Table 9.
The functional assessment of non-synonymous amino acid substitutions in four structural SARS-CoV-2 proteins (E, M, N, S). The functional assessment of mutation is predicted on utilizing two different measures (PROVEAN score and stability value).
| Protein | Substitution | PROVEAN score | Type | ΔΔG prediction | RI | Freq. |
|---|---|---|---|---|---|---|
| E | V62F | 0 | Neutral | −1.65 | 8 | 1 |
| V75F | −1.414 | Neutral | −1.57 | 9 | 1 | |
| M | A142V | 0.18 | Neutral | 0.25 | 5 | 2 |
| L29F | −1.646 | Neutral | −0.91 | 7 | 1 | |
| A63V | −1.937 | Neutral | 0.14 | 0 | 1 | |
| A69S | −1.991 | Neutral | −0.82 | 9 | 1 | |
| V70F | −1.365 | Neutral | −1.66 | 10 | 1 | |
| R107L | −4.03 | Deleterious | −0.33 | 4 | 1 | |
| H125Y | 0.799 | Neutral | 0.06 | 5 | 1 | |
| N | S194L | −4.272 | Deleterious | −0.38 | 2 | 158 |
| P13L | −1.23 | Neutral | −0.48 | 3 | 23 | |
| S202N | −0.404 | Neutral | −0.78 | 0 | 20 | |
| R203K | −1.604 | Neutral | −0.93 | 6 | 14 | |
| R203K | −1.604 | Neutral | −0.93 | 6 | 14 | |
| G204R | −1.656 | Neutral | −0.52 | 5 | 14 | |
| T205I | −1.562 | Neutral | −0.53 | 3 | 6 | |
| S193I | −2.755 | Deleterious | −0.36 | 2 | 4 | |
| G97S | −1.98 | Neutral | −1.33 | 8 | 3 | |
| A156S | −0.457 | Neutral | −0.83 | 9 | 3 | |
| P6T | −0.223 | Neutral | −1.1 | 8 | 2 | |
| S33I | −1.372 | Neutral | 0.27 | 6 | 2 | |
| S180I | −3.465 | Deleterious | −0.14 | 3 | 2 | |
| M234I | 0.044 | Neutral | −0.03 | 1 | 2 | |
| D22N | −0.541 | Neutral | −1.4 | 6 | 1 | |
| D22N | −0.541 | Neutral | −1.4 | 6 | 1 | |
| E31Q | 0.054 | Neutral | −0.7 | 5 | 1 | |
| G34W | −1.609 | Neutral | −0.13 | 2 | 1 | |
| R92S | −3.718 | Deleterious | −1.23 | 6 | 1 | |
| G120R | −0.733 | Neutral | −0.29 | 1 | 1 | |
| A134V | −2.811 | Deleterious | −0.12 | 2 | 1 | |
| L139F | −0.697 | Neutral | −0.85 | 8 | 1 | |
| D144Y | −1.764 | Neutral | 0.2 | 1 | 1 | |
| A152S | 1.463 | Neutral | −0.92 | 9 | 1 | |
| R191L | −3.269 | Deleterious | −0.58 | 3 | 1 | |
| R203G | −3.247 | Deleterious | −1.6 | 7 | 1 | |
| R203K | −1.604 | Neutral | −0.93 | 6 | 1 | |
| G204R | −1.656 | Neutral | −0.52 | 5 | 1 | |
| G204T | −1.76 | Neutral | −0.96 | 7 | 1 | |
| A218V | 0.171 | Neutral | 0.21 | 1 | 1 | |
| M234I | 0.044 | Neutral | −0.03 | 1 | 1 | |
| G236C | −2.269 | Neutral | −0.27 | 5 | 1 | |
| H300Y | −1.577 | Neutral | 0.46 | 5 | 1 | |
| P302S | −4.043 | Deleterious | −1.3 | 7 | 1 | |
| P344S | −4.031 | Deleterious | −1.46 | 8 | 1 | |
| D348Y | −0.588 | Neutral | −0.41 | 2 | 1 | |
| T362I | −1.722 | Neutral | −0.35 | 3 | 1 | |
| T393I | −0.613 | Neutral | 0.1 | 2 | 1 | |
| S | D614G | 0.598 | Neutral | −0.93 | 3 | 405 |
