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Aliases for NGLY1 Gene

Aliases for NGLY1 Gene

  • N-Glycanase 1 2 3 4 5
  • Peptide-N(4)-(N-Acetyl-Beta-Glucosaminyl)Asparagine Amidase 2 3
  • Peptide:N-Glycanase 3 4
  • EC 3.5.1.52 4 61
  • HPNGase 3 4
  • PNGase 3 4
  • PNG1 3 4
  • CDG1V 3
  • CDDG 3

External Ids for NGLY1 Gene

Previous GeneCards Identifiers for NGLY1 Gene

  • GC03M025468
  • GC03M025610
  • GC03M025735

Summaries for NGLY1 Gene

Entrez Gene Summary for NGLY1 Gene

  • This gene encodes an enzyme that catalyzes hydrolysis of an N(4)-(acetyl-beta-D-glucosaminyl) asparagine residue to N-acetyl-beta-D-glucosaminylamine and a peptide containing an aspartate residue. The encoded enzyme may play a role in the proteasome-mediated degradation of misfolded glycoproteins. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Feb 2009]

GeneCards Summary for NGLY1 Gene

NGLY1 (N-Glycanase 1) is a Protein Coding gene. Diseases associated with NGLY1 include Congenital Disorder Of Deglycosylation and Ngly1-Cdg. Among its related pathways are Transport to the Golgi and subsequent modification and Calnexin/calreticulin cycle. GO annotations related to this gene include damaged DNA binding and peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity.

UniProtKB/Swiss-Prot for NGLY1 Gene

  • Specifically deglycosylates the denatured form of N-linked glycoproteins in the cytoplasm and assists their proteasome-mediated degradation. Cleaves the beta-aspartyl-glucosamine (GlcNAc) of the glycan and the amide side chain of Asn, converting Asn to Asp. Prefers proteins containing high-mannose over those bearing complex type oligosaccharides. Can recognize misfolded proteins in the endoplasmic reticulum that are exported to the cytosol to be destroyed and deglycosylate them, while it has no activity toward native proteins. Deglycosylation is a prerequisite for subsequent proteasome-mediated degradation of some, but not all, misfolded glycoproteins.

Gene Wiki entry for NGLY1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NGLY1 Gene

Genomics for NGLY1 Gene

Regulatory Elements for NGLY1 Gene

Enhancers for NGLY1 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
GH03F025820 0.7 Ensembl ENCODE 11.6 -30.6 -30596 1.2 BHLHE40 MAFG ZNF316 HMBOX1 NFE2 FOS MAFK EMSY NFE2L2 NGLY1 OXSM GC03P025816 LOC105377000
GH03F025723 0.2 ENCODE 11.3 +65.0 64981 2.5 GATA3 PKNOX1 RFX1 CTBP1 MNT FOS FOSL2 SUPT5H OXSM NGLY1 GC03M025722 PIR50853
GH03F025653 0.4 Ensembl 11.2 +134.6 134639 4.4 PKNOX1 ZFP3 SCRT2 CEBPB FEZF1 EBF1 OXSM NGLY1 TOP2B MIR4442 GC03M025633
GH03F025854 1.1 Ensembl ENCODE 11 -64.6 -64598 0.9 DPF2 ZNF217 GATA3 CTBP1 MAFF FOSL2 FOS NFE2 MAFK EZH2 NGLY1 OXSM LINC00692 LOC105377000
GH03F026103 1 FANTOM5 ENCODE 6.7 -315.2 -315154 3.2 PKNOX1 EED TCF7 EBF1 EP300 SPI1 NGLY1 TOP2B GC03M026123 PIR51645
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around NGLY1 on UCSC Golden Path with GeneCards custom track

Promoters for NGLY1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001359683 238 2400 HDGF PKNOX1 CREB3L1 MLX WRNIP1 ZFP64 ARID4B SIN3A DMAP1 ZNF2

Genomic Location for NGLY1 Gene

Chromosome:
3
Start:
25,718,944 bp from pter
End:
25,790,039 bp from pter
Size:
71,096 bases
Orientation:
Minus strand

Genomic View for NGLY1 Gene

Genes around NGLY1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NGLY1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NGLY1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NGLY1 Gene

