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DNA Labs India

HCFC1 Gene Mental retardation, X-linked type 3 NGS Genetic Test

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HCFC1 Gene Mental retardation, X-linked type 3 NGS Genetic Test

Short Name: HCFC1 XLMR3 NGS

Also known as: MRX3, X-linked mental retardation type 3, HCFC1-associated intellectual disability

HCFC1 Gene Mental retardation, X-linked type 3 NGS Genetic Test test available at DNA Labs India for ₹20,000. Uses Next Generation Sequencing (NGS) on Blood, Extracted DNA, or Dried Blood Spot on FTA Card samples. Results in Results are typically delivered within 3 to 4 weeks after sample reaching the laboratory.. Free home collection in 300+ cities across India.

NGS Genetic TestMale / FemaleChildren, Adolescents, Adults🏠 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 test is to detect pathogenic variants in the HCFC1 gene in individuals suspected of having X-linked mental retardation type 3, confirming the clinical diagnosis and enabling appropriate genetic counseling and family planning.

Test Code
4272
Price
₹20,000
Sample Type
Blood, Extracted DNA, or Dried Blood Spot on FTA Card
Result Time
Results are typically delivered within 3 to 4 weeks after sample reaching the laboratory.
Fasting Required
No
Method
Next Generation Sequencing (NGS)
Step 1

Sample Collection

No special preparation is required. A detailed clinical history of the patient is essential, and a genetic counseling session to draw a pedigree chart of affected family members is recommended. Please provide any prior genetic testing results.

Method: Venipuncture / Buccal swab / FTA card spotting

Step 2

Laboratory Analysis

A trained phlebotomist will collect a blood sample or a buccal swab. For FTA card samples, a few drops of blood are applied to the card and allowed to air dry.

Step 3

Report Delivery

No limitations or downtime. You can resume normal activities immediately.

Timeline: Results are typically delivered within 3 to 4 weeks after sample reaching the laboratory.

Patient Instructions

1
Before the Test:No special preparation is required. A detailed clinical history and a family pedigree are essential for accurate interpretation. Please provide any prior genetic testing results.
2
During the Test:A trained phlebotomist will collect a blood sample or a buccal swab. For FTA card samples, a few drops of blood are applied to the card and allowed to air dry.
3
After the Test:No limitations or downtime. You can resume normal activities immediately.

About This Test

Who Should Get This Test

The purpose of this test is to detect pathogenic variants in the HCFC1 gene in individuals suspected of having X-linked mental retardation type 3, confirming the clinical diagnosis and enabling appropriate genetic counseling and family planning.

How to Prepare

  • For blood collection, use EDTA (lavender top) vacutainer.
  • For FTA card, spot 3-5 blood drops directly onto the card.
  • For extracted DNA, ensure it is dissolved in sterile water or Tris-EDTA buffer.
  • Label all tubes/cards with patient name, ID, and collection date.
  • Ship samples at ambient temperature via courier.

Doctor's Notes

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

"Genetic testing for X-linked intellectual disability is essential not only for confirming the diagnosis in affected males but also for providing accurate reproductive risk counseling for carrier females."

Last medically reviewed: September 7, 2026

Test Parameters & Specifications

Sample TypeBlood, Extracted DNA, or Dried Blood Spot on FTA Card
Sample Volume3-5 mL whole blood / 3-5 blood spots on FTA card
ContainerEDTA vacutainer / DNA tube / FTA Card
Collection MethodVenipuncture / Buccal swab / FTA card spotting

Sample Stability

Whole blood (EDTA): 2-8°C for 1 week, ambient temperature for 3-4 days
Extracted DNA: stable at 4°C for 6 months, -20°C for 2 years
FTA card: stable at room temperature for several years
Sample Rejection Criteria:
  • Clotted or hemolyzed blood
  • Insufficient sample quantity
  • Leaked or expired collection tubes
  • Mislabeled or unlabeled sample
  • Samples received without clinical history

Understanding Your Results

The genomic DNA was extracted and subjected to NGS for the HCFC1 gene. Variants were classified according to ACMG guidelines. The result should be interpreted in the context of the patient's clinical presentation and family history.
📊

Pathogenic/likely pathogenic variant detected

The detected variant is associated with HCFC1 gene-related X-linked mental retardation type 3. This result confirms the clinical diagnosis and has significant implications for the patient and family.

