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

Gene Gene information from NCBI Gene database. Gene SNPs Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	84572
Gene name	N-acetylglucosamine-1-phosphate transferase subunit gamma
Gene symbol	GNPTG
Synonyms (NCBI Gene)	C16orf27GNPTAGLP2537RJD9
Chromosome	16
Chromosome location	16p13.3
Summary	This gene encodes the gamma sunbunit of the N-acetylglucosamine-1-phosphotransferase complex. This hexameric complex, composed of alpha, beta and gamma subunits, catalyzes the first step in synthesis of a mannose 6-phosphate lysosomal recognition marker.

Show/Hide all (31)

SNP ID	Visualize variation	Clinical significance	Consequence
rs76594024	G>A,C	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Synonymous variant, 5 prime UTR variant, coding sequence variant
rs112850896	G>A,C	Likely-pathogenic	Splice acceptor variant
rs137852884	G>A	Pathogenic	5 prime UTR variant, coding sequence variant, stop gained
rs137852885	G>A	Pathogenic	5 prime UTR variant, coding sequence variant, missense variant
rs193302847	G>A,C	Likely-pathogenic, pathogenic	Splice acceptor variant
rs193302848	C>T	Pathogenic	Stop gained, coding sequence variant, 5 prime UTR variant
rs193302849	ACA>-	Likely-pathogenic, pathogenic	Coding sequence variant, inframe deletion, 5 prime UTR variant
rs193302850	GACGCCTGCCGTT>-	Pathogenic	Frameshift variant, coding sequence variant
rs193302851	->C	Pathogenic	Frameshift variant, coding sequence variant
rs193302853	GTGGGCCTGGCTGGGAGCTGGGTGCTGCCCCTGC>-	Pathogenic	Intron variant
rs193302854	G>C,T	Pathogenic	Splice acceptor variant
rs193302855	A>G	Pathogenic	Splice acceptor variant
rs193302856	G>-	Pathogenic	Splice acceptor variant, coding sequence variant
rs193302857	->T	Pathogenic	Frameshift variant, coding sequence variant
rs193302858	TT>-,T	Pathogenic	Stop gained, frameshift variant, coding sequence variant
rs193302859	GAGGATGCTGGCTACTTAAAGACCCCAG>-	Pathogenic	Frameshift variant, coding sequence variant
rs281864956	G>-	Pathogenic	Frameshift variant, coding sequence variant
rs376679416	G>A,C,T	Likely-pathogenic	Splice donor variant
rs756225251	->C	Likely-pathogenic	Frameshift variant, coding sequence variant
rs756959430	C>-,CC	Pathogenic	Frameshift variant, coding sequence variant
rs763678034	G>A,C,T	Pathogenic	Missense variant, coding sequence variant, 5 prime UTR variant, stop gained
rs775359476	G>A,C	Likely-pathogenic	Coding sequence variant, missense variant
rs1060499690	G>A	Likely-pathogenic	Stop gained, 5 prime UTR variant, coding sequence variant
rs1060499691	G>A	Likely-pathogenic	Intron variant
rs1260510628	G>C,T	Likely-pathogenic	Splice donor variant
rs1336176104	G>A,C	Pathogenic	Intron variant
rs1555451608	T>A,C	Likely-pathogenic	Splice donor variant
rs1555451643	AT>-	Likely-pathogenic	Stop gained, 5 prime UTR variant, coding sequence variant
rs1555451866	G>C	Likely-pathogenic	Splice acceptor variant
rs1555451874	AACCGGCTGGC>-	Pathogenic	Frameshift variant, coding sequence variant
rs1555451988	->C	Pathogenic	Frameshift variant, coding sequence variant

Show/Hide all (11)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	26385638, 28514442
GO:0005576	Component	Extracellular region	IEA
GO:0005794	Component	Golgi apparatus	IBA
GO:0005794	Component	Golgi apparatus	IDA	27038293
GO:0005794	Component	Golgi apparatus	IEA
GO:0005794	Component	Golgi apparatus	ISS
GO:0016256	Process	N-glycan processing to lysosome	NAS	25505245
GO:0042803	Function	Protein homodimerization activity	ISS
GO:0046835	Process	Carbohydrate phosphorylation	IDA	19955174
GO:0070062	Component	Extracellular exosome	HDA	19199708
GO:0070622	Component	UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase complex	IPI	26385638

MIM	HGNC	e!Ensembl
607838	23026	ENSG00000090581

Q9UJJ9

Protein name

N-acetylglucosamine-1-phosphotransferase subunit gamma (GlcNAc-1-phosphotransferase subunit gamma) (UDP-N-acetylglucosamine-1-phosphotransferase subunit gamma)

Protein function

Non-catalytic subunit of the N-acetylglucosamine-1-phosphotransferase complex, an enzyme that catalyzes the formation of mannose 6-phosphate (M6P) markers on high mannose type oligosaccharides in the Golgi apparatus. Binds and presents the high

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF13015	PRKCSH_1	48 → 211	Glucosidase II beta subunit-like protein	Family

Tissue specificity

TISSUE SPECIFICITY: Widely expressed. {ECO:0000269|PubMed:10712439}.

