CPT2

Carnitine Palmitoyltransferase II (CPT II) Deficiency

Introduction

The CPT2 gene, carnitine palmitoyltransferase 2, is located on chromosome 1p32.3 and has 5 exons spanning ~20kb (1). It encodes a 685 amino acid nuclear protein, carnitine palmitoyltransferase II or CPT II, which is transported to the mitochondrial inner membrane (2). Together with carnitine palmitoyltransferase I, carnitine palmitoyltransferase II oxidizes long-chain fatty acids in the mitochondria (3). The protein is involved in the intramitochondrial synthesis of acylcarnitines from accumulated acyl-CoA metabolites (4,5) and their reconversion back into the respective acyl-CoA esters that can then undergo beta-oxidation, an essential step for the mitochondrial uptake of long-chain fatty acids and their subsequent beta-oxidation in the mitochondrion. The enzyme is active with medium (C8-C12) and long-chain (C14-C18) acyl-CoA esters (5).

The protein is expressed in liver, colon and other tissues (6).

More than 160 disease-causing variants in the CPT2 gene have been identified in CPT Ⅱ patients and are represented in this database. The variants occur across the entire length of the gene and include frameshift, splice site, copy-number, nonsense and missense variants (7).

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	Phenotype	PMID	Location	Present in ClinVar

