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HMGCS2 Gene

protein-coding   GIFtS: 66
GCID: GC01M120290

3-Hydroxy-3-Methylglutaryl-CoA Synthase 2 (Mitochondrial)

(Previous name: 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2 (mitochondrial))
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 2 (Mitochondrial)1 2
3-Hydroxy-3-Methylglutaryl-Coenzyme A Synthase 2 (Mitochondrial)1 2
HMG-CoA Synthase2 3
EC 2.3.3.103 8
Hydroxymethylglutaryl-CoA Synthase, Mitochondrial2
3-Hydroxy-3-Methylglutaryl Coenzyme A Synthase3

External Ids:    HGNC: 50081   Entrez Gene: 31582   Ensembl: ENSG000001342407   OMIM: 6002345   UniProtKB: P548683   

Export aliases for HMGCS2 gene to outside databases

Previous GC identifers: GC01M120737 GC01M119128 GC01M119438 GC01M119637 GC01M120003 GC01M120092 GC01M118149


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for HMGCS2 Gene:
The protein encoded by this gene belongs to the HMG-CoA synthase family. It is a mitochondrial enzyme that
catalyzes the first reaction of ketogenesis, a metabolic pathway that provides lipid-derived energy for various
organs during times of carbohydrate deprivation, such as fasting. Mutations in this gene are associated with
HMG-CoA synthase deficiency. Alternatively spliced transcript variants encoding different isoforms have been
found for this gene.(provided by RefSeq, Oct 2009)

GeneCards Summary for HMGCS2 Gene:
HMGCS2 (3-hydroxy-3-methylglutaryl-CoA synthase 2 (mitochondrial)) is a protein-coding gene. Diseases associated with HMGCS2 include 3-hydroxy-3-methylglutaryl-coa synthase 2 deficiency, and hmg-coa synthase-2 deficiency. GO annotations related to this gene include hydroxymethylglutaryl-CoA synthase activity. An important paralog of this gene is HMGCS1.

UniProtKB/Swiss-Prot: HMCS2_HUMAN, P54868
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_000001.11  NC_018912.2  NT_032977.10  
Regulatory elements:
   Regulatory transcription factor binding sites in the HMGCS2 gene promoter:
         C/EBPbeta   RelA   LUN-1   NF-kappaB   C/EBPalpha   E47   MEF-2A   ARP-1   Hand1   NF-kappaB1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidHMGCS2 promoter sequence
   Search Chromatin IP Primers for HMGCS2

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat HMGCS2


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

Entrez Gene cytogenetic band: 1p13-p12   Ensembl cytogenetic band:  1p12   HGNC cytogenetic band: 1p13-p12

HMGCS2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
HMGCS2 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01M120290:  view genomic region     (about GC identifiers)

Start:
120,290,619 bp from pter      End:
120,311,555 bp from pter
Size:
20,937 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: HMCS2_HUMAN, P54868 (See protein sequence)
Recommended Name: Hydroxymethylglutaryl-CoA synthase, mitochondrial precursor  
Size: 508 amino acids; 56635 Da
Subunit: Homodimer
1 PDB 3D structure from and Proteopedia for HMGCS2:
2WYA (3D)    
Secondary accessions: B7Z8R3 D3Y5K6 Q5SZU2 Q6IBF4
Alternative splicing: 3 isoforms:  P54868-1   P54868-2   P54868-3   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for HMGCS2: NX_P54868

Explore proteomics data for HMGCS2 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys137
  • Modification sites at PhosphoSitePlus
  • Selected DME Specific Peptides for HMGCS2 (P54868) (see all 15)
     VQKSLAR  CYLRALD  VVCGDIA  YGCLASLL 


    See HMGCS2 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_001159579.1  NP_005509.1  

    ENSEMBL proteins: 
     ENSP00000358414   ENSP00000439495  
    Reactome Protein details: P54868

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    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 P54868

