Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
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

Show/Hide all (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
rs532007026	C>G	Likely-pathogenic, pathogenic	Splice acceptor variant
rs587776982	G>-	Pathogenic, likely-pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant, 3 prime UTR variant, genic downstream transcript variant
rs587777265	->C	Pathogenic	Intron variant, coding sequence variant, non coding transcript variant, frameshift variant
rs587777266	TCT>-	Pathogenic	Coding sequence variant, non coding transcript variant, inframe deletion
rs745814294	G>A	Pathogenic	Coding sequence variant, non coding transcript variant, synonymous variant
rs755009745	G>A	Likely-pathogenic	Non coding transcript variant, coding sequence variant, stop gained
rs757712371	T>C,G	Likely-pathogenic	Intron variant, non coding transcript variant, missense variant, coding sequence variant
rs761634625	GCT>-	Likely-pathogenic	Inframe indel, non coding transcript variant, coding sequence variant
rs765211108	ATTG>-	Likely-pathogenic, pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant
rs767388144	C>G,T	Pathogenic	Coding sequence variant, non coding transcript variant, stop gained, missense variant
rs768131676	G>A	Pathogenic	Coding sequence variant, non coding transcript variant, intron variant, stop gained
rs771354261	C>A	Likely-pathogenic	Non coding transcript variant, coding sequence variant, missense variant
rs772184143	C>T	Likely-pathogenic	Genic downstream transcript variant, intron variant
rs772994617	G>A	Pathogenic, likely-pathogenic	Non coding transcript variant, coding sequence variant, stop gained
rs907852687	G>C,T	Pathogenic	Non coding transcript variant, stop gained, coding sequence variant
rs992161646	C>A	Likely-pathogenic	Intron variant, non coding transcript variant, coding sequence variant, stop gained
rs1060499777	A>C	Likely-pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs1135401728	C>G,T	Pathogenic, likely-pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs1135401729	A>G	Pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs1135401730	A>-	Pathogenic, likely-pathogenic	3 prime UTR variant, stop gained, genic downstream transcript variant, non coding transcript variant, coding sequence variant
rs1135401731	C>A	Pathogenic	Intron variant
rs1261363915	C>A,T	Pathogenic	Splice donor variant, genic downstream transcript variant, intron variant
rs1375323331	TCGATTGCTGAACTGGC>-	Pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs1470912253	->A	Likely-pathogenic	Frameshift variant, coding sequence variant, genic downstream transcript variant, non coding transcript variant
rs1553649843	T>-	Likely-pathogenic	Non coding transcript variant, genic downstream transcript variant, frameshift variant, 3 prime UTR variant, coding sequence variant
rs1553652151	->T	Pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant
rs1553666033	C>-	Pathogenic	Upstream transcript variant, non coding transcript variant, intron variant, genic upstream transcript variant, frameshift variant, coding sequence variant
rs1575612023	ACAAAGGT>-	Likely-pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant
rs1575614945	G>A	Pathogenic	Intron variant, coding sequence variant, stop gained, non coding transcript variant
rs1575616394	A>-	Pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant
rs1575622147	G>-	Likely-pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant
rs1575650389	C>T	Likely-pathogenic	Splice acceptor variant

Show/Hide all (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
MIRT1184205	hsa-miR-548c-3p	CLIP-seq
MIRT1184206	hsa-miR-124	CLIP-seq
MIRT1184207	hsa-miR-3714	CLIP-seq
MIRT1184208	hsa-miR-3910	CLIP-seq
MIRT1184209	hsa-miR-506	CLIP-seq
MIRT1184210	hsa-miR-579	CLIP-seq
MIRT2282620	hsa-miR-1183	CLIP-seq
MIRT2282621	hsa-miR-1293	CLIP-seq
MIRT2282622	hsa-miR-142-5p	CLIP-seq
MIRT2282623	hsa-miR-23a	CLIP-seq
MIRT2282624	hsa-miR-23b	CLIP-seq
MIRT2282625	hsa-miR-23c	CLIP-seq
MIRT2282626	hsa-miR-3146	CLIP-seq
MIRT2282627	hsa-miR-340	CLIP-seq
MIRT2282628	hsa-miR-433	CLIP-seq
MIRT2282629	hsa-miR-4483	CLIP-seq
MIRT2282630	hsa-miR-4666-5p	CLIP-seq
MIRT2282631	hsa-miR-4775	CLIP-seq
MIRT2282632	hsa-miR-4795-3p	CLIP-seq
MIRT2282633	hsa-miR-590-3p	CLIP-seq
MIRT2282634	hsa-miR-621	CLIP-seq

