J Pediatr Endocrinol Metab 2020; aop Case Report Aman Ullah, Bibi Zubaida, Huma Arshad Cheema and Muhammad Naeem* Identification of two novel variants in GAA underlying infantile-onset Pompe disease in two Pakistani families https://doi.org/10.1515/jpem-2019-0477 Received October 13, 2019; accepted December 22, 2019 Abstract Background: Pompe disease (PD) is an autosomal reces- sive metabolic myopathy with an average incidence of one in 40,000 live births. It has a variable age of onset and can be diagnosed within the first 3 months. Heart involvement and muscle weakness are its primary manifestations. Case presentation: We describe two families affected by PD with two rare, novel variants. To date, pathogenic vari- ants in acid α-glucosidase (GAA) alone have accounted for all cases of the disease. Both families were screened for pathogenic sequence variations. This study presents the implications of regulatory or modifier sequences in the disease pathogenesis for the first time. A homozygous missense p.Arg854Gln variant in family A and a single het- erozygous variant (p.Asn925His) in family B were found to be segregating according to the disease phenotype. The variants were not detected in our in-house database com- prising 50 whole-exome sequences of healthy individuals from a local unrelated Pakistani population. In silico anal- yses predicted that the variants would have deleterious effects on the protein structure. Conclusions: The variants likely underlie the infantile- onset PD (IOPD) in these Pakistani families. The study expands the mutation spectrum of GAA associated with IOPD and highlights the insufficiency of screening the GAA coding sequence to determine the cause of IOPD. The work should be helpful in carrier identification, improving genetic counselling, and prenatal diagnosis. Keywords: α-1,4-glucosidase; infantile-onset Pompe disease; molecular diagnosis. What is new? 1. The segregation of single heterozygous variants was observed in families affected with autosomal reces- sive infantile-onset Pompe disease (IOPD). 2. The results have implications in regulatory or modi- fier sequences in the disease aetiology. 3. Evidence is provided for the insufficiency of acid α-glucosidase (GAA) coding sequence screening to define the genetic cause of PD. Introduction Pompe disease (PD) (glycogen storage disease II [GSDII]; OMIM: 232300) is a progressive and debilitat- ing neuromuscular disease caused by deficiency of acid α-glucosidase (GAA), which leads to the accumulation of glycogen in the lysosomes present in skeletal, cardiac, and smooth muscles. The deficiency is caused by muta- tions in the GAA gene on chromosome 17q25.3. PD is a rare condition, and the reported prevalence estimates vary widely depending on ethnicity. It is classified as infantile- onset Pompe disease (IOPD) or late-onset Pompe disease (LOPD) based on the age of onset, organ involvement, and rate of progression. The frequency of IOPD has been esti- mated as one in 8684–138,000 worldwide [1–3]. PD is clini- cally heterogeneous and multisystemic, and it follows an autosomal recessive mode of inheritance. IOPD is diag- nosed in infants with an onset before the age of 12 months in cases of cardiomegaly [3]. GAA enzyme (EC 3.2.1.20) activity is differently impacted by different mutations. Some GAA variations *Corresponding author: Muhammad Naeem, PhD, Medical Genetics Research Laboratory, Department of Biotechnology, Quaid-i-Azam University, Islamabad 45320, Pakistan, Phone: +925190644122, Cell: +92-333-5324922, E-mail: mnaeem@qau.edu.pk. https://orcid.org/0000-0002-3894-3085 Aman Ullah and Bibi Zubaida: Medical Genetics Research Laboratory, Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan. https://orcid.org/0000-0003-1062-2586 (A. Ullah) Huma Arshad Cheema: Department of Pediatric Gastroenterology, The Children’s Hospital and The Institute of Child Health, Lahore, Pakistan Brought to you by | The University of Texas at Austin Authenticated Download Date | 2/17/20 8:19 PM