Summary and Pricing
Test MethodExome Sequencing with CNV Detection
|Test Code||Test Copy Genes||Gene CPT Codes Copy CPT Codes|
|10075||SLC3A1||81479,81479||Order Options and Pricing|
|Test Code||Test Copy Genes||Panel CPT Code||Gene CPT Codes Copy CPT Code||Base Price|
|10075||Genes x (2)||81479||81479||$890||Order Options and Pricing|
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.
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.
For ordering sequencing of targeted known variants, go to our Targeted Variants page.
Clinical Features and Genetics
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 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).
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.
Candidates for this test are patients with cystinuria.
|Official Gene Symbol||OMIM ID|
- 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-Llitjós 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
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.
- 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.