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Aliases for POMGNT2 Gene

Aliases for POMGNT2 Gene

  • Protein O-Linked Mannose N-Acetylglucosaminyltransferase 2 (Beta 1,4-) 2 3 5
  • Glycosyltransferase-Like Domain-Containing Protein 2 3 4
  • Glycosyltransferase-Like Domain Containing 2 2 3
  • C3orf39 3 4
  • GTDC2 3 4
  • AGO61 3 4
  • Protein O-Linked-Mannose Beta-1,4-N-Acetylglucosaminyltransferase 2 3
  • Extracellular O-Linked N-Acetylglucosamine Transferase-Like 4
  • Chromosome 3 Open Reading Frame 39 2
  • EC 2.4.1.- 4
  • POMGnT2 4
  • MDDGA8 3
  • EOGTL 4

External Ids for POMGNT2 Gene

Previous HGNC Symbols for POMGNT2 Gene

  • C3orf39
  • GTDC2

Summaries for POMGNT2 Gene

Entrez Gene Summary for POMGNT2 Gene

  • This gene encodes a protein with glycosyltransferase activity although its function is not currently known. [provided by RefSeq, Sep 2012]

GeneCards Summary for POMGNT2 Gene

POMGNT2 (Protein O-Linked Mannose N-Acetylglucosaminyltransferase 2 (Beta 1,4-)) is a Protein Coding gene. Diseases associated with POMGNT2 include Muscular Dystrophy-Dystroglycanopathy (Congenital With Brain And Eye Anomalies, Type A, 8 and Walker-Warburg Syndrome. Among its related pathways are Mannose type O-glycan biosynthesis and O-linked glycosylation. GO annotations related to this gene include transferase activity, transferring glycosyl groups and protein O-GlcNAc transferase activity. An important paralog of this gene is EOGT.

UniProtKB/Swiss-Prot for POMGNT2 Gene

  • O-linked mannose beta-1,4-N-acetylglucosaminyltransferase that tranfers UDP-N-acetyl-D-glucosamine to the 4-position of the mannose to generate N-acetyl-D-glucosamine-beta-1,4-O-D-mannosylprotein. Involved in the biosynthesis of the phosphorylated O-mannosyl trisaccharide (N-acetylgalactosamine-beta-3-N-acetylglucosamine-beta-4-(phosphate-6-)mannose), a carbohydrate structure present in alpha-dystroglycan (DAG1), which is required for binding laminin G-like domain-containing extracellular proteins with high affinity.

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for POMGNT2 Gene

Genomics for POMGNT2 Gene

Regulatory Elements for POMGNT2 Gene

Enhancers for POMGNT2 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH03G043011 1.3 Ensembl ENCODE dbSUPER 16.8 +87.4 87414 14.5 ZBTB21 ZFP64 TAL1 ZBTB40 ZIC2 FOSL1 TCF12 NFE2 TRIM24 MAFK POMGNT2 FAM198A HIGD1A PIR62180 PIR49761
GH03G042759 1.6 Ensembl ENCODE dbSUPER 10.6 +344.5 344461 3.6 HDGF PKNOX1 MLX ZFP64 ARID4B SIN3A DMAP1 FEZF1 ZNF2 YY1 CCDC13-AS1 KRBOX1 SEC22C POMGNT2 HIGD1A LINC02158
GH03G042700 1.5 Ensembl ENCODE dbSUPER 10.6 +403.9 403872 2.5 PKNOX1 ZFP64 ARID4B SIN3A ZNF2 ZNF48 SLC30A9 ZNF143 KLF13 KDM4B KRBOX1 SEC22C POMGNT2 HHATL HHATL-AS1 KLHL40
GH03G042819 1.3 ENCODE dbSUPER 10.6 +286.1 286107 1.3 PKNOX1 FOXA2 ARNT FEZF1 ZNF2 ZNF121 GLIS2 ZNF302 FOS KLF7 SEC22C POMGNT2 NKTR KRBOX1 ENSG00000235288
GH03G043105 1 ENCODE 13.5 +0.2 200 1.6 ATF1 CREB3L1 ARID4B SIN3A YY1 ETS1 GLIS2 GATA2 ZNF207 ZNF143 POMGNT2 HIGD1A ENSG00000271941 ENSG00000227245
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around POMGNT2 on UCSC Golden Path with GeneCards custom track

