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

Gene Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	55624
Gene name Gene Name - the full gene name approved by the HGNC.	Protein O-linked mannose N-acetylglucosaminyltransferase 1 (beta 1,2-)
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	POMGNT1
Synonyms (NCBI Gene) Gene synonyms aliases	GNTI.2, GnT I.2, LGMD2O, LGMDR15, MEB, MGAT1.2, RP76, gnT-I.2
Chromosome Chromosome number	1
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	1p34.1
Summary Summary of gene provided in NCBI Entrez Gene.	This gene encodes a type II transmembrane protein that resides in the Golgi apparatus. It participates in O-mannosyl glycosylation and is specific for alpha linked terminal mannose. Mutations in this gene may be associated with muscle-eye-brain disease an

Show/Hide all(8)

SNP ID	Visualize variation	Clinical significance	Consequence
rs138950267	G>A	Conflicting-interpretations-of-pathogenicity, uncertain-significance	5 prime UTR variant, synonymous variant, coding sequence variant
rs193919337	G>A	Pathogenic	Stop gained, coding sequence variant, 5 prime UTR variant
rs386834027	->G	Likely-pathogenic	Frameshift variant, coding sequence variant, upstream transcript variant, genic upstream transcript variant
rs398124310	->T	Pathogenic	Frameshift variant, coding sequence variant, upstream transcript variant, genic upstream transcript variant
rs1057516478	CCAG>TCAC	Likely-pathogenic	Stop gained, upstream transcript variant, coding sequence variant, genic upstream transcript variant
rs1057516871	T>C	Likely-pathogenic	Intron variant, splice acceptor variant
rs1057517153	->T	Likely-pathogenic	5 prime UTR variant, coding sequence variant, frameshift variant
rs1571672866	A>-	Pathogenic	Frameshift variant, coding sequence variant, genic upstream transcript variant, upstream transcript variant

Show/Hide all(107)

