Objective Generalized epilepsy with febrile seizures plus (GEFS+) and severe myoclonic epilepsy in infancy (SMEI) are associated with sodium channel α-subunit type-1 gene (SCN1A) mutations, although previous studies failed to correlate the functional defects (funotypes) with phenotypes.Febrile seizures and partial epilepsy are the two common features of GEFS+ and SMEI.It is thus suspected that partial epilepsy with antecedent febrile seizures (PEFS+) may also be a phenotype of SCN1A abnormalities.Seizure aggravation induced by antiepileptic drugs (AEDs), a feature of SMEI, is considered here as a clue to find SCN1A mutations in isolated PEFS+ patients.Methods Two isolated PEFS+ patients with AEDs-induced seizure aggravation were screened for mutations in SCN1A, SCN2A, SCN1B, and GABRG2 using denaturing high-performance liquid chromatography and direct sequencing.The biophysiological features of two newly defined mutants were studied in transfected tsA201 cells using whole-cell patch-clamp technique.To characterize PEFS+ biologically, the genotype-funotype-phenotype relationships in all previously reported SCN1A mutations were analyzed.Results One PEFS+ patient each had heterozygous de novo mutations of c.2837G>A/p.R946H and c.5295 T>A/p.F1765L in SCN1A, which cause the loss of function of the mutants.With the defining of PEFS+, classifying the funotype in detail, and considering the subtle differences in the amino acid substitution, a close genotype-funotype-phenotype relationship was found in epilepsies with SCN1A mutations at a submolecular level.GEFS+ is clinically mild, with also mild channel dysfunction and mutations outside the pore region.PEFS+ is clinically similar to GEFS+, but distinct from GEFS+ in its funotype and AEDs-induced seizure aggravation.PEFS+ is much milder than SMEI clinically, similar to SMEI biophysiologically with features of loss of function but less in degree, structurally different from SMEI by substitutions without changes in polarity.Conclusions PEFS+ may be a distinct phenotype of SCN1A mutations.Sodium channel blocking-AEDs should be avoided in PEFS+ patients to prevent seizure aggravation.The submolecular variations in the sodium channel may determine the funotype and phenotype, suggesting further research on the relationship of a molecule to multiple phenotypes (or diseases), setting a submolecular stage in medicine.