Aliases for HMGCLL1 Gene

Aliases for HMGCLL1 Gene

  • 3-Hydroxymethyl-3-Methylglutaryl-CoA Lyase Like 1 2 3 5
  • Endoplasmic Reticulum 3-Hydroxy-3-Methylglutaryl-CoA Lyase 3 4
  • 3-Hydroxymethyl-3-Methylglutaryl-Coenzyme A Lyase-Like 1 2 3
  • 3-Hydroxy-3-Methylglutaryl-CoA Lyase-Like Protein 1 3 4
  • EC 4 52
  • Er-CHL 3 4
  • Endoplasmic Reticulum 3-Hydroxymethyl-3-Methylglutaryl-CoA Lyase 3
  • 3-Hydroxymethyl-3-Methylglutaryl-CoA Lyase-Like Protein 1 3
  • 3-Hydroxymethyl-3-Methylglutaryl-CoA Lyase, Cytoplasmic 3
  • Probable 3-Hydroxymethyl-3-Methylglutaryl-CoA Lyase 2 3
  • 3-Hydroxy-3-Methylglutaryl-CoA Lyase, Cytoplasmic 4
  • BA418P12.1 3

External Ids for HMGCLL1 Gene

Previous GeneCards Identifiers for HMGCLL1 Gene

  • GC06M055300
  • GC06M055346
  • GC06M055133
  • GC06M055299

Summaries for HMGCLL1 Gene

GeneCards Summary for HMGCLL1 Gene

HMGCLL1 (3-Hydroxymethyl-3-Methylglutaryl-CoA Lyase Like 1) is a Protein Coding gene. Diseases associated with HMGCLL1 include Breast Adenoid Cystic Carcinoma and Hepatic Infarction. Among its related pathways are Valine, leucine and isoleucine degradation and Ketone body metabolism. Gene Ontology (GO) annotations related to this gene include lyase activity and hydroxymethylglutaryl-CoA lyase activity. An important paralog of this gene is HMGCL.

UniProtKB/Swiss-Prot Summary for HMGCLL1 Gene

  • Non-mitochondrial 3-hydroxymethyl-3-methylglutaryl-CoA lyase that catalyzes a cation-dependent cleavage of (S)-3-hydroxy-3-methylglutaryl-CoA into acetyl-CoA and acetoacetate, a key step in ketogenesis, the products of which support energy production in nonhepatic animal tissues.

Additional gene information for HMGCLL1 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for HMGCLL1 Gene

Genomics for HMGCLL1 Gene

GeneHancer (GH) Regulatory Elements for HMGCLL1 Gene

Promoters and enhancers for HMGCLL1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06J055578 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE CraniofacialAtlas 513.9 +100.6 100567 1.4 ZNF217 EP300 ZNF10 ZIC2 ZBTB10 ZNF423 ZBTB26 KLF4 KLF7 ZEB1 HMGCLL1 piR-41880-024 HSALNG0050757
GH06J055678 Enhancer 0.6 Ensembl 500.7 +0.8 767 1 ATF2 ZNF335 IKZF3 POLR2A FOXP2 PRDM6 GLIS1 ZFP69B ZBTB21 TRIM28 HMGCLL1 piR-41880-024
GH06J055680 Enhancer 0.3 Ensembl 500.7 -1.1 -1133 0.4 ZNF335 ZBTB44 ENSG00000220725 HMGCLL1 lnc-BMP5-1
GH06J055635 Enhancer 0.9 Ensembl ENCODE 10.9 +43.0 43021 3.2 ZNF217 TCF12 FOS CUX1 CHD1 CTBP1 MBD2 POLR2A FOSL2 CEBPB HMGCLL1 ENSG00000224984 piR-41880-024
GH06J055704 Enhancer 0.6 Ensembl ENCODE 10.9 -25.1 -25133 1.6 FOS JUN BATF JUND HMGCLL1 piR-46002-485 BMP5
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HMGCLL1 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for HMGCLL1

Top Transcription factor binding sites by QIAGEN in the HMGCLL1 gene promoter:
  • C/EBPalpha
  • Gfi-1
  • Hlf
  • NF-1
  • NF-1/L
  • NF-kappaB
  • NF-kappaB1
  • Pax-5
  • PPAR-gamma1
  • PPAR-gamma2

