Background: Genetic diseases collectively affect more than 300 million individuals worldwide, posing a significant health burden, as diagnosis is often challenging and therapeutic options are limited. Recent genetic technological advancements are improving the management of many inherited disorders, including genetic kidney disorders (GKDs), the leading cause of early-onset chronic kidney disease (CKD) and the cause of 10–15% of kidney replacement therapy in adults. Summary: GKDs fall into different clinical categories, including cystic and fibro-cystic diseases in the setting of ciliopathies, rare conditions caused by the dysfunction of the primary cilium, typically characterized by multiorgan dysfunction. CKD is a significant cause of morbidity and mortality in these patients and a correct diagnosis is crucial for patient’s management. Key Message: The present review analyzes whether advances in genomic technologies have provided benefit in the ciliopathy field, in both modeling renal diseases and improving patient’s care.

INTRODUCTION:CFHR5 nephropathy is considered a subtype of C3 glomerulopathy. It was originally described in Greek Cypriot families and it is characterized by the time with the development of microscopic hematuria and proteinuria associated with a fast progression toward ESKD, especially in men. These symptoms present an autosomal dominant inheritance pattern and are associated with the exon 2 to 3 duplication of the CFHR5 gene. CASE PRESENTATION:Here, we describe a novel clinical phenotype associated with a variant of the CFHR5. The affected subjects present the clinical features of autosomal dominant tubulo-interstitial kidney disease. They present with CKD of unknown origin with no hematuria nor proteinuria. Like the classical CFHR5 nephropathy, males have a worse prognosis than females, with a fast progression toward ESKD in the second-third decade of life. Kidney pathology shows severe tubular atrophy and interstitial fibrosis and infiltrate. Arteries involvement is characterized by thickening of the intima layer, while no major alterations are described at the glomerular level. Electron microscopy confirms no interstitial or glomerular filtration barrier alterations. CONCLUSION:The exact mechanism behind this phenomenon remains unclear; we hope that our case will encourage further investigation.

Sotos syndrome is a rare genetic disorder characterized by distinctive facial features, including a broad and prominent forehead, dolichocephaly, and learning disabilities ranging from mild to severe intellectual impairment. Affected individuals often show overgrowth in height and head circumference over two standard deviations. The syndrome is caused by haploinsufficiency of the NSD1 gene, with no evidence of genetic heterogeneity to date. Here we describe the unsolved case of a child of 4 years of age with a clinical diagnosis of Sotos syndrome. However, trio exome sequencing (ES) and exon chromosomal microarray (CMA) analysis excluded both small and large mutations in the NSD1 gene. As part of the Telethon Undiagnosed Programme, we used additional tools to investigate the possibility of new genes or elusive mutations that may have been missed by previous molecular diagnostic approaches. Therefore, we performed Nanopore long-read sequencing. This revealed a 447 bp insertion in exon 13 of the NSD1 gene. mRNA analysis confirmed in-frame skipping of exon 13 that encodes for two PHD domains. The genomic insertion shows 100% identity with an intronic region, although inverted, containing an AluSx1 element 2 kb upstream of the skipped exon, which may drive the event by masking the splice acceptor site of exon 13. Interestingly, this is the first case of Sotos syndrome linked to a pathogenic mechanism involving an insertion enclosing a transposable element generating a protein devoid of two PHDs, which are required for reading histone post-translational modifications.

Background: Multiple genes can disrupt hypothalamic–pituitary axis development, causing multiple pituitary hormone deficiencies (MPHD). Despite advances in next-generation sequencing (NGS) identifying over 30 key genes, 85% of cases remain unsolved, indicating complex genotype–phenotype correlations and variable inheritance patterns. Objective: This study aimed to identify the MPHD genetics in three probands from two unrelated families. Methods: Family A had one affected child, while Family B had two affected siblings. All probands exhibited poor growth since birth, and family B’s probands were born small for gestational age. Growth hormone deficiency was confirmed in all subjects. Family B’s probands responded poorly to growth hormone treatment compared to the first patient. Furthermore, Family A’s proband and Family B’s younger sibling developed central hypothyroidism, while Family B’s older sibling presented hypogonadotropic hypogonadism. Brain magnetic resonance imaging (MRI) revealed pituitary hypoplasia, ectopic posterior pituitary gland, and small sella turcica in all probands. Patients and their available relatives underwent NGS. Results: NGS identified the same novel and likely pathogenic LHX4 variant (c.481C>G) in all probands despite the families being unrelated. Additionally, Family A’s proband carried a GLI2 variant (c.2105C>A), and Family B’s probands carried an IGF1R variant (c.166G>A), both interpreted as being of uncertain significance. Conclusions: This study confirms that heterozygous pathogenic variants of LHX4 can cause MPHD associated with a specific neuroradiological triad of abnormalities despite incomplete penetrance and variable phenotype. Moreover, the co-occurrence of the other two gene variants was debated. The IGF1R variant could explain the unusually poor response to growth hormone therapy in Family B, suggesting an oligogenic mechanism underlying the phenotype.

Introduction:Chronic kidney disease (CKD) is a critical prognostic factor in Bardet-Biedl syndrome (BBS). Early diagnosis and intervention are essential for improving patient outcomes. The present study analyzed kidney function in patients with BBS, with the aim to explore the impact of genetic variants and common risk factors for kidney disease. Methods:A monocentric cross-sectional study was conducted. Patients underwent genetic analysis via next generation sequencing; renal function was assessed and the relationship with the following: (i) age, obesity, hypertension and (ii) genetic mutations was analyzed. Results:A total of 65 patients with BBS were enrolled in the study; renal function was variable, with 25% of patients showing an estimated glomerular filtration rate (eGFR) < 60 ml/min per 1.73 m2. Patients' age was inversely correlated with the eGFR (P = 0.002). Reduced eGFR significantly correlated with truncating mutations in any BBS gene and hypertension; moreover, multivariate analysis using eGFR as an objective variable and multiple risk factors as explanatory variables, showed that body mass index (BMI) was independently associated with eGFR decline (β = -2.45, P < 0.0001), in addition to age. Interestingly, significant discordance in renal phenotype was revealed in 50% of subgroups of consanguineous or nonconsanguineous patients sharing the same pathogenic variants, indicating clinical variability even in this setting. Conclusion:The present study suggests that BBS is a condition of vulnerability to develop kidney disease, and that age, hypertension and obesity are associated with eGFR decline in adult patients with BBS. Whether effective interventions to treat modifiable factors will reduce CKD risk requires further studies.

Heterozygous mutations in the gene encoding RagD GTPase were shown to cause a novel autosomal dominant condition characterized by kidney tubulopathy and cardiomyopathy. We previously demonstrated that RagD, and its paralogue RagC, mediate a non-canonical mTORC1 signaling pathway that inhibits the activity of TFEB and TFE3, transcription factors of the MiT/TFE family and master regulators of lysosomal biogenesis and autophagy. Here we show that RagD mutations causing kidney tubulopathy and cardiomyopathy are “auto- activating”, even in the absence of Folliculin, the GAP responsible for RagC/D activation, and cause constitutive phosphorylation of TFEB and TFE3 by mTORC1, without affecting the phosphorylation of “canonical” mTORC1 substrates, such as S6K. By using HeLa and HK-2 cell lines, human induced pluripotent stem cell-derived cardiomyocytes and patient-derived primary fibroblasts, we show that RRAGD auto-activating mutations lead to inhibition of TFEB and TFE3 nuclear translocation and transcriptional activity, which impairs the response to lysosomal and mitochondrial injury. These data suggest that inhibition of MiT/TFE factors plays a key role in kidney tubulopathy and cardiomyopathy syndrome.

Aymé-Gripp Syndrome (AGS) is an ultra-rare syndrome characterized by peculiar facial traits combined with early bilateral cataracts, sensorineural hearing loss, and variable neurodevelopmental abnormalities. Only a few cases carrying a pathogenic variant in MAF have been described to date. A significant effort is then required to expand the genotypic and phenotypic spectrum of this condition. In this paper, we report the peculiar case of a 6-year-old girl carrying a de novo missense pathogenic variant in MAF, being the first case reported to show a milder phenotype with no cataracts and deafness displayed. Furthermore, we performed a systematic review of previously published cases, focusing on clinical manifestation and genotype.

Disrupting variants in the DMD gene are associated with Duchenne or Becker muscular dystrophy (DMD/BMD) or with hyperCKemia, all of which present very different degrees of clinical severity. The clinical phenotypes of these disorders could not be distinguished in infancy or early childhood. Accurate phenotype prediction based on DNA variants may therefore be required in addition to invasive tests, such as muscle biopsy. Transposon insertion is one of the rarest mutation types. Depending on their position and characteristics, transposon insertions may affect the quality and/or quantity of dystrophin mRNA, leading to unpredictable alterations in gene products. Here, we report the case of a three-year-old boy showing initial skeletal muscle involvement in whom we characterized a transposon insertion (Alu sequence) in exon 15 of the DMD gene. In similar cases, the generation of a null allele is predicted, resulting in a DMD phenotype. However, mRNA analysis of muscle biopsy tissue revealed skipping of exon 15, which restored the reading frame, thus predicting a milder phenotype. This case is similar to very few others already described in the literature. This case further enriches our knowledge of the mechanisms perturbing splicing and causing exon skipping in DMD, helping to properly guide clinical diagnosis.

