Reconciling newborn screening and a novel splice variant in BTD associated with partial biotinidase deficiency: a BabySeq Project case report

• Published in: Cold Spring Harbor molecular case studies 2018-08, Vol.4 (4), p.a002873
• Main Authors: Murry, Jaclyn B, Machini, Kalotina, Ceyhan-Birsoy, Ozge, Kritzer, Amy, Krier, Joel B, Lebo, Matthew S, Fayer, Shawn, Genetti, Casie A, VanNoy, Grace E, Yu, Timothy W, Agrawal, Pankaj B, Parad, Richard B, Holm, Ingrid A, McGuire, Amy L, Green, Robert C, Beggs, Alan H, Rehm, Heidi L
• Format: Article
• Language: English
• Subjects: Alternative splicing; Biotinidase; Biotinidase - genetics; Case reports; Diagnostic systems; Enzymatic activity; Enzyme activity; Female; Homozygosity; Humans; Impact prediction; Infant, Newborn; Loss of Function Mutation; Medical screening; Neonatal Screening; Rapid Communication; Reclassification; RNA Splicing; Splicing; Whole Exome Sequencing
• ISSN: 2373-2865; 2373-2873
• DOI: 10.1101/mcs.a002873

Here, we report a newborn female infant from the well-baby cohort of the BabySeq Project who was identified with compound heterozygous gene variants. The two identified variants included a well-established pathogenic variant (c.1612C>T, p.Arg538Cys) that causes profound biotinidase deficiency (BTD) in homozygosity. In addition, a novel splice variant (c.44+1G>A, p.?) was identified in the invariant splice donor region of intron 1, potentially predictive of loss of function. The novel variant was predicted to impact splicing of exon 1; however, given the absence of any reported pathogenic variants in exon 1 and the presence of alternative splicing with exon 1 absent in most tissues in the GTEx database, we assigned an initial classification of uncertain significance. Follow-up medical record review of state-mandated newborn screen (NBS) results revealed an initial out-of-range biotinidase activity level. Levels from a repeat NBS sample barely passed cutoff into the normal range. To determine whether the infant was biotinidase-deficient, subsequent diagnostic enzyme activity testing was performed, confirming partial BTD, and resulted in a change of management for this patient. This led to reclassification of the novel splice variant based on these results. In conclusion, combining the genetic and NBS results together prompted clinical follow-up that confirmed partial BTD and informed this novel splice site's reclassification, emphasizing the importance of combining iterative genetic and phenotypic evaluations.