2 DY
M tested
tested tested
tested 3
JT F
tested -
tested tested
4 RA
M tested
tested tested
tested 5
RGP M
tested tested
tested tested
6 DM
M tested
tested tested
tested 7
NTW M
tested tested
tested tested
8 DS
F tested
- tested
tested 9
AAI M
tested tested
tested tested
10 JO
F tested
- tested
tested 11
RA M
tested tested
tested tested
12 AK
M tested
tested tested
tested 13
DAT M
tested tested
tested tested
14 PH
M tested
tested tested
tested 15
RA F
tested -
tested tested
16 D
M tested
tested tested
tested 17
LA F
tested -
tested tested
18 AA
M tested
tested tested
tested 19
R F
tested -
tested tested
20 FAE
M tested
tested tested
tested 21
DB F
tested -
tested tested
22 SB
M tested
tested tested
tested 23
DBP M
tested tested
tested tested
24 EA
F tested
- tested
tested 25
FRHP M
tested tested
tested tested
26 D
F tested
- tested
tested 27
J F
tested -
tested tested
28 Yosepin
F tested
- tested
tested 29
Aris Masari M
tested tested
tested tested
30 Yuda
M tested
tested tested
tested 31
Evi F
tested -
tested tested
IV.3.1 SCN1A
SCN1A were chosen because it is involved in channelopathies, one of the basic pathogenesis of epilepsy. It is tested for all patients males and females, it was chosen to be first
tested due to its high prevalence that in the society. It is also a well known gene for FS, GEFS+, and SMEI
13
.
First step was designed the primers of SCN1A. PCR product were run on the gel and got the results. If there are product on the gel, then the primer worked. Here is the example of the
PCR product of the tested SCN1A primers. After purified the DNA then sequencing were performed.
Figure 7. Results of SCN1A primers with three controls and 26 exons tested.
Figure 8. Some of the results of SCN1A sequencing.
Analyzing whether this results are real mutation or just SNPs were performed using Alamut software. Some of the results are new SNPs, it might be not recorded yet because mostly
Javanese population were sequenced. After comparation from Alamut software that mostly came from Caucasians population, conclusion were drawned.
Table 6.
SNPs Results from SCN1A screening examination
exon Intron SNPs
Protein RS number
Total Caucassian
Control From 31
2 c.383+66 TC
rs8191987 TC 12
38,71 66,7
5 c.603-106 GT
rs3812719 GT 2
6,45 c.603-91 GA
rs3812718 GA 11
35,48 6
c.964+116 AT rs6750294 AT
9 29,03
66,7 c.964+199 TG
rs6706163 TG 7
22,58 7
c.965-21 CT rs994399 CT
3 9,68
33,3 c.1028+21 TC
rs1542484 TC 13
41,93 8
c.1029-68 CT rs1461193 CT
1 3,23
c.1170+75 CA
rs11690962 CA 7
22,58 33,3
c.1170+112 CT
rs11690959 CT 4
12,9 9
c.1212 AG rs7580482 AG
4 12,9
c.1377+52 GA
rs6432861 GA 4
12,9 11
c.1663-47 TG rs6753355 TG
1 3,23
12 c.2143+44 CT
New finding 2
6,45 13
c.2259 TC rs6432860 TC
5 16,13
33,3 15
c.2808 GA p.V936V
New finding 1
3,23 c.2913+56
AG rs2020318 AG
4 12,9
16 c.3167 GA
rs2298771 GA 2
6,45 22
c.4305+74 CT rs4305294 CT
3 9,68
23 c.4443+33
GA rs73969742
GA 3
9,68
Two unclassified varients in the intron 12 and exon 15 were found. These variants are believed to be rare nonpathogenic variants, since they did not lead to a change in the amino acid
sequence of the protein. Therefore, they are believed not to explain MR and epilepsy from the patients list.
Splice site prediction programs already performed to those SNPs. Yet, no changes were found and proven influencing on gene splicing process.
IV.3.2 ARX
