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Neuromuscular diseases (NMDs) encompass a variety of ailments from muscular dystrophies to ataxias, in the course of which the functioning of the muscles is eventually either directly or indirectly impaired. The clinical diagnosis of a particular NMD is not always straightforward due to the clinical and genetic heterogeneity of the disorders under investigation. Traditional diagnostic tools such as electrophysiological tests and muscle biopsies are both invasive and painful methods, causing the patients to be reluctant. Next-generation sequencing, on the other hand, emerged as an alternative method for the diagnosis of NMDs, both with its minimally invasive nature and fast processing period. In this study, clinical exome sequencing (CES) was applied to a cohort of 70 probands in Turkey, 44 of whom received a final diagnosis, representing a diagnostic rate of 62.9%. Out of the 50 mutations identified to be causal, 26 were novel in the known 27 NMD genes. Two probands had complex/blended phenotypes. Molecular confirmation of clinical diagnosis of NMDs has a major prognostic impact and is crucial for the management and the possibility of alternative reproductive options. CES, which has been increasingly adopted to diagnose single-gene disorders, is also a powerful tool for revealing the etiopathogenesis in complex/blended phenotypes, as observed in two probands of the cohort. [ABSTRACT FROM AUTHOR]

Background Cornelia de Lange syndrome (CdLS) is a multisystem disorder with distinctive facial appearance, intellectual disability and growth failure as prominent features. Most individuals with typical CdLS have de novo heterozygous loss-of-function mutations in NIPBL with mosaic individuals representing a significant proportion. Mutations in other cohesin components, SMC1A, SMC3, HDAC8 and RAD21 cause less typical CdLS. Methods We screened 163 affected individuals for coding region mutations in the known genes, 90 for genomic rearrangements, 19 for deep intronic variants in NIPBL and 5 had whole-exome sequencing. Results Pathogenic mutations [including mosaic changes] were identified in: NIPBL 46 [3] (28.2%); SMC1A 5 [1] (3.1%); SMC3 5 [1] (3.1%); HDAC8 6 [0] (3.6%) and RAD21 1 [0] (0.6%). One individual had a de novo 1.3 Mb deletion of 1p36.3. Another had a 520 kb duplication of 12q13.13 encompassing ESPL1, encoding separase, an enzyme that cleaves the cohesin ring. Three de novo mutations were identified in ANKRD11 demonstrating a phenotypic overlap with KBG syndrome. To estimate the number of undetected mosaic cases we used recursive partitioning to identify discriminating features in the NIPBL-positive subgroup. Filtering of the mutation-negative group on these features classified at least 18% as 'NIPBL-like'. A computer composition of the average face of this NIPBL-like subgroup was also more typical in appearance than that of all others in the mutationnegative group supporting the existence of undetected mosaic cases. Conclusions Future diagnostic testing in 'mutationnegative' CdLS thus merits deeper sequencing of multiple DNA samples derived from different tissues. [ABSTRACT FROM AUTHOR]

Autosomal recessive cutis laxa (ARCL) syndromes are phenotypically overlapping, but genetically heterogeneous disorders. Mutations in the ATP6V0A2 gene were found to underlie both, autosomal recessive cutis laxa type 2 (ARCL2), Debré type, and wrinkly skin syndrome (WSS). The ATP6V0A2 gene encodes the a2 subunit of the V-type H-ATPase, playing a role in proton translocation, and possibly also in membrane fusion. Here, we describe a highly variable phenotype in 13 patients with ARCL2, including the oldest affected individual described so far, who showed strikingly progressive dysmorphic features and heterotopic calcifications. In these individuals we identified 17 ATP6V0A2 mutations, 14 of which are novel. Furthermore, we demonstrate a localization of ATP6V0A2 at the Golgi-apparatus and a loss of the mutated ATP6V0A2 protein in patients' dermal fibroblasts. Investigation of brefeldin A-induced Golgi collapse in dermal fibroblasts as well as in HeLa cells deficient for ATP6V0A2 revealed a delay, which was absent in cells deficient for the ARCL-associated proteins GORAB or PYCR1. Furthermore, fibroblasts from patients with ATP6V0A2 mutations displayed elevated TGF-β signalling and increased TGF-β1 levels in the supernatant. Our current findings expand the genetic and phenotypic spectrum and suggest that, besides the known glycosylation defect, alterations in trafficking and signalling processes are potential key events in the pathogenesis of ATP6V0A2-related ARCL. [ABSTRACT FROM AUTHOR]

