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SMPD1 Gene

protein-coding   GIFtS: 70
GCID: GC11P006411

Sphingomyelin Phosphodiesterase 1, Acid Lysosomal

  See SMPD1-related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Sphingomyelin Phosphodiesterase 1, Acid Lysosomal1 2     ASMASE2
Acid Sphingomyelinase1 2 3     Sphingomyelin Phosphodiesterase2
ASM2 3     EC 3.1.4.123
NPD2 5     aSMase3

External Ids:    HGNC: 111201   Entrez Gene: 66092   Ensembl: ENSG000001663117   OMIM: 6076085   UniProtKB: P174053   

Export aliases for SMPD1 gene to outside databases

Previous GC identifers: GC11P007154 GC11P006873 GC11P006370 GC11P006376 GC11P006368 GC11P006070


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for SMPD1 Gene:
The protein encoded by this gene is a lysosomal acid sphingomyelinase that converts sphingomyelin to ceramide. The
encoded protein also has phospholipase C activity. Defects in this gene are a cause of Niemann-Pick disease type
A (NPA) and Niemann-Pick disease type B (NPB). Multiple transcript variants encoding different isoforms have been
identified. (provided by RefSeq, Jul 2010)

GeneCards Summary for SMPD1 Gene:
SMPD1 (sphingomyelin phosphodiesterase 1, acid lysosomal) is a protein-coding gene. Diseases associated with SMPD1 include niemann-pick disease, and sea-blue histiocytosis. GO annotations related to this gene include hydrolase activity, acting on glycosyl bonds and sphingomyelin phosphodiesterase activity. An important paralog of this gene is SMPDL3A.

UniProtKB/Swiss-Prot: ASM_HUMAN, P17405
Function: Converts sphingomyelin to ceramide. Also has phospholipase C activities toward
1,2-diacylglycerolphosphocholine and 1,2-diacylglycerolphosphoglycerol. Isoform 2 and isoform 3 have lost
catalytic activity

Gene Wiki entry for SMPD1 (Sphingomyelin phosphodiesterase 1) Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000011.9  NT_009237.19  NC_018922.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the SMPD1 gene promoter:
         NF-1   Nkx2-5   RORalpha2   NF-AT   NF-AT4   NF-AT2   NF-AT3   ZID   Meis-1   NF-AT1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSMPD1 promoter sequence
   Search Chromatin IP Primers for SMPD1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SMPD1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 11p15.4-p15.1   Ensembl cytogenetic band:  11p15.4   HGNC cytogenetic band: 11p15.4-p15.1

SMPD1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SMPD1 gene location

GeneLoc information about chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11P006411:  view genomic region     (about GC identifiers)

Start:
6,411,644 bp from pter      End:
6,416,228 bp from pter
Size:
4,585 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: ASM_HUMAN, P17405 (See protein sequence)
Recommended Name: Sphingomyelin phosphodiesterase precursor  
Size: 629 amino acids; 69752 Da
Subunit: Monomer
Miscellaneous: There are two types of sphingomyelinases: ASM (acid), and NSM (neutral)
Secondary accessions: A8K8M3 E9PKS3 P17406 Q13811 Q16837 Q16841
Alternative splicing: 4 isoforms:  P17405-1   P17405-2   P17405-3   P17405-4   (Low abundance (<1%))

Explore the universe of human proteins at neXtProt for SMPD1: NX_P17405

Explore proteomics data for SMPD1 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn86, Asn175, Asn335, Asn395, Asn520
  • Modification sites at PhosphoSitePlus

  • See SMPD1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_000534.3  NP_001007594.2  

    ENSEMBL proteins: 
     ENSP00000340409   ENSP00000431479   ENSP00000434353   ENSP00000435350   ENSP00000435950  
     ENSP00000432625   ENSP00000436278   ENSP00000299397   ENSP00000349203  
    Reactome Protein details: P17405

    SMPD1 Human Recombinant Protein Products:

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    OriGene Protein Over-expression Lysate for SMPD1
    OriGene Custom MassSpec
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    Novus Biologicals SMPD1 Protein
    Novus Biologicals SMPD1 Lysate
    Sino Biological Recombinant Protein for SMPD1
    Sino Biological Cell Lysate for SMPD1
    Browse ProSpec Recombinant Proteins
    Browse Proteins at Cloud-Clone Corp.