Genomic Locations for HMGCLL1 Gene

Genomic Locations for HMGCLL1 Gene
245,300 bases
Minus strand
144,846 bases
Minus strand

Genomic View for HMGCLL1 Gene

Genes around HMGCLL1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HMGCLL1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HMGCLL1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HMGCLL1 Gene

Proteins for HMGCLL1 Gene

  • Protein details for HMGCLL1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    3-hydroxy-3-methylglutaryl-CoA lyase, cytoplasmic
    Protein Accession:
    Secondary Accessions:
    • B1AQ42
    • B3KNV0
    • B7Z1S7
    • F8W793
    • Q6ZSA9

    Protein attributes for HMGCLL1 Gene

    370 amino acids
    Molecular mass:
    39514 Da
    Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
    Quaternary structure:
    No Data Available
    • [Isoform 3]: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.
    • Sequence=BAC87045.1; Type=Frameshift; Evidence={ECO:0000305}; Sequence=BAG51462.1; Type=Erroneous translation; Note=Wrong choice of CDS.; Evidence={ECO:0000305};

    Alternative splice isoforms for HMGCLL1 Gene


neXtProt entry for HMGCLL1 Gene

Selected DME Specific Peptides for HMGCLL1 Gene


Post-translational modifications for HMGCLL1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Domains & Families for HMGCLL1 Gene

Gene Families for HMGCLL1 Gene

Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Protein Domains for HMGCLL1 Gene


Suggested Antigen Peptide Sequences for HMGCLL1 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ57919 (B7Z212_HUMAN)
  • cDNA FLJ57397 (B7Z4D4_HUMAN)
  • 3-hydroxymethyl-3-methylglutaryl-CoA lyase-like protein 1 (HMGC2_HUMAN)

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 HMGCLL1: view

Function for HMGCLL1 Gene

Molecular function for HMGCLL1 Gene

UniProtKB/Swiss-Prot Function:
Non-mitochondrial 3-hydroxymethyl-3-methylglutaryl-CoA lyase that catalyzes a cation-dependent cleavage of (S)-3-hydroxy-3-methylglutaryl-CoA into acetyl-CoA and acetoacetate, a key step in ketogenesis, the products of which support energy production in nonhepatic animal tissues.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=(3S)-hydroxy-3-methylglutaryl-CoA = acetoacetate + acetyl-CoA; Xref=Rhea:RHEA:24404, ChEBI:CHEBI:13705, ChEBI:CHEBI:43074, ChEBI:CHEBI:57288; EC=; Evidence={ECO:0000269 PubMed:22847177, ECO:0000269 PubMed:22865860};.
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=40 uM for (S)-3-hydroxy-3-methylglutaryl-CoA (at pH 9) {ECO:0000269 PubMed:22847177}; KM=75 uM for (S)-3-hydroxy-3-methylglutaryl-CoA (at pH 8) {ECO:0000269 PubMed:22847177}; KM=28 uM for (S)-3-hydroxy-3-methylglutaryl-CoA {ECO:0000269 PubMed:22865860}; KM=49 uM for (S)-3-hydroxy-3-methylglutaryl-CoA (in presence of magnesium) {ECO:0000269 PubMed:22865860}; KM=0.18 uM for (S)-3-hydroxy-3-methylglutaryl-CoA (in presence of manganese) {ECO:0000269 PubMed:22865860}; Vmax=12 nmol/min/mg enzyme with (S)-3-hydroxy-3-methylglutaryl- CoA as substrate at pH 9 {ECO:0000269 PubMed:22847177}; Vmax=25 nmol/min/mg enzyme with (S)-3-hydroxy-3-methylglutaryl- CoA as substrate at pH 8 {ECO:0000269 PubMed:22847177};

Enzyme Numbers (IUBMB) for HMGCLL1 Gene

Phenotypes From GWAS Catalog for HMGCLL1 Gene

Gene Ontology (GO) - Molecular Function for HMGCLL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004419 hydroxymethylglutaryl-CoA lyase activity ISS,IEA --
GO:0016829 lyase activity IEA --
GO:0046872 metal ion binding TAS 22865860
genes like me logo Genes that share ontologies with HMGCLL1: view
genes like me logo Genes that share phenotypes with HMGCLL1: view

Animal Model Products

CRISPR Products

Clone Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for HMGCLL1 Gene

Localization for HMGCLL1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HMGCLL1 Gene

Cytoplasm, cytosol. Endoplasmic reticulum membrane; Peripheral membrane protein.