Proteins for NGLY1 Gene

  • Protein details for NGLY1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96IV0-NGLY1_HUMAN
    Recommended name:
    Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase
    Protein Accession:
    Q96IV0
    Secondary Accessions:
    • B4DJE9
    • Q59FB1
    • Q6PJD8
    • Q9BVR8
    • Q9NR70

    Protein attributes for NGLY1 Gene

    Size:
    654 amino acids
    Molecular mass:
    74390 Da
    Cofactor:
    Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
    Quaternary structure:
    • Component of a complex required to couple retrotranslocation, ubiquitination and deglycosylation composed of NGLY1, SAKS1, AMFR, VCP and RAD23B. Interacts with the proteasome components RAD23B and PSMC1. Interacts with directly with VCP. Interacts with DERL1, bringing it close to the endoplasmic reticulum membrane. Interacts with SAKS1.
    Miscellaneous:
    • In case of infection by cytomegaloviruses, it is not essential for degradation of MHC class I heavy chains.
    SequenceCaution:
    • Sequence=AAH17220.1; Type=Erroneous termination; Positions=77; Note=Translated as Glu.; Evidence={ECO:0000305}; Sequence=BAD92786.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for NGLY1 Gene

    Alternative splice isoforms for NGLY1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for NGLY1 Gene

Selected DME Specific Peptides for NGLY1 Gene

Q96IV0:
  • AFSTRLLPVRGAVECLFEMGF
  • ISWKFEC
  • SYVIAFS
  • DVTWRYSCKH
  • EKYRSIR
  • DDELKWGAK
  • GRCGEWANCF
  • DHVWTEVYS
  • GFEARYV
  • EDFLLLELL
  • AWQHTQLFR
  • VELVEFISPK
  • CDKPLLYE
  • MVYLARKEGSS
  • QLFRQSL

Post-translational modifications for NGLY1 Gene

  • Ubiquitination at Lys 92, Lys 123, Lys 204, Lys 272, Lys 300, Lys 419, Lys 448, Lys 451, Lys 477, and Lys 501
  • Modification sites at PhosphoSitePlus

Domains & Families for NGLY1 Gene

Graphical View of Domain Structure for InterPro Entry

Q96IV0

UniProtKB/Swiss-Prot:

NGLY1_HUMAN :
  • The PUB domain mediates the interaction with VCP.
  • Belongs to the transglutaminase-like superfamily. PNGase family.
Domain:
  • The PUB domain mediates the interaction with VCP.
  • Contains 1 PAW domain.
  • Contains 1 PUB (PUG) domain.
Family:
  • Belongs to the transglutaminase-like superfamily. PNGase family.
genes like me logo Genes that share domains with NGLY1: view

No data available for Gene Families for NGLY1 Gene

Function for NGLY1 Gene

Molecular function for NGLY1 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
Hydrolysis of an N(4)-(acetyl-beta-D-glucosaminyl)asparagine residue in which the glucosamine residue may be further glycosylated, to yield a (substituted) N-acetyl-beta-D-glucosaminylamine and a peptide containing an aspartate residue.
UniProtKB/Swiss-Prot EnzymeRegulation:
Inhibited by Z-VAD-fmk, a well-known caspase inhibitor, which inhibits enzyme activity through covalent binding of the carbohydrate to the single Cys-306 residue.
UniProtKB/Swiss-Prot Function:
Specifically deglycosylates the denatured form of N-linked glycoproteins in the cytoplasm and assists their proteasome-mediated degradation. Cleaves the beta-aspartyl-glucosamine (GlcNAc) of the glycan and the amide side chain of Asn, converting Asn to Asp. Prefers proteins containing high-mannose over those bearing complex type oligosaccharides. Can recognize misfolded proteins in the endoplasmic reticulum that are exported to the cytosol to be destroyed and deglycosylate them, while it has no activity toward native proteins. Deglycosylation is a prerequisite for subsequent proteasome-mediated degradation of some, but not all, misfolded glycoproteins.

