CPT1A (carnitine palmitoyltransferase 1A)

Gene

• Entrez ID: 1374
• Gene name: Carnitine palmitoyltransferase 1A
• Gene symbol: CPT1A
• Synonyms: CPT1, CPT1-L, L-CPT1
• Chromosome: 11
• Chromosome location: 11q13.3
• Summary: The mitochondrial oxidation of long-chain fatty acids is initiated by the sequential action of carnitine palmitoyltransferase I (which is located in the outer membrane and is detergent-labile) and carnitine palmitoyltransferase II (which is located in the inner membrane and is detergent-stable), together with a carnitine-acylcarnitine translocase. CPT I is the key enzyme in the carnitine-dependent transport across the mitochondrial inner membrane and its deficiency results in a decreased rate of fatty acid beta-oxidation. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs28936374	C>T	Pathogenic	Coding sequence variant, missense variant
rs80356774	G>A	Pathogenic, likely-pathogenic	Coding sequence variant, stop gained
rs80356775	G>A	Pathogenic, uncertain-significance	Missense variant, coding sequence variant
rs80356776	G>A	Pathogenic	Missense variant, coding sequence variant
rs80356777	G>A	Pathogenic	Missense variant, coding sequence variant
rs80356778	T>C	Pathogenic	Missense variant, coding sequence variant
rs80356779	G>A	Pathogenic, benign, conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs80356780	C>T	Pathogenic, likely-pathogenic	Missense variant, coding sequence variant
rs80356782	G>A	Pathogenic	Coding sequence variant, stop gained
rs80356783	A>C	Pathogenic	Missense variant, coding sequence variant
rs80356784	C>A,T	Pathogenic, uncertain-significance	Missense variant, coding sequence variant
rs80356785	G>C,T	Pathogenic	Coding sequence variant, stop gained
rs80356786	A>C	Pathogenic	Coding sequence variant, stop gained
rs80356787	T>C	Pathogenic	Missense variant, coding sequence variant
rs80356789	G>A,C	Pathogenic	Missense variant, coding sequence variant, synonymous variant
rs80356790	G>A	Pathogenic	Missense variant, coding sequence variant
rs80356793	A>G	Pathogenic	Missense variant, coding sequence variant
rs80356794	C>T	Pathogenic	Coding sequence variant, stop gained
rs80356795	A>C,G,T	Pathogenic	Synonymous variant, coding sequence variant, stop gained
rs80356796	G>A,C	Pathogenic, uncertain-significance	Missense variant, coding sequence variant
rs80356798	C>G,T	Likely-pathogenic	Splice acceptor variant
rs80356799	ACTT>-	Pathogenic	Splice donor variant, coding sequence variant, intron variant
rs80356800	C>-	Pathogenic	Frameshift variant, coding sequence variant
rs80356801	G>-	Pathogenic	Coding sequence variant, stop gained
rs112498048	C>T	Likely-pathogenic	Splice donor variant
rs139789100	G>A	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant
rs148059333	C>T	Pathogenic	Splice donor variant
rs151271754	T>C	Conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs189174414	T>G	Likely-pathogenic	Coding sequence variant, missense variant
rs191107774	C>T	Pathogenic	Splice donor variant
rs199640034	C>T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant
rs397515543	G>A	Pathogenic	Stop gained, coding sequence variant
rs397515544	C>T	Pathogenic	Missense variant, coding sequence variant
rs398123654	G>A,C,T	Pathogenic, likely-pathogenic	Synonymous variant, stop gained, coding sequence variant
rs753776604	G>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs761944958	C>A,T	Likely-pathogenic	Missense variant, coding sequence variant
rs765161206	G>A	Likely-pathogenic	Coding sequence variant, stop gained
rs773153659	G>A	Pathogenic	Coding sequence variant, stop gained
rs779893091	G>A,T	Likely-pathogenic	Stop gained, coding sequence variant, synonymous variant
rs886042250	CA>-	Pathogenic	Frameshift variant, coding sequence variant
rs1055176086	C>A,G,T	Likely-pathogenic	Splice donor variant
rs1057516304	T>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1057516396	G>A	Likely-pathogenic	Stop gained, coding sequence variant
rs1057516434	C>T	Likely-pathogenic	Stop gained, coding sequence variant
rs1057516586	G>A	Likely-pathogenic	Stop gained, coding sequence variant
rs1057516800	->TTTT	Likely-pathogenic	Stop gained, coding sequence variant
rs1057517046	C>T	Likely-pathogenic	Splice acceptor variant
rs1057517188	C>T	Likely-pathogenic	Splice acceptor variant
rs1057517245	T>C	Likely-pathogenic	Splice acceptor variant
rs1169875761	AAAAAAAAA>-,AA,AAA,AAAAAAA,AAAAAAAA,AAAAAAAAAA,AAAAAAAAAAA,AAAAAAAAAAAA,AAAAAAAAAAAAAAA	Pathogenic	Intron variant
rs1224226554	A>G	Likely-pathogenic	Splice donor variant
rs1269472669	G>A,C	Likely-pathogenic	Coding sequence variant, missense variant, synonymous variant
rs1282293820	C>A,T	Likely-pathogenic	Splice donor variant
rs1405682081	G>A,C	Likely-pathogenic	Coding sequence variant, missense variant
rs1555226417	A>C	Likely-pathogenic	Splice donor variant
rs1555227607	T>C	Likely-pathogenic	Splice acceptor variant
rs1555228470	C>T	Likely-pathogenic	Splice donor variant
rs1555228640	CCTGTCGTA>-	Likely-pathogenic	Coding sequence variant, splice donor variant, intron variant
rs1555229059	A>G	Likely-pathogenic	Splice donor variant
rs1555230326	C>T	Likely-pathogenic	Splice acceptor variant
rs1555230494	C>G	Likely-pathogenic	Splice donor variant
rs1555230518	T>C	Likely-pathogenic	Splice acceptor variant
rs1594313040	->AGG	Likely-pathogenic	Intron variant, inframe insertion, coding sequence variant
rs1594334937	G>A	Pathogenic	Coding sequence variant, stop gained

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT004535	hsa-miR-370-3p	Luciferase reporter assay, qRT-PCR, Western blot	20124555
MIRT020838	hsa-miR-155-5p	Proteomics	18668040
MIRT031747	hsa-miR-16-5p	Proteomics	18668040
MIRT048093	hsa-miR-197-3p	CLASH	23622248
MIRT538397	hsa-miR-5581-3p	PAR-CLIP	22012620
MIRT538398	hsa-miR-6716-5p	PAR-CLIP	22012620
MIRT538399	hsa-miR-1298-5p	PAR-CLIP	22012620
MIRT538400	hsa-miR-194-3p	PAR-CLIP	22012620
MIRT538401	hsa-miR-1324	PAR-CLIP	22012620
MIRT637837	hsa-miR-6789-3p	HITS-CLIP	23824327
MIRT637838	hsa-miR-4707-3p	HITS-CLIP	23824327
MIRT637839	hsa-miR-4258	HITS-CLIP	23824327
MIRT637840	hsa-miR-153-5p	HITS-CLIP	23824327
MIRT637841	hsa-miR-1250-3p	HITS-CLIP	23824327
MIRT659384	hsa-miR-129-5p	HITS-CLIP	23824327
MIRT659385	hsa-miR-7151-3p	HITS-CLIP	23824327
MIRT659386	hsa-miR-5095	HITS-CLIP	23824327
MIRT659387	hsa-miR-4438	HITS-CLIP	23824327
MIRT688663	hsa-miR-5089-5p	HITS-CLIP	23313552
MIRT688664	hsa-miR-6878-3p	HITS-CLIP	23313552
MIRT688665	hsa-miR-6744-3p	HITS-CLIP	23313552
MIRT688666	hsa-miR-4757-5p	HITS-CLIP	23313552
MIRT688667	hsa-miR-5589-5p	HITS-CLIP	23313552
MIRT688668	hsa-miR-4731-5p	HITS-CLIP	23313552
MIRT688669	hsa-miR-6778-3p	HITS-CLIP	23313552
MIRT688670	hsa-miR-6506-5p	HITS-CLIP	23313552
MIRT688671	hsa-miR-619-5p	HITS-CLIP	23313552
MIRT688672	hsa-miR-150-5p	HITS-CLIP	23313552
MIRT688673	hsa-miR-212-5p	HITS-CLIP	23313552
MIRT688674	hsa-miR-186-3p	HITS-CLIP	23313552
MIRT688675	hsa-miR-520h	HITS-CLIP	23313552
MIRT688676	hsa-miR-520g-3p	HITS-CLIP	23313552
MIRT688677	hsa-miR-512-3p	HITS-CLIP	23313552
MIRT688678	hsa-miR-93-5p	HITS-CLIP	23313552
MIRT688679	hsa-miR-526b-3p	HITS-CLIP	23313552
MIRT688680	hsa-miR-519d-3p	HITS-CLIP	23313552
MIRT688681	hsa-miR-20b-5p	HITS-CLIP	23313552
MIRT688682	hsa-miR-20a-5p	HITS-CLIP	23313552
MIRT688683	hsa-miR-17-5p	HITS-CLIP	23313552
MIRT688684	hsa-miR-106b-5p	HITS-CLIP	23313552
MIRT688685	hsa-miR-106a-5p	HITS-CLIP	23313552
