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Aliases for SMPD2 Gene

Aliases for SMPD2 Gene

  • Sphingomyelin Phosphodiesterase 2 2 3 5
  • Neutral Sphingomyelinase 2 3 4
  • Lyso-Platelet-Activating Factor-Phospholipase C 3 4
  • Lyso-PAF-PLC 3 4
  • N-SMase 3 4
  • NSMASE 3 4
  • Sphingomyelin Phosphodiesterase 2, Neutral Membrane (Neutral Sphingomyelinase) 2
  • EC 3.1.4.12 4
  • NSMASE1 3
  • ISC1 3

External Ids for SMPD2 Gene

Previous GeneCards Identifiers for SMPD2 Gene

  • GC06P109597
  • GC06P109784
  • GC06P109807
  • GC06P109868
  • GC06P109761
  • GC06P107328

Summaries for SMPD2 Gene

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) is a Protein Coding gene. Diseases associated with SMPD2 include Lipid Storage Disease. Among its related pathways are Metabolism and DREAM Repression and Dynorphin Expression. GO annotations related to this gene include sphingomyelin phosphodiesterase activity.

UniProtKB/Swiss-Prot for SMPD2 Gene

  • 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

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SMPD2 Gene

Genomics for SMPD2 Gene

Regulatory Elements for SMPD2 Gene

Enhancers for SMPD2 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH06F109373 0.9 Ensembl ENCODE 33.6 -66.6 -66647 1.7 HDGF TBL1XR1 BMI1 RAD21 CBX5 SCRT2 ETV6 CREM MIXL1 CBFB SMPD2 ENSG00000260273 PPIL6 PTCHD3P3 ENSG00000233908 CCDC162P ZBTB24 CD164 LOC101927538
GH06F109379 0.2 ENCODE 32.8 -58.3 -58293 6.3 CREB3L1 MLX FEZF1 DMAP1 YY1 SLC30A9 ZNF143 ZNF263 SP3 TBX21 ZBTB24 SMPD2 ENSG00000271730 ENSG00000260273 MICAL1 AK9 PPIL6 ENSG00000233908 PTCHD3P3 CCDC162P
GH06F109371 0.2 ENCODE 32.3 -69.1 -69074 0.1 POLR2A FOS SMPD2 PPIL6 ENSG00000233908 PTCHD3P3 CCDC162P ZBTB24 CD164 LOC101927538
GH06F109461 0.6 ENCODE 31.4 +21.5 21507 1.5 SMARCA5 CTCF ZNF146 ZNF280D ZMYM3 REST RAD21 CHAMP1 ZNF121 HDAC2 SMPD2 MICAL1 ZBTB24 LOC105377935 PPIL6 PIR52480
GH06F109453 1.2 FANTOM5 ENCODE 25.1 +16.5 16514 7.8 HDGF PKNOX1 WRNIP1 ARID4B GLI4 GLIS2 KLF7 KLF13 SP3 REST SMPD2 ZBTB24 MICAL1 ENSG00000233908 RN7SL617P ENSG00000260273 METTL24 LOC105377935 FIG4 PPIL6
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around SMPD2 on UCSC Golden Path with GeneCards custom track

Promoters for SMPD2 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001224185 -145 2600 CREB3L1 SIN3A DMAP1 YY1 ZNF143 KLF13 ZNF263 SP3 SP5 REST

Genomic Location for SMPD2 Gene

Chromosome:
6
Start:
109,440,646 bp from pter
End:
109,443,922 bp from pter
Size:
3,277 bases
Orientation:
Plus strand

Genomic View for SMPD2 Gene

Genes around SMPD2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SMPD2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SMPD2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SMPD2 Gene

Proteins for SMPD2 Gene

  • Protein details for SMPD2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O60906-NSMA_HUMAN
    Recommended name:
    Sphingomyelin phosphodiesterase 2
    Protein Accession:
    O60906
    Secondary Accessions:
    • Q5TED1
    • Q9BWR3

    Protein attributes for SMPD2 Gene

    Size:
    423 amino acids
    Molecular mass:
    47646 Da
    Cofactor:
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
    Quaternary structure:
    No Data Available

neXtProt entry for SMPD2 Gene

Post-translational modifications for SMPD2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SMPD2 Gene

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for SMPD2 (SMPD2)
  • Abcam antibodies for SMPD2
  • Cloud-Clone Corp. Antibodies for SMPD2

No data available for DME Specific Peptides for SMPD2 Gene

Domains & Families for SMPD2 Gene

Protein Domains for SMPD2 Gene

Graphical View of Domain Structure for InterPro Entry

O60906

UniProtKB/Swiss-Prot:

NSMA_HUMAN :
  • Belongs to the neutral sphingomyelinase family.
Family:
  • Belongs to the neutral sphingomyelinase family.
genes like me logo Genes that share domains with SMPD2: view

No data available for Gene Families for SMPD2 Gene

Function for SMPD2 Gene

Molecular function for SMPD2 Gene

UniProtKB/Swiss-Prot BiophysicochemicalProperties:
pH dependence: Optimum pH is 6.5-7.5.;
UniProtKB/Swiss-Prot CatalyticActivity:
Sphingomyelin + H(2)O = N-acylsphingosine + phosphocholine.
UniProtKB/Swiss-Prot 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.

