Cell modeling and rescue of a novel noncoding genetic cause of glycogen storage disease IX

Delayed diagnosis of Mendelian disease prevents early therapeutic intervention that could improve symptoms and prognosis. One major contributing challenge is functional interpretation of noncoding variants that alter splicing. Here, we aimed to better understand both how splice altering variants contribute to Mendelian disease and how to identify such mechanisms via an instrumental case study of 2 siblings with glycogen storage disease (GSD) IX γ2.

The siblings had a classic clinical presentation, enzyme deficiency, and a known pathogenic splice variant on 1 allele of PHKG2 (HGNC:8931). Despite the autosomal recessive nature of the disease, no coding variant on the second allele was identified by targeted sequencing. We evaluated potential noncoding pathogenic variants using genome sequencing and RNA sequencing and created an isogenic model of the candidate variant using CRISPR/Cas9 genome editing.

In both siblings, we identified a second variant (NC_000016.10:g.30754626T>G [GRCh38]): a deep intronic variant that caused a 76-bp pseudoexon inclusion in PHKG2. In a HEK293T cell model in which we installed that variant, we confirmed its effects on splicing in addition to multiple biochemical and cellular phenotypes consistent with GSD IX. We then reversed aberrant splicing using antisense oligonucleotide technology.

As evidenced by RNA sequencing, population and allelic segregation data, and phenotyping of an isogenic cell culture model of the variant, we concluded that PHKG2 c.556+1069T>G causes GSD IX γ2 and can be targeted using antisense oligonucleotides. This demonstrates a novel and robust pathway for detecting, validating, and reversing the impacts of noncoding causes of rare disease.