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Aliases for HMGCS2 Gene

Aliases for HMGCS2 Gene

  • 3-Hydroxy-3-Methylglutaryl-CoA Synthase 2 (Mitochondrial) 2 3
  • EC 4 63
  • 3-Hydroxy-3-Methylglutaryl-Coenzyme A Synthase 2 (Mitochondrial) 2
  • 3-Hydroxy-3-Methylglutaryl Coenzyme A Synthase 4
  • HMG-CoA Synthase 4

External Ids for HMGCS2 Gene

Previous GeneCards Identifiers for HMGCS2 Gene

  • GC01M120737
  • GC01M119128
  • GC01M119438
  • GC01M119637
  • GC01M120003
  • GC01M120092
  • GC01M120290
  • GC01M118149

Summaries for HMGCS2 Gene

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 hmg-coa synthase-2 deficiency and 3-hydroxy-3-methylglutaryl-coa synthase deficiency. Among its related pathways are Metabolism and Metabolism. GO annotations related to this gene include hydroxymethylglutaryl-CoA synthase activity. An important paralog of this gene is HMGCS1.

UniProtKB/Swiss-Prot for HMGCS2 Gene

  • This enzyme condenses acetyl-CoA with acetoacetyl-CoA to form HMG-CoA, which is the substrate for HMG-CoA reductase

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HMGCS2 Gene

Genomics for HMGCS2 Gene

Regulatory Elements for HMGCS2 Gene

Genomic Location for HMGCS2 Gene

119,747,996 bp from pter
119,768,932 bp from pter
20,937 bases
Minus strand

Genomic View for HMGCS2 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for HMGCS2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HMGCS2 Gene

Proteins for HMGCS2 Gene

  • Protein details for HMGCS2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Hydroxymethylglutaryl-CoA synthase, mitochondrial
    Protein Accession:
    Secondary Accessions:
    • B7Z8R3
    • D3Y5K6
    • Q5SZU2
    • Q6IBF4

    Protein attributes for HMGCS2 Gene

    508 amino acids
    Molecular mass:
    56635 Da
    Quaternary structure:
    • Homodimer.

    Three dimensional structures from OCA and Proteopedia for HMGCS2 Gene

    Alternative splice isoforms for HMGCS2 Gene


neXtProt entry for HMGCS2 Gene

Proteomics data for HMGCS2 Gene at MOPED

Post-translational modifications for HMGCS2 Gene

  • Ubiquitination at Lys137
  • Modification sites at PhosphoSitePlus

Other Protein References for HMGCS2 Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

Antibody Products

Domains for HMGCS2 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the HMG-CoA synthase family.
  • Belongs to the HMG-CoA synthase family.
genes like me logo Genes that share domains with HMGCS2: view

No data available for Gene Families for HMGCS2 Gene

Function for HMGCS2 Gene

Molecular function for HMGCS2 Gene

GENATLAS Biochemistry:
3-hydroxy-3-methylglutaryl-CoA synthase 2,mitochondrial,first and regulating enzyme of ketogenic pathway,through association with PPARA
UniProtKB/Swiss-Prot CatalyticActivity:
Acetyl-CoA + H(2)O + acetoacetyl-CoA = (S)-3-hydroxy-3-methylglutaryl-CoA + CoA.
UniProtKB/Swiss-Prot Function:
This enzyme condenses acetyl-CoA with acetoacetyl-CoA to form HMG-CoA, which is the substrate for HMG-CoA reductase

Enzyme Numbers (IUBMB) for HMGCS2 Gene

Gene Ontology (GO) - Molecular Function for HMGCS2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003824 catalytic activity --
GO:0004421 hydroxymethylglutaryl-CoA synthase activity IEA --
genes like me logo Genes that share ontologies with HMGCS2: view

Phenotypes for HMGCS2 Gene

GenomeRNAi human phenotypes for HMGCS2:
genes like me logo Genes that share phenotypes with HMGCS2: view