miRTarBase ID	miRNA	Experiments	Reference
MIRT049784	hsa-miR-92a-3p	CLASH	23622248
MIRT048358	hsa-miR-103a-3p	CLASH	23622248
MIRT046794	hsa-miR-222-3p	CLASH	23622248
MIRT038869	hsa-miR-93-3p	CLASH	23622248
MIRT038246	hsa-miR-330-5p	CLASH	23622248
MIRT037663	hsa-miR-744-5p	CLASH	23622248
MIRT654919	hsa-miR-1470	HITS-CLIP	23824327
MIRT666875	hsa-miR-4667-3p	HITS-CLIP	23824327
MIRT654918	hsa-miR-5193	HITS-CLIP	23824327
MIRT666874	hsa-miR-660-3p	HITS-CLIP	23824327
MIRT654917	hsa-miR-6852-5p	HITS-CLIP	23824327
MIRT654916	hsa-miR-3121-5p	HITS-CLIP	23824327
MIRT654915	hsa-miR-4469	HITS-CLIP	23824327
MIRT654914	hsa-miR-7106-3p	HITS-CLIP	23824327
MIRT654913	hsa-miR-4489	HITS-CLIP	23824327
MIRT654912	hsa-miR-4283	HITS-CLIP	23824327
MIRT654911	hsa-miR-185-3p	HITS-CLIP	23824327
MIRT654910	hsa-miR-6835-5p	HITS-CLIP	23824327
MIRT654909	hsa-miR-6752-5p	HITS-CLIP	23824327
MIRT654908	hsa-miR-6842-5p	HITS-CLIP	23824327
MIRT654907	hsa-miR-7110-5p	HITS-CLIP	23824327
MIRT654906	hsa-miR-1275	HITS-CLIP	23824327
MIRT654905	hsa-miR-4665-5p	HITS-CLIP	23824327
MIRT654903	hsa-miR-7109-5p	HITS-CLIP	23824327
MIRT654904	hsa-miR-6751-5p	HITS-CLIP	23824327
MIRT654902	hsa-miR-6803-5p	HITS-CLIP	23824327
MIRT654901	hsa-miR-450a-2-3p	HITS-CLIP	23824327
MIRT654900	hsa-miR-4260	HITS-CLIP	23824327
MIRT654899	hsa-miR-5572	HITS-CLIP	23824327
MIRT654919	hsa-miR-1470	HITS-CLIP	23824327
MIRT654918	hsa-miR-5193	HITS-CLIP	23824327
MIRT654917	hsa-miR-6852-5p	HITS-CLIP	23824327
MIRT654916	hsa-miR-3121-5p	HITS-CLIP	23824327
MIRT654915	hsa-miR-4469	HITS-CLIP	23824327
MIRT654914	hsa-miR-7106-3p	HITS-CLIP	23824327
MIRT654913	hsa-miR-4489	HITS-CLIP	23824327
MIRT654912	hsa-miR-4283	HITS-CLIP	23824327
MIRT654911	hsa-miR-185-3p	HITS-CLIP	23824327
MIRT654910	hsa-miR-6835-5p	HITS-CLIP	23824327
MIRT654909	hsa-miR-6752-5p	HITS-CLIP	23824327
MIRT654908	hsa-miR-6842-5p	HITS-CLIP	23824327
MIRT654907	hsa-miR-7110-5p	HITS-CLIP	23824327
MIRT654906	hsa-miR-1275	HITS-CLIP	23824327
MIRT654905	hsa-miR-4665-5p	HITS-CLIP	23824327
MIRT654903	hsa-miR-7109-5p	HITS-CLIP	23824327
MIRT654904	hsa-miR-6751-5p	HITS-CLIP	23824327
MIRT654902	hsa-miR-6803-5p	HITS-CLIP	23824327
MIRT654901	hsa-miR-450a-2-3p	HITS-CLIP	23824327
MIRT654900	hsa-miR-4260	HITS-CLIP	23824327
MIRT654899	hsa-miR-5572	HITS-CLIP	23824327
MIRT654919	hsa-miR-1470	HITS-CLIP	23824327
MIRT666875	hsa-miR-4667-3p	HITS-CLIP	23824327
