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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 p75(NTR)-mediated signaling and TNF signaling (REACTOME). Gene Ontology (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

Additional gene information for SMPD2 Gene

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

Genomics for SMPD2 Gene

GeneHancer (GH) Regulatory Elements for SMPD2 Gene

Promoters and enhancers for SMPD2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06I109438 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 582.2 0.0 -42 3.4 ARNT ARID4B SIN3A DMAP1 IRF4 YY1 ZNF766 ZNF213 ZNF207 ZNF143 SMPD2 PPIL6 ZBTB24 ENSG00000260273 AK9 MICAL1 FIG4 GC06P109389 PIR52905
GH06I109379 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 32.8 -58.3 -58292 6.3 CLOCK MLX FEZF1 DMAP1 YY1 ZNF213 E2F8 ZNF143 SP3 SSRP1 ENSG00000260273 CD164 ZBTB24 SMPD2 MICAL1 AK9 PPIL6 PTCHD3P3 ENSG00000233908 CCDC162P
GH06I109453 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 25.1 +16.5 16514 7.8 HDGF PKNOX1 FOXA2 ARID4B ZBTB7B IRF4 ZNF143 SP3 REST SMARCA4 MICAL1 SMPD2 ZBTB24 METTL24 ENSG00000260273 LOC105377935 FOXO3 FIG4 PPIL6 CD164
GH06I109690 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 31.1 +250.5 250455 2.2 HDGF PKNOX1 ARID4B SIN3A YY1 SLC30A9 ZNF766 ZNF207 ZNF143 KLF13 AK9 FIG4 SMPD2 ZBTB24 ENSG00000260273
GH06I109481 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 23 +42.8 42760 3.1 ATF1 ARID4B SIN3A DMAP1 YY1 GLIS2 ZNF213 ELK1 ZNF207 RUNX3 ZBTB24 LOC105377935 SMPD2 ENSG00000260273 PPIL6 MICAL1 SESN1 AK9
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SMPD2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SMPD2 gene promoter:

Genomic Locations for SMPD2 Gene

Genomic Locations for SMPD2 Gene
chr6:109,440,646-109,443,922
(GRCh38/hg38)
Size:
3,277 bases
Orientation:
Plus strand
chr6:109,761,931-109,765,122
(GRCh37/hg19)

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

No Post-translational modifications

Other Protein References for SMPD2 Gene

No data available for DME Specific Peptides for SMPD2 Gene

Domains & Families for SMPD2 Gene

Gene Families for SMPD2 Gene

Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins
  • Predicted membrane proteins

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

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

Phenotypes From GWAS Catalog 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

CRISPR Products

Inhibitory RNA 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
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SMPD2 gene
Compartment Confidence
plasma membrane 5
mitochondrion 3
endoplasmic reticulum 2
cytosol 2
lysosome 2
extracellular 1
nucleus 1
golgi apparatus 1
endosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cell Junctions (2)
  • Plasma membrane (2)
  • Vesicles (2)
See all subcellular structures

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
Magnesium Approved Nutra 0
Water Approved Pharma 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:

CRISPR Products

Inhibitory RNA 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 CGAP 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

Evidence on tissue expression from TISSUES for SMPD2 Gene

  • Nervous system(4.4)
genes like me logo Genes that share expression patterns with SMPD2: view

Primer Products

No data available for Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer 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 33 34
  • 99.37 (n)
cow
(Bos Taurus)
Mammalia SMPD2 33 34
  • 87.47 (n)
dog
(Canis familiaris)
Mammalia SMPD2 33 34
  • 86.05 (n)
rat
(Rattus norvegicus)
Mammalia Smpd2 33
  • 83.18 (n)
mouse
(Mus musculus)
Mammalia Smpd2 33 16 34
  • 81.86 (n)
oppossum
(Monodelphis domestica)
Mammalia SMPD2 34
  • 55 (a)
OneToOne
chicken
(Gallus gallus)
Aves SMPD2 33 34
  • 65.3 (n)
lizard
(Anolis carolinensis)
Reptilia SMPD2 34
  • 45 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia smpd2 33
  • 55.52 (n)
zebrafish
(Danio rerio)
Actinopterygii LOC797914 33
  • 54.99 (n)
smpd2a 34
  • 41 (a)
OneToMany
SMPD2 (2 of 2) 34
  • 40 (a)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008053 33
  • 51.21 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG12034 35 33 34
  • 48.27 (n)
worm
(Caenorhabditis elegans)
Secernentea T27F6.6 35 33 34
  • 49.83 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes ISC1 34 36
  • 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 Variation AA Info Type
rs1000982062 -- 109,440,564(+) G/A/C/T upstream_transcript_variant
rs1000992004 -- 109,440,354(+) C/G upstream_transcript_variant
rs1001982428 -- 109,441,218(+) A/G genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1002211252 -- 109,440,121(+) AAAAAA/AAAAA/AAAAAAA upstream_transcript_variant
rs1003207558 -- 109,438,994(+) C/G upstream_transcript_variant

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)

Additional Variant Information 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

Additional Disease Information for SMPD2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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 (Proceedings of the National Academy of Sciences of the United States of America 1998) 2 3 4 22 58
  2. Function of the cloned putative neutral sphingomyelinase as lyso-platelet activating factor-phospholipase C. (PMID: 10608884) Sawai H … Hannun YA (The Journal of biological chemistry 1999) 3 4 22 58
  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 SD … DREAM investigators (Diabetes care 2010) 3 44 58
  4. Sequential use of transcriptional profiling, expression quantitative trait mapping, and gene association implicates MMP20 in human kidney aging. (PMID: 19834535) Wheeler HE … Kim SK (PLoS genetics 2009) 3 44 58
  5. 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 (Biochimica et biophysica acta 2009) 3 22 58

Products for SMPD2 Gene

Sources for SMPD2 Gene

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