Show/Hide all (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
GO:0005634	Component	Nucleus	IBA
GO:0005737	Component	Cytoplasm	IDA	15358861
GO:0005737	Component	Cytoplasm	IEA
GO:0005829	Component	Cytosol	IBA
GO:0005829	Component	Cytosol	TAS
GO:0006457	Process	Protein folding	TAS
GO:0006516	Process	Glycoprotein catabolic process	IBA
GO:0006516	Process	Glycoprotein catabolic process	IDA	15358861
GO:0006516	Process	Glycoprotein catabolic process	IEA
GO:0016787	Function	Hydrolase activity	IEA
GO:0030513	Process	Positive regulation of BMP signaling pathway	IBA
GO:0046872	Function	Metal ion binding	IEA

MIM	HGNC	e!Ensembl
610661	17646	ENSG00000151092

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
FSTRLLPVRGAVECLFEMGFEEGETHLIFPKKASVEQLQKIRDLIAIERSSRLDGSNKSH
KVKSSQQPAASTQLPTTPSSNPSGLNQHTRNRQGQSSDPPSASTVAADSAILEVLQSNIQ
HVLVYENPALQEKALACIPVQELKRKSQEKLSRARKLDKGINISDEDFLLLELLHWFKEE
FFHWVNNVLCSKCGGQTRSRDRSLLPSDDELKWGAKEVEDHYCDACQFSNRFPRYNNPEK
LLETRCGRCGEWANCFTLCCRAVGFEARYVWDYTDHVWTEVYSPSQQRWLHCDACEDVCD
KPLLYEIGWGKKLSYVIAFSKDEVVDVTWRYSCKHEEVIARRTKVKEALLRDTINGLNKQ
RQLFLSENRRKELLQRIIVELVEFISPKTPKPGELGGRISGSVAWRVARGEMGLQRKETL
FIPCENEKISKQLHLCYNIVKDRYVRVSNNNQTISGWENGVWKMESIFRKVETDWHMVYL
ARKEGSSFAYISWKFECGSVGLKVDSISIRTSSQTFQTGTVEWKLRSDTAQVELTGDNSL
HSYADFSGATEVILEAELSRGDGDVAWQHTQLFRQSLNDHEENCLEIIIKFSDL

Sequence length

654

Interactions

View interactions

	KEGG		Reactome
	Protein processing in endoplasmic reticulum		N-glycan trimming in the ER and Calnexin/Calreticulin cycle

836

Show/Hide Causal Diseases (10)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Abnormal brain morphology	Likely pathogenic	rs1060499777	RCV000454236
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 RCV001383339 RCV001384997 RCV001821867 RCV003741278 RCV000114362 RCV000114363 RCV000114364 RCV001807983 RCV001887334 RCV001921089 RCV001993184 RCV001942125 RCV001883252 RCV001975014 RCV001972519 RCV001896433 RCV003111692 RCV002695411 RCV002839251 RCV002928151 RCV002970806 RCV003036530 RCV000496180 RCV000496208 RCV000496158 RCV000496154 RCV000496137 RCV000496134 RCV000496176 RCV003123511 RCV003236264 RCV003581910 RCV003582251 RCV003582470 RCV003581376 RCV003581216 RCV003581265 RCV003582690 RCV003582759 RCV003582927 RCV003582801 RCV003582028 RCV003741363 RCV003741361 RCV003741644 RCV003741714 RCV003741696 RCV003741765 RCV003742015 RCV003741985 RCV003741986 RCV003742235 RCV003742261 RCV003742264 RCV003742308 RCV003742447 RCV003740730 RCV003742510 RCV003740781 RCV003740881 RCV003740833 RCV000763511 RCV000543687 RCV000651488 RCV002532690 RCV003741212 RCV000651484 RCV000699456 RCV000802056 RCV000796100 RCV000824894 RCV000043662 RCV000043663 RCV000991415 RCV000995586 RCV000995587 RCV001860591 RCV001860596 RCV001213883 RCV001027428 RCV001046154 RCV001242867 RCV001270699 RCV001270700 RCV001270701
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 RCV002283973 RCV003992727 RCV005025336 RCV003325266 RCV004554919 RCV004554920 RCV004555912 RCV004760485 RCV005034113 RCV004796241 RCV005027733 RCV002468595 RCV003338810 RCV003147331 RCV002477142 RCV002468613 RCV002471069
Intellectual disability	Pathogenic	rs765211108	RCV000662298
Malignant tumor of urinary bladder	Likely pathogenic	rs772184143	RCV005898560
Neurodevelopmental abnormality	Likely pathogenic	rs762276611	RCV001264673
Neurodevelopmental delay	Pathogenic; Likely pathogenic	rs2125485574, rs201791209	RCV002274358 RCV002273988
Neuromotor delay	Pathogenic	rs765211108	RCV000662298
NGLY1-related disorder	Pathogenic	rs1043604336	RCV004756541
Peripheral neuropathy	Pathogenic	rs765211108	RCV000662298

