Atlas of Genetics and Cytogenetics in Oncology and Haematology


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HMGCS1 (3-hydroxy-3-methylglutaryl-CoA synthase 1)

Identity

Other aliasHMGCS
HGNC (Hugo) HMGCS1
LocusID (NCBI) 3157
Atlas_Id 56992
Location 5p12  [Link to chromosome band 5p12]
Location_base_pair Starts at 43287470 and ends at 43313512 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)
ABCA8 (17q24.2) / HMGCS1 (5p12)HMGCS1 (5p12) / HMGCS1 (5p12)HMGCS1 (5p12) / OXCT1 (5p13.1)
NUPL2 (7p15.3) / HMGCS1 (5p12)ZC3HC1 (7q32.2) / HMGCS1 (5p12)

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)HMGCS1   5007
Cards
Entrez_Gene (NCBI)HMGCS1  3157  3-hydroxy-3-methylglutaryl-CoA synthase 1
AliasesHMGCS
GeneCards (Weizmann)HMGCS1
Ensembl hg19 (Hinxton) [Gene_View]
Ensembl hg38 (Hinxton) [Gene_View]  chr5:43287470-43313512 [Contig_View]  HMGCS1 [Vega]
TCGA cBioPortalHMGCS1
AceView (NCBI)HMGCS1
Genatlas (Paris)HMGCS1
WikiGenes3157
SOURCE (Princeton)HMGCS1
Genetics Home Reference (NIH)HMGCS1
Genomic and cartography
GoldenPath hg38 (UCSC)HMGCS1  -     chr5:43287470-43313512 -  5p12   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)HMGCS1  -     5p12   [Description]    (hg19-Feb_2009)
EnsemblHMGCS1 - 5p12 [CytoView hg19]  HMGCS1 - 5p12 [CytoView hg38]
Mapping of homologs : NCBIHMGCS1 [Mapview hg19]  HMGCS1 [Mapview hg38]
OMIM142940   
Gene and transcription
Genbank (Entrez)AK095492 AK315593 AL050004 BC000297 BC082234
RefSeq transcript (Entrez)NM_001098272 NM_001324219 NM_001324220 NM_001324222 NM_001324223 NM_001324224 NM_001330663 NM_002130
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)HMGCS1
Cluster EST : UnigeneHs.741287 [ NCBI ]
CGAP (NCI)Hs.741287
Gene ExpressionHMGCS1 [ NCBI-GEO ]   HMGCS1 [ EBI - ARRAY_EXPRESS ]   HMGCS1 [ SEEK ]   HMGCS1 [ MEM ]
Gene Expression Viewer (FireBrowse)HMGCS1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)3157
GTEX Portal (Tissue expression)HMGCS1
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ01581   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ01581  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ01581
Splice isoforms : SwissVarQ01581
Catalytic activity : Enzyme2.3.3.10 [ Enzyme-Expasy ]   2.3.3.102.3.3.10 [ IntEnz-EBI ]   2.3.3.10 [ BRENDA ]   2.3.3.10 [ KEGG ]   
PhosPhoSitePlusQ01581
Domaine pattern : Prosite (Expaxy)HMG_COA_SYNTHASE (PS01226)   
Domains : Interpro (EBI)HMG_CoA_synt_AS    HMG_CoA_synt_C_dom    HMG_CoA_synth_N    HMG_CoA_synthase_euk    Thiolase-like   
Domain families : Pfam (Sanger)HMG_CoA_synt_C (PF08540)    HMG_CoA_synt_N (PF01154)   
Domain families : Pfam (NCBI)pfam08540    pfam01154   
Conserved Domain (NCBI)HMGCS1
DMDM Disease mutations3157
Blocks (Seattle)HMGCS1
PDB (SRS)2P8U   
PDB (PDBSum)2P8U   
PDB (IMB)2P8U   
PDB (RSDB)2P8U   
Structural Biology KnowledgeBase2P8U   
SCOP (Structural Classification of Proteins)2P8U   
CATH (Classification of proteins structures)2P8U   
SuperfamilyQ01581
Peptide AtlasQ01581
IPIIPI00008475   IPI00963899   
Protein Interaction databases
DIP (DOE-UCLA)Q01581
IntAct (EBI)Q01581
BioGRIDHMGCS1
STRING (EMBL)HMGCS1
ZODIACHMGCS1
Ontologies - Pathways
QuickGOQ01581
