Carnitine Deficiency Workup

Updated: Dec 13, 2019
  • Author: Fernando Scaglia, MD, FACMG; Chief Editor: Maria Descartes, MD  more...
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Laboratory Studies

If the patient is suspected of having primary carnitine deficiency or other metabolic disorders associated with secondary carnitine deficiency and is presenting with a metabolic emergency, the following studies are indicated:

  • Immediate assessment: Immediately check blood glucose and urine ketones if a child presents to the emergency room with lethargy, seizures, apnea, or any episode of decreased consciousness. The absence or low amounts of ketones in the urine, combined with the episode of hypoglycemia in primary carnitine deficiency (as well as in other defects in the carnitine cycle or fatty acid oxidation), causes secondary carnitine deficiency.

  • Ammonia level, liver enzymes (ie, aspartate aminotransferase [AST], alanine aminotransferase [ALT], glutamyltransferase [GGT]), chemistry panel, uric acid, creatine kinase (CK), lactic acid, and coagulation tests

    • Ammonia levels can be moderately elevated, especially in primary carnitine deficiency and particularly if the child has a presentation similar to that of Reye syndrome.

    • Transaminases are usually moderately elevated in primary carnitine deficiency.

    • In some defects of the carnitine cycle that cause secondary carnitine deficiency (eg, CPT-II deficiency), a hepatocardiomuscular form can present with liver involvement. Other fatty acid oxidation disorders, such as long-chain 3-hydroxyacyl-CoA dehydrogenase (LCHAD) deficiency, can present with liver involvement.

    • A chemistry panel may show evidence of metabolic acidosis.

    • Hyperuricemia may be present in carnitine deficiency because carnitine competes for renal tubular excretion.

    • Elevated serum CK levels may be observed in primary carnitine deficiency and in fatty acid oxidation disorders.

    • Elevated lactate can be observed in respiratory chain defects or in LCHAD deficiency.

    • Altered coagulation with prolonged prothrombin time may be found.

  • Plasma carnitine level: In primary carnitine deficiency, the carnitine level in plasma is usually less than 5% of normal, with acylcarnitines proportionately reduced. The ratio between acylcarnitine and free carnitine is normal. A feature of most fatty acid oxidation disorders is that they are associated with decreased plasma carnitine concentrations. This feature is also observed in other inborn errors of metabolism that cause secondary carnitine deficiency, such as organic acidemias caused by the formation of carnitine esters.

  • Urine carnitine level: This is only useful in primary carnitine deficiency in which the transporter in kidney cells has decreased capacity for reabsorption, causing increased carnitine excretion.

  • Newborn screen (see Other Tests): Recently, several patients with primary carnitine deficiency have been ascertained through newborn screening programs. In these cases, the acylcarnitine profile reveals a low level of free carnitine and all acylcarnitine species. However, plasma carnitine levels can be within the reference range if obtained too early, due to the transfer of carnitine through the placenta to the fetus.

  • Urine organic acid levels: In primary carnitine deficiency, the urine organic acid analysis usually is normal. In cases of fatty acid oxidation disorders that cause secondary carnitine deficiency, inappropriate dicarboxylic aciduria occurs during periods of illness. Urinary organic acid profile usually is normal in these patients when they are well, except in cases of medium-chain 3-hydroxyacyl-CoA dehydrogenase (MCAD) deficiency. In some disorders (eg, MCAD, LCHAD, short-chain acyl-CoA dehydrogenase [SCAD] deficiency) specific patterns can be seen. Collecting this specimen during illness is important.

  • Urine acylglycine level: In MCAD deficiency, the urine contains increased amounts of glycine conjugates. The test may also be used in individuals with suspected glutaric aciduria type II or SCAD deficiency.

  • Acylcarnitine profile and free fatty acid levels: Tandem mass spectrometry analyses of acylcarnitine profile and free fatty acids may be used to detect metabolic defects that cause secondary carnitine deficiency (eg, fatty acid oxidation disorders, organic acidemias) because acyl-CoA intermediates proximal to the block in fatty acid or amino acid oxidative pathway may be transesterified to carnitine. Modest amounts of long-chain 3-hydroxy fatty acids consistently are found in the plasma of patients with LCHAD deficiency, even if these patients are asymptomatic.

  • Fasting test: In a fasting test, patients undergo a controlled and prolonged fast under strict medical supervision. Take blood samples at regular intervals to measure glucose, ketone bodies, and free fatty acids. Acylcarnitine profile may be obtained at the same time. Fasting may be continued in children for up to 24 hours, unless blood glucose drops to less than 3 mmol/L. An inadequate production of ketones with a high free fatty acid–to–ketone bodies ratio suggests a defect in long-chain fatty acid oxidation.

