We examined the burden of large, rare, copy-number variants (CNVs) in 192 individuals with renal hypodysplasia (RHD) and replicated findings in 330 RHD cases from two independent cohorts. CNV distribution was significantly skewed toward larger gene-disrupting events in RHD cases compared to 4,733 ethnicity-matched controls (p = 4.8 × 10(-11)). This excess was attributable to known and novel (i.e., not present in any database or in the literature) genomic disorders. All together, 55/522 (10.5%) RHD cases harbored 34 distinct known genomic disorders, which were detected in only 0.2% of 13,839 population controls (p = 1.2 × 10(-58)). Another 32 (6.1%) RHD cases harbored large gene-disrupting CNVs that were absent from or extremely rare in the 13,839 population controls, identifying 38 potential novel or rare genomic disorders for this trait. Deletions at the HNF1B locus and the DiGeorge/velocardiofacial locus were most frequent. However, the majority of disorders were detected in a single individual. Genomic disorders were detected in 22.5% of individuals with multiple malformations and 14.5% of individuals with isolated urinary-tract defects; 14 individuals harbored two or more diagnostic or rare CNVs. Strikingly, the majority of the known CNV disorders detected in the RHD cohort have previous associations with developmental delay or neuropsychiatric diseases. Up to 16.6% of individuals with kidney malformations had a molecular diagnosis attributable to a copy-number disorder, suggesting kidney malformations as a sentinel manifestation of pathogenic genomic imbalances. A search for pathogenic CNVs should be considered in this population for the diagnosis of their specific genomic disorders and for the evaluation of the potential for developmental delay.

BACKGROUND The DiGeorge syndrome, the most common of the microdeletion syndromes, affects multiple organs, including the heart, the nervous system, and the kidney. It is caused by deletions on chromosome 22q11.2; the genetic driver of the kidney defects is unknown. METHODS We conducted a genomewide search for structural variants in two cohorts: 2080 patients with congenital kidney and urinary tract anomalies and 22,094 controls. We performed exome and targeted resequencing in samples obtained from 586 additional patients with congenital kidney anomalies. We also carried out functional studies using zebrafish and mice. RESULTS We identified heterozygous deletions of 22q11.2 in 1.1% of the patients with congenital kidney anomalies and in 0.01% of population controls (odds ratio, 81.5; P=4.5×10−14). We localized the main drivers of renal disease in the DiGeorge syndrome to a 370-kb region containing nine genes. In zebrafish embryos, an induced loss of function in snap29, aifm3, and crkl resulted in renal defects; the loss of crkl alone was sufficient to induce defects. Five of 586 patients with congenital urinary anomalies had newly identified, heterozygous protein-altering variants, including a premature termination codon, in CRKL. The inactivation of Crkl in the mouse model induced developmental defects similar to those observed in patients with congenital urinary anomalies. CONCLUSIONS We identified a recurrent 370-kb deletion at the 22q11.2 locus as a driver of kidney defects in the DiGeorge syndrome and in sporadic congenital kidney and urinary tract anomalies. Of the nine genes at this locus, SNAP29, AIFM3, and CRKL appear to be critical to the phenotype, with haploinsufficiency of CRKL emerging as the main genetic driver. (Funded by the National Institutes of Health and others.)

Renal agenesis and hypodysplasia (RHD) are major causes of pediatric chronic kidney disease and are highly genetically heterogeneous. We conducted whole-exome sequencing in 202 case subjects with RHD and identified diagnostic mutations in genes known to be associated with RHD in 7/202 case subjects. In an additional affected individual with RHD and a congenital heart defect, we found a homozygous loss-of-function (LOF) variant in SLIT3, recapitulating phenotypes reported with Slit3 inactivation in the mouse. To identify genes associated with RHD, we performed an exome-wide association study with 195 unresolved case subjects and 6,905 control subjects. The top signal resided in GREB1L, a gene implicated previously in Hoxb1 and Shha signaling in zebrafish. The significance of the association, which was p = 2.0 × 10 for novel LOF, increased to p = 4.1 × 10 for LOF and deleterious missense variants combined, and augmented further after accounting for segregation and de novo inheritance of rare variants (joint p = 2.3 × 10). Finally, CRISPR/Cas9 disruption or knockdown of greb1l in zebrafish caused specific pronephric defects, which were rescued by wild-type human GREB1L mRNA, but not mRNA containing alleles identified in case subjects. Together, our study provides insight into the genetic landscape of kidney malformations in humans, presents multiple candidates, and identifies SLIT3 and GREB1L as genes implicated in the pathogenesis of RHD.