Enzyme Numbers (IUBMB) for SMPD2 Gene

Gene Ontology (GO) - Molecular Function for SMPD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004767 sphingomyelin phosphodiesterase activity IEA --
GO:0016787 hydrolase activity IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with SMPD2: view
genes like me logo Genes that share phenotypes with SMPD2: view

Animal Models for SMPD2 Gene

MGI Knock Outs for SMPD2:

Animal Model Products

  • Taconic Biosciences Mouse Models for SMPD2

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for SMPD2 Gene

Localization for SMPD2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SMPD2 Gene

Membrane; Multi-pass membrane protein.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for SMPD2 Gene COMPARTMENTS Subcellular localization image for SMPD2 gene
Compartment Confidence
plasma membrane 5
mitochondrion 3
cytosol 2
lysosome 2
vacuole 2
endoplasmic reticulum 1
extracellular 1
golgi apparatus 1
nucleus 1

Gene Ontology (GO) - Cellular Components for SMPD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IEA --
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane TAS 9520418
GO:0005901 caveola IEA --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with SMPD2: view

Pathways & Interactions for SMPD2 Gene

genes like me logo Genes that share pathways with SMPD2: view

UniProtKB/Swiss-Prot O60906-NSMA_HUMAN

  • Pathway: Lipid metabolism; sphingolipid metabolism.

Gene Ontology (GO) - Biological Process for SMPD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006629 lipid metabolic process IEA --
GO:0006665 sphingolipid metabolic process IEA --
GO:0006684 sphingomyelin metabolic process TAS 9520418
GO:0006687 glycosphingolipid metabolic process TAS --
GO:0009612 response to mechanical stimulus IEA --
genes like me logo Genes that share ontologies with SMPD2: view

No data available for SIGNOR curated interactions for SMPD2 Gene

Drugs & Compounds for SMPD2 Gene

(11) Drugs for SMPD2 Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Water Approved Pharma 0
Magnesium Nutra 0

(132) Additional Compounds for SMPD2 Gene - From: HMDB and Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
phosphorylcholine
  • Choline phosphate
  • N-Trimethyl-2-aminoethylphosphonate
  • O-Phosphocholine
  • Phosphocholine
  • Phosphoryl-choline
3616-04-4
3-O-Sulfogalactosylceramide (d18:1/12:0)
  • 3'-O-Sulphogalactosylceramide
  • 3-O-Sulfo-beta-D-galactosylceramide
  • 3-O-Sulfo-beta-delta-galactosylceramide
  • 3-O-Sulfogalactosylceramide
  • Cerebroside 3-sulfate
852100-88-0
3-O-Sulfogalactosylceramide (d18:1/14:0)
  • 3'-O-Sulphogalactosylceramide
  • 3-O-Sulfo-beta-D-galactosylceramide
  • 3-O-Sulfo-beta-delta-galactosylceramide
  • 3-O-Sulfogalactosylceramide
  • Cerebroside 3-sulfate
3-O-Sulfogalactosylceramide (d18:1/16:0)
  • 3'-O-Sulphogalactosylceramide
  • 3-O-Sulfo-beta-D-galactosylceramide
  • 3-O-Sulfo-beta-delta-galactosylceramide
  • 3-O-Sulfogalactosylceramide
  • Cerebroside 3-sulfate
862509-48-6
3-O-Sulfogalactosylceramide (d18:1/18:0)
  • 3'-O-Sulphogalactosylceramide
  • 3-O-Sulfo-beta-D-galactosylceramide
  • 3-O-Sulfo-beta-delta-galactosylceramide
  • 3-O-Sulfogalactosylceramide
  • Cerebroside 3-sulfate
244215-65-4
genes like me logo Genes that share compounds with SMPD2: view

Transcripts for SMPD2 Gene

Unigene Clusters for SMPD2 Gene

Sphingomyelin phosphodiesterase 2, neutral membrane (neutral sphingomyelinase):
Representative Sequences:

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for SMPD2 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b · 2c ^ 3a · 3b ^ 4a · 4b ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10a · 10b
SP1: - - -
SP2: - - -
SP3: -
SP4: - -
SP5:
SP6: -

Relevant External Links for SMPD2 Gene

GeneLoc Exon Structure for
SMPD2
ECgene alternative splicing isoforms for
SMPD2

Expression for SMPD2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SMPD2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SMPD2 Gene

This gene is overexpressed in Testis (x6.0).

