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Cystinosis via the CTNS Gene

Summary and Pricing

Test Method

Exome Sequencing with CNV Detection
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
CTNS 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
9565CTNS81479 81479,81479 $990 Order Options and Pricing

Pricing Comments

Our favored testing approach is exome based NextGen sequencing with CNV analysis. This will allow cost effective reflexing to PGxome or other exome based tests. However, if full gene Sanger sequencing is desired for STAT turnaround time, insurance, or other reasons, please see link below for Test Code, pricing, and turnaround time information.

An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.

Click here for costs to reflex to whole PGxome (if original test is on PGxome Sequencing platform).

Click here for costs to reflex to whole PGnome (if original test is on PGnome Sequencing platform).

The Sanger Sequencing method for this test is NY State approved.

For Sanger Sequencing click here.

Turnaround Time

3 weeks on average for standard orders or 2 weeks on average for STAT orders.

Please note: Once the testing process begins, an Estimated Report Date (ERD) range will be displayed in the portal. This is the most accurate prediction of when your report will be complete and may differ from the average TAT published on our website. About 85% of our tests will be reported within or before the ERD range. We will notify you of significant delays or holds which will impact the ERD. Learn more about turnaround times here.

Targeted Testing

For ordering sequencing of targeted known variants, go to our Targeted Variants page.


Genetic Counselors


  • McKenna Kyriss, PhD

Clinical Features and Genetics

Clinical Features

Cystinosis is a condition characterized by the accumulation of the amino acid cystine within the lysosomes of cells. Excess cystine in cells results in crystal formation which is damaging to many organs and tissues. In particular, the kidneys and eyes of individuals with cystinosis are especially vulnerable. Children with cystinosis are normal at birth, but develop signs of renal tubular Fanconi syndrome between 6 and 12 months of age (Nesterova and Gahl 2014; Gahl and Thoene 2014). Symptoms include failure to thrive, vomiting, acidosis, polyuria, excessive thirst, dehydration, electrolyte imbalances and hypophosphatemic rickets (Gahl and Thoene 2014). If left untreated, the major clinical manifestation is renal failure at around 9-10 years of age (Nesterova and Gahl 2014). Corneal cystine crystals can cause photophobia which is always present by two years of age. An intermediate form of cystinosis can also occur, but typically onset is not until adolescence, and symptoms are not as severe. Ocular cystinosis (non-nephropathic) presents with photophobia, but cystine crystals are present in the bone marrow and conjunctiva as well as the corneas. Diagnosis is typically made on a routine eye exam with a slit lamp.

Cystine depletion therapy with cysteamine bitartrate can reduce 90% of cysteine content in cells. With early, diligent treatment, end stage renal disease can be delayed or even prevented (Nesterova and Gahl 2014). Supplementation with phosphate, vitamin D, and good nutrition will reduce growth deficiencies and prevent hypophosphatemic rickets (Nesterova and Gahl 2014). Prior to the use of renal transplant and cystine depletion therapy, the nephropathic patient lifespan was no longer than ten years. With these therapies, affected individuals can survive into forties and fifties.


Cystinosis is an autosomal recessive disorder caused by pathogenic variants in the CTNS gene located on chromosome 17p13.2. CTNS encodes the cystinosin protein (327 amino acids) which transports cystine out of the lysosome into the cytoplasm. It contains seven transmembrane domains and two lysosomal targeting motifs.

CTNS is the only gene which is associated with cystinosis. The incidence of infantile nephropathic cystinosis is approximately 1 per 100,000 to 200,000 live births (Levtchenko et al. 2014). The French region of Brittany has a higher incidence of 1 per 26,000. The most common pathogenic variant is a 57 kb deletion which includes exons 1-9 and part of exon 10 (Levtchenko et al. 2014; Touchman et al. 2000). In people of Northern European ancestry, approximately 50% of patients with nephropathic cystinosis are homozygous for the 57 kb deletion (Nesterova and Gahl 2014). Other pathogenic variants include missense, nonsense, splice site variants, insertions, and deletions (Human Gene Mutation Database). The missense variants are typically present in the transmembrane region of the cystinosin protein.

Clinical Sensitivity - Sequencing with CNV PGxome

Sanger sequencing combined with the common 57 kb deletion test will detect pathogenic variants in 85-95% of patients who present with typical cystinosis symptoms. In a cohort of 12 Turkish patients, 92% of patients had a molecular diagnosis detectable by these methods (Topaloglu et al. 2012). In another study of 13 Egyptian patients, 85% had identifiable pathogenic variants (Soliman et al. 2014). In people of Northern European ancestry, approximately 50% of patients with nephropathic cystinosis are homozygous for the 57 kb deletion (Nesterova and Gahl 2014). In addition to the common 57 kb deletion, a number of other gross deletions in CTNS have been reported to be causative for cystinosis.

