Carnitine Palmitoyltransferase I (CPT I) Deficiency


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Introduction

The CPT1A gene, which stands for carnitine palmitoyltransferase 1A, is located on chromosome 11q13.3, has 19 exons spanning ~60kb and encodes a 774 amino acid protein, Carnitine Palmitoyltransferase I or CPT I (1). The mitochondrial oxidation of long-chain fatty acids is initiated by the sequential action of carnitine palmitoyltransferase I (located in the outer membrane) and carnitine palmitoyltransferase II (located in the inner membrane), together with a carnitine-acylcarnitine translocase (2). 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 (2). The protein 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 (3).

The CPT I protein is expressed at high levels in kidney and heart and at lower levels in liver and skeletal muscle (3).

More than 94 unique disease-causing variants in the CPT1A gene have been identified in CPT I patients and are represented in this database (4). The variants occur across the entire length of the gene and include frameshift, splice site, copy-number, nonsense and missense variants.

Variant List

To see more information, click on the Variant in the table. Hover on the Variant in the table to see its location on the gene. For more information on table headers, HGVS nomenclature, and ACMG classification please use the following links here.

Gene Structure
Variant IDVariantAmino Acid ChangeGene SymbolVariant TypeEffect TypeDisplay ACMG CallDisease SubtypeTimes ObservedPhenotypePMIDLocationPresent in ClinVar
CPT1A_0095c.694-?_967+?dupGain (Exons 7-9)CPT1ALikely PathogenicCPT I<5Unknown
CPT1A_0001c.2246G>Ap.Arg749HisCPT1ASNVMissenseLikely PathogenicCPT I<5Developmental delay34374989, 35360862Exon 19No
CPT1A_0002c.2238T>Gp.Asp746GluCPT1ASNVMissenseUncertain SignificanceCPT I<5MyopathyExon 19Yes
CPT1A_0096c.2235+4T>CIntronicCPT1ASNVSplice regionUncertain SignificanceCPT I<5Elevated circulating creatine kinase concentrationIntron 18Yes
CPT1A_0003c.2215A>Gp.Lys739GluCPT1ASNVMissenseLikely PathogenicCPT I<533123633Exon 18No
CPT1A_0004c.2201T>Cp.Phe734SerCPT1ASNVMissenseUncertain SignificanceCPT I<534233743Exon 18No
CPT1A_0005c.2198A>Gp.Asn733SerCPT1ASNVMissenseUncertain SignificanceCPT I<534023347Exon 18Yes
CPT1A_0006c.2156G>Ap.Gly719AspCPT1ASNVMissenseLikely PathogenicCPT I<519345525Exon 18No
CPT1A_0007c.2142G>Ap.Pro714=CPT1ASNVSilentUncertain SignificanceCPT I<5Exon 17Yes
CPT1A_0009c.2136delp.Phe712Leufs*43CPT1ADeletionFrameshiftLikely PathogenicCPT I<530887117Exon 17Yes
CPT1A_0010c.2129G>Ap.Gly710GluCPT1ASNVMissenseLikely PathogenicCPT I11-20Deep vein thrombosis, Dehydration, Developmental delay, Diarrhea, Encephalopathy....11350182, 11350183, 1403388Exon 17Yes
CPT1A_0011c.2126G>Ap.Gly709GluCPT1ASNVMissenseLikely PathogenicCPT I<5Abnormality of metabolism/homeostasis, Arrhythmia, Cardiac-other, Hypoglycemia, Hypotonic, Liver abnormality, Peripheral oedema14517221, 9048718Exon 17Yes
CPT1A_0012c.2125G>Ap.Gly709ArgCPT1ASNVMissenseLikely PathogenicCPT I<535281663, 35360862Exon 17Yes