📊

Variant of uncertain significance (VUS) detected

The variant is currently of unknown clinical significance. Additional family studies, segregation analysis, or functional studies may be required to clarify its role. Consultation with a geneticist is advised.

📊

No pathogenic variant detected

No disease-causing variant was found in the coding regions of the HCFC1 gene. However, this does not completely exclude a genetic cause; clinical re-evaluation and possibly other genetic tests are recommended.

⚠️ When to Consult a Doctor:

If your result is positive or shows a VUS, consult a clinical geneticist, neurologist, or your referring physician for a detailed explanation and personalized management plan. Family members at risk should also be offered genetic counseling.

Limitations

  • ⚠NGS may not detect large deletions/duplications, trinucleotide repeat expansions, or deep intronic variants.
  • ⚠Variant interpretation may be inconclusive; variants of uncertain significance may be reported.
  • ⚠The test does not evaluate all genes associated with intellectual disability.
  • ⚠Negative results do not exclude all hereditary causes and additional testing may be required.

Risks & Considerations

  • ●Minimal physical risk from blood collection
  • ●Potential psychological stress from a genetic diagnosis
  • ●Possible insurance or employment discrimination (though prohibited by law)

Interfering Factors

  • ●Poor DNA quality or degradation
  • ●Hemolyzed or clotted blood sample
  • ●Sample contamination or mix-up
  • ●PCR inhibitors in extracted DNA
  • ●Incomplete clinical history or pedigree information

Frequently Asked Questions

What is HCFC1 gene mental retardation type 3?
HCFC1 gene mental retardation type 3 (MRX3) is a rare X-linked genetic disorder caused by mutations in the HCFC1 gene. It predominantly affects males and is characterized by intellectual disability, speech delay, behavioral issues, seizures, and distinctive facial features.
Who should undergo this NGS genetic test?
Individuals, especially males, with unexplained intellectual disability/developmental delay, seizures, and dysmorphic features suggestive of X-linked inheritance, as well as female relatives seeking carrier status, may be appropriate candidates. A clinical geneticist or neurologist should evaluate the indication.
How is the HCFC1 gene NGS test performed?
The test uses next-generation sequencing (NGS) to analyze the protein-coding regions and splice sites of the HCFC1 gene. DNA extracted from the sample is massively parallel sequenced to identify variants that may be pathogenic.
What sample types are accepted for this test?
We accept whole blood in EDTA tubes, extracted DNA, or dried blood spots on FTA cards. For sample quality, the preferred sample is peripheral blood.
Is fasting required before the test?
No, this is a genetic test and fasting is not required. You can eat and drink normally.
What is the cost of the HCFC1 gene NGS test?
The cost is INR 20,000. This includes home sample collection across India and the full clinical report along with raw data files (FASTQ, VCF) for transparency.
What is the turnaround time for results?
Reports are typically available within 3 to 4 weeks after the sample reaches the laboratory. The exact time may vary depending on the sample quality and any repeat testing.
What does a positive result mean?
A positive result indicates the presence of a pathogenic or likely pathogenic variant in the HCFC1 gene, confirming the diagnosis of X-linked mental retardation type 3. Genetic counseling is strongly recommended.
What does a negative result mean?
A negative result means no pathogenic variant was detected in the coding regions analyzed. It does not exclude a genetic cause, as mutations may be in non-coding regions or in other genes.
Will my insurance cover this test?
Coverage depends on the policy and insurer. We recommend contacting your insurance provider. Some schemes under PMJAY, CGHS, ECHS, or private insurance may partially or fully cover specific genetic tests under certain conditions.
Is home sample collection available?
Yes, we offer free home sample collection for patients located across India, including all major cities. A trained phlebotomist will visit your preferred address.
Why does DNA Labs India provide raw data files?
DNA Labs India believes in complete transparency. Providing raw data files (FASTQ, BAM, VCF) enables future reanalysis, second opinions, and lifelong utility of your test 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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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.

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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.

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