NAGPA (N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase)

Gene

• Entrez ID: 51172
• Gene name: N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase
• Gene symbol: NAGPA
• Synonyms (NCBI Gene): APAA, UCE
• Chromosome: 16
• Chromosome location: 16p13.3
• Summary: Hydrolases are transported to lysosomes after binding to mannose 6-phosphate receptors in the trans-Golgi network. This gene encodes the enzyme that catalyzes the second step in the formation of the mannose 6-phosphate recognition marker on lysosomal hydr

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT019717	hsa-miR-375	Microarray	20215506
MIRT044896	hsa-miR-193a-3p	CLASH	23622248
MIRT1173074	hsa-miR-203	CLIP-seq
MIRT1173075	hsa-miR-298	CLIP-seq
MIRT1173076	hsa-miR-3158-5p	CLIP-seq
MIRT1173077	hsa-miR-331-3p	CLIP-seq
MIRT1173078	hsa-miR-3679-3p	CLIP-seq
MIRT1173079	hsa-miR-4786-3p	CLIP-seq
MIRT1173080	hsa-miR-513a-3p	CLIP-seq
MIRT1173075	hsa-miR-298	CLIP-seq
MIRT1173076	hsa-miR-3158-5p	CLIP-seq
MIRT1173077	hsa-miR-331-3p	CLIP-seq
MIRT1173078	hsa-miR-3679-3p	CLIP-seq
MIRT2050128	hsa-miR-4514	CLIP-seq
MIRT2050129	hsa-miR-4692	CLIP-seq
MIRT1173079	hsa-miR-4786-3p	CLIP-seq
MIRT1173080	hsa-miR-513a-3p	CLIP-seq
MIRT2279056	hsa-miR-1307	CLIP-seq
MIRT2279057	hsa-miR-1972	CLIP-seq
MIRT2279058	hsa-miR-214	CLIP-seq
MIRT2279059	hsa-miR-3166	CLIP-seq
MIRT2279060	hsa-miR-3619-5p	CLIP-seq
MIRT2050128	hsa-miR-4514	CLIP-seq
MIRT2279061	hsa-miR-4638-5p	CLIP-seq
MIRT2050129	hsa-miR-4692	CLIP-seq
MIRT2279062	hsa-miR-761	CLIP-seq
MIRT2279063	hsa-miR-885-3p	CLIP-seq
MIRT2279064	hsa-miR-922	CLIP-seq
MIRT2279065	hsa-miR-940	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003944	Function	N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase activity	IEA
GO:0003944	Function	N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase activity	TAS	10551838
GO:0005515	Function	Protein binding	IPI	26544806
GO:0005794	Component	Golgi apparatus	IEA
GO:0005975	Process	Carbohydrate metabolic process	TAS	10551838
GO:0006486	Process	Protein glycosylation	IEA
GO:0006622	Process	Protein targeting to lysosome	TAS	10551838
GO:0007040	Process	Lysosome organization	TAS	10551838
GO:0016020	Component	Membrane	IEA
GO:0016020	Component	Membrane	TAS	10551838
GO:0016787	Function	Hydrolase activity	IEA
GO:0032580	Component	Golgi cisterna membrane	IEA
GO:0033299	Process	Secretion of lysosomal enzymes	IBA
GO:0033299	Process	Secretion of lysosomal enzymes	IEA
GO:0036211	Process	Protein modification process	TAS	10551838

Other IDs

• MIM: 607985
• HGNC: 17378
• e!Ensembl: ENSG00000103174

Protein

• UniProt ID: Q9UK23
• Protein name: N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase (EC 3.1.4.45) (Mannose 6-phosphate-uncovering enzyme) (Phosphodiester alpha-GlcNAcase)
• Protein function: Catalyzes the second step in the formation of the mannose 6-phosphate targeting signal on lysosomal enzyme oligosaccharides by removing GlcNAc residues from GlcNAc-alpha-P-mannose moieties, which are formed in the first step. Also hydrolyzes UDP
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF09992	NAGPA	130 → 325	Phosphodiester glycosidase	Domain

• Tissue specificity: TISSUE SPECIFICITY: Isoform 2 may be brain-specific.
• Sequence:

  MATSTGRWLLLRLALFGFLWEASGGLDSGASRDDDLLLPYPRARARLPRDCTRVRAGNRE
  HESWPPPPATPGAGGLAVRTFVSHFRDRAVAGHLTRAVEPLRTFSVLEPGGPGGCAARRR
  ATVEETARAADCRVAQNGGFFRMNSGECLGNVVSDERRVSSSGGLQNAQFGIRRDGTLVT
  GYLSEEEVLDTENPFVQLLSGVVWLIRNGSIYINESQATECDETQETGSFSKFVNVISAR
  TAIGHDRKGQLVLFHADGQTEQRGINLWEMAEFLLKQDVVNAINLDGGGSATFVLNGTLA
  SYPSDHCQDNMWRCPRQVSTVVCVHEPRCQPPDCHGHGTCVDGHCQCTGHFWRGPGCDEL
  DCGPSNCSQHGLCTETGCRCDAGWTGSNCSEECPLGWHGPGCQRPCKCEHHCPCDPKTGN
  CSVSRVKQCLQPPEATLRAGELSFFTRTAWLALTLALAFLLLISTAANLSLLLSRAERNR
  RLHGDYAYHPLQEMNGEPLAAEKEQPGGAHNPFKD

• Sequence length: 515

Pathways

KEGG:

Lysosome

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)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Cholangiocarcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant lymphoma, large B-cell, diffuse	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MUCOCUTANEOUS LYMPH NODE SYNDROME	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NAGPA-related disorder	Likely benign; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCOLIOSIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Stuttering, familial persistent, 2	Uncertain significance; Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Variant of unknown significance	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
VASCULITIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Developmental reading disorder	Developmental dyslexia	BEFREE	25643770		★☆☆☆☆ Found in Text Mining only
Dyslexia	Dyslexia	BEFREE	25643770		★☆☆☆☆ Found in Text Mining only
Dyslexia	Dyslexia	Pubtator	25643770	Associate	★☆☆☆☆ Found in Text Mining only
MPS III B	Mucopolysaccharidosis	BEFREE	30657762		★☆☆☆☆ Found in Text Mining only
Mucocutaneous Lymph Node Syndrome	Kawasaki disease	Pubtator	33993232	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Mucolipidoses	Mucolipidosis	Pubtator	20147709	Associate	★☆☆☆☆ Found in Text Mining only
Mucolipidoses	Mucolipidosis	BEFREE	22884963		★☆☆☆☆ Found in Text Mining only
MUCOLIPIDOSIS II ALPHA/BETA (disorder)	Mucolipidosis	BEFREE	26130485		★☆☆☆☆ Found in Text Mining only
Multiple Myeloma	Multiple myeloma	Pubtator	31948430	Associate	★☆☆☆☆ Found in Text Mining only
Neurodegenerative Disorders	Neurodegenerative Disorders	BEFREE	30657762		★☆☆☆☆ Found in Text Mining only
Pseudo-Hurler Polydystrophy	Pseudo-Hurler Polydystrophy	BEFREE	26130485		★☆☆☆☆ Found in Text Mining only
Specific language impairment	Specific Language Impairment	BEFREE	24807205		★☆☆☆☆ Found in Text Mining only
Vasculitis	Vasculitis	Pubtator	33993232	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations