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    CRAT carnitine O-acetyltransferase [ Homo sapiens (human) ]

    Gene ID: 1384, updated on 2-Nov-2024

    Summary

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    Official Symbol
    CRATprovided by HGNC
    Official Full Name
    carnitine O-acetyltransferaseprovided by HGNC
    Primary source
    HGNC:HGNC:2342
    See related
    Ensembl:ENSG00000095321 MIM:600184; AllianceGenome:HGNC:2342
    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
    CAT; CAT1; NBIA8
    Summary
    This gene encodes carnitine O-acetyltransferase, a member of the carnitine acyltransferase family and a key metabolic pathway enzyme which plays an important role in energy homeostasis and fat metabolism. This enzyme catalyzes the reversible transfer of acyl groups from an acyl-CoA thioester to carnitine and regulates the ratio of acyl-CoA/CoA. It is found in both the mitochondria and the peroxisome. Alternative splicing results in transcript variants encoding different isoforms that may localize to different subcellular compartments. [provided by RefSeq, Oct 2016]
    Expression
    Broad expression in testis (RPKM 76.6), duodenum (RPKM 25.0) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CRAT in Genome Data Viewer
    Location:
    9q34.11
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (129094794..129110793, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (141298255..141314668, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (131857073..131873072, complement)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene mitoguardin 2 Neighboring gene uncharacterized LOC124902334 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29102 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131833123-131834072 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131834073-131835022 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20359 Neighboring gene dolichyldiphosphatase 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:131864095-131864840 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20360 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:131873890-131874430 Neighboring gene protein phosphatase 2 phosphatase activator Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131889125-131890047 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131893809-131894363 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:131895457-131895957 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131900767-131901394 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29104 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131902025-131902652 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131902653-131903282 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29107 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131905799-131906426 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131907685-131908314 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29108 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:131910837-131911337 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131929576-131930565 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20363 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131937384-131938105 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20365 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20366 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20367 Neighboring gene Sharpr-MPRA regulatory region 13939 Neighboring gene immediate early response 5 like

    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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    Related articles in PubMed

    1. Carnitine, mitochondrial function and therapy. Zammit VA, et al. Adv Drug Deliv Rev, 2009 Nov 30. PMID 19716391
    2. A snapshot of carnitine acetyltransferase. Ramsay RR, et al. Trends Biochem Sci, 2003 Jul. PMID 12877997
    3. Structure of human carnitine acetyltransferase. Molecular basis for fatty acyl transfer. Wu D, et al. J Biol Chem, 2003 Apr 11. PMID 12562770
    4. CRAT missense variants cause abnormal carnitine acetyltransferase function in an early-onset case of Leigh syndrome. Laera L, et al. Hum Mutat, 2020 Jan. PMID 31448845
    5. Crystallization and preliminary X-ray crystallographic studies on recombinant human carnitine acetyltransferase. Lian W, et al. Acta Crystallogr D Biol Crystallogr, 2002 Jul. PMID 12077440

