Functional prediction of human hypothetical proteins remains a major project for biologist to carry out their further research in various life science and healthcare segments. Human chromosome 1 is the one which is very largest and has many hypothetical proteins. So it is attempted to find the function of some of the human chromosome 1 hypothetical proteins, the proteins are clustered based on their sequence similarities and identify the consensus sequence in those proteins. Using various prediction methods their functional annotations are carried out and a domain was predicted which is involved in the pathogenic functionality.