Pathogenic sequence variants in the IQ motif- and Sec7 domain-containing protein 2 (IQSEC2) gene have been confirmed as causative in the aetiopathogenesis of neurodevelopmental disorders (intellectual disability, autism) and epilepsy. We report on a case of a family with three sons; two of them manifest delayed psychomotor development and epilepsy. Initially proband A was examined using a multistep molecular diagnostics algorithm, including karyotype and array-comparative genomic hybridization analysis, both with negative results. Therefore, probands A and B and their unaffected parents were enrolled for an analysis using targeted "next-generation" sequencing (NGS) with a gene panel ClearSeq Inherited DiseaseXT (Agilent Technologies) and verification analysis by Sanger sequencing. A novel frameshift variant in the X-linked IQSEC2 gene NM_001111125.2:c.1813_1814del, p.(Asp605Profs*3) on protein level, was identified in both affected probands and their asymptomatic mother, having skewed X chromosome inactivation (XCI) (100:0). As the IQSEC2 gene is a known gene escaping from XCI in humans, we expect the existence of mechanisms maintaining the normal or enough level of the IQSEC2 protein in the asymptomatic mother. Further analyses may help to the characterization of the presented novel frameshift variant in the IQSEC2 gene as well as to elucidate the mechanisms leading to the rare asymptomatic phenotypes in females.
- MeSH
- Algorithms MeSH
- Gene Deletion MeSH
- Child MeSH
- Epilepsy complications genetics MeSH
- Phenotype MeSH
- Genetic Variation * MeSH
- X Chromosome Inactivation MeSH
- Karyotyping MeSH
- Humans MeSH
- Neurodevelopmental Disorders complications genetics MeSH
- Frameshift Mutation MeSH
- Child, Preschool MeSH
- Chromosome Banding MeSH
- Oligonucleotide Array Sequence Analysis MeSH
- Comparative Genomic Hybridization * MeSH
- Guanine Nucleotide Exchange Factors genetics MeSH
- High-Throughput Nucleotide Sequencing MeSH
- Check Tag
- Child MeSH
- Humans MeSH
- Male MeSH
- Child, Preschool MeSH
- Female MeSH
- Publication type
- Journal Article MeSH
- Case Reports MeSH
- Research Support, Non-U.S. Gov't MeSH
Východiska: Liův-Fraumeniho syndrom (LFS) je vzácné autozomálně dominantní onemocnění charakterizované extrémním celoživotním rizikem vzniku mnohočetných a časně se objevujících zhoubných nádorů, za jehož vznik odpovídají dědičné patogenní mutace v genu TP53. Zatímco somatické mutace v TP53 patří mezi nejčastější genetické alterace u nádorových onemocnění, dědičné mutace jsou raritní. Poslední dekáda přinesla řadu změn v diagnostice LFS a nových poznatků o rizicích asociovaných nádorových onemocnění, které se promítají do preventivních opatření. Cíl: Předkládaný přehled ilustruje vývoj diagnostiky LFS a změny v indikačních kritériích pro testování germinálních variant v TP53, které umožnily definici širší nozologické jednotky – syndromu dědičné nádorové predispozice související s TP53 (hTP53rc – heritable TP53-related cancer syndrome). Posun v molekulárně biologické diagnostice směrem k sekvenování nové generace zjednodušil postup a dostupnost vyšetření nádorové predispozice. Analýza genu TP53 na germinální úrovni se stala součástí vyšetření téměř u všech osob indikovaných k testování dědičné nádorové predispozice, i když se nejedná o osoby s LFS fenotypem. Identifikace skutečných zárodečných patogenních variant TP53 představuje výzvu v jejich odlišení od mozaicizmu či somatických patogenních variant TP53 vznikajících v důsledku klonální hematopoézy neurčitého potenciálu. Pro jejich odlišení je nezbytná konfirmační analýza ze vzorku tkáně s vyjádřením alelické frakce variantní alely. Výzvou je i hodnocení patogenity vzácných germinálních variant TP53, která vyžaduje komplexní analýzu korelace genotypu s fenotypem. Pro potvrzení patogenity germinálních variant TP53 byla recentně publikována genově specifická kritéria American College of Medical Genetics and Genomics / Association for Molecular Pathology. Pouze nosiči jednoznačně prokázané zárodečné patogenní varianty by měli být zařazeni do intenzivního klinického preventivního programu. Závěr: Předložená práce upozorňuje na posun v poznání a diagnostice jedné z nejsilnějších predispozic ke vzniku nádorových onemocnění a měla by sloužit jako východisko pro další diskuzi týkající se organizace péče o vysoce rizikové nosiče patogenních variant TP53 nejen v dětském, ale i dospělém věku v ČR.
