Treatment resistant epileptic encephalopathy (EE) in childhood in a significant amount due to genetic damage or congenital abnormalities of the brain. The literature described a rare microcephalic-capillary malformation syndrome (Microcephaly-capillary malformation, MIC-CAP), manifested from the first month of life by the early onset of treatment-resistant epilepsy, severe progressive microcephaly, spastic tetraparesis, severe delay in psychomotor development, multiple, small-sized capillary angiomas on the body and underdevelopment of the fingers. The boy was diagnosed with a previously described variant of the nucleotide sequence in exon 2 of the STAMBP chr2 gene:74058171rs781694797 188A>G in the homozygous state, leading to the replacement of the amino acid p.Tyr63Cys in 63 protein position. This type of mutation chr2:74058171rs781694797 188A>G was also detected in the father and mother in the heterozygous state. This variant is considered as pathogenic, related to the patient’s phenotype. The article presents a literature review of this syndrome and the case report.