    ProtoNet protein and cluster: P54868

    1 Blocks protein domain: IPB000590 Hydroxymethylglutaryl-coenzyme A synthase

    UniProtKB/Swiss-Prot: HMCS2_HUMAN, P54868
    Similarity: Belongs to the HMG-CoA synthase family


    HMGCS2 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: HMCS2_HUMAN, P54868
    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 HMGCS2:
    3-hydroxy-3-methylglutaryl-CoA synthase 2,mitochondrial,first and regulating enzyme of ketogenic pathway,through
    association with PPARA

         Enzyme Number (IUBMB): EC 2.3.3.101 2

         Gene Ontology (GO): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003824catalytic activity ----
    GO:0004421hydroxymethylglutaryl-CoA synthase activity IEA--
         
    HMGCS2 for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for HMGCS2:
     Decreased Wnt reporter activit 

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for HMGCS2
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       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for HMGCS2
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    1 qRT-PCR Assays for microRNA that regulate HMGCS2:
    hsa-miR-136
    SwitchGear 3'UTR luciferase reporter plasmidHMGCS2 3' UTR sequence
    Inhib. RNA
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    Sino Biological Human cDNA Clone for HMGCS2
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat HMGCS2

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    (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
    HMCS2_HUMAN, P54868: Mitochondrion
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    mitochondrion5
    cytosol2
    nucleus1
    peroxisome1

    Gene Ontology (GO): 3 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005739mitochondrion TAS7851882
    GO:0005743mitochondrial inner membrane IEA--
    GO:0005759mitochondrial matrix TAS--

    HMGCS2 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 HMGCS2 About   (see all 8)                                                                                              See pathways by source

    SuperPathContained pathways About
    1Fatty 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
    ketogenesis0.00
    2superpathway of cholesterol biosynthesis
    superpathway of cholesterol biosynthesis0.85
    mevalonate pathway I0.00
    Terpenoid backbone biosynthesis0.34
    superpathway of geranylgeranyldiphosphate biosynthesis I (via mevalonate)0.00
    3Synthesis and Degradation of Ketone Bodies
    Synthesis and Degradation of Ketone Bodies0.43
    Synthesis of Ketone Bodies0.00
    Ketone body metabolism0.00
    4Metabolism
    Metabolism0.38
    Metabolism of lipids and lipoproteins0.37
    Metabolic pathways0.38
    5Butanoate metabolism
    Butanoate metabolism
    Synthesis and degradation of ketone bodies0.00

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    Selected BioSystems Pathways for HMGCS2 (see all 6)
        Synthesis and Degradation of Ketone Bodies
    ketogenesis
    mevalonate pathway I
    superpathway of cholesterol biosynthesis
    Validated targets of C-MYC transcriptional repression


    2 Reactome Pathways for HMGCS2
        Synthesis of Ketone Bodies
    PPARA activates gene expression


    Selected Kegg Pathways  (Kegg details for HMGCS2) (see all 6):
        Synthesis and degradation of ketone bodies
    Valine, leucine and isoleucine degradation
    Butanoate metabolism
    Terpenoid backbone biosynthesis
    Metabolic pathways

    UniProtKB/Swiss-Prot: HMCS2_HUMAN, P54868
    Pathway: Metabolic intermediate biosynthesis; (R)-mevalonate biosynthesis; (R)-mevalonate from acetyl-CoA: step
    2/3


    HMGCS2 for pathways           About GeneDecksing

        Pathway & Disease-focused RT2 Profiler PCR Arrays including HMGCS2: 

              Fatty Acid Metabolism in human mouse rat
              Lipoprotein Signaling & Cholesterol Metabolism in human mouse rat
              PPAR Targets in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for HMGCS2