Animal Model Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for HMGCS2

In Situ Assay Products

Flow Cytometry Products

No data available for Animal Models , miRNA , Transcription Factor Targeting and HOMER Transcription for HMGCS2 Gene

Localization for HMGCS2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HMGCS2 Gene


Subcellular locations from

Jensen Localization Image for HMGCS2 Gene COMPARTMENTS Subcellular localization image for HMGCS2 gene
Compartment Confidence
mitochondrion 5
cytosol 2
nucleus 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for HMGCS2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion TAS 7851882
GO:0005743 mitochondrial inner membrane IEA --
GO:0005759 mitochondrial matrix TAS --
genes like me logo Genes that share ontologies with HMGCS2: view

Pathways for HMGCS2 Gene

genes like me logo Genes that share pathways with HMGCS2: view

PCR Array Products

UniProtKB/Swiss-Prot P54868-HMCS2_HUMAN

  • Pathway: Metabolic intermediate biosynthesis; (R)-mevalonate biosynthesis; (R)-mevalonate from acetyl-CoA: step 2/3

Gene Ontology (GO) - Biological Process for HMGCS2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006695 cholesterol biosynthetic process IEA --
GO:0008152 metabolic process --
GO:0008299 isoprenoid biosynthetic process IEA --
GO:0044255 cellular lipid metabolic process TAS --
GO:0044281 small molecule metabolic process TAS --
genes like me logo Genes that share ontologies with HMGCS2: view

Compounds for HMGCS2 Gene

(6) HMDB Compounds for HMGCS2 Gene

Compound Synonyms Cas Number PubMed IDs
  • (S)-3-hydroxy-3-methylglutaryl-CoA
  • (-)-7-dehydrocholesterol
  • 3-acetoacetyl-CoA
  • S-Acetyl coenzyme A
Coenzyme A
  • Acetoacetyl coenzyme A sodium salt

(2) Novoseek inferred chemical compound relationships for HMGCS2 Gene

Compound -log(P) Hits PubMed IDs
3-hydroxy-3-methylglutaryl-coa 86.2 6
fatty acid 36.9 1
genes like me logo Genes that share compounds with HMGCS2: view

Transcripts for HMGCS2 Gene

Unigene Clusters for HMGCS2 Gene

3-hydroxy-3-methylglutaryl-CoA synthase 2 (mitochondrial):
Representative Sequences:

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for HMGCS2

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for HMGCS2 Gene

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

Relevant External Links for HMGCS2 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for HMGCS2 Gene

mRNA expression in normal human tissues for HMGCS2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for HMGCS2 Gene

This gene is overexpressed in Liver (32.3) and Colon - Transverse (9.9).

Protein differential expression in normal tissues for HMGCS2 Gene

This gene is overexpressed in Liver (39.1), Liver, secretome (8.5), and Fetal Liver (6.3).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for HMGCS2 Gene

SOURCE GeneReport for Unigene cluster for HMGCS2 Gene Hs.59889

mRNA Expression by UniProt/SwissProt for HMGCS2 Gene

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%).
genes like me logo Genes that share expressions with HMGCS2: view

