We identified two risk genes, SLC2A1 for EHR-defined depression (OR = 6.01, 95% CI = 3.03–11.94, p = 2.96 × 10−7) and NOG (OR = 8.43, 95% CI = 3.50–20.33, p = 2.03 × 10−6) for Psypsy-defined depression through damaging missense variant burden association analysis in UKB whole-exome sequencing data (Supplementary Data 18a, b and Supplementary Fig. 8). The gene discussed is SLC2A1; the disease is depressive symptom measurement.