We identified two transcriptome-wide significant signals: TMEM106B for depression with anxiety (panel CMC DLPFC splicing, p = 1.23 × 10−6) and ATP2A1 for depression with weight gain (panel PsychENCODE, p = 1.34 × 10−6); no significant features were identified for TRD. This evidence concerns the gene ATP2A1 and major depressive disorder.