Table 1.
Profile of 49 pathogenic or likely pathogenic sequence variants.
| Case | Gene | Variant (RefSeq:DNA base:amino acid) | Inheritance | ACMG criteria | ACMG classification | ClinVar | HGMD |
|---|---|---|---|---|---|---|---|
| Case 29 | ARHGEF9 | NM_001173479:c.1355G>A:p.Trp452* | From mosaic carrier mother | PVS1, PM2, PP1 | Pathogenic | ||
| Case 75 | ATP1A2 | NM_000702:c.1096G>T:p.Gly366Cys | De novo | PS2, PM1, PM2, PP2, PP3 | Pathogenic | ||
| Case 8 | ATP1A3 | NM_152296:c.1088T>C:p. Ile363Thr | Not evaluated | PM1, PM2, PM5, PP2, PP3 | Likely Pathogenic | ||
| Case 5 | GABRA1 | NM_001127648:c.1015A>G:p.Lys339Glu | From asymptomatic mosaic mother | PM2, PM6+, PP2, PP3 | Likely Pathogenic | ||
| Case 66 | GABRB3 | NM_001191320:c.577C>T:p.Leu193Phe | De novo | PS2, PM2, PP2, PP3 | Likely Pathogenic | ||
| Case 2 | GLRA1 | NM_001292000:c.494_495insAC:p.Met165fs | From asymptomatic father | PVS1, PM2 | Likely Pathogenic | ||
| Case 82 | HCN1 | NM_021072:c.1171G>A:p.Gly391Ser | De novo | PS2, PM2, PP2, PP3 | Likely Pathogenic | ||
| Case 73 | KCNA2 | NM_004974:c.971G>A:p.Ser324Asn | De Novo | PS2, PM2, PP2, PP3 | Likely Pathogenic | ||
| Case 85 | KCNQ2 | NM_004518:c.727C>G:p.Leu243Val | De novo | PS2, PM2, PP2, PP3 | Pathogenic | ||
| Case 14 | KCNQ2 | NM_004518:c.766G>T:p.Gly256Trp | De novo | PS2, PM1, PM2, PP2, PP3, PP4 | Pathogenic | ||
| Case 11 | KCNQ2 | NM_004518:c.997C>T:p.Arg333Trp | Not evaluated | PS2, PS4, PM2, PP2, PP3 | Pathogenic | Pathogenic | DM |
| Case 57 | KCNQ2 | NM_004518:c.998G>A:p.Arg333Gln | From asymptomatic father | PS3, PS4, PM2, PP1, PP2 | Pathogenic | Pathogenic | DM |
| Case 68 | KCNQ2 | NM_004518:c.1130dupC:p.Pro377fs | From asymptomatic father | PVS1, PM2, PP1 | Pathogenic | ||
| Case 39 | KCNQ3 | NM_001204824:c.590T>C:p.Ile197Thr | From symptomatic father | PM1, PM2, PP1, PP2, PP3 | Likely Pathogenic | DM | |
| Case 56 | PCDH19 | NM_001105243:c.595G>T:p.Glu199* | Not evaluated | PVS1, PM2 | Likely Pathogenic | Pathogenic | |
| Case 96 | PCDH19 | NM_001105243:c.1105G>C:p.Ala369Pro | From asymptomatic father | PM2, PP1, PP2, PP3, PP4 | Likely Pathogenic | ||
| Case 51 | PRRT2 | NM_001256442:c.649delC:p.Ala217fs | From asymptomatic father | PVS1, PS4, PM1 | Pathogenic | Pathogenic | |
| Case 43 | PRRT2 | NM_001256442:c.649dupC:p.Ala217fs | From symptomatic father | PVS1, PS4, PM1, PP1 | Pathogenic | Pathogenic | |
| Case 58 | PRRT2 | NM_001256442:c.649dupC:p.Ala217fs | Not evaluated | PVS1, PS4, PM1 | Pathogenic | Pathogenic | |
| Case 71 | PRRT2 | NM_0012564c.649dupC:p.Ala217fs | Not evaluated | PVS1, PS4, PM1 | Pathogenic | Pathogenic | |
| Case 77 | PRRT2 | NM_001256442:c.649dupC:p.Ala217fs | Not evaluated | PVS1, PS4, PM1 | Pathogenic | Pathogenic | |
| Case 78 | PRRT2 | NM_001256442:c.649dupC:p.Ala217fs | From asymptomatic father | PVS1, PS4, PM1 | Pathogenic | Pathogenic | |
| Case 81 | PRRT2 | NM_001256442:c.649dupC:p.Ala217fs | From symptomatic mother | PVS1, PS4, PP1 | Pathogenic | Pathogenic | |
