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The Major Histocompatibility Complex (MHC) contains highly variable   multi-gene families, which play a key role in the adaptive immune response   within vertebrates. Among the Capra MHC class II genes, the expressed DRB   locus is highly polymorphic, particularly in exon 2, which encodes the   antigen-binding site. Models of variable non-synonymous/synonymous rate   ratios among sites may provide important insights into functional constraints   at different amino acid sites and may be used to detect sites under positive   selection. Many non-synonymous single nucleotide polymorphisms (nsSNPs) at   the DRB locus in goats are suspected to impact protein function. This study,   therefore, aimed at comparing the efficiency of six computational approaches   to predict the likelihood of a particular non-synonymous (amino acid change)   coding SNP to cause a functional impact on the protein. This involved the use   of PANTHER, SNAP, SIFT, PolyPhen-2, PROVEAN and nsSNPAnalyzer bioinformatics   analytical tools in detecting harmful and beneficial effects at H57G, Y89R,   V104D and Y112I substitutions in the peptide binding region of the DRB gene   of Nigerian goats. The results from PANTHER analysis revealed that H57G, Y89R   and Y112I substitutions (Pdeleterious= 0.113, 0.204 and 0.472, respectively)   were beneficial; while that of V104D was deleterious (Pdeleterious= 0.756),   an indication that it was non-neutral. As regards the SNAP approach, H57G and   Y89R substitutions were returned neutral with expected accuracy of 53 and   69%, respectively while V104D and Y112I substitutions were harmful. H57G and   Y89R substitutions were also found harmless in the SIFT analysis. However,   only H57G (PROVEAN) and V104D (nsSNPAnalyzer) amino acid substitutions were   found to be beneficial. Interestingly, the predicted 3D structures of both   native and mutant DRB protein appeared similar as validated by Ramachandran   plots. The consensus reached by PANTHER, SNAP, SIFT and PolyPhen-2 approaches   on the neutrality especially of H57G (PROVEAN inclusive) and Y89R amino acid   substitutions may be used in search of disease resistant genotypes at the DRB   locus of Nigerian goats

Application of computational algorithms to assess the functionality of non-synonymous substitutions in MHC DRB gene of Nigerian goats