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    HMGCLL1 3-hydroxy-3-methylglutaryl-CoA lyase like 1 [ Homo sapiens (human) ]

    Gene ID: 54511, updated on 2-Nov-2024

    Summary

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    Official Symbol
    HMGCLL1provided by HGNC
    Official Full Name
    3-hydroxy-3-methylglutaryl-CoA lyase like 1provided by HGNC
    Primary source
    HGNC:HGNC:21359
    See related
    Ensembl:ENSG00000146151 MIM:619050; AllianceGenome:HGNC:21359
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    ERCHL; er-cHL; bA418P12.1
    Summary
    Enables hydroxymethylglutaryl-CoA lyase activity. Involved in ketone body biosynthetic process. Located in several cellular components, including cytosol; endoplasmic reticulum; and perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in brain (RPKM 2.9), adrenal (RPKM 1.2) and 14 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See HMGCLL1 in Genome Data Viewer
    Location:
    6p12.1
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (55434373..55678919, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (55273980..55518567, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (55299171..55443990, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901491 Neighboring gene hypocretin receptor 2 Neighboring gene GDNF family receptor alpha like Neighboring gene Sharpr-MPRA regulatory region 3486 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:55558913-55559433 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_92273 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_92293 Neighboring gene NANOG hESC enhancer GRCh37_chr6:55639263-55639806 Neighboring gene bone morphogenetic protein 5 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:55724930-55725119 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:55774580-55775114 Neighboring gene nucleophosmin 1 pseudogene 36

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. there are nine mature transcripts for the novel gene HMGCLL1
      Title: Characterization of a novel HMG-CoA lyase enzyme with a dual location in endoplasmic reticulum and cytosol.
    2. analysis of HMGCLL1 as an extramitochondrial human 3-hydroxy-3-methylglutaryl-CoA lyase and comparison with MHGCL
      Title: Identification and characterization of an extramitochondrial human 3-hydroxy-3-methylglutaryl-CoA lyase.
    3. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • DKFZp434G1411

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables hydroxymethylglutaryl-CoA lyase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables hydroxymethylglutaryl-CoA lyase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables hydroxymethylglutaryl-CoA lyase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables metal ion binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables metal ion binding TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in L-leucine catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in ketone body biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in ketone body biosynthetic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    is_active_in endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endoplasmic reticulum membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in perinuclear region of cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    3-hydroxymethyl-3-methylglutaryl-CoA lyase, cytoplasmic
    Names
    3-hydroxy-3-methylglutaryl-CoA lyase, cytoplasmic
    3-hydroxy-3-methylglutaryl-CoA lyase-like protein 1
    3-hydroxymethyl-3-methylglutaryl-CoA lyase L1
    3-hydroxymethyl-3-methylglutaryl-CoA lyase like 1
    3-hydroxymethyl-3-methylglutaryl-CoA lyase-like protein 1
    3-hydroxymethyl-3-methylglutaryl-Coenzyme A lyase-like 1
    HMGCL-like 1
    endoplasmic reticulum 3-hydroxy-3-methylglutaryl-CoA lyase
    endoplasmic reticulum 3-hydroxymethyl-3-methylglutaryl-CoA lyase
    endoplasmic reticulum and cytosol HMG-CoA lyase
    probable 3-hydroxymethyl-3-methylglutaryl-CoA lyase 2
    NP_001035865.1
    NP_001274670.1
    NP_001274675.1
    NP_001274682.1
    NP_061909.2
    XP_047274858.1
    XP_047274859.1
    XP_047274860.1
    XP_054211653.1
    XP_054211654.1
    XP_054211655.1
    XP_054211656.1

    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.

    mRNA and Protein(s)

    1. NM_001042406.2 → NP_001035865.1  3-hydroxymethyl-3-methylglutaryl-CoA lyase, cytoplasmic isoform b

      See identical proteins and their annotated locations for NP_001035865.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. It encodes isoform b, which is shorter than isoform a.
      Source sequence(s)
      AF131827, AL137605, AL590406, BC024194, DA508472
      Consensus CDS
      CCDS43474.1
      UniProtKB/Swiss-Prot
      Q8TB92
      UniProtKB/TrEMBL
      O95896, Q9NT06
      Related
      ENSP00000274901.4, ENST00000274901.9
      Conserved Domains (1) summary
      PLN02746
      Location:41 → 336
      PLN02746; hydroxymethylglutaryl-CoA lyase