    See all (49) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Carnitine acetyltransferase deficiency mediates mitochondrial dysfunction-induced cellular senescence in dermal fibroblasts.
      Title: Carnitine acetyltransferase deficiency mediates mitochondrial dysfunction-induced cellular senescence in dermal fibroblasts.
    2. Skeletal muscle mitochondrial inertia is associated with carnitine acetyltransferase activity and physical function in humans.
      Title: Skeletal muscle mitochondrial inertia is associated with carnitine acetyltransferase activity and physical function in humans.
    3. CRAT missense variants cause abnormal carnitine acetyltransferase function in an early-onset case of Leigh syndrome.
      Title: CRAT missense variants cause abnormal carnitine acetyltransferase function in an early-onset case of Leigh syndrome.
    4. We provide evidence that the downregulation of hsa-miR-124-3p, hsa-miR-129-5p and hsa-miR-378 induced an increase in both expression and activity of CPT1A, CACT and CrAT in malignant prostate cells.
      Title: Deregulation of MicroRNAs mediated control of carnitine cycle in prostate cancer: molecular basis and pathophysiological consequences.
    5. CrAT turned out to be active towards some but not all the BCAAO intermediates tested and no activity was found with dicarboxylic acyl-CoA esters.
      Title: Substrate specificity of human carnitine acetyltransferase: Implications for fatty acid and branched-chain amino acid metabolism.
    6. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    7. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
    8. Data show that CrAT overexpression in primary human skeletal myocytes increased glucose uptake and attenuated lipid-induced suppression of glucose oxidation.
      Title: Carnitine insufficiency caused by aging and overnutrition compromises mitochondrial performance and metabolic control.
    9. structure of a binary complex of human peroxisomal carnitine acetyltransferase and the substrate l-carnitine, refined to a resolution of 1.8; site-directed mutagenesis and kinetic characterization
      Title: Structural and mutational characterization of L-carnitine binding to human carnitine acetyltransferase.
    10. The structure and reactions of this enzyme are examined.
      Title: Structure of human carnitine acetyltransferase. Molecular basis for fatty acyl transfer.
    Submit: New GeneRIF Correction See all GeneRIFs (12)

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Neurodegeneration with brain iron accumulation 8
    MedGen: C4693587 OMIM: 617917 GeneReviews: Not available
    		not available

    EBI GWAS Catalog

    Description
    An atlas of genetic influences on human blood metabolites.
    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables acyl-CoA oxidase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables carnitine O-acetyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables carnitine O-acetyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables carnitine O-acetyltransferase activity TAS
    Traceable Author Statement
    more info
    		  
    enables carnitine O-octanoyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in carnitine metabolic process, CoA-linked IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in carnitine metabolic process, CoA-linked IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in fatty acid beta-oxidation using acyl-CoA oxidase IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in fatty acid beta-oxidation using acyl-CoA oxidase TAS
    Traceable Author Statement
    more info
    		  
    involved_in medium-chain fatty acid metabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in short-chain fatty acid metabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in endoplasmic reticulum IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in mitochondrial inner membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in mitochondrion HDA PubMed 
    located_in mitochondrion HTP PubMed 
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in peroxisomal matrix TAS
    Traceable Author Statement
    more info
    		  
    is_active_in peroxisome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in peroxisome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    carnitine O-acetyltransferase
    Names
    carnitine acetylase
    NP_000746.3
    NP_001244292.2
    NP_001333475.2
    NP_001333476.2
    NP_001333477.2
    NP_001333478.2
    NP_003994.3
    XP_005251765.1
    XP_016869764.1
    XP_047278726.1
    XP_047278727.1
    XP_047278728.1
    XP_054217957.1
    XP_054217958.1
    XP_054217959.1
    XP_054217960.1
    XP_054217961.1

    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_000755.5 → NP_000746.3  carnitine O-acetyltransferase isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes isoform 1.
      Source sequence(s)
      AL158151
      Consensus CDS
      CCDS6919.1
      UniProtKB/Swiss-Prot
      P43155, Q5T952, Q9BW16
      UniProtKB/TrEMBL
      A0A7P0TBF3
      Related
      ENSP00000315013.2, ENST00000318080.7
      Conserved Domains (1) summary
      pfam00755
      Location:35 → 611
      Carn_acyltransf; Choline/Carnitine o-acyltransferase

    2. NM_001257363.3 → NP_001244292.2  carnitine O-acetyltransferase isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) contains an alternate exon in the 5' region and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (2) is shorter at the N-terminus, compared to isoform 1. Variants 2 and 6 encode the same protein.
      Source sequence(s)
      AL158151
      UniProtKB/TrEMBL
      A0A7P0TBF3
      Conserved Domains (1) summary
      pfam00755
      Location:14 → 594
      Carn_acyltransf; Choline/Carnitine o-acyltransferase

