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Aliases for SMPD1 Gene

Aliases for SMPD1 Gene

  • Sphingomyelin Phosphodiesterase 1, Acid Lysosomal 2 3
  • Acid Sphingomyelinase 2 3 4
  • ASMASE 3 4
  • ASM 3 4
  • NPD 3 6
  • Sphingomyelin Phosphodiesterase 3
  • EC 3.1.4.12 4

External Ids for SMPD1 Gene

Previous GeneCards Identifiers for SMPD1 Gene

  • GC11P007154
  • GC11P006873
  • GC11P006370
  • GC11P006376
  • GC11P006368
  • GC11P006070
  • GC11P006411

Summaries for SMPD1 Gene

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 niemann-pick disease, type a. Among its related pathways are Sphingolipid metabolism and Sphingolipid metabolism. 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 for SMPD1 Gene

  • 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 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SMPD1 Gene

Genomics for SMPD1 Gene

Regulatory Elements for SMPD1 Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for SMPD1 Gene

Start:
6,390,331 bp from pter
End:
6,394,998 bp from pter
Size:
4,668 bases
Orientation:
Plus strand

Genomic View for SMPD1 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for SMPD1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SMPD1 Gene

Proteins for SMPD1 Gene

  • Protein details for SMPD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P17405-ASM_HUMAN
    Recommended name:
    Sphingomyelin phosphodiesterase
    Protein Accession:
    P17405
    Secondary Accessions:
    • A8K8M3
    • E9PKS3
    • P17406
    • Q13811
    • Q16837
    • Q16841

    Protein attributes for SMPD1 Gene

    Size:
    629 amino acids
    Molecular mass:
    69752 Da
    Quaternary structure:
    • Monomer
    Miscellaneous:
    • There are two types of sphingomyelinases: ASM (acid), and NSM (neutral)

    Alternative splice isoforms for SMPD1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SMPD1 Gene

Proteomics data for SMPD1 Gene at MOPED

Post-translational modifications for SMPD1 Gene

  • Glycosylation at Asn86, Asn175, Asn335, Asn395, and Asn520
  • Modification sites at PhosphoSitePlus

Other Protein References for SMPD1 Gene

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for SMPD1 (SMPD1)

No data available for DME Specific Peptides for SMPD1 Gene

Domains for SMPD1 Gene

Protein Domains for SMPD1 Gene

Graphical View of Domain Structure for InterPro Entry

P17405

UniProtKB/Swiss-Prot:

ASM_HUMAN :
  • P17405
Domain:
  • Contains 1 saposin B-type domain.
Family:
  • Belongs to the acid sphingomyelinase family.
genes like me logo Genes that share domains with SMPD1: view

No data available for Gene Families for SMPD1 Gene

Function for SMPD1 Gene

Molecular function for SMPD1 Gene

GENATLAS Biochemistry: sphingomyelin phosphodiesterase 1,lysosomal (acid sphingomyelinase),hydrolyzing sphingomyelin to ceramide and phosphocholine,activated by TNFRSF1A and initiating the apoptotic pathway
UniProtKB/Swiss-Prot CatalyticActivity: Sphingomyelin + H(2)O = N-acylsphingosine + phosphocholine
UniProtKB/Swiss-Prot 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

Enzyme Numbers (IUBMB) for SMPD1 Gene

Gene Ontology (GO) - Molecular Function for SMPD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004767 sphingomyelin phosphodiesterase activity IEA --
GO:0005515 protein binding IPI 21157428
GO:0016787 hydrolase activity --
GO:0016798 hydrolase activity, acting on glycosyl bonds IEA --
genes like me logo Genes that share ontologies with SMPD1: view
genes like me logo Genes that share phenotypes with SMPD1: view

Animal Models for SMPD1 Gene

MGI Knock Outs for SMPD1:

Animal Model Products

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for SMPD1

In Situ Assay Products

Flow Cytometry Products

No data available for miRNA , Transcription Factor Targeting and HOMER Transcription for SMPD1 Gene

Localization for SMPD1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SMPD1 Gene

Lysosome.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for SMPD1 Gene COMPARTMENTS Subcellular localization image for SMPD1 gene
Compartment Confidence
lysosome 5
vacuole 5
endosome 2
extracellular 2
mitochondrion 2
plasma membrane 2
cytoskeleton 1
cytosol 1
endoplasmic reticulum 1
nucleus 1

Gene Ontology (GO) - Cellular Components for SMPD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space IEA --
GO:0005764 lysosome IDA 20956541
GO:0005768 endosome IDA 20956541
GO:0005886 plasma membrane IDA 20956541
GO:0042599 lamellar body IEA --
genes like me logo Genes that share ontologies with SMPD1: view

