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 GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
8067 TRAP1 81479 81479,81479 $890 Order Options and Pricing
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
8067TRAP181479 81479 $890 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.

For Reflex to PGxome pricing click here.

The Sanger Sequencing method for this test is NY State approved.

For Sanger Sequencing 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

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.

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 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.

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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