# Reassessing Benign ASXL1 Variants in Bohring–Opitz Syndrome: The Role of Population Databases in Variant Reinterpretation

## TL;DR

This study uses structural modeling to reassess the significance of certain ASXL1 gene variants linked to Bohring–Opitz syndrome, showing how they might affect protein function.

## Contribution

The study introduces structural modeling as a tool to reinterpret ASXL1 missense variants previously classified as benign or uncertain.

## Key findings

- Structural modeling revealed that p.Q1448R alters polar interactions and introduces steric constraints near a conserved domain.
- Variants p.R265H and p.T297M disrupt stabilizing interactions in the DEUBAD domain, while p.Y358C affects a polar microenvironment.
- Except for p.T297M, all variants localized to evolutionarily conserved regions, suggesting potential functional impact.

## Abstract

Background/Objectives: ASXL1 is a chromatin-associated gene implicated in both hematologic malignancies and neurodevelopmental disorders, including Bohring–Opitz syndrome (BOS). Although many ASXL1 variants are well classified, a substantial proportion remain variants of uncertain significance (VUS), complicating molecular diagnosis and genetic counseling. The objective of this study was to evaluate whether structural context can inform the interpretation of selected ASXL1 missense variants in a clinical setting. Methods: We describe a 17-year-old female with clinical features consistent with BOS carrying the heterozygous ASXL1 variant p.Q1448R, currently classified as benign under ACMG/AMP guidelines. Three-dimensional in silico structural modeling was performed using AlphaFold3 and available crystallographic data. Three additional ASXL1 missense variants classified as VUS in ClinVar (p.R265H, p.T297M, and p.Y358C) were also analyzed. Evolutionary conservation, domain localization, and residue-level interactions were assessed. Results: Structural modeling indicated that the p.Q1448R substitution alters polar interactions and introduces a steric constraint near a conserved PHD-type zinc finger domain. Variants p.R265H and p.T297M affected stabilizing interactions within the DEUBAD, which is involved in BAP1 activation, while p.Y358C altered a polar microenvironment adjacent to a chromatin-interacting region. All analyzed variants, except p.T297M, localized to evolutionarily conserved regions. Conclusions: This study demonstrates that in silico structural analysis can provide complementary, domain-level insights for the interpretation of ASXL1 missense variants that remain classified as benign, likely benign or VUS under current frameworks. Such approaches may assist in prioritizing variants for further functional evaluation and refining molecular interpretation when experimental data are limited.