CPT1A

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

CPT1A_0001	c.2246G>A	p.Arg749His	CPT1A	SNV	Missense	Likely Pathogenic	CPT1	3-5	Developmental delay	34374989, 35360862	Exon 19
CPT1A_0002	c.2238T>G	p.Asp746Glu	CPT1A	SNV	Missense	Uncertain Significance	CPT1	<3			Exon 19
CPT1A_0003	c.2215A>G	p.Lys739Glu	CPT1A	SNV	Missense	Likely Pathogenic	CPT1	<3		33123633	Exon 18
CPT1A_0004	c.2201T>C	p.Phe734Ser	CPT1A	SNV	Missense	Uncertain Significance	CPT1	<3		34233743	Exon 18
CPT1A_0005	c.2198A>G	p.Asn733Ser	CPT1A	SNV	Missense	Uncertain Significance	CPT1	<3		34023347	Exon 18
CPT1A_0006	c.2156G>A	p.Gly719Asp	CPT1A	SNV	Missense	Likely Pathogenic	CPT1	<3		19345525	Exon 18
CPT1A_0007	c.2142G>A	p.Pro714=	CPT1A	SNV	Silent	Uncertain Significance	CPT1	30+			Exon 17
CPT1A_0008	c.2142G>A	Silent	CPT1A	SNV	Silent	Uncertain Significance	CPT1	<3			Exon 17
CPT1A_0009	c.2136del	p.Phe712Leufs*43	CPT1A	Deletion	Frameshift	Likely Pathogenic	CPT1	<3		30887117	Exon 17
CPT1A_0010	c.2129G>A	p.Gly710Glu	CPT1A	SNV	Missense	Likely Pathogenic	CPT1	11-20	Abnormal liver morph....	11350182, 11350183, 1403388	Exon 17
CPT1A_0011	c.2126G>A	p.Gly709Glu	CPT1A	SNV	Missense	Likely Pathogenic	CPT1	<3	Abnormal liver morph....	14517221, 9048718	Exon 17
CPT1A_0012	c.2125G>A	p.Gly709Arg	CPT1A	SNV	Missense	Likely Pathogenic	CPT1	3-5		35281663, 35360862	Exon 17
CPT1A_0013	c.2122A>C	p.Ser708Arg	CPT1A	SNV	Missense	Likely Pathogenic	CPT1	6-10	Abnormality of metab....	35822099	Exon 17
CPT1A_0014	c.2028+3_2028+6del	Intronic	CPT1A	Deletion	Splice region	Likely Pathogenic	CPT1	<3		12111367	Intron 16
CPT1A_0015	c.1964G>A	p.Arg655His	CPT1A	SNV	Missense	Uncertain Significance	CPT1	<3	Abnormal liver morph....	31234250	Exon 16
CPT1A_0016	c.1948G>A	p.Gly650Ser	CPT1A	SNV	Missense	Uncertain Significance	CPT1	<3		35281663	Exon 16
CPT1A_0018	c.1910C>T	p.Ser637Phe	CPT1A	SNV	Missense	Uncertain Significance	CPT1	<3		36246604	Exon 16
CPT1A_0017	c.1910C>A	p.Ser637Tyr	CPT1A	SNV	Missense	Likely Pathogenic	CPT1	3-5		35360862	Exon 16
CPT1A_0019	c.1907C>T	p.Ala636Val	CPT1A	SNV	Missense	Uncertain Significance	CPT1	<3		30617651	Exon 16
CPT1A_0020	c.1889T>G	p.Leu630Arg	CPT1A	SNV	Missense	Uncertain Significance	CPT1	<3		34728707	Exon 16
CPT1A_0021	c.1850G>A	p.Arg617Gln	CPT1A	SNV	Missense	Uncertain Significance	CPT1	30+			Exon 15
CPT1A_0022	c.1817G>A	p.Arg606His	CPT1A	SNV	Missense	Uncertain Significance	CPT1	<3		35360862	Exon 15
CPT1A_0023	c.1783C>T	p.Arg595Trp	CPT1A	SNV	Missense	Likely Pathogenic	CPT1	<3	Abnormal liver morph....	23430932	Exon 15
CPT1A_0024	c.1762_1766dup	p.Tyr589*	CPT1A	Insertion	Frameshift	Pathogenic	CPT1	<3	Abnormal liver morph....	23430491	Exon 15
CPT1A_0025	c.1737C>A	p.Tyr579*	CPT1A	SNV	Nonsense	Pathogenic	CPT1	<3	Apathy, Encephalopat....	16146704	Exon 14