Pathways for SMPD1 Gene

genes like me logo Genes that share pathways with SMPD1: view

PCR Array Products

  • Pathway & Disease-focused RT² Profiler PCR Arrays

Gene Ontology (GO) - Biological Process for SMPD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006665 sphingolipid metabolic process TAS --
GO:0006684 sphingomyelin metabolic process TAS 7670466
GO:0006685 sphingomyelin catabolic process IEA --
GO:0006687 glycosphingolipid metabolic process TAS --
GO:0007165 signal transduction TAS 7670466
genes like me logo Genes that share ontologies with SMPD1: view

Compounds for SMPD1 Gene

(152) HMDB Compounds for SMPD1 Gene

Compound Synonyms Cas Number PubMed IDs
3-O-Sulfogalactosylceramide (d18:1/12:0)
  • Sulfatide (d18:1/12:0)
852100-88-0
3-O-Sulfogalactosylceramide (d18:1/14:0)
  • Sulfatide (d18:1/14:0)
Not Available
3-O-Sulfogalactosylceramide (d18:1/16:0)
  • Sulfatide (d18:1/16:0)
862509-48-6
3-O-Sulfogalactosylceramide (d18:1/18:0)
  • Sulfatide (d18:1/18:0)
244215-65-4
3-O-Sulfogalactosylceramide (d18:1/18:1(9Z))
  • Sulfatide (d18:1/18:1(9Z))
Not Available

(1) Drugbank Compounds for SMPD1 Gene

Compound Synonyms Cas Number Type Actions PubMed IDs
Desipramine
  • Demethylimipramine
50-47-5 target inhibitor

(48) Novoseek inferred chemical compound relationships for SMPD1 Gene

Compound -log(P) Hits PubMed IDs
ceramide 94.5 153
fantofarone 86.4 5
ceramides 72.1 7
phosphorylcholine 71.6 16
ceramide 1-phosphate 69.2 5
genes like me logo Genes that share compounds with SMPD1: view

Transcripts for SMPD1 Gene

Unigene Clusters for SMPD1 Gene

Sphingomyelin phosphodiesterase 1, acid lysosomal:
Representative Sequences:

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for SMPD1

Primer Products

  • OriGene qSTAR qPCR primer pairs in human,mouse,rat for SMPD1

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for SMPD1 Gene

No ASD Table

Relevant External Links for SMPD1 Gene

GeneLoc Exon Structure for
SMPD1
ECgene alternative splicing isoforms for
SMPD1

Expression for SMPD1 Gene

mRNA expression in normal human tissues for SMPD1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for SMPD1 Gene

SOURCE GeneReport for Unigene cluster for SMPD1 Gene Hs.498173

genes like me logo Genes that share expressions with SMPD1: view

In Situ Assay Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for SMPD1 Gene

Orthologs for SMPD1 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for SMPD1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SMPD1 35
  • 98.99 (n)
  • 99.04 (a)
SMPD1 36
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SMPD1 35
  • 86.08 (n)
  • 85.6 (a)
SMPD1 36
  • 86 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SMPD1 35
  • 85.88 (n)
  • 86.15 (a)
SMPD1 36
  • 86 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Smpd1 35
  • 82.93 (n)
  • 83.04 (a)
Smpd1 16
Smpd1 36
  • 82 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SMPD1 36
  • 73 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SMPD1 36
  • 78 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Smpd1 35
  • 83.2 (n)
  • 83.36 (a)
chicken
(Gallus gallus)
Aves SMPD1 35
  • 68.22 (n)
  • 66.12 (a)
SMPD1 36
  • 65 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SMPD1 36
  • 66 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.2147 35
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100487433 35
  • 64.43 (n)
  • 63.41 (a)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.3961 35
zebrafish
(Danio rerio)
Actinopterygii smpd1 35
  • 59.73 (n)
  • 59.3 (a)
smpd1 36
  • 48 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP011940 35
  • 52.65 (n)
  • 43.52 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG15533 36
  • 5 (a)
OneToMany
CG15534 36
  • 7 (a)
OneToMany
CG3376 35
  • 52.78 (n)
  • 42.61 (a)
CG3376 36
  • 29 (a)
OneToMany
CG15534 37
  • 32 (a)
CG3376 37
  • 38 (a)
CG15533 37
  • 32 (a)
worm
(Caenorhabditis elegans)
Secernentea asm-2 35
  • 45.49 (n)
  • 38.58 (a)
asm-2 36
  • 8 (a)
OneToOne
ZK455.4 37
  • 33 (a)
B0252.2 37
  • 34 (a)
W03G1.7 37
  • 30 (a)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ACL091C 35
  • 44.39 (n)
  • 32.67 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PPN1 36
  • 13 (a)
OneToMany
bread mold
(Neurospora crassa)
Ascomycetes NCU06697 35
  • 43.77 (n)
  • 31.91 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 10 (a)
OneToOne
Species with no ortholog for SMPD1:
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SMPD1 Gene

