Table 2.
Potentially pathogenic variants identified by whole-exome sequencing in 18 EA patients.
| Patient No | Family History | Gene | Exon | mRNA | Protein | Variant effect | SIFT | LRT | Polyphen | Mutation taster | GERP | MAF | Pathogenic |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | + | CACNA1A | 16 | c.2030 G > A | p.Gly677Glu | missense | D | D | B | D | 4.58 | — | possible |
| 2 | + | CACNA1A | 40 | c.5956 C > T | p.Gln1986* | nonsense | — | — | — | — | — | — | probable |
| UBR4 | 100 | c.14630 A > G | p.Tyr4877Cys | missense | D | D | D | D | 5.75 | — | possible | ||
| 3 | + | CACNA1A | 23 | c.3871_3873delGAG | p.Glu1294 DEL | deletion | — | — | — | — | — | — | probable |
| SLC1A3 | 7 | c.985 G > A | p.Ala329Thr | missense | D | D | P | D | 5.71 | 0.0003† | probable | ||
| 4 | + | CACNA1A | 5 | c.742 T > A | p.Tyr248Asn | missense | D | D | D | D | 5.55 | — | possible |
| 5 | + | CACNA1A | 32 | c.5005 C > T | p.Arg1669* | nonsense | — | — | — | — | — | — | probable |
| CACNA1A | 19 | c.2992 G > C | p.Glu998Gln | missense | T | N | B | D | 1.91 | — | possible | ||
| UBR4 | 83 | c.12332 G > A | p.Arg4111His | missense | T | D | P | D | 5.25 | 0.0001† | possible | ||
| 6 | + | SLC1A3 | 8 | c.1177 G > A | p.Val393Ile | missense | T | D | P | D | 5.8 | — | probable |
| 11 | + | TTBK2 | 15 | c.3467 G > A | p.Arg1156Gln | missense | D | D | D | D | 5.13 | 0.00002† | possible |
| 12 | + | TGM6 | 10 | c.1478 C > T | p.Pro493Leu | missense | T | N | D | D | 4.67 | 0.0001† | possible |
| 15 | − | CACNA1A | 20 | c.3321_3322insC | p.Gly1108Argfs40* | insertion | — | — | — | — | — | — | probable |
| CACNA1A | 46 | c.6605_6616delACC AGGAGCGGG | p.Asp2202_Arg2205DEL | deletion | — | — | — | — | — | 0.0005† | possible | ||
| 16 | − | CACNA1A | 29 | c.4645 C > T | p.Arg1549* | nonsense | — | — | — | — | — | — | probable |
| 19 | − | ATP1A2 | 6 | c.586 C > T | p.Arg196Cys | missense | D | D | D | D | 5.11 | 0.00003† | possible |
| 22 | − | SCN1A | 26 | c.5516 T > G | p.Ile1839Ser | missense | D | D | D | D | 5.6 | 0.000008† | possible |
| 23 | − | SLC1A3 | 7 | c.952 A > G | p.Thr318Ala | missense | T | D | B | D | 6.07 | 0.0002† | possible |
| 26 | − | UBR4 | 103 | c.15125 C > T | p.Ala5042Val | missense | T | D | D | D | 5.39 | 0.0002‡ | possible |
| 28 | − | UBR4 | 52 | c.7742 C > T | p.Ala2581Val | missense | D | D | D | D | 5.95 | — | possible |
| 30 | − | SCN1A | 11 | c.1688T > A | p.Leu563Gln | missense | D | D | D | D | 5.59 | — | possible |
| 32 | − | FGF14 | 1 | c.31 A > G | p.Thr11Ala | missense | D | N | B | D | 4.73 | — | possible |
| 33 | − | KCND3 | 4 | c.1291 C > T | p.Arg431Cys | missense | D | D | D | D | 5.25 | 0.000009† | possible |
Transcript ID: ATP1A2, NM_000702.3 (NP_000693.1); CACNA1A, NM_023035.2 (NP_075461.2); FGF14, NM_175959.2 (NP_787125.1); KCND3, NM_004890.4(NP_004971.2); SCN1A, NM_006920.4 (NP_008851.3); SLC1A3, NM_004172.4 (NP_00416.3); TGM6, NM_198994.2 (NP_945345.2); TTBK2, NM_173500.3 (NP_775771.3); UBR4, NM_020765.2 (NP_065816.2). SIFT- D (damaging), T (tolerated); LRT- D (deleterious), N (neutral); Polyphen- D (probably damaging), P (possibly damaging), B (benign); MutationTaster- D (disease_causing). †MAF based on the Exome Aggregation Consortium (ExAC), ‡MAF based on the 1000 Genomes Project.