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 HMGCLL1 gene
Compartment Confidence
endoplasmic reticulum 5
cytosol 5
mitochondrion 3
extracellular 1
peroxisome 1
nucleus 1

Gene Ontology (GO) - Cellular Components for HMGCLL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005783 endoplasmic reticulum IBA,IDA 22847177
GO:0005789 endoplasmic reticulum membrane IEA --
GO:0005829 cytosol TAS --
GO:0016020 membrane IDA,IEA 22865860
genes like me logo Genes that share ontologies with HMGCLL1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for HMGCLL1 Gene

Pathways & Interactions for HMGCLL1 Gene

genes like me logo Genes that share pathways with HMGCLL1: view

UniProtKB/Swiss-Prot Q8TB92-HMGC2_HUMAN

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

Interacting Proteins for HMGCLL1 Gene


Gene Ontology (GO) - Biological Process for HMGCLL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006552 leucine catabolic process IBA 21873635
GO:0006629 lipid metabolic process IBA 21873635
GO:0046951 ketone body biosynthetic process TAS,IEA --
genes like me logo Genes that share ontologies with HMGCLL1: view

No data available for SIGNOR curated interactions for HMGCLL1 Gene

Drugs & Compounds for HMGCLL1 Gene

(1) Drugs for HMGCLL1 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Acetoacetic acid Experimental Pharma 0

(2) Additional Compounds for HMGCLL1 Gene - From: 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-coenzyme A
  • AcCoA
  • Acetyl coenzyme A
  • S-Acetyl-CoA
  • S-Acetyl-coenzyme A
  • Ac-CoA
genes like me logo Genes that share compounds with HMGCLL1: view

Transcripts for HMGCLL1 Gene

mRNA/cDNA for HMGCLL1 Gene

10 NCBI additional mRNA sequence :
9 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for HMGCLL1 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9a · 9b ^ 10 ^ 11 ^ 12a · 12b ^ 13a · 13b
SP1: - - - -
SP2: - - - -
SP3: - - - - -
SP4: - - -
SP5: - - - - - - - - - -
SP6: - - - - - -

Relevant External Links for HMGCLL1 Gene

GeneLoc Exon Structure for

Expression for HMGCLL1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for HMGCLL1 Gene

mRNA differential expression in normal tissues according to GTEx for HMGCLL1 Gene

This gene is overexpressed in Brain - Anterior cingulate cortex (BA24) (x4.7), Brain - Frontal Cortex (BA9) (x4.5), and Brain - Hypothalamus (x4.3).

Protein differential expression in normal tissues from HIPED for HMGCLL1 Gene

This gene is overexpressed in Heart (36.6) and Liver (32.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for HMGCLL1 Gene

Protein tissue co-expression partners for HMGCLL1 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for HMGCLL1

SOURCE GeneReport for Unigene cluster for HMGCLL1 Gene:


Evidence on tissue expression from TISSUES for HMGCLL1 Gene

  • Nervous system(4.7)
genes like me logo Genes that share expression patterns with HMGCLL1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for HMGCLL1 Gene

Orthologs for HMGCLL1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for HMGCLL1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia HMGCLL1 31 30
  • 99.59 (n)
(Canis familiaris)
Mammalia HMGCLL1 31 30
  • 94.51 (n)
(Bos Taurus)
Mammalia HMGCLL1 31 30
  • 89.31 (n)
(Mus musculus)
Mammalia Hmgcll1 17 31 30
  • 88.43 (n)
(Rattus norvegicus)
Mammalia Hmgcll1 30
  • 88.14 (n)
(Monodelphis domestica)
Mammalia HMGCLL1 31
  • 75 (a)
(Ornithorhynchus anatinus)
Mammalia HMGCLL1 31
  • 58 (a)
(Gallus gallus)
Aves HMGCLL1 31 30
  • 78.54 (n)
(Anolis carolinensis)
Reptilia HMGCLL1 31
  • 78 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia hmgcll1 30
  • 72.85 (n)
(Danio rerio)
Actinopterygii hmgcll1 31 30
  • 66.47 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG10399 31
  • 56 (a)
(Caenorhabditis elegans)
Secernentea Y71G12B.10 31
  • 50 (a)
(Oryza sativa)
Liliopsida Os12g0134000 30
  • 62.39 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 58 (a)
Species where no ortholog for HMGCLL1 was found in the sources mined by GeneCards:
  • 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)
  • baker's yeast (Saccharomyces cerevisiae)
  • 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)
  • wheat (Triticum aestivum)

