Table 2 Gene testing results of all the 38 patients and the affected family members and pathogenic analysis of the variants
Case ID | Genetic testing method | Gene | OMIM/ literature inheritance pattern | Genotype | Ensembl transcript ID | Coding DNA change | Amino acid change | Origin | ACMG |
|---|---|---|---|---|---|---|---|---|---|
P1 | Trio-based WES | PPT1 | reccessive | het | ENST00000433473 | c.372_373insTG | p.Ala125TrpfsTer10 | Maternal | Pathogenic |
reccessive | het | ENST00000433473 | c.413C > T | p.Ser138Leu | Paternal | Likely pathogenic | |||
P2 | Trio-based WES | PPT1 | reccessive | het | ENST00000433473 | c.413C > T | p.Ser138Leu | Paternal | Likely pathogenic |
reccessive | het | ENST00000433473 | c.713C > T | p.Pro238Leu | Maternal | Uncertain significance | |||
P3 | Sanger sequencing of TPP1 | TPP1 | reccessive | hom | ENST00000299427 | c.177_180delAAGA [12] | p.Glu59AspfsTer21 | Paternal and maternal | Pathogenic |
P4 | NGS panels of epilepsy | TPP1 | reccessive | hom | ENST00000299427 | c.515delG | p.Gly172AspfsTer11 | Paternal and maternal | Pathogenic |
P5 | Trio-based WES | TPP1 | reccessive | het | ENST00000299427 | c.1424C > T [13] | p.Ser475Leu | Maternal | Likely pathogenic |
reccessive | het | ENST00000299427 | c.1222_1224del | p.Ser408del | Paternal | Likely pathogenic | |||
P6–1 | Trio-based WES and qPCR | TPP1 | reccessive | het | ENST00000299427 | c.1613C > A | p.Ser538Tyr | Maternal | Likely pathogenic |
reccessive | het | ENST00000299427 | 1–3 exon deletion | / | Paternal | Pathogenic | |||
P6–2 | Sanger sequencing and qPCR | TPP1 | reccessive | het | ENST00000299427 | c.1613C > A | p.Ser538Tyr | Maternal | Likely pathogenic |
reccessive | het | ENST00000299427 | 1–3 exon deletion | / | Paternal | Pathogenic | |||
P7 | NGS panels of epilepsy | TPP1 | reccessive | het | ENST00000299427 | c.1424C > T [13] | p.S475L | Paternal | Likely pathogenic |
reccessive | het | ENST00000299427 | c.177_180delAAGA [12] | p.Glu59AspfsTer21 | Maternal | Pathogenic | |||
P8 | Trio-based WES | TPP1 | reccessive | het | ENST00000299427 | c.1622_1633del | p.Gly541_Pro544del | Maternal | Uncertain significance uncertain |
reccessive | het | ENST00000299427 | c.1145 + 3_1145 + 4insGTACTCTAGGTAAGTAAGTACTCTAGGCTAGGTAAGTACTCTACCCTGCCTCCAGGTAGTACTCTAGGTAAGTAAGTACTCTAGGCTGGTA | / | Paternal | Uncertain significance | |||
P9 | Trio-based WES | CLN3 | reccessive | het | ENST00000360019 | c.946G > A | p.Ala316Thr | Paternal | Uncertain significance |
/ | / | / | / | / | / | / | |||
P10 | Trio-based WES | CLN5 | reccessive | hom | ENST00000377453 | c.451 T > C | p.Trp151Arg | Paternal and maternal | Uncertain significance |
P11 | NGS panels of epilepsy | CLN6 | reccessive | het | ENST00000249806 | c.41delG | p.Gly14AlafsTer19 | Maternal | Pathogenic |
reccessive | het | ENST00000249806 | c.184C > T [14] | p.Arg62Cys | Paternal | Likely pathogenic | |||
P12 | Trio-based WES | MFSD8 | reccessive | het | ENST00000296468 | c.1351-1G > A | / | Maternal | Pathogenic |
reccessive | het | ENST00000296468 | c.557 T > G | p.Phe186Cys | Paternal | Likely pathogenic | |||
P13–1 | NGS panels of epilepsy | MFSD8 | reccessive | het | ENST00000296468 | c.1351-1G > A | / | Paternal | Pathogenic |
