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SLC9A6 Gene Mental retardation, X-linked syndromic, Christianson type NGS Genetic Test

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SLC9A6 Gene Mental retardation, X-linked syndromic, Christianson type NGS Genetic Test

Short Name: SLC9A6 Christianson Syndrome NGS Test

Also known as: Christianson Syndrome, MRXSCH, SLC9A6-related X-linked Intellectual Disability, X-linked Angelman-like Syndrome, SLC9A6 Gene Panel

SLC9A6 Gene Mental retardation, X-linked syndromic, Christianson type 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 Results are available within 3 to 4 weeks from sample receipt at the laboratory.. Free home collection in 300+ cities across India.

Next Generation Sequencing (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 SLC9A6 Gene Christianson Syndrome NGS Genetic Test is performed to identify pathogenic mutations in the SLC9A6 gene that cause X-linked syndromic mental retardation (Christianson Syndrome). The primary purpose is to confirm a clinical diagnosis in individuals presenting with intellectual disability, absent speech, seizures, ataxia, and other characteristic features. This test is also used for carrier identification in at-risk female family members and for informed reproductive planning. Molecular confirmation through NGS allows differentiation from phenotypically similar conditions such as Angelman Syndrome, Rett Syndrome, and other X-linked intellectual disability syndromes, enabling targeted clinical management and appropriate genetic counselling.

Test Code
1699
CPT Code
81470
ICD Code
Q87.8
Price
₹20,000
Sample Type
Blood or Extracted DNA or One drop Blood on FTA Card
Result Time
Results are available within 3 to 4 weeks from sample receipt at the laboratory.
Fasting Required
No
Method
Next Generation Sequencing (NGS)
Step 1

Sample Collection

No special preparation or fasting is required. Ensure genetic counselling is completed and informed consent is obtained prior to sample collection. Provide a detailed clinical history and family pedigree chart.

Method: Venipuncture

Step 2

Laboratory Analysis

A trained phlebotomist will collect 3-5 mL of venous blood in an EDTA (lavender top) vacutainer via standard venipuncture technique. Alternatively, a single drop of blood on an FTA card or previously extracted DNA may be submitted.

Step 3

Report Delivery

Label the sample correctly with patient details. Store at ambient room temperature and transport to the laboratory within 48 hours. Avoid freezing whole blood samples.

Timeline: Results are available within 3 to 4 weeks from sample receipt at the laboratory.

Patient Instructions

1
Before the Test:A genetic counselling session is recommended prior to testing. During this session, a detailed clinical history of the patient and a pedigree chart of family members affected with intellectual disability, seizures, or related neurological features will be drawn. Informed consent must be obtained. No fasting or special preparation is required for blood sample collection.
2
During the Test:The blood sample is collected via venipuncture (3-5 mL in an EDTA tube) or a single blood drop on an FTA card. DNA is extracted in the laboratory and subjected to Next Generation Sequencing (NGS) targeting the entire coding region and flanking intronic sequences of the SLC9A6 gene. Bioinformatic analysis is performed to identify variants, which are then classified according to ACMG guidelines.
3
After the Test:Results are typically available within 3 to 4 weeks and delivered via the online portal, email, or WhatsApp. The clinical report includes variant classification, clinical significance, and recommendations. DNA Labs India also provides raw data files (FASTQ and VCF) for independent review. A follow-up genetic counselling session is recommended to discuss results and plan next steps.

About This Test

Who Should Get This Test

The SLC9A6 Gene Christianson Syndrome NGS Genetic Test is performed to identify pathogenic mutations in the SLC9A6 gene that cause X-linked syndromic mental retardation (Christianson Syndrome). The primary purpose is to confirm a clinical diagnosis in individuals presenting with intellectual disability, absent speech, seizures, ataxia, and other characteristic features. This test is also used for carrier identification in at-risk female family members and for informed reproductive planning. Molecular confirmation through NGS allows differentiation from phenotypically similar conditions such as Angelman Syndrome, Rett Syndrome, and other X-linked intellectual disability syndromes, enabling targeted clinical management and appropriate genetic counselling.

How to Prepare

  • Collect 3-5 mL venous blood in an EDTA (Lavender Top) vacutainer
  • Alternatively, use one drop of blood on an FTA Card or submit extracted DNA
  • Do not use heparinized tubes as heparin can interfere with NGS library preparation
  • Label the sample with patient name, date of birth, and sample ID
  • Store at ambient room temperature (15-30°C); do not freeze
  • Transport to laboratory within 48 hours of collection
  • Ensure informed consent form is signed and accompany the sample

Doctor's Notes

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

"Christianson Syndrome is frequently underdiagnosed due to phenotypic overlap with Angelman Syndrome and other X-linked intellectual disability syndromes. Confirmatory genetic testing via NGS of the SLC9A6 gene is essential for an accurate diagnosis. Early identification allows for targeted seizure management, neurodevelopmental support, and informed genetic counselling for at-risk family members. Carrier testing for females in the family is also recommended as they may exhibit mild cognitive or behavioural features. Families should undergo pre-test genetic counselling to understand X-linked inheritance, recurrence risks, and reproductive options."

