Fibroblast growth factor homologous factors (FHFs) belong to a subclass of Fibroblast Growth Factor (FGF) family owing to their high sequence and structural similarities with FGFs. However, despite these similarities, there are properties which set them apart from FGFs. FHFs lack the secretion signal sequence unlike other FGF members, except FGF1 and 2. It may be possible that FGF1 partially unfolds and secretes outside the cell, suggesting that lower stability of protein may be trade-off for secretion. Unlike FGFs, FHFs are not able to bind to FGF receptors (FGFRs) and trigger a cascade of cellular events. FHFs have been implicated in development of mammalian nervous system by binding to intracellular domains of voltage-gated sodium channels (VGSCs), neuronal MAP kinase scaffold protein and islet-brain-2 (IB2). The two amino acids Arg-52 and Val95 are conserved in all FHFs and mutation of these residues lead to its inability to bind with VGSC/IB2. However, it is not clear whether the loss of binding is due to destabilization of the protein on mutation leading to partial denaturation or due to involvement of Arg52 and Val95 in conferring functionality to FHFs. In the present study, we have mutated two conserved residues of FHF2 (Arg-52 and Val-95) with its corresponding FGF counterpart amino acids and studied the effects of the mutations on the overall stability and conformations of the protein using several biophysical methods like isothermal equilibrium denaturation study, ANS fluorescence, intrinsic fluorescence, acrylamide quenching, circular dichroism studies as well as using computational approaches.