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HMGCL Gene

protein-coding   GIFtS: 65
GCID: GC01M024128

3-Hydroxymethyl-3-Methylglutaryl-CoA Lyase

(Previous name: 3-hydroxymethyl-3-methylglutaryl-Coenzyme A lyase)
  See HMGCL-related diseases
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-Hydroxymethyl-3-Methylglutaryl-CoA Lyase1 2     HMG-CoA Lyase2 3
3-Hydroxymethyl-3-Methylglutaryl-Coenzyme A Lyase1 2     EC 4.1.3.43 8
hydroxymethylglutaricaciduria1 2     3-Hydroxy-3-Methylglutaryl-CoA Lyase2
3-Hydroxy-3-Methylglutarate-CoA Lyase2 3     Hydroxymethylglutaryl-CoA Lyase, Mitochondrial2
HL2 3     Mitochondrial 3-Hydroxy-3-Methylglutaryl-CoA Lyase2

External Ids:    HGNC: 50051   Entrez Gene: 31552   Ensembl: ENSG000001173057   OMIM: 6138985   UniProtKB: P359143   

Export aliases for HMGCL gene to outside databases

Previous GC identifers: GC01M023686 GC01M023199 GC01M023597 GC01M023873 GC01M024001 GC01M022379


(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 HMGCL Gene:
The protein encoded by this gene belongs to the HMG-CoA lyase family. It is a mitochondrial enzyme that catalyzes
the final step of leucine degradation and plays a key role in ketone body formation. Mutations in this gene are
associated with HMG-CoA lyase deficiency. Alternatively spliced transcript variants encoding different isoforms
have been found for this gene. (provided by RefSeq, Oct 2009)

GeneCards Summary for HMGCL Gene:
HMGCL (3-hydroxymethyl-3-methylglutaryl-CoA lyase) is a protein-coding gene. Diseases associated with HMGCL include 3-hydroxy-3-methylglutaryl-coenzyme a lyase deficiency, and hmg coa lyase deficiency. GO annotations related to this gene include magnesium ion binding and protein homodimerization activity. An important paralog of this gene is HMGCLL1.

UniProtKB/Swiss-Prot: HMGCL_HUMAN, P35914
Function: Key enzyme in ketogenesis (ketone body formation). Terminal step in leucine catabolism. Ketone bodies
(beta-hydroxybutyrate, acetoacetate and acetone) are essential as an alternative source of energy to glucose, as
lipid precursors and as regulators of metabolism




(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 at NCBI GenBank:
NC_000001.10  NC_018912.2  NT_032977.10  
Regulatory elements:
   Regulatory transcription factor binding sites in the HMGCL gene promoter:
         STAT4   STAT1beta   CUTL1   STAT1alpha   CREB   deltaCREB   HSF2   STAT2   STAT3   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidHMGCL promoter sequence
   Search Chromatin IP Primers for HMGCL

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


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

Entrez Gene cytogenetic band: 1p36.1-p35   Ensembl cytogenetic band:  1p36.11   HGNC cytogenetic band: 1p36.1-p35

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

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01M024128:  view genomic region     (about GC identifiers)

Start:
24,128,367 bp from pter      End:
24,165,110 bp from pter
Size:
36,744 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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: HMGCL_HUMAN, P35914 (See protein sequence)
Recommended Name: Hydroxymethylglutaryl-CoA lyase, mitochondrial precursor  
Size: 325 amino acids; 34360 Da
Cofactor: Divalent metal cations
Subunit: Homodimer; disulfide-linked. Can also form homotetramers
4 PDB 3D structures from and Proteopedia for HMGCL:
2CW6 (3D)        3MP3 (3D)        3MP4 (3D)        3MP5 (3D)    
Secondary accessions: B4DUP4 B7UCC6 D3Y5K7 Q6IBC0 Q96FP8
Alternative splicing: 3 isoforms:  P35914-1   P35914-2   P35914-3   (Very low expression. The transcript is not translated, but would result in a catatically inactive product if it was)

Explore the universe of human proteins at neXtProt for HMGCL: NX_P35914

Explore proteomics data for HMGCL at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus
  • Selected DME Specific Peptides for HMGCL (P35914) (see all 14)
     PRRLVGL  YPVLTPN  NCSIEES  VRGYVSC 


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

    REFSEQ proteins (2 alternative transcripts): 
    NP_000182.2  NP_001159531.1  

    ENSEMBL proteins: 
     ENSP00000363614   ENSP00000389281   ENSP00000363611   ENSP00000235958   ENSP00000363607  
    Reactome Protein details: P35914

    HMGCL Human Recombinant Protein Products:

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    Novus Biologicals HMGCL Proteins
    Novus Biologicals HMGCL Lysates
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    Cloud-Clone Corp. Proteins for HMGCL

     
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    Search eBioscience for ELISAs for HMGCL 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    4 InterPro protein domains:
     IPR013785 Aldolase_TIM
     IPR000891 PYR_CT
     IPR000138 HMG_CoA_lyase_AS
     IPR027167 HMG-CoA_lyase

    Graphical View of Domain Structure for InterPro Entry P35914

    ProtoNet protein and cluster: P35914

    1 Blocks protein domain: IPB000138 Hydroxymethylglutaryl-coenzyme A lyase active site

    UniProtKB/Swiss-Prot: HMGCL_HUMAN, P35914
    Similarity: Belongs to the HMG-CoA lyase family


    Find genes that share domains with HMGCL           About GenesLikeMe


    (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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: HMGCL_HUMAN, P35914
    Function: Key enzyme in ketogenesis (ketone body formation). Terminal step in leucine catabolism. Ketone bodies
    (beta-hydroxybutyrate, acetoacetate and acetone) are essential as an alternative source of energy to glucose, as
    lipid precursors and as regulators of metabolism
    Catalytic activity: (S)-3-hydroxy-3-methylglutaryl-CoA = acetyl-CoA + acetoacetate
    Enzyme regulation: Stimulated by reducing agents such as dithiothreitol (DTT)
    Biophysicochemical properties: Kinetic parameters: KM=200 uM for magnesium ion; KM=48 uM for HMG-CoA; Vmax=191
    umol/min/mg enzyme;

         Genatlas biochemistry entry for HMGCL:
    3-hydroxy-3-methylglutaryl-CoA lyase,homodimeric mitochondrial and peroxisomal matrix enzyme,branched chain,last
    enzyme of ketogenesis from fatty acids and also leucine catabolism,lethal in HMGCL-deficient mice

         Enzyme Number (IUBMB): EC 4.1.3.41 2

         Gene Ontology (GO): Selected molecular function terms (see all 9):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000062fatty-acyl-CoA binding IEA--
    GO:0000287magnesium ion binding IDA9200711
    GO:0003824catalytic activity ----
    GO:0004419hydroxymethylglutaryl-CoA lyase activity TAS--
    GO:0005102receptor binding IPI--
         
    Find genes that share ontologies with HMGCL           About GenesLikeMe


    Phenotypes:
         8 MGI mutant phenotypes (inferred from 2 alleles(MGI details for Hmgcl):
     behavior/neurological  cardiovascular system  cellular  embryogenesis  growth/size/body 
     homeostasis/metabolism  liver/biliary system  mortality/aging 

    Find genes that share phenotypes with HMGCL           About GenesLikeMe

    Animal Models:
         MGI mouse knock-out Hmgcltm1Gam for HMGCL

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

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

    miRNA
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    miRTarBase miRNAs that target HMGCL:
    hsa-mir-106b-5p (MIRT044352)

    Block miRNA regulation of human, mouse, rat HMGCL using miScript Target Protectors
    3 qRT-PCR Assays for microRNAs that regulate HMGCL:
    hsa-miR-571 hsa-miR-548c-3p hsa-miR-1305
    SwitchGear 3'UTR luciferase reporter plasmidHMGCL 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat HMGCL

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    GenScript: all cDNA clones in your preferred vector (see all 2): HMGCL (NM_000191)
    Sino Biological Human cDNA Clone for HMGCL
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for HMGCL
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat HMGCL
    Addgene plasmids for HMGCL 

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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for HMGCL


    (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
    HMGCL_HUMAN, P35914: Mitochondrion matrix. Peroxisome. Note=Unprocessed form is peroxisomal
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    mitochondrion5
    peroxisome5
    cytosol1

    Gene Ontology (GO): 4 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005739mitochondrion IDA9869651
    GO:0005743mitochondrial inner membrane IEA--
    GO:0005759mitochondrial matrix TAS--
    GO:0005777peroxisome IDA9869651

    Find genes that share ontologies with HMGCL           About GenesLikeMe


    (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 HMGCL About   (see all 6)  
    See pathways by source

    SuperPathContained pathways About
    1Synthesis and Degradation of Ketone Bodies
    Synthesis and Degradation of Ketone Bodies0.43
    Synthesis of Ketone Bodies0.00
    Ketone body metabolism0.00
    2Metabolism
    Metabolism0.38
    Metabolism of lipids and lipoproteins0.37
    Metabolic pathways0.38
    3Butanoate metabolism
    Butanoate metabolism
    Synthesis and degradation of ketone bodies0.00
    4Fatty acid, triacylglycerol, and ketone body metabolism
    Fatty acid, triacylglycerol, and ketone body metabolism0.65
    5Valine, leucine and isoleucine degradation
    Valine, leucine and isoleucine degradation0.31


    Find genes that share SuperPaths with HMGCL           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 BioSystems Pathway for HMGCL
        Synthesis and Degradation of Ketone Bodies


    1 Reactome Pathway for HMGCL
        Synthesis of Ketone Bodies


    5 Kegg Pathways  (Kegg details for HMGCL):
        Synthesis and degradation of ketone bodies
    Valine, leucine and isoleucine degradation
    Butanoate metabolism
    Metabolic pathways
    Peroxisome

    UniProtKB/Swiss-Prot: HMGCL_HUMAN, P35914
    Pathway: Metabolic intermediate metabolism; (S)-3-hydroxy-3-methylglutaryl-CoA degradation; acetoacetate from
    (S)-3-hydroxy-3-methylglutaryl-CoA: step 1/1

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

              Fatty Acid Metabolism in human mouse rat
              Amino Acid Metabolism I in human mouse rat

    Interactions:

        Search GeneGlobe Interaction Network for HMGCL

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

    Selected Interacting proteins for HMGCL (P359142, 3 ENSP000003636144) via UniProtKB, MINT, STRING, and/or I2D (see all 38)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ADAMTS10Q9H3242, 3, ENSP000002703284MINT-8258164 I2D: score=2 STRING: ENSP00000270328
    ARL6IP1Q150412, 3, ENSP000003067884MINT-8258175 I2D: score=2 STRING: ENSP00000306788
    DNAJA1P316892, 3, ENSP000003691274MINT-8258186 I2D: score=2 STRING: ENSP00000369127
    HES1Q144692, 3MINT-8258197 I2D: score=2 
    RNF126Q9BV682, 3, ENSP000002923634MINT-8258208 I2D: score=2 STRING: ENSP00000292363
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 13):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001889liver development IEA--
    GO:0006552leucine catabolic process NAS9200711
    GO:0006637acyl-CoA metabolic process IEA--
    GO:0007005mitochondrion organization IEA--
    GO:0007584response to nutrient IEA--

    Find genes that share ontologies with HMGCL           About GenesLikeMe



    (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 HMGCL

    4 HMDB Compounds for HMGCL    About this table
    CompoundSynonyms CAS #PubMed Ids
    3-Hydroxy-3-methylglutaryl-CoA(S)-3-hydroxy-3-methylglutaryl-CoA (see all 15)1553-55-5--
    3-Hydroxymethylglutaric acid3-Hydroxy-3-methylglutarate (see all 14)503-49-1--
    Acetoacetic acid3-Ketobutyrate (see all 9)541-50-4--
    Acetyl-CoAS-Acetyl coenzyme A (see all 13)72-89-9--

    1 DrugBank Compound for HMGCL    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    3-hydroxyglutaric acid-- 638-18-6target----

    6 Novoseek inferred chemical compound relationships for HMGCL gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    3-hydroxy-3-methylglutaryl-coa 91.4 23 12746442 (3), 1302289 (2), 8617516 (2), 9776534 (1) (see all 16)
    4-hydroxy-2-oxovalerate 83.8 1 15122894 (1)
    leucine 70.8 13 9658458 (2), 15752612 (1), 16876013 (1), 15164951 (1) (see all 10)
    acetoacetate 65.4 2 8617516 (1), 9658458 (1)
    acetyl-coa 55.6 2 8617516 (1), 9658458 (1)
    cysteine 8.5 1 1304393 (1)



    Find genes that share compounds with HMGCL           About GenesLikeMe



    (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,
    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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for HMGCL gene (2 alternative transcripts): 
    NM_000191.2  NM_001166059.1  

    Unigene Cluster for HMGCL:

    3-hydroxymethyl-3-methylglutaryl-CoA lyase
    Hs.533444  [show with all ESTs]
    Unigene Representative Sequence: AK122801
    10 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000374490(uc001bib.3 uc010oec.2) ENST00000436439(uc021oii.1)
    ENST00000374487 ENST00000235958 ENST00000509389(uc009vqs.1) ENST00000496907
    ENST00000513148 ENST00000479458 ENST00000498698 ENST00000374483(uc001bic.3)

    miRNA
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    hsa-miR-571 hsa-miR-548c-3p hsa-miR-1305
    SwitchGear 3'UTR luciferase reporter plasmidHMGCL 3' UTR sequence
    Inhib. RNA
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      QuantiFast Probe-based Assays in human, mouse, rat HMGCL

    Additional mRNA sequence: 

    AK122801.1 AK300733.1 AK309129.1 AK313869.1 BC010570.1 BC021145.1 BT009792.1 CR456884.1 
    FJ472654.1 GU433941.1 L07033.1 

    Selected DOTS entries (see all 25):

    DT.216731  DT.100815335  DT.100815338  DT.100024518  DT.100661763  DT.95155278  DT.121382195  DT.95155290 
    DT.91751665  DT.95155277  DT.121382156  DT.75178439  DT.99995662  DT.91806374  DT.91928535  DT.92022788 
    DT.95155271  DT.95155276  DT.95155279  DT.97854087  DT.100663977  DT.91668479  DT.100813339  DT.102836787 

    Selected AceView cDNA sequences (see all 715):

    BI870763 CR612765 BG033962 BU553183 CF529487 AK122801 AI051126 CA418761 
    BI914327 BM846841 BF344949 CR592211 CR620370 AI123937 BG751626 AI733004 
    BG283060 BE384675 CB305984 CR623692 AL527902 AI719061 CD675757 AW631350 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for HMGCL (see all 7)    About this scheme

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


    ECgene alternative splicing isoforms for HMGCL

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

    HMGCL Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    HMGCL Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.533444

    UniProtKB/Swiss-Prot: HMGCL_HUMAN, P35914
    Tissue specificity: Highest expression in liver. Expressed in pancreas, kidey, intestine, testis, fibroblasts and
    lymphoblasts. Very low expression in brain and skeletal muscle. The relative expression of isoform 2 (at mRNA
    level) is highest in heart (30%), skeletal muscle (22%), and brain (14%)

        Pathway & Disease-focused RT2 Profiler PCR Arrays including HMGCL: 
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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 HMGCL gene from Selected species (see all 21)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Hmgcl1 , 5 3-hydroxy-3-methylglutaryl-Coenzyme A lyase1, 5 84.92(n)1
    88(a)1
      4 (68.14 cM)5
    153561  NM_008254.21  NP_032280.21 
     1359464485 
    chicken
    (Gallus gallus)
    Aves HMGCL1 3-hydroxymethyl-3-methylglutaryl-CoA lyase 75.13(n)
    78.68(a)
      396316  NM_001198714.1  NP_001185643.1 
    lizard
    (Anolis carolinensis)
    Reptilia HMGCL6
    3-hydroxymethyl-3-methylglutaryl-CoA lyase
    79(a)
    1 ↔ 1
    GL343498.1(82923-90129)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia LOC1004949041 hydroxymethylglutaryl-CoA lyase, mitochondrial-like 68.92(n)
    72.67(a)
      100494904  XM_002934559.2  XP_002934605.1 
    zebrafish
    (Danio rerio)
    Actinopterygii BC046023.12   -- 76.18(n)   394190  BC046023.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG103991 , 3 hydroxymethylglutaryl-CoA lyase3
    CG103991
    62(a)3
    60.82(n)1
    61.36(a)1
      27C73
    339781  NM_135245.21  NP_609089.11 
    worm
    (Caenorhabditis elegans)
    Secernentea Y71G12B.101 , 3 Y71G12B.101 51(a)3
    55.77(n)1
    53.27(a)1
      I(1751494-1754316)3
    1717381  NM_058488.51  NP_490889.11 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT2G268001 AT2G26800 61.43(n)
    64.16(a)
      817221  NM_179756.3  NP_850087.1 
    rice
    (Oryza sativa)
    Liliopsida Os.178682 Oryza sativa (japonica cultivar-group) cDNA cloneJ more 74.1(n)    AK066940.1 