Evolution for HMGCLL1 Gene

Gene Tree for HMGCLL1 (if available)
Gene Tree for HMGCLL1 (if available)
Evolutionary constrained regions (ECRs) for HMGCLL1: view image

Paralogs for HMGCLL1 Gene

Paralogs for HMGCLL1 Gene

(2) SIMAP similar genes for HMGCLL1 Gene using alignment to 5 proteins:

  • B7Z212_HUMAN
  • B7Z4D4_HUMAN
  • G5E9S9_HUMAN
genes like me logo Genes that share paralogs with HMGCLL1: view

Variants for HMGCLL1 Gene

Additional dbSNP identifiers (rs#s) for HMGCLL1 Gene

Structural Variations from Database of Genomic Variants (DGV) for HMGCLL1 Gene

Variant ID Type Subtype PubMed ID
dgv3318n106 CNV deletion 24896259
dgv5965n100 CNV gain 25217958
esv1503742 CNV deletion 17803354
esv22238 CNV loss 19812545
esv2659563 CNV deletion 23128226
esv2662832 CNV deletion 23128226
esv2674357 CNV deletion 23128226
esv2732109 CNV deletion 23290073
esv2732110 CNV deletion 23290073
esv2732111 CNV deletion 23290073
esv2732112 CNV deletion 23290073
esv2732113 CNV deletion 23290073
esv3539771 CNV deletion 23714750
esv3571076 CNV loss 25503493
esv3571077 CNV loss 25503493
esv3609067 CNV loss 21293372
esv3609070 CNV loss 21293372
esv4242 CNV loss 18987735
esv5756 CNV loss 19470904
nsv1018622 CNV loss 25217958
nsv1020349 CNV loss 25217958
nsv1025276 CNV loss 25217958
nsv1031992 CNV loss 25217958
nsv1034037 CNV gain 25217958
nsv1073980 CNV deletion 25765185
nsv1074933 CNV deletion 25765185
nsv1117622 CNV deletion 24896259
nsv1137081 CNV deletion 24896259
nsv1161382 CNV duplication 26073780
nsv349134 CNV deletion 16902084
nsv462948 CNV gain 19166990
nsv470819 CNV gain 18288195
nsv5311 CNV deletion 18451855
nsv603163 CNV gain 21841781
nsv955791 CNV deletion 24416366
nsv956550 CNV deletion 24416366

Variation tolerance for HMGCLL1 Gene

Residual Variation Intolerance Score: 44% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.35; 26.78% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HMGCLL1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for HMGCLL1 Gene

Disorders for HMGCLL1 Gene

MalaCards: The human disease database

(2) MalaCards diseases for HMGCLL1 Gene - From: DISEASES

Disorder Aliases PubMed IDs
breast adenoid cystic carcinoma
  • adenoid cystic carcinoma of breast
hepatic infarction
  • infarct of liver
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for HMGCLL1

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with HMGCLL1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for HMGCLL1 Gene

Publications for HMGCLL1 Gene

  1. Characterization of a novel HMG-CoA lyase enzyme with a dual location in endoplasmic reticulum and cytosol. (PMID: 22847177) Arnedo M … Pié J (Journal of lipid research 2012) 3 4 54
  2. Identification and characterization of an extramitochondrial human 3-hydroxy-3-methylglutaryl-CoA lyase. (PMID: 22865860) Montgomery C … Miziorko HM (The Journal of biological chemistry 2012) 3 4 54
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 41 54
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 54
  5. Large-scale concatenation cDNA sequencing. (PMID: 9110174) Yu W … Gibbs RA (Genome research 1997) 2 3 54

Products for HMGCLL1 Gene

Sources for HMGCLL1 Gene