Variants of uncertain significance in 15 focal epilepsy genes
| Patient ID, sex, age at onset (years) | Epilepsy phenotype | Gene (transcript) variants | In silico (CADD, pph2 and SIFT) | Allele frequency (gnomAD) |
| 1, f, 6 | MRI-negative TLE |
LGI1
NM_005097.3: c.1208G>A p.(Ser403Asn) | 25.5, D, D | 0 |
|
NPRL3
NM_001077350.2: c.1561G>A p.(Ala521Thr) | 24.7, D, T | 0.00002 | ||
| 7, f, 1 | MRI-negative TLE |
SCN8A
NM_014191.3: c.3185A>C p.(Asn1062Thr) | 23.6, PD, D | 0 |
| 19, f, 12 | MRI-negative TLE |
LGI1
NM_005097.2: c.1124C>T p.(Ala375Val) | 20.2, B, T | 0.000018 |
| 31, f, 3 | MRI-negative FLE |
CHRNA4
NM_000744.6: c.419A>G p.(Lys140Arg) | 25.1, D, D | 0 |
| 43, m, 1 | MRI-negative TLE |
RELN
NM_005045.3: c.3479A>G p.(Asn1160Ser) | 23.6, D, D | 0.000007 |
| 49, f, 10 | MRI-negative FLE |
KCNT1
NM_020822.2: c.2061_2066delCGGTGG p.(Gly691_Gly692del) | N/A (indel) | 0.000034 |
| 50, f, 54 | MRI-negative TLE |
KCNQ3
NM_004519.3: c.1709T>C p.(Met570Thr) | 23.7, PD, D | 0.000024 |
| 55, m, 14 | MRI-negative TLE |
NPRL3
NM_001077350.2: c.745G>A p.(Glu249Lys) | 35, D, T | 0.000099 |
| 61, f, 49 | MRI-negative TLE |
KCNQ3
NM_004519.3: c.2237C>T p.(Thr746Met) | 23.2, D, D | 0.000035 |
| 70, m, 18 | MRI-negative TLE |
RELN
NM_005045.3: c.1795C>T p.(Arg599Cys) | 34, PD, D | 0.000028 |
| 84, m, 7 | MRI-negative FLE |
RELN
NM_005045.3: c.8492C>T p.(Pro2831Leu) | 21.9, D, T | 0.000036 |
| 90, m, 34 | MRI-negative TLE |
DEPDC5
NM_001242896.1: c.1526G>A p.(Arg509His) | 23.6, D, T | 0.000036 |
| 91, f, 13 | MRI-negative FLE |
DEPDC5
NM_001242896.1: c.3521C>T p.(Ser1174Phe) | 27.8, PD, D | 0 |
| 101, m, 23 | MRI-negative UFE |
NPRL3
NM_001077350.2: c.1053G>C p.(Gln351His) | 20.3, B, T | 0 |
| 108, m, 3 | MRI-negative FLE |
SCN2A
NM_021007.2: c.3545G>A p.(Cys1182Tyr) | 29.2, PD, D | 0 |
| 110, f, 15 | HS/HA-TLE |
RELN
NM_005045.3: c.10210C>T p.(Arg3404Cys) | 35, D, T | 0.000012 |
Patients with multiple rare variants are highlighted in grey.
CADD, combined annotation-dependent depletion; f, female; FLE, frontal lobe epilepsy; gnomAD, Genome Aggregation Database; HA, hippocampal atrophy; HS, hippocampal sclerosis; m, male; N/A, not applicable; pph2, PolyPhen-2 (B, benign; D, probably damaging; PD. possibly damaging); SIFT, sorting intolerant from tolerant (D, deleterious; T, tolerated); TLE, temporal lobe epilepsy; UFE, unclassified focal epilepsy.