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INTRODUCTION: Neurodevelopmental disorders (NDDs) are diverse and can be explained by either genomic aberrations or single nucleotide variants. Most likely due to methodological approaches and/or disadvantages, the concurrence of both genetic events in a single patient has hardly been reported and even more rarely the pathogenic variant has been regarded as the cause of the phenotype when a chromosomal alteration is initially identified. CASE PRESENTATION: Here, we describe a NDD patient with a 6p nonpathogenic paracentric inversion paternally transmitted and a de novo pathogenic variant in the GRIN2B gene. Molecular-cytogenetic studies characterized the familial 6p inversion and revealed a paternal 9q inversion not transmitted to the patient. Subsequent whole-genome sequencing in the patient-father dyad corroborated the previous findings, discarded inversions-related cryptic genomic rearrangements as causative of the patient's phenotype, and unveiled a novel heterozygous GRIN2B variant (p.(Ser570Pro)) only in the proband. In addition, Sanger sequencing ruled out such a variant in her mother and thereby confirmed its de novo origin. Due to predicted disturbances in the local secondary structure, this variant may alter the ion channel function of the M1 transmembrane domain. Other pathogenic variants in GRIN2B have been related to the autosomal dominant neurodevelopmental disorder MRD6 (intellectual developmental disorder, autosomal dominant 6, with or without seizures), which presents with a high variability ranging from mild intellectual disability (ID) without seizures to a more severe encephalopathy. In comparison, our patient's clinical manifestations include, among others, mild ID and brain anomalies previously documented in subjects with MRD6. CONCLUSION: Occasionally, gross chromosomal abnormalities can be coincidental findings rather than a prime cause of a clinical phenotype (even though they appear to be the causal agent). In brief, this case underscores the importance of comprehensive genomic analysis in unraveling the wide-ranging genetic causes of NDDs and may bring new insights into the MRD6 variability.
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Germline or constitutional chromoanagenesis-related complex chromosomal rearrangements (CCRs) are rare, apparently "all-at-once", catastrophic events that occur in a single cell cycle, exhibit an unexpected complexity, and sometimes correlate with a severe abnormal phenotype. The term chromoanagenesis encompasses three distinct phenomena, namely chromothripsis, chromoanasynthesis, and chromoplexy. Herein, we found hallmarks of chromothripsis and chromoplexy in an ultra-complex t(5;7;21)dn involving several disordered breakpoint junctions (BPJs) accompanied by some microdeletions and the disruption of neurodevelopmental genes in a patient with a phenotype resembling autosomal dominant MRD44 (OMIM 617061). G-banded chromosomes and FISH showed that the CCR implied the translocation of the 5p15.2âpter segment onto 7q11.23; in turn, the fragment 7q11.23âqter of der(7) separated into two pieces: the segment q11.23âq32 translocated onto 5p15.2 and fused to 21q22.1âter in the der(5) while the distal 7q32âqter segment translocated onto der(21) at q22.1. Subsequent whole-genome sequencing unveiled that CCT5, CMBL, RETREG1, MYO10, and TRIO from der(5), IMMP2L, TES, VPS37D, DUS4L, TYW1B, and FEZF1-AS1 from der(7), and TIAM1 and SOD1 from der(21), were disrupted by BPJs, whereas some other genes (predicted to be haplosufficient or inconsequential) were completely deleted. Although remarkably CCT5, TRIO, TES, MYO10, and TIAM1 (and even VPS37D) cooperate in key biological processes for normal neuronal development such as cell adhesion, migration, growth, and/or cytoskeleton formation, the disruption of TRIO most likely caused the patient's MRD44-like phenotype, including intellectual disability, microcephaly, finger anomalies, and facial dysmorphia. Our observation represents the first truncation of TRIO related to a chromoanagenesis event and therefore expands the mutational spectrum of this crucial gene. Moreover, our findings indicate that more than one mechanism is involved in modeling the architecture of ultra-complex rearrangements.