     
    Search eBioscience for Proteins for SMPD1 

    SMPD1 Antibody Products:

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    Search eBioscience for ELISAs for SMPD1 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    4 InterPro protein domains:
     IPR011160 Sphingomy_PDE
     IPR004843 PEstase_dom
     IPR011001 Saposin-like
     IPR008139 SaposinB

    Graphical View of Domain Structure for InterPro Entry P17405

    ProtoNet protein and cluster: P17405

    1 Blocks protein domain: IPB008139 Saposin B

    UniProtKB/Swiss-Prot: ASM_HUMAN, P17405
    Similarity: Belongs to the acid sphingomyelinase family
    Similarity: Contains 1 saposin B-type domain


    Find genes that share domains with SMPD1           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: ASM_HUMAN, P17405
    Function: Converts sphingomyelin to ceramide. Also has phospholipase C activities toward
    1,2-diacylglycerolphosphocholine and 1,2-diacylglycerolphosphoglycerol. Isoform 2 and isoform 3 have lost
    catalytic activity
    Catalytic activity: Sphingomyelin + H(2)O = N-acylsphingosine + phosphocholine

         Genatlas biochemistry entry for SMPD1:
    sphingomyelin phosphodiesterase 1,lysosomal (acid sphingomyelinase),hydrolyzing sphingomyelin to ceramide and
    phosphocholine,activated by TNFRSF1A and initiating the apoptotic pathway

         Enzyme Number (IUBMB): EC 3.1.4.121

         Gene Ontology (GO): 4 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004767sphingomyelin phosphodiesterase activity IEA--
    GO:0005515protein binding IPI--
    GO:0016787hydrolase activity ----
    GO:0016798hydrolase activity, acting on glycosyl bonds IEA--
         
    Find genes that share ontologies with SMPD1           About GenesLikeMe


    Phenotypes:
         4 GenomeRNAi human phenotypes for SMPD1:
     Decreased POU5F1-GFP protein e  Downregulation of NF-kappaB pa  Downregulation of NF-kappaB pa  Increased cell number in S and 

         11 MGI mutant phenotypes (inferred from 2 alleles(MGI details for Smpd1):
     behavior/neurological  cellular  growth/size/body  hematopoietic system  homeostasis/metabolism 
     immune system  liver/biliary system  mortality/aging  nervous system  reproductive system 
     respiratory system 

    Find genes that share phenotypes with SMPD1           About GenesLikeMe

    Animal Models:
         MGI mouse knock-outs for SMPD1: Smpd1tm1Wst Smpd1tm1Esc

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for SMPD1
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       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for SMPD1
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for SMPD1

    miRNA
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    hsa-miR-424 hsa-miR-15a hsa-miR-16 hsa-miR-195 hsa-miR-497 hsa-miR-15b
    SwitchGear 3'UTR luciferase reporter plasmidSMPD1 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat SMPD1

    Gene Editing
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    Clone
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    GenScript: all cDNA clones in your preferred vector (see all 2): SMPD1 (NM_000543)
    Sino Biological Human cDNA Clone for SMPD1
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for SMPD1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SMPD1

    Cell Line
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    ESI BIO PureStem Progenitor for SMPD1: 
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    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SMPD1


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    ASM_HUMAN, P17405: Lysosome
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    lysosome5
    vacuole5
    endosome2
    extracellular2
    mitochondrion2
    plasma membrane2
    cytoskeleton1
    cytosol1
    endoplasmic reticulum1
    nucleus1

    Gene Ontology (GO): 3 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005615extracellular space IEA--
    GO:0042599lamellar body IEA--
    GO:0043202lysosomal lumen TAS--

