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Aliases for BPNT1 Gene

Aliases for BPNT1 Gene

  • 3'(2'), 5'-Bisphosphate Nucleotidase 1 2 3
  • Bisphosphate 3-Nucleotidase 1 3 4
  • PIP 3 4
  • 3(2), 5-Bisphosphate Nucleotidase 1 5
  • 3(2),5-Bisphosphate Nucleotidase 1 3
  • Testicular Tissue Protein Li 29 3
  • Epididymis Luminal Protein 20 3
  • PAP-Inositol-1,4-Phosphatase 3
  • PAP-Inositol 1,4-Phosphatase 4
  • EC 4
  • BPntase 3
  • HEL20 3

External Ids for BPNT1 Gene

Previous GeneCards Identifiers for BPNT1 Gene

  • GC01M218827
  • GC01M216074
  • GC01M216777
  • GC01M217287
  • GC01M216619
  • GC01M218297
  • GC01M220230
  • GC01M190905

Summaries for BPNT1 Gene

Entrez Gene Summary for BPNT1 Gene

  • BPNT1, also called bisphosphate 3-prime-nucleotidase, or BPntase, is a member of a magnesium-dependent phosphomonoesterase family. Lithium, a major drug used to treat manic depression, acts as an uncompetitive inhibitor of BPntase. The predicted human protein is 92% identical to mouse BPntase. BPntase's physiologic role in nucleotide metabolism may be regulated by inositol signaling pathways. The inhibition of human BPntase may account for lithium-induced nephrotoxicity. [provided by RefSeq, Jul 2008]

GeneCards Summary for BPNT1 Gene

BPNT1 (3'(2'), 5'-Bisphosphate Nucleotidase 1) is a Protein Coding gene. Among its related pathways are Metabolism and Cytochrome P450 - arranged by substrate type. Gene Ontology (GO) annotations related to this gene include magnesium ion binding and 3(2),5-bisphosphate nucleotidase activity. An important paralog of this gene is IMPAD1.

UniProtKB/Swiss-Prot for BPNT1 Gene

  • Converts adenosine 3-phosphate 5-phosphosulfate (PAPS) to adenosine 5-phosphosulfate (APS) and 3(2)-phosphoadenosine 5- phosphate (PAP) to AMP. Has 1000-fold lower activity towards inositol 1,4-bisphosphate (Ins(1,4)P2) and inositol 1,3,4-trisphosphate (Ins(1,3,4)P3), but does not hydrolyze Ins(1)P, Ins(3,4)P2, Ins(1,3,4,5)P4 or InsP6.

Additional gene information for BPNT1 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for BPNT1 Gene

Genomics for BPNT1 Gene

GeneHancer (GH) Regulatory Elements for BPNT1 Gene

Promoters and enhancers for BPNT1 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
GH01J220088 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 650.7 +0.7 682 2 HDGF PKNOX1 FOXA2 ARNT ARID4B NEUROD1 SIN3A DMAP1 IRF4 YY1 BPNT1 RPS15AP12 ZC3H11B RIMKLBP2 EPRS PIR35692
GH01J220270 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 4.4 -181.7 -181730 2.6 HDGF PKNOX1 ARNT ARID4B SIN3A FEZF1 DMAP1 ZBTB7B YY1 POLR2B RAB3GAP2 RPS15AP12 SNX2P1 ZC3H11B BPNT1 AURKAPS1
GH01J220219 Enhancer 1.1 FANTOM5 ENCODE 1.8 -130.6 -130562 3.8 PKNOX1 STAT5A ATF7 BCLAF1 IKZF2 RUNX3 CREM SMARCA5 SMAD5 JUNB ENSG00000270708 RAB3GAP2 BPNT1 EPRS GC01P220248
GH01J220086 Enhancer 0.7 ENCODE 0.7 +4.1 4118 0.2 HDGF CTCF ATF1 E4F1 PRPF4 ZNF143 RUNX3 CREM SMARCE1 SMARCA5 BPNT1 PIR35692
GH01J220084 Enhancer 0.5 ENCODE 0.4 +5.6 5581 1.4 GATA3 RXRA HLF CEBPA HNF4A PPARG BPNT1 PIR35692
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around BPNT1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the BPNT1 gene promoter:
  • HEN1
  • GATA-1
  • Arnt
  • POU2F1a
  • POU2F1
  • Ik-3
  • GATA-2
  • FOXJ2 (long isoform)
  • FOXJ2
  • FOXD3

Genomic Locations for BPNT1 Gene

Genomic Locations for BPNT1 Gene
32,981 bases
Minus strand
32,981 bases
Minus strand

Genomic View for BPNT1 Gene

Genes around BPNT1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
BPNT1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for BPNT1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for BPNT1 Gene

