Vascular Malformations Panel, Sequencing and Deletion/Duplication

Last Literature Review: May 2022 Last Update:
  • 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.

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.

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

SyndromePrevalence
HHT1 in 5,000 to 1 in 10,000 , 
CCM1 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 syndrome1 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 ClassAnalytic Sensitivity (PPA) Estimatea (%) and 95% Credibility RegionAnalytic Specificity (NPA) Estimate (%)
SNVs>99 (96.9-99.4)>99.9
Deletions 1-10 bpb93.8 (84.3-98.2)>99.9
Insertions 1-10 bpb94.8 (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 duplications83.3 (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

GeneMIM NumberDisorderInheritance
ACVRL1601284Hereditary hemorrhagic telangiectasia, type 2AD
AKT1164730Proteus syndromeAD with somatic mosaicism
BMPR2600799

Primary pulmonary hypertension 1

Pulmonary venoocclusive disease 1, autosomal dominant

AD
CCBE1612753Hennekam lymphangiectasia-lymphedema syndrome 1AR
CCM2607929Cerebral cavernous malformations 2AD
EIF2AK4609280Pulmonary venoocclusive disease 2, autosomal recessiveAR
ELMO2606421Primary intraosseous vascular malformationAR
ENG131195Hereditary hemorrhagic telangiectasia type 1AD
EPHB4600011Capillary malformation-arteriovenous malformation syndromeAD
FAT4612411

Van Maldergem syndrome 2

Hennekam lymphangiectasia-lymphedema syndrome 2

AR
FLT4136352

Hereditary lymphedema IA

Capillary infantile hemangioma

AD
FOXC2602402Lymphedema-distichiasis syndromeAD
GATA2137295

Primary lymphedema with myelodysplasia

Emberger syndrome

AD
GDF2 (BMP9)605120Hereditary hemorrhagic telangiectasia type 5AD
GJC2608803Hereditary lymphedema ICAD
GLMN601749Glomuvenous malformationsAD
KCNK3603220Primary pulmonary hypertension 4AD
KRIT1604214Cerebral cavernous malformationsAD
PDCD10609118Cerebral cavernous malformations 3AD
PIEZO1611184Hereditary lymphedema IIIAR
PTEN601728

PTEN hamartoma tumor syndrome

PTEN-related Proteus syndrome

AD
RASA1139150

Capillary malformation-arteriovenous malformation syndrome

Parkes Weber syndrome

AD
SMAD4600993Juvenile polyposis/hereditary hemorrhagic telangiectasia syndromeAD
SMAD9603295Primary pulmonary hypertension 2AD
SOX18601618Hypotrichosis-lymphedema-telangiectasia-renal defect syndromeAD
Hypotrichosis-lymphedema-telangiectasia syndromeAR
STAMBP606247Microcephaly-capillary malformation syndromeAR
TEK600221Multiple cutaneous and mucosal venous malformationsAD
VEGFC601528Hereditary lymphedema IDAD
AD, autosomal dominant; AR, autosomal recessive

References