The protein encoded by this gene regulates the turnover of diphosphoinositol polyphosphates. The turnover of these high-energy diphosphoinositol polyphosphates represents a molecular switching activity with important regulatory consequences. Molecular switching by diphosphoinositol polyphosphates may contribute to regulating intracellular trafficking. Several alternatively spli... See more...

Aliases for NUDT4 Gene

Aliases for NUDT4 Gene

  • Nudix Hydrolase 4 2 3 5
  • Nudix (Nucleoside Diphosphate Linked Moiety X)-Type Motif 4 2 3
  • Diphosphoinositol Polyphosphate Phosphohydrolase Type 2 2 3
  • Diadenosine 5',5'''-P1,P6-Hexaphosphate Hydrolase 2 3 4
  • Diphosphoinositol Polyphosphate Phosphohydrolase 2 3 4
  • DIPP-2 3 4
  • DIPP2 3 4
  • Diphosphoinositol Polyphosphate Phosphohydrolase NUDT4B 3
  • Nucleoside Diphosphate-Linked Moiety X Motif 4B 3
  • Nucleoside Diphosphate-Linked Moiety X Motif 4 4
  • Nudix Hydrolase 4B 3
  • Nudix Motif 4B 3
  • Nudix Motif 4 4
  • EC 3.6.1.52 4
  • DIPP2alpha 3
  • DIPP2beta 3
  • HDCMB47P 3
  • KIAA0487 4
  • DIPP-2B 3
  • NUDT4B 3

External Ids for NUDT4 Gene

Previous GeneCards Identifiers for NUDT4 Gene

  • GC12P094293
  • GC12P093704
  • GC12P092274
  • GC12P093771

Summaries for NUDT4 Gene

Entrez Gene Summary for NUDT4 Gene

  • The protein encoded by this gene regulates the turnover of diphosphoinositol polyphosphates. The turnover of these high-energy diphosphoinositol polyphosphates represents a molecular switching activity with important regulatory consequences. Molecular switching by diphosphoinositol polyphosphates may contribute to regulating intracellular trafficking. Several alternatively spliced transcript variants have been described, but the full-length nature of some variants has not been determined. Isoforms DIPP2alpha and DIPP2beta are distinguishable from each other solely by DIPP2beta possessing one additional amino acid due to intron boundary skidding in alternate splicing. [provided by RefSeq, Jul 2008]

GeneCards Summary for NUDT4 Gene

NUDT4 (Nudix Hydrolase 4) is a Protein Coding gene. Diseases associated with NUDT4 include Testis Seminoma and Peroxisome Biogenesis Disorder 1B. Among its related pathways are Metabolism and Inositol phosphate metabolism. Gene Ontology (GO) annotations related to this gene include hydrolase activity and m7G(5')pppN diphosphatase activity. An important paralog of this gene is NUDT4B.

UniProtKB/Swiss-Prot Summary for NUDT4 Gene

  • Cleaves a beta-phosphate from the diphosphate groups in PP-InsP5 (diphosphoinositol pentakisphosphate), PP-InsP4 and [PP]2-InsP4 (bisdiphosphoinositol tetrakisphosphate), suggesting that it may play a role in signal transduction. Also able to catalyze the hydrolysis of dinucleoside oligophosphate Ap6A, but not Ap5A. The major reaction products are ADP and p4a from Ap6A. Also able to hydrolyze 5-phosphoribose 1-diphosphate. Does not play a role in U8 snoRNA decapping activity. Binds U8 snoRNA.

