Alport Syndrome via the COL4A5 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 | |
|---|---|---|---|---|---|
| 3053 | COL4A5 | 81408 | 81408,81407 | $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
Alport Syndrome (AS) is a hereditary nephritis caused by defects of the collagen type IV protein, which is responsible for basement membrane formation in the kidney, ear and eye. The disease affects approximately 1 in 50000 individuals and is characterized by progressive renal failure, sensorineural hearing loss and eye abnormalities. The most common symptoms include persistent microhematuria at early childhood, progressive proteinuria, bilateral high frequency sensorineural hearing loss and anterior lenticonus in late childhood and adolescence. Approximately 80% of cases of the disease display X-linked inheritance. Almost all X-linked male patients will reach the end stage of renal failure by age 40, whereas female patients may only manifest hematuria (Lemmink et al. 1997; Hertz et al. 2001; Nagel et al. 2005; Hertz. 2009; Kashtan 2010).
Genetics
Alport syndrome can be caused by mutations in COL4A3, COL4A4 and COL4A5. The X-linked Alport syndrome is caused by mutations in the COL4A5 gene. The COL4A5 gene encodes alpha-5 chain of type IV collagen, a major structural component of basement membranes. Mutations in the COL4A5 gene explain approximately 90% of clinically diagnosed X-linked Alports syndrome. To date, more than 600 causative mutations were reported throughout the gene including missense (~35%), truncating (~30%), splicing (15%) and large del/dup (~20%). Large deletions involving 5’ ends of the COL4A5 gene and a breakpoint within the intron 2 of the COL4A6 gene were reported to cause diffuse leiomyomatosis. Glycine substitutions in Gly-Xaa-Yaa repeat sequence in the collagenous domain account for 85% of the missense mutations (Hertz 2009).
Clinical Sensitivity - Sequencing with CNV PG-Select
A large panel study showed that the overall detection rate is 53%, and a likely causative mutation was identified in 82% (23/28) of families with clear X-linked cases (Hertz 2009).
Testing Strategy
This test provides full coverage of all coding exons of the COL4A5 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 symptoms consistent with X-linked Alport syndrome and the family members of patients who have known COL4A5 mutations.
Candidates for this test are patients with symptoms consistent with X-linked Alport syndrome and the family members of patients who have known COL4A5 mutations.
Gene
| Official Gene Symbol | OMIM ID |
|---|---|
| COL4A5 | 303630 |
| Inheritance | Abbreviation |
|---|---|
| Autosomal Dominant | AD |
| Autosomal Recessive | AR |
| X-Linked | XL |
| Mitochondrial | MT |
Disease
| Name | Inheritance | OMIM ID |
|---|---|---|
| Alport Syndrome, X-Linked Recessive | XL | 301050 |
Citations
- Hertz et al. Detection of mutations in the COL4A5 gene by SSCP in X-linked Alport syndrome. Hum Mutat 18(2):141-8, 2001. PubMed ID: 11462238
- Hertz JM. 2009. Alport syndrome. Molecular genetic aspects. Dan Med Bull 56: 105–152. PubMed ID: 19728970
- Kashtan CE. 2013. Alport Syndrome and Thin Basement Membrane Nephropathy. In: Pagon RA, Adam MP, Ardinger HH, Bird TD, Dolan CR, Fong C-T, Smith RJ, and Stephens K, editors. GeneReviews(®), Seattle (WA): University of Washington, Seattle. PubMed ID: 20301386
- Lemmink et al. The clinical spectrum of type IV collagen mutations. Hum Mutat 9(6): 477-499, 1997. PubMed ID: 9195222
- Nagel et al. Novel COL4A5, COL4A4, and COL4A3 mutations in Alport syndrome. Hum Mutat 26(1): 60. 2005. PubMed ID: 15954103
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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