U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    SMPD2 sphingomyelin phosphodiesterase 2 [ Homo sapiens (human) ]

    Gene ID: 6610, updated on 27-Nov-2024

    Summary

    Official Symbol
    SMPD2provided by HGNC
    Official Full Name
    sphingomyelin phosphodiesterase 2provided by HGNC
    Primary source
    HGNC:HGNC:11121
    See related
    Ensembl:ENSG00000135587 MIM:603498; AllianceGenome:HGNC:11121
    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
    ISC1; NSMASE; NSMASE1
    Summary
    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]
    Expression
    Broad expression in testis (RPKM 17.9), skin (RPKM 6.8) and 24 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SMPD2 in Genome Data Viewer
    Location:
    6q21
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (109440724..109443919)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (110618762..110621957)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (109761927..109765122)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene coiled-coil domain containing 162, pseudogene Neighboring gene OCT4 hESC enhancer GRCh37_chr6:109649788-109650315 Neighboring gene ribosomal protein L7 pseudogene 28 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17458 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:109703563-109704072 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24923 Neighboring gene Sharpr-MPRA regulatory region 15445 Neighboring gene CD164 molecule Neighboring gene ReSE screen-validated silencer GRCh37_chr6:109761883-109762088 Neighboring gene peptidylprolyl isomerase like 6 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24924 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24925 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17460 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24926 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24927 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:109775979-109776487 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17462 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24928 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24929 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24930 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:109801913-109802414 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17463 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17464 Neighboring gene microtubule associated monooxygenase, calponin and LIM domain containing 1 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:109811810-109812520 Neighboring gene ZBTB24 divergent transcript Neighboring gene zinc finger and BTB domain containing 24 Neighboring gene adenylate kinase 9

    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
    Many sequence variants affecting diversity of adult human height.
    EBI GWAS Catalog

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env Treatment of cells with sphingomyelinase inhibits viral fusion after the engagement of HIV-1 gp120 with CD4 and sphingomyelinase restricts CD4 mobility. This inhibition is dependent on CD4 expression levels 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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    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 
    Process Evidence Code Pubs
    involved_in ceramide biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in sphingolipid catabolic process IBA
    Inferred from Biological aspect of Ancestor
    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
     
    Component Evidence Code Pubs
    is_active_in caveola IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    is_active_in cell periphery IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    is_active_in endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    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 2
    Names
    N-SMase
    lyso-PAF-PLC
    lyso-platelet-activating factor-phospholipase C
    neutral sphingomyelinase
    NP_003071.2
    XP_011534381.1
    XP_054212238.1

    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_003080.3NP_003071.2  sphingomyelin phosphodiesterase 2

      See identical proteins and their annotated locations for NP_003071.2

      Status: VALIDATED

      Source sequence(s)
      AJ222801, AL109947, CA314251, DA672570
      Consensus CDS
      CCDS5075.1
      UniProtKB/Swiss-Prot
      O60906, Q5TED1, Q9BWR3
      UniProtKB/TrEMBL
      B2R8U8
      Related
      ENSP00000258052.3, ENST00000258052.8
      Conserved Domains (1) summary
      cl00490
      Location:14279
      EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      109440724..109443919
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011536079.2XP_011534381.1  sphingomyelin phosphodiesterase 2 isoform X1

      Conserved Domains (1) summary
      cl00490
      Location:6174
      EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

    RNA

    1. XR_942566.3 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      110618762..110621957
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054356263.1XP_054212238.1  sphingomyelin phosphodiesterase 2 isoform X1

    RNA

    1. XR_008487431.1 RNA Sequence