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Rare diseases are thought to affect a smaller number of people, but together they become a major health concern. Due to advancements in molecular techniques, early diagnosis is essential to the genetic cause of these diseases. This may improve medical care and the survival of affected individuals. Copy number variations or pathogenic single gene mutations are the cause of most of these disorders. Two main rare disease categories were in the focus of our research: congenital heart defects and non-syndromic intellectual disability. Genetic factors, including copy number variations (CNVs), play an important role in the development of CHDs. The most common CNVs are found on chromosome 22q11.2. The genomic instability of this region, caused by the eight low copy repeats (LCR A-H), may result in several recurrent and/or rare microdeletions and duplications, including the most common, ~3Mb large LCR A-D deletion (classical 22q.11.2 deletion syndrome, known as DiGeorge syndrome). Many patients with 22q11.2 CNVs, especially in the adult population may remain undiagnosed due to the high phenotypical variability of these CNVs. Therefore, we aimed to perform a systemic molecular genetic screening for 22q11.2 CNVs in the paediatric and adult patients of the Southern-Hungarian CHD Registry, regardless of the type of their CHDs. All the enrolled participants were cardiologically diagnosed with non-syndromic CHDs. A combination of multiplex ligation-dependent probe amplification, chromosomal microarray analysis and droplet digital PCR methods were used to comprehensively assess the detected 22q11.2 CNVs in overall 212 CHD-patients. Additionally, capillary sequencing was performed to detect variants in the TBX1 gene, a cardinal gene located in 22q11.2. Pathogenic CNVs were detected in 5.2% (11/212), VUS in 0.9% and benign CNVs in 1.8% of the overall CHD cohort. In patients with tetralogy of Fallot the rate of pathogenic CNVs was 17% (5/30). Sixty-four percent of all CNVs were typical proximal deletions (LCR A-D). However, nested (LCR A-B) and central deletions (LCR C-D), proximal (LCR A-D) and distal duplications (LCR D-E, LCR D-H, LCR E-H, LCR F-H) and rare combinations of deletions and duplications were also identified. Segregation analysis detected familial occurrence in 18% (2/11) of the pathogenic variants. Based on in-depth clinical information, a detailed phenotype–genotype comparison was performed. No pathogenic variant was identified in the TBX1 gene, which may question the ethiopathogenetic role of TBX1 mutations alone in the development of CHDs and DiGeorge syndrome. Our findings confirmed the previously described large phenotypic diversity in the 22q11.2 CNVs. MLPA proved to be a highly efficient and cost-effective genetic screening method for our CHD-cohort. Our results highlight the necessity for large-scale genetic screening of CHD-patients and the importance of early genetic diagnosis in their adequate clinical management. In the frame of genetic examinations in X-linked non-syndromic intellectual disabilities we identified a novel mutation in PAK3 gene in a 14-years-old boy. PAK3 is a p21-activated serine/threonine kinase, an essential downstream effector in the Rho-GTPase signaling. It has been reported to play an important role in dendritic spine morphogenesis, synaptic network dynamics and neuronal plasticity. PAK3 gene mutations has been described to cause non-syndromic X-linked intellectual disability with neuropsychiatric disorders and dysmorphic but not distinctive features in the affected individuals. Our patient presented with cognitive impairment, autistic features, temper tantrums, episodic aggression, prior episodes of convulsions, spina bifida occulta, mildly dysmorphic facial features and microcephaly without structural brain abnormalities. Exome sequencing identified a novel hemizygous missense variant in the kinase domain of PAK3 gene (c.976G>C; p.V326L) which is interspecies highly conserved. In silico variant predictions, in silico functional modeling and segregation analysis in the family supported the ethiopathogenicity of the variant. Our detailed clinical findings together with the data from the few reported families allowed further insight in the phenotype of the disease, to expand the mutation spectrum of PAK3 gene and support the importance of PAK3 in neural synaptic function.

Congenital heart defects (CHD) are the most common developmental abnormalities, affecting approximately 0.9% of livebirths. Genetic factors, including copy number variations (CNVs), play an important role in their development. The most common CNVs are found on chromosome 22q11.2. The genomic instability of this region, caused by the eight low copy repeats (LCR A-H), may result in several recurrent and/or rare microdeletions and duplications, including the most common, ∼3 Mb large LCR A-D deletion (classical 22q.11.2 deletion syndrome). We aimed to screen 22q11.2 CNVs in a large Hungarian pediatric and adult CHD cohort, regardless of the type of their CHDs. All the enrolled participants were cardiologically diagnosed with non-syndromic CHDs. A combination of multiplex ligation-dependent probe amplification (MLPA), chromosomal microarray analysis and droplet digital PCR methods were used to comprehensively assess the detected 22q11.2 CNVs in 212 CHD-patients. Additionally, capillary sequencing was performed to detect variants in the TBX1 gene, a cardinal gene located in 22q11.2. Pathogenic CNVs were detected in 5.2% (11/212), VUS in 0.9% and benign CNVs in 1.8% of the overall CHD cohort. In patients with tetralogy of Fallot the rate of pathogenic CNVs was 17% (5/30). Fifty-four percent of all CNVs were typical proximal deletions (LCR A-D). However, nested (LCR A-B) and central deletions (LCR C-D), proximal (LCR A-D) and distal duplications (LCR D-E, LCR D-H, LCR E-H, LCR F-H) and rare combinations of deletions and duplications were also identified. Segregation analysis detected familial occurrence in 18% (2/11) of the pathogenic variants. Based on in-depth clinical information, a detailed phenotype–genotype comparison was performed. No pathogenic variant was identified in the TBX1 gene. Our findings confirmed the previously described large phenotypic diversity in the 22q11.2 CNVs. MLPA proved to be a highly efficient genetic screening method for our CHD-cohort. Our results highlight the necessity for large-scale genetic screening of CHD-patients and the importance of early genetic diagnosis in their clinical management.