Complex genetic syndromes represent a diagnostic challenge due to their diverse phenotypic presentations, which often evolve over time and may not be fully evident at birth. Disorders of sex development (DSD) comprise congenital conditions with discordance between chromosomal, gonadal, and/or genital sex. In 46,XY gonadal dysgenesis, undervirilisation or female-appearing genitalia may occur despite a normal karyotype, and diagnosis increasingly relies on genomic approaches. Prenatal and postnatal growth failure has been described in patients with syndromic 46,XY DSD. We report a male patient with SGA, lack of postnatal catch-up growth, and syndromic dysgenetic 46,XY DSD followed longitudinally from infancy to 11 years, in whom whole-exome sequencing (WES) reanalysis revealed a pathogenic 2.7 Mb microdeletion at 3q27.1q27.2. Systematic review of previously reported 3q27.1 deletions identified overlapping phenotypes but limited documentation of gonadal dysfunction. Curation of 71 genes within the deleted region highlighted DVL3 and CLCN2 as potential contributors to the gonadal phenotype, although functional evidence remains lacking. This case expands the phenotypic spectrum of 3q27.1 microdeletion syndrome, suggesting that 46,XY gonadal dysgenesis may represent an under-recognised feature. It also underscores the importance of copy number variant (CNV) analysis and periodic re-evaluation of sequencing data to increase diagnostic yield.

3p deletion syndrome is a rare monosomal disease that encompasses deletions throughout the short arm of chromosome 3. It is often in the distal region (3p25-pter), but variations in breakpoints and a complex clinical manifestation exist, with congenital heart defects being considered rare. We present the first case of hypoplastic left heart syndrome and minor dysmorphic features associated with 3p- syndrome. Furthermore, we aim to establish a gene-phenotype association. The diagnosis was made by karyotyping, followed by a literature investigation and in silico bioinformatic analysis about the possible candidate genes associated with congenital heart defects or hypoplastic left heart syndrome in 3p- syndrome. All genes analyzed that could affect heart formation are located in the 3p25.3 region, adjacent to the deleted region in the newborn from our case (3p26). Taking into account the technical limitations of the karyotype and the strength of evidence from each gene evaluated and locus proximity, it is likely that an unidentified partial break in the CAV3 gene occurred. We identified an indirect relation between gene CAV3 and hypoplastic left heart syndrome due to its strong association with cardiomyopathies and isolated cardiac defects. Furthermore, the cytogenetic band from our case is new information for the delimitation of a critical cardiac region on 3p syndrome, a discussion that has been ongoing since 1986. Thus, we reinforce the importance of cytogenetic investigation in patients with hypoplastic hearts and dysmorphia, assisting in diagnosis, definition of prognosis, and genetic counseling for the family. A síndrome da deleção 3p é uma doença monossômica rara que engloba deleções em todo o braço curto do cromossomo 3. Frequentemente está na região distal (3p25-pter), mas apresenta variações nos pontos de quebra e uma manifestação clínica complexa, cujas cardiopatias congênitas são consideradas raras. Apresentamos aqui o primeiro caso de síndrome do coração esquerdo hipoplásico e características dismórficas menores na síndrome 3p-. Além disso, buscamos estabelecer uma associação gene-fenótipo. O diagnóstico foi feito por cariótipo e procedeu-se a uma investigação bibliográfica e análise bioinformática in silico sobre os possíveis genes associados a cardiopatias congênitas ou síndrome do coração esquerdo hipoplásico na síndrome da deleção 3p. Todos os genes analisados que poderiam afetar a formação do coração estão localizados na região 3p25.3, adjacente à região deletada no recém-nascido do nosso caso (3p26). Tendo em conta as limitações técnicas do cariótipo, a força da evidência de cada gene avaliado e a proximidade do locus, é provável que tenha ocorrido uma quebra parcial não identificada no gene CAV3. Identificamos uma relação indireta entre o gene CAV3 e a síndrome do coração hipoplásico esquerdo, em razão da sua forte associação com cardiomiopatias e defeitos cardíacos isolados. Além disso, a banda citogenética do nosso caso é uma informação nova para a delimitação de uma região cardíaca crítica na síndrome 3p, discussão que está em andamento desde 1986. Assim, reforçamos a importância da investigação citogenética em pacientes com coração hipoplásico e dismorfias auxiliando no diagnóstico, definição de prognóstico e aconselhamento genético para a família.