CPT1A_0026	c.1683del	p.Lys561Asnfs*33	CPT1A	Deletion	Frameshift	Likely Pathogenic	CPT1	<3		28771436	Exon 14
CPT1A_0027	c.1600del	p.Leu534*	CPT1A	Deletion	Frameshift	Pathogenic	CPT1	<3	Encephalopathy, Hypoglycemia	16146704	Exon 14
CPT1A_0028	c.1518C>T	p.Gly506=	CPT1A	SNV	Silent	Uncertain Significance	CPT1	30+			Exon 13
CPT1A_0029	c.1497G>A	Silent	CPT1A	SNV	Silent	Uncertain Significance	CPT1	<3			Exon 13
CPT1A_0031	c.1493A>C	p.Tyr498Ser	CPT1A	SNV	Missense	Likely Pathogenic	CPT1	<3	Abnormality of metab....	17060594, 21962599	Exon 13
CPT1A_0030	c.1493A>G	p.Tyr498Cys	CPT1A	SNV	Missense	Likely Pathogenic	CPT1	<3	Abnormal liver morph....	12189492, 2768784	Exon 13
CPT1A_0032	c.1456_1458+1del	Intronic	CPT1A	Deletion	Splice donor	Pathogenic	CPT1	<3	Hepatic failure, Hyperammonemia, Hypoglycemia	30617651	Exon 12, Intron 12
CPT1A_0033	c.1451T>C	p.Leu484Pro	CPT1A	SNV	Missense	Likely Pathogenic	CPT1	<3		11441142, 3211616	Exon 12
CPT1A_0034	c.1436C>T	p.Pro479Leu	CPT1A	SNV	Missense	Conflict	CPT1	30+		11441142, 19181627, 30887117, 35442417, 36109795	Exon 12
CPT1A_0035	c.1433C>T	p.Ala478Val	CPT1A	SNV	Missense	Likely Pathogenic	CPT1	<3	Recurrent acute pancreatitis	23700290	Exon 12
CPT1A_0036	c.1394G>A	p.Gly465Glu	CPT1A	SNV	Missense	Likely Pathogenic	CPT1	3-5	Abnormal liver morph....	32781271	Exon 12
CPT1A_0037	c.1393G>T	p.Gly465Trp	CPT1A	SNV	Missense	Likely Pathogenic	CPT1	3-5	Encephalopathy, Hypoketotic hypoglycemia	15110323	Exon 12
CPT1A_0038	c.1393G>A	p.Gly465Arg	CPT1A	SNV	Missense	Likely Pathogenic	CPT1	<3	Abnormal liver morph....	27066452	Exon 12
CPT1A_0039	c.1367C>T	p.Ser456Leu	CPT1A	SNV	Missense	Likely Pathogenic	CPT1	<3	Recurrent acute pancreatitis	23700290	Exon 12
CPT1A_0040	c.1364A>C	p.Lys455Thr	CPT1A	SNV	Missense	Pathogenic	CPT1	11-20	Abnormal liver morph....	15970898, 17060594, 21962599	Exon 12
CPT1A_0041	c.1361A>G	p.Asp454Gly	CPT1A	SNV	Missense	Likely Pathogenic	CPT1	3-5	Abnormal liver morph....	9691089	Exon 12
CPT1A_0042	c.1339C>T	p.Arg447*	CPT1A	SNV	Nonsense	Pathogenic	CPT1	<3		19345525	Exon 11
CPT1A_0043	c.1336G>A	p.Gly446Ser	CPT1A	SNV	Missense	Likely Pathogenic	CPT1	3-5		30904546, 34869124, 35360862	Exon 11
CPT1A_0044	c.1328T>C	p.Leu443Pro	CPT1A	SNV	Missense	Likely Pathogenic	CPT1	3-5		35360862	Exon 11
CPT1A_0045	c.1318G>A	p.Ala440Thr	CPT1A	SNV	Missense	Likely Pathogenic	CPT1	6-10		27295194, 34233743	Exon 11
CPT1A_0046	c.1295C>T	p.Pro432Leu	CPT1A	SNV	Missense	Likely Pathogenic	CPT1	<3		35360862	Exon 11
CPT1A_0047	c.1241C>T	p.Ala414Val	CPT1A	SNV	Missense	Pathogenic	CPT1	3-5	Abnormal liver morph....	12189492, 27295194, 2768784	Exon 11
CPT1A_0048	c.1199G>C	p.Gly400Ala	CPT1A	SNV	Missense	Uncertain Significance	CPT1	30+			Exon 11
CPT1A_0049	c.1184_1186del	p.Arg395del	CPT1A	Deletion	Deletion	Likely Pathogenic	CPT1	<3	Dehydration, Diarrhea, Hypoglycemia, Seizure	11441142	Exon 11
