Two cases of TBL1XR1 heterozygous variants in children: a new splicing site variant identification and functional analysis through molecular docking and molecular dynamics simulation

Transducin β-like 1 X-linked receptor 1 (TBL1XR1) protein is an important component of NCoR/SMRT complex. The variants of TBL1XR1 are associated with Pierpont syndrome (PS) and developmental delay (DD). This study aimed to discover new TBL1XR1 variants, their clinical manifestations, and protein-level changes. Whole-exome sequencing was used to identify patients with TBL1XR1 variants in 2024. Minigene assay was used to investigate specific splice site, which was further validated by Sanger sequencing. Structural changes in the TBL1XR1 protein were analyzed using PyMOL and molecular dynamics (MD) simulations. Potential binding partners were predicted via Genecards, STRING, and Cytoscape, while molecular docking was employed to assess how variants affect protein complex interactions. Two novel TBL1XR1 variants (c.1048-8_1049del and c.865-7A>G) were identified in two patients. Patient 1 exhibits global developmental delay (GDD), while patient 2 displays with facial dysmorphism and autism spectrum disorder. c.865-7A>G is a non-canonical splicing variant causing abnormal mRNA splicing. SpliceAI and RDDC predicted its splicing pattern. Minigene analysis found a 6 bp (TCTCAG) insertion in mRNA, leading to two amino acid (SQ) insertion in the TBL1XR1 protein. Therefore, P2 was diagnosed with PS. Variant changed the local hydrogen bond network and electrostatic potential. MD simulations showed variant changed the conformation of TBL1XR1 protein. Protein–protein interaction analysis selected NCOR1 for docking with TBL1XR1. Their interaction was reduced after the insertion of SQ, which may contribute to the occurrence of PS. This study reported two patients manifesting with GDD and PS, which were identified with two novel variants of TBL1XR1 (c.1048-8_1049del, p.(N350X)) and (c.865-7A>G, p.K288_T289insSQ), respectively. c.865-7A>G variant might lead to PS by reducing its interaction with NCOR1.