Skip to main content
DNA Labs India

CLN3 Gene Ceroid lipofuscinosis neuronal type 3 NGS Genetic Test

DNA Labs India | ISO 9001:2015 Certified

CLN3 Gene Ceroid lipofuscinosis neuronal type 3 NGS Genetic Test

Short Name: CLN3 Gene NGS Test

Also known as: Juvenile Batten Disease, Juvenile Neuronal Ceroid Lipofuscinosis, JNCL, Batten Disease Type 3, CLN3 Disease

CLN3 Gene Ceroid lipofuscinosis neuronal type 3 NGS Genetic Test test available at DNA Labs India for ₹20,000. Uses Next-Generation Sequencing (NGS) on Blood or Extracted DNA or One drop Blood on FTA Card samples. Results in 3 to 4 Weeks. Free home collection in 300+ cities across India.

NGS Genetic TestUnisexAll 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 CLN3 Gene NGS Genetic Test is to detect mutations in the CLN3 gene to confirm a diagnosis of Juvenile Neuronal Ceroid Lipofuscinosis (Juvenile Batten Disease). This test is used to identify disease-causing genetic variants in individuals presenting with symptoms suggestive of CLN3 disease, to determine carrier status in family members, to assist in genetic counseling and family planning, and to facilitate enrollment in clinical trials or emerging therapeutic programs when available.

Test Code
1922
Price
₹20,000
Sample Type
Blood or Extracted DNA or One drop Blood on FTA Card
Result Time
3 to 4 Weeks
Fasting Required
No
Method
Next-Generation Sequencing (NGS)
Step 1

Sample Collection

No special preparation or fasting is required before sample collection. A genetic counseling session is strongly recommended prior to testing to discuss the clinical indication, test implications, possible outcomes, and family history. Please provide a detailed clinical history of the patient and a pedigree chart of family members affected with Ceroid Lipofuscinosis Neuronal Type 3 or related metabolic disorders.

Method: Venipuncture

Step 2

Laboratory Analysis

A trained phlebotomist will collect approximately 3-5 mL of venous blood from a vein in the arm using standard venipuncture technique. Alternatively, a single drop of blood may be collected on an FTA card. The collection procedure typically takes 5-10 minutes. The sample will be labeled, stored appropriately, and transported to the laboratory for DNA extraction and NGS analysis.

Step 3

Report Delivery

After sample collection, apply gentle pressure on the puncture site with sterile cotton for 3-5 minutes to prevent bruising. You may resume normal activities immediately after blood draw. Keep the puncture site clean and dry. Results will be available within 3 to 4 weeks via the online portal, email, or WhatsApp.

Timeline: 3 to 4 Weeks

Patient Instructions

1
Before the Test:A genetic counseling session is recommended before testing to discuss the purpose, implications, and possible outcomes of the test. Provide the clinical history of the patient and a pedigree chart of family members affected with Ceroid Lipofuscinosis Neuronal Type 3 or related conditions. No fasting or special preparation is required.
2
During the Test:A blood sample of approximately 3-5 mL will be collected via venipuncture, or a single drop of blood may be placed on an FTA card. The collection procedure takes about 5-10 minutes. The sample is then sent to the laboratory for DNA extraction and Next-Generation Sequencing analysis of the CLN3 gene.
3
After the Test:You may resume normal activities immediately after the blood draw. Mild soreness at the puncture site is normal and resolves quickly. Results are typically available within 3 to 4 weeks and will be delivered through the online portal, email, or WhatsApp. A follow-up genetic counseling session is recommended to discuss the results.

About This Test

Who Should Get This Test

The purpose of the CLN3 Gene NGS Genetic Test is to detect mutations in the CLN3 gene to confirm a diagnosis of Juvenile Neuronal Ceroid Lipofuscinosis (Juvenile Batten Disease). This test is used to identify disease-causing genetic variants in individuals presenting with symptoms suggestive of CLN3 disease, to determine carrier status in family members, to assist in genetic counseling and family planning, and to facilitate enrollment in clinical trials or emerging therapeutic programs when available.

