Reassessing Benign ASXL1 Variants in Bohring-Opitz Syndrome: The Role of Population Databases in Variant...

Area of Science:

• Genetics
• Molecular Biology
• Bioinformatics

Background:

• ASXL1 gene mutations are linked to hematologic malignancies and neurodevelopmental disorders like Bohring-Opitz syndrome (BOS).
• Many ASXL1 variants are classified, but a significant number remain variants of uncertain significance (VUS), complicating clinical diagnosis and genetic counseling.
• Interpreting the pathogenicity of ASXL1 missense variants is crucial for accurate molecular diagnosis.

Purpose of the Study:

• To evaluate the utility of structural context in interpreting selected ASXL1 missense variants.
• To assess if in silico structural modeling can inform the classification of ASXL1 variants currently deemed benign or VUS.
• To provide complementary insights for refining molecular interpretation when experimental data is limited.

Main Methods:

• In silico 3D structural modeling using AlphaFold3 and crystallographic data for ASXL1 variants.
• Analysis of a patient with Bohring-Opitz syndrome (BOS) carrying the ASXL1 p.Q1448R variant.
• Assessment of evolutionary conservation, domain localization, and residue-level interactions for selected ASXL1 missense variants (p.Q1448R, p.R265H, p.T297M, p.Y358C).

Main Results:

• The ASXL1 p.Q1448R variant was predicted to alter polar interactions and introduce steric constraints near a zinc finger domain.
• Variants p.R265H and p.T297M impacted stabilizing interactions in the DEUBAD domain, crucial for BAP1 activation.
• Variant p.Y358C affected a polar microenvironment near a chromatin-interacting region; most variants were in conserved regions.

Conclusions:

• In silico structural analysis offers valuable domain-level insights for interpreting ASXL1 missense variants.
• This approach can aid in classifying variants currently categorized as benign, likely benign, or VUS.
• Structural modeling can help prioritize variants for functional studies and improve molecular interpretation in cases with limited experimental data.