PRUNE1 Gene (Protein Coding)

Prune Exopolyphosphatase 1

GC01P151008
GIFtS:
33
This gene encodes a member of the DHH protein superfamily of phosphoesterases. This protein has been found to function as both a nucleotide phosphodiesterase and an exopolyphosphatase. This protein is believed to stimulate cancer progression and metastases through the induction of cell motility. A pseuodgene has been identified on chromosome 13. Alternative splicing results in ... See more...

Aliases for PRUNE1 Gene

Aliases for PRUNE1 Gene

  • Prune Exopolyphosphatase 1 2 3 5
  • Drosophila-Related Expressed Sequence 17 3 4
  • Exopolyphosphatase PRUNE1 3 4
  • Protein Prune Homolog 1 3 4
  • DRES-17 3 4
  • DRES17 3 4
  • PRUNE 3 4
  • Prune Homolog (Drosophila) 2
  • Protein Prune Homolog 3
  • EC 3.6.1.1 4
  • H-PRUNE 3
  • HTCD37 3
  • NMIHBA 3
  • HTcD37 4
  • HPrune 4

External Ids for PRUNE1 Gene

Previous HGNC Symbols for PRUNE1 Gene

  • PRUNE

Summaries for PRUNE1 Gene

Entrez Gene Summary for PRUNE1 Gene

  • This gene encodes a member of the DHH protein superfamily of phosphoesterases. This protein has been found to function as both a nucleotide phosphodiesterase and an exopolyphosphatase. This protein is believed to stimulate cancer progression and metastases through the induction of cell motility. A pseuodgene has been identified on chromosome 13. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]

GeneCards Summary for PRUNE1 Gene

PRUNE1 (Prune Exopolyphosphatase 1) is a Protein Coding gene. Diseases associated with PRUNE1 include Neurodevelopmental Disorder With Microcephaly, Hypotonia, And Variable Brain Anomalies and Prune Belly Syndrome. Among its related pathways are Metabolism and Metabolism of nucleotides.

UniProtKB/Swiss-Prot Summary for PRUNE1 Gene

  • Phosphodiesterase (PDE) that has higher activity toward cAMP than cGMP, as substrate. Plays a role in cell proliferation, migration and differentiation, and acts as a negative regulator of NME1. Plays a role in the regulation of neurogenesis (PubMed:28334956). Involved in the regulation of microtubule polymerization (PubMed:28334956).

Additional gene information for PRUNE1 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PRUNE1 Gene

Genomics for PRUNE1 Gene

GeneHancer (GH) Regulatory Elements for PRUNE1 Gene

Promoters and enhancers for PRUNE1 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 PRUNE1 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PRUNE1

Genomic Locations for PRUNE1 Gene

Genomic Locations for PRUNE1 Gene
chr1:151,008,391-151,035,713
(GRCh38/hg38)
Size:
27,323 bases
Orientation:
Plus strand
chr1:150,980,896-151,008,189
(GRCh37/hg19)
Size:
27,294 bases
Orientation:
Plus strand

Genomic View for PRUNE1 Gene

Genes around PRUNE1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PRUNE1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PRUNE1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for PRUNE1 Gene

Proteins for PRUNE1 Gene

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  2. Protein
  3. Assay

  • Protein details for PRUNE1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q86TP1-PRUN1_HUMAN
    Recommended name:
    Exopolyphosphatase PRUNE1
    Protein Accession:
    Q86TP1
    Secondary Accessions:
    • B2RCH8
    • B4DFL7
    • Q5SZF9
    • Q659E5
    • Q6P4E0
    • Q8N654
    • Q96JU5
    • Q9C071
    • Q9C072
    • Q9UIV0

    Protein attributes for PRUNE1 Gene

    Size:
    453 amino acids
    Molecular mass:
    50200 Da
    Cofactor:
    Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
    Quaternary structure:
    • Homooligomer. Able to homodimerize via its C-terminal domain. Interacts with NME1. Interacts with GSK3; at focal adhesion complexes where paxillin and vinculin are colocalized. Interacts with alpha and beta tubulin (PubMed:28334956).
    SequenceCaution:
    • Sequence=BAB55423.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAG60534.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for PRUNE1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PRUNE1 Gene

Post-translational modifications for PRUNE1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for PRUNE1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PRUNE1 Gene

Domains & Families for PRUNE1 Gene

Gene Families for PRUNE1 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Potential drug targets
  • Predicted intracellular proteins

