AFF2 Gene Mental retardation, X-linked, associated with fragile site FRAXE NGS Genetic Test
Short Name: AFF2 Gene FRAXE NGS Test
Also known as: FRAXE Syndrome Test, FMR2-Related Intellectual Disability Test, AFF2 Gene Mutation Analysis, Fragile Site FRAXE Genetic Test, X-linked FRAXE Mental Retardation NGS Test
AFF2 Gene Mental retardation, X-linked, associated with fragile site FRAXE NGS Genetic Test test available at DNA Labs India for ₹20,000. Uses Next-Generation Sequencing (NGS) 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, or WhatsApp as per the patient's preference.. 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 the AFF2 Gene FRAXE NGS Genetic Test is to identify pathogenic mutations, including CGG trinucleotide repeat expansions and other sequence variants in the AFF2 gene, to confirm or rule out a diagnosis of X-linked intellectual disability associated with fragile site FRAXE. This test aids clinicians in establishing a definitive molecular diagnosis, differentiating FRAXE-related mental retardation from other causes of intellectual disability, guiding therapeutic management, informing genetic counseling and family planning, and enabling carrier detection in at-risk family members.
- Test Code
- 1706
- CPT Code
- 81479
- ICD Code
- Q99.2
- 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, or WhatsApp as per the patient's preference.
- Fasting Required
- No
- Method
- Next-Generation Sequencing (NGS)
Sample Collection
A genetic counseling session is recommended prior to sample collection. The clinical history of the patient and a pedigree chart of family members affected with X-linked mental retardation should be prepared. No fasting is required. Ensure all patient consent forms are completed.
Method: Venipuncture
Laboratory Analysis
A standard venipuncture blood draw of approximately 5 mL will be collected into an EDTA (lavender-top) tube. The sample will be labeled with patient identifiers and handled according to laboratory protocols.
Report Delivery
The blood sample will be transported to the laboratory under ambient temperature conditions. Results will be available in 3 to 4 weeks. The genetic counselor will follow up to discuss findings and implications.
Timeline: Results are typically available within 3 to 4 weeks from the date of sample collection. Results are delivered via the online portal, email, or WhatsApp as per the patient's preference.
Patient Instructions
About This Test
Who Should Get This Test
The purpose of the AFF2 Gene FRAXE NGS Genetic Test is to identify pathogenic mutations, including CGG trinucleotide repeat expansions and other sequence variants in the AFF2 gene, to confirm or rule out a diagnosis of X-linked intellectual disability associated with fragile site FRAXE. This test aids clinicians in establishing a definitive molecular diagnosis, differentiating FRAXE-related mental retardation from other causes of intellectual disability, guiding therapeutic management, informing genetic counseling and family planning, and enabling carrier detection in at-risk family members.
How to Prepare
- No fasting is required before sample collection
- Provide complete clinical history and family pedigree before sample collection
- Genetic counseling session must be completed prior to testing
- Ensure the sample is collected in an EDTA (lavender-top) tube
- Label the sample clearly with patient name, date of birth, and sample date
- Transport the sample at ambient room temperature to the laboratory
- Inform the laboratory of any recent blood transfusions or bone marrow transplants
Doctor's Notes
Reviewed by Dr SULOCHANA HEMCHANDRA HOLLA — MBBS, MD (Medical Genetics) · Reg. No. 8532
"X-linked intellectual disability associated with the AFF2 gene frequently presents in early childhood with speech and language delays, learning difficulties, and behavioral challenges. Precise identification of AFF2 mutations through NGS technology is essential for early intervention strategies, tailored therapeutic planning, and accurate genetic counseling for affected families. I recommend this test for any patient presenting with unexplained intellectual disability and a suspected X-linked inheritance pattern."
Last medically reviewed: September 7, 2026
Test Parameters & Specifications
Sample Stability
- Hemolyzed, clotted, or inadequately labeled samples
- Samples collected in incorrect tube type (non-EDTA tubes)
- Samples with insufficient volume (less than 2 mL)
- Samples received without completed requisition form or clinical history
- Contaminated or leaking samples
Understanding Your Results
No Pathogenic Variant Detected
No disease-causing mutations were identified in the AFF2 gene. Clinical correlation with other diagnostic evaluations is recommended if symptoms persist.
