Affective disorders, which can be categorized into depressive and bipolar disorders, represent a leading cause of disability worldwide. Despite their considerable prevalence, the intricate molecular and cellular mechanisms underlying these conditions remain elusive, mainly due to their complex etiologies and heterogeneous clinical presentations. Over the past years, the serotonergic system has emerged as a focal point in understanding the pathophysiological and therapeutic responses of affective disorders. Among the major regulators of this system, the serotonin transporter (SERT), which mediates serotonin neurotransmission and reuptake, represents a key target for pharmacological intervention in cases of depressive disorders. However, the extent to which impaired SERT contributes to the development of such disorders remains to be determined. In this study, we identified two previously uncharacterized SERT coding variants (SERT-N217S and SERT-A500T) significantly enriched among a cohort of 144 Danish patients presenting treatment-resistant chronic affective disorders along with a history of electroconvulsive therapy. Although their overall effects converge towards a partial loss-of-function phenotype, both SERT mutations seem to exert distinct molecular and functional perturbations. Indeed, while the SERT-A500T variant appears to compromise the catalytic activity of the transporter, the SERT-N217S missense mutation abolishes one glycosylation site present within the second extracellular loop of the SERT, thereby impairing its proper trafficking. Our results also suggest that the trafficking deficiency of the SERT-N217S could be amenable to pharmacological chaperoning by noribogaine. Collectively, our findings describe the first disease-associated loss-of-function SERT variants and implicate serotonergic disturbances arising from SERT dysfunction as a risk factor for chronic affective disorders.