Table 3. Somatic EPHA2 coding SNVs found in the paired clear lens panel (VAF >3%).
| Chr | Start/End | Ref | Alt | ExonicFunc.refGene | AAChange.refGene | cosmic70 | snp138 | exac01 | SIFT | Depth | VAF |
|---|---|---|---|---|---|---|---|---|---|---|---|
| chr1 | 16451690 | G* | A* | UTR-3 | NM_004431:c.*20C>T | 1.58E-05 | 3502 | 3.94% | |||
| chr1 | 16451707 | G* | A* | UTR-3 | NM_004431:c.*3C>T | 4181 | 3.28% | ||||
| chr1 | 16451720 | A | G | nonsynonymous SNV | EPHA2:NM_004431:exon17:c.T2921C:p.I974T | D | 4172 | 3.96% | |||
| chr1 | 16451809 | G* | A* | synonymous SNV | EPHA2:NM_004431:exon17:c.C2832T:p.I944I | 1416 | 4.31% | ||||
| chr1 | 16451815 | G | A | synonymous SNV | EPHA2:NM_004431:exon17:c.C2826T:p.D942D | rs143828420 | 8.69E-05 | 1417 | 4.10% | ||
| chr1 | 16455972 | C* | T* | nonsynonymous SNV | EPHA2:NM_004431:exon16:c.G2782A:p.A928T | D | 3242 | 12.94% | |||
| chr1 | 16456009 | G* | A* | synonymous SNV | EPHA2:NM_004431:exon16:c.C2745T:p.S915S | 7158 | 13.87% | ||||
| chr1 | 16456014 | C | A | stopgain | EPHA2:NM_004431:exon16:c.G2740T:p.E914X | ID = COSM3934228 | D | 3242 | 8.34% | ||
| chr1 | 16456016 | A | G | nonsynonymous SNV | EPHA2:NM_004431:exon16:c.T2738C:p.L913P | D | 3048 | 3.28% | |||
| chr1 | 16456023 | C* | T* | nonsynonymous SNV | EPHA2:NM_004431:exon16:c.G2731A:p.E911K | rs376030072 | D | 3991 | 4.44% | ||
| chr1 | 16456039 | G* | A* | synonymous SNV | EPHA2:NM_004431:exon16:c.C2715T:p.P905P | 3055 | 5.24% | ||||
| chr1 | 16456067 | G* | A* | nonsynonymous SNV | EPHA2:NM_004431:exon16:c.C2687T:p.P896L | T | 2950 | 5.29% | |||
| chr1 | 16456744 | C* | T* | synonymous SNV | EPHA2:NM_004431:exon15:c.G2646A:p.K882K | 4205 | 4.04% | ||||
| chr1 | 16456822 | C | A | nonsynonymous SNV | EPHA2:NM_004431:exon15:c.G2568T:p.Q856H | D | 4309 | 7.80% | |||
| chr1 | 16458240 | G* | A* | synonymous SNV | EPHA2:NM_004431:exon14:c.C2451T:p.P817P | 6056 | 3.32% | ||||
| chr1 | 16458257 | T | C | nonsynonymous SNV | EPHA2:NM_004431:exon14:c.A2434G:p.T812A | D | 5718 | 3.06% | |||
| chr1 | 16458352 | G* | A* | nonsynonymous SNV | EPHA2:NM_004431:exon14:c.C2339T:p.P780L | D | 1668 | 8.69% | |||
| chr1 | 16458353 | G* | A* | nonsynonymous SNV | EPHA2:NM_004431:exon14:c.C2338T:p.P780S | D | 1668 | 5.28% | |||
| chr1 | 16458579 | C* | T* | nonsynonymous SNV | EPHA2:NM_004431:exon13:c.G2305A:p.E769K | rs367724183 | 2.37E-05 | D | 1247 | 6.52% | |
| chr1 | 16458598 | G | A | synonymous SNV | EPHA2:NM_004431:exon13:c.C2286T:p.R762R | 2564 | 33.35% | ||||
| chr1 | 16458890 | G* | A* | synonymous SNV | EPHA2:NM_004431:exon12:c.C2098T:p.L700L | 1776 | 3.72% | ||||
