Assessing the pathogenicity of missense single nucleotide polymorphisms in the human FUCA1 gene using multiple bioinformatics tools

INTRODUCTION: Fucosidosis is a rare lysosomal storage disorder caused by mutations in the FUCA1 gene leading to a deficiency in α-L-fucosidase. This study aimed to investigate the pathogenic missense mutations in the FUCA1 gene and their effects on protein stability using various bioinformatics tools.
METHODS: Initially, 438 missense mutations were retrieved from the NCBI database, of which 43 mutations were identified by SIFT. The impact of these mutations on protein stability was assessed using I-MUTANT2.0 and MUPRO. Additionally, protein flexibility was analyzed using MEDUSA.
RESULTS: Among the 43 mutations, SIFT predicted 20 mutations as "deleterious". PANTHER database predicted 21 mutations as "probably damaging" and 4 mutations as "possibly damaging", PolyPhen-2 tool identified 14 mutations as "probably damaging", and 6 mutations as "possibly damaging", PHD-SNP tool predicted 21 mutations as "disease-related", PROVEAN tool predicted 27 mutations as "deleterious", PMUT tool predicted 18 mutations as "disease-related", and SNP&GO tool predicted 24 mutations as "disease-related". Nine mutations (R173Q, W145R, W188C, R36C, R162Q, R308H, R162W, G425R, A368T) were commonly predicted by all the seven tools. The impact of these mutations on protein stability was assessed using I-MUTANT2.0 and MUPRO tools. The I-MUTANT2.0 tool indicated that all nine mutations result in a decrease in protein stability. Similarly, MUPRO tool showed that eight of the nine mutations decrease protein stability, and one mutation, G425R, was found to increase protein stability. Additionally, protein flexibility was analyzed using MEDUSA tool, which revealed that the positions of all 9 SNPs were rigid, except R36C and G425R which were flexible.
DISCUSSION AND CONCLUSION: We hope that these findings could contribute to understanding the molecular basis of diseases associated with FUCA1 gene mutations. However, Experimental validation is recommended to confirm these results and guide future therapeutic strategies.