Comprehensive study of 28 individuals with *SIN3A*-related disorder underscoring the associated mild cognitive and distinctive facial phenotype

Witteveen-Kolk syndrome (OMIM #613406), first described in 2016, is characterized by distinctive facial features, microcephaly, short stature, mild intellectual disability (ID), delayed cognitive and motor development, and subtle brain MRI anomalies. Frameshift and missense variants in the *SIN3A* gene (OMIM *607776*) have been associated with this syndrome, typically presenting with a mild clinical picture. The *SIN3A* gene, located on chromosome 15q24, is considered a critical gene in the atypical 15q24 microdeletion syndrome due to its location within the shortest region of overlap of various reported deletions. *SIN3A* encodes a transcriptional regulatory protein involved in the histone deacetylase complex, playing a crucial role in gene expression regulation. Prior research has indicated *SIN3A*'s involvement in cortical neurogenesis, suggesting that variants affecting its function may lead to a broad spectrum of developmental and neurological issues. This study aimed to comprehensively characterize the phenotype of *SIN3A*-related disorder, focusing on developmental and behavioral aspects and investigating genotype-phenotype correlations by identifying and analyzing an additional 28 patients with *SIN3A* variants.

The initial description of Witteveen-Kolk syndrome highlighted its key features, but further research was needed to fully understand its phenotypic spectrum. Previous studies have reported individual cases or small cohorts of patients with *SIN3A* variants, demonstrating a generally mild clinical presentation, but lacked the comprehensive analysis needed to fully define the associated developmental and behavioral traits. This gap in knowledge underscored the importance of this study in expanding the understanding of *SIN3A*-related neurodevelopmental disorders. The existing literature provided a foundation for understanding the role of *SIN3A* in development and neurological function, suggesting a link between *SIN3A* variants and a range of clinical manifestations. However, a detailed, multi-faceted characterization of the phenotype associated with *SIN3A* variants was needed to better inform clinical diagnosis and management.

This study involved the recruitment of 28 individuals with previously unreported *SIN3A* variants. Patient identification was facilitated through collaborations with the Deciphering Developmental Disorders (DDD) study, GeneMatcher, and DECIPHER databases. These resources enabled the identification of individuals with developmental delay/intellectual disability (DD/ID) and related phenotypes harboring rare *SIN3A* variants. Clinicians independently identified these individuals during routine diagnostic genetic testing. The DDD study application provided access to anonymized patient data. Clinicians then contacted families to invite participation. Comprehensive clinical analysis was performed, including medical history review, physical examinations, and observational analysis of behavioral characteristics supported by family-reported histories. Exome sequencing and variant filtering were performed using standard protocols at each institute. Only patients with class 4 or 5 *SIN3A* variants (likely pathogenic or pathogenic) according to the American College of Medical Genetics (ACMG) criteria were included. Informed consent for publication was obtained from all participants or their guardians. Patients with additional genetic diagnoses, chromosomal anomalies, or *SIN3A* variants of uncertain significance without clinical correlation were excluded. All identified variants were submitted to the DECIPHER database.

The study identified 28 patients with *SIN3A* variants classified as pathogenic or likely pathogenic. Twenty-seven variants were novel. The majority (24/28) were truncating variants predicted to cause loss-of-function. The remaining four variants included three missense variants and one large in-frame insertion. The mean age of the cohort was 8.2 years (17 males, 11 females). Cognitive assessment revealed that, among the 16 patients aged 8 years or older, 8 (50%) had mild intellectual disability, 4 (25%) had moderate intellectual disability, 1 (6%) had severe intellectual disability, and 4 (25%) showed no cognitive impairment. Other neurological features included seizures (4/28) and hypotonia (12/28). Behavioral problems were less common, with three out of 23 patients aged 2 years or older diagnosed with Autism Spectrum Disorder (ASD) and four with Attention Deficit Hyperactivity Disorder (ADHD). Growth abnormalities were also prevalent; 13/28 patients (46%) had microcephaly, 8/28 (29%) had low weight, and 5/28 (18%) had low height. Feeding difficulties were reported in 15/28 (54%) patients. Craniofacial dysmorphism was observed in 14/28 (50%) patients. Analysis of missense variants used a 3D model of mouse SIN3A, revealing that variants were predicted to disrupt critical functional domains involved in protein interactions, contributing to pathogenicity.

This comprehensive study significantly expands the understanding of the phenotypic spectrum associated with *SIN3A* variants. The findings confirm the association between *SIN3A* haploinsufficiency and mild intellectual disability, growth retardation, and characteristic facial features. The high prevalence of feeding difficulties highlights the need for early intervention in affected individuals. The identification of both truncating and missense variants, along with the detailed clinical characterization, enhances the genotype-phenotype correlation. The study’s findings underscore the importance of considering *SIN3A* as a potential candidate gene in individuals with developmental delay, intellectual disability, and associated features. The multidisciplinary approach, involving geneticists, pediatricians, and neurologists, is crucial for optimal patient management.

This study provides a comprehensive clinical and molecular characterization of 28 individuals with *SIN3A*-related disorder. It confirms the association of *SIN3A* variants with a range of developmental and neurological problems, including mild intellectual disability, growth retardation, craniofacial dysmorphism, and behavioral issues. The identification of novel variants expands the mutational spectrum of *SIN3A*, aiding in genetic diagnosis. The findings highlight the importance of multidisciplinary care for these patients and suggest that future research should focus on the functional consequences of the identified variants to better understand the disease mechanisms and develop potential therapeutic strategies.

The retrospective nature of the study limits the generalizability of findings. The limited number of patients with formally assessed IQ scores and the variable age range of the patients may affect the ability to establish precise genotype-phenotype correlations. The reliance on clinical assessment and family-reported information could have introduced some bias. Additionally, the study did not evaluate the long-term effects of *SIN3A* variants, necessitating further longitudinal studies.