    3. NM_001346546.2 → NP_001333475.2  carnitine O-acetyltransferase isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) contains an alternate exon in the 5' region and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (3) is longer and has a distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      AL158151
      UniProtKB/TrEMBL
      A0A7P0TBF3
      Conserved Domains (1) summary
      pfam00755
      Location:36 → 616
      Carn_acyltransf; Choline/Carnitine o-acyltransferase

    4. NM_001346547.2 → NP_001333476.2  carnitine O-acetyltransferase isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (4) is shorter than isoform 1.
      Source sequence(s)
      AL158151
      Consensus CDS
      CCDS94505.1
      UniProtKB/TrEMBL
      A0A7P0TAR1, A0A7P0TBF3
      Related
      ENSP00000506267.1, ENST00000681627.1
      Conserved Domains (1) summary
      pfam00755
      Location:35 → 591
      Carn_acyltransf; Choline/Carnitine o-acyltransferase

    5. NM_001346548.2 → NP_001333477.2  carnitine O-acetyltransferase isoform 5

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) contains an alternate exon in the 5' region, initiates translation at a downstream start codon, and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (5) is shorter than isoform 1.
      Source sequence(s)
      AL158151
      UniProtKB/TrEMBL
      A0A7P0TBF3
      Conserved Domains (1) summary
      pfam00755
      Location:14 → 570
      Carn_acyltransf; Choline/Carnitine o-acyltransferase

    6. NM_001346549.2 → NP_001333478.2  carnitine O-acetyltransferase isoform 6

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. The encoded isoform (6) is shorter than isoform 1.
      Source sequence(s)
      AL158151
      Consensus CDS
      CCDS94506.1
      UniProtKB/TrEMBL
      A0A7P0TBF3, H0Y4Z7
      Related
      ENSP00000395458.2, ENST00000455396.2
      Conserved Domains (1) summary
      pfam00755
      Location:35 → 575
      Carn_acyltransf; Choline/Carnitine o-acyltransferase

    7. NM_004003.4 → NP_003994.3  carnitine O-acetyltransferase isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) contains an alternate exon in the 5' region and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (2) is shorter at the N-terminus, compared to isoform 1. Variants 2 and 6 encode the same protein.
      Source sequence(s)
      AL158151
      UniProtKB/TrEMBL
      A0A7P0TBF3
      Conserved Domains (1) summary
      pfam00755
      Location:14 → 594
      Carn_acyltransf; Choline/Carnitine o-acyltransferase

    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_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      129094794..129110793 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005251708.5 → XP_005251765.1  carnitine O-acetyltransferase isoform X3

      UniProtKB/TrEMBL
      A0A7P0TBF3
      Conserved Domains (1) summary
      pfam00755
      Location:14 → 594
      Carn_acyltransf; Choline/Carnitine o-acyltransferase

    2. XM_047422771.1 → XP_047278727.1  carnitine O-acetyltransferase isoform X3

    3. XM_047422770.1 → XP_047278726.1  carnitine O-acetyltransferase isoform X2

    4. XM_017014275.2 → XP_016869764.1  carnitine O-acetyltransferase isoform X1

      UniProtKB/TrEMBL
      A0A7P0TBF3
      Conserved Domains (1) summary
      pfam00755
      Location:36 → 616
      Carn_acyltransf; Choline/Carnitine o-acyltransferase

    5. XM_047422772.1 → XP_047278728.1  carnitine O-acetyltransferase isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      141298255..141314668 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054361983.1 → XP_054217958.1  carnitine O-acetyltransferase isoform X4

    2. XM_054361985.1 → XP_054217960.1  carnitine O-acetyltransferase isoform X3

    3. XM_054361986.1 → XP_054217961.1  carnitine O-acetyltransferase isoform X3

    4. XM_054361984.1 → XP_054217959.1  carnitine O-acetyltransferase isoform X2

    5. XM_054361982.1 → XP_054217957.1  carnitine O-acetyltransferase isoform X1

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_144782.1: Suppressed sequence

      Description
      NM_144782.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P43155.5 GenPept UniProtKB/Swiss-Prot:P43155

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