Co-existence pathogenic copy number variation with aneuploidy is a rare phenomenon. Whole TBL1XR1 gene deletions are described and associated with autosomal dominant intellectual development disorder-41 (#616944). However, the phenotypical expression of the TBL1XR1 partial deletion is poorly described. We describe the case of a male, aged 18 months, who presented delayed motor development, gait disturbance, mild generalized hypotonia, minor dysmorphic features, and growth failure, in addition to Klinefelter syndrome (KS). The single nucleotide polymorphism array revealed the de novo pathogenic interstitial deletion of chromosome 3q26.32 of 202 kb size that encompassed the first two exons of one relevant coding gene: TBL1XR1 (*608,628). We report a male without clinical signs of KS and overlapped phenotypical features with another TBL1XR1-related disease: Pierpont syndrome (#602342). This patient extends the phenotypic spectrum of TBL1XR1 gene pathogenic variants.

Optical genome mapping (OGM), which allows analysis of ultra-high molecular weight (UHMW) DNA molecules, represents a response to the restriction created by short-read next-generation-sequencing, even in cases where the causative variant is a neutral copy-number-variant insensitive to quantitative investigations. This study aimed to provide a molecular diagnosis to a boy with Marfan syndrome (MFS) and intellectual disability (ID) carrying a de novo translocation involving chromosomes 3, 4, and 13 and a 1.7 Mb deletion at the breakpoint of chromosome 3. No FBN1 alteration explaining his Marfan phenotype was highlighted. UHMW gDNA was isolated from both the patient and his parents and processed using OGM. Genome assembly was followed by variant calling and annotation. Multiple strategies confirmed the results. The 3p deletion, which disrupted ROBO2, (MIM*602431) included three copy-neutral insertions. Two came from chromosome 13; the third contained 15q21.1, including the FBN1 from intron-45 onwards, thus explaining the MFS phenotype. We could not attribute the ID to a specific gene variant nor to the reshuffling of topologically associating domains (TADs). Our patient did not have vesicular reflux-2, as reported by missense alterations of ROBO2 (VUR2, MIM#610878), implying that reduced expression of all or some isoforms has a different effect than some of the point mutations. Indeed, the ROBO2 expression pattern and its role as an axon-guide suggests that its partial deletion is responsible for the patient's neurological phenotype. Conclusion: OGM testing 1) highlights copy-neutral variants that could remain invisible if no loss of heterozygosity is observed and 2) is mandatory before other molecular studies in the presence of any chromosomal rearrangement for an accurate genotype-phenotype relationship.

3q29 deletion syndrome is characterized by various developmental abnormalities, medical issues, and neuropsychiatric symptoms, including psychosis. Although this syndrome may confer the greatest risk for schizophrenia of any copy number variation, response to antipsychotic medication has infrequently been described in the literature, and no reviews on the topic currently exist. As such, the purpose of this article was to review treatment response in 3q29 deletion syndrome-associated psychosis. A review of the literature was completed in December 2022 for English language articles that described treatment response to antipsychotic medications in affected individuals with schizophrenia-like presentations. Five articles that collectively described eight individuals were included. Four individuals had a poor treatment response to non-clozapine antipsychotic medications, three had a partial response, and one individual's response to treatment was not described, despite having taken psychotropic medications of some kind. Additionally, three individuals received clozapine; one of whom partially responded, while two exhibited a good response. Treatment response did not clearly differ according to developmental history. 3q29 deletion syndrome may be associated with treatment-resistant psychotic symptoms. As such, clozapine therapy should be considered in such individuals, provided they meet criteria for treatment-resistant schizophrenia and no contraindications exist. However, this mini-review also highlights the need for more published case reports/series before more specific treatment recommendations can be made.