Congenital Abnormalities of Kidney and Urinary Tract (CAKUT) and VACTERL Association via the TRAP1 Gene
Summary and Pricing 
Test Method
Exome Sequencing with CNV Detection
| Test Code | Test Copy Genes | Test CPT Code | Gene CPT Codes Copy CPT Code | Base Price | |
|---|---|---|---|---|---|
| 8067 | TRAP1 | 81479 | 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. If the Sanger option is selected, CNV detection may be ordered through Test #600.
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.
Clinical Features and Genetics
Clinical Features
Congenital anomalies of kidney and urinary tract (CAKUT) represent a wide spectrum of defects in the morphogenesis of the kidney and/or urinary tract, accounting for about 40-50% of children with chronic kidney disease worldwide (Vivante et al. 2014). Clinical features of CAKUT include renal agenesis, renal hypodysplasia, multicystic dysplastic kidney, hydronephrosis, ureteropelvic junction obstruction, megaureter, ureter duplex, vesicoureteral reflux, and posterior urethral valves. CAKUT usually occurs isolated, but it can be associated with extrarenal presentations such as VACTERL association, which is a rare multi-organ disorder. VACTERL stands for vertebral defects, anal atresia, cardiac defects, tracheo-esophageal fistula, renal anomalies, and limb abnormalities. Recessive mutations in the TRAP1 gene can cause CAKUT or CAKUT with VACTERL association (Saisawat et al. 2014).
Genetics
CAKUT is a group of highly genetically heterogeneous diseases and dozens of genes have been associated with this spectrum (Vivante et al. 2014). TRAP1-caused CAKUT is inherited in an autosomal recessive manner (Saisawat et al. 2014). TRAP1 has 18 coding exons that encode TNF receptor-associated protein 1, which plays a key role in the maintenance of mitochondrial integrity and in protection against oxidative cell damage. Genetic defects documented to date in TRAP1 only include missense variants and small indels (Human Gene Mutation Database).
Clinical Sensitivity - Sequencing with CNV PGxome
In a study of a total of 677 CAKUT patients and 301 patients with VACTERL association, Saisawat et al. identified TRAP1 recessive mutations in about 0.5% of these patients (Saisawat et al. 2014).
Testing Strategy
This test provides full coverage of all coding exons of the TRAP1 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 CAKUT or CAKUT with VACTERL association. Testing is also indicated for family members of patients who have known TRAP1 mutations. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in TRAP1.
Candidates for this test are patients with CAKUT or CAKUT with VACTERL association. Testing is also indicated for family members of patients who have known TRAP1 mutations. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in TRAP1.
Gene
| Official Gene Symbol | OMIM ID |
|---|---|
| TRAP1 | 606219 |
| Inheritance | Abbreviation |
|---|---|
| Autosomal Dominant | AD |
| Autosomal Recessive | AR |
| X-Linked | XL |
| Mitochondrial | MT |
Disease
| Name | Inheritance | OMIM ID |
|---|---|---|
| Vater Association | 192350 |
Citations
- Human Gene Mutation Database (Bio-base).
- Saisawat P, Kohl S, Hilger AC, Hwang D-Y, Yung Gee H, Dworschak GC, Tasic V, Pennimpede T, Natarajan S, Sperry E, Matassa DS, Stajic N, Bogdanovic R, de Blaauw I, Marcelis CL, Wijers CH, Bartels E, Schmiedeke E, Schmidt D, Märzheuser S, Grasshoff-Derr S, Holland-Cunz S, Ludwig M, Nöthen MM, Draaken M, Brosens E, Heij H, Tibboel D, Herrmann BG, Solomon BD, de Klein A, van Rooij IA, Esposito F, Reutter HM, Hildebrandt F. 2014. Whole-exome resequencing reveals recessive mutations in TRAP1 in individuals with CAKUT and VACTERL association. Kidney Int. 85: 1310–1317. PubMed ID: 24152966
- Vivante A, Kohl S, Hwang D-Y, Dworschak GC, Hildebrandt F. 2014. Single-gene causes of congenital anomalies of the kidney and urinary tract (CAKUT) in humans. Pediatr. Nephrol. 29: 695-704. PubMed ID: 24398540
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.
- 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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ORDER OPTIONS
View Ordering Instructions1) Select Test Type
2) Select Additional Test Options
No Additional Test Options are available for this test.