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PURPOSE: Mendelian disease genomic research has undergone a massive transformation over the past decade. With increasing availability of exome and genome sequencing, the role of Mendelian research has expanded beyond data collection, sequencing, and analysis to worldwide data sharing and collaboration. METHODS: Over the past 10 years, the National Institutes of Health–supported Centers for Mendelian Genomics (CMGs) have played a major role in this research and clinical evolution. RESULTS: We highlight the cumulative gene discoveries facilitated by the program, biomedical research leveraged by the approach, and the larger impact on the research community. Beyond generating a list of gene-phenotype relationships and participating in widespread data sharing, the CMGs have created resources, tools, and training for the larger community to foster understanding of genes and genome variation. The CMGs have participated in a wide range of data sharing activities, including deposition of all eligible CMG data into the Analysis, Visualization, and Informatics Lab-space (AnVIL), sharing candidate genes through the Matchmaker Exchange and the CMG website, and sharing variants in Genotypes to Mendelian Phenotypes (Geno2MP) and VariantMatcher. CONCLUSION: The work is far from complete; strengthening communication between research and clinical realms, continued development and sharing of knowledge and tools, and improving access to richly characterized data sets are all required to diagnose the remaining molecularly undiagnosed patients.

To elucidate the pathogenesis of vein of Galen malformations (VOGMs), the most common and severe congenital brain arteriovenous malformation, we performed an integrated analysis of 310 VOGM proband-family exomes and 336,326 human cerebrovasculature single-cell transcriptomes. We found the Ras suppressor p120 RasGAP (RASA1) harbored a genome-wide significant burden of loss-of-functionde novovariants (p=4.79×10-7). Rare, damaging transmitted variants were enriched in Ephrin receptor-B4 (EPHB4) (p=1.22×10-5), which cooperates with p120 RasGAP to limit Ras activation. Other probands had pathogenic variants inACVRL1,NOTCH1,ITGB1, andPTPN11.ACVRL1variants were also identified in a multi-generational VOGM pedigree. Integrative genomics defined developing endothelial cells as a key spatio-temporal locus of VOGM pathophysiology. Mice expressing a VOGM-specificEPHB4kinase-domain missense variant exhibited constitutive endothelial Ras/ERK/MAPK activation and impaired hierarchical development of angiogenesis-regulated arterial-capillary-venous networks, but only when carrying a “second-hit” allele. These results illuminate human arterio-venous development and VOGM pathobiology and have clinical implications.

Context Familial pituitary diabetes insipidus has been described only in an autosomal dominant or recessive mode of inheritance. Objective This work aims to determine the cause of a novel form of familial diabetes insipidus (DI) that is controlled by desmopressin therapy but segregates in an X-linked recessive manner. Methods Thirteen members from 3 generations of the kindred with familial DI were studied. Water intake, urine volume, urine osmolality, plasma osmolality, and plasma vasopressin were measured under basal conditions, during fluid deprivation, 3% saline infusion, and water loading. Magnetic resonance images of the posterior pituitary also were obtained. In affected males, the effects of desmopressin therapy and linkage of the DI to markers for chromosome Xq28 were determined. In addition, the genes encoding vasopressin, aquaporin-2, the AVPR2 receptor, and its flanking regions were sequenced. Results This study showed that 4 males from 3 generations of the kindred have DI that is due to a deficiency of vasopressin, is corrected by standard doses of desmopressin, and segregates with markers for the AVPR2 gene in Xq28. However, no mutations were found in AVPR2 or its highly conserved flanking regions. Exome sequencing confirmed these findings and also revealed no deleterious variants in the provasopressin and aquaporin-2 genes. The 4 obligate female carriers osmo-regulated vasopressin in the low normal range. Conclusion X-linked recessive transmission of DI can be due to a defect in either the secretion or the action of vasopressin. Other criteria are necessary to differentiate and manage the 2 disorders correctly.

