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The diagnosis of Mendelian disorders has notably advanced with integration of whole exome and genome sequencing (WES and WGS) in clinical practice. However, challenges in variant interpretation and uncovered variants by WES still leave a substantial percentage of patients undiagnosed. In this context, integrating RNA sequencing (RNA-seq) improves diagnostic workflows, particularly for WES inconclusive cases. Additionally, functional studies are often necessary to elucidate the impact of prioritized variants on gene expression and protein function. Our study focused on three unrelated male patients (P1-P3) with ATP6AP1-CDG (congenital disorder of glycosylation), presenting with intellectual disability and varying degrees of hepatopathy, glycosylation defects, and an initially inconclusive diagnosis through WES. Subsequent RNA-seq was pivotal in identifying the underlying genetic causes in P1 and P2, detecting ATP6AP1 underexpression and aberrant splicing. Molecular studies in fibroblasts confirmed these findings and identified the rare intronic variants c.289-233C > T and c.289-289G > A in P1 and P2, respectively. Trio-WGS also revealed the variant c.289-289G > A in P3, which was a de novo change in both patients. Functional assays expressing the mutant alleles in HAP1 cells demonstrated the pathogenic impact of these variants by reproducing the splicing alterations observed in patients. Our study underscores the role of RNA-seq and WGS in enhancing diagnostic rates for genetic diseases such as CDG, providing new insights into ATP6AP1-CDG molecular bases by identifying the first two deep intronic variants in this X-linked gene. Additionally, our study highlights the need to integrate RNA-seq and WGS, followed by functional validation, in routine diagnostics for a comprehensive evaluation of patients with an unidentified molecular etiology., Competing Interests: Declaration of competing interest The authors declare no conflict of interest., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Phosphoglucomutase 1 deficiency is a congenital disorder of glycosylation (CDG) with multiorgan involvement affecting carbohydrate metabolism, N-glycosylation and energy production. The metabolic management consists of dietary D-galactose supplementation that ameliorates hypoglycemia, hepatic dysfunction, endocrine anomalies and growth delay. Previous studies suggest that D-galactose administration in juvenile patients leads to more significant and long-lasting effects, stressing the urge of neonatal diagnosis (0-6 months of age). Here, we detail the early clinical presentation of PGM1-CDG in eleven infantile patients, and applied the modified Beutler test for screening of PGM1-CDG in neonatal dried blood spots (DBSs). All eleven infants presented episodic hypoglycemia and elevated transaminases, along with cleft palate and growth delay (10/11), muscle involvement (8/11), neurologic involvement (5/11), cardiac defects (2/11). Standard dietary measures for suspected lactose intolerance in four patients prior to diagnosis led to worsening of hypoglycemia, hepatic failure and recurrent diarrhea, which resolved upon D-galactose supplementation. To investigate possible differences in early vs. late clinical presentation, we performed the first systematic literature review for PGM1-CDG, which highlighted respiratory and gastrointestinal symptoms as significantly more diagnosed in neonatal age. The modified Butler-test successfully identified PGM1-CDG in DBSs from seven patients, including for the first time Guthrie cards from newborn screening, confirming the possibility of future inclusion of PGM1-CDG in neonatal screening programs. In conclusion, severe infantile morbidity of PGM1-CDG due to delayed diagnosis could be prevented by raising awareness on its early presentation and by inclusion in newborn screening programs, enabling early treatments and galactose-based metabolic management., Competing Interests: Declaration of Competing Interest The authors have no conflicts of interest to disclose., (Copyright © 2020 The Authors. Published by Elsevier Inc. All rights reserved.)

Many proteins regulating coagulation, including factor IX, factor XI, Antithrombin-III, Protein C and Protein S are deficient or decreased in activity in congenital disorders of glycosylation (CDG). Because of the imbalance of coagulation and anticoagulation factors, some patients develop acute vascular events, such as thrombosis. Identifying patients with increased risk for thrombotic events could prevent serious complications and even mortality. We performed a systematic review on patients diagnosed with the most common CDG form; PMM2-CDG, reported between 1990 and 2012 in medical literature. We also evaluated our PMM2-CDG patient-cohort of 15 patients. In total, based on the availability of comprehensive clinical descriptions, 100 patients were included in the study. Patients with and without thrombotic events were compared based on the alterations of the following glycosylated coagulation and anticoagulation factors: Antithrombin-III, Protein C, Protein S, factors IX and XI. We also assessed the global hemostasis, family history and provoking events. In the group of 100 PMM2-CDG patients 14 had suffered a venous or arterial thrombotic event. Low activity of several anticoagulation factors correlated with thrombotic events. Relatively high factor IX and XI activities were not associated with thrombosis. Prolonged PT and aPTT did not seem to protect against thrombosis in patients. Surgical procedures were frequently associated with thrombotic events. Based on the association of thrombosis and surgery in PMM2-CDG we advise to avoid elective surgical procedures in PMM2-CDG patients. Easily preventable risk factors like immobility should be treated with regular physiotherapy. We suggest a yearly follow-up for Antithrombin-III and Protein C levels and parent education for early thrombotic signs in CDG., (Copyright © 2012 Elsevier Inc. All rights reserved.)

Glycoproteins are essential in the production, transport, storage and regulation of thyroid hormones. Altered glycosylation has a potential impact on thyroid function. Abnormal thyroid function tests have been described in patients with congenital disorders of glycosylation. We evaluated the reliability of biochemical markers and investigated thyroid function in 18 PMM2-CDG patients. We propose an expectative therapeutic approach for neonates with thyroid abnormalities in CDG., (Copyright © 2012 Elsevier Inc. All rights reserved.)

We found that the missense mutation p.Pro1205Leu in the PHKA2 gene is a common cause of hepatic phosphorylase-kinase deficiency in Dutch patients, suggesting a founder-effect. Most patients presented with isolated growth delay and diarrhea, prior to the occurrence of hepatomegaly, delaying diagnosis. Tetraglucoside excretion correlated with disease severity and was used to follow compliance. The clinical presentation and therapeutic requirements in the same mutation carriers were variable, and PhK deficiency necessitated tube-feeding in some children., (Copyright © 2011 Elsevier Inc. All rights reserved.)

The association of fetal hydrops with Congenital Disorders of Glycosylation (CDG) has been reported previously. Pericardial fluid accumulation and ascites were also observed in a few young patients with CDG type Ia. Here we describe the clinical and biochemical features in three children developing life-threatening extravascular fluid accumulation. All patients carried severe PMM2 mutations comparable to the earlier reported patients with fetal hydrops. One patient was successfully treated with a pericardial-pleural shunt placement. Pericardial fluid accumulation and generalized oedema resolved temporarily in the other two children on regular albumin infusions and the use of diuretics. Sequential abdominal punctures were unsuccessful in the treatment of the extensive ascites production. The use of non-steroid anti-inflammatory agents and the application of high dose steroids had no clinical effect. Severe extravascular fluid accumulation progressed to decompensation and death. Biochemical investigations of the abdominal fluid and pericardial fluid demonstrated a high extracellular protein concentration, increased cytokine concentrations and an abnormal transferrin isoelectric focusing pattern characteristic of CDG type I. Our results are consistent with a local activation of the cytokine pathways and subsequent protein transport through the endothelial surface to the extravascular space. Normal glycosylation of cell surface proteins is essential for the normal fluid balance and protein transport through the pericardial and peritoneal membrane. Future therapeutic efforts should be directed to inhibit the abnormal immune response and excessive protein transport in this life-threatening complication of CDG syndrome.