Table 2 Genetic variants with corresponding variant localization, frequency (gnomAD), in silico predictions, PhyloP scores, pathogenicity classifications (ACMG class), and novelty status
From: Genetic heterogeneity in epilepsy and comorbidities: insights from Pakistani families
Genetic Variant | Variant Localization | Frequency (gnomAD) | In silico prediction | PhyloP score | Pathogenicity (ACMG class) | Novelty Status |
|---|---|---|---|---|---|---|
NM_030582.3 (COL18A1): c.1339–6 C > T, p.? (ENSG00000182871) | Splice acceptor site of the intron 4 | Overall: 0.0000323 South Asian: 0.0000654 Homozygotes:0 | Likely Benign | -0.902 | Uncertain Significance (PP1, PM2) | Novel |
NM_018359.3(UFSP2): c.344T > A, p. Val115Glu (ENSG00000109775) | Exon 5 | Overall: 0.0000713 South Asian: 0.000847 Homozygotes:0 | Likely pathogenic | 6.331 | a. Pathogenic b. (PS3, PM1, PP1, PP2, PP4, PP5) | PMID: 33,473,208 |
NM_015346.4 (ZFYVE26): c.1926_1941del, p. Tyr643MetfsX2 (ENSG00000072121) | Exon 11 | Overall: 0 South Asian:0 Homozygotes:0 | Likely pathogenic | 2.421 | Likely Pathogenic (PVS1) | Novel |
NM_022089.4(ATP13A2): c.1208 C > A, p. Ala403Glu (ENSG00000159363) | Exon 13 | Overall:  0.0000297 South Asian: 0.0005271 Homozygotes: 0 | Damaging | 4.442 | a. Uncertain Significance (PM1, PM2, PP1) | Reported in ClinVar (Accession #: SCV000351396) |