NUDT2 nudix hydrolase 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: NUDT2provided by HGNC
Official Full Name: nudix hydrolase 2provided by HGNC
Primary source: HGNC:HGNC:8049
See related: Ensembl:ENSG00000164978 MIM:602852; AllianceGenome:HGNC:8049
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: APAH1; IDDPN
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 asymmetrically hydrolyzes Ap4A to yield AMP and ATP and is responsible for maintaining the intracellular level of the dinucleotide Ap4A, the function of which has yet to be established. This gene may be a candidate tumor suppressor gene. Alternative splicing has been observed at this locus and four transcript variants, all encoding the same protein, have been identified. [provided by RefSeq, Sep 2011]
Expression: Ubiquitous expression in ovary (RPKM 11.6), prostate (RPKM 10.9) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 9p13.3

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	9	NC_000009.12 (34329569..34343699)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	9	NC_060933.1 (34348133..34362241)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	9	NC_000009.11 (34329567..34343697)

Chromosome 9 - NC_000009.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Biallelic NUDT2 variants defective in mRNA decapping cause a neurodevelopmental disease.
Title: Biallelic NUDT2 variants defective in mRNA decapping cause a neurodevelopmental disease.
Role of Nudt2 in Anchorage-Independent Growth and Cell Migration of Human Melanoma.
Title: Role of Nudt2 in Anchorage-Independent Growth and Cell Migration of Human Melanoma.
NUDT2 initiates viral RNA degradation by removal of 5'-phosphates.
Title: NUDT2 initiates viral RNA degradation by removal of 5'-phosphates.
NUDT2 is a novel complex formation enhancing factor regulating mTORC1-Rag GTPase signaling that is crucial for cell growth control.
Title: Nudix-type motif 2 contributes to cancer proliferation through the regulation of Rag GTPase-mediated mammalian target of rapamycin complex 1 localization.
Regulation of gene expression is one of several roles proposed for the stress-induced nucleotide diadenosine tetraphosphate (Ap4A). We have examined this directly by a comparative RNA-Seq analysis of KBM-7 chronic myelogenous leukemia cells and KBM-7 cells in which the NUDT2 Ap4A hydrolase gene had been disrupted (NuKO cells), causing a 175-fold increase in intracellular Ap4A.
Title: NUDT2 Disruption Elevates Diadenosine Tetraphosphate (Ap4A) and Down-Regulates Immune Response and Cancer Promotion Genes.
This paper presents the crystal structure of wild-type and E58A mutant human Ap4A hydrolase.
Title: Crystal structure of wild-type and mutant human Ap4A hydrolase.
High NUDT2 is associated with breast carcinoma.
Title: Nudix-type motif 2 in human breast carcinoma: a potent prognostic factor associated with cell proliferation.
Observational study of gene-disease association. (HuGE Navigator)
Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
In this study the authors present data demonstrating that the SARS-CoV 7a protein interacts with human Ap4A-hydrolase (asymmetrical diadenosine tetraphosphate hydrolase, EC 3.6.1.17).
Title: SARS coronavirus protein 7a interacts with human Ap4A-hydrolase.
NMR resonance assignments
Title: 1H, 13C, and 15N resonance assignments of the 17 kDa Ap4A hydrolase from Homo sapiens in the presence and absence of ATP.

Submit: New GeneRIF Correction See all GeneRIFs (11)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Intellectual developmental disorder with or without peripheral neuropathy MedGen: C5676969 OMIM: 619844 GeneReviews: Not available	not available

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables GTP binding	IEA Inferred from Electronic Annotation more info
enables bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity	IBA Inferred from Biological aspect of Ancestor more info
enables bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity	TAS Traceable Author Statement more info
enables bis(5'-nucleosyl)-tetraphosphatase (symmetrical) activity	TAS Traceable Author Statement more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in AMP biosynthetic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in ATP biosynthetic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in apoptotic process	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in cellular response to oxidative stress	TAS Traceable Author Statement more info
involved_in nucleobase-containing compound metabolic process	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in mitochondrial matrix	TAS Traceable Author Statement more info

General protein information

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Preferred Names: bis(5'-nucleosyl)-tetraphosphatase [asymmetrical]