Promoters for POMGNT2 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000151442 183 1400 ATF1 CREB3L1 ARID4B SIN3A YY1 ETS1 GLIS2 GATA2 ZNF207 ZNF143

Genomic Location for POMGNT2 Gene

Chromosome:
3
Start:
43,079,229 bp from pter
End:
43,106,083 bp from pter
Size:
26,855 bases
Orientation:
Minus strand

Genomic View for POMGNT2 Gene

Genes around POMGNT2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
POMGNT2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for POMGNT2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for POMGNT2 Gene

Proteins for POMGNT2 Gene

  • Protein details for POMGNT2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8NAT1-PMGT2_HUMAN
    Recommended name:
    Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
    Protein Accession:
    Q8NAT1
    Secondary Accessions:
    • B3KWC3
    • Q96SY3

    Protein attributes for POMGNT2 Gene

    Size:
    580 amino acids
    Molecular mass:
    66615 Da
    Quaternary structure:
    No Data Available

neXtProt entry for POMGNT2 Gene

Post-translational modifications for POMGNT2 Gene

  • Glycosylation at Thr43, Asn99, and posLast=276276
  • Modification sites at PhosphoSitePlus

Other Protein References for POMGNT2 Gene

No data available for DME Specific Peptides for POMGNT2 Gene

Domains & Families for POMGNT2 Gene

Gene Families for POMGNT2 Gene

Protein Domains for POMGNT2 Gene

Suggested Antigen Peptide Sequences for POMGNT2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q8NAT1

UniProtKB/Swiss-Prot:

PMGT2_HUMAN :
  • Belongs to the glycosyltransferase 61 family.
Family:
  • Belongs to the glycosyltransferase 61 family.
genes like me logo Genes that share domains with POMGNT2: view

Function for POMGNT2 Gene

Molecular function for POMGNT2 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
UDP-N-acetyl-alpha-D-glucosamine + O-alpha-D-mannosylprotein = UDP + N-acetyl-beta-D-glucosaminyl-(1->4)-O-alpha-D-mannosylprotein.
UniProtKB/Swiss-Prot Function:
O-linked mannose beta-1,4-N-acetylglucosaminyltransferase that tranfers UDP-N-acetyl-D-glucosamine to the 4-position of the mannose to generate N-acetyl-D-glucosamine-beta-1,4-O-D-mannosylprotein. Involved in the biosynthesis of the phosphorylated O-mannosyl trisaccharide (N-acetylgalactosamine-beta-3-N-acetylglucosamine-beta-4-(phosphate-6-)mannose), a carbohydrate structure present in alpha-dystroglycan (DAG1), which is required for binding laminin G-like domain-containing extracellular proteins with high affinity.

Enzyme Numbers (IUBMB) for POMGNT2 Gene

Gene Ontology (GO) - Molecular Function for POMGNT2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25416956
GO:0008375 acetylglucosaminyltransferase activity TAS --
GO:0016740 transferase activity IEA --
GO:0016757 transferase activity, transferring glycosyl groups IEA --
GO:0097363 protein O-GlcNAc transferase activity IDA 23929950
genes like me logo Genes that share ontologies with POMGNT2: view
genes like me logo Genes that share phenotypes with POMGNT2: view

Human Phenotype Ontology for POMGNT2 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for POMGNT2 Gene

MGI Knock Outs for POMGNT2:

Animal Model Products

CRISPR Products

miRNA for POMGNT2 Gene

miRTarBase miRNAs that target POMGNT2

Inhibitory RNA Products

No data available for Transcription Factor Targets and HOMER Transcription for POMGNT2 Gene

Localization for POMGNT2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for POMGNT2 Gene

Endoplasmic reticulum membrane; Single-pass type II membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for POMGNT2 gene
Compartment Confidence
endoplasmic reticulum 5
extracellular 2
plasma membrane 1
cytosol 1
lysosome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for POMGNT2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum IEA,IDA 23929950
GO:0005789 endoplasmic reticulum membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with POMGNT2: view

Pathways & Interactions for POMGNT2 Gene

genes like me logo Genes that share pathways with POMGNT2: view

Pathways by source for POMGNT2 Gene

UniProtKB/Swiss-Prot Q8NAT1-PMGT2_HUMAN

  • Pathway: Protein modification; protein glycosylation.