Background: Li-Fraumeni syndrome (LFS) is a rare autosomal dominant disorder characterized by an extreme lifetime risk of multiple and early-onset tumors, driven by inherited pathogenic variants in the TP53 gene. While somatic mutations in TP53 are among the most frequent genetic alterations in cancer, germline mutations remain rare. Although LFS has long been recognized as a prototypical cancer predisposition syndrome, recent advances have significantly reshaped its diagnostic criteria and deepened our understanding of its associated cancer risks. Objective: The review illustrates the evolving diagnostic landscape of LFS and the updated indication criteria for germline TP53 testing, which have broadened the definition of the syndrome into the more inclusive entity of heritable TP53-related cancer predisposition syndrome (hTP53rc). The adoption of NGS has streamlined molecular diagnostics in hereditary cancer syndromes. Germline analysis of TP53 has become standard practice in hereditary cancer predisposition testing, even if a proband does not exhibit a LFS phenotype. However, the accurate identification of germline pathogenic TP53 variants remains challenging, particularly due to confounding factors, such as mosaicism or clonal hematopoiesis of indeterminate potential. Confirmatory testing using an independent tissue sample, along with estimation of allelic fraction is necessary to distinguish true germline variants. Another major hurdle is the assessment of the pathogenicity of rare germline TP53 variants, which requires a thorough genotype-phenotype correlation analyses. Recently, gene-specific American College of Medical Genetics and Genomics / Association for Molecular Pathology criteria have been introduced to support the classification of germline TP53 variants. Importantly, only carriers of a clearly established germline pathogenic variant should be considered for inclusion in an intensive clinical surveillance and prevention program. Conclusion: The present work underscores a paradigm shift in the understanding of one of the most significant cancer predisposition syndromes and aims to stimulate further discussion on the organization of care for high-risk carriers of pathogenic TP53 variants in the Czech Republic.
Familiární hypercholesterolemie je jedno z nejčastějších metabolických onemocnění. Nejčastěji je spojována s patogenními variantami v genu pro LDL-receptorový protein (LDLR). Ve veřejných databázích je popsáno již více než 2 700 variant, které byly v tomto genu celosvětově nalezeny. I přes zásadní technologické pokroky v molekulární biologii zůstává stěžejním úkolem interpretace nalezených sekvenčních variant ve vztahu ke konkrétnímu hodnocenému klinickému projevu u konkrétního pacienta. V rámci mezinárodní expertní skupiny byla vypracována kritéria pro hodnocení kauzality sekvenčních variant v genu LDLR ve snaze sjednotit rozdílné interpretační algoritmy. Tato kritéria by následně měla být aplikována do klinické a diagnostické praxe.
Familial hypercholesterolemia is one of the most common metabolic diseases. It is mostly associated with pathogenic variants in the LDLR gene. Public databases contain more than 3,000 sequence variants that have been reported in this gene worldwide. Despite crucial technological advances in molecular biology, the interpretation of detected sequence variants in relation to the specific evaluated clinical phenotype in a particular patient remains a key task. Within an international expert group, criteria for evaluation of causality of sequence variants in the LDLR gene were developed to unify different interpretation algorithms. These criteria should then be applied to the clinical and diagnostic practice.