Enzyme Numbers (IUBMB) for NGLY1 Gene

Gene Ontology (GO) - Molecular Function for NGLY1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000224 peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity IBA --
GO:0005515 protein binding IPI 15358861
GO:0016787 hydrolase activity IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with NGLY1: view
genes like me logo Genes that share phenotypes with NGLY1: view

Human Phenotype Ontology for NGLY1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

  • Taconic Biosciences Mouse Models for NGLY1

miRNA for NGLY1 Gene

miRTarBase miRNAs that target NGLY1

Flow Cytometry Products

No data available for Animal Models , Transcription Factor Targets and HOMER Transcription for NGLY1 Gene

Localization for NGLY1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NGLY1 Gene

Cytoplasm.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for NGLY1 Gene COMPARTMENTS Subcellular localization image for NGLY1 gene
Compartment Confidence
cytosol 3
endoplasmic reticulum 2
nucleus 2
extracellular 1
vacuole 1

Gene Ontology (GO) - Cellular Components for NGLY1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA --
GO:0005737 cytoplasm IDA 15358861
GO:0005829 cytosol IBA --
genes like me logo Genes that share ontologies with NGLY1: view

Pathways & Interactions for NGLY1 Gene

genes like me logo Genes that share pathways with NGLY1: view

Gene Ontology (GO) - Biological Process for NGLY1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006515 misfolded or incompletely synthesized protein catabolic process IBA --
GO:0006516 glycoprotein catabolic process IDA 15358861
GO:0006517 protein deglycosylation IBA --
genes like me logo Genes that share ontologies with NGLY1: view

No data available for SIGNOR curated interactions for NGLY1 Gene

Drugs & Compounds for NGLY1 Gene

(1) Drugs for NGLY1 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Glucosamine Approved Nutra 182
genes like me logo Genes that share compounds with NGLY1: view

Transcripts for NGLY1 Gene

Unigene Clusters for NGLY1 Gene

N-glycanase 1:
Representative Sequences:

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for NGLY1 Gene

ExUns: 1 ^ 2a · 2b · 2c · 2d · 2e ^ 3 ^ 4a · 4b · 4c · 4d ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9 ^ 10a · 10b · 10c ^ 11a · 11b ^ 12 ^ 13 ^ 14 ^ 15a ·
SP1: - - - - - - -
SP2: - - - - - -
SP3: - - - - - - -
SP4: - - - - - -
SP5: - - - - -
SP6: - - - -
SP7: - - - - - - -
SP8: - -
SP9: - -
SP10: - - - - - - -
SP11:
SP12: - -
SP13: -

ExUns: 15b ^ 16 ^ 17a · 17b · 17c
SP1:
SP2:
SP3: -
SP4:
SP5:
SP6: -
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:

Relevant External Links for NGLY1 Gene

GeneLoc Exon Structure for
NGLY1
ECgene alternative splicing isoforms for
NGLY1

Expression for NGLY1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for NGLY1 Gene

Protein differential expression in normal tissues from HIPED for NGLY1 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (12.2) and Testis (6.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for NGLY1 Gene



Protein tissue co-expression partners for NGLY1 Gene

NURSA nuclear receptor signaling pathways regulating expression of NGLY1 Gene:

NGLY1

SOURCE GeneReport for Unigene cluster for NGLY1 Gene:

Hs.368960
genes like me logo Genes that share expression patterns with NGLY1: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for NGLY1 Gene

Orthologs for NGLY1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for NGLY1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia NGLY1 34 35
  • 99.18 (n)
dog
(Canis familiaris)
Mammalia NGLY1 34 35
  • 92.09 (n)
cow
(Bos Taurus)
Mammalia NGLY1 34 35
  • 85.83 (n)
mouse
(Mus musculus)
Mammalia Ngly1 34 16 35
  • 85.26 (n)
rat
(Rattus norvegicus)
Mammalia Ngly1 34
  • 83.65 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia NGLY1 35
  • 73 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia NGLY1 35
  • 71 (a)
OneToOne
chicken
(Gallus gallus)
Aves NGLY1 34 35
  • 70.25 (n)
lizard
(Anolis carolinensis)
Reptilia NGLY1 35
  • 69 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ngly1 34
  • 67.25 (n)
zebrafish
(Danio rerio)
Actinopterygii ngly1 34 35
  • 60.66 (n)
fruit fly
(Drosophila melanogaster)
Insecta Pngl 34 35
  • 46.22 (n)
PNGase 36
  • 33 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007390 34
  • 45.29 (n)
worm
(Caenorhabditis elegans)
Secernentea png-1 34 35
  • 46.81 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PNG1 34 35 37
  • 49.77 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0E24223g 34
  • 46.99 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ABR193W 34
  • 44.98 (n)
wheat
(Triticum aestivum)
Liliopsida Ta.7525 34
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPBC1709.14 34
  • 49.95 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU00651 34
  • 48.3 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 41 (a)
OneToMany
-- 35
  • 29 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.8469 34
Species where no ortholog for NGLY1 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • 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 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)