CPT2_0011	c.?	p.Leu72Phe	CPT2			Likely Pathogenic	CPT II	<5	Hypoglycemia, Liver abnormality	14605500		Unknown
CPT2_0004	c.?	p.His369Gln	CPT2			Likely Pathogenic	CPT II	<5	Muscle switching, Myalgia, Myoglobinuria	23911907		Unknown
CPT2_0001	c.?	p.Tyr290*	CPT2			Pathogenic	CPT II	<5	Abnormal renal morphology, Renal insufficiency/failure	14605500		Unknown
CPT2_0008	c.?	p.Gly600Arg	CPT2			Pathogenic	CPT II	<5	Arrhythmia, Liver abnormality	14605500		Unknown
CPT2_0007	c.?	p.Phe448Leu	CPT2			Likely Pathogenic	CPT II	<5	Abnormal renal morphology, Abnormality of metabolism/homeostasis, Absence of cor....	11477613		Unknown
CPT2_0010	c.?	p.Val605Leu	CPT2			Pathogenic	CPT II	<5	Bilateral oculomotor disturbance, Bilateral ptosis, Cataracts, Cognitive decline....	31348995		Unknown
CPT2_0012	c.28_29insAGCAAG	p.Trp10*	CPT2	Insertion	Nonsense	Pathogenic	CPT II	<5	Abnormal renal morphology, Facial dysmorphia, Polymicrogyria of cns with calcification	30293990	Exon 1	Yes
CPT2_0013	c.38del	p.Gly13Alafs*60	CPT2	Deletion	Frameshift	Pathogenic	CPT II	<5		16996287	Exon 1	Yes
CPT2_0014	c.36_43dup	p.Ala15Glyfs*61	CPT2	Duplication	Frameshift	Pathogenic	CPT II	<5		16996287	Exon 1	No
CPT2_0015	c.62C>A	p.Pro21His	CPT2	SNV	Missense	Likely Pathogenic	CPT II	<5	Gastrointestinal-other, Hypotonia, Muscle weakness, Poor oral intake	22494076	Exon 1	Yes
CPT2_0016	c.98del	p.Gln33Argfs*40	CPT2	Deletion	Frameshift	Pathogenic	CPT II	<5	Muscle weakness, Myoglobinuria	21913903, 30957255	Exon 1	Yes
CPT2_0017	c.99G>C	p.Gln33His	CPT2	SNV	Missense	Likely Pathogenic	CPT II	<5	Gastrointestinal-other, Hypotonia, Muscle weakness, Poor oral intake	22494076	Exon 1	Yes
CPT2_0018	c.110_111dup	p.Ser38Alafs*36	CPT2	Duplication	Frameshift	Pathogenic	CPT II	5-10	Abnormal renal morphology, Abnormality of metabolism/homeostasis, Arrhythmia, Ca....	10862092, 12410208, 12673791, 12840153, 16996287, 20505667, 21378393, 24898617, 30007356	Exon 1	Yes
CPT2_0019	c.122C>T	p.Pro41Leu	CPT2	SNV	Missense	Uncertain Significance	CPT II	<5	Rhabdomyolysis	22899091	Exon 1	Yes
CPT2_0020	c.122_130del	p.Pro41_Met43del	CPT2	Deletion	Deletion	Uncertain Significance	CPT II	<5	Encephalopathy, Seizure	35281663	Exon 1	No
CPT2_0021	c.131_133delinsCCC	p.His44_Tyr45delinsProHis	CPT2	Delins	Missense	Uncertain Significance	CPT II	<5	Elevated circulating creatine kinase concentration, Myopathy, Rhabdomyolysis		Exon 1	Yes
CPT2_0022	c.136C>T	p.Gln46*	CPT2	SNV	Nonsense	Pathogenic	CPT II	<5	Abnormality of metabolism/homeostasis, Hyperammonemia, Hypoglycemia, Hypothermia	31638495	Exon 1	No
CPT2_0023	c.149C>A	p.Pro50His	CPT2	SNV	Missense	Pathogenic	CPT II	30+	Decreased feeding, Diarrhea, Elevated circulating creatine kinase concentration,....	10398218, 10862092, 12410208, 12673791, 12707442, 15622536, 16996287, 17936304, 20505667, 24602495, 29478820, 30455135, 30897730, 30957255, 31554424, 33123633, 34449523, 7711730, 9048718	Exon 1	Yes
CPT2_0024	c.151A>G	p.Arg51Gly	CPT2	SNV	Missense	Uncertain Significance	CPT II	<5	Abnormality of metabolism/homeostasis, Hypoglycemia, Liver abnormality, Myalgia, Reye syndrome-like episodes, Seizure, Unconsciousness	22841441, 29552494	Exon 1	No
CPT2_0025	c.152+5G>A	Intronic	CPT2	SNV	Splice region	Pathogenic	CPT II	5-10	Cardiomyopathy, Elevated circulating creatine kinase concentration, Encephalopathy		Intron 1	Yes
CPT2_0026	c.161T>G	p.Ile54Ser	CPT2	SNV	Missense	Uncertain Significance	CPT II	<5	Fever, Reduced feeding, Vomiting	35859960	Exon 2	No
CPT2_0027	c.164C>G	p.Pro55Arg	CPT2	SNV	Missense	Likely Pathogenic	CPT II	<5	Abnormal renal morphology, Developmental delay, Periventricular calcifications, Prominent lenticulostriate vascular markings, Ventriculomegaly	18550408	Exon 2	Yes
CPT2_0028	c.182_203del	p.Ile61Argfs*5	CPT2	Deletion	Frameshift	Pathogenic	CPT II	<5	Muscle weakness, Myoglobinuria	23475205, 30455135, 30897730	Exon 2	No
CPT2_0029	c.200C>G	p.Ala67Gly	CPT2	SNV	Missense	Uncertain Significance	CPT II	<5	Myalgia, Rhabdomyolysis, Vomiting	29478820	Exon 2	Yes
