Primary Hyperoxaluria Type 1 via the AGXT Gene
Summary and Pricing 
Test Method
Sequencing and CNV Detection via NextGen Sequencing using PG-Select Capture Probes| Test Code | Test Copy Genes | Test CPT Code | Gene CPT Codes Copy CPT Code | Base Price | |
|---|---|---|---|---|---|
| 7247 | AGXT | 81479 | 81479,81479 | $990 | Order Options and Pricing |
Pricing Comments
Testing run on PG-select capture probes includes CNV analysis for the gene(s) on the panel but does not permit the optional add on of exome-wide CNV analysis. Any of the NGS platforms allow reflex to other clinically relevant genes, up to whole exome or whole genome sequencing depending upon the base platform selected for the initial test.
An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.
This test is also offered via a custom panel (click here) on our exome or genome backbone which permits the optional add on of exome-wide CNV or genome-wide SV analysis.
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
Primary hyperoxaluria type 1 (PH1; OMIM# 259900) is an inherited disorder of glyoxylate metabolism due to deficiency of the alanine glyoxylate aminotransferase (AGT) enzyme (Coulter-Mackie et al. 2011). This disease is characterized by an accumulation of endogenous calcium oxalate in various organs, particularly the kidneys, leading to recurrent nephrolithiasis, nephrocalcinosis, or end-stage renal disease (ESRD). Age at onset of PH1 ranges from the first year of life to adulthood with varied disease severity.
Genetics
Primary hyperoxaluria type 1 is an autosomal recessive disorder caused by defects in the AGXT gene (Purdue et al. 1990; Monico et al. 2007; Williams et al. 2009). 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 mutations, and small deletion/insertions (Human Gene Mutation Database). Exon-level large deletions involving AGXT have also been reported, but are relatively uncommon.
Clinical Sensitivity - Sequencing with CNV PG-Select
Sequence analysis can detect at least one pathogenic AGXT allele in 100% of affected individuals (Coulter-Mackie et al. 2011).
Testing Strategy
This test provides full coverage of all coding exons of the AGXT gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.
Indications for Test
Candidates for this test are patients with primary hyperoxaluria type 1. Testing is also indicated for family members of patients who have known AGXT mutations. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in AGXT.
Candidates for this test are patients with primary hyperoxaluria type 1. Testing is also indicated for family members of patients who have known AGXT mutations. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in AGXT.
Gene
| Official Gene Symbol | OMIM ID |
|---|---|
| AGXT | 604285 |
| Inheritance | Abbreviation |
|---|---|
| Autosomal Dominant | AD |
| Autosomal Recessive | AR |
| X-Linked | XL |
| Mitochondrial | MT |
Disease
| Name | Inheritance | OMIM ID |
|---|---|---|
| Primary Hyperoxaluria, Type I | AR | 259900 |
Related Tests
| Name |
|---|
| Nephrolithiasis and Nephrocalcinosis Panel |
| Primary Hyperoxaluria Panel |
Citations
- Coulter-Mackie MB, White CT, Hurley RM, Chew BH, Lange D. 2011. Primary Hyperoxaluria Type 1. In: Pagon RA, Adam MP, Bird TD, Dolan CR, Fong C-T, and Stephens K, editors. GeneReviews™, Seattle (WA): University of Washington, Seattle. PubMed ID: 20301460
- Human Gene Mutation Database (Bio-base).
- Monico CG, Rossetti S, Schwanz HA, Olson JB, Lundquist PA, Dawson DB, Harris PC, Milliner DS. 2007. Comprehensive mutation screening in 55 probands with type 1 primary hyperoxaluria shows feasibility of a gene-based diagnosis. J. Am. Soc. Nephrol. 18: 1905-1914. PubMed ID: 17460142
- Purdue PE, Takada Y, Danpure CJ. 1990. Identification of mutations associated with peroxisome-to-mitochondrion mistargeting of alanine/glyoxylate aminotransferase in primary hyperoxaluria type 1. J. Cell Biol. 111: 2341-2351. PubMed ID: 1703535
- Williams EL, Acquaviva C, Amoroso A, Chevalier F, Coulter-Mackie M, Monico CG, Giachino D, Owen T, Robbiano A, Salido E, Waterham H, Rumsby G. 2009. Primary hyperoxaluria type 1: update and additional mutation analysis of the AGXT gene. Hum. Mutat. 30: 910-917. PubMed ID: 19479957
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
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ORDER OPTIONS
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2) Select Additional Test Options
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