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PSAT1 Gene Phosphoserine aminotransferase deficiency NGS Genetic Test

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PSAT1 Gene Phosphoserine aminotransferase deficiency NGS Genetic Test

Short Name: PSAT1 Gene NGS Test

Also known as: PSAT1 Deficiency Test, Phosphoserine Aminotransferase Deficiency Genetic Test, PSAT1 Gene Sequencing, Serine Biosynthesis Disorder NGS Test, PSAT1 Mutation Analysis

PSAT1 Gene Phosphoserine aminotransferase deficiency NGS Genetic Test test available at DNA Labs India for ₹20,000. Uses Next Generation Sequencing (NGS), Sanger Confirmation (if required), Bioinformatics Pipeline Analysis on Blood or Extracted DNA or One Drop Blood on FTA Card samples. Results in Results are typically available within 3 to 4 weeks from the date of sample receipt at the laboratory. Reports are delivered via the DNA Labs India online portal, email, and WhatsApp. Urgent processing may be available upon request.. Free home collection in 300+ cities across India.

NGS Genetic TestAll Ages🏠 Home Collection

🩺 Medically Reviewed By

Overview

The primary purpose of this test is to identify pathogenic mutations in the PSAT1 gene to confirm or rule out a diagnosis of phosphoserine aminotransferase deficiency. This test is used for diagnostic confirmation in symptomatic individuals, carrier detection in at-risk family members, and informing recurrence risk assessment for family planning. Early molecular diagnosis enables timely initiation of serine and glycine supplementation therapy, which may improve neurological outcomes when started early in life.

Test Code
2213
CPT Code
81479
ICD Code
E72.8
Price
₹20,000
Sample Type
Blood or Extracted DNA or One Drop Blood on FTA Card
Result Time
Results are typically available within 3 to 4 weeks from the date of sample receipt at the laboratory. Reports are delivered via the DNA Labs India online portal, email, and WhatsApp. Urgent processing may be available upon request.
Fasting Required
No
Method
Next Generation Sequencing (NGS), Sanger Confirmation (if required), Bioinformatics Pipeline Analysis
Step 1

Sample Collection

Genetic counseling session is recommended before sample collection. A pedigree chart of family members affected with phosphoserine aminotransferase deficiency should be prepared. Provide complete clinical history of the patient. No fasting is required.

Method: Venipuncture / Heel prick (neonates)

Step 2

Laboratory Analysis

A trained phlebotomist collects approximately 3 mL of venous blood in an EDTA (lavender top) vacutainer. For neonates, a heel prick blood drop may be collected on an FTA card. The procedure typically takes less than 5 minutes and involves minimal discomfort.

Step 3

Report Delivery

The sample is labeled, stored at ambient room temperature, and transported to the DNA Labs India testing facility under controlled conditions. Avoid exposure to extreme temperatures. The clinical report, along with raw data files (FASTQ and VCF), is delivered within 3 to 4 weeks.

Timeline: Results are typically available within 3 to 4 weeks from the date of sample receipt at the laboratory. Reports are delivered via the DNA Labs India online portal, email, and WhatsApp. Urgent processing may be available upon request.

Patient Instructions

1
Before the Test:A genetic counseling session is recommended prior to testing. Prepare a detailed pedigree chart of family members affected with phosphoserine aminotransferase deficiency or related metabolic disorders. Provide the complete clinical history of the patient, including developmental milestones, seizure history, neuroimaging findings, and any prior biochemical test results. No fasting is required for this test. Inform the lab of any recent blood transfusions.
2
During the Test:A trained phlebotomist collects a venous blood sample (approximately 3 mL) in an EDTA vacutainer, or a heel prick blood spot on an FTA card for neonates. The sample is transported to DNA Labs India's laboratory under controlled ambient conditions. DNA is extracted, and next-generation sequencing is performed to analyze the complete coding region and flanking intronic sequences of the PSAT1 gene.
3
After the Test:After sample collection, pressure is applied to the venipuncture site to prevent bruising. No special post-collection care is needed. The clinical report along with raw data files (FASTQ and VCF) will be delivered within 3 to 4 weeks via online portal, email, or WhatsApp. Genetic counseling is available after receiving results to discuss findings, implications, and next steps.

About This Test

Who Should Get This Test

The primary purpose of this test is to identify pathogenic mutations in the PSAT1 gene to confirm or rule out a diagnosis of phosphoserine aminotransferase deficiency. This test is used for diagnostic confirmation in symptomatic individuals, carrier detection in at-risk family members, and informing recurrence risk assessment for family planning. Early molecular diagnosis enables timely initiation of serine and glycine supplementation therapy, which may improve neurological outcomes when started early in life.

