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

Gene Gene information from NCBI Gene database. Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	4247
Gene name	Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase
Gene symbol	MGAT2
Synonyms (NCBI Gene)	CDG2ACDGS2GLCNACTIIGNT-IIGNT2
Chromosome	14
Chromosome location	14q21.3
Summary	The product of this gene is a Golgi enzyme catalyzing an essential step in the conversion of oligomannose to complex N-glycans. The enzyme has the typical glycosyltransferase domains: a short N-terminal cytoplasmic domain, a hydrophobic non-cleavable sign

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miRTarBase ID	miRNA	Experiments	Reference
MIRT047885	hsa-miR-30c-5p	CLASH	23622248
MIRT1146871	hsa-miR-188-5p	CLIP-seq
MIRT1146872	hsa-miR-200b	CLIP-seq
MIRT1146873	hsa-miR-200c	CLIP-seq
MIRT1146874	hsa-miR-3065-3p	CLIP-seq
MIRT1146875	hsa-miR-3149	CLIP-seq
MIRT1146876	hsa-miR-320e	CLIP-seq
MIRT1146877	hsa-miR-3647-3p	CLIP-seq
MIRT1146878	hsa-miR-3662	CLIP-seq
MIRT1146879	hsa-miR-3667-3p	CLIP-seq
MIRT1146880	hsa-miR-374c	CLIP-seq
MIRT1146881	hsa-miR-429	CLIP-seq
MIRT1146882	hsa-miR-4477a	CLIP-seq
MIRT1146883	hsa-miR-4700-3p	CLIP-seq
MIRT1146884	hsa-miR-4724-5p	CLIP-seq
MIRT1146885	hsa-miR-570	CLIP-seq
MIRT1146886	hsa-miR-595	CLIP-seq
MIRT1146887	hsa-miR-607	CLIP-seq
MIRT1146888	hsa-miR-629	CLIP-seq
MIRT1146889	hsa-miR-655	CLIP-seq
MIRT1146890	hsa-miR-943	CLIP-seq
MIRT1146891	hsa-miR-944	CLIP-seq
MIRT1146872	hsa-miR-200b	CLIP-seq
MIRT1146873	hsa-miR-200c	CLIP-seq
MIRT2041824	hsa-miR-2052	CLIP-seq
MIRT2041825	hsa-miR-3671	CLIP-seq
MIRT1146880	hsa-miR-374c	CLIP-seq
MIRT2041826	hsa-miR-375	CLIP-seq
MIRT1146881	hsa-miR-429	CLIP-seq
MIRT2041827	hsa-miR-4464	CLIP-seq
MIRT2041828	hsa-miR-4705	CLIP-seq
MIRT2041829	hsa-miR-4718	CLIP-seq
MIRT2041830	hsa-miR-4738-3p	CLIP-seq
MIRT2041831	hsa-miR-4748	CLIP-seq
MIRT2041832	hsa-miR-488	CLIP-seq
MIRT1146886	hsa-miR-595	CLIP-seq
MIRT1146888	hsa-miR-629	CLIP-seq
MIRT1146889	hsa-miR-655	CLIP-seq
MIRT2041833	hsa-miR-885-5p	CLIP-seq
MIRT2271375	hsa-miR-1323	CLIP-seq
MIRT1146874	hsa-miR-3065-3p	CLIP-seq
MIRT2271376	hsa-miR-3148	CLIP-seq
MIRT2271377	hsa-miR-335	CLIP-seq
MIRT1146878	hsa-miR-3662	CLIP-seq
MIRT2271378	hsa-miR-371b-5p	CLIP-seq
MIRT2271379	hsa-miR-4693-3p	CLIP-seq
MIRT2041830	hsa-miR-4738-3p	CLIP-seq
MIRT2271380	hsa-miR-4768-5p	CLIP-seq
MIRT2271381	hsa-miR-496	CLIP-seq
MIRT2271382	hsa-miR-548o	CLIP-seq
MIRT2271383	hsa-miR-592	CLIP-seq
MIRT1146886	hsa-miR-595	CLIP-seq
MIRT2271384	hsa-miR-597	CLIP-seq
MIRT2271385	hsa-miR-603	CLIP-seq
MIRT2271386	hsa-miR-888	CLIP-seq
MIRT2271387	hsa-miR-942	CLIP-seq
MIRT1146872	hsa-miR-200b	CLIP-seq
MIRT1146873	hsa-miR-200c	CLIP-seq
MIRT1146880	hsa-miR-374c	CLIP-seq
MIRT2041826	hsa-miR-375	CLIP-seq
MIRT2570557	hsa-miR-425	CLIP-seq
MIRT1146881	hsa-miR-429	CLIP-seq
MIRT2570558	hsa-miR-4328	CLIP-seq
MIRT2570559	hsa-miR-4645-3p	CLIP-seq
MIRT2041830	hsa-miR-4738-3p	CLIP-seq
MIRT2570560	hsa-miR-4803	CLIP-seq
MIRT2570561	hsa-miR-495	CLIP-seq
MIRT2570562	hsa-miR-513a-3p	CLIP-seq
MIRT2570563	hsa-miR-609	CLIP-seq
MIRT1146888	hsa-miR-629	CLIP-seq
MIRT1146889	hsa-miR-655	CLIP-seq
MIRT2041833	hsa-miR-885-5p	CLIP-seq
MIRT1146872	hsa-miR-200b	CLIP-seq
MIRT1146873	hsa-miR-200c	CLIP-seq
MIRT1146880	hsa-miR-374c	CLIP-seq
MIRT2041826	hsa-miR-375	CLIP-seq
MIRT2570557	hsa-miR-425	CLIP-seq
MIRT1146881	hsa-miR-429	CLIP-seq
MIRT2570558	hsa-miR-4328	CLIP-seq
MIRT2570559	hsa-miR-4645-3p	CLIP-seq
MIRT2041830	hsa-miR-4738-3p	CLIP-seq
MIRT2570560	hsa-miR-4803	CLIP-seq
MIRT2570561	hsa-miR-495	CLIP-seq
MIRT2570563	hsa-miR-609	CLIP-seq
MIRT1146888	hsa-miR-629	CLIP-seq
MIRT1146889	hsa-miR-655	CLIP-seq
MIRT2041833	hsa-miR-885-5p	CLIP-seq