Last medically reviewed: September 7, 2026

Test Parameters & Specifications

Sample TypeBlood or Extracted DNA or One drop Blood on FTA Card
Sample Volume3 to 5 mL
ContainerEDTA (Lavender Top) Vacutainer or FTA Card
Collection MethodVenipuncture

Sample Stability

Whole blood in EDTA: Stable up to 72 hours at ambient room temperature (15-30°C)
FTA Card: Stable at room temperature for extended periods when stored properly
Extracted DNA: Stable at 2-8°C for up to 6 months or at -20°C for long-term storage
Sample Rejection Criteria:
  • Sample collected in heparinized tube
  • Hemolyzed, clotted, or insufficient sample volume
  • Sample without proper labeling or patient identification
  • Sample older than 72 hours at ambient temperature (whole blood)
  • Missing or incomplete consent form
  • Sample transported at improper temperature conditions

Understanding Your Results

The results of the SLC9A6 Gene NGS Genetic Test are interpreted based on the presence or absence of pathogenic or likely pathogenic variants in the SLC9A6 gene. Variants are classified according to the American College of Medical Genetics and Genomics (ACMG) guidelines into five categories: Pathogenic, Likely Pathogenic, Variant of Uncertain Significance (VUS), Likely Benign, and Benign. A positive result confirms the molecular diagnosis of Christianson Syndrome and enables targeted clinical management, genetic counselling, and carrier testing of family members. A negative result does not exclude all genetic causes of the patient's clinical presentation, and additional genetic testing may be recommended by the treating physician or geneticist.
📊

Confirms diagnosis of Christianson Syndrome (MRXSCH). The identified mutation in SLC9A6 is known to cause the disorder. Genetic counselling, carrier testing of family members, and targeted clinical management are recommended.

High

Result type: Pathogenic Variant Detected

📊

Strongly suggestive of Christianson Syndrome. The variant is predicted to be disease-causing based on available evidence. Correlation with clinical features and family studies is advised. Follow-up genetic counselling is recommended.

High

Result type: Likely Pathogenic Variant Detected

📊

A genetic change in SLC9A6 was identified but current evidence is insufficient to classify it as pathogenic or benign. Clinical correlation is essential. Periodic reclassification is recommended as new data become available. This result should not be used alone for clinical decision-making.

Uncertain

Result type: Variant of Uncertain Significance (VUS)

📊

The identified variant is unlikely to be the cause of the patient's clinical features. No action required for this specific variant.

Low

Result type: Likely Benign Variant Detected

📊

No disease-causing mutations were identified in the SLC9A6 gene. This result does not exclude a genetic basis for the patient's condition. Additional testing such as Whole Exome Sequencing, Chromosomal Microarray, or evaluation of other genes may be considered.

Negative

Result type: No Pathogenic Variant Detected

⚠️ When to Consult a Doctor:

Consult a clinical geneticist or neurologist if genetic testing reveals a pathogenic or likely pathogenic variant in the SLC9A6 gene, if a variant of uncertain significance is identified, or if clinical symptoms persist despite a negative result. Families with confirmed Christianson Syndrome should seek genetic counselling for recurrence risk assessment and reproductive planning. Early referral for neurodevelopmental assessment, seizure management, and rehabilitation services is strongly recommended.

Limitations

  • ⚠This test targets only the SLC9A6 gene and does not detect mutations in other genes associated with intellectual disability
  • ⚠Large deletions or duplications involving the SLC9A6 gene may require confirmatory testing by MLPA or CMA
  • ⚠Deep intronic regulatory region variants outside the sequenced target may not be detected
  • ⚠Variants of uncertain significance (VUS) may be identified and require periodic reclassification
  • ⚠This test does not detect mitochondrial DNA variants or trinucleotide repeat expansions
  • ⚠A negative result does not completely exclude a genetic basis for the patient's condition

Risks & Considerations

  • ●Minor bruising or discomfort at the venipuncture site
  • ●Very rare risk of infection at the blood draw site
  • ●Psychological impact of genetic diagnosis on the patient and family
  • ●Potential identification of variants of uncertain significance that may cause anxiety
  • ●Risk of incidental findings unrelated to the primary indication (minimal with targeted gene panel)

Interfering Factors

  • ●Degraded or insufficient DNA quality may affect sequencing results
  • ●Blood sample collected in incorrect anticoagulant (e.g., heparin instead of EDTA)
  • ●Recent blood transfusion within the past 4 weeks may affect results
  • ●Contamination during sample collection or transport