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

    Selected Interacting proteins for HMGCS2 (P548682, 3 ENSP000003584144) via UniProtKB, MINT, STRING, and/or I2D (see all 140)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    YWHAQP273482, 3, ENSP000002380814MINT-7900157 I2D: score=1 STRING: ENSP00000238081
    YWHAZP631042, ENSP000003095034MINT-7900157 STRING: ENSP00000309503
    ACTBP607092, ENSP000003499604MINT-7900157 STRING: ENSP00000349960
    ACTA2P627362MINT-7900157
    ANKRD18AQ8IVF62MINT-7900157
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006695cholesterol biosynthetic process IEA--
    GO:0008152metabolic process ----
    GO:0008299isoprenoid biosynthetic process IEA--
    GO:0044255cellular lipid metabolic process TAS--
    GO:0044281small molecule metabolic process TAS--

    HMGCS2 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 HMGCS2 (HMCS2)

    6 HMDB Compounds for HMGCS2    About this table
    CompoundSynonyms CAS #PubMed Ids
    7-Dehydrocholesterol(-)-7-dehydrocholesterol (see all 26)434-16-29548596
    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--

    2 Novoseek inferred chemical compound relationships for HMGCS2 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    3-hydroxy-3-methylglutaryl-coa 86.2 10 16713539 (2), 12027802 (1), 19389950 (1), 1356769 (1) (see all 5)
    fatty acid 36.9 2 19389950 (1)



    HMGCS2 for compounds           About GeneDecksing



    (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 HMGCS2 gene (2 alternative transcripts): 
    NM_001166107.1  NM_005518.3  

    Unigene Cluster for HMGCS2:

    3-hydroxy-3-methylglutaryl-CoA synthase 2 (mitochondrial)
    Hs.59889  [show with all ESTs]
    Unigene Representative Sequence: NM_005518
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000369406(uc001eid.3 uc010oxj.2) ENST00000544913(uc021osw.1)
    ENST00000472375 ENST00000476640(uc021osx.1)
    Congresses - knowledge worth sharing:
    European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) 10 - 13 May 2014

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    Inhib. RNA
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      QuantiTect SYBR Green Assays in human, mouse, rat HMGCS2
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    Additional mRNA sequence: 

    AK301594.1 AK302276.1 AK303777.1 AK313590.1 BC044217.1 CR456850.1 GU433940.1 U12788.1 
    U12789.1 X83618.1 

    13 DOTS entries:

    DT.447712  DT.75172745  DT.91761654  DT.95170169  DT.91761649  DT.91761656  DT.95170168  DT.100664062 
    DT.100829345  DT.121342069  DT.447711  DT.95309941  DT.217562 

    Selected AceView cDNA sequences (see all 185):

    CB161812 BX101808 CB157381 BX504512 AA399107 CR618114 W92241 AI215948 
    CB156021 BQ083175 CB132569 BI826589 AI832798 AA902856 AI025465 CB164460 
    CB161471 AA496149 AL048890 AA687814 CB159372 CB161374 BM746643 AI223006 

    GeneLoc Exon Structure

    5 Alternative Splicing Database (ASD) splice patterns (SP) for HMGCS2    About this scheme

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


    ECgene alternative splicing isoforms for HMGCS2

    (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)
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    HMGCS2 expression in normal human tissues (normalized intensities)      HMGCS2 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TGTTAGAACT
    HMGCS2 Expression
    About this image


    HMGCS2 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 14) fully expand
     
     Neural Tube (Nervous System)    fully expand to see all 4 entries
             Metencephalon
     
     Brain (Nervous System)    fully expand to see all 3 entries
             Medulla Oblongata
     
     Kidney (Urinary System)    fully expand to see all 2 entries
             Renal Collecting Duct System
     
     Liver (Hepatobiliary System)    fully expand to see all 2 entries
             Hepatocytes Liver Lobule
             Hepatocyte-like cells
     
     Heart (Cardiovascular System)    fully expand to see all 2 entries
             Atrioventricular Canal Cells Atrioventricular Canal
    HMGCS2 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    HMGCS2 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.59889

