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CPT2 Gene Carnitine palmitoyltransferase 2 deficiency, infantile NGS Genetic Test

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CPT2 Gene Carnitine palmitoyltransferase 2 deficiency, infantile NGS Genetic Test

Short Name: CPT2 Gene NGS Test

Also known as: CPT II Deficiency Genetic Test, Carnitine Palmitoyltransferase II Gene Sequencing, CPT2 Mutation Analysis, CPT2 NGS Sequencing Test, Infantile CPT2 Deficiency Panel

CPT2 Gene Carnitine palmitoyltransferase 2 deficiency, infantile NGS Genetic Test test available at DNA Labs India for ₹20,000. Uses Next-Generation Sequencing (NGS), Sanger Sequencing (confirmation of detected variants) on Blood or Extracted DNA or One drop Blood on FTA Card samples. Results in Results are typically available within 3 to 4 weeks from the date of sample collection. You will be notified via your preferred communication channel (online portal, email, or WhatsApp) once your report is ready.. Free home collection in 300+ cities across India.

NGS Genetic TestAll Ages🏠 Home Collection

✍️ Written By

🩺 Medically Reviewed By

Dr SULOCHANA HEMCHANDRA HOLLA

Dr SULOCHANA HEMCHANDRA HOLLA

Consultant Medical Geneticist · Reg: 8532

Last reviewed: September 7, 2026

Overview

The purpose of the CPT2 Gene NGS Genetic Test is to identify pathogenic or likely pathogenic variants in the CPT2 gene that are responsible for carnitine palmitoyltransferase 2 deficiency. This test enables accurate molecular diagnosis of the infantile form of CPT2 deficiency, facilitates carrier testing for family members, supports genetic counselling regarding inheritance patterns and recurrence risks, and guides clinical management strategies including dietary modifications and emergency treatment protocols to prevent metabolic decompensation.

Test Code
1906
CPT Code
81404
ICD Code
E71.312
Price
₹20,000
Sample Type
Blood or Extracted DNA or One drop Blood on FTA Card
Result Time
Results are typically available within 3 to 4 weeks from the date of sample collection. You will be notified via your preferred communication channel (online portal, email, or WhatsApp) once your report is ready.
Fasting Required
No
Method
Next-Generation Sequencing (NGS), Sanger Sequencing (confirmation of detected variants)
Step 1

Sample Collection

A genetic counselling session is recommended prior to sample collection to draw a detailed pedigree chart of family members affected with CPT2 deficiency or related metabolic disorders. Clinical history of the patient, including presenting symptoms, family history, and any prior metabolic workup results, should be documented. No fasting is required for this genetic test.

Method: Venipuncture / Heel-stick (neonates)

Step 2

Laboratory Analysis

A blood sample (3–5 mL) is collected via venipuncture into an EDTA (lavender-top) tube. For neonates, a heel-stick blood collection onto an FTA card is an acceptable alternative. The sample should be gently mixed with the anticoagulant and labelled correctly with patient details.

Step 3

Report Delivery

The sample is transported to the laboratory under ambient room temperature conditions. DNA is extracted and subjected to NGS-based sequencing of the CPT2 gene. Results are typically available within 3 to 4 weeks and are delivered via the online portal, email, or WhatsApp.

Timeline: Results are typically available within 3 to 4 weeks from the date of sample collection. You will be notified via your preferred communication channel (online portal, email, or WhatsApp) once your report is ready.

Patient Instructions

1
Before the Test:Prior to testing, a genetic counselling session is recommended to document the patient's clinical history, presenting symptoms, family history, and to construct a pedigree chart of family members affected with CPT2 deficiency or related metabolic disorders. No fasting is required. Inform the laboratory about any recent blood transfusions.
2
During the Test:A small blood sample (3–5 mL) is drawn via venipuncture into an EDTA tube, or a heel-stick blood sample is collected onto an FTA card for neonates. The procedure is minimally invasive and takes only a few minutes. DNA is then extracted in the laboratory for NGS analysis.
3
After the Test:After sample collection, normal activities can be resumed immediately. The sample undergoes DNA extraction and next-generation sequencing of the CPT2 gene. Results are typically available within 3 to 4 weeks and will be communicated via the online portal, email, or WhatsApp. A post-test genetic counselling session is recommended to interpret results and discuss management options.

About This Test

Who Should Get This Test

The purpose of the CPT2 Gene NGS Genetic Test is to identify pathogenic or likely pathogenic variants in the CPT2 gene that are responsible for carnitine palmitoyltransferase 2 deficiency. This test enables accurate molecular diagnosis of the infantile form of CPT2 deficiency, facilitates carrier testing for family members, supports genetic counselling regarding inheritance patterns and recurrence risks, and guides clinical management strategies including dietary modifications and emergency treatment protocols to prevent metabolic decompensation.