Evolution for NGLY1 Gene

ENSEMBL:
Gene Tree for NGLY1 (if available)
TreeFam:
Gene Tree for NGLY1 (if available)

Paralogs for NGLY1 Gene

No data available for Paralogs for NGLY1 Gene

Variants for NGLY1 Gene

Sequence variations from dbSNP and Humsavar for NGLY1 Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type
rs201337954 Pathogenic 25,733,931(+) TCTTC(A/C/T)GGCAA nc-transcript-variant, reference, missense, utr-variant-3-prime, stop-gained
rs528583612 Pathogenic 25,720,179(+) CTTTC(A/G)GGCCA intron-variant, nc-transcript-variant, reference, stop-gained
rs587776982 Pathogenic 25,719,534(+) CAGCT(-/G)GGTGT nc-transcript-variant, reference, utr-variant-3-prime, frameshift-variant
rs587777265 Pathogenic 25,732,374(+) TCTTC(-/C)CCCCA intron-variant, nc-transcript-variant, reference, frameshift-variant
rs587777266 Pathogenic 25,733,925(+) CTTAG(-/TTC)TTCTG nc-transcript-variant, cds-indel

Structural Variations from Database of Genomic Variants (DGV) for NGLY1 Gene

Variant ID Type Subtype PubMed ID
dgv71n17 CNV loss 16327808
esv2725055 CNV deletion 23290073
esv2763742 CNV gain 21179565
esv3561630 CNV deletion 23714750
esv3893676 CNV loss 25118596
nsv3736 CNV insertion 18451855
nsv965150 CNV duplication 23825009

Variation tolerance for NGLY1 Gene

Residual Variation Intolerance Score: 16.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.23; 40.17% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for NGLY1 Gene

Human Gene Mutation Database (HGMD)
NGLY1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
NGLY1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NGLY1 Gene

Disorders for NGLY1 Gene

MalaCards: The human disease database

(6) MalaCards diseases for NGLY1 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
congenital disorder of deglycosylation
  • ngly1-deficiency
ngly1-cdg
  • congenital disorder of glycosylation, type iv
juvenile astrocytoma
  • pediatric astrocytoma
childhood pilocytic astrocytoma
  • pediatric pilocytic astrocytoma
juvenile pilocytic astrocytoma
- elite association - COSMIC cancer census association via MalaCards
Search NGLY1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

NGLY1_HUMAN
  • Congenital disorder of deglycosylation (CDDG) [MIM:615273]: A multisystem disorder characterized by developmental delay, hypotonia, abnormal involuntary movements and alacrima or poor tear production. Other features include microcephaly, intractable seizures, abnormal eye movements and evidence of liver dysfunction, probably due to cytoplasmic accumulation of storage material in vacuoles. {ECO:0000269 PubMed:22581936, ECO:0000269 PubMed:24651605}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for NGLY1

Genetic Association Database (GAD)
NGLY1
Human Genome Epidemiology (HuGE) Navigator
NGLY1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
NGLY1
genes like me logo Genes that share disorders with NGLY1: view

No data available for Genatlas for NGLY1 Gene

Publications for NGLY1 Gene

  1. A glycosylated type I membrane protein becomes cytosolic when peptide: N-glycanase is compromised. (PMID: 14749736) Blom D. … Ploegh H.L. (EMBO J. 2004) 3 4 22 64
  2. Mutations in NGLY1 cause an inherited disorder of the endoplasmic reticulum-associated degradation pathway. (PMID: 24651605) Enns G.M. … Goldstein D.B. (Genet. Med. 2014) 3 4 64
  3. The PUB domain functions as a p97 binding module in human peptide N- glycanase. (PMID: 16807242) Allen M.D. … Bycroft M. (J. Biol. Chem. 2006) 3 4 64
  4. The retrotranslocation protein derlin-1 binds peptide:N-glycanase to the endoplasmic reticulum. (PMID: 16055502) Katiyar S. … Lennarz W.J. (Mol. Biol. Cell 2005) 3 4 64
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64

Products for NGLY1 Gene

Sources for NGLY1 Gene

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