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Aliases for PRUNE2 Gene

Aliases for PRUNE2 Gene

  • Prune Homolog 2 2 3 5
  • KIAA0367 2 3 4
  • BNIP2 Motif-Containing Molecule At The C-Terminal Region 1 3 4
  • Olfaxin 2 3
  • C9orf65 3 4
  • BNIPXL 3 4
  • BMCC1 3 4
  • BNIP2 Motif Containing Molecule At The Carboxyl Terminal Region 1 3
  • BCH Motif-Containing Molecule At The Carboxyl Terminal Region 1 3
  • Chromosome 9 Open Reading Frame 65 2
  • Prune Homolog 2 (Drosophila) 2
  • Protein Prune Homolog 2 3
  • Truncated PRUNE2 3

External Ids for PRUNE2 Gene

Previous HGNC Symbols for PRUNE2 Gene

  • C9orf65
  • KIAA0367

Previous GeneCards Identifiers for PRUNE2 Gene

  • GC09M078594
  • GC09M078627
  • GC09M079226
  • GC09M049055

Summaries for PRUNE2 Gene

Entrez Gene Summary for PRUNE2 Gene

  • The protein encoded by this gene belongs to the B-cell CLL/lymphoma 2 and adenovirus E1B 19 kDa interacting family, whose members play roles in many cellular processes including apotosis, cell transformation, and synaptic function. Several functions for this protein have been demonstrated including suppression of Ras homolog family member A activity, which results in reduced stress fiber formation and suppression of oncogenic cellular transformation. A high molecular weight isoform of this protein has also been shown to colocalize with Adaptor protein complex 2, beta-Adaptin and endodermal markers, suggesting an involvement in post-endocytic trafficking. In prostate cancer cells, this gene acts as a tumor suppressor and its expression is regulated by prostate cancer antigen 3, a non-protein coding gene on the opposite DNA strand in an intron of this gene. Prostate cancer antigen 3 regulates levels of this gene through formation of a double-stranded RNA that undergoes adenosine deaminase actin on RNA-dependent adenosine-to-inosine RNA editing. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2015]

GeneCards Summary for PRUNE2 Gene

PRUNE2 (Prune Homolog 2) is a Protein Coding gene. Diseases associated with PRUNE2 include Intraductal Papilloma and Prostate Cancer. Gene Ontology (GO) annotations related to this gene include pyrophosphatase activity. An important paralog of this gene is ATCAY.

UniProtKB/Swiss-Prot for PRUNE2 Gene

  • May play an important role in regulating differentiation, survival and aggressiveness of the tumor cells.

Gene Wiki entry for PRUNE2 Gene

Additional gene information for PRUNE2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PRUNE2 Gene

Genomics for PRUNE2 Gene

GeneHancer (GH) Regulatory Elements for PRUNE2 Gene

Promoters and enhancers for PRUNE2 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
GH09J076905 Promoter/Enhancer 1.6 Ensembl ENCODE dbSUPER 650.7 -0.1 -63 1.3 CLOCK INSM2 KLF17 SIN3A FEZF1 KLF14 RFX5 ZNF335 GLIS2 ELK1 PRUNE2 VPS13A GC09M076829
GH09J076687 Enhancer 1.4 FANTOM5 Ensembl ENCODE dbSUPER 67.6 +218.1 218066 2.2 RARA ZNF121 ZNF614 FOS THAP11 MIXL1 RXRA CEBPB PPARG KAT8 PRUNE2 GCNT1 PCA3 LOC105376095
GH09J076700 Enhancer 0.8 Ensembl ENCODE dbSUPER 95.1 +205.0 204958 2.5 JUND POLR2A ZNF24 PRUNE2 PCA3 GC09P076757
GH09J076691 Enhancer 1 Ensembl ENCODE dbSUPER 75.5 +213.9 213933 1.7 USF1 L3MBTL2 SIN3A USF2 MITF ZFP69B ZNF366 PATZ1 ZXDB ZBTB17 PCA3 PRUNE2 GC09P076757
GH09J076704 Enhancer 0.8 Ensembl ENCODE 93.8 +201.4 201430 0.5 CTCF STAT1 ZNF654 TEAD4 MAFG REST RAD21 SREBF1 SMC3 ZNF143 PRUNE2 PCA3 GC09P076757
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PRUNE2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PRUNE2 gene promoter:
  • ATF
  • POU2F1a
  • POU2F1
  • NF-1/L
  • NF-1
  • RP58
  • ZID
  • Arnt
  • AhR
  • C/EBPalpha

Genomic Locations for PRUNE2 Gene

Genomic Locations for PRUNE2 Gene
294,845 bases
Minus strand
294,712 bases
Minus strand

Genomic View for PRUNE2 Gene

Genes around PRUNE2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PRUNE2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PRUNE2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PRUNE2 Gene

