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 st... See more...

Aliases for PRUNE2 Gene

Aliases for PRUNE2 Gene

  • Prune Homolog 2 With BCH Domain 2 3 5
  • KIAA0367 2 3 4
  • BNIP2 Motif-Containing Molecule At The C-Terminal Region 1 3 4
  • Protein Prune Homolog 2 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
  • Truncated PRUNE2 3
  • Prune Homolog 2 2

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 With BCH Domain) is a Protein Coding gene. Diseases associated with PRUNE2 include Prostate Sarcoma and Pelvic Lipomatosis. Gene Ontology (GO) annotations related to this gene include pyrophosphatase activity. An important paralog of this gene is BNIP2.

UniProtKB/Swiss-Prot Summary 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 , Rfam classification 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
Score
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 1.7 Ensembl ENCODE CraniofacialAtlas dbSUPER 506.2 +1.0 950 3.3 USF1 TEAD4 ZIC2 REST ZBTB26 TRIM28 KLF4 HDAC2 CTBP1 ZNF341 PRUNE2 RF00017-7636 VPS13A
GH09J076691 Promoter/Enhancer 1.7 Ensembl ENCODE CraniofacialAtlas dbSUPER 75.5 +213.9 213933 1.7 EP300 USF1 TEAD4 ZBTB17 ZNF263 ZNF76 YY1 SPI1 SIN3A MITF PCA3 PRUNE2 piR-50437-667
GH09J076700 Enhancer 1 Ensembl ENCODE dbSUPER 96.9 +205.3 205319 8.6 CTCF REST RAD21 SMC3 ZNF316 MAFF ZKSCAN1 MAFK POLR2A NR2F2 PRUNE2 piR-50437-667 PCA3 DQ374659
GH09J076687 Enhancer 1.1 FANTOM5 ENCODE dbSUPER 67.6 +218.1 218066 2.2 EP300 NCOR1 POLR2A TCF7 RFX1 TEAD1 CEBPB FOS MIER3 GABPB1 PRUNE2 GCNT1 PCA3 piR-55361-570
GH09J076628 Enhancer 0.9 Ensembl dbSUPER 25.2 +277.0 277019 5.6 HDAC3 NCOR1 NEUROD1 NFIC PBX2 TAL1 STAT5A HDAC2 NCOA1 TCF12 PRUNE2 GCNT1 lnc-RFK-5 lnc-RFK-6 LOC105376095
- 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

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PRUNE2

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

Genomic Locations for PRUNE2 Gene

Genomic Locations for PRUNE2 Gene
chr9:76,611,376-76,906,220
(GRCh38/hg38)
Size:
294,845 bases
Orientation:
Minus strand
chr9:79,226,292-79,521,003
(GRCh37/hg19)
Size:
294,712 bases
Orientation:
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:
    Q8WUY3-PRUN2_HUMAN
    Recommended name:
    Protein prune homolog 2
    Protein Accession:
    Q8WUY3
    Secondary Accessions:
    • B3KYC4
    • B4DQH8
    • O15073
    • Q58A63
    • Q5JUB6
    • Q5T304
    • Q5T476
    • Q6T2V6
    • Q6T2V7
    • Q8N665

    Protein attributes for PRUNE2 Gene

    Size:
    3088 amino acids
    Molecular mass:
    340635 Da
    Quaternary structure:
    No Data Available
    Miscellaneous:
    • 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.
    SequenceCaution:
    • Sequence=AAH22571.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=AAH22571.1; Type=Miscellaneous discrepancy; Note=Aberrant splicing.; Evidence={ECO:0000305}; Sequence=AAR15150.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=AAR15151.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=BAD93351.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};

    Alternative splice isoforms for PRUNE2 Gene

    UniProtKB/Swiss-Prot:

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

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

Protein Domains for PRUNE2 Gene

Suggested Antigen Peptide Sequences for PRUNE2 Gene

GenScript: Design optimal peptide antigens:
  • Prune homolog 2 (Drosophila) (B3KYC4_HUMAN)
  • cDNA FLJ59118 (B4DJW7_HUMAN)
  • cDNA FLJ54876 (B4DSQ3_HUMAN)
  • PRUNE2 protein (B9EK61_HUMAN)
  • Prune homolog 2 (D6RTK6_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8WUY3

UniProtKB/Swiss-Prot:

PRUN2_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 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 21873635
GO:0016462 pyrophosphatase activity IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with PRUNE2: view
genes like me logo Genes that share phenotypes with PRUNE2: view

Animal Models for PRUNE2 Gene

MGI Knock Outs for PRUNE2:
  • Prune2 Prune2<tm1e(KOMP)Wtsi>

Animal Model Products

CRISPR Products

Clone Products

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

Localization for PRUNE2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PRUNE2 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 PRUNE2 gene
Compartment Confidence
nucleus 3
cytosol 3
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
endosome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for PRUNE2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA,IBA 21873635
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

PathCards logo

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 21873635
GO:0006915 apoptotic process IBA 21873635
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

8 REFSEQ mRNAs :
19 NCBI additional mRNA sequence :
15 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

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: - -
SP4:
SP5: - - - -
SP6: - -
SP7:
SP8: -
SP9: - - -
SP10:

Relevant External Links for PRUNE2 Gene

GeneLoc Exon Structure for
PRUNE2

Expression for PRUNE2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PRUNE2

SOURCE GeneReport for Unigene cluster for PRUNE2 Gene:

Hs.262857

mRNA Expression by UniProt/SwissProt for PRUNE2 Gene:

Q8WUY3-PRUN2_HUMAN
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
chimpanzee
(Pan troglodytes)
Mammalia PRUNE2 31 30
  • 99.34 (n)
OneToOne
dog
(Canis familiaris)
Mammalia PRUNE2 31 30
  • 83.76 (n)
OneToOne
cow
(Bos Taurus)
Mammalia PRUNE2 31 30
  • 82.53 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Prune2 17 31 30
  • 77.04 (n)
rat
(Rattus norvegicus)
Mammalia Prune2 30
  • 76.58 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia PRUNE2 31
  • 76 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia PRUNE2 31
  • 55 (a)
OneToOne
chicken
(Gallus gallus)
Aves PRUNE2 31
  • 40 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PRUNE2 31
  • 40 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii prune2 31
  • 65 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG11593 31
  • 33 (a)
OneToMany
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

ENSEMBL:
Gene Tree for PRUNE2 (if available)
TreeFam:
Gene Tree for PRUNE2 (if available)
Aminode:
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:

  • PRUN2_HUMAN
  • B4DJW7_HUMAN
  • B4DSQ3_HUMAN
  • B9EK61_HUMAN
  • D6RTK6_HUMAN
  • E9PDC2_HUMAN
  • G8XWS8_HUMAN
  • G8XWS9_HUMAN
  • H7BZH9_HUMAN
  • L8E865_HUMAN
  • Q5JUB8_HUMAN
  • Q5JUB9_HUMAN
genes like me logo Genes that share paralogs with PRUNE2: view

Variants for PRUNE2 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PRUNE2 Gene

SNP ID Clinical significance and condition Chr 09 pos Variation AA Info Type
708874 Benign: not provided 76,703,950(-) G/T MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT
708875 Benign: not provided 76,704,864(-) C/T NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT
708876 Benign: not provided 76,707,219(-) T/C NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT
718914 Benign: not provided 76,706,075(-) C/T MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT
731448 Benign: not provided 76,706,181(-) T/C NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for PRUNE2 Gene

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)
PRUNE2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PRUNE2

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

Disorders for PRUNE2 Gene

MalaCards: The human disease database

(5) MalaCards diseases for PRUNE2 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
prostate sarcoma
  • sarcoma of the prostate
pelvic lipomatosis
  • excess of mature unencapsulated fatty tissue in the pelvis
leiomyosarcoma
  • leiomyosarcomas
prostate cancer
  • prostate cancer, somatic
bladder sarcoma
  • sarcoma of bladder
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for PRUNE2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
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 54
  2. BMCC1 is an AP-2 associated endosomal protein in prostate cancer cells. (PMID: 24040105) Harris JL … Lavin MF (PloS one 2013) 2 3 54
  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 41 54
  4. Investigation of genetic susceptibility factors for human longevity - a targeted nonsynonymous SNP study. (PMID: 20800603) Flachsbart F … Nebel A (Mutation research 2010) 3 41 54
  5. Differential expression of PCA3 and its overlapping PRUNE2 transcript in prostate cancer. (PMID: 19760627) Salagierski M … Schalken JA (The Prostate 2010) 3 4 54

Products for PRUNE2 Gene

Sources for PRUNE2 Gene