Whole-exome sequencing of 13 individuals with developmental delay commonly accompanied by abnormal muscle tone and seizures identified de novo missense mutations enriched within a sub-region of GNB1, a gene encoding the guanine nucleotide-binding protein subunit beta-1, Gβ. These 13 individuals were identified among a base of 5,855 individuals recruited for various undiagnosed genetic disorders. The probability of observing 13 or more de novo mutations by chance among 5,855 individuals is very low (p = 7.1 × 10(-21)), implicating GNB1 as a genome-wide-significant disease-associated gene. The majority of these 13 mutations affect known Gβ binding sites, which suggests that a likely disease mechanism is through the disruption of the protein interface required for Gα-Gβγ interaction (resulting in a constitutively active Gβγ) or through the disruption of residues relevant for interaction between Gβγ and certain downstream effectors (resulting in reduced interaction with the effectors). Strikingly, 8 of the 13 individuals recruited here for a neurodevelopmental disorder have a germline de novo GNB1 mutation that overlaps a set of five recurrent somatic tumor mutations for which recent functional studies demonstrated a gain-of-function effect due to constitutive activation of G protein downstream signaling cascades for some of the affected residues.

De novo germline mutations in GNB1 have been associated with a neurodevelopmental phenotype. To date, 28 patients with variants classified as pathogenic have been reported. We add 18 patients with de novo mutations to this cohort, including a patient with mosaicism for a GNB1 mutation who presented with a milder phenotype. Consistent with previous reports, developmental delay in these patients was moderate to severe, and more than half of the patients were non-ambulatory and nonverbal. The most observed substitution affects the p.Ile80 residue encoded in exon 6, with 28% of patients carrying a variant at this residue. Dystonia and growth delay were observed more frequently in patients carrying variants in this residue, suggesting a potential genotype-phenotype correlation. In the new cohort of 18 patients, 50% of males had genitourinary anomalies and 61% of patients had gastrointestinal anomalies, suggesting a possible association of these findings with variants in GNB1. In addition, cutaneous mastocytosis, reported once before in a patient with a GNB1 variant, was observed in three additional patients, providing further evidence for an association to GNB1. We will review clinical and molecular data of these new cases and all previously reported cases to further define the phenotype and establish possible genotype-phenotype correlations.

The association between 1p32-p31 contiguous gene deletions and a distinct phenotype that includes anomalies of the corpus callosum, ventriculomegaly, developmental delay, seizures, and dysmorphic features has been long recognized and described. Recently, the observation of overlapping phenotypes in patients with chromosome translocations that disrupt NFIA (Nuclear factor I/A), a gene within this deleted region, and NFIA intragenic deletions has led to the hypothesis that NFIA is a critical gene within this region. The wide application and increasing accessibility of whole exome sequencing (WES) has helped identify new cases to support this hypothesis. Here, we describe four patients with loss-of-function variants in the NFIA gene identified through WES. The clinical presentation of these patients significantly overlaps with the phenotype described in previously reported cases of 1p32-p31 deletion syndrome, NFIA gene disruptions and intragenic NFIA deletions. Our cohort includes a mother and daughter as well as an unrelated individual who share the same nonsense variant (c.205C>T, p.Arg69Ter; NM_001145512.1). We also report a patient with a frameshift NFIA variant (c.159_160dupCC, p.Gln54ProfsTer49). We have compared published cases of 1p32-p31 microdeletion syndrome, translocations resulting in NFIA gene disruption, intragenic deletions, and loss-of-function mutations (including our four patients) to reveal that abnormalities of the corpus callosum, ventriculomegaly/hydrocephalus, macrocephaly, Chiari I malformation, dysmorphic features, developmental delay, hypotonia, and urinary tract defects are common findings. The consistent overlap in clinical presentation provides further evidence of the critical role of NFIA haploinsufficiency in the development of the 1p32-p31 microdeletion syndrome phenotype.