CPT2_0030	c.213_214del	p.Leu72Glufs*2	CPT2	Deletion	Frameshift	Pathogenic	CPT II	<5	Elevated circulating creatine kinase concentration, Other		Exon 2	Yes
CPT2_0031	c.233+2T>A	Intronic	CPT2	SNV	Splice donor	Pathogenic	CPT II	<5		28747690	Intron 2	No
CPT2_0032	c.234-1G>A	Intronic	CPT2	SNV	Splice acceptor	Pathogenic	CPT II	5-10	Arrhythmia, Cardiac-other, Hypotonia, Lethargy, Liver abnormality, Pulmonary/respiratory, Seizure	12560872	Intron 2	Yes
CPT2_0033	c.250T>C	p.Cys84Arg	CPT2	SNV	Missense	Uncertain Significance	CPT II	<5		16996287	Exon 3	No
CPT2_0034	c.256_257del	p.Ser86Phefs*2	CPT2	Deletion	Frameshift	Pathogenic	CPT II	<5		16996287	Exon 3	Yes
CPT2_0035	c.298del	p.Val100Leufs*30	CPT2	Deletion	Frameshift	Pathogenic	CPT II	<5	Myalgia, Rhabdomyolysis	36109795	Exon 3	Yes
CPT2_0036	c.302C>T	p.Ala101Val	CPT2	SNV	Missense	Likely Benign	CPT II	<5	Rhabdomyolysis	16996287, 32978841	Exon 3	Yes
CPT2_0037	c.313C>T	p.Gln105*	CPT2	SNV	Nonsense	Pathogenic	CPT II	<5	Rhabdomyolysis	28801073	Exon 3	No
CPT2_0038	c.338C>T	p.Ser113Leu	CPT2	SNV	Missense	Pathogenic	CPT II	30+	Abnormal emg, Abnormality of metabolism/homeostasis, Acute rhabdomyolysis, Ameno....	10090476, 10398215, 10398218, 10734268, 10738923, 10862092, 10868782, 11001791, 11585077, 11595519, 11994355, 11999976, 12362414, 12673791, 12707442, 12809643, 12840153, 14605500, 14970749, 15613406, 15622536, 15776096, 16168441, 16225172, 16671104, 16996287, 17936304, 18471680, 18550408, 18645163, 20505667, 20810031, 21378393, 21913903, 23184072, 23475205, 24305961, 24398345, 24563797, 24602495, 24786990, 24843804, 24898617, 25513977, 26913919, 27034144, 27067077, 27085974, 27629963, 27843283, 28468868, 28779239, 28801073, 28871440, 29478820, 29731937, 29744303, 30007356, 30149802, 30262761, 30455135, 30514913, 30881520, 30897730, 30957255, 31070454, 31191612, 31235404, 31407473, 31517061, 31624327, 31638495, 32463482, 32721234, 32793418, 32928639, 32978841, 33122977, 33123633, 33201363, 33304817, 35256318, 36109795, 36422281, 36473042, 36478999, 36685561, 7711426, 7711730, 8651281, 9048718, 9309694, 9562964, 9758712	Exon 3	Yes
CPT2_0039	c.340+1G>A	Intronic	CPT2	SNV	Splice donor	Pathogenic	CPT II	<5	Muscle weakness, Myoglobinuria	23475205, 30455135, 30897730	Intron 3	Yes
CPT2_0040	c.340+3A>T	Intronic	CPT2	SNV	Splice region	Likely Pathogenic	CPT II	<5		28871440, 32928639	Intron 3	No
CPT2_0041	c.340+5G>A	Intronic	CPT2	SNV	Splice region	Likely Pathogenic	CPT II	<5	Muscle weakness, Myalgia, Rhabdomyolysis	12809643, 30455135, 30897730	Intron 3	Yes
CPT2_0042	c.341-2621_1121del	Intronic	CPT2	Deletion	Splice acceptor	Uncertain Significance	CPT II	<5	Atn, Myoglobinuria, Myopathy, Rhabdomyolysis	36109795	Exon 4, Intron 3	No
CPT2_0043	c.341-2A>G	Intronic	CPT2	SNV	Splice acceptor	Pathogenic	CPT II	<5		30957255	Intron 3	Yes
CPT2_0044	c.359A>G	p.Tyr120Cys	CPT2	SNV	Missense	Pathogenic	CPT II	5-10	Elevated circulating creatine kinase concentration, Hypoglycemia, Liver abnormality, Myoglobinuria, Myopathy, Other, Rhabdomyolysis	10862092, 16996287, 18550408	Exon 4	Yes
CPT2_0045	c.362T>A	p.Leu121Gln	CPT2	SNV	Missense	Likely Pathogenic	CPT II	<5	Myoglobinuria	21913903	Exon 4	No
CPT2_0046	c.365C>T	p.Ser122Phe	CPT2	SNV	Missense	Likely Pathogenic	CPT II	<5	Encephalopathy, Febrile episode, Rhabdomyolysis	30514913	Exon 4	Yes
CPT2_0047	c.370C>T	p.Arg124*	CPT2	SNV	Nonsense	Pathogenic	CPT II	5-10	Abnormal renal morphology, Abnormality of metabolism/homeostasis, Arrhythmia, Ca....	16996287, 18645163, 22652984, 24305961, 32463482, 9562964	Exon 4	Yes
CPT2_0049	c.371G>C	p.Arg124Pro	CPT2	SNV	Missense	Pathogenic	CPT II	<5	Abnormality of metabolism/homeostasis, Hyperammonemia, Hypoglycemia, Hypothermia	31638495	Exon 4	Yes
CPT2_0048	c.371G>A	p.Arg124Gln	CPT2	SNV	Missense	Likely Pathogenic	CPT II	<5	Rhabdomyolysis	12673791, 12840153, 21378393, 24898617	Exon 4	Yes
