Rapid whole-genome sequencing identifies a homozygous novel variant, His540Arg, in HSD17B4 resulting in D-bifunctional protein deficiency disorder diagnosis

Cold Spring Harb Mol Case Stud. 2020 Dec 17;6(6):a005496. doi: 10.1101/mcs.a005496. Print 2020 Dec.


Rapid whole-genome sequencing (rWGS) allows for a diagnosis to be made quickly and impact medical management, particularly in critically ill children. Variants identified by this approach are often not identified using other testing methodologies, such as carrier screening or gene sequencing panels, targeted panels, or chromosomal microarrays. However, rWGS can identify variants of uncertain significance (VUSs), which challenges clinicians in the rapid return of information to families. Here we present a case of the metabolic condition D-bifunctional protein deficiency in a neonate with epilepsy and hypotonia born to consanguineous parents. Sequencing revealed a homozygous VUS in HSD17B4, c.1619A > G (p.His540Arg). Preliminary results were delivered within 3 d of sample receipt. Previous parental carrier screening included the HSD17B4 gene but was reported as negative. The molecular finding directed the clinical team to assess phenotypic overlap and investigate next steps in terms of confirmation of the findings and potential medical management of the patient. Clinical metabolic testing of fatty acids confirmed the diagnosis. Computational analysis of HSD17B4 His540Arg showed the change to likely impact dimerization based on structural insights, with the histidine conserved and selected throughout all 223 species assessed for this amino acid. This variant clusters around several pathogenic and likely pathogenic variants in HSD17B4 This case demonstrates the utility of rWGS, the potential for receiving uncertain results, and the downstream implications for confirmation or rejection of a molecular diagnosis by the clinical team.

Keywords: generalized neonatal hypotonia; infantile spasms; respiratory difficulties; respiratory insufficiency due to muscle weakness; very long chain fatty acid accumulation.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Fatty Acids
  • Female
  • Genetic Predisposition to Disease / genetics
  • Homozygote*
  • Humans
  • Infant
  • Models, Molecular
  • Muscle Hypotonia
  • Pathology, Molecular / methods
  • Peroxisomal Multifunctional Protein-2 / chemistry
  • Peroxisomal Multifunctional Protein-2 / deficiency*
  • Peroxisomal Multifunctional Protein-2 / genetics*
  • Protein Conformation
  • Protein Deficiency / genetics*
  • Whole Genome Sequencing*


  • Fatty Acids
  • Peroxisomal Multifunctional Protein-2
  • HSD17B4 protein, human