Pathogenic or Likely Pathogenic Variant Detected
A mutation known to cause or likely to cause FRAXE-associated intellectual disability has been identified. Genetic counseling is strongly recommended to discuss implications, inheritance pattern, and family planning options.
CGG Repeat Expansion - Full Mutation (>200 repeats) with Methylation
Full mutation at the FRAXE locus with hypermethylation of the AFF2 promoter region, consistent with FRAXE mental retardation. Gene silencing is likely.
CGG Repeat Expansion - Intermediate or Premutation (40-200 repeats)
Intermediate or premutation alleles identified. These may not cause clinical symptoms but carry a risk of expansion to full mutation in subsequent generations. Genetic counseling is recommended.
Variant of Uncertain Significance (VUS)
A variant was identified whose clinical significance is currently unknown. Further family studies and functional analyses may be needed. Periodic reclassification may be warranted.
Carrier Status (Heterozygous Female)
A female carrier of an AFF2 pathogenic variant has been identified. While carriers may be asymptomatic or mildly affected, they have a risk of transmitting the mutation to offspring.
Consult a neurologist or clinical geneticist if you or your child experience unexplained intellectual disability, speech and language delays, learning difficulties, or behavioral challenges, particularly if there is a family history of X-linked mental retardation. Early consultation allows for timely genetic testing, appropriate interventions, and informed family planning.
Limitations
- ⚠This test may not detect all types of mutations including deep intronic variants and regulatory region changes outside the targeted regions
- ⚠Mosaicism for CGG repeat expansions may be present and difficult to fully characterize
- ⚠Variants of uncertain significance (VUS) may be identified and may require further investigation
- ⚠This test does not replace comprehensive clinical evaluation and neurodevelopmental assessment
- ⚠Negative result does not completely exclude other genetic causes of intellectual disability
Risks & Considerations
- ●Minimal risk associated with blood collection: slight bruising or discomfort at the venipuncture site
- ●Risk of identifying variants of uncertain significance (VUS) which may cause anxiety and require additional follow-up testing
- ●Genetic results may have psychological and familial implications, including impacts on family planning
- ●Risk of incidental findings in genes other than AFF2 if broader analysis is performed
Interfering Factors
- ●Blood sample contamination or degradation due to improper storage or transport
- ●Recent blood transfusion within the past 4 weeks may affect DNA quality
- ●Insufficient sample volume or hemolyzed samples
- ●Mosaicism in repeat expansion size may complicate interpretation
Compare With Similar Tests
| Test | AFF2 Gene Mental retardation, X-linked, associated with fragile site FRAXE NGS Genetic Test | ||||
|---|---|---|---|---|---|
| Comparison | AFF2 Gene Mental retardation, X-linked, associated with fragile site FRAXE NGS Genetic Test | Targets the FMR1 gene at fragile site FRAXA, the most common inherited cause of intellectual disability. While Fragile X and FRAXE share clinical features, they involve different genes and distinct trinucleotide repeat expansions. Both tests may be ordered together for comprehensive evaluation. | A broader panel that simultaneously analyzes multiple genes associated with X-linked intellectual disability, including AFF2, FMR1, ARX, MED12, and others. This panel provides more comprehensive coverage when the specific gene involved is unknown. | Detects copy number variants (deletions and duplications) across the entire genome. CMA does not detect trinucleotide repeat expansions such as those at the FRAXE locus, making the AFF2 NGS test necessary for specific FRAXE diagnosis. | Analyzes all protein-coding genes in the genome. WES may detect point mutations in AFF2 but may not reliably detect trinucleotide repeat expansions. Targeted AFF2 testing is recommended when FRAXE is specifically suspected. |
Frequently Asked Questions
What is the AFF2 Gene FRAXE NGS Genetic Test?
Who should get the AFF2 Gene FRAXE Genetic Test?
What is the cost of the AFF2 Gene FRAXE NGS Genetic Test at DNA Labs India?
How is the blood sample collected for this test?
What is the turnaround time for receiving results?
Is the AFF2 Gene FRAXE Genetic Test available across India?
What does a positive (pathogenic variant detected) result mean?
Can female carriers of AFF2 gene mutations be detected with this test?
Is genetic counseling included with this test?
Is this genetic test covered by health insurance in India?
How accurate is NGS testing for AFF2 gene mutations?
What happens after a diagnosis of FRAXE-associated intellectual disability is confirmed?
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