Atlas of Genetics and Cytogenetics in Oncology and Haematology


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SMPD4 (sphingomyelin phosphodiesterase 4)

Identity

Alias_namessphingomyelin phosphodiesterase 4
Alias_symbol (synonym)FLJ20297
FLJ20756
nSMase-3
KIAA1418
NSMASE3
NET13
Other aliasNSMASE-3
HGNC (Hugo) SMPD4
LocusID (NCBI) 55627
Atlas_Id 50381
Location 2q21.1  [Link to chromosome band 2q21]
Location_base_pair Starts at 130151392 and ends at 130181757 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2016)
SMPD4 (2q21.1) / MDH1 (2p15)SMPD4 (2q21.1) / MTCH1 (6p21.2)

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 


External links

Nomenclature
HGNC (Hugo)SMPD4   32949
Cards
Entrez_Gene (NCBI)SMPD4  55627  sphingomyelin phosphodiesterase 4
AliasesNET13; NSMASE-3; NSMASE3
GeneCards (Weizmann)SMPD4
Ensembl hg19 (Hinxton)ENSG00000136699 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000136699 [Gene_View]  chr2:130151392-130181757 [Contig_View]  SMPD4 [Vega]
ICGC DataPortalENSG00000136699
TCGA cBioPortalSMPD4
AceView (NCBI)SMPD4
Genatlas (Paris)SMPD4
WikiGenes55627
SOURCE (Princeton)SMPD4
Genetics Home Reference (NIH)SMPD4
Genomic and cartography
GoldenPath hg38 (UCSC)SMPD4  -     chr2:130151392-130181757 -  2q21.1   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SMPD4  -     2q21.1   [Description]    (hg19-Feb_2009)
EnsemblSMPD4 - 2q21.1 [CytoView hg19]  SMPD4 - 2q21.1 [CytoView hg38]
Mapping of homologs : NCBISMPD4 [Mapview hg19]  SMPD4 [Mapview hg38]
OMIM610457   
Gene and transcription
Genbank (Entrez)AA232420 AB037839 AF052134 AI393912 AK000304
RefSeq transcript (Entrez)NM_001171083 NM_001171084 NM_017751 NM_017951
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SMPD4
Cluster EST : UnigeneHs.516450 [ NCBI ]
CGAP (NCI)Hs.516450
Alternative Splicing GalleryENSG00000136699
Gene ExpressionSMPD4 [ NCBI-GEO ]   SMPD4 [ EBI - ARRAY_EXPRESS ]   SMPD4 [ SEEK ]   SMPD4 [ MEM ]
Gene Expression Viewer (FireBrowse)SMPD4 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)55627
GTEX Portal (Tissue expression)SMPD4
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9NXE4   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9NXE4  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9NXE4
Splice isoforms : SwissVarQ9NXE4
Catalytic activity : Enzyme3.1.4.12 [ Enzyme-Expasy ]   3.1.4.123.1.4.12 [ IntEnz-EBI ]   3.1.4.12 [ BRENDA ]   3.1.4.12 [ KEGG ]   
PhosPhoSitePlusQ9NXE4
Domains : Interpro (EBI)Sphingomy_SMPD4   
Domain families : Pfam (Sanger)mit_SMPDase (PF14724)   
Domain families : Pfam (NCBI)pfam14724   
Conserved Domain (NCBI)SMPD4
DMDM Disease mutations55627
Blocks (Seattle)SMPD4
SuperfamilyQ9NXE4
Human Protein AtlasENSG00000136699
Peptide AtlasQ9NXE4
HPRD13374
IPIIPI00827746   IPI00828125   IPI00828176   IPI00743121   IPI00909249   IPI00910965   IPI01016049   IPI00940103   IPI00910464   IPI00793691   IPI00903175   IPI00852777   IPI00915805   IPI00917957   IPI00917450   IPI00916412   IPI00916439   IPI00916086   
Protein Interaction databases
DIP (DOE-UCLA)Q9NXE4
IntAct (EBI)Q9NXE4
FunCoupENSG00000136699
BioGRIDSMPD4
STRING (EMBL)SMPD4
ZODIACSMPD4
Ontologies - Pathways
QuickGOQ9NXE4
Ontology : AmiGOGolgi membrane  sphingomyelin phosphodiesterase activity  endoplasmic reticulum  endoplasmic reticulum membrane  Golgi apparatus  trans-Golgi network  sphingomyelin catabolic process  glycosphingolipid metabolic process  integral component of membrane  glycerophospholipid catabolic process  ceramide biosynthetic process  metal ion binding  sphingomyelin phosphodiesterase D activity  cellular response to tumor necrosis factor  
Ontology : EGO-EBIGolgi membrane  sphingomyelin phosphodiesterase activity  endoplasmic reticulum  endoplasmic reticulum membrane  Golgi apparatus  trans-Golgi network  sphingomyelin catabolic process  glycosphingolipid metabolic process  integral component of membrane  glycerophospholipid catabolic process  ceramide biosynthetic process  metal ion binding  sphingomyelin phosphodiesterase D activity  cellular response to tumor necrosis factor  
Pathways : KEGGSphingolipid metabolism   
NDEx NetworkSMPD4
Atlas of Cancer Signalling NetworkSMPD4
Wikipedia pathwaysSMPD4
Orthology - Evolution
OrthoDB55627
GeneTree (enSembl)ENSG00000136699
Phylogenetic Trees/Animal Genes : TreeFamSMPD4
HOVERGENQ9NXE4
HOGENOMQ9NXE4
Homologs : HomoloGeneSMPD4
Homology/Alignments : Family Browser (UCSC)SMPD4
Gene fusions - Rearrangements
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSMPD4 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SMPD4
dbVarSMPD4
ClinVarSMPD4
1000_GenomesSMPD4 
Exome Variant ServerSMPD4
ExAC (Exome Aggregation Consortium)SMPD4 (select the gene name)
Genetic variants : HAPMAP55627
Genomic Variants (DGV)SMPD4 [DGVbeta]
DECIPHERSMPD4 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSMPD4 
Mutations
ICGC Data PortalSMPD4 
TCGA Data PortalSMPD4 
Broad Tumor PortalSMPD4
OASIS PortalSMPD4 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSMPD4  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDSMPD4
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch SMPD4
DgiDB (Drug Gene Interaction Database)SMPD4
DoCM (Curated mutations)SMPD4 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SMPD4 (select a term)
intoGenSMPD4
Cancer3DSMPD4(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM610457   
Orphanet
MedgenSMPD4
Genetic Testing Registry SMPD4
NextProtQ9NXE4 [Medical]
TSGene55627
GENETestsSMPD4
Target ValidationSMPD4
Huge Navigator SMPD4 [HugePedia]
snp3D : Map Gene to Disease55627
BioCentury BCIQSMPD4
ClinGenSMPD4
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD55627
Chemical/Pharm GKB GenePA145148067
Clinical trialSMPD4
Miscellaneous
canSAR (ICR)SMPD4 (select the gene name)
Probes
Litterature
PubMed24 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSMPD4
EVEXSMPD4
GoPubMedSMPD4
iHOPSMPD4
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Wed Jun 7 12:56:35 CEST 2017

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