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Table 1 Results of mutation analysis in 25 patients with pathogenic or likely pathogenic mutations involving single nucleotide or several exons according to ACMG guideline

From: Efficient strategy for the molecular diagnosis of intractable early-onset epilepsy using targeted gene sequencing

Patient Gene Inheritance NM Nucleotide change Amino acid change Zygosity ACMG classification ACMG evidence components Origin of variant
P1 STXBP1 AD NM_003165.3 c.733C > G p.His245Asp Heterozygosity Pathogenic PS2, PM2, PM5, PP3, PP4 de novo
P2 STXBP1 AD NM_003165.3 c.874C > T p.Arg292Cys Heterozygosity Pathogenic PS1, PS2, PM2, PP4 de novo
P3 STXBP1 AD NM_003165.3 c.1216C > T p.Arg406Cys Heterozygosity Pathogenic PS1, PS2, PM2, PM5, PP3, PP4 de novo
P4 CDKL5 XD NM_003159.2 c.511 T > A p.Tyr171Asn Heterozygosity Pathogenic PS2, PM2, PM5, PP3, PP4 de novo
P5 CDKL5 XD NM_003159.2 c.282 + 1G > A splice site Heterozygosity Pathogenic PVS1, PS2, PM2, PP4, PP5 de novo
P6 KCNQ2 AD NM_172107.2 c.917C > T p.Ala306Val Heterozygosity Pathogenic PS2, PM2, PP2, PP3, PP4, PP5 de novo
P7 KCNQ2 AD NM_172107.2 c.593G > A p.Arg198Gln Heterozygosity Pathogenic PS2, PM2, PP2, PP3, PP4, PP5 de novo
P8 SCN1A AD NM_001165963.1 c.5068_5069delinsG p.Ser1690AlafsTer25 Heterozygosity Pathogenic PVS1, PM2, PP4 NA
P9 SCN1A AD NM_001165963.1 c.1209dupT p.Val404CysfsTer46 Heterozygosity Pathogenic PVS1, PM2, PP4 NA
P10 SYNGAP1 AD NM_006772.2 c.980 T > C p.Leu327Pro Heterozygosity Likely pathogenic PS2, PM2, PP3, PP4, PP5 de novo
P11 SYNGAP1 AD NM_006772.2 c.1735C > T p.Arg579Ter Heterozygosity Pathogenic PVS1, PM2, PP4, PP5 NA
P12 GNAO1 AD NM_020988.2 c.118G > T p.Gly40Trp Heterozygosity Pathogenic PS2, PM2, PM5, PP3, PP4 de novo
P13 GNAO1 AD NM_020988.2 c.155A > C p.Gln52Pro Heterozygosity Likely pathogenic PS2, PM2, PP3, PP4 de novo
P14 KCNT1 AD NM_020822.2 c.2800G > A p.Ala934Thr Heterozygosity Likely pathogenic PS1, PM2, PP4 NA
P15 KCNT1 AD NM_020822.2 c.1038C > G p.Phe346Leu Heterozygosity Likely pathogenic PS2, PM2, PP2, PP4 de novo
P16 BRAT1 AR NM_152743.3 c.1576C > T p.Gln526Ter Heterozygosity Likely pathogenic PVS1, PM2, PP4 maternal inheritance
P16 BRAT1 AR NM_152743.3 exon 2–3 deletion _ Heterozygosity Likely pathogenic PM2, PM3, PP4, PP5 NA
P17 WWOX AR NM_016373.2 c.1060C > T p.Gln354Ter Heterozygosity Pathogenic PVS1, PM2, PM3, PP4 maternal inheritance
P17 WWOX AR NM_016373.2 exon 6–8 duplication _ Heterozygosity Likely pathogenic PM2, PM3, PP4, PP5 paternal inheritance
P18 ZEB2 AD NM_014795.3 c.1956C > A p.Tyr652Ter Heterozygosity Pathogenic PVS1, PS1, PM2, PP4 NA
P19 CHD2 AD NM_001271.3 c.1269dupA p.Glu424ArgfsTer3 Heterozygosity Pathogenic PVS1, PM2, PP4 NA
P20 PRICKLE2 AD NM_198859.3 c.2129_2147del p.Arg710LeufsTer2 Heterozygosity Likely pathogenic PVS1, PM2 NA
P21 COL4A1 AD NM_001845.4 c.2897G > A p.Gly966Glu Heterozygosity Likely pathogenic PS2, PM2, PP2, PP3, PP4 de novo
P22 DNM1 AD NM_004408.2 c.1195A > G p.Arg399Gly Heterozygosity Likely pathogenic PS2, PM2, PP2, PP3, PP4 de novo
P23 SCN8A AD NM_014191.3 c.782G > T p.Cys261Phe Heterozygosity Likely pathogenic PS2, PM2, PP2, PP3, PP4 de novo
P24 MECP2 XD NM_004992.3 c.1164_1207del p.Pro389Ter Heterozygosity Pathogenic PVS1, PM1, PM2, PP4 NA
P25 SLC9A6 XD NM_006359.2 c.316_325 + 28del splice site Heterozygosity Pathogenic PVS1, PS2, PM2, PP4 de novo
  1. AD autosomal dominant, XD X dominant, AR autosomal recessive, VUS variant of unknown significance, PVS pathogenic very strong, PS pathogenic strong, PM pathogenic moderate, PP pathogenic supporting, NA not available