MIRT704466	hsa-miR-520e	HITS-CLIP	23313552
MIRT704467	hsa-miR-520d-3p	HITS-CLIP	23313552
MIRT704468	hsa-miR-520c-3p	HITS-CLIP	23313552
MIRT704469	hsa-miR-520b	HITS-CLIP	23313552
MIRT704470	hsa-miR-520a-3p	HITS-CLIP	23313552
MIRT704471	hsa-miR-372-3p	HITS-CLIP	23313552
MIRT704472	hsa-miR-373-3p	HITS-CLIP	23313552
MIRT704473	hsa-miR-302e	HITS-CLIP	23313552
MIRT704474	hsa-miR-302d-3p	HITS-CLIP	23313552
MIRT704475	hsa-miR-302c-3p	HITS-CLIP	23313552
MIRT704476	hsa-miR-302a-3p	HITS-CLIP	23313552
MIRT704477	hsa-miR-302b-3p	HITS-CLIP	23313552
MIRT704478	hsa-miR-7162-3p	HITS-CLIP	23313552
MIRT704479	hsa-miR-4786-5p	HITS-CLIP	23313552
MIRT704480	hsa-miR-544b	HITS-CLIP	23313552
MIRT704481	hsa-miR-6849-3p	HITS-CLIP	23313552
MIRT704482	hsa-miR-4459	HITS-CLIP	23313552
MIRT704483	hsa-miR-4433a-3p	HITS-CLIP	23313552
MIRT704484	hsa-miR-4768-3p	HITS-CLIP	23313552
MIRT704485	hsa-miR-3622b-3p	HITS-CLIP	23313552
MIRT704486	hsa-miR-3622a-3p	HITS-CLIP	23313552
MIRT704487	hsa-miR-1272	HITS-CLIP	23313552
MIRT704488	hsa-miR-1322	HITS-CLIP	23313552
MIRT704489	hsa-miR-4293	HITS-CLIP	23313552
MIRT704490	hsa-miR-4517	HITS-CLIP	23313552
MIRT725559	hsa-miR-4322	HITS-CLIP	19536157
MIRT725560	hsa-miR-4296	HITS-CLIP	19536157
MIRT725561	hsa-miR-4265	HITS-CLIP	19536157
MIRT725562	hsa-miR-6514-3p	HITS-CLIP	19536157
MIRT725563	hsa-miR-4666b	HITS-CLIP	19536157
MIRT725564	hsa-miR-7977	HITS-CLIP	19536157
MIRT725565	hsa-miR-4417	HITS-CLIP	19536157
MIRT725566	hsa-miR-6781-5p	HITS-CLIP	19536157
MIRT725567	hsa-miR-6877-5p	HITS-CLIP	19536157
MIRT725568	hsa-miR-24-3p	HITS-CLIP	19536157
MIRT725569	hsa-miR-4284	HITS-CLIP	19536157
MIRT725570	hsa-miR-6847-3p	HITS-CLIP	19536157
MIRT725571	hsa-miR-6811-3p	HITS-CLIP	19536157
MIRT725572	hsa-miR-214-5p	HITS-CLIP	19536157
MIRT725573	hsa-miR-6869-3p	HITS-CLIP	19536157
MIRT725574	hsa-miR-299-3p	HITS-CLIP	19536157
MIRT731519	hsa-miR-33a-5p	Luciferase reporter assay, qRT-PCR, Western blot	27199118

