Table 2.
Genetic variations in SCN10A in lone AF patients
| ESP6500
|
|||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Exon | rsID | GVS Function |
Amino Acid Pos. |
cDNA Pos. |
EA Allele # | AA Allele # | ALL Allele # | MAF (%) (EA/AA/AII) |
PolyPhen- 2 Prediction |
SIFT | Grantham | Conservation | Agreement ≥3 |
| 1 | rs141207048 | missense | R14L | 41 | A=26/C=8574 | A=2/C=4404 | A=28/C=12978 | 0.30/0.045/0.21 | Probably-damaging | Damaging | 102 | Conserved | D |
| 1 | rs34314583 | coding-synonymous | R15R | 45 | A=92/G=8508 | A=15/G=4391 | A=107/G=12899 | 1.07/0.34/0.82 | - | - | - | Conserved | - |
| 2 | rs202143516 | missense | V94G | 281 | C=1/A=8599 | C=0/A=4406 | C=1/A=13005 | 0.012/0.0/0.0077 | Probably-damaging | Damaging | 109 | Conserved | D |
| 4 | rs202192818 | missense-near-splice | Y158D | 472 | C=5/A=8595 | C=0/A=4406 | C=5/A=13001 | 0.058/0.0/0.038 | Probably-damaging | Damaging | 160 | Conserved | D |
| 4 | rs75991777 | splice-5 | None | c.599+1 | - | - | - | - | - | - | - | Conserved | - |
| 5 | rs74717885 | missense | I206M | 618 | C=137/T=8463 | C=14/T=4392 | C=151/T=12855 | 1.59/0.32/1.16 | Benign | Tolerated | 10 | Conserved | B |
| 9 | rs62244070 | coding-synonymous | E428E | 1284 | T=2158/C=6442 | T=474/C=3932 | T=2632/C=10374 | 25.09/10.76/20.24 | - | - | - | Conserved | - |
| 11 | rs7617919 | coding-synonymous | L492L | 1476 | A=2169/G=6429 | A=471/G=3935 | A=2640/G=10364 | 25.23/10.69/20.30 | - | - | - | Conserved | - |
| 11 | rs7630989 | missense | S509P | 1525 | G=241/A=8359 | G=925/A=3481 | G=1166/A=11840 | 2.80/20.99/8.97 | Benign | Tolerated | 74 | Conserved | B |
| 15 | rs139861061 | missense | R814H | 2441 | T=6/C=8594 | T=1/C=4405 | T=7/C=12999 | 0.07/0.023/0.054 | Possibly-damaging | Damaging | 29 | Not Conserved | B |
| 15 | rs146028829 | missense | E825D | 2475 | G=19/T=8581 | G=2/T=4404 | G=21/T=12985 | 0.22/0.045/0.16 | Benign | Tolerated | 45 | Not Conserved | B |
| 16 | rs7374804 | coding-synonymous | K950K | 2850 | C=557/T=8043 | C=362/T=4044 | C=919/T=12087 | 6.48/8.22/7.07 | - | - | - | Not Conserved | - |
| 16 | rs57326399 | missense | I962V | 2884 | C=2253/T=6347 | C=482/T=3924 | C=2735/T=10271 | 26.20/10.94/21.03 | Benign | Tolerated | 29 | Not Conserved | B |
| 16 | rs59468016 | coding-synonymous | G979G | 2937 | A=2248/G=6352 | A=224/G=4182 | A=2472/G=10534 | 26.14/5.08/19.01 | - | - | - | Not Conserved | - |
| 16 | unknown | missense | I999L | 2995 | - | - | - | - | Benign | Tolerated | 5 | Conserved | B |
| 17 | rs73062575 | missense | P1045T | 3133 | T=273/G=8327 | T=22/G=4384 | T=295/G=12711 | 3.17/0.5/2.27 | Benign | Tolerated | 38 | Not Conserved | B |
| 17 | rs6791171 | coding-synonymous | T1064T | 3192 | T=1216/C=7384 | T=880/C=3526 | T=2096/C=10910 | 14.14/19.97/16.12 | - | - | - | Not Conserved | - |
| 17 | rs6795970 | missense | A1073 | 3218 | G=5176/A=3424 | G=3961/A=445 | G=9137/A=3869 | 39.81/10.01/29.74 | Benign | Tolerated | 64 | Not Conserved | B |
| 18 | rs12632942 | missense | P1092 | 3275 | G=2236/A=6364 | G=625/A=3781 | G=2861/A=10145 | 26.0/14.18/21.99 | Benign | Tolerated | 98 | Not Conserved | B |
| 18 | unknown | coding-synonymous | D1113D | 3339 | - | - | - | - | - | - | - | Not Conserved | - |
| 19 | rs6771157 | coding-synonymous | T1131T | 3393 | C=2238/G=6362 | C=626/G=3780 | C=2864/G=10142 | 26.02/14.21/22.02 | - | - | - | Not Conserved | - |
| 21 | rs138832868 | missense-near-splice | R1268Q | 3803 | T=24/C=8576 | T=3/C=4403 | T=27/C=12979 | 0.279/0.068/0.20 | Probably-damaging | Damaging | 43 | Conserved | D |
| 22 | rs11711062 | missense | S1337T | 4009 | T=56/A=8544 | T=3/A=4403 | T=59/A=12947 | 0.65/0.07/0.45 | Benign | Tolerated | 58 | Conserved | B |
| 25 | rs6790627 | coding-synonymous | K1441K | 4323 | C=1230/T=7370 | C=1500/T=2906 | C=2730/T=10276 | 14.30/34.04/20.99 | - | - | - | Conserved | - |
| 26 | rs142217269 | missense | C1523Y | 4568 | T=23/C=8577 | T=1/C=4405 | T=24/C=12982 | 0.27/0.02/0.18 | Probably-damaging | Damaging | 194 | Conserved | D |
| 27 | rs78425180 | coding-synonymous | T1570T | 4710 | T=122/C=8478 | T=16/C=4390 | T=138/C=12868 | 1.41/0.36/1.06 | - | - | - | Conserved | - |
| 27 | unknown | missense | R1588Q | 4763 | T=0/C=8600 | T=1/C=4405 | T=1/C=13005 | 0.0/0.023/0.008 | Probably-damaging | Damaging | 43 | Conserved | D |
| 27 | rs6599242 | coding-synonymous | S1622S | 4866 | G=7870/A=730 | G=4232/A=174 | G=12102/A=904 | 8.49/3.95/6.95 | - | - | - | Conserved | - |
| 27 | rs77804526 | missense | V1697I | 5089 | T=118/C=8482 | T=13/C=4393 | T=131/C=12875 | 1.37/0.3/1.01 | Benign | Tolerated | 29 | Conserved | B |
| 27 | rs116353929 | coding-synonymous | D1739D | 5217 | A=265/G=8335 | A=36/G=4370 | A=301/G=12705 | 3.08/0.82/2.31 | - | - | - | Conserved | - |
Positions of the variants found in lone AF cohort. The frequency and MAF of the alleles are reported from ESP6500 exome server. PolyPhen-2 prediction reports the possible impact of an amino acid substitution on protein structure and function based on Polymorphism Phenotyping-2 (PolyPhen-2) program. D: Disease Causing; B: Benign; EA: European American; AA: African American; ESP 6500 exomes: Exome Variant Server (chromosomes 1–22, and X); MAF (%) (EA/AA/All): the minor-allele frequency in percent listed in the order of European American (EA), African American (AA) and all populations (All). (delimited by /)