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	84892
Gene name	Protein O-linked mannose N-acetylglucosaminyltransferase 2 (beta 1,4-)
Gene symbol	POMGNT2
Synonyms (NCBI Gene)	AGO61C3orf39GTDC2MDDGA8MDDGC8
Chromosome	3
Chromosome location	3p22.1
Summary	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

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

442

Show/Hide Causal Diseases (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8	Likely pathogenic; Pathogenic	rs747691921, rs2125699699, rs747569790, rs2125700641, rs2125700808, rs2125700249, rs2089853535, rs2089847365, rs2089842285, rs2528901921, rs2528893606, rs2528899846, rs2528895339, rs1553618354, rs387907299 View all (6 more)	RCV001368082 RCV001364032 RCV001391258 RCV001844390 RCV001994733 RCV002037757 RCV001896689 RCV001888172 RCV003076417 RCV002823899 RCV002947168 RCV002928438 RCV003867011 RCV000500387 RCV000030787 RCV000856628 RCV000656413 RCV000691508 RCV000817910 RCV002549296 RCV001065611
Muscular dystrophy-dystroglycanopathy (limb-girdle), type C, 8	Likely pathogenic; Pathogenic	rs374042455, rs1559414655	RCV000684835 RCV000684836

Show/Hide Unknown Diseases (4)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
concomitant exotropia	Conflicting classifications of pathogenicity	rs199612856	RCV004731059
Neonatal death	Conflicting classifications of pathogenicity	rs387907300	RCV000162139
POMGNT2-related disorder	Likely benign; Benign; Conflicting classifications of pathogenicity; Uncertain significance	rs572228301, rs149948290, rs1211672309, rs375314883, rs143394182, rs139245562, rs140389725, rs201114442, rs201572917, rs549430013, rs373276653, rs59831271, rs377724350, rs199612856	RCV003900395 RCV003927804 RCV003909798 RCV003970182 RCV003925438 RCV004730963 RCV003935501 RCV003925683 RCV003935502 RCV003420214 RCV003948227 RCV003908297 RCV003910526 RCV003958276
Severe hydrocephalus	Conflicting classifications of pathogenicity	rs387907300	RCV000162139

Show/Hide Text Mining Associations (5)

Disease Name	Relationship Type	References
Associations from Text MiningDisease 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-))