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HMGCL 3-hydroxy-3-methylglutaryl-CoA lyase [ Homo sapiens (human) ]

Gene ID: 3155, updated on 4-Jan-2025

Summary

Official Symbol
HMGCLprovided by HGNC
Official Full Name
3-hydroxy-3-methylglutaryl-CoA lyaseprovided by HGNC
Primary source
HGNC:HGNC:5005
See related
Ensembl:ENSG00000117305 MIM:613898; AllianceGenome:HGNC:5005
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HL; HMGCL1
Summary
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]
Expression
Ubiquitous expression in liver (RPKM 67.1), kidney (RPKM 50.9) and 24 other tissues See more
Orthologs
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Genomic context

See HMGCL in Genome Data Viewer
Location:
1p36.11
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (23801885..23825429, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (23636860..23660403, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (24128375..24151919, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376860 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 423 Neighboring gene lysophospholipase 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 424 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 425 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 426 Neighboring gene UDP-galactose-4-epimerase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 377 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:24137325-24137530 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:24151920-24152788 Neighboring gene uncharacterized LOC105376861 Neighboring gene alpha-L-fucosidase 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:24191742-24192941 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 427

Genomic regions, transcripts, and products

Expression

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Deficiency of hydroxymethylglutaryl-CoA lyase
MedGen: C0268601 OMIM: 246450 GeneReviews: Not available
Compare labs

Pathways from PubChem

Interactions

General gene information

Potential readthrough

Included gene: GALE

Gene Ontology Provided by GOA

Component Evidence Code Pubs
located_in cytosol  
located_in mitochondrial matrix PubMed 
located_in mitochondrial matrix  
located_in mitochondrion PubMed 
is_active_in mitochondrion  
located_in mitochondrion PubMed 
located_in peroxisomal matrix  
located_in peroxisome PubMed 
part_of protein-containing complex PubMed 

General protein information

Preferred Names
hydroxymethylglutaryl-CoA lyase, mitochondrial
Names
3-hydroxy-3-methylglutarate-CoA lyase
3-hydroxymethyl-3-methylglutaryl-CoA lyase
3-hydroxymethyl-3-methylglutaryl-Coenzyme A lyase
HMG-CoA lyase
hydroxymethylglutaricaciduria
mitochondrial 3-hydroxy-3-methylglutaryl-CoA lyase
NP_000182.2
NP_001159531.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_013061.1 RefSeqGene

    Range
    5031..28575
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000191.3NP_000182.2  hydroxymethylglutaryl-CoA lyase, mitochondrial isoform 1 precursor

    See identical proteins and their annotated locations for NP_000182.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AI202943, AL031295, AL590728
    Consensus CDS
    CCDS243.1
    UniProtKB/Swiss-Prot
    B4DUP4, B7UCC6, D3Y5K7, P35914, Q6IBC0, Q96FP8
    UniProtKB/TrEMBL
    A6NMQ0, B1AK13
    Related
    ENSP00000363614.3, ENST00000374490.8
    Conserved Domains (1) summary
    cd07938
    Location:35308
    DRE_TIM_HMGL; 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain
  2. NM_001166059.2NP_001159531.1  hydroxymethylglutaryl-CoA lyase, mitochondrial isoform 2 precursor

    See identical proteins and their annotated locations for NP_001159531.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant is missing two consecutive in-frame coding exons compared to variant 1, resulting in a shorter isoform (2) lacking an internal protein segment compared to isoform 1.
    Source sequence(s)
    BC010570, CA306929, DA425822, L07033
    Consensus CDS
    CCDS53279.1
    UniProtKB/Swiss-Prot
    P35914
    Related
    ENSP00000389281.2, ENST00000436439.6
    Conserved Domains (2) summary
    PLN02746
    Location:17254
    PLN02746; hydroxymethylglutaryl-CoA lyase
    pfam00682
    Location:32235
    HMGL-like; HMGL-like

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    23801885..23825429 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    23636860..23660403 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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