NUDT3 nudix hydrolase 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: NUDT3provided by HGNC
Official Full Name: nudix hydrolase 3provided by HGNC
Primary source: HGNC:HGNC:8050
See related: Ensembl:ENSG00000272325 MIM:609228; AllianceGenome:HGNC:8050
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: DIPP; DIPP1; DIPP-1
Summary: NUDT3 belongs to the MutT, or Nudix, protein family. Nudix proteins act as homeostatic checkpoints at important stages in nucleoside phosphate metabolic pathways, guarding against elevated levels of potentially dangerous intermediates, like 8-oxo-dGTP, which promotes AT-to-CG transversions (Safrany et al., 1998 [PubMed 9822604]).[supplied by OMIM, Feb 2011]
Expression: Ubiquitous expression in brain (RPKM 33.6), thyroid (RPKM 19.6) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 6p21.31

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (34279679..34392669, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (34103325..34216339, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (34247456..34360446, complement)

Chromosome 6 - NC_000006.12 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
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?

Uterine leiomyoma with RAD51B::NUDT3 fusion: a report of 2 cases.
Title: Uterine leiomyoma with RAD51B::NUDT3 fusion: a report of 2 cases.
Polyphosphate degradation by Nudt3-Zn(2+) mediates oxidative stress response.
Title: Polyphosphate degradation by Nudt3-Zn(2+) mediates oxidative stress response.
New structural insights reveal an expanded reaction cycle for inositol pyrophosphate hydrolysis by human DIPP1.
Title: New structural insights reveal an expanded reaction cycle for inositol pyrophosphate hydrolysis by human DIPP1.
InsP7 is a small-molecule regulator of NUDT3-mediated mRNA decapping and processing-body dynamics.
Title: InsP(7) is a small-molecule regulator of NUDT3-mediated mRNA decapping and processing-body dynamics.
NUDT3 and KLF5 were found to associate with lean mass and HLA-DQB1-AS1 for hand grip strength as candidate genes to target for these phenotypes in sarcopenia. The associated regulatory SNPs are rs464553, rs1028883 and rs3129753 respectively.
Title: Disentangling the genetics of sarcopenia: prioritization of NUDT3 and KLF5 as genes for lean mass & HLA-DQB1-AS1 for hand grip strength with the associated enhancing SNPs & a scoring system.
Nudt3 is an mRNA decapping enzyme that orchestrates expression of a subset of mRNAs to modulate cell migration and further substantiates the existence of multiple decapping enzymes functioning in distinct cellular pathways in mammals
Title: Nudt3 is an mRNA decapping enzyme that modulates cell migration.
results suggest that NUDT3 rs206936 is associated with body mass index in Japanese women
Title: NUDT3 rs206936 is associated with body mass index in obese Japanese women.

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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

EBI GWAS Catalog

Description
Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index. EBI GWAS Catalog EBI GWAS CatalogPubMed
Identification of 15 loci influencing height in a Korean population. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
Knockdown of nudix (nucleoside diphosphate linked moiety X)-type motif 3 (NUDT3) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D11S2921 (e-PCR)
- UniSTS:152074

L17705 (e-PCR)
- UniSTS:66091

D1S1361 (e-PCR)
- UniSTS:149557

D11S3674 (e-PCR)
- UniSTS:152908

D7S2067E (e-PCR)
- UniSTS:151120

G42665 (e-PCR)
- UniSTS:94565

D10S16 (e-PCR)
- UniSTS:155756

1866 (e-PCR)
- UniSTS:7030

RH37434 (e-PCR)
- UniSTS:83328

D8S1027 (e-PCR)
- UniSTS:149197

D11S3316 (e-PCR)
- UniSTS:152558

Readthrough RPS10-NUDT3

Readthrough gene: RPS10-NUDT3, Included gene: RPS10

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity	IDA Inferred from Direct Assay more info	PubMed
enables 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity	IDA Inferred from Direct Assay more info	PubMed
enables bis(5'-adenosyl)-hexaphosphatase activity	IBA Inferred from Biological aspect of Ancestor more info
enables bis(5'-adenosyl)-pentaphosphatase activity	IBA Inferred from Biological aspect of Ancestor more info
enables diphosphoinositol-polyphosphate diphosphatase activity	IBA Inferred from Biological aspect of Ancestor more info
enables diphosphoinositol-polyphosphate diphosphatase activity	IDA Inferred from Direct Assay more info	PubMed
enables endopolyphosphatase activity	IBA Inferred from Biological aspect of Ancestor more info
enables endopolyphosphatase activity	IDA Inferred from Direct Assay more info	PubMed
enables inositol diphosphate pentakisphosphate diphosphatase activity	IDA Inferred from Direct Assay more info	PubMed
enables inositol diphosphate pentakisphosphate diphosphatase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables inositol diphosphate tetrakisphosphate diphosphatase activity	IDA Inferred from Direct Assay more info	PubMed
enables inositol diphosphate tetrakisphosphate diphosphatase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables inositol-3,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity	IEA Inferred from Electronic Annotation more info
enables inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity	IEA Inferred from Electronic Annotation more info
enables magnesium ion binding	IDA Inferred from Direct Assay more info	PubMed
enables manganese ion binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables zinc ion binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in RNA decapping	IDA Inferred from Direct Assay more info	PubMed
involved_in RNA decapping	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in adenosine 5'-(hexahydrogen pentaphosphate) catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell-cell signaling	TAS Traceable Author Statement more info	PubMed
involved_in diadenosine hexaphosphate catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in diadenosine hexaphosphate catabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in diadenosine pentaphosphate catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in diadenosine polyphosphate catabolic process	TAS Traceable Author Statement more info	PubMed
involved_in diphosphoinositol polyphosphate catabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in diphosphoinositol polyphosphate metabolic process	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info
located_in cytosol	TAS Traceable Author Statement more info
located_in glutamatergic synapse	IEA Inferred from Electronic Annotation more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: diphosphoinositol polyphosphate phosphohydrolase 1

Names: ap6A hydrolase; diadenosine 5',5'''-P1,P6-hexaphosphate hydrolase 1; diadenosine hexaphosphate hydrolase; endopolyphosphatase; m7GpppN-mRNA hydrolase; m7GpppX diphosphatase; nucleoside diphosphate-linked moiety X motif 3; nudix (nucleoside diphosphate linked moiety X)-type motif 3; nudix motif 3

NP_006694.1

EC 3.6.1.10

EC 3.6.1.52

EC 3.6.1.59

EC 3.6.1.61

EC 3.6.1.62

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_006703.4 → NP_006694.1 diphosphoinositol polyphosphate phosphohydrolase 1

See identical proteins and their annotated locations for NP_006694.1

Status: VALIDATED

Source sequence(s)

AL354740, BC007727, CA430332, DA803962, Z98036

Consensus CDS

CCDS4791.1

UniProtKB/Swiss-Prot

B2R8N4, O95989

Related

ENSP00000476119.1, ENST00000607016.2

Conserved Domains (1) summary

cd04666
Location:19 → 131

Nudix_Hydrolase_9; Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly ...