The transcription/export (TREX) complex is a conserved and ubiquitous model essential for gene expression and mRNA export from nucleus to cytoplasm. TREX is a multiprotein complex consisting of THO complex (THO complex subunits 1, 2, 5, 6, 7) and other proteins. Mutations in these proteins have been implicated in neurodevelopmental disorders. THOC2 gene that encodes for a THO complex subunit 2 have been reported in patients with non-syndromic X-linked intellectual disability (XLID). In this study, we performed G-banded karyotyping to identify chromosomal anomalies, whole exome sequencing to identify mutations and Sanger sequencing to study segregation of the potentially pathogenic mutation in the family. Clinical investigations of these two patients revealed truncal obesity, small penis, macroorchidism, dysmorphic features along with mild to moderate intellectual disability. Whole exome sequencing of both the male siblings and unaffected mother revealed a novel hemizygous c.1942G>T variant that resulted in a missense mutation p.Ala648Ser in THOC2. Our study expands the genotypes and clinical phenotypes known in THOC2 associated XLID that will aid in clinical diagnosis and management.