1. Reticular dysgenesis caused by an intronic pathogenic variant in AK2 .
- Author
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Ichikawa S, Prockop S, Cunningham-Rundles C, Sifers T, Conner BR, Wu S, Karam R, Walsh MF, and Fiala E
- Subjects
- Alleles, DNA Mutational Analysis, Exons, Humans, Infant, Infant, Newborn, Leukopenia therapy, Male, Mutation, Peripheral Blood Stem Cell Transplantation, Phenotype, RNA Splicing, Severe Combined Immunodeficiency therapy, Treatment Outcome, Adenylate Kinase genetics, Genetic Association Studies, Genetic Predisposition to Disease, Genetic Variation, Introns, Leukopenia diagnosis, Leukopenia genetics, Severe Combined Immunodeficiency diagnosis, Severe Combined Immunodeficiency genetics
- Abstract
Reticular dysgenesis is a form of severe combined immunodeficiency (SCID) caused by biallelic pathogenic variants in AK2 Here we present the case of a boy diagnosed with SCID following a positive newborn screen (NBS). Genetic testing revealed a homozygous variant: AK2 c.330 + 5G > A. In silico analyses predicted weakened native donor splice site. However, this variant was initially classified as a variant of uncertain significance (VUS) given lack of direct evidence. To determine the impact on splicing, we analyzed RNA from the proband and his parents, using massively parallel RNA-seq of cloned RT-PCR products. Analysis showed that c.330 + 5G > A results in exon 3 skipping, which encodes a critical region of the AK2 protein. With these results, the variant was upgraded to pathogenic, and the patient was given a diagnosis of reticular dysgenesis. Interpretation of VUS at noncanonical splice site nucleotides presents a challenge. RNA sequencing provides an ideal platform to perform qualitative and quantitative assessment of intronic VUS, which can lead to reclassification if a significant impact on mRNA is observed. Genetic disorders of hematopoiesis and immunity represent fruitful areas to apply RNA-based analysis for variant interpretation given the high expression of RNA in blood., (© 2020 Ichikawa et al.; Published by Cold Spring Harbor Laboratory Press.)
- Published
- 2020
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