Radial spokes (RSs) are T-shaped multiprotein complexes in the 9+2 axoneme of motile cilia and flagella that couple the central pair to the peripheral doublet microtubules. RS1, RS2, and RS3 are repeated along the outer microtubule of the axoneme and modulate the activity of dynein, thus ciliary and flagella movement. RS substructures are distinct in spermatozoa from other cells harboring motile cilia in mammals. However, the molecular components of the cell-type specific RS substructures remain largely unknown. Here, we report a leucine-rich repeat-containing protein, LRRC23, is a RS head component indispensable for the RS3 head assembly and flagellar movement in human and mouse sperm. From a Pakistani consanguineous family with infertile males due to reduced sperm motility, we identified a splice site variant of LRRC23 that leads to truncate LRRC23 at the C-terminus. In mutant mouse model mimicking the identified variant, the truncated LRRC23 protein is produced in testis but fails to localize in the mature sperm tail, causing severe sperm motility defects and male infertility. Purified recombinant human LRRC23 does not interacts with RS stalk proteins, but with a head protein, RSPH9, which is abolished by the C-terminus truncation of LRRC23. Cryo-electron tomography and sub-tomogram averaging unambiguously visualized that the RS3 head and sperm-specific RS2-RS3 bridge structure is missing in the LRRC23 mutant sperm. Our study provides new insights into RS3 structure and function in mammalian sperm flagella as well as molecular pathogenicity ofLRRC23underlying reduced sperm motility in infertile human males.

Background: About 40 disease genes have been described to date for isolated congenital anomalies of the kidneys and urinary tract (CAKUT), the most common cause of childhood chronic kidney disease. However, these genes account for only 20% of cases. ARHGEF6, a guanine nucleotide exchange factor that is implicated in such biologic processes as cell migration and focal adhesion, acts downstream of integrin linked kinase (ILK) and parvin proteins. A genetic variant of ILK that causes murine renal agenesis abrogates the interaction of ILK with a murine focal adhesion protein encoded by Parva, leading to CAKUT in mice with this variant. Methods: To identify novel genes that, when mutated, result in CAKUT, we performed exome sequencing in an international cohort of 1265 families with CAKUT. We also assessed the effects in vitro of wild-type and mutant ARHGEF6 proteins, as well as the effects of Arhgef6 deficiency in mouse and frog models. Results: We detected six different hemizygous variants in the gene ARHGEF6 (which is located on the X chromosome in humans) in eight individuals from six families with CAKUT. In kidney cells, overexpression of wild-type ARHGEF6—but not proband-derived mutant ARHGEF6— increased active levels of CDC42/RAC1, induced lamellipodia formation, and stimulated PARVAdependent cell spreading. ARHGEF6 mutant proteins showed loss of interaction with PARVA. Three-dimensional MDCK cell cultures expressing ARHGEF6 mutant proteins exhibited reduced lumen formation and polarity defects. Arhgef6 deficiency in mouse and frog models recapitulated features of human CAKUT. Conclusions: Deleterious variants in ARHGEF6 may cause dysregulation of integrin-parvinRAC1/CDC42 signaling, thereby leading to X-linked CAKUT.

Nephrolithiasis (NL) affects 1 in 11 individuals worldwide, leading to significant patient morbidity. NL is associated with nephrocalcinosis (NC), a risk factor for chronic kidney disease. Causative genetic variants are detected in 11-28% of NL and/or NC, suggesting additional NL/NC-associated genetic loci await discovery. Therefore, we employed genomic approaches to discover novel genetic forms of NL/NC.Exome sequencing and directed sequencing of the OXGR1 locus were performed in a worldwide NL/NC cohort. Putatively deleterious rare OXGR1 variants were functionally characterized.Exome sequencing revealed a heterozygous OXGR1 missense variant (c.371TG, p.L124R) co-segregating with calcium oxalate NL and/or NC disease in an autosomal dominant inheritance pattern within a multi-generational family with five affected individuals. OXGR1 encodes 2-oxoglutarate (α-ketoglutarate) receptor 1 in the distal nephron. In response to its ligand α-ketoglutarate (AKG), OXGR1 stimulates the chloride-bicarbonate exchanger Pendrin, which also regulates transepithelial calcium transport in cortical connecting tubules. Strong amino acid conservation in orthologues and paralogues, severe in silico prediction scores, and extreme rarity in exome population databases suggested the variant was deleterious. Interrogation of the OXGR1 locus in 1107 additional NL/NC families identified five additional deleterious dominant variants in five families with calcium oxalate NL/NC. Rare, potentially deleterious OXGR1 variants were enriched in NL/NC subjects relative to ExAC controls (ΧRare, dominant loss-of-function OXGR1 variants are associated with recurrent calcium oxalate NL/NC disease.