Transcription factors

Transcription factor	Regulation	Reference
PPARA	Repression	17150915

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001676	Process	Long-chain fatty acid metabolic process	IDA	11350182
GO:0004095	Function	Carnitine O-palmitoyltransferase activity	IBA	21873635
GO:0004095	Function	Carnitine O-palmitoyltransferase activity	IDA	7892212, 11350182
GO:0004095	Function	Carnitine O-palmitoyltransferase activity	IMP	9691089, 14517221
GO:0005739	Component	Mitochondrion	IBA	21873635
GO:0005739	Component	Mitochondrion	IDA	11350182
GO:0005741	Component	Mitochondrial outer membrane	IMP	14517221
GO:0005741	Component	Mitochondrial outer membrane	TAS
GO:0006006	Process	Glucose metabolic process	IEA
GO:0006631	Process	Fatty acid metabolic process	IBA	21873635
GO:0006635	Process	Fatty acid beta-oxidation	IEA
GO:0006641	Process	Triglyceride metabolic process	IEA
GO:0006853	Process	Carnitine shuttle	TAS
GO:0007623	Process	Circadian rhythm	TAS
GO:0009437	Process	Carnitine metabolic process	IBA	21873635
GO:0009437	Process	Carnitine metabolic process	IDA	11350182
GO:0010883	Process	Regulation of lipid storage	IEA
GO:0014070	Process	Response to organic cyclic compound	IEA
GO:0016020	Component	Membrane	HDA	19946888
GO:0019216	Process	Regulation of lipid metabolic process	TAS
GO:0030855	Process	Epithelial cell differentiation	IEP	21492153
GO:0031307	Component	Integral component of mitochondrial outer membrane	ISS
GO:0031667	Process	Response to nutrient levels	IEA
GO:0032000	Process	Positive regulation of fatty acid beta-oxidation	IEA
GO:0042493	Process	Response to drug	IEA
GO:0042755	Process	Eating behavior	IEA
GO:0042802	Function	Identical protein binding	IEA
GO:0043279	Process	Response to alkaloid	IEA
GO:0045471	Process	Response to ethanol	IEA
GO:0046677	Process	Response to antibiotic	IEA
GO:0050796	Process	Regulation of insulin secretion	IEA
GO:0071398	Process	Cellular response to fatty acid	IEA
GO:0097421	Process	Liver regeneration	IEA
GO:1904772	Process	Response to tetrachloromethane	IEA
GO:1990698	Function	Palmitoleoyltransferase activity	IEA

Other IDs

• MIM: 600528
• HGNC: 2328
• e!Ensembl: ENSG00000110090

Protein

• UniProt ID: P50416
• Protein name: Carnitine O-palmitoyltransferase 1, liver isoform (CPT1-L) (EC 2.3.1.21) (Carnitine O-palmitoyltransferase I, liver isoform) (CPT I) (CPTI-L) (Carnitine palmitoyltransferase 1A)
• Protein function: Catalyzes the transfer of the acyl group of long-chain fatty acid-CoA conjugates onto carnitine, an essential step for the mitochondrial uptake of long-chain fatty acids and their subsequent beta-oxidation in the mitochondrion (PubMed:9691089, PubMed:11350182, PubMed:14517221). Plays an important role in hepatic triglyceride metabolism (By similarity).
• PDB: 2LE3
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF16484	CPT_N	1 → 47	Carnitine O-palmitoyltransferase N-terminus	Domain
  PF00755	Carn_acyltransf	171 → 762	Choline/Carnitine o-acyltransferase	Family

• Sequence:

  MAEAHQAVAFQFTVTPDGIDLRLSHEALRQIYLSGLHSWKKKFIRFKNGIITGVYPASPS
  SWLIVVVGVMTTMYAKIDPSLGIIAKINRTLETANCMSSQTKNVVSGVLFGTGLWVALIV
  TMRYSLKVLLSYHGWMFTEHGKMSRATKIWMGMVKIFSGRKPMLYSFQTSLPRLPVPAVK
  DTVNRYLQSVRPLMKEEDFKRMTALAQDFAVGLGPRLQWYLKLKSWWATNYVSDWWEEYI
  YLRGRGPLMVNSNYYAMDLLYILPTHIQAARAGNAIHAILLYRRKLDREEIKPIRLLGST
  IPLCSAQWERMFNTSRIPGEETDTIQHMRDSKHIVVYHRGRYFKVWLYHDGRLLKPREME
  QQMQRILDNTSEPQPGEARLAALTAGDRVPWARCRQAYFGRGKNKQSLDAVEKAAFFVTL
  DETEEGYRSEDPDTSMDSYAKSLLHGRCYDRWFDKSFTFVVFKNGKMGLNAEHSWADAPI
  VAHLWEYVMSIDSLQLGYAEDGHCKGDINPNIPYPTRLQWDIPGECQEVIETSLNTANLL
  ANDVDFHSFPFVAFGKGIIKKCRTSPDAFVQLALQLAHYKDMGKFCLTYEASMTRLFREG
  RTETVRSCTTESCDFVRAMVDPAQTVEQRLKLFKLASEKHQHMYRLAMTGSGIDRHLFCL
  YVVSKYLAVESPFLKEVLSEPWRLSTSQTPQQQVELFDLENNPEYVSSGGGFGPVADDGY
  GVSYILVGENLINFHISSKFSCPETDSHRFGRHLKEAMTDIITLFGLSSNSKK

• Sequence length: 773