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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
  • DIPP-2 3 4
  • DIPP2 3 4
  • Diphosphoinositol Polyphosphate Phosphohydrolase 2 3
  • Nucleoside Diphosphate-Linked Moiety X Motif 4 4
  • Nudix Motif 4 4
  • EC 4
  • DIPP2alpha 3
  • EC 3.6.1.- 4
  • DIPP2beta 3
  • HDCMB47P 3
  • KIAA0487 4

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. Among its related pathways are Metabolism and Inositol phosphate metabolism (REACTOME). 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 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 , fRNAdb sequence ontologies and piRNA Summary for NUDT4 Gene

Genomics for NUDT4 Gene

GeneHancer (GH) Regulatory Elements for NUDT4 Gene

Promoters and enhancers for NUDT4 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH12I093375 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 557.4 +1.0 981 6.7 HDGF PKNOX1 ARNT ARID4B SIN3A ZNF2 YY1 POLR2B ZNF766 FOS ENSG00000257252 NUDT4 LOC643339 ENSG00000257512 UBE2N MRPL42 GC12P093403 GC12P093405 PIR61938 GC12M093281
GH12I093373 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 17 -3.9 -3895 1.7 HDGF SMAD1 ATF1 ARNT NCOA2 TCF12 POLR2B ZNF766 ATF7 CAVIN1 GC12P093373 ENSG00000257252 NUDT4 ENSG00000257512 CRADD LOC643339 GC12M093281 GC12P093160
GH12I093126 Enhancer 1.2 Ensembl ENCODE 9.4 -250.3 -250265 2.1 PKNOX1 FOXA2 MLX ZFP64 ARID4B DMAP1 ZNF48 ETS1 YY1 ATF7 NACAP3 NUDT4 GC12M093120 ENSG00000257322 LOC643339
GH12I093134 Enhancer 1.4 Ensembl ENCODE dbSUPER 4.6 -242.4 -242391 2.7 PKNOX1 FOXA2 ARID4B FEZF1 DMAP1 ZNF2 YY1 ZNF213 ATF7 RUNX3 GC12M093134 GC12M093135 GC12M093136 GC12P093136 NUDT4 NACAP3 ENSG00000257322 LOC643339
GH12I093406 Enhancer 0.5 dbSUPER 5.9 +29.5 29477 1.2 NCOA6 NFIC POLR2A ZNF189 ZSCAN16 PRDM4 SUPT5H MRPL42 UBE2N NUDT4 ENSG00000257252 GC12M093281 PIR47591 GC12P093160
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around NUDT4 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the NUDT4 gene promoter:

Genomic Locations for NUDT4 Gene

Genomic Locations for NUDT4 Gene
30,264 bases
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:
    Recommended name:
    Diphosphoinositol polyphosphate phosphohydrolase 2
    Protein Accession:
    Secondary Accessions:
    • B7Z916
    • Q4AEJ6
    • Q53EZ2
    • Q68DD7
    • Q9NPC5
    • Q9NS30
    • Q9NZK0
    • Q9NZK1

    Protein attributes for NUDT4 Gene

    180 amino acids
    Molecular mass:
    20306 Da
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
    Quaternary structure:
    No Data Available
    • Sequence=AAF75563.1; Type=Erroneous termination; Positions=181; Note=Translated as stop.; Evidence={ECO:0000305}; Sequence=BAE16985.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for NUDT4 Gene

    Alternative splice isoforms for NUDT4 Gene


neXtProt entry for NUDT4 Gene

Post-translational modifications for NUDT4 Gene

No Post-translational modifications

No data available for DME Specific Peptides for NUDT4 Gene

Domains & Families for NUDT4 Gene

Gene Families for NUDT4 Gene

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

Protein Domains for NUDT4 Gene

Suggested Antigen Peptide Sequences for NUDT4 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the Nudix hydrolase family. DIPP subfamily.
  • 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 BiophysicochemicalProperties:
Kinetic parameters: KM=4.2 nM for PP-InsP5 {ECO:0000269 PubMed:10777568};
UniProtKB/Swiss-Prot CatalyticActivity:
Diphospho-myo-inositol polyphosphate + H(2)O = myo-inositol polyphosphate + phosphate.
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.