CPT2_0050	c.437A>C	p.Asn146Thr	CPT2	SNV	Missense	Likely Pathogenic	CPT II	<5	Rhabdomyolysis	12673791, 12840153, 21378393	Exon 4	No
CPT2_0051	c.451C>T	p.Arg151Trp	CPT2	SNV	Missense	Pathogenic	CPT II	5-10	Abnormality of metabolism/homeostasis, Cardiac arrest, Cardiac-other, Cardiomyop....	17936304, 28529889, 28801073, 30514913, 32489884	Exon 4	Yes
CPT2_0052	c.452G>A	p.Arg151Gln	CPT2	SNV	Missense	Pathogenic	CPT II	11-20	Exercise intolerance, Hypotonia, Liver abnormality, Muscle spasm, Myalgia, Myogl....	12673791, 14605500, 17936304, 18645163, 21913903, 27843283, 30455135, 30897730, 9758712	Exon 4	Yes
CPT2_0053	c.481C>T	p.Arg161Trp	CPT2	SNV	Missense	Likely Pathogenic	CPT II	5-10	Cardiac arrest, Cola colored urine, Diffuse brain edema, Encephalopathy, General....	12673791, 22854105, 28801073, 30514913, 31235404, 33123633	Exon 4	Yes
CPT2_0054	c.482G>A	p.Arg161Gln	CPT2	SNV	Missense	Likely Pathogenic	CPT II	<5	Anuria, Fever, Malaise/fatigue, Myalgia, Pulmonary/respiratory, Renal insufficiency/failure, Rhabdomyolysis, Urine discoloration	31770251	Exon 4	Yes
CPT2_0055	c.517C>T	p.Pro173Ser	CPT2	SNV	Missense	Uncertain Significance	CPT II	<5	Muscle weakness, Myoglobinuria	21913903	Exon 4	No
CPT2_0056	c.520G>A	p.Glu174Lys	CPT2	SNV	Missense	Pathogenic	CPT II	5-10	Abnormality of metabolism/homeostasis, Arrhythmia, Cardiac arrest, Cardiac-other....	18577113, 22841441, 25919294, 2752669, 28801073, 29552494, 30514913, 35360862, 8682496, 9600456	Exon 4	Yes
CPT2_0057	c.534_558delinsT	p.Leu178_Ile186delinsPhe	CPT2	Delins	Protein altering	Pathogenic	CPT II	11-20	Abnormality of metabolism/homeostasis, Arrhythmia, Cardiac-other, Dandy-walker s....	10862092, 12560872, 16168441, 16996287, 17936304, 21641254, 21913903, 30957255, 9758712	Exon 4	Yes
CPT2_0058	c.563T>C	p.Phe188Ser	CPT2	SNV	Missense	Likely Pathogenic	CPT II	<5	Myalgia, Rhabdomyolysis	15613406	Exon 4	No
CPT2_0059	c.577C>T	p.Arg193Cys	CPT2	SNV	Missense	Likely Pathogenic	CPT II	<5	Limb-girdle muscular dystrophy, Myalgia	26436962	Exon 4	Yes
CPT2_0060	c.587C>T	p.Pro196Leu	CPT2	SNV	Missense	Uncertain Significance	CPT II	<5		35281663	Exon 4	Yes
CPT2_0061	c.593C>G	p.Ser198Cys	CPT2	SNV	Missense	Uncertain Significance	CPT II	<5	Dysphonia, Elevated circulating creatine kinase concentration, Hoarseness, Respiratory tract infection, Visceral leishmaniasis	35572607	Exon 4	No
CPT2_0062	c.602G>A	p.Trp201*	CPT2	SNV	Nonsense	Pathogenic	CPT II	<5	Pain, Rhabdomyolysis	20505667, 30007356	Exon 4	Yes
CPT2_0063	c.611C>T	p.Ala204Val	CPT2	SNV	Missense	Uncertain Significance	CPT II	<5			Exon 4	Yes
CPT2_0064	c.628T>G	p.Tyr210Asp	CPT2	SNV	Missense	Likely Pathogenic	CPT II	<5	Cardiomyopathy	14605500	Exon 4	No
CPT2_0065	c.631C>T	p.Pro211Ser	CPT2	SNV	Missense	Likely Pathogenic	CPT II	<5	Limb-girdle muscle weakness, Muscle weakness, Myalgia, Myoglobinuria, Rhabdomyolysis	35342266	Exon 4	Yes
CPT2_0066	c.638A>G	p.Asp213Gly	CPT2	SNV	Missense	Pathogenic	CPT II	<5	Apnoea, Hypoglycemia, Hypothermia, Lethargy, Poor feeding, Pulmonary/respiratory	15622536, 34626609	Exon 4	Yes
CPT2_0067	c.641T>C	p.Met214Thr	CPT2	SNV	Missense	Pathogenic	CPT II	<5	Rhabdomyolysis	12707442, 28801073, 30514913	Exon 4	Yes
CPT2_0068	c.647A>G	p.Gln216Arg	CPT2	SNV	Missense	Likely Pathogenic	CPT II	<5		21921422	Exon 4	No
CPT2_0069	c.656G>A	p.Arg219Gln	CPT2	SNV	Missense	Uncertain Significance	CPT II	<5		30514913	Exon 4	Yes
CPT2_0070	c.680C>T	p.Pro227Leu	CPT2	SNV	Missense	Pathogenic	CPT II	11-20	Abnormal cerebral cortex morphology, Abnormal renal morphology, Arrhythmia, Bila....	18550408, 25827434, 9758712, None (Abstract only)	Exon 4	Yes
CPT2_0071	c.691C>T	p.Arg231Trp	CPT2	SNV	Missense	Likely Pathogenic	CPT II	<5	Myalgia, Myoglobinuria	16996287, 24602495, 30455135, 30897730	Exon 4	Yes
CPT2_0072	c.733G>A	p.Val245Ile	CPT2	SNV	Missense	Uncertain Significance	CPT II	<5			Exon 4	Yes
CPT2_0073	c.739A>T	p.Arg247Trp	CPT2	SNV	Missense	Likely Pathogenic	CPT II	<5	Exercise intolerance, Myalgia, Myoglobinuria, Renal insufficiency/failure	17936304	Exon 4	Yes
