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SMPD2 Gene

protein-coding   GIFtS: 61
GCID: GC06P109761

Sphingomyelin Phosphodiesterase 2, Neutral Membrane (Neutral...

  See SMPD2-related disease
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 2, Neutral Membrane (Neutral
Sphingomyelinase)1 2
     NSMASE12
Lyso-Platelet-Activating Factor-Phospholipase C2 3     lyso-PAF-PLC2
Neutral Sphingomyelinase2 3     Sphingomyelin Phosphodiesterase 22
N-SMase2 3     EC 3.1.4.123
ISC12     Lyso-PAF-PLC3
NSMASE2     nSMase3

External Ids:    HGNC: 111211   Entrez Gene: 66102   Ensembl: ENSG000001355877   OMIM: 6034985   UniProtKB: O609063   

Export aliases for SMPD2 gene to outside databases

Previous GC identifers: GC06P109597 GC06P109784 GC06P109807 GC06P109868 GC06P107328


(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 SMPD2 Gene:
This gene encodes a protein which was initially identified as a sphingomyelinase based on sequence similarity
between bacterial sphingomyelinases and a yeast protein. Subsequent studies showed that its biological function
is less likely to be as a sphingomyelinase and instead as a lysophospholipase. (provided by RefSeq, Oct 2009)

GeneCards Summary for SMPD2 Gene:
SMPD2 (sphingomyelin phosphodiesterase 2, neutral membrane (neutral sphingomyelinase)) is a protein-coding gene. Diseases associated with SMPD2 include lipid storage disease. GO annotations related to this gene include sphingomyelin phosphodiesterase activity.

UniProtKB/Swiss-Prot: NSMA_HUMAN, O60906
Function: Converts sphingomyelin to ceramide. Hydrolyze 1-acyl-2-lyso-sn-glycero-3-phosphocholine (lyso-PC) and
1-O-alkyl-2-lyso-sn-glycero-3-phosphocholine (lyso-platelet-activating factor). The physiological substrate seems
to be Lyso-PAF

Gene Wiki entry for SMPD2 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_000006.11  NT_025741.16  NC_018917.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the SMPD2 gene promoter:
         AP-1   ATF-2   MyoD   c-Jun   NF-kappaB   NF-kappaB1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSMPD2 promoter sequence
   Search Chromatin IP Primers for SMPD2

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SMPD2


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

Entrez Gene cytogenetic band: 6q21   Ensembl cytogenetic band:  6q21   HGNC cytogenetic band: 6q21

SMPD2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SMPD2 gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06P109761:  view genomic region     (about GC identifiers)

Start:
109,761,931 bp from pter      End:
109,765,122 bp from pter
Size:
3,192 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: NSMA_HUMAN, O60906 (See protein sequence)
Recommended Name: Sphingomyelin phosphodiesterase 2  
Size: 423 amino acids; 47646 Da
Cofactor: Magnesium
Secondary accessions: Q5TED1 Q9BWR3

Explore the universe of human proteins at neXtProt for SMPD2: NX_O60906

Explore proteomics data for SMPD2 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See SMPD2 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_003071.2  
    ENSEMBL proteins: 
     ENSP00000258052   ENSP00000399731  
    Reactome Protein details: O60906

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    Browse Proteins at Cloud-Clone Corp.

     
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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    1 InterPro protein domain:
     IPR005135 Endo/exonuclease/phosphatase

    Graphical View of Domain Structure for InterPro Entry O60906

    ProtoNet protein and cluster: O60906

    UniProtKB/Swiss-Prot: NSMA_HUMAN, O60906
    Similarity: Belongs to the neutral sphingomyelinase family


    Find genes that share domains with SMPD2           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: NSMA_HUMAN, O60906
    Function: Converts sphingomyelin to ceramide. Hydrolyze 1-acyl-2-lyso-sn-glycero-3-phosphocholine (lyso-PC) and
    1-O-alkyl-2-lyso-sn-glycero-3-phosphocholine (lyso-platelet-activating factor). The physiological substrate seems
    to be Lyso-PAF
    Catalytic activity: Sphingomyelin + H(2)O = N-acylsphingosine + phosphocholine
    Biophysicochemical properties: pH dependence: Optimum pH is 6.5-7.5;

         Enzyme Number (IUBMB): EC 3.1.4.121

         Gene Ontology (GO): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004767sphingomyelin phosphodiesterase activity IEA--
    GO:0046872metal ion binding IEA--
         
