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HMGCS2 3-hydroxy-3-methylglutaryl-CoA synthase 2 [ Homo sapiens (human) ]

Gene ID: 3158, updated on 5-Aug-2018

Summary

Official Symbol
HMGCS2provided by HGNC
Official Full Name
3-hydroxy-3-methylglutaryl-CoA synthase 2provided by HGNC
Primary source
HGNC:HGNC:5008
See related
Ensembl:ENSG00000134240 MIM:600234; Vega:OTTHUMG00000012101
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
Summary
The protein encoded by this gene belongs to the HMG-CoA synthase family. It is a mitochondrial enzyme that catalyzes the first reaction of ketogenesis, a metabolic pathway that provides lipid-derived energy for various organs during times of carbohydrate deprivation, such as fasting. Mutations in this gene are associated with HMG-CoA synthase deficiency. Alternatively spliced transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Oct 2009]
Expression
Biased expression in liver (RPKM 471.6), colon (RPKM 127.8) and 5 other tissues See more
Orthologs

Genomic context

See HMGCS2 in Genome Data Viewer
Location:
1p12
Exon count:
10
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 1 NC_000001.11 (119747996..119768932, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (120290619..120311555, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378937 Neighboring gene uncharacterized LOC105378936 Neighboring gene phosphoglycerate dehydrogenase Neighboring gene regenerating family member 4 Neighboring gene uncharacterized LOC105378938 Neighboring gene NBPF member 7

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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
hydroxymethylglutaryl-CoA synthase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
hydroxymethylglutaryl-CoA synthase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
hydroxymethylglutaryl-CoA synthase activity TAS
Traceable Author Statement
more info
 
Process Evidence Code Pubs
acetyl-CoA metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cholesterol biosynthetic process IEA
Inferred from Electronic Annotation
more info
 
farnesyl diphosphate biosynthetic process, mevalonate pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
isoprenoid biosynthetic process IEA
Inferred from Electronic Annotation
more info
 
ketone body biosynthetic process TAS
Traceable Author Statement
more info
 
regulation of lipid metabolic process TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
mitochondrial matrix TAS
Traceable Author Statement
more info
 
mitochondrion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mitochondrion IDA
Inferred from Direct Assay
more info
 

General protein information

Preferred Names
hydroxymethylglutaryl-CoA synthase, mitochondrial
Names
3-hydroxy-3-methylglutaryl-CoA synthase 2 (mitochondrial)
3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2 (mitochondrial)
HMG-CoA synthase
testicular tissue protein Li 88
NP_001159579.1
NP_005509.1
XP_011539615.1

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.

Genomic

  1. NG_013348.1 RefSeqGene

    Range
    5001..25937
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_447

mRNA and Protein(s)

  1. NM_001166107.1NP_001159579.1  hydroxymethylglutaryl-CoA synthase, mitochondrial isoform 2 precursor

    See identical proteins and their annotated locations for NP_001159579.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) is missing an in-frame coding exon compared to variant 1. This results in a shorter isoform (2) lacking an internal protein segment compared to isoform 1.
    Source sequence(s)
    AI215948, AK303777, BC044217, BP420631, BX104280
    Consensus CDS
    CCDS53353.1
    UniProtKB/Swiss-Prot
    P54868
    Related
    ENSP00000439495.2, OTTHUMP00000243996, ENST00000544913.2, OTTHUMT00000409524
    Conserved Domains (3) summary
    TIGR01833
    Location:50464
    HMG-CoA-S_euk; 3-hydroxy-3-methylglutaryl-CoA-synthase, eukaryotic clade
    pfam08540
    Location:187464
    HMG_CoA_synt_C; Hydroxymethylglutaryl-coenzyme A synthase C terminal
    cl09938
    Location:53187
    cond_enzymes; Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the ...
  2. NM_005518.3NP_005509.1  hydroxymethylglutaryl-CoA synthase, mitochondrial isoform 1 precursor

    See identical proteins and their annotated locations for NP_005509.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AI215948, BC044217, BP420631, BX104280
    Consensus CDS
    CCDS905.1
    UniProtKB/Swiss-Prot
    P54868
    UniProtKB/TrEMBL
    A0A140VJL2
    Related
    ENSP00000358414.3, OTTHUMP00000013928, ENST00000369406.7, OTTHUMT00000033469
    Conserved Domains (1) summary
    TIGR01833
    Location:50506
    HMG-CoA-S_euk; 3-hydroxy-3-methylglutaryl-CoA-synthase, eukaryotic clade

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p12 Primary Assembly

    Range
    119747996..119768932 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011541313.2XP_011539615.1  hydroxymethylglutaryl-CoA synthase, mitochondrial isoform X1

    UniProtKB/Swiss-Prot
    P54868
    Conserved Domains (3) summary
    TIGR01833
    Location:50451
    HMG-CoA-S_euk; 3-hydroxy-3-methylglutaryl-CoA-synthase, eukaryotic clade
    pfam01154
    Location:53223
    HMG_CoA_synt_N; Hydroxymethylglutaryl-coenzyme A synthase N terminal
    pfam08540
    Location:231451
    HMG_CoA_synt_C; Hydroxymethylglutaryl-coenzyme A synthase C terminal
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