CPT1A_0050	c.1163+5G>A	Intronic	CPT1A	SNV	Splice region	Uncertain Significance	CPT1	<3		30271085	Intron 10
CPT1A_0051	c.1163+4C>T	Intronic	CPT1A	SNV	Splice region	Uncertain Significance	CPT1	<3			Intron 10
CPT1A_0052	c.1163+1G>A	Intronic	CPT1A	SNV	Splice donor	Pathogenic	CPT1	3-5	Abnormal liver morph....	27066452, 28748224	Intron 10
CPT1A_0053	c.1131G>C	p.Glu377Asp	CPT1A	SNV	Missense	Likely Pathogenic	CPT1	<3		34869124, 35360862	Exon 10
CPT1A_0054	c.1079A>G	p.Glu360Gly	CPT1A	SNV	Missense	Likely Pathogenic	CPT1	<3	Hypoketotic hypoglyc....	12111367	Exon 10
CPT1A_0055	c.1069C>T	p.Arg357Trp	CPT1A	SNV	Missense	Likely Pathogenic	CPT1	3-5	Abnormal liver morph....	11441142, 3211616	Exon 10
CPT1A_0056	c.1065G>A	p.Lys355Lys	CPT1A	SNV	Silent	Uncertain Significance	CPT1	<3		36246604	Exon 10
CPT1A_0057	c.1027T>G	p.Phe343Val	CPT1A	SNV	Missense	Likely Pathogenic	CPT1	<3	Encephalopathy, Hypoglycemia	15110323	Exon 10
CPT1A_0058	c.1015C>T	p.Arg339*	CPT1A	SNV	Nonsense	Pathogenic	CPT1	<3		29519241	Exon 10
CPT1A_0059	c.1006G>A	p.Val336Met	CPT1A	SNV	Missense	Uncertain Significance	CPT1	<3	Hypoglycemia, Reyes syndrome	28466427	Exon 10
CPT1A_0060	c.979C>T	p.His327Tyr	CPT1A	SNV	Missense	Uncertain Significance	CPT1	<3		35360862	Exon 10
CPT1A_0061	c.968-3C>G	Intronic	CPT1A	SNV		Uncertain Significance	CPT1	<3		31319225	Intron 9
CPT1A_0062	c.968-11G>A	Intronic	CPT1A	SNV	Intronic	Uncertain Significance	CPT1	<3	Abnormal liver morph....	31234250	Intron 9
CPT1A_0063	c.956G>T	p.Gly319Val	CPT1A	SNV	Missense	Uncertain Significance	CPT1	<3		35360862	Exon 9
CPT1A_0064	c.948del	p.Ile317Serfs*12	CPT1A	Deletion	Frameshift	Pathogenic	CPT1	<3	Abnormal liver morph....	14517221, 9048718	Exon 9
CPT1A_0065	c.947G>A	p.Arg316Gln	CPT1A	SNV	Missense	Likely Pathogenic	CPT1	<3	Abnormal liver morph....	23969540, 29519241	Exon 9
CPT1A_0066	c.946C>G	p.Arg316Gly	CPT1A	SNV	Missense	Uncertain Significance	CPT1	3-5		15110323	Exon 9
CPT1A_0067	c.941C>T	p.Thr314Ile	CPT1A	SNV	Missense	Likely Pathogenic	CPT1	<3	Abnormal renal morph....	15669684	Exon 9
CPT1A_0068	c.929G>A	p.Arg310Gln	CPT1A	SNV	Missense	Uncertain Significance	CPT1	<3			Exon 9
CPT1A_0069	c.912C>G	p.Cys304Trp	CPT1A	SNV	Missense	Likely Pathogenic	CPT1	<3	Abnormal liver morph....	11441142	Exon 9
CPT1A_0070	c.884G>A	p.Arg295His	CPT1A	SNV	Missense	Uncertain Significance	CPT1	<3			Exon 9
CPT1A_0071	c.837_838insT	p.Leu280Serfs*34	CPT1A	Insertion	Frameshift	Pathogenic	CPT1	<3	Abnormal liver morph....	23969540, 29519241	Exon 8
CPT1A_0072	c.823G>A	p.Ala275Thr	CPT1A	SNV	Missense	Conflict	CPT1	6-10	Abnormal liver morph....	11441142, 12189492, 15669684, 22494076, 2768784	Exon 8
CPT1A_0073	c.748G>T	p.Val250Leu	CPT1A	SNV	Missense	Uncertain Significance	CPT1	<3		29519241	Exon 7
CPT1A_0074	c.740C>T	p.Pro247Leu	CPT1A	SNV	Missense	Likely Pathogenic	CPT1	3-5		35360862	Exon 7
