Table 1 Summary of all 69 nsSNPs predicted 504 to be damaging/deleterious by at least two of the used tools
From: In silico SNP analysis of the breast cancer antigen NY-BR-1
SNP ID | Location on chromosome | Location in protein | Nucleotide variation | Protein variation | SIFT prediction | Provean prediction | Polyphen prediction | AA change | In ANK domain | Minor Allele Frequency |
|---|---|---|---|---|---|---|---|---|---|---|
rs113525905 | 37447451 | 613 | G/A | G/R | Damaging(0.013) | Neutral(−1.25) | probably damaging(0.998) | hydrophobe > hydrophile | 0,19 | |
rs1200875 | 37505192 | 985 | C/T | R/C | Damaging(0.001) | Neutral(0.32) | possibly damaging(0.762) | hydrophile > hydrophile | 12,89 | |
rs140013037 | 37505242 | 1001 | G/C | K/N | Damaging(0.016) | Deleterious(−3.58) | probably damaging(0.963) | hydrophile > hydrophile | 0,17 | |
rs144539033 | 37430978 | 385 | T/C | W/R | Damaging(0) | Neutral(−1.04) | possibly damaging(0.943) | hydrophobe > hydrophile | 0,15 | |
rs17590850 | 37470375 | 730 | A/C | N/H | Damaging(0.002) | Neutral(−0.35) | possibly damaging(0.94) | hydrophile > hydrophile | NA | |
rs17606645 | 37470263 | 723 | A/T | K/N | Damaging(0.004) | Neutral(−0.44) | possibly damaging(0.851) | hydrophile > hydrophile | NA | |
rs183760470 | 37451752 | 660 | A/C | K/Q | Damaging(0.002) | Neutral(−0.78) | possibly damaging(0.851) | hydrophile > hydrophile | 0,01 | |
rs184702413 | 37481992 | 838 | A/G | E/G | Damaging(0.017) | Neutral(−1.16) | possibly damaging(0.851) | hydrophile > hydrophobe | 0,41 | |
rs185294248 | 37508038 | 1133 | T/C | F/S | Damaging(0.012) | Deleterious(−4.37) | benign(0.006) | hydrophobe > hydrophile | 0,11 | |
rs190686350 | 37419160 | 122 | G/A | A/T | Damaging(0.012) | Deleterious(−3.27) | probably damaging(0.997) | hydrophobe > hydrophile | Yes | 0,01 |
rs199571878 | 37438753 | 541 | A/C | K/Q | Damaging(0) | Neutral(−0.47) | possibly damaging(0.947) | hydrophile > hydrophile | 0,079 | |
rs199691521 | 37488715 | 926 | A/T | E/V | Damaging(0.02) | Neutral(−1.16) | probably damaging(0.994) | hydrophile > hydrophobe | NA | |
rs199795040 | 37508139 | 1167 | C/A | Q/K | Damaging(0.002) | Neutral(−2.3) | possibly damaging(0.886) | hydrophile > hydrophile | NA | |
rs199841724 | 37508538 | 1300 | C/A | H/N | Damaging(0.032) | Deleterious(−3.11) | benign(0.03) | hydrophile > hydrophile | NA | |
rs199874591 | 37451705 | 644 | C/A | P/H | Damaging(0.001) | Neutral(−1.11) | probably damaging(0.997) | hydrophobe > hydrophile | NA | |
rs200114350 | 37486388 | 899 | A/G | N/S | Damaging(0.006) | Neutral(−1.64) | possibly damaging(0.713) | hydrophile > hydrophile | NA | |
rs200264724 | 37431045 | 407 | C/T | T/M | Damaging(0.001) | Neutral(0.55) | probably damaging(0.989) | hydrophile > hydrophobe | NA | |
rs200331751 | 37478422 | 817 | G/A | D/N | Damaging(0.028) | Neutral(−0.12) | possibly damaging(0.818) | hydrophile > hydrophile | NA | |
rs200399695 | 37506718 | 1060 | G/C | R/T | Damaging(0.029) | Deleterious(−2.91) | benign(0.013) | hydrophile > hydrophile | NA | |
rs200639888 | 37419170 | 125 | T/C | L/P | Damaging(0) | Deleterious(−5.96) | probably damaging(0.997) | hydrophobe > hydrophobe | Yes | NA |
rs200651327 | 37418912 | 105 | G/A | E/K | Tolerated(0.081) | Deleterious(−3.37) | probably damaging(0.999) | hydrophile > hydrophile | Yes | NA |
