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Aliases for SMPD3 Gene

Aliases for SMPD3 Gene

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

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 Deafness, Autosomal Recessive 89. Among its related pathways are TNF signaling (REACTOME) and Metabolism. Gene Ontology (GO) annotations related to this gene include sphingomyelin phosphodiesterase activity.

UniProtKB/Swiss-Prot 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

Additional gene information for SMPD3 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SMPD3 Gene

Genomics for SMPD3 Gene

GeneHancer (GH) Regulatory Elements for SMPD3 Gene

Promoters and enhancers for SMPD3 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
GH16I068448 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 550.8 0.0 -2 1 HDGF FOXA2 MLX ARID4B SIN3A DMAP1 YY1 SLC30A9 ZNF766 ZNF207 ENSG00000274698 PIR55988 SMPD3 ZFP90
GH16I068414 Enhancer 1.3 FANTOM5 Ensembl ENCODE 11.8 +31.4 31447 4.6 PKNOX1 FOXA2 SMAD1 NFIB RAD21 YY1 ZNF335 RXRA JUNB REST SLC7A6OS SMPD3 ZFP90 PRMT7 RNU4-36P UTP4 CDH1 NFATC3 PSMB10 DPEP2
GH16I068509 Enhancer 1.2 FANTOM5 Ensembl ENCODE 12.2 -61.4 -61447 1 ELF3 RB1 ARID4B ZNF48 RAD21 ZNF143 BCLAF1 RUNX3 CREM THAP11 GC16M068509 PIR38497 SMPD3 RNU4-36P ZFP90 LOC105371321
GH16I068489 Enhancer 1.1 FANTOM5 ENCODE dbSUPER 12.3 -43.3 -43284 4.1 GTF2F1 PKNOX1 USF1 ZIC2 RFX5 ZNF507 HNF4G FOS FOSL2 ZNF687 SMPD3 RNU4-36P ZFP90 GC16M068485 GC16M068494 PIR40396
GH16I068520 Enhancer 1.1 Ensembl ENCODE 11.3 -72.1 -72122 0.8 ATF1 ZFP64 ARID4B NEUROD1 SIN3A DMAP1 ZNF2 ZNF48 ETS1 SLC30A9 ZFP90 SMPD3 PRMT7 SLC7A6OS LOC105371321
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SMPD3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SMPD3 gene promoter:

Genomic Locations for SMPD3 Gene

Genomic Locations for SMPD3 Gene
chr16:68,358,325-68,448,688
(GRCh38/hg38)
Size:
90,364 bases
Orientation:
Minus strand
chr16:68,392,230-68,482,591
(GRCh37/hg19)

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.

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

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 BiophysicochemicalProperties:
pH dependence: Optimum pH is 7.5.;
UniProtKB/Swiss-Prot CatalyticActivity:
Sphingomyelin + H(2)O = N-acylsphingosine + phosphocholine.
UniProtKB/Swiss-Prot EnzymeRegulation:
Activated by unsaturated fatty acids and phosphatidylserine.
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.

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:0004767 sphingomyelin phosphodiesterase activity IEA --
GO:0005515 protein binding IPI 20080539
GO:0016787 hydrolase activity IEA --
GO:0046872 metal ion 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:

miRNA for SMPD3 Gene

miRTarBase miRNAs that target SMPD3

Clone Products

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
extracellular 3
golgi apparatus 3
endosome 2
peroxisome 1
nucleus 1
cytosol 1
lysosome 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:0005794 Golgi apparatus IEA --
GO:0005886 plasma membrane TAS --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with SMPD3: view

Pathways & Interactions for SMPD3 Gene

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

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:0002244 hematopoietic progenitor cell differentiation IEA --
GO:0006629 lipid metabolic process IEA --
GO:0006665 sphingolipid metabolic process IEA --
GO:0006684 sphingomyelin metabolic process IEA --
GO:0006685 sphingomyelin catabolic process TAS 10823942
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
Water Approved Pharma 0
Magnesium Approved Nutra 0
PHOSPHATIDYLSERINE Pharma 0

(248) 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

Unigene Clusters for SMPD3 Gene

Sphingomyelin phosphodiesterase 3, neutral membrane (neutral sphingomyelinase II):
Representative Sequences:

Clone Products

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
ECgene alternative splicing isoforms for
SMPD3

Expression for SMPD3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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, PaxDb, and MOPED for SMPD3 Gene



NURSA nuclear receptor signaling pathways regulating expression of SMPD3 Gene:

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(4.4)
  • Liver(4.2)
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 33 34
  • 99.39 (n)
dog
(Canis familiaris)
Mammalia SMPD3 33 34
  • 88.35 (n)
cow
(Bos Taurus)
Mammalia SMPD3 33 34
  • 88.18 (n)
rat
(Rattus norvegicus)
Mammalia Smpd3 33
  • 87.17 (n)
mouse
(Mus musculus)
Mammalia Smpd3 33 16 34
  • 86.93 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SMPD3 34
  • 71 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SMPD3 34
  • 68 (a)
OneToOne
chicken
(Gallus gallus)
Aves SMPD3 33 34
  • 69.89 (n)
lizard
(Anolis carolinensis)
Reptilia SMPD3 34
  • 71 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia smpd3 33
  • 67.69 (n)
zebrafish
(Danio rerio)
Actinopterygii smpd3 33 34
  • 62.37 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 28 (a)
OneToOne
Species where no ortholog for SMPD3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 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)

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

Sequence variations from dbSNP and Humsavar for SMPD3 Gene

SNP ID Clin Chr 16 pos Variation AA Info Type
rs1000003195 -- 68,396,382(-) A/G genic_upstream_transcript_variant, intron_variant
rs1000015622 -- 68,380,201(-) T/A intron_variant
rs1000036009 -- 68,402,803(-) A/T genic_upstream_transcript_variant, intron_variant
rs1000103101 -- 68,416,298(-) T/G genic_upstream_transcript_variant, intron_variant
rs1000154444 -- 68,448,363(-) GGG/GG 5_prime_UTR_variant, genic_upstream_transcript_variant

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SMPD3 Gene

Disorders for SMPD3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for SMPD3 Gene - From: DISEASES

Disorder Aliases PubMed IDs
deafness, autosomal recessive 89
  • dfnb89
- 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
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 22 58
  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 22 25 58
  3. Hydrolysis of sphingosylphosphocholine by neutral sphingomyelinases. (PMID: 14741383) Miura Y … Hanada K (FEBS letters 2004) 3 4 22 58
  4. 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 22 58
  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 58

Products for SMPD3 Gene

Sources for SMPD3 Gene

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