60Mutations that alter signaling of RAS/MAPK-family proteins give rise to a group 61 of Mendelian diseases known as RASopathies, but the matrix of genotype-phenotype 62 relationships is still incomplete, in part because there are many RAS-related proteins, 63 and in part because the phenotypic consequences may be variable and/or pleiotropic. 64Here, we describe a cohort of ten cases, drawn from six clinical sites and over 16,000 65 sequenced probands, with de novo protein-altering variation in RALA, a RAS-like small 66 GTPase. All probands present with speech and motor delays, and most have intellectual 67 disability, low weight, short stature, and facial dysmorphism. The observed rate of de 68 novo RALA variants in affected probands is significantly higher (p=4.93 x 10 -11 ) than 69 expected from the estimated mutation rate. Further, all de novo variants described 70 here affect conserved residues within the GTP/GDP-binding region of RALA; in fact, six 71 alleles arose at only two codons, Val25 and Lys128. We directly assayed GTP hydrolysis 72 and RALA effector-protein binding, and all but one tested variant significantly reduced 73 both activities. The one exception, S157A, reduced GTP hydrolysis but significantly 74 increased RALA-effector binding, an observation similar to that seen for oncogenic RAS 75 variants. These results show the power of data sharing for the interpretation and 76 analysis of rare variation, expand the spectrum of molecular causes of developmental 77 disability to include RALA, and provide additional insight into the pathogenesis of78 human disease caused by mutations in small GTPases.79 80 81 5 82 Author Summary 83 While many causes of developmental disabilities have been identified, a large number of 84 affected children cannot be diagnosed despite extensive medical testing. Previously 85 unknown genetic factors are likely to be the culprits in many of these cases. Using DNA 86 sequencing, and by sharing information among many doctors and researchers, we have 87 identified a set of individuals with developmental problems who all have changes to the 88 same gene, RALA. The affected individuals all have similar symptoms, including 89 intellectual disability, speech delay (or no speech), and problems with motor skills like 90walking. In nearly all of these cases (10 of 11), the genetic change found in the child was 91 not inherited from either parent. The locations and biological properties of these 92 changes suggest that they are likely to disrupt the normal functions of RALA and cause 93 significant health problems. We also performed experiments to show that the genetic 94 changes found in these individuals alter two key functions of RALA. Together, we have 95 provided evidence that genetic changes in RALA can cause DD/ID. These results will 96 allow doctors and researchers to identify additional children with the same condition, 97 providing a clinical diagnosis to these families and leading to new research 98 opportunities. 99 100 101 Developmental delay and intellectual disabili...

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Mutations that alter signaling of RAS/MAPK-family proteins give rise to a group of Mendelian diseases known as RASopathies. However, among RASopathies, the matrix of genotype-phenotype relationships is still incomplete, in part because there are many RAS-related proteins and in part because the phenotypic consequences may be variable and/or pleiotropic. Here, we describe a cohort of ten cases, drawn from six clinical sites and over 16,000 sequenced probands, with de novo protein-altering variation in RALA, a RAS-like small GTPase. All probands present with speech and motor delays, and most have intellectual disability, low weight, short stature, and facial dysmorphism. The observed rate of de novo RALA variants in affected probands is significantly higher (p = 4.93 x 10−11) than expected from the estimated random mutation rate. Further, all de novo variants described here affect residues within the GTP/GDP-binding region of RALA; in fact, six alleles arose at only two codons, Val25 and Lys128. The affected residues are highly conserved across both RAL- and RAS-family genes, are devoid of variation in large human population datasets, and several are homologous to positions at which disease-associated variants have been observed in other GTPase genes. We directly assayed GTP hydrolysis and RALA effector-protein binding of the observed variants, and found that all but one tested variant significantly reduced both activities compared to wild-type. The one exception, S157A, reduced GTP hydrolysis but significantly increased RALA-effector binding, an observation similar to that seen for oncogenic RAS variants. These results show the power of data sharing for the interpretation and analysis of rare variation, expand the spectrum of molecular causes of developmental disability to include RALA, and provide additional insight into the pathogenesis of human disease caused by mutations in small GTPases.

Chromosome 4q deletion syndrome is a rare intellectual disability disorder caused by a variety of non-recurrent deletions of 4q. We describe the evolution of the phenotypic features of a female patient with a previously unreported deletion of 4q12-4q21.21 (hg 18; 54,711,575-79,601,919). By review reported individuals with interstitial deletions extending telomeric from 4q12 have syndromic intellectual disability with variable piebaldism. We expand the phenotype to include dolichocephaly, pectus excavatum, hip dysplasia, pes planus, myopia, lens opacities, and an absence of spoken language but not of communication through sign. The proposita also did not have piebaldism suggesting again that piebaldism arises from a mechanism more complex than simple haploinsufficiency of KIT. Comparing deletions among affected individuals localizes the critical interval within 4q12-4q13.1, although the absence of molecular boundaries for nearly all reported cases precludes precise delineation and genotype-phenotype correlation.

With an expected incidence of more than 1 million cases by 2025, liver cancer remains a problem for world health. With over 90% of cases, hepatocellular carcinoma (HCC) is the most prevalent kind of liver cancer. In this review, we presented the range of experimental therapeutics for patients with advanced HCC, the successes and failures of new treatments, areas for future development, the evaluation of dose-limiting toxicity in different drugs, and the safety profile in patients with liver dysfunction related to the underlying chronic liver disease. In addition to the unmet demand for biomarkers to guide treatment decisions and the burgeoning fields of immunotherapy and systemic therapy in hepatocellular carcinoma, the development of old and new drugs, including their failures and current advancements, has been reviewed. This review aims to evaluate the updated optimal clinical treatment of unresectable hepatocellular carcinomas in clinical practice, mainly through targeted therapy. Although surgical treatment can significantly enhance the survival probability of early and intermediate-stage patients, it is unsuitable for most HCC patients due to a lack of donors. Due to their severe toxicity, the few first-line anti-HCC drugs, such as sorafenib, are often reserved for advanced HCC patients for whom other therapies have failed. The second-line drugs are usually alternatives for patients with intolerance or resistance. Consequently, the ongoing growth of possible preclinical drugs and studies on miRNAs, lncRNAs, and numerous other signaling pathway targets for developing novel drugs may introduce additional treatment prospects for HCC.