CPT1A_0013c.2122A>Cp.Ser708ArgCPT1ASNVMissenseLikely PathogenicCPT I5-10Abnormality of metabolism/homeostasis, Coagulopathy, Encephalopathy, Global cere....35822099Exon 17No
CPT1A_0014c.2028+3_2028+6delIntronicCPT1ADeletionSplice regionLikely PathogenicCPT I<5Hypoglycemia, Reye syndrome-like episodes12111367Intron 16Yes
CPT1A_0015c.1964G>Ap.Arg655HisCPT1ASNVMissenseUncertain SignificanceCPT I<5Acute severe pancreatitis, Fever, Hemolysis, Jaundice, Liver abnormality, Renal tubular acidosis31234250Exon 16No
CPT1A_0016c.1948G>Ap.Gly650SerCPT1ASNVMissenseUncertain SignificanceCPT I<535281663Exon 16Yes
CPT1A_0017c.1910C>Ap.Ser637TyrCPT1ASNVMissenseLikely PathogenicCPT I<535360862Exon 16No
CPT1A_0018c.1910C>Tp.Ser637PheCPT1ASNVMissenseUncertain SignificanceCPT I<536246604Exon 16Yes
CPT1A_0019c.1907C>Tp.Ala636ValCPT1ASNVMissenseUncertain SignificanceCPT I<530617651Exon 16Yes
CPT1A_0020c.1889T>Gp.Leu630ArgCPT1ASNVMissenseUncertain SignificanceCPT I<534728707Exon 16No
CPT1A_0097c.1876G>Cp.Val626LeuCPT1ASNVMissenseUncertain SignificanceCPT I<5Exon 16Yes
CPT1A_0021c.1850G>Ap.Arg617GlnCPT1ASNVMissenseUncertain SignificanceCPT I<5Exon 15Yes
CPT1A_0022c.1817G>Ap.Arg606HisCPT1ASNVMissenseUncertain SignificanceCPT I<535360862Exon 15Yes
CPT1A_0098c.1813G>Ap.Val605MetCPT1ASNVMissenseUncertain SignificanceCPT I<5Elevated circulating creatine kinase concentration, Myopathy, Other, Peripheral neuropathyExon 15Yes
CPT1A_0023c.1783C>Tp.Arg595TrpCPT1ASNVMissenseLikely PathogenicCPT I<5Anorexia, Cerebral hyperexcitability, Coma, Dehydration, Developmental delay, Di....23430932Exon 15Yes
CPT1A_0024c.1762_1766dupp.Tyr589*CPT1AInsertionFrameshiftPathogenicCPT I<5Cough, Diarrhea, Fever, Gastrointestinal-other, Hypoglycemia, Jaundice, Liver abnormality, Muscle weakness, Pulmonary/respiratory, Vomiting23430491Exon 15Yes
CPT1A_0025c.1737C>Ap.Tyr579*CPT1ASNVNonsensePathogenicCPT I<5Apathy, Encephalopathy, Lethargy, Otitis media, Vomiting16146704Exon 14Yes
CPT1A_0099c.1685G>Cp.Cys562SerCPT1ASNVMissenseUncertain SignificanceCPT I<5Exon 14Yes
CPT1A_0026c.1683delp.Lys561Asnfs*33CPT1ADeletionFrameshiftLikely PathogenicCPT I<528771436Exon 14No
CPT1A_0100c.1658C>Tp.Ala553ValCPT1ASNVMissenseUncertain SignificanceCPT I<5Exon 14Yes
CPT1A_0101c.1625A>Gp.Asn542SerCPT1ASNVMissenseUncertain SignificanceCPT I<5Exon 14No
CPT1A_0027c.1600delp.Leu534*CPT1ADeletionFrameshiftPathogenicCPT I<5Encephalopathy, Hypoglycemia16146704Exon 14Yes
CPT1A_0028c.1518C>Tp.Gly506=CPT1ASNVSilentUncertain SignificanceCPT I<5Exon 13Yes
CPT1A_0107c.1497G>Ap.Ala499=CPT1ASNVSilentUncertain SignificanceCPT I<5Exon 13Yes
CPT1A_0102c.1496C>Tp.Ala499ValCPT1ASNVMissenseUncertain SignificanceCPT I<5Elevated circulating creatine kinase concentration, Hypoglycemia, RhabdomyolysisExon 13Yes
CPT1A_0030c.1493A>Gp.Tyr498CysCPT1ASNVMissenseLikely PathogenicCPT I<5Abnormal truncal coordination, Abnormality of metabolism/homeostasis, Aminoacidu....12189492, 2768784Exon 13Yes
CPT1A_0031c.1493A>Cp.Tyr498SerCPT1ASNVMissenseLikely PathogenicCPT I<5Abnormality of metabolism/homeostasis, Encephalopathy, Hyperlipidemia, Hypoglycemia, Renal tubular acidosis17060594, 21962599Exon 13No
