Data from: Krabbe disease variant classification using parental blood-based diagnostic RNA-seq
Chakravorty, Samya (2021), Data from: Krabbe disease variant classification using parental blood-based diagnostic RNA-seq, Dryad, Dataset, https://doi.org/10.5061/dryad.n2z34tmvx
Krabbe disease (KD) is a rare autosomal recessive lysosomal storage disorder (LSD) associated with severe neurodegeneration and high mortality and is one of most prevalent LSDs at a recent estimate of 1 in 12,080 live births. The disease pathogenesis is related to low/undetectable galactocerebrosidase (GALC) activity resulting in an accumulation of a cytotoxic GALC substrate, psychosine (Psy), that leads to diffuse demyelination, psychomotor delays, and high morbidity/mortality across the disease spectrum. Although phenotypic prediction in newborns with a more common, homozygous 30kb deletion and very high Psy levels is straightforward, there is a larger subset of patients identified through newborn screening with missense variants of uncertain significance (VUSs) that present with mildly elevated Psy levels that are difficult to interpret. Functional data for a small set of missense variants support altered GALC trafficking and lysosomal localization in KD compared to a loss of catalytic function; however, there are >130 unclassified GALC VUSs (ClinVar; 73 missense) with no clear prognostic impact and differential onset. We are starting to performed blood-based diagnostic RNAseq (whole transcriptomics) to classify such VUSs. Here in this dataset, we performed blood-based diagnostic RNAseq on a couple to try to classify GALC gene variants in a family with Krabbe Disease (KD) and Phenylketonuria (PKU) clinical history. The single p.T513M variant carried by one of the couple was known to be pathogenic or likely pathogenic variant (ClinVar). Using RNAseq, we identified leaky splicing abnormality of portion of transcripts skipping of GALC exon 14 casuig a frameshift and a premature stop codon allowing us to confirm its classifciation as pathogenic. The single c.442+5G>A GALC variant carried by the other individual did not show any splicing defect suggesting this variant to be likely benign. This shows that blood-based targeted or whole mRNAseq can be perforemd for fater effieicnt diagnostis and varoant classification of GALC gene and confirmation of molecular diagnosis of KD. This dataset also shows that carrier individuals or parental RNAseq can be performed if children peripheral blood or dried blood spots (DBSs) are not available to diagnose and classify GALC variants. This type of usafe of clinical-grade functional omics platforms will enahance rare neurological disease diagnosis.
Blood-based parental diagnostic RNAseq and analysis.