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SPTLC3 (serine palmitoyltransferase long chain base subunit 3)

Identity

Alias_namesC20orf38
SPTLC2L
chromosome 20 open reading frame 38
serine palmitoyltransferase, long chain base subunit 2-like (aminotransferase 2)
Alias_symbol (synonym)LCB2B
FLJ11112
hLCB2b
Other aliasLCB 3
LCB3
SPT 3
SPT3
dJ718P11
dJ718P11.1
HGNC (Hugo) SPTLC3
LocusID (NCBI) 55304
Atlas_Id 881
Location 20p12.1  [Link to chromosome band 20p12]
Location_base_pair Starts at 13008954 and ends at 13166764 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2016)
BHMT2 (5q14.1) / SPTLC3 (20p12.1)CCDC69 (5q33.1) / SPTLC3 (20p12.1)SPTLC3 (20p12.1) / AC040934.1 ()
SPTLC3 (20p12.1) / MAOA (Xp11.3)SPTLC3 (20p12.1) / PLPP1 (5q11.2)SPTLC3 20p12.1 AC040934.1
SPTLC3 20p12.1 / PPAP2A 5q11.2

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

 


Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 1 ]
  Lung: Translocations in Adenocarcinoma


External links

Nomenclature
HGNC (Hugo)SPTLC3   16253
Cards
Entrez_Gene (NCBI)SPTLC3  55304  serine palmitoyltransferase long chain base subunit 3
AliasesC20orf38; LCB; LCB2B; LCB3; 
SPT; SPT3; SPTLC2L; dJ718P11; dJ718P11.1; hLCB2b
GeneCards (Weizmann)SPTLC3
Ensembl hg19 (Hinxton)ENSG00000172296 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000172296 [Gene_View]  chr20:13008954-13166764 [Contig_View]  SPTLC3 [Vega]
ICGC DataPortalENSG00000172296
TCGA cBioPortalSPTLC3
AceView (NCBI)SPTLC3
Genatlas (Paris)SPTLC3
WikiGenes55304
SOURCE (Princeton)SPTLC3
Genetics Home Reference (NIH)SPTLC3
Genomic and cartography
GoldenPath hg38 (UCSC)SPTLC3  -     chr20:13008954-13166764 +  20p12.1   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SPTLC3  -     20p12.1   [Description]    (hg19-Feb_2009)
EnsemblSPTLC3 - 20p12.1 [CytoView hg19]  SPTLC3 - 20p12.1 [CytoView hg38]
Mapping of homologs : NCBISPTLC3 [Mapview hg19]  SPTLC3 [Mapview hg38]
OMIM611120   
Gene and transcription
Genbank (Entrez)AK001974 AK075271 AK300184 AL844429 BC005205
RefSeq transcript (Entrez)NM_001349945 NM_018327
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SPTLC3
Cluster EST : UnigeneHs.425023 [ NCBI ]
CGAP (NCI)Hs.425023
Alternative Splicing GalleryENSG00000172296
Gene ExpressionSPTLC3 [ NCBI-GEO ]   SPTLC3 [ EBI - ARRAY_EXPRESS ]   SPTLC3 [ SEEK ]   SPTLC3 [ MEM ]
Gene Expression Viewer (FireBrowse)SPTLC3 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)55304
GTEX Portal (Tissue expression)SPTLC3
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9NUV7   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9NUV7  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9NUV7
Splice isoforms : SwissVarQ9NUV7
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 ]   
PhosPhoSitePlusQ9NUV7
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_major_sub1    PyrdxlP-dep_Trfase_major_sub2   
Domain families : Pfam (Sanger)Aminotran_1_2 (PF00155)   
Domain families : Pfam (NCBI)pfam00155   
Conserved Domain (NCBI)SPTLC3
DMDM Disease mutations55304
Blocks (Seattle)SPTLC3
SuperfamilyQ9NUV7
Human Protein AtlasENSG00000172296
Peptide AtlasQ9NUV7
HPRD12765
IPIIPI00794843   IPI00910557   IPI01018293   IPI00641753   IPI00640240   
Protein Interaction databases
DIP (DOE-UCLA)Q9NUV7
IntAct (EBI)Q9NUV7
FunCoupENSG00000172296
BioGRIDSPTLC3
STRING (EMBL)SPTLC3
ZODIACSPTLC3
Ontologies - Pathways
QuickGOQ9NUV7
Ontology : AmiGOserine C-palmitoyltransferase activity  serine C-palmitoyltransferase activity  endoplasmic reticulum membrane  integral component of membrane  serine C-palmitoyltransferase complex  sphingolipid biosynthetic process  pyridoxal phosphate binding  sphingoid biosynthetic process  
Ontology : EGO-EBIserine C-palmitoyltransferase activity  serine C-palmitoyltransferase activity  endoplasmic reticulum membrane  integral component of membrane  serine C-palmitoyltransferase complex  sphingolipid biosynthetic process  pyridoxal phosphate binding  sphingoid biosynthetic process  
Pathways : KEGGSphingolipid metabolism   
NDEx NetworkSPTLC3
Atlas of Cancer Signalling NetworkSPTLC3
Wikipedia pathwaysSPTLC3
Orthology - Evolution
OrthoDB55304
GeneTree (enSembl)ENSG00000172296
Phylogenetic Trees/Animal Genes : TreeFamSPTLC3
HOVERGENQ9NUV7
HOGENOMQ9NUV7
Homologs : HomoloGeneSPTLC3
Homology/Alignments : Family Browser (UCSC)SPTLC3
Gene fusions - Rearrangements
Fusion : MitelmanSPTLC3/MAOA [20p12.1/Xp11.3]  
Fusion : MitelmanSPTLC3/PPAP2A [20p12.1/5q11.2]  [t(5;20)(q11;p12)]  
Fusion: TCGASPTLC3 20p12.1 AC040934.1 BRCA
Fusion: TCGASPTLC3 20p12.1 PPAP2A 5q11.2 OV
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSPTLC3 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SPTLC3
dbVarSPTLC3
ClinVarSPTLC3
1000_GenomesSPTLC3 
Exome Variant ServerSPTLC3
ExAC (Exome Aggregation Consortium)SPTLC3 (select the gene name)
Genetic variants : HAPMAP55304
Genomic Variants (DGV)SPTLC3 [DGVbeta]
DECIPHERSPTLC3 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSPTLC3 
Mutations
ICGC Data PortalSPTLC3 
TCGA Data PortalSPTLC3 
Broad Tumor PortalSPTLC3
OASIS PortalSPTLC3 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSPTLC3  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDSPTLC3
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 SPTLC3
DgiDB (Drug Gene Interaction Database)SPTLC3
DoCM (Curated mutations)SPTLC3 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SPTLC3 (select a term)
intoGenSPTLC3
Cancer3DSPTLC3(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM611120   
Orphanet
MedgenSPTLC3
Genetic Testing Registry SPTLC3
NextProtQ9NUV7 [Medical]
TSGene55304
GENETestsSPTLC3
Target ValidationSPTLC3
Huge Navigator SPTLC3 [HugePedia]
snp3D : Map Gene to Disease55304
BioCentury BCIQSPTLC3
ClinGenSPTLC3
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD55304
Chemical/Pharm GKB GenePA162404677
Clinical trialSPTLC3
Miscellaneous
canSAR (ICR)SPTLC3 (select the gene name)
Probes
Litterature
PubMed22 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSPTLC3
EVEXSPTLC3
GoPubMedSPTLC3
iHOPSPTLC3
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Mon Sep 25 19:32:55 CEST 2017

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