Gene Gene information from NCBI Gene database.
Entrez ID 55768
Gene name N-glycanase 1
Gene symbol NGLY1
Synonyms (NCBI Gene)
CDDGCDG1VPNG-1PNG1PNGase
Chromosome 3
Chromosome location 3p24.2
Summary 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-media
SNPs SNP information provided by dbSNP.
37
SNP ID Visualize variation Clinical significance Consequence
rs146140738 G>A Pathogenic, likely-pathogenic Stop gained, coding sequence variant, non coding transcript variant
rs200561967 G>A Pathogenic Coding sequence variant, non coding transcript variant, stop gained
rs201337954 T>A,C Pathogenic Coding sequence variant, non coding transcript variant, missense variant, stop gained
rs201791209 C>A,T Pathogenic-likely-pathogenic Coding sequence variant, missense variant, non coding transcript variant, stop gained
rs528583612 G>A Pathogenic Non coding transcript variant, intron variant, coding sequence variant, genic downstream transcript variant, stop gained
miRNA miRNA information provided by mirtarbase database.
26
miRTarBase ID miRNA Experiments Reference
MIRT045306 hsa-miR-186-5p CLASH 23622248
MIRT1184201 hsa-miR-383 CLIP-seq
MIRT1184202 hsa-miR-4266 CLIP-seq
MIRT1184203 hsa-miR-4735-5p CLIP-seq
MIRT1184204 hsa-miR-4772-5p CLIP-seq
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
17
GO ID Ontology Definition Evidence Reference
GO:0000224 Function Peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity IBA
GO:0000224 Function Peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity IEA
GO:0000224 Function Peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity IGI 28826503
GO:0000224 Function Peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity TAS
GO:0005515 Function Protein binding IPI 15358861, 22119785, 25416956, 28514442, 31515488, 32296183, 33961781
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
610661 17646 ENSG00000151092
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
Q96IV0
Protein name Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase (PNGase) (hPNGase) (EC 3.5.1.52) (N-glycanase 1) (Peptide:N-glycanase)
Protein 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
PDB 2CCQ , 2CM0
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF09409 PUB 25 103 PUB domain Domain
PF01841 Transglut_core 258 354 Transglutaminase-like superfamily Family
PF04721 PAW 457 651 PNGase C-terminal domain, mannose-binding module PAW Domain
Sequence
MAAAALGSSSGSASPAVAELCQNTPETFLEASKLLLTYADNILRNPNDEKYRSIRIGNTA
FSTRLLPVRGAVECLFEMGFEEGETHLIFPKKASVEQLQKIRD
LIAIERSSRLDGSNKSH
KVKSSQQPAASTQLPTTPSSNPSGLNQHTRNRQGQSSDPPSASTVAADSAILEVLQSNIQ
HVLVYENPALQEKALACIPVQELKRKSQEKLSRARKLDKGINISDEDFLLLELLHWFKEE
FFHWVNNVLCSKCGGQTRSRDRSLLPSDDELKWGAKEVEDHYCDACQFSNRFPRYNNPEK
LLETRCGRCGEWANCFTLCCRAVGFEARYVWDYTDHVWTEVYSPSQQRWLHCDA
CEDVCD
KPLLYEIGWGKKLSYVIAFSKDEVVDVTWRYSCKHEEVIARRTKVKEALLRDTINGLNKQ
RQLFLSENRRKELLQRIIVELVEFISPKTPKPGELGGRISGSVAWRVARGEMGLQRKETL
FIPCENEKISKQLHLCYNIVKDRYVRVSNNNQTISGWENGVWKMESIFRKVETDWHMVYL
ARKEGSSFAYISWKFECGSVGLKVDSISIRTSSQTFQTGTVEWKLRSDTAQVELTGDNSL
HSYADFSGATEVILEAELSRGDGDVAWQHTQLFRQSLNDHEENCLEIIIKF
SDL
Sequence length 654
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  Protein processing in endoplasmic reticulum   N-glycan trimming in the ER and Calnexin/Calreticulin cycle
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
21
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Abnormal brain morphology Likely pathogenic rs1060499777 RCV000454236
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Congenital disorder of deglycosylation Likely pathogenic; Pathogenic rs2125460077, rs765145201, rs2125442838, rs1705416478, rs2125459914, rs2125478800, rs2125321733, rs376678889, rs2125442722, rs587777265, rs587777266, rs528583612, rs2125466047, rs762131179, rs750294252
View all (74 more)
RCV001377043
RCV001383326
RCV001386057
RCV001390877
RCV001381919
View all (85 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Congenital disorder of deglycosylation 1 Likely pathogenic; Pathogenic rs2125321733, rs376678889, rs2125442722, rs528583612, rs2125442902, rs2470672967, rs1383370693, rs200561967, rs2470535952, rs765492483, rs2470552567, rs2470553648, rs532007026, rs772994617, rs768131676
View all (7 more)
RCV005023144
RCV005038257
RCV003147674
RCV005025175
RCV005025509
View all (17 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Intellectual disability Pathogenic rs765211108 RCV000662298
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
Cervical cancer Likely benign; Benign; - ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma Benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Familial cancer of breast Uncertain significance ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Fetal growth restriction Uncertain significance ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Alacrima Alacrima HPO_DG
★☆☆☆☆
Found in Text Mining only
Alacrimia-choreoathetosis-liver dysfunction syndrome Alacrimia-Choreoathetosis-Liver Dysfunction Syndrome Orphanet
★☆☆☆☆
Found in Text Mining only
Amyotrophic Lateral Sclerosis Amyotrophic lateral sclerosis Pubtator 25220016 Associate
★☆☆☆☆
Found in Text Mining only
Amyotrophic Lateral Sclerosis Amyotrophic Lateral Sclerosis BEFREE 30867060
★☆☆☆☆
Found in Text Mining only
Anhidrosis Anhidrosis HPO_DG
★☆☆☆☆
Found in Text Mining only
Ataxia Ataxia Pubtator 32265286 Associate
★☆☆☆☆
Found in Text Mining only
Blepharoptosis Ptosis HPO_DG
★☆☆☆☆
Found in Text Mining only
Brachycephaly Brachycephaly HPO_DG
★☆☆☆☆
Found in Text Mining only
Brain Diseases Brain disease Pubtator 35322011 Associate
★☆☆☆☆
Found in Text Mining only
Central visual impairment Central Visual Impairment BEFREE 26350515
★☆☆☆☆
Found in Text Mining only