_011534979.1  protein O-mannosyl-transferase 2 isoform X7

      UniProtKB/TrEMBL
      A0A804HJN3
      Conserved Domains (4) summary
      smart00472
      Location:251 → 306
      MIR; Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases
      COG1928
      Location:50 → 660
      PMT1; Dolichyl-phosphate-mannose--protein O-mannosyl transferase [Posttranslational modification, protein turnover, chaperones]
      pfam16192
      Location:385 → 658
      PMT_4TMC; C-terminal four TMM region of protein-O-mannosyltransferase
      cl21590
      Location:62 → 168
      PMT_2; Dolichyl-phosphate-mannose-protein mannosyltransferase

    4. XM_047431316.1 → XP_047287272.1  protein O-mannosyl-transferase 2 isoform X6

    5. XM_011536675.3 → XP_011534977.1  protein O-mannosyl-transferase 2 isoform X2

      UniProtKB/TrEMBL
      A0A804HJN3
      Conserved Domains (4) summary
      smart00472
      Location:404 → 459
      MIR; Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases
      COG1928
      Location:50 → 813
      PMT1; Dolichyl-phosphate-mannose--protein O-mannosyl transferase [Posttranslational modification, protein turnover, chaperones]
      pfam02366
      Location:62 → 306
      PMT; Dolichyl-phosphate-mannose-protein mannosyltransferase
      pfam16192
      Location:538 → 811
      PMT_4TMC; C-terminal four TMM region of protein-O-mannosyltransferase

    6. XM_047431313.1 → XP_047287269.1  protein O-mannosyl-transferase 2 isoform X3

    7. XM_047431312.1 → XP_047287268.1  protein O-mannosyl-transferase 2 isoform X1

    8. XM_047431320.1 → XP_047287276.1  protein O-mannosyl-transferase 2 isoform X11

    9. XM_047431319.1 → XP_047287275.1  protein O-mannosyl-transferase 2 isoform X10

      Related
      ENST00000682955.1

    10. XM_047431317.1 → XP_047287273.1  protein O-mannosyl-transferase 2 isoform X8

    11. XM_047431315.1 → XP_047287271.1  protein O-mannosyl-transferase 2 isoform X5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      71484305..71530246 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054375925.1 → XP_054231900.1  protein O-mannosyl-transferase 2 isoform X4

    2. XM_054375930.1 → XP_054231905.1  protein O-mannosyl-transferase 2 isoform X9

    3. XM_054375928.1 → XP_054231903.1  protein O-mannosyl-transferase 2 isoform X7

    4. XM_054375927.1 → XP_054231902.1  protein O-mannosyl-transferase 2 isoform X6

    5. XM_054375923.1 → XP_054231898.1  protein O-mannosyl-transferase 2 isoform X2

    6. XM_054375924.1 → XP_054231899.1  protein O-mannosyl-transferase 2 isoform X3

    7. XM_054375922.1 → XP_054231897.1  protein O-mannosyl-transferase 2 isoform X1

    8. XM_054375932.1 → XP_054231907.1  protein O-mannosyl-transferase 2 isoform X11

    9. XM_054375931.1 → XP_054231906.1  protein O-mannosyl-transferase 2 isoform X10

    10. XM_054375929.1 → XP_054231904.1  protein O-mannosyl-transferase 2 isoform X8

    11. XM_054375926.1 → XP_054231901.1  protein O-mannosyl-transferase 2 isoform X5

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UKY4.2 GenPept UniProtKB/Swiss-Prot:Q9UKY4

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