Background: Information about renal diseases in children is available from national registries of renal biopsies. Aim of the study was to compare the clinical presentation of glomerular diseases and tubulointerstitial space diseases with pathohistological diagnosis of indicated renal biopsies from pediatric population in the Croatian region of Dalmatia. Methods: Out of 231 pediatric patients with suspected glomerular and tubulointerstitial diseases, 54 underwent ultrasound-guided renal biopsy at University Hospital of Split. Kidney allograft biopsy, and re-biopsy were excluded. The biopsy sections were examined under light microscopy, immunofluorescence and electron microscopy. The data was reviewed to determine the pathohistological spectrum and clinicopathologic correlations. We retrospectively analyzed kidney biopsy data from 2008 to 2017 and compared them to that between 1995 and 2005.Results: The mean age of patients was 9.84 ± 5.4 years. Male:female ratio was 1.2:1. The main indications for biopsy were pure nephrotic syndrome without hematuria (25.9%), non-nephrotic proteinuria with haematuria (22.2%), nephritic syndrome with nephrotic proteinuria (18.5%), and isolated hematuria (16.7%). The most common pathohistological findings were IgA nephropathy (IgAN, 24.1%), minimal change disease (MCD, 16.7%), Henoch-Schönlein purpura glomerulonephritis (HSPN, 14.8%), Alport syndrome and focal segmental glomerulosclerosis (AS and FSGS, 11.1% each), tubulointerstitial nephritis and membranous glomerulopathy (TIN and MGN, 3.7% each), while other cases were diagnosed rarely. Conclusions:Changes in epidemiology of renal diseases in children between the analyzed periods showed an increasing trend of IgAN, MCD, HSPN, AS and FSGS, while mesangioproliferative glomerulonephritis (MesPGN) and endoproliferative glomerulonephritis (EDGN) showed a decreasing trend that can be explained with the new pathohistological classification.

Purpose: The aim of this study was to analyze the incidence of intrarenal reflux (IRR) among vesicoureteral refluxes (VURs), diagnosed by contrast-enhanced voiding urosonography (ceVUS), to define VURs which are positive to IRR and their locations in the kidney.Materials and Methods: Seventy patients with VURs, including 103 uretero-renal units (URUs) with VURs of grades II–V (37 URUs were excluded because of renal anomalies or absence of VUR) were examined with ceVUS due to recurrent febrile UTI or first febrile UTI accompanied by abnormalities on renal ultrasonography. Patients were examined on GE Logiq S8 ultrasound machine, using second generation of ultrasound contrast agent.Results: Out of 103 VURs, 51 (49.51%) had IRR regardless the grade of VUR, showing increase in IRR incidence with VUR severity (p < 0.0001). The median age at the time of IRR diagnosis was 5 months (IQR, 3–14.3), whereas in patients without IRR, it was 15.5 months (IQR, 5–41.5), (p = 0.0069). IRR was most common in superior pole (80%), followed by inferior pole (62.7%), and middle segments (37%), and to all segments (27%) (p < 0.0001).Conclusion: In the present study, patients with IRR-associated VUR showed earlier clinical presentation. The distribution of IRRs corresponded to the natural distribution of composed papillae types II and III, while the incidence of IRR increased with severity of VUR. Further clinical studies may point to the importance of considering IRR in the future classification of VUR.