Alpha-1 Antitrypsin Deficiency via the SERPINA1 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 | |
|---|---|---|---|---|---|
| 7813 | SERPINA1 | 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
Alpha-1 antitrypsin deficiency primarily affects the lungs and liver (Crystal 1990; Stockley et al. 2014). Patients commonly develop lung disease by the third to fourth decade, which is characterized by emphysema including difficulty breathing, a hacking cough and a barrel-shaped chest. Liver disease is less common, and presents with jaundice and cholestasis in children and cirrhosis in adults. In some rare cases, patients can develop a skin condition called panniculitis. Onset age and severity of different signs and symptoms vary greatly among patients depending in part on genotype.
Genetics
Alpha-1 antitrypsin deficiency is an autosomal recessive disorder caused by SERPINA1 pathogenic variants (Medicina et al. 2009; Ferrarotti et al. 2014). The SERPINA1 gene has 4 coding exons that encode alpha-1-antitrypsin (AAT), also known as protease inhibitor (PI), a major plasma serine protease inhibitor. Genetic defects of SERPINA1 found to date include missense, nonsense, splicing mutations, and small and large deletions (Human Gene Mutation Database).
Clinical Sensitivity - Sequencing with CNV PG-Select
Detection rate of pathogenic variants in the SERPINA1 gene in a large cohort of patients with alpha-1 antitrypsin deficiency is unknown in the literature because only a limited number of cases have been reported, but is expected to be high via Sanger sequencing since large deletions appear to be rare. SERPINA1 is the only gene known to be involved in this disorder.
Testing Strategy
This test provides full coverage of all coding exons of the SERPINA1 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 alpha-1 antitrypsin deficiency. Testing is also indicated for family members of patients who have known pathogenic variants in the SERPINA1 gene. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in SERPINA1.
Candidates for this test are patients with alpha-1 antitrypsin deficiency. Testing is also indicated for family members of patients who have known pathogenic variants in the SERPINA1 gene. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in SERPINA1.
Gene
| Official Gene Symbol | OMIM ID |
|---|---|
| SERPINA1 | 107400 |
| Inheritance | Abbreviation |
|---|---|
| Autosomal Dominant | AD |
| Autosomal Recessive | AR |
| X-Linked | XL |
| Mitochondrial | MT |
Disease
| Name | Inheritance | OMIM ID |
|---|---|---|
| Alpha-1-Antitrypsin Deficiency | AR | 613490 |
Citations
- Crystal RG. 1990. The Journal of Clinical Investigation. 85: 1343-52. PubMed ID: 2185272
- Ferrarotti I., Carroll TP. 2014. Orphanet Journal of Rare Diseases. 9: 172. PubMed ID: 25425243
- Human Gene Mutation Database (Bio-base).
- Medicina D. et al. 2009. Human Mutation. 30: E771-81. PubMed ID: 19437508
- Stockley RA., Turner AM. 2014. Trends in Molecular Medicine. 20: 105-15. PubMed ID: 24380646
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
No Additional Test Options are available for this test.