Whole Exome Sequencing Identifies Truncating Variants in Nuclear Envelope Genes in Patients With Cardiovascular Disease

Circ Cardiovasc Genet. 2017 Jun;10(3):e001443. doi: 10.1161/CIRCGENETICS.116.001443.


Background: The genetic variation underlying many heritable forms of cardiovascular disease is incompletely understood, even in patients with strong family history or early age at onset.

Methods and results: We used whole exome sequencing to detect pathogenic variants in 55 patients with suspected monogenic forms of cardiovascular disease. Diagnostic analysis of established disease genes identified pathogenic variants in 21.8% of cases and variants of uncertain significance in 34.5% of cases. Three patients harbored heterozygous nonsense or splice-site variants in the nucleoporin genes NUP37, NUP43, and NUP188, which have not been implicated previously in cardiac disease. We also identified a heterozygous splice site variant in the nuclear envelope gene SYNE1 in a child with severe dilated cardiomyopathy that underwent transplant, as well as in his affected father. To confirm a cardiovascular role for these candidate genes in vivo, we used morpholinos to reduce SYNE1, NUP37, and NUP43 gene expression in zebrafish. Morphant embryos displayed cardiac abnormalities, including pericardial edema and heart failure. Furthermore, lymphoblasts from the patient carrying a SYNE1 splice-site variant displayed changes in nuclear morphology and protein localization that are consistent with disruption of the nuclear envelope.

Conclusions: These data expand the repertoire of pathogenic variants associated with cardiovascular disease and validate the diagnostic and research use of whole exome sequencing. We identify NUP37, NUP43, and NUP188 as novel candidate genes for cardiovascular disease, and suggest that dysfunction of the nuclear envelope may be an under-recognized component of inherited cardiac disease in some cases.

Keywords: animals; cardiomyopathy; dilated cardiomyopathy; edema; genetic variation.

MeSH terms

  • Animals
  • Cardiovascular Diseases / diagnosis*
  • Cardiovascular Diseases / genetics
  • Cardiovascular Diseases / pathology
  • Cytoskeletal Proteins
  • Databases, Genetic
  • Embryo, Nonmammalian / metabolism
  • Genetic Variation
  • Heterozygote
  • Humans
  • Lamin Type A / metabolism
  • Morpholinos / metabolism
  • Mutation, Missense
  • Nerve Tissue Proteins / metabolism
  • Nuclear Pore Complex Proteins / antagonists & inhibitors
  • Nuclear Pore Complex Proteins / genetics*
  • Nuclear Pore Complex Proteins / metabolism
  • Nuclear Proteins / metabolism
  • Phenotype
  • RNA Interference
  • RNA Splice Sites / genetics
  • Sequence Analysis, DNA
  • Whole Exome Sequencing
  • Zebrafish


  • Cytoskeletal Proteins
  • Lamin Type A
  • Morpholinos
  • Nerve Tissue Proteins
  • Nuclear Pore Complex Proteins
  • Nuclear Proteins
  • RNA Splice Sites
  • SYNE1 protein, human