Table 2.
Loss-of-function variants detected in case and control cohorts
| Symbol | CDS changea | Protein change | dbSNP identifier | Cases | Control participants | Consequence | EVS European MAF | ExAC non-Finnish European MAF |
|---|---|---|---|---|---|---|---|---|
| ADAM29 | c.2020A > T | p.Lys674Ter | – | 1 | 0 | Stop-gained | 0 | 0 |
| CASP8 | c.379C > T | p.Arg127Ter | – | 1 | 0 | Stop-gained | 0 | 0 |
| CDKN2A | c.225_243delCGCCACTCTCACCCGACCC | p.Ala76CysfsTer64 | – | 1 | 0 | Frame shift | 0 | 0 |
| CDKN2B | c.149_150delCG | p.Ala50AspfsTer36 | – | 0 | 1 | Frame shift | 0 | < 0.0001 |
| DCLRE1B | c.189 + 1G > C | – | 1 | 0 | Splice donor | 0 | 0 | |
| DCLRE1B | c.256G > T | p.Gly86Ter | – | 0 | 1 | Stop-gained | 0 | 0 |
| FTO | c.11delC | p.Pro5ArgfsTer13 | – | 1 | 0 | Frame shift | 0 | 0 |
| LGR6 | c.858-2A > C | – | 1 | 0 | Splice acceptor | < 0.0001 | < 0.0001 | |
| MUS81 | c.1314delC | p.Pro439LeufsTer6 | – | 1 | 0 | Frame shift | 0 | 0 |
| MUS81 | c.1062delC | p.Arg355GlyfsTer2 | – | 0 | 1 | Frame shift | 0 | 0 |
| NFRKB | c.2149G > T | p.Glu717Ter | – | 1 | 0 | Stop-gained | 0 | 0 |
| NFRKB | c.794C > G | p.Ser265Ter | – | 0 | 1 | Stop-gained | 0 | < 0.0001 |
| NRIP1 | c.40_41insT | p.Asp14ValfsTer25 | – | 1 | 0 | Frame shift | 0 | 0 |
| NRIP1 | c.2750C > G | p.Ser917Ter | – | 1 | 0 | Stop-gained | 0 | 0 |
| NRIP1 | c.1968dupT | p.Gly657TrpfsTer5 | – | 1 | 0 | Frame shift | 0 | 0 |
| PDE4D | c.2400_2410dupTGTCATAGATG | p.Asp804ValfsTer3 | – | 1 | 0 | Frame shift | 0 | 0 |
| RAD51B | c.139C > T | p.Arg47Ter | rs200355697 | 2 | 0 | Stop-gained | 0 | 0.0001 |
| SETMAR | c.823_826delAAAG | p.Glu276GlyfsTer2 | – | 1 | 0 | Frame shift | 0 | < 0.0001 |
| SETMAR | c.706C > T | p.Arg236Ter | – | 0 | 1 | Stop-gained | 0 | 0.0001 |
| SETMAR | c.1635C > G | p.Tyr545Ter | – | 0 | 1 | Stop-gained | 0 | 0 |
| SLC4A7 | c.1663G > T | p.Gly555Ter | – | 1 | 0 | Stop-gained | 0 | 0 |
| SNX32 | c.1111C > T | p.Arg371Ter | – | 1 | 0 | Stop-gained | 0 | < 0.0001 |
| SNX32 | c.825 + 2 T > G | – | 1 | 0 | Splice donor | 0 | 0 | |
| TCF7L2 | c.1804_1805insAAT | p.Glu602_Glu603insTer | – | 0 | 1 | Stop-gained | 0 | 0 |
| TET2 | c.1085_1086insT | p.Pro363SerfsTer6 | – | 1 | 0 | Frame shift | 0 | 0 |
| TET2 | c.2072delC | p.Thr691MetfsTer9 | – | 1 | 0 | Frame shift | 0 | 0 |
| TET2 | c.3646C > T | p.Arg1216Ter | – | 1 | 0 | Stop-gained | 0 | 0 |
| TET2 | c.4361_4362insG | p.Arg1455GlnfsTer23 | – | 1 | 0 | Frame shift | 0 | 0 |
| TET2 | c.3812_3820delGCGCCTGTC | p.Cys1271_Gln1274delinsTer | – | 1 | 0 | Stop-gained | 0 | 0 |
| TET2 | c.832C > T | p.Gln278Ter | – | 0 | 1 | Stop-gained | 0 | 0 |
| TET2 | c.1458delC | p.Asn486LysfsTer11 | – | 0 | 1 | Frame shift | 0 | 0 |
| TPK1 | c.185 + 1G > A | – | 0 | 1 | Splice donor | 0 | 0 | |
| USHBP1 | c.1220 + 1G > T | rs144791770 | 1 | 0 | Splice donor | 0.0002 | 0.0001 | |
| USHBP1 | c.258dupA | p.Val87SerfsTer103 | – | 0 | 1 | Frame shift | 0.0001 | < 0.0001 |
| ZNF226 | c.1229_1230delAA | p.Arg411SerfsTer11 | – | 1 | 0 | Frame shift | 0 | 0.0001 |
| ZNF226 | c.2239C > T | p.Arg747Ter | – | 1 | 0 | Stop-gained | 0 | 0 |
| ZNF226 | c.2380G > T | p.Glu794Ter | rs201830106 | 0 | 1 | Stop-gained | 0.0007 | 0.0003 |
| ZNF226 | c.582delT | p.Asn194LysfsTer41 | – | 0 | 1 | Frame shift | 0 | 0 |
Abbreviations: CDS Coding DNA sequence, EVS Exome Variant Server, ExAC Exome Aggregation Consortium, MAF Minor allele frequency, dbSNP Single-nucleotide polymorphism database
aCanonical transcript for each gene according to Ensembl definition