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HMGCS1 Gene

protein-coding   GIFtS: 63
GCID: GC05M043326

3-Hydroxy-3-Methylglutaryl-CoA Synthase 1 (Soluble)

(Previous name: 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1 (soluble))
(Previous symbol: HMGCS)
Microbiology & Infectious Diseases Congress
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at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
3-Hydroxy-3-Methylglutaryl-CoA Synthase 1 (Soluble)1 2     EC 2.3.3.103 8
HMGCS1 2 3     Hydroxymethylglutaryl-CoA Synthase, Cytoplasmic2
3-Hydroxy-3-Methylglutaryl-Coenzyme A Synthase 1 (Soluble)1 2     3-Hydroxy-3-Methylglutaryl Coenzyme A Synthase3
3-Hydroxy-3-Methylglutaryl Coenzyme A (HMG-CoA) Synthase1 2     HMG-CoA Synthase3

External Ids:    HGNC: 50071   Entrez Gene: 31572   Ensembl: ENSG000001129727   OMIM: 1429405   UniProtKB: Q015813   

Export aliases for HMGCS1 gene to outside databases

Previous GC identifers: GC05M043596 GC05M044466 GC05M043289 GC05M043336


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for HMGCS1 Gene:
HMGCS1 (3-hydroxy-3-methylglutaryl-CoA synthase 1 (soluble)) is a protein-coding gene. Diseases associated with HMGCS1 include labyrinthitis, and pneumonia. GO annotations related to this gene include isomerase activity and protein homodimerization activity. An important paralog of this gene is HMGCS2.

UniProtKB/Swiss-Prot: HMCS1_HUMAN, Q01581
Function: This enzyme condenses acetyl-CoA with acetoacetyl-CoA to form HMG-CoA, which is the substrate for
HMG-CoA reductase




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000005.10  NT_006576.17  NC_018916.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the HMGCS1 gene promoter:
         AhR   AML1a   GCNF   RREB-1   AREB6   S8   GCNF-1   NF-Y   GCNF-2   CBF(2)   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidHMGCS1 promoter sequence
   Search Chromatin IP Primers for HMGCS1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat HMGCS1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 5p14-p13   Ensembl cytogenetic band:  5p12   HGNC cytogenetic band: 5p14-p13

HMGCS1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
HMGCS1 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05M043326:  view genomic region     (about GC identifiers)

Start:
43,289,493 bp from pter      End:
43,313,614 bp from pter
Size:
24,122 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: HMCS1_HUMAN, Q01581 (See protein sequence)
Recommended Name: Hydroxymethylglutaryl-CoA synthase, cytoplasmic  
Size: 520 amino acids; 57294 Da
Sequence caution: Sequence=AAH00297.2; Type=Erroneous initiation;
1 PDB 3D structure from and Proteopedia for HMGCS1:
2P8U (3D)    
Secondary accessions: B2RDL8

Explore the universe of human proteins at neXtProt for HMGCS1: NX_Q01581

Explore proteomics data for HMGCS1 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys46, Lys100, Lys206, Lys273, Lys291, Lys317, Lys321, Lys330, Lys368, Lys400,
                                 Lys409, Lys428
  • Modification sites at PhosphoSitePlus
  • Selected DME Specific Peptides for HMGCS1 (Q01581) (see all 17)
     VQKSLAR  LIGPNAP  DKSKSVK  GNARPTGG 


    See HMGCS1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_001091742.1  NP_002121.4  

    ENSEMBL proteins: 
     ENSP00000322706   ENSP00000399402   ENSP00000427339  
    Reactome Protein details: Q01581

    HMGCS1 Human Recombinant Protein Products:

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    OriGene Purified Proteins for HMGCS1
    OriGene Protein Over-expression Lysate for HMGCS1
    OriGene MassSpec for HMGCS1
    OriGene Custom Protein Services for HMGCS1
    GenScript Custom Purified and Recombinant Proteins Services for HMGCS1
    Novus Biologicals HMGCS1 Protein
    Novus Biologicals HMGCS1 Lysates
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates
    Browse ProSpec Recombinant Proteins
    Browse Proteins at Cloud-Clone Corp.

