Glycogen storage disorders (GSD) GSD-IX are characterized by deficiencies in muscular and/or hepatic phosphorylase enzymes. GSD type IX za is an X-linked disorder, while IXb and IXc are autosomal recessive disorders resulting from pathogenic variants in the genes encoding the Phosphorylase b Kinase regulatory subunit alpha (PHKA), beta (PHKB), and gamma (PHKG), respectively. Despite progress in understanding these diseases, there are still unclear questions regarding their clinical manifestations, genetic variations, and the relationship between genotype and phenotype. Therefore, this review focuses on variants of GSD IX subtypes and all clinical findings to establish a genotype–phenotype relationship as well as highlighting the wide spectrum of disease-causing variants. Such information is beneficial for the establishment of a privileged mutation screening process in a specific region or ethnic group. Diagnosis is based on clinical manifestations and laboratory test results, but molecular analysis is often necessary to distinguish the various forms with similar presentations.