CPT1A_0032c.1456_1458+1delIntronicCPT1ADeletionSplice donorPathogenicCPT I<5Hyperammonemia, Hypoglycemia, Liver abnormality30617651Exon 12, Intron 12No
CPT1A_0033c.1451T>Cp.Leu484ProCPT1ASNVMissenseLikely PathogenicCPT I<511441142, 3211616Exon 12Yes
CPT1A_0034c.1436C>Tp.Pro479LeuCPT1ASNVMissenseConflictCPT I30+Asthma, Eczema, Encephalopathy, Hypoglycemia, Liver abnormality, Loss of consciousness, Muscle cramping, Pain, Rhabdomyolysis, Seizure, Vomiting11441142, 19181627, 30887117, 35442417, 36109795Exon 12Yes
CPT1A_0035c.1433C>Tp.Ala478ValCPT1ASNVMissenseLikely PathogenicCPT I<5Recurrent acute pancreatitis23700290Exon 12Yes
CPT1A_0036c.1394G>Ap.Gly465GluCPT1ASNVMissenseLikely PathogenicCPT I<5Autism/behavior, Developmental delay, Hypertelorism, Hypotonia, Liver abnormalit....32781271Exon 12Yes
CPT1A_0038c.1393G>Ap.Gly465ArgCPT1ASNVMissenseLikely PathogenicCPT I<5Abnormal renal morphology, Abnormality of metabolism/homeostasis, Craniosynostos....27066452Exon 12Yes
CPT1A_0037c.1393G>Tp.Gly465TrpCPT1ASNVMissenseLikely PathogenicCPT I<5Hepatic encephalopathy, Hypoglycemia15110323Exon 12Yes
CPT1A_0039c.1367C>Tp.Ser456LeuCPT1ASNVMissenseLikely PathogenicCPT I<5Recurrent acute pancreatitis23700290Exon 12Yes
CPT1A_0040c.1364A>Cp.Lys455ThrCPT1ASNVMissensePathogenicCPT I11-20Abnormality of metabolism/homeostasis, Anemia, Encephalopathy, Hyperammonemia, H....15970898, 17060594, 21962599Exon 12Yes
CPT1A_0041c.1361A>Gp.Asp454GlyCPT1ASNVMissenseLikely PathogenicCPT I<5Abnormality of metabolism/homeostasis, Diarrhea, Encephalopathy, Feeding difficulties, Hypoglycemia, Hypotonia, Lethargy, Liver abnormality9691089Exon 12Yes
CPT1A_0042c.1339C>Tp.Arg447*CPT1ASNVNonsensePathogenicCPT I<519345525Exon 11Yes
CPT1A_0043c.1336G>Ap.Gly446SerCPT1ASNVMissenseLikely PathogenicCPT I<530904546, 34869124, 35360862Exon 11No
CPT1A_0044c.1328T>Cp.Leu443ProCPT1ASNVMissenseLikely PathogenicCPT I<535360862Exon 11No
CPT1A_0045c.1318G>Ap.Ala440ThrCPT1ASNVMissenseLikely PathogenicCPT I5-1027295194, 34233743Exon 11No
CPT1A_0046c.1295C>Tp.Pro432LeuCPT1ASNVMissenseLikely PathogenicCPT I<535360862Exon 11No
CPT1A_0047c.1241C>Tp.Ala414ValCPT1ASNVMissensePathogenicCPT I<5Abnormal truncal coordination, Abnormality of metabolism/homeostasis, Aminoacidu....12189492, 27295194, 2768784Exon 11Yes
CPT1A_0048c.1199G>Cp.Gly400AlaCPT1ASNVMissenseUncertain SignificanceCPT I<5Exon 11Yes
CPT1A_0049c.1184_1186delp.Arg395delCPT1ADeletionDeletionLikely PathogenicCPT I<5Dehydration, Diarrhea, Hypoglycemia, Seizure11441142Exon 11No
CPT1A_0050c.1163+5G>AIntronicCPT1ASNVSplice regionUncertain SignificanceCPT I<5Decreased body weight, Developmental delay, High procalcitonin levels, Jaundice,....30271085Intron 10Yes
CPT1A_0051c.1163+4C>TIntronicCPT1ASNVSplice regionUncertain SignificanceCPT I<5Intron 10Yes
CPT1A_0052c.1163+1G>AIntronicCPT1ASNVSplice donorPathogenicCPT I<5Abnormal renal morphology, Abnormality of metabolism/homeostasis, Craniosynostos....27066452, 28748224Intron 10Yes
CPT1A_0053c.1131G>Cp.Glu377AspCPT1ASNVMissenseLikely PathogenicCPT I<534869124, 35360862Exon 10No
CPT1A_0103c.1112C>Tp.Ser371LeuCPT1ASNVMissenseUncertain SignificanceCPT I<5Liver abnormalityExon 10Yes