reccessive | het | ENST00000296468 | c.300 T > G | p.Tyr100Ter | Maternal | Pathogenic | |||
P13–2 | NGS panels of epilepsy | MFSD8 | reccessive | het | ENST00000296468 | c.1351-1G > A | / | Paternal | Pathogenic |
reccessive | het | ENST00000296468 | c.300 T > G | p.Tyr100Ter | Maternal | Pathogenic | |||
P13–3 | Not done | NA | / | / | / | / | / | / | / |
/ | / | / | / | / | / | / | |||
P14 | NGS panels of epilepsy | NEU1 | reccessive | het | ENST00000375631 | c.544 A > G [15] | p.Ser182Gly | Paternal | Pathogenic |
reccessive | het | ENST00000375631 | c.239 C > T [16] | p.Pro80Leu | Maternal | Pathogenic | |||
P15–1 | Sanger sequencing of NEU1 | NEU1 | reccessive | het | ENST00000375631 | c.544A > G [15] | p.Ser182Gly | Paternal | Pathogenic |
reccessive | het | ENST00000375631 | c.239C > T [16] | p.Pro80Leu | Maternal | Pathogenic | |||
P15–2 | Sanger sequencing of NEU1 | NEU1 | reccessive | het | ENST00000375631 | c.544A > G [15] | p.Ser182Gly | Paternal | Pathogenic |
reccessive | het | ENST00000375631 | c.239C > T [16] | p.Pro80Leu | Maternal | Pathogenic | |||
P16–1 | Sanger sequencing of GBA | GBA | reccessive | het | ENST00000327247 | c.680A > G [17] | p.Asn227Ser | Paternal | Pathogenic |
reccessive | het | ENST00000327247 | c.1448 T > C [18] | p.Leu483Pro | Maternal | Pathogenic | |||
reccessive | het | ENST00000327247 | c.1342G > C [19] | p.Asp448His | Maternal | Pathogenic | |||
P16–2 | Sanger sequencing of GBA | GBA | reccessive | het | ENST00000327247 | c.680A > G [17] | p.Asn227Ser | Paternal | Pathogenic |
reccessive | het | ENST00000327247 | c.1448 T > C [18] | p.Leu483Pro | Maternal | Pathogenic | |||
reccessive | het | ENST00000327247 | c.1342G > C [19] | p.Asp448His | Maternal | Pathogenic | |||
P17 | Sanger sequencing of GBA | GBA | reccessive | het | ENST00000327247 | c.907C > A | p.Leu303Ile | Paternal | Likely pathogenic |
reccessive | het | ENST00000327247 | c.1265_1319del [20] | p.Leu422ProfsTer4 | Maternal | Pathogenic | |||
P18–1 | NGS panels of epilepsy | ASAH1 | reccessive | het | ENST00000381733 | c.304_305insA [9] | p.Thr102AsnfsTer14 | Paternal | Pathogenic |
reccessive | het | ENST00000381733 | c.173C > T [9] | p.Thr58Met | Maternal | Likely pathogenic | |||
P18–2 | NGS panels of epilepsy | ASAH1 | reccessive | het | ENST00000381733 | c.304_305insA [9] | p.Thr102AsnfsTer14 | Paternal | Pathogenic |
reccessive | het | ENST00000381733 | c.173C > T [9] | p.Thr58Met | Maternal | Likely pathogenic | |||
P19 | Trio-based WES | KCNC1 | dominant | het | ENST00000265969 | c.1262C > T [9] | p.Ala421Val | De novo | Pathogenic |
P20 | Trio-based WES | KCNC1 | dominant | het | ENST00000265969 | c.1262C > T [9] | p.Ala421Val | De novo | Pathogenic |
P21 | Trio-based WES | KCNC1 | dominant | het | ENST00000265969 | c.959G > A [9] | p.Arg320His | De novo | Pathogenic |
P22 | Trio-based WES | KCNC1 | dominant | het | ENST00000265969 | c.959G > A [9] | p.Arg320His | De novo | Pathogenic |
P23 | NGS panels of epilepsy | KCTD7 | reccessive | het | ENST00000275532 | c.458G > A [21] | p.Arg153His | Paternal | Uncertain significance |
