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Nephrolithiasis via the SLC26A1 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
8583 SLC26A1 81479 81479,81479 $890 Order Options and Pricing
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
8583SLC26A181479 81479,81479 $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.

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 backbone).

Click here for costs to reflex to whole PGnome (if original test is on PGnome Sequencing backbone).

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 13 days 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.

EMAIL CONTACTS

Genetic Counselors

Geneticist

  • Angela Gruber, PhD

Clinical Features and Genetics

Clinical Features

Nephrolithiasis is a clinical condition in which urinary supersaturation leads to stone formation in the urinary system (the lumen of the collecting system, ureter, and bladder) (Braun et al. 2016; Halbritter et al. 2015; Gee et al. 2016). Patients with kidney stones may have no symptoms or may present with flank pain, gross or microscopic hematuria, obstruction of one or both kidneys, and urinary infections. It affects 10%-15% of adults in their lifetime. Defects in the SLC26A1 gene cause calcium oxalate nephrolithiasis (Gee et al. 2016). The index patient reported by Gee et al. presented with acute renal failure due to ureteral obstruction with calculi at the age of five.

Genetics

SLC26A1-associated nephrolithiasis is an autosomal recessive disorder (Gee et al. 2016). The SLC26A1 gene (two coding exons) encodes solute carrier family 26 member 1, which plays a critical role in oxalate and sulfate homeostasis. To date, documented genetic defects of SLC26A1 for nephrolithiasis are only missense variants that result in decreased transporter activity (Human Gene Mutation Database). A large deletion encompassing SLC26A1 has been reported in a study of epileptic encephalopathies, but the contribution of SLC26A1 to disease is uncertain (Mefford et al. 2011).

Clinical Sensitivity - Sequencing with CNV PGxome

In the original report of SLC26A1-associated nephrolithiasis, 2 out of 348 (~0.6%) unrelated patients with kidney stones were found to have biallelic pathogenic SLC26A1 variants (Gee et al. 2016).

Testing Strategy

This test provides full coverage of all coding exons of the SLC26A1 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 calcium oxalate nephrolithiasis. Testing is also indicated for family members of patients who have known pathogenic variants in the SLC26A1 gene. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in SLC26A1.

Gene

Official Gene Symbol OMIM ID
SLC26A1 610130
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Disease

Name Inheritance OMIM ID
Nephrolithiasis, Calcium Oxalate AR 167030

Citations

  • Braun D.A. et al. 2016. Clinical Journal of the American Society of Nephrology. 11: 664-72. PubMed ID: 26787776
  • Gee H.Y. et al. 2016. American Journal of Human Genetics. 98: 1228-34. PubMed ID: 27210743
  • Halbritter et al. 2015. PubMed ID: 25296721
  • Human Gene Mutation Database (Bio-base).
  • Mefford H.C. et al. 2011. Annals of Neurology. 70: 974-85. PubMed ID: 22190369

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


Specimen Types

Specimen Requirements and Shipping Details

PGxome (Exome) Sequencing Panel

PGnome (Genome) Sequencing Panel

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ORDER OPTIONS

View Ordering Instructions

1) Select Test Method (Backbone)


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.
Total Price: $
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