Free for academic non-profit institutions. Other users need a Commercial license

Aliases for HMGCL Gene

Aliases for HMGCL Gene

  • 3-Hydroxymethyl-3-Methylglutaryl-CoA Lyase 2 3 5
  • 3-Hydroxymethyl-3-Methylglutaryl-Coenzyme A Lyase 2 3
  • 3-Hydroxy-3-Methylglutarate-CoA Lyase 3 4
  • Hydroxymethylglutaricaciduria 2 3
  • HMG-CoA Lyase 3 4
  • EC 4 58
  • HL 3 4
  • Mitochondrial 3-Hydroxy-3-Methylglutaryl-CoA Lyase 3
  • Hydroxymethylglutaryl-CoA Lyase, Mitochondrial 3
  • 3-Hydroxy-3-Methylglutaryl-CoA Lyase 3

External Ids for HMGCL Gene

Previous GeneCards Identifiers for HMGCL Gene

  • GC01M023686
  • GC01M023199
  • GC01M023597
  • GC01M023873
  • GC01M024001
  • GC01M024128
  • GC01M022379

Summaries for HMGCL Gene

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 Hmg-Coa Lyase Deficiency and 3-Hydroxy-3-Methylglutaryl-Coenzyme A Lyase Deficiency. Among its related pathways are Ketone body metabolism and Metabolism. GO annotations related to this gene include protein homodimerization activity and magnesium ion binding. An important paralog of this gene is HMGCLL1.

UniProtKB/Swiss-Prot for HMGCL Gene

  • 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.

Additional gene information for HMGCL Gene

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

Genomics for HMGCL Gene

Regulatory Elements for HMGCL Gene

Enhancers for HMGCL Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01H023829 0.8 ENCODE 7.9 +8.3 8276 0.9 HDGF FOXA2 TAL1 MAX YY1 TCF12 NCOR1 ADNP TRIM24 SMARCE1 FUCA1 HMGCL GC01P023838 PIR41142
GH01H023726 1.2 Ensembl ENCODE 4.7 +110.5 110485 3.1 PKNOX1 FOXA2 ARID4B SIN3A DMAP1 YY1 ZNF207 ATF7 RUNX3 MXD4 FUCA1 HMGCL GC01P023723 GC01M023736
GH01H024432 0.4 dbSUPER 6.7 -594.6 -594634 1.9 ZNF664 STPG1 NIPAL3 HMGCL GC01P024477
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around HMGCL on UCSC Golden Path with GeneCards custom track

Promoters for HMGCL Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000003098 -180 801 HDAC1 HDGF ARID4B YY1 GLIS2 EGR1 CREM EGR2 SP3 ZNF362

Genomic Locations for HMGCL Gene

Genomic Locations for HMGCL Gene
36,744 bases
Minus strand

Genomic View for HMGCL Gene

Genes around HMGCL on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HMGCL Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HMGCL Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HMGCL Gene

Proteins for HMGCL Gene

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

    Protein Symbol:
    Recommended name:
    Hydroxymethylglutaryl-CoA lyase, mitochondrial
    Protein Accession:
    Secondary Accessions:
    • B4DUP4
    • B7UCC6
    • D3Y5K7
    • Q6IBC0
    • Q96FP8

    Protein attributes for HMGCL Gene

    325 amino acids
    Molecular mass:
    34360 Da
    Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
    Quaternary structure:
    • Homodimer; disulfide-linked. Can also form homotetramers.