| chr1 | 16458893 | C* | T* | nonsynonymous SNV | EPHA2:NM_004431:exon12:c.G2095A:p.A699T | ID = COSM1727288 | D | 1780 | 4.22% | ||
| chr1 | 16458896 | C* | T* | nonsynonymous SNV | EPHA2:NM_004431:exon12:c.G2092A:p.G698R | D | 1781 | 4.27% | |||
| chr1 | 16458911 | C* | T* | nonsynonymous SNV | EPHA2:NM_004431:exon12:c.G2077A:p.E693K | D | 1776 | 4.23% | |||
| chr1 | 16458927 | G* | A* | synonymous SNV | EPHA2:NM_004431:exon12:c.C2061T:p.P687P | 1775 | 3.90% | ||||
| chr1 | 16459729 | T | C | nonsynonymous SNV | EPHA2:NM_004431:exon11:c.A1999G:p.M667V | D | 2940 | 8.80% | |||
| chr1 | 16459977 | T | C | synonymous SNV | EPHA2:NM_004431:exon10:c.A1863G:p.A621A | 3560 | 3.65% | ||||
| chr1 | 16460030 | A | G | nonsynonymous SNV | EPHA2:NM_004431:exon10:c.T1810C:p.F604L | D | 2125 | 4.33% | |||
| chr1 | 16460049 | G* | A* | synonymous SNV | EPHA2:NM_004431:exon10:c.C1791T:p.P597P | 3711 | 3.18% | ||||
| chr1 | 16460050 | G* | A* | nonsynonymous SNV | EPHA2:NM_004431:exon10:c.C1790T:p.P597L | D | 3700 | 3.22% | |||
| chr1 | 16460066 | G* | A* | nonsynonymous SNV | EPHA2:NM_004431:exon10:c.C1774T:p.H592Y | D | 3736 | 3.28% | |||
| chr1 | 16460068 | G* | A* | nonsynonymous SNV | EPHA2:NM_004431:exon10:c.C1772T:p.P591L | D | 3486 | 3.30% | |||
| chr1 | 16460401 | G* | A* | synonymous SNV | EPHA2:NM_004431:exon9:c.C1692T:p.N564N | 1197 | 7.20% | ||||
| chr1 | 16460407 | C* | T* | synonymous SNV | EPHA2:NM_004431:exon9:c.G1686A:p.R562R | 2464 | 20.06% | ||||
| chr1 | 16460962 | C* | T* | splicing | NM_004431:exon9:c.1682+1G>A | 4208 | 5.28% | ||||
| chr1 | 16461003 | G* | A* | nonsynonymous SNV | EPHA2:NM_004431:exon8:c.C1642T:p.L548F | D | 1415 | 3.67% | |||
| chr1 | 16461007 | G* | A* | synonymous SNV | EPHA2:NM_004431:exon8:c.C1638T:p.V546V | 3799 | 5.00% | ||||
| chr1 | 16461024 | C | T | nonsynonymous SNV | EPHA2:NM_004431:exon8:c.G1621A:p.V541M | rs61731097 | 2.26E-03 | D | 3766 | 3.58% | |
| chr1 | 16462157 | C | T | nonsynonymous SNV | EPHA2:NM_004431:exon6:c.G1421A:p.R474H | D | 4070 | 3.02% | |||
| chr1 | 16464354 | G* | A* | stopgain | EPHA2:NM_004431:exon5:c.C1306T:p.Q436X | D | 4515 | 3.43% | |||
| chr1 | 16464480 | G* | A* | nonsynonymous SNV | EPHA2:NM_004431:exon5:c.C1180T:p.R394C | 2.37E-05 | D | 4989 | 5.46% | ||
| chr1 | 16464490 | G | A | synonymous SNV | EPHA2:NM_004431:exon5:c.C1170T:p.H390H | rs113173342 | 1.02E-03 | 4613 | 4.10% | ||
| chr1 | 16464498 | G* | A* | nonsynonymous SNV | EPHA2:NM_004431:exon5:c.C1162T:p.P388S | D | 4640 | 5.07% | |||
