We conducted variable threshold gene-based burden tests for all nonsynonymous variants imputed with MTFS sequences with minimac RSQ > .3, a conventional cutoff. After considering only genes that had at least two called SNPs with a burden allele count of three or greater, the number of genes tested ranged from 16,070 to 16,263, with corresponding Bonferroni cutoffs of ~2.8e-6. Four genes were significantly associated with an endophenotype and are displayed in Table 4. The variable threshold collapsing and multivariante count (VTCMC) test identified two genes, annexin A3 (ANXA3) associated with antisaccade, and solute carrier family 27 (fatty acid transporter) member 6 (SLC27A6) associated with aversive difference startle modulation. The SKAT test also identified two genes, GBX2 and KIF18A, as significantly associated with EEG beta power and pleasant difference startle modulation, respectively.