How to Prepare

  • No fasting is required prior to sample collection.
  • A pre-test genetic counselling session is strongly recommended to document family history and draw a pedigree chart.
  • For venipuncture: 3–5 mL of blood in an EDTA (lavender-top) tube. For neonates: heel-stick blood on FTA card is acceptable.
  • Gently invert the EDTA tube 8–10 times immediately after collection to prevent clotting.
  • Ensure the sample is correctly labelled with the patient's full name, date of birth, and unique identifier.
  • Store and transport the sample at ambient room temperature (15–30°C). Avoid extreme heat or cold.
  • Inform the laboratory of any recent blood transfusions (within the last 120 days), as this may affect results.

Doctor's Notes

Reviewed by — MBBS, MD (Medical Genetics) · Reg. No. 8532

"Infantile-onset CPT2 deficiency is a life-threatening metabolic emergency. Early genetic diagnosis through NGS testing allows for timely dietary interventions—such as avoidance of prolonged fasting and use of medium-chain triglyceride (MCT) supplementation—that can prevent fatal metabolic crises. Families with a confirmed genetic diagnosis can also benefit from prenatal and preconception counselling for future pregnancies. I strongly recommend CPT2 gene testing for any infant presenting with unexplained hypoglycemia, hepatomegaly, or cardiomyopathy, particularly when triggered by fasting or intercurrent illness."

Last medically reviewed: September 7, 2026

Test Parameters & Specifications

Sample TypeBlood or Extracted DNA or One drop Blood on FTA Card
Sample Volume3–5 mL
ContainerEDTA Tube (Lavender/Purple Top) or FTA Card
Collection MethodVenipuncture / Heel-stick (neonates)

Sample Stability

EDTA whole blood: Stable at 15–30°C for up to 7 days; at 2–8°C for up to 14 days.
Extracted DNA: Stable at 2–8°C for up to 6 months; at -20°C for long-term storage.
FTA Card with blood spot: Stable at room temperature for up to several years when stored dry.
Sample Rejection Criteria:
  • Clotted blood sample (failure to mix with EDTA anticoagulant)
  • Severely hemolyzed or lipemic sample
  • Insufficient sample volume (less than 1 mL for DNA extraction)
  • Sample received without proper patient identification or labelling
  • Sample collected in incorrect container (e.g., heparin tube instead of EDTA)
  • Sample contaminated or showing signs of microbial growth

Understanding Your Results

The results of the CPT2 Gene NGS Genetic Test will indicate whether pathogenic or likely pathogenic variants in the CPT2 gene have been identified. Since CPT2 deficiency follows autosomal recessive inheritance, the presence of two pathogenic variants (either homozygous or compound heterozygous) is consistent with a diagnosis of CPT2 deficiency. A single pathogenic variant indicates carrier status. Results should always be interpreted in conjunction with clinical presentation, family history, biochemical findings (acylcarnitine profile, free and total carnitine levels), and other relevant investigations. Genetic counselling is strongly recommended following result disclosure.
📊

Two pathogenic or likely pathogenic variants detected (homozygous or compound heterozygous)

Consistent with a molecular diagnosis of CPT2 deficiency. Clinical correlation with symptoms and biochemical markers is essential. Genetic counselling and initiation of dietary management strategies are recommended.

Clinical action: Referral to metabolic specialist. Avoidance of prolonged fasting. MCT oil supplementation. Emergency protocol letter for metabolic crises.

📊

One pathogenic or likely pathogenic variant detected

The individual is a carrier of CPT2 deficiency. Carriers are typically asymptomatic but have a 50% chance of passing the variant to offspring. Partner testing may be recommended.

Clinical action: Genetic counselling for reproductive planning. Partner testing if planning pregnancy.

📊

Variant of Uncertain Significance (VUS) detected

A genetic variant was identified, but there is currently insufficient evidence to classify it as pathogenic or benign. Further family studies and functional analysis may be needed.

Clinical action: Genetic counselling recommended. Correlation with clinical and biochemical findings. Family segregation analysis may be considered.

📊

No pathogenic variants detected

No disease-causing mutations in the CPT2 gene were identified by NGS. This result does not completely exclude CPT2 deficiency if large deletions/duplications or deep intronic variants are present. Clinical correlation is advised.

Clinical action: If clinical suspicion remains high, consider MLPA for copy number variant analysis, repeat biochemical testing, or evaluation of other fatty acid oxidation disorder genes.

⚠️ When to Consult a Doctor:

Consult a metabolic specialist or clinical geneticist immediately if your child is experiencing recurrent episodes of low blood sugar (hypoglycemia), unexplained muscle weakness, an enlarged liver, seizures, or any metabolic crisis symptoms—especially if triggered by fasting, illness, or prolonged exercise. Early consultation is critical for timely diagnosis and prevention of life-threatening complications. If your child has received a positive or uncertain genetic test result, schedule a genetic counselling session to understand the implications, management options, and recurrence risks for future pregnancies.

Limitations

  • ⚠This test does not detect large deletions or duplications (copy number variants) unless specified by CNV analysis algorithms. Confirmatory testing such as MLPA may be recommended.
  • ⚠Deep intronic variants and regulatory region mutations outside the coding exons and flanking intronic regions may not be detected.
  • ⚠The test cannot predict disease severity, age of onset, or clinical progression with certainty.
  • ⚠Variants of Uncertain Significance (VUS) may be reported; clinical correlation and family studies are recommended.
  • ⚠This test does not substitute for biochemical testing such as acylcarnitine profile analysis, which should be performed alongside genetic testing.

