D-bifunctional protein deficiency caused by splicing variants in a neonate with severe peroxisomal dysfunction and persistent hypoglycemia

Abstract

D-bifunctional protein (DBP) deficiency is a rare, autosomal recessive peroxisomal enzyme deficiency resulting in a high burden of morbidity and early mortality. Patients with DBP deficiency resemble those with a severe Zellweger phenotype, with neonatal hypotonia, seizures, craniofacial dysmorphisms, psychomotor delay, deafness, blindness, and death typically within the first 2 years of life, although patients with residual enzyme function can survive longer. The clinical severity of the disease depends on the degree of enzyme deficiency. Loss-of-function variants typically result in no residual enzyme activity; however, splice variants may result in protein with residual function. We describe a full-term newborn presenting with hypotonia, seizures, and unexplained hypoglycemia, who was later found to have rickets at follow up. Rapid whole genome sequencing identified two HSD17B4 variants in trans; one likely pathogenic variant and one variant of uncertain significance (VUS) located in the polypyrimidine tract of intron 13. To determine the functional consequence of the VUS, we analyzed RNA from the patient's father with RNA-seq which showed skipping of Exon 14, resulting in a frameshift mutation three amino acids from the new reading frame. This RNA-seq analysis was correlated with virtually absent enzyme activity, elevated very-long-chain fatty acids in fibroblasts, and a clinically severe phenotype. Both variants are reclassified as pathogenic. Due to the clinical spectrum of DBP deficiency, this provides important prognostic information, including early mortality. Furthermore, we add persistent hypoglycemia to the clinical spectrum of the disease, and advocate for the early management of fat-soluble vitamin deficiencies to reduce complications.

Keywords: D-bifunctional protein deficiency; Zellweger spectrum disorders; peroxisomal biogenesis disorders; rapid whole genome sequencing; very-long-chain fatty acids.

FIGURE 1

X-ray of right leg. Long bone metaphyses are symmetrically frayed and cupped in the bilateral upper and lower extremities, most striking around the knees and ankles. The zone of provisional calcification is obliterated throughout the long bone metaphyses

FIGURE 2

Integrated Genomics Viewer (IGV) image of RNA-seq alignments from the patient’s father and whole genome sequence (WGS) from the patient. (a) Coverage of alignments for exons 13 and 14 of HSD17B4. The number of reads for exon 14 (26 reads) is half that of exon 13 (52 reads). The total coverage for exon 15 is 92 reads (not shown). (b) Exon junctions track show that for some reads, exon 14 is spliced in the transcript, and for others (red arrow), exon 14 is skipped. (c) Alignments of RNA-seq reads from the father. (d) Alignments of WGS data from the patient. The red arrow points to the c.1210-11C>G variant. (e) Exon boundaries for various HSD17B4 transcripts, in the canonical transcript NM_000414, they are exons 13 and 14