    HMGCS1 Antibody Products:

    Browse EMD Millipore's Extensive Line of Mono- and Polyclonal Antibodies
    Browse R&D Systems for Antibodies
    Browse OriGene Antibodies
    OriGene Custom Antibody Services for HMGCS1
    Novus Biologicals HMGCS1 Antibodies
    Abcam antibodies for HMGCS1
    Browse Antibodies at Cloud-Clone Corp.
    ThermoFisher Antibody for HMGCS1
    LSBio Antibodies in human, mouse, rat for HMGCS1

    HMGCS1 Assay Products:

    Browse Kits and Assays available from EMD Millipore
    OriGene Custom Assay Services for HMGCS1
    Browse R&D Systems for biochemical assays
    GenScript Custom Assay Services for HMGCS1
    Browse Enzo Life Sciences for kits & assays
    Browse ELISAs at Cloud-Clone Corp.
    Browse CLIAs at Cloud-Clone Corp.


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    IUPHAR Guide to PHARMACOLOGY protein family classification: hydroxymethylglutaryl-CoA synthase
    Lanosterol biosynthesis pathway

    Selected InterPro protein domains (see all 6):
     IPR016038 Thiolase-like_subgr
     IPR010122 HMG_CoA_synthase_euk
     IPR000590 HMG_CoA_synt_AS
     IPR013746 HMG_CoA_synt_C
     IPR016039 Thiolase-like

    Graphical View of Domain Structure for InterPro Entry Q01581

    ProtoNet protein and cluster: Q01581

    1 Blocks protein domain: IPB000590 Hydroxymethylglutaryl-coenzyme A synthase

    UniProtKB/Swiss-Prot: HMCS1_HUMAN, Q01581
    Similarity: Belongs to the HMG-CoA synthase family


    HMGCS1 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: HMCS1_HUMAN, Q01581
    Function: This enzyme condenses acetyl-CoA with acetoacetyl-CoA to form HMG-CoA, which is the substrate for
    HMG-CoA reductase
    Catalytic activity: Acetyl-CoA + H(2)O + acetoacetyl-CoA = (S)-3-hydroxy-3-methylglutaryl-CoA + CoA

         Genatlas biochemistry entry for HMGCS1:
    3-hydroxy-3-methylglutaryl-CoA synthase 1,cytoplasmic

         Enzyme Number (IUBMB): EC 2.3.3.101 2

         Gene Ontology (GO): Selected molecular function terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003824catalytic activity ----
    GO:0004421hydroxymethylglutaryl-CoA synthase activity IEA--
    GO:0008144drug binding IEA--
    GO:0016853isomerase activity IEA--
    GO:0042803protein homodimerization activity IEA--
         
    HMGCS1 for ontologies           About GeneDecksing


    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for HMGCS1
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for HMGCS1

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for HMGCS1
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for HMGCS1

    miRNA
    Products:
        
    miRTarBase miRNAs that target HMGCS1:
    hsa-mir-186-5p (MIRT021092), hsa-let-7b-5p (MIRT052336), hsa-mir-19b-3p (MIRT031085), hsa-mir-192-5p (MIRT026269), hsa-mir-18a-5p (MIRT031353), hsa-mir-769-3p (MIRT039071), hsa-mir-3176 (MIRT052793), hsa-mir-335-5p (MIRT017138), hsa-mir-96-5p (MIRT027892), hsa-mir-1301-3p (MIRT035970), hsa-mir-92a-3p (MIRT049260)

    Block miRNA regulation of human, mouse, rat HMGCS1 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate HMGCS1 (see all 49):
    hsa-miR-4317 hsa-miR-142-5p hsa-miR-323-3p hsa-miR-4291 hsa-miR-607 hsa-miR-513a-5p hsa-miR-29a hsa-miR-200a
    SwitchGear 3'UTR luciferase reporter plasmidHMGCS1 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for HMGCS1
    Predesigned siRNA for gene silencing in human, mouse, rat HMGCS1

    Gene Editing
    Products:
    DNA2.0 Custom Protein Engineering Service for HMGCS1

    Clone
    Products:
         
