A case of DEE98, a rare developmental and epileptic encephalopathy related to previously reported the de novo missense mutation p.Arg908Gln in the ATP1A2 gene, is described. A girl examined first time in 11 months had microcephaly, severe mental and motor delay, strabismus, spastic paraparesis and pachypolymicrogyria on brain MRI that is atypical for DEE98. Epilepsy with polymorphic seizures started at the age of 15 months. There was a remission lasting 9 months, after which seizures renewed. DEE98 was diagnosed at the age of 2 years 9 months by exome sequencing verified by trio Sanger sequencing. Another finding from high-throughput exome sequencing were two previously undescribed heterozygous variants of uncertain pathogenicity in the SPART gene, which causes autosomal recessive spastic paraplegia type 20 (SPG20); Sanger sequencing confirmed the trans position of the variants. The common clinical sign with typical SPG20 was early spastic paraparesis with contractures; other symptoms did not coincide. Considering the phenotypic diversity of SPG20 and the possibility of a combination of two independent diseases, we performed an additional study of the pathogenicity of SPART variants at the mRNA level: pathogenicity was not confirmed, and there were no grounds to diagnose SPG20.