rs200845385 | 37430796 | 324 | C/T | T/I | Damaging(0.002) | Neutral(−0.78) | possibly damaging(0.898) | hydrophile > hydrophobe | NA | |
rs200929491 | 37508788 | 1383 | G/A | R/H | Damaging(0.002) | Deleterious(−3.55) | probably damaging(0.987) | hydrophile > hydrophile | NA | |
rs201234943 | 37447491 | 626 | A/T | K/M | Damaging(0) | Neutral(−1.29) | probably damaging(0.98) | hydrophile > hydrophobe | 0,01 | |
rs201628233 | 37478440 | 823 | G/T | A/S | Damaging(0.022) | Neutral(−0.44) | possibly damaging(0.841) | hydrophobe > hydrophile | 0,39 | |
rs201669885 | 37447325 | 602 | C/G | P/A | Damaging(0.012) | Neutral(−1.66) | possibly damaging(0.924) | hydrophobe > hydrophobe | 0,01 | |
rs201764363 | 37508814 | 1392 | G/C | A/P | Damaging(0.002) | Deleterious(−4.03) | probably damaging(0.969) | hydrophobe > hydrophobe | 0,01 | |
rs201858051 | 37508539 | 1300 | A/G | H/R | Tolerated(0.108) | Deleterious(−3.06) | possibly damaging(0.651) | hydrophile > hydrophile | NA | |
rs201885728 | 37451744 | 657 | T/C | L/S | Damaging(0.01) | Neutral(−0.08) | possibly damaging(0.932) | hydrophobe > hydrophile | 0,01 | |
rs201943652 | 37421175 | 173 | T/C | L/P | Damaging(0.011) | Deleterious(−4.76) | probably damaging(0.995) | hydrophobe > hydrophobe | Yes | NA |
rs201976592 | 37447446 | 611 | C/A | T/N | Damaging(0.002) | Neutral(−1.14) | possibly damaging(0.851) | hydrophile > hydrophile | 0,05 | |
rs202090351 | 37430699 | 292 | C/A | P/T | Damaging(0.001) | Neutral(−1.91) | probably damaging(0.998) | hydrophobe > hydrophile | NA | |
rs202098264 | 37430875 | 350 | C/G | F/L | Damaging(0.003) | Neutral(−1.01) | probably damaging(0.965) | hydrophobe > hydrophobe | NA | |
rs202200263 | 37454055 | 679 | A/G | D/G | Damaging(0.001) | Neutral(−1.04) | possibly damaging(0.924) | hydrophile > hydrophobe | 0,01 | |
rs267602477 | 37419220 | 142 | G/A | A/T | Damaging(0.016) | Deleterious(−3.41) | probably damaging(0.997) | hydrophobe > hydrophile | Yes | NA |
rs267602481 | 37438727 | 532 | C/T | S/F | Damaging(0.001) | Neutral(−1.27) | possibly damaging(0.842) | hydrophile > hydrophobe | NA | |
rs267602482 | 37441009 | 556 | C/T | S/F | Damaging(0) | Neutral(−1.66) | probably damaging(0.99) | hydrophile > hydrophobe | NA | |
rs267602485 | 37507968 | 1110 | G/A | E/K | Damaging(0.021) | Deleterious(−3.34) | probably damaging(0.98) | hydrophile > hydrophile | NA | |
rs367841401 | 37508002 | 1121 | T/C | L/P | Damaging(0) | Deleterious(−4.47) | probably damaging(0.969) | hydrophobe > hydrophobe | NA | |
rs368559588 | 37508121 | 1161 | G/A | A/T | Damaging(0.04) | Neutral(−0.75) | possibly damaging(0.618) | hydrophobe > hydrophile | 0,05 | |
rs368660392 | 37442552 | 587 | A/G | H/R | Damaging(0.003) | Neutral(−1.4) | possibly damaging(0.932) | hydrophile > hydrophile | 0,01 | |
rs369099906 | 37508651 | 1337 | A/T | L/F | Damaging(0.001) | Deleterious(−3.22) | probably damaging(0.999) | hydrophobe > hydrophobe | NA | |
rs369118323 | 37422851 | 209 | C/T | L/F | Damaging(0.01) | Neutral(−1.52) | probably damaging(0.993) | hydrophobe > hydrophobe | Yes | NA |
rs369532435 | 37438591 | 519 | A/T | K/M | Damaging(0) | Neutral(−1.13) | probably damaging(0.996) | hydrophile > hydrophobe | 0,01 | |
rs371253665 | 37451583 | 636 | C/T | P/L | Damaging(0.001) | Neutral(−0.77) | probably damaging(0.994) | hydrophobe > hydrophobe | 0,01 | |