    Find genes that share ontologies with SMPD1           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for SMPD1 About   (see all 18)  
    See pathways by source

    SuperPathContained pathways About
    1Sphingolipid metabolism
    Sphingolipid metabolism0.61
    Glycosphingolipid metabolism0.56
    Sphingolipid metabolism0.61
    2Metabolism
    Metabolism0.38
    Metabolism of lipids and lipoproteins0.37
    Metabolic pathways0.38
    3Ceramide Pathway
    Ceramide Pathway0.32
    TNF-Induced Apoptosis Implicating Sphingolipids0.32
    4FAS (CD95) signaling pathway
    TRAIL signaling pathway0.30
    FAS (CD95) signaling pathway0.30
    5NGF Pathway
    NGF Pathway0.75


    Find genes that share SuperPaths with SMPD1           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    Selected Downloadable PowerPoint Slides of GeneGlobe Pathway Central Maps for SMPD1 (see all 9)
        Caspase Cascade
    S-1P Stimulated Signaling
    TNF-Induced Apoptosis Implicating Sphingolipids
    LDL Oxidation in Atherogenesis
    Fas Signaling

    1 Cell Signaling Technology (CST) Pathway for SMPD1
        Ca, cAMP and Lipid Signaling

    Selected BioSystems Pathways for SMPD1 (see all 7)
        Ovarian Infertility Genes
    sphingomyelin metabolism/ceramide salvage
    TRAIL signaling pathway
    IL2 signaling events mediated by PI3K
    Ceramide signaling pathway


    1 Reactome Pathway for SMPD1
        Glycosphingolipid metabolism


    3 Kegg Pathways  (Kegg details for SMPD1):
        Sphingolipid metabolism
    Metabolic pathways
    Lysosome

        Pathway & Disease-focused RT2 Profiler PCR Array including SMPD1: 
              Molecular Toxicology PathwayFinder 384HT in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for SMPD1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for SMPD1 (P174051, 2, 3 ENSP000003404094) via UniProtKB, MINT, STRING, and/or I2D (see all 70)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    CASP7P552101, 2, 3EBI-7095800,EBI-523958 MINT-8095356 MINT-8095286 MINT-8095296 MINT-8095342 MINT-8095383 MINT-8095372 I2D: score=1 
    CASP8Q147902, 3, ENSP000003512734MINT-8095252 MINT-8095356 MINT-8095243 I2D: score=1 STRING: ENSP00000351273
    ANXA7P200732, 3MINT-8248724 I2D: score=2 
    DUSP23Q9BVJ72, 3MINT-8254754 I2D: score=2 
    NR1H2P550552, 3MINT-8263940 I2D: score=2 
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    Gene Ontology (GO): Selected biological process terms (see all 15):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006665sphingolipid metabolic process TAS--
    GO:0006684sphingomyelin metabolic process TAS7670466
    GO:0006685sphingomyelin catabolic process IEA--
    GO:0006687glycosphingolipid metabolic process TAS--
    GO:0007165signal transduction TAS7670466

    Find genes that share ontologies with SMPD1           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Enzo Life Sciences drugs & compounds for SMPD1
      Browse compounds at ApexBio 

    Browse Tocris compounds for SMPD1 (ASM)