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for HMGCL gene
    HMGCLL12  
    2 SIMAP similar genes for HMGCL using alignment to 6 protein entries:     HMGCL_HUMAN (see all proteins):
    HMGCLL1    DKFZp434G1411

    Find genes that share paralogs with HMGCL           About GenesLikeMe



    (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 HMGCL (see all 569)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1995878951,2,,4
    3-hydroxy-3-methylglutaryl-CoA lyase deficiency (HMGCLD)4 --22392260(+) ACCCCC/TGCACA 3 Q R mis1 int10--------
    VAR_0584474
    3-hydroxy-3-methylglutaryl-CoA lyase deficiency (HMGCLD)4--see VAR_0584472 S Y mis40--------
    VAR_0584424
    3-hydroxy-3-methylglutaryl-CoA lyase deficiency (HMGCLD)4--see VAR_0584422 S R mis40--------
    VAR_0584414
    3-hydroxy-3-methylglutaryl-CoA lyase deficiency (HMGCLD)4--see VAR_0584412 K N mis40--------
    VAR_0037464
    3-hydroxy-3-methylglutaryl-CoA lyase deficiency (HMGCLD)4--see VAR_0037462 D G mis40--------
    VAR_0037494
    3-hydroxy-3-methylglutaryl-CoA lyase deficiency (HMGCLD)4--see VAR_0037492 H R mis40--------
    VAR_0037454
    3-hydroxy-3-methylglutaryl-CoA lyase deficiency (HMGCLD)4--see VAR_0037452 D E mis40--------
    VAR_0037444
    3-hydroxy-3-methylglutaryl-CoA lyase deficiency (HMGCLD)4--see VAR_0037442 R Q mis40--------
    VAR_0584484
    3-hydroxy-3-methylglutaryl-CoA lyase deficiency (HMGCLD)4--see VAR_0584482 G E mis40--------
    rs289348941,2,4
    3-hydroxy-3-methylglutaryl-CoA lyase deficiency (HMGCLD)4--see VAR_0142022 mis40--------

    HapMap Linkage Disequilibrium report for HMGCL (24128367 - 24165110 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for HMGCL: --
    Human Gene Mutation Database (HGMD): HMGCL
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing HMGCL
    DNA2.0 Custom Variant and Variant Library Synthesis for HMGCL

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 613898   
    OMIM disorders: 246450  
    UniProtKB/Swiss-Prot: HMGCL_HUMAN, P35914
  • 3-hydroxy-3-methylglutaryl-CoA lyase deficiency (HMGCLD) [MIM:246450]: An autosomal recessive disease
    affecting ketogenesis and L-leucine catabolism. The disease usually appears in the first year of life after a
    fasting period and its clinical acute symptoms include vomiting, seizures, metabolic acidosis, hypoketotic
    hypoglycemia and lethargy. These symptoms sometimes progress to coma, with fatal outcome in some cases. Note=The
    disease is caused by mutations affecting the gene represented in this entry

  • 13 diseases for HMGCL:    
    About MalaCards
    3-hydroxy-3-methylglutaryl-coenzyme a lyase deficiency    hmg coa lyase deficiency    reye syndrome    propionic acidemia
    ornithine carbamoyltransferase deficiency    3-methylcrotonyl-coa carboxylase deficiency    organic acidemia    the organic acidemias: an
    isovaleric acidemia    maple syrup urine disease    ketothiolase deficiency    beta-ketothiolase deficiency
    methylmalonic acidemia

    9 diseases from the University of Copenhagen DISEASES database for HMGCL:
    3-Methylcrotonyl-CoA carboxylase deficiency     beta-ketothiolase deficiency     Isovaleric acidemia     Maple syrup urine disease
    Propionic acidemia     Metabolic acidosis     Methylmalonic acidemia     Hypoglycemia
    Ornithine carbamoyltransferase deficiency

