Table 1.
Rare (<0.5 and 1.0% minor allele frequency) compound heterozygous variants in Epi4k participants.
| Gene | Transcript | Sex | Phena. | Ancb. | Chr:bp* | dbSNP ID | REF/ ALT | Exac ALL AFc |
ExAC NFE AF |
Peptide change | Epi4k # (1%) | 1 kg # (1%) | p-value | Epi4k # (0.5%) | 1 kg # (0.5%) | p-value |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| EU (y/n)d: All (y/n) | EU (y/n): All (y/n) | EU:All | EU (y/n): All (y/n) | EU (y/n): All (s/n) | EU:All | |||||||||||
| PRTG | ENST000 00389286 |
F | IS | EU | 15:56032666 | rs373423650 | T/C | 9.94E-05 | 1.65E-04 | E104G | 3/204: 3/261 | 0/503: 0/2504 | 0.0245: 0.00086 | 2/205: 2/262 | 0/503: 0/2504 | 0.0847: 0.0091 |
| 15:56032666 | rs185716584 | C/G | 0.003022 | 0.004315 | E104D | |||||||||||
| M | LGS | EU | 15:56032665 | rs372777171 | C/A | 8.28E-06 | 1.50E-05 | E575* | ||||||||
| 15:55965698 | rs185716584 | C/G | 0.003022 | 0.004315 | E104D | |||||||||||
| M | LGS | EU | 15:56032665 | rs35718474 | G/A | 0.003033 | 0.006701 | P13S | ||||||||
| 15:56035093 | rs148011047 | T/G | 0.002611 | 0.003608 | K977T | |||||||||||
| OSBP2 | ENST000 00332585 |
M | IS | EU | 15:55916703 | rs200118898 | C/G | 1.09E-04 | 1.98E-04 | S143W | 2/205: 2/262 | 0/503: 0/2504 | 0.0847: 0.0091 | 2/205: 2/262 | 0/503: 0/2504 | 0.292: 0.0091 |
| 22:31091324 | rs201298398 | G/A | 3.20E-04 | 5.19E-04 | R262Q | |||||||||||
| M | LGS | E Asia | 22:31137288 | rs576508023 | G/C | 8.42E-06 | 0 | G115R | ||||||||
| 22:31091239 | NA | C/T | 1.66E-05 | 0 | R383W | |||||||||||
| ABCC11 | ENST000 00394747 |
F | IS | EU | 22:31283452 | rs529824818 | C/T | 8.24E-06 | 0 | C543Y | 2/205: 2/262 | 0/503: 2/2502 | 0.0847: 0.0478 | 2/205: 2/262 | 0/503: 1/2502 | 0.0847: 0.0255 |
| 16:48242388 | rs199839251 | C/T | 8.29E-06 | 1.51E-05 | E273K | |||||||||||
| M | LGS | EU | 16:48250159 | NA | C/A | NA | NA | R889M | ||||||||
| 16:48226471 | NA | C/A | NA | NA | G636V | |||||||||||
| TNC | ENST000 00345230 |
M | IS | EU | 16:48234362 | rs200401362 | C/T | 8.24E-06 | 0 | G861R | 2/205: 3/261 | 0/503: 4/2500 | 0.0847: 0.022 | 1/206: 2/262 | 0/503: 2/2502 | 0.29: 0.0478 |
| 9:117840315 | rs117058692 | C/G | 7.77E-04 | 0.001248 | G171R | |||||||||||
| 9:117849499 | rs143586851 | C/T | 2.23E-04 | 3.90E-04 | A39T | |||||||||||
| M | IS | C/S Asia | 9:117853183 | rs149986851 | C/A | 2.06E-04 | 3.75E-04 | G203V | ||||||||
| 9:117849402 | rs139280264 | G/A | 8.51E-04 | 0.001247 | R1066C | |||||||||||
| M | IS | EU | 9:117835900 | rs371055558 | C/T | 2.54E-05 | 3.07E-05 | G576S | ||||||||
| 9:117848284 | rs144032672 | C/T | 0.001336 | 0.002026 | G210S | |||||||||||
| MACF1 | ENST000 00289893 |
M | IS | EU | 9:117849382 | NA | G/A | 1.65E-05 | 3.00E-05 | R4344Q | 3/204: 3/261 | 1/502: 11/2493 | 0.0769: 0.142 | 3/204: 3/261 | 0/503: 6/2498 | 0.0245: 0.0478 |
| 1:39900231 | rs141949859 | G/T | 6.34E-04 | 1.12E-03 | V3535F | |||||||||||
| M | IS | EU | 1:39853797 | rs145271544 | G/T | NA | NA | A3264S | ||||||||
| 1:39852984 | rs138819868 | T/G | 2.46E-03 | 3.85E-03 | F5885L | |||||||||||
| M | LGS | EU | 1:39951304 | NA | A/G | 8.28E-06 | 0 | I1066V | ||||||||
| 1:39800136 | NA | G/C | 8.264 | 1.50E-05 | W4967C | |||||||||||
| STAB1 | ENST000 00321725 |
M | IS | ME | 1:39910474 | rs145751447 | G/A | 9.17E-05 | 0 | D1289N | 0/207: 2/262 | 1/502: 6/2498 | 0.99: 0.173 | 0/207: 2/262 | 1/502: 2/2502 | 0.99: 0.0478 |
| 3:52549439 | rs147953260 | G/A | 0.001512 | 0.002524 | R1872H | |||||||||||
| F | IS | C/S Asia | 3:52554531 | rs189303343 | A/G | 4.05E-05 | 3.66E-05 | I590V | ||||||||
| 3:52540204 | NA | C/T | NA | NA | R2351W |
aPhen = phenotype, bAnc = ancestry, cAF = allele frequency, dy/n corresponds to yes/no counts of individuals with qualifying variants.
*bp (base pair position) in hg19/Build37.
Ancestries: EU = European, E Asia = East Asia, C/S Asia = Central/South Asia, ME = Middle East. Phenotypes: IS = Infantile spasms, LGS = Lennox-Gastaut syndrome.
p-values in bold are the most significant for the specific analysis.