Risks & Considerations

  • ●Minor bruising or discomfort at the venipuncture site
  • ●Slight risk of infection at the blood draw site (extremely rare with proper technique)
  • ●For heel-stick in neonates: minor discomfort during the procedure
  • ●Psychological impact of results — genetic counselling is recommended before and after testing

Interfering Factors

  • ●Recent blood transfusion (within 120 days) may interfere with accurate genotyping of patient DNA
  • ●Degraded or insufficient DNA quality may affect NGS coverage and variant detection sensitivity
  • ●Clotted or hemolyzed blood samples may yield suboptimal DNA extraction
  • ●Contamination of the sample during collection or transport may compromise results

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Frequently Asked Questions

What is CPT2 deficiency?
Carnitine palmitoyltransferase 2 (CPT2) deficiency is a rare inherited metabolic disorder in which the body cannot properly break down long-chain fatty acids for energy due to mutations in the CPT2 gene. This leads to a reduced ability to use fat as a fuel source, particularly during fasting, illness, or exercise.
What causes CPT2 deficiency?
CPT2 deficiency is caused by mutations in the CPT2 gene located on chromosome 1p32.3. This gene provides instructions for making the carnitine palmitoyltransferase 2 enzyme, which is necessary for transporting fatty acids into the mitochondria for energy production. Mutations reduce or eliminate enzyme activity.
How is CPT2 deficiency inherited?
CPT2 deficiency follows an autosomal recessive inheritance pattern. This means an affected child must inherit two mutated copies of the CPT2 gene—one from each parent. Parents who carry one mutated copy are typically asymptomatic carriers with a 25% chance of having an affected child in each pregnancy.
What are the symptoms of infantile CPT2 deficiency?
The infantile form of CPT2 deficiency typically presents in the first year of life with recurrent hypoglycemia (low blood sugar), hepatomegaly (enlarged liver), liver dysfunction, cardiomyopathy, muscle weakness, and metabolic crises. Seizures, coma, and sudden death can occur if the condition is not diagnosed and managed promptly.
How is CPT2 deficiency diagnosed?
Diagnosis involves a combination of clinical evaluation, biochemical testing (acylcarnitine profile, carnitine levels), and confirmatory genetic testing. Newborn screening may detect abnormal acylcarnitine patterns. The CPT2 gene NGS test provides a definitive molecular diagnosis by identifying causative mutations.
What is NGS genetic testing and how does it work?
Next-generation sequencing (NGS) is an advanced genetic testing technology that can rapidly sequence large portions of DNA, including entire genes. For the CPT2 gene test, NGS reads the DNA sequence of the CPT2 gene to identify mutations such as missense, nonsense, splice-site variants, and small insertions or deletions that may be causing the disorder.
What sample is required for the CPT2 gene test?
The test can be performed using a blood sample (3–5 mL in an EDTA tube), extracted DNA, or one drop of blood on an FTA card. For newborns and infants, a heel-stick blood collection onto an FTA card is commonly used. No fasting is required.
How long does it take to get the results of the CPT2 gene test?
Results are typically available within 3 to 4 weeks from the date of sample collection. You will receive your report through the online portal, email, or WhatsApp as per your preference.
Is genetic counselling included with the CPT2 gene test at DNA Labs India?
Yes, DNA Labs India includes genetic counselling as part of the testing process. A pre-test counselling session helps document clinical and family history and draw a pedigree chart, while a post-test session helps interpret results, discuss management options, and address recurrence risks.
Can CPT2 deficiency be treated?
While there is no cure for CPT2 deficiency, the condition can be managed effectively with dietary modifications. Key strategies include avoidance of prolonged fasting, frequent meals with complex carbohydrates, medium-chain triglyceride (MCT) oil supplementation, and having an emergency protocol in place during illness to prevent metabolic crises.
Who should get tested for CPT2 deficiency?
Testing is recommended for infants and children presenting with unexplained hypoglycemia, hepatomegaly, cardiomyopathy, or muscle weakness suggestive of a fatty acid oxidation disorder; individuals with abnormal acylcarnitine profiles or abnormal newborn screening results; and family members of known CPT2 deficiency patients for carrier testing or confirmatory diagnosis.
Is the CPT2 gene NGS test available across India?
Yes, DNA Labs India offers free home sample collection for the CPT2 gene NGS genetic test across numerous cities in India, including Mumbai, Delhi, Bangalore, Hyderabad, Chennai, Kolkata, Pune, Ahmedabad, Jaipur, Lucknow, Chandigarh, and many more. You can book the test online and have a phlebotomist visit your home for sample collection.
Worried about the process? Our certified phlebotomists collect thousands of samples every month across India. The process takes under 5 minutes and is virtually painless. Questions? Message us on WhatsApp — we're here 7 days a week.

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