Atlas of Genetics and Cytogenetics in Oncology and Haematology

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SPTLC2 (serine palmitoyltransferase long chain base subunit 2)

Identity

Alias_symbol (synonym)KIAA0526
LCB2
LCB2A
hLCB2a
Other aliasHSN1C
NSAN1C
SPT2
HGNC (Hugo) SPTLC2
LocusID (NCBI) 9517
Atlas_Id 74218
Location 14q24.3  [Link to chromosome band 14q24]
Location_base_pair Starts at 77505997 and ends at 77616767 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)
SPTLC2 (14q24.3) / ACTB (7p22.1)SPTLC2 (14q24.3) / PID1 (2q36.3)SPTLC2 (14q24.3) / SPTLC2 (14q24.3)
SURF4 (9q34.2) / SPTLC2 (14q24.3)

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)SPTLC2   11278
LRG (Locus Reference Genomic)LRG_371
Cards
Entrez_Gene (NCBI)SPTLC2  9517  serine palmitoyltransferase long chain base subunit 2
AliasesHSN1C; LCB2; LCB2A; NSAN1C; 
SPT2; hLCB2a
GeneCards (Weizmann)SPTLC2
Ensembl hg19 (Hinxton)ENSG00000100596 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000100596 [Gene_View]  ENSG00000100596 [Sequence]  chr14:77505997-77616767 [Contig_View]  SPTLC2 [Vega]
ICGC DataPortalENSG00000100596
TCGA cBioPortalSPTLC2
AceView (NCBI)SPTLC2
Genatlas (Paris)SPTLC2
WikiGenes9517
SOURCE (Princeton)SPTLC2
Genetics Home Reference (NIH)SPTLC2
Genomic and cartography
GoldenPath hg38 (UCSC)SPTLC2  -     chr14:77505997-77616767 -  14q24.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SPTLC2  -     14q24.3   [Description]    (hg19-Feb_2009)
GoldenPathSPTLC2 - 14q24.3 [CytoView hg19]  SPTLC2 - 14q24.3 [CytoView hg38]
ImmunoBaseENSG00000100596
Mapping of homologs : NCBISPTLC2 [Mapview hg19]  SPTLC2 [Mapview hg38]
OMIM605713   613640   
Gene and transcription
Genbank (Entrez)AB011098 BC005123 BG024616 BM992457 BQ338973
RefSeq transcript (Entrez)NM_004863
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SPTLC2
Cluster EST : UnigeneHs.435661 [ NCBI ]
CGAP (NCI)Hs.435661
Alternative Splicing GalleryENSG00000100596
Gene ExpressionSPTLC2 [ NCBI-GEO ]   SPTLC2 [ EBI - ARRAY_EXPRESS ]   SPTLC2 [ SEEK ]   SPTLC2 [ MEM ]
Gene Expression Viewer (FireBrowse)SPTLC2 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)9517
GTEX Portal (Tissue expression)SPTLC2
Human Protein AtlasENSG00000100596-SPTLC2 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtO15270   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtO15270  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProO15270
Splice isoforms : SwissVarO15270
Catalytic activity : Enzyme2.3.1.50 [ Enzyme-Expasy ]   2.3.1.502.3.1.50 [ IntEnz-EBI ]   2.3.1.50 [ BRENDA ]   2.3.1.50 [ KEGG ]   
PhosPhoSitePlusO15270
Domaine pattern : Prosite (Expaxy)AA_TRANSFER_CLASS_2 (PS00599)   
Domains : Interpro (EBI)Aminotrans_II_pyridoxalP_BS    Aminotransferase_I/II    PyrdxlP-dep_Trfase    PyrdxlP-dep_Trfase_dom1    PyrdxlP-dep_Trfase_major   
Domain families : Pfam (Sanger)Aminotran_1_2 (PF00155)   
Domain families : Pfam (NCBI)pfam00155   
Conserved Domain (NCBI)SPTLC2
DMDM Disease mutations9517
Blocks (Seattle)SPTLC2
SuperfamilyO15270
Human Protein Atlas [tissue]ENSG00000100596-SPTLC2 [tissue]
Peptide AtlasO15270
HPRD05755
IPIIPI00005751   IPI01025835   IPI01025616   
Protein Interaction databases
DIP (DOE-UCLA)O15270
IntAct (EBI)O15270
FunCoupENSG00000100596
BioGRIDSPTLC2
STRING (EMBL)SPTLC2
ZODIACSPTLC2
Ontologies - Pathways