An abbreviated tract of five thymidines (5T) in intron 8 of the cystic fibrosis transmembrane conductance regulator (CFTR) gene is found in approximately 10% of individuals in the general population. When found in trans with a severe CFTR mutation, 5T can result in male infertility, nonclassic cystic fibrosis, or a normal phenotype. To test whether the number of TG repeats adjacent to 5T influences disease penetrance, we determined TG repeat number in 98 patients with male infertility due to congenital absence of the vas deferens, 9 patients with nonclassic CF, and 27 unaffected individuals (fertile men). Each of the individuals in this study had a severe CFTR mutation on one CFTR gene and 5T on the other. Of the unaffected individuals, 78% (21 of 27) had 5T adjacent to 11 TG repeats, compared with 9% (10 of 107) of affected individuals. Conversely, 91% (97 of 107) of affected individuals had 12 or 13 TG repeats, versus only 22% (6 of 27) of unaffected individuals (P<.00001). Those individuals with 5T adjacent to either 12 or 13 TG repeats were substantially more likely to exhibit an abnormal phenotype than those with 5T adjacent to 11 TG repeats (odds ratio 34.0, 95% CI 11.1-103.7, P<.00001). Thus, determination of TG repeat number will allow for more accurate prediction of benign versus pathogenic 5T alleles.
Pathogenic sequence variant in the GNAI1 gene were recently introduced as a cause of novel syndrome with a manifestation of variable developmental delay and autistic features. In our study, we report a case of monozygotic twins with severe intellectual disability and motor delay and developmental dysphasia. Both probands and their parents were examined using multi-step molecular diagnostic algorithm including whole-exome sequencing (WES), resulting in the identification of a novel, de novo pathogenic sequence variant in the GNAI1 gene, NM_002069.6:c.815 A>G, p.(Asp272Gly) in probands. Using WES we also verified the microarray findings of a familial 8q24.23q24.3 duplication and heterozygous 5q13.2 deletion, not associated with clinical symptoms in probands. Our results confirmed the role of the GNAI1 gene in the pathogenesis of syndromic neurodevelopmental disorders. They support trio- or quatro-based WES as a suitable molecular diagnostics method for the simultaneous detection of clinically relevant sequence variants and CNVs in individuals with neurodevelopmental disorders and rare diseases.
Viroid-caused pathogenesis is a specific process dependent on viroid and host genotype(s), and may involve viroid-specific small RNAs (vsRNAs). We describe a new PSTVd variant C3, evolved through sequence adaptation to the host chamomile (Matricaria chamomilla) after biolistic inoculation with PSTVd-KF440-2, which causes extraordinary strong ('lethal') symptoms. The deletion of a single adenine A in the oligoA stretch of the pathogenicity (P) domain appears characteristic of PSTVd-C3. The pathogenicity and the vsRNA pool of PSTVd-C3 were compared to those of lethal variant PSTVd-AS1, from which PSTVd-C3 differs by five mutations located in the P domain. Both lethal viroid variants showed higher stability and lower variation in analyzed vsRNA pools than the mild PSTVd-QFA. PSTVd-C3 and -AS1 caused similar symptoms on chamomile, tomato, and Nicotiana benthamiana, and exhibited similar but species-specific distributions of selected vsRNAs as quantified using TaqMan probes. Both lethal PSTVd variants block biosynthesis of lignin in roots of cultured chamomile and tomato. Four 'expression markers' (TCP3, CIPK, VSF-1, and VPE) were selected from a tomato EST library to quantify their expression upon viroid infection; these markers were strongly downregulated in tomato leaf blades infected by PSTVd-C3- and -AS1 but not by PSTVd-QFA.
