ObjectiveThis study is an example of the contribution of exome sequencing (ES) in selected prenatal indications, while illustrating the complexity of interpreting prenatal genetic testing. Therefore, one of the aims of this study was to better describe antenatal phenotypes.MethodsThis was a multicenter, comparative, prospective study assessing high-throughput sequencing performance (targeted gene panel versus exome sequencing) in selected prenatal indications.ResultsTrio-ES was performed on 86 fetuses, allowed making a definite etiological diagnosis in 28% of cases (24/86). One-third of diagnoses were obtained only after exome analysis (8/24, 33%). The diagnostic yield varied according to the indication and was the highest for vermian hypoplasia (5/12, 42%) and polymalformative syndromes (30%, 8/27) indications. The variants identified were mainly missense variants in ciliopathy (18%, 6/33) and cytoskeleton (15%, 5/33) genes. Among the etiological diagnoses, one fetus carried a postzygotic mosaic variant in RHOA.ConclusionIn selected indications, the diagnostic yield of ES was close to 30% and varied according to the indications, showing the importance of clearly define the malformations justifying this approach. An etiological diagnosis was made in 23 families, within a timeframe compatible with pregnancy, thus improving the management of the pregnancy and/or the unborn child.

The SMARCA4 gene encodes a catalytic subunit of the BRG1/BRM-associated factor complex, which regulates gene expression through chromatin remodeling. Heterozygous missense variants in this gene have been linked to Coffin-Siris syndrome, characterized by intellectual development disorder and various congenital anomalies (distinctive facial features, hypoplastic fifth digits, and malformations of the heart and central nervous system), but it is not typically associated with structural eye anomalies. Truncating variants in SMARCA4 have been associated with rhabdoid tumors predisposition syndrome, a group of rare and aggressive tumors occurring predominantly in infancy. Through pangenomic analyses (whole-exome or whole-genome sequencing), we identified loss-of-function variants in SMARCA4 in three unrelated individuals with microphthalmia and/or coloboma. None of these individuals had a history of rhabdoid tumors; however, a regular oncological follow-up was established following the SMARCA4 variant identification. Systemic features observed in these individuals consisted of developmental delay and brain anomalies. However, their clinical presentation does not align with classic features of Coffin-Siris syndrome. Although eye development anomalies have occasionally been reported in individuals with a pathogenic variant in SMARCA4, no clear association has been established to date. The description of these three new individuals provides further evidence supporting the role of SMARCA4 in eye development and its likely involvement in structural eye malformations.

Biallelic pathogenic variants of the Reticulon 4 interacting protein 1 (RTN4IP1) gene are responsible for optic atrophy, either isolated or associated with ataxia, mental retardation, and seizures. They are identified as a cause of hereditary optic neuropathy in 7% of patients diagnosed before the age of 20. We have built a dataset for this gene by collating all the clinical cases available in the literature, and unpublished patients diagnosed at our centre, using standard nomenclature to describe both the molecular and phenotypic features. We performed a comprehensive data analysis, based on computational reasoning, to provide an overall picture of the dataset and validate its relevance. This new dataset provides an updated genetic map of the reported pathogenic variants, an ontological annotation of phenotypic abnormalities in a grid format showing clinical heterogeneity, and a full interoperability with the databases of other genetic forms of optic neuropathies.

Congenital aniridia is a rare disorder presenting as a panocular malformation with variable severity, often complicated by progressive keratopathy. The purpose of this study was to characterise the tear-film proteome in adults with PAX6-related congenital aniridia and to identify dysregulated pathways linked to aniridia associated keratopathy (AAK). Tears were obtained with Schirmer strips from four genetically confirmed patients and four age- and sex-matched healthy volunteers. Peptides prepared with the single-pot, solid-phase–enhanced (SP3) protocol were analysed by data-independent nanoLC-MS/MS. Proteins were identified with a false discovery rate (FDR) <1

