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.

SCN1A, the gene encoding for the Nav1.1 channel, exhibits dominant interneuron-specific expression, whereby variants disrupting the channel’s function affect the initiation and propagation of action potentials and neuronal excitability causing various types of epilepsy. Dravet syndrome (DS), the first described clinical presentation of SCN1A channelopathy, is characterized by severe myoclonic epilepsy in infancy (SMEI). Variants’ characteristics and other genetic or epigenetic factors lead to extreme clinical heterogeneity, ranging from non-epileptic conditions to developmental and epileptic encephalopathy (DEE). This current study reports on findings from 343 patients referred by physicians in hospitals and tertiary care centers in Greece between 2017 and 2023. Positive family history for specific neurologic disorders was disclosed in 89 cases and the one common clinical feature was the onset of seizures, at a mean age of 17 months (range from birth to 15 years old). Most patients were specifically referred for SCN1A investigation (Sanger Sequencing and MLPA) and only five for next generation sequencing. Twenty-six SCN1A variants were detected, including nine novel causative variants (c.4567A>Τ, c.5564C>A, c.2176+2T>C, c.3646G>C, c.4331C>A, c.1130_1131delGAinsAC, c.1574_1580delCTGAGGA, c.4620A>G and c.5462A>C), and are herein presented, along with subsequent genotype–phenotype associations. The identification of novel variants complements SCN1A databases extending our expertise on genetic counseling and patient and family management including gene-based personalized interventions.

We report a thirty-six-year-old woman with intellectual disability who was referred for evaluation of suspected obstructive sleep apnea. The initial clinical impression suggested a syndromic case, so comprehensive genetic testing was undertaken. Overnight polysomnography revealed a severe rapid eye movement–predominant obstructive sleep apnea syndrome with an apnea–hypopnea index of 31.9 events per hour, rapid eye movement apnea–hypopnea index of 113.8 events per hour, and lowest oxygen saturation of 66%. Treatment with continuous positive airway pressure improved respiratory and sleep quality indices and was well tolerated. Whole-exome sequencing identified a de novo splice site variant in the pleckstrin homology domain interacting protein gene (c.41-1G > A), confirming a molecular diagnosis of Chung–Jansen Syndrome. Chung–Jansen syndrome is a rare neurodevelopmental disorder caused by heterozygous pathogenic variants in the pleckstrin homology domain interacting protein gene, marked by developmental delay, intellectual disability, behavioral abnormalities, dysmorphism, and progressive obesity. PHIP influences central and peripheral pathways controlling satiety, pancreatic function, and body weight. Despite frequent reports of sleep problems, systematic evaluation of sleep-disordered breathing has been limited. This adult case provides the first polysomnographic confirmation in the syndrome, supporting proactive screening for obstructive sleep apnea—especially in those with obesity. Integrating genetic assessment into sleep care can reduce diagnostic delays and better guide therapy and prognosis.

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.