Mutations in COL4A3-A5 cause a spectrum of glomerular disorders, including thin basement membrane nephropathy (TBMN) and Alport syndrome (AS). The wide application of next-generation sequencing (NGS) in the last few years has revealed that mutations in these genes are not limited to these clinical entities. In this study, 176 individuals with a clinical diagnosis of inherited kidney disorders underwent an NGS-based analysis to address the underlying cause; those who changed or perfected the clinical diagnosis after molecular analysis were selected. In 5 out of 83 individuals reaching a molecular diagnosis, the genetic result was unexpected: three individuals showed mutations in collagen type IV genes. These patients showed the following clinical pictures: (1) familial focal segmental glomerulosclerosis; (2) end-stage renal disease (ESRD) diagnosed incidentally in a 49-year-old man, with diffuse cortical calcifications on renal imaging; and (3) dysmorphic and asymmetric kidneys with multiple cysts and signs of tubule–interstitial defects. Genetic analysis revealed rare heterozygote/compound heterozygote COL4A4-A5 variants. Our study highlights the key role of NGS in the diagnosis of inherited renal disorders and shows the phenotype variability in patients carrying mutations in collagen type IV genes.

Glycosylphosphatidylinositol biosynthesis defect 15 is a rare autosomal recessive disorder due to biallelic loss of function of GPAA1. At the moment, less than twenty patients have been reported, usually compound heterozygous for GPAA1 variants. The main clinical features are intellectual disability, hypotonia, seizures, and cerebellar atrophy. We describe a 4-year-old male with a novel, homozygous variant. The patient presents with typical features, such as developmental delay, hypotonia, seizures, and atypical features, such as macrocephaly, preauricular, and cheek appendages. When he was 15 months, the cerebellum was normal. When he was 33 months old, after the molecular diagnosis, magnetic resonance imaging was repeated, showing cerebellar atrophy. This case extends the clinical spectrum of the GPAA1-related disorder and helps to delineate phenotypic differences with defects of other subunits of the transamidase complex.

Chronic kidney disease (CKD) is a major clinical sign of patients with Bardet-Biedl syndrome (BBS), especially in those carrying BBS10 mutations. Twenty-nine patients with BBS and 30 controls underwent a serum-targeted metabolomic analysis. In vitro studies were conducted in two kidney-derived epithelial cell lines, where Bbs10 was stably deleted (IMCD3-Bbs10-/-cells) and over-expressed. The CKD status affected plasmatic metabolite fingerprinting in both patents with BBS and controls. Specific phosphatdylcholinc and acylcarnitines discriminated eGFR decline only in patients with. BBS. IMCD3-Bbs10-/ cells displayed intracellular lipidaccumulation, reduced mitochondrial potential membrane and citrate synthase staining. Mass-Spectrometry-based analysis revealed that human BBS10 interacted with six mitochondrial proteins, in vitro. In conclusion, renal dysfunction correlated with abnormal phosphatidylcholine and acylcarnitines plasma levels in patients with BBS; in vitro, Bbs10 depletion caused mitochondrial defects while human BBS10 interacted with several mitochon-dria-related proteins, suggesting an unexplored role of this protein.

Neonatal cholestasis (NC) may be due to multiple surgical and non-surgical causes, some of which are potentially fatal. The list of potential causes of NC is long, and the systematic search for each of them is challenging in infants, especially when overt signs of underlying disease are lacking. Endocrinological diseases as causes of NC are rare and sometimes misdiagnosed. We report the case of an infant with prolonged cholestatic jaundice due to adrenal insufficiency suspected because of a single episode of hypoglycemia occurring at birth in the absence of clinical signs of adrenal impairment. Clinical exome analysis identified a new homozygous variant in MC2R gene as a putative responsible for familial glucocorticoid deficiency (FGD). Adrenal insufficiency should always be considered in all cholestatic infants, even in the absence of specific symptoms, since early recognition and treatment is essential to prevent life-threatening events.

Next generation sequencing (NGS) has changed our approach to diagnosis of genetic disorders. Nowadays, the most comprehensive application of NGS is whole genome sequencing (WGS) that is able to detect virtually all DNA variations. However, even after accurate WGS, many genetic conditions remain unsolved. This may be due to the current NGS protocols, based on DNA fragmentation and short reads. To overcome these limitations, we applied a linked-read sequencing technology that combines single-molecule barcoding with short-read WGS. We were able to assemble haplotypes and distinguish between alleles along the genome. As an exemplary case, we studied the case of a female carrier of X-linked muscular dystrophy with an unsolved genetic status. A deletion of exons 16–29 in DMD gene was responsible for the disease in her family, but she showed a normal dosage of these exons by Multiplex Ligation-dependent Probe Amplification (MLPA) and array CGH. This situation is usually considered compatible with a “non-carrier” status. Unexpectedly, the girl also showed an increased dosage of flanking exons 1–15 and 30–34. Using linked-read WGS, we were able to distinguish between the two X chromosomes. In the first allele, we found the 16–29 deletion, while the second allele showed a 1–34 duplication: in both cases, linked-read WGS correctly mapped the borders at single-nucleotide resolution. This duplication in trans apparently restored the normal dosage of exons 16–29 seen by quantitative assays. This had a dramatic impact in genetic counselling, by converting a non-carrier into a double carrier status prediction. We conclude that linked-read WGS should be considered as a valuable option to improve our understanding of unsolved genetic conditions.