Protein Domains for PRUNE1 Gene

Blocks:
  • Phosphoesterase, RecJ-like
  • DHHA2 domain
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for PRUNE1 Gene

GenScript: Design optimal peptide antigens:
  • HTcD37 (PRUNE_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q86TP1

UniProtKB/Swiss-Prot:

PRUN1_HUMAN :
  • Belongs to the PPase class C family. Prune subfamily.
Family:
  • Belongs to the PPase class C family. Prune subfamily.
genes like me logo Genes that share domains with PRUNE1: view

Function for PRUNE1 Gene

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  2. CRISPR
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Molecular function for PRUNE1 Gene

UniProtKB/Swiss-Prot Function:
Phosphodiesterase (PDE) that has higher activity toward cAMP than cGMP, as substrate. Plays a role in cell proliferation, migration and differentiation, and acts as a negative regulator of NME1. Plays a role in the regulation of neurogenesis (PubMed:28334956). Involved in the regulation of microtubule polymerization (PubMed:28334956).
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=diphosphate + H2O = H(+) + 2 phosphate; Xref=Rhea:RHEA:24576, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:33019, ChEBI:CHEBI:43474; EC=3.6.1.1;.
UniProtKB/Swiss-Prot EnzymeRegulation:
Activated by magnesium ions and inhibited by manganese ions. Inhibited by dipyridamole, moderately sensitive to IBMX and inhibited by vinpocetine.
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=0.91 uM for cAMP {ECO:0000269 PubMed:14998490, ECO:0000269 PubMed:17655525}; KM=2.3 uM for cGMP {ECO:0000269 PubMed:14998490, ECO:0000269 PubMed:17655525}; Vmax=12.8 pmol/min/ug enzyme with cAMP as substrate {ECO:0000269 PubMed:14998490, ECO:0000269 PubMed:17655525}; Vmax=0.8 pmol/min/ug enzyme with cGMP as substrate {ECO:0000269 PubMed:14998490, ECO:0000269 PubMed:17655525};

Enzyme Numbers (IUBMB) for PRUNE1 Gene

Phenotypes From GWAS Catalog for PRUNE1 Gene

Gene Ontology (GO) - Molecular Function for PRUNE1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004309 exopolyphosphatase activity IBA 21873635
GO:0004427 inorganic diphosphatase activity IEA --
GO:0005515 protein binding IPI 10602478
GO:0015631 tubulin binding IDA 28334956
GO:0016462 pyrophosphatase activity IEA --
genes like me logo Genes that share ontologies with PRUNE1: view
genes like me logo Genes that share phenotypes with PRUNE1: view

Human Phenotype Ontology for PRUNE1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PRUNE1 Gene

MGI Knock Outs for PRUNE1:
  • Prune1 Prune1<tm1.1(KOMP)Vlcg>

Animal Model Products

CRISPR Products

miRNA for PRUNE1 Gene

miRTarBase miRNAs that target PRUNE1

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PRUNE1

Clone Products

No data available for Transcription Factor Targets and HOMER Transcription for PRUNE1 Gene

Localization for PRUNE1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PRUNE1 Gene

Cytoplasm. Nucleus. Cell junction, focal adhesion. Note=In some transfected cells a nuclear staining is also observed.

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 PRUNE1 gene
Compartment Confidence
nucleus 5
cytosol 5
plasma membrane 2
extracellular 2
cytoskeleton 2
mitochondrion 2
peroxisome 1
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PRUNE1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005737 cytoplasm IBA 21873635
GO:0005829 cytosol IDA --
GO:0005925 focal adhesion IEA --
GO:0030054 cell junction IEA --
genes like me logo Genes that share ontologies with PRUNE1: view

Pathways & Interactions for PRUNE1 Gene

PathCards logo

SuperPathways for PRUNE1 Gene

SuperPathway Contained pathways
1 Metabolism
Metabolic pathways
.40
2 Metabolism of nucleotides
Purine metabolism
.35
genes like me logo Genes that share pathways with PRUNE1: view

Pathways by source for PRUNE1 Gene

2 KEGG pathways for PRUNE1 Gene

Gene Ontology (GO) - Biological Process for PRUNE1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006798 polyphosphate catabolic process IBA 21873635
GO:0016311 dephosphorylation IEA --
GO:0031113 regulation of microtubule polymerization IMP 28334956
GO:0050767 regulation of neurogenesis IMP 28334956
genes like me logo Genes that share ontologies with PRUNE1: view

