Genome sequencing reveals novel noncoding variants in PLA2G6 and LMNB1 causing progressive neurologic disease.

Neurodegenerative disorders and leukodystrophies are progressive neurologic conditions that can occur following the disruption of intricately coordinated patterns of gene expression. Exome sequencing has been adopted as an effective diagnostic tool for determining the underlying genetic etiology of Mendelian neurologic disorders, however genome sequencing offer advantages in its ability to identify and characterize copy number, structural, and sequence variants in noncoding regions. Genome sequencing from peripheral leukocytes was performed on two patients with progressive neurologic disease of unknown etiology following negative genetic investigations including exome sequencing. RNA sequencing from peripheral blood was performed to determine gene expression patterns in one of the patients. Potential causative variants were matched to the patients' clinical presentation. The first proband was found to be heterozygous for a likely pathogenic missense variant in PLA2G6 (c.386T>C; p.Leu129Pro) and have an additional deep intronic variant in PLA2G6 (c.2035-926G>A). RNA sequencing indicated this latter variant created a splice acceptor site leading to the incorporation of a pseudo-exon introducing a premature termination codon. The second proband was heterozygous for a 261 kb deletion upstream of LMNB1 that included an enhancer region. Previous reports of copy number variants spanning this region of cis-acting regulatory elements corroborated its pathogenicity. When combined with clinical presentations, these findings led to a definitive diagnosis of autosomal recessive infantile neuroaxonal dystrophy and autosomal dominant adult-onset demyelinating leukodystrophy, respectively. In patients with progressive neurologic disease of unknown etiology, genome sequencing with the addition of RNA analysis where appropriate should be considered for the identification of causative noncoding pathogenic variants.

Bilateral choanal stenosis in auriculocondylar syndrome caused by a PLCB4 variant.

Auriculocondylar syndrome (ARCND) is characterized by a distinguished feature of question mark ears and a variation of other minor and major malformations. Monoallelic or biallelic PLCB4 variants have been reported in a subset of affected individuals, referred to as ARCND2. We report on a 3-year-old female with ARCND who presented at birth with question mark ears, micrognathia, and bilateral choanal stenosis that was characterized by difficulty in breathing. She was found to be heterozygous for a novel PLCB4 variant, p.Glu358Gly. Respiratory distress is rare in autosomal dominant ARCND2 and choanal stenosis has not been reported. Our study expands the clinical phenotype of ARCND by adding choanal stenosis as a finding and suggests that PLCB4 play a role in the development of choanal structures.