    2. NM_001287741.2 → NP_001274670.1  3-hydroxymethyl-3-methylglutaryl-CoA lyase, cytoplasmic isoform c

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks two alternate exons in the 5' coding region, compared to variant 1. It encodes isoform c, which is shorter than isoform a.
      Source sequence(s)
      AF131827, AK293856, AL590406, DA508472, DB179645
      Consensus CDS
      CCDS75473.1
      UniProtKB/Swiss-Prot
      Q8TB92
      UniProtKB/TrEMBL
      O95896
      Related
      ENSP00000309737.4, ENST00000308161.8
      Conserved Domains (1) summary
      PLN02746
      Location:41 → 304
      PLN02746; hydroxymethylglutaryl-CoA lyase

    3. NM_001287746.2 → NP_001274675.1  3-hydroxymethyl-3-methylglutaryl-CoA lyase, cytoplasmic isoform d

      See identical proteins and their annotated locations for NP_001274675.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream start codon, compared to variant 1. It encodes isoform d, which is shorter at the N-terminus, compared to isoform a.
      Source sequence(s)
      AF131827, AK055075, AL590406, DA508472, DB179645
      UniProtKB/Swiss-Prot
      Q8TB92
      UniProtKB/TrEMBL
      O95896
      Conserved Domains (1) summary
      PLN02746
      Location:1 → 237
      PLN02746; hydroxymethylglutaryl-CoA lyase

    4. NM_001287753.2 → NP_001274682.1  3-hydroxymethyl-3-methylglutaryl-CoA lyase, cytoplasmic isoform e

      See identical proteins and their annotated locations for NP_001274682.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) lacks several exons in the coding region, compared to variant 1. It encodes isoform e, which is shorter than isoform a.
      Source sequence(s)
      AF131827, AK294210, AL590406, DB179645
      Consensus CDS
      CCDS75472.1
      UniProtKB/TrEMBL
      B7Z212
      Related
      ENSP00000359887.2, ENST00000370850.6
      Conserved Domains (1) summary
      PLN02746
      Location:41 → 233
      PLN02746; hydroxymethylglutaryl-CoA lyase

    5. NM_019036.3 → NP_061909.2  3-hydroxymethyl-3-methylglutaryl-CoA lyase, cytoplasmic isoform a

      See identical proteins and their annotated locations for NP_061909.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (a).
      Source sequence(s)
      AF131827, AK055075, AK127587, AL590406, DB179645
      Consensus CDS
      CCDS43475.1
      UniProtKB/Swiss-Prot
      B1AQ42, B3KNV0, B7Z1S7, F8W793, Q6ZSA9, Q8TB92
      Related
      ENSP00000381654.2, ENST00000398661.6
      Conserved Domains (1) summary
      PLN02746
      Location:56 → 366
      PLN02746; hydroxymethylglutaryl-CoA lyase

    RNA

    1. NR_109867.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) lacks several exons and its 3' terminal exon extends past a splice site that is used in variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
      Source sequence(s)
      AL137605, AL590406, DA508472, DB179645
      Related
      ENST00000428842.1

    2. NR_109869.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (7) lacks several exons in the coding region, compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
      Source sequence(s)
      AF131827, AK297191, AL590406, DA508472, DB179645

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      55434373..55678919 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047418902.1 → XP_047274858.1  3-hydroxymethyl-3-methylglutaryl-CoA lyase, cytoplasmic isoform X1

    2. XM_047418904.1 → XP_047274860.1  3-hydroxymethyl-3-methylglutaryl-CoA lyase, cytoplasmic isoform X2

    3. XM_047418903.1 → XP_047274859.1  3-hydroxymethyl-3-methylglutaryl-CoA lyase, cytoplasmic isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      55273980..55518567 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054355678.1 → XP_054211653.1  3-hydroxymethyl-3-methylglutaryl-CoA lyase, cytoplasmic isoform X1

    2. XM_054355681.1 → XP_054211656.1  3-hydroxymethyl-3-methylglutaryl-CoA lyase, cytoplasmic isoform X2

    3. XM_054355680.1 → XP_054211655.1  3-hydroxymethyl-3-methylglutaryl-CoA lyase, cytoplasmic isoform X2

    4. XM_054355679.1 → XP_054211654.1  3-hydroxymethyl-3-methylglutaryl-CoA lyase, cytoplasmic isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8TB92.3 GenPept UniProtKB/Swiss-Prot:Q8TB92

    Gene LinkOut

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