Rats of the WAG/Rij strain represent an accepted rodent model of childhood absence epilepsy. Thalamocortical (TC) neurons of WAG/Rij rats are characterized by an increased HCN1 expression, a negative shift in I_h activation curve, and an altered responsiveness of I_h to cAMP. We cloned HCN1 channels from WAG/Rij rat thalamic cDNA libraries (WAG-HCN1), and found an N-terminal deletion of 37 amino acids. In addition, WAG-HCN1 had a stretch of six amino acids, directly following the deletion, where the wild-type sequence (GNSVCF) was changed to a polyserine motif. These alterations were found solely in thalamic mRNA, but not genomic DNA. The truncated WAG-HCN1 was detected late postnatal in WAG/Rij rats and was not passed on to rats obtained from pairing WAG/Rij and non-epileptic ACI rats. Heterologous expression in Xenopus oocytes revealed 2.1-fold increased current amplitude of WAG-HCN1 compared to rat HCN1. While WAG-HCN1 channels revealed unaltered current kinetics and unchanged regulation by protein kinases, fluorescence imaging demonstrated stronger surface expression of WAG-HCN1. Using co-expression experiments, we found that WAG-HCN1 channels suppressed heteromeric HCN2 and HCN4 currents. Moreover, heteromeric channels of WAG-HCN1 with HCN2 showed a negative shift in the activation curve and an altered cAMP sensitivity. Functional studies revealed that the gain-of-function of WAG-HCN1 is not caused by the N-terminal deletion alone, thus requiring a change of the N-terminal GNSVCF motif. Our findings explain previous observations in WAG/Rij TC neurons and indicate that WAG-HCN1 may contribute to the genesis of absence seizures in WAG/Rij rats.