CPT1A_0075	c.734G>A	p.Arg245Gln	CPT1A	SNV	Missense	Likely Pathogenic	CPT1	<3		30904546, 34869124	Exon 7
CPT1A_0076	c.733C>T	p.Arg245*	CPT1A	SNV	Nonsense	Pathogenic	CPT1	<3	Arrhythmia, Hyperamm....	28468868	Exon 7
CPT1A_0077	c.693+1G>A	Intronic	CPT1A	SNV	Splice donor	Likely Pathogenic	CPT1	<3		30887117	Intron 6
CPT1A_0078	c.627del	p.Phe209Leufs*13	CPT1A	Deletion	Frameshift	Pathogenic	CPT1	<3	Hypoglycemia, Reyes syndrome	28466427	Exon 6
CPT1A_0079	c.619C>T	p.Gln207*	CPT1A	SNV	Nonsense	Pathogenic	CPT1	<3		33123633	Exon 6
CPT1A_0080	c.601C>T	p.Arg201Trp	CPT1A	SNV	Missense	Uncertain Significance	CPT1	<3			Exon 6
CPT1A_0081	c.577del	p.Met194*	CPT1A	Deletion	Frameshift	Pathogenic	CPT1	<3		35360862	Exon 6
CPT1A_0082	c.526G>T	p.Val176Phe	CPT1A	SNV	Missense	Uncertain Significance	CPT1	<3	Abnormal liver morph....	23430491	Exon 5
CPT1A_0083	c.497G>T	p.Ser166Ile	CPT1A	SNV	Missense	Uncertain Significance	CPT1	<3		23700290	Exon 5
CPT1A_0084	c.478C>T	p.Arg160*	CPT1A	SNV	Nonsense	Pathogenic	CPT1	3-5	Abnormal liver morph....	15110323, 16146704	Exon 5
CPT1A_0085	c.434G>A	p.Arg145His	CPT1A	SNV	Missense	Uncertain Significance	CPT1	<3			Exon 4
CPT1A_0086	c.367C>T	p.Arg123Cys	CPT1A	SNV	Missense	Likely Pathogenic	CPT1	<3	Hypoglycemia, Otitis....	11441142	Exon 4
CPT1A_0087	c.319G>A	p.Gly107Ser	CPT1A	SNV	Missense	Uncertain Significance	CPT1	<3			Exon 4
CPT1A_0088	c.298C>T	p.Gln100*	CPT1A	SNV	Nonsense	Pathogenic	CPT1	<3	Hypoketotic hypoglycemia	12189492	Exon 4
CPT1A_0089	c.281+1G>A	Intronic	CPT1A	SNV	Splice donor	Pathogenic	CPT1	<3		35360862	Intron 3
CPT1A_0090	c.272T>C	p.Leu91Pro	CPT1A	SNV	Missense	Likely Pathogenic	CPT1	<3		23700290, 34869124	Exon 3
CPT1A_0091	c.205G>A	p.Val69Met	CPT1A	SNV	Missense	Uncertain Significance	CPT1	<3		35360862	Exon 3
CPT1A_0092	c.167C>T	p.Pro56Leu	CPT1A	SNV	Missense	Likely Pathogenic	CPT1	3-5	Cardiac-other, Diarr....	23430868	Exon 3
CPT1A_0093	c.100T>C	p.Ser34Pro	CPT1A	SNV	Missense	Uncertain Significance	CPT1	30+		35822099	Exon 2
CPT1A_0094	c.96T>G	p.Tyr32*	CPT1A	SNV	Nonsense	Pathogenic	CPT1	<3	Hypoketotic hypoglyc....	12111367	Exon 2

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.

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

References:

Gobin, S. et al., Organization of the human liver carnitine palmitoyltransferase 1 gene (CPT1A) and identification of novel mutations in hypoketotic hypoglycaemia. Hum Genet. 2002 Aug;111(2):179-89.
https://www.ncbi.nlm.nih.gov/gene/1374
https://www.genecards.org/cgi-bin/carddisp.pl?gene=CPT1A&keywords=cpt1a
Richbourg et al. (2023) Phenotype associations from a comprehensive database of long-chain fatty acid oxidation disorder gene variants (Abstract and poster presentation, American Society of Human Genetics 2023).

Introduction

Variant List

Gene Structure

Give us a moment while we fetch the data.