Telomere maintenance 2 (TELO2) is a gene located at 16p13.3 which encodes a protein that functions as ‘S-phase checkpoint’ in the cell cycle and may play a role in DNA repair. Loss of function in TELO2 has been recently reported as a novel gene associated with autosomal recessive syndromic form of learning disability characterized by microcephaly, abnormal balance, involuntary movements, vision and auditory impairments, and some dysmorphic facial features. We report a pair of sisters, aged 9 and 6 years who were found to have compound heterozygous mutations in TELO2 gene. The elder sibling presented with refractory seizures since infancy, not fully responsive to multiple oral anti-convulsants, steroids and even ketogenic diet, but her younger sibling only has hypotonia with global developmental delay. Whole exome sequencing discovered c.901C>T:p.(Gln301*), a ‘novel mutation’ and c.1826G>A:p.(Arg609His) mutations in both sisters. Our family showed that TELO2 mutations can be associated with intra-familial phenotypic variable expression and early onset epilepsy can be a feature in more severely affected individuals.