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Aliases for HMGCLL1 Gene

Aliases for HMGCLL1 Gene

  • 3-Hydroxymethyl-3-Methylglutaryl-CoA Lyase-Like 1 2 3 5
  • Endoplasmic Reticulum 3-Hydroxymethyl-3-Methylglutaryl-CoA Lyase 3 4
  • 3-Hydroxymethyl-3-Methylglutaryl-CoA Lyase-Like Protein 1 3 4
  • 3-Hydroxymethyl-3-Methylglutaryl-Coenzyme A Lyase-Like 1 2 3
  • EC 4 63
  • Er-CHL 3 4
  • Probable 3-Hydroxymethyl-3-Methylglutaryl-CoA Lyase 2 3
  • 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. Among its related pathways are Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha) and Valine, leucine and isoleucine degradation. 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 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.

No data available for Entrez Gene Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HMGCLL1 Gene

Genomics for HMGCLL1 Gene

Regulatory Elements for HMGCLL1 Gene

Enhancers for HMGCLL1 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around HMGCLL1 on UCSC Golden Path with GeneCards custom track

Genomic Location for HMGCLL1 Gene

55,434,369 bp from pter
55,679,668 bp from pter
245,300 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-hydroxymethyl-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
    • Sequence=BAC87045.1; Type=Frameshift; Positions=253; 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

Proteomics data for HMGCLL1 Gene at MOPED

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

Protein Domains for HMGCLL1 Gene


Suggested Antigen Peptide Sequences for HMGCLL1 Gene

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

No data available for Gene Families for HMGCLL1 Gene

Function for HMGCLL1 Gene

Molecular function for HMGCLL1 Gene

UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=40 uM for (S)-3-hydroxy-3-methylglutaryl-CoA (at pH 9) {ECO:0000269 PubMed:22847177, ECO:0000269 PubMed:22865860}; KM=75 uM for (S)-3-hydroxy-3-methylglutaryl-CoA (at pH 8) {ECO:0000269 PubMed:22847177, ECO:0000269 PubMed:22865860}; KM=28 uM for (S)-3-hydroxy-3-methylglutaryl-CoA {ECO:0000269 PubMed:22847177, ECO:0000269 PubMed:22865860}; KM=49 uM for (S)-3-hydroxy-3-methylglutaryl-CoA (in presence of magnesium) {ECO:0000269 PubMed:22847177, ECO:0000269 PubMed:22865860}; KM=0.18 uM for (S)-3-hydroxy-3-methylglutaryl-CoA (in presence of manganese) {ECO:0000269 PubMed:22847177, 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, ECO:0000269 PubMed:22865860}; Vmax=25 nmol/min/mg enzyme with (S)-3-hydroxy-3-methylglutaryl- CoA as substrate at pH 8 {ECO:0000269 PubMed:22847177, ECO:0000269 PubMed:22865860};
UniProtKB/Swiss-Prot CatalyticActivity:
(S)-3-hydroxy-3-methylglutaryl-CoA = acetyl-CoA + acetoacetate.
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.

Enzyme Numbers (IUBMB) for HMGCLL1 Gene

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

Animal Model Products

CRISPR Products

No data available for Gene Ontology (GO) - Molecular Function , 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

Jensen Localization Image for HMGCLL1 Gene COMPARTMENTS Subcellular localization image for HMGCLL1 gene
Compartment Confidence
cytosol 5
endoplasmic reticulum 5
mitochondrion 3
nucleus 2
extracellular 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for HMGCLL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005789 endoplasmic reticulum membrane IEA --
GO:0005829 cytosol IDA,TAS --
GO:0016020 membrane IEA,IDA 22865860
GO:0048471 perinuclear region of cytoplasm IDA 22865860
genes like me logo Genes that share ontologies with HMGCLL1: view

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


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-CoA
  • Ac-CoA
  • Ac-Coenzyme A
  • Ac-S-CoA
  • Ac-S-Coenzyme A
  • Acetyl coenzyme-A
genes like me logo Genes that share compounds with HMGCLL1: view

Transcripts for HMGCLL1 Gene

Unigene Clusters for HMGCLL1 Gene

3-hydroxymethyl-3-methylglutaryl-CoA lyase-like 1:
Representative Sequences:

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
ECgene alternative splicing isoforms for

Expression for HMGCLL1 Gene

mRNA expression in normal human tissues 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, PaxDb, and MOPED for HMGCLL1 Gene

