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FeedbackMassively Parallel Sequencing
Capillary malformation-arteriovenous malformation (CM-AVM) syndrome is a disorder of the vascular system characterized by enlarged capillaries that appear as small, round dots on the skin. Some affected individuals also have fast-flow vascular anomalies, including arteriovenous malformations (AVMs) or arteriovenous fistulas (AVFs) in the skin, muscle, bone, spine, or brain. These lesions may cause life-threatening complications such as bleeding, congestive heart failure, or neurological consequences. Additional manifestations include lymphatic abnormalities, recurrent epistaxis (CM-AVM2), dermal telangiectasias (CM-AVM2), and bier spots (CM-AVM2). Genetic testing can confirm diagnosis of RASA1-related CM-AVM disorder (CM-AVM1) or EPHB4-related CM-AVM disorder (CM-AVM2) in individuals with clinical findings suggestive of CM-AVM.
Disease Overview
Incidence
- Approximately 1/20,000 for CM-AVM1
- Approximately 1/12,000 for CM-AVM2
Genetics
Genes
- EPHB4 (NM_004444) and RASA1 (NM_002890)
- See Genes Tested table for more information
Inheritance
- Autosomal dominant
- De novo variants
- Approximately 33% of cases for RASA1
- Approximately 20% of cases for EPHB4
- Somatic mosaicism has been described
Penetrance
Test Interpretation
Methodology
This test is performed using the following sequence of steps:
- Selected genomic regions, primarily coding exons and exon-intron boundaries, from the targeted genes are isolated from extracted genomic DNA using a probe-based hybrid capture enrichment workflow.
- Enriched DNA is sequenced by massively parallel sequencing (MPS; also known as next generation sequencing [NGS]) followed by paired-end read alignment and variant calling using a custom bioinformatics pipeline. The pipeline includes an algorithm for detection of large (single exon-level or larger) deletions and duplications.
- Sanger sequencing is performed as necessary to fill in regions of low coverage and in certain situations, to confirm variant calls.
- Large deletion/duplication calls made using MPS are confirmed by an orthogonal exon-level microarray when sample quality and technical conditions allow.
Clinical Sensitivity
Clinical sensitivity is not well established but is estimated at 60%
- EPHB4
- RASA1
-
- 92% of detectable RASA1 pathogenic variants are sequence variants and 8% are large deletions/duplications
Analytic Sensitivity
| Variant Class | Analytic Sensitivity (PPA) Estimatea (%) and 95% Credibility Region | Analytic Specificity (NPA) |
|---|---|---|
|
SNVs |
>99 (96.9-99.4) |
>99.9 |
|
Deletions 1-10 bpb |
93.8 (84.3-98.2) |
>99.9 |
|
Insertions 1-10 bpb |
94.8 (86.8-98.5) |
>99.9 |
|
Exon-levelc deletions |
97.8 (90.3-99.8) [2 exons or larger] 62.5 (38.3-82.6) [single exon] |
>99.9 |
|
Exon-levelc duplications |
83.3 (56.4-96.4) [3 exons or larger] |
>99.9 |
|
aGenes included on this test are a subset of a larger methods-based validation from which the PPA values are derived. bVariants greater than 10 bp may be detected, but the analytic sensitivity may be reduced. cIn most cases, a single exon deletion or duplication is less than 450 bp and 3 exons span a genomic region larger than 700 bp. bp, base pairs; NPA, negative percent agreement; PPA, positive percent agreement; SNVs, single nucleotide variants |
||
Results
| Result | Variant(s) Detected | Clinical Significance |
|---|---|---|
|
Positive |
Pathogenic EPHB4 or RASA1 variant detected |
Confirms diagnosis of CM-AVM in a symptomatic individual |
|
Negative |
No known pathogenic EPHB4 or RASA1 variant detected |
Reduces possibility of, but does not exclude, a diagnosis of CM-AVM |
|
Inconclusive |
Variant of uncertain clinical significance detected in EPHB4 or RASA1 |
Unclear if variant is disease causing or benign |
Limitations
- A negative result does not exclude a diagnosis of CM-AVM.
- Diagnostic errors can occur due to rare sequence variations.
- Interpretation of the test result may be impacted if the 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
- The following may not be detected:
- Deletions/duplications/insertions of any size by MPS
- Large duplications less than 3 exons in size
- Noncoding transcripts
- Some variants, due to technical limitations in the presence of pseudogenes or repetitive or homologous regions
- Low-level somatic variants
Genes Tested
| Gene | MIM# | Disorder | Inheritance |
|---|---|---|---|
| EPHB4 | 600011 |
CM-AVM2 Lymphatic malformation 7 |
AD |
| RASA1 | 139150 | CM-AVM1 | AD |
| AD, autosomal dominant | |||
References
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28687708
Amyere M, Revencu N, Helaers R, et al. Germline loss-of-function mutations in EPHB4 cause a second form of capillary malformation-arteriovenous malformation (CM-AVM2) deregulating RAS-MAPK signaling. Circulation. 2017;136(11):1037-1048.
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GeneReviews - Capillary Malformation-Arteriovenous Malformation Syndrome
Bayrak-Toydemir P, Stevenson D. Capillary malformation-arteriovenous malformation syndrome. In: Adam MP, Ardinger HH, Pagon RA, et al, eds. GeneReviews. University of Washington, Seattle. Last update Sep 2019; accessed Nov 2020.
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22200646
Wooderchak-Donahue W, Stevenson DA, McDonald J , et al. RASA1 analysis: clinical and molecular findings in a series of consecutive cases. Eur J Med Genet. 2012;55(2):91-95.
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24038909
Revencu N, Boon LM, Mendola A, et al. RASA1 mutations and associated phenotypes in 68 families with capillary malformation-arteriovenous malformation. Hum Mutat. 2013;34(12):1632-1641.
Use to detect CM-AVM. If vascular symptoms are expanded beyond CM-AVM, consider testing for a hereditary vascular malformation disorder. If a familial sequence variant has been previously identified, targeted sequencing for that variant may be appropriate. Refer to the Laboratory Test Directory for additional information.