Aliases for SMPD3 Gene

Aliases for SMPD3 Gene

  • Sphingomyelin Phosphodiesterase 3 2 3 4 5
  • Neutral Sphingomyelinase II 2 3 4
  • Neutral Sphingomyelinase 2 3 4
  • NSMase-2 3 4
  • NSMASE2 2 3
  • Sphingomyelin Phosphodiesterase 3, Neutral Membrane (Neutral Sphingomyelinase II) 2
  • EC 3.1.4.12 4
  • NSMase2 4
  • SMPD3 5

External Ids for SMPD3 Gene

Previous GeneCards Identifiers for SMPD3 Gene

  • GC16M059090
  • GC16M068772
  • GC16M068130
  • GC16M068171
  • GC16M066949
  • GC16M068392
  • GC16M054265

Summaries for SMPD3 Gene

GeneCards Summary for SMPD3 Gene

SMPD3 (Sphingomyelin Phosphodiesterase 3) is a Protein Coding gene. Diseases associated with SMPD3 include Pituitary Hormone Deficiency, Combined, 2 and Coffin-Siris Syndrome 1. Among its related pathways are Signaling by GPCR and NGF Pathway. Gene Ontology (GO) annotations related to this gene include sphingomyelin phosphodiesterase activity.

UniProtKB/Swiss-Prot Summary for SMPD3 Gene

  • Catalyzes the hydrolysis of sphingomyelin to form ceramide and phosphocholine. Ceramide mediates numerous cellular functions, such as apoptosis and growth arrest, and is capable of regulating these 2 cellular events independently. Also hydrolyzes sphingosylphosphocholine. Regulates the cell cycle by acting as a growth suppressor in confluent cells. Probably acts as a regulator of postnatal development and participates in bone and dentin mineralization.

Gene Wiki entry for SMPD3 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SMPD3 Gene

Genomics for SMPD3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SMPD3 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SMPD3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SMPD3

Top Transcription factor binding sites by QIAGEN in the SMPD3 gene promoter:
  • AP-1
  • ATF-2
  • c-Jun
  • E47
  • Egr-2
  • FOXI1
  • HFH-1
  • HFH-3
  • POU2F1b
  • Tal-1beta

Genomic Locations for SMPD3 Gene

Genomic Locations for SMPD3 Gene
chr16:68,358,327-68,448,703
(GRCh38/hg38)
Size:
90,377 bases
Orientation:
Minus strand
chr16:68,392,230-68,482,591
(GRCh37/hg19)
Size:
90,362 bases
Orientation:
Minus strand

Genomic View for SMPD3 Gene

Genes around SMPD3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SMPD3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SMPD3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SMPD3 Gene

Proteins for SMPD3 Gene

  • Protein details for SMPD3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NY59-NSMA2_HUMAN
    Recommended name:
    Sphingomyelin phosphodiesterase 3
    Protein Accession:
    Q9NY59
    Secondary Accessions:
    • B7ZL82
    • Q2M1S8

    Protein attributes for SMPD3 Gene

    Size:
    655 amino acids
    Molecular mass:
    71081 Da
    Cofactor:
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for SMPD3 Gene

    Alternative splice isoforms for SMPD3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SMPD3 Gene

Post-translational modifications for SMPD3 Gene

  • Palmitoylated, palmitoylation-deficient proteins are targeted for lysosomal degradation.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for SMPD3 Gene

Domains & Families for SMPD3 Gene

Gene Families for SMPD3 Gene

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

Protein Domains for SMPD3 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SMPD3 Gene

GenScript: Design optimal peptide antigens:
  • Sphingomyelin phosphodiesterase (C8CHW6_HUMAN)
  • Neutral sphingomyelinase type 2 (D6Q0F1_HUMAN)
  • Neutral sphingomyelinase II (NSMA2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9NY59

UniProtKB/Swiss-Prot:

NSMA2_HUMAN :
  • Belongs to the neutral sphingomyelinase family.
Family:
  • Belongs to the neutral sphingomyelinase family.
genes like me logo Genes that share domains with SMPD3: view

Function for SMPD3 Gene

Molecular function for SMPD3 Gene

UniProtKB/Swiss-Prot Function:
Catalyzes the hydrolysis of sphingomyelin to form ceramide and phosphocholine. Ceramide mediates numerous cellular functions, such as apoptosis and growth arrest, and is capable of regulating these 2 cellular events independently. Also hydrolyzes sphingosylphosphocholine. Regulates the cell cycle by acting as a growth suppressor in confluent cells. Probably acts as a regulator of postnatal development and participates in bone and dentin mineralization.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=H2O + sphingomyelin = an N-acylsphing-4-enine + H(+) + phosphocholine; Xref=Rhea:RHEA:19253, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:17636, ChEBI:CHEBI:52639, ChEBI:CHEBI:295975; EC=3.1.4.12;.
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
pH dependence: Optimum pH is 7.5.;
UniProtKB/Swiss-Prot EnzymeRegulation:
Activated by unsaturated fatty acids and phosphatidylserine.

