Precise pre-mRNA splicing, essential for appropriate protein translation, depends on the presence of consensus “cis” sequences that define exon-intron boundaries and regulatory sequences recognized by splicing machinery. Point mutations at these consensus sequences can cause improper exon and intron recognition and may result in the formation of an aberrant transcript of the mutated gene. The splicing mutation may occur in both introns and exons and disrupt existing splice sites or splicing regulatory sequences (intronic and exonic splicing silencers and enhancers), create new ones, or activate the cryptic ones. Usually such mutations result in errors during the splicing process and may lead to improper intron removal and thus cause alterations of the open reading frame. Recent research has underlined the abundance and importance of splicing mutations in the etiology of inherited diseases. The application of modern techniques allowed to identify synonymous and nonsynonymous variants as well as deep intronic mutations that affected pre-mRNA splicing. The bioinformatic algorithms can be applied as a tool to assess the possible effect of the identified changes. However, it should be underlined that the results of such tests are only predictive, and the exact effect of the specific mutation should be verified in functional studies. This article summarizes the current knowledge about the “splicing mutations” and methods that help to identify such changes in clinical diagnosis.

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The original version on this paper contained an error. The first names and last names of Anna Abramowicz and Monika Gos are inadvertently interchanged and are incorrectly displayed in indexing sites. The correct names are presented above. Publisher's note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Craniosynostosis (occurrence: 1/2500 live births) is a result of premature fusion of cranial sutures, leading to alterations of the pattern of cranial growth, resulting in abnormal shape of the head and dysmorphic facial features. In approximately 85% of cases, the disease is isolated and nonsyndromic and mainly involves only one suture. Syndromic craniosynostoses such as Crouzon, Apert, Pfeiffer, Muenke, and Saethre-Chotzen syndromes not only affect multiple sutures, but are also associated with the presence of additional clinical symptoms, including hand and feet malformations, skeletal and cardiac defects, developmental delay, and others. The etiology of craniosynostoses may involve genetic (also somatic mosaicism and regulatory mutations) and epigenetic factors, as well as environmental factors. According to the published data, chromosomal aberrations, mostly submicroscopic ones, account for about 6.7-40% of cases of syndromic craniosynostoses presenting with premature fusion of metopic or sagittal sutures. The best characterized is the deletion or translocation of the 7p21 region containing the TWIST1 gene. The deletions of 9p22 or 11q23-qter (Jacobsen syndrome) are both associated with trigonocephaly. The genes related to the pathogenesis of the craniosynostoses itself are those encoding transcription factors, e.g., TWIST1, MSX2, EN1, and ZIC1, and proteins involved in osteogenic proliferation, differentiation, and homeostasis, such as FGFR1, FGFR2, RUNX2, POR, and many others. In this review, we present the clinical and molecular features of selected craniosynostosis syndromes, genotype-phenotype correlation, family genetic counseling, and propose the most appropriate diagnostic algorithm.

Noonan syndrome (NS) is a common developmental disorder presenting with dysmorphic craniofacial features, heart defects, and short stature. It belongs to the group of RASopathies caused by germline mutations in genes encoding proteins involved in the RAS/MAPK signaling pathway. Although mutations in nine genes are known to cause NS, approximately 30% of the cases still have unexplained etiology. To identify the new causative genes, 42 patients with a clinical diagnosis of NS, who had negative results on Sanger sequencing of PTPN11, SOS1, and RAF1 (the most common NS genes), were selected for whole exome sequencing. In two patients, mutations in recently described new NS gene—RIT1 were found (c.244T>G [p.Phe82Val] and c.270G>C [p.Met90Ile]). Further analysis of a larger cohort (n = 64) of NS patients with classic Sanger sequencing revealed the presence of RIT1 mutation c.284G>C (p.Gly95Ala) in two additional patients. All the detected mutations were localized in switch II domain responsible for GTPase activity. The modeling of RIT1 protein structure revealed that the mutated amino acids and their interacting residues are evolutionary conserved and any residue replacement might change the structural stability and/or protein internal dynamics influencing catalytic activity of the protein. It seems that the identified mutations might alter protein function and therefore, the activity of ERK and P38 MAPK pathways, thus underlying the specific phenotype observed in NS patients. Our study independently confirms the role of RIT1 in the pathogenesis of Noonan syndrome. © 2014 Wiley Periodicals, Inc.