CPT2_0074	c.746del	p.Gly249Glufs*16	CPT2	Deletion	Frameshift	Pathogenic	CPT II	<5	Brain edema, Bulged anterior fontanelle, Lethargy, Seizure, Sudden death	21921422, 25919294	Exon 4	No
CPT2_0075	c.748_749del	p.Asn250Phefs*5	CPT2	Deletion	Frameshift	Pathogenic	CPT II	<5		18925671	Exon 4	Yes
CPT2_0161	c.755A>T	p.Tyr252Phe	CPT2	SNV	Missense	Uncertain Significance	CPT II	<5	Cardiomyopathy, Elevated circulating creatine kinase concentration, Liver abnorm....		Exon 4	Yes
CPT2_0076	c.853G>A	p.Glu285Lys	CPT2	SNV	Missense	Uncertain Significance	CPT II	<5			Exon 4	Yes
CPT2_0162	c.878G>T	p.Ser293Ile	CPT2	SNV	Missense	Uncertain Significance	CPT II	<5	Elevated circulating creatine kinase concentration, Hypoglycemia, Liver abnormality, Rhabdomyolysis		Exon 4	Yes
CPT2_0077	c.886C>T	p.Arg296*	CPT2	SNV	Nonsense	Pathogenic	CPT II	<5	Myalgia, Rhabdomyolysis	14605500, 34394177	Exon 4	Yes
CPT2_0079	c.887G>T	p.Arg296Leu	CPT2	SNV	Missense	Likely Pathogenic	CPT II	<5	Muscle weakness, Myoglobinuria	21913903	Exon 4	No
CPT2_0078	c.887G>A	p.Arg296Gln	CPT2	SNV	Missense	Pathogenic	CPT II	<5	Dehydration, Liver abnormality, Myalgia, Restlessness, Rhabdomyolysis, Seizure, Vomiting	14605500, 35028265	Exon 4	Yes
CPT2_0080	c.896_906dup	p.Arg303Glyfs*8	CPT2	Duplication	Frameshift	Pathogenic	CPT II	<5		35360862	Exon 4	Yes
CPT2_0081	c.921_923del	p.Met307_Ser308delinsIle	CPT2	Deletion	Deletion	Uncertain Significance	CPT II	<5			Exon 4	Yes
CPT2_0082	c.930C>T	p.Gly310=	CPT2	SNV	Silent	Uncertain Significance	CPT II	<5		16996287	Exon 4	Yes
CPT2_0083	c.969_970del	p.Phe323Leufs*6	CPT2	Deletion	Frameshift	Pathogenic	CPT II	<5	Cardiac arrest, Lost consciousness, Reyes-like syndrome	28649538	Exon 4	No
CPT2_0084	c.977G>A	p.Cys326Tyr	CPT2	SNV	Missense	Uncertain Significance	CPT II	<5	Myoglobinuria	21913903	Exon 4	Yes
CPT2_0085	c.983A>G	p.Asp328Gly	CPT2	SNV	Missense	Pathogenic	CPT II	5-10	Arrhythmia, Cardiomyopathy, Gastrointestinal-other, Hypoglycemia, Hyporeactivity, Hypotonia, Liver abnormality, Renal insufficiency/failure	12673791, 12840153, 14634971, 21378393	Exon 4	Yes
CPT2_0086	c.989dup	p.Ile332Hisfs*2	CPT2	Duplication	Frameshift	Pathogenic	CPT II	<5		35360862	Exon 4	Yes
CPT2_0087	c.1048C>T	p.Arg350Cys	CPT2	SNV	Missense	Uncertain Significance	CPT II	<5	Elevated circulating creatine kinase concentration, Myopathy, Rhabdomyolysis		Exon 4	Yes
CPT2_0088	c.1054T>C	p.Phe352Leu	CPT2	SNV	Missense	Likely Pathogenic	CPT II	<5		35360862	Exon 4	No
CPT2_0089	c.1073T>G	p.Leu358Arg	CPT2	SNV	Missense	Likely Pathogenic	CPT II	<5	Apnoea, Hypoglycemia, Hypothermia, Lethargy, Poor feeding, Pulmonary/respiratory	34626609	Exon 4	No
CPT2_0090	c.1115_1116delinsTT	p.His372Leu	CPT2	Delins	Missense	Uncertain Significance	CPT II	<5			Exon 4	Yes
CPT2_0091	c.1117T>C	p.Ser373Pro	CPT2	SNV	Missense	Likely Pathogenic	CPT II	<5	Cerebral palsy, Hemiparesis, Mild cognitive delay, Muscle weakness, Myopathy, Rhabdomyolysis	30149802	Exon 4	No
CPT2_0092	c.1121G>A	p.Trp374*	CPT2	SNV	Nonsense	Pathogenic	CPT II	<5	Gastrointestinal-other	28801073	Exon 4	Yes
CPT2_0163	c.1124G>T	p.Gly375Val	CPT2	SNV	Missense	Uncertain Significance	CPT II	<5	Elevated circulating creatine kinase concentration, Myopathy, Peripheral neuropathy		Exon 4	Yes
CPT2_0093	c.1130G>A	p.Gly377Asp	CPT2	SNV	Missense	Likely Pathogenic	CPT II	<5	Pain, Rhabdomyolysis	20505667, 30007356	Exon 4	No
CPT2_0094	c.1145G>A	p.Arg382Lys	CPT2	SNV	Missense	Uncertain Significance	CPT II	<5		10607472	Exon 4	Yes
CPT2_0164	c.1145G>C	p.Arg382Thr	CPT2	SNV	Missense	Uncertain Significance	CPT II	<5	Cardiomyopathy, Liver abnormality		Exon 4	Yes
CPT2_0095	c.1148T>A	p.Phe383Tyr	CPT2	SNV	Missense	Pathogenic	CPT II	30+	Abnormality of metabolism/homeostasis, Acute muscle weakness, Ankle dorsiflexor ....	12673791, 17709715, 18363739, 21227726, 22854105, 23700290, 25919294, 27363342, 28516040, 28649538, 28747690, 28801073, 29552494, 30514913, 31372341, 32489884, 34394177, 34539730, 8682496, 9600456	Exon 4	Yes
