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    SMPD1 sphingomyelin phosphodiesterase 1, acid lysosomal [ Homo sapiens (human) ]

    Gene ID: 6609, updated on 22-May-2013
    Official Symbol
    SMPD1provided by HGNC
    Official Full Name
    sphingomyelin phosphodiesterase 1, acid lysosomalprovided by HGNC
    Primary source
    HGNC:11120
    See related
    Ensembl:ENSG00000166311; HPRD:06353; MIM:607608; Vega:OTTHUMG00000165453
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    ASM; NPD; ASMASE
    Summary
    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]
    Location :
    11p15.4-p15.1
    Sequence :
    Chromosome: 11; NC_000011.9 (6411644..6416228)
    See SMPD1 in Epigenomics, MapViewer

    Chromosome 11 - NC_000011.9Genomic Context describing neighboring genes Neighboring gene cholecystokinin B receptor Neighboring gene protein kinase C, delta binding protein Neighboring gene amyloid beta (A4) precursor protein-binding, family B, member 1 (Fe65) Neighboring gene hemopexin

    GeneRIFs: Gene References Into Functions What's a GeneRIF?

    Niemann-Pick disease, type A

    Summary from GeneReviews: Acid Sphingomyelinase Deficiency Go to GeneReviews

    Disease Characteristics
    Acid sphingomyelinase (ASM) deficiency has been categorized in the past as either neuronopathic (Niemann-Pick disease type A [NPD-A]), with death in early childhood, or non-neuronopathic (Niemann-Pick disease type B [NPD-B]). While forms intermediate to these two extremes occur, all ASM deficiency that is not NPD-A is designated in this review as NPD-B, despite its wide range of manifestations and severity. The first symptom in NPD-A is hepatosplenomegaly, usually noted by age three months; over time the liver and spleen become massive. Psychomotor development progresses no further than the 12-month level, after which neurologic deterioration is relentless. A classic cherry-red spot of the macula of the retina, which may not be present in the first few months, is eventually present in all affected children. Interstitial lung disease caused by storage of sphingomyelin in pulmonary macrophages results in frequent respiratory infections and often respiratory failure. Most children succumb before the third year. NPD type B, later in onset and milder in manifestations than NPD type A, is characterized by hepatosplenomegaly with progressive hypersplenism and stable liver dysfunction, gradual deterioration in pulmonary function, and atherogenic lipid profile. Progressive and/or clinically significant neurologic manifestations occur infrequently. Survival to adulthood can occur.
    Diagnosis Testing
    The diagnosis of ASM deficiency is established when residual ASM enzyme activity in peripheral blood lymphocytes or cultured skin fibroblasts is less than 10% of controls. SMPD1 is the only gene known to be associated with ASM deficiency. Sequence analysis of SMPD1 detects mutations in more than 95% of individuals with enzymatically confirmed ASM deficiency. Targeted mutation analysis for common population-specific mutations is available for individuals of Ashkenazi Jewish background with NPD-A, individuals of North African descent with NPD-B, and certain other populations.
    Genetic Counseling
    Acid sphingomyelinase (ASM) deficiency is inherited in an autosomal recessive manner. At conception, each sib of an affected individual has a 25% chance of being affected, a 50% chance of being an asymptomatic carrier, and a 25% chance of being unaffected and not a carrier. Carrier testing for at-risk relatives is possible if both disease-causing alleles in the family are known. Prenatal diagnosis for pregnancies at 25% risk is possible by biochemical testing of ASM enzyme activity and/or by molecular genetic testing if both disease-causing alleles in the family are known.
    References

    Niemann-Pick disease, type B

    Summary from GeneReviews: Acid Sphingomyelinase Deficiency Go to GeneReviews

    Disease Characteristics
    Acid sphingomyelinase (ASM) deficiency has been categorized in the past as either neuronopathic (Niemann-Pick disease type A [NPD-A]), with death in early childhood, or non-neuronopathic (Niemann-Pick disease type B [NPD-B]). While forms intermediate to these two extremes occur, all ASM deficiency that is not NPD-A is designated in this review as NPD-B, despite its wide range of manifestations and severity. The first symptom in NPD-A is hepatosplenomegaly, usually noted by age three months; over time the liver and spleen become massive. Psychomotor development progresses no further than the 12-month level, after which neurologic deterioration is relentless. A classic cherry-red spot of the macula of the retina, which may not be present in the first few months, is eventually present in all affected children. Interstitial lung disease caused by storage of sphingomyelin in pulmonary macrophages results in frequent respiratory infections and often respiratory failure. Most children succumb before the third year. NPD type B, later in onset and milder in manifestations than NPD type A, is characterized by hepatosplenomegaly with progressive hypersplenism and stable liver dysfunction, gradual deterioration in pulmonary function, and atherogenic lipid profile. Progressive and/or clinically significant neurologic manifestations occur infrequently. Survival to adulthood can occur.
    Diagnosis Testing
    The diagnosis of ASM deficiency is established when residual ASM enzyme activity in peripheral blood lymphocytes or cultured skin fibroblasts is less than 10% of controls. SMPD1 is the only gene known to be associated with ASM deficiency. Sequence analysis of SMPD1 detects mutations in more than 95% of individuals with enzymatically confirmed ASM deficiency. Targeted mutation analysis for common population-specific mutations is available for individuals of Ashkenazi Jewish background with NPD-A, individuals of North African descent with NPD-B, and certain other populations.
    Genetic Counseling
    Acid sphingomyelinase (ASM) deficiency is inherited in an autosomal recessive manner. At conception, each sib of an affected individual has a 25% chance of being affected, a 50% chance of being an asymptomatic carrier, and a 25% chance of being unaffected and not a carrier. Carrier testing for at-risk relatives is possible if both disease-causing alleles in the family are known. Prenatal diagnosis for pregnancies at 25% risk is possible by biochemical testing of ASM enzyme activity and/or by molecular genetic testing if both disease-causing alleles in the family are known.
    References
    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 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, p27 nef HIV-1 Nef expression in human glial cells modulates the sphingomyelinase signaling pathway triggered by TNF-alpha PubMed