Show/Hide all (26)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000139	Component	Golgi membrane	IBA
GO:0000139	Component	Golgi membrane	IDA	20378551
GO:0000139	Component	Golgi membrane	IEA
GO:0000139	Component	Golgi membrane	TAS
GO:0005794	Component	Golgi apparatus	IDA
GO:0005794	Component	Golgi apparatus	IEA
GO:0005795	Component	Golgi stack	IEA
GO:0006486	Process	Protein glycosylation	IEA
GO:0006487	Process	Protein N-linked glycosylation	IBA
GO:0008455	Function	Alpha-1,6-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity	IBA
GO:0008455	Function	Alpha-1,6-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity	IDA	7635144, 29666272
GO:0008455	Function	Alpha-1,6-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity	IEA
GO:0008455	Function	Alpha-1,6-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity	IMP	8808595
GO:0008455	Function	Alpha-1,6-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity	TAS
GO:0009312	Process	Oligosaccharide biosynthetic process	IEA
GO:0016020	Component	Membrane	HDA	19946888
GO:0016020	Component	Membrane	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0016757	Function	Glycosyltransferase activity	IEA
GO:0018279	Process	Protein N-linked glycosylation via asparagine	IDA	7635144, 29666272
GO:0018279	Process	Protein N-linked glycosylation via asparagine	IEA
GO:0018279	Process	Protein N-linked glycosylation via asparagine	IMP	8808595
GO:0019082	Process	Viral protein processing	TAS
GO:0030145	Function	Manganese ion binding	IDA	29666272
GO:0042803	Function	Protein homodimerization activity	IDA	20378551
GO:0046872	Function	Metal ion binding	IEA

MIM	HGNC	e!Ensembl
602616	7045	ENSG00000168282

Q10469

Protein name

Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase (EC 2.4.1.143) (Beta-1,2-N-acetylglucosaminyltransferase II) (GlcNAc-T II) (GNT-II) (Mannoside acetylglucosaminyltransferase 2) (N-glycosyl-oligosaccharide-glycoprotein N-acetylglucosa

Protein function

Plays an essential role in protein N-glycosylation. Catalyzes the transfer of N-acetylglucosamine (GlcNAc) onto the free terminal mannose moiety in the core structure of the nascent N-linked glycan chain, giving rise to the second branch in comp

PDB

5VCM , 5VCR , 5VCS

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF05060	MGAT2	92 → 440	N-acetylglucosaminyltransferase II (MGAT2)	Family

Sequence

MRFRIYKRKVLILTLVVAACGFVLWSSNGRQRKNEALAPPLLDAEPARGAGGRGGDHPSV
AVGIRRVSNVSAASLVPAVPQPEADNLTLRYRSLVYQLNFDQTLRNVDKAGTWAPRELVL
VVQVHNRPEYLRLLLDSLRKAQGIDNVLVIFSHDFWSTEINQLIAGVNFCPVLQVFFPFS
IQLYPNEFPGSDPRDCPRDLPKNAALKLGCINAEYPDSFGHYREAKFSQTKHHWWWKLHF
VWERVKILRDYAGLILFLEEDHYLAPDFYHVFKKMWKLKQQECPECDVLSLGTYSASRSF
YGMADKVDVKTWKSTEHNMGLALTRNAYQKLIECTDTFCTYDDYNWDWTLQYLTVSCLPK
FWKVLVPQIPRIFHAGDCGMHHKKTCRPSTQSAQIESLLNNNKQYMFPETLTISEKFTVV
AISPPRKNGGWGDIRDHELCKSYRRLQ

Sequence length

447

Interactions

View interactions

	KEGG		Reactome
	N-Glycan biosynthesis Various types of N-glycan biosynthesis Metabolic pathways		Defective MGAT2 causes MGAT2-CDG (CDG-2a) Reactions specific to the complex N-glycan synthesis pathway

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 (5)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Abnormal facial shape	Likely pathogenic	rs730882218	RCV000162128	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Abnormal glycosylation	Likely pathogenic	rs730882218	RCV000162128	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Global developmental delay	Likely pathogenic	rs730882218	RCV000162128	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
MGAT2-congenital disorder of glycosylation	Pathogenic; Likely pathogenic	rs104894447, rs104894448, rs104894449, rs1882879689, rs2502745152, rs730882218, rs1566504935, rs1310787426, rs1566505013	RCV000007406 RCV000007407 RCV000007408 RCV003984967 RCV003990102 View all (4 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
MGAT2-related disorder	Likely pathogenic	rs2502745152	RCV004731583	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (4)

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.
Congenital disorder of glycosylation	Uncertain significance; Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL DISORDER OF GLYCOSYLATION TYPE 2A	—	CTD, Disgenet CTD, Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL DISORDER OF GLYCOSYLATION, TYPE IIA	—	HPO	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL DISORDERS OF GLYCOSYLATION	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

MGAT2 (alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase)