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    HMGCS2 3-hydroxy-3-methylglutaryl-CoA synthase 2 [ Homo sapiens (human) ]

    Gene ID: 3158, updated on 8-Jul-2021

    Summary

    Official Symbol
    HMGCS2provided by HGNC
    Official Full Name
    3-hydroxy-3-methylglutaryl-CoA synthase 2provided by HGNC
    Primary source
    HGNC:HGNC:5008
    See related
    Ensembl:ENSG00000134240 MIM:600234
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    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]
    Expression
    Biased expression in liver (RPKM 471.6), colon (RPKM 127.8) and 5 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See HMGCS2 in Genome Data Viewer
    Location:
    1p12
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    109.20210514 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (119747996..119768932, complement)
    105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (120290619..120311555, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378937 Neighboring gene uncharacterized LOC105378936 Neighboring gene phosphoglycerate dehydrogenase Neighboring gene regenerating family member 4 Neighboring gene uncharacterized LOC105378938 Neighboring gene NBPF member 7, pseudogene

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables hydroxymethylglutaryl-CoA synthase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables hydroxymethylglutaryl-CoA synthase activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables hydroxymethylglutaryl-CoA synthase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables hydroxymethylglutaryl-CoA synthase activity TAS
    Traceable Author Statement
    more info
     
    enables identical protein binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in acetyl-CoA metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in acetyl-CoA metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cholesterol biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in farnesyl diphosphate biosynthetic process, mevalonate pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in ketone body biosynthetic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in ketone body biosynthetic process TAS
    Traceable Author Statement
    more info
     
    Component Evidence Code Pubs
    located_in mitochondrial matrix TAS
    Traceable Author Statement
    more info
     
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
     

    General protein information

    Preferred Names
    hydroxymethylglutaryl-CoA synthase, mitochondrial
    Names
    3-hydroxy-3-methylglutaryl-CoA synthase 2 (mitochondrial)
    3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2 (mitochondrial)
    HMG-CoA synthase
    testicular tissue protein Li 88
    NP_001159579.1
    NP_005509.1
    XP_011539615.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_013348.1 RefSeqGene

      Range
      5001..25937
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_447

    mRNA and Protein(s)

    1. NM_001166107.1NP_001159579.1  hydroxymethylglutaryl-CoA synthase, mitochondrial isoform 2 precursor

      See identical proteins and their annotated locations for NP_001159579.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) is missing an in-frame coding exon compared to variant 1. This results in a shorter isoform (2) lacking an internal protein segment compared to isoform 1.
      Source sequence(s)
      AI215948, AK303777, BC044217, BP420631, BX104280
      Consensus CDS
      CCDS53353.1
      UniProtKB/Swiss-Prot
      P54868
      Related
      ENSP00000439495.2, ENST00000544913.2
      Conserved Domains (3) summary
      TIGR01833
      Location:50464
      HMG-CoA-S_euk; 3-hydroxy-3-methylglutaryl-CoA-synthase, eukaryotic clade
      pfam08540
      Location:187464
      HMG_CoA_synt_C; Hydroxymethylglutaryl-coenzyme A synthase C terminal
      cl09938
      Location:53187
      cond_enzymes; Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the ...
    2. NM_005518.4NP_005509.1  hydroxymethylglutaryl-CoA synthase, mitochondrial isoform 1 precursor

      See identical proteins and their annotated locations for NP_005509.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AI215948, BC044217, BP420631, BX104280
      Consensus CDS
      CCDS905.1
      UniProtKB/Swiss-Prot
      P54868
      UniProtKB/TrEMBL
      A0A140VJL2
      Related
      ENSP00000358414.3, ENST00000369406.8
      Conserved Domains (1) summary
      TIGR01833
      Location:50506
      HMG-CoA-S_euk; 3-hydroxy-3-methylglutaryl-CoA-synthase, eukaryotic clade

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

      Range
      119747996..119768932 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011541313.2XP_011539615.1  hydroxymethylglutaryl-CoA synthase, mitochondrial isoform X1

      UniProtKB/Swiss-Prot
      P54868
      Conserved Domains (3) summary
      TIGR01833
      Location:50451
      HMG-CoA-S_euk; 3-hydroxy-3-methylglutaryl-CoA-synthase, eukaryotic clade
      pfam01154
      Location:53223
      HMG_CoA_synt_N; Hydroxymethylglutaryl-coenzyme A synthase N terminal
      pfam08540
      Location:231451
      HMG_CoA_synt_C; Hydroxymethylglutaryl-coenzyme A synthase C terminal
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