reccessive | het | ENST00000275532 | c.533C > T [22] | p.Ala178Val | Maternal | Uncertain significance | |||
P24 | NGS panels of epilepsy | KCTD7 | reccessive | het | ENST00000275532 | c.184 T > G | p.Phe62Val | Paternal | Likely pathogenic |
reccessive | het | ENST00000275532 | c.341G > A | p.Gly114Glu | Maternal | Likely pathogenic | |||
P25–1 | Trio-based WES | KCTD7 | reccessive | het | ENST00000275532 | c.440 T > C | p.Leu147Pro | Maternal | Likely pathogenic |
reccessive | het | ENST00000275532 | c.520G > A | p.Ala174Thr | Paternal | Uncertain significance | |||
P25–2 | Trio-based WES | KCTD7 | reccessive | het | ENST00000275532 | c.440 T > C | p.Leu147Pro | Maternal | Likely pathogenic |
reccessive | het | ENST00000275532 | c.520G > A | p.Ala174Thr | Paternal | Uncertain significance | |||
P26 | Trio-based WES | KCTD7 | reccessive | het | ENST00000275532 | c.384G > C | p.Glu128Asp | Paternal | Uncertain significance |
reccessive | het | ENST00000275532 | c.845A > G | p.Tyr282Cys | Maternal | Uncertain significance | |||
P27 | NGS panels of epilepsy | TBC1D24 | reccessive | het | ENST00000567020 | c.241_252del [9] | p.81_84del | Paternal | Pathogenic |
reccessive | het | ENST00000567020 | c.1153C > T [9] | p.Gln385Ter | Maternal | Pathogenic | |||
P28 | Trio-based WES | TBC1D24 | reccessive | het | ENST00000567020 | c.241_252del [9] | p.81_84del | Maternal | Pathogenic |
reccessive | het | ENST00000567020 | c.139A > G [9] | p.Ser47Gly | De novo | Likely pathogenic | |||
P29–1 | Trio-based WES | GOSR2 | reccessive | het | ENST00000225567 | c.146delA [9] | p.Glu49AspfsTer25 | Maternal | Pathogenic |
reccessive | het | ENST00000225567 | c.478-16 T > A [9] | / | Paternal | Uncertain significance | |||
P29–2 | Trio-based WES | GOSR2 | reccessive | het | ENST00000225567 | c.146delA [9] | p.Glu49AspfsTer25 | Maternal | Pathogenic |
reccessive | het | ENST00000225567 | c.478-16 T > A [9] | / | Paternal | Uncertain significance | |||
P30–1 | Trio-based WES and detection of trinucleotide (CAG) repeat number | ATN1 | dominant | het | / | CAG repeats was 70 [9] | / | Paternal | / |
P30–2 | Detection of trinucleotide (CAG) repeat number | ATN1 | dominant | het | / | / | / | / | / |
P30–3 | Not done | NA | / | / | / | / | / | / | / |
P31–1 | Trio-based WES and detection of trinucleotide (CAG) repeat number | ATN1 | dominant | het | / | CAG repeats was 73 | / | Paternal | / |
P31–2 | Detection of trinucleotide (CAG) repeat number | ATN1 | dominant | het | / | CAG repeats was 74 | / | / | / |
P31–3 | Detection of trinucleotide (CAG) repeat number | ATN1 | dominant | het | / | CAG repeats was 63 | / | / | / |
P31–4 | Not done | NA | / | / | / | / | / | / | / |
P31–5 | Not done | NA | / | / | / | / | / | / | / |
P32–1 | Trio-based WES | Negative | / | / | / | / | / | / | / |
P32–2 | Trio-based WES | Negative | / | / | / | / | / | / | / |
P33 | Trio-based WES | Negative | / | / | / | / | / | / | / |
P34 | Trio-based WES | Negative | / | / | / | / | / | / | / |
P35 | Trio-based WES | Negative | / | / | / | / | / | / | / |
P36 | Trio-based WES | Negative | / | / | / | / | / | / | / |
P37 | Trio-based WES | Negative | / | / | / | / | / | / | / |
P38 | Trio-based WES | Negative | / | / | / | / | / | / | / |