    UniProtKB/Swiss-Prot: HMCS2_HUMAN, P54868
    Tissue specificity: Expression in liver is 200-fold higher than in any other tissue. Low expression in colon,
    kidney, testis, and pancreas. Very low expression in heart and skeletal muscle. Not detected in brain. The
    relative expression of isoform 3 (at mRNA level) is highest in heart (70%) and skeletal muscle (60%)

        Pathway & Disease-focused RT2 Profiler PCR Arrays including HMGCS2: 
              Fatty Acid Metabolism in human mouse rat
              Lipoprotein Signaling & Cholesterol Metabolism in human mouse rat
              PPAR Targets in human mouse rat

    Primer
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for HMGCS2

    (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 HMGCS2 gene from Selected species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Hmgcs21 , 5 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 21, 5 86.35(n)1
    89.37(a)1
      3 (42.74 cM)5
    153601  NM_008256.41  NP_032282.21 
     982804355 
    chicken
    (Gallus gallus)
    Aves HMGCS21 3-hydroxy-3-methylglutaryl-CoA synthase 2 (mitochondrial) 72.45(n)
    72.52(a)
      424380  XM_422225.4  XP_422225.3 
    lizard
    (Anolis carolinensis)
    Reptilia HMGCS26
    3-hydroxy-3-methylglutaryl-CoA synthase 2 (mitocho...
    68(a)
    1 ↔ 1
    GL343782.1(104365-134893)
    fruit fly
    (Drosophila melanogaster)
    Insecta Hmgs3 hydroxymethylglutaryl-CoA synthase 60(a)   53B5   --
    worm
    (Caenorhabditis elegans)
    Secernentea F25B4.63 hydroxymethlglutaryl-CoA synthase 43(a)   V(5685458-5687182)   --
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes ERG136
    3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) synthase,...
    43(a)
    1 → many
    XIII(19060-20535) YML126C
    rice
    (Oryza sativa)
    Liliopsida Os.327822 Oryza sativa (japonica cultivar-group) cDNA cloneJ more 74.35(n)    AK102923.1 


    ENSEMBL Gene Tree for HMGCS2 (if available)
    TreeFam Gene Tree for HMGCS2 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for HMGCS2 gene
    HMGCS12  
    1 SIMAP similar gene for HMGCS2 using alignment to 1 protein entry:     HMCS2_HUMAN:
    HMGCS1

    HMGCS2 for paralogs           About GeneDecksing



    (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 HMGCS2 (see all 516)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0327604
    HMG-CoA synthase deficiency (HMGCS deficiency)4--see VAR_0327602 R H mis40--------
    VAR_0327584
    HMG-CoA synthase deficiency (HMGCS deficiency)4--see VAR_0327582 Y C mis40--------
    VAR_0327594
    HMG-CoA synthase deficiency (HMGCS deficiency)4--see VAR_0327592 G R mis40--------
    VAR_0327114
    HMG-CoA synthase deficiency (HMGCS deficiency)4--see VAR_0327112 F L mis40--------
    rs1378526371,2
    Cpathogenic1120367592(-) CATTTC/TGAGTA 4 R * stg11Minor allele frequency- T:0.00NA 4550
    rs1378526381,2
    Cpathogenic1120374195(-) GGGCCG/AGAGCT 3 /R /G mis1 int11Minor allele frequency- A:0.00NA 4552
    rs1135937861,2
    C--118150560(+) CCCCCCT/-CCCTC 2 -- int11Minor allele frequency- -:0.50CSA 2
    rs5091841,2
    C,F--118150561(+) CCCCCC/TCCCTC 2 -- int1 trp34Minor allele frequency- T:0.42NA EA 1468
    rs763166911,2
    C--118150561(+) CCCCC-/T/TC  
            
    TCCCT
    2 -- int10--------
    rs37906981,2
    C--118151117(-) GAACCA/C/TAGGTA 2 -- int11NA 2

    HapMap Linkage Disequilibrium report for HMGCS2 (120290619 - 120311555 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 6 variations for HMGCS2:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv831215CNV Gain17160897
    nsv524681CNV Gain19592680
    nsv428201CNV Gain18775914
    nsv831204CNV Gain+Loss17160897
    dgv94e1CNV Complex17122850
    dgv93e1CNV Complex17122850