How to Prepare

  • Use an EDTA (lavender top) vacutainer for blood collection
  • Do NOT use heparin anticoagulant as it can interfere with DNA extraction
  • Ensure the sample is gently mixed after collection to prevent clotting
  • Store the sample at ambient room temperature (15-30°C) until dispatch
  • Do not freeze the blood sample prior to DNA extraction
  • For FTA card collection, allow the blood spot to air dry completely before packaging
  • Label the sample with patient name, date of collection, and sample ID

Doctor's Notes

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

"PSAT1 gene phosphoserine aminotransferase deficiency is a rare autosomal recessive inborn error of serine biosynthesis. Early identification through genetic testing is critical, particularly in families with a history of developmental delays, seizures, or microcephaly in infancy. Prenatal and carrier testing should be considered for at-risk couples with a known family history. Genetic counseling before and after testing is strongly recommended to help families understand inheritance patterns, recurrence risks, and available management strategies. Referral for metabolic evaluation and long-term developmental follow-up is advised upon diagnosis."

Last medically reviewed: September 7, 2026

Test Parameters & Specifications

Sample TypeBlood or Extracted DNA or One Drop Blood on FTA Card
Sample Volume3 mL whole blood in EDTA tube
ContainerEDTA (Lavender Top) Vacutainer or FTA Card
Collection MethodVenipuncture / Heel prick (neonates)

Sample Stability

Whole blood in EDTA at room temperature
Extracted DNA at 2-8°C
Extracted DNA at -20°C
Blood on FTA card at room temperature
Sample Rejection Criteria:
  • Sample collected in heparin anticoagulant
  • Hemolyzed, clotted, or insufficient sample volume
  • Sample without proper labeling or identification
  • Sample contaminated or improperly stored
  • Sample collected after recent blood transfusion (within 120 days) for blood-based testing

Understanding Your Results

The PSAT1 Gene NGS Genetic Test report provides a detailed analysis of the PSAT1 gene, including any detected variants, their classification according to ACMG/AMP guidelines, zygosity, and clinical significance. Results should be interpreted by a qualified geneticist or metabolic specialist in the context of the patient's clinical presentation, family history, and biochemical findings.
📊

No pathogenic or likely pathogenic variants detected

No mutations in the PSAT1 gene were identified. This result reduces the likelihood of PSAT1 phosphoserine aminotransferase deficiency but does not exclude it entirely, as mutations in deep intronic regions or large rearrangements may not be detected by this method. Clinical correlation and consideration of other genetic causes is advised.

📊

Homozygous pathogenic variant detected

Two copies of the same pathogenic variant were identified in the PSAT1 gene, consistent with autosomal recessive inheritance. This finding supports a diagnosis of phosphoserine aminotransferase deficiency. Carrier testing for parents is recommended to confirm segregation.

📊

Compound heterozygous pathogenic variants detected

Two different pathogenic or likely pathogenic variants were identified in the PSAT1 gene (one on each allele). This finding supports a diagnosis of phosphoserine aminotransferase deficiency. Parental testing is recommended for confirmation.

📊

Heterozygous pathogenic variant detected (carrier)

A single pathogenic variant was identified, indicating carrier status. The individual is typically unaffected but has a 50% chance of passing the variant to offspring. If the partner is also a carrier, there is a 25% risk of having an affected child.

📊

Variant of Uncertain Significance (VUS) detected

A genetic variant was identified in the PSAT1 gene, but current evidence is insufficient to classify it as pathogenic or benign. Clinical correlation, family studies, and functional analysis may help determine significance. Genetic counseling is recommended.

⚠️ When to Consult a Doctor:

Consult a clinical geneticist or metabolic specialist if the test detects any pathogenic, likely pathogenic, or uncertain variants. Also consult a doctor if the patient exhibits symptoms such as developmental delays, seizures, microcephaly, hypotonia, or low serine levels, even if genetic testing is normal. Families planning future pregnancies should seek genetic counseling regarding recurrence risk and prenatal testing options.

Limitations

  • This test does not detect large genomic rearrangements, copy number variations, or deep intronic mutations outside covered regions
  • Variants of Uncertain Significance (VUS) may be identified and may require further clinical correlation
  • A negative result does not completely exclude other genetic causes of the clinical phenotype
  • This test is specific to the PSAT1 gene and does not screen for mutations in other serine biosynthesis pathway genes (PHGDH, PSPH)
  • Results should always be interpreted in conjunction with clinical findings, family history, and biochemical data

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 further testing
  • Potential for incidental findings related to carrier status that may have implications for family planning
  • Emotional and psychological impact of a positive diagnosis — genetic counseling support is recommended

Interfering Factors

  • Degraded or insufficient DNA quality may affect sequencing accuracy
  • Blood sample contaminated or improperly stored may require recollection
  • Recent blood transfusion (within 120 days) may affect results in blood-based samples
  • Heparin anticoagulant can interfere with downstream molecular processing

