Rare Disease Genes

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.

Variant ID	Variant	Amino Acid Change	Gene Symbol	Variant Type	Effect Type	Display ACMG Call	Disease Subtype	Times Observed	Phenotype	PMID	Location	Present in ClinVar

CPT1A_0095	c.694-?_967+?dup	Gain (Exons 7-9)	CPT1A			Likely Pathogenic	CPT I	<5				Unknown
CPT1A_0001	c.2246G>A	p.Arg749His	CPT1A	SNV	Missense	Likely Pathogenic	CPT I	<5	Developmental delay	34374989, 35360862	Exon 19	No
CPT1A_0002	c.2238T>G	p.Asp746Glu	CPT1A	SNV	Missense	Uncertain Significance	CPT I	<5	Myopathy		Exon 19	Yes
CPT1A_0096	c.2235+4T>C	Intronic	CPT1A	SNV	Splice region	Uncertain Significance	CPT I	<5	Elevated circulating creatine kinase concentration		Intron 18	Yes
CPT1A_0003	c.2215A>G	p.Lys739Glu	CPT1A	SNV	Missense	Likely Pathogenic	CPT I	<5		33123633	Exon 18	No
CPT1A_0004	c.2201T>C	p.Phe734Ser	CPT1A	SNV	Missense	Uncertain Significance	CPT I	<5		34233743	Exon 18	No
CPT1A_0005	c.2198A>G	p.Asn733Ser	CPT1A	SNV	Missense	Uncertain Significance	CPT I	<5		34023347	Exon 18	Yes
CPT1A_0006	c.2156G>A	p.Gly719Asp	CPT1A	SNV	Missense	Likely Pathogenic	CPT I	<5		19345525	Exon 18	No
CPT1A_0007	c.2142G>A	p.Pro714=	CPT1A	SNV	Silent	Uncertain Significance	CPT I	<5			Exon 17	Yes
CPT1A_0009	c.2136del	p.Phe712Leufs*43	CPT1A	Deletion	Frameshift	Likely Pathogenic	CPT I	<5		30887117	Exon 17	Yes
CPT1A_0010	c.2129G>A	p.Gly710Glu	CPT1A	SNV	Missense	Likely Pathogenic	CPT I	11-20	Deep vein thrombosis, Dehydration, Developmental delay, Diarrhea, Encephalopathy....	11350182, 11350183, 1403388	Exon 17	Yes
CPT1A_0011	c.2126G>A	p.Gly709Glu	CPT1A	SNV	Missense	Likely Pathogenic	CPT I	<5	Abnormality of metabolism/homeostasis, Arrhythmia, Cardiac-other, Hypoglycemia, Hypotonic, Liver abnormality, Peripheral oedema	14517221, 9048718	Exon 17	Yes
CPT1A_0012	c.2125G>A	p.Gly709Arg	CPT1A	SNV	Missense	Likely Pathogenic	CPT I	<5		35281663, 35360862	Exon 17	Yes
CPT1A_0013	c.2122A>C	p.Ser708Arg	CPT1A	SNV	Missense	Likely Pathogenic	CPT I	5-10	Abnormality of metabolism/homeostasis, Coagulopathy, Encephalopathy, Global cere....	35822099	Exon 17	No
CPT1A_0014	c.2028+3_2028+6del	Intronic	CPT1A	Deletion	Splice region	Likely Pathogenic	CPT I	<5	Hypoglycemia, Reye syndrome-like episodes	12111367	Intron 16	Yes
CPT1A_0015	c.1964G>A	p.Arg655His	CPT1A	SNV	Missense	Uncertain Significance	CPT I	<5	Acute severe pancreatitis, Fever, Hemolysis, Jaundice, Liver abnormality, Renal tubular acidosis	31234250	Exon 16	No
CPT1A_0016	c.1948G>A	p.Gly650Ser	CPT1A	SNV	Missense	Uncertain Significance	CPT I	<5		35281663	Exon 16	Yes
