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PAX6 Gene Foveal Hypoplasia Type 1 NGS Genetic Test

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PAX6 Gene Foveal Hypoplasia Type 1 NGS Genetic Test

Also known as: PAX6 Gene Mutation Test, Foveal Hypoplasia Type 1 Genetic Test, PAX6 NGS Sequencing

PAX6 Gene Foveal Hypoplasia Type 1 NGS Genetic Test test available at DNA Labs India for ₹20,000. Uses Next Generation Sequencing (NGS), Sanger confirmation 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 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 this NGS genetic test is to identify pathogenic variants in the PAX6 gene that are associated with foveal hypoplasia type 1. This helps confirm the clinical diagnosis in symptomatic individuals, facilitate early intervention and visual rehabilitation, provide accurate recurrence risk information for family planning, and enable genetic counseling for affected families. The test also helps differentiate foveal hypoplasia type 1 from other inherited eye conditions with similar symptoms.

Test Code
3825
CPT Code
81406
ICD Code
H35.879
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), Sanger confirmation
Step 1

Sample Collection

No special preparation required. Patient should provide complete clinical history and any previous ophthalmological reports. A genetic counseling session is recommended to draw a pedigree chart of family members affected with PAX6 gene-associated conditions.

Method: Venipuncture / Finger-prick blood spot

Step 2

Laboratory Analysis

Blood sample is collected by venipuncture into an EDTA tube or a finger-prick blood spot on an FTA card. Ensure proper labeling and chain of custody.

Step 3

Report Delivery

No restrictions. The sample should be transported to the laboratory at ambient temperature (15-25°C) within 48 hours.

Timeline: 3 to 4 Weeks

Patient Instructions

1
Before the Test:Our genetic counselor will collect a detailed family history and draw a pedigree chart. Patients should bring all prior eye examination reports and any family records of genetic eye disorders. No special preparation or fasting is required.
2
During the Test:A small blood sample is taken by a trained phlebotomist at your home or at a DNA Labs India center. The procedure is quick and minimally invasive; no sedation or anesthesia is needed. For FTA card collection, a simple finger-prick is performed.
3
After the Test:After sample collection, you can resume normal activities immediately. The laboratory will process your sample, and results will be reported in 3 to 4 weeks. Genetic counseling is provided to discuss results and implications.

About This Test

Who Should Get This Test

The purpose of this NGS genetic test is to identify pathogenic variants in the PAX6 gene that are associated with foveal hypoplasia type 1. This helps confirm the clinical diagnosis in symptomatic individuals, facilitate early intervention and visual rehabilitation, provide accurate recurrence risk information for family planning, and enable genetic counseling for affected families. The test also helps differentiate foveal hypoplasia type 1 from other inherited eye conditions with similar symptoms.

How to Prepare

  • For blood sample, use sterile venipuncture technique and collect into EDTA vacutainer.
  • If using FTA card, apply one full drop of blood onto each designated circle.
  • Allow FTA card to air dry for at least 1 hour before placing in the provided envelope.
  • Avoid repeated freezing-thawing of extracted DNA samples.
  • Label the sample with patient name, date of birth, and collection date.

Doctor's Notes

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

"PAX6 gene mutations are a known cause of foveal hypoplasia type 1, a rare ocular developmental disorder. This NGS-based genetic test provides a definitive diagnosis for affected individuals and enables accurate genetic counseling for family planning and recurrence risk assessment."

Last medically reviewed: September 7, 2026

Test Parameters & Specifications

Sample TypeBlood or Extracted DNA or One drop Blood on FTA Card
Sample Volume2-3 ml whole blood or equivalent extracted DNA
ContainerEDTA vacutainer / FTA card
Collection MethodVenipuncture / Finger-prick blood spot

Sample Stability

48 hours
6 months
1 year
Sample Rejection Criteria:
  • Hemolyzed blood sample
  • Coagulated blood in EDTA tube
  • Incorrectly labeled specimen
  • Insufficient sample volume
  • Sample received after prolonged transit without temperature control

Understanding Your Results

The genetic test report will provide a clear interpretation of identified variants in the PAX6 gene, including pathogenicity classification based on American College of Medical Genetics (ACMG) guidelines. Positive, negative, and uncertain results are explained with precision, followed by clinical correlation and genetic counseling.
📊

A pathogenic or likely pathogenic variant in the PAX6 gene confirms the diagnosis of foveal hypoplasia type 1. Family members should be offered predictive testing.

Confirms clinical diagnosis and enables early intervention, visual rehabilitation, and informed family planning.

