Significance Na _v 1.1 is a major Na _v subtype in the brain. Up to 900 nonsense and missense mutations in SCN1A , the coding gene for Na _v 1.1, have been identified in patients with epilepsy syndromes. Here, we report the cryo-EM structure of the human Na _v 1.1–β4 complex. Comparative structural analysis of hundreds of missense disease mutations in Na _v 1.1 and Na _v 1.5, whose structure is reported in the accompanying paper, reveals 70 loci that are common in these two channels. Several clusters, defined as the mutational hotspots, are identified and generally classified as the structural mutations and functional mutations. Our comparative structural analyses establish a framework for structure–function relationship dissection of Na _v disease variants and will facilitate development of precision medicine for various sodium channelopathies.