SLC9A3R1 Gene Nephrolithiasis/osteoporosis, hypophosphatemic, type 2 NGS Genetic Test
Short Name: SLC9A3R1 Gene NGS Test
Also known as: SLC9A3R1 Mutation Analysis, NHERF1 Gene Test, NPHLOP2 Genetic Test, Hypophosphatemic Type 2 Gene Panel, SLC9A3R1 Sequencing Test
SLC9A3R1 Gene Nephrolithiasis/osteoporosis, hypophosphatemic, type 2 NGS Genetic Test test available at DNA Labs India for ₹20,000. Uses Next-Generation Sequencing (NGS), Sanger Confirmation (if required), Bioinformatics Pipeline Analysis, ACMG/AMP Variant Classification 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.. Free home collection in 300+ cities across India.
🩺 Medically Reviewed By
Dr SULOCHANA HEMCHANDRA HOLLA
Consultant Medical Geneticist · Reg: 8532
Last reviewed: September 3, 2026
Overview
The purpose of this test is to identify pathogenic or likely pathogenic variants in the SLC9A3R1 gene that cause hypophosphatemic nephrolithiasis/osteoporosis type 2. Genetic confirmation enables accurate diagnosis, guides treatment decisions including phosphate and calcitriol supplementation, facilitates family screening, and supports genetic counselling regarding recurrence risk and family planning.
- Test Code
- 5466
- CPT Code
- 81479
- ICD Code
- E83.30
- 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.
- Fasting Required
- No
- Method
- Next-Generation Sequencing (NGS), Sanger Confirmation (if required), Bioinformatics Pipeline Analysis, ACMG/AMP Variant Classification
Sample Collection
No special preparation such as fasting is required. A genetic counselling session is recommended prior to sample collection to document the clinical history of the patient and to draw a pedigree chart of family members affected with similar symptoms.
Method: Venipuncture / FTA Card Spot
Laboratory Analysis
A 3 mL venous blood sample is collected in an EDTA (lavender-top) vacutainer. Alternatively, one drop of blood can be spotted on an FTA card. The collection procedure is similar to a routine blood draw and typically takes less than 5 minutes.
Report Delivery
The sample is labelled, stored at ambient room temperature, and transported to the DNA Labs India molecular genetics laboratory. No post-collection restrictions apply. Patients may resume normal activities immediately.
Timeline: Results are typically available within 3 to 4 weeks from the date of sample receipt at the laboratory.
Patient Instructions
About This Test
Who Should Get This Test
The purpose of this test is to identify pathogenic or likely pathogenic variants in the SLC9A3R1 gene that cause hypophosphatemic nephrolithiasis/osteoporosis type 2. Genetic confirmation enables accurate diagnosis, guides treatment decisions including phosphate and calcitriol supplementation, facilitates family screening, and supports genetic counselling regarding recurrence risk and family planning.
How to Prepare
- Collect 3 mL venous blood in an EDTA (lavender-top) vacutainer under aseptic conditions
- Alternatively, spot one drop of blood on the provided FTA card and allow it to dry completely
- Label the sample clearly with patient name, date of birth, and unique sample ID
- Store at ambient room temperature (15–30°C); do not freeze
- Transport to the laboratory within 72 hours of collection
- Include the signed test requisition form and informed consent document with the sample
Doctor's Notes
Reviewed by Dr SULOCHANA HEMCHANDRA HOLLA — MBBS, MD (Medical Genetics) · Reg. No. 8532
"Patients presenting with recurrent kidney stones, unexplained hypophosphatemia, or early-onset osteoporosis should be evaluated for inherited phosphate-wasting disorders. The SLC9A3R1 gene test using NGS technology allows comprehensive variant detection and helps guide targeted treatment strategies, including phosphate supplementation and monitoring of bone mineral density. Early genetic diagnosis can prevent long-term complications such as chronic kidney disease and pathological fractures."
