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    BPNT1 3'(2'), 5'-bisphosphate nucleotidase 1 [ Homo sapiens (human) ]

    Gene ID: 10380, updated on 20-Apr-2024

    Summary

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    Official Symbol
    BPNT1provided by HGNC
    Official Full Name
    3'(2'), 5'-bisphosphate nucleotidase 1provided by HGNC
    Primary source
    HGNC:HGNC:1096
    See related
    Ensembl:ENSG00000162813 MIM:604053; AllianceGenome:HGNC:1096
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    PIP; HEL20; HsPIP
    Summary
    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]
    Expression
    Ubiquitous expression in small intestine (RPKM 11.4), duodenum (RPKM 10.5) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    1q41
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (220057482..220089788, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (219296762..219329190, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (220230824..220263130, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA U3 Neighboring gene glutamyl-prolyl-tRNA synthetase 1 Neighboring gene small nucleolar RNA U13 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_4879 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:220200073-220200574 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:220219000-220219557 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2551 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2552 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_4904 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2553 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2554 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1822 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1823 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:220267703-220268202 Neighboring gene uncharacterized LOC105373475 Neighboring gene isoleucyl-tRNA synthetase 2, mitochondrial Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_4917 Neighboring gene uncharacterized LOC124904515 Neighboring gene microRNA 215

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Cloning and characterization of a mammalian lithium-sensitive bisphosphate 3'-nucleotidase inhibited by inositol 1,4-bisphosphate. Spiegelberg BD, et al. J Biol Chem, 1999 May 7. PMID 10224133
    2. Evaluation of candidate stromal epithelial cross-talk genes identifies association between risk of serous ovarian cancer and TERT, a cancer susceptibility "hot-spot". Johnatty SE, et al. PLoS Genet, 2010 Jul 8. PMID 20628624, Free PMC Article
    3. AIMP2-DX2 provides therapeutic interface to control KRAS-driven tumorigenesis. Kim DG, et al. Nat Commun, 2022 May 11. PMID 35546148, Free PMC Article
    4. N(6)-Methyladenosine on mRNA facilitates a phase-separated nuclear body that suppresses myeloid leukemic differentiation. Cheng Y, et al. Cancer Cell, 2021 Jul 12. PMID 34048709, Free PMC Article
    5. Parkinson's disease-associated LRRK2-G2019S mutant acts through regulation of SERCA activity to control ER stress in astrocytes. Lee JH, et al. Acta Neuropathol Commun, 2019 May 2. PMID 31046837, Free PMC Article

    See all (26) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. CircRNA HLCS regulates lens epithelial cell apoptosis via miR-338-3p/BPNT1 axis.
      Title: CircRNA HLCS regulates lens epithelial cell apoptosis via miR-338-3p/BPNT1 axis.
    2. Meta-analysis of gene-disease association. (HuGE Navigator)
      Title: Evaluation of candidate stromal epithelial cross-talk genes identifies association between risk of serous ovarian cancer and TERT, a cancer susceptibility "hot-spot".
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables 3'(2'),5'-bisphosphate nucleotidase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables 3'(2'),5'-bisphosphate nucleotidase activity TAS
    Traceable Author Statement
    more info
    		  
    enables inositol-1,4-bisphosphate 1-phosphatase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in 3'-phosphoadenosine 5'-phosphosulfate metabolic process TAS
    Traceable Author Statement
    more info
    		  
    involved_in nervous system development TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in nucleobase-containing compound metabolic process TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in phosphatidylinositol phosphate biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    3'(2'),5'-bisphosphate nucleotidase 1
    Names
    3'-phosphoadenosine 5'-phosphate phosphatase
    BPntase
    BPntase 1
    PAP phosphatase
    PAP-inositol-1,4-phosphatase
    bisphosphate 3'-nucleotidase 1
    epididymis luminal protein 20
    inositol-polyphosphate 1-phosphatase
    testicular tissue protein Li 29
    NP_001273078.1
    NP_001273079.1
    NP_001273080.1
    NP_006076.4
    XP_005273055.1
    XP_005273056.1
    XP_005273057.1
    XP_005273061.1
    XP_005273062.1
    XP_006711177.1
    XP_011507365.1
    XP_011507367.1
    XP_016855532.1
    XP_016855534.1
    XP_047285423.1
    XP_047285529.1
    XP_047285580.1
    XP_047285622.1
    XP_054189789.1
    XP_054189790.1
    XP_054189791.1
    XP_054189792.1
    XP_054189793.1
    XP_054189794.1
    XP_054189795.1
    XP_054189796.1
    XP_054189797.1
    XP_054189798.1
    XP_054189799.1
    XP_054189800.1
    XP_054189801.1
    XP_054189802.1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001286149.2 → NP_001273078.1  3'(2'),5'-bisphosphate nucleotidase 1 isoform 2

