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    SMPD3 sphingomyelin phosphodiesterase 3 [ Homo sapiens (human) ]

    Gene ID: 55512, updated on 17-Jun-2024

    Summary

    Official Symbol
    SMPD3provided by HGNC
    Official Full Name
    sphingomyelin phosphodiesterase 3provided by HGNC
    Primary source
    HGNC:HGNC:14240
    See related
    Ensembl:ENSG00000103056 MIM:605777; AllianceGenome:HGNC:14240
    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
    NSMASE2
    Summary
    Predicted to enable phosphatidic acid binding activity; phosphatidylserine binding activity; and sphingomyelin phosphodiesterase activity. Predicted to be involved in positive regulation of exosomal secretion and sphingomyelin metabolic process. Predicted to act upstream of or within several processes, including animal organ development; enzyme linked receptor protein signaling pathway; and sphingolipid metabolic process. Predicted to be located in Golgi apparatus and plasma membrane. Predicted to be active in cytoplasm. Biomarker of pulmonary emphysema. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in duodenum (RPKM 22.0), small intestine (RPKM 21.4) and 11 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SMPD3 in Genome Data Viewer
    Location:
    16q22.1
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (68358327..68448508, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (74154167..74244330, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (68392230..68482411, complement)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA U13 Neighboring gene protein arginine methyltransferase 7 Neighboring gene RNA, U4 small nuclear 30, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:68382607-68383107 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11013 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:68396471-68397283 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:68397284-68398095 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:68400892-68401445 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:68401446-68401998 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11014 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11015 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:68413436-68413938 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:68413939-68414439 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:68415806-68416642 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:68416643-68417477 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:68422765-68423592 Neighboring gene Sharpr-MPRA regulatory region 9240 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:68431713-68432213 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:68432795-68433424 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:68433425-68434052 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:68442570-68443549 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:68444678-68445630 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:68445631-68446581 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7646 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11016 Neighboring gene uncharacterized LOC124903705 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:68504627-68505126 Neighboring gene ribosomal protein L35a pseudogene 33

    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?

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env A redox-regulated translocation of neutral sphingomyelinase-2 to the plasma membrane is required for HIV-1 gp120-induced enlargement and stabilization of the structure of lipid microdomains on dendrites PubMed
    env HIV-1 gp120 binding to CXCR4 induces NADPH oxidase-mediated production of superoxide radicals in neurons, which is involved in the activation of neutral sphingomyelinase PubMed
    env In human primary neurons, HIV-1 gp120 induces the activation of sphingomyelinases (primarily neutral sphingomyelinase); antisense knockdown of neutral sphingomyelinase markedly inhibits gp120-mediated apoptosis and cell death of primary neurons PubMed
    Nef nef HIV-1 Nef inhibits sphingomyelinase activity in human podocyte 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

    • FLJ22593, MGC138443

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables identical protein binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables neutral sphingomyelin phosphodiesterase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables phosphatidic acid binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables phosphatidylserine binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables phosphoric diester hydrolase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables sphingomyelin phosphodiesterase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables sphingomyelin phosphodiesterase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables sphingomyelin phosphodiesterase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Process Evidence Code Pubs
    involved_in BMP signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in DNA biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in G1 to G0 transition IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in bone growth IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in bone mineralization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to hydrogen peroxide IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to magnesium ion IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to oxidised low-density lipoprotein particle stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to peptide IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to redox state IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to tumor necrosis factor IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in ceramide metabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in chondrocyte development involved in endochondral bone morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in collagen metabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in dentinogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in endochondral ossification IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in extracellular matrix assembly IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in hematopoietic progenitor cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in lung alveolus development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in mitotic nuclear division IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in multicellular organism growth IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of hyaluronan biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in peptide hormone secretion IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in platelet-derived growth factor receptor signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in polysaccharide transport IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of exosomal secretion ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of mitotic nuclear division IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of smooth muscle cell proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of cartilage development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of leukocyte migration IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of protein phosphorylation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in sphingolipid mediated signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in sphingomyelin catabolic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in sphingomyelin metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in sphingomyelin metabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    located_in Golgi cis cisterna IEA
    Inferred from Electronic Annotation
    more info
     
