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CSMD1 is a gene involved in various biological processes and is highly expressed in the central nervous system, where it plays a key role in complement activity, brain circuit development, and cognitive function. It has been implicated as a susceptibility gene for schizophrenia and a causative factor in developmental epileptic encephalopathy, neurodevelopmental disorders, and intellectual disability. However, no MIM phenotype number has been assigned to CSMD1 for a specific disorder. Here, we report an individual presenting with moderate intellectual disability, anxiety disorder, obsessive–compulsive personality traits, and facial dysmorphisms. Trio-based whole-exome sequencing (WES) identified two heterozygous CSMD1 variants, c.8095A>G and c.5315T>C, both classified as variants of uncertain significance (VUS) according to ACMG criteria. Computational analysis using the DOMINO tool supported an autosomal recessive inheritance model for CSMD1. This study contributes to the growing evidence linking CSMD1 to neurodevelopmental phenotypes, highlighting the need for further investigations to clarify its pathogenic role.

PHF21A (PHD finger protein 21A) gene, located in the short arm of chromosome 11, encodes for BHC80, a component of the Lysine Specific Demethylase 1, Corepressor of REST (LSD1-CoREST) complex. BHC80 is mainly expressed in the human fetal brain and skeletal muscle and acts as a modulator of several neuronal genes during embryogenesis. Data from literature relates PHF21A variants with Potocki–Shaffer Syndrome (PSS), a contiguous gene deletion disorder caused by the haploinsufficiency of PHF21A, ALX4, and EXT2 genes. Clinical cardinal features of PSS syndrome are multiple exostoses (due to the EXT2 involvement), biparietal foramina (due to the ALX4 involvement), intellectual disability, and craniofacial anomalies (due to the PHF21A involvement). To date, to the best of our knowledge, a detailed description of PHF21A-related disorder clinical phenotype is not described in the literature; in fact, only 14 subjects with microdeletion frameshift or nonsense variants concerning only PHF21A gene have been reported. All reported cases did not present ALX4 or EXT2 variants, and their clinical features did not fit with PSS diagnosis. Herein, by using Exome sequencing, and Sanger sequencing of the region of interest, we describe a case of a child with a paternally inherited (mosaicism of 5%) truncating variant of the PHF21A gene (c.649_650del; p.Gln217ValfsTer6), and discuss the new evidence. In conclusion, these patients showed varied clinical expressions, mainly including the presence of intellectual disability, epilepsy, hypotonia, and dysmorphic features. Our study contributes to describing the genotype–phenotype spectrum of patients with PHF21A-related disorder; however, the limited data in the literature have been unable to provide a precise diagnostic protocol for patients with PHF21A-related disorder.

E3 ubiquitin protein ligase encoded by ARIH2 gene catalyses the ubiquitination of target proteins and plays a crucial role in posttranslational modifications across various cellular processes. As prior documented, mutations in genes involved in the ubiquitination process are often associated with autism spectrum disorder (ASD) and/or intellectual disability (ID). In the current study, a de novo heterozygous mutation was identified in the splicing intronic region adjacent to the last exon of the ARIH2 gene using whole exome sequencing (WES). We hypothesize that this mutation, found in an ASD/ID patient, disrupts the protein Ariadne domain which is involved in the autoinhibition of ARIH2 enzyme. Predictive analyses elucidated the implications of the novel mutation in the splicing process and confirmed its autosomal dominant inheritance model. Nevertheless, we cannot exclude the possibility that other genetic factors, undetectable by WES, such as mutations in non-coding regions and polygenic risk in inter-allelic complementation, may contribute to the patient's phenotype. This work aims to suggest potential relationship between the detected mutation in ARIH2 gene and both ASD and ID, even though functional studies combined with new sequencing approaches will be necessary to validate this hypothesis.