    Three dimensional structures from OCA and Proteopedia for HMGCL Gene

    Alternative splice isoforms for HMGCL Gene


neXtProt entry for HMGCL Gene

Selected DME Specific Peptides for HMGCL Gene


Post-translational modifications for HMGCL Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for HMGCL Gene

Domains & Families for HMGCL Gene

Gene Families for HMGCL Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Plasma proteins
  • Potential drug targets
  • Predicted intracellular proteins
  • Predicted secreted proteins

Graphical View of Domain Structure for InterPro Entry



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

Function for HMGCL Gene

Molecular function for HMGCL Gene

GENATLAS Biochemistry:
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
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=200 uM for magnesium ion {ECO:0000269 PubMed:12874287, ECO:0000269 PubMed:15122894}; KM=48 uM for HMG-CoA {ECO:0000269 PubMed:12874287, ECO:0000269 PubMed:15122894}; Vmax=191 umol/min/mg enzyme {ECO:0000269 PubMed:12874287, ECO:0000269 PubMed:15122894};
UniProtKB/Swiss-Prot CatalyticActivity:
(S)-3-hydroxy-3-methylglutaryl-CoA = acetyl-CoA + acetoacetate.
UniProtKB/Swiss-Prot EnzymeRegulation:
Stimulated by reducing agents such as dithiothreitol (DTT).
UniProtKB/Swiss-Prot 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.

Enzyme Numbers (IUBMB) for HMGCL Gene

Phenotypes From GWAS Catalog for HMGCL Gene

Gene Ontology (GO) - Molecular Function for HMGCL Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000062 fatty-acyl-CoA binding IEA --
GO:0000287 magnesium ion binding IDA 9200711
GO:0003824 catalytic activity IEA --
GO:0004419 hydroxymethylglutaryl-CoA lyase activity TAS,IEA --
GO:0005102 receptor binding IPI 20178365
genes like me logo Genes that share ontologies with HMGCL: view
genes like me logo Genes that share phenotypes with HMGCL: view

Human Phenotype Ontology for HMGCL Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for HMGCL Gene

MGI Knock Outs for HMGCL:

Animal Model Products

miRNA for HMGCL Gene

miRTarBase miRNAs that target HMGCL

Clone Products

  • Addgene plasmids for HMGCL

No data available for Transcription Factor Targets and HOMER Transcription for HMGCL Gene

Localization for HMGCL Gene

Subcellular locations from UniProtKB/Swiss-Prot for HMGCL Gene

Mitochondrion matrix. Peroxisome. Note=Unprocessed form is peroxisomal.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for HMGCL gene
Compartment Confidence
mitochondrion 5
peroxisome 5
cytosol 1

Gene Ontology (GO) - Cellular Components for HMGCL Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion IDA,IEA 9869651
GO:0005743 mitochondrial inner membrane IEA --
GO:0005759 mitochondrial matrix TAS --
GO:0005777 peroxisome IEA,IDA 9869651
genes like me logo Genes that share ontologies with HMGCL: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for HMGCL Gene

Pathways & Interactions for HMGCL Gene

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

UniProtKB/Swiss-Prot P35914-HMGCL_HUMAN

  • Pathway: Metabolic intermediate metabolism; (S)-3-hydroxy-3-methylglutaryl-CoA degradation; acetoacetate from (S)-3-hydroxy-3-methylglutaryl-CoA: step 1/1.

Gene Ontology (GO) - Biological Process for HMGCL Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001889 liver development IEA --
GO:0006552 leucine catabolic process TAS,NAS 8027038
GO:0006629 lipid metabolic process IDA 8027038
GO:0006637 acyl-CoA metabolic process IEA --
GO:0007005 mitochondrion organization IEA --
genes like me logo Genes that share ontologies with HMGCL: view

No data available for SIGNOR curated interactions for HMGCL Gene

Drugs & Compounds for HMGCL Gene

(5) Drugs for HMGCL Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
acetic acid Approved Nutra Full agonist, Agonist 115
3-hydroxyglutaric acid Experimental Pharma Target 0
Acetoacetic acid Experimental Pharma 0