      See identical proteins and their annotated locations for NP_001273078.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and lacks a portion of the 5' coding region, compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (2) with a shorter N-terminus, compared to isoform 1. Variants 2 and 4 encode the same isoform (2).
      Source sequence(s)
      AC103590, AK298476
      Consensus CDS
      CCDS65787.1
      UniProtKB/TrEMBL
      B7Z9J7
      Conserved Domains (1) summary
      cd01640
      Location:1 → 242
      IPPase; IPPase; Inositol polyphosphate-1-phosphatase, a member of the Mg++ dependent family of inositol monophosphatase-like domains, hydrolyzes the 1' position phosphate from inositol 1,3,4-trisphosphate and inositol 1,4-bisphosphate. Members in this group may ...

    2. NM_001286150.2 → NP_001273079.1  3'(2'),5'-bisphosphate nucleotidase 1 isoform 3

      See identical proteins and their annotated locations for NP_001273079.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an in-frame exon in the 5' coding region compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
      Source sequence(s)
      AC103590, AK300777
      Consensus CDS
      CCDS65788.1
      UniProtKB/TrEMBL
      A6NF51
      Related
      ENSP00000410348.2, ENST00000414869.6
      Conserved Domains (1) summary
      cd01640
      Location:11 → 261
      IPPase; Inositol polyphosphate-1-phosphatase, a member of the Mg++ dependent family of inositol monophosphatase-like domains, hydrolyzes the 1' position phosphate from inositol 1,3,4-trisphosphate and inositol 1,4-bisphosphate. Members in this group may also ...

    3. NM_001286151.2 → NP_001273080.1  3'(2'),5'-bisphosphate nucleotidase 1 isoform 2

      See identical proteins and their annotated locations for NP_001273080.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and lacks a portion of the 5' coding region, compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (2) with a shorter N-terminus, compared to isoform 1. Variants 2 and 4 encode the same isoform (2).
      Source sequence(s)
      AC103590, AK315962
      Consensus CDS
      CCDS65787.1
      UniProtKB/TrEMBL
      B7Z9J7
      Related
      ENSP00000444398.1, ENST00000544404.5
      Conserved Domains (1) summary
      cd01640
      Location:1 → 242
      IPPase; IPPase; Inositol polyphosphate-1-phosphatase, a member of the Mg++ dependent family of inositol monophosphatase-like domains, hydrolyzes the 1' position phosphate from inositol 1,3,4-trisphosphate and inositol 1,4-bisphosphate. Members in this group may ...

    4. NM_006085.6 → NP_006076.4  3'(2'),5'-bisphosphate nucleotidase 1 isoform 1

      See identical proteins and their annotated locations for NP_006076.4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC103590, AK291943
      Consensus CDS
      CCDS41469.1
      UniProtKB/Swiss-Prot
      A8K7C8, B4DPS5, B4DUS9, D3DTA9, O95861, Q8WVL5, Q9UGJ3
      UniProtKB/TrEMBL
      A6NF51, V9HWF9
      Related
      ENSP00000318852.7, ENST00000322067.12
      Conserved Domains (1) summary
      cd01640
      Location:11 → 297
      IPPase; Inositol polyphosphate-1-phosphatase, a member of the Mg++ dependent family of inositol monophosphatase-like domains, hydrolyzes the 1' position phosphate from inositol 1,3,4-trisphosphate and inositol 1,4-bisphosphate. Members in this group may also ...