rs371384886 | 37430859 | 345 | C/T | A/V | Damaging(0.001) | Neutral(−0.56) | probably damaging(0.997) | hydrophobe > hydrophobe | 0,01 | |
rs371443557 | 37431010 | 395 | T/G | I/M | Damaging(0.004) | Neutral(−0.28) | possibly damaging(0.676) | hydrophobe > hydrophobe | NA | |
rs371878855 | 37508548 | 1303 | A/G | Q/R | Damaging(0.012) | Deleterious(−2.52) | possibly damaging(0.808) | hydrophile > hydrophile | NA | |
rs371981371 | 37508671 | 1344 | C/A | A/D | Damaging(0.003) | Deleterious(−4.6) | probably damaging(0.989) | hydrophobe > hydrophile | NA | |
rs372199195 | 37430803 | 326 | T/G | D/E | Damaging(0) | Neutral(−0.13) | possibly damaging(0.643) | hydrophile > hydrophile | NA | |
rs372420008 | 37430922 | 366 | A/G | K/R | Damaging(0.007) | Neutral(−0.62) | possibly damaging(0.956) | hydrophile > hydrophile | NA | |
rs372878721 | 37442530 | 580 | G/A | V/M | Damaging(0.013) | Neutral(−0.77) | probably damaging(0.976) | hydrophobe > hydrophobe | NA | |
rs373377344 | 37508379 | 1247 | G/A | E/K | Damaging(0.048) | Deleterious(−2.78) | possibly damaging(0.898) | hydrophile > hydrophile | NA | |
rs373380909 | 37422972 | 249 | G/T | G/V | Damaging(0.003) | Neutral(−2.41) | probably damaging(0.999) | hydrophobe > hydrophobe | Yes | NA |
rs373997768 | 37505217 | 993 | A/C | K/T | Damaging(0.003) | Deleterious(−2.76) | probably damaging(0.963) | hydrophile > hydrophile | NA | |
rs374024060 | 37430943 | 373 | C/T | T/M | Damaging(0.011) | Neutral(−0.76) | probably damaging(0.975) | hydrophile > hydrophobe | NA | |
rs374037740 | 37441038 | 566 | T/G | W/G | Damaging(0.009) | Neutral(−1.82) | possibly damaging(0.826) | hydrophobe > hydrophobe | NA | |
rs374739457 | 37454063 | 682 | G/C | E/Q | Damaging(0.018) | Neutral(−0.76) | possibly damaging(0.851) | hydrophile > hydrophile | NA | |
rs374753521 | 37508446 | 1269 | A/C | Y/S | Damaging(0.031) | Deleterious(−4.18) | benign(0.347) | hydrophile > hydrophile | NA | |
rs375945698 | 37505306 | 1023 | G/C | E/Q | Damaging(0.018) | Neutral(−2.17) | probably damaging(0.999) | hydrophile > hydrophile | NA | |
rs376116213 | 37505157 | 973 | G/A | R/K | Damaging(0.004) | Neutral(−2.23) | probably damaging(0.976) | hydrophile > hydrophile | 0,01 | |
rs376821949 | 37438772 | 547 | G/A | R/K | Damaging(0) | Neutral(0.04) | possibly damaging(0.643) | hydrophile > hydrophile | NA | |
rs377410013 | 37440994 | 551 | T/C | M/T | Damaging(0.045) | Neutral(−0.42) | possibly damaging(0.717) | hydrophobe > hydrophile | NA | |
rs377740138 | 37430720 | 299 | G/A | V/M | Damaging(0.002) | Neutral(−0.39) | possibly damaging(0.845) | hydrophobe > hydrophobe | NA | |
rs377744149 | 37508352 | 1238 | G/A | D/N | Tolerated(0.083) | Deleterious(−3.19) | probably damaging(0.971) | hydrophile > hydrophile | 0,01 | |
rs377750885 | 37508803 | 1388 | A/T | E/V | Damaging(0) | Deleterious(−5.87) | probably damaging(0.997) | hydrophile > hydrophobe | NA | |
rs41276130 | 37451768 | 665 | T/G | L/W | Damaging(0.002) | Neutral(−0.98) | probably damaging(0.983) | hydrophobe > hydrophobe | 4,17 | |
rs45515098 | 37440991 | 550 | C/T | P/L | Damaging(0.028) | Neutral(−1.27) | possibly damaging(0.581) | hydrophobe > hydrophobe | 0,01 | |
rs61737412 | 37419218 | 141 | C/T | T/M | Damaging(0.035) | Deleterious(−5.03) | possibly damaging(0.951) | hydrophile > hydrophobe | Yes | 4,13 |