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SCN1A Gene Generalized epilepsy with febrile seizures plus type 2 NGS Genetic Test

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SCN1A Gene Generalized epilepsy with febrile seizures plus type 2 NGS Genetic Test

Short Name: SCN1A GEFS+ Type 2 NGS

Also known as: SCN1A Gene Mutation Analysis, SCN1A Sequencing Test, GEFS+ Type 2 Genetic Test, Febrile Seizures Plus Genetic Test

SCN1A Gene Generalized epilepsy with febrile seizures plus type 2 NGS Genetic Test test available at DNA Labs India for ₹20,000. Uses Next-Generation Sequencing (NGS) on Blood or Extracted DNA or FTA Card Blood Spot samples. Results in Reports are typically available within 3 to 4 weeks after the sample is received by the laboratory. The turnaround time includes quality control, NGS sequencing, bioinformatics analysis, variant interpretation, and clinical review.. Free home collection in 300+ cities across India.

NGS Genetic TestAll Age Groups🏠 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 SCN1A gene NGS test is to identify pathogenic mutations in the SCN1A gene that cause Generalized Epilepsy with Febrile Seizures Plus Type 2 (GEFS+ type 2). This helps confirm clinical diagnosis, guide treatment decisions, assess the risk of associated conditions (e.g., Dravet syndrome), and provide information for genetic counseling and family planning.

Test Code
4098
ICD Code
G40.89
Price
₹20,000
Sample Type
Blood or Extracted DNA or FTA Card Blood Spot
Result Time
Reports are typically available within 3 to 4 weeks after the sample is received by the laboratory. The turnaround time includes quality control, NGS sequencing, bioinformatics analysis, variant interpretation, and clinical review.
Fasting Required
No
Method
Next-Generation Sequencing (NGS)
Step 1

Sample Collection

No specific fasting is required for this test. However, it is important to inform the clinician about any blood transfusions, stem cell transplants, or haematological disorders. A prior consultation and genetic counselling session is recommended to draw a pedigree chart of family members affected with SCN1A-related conditions.

Method: Peripheral blood draw or FTA card blood spot

Step 2

Laboratory Analysis

A trained phlebotomist will collect 3-5 mL of peripheral blood in an EDTA tube. For FTA card samples, a few drops of blood will be placed on the designated card. The procedure takes only a few minutes and involves minimal discomfort.

Step 3

Report Delivery

You can resume all normal activities immediately. There are no restrictions. The sample will be transported to the laboratory at controlled temperature. Results will be available through the online portal, email, or WhatsApp in the provided turnaround time.

Timeline: Reports are typically available within 3 to 4 weeks after the sample is received by the laboratory. The turnaround time includes quality control, NGS sequencing, bioinformatics analysis, variant interpretation, and clinical review.

Patient Instructions

1
Before the Test:Before undergoing the SCN1A gene NGS test, a genetic counselling session is recommended to review the family history and explain the test's benefits, limitations, and possible outcomes. This session helps the patient and family understand the medical, psychological, and reproductive implications of testing.
2
During the Test:During the test, the sample is processed in the Molecular Genetics laboratory. DNA is extracted from the blood or FTA card, enriched for the SCN1A gene region, and sequenced using NGS technology. Bioinformatic analysis is performed to identify variants, which are then classified and interpreted.
3
After the Test:After the test, you will receive a comprehensive clinical report via email, WhatsApp, or the online portal. The laboratory provides the raw data (FASTQ, VCF) upon request for independent analysis. A follow-up genetic counselling session may be scheduled to explain the results and discuss management options.

About This Test

Who Should Get This Test

The purpose of the SCN1A gene NGS test is to identify pathogenic mutations in the SCN1A gene that cause Generalized Epilepsy with Febrile Seizures Plus Type 2 (GEFS+ type 2). This helps confirm clinical diagnosis, guide treatment decisions, assess the risk of associated conditions (e.g., Dravet syndrome), and provide information for genetic counseling and family planning.

How to Prepare

  • Please carry a valid ID proof and the filled test requisition form when you visit the lab for sample collection.
  • Ensure the EDTA tube is properly labelled with your name and date of birth.
  • For home collection, the phlebotomist will use sterile equipment and follow standard safety protocols.
  • For FTA card collection, allow the blood spot to air dry completely before packaging.

Doctor's Notes

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

"Genetic testing for SCN1A is essential when epilepsy with febrile seizures runs in families, as early diagnosis aids in targeted treatment and reproductive planning."

Last medically reviewed: September 7, 2026

Test Parameters & Specifications

Sample TypeBlood or Extracted DNA or FTA Card Blood Spot
Sample Volume3-5 mL blood or equivalent DNA
ContainerEDTA vacutainer (for blood) or Sterile vial with extracted DNA
Collection MethodPeripheral blood draw or FTA card blood spot

Sample Stability

Whole blood (EDTA): 48 hours at room temperature (22-25°C); up to 7 days at 2-8°C.
Extracted DNA: Stable for several years when stored at -20°C.
FTA card blood spot: Stable at room temperature for several months.
Sample Rejection Criteria:
  • Hemolysed or clotted blood samples are unsuitable.
  • Incorrectly labelled samples will be rejected.
  • Sample volume insufficient for DNA extraction.
  • Improper storage or shipping causing sample degradation.

