Primary Hyperoxaluria Type 3 via the HOGA1 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 | |
|---|---|---|---|---|---|
| 7251 | HOGA1 | 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 (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).
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 Primary Hyperoxaluria 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.
Testing Strategy
This test provides full coverage of all coding exons of the HOGA1 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 3. Testing is also indicated for family members of patients who have known HOGA1 mutations. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in HOGA1.
Candidates for this test are patients with primary hyperoxaluria type 3. Testing is also indicated for family members of patients who have known HOGA1 mutations. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in HOGA1.
Gene
| Official Gene Symbol | OMIM ID |
|---|---|
| HOGA1 | 613597 |
| Inheritance | Abbreviation |
|---|---|
| Autosomal Dominant | AD |
| Autosomal Recessive | AR |
| X-Linked | XL |
| Mitochondrial | MT |
Disease
| Name | Inheritance | OMIM ID |
|---|---|---|
| Primary Hyperoxaluria, Type III | AR | 613616 |
Related Tests
| Name |
|---|
| Nephrolithiasis and Nephrocalcinosis Panel |
| Primary Hyperoxaluria Panel |
| Primary Hyperoxaluria Type 1 via the AGXT Gene |
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.
- 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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