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

Gene ID: 54511, updated on 11-Apr-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, Apr 2022]
Expression
Broad expression in brain (RPKM 2.9), adrenal (RPKM 1.2) and 14 other tissues See more
Orthologs
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Genomic context

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Location:
6p12.1
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (55434373..55678919, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (55273980..55518567, complement)
105.20220307 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
  • 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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Related articles in PubMed

  1. Characterization of a novel HMG-CoA lyase enzyme with a dual location in endoplasmic reticulum and cytosol. Arnedo M, et al. J Lipid Res, 2012 Oct. PMID 22847177, Free PMC Article
  2. 3-Hydroxy-3-methylglutaryl coenzyme A lyase (HL). Cloning of human and chicken liver HL cDNAs and characterization of a mutation causing human HL deficiency. Mitchell GA, et al. J Biol Chem, 1993 Feb 25. PMID 8440722
  3. Identification and characterization of an extramitochondrial human 3-hydroxy-3-methylglutaryl-CoA lyase. Montgomery C, et al. J Biol Chem, 2012 Sep 28. PMID 22865860, Free PMC Article
  4. Large-scale concatenation cDNA sequencing. Yu W, et al. Genome Res, 1997 Apr. PMID 9110174, Free PMC Article
  5. A "double adaptor" method for improved shotgun library construction. Andersson B, et al. Anal Biochem, 1996 Apr 5. PMID 8619474

See all (15) citations in PubMed

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)

Genotypes

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_2023_10

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

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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