Whole-Exome Sequencing (WES) has proven valuable in the characterization of underlying genetic defects in most rare diseases (RDs). Copy Number Variants (CNVs) were initially thought to escape detection. Recent technological advances enabled CNV calling from WES data with the use of accurate and highly sensitive bioinformatic tools. Amongst 920 patients referred for WES, 454 unresolved cases were further analysed using the ExomeDepth algorithm. CNVs were called, evaluated and categorized according to ACMG/ClinGen recommendations. Causative CNVs were identified in 40 patients, increasing the diagnostic yield of WES from 50.7% (466/920) to 55% (506/920). Twenty-two CNVs were available for validation and were all confirmed; of these, five were novel. Implementation of the ExomeDepth tool promoted effective identification of phenotype-relevant and/or novel CNVs. Among the advantages of calling CNVs from WES data, characterization of complex genotypes comprising both CNVs and SNVs minimizes cost and time to final diagnosis, while allowing differentiation between true or false homozygosity, as well as compound heterozygosity of variants in AR genes. The use of a specific algorithm for calling CNVs from WES data enables ancillary detection of different types of causative genetic variants, making WES a critical first-tier diagnostic test for patients with RDs.

Alport syndrome (AS) is a hereditary glomerulopathy due to pathogenic variants in COL4A3, COL4A4, and COL4A5. Treatment with Renin–Angiotensin–Aldosterone System (RAAS) inhibitors can delay progression to end stage renal disease (ESRD). From 2018 until today, we performed Whole Exome Sequencing (WES) in 19 patients with AS phenotype with or without positive family history. Fourteen of these patients were children. Genetic testing was extended to family members at risk. All patients received a genetic diagnosis of AS: five X-linked AS (XLAS) males, five X-linked AS (XLAS) females, six autosomal dominant AS (ADAS), and one autosomal recessive AS (ARAS). After cascade screening four XLAS males and eight XLAS females, six ADAS and three ARAS heterozygotes were added to our initial results. Fifteen patients were eligible to start treatment with RAAS inhibitors after their diagnosis. All XLAS female patients, ARAS heterozygotes, and ADAS have been advised to be followed up, so that therapeutic intervention can begin in the presence of microalbuminuria. Genetic diagnosis of AS ensures early therapeutic intervention and appropriate follow up to delay progression to chronic kidney disease, especially in thet pediatric population.

Marinesco–Sjögren syndrome (MSS) is a rare autosomal recessive neuromuscular disorder marked by ataxia, muscle weakness, cataracts, and often intellectual and skeletal abnormalities. It is commonly caused by loss-of-function variants in the SIL1 gene, which impair binding immunoglobulin protein (BiP) function, leading to protein misfolding and activation of the unfolded protein response. In a 2-year-old patient with typical MSS symptoms, we identified a previously unreported c.1024G>A (p.E342K) variant in SIL1 via whole-exome sequencing. The pathogenicity of this Sil1 variant was supported by evidence of structural changes revealed through in silico predictions, circular dichroism, and native gel electrophoresis. Patient-derived fibroblasts exhibited reduced Sil1 protein levels, likely due to misfolding and degradation, which was partially rescued by proteasome inhibition. Proteomics revealed a profile similar to known MSS cases and a distinctive MSS transcriptional signature. Ultrastructural analysis confirmed typical MSS features, such as autophagic vacuoles and lipid droplets. Although the p.E342K phenotype appears milder than the reference pathogenic variant R111X, our findings support the reclassification of this novel variant as pathogenic, in accordance with the American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) 2015 guidelines and the refinements proposed by the Clinical Genome Resource Sequence Variant Interpretation (ClinGen SVI) recommendations. Furthermore, the overall evidence also provides important insights into the genotype–phenotype correlation and the underlying pathogenic mechanism of the p.E342K variant.

Background/Objectives: To date, approximately 360 pathogenic variants of the OCRL gene have been reported, including frameshift, substitution, gross inversion, nonsense, and missense mutations. These genetic alterations have been associated with a broad phenotypic spectrum of Lowe syndrome, contributing to considerable variability in disease severity and clinical presentation. Missense variants are typically associated with preserved messenger RNA expression in fibroblasts, whereas more deleterious mutations result in markedly reduced expression of the OCRL transcript or protein product. Pathogenic variants in the OCRL gene have also been identified in patients with Dent’s disease type 2. Case presentation: This case report describes a pediatric male patient with autism spectrum disorder and renal dysfunction, who was found to harbor a variant of uncertain clinical significance in the OCRL gene and a pathogenic 16p11.2 chromosomal deletion. The patient, a 12-year-old boy with autism, presented with proteinuria during hospitalization for febrile gastroenteritis and streptococcal infection. Further evaluation revealed focal glomerulosclerosis, tubular calcium phosphate deposits, albuminuria, and hypercalciuria. Ophthalmologic examination additionally demonstrated bilateral lens opacities in the absence of congenital cataracts, as well as hyperopia. The coexistence of these clinical manifestations together with the identified OCRL gene variant raises the possibility of an atypical presentation of Dent disease type 2. Nevertheless, continued clinical and genetic follow-up remains warranted to further clarify the pathogenic significance of the detected variant and to establish a definitive diagnosis. Conclusions: The uniqueness of this case resides in the coexistence of two independent genetic findings presenting a phenotype-attribution challenge. Furthermore, the identified phenotype may warrant consideration as a possible previously unreported phenotypic presentation situated along the clinical spectrum between Lowe syndrome and Dent disease type 2. The main contribution of this report is to illustrate the interpretative challenges of a concurrent pathogenic 16p11.2 deletion and an OCRL variant of uncertain significance in a patient with renal disease and neurodevelopmental features.