    Selected HMDB Compounds for SMPD1 (see all 152)    About this table
    CompoundSynonyms CAS #PubMed Ids
    3-O-Sulfogalactosylceramide (d18:1/12:0)Sulfatide (d18:1/12:0) (see all 13)852100-88-0--
    3-O-Sulfogalactosylceramide (d18:1/14:0)Sulfatide (d18:1/14:0) (see all 13)----
    3-O-Sulfogalactosylceramide (d18:1/16:0)Sulfatide (d18:1/16:0) (see all 13)862509-48-6--
    3-O-Sulfogalactosylceramide (d18:1/18:0)Sulfatide (d18:1/18:0) (see all 13)244215-65-4--
    3-O-Sulfogalactosylceramide (d18:1/18:1(9Z))Sulfatide (d18:1/18:1(9Z)) (see all 13)----
    3-O-Sulfogalactosylceramide (d18:1/20:0)Sulfatide (d18:1/20:0) (see all 13)265096-81-9--
    3-O-Sulfogalactosylceramide (d18:1/22:0)Sulfatide (d18:1/22:0) (see all 13)265096-83-1--
    3-O-Sulfogalactosylceramide (d18:1/24:0)Sulfatide (d18:1/24:0) (see all 16)151122-71-3--
    3-O-Sulfogalactosylceramide (d18:1/24:1(15Z))Sulfatide (d18:1/24:1(15Z)) (see all 13)151057-28-2--
    3-O-Sulfogalactosylceramide (d18:1/26:1(17Z))Sulfatide (d18:1/26:1(17Z)) (see all 13)928346-40-1--

    1 DrugBank Compound for SMPD1    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    DesipramineDemethylimipramine (see all 11)50-47-5targetinhibitor7945993 20502000 16803890 14689449 15705795 14960314

    Selected Novoseek inferred chemical compound relationships for SMPD1 gene (see all 48)    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    ceramide 94.5 266 9516458 (6), 15888438 (5), 19635928 (5), 16636669 (4) (see all 99)
    fantofarone 86.4 6 10930579 (1), 9716505 (1), 17329567 (1), 15201971 (1) (see all 5)
    ceramides 72.1 8 16034716 (2), 9500792 (1), 17329567 (1), 19416641 (1) (see all 6)
    phosphorylcholine 71.6 27 8053910 (1), 7727545 (1), 12631268 (1), 14515991 (1) (see all 16)
    ceramide 1-phosphate 69.2 6 14523050 (2), 15978590 (1), 18510950 (1), 19416641 (1)
    glucosylceramide 68.4 5 15271800 (2), 12586734 (1), 15679111 (1)
    desipramine 63.4 20 16803890 (3), 15705795 (2), 7945993 (1), 14689449 (1) (see all 12)
    sphingosine 63.1 4 16034716 (2), 18547682 (1), 12485859 (1)
    mannose 6-phosphate 61.8 2 16787399 (2)
    myriocin 61.5 1 16131844 (1)



    Find genes that share compounds with SMPD1           About GenesLikeMe



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for SMPD1 gene (2 alternative transcripts): 
    NM_000543.4  NM_001007593.2  

    Unigene Cluster for SMPD1:

    Sphingomyelin phosphodiesterase 1, acid lysosomal
    Hs.498173  [show with all ESTs]
    Unigene Representative Sequence: NM_000543
    12 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000342245(uc021qcz.1 uc001mcv.2 uc009yew.3 uc001mcw.3 uc021qda.1)
    ENST00000533196 ENST00000530395 ENST00000534405 ENST00000527275 ENST00000533123
    ENST00000531303 ENST00000526280 ENST00000531336 ENST00000532367 ENST00000299397
    ENST00000356761(uc009yex.3)
    miRNA
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    hsa-miR-424 hsa-miR-15a hsa-miR-16 hsa-miR-195 hsa-miR-497 hsa-miR-15b
    SwitchGear 3'UTR luciferase reporter plasmidSMPD1 3' UTR sequence
    Inhib. RNA
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    Primer
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      QuantiTect SYBR Green Assays in human, mouse, rat SMPD1
      QuantiFast Probe-based Assays in human, mouse, rat SMPD1

    Additional mRNA sequence: 

    AB209775.1 AK292388.1 HQ132745.1 HQ132746.1 HQ132747.1 HQ132748.1 M59916.1 X52678.1 
    X52679.1 X59960.1 

    11 DOTS entries:

    DT.97789320  DT.87017024  DT.95141668  DT.92431744  DT.95141654  DT.95141666  DT.95259806  DT.100788912 
    DT.100788914  DT.120699666  DT.95141656 

    Selected AceView cDNA sequences (see all 259):