No data available for SIGNOR curated interactions for PRUNE1 Gene

Drugs & Compounds for PRUNE1 Gene

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  1. Drug

(5) Drugs for PRUNE1 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
cyclic amp Experimental Pharma 0

(4) Additional Compounds for PRUNE1 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Guanosine 3',5'-bis(diphosphate)
  • Guanosine 3'-diphosphate 5'-diphosphate
  • Guanosine 5'-diphosphate,3'-diphosphate
  • GUANOSINE-5',3'-tetraphosphATE
  • Guanosine 3'-diphosphoric acid 5'-diphosphoric acid
  • Guanosine 3',5'-bis(diphosphoric acid)
Guanosine 3'-diphosphate 5'-triphosphate
  • Guanosine 5'-triphosphate,3'-diphosphate
  • Guanosine pentaphosphate
  • Guanosine 5'-triphosphoric acid,3'-diphosphoric acid
  • Guanosine 3'-diphosphoric acid 5'-triphosphoric acid
  • Guanosine pentaphosphoric acid
Phosphate
  • [po(OH)3]
  • Acide phosphorique
  • Acidum phosphoricum
  • H3PO4
  • Orthophosphoric acid
 14066-19-4, 14265-44-2
pyrophosphate
  • [(ho)2P(O)OP(O)(OH)2]
  • Acide diphosphorique
  • Diphosphorsaeure
  • H4P2O7
  • PYROphosphATE
 14000-31-8
genes like me logo Genes that share compounds with PRUNE1: view

Transcripts for PRUNE1 Gene

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  1. CRISPR
  2. miRNA
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mRNA/cDNA for PRUNE1 Gene

4 REFSEQ mRNAs :
18 NCBI additional mRNA sequence :
11 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PRUNE1

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PRUNE1 Gene

No ASD Table

Relevant External Links for PRUNE1 Gene

GeneLoc Exon Structure for
PRUNE1

Expression for PRUNE1 Gene

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  1. Primer
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Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PRUNE1

mRNA Expression by UniProt/SwissProt for PRUNE1 Gene:

Q86TP1-PRUN1_HUMAN
Tissue specificity: Ubiquitously expressed. Seems to be overexpressed in aggressive sarcoma subtypes, such as leiomyosarcomas and malignant fibrous histiocytomas (MFH) as well as in the less malignant liposarcomas.

Evidence on tissue expression from TISSUES for PRUNE1 Gene

  • Nervous system(4.7)
  • Kidney(4.3)
  • Thyroid gland(4.3)
  • Blood(4.2)

No data available for mRNA expression in normal human tissues , mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for PRUNE1 Gene

Orthologs for PRUNE1 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for PRUNE1 Gene

Organism Taxonomy Gene Similarity Type Details
dog
(Canis familiaris)
 Mammalia PRUNE 31 30
  • 91.02 (n)
 OneToOne
cow
(Bos Taurus)
 Mammalia PRUNE 31 30
  • 89.77 (n)
 OneToOne
mouse
(Mus musculus)
 Mammalia Prune 31 30
  • 85.28 (n)
 OneToOne
Prune1 17
rat
(Rattus norvegicus)
 Mammalia Prune 30
  • 84.92 (n)
oppossum
(Monodelphis domestica)
 Mammalia PRUNE 31
  • 70 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia PRUNE 31
  • 37 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves LOC100857290 30
  • 58.74 (n)
PRUNE 31
  • 56 (a)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia PRUNE 31
  • 54 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia prune 30
  • 58.15 (n)
Str.16711 30
African clawed frog
(Xenopus laevis)
 Amphibia Xl.14865 30
zebrafish
(Danio rerio)
 Actinopterygii LOC563343 30
  • 57.87 (n)
prune 31
  • 49 (a)
 OneToOne
fruit fly
(Drosophila melanogaster)
 Insecta pn 31 30
  • 48.4 (n)
 OneToOne
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP004314 30
  • 44.89 (n)
baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes PPX1 33 31 30
  • 43 (n)
A. gosspyii yeast
(Ashbya gossypii)
 Saccharomycetes AGOS_ABL083W 30
  • 41.57 (n)
K. lactis yeast
(Kluyveromyces lactis)
 Saccharomycetes KLLA0B03806g 30
  • 41.03 (n)
fission yeast
(Schizosaccharomyces pombe)
 Schizosaccharomycetes SPAC2F3.11 30
  • 39.74 (n)
bread mold
(Neurospora crassa)
 Ascomycetes NCU06310 30
  • 38.38 (n)
sea squirt
(Ciona savignyi)
 Ascidiacea -- 31
  • 28 (a)
 OneToOne
Species where no ortholog for PRUNE1 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • chimpanzee (Pan troglodytes)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for PRUNE1 Gene