Primer Products

In Situ Assay Products

No data available for Expression partners for HMGCS2 Gene

Orthologs for HMGCS2 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for HMGCS2 Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia HMGCS2 35
  • 86.55 (n)
  • 87.6 (a)
  • 88 (a)
(Canis familiaris)
Mammalia HMGCS2 35
  • 88.39 (n)
  • 89.17 (a)
  • 89 (a)
(Mus musculus)
Mammalia Hmgcs2 35
  • 86.35 (n)
  • 89.37 (a)
Hmgcs2 16
Hmgcs2 36
  • 89 (a)
(Pan troglodytes)
Mammalia HMGCS2 35
  • 99.61 (n)
  • 99.61 (a)
  • 100 (a)
(Rattus norvegicus)
Mammalia Hmgcs2 35
  • 85.56 (n)
  • 89.17 (a)
(Monodelphis domestica)
Mammalia HMGCS2 36
  • 81 (a)
(Ornithorhynchus anatinus)
Mammalia HMGCS2 36
  • 71 (a)
(Gallus gallus)
Aves HMGCS2 35
  • 72.45 (n)
  • 72.52 (a)
  • 70 (a)
(Anolis carolinensis)
Reptilia HMGCS2 36
  • 68 (a)
fruit fly
(Drosophila melanogaster)
Insecta Hmgs 37
  • 60 (a)
Hmgs 36
  • 59 (a)
(Caenorhabditis elegans)
Secernentea F25B4.6 37
  • 43 (a)
hmgs-1 36
  • 42 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes ERG13 36
  • 43 (a)
(Oryza sativa)
Liliopsida Os.32782 35
sea squirt
(Ciona savignyi)
Ascidiacea CSA.9481 36
  • 51 (a)
Species with no ortholog for HMGCS2:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • zebrafish (Danio rerio)

Evolution for HMGCS2 Gene

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

Paralogs for HMGCS2 Gene

Paralogs for HMGCS2 Gene

(1) SIMAP similar genes for HMGCS2 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with HMGCS2: view

Variants for HMGCS2 Gene

Sequence variations from dbSNP and Humsavar for HMGCS2 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type MAF
rs4716 -- 119,755,461(-) CCTCA(A/T)CCCTG missense, reference
rs15609 -- 119,753,314(-) AGTTT(C/T)TTTTC reference, synonymous-codon
rs509184 -- 119,749,398(+) CCCCC(C/T)CCCTC intron-variant
rs532208 -- 119,749,656(+) TCCCA(G/T)CGGTA intron-variant
rs536662 -- 119,750,110(+) CAGAA(A/G)GAATC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for HMGCS2 Gene

Variant ID Type Subtype PubMed ID
nsv524681 CNV Gain 19592680
nsv831204 CNV Gain+Loss 17160897
nsv831215 CNV Gain 17160897
dgv93e1 CNV Complex 17122850
nsv428201 CNV Gain 18775914
dgv94e1 CNV Complex 17122850

Relevant External Links for HMGCS2 Gene

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)
Locus Specific Mutation Databases (LSDB)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HMGCS2 Gene

Disorders for HMGCS2 Gene

(1) OMIM Diseases for HMGCS2 Gene (600234)


  • 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. {ECO:0000269 PubMed:11228257, ECO:0000269 PubMed:11479731, ECO:0000269 PubMed:12647205}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Genatlas disease for HMGCS2 Gene

defective ketogenesis with recurrent hypoketotic hypoglycemia during fasting

Relevant External Links for HMGCS2

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
genes like me logo Genes that share disorders with HMGCS2: view

No data available for University of Copenhagen DISEASES and Novoseek inferred disease relationships for HMGCS2 Gene

Publications for HMGCS2 Gene

  1. Genetic basis of mitochondrial HMG-CoA synthase deficiency. (PMID: 11479731) Aledo R. … Hegardt F.G. (Hum. Genet. 2001) 3 4 23
  2. Human mitochondrial HMG CoA synthase: liver cDNA and partial genomic cloning, chromosome mapping to 1p12-p13, and possible role in vertebrate evolution. (PMID: 7851882) Boukaftane Y. … Mitchell G.A. (Genomics 1994) 2 3 4
  3. Molecular cloning and tissue expression of human mitochondrial 3- hydroxy-3-methylglutaryl-CoA synthase. (PMID: 7893153) Mascaro C. … Hegardt F.G. (Arch. Biochem. Biophys. 1995) 2 3 4
  4. Cloning and characterization of the human mitochondrial 3-hydroxy-3- methylglutaryl CoA synthase gene. (PMID: 9305755) Boukaftane Y. … Mitchell G.A. (Gene 1997) 3 4
  5. Mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency: clinical course and description of causal mutations in two patients. (PMID: 11228257) Bouchard L. … Mitchell G.A. (Pediatr. Res. 2001) 3 4

Products for HMGCS2 Gene

Sources for HMGCS2 Gene

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