    OriGene clones in human, mouse for HMGCS1 (see all 11)
    OriGene ORF clones in mouse, rat for HMGCS1
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 2): HMGCS1 (NM_002130)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for HMGCS1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat HMGCS1

    Cell Line
    Products:
         
    GenScript Custom overexpressing Cell Line Services for HMGCS1
    Browse ESI BIO Cell Lines and PureStem Progenitors for HMGCS1 
    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for HMGCS1


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    HMCS1_HUMAN, Q01581: Cytoplasm
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    cytosol4
    nucleus4
    plasma membrane4
    endoplasmic reticulum1
    extracellular1
    mitochondrion1
    peroxisome1

    Gene Ontology (GO): 5 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA--
    GO:0005730NOT nucleolus IDA--
    GO:0005737cytoplasm IDA--
    GO:0005829cytosol TAS--
    GO:0005886plasma membrane IDA--

    HMGCS1 for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for HMGCS1 About   (see all 10)                                                                                              See pathways by source

    SuperPathContained pathways About
    1superpathway of cholesterol biosynthesis
    superpathway of cholesterol biosynthesis0.85
    Terpenoid backbone biosynthesis0.34
    Cholesterol biosynthesis0.85
    superpathway of geranylgeranyldiphosphate biosynthesis I (via mevalonate)0.00
    Cholesterol biosynthesis0.62
    mevalonate pathway I0.00
    2Regulation of Cholesterol Biosynthesis by SREBP (SREBF)
    Regulation of Cholesterol Biosynthesis by SREBP (SREBF)0.75
    SREBP signalling0.31
    Activation of Gene Expression by SREBP (SREBF)0.75
    3Metabolism
    Metabolism0.38
    Metabolism of lipids and lipoproteins0.37
    Metabolic pathways0.38
    4Fatty acid, triacylglycerol, and ketone body metabolism
    Fatty acid, triacylglycerol, and ketone body metabolism0.65
    PPARA Activates Gene Expression0.63
    Regulation of Lipid Metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha)0.65
    5Butanoate metabolism
    Butanoate metabolism
    Synthesis and degradation of ketone bodies0.00

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    Selected BioSystems Pathways for HMGCS1 (see all 8)
        Cholesterol biosynthesis
    SREBP signalling
    SREBF and miR33 in cholesterol and lipid homeostasis
    Endochondral Ossification
    mevalonate pathway I

    3 Reactome Pathways for HMGCS1
        PPARA activates gene expression
    Cholesterol biosynthesis
    Activation of gene expression by SREBF (SREBP)

    1 PharmGKB Pathway for HMGCS1
        Bisphosphonate Pathway, Pharmacodynamics

    5 Kegg Pathways  (Kegg details for HMGCS1):
        Synthesis and degradation of ketone bodies
    Valine, leucine and isoleucine degradation
    Butanoate metabolism
    Terpenoid backbone biosynthesis
    Metabolic pathways

    UniProtKB/Swiss-Prot: HMCS1_HUMAN, Q01581
    Pathway: Metabolic intermediate biosynthesis; (R)-mevalonate biosynthesis; (R)-mevalonate from acetyl-CoA: step
    2/3


    HMGCS1 for pathways           About GeneDecksing

        Pathway & Disease-focused RT2 Profiler PCR Arrays including HMGCS1: 

              Parkinson's Disease in human mouse rat
              Fatty Acid Metabolism in human mouse rat
              Amino Acid Metabolism I in human mouse rat
              Lipoprotein Signaling & Cholesterol Metabolism in human mouse rat

    Interactions:

        Search GeneGlobe Interaction Network for HMGCS1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for HMGCS1 (Q015813 ENSP000003227064) via UniProtKB, MINT, STRING, and/or I2D (see all 191)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HIST1H4AP628053I2D: score=1 
    HIST1H4BP628053I2D: score=1 
    HIST1H4CP628053I2D: score=1 
    HIST1H4DP628053I2D: score=1 
    HIST1H4EP628053I2D: score=1 
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 24):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001101response to acid IEA--
    GO:0001889liver development IEA--
    GO:0006629lipid metabolic process NAS7913309
    GO:0006695cholesterol biosynthetic process TAS--
    GO:0007420brain development IEA--