    located_in Golgi membrane IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
     
    located_in plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    sphingomyelin phosphodiesterase 3
    Names
    nSMase-2
    neutral sphingomyelinase 2
    neutral sphingomyelinase II
    NP_061137.1
    XP_005256089.1
    XP_011521509.1
    XP_011521512.1
    XP_016878895.1
    XP_047290292.1
    XP_047290293.1
    XP_047290294.1
    XP_047290295.1
    XP_047290296.1
    XP_047290297.1
    XP_054169385.1
    XP_054169386.1
    XP_054169387.1
    XP_054169388.1
    XP_054169389.1
    XP_054169390.1
    XP_054169391.1
    XP_054169392.1
    XP_054169393.1
    XP_054169394.1
    XP_054169395.1

    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.

    mRNA and Protein(s)

    1. NM_018667.4NP_061137.1  sphingomyelin phosphodiesterase 3

      See identical proteins and their annotated locations for NP_061137.1

      Status: VALIDATED

      Source sequence(s)
      AC099521, AK289651, BC112238
      Consensus CDS
      CCDS10867.1
      UniProtKB/Swiss-Prot
      B7ZL82, Q2M1S8, Q9NY59
      UniProtKB/TrEMBL
      A8K0T6
      Related
      ENSP00000219334.5, ENST00000219334.10
      Conserved Domains (2) summary
      cd09078
      Location:338646
      nSMase; Neutral sphingomyelinases (nSMase) catalyze the hydrolysis of sphingomyelin in biological membranes to ceramide and phosphorylcholine
      PHA03307
      Location:171321
      PHA03307; transcriptional regulator ICP4; Provisional

    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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      68358327..68448508 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011523207.2XP_011521509.1  sphingomyelin phosphodiesterase 3 isoform X1

      See identical proteins and their annotated locations for XP_011521509.1

      UniProtKB/Swiss-Prot
      B7ZL82, Q2M1S8, Q9NY59
      UniProtKB/TrEMBL
      A8K0T6
      Conserved Domains (2) summary
      cd09078
      Location:338646
      nSMase; Neutral sphingomyelinases (nSMase) catalyze the hydrolysis of sphingomyelin in biological membranes to ceramide and phosphorylcholine
      PHA03307
      Location:171321
      PHA03307; transcriptional regulator ICP4; Provisional
    2. XM_047434339.1XP_047290295.1  sphingomyelin phosphodiesterase 3 isoform X1

      UniProtKB/Swiss-Prot
      B7ZL82, Q2M1S8, Q9NY59
      UniProtKB/TrEMBL
      A8K0T6
    3. XM_017023406.2XP_016878895.1  sphingomyelin phosphodiesterase 3 isoform X1

      UniProtKB/Swiss-Prot
      B7ZL82, Q2M1S8, Q9NY59
      UniProtKB/TrEMBL
      A8K0T6
      Conserved Domains (2) summary
      cd09078
      Location:338646
      nSMase; Neutral sphingomyelinases (nSMase) catalyze the hydrolysis of sphingomyelin in biological membranes to ceramide and phosphorylcholine
      PHA03307
      Location:171321
      PHA03307; transcriptional regulator ICP4; Provisional
    4. XM_047434340.1XP_047290296.1  sphingomyelin phosphodiesterase 3 isoform X1

      UniProtKB/Swiss-Prot
      B7ZL82, Q2M1S8, Q9NY59
      UniProtKB/TrEMBL
      A8K0T6
    5. XM_047434338.1XP_047290294.1  sphingomyelin phosphodiesterase 3 isoform X1

      UniProtKB/Swiss-Prot
      B7ZL82, Q2M1S8, Q9NY59
      UniProtKB/TrEMBL
      A8K0T6
    6. XM_047434336.1XP_047290292.1  sphingomyelin phosphodiesterase 3 isoform X1

      UniProtKB/Swiss-Prot
      B7ZL82, Q2M1S8, Q9NY59
      UniProtKB/TrEMBL
      A8K0T6
      Related
      ENSP00000455955.1, ENST00000563226.1
    7. XM_047434337.1XP_047290293.1  sphingomyelin phosphodiesterase 3 isoform X1

