ABCA1 Gene HDL deficiency, type 2 NGS Genetic Test
Short Name: ABCA1 HDL Deficiency Type 2
Also known as: ABCA1 Gene Mutation Analysis, Tangier Disease Genetic Test, Familial HDL Deficiency NGS Test, ABCA1 Sequencing Test, High-Density Lipoprotein Deficiency Type 2 Genetic Test
ABCA1 Gene HDL deficiency, type 2 NGS Genetic Test test available at DNA Labs India for ₹20,000. Uses Next-Generation Sequencing (NGS), Sanger Confirmation (if required), Bioinformatics Analysis on Blood samples. Results in Results are typically available within 3 to 4 weeks from the date of sample collection. Results are delivered via the online portal, email, and WhatsApp.. Free home collection in 300+ cities across India.
🩺 Medically Reviewed By
Dr SULOCHANA HEMCHANDRA HOLLA
Consultant Medical Geneticist · Reg: 8532
Last reviewed: September 7, 2026
Overview
The purpose of this test is to identify pathogenic or likely pathogenic mutations in the ABCA1 gene that cause HDL deficiency type 2. The test confirms a clinical diagnosis, guides treatment decisions, enables cascade family screening, facilitates genetic counselling regarding inheritance and recurrence risk, and supports research into cardiovascular disease susceptibility linked to HDL metabolism defects.
- Test Code
- 2066
- CPT Code
- 81479
- ICD Code
- E78.6
- Price
- ₹20,000
- Sample Type
- Blood
- Result Time
- Results are typically available within 3 to 4 weeks from the date of sample collection. Results are delivered via the online portal, email, and WhatsApp.
- Fasting Required
- No
- Method
- Next-Generation Sequencing (NGS), Sanger Confirmation (if required), Bioinformatics Analysis
Sample Collection
A genetic counselling session is mandatory before sample collection. During this session, a detailed clinical history of the patient and a pedigree chart of family members affected with HDL deficiency type 2 will be prepared. No fasting is required. Maintain the sample at ambient room temperature.
Method: Venipuncture
Laboratory Analysis
A trained phlebotomist will collect approximately 5 mL of venous blood in an EDTA (lavender top) vacutainer under aseptic conditions. The sample will be labelled with patient details and barcoded for tracking.
Report Delivery
The blood sample will be transported to the laboratory under controlled ambient conditions. DNA will be extracted, and NGS analysis will be performed. Results will be available within 3 to 4 weeks and delivered via the online portal, email, or WhatsApp.
Timeline: Results are typically available within 3 to 4 weeks from the date of sample collection. Results are delivered via the online portal, email, and WhatsApp.
Patient Instructions
About This Test
Who Should Get This Test
The purpose of this test is to identify pathogenic or likely pathogenic mutations in the ABCA1 gene that cause HDL deficiency type 2. The test confirms a clinical diagnosis, guides treatment decisions, enables cascade family screening, facilitates genetic counselling regarding inheritance and recurrence risk, and supports research into cardiovascular disease susceptibility linked to HDL metabolism defects.
How to Prepare
- Schedule a genetic counselling session prior to sample collection
- Bring a detailed family history and any previous lipid profile reports
- No fasting is required before blood sample collection
- Inform the phlebotomist of any recent blood transfusions or bone marrow transplants
- Wear a short-sleeved shirt or loose-fitting clothing for easy venipuncture access
- Stay hydrated before the blood draw to ensure smooth collection
Doctor's Notes
Reviewed by Dr SULOCHANA HEMCHANDRA HOLLA — MBBS, MD (Medical Genetics) · Reg. No. 8532
"ABCA1 gene mutations are a significant cause of familial HDL deficiency and Tangier disease. Patients presenting with markedly reduced HDL cholesterol, especially below 20 mg/dL, alongside hepatosplenomegaly or peripheral neuropathy, should be evaluated for ABCA1 mutations. Early genetic diagnosis allows for proactive cardiovascular risk management and family screening. I recommend this test for individuals with unexplained very low HDL levels and a family history of premature cardiovascular disease."
Last medically reviewed: September 7, 2026
Test Parameters & Specifications
Sample Stability
- Sample received in a heparin tube instead of EDTA tube
- Insufficient sample volume (less than 2 mL)
- Sample labelled incorrectly or missing patient identification
- Haemolysed, clotted, or contaminated sample
- Sample received without prior genetic counselling documentation
Understanding Your Results
Two pathogenic mutations identified in the ABCA1 gene, consistent with a diagnosis of Tangier disease or severe familial HDL deficiency. The patient is expected to have significantly reduced or absent HDL cholesterol, with increased risk of cardiovascular disease, peripheral neuropathy, and organomegaly. Cascade screening of family members is recommended.