CPT1A_0017	c.1910C>A	p.Ser637Tyr	CPT1A	SNV	Missense	Likely Pathogenic	CPT I	<5		35360862	Exon 16	No
CPT1A_0018	c.1910C>T	p.Ser637Phe	CPT1A	SNV	Missense	Uncertain Significance	CPT I	<5		36246604	Exon 16	Yes
CPT1A_0019	c.1907C>T	p.Ala636Val	CPT1A	SNV	Missense	Uncertain Significance	CPT I	<5		30617651	Exon 16	Yes
CPT1A_0020	c.1889T>G	p.Leu630Arg	CPT1A	SNV	Missense	Uncertain Significance	CPT I	<5		34728707	Exon 16	No
CPT1A_0097	c.1876G>C	p.Val626Leu	CPT1A	SNV	Missense	Uncertain Significance	CPT I	<5			Exon 16	Yes
CPT1A_0021	c.1850G>A	p.Arg617Gln	CPT1A	SNV	Missense	Uncertain Significance	CPT I	<5			Exon 15	Yes
CPT1A_0022	c.1817G>A	p.Arg606His	CPT1A	SNV	Missense	Uncertain Significance	CPT I	<5		35360862	Exon 15	Yes
CPT1A_0098	c.1813G>A	p.Val605Met	CPT1A	SNV	Missense	Uncertain Significance	CPT I	<5	Elevated circulating creatine kinase concentration, Myopathy, Other, Peripheral neuropathy		Exon 15	Yes
CPT1A_0023	c.1783C>T	p.Arg595Trp	CPT1A	SNV	Missense	Likely Pathogenic	CPT I	<5	Anorexia, Cerebral hyperexcitability, Coma, Dehydration, Developmental delay, Di....	23430932	Exon 15	Yes
CPT1A_0024	c.1762_1766dup	p.Tyr589*	CPT1A	Insertion	Frameshift	Pathogenic	CPT I	<5	Cough, Diarrhea, Fever, Gastrointestinal-other, Hypoglycemia, Jaundice, Liver abnormality, Muscle weakness, Pulmonary/respiratory, Vomiting	23430491	Exon 15	Yes
CPT1A_0025	c.1737C>A	p.Tyr579*	CPT1A	SNV	Nonsense	Pathogenic	CPT I	<5	Apathy, Encephalopathy, Lethargy, Otitis media, Vomiting	16146704	Exon 14	Yes
CPT1A_0099	c.1685G>C	p.Cys562Ser	CPT1A	SNV	Missense	Uncertain Significance	CPT I	<5			Exon 14	Yes
CPT1A_0026	c.1683del	p.Lys561Asnfs*33	CPT1A	Deletion	Frameshift	Likely Pathogenic	CPT I	<5		28771436	Exon 14	No
CPT1A_0100	c.1658C>T	p.Ala553Val	CPT1A	SNV	Missense	Uncertain Significance	CPT I	<5			Exon 14	Yes
CPT1A_0101	c.1625A>G	p.Asn542Ser	CPT1A	SNV	Missense	Uncertain Significance	CPT I	<5			Exon 14	No
CPT1A_0027	c.1600del	p.Leu534*	CPT1A	Deletion	Frameshift	Pathogenic	CPT I	<5	Encephalopathy, Hypoglycemia	16146704	Exon 14	Yes
CPT1A_0028	c.1518C>T	p.Gly506=	CPT1A	SNV	Silent	Uncertain Significance	CPT I	<5			Exon 13	Yes
CPT1A_0107	c.1497G>A	p.Ala499=	CPT1A	SNV	Silent	Uncertain Significance	CPT I	<5			Exon 13	Yes
CPT1A_0102	c.1496C>T	p.Ala499Val	CPT1A	SNV	Missense	Uncertain Significance	CPT I	<5	Elevated circulating creatine kinase concentration, Hypoglycemia, Rhabdomyolysis		Exon 13	Yes
CPT1A_0030	c.1493A>G	p.Tyr498Cys	CPT1A	SNV	Missense	Likely Pathogenic	CPT I	<5	Abnormal truncal coordination, Abnormality of metabolism/homeostasis, Aminoacidu....	12189492, 2768784	Exon 13	Yes
