Atlas of Genetics and Cytogenetics in Oncology and Haematology


Home   Genes   Leukemias   Solid Tumors   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

X Y 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 NA

SPTLC1 (serine palmitoyltransferase long chain base subunit 1)

Identity

Alias (NCBI)HSAN1
HSN1
LBC1
LCB1
SPT1
SPTI
HGNC (Hugo) SPTLC1
HGNC Alias symbLCB1
SPTI
HSAN1
hLCB1
HGNC Previous nameHSN1
HGNC Previous namehereditary sensory neuropathy, type 1
LocusID (NCBI) 10558
Atlas_Id 54668
Location 9q22.31  [Link to chromosome band 9q22]
Location_base_pair Starts at 92079061 and ends at 92115413 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)
ACSS1 (20p11.21) / SPTLC1 (9q22.31)DTNB (2p23.3) / SPTLC1 (9q22.31)ITIH3 (3p21.1) / SPTLC1 (9q22.31)
MRPL51 (12p13.31) / SPTLC1 (9q22.31)PLD5 (1q43) / SPTLC1 (9q22.31)SPTLC1 (9q22.31) / SPTLC1 (9q22.31)

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 ]
  t(2;9)(p23;q22) DTNB/SPTLC1


External links

Nomenclature
HGNC (Hugo)SPTLC1   11277
LRG (Locus Reference Genomic)LRG_272
Cards
Entrez_Gene (NCBI)SPTLC1  10558  serine palmitoyltransferase long chain base subunit 1
AliasesHSAN1; HSN1; LBC1; LCB1; 
SPT1; SPTI
GeneCards (Weizmann)SPTLC1
Ensembl hg19 (Hinxton)ENSG00000090054 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000090054 [Gene_View]  ENSG00000090054 [Sequence]  chr9:92079061-92115413 [Contig_View]  SPTLC1 [Vega]
ICGC DataPortalENSG00000090054
TCGA cBioPortalSPTLC1
AceView (NCBI)SPTLC1
Genatlas (Paris)SPTLC1
WikiGenes10558
SOURCE (Princeton)SPTLC1
Genetics Home Reference (NIH)SPTLC1
Genomic and cartography
GoldenPath hg38 (UCSC)SPTLC1  -     chr9:92079061-92115413 -  9q22.31   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SPTLC1  -     9q22.31   [Description]    (hg19-Feb_2009)
GoldenPathSPTLC1 - 9q22.31 [CytoView hg19]  SPTLC1 - 9q22.31 [CytoView hg38]
ImmunoBaseENSG00000090054
genome Data Viewer NCBISPTLC1 [Mapview hg19]  
OMIM162400   605712   
Gene and transcription
Genbank (Entrez)AB209757 AF147304 AK098344 AK291546 AK299153
RefSeq transcript (Entrez)NM_001281303 NM_001368272 NM_001368273 NM_006415 NM_178324
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SPTLC1
Alternative Splicing GalleryENSG00000090054
Gene ExpressionSPTLC1 [ NCBI-GEO ]   SPTLC1 [ EBI - ARRAY_EXPRESS ]   SPTLC1 [ SEEK ]   SPTLC1 [ MEM ]
Gene Expression Viewer (FireBrowse)SPTLC1 [ Firebrowse - Broad ]
GenevisibleExpression of SPTLC1 in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)10558
GTEX Portal (Tissue expression)SPTLC1
Human Protein AtlasENSG00000090054-SPTLC1 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtO15269   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtO15269  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProO15269
Splice isoforms : SwissVarO15269
PhosPhoSitePlusO15269
Domains : Interpro (EBI)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)SPTLC1
DMDM Disease mutations10558
Blocks (Seattle)SPTLC1
SuperfamilyO15269
Human Protein Atlas [tissue]ENSG00000090054-SPTLC1 [tissue]
Peptide AtlasO15269
HPRD05754
IPIIPI00005745   IPI00259092   
Protein Interaction databases
DIP (DOE-UCLA)O15269
IntAct (EBI)O15269
FunCoupENSG00000090054
BioGRIDSPTLC1
STRING (EMBL)SPTLC1
ZODIACSPTLC1
Ontologies - Pathways
QuickGOO15269
