Genetic testing is currently available through Natera’s Renasight program and Invitae’s Expanded Rare Disease Panel.
Visit their respective websites for additional details.
As discussed at length on our genetics page, Alport syndrome has several different modes of inheritance; XLAS, ARAS, and ADAS, that can be identified by verifying mutations on one or more of the 3 associated type IV collagen chains (exomes) COL4A5, and COL4A3, and COL4A4. There are two primary types of genetic testing methods that identify which chain is affected, and what kind of mutation occurred, which can provide comprehensive diagnostic and prognostic information: Sanger Sequencing (also known as “single gene sequencing” or “capillary electrophoresis”) is a test conducted on an individual DNA protein chain, while Next Generation Sequencing (NGS) analyzes panels of multiple chains simultaneously. NGS is commonly referred to as exome sequencing, whole exome sequencing, or Massively Parallel Sequencing (MPS) because it can observe entire regions of exomes simultaneously.
Determining which method of testing, or which panels to select for NGS depends on an individual’s family medical history, severity of symptoms, and purposes for pursuing genetic testing (diagnosis, mutation confirmation, risk assessment, screening, etc.). However, recent research suggests that while conventional Sanger Sequencing tests and modern NGS tests have shown to be equally diagnostically reliable, NGS is more comprehensive when identifying other inherited conditions or mutations that Sanger Sequencing may have missed (Yamamura et al. 2019). Because NGS is able to explore multiple genes at once, it can be more cost-effective to test a given sample for all Alport-related genes rather than covering the cost of multiple single gene sequence tests.
For example, genetic research on Alport Syndrome shows that about 80% of patients can be diagnosed with XLAS as a result of identifying mutations on the COL4A5 gene. With an 80% probability, it is not unreasonable for a physician to default to ordering a Sanger Sequencing test on COL4A5 to confirm XLAS mode of inheritance. However, for about the same cost, the physician could opt for a multi-gene NGS panel, which would find any mutations in COL4A3, COL4A4, COL4A5, and/or hundreds to thousands of any other DNA chains or regions of interest at the same time. If the aforementioned Sanger Sequencing test for COL4A5 showed no mutations, and the physician wanted to continue looking for Alport-related variants (or any other inherited disorders), they would need to order an additional test for a different chain (e.g. COL4A3) at an additional cost. Furthermore, Sanger Sequencing requires a specialized laboratory with skilled operators, and can take days or weeks to process samples and return results. In comparison, NGS technology is portable, widely available, and utilized as a standard in most hospitals and genetic counseling clinics.
Genetic Testing Laboratories
Most labs that were formerly known for providing specialized Sanger Sequencing now also provide NGS testing as well. Traditionally, genetic testing for Alport Syndrome has been limited to those who had access to Sanger Sequencing labs, but now that NGS has dramatically simplified the process of analyzing genes, Sanger Sequencing has transitioned from being standard to being used primarily for confirming results from NGS analysis. A number of labs that are still actively conducting Sanger Sequencing are listed below. For a comprehensive list of genetic services for Alport Syndrome including NGS and Sanger facilities, visit The American College of Medical Genetics and Genomics; their database is searchable by location, service type, or center name.
University clinics can also be useful resources when considering genetic counseling, and studies involving Alport Syndrome often require and cover costs for genetic testing of willing participants.
Following is a partial list of laboratories that offer genetic testing for Alport syndrome (for a fee). There may be other laboratories of which ASF is unaware.
GeneDx, Inc.
Toll Free (888) 729-1206
Phone: (301) 519-2100
Fax: (201) 421-2010
Blueprint Genetics
Phone: (650) 452-9340
Fax: (650) 446-7790
2505 3rd Ave,Suite 204
Seattle, WA 98121
Connective Tissue Gene Tests
Phone: (484) 244-2900
Fax: (484) 244-2904
Fulgent Genetics
Phone: +1 (626) 350-0537
Fax: +1 (626) 454-1667
4978 Santa Anita Ave
Temple City, CA 91780
Machaon Diagnostics
Phone : 510-839-5600
Fax: 510-839-6153
3023 Summit Street
Oakland, CA 94609
Sistemas Geneticos
Phone: +34 961 366 150
Fax: +34 961 366 151
Parque Tecnológico de Paterna
R. Guillermo Marconi, 6
46980 – Paterna, Valencia
(ESPAÑA)
ARUP Genetics
Phone: (800) 522-2787
Fax: (800) 522-2706
500 Chipeta Way
Salt Lake City, Utah 84108
Detecting Alport Syndrome Genetic Mutations
Because Alport Syndrome is typically genetically heterogeneous (abnormalities occuring on more than one gene), genetic testing for multiple mutations involves various methods. Some known types of genetic variation associated with Alport Syndrome include nonsense variants, exonix deletions/insertions/duplications (also known as copy-number variations CNV’s), mutations located in consensus splicing sites, mutations located out with consensus splicing sites, glycine missense variants in intermediate collagenous domains, and missense variants in non-collagenous domains. Because there are so many possibilities of genetic variance in multiple locations, neither NGS nor Sanger alone can always identify mutations without administering further testing with specialized methods related to suspected mutations. As such, methods for diagnostic testing for Alport Syndrome follow the following procedures.
Next Generation Sequencing Analysis
- Step 1: Targeted Exome Sequensing of COL4A3, COL4A4, and COL4A5
- Step 2: If no pathogenic variant detected, pair analysis for CNVs using Deletion / Duplication (DEL/DUP).
- Step 3: If CNVs are found with DEL/DUP, pair analysis for Multiplex Ligation-Dependant Probe Amplification (MLPA) to confirm CNVs.
- Step 4: If no variants are detected from steps 1-3, conduct RNA sequencing via reverse transcription polymerase chain reaction (PCR) to check for aberrant splicing by intrionic variants.
Sanger Sequencing Analysis
- Step 1: Sanger Sequencing for one or each COL4A3, COL4A4, and/or COL4A5.
- Step 2: If no pathogenic variant detected, pair analysis for MLPA to detect CNVs.
- Step 3: If no variants are detected from MLPA, pair analysis for RNA sequencing.
Some common testing methods for DEL/DUP analysis include Microarray Analysis and VisCap Analysis. PCR tests are for targeted variant analysis. More information on genetic testing methodology can be found at the National Center for Biotechnology Information (NCBI).
When ordering panels for Alport Syndrome, most genetic testing labs have “off the shelf” multigene panels already existing. Gene panels can also be customized by request of a physican, and cost of testing typically depends on how large of a panel is being analyzed. Below are three examples of existing “off the shelf” panels that can identify genetic mutations associated with Alport Syndrome, each with different subsequent testing.
