Two Novel Variants Affecting CDKL5 Transcript Associated with Epileptic Encephalopathy.

BACKGROUND: Variants in the human X-linked cyclin-dependent kinase-like 5 (CDKL5) gene have been reported as being etiologically associated with early infantile epileptic encephalopathy type 2 (EIEE2). We report on two patients, a boy and a girl, with EIEE2 that present with early onset epilepsy, hypotonia, severe intellectual disability, and poor eye contact. METHODS: Massively parallel sequencing (MPS) of a custom-designed gene panel for epilepsy and epileptic encephalopathy containing 112 epilepsy-related genes was performed. Sanger sequencing was used to confirm the novel variants. For confirmation of the functional consequence of an intronic CDKL5 variant in patient 2, an RNA study was done. RESULTS: DNA sequencing revealed de novo variants in CDKL5, a c.2578C>T (p. Gln860*) present in a hemizygous state in a 3-year-old boy, and a potential splice site variant c.463+5G>A in heterozygous state in a 5-year-old girl. Multiple in silico splicing algorithms predicted a highly reduced splice site score for c.463+5G>A. A subsequent mRNA study confirmed an aberrant shorter transcript lacking exon 7. CONCLUSIONS: Our data confirmed that variants in the CDKL5 are associated with EIEE2. There is credible evidence that the novel identified variants are pathogenic and, therefore, are likely the cause of the disease in the presented patients. In one of the patients a stop codon variant is predicted to produce a truncated protein, and in the other patient an intronic variant results in aberrant splicing.

Point mutations in Czech DMD/BMD patients and their phenotypic outcome.

Duchenne and Becker muscular dystrophies (DMD/BMD) are associated with mutations in the DMD gene. We determined the mutation status of 47 patients with dystrophinopathy without deletion or duplication in the DMD gene by screening performed by reverse transcription-PCR, protein truncation test, and DNA sequencing. We describe three patients with a mutation creating a premature termination codon (p.E55X, p.E1110X, and p.S3497PfsX2) but with a mild phenotype, which present three different ways of rescuing the DMD phenotype. In one patient we detected the insertion of a repetitive sequence AluYa5 in intron 56, which led to skipping of exon 57. Further, using quantitative analysis of DMD mRNA carrying various mutated alleles, we examine levels of mRNA degradation due to nonsense mediated mRNA decay. The quantity of dystrophin mRNA is different depending on the presence of a mutation leading to a premature termination codon, and position of the analysed mRNA region with respect to its 5' end or 3' end. Average relative amounts of DMD mRNAs carrying a premature termination codon is 48% and 17%, when using primers amplifying the 5' and 3' cDNA regions, respectively.

Emery-Dreifuss muscular dystrophy: a novel mutation in the LMNA gene.

Described here is the phenotypical expression of a novel LMNA mutation c.1157 G>T in a Czech patient with an early-onset form of Emery-Dreifuss muscular dystrophy. The mutation predicts aberrant splicing. Now 21 years old, the patient has had slowly progressing muscle dystrophy since the age of one and early contractures of elbows. He is the only family member affected. Even though the dystrophy typically affects the heart as well, in the present case these signs are not yet expressed.

Analysis of point mutations in the SMN1 gene in SMA patients bearing a single SMN1 copy.

Spinal muscular atrophy (SMA) is caused by homozygous deletion of the SMN1 gene in approximately 96% of cases. Four percent of SMA patients have a combination of the deletion or conversion on one allele and an intragenic mutation on the second one. We performed analysis of point mutations in a set of our patients with suspicion of SMA and without homozygous deletion of the SMN1 gene. A quantitative test determining SMN1 copy number (using real-time PCR and/or MLPA analysis) was performed in 301 patients and only 1 SMN1 copy was detected in 14 of them. When these 14 patients were screened for the presence of point mutations we identified 6 mutations, p.Y272C (in three patients) and p.T274I, p.I33IfsX6, and p.A188S (each in one case). The mutations p.I33IfsX6 and p.A188S were found in two SMAI patients and were not detected previously. Further, evaluation of the relationship between mutation type, copy number of the SMN2 gene and clinical findings was performed. Among our SMA patients with a SMN1 homozygous deletion, we found a family with two patients: the son with SMAII possesses 3 SMN2 copies and the nearly asymptomatic father has a homozygous deletion of SMN1 exon 7 and carries 4 SMN2 copies. Generally, our results illustrate that an increased SMN2 gene copy number is associated with a milder SMA phenotype.

Quantitative analysis of CAPN3 transcripts in LGMD2A patients: involvement of nonsense-mediated mRNA decay.

Limb girdle muscular dystrophy type 2A (LGMD2A) is caused by single or small nucleotide changes widespread along the CAPN3 gene, which encodes the muscle-specific proteolytic enzyme calpain-3. About 356 unique allelic variants of CAPN3 have been identified to date. We performed analysis of the CAPN3 gene in LGMD2A patients at both the mRNA level using reverse transcription-PCR, and at the DNA level using PCR and denaturing high performance liquid chromatography. In four patients, we detected homozygous occurrence of a missense mutation or an in-frame deletion at the mRNA level although the DNA was heterozygous for this mutation in conjunction with a frame-shift mutation. The relationship observed in 12 patients between the quantity of CAPN3 mRNA, determined using real-time PCR, and the genotype leads us to propose that CAPN3 mRNAs which contain frame-shift mutations are degraded by nonsense-mediated mRNA decay. Our results illustrate the importance of DNA analysis for reliable establishment of mutation status, and provide a new insight into the process of mRNA decay in cells of LGMD2A patients.

Mutations in Czech LGMD2A patients revealed by analysis of calpain3 mRNA and their phenotypic outcome.

Calpain3 (CAPN3, p94) is a muscle-specific nonlysosomal cysteine proteinase. Loss of proteolytic function or change of other properties of this enzyme (such as stability or ability to interact with other muscular proteins) is manifested as limb girdle muscular dystrophy type 2A (LGMD2A, calpainopathy). These pathological changes in properties of calpain3 are caused by mutations in the calpain3 gene. The fact that the human gene for calpain3 is quite long led us to analyse its coding sequence by reverse transcription-PCR followed by sequence analysis. This study reports nine mutations that we found by analysing mRNA of seven unrelated LGMD patients in the Czech Republic. Three of these mutations were novel, not described on the Leiden muscular dystrophy pages so far. Further, we observed a reduction of dysferlin in muscle membrane in five of our seven LGMD2A patients by immunohistochemical analysis of muscle sections.