Primary Hyperoxaluria Panel

Summary and Pricing

Test Method

Sequencing and CNV Detection via NextGen Sequencing using PG-Select Capture Probes
Test Code Test Copy Genes Gene CPT Codes Copy CPT Codes
4531 AGXT 81479,81479 Order Options and Pricing
GRHPR 81479,81479
HOGA1 81479,81479
Test Code Test Copy Genes Panel CPT Code Gene CPT Codes Copy CPT Code Base Price
4531Genes x (3)81479 81479 $640 Order Options and Pricing

Pricing Comments

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.

This test is also offered via our exome backbone with CNV detection (click here). The exome-based test may be higher priced, but permits reflex to the entire exome or to any other set of clinically relevant genes.

An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.

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

Primary hyperoxaluria (PH) is an autosomal recessive disorder of endogenous glyoxylate metabolism characterized by an accumulated urinary excretion of calcium oxalate (Rumsby 2008; Coulter-Mackie et al. 2002; Milliner et al. 2015). The increased oxalate excretion causes nephrolithiasis, nephrocalcinosis and renal failure followed by systemic oxalate deposition. The age at onset of PH ranges from the first year of life to adulthood with varied disease severity. AGXT-causative type 1 PH is the most severe form, accounting for up to 80% of genetically characterized PH patients (Hopp et al. 2015). GRHPR-causative type 2 PH is less severe than type 1, accounting for about 10% of genetically characterized PH patients. HOGA1-causative type 3 PH is the least severe, accounting for the remaining about 10% of genetically characterized PH patients.

Genetics

Primary hyperoxaluria is an autosomal recessive disorder, which comprises three types depending on the causative genes: type 1 (AGXT), type 2 (GRHPR) and type 3 (HOGA1) (Hopp et al. 2015).

AGXT has 11 coding exons that encode the liver peroxisomal enzyme alanine:glyoxylate-aminotransferase (AGT), which catalyzes the conversion of glyoxylate to glycine. Genetic defects of AGXT throughout the whole coding region include missense, nonsense, splicing site pathogenic variants, and small deletion/insertions (Human Gene Mutation Database). Exon-level large deletions involving AGXT have also been reported, but are relatively uncommon.

GRHPR has 9 coding exons that encode the glyoxylate reductase/hydroxypyruvate reductase, which catalyzes the reduction of hydroxypyruvate to D-glycerate, the reduction of glyoxylate to glycolate and the oxidation of D-glycerate to hydroxypyruvate. Genetic defects of GRHPR throughout the whole coding region include missense, nonsense, splicing site pathogenic variants and small deletion/insertions (Human Gene Mutation Database). Exon-level large deletions and duplications involving GRHPR have not been reported.

HOGA1 (formerly DHDPSL) has 7 coding exons that encode the 4-hydroxy-2-oxoglutarate aldolase, which catalyzes the final step in the metabolic pathway of hydroxyproline. Genetic defects of HOGA1 throughout the whole coding region include missense, nonsense, splicing site pathogenic variants and small deletion/insertions (Human Gene Mutation Database). Exon-level large deletions and duplications involving HOGA1 have not been reported.

Clinical Sensitivity - Sequencing with CNV PG-Select

In a sequencing study of 301 PH families (355 patients), defects in the AGXT, GRHPR and HOGA1 genes were found in 68.4%, 9.3% and 11% of these families, respectively (Hopp et al. 2015). The remaining 11.3% had no pathogenic variants found in these three genes.

Large deletions and/or duplications have not been documented in GRHPR or HOGA1 in Human Gene Mutation Database (HGMD) while large deletions involving AGXT have been reported, but are relatively uncommon.

Testing Strategy

This panel provides 100% coverage of all coding exons of the genes listed, plus ~10 bases of flanking noncoding DNA. We define coverage as ≥20X NGS reads or Sanger sequencing.

Indications for Test

Candidates for this test are patients with primary hyperoxaluria.

Genes

Official Gene Symbol OMIM ID
AGXT 604285
GRHPR 604296
HOGA1 613597
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Related Test

Name
PGxome®

Citations

  • Coulter-Mackie M.B. et al. 2002. Primary Hyperoxaluria Type 1. In: Pagon RA, Adam MP, Bird TD, Dolan CR, Fong C-T, Smith RJ, and Stephens K, editors. GeneReviews™, Seattle (WA): University of Washington, Seattle. PubMed ID: 20301460
  • Hopp K. et al. 2015. Journal of the American Society of Nephrology. 26: 2559-70. PubMed ID: 25644115
  • Human Gene Mutation Database (Bio-base).
  • Milliner D.S. et al. 2015. Primary Hyperoxaluria Type 3. In: Pagon RA, Adam MP, Bird TD, Dolan CR, Fong C-T, Smith RJ, and Stephens K, editors. GeneReviews™, Seattle (WA): University of Washington, Seattle. PubMed ID: 26401545
  • Rumsby G. 2008. Primary Hyperoxaluria Type 2. In: Pagon RA, Adam MP, Bird TD, Dolan CR, Fong C-T, Smith RJ, and Stephens K, editors. GeneReviews™, Seattle (WA): University of Washington, Seattle. PubMed ID: 20301742

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

loading Loading... ×

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.

Total Price: $
×
Copy Text to Clipboard
×