    HMGCS1 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for HMGCS1 (HMCS1)

    5 HMDB Compounds for HMGCS1    About this table
    CompoundSynonyms CAS #PubMed Ids
    3-Hydroxy-3-methylglutaryl-CoA(S)-3-hydroxy-3-methylglutaryl-CoA (see all 15)1553-55-5--
    Acetoacetyl-CoA3-acetoacetyl-CoA (see all 9)1420-36-6--
    Acetyl-CoAS-Acetyl coenzyme A (see all 13)72-89-9--
    Coenzyme AAcetoacetyl coenzyme A sodium salt (see all 21)85-61-0--
    WaterDihydrogen oxide (see all 2)7732-18-5--

    1 DrugBank Compound for HMGCS1    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    (3R,5S,7R,12S,13R)-13-FORMYL-12,14-DIHYDROXY-3,5,7-TRIMETHYLTETRADECANOIC ACID-- --target--10592235

    1 IUPHAR Ligand for HMGCS1 (hydroxymethylglutaryl-CoA synthase)    About this table
    LigandTypeActionAffinityPubmed IDs
    (S)-3-hydroxy-3-methylglutaryl-CoA
    InhibitorFeedback inhibition5.5 - 5.919706283



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for HMGCS1 gene (2 alternative transcripts): 
    NM_001098272.2  NM_002130.7  

    Unigene Cluster for HMGCS1:

    3-hydroxy-3-methylglutaryl-CoA synthase 1 (soluble)
    Hs.397729  [show with all ESTs]
    Unigene Representative Sequence: NM_001098272
    7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000325110(uc003jnr.4) ENST00000433297(uc003jnp.4 uc003jnq.4)
    ENST00000508319 ENST00000514610 ENST00000507004 ENST00000507293 ENST00000511774

    Congresses - knowledge worth sharing:
    European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) 10 - 13 May 2014

    miRNA
    Products:
         
    Block miRNA regulation of human, mouse, rat HMGCS1 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate HMGCS1 (see all 49):
    hsa-miR-4317 hsa-miR-142-5p hsa-miR-323-3p hsa-miR-4291 hsa-miR-607 hsa-miR-513a-5p hsa-miR-29a hsa-miR-200a
    SwitchGear 3'UTR luciferase reporter plasmidHMGCS1 3' UTR sequence
    Inhib. RNA
    Products:
         
    OriGene RNAi products in human, mouse, rat for HMGCS1
    Predesigned siRNA for gene silencing in human, mouse, rat HMGCS1
    Clone
    Products:
         
    OriGene clones in human, mouse for HMGCS1 (see all 11)
    OriGene ORF clones in mouse, rat for HMGCS1
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 2): HMGCS1 (NM_002130)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for HMGCS1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat HMGCS1
    Primer
    Products:
        
    OriGene qPCR primer pairs and template standards for HMGCS1
    OriGene qSTAR qPCR primer pairs in human, mouse for HMGCS1
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat HMGCS1
      QuantiTect SYBR Green Assays in human, mouse, rat HMGCS1
      QuantiFast Probe-based Assays in human, mouse, rat HMGCS1

    Additional mRNA sequence: 

    AK095492.1 AK315593.1 AL050004.1 BC000297.2 BC082234.1 BC083514.1 BT007302.1 L25798.1 
    X66435.1 

    24 DOTS entries:

    DT.92444019  DT.99933619  DT.100830773  DT.75199564  DT.100885377  DT.120849854  DT.100885373  DT.100885385 
    DT.306316  DT.100885378  DT.100885382  DT.97859142  DT.92046034  DT.100885380  DT.100885383  DT.120849834 
    DT.120849878  DT.120849928  DT.427418  DT.120849887  DT.411725  DT.92444036  DT.95177279  DT.97861163 

    Selected AceView cDNA sequences (see all 315):