QuickGOO15270
Ontology : AmiGOserine C-palmitoyltransferase activity  serine C-palmitoyltransferase activity  endoplasmic reticulum membrane  sphingomyelin biosynthetic process  integral component of membrane  serine C-palmitoyltransferase complex  sphingolipid biosynthetic process  sphingolipid biosynthetic process  pyridoxal phosphate binding  sphinganine biosynthetic process  sphingosine biosynthetic process  ceramide biosynthetic process  adipose tissue development  positive regulation of lipophagy  
Ontology : EGO-EBIserine C-palmitoyltransferase activity  serine C-palmitoyltransferase activity  endoplasmic reticulum membrane  sphingomyelin biosynthetic process  integral component of membrane  serine C-palmitoyltransferase complex  sphingolipid biosynthetic process  sphingolipid biosynthetic process  pyridoxal phosphate binding  sphinganine biosynthetic process  sphingosine biosynthetic process  ceramide biosynthetic process  adipose tissue development  positive regulation of lipophagy  
Pathways : KEGGSphingolipid metabolism   
NDEx NetworkSPTLC2
Atlas of Cancer Signalling NetworkSPTLC2
Wikipedia pathwaysSPTLC2
Orthology - Evolution
OrthoDB9517
GeneTree (enSembl)ENSG00000100596
Phylogenetic Trees/Animal Genes : TreeFamSPTLC2
HOGENOMO15270
Homologs : HomoloGeneSPTLC2
Homology/Alignments : Family Browser (UCSC)SPTLC2
Gene fusions - Rearrangements
Fusion : QuiverSPTLC2
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSPTLC2 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SPTLC2
dbVarSPTLC2
ClinVarSPTLC2
1000_GenomesSPTLC2 
Exome Variant ServerSPTLC2
ExAC (Exome Aggregation Consortium)ENSG00000100596
GNOMAD BrowserENSG00000100596
Varsome BrowserSPTLC2
Genetic variants : HAPMAP9517
Genomic Variants (DGV)SPTLC2 [DGVbeta]
DECIPHERSPTLC2 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSPTLC2 
Mutations
ICGC Data PortalSPTLC2 
TCGA Data PortalSPTLC2 
Broad Tumor PortalSPTLC2
OASIS PortalSPTLC2 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSPTLC2  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DSPTLC2
Mutations and Diseases : HGMDSPTLC2
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)Leiden Muscular Dystrophy pages
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
LOVD (Leiden Open Variation Database)MSeqDR-LSDB Mitochondrial Disease Locus Specific Database
BioMutasearch SPTLC2
DgiDB (Drug Gene Interaction Database)SPTLC2
DoCM (Curated mutations)SPTLC2 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SPTLC2 (select a term)
intoGenSPTLC2
Cancer3DSPTLC2(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM605713    613640   
Orphanet10423   
DisGeNETSPTLC2
MedgenSPTLC2
Genetic Testing Registry SPTLC2
NextProtO15270 [Medical]
TSGene9517
GENETestsSPTLC2
Target ValidationSPTLC2
Huge Navigator SPTLC2 [HugePedia]
snp3D : Map Gene to Disease9517
BioCentury BCIQSPTLC2
ClinGenSPTLC2
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD9517
Chemical/Pharm GKB GenePA36107
Clinical trialSPTLC2
Miscellaneous
canSAR (ICR)SPTLC2 (select the gene name)
DataMed IndexSPTLC2
Probes
Litterature
PubMed37 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSPTLC2
EVEXSPTLC2
GoPubMedSPTLC2
iHOPSPTLC2
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Tue Sep 3 16:08:38 CEST 2019
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