Interacting Proteins for POMGNT2 Gene

Gene Ontology (GO) - Biological Process for POMGNT2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001764 neuron migration ISS --
GO:0006486 protein glycosylation IEA --
GO:0006493 protein O-linked glycosylation TAS --
GO:0035269 protein O-linked mannosylation ISS --
genes like me logo Genes that share ontologies with POMGNT2: view

No data available for SIGNOR curated interactions for POMGNT2 Gene

Drugs & Compounds for POMGNT2 Gene

(17) Drugs for POMGNT2 Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Uridine-5'-Diphosphate Experimental Pharma 0

(36) Additional Compounds for POMGNT2 Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Uridine diphosphate-N-acetylglucosamine
  • N-[2-[[[5-[(2,4-Dioxo-1H-pyrimidin-1-yl)]-3,4-dihydroxy-tetrahydrofuran-2-yl]methoxy-hydroxy-phosphinoyl]oxy-hydroxy-phosphinoyl]oxy-4,5-dihydroxy-6-(hydroxymethyl)tetrahydropyran-3-yl]acetamide
  • UDP-a-D-N-Acetylglucosamine
  • UDP-Acetyl-D-glucosamine
  • UDP-Acetyl-delta-glucosamine
  • UDP-Acetylglucosamine
528-04-1
genes like me logo Genes that share compounds with POMGNT2: view

Transcripts for POMGNT2 Gene

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for POMGNT2 Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b
SP1:
SP2: -

Relevant External Links for POMGNT2 Gene

GeneLoc Exon Structure for
POMGNT2
ECgene alternative splicing isoforms for
POMGNT2

Expression for POMGNT2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for POMGNT2 Gene

Protein differential expression in normal tissues from HIPED for POMGNT2 Gene

This gene is overexpressed in Nasal epithelium (60.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for POMGNT2 Gene



Protein tissue co-expression partners for POMGNT2 Gene

NURSA nuclear receptor signaling pathways regulating expression of POMGNT2 Gene:

POMGNT2

mRNA Expression by UniProt/SwissProt for POMGNT2 Gene:

Q8NAT1-PMGT2_HUMAN
Tissue specificity: Highly expressed in the brain, muscle, heart, and kidney in both fetus and adult. In the brain, highest expression in the cortex and cerebellum. Highly expressed in the pancreas.

Evidence on tissue expression from TISSUES for POMGNT2 Gene

  • Nervous system(4.4)

Phenotype-based relationships between genes and organs from Gene ORGANizer for POMGNT2 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • endocrine
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Organs:
Head and neck:
  • brain
  • cerebellum
  • cerebrospinal fluid
  • cheek
  • chin
  • cranial nerve
  • ear
  • eye
  • face
  • forehead
  • head
  • inner ear
  • jaw
  • lip
  • mandible
  • maxilla
  • meninges
  • middle ear
  • mouth
  • neck
  • nose
  • outer ear
  • pituitary gland
  • skull
  • tongue
Thorax:
  • breast
  • chest wall
  • clavicle
  • heart
  • heart valve
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
Abdomen:
  • intestine
  • kidney
  • large intestine
Pelvis:
  • anus
  • ovary
  • pelvis
  • penis
  • prostate
  • rectum
  • testicle
  • ureter
  • uterus
  • vagina
  • vulva
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • blood
  • blood vessel
  • hair
  • peripheral nerve
  • peripheral nervous system
  • red blood cell
  • skin
  • spinal column
  • spinal cord
  • vertebrae
genes like me logo Genes that share expression patterns with POMGNT2: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for POMGNT2 Gene

Orthologs for POMGNT2 Gene

This gene was present in the common ancestor of animals.

