Anorectal malformations (ARM) are individually common, but Congenital Pouch Colon (CPC) is a rare anorectal anomaly that causes a dilated pouch and communication with the genitourinary tract. In this work, we attempted to identify de novo heterozygous missense variants, and further discovered variants of unknown significance (VUS) which could provide insights into CPC manifestation. From whole exome sequencing (WES) performed earlier, the trio exomes were analyzed from those who were admitted to J.K. Lon Hospital, SMS Medical College, Jaipur, India, between 2011 and 2017. The proband exomes were compared with the unaffected sibling/family members, and we sought to ask whether any variants of significant interest were associated with the CPC manifestation. The WES data from a total of 64 samples including 16 affected neonates (11 male and 5 female) with their parents and unaffected siblings were used for the study. We examined the role of rare allelic variation associated with CPC in a 16 proband/parent trio family, comparing the mutations to those of their unaffected parents/siblings. We also performed RNA-Seq as a pilot to find whether or not the genes harboring these mutations were differentially expressed. Our study revealed extremely rare variants, viz.,TAF1B,MUC5BandFRG1, which were further validated for disease-causing mutations associated with CPC, further closing the gaps of surgery by bringing intervention in therapies.