CPT1A_0031	c.1493A>C	p.Tyr498Ser	CPT1A	SNV	Missense	Likely Pathogenic	CPT I	<5	Abnormality of metabolism/homeostasis, Encephalopathy, Hyperlipidemia, Hypoglycemia, Renal tubular acidosis	17060594, 21962599	Exon 13	No
CPT1A_0032	c.1456_1458+1del	Intronic	CPT1A	Deletion	Splice donor	Pathogenic	CPT I	<5	Hyperammonemia, Hypoglycemia, Liver abnormality	30617651	Exon 12, Intron 12	No
CPT1A_0033	c.1451T>C	p.Leu484Pro	CPT1A	SNV	Missense	Likely Pathogenic	CPT I	<5		11441142, 3211616	Exon 12	Yes
CPT1A_0034	c.1436C>T	p.Pro479Leu	CPT1A	SNV	Missense	Conflict	CPT I	30+	Asthma, Eczema, Encephalopathy, Hypoglycemia, Liver abnormality, Loss of consciousness, Muscle cramping, Pain, Rhabdomyolysis, Seizure, Vomiting	11441142, 19181627, 30887117, 35442417, 36109795	Exon 12	Yes
CPT1A_0035	c.1433C>T	p.Ala478Val	CPT1A	SNV	Missense	Likely Pathogenic	CPT I	<5	Recurrent acute pancreatitis	23700290	Exon 12	Yes
CPT1A_0036	c.1394G>A	p.Gly465Glu	CPT1A	SNV	Missense	Likely Pathogenic	CPT I	<5	Autism/behavior, Developmental delay, Hypertelorism, Hypotonia, Liver abnormalit....	32781271	Exon 12	Yes
CPT1A_0038	c.1393G>A	p.Gly465Arg	CPT1A	SNV	Missense	Likely Pathogenic	CPT I	<5	Abnormal renal morphology, Abnormality of metabolism/homeostasis, Craniosynostos....	27066452	Exon 12	Yes
CPT1A_0037	c.1393G>T	p.Gly465Trp	CPT1A	SNV	Missense	Likely Pathogenic	CPT I	<5	Hepatic encephalopathy, Hypoglycemia	15110323	Exon 12	Yes
CPT1A_0039	c.1367C>T	p.Ser456Leu	CPT1A	SNV	Missense	Likely Pathogenic	CPT I	<5	Recurrent acute pancreatitis	23700290	Exon 12	Yes
CPT1A_0040	c.1364A>C	p.Lys455Thr	CPT1A	SNV	Missense	Pathogenic	CPT I	11-20	Abnormality of metabolism/homeostasis, Anemia, Encephalopathy, Hyperammonemia, H....	15970898, 17060594, 21962599	Exon 12	Yes
CPT1A_0041	c.1361A>G	p.Asp454Gly	CPT1A	SNV	Missense	Likely Pathogenic	CPT I	<5	Abnormality of metabolism/homeostasis, Diarrhea, Encephalopathy, Feeding difficulties, Hypoglycemia, Hypotonia, Lethargy, Liver abnormality	9691089	Exon 12	Yes
CPT1A_0042	c.1339C>T	p.Arg447*	CPT1A	SNV	Nonsense	Pathogenic	CPT I	<5		19345525	Exon 11	Yes
CPT1A_0043	c.1336G>A	p.Gly446Ser	CPT1A	SNV	Missense	Likely Pathogenic	CPT I	<5		30904546, 34869124, 35360862	Exon 11	No
CPT1A_0044	c.1328T>C	p.Leu443Pro	CPT1A	SNV	Missense	Likely Pathogenic	CPT I	<5		35360862	Exon 11	No
CPT1A_0045	c.1318G>A	p.Ala440Thr	CPT1A	SNV	Missense	Likely Pathogenic	CPT I	5-10		27295194, 34233743	Exon 11	No
CPT1A_0046	c.1295C>T	p.Pro432Leu	CPT1A	SNV	Missense	Likely Pathogenic	CPT I	<5		35360862	Exon 11	No