  • Fatty acid oxidation study: This is used if a fatty acid oxidation defect is suspected. The most appropriate first line of investigation in these patients is to study the entire fatty acid oxidation pathway. Methods involve (1) monitoring the rate of production of radioactive end products of fatty acid oxidation disorders for radiolabeled precursor fatty acids or (2) measuring by tandem mass spectrometry the disease-specific acylcarnitines produced when stable isotope fatty acid precursors are incubated with cells in the presence of excess L-carnitine. [11]

  • Enzyme assay: This criterion standard for demonstrating an enzyme defect measures the activity in cultured fibroblasts or in some other tissue, such as muscle or liver. To account for the frequent finding of overlapping chain-length specificities, complex analysis using a mixture of different chain-length substrates and immunoprecipitation with antibodies to different enzymes is required.

  • Carnitine transport assay: Carnitine transport assay in cultured fibroblasts specifically demonstrates the absence of active carnitine transport in cultured fibroblasts. This finding is specific for primary carnitine deficiency.

  • Molecular diagnosis: Molecular diagnosis provides information on the gene for the carnitine transporter defective in primary carnitine deficiency, which has been cloned (SLC22A5) and can be screened for mutations. Most patients have private mutations. However, the R245X mutation has been found in Taiwanese, Saudi, and Lebanese kindreds. [12] The R245X and V295X mutations are associated with cardiomyopathy as the only clinical phenotype. Phenotypic variability has been observed among patients harboring the same mutations raising the possibility of modifier genes or epigenetic factors as responsible for these differences.

  • Mutation analysis: The genes for most of the enzymes of fatty acid oxidation that are defective in fatty acid oxidation disorders and may cause secondary carnitine deficiency have been identified, and mutation analysis is available for numerous genes (eg, CPT1, CPT2, VLCAD, TFP, MCAD). Prevalent mutations have been identified in patients with MCAD deficiency (A985G) and LCHAD deficiency (G1528C). In the adult form of CPT-II deficiency, a C439T mutation accounts for 60% of mutations in patients with adult onset.


Imaging Studies

The following imaging studies may be indicated:

  • Roentgenograms reveal cardiac enlargement in primary carnitine deficiency and fatty acid oxidation disorders, such as LCHAD or very long-chain acyl-CoA dehydrogenase (VLCAD) deficiency, which may cause secondary carnitine deficiency.

  • In primary carnitine deficiency (as well as in fatty acid oxidation disorders, which also may present with cardiomyopathy), the echocardiogram may reveal cardiac enlargement and increased thickness of the left ventricular wall.

  • Brain imaging studies (eg, cranial ultrasound, brain MRI) may show cystic lesions in glutaric aciduria type II or basal ganglia involvement in mitochondrial disorders that may be associated with secondary carnitine deficiency.


Other Tests

The following other tests may be indicated:

  • ECG: The ECG reveals left ventricular hypertrophy and peaked T waves in primary carnitine deficiency. Cardiac arrhythmias can be observed in translocase deficiency and in the lethal neonatal form of carnitine palmitoyltransferase II (CPT-II) deficiency.

  • Newborn screen

    • Primary carnitine deficiency can be identified in infants by expanded newborn screening using tandem mass spectrometry by detection of low levels of free carnitine (C0). In addition, newborns’ low carnitine levels may result from primary carnitine deficiency in their affected mothers.

    • Pediatrician needs to contact the family to inform them of the newborn screening result and ascertain clinical status and whether the newborn presents with poor feeding, lethargy, or tachypnea.

    • Consultation with a pediatric metabolic specialist has to be immediately activated and the newborn should be evaluated for tachycardia, hepatomegaly, or reduced muscle tone. After obtaining confirmatory testing with total and free plasma carnitine levels in the newborn and mother, carnitine supplementation with 100 mg/kg/d by mouth in 3 divided doses should be initiated by the metabolic specialist.

    • Confirmatory and diagnostic testing can be performed with carnitine uptake assay in cultured fibroblasts and SLC22A5 gene sequencing.

    • Clinical availability of SLC22A5 gene sequencing may preclude the need of a skin biopsy and carnitine uptake assay on cultured fibroblasts.

    • The family has to be educated about signs, symptoms and need for urgent treatment if infant becomes ill.



Skin biopsy can be performed to confirm diagnosis of primary carnitine deficiency by demonstrating reduced carnitine transport in fibroblasts that express the transporter. Fibroblasts may be used for fatty acid oxidation studies or enzyme assay. However, with the clinical availability of SLC22A5 sequencing, it may not be strictly necessary to perform a skin biopsy for the transport assay on cultured fibroblasts.

Muscle biopsy may be necessary to confirm the diagnosis of some conditions that may cause secondary carnitine deficiency (eg, respiratory chain defect) or to measure the carnitine concentration in muscle in cases of myopathic carnitine deficiency.


Histologic Findings

Biopsy of the liver may show microvesicular lipid steatosis that, along with the rest of the clinical picture, may lead to a diagnosis of Reye syndrome. If muscle biopsy is performed, very low fatty infiltration may be seen.