CPT2_0096	c.1171A>G	p.Ser391Gly	CPT2	SNV	Missense	Uncertain Significance	CPT II	<5	Myalgia, Renal insufficiency/failure, Rhabdomyolysis	29478820	Exon 4	No
CPT2_0097	c.1223_1224del	p.Ser408Tyrfs*13	CPT2	Deletion	Frameshift	Pathogenic	CPT II	<5	Malaise/fatigue, Myalgia, Pulmonary/respiratory, Renal insufficiency/failure, Rhabdomyolysis, Urine discoloration	15754283, 18363739	Exon 4	Yes
CPT2_0098	c.1234G>T	p.Val412Leu	CPT2	SNV	Missense	Uncertain Significance	CPT II	<5	Myalgia	35342266	Exon 4	Yes
CPT2_0099	c.1239G>A	p.Gln413=	CPT2	SNV	Silent	Uncertain Significance	CPT II	<5	Asthenia, Muscle stiffness, Myalgia, Myoglobinuria	20810031	Exon 4	No
CPT2_0006	c.1239_1240delGA	p.Lys414Thrfs*7	CPT2	Deletion	Frameshift	Pathogenic	CPT II	<5	Abnormal renal morphology, Abnormality of metabolism/homeostasis, Arrhythmia, Ca....	12410208	Exon 4	Yes
CPT2_0100	c.1239_1240del	p.Lys414Thrfs*7	CPT2	Deletion	Frameshift	Pathogenic	CPT II	30+	Abnormal renal morphology, Abnormality of metabolism/homeostasis, Absence of cor....	10090476, 10398218, 11477613, 12362414, 12673791, 12707442, 14970749, 16996287, 18645163, 19335026, 21913903, 24602495, 28871440, 30455135, 30897730, 31428121, 31624327, 32928639	Exon 4	Yes
CPT2_0165	c.1259C>G	p.Thr420Ser	CPT2	SNV	Missense	Uncertain Significance	CPT II	<5			Exon 4	Yes
CPT2_0101	c.1273_1274del	p.Thr425Trpfs*6	CPT2	Deletion	Frameshift	Pathogenic	CPT II	<5		16996287	Exon 4	Yes
CPT2_0102	c.1301T>C	p.Phe434Ser	CPT2	SNV	Missense	Uncertain Significance	CPT II	<5		35360862	Exon 4	No
CPT2_0009	c.1333T>C	p.Cys445Arg	CPT2	SNV	Missense	Uncertain Significance	CPT II	<5		30881520	Exon 4	Yes
CPT2_0103	c.1342T>C	p.Phe448Leu	CPT2	SNV	Missense	Uncertain Significance	CPT II	21-30	Abnormal renal morphology, Cardiac-other, Elevated circulating creatine kinase c....	10090476, 10398218, 12673791, 12707442, 19335026, 28871440, 31624327, 32928639	Exon 4	Yes
CPT2_0104	c.1345C>A	p.Gln449Lys	CPT2	SNV	Missense	Uncertain Significance	CPT II	<5	Hypoglycemia	28801073, 30514913	Exon 4	No
CPT2_0105	c.1348A>T	p.Arg450*	CPT2	SNV	Nonsense	Pathogenic	CPT II	<5	Asthenia, Elevated circulating creatine kinase concentration, Exercise intoleran....	20810031, 21913903, 31517061	Exon 4	Yes
CPT2_0003	c.1352G>A	p.Gly451Glu	CPT2	SNV	Missense	Uncertain Significance	CPT II	<5	Myoglobinuria	23475205	Exon 4	No
CPT2_0106	c.1369A>T	p.Lys457*	CPT2	SNV	Nonsense	Pathogenic	CPT II	<5	Chest tightness, Decreased feeding, Myalgia, Myoglobinuria, Pain, Vomiting	16996287, 30094188, 33123633, 34449523	Exon 4	Yes
CPT2_0107	c.1420G>C	p.Ala474Pro	CPT2	SNV	Missense	Uncertain Significance	CPT II	<5	Myalgia, Renal insufficiency/failure, Rhabdomyolysis	29478820	Exon 4	No
CPT2_0108	c.1429C>T	p.Arg477Trp	CPT2	SNV	Missense	Uncertain Significance	CPT II	<5	Hyperck, Rhabdomyolysis	28801073, 29552494, 31372341	Exon 4	Yes
CPT2_0109	c.1436A>G	p.Tyr479Cys	CPT2	SNV	Missense	Likely Pathogenic	CPT II	<5		18925671	Exon 4	Yes
CPT2_0005	c.1436A>T	p.Tyr479Phe	CPT2	SNV	Missense	Likely Pathogenic	CPT II	<5	Myoglobinuria	12707442, 24602495	Exon 4	Yes
CPT2_0110	c.1438G>A	p.Gly480Arg	CPT2	SNV	Missense	Uncertain Significance	CPT II	<5		16996287	Exon 4	Yes
CPT2_0111	c.1444_1447del	p.Thr482Trpfs*49	CPT2	Deletion	Frameshift	Pathogenic	CPT II	<5		16996287, 33123633	Exon 4	Yes
CPT2_0112	c.1459G>A	p.Glu487Lys	CPT2	SNV	Missense	Likely Pathogenic	CPT II	<5	Myalgia, Myoglobinuria, Pigmenturia	10868782, 30455135, 30897730	Exon 4	Yes
CPT2_0113	c.1460A>C	p.Glu487Ala	CPT2	SNV	Missense	Pathogenic	CPT II	<5			Exon 4	Yes
CPT2_0114	c.1489G>A	p.Gly497Ser	CPT2	SNV	Missense	Pathogenic	CPT II	<5	Muscle switching, Myalgia, Myoglobinuria	23911907, 30887117	Exon 4	Yes
CPT2_0115	c.1493G>T	p.Arg498Leu	CPT2	SNV	Missense	Uncertain Significance	CPT II	<5	Anuria, Fever, Malaise/fatigue, Myalgia, Pulmonary/respiratory, Renal insufficiency/failure, Rhabdomyolysis, Urine discoloration	31770251	Exon 4	No
CPT2_0116	c.1505T>C	p.Ile502Thr	CPT2	SNV	Missense	Pathogenic	CPT II	5-10	Myoglobinuria	10398215, 10862092, 30957255	Exon 4	Yes