(7) Additional Compounds for HMGCL Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • (S)-3-hydroxy-3-methylglutaryl-CoA
  • (S)-3-hydroxy-3-methylglutaryl-Coenzyme A
  • 3-Hydroxy-3-methyl-Glutaryl-CoA
  • 3-Hydroxy-3-methyl-Glutaryl-Coenzyme A
  • 3-Hydroxy-3-methylglutaryl-CoA
  • Ac-CoA
  • Ac-Coenzyme A
  • Ac-S-CoA
  • Ac-S-Coenzyme A
  • Acetyl coenzyme-A
3-Hydroxymethylglutaric acid
  • 3-Hydroxy-3-methyl-Glutaric acid
  • 3-Hydroxy-3-methylglutarate
  • 3-Hydroxy-3-methylglutaric acid
  • 3-Hydroxymethylglutarate
  • 3-Hydroxymethylglutaric acid
genes like me logo Genes that share compounds with HMGCL: view

Transcripts for HMGCL Gene

Unigene Clusters for HMGCL Gene

3-hydroxymethyl-3-methylglutaryl-CoA lyase:
Representative Sequences:

Clone Products

  • Addgene plasmids for HMGCL

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

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: - - - - - -
SP6: - -

Relevant External Links for HMGCL Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for HMGCL Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HMGCL Gene

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

This gene is overexpressed in Liver (x8.3).

Protein differential expression in normal tissues from HIPED for HMGCL Gene

This gene is overexpressed in Liver, secretome (16.0) and Liver (8.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for HMGCL Gene

Protein tissue co-expression partners for HMGCL Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of HMGCL Gene:


SOURCE GeneReport for Unigene cluster for HMGCL Gene:


mRNA Expression by UniProt/SwissProt for HMGCL Gene:

Tissue specificity: Highest expression in liver. Expressed in pancreas, kidney, 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%).

Evidence on tissue expression from TISSUES for HMGCL Gene

  • Nervous system(4.6)
  • Liver(4.5)
  • Muscle(4.3)
  • Kidney(2.7)

Phenotype-based relationships between genes and organs from Gene ORGANizer for HMGCL Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • digestive
  • endocrine
  • immune
  • integumentary
  • nervous
  • reproductive
Head and neck:
  • brain
  • cerebellum
  • ear
  • eye
  • head
  • heart
  • adrenal gland
  • liver
  • penis
  • testicle
  • blood
  • peripheral nerve
  • peripheral nervous system
  • red blood cell
  • skin
  • sweat gland
  • white blood cell
genes like me logo Genes that share expression patterns with HMGCL: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery for HMGCL Gene

Orthologs for HMGCL Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for HMGCL Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia HMGCL 33 34
  • 99.49 (n)
(Bos Taurus)
Mammalia HMGCL 33 34
  • 88.82 (n)
(Canis familiaris)
Mammalia HMGCL 33 34
  • 88.1 (n)
(Mus musculus)
Mammalia Hmgcl 33 16 34
  • 84.92 (n)
(Rattus norvegicus)
Mammalia Hmgcl 33
  • 84.62 (n)
(Monodelphis domestica)
Mammalia HMGCL 34
  • 78 (a)
(Ornithorhynchus anatinus)
Mammalia HMGCL 34
  • 57 (a)
(Gallus gallus)
Aves HMGCL 33 34
  • 75.13 (n)
(Anolis carolinensis)
Reptilia HMGCL 34
  • 79 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100494904 33
  • 68.92 (n)
(Danio rerio)
Actinopterygii hmgcl 33 34
  • 69.57 (n)
-- 33
fruit fly
(Drosophila melanogaster)
Insecta CG10399 35 33 34
  • 60.82 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008717 33
  • 59.66 (n)
(Caenorhabditis elegans)
Secernentea Y71G12B.10 35 33 34
  • 55.77 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT2G26800 33
  • 61.43 (n)
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.372 33
(Oryza sativa)
Liliopsida Os01g0269000 33
  • 62.34 (n)
Os.17868 33
(Hordeum vulgare)
Liliopsida Hv.1703 33
(Triticum aestivum)
Liliopsida Ta.9483 33
(Zea mays)
Liliopsida Zm.6728 33
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 58 (a)
Species where no ortholog for HMGCL was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • 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)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)

Evolution for HMGCL Gene

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

Paralogs for HMGCL Gene

Paralogs for HMGCL Gene

(2) SIMAP similar genes for HMGCL Gene using alignment to 6 proteins:

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

Variants for HMGCL Gene

Sequence variations from dbSNP and Humsavar for HMGCL Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs121964996 Pathogenic, 3-hydroxy-3-methylglutaryl-CoA lyase deficiency (HMGCLD) [MIM:246450] 23,817,520(-) TCTCT(C/G)TTATA reference, missense
rs121964997 Pathogenic, 3-hydroxy-3-methylglutaryl-CoA lyase deficiency (HMGCLD) [MIM:246450] 23,820,532(-) TCCCC(A/G)AGATG reference, missense
rs199587895 3-hydroxy-3-methylglutaryl-CoA lyase deficiency (HMGCLD) [MIM:246450] 23,814,193(+) ACCCC(C/G/T)GCACA intron-variant, reference, missense
rs28934894 3-hydroxy-3-methylglutaryl-CoA lyase deficiency (HMGCLD) [MIM:246450]
rs727503963 Pathogenic, 3-hydroxy-3-methylglutaryl-CoA lyase deficiency (HMGCLD) [MIM:246450] 23,808,187(-) TGTCC(A/G)CTGCC reference, missense

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

Variant ID Type Subtype PubMed ID
nsv1113088 CNV deletion 24896259

Variation tolerance for HMGCL Gene

Residual Variation Intolerance Score: 22.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.00; 20.65% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for HMGCL Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

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

Disorders for HMGCL Gene

MalaCards: The human disease database

(16) MalaCards diseases for HMGCL Gene - From: HGMD, OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
hmg-coa lyase deficiency
  • hmg coa lyase deficiency
3-hydroxy-3-methylglutaryl-coenzyme a lyase deficiency
  • hmg-coa lyase deficiency
reye syndrome
  • reye's syndrome
organic acidemia
  • organic acid metabolism disorder
metabolic acidosis
- elite association - COSMIC cancer census association via MalaCards
Search HMGCL in MalaCards View complete list of genes associated with diseases


  • 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. {ECO:0000269 PubMed:11129331, ECO:0000269 PubMed:12746442, ECO:0000269 PubMed:16601870, ECO:0000269 PubMed:17173698, ECO:0000269 PubMed:17459752, ECO:0000269 PubMed:19036343, ECO:0000269 PubMed:19177531, ECO:0000269 PubMed:8798725, ECO:0000269 PubMed:9463337, ECO:0000269 PubMed:9784232}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Genatlas disease for HMGCL Gene

defective ketogenesis characterized by recurrent non ketotic hypoglycemia with acidosis,hyperammonemia and hydroxymethylglutaricaciduria

Relevant External Links for HMGCL

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with HMGCL: view

Publications for HMGCL Gene

  1. Ten novel HMGCL mutations in 24 patients of different origin with 3-hydroxy-3-methyl-glutaric aciduria. (PMID: 19177531) Menao S … Pié J (Human mutation 2009) 3 4 22 60
  2. C-terminal end and aminoacid Lys48 in HMG-CoA lyase are involved in substrate binding and enzyme activity. (PMID: 17459752) Carrasco P … Casals N (Molecular genetics and metabolism 2007) 3 4 22 60
  3. Mutations underlying 3-hydroxy-3-methylglutaryl CoA lyase deficiency in the Saudi population. (PMID: 17173698) Al-Sayed M … Meyer BF (BMC medical genetics 2006) 3 4 22 60
  4. Evaluation of 3-hydroxy-3-methylglutaryl-coenzyme A lyase arginine-41 as a catalytic residue: use of acetyldithio-coenzyme A to monitor product enolization. (PMID: 15122894) Tuinstra RL … Miziorko HM (Biochemistry 2004) 3 4 22 60
  5. HMG CoA lyase deficiency: identification of five causal point mutations in codons 41 and 42, including a frequent Saudi Arabian mutation, R41Q. (PMID: 9463337) Mitchell GA … Miziorko H (American journal of human genetics 1998) 3 4 22 60

Products for HMGCL Gene

Sources for HMGCL Gene

Loading form....