Result type: Positive

📊

No pathogenic variants detected in the PAX6 gene. Foveal hypoplasia type 1 due to PAX6 is unlikely, but other genetic or non-genetic causes should be explored.

Negative result does not completely exclude genetic cause; consultation with ophthalmologist and geneticist recommended.

Result type: Negative

📊

A genetic variant was found but its clinical significance is unclear. Additional familial segregation analysis may clarify pathogenicity.

Genetic counseling is strongly advised to discuss further testing options and family screening.

Result type: Variant of Uncertain Significance (VUS)

📊

A single pathogenic PAX6 variant in an autosomal dominant pattern would indicate affected individual; carrier status is not typically applicable unless other inheritance pattern is considered.

Not applicable for foveal hypoplasia type 1 (typically autosomal dominant); report interpreted by clinical geneticist.

Result type: Carrier

⚠️ When to Consult a Doctor:

Consult your ophthalmologist if you or your child have symptoms such as reduced vision, nystagmus, or photophobia. A referral for genetic testing is appropriate when foveal hypoplasia is observed on retinal imaging or if there is a known family history of PAX6-associated conditions.

Limitations

  • ⚠NGS may not detect deep intronic mutations or large structural variations beyond the analyzed regions
  • ⚠Variant of uncertain significance may require further familial segregation studies
  • ⚠This test does not assess other genes associated with foveal hypoplasia (e.g., SLC38A8, GPR143)
  • ⚠Test results should be interpreted in the context of clinical and ophthalmological findings
  • ⚠Somatic mosaicism may lead to lower sensitivity in detecting low-level variants

Risks & Considerations

  • ●Minimal risk of bruising or infection at the venipuncture site
  • ●Mild discomfort during blood collection
  • ●Emotional or psychological stress after receiving genetic results
  • ●Potential for discovering incidental findings or unsolicited genetic information

Interfering Factors

  • ●Poor quality or degraded DNA sample can affect test accuracy
  • ●Contamination of sample during collection or transport
  • ●Maternal cell contamination if sample is from cord blood
  • ●Presence of large genomic rearrangements might be missed if only NGS sequencing is performed without CNV analysis

Compare With Similar Tests

TestPAX6 Gene Foveal Hypoplasia Type 1 NGS Genetic Test
ComparisonPAX6 Gene Foveal Hypoplasia Type 1 NGS Genetic Test

Frequently Asked Questions

What is foveal hypoplasia type 1?
Foveal hypoplasia type 1 is a genetic disorder characterized by underdevelopment of the fovea, the area of the retina responsible for sharp central vision. It is caused by mutations in the PAX6 gene and leads to symptoms like reduced visual acuity, nystagmus, and photophobia.
How is PAX6 gene foveal hypoplasia type 1 diagnosed?
Diagnosis is suspected through comprehensive eye examination including visual acuity testing, eye movement assessment, and retinal imaging. NGS genetic testing of the PAX6 gene confirms the diagnosis by identifying pathogenic mutations.
What does the NGS genetic test for PAX6 detect?
The test sequences the entire coding region and exon-intron boundaries of the PAX6 gene to detect pathogenic variants, deletions, or duplications associated with foveal hypoplasia type 1 and other PAX6-related disorders.
What sample is required for the test?
The test requires 2-3 ml of blood in an EDTA tube, or extracted DNA, or one drop of blood on an FTA card. Home collection is available at no extra cost for online bookings.
Is fasting required before the test?
No, fasting is not required for this genetic test.
How long does it take to get the results?
The turnaround time is 3 to 4 weeks from the date the sample is received at the laboratory.
What is the cost of the test?
The cost is INR 20,000. This includes the genetic counseling session, testing, clinical report, and access to raw data files (FASTQ, VCF).
Will I receive raw data files?
Yes, DNA Labs India is the only laboratory that shares raw data files (FASTQ, VCF) along with the conclusive clinical report, ensuring transparency.
How do I interpret a positive test result?
A positive result indicates a pathogenic or likely pathogenic variant in the PAX6 gene, confirming the diagnosis of foveal hypoplasia type 1. Your genetic counselor will explain the inheritance and implications for family members.
Can this test be used for prenatal diagnosis?
Yes, if a familial PAX6 pathogenic variant is known, prenatal testing can be performed on fetal DNA from amniocentesis or CVS samples after genetic counseling.
Are there any limitations to NGS testing?
NGS may not detect large structural rearrangements or deep intronic variants. In some cases, CNV analysis is required. This test is limited to the PAX6 gene and does not cover other genes linked to foveal hypoplasia.
Is genetic counseling included?
Yes, the test price includes a genetic counseling session before and after testing to help you understand risks, benefits, and results.
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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