Vascular Malformations Panel, Sequencing and Deletion/Duplication

  • Use to confirm a clinical diagnosis of a hereditary vascular malformation disorder, if no single specific diagnosis is strongly suspected
  • If an individual meets clinical criteria for a specific disorder or if a specific diagnosis is suspected, consider more targeted gene testing first.

Assess for a known familial sequence variant previously identified in a family member

Vascular malformation syndromes are caused by defects of blood vessels, which can affect multiple vessel types (venous, arterial, capillary, or combined). Examples include capillary malformation, arteriovenous malformation, cerebral cavernous malformation (CCM), glomuvenous malformation, hereditary hemorrhagic telangiectasia (HHT), multiple cutaneous and mucosal venous malformations, pulmonary arterial hypertension, and hereditary lymphedema syndromes. Potential findings of vascular malformation syndromes include hemorrhage and/or epistaxis, localized pain and/or lymphedema, destruction or deformation of surrounding tissue, localized intravascular coagulopathy (LIC), stroke, and congestive heart failure. If no single specific diagnosis is strongly suspected, a multigene panel test can confirm a clinical diagnosis of a hereditary vascular malformation disorder.

Genetics

Genes

Analysis includes the coding regions and intron-exon boundaries of the genes tested (see Genes Tested table), the 5' untranslated region of ENG, a region of ACVRL1 intron 9 encompassing the CT-rich variant hotspot region, and select PTEN promoter variants.

Etiology

Pathogenic variants in vascular malformation genes lead to defects of blood vessels that can cause fast-flow or slow-flow lesions, shunting, swelling, or skin findings. For some disorders, this may lead to potentially life-threatening hemorrhage, stroke, or heart failure.

Prevalence

Syndrome Prevalence

HHT

1 in 5,000 to 1 in 10,000  

CCM

1 in 2,000 to 1 in 10,000 

CM-AVM

RASA1-CM-AVM: 1 in 20,000 

EPHB4-CM-AVM: 1 in 12,000 

PTEN hamartoma tumor syndrome:

1 in 200,000 

AKT1-related proteus syndrome

1 in 1 million 

CM-AVM, capillary malformation-arteriovenous malformation syndrome

Sources: McDonald, 2017 ; Faughnan, 2020 ; Zafar, 2019 ; Amyere, 2017 ; Nelen, 1999 ; Biesecker, 2019 

Genotype-Phenotype Correlation

  • Vascular malformation syndromes are typically categorized according to vessel type affected and fast- versus slow-flow lesions.
  • Most vascular malformations are sporadic.
  • Inherited forms are characterized by multiple lesions, which are often smaller and less often congenital than their sporadic counterparts.
  • Penetrance is often age-related and variable.

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.
  • Bidirectional Sanger sequencing is performed on the following gene(s):
    • PTEN (NM_000314) 9

Clinical Sensitivity

Variable and dependent upon specific disorder

Analytic Sensitivity

Variant Class Analytic Sensitivity (PPA) Estimatea (%) and 95% Credibility Region Analytic Specificity (NPA) Estimate (%)

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

aPPA values are derived from larger methods-based MPS and/or Sanger validations. These values do not apply to testing performed by multiplex ligation-dependent probe amplification (MLPA) unless otherwise indicated.

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; PPA, positive percent agreement; NPA, negative percent agreement; SNVs, single nucleotide variants

