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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 4.1.3.4 4 61
  • Er-CHL 3 4
  • 3-Hydroxymethyl-3-Methylglutaryl-CoA Lyase, Cytoplasmic 3
  • 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 Metabolism and Peroxisome. 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 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
GH06F055578 0.2 ENCODE 13.9 +100.5 100518 0.7 RAD21 ZNF2 ZEB1 GLIS2 SCRT2 RCOR1 KLF7 ZNF202 ZNF263 SP3 HMGCLL1 GC06P055585 GC06M055481
GH06F055553 0.4 FANTOM5 11.4 +125.8 125806 0.1 HMGCLL1 GC06P055585 GC06M055481
GH06F055704 0.7 ENCODE 10.9 -25.0 -24979 1.2 JUND JUN FOS PRDM1 FOXA1 NR2F2 HMGCLL1 PIR48007 GC06P055722
GH06F055705 0.2 ENCODE 10.9 -25.9 -25850 0.2 HMGCLL1 PIR48007 GC06P055722
GH06F055635 1 ENCODE 10.9 +43.0 43021 3.2 JUN CEBPB ZHX2 DPF2 CEBPG ZNF217 MBD2 GATA3 CTBP1 JUND HMGCLL1 ENSG00000224984 GC06P055627 GC06P055628 GC06P055629 GC06P055630 GC06P055631 GC06P055632 GC06P055633 GC06P055634
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around HMGCLL1 on UCSC Golden Path with GeneCards custom track

Genomic Location for HMGCLL1 Gene

Chromosome:
6
Start:
55,434,369 bp from pter
End:
55,679,668 bp from pter
Size:
245,300 bases
Orientation:
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:
    Q8TB92-HMGC2_HUMAN
    Recommended name:
    3-hydroxymethyl-3-methylglutaryl-CoA lyase, cytoplasmic
    Protein Accession:
    Q8TB92
    Secondary Accessions:
    • B1AQ42
    • B3KNV0
    • B7Z1S7
    • F8W793
    • Q6ZSA9

    Protein attributes for HMGCLL1 Gene

    Size:
    370 amino acids
    Molecular mass:
    39514 Da
    Cofactor:
    Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • 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

    UniProtKB/Swiss-Prot:

neXtProt entry for HMGCLL1 Gene

Selected DME Specific Peptides for HMGCLL1 Gene

Q8TB92:
  • EVGPRDGLQNE
  • NCSIEES
  • ALAVHCHDTYGQAL
  • GASGNVATEDL
  • YPVLTPN
  • MGCYEISLGDTIGVGTPG

Post-translational modifications for HMGCLL1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Domains & Families for HMGCLL1 Gene

Protein Domains for HMGCLL1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for HMGCLL1 Gene

Graphical View of Domain Structure for InterPro Entry

Q8TB92

UniProtKB/Swiss-Prot:

HMGC2_HUMAN :
  • Contains 1 pyruvate carboxyltransferase domain.
  • Belongs to the HMG-CoA lyase family.
Domain:
  • Contains 1 pyruvate carboxyltransferase domain.
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

Gene Ontology (GO) - Molecular Function for HMGCLL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004419 hydroxymethylglutaryl-CoA lyase activity IEA,TAS --
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

Inhibitory RNA Products

Flow Cytometry 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

COMPARTMENTS
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:0005737 cytoplasm IEA --
GO:0005783 endoplasmic reticulum IEA,IDA 22847177
GO:0005789 endoplasmic reticulum membrane IEA --
GO:0005829 cytosol TAS --
GO:0016020 membrane IEA,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

GO ID Qualified GO term Evidence PubMed IDs
GO:0046951 ketone body biosynthetic process IEA,TAS --
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
3-hydroxy-3-methylglutaryl-coa
  • (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
1553-55-5
acetyl-coa
  • Ac-CoA
  • Ac-Coenzyme A
  • Ac-S-CoA
  • Ac-S-Coenzyme A
  • Acetyl coenzyme-A
72-89-9
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:

Inhibitory RNA Products

Flow Cytometry 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: - - - - - -
SP7:

Relevant External Links for HMGCLL1 Gene

GeneLoc Exon Structure for
HMGCLL1
ECgene alternative splicing isoforms for
HMGCLL1

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, PaxDb, and MOPED for HMGCLL1 Gene



Protein tissue co-expression partners for HMGCLL1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of HMGCLL1 Gene:

HMGCLL1

SOURCE GeneReport for Unigene cluster for HMGCLL1 Gene:

Hs.147054
genes like me logo Genes that share expression patterns with HMGCLL1: view

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
chimpanzee
(Pan troglodytes)
Mammalia HMGCLL1 34 35
  • 99.59 (n)
dog
(Canis familiaris)
Mammalia HMGCLL1 34 35
  • 94.51 (n)
cow
(Bos Taurus)
Mammalia HMGCLL1 34 35
  • 89.31 (n)
mouse
(Mus musculus)
Mammalia Hmgcll1 34 16 35
  • 88.43 (n)
rat
(Rattus norvegicus)
Mammalia Hmgcll1 34
  • 88.14 (n)
oppossum
(Monodelphis domestica)
Mammalia HMGCLL1 35
  • 75 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia HMGCLL1 35
  • 58 (a)
OneToOne
chicken
(Gallus gallus)
Aves HMGCLL1 34 35
  • 78.54 (n)
lizard
(Anolis carolinensis)
Reptilia HMGCLL1 35
  • 78 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia hmgcll1 34
  • 72.85 (n)
zebrafish
(Danio rerio)
Actinopterygii hmgcll1 34 35
  • 66.47 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG10399 35
  • 56 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea Y71G12B.10 35
  • 50 (a)
OneToMany
rice
(Oryza sativa)
Liliopsida Os12g0134000 34
  • 62.39 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 58 (a)
OneToMany
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

ENSEMBL:
Gene Tree for HMGCLL1 (if available)
TreeFam:
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
rs10223668 -- 55,511,788(+) ATAAG(A/G)TATTT intron-variant
rs10456184 -- 55,463,275(+) AAACC(A/G)CCTAC intron-variant
rs10456185 -- 55,465,517(+) GTGAT(G/T)GGTAC intron-variant
rs10456714 -- 55,488,356(+) ATACA(C/T)ACAAC intron-variant
rs10456715 -- 55,491,895(+) CAACA(A/G)TCTCT intron-variant

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)

Relevant External Links for HMGCLL1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
HMGCLL1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HMGCLL1 Gene

Disorders for HMGCLL1 Gene

Relevant External Links for HMGCLL1

Genetic Association Database (GAD)
HMGCLL1
Human Genome Epidemiology (HuGE) Navigator
HMGCLL1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
HMGCLL1

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 64
  2. 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 4 64
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 46 64
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  5. Large-scale concatenation cDNA sequencing. (PMID: 9110174) Yu W. … Gibbs R.A. (Genome Res. 1997) 2 3 64

Products for HMGCLL1 Gene

Sources for HMGCLL1 Gene

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