Testing Strategy

This test provides full coverage of all coding exons of the CTNS gene plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define full coverage as >20X NGS reads or Sanger sequencing. PGnome panels typically provide slightly increased coverage over the PGxome equivalent. PGnome sequencing panels have the added benefit of additional analysis and reporting of deep intronic regions (where applicable).

This testing also includes coverage for the c.-520G>T, c.-512G>C and c.141-24T>C pre-coding or intronic variants, as well as ~10 bp of adjacent sequence.

Dependent on the sequencing backbone selected for this testing, discounted reflex testing to any other similar backbone-based test is available (i.e., PGxome panel to whole PGxome; PGnome panel to whole PGnome).

Indications for Test

Candidates for this test are patients with symptoms consistent with cystinosis and increased cystine levels in polymorphonuclear leukocytes. Testing is also indicated for family members of patients who have known CTNS pathogenic variants. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in CTNS.


Official Gene Symbol OMIM ID
CTNS 606272
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Related Test

Cystinosis via the CTNS Gene, 57-kb Deletion


  • Gahl W.A., Thoene J.G. 2014. Cystinosis: A Disorder of Lysosomal Membrane Transport. OMMBID - The Online Metabolic and Molecular Bases of Inherited Diseases., New York, NY: The McGraw-Hill Companies, Inc.
  • Human Gene Mutation Database (Bio-base).
  • Levtchenko E., van den Heuvel L., Emma F., Antignac C. 2014. Clinical utility gene card for: Cystinosis. European Journal of Human Genetics 22:5. PubMed ID: 24045844
  • Nesterova, G., Gahl, WA. 2014. Cystinosis. In: Pagon RA, Adam MP, Ardinger HH, Bird TD, Dolan CR, Fong C-T, Smith RJ, and Stephens K, editors. GeneReviews(), Seattle (WA): University of Washington, Seattle. PubMed ID: 20301574
  • Soliman NA, Elmonem MA, Heuvel L van den, Hamid RHA, Gamal M, Bongaers I, Marie S, Levtchenko E. 2014. Mutational Spectrum of the CTNS Gene in Egyptian Patients with Nephropathic Cystinosis. JIMD Rep. PubMed ID: 24464559
  • Topaloglu R, Vilboux T, Coskun T, Ozaltin F, Tinloy B, Gunay-Aygun M, Bakkaloglu A, Besbas N, van den Heuvel L, Kleta R, Gahl WA. 2012. Genetic basis of cystinosis in Turkish patients: a single-center experience. Pediatr Nephrol 27: 115121. PubMed ID: 21786142
  • Touchman J.W., Anikster Y., Dietrich N.L., Maduro V.V.B., McDowell G., Shotelersuk V., Bouffard G.G., Beckstrom-Sternberg S.M., Gahl W.A., Green E.D. 2000. The Genomic Region Encompassing the Nephropathic Cystinosis Gene (CTNS): Complete Sequencing of a 200-kb Segment and Discovery of a Novel Gene within the Common Cystinosis-Causing Deletion. Genome Res 10: 165173. PubMed ID: 10673275


Ordering Options

We offer several options when ordering sequencing tests. For more information on these options, see our Ordering Instructions page. To view available options, click on the Order Options button within the test description.

myPrevent - Online Ordering

  • The test can be added to your online orders in the Summary and Pricing section.
  • Once the test has been added log in to myPrevent to fill out an online requisition form.
  • PGnome sequencing panels can be ordered via the myPrevent portal only at this time.

Requisition Form

  • A completed requisition form must accompany all specimens.
  • Billing information along with specimen and shipping instructions are within the requisition form.
  • All testing must be ordered by a qualified healthcare provider.

For Requisition Forms, visit our Forms page

If ordering a Duo or Trio test, the proband and all comparator samples are required to initiate testing. If we do not receive all required samples for the test ordered within 21 days, we will convert the order to the most effective testing strategy with the samples available. Prior authorization and/or billing in place may be impacted by a change in test code.

Specimen Types

Specimen Requirements and Shipping Details

PGxome (Exome) Sequencing Panel

PGnome (Genome) Sequencing Panel

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Note: acceptable specimen types are whole blood and DNA from whole blood only.
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