    Find genes that share disorders with HMGCL           About GenesLikeMe

    Selected Novoseek inferred disease relationships for HMGCL gene (see all 12)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    aciduria organic 74.9 2 17173698 (1), 15308132 (1)
    metabolic acidosis 73.5 2 2225463 (1), 19932602 (1)
    hyperammonemia 70.3 1 2225463 (1)
    hypoglycemia 68.8 5 8440722 (1), 2225463 (1), 19932602 (1), 8617516 (1) (see all 5)
    reye syndrome 68.4 1 7777393 (1)
    propionic acidemia 68 1 1588014 (1)
    maple syrup urine disease 60.6 1 16398167 (1)
    methylmalonic aciduria 59 1 1588014 (1)
    homocystinuria 53.8 1 16398167 (1)
    genetic disorder 51.1 4 15752612 (1), 17692550 (1), 19932602 (1)

    Genatlas disease: HMGCL
    defective ketogenesis characterized by recurrent non ketotic hypoglycemia with acidosis,hyperammonemia and
    hydroxymethylglutaricaciduria

    Genetic Association Database (GAD): HMGCL
    Human Genome Epidemiology (HuGE) Navigator: HMGCL (3 documents)

    Export disorders for HMGCL 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 HMGCL gene, integrated from 10 sources (see all 85):
    (articles sorted by number of sources associating them with HMGCL)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. 3-hydroxy-3-methylglutaryl coenzyme A lyase (HL). Cloning of human and chicken liver HL cDNAs and characterization of a mutation causing human HL deficiency. (PubMed id 8440722)1, 2, 9 Mitchell G.A....Miziorko H.M. (J. Biol. Chem. 1993)
    2. 3-hydroxy-3-methylglutaryl CoA lyase (HL): mouse and human HL gene (HMGCL) cloning and detection of large gene deletions in two unrelated HL-deficient patients. (PubMed id 8617516)1, 2, 9 Wang S.P.... Mitchell G.A. (Genomics 1996)
    3. 3-Hydroxy-3-methylglutaryl coenzyme A lyase (HL): cloning and characterization of a mouse liver HL cDNA and subchromosomal mapping of the human and mouse HL genes. (PubMed id 8102917)1, 3, 9 Wang S....Miziorko H. (Mamm. Genome 1993)
    4. 3-Hydroxy-3-methylglutaryl-CoA lyase is present in mouse and human liver peroxisomes. (PubMed id 7527399)1, 2, 9 Ashmarina L.I.... Mitchell G.A. (J. Biol. Chem. 1994)
    5. Aberrantly spliced mRNAs of the 3-hydroxy-3-methylglutaryl coenzyme A lyase (HL) gene with a donor splice-site point mutation produce hereditary HL deficiency. (PubMed id 8978493)1, 3, 9 Buesa C....Hegardt F.G. (J. Lipid Res. 1996)
    6. Ten novel HMGCL mutations in 24 patients of different origin with 3- hydroxy-3-methyl-glutaric aciduria. (PubMed id 19177531)1, 2, 9 Menao S....Pie J. (Hum. Mutat. 2009)
    7. Evaluation of 3-hydroxy-3-methylglutaryl-coenzyme A lyase arginine-41 as a catalytic residue: use of acetyldithio-coenzyme A to monitor product enolization. (PubMed id 15122894)1, 2, 9 Tuinstra R.L.... Miziorko H.M. (Biochemistry 2004)
    8. C-terminal end and aminoacid Lys48 in HMG-CoA lyase are involved in substrate binding and enzyme activity. (PubMed id 17459752)1, 2, 9 Carrasco P.... Casals N. (Mol. Genet. Metab. 2007)
    9. Mutations underlying 3-hydroxy-3-methylglutaryl CoA lyase deficiency in the Saudi population. (PubMed id 17173698)1, 2, 9 Al-Sayed M.... Meyer B.F. (BMC Med. Genet. 2006)
    10. HMG CoA lyase deficiency: identification of five causal point mutations in codons 41 and 42, including a frequent Saudi Arabian mutation, R41Q. (PubMed id 9463337)1, 2, 9 Mitchell G.A....Miziorko H. (Am. J. Hum. Genet. 1998)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    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: 3155 HGNC: 5005 AceView: HMGCLandGALE Ensembl:ENSG00000117305 euGenes: HUgn3155
    ECgene: HMGCL Kegg: 3155 H-InvDB: HMGCL

    (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 HMGCL Pharmacogenomics, SNPs, Pathways
    GeneReviewshttp://www.ncbi.nlm.nih.gov/books/NBK1116/?term=HMGCL[genesymbol]

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

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



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