- MeSH
- Adaptation, Physiological * MeSH
- Genetic Markers genetics MeSH
- Host-Pathogen Interactions MeSH
- Lignin metabolism MeSH
- RNA, Small Untranslated genetics MeSH
- Matricaria virology MeSH
- RNA, Messenger genetics metabolism MeSH
- Evolution, Molecular * MeSH
- Molecular Sequence Data MeSH
- RNA, Viral genetics MeSH
- Base Sequence MeSH
- Solanum lycopersicum virology MeSH
- Solanum tuberosum metabolism virology MeSH
- Thermodynamics MeSH
- Viroids genetics pathogenicity physiology MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Mutations in CACNA1C, the gene encoding Cav1.2 voltage-gated calcium channels, are associated with a spectrum of disorders, including Timothy syndrome and other neurodevelopmental and cardiac conditions. In this study, we report a child with a de novo heterozygous missense variant (c.1973T > C; L658P) in CACNA1C, presenting with refractory epilepsy, global developmental delay, hypotonia, and multiple systemic abnormalities, but without overt cardiac dysfunction. Electrophysiological analysis of the recombinant Cav1.2 L658P variant revealed profound gating alterations, most notably a significant hyperpolarizing shift in the voltage dependence of activation and inactivation. Additionally, molecular modeling suggested that the L658P mutation disrupts interactions within the IIS5 transmembrane segment, reducing the energy barrier for state transitions and facilitating channel opening at more negative voltages. These findings establish L658P as a pathogenic CACNA1C variant primarily associated with severe neurological dysfunction and expands the phenotypic spectrum of CACNA1C-related disorders.
- MeSH
- Child MeSH
- Ion Channel Gating * MeSH
- Humans MeSH
- Mutation, Missense genetics MeSH
- Models, Molecular MeSH
- Neurodevelopmental Disorders * genetics MeSH
- Child, Preschool MeSH
- Amino Acid Sequence MeSH
- Calcium Channels, L-Type * genetics MeSH
- Check Tag
- Child MeSH
- Humans MeSH
- Male MeSH
- Child, Preschool MeSH
- Female MeSH
- Publication type
- Journal Article MeSH
- Case Reports MeSH
Východiska: Hereditární nádorové syndromy tvoří významnou podskupinu zhoubných nádorových onemocnění způsobených patogenními variantami v některém z mnoha známých nádorových predispozičních genů. Diagnostika nádorové predispozice je založena na genetickém testování pomocí sekvenování nové generace. To umožňuje analýzu mnoha genů najednou, nicméně zároveň se zvyšuje počet identifikovaných variant. Správná klasifikace nalezených variant je zásadní pro klinickou interpretaci výsledků genetického testování. Cíl: Cílem práce je shrnutí pravidel pro klasifikaci identifikovaných variant v rámci jednotlivých pracovišť a představení procesu tvorby společné klasifikace. Sdílení nalezených genetických variant a tvorba jejich konsenzuální klasifikace v rámci národních laboratorně diagnostických komunit probíhá v ČR v rámci konzorcia Czech Cancer Panel for Clinical Application (CZECANCA) sdružujícího výzkumné a diagnostické onkogenetické laboratoře. Tvorba konsenzu pro klasifikaci variant probíhá podle definovaného protokolu. Sdílení výsledků a konsenzuální klasifikace zrychluje a zpřesňuje vydávání výsledků genetického testování, harmonizuje výsledky mezi laboratořemi a přispívá tak ke zkvalitnění péče o jedince ve vysokém riziku vzniku nádorových onemocnění a jejich příbuzné.
Background: Hereditary cancer syndromes are an important subset of malignant cancers caused by pathogenic variants in one of many known cancer predisposition genes. Diagnosis of cancer predisposition is based on genetic testing using next-generation sequencing. This allows many genes to be analysed at once, increasing the number of variants identified. The correct classification of the variants found is essential for the clinical interpretation of genetic test results. Purpose: The aim of this study is to summarise the rules for classifying identified variants within individual laboratories and to present the process for creating a common classification. In the Czech Republic, the sharing of identified genetic variants and the development of their consensus classification among national laboratory diagnostic communities is carried out within the Czech Cancer Panel for Clinical Application (CZECANCA) consortium of scientific and diagnostic oncogenetic laboratories. Consensus for variant classification follows a defined protocol. Sharing the results and consensus classification accelerates and refines the release of genetic test results, harmonises results between laboratories and thus contributes to improving the care of individuals at high risk of cancer and their relatives.
