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

Gene ID: 29954, updated on 23-Nov-2023

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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (77274956..77320883, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (71484305..71530246, complement)
105.20220307 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 (Junior 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
  • 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. Limb girdle muscular dystrophy due to mutations in POMT2. Østergaard ST, et al. J Neurol Neurosurg Psychiatry, 2018 May. PMID 29175898
  3. Noncompaction cardiomyopathy in an infant with Walker-Warburg syndrome. Abdullah S, et al. Am J Med Genet A, 2017 Nov. PMID 28980384
  4. 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
  5. 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

See all (46) 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

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_2023_10

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

    UniProtKB/TrEMBL
    Q6AHY3

  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

    UniProtKB/TrEMBL
    A0A804HJN3

  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

    UniProtKB/TrEMBL
    A0A804HJN3

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

    UniProtKB/TrEMBL
    A0A804HJN3

  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

    UniProtKB/TrEMBL
    Q6AHY3

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

    UniProtKB/TrEMBL
    Q59GJ5

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

    UniProtKB/TrEMBL
    Q6AHY3

  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

    UniProtKB/TrEMBL
    A0A804HJN3

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

    UniProtKB/TrEMBL
    A0A804HJN3

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

    UniProtKB/TrEMBL
    A0A804HJN3

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

    UniProtKB/TrEMBL
    A0A804HJN3

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

    UniProtKB/TrEMBL
    A0A804HJN3

  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

    UniProtKB/TrEMBL
    Q6AHY3

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

    UniProtKB/TrEMBL
    Q59GJ5
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9UKY4.2 GenPept UniProtKB/Swiss-Prot:Q9UKY4

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