SOURCE GeneReport for Unigene cluster for HMGCLL1 Gene Hs.147054

genes like me logo Genes that share expression patterns with HMGCLL1: view

Protein tissue co-expression partners for HMGCLL1 Gene

- Elite partner

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA Expression by UniProt/SwissProt 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
(Bos Taurus)
Mammalia HMGCLL1 35
  • 89.31 (n)
  • 93.24 (a)
  • 95 (a)
(Canis familiaris)
Mammalia HMGCLL1 35
  • 94.51 (n)
  • 96.47 (a)
  • 96 (a)
(Mus musculus)
Mammalia Hmgcll1 35
  • 88.43 (n)
  • 92.65 (a)
Hmgcll1 16
Hmgcll1 36
  • 92 (a)
(Pan troglodytes)
Mammalia HMGCLL1 35
  • 99.59 (n)
  • 99.09 (a)
  • 99 (a)
(Rattus norvegicus)
Mammalia Hmgcll1 35
  • 88.14 (n)
  • 92.06 (a)
(Monodelphis domestica)
Mammalia HMGCLL1 36
  • 75 (a)
(Ornithorhynchus anatinus)
Mammalia HMGCLL1 36
  • 58 (a)
(Gallus gallus)
Aves HMGCLL1 35
  • 78.54 (n)
  • 83.09 (a)
  • 81 (a)
(Anolis carolinensis)
Reptilia HMGCLL1 36
  • 78 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia hmgcll1 35
  • 72.85 (n)
  • 73.65 (a)
(Danio rerio)
Actinopterygii hmgcll1 35
  • 66.47 (n)
  • 70.96 (a)
hmgcll1 36
  • 72 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG10399 36
  • 56 (a)
(Caenorhabditis elegans)
Secernentea Y71G12B.10 36
  • 50 (a)
(Oryza sativa)
Liliopsida Os12g0134000 35
  • 62.39 (n)
  • 64.53 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 58 (a)
Species with no ortholog for HMGCLL1:
  • 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)

Paralogs for HMGCLL1 Gene

Paralogs for HMGCLL1 Gene

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

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

Variants for HMGCLL1 Gene

Sequence variations from dbSNP and Humsavar for HMGCLL1 Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs4998850 -- 55,452,283(+) TGGAC(C/T)TAAAT intron-variant
rs5876450 -- 55,449,939(+) TTAGT(-/TAGT)CAGTT intron-variant
rs5876451 -- 55,452,418(+) CAGAG(-/A)AATTC intron-variant
rs5876452 -- 55,455,366(+) AATAA(-/T)TTTTT intron-variant
rs5876453 -- 55,504,685(+) TAAAA(-/AT)ATTTT intron-variant

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

Variant ID Type Subtype PubMed ID
dgv6849n71 CNV Gain 21882294
nsv470819 CNV Gain 18288195
nsv462948 CNV Gain 19166990
nsv5311 CNV Loss 18451855
esv2732109 CNV Deletion 23290073
esv2732110 CNV Deletion 23290073
esv2732111 CNV Deletion 23290073
esv2659563 CNV Deletion 23128226
esv4242 CNV Deletion 18987735
esv2732112 CNV Deletion 23290073
esv5756 CNV Loss 19470904
esv2662832 CNV Deletion 23128226
nsv349134 CNV Loss 16902084
esv1503742 CNV Deletion 17803354
esv2674357 CNV Deletion 23128226
esv22238 CNV Loss 19812545
esv2732113 CNV Deletion 23290073

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)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Relevant External Links for HMGCLL1 Gene

Disorders for HMGCLL1 Gene

Relevant External Links for HMGCLL1

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for HMGCLL1 Gene.

No data available for MalaCards , 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. … Pie J. (J. Lipid Res. 2012) 3 4 67
  2. Large-scale concatenation cDNA sequencing. (PMID: 9110174) Yu W. … Gibbs R.A. (Genome Res. 1997) 2 3
  3. A "double adaptor" method for improved shotgun library construction. (PMID: 8619474) Andersson B. … Gibbs R.A. (Anal. Biochem. 1996) 2 3
  4. Identification and characterization of an extramitochondrial human 3- Hydroxy-3-methylglutaryl-CoA lyase. (PMID: 22865860) Montgomery C. … Miziorko H.M. (J. Biol. Chem. 2012) 3
  5. Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. (PMID: 23251661) Comuzzie A.G. … Butte N.F. (PLoS ONE 2012) 3

Products for HMGCLL1 Gene

Sources for HMGCLL1 Gene