Unmasking Compound Heterozygosity in GYG1 Myopathy: Diagnostic Insights From RNA-Seq and Long-Read Genomics

Polyglucosan body myopathy type 2 (PGBM2; OMIM #616199) is an autosomal recessive myopathy caused by biallelic variants in GYG1, which encodes glycogenin-1. It is characterized by progressive muscle weakness and PAS-positive, diastase-resistant polyglucosan inclusions on muscle biopsy. We report a 64-year-old woman who developed progressive proximal weakness beginning in her early 50s, with polyglucosan bodies identified on muscle histopathology. Genome sequencing (GS) detected a single heterozygous pathogenic splice-site variant, NM_004130.4(GYG1):c.143+3G>C. Given strong histopathologic evidence of PGBM2, GS data were reanalyzed, revealing an additional rare deep intronic variant, NM_004130.4(GYG1):c.7+992T>G, predicted to activate a cryptic exon. RNA sequencing (RNA-seq) confirmed aberrant splicing from both variants, demonstrating exon 2 skipping associated with c.143+3G>C and cryptic exon inclusion caused by c.7+992T>G. Variant phasing posed a diagnostic challenge due to unavailable parental DNA, and long-range PCR results were inconclusive. Long-read GS definitively demonstrated that the two variants were in trans, establishing compound heterozygosity and confirming the molecular diagnosis. These findings enabled reclassification of the deep intronic variant as likely pathogenic. This case highlights the diagnostic limitations of conventional phasing approaches in adult-onset recessive disorders and demonstrates the clinical utility of integrating genome reanalysis, RNA-seq, and long-read GS for resolving complex phasing challenges.