| chr1 | 16464513 | C | T | nonsynonymous SNV | EPHA2:NM_004431:exon5:c.G1147A:p.V383M | ID = COSM1205441 | D | 7947 | 3.60% | ||
| chr1 | 16464529 | C* | T* | synonymous SNV | EPHA2:NM_004431:exon5:c.G1131A:p.G377G | 2588 | 3.21% | ||||
| chr1 | 16464550 | C* | T* | stopgain | EPHA2:NM_004431:exon5:c.G1110A:p.W370X | T | 7850 | 3.80% | |||
| chr1 | 16464553 | G* | A* | synonymous SNV | EPHA2:NM_004431:exon5:c.C1107T:p.C369C | 2488 | 12.42% | ||||
| chr1 | 16464583 | G | A | synonymous SNV | EPHA2:NM_004431:exon5:c.C1077T:p.D359D | 5120 | 3.03% | ||||
| chr1 | 16464596 | C* | T* | nonsynonymous SNV | EPHA2:NM_004431:exon5:c.G1064A:p.G355E | D | 2489 | 3.50% | |||
| chr1 | 16464607 | A | G | synonymous SNV | EPHA2:NM_004431:exon5:c.T1053C:p.P351P | 1090 | 3.13% | ||||
| chr1 | 16464618 | A | G | nonsynonymous SNV | EPHA2:NM_004431:exon5:c.T1042C:p.W348R | D | 1808 | 3.98% | |||
| chr1 | 16464621 | G | A | nonsynonymous SNV | EPHA2:NM_004431:exon5:c.C1039T:p.R347C | 7.90E-06 | D | 1442 | 3.81% | ||
| chr1 | 16464625 | C* | T* | synonymous SNV | EPHA2:NM_004431:exon5:c.G1035A:p.E345E | 1659 | 18.26% | ||||
| chr1 | 16464641 | A | G | nonsynonymous SNV | EPHA2:NM_004431:exon5:c.T1019C:p.M340T | D | 1011 | 4.95% | |||
| chr1 | 16464655 | G* | A* | synonymous SNV | EPHA2:NM_004431:exon5:c.C1005T:p.L335L | 2505 | 4.47% | ||||
| chr1 | 16464658 | G* | A* | synonymous SNV | EPHA2:NM_004431:exon5:c.C1002T:p.Y334Y | 2078 | 8.81% | ||||
| chr1 | 16464664 | T | C | synonymous SNV | EPHA2:NM_004431:exon5:c.A996G:p.P332P | 2070 | 3.54% | ||||
| chr1 | 16464822 | A | G | synonymous SNV | EPHA2:NM_004431:exon4:c.T927C:p.C309C | 6671 | 3.36% | ||||
| chr1 | 16475091 | G* | A* | nonsynonymous SNV | EPHA2:NM_004431:exon3:c.C605T:p.P202L | D | 3906 | 4.74% | |||
| chr1 | 16475108 | G* | A* | synonymous SNV | EPHA2:NM_004431:exon3:c.C588T:p.V196V | 3928 | 3.39% | ||||
| chr1 | 16475144 | A | G | synonymous SNV | EPHA2:NM_004431:exon3:c.T552C:p.D184D | 2676 | 10.31% | ||||
| chr1 | 16475374 | A | G | nonsynonymous SNV | EPHA2:NM_004431:exon3:c.T322C:p.F108L | rs149867517 | 7.89E-06 | T | 5817 | 4.06% | |
| chr1 | 16475408 | A | G | synonymous SNV | EPHA2:NM_004431:exon3:c.T288C:p.I96I | 4013 | 12.52% | ||||
| chr1 | 16475446 | T | C | nonsynonymous SNV | EPHA2:NM_004431:exon3:c.A250G:p.N84D | T | 5681 | 3.15% | |||
| chr1 | 16475451 | C | T | nonsynonymous SNV | EPHA2:NM_004431:exon3:c.G245A:p.R82H | 1.58E-05 | D | 5662 | 3.55% | ||
| chr1 | 16477406 | G* | A* | synonymous SNV | EPHA2:NM_004431:exon2:c.C138T:p.H46H | 7.89E-06 | 4868 | 4.36% |
*SNV at di-pyrimidine site. D—damaging, T—tolerated.