Massively Parallel Sequencing/ Multiplex Ligation-dependent Probe Amplification
- Recommended test to confirm carrier status or a diagnosis of AS or MYH9-related disease.
- Regions of low coverage and reported variants are confirmed by Sanger sequencing as necessary.
Polymerase Chain Reaction/Sequencing
- Recommended test for a sequence variant previously identified in a family member.
- A copy of the family member’s test result is required.
Multiplex Ligation-dependent Probe Amplification
- Recommended test for a large deletion/duplication previously identified in a family member.
- A copy of the family member’s test result is recommended.
Alport syndrome (AS) is a spectrum of disorders that may range from isolated nonprogressive microscopic hematuria and proteinuria to progressive renal insufficiency, end stage renal disease (ESRD), eye findings, and sensorineural hearing loss (SNHL). The three main genes causative for AS (COL4A3, COL4A4, and COL4A5) are critical to the collagen IV a345 network of basement membranes. Pathogenic variants in COL4A5, causative for approximately 80-85% of AS, are inherited in an X-linked recessive (XLR) manner. Approximately 15-20% of AS is autosomal dominant (AD) or autosomal recessive (AR) due to pathogenic variants in the COL4A3 or COL4A4 genes.
Disease Overview
Symptoms
Symptom Categories | X-Linked and Autosomal Recessive AS | Autosomal Dominant AS | MYH9-Related Disease |
---|---|---|---|
Renal symptoms |
Renal disease progressing from microhematuria and proteinuria to renal insufficiency and ESRD
|
Slowly progressive renal insufficiency presenting later in life |
Early adult onset of renal disease, initially presenting as glomerular nephropathy |
Hearing loss |
Progressive SNHL in late childhood |
Slowly progressive SNHL later in life |
SNHL |
Ocular issues |
Anterior lenticonus
Maculopathy
Corneal endothelial vesicles or corneal erosion in X-linked AS Posterior subcapsular cataracts in X-linked AS |
Ocular lesions are uncommon |
Cataracts |
Other |
Diffuse leiomyomatosis (benign smooth muscle cell proliferation) of the esophagus and tracheobronchial tree may occur in X-linked AS Thoracic and abdominal aortic aneurysms in a few males with X-linked AS at <40 years |
– |
Congenital presentation of large platelets and thrombocytopenia Adult onset of elevated liver enzymes |
Etiology of Alport Syndrome
AS is caused by pathogenic variants in collagen genes that contribute to the collagen IV network of basement membranes.
Penetrance of Alport Syndrome and MYH9-Related Disease
- Complete for males with X-linked AS and both males and females with AR COL4A3 and COL4A4 variants and MYH9-related disease
- Possible incomplete penetrance for AD COL4A3 and COL4A4 variants
Prevalence of Alport Syndrome
Inheritance
- COL4A5: XLR
- COL4A3 and COL4A4: AD and AR, depending on the variant
- MYH9: AD
Genotype-Phenotype Correlation
- Large COL4A5 rearrangements, nonsense, frameshift, and splice site variants are associated with a 50% risk for ESRD by age 20, 90% risk of ESRD by age 30, and a 50% risk for SNHL by age 10.
- Pathogenic missense COL4A5 variants confer a 50% risk for ESRD by age 30 and 50% risk of SNHL by age 20.
- Leiomyomatosis only occurs in individuals with a deletion of both COL4A5 and COL4A6 when the COL4A6 breakpoint is in the second intron of the gene.
Test Interpretation
Clinical Sensitivity
Analytical Sensitivity
For massively parallel sequencing:
Variant Class | Analytical Sensitivity (PPA) Estimatea (%) | Analytical Sensitivity (PPA) 95% Credibility Regiona (%) |
---|---|---|
SNVs |
99.2 |
96.9-99.4 |
Deletions 1-10 bp |
93.8 |
84.3-98.2 |
Deletions 11-44 bp |
99.9 |
87.8-100 |
Insertions 1-10 bp |
94.8 |
86.8-98.5 |
Insertions 11-23 bp |
99.9 |
62.1-100 |
aGenes included on this test are a subset of a larger methods-based validation from which the PPA values are derived. bp, base pairs; PPA, positive percent agreement; SNVs, single nucleotide variants |
Limitations
- A negative result does not exclude a diagnosis of AS or MYH9-related disease.
- Diagnostic errors can occur due to rare sequence variations.
- Interpretation of this test result may be impacted if this patient has had an allogeneic stem cell transplantation.
- The following will not be evaluated:
- Variants outside the coding regions and intron-exon boundaries of targeted genes
- Regulatory region and deep intronic variants
- Breakpoints of large deletions/duplications
- Deletions/duplications in COL4A3, COL4A4, and MYH9 genes
- Noncoding transcripts
- The following may not be detected:
- Deletions/duplications/insertions of any size by massively parallel sequencing
- Some variants due to technical limitations in the presence of pseudogenes, repetitive, or homologous regions
- Low-level somatic variants
- Single exon deletions/duplications in the following exons:
- COL4A5 (NM_000495) 8, 25, 40, 42, 43
Genes Tested
Gene Symbol | MIM # | Disorders | Inheritance |
---|---|---|---|
COL4A3 |
120070 |
Alport syndrome 2 Alport syndrome 3 Hematuria, benign familial |
AR/AD |
COL4A4 |
120131 |
Alport syndrome 2 Hematuria, familial benign |
AR/AD |
COL4A5 |
303630 |
Alport syndrome 1, X-linked |
XLR |
MYH9 |
160775 |
Deafness 17 Macrothrombocytopenia and granulocyte inclusions with or without nephritis or sensorineural hearing loss |
AD |
References
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