CPT1A_0047	c.1241C>T	p.Ala414Val	CPT1A	SNV	Missense	Pathogenic	CPT I	<5	Abnormal truncal coordination, Abnormality of metabolism/homeostasis, Aminoacidu....	12189492, 27295194, 2768784	Exon 11	Yes
CPT1A_0048	c.1199G>C	p.Gly400Ala	CPT1A	SNV	Missense	Uncertain Significance	CPT I	<5			Exon 11	Yes
CPT1A_0049	c.1184_1186del	p.Arg395del	CPT1A	Deletion	Deletion	Likely Pathogenic	CPT I	<5	Dehydration, Diarrhea, Hypoglycemia, Seizure	11441142	Exon 11	No
CPT1A_0050	c.1163+5G>A	Intronic	CPT1A	SNV	Splice region	Uncertain Significance	CPT I	<5	Decreased body weight, Developmental delay, High procalcitonin levels, Jaundice,....	30271085	Intron 10	Yes
CPT1A_0051	c.1163+4C>T	Intronic	CPT1A	SNV	Splice region	Uncertain Significance	CPT I	<5			Intron 10	Yes
CPT1A_0052	c.1163+1G>A	Intronic	CPT1A	SNV	Splice donor	Pathogenic	CPT I	<5	Abnormal renal morphology, Abnormality of metabolism/homeostasis, Craniosynostos....	27066452, 28748224	Intron 10	Yes
CPT1A_0053	c.1131G>C	p.Glu377Asp	CPT1A	SNV	Missense	Likely Pathogenic	CPT I	<5		34869124, 35360862	Exon 10	No
CPT1A_0103	c.1112C>T	p.Ser371Leu	CPT1A	SNV	Missense	Uncertain Significance	CPT I	<5	Liver abnormality		Exon 10	Yes
CPT1A_0054	c.1079A>G	p.Glu360Gly	CPT1A	SNV	Missense	Likely Pathogenic	CPT I	<5	Hypoglycemia, Reye syndrome-like episodes	12111367	Exon 10	Yes
CPT1A_0055	c.1069C>T	p.Arg357Trp	CPT1A	SNV	Missense	Likely Pathogenic	CPT I	<5	Abnormality of metabolism/homeostasis, Coma, Flulike illness, Liver abnormality	11441142, 3211616	Exon 10	Yes
CPT1A_0056	c.1065G>A	p.Lys355Lys	CPT1A	SNV	Silent	Uncertain Significance	CPT I	<5		36246604	Exon 10	Yes
CPT1A_0057	c.1027T>G	p.Phe343Val	CPT1A	SNV	Missense	Likely Pathogenic	CPT I	<5	Hepatic encephalopathy, Hypoglycemia	15110323	Exon 10	Yes
CPT1A_0058	c.1015C>T	p.Arg339*	CPT1A	SNV	Nonsense	Pathogenic	CPT I	<5		29519241	Exon 10	Yes
CPT1A_0059	c.1006G>A	p.Val336Met	CPT1A	SNV	Missense	Uncertain Significance	CPT I	<5	Hypoglycemia, Reyes syndrome	28466427	Exon 10	No
CPT1A_0060	c.979C>T	p.His327Tyr	CPT1A	SNV	Missense	Uncertain Significance	CPT I	<5		35360862	Exon 10	No
CPT1A_0061	c.968-3C>G	Intronic	CPT1A	SNV	Splice region	Uncertain Significance	CPT I	<5		31319225	Intron 9	Yes
CPT1A_0062	c.968-11G>A	Intronic	CPT1A	SNV	Intronic	Uncertain Significance	CPT I	<5	Acute severe pancreatitis, Fever, Hemolysis, Jaundice, Liver abnormality, Renal tubular acidosis	31234250	Intron 9	Yes
CPT1A_0063	c.956G>T	p.Gly319Val	CPT1A	SNV	Missense	Uncertain Significance	CPT I	<5		35360862	Exon 9	No