    BG939305 BM724639 BU845962 R85045 BM694250 BQ681310 AI708247 CA449771 
    CR615854 BU727943 CK904688 AI223155 BQ187351 BX280171 BI868721 BM977655 
    CN482223 BQ684187 CA417896 BU625428 BM558202 BU197048 CD365316 BQ021596 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

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    SMPD1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GAGTAGAGGC
    SMPD1 Expression
    About this image


    SMPD1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 4) fully expand
     
     Brain (Nervous System)    fully expand to see all 4 entries
             Cerebral Cortex
     
     Neural Tube (Nervous System)    fully expand to see all 2 entries
             Metencephalon
     
     Blood (Hematopoietic System)
             T-Cytotoxic Cells Peripheral Blood
     
     Eye (Sensory Organs)
             Lens
    SMPD1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SMPD1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.498173
        Pathway & Disease-focused RT2 Profiler PCR Array including SMPD1: 
              Molecular Toxicology PathwayFinder 384HT in human mouse rat

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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals and fungi.

    Orthologs for SMPD1 gene from Selected species (see all 20)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Smpd11 , 5 sphingomyelin phosphodiesterase 1, acid lysosomal1, 5 82.93(n)1
    83.04(a)1
      7 (55.90 cM)5
    205971  NM_011421.21  NP_035551.11 
     1055543605 
    chicken
    (Gallus gallus)
    Aves SMPD11 sphingomyelin phosphodiesterase 1, acid lysosomal 68.22(n)
    66.12(a)
      419077  XM_003640615.2  XP_003640663.2 
    lizard
    (Anolis carolinensis)
    Reptilia SMPD16
    sphingomyelin phosphodiesterase 1, acid lysosomal
    66(a)
    1 ↔ 1
    GL344762.1(9508-14800)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.21472 Xenopus laevis transcribed sequence with weak similarity more 79.79(n)    BQ399327.1 
    zebrafish
    (Danio rerio)
    Actinopterygii CD597777.12   -- 73.1(n)    CD597777.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG33761 , 3 sphingomyelin phosphodiesterase3
    CG33761
    38(a)
    (best of 3)3
    52.78(n)1
    42.61(a)1
      60C43
    378841  NM_138060.21  NP_611904.11 
    worm
    (Caenorhabditis elegans)
    Secernentea B0252.23
    asm-21
    Spingomyelin phosphodiesterase3
    asm-21
    34(a)
    (best of 3)3
    45.49(n)1
    38.58(a)1
      II(6910015-6912507)3
    1813231  NM_077493.41  NP_509894.21 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes PPN16
    Vacuolar endopolyphosphatase with a role in phosph...
    13(a)
    1 → many
    IV(1362878-1364902) YDR452W


    ENSEMBL Gene Tree for SMPD1 (if available)
    TreeFam Gene Tree for SMPD1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SMPD1 gene
    SMPDL3A2  SMPDL3B2  
    1 SIMAP similar gene for SMPD1 using alignment to 17 protein entries:     ASM_HUMAN (see all proteins):
    ASM

    Find genes that share paralogs with SMPD1           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Polymorphic Variants from UniProtKB/Swiss-Prot
    ASM_HUMAN, P17405: A common polymorphism arises from a variable number of hexanucleotide repeat sequence within the
    signal peptide region


    Selected SNPs for SMPD1 (see all 385)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 11 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0609074
    Niemann-Pick disease B (NPDB)4--see VAR_0609072 C R mis40--------
    VAR_0050584
    Niemann-Pick disease B (NPDB)4--see VAR_0050582 G R mis40--------
    VAR_0609164
    Niemann-Pick disease A (NPDA)4--see VAR_0609162 A E mis40--------
    VAR_0609064
    Niemann-Pick disease A (NPDA)4--see VAR_0609062 H R mis40--------
    VAR_0608844
    Niemann-Pick disease B (NPDB)4--see VAR_0608842 G D mis40--------
    VAR_0609054
    Niemann-Pick disease B (NPDB)4--see VAR_0609052 A V mis40--------
    VAR_0608924
    Niemann-Pick disease B (NPDB)4--see VAR_0608922 R H mis40--------
    VAR_0609034
    Niemann-Pick disease B (NPDB)4--see VAR_0609032 S P mis40--------
    VAR_0684374
    Niemann-Pick disease B (NPDB)4--see VAR_0684372 V M mis40--------
    VAR_0684384
    Niemann-Pick disease B (NPDB)4--see VAR_0684382 H R mis40--------

    HapMap Linkage Disequilibrium report for SMPD1 (6411644 - 6416228 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for SMPD1: --
    Human Gene Mutation Database (HGMD): SMPD1
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing SMPD1
    DNA2.0 Custom Variant and Variant Library Synthesis for SMPD1

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 607608   
    OMIM disorders: 257200  607616  
    UniProtKB/Swiss-Prot: ASM_HUMAN, P17405
  • Niemann-Pick disease A (NPDA) [MIM:257200]: An early-onset lysosomal storage disorder caused by failure
    to hydrolyze sphingomyelin to ceramide. It results in the accumulation of sphingomyelin and other metabolically
    related lipids in reticuloendothelial and other cell types throughout the body, leading to cell death.
    Niemann-Pick disease type A is a primarily neurodegenerative disorder characterized by onset within the first
    year of life, mental retardation, digestive disorders, failure to thrive, major hepatosplenomegaly, and severe
    neurologic symptoms. The severe neurological disorders and pulmonary infections lead to an early death, often
    around the age of four. Clinical features are variable. A phenotypic continuum exists between type A (basic
    neurovisceral) and type B (purely visceral) forms of Niemann-Pick disease, and the intermediate types encompass a
    cluster of variants combining clinical features of both types A and B. Note=The disease is caused by mutations
    affecting the gene represented in this entry
  • Niemann-Pick disease B (NPDB) [MIM:607616]: A late-onset lysosomal storage disorder caused by failure to
    hydrolyze sphingomyelin to ceramide. It results in the accumulation of sphingomyelin and other metabolically
    related lipids in reticuloendothelial and other cell types throughout the body, leading to cell death. Clinical
    signs involve only visceral organs. The most constant sign is hepatosplenomegaly which can be associated with
    pulmonary symptoms. Patients remain free of neurologic manifestations. However, a phenotypic continuum exists
    between type A (basic neurovisceral) and type B (purely visceral) forms of Niemann-Pick disease, and the
    intermediate types encompass a cluster of variants combining clinical features of both types A and B. In
    Niemann-Pick disease type B, onset of the first symptoms occurs in early childhood and patients can survive into
    adulthood. Note=The disease is caused by mutations affecting the gene represented in this entry

  • 11 diseases for SMPD1:    
    About MalaCards
    niemann-pick disease    sea-blue histiocytosis    acid sphingomyelinase deficiency    narcissistic personality disorder
    mucolipidosis ii    pick's disease    mucolipidosis    hemihypertrophy
    pulmonary edema    familial adenomatous polyposis    beckwith-wiedemann syndrome

    3 diseases from the University of Copenhagen DISEASES database for SMPD1:
    Niemann-Pick disease     Narcissistic personality disorder     Systemic mastocytosis

    Find genes that share disorders with SMPD1           About GenesLikeMe

    Selected Novoseek inferred disease relationships for SMPD1 gene (see all 35)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    niemann-pick diseases 97.9 123 16099409 (3), 19944693 (2), 17011332 (2), 11023983 (2) (see all 71)
    niemann-picks disease type b 94 7 10515006 (1), 12436303 (1), 8225311 (1), 12142792 (1) (see all 7)
    i-cell disease 71.1 2 15997205 (1), 8106525 (1)
    niemann-picks disease type c 59.2 3 16143556 (1), 8025130 (1), 16802107 (1)
    lysosomal storage diseases 49.9 2 1618760 (1), 7600574 (1)
    lipidosis 47.5 3 14736491 (2), 2153272 (1)
    hemihypertrophy 41 1 11310411 (1)
    necrosis 36.2 15 11255263 (2), 7981153 (2), 16803890 (1), 10601312 (1) (see all 10)
    oligodendroglioma 34.9 1 15086520 (1)
    beckwith-wiedemann syndrome 27.3 4 11173664 (2), 11310411 (1)