    BG681747 BM968193 AI824743 BM477536 BX284043 BC000297 CA440194 AW249691 
    CB138968 BQ775593 C00010 CB114547 BQ002743 T91394 BI492525 CR591410 
    AK095492 BF219764 AI520729 BM474567 CN480717 AW951421 AU131382 T29665 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for HMGCS1 (see all 9)    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6a · 6b · 6c ^ 7a · 7b ^ 8a · 8b · 8c ^ 9 ^ 10a · 10b ^ 11a · 11b ^ 12 ^ 13 ^ 14
    SP1:                                                                                                                                                
    SP2:              -     -                 -                                         -                                                               
    SP3:                                                                                -                                                               
    SP4:                                                                                -                                                               
    SP5:                                                                                                                                                


    ECgene alternative splicing isoforms for HMGCS1

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

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    HMGCS1 expression in normal human tissues (normalized intensities)      HMGCS1 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    HMGCS1 Expression
    About this image


    HMGCS1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 9) fully expand
     
     Brain (Nervous System)    fully expand to see all 7 entries
             Cerebral Cortex
     
     Neural Tube (Nervous System)    fully expand to see all 3 entries
             Metencephalon
     
     Liver (Hepatobiliary System)
             Hepatocytes Liver Lobule
     
     Gonad (Reproductive System)
             Primordial Germ Cells Primitive Gonad
     
     Inner Cell Mass (Early Embryonic Tissues)
             Inner Cell Mass Cells Inner Cell Mass
    HMGCS1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    HMGCS1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.397729
        Pathway & Disease-focused RT2 Profiler PCR Arrays including HMGCS1: 
              Parkinson's Disease in human mouse rat
              Fatty Acid Metabolism in human mouse rat
              Amino Acid Metabolism I in human mouse rat
              Lipoprotein Signaling & Cholesterol Metabolism in human mouse rat

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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of eukaryotes.

    Orthologs for HMGCS1 gene from Selected species (see all 29)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Hmgcs11 , 5 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 11, 5 89.29(n)1
    94.62(a)1
      135
    2087151  NM_145942.41  NP_666054.21 
     1196904625 
    chicken
    (Gallus gallus)
    Aves HMGCS11 3-hydroxy-3-methylglutaryl-CoA synthase 1 (soluble) 79.04(n)
    84.23(a)
      396379  NM_205411.1  NP_990742.1 
    lizard
    (Anolis carolinensis)
    Reptilia HMGCS16
    3-hydroxy-3-methylglutaryl-CoA synthase 1 (soluble...
    82(a)
    1 ↔ 1
    2(6150939-6167805)
    African clawed frog
    (Xenopus laevis)
    Amphibia hmgcs1-prov2 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1 76.66(n)    BC042929.1 
    zebrafish
    (Danio rerio)
    Actinopterygii zgc564812 similar to 3-hydroxy-3-methylglutaryl-Coenzyme A synthase more 76.37(n)   394060  BC049456.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Hmgs1 , 3 hydroxymethylglutaryl-CoA synthase3
    HMG Coenzyme A synthase1
    64(a)3
    59.12(n)1
    64.62(a)1
      53B53
    441541  NM_166169.21  NP_725570.11 
    worm
    (Caenorhabditis elegans)
    Secernentea F25B4.63 hydroxymethlglutaryl-CoA synthase 41(a)   V(5685458-5687182)   --
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes ERG13(YML126C)4
    ERG131
    3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) synthase, more4
    ERG131
    56.09(n)1
    50.91(a)1
      13(20535-19060)4
    8549131, 4  NP_013580.11, 4 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons MVA11 MVA1 55.41(n)
    50.11(a)
      826788  NM_117251.2  NP_192919.1 
    rice
    (Oryza sativa)
    Liliopsida AK063755.12   -- 72.33(n)    AK063755.1 


    ENSEMBL Gene Tree for HMGCS1 (if available)
    TreeFam Gene Tree for HMGCS1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for HMGCS1 gene
    HMGCS22  
    1 SIMAP similar gene for HMGCS1 using alignment to 3 protein entries:     HMCS1_HUMAN (see all proteins):
    HMGCS2

    HMGCS1 for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for HMGCS1
    PGOHUM00000245270