CPT1A_0064	c.948del	p.Ile317Serfs*12	CPT1A	Deletion	Frameshift	Pathogenic	CPT I	<5	Abnormality of metabolism/homeostasis, Arrhythmia, Cardiac-other, Hypoglycemia, Hypotonic, Liver abnormality, Peripheral oedema	14517221, 9048718	Exon 9	Yes
CPT1A_0065	c.947G>A	p.Arg316Gln	CPT1A	SNV	Missense	Likely Pathogenic	CPT I	<5	Developmental delay, Hemolytic anemia, Lethargy, Liver abnormality, Rhabdomyolysis, Vomiting	23969540, 29519241	Exon 9	No
CPT1A_0066	c.946C>G	p.Arg316Gly	CPT1A	SNV	Missense	Uncertain Significance	CPT I	5-10		15110323	Exon 9	Yes
CPT1A_0067	c.941C>T	p.Thr314Ile	CPT1A	SNV	Missense	Likely Pathogenic	CPT I	<5	Abnormal renal morphology, Abnormality of metabolism/homeostasis, Dehydration, H....	15669684	Exon 9	Yes
CPT1A_0068	c.929G>A	p.Arg310Gln	CPT1A	SNV	Missense	Uncertain Significance	CPT I	<5			Exon 9	Yes
CPT1A_0069	c.912C>G	p.Cys304Trp	CPT1A	SNV	Missense	Likely Pathogenic	CPT I	<5	Dehydration, Diarrhea, Liver abnormality, Vomiting	11441142	Exon 9	No
CPT1A_0070	c.884G>A	p.Arg295His	CPT1A	SNV	Missense	Uncertain Significance	CPT I	<5			Exon 9	Yes
CPT1A_0071	c.837_838insT	p.Leu280Serfs*34	CPT1A	Insertion	Frameshift	Pathogenic	CPT I	<5	Developmental delay, Hemolytic anemia, Lethargy, Liver abnormality, Rhabdomyolysis, Vomiting	23969540, 29519241	Exon 8	No
CPT1A_0072	c.823G>A	p.Ala275Thr	CPT1A	SNV	Missense	Conflict	CPT I	5-10	Abnormal renal morphology, Abnormal truncal coordination, Abnormality of metabol....	11441142, 12189492, 15669684, 22494076, 2768784	Exon 8	Yes
CPT1A_0073	c.748G>T	p.Val250Leu	CPT1A	SNV	Missense	Uncertain Significance	CPT I	<5		29519241	Exon 7	No
CPT1A_0074	c.740C>T	p.Pro247Leu	CPT1A	SNV	Missense	Likely Pathogenic	CPT I	<5		35360862	Exon 7	Yes
CPT1A_0075	c.734G>A	p.Arg245Gln	CPT1A	SNV	Missense	Likely Pathogenic	CPT I	<5		30904546, 34869124	Exon 7	No
CPT1A_0076	c.733C>T	p.Arg245*	CPT1A	SNV	Nonsense	Pathogenic	CPT I	<5	Arrhythmia, Hyperammonemia, Hypoglycemia, Reye syndrome-like episodes	28468868	Exon 7	Yes
CPT1A_0077	c.693+1G>A	Intronic	CPT1A	SNV	Splice donor	Likely Pathogenic	CPT I	<5		30887117	Intron 6	Yes
CPT1A_0078	c.627del	p.Phe209Leufs*13	CPT1A	Deletion	Frameshift	Pathogenic	CPT I	<5	Hypoglycemia, Reyes syndrome	28466427	Exon 6	No
CPT1A_0079	c.619C>T	p.Gln207*	CPT1A	SNV	Nonsense	Pathogenic	CPT I	<5		33123633	Exon 6	Yes
CPT1A_0080	c.601C>T	p.Arg201Trp	CPT1A	SNV	Missense	Uncertain Significance	CPT I	<5			Exon 6	Yes
CPT1A_0081	c.577del	p.Met194*	CPT1A	Deletion	Frameshift	Pathogenic	CPT I	<5		35360862	Exon 6	No
CPT1A_0082	c.526G>T	p.Val176Phe	CPT1A	SNV	Missense	Uncertain Significance	CPT I	<5	Cough, Diarrhea, Fever, Gastrointestinal-other, Hypoglycemia, Jaundice, Liver abnormality, Muscle weakness, Pulmonary/respiratory, Vomiting	23430491	Exon 5	No
