Deletion of a phenylalanine at position 1617 (delF1617) in the extracellular linker between the S3 and S4 segments in domain IV of the human heart Na channel (hH1a) has been tentatively associated with the long QT syndrome, LQT3. In a mammalian cell expression system we compared whole-cell currents, gating currents and single channel currents of delF1617 to wild-type hH1a. The half-points of the peak activation-voltage curve for the two channels were similar as were the deactivation time constants at hyperpolarized test potentials. However, delF1617 demonstrated a significant negative shift of -7 mV in the half-point of the voltage-dependent Na channel availability curve compared to wild-type. In addition, both the time course of decay of I_Na and two-pulse development of inactivation of delF1617 were faster at negative test potentials while they tended to be slower at positive potentials compared to wild-type. Mean channel open times for delF1617 were shorter at potentials less than 0 mV while they were longer than wild-type at potentials greater than 0 mV. Using Anthopleurin-A toxin, a site-3 toxin that inhibits movement of the S4 segment in domain IV (S4-DIV), we found that the gating charge contributed by the S4-DIV in delF1617 was reduced by 37% compared to that from wild-type. We conclude that deletion of a single amino acid in the S3-S4 linker of domain IV alters the voltage dependence of fast inactivation by a reduction in the gating charge contributed by S4-DIV, and can cause either a gain or loss of sodium current depending upon the membrane potential.