Proteins for BPNT1 Gene

  • Protein details for BPNT1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    3(2),5-bisphosphate nucleotidase 1
    Protein Accession:
    Secondary Accessions:
    • A8K7C8
    • B4DPS5
    • B4DUS9
    • D3DTA9
    • Q8WVL5
    • Q9UGJ3

    Protein attributes for BPNT1 Gene

    308 amino acids
    Molecular mass:
    33392 Da
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for BPNT1 Gene

    Alternative splice isoforms for BPNT1 Gene


neXtProt entry for BPNT1 Gene

Post-translational modifications for BPNT1 Gene

  • Ubiquitination at posLast=4949
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for BPNT1 Gene

Domains & Families for BPNT1 Gene

Gene Families for BPNT1 Gene

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

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the inositol monophosphatase superfamily.
  • Belongs to the inositol monophosphatase superfamily.
genes like me logo Genes that share domains with BPNT1: view

Function for BPNT1 Gene

Molecular function for BPNT1 Gene

UniProtKB/Swiss-Prot Function:
Converts adenosine 3-phosphate 5-phosphosulfate (PAPS) to adenosine 5-phosphosulfate (APS) and 3(2)-phosphoadenosine 5- phosphate (PAP) to AMP. Has 1000-fold lower activity towards inositol 1,4-bisphosphate (Ins(1,4)P2) and inositol 1,3,4-trisphosphate (Ins(1,3,4)P3), but does not hydrolyze Ins(1)P, Ins(3,4)P2, Ins(1,3,4,5)P4 or InsP6.
UniProtKB/Swiss-Prot CatalyticActivity:
Adenosine 3,5-bisphosphate + H(2)O = adenosine 5-phosphate + phosphate.
UniProtKB/Swiss-Prot EnzymeRegulation:
Uncompetitive inhibition by micromolar concentrations of lithium. Competitive inhibition by inositol 1,4-bisphosphate.

Enzyme Numbers (IUBMB) for BPNT1 Gene

Gene Ontology (GO) - Molecular Function for BPNT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008441 3(2),5-bisphosphate nucleotidase activity TAS --
GO:0016787 hydrolase activity IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with BPNT1: view
genes like me logo Genes that share phenotypes with BPNT1: view

Animal Models for BPNT1 Gene

MGI Knock Outs for BPNT1:

Animal Model Products

  • Taconic Biosciences Mouse Models for BPNT1

miRNA for BPNT1 Gene

miRTarBase miRNAs that target BPNT1

Clone Products

No data available for Phenotypes From GWAS Catalog , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for BPNT1 Gene

Localization for BPNT1 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 BPNT1 gene
Compartment Confidence
extracellular 5
cytosol 5
mitochondrion 3
nucleus 3

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear speckles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for BPNT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005829 cytosol TAS --
GO:0070062 extracellular exosome HDA --
genes like me logo Genes that share ontologies with BPNT1: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for BPNT1 Gene

Pathways & Interactions for BPNT1 Gene

genes like me logo Genes that share pathways with BPNT1: view

Pathways by source for BPNT1 Gene

Gene Ontology (GO) - Biological Process for BPNT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006139 nucleobase-containing compound metabolic process TAS 10224133
GO:0007399 nervous system development TAS 10224133
GO:0016311 dephosphorylation IEA --
GO:0046854 phosphatidylinositol phosphorylation IEA --
GO:0050427 3-phosphoadenosine 5-phosphosulfate metabolic process TAS --
genes like me logo Genes that share ontologies with BPNT1: view

No data available for SIGNOR curated interactions for BPNT1 Gene

Drugs & Compounds for BPNT1 Gene

(7) Drugs for BPNT1 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Lithium Approved Pharma 0
Phosphoric acid Approved Pharma 0
Water Approved Pharma 0
Zolpidem Approved Pharma Full agonist, Allosteric regulator 110
Adenosine monophosphate Approved, Investigational Nutra 0

(3) Additional Compounds for BPNT1 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Adenosine 3',5'-diphosphate
  • 3'-Phosphoadenylate
  • Adenosine 3',5'-bisphosphate
  • PAP
  • Phosphoadenosine phosphate
  • 3'-Phosphoadenylic acid
  • [po(OH)3]
  • Acide phosphorique
  • Acidum phosphoricum
  • H3PO4
  • Orthophosphoric acid
Phosphoadenosine phosphosulfate
  • 3'-Phosphoadenosine 5'-phosphosulfate
  • 3'-Phosphoadenylyl sulfate
  • PAPS
  • 3'-Phosphoadenosine 5'-phosphosulfuric acid
  • 3'-Phosphoadenosine 5'-phosphosulphate
genes like me logo Genes that share compounds with BPNT1: view