Last medically reviewed: September 3, 2026
Test Parameters & Specifications
Sample Stability
- Hemolyzed or clotted blood sample
- Sample collected in incorrect anticoagulant (e.g., heparin tube instead of EDTA)
- Unlabelled or mislabelled sample
- Sample received without requisition form or informed consent
- Severely degraded DNA with insufficient quantity for NGS library preparation
Understanding Your Results
Pathogenic Variant Detected
A variant classified as pathogenic was identified in the SLC9A3R1 gene. This confirms a genetic diagnosis of hypophosphatemic nephrolithiasis/osteoporosis type 2 (NPHLOP2). Clinical management including phosphate supplementation, calcitriol therapy, and bone density monitoring should be initiated. Family members should be offered cascade genetic testing.
Likely Pathogenic Variant Detected
A variant classified as likely pathogenic was identified. This strongly supports a genetic diagnosis of NPHLOP2. Clinical correlation and family segregation studies are recommended to further confirm pathogenicity. Management should be guided by the treating nephrologist or endocrinologist.
Variant of Uncertain Significance (VUS)
A variant was identified that cannot currently be classified as pathogenic or benign. This result is not diagnostic. Clinical correlation, family studies, and periodic re-evaluation of variant classification as new evidence becomes available are recommended.
No Pathogenic Variant Detected
No pathogenic or likely pathogenic variants were identified in the SLC9A3R1 gene. This result does not completely exclude a genetic etiology, as mutations in other genes (such as SLC34A1, SLC34A3) may also cause similar phosphate wasting conditions. Clinical correlation and further genetic evaluation may be considered.
Consult a nephrologist, endocrinologist, or clinical geneticist if you experience recurrent kidney stones, unexplained bone pain or fractures, muscle weakness, fatigue, delayed growth in children, or if blood tests reveal persistently low phosphate levels. Individuals with a family history of hypophosphatemic disorders should seek genetic counselling to discuss the appropriateness of this test.
Limitations
- ⚠This test does not detect large genomic rearrangements, copy number variations, or deep intronic variants outside the targeted regions
- ⚠Variants of uncertain significance (VUS) may be identified and may require further investigation or family studies
- ⚠A negative result does not completely exclude a genetic basis for the patient's condition, as other genes may be involved
- ⚠This test is not validated for prenatal diagnosis or preimplantation genetic testing
- ⚠Results should always be interpreted in the context of clinical findings and family history by a qualified geneticist or nephrologist
Risks & Considerations
- ●Minimal risk associated with blood draw: minor bruising, slight pain at the puncture site, or very rarely, infection
- ●Psychological impact of receiving genetic test results, including anxiety or distress
- ●Potential implications for insurance or employment in the absence of genetic non-discrimination protections
- ●Identification of variants of uncertain significance (VUS) may cause confusion or concern
Interfering Factors
- ●Hemolyzed or degraded DNA samples may affect sequencing quality
- ●Recent blood transfusion within the past 4 weeks may lead to mixed DNA profiles
- ●Insufficient sample volume may result in inadequate DNA extraction
- ●Presence of somatic mosaicism may not be fully detected by standard NGS pipelines
Compare With Similar Tests
| Test | SLC9A3R1 Gene Nephrolithiasis/osteoporosis, hypophosphatemic, type 2 NGS Genetic Test | |||||
|---|---|---|---|---|---|---|
| Comparison | SLC9A3R1 Gene Nephrolithiasis/osteoporosis, hypophosphatemic, type 2 NGS Genetic Test |
Frequently Asked Questions
What is the SLC9A3R1 gene and what does it do?
What conditions are associated with SLC9A3R1 gene mutations?
Who should consider getting the SLC9A3R1 Gene NGS Genetic Test?
What sample is required for this genetic test?
How long does it take to get the results?
Is genetic counselling recommended before and after this test?
Can this test be performed on children?
What happens if a pathogenic mutation is found?
Is this genetic test covered by insurance or government health schemes?
How accurate is NGS-based genetic testing for the SLC9A3R1 gene?
What is the difference between this test and a standard blood test for phosphate levels?
Does DNA Labs India provide raw genetic data files along with the clinical report?
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