Compare With Similar Tests

TestSLC9A6 Gene Mental retardation, X-linked syndromic, Christianson type NGS Genetic TestFragile X Syndrome (FMR1 Gene) Genetic TestAngelman Syndrome (UBE3A Gene) Methylation-Specific MLPAWhole Exome Sequencing (WES)Chromosomal Microarray Analysis (CMA)
ComparisonSLC9A6 Gene Mental retardation, X-linked syndromic, Christianson type NGS Genetic Test

Frequently Asked Questions

What is the SLC9A6 Gene Christianson Syndrome NGS Genetic Test?
This is a Next Generation Sequencing (NGS) based genetic test that analyzes the SLC9A6 gene for mutations causing Christianson Syndrome, an X-linked syndromic form of intellectual disability. The test provides comprehensive sequencing of the gene's coding regions and flanking intronic sequences to detect pathogenic variants responsible for the disorder.
Who should get tested for Christianson Syndrome?
This test is recommended for males presenting with moderate to severe intellectual disability, absent or limited speech, early-onset seizures, cerebellar ataxia, hyperkinesis, and a happy demeanour, particularly when other common causes such as Angelman Syndrome or Fragile X Syndrome have been excluded. It is also recommended for carrier testing in females from families with known SLC9A6 mutations.
What sample is required for this genetic test?
The test can be performed using 3-5 mL of venous blood collected in an EDTA (lavender top) vacutainer, extracted DNA, or a single drop of blood on an FTA card. No fasting is required prior to sample collection.
How long does it take to get the results?
Results are typically available within 3 to 4 weeks from the date the sample is received at the laboratory. The report is delivered via the online portal, email, or WhatsApp.
What is the cost of the SLC9A6 Gene NGS Genetic Test?
The cost of the SLC9A6 Gene Christianson Syndrome NGS Genetic Test at DNA Labs India is Rs 20,000 (INR). This includes NGS sequencing, variant analysis, the clinical report, and raw data files (FASTQ and VCF). Free home sample collection is available in select cities across India.
Is home sample collection available for this test?
Yes, DNA Labs India offers free home sample collection for online bookings of this test across a wide network of cities in India. A trained phlebotomist will visit your home to collect the blood sample at a scheduled time convenient for you.
What are the main symptoms of Christianson Syndrome?
The main symptoms include moderate to severe intellectual disability, absent or severely delayed speech, early-onset seizures, progressive cerebellar ataxia, hyperkinesis, microcephaly (in some cases), abnormal eye movements (ophthalmoplegia), muscle weakness, a characteristic happy demeanour with frequent smiling, and recurrent infections.
How is Christianson Syndrome inherited?
Christianson Syndrome follows an X-linked recessive inheritance pattern. The SLC9A6 gene is located on the X chromosome. Males (who have one X chromosome) are predominantly affected as they need only one mutated copy to manifest the disorder. Females with one mutated copy are typically carriers who may show mild symptoms due to random X-inactivation. If the mother is a carrier, there is a 50% chance of passing the mutation to each son (who would be affected) and a 50% chance of passing it to each daughter (who would be a carrier).
Can Christianson Syndrome be detected during pregnancy?
If a familial SLC9A6 mutation has been previously identified, prenatal testing or preimplantation genetic testing (PGT) may be available for at-risk pregnancies. Prenatal testing can be performed on chorionic villus samples (CVS) at 10-13 weeks or amniotic fluid at 15-18 weeks of gestation. Consult your genetic counsellor or obstetrician for guidance on prenatal testing options.
Why is genetic counselling important before and after this test?
Pre-test genetic counselling helps families understand the purpose of the test, the inheritance pattern of Christianson Syndrome, the implications of possible results (positive, negative, or VUS), and reproductive options. Post-test counselling is essential to interpret results, plan clinical management, discuss recurrence risks, and offer carrier testing to other family members. A detailed family pedigree is drawn during counselling to identify at-risk relatives.
Does DNA Labs India share raw data and sequencing files with patients?
Yes. DNA Labs India is the only laboratory in India that transparently provides raw data, FASTQ files, and VCF files alongside the clinical test report for this test. This allows patients, families, and their physicians to independently review the sequencing data or seek second opinions from other geneticists or bioinformaticians.
What should I do if the test result is negative but symptoms persist?
A negative result means no pathogenic variant was detected in the SLC9A6 gene. This does not rule out all genetic causes of the patient's condition. Your physician or geneticist may recommend additional testing such as Whole Exome Sequencing (WES), Chromosomal Microarray Analysis (CMA), or a broader intellectual disability gene panel to identify the underlying cause. Discuss further evaluation options with your healthcare provider.
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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