How to Prepare

  • Ensure proper labeling of the sample tube with patient name, date of birth, and unique identification number
  • For FTA card collection, allow the blood drop to dry completely at room temperature before packaging
  • Transport blood samples at ambient room temperature to the laboratory within 72 hours of collection
  • Complete the test requisition form with detailed clinical history, family pedigree information, and referring physician details
  • If extracted DNA is being submitted, ensure DNA concentration and quality meet minimum laboratory requirements

Doctor's Notes

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

"Early genetic diagnosis of CLN3 disease through NGS testing is crucial for initiating supportive therapies, planning appropriate long-term care, and providing accurate genetic counseling to families. Identifying the specific CLN3 mutations helps in understanding disease prognosis, assessing recurrence risk for future pregnancies, and may open avenues for participation in clinical trials for emerging therapies. Families with a confirmed genetic diagnosis are better equipped to access multidisciplinary care and community support resources."

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 top) or FTA Card
Collection MethodVenipuncture

Sample Stability

EDTA blood
FTA Card blood
Extracted DNA
Sample Rejection Criteria:
  • Clotted blood sample in EDTA tube
  • Insufficient sample volume for DNA extraction
  • Sample contaminated or severely hemolyzed
  • Improperly labeled or unlabeled sample
  • Sample received beyond the stability period

Understanding Your Results

The results of the CLN3 Gene NGS Genetic Test provide information about the presence or absence of genetic variants in the CLN3 gene. Results should be interpreted by a qualified geneticist or genetic counselor in the context of the patient's clinical presentation, family history, and other diagnostic findings. The following categories describe possible test outcomes:
📊

Pathogenic Variant(s) Detected

Disease-causing mutation(s) have been identified in the CLN3 gene. In the context of compatible clinical features, this confirms a diagnosis of CLN3 disease (Juvenile Batten Disease). Genetic counseling is recommended to discuss inheritance patterns, recurrence risk for future pregnancies, and management options.

📊

Likely Pathogenic Variant(s) Detected

Variant(s) have been identified in the CLN3 gene that are likely disease-causing based on available scientific evidence. Clinical correlation and genetic counseling are recommended. Confirmation in parents (segregation analysis) may be advised.

📊

Variant of Uncertain Significance (VUS)

A genetic variant has been detected in the CLN3 gene, but its clinical significance is currently unknown based on available evidence. This result alone is insufficient for diagnosis. Clinical correlation, family studies, functional studies, and periodic reassessment as scientific knowledge evolves are recommended.

📊

No Pathogenic Variant Detected

No disease-causing mutations were identified in the CLN3 gene using NGS. This result significantly reduces the likelihood of CLN3 disease but does not completely exclude it, particularly if deep intronic variants or large structural rearrangements are present. If clinical suspicion remains high, additional testing or evaluation of other NCL-associated genes may be considered.

📊

Carrier Status (Heterozygous)

A single pathogenic variant in the CLN3 gene has been identified, indicating the individual is a carrier of CLN3 disease. Carriers are typically unaffected but have a 50% chance of passing the variant to each offspring. Genetic counseling is recommended for family planning.

⚠️ When to Consult a Doctor:

Consult a geneticist or neurologist if the CLN3 Gene NGS Test detects pathogenic or likely pathogenic mutations, if a Variant of Uncertain Significance is identified, or if your child develops progressive vision loss, seizures, cognitive decline, motor dysfunction, or behavioral changes between the ages of 4 and 10 years. Families with a confirmed or suspected diagnosis of Batten disease should seek referral to a center experienced in managing neurodegenerative disorders and genetic counseling services.