Gene Wiki entry for NUDT4 Gene

Additional gene information for NUDT4 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for NUDT4 Gene

Genomics for NUDT4 Gene

GeneHancer (GH) Regulatory Elements for NUDT4 Gene

Promoters and enhancers for NUDT4 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NUDT4 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for NUDT4

Top Transcription factor binding sites by QIAGEN in the NUDT4 gene promoter:
  • AP-1
  • c-Fos
  • E2F
  • E2F-1
  • E2F-2
  • E2F-3a
  • E2F-4
  • E2F-5
  • FOXL1
  • Pbx1a

Genomic Locations for NUDT4 Gene

Genomic Locations for NUDT4 Gene
chr12:93,377,883-93,408,146
(GRCh38/hg38)
Size:
30,264 bases
Orientation:
Plus strand
chr12:93,771,659-93,797,024
(GRCh37/hg19)
Size:
25,366 bases
Orientation:
Plus strand

Genomic View for NUDT4 Gene

Genes around NUDT4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NUDT4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NUDT4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NUDT4 Gene

Proteins for NUDT4 Gene

  • Protein details for NUDT4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NZJ9-NUDT4_HUMAN
    Recommended name:
    Diphosphoinositol polyphosphate phosphohydrolase 2
    Protein Accession:
    Q9NZJ9
    Secondary Accessions:
    • B7Z916
    • Q4AEJ6
    • Q53EZ2
    • Q68DD7
    • Q9NPC5
    • Q9NS30
    • Q9NZK0
    • Q9NZK1

    Protein attributes for NUDT4 Gene

    Size:
    180 amino acids
    Molecular mass:
    20306 Da
    Cofactor:
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAF75563.1; Type=Erroneous termination; Note=Extended C-terminus.; Evidence={ECO:0000305}; Sequence=BAE16985.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for NUDT4 Gene

    Alternative splice isoforms for NUDT4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for NUDT4 Gene

Post-translational modifications for NUDT4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for NUDT4 Gene

Domains & Families for NUDT4 Gene

Gene Families for NUDT4 Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Protein Domains for NUDT4 Gene

Blocks:
  • NUDIX hydrolase
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for NUDT4 Gene

GenScript: Design optimal peptide antigens:
  • Nucleoside diphosphate-linked moiety X motif 4 (NUDT4_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9NZJ9

UniProtKB/Swiss-Prot:

NUDT4_HUMAN :
  • Belongs to the Nudix hydrolase family. DIPP subfamily.
Family:
  • Belongs to the Nudix hydrolase family. DIPP subfamily.
genes like me logo Genes that share domains with NUDT4: view

Function for NUDT4 Gene

Molecular function for NUDT4 Gene

UniProtKB/Swiss-Prot Function:
Cleaves a beta-phosphate from the diphosphate groups in PP-InsP5 (diphosphoinositol pentakisphosphate), PP-InsP4 and [PP]2-InsP4 (bisdiphosphoinositol tetrakisphosphate), suggesting that it may play a role in signal transduction. Also able to catalyze the hydrolysis of dinucleoside oligophosphate Ap6A, but not Ap5A. The major reaction products are ADP and p4a from Ap6A. Also able to hydrolyze 5-phosphoribose 1-diphosphate. Does not play a role in U8 snoRNA decapping activity. Binds U8 snoRNA.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=Diphospho-myo-inositol polyphosphate + H(2)O = myo-inositol polyphosphate + phosphate.; EC=3.6.1.52; Evidence=. ;.
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=4.2 nM for PP-InsP5 {ECO:0000269 PubMed:10777568};

Enzyme Numbers (IUBMB) for NUDT4 Gene

Phenotypes From GWAS Catalog for NUDT4 Gene

Gene Ontology (GO) - Molecular Function for NUDT4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000298 endopolyphosphatase activity IBA 21873635
GO:0003723 RNA binding IEA --
GO:0005515 protein binding IPI 25416956
GO:0008486 diphosphoinositol-polyphosphate diphosphatase activity IDA,TAS 10777568
GO:0016787 hydrolase activity IEA --
genes like me logo Genes that share ontologies with NUDT4: view
genes like me logo Genes that share phenotypes with NUDT4: view

Animal Model Products

CRISPR Products

Clone Products

  • Addgene plasmids for NUDT4

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for NUDT4 Gene

Localization for NUDT4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NUDT4 Gene

Cytoplasm.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for NUDT4 gene
Compartment Confidence
nucleus 4
cytosol 4
extracellular 1
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for NUDT4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA 21873635
GO:0005737 cytoplasm IBA 21873635
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with NUDT4: view