      UniProtKB/Swiss-Prot
      B7ZL82, Q2M1S8, Q9NY59
      UniProtKB/TrEMBL
      A8K0T6
    8. XM_005256032.4XP_005256089.1  sphingomyelin phosphodiesterase 3 isoform X1

      See identical proteins and their annotated locations for XP_005256089.1

      UniProtKB/Swiss-Prot
      B7ZL82, Q2M1S8, Q9NY59
      UniProtKB/TrEMBL
      A8K0T6
      Conserved Domains (2) summary
      cd09078
      Location:338646
      nSMase; Neutral sphingomyelinases (nSMase) catalyze the hydrolysis of sphingomyelin in biological membranes to ceramide and phosphorylcholine
      PHA03307
      Location:171321
      PHA03307; transcriptional regulator ICP4; Provisional
    9. XM_047434341.1XP_047290297.1  sphingomyelin phosphodiesterase 3 isoform X1

      UniProtKB/Swiss-Prot
      B7ZL82, Q2M1S8, Q9NY59
      UniProtKB/TrEMBL
      A8K0T6
    10. XM_011523210.3XP_011521512.1  sphingomyelin phosphodiesterase 3 isoform X2

      Conserved Domains (1) summary
      cl00490
      Location:338441
      EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

    RNA

    1. XR_933371.3 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      74154167..74244330 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054313412.1XP_054169387.1  sphingomyelin phosphodiesterase 3 isoform X1

      UniProtKB/Swiss-Prot
      B7ZL82, Q2M1S8, Q9NY59
      UniProtKB/TrEMBL
      A8K0T6
    2. XM_054313415.1XP_054169390.1  sphingomyelin phosphodiesterase 3 isoform X1

      UniProtKB/Swiss-Prot
      B7ZL82, Q2M1S8, Q9NY59
      UniProtKB/TrEMBL
      A8K0T6
    3. XM_054313410.1XP_054169385.1  sphingomyelin phosphodiesterase 3 isoform X1

      UniProtKB/Swiss-Prot
      B7ZL82, Q2M1S8, Q9NY59
      UniProtKB/TrEMBL
      A8K0T6
    4. XM_054313416.1XP_054169391.1  sphingomyelin phosphodiesterase 3 isoform X1

      UniProtKB/Swiss-Prot
      B7ZL82, Q2M1S8, Q9NY59
      UniProtKB/TrEMBL
      A8K0T6
    5. XM_054313414.1XP_054169389.1  sphingomyelin phosphodiesterase 3 isoform X1

      UniProtKB/Swiss-Prot
      B7ZL82, Q2M1S8, Q9NY59
      UniProtKB/TrEMBL
      A8K0T6
    6. XM_054313418.1XP_054169393.1  sphingomyelin phosphodiesterase 3 isoform X1

      UniProtKB/Swiss-Prot
      B7ZL82, Q2M1S8, Q9NY59
      UniProtKB/TrEMBL
      A8K0T6
    7. XM_054313413.1XP_054169388.1  sphingomyelin phosphodiesterase 3 isoform X1

      UniProtKB/Swiss-Prot
      B7ZL82, Q2M1S8, Q9NY59
      UniProtKB/TrEMBL
      A8K0T6
    8. XM_054313411.1XP_054169386.1  sphingomyelin phosphodiesterase 3 isoform X1

      UniProtKB/Swiss-Prot
      B7ZL82, Q2M1S8, Q9NY59
      UniProtKB/TrEMBL
      A8K0T6
    9. XM_054313417.1XP_054169392.1  sphingomyelin phosphodiesterase 3 isoform X1

      UniProtKB/Swiss-Prot
      B7ZL82, Q2M1S8, Q9NY59
      UniProtKB/TrEMBL
      A8K0T6
    10. XM_054313420.1XP_054169395.1  sphingomyelin phosphodiesterase 3 isoform X2

    11. XM_054313419.1XP_054169394.1  sphingomyelin phosphodiesterase 3 isoform X2

    RNA

    1. XR_008484705.1 RNA Sequence