Limitations

  • ⚠This test targets the CLN3 gene and may not detect mutations in other genes associated with neuronal ceroid lipofuscinosis
  • ⚠Deep intronic mutations, regulatory region variants, or large structural rearrangements beyond the detection capability of NGS may be missed
  • ⚠This test cannot predict the age of symptom onset, disease severity, or rate of progression
  • ⚠A negative result does not completely exclude CLN3 disease if clinical suspicion remains high, as novel or private mutations may exist
  • ⚠Results should always be interpreted in the context of clinical findings, family history, and other diagnostic investigations

Risks & Considerations

  • ●Minimal physical risk from blood draw, including minor bruising or soreness at the puncture site
  • ●Rare risk of infection or hematoma at the venipuncture site
  • ●Potential psychological and emotional impact of receiving genetic test results
  • ●Risk of uncertain or inconclusive findings (VUS) that may cause anxiety and require further investigation
  • ●Implications for family members who may also carry the mutation

Interfering Factors

  • ●Degraded or low-quality DNA may affect the accuracy of sequencing results
  • ●Contamination of the sample with foreign DNA may lead to erroneous results
  • ●Insufficient sample volume or very low DNA concentration may require repeat collection
  • ●Presence of blood transfusion within 72 hours prior to sample collection may affect results

Compare With Similar Tests

TestCLN3 Gene Ceroid lipofuscinosis neuronal type 3 NGS Genetic Test
ComparisonCLN3 Gene Ceroid lipofuscinosis neuronal type 3 NGS Genetic Test