CPT1A_0054c.1079A>Gp.Glu360GlyCPT1ASNVMissenseLikely PathogenicCPT I<5Hypoglycemia, Reye syndrome-like episodes12111367Exon 10Yes
CPT1A_0055c.1069C>Tp.Arg357TrpCPT1ASNVMissenseLikely PathogenicCPT I<5Abnormality of metabolism/homeostasis, Coma, Flulike illness, Liver abnormality11441142, 3211616Exon 10Yes
CPT1A_0056c.1065G>Ap.Lys355LysCPT1ASNVSilentUncertain SignificanceCPT I<536246604Exon 10Yes
CPT1A_0057c.1027T>Gp.Phe343ValCPT1ASNVMissenseLikely PathogenicCPT I<5Hepatic encephalopathy, Hypoglycemia15110323Exon 10Yes
CPT1A_0058c.1015C>Tp.Arg339*CPT1ASNVNonsensePathogenicCPT I<529519241Exon 10Yes
CPT1A_0059c.1006G>Ap.Val336MetCPT1ASNVMissenseUncertain SignificanceCPT I<5Hypoglycemia, Reyes syndrome28466427Exon 10No
CPT1A_0060c.979C>Tp.His327TyrCPT1ASNVMissenseUncertain SignificanceCPT I<535360862Exon 10No
CPT1A_0061c.968-3C>GIntronicCPT1ASNVSplice regionUncertain SignificanceCPT I<531319225Intron 9Yes
CPT1A_0062c.968-11G>AIntronicCPT1ASNVIntronicUncertain SignificanceCPT I<5Acute severe pancreatitis, Fever, Hemolysis, Jaundice, Liver abnormality, Renal tubular acidosis31234250Intron 9Yes
CPT1A_0063c.956G>Tp.Gly319ValCPT1ASNVMissenseUncertain SignificanceCPT I<535360862Exon 9No
CPT1A_0064c.948delp.Ile317Serfs*12CPT1ADeletionFrameshiftPathogenicCPT I<5Abnormality of metabolism/homeostasis, Arrhythmia, Cardiac-other, Hypoglycemia, Hypotonic, Liver abnormality, Peripheral oedema14517221, 9048718Exon 9Yes
CPT1A_0065c.947G>Ap.Arg316GlnCPT1ASNVMissenseLikely PathogenicCPT I<5Developmental delay, Hemolytic anemia, Lethargy, Liver abnormality, Rhabdomyolysis, Vomiting23969540, 29519241Exon 9No
CPT1A_0066c.946C>Gp.Arg316GlyCPT1ASNVMissenseUncertain SignificanceCPT I5-1015110323Exon 9Yes
CPT1A_0067c.941C>Tp.Thr314IleCPT1ASNVMissenseLikely PathogenicCPT I<5Abnormal renal morphology, Abnormality of metabolism/homeostasis, Dehydration, H....15669684Exon 9Yes
CPT1A_0068c.929G>Ap.Arg310GlnCPT1ASNVMissenseUncertain SignificanceCPT I<5Exon 9Yes
CPT1A_0069c.912C>Gp.Cys304TrpCPT1ASNVMissenseLikely PathogenicCPT I<5Dehydration, Diarrhea, Liver abnormality, Vomiting11441142Exon 9No
CPT1A_0070c.884G>Ap.Arg295HisCPT1ASNVMissenseUncertain SignificanceCPT I<5Exon 9Yes
CPT1A_0071c.837_838insTp.Leu280Serfs*34CPT1AInsertionFrameshiftPathogenicCPT I<5Developmental delay, Hemolytic anemia, Lethargy, Liver abnormality, Rhabdomyolysis, Vomiting23969540, 29519241Exon 8No
CPT1A_0072c.823G>Ap.Ala275ThrCPT1ASNVMissenseConflictCPT I5-10Abnormal renal morphology, Abnormal truncal coordination, Abnormality of metabol....11441142, 12189492, 15669684, 22494076, 2768784Exon 8Yes
CPT1A_0073c.748G>Tp.Val250LeuCPT1ASNVMissenseUncertain SignificanceCPT I<529519241Exon 7No
CPT1A_0074c.740C>Tp.Pro247LeuCPT1ASNVMissenseLikely PathogenicCPT I<535360862Exon 7Yes
CPT1A_0075c.734G>Ap.Arg245GlnCPT1ASNVMissenseLikely PathogenicCPT I<530904546, 34869124Exon 7No
CPT1A_0076c.733C>Tp.Arg245*CPT1ASNVNonsensePathogenicCPT I<5Arrhythmia, Hyperammonemia, Hypoglycemia, Reye syndrome-like episodes28468868Exon 7Yes
CPT1A_0077c.693+1G>AIntronicCPT1ASNVSplice donorLikely PathogenicCPT I<530887117Intron 6Yes