Protein differential expression in normal tissues from HIPED for SMPD2 Gene

This gene is overexpressed in Nasal epithelium (64.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SMPD2 Gene



NURSA nuclear receptor signaling pathways regulating expression of SMPD2 Gene:

SMPD2

SOURCE GeneReport for Unigene cluster for SMPD2 Gene:

Hs.55235
genes like me logo Genes that share expression patterns with SMPD2: view

Primer Products

No data available for Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt for SMPD2 Gene

Orthologs for SMPD2 Gene

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

Orthologs for SMPD2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SMPD2 34 35
  • 99.37 (n)
cow
(Bos Taurus)
Mammalia SMPD2 34 35
  • 87.47 (n)
dog
(Canis familiaris)
Mammalia SMPD2 34 35
  • 86.05 (n)
rat
(Rattus norvegicus)
Mammalia Smpd2 34
  • 83.18 (n)
mouse
(Mus musculus)
Mammalia Smpd2 34 16 35
  • 81.86 (n)
oppossum
(Monodelphis domestica)
Mammalia SMPD2 35
  • 55 (a)
OneToOne
chicken
(Gallus gallus)
Aves SMPD2 34 35
  • 65.3 (n)
lizard
(Anolis carolinensis)
Reptilia SMPD2 35
  • 45 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia smpd2 34
  • 55.52 (n)
zebrafish
(Danio rerio)
Actinopterygii LOC797914 34
  • 54.99 (n)
smpd2a 35
  • 41 (a)
OneToMany
SMPD2 (2 of 2) 35
  • 40 (a)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008053 34
  • 51.21 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG12034 36 34 35
  • 48.27 (n)
worm
(Caenorhabditis elegans)
Secernentea T27F6.6 36 34 35
  • 49.83 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes ISC1 35 37
  • 22 (a)
OneToOne
Species where no ortholog for SMPD2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • 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)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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 SMPD2 Gene

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

Paralogs for SMPD2 Gene

No data available for Paralogs for SMPD2 Gene

Variants for SMPD2 Gene

Sequence variations from dbSNP and Humsavar for SMPD2 Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs1048197 -- 109,441,129(-) AGTTG(A/G)GCTTC nc-transcript-variant, upstream-variant-2KB, reference, missense, utr-variant-5-prime
rs1048203 -- 109,441,033(-) CTCCC(C/T)AGACC nc-transcript-variant, upstream-variant-2KB, utr-variant-5-prime
rs1048210 -- 109,440,889(-) CCGCT(A/G)CCGAA nc-transcript-variant, upstream-variant-2KB, utr-variant-5-prime
rs111369755 -- 109,440,824(+) CGGGG(C/G)CGCTC nc-transcript-variant, upstream-variant-2KB, utr-variant-5-prime
rs111892331 -- 109,442,745(+) TGGTT(C/T)CCCCA intron-variant, upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for SMPD2 Gene

Variant ID Type Subtype PubMed ID
esv3576210 CNV gain 25503493
nsv950493 CNV deletion 24416366

Variation tolerance for SMPD2 Gene

Residual Variation Intolerance Score: 16.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.04; 80.22% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SMPD2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SMPD2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SMPD2 Gene

Disorders for SMPD2 Gene

MalaCards: The human disease database

(1) MalaCards diseases for SMPD2 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
lipid storage disease
  • inborn lipid storage disorder
- elite association - COSMIC cancer census association via MalaCards
Search SMPD2 in MalaCards View complete list of genes associated with diseases

Relevant External Links for SMPD2

Genetic Association Database (GAD)
SMPD2
Human Genome Epidemiology (HuGE) Navigator
SMPD2
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SMPD2
genes like me logo Genes that share disorders with SMPD2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SMPD2 Gene

Publications for SMPD2 Gene

  1. Cloned mammalian neutral sphingomyelinase: functions in sphingolipid signaling? (PMID: 9520418) Tomiuk S. … Stoffel W. (Proc. Natl. Acad. Sci. U.S.A. 1998) 2 3 4 22 64
  2. Function of the cloned putative neutral sphingomyelinase as lyso- platelet activating factor-phospholipase C. (PMID: 10608884) Sawai H. … Hannun Y.A. (J. Biol. Chem. 1999) 3 4 22 64
  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. (PMID: 20628086) Bailey S.D. … Anand S. (Diabetes Care 2010) 3 46 64
  4. Transcriptional regulation of neutral sphingomyelinase 2 gene expression of a human breast cancer cell line, MCF-7, induced by the anti-cancer drug, daunorubicin. (PMID: 19698806) Ito H. … Murate T. (Biochim. Biophys. Acta 2009) 3 22 64
  5. Aggregated low density lipoprotein induces tissue factor by inhibiting sphingomyelinase activity in human vascular smooth muscle cells. (PMID: 19817993) Camino-LA^pez S. … Llorente-CortAcs V. (J. Thromb. Haemost. 2009) 3 22 64

Products for SMPD2 Gene

Sources for SMPD2 Gene

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