Enzyme Numbers (IUBMB) for SMPD3 Gene

Phenotypes From GWAS Catalog for SMPD3 Gene

Gene Ontology (GO) - Molecular Function for SMPD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004620 phospholipase activity IBA 21873635
GO:0004767 sphingomyelin phosphodiesterase activity IBA 21873635
GO:0005515 protein binding IPI 20080539
GO:0016787 hydrolase activity IEA --
GO:0042802 identical protein binding IEA --
genes like me logo Genes that share ontologies with SMPD3: view
genes like me logo Genes that share phenotypes with SMPD3: view

Animal Models for SMPD3 Gene

MGI Knock Outs for SMPD3:

Animal Model Products

  • Taconic Biosciences Mouse Models for SMPD3

CRISPR Products

miRNA for SMPD3 Gene

miRTarBase miRNAs that target SMPD3

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SMPD3

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SMPD3 Gene

Localization for SMPD3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SMPD3 Gene

Golgi apparatus membrane. Lipid-anchor. Cell membrane. Lipid-anchor. Note=May localize to detergent-resistant subdomains of Golgi membranes of hypothalamic neurosecretory neurons (PubMed:10823942). Localizes to plasma membrane in confluent contact-inhaibited cells (PubMed:15051724).

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 SMPD3 gene
Compartment Confidence
plasma membrane 5
golgi apparatus 4
extracellular 3
cytoskeleton 2
mitochondrion 2
nucleus 2
endoplasmic reticulum 2
endosome 2
cytosol 2
lysosome 2
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Endoplasmic reticulum (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SMPD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000137 Golgi cis cisterna IEA --
GO:0000139 Golgi membrane IEA --
GO:0005737 cytoplasm IBA 21873635
GO:0005794 Golgi apparatus IEA --
GO:0005886 plasma membrane TAS --
genes like me logo Genes that share ontologies with SMPD3: view

Pathways & Interactions for SMPD3 Gene

PathCards logo

SuperPathways for SMPD3 Gene

genes like me logo Genes that share pathways with SMPD3: view

Pathways by source for SMPD3 Gene

2 KEGG pathways for SMPD3 Gene
9 Qiagen pathways for SMPD3 Gene
  • Caspase Cascade
  • Ceramide Pathway
  • Fas Signaling
  • LDL Oxidation in Atherogenesis
  • NGF Pathway

UniProtKB/Swiss-Prot Q9NY59-NSMA2_HUMAN

  • Pathway: Lipid metabolism; sphingolipid metabolism.

Gene Ontology (GO) - Biological Process for SMPD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001501 skeletal system development IEA --
GO:0001503 ossification IEA --
GO:0001932 regulation of protein phosphorylation IEA --
GO:0001958 endochondral ossification IEA --
GO:0002063 chondrocyte development IEA --
genes like me logo Genes that share ontologies with SMPD3: view

No data available for SIGNOR curated interactions for SMPD3 Gene

Drugs & Compounds for SMPD3 Gene

(8) Drugs for SMPD3 Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Phosphatidyl serine Approved, Investigational Nutra Target 0
Magnesium Approved, Experimental, Investigational Pharma 0
Water Approved Pharma 0
PHOSPHATIDYLSERINE Pharma 0

(276) Additional Compounds for SMPD3 Gene - From: HMDB and Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
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
3-O-Sulfogalactosylceramide (d18:1/18:1(9Z))
  • 3'-O-Sulphogalactosylceramide
  • 3-O-SulfO-beta-D-galactosylceramide
  • 3-O-SulfO-beta-delta-galactosylceramide
  • 3-O-Sulfogalactosylceramide
  • Cerebroside 3-sulfate
genes like me logo Genes that share compounds with SMPD3: view

Transcripts for SMPD3 Gene

mRNA/cDNA for SMPD3 Gene

1 REFSEQ mRNAs :
15 NCBI additional mRNA sequence :
12 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SMPD3

Alternative Splicing Database (ASD) splice patterns (SP) for SMPD3 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9a · 9b ^ 10 ^ 11a · 11b ^ 12
SP1: - - - - -
SP2: - - - -
SP3: -
SP4: - - -
SP5: -
SP6: -
SP7:

Relevant External Links for SMPD3 Gene

GeneLoc Exon Structure for
SMPD3

Expression for SMPD3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SMPD3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SMPD3 Gene

This gene is overexpressed in Small Intestine - Terminal Ileum (x5.4) and Colon - Transverse (x5.2).