Compare With Similar Tests

TestPSAT1 Gene Phosphoserine aminotransferase deficiency NGS Genetic TestSanger Sequencing of PSAT1 GeneTargeted Mutation Panel (Metabolic Disorders)Whole Exome Sequencing (WES)Biochemical Serine Levels (Plasma/CSF)
ComparisonPSAT1 Gene Phosphoserine aminotransferase deficiency NGS Genetic Test

Frequently Asked Questions

What is PSAT1 Gene Phosphoserine Aminotransferase Deficiency?
PSAT1 gene phosphoserine aminotransferase deficiency is a rare autosomal recessive genetic disorder caused by mutations in the PSAT1 gene. This gene encodes the enzyme phosphoserine aminotransferase, which is essential for the biosynthesis of serine, an amino acid critical for brain development, protein synthesis, and nucleotide metabolism. Deficiency of this enzyme leads to low serine levels, resulting in neurological and developmental abnormalities including intellectual disability, seizures, and microcephaly.
What does the PSAT1 Gene NGS Genetic Test involve?
The test involves collecting a blood sample (or extracted DNA), which is then analyzed using next-generation sequencing (NGS) technology. The entire coding region and flanking intronic sequences of the PSAT1 gene are sequenced to detect pathogenic variants, including single nucleotide variants, small insertions, deletions, and splice-site mutations. Results are interpreted according to ACMG/AMP variant classification guidelines and presented in a comprehensive clinical report.
Who should get tested for PSAT1 deficiency?
This test is recommended for individuals who present with symptoms suggestive of serine biosynthesis disorder, such as developmental delays, seizures, intellectual disability, microcephaly, or hypotonia. It is also recommended for carrier testing in parents or siblings of an affected individual and for prenatal testing in families with a known PSAT1 mutation. A physician or genetic counselor can help determine if this test is appropriate.
What is the cost of the PSAT1 Gene NGS Genetic Test at DNA Labs India?
The cost of the PSAT1 Gene Phosphoserine Aminotransferase Deficiency NGS Genetic Test at DNA Labs India is INR 20,000. This price includes home sample collection, DNA extraction, NGS sequencing, bioinformatics analysis, variant interpretation, clinical reporting, and provision of raw data files (FASTQ and VCF formats). Free home collection is available across 300+ cities in India.
How long does it take to receive the test results?
Results are typically available within 3 to 4 weeks from the date of sample receipt at the laboratory. The clinical report, along with raw data files (FASTQ and VCF), is delivered via the DNA Labs India online portal, email, and WhatsApp.
What sample is required for this test?
The test requires either 3 mL of whole blood collected in an EDTA (lavender top) vacutainer, extracted DNA, or one drop of blood on an FTA card. No fasting is required. The sample can be collected at home through our free home collection service or at a walk-in center.
Is genetic counseling required before taking this test?
While not mandatory, genetic counseling is strongly recommended before and after the test. A pre-test counseling session helps prepare a family pedigree, understand the inheritance pattern, and set appropriate expectations. Post-test counseling helps interpret the results, discuss implications for the patient and family members, and plan next steps.
What does a positive result mean?
A positive result means that pathogenic or likely pathogenic variants were identified in the PSAT1 gene. For a person showing two variants (homozygous or compound heterozygous), this confirms a diagnosis of phosphoserine aminotransferase deficiency. A single variant indicates carrier status. Your genetic counselor and treating physician will discuss the implications and management options based on the specific findings.
What is the difference between NGS and Sanger sequencing for this test?
Next-generation sequencing (NGS) allows simultaneous sequencing of multiple regions of the PSAT1 gene with high throughput and deep coverage, making it more efficient, comprehensive, and cost-effective than Sanger sequencing. Sanger sequencing is typically used as a confirmation method for specific variants identified by NGS. DNA Labs India uses NGS as the primary method with Sanger confirmation available when needed.
Does DNA Labs India provide raw data files along with the report?
Yes. DNA Labs India is one of the only labs in India that transparently shares raw data files (FASTQ and VCF formats) along with the conclusive clinical report. This allows patients, families, and their physicians to independently verify results, seek second opinions, or use the data for future clinical needs.
Is home sample collection available for this test?
Yes, DNA Labs India offers free home sample collection for the PSAT1 Gene NGS Genetic Test when booked online. This service is available in over 300 cities across India, including Mumbai, Delhi, Bangalore, Hyderabad, Chennai, Kolkata, Pune, Ahmedabad, and many more. A trained phlebotomist will visit your location at a scheduled time to collect the sample.
Can this test be used for prenatal diagnosis?
Yes, if the familial PSAT1 mutations have been previously identified in an affected family member, targeted testing can be performed on prenatal samples such as chorionic villus sampling (CVS) or amniocentesis. It is essential to consult with a genetic counselor and your obstetrician before opting for prenatal testing. Prenatal testing should be performed only after appropriate genetic counseling.
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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