Microphthalmia and anophthalmia (M/A) are rare congenital eye anomalies with a birth prevalence of up to 1 in 10,000 births. The etiology of M/A can involve environmental and/or genetic factors, with a genetic origin identified in approximately 50% of cases through analysis of key genes. The transcription factor SOX2 is the most commonly implicated gene, accounting for around 15% of M/A cases. Recent studies have shown that the RNA-binding protein Rbm24 post-transcriptionally regulates Sox2 expression in mice and zebrafish, with Rbm24 null models exhibiting eye phenotypes in both species. Rbm24 can bind to Sox2 mRNA via three AU-Rich elements (AREs) located in its 3' untranslated region (UTR). In this study, we aimed to determine whether pathogenic variants within RBM24 or the SOX2 3'UTR AREs were present in a cohort of 50 individuals with M/A with no identified genetic cause for their condition. Despite the ocular defects observed in animal models, we did not detect any variant of interest in these candidate regions in our cohort. Although we cannot exclude the involvement of pathogenic variations in RBM24 or the SOX2 3'UTR AREs in ocular developmental defects, our study shows that they are unlikely to represent a frequent cause of M/A.

Purpose:FOXE3 encodes a highly conserved, lens-enriched transcription factor essential for eye development. Biallelic mutations in FOXE3 are associated with a spectrum of ocular anomalies, ranging from congenital cataracts to complex microphthalmia (CM), with severity and penetrance correlating with genotype. This study aimed to investigate the regulatory landscape of FOXE3 and its contribution to CM. Methods:In a patient with CM, a truncating FOXE3 variation (p.Cys240*) was identified alongside a second, trans-acting regulatory variant (rv: rs745674596G>A) located 3 kb upstream of FOXE3. To investigate its functional impact, mouse models were generated carrying either the rv or a frameshift (fs) mutation in homozygosity (Foxe3rv/rv, Foxe3fs/fs) or in compound heterozygosity (Foxe3rv/fs). Ocular phenotypes were characterized, and molecular analyses were conducted to assess FOXE3 expression and transcriptional regulation. Results:Phenotypic severity followed a progressive pattern from Foxe3rv/rv to Foxe3rv/fs, with Foxe3fs/fs consistently exhibiting CM, mirroring genotype-dependent effects observed in humans. Protein levels, but not mRNA levels, correlated with ocular phenotype, with the frameshift mutation leading to pronounced mRNA overexpression in embryos. In Foxe3fs/fs mice, CM resulted from early anterior lens epithelium disorganization, triggering progressive lens degeneration and ocular involution. Transcription factor binding studies identified USF2 as a key regulator of FOXE3 expression, positioning it as a novel candidate in ocular development and disease. Conclusions:This study highlights the critical role of regulatory variants in ocular pathology, proposes a potentially novel mechanism for microphthalmia through lens degeneration, and identifies USF2 as a potential contributor to the FOXE3-regulatory network that remains largely unknown.

Variants in gap junction protein alpha 8 (GJA8), the gene encoding connexin 50 (Cx50), are primarily associated with developmental cataract, although some are associated with severe structural eye anomalies, such as aphakia (absent lens), microphthalmia (small eyes), and sclerocornea. To further define the relationship of GJA8 variants to ocular developmental disorders, we screened four large international cohorts with structural eye anomalies, including anophthalmia, microphthalmia, and coloboma (AMC) or cataracts. We identified 15 new families carrying 14 different heterozygous GJA8 variants (12 missense variants and two 1q21 microdeletions). The missense variants comprised 10 previously reported alterations in cases with eye anomalies [p.(Gly22Ser), p.(Val44Met), p.(Asp67Gly), p.(Arg76Cys), p.(Pro88Leu), p.(Gly94Glu), p.(Gly94Arg), p.(His98Arg), p.(Pro189Ser), and p.(Arg198Trp)] and two not yet linked with disease [p.(Thr39Met) and p.(Tyr66Asp)]. Their associated phenotypes ranged from isolated cataracts to a combination of microphthalmia and cataract with/without sclerocornea. Our study confirms GJA8 variants as an important source of genetic diagnoses for families with structural eye anomalies in addition to cataract and highlights specific mutational hotspots. Furthermore, we confirm an important genotype-phenotype correlation between sclerocornea and the p.(Gly94Arg) variant, and detail intra- and inter-familial phenotypic variability, which is important for clinical assessment and genetic counselling.

