GALNT3 Gene Tumoral calcinosis, hyperphosphatemic, familial, type 1 NGS Genetic Test
Short Name: GALNT3 Gene HFTC1 NGS Test
Also known as: HFTC1 NGS Genetic Test, GALNT3 Gene Mutation Analysis, Hyperphosphatemic Familial Tumoral Calcinosis Type 1 Gene Test, GALNT3 Sequencing Test, Familial Tumoral Calcinosis DNA Test
GALNT3 Gene Tumoral calcinosis, hyperphosphatemic, familial, type 1 NGS Genetic Test test available at DNA Labs India for ₹20,000. Uses Next-Generation Sequencing (NGS), Sanger Confirmation (if required), Bioinformatic Variant 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. Results are delivered through the DNA Labs India online portal, email, and WhatsApp.. 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 GALNT3 Gene NGS Genetic Test is to identify pathogenic or likely pathogenic mutations in the GALNT3 gene that cause hyperphosphatemic familial tumoral calcinosis type 1 (HFTC1). This test enables definitive molecular diagnosis, guides clinical management decisions, facilitates carrier detection in family members, and supports genetic counseling for affected families including prenatal and preconception planning.
- Test Code
- 2275
- CPT Code
- 81479
- ICD Code
- E83.59
- 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. Results are delivered through the DNA Labs India online portal, email, and WhatsApp.
- Fasting Required
- No
- Method
- Next-Generation Sequencing (NGS), Sanger Confirmation (if required), Bioinformatic Variant Analysis
Sample Collection
A pre-test Genetic Counselling session is recommended to draw a detailed pedigree chart of family members affected with tumoral calcinosis, hyperphosphatemia, or related metabolic disorders. Clinical history of the patient, including prior imaging and laboratory results (serum phosphorus, calcium, FGF23 levels), should be documented. No fasting is required. Inform the laboratory of any recent blood transfusions.
Method: Venipuncture or FTA Card finger-prick
Laboratory Analysis
Blood sample (3-5 mL) is collected via venipuncture into an EDTA (lavender-top) vacutainer. Alternatively, a single drop of blood can be spotted onto an FTA card. For extracted DNA, submit at least 1 microgram of high-quality genomic DNA in TE buffer or equivalent. Label the sample clearly with patient identifiers. Maintain ambient room temperature during transport; do not freeze whole blood samples.
Report Delivery
The sample is transported to the DNA Labs India molecular genetics laboratory. DNA is extracted, quantified, and subjected to NGS library preparation and sequencing. Bioinformatic analysis is performed to identify variants in the GALNT3 gene. Results are reviewed by a clinical geneticist, and a comprehensive report is generated within 3 to 4 weeks. Results are delivered via online portal, email, or WhatsApp. Raw data files (FASTQ and VCF) are provided alongside the clinical report.
Timeline: Results are typically available within 3 to 4 weeks from the date of sample receipt at the laboratory. Results are delivered through the DNA Labs India online portal, email, and WhatsApp.
Patient Instructions
About This Test
Who Should Get This Test
The purpose of the GALNT3 Gene NGS Genetic Test is to identify pathogenic or likely pathogenic mutations in the GALNT3 gene that cause hyperphosphatemic familial tumoral calcinosis type 1 (HFTC1). This test enables definitive molecular diagnosis, guides clinical management decisions, facilitates carrier detection in family members, and supports genetic counseling for affected families including prenatal and preconception planning.
How to Prepare
- Collect 3-5 mL of venous blood in an EDTA (lavender-top) vacutainer or use an FTA card for a single blood drop
- Gently invert the EDTA tube 8-10 times immediately after collection to prevent clotting
- Ensure proper patient identification and labeling on the sample container
- Store and transport at ambient room temperature; do not freeze whole blood
- If using extracted DNA, ensure a minimum of 1 microgram at a concentration of ≥50 ng/µL
- Complete the test requisition form with clinical history and family pedigree information
- Schedule free home sample collection through the DNA Labs India online booking portal if preferred
Doctor's Notes
Reviewed by Dr SULOCHANA HEMCHANDRA HOLLA — MBBS, MD (Medical Genetics) · Reg. No. 8532
"Hyperphosphatemic familial tumoral calcinosis type 1 caused by GALNT3 mutations is a rare but clinically significant condition that should be suspected in patients presenting with periarticular calcified masses and persistent hyperphosphatemia. Early genetic confirmation through NGS allows clinicians to differentiate HFTC1 from other causes of soft tissue calcification, initiate phosphate-lowering strategies, and offer carrier screening and prenatal counseling to at-risk families. I recommend this test for any patient with unexplained tumoral calcinosis or a suggestive family history of autosomal recessive inheritance."
Last medically reviewed: September 7, 2026
Test Parameters & Specifications
Sample Stability
- Clotted blood sample in EDTA tube
- Sample collected in incorrect anticoagulant (e.g., heparin, which can inhibit PCR and NGS library preparation)
- Insufficient sample volume (less than 2 mL whole blood)
- Severely hemolyzed, lipemic, or icteric sample
- Sample received without proper identification or requisition form
- Sample contaminated or improperly stored (e.g., frozen whole blood)
Understanding Your Results
Pathogenic or Likely Pathogenic Variant Detected (Homozygous)
Confirms a molecular diagnosis of HFTC1. The patient has two copies of a disease-causing mutation in the GALNT3 gene, consistent with autosomal recessive inheritance. Clinical correlation with hyperphosphatemia and tumoral calcinosis is expected. Phosphate-lowering management and genetic counseling for family members should be initiated.
