Novel approaches to uncover the molecular etiology of neurodevelopmental disorders (NDD) are highly needed. Even using a powerful tool such as whole exome sequencing (WES), the diagnostic process may still prove long and arduous due to the high clinical and genetic heterogeneity of these conditions. The main strategies to improve the diagnostic rate are based on family segregation, re-evaluation of the clinical features by reverse-phenotyping, re-analysis of unsolved NGS-based cases and epigenetic functional studies. In this article, we described three selected cases from a cohort of patients with NDD in which trio WES was applied, in order to underline the typical challenges encountered during the diagnostic process: (1) an ultra-rare condition caused by a missense variant in MEIS2, identified through the updated Solve-RD re-analysis; (2) a patient with Noonan-like features in which the NGS analysis revealed a novel variant in NIPBL causing Cornelia de Lange syndrome; and (3) a case with de novo variants in genes involved in the chromatin-remodeling complex, for which the study of the epigenetic signature excluded a pathogenic role. In this perspective, we aimed to (i) provide an example of the relevance of the genetic re-analysis of all unsolved cases through network projects on rare diseases; (ii) point out the role and the uncertainties of the reverse phenotyping in the interpretation of the genetic results; and (iii) describe the use of methylation signatures in neurodevelopmental syndromes for the validation of the variants of uncertain significance.

Background: Autosomal dominant polycystic kidney disease (ADPKD) is the most common inherited kidney disease, affecting approximately 1 in 1000 individuals. This genetically heterogeneous condition is primarily caused by monoallelic pathogenic or likely pathogenic variants in the PKD1 and PKD2 genes, accounting for 78% and 15% of typical cases, respectively. Recently, the application of NGS methods has led to the identification of additional genes associated with ADPKD, which have been incorporated into routine diagnostic testing for detecting phenocopies of the disease. Methods: In this study, targeted NGS (tNGS) analysis of the main cystogenes associated with classic and atypical ADPKD was performed in a cohort of 218 patients clinically diagnosed with cystic nephropathies. Results: Genetic testing identified variants in 175 out of 218 cases (80.3%). Among these, 133 probands (76%) harbored likely pathogenic or pathogenic variants in one or more genes of the panel, while 42 individuals (24%) had a variant of unknown significance (VUS). Specifically, one or more class 4/5 variants in PKD1, PKD2, or both were identified in 111 (83.5%) probands. Remarkably, a pathogenic variant in the IFT140 gene was identified in 14 index cases (8% of positive individuals, 6.4% of the global cohort): 10 distinct loss-of-function (LoF) variants were identified (including four frameshift variants, four nonsense variants, and two splice site defects); one individual carried a second IFT140 missense variant classified as VUS. Furthermore, five affected family members were found to carry a P/LP LoF variant in IFT140. Conclusions: Our data support that IFT140 heterozygous IFT140 LoF variants result in an atypical, mild form of ADPKD, consisting of bilateral kidney cysts and renal functional decline at older ages. Furthermore, we describe the second pediatric patient with a mild form of ADPKD due to an IFT140 variant and discuss hyperuricemia as a previously unappreciated feature of this condition.

Background/Objectives: The TECTA gene variant is one of the most common causes of nonsyndromic congenital hearing loss affecting the mid-frequency range. Situated on chromosome 11q22–q24, the TECTA gene encodes α-tectorin, a non-collagenous protein of the tectorial membrane. Pathogenetic variants of TECTA are relatively rare, and numerous variants have been described, complicating the delineation of a clear and recognizable clinical phenotype. This scoping review aims to provide an up-to-date overview of the known TECTA variants causing autosomal dominant sensorineural hearing loss (ADSNHL) and their associated audiological phenotypes. Methods: A review of the English-language literature on hearing loss associated with TECTA variants was conducted using PubMed, Scopus, Google Scholar, and MEDLINE databases, in accordance with the “Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA)” criteria for scoping review. Results: Eighteen studies met all inclusion criteria. Overall, 44 unique TECTA variants were identified after recurrent reports of the same cDNA-level variant were consolidated. Of these, 14 were classified as pathogenic or likely pathogenic (P/LP), 9 as variants of uncertain significance (VUS), while the remaining 21 had conflicting, benign/likely benign, or unavailable classification. Domain-based analysis showed a marked prevalence of variants in the ZA domain (21 variants, 47.73%), followed by the ZP domain (14 variants, 31.82%) and the ENT domain (5 variants, 11.36%). Thirty-two variant occurrences were reported in association with hearing loss in the mid frequencies and 12 in the high frequencies. Stable hearing loss was reported for 15 variant occurrences, whereas progressive hearing loss was reported for 13. Conclusions: The identification and characterization of novel genetic variants associated with hearing loss are essential for improving phenotype–genotype correlations. Early identification of the genetic etiology of hearing loss is becoming increasingly important, particularly in light of recent advances in gene therapy for pediatric hearing loss.