Table 3 Stop-gain variants identified in SLIC probands.
Variant Position | Gene | dbSNP137 | Ref | Var | Proband ID | 1000G (ALL) variant freq | EVS (5400_ALL) variant freq | Variant status | Coding change | % of protein missing | PhyloP | Phast Cons | SIFT |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
chr1:158532597 | OR6P1 | rs142215019 | G | T | 34 | 0.10% | 0.22% | rare | NM_001160325:exon1: c.C798A:p.Y266X | 16.4% | −0.62 | 0.00 | 1.00 |
chr3:63466576a | SYNPR | rs376661036 | C | A | 30 | NA | 0.01% | rare | NM_144642:exon2: c.C93A:p.C31X | 84.7% | −0.72 | 0.60 | 1.00 |
chr8:107738486 | OXR1 | rs145739822 | G | A | 29 | 0.14% | NA | rare | NM_001198534:exon1: c.G15A:p.W5X | 97.7% | 4.24 | 1.00 | 1.00 |
chr8:39847306 | IDO2 | rs199869245 | C | T | 11 | NA | 0.05% | rare | NM_194294:exon8: c.C655T:p.R219X | 49.5% | 1.90 | 0.95 | 1.00 |
chr11:1027390 | MUC6 | rs200217410 | G | T | 8 | NA | 0.06% | rare | NM_005961:exon17: c.C2109A:p.C703X | 71.2% | 0.40 | 1.00 | 1.00 |
chr11:6190828a | OR52B2 | rs190537696 | A | T | 19 | 0.14% | 0.10% | rare | NM_001004052:exon1: c.T729A:p.C243X | 25.0% | 0.59 | 1.00 | 1.00 |
chr16:4745030 | NUDT16L1 | rs146701095 | C | T | 9 | 0.05% | 0.04% | rare | NM_001193452:exon3: c.C556T:p.Q186X | 3.6% | 1.77 | 1.00 | 1.00 |