Enzyme Numbers (IUBMB) for NUDT4 Gene

Gene Ontology (GO) - Molecular Function for NUDT4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000298 endopolyphosphatase activity IBA --
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

Clone Products

No data available for Phenotypes From GWAS Catalog , 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


Subcellular locations from

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

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:0005622 intracellular TAS 10777568
GO:0005634 nucleus IBA --
GO:0005737 cytoplasm IBA --
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with NUDT4: view

Pathways & Interactions for NUDT4 Gene

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

Pathways by source for NUDT4 Gene

Interacting Proteins for NUDT4 Gene

Gene Ontology (GO) - Biological Process for NUDT4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0009187 cyclic nucleotide metabolic process TAS 10777568
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 --
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

(4) Drugs for NUDT4 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Phosphoric acid Approved Pharma 0
Water Approved Pharma 0
Magnesium Approved Nutra 0
Manganese Approved Nutra 37

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

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
5-Diphosphoinositol pentakisphosphate
  • 1,2,3,4,6-Pentakis-O-phosphono-1D-myo-inositol 5-(trihydrogen diphosphate)
  • 1D-Myo-inositol 5-diphosphate pentakisphosphate
  • 5-Diphospho-1D-myo-inositol 1,2,3,4,6-pentakisphosphate
  • 5-Diphospho-1D-myo-inositol pentakisphosphate
  • 5-PP-InsP5
Myo-inositol hexakisphosphate
  • 1D-Myo-Inositol 1,2,3,4,5,6-hexakisphosphate
  • 1D-Myo-inositol hexakisphosphate
  • D-Myo-Inositol 1,2,3,4,5,6-hexakisphosphate
  • Inositol 1,2,3,4,5,6-hexakisphosphate
  • Myo-Inositol 1,2,3,4,5,6-hexakisphosphate
  • NFB Orthophosphate
  • O-Phosphoric acid
  • Ortho-phosphate
  • Orthophosphate (PO43-)
  • Orthophosphate(3-)
genes like me logo Genes that share compounds with NUDT4: view

Transcripts for NUDT4 Gene

Unigene Clusters for NUDT4 Gene

Nudix (nucleoside diphosphate linked moiety X)-type motif 4:
Representative Sequences:

Clone Products

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
SP2: - - - - - -
SP3: - - - - - -
SP4: - - - - -
SP5: - - -
SP6: - - - - - - -
SP7: -

Relevant External Links for NUDT4 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for NUDT4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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, PaxDb, MaxQB, and MOPED for NUDT4 Gene

Protein tissue co-expression partners for NUDT4 Gene

NURSA nuclear receptor signaling pathways regulating expression of NUDT4 Gene:


SOURCE GeneReport for Unigene cluster for NUDT4 Gene:


mRNA Expression by UniProt/SwissProt for NUDT4 Gene:

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
(Pan troglodytes)
Mammalia NUDT4 33 34
  • 99.82 (n)
(Bos Taurus)
Mammalia -- 34
  • 96 (a)
NUDT4 33 34
  • 91.9 (n)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 96 (a)
(Canis familiaris)
Mammalia NUDT4 33 34
  • 94.11 (n)
(Mus musculus)
Mammalia Nudt4 33 16 34
  • 90.32 (n)
(Rattus norvegicus)
Mammalia Nudt4 33
  • 88.08 (n)
(Monodelphis domestica)
Mammalia -- 34
  • 84 (a)
-- 34
  • 73 (a)
-- 34
  • 61 (a)
(Gallus gallus)
Aves -- 34
  • 88 (a)
NUDT4 33
  • 80.31 (n)
(Anolis carolinensis)
Reptilia -- 34
  • 94 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia nudt4 33
  • 80.19 (n)
Str.6375 33
(Danio rerio)
Actinopterygii nudt4b 33 34
  • 68.79 (n)
nudt4a 34
  • 62 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG6391 35
  • 58 (a)
Aps 34
  • 53 (a)
(Caenorhabditis elegans)
Secernentea Y92H12BL.5 34
  • 38 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.8787 34
  • 40 (a)
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

Gene Tree for NUDT4 (if available)
Gene Tree for NUDT4 (if available)

Paralogs for NUDT4 Gene

Paralogs for NUDT4 Gene

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

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

Variants for NUDT4 Gene

Sequence variations from dbSNP and Humsavar for NUDT4 Gene

SNP ID Clin Chr 12 pos Variation AA Info Type
rs1000036192 -- 93,393,531(+) A/C intron_variant
rs1000094935 -- 93,402,348(+) T/A/C 3_prime_UTR_variant
rs1000325312 -- 93,393,942(+) A/G intron_variant
rs1000591747 -- 93,396,377(+) C/T intron_variant
rs1000897841 -- 93,377,885(+) A/C upstream_transcript_variant

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NUDT4 Gene

Disorders for NUDT4 Gene

Additional Disease Information for NUDT4

No disorders were found for NUDT4 Gene.

No data available for MalaCards , 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 22 58
  2. Genetic rationale for microheterogeneity of human diphosphoinositol polyphosphate phosphohydrolase type 2. (PMID: 11376937) Caffrey JJ … Shears SB (Gene 2001) 2 3 22 58
  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 58
  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 58
  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 58

Products for NUDT4 Gene

Sources for NUDT4 Gene

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