CPT2_0117	c.1507C>T	p.Arg503Cys	CPT2	SNV	Missense	Pathogenic	CPT II	11-20	Abnormality of metabolism/homeostasis, Cardiac-other, Carnitine palmitoyltransfe....	10090476, 10398218, 10873395, 11001791, 17372854, 19762733, 21913903, 8515756	Exon 4	Yes
CPT2_0118	c.1511C>T	p.Pro504Leu	CPT2	SNV	Missense	Pathogenic	CPT II	11-20	Abnormality of metabolism/homeostasis, Acute cardiomyopathy, Cardiac-other, Cere....	16996287, 17936304, 18306170, 18550408, 26537576, 28801073, 28871440, 30514913, 31638495, 32928639	Exon 4	Yes
CPT2_0119	c.1525A>G	p.Thr509Ala	CPT2	SNV	Missense	Likely Benign	CPT II	<5		28801073, 30514913	Exon 4	No
CPT2_0120	c.1547T>C	p.Phe516Ser	CPT2	SNV	Missense	Pathogenic	CPT II	<5	Asthenia, Contractures, Encephalopathy, Muscle spasm, Muscle weakness, Myalgia, Myoglobinuria, Pulmonary/respiratory, Seizure	20810031, 21913903, 35281663	Exon 4	Yes
CPT2_0121	c.1569_1570del	p.His523Glnfs*4	CPT2	Deletion	Frameshift	Pathogenic	CPT II	<5		16996287	Exon 4	Yes
CPT2_0122	c.1579G>A	p.Glu527Lys	CPT2	SNV	Missense	Uncertain Significance	CPT II	<5	Myalgia, Rhabdomyolysis	28801073	Exon 4	No
CPT2_0123	c.1634A>C	p.Glu545Ala	CPT2	SNV	Missense	Conflict	CPT II	<5	Rhabdomyolysis	20952238, 28801073, 30514913	Exon 4	Yes
CPT2_0124	c.1634_1636del	p.Glu545del	CPT2	Deletion	Deletion	Uncertain Significance	CPT II	<5		16996287	Exon 4	No
CPT2_0125	c.1645+5G>A	Intronic	CPT2	SNV	Splice region	Uncertain Significance	CPT II	<5		16996287	Intron 4	No
CPT2_0126	c.1645+20C>T	Intronic	CPT2	SNV	Intronic	Uncertain Significance	CPT II	<5			Intron 4	Yes
CPT2_0127	c.1646-1G>T	Intronic	CPT2	SNV	Splice acceptor	Pathogenic	CPT II	<5		30957255	Intron 4	No
CPT2_0128	c.1646G>A	p.Gly549Asp	CPT2	SNV	Missense	Pathogenic	CPT II	<5		10398218, 16996287	Exon 5	Yes
CPT2_0129	c.1647_1650del	p.Gln550Alafs*32	CPT2	Deletion	Frameshift	Pathogenic	CPT II	<5	Myoglobinuria	24602495	Exon 5	No
CPT2_0130	c.1649A>G	p.Gln550Arg	CPT2	SNV	Missense	Uncertain Significance	CPT II	<5		9758712	Exon 5	No
CPT2_0131	c.1657G>A	p.Asp553Asn	CPT2	SNV	Missense	Pathogenic	CPT II	<5	Myoglobinuria	17936304, 7711730	Exon 5	Yes
CPT2_0132	c.1660C>T	p.Arg554*	CPT2	SNV	Nonsense	Pathogenic	CPT II	<5	Myoglobinuria	17936304	Exon 5	Yes
CPT2_0133	c.1665C>G	p.His555Gln	CPT2	SNV	Missense	Uncertain Significance	CPT II	<5	Lethargy, Muscle spasm, Muscle weakness, Myalgia, Urine discoloration	29744303	Exon 5	Yes
CPT2_0134	c.1666_1667del	p.Leu556Valfs*16	CPT2	Deletion	Frameshift	Pathogenic	CPT II	5-10	Diarrhea, Muscle weakness, Myalgia, Renal insufficiency/failure, Rhabdomyolysis	28871440, 29478820, 32928639	Exon 5	Yes
CPT2_0135	c.1678C>T	p.Arg560Trp	CPT2	SNV	Missense	Likely Pathogenic	CPT II	<5	Rhabdomyolysis	30514913	Exon 5	Yes
CPT2_0136	c.1679G>A	p.Arg560Gln	CPT2	SNV	Missense	Likely Pathogenic	CPT II	<5		16996287	Exon 5	Yes
CPT2_0137	c.1711C>A	p.Pro571Thr	CPT2	SNV	Missense	Pathogenic	CPT II	5-10		28771436, 35360862	Exon 5	Yes
CPT2_0138	c.1724T>C	p.Leu575Pro	CPT2	SNV	Missense	Likely Pathogenic	CPT II	<5	Asthenia, Malaise/fatigue, Muscle weakness, Myoglobinuria, Pulmonary/respiratory	20810031, 21913903	Exon 5	No
CPT2_0139	c.1727A>G	p.Asp576Gly	CPT2	SNV	Missense	Likely Pathogenic	CPT II	<5	Myoglobinuria	17936304	Exon 5	No
CPT2_0140	c.1737del	p.Tyr579*	CPT2	Deletion	Frameshift	Pathogenic	CPT II	<5	Arrhythmia, Cardiac-other, Cyanosis, Intra-alveolar hemorrhage, Liver abnormality, Pleural effusion	18577113	Exon 5	Yes
CPT2_0141	c.1749C>A	p.Asn583Lys	CPT2	SNV	Missense	Uncertain Significance	CPT II	<5		34539730	Exon 5	Yes
CPT2_0142	c.1763C>G	p.Ser588Cys	CPT2	SNV	Missense	Likely Benign	CPT II	<5		16996287	Exon 5	Yes
CPT2_0002	c.1769G>A	p.Ser590Asn	CPT2	SNV	Missense	Likely Pathogenic	CPT II	<5	Myalgia, Myoglobinuria	23475205	Exon 5	Yes
CPT2_0143	c.1784del	p.Pro595Glnfs*3	CPT2	Deletion	Frameshift	Pathogenic	CPT II	<5	Abnormal renal morphology, Developmental delay, Periventricular calcifications, ....	18550408, 22899091	Exon 5	Yes
