Cystinosis via the CTNS Gene, 57-kb Deletion

  • Summary and Pricing
  • Clinical Features and Genetics
  • Citations
  • Methods
  • Ordering/Specimens
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Targeted Deletion

Test Code Test Copy GenesPriceCPT Code Copy CPT Codes
1636 CTNS$490.00 81479 Add to Order
Turnaround Time

The great majority of tests are completed within 18 days.

Clinical Sensitivity

About 50% of cystinosis patients of Northern European descent are found to be homozygous for this deletion (Nesterova and Gahl 2014).

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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 6-12 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 to 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 cornea. 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 mutation 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.

Testing Strategy

This test involves amplification of patient DNA with several sets of specific PCR primers that flank the common CTNS 57-kb deletion. In a patient with the deletion, two separate primer sets amplify across the deletion resulting in 485 bp and 601 bp products. Other control primers are used to detect the normal allele. Sanger sequencing of the deletion products will also be done to confirm breakpoint positions. This test permits the identification of patients with normal genotypes, patients who are homozygous for the deletion, and heterozygous carriers. PreventionGenetics also offers a sequencing test for the CTNS gene (Test #1561).

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.


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


Genetic Counselors
  • 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
  • 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: 165–173. PubMed ID: 10673275
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Targeted Deletion Testing via PCR

Test Procedure

See methodology section in the supplemental information included in test reports.

Analytical Validity
Analytical Limitations
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Ordering Options

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.
  • 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.


(Delivery accepted Monday - Saturday)

  • Collect 3 ml -5 ml (5 ml preferred) of whole blood in EDTA (purple top tube) or ACD (yellow top tube). For Test #500-DNA Banking only, collect 10 ml -20 ml of whole blood.
  • For small babies, we require a minimum of 1 ml of blood.
  • Only one blood tube is required for multiple tests.
  • Ship blood tubes at room temperature in an insulated container. Do not freeze blood.
  • During hot weather, include a frozen ice pack in the shipping container. Place a paper towel or other thin material between the ice pack and the blood tube.
  • In cold weather, include an unfrozen ice pack in the shipping container as insulation.
  • At room temperature, blood specimen is stable for up to 48 hours.
  • If refrigerated, blood specimen is stable for up to one week.
  • Label the tube with the patient name, date of birth and/or ID number.


(Delivery accepted Monday - Saturday)

  • Send in screw cap tube at least 5 µg -10 µg of purified DNA at a concentration of at least 20 µg/ml for NGS and Sanger tests and at least 5 µg of purified DNA at a concentration of at least 100 µg/ml for gene-centric aCGH, MLPA, and CMA tests, minimum 2 µg for limited specimens.
  • For requests requiring more than one test, send an additional 5 µg DNA per test ordered when possible.
  • DNA may be shipped at room temperature.
  • Label the tube with the composition of the solute, DNA concentration as well as the patient’s name, date of birth, and/or ID number.
  • We only accept genomic DNA for testing. We do NOT accept products of whole genome amplification reactions or other amplification reactions.


(Delivery preferred Monday - Thursday)

  • PreventionGenetics should be notified in advance of arrival of a cell culture.
  • Culture and send at least two T25 flasks of confluent cells.
  • Some panels may require additional flasks (dependent on size of genes, amount of Sanger sequencing required, etc.). Multiple test requests may also require additional flasks. Please contact us for details.
  • Send specimens in insulated, shatterproof container overnight.
  • Cell cultures may be shipped at room temperature or refrigerated.
  • Label the flasks with the patient name, date of birth, and/or ID number.
  • We strongly recommend maintaining a local back-up culture. We do not culture cells.
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