Frequently Asked Questions

What is CLN3 Gene Ceroid Lipofuscinosis Neuronal Type 3?
CLN3 Gene Ceroid Lipofuscinosis Neuronal Type 3, also known as Juvenile Batten Disease or Juvenile Neuronal Ceroid Lipofuscinosis (JNCL), is a rare autosomal recessive neurodegenerative disorder caused by mutations in the CLN3 gene. It leads to progressive vision loss, seizures, cognitive decline, and motor deterioration, typically beginning between ages 5 and 10. The disease results from abnormal accumulation of lipopigments (ceroid and lipofuscin) in the brain and other tissues due to defective lysosomal function.
What is the CLN3 Gene NGS Genetic Test?
The CLN3 Gene NGS Genetic Test is a molecular diagnostic test that uses Next-Generation Sequencing (NGS) technology to analyze the CLN3 gene for disease-causing mutations. This test can detect a wide range of genetic variations including point mutations, small insertions, deletions, and large copy number variations such as the common 1.02 kb deletion. It is the gold standard for confirming a diagnosis of Juvenile Batten Disease at the molecular level.
Who should undergo the CLN3 Gene NGS Genetic Test?
This test is recommended for individuals who present with symptoms suggestive of Juvenile Batten Disease, such as progressive vision loss beginning in childhood, seizures, cognitive decline, motor dysfunction, or behavioral changes. It is also recommended for individuals with a family history of neuronal ceroid lipofuscinosis, for carrier testing in parents or siblings of affected individuals, and for prenatal testing in families with known CLN3 mutations.
What are the symptoms of CLN3 disease (Juvenile Batten Disease)?
Symptoms of CLN3 disease typically appear between ages 5 and 10 and include progressive vision loss leading to blindness, seizures, muscle weakness, speech difficulties, delayed mental and physical development, behavioral changes (anxiety, attention difficulties, personality changes), and progressive loss of motor skills. The symptoms worsen over time, and affected individuals eventually become completely dependent on others for daily activities.
How is the CLN3 Gene NGS Test performed?
The test begins with collection of a blood sample (3-5 mL in an EDTA tube) or a blood drop on an FTA card. DNA is extracted from the sample in the laboratory. The CLN3 gene is then analyzed using Next-Generation Sequencing technology, which reads the DNA sequence at high depth to identify any mutations. Detected variants are classified according to ACMG/AMP guidelines and included in the final genetic report.
What sample is required for the CLN3 Gene Test?
The test can be performed using 3-5 mL of peripheral venous blood collected in an EDTA (lavender-top) tube, extracted genomic DNA, or a single drop of blood on an FTA card. No fasting is required before sample collection. The sample can be collected at home with free home collection offered by DNA Labs India.
How long does it take to get the CLN3 Gene Test results?
The turnaround time for the CLN3 Gene NGS Genetic Test is approximately 3 to 4 weeks from the date of sample collection. This timeframe includes DNA extraction, NGS sequencing, bioinformatics analysis, variant interpretation, and expert review of results. Reports are delivered via the online portal, email, or WhatsApp.
What is the cost of the CLN3 Gene NGS Genetic Test in India?
The cost of the CLN3 Gene NGS Genetic Test at DNA Labs India is ?20,000 (Indian Rupees). This price includes sample collection (with free home collection facility across India), DNA extraction, NGS analysis, detailed genetic report, and expert geneticist review. The test may be covered under certain insurance plans; patients should check with their insurance provider.
Is the CLN3 Gene Test covered by insurance in India?
Some private insurance plans in India may cover genetic testing for diagnostic purposes, but coverage varies by policy and provider. Government health schemes such as PMJAY, CGHS, ECHS, and ESIC may provide partial or full coverage depending on the specific case and policy terms. It is recommended to check directly with your insurance provider or scheme administrator for coverage eligibility before booking the test.
Can the CLN3 Gene Test be done at home?
Yes, DNA Labs India offers free home sample collection for the CLN3 Gene NGS Genetic Test across India. A trained phlebotomist will visit your home to collect the blood sample at your convenience. This service is available in numerous cities including Mumbai, Delhi, Bangalore, Hyderabad, Chennai, Kolkata, Pune, Ahmedabad, Jaipur, and many more. You can book the home collection service online or by calling our helpline.
What happens if the test detects a mutation in the CLN3 gene?
If the test identifies pathogenic or likely pathogenic mutations in the CLN3 gene, this confirms a molecular diagnosis of CLN3 disease (Juvenile Batten Disease). A genetic counselor or medical geneticist will help explain the results, discuss the inheritance pattern and recurrence risk for future pregnancies, and guide you toward appropriate management strategies, supportive care options, and available clinical trials. Referral to a neurologist experienced in managing neurodegenerative disorders will also be recommended.
Is genetic counseling recommended before and after the CLN3 Gene Test?
Yes, genetic counseling is strongly recommended both before and after the CLN3 Gene NGS Genetic Test. Pre-test counseling helps families understand the purpose of testing, possible outcomes, implications for family members, and reproductive options. Post-test counseling is essential to help interpret results, understand the diagnosis, discuss management options, assess recurrence risk, and connect families with appropriate support resources and clinical trials.
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.

Related Tests

Angelman Syndrome Test

₹10,000

Duchenne / Becker Muscular Dystrophy (DMD / BMD) Gene Mutation Test

₹14,000

Episodic Ataxia Type 1 Hotspot Test

₹11,500

Episodic Ataxia Comprehensive Profile Hotspot Test

₹16,000

Megalencephalic Leukoencephalopathy with Subcortical Cysts Van Der Knaap and Nalband MLC Gene Hotspot Mutation Test

₹7,500

Analyzer 18 SMA 18 Test Panel

₹1,755
For Hospitals & Clinics

Reference Laboratory Services

We serve as a reference laboratory for hospitals and clinics across India. Send samples from your facility with same-day pickup, priority processing, and results delivered through our online portal. Competitive institutional pricing available.

LIMS Integration

Your Data Privacy

Your medical data is protected under Indian law.

✓ Stored in India: All patient records are stored on servers located in India. No data is transferred outside the country.

✓ DPDP Act Compliant: Under the Digital Personal Data Protection Act 2023, you can request deletion of your records at any time by contacting support.

Book Your Test

Enter your details and we'll connect you within 15 minutes.

🧬

Quick Connect

Enter your mobile number and we’ll connect you with the team.

+91

✅ Connecting you now...

🔒 Your number is used to respond to this request.