Proteins for PRUNE2 Gene

  • Protein details for PRUNE2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein prune homolog 2
    Protein Accession:
    Secondary Accessions:
    • B3KYC4
    • B4DQH8
    • O15073
    • Q58A63
    • Q5JUB6
    • Q5T304
    • Q5T476
    • Q6T2V6
    • Q6T2V7
    • Q8N665

    Protein attributes for PRUNE2 Gene

    3088 amino acids
    Molecular mass:
    340635 Da
    Quaternary structure:
    No Data Available
    • PRUNE2/BMCC1 and PCA3, one of the most prostate cancer specific markers are overlapping genes in reverse orientation. However, they do not appear to be coregulated.
    • Sequence=AAH22571.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAH22571.1; Type=Miscellaneous discrepancy; Note=Aberrant splicing.; Evidence={ECO:0000305}; Sequence=AAR15150.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAR15151.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAD93351.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=CAI10915.2; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=CAI16084.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=CAI39750.2; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Alternative splice isoforms for PRUNE2 Gene


neXtProt entry for PRUNE2 Gene

Post-translational modifications for PRUNE2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for PRUNE2 Gene

Domains & Families for PRUNE2 Gene

Gene Families for PRUNE2 Gene

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

Protein Domains for PRUNE2 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the PPase class C family. Prune subfamily.
  • Belongs to the PPase class C family. Prune subfamily.
genes like me logo Genes that share domains with PRUNE2: view

Function for PRUNE2 Gene

Molecular function for PRUNE2 Gene

UniProtKB/Swiss-Prot Function:
May play an important role in regulating differentiation, survival and aggressiveness of the tumor cells.
UniProtKB/Swiss-Prot Induction:
Down-regulated after NGF-induced differentiation, and up-regulated during the NGF-depletion-induced apoptosis.

Phenotypes From GWAS Catalog for PRUNE2 Gene

Gene Ontology (GO) - Molecular Function for PRUNE2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004309 exopolyphosphatase activity IBA --
GO:0016462 pyrophosphatase activity IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with PRUNE2: view

Phenotypes for PRUNE2 Gene

genes like me logo Genes that share phenotypes with PRUNE2: view

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PRUNE2 Gene

Localization for PRUNE2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PRUNE2 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 PRUNE2 gene
Compartment Confidence
nucleus 3
cytosol 3
golgi apparatus 2

Gene Ontology (GO) - Cellular Components for PRUNE2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with PRUNE2: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PRUNE2 Gene

Pathways & Interactions for PRUNE2 Gene

SuperPathways for PRUNE2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PRUNE2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006798 polyphosphate catabolic process IBA --
GO:0006915 apoptotic process IEA --
genes like me logo Genes that share ontologies with PRUNE2: view

No data available for Pathways by source and SIGNOR curated interactions for PRUNE2 Gene

Drugs & Compounds for PRUNE2 Gene

No Compound Related Data Available

Transcripts for PRUNE2 Gene

mRNA/cDNA for PRUNE2 Gene

(37) REFSEQ mRNAs :
(14) Additional mRNA sequences :
(11) Selected AceView cDNA sequences:
(15) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for PRUNE2 Gene

Prune homolog 2 (Drosophila):
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PRUNE2 Gene

ExUns: 1 ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14a · 14b ^ 15 ^ 16a · 16b ^ 17a · 17b · 17c
SP1: - -
SP2: - - - - -
SP3: - -
SP5: - - - -
SP6: - -
SP8: -
SP9: - - -

Relevant External Links for PRUNE2 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PRUNE2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PRUNE2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PRUNE2 Gene

This gene is overexpressed in Esophagus - Muscularis (x4.5).

Protein differential expression in normal tissues from HIPED for PRUNE2 Gene

This gene is overexpressed in Testis (40.1) and Urinary Bladder (10.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PRUNE2 Gene

NURSA nuclear receptor signaling pathways regulating expression of PRUNE2 Gene:


SOURCE GeneReport for Unigene cluster for PRUNE2 Gene:


mRNA Expression by UniProt/SwissProt for PRUNE2 Gene:

Tissue specificity: A high level of expression seen in the nervous system (brain, cerebellum and spinal cord) as well as adrenal gland. Expressed at high levels in noneuroblastoma, rhabdomyosarcoma, melanoma and some osteosarcoma cell lines, whereas at only low levels in cancer cell lines of liver, breast, thyroid and colon. Expression is significantly higher in favorable tumors than aggressive ones.

Evidence on tissue expression from TISSUES for PRUNE2 Gene

  • Nervous system(5)
  • Kidney(4.3)
  • Liver(4)
genes like me logo Genes that share expression patterns with PRUNE2: view

No data available for Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for PRUNE2 Gene

Orthologs for PRUNE2 Gene

This gene was present in the common ancestor of animals.