Transcripts for BPNT1 Gene

Unigene Clusters for BPNT1 Gene

3(2), 5-bisphosphate nucleotidase 1:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for BPNT1 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9a · 9b ^ 10
SP1: - -
SP2: -
SP3: -
SP4: - - -

Relevant External Links for BPNT1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for BPNT1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for BPNT1 Gene

Protein differential expression in normal tissues from HIPED for BPNT1 Gene

This gene is overexpressed in Skin (11.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for BPNT1 Gene

Protein tissue co-expression partners for BPNT1 Gene

NURSA nuclear receptor signaling pathways regulating expression of BPNT1 Gene:


SOURCE GeneReport for Unigene cluster for BPNT1 Gene:


mRNA Expression by UniProt/SwissProt for BPNT1 Gene:

Tissue specificity: Highly expressed in kidney, liver, pancreas and heart. Detected at lower levels in brain, placenta, lung and skeletal muscle.

Evidence on tissue expression from TISSUES for BPNT1 Gene

  • Liver(4.3)
  • Muscle(4.2)
  • Nervous system(2.2)
genes like me logo Genes that share expression patterns with BPNT1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for BPNT1 Gene

Orthologs for BPNT1 Gene

This gene was present in the common ancestor of animals.

Orthologs for BPNT1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia BPNT1 34 33
  • 99.89 (n)
(Canis familiaris)
Mammalia BPNT1 34 33
  • 91.99 (n)
(Bos Taurus)
Mammalia BPNT1 34 33
  • 90.04 (n)
(Ornithorhynchus anatinus)
Mammalia BPNT1 34
  • 87 (a)
(Mus musculus)
Mammalia Bpnt1 16 34 33
  • 85.06 (n)
(Rattus norvegicus)
Mammalia Bpnt1 33
  • 84.96 (n)
(Monodelphis domestica)
Mammalia BPNT1 34
  • 57 (a)
(Gallus gallus)
Aves BPNT1 34 33
  • 77.02 (n)
(Anolis carolinensis)
Reptilia BPNT1 34
  • 84 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia bpnt1 33
  • 74.13 (n)
Str.3809 33
(Danio rerio)
Actinopterygii bpnt1 34 33
  • 68.19 (n)
Dr.15386 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.14199 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP004654 33
  • 54.08 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG7789 34 35 33
  • 52.98 (n)
(Caenorhabditis elegans)
Secernentea tag-231 34 33
  • 55.36 (n)
ZK430.2 35
  • 42 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 45 (a)
Cin.15563 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.15563 33
Species where no ortholog for BPNT1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • 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 BPNT1 Gene

Gene Tree for BPNT1 (if available)
Gene Tree for BPNT1 (if available)
Evolutionary constrained regions (ECRs) for BPNT1: view image

Paralogs for BPNT1 Gene

Paralogs for BPNT1 Gene

(1) SIMAP similar genes for BPNT1 Gene using alignment to 8 proteins:

  • A6NF51_HUMAN
  • F8W1J0_HUMAN
genes like me logo Genes that share paralogs with BPNT1: view

Variants for BPNT1 Gene

Sequence variations from dbSNP and Humsavar for BPNT1 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000014211 -- 220,072,629(-) A/G intron_variant
rs1000041751 -- 220,072,392(-) C/A intron_variant
rs1000176619 -- 220,087,419(-) G/A intron_variant
rs1000192372 -- 220,078,984(-) A/G intron_variant
rs1000385622 -- 220,065,131(-) T/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for BPNT1 Gene

Variant ID Type Subtype PubMed ID
esv3588892 CNV loss 21293372
nsv1144433 CNV deletion 24896259
nsv4632 CNV insertion 18451855
nsv549222 CNV loss 21841781
nsv832636 CNV loss 17160897

Variation tolerance for BPNT1 Gene

Residual Variation Intolerance Score: 44.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.64; 31.45% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for BPNT1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for BPNT1 Gene

Disorders for BPNT1 Gene

Additional Disease Information for BPNT1

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for BPNT1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for BPNT1 Gene

Publications for BPNT1 Gene

  1. Cloning and characterization of a mammalian lithium-sensitive bisphosphate 3'-nucleotidase inhibited by inositol 1,4-bisphosphate. (PMID: 10224133) Spiegelberg BD … York JD (The Journal of biological chemistry 1999) 2 3 4 22 58
  2. Evaluation of candidate stromal epithelial cross-talk genes identifies association between risk of serous ovarian cancer and TERT, a cancer susceptibility "hot-spot". (PMID: 20628624) Johnatty SE … Australian Cancer Study (Ovarian Cancer) (PLoS genetics 2010) 3 44 58
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  4. 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
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58

Products for BPNT1 Gene

Sources for BPNT1 Gene

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