CPT1A_0083	c.497G>T	p.Ser166Ile	CPT1A	SNV	Missense	Uncertain Significance	CPT I	<5		23700290	Exon 5	No
CPT1A_0084	c.478C>T	p.Arg160*	CPT1A	SNV	Nonsense	Pathogenic	CPT I	<5	Encephalopathy, Hepatic encephalopathy, Hypoglycemia, Liver abnormality, Vomiting	15110323, 16146704	Exon 5	Yes
CPT1A_0104	c.454-6C>G	Intronic	CPT1A	SNV	Splice region	Uncertain Significance	CPT I	<5			Intron 4	No
CPT1A_0085	c.434G>A	p.Arg145His	CPT1A	SNV	Missense	Uncertain Significance	CPT I	<5			Exon 4	Yes
CPT1A_0086	c.367C>T	p.Arg123Cys	CPT1A	SNV	Missense	Likely Pathogenic	CPT I	<5	Hypoglycemia, Otitis media, Seizure, Toroviruspositive diarrhea	11441142	Exon 4	Yes
CPT1A_0087	c.319G>A	p.Gly107Ser	CPT1A	SNV	Missense	Uncertain Significance	CPT I	<5			Exon 4	Yes
CPT1A_0105	c.304A>C	p.Lys102Gln	CPT1A	SNV	Missense	Uncertain Significance	CPT I	<5	Liver abnormality, Myopathy, Other, Peripheral neuropathy		Exon 4	Yes
CPT1A_0088	c.298C>T	p.Gln100*	CPT1A	SNV	Nonsense	Pathogenic	CPT I	<5	Hypoglycemia	12189492	Exon 4	Yes
CPT1A_0089	c.281+1G>A	Intronic	CPT1A	SNV	Splice donor	Pathogenic	CPT I	<5		35360862	Intron 3	Yes
CPT1A_0090	c.272T>C	p.Leu91Pro	CPT1A	SNV	Missense	Likely Pathogenic	CPT I	<5		23700290, 34869124	Exon 3	No
CPT1A_0106	c.223G>A	p.Ala75Thr	CPT1A	SNV	Missense	Uncertain Significance	CPT I	<5			Exon 3	Yes
CPT1A_0091	c.205G>A	p.Val69Met	CPT1A	SNV	Missense	Uncertain Significance	CPT I	<5		35360862	Exon 3	No
CPT1A_0092	c.167C>T	p.Pro56Leu	CPT1A	SNV	Missense	Likely Pathogenic	CPT I	5-10	Cardiac-other, Diarrhea, Fever, Hypotonia, Lethargy	23430868	Exon 3	Yes
CPT1A_0093	c.100T>C	p.Ser34Pro	CPT1A	SNV	Missense	Uncertain Significance	CPT I	30+		35822099	Exon 2	Yes
CPT1A_0094	c.96T>G	p.Tyr32*	CPT1A	SNV	Nonsense	Pathogenic	CPT I	<5	Hypoglycemia, Reye syndrome-like episodes	12111367	Exon 2	Yes

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Variant ID
Variant
Amino Acid Change
Gene Symbol
Variant Type
Effect Type
Display ACMG Call
Disease Subtype
Times Observed
Phenotype
PMID
Article Count
Location
Variant Start
AA Position
Protein Domain
ACMG Call Last Revised Date
GRCh38
Record Last Revised Date
Present in ClinVar
ACMG Call
Predicted ACMG Call
Thousand Genomes Allele Frequency
Ontology Relations
ExAC Allele Frequency
GnomAD Alleles
Associated Geography
Variants Seen With

Carnitine Palmitoyltransferase I (CPT I) Deficiency

Introduction

Variant List

Gene Structure

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