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for HMGCS1 (see all 545)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 5 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs563055091,2
    C--43251985(+) GCATT-/GTTCAGA 2 -- int10--------
    rs1810502801,2
    --43287127(+) AGAATA/CCATTT 2 -- ds50010--------
    rs1841755941,2
    --43287146(+) ACTTTC/GTAGAG 2 -- ds50010--------
    rs674156721,2
    C,F--43287161(+) CCTGCT/CTTCCT 2 -- ds50018Minor allele frequency- C:0.35WA NA CSA EA 368
    rs1428371531,2
    C--43287174(+) GCTCAC/TGGTCA 2 -- ds50010--------
    rs1451162171,2
    C--43287283(+) TAAAGA/TCCCAC 2 -- ds50010--------
    rs1884807011,2
    --43287314(+) CAGACA/CATCCA 2 -- ds50010--------
    rs1812999151,2
    C--43287427(+) TGGGAC/GGGCAT 2 -- ds50010--------
    rs104733061,2
    C,F,H--43287437(+) TCATTC/GTGCAA 2 -- ds50017Minor allele frequency- G:0.07NS EA WA CSA 542
    rs1859520481,2
    --43287479(+) CTCCAA/CTCTCC 2 -- ds50010--------

    HapMap Linkage Disequilibrium report for HMGCS1 (43289493 - 43313614 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 1 variation for HMGCS1:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv508352CNV Loss20534489

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing HMGCS1
    DNA2.0 Custom Variant and Variant Library Synthesis for HMGCS1

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 142940    OMIM disorders: --

    9 diseases for HMGCS1:    About MalaCards
    labyrinthitis    pneumonia    parkinson's disease    neuroblastoma
    malaria    alzheimer's disease    hepatitis    cerebritis
    leukemia


    HMGCS1 for disorders           About GeneDecksing


    Congresses - knowledge worth sharing:
    Alzheimer's & Parkinson's Diseases Congress (ADPD) 18 - 22 March 2015
    Genetic Association Database (GAD): HMGCS1
    Human Genome Epidemiology (HuGE) Navigator: HMGCS1 (5 documents)

    Export disorders for HMGCS1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for HMGCS1 gene, integrated from 10 sources (see all 43):
    (articles sorted by number of sources associating them with HMGCS1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Polymorphisms in the estrogen receptor 1 and vitamin C and matrix metalloproteinase gene families are associated with susceptibility to lymphoma. (PubMed id 18636124)1, 4 Skibola C.F....Smith M.T. (PLoS ONE 2008)
    2. Multiple genetic variants along candidate pathways influence plasma high-density lipoprotein cholesterol concentrations. (PubMed id 18660489)1, 4 Lu Y....Boer J.M. (J. Lipid Res. 2008)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    5. Human cytoplasmic 3-hydroxy-3-methylglutaryl coenzyme A synthase: expression, purification, and characterization of recombinant wild- type and Cys129 mutant enzymes. (PubMed id 7913309)1, 2 Rokosz L.L.... Hermes J.D. (Arch. Biochem. Biophys. 1994)
    6. Amplification and direct sequencing of a cDNA encoding human cytosolic 3-hydroxy-3-methylglutaryl-coenzyme A synthase. (PubMed id 1358203)1, 2 Russ A.P.... Gross W. (Biochim. Biophys. Acta 1992)
    7. Crystal structures of human HMG-CoA synthase isoforms provide insights into inherited ketogenesis disorders and inhibitor design. (PubMed id 20346956)1, 9 Shafqat N.... Yue W.W. (J. Mol. Biol. 2010)
    8. Transcriptional regulation of HMG-CoA synthase and HMG-CoA reductase genes by human ACBP. (PubMed id 19088433)1, 9 Vock C....Nitz I. (Cell. Physiol. Biochem. 2008)
    9. Drafting the CLN3 protein interactome in SH-SY5Y human neuroblastoma cells: a label-free quantitative proteomics approach. (PubMed id 23464991)1 Scifo E....Lalowski M. (J. Proteome Res. 2013)
    10. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (Cell 2012)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 3157 HGNC: 5007 AceView: HMGCS1 Ensembl:ENSG00000112972 euGenes: HUgn3157
    ECgene: HMGCS1 Kegg: 3157 H-InvDB: HMGCS1

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for HMGCS1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for HMGCS1 gene:
    Search GeneIP for patents involving HMGCS1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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