Ontology : AmiGOliver development  hydroxymethylglutaryl-CoA synthase activity  cytoplasm  cytosol  lipid metabolic process  cholesterol biosynthetic process  brain development  drug binding  isoprenoid biosynthetic process  male gonad development  response to low light intensity stimulus  response to purine-containing compound  isomerase activity  regulation of lipid metabolic process  response to vitamin E  response to drug  protein homodimerization activity  organic acid binding  regulation of cholesterol biosynthetic process  response to tellurium ion  response to lipoprotein particle  cellular response to follicle-stimulating hormone stimulus  cellular response to cholesterol  
Ontology : EGO-EBIliver development  hydroxymethylglutaryl-CoA synthase activity  cytoplasm  cytosol  lipid metabolic process  cholesterol biosynthetic process  brain development  drug binding  isoprenoid biosynthetic process  male gonad development  response to low light intensity stimulus  response to purine-containing compound  isomerase activity  regulation of lipid metabolic process  response to vitamin E  response to drug  protein homodimerization activity  organic acid binding  regulation of cholesterol biosynthetic process  response to tellurium ion  response to lipoprotein particle  cellular response to follicle-stimulating hormone stimulus  cellular response to cholesterol  
Pathways : BIOCARTASREBP control of lipid synthesis [Genes]   
Pathways : KEGGSynthesis and degradation of ketone bodies    Valine, leucine and isoleucine degradation    Butanoate metabolism    Terpenoid backbone biosynthesis   
NDEx NetworkHMGCS1
Atlas of Cancer Signalling NetworkHMGCS1
Wikipedia pathwaysHMGCS1
Orthology - Evolution
OrthoDB3157
Phylogenetic Trees/Animal Genes : TreeFamHMGCS1
HOVERGENQ01581
HOGENOMQ01581
Homologs : HomoloGeneHMGCS1
Homology/Alignments : Family Browser (UCSC)HMGCS1
Gene fusions - Rearrangements
Tumor Fusion PortalHMGCS1
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerHMGCS1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)HMGCS1
dbVarHMGCS1
ClinVarHMGCS1
1000_GenomesHMGCS1 
Exome Variant ServerHMGCS1
ExAC (Exome Aggregation Consortium)
Genetic variants : HAPMAP3157
Genomic Variants (DGV)HMGCS1 [DGVbeta]
DECIPHERHMGCS1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisHMGCS1 
Mutations
ICGC Data PortalHMGCS1 
TCGA Data PortalHMGCS1 
Broad Tumor PortalHMGCS1
OASIS PortalHMGCS1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICHMGCS1  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDHMGCS1
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 HMGCS1
DgiDB (Drug Gene Interaction Database)HMGCS1
DoCM (Curated mutations)HMGCS1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)HMGCS1 (select a term)
intoGenHMGCS1
Cancer3DHMGCS1(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM142940   
Orphanet
DisGeNETHMGCS1
MedgenHMGCS1
Genetic Testing Registry HMGCS1
NextProtQ01581 [Medical]
TSGene3157
GENETestsHMGCS1
Target ValidationHMGCS1
Huge Navigator HMGCS1 [HugePedia]
snp3D : Map Gene to Disease3157
BioCentury BCIQHMGCS1
ClinGenHMGCS1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD3157
Chemical/Pharm GKB GenePA29337
Clinical trialHMGCS1
Miscellaneous
canSAR (ICR)HMGCS1 (select the gene name)
Probes
Litterature
PubMed23 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineHMGCS1
EVEXHMGCS1
GoPubMedHMGCS1
iHOPHMGCS1
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Mon Nov 20 20:39:54 CET 2017

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