Cryptic intronic NBAS variant reveals the genetic basis of recurrent liver failure in a child

Mol Genet Metab. 2019 Jan;126(1):77-82. doi: 10.1016/j.ymgme.2018.12.002. Epub 2018 Dec 11.


Background: In almost half of patients with acute liver failure the cause is unknown, making targeted treatment and decisions about liver transplantation a challenge. Monogenic disorders may contribute to a significant proportion of these undiagnosed patients, and so the incorporation of technologies such as next generation sequencing (NGS) in the clinic could aid in providing a definitive diagnosis. However, this technology may present a major challenge in interpretation of sequence variants, particularly those in non-coding regions.

Results: In this report we describe a case of Infantile liver failure syndrome 2 (ILFS2; MIM 616483) due to novel bi-allelic variants in the NBAS gene. A missense variant NM_015909.3(NBAS):c.2617C > T, NP_056993.2(NBAS):p.(Arg873Trp) was identified by whole genome sequencing (WGS). By combining WGS and reverse transcription-polymerase chain reaction (RT-PCR) we were able to identify a novel deep intronic variant, NM_015909.3(NBAS):c.2423 + 404G > C, leading to the inclusion of a pseudo-exon. This mechanism has not been described previously in this syndrome.

Conclusions: This study highlights the utility of analyzing NGS data in conjunction with investigating complementary DNA (cDNA) using techniques such as RT-PCR for detection of variants that otherwise would be likely to be missed in common NGS bioinformatic analysis pipelines. Combining these approaches, particularly when the phenotype match is strong, could lead to an increase in the diagnostic yield in acute liver failure and thus aid in targeted treatment, accurate genetic counseling and restoration of reproductive confidence.

Keywords: Deep-intronic; Liver failure; Pseudo-exon; Whole Genome Sequencing.

Publication types

  • Case Reports
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles
  • Child
  • Computational Biology
  • Genetic Variation*
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Introns*
  • Liver Failure, Acute / diagnosis
  • Liver Failure, Acute / genetics*
  • Liver Transplantation
  • Mutation
  • Neoplasm Proteins / genetics*
  • Phenotype
  • Whole Genome Sequencing


  • NBAS protein, human
  • Neoplasm Proteins