Pathways & Interactions for NUDT4 Gene

PathCards logo

SuperPathways for NUDT4 Gene

genes like me logo Genes that share pathways with NUDT4: view

Pathways by source for NUDT4 Gene

Gene Ontology (GO) - Biological Process for NUDT4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0019722 calcium-mediated signaling TAS 10777568
GO:0019935 cyclic-nucleotide-mediated signaling TAS 10777568
GO:0035556 intracellular signal transduction NAS 10777568
GO:0043647 inositol phosphate metabolic process TAS --
GO:0071543 diphosphoinositol polyphosphate metabolic process IBA 21873635
genes like me logo Genes that share ontologies with NUDT4: view

No data available for SIGNOR curated interactions for NUDT4 Gene

Drugs & Compounds for NUDT4 Gene

(5) Drugs for NUDT4 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Magnesium Approved, Experimental, Investigational Pharma 0
Phosphoric acid Approved Pharma 0
Water Approved Pharma 0
Manganese Approved Nutra 51
Fytic acid Investigational Pharma 0

(2) Additional Compounds for NUDT4 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
5-Diphosphoinositol pentakisphosphate
  • (1R,2R,3S,4S,5R,6S)-2,3,4,5,6-Pentakis(phosphonooxy)cyclohexyl trihydrogen diphosphate
  • 1D-myo-Inositol 5-diphosphate 1,2,3,4,6-pentakisphosphate
  • 1D-myo-Inositol 5-diphosphate pentakisphosphate
  • 5-PP-InsP5
  • (1R,2R,3S,4S,5R,6S)-2,3,4,5,6-Pentakis(phosphonooxy)cyclohexyl trihydrogen diphosphoric acid
Phosphate
  • [po(OH)3]
  • Acide phosphorique
  • Acidum phosphoricum
  • H3PO4
  • Orthophosphoric acid
14066-19-4, 14265-44-2
genes like me logo Genes that share compounds with NUDT4: view

Transcripts for NUDT4 Gene

mRNA/cDNA for NUDT4 Gene

5 REFSEQ mRNAs :
24 NCBI additional mRNA sequence :
7 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

  • Addgene plasmids for NUDT4

Alternative Splicing Database (ASD) splice patterns (SP) for NUDT4 Gene

ExUns: 1 ^ 2 ^ 3a · 3b · 3c ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9a · 9b · 9c · 9d
SP1:
SP2: - - - - - -
SP3: - - - - - -
SP4: - - - - -
SP5: - - -
SP6: - - - - - - -
SP7: -

Relevant External Links for NUDT4 Gene

GeneLoc Exon Structure for
NUDT4

Expression for NUDT4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for NUDT4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for NUDT4 Gene

This gene is overexpressed in Heart - Left Ventricle (x5.2).

Protein differential expression in normal tissues from HIPED for NUDT4 Gene

This gene is overexpressed in Skin (16.2), Ovary (6.5), and Salivary gland (6.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for NUDT4 Gene



Protein tissue co-expression partners for NUDT4 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for NUDT4

SOURCE GeneReport for Unigene cluster for NUDT4 Gene:

Hs.506325

mRNA Expression by UniProt/SwissProt for NUDT4 Gene:

Q9NZJ9-NUDT4_HUMAN
Tissue specificity: Expressed in heart and, at lower level in skeletal muscle, pancreas and kidney.

Evidence on tissue expression from TISSUES for NUDT4 Gene

  • Nervous system(4.9)
  • Eye(4.2)
  • Intestine(2.8)
  • Heart(2.6)
  • Kidney(2.2)
  • Muscle(2.1)
  • Skin(2.1)
  • Liver(2)
genes like me logo Genes that share expression patterns with NUDT4: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for NUDT4 Gene

Orthologs for NUDT4 Gene

This gene was present in the common ancestor of animals.