Using homozygosity mapping and locus resequencing, we found that alterations in the homeodomain of the IRX5 transcription factor cause a recessive congenital disorder affecting face, brain, blood, heart, bone and gonad development. We found through in vivo modeling in Xenopus laevis embryos that Irx5 modulates the migration of progenitor cell populations in branchial arches and gonads by repressing Sdf1. We further found that transcriptional control by Irx5 is modulated by direct protein-protein interaction with two GATA zinc-finger proteins, GATA3 and TRPS1; disruptions of these proteins also cause craniofacial dysmorphisms. Our findings suggest that IRX proteins integrate combinatorial transcriptional inputs to regulate key signaling molecules involved in the ontogeny of multiple organs during embryogenesis and homeostasis. [ABSTRACT FROM AUTHOR]

Patients with multiple congenital abnormalities and mental retardation are the most frequent patient group who are referred to a genetic clinic. Specific diagnosis for these patients will provide a better understanding of the possible reasons of pathogenesis, thereby providing more true information to families on recurrence risk, prognosis, possible treatment options and prenatal diagnosis. With the aim of finding out the etiology of the genetic diseases, 4659 patients who were classified into mental retardation or multiple congenital anomaly and mental retardation (MR or MCA/MR) group who were referred to Istanbul University, Departments of Medical Genetics of Cerrahpasa Medical Faculty and Istanbul Medical Faculty in between 1985 and 2005 were analyzed retrospectively and a two step study was generated: first step involved the etiologic classification of MR or MCA/MR group and the second evaluation of the factors that help in finding out the etiologies such as age at first observation, number and periods of observations and completion of laboratory tests. In the first part of the study, etiologic classification of the patients with MR or MCA/MR who were referred to genetic clinics of the two medical faculty of Istanbul University were mentioned. 2847 patients have had an etiological diagnosis (61.10%): from these patients, 1541 out of them had a chromosomal abnormality (33.07%), 555 were known single gene mutations (11.91%), 20 were recognized syndromes (00.42%), 567 were sequences (12.16%), 6 were associations (00.12%), 29 had spectrums (00.62%), 98 had structural abnormality of CNS (2.10%), and finally, 31 suffered from prematurity and its complications, toxic drugs, infections and hypoxic ischemic encephalopathy. This study will be the one of the biggest studies in Turkey and also around the world, evaluating the most frequent patient group referred to genetic clinics: MCA or MR. [ABSTRACT FROM AUTHOR]

Background: Pallister Killian syndrome (PKS, OMIM 601803) is a rare genetic disorder with a distinct phenotype caused by tissue- limited mosaicism tetrasomy of the short arm of chromosome 12, which usually cytogenetically presents as an extra isochromosome 12p. Wide phenotypic variability in PKS has been reported, ranging from pre-to perinatal death due to multiple congenital anomalies, especially diaphragmatic hernia, and classic phenotypes including seizures, severe developmental delay, macrosomia at birth, deafness, and distinct dysmorphic features, such as coarse face, temporal alopecia, a small nose with anteverted nostrils, long philtrum, and hypo−/hyper- pigmented streaks on the skin. Results: Karyotypes obtained from cultured peripheral lymphocytes of 13 cases, who were diagnosed as PKS, were normal, while karyotypes obtained from cultured skin samples and buccal mucosa revealed the supernumerary mosaic i(12p). Mosaic karyotype was found in both fibroblast and buccal mucosa in 14 of 15 patients in our series, whereas in one stillbirth, following the clinical diagnosis of PKS, skin and buccal smear samples were taken, and all karyotypes from cultured fibroblasts revealed a supernumerary i(12p), while I-FISH study showed 60% mosaicism in mucosal cells. Conclusions: We here share the clinical, cytogenetic and molecular cytogenetic findings of 15 cases with PKS phenotype and the parental origin of seven i(12p) identified by molecular analyses. To our knowledge, this is the largest series of PKS patients with parental origin study from a single center. We believe that our study makes a significant contribution to the literature because we specifically found no differences in the phenotypes of cases with either a maternal or paternal origin of the extra element and differential imprinting appeared not to be a factor. [ABSTRACT FROM AUTHOR]

The genetic disorder Kabuki syndrome (KS) is characterized by developmental delay and congenital anomalies. Dominant mutations in the chromatin regulators lysine (K)--specific methyltransferase 2D (KMT2D) (also known as MLL2) and lysine (K)--specific demethylase 6A (KDM6A) underlie the majority of cases. Although the functions of these chromatin-modifying proteins have been studied extensively, the physiological systems regulated by them are largely unknown. Using whole-exome sequencing, we identified a mutation in RAP1A that was converted to homozygosity as the result of uniparental isodisomy (UPD) in a patient with KS and a de novo, dominant mutation in RAP1B in a second individual with a KS-like phenotype. We elucidated a genetic and functional interaction between the respective KS-associated genes and their products in zebrafish models and patient cell lines. Specifically, we determined that dysfunction of known KS genes and the genes identified in this study results in aberrant MEK/ERK signaling as well as disruption of F-actin polymerization and cell intercalation. Moreover, these phenotypes could be rescued in zebrafish models by rebalancing MEK/ERK signaling via administration of small molecule inhibitors of MEK. Taken together, our studies suggest that the KS pathophysiology overlaps with the RASopathies and provide a potential direction for treatment design. [ABSTRACT FROM AUTHOR]