Orthologs for POMGNT2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia GTDC2 34 35
  • 99.71 (n)
cow
(Bos Taurus)
Mammalia GTDC2 34 35
  • 90 (n)
dog
(Canis familiaris)
Mammalia GTDC2 34 35
  • 89.6 (n)
mouse
(Mus musculus)
Mammalia Pomgnt2 34 16 35
  • 88.68 (n)
rat
(Rattus norvegicus)
Mammalia Pomgnt2 34
  • 88.33 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia POMGNT2 35
  • 80 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia POMGNT2 35
  • 67 (a)
OneToOne
chicken
(Gallus gallus)
Aves POMGNT2 35
  • 80 (a)
OneToOne
C2H3ORF39 34
  • 75.1 (n)
lizard
(Anolis carolinensis)
Reptilia POMGNT2 35
  • 81 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia pomgnt2 34
  • 68.17 (n)
Str.19414 34
zebrafish
(Danio rerio)
Actinopterygii pomgnt2 34 35
  • 70.24 (n)
fruit fly
(Drosophila melanogaster)
Insecta Eogt 35
  • 18 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea H12D21.10 35
  • 15 (a)
OneToMany
Species where no ortholog for POMGNT2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for POMGNT2 Gene

ENSEMBL:
Gene Tree for POMGNT2 (if available)
TreeFam:
Gene Tree for POMGNT2 (if available)

Paralogs for POMGNT2 Gene

Paralogs for POMGNT2 Gene

genes like me logo Genes that share paralogs with POMGNT2: view

Variants for POMGNT2 Gene

Sequence variations from dbSNP and Humsavar for POMGNT2 Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type
rs387907300 Pathogenic, Muscular dystrophy-dystroglycanopathy congenital with brain and eye anomalies A8 (MDDGA8) [MIM:614830] 43,080,959(-) CAACC(A/G)CTTCA reference, missense
rs387907299 Pathogenic 43,080,099(-) TCTTC(C/T)GAATC reference, stop-gained
rs138980930 Likely benign 43,080,758(+) GCAGC(C/T)GGCCC reference, missense
rs141319921 Likely benign 43,080,466(+) TCCAG(C/G)GACAC reference, synonymous-codon
rs143832191 Likely benign 43,079,830(+) GGCAC(A/G)TAGGT reference, synonymous-codon

Structural Variations from Database of Genomic Variants (DGV) for POMGNT2 Gene

Variant ID Type Subtype PubMed ID
esv3377835 CNV insertion 20981092
nsv590149 CNV gain 21841781
nsv834672 CNV loss 17160897
nsv954473 CNV deletion 24416366

Variation tolerance for POMGNT2 Gene

Residual Variation Intolerance Score: 75.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.13; 61.33% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for POMGNT2 Gene

Human Gene Mutation Database (HGMD)
POMGNT2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
POMGNT2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for POMGNT2 Gene

Disorders for POMGNT2 Gene

MalaCards: The human disease database

(17) MalaCards diseases for POMGNT2 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies, type a, 8
  • muscular dystrophy-dystroglycanopathy congenital with brain and eye anomalies a8
walker-warburg syndrome
  • cerebroocular dysplasia-muscular dystrophy syndrome
gtdc2-related muscle diseases
  • mddga8
hereditary multiple osteochondromas
  • hereditary multiple exostoses
exostosis
  • bone spur
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

PMGT2_HUMAN
  • Muscular dystrophy-dystroglycanopathy congenital with brain and eye anomalies A8 (MDDGA8) [MIM:614830]: An autosomal recessive disorder characterized by congenital muscular dystrophy associated with cobblestone lissencephaly and other brain anomalies, eye malformations, profound mental retardation, and death usually in the first years of life. Included diseases are the more severe Walker-Warburg syndrome and the slightly less severe muscle-eye-brain disease. {ECO:0000269 PubMed:22958903}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for POMGNT2

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
POMGNT2
genes like me logo Genes that share disorders with POMGNT2: view

No data available for Genatlas for POMGNT2 Gene

Publications for POMGNT2 Gene

  1. SGK196 is a glycosylation-specific O-mannose kinase required for dystroglycan function. (PMID: 23929950) Yoshida-Moriguchi T. … Campbell K.P. (Science 2013) 3 4 64
  2. Exome sequencing and functional validation in zebrafish identify GTDC2 mutations as a cause of Walker-Warburg syndrome. (PMID: 22958903) Manzini M.C. … Walsh C.A. (Am. J. Hum. Genet. 2012) 3 4 64
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg R.L. … Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002) 2 3 64

Products for POMGNT2 Gene

Sources for POMGNT2 Gene

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