MIRT654918	hsa-miR-5193	HITS-CLIP	23824327
MIRT666874	hsa-miR-660-3p	HITS-CLIP	23824327
MIRT654917	hsa-miR-6852-5p	HITS-CLIP	23824327
MIRT654916	hsa-miR-3121-5p	HITS-CLIP	23824327
MIRT654915	hsa-miR-4469	HITS-CLIP	23824327
MIRT654914	hsa-miR-7106-3p	HITS-CLIP	23824327
MIRT654913	hsa-miR-4489	HITS-CLIP	23824327
MIRT654912	hsa-miR-4283	HITS-CLIP	23824327
MIRT654911	hsa-miR-185-3p	HITS-CLIP	23824327
MIRT654910	hsa-miR-6835-5p	HITS-CLIP	23824327
MIRT654909	hsa-miR-6752-5p	HITS-CLIP	23824327
MIRT654908	hsa-miR-6842-5p	HITS-CLIP	23824327
MIRT654907	hsa-miR-7110-5p	HITS-CLIP	23824327
MIRT654906	hsa-miR-1275	HITS-CLIP	23824327
MIRT654905	hsa-miR-4665-5p	HITS-CLIP	23824327
MIRT654903	hsa-miR-7109-5p	HITS-CLIP	23824327
MIRT654904	hsa-miR-6751-5p	HITS-CLIP	23824327
MIRT654902	hsa-miR-6803-5p	HITS-CLIP	23824327
MIRT654901	hsa-miR-450a-2-3p	HITS-CLIP	23824327
MIRT654900	hsa-miR-4260	HITS-CLIP	23824327
MIRT654899	hsa-miR-5572	HITS-CLIP	23824327
MIRT654919	hsa-miR-1470	HITS-CLIP	23824327
MIRT654918	hsa-miR-5193	HITS-CLIP	23824327
MIRT654917	hsa-miR-6852-5p	HITS-CLIP	23824327
MIRT654916	hsa-miR-3121-5p	HITS-CLIP	23824327
MIRT654915	hsa-miR-4469	HITS-CLIP	23824327
MIRT654914	hsa-miR-7106-3p	HITS-CLIP	23824327
MIRT654913	hsa-miR-4489	HITS-CLIP	23824327
MIRT654912	hsa-miR-4283	HITS-CLIP	23824327
MIRT654911	hsa-miR-185-3p	HITS-CLIP	23824327
MIRT654910	hsa-miR-6835-5p	HITS-CLIP	23824327
MIRT654909	hsa-miR-6752-5p	HITS-CLIP	23824327
MIRT654908	hsa-miR-6842-5p	HITS-CLIP	23824327
MIRT654907	hsa-miR-7110-5p	HITS-CLIP	23824327
MIRT654906	hsa-miR-1275	HITS-CLIP	23824327
MIRT654905	hsa-miR-4665-5p	HITS-CLIP	23824327
MIRT654903	hsa-miR-7109-5p	HITS-CLIP	23824327
MIRT654904	hsa-miR-6751-5p	HITS-CLIP	23824327
MIRT654902	hsa-miR-6803-5p	HITS-CLIP	23824327
MIRT654901	hsa-miR-450a-2-3p	HITS-CLIP	23824327
MIRT654900	hsa-miR-4260	HITS-CLIP	23824327
MIRT654899	hsa-miR-5572	HITS-CLIP	23824327
MIRT1250051	hsa-miR-1909	CLIP-seq
MIRT1250052	hsa-miR-4290	CLIP-seq
MIRT1250053	hsa-miR-4645-5p	CLIP-seq
MIRT1250054	hsa-miR-4673	CLIP-seq
MIRT1250055	hsa-miR-609	CLIP-seq
MIRT2688360	hsa-miR-1207-3p	CLIP-seq
MIRT2688361	hsa-miR-2861	CLIP-seq
MIRT2688362	hsa-miR-296-5p	CLIP-seq
MIRT2688363	hsa-miR-299-3p	CLIP-seq
MIRT2688364	hsa-miR-4265	CLIP-seq
MIRT2688365	hsa-miR-4296	CLIP-seq
MIRT2688366	hsa-miR-4322	CLIP-seq
MIRT2688367	hsa-miR-4417	CLIP-seq