Moebius syndrome (MBS) is a rare congenital disorder characterized by rhombencephalic mal development, mainly presenting with facial palsy with limited gaze abduction. Most cases are sporadic, possibly caused by a combination of environmental and genetic factors; however, no proven specific associations have been yet established. Hereditary congenital facial palsy (HCFP) is an autosomal dominant congenital dysinnervation syndrome, recognizable by the isolated dysfunction of the seventh cranial nerve. Mutant mice for Hoxb1 were reported to present with facial weakness, resembling MBS. Recently a homozygous mutation altering arg 5 residue of HOXB1 homeodomain into cys 5 was identified in two families with HCFP. We screened 95 sporadic patients diagnosed as MBS or HCFP for mutations in HOXB1. A novel homozygous alteration was identified in one HCFP case, affecting the same residue, resulting to his 5. In silico protein analysis predicted stronger HOXB1-DNA binding properties for his 5 than cys 5 that resulted to milder phenotype. It should be noted that, inclusive of the previous report, only two mutations revealed in HOXB1 associated with HCFP involved the same amino acid arg 5 in HOXB1 residing in HOXB1-DNA-PBX1 ternary complex. [ABSTRACT FROM AUTHOR]

Robinow syndrome is a genetically heterogeneous disorder characterized by mesomelic limb shortening, genital hypoplasia, and distinctive facial features and for which both autosomal-recessive and autosomal-dominant inheritance patterns have been described. Causative variants in the non-canonical signaling gene WNT5A underlie a subset of autosomal-dominant Robinow syndrome (DRS) cases, but most individuals with DRS remain without a molecular diagnosis. We performed whole-exome sequencing in four unrelated DRS-affected individuals without coding mutations in WNT5A and found heterozygous DVL1 exon 14 mutations in three of them. Targeted Sanger sequencing in additional subjects with DRS uncovered DVL1 exon 14 mutations in five individuals, including a pair of monozygotic twins. In total, six distinct frameshift mutations were found in eight subjects, and all were heterozygous truncating variants within the penultimate exon of DVL1 . In five families in which samples from unaffected parents were available, the variants were demonstrated to represent de novo mutations. All variant alleles are predicted to result in a premature termination codon within the last exon, escape nonsense-mediated decay (NMD), and most likely generate a C-terminally truncated protein with a distinct −1 reading-frame terminus. Study of the transcripts extracted from affected subjects’ leukocytes confirmed expression of both wild-type and variant alleles, supporting the hypothesis that mutant mRNA escapes NMD. Genomic variants identified in our study suggest that truncation of the C-terminal domain of DVL1, a protein hypothesized to have a downstream role in the Wnt-5a non-canonical pathway, is a common cause of DRS. [ABSTRACT FROM AUTHOR]

Abstract: Autosomal recessive cutis laxa type 2B (ARCL2B; OMIM # 612940) is a segmental progeroid disorder caused by mutations in PYCR1 encoding pyrroline-5-carboxylate reductase 1, which is part of the conserved proline de novo synthesis pathway. Here we describe 33 patients with PYCR1-related ARCL from 27 families with initial diagnoses varying between wrinkly skin syndrome, gerodermia osteodysplastica, De Barsy syndrome or more severe progeria syndromes. Given the difficult differential diagnosis of ARCL syndromes we performed a systematic comparison of clinical features of PYCR1-related ARCL. Intrauterine growth retardation, a characteristic triangular facial gestalt, psychomotor retardation, and hypotonia were the most relevant distinctive hallmarks of ARCL due to proline de novo synthesis defects. Corneal clouding or cataracts, athetoid movements, and finger contractures were rather rare features, but had a high predictive value. In our cohort we identified 20 different PYCR1 mutations of which seven were novel. Most of the mutations accumulated in exons 4 to 6. Missense alterations of highly conserved residues were most frequent followed by splice site changes and a single nonsense mutation. Analysis of genotype–phenotype correlation revealed that patients with mutations in the first two exons had lower average clinical scores and absent or only mild intellectual disability. Structural analyses predicted interference with PYCR1 multimerization for a subset of missense mutations. These findings have implications for the clinics as well as the pathomechanism of PYCR1-related ARCL. [Copyright &y& Elsevier]