CPT1A_0078c.627delp.Phe209Leufs*13CPT1ADeletionFrameshiftPathogenicCPT I<5Hypoglycemia, Reyes syndrome28466427Exon 6No
CPT1A_0079c.619C>Tp.Gln207*CPT1ASNVNonsensePathogenicCPT I<533123633Exon 6Yes
CPT1A_0080c.601C>Tp.Arg201TrpCPT1ASNVMissenseUncertain SignificanceCPT I<5Exon 6Yes
CPT1A_0081c.577delp.Met194*CPT1ADeletionFrameshiftPathogenicCPT I<535360862Exon 6No
CPT1A_0082c.526G>Tp.Val176PheCPT1ASNVMissenseUncertain SignificanceCPT I<5Cough, Diarrhea, Fever, Gastrointestinal-other, Hypoglycemia, Jaundice, Liver abnormality, Muscle weakness, Pulmonary/respiratory, Vomiting23430491Exon 5No
CPT1A_0083c.497G>Tp.Ser166IleCPT1ASNVMissenseUncertain SignificanceCPT I<523700290Exon 5No
CPT1A_0084c.478C>Tp.Arg160*CPT1ASNVNonsensePathogenicCPT I<5Encephalopathy, Hepatic encephalopathy, Hypoglycemia, Liver abnormality, Vomiting15110323, 16146704Exon 5Yes
CPT1A_0104c.454-6C>GIntronicCPT1ASNVSplice regionUncertain SignificanceCPT I<5Intron 4No
CPT1A_0085c.434G>Ap.Arg145HisCPT1ASNVMissenseUncertain SignificanceCPT I<5Exon 4Yes
CPT1A_0086c.367C>Tp.Arg123CysCPT1ASNVMissenseLikely PathogenicCPT I<5Hypoglycemia, Otitis media, Seizure, Toroviruspositive diarrhea11441142Exon 4Yes
CPT1A_0087c.319G>Ap.Gly107SerCPT1ASNVMissenseUncertain SignificanceCPT I<5Exon 4Yes
CPT1A_0105c.304A>Cp.Lys102GlnCPT1ASNVMissenseUncertain SignificanceCPT I<5Liver abnormality, Myopathy, Other, Peripheral neuropathyExon 4Yes
CPT1A_0088c.298C>Tp.Gln100*CPT1ASNVNonsensePathogenicCPT I<5Hypoglycemia12189492Exon 4Yes
CPT1A_0089c.281+1G>AIntronicCPT1ASNVSplice donorPathogenicCPT I<535360862Intron 3Yes
CPT1A_0090c.272T>Cp.Leu91ProCPT1ASNVMissenseLikely PathogenicCPT I<523700290, 34869124Exon 3No
CPT1A_0106c.223G>Ap.Ala75ThrCPT1ASNVMissenseUncertain SignificanceCPT I<5Exon 3Yes
CPT1A_0091c.205G>Ap.Val69MetCPT1ASNVMissenseUncertain SignificanceCPT I<535360862Exon 3No
CPT1A_0092c.167C>Tp.Pro56LeuCPT1ASNVMissenseLikely PathogenicCPT I5-10Cardiac-other, Diarrhea, Fever, Hypotonia, Lethargy23430868Exon 3Yes
CPT1A_0093c.100T>Cp.Ser34ProCPT1ASNVMissenseUncertain SignificanceCPT I30+35822099Exon 2Yes
CPT1A_0094c.96T>Gp.Tyr32*CPT1ASNVNonsensePathogenicCPT I<5Hypoglycemia, Reye syndrome-like episodes12111367Exon 2Yes
    Notes:
  • * Click the PMID number to go to the corresponding publication.
  • * All variants are referencing NM_001876.4 and there is no change between these versions with respect to the coding sequence.
  • * Genomic coordinates are calculated based on variant data provided: in some cases coordinates are estimated in order to allow users to sort the variants linearly, by approximation.
  • * Click the Present in ClinVar link to go to the corresponding ClinVar VariationID.
    Definition of acronyms:
  • "*": Referenced a stop codon insertion when listed under amino acid change.
  • ACMG: American College of Medical Genetics and Genomics
  • CNV: Copy number variant which here describes a change 100 DNA nucleotides or larger.
  • SNV: Single DNA nucleotide variant
  • del: Deletion
  • dup: Duplication
  • fs: Frameshift
  • ins: Insertion

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