Table 2.
Identification of gene variants of SCN11A, SCN10A, and SCN9A in a cohort of FEPS candidates.
| Gene | c.Position | p.Position | Number of Patients | Location (GRCh38.p14) |
ToMMo 38KJPN Allele Frequency |
Variant Classification |
dbSNP | * Reference |
|---|---|---|---|---|---|---|---|---|
| SCN11A | c.598T>C | p.S200P | 1 | chr3:38926822 | na | likely pathogenic | na | |
| c.665G>A | p.R222H | 25 | chr3:38925462 | 0.000013 | pathogenic | rs1230622899 | [8,9] | |
| c.664C>A | p.R222S | 1 | chr3:38925463 | na | pathogenic | rs775199760 | [8] | |
| c.673C>T | p.R225C | 3 | chr3:38925454 | na | pathogenic | rs138607170 | [10,13] | |
| c.923C>T | p.P308L | 2 | chr3:38919971 | 0.001846 | likely pathogenic | rs751477540 | ||
| c.2410A>G | p.N804D | 1 | chr3:38894958 | na | likely pathogenic | na | ||
| c.2431C>T | p.L811F | 1 | chr3:38894937 | na | pathogenic | na | ||
| c.2441T>G | p.F814C | 1 | chr3:38894927 | na | likely pathogenic | na | [10] | |
| c.2669G>A | p.G890D | 1 | chr3:38894699 | 0.000581 | likely benign | rs769754010 | ||
| c.3437T>C | p.F1146S | 5 | chr3:38872251 | na | pathogenic | na | [10] | |
| c.3551T>C | p.V1184A | 1 | chr3:38871653 | na | likely pathogenic | na | [10,14] | |
| c.4229C>T | p.T1410M | 1 | chr3:38850579 | 0.000129 | likely pathogenic | rs771241253 | ||
| c.4699T>C | p.C1567R | 1 | chr3:38847371 | 0.002595 | likely pathogenic | rs201595463 | ||
| c.5309T>C | p.L1770P | 3 | chr3:38846761 | 0.005023 | VUS | rs148328451 | ||
| SCN10A | c.53C>T | p.P18L | 4 | chr3:38793958 | 0.006521 | likely pathogenic | rs190176472 | |
| c.110C>T | p.A37V | 1 | chr3:38793901 | na | VUS | na | ||
| c.349A>C | p.N117H | 2 | chr3:38792090 | 0.000852 | likely benign | rs774462243 | ||
| c.565T>A | p.W189R | 1 | chr3:38771313 | 0.000245 | likely pathogenic | rs1379282429 | ||
| c.1157T>G | p.F386C | 4 | chr3:38756807 | 0.0043 | likely pathogenic | rs78555408 | ||
| c.1277G>A | p.R426Q | 2 | chr3:38756687 | 0.001485 | likely benign | rs143033805 | ||
| c.1489C>T | p.R497C | 1 | chr3:38752485 | 0.000077 | likely pathogenic | rs370009920 | ||
| c.1549C>T | p.P517S | 2 | chr3:38752425 | 0.000413 | likely benign | rs2063758700 | ||
| c.2161C>T | p.P721S | 3 | chr3:38739634 | 0.000723 | likely pathogenic | rs747114420 | ||
| c.2311C>T | p.P771S | 1 | chr3:38728871 | 0.000026 | likely pathogenic | na | ||
| c.3670C>T | p.L1224F | 2 | chr3:38718664 | 0.001265 | likely pathogenic | rs200597401 | ||
| c.4379G>C | p.R1460P | 1 | chr3:38707286 | na | likely pathogenic | rs369399424 | ||
| c.4580T>C | p.M1527T | 1 | chr3:38701916 | na | VUS | na | ||
| c.5047C>T | p.P1683S | 1 | chr3:38698173 | 0.006637 | VUS | rs146999807 | ||
| c.5122_5124del | p.I1708del | 1 | chr3:38698103_38698105 | na | pathogenic | na | ||
| c.5536C>A | p.L1846I | 3 | chr3:38697684 | 0.001911 | VUS | rs1001583386 | ||
| c.5605C>T | p.R1869C | 2 | chr3:38697615 | 0.002247 | likely pathogenic | rs141648641 | ||
| c.5831A>T | p.D1944V | 1 | chr3:38697389 | na | VUS | rs768502791 | ||
| SCN9A | c.29A>G | p.Q10R | 2 | chr2:166311728 | 0.001111 | pathogenic | rs267607030 | [16] |
| c.130G>C | p.E44Q | 1 | chr2:166311627 | 0.000039 | pathogenic | rs757848676 | [13] | |
| c.1818T>G | p.S606R | 3 | chr2:166284609 | 0.004855 | likely benign | rs202141567 | ||
| c.3179T>C | p.M1060T | 1 | chr2:166272538 | na | VUS | rs781223783 | ||
| c.3312C>A | p.S1104R | 1 | chr2:166272405 | 0.000362 | VUS | rs767904709 | ||
| c.3335G>A | p.S1112N | 3 | chr2:166251869 | 0.006529 | likely pathogenic | rs141040985 | ||
| c.4739T>C | p.V1580A | 1 | chr2:166203957 | na | likely pathogenic | rs1574705360 | ||
| c.5678G>A | p.R1893H | 3 | chr2:166198928 | 0.007657 | likely pathogenic | rs79805025 |
na: not applicable. * The variant is previously reported.