The 26S proteasome is a large, ATP-dependent proteolytic complex responsible for degrading ubiquitinated proteins in eukaryotic cells. It plays a crucial role in maintaining cellular protein homeostasis by selectively eliminating misfolded, damaged, or regulatory proteins marked for degradation. In this study, whole-exome sequencing (WES) was performed on an individual presenting with developmental delay and mild intellectual disability, as well as on both of his unaffected parents. This analysis identified a de novo variant, c.959C>G (p.Pro320Arg), in the PSMC5 gene. As predicted, this gene shows a very likely autosomal dominant inheritance pattern. Notably, PSMC5 has not previously been associated with any phenotype in the OMIM database. This variant was recently submitted to the ClinVar database as a variant of uncertain significance (VUS) and remains absent in both gnomAD and dbSNP. Notably, it has been identified in six unrelated individuals presenting with clinical features comparable to those observed in the patient described in this study. Multiple in silico prediction tools classified the variant as pathogenic, and a PhyloP conservation score supports strong evolutionary conservation of the mutated nucleotide. Protein structure predictions using the AlphaFold3 algorithm revealed notable structural differences between the mutant and wild-type PSMC5 proteins. We hypothesize that the p.Pro320Arg substitution alters the structure and function of PSMC5 as a regulatory subunit of the 26S proteasome, potentially impairing the stability and activity of the entire complex. Although functional studies are imperative, this study contributes to a deeper understanding of PSMC5, expands the spectrum of associated neurodevelopmental phenotypes, and highlights its potential as a therapeutic target. Furthermore, this study resulted in the submission of the identified variant to the ClinVar database (SCV006083352), where it was classified as pathogenic.

Tooth agenesis (TA), the congenital absence of one or more teeth, is the most common manifestation of defective dental morphogenesis in humans. TA can occur as an isolated (non-syndromic) condition or as part of a broader syndromic presentation. In this review, we analyzed a total of 73 manuscripts to provide a comprehensive update on the genetic landscape of TA. To investigate the genes, variants, and associated phenotypes, we reviewed data from curated databases including Human Phenotype Ontology (HPO), OMIM, ClinVar and MalaCards. Based on the current evidence, the genes most frequently implicated in TA are MSX1, EDA, and PAX9. However, chromosomal abnormalities, such as those seen in Down syndrome and Williams syndrome, along with structural variations (e.g., deletions and duplications), also contribute significantly to TA etiology. The most involved pathways include TNF receptor binding, encompassing genes such as EDA, EDA2R, EDAR, and EDARADD, and the mTOR signaling pathway, which includes AXIN2, FGFR1, LRP6, WNT10A, and WNT10B. The aim of this review is to provide an critical synthesis of the genetic mechanisms underlying TA, highlighting the contribution of major signaling pathways, regulatory networks, and emerging molecular insights that may inform diagnostic and therapeutic advances.

Background and Objectives: Autism spectrum disorder (ASD) is a neurodevelopmental disorder that belong to genetic and epigenetic mechanism. Despite the recent advantages in next-generation sequencing (NGS) technology, ASD etiology is still unclear. Materials and Methods: In this study, we tested a customized target genetic panel consisting of 74 genes in a cohort of 53 ASD individuals. The tested panel was designed from the SFARI database. Results: Among 53 patients analyzed using a targeted genetic panel, 102 rare variants were identified, with nine individuals carrying likely pathogenic or pathogenic variants considered genetically “positive.” We identified six de novo variants across five genes (POGZ 2 variants, NCOR1, CHD2, ADNP, and GRIN2B), including two variants of uncertain significance in POGZ p.Thr451Met and NCOR1 p.Glu1137Lys, one likely pathogenic variant in GRIN2B p.Leu714Gln, and three pathogenic variants in POGZ p.Leu775Valfs32, CHD2 p.Thr1108Metfs8, and ADNP p.Pro5Argfs*2. Conclusions: This study presents a comprehensive characterization of the targeted gene panel used for genetic analysis, while critically evaluating its diagnostic limitations within the context of contemporary genomic approaches. A pivotal accomplishment of this study was the ClinVar submission of novel de novo variants which expands the documented mutational spectrum of ASD-associated genes and enhances future diagnostic interpretation.

