Autosomal Recessive Pseudohypoaldosteronism Type 1 via the SCNN1A Gene
Summary and Pricing 
Test Method
Exome Sequencing with CNV Detection
| Test Code | Test Copy Genes | Test CPT Code | Gene CPT Codes Copy CPT Code | Base Price | |
|---|---|---|---|---|---|
| 11647 | SCNN1A | 81406 | 81406,81479 | $990 | 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.
Click here for costs to reflex to whole PGxome (if original test is on PGxome Sequencing platform).
Click here for costs to reflex to whole PGnome (if original test is on PGnome Sequencing platform).
The Sanger Sequencing method for this test is NY State approved.
For Sanger Sequencing click here.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
Autosomal recessive pseudohypoaldosteronism type 1 (PHA1; OMIM #264350) is a multi-organ life-threatening disorder characterized by severe neonatal onset salt wasting and high concentrations of sodium in sweat, stool, and saliva (Chang et al. Nat Genet 12(3):248-253, 1996; Scheinman et al. N Engl J Med 340(15):1177-1187, 1999). Clinical features include hyponatremia, hyperkalaemia, metabolic acidosis, unresponsiveness to mineralocorticoid hormones, and increased plasma renin activity with high serum aldosterone concentrations. Compared with autosomal dominant PHA1, the recessive form of the disease is a more severe systemic condition with persistence into adulthood. Some patients have recurrent respiratory problems (Chang et al., 1996; Schaedel et al. J Pediatr 135(6):739-745, 1999). Genetic confirmation is essential for distinguishing autosomal recessive PHA1 from cystic fibrosis-like disease (Sheridan et al. Hum Mol Genet 14(22):3493-3498, 2005; Azad et al. Hum Mutat 30(7):1093-1103, 2009; Mora-Lopez et al. Eur J Pediatr 171(6):997-1000, 2012).
Genetics
Autosomal recessive PHA1 can be caused by mutations in any one of the three genes encoding the epithelial sodium channel (ENaC) including SCNN1A, SCNN1B and SCNN1G (Hansson et al. Nat Genet 11(1):76-82, 1995; Chang et al., 1996). These amiloride-sensitive channels play a key role in electrolyte transportation across epithelia in many organs. SCNN1A has 12 coding exons that encode the alpha subunit of ENaC. Genetic defects located throughout the SCNN1A gene include missense, nonsense, splicing mutations and small deletion/insertions. To date, one gross deletion within the SCNN1A gene has also been reported (Human Gene Mutation Database).
Clinical Sensitivity - Sequencing with CNV PGxome
SCNN1A mutation detection rates in autosomal recessive PHA1 patients via Sanger sequencing varied from 50% to 100% in different studies, each of which had a limited number of patients (Kerem et al. N Engl J Med 341(3):156-162, 1999; Saxena et al. J Clin Endocrinol Metab 87(7):3344-3350, 2002; Welzel et al. Eur J Endocrinol 168(5):707-715, 2013).
Testing Strategy
This test provides full coverage of all coding exons of the SCNN1A 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 autosomal recessive PHA1. Testing is also indicated for family members of patients who have known SCNN1A mutations. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in SCNN1A.
Candidates for this test are patients with autosomal recessive PHA1. Testing is also indicated for family members of patients who have known SCNN1A mutations. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in SCNN1A.
Gene
| Official Gene Symbol | OMIM ID |
|---|---|
| SCNN1A | 600228 |
| Inheritance | Abbreviation |
|---|---|
| Autosomal Dominant | AD |
| Autosomal Recessive | AR |
| X-Linked | XL |
| Mitochondrial | MT |
Disease
| Name | Inheritance | OMIM ID |
|---|---|---|
| Pseudohypoaldosteronism Type 1 Autosomal Recessive | AR | 264350 |
Citations
- Azad, A. et al. (2009). "Mutations in the amiloride-sensitive epithelial sodium channel in patients with cystic fibrosis-like disease." Hum Mutat 30(7):1093-1103. PubMed ID: 19462466
- Chang, S. et al. (1996). "Mutations in subunits of the epithelial sodium channel cause salt wasting with hyperkalaemic acidosis, pseudohypoaldosteronism type 1." Nat Genet 12(3):248-253. PubMed ID: 8589714
- Hansson, J. et al. (1995). "Hypertension caused by a truncated epithelial sodium channel gamma subunit: genetic heterogeneity of Liddle syndrome." Nat Genet 11(1):76-82. PubMed ID: 7550319
- Human Gene Mutation Database (Bio-base).
- Kerem, E. et al. (1999). "Pulmonary epithelial sodium-channel dysfunction and excess airway liquid in pseudohypoaldosteronism." N Engl J Med 341(3):156-162. PubMed ID: 10403853
- Mora-Lopez, F. et al. (2012). “Novel mutation in the epithelial sodium channel causing type I pseudohypoaldosteronism in a patient misdiagnosed with cystic fibrosis.” Eur J Pediatr 171(6):997-1000. PubMed ID: 22371258
- Saxena, A. et al. (2002). “Novel mutations responsible for autosomal recessive multisystem pseudohypoaldosteronism and sequence variants in epithelial sodium channel alpha-, beta-, and gamma-subunit genes.” J Clin Endocrinol Metab 87(7):3344-3350. PubMed ID: 12107247
- Schaedel, C. et al. (1999). "Lung symptoms in pseudohypoaldosteronism type 1 are associated with deficiency of the alpha-subunit of the epithelial sodium channel." J Pediatr 135(6):739-745. PubMed ID: 10586178
- Scheinman, S. et al. (1999). “Genetic disorders of renal electrolyte transport.” N Engl J Med 340(15):1177-1187. PubMed ID: 10202170
- Sheridan, M. et al. (2005). “Mutations in the beta-subunit of the epithelial Na+ channel in patients with a cystic fibrosis-like syndrome.” Hum Mol Genet 14(22):3493-3498. PubMed ID: 16207733
- Welzel, M. et al. (2013). "Five novel mutations in the SCNN1A gene causing autosomal recessive pseudohypoaldosteronism type 1." Eur J Endocrinol 168(5):707-715. PubMed ID: 23416952
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
PGxome (Exome) Sequencing Panel
PGnome (Genome) Sequencing Panel
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ORDER OPTIONS
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2) Select Additional Test Options
No Additional Test Options are available for this test.