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      220057482..220089788 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011509063.3 → XP_011507365.1  3'(2'),5'-bisphosphate nucleotidase 1 isoform X5

      UniProtKB/TrEMBL
      B7Z9J7
      Conserved Domains (1) summary
      cd01640
      Location:1 → 257
      IPPase; IPPase; Inositol polyphosphate-1-phosphatase, a member of the Mg++ dependent family of inositol monophosphatase-like domains, hydrolyzes the 1' position phosphate from inositol 1,3,4-trisphosphate and inositol 1,4-bisphosphate. Members in this group may ...

    2. XM_047429573.1 → XP_047285529.1  3'(2'),5'-bisphosphate nucleotidase 1 isoform X8

    3. XM_006711114.4 → XP_006711177.1  3'(2'),5'-bisphosphate nucleotidase 1 isoform X3

      See identical proteins and their annotated locations for XP_006711177.1

      UniProtKB/TrEMBL
      A6NF51
      Conserved Domains (1) summary
      cd01640
      Location:11 → 276
      IPPase; Inositol polyphosphate-1-phosphatase, a member of the Mg++ dependent family of inositol monophosphatase-like domains, hydrolyzes the 1' position phosphate from inositol 1,3,4-trisphosphate and inositol 1,4-bisphosphate. Members in this group may also ...

    4. XM_005273004.4 → XP_005273061.1  3'(2'),5'-bisphosphate nucleotidase 1 isoform X6

      See identical proteins and their annotated locations for XP_005273061.1

      Conserved Domains (1) summary
      cd01640
      Location:11 → 231
      IPPase; IPPase; Inositol polyphosphate-1-phosphatase, a member of the Mg++ dependent family of inositol monophosphatase-like domains, hydrolyzes the 1' position phosphate from inositol 1,3,4-trisphosphate and inositol 1,4-bisphosphate. Members in this group may ...

    5. XM_005272998.4 → XP_005273055.1  3'(2'),5'-bisphosphate nucleotidase 1 isoform X1

      See identical proteins and their annotated locations for XP_005273055.1

      UniProtKB/TrEMBL
      A6NF51
      Related
      ENSP00000346862.3, ENST00000354807.7
      Conserved Domains (1) summary
      cd01640
      Location:11 → 312
      IPPase; Inositol polyphosphate-1-phosphatase, a member of the Mg++ dependent family of inositol monophosphatase-like domains, hydrolyzes the 1' position phosphate from inositol 1,3,4-trisphosphate and inositol 1,4-bisphosphate. Members in this group may also ...

    6. XM_017000043.2 → XP_016855532.1  3'(2'),5'-bisphosphate nucleotidase 1 isoform X4

      UniProtKB/TrEMBL
      A6NF51
      Conserved Domains (1) summary
      cd01640
      Location:11 → 261
      IPPase; Inositol polyphosphate-1-phosphatase, a member of the Mg++ dependent family of inositol monophosphatase-like domains, hydrolyzes the 1' position phosphate from inositol 1,3,4-trisphosphate and inositol 1,4-bisphosphate. Members in this group may also ...

    7. XM_047429467.1 → XP_047285423.1  3'(2'),5'-bisphosphate nucleotidase 1 isoform X3

    8. XM_005273005.5 → XP_005273062.1  3'(2'),5'-bisphosphate nucleotidase 1 isoform X6

      See identical proteins and their annotated locations for XP_005273062.1

      Conserved Domains (1) summary
      cd01640
      Location:11 → 231
      IPPase; IPPase; Inositol polyphosphate-1-phosphatase, a member of the Mg++ dependent family of inositol monophosphatase-like domains, hydrolyzes the 1' position phosphate from inositol 1,3,4-trisphosphate and inositol 1,4-bisphosphate. Members in this group may ...

