Table 3. Pathogenic or likely pathogenic variants according to the ACMG guideline.
| Gene | Chr. | Position | HGVS.p | OR | 95% CI | ACMG Criteria | Interpretation |
|---|---|---|---|---|---|---|---|
| ADGRV1 | chr5 | 89,977,183 | p.His1859Arg | 11.7 | 3.6–37.6 | PS4, PM6, PP3, PP5 | Likely pathogenic |
| CHRNA4 | chr20 | 61,981,730 | p.Arg345Cys | NA | NA | PS1, PS3, PM2, PM6, PP3 | Pathogenic |
| CNTNAP2 | chr7 | 146,741,111 | p.Ile172Thr | 35.7 | 4.3–290.5 | PS4, PM6, PP3, PP5 | Likely pathogenic |
| chr7 | 148,112,574 | p.Arg1288Cys | 83.3 | 8.6–802.2 | PS4, PM6, PP3, PP5 | Likely pathogenic | |
| DEPDC5 | chr22 | 32,215,100 | p.Arg587X | NA | NA | PVS1, PS3, PM2, PM6, PP3 | Pathogenic |
| chr22 | 32,242,890 | p.Pro1031His | 7.0 | 1.7–28.7 | PS4, PM6, PP3 | Likely pathogenic | |
| EFHC1 | chr6 | 52,319,049 | p.Arg294Cys | 125.2 | 11.3–1382.9 | PS4, PM5, PP3, PP5 | Likely pathogenic |
| GABRG2 | chr5 | 161,495,029 | p.Ser8Arg | 250.6 | 35.2–1782.6 | PS4. PM6, PP3, PP5 | Likely pathogenic |
| HCN1 | chr5 | 45,695,898 | p.Ser100Ala | 235.5 | 14.7–3770.7 | PS4, PM5, PM6, PP3 | Likely pathogenic |
| KCNB1 | chr20 | 47,990,709 | p.Ile463Thr | 14.7 | 1.9–110.8 | PS4, PM6, PP3 | Likely pathogenic |
| KCNT1 | chr9 | 138,670,613 | p.Glu892Lys | 24.9 | 3.1–194.6 | PS4, PM6, PP3, PP5 | Likely pathogenic |
| PRICKLE1 | chr12 | 42,858,215 | p.Ala541Ser | 376.9 | 62.8–2260.6 | PS4, PM6, PP3, PP5 | Likely pathogenic |
| RELN | chr7 | 103,197,510 | p.Thr1904Met | 23.6 | 5.5–100.9 | PS4, PM6, PP3, PP5 | Likely pathogenic |
| chr7 | 103,276,733 | p.Lys751Thr | 9.6 | 1.3–71.1 | PS4, PM6, PP3, PP5 | Likely pathogenic | |
| SCN1A | chr2 | 166,850,785 | p.Arg1575Cys | 55.3 | 11.9–256.8 | PS4, PM6, PP3, PP5 | Likely pathogenic |
| chr2 | 166,903,464 | p.Thr398Met | 250.3 | 15.6–4007.8 | PS4, PM6, PP3 | Likely pathogenic | |
| chr2 | 166,894,321 | p.Val971Ile | 55.3 | 11.9–256.7 | PS4, PM6, PP3, PP5 | Likely pathogenic | |
| SCN9A | chr2 | 167,141,015 | p.Asn641Ser | 123.3 | 11.2–1362.3 | PS4, PM5, PM6, PP3 | Likely pathogenic |
| TSC1 | chr9 | 135,771,689 | p.Pro1143Leu | 83.4 | 8.7–803.3 | PS4, PM6, PP3, PP5 | Likely pathogenic |
| chr9 | 135,772,927 | p.Thr899Ser | 41.8 | 9.3–187.3 | PS4, PM6, PP3, PP5 | Likely pathogenic | |
| chr9 | 135,776,993 | p.Ser829Arg | 62.4 | 13.2–294.6 | PS4, PM6, PP3, PP5 | Likely pathogenic | |
| TSC2 | chr16 | 2,134,649 | p.Glu1476Gln | 62.1 | 6.9–556.7 | PS4, PM5, PM6, PP3, PP5 | Pathogenic |
| chr16 | 2,135,247 | p.Arg1529Gln | 13.3 | 1.8–100.2 | PS4, PM6, PP3, PP5 | Likely pathogenic | |
| chr16 | 2,127,648 | p.Val963Met | 41.7 | 5.0–347.2 | PS4, PM6, PP3, PP5 | Likely pathogenic | |
| chr16 | 2,129,146 | p.Leu1027Pro | NA | NA | PM2, PM6, PP3, PP5 | Likely pathogenic | |
| chr16 | 2,134,692 | p.Glu1490Gly | 14.5 | 1.9–108.7 | PS4, PM6, PP3, PP5 | Likely pathogenic |
Note:
ACMG, American College of Medical Genetics and Genomics; Chr, chromosome; HGCV.p, Human Genome Variation Society nomenclature for protein; OR, odds ratio; CI, confidence interval; NA, not available.