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    INPP5D inositol polyphosphate-5-phosphatase D [ Homo sapiens (human) ]

    Gene ID: 3635, updated on 1-Jul-2024

    Summary

    Official Symbol
    INPP5Dprovided by HGNC
    Official Full Name
    inositol polyphosphate-5-phosphatase Dprovided by HGNC
    Primary source
    HGNC:HGNC:6079
    See related
    Ensembl:ENSG00000168918 MIM:601582; AllianceGenome:HGNC:6079
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SHIP; SHIP1; SHIP-1; hp51CN; SIP-145; p150Ship
    Summary
    This gene is a member of the inositol polyphosphate-5-phosphatase (INPP5) family and encodes a protein with an N-terminal SH2 domain, an inositol phosphatase domain, and two C-terminal protein interaction domains. Expression of this protein is restricted to hematopoietic cells where its movement from the cytosol to the plasma membrane is mediated by tyrosine phosphorylation. At the plasma membrane, the protein hydrolyzes the 5' phosphate from phosphatidylinositol (3,4,5)-trisphosphate and inositol-1,3,4,5-tetrakisphosphate, thereby affecting multiple signaling pathways. The protein is also partly localized to the nucleus, where it may be involved in nuclear inositol phosphate signaling processes. Overall, the protein functions as a negative regulator of myeloid cell proliferation and survival. Mutations in this gene are associated with defects and cancers of the immune system. Deficiencies in the encoded protein, SHIP1, have been associated with Inflammatory Bowel Disease types such as Crohn's Disease and Ulcerative Colitis. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jul 2020]
    Expression
    Broad expression in lymph node (RPKM 33.2), spleen (RPKM 31.1) and 21 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See INPP5D in Genome Data Viewer
    Location:
    2q37.1
    Exon count:
    27
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (233060342..233207903)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (233547692..233695995)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (233925052..234116549)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene neuronal guanine nucleotide exchange factor Neighboring gene uncharacterized LOC101928881 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12465 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17328 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12466 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17329 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:233926783-233927376 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:233927377-233927970 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17330 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12468 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:233937995-233938700 Neighboring gene neuraminidase 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17331 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17332 Neighboring gene Sharpr-MPRA regulatory region 10619 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17333 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:233953501-233954000 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:233972121-233972622 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:233972623-233973122 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17334 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:233982267-233982860 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:233987251-233987751 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:233988888-233989435 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:233989436-233989982 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:233993677-233994176 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:234072305-234072918 Neighboring gene NANOG hESC enhancer GRCh37_chr2:234125377-234125936 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:234131944-234132095 Neighboring gene RNA, 7SL, cytoplasmic 32, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr2:234151441-234151635 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:234155927-234157126 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17335 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17336 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17337 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12469 Neighboring gene autophagy related 16 like 1 Neighboring gene NANOG hESC enhancer GRCh37_chr2:234197330-234197831 Neighboring gene small Cajal body-specific RNA 5 Neighboring gene small Cajal body-specific RNA 6

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    A genome-wide scan of Ashkenazi Jewish Crohn's disease suggests novel susceptibility loci.
    EBI GWAS Catalog
    Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
    EBI GWAS Catalog
    Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease.
    EBI GWAS Catalog
    Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease.
    EBI GWAS Catalog
    Variants in the 1q21 risk region are associated with a visual endophenotype of autism and schizophrenia.
    EBI GWAS Catalog

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env HIV-1 gp120 upregulates the expression of inositol polyphosphate-5-phosphatase, 145kDa (INPP5D) in human B cells PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC104855, MGC142140, MGC142142

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in T cell receptor signaling pathway TAS
    Traceable Author Statement
    more info
     
    involved_in apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in determination of adult lifespan IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in immunoglobulin mediated immune response IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in intracellular signal transduction IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of B cell proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of bone resorption IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in negative regulation of immune response IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of interleukin-6 production IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of monocyte differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of neutrophil differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in negative regulation of osteoclast differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of signal transduction IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in phosphate-containing compound metabolic process TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in phosphatidylinositol biosynthetic process TAS
    Traceable Author Statement
    more info
     
    involved_in phosphatidylinositol dephosphorylation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of B cell differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of erythrocyte differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of immune response IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in signal transduction TAS
    Traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in cytoskeleton IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
     
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in membrane raft IEA
    Inferred from Electronic Annotation
    more info
     
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1
    Names
    SH2 domain-containing inositol 5'-phosphatase 1
    inositol polyphosphate-5-phosphatase, 145kD
    inositol polyphosphate-5-phosphatase, 145kDa
    phosphatidylinositol 4,5-bisphosphate 5-phosphatase
    signaling inositol polyphosphate 5 phosphatase SIP-145
    signaling inositol polyphosphate phosphatase SHIP II
    NP_001017915.1
    NP_005532.2
    XP_047300175.1
    XP_047300176.1
    XP_054187655.1
    XP_054187656.1
    XP_054197847.1
    XP_054197848.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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.

    Genomic

    1. NG_033988.1 RefSeqGene

      Range
      5376..152937
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001017915.3NP_001017915.1  phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1 isoform a

      See identical proteins and their annotated locations for NP_001017915.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
      Source sequence(s)
      AW503130, BC099920, U53470
      Consensus CDS
      CCDS74672.1
      UniProtKB/Swiss-Prot
      O00145, Q13544, Q13545, Q6P5A4, Q92656, Q92835, Q9UE80
      Related
      ENSP00000405338.2, ENST00000445964.6
      Conserved Domains (3) summary
      cd09100
      Location:404710
      INPP5c_SHIP1-INPP5D; Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of SH2 domain containing inositol polyphosphate 5-phosphatase-1 and related proteins
      cd10343
      Location:1102
      SH2_SHIP; Src homology 2 (SH2) domain found in SH2-containing inositol-5'-phosphatase (SHIP) and SLAM-associated protein (SAP)
      PHA03307
      Location:8991127
      PHA03307; transcriptional regulator ICP4; Provisional
    2. NM_005541.5NP_005532.2  phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1 isoform b

      See identical proteins and their annotated locations for NP_005532.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1, resulting in an isoform (b) that is 1 aa shorter than isoform a.
      Source sequence(s)
      AW503130, BC099920, X98429
      Consensus CDS
      CCDS77543.1
      UniProtKB/Swiss-Prot
      Q92835
      Related
      ENSP00000352575.7, ENST00000359570.9
      Conserved Domains (2) summary
      cd09100
      Location:403709
      INPP5c_SHIP1-INPP5D; Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of SH2 domain containing inositol polyphosphate 5-phosphatase-1 and related proteins
      cd10343
      Location:1102
      SH2_SHIP; Src homology 2 (SH2) domain found in SH2-containing inositol-5'-phosphatase (SHIP) and SLAM-associated protein (SAP)

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      233060342..233207903
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047444219.1XP_047300175.1  phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1 isoform X1

    2. XM_047444220.1XP_047300176.1  phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1 isoform X2

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_011332690.1 Reference GRCh38.p14 PATCHES

      Range
      5680..153241
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054331680.1XP_054187655.1  phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1 isoform X1

    2. XM_054331681.1XP_054187656.1  phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1 isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      233547692..233695995
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054341872.1XP_054197847.1  phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1 isoform X1

    2. XM_054341873.1XP_054197848.1  phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1 isoform X2