Glycosylation is a post-translational modification essential for proper protein folding and function, with significant roles in diverse biological processes, including neurogenesis. MAN2A2 enzyme is required for proper N -glycan trimming/maturation in the N -glycosylation pathway. Whole-exome sequencing of a trio revealed two potentially causative variants in the MAN2A2 gene in a patient with autism spectrum disorder (ASD) and cognitive delay. The first variant, c.1679G > A (p.Arg560Gln), was inherited from the unaffected father. It is located within the alpha-mannosidase middle functional domain, a region essential for mannose metabolism and alpha-mannosidase enzymatic activity. The second variant, c.3292C > T (p.Gln1098Ter), was inherited from the mother and it generated a premature stop codon. These variants resulted in a compound heterozygous condition in the patient. Prediction using the DOMINO tool suggested an autosomal recessive inheritance pattern. Notably, the MAN2A2 gene is highly expressed in several brain regions. The encoded enzyme, an alpha-mannosidase, is localized to the Golgi apparatus, the cellular organelle where the processing and maturation of N -glycans occurs. In silico analyses consistently classified both variants as likely pathogenic, supported by structural prediction analyses that indicated significant disruptions in protein architecture. Glycosylation analyses demonstrated impaired N -glycosylation, evidenced by the accumulation of immature serum glycoprotein N -glycans including disease-specific hybrid-type species. Further investigations are essential to elucidate the role of this gene in ASD and cognitive delay.

Background and Objectives: Zinc finger proteins are important transcription factors that regulate gene expression and play a critical role in neurodevelopment including autism spectrum disorders (ASDs). They are involved in a variety of cellular processes, including cell proliferation, differentiation, and apoptosis. Materials and Methods: Whole-exome sequencing (WES) analysis on a patient diagnosed with ASD. Results: Sequencing identified a homozygous insertion causing a stop codon, resulting in the removal of several functional domains including the zinc finger C2HC/C3H type of the ZC2HC1C protein. To date, no MIM entry has been assigned to the detected gene. In silico predictions described the variant as likely pathogenic, indicating an autosomal recessive inheritance pattern. In this study, we hypothesize that this homozygous mutation disrupts protein function and may represent a susceptibility gene for autism. The parents and the patient’s sister were healthy and carry the variant in the heterozygous condition. This gene is expressed in brain tissues showing high expression in both the choroid plexus (ChP) and midbrain, whose dysfunctions, as reported, may lead to ASD. Moreover, predictive pathway analyses indicated the probable involvement of this gene in primary cilia development. This process has been frequently linked to neurodevelopmental impairments, such as autism, as documented in previous studies. Conclusions: Further analyses are needed via in vitro functional assays or by ZC2HC1C gene knockout to validate its functional role.

Recessive mutations in the POLR3A gene cause POLR3-HLD (the second-most-common form of childhood-onset hypomyelinating leukodystrophy), a neurodegenerative disorder featuring deficient cerebral myelin formation. To date, more than 140 POLR3A (NM_007055.3) missense mutations are related to the pathogenesis of POLR3-related leukodystrophy and spastic ataxia. Herein, in a cohort of five families from Sicily (Italy), we detected two cases of patients affected by POLR3-related leukodystrophy, one due to a compound heterozygous mutation in the POLR3A gene, including a previously undescribed missense mutation (c.328A > G (p.Lys110Glu)). Our study used an in-house NGS gene panel comprising 41 known leukodystrophy genes. Successively, we used a predictive test supporting the missense mutation as causative of disease, thus this mutation can be considered “Likely Pathogenic” and could be as a new pathogenetic mutation of the POLR3A gene causing a severe form of POLR3-HLD.

Zinc finger proteins are frequently implicated in a wide range of neurodevelopmental disorders (NDDs). In this study, we report a case of mild intellectual disability (ID), global developmental delay (GDD), and developmental coordination disorder (DCD) in an individual with unaffected parents. Trio-based whole-exome sequencing (WES) identified a de novo variant (c.1530dup, p.Glu511ArgfsTer16) in the ZNF496 gene of the proband. According to ACMG guidelines, this novel variant is classified as pathogenic. It creates a frameshift that introduces a premature stop codon, resulting in a truncated protein of 525 amino acids (compared to the wild-type 587 residues). Notably, NMDEscPredictor analysis predicted that the transcript escapes nonsense-mediated decay (NMD) despite the frameshift. Computational analyses suggest the potential pathogenetic effects of the identified variant. As documented, ZNF496 interacts with JARID2, a gene associated with NDDs, ID and facial dysmorphism (MIM: #620098). In silico analyses suggest that the identified mutation disrupts this interaction by deleting ZNF496’s C2H2 domain, potentially dysregulating JARID2 target genes. To our knowledge, this is the first reported association between ZNF496 and NDDs, and the variant has been submitted to the ClinVar database (SCV006100880). Functional studies are imperative to validate ZNF496’s role in NDDs and confirm the mutation’s impact on ZNF496-JARID2 interactions.