Sequence

MAAGLARLLLLLGLSAGGPAPAGAAKMKVVEEPNAFGVNNPFLPQASRLQAKRDPSPVSG
PVHLFRLSGKCFSLVESTYKYEFCPFHNVTQHEQTFRWNAYSGILGIWHEWEIANNTFTG
MWMRDGDACRSRSRQSKVELACGKSNRLAHVSEPSTCVYALTFETPLVCHPHALLVYPTL
PEALQRQWDQVEQDLADELITPQGHEKLLRTLFEDAGYLKTPEENEPTQLEGGPDSLGFE
TLENCRKAHKELSKEIKRLKGLLTQHGIPYTRPTETSNLEHLGHETPRAKSPEQLRGDPG
LRGSL

Sequence length

305

Interactions

View interactions

	KEGG
	Lysosome

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)

Show/Hide Causal Diseases (7)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Familial cancer of breast	Likely pathogenic	rs2141632749	RCV005912612	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
GNPTG-mucolipidosis	Likely pathogenic; Pathogenic	rs2141632749, rs988175540, rs1451538466, rs2141861740, rs552402857, rs193302858, rs2141864418, rs368983807, rs2548190467, rs2548185540, rs771844889, rs193302856, rs1335120510, rs193302859, rs137852884 View all (39 more)	RCV005014520 RCV001831373 RCV004770133 RCV001843409 RCV004776305 View all (55 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Melanoma	Pathogenic	rs112850896	RCV005924378	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Mucolipidosis	Likely pathogenic	rs1060499690, rs1596603769	RCV000825527 RCV000825528	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Nonpapillary renal cell carcinoma	Pathogenic	rs112850896	RCV005924377	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Retinal dystrophy	Pathogenic; Likely pathogenic	rs193302848, rs193302849	RCV004814911 RCV004814912	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Rod-cone dystrophy	Likely pathogenic; Pathogenic	rs193302849, rs756225251	RCV003105776 RCV003106016	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (11)

Phenotype Name	Clinical Significance	Source	Evidence Score
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.
Cervical cancer	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DESBUQUOIS SYNDROME	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GNPTG-related disorder	Likely benign; Benign; Conflicting classifications of pathogenicity; Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of urinary bladder	Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MUCOLIPIDOSES	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MUCOLIPIDOSIS III GAMMA	—	CTD, Disgenet, HPO CTD, Disgenet, HPO CTD, Disgenet, HPO	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MUCOLIPIDOSIS TYPE III GAMMA	—	Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RETINITIS PIGMENTOSA 1	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (31)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Aortic Valve Insufficiency	Aortic Valve Insufficiency	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Aortic Valve Stenosis	Aortic Valve Sclerosis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Atrial Fibrillation	Atrial fibrillation	Pubtator	39864423	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital pectus carinatum	Congenital Pectus Carinatum	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Dyslexia	Dyslexia	BEFREE	25643770		★★★★★ ★☆☆☆☆ Found in Text Mining only
Mild Mental Retardation	Mental retardation	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Mucolipidoses	Mucolipidosis	BEFREE	22884963, 26935170, 30882951		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Mucolipidoses	Mucolipidosis	Pubtator	26130485, 27038293, 29872134, 35939698	Associate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Mucolipidoses	Mucolipidosis	CLINVAR_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Mucolipidosis II Alpha Beta	Mucolipidosis	Pubtator	26130485, 29872134	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
MUCOLIPIDOSIS II ALPHA/BETA (disorder)	Mucolipidosis	BEFREE	26130485		★★★★★ ★☆☆☆☆ Found in Text Mining only
MUCOLIPIDOSIS II ALPHA/BETA (disorder)	Mucolipidosis	CLINVAR_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Mucolipidosis III Gamma	Mucolipidosis	CLINVAR_DG	10712439, 15060128, 23430803, 24316125, 25182519, 26935170, 27243974, 27896079		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Mucolipidosis III Gamma	Mucolipidosis	UNIPROT_DG	10712439, 15060128, 15532026, 19370764, 24316125, 26108976, 27038293		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Mucolipidosis III Gamma	Mucolipidosis	BEFREE	19370764, 19708128, 20034096, 20951619, 21792934, 24316125, 30235039		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Mucolipidosis III Gamma	Mucolipidosis	GENOMICS_ENGLAND_DG	19370764, 19659762, 27604308		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Mucolipidosis III Gamma	Mucolipidosis	ORPHANET_DG	19708128, 20034096		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Mucolipidosis III Gamma	Mucolipidosis	Pubtator	26130485, 27038293, 28950892, 37752499	Associate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Mucolipidosis III Gamma	Mucolipidosis	CTD_human_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Mucolipidosis type III gamma	Mucolipidosis	Orphanet			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Mucopolysaccharidosis IV	Mucopolysaccharidosis	BEFREE	21792934		★★★★★ ★☆☆☆☆ Found in Text Mining only
Myopia	Myopia	Pubtator	29346494	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Myopia	Myopia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Pfaundler-Hurler Syndrome	Pfaundler-Hurler Syndrome	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Pseudo-Hurler Polydystrophy	Pseudo-Hurler Polydystrophy	BEFREE	26130485, 27038293		★★★★★ ★☆☆☆☆ Found in Text Mining only
Retinitis Pigmentosa	Retinitis Pigmentosa	BEFREE	21792934		★★★★★ ★☆☆☆☆ Found in Text Mining only
Retinitis Pigmentosa	Retinitis pigmentosa	Pubtator	37752499	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Scleroderma Systemic	Systemic sclerosis	Pubtator	28950892	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Scoliosis, unspecified	Scoliosis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Type II Mucolipidosis	Mucolipidosis	BEFREE	16835905, 19659762, 19938078, 26130485, 29872134		★★★★★ ★☆☆☆☆ Found in Text Mining only

GNPTG (N-acetylglucosamine-1-phosphate transferase subunit gamma)