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

Paralogs for SMPD1 Gene

Paralogs for SMPD1 Gene

genes like me logo Genes that share paralogs with SMPD1: view

Variants for SMPD1 Gene

Polymorphic Variants from UniProtKB/Swiss-Prot for SMPD1 Gene

P17405-ASM_HUMAN
A common polymorphism arises from a variable number of hexanucleotide repeat sequence within the signal peptide region

Sequence variations from dbSNP and Humsavar for SMPD1 Gene

SNP ID Clin Chr 11 pos Sequence Context AA Info Type MAF
rs1050228 Benign, - 6,390,705(+) CCTGG(C/T)GCTGG missense, reference
rs1050233 - 6,392,036(+) AAGCA(C/T)ACCTG reference, missense
rs1050239 Benign, - 6,394,233(+) ACTCC(A/G)GGAGC missense, reference, utr-variant-3-prime
rs1542705 -- 6,389,167(-) TGAGG(A/G)ATCCT upstream-variant-2KB
rs1803161 -- 6,391,937(+) GACTC(A/G)TCAGG missense, reference

Relevant External Links for SMPD1 Gene

HapMap Linkage Disequilibrium report
SMPD1
Human Gene Mutation Database (HGMD)
SMPD1

No data available for Structural Variations from Database of Genomic Variants (DGV) for SMPD1 Gene

Disorders for SMPD1 Gene

(2) OMIM Diseases for SMPD1 Gene (607608)

UniProtKB/Swiss-Prot

ASM_HUMAN
  • 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. {ECO:0000269 PubMed:12556236, ECO:0000269 PubMed:1391960, ECO:0000269 PubMed:15221801, ECO:0000269 PubMed:15877209, ECO:0000269 PubMed:1618760, ECO:0000269 PubMed:1718266, ECO:0000269 PubMed:19405096, ECO:0000269 PubMed:2023926, ECO:0000269 PubMed:20386867, ECO:0000269 PubMed:8680412, ECO:0000269 PubMed:8693491, ECO:0000269 PubMed:9266408}. 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. {ECO:0000269 PubMed:12369017, ECO:0000269 PubMed:12556236, ECO:0000269 PubMed:1301192, ECO:0000269 PubMed:15241805, ECO:0000269 PubMed:16010684, ECO:0000269 PubMed:1618760, ECO:0000269 PubMed:16472269, ECO:0000269 PubMed:1885770, ECO:0000269 PubMed:19050888, ECO:0000269 PubMed:19405096, ECO:0000269 PubMed:20386867, ECO:0000269 PubMed:22613662, ECO:0000269 PubMed:8051942, ECO:0000269 PubMed:8664904}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(35) Novoseek inferred disease relationships for SMPD1 Gene

Disease -log(P) Hits PubMed IDs
niemann-pick diseases 97.9 85
niemann-picks disease type b 94 7
i-cell disease 71.1 2
niemann-picks disease type c 59.2 3
lysosomal storage diseases 49.9 2

Genatlas disease for SMPD1 Gene

Niemann-Pick disease,types A & B

Relevant External Links for SMPD1

GeneTests
SMPD1
GeneReviews
SMPD1
Genetic Association Database (GAD)
SMPD1
Human Genome Epidemiology (HuGE) Navigator
SMPD1
genes like me logo Genes that share disorders with SMPD1: view

Publications for SMPD1 Gene

  1. Identification and expression of a common missense mutation (L302P) in the acid sphingomyelinase gene of Ashkenazi Jewish type A Niemann- Pick disease patients. (PMID: 1391960) Levran O. … Schuchman E.H. (Blood 1992) 3 4 23
  2. 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. (PMID: 1618760) Takahashi T. … Schuchman E.H. (J. Biol. Chem. 1992) 3 4 23
  3. Niemann-Pick disease: a frequent missense mutation in the acid sphingomyelinase gene of Ashkenazi Jewish type A and B patients. (PMID: 2023926) Levran O. … Schuchman E.H. (Proc. Natl. Acad. Sci. U.S.A. 1991) 3 4 23
  4. Molecular basis of acid sphingomyelinase deficiency in a patient with Niemann-Pick disease type A. (PMID: 1718266) Ferlinz K. … Sandhoff K. (Biochem. Biophys. Res. Commun. 1991) 3 4 23
  5. Structural organization and complete nucleotide sequence of the gene encoding human acid sphingomyelinase (SMPD1). (PMID: 1740330) Schuchman E.H. … Desnick R.J. (Genomics 1992) 3 4 23

Products for SMPD1 Gene

Sources for SMPD1 Gene

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