Atlas of Genetics and Cytogenetics in Oncology and Haematology


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SMPD2 (sphingomyelin phosphodiesterase 2)

Identity

Alias (NCBI)ISC1
NSMASE
NSMASE1
HGNC (Hugo) SMPD2
HGNC Alias symbnSMase
ISC1
HGNC Alias nameneutral sphingomyelinase
HGNC Previous namesphingomyelin phosphodiesterase 2, neutral membrane (neutral sphingomyelinase)
LocusID (NCBI) 6610
Atlas_Id 52064
Location 6q21  [Link to chromosome band 6q21]
Location_base_pair Starts at 109440724 and ends at 109443919 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)

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)SMPD2   11121
Cards
Entrez_Gene (NCBI)SMPD2  6610  sphingomyelin phosphodiesterase 2
AliasesISC1; NSMASE; NSMASE1
GeneCards (Weizmann)SMPD2
Ensembl hg19 (Hinxton)ENSG00000135587 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000135587 [Gene_View]  ENSG00000135587 [Sequence]  chr6:109440724-109443919 [Contig_View]  SMPD2 [Vega]
ICGC DataPortalENSG00000135587
TCGA cBioPortalSMPD2
AceView (NCBI)SMPD2
Genatlas (Paris)SMPD2
WikiGenes6610
SOURCE (Princeton)SMPD2
Genetics Home Reference (NIH)SMPD2
Genomic and cartography
GoldenPath hg38 (UCSC)SMPD2  -     chr6:109440724-109443919 +  6q21   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SMPD2  -     6q21   [Description]    (hg19-Feb_2009)
GoldenPathSMPD2 - 6q21 [CytoView hg19]  SMPD2 - 6q21 [CytoView hg38]
ImmunoBaseENSG00000135587
genome Data Viewer NCBISMPD2 [Mapview hg19]  
OMIM603498   
Gene and transcription
Genbank (Entrez)AJ222801 AK310148 AK313515 BC000038 CA314251
RefSeq transcript (Entrez)NM_003080
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SMPD2
Alternative Splicing GalleryENSG00000135587
Gene ExpressionSMPD2 [ NCBI-GEO ]   SMPD2 [ EBI - ARRAY_EXPRESS ]   SMPD2 [ SEEK ]   SMPD2 [ MEM ]
Gene Expression Viewer (FireBrowse)SMPD2 [ Firebrowse - Broad ]
GenevisibleExpression of SMPD2 in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)6610
GTEX Portal (Tissue expression)SMPD2
Human Protein AtlasENSG00000135587-SMPD2 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtO60906   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtO60906  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProO60906
Splice isoforms : SwissVarO60906
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 ]   [ MEROPS ]
PhosPhoSitePlusO60906
Domains : Interpro (EBI)Endo/exonu/phosph_ase_sf    Endo/exonuclease/phosphatase    SMPD2-like   
Domain families : Pfam (Sanger)Exo_endo_phos (PF03372)   
Domain families : Pfam (NCBI)pfam03372   
Conserved Domain (NCBI)SMPD2
DMDM Disease mutations6610
Blocks (Seattle)SMPD2
SuperfamilyO60906
Human Protein Atlas [tissue]ENSG00000135587-SMPD2 [tissue]
Peptide AtlasO60906
HPRD04608
IPIIPI00017670   IPI00646648   IPI00514319   
Protein Interaction databases
DIP (DOE-UCLA)O60906
IntAct (EBI)O60906
FunCoupENSG00000135587
BioGRIDSMPD2
STRING (EMBL)SMPD2
ZODIACSMPD2
Ontologies - Pathways
QuickGOO60906
Ontology : AmiGOsphingomyelin phosphodiesterase activity  endoplasmic reticulum  plasma membrane  integral component of plasma membrane  caveola  sphingomyelin metabolic process  sphingomyelin catabolic process  glycosphingolipid metabolic process  response to mechanical stimulus  membrane  sphingolipid catabolic process  intracellular signal transduction  ceramide biosynthetic process  ceramide biosynthetic process  metal ion binding  cell periphery  positive regulation of ceramide biosynthetic process  
Ontology : EGO-EBIsphingomyelin phosphodiesterase activity  endoplasmic reticulum  plasma membrane  integral component of plasma membrane  caveola  sphingomyelin metabolic process  sphingomyelin catabolic process  glycosphingolipid metabolic process  response to mechanical stimulus  membrane  sphingolipid catabolic process  intracellular signal transduction  ceramide biosynthetic process  ceramide biosynthetic process  metal ion binding  cell periphery  positive regulation of ceramide biosynthetic process  
Pathways : KEGGSphingolipid metabolism   
NDEx NetworkSMPD2
Atlas of Cancer Signalling NetworkSMPD2
Wikipedia pathwaysSMPD2
Orthology - Evolution
OrthoDB6610
GeneTree (enSembl)ENSG00000135587
Phylogenetic Trees/Animal Genes : TreeFamSMPD2
HOGENOMO60906
Homologs : HomoloGeneSMPD2
Homology/Alignments : Family Browser (UCSC)SMPD2
Gene fusions - Rearrangements
Fusion : QuiverSMPD2
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSMPD2 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SMPD2
dbVarSMPD2
ClinVarSMPD2
MonarchSMPD2
1000_GenomesSMPD2 
Exome Variant ServerSMPD2
GNOMAD BrowserENSG00000135587
Varsome BrowserSMPD2
Genetic variants : HAPMAP6610
Genomic Variants (DGV)SMPD2 [DGVbeta]
DECIPHERSMPD2 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSMPD2 
Mutations
ICGC Data PortalSMPD2 
TCGA Data PortalSMPD2 
Broad Tumor PortalSMPD2
OASIS PortalSMPD2 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSMPD2  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DSMPD2
Mutations and Diseases : HGMDSMPD2
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 SMPD2
DgiDB (Drug Gene Interaction Database)SMPD2
DoCM (Curated mutations)SMPD2 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SMPD2 (select a term)
intoGenSMPD2
Cancer3DSMPD2(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM603498   
Orphanet
DisGeNETSMPD2
MedgenSMPD2
Genetic Testing Registry SMPD2
NextProtO60906 [Medical]
TSGene6610
GENETestsSMPD2
Target ValidationSMPD2
Huge Navigator SMPD2 [HugePedia]
snp3D : Map Gene to Disease6610
BioCentury BCIQSMPD2
ClinGenSMPD2
Clinical trials, drugs, therapy
Protein Interactions : CTD6610
Pharm GKB GenePA35970
Clinical trialSMPD2
Miscellaneous
canSAR (ICR)SMPD2 (select the gene name)
HarmonizomeSMPD2
DataMed IndexSMPD2
Probes
Litterature
PubMed42 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSMPD2
EVEXSMPD2
GoPubMedSMPD2
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Mon Sep 14 14:33:31 CEST 2020

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