Table 2 Results of protein structure stability and functional analysis
Gene | SNV ID | Variant | MutPred2 | PredictSNP | I-Mutant2.0 | MuPro | Michelanglo-VENUS | |||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
|  |  |  | Score | Prediction | Score | Prediction | Score | Prediction | Score | Prediction | Gibbs free energy (∆∆G value) | Amino acid change |
BRCA1 | rs1555587813 | Asp1131Gly | 0.256 | No pathogenic effect | 51% | Deleterious | − 1.58 | Decrease Stability | − 2.06 | Decrease stability | Variant is unlikely to significantly affect the stability of the protein | Amino acid Aspartate (D)- acidic, polar, hydrophilic negatively charged changed to the amino acid Glycine (G)- neutral charge at physiological pH, hydrophilic (weak hydrophobic tendencies), smaller more flexible |
BRIP1 | rs45437094 | Arg1035Cys | 0.102 | No pathogenic effect | 51% | Deleterious | − 0.16 | Decrease Stability | − 0.89 | Decrease stability | Variant is unlikely to significantly affect the stability of the protein | Amino acid Arginine -positively charged hydrophilic basic changed to the amino acid Cysteine—neutral, hydrophilic amino acid |
CHEK2 | rs375507194 | Gln20His | 0.139 | No pathogenic effect | 55% | Deleterious | − 0.29 | Decrease Stability | − 1.05 | Decrease stability | Variant is unlikely to significantly affect the stability of the protein | The amino acid Glutamine (Q)-acidic, polar negatively charged changed to the amino acid Histidine (H) neutral charge smaller more flexible |
MET | rs1207381066 | Arg280Ser | 0.915 | Possibly pathogenic | 72% | Deleterious | − 2.14 | Decrease Stability | − 0.54 | Decrease stability | Suggested few changes in the motifs | Amino acid Arginine -basic positively charged, hydrophilic, polar changed to amino acid Serine- polar hydrophilic uncharged |
STK11 | rs545015076 | Asn119Asp | 0.668 | Possibly pathogenic | 83% | Neutral | − 1.25 | Decrease Stability | − 1.26 | Decrease stability | Variant is unlikely to significantly affect the stability of the protein | Amino acid Asparagine (N)-polar, hydrophilic uncharged neutral changed to Aspartate (D) polar negatively charged and hydrophilic. But both are equal in size |