Names: Ap4A hydrolase 1; Ap4Aase; bis(5'-nucleosyl)-tetraphosphatase (asymmetrical); diadenosine 5',5'''-P1,P4-tetraphosphate asymmetrical hydrolase; diadenosine 5',5''-P1,P4-tetraphosphate pyrophosphohydrolase; diadenosine tetraphosphatase; nucleoside diphosphate-linked moiety X motif 2; nudix (nucleoside diphosphate linked moiety X)-type motif 2; nudix motif 2

NP_001152.1

EC 3.6.1.17

NP_001231319.1

EC 3.6.1.17

NP_671701.1

EC 3.6.1.17

NP_671702.1

EC 3.6.1.17

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001161.5 → NP_001152.1 bis(5'-nucleosyl)-tetraphosphatase [asymmetrical]

See identical proteins and their annotated locations for NP_001152.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) is the full-length transcript. All four variants encode the same protein.

Source sequence(s)

AA398857, AL356494, BG825757, BQ007098

Consensus CDS

CCDS6552.1

UniProtKB/Swiss-Prot

D3DRM0, P50583, Q5T589

Related

ENSP00000368455.1, ENST00000379158.7

Conserved Domains (1) summary

cd03428
Location:2 → 140

Ap4A_hydrolase_human_like; Diadenosine tetraphosphate (Ap4A) hydrolase is a member of the Nudix hydrolase superfamily. Ap4A hydrolases are well represented in a variety of prokaryotic and eukaryotic organisms. Phylogenetic analysis reveals two distinct subgroups where plant ...
NM_001244390.2 → NP_001231319.1 bis(5'-nucleosyl)-tetraphosphatase [asymmetrical]

See identical proteins and their annotated locations for NP_001231319.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks two alternate 5' UTR exons compared to variant 1. All four variants encode the same protein.

Source sequence(s)

AA310093, BQ007098

Consensus CDS

CCDS6552.1

UniProtKB/Swiss-Prot

D3DRM0, P50583, Q5T589

Related

ENSP00000482384.1, ENST00000618590.1

Conserved Domains (1) summary

cd03428
Location:2 → 140

Ap4A_hydrolase_human_like; Diadenosine tetraphosphate (Ap4A) hydrolase is a member of the Nudix hydrolase superfamily. Ap4A hydrolases are well represented in a variety of prokaryotic and eukaryotic organisms. Phylogenetic analysis reveals two distinct subgroups where plant ...
NM_147172.3 → NP_671701.1 bis(5'-nucleosyl)-tetraphosphatase [asymmetrical]

See identical proteins and their annotated locations for NP_671701.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate splice site on a 5' non-coding exon, compared to variant 1. All four variants encode the same protein.

Source sequence(s)

BG622439, BQ007098

Consensus CDS

CCDS6552.1

UniProtKB/Swiss-Prot

D3DRM0, P50583, Q5T589

Related

ENSP00000368452.5, ENST00000379155.9

Conserved Domains (1) summary

cd03428
Location:2 → 140

Ap4A_hydrolase_human_like; Diadenosine tetraphosphate (Ap4A) hydrolase is a member of the Nudix hydrolase superfamily. Ap4A hydrolases are well represented in a variety of prokaryotic and eukaryotic organisms. Phylogenetic analysis reveals two distinct subgroups where plant ...
NM_147173.3 → NP_671702.1 bis(5'-nucleosyl)-tetraphosphatase [asymmetrical]

See identical proteins and their annotated locations for NP_671702.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks a 5' non-coding exon, compared to variant 1. All four variants encode the same protein.

Source sequence(s)

AA398857, BQ007098, DN992111

Consensus CDS

CCDS6552.1

UniProtKB/Swiss-Prot

D3DRM0, P50583, Q5T589

Related

ENSP00000344187.4, ENST00000346365.9

Conserved Domains (1) summary

cd03428
Location:2 → 140

Ap4A_hydrolase_human_like; Diadenosine tetraphosphate (Ap4A) hydrolase is a member of the Nudix hydrolase superfamily. Ap4A hydrolases are well represented in a variety of prokaryotic and eukaryotic organisms. Phylogenetic analysis reveals two distinct subgroups where plant ...