Ocular malformations (OMs) arise from early defects during embryonic eye development. Despite the identification of over 100 genes linked to this heterogeneous group of disorders, the genetic cause remains unknown for half of the individuals following Whole-Exome Sequencing. Diagnosis procedures are further hampered by the difficulty of studying samples from clinically relevant tissue, which is one of the main obstacles in OMs. Whole-Genome Sequencing (WGS) to screen for non-coding regions and structural variants may unveil new diagnoses for OM individuals. In this study, we report a patient exhibiting a syndromic OM with a de novo 3.15 Mb inversion in the 6p25 region identified by WGS. This balanced structural variant was located 100 kb away from the FOXC1 gene, previously associated with ocular defects in the literature. We hypothesized that the inversion disrupts the topologically associating domain of FOXC1 and impairs the expression of the gene. Using a new type of samples to study transcripts, we were able to show that the patient presented monoallelic expression of FOXC1 in conjunctival cells, consistent with the abolition of the expression of the inverted allele. This report underscores the importance of investigating structural variants, even in non-coding regions, in individuals affected by ocular malformations.

The association of early-onset non-progressive ataxia and miosis is an extremely rare phenotypic entity occasionally reported in the literature. To date, only one family (two siblings and their mother) has benefited from a genetic diagnosis by the identification of a missense heterozygous variant (p.Arg36Cys) in the ITPR1 gene. This gene encodes the inositol 1,4,5-trisphosphate receptor type 1, an intracellular channel that mediates calcium release from the endoplasmic reticulum. Deleterious variants in this gene are known to be associated with two types of spinocerebellar ataxia, SCA15 and SCA29, and with Gillespie syndrome that is associated with ataxia, partial iris hypoplasia, and intellectual disability. In this work, we describe a novel individual carrying a heterozygous missense variant (p.Arg36Pro) at the same position in the N-terminal suppressor domain of ITPR1 as the family previously reported, with the same phenotype associating early-onset non-progressive ataxia and miosis. This second report confirms the implication of ITPR1 in the miosis-ataxia syndrome and therefore broadens the clinical spectrum of the gene. Moreover, the high specificity of the phenotype makes it a recognizable syndrome of genetic origin.

Purpose: Imbalances in protein homeostasis affect human brain development, with the ubiquitin-proteasome system (UPS) and autophagy playing crucial roles in neurodevelopmental disorders (NDD). This study explores the impact of biallelic USP14 variants on neurodevelopment, focusing on its role as a key hub connecting UPS and autophagy. Methods: Here, we identi fi ed biallelic USP14 variants in 4 individuals from 3 unrelated families: 1 fetus, a newborn with a syndromic NDD and 2 siblings affected by a progressive neurological disease. Speci fi cally, the 2 siblings from the latter family carried 2 compound heterozygous variants c.8T > C p.(Leu3Pro) and c.988C > T p.(Arg330 * ), whereas the fetus had a homozygous frameshift c.899_902del p.(Lys300Serfs * 24) variant, and the newborn patient harbored a homozygous frameshift c.233_236del p.(Leu78Glnfs * 11) variant. Functional studies were conducted using sodium dodecyl-sulfate polyacrylamide gel electrophoresis, western blotting, and mass spectrometry analyses in both patient -derived and CRISPR-Cas9-generated cells. Results: Our investigations indicated that the USP14 variants correlated with reduced N -terminal methionine excision, along with profound alterations in proteasome, autophagy, and mitophagy activities. Conclusion: Biallelic USP14 variants in NDD patients perturbed protein degradation pathways, potentially contributing to disorder etiology. Altered UPS, autophagy, and mitophagy activities underscore the intricate interplay, elucidating their signi fi cance in maintaining proper protein homeostasis during brain development. (c) 2024 The Authors. Published by Elsevier Inc. on behalf of American College of Medical Genetics and Genomics. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

Pulmonary hypoplasia, Diaphragmatic anomalies, Anophthalmia/microphthalmia, and Cardiac defects (PDAC) syndrome is a genetically heterogeneous multiple congenital malformation syndrome. Although pathogenic variants in RARB and STRA6 are established causes of PDAC, many PDAC cases remain unsolved at the molecular level. Recently, we proposed biallelic WNT7B variants as a novel etiology based on several families with typical features of PDAC syndrome albeit with variable expressivity. Here, we report three patients from two families that share a novel founder variant in WNT7B (c.739C > T; Arg247Trp). The phenotypic expression of this variant ranges from typical PDAC features to isolated genitourinary anomalies. Similar to previously reported PDAC-associated WNT7B variants, this variant was found to significantly impair WNT7B signaling activity further corroborating its proposed pathogenicity. This report adds further evidence to WNT7B -related PDAC and expands its variable expressivity.