| Case 83 | PRRT2 | NM_001256442:c.649dupC:p.Ala217fs | From symptomatic father | PVS1, PS4, PP1 | Pathogenic | Pathogenic | |
| Case 105 | PRRT2 | NM_001256442:c.649dupC:p.Ala217fs | From symptomatic mother | PVS1, PS4, PP1 | Pathogenic | Pathogenic | |
| Case 34 | PRRT2 | NM_001256442:c.796_797insGG:p.Arg266fs | From symptomatic father | PVS1, PS4, PP1 | Pathogenic | ||
| Case 26 | SCN1A | NM_001165963:c.596_602del:p.Thr199fs | Not evaluated | PVS1, PM2, PP4 | Pathogenic | ||
| Case 101 | SCN1A | NM_001165963:c.2244G>A:p.Trp748* | Not evaluated | PVS1, PS4, PM2, PP4 | Pathogenic | ||
| Case 48 | SCN1A | NM_001202435:c.2947-1G>A | Not evaluated | PVS1, PM2, PP4 | Pathogenic | Likely Pathogenic | |
| Case 40 | SCN1A | NM_001165963:c.4201G>C:p.Glu1401Gln | Not evaluated | PM1, PM2, PP2, PP3, PP4 | Likely Pathogenic | ||
| Case 13 | SCN1A | NM_001165963:c.4219C>T:p.Arg1407* | Not evaluated | PVS1, PM2, PP4 | Pathogenic | Pathogenic | DM |
| Case 54 | SCN1A | NM_001165963:c.5288T>A:p.Ile1763Asn | From symptomatic mother | PS4,PM2, PP1, PP2, PP3, PP4 | Pathogenic | DM | |
| Case 100 | SCN1B | NM_001037:c.373C>T:p.Arg125Cys | Not evaluated | PS3, PM2, PP1, PP2, PP3 | Pathogenic | Pathogenic | DM |
| Case 25 | SCN2A | NM_001040143:c.466A>G:p.Lys156Glu | De novo | PS2, PM2, PP2, PP3, PP4 | Likely Pathogenic | ||
| Case 45 | SCN2A | NM_001040143:c.605C>T:p.Ala202Val | De novo | PS2, PM2, PP2, PP3 | Likely Pathogenic | Uncertain Significance | |
| Case 33 | SCN2A | NM_001040143:c.1879C>T:p.Gln627* | Not evaluated | PVS1, PM2 | Likely Pathogenic | ||
| Case 31 | SCN2A | NM_001040143:c.2932T>C:p.Phe978Leu | De novo | PS2, PM2, PP2, PP3 | Likely Pathogenic | ||
| Case 104 | SCN8A | NM_001177984:c.3820G>A:p.Val1274Met | De novo | PS2, PM2, PP2, PP3 | Likely Pathogenic | ||
| Case 111 | SCN8A | NM_014191:c.4423G>A.:p.Gly1475Arg | Not evaluated | PM2, PP2, PP3, PP4, PP5 | Likely Pathogenic | Pathogenic/Likely Pathogenic | |
| Case 79 | SCN8A | NM_001177984:c.5491C>T:p.Arg1831Trp | De novo | PS2, PM2, PP2, PP3 | Likely Pathogenic | Pathogenic | DM |
| Case 47 | SLC2A1 | NM_006516:c.223C>A:p.Gly75Arg | De novo | PS2, PM2, PP2, PP3 | Likely Pathogenic | ||
| Case 12 | SLC2A1 | NM_006516:c.940G>C:p.Gly314Arg | Inherited from symptomatic mother | PM2, PM5, PP1, PP2, PP3 | Likely Pathogenic | ||
| Case 93 | SLC2A1 | NM_006516:c.1255G>C:p.Gly419Arg | De novo | PS2, PM2, PP2, PP3 | Likely Pathogenic | ||
| Case 17 | STXBP1 | NM_001032221:c.703C>T:p.Arg235* | De novo | PVS1, PS2, PM2 | Pathogenic | Pathogenic | DM |
| Case 109 | STXBP1 | NM_001032221:c.1099C>T:p.Arg367* | Not evaluated | PVS1, PM2 | Likely Pathogenic | Pathogenic | DM |
| Case 64 | STXBP1 | NM_001032221:c.1212A>C:p.Lys404Asn | De novo | PS2, PM2, PP2, PP3 | Pathogenic | ||
| Case 1 | SYNGAP1 | NM_006772:c.2116-1G>A | De novo | PVS1, PS2, PM2 | Pathogenic | ||
| Case 36 | SYNGAP1 | NM_006772:c.3718C>T:p.Arg1240* | De novo | PVS1, PS2, PM2 | Pathogenic |
ACMG, American College of Medical Genetics; DM, Disease causing Mutation; HGMD, Human Gene Mutation Database;
*
Indicates stopgain.