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

Gene

• Entrez ID: 84892
• Gene name: Protein O-linked mannose N-acetylglucosaminyltransferase 2 (beta 1,4-)
• Gene symbol: POMGNT2
• Synonyms (NCBI Gene): AGO61, C3orf39, GTDC2, MDDGA8, MDDGC8
• 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]

SNPs

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

miRNA

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

Gene ontology (GO)

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

Other IDs

• MIM: 614828
• HGNC: 25902
• e!Ensembl: 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

Pathways

KEGG:

Mannose type O-glycan biosynthesis
Metabolic pathways

Reactome:

O-linked glycosylation

Associated diseases

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)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
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, rs752069645, rs374042455, rs755487513, rs1021357430, rs1575461722, rs2089839448	RCV001368082 RCV001364032 RCV001391258 RCV001844390 RCV001994733 RCV002037757 RCV001896689 RCV001888172 RCV003076417 RCV002823899 RCV002947168 RCV002928438 RCV003867011 RCV000500387 RCV000030787 RCV000856628 RCV000656413 RCV000691508 RCV000817910 RCV002549296 RCV001065611	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Muscular dystrophy-dystroglycanopathy (limb-girdle), type C, 8	Likely pathogenic; Pathogenic	rs374042455, rs1559414655	RCV000684835 RCV000684836	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
ATTENTION DEFICIT HYPERACTIVITY DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BIPOLAR DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
concomitant exotropia	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INSOMNIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MAJOR DEPRESSIVE DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MENTAL OR BEHAVIOURAL DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MUSCLE EYE BRAIN DISEASE	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Neonatal death	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OBESITY	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
POMGNT2-related disorder	Likely benign; Benign; Conflicting classifications of pathogenicity; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
POST-TRAUMATIC STRESS DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCHIZOPHRENIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Severe hydrocephalus	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SUBSTANCE ABUSE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
WALKER-WARBURG CONGENITAL MUSCULAR DYSTROPHY	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
WALKER-WARBURG SYNDROME	—	CTD, Orphanet CTD, Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Absence of septum pellucidum	Absence Of Septum Pellucidum	HPO_DG			★☆☆☆☆ Found in Text Mining only
Agenesis of corpus callosum	Agenesis Of Corpus Callosum	HPO_DG			★☆☆☆☆ Found in Text Mining only
alpha-Dystroglycanopathies	alpha-Dystroglycanopathy	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Anophthalmos	Syndromic microphthalmia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cataract	Cataract	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cerebellar Hypoplasia	Cerebellar Hypoplasia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cobblestone Lissencephaly	Cobblestone Lissencephaly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital coloboma of iris	Congenital Coloboma Of Iris	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital hypoplasia of penis	Congenital Hypoplasia Of Penis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cryptorchidism	Cryptorchidism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Dandy-Walker Syndrome	Dandy-Walker Syndrome	HPO_DG			★☆☆☆☆ Found in Text Mining only
Fukuyama Type Congenital Muscular Dystrophy	Fukuyama Type Congenital Muscular Dystrophy	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Glaucoma	Glaucoma	HPO_DG			★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hydrocephalus	Hydrocephalus	BEFREE	22958903		★☆☆☆☆ Found in Text Mining only
Hydrocephalus	Hydrocephalus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Leukemia, Myelocytic, Acute	Leukemia	GWASCAT_DG	27903959		★☆☆☆☆ Found in Text Mining only
Macrocephaly	Macrocephaly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Malformations of Cortical Development	Cortical development malformation	Pubtator	32570172, 34301702	Associate	★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Microcornea	Microcornea	HPO_DG			★☆☆☆☆ Found in Text Mining only
Microphthalmos	Microphthalmos	HPO_DG			★☆☆☆☆ Found in Text Mining only
Muscle eye brain disease	Muscle Eye Brain Disease	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Muscular Dystrophies, Limb-Girdle	Limb-Girdle Muscular Dystrophy	GENOMICS_ENGLAND_DG	27066570		★☆☆☆☆ Found in Text Mining only
Muscular Dystrophy	Muscular dystrophy	BEFREE	22958903		★☆☆☆☆ Found in Text Mining only
Muscular Dystrophy	Muscular dystrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
MUSCULAR DYSTROPHY, LIMB-GIRDLE, TYPE 2K	Limb-girdle muscular dystrophy	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Muscular Dystrophy-Dystroglycanopathy (Congenital with Brain and Eye Anomalies) Type A, 1	Muscular Dystrophy-Dystroglycanopathy	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (CONGENITAL WITH BRAIN AND EYE ANOMALIES), TYPE A, 8	Congenital Muscular Dystrophy-Dystroglycanopathy With Brain And Eye Anomalies	GENOMICS_ENGLAND_DG	22958903, 27066570		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (CONGENITAL WITH BRAIN AND EYE ANOMALIES), TYPE A, 8	Congenital Muscular Dystrophy-Dystroglycanopathy With Brain And Eye Anomalies	UNIPROT_DG	22958903		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (CONGENITAL WITH BRAIN AND EYE ANOMALIES), TYPE A, 8	Congenital Muscular Dystrophy-Dystroglycanopathy With Brain And Eye Anomalies	CLINVAR_DG			★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (LIMB-GIRDLE), TYPE C, 8	Limb-Girdle Muscular Dystrophy-Dystroglycanopathy	UNIPROT_DG	27066570		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (LIMB-GIRDLE), TYPE C, 8	Limb-Girdle Muscular Dystrophy-Dystroglycanopathy	CLINVAR_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Optic Atrophy	Optic Atrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Pachygyria	Pachygyria	HPO_DG			★☆☆☆☆ Found in Text Mining only
Polymicrogyria	Polymicrogyria	HPO_DG			★☆☆☆☆ Found in Text Mining only
Posteriorly rotated ear	Posteriorly Rotated Ear	HPO_DG			★☆☆☆☆ Found in Text Mining only
Retinal Detachment	Retinal Detachment	HPO_DG			★☆☆☆☆ Found in Text Mining only
Retinal Dysplasia	Retinal Dysplasia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Retinal Dystrophies	Retinal Dystrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Specific learning disability	Specific Learning Disorder	HPO_DG			★☆☆☆☆ Found in Text Mining only
Submucous cleft of hard palate	Submucosal cleft palate	HPO_DG			★☆☆☆☆ Found in Text Mining only
Walker-Warburg congenital muscular dystrophy	Walker-Warburg Congenital Muscular Dystrophy	BEFREE	22958903, 24041696		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Walker-Warburg congenital muscular dystrophy	Walker-Warburg Congenital Muscular Dystrophy	ORPHANET_DG	22958903		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Walker-Warburg congenital muscular dystrophy	Walker-Warburg Congenital Muscular Dystrophy	GENOMICS_ENGLAND_DG	27066570		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Walker-Warburg congenital muscular dystrophy	Walker-Warburg Congenital Muscular Dystrophy	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Walker-Warburg syndrome	Walker-Warburg Syndrome	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations