Background/Objectives: Hereditary hearing loss (HHL) is a genetically heterogeneous condition, involving more than 150 genes in non-syndromic cases and associated with over 400 distinct disorders in syndromic forms. Although whole-exome sequencing (WES) has markedly increased diagnostic yield, a substantial number of cases remain unsolved, often due to intronic variants that affect splicing and are difficult to interpret. This study aimed to characterize the potential impact of intronic variants predicted to alter splicing in families affected by HHL. Methods: The effect of seven intronic variants, previously identified in a diagnostic setting by WES within ADGRV1, ATP11A, GSDME, OTOF, OTOGL, and USH2A genes, was evaluated. To functionally validate these predictions, in vitro minigene splicing assays were subsequently performed. Results: All the identified variants were predicted to disrupt normal RNA splicing. The functional studies with minigene assays confirmed this observation and showed that the tested variants induced both exon skipping and activation of cryptic splice sites. In five out of seven cases, these splicing alterations caused a frameshift and introduced a premature termination codon, ultimately resulting in nonsense-mediated mRNA decay and protein degradation. Conclusions: This study expands the mutational spectrum of HL-related genes and highlights the importance of integrating in silico predictions with minigene assays. Such a combined approach is crucial for accurate interpretation of splicing variants, particularly when patient-derived RNA samples are unavailable.

Background: Pathogenic variants in the PPP1R12A gene have been associated with a malformation syndrome involving the brain and the genitourinary systems (GUBS, MIM #618820). To date, neither hearing loss (HL) nor inner ear malformations have been reported in affected individuals, and these features are therefore not currently regarded as part of the PPP1R12A-related phenotype. Moreover, functional evidence supporting the pathogenicity of several reported variants remains limited. Methods: We investigated a 12.5-year-old patient presenting with profound bilateral sensorineural hearing loss associated with inner ear malformations, genitourinary and central nervous system abnormalities. The patient underwent comprehensive clinical, audiological and radiological assessments, followed by genetic testing via trio-based whole-exome sequencing (WES). The molecular consequences of the identified variant were evaluated through minigene splicing assay and RT–PCR analysis on RNA extracted from peripheral blood cells. Results: WES identified a novel heterozygous splicing variant (c.792+3A>C) in the PPP1R12A gene (NM_002480.3). Functional studies demonstrated that this variant causes complete skipping of exon 5, resulting in a frameshift and the introduction of a premature termination codon. RT–PCR analysis confirmed the presence of the alternatively spliced transcript lacking exon 5. In addition, an extensive review of the literature indicated that no clear genotype–phenotype correlation has yet been established for PPP1R12A-related disorders and, whereas the majority of previously reported patients share brain and genitourinary malformations our patient additionally presented with profound bilateral sensorineural HL and inner ear malformations. Conclusions: Our findings suggest that PPP1R12A-related disorders may exhibit a broader phenotypic variability than previously recognized and we further propose that HL and inner ear malformations may represent novel features associated with this clinical spectrum. Moreover, our study underscores the importance of functional studies for accurately defining the molecular consequences of novel variants and establishing appropriate clinical correlations.