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

Gene ID: 1384, updated on 3-Apr-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
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Genomic context

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Location:
9q34.11
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (129094794..129110793, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (141298255..141314668, complement)
105.20220307 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
  • 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. Skeletal muscle mitochondrial inertia is associated with carnitine acetyltransferase activity and physical function in humans. Mancilla RF, et al. JCI Insight, 2023 Jan 10. PMID 36413408, Free PMC Article
  2. 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
  3. Carnitine, mitochondrial function and therapy. Zammit VA, et al. Adv Drug Deliv Rev, 2009 Nov 30. PMID 19716391
  4. Carnitine insufficiency caused by aging and overnutrition compromises mitochondrial performance and metabolic control. Noland RC, et al. J Biol Chem, 2009 Aug 21. PMID 19553674, Free PMC Article
  5. Structure and function of carnitine acyltransferases. Jogl G, et al. Ann N Y Acad Sci, 2004 Nov. PMID 15591000

See all (46) 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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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

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
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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)

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

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 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_2023_10

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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