Limitations

  • A negative result does not exclude a heritable form of a vascular malformation disorder.
  • Diagnostic errors can occur due to rare sequence variations.
  • Interpretation of this test result may be impacted if this individual has had an allogeneic stem cell transplantation.
  • The following will not be evaluated:
    • Variants outside the coding regions and intron-exon boundaries of the targeted genes
    • Regulatory region variants and deep intronic variants
    • Breakpoints of large deletions/duplications
    • The following exons are not sequenced due to technical limitations of the assay:
      • CCM2 (NM_001363458) exon(s) 7
      • CCM2 (NM_001363459) exon(s) 6
      • FLT4 (NM_001354989) exon(s) 30
      • GJC2 (NM_020435) partial exon(s) 2(Chr1:228346380-228346419)
      • PTEN (NM_000314) exon(s) 9
      • PTEN (NM_001304717) exon(s) 10
      • PTEN (NM_001304718) exon(s) 9
      • SOX18 (NM_018419) partial exon(s) 1(Chr20:62680707-62680791)
      • STAMBP (NM_001353969) exon(s) 10
      • STAMBP (NM_001353970) exon(s) 11
      • STAMBP (NM_001353976) exon(s) 10
  • The following may not be detected:
    • Deletions/duplications/insertions of any size by MPS
    • Large duplications less than 3 exons in size
    • Noncoding transcripts
    • Deletions/duplications less than 1kb in the targeted genes by array
    • Some variants due to technical limitations in the presence of pseudogenes and/or repetitive/homologous regions
    • Low-level somatic variants
    • Single exon deletions/duplications in the following exons:
      • CCM2 (NM_001363458) 7; CCM2 (NM_001363459) 6; ENG (NM_001114753) 1; ENG (NM_000118) 1; FLT4 (NM_001354989) 30; GLMN (NM_053274) 16; GLMN (NM_001319683) 15; PIEZO1 (NM_001142864) 1,25,47; PTEN (NM_000314) 9; PTEN (NM_001304717) 1,10; PTEN (NM_001304718) 9; STAMBP (NM_001353969) 10; STAMBP (NM_001353970) 11; STAMBP (NM_001353976) 10

Genes Tested

Gene MIM Number Disorder Inheritance

ACVRL1

601284

Hereditary hemorrhagic telangiectasia, type 2

AD

AKT1

164730

Proteus syndrome

AD with somatic mosaicism

BMPR2

600799

Primary pulmonary hypertension 1

Pulmonary venoocclusive disease 1, autosomal dominant

AD

CCBE1

612753

Hennekam lymphangiectasia-lymphedema syndrome 1

AR

CCM2

607929

Cerebral cavernous malformations 2

AD

EIF2AK4

609280

Pulmonary venoocclusive disease 2, autosomal recessive

AR

ELMO2

606421

Primary intraosseous vascular malformation

AR

ENG

131195

Hereditary hemorrhagic telangiectasia type 1

AD

EPHB4

600011

Capillary malformation-arteriovenous malformation syndrome

AD

FAT4

612411

Van Maldergem syndrome 2

Hennekam lymphangiectasia-lymphedema syndrome 2

AR

FLT4

136352

Hereditary lymphedema IA

Capillary infantile hemangioma

AD

FOXC2

602402

Lymphedema-distichiasis syndrome

AD

GATA2

137295

Primary lymphedema with myelodysplasia

Emberger syndrome

AD

GDF2 (BMP9)

605120

Hereditary hemorrhagic telangiectasia type 5

AD

GJC2

608803

Hereditary lymphedema IC

AD

GLMN

601749

Glomuvenous malformations

AD

KCNK3

603220

Primary pulmonary hypertension 4

AD

KRIT1

604214

Cerebral cavernous malformations

AD

PDCD10

609118

Cerebral cavernous malformations 3

AD

PIEZO1

611184

Hereditary lymphedema III

AR

PTEN

601728

PTEN hamartoma tumor syndrome

PTEN-related Proteus syndrome

AD

RASA1

139150

Capillary malformation-arteriovenous malformation syndrome

Parkes Weber syndrome

AD

SMAD4

600993

Juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome

AD

SMAD9

603295

Primary pulmonary hypertension 2

AD

SOX18

601618

Hypotrichosis-lymphedema-telangiectasia-renal defect syndrome

AD

Hypotrichosis-lymphedema-telangiectasia syndrome AR

STAMBP

606247

Microcephaly-capillary malformation syndrome

AR

TEK

600221

Multiple cutaneous and mucosal venous malformations

AD

VEGFC

601528

Hereditary lymphedema ID

AD

AD, autosomal dominant; AR, autosomal recessive

References

Additional Resources