Clinical action: Refer to lipid specialist or cardiologist. Initiate aggressive cardiovascular risk factor management. Arrange family screening. Genetic counselling for reproductive planning.
Result type: Pathogenic Variant Detected - Homozygous/Compound Heterozygous
One pathogenic mutation identified, indicating carrier status. Heterozygous carriers typically have moderately reduced HDL cholesterol levels (typically 20-40 mg/dL) and may have a 2- to 4-fold increased risk of coronary artery disease compared to the general population.
Clinical action: Monitor lipid profiles regularly. Assess cardiovascular risk factors. Genetic counselling to discuss carrier status, partner testing, and offspring risk. Lifestyle modifications and appropriate lipid management as indicated.
Result type: Pathogenic Variant Detected - Heterozygous Carrier
A genetic variant in the ABCA1 gene was identified, but there is currently insufficient evidence to classify it as pathogenic or benign. This result cannot be used to confirm or exclude a diagnosis of ABCA1-related HDL deficiency.
Clinical action: Clinical correlation is advised. Repeat testing or family segregation analysis may be helpful. The variant may be reclassified as new scientific evidence becomes available. Continue clinical monitoring.
Result type: Variant of Uncertain Significance (VUS)
No disease-causing mutations were identified in the ABCA1 gene. This result reduces but does not completely eliminate the possibility of ABCA1-related HDL deficiency, as large deletions or mutations in regulatory regions may not be detected by this method. Other genetic or non-genetic causes of low HDL should be considered.
Clinical action: Consider testing for other genes involved in HDL metabolism (e.g., LCAT, CETP, LIPG). Evaluate secondary causes of low HDL. Clinical follow-up as appropriate.
Result type: No Pathogenic Variant Detected
Consult your physician or genetic specialist if your test reveals any pathogenic variant in the ABCA1 gene, if you have persistently very low HDL cholesterol levels, if you experience symptoms such as orange-coloured tonsils, unexplained numbness or tingling in extremities, or if you have a family history of premature heart disease. Early consultation allows for proactive cardiovascular risk management and family screening.
Limitations
- ⚠This test does not detect large genomic rearrangements, copy number variations (CNVs), or deep intronic mutations outside standard NGS capture regions
- ⚠Variants of Uncertain Significance (VUS) may be identified and cannot be used for definitive clinical diagnosis without further evidence
- ⚠The test does not evaluate other genes involved in HDL metabolism such as LCAT, CETP, or LIPG
- ⚠Negative results do not completely exclude HDL deficiency caused by other genetic or non-genetic factors
- ⚠Genotype-phenotype correlations may vary; the presence of a pathogenic variant does not always predict disease severity
Risks & Considerations
- ●Minor bruising or discomfort at the blood collection site
- ●Rarely, slight dizziness or lightheadedness during venipuncture
- ●Psychological impact of genetic test results; genetic counselling is provided to address this
- ●Potential identification of Variants of Uncertain Significance (VUS) which may cause anxiety without definitive clinical guidance
Interfering Factors
- ●Recent blood transfusion (within 4 weeks) may affect DNA quality and introduce donor DNA
- ●Contamination of the blood sample during collection or transport
- ●Degraded DNA due to improper sample storage or prolonged transit time
- ●Presence of somatic mosaicism may lead to low-level variant detection challenges
Compare With Similar Tests
| Test | ABCA1 Gene HDL deficiency, type 2 NGS Genetic Test | ABCA1 Single Gene Sanger Sequencing | Lipid Profile Panel | Dyslipidemia Gene Panel (Multi-Gene) | Whole Exome Sequencing (WES) |
|---|---|---|---|---|---|
| Comparison | ABCA1 Gene HDL deficiency, type 2 NGS Genetic Test |
Frequently Asked Questions
What is the ABCA1 Gene HDL Deficiency Type 2 NGS Genetic Test?
Who should get the ABCA1 Gene HDL Deficiency Type 2 Genetic Test?
What is the cost of the ABCA1 Gene HDL Deficiency Type 2 NGS Genetic Test?
Is fasting required for the ABCA1 Gene HDL Deficiency Type 2 NGS Genetic Test?
How long does it take to get the results of the ABCA1 Gene HDL Deficiency Type 2 NGS Genetic Test?
What sample is required for the ABCA1 Gene HDL Deficiency Type 2 NGS Genetic Test?
What is Tangier disease and how is it related to ABCA1 gene mutations?
What does it mean if I am a carrier (heterozygous) for an ABCA1 mutation?
Is free home sample collection available for this test?
What is the difference between this NGS test and a lipid profile blood test?
Can this test be used for family screening and carrier detection?
What happens after I receive my test results?
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