    Human Gene Mutation Database (HGMD): HMGCS2
    Locus Specific Mutation Databases (LSDB): HMGCS2

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing HMGCS2
    DNA2.0 Custom Variant and Variant Library Synthesis for HMGCS2

    (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: 600234   
    OMIM disorders: 605911  
    UniProtKB/Swiss-Prot: HMCS2_HUMAN, P54868
  • HMG-CoA synthase deficiency (HMGCS deficiency) [MIM:605911]: Affected individuals present with severe
    hypoketotic hypoglycemia, mild hepatomegaly, or fatty liver, and a nondiagnostic pattern of urinary organic acids
    with increase of medium and short chain dicarboxylic acids. Note=The disease is caused by mutations affecting the
    gene represented in this entry

  • 10 diseases for HMGCS2:    About MalaCards
    3-hydroxy-3-methylglutaryl-coa synthase 2 deficiency    hmg-coa synthase-2 deficiency    hypoglycemia    meningitis
    pneumonia    choroiditis    alzheimer's disease    multiple myeloma
    myeloma    hepatitis


    HMGCS2 for disorders           About GeneDecksing


    Congresses - knowledge worth sharing:
    Alzheimer's & Parkinson's Diseases Congress (ADPD) 18 - 22 March 2015
    Genatlas disease: HMGCS2
    defective ketogenesis with recurrent hypoketotic hypoglycemia during fasting

    Genetic Association Database (GAD): HMGCS2
    Human Genome Epidemiology (HuGE) Navigator: HMGCS2 (11 documents)

    Export disorders for HMGCS2 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 HMGCS2 gene, integrated from 10 sources (see all 37):
    (articles sorted by number of sources associating them with HMGCS2)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Molecular cloning and tissue expression of human mitochondrial 3- hydroxy-3-methylglutaryl-CoA synthase. (PubMed id 7893153)1, 2, 3 Mascaro C.... Hegardt F.G. (Arch. Biochem. Biophys. 1995)
    2. Human mitochondrial HMG CoA synthase: liver cDNA and partial genomic cloning, chromosome mapping to 1p12-p13, and possible role in vertebrate evolution. (PubMed id 7851882)1, 2, 3 Boukaftane Y.... Mitchell G.A. (Genomics 1994)
    3. Genetic basis of mitochondrial HMG-CoA synthase deficiency. (PubMed id 11479731)1, 2, 9 Aledo R.... Hegardt F.G. (Hum. Genet. 2001)
    4. Characterization of splice variants of the genes encoding human mitochondrial HMG-CoA lyase and HMG-CoA synthase, the main enzymes of the ketogenesis pathway. (PubMed id 21952825)1, 2 Puisac B....Pie J. (Mol. Biol. Rep. 2012)
    5. Crystal structures of human HMG-CoA synthase isoforms provide insights into inherited ketogenesis disorders and inhibitor design. (PubMed id 20346956)1, 2 Shafqat N.... Yue W.W. (J. Mol. Biol. 2010)
    6. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PubMed id 20877624)1, 4 Hendrickson S.L....O'Brien S.J. (PLoS ONE 2010)
    7. Genome-wide searching of rare genetic variants in WTCCC data. (PubMed id 20549515)1, 4 Feng T. and Zhu X. (Hum. Genet. 2010)
    8. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PubMed id 20628086)1, 4 Bailey S.D....Anand S. (Diabetes Care 2010)
    9. 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)
    10. 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)

    (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: 3158 HGNC: 5008 AceView: HMGCS2 Ensembl:ENSG00000134240 euGenes: HUgn3158
    ECgene: HMGCS2 Kegg: 3158 H-InvDB: HMGCS2

    (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 HMGCS2 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 HMGCS2 gene:
    Search GeneIP for patents involving HMGCS2

    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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