Either confluence or serum withdrawal may cause growth arrest of cultured non-transformed cells. Here, we compared sparsely populated and confluent C3H10T1/2 cells with and without serum-containing medium. The following proliferation-relevant end points were examined: cell-cycle distribution, Ki-67 antigen presence, the level of the von Hippel-Lindau (VHL) protein, and gene expression, determined using a microarray approach. In sparse/logarithmic cultures, the fraction of cells in G(0)/G(1) phase increased from 55 to 85% following serum withdrawal. Moreover, the fraction of Ki-67 positive cells dropped from 89 to 47%. In confluent cultures, the majority of cells (80%) were in G(0)/G(1) phase and only 25-30% were Ki-67 positive, regardless of serum presence. In both serum-deprived and contact-inhibited cultures, significant and distinct changes in gene expression were observed. Serum deprivation of sparsely cultured cells resulted in significant over-expression of several transcription factors, while confluent cells showed elevated expression of genes coding for Wnt6, uPar, Tdag51, Egr1, Ini1a and Mor1. These results indicate that contact inhibition and serum withdrawal lead to cellular quiescence through distinct genetic and molecular mechanisms.

Purpose: Mutations in the CDKL5 gene have been associated with an X-linked dominant early infantile epileptic encephalopathy-2. The clinical presentation is usually of severe encephalopathy with refractory seizures and Rett syndrome (RTT)-like phenotype. We attempted to assess the role of mosaic intragenic copy number variation in CDKL5. Methods: We have used comparative genomic hybridization with a custom-designed clinical oligonucleotide array targeting exons of selected disease and candidate genes, including CDKL5. Results: We have identified mosaic exonic deletions of CDKL5 in one male and two females with developmental delay and medically intractable seizures. These three mosaic changes represent 60% of all deletions detected in 12,000 patients analyzed by array comparative genomic hybridization and involving the exonic portion of CDKL5. Conclusion: We report the first case of an exonic deletion of CDKL5 in a male and emphasize the importance of underappreciated mosaic exonic copy number variation in patients with early-onset seizures and RTT-like features of both genders. Genet T he cyclin-dependent kinase-like 5 (CDKL5) gene (also known as seronine-threonine kinase 9) encodes a protein of 1030 amino acids with highly conserved serine-threonine kinase domain in the N-terminal region and a large C-terminal region involved in either the catalytic activity or the subcellular localization. 1 CDKL5 is particularly expressed in the brain and has homology to the mitogen-activated protein kinase and CDK families. 2 Mutations in CDKL5 (OMIM# 300203) are X-linked dominant and have been described in females with severe neurodevelopmental disorders characterized by early-onset seizures, infantile spasms and severe psychomotor impairments, and Rett Syndrome (RTT)-like phenotypes. 3 The phenotypic resemblance to Rett syndrome is likely related to similar function of the CDKL5 and MeCP2 proteins in the molecular pathways and regional pattern of expression during neurodevelopment. 4,5 Recently, copy number variations (CNVs) involving the CDKL5 gene have been reported in girls with severe epilepsy and a RTT-like phenotype. The increasing availability of array comparative genomic hybridization (CGH) has led to several publications describing different deletions in CDKL5 in females. 6 -9 These data emphasize that deletion CNVs involving CDKL5 are more common than first appreciated, especially in females.CDKL5 mutations have been found very rarely in males, suggesting that nullisomy might be incompatible with life. To date, only two frameshifts and four missense mutations have been reported in males with severe encephalopathy and early-onset intractable epilepsy. 10 -13 In addition, an approximately 2.8-Mb deletion involving CDKL5 and 15 other genes has been reported in a boy with severe encephalopathy, tetralogy of Fallot, and bilateral cataracts. 14 Also, an approximately 136-kb deletion disrupting exons 17-20 of CDKL5 and the RS1 and PPEF1 genes has been described in a male with retinoschisis and epilepsy. 15 We report ...

MED12 is a member of the large Mediator complex that controls cell growth, development, and differentiation. Mutations in MED12 disrupt neuronal gene expression and lead to at least three distinct X-linked intellectual disability syndromes (FG, Lujan-Fryns, and Ohdo). Here, we describe six families with missense variants in MED12 (p.(Arg815Gln), p.(Val954Gly), p.(Glu1091Lys), p.(Arg1295Cys), p.(Pro1371Ser), and p.(Arg1148His), the latter being first reported in affected females) associated with a continuum of symptoms rather than distinct syndromes. The variants expanded the genetic architecture and phenotypic spectrum of MED12-related disorders. New clinical symptoms included brachycephaly, anteverted nares, bulbous nasal tip, prognathism, deep set eyes, and single palmar crease. We showed that MED12 variants, initially implicated in X-linked recessive disorders in males, may predict a potential risk for phenotypic expression in females, with no correlation of the X chromosome inactivation pattern in blood cells. Molecular modeling (Yasara Structure) performed to model the functional effects of the variants strongly supported the pathogenic character of the variants examined. We showed that molecular modeling is a useful method for in silico testing of the potential functional effects of MED12 variants and thus can be a valuable addition to the interpretation of the clinical and genetic findings.