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Cystinuria via the SLC7A9 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
11691 SLC7A9 81479 81479,81479 $990 Order Options and Pricing
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
11691SLC7A981479 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


  • Angela Gruber, PhD

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).


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 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%) have 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 provides full coverage of all coding exons of the SLC7A9 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).

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 cystinuria. Testing is also indicated for family members of patients who have known mutations in the SLC7A9 gene. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in SLC7A9.


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


Name Inheritance OMIM ID
Cystinuria AD,AR 220100


  • 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 (HGMD).
  • Schmidt C. et al. 2003. Kidney International. 64: 1564-72. PubMed ID: 14531788


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

Specimen Types

Specimen Requirements and Shipping Details

PGxome (Exome) Sequencing Panel

PGnome (Genome) Sequencing Panel

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View Ordering Instructions

1) Select Test Method (Platform)

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.

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