    Find genes that share ontologies with SMPD2           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for SMPD2:
     Upregulation of Wnt/beta-caten 

         2 MGI mutant phenotypes (inferred from 1 allele(MGI details for Smpd2):
     homeostasis/metabolism  normal 

    Find genes that share phenotypes with SMPD2           About GenesLikeMe

    Animal Models:
         MGI mouse knock-out Smpd2tm1Wst for SMPD2

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for SMPD2
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    (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
    NSMA_HUMAN, O60906: Membrane; Multi-pass membrane protein
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane4
    cytosol2
    mitochondrion2
    nucleus2
    endoplasmic reticulum1
    extracellular1
    golgi apparatus1
    lysosome1
    vacuole1

    Gene Ontology (GO): 4 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005886plasma membrane TAS--
    GO:0005887integral component of plasma membrane TAS9520418
    GO:0005901caveola IEA--
    GO:0016020membrane ----

    Find genes that share ontologies with SMPD2           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 SMPD2 About   (see all 17)  
    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
    3p75(NTR)-mediated signaling
    Ceramide signalling0.00
    p75(NTR)-mediated signaling
    4NGF Pathway
    NGF Pathway0.75
    5p75 NTR receptor-mediated signalling
    p75 NTR receptor-mediated signalling0.74


    Find genes that share SuperPaths with SMPD2           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    Selected Downloadable PowerPoint Slides of GeneGlobe Pathway Central Maps for SMPD2 (see all 7)
        Caspase Cascade
    UVA-Induced MAPK Signaling
    S-1P Stimulated Signaling
    UVC-Induced MAPK Signaling
    NGF Pathway

    2 Cell Signaling Technology (CST) Pathways for SMPD2
        Apoptosis and Autophagy
    Ca, cAMP and Lipid Signaling

    3 BioSystems Pathways for SMPD2
        sphingomyelin metabolism/ceramide salvage
    p75(NTR)-mediated signaling
    TNF receptor signaling pathway


    2 Reactome Pathways for SMPD2
        Glycosphingolipid metabolism
    Ceramide signalling


    2 Kegg Pathways  (Kegg details for SMPD2):
        Sphingolipid metabolism
    Metabolic pathways

    UniProtKB/Swiss-Prot: NSMA_HUMAN, O60906
    Pathway: Lipid metabolism; sphingolipid metabolism

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for SMPD2
    Interactions:

        GeneGlobe Interaction Network for SMPD2

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

    Selected Interacting proteins for SMPD2 (O609063 ENSP000002580524) via UniProtKB, MINT, STRING, and/or I2D (see all 131)

    InteractantInteraction Details
    GeneCardExternal ID(s)
    PIK3CGP487363, ENSP000003521214I2D: score=2 STRING: ENSP00000352121
    FA2HQ7L5A83, ENSP000002193684I2D: score=1 STRING: ENSP00000219368
    PPP6CO007433, ENSP000003921474I2D: score=1 STRING: ENSP00000392147
    SPTLC1O152693, ENSP000002625544I2D: score=1 STRING: ENSP00000262554
    SC5DO758453, ENSP000002640274I2D: score=1 STRING: ENSP00000264027
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 8):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006665sphingolipid metabolic process TAS--
    GO:0006684sphingomyelin metabolic process TAS9520418
    GO:0006687glycosphingolipid metabolic process TAS--
    GO:0009612response to mechanical stimulus IEA--
    GO:0044281small molecule metabolic process TAS--

    Find genes that share ontologies with SMPD2           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
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for SMPD2 (NSMA)

    Selected HMDB Compounds for SMPD2 (see all 154)    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--

    Selected Novoseek inferred chemical compound relationships for SMPD2 gene (see all 20)    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    ceramide 92 68 14871831 (3), 15642349 (3), 15741222 (3), 11901191 (2) (see all 39)
    c2ceramide 75.3 3 16777978 (3)
    manumycin 73.7 3 14563682 (1), 12270134 (1), 11597471 (1)
    phosphorylcholine 62.3 2 16517606 (1), 9763522 (1)
    lactosylceramide 54.4 1 16691498 (1)
    sphingosine 38.6 1 8379453 (1)
    sterol 36.5 1 9763522 (1)
    n acetylcysteine 32 4 12387875 (1), 17707397 (1)
    lipid 29.7 5 11001565 (1), 19572936 (1), 8379453 (1), 9520418 (1)
    dithiothreitol 29.7 3 9195931 (1), 10832103 (1)