Ontology : AmiGOserine C-palmitoyltransferase activity  serine C-palmitoyltransferase activity  protein binding  endoplasmic reticulum  endoplasmic reticulum  endoplasmic reticulum membrane  sphingolipid metabolic process  sphingomyelin biosynthetic process  integral component of membrane  serine C-palmitoyltransferase complex  sphingolipid biosynthetic process  sphingolipid biosynthetic process  pyridoxal phosphate binding  SPOTS complex  sphinganine biosynthetic process  sphingosine biosynthetic process  ceramide biosynthetic process  ceramide biosynthetic process  positive regulation of lipophagy  regulation of fat cell apoptotic process  
Ontology : EGO-EBIserine C-palmitoyltransferase activity  serine C-palmitoyltransferase activity  protein binding  endoplasmic reticulum  endoplasmic reticulum  endoplasmic reticulum membrane  sphingolipid metabolic process  sphingomyelin biosynthetic process  integral component of membrane  serine C-palmitoyltransferase complex  sphingolipid biosynthetic process  sphingolipid biosynthetic process  pyridoxal phosphate binding  SPOTS complex  sphinganine biosynthetic process  sphingosine biosynthetic process  ceramide biosynthetic process  ceramide biosynthetic process  positive regulation of lipophagy  regulation of fat cell apoptotic process  
Pathways : KEGGSphingolipid metabolism   
NDEx NetworkSPTLC1
Atlas of Cancer Signalling NetworkSPTLC1
Wikipedia pathwaysSPTLC1
Orthology - Evolution
OrthoDB10558
GeneTree (enSembl)ENSG00000090054
Phylogenetic Trees/Animal Genes : TreeFamSPTLC1
HOGENOMO15269
Homologs : HomoloGeneSPTLC1
Homology/Alignments : Family Browser (UCSC)SPTLC1
Gene fusions - Rearrangements
Fusion : MitelmanDTNB/SPTLC1 [2p23.3/9q22.31]  
Fusion : QuiverSPTLC1
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSPTLC1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SPTLC1
dbVarSPTLC1
ClinVarSPTLC1
MonarchSPTLC1
1000_GenomesSPTLC1 
Exome Variant ServerSPTLC1
GNOMAD BrowserENSG00000090054
Varsome BrowserSPTLC1
Genetic variants : HAPMAP10558
Genomic Variants (DGV)SPTLC1 [DGVbeta]
DECIPHERSPTLC1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSPTLC1 
Mutations
ICGC Data PortalSPTLC1 
TCGA Data PortalSPTLC1 
Broad Tumor PortalSPTLC1
OASIS PortalSPTLC1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSPTLC1  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DSPTLC1
Mutations and Diseases : HGMDSPTLC1
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
BioMutasearch SPTLC1
DgiDB (Drug Gene Interaction Database)SPTLC1
DoCM (Curated mutations)SPTLC1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SPTLC1 (select a term)
intoGenSPTLC1
Cancer3DSPTLC1(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM162400    605712   
Orphanet10423   
DisGeNETSPTLC1
MedgenSPTLC1
Genetic Testing Registry SPTLC1
NextProtO15269 [Medical]
TSGene10558
GENETestsSPTLC1
Target ValidationSPTLC1
Huge Navigator SPTLC1 [HugePedia]
snp3D : Map Gene to Disease10558
BioCentury BCIQSPTLC1
ClinGenSPTLC1
Clinical trials, drugs, therapy
Protein Interactions : CTD10558
Pharm GKB GenePA36106
Clinical trialSPTLC1
Miscellaneous
canSAR (ICR)SPTLC1 (select the gene name)
HarmonizomeSPTLC1
DataMed IndexSPTLC1
Probes
Litterature
PubMed85 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSPTLC1
EVEXSPTLC1
GoPubMedSPTLC1
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 14 14:34:14 CEST 2020

Home   Genes   Leukemias   Solid Tumors   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

For comments and suggestions or contributions, please contact us

jlhuret@AtlasGeneticsOncology.org.