    9. XM_005273000.6 → XP_005273057.1  3'(2'),5'-bisphosphate nucleotidase 1 isoform X2

      See identical proteins and their annotated locations for XP_005273057.1

      UniProtKB/Swiss-Prot
      A8K7C8, B4DPS5, B4DUS9, D3DTA9, O95861, Q8WVL5, Q9UGJ3
      UniProtKB/TrEMBL
      A6NF51, V9HWF9
      Conserved Domains (1) summary
      cd01640
      Location:11 → 297
      IPPase; Inositol polyphosphate-1-phosphatase, a member of the Mg++ dependent family of inositol monophosphatase-like domains, hydrolyzes the 1' position phosphate from inositol 1,3,4-trisphosphate and inositol 1,4-bisphosphate. Members in this group may also ...

    10. XM_005272999.6 → XP_005273056.1  3'(2'),5'-bisphosphate nucleotidase 1 isoform X1

      See identical proteins and their annotated locations for XP_005273056.1

      UniProtKB/TrEMBL
      A6NF51
      Conserved Domains (1) summary
      cd01640
      Location:11 → 312
      IPPase; Inositol polyphosphate-1-phosphatase, a member of the Mg++ dependent family of inositol monophosphatase-like domains, hydrolyzes the 1' position phosphate from inositol 1,3,4-trisphosphate and inositol 1,4-bisphosphate. Members in this group may also ...

    11. XM_047429666.1 → XP_047285622.1  3'(2'),5'-bisphosphate nucleotidase 1 isoform X10

    12. XM_017000045.3 → XP_016855534.1  3'(2'),5'-bisphosphate nucleotidase 1 isoform X9

    13. XM_011509065.4 → XP_011507367.1  3'(2'),5'-bisphosphate nucleotidase 1 isoform X7

      Conserved Domains (1) summary
      cl00289
      Location:11 → 157
      FIG; FIG, FBPase/IMPase/glpX-like domain. A superfamily of metal-dependent phosphatases with various substrates. Fructose-1,6-bisphospatase (both the major and the glpX-encoded variant) hydrolyze fructose-1,6,-bisphosphate to fructose-6-phosphate in ...

    14. XM_047429624.1 → XP_047285580.1  3'(2'),5'-bisphosphate nucleotidase 1 isoform X9

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      219296762..219329190 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054333818.1 → XP_054189793.1  3'(2'),5'-bisphosphate nucleotidase 1 isoform X3

    2. XM_054333822.1 → XP_054189797.1  3'(2'),5'-bisphosphate nucleotidase 1 isoform X6

    3. XM_054333815.1 → XP_054189790.1  3'(2'),5'-bisphosphate nucleotidase 1 isoform X1

    4. XM_054333819.1 → XP_054189794.1  3'(2'),5'-bisphosphate nucleotidase 1 isoform X4

    5. XM_054333816.1 → XP_054189791.1  3'(2'),5'-bisphosphate nucleotidase 1 isoform X2

      UniProtKB/Swiss-Prot
      A8K7C8, B4DPS5, B4DUS9, D3DTA9, O95861, Q8WVL5, Q9UGJ3
      UniProtKB/TrEMBL
      V9HWF9

    6. XM_054333820.1 → XP_054189795.1  3'(2'),5'-bisphosphate nucleotidase 1 isoform X5

    7. XM_054333824.1 → XP_054189799.1  3'(2'),5'-bisphosphate nucleotidase 1 isoform X8

    8. XM_054333817.1 → XP_054189792.1  3'(2'),5'-bisphosphate nucleotidase 1 isoform X3

    9. XM_054333821.1 → XP_054189796.1  3'(2'),5'-bisphosphate nucleotidase 1 isoform X6

    10. XM_054333814.1 → XP_054189789.1  3'(2'),5'-bisphosphate nucleotidase 1 isoform X1

    11. XM_054333826.1 → XP_054189801.1  3'(2'),5'-bisphosphate nucleotidase 1 isoform X9

    12. XM_054333827.1 → XP_054189802.1  3'(2'),5'-bisphosphate nucleotidase 1 isoform X10

    13. XM_054333825.1 → XP_054189800.1  3'(2'),5'-bisphosphate nucleotidase 1 isoform X9

    14. XM_054333823.1 → XP_054189798.1  3'(2'),5'-bisphosphate nucleotidase 1 isoform X7

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O95861.1 GenPept UniProtKB/Swiss-Prot:O95861

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