Orthologs for PRUNE2 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PRUNE2 34 33
  • 99.34 (n)
(Canis familiaris)
Mammalia PRUNE2 34 33
  • 83.76 (n)
(Bos Taurus)
Mammalia PRUNE2 34 33
  • 82.53 (n)
(Mus musculus)
Mammalia Prune2 16 34 33
  • 77.04 (n)
(Rattus norvegicus)
Mammalia Prune2 33
  • 76.58 (n)
(Ornithorhynchus anatinus)
Mammalia PRUNE2 34
  • 76 (a)
(Monodelphis domestica)
Mammalia PRUNE2 34
  • 55 (a)
(Gallus gallus)
Aves PRUNE2 34
  • 40 (a)
(Anolis carolinensis)
Reptilia PRUNE2 34
  • 40 (a)
(Danio rerio)
Actinopterygii prune2 34
  • 65 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG11593 34
  • 33 (a)
Species where no ortholog for PRUNE2 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 squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for PRUNE2 Gene

Gene Tree for PRUNE2 (if available)
Gene Tree for PRUNE2 (if available)
Evolutionary constrained regions (ECRs) for PRUNE2: view image

Paralogs for PRUNE2 Gene

Paralogs for PRUNE2 Gene

(8) SIMAP similar genes for PRUNE2 Gene using alignment to 12 proteins:

  • B9EK61_HUMAN
  • L8E865_HUMAN
genes like me logo Genes that share paralogs with PRUNE2: view

Variants for PRUNE2 Gene

Sequence variations from dbSNP and Humsavar for PRUNE2 Gene

SNP ID Clin Chr 09 pos Variation AA Info Type
rs1000000129 -- 76,796,630(-) T/C/G genic_upstream_transcript_variant, intron_variant
rs1000003097 -- 76,664,568(-) T/C intron_variant
rs1000022536 -- 76,897,980(-) C/G/T genic_upstream_transcript_variant, intron_variant
rs1000027520 -- 76,820,501(-) T/G genic_upstream_transcript_variant, intron_variant
rs1000035301 -- 76,765,489(-) AGAGA/AGA genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for PRUNE2 Gene

Variant ID Type Subtype PubMed ID
dgv1484e214 CNV gain 21293372
esv2663601 CNV deletion 23128226
esv2670071 CNV deletion 23128226
esv2738601 CNV deletion 23290073
esv2738602 CNV deletion 23290073
esv2738603 CNV deletion 23290073
esv2759697 CNV loss 17122850
esv3303407 CNV mobile element insertion 20981092
esv3307144 CNV mobile element insertion 20981092
esv3308196 CNV mobile element insertion 20981092
esv3345565 CNV insertion 20981092
esv3390142 CNV insertion 20981092
esv3439544 CNV insertion 20981092
esv3441383 CNV insertion 20981092
esv3620746 CNV loss 21293372
esv3620750 CNV loss 21293372
esv3620751 CNV loss 21293372
esv3620752 CNV loss 21293372
esv4747 CNV loss 18987735
esv5447 CNV gain 19470904
nsv1040363 CNV gain 25217958
nsv1054381 CNV loss 25217958
nsv1141000 CNV deletion 24896259
nsv1147298 CNV duplication 26484159
nsv510193 OTHER sequence alteration 20534489
nsv527438 CNV gain 19592680
nsv6571 CNV insertion 18451855
nsv824952 CNV loss 20364138
nsv8526 CNV loss 18304495

Variation tolerance for PRUNE2 Gene

Residual Variation Intolerance Score: 98.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 22.38; 99.42% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PRUNE2 Gene

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PRUNE2 Gene

Disorders for PRUNE2 Gene

MalaCards: The human disease database

(2) MalaCards diseases for PRUNE2 Gene - From: HGMD, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
intraductal papilloma
  • ductal papilloma
prostate cancer
  • prostate cancer, susceptibility to
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for PRUNE2

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with PRUNE2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PRUNE2 Gene

Publications for PRUNE2 Gene

  1. Increased expression of proapoptotic BMCC1, a novel gene with the BNIP2 and Cdc42GAP homology (BCH) domain, is associated with favorable prognosis in human neuroblastomas. (PMID: 16288218) Machida T … Nakagawara A (Oncogene 2006) 2 3 4 58
  2. Differential expression of PCA3 and its overlapping PRUNE2 transcript in prostate cancer. (PMID: 19760627) Salagierski M … Schalken JA (The Prostate 2010) 3 4 58
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  4. Investigation of genetic susceptibility factors for human longevity - a targeted nonsynonymous SNP study. (PMID: 20800603) Flachsbart F … Nebel A (Mutation research 2010) 3 44 58
  5. Hippocampal atrophy as a quantitative trait in a genome-wide association study identifying novel susceptibility genes for Alzheimer's disease. (PMID: 19668339) Potkin SG … Alzheimer's Disease Neuroimaging Initiative (PloS one 2009) 3 44 58

Products for PRUNE2 Gene

Sources for PRUNE2 Gene

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