    Go to the HIV-1, Human Protein Interaction Database

    Products Interactant Other Gene Complex Source Pubs Description
    P17405 Q13510 ASAH1    HPRD  PubMed  
    P17405 Q00994 NGFRAP1    HPRD  PubMed  
    BioGRID:112493 BioGRID:106804 ANXA4    BioGRID  PubMed Two-hybrid 
    BioGRID:112493 BioGRID:106807 ANXA7    BioGRID  PubMed Two-hybrid 
    BioGRID:112493 BioGRID:120275 DUSP23    BioGRID  PubMed Two-hybrid 
    BioGRID:112493 BioGRID:108309 ELAVL1    BioGRID  PubMed Affinity Capture-RNA 
    BioGRID:112493 BioGRID:115114 KIAA0101    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:112493 BioGRID:113222 NR1H2    BioGRID  PubMed Two-hybrid 

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    hydrolase activity, acting on glycosyl bonds IEA
    Inferred from Electronic Annotation
    more info
     
    sphingomyelin phosphodiesterase activity IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    cell death IEA
    Inferred from Electronic Annotation
    more info
     
    ceramide biosynthetic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    glycosphingolipid metabolic process TAS
    Traceable Author Statement
    more info
     
    negative regulation of MAP kinase activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    nervous system development TAS
    Traceable Author Statement
    more info
    PubMed 
    positive regulation of apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of protein dephosphorylation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    response to cocaine IEA
    Inferred from Electronic Annotation
    more info
     
    response to drug IEA
    Inferred from Electronic Annotation
    more info
     
    signal transduction TAS
    Traceable Author Statement
    more info
    PubMed 
    small molecule metabolic process TAS
    Traceable Author Statement
    more info
     
    sphingolipid metabolic process TAS
    Traceable Author Statement
    more info
     
    sphingomyelin catabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    sphingomyelin metabolic process TAS
    Traceable Author Statement
    more info
    PubMed 
    termination of signal transduction IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    extracellular space IEA
    Inferred from Electronic Annotation
    more info
     
    lamellar body IEA
    Inferred from Electronic Annotation
    more info
     
    lysosomal lumen TAS
    Traceable Author Statement
    more info
     
    Preferred Names
    sphingomyelin phosphodiesterase
    Names
    sphingomyelin phosphodiesterase
    acid sphingomyelinase
    NP_000534.3
    NP_001007594.2

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_011780.1 RefSeqGene

      Range
      4990..9574
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_000543.4NP_000534.3  sphingomyelin phosphodiesterase isoform 1 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AA746054, AB209775, BI599208, M59916
      Consensus CDS
      CCDS44531.1
      UniProtKB/Swiss-Prot
      P17405
      UniProtKB/TrEMBL
      Q59EN6
      Related
      ENSP00000340409, OTTHUMP00000229836, ENST00000342245, OTTHUMT00000384205
      Conserved Domains (3) summary
      cd00842
      Location:203498
      Blast Score: 987
      MPP_ASMase; acid sphingomyelinase and related proteins, metallophosphatase domain
      smart00741
      Location:89162
      Blast Score: 121
      SapB; Saposin (B) Domains
      pfam00149
      Location:269463
      Blast Score: 136
      Metallophos; Calcineurin-like phosphoesterase
    2. NM_001007593.2NP_001007594.2  sphingomyelin phosphodiesterase isoform 2 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. The encoded protein (isoform 2) is one amino acid shorter than isoform 1.
      Source sequence(s)
      AA746054, AB209775, BI599208, M59916
      Consensus CDS
      CCDS31409.2
      UniProtKB/TrEMBL
      E9PKS3
      UniProtKB/Swiss-Prot
      P17405
      UniProtKB/TrEMBL
      Q59EN6
      Related
      ENSP00000435350, OTTHUMP00000232789, ENST00000527275, OTTHUMT00000389550
      Conserved Domains (3) summary
      cd00842
      Location:202497
      Blast Score: 986
      MPP_ASMase; acid sphingomyelinase and related proteins, metallophosphatase domain
      smart00741
      Location:89161
      Blast Score: 113
      SapB; Saposin (B) Domains
      pfam00149
      Location:268462
      Blast Score: 135
      Metallophos; Calcineurin-like phosphoesterase

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 104

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

    Reference GRCh37.p10 Primary Assembly

    Genomic

    1. NC_000011.9 Reference GRCh37.p10 Primary Assembly

      Range
      6411644..6416228
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate HuRef

    Genomic

    1. AC_000143.1 Alternate HuRef

      Range
      6070739..6075337
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate CHM1_1.0

    Genomic

    1. NC_018922.1 Alternate CHM1_1.0

      Range
      6325982..6330567
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NR_027400.1: Suppressed sequence

      Description
      NR_027400.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript.

      Supplemental Content

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