Characterizing ARID1B-related disorders and variants of uncertain significance using DNA methylation

Sequence variants in ARID1B, a subunit of the BRG1 (BRM)-associated factors (BAF) complex, are often challenging to classify clinically due to the broad phenotypic spectrum of ARID1B-related disorders (ARID1B-RD). Our previous work has shown that pathogenic variants in epigenetic regulatory genes are associated with DNA methylation (DNAm) signatures, which have proven diagnostic utility for variant classification. Given the role of ARID1B in chromatin remodeling, we profiled whole-blood DNAm for 22 individuals with ARID1B variants and 240 typically developing individuals using Illumina's Infinium EPIC array. We identified a unique DNAm signature for ARID1B-RD of 160 CpG sites (FDR < 0.05; Δβ > 5%) in six individuals with ARID1B-RD, validating this signature in two more individuals with ARID1B-RD and demonstrating its diagnostic utility by classifying 14 additional individuals with ARID1B variants. Collectively, our findings support the use of DNAm to clarify the interpretation of ARID1B variants, particularly missense and in-frame variants that are rarely reported and challenging to classify, as well as truncating variants in exons 1 and 3 that have been previously reported in unaffected individuals. Comparing the DNAm profiles of individuals with ARID1B-RD to individuals with other disorders of the BAF complex, we saw a spectrum of shared DNAm changes. The ARID1B-RD DNAm signature was able to distinguish the DNAm profiles of individuals with pathogenic variants in ARID1B from those with pathogenic variants in SMARCA2, ARID1A, and ATRX. However, it was not able to distinguish between individuals with pathogenic variants in ARID1B and SMARCB1.