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SMPD1 sphingomyelin phosphodiesterase 1 [ Homo sapiens (human) ]

Gene ID: 6609, updated on 9-Jul-2017
Official Symbol
SMPD1provided by HGNC
Official Full Name
sphingomyelin phosphodiesterase 1provided by HGNC
Primary source
HGNC:HGNC:11120
See related
Ensembl:ENSG00000166311 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]
Orthologs
Location:
11p15.4
Exon count:
6
Annotation release Status Assembly Chr Location
108 current GRCh38.p7 (GCF_000001405.33) 11 NC_000011.10 (6390301..6394998)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (6411644..6416228)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene cholecystokinin B receptor Neighboring gene uncharacterized LOC101927825 Neighboring gene caveolae associated protein 3 Neighboring gene amyloid beta precursor protein binding family B member 1 Neighboring gene hemopexin

  • 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 Jun 15 11:32:44 2016

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

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 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
nef HIV-1 Nef expression in human glial cells modulates the sphingomyelinase signaling pathway triggered by TNF-alpha PubMed
Tat tat HIV-1 Tat upregulates sphingomyelin phosphodiesterase 1, acid lysosomal (SMPD1) expression in Jurkat T-cells PubMed

Go to the HIV-1, Human Interaction Database

Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
acid sphingomyelin phosphodiesterase activity IDA
Inferred from Direct Assay
more info
PubMed 
hydrolase activity, acting on glycosyl bonds IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
sphingomyelin phosphodiesterase activity TAS
Traceable Author Statement
more info
 
zinc ion binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
ceramide biosynthetic process IDA
Inferred from Direct Assay
more info
PubMed 
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 
sphingomyelin catabolic process IDA
Inferred from Direct Assay
more info
PubMed 
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
endosome IDA
Inferred from Direct Assay
more info
PubMed 
extracellular exosome IDA
Inferred from Direct Assay
more info
PubMed 
extracellular space IDA
Inferred from Direct Assay
more info
PubMed 
lamellar body IEA
Inferred from Electronic Annotation
more info
 
lysosomal lumen TAS
Traceable Author Statement
more info
 
lysosome IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
Preferred Names
sphingomyelin phosphodiesterase
Names
acid sphingomyelinase
sphingomyelin phosphodiesterase 1, acid lysosomal
NP_000534.3
NP_001007594.2
NP_001305016.1
NP_001305017.1
XP_011518605.1
XP_011518606.1

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

    See identical proteins and their annotated locations for NP_000534.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AA746054, AB209775, BI599208, M59916
    Consensus CDS
    CCDS44531.1
    UniProtKB/Swiss-Prot
    P17405
    UniProtKB/TrEMBL
    Q59EN6
    Related
    ENSP00000340409.4, OTTHUMP00000229836, ENST00000342245.8, OTTHUMT00000384205
    Conserved Domains (3) summary
    smart00741
    Location:89162
    SapB; Saposin (B) Domains
    cd00842
    Location:203498
    MPP_ASMase; acid sphingomyelinase and related proteins, metallophosphatase domain
    pfam00149
    Location:256463
    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/Swiss-Prot
    P17405
    UniProtKB/TrEMBL
    Q59EN6
    Related
    ENSP00000435350.1, OTTHUMP00000232789, ENST00000527275.5, OTTHUMT00000389550
    Conserved Domains (3) summary
    smart00741
    Location:89161
    SapB; Saposin (B) Domains
    cd00842
    Location:202497
    MPP_ASMase; acid sphingomyelinase and related proteins, metallophosphatase domain
    pfam00149
    Location:255462
    Metallophos; Calcineurin-like phosphoesterase
  3. NM_001318087.1NP_001305016.1  sphingomyelin phosphodiesterase isoform 3 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate splice site in its 3' exon resulting in a frameshift and an early stop codon compared to variant 1. The encoded isoform (3) has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AA746054, BC041164, BI599208, HQ132747, M59916
    UniProtKB/Swiss-Prot
    P17405
    UniProtKB/TrEMBL
    E9LUE8, Q8IUN0
    Conserved Domains (3) summary
    smart00741
    Location:89162
    SapB; Saposin (B) Domains
    cd00842
    Location:203495
    MPP_ASMase; acid sphingomyelinase and related proteins, metallophosphatase domain
    pfam00149
    Location:256463
    Metallophos; Calcineurin-like phosphoesterase
  4. NM_001318088.1NP_001305017.1  sphingomyelin phosphodiesterase isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and uses an alternate translation start site compared to variant 1. The encoded isoform (4) has a shorter and distinct N-terminus, and lacks a predicted signal peptide compared to isoform 1.
    Source sequence(s)
    AB209775, BI599208, BM977655, HQ132748, M59916
    UniProtKB/Swiss-Prot
    P17405
    UniProtKB/TrEMBL
    E9LUE9, Q59EN6
    Conserved Domains (2) summary
    COG1409
    Location:95214
    CpdA; 3',5'-cyclic AMP phosphodiesterase CpdA [Signal transduction mechanisms]
    cd00842
    Location:47191
    MPP_ASMase; acid sphingomyelinase and related proteins, metallophosphatase domain

RNA

  1. NR_027400.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (ASM-3) lacks an alternate internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AA746054, BC041164, HY095805
    Related
    ENST00000533123.5, OTTHUMT00000384206
  2. NR_134502.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) uses an alternate splice site in an internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AY649987, BI599208, BM977655, M59916

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

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

Reference GRCh38.p7 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p7 Primary Assembly

    Range
    6390301..6394998
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011520303.1XP_011518605.1  sphingomyelin phosphodiesterase isoform X1

    See identical proteins and their annotated locations for XP_011518605.1

    Conserved Domains (3) summary
    smart00741
    Location:89162
    SapB; Saposin (B) Domains
    cd00842
    Location:203454
    MPP_ASMase; acid sphingomyelinase and related proteins, metallophosphatase domain
    pfam00149
    Location:256419
    Metallophos; Calcineurin-like phosphoesterase
  2. XM_011520304.1XP_011518606.1  sphingomyelin phosphodiesterase isoform X2

    Conserved Domains (3) summary
    smart00741
    Location:89162
    SapB; Saposin (B) Domains
    cd00842
    Location:203451
    MPP_ASMase; acid sphingomyelinase and related proteins, metallophosphatase domain
    pfam00149
    Location:256419
    Metallophos; Calcineurin-like phosphoesterase

RNA

  1. XR_001747940.1 RNA Sequence

Alternate CHM1_1.1

Genomic

  1. NC_018922.2 Alternate CHM1_1.1

    Range
    6410778..6415363
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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