Understanding Your Results

The genetic test report is interpreted by a clinical geneticist in correlation with clinical presentation and family history. The report will list all detected variants and classify them based on ACMG guidelines.
Positive for a pathogenic or likely pathogenic variant: Confirms the clinical diagnosis of GEFS+ type 2 (or the associated SCN1A phenotype). Allows predictive testing of family members.
Variant of uncertain significance (VUS): The variant does not yet have enough evidence to confirm or exclude a diagnosis. Additional segregation studies may be needed.
Negative result (no pathogenic variant): Does not rule out the condition if clinical suspicion is high. Other genetic or non-genetic causes should be considered.
Carrier status: Not applicable for autosomal dominant SCN1A-related conditions; a pathogenic variant in one allele is sufficient for the disease phenotype.
⚠️ When to Consult a Doctor:

Consult your neurologist or geneticist if the test result is positive or inconclusive. Also seek medical advice before genetic testing if you have a family history of epilepsy with febrile seizures, or if you are planning a pregnancy and want to assess risks.

Limitations

  • ⚠This NGS test primarily detects single nucleotide variants and small indels. Large structural rearrangements may not be consistently identified.
  • ⚠Deep intronic variants, regulatory region changes, and large CNVs may not be detected; additional testing such as MLPA or Sanger sequencing may be required for specific indications.
  • ⚠A negative or inconclusive result does not rule out genetic causes if clinical suspicion remains high.
  • ⚠Genetic variants of uncertain significance (VUS) require further familial segregation analysis to clarify pathogenicity.

Risks & Considerations

  • ●Risk of bruising or minor bleeding at the blood collection site.
  • ●Mild discomfort during venepuncture.
  • ●Psychological stress related to test results.
  • ●Possible result of Variant of Uncertain Significance (VUS) causing anxiety.
  • ●No risk of contracting infection as sterile equipment is used.

Interfering Factors

  • ●Recent blood transfusion within the last 3 months can dilute patient DNA and cause false results.
  • ●Active haematological malignancies or bone marrow transplantation may affect DNA analysis.
  • ●Inadequate DNA yield or poor quality DNA may lead to test failure.
  • ●Contamination during sample collection or processing.
  • ●Variant interpretation may be inconclusive in rare cases of variants of uncertain significance (VUS).

Compare With Similar Tests

TestSCN1A Gene Generalized epilepsy with febrile seizures plus type 2 NGS Genetic TestSCN1A Single Gene Sanger SequencingComprehensive Epilepsy NGS PanelChromosomal Microarray (CMA)
ComparisonSCN1A Gene Generalized epilepsy with febrile seizures plus type 2 NGS Genetic Test

Frequently Asked Questions

What is the cost of the SCN1A gene NGS genetic test for GEFS+ type 2?
The cost is Rs 20,000 INR. This includes free home sample collection, NGS sequencing, clinical report, and raw data (FASTQ, VCF files) at DNA Labs India.
What is Generalized Epilepsy with Febrile Seizures Plus Type 2 (GEFS+ type 2)?
GEFS+ type 2 is a rare genetic epilepsy disorder caused by mutations in the SCN1A gene. It is characterized by febrile seizures (seizures triggered by fever) that begin in childhood and may persist beyond age 5, sometimes progressing to non-fever-related seizures.
How is the SCN1A NGS genetic test performed?
The test uses Next-Generation Sequencing (NGS) to analyze the entire SCN1A gene, including all coding exons and splice junction regions. DNA is extracted from your blood sample and sequenced to identify mutations.
What sample type is required for this test?
The test can be done on 3-5 mL of peripheral blood in an EDTA tube, extracted DNA, or a dried blood spot on an FTA card. Free home collection is available for online bookings.
Is fasting required before the test?
No, fasting is not required. You can eat and drink normally. There are no specific dietary or medication restrictions before giving a blood sample for genetic testing.
How long does it take to get the test report?
The turnaround time is 3 to 4 weeks. The report is sent to you via email, WhatsApp, or the online patient portal. You can also request the raw data files (FASTQ, VCF) for further analysis.
What does a positive result mean?
A positive result indicates the presence of a pathogenic or likely pathogenic variant in the SCN1A gene. This confirms the genetic basis for GEFS+ type 2 and helps guide treatment and genetic counseling for the family.
Can this test detect Dravet syndrome?
Dravet syndrome is a severe form of epilepsy also caused by SCN1A mutations. Since this test sequences the entire SCN1A gene, it can detect mutations associated with Dravet syndrome as well. However, clinical correlation is required for diagnosis.
What should I do if the result shows a variant of uncertain significance (VUS)?
If a VUS is found, your genetic counselor or neurologist may recommend additional testing, such as segregation analysis of family members, to help classify the variant. In some cases, the variant may be reclassified over time as more data becomes available.
Are there any risks associated with this genetic test?
The physical risks are minimal, similar to routine blood collection, such as slight bruising or discomfort. There can be emotional or psychological risks related to test results, which is why genetic counseling is strongly recommended before and after the test.
Will I receive the raw data (FASTQ, VCF) along with the clinical report?
Yes, DNA Labs India is transparent and provides the raw data files (FASTQ, VCF) along with the conclusive clinical report. This allows independent verification and future re-analysis if needed.
Does the test require any pre-test genetic counseling?
Yes, we recommend a genetic counseling session before the test to draw a family pedigree and discuss the implications of the test result. This is included in the test price and helps ensure informed decision-making.
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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