Dane Witmer

The RET (rearranged during transfection) gene encodes a trans-membrane protein belonging to the receptor tyrosine kinase (RTK) family. It plays a crucial role in the early development of precursor cells of the neural crest, including enteric ganglia, urogenital tract, and testis germ cells. Loss-of-function variants in RET constitute the most common monogenic, nonsyndromic cause of Hirschsprung susceptibility. Notably, RET variants have also been implicated in renal agenesis in humans, and other phenotypes within the congenital anomalies of the kidney and urinary tract (CAKUT) spectrum (eg, kidney dysplasia/hypoplasia). A monogenic etiology is attributed to approximately 10-20% of individuals with CAKUT, with around 5% suspected to have variants in the RET signaling pathway. Here, we present two unrelated patients with severe forms of Hirschsprung disease and CAKUT, both harboring the same novel germline missense variant in RET. Patient 1 is a 3-year-old female with a prenatal history of intrauterine growth restriction and oligohydramnios who was delivered via emergent C-section at 36 weeks gestation. Her postnatal course was complicated by acute kidney injury (AKI) and failure to pass meconium and subsequent work-up was consistent with total intestinal aganglionosis. Exome sequencing trio through a clinical laboratory identified an apparently de novo heterozygous variant in RET [NM_020975.6: c.2617C>T, p.(Arg873Trp)]. Increased renal echogenicity suggestive of medical renal disease was noted on ultrasound at 6 months, and the kidney length was noted to be small for age by 2 years. There was a steady progression from AKI to chronic kidney disease (CKD), but at 2-years-old, there was an unexplained precipitous progression to stage 3 CKD which raised questions about a potential association between her RET variant and her renal phenotype. Patient 2 had a prenatal diagnosis of bilateral renal agenesis, underwent serial amnioinfusion for associated anhydramnios and was delivered at 35 weeks gestation. Concern for Hirschsprung disease arose after postnatal failure to pass meconium, so clinical exome sequencing trio was ordered. Biopsy confirmed a diagnosis of near total intestinal aganglionosis and the exome sequencing trio identified a heterozygous RET [NM_020975.6: c.2617C>T, p.(Arg873Trp)] variant. The proband’s mother’s saliva specimen demonstrated low-level mosaicism for this variant. Her medical history was significant for hearing loss and seizures, but no other known issues. Unfortunately, the baby passed away at 6 months. Herein, we present two unrelated patients with heterozygosity for a novel germline variant, c.2617C>T, p.(Arg873Trp) in RET and medical histories of severe forms of Hirschsprung disease as well as CAKUT. This variant is absent from a large population dataset and to our knowledge, has not previously been reported in the literature as a germline variant. This substitution is situated in the intracellular tyrosine kinase domain of the protein product, where other Hirschsprung disease-associated variants are localized. Bioinformatic tools predict a decrease in structural stability. Importantly, the arginine residue appears to be highly conserved across available vertebrate species. Based on current evidence, this variant is classified as likely pathogenic, but it is suspected to be causative of each patients’ findings. Further investigational studies are needed to assess the potential deleterious effects of this variant and to explore its association with CAKUT. For example, bioinformatic analysis predicts that this substitution will not affect exon 15 splicing, but this has not been confirmed in the laboratory setting. Tissue-specific analyses could be utilized as a tool to evaluate for an effect on gene expression in the kidneys. Based on our search of publicly available online resources, this variant has been identified in at least 3 patients with overlapping phenotypes. This variant has likely been identified in additional patients undergoing broad genetic testing through clinical laboratories but remains unreported in the literature.