ENSEMBL:
Gene Tree for PRUNE1 (if available)
TreeFam:
Gene Tree for PRUNE1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PRUNE1: view image

Paralogs for PRUNE1 Gene

Pseudogenes.org Pseudogenes for PRUNE1 Gene

genes like me logo Genes that share paralogs with PRUNE1: view

No data available for Paralogs for PRUNE1 Gene

Variants for PRUNE1 Gene

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PRUNE1 Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
767697 Benign: not provided 151,024,679(+) G/A MISSENSE_VARIANT,FIVE_PRIME_UTR_VARIANT,INTRON_VARIANT
rs1057521927 Likely Pathogenic: Abnormality of brain morphology; Neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies; not provided. Neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies (NMIHBA) [MIM:617481] 151,017,860(+) G/Ap.Asp30Asn MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT,FIVE_PRIME_UTR_VARIANT
rs1085308033 Pathogenic: Neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies. Neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies (NMIHBA) [MIM:617481] 151,018,494(+) C/Ap.Pro54Thr MISSENSE_VARIANT,FIVE_PRIME_UTR_VARIANT,INTRON_VARIANT
rs137929776 Pathogenic: not provided 151,018,530(+) C/T NONSENSE,FIVE_PRIME_UTR_VARIANT,INTRON_VARIANT
rs1553251507 Pathogenic: Inborn genetic diseases 151,008,634(+) T/TGGAGG INITIATIOR_CODON_VARIANT,FRAMESHIFT_VARIANT,NON_CODING_TRANSCRIPT_VARIANT,FIVE_PRIME_UTR_VARIANT

Additional dbSNP identifiers (rs#s) for PRUNE1 Gene

Structural Variations from Database of Genomic Variants (DGV) for PRUNE1 Gene

Variant ID Type Subtype PubMed ID
nsv1127030 CNV deletion 24896259
nsv522840 CNV gain 19592680

Variation tolerance for PRUNE1 Gene

Residual Variation Intolerance Score: 61.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.76; 73.45% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PRUNE1 Gene

Human Gene Mutation Database (HGMD)
PRUNE1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PRUNE1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PRUNE1 Gene

Disorders for PRUNE1 Gene

MalaCards: The human disease database

(15) MalaCards diseases for PRUNE1 Gene - From: UniProtKB/Swiss-Prot, OMIM, ClinVar, Orphanet, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

PRUN1_HUMAN
  • Neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies (NMIHBA) [MIM:617481]: An autosomal recessive neurodevelopmental and degenerative disorder characterized by primary microcephaly, profound global developmental delay, and severe intellectual disability. Additional clinical features include dysmorphic features, truncal hypotonia, peripheral spasticity, and lack of independent ambulation or speech acquisition. Brain imaging shows cortical atrophy, thin corpus callosum, cerebellar hypoplasia, and delayed myelination. {ECO:0000269 PubMed:26539891, ECO:0000269 PubMed:28211990, ECO:0000269 PubMed:28334956}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for PRUNE1

ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with PRUNE1: view

No data available for Genatlas for PRUNE1 Gene

Publications for PRUNE1 Gene

  1. Amplification and overexpression of PRUNE in human sarcomas and breast carcinomas-a possible mechanism for altering the nm23-H1 activity. (PMID: 11687967) Forus A … Zollo M (Oncogene 2001) 2 3 4 54
  2. Evidence for interaction between human PRUNE and nm23-H1 NDPKinase. (PMID: 10602478) Reymond A … Zollo M (Oncogene 1999) 2 3 4 54
  3. PRUNE is crucial for normal brain development and mutated in microcephaly with neurodevelopmental impairment. (PMID: 28334956) Zollo M … Baple EL (Brain : a journal of neurology 2017) 3 4 54
  4. Homozygous mutation in PRUNE1 in an Oji-Cree male with a complex neurological phenotype. (PMID: 28211990) Costain G … Kannu P (American journal of medical genetics. Part A 2017) 3 4 54
  5. Human metastasis regulator protein H-prune is a short-chain exopolyphosphatase. (PMID: 18700747) Tammenkoski M … Lahti R (Biochemistry 2008) 2 3 54

ExternalLinks

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