| L54F | −0.435 | Neutral | −1.14 | 4 | 80 | |
| E583D | −0.819 | Neutral | −0.44 | 3 | 14 | |
| R78M | 0.986 | Neutral | −0.84 | 7 | 12 | |
| T572I | −0.649 | Neutral | 0 | 3 | 10 | |
| Q677H | 0.002 | Neutral | −0.67 | 5 | 5 | |
| L5F | −1.126 | Neutral | −0.98 | 3 | 3 | |
| Q690H | −0.796 | Neutral | −0.86 | 6 | 3 | |
| S12F | −0.65 | Neutral | 0.14 | 2 | 2 | |
| W152L | −0.159 | Neutral | −0.89 | 7 | 2 | |
| S155I | −0.503 | Neutral | 0 | 4 | 2 | |
| M177I | 0.579 | Neutral | −0.61 | 5 | 2 | |
| G181A | 0.396 | Neutral | −0.58 | 1 | 2 | |
| W258L | −1.084 | Neutral | −0.65 | 7 | 2 | |
| A706S | 0.183 | Neutral | −0.85 | 9 | 2 | |
| A879S | −0.361 | Neutral | 0.54 | 7 | 2 | |
| H1083Q | −1.006 | Neutral | −0.34 | 5 | 2 | |
| C1243F | −4.53 | Deleterious | −0.09 | 2 | 2 | |
| F2L | −0.902 | Neutral | −1.22 | 9 | 1 | |
| S13I | −1.187 | Neutral | 0.27 | 0 | 1 | |
| Y28H | −0.443 | Neutral | −1.38 | 4 | 1 | |
| G35V | −2.112 | Neutral | −0.68 | 7 | 1 | |
| T76I | −0.115 | Neutral | −0.72 | 6 | 1 | |
| K97Q | −0.113 | Neutral | −0.92 | 7 | 1 | |
| N148Y | −0.177 | Neutral | 0.1 | 4 | 1 | |
| M153I | 0.244 | Neutral | −0.98 | 6 | 1 | |
| E156D | 0.958 | Neutral | −0.52 | 4 | 1 | |
| S162I | 0.231 | Neutral | 0.02 | 1 | 1 | |
| Q173H | −0.299 | Neutral | −1.02 | 7 | 1 | |
| S255F | −0.423 | Neutral | −0.03 | 3 | 1 | |
| G261S | 0.485 | Neutral | −1.13 | 8 | 1 | |
| A262S | 0.154 | Neutral | −0.64 | 9 | 1 | |
| Q271R | −0.48 | Neutral | −0.27 | 5 | 1 | |
| C301F | −8.689 | Deleterious | 0.2 | 4 | 1 | |
| E471Q | 0.445 | Neutral | −0.59 | 7 | 1 | |
| D574Y | 0.858 | Neutral | 0.36 | 2 | 1 | |
| Q613H | −0.917 | Neutral | −0.86 | 6 | 1 | |
| H655Y | −0.814 | Neutral | 0.08 | 4 | 1 | |
| A688V | 0.498 | Neutral | −0.37 | 5 | 1 | |
| A701V | 0.597 | Neutral | −0.25 | 4 | 1 | |
| M731I | −0.598 | Neutral | −0.25 | 3 | 1 | |
| K795Q | 0.072 | Neutral | −0.61 | 3 | 1 | |
| P809S | 1.024 | Neutral | −1.55 | 8 | 1 | |
| T827I | −0.378 | Neutral | −0.45 | 6 | 1 | |
| A892V | −1.901 | Neutral | 0.2 | 1 | 1 | |
| A930V | −3.727 | Deleterious | −0.2 | 3 | 1 | |
| T1077I | −1.511 | Neutral | −0.13 | 1 | 1 | |
| V1104L | −0.604 | Neutral | −0.7 | 1 | 1 | |
| D1153Y | −3.275 | Deleterious | −1.52 | 2 | 1 | |
| K1181R | −0.522 | Neutral | −0.48 | 7 | 1 | |
| N1187K | −0.467 | Neutral | −0.29 | 4 | 1 | |
| Q1201K | 1.409 | Neutral | −0.29 | 3 | 1 | |
| C1250F | −5.057 | Deleterious | −0.09 | 2 | 1 | |
| D1259Y | 3.924 | Neutral | −0.21 | 3 | 1 |
The substitutions with either high PROVEAN score (< − 2.5, type: deleterious) or large increase stability (ΔΔG < − 0.5) or both are shown in bold.