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Cromotripsia , Aberrações Cromossômicas , Rearranjo Gênico , Humanos , Translocação Genética , Sequenciamento Completo do GenomaRESUMO
BACKGROUND: 4q deletion syndrome is a rare chromosomal disorder that mostly arises de novo. The syndrome is characterized by craniofacial dysmorphism, digital abnormalities, skeletal alterations, heart malformations, developmental delay, growth retardation, Pierre Robin sequence, autistic spectrum and attention deficit-hyperactivity disorder, although not every patient shows the same features. Array comparative genomic hybridization (aCGH) use improves the detection of tiny chromosomal deletions and allows for a better understanding of genotype-phenotype correlations in affected patients. We report the case of a 6-year-old female patient showing mild dysmorphic features, mild mental disabilities and a coagulation disorder as a consequence of a de novo del(4)(q34.1) characterized by aCGH. CASE PRESENTATION: A 6-year-old female patient exhibited special craniofacial features, such as backward-rotated ears, upslanted palpebral fissures, broad nasal bridges, anteverted nares, broad nasal alae, smooth philtrums, smooth nasolabial folds, thin lips, horizontal labial commissures, and retrognathia. In the oral cavity, maxillary deformation, a high arched palate, agenesis of both mandibular canines and fusion of two mandibular incisors were observed. She also displayed bilateral implantation of the proximal thumbs, widely spaced nipples, dorsal kyphosis, hyperlordosis, and clitoral hypertrophy. In addition, the patient presented with coagulopathy, psychomotor delay, attention deficit-hyperactivity disorder, and mild mental disability. A chromosomal study showed the karyotype 46,XX,del(4)(q34.1), while an aCGH analysis revealed an 18.9 Mb deletion of a chromosome 4q subtelomeric region spanning 93 known genes. CONCLUSION: The clinical manifestations of this patient were similar to those reported in other individuals with 4q deletion syndrome. Although most of the patients with a 4q34 terminal deletion share similarities, variations in phenotype are also common. In general, clinical effects of chromosomal deletion syndromes depend on the length of the deleted chromosomal segment and, consequently, on the number of lost genes; however, in all of these syndromes, there is no simple correlation between the phenotype and the chromosomal region involved, particularly in cases of 4q deletion.
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The Williams-Beuren (SWB; OMIM 194050) syndrome is an autosomal dominant multisystem disorder that occurs in ~ 1 in 20,000 live births and results from a 7q11.23 deletion spanning ~ 28 genes. This deletion is caused by a nonallelic homologous recombination (NAHR) between low copy repeats present therein. The SWB phenotype is characterized by neonatal hypercalcemia, mental disability, distinctive personality and cognitive profile, short stature, dysmorphic facies, connective tissue disorders and supravalvular aortic stenosis. Ninety percent of the deletions are of 1.5 Mb, 8% of 1.84Mb, and only 2% are atypical. Although only ~ 40 atypical deletions have been described, they have contributed to clarify the genotype-phenotype correlation and allowed for a more integrative management. In this review we highlight the importance of detecting atypical deletions in patients with SWB.
El síndrome Williams-Beuren (SWB; OMIM 194050) es un trastorno multisistémico autosómico dominante que ocurre en ~ 1 de cada 20 000 nacidos vivos, y se debe a una deleción en 7q11.23 de ~ 28 genes. Esta deleción resulta de una recombinación homóloga no alélica entre repeticiones de bajo número de copias presentes en dicha región. El fenotipo SWB se caracteriza por hipercalcemia neonatal, discapacidad mental, personalidad y perfil cognitivo distintivos, baja estatura, facies dismórficas, trastornos del tejido conectivo y estenosis aórtica supravalvular. El 90% de las deleciones son de 1.5 Mb, 8% de 1.84 Mb, y solo el 2% son atípicas. Aunque solo se han descrito ~ 40 deleciones atípicas, estas han contribuido a esclarecer la correlación genotipo-fenotipo y permitido un manejo integral. En esta revisión se destaca la importancia de la detección de deleciones atípicas en pacientes con SWB.