CPT2_0144	c.1798G>A	p.Gly600Arg	CPT2	SNV	Missense	Pathogenic	CPT II	<5		33123633	Exon 5	Yes
CPT2_0145	c.1803del	p.Phe602Leufs*20	CPT2	Deletion	Frameshift	Pathogenic	CPT II	<5	Abnormality of metabolism/homeostasis, Hypoglycemia, Liver abnormality	23700290	Exon 5	No
CPT2_0146	c.1806del	p.Phe602Leufs*20	CPT2	Deletion	Frameshift	Pathogenic	CPT II	<5	Abnormal renal morphology, Liver abnormality, Micrognathia, Oligohydramnios, Pulmonary/respiratory	31599017	Exon 5	Yes
CPT2_0147	c.1810C>T	p.Pro604Ser	CPT2	SNV	Missense	Likely Pathogenic	CPT II	<5		16996287, 9758712	Exon 5	Yes
CPT2_0148	c.1813G>C	p.Val605Leu	CPT2	SNV	Missense	Pathogenic	CPT II	5-10	Cardiac arrest, Coma, Encephalopathy, Hypoglycemia, Hypotonia, Loss of conscious....	18306170, 18363739, 28649538, 28801073, 30514913	Exon 5	Yes
CPT2_0149	c.1816_1817del	p.Val606Leufs*2	CPT2	Deletion	Frameshift	Pathogenic	CPT II	<5		16996287	Exon 5	Yes
CPT2_0150	c.1822G>C	p.Asp608His	CPT2	SNV	Missense	Likely Pathogenic	CPT II	<5	Pain, Rhabdomyolysis	12673791, 20505667	Exon 5	Yes
CPT2_0151	c.1838G>A	p.Gly613Glu	CPT2	SNV	Missense	Uncertain Significance	CPT II	<5	Abnormal renal morphology, Cardiomyopathy, Hypoglycemia, Iugr	28468868	Exon 5	No
CPT2_0152	c.1858T>C	p.Trp620Arg	CPT2	SNV	Missense	Uncertain Significance	CPT II	<5			Exon 5	Yes
CPT2_0153	c.1883A>C	p.Tyr628Ser	CPT2	SNV	Missense	Pathogenic	CPT II	5-10	Abnormality of metabolism/homeostasis, Arrhythmia, Cardiac arrest, Cardiac-other....	10398215, 10734268, 12673791, 15613406, 1999498, 20661589, 21378393, 8651281	Exon 5	Yes
CPT2_0154	c.1891C>T	p.Arg631Cys	CPT2	SNV	Missense	Pathogenic	CPT II	30+	Cardiac-other, Cardiomyopathy, Coma, Dehydration, Exercise intolerance, Fever, H....	1528846, 15754283, 16996287, 17651973, 17936304, 18363739, 18645163, 20810031, 21913903, 28801073, 32463482, 35028265, 35372350, 36422281	Exon 5	Yes
CPT2_0155	c.1892G>A	p.Arg631His	CPT2	SNV	Missense	Likely Pathogenic	CPT II	<5	Muscle weakness, Myalgia, Rhabdomyolysis	35256318	Exon 5	Yes
CPT2_0156	c.1925_1937del	p.Lys642Thrfs*6	CPT2	Deletion	Frameshift	Pathogenic	CPT II	<5	Abnormal renal morphology, Abnormality of metabolism/homeostasis, Absence of cor....	18550408	Exon 5	Yes
CPT2_0157	c.1931T>C	p.Leu644Ser	CPT2	SNV	Missense	Likely Pathogenic	CPT II	<5	Cardiac arrest	21227726	Exon 5	No
CPT2_0158	c.1932dup	p.Glu645Argfs*5	CPT2	Duplication	Frameshift	Pathogenic	CPT II	5-10	Elevated circulating creatine kinase concentration, Myalgia, Myoglobinuria, Rhabdomyolysis, Seizure	17936304, 20810031, 21913903	Exon 5	Yes
CPT2_0159	c.1933G>T	p.Glu645*	CPT2	SNV	Nonsense	Pathogenic	CPT II	<5	Rhabdomyolysis	30514913	Exon 5	No
CPT2_0160	c.1964C>A	p.Ser655Tyr	CPT2	SNV	Missense	Uncertain Significance	CPT II	<5	Elevated circulating creatine kinase concentration, Myopathy		Exon 5	Yes

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Column Name	Table View	Detail View
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

Notes:

* Click the PMID number to go to the corresponding publication.
* All variants are referencing NM_000098.3 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

References:

Verderio, E. et al., Carnitine palmitoyltransferase II deficiency: structure of the gene and characterization of two novel disease-causing mutations. Human Mol Genet. 1995 Jan;4(1):19-29.
https://www.ncbi.nlm.nih.gov/gene/1376
https://www.omim.org/entry/600650?search=cpt2&highlight=cpt2
Yasuno et al. Biochem Biophys Res Commun. 2014 30;448(2):175-81
Violante, S. et al., Carnitine palmitoyltransferase 2: New insights on the substrate specificity and implications for acylcarnitine profiling. Biochim Biophys Acta. 2010 Sep;1802(9):728-32.
https://www.uniprot.org/uniprotkb/P23786/entry#expression
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).

Carnitine Palmitoyltransferase II (CPT II) Deficiency

Introduction

Variant List

Gene Structure

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