Table 4 Genes with more than one rare variant in the same SLIC proband.
Variant Position | Gene | dbSNP137 | Ref | Var | Proband IDs | 1000G (ALL) variant freq | EVS variant freq | Variant status | Coding change | PhyloP | Phast Cons | SIFT | Poly Phen | Notes |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
chr2:167089942 | SCN9A | rs180922748 | G | C | 2 | 0.14% | 0.20% | rare | NM_002977:exon21:c.C3799G:p.L1267V | 2.07 | 1.00 | 0.13 | 0.99 | |
chr2:167094638 | SCN9A | rs141268327 | T | C | 0.41% | 0.53% | rare | NM_002977:exon20:c.A3734G:p.N1245S | 4.93 | 1.00 | 0.00 | 1.00 | ||
chr2:32689842 | BIRC6 | rs61754195 | C | T | 26, 42 | 0.46% | 0.98% | rare | NM_016252:exon25:c.C5207T:p.P1736L | 3.09 | 0.99 | 0.01 | 0.60 | |
chr2:32740353 | BIRC6 | rs61757638 | C | T | 0.18% | 0.25% | rare | NM_016252:exon55:c.C10865T:p.A3622V | 6.06 | 1.00 | 0.00 | 0.99 | ||
chr3:58104626 | FLNB | rs139875974 | G | T | 40 | 0.05% | 0.07% | rare | NM_001164317:exon19:c.G2773T:p.G925C | 6.33 | 1.00 | 0.00 | 1.00 | |
chr3:58110119 | FLNB | rs111330368 | G | C | 0.23% | 0.41% | rare | NM_001164317:exon22:c.G3785C:p.G1262A | 6.18 | 1.00 | 0.00 | 1.00 | ||
chr11:6190710 | OR52B2 a | rs372373798 | C | T | 19 | NA | 0.01% | novel | NM_001004052:exon1:c.G847A:p.V283M | 2.69 | 1.00 | 0.08 | 1.00 | |
chr11:6190828 | OR52B2 ab | rs190537696 | A | T | 0.14% | 0.10% | rare | NM_001004052:exon1:c.T729A:p.C243X | 0.59 | 1.00 | 1.00 | . | STOP | |
chr11:92086828 | FAT3 | rs139595720 | T | C | 7 | 0.46% | 0.66% | rare | NM_001008781:exon1:c.T1550C:p.L517S | 3.32 | 0.82 | 0.72 | 1.00 | |
chr11:92624235 | FAT3 | rs187159256 | C | T | 0.14% | 0.17% | rare | NM_001008781:exon25:c.C13630T:p.L4544F | 0.94 | 0.96 | 0.03 | 0.37 | ||
chr12:49418717 | KMT2D a | rs201481646 | C | T | 12 | NA | 0.07% | rare | NM_003482:exon49:c.G15797A:p.R5266H | 2.39 | 1.00 | 0.00 | 1.00 | |
chr12:49432365 | KMT2D a | rs199547661 | G | A | 0.09% | 0.24% | rare | NM_003482:exon34:c.C8774T:p.A2925V | 0.77 | 0.38 | 0.00 | 0.00 | ||
chr13:109613971 | MYO16 | rs374252281 | G | A | 28 | NA | 0.01% | rare | NM_001198950:exon18:c.G2122A:p.A708T | 4.62 | 1.00 | 0.01 | 1.00 | |
chr13:109617108 | MYO16 | G | A | NA | NA | novel | NM_001198950:exon20:splice acceptor lost | 4.87 | 1.00 | . | . | SPLICE | ||
chr14:58924684 | KIAA0586 a | rs61742715 | T | A | 19 | 0.23% | 0.39% | rare | NM_001244189:exon13:c.T1729A:p.L577I | 0.28 | 0.81 | 0.43 | 1.00 | |
chr14:59014632 | KIAA0586 a | rs61745066 | G | A | 0.18% | 0.24% | rare | NM_001244189:exon34:c.G4873A:p.G1625R | −1.15 | 0.41 | 0.00 | 0.00 | ||
chr15:42977116 | STARD9 a | rs79165890 | T | C | 12 | 0.05% | 0.22% | rare | NM_020759:exon23:c.T3340C:p.C1114R | 1.98 | 0.51 | 0.00 | 0.05 | |
chr15:42977810 | STARD9 a | rs140924205 | T | G | 19 | 0.32% | 0.40% | rare | NM_020759:exon23:c.T4034G:p.I1345S | 0.269 | 0.001 | 0.00 | 0.27 | |
chr15:42978141 | STARD9 a | rs376229251 | A | C | 19 | NA | 0.09% | rare | NM_020759:exon23:c.A4365C:p.E1455D | 0.553 | 0.067 | 0.00 | 0.99 | |
chr15:42981101 | STARD9 a | rs202017657 | C | G | 12, 19 | NA | 0.15% | rare | NM_020759:exon23:c.C7325G:p.P2442R | 0.28 | 0.01 | 0.00 | 0.99 | |
chr15:42982237 | STARD9 a | rs201340789 | G | C | 12, 19 | NA | 0.19% | rare | NM_020759:exon23:c.G8461C:p.V2821L | 0.28 | 0.01 | 0.00 | 0.99 | |
chr16:23635348 | PALB2 | rs45478192 | A | C | 13 | 0.09% | 0.17% | rare | NM_024675:exon8:c.T2816G:p.L939W | 2.83 | 1.00 | 0.00 | 1.00 | |
chr16:23641275 | PALB2 | rs45543843 | T | A | NA | 0.01% | rare | NM_024675:exon5:c.A2200T:p.T734S | 2.90 | 0.97 | 0.11 | 1.00 | ||
chr17:34861135 | MYO19 | rs200572125 | C | T | 25 | NA | 0.03% | rare | NM_001163735:splice donor lost, exon20 | 4.98 | 1.00 | . | . | SPLICE |
chr17:34871802 | MYO19 | rs187710120 | T | C | 0.05% | 0.19% | rare | NM_001163735:exon8:c.A446G:p.Y149C | 4.52 | 1.00 | 0.00 | 1.00 |