Pathogenic or Likely Pathogenic Variant Detected (Compound Heterozygous)
Confirms a molecular diagnosis of HFTC1. The patient carries two different pathogenic variants in the GALNT3 gene on separate alleles, consistent with autosomal recessive inheritance. Clinical management and family screening are recommended.
Single Heterozygous Pathogenic Variant Detected
The patient is a carrier of one pathogenic GALNT3 variant. Carrier individuals are typically unaffected but have a 50% chance of passing the variant to each offspring. If the partner is also a carrier, there is a 25% risk of affected offspring. Carrier testing of the partner and genetic counseling are recommended.
Variant of Uncertain Significance (VUS) Detected
A genetic variant in GALNT3 was identified, but current evidence is insufficient to classify it as pathogenic or benign. This result is not diagnostic. Family segregation analysis, functional studies, and longitudinal clinical follow-up may help clarify the significance. Repeat analysis or consultation with a genetic specialist is recommended.
No Pathogenic Variant Detected
No pathogenic or likely pathogenic variants were identified in the coding regions and splice sites of the GALNT3 gene. This result does not fully exclude GALNT3-related disease if deep intronic or regulatory variants are suspected, nor does it exclude other genetic causes of tumoral calcinosis (e.g., FGF23 or KL gene mutations). Clinical correlation and additional testing may be warranted.
Consult your physician or clinical geneticist if the test reveals a pathogenic or likely pathogenic variant in the GALNT3 gene, a variant of uncertain significance, or a result that does not align with the clinical presentation. Additionally, seek medical attention if you or a family member develop new calcified masses, worsening joint pain or stiffness, unexplained hyperphosphatemia on routine blood work, or reduced range of motion. Genetic counseling is strongly recommended for all family members of an affected individual to understand carrier status, reproductive risks, and management options.
Limitations
- ⚠This test targets coding exons and intron-exon boundaries of the GALNT3 gene; deep intronic variants, regulatory region mutations, and large copy number variants may not be detected
- ⚠Variants of uncertain significance (VUS) cannot be used for definitive clinical diagnosis and may require family segregation analysis
- ⚠A negative result does not exclude other genetic or non-genetic causes of tumoral calcinosis or hyperphosphatemia
- ⚠Somatic mosaicism at low allele frequencies may not be reliably detected
- ⚠This test is not validated for prenatal diagnosis from chorionic villus sampling or amniotic fluid
Risks & Considerations
- ●Minor bruising or discomfort at the blood draw site
- ●Very rare risk of infection at the venipuncture site
- ●Emotional or psychological impact of genetic test results, particularly for carrier or affected status
- ●Potential for variants of uncertain significance that may cause anxiety without providing a definitive diagnosis
Interfering Factors
- ●Degraded or insufficient DNA quality from the submitted sample may affect sequencing results
- ●Recent blood transfusion within the past 4 weeks may interfere with DNA analysis
- ●Contamination of the sample during collection or transport
- ●Large structural rearrangements or deep intronic variants may not be fully detected by standard NGS coding-region panels
Compare With Similar Tests
| Test | GALNT3 Gene Tumoral calcinosis, hyperphosphatemic, familial, type 1 NGS Genetic Test | Sanger Sequencing of GALNT3 | Serum Phosphorus Level | FGF23 Gene Sequencing | Imaging (X-ray, CT, MRI) |
|---|---|---|---|---|---|
| Comparison | GALNT3 Gene Tumoral calcinosis, hyperphosphatemic, familial, type 1 NGS Genetic Test | Sanger sequencing targets specific exons and is suitable for confirming known familial variants but is less efficient for comprehensive gene screening. NGS covers all coding exons simultaneously with higher throughput and sensitivity, making it the preferred first-line molecular test. | Elevated serum phosphorus is a biochemical hallmark of HFTC1 but is non-specific and can be elevated in chronic kidney disease, hypoparathyroidism, and other conditions. NGS genetic testing provides a definitive etiological diagnosis. | FGF23 mutations cause hyperphosphatemic familial tumoral calcinosis type 2 (HFTC2), which can mimic HFTC1 clinically. NGS of GALNT3 specifically differentiates HFTC1 from HFTC2. A comprehensive panel including both genes may be considered. | Imaging detects the presence and extent of calcified soft tissue masses but cannot determine the underlying genetic etiology. Genetic testing with NGS identifies the causative mutation, enabling precise diagnosis, prognosis, and family screening. |
Frequently Asked Questions
What is the GALNT3 gene and how does it relate to tumoral calcinosis?
How is HFTC1 inherited?
What are the main symptoms of GALNT3 gene tumoral calcinosis?
How is the NGS genetic test performed for GALNT3?
What sample is required for this genetic test?
What is the cost of the GALNT3 NGS Genetic Test in India?
How long does it take to get the test results?
Can this test be performed during pregnancy?
Is genetic counseling required before taking this test?
What does a positive test result mean for me and my family?
Why does DNA Labs India share raw data files along with the clinical report?
Can this test detect all types of mutations in the GALNT3 gene?
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