| Literature DB >> 35247231 |
Nicholas Borja1, Stephanie Bivona1, Lé Shon Peart1, Brittany Johnson1, Joanna Gonzalez1, Deborah Barbouth1, Henry Moore2, Shengru Guo3, Guney Bademci1, Mustafa Tekin1,3.
Abstract
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.Entities:
Keywords: zzm321990LMNB1zzm321990; zzm321990PLA2G6zzm321990; noncoding variants; progressive neurologic disease
Mesh:
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Year: 2022 PMID: 35247231 PMCID: PMC9000935 DOI: 10.1002/mgg3.1892
Source DB: PubMed Journal: Mol Genet Genomic Med ISSN: 2324-9269 Impact factor: 2.183
FIGURE 1Brain MRI images of probands. Proband 1 (A.a) Axial T2W scans demonstrate diffuse increased signal abnormality within bilateral caudate and putamen and probable involvement of bilateral thalami with relative sparing of globus pallidus (A.b) Moderate cerebellar atrophy with prominence of cerebellar folia on axial T2W image through the level of posterior fossa. Proband 2 (B.a) Axial T2W and FLAIR images show extensive bilateral white matter signal hyperintensities. Basal ganglia were spared (not shown). (B.b) Axial T2W scans demonstrate increased signal within the bilateral internal capsules, and midbrain, including cerebral white matter. Middle cerebellar peduncles, pons, and medulla were also involved (not shown). (B.c) Axial T2W and FLAIR images reveal right inferior cerebellar encephalomalacia presumed to be due to prior vascular insult
FIGURE 2Molecular studies. (a) The PLA2G6(NM_003560.4): c.2035‐926G>A is a single nucleic acid substitution that creates a splice site acceptor gain site. As a consequence, a pseudo‐exon 145 base pairs in length is incorporated into the transcript. A premature stop codon within the pseudo‐exon is anticipated to produce nonsense‐mediated decay of the mRNA transcript. (b) Pseudo‐exon donor site found to be active in two other PLA2G6 transcripts based on information in Ensembl GRCh37/hg19. (c) Relative expression of PLA2G6 in whole blood of proband 1 found to be reduced when compared to controls as measured by PLA2G6 mRNA read counts normalized to total transcriptome exonic reads. Mean of three controls ± SD shown in graph
FIGURE 3A 261 kb copy number variant was discovered at chr5:125844053‐126105052, upstream of LMNB1 as depicted. The deletion overlies a putative enhancer region for LMNB1 and five prior patients who are heterozygous for deletions overlying this area have been reported in the literature and share the autosomal dominant adult‐onset demyelinating leukodystrophy phenotype (this is based on information from the UCSC genome browser assembly GRCh37/hg19)