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

Gene ID: 54511, updated on 21-Oct-2020

Summary

Official Symbol
HMGCLL1provided by HGNC
Official Full Name
3-hydroxymethyl-3-methylglutaryl-CoA lyase like 1provided by HGNC
Primary source
HGNC:HGNC:21359
See related
Ensembl:ENSG00000146151 MIM:619050
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
Expression
Broad expression in brain (RPKM 2.9), adrenal (RPKM 1.2) and 14 other tissues See more
Orthologs

Genomic context

See HMGCLL1 in Genome Data Viewer
Location:
6p12.1
Exon count:
14
Annotation release Status Assembly Chr Location
109.20200815 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (55434373..55607573, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (55299171..55444012, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene hypocretin receptor 2 Neighboring gene GDNF family receptor alpha like Neighboring gene bone morphogenetic protein 5 Neighboring gene nucleophosmin 1 pseudogene 36

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
GeneReviews: Not available

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • DKFZp434G1411

Gene Ontology Provided by GOA

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

General protein information

Preferred Names
3-hydroxymethyl-3-methylglutaryl-CoA lyase, cytoplasmic
Names
3-hydroxy-3-methylglutaryl-CoA lyase-like protein 1
3-hydroxymethyl-3-methylglutaryl-CoA lyase-like protein 1
3-hydroxymethyl-3-methylglutaryl-Coenzyme A lyase-like 1
endoplasmic reticulum 3-hydroxy-3-methylglutaryl-CoA lyase
endoplasmic reticulum 3-hydroxymethyl-3-methylglutaryl-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_011513002.1
XP_024302237.1
XP_024302238.1
XP_024302239.1

NCBI Reference Sequences (RefSeq)

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_001042406.2NP_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, ENST00000274901.8
    Conserved Domains (1) summary
    PLN02746
    Location:41336
    PLN02746; hydroxymethylglutaryl-CoA lyase
  2. NM_001287741.2NP_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:41304
    PLN02746; hydroxymethylglutaryl-CoA lyase
  3. NM_001287746.2NP_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:1237
    PLN02746; hydroxymethylglutaryl-CoA lyase
  4. NM_001287753.2NP_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, O95896
    Related
    ENSP00000359887.2, ENST00000370850.6
    Conserved Domains (1) summary
    PLN02746
    Location:41233
    PLN02746; hydroxymethylglutaryl-CoA lyase
  5. NM_019036.3NP_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
    Q8TB92
    UniProtKB/TrEMBL
    O95896
    Related
    ENSP00000381654.2, ENST00000398661.6
    Conserved Domains (1) summary
    PLN02746
    Location:56366
    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: Homo sapiens Updated Annotation Release 109.20200815

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p13 Primary Assembly

    Range
    55434373..55607573 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024446471.1XP_024302239.1  3-hydroxymethyl-3-methylglutaryl-CoA lyase, cytoplasmic isoform X3

    Conserved Domains (1) summary
    PLN02746
    Location:3175
    PLN02746; hydroxymethylglutaryl-CoA lyase
  2. XM_024446469.1XP_024302237.1  3-hydroxymethyl-3-methylglutaryl-CoA lyase, cytoplasmic isoform X2

    Conserved Domains (1) summary
    PLN02746
    Location:1237
    PLN02746; hydroxymethylglutaryl-CoA lyase
  3. XM_024446470.1XP_024302238.1  3-hydroxymethyl-3-methylglutaryl-CoA lyase, cytoplasmic isoform X3

    Conserved Domains (1) summary
    PLN02746
    Location:3175
    PLN02746; hydroxymethylglutaryl-CoA lyase
  4. XM_011514700.3XP_011513002.1  3-hydroxymethyl-3-methylglutaryl-CoA lyase, cytoplasmic isoform X1

    See identical proteins and their annotated locations for XP_011513002.1

    Conserved Domains (1) summary
    cd07938
    Location:50265
    DRE_TIM_HMGL; 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain
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