Protein differential expression in normal tissues from HIPED for SMPD3 Gene

This gene is overexpressed in Pancreatic juice (22.2), Urine (12.9), Ovary (10.9), Lung (8.7), and Fetal Brain (6.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SMPD3 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SMPD3

SOURCE GeneReport for Unigene cluster for SMPD3 Gene:

Hs.368421

mRNA Expression by UniProt/SwissProt for SMPD3 Gene:

Q9NY59-NSMA2_HUMAN
Tissue specificity: Predominantly expressed in brain.

Evidence on tissue expression from TISSUES for SMPD3 Gene

  • Nervous system(4.5)
  • Liver(4.4)
  • Heart(2.2)
  • Skin(2.1)
  • Muscle(2.1)
genes like me logo Genes that share expression patterns with SMPD3: view

No data available for Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for SMPD3 Gene

Orthologs for SMPD3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for SMPD3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SMPD3 30 31
  • 99.39 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia SMPD3 30 31
  • 88.35 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia SMPD3 30 31
  • 88.18 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Smpd3 30
  • 87.17 (n)
Mouse
(Mus musculus)
Mammalia Smpd3 30 17 31
  • 86.93 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia SMPD3 31
  • 71 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia SMPD3 31
  • 68 (a)
OneToOne
Chicken
(Gallus gallus)
Aves SMPD3 30 31
  • 69.89 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SMPD3 31
  • 71 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia smpd3 30
  • 67.69 (n)
Zebrafish
(Danio rerio)
Actinopterygii smpd3 30 31
  • 62.37 (n)
OneToOne
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 28 (a)
OneToOne
Species where no ortholog for SMPD3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • 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)
  • Fruit Fly (Drosophila melanogaster)
  • 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)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • 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)
  • Worm (Caenorhabditis elegans)

Evolution for SMPD3 Gene

ENSEMBL:
Gene Tree for SMPD3 (if available)
TreeFam:
Gene Tree for SMPD3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SMPD3: view image

Paralogs for SMPD3 Gene

Pseudogenes.org Pseudogenes for SMPD3 Gene

genes like me logo Genes that share paralogs with SMPD3: view

No data available for Paralogs for SMPD3 Gene

Variants for SMPD3 Gene

Additional dbSNP identifiers (rs#s) for SMPD3 Gene

Structural Variations from Database of Genomic Variants (DGV) for SMPD3 Gene

Variant ID Type Subtype PubMed ID
esv2714652 CNV deletion 23290073
esv3582280 CNV loss 25503493
esv3638906 CNV loss 21293372
nsv1847 CNV insertion 18451855
nsv1848 CNV insertion 18451855
nsv475103 CNV novel sequence insertion 20440878

Variation tolerance for SMPD3 Gene

Residual Variation Intolerance Score: 49.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.63; 56.68% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SMPD3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SMPD3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SMPD3 Gene

Disorders for SMPD3 Gene

MalaCards: The human disease database

(3) MalaCards diseases for SMPD3 Gene - From: DISEASES and Novoseek

- elite association - COSMIC cancer census association via MalaCards
Search SMPD3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SMPD3

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with SMPD3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SMPD3 Gene

Publications for SMPD3 Gene

  1. Analysis of membrane topology of neutral sphingomyelinase 2. (PMID: 17349629) Tani M … Hannun YA (FEBS letters 2007) 3 4 23
  2. Novel tumor necrosis factor-responsive mammalian neutral sphingomyelinase-3 is a C-tail-anchored protein. (PMID: 16517606) Krut O … Krönke M (The Journal of biological chemistry 2006) 3 23 26
  3. Role for mammalian neutral sphingomyelinase 2 in confluence-induced growth arrest of MCF7 cells. (PMID: 15051724) Marchesini N … Hannun YA (The Journal of biological chemistry 2004) 3 4 23
  4. Hydrolysis of sphingosylphosphocholine by neutral sphingomyelinases. (PMID: 14741383) Miura Y … Hanada K (FEBS letters 2004) 3 4 23
  5. Cloning and characterization of the mammalian brain-specific, Mg2+-dependent neutral sphingomyelinase. (PMID: 10823942) Hofmann K … Stoffel W (Proceedings of the National Academy of Sciences of the United States of America 2000) 2 3 4

Products for SMPD3 Gene

Sources for SMPD3 Gene