Single Nucleotide Polymorphisms (SNPs) are the most abundant sequence variations encountered in a genome and play a major role in understanding of the genetic basis of many complex human diseases. The genetics of human phenotype variation could be understood by knowing the functions of these SNPs. It is still a major challenge to identify the functional SNPs in a disease-related gene. In this work, we have analyzed the genetic variation that can alter the expression and function of GALC gene using computational methods. Of the total 1615 SNPs, 12 were found to be nonsynonymous SNPs (nsSNPs). Among these 12 nsSNPs, 3 are deleterious analyzed by SIFT program. 4 nsSNPs are damaged found by PolyPhen. 3 nsSNPs that were observed to be deleterious and damaged by using both SIFT and PolyPhen program. From this a comparison of stabilizing residues are done by RMSD of native and mutant proteins, higher the RMSD value is the more deviation between two structure, so we propose that an nsSNP rs73312829 with a mutation of Arginine to Cystine at position 79 could be the main target mutation for the Krabbe disease.