Ocular coloboma (OC) is a congenital disorder caused by the incomplete closure of the embryonic ocular fissure. OC can present as a simple anomaly or, in more complex forms, be associated with additional ocular abnormalities. It can occur in isolation or as part of a broader syndrome, exhibiting considerable genetic heterogeneity. Diagnostic yield for OC remains below 30%, indicating the need for further genetic exploration. Mutations in the Wnt receptor FZD5, which is expressed throughout eye development, have been linked to both isolated and complex forms of coloboma. These mutations often result in a dominant-negative effect, where the mutated FZD5 protein disrupts WNT signaling by sequestering WNT ligands. Here, we describe a case of syndromic bilateral OC with additional features such as microcornea, bone developmental anomalies, and mild intellectual disability. Whole exome sequencing revealed a homozygous rare missense variant in FZD5. Consistent with a loss-of-function effect, overexpressing of fzd5 mRNA harboring the missense variant in zebrafish embryos does not influence embryonic development, whereas overexpression of wild-type fzd5 mRNA results in body axis duplications. However, in vitro TOPFlash assays revealed that the missense variant only caused partial loss-of-function, behaving as a hypomorphic mutation. We further showed that the mutant protein still localized to the cell membrane and maintained proper conformation when modeled in silico, suggesting that the impairment lies in signal transduction. This hypothesis is further supported by the fact that the variant affects a highly conserved amino acid known to be crucial for protein-protein interactions.

Radiculomegaly is a rare dental anomaly characterised by the enlargement of the root canals of teeth. It is usually associated with oculo-facio-cardio-dental (OFCD) syndrome due to truncating variants in BCL-6 transcriptional corepressor (BCOR) (MIM*300485). We present the case of a 21-year-old female patient who was referred to genetics for a polymalformative syndrome including bilateral glaucoma and dental anomalies, especially radiculomegaly. Some others dysmorphic features were right superior lip notch, ogival palate, long philtrum, difficulty in pronation, caf & eacute;-au-lait spots, II-III toe bilateral syndactyly, and macrocephaly. Cone-beam CT confirmed radiculomegaly. The genetic analysis identified a heterozygous pathogenic variant NM_001123385.1:c.2093del (p.Pro698Glnfs*17) in the BCOR gene. After genetic diagnosis of OFCD syndrome, cardiac CT-scan revealed a large asymptomatic atrial septal defect that was subsequently surgically closed. Reviews of the literature have previously highlighted the prevalence of radiculomegaly in OFCD syndrome with a positive predictive value of 88.23% and a sensitivity of 75.94%. This case report highlights the importance of radiculomegaly as a clinical sign of OFCD syndrome, emphasising the rarity of non-syndromic radiculomegaly and the benefits of its diagnosis in clinical management, especially in cardiac screening.

AbstractAnophthalmia, microphthalmia and coloboma (AMC) comprise a spectrum of developmental eye disorders, accounting for approximately 20% of childhood visual impairment. While non-coding regulatory sequences are increasingly recognised as contributing to disease burden, characterising their impact on gene function and phenotype remains challenging. Furthermore, little is known of the nature and extent of their contribution to AMC phenotypes. We report two families with variants in or near MAB21L2, a gene where genetic variants are known to cause AMC in humans and animal models. The first proband, presenting with microphthalmia and coloboma, has a likely pathogenic missense variant (c.338 G > C; p.[Trp113Ser]), segregating within the family. The second individual, presenting with microphthalmia, carries an ~ 113.5 kb homozygous deletion 19.38 kb upstream of MAB21L2. Modelling of the deletion results in transient small lens and coloboma as well as midbrain anomalies in zebrafish, and microphthalmia and coloboma in Xenopus tropicalis. Using conservation analysis, we identify 15 non-coding conserved elements (CEs) within the deleted region, while ChIP-seq data from mouse embryonic stem cells demonstrates that two of these (CE13 and 14) bind Otx2, a protein with an established role in eye development. Targeted disruption of CE14 in Xenopus tropicalis recapitulates an ocular coloboma phenotype, supporting its role in eye development. Together, our data provides insights into regulatory mechanisms underlying eye development and highlights the importance of non-coding sequences as a source of genetic diagnoses in AMC.