Show/Hide Unknown Diseases (11)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Cervical cancer	Likely benign; Benign; -	rs183348716, rs79623349, rs2470554000	RCV005917551 RCV005925291 RCV005930255
Cholangiocarcinoma	Benign	rs79623349	RCV005925292
Familial cancer of breast	Uncertain significance	rs778126026	RCV005932135
Fetal growth restriction	Uncertain significance	rs771354261	RCV001003583
Gastric cancer	Likely benign	rs183348716, rs181461044	RCV005917552 RCV005896994
Global developmental delay	Uncertain significance	rs771354261	RCV001003583
Lactic acidosis	Uncertain significance	rs771354261	RCV001003583
Lung cancer	Uncertain significance	rs757626321	RCV005911254
Malignant tumor of esophagus	Conflicting classifications of pathogenicity	rs138477428	RCV005896993
Ovarian serous cystadenocarcinoma	Likely benign	rs76180231, rs774909250	RCV005916131 RCV005935085
Uterine corpus endometrial carcinoma	Likely benign; Benign; Conflicting classifications of pathogenicity; Uncertain significance	rs76180231, rs79623349, rs745814294, rs775894258	RCV005916132 RCV005925293 RCV005893790 RCV005913585

Show/Hide Text Mining Associations (58)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Addison Disease	Associate	30740912
Adenomatous Polyposis Coli	Associate	31663907
Adrenal Insufficiency	Associate	30740912
Alacrima	Associate	24651605, 25900930, 36528660
Alacrima Congenital	Associate	30740912
Amyotrophic Lateral Sclerosis	Associate	25220016
Ataxia	Associate	32265286
Brain Diseases	Associate	35322011
Cardiac Output Low	Associate	35322011
Chemical and Drug Induced Liver Injury	Associate	25900930, 32576142
Cognitive Dysfunction	Associate	25220016, 31957011
Cone Dystrophy	Associate	27388694
Congenital Abnormalities	Associate	31957011
Congenital Hereditary and Neonatal Diseases and Abnormalities	Associate	27388694, 32576142
Constipation	Associate	32265286, 32576142
Conversion Disorder	Associate	25220016
Corneal Opacity	Associate	25220016
Death	Associate	30740912
Deglutition Disorders	Associate	28512024
Developmental Disabilities	Associate	25900930, 27388694, 28512024, 32265286, 32576142, 36528660, 38039131
Disease	Associate	31957011
Epilepsies Myoclonic	Associate	31957011
Epilepsy	Associate	32576142
Genetic Diseases Inborn	Associate	22581936, 24651605, 36102038
Heredodegenerative Disorders Nervous System	Associate	25220016
Hyperkinesis	Associate	27388694, 28512024
Hyperpigmentation	Associate	30740912
Immunologic Deficiency Syndromes	Associate	35322011
Intellectual Disability	Associate	25220016, 31957011, 32576142, 38039131
Joint Instability	Associate	27388694
Leiomyoma	Associate	36948524
Liver Diseases	Associate	24651605
Liver Failure	Associate	28512024
Measles	Associate	27388694
Melanoma Cutaneous Malignant	Associate	33057211
Microcephaly	Associate	35322011
Mitochondrial Diseases	Associate	31957011, 38039131
Movement Disorders	Associate	32265286, 36528660
Muscle Hypotonia	Associate	34970863
N acetyltransferase deficiency	Inhibit	25900930, 34619643, 35322011, 36102038
N acetyltransferase deficiency	Associate	34619643
N syndrome	Associate	34051448
N syndrome	Inhibit	34051448
Neoplasms	Associate	36948524
Nervous System Diseases	Associate	25220016, 31957011, 38039131
Neurologic Manifestations	Associate	24651605, 30740912, 35322011
Neuromuscular Diseases	Associate	32265286
NGLY1 deficiency	Associate	24651605, 30612078, 31326749, 32576142
NGLY1 deficiency	Inhibit	27388694, 30612078, 31326749, 36528660, 38581946
Night blindness congenital stationary	Inhibit	38039131
Optic Atrophy	Associate	27388694
Parkinson Disease	Associate	25220016
Peripheral Nervous System Diseases	Associate	25900930
Polyneuropathies	Associate	31957011
Retinal Diseases	Associate	27388694
Rubella	Associate	27388694
Seizures	Associate	24651605, 25900930, 28512024, 32265286, 32576142, 38039131
Vision Disorders	Associate	26350515

NGLY1 (N-glycanase 1)