Mutations in SPAG1, a dynein axonemal assembly factor (DNAAF) that facilitates the assembly of dynein arms in the cytoplasm before their transport into the cilium, result in primary ciliary dyskinesia (PCD), a genetically heterogenous disorder characterized by chronic oto-sino-pulmonary disease, infertility and laterality defects. To further elucidate the role of SPAG1 in dynein assembly, we examined its expression, interactions and ciliary defects in control and PCD human airway epithelia. Immunoprecipitations showed that SPAG1 interacts with multiple DNAAFs, dynein chains and canonical components of the R2TP complex. Protein levels of dynein heavy chains (DHCs) and interactions between DHCs and dynein intermediate chains (DICs) were reduced in SPAG1 mutants. We also identified a previously uncharacterized 60 kDa SPAG1 isoform, through examination of PCD subjects with an atypical ultrastructural defect for SPAG1 variants, that can partially compensate for the absence of full-length SPAG1 to assemble a reduced number of outer dynein arms. In summary, our data show that SPAG1 is necessary for axonemal dynein arm assembly by scaffolding R2TP-like complexes composed of several DNAAFs that facilitate the folding and/or binding of the DHCs to the DIC complex.

Coexistence of TAPVC (total anomalous pulmonary venous connection) and coarctation of aorta rarely occurs. Newborn weighing 2.4 kg admitted in Sangli civil hospital NICU with respiratory distress with cyanosis. Chest X-ray of baby was suggestive of ground glass appearance of bilateral lung fields and cardiomegaly. SpO2 of baby was fluctuating between 85 to 90% on nasal CPAP. 2D echo showed baby was having obstructed supracardiac TAPVC with severe discrete post-ductal coarctation of aorta. There was stretched PFO shunting R-L and small PDA shunting R-L. Baby was planned for emergency surgery but couldn’t make it to operation theatre and succumbed within 30 hours of life. Till now there are very few case reports of TAPVC with coarctation but no case of obstructed supracardiac TAPVC with coarctation has been reported.

Multisystem inflammatory syndrome (MIS-C) in children (MIS-C) associated with severe acute respiratory syndrome coronavirus-2 (SARS-CoV2) is well recognised in children, however, rarely reported in newborns. It usually presents as fever and multiorgan involvement, with blood investigations showing increased inflammatory markers weeks after exposure to SARS-CoV-2. Unlike older children, the mechanism is unique in neonates as COVID-19 infection and the subsequent inflammatory reaction leading to MIS-C occur in two different individuals. We reviewed the perinatal history, clinical features, and outcomes of 3 neonates with features consistent with MIS-N related to maternal SARS-CoV-2, from August 2021 to December 2021. Anti-SARS-CoV-2 IgG and IgM antibodies were tested in all neonates. Clinical picture comprised multiorgan dysfunction (gastrointestinal, cardiorespiratory, haematological and dermatological), positive inflammatory markers, high ferritin and high D-dimer levels, elevated Cardiac enzymes. Blood cultures were sterile. Positive anti-SARS-CoV-2 IgG in both the mother and the infant, along with epidemiological evidence of maternal contact with COVID-19, clinched the diagnosis of MIS-C. Immunomodulatory drugs (intravenous immunoglobulin and systemic steroids) were administered. Multisystem inflammatory syndrome should be considered as a differential diagnosis in all critically ill neonates, particularly with maternal history of COVID-19 infection or epidemiological contact. This neonatal presentation is the reflection of fetal inflammatory response syndrome associated with maternal SARS-CoV-2 infection. Having no fever throughout the course of illness, in some neonates, suggests that neonates respond differently compared with children.