Cystinuria Panel

Summary and Pricing

Test Method

Exome Sequencing with CNV Detection
Test Code Test Copy Genes Gene CPT Codes Copy CPT Codes
10075 SLC3A1 81479,81479 Order Options and Pricing
SLC7A9 81479,81479
Test Code Test Copy Genes Panel CPT Code Gene CPT Codes Copy CPT Code Base Price
10075Genes x (2)81479 81479 $890 Order Options and Pricing

Pricing Comments

We are happy to accommodate requests for testing single genes in this panel or a subset of these genes. The price will remain the list price. If desired, free reflex testing to remaining genes on panel is available. Alternatively, a single gene or subset of genes can also be ordered via our PGxome Custom Panel tool.

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

For Reflex to PGxome pricing click here.

Turnaround Time

18 days on average for standard orders or 14 days on average for STAT orders.

Once a specimen has started the testing process in our lab, the most accurate prediction of TAT will be displayed in the myPrevent portal as an Estimated Report Date (ERD) range. We calculate the ERD for each specimen as testing progresses; therefore the ERD range may differ from our published average TAT. View more about turnaround times here.

Targeted Testing

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

EMAIL CONTACTS

Genetic Counselors

Geneticist

Clinical Features and Genetics

Clinical Features

Cystinuria is characterized by impaired transport of cystine and dibasic amino acids in the proximal renal tubule and gastrointestinal tract (Barbosa et al. 2012). The defective renal reabsorption of cystine leads to the formation of calculi in the urinary tract and consequently, obstructive uropathy, pyelonephritis, and even renal failure. Classification of cystinuria can be based on urine excretion of cystine and dibasic amino acids or genetic profiling (Font-Llitjós et al. 2005; Dello Strologo et al. 2002).

Genetics

The inheritance of cystinuria is not clear cut (Dello Strologo et al. 2002). In general, cystinuria shows classic autosomal recessive inheritance. However, obligate heterozygote carriers have variable urinary excretion of cystine and dibasic amino acids and may develop nephrolithiasis. Therefore, cystinuria sometimes can be regarded as an autosomal dominant disorder with incomplete penetrance (Barbosa et al. 2012). SLC3A1 and SLC7A9 are the two known cystinuria causative genes.

The SLC3A1 gene (10 coding exons) encodes a type II membrane glycoprotein which is one of the components of the renal amino acid transporter which transports neutral and basic amino acids in the renal tubule and intestinal tract. To date, documented genetic defects of SLC3A1 include missense, nonsense, splicing variants, small indels and large deletions/duplications (Human Gene Mutation Database).

The SLC7A9 gene (12 coding exons) encodes a member protein of light subunits of amino acid transporters, which functions in the reabsorption of cystine in the kidney tubule. To date, documented genetic defects of SLC7A9 include missense, nonsense, splicing variants, small indels and large deletions/duplications (Human Gene Mutation Database).

In particular, large deletions and duplications are common in both SLC3A1 and SLC7A9 (Schmidt et al. 2003; Barbosa et al. 2012).

Clinical Sensitivity - Sequencing with CNV PGxome

86.8% of mutant alleles were identified in a mutation screen for SLC3A1 and SLC7A9 in 164 probands from the International Cystinuria Consortium (Font-Llitjós et al. 2005). Of the fully explained probands, 56 (34.1%) and 68 (41.5%) had two pathogenic variants found in SLC3A1 and SLC7A9, respectively.

Large deletions and duplications are common in both SLC3A1 and SLC7A9 (Schmidt et al. 2003; Barbosa et al. 2012). Large rearrangements were found in 33.3% of mutant alleles (5 in SLC3A1 and 1 in SLC7A9) in a cohort of 12 Portuguese patients affected with cystinuria (Barbosa et al. 2012). In another cohort of 49 patients, 7 and 3 showed copy number variants in SLC3A1 and SLC7A9, respectively (Schmidt et al. 2003).

Testing Strategy

This test is performed using Next-Gen sequencing with additional Sanger sequencing as necessary.

This panel provides 100% coverage of all coding exons of the genes 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 coverage as ≥20X NGS reads or Sanger sequencing.

Since this test is performed using exome capture probes, a reflex to any of our exome based tests is available (PGxome, PGxome Custom Panels).

Indications for Test

Candidates for this test are patients with cystinuria.

Genes

Official Gene Symbol OMIM ID
SLC3A1 104614
SLC7A9 604144
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Disease

Name Inheritance OMIM ID
Cystinuria AD,AR 220100

Related Test

Name
PGxome®

Citations

  • Barbosa M. et al. 2012. Clinical Genetics. 81: 47-55. PubMed ID: 21255007
  • Dello Strologo L. et al. 2002. Journal of the American Society of Nephrology : Jasn. 13: 2547-53. PubMed ID: 12239244
  • Font-Llitj√≥s M. et al. 2005. Journal of Medical Genetics. 42: 58-68. PubMed ID: 15635077
  • Human Gene Mutation Database (Bio-base).
  • Schmidt C. et al. 2003. Kidney International. 64: 1564-72. PubMed ID: 14531788

Ordering/Specimens

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.

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


Specimen Types

Specimen Requirements and Shipping Details

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ORDER OPTIONS

View Ordering Instructions

1) Select Test Type


2) Select Additional Test Options

STAT and Prenatal Test Options are not available with Patient Plus.

No Additional Test Options are available for this test.

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