- Keywords
- CZECANCA,
- MeSH
- Neoplastic Syndromes, Hereditary * diagnosis genetics classification MeSH
- Genetic Predisposition to Disease genetics prevention & control MeSH
- Genetic Testing methods MeSH
- Classification MeSH
- Consensus * MeSH
- Humans MeSH
- Neoplasms genetics classification MeSH
- High-Throughput Nucleotide Sequencing methods MeSH
- Germ-Line Mutation genetics MeSH
- Check Tag
- Humans MeSH
- Publication type
- Research Support, Non-U.S. Gov't MeSH
- Review MeSH
- Geographicals
- Czech Republic MeSH
Objective: To investigate the pathogenicity of a novel homozygous BRAT1 variant in 2 siblings with nonprogressive cerebellar ataxia (NPCA) through functional studies on primary and immortalized patient cell lines. Methods: BRAT1 protein levels and ataxia-telangiectasia mutated (ATM) kinase activity in patient-derived and control cell lines were assessed by Western blotting. The impact of the novel BRAT1 variants on mitochondrial function was also assessed, by comparing patient and control cell lines for rates of oxygen consumption and for phosphorylation (S293) of the E1⍺ subunit of pyruvate dehydrogenase (PDH). Results: Two male siblings with NPCA, mild intellectual disability, and isolated cerebellar atrophy were found to be homozygous for a c.185T>A (p.Val62Glu) variant in BRAT1 by whole exome sequencing. Western blotting revealed markedly decreased BRAT1 protein levels in lymphocytes and/or fibroblast cells from both affected siblings compared to control cell lines. There were no differences between the patient and control cells in ATM kinase activation, following ionizing radiation. Mitochondrial studies were initially suggestive of a defect in regulation of PDH activity, but there was no evidence of increased phosphorylation of the E1⍺ subunit of the PDH complex. Measurement of oxygen consumption rates similarly failed to identify differences between patient and control cells. Conclusions: Biallelic pathogenic variants in BRAT1 can be associated with NPCA, a phenotype considerably milder than previously reported. Surprisingly, despite the molecular role currently proposed for BRAT1 in ATM regulation, this disorder is unlikely to result from defective ATM kinase or mitochondrial dysfunction.
- Publication type
- Journal Article MeSH
BACKGROUND: Cardiac-urogenital syndrome [MIM # 618280] is a newly described very rare syndrome associated with pathogenic variants in the myelin regulatory factor (MYRF) gene that leads to loss of protein function. MYRF is a transcription factor previously associated only with the control of myelin-related gene expression. However, it is also highly expressed in other tissues and associated with various organ anomalies. The clinical picture is primarily dominated by complex congenital cardiac developmental defects, pulmonary hypoplasia, congenital diaphragmatic hernia, and urogenital malformations. CASE PRESENTATION: We present case reports of two siblings of unrelated parents in whom whole-exome sequencing was indicated due to familial occurrence of extensive developmental defects. A new, previously undescribed splicing pathogenic variant c.1388+2T>G in the MYRF gene has been identified in both patients. Both parents are unaffected, tested negative, and have another healthy daughter. The identical de novo event in siblings suggests gonadal mosaicism, which can mimic recessive inheritance. CONCLUSIONS: To our knowledge, this is the first published case of familial cardiac-urogenital syndrome indicating gonadal mosaicism.
- MeSH
- Humans MeSH
- Mosaicism * MeSH
- Exome Sequencing MeSH
- Siblings * MeSH
- Syndrome MeSH
- Transcription Factors genetics MeSH
- Check Tag
- Humans MeSH
- Female MeSH
- Publication type
- Journal Article MeSH
- Case Reports MeSH
- Research Support, Non-U.S. Gov't MeSH