Orthologs for NUDT4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia NUDT4 31 30
  • 99.82 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 96 (a)
OneToMany
cow
(Bos Taurus)
Mammalia -- 31
  • 96 (a)
OneToMany
NUDT4 31 30
  • 91.9 (n)
OneToMany
dog
(Canis familiaris)
Mammalia NUDT4 31 30
  • 94.11 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Nudt4 17 31 30
  • 90.32 (n)
rat
(Rattus norvegicus)
Mammalia Nudt4 30
  • 88.08 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 31
  • 84 (a)
ManyToMany
-- 31
  • 73 (a)
ManyToMany
-- 31
  • 61 (a)
ManyToMany
chicken
(Gallus gallus)
Aves -- 31
  • 88 (a)
OneToMany
NUDT4 30
  • 80.31 (n)
lizard
(Anolis carolinensis)
Reptilia -- 31
  • 94 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia nudt4 30
  • 80.19 (n)
Str.6375 30
zebrafish
(Danio rerio)
Actinopterygii nudt4b 31 30
  • 68.79 (n)
ManyToMany
nudt4a 31
  • 62 (a)
ManyToMany
fruit fly
(Drosophila melanogaster)
Insecta CG6391 32
  • 58 (a)
Aps 31
  • 53 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea Y92H12BL.5 31
  • 38 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.8787 31
  • 40 (a)
OneToMany
Species where no ortholog for NUDT4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for NUDT4 Gene

ENSEMBL:
Gene Tree for NUDT4 (if available)
TreeFam:
Gene Tree for NUDT4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for NUDT4: view image

Paralogs for NUDT4 Gene

Paralogs for NUDT4 Gene

(4) SIMAP similar genes for NUDT4 Gene using alignment to 3 proteins:

  • NUDT4_HUMAN
  • F8VRL4_HUMAN
  • F8VRR0_HUMAN

Pseudogenes.org Pseudogenes for NUDT4 Gene

genes like me logo Genes that share paralogs with NUDT4: view

Variants for NUDT4 Gene

Additional dbSNP identifiers (rs#s) for NUDT4 Gene

Structural Variations from Database of Genomic Variants (DGV) for NUDT4 Gene

Variant ID Type Subtype PubMed ID
dgv851n106 CNV duplication 24896259
esv23701 CNV loss 19812545
esv3630396 CNV loss 21293372
nsv1044304 CNV gain 25217958
nsv518120 CNV loss 19592680
nsv7234 OTHER inversion 18451855
nsv822 CNV deletion 18451855
nsv952465 CNV duplication 24416366
nsv973103 CNV duplication 23825009

Variation tolerance for NUDT4 Gene

Residual Variation Intolerance Score: 72.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.01; 0.28% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NUDT4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
NUDT4

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for NUDT4 Gene

Disorders for NUDT4 Gene

MalaCards: The human disease database

(2) MalaCards diseases for NUDT4 Gene - From: DISEASES

Disorder Aliases PubMed IDs
testis seminoma
  • seminoma
peroxisome biogenesis disorder 1b
  • pbd1b
- elite association - COSMIC cancer census association via MalaCards
Search NUDT4 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for NUDT4

genes like me logo Genes that share disorders with NUDT4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for NUDT4 Gene

Publications for NUDT4 Gene

  1. Discovery of molecular and catalytic diversity among human diphosphoinositol-polyphosphate phosphohydrolases. An expanding Nudt family. (PMID: 10777568) Caffrey JJ … Shears SB (The Journal of biological chemistry 2000) 2 3 4 23 54
  2. Genetic rationale for microheterogeneity of human diphosphoinositol polyphosphate phosphohydrolase type 2. (PMID: 11376937) Caffrey JJ … Shears SB (Gene 2001) 2 3 23 54
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 54
  4. Nudix hydrolases that degrade dinucleoside and diphosphoinositol polyphosphates also have 5-phosphoribosyl 1-pyrophosphate (PRPP) pyrophosphatase activity that generates the glycolytic activator ribose 1,5-bisphosphate. (PMID: 12370170) Fisher DI … Cartwright JL (The Journal of biological chemistry 2002) 3 4 54
  5. Cloning and characterisation of hAps1 and hAps2, human diadenosine polyphosphate-metabolising Nudix hydrolases. (PMID: 12121577) Leslie NR … Safrany ST (BMC biochemistry 2002) 3 4 54

Products for NUDT4 Gene

Sources for NUDT4 Gene