    Find genes that share compounds with SMPD2           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 SMPD2 gene: 
    NM_003080.2  

    Unigene Cluster for SMPD2:

    Sphingomyelin phosphodiesterase 2, neutral membrane (neutral sphingomyelinase)
    Hs.55235  [show with all ESTs]
    Unigene Representative Sequence: NM_003080
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000258052(uc010kdq.3 uc003pti.3) ENST00000439615 ENST00000458487

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    Additional mRNA sequence: 

    AJ222801.1 AK310148.1 AK313515.1 BC000038.2 

    3 DOTS entries:

    DT.311601  DT.40132320  DT.95264543 

    Selected AceView cDNA sequences (see all 88):

    BM790786 CR591613 AI380803 BU726050 CA314251 BI869842 AI274249 AI420934 
    BM785558 AI083508 BM840848 BM544667 BU726647 BM769617 BM769176 BM966928 
    BM769177 BM795556 BM769106 BQ083596 AL537110 BP363117 AA554704 BP371432 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for SMPD2 (see all 6)    About this scheme

    ExUns: 1a · 1b · 1c ^ 2a · 2b · 2c ^ 3a · 3b ^ 4a · 4b ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10a · 10b
    SP1:                    -                       -     -                                                         
    SP2:                    -                       -     -                                                         
    SP3:                                            -                                                               
    SP4:                                            -     -                                                         
    SP5:                                                                                                            


    ECgene alternative splicing isoforms for SMPD2

    (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)
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    SMPD2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TGCTAGGAAG
    SMPD2 Expression
    About this image


    SMPD2 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 5) fully expand
     
     Neural Tube (Nervous System)
             Telencephalon
     
     Brain (Nervous System)
             Cerebral Cortex
     
     Lung (Respiratory System)
     
     Spinal Cord (Nervous System)
     
     Stomach (Gastrointestinal Tract)
    SMPD2 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SMPD2 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.55235
        Custom PCR Arrays for SMPD2
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SMPD2

    (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 SMPD2 gene from Selected species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Smpd21 , 5 sphingomyelin phosphodiesterase 2, neutral1, 5 81.86(n)1
    77.09(a)1
      10 (22.42 cM)5
    205981  NM_009213.21  NP_033239.11 
     414856425 
    chicken
    (Gallus gallus)
    Aves SMPD21 sphingomyelin phosphodiesterase 2, neutral membrane more 65.3(n)
    56.92(a)
      770663  XM_001232515.3  XP_001232516.1 
    lizard
    (Anolis carolinensis)
    Reptilia SMPD26
    sphingomyelin phosphodiesterase 2, neutral membran...
    45(a)
    1 ↔ 1
    4(124269525-124283302)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia smpd21 sphingomyelin phosphodiesterase 2, neutral membrane more 55.52(n)
    49.69(a)
      100145256  NM_001126737.1  NP_001120209.1 
    zebrafish
    (Danio rerio)
    Actinopterygii LOC7979141 sphingomyelin phosphodiesterase 2-like 54.99(n)
    49.84(a)
      797914  XM_001338333.4  XP_001338369.2 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG120341 , 3 sphingomyelin phosphodiesterase3
    CG120341
    34(a)3
    48.27(n)1
    36.92(a)1
      63B143
    383961  NM_139533.41  NP_647790.11 
    worm
    (Caenorhabditis elegans)
    Secernentea T27F6.61 , 3 T27F6.61 41(a)3
    49.83(n)1
    42.51(a)1
      I(12499033-12502413)3
    1731181  NM_060768.41  NP_493169.21 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes ISC1(YER019W)4 Mitochondrial membrane localized inositol phosphosphingolipid more   --   5(192797-194230) 856739  NP_010935.1 


    ENSEMBL Gene Tree for SMPD2 (if available)
    TreeFam Gene Tree for SMPD2 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section

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    (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)
    About This Section