    Genatlas disease: SMPD1
    Niemann-Pick disease,types A & B

    GeneTests: SMPD1
    GeneReviews: SMPD1
    Genetic Association Database (GAD): SMPD1
    Human Genome Epidemiology (HuGE) Navigator: SMPD1 (8 documents)

    Export disorders for SMPD1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for SMPD1 gene, integrated from 10 sources (see all 346):
    (articles sorted by number of sources associating them with SMPD1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Identification and expression of five mutations in the human acid sphingomyelinase gene causing types A and B Niemann-Pick disease. Molecular evidence for genetic heterogeneity in the neuronopathic and non-neuronopathic forms. (PubMed id 1618760)1, 2, 9 Takahashi T.... Schuchman E.H. (J. Biol. Chem. 1992)
    2. Structural organization and complete nucleotide sequence of the gene encoding human acid sphingomyelinase (SMPD1). (PubMed id 1740330)1, 2, 9 Schuchman E.H.... Desnick R.J. (Genomics 1992)
    3. Niemann-Pick disease: a frequent missense mutation in the acid sphingomyelinase gene of Ashkenazi Jewish type A and B patients. (PubMed id 2023926)1, 2, 9 Levran O.... Schuchman E.H. (Proc. Natl. Acad. Sci. U.S.A. 1991)
    4. Sphingomyelin phosphodiesterase-1 (SMPD1) coding variants do not contribute to low levels of high-density lipoprotein cholesterol. (PubMed id 18088425)1, 2, 9 Dastani Z.... Marcil M. (BMC Med. Genet. 2007)
    5. Functional characterization of the N-glycosylation sites of human acid sphingomyelinase by site-directed mutagenesis. (PubMed id 9030779)1, 2, 9 Ferlinz K....Sandhoff K. (Eur. J. Biochem. 1997)
    6. Identification and expression of a common missense mutation (L302P) in the acid sphingomyelinase gene of Ashkenazi Jewish type A Niemann- Pick disease patients. (PubMed id 1391960)1, 2, 9 Levran O.... Schuchman E.H. (Blood 1992)
    7. Functional in vitro characterization of 14 SMPD1 mutations identified in Italian patients affected by Niemann Pick type B disease. (PubMed id 16010684)1, 2, 9 Dardis A....Pittis M.G. (Hum. Mutat. 2005)
    8. Acid sphingomyelinase: identification of nine novel mutations among Italian Niemann Pick type B patients and characterization of in vivo functional in-frame start codon. (PubMed id 15241805)1, 2, 9 Pittis M.G.... Bembi B. (Hum. Mutat. 2004)
    9. Identification and expression of a missense mutation (Y446C) in the acid sphingomyelinase gene from a Japanese patient with type A Niemann-Pick disease. (PubMed id 8693491)1, 2, 9 Takahashi T.... Takada G. (Tohoku J. Exp. Med. 1995)
    10. Acid sphingomyelinase deficiency. Phenotype variability with prevalence of intermediate phenotype in a series of twenty-five Czech and Slovak patients. A multi-approach study. (PubMed id 15877209)1, 2, 9 Pavluu-Pereira H....Elleder M. (J. Inherit. Metab. Dis. 2005)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 6609 HGNC: 11120 AceView: SMPD1 Ensembl:ENSG00000166311 euGenes: HUgn6609
    ECgene: SMPD1 Kegg: 6609 H-InvDB: SMPD1

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
    About This Section

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    NameDescription
    PharmGKB entry for SMPD1 Pharmacogenomics, SNPs, Pathways
    GeneReviewshttp://www.ncbi.nlm.nih.gov/books/NBK1116/?term=SMPD1[genesymbol]

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for SMPD1 gene:
    Search GeneIP for patents involving SMPD1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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