SATB2-associated syndrome (SAS) is a multisystemic disorder characterized by developmental delay, moderate to profound intellectual disability, speech delay and/or absent speech, behavioral issues such as autistic tendencies, agitation or aggressive outbursts, self-injury, impulsivity, hyperactivity, anxiety and sleeping difficulties. Alterations in the SATB2 gene have been identified as pathogenic causes of SAS. No formal clinical diagnostic criteria have been established for SAS, and molecular disruption of SATB2 is necessary to confirm the diagnosis. To investigate the molecular pathogenesis of five sporadic patients with intellectual disability, and to delineate the comprehensive clinical characteristics of SAS patients. Whole-exome sequencing analysis was performed in five unrelated patients, and RNA analysis was employed to validate the impact of genetic variation on aberrant splicing. Five SATB2 variants were identified, three of which were novel, including three frameshift variants, one nonsense variant, and a missense variant resulting in aberrant splicing was verified by RNA analysis. A comparative analysis was conducted between the clinical features of our patients and those reported in the literature. In addition to intellectual disability and impaired speech, abnormalities in palmar creases and postnatal growth delay were highlighted as clinically significant features for the diagnosis of SAS. Language regression, as well as joints and fingers abnormalities were also observed in our cohort. Our findings demonstrate that effective mRNA analysis is helpful for understanding the pathogenic mechanisms of novel variants. This study broadens the genetic and phenotypic spectrum of SAS and enhances our knowledge to facilitate accurate genetic counseling and appropriate treatment options.

SATB2-associated syndrome is an autosomal dominant neurodevelopmental syndrome caused by genetic alterations in the transcription factor SATB2. The associated phenotype is variable, and genotype-phenotype correlation studies have not yet been able to explain differences in severity and symptoms across affected individuals. While haploinsufficiency is the most often described disease mechanism, with the majority of variants consisting of whole- or partial-gene deletions and protein truncating variants with predicted loss of function, approximately one-third of affected individuals carry a SATB2 missense variant with an unknown effect. In this study, we sought to functionally characterize these missense variants to uncover associated pathogenic mechanisms. We combined a set of human cell-based experiments to screen 31 etiological SATB2 missense variants for effects on nuclear localization, global chromatin binding, and transcriptional activity. Our data indicate partial loss-of-function effects for most of the studied missense variants but identify at least eight variants with increased SATB2 function showing a combination (or subset) of features that include stronger co-localization with DNA, decreased nuclear protein mobility suggesting increased overall chromatin binding, and maintained or increased transcriptional activity. These results demonstrate that phenotypes associated with variants in SATB2 may have distinct underlying disease mechanisms, and the data could provide a resource for future studies investigating disease variability and potential therapies for this condition.

SATB2-associated syndrome (SAS), also known as Glass syndrome, is a neurodevelopmental disorder (NDD) characterized by intellectual disability, developmental delay, absent or limited speech, and distinctive craniofacial and dental anomalies. It is caused by autosomal dominant pathogenic variants in the SATB2 gene, which plays a crucial role in brain, dental, and jaw development. Due to its variable phenotype, clinical diagnosis can be challenging, necessitating genetic confirmation. We present six new cases of SAS with SATB2 germline variants identified through next generation sequencing (NGS) technologies, expanding the known genetic and clinical spectrum of the syndrome. Detailed clinical phenotyping was performed for all patients. Our cohort exhibits a broad range of clinical manifestations consistent with SAS, encompassing severe intellectual disability, profound speech delay, various palatal and dental abnormalities. We report the oldest adult patient (56 years old) carrying an in-frame duplication, and a pediatric patient with a missense variant who presented a significant reduction in visual acuity, likely of neurological or cortical origin, in the absence of ophthalmological abnormalities. SATB2 variants include three missenses, two in-frame deletion/duplication and one frameshift variant, several of which are novel and classified as likely pathogenic or pathogenic according to ACMG guidelines. This report provides new clinical and genetic insights into the landscape of SAS. Our findings confirm the phenotypic heterogeneity of SAS and highlight the critical role of comprehensive genetic testing for accurate diagnosis in NDD patients.

SATB2-associated syndrome (SAS) is characterized by intellectual disability, neurodevelopmental disorders, cleft palate, and dental abnormalities. SAS is caused by variants in the special AT-rich sequence-binding protein 2 (SATB2), which encodes a transcription factor containing two CUT domains and a homeobox (HOX) domain. Here, we report the case of a 16-year-old male diagnosed with SAS using exome sequencing and investigate the functional consequences of previously reported SATB2 variants, including those in this case. The patient carried a heterozygous missense variant (c.1147G>C, p.A383P) in SATB2, which was predicted to be pathogenic in silico but was absent from public databases. Immunofluorescence assays demonstrated that SATB2 proteins with variants in the CUT2 domain predominantly localized to the cytoplasm. Functional analysis further revealed that wild-type SATB2 increased the activity of the Msx1 promoter, which is involved in palatogenesis and tooth development, whereas variants in the CUT1 domain disrupted this transcriptional activation. These findings suggest that the nuclear localization signal of SATB2 resides in the CUT2 domain and that Msx1 promoter impairment owing to SATB2 variants may contribute to the pathogenesis of cleft palate and tooth agenesis in SAS. This research highlights a novel pathogenic variant and the functional implications for understanding SAS.

Special AT-rich sequence-binding protein 2 (SATB2) is a master regulator of gene expression. Mutations of the SATB2 gene results in the SATB2-associated syndrome (SAS), a genetic disorder characterized by neurodevelopmental disabilities and autism-related phenotype. The importance of plasma as an indicator of SAS phenotypes is unknown. We aim to investigate if pathogenic variants in SATB2 are associated with alteration to relevant pathways in the plasma of SAS patients and identify key differentially regulated proteins which may serve as biomarkers to improve diagnostic and future pharmacological approaches. We used well-validated proteomic technologies to determine the proteomic profile of plasma from SAS patients compared to healthy control subjects. Bioinformatical analysis was performed to identify significant proteins and functionally enriched pathways. We identified differentially expressed proteins in the plasma of SAS patients that are significantly involved in metabolism-related pathways. Energy metabolism, glucose metabolism and vitamin metabolism pathways are significantly enriched in SAS patients as compared to healthy controls. Our study linked SATB2 mutations to the impairment of plasma proteins involved in different metabolic pathways in SAS patients.