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    Selected SNPs for SMPD2 (see all 22)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 6 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs14763861,2
    C,F,O,A,H--109764404(+) GTAGCC/TGGGAG 1 -- int117Minor allele frequency- T:0.06NS EA NA WA EU 2931
    rs2002575531,2
    --109764452(+) TCTCTG/TGCCCT 1 -- int10--------
    rs1998115811,2
    --109764516(+) CACTAC/TAGGCT 2 T I mis10--------
    rs14763871,2,,4
    C,F,A,H--109764535(+) CACAGA/G/TGGCAC 3 R S syn1 mis1 ese332EA NA MN NS WA CSA EU 8969
    rs2015576731,2
    --109764690(+) ACTCTC/TTCCTG 1 -- int10--------
    rs93868061,2,4
    ----see VAR_0503062 mis40--------
    rs10481971,2,4
    ----see VAR_0503052 mis40--------
    rs1463184701,2
    ----109764755(+) TGCTAA/CAGGAG 2 K Q mis10--------
    rs3770157321,2
    ----109764689(+) GACTCC/TCTCCT 1 -- int10--------
    rs3690420851,2
    ----109764623(+) CCCACA/GGTGAG 2 R G mis10--------

    HapMap Linkage Disequilibrium report for SMPD2 (109761931 - 109765122 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for SMPD2: --
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing SMPD2
    DNA2.0 Custom Variant and Variant Library Synthesis for SMPD2

    (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: 603498    OMIM disorders: --

    1 disease for SMPD2:    
    About MalaCards
    lipid storage disease

    1 disease from the University of Copenhagen DISEASES database for SMPD2:
    Niemann-Pick disease

    Find genes that share disorders with SMPD2           About GenesLikeMe

    7 Novoseek inferred disease relationships for SMPD2 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    necrosis 50.4 6 12531545 (1), 14689449 (1), 11001563 (1), 14670935 (1) (see all 6)
    tumors 28.6 5 12531545 (1), 14689449 (1), 11001563 (1), 14670935 (1) (see all 5)
    heart failure 8.48 2 11001563 (1), 9763522 (1)
    atherosclerosis 3.52 3 11001563 (2), 9763522 (1)
    leukemia 0 1 9556624 (1)
    stroke 0 2 11001563 (1), 9763522 (1)
    carcinoma 0 1 9556624 (1)

    Genetic Association Database (GAD): SMPD2
    Human Genome Epidemiology (HuGE) Navigator: SMPD2 (4 documents)

    Export disorders for SMPD2 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 SMPD2 gene, integrated from 10 sources (see all 117):
    (articles sorted by number of sources associating them with SMPD2)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Cloned mammalian neutral sphingomyelinase: functions in sphingolipid signaling? (PubMed id 9520418)1, 2, 3, 9 Tomiuk S.... Stoffel W. (Proc. Natl. Acad. Sci. U.S.A. 1998)
    2. Function of the cloned putative neutral sphingomyelinase as lyso- platelet activating factor-phospholipase C. (PubMed id 10608884)1, 2, 9 Sawai H.... Hannun Y.A. (J. Biol. Chem. 1999)
    3. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PubMed id 20628086)1, 4 Bailey S.D....Anand S. (Diabetes Care 2010)
    4. Sequential use of transcriptional profiling, expression quantitative trait mapping, and gene association implicates MMP20 in human kidney aging. (PubMed id 19834535)1, 4 Wheeler H.E....Kim S.K. (PLoS Genet. 2009)
    5. Many sequence variants affecting diversity of adult human height. (PubMed id 18391951)1, 4 Gudbjartsson D.F....Stefansson K. (Nat. Genet. 2008)
    6. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    7. Human immunodeficiency virus type 1 gp120 induces apoptosis in human primary neurons through redox-regulated activation of neutral sphingomyelinase. (PubMed id 15509740)1, 9 Jana A. and Pahan K. (J. Neurosci. 2004)
    8. Regulation of sphingomyelinases in cells of the oligodendrocyte lineage. (PubMed id 14689449)1, 9 Testai F.D....Dawson G. (J. Neurosci. Res. 2004)
    9. Transcriptional regulation of neutral sphingomyelinase 2 gene expression of a human breast cancer cell line, MCF-7, induced by the anti-cancer drug, daunorubicin. (PubMed id 19698806)1, 9 Ito H....Murate T. (Biochim. Biophys. Acta 2009)
    10. Aggregated low density lipoprotein induces tissue factor by inhibiting sphingomyelinase activity in human vascular smooth muscle cells. (PubMed id 19817993)1, 9 Camino-LA^pez S....Llorente-CortAcs V. (J. Thromb. Haemost. 2009)

    (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: 6610 HGNC: 11121 AceView: SMPD2 Ensembl:ENSG00000135587 euGenes: HUgn6610
    ECgene: SMPD2 Kegg: 6610 H-InvDB: SMPD2

    (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 SMPD2 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section

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    Patent Information for SMPD2 gene:
    Search GeneIP for patents involving SMPD2

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



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