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

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	84892
Gene name Gene Name - the full gene name approved by the HGNC.	Protein O-linked mannose N-acetylglucosaminyltransferase 2 (beta 1,4-)
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	POMGNT2
Synonyms (NCBI Gene) Gene synonyms aliases	AGO61, C3orf39, GTDC2, MDDGA8, MDDGC8
Chromosome Chromosome number	3
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	3p22.1
Summary Summary of gene provided in NCBI Entrez Gene.	This gene encodes a protein with glycosyltransferase activity although its function is not currently known. [provided by RefSeq, Sep 2012]

Show/Hide all(18)

SNP ID	Visualize variation	Clinical significance	Consequence
rs142190930	T>C	Conflicting-interpretations-of-pathogenicity, benign	Synonymous variant, coding sequence variant
rs143394182	C>T	Conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs146511234	C>T	Conflicting-interpretations-of-pathogenicity, benign	Coding sequence variant, missense variant
rs147429438	G>A,C	Conflicting-interpretations-of-pathogenicity, likely-benign	Coding sequence variant, synonymous variant, missense variant
rs200535361	T>C	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, missense variant
rs371749889	T>C	Conflicting-interpretations-of-pathogenicity, likely-benign	Coding sequence variant, synonymous variant
rs374042455	G>A	Pathogenic	Coding sequence variant, missense variant
rs387907299	G>A,T	Pathogenic	Coding sequence variant, stop gained, synonymous variant
rs387907300	C>T	Likely-pathogenic, pathogenic	Missense variant, coding sequence variant
rs576598140	C>T	Conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs752069645	C>T	Pathogenic	Stop gained, coding sequence variant
rs768063378	C>T	Pathogenic	Coding sequence variant, missense variant
rs774277094	AGAGGTCGAAGT>-	Likely-pathogenic	Coding sequence variant, inframe deletion
rs780525490	C>A,G	Pathogenic	Missense variant, stop gained, coding sequence variant
rs1021357430	G>A	Likely-pathogenic	Coding sequence variant, stop gained
rs1553618354	G>A	Pathogenic	Stop gained, coding sequence variant
rs1559414655	A>G	Pathogenic	Missense variant, coding sequence variant
rs1575461722	C>-	Likely-pathogenic	Frameshift variant, coding sequence variant

Show/Hide all(12)

miRTarBase ID	miRNA	Experiments	Reference
MIRT740377	hsa-miR-329-3p	HITS-CLIP	19536157
MIRT740378	hsa-miR-362-3p	HITS-CLIP	19536157
MIRT740379	hsa-miR-4729	HITS-CLIP	19536157
MIRT740380	hsa-miR-5696	HITS-CLIP	19536157
MIRT740377	hsa-miR-329-3p	HITS-CLIP	19536157
MIRT740378	hsa-miR-362-3p	HITS-CLIP	19536157
MIRT740379	hsa-miR-4729	HITS-CLIP	19536157
MIRT740380	hsa-miR-5696	HITS-CLIP	19536157
MIRT740377	hsa-miR-329-3p	HITS-CLIP	19536157
MIRT740378	hsa-miR-362-3p	HITS-CLIP	19536157
MIRT740379	hsa-miR-4729	HITS-CLIP	19536157
MIRT740380	hsa-miR-5696	HITS-CLIP	19536157

Show/Hide all(25)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001764	Process	Neuron migration	IEA
GO:0001764	Process	Neuron migration	ISS
GO:0005515	Function	Protein binding	IPI	25416956
GO:0005783	Component	Endoplasmic reticulum	IBA
GO:0005783	Component	Endoplasmic reticulum	IDA	23929950, 27066570
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	TAS
GO:0006486	Process	Protein glycosylation	IEA
GO:0006493	Process	Protein O-linked glycosylation	IDA	23929950
GO:0006493	Process	Protein O-linked glycosylation	IEA
GO:0006493	Process	Protein O-linked glycosylation	IMP	27066570
GO:0006493	Process	Protein O-linked glycosylation	TAS
GO:0008375	Function	Acetylglucosaminyltransferase activity	IDA	23929950
GO:0008375	Function	Acetylglucosaminyltransferase activity	IEA
GO:0008375	Function	Acetylglucosaminyltransferase activity	TAS
GO:0016020	Component	Membrane	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0016757	Function	Glycosyltransferase activity	IEA
GO:0035269	Process	Protein O-linked glycosylation via mannose	IBA
GO:0035269	Process	Protein O-linked glycosylation via mannose	IEA
GO:0035269	Process	Protein O-linked glycosylation via mannose	ISS
GO:0097363	Function	Protein O-acetylglucosaminyltransferase activity	IBA
GO:0097363	Function	Protein O-acetylglucosaminyltransferase activity	IDA	23929950
GO:0097363	Function	Protein O-acetylglucosaminyltransferase activity	IMP	27066570

