NUDT2 (nudix hydrolase 2)

Gene

• Entrez ID: 318
• Gene name: Nudix hydrolase 2
• Gene symbol: NUDT2
• Synonyms (NCBI Gene): APAH1, IDDPN
• Chromosome: 9
• Chromosome location: 9p13.3
• Summary: This gene encodes a member of the MutT family of nucleotide pyrophosphatases, a subset of the larger NUDIX hydrolase family. The gene product possesses a modification of the MutT sequence motif found in certain nucleotide pyrophosphatases. The enzyme asym

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs529087882	A>-	Likely-pathogenic	Coding sequence variant, frameshift variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT042526	hsa-miR-423-3p	CLASH	23622248
MIRT037637	hsa-miR-744-5p	CLASH	23622248
MIRT1198047	hsa-miR-4537	CLIP-seq
MIRT1198048	hsa-miR-4686	CLIP-seq
MIRT1198049	hsa-miR-4719	CLIP-seq
MIRT1198050	hsa-miR-4762-5p	CLIP-seq
MIRT1198051	hsa-miR-513b	CLIP-seq
MIRT1198052	hsa-miR-767-3p	CLIP-seq
MIRT1198053	hsa-miR-4687-3p	CLIP-seq
MIRT1198054	hsa-miR-634	CLIP-seq
MIRT2057338	hsa-miR-142-5p	CLIP-seq
MIRT2057339	hsa-miR-340	CLIP-seq
MIRT2057340	hsa-miR-548a-5p	CLIP-seq
MIRT2057341	hsa-miR-548ab	CLIP-seq
MIRT2057342	hsa-miR-548ak	CLIP-seq
MIRT2057343	hsa-miR-548b-5p	CLIP-seq
MIRT2057344	hsa-miR-548c-5p	CLIP-seq
MIRT2057345	hsa-miR-548d-5p	CLIP-seq
MIRT2057346	hsa-miR-548h	CLIP-seq
MIRT2057347	hsa-miR-548i	CLIP-seq
MIRT2057348	hsa-miR-548j	CLIP-seq
MIRT2057349	hsa-miR-548k	CLIP-seq
MIRT2057350	hsa-miR-548l	CLIP-seq
MIRT2057351	hsa-miR-548w	CLIP-seq
MIRT2057352	hsa-miR-548y	CLIP-seq
MIRT2057353	hsa-miR-559	CLIP-seq
MIRT2057354	hsa-miR-624	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0004081	Function	Bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity	IBA
GO:0004081	Function	Bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity	IEA
GO:0004081	Function	Bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity	ISS	11738085
GO:0004081	Function	Bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity	TAS
GO:0005515	Function	Protein binding	IPI	25416956, 32296183
GO:0005525	Function	GTP binding	IEA
GO:0005759	Component	Mitochondrial matrix	TAS
GO:0006139	Process	Nucleobase-containing compound metabolic process	TAS	7487923
GO:0006167	Process	AMP biosynthetic process	IBA
GO:0006754	Process	ATP biosynthetic process	IBA
GO:0006915	Process	Apoptotic process	ISS	11937063
GO:0008796	Function	Bis(5'-nucleosyl)-tetraphosphatase activity	IEA
GO:0008803	Function	Bis(5'-nucleosyl)-tetraphosphatase (symmetrical) activity	TAS	7487923
GO:0016787	Function	Hydrolase activity	IEA
GO:0034599	Process	Cellular response to oxidative stress	TAS

Other IDs

• MIM: 602852
• HGNC: 8049
• e!Ensembl: ENSG00000164978

Protein

• UniProt ID: P50583
• Protein name: Bis(5'-nucleosyl)-tetraphosphatase [asymmetrical] (EC 3.6.1.17) (Diadenosine 5',5'''-P1,P4-tetraphosphate asymmetrical hydrolase) (Ap4A hydrolase) (Ap4Aase) (Diadenosine tetraphosphatase) (Nucleoside diphosphate-linked moiety X motif 2) (Nudix motif 2)
• Protein function: Catalyzes the asymmetric hydrolysis of diadenosine 5',5'''-P1,P4-tetraphosphate (Ap4A) to yield AMP and ATP (By similarity). Exhibits decapping activity towards FAD-capped RNAs and dpCoA-capped RNAs in vitro (By similarity). {ECO:0000250|UniProt
• PDB: 1XSA, 1XSB, 1XSC, 3U53, 4ICK, 4IJX
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00293	NUDIX	12 → 137	NUDIX domain	Domain

• Sequence:

  MALRACGLIIFRRCLIPKVDNNAIEFLLLQASDGIHHWTPPKGHVEPGEDDLETALRETQ
  EEAGIEAGQLTIIEGFKRELNYVARNKPKTVIYWLAEVKDYDVEIRLSHEHQAYRWLGLE
  EACQLAQFKEMKAALQEGHQFLCSIEA

• Sequence length: 147

Pathways

KEGG:

Purine metabolism
Pyrimidine metabolism
Metabolic pathways

Reactome:

Detoxification of Reactive Oxygen Species

Associated diseases

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Complex neurodevelopmental disorder	Likely pathogenic; Pathogenic	rs529087882	RCV002225120
Intellectual developmental disorder with or without peripheral neuropathy	Likely pathogenic; Pathogenic	rs148119952, rs772730170, rs529087882	RCV002248318 RCV003156721 RCV002251755
Intellectual disability	Likely pathogenic; Pathogenic	rs529087882	RCV001533201
NUDT2-associated condition	Likely pathogenic; Pathogenic	rs529087882	RCV000850407

Associations from Text Mining
Disease Name	Relationship Type	References
Attention Deficit Disorder with Hyperactivity	Associate	38243213
Basal Ganglia Diseases	Associate	38141063
Disease	Associate	38141063
Gait Disorders Neurologic	Associate	38141063
Heredodegenerative Disorders Nervous System	Associate	38141063
Hypersensitivity Delayed	Associate	38243213
Inflammation	Associate	27144453
Intellectual Disability	Associate	33058507, 38243213
Muscle Weakness	Associate	33058507
Neoplasms	Associate	27144453
Nervous System Diseases	Associate	38141063
Paraparesis	Associate	33058507
Peripheral Nervous System Diseases	Associate	38141063
Polyneuropathies	Associate	33058507
Sensorimotor neuropathy with ataxia autosomal dominant	Associate	33058507
Somnambulism	Associate	38243213