Transcription factors

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Transcription factor	Regulation	Reference
ZNF202	Repression	22419172

Show/Hide all(38)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000139	Component	Golgi membrane	IBA
GO:0000139	Component	Golgi membrane	IDA	17034757
GO:0000139	Component	Golgi membrane	IEA
GO:0000139	Component	Golgi membrane	TAS
GO:0005515	Function	Protein binding	IPI	17034757, 25416956, 28514442, 29892012, 32296183, 32707033, 33961781
GO:0005794	Component	Golgi apparatus	IEA
GO:0006486	Process	Protein glycosylation	IEA
GO:0006486	Process	Protein glycosylation	IEA
GO:0006493	Process	Protein O-linked glycosylation	IDA	11709191
GO:0006493	Process	Protein O-linked glycosylation	IEA
GO:0006493	Process	Protein O-linked glycosylation	IEA
GO:0006493	Process	Protein O-linked glycosylation	IMP	26908613, 27391550
GO:0006493	Process	Protein O-linked glycosylation	TAS
GO:0007420	Process	Brain development	IEA
GO:0007605	Process	Sensory perception of sound	IEA
GO:0008375	Function	Acetylglucosaminyltransferase activity	IDA	27493216
GO:0008375	Function	Acetylglucosaminyltransferase activity	IEA
GO:0008375	Function	Acetylglucosaminyltransferase activity	IMP	26908613, 27391550
GO:0010467	Process	Gene expression	IEA
GO:0016020	Component	Membrane	IEA
GO:0016020	Component	Membrane	IMP	27493216
GO:0016266	Process	Protein O-linked glycosylation via N-acetyl-galactosamine	IBA
GO:0016266	Process	Protein O-linked glycosylation via N-acetyl-galactosamine	IDA	27493216
GO:0016740	Function	Transferase activity	IEA
GO:0016757	Function	Glycosyltransferase activity	IEA
GO:0021542	Process	Dentate gyrus development	IEA
GO:0030145	Function	Manganese ion binding	IDA	27493216
GO:0030246	Function	Carbohydrate binding	IEA
GO:0035269	Process	Protein O-linked glycosylation via mannose	IEA
GO:0036211	Process	Protein modification process	IEA
GO:0042552	Process	Myelination	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0047223	Function	Beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity	IBA
GO:0047223	Function	Beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity	IDA	11742540
GO:0047223	Function	Beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity	TAS
GO:0051674	Process	Localization of cell	IEA
GO:0071711	Process	Basement membrane organization	IEA
GO:0150103	Process	Reactive gliosis	IEA

MIM	HGNC	e!Ensembl
606822	19139	ENSG00000085998

Protein

UniProt ID

Q8WZA1

Protein name

Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1 (POMGnT1) (EC 2.4.1.-) (UDP-GlcNAc:alpha-D-mannoside beta-1,2-N-acetylglucosaminyltransferase I.2) (GnT I.2)

Protein function

Participates in O-mannosyl glycosylation by catalyzing the addition of N-acetylglucosamine to O-linked mannose on glycoproteins (PubMed:11709191, PubMed:27493216, PubMed:28512129). Catalyzes the synthesis of the GlcNAc(beta1-2)Man(alpha1-)O-Ser/

PDB

5GGF , 5GGG , 5GGI , 5GGJ , 5GGK , 5GGL , 5GGN , 5GGO , 5GGP , 5XFC

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF15711	ILEI	129 → 218	Interleukin-like EMT inducer	Domain
PF03071	GNT-I	293 → 609	GNT-I family	Family

Tissue specificity

TISSUE SPECIFICITY: Constitutively expressed. An additional weaker band is also detected in spinal cord, lymph node, and trachea. Expressed especially in astrocytes. Also expressed in immature and mature neurons. {ECO:0000269|PubMed:11709191, ECO:0000269|

Sequence

MDDWKPSPLIKPFGARKKRSWYLTWKYKLTNQRALRRFCQTGAVLFLLVTVIVNIKLILD
TRRAISEANEDPEPEQDYDEALGRLEPPRRRGSGPRRVLDVEVYSSRSKVYVAVDGTTVL
EDEAREQGRGIHVIVLNQATGHVMAKRVFDTYSPHEDEAMVLFLNMVAPGRVLICTVKDE
GSFHLKDTAKALLRSLGSQAGPALGWRDTWAFVGRKGGPVFGEKHSKSPALSSWGDPVLL
KTDVPLSSAEEAECHWADTELNRRRRRFCSKVEGYGSVCSCKDPTPIEFSPDPLPDNKVL
NVPVAVIAGNRPNYLYRMLRSLLSAQGVSPQMITVFIDGYYEEPMDVVALFGLRGIQHTP
ISIKNARVSQHYKASLTATFNLFPEAKFAVVLEEDLDIAVDFFSFLSQSIHLLEEDDSLY
CISAWNDQGYEHTAEDPALLYRVETMPGLGWVLRRSLYKEELEPKWPTPEKLWDWDMWMR
MPEQRRGRECIIPDVSRSYHFGIVGLNMNGYFHEAYFKKHKFNTVPGVQLRNVDSLKKEA
YEVEVHRLLSEAEVLDHSKNPCEDSFLPDTEGHTYVAFIRMEKDDDFTTWTQLAKCLHIW
DLDVRGNHRGLWRLFRKKNHFLMVGVPASPYSVKKPPSVTPIFLEPPPKEEGAPGAPEQT

Sequence length

660

Interactions

View interactions

	KEGG		Reactome
	Mannose type O-glycan biosynthesis Metabolic pathways		Defective POMGNT1 causes MDDGA3, MDDGB3 and MDDGC3 O-linked glycosylation

Show/Hide Causal Diseases (5)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Congenital Muscular Dystrophy-Dystroglycanopathy With Brain And Eye Anomalies	Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A3	rs386834038, rs386834012, rs1553163077, rs587777822, rs1057517247, rs1553162872, rs386834017, rs1057516986, rs267606961, rs28942068, rs150877512, rs386834032, rs386834035, rs1268759044, rs587777821 View all (5 more)	N/A
Limb-girdle muscular dystrophy	Autosomal recessive limb-girdle muscular dystrophy, Autosomal recessive limb-girdle muscular dystrophy type 2O	rs193919335, rs150877512, rs138642840, rs28940869, rs193919336, rs386834012, rs386834019	N/A
Muscle Eye Brain Disease	muscle eye brain disease	rs1553163077, rs1553162601, rs386834020, rs1057517247, rs386834028, rs386834013, rs1553162873, rs386834017, rs1057516986, rs386834021, rs386834039, rs386834015, rs1553163360, rs386834022, rs386834029 View all (51 more)	N/A
muscular dystrophy-dystroglycanopathy	Muscular dystrophy-dystroglycanopathy	rs1176001640, rs749332339, rs386834038, rs386834028, rs150877512, rs1057517355, rs386834040, rs138642840, rs386834024, rs386834035, rs1424631447, rs193919336	N/A
Retinitis Pigmentosa	retinitis pigmentosa 76	rs193919337, rs28940869, rs386834024, rs886037947, rs886037948, rs886037949, rs386834012, rs386834019	N/A

Show/Hide Unknown Diseases (4)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Congenital muscular dystrophy	Congenital Muscular Dystrophy, alpha-dystroglycan related	N/A	N/A	ClinVar
Mental retardation	muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B3	N/A	N/A	GenCC
Myopathy	myopathy caused by variation in POMGNT1	N/A	N/A	GenCC
retinal dystrophy	Retinal dystrophy	N/A	N/A	ClinVar

Show/Hide Text Mining Associations (19)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Acute Disease	Associate	29101272
Brachydactyly type A3	Associate	30961548
Brain Diseases	Associate	40244109
Cone Rod Dystrophies	Associate	40244109
Disorders of Excessive Somnolence	Associate	31580529
Eye Infections	Associate	28765568
Fabry Disease	Associate	28765568
Hydrocephalus	Associate	35843586
Hydrocephalus Normal Pressure	Associate	34360799
Malformations of Cortical Development Group II	Associate	11709191
Mannose Binding Protein Deficiency	Inhibit	33610554
Muscular Dystrophies	Associate	11709191, 30961548, 40244109
Muscular Dystrophies Limb Girdle	Associate	22419172
Obesity	Associate	34239500
Respiratory Tract Neoplasms	Associate	22727687
Retinal Diseases	Associate	40244109
Retinal Dystrophies	Associate	40244109
Signs and Symptoms Respiratory	Associate	29101272
Walker Warburg Syndrome	Associate	11709191, 12369018, 18752264, 19266496, 20215985, 21361872, 22419172, 22554691, 23217329, 28765568, 29101272, 31580529, 32115343, 32627857, 33610554, 35863218, 40244109 View all (2 more)

POMGNT1 (protein O-linked mannose N-acetylglucosaminyltransferase 1 (beta 1,2-))