MIM	HGNC	e!Ensembl
614828	25902	ENSG00000144647

Protein

UniProt ID

Q8NAT1

Protein name

Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2 (POMGnT2) (EC 2.4.1.312) (Extracellular O-linked N-acetylglucosamine transferase-like) (Glycosyltransferase-like domain-containing protein 2)

Protein function

O-linked mannose beta-1,4-N-acetylglucosaminyltransferase that transfers UDP-N-acetyl-D-glucosamine to the 4-position of the mannose to generate N-acetyl-D-glucosamine-beta-1,4-O-D-mannosylprotein. Involved in the biosynthesis of the phosphoryla

PDB

6XFI , 8KB7

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF04577	DUF563	162 → 395	Protein of unknown function (DUF563)	Family

Tissue specificity

TISSUE SPECIFICITY: Highly expressed in the brain, muscle, heart, and kidney in both fetus and adult. In the brain, highest expression in the cortex and cerebellum. Highly expressed in the pancreas. {ECO:0000269|PubMed:22958903}.

Sequence

MHLSAVFNALLVSVLAAVLWKHVRLREHAATLEEELALSRQATEPAPALRIDYPKALQIL
MEGGTHMVCTGRTHTDRICRFKWLCYSNEAEEFIFFHGNTSVMLPNLGSRRFQPALLDLS
TVEDHNTQYFNFVELPAAALRFMPKPVFVPDVALIANRFNPDNLMHVFHDDLLPLFYTLR
QFPGLAHEARLFFMEGWGEGAHFDLYKLLSPKQPLLRAQLKTLGRLLCFSHAFVGLSKIT
TWYQYGFVQPQGPKANILVSGNEIRQFARFMTEKLNVSHTGVPLGEEYILVFSRTQNRLI
LNEAELLLALAQEFQMKTVTVSLEDHTFADVVRLVSNASMLVSMHGAQLVTTLFLPRGAT
VVELFPYAVNPDHYTPYKTLAMLPGMDLQYVAWRNMMPENTVTHPERPWDQGGITHLDRA
EQARILQSREVPRHLCCRNPEWLFRIYQDTKVDIPSLIQTIRRVVKGRPGPRKQKWTVGL
YPGKVREARCQASVHGASEARLTVSWQIPWNLKYLKVREVKYEVWLQEQGENTYVPYILA
LQNHTFTENIKPFTTYLVWVRCIFNKILLGPFADVLVCNT

Sequence length

580

Interactions

View interactions

	KEGG		Reactome
	Mannose type O-glycan biosynthesis Metabolic pathways		O-linked glycosylation

Show/Hide Causal Diseases (2)

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 a, 8	rs387907299, rs752069645, rs1553618354, rs374042455, rs755487513, rs1021357430, rs1575461722, rs2089839448	N/A
Limb-Girdle Muscular Dystrophy-Dystroglycanopathy	muscular dystrophy-dystroglycanopathy (limb-girdle), type c, 8	rs374042455, rs1559414655	N/A

Show/Hide Unknown Diseases (3)

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.
Insomnia	Insomnia	N/A	N/A	GWAS
Muscular dystrophy	muscular dystrophy-dystroglycanopathy, type A	N/A	N/A	GenCC
Myopathy	myopathy caused by variation in POMGNT2	N/A	N/A	GenCC

Show/Hide Text Mining Associations (5)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Exotropia	Associate	39773702
Malformations of Cortical Development	Associate	32570172, 34301702
Muscular Dystrophies	Associate	23929950
Muscular Dystrophies Limb Girdle	Associate	33825709
Walker Warburg Syndrome	Associate	22958903, 33825709

POMGNT2 (protein O-linked mannose N-acetylglucosaminyltransferase 2 (beta 1,4-))