Table 5.
List of identified variants of unknown significance
| Patient | Gene | Nucleotide | Protein | rs number | EXaC MAF | ClinVar/VarSome classification | SIFT | PP2 | MA | Damag. acc. to ≥2 software |
|---|---|---|---|---|---|---|---|---|---|---|
| With SMN | ||||||||||
| OL0134 | BLM | c.11T>C | p.Val4Ala | rs144706057 | 0.0017 | 1–3/3 | 0 | 0.132 | 2.14 | Y |
| OL0135 | PTCH1 | c.2597G>A | p.Gly866Glu | NA | NA | 3/3 | 0.08 | 0.999 | 2.31 | Y |
| ATM | c.3208G>A | p.Val1070Ile | NA | NA | 3/3 | 0.35 | 0.026 | 2.135 | N | |
| OL0136 | PLA2G2A | c.185G>A | p.Arg62His | NA | 8.34E-05 | NA/3 | 0.02 | 0.888 | 3.005 | Y |
| LRIG1 | c.2195C>T | p.Pro732Leu | rs61746346 | 0.0022 | NA/3 | 0 | 0.991 | 1.975 | Y | |
| RECQL5 | c.1801G>A | p.Val601Met | NA | NA | NA/3 | 0.3 | 0.04 | 1.905 | N | |
| OL0138 | PREX2 | c.C1672G | p.Pro558Ala | rs199541834 | 0.0001 | NA/3 | 0.15 | 0.145 | 0.46 | N |
| PARP1 | c.C659T | p.Ala220Val | rs139232092 | 0.0006 | NA/3 | 0.15 | 0.003 | 1.155 | N | |
| Without SMN | ||||||||||
| OL0041 | BUB1B | c.1042G>A | p.Ala348Thr | NA | 8.24E-06 | NA/3 | 0.33 | 0.85 | 2.175 | N |
| MRE11A | c.C1475A | p.Ala492Asp | rs61749249 | 0.0034 | 1–3/3 | 0.43 | 0.754 | 1.735 | N | |
| OL0130 | XRCC1 | c.632A>G | p.Tyr211Cys | NA | 1.74E-05 | NA/3 | 0.15 | 0.998 | 2.175 | Y |
| OL0131 | 0 | |||||||||
| OL0132 | GRB7 | c.1439T>C | p.Val480Ala | rs143372931 | 0.0004 | NA/3 | 0 | 0.848 | 3.07 | Y |
| RAD9A | c.215G>A | p.Arg72His | rs377299831 | 1.65E-05 | NA/3 | 0.58 | 0.019 | 1.2 | N | |
| OL0133 | EXT2 | c.1859C>T | p.Thr620Met | rs138495222 | 0.0006 | 2–3/3 | 0.02 | 0.999 | 2.24 | Y |
| MLH3a | c.3281-1G>C | – | NA | NA | NA/3 | – | – | – | – | |
| OL0137 | PREX2 | c.2167A>G | p.Asn723Asp | NA | 1.65E-05 | NA/3 | 0.03 | 0.614 | 1.63 | N |
| HELQ | c.1418G>A | p.Arg473His | NA | 2.48E-05 | NA/3 | 0 | 1 | 4.545 | Y | |
| RFC4 | c.908C>T | p.Ala303Val | rs144238574 | 9.07E-05 | NA/3 | 0.44 | 0.027 | 1.235 | N | |
| OL0139 | RHBDF2 | c.940G>A | p.Ala314Thr | rs140433374 | 0.0008 | NA/3 | 0.33 | 0.952 | 1.78 | N |
| MDM4 | c.1162C>G | p.Pro388Ala | rs61754765 | 0.0006 | NA/3 | 0.92 | 0.997 | 1.1 | N | |
| OL0140 | FANCM | c.3407T>C | p.Leu1136Ser | NA | 1.65E-05 | NA/3 | 0.01 | 0.963 | 1.905 | Y |
| POLE | c.1601T>C | p.Leu534Pro | NA | NA | NA/3 | 0 | 0.991 | 3.565 | Y | |
| OL0141 | 0 | |||||||||
| OL0142 | RAD54L | c.1817G>A | p.Arg606Gln | rs374574941 | 2.47E-05 | NA/3 | 0 | 1 | 4.735 | Y |
| POLD1 | c.2116C>G | p.Pro706Ala | NA | NA | 3/3 | 0.01 | 0.733 | 2.41 | Y | |
| OL0144 | CWF19L2 | c.2240A>C | p.Lys747Ther | NA | NA | NA/3 | 0.08 | 0.697 | 1.915 | N |
| SETX | c.967A>G | p.Ser323Gly | NA | 1.65E-05 | NA/3 | 0 | 0.994 | 0.975 | Y | |
| OL0157 | TP53BP1 | c.2226A>T | p.Glu742Asp | rs150423877 | 0.0004 | NA/3 | 0.48 | 0.987 | 0.46 | N |
| PCI77 | 0 | |||||||||
| PCI15 | PTCH1 | c.3376G>A | p.Val1126Ile | rs147025073 | 0.0005 | 3/3 | 0.26 | 0.927 | 1.77 | N |
| NCAM1 | c.1481C>A | p.Thr494Asn | NA | NA | NA/3 | 0.01 | 0.347 | NA | N | |
| PCI39 | 0 | |||||||||
| PCO11 | BRCA1 | c.3929C>A | p.Thr1310Lys | rs80357257 | 8.24E-06 | 1–3/3 | 0.01 | 0.787 | 1.895 | N |
| AURKA | c.1028G>A | p.Arg343Gln | rs200181472 | 0.0002 | NA/3 | 0.04 | 0.027 | 0.71 | N | |
| EXO1 | c.820G>A | p.Gly274Arg | rs149397534 | 0.0021 | NA/3 | 0.16 | 0.999 | 1.295 | N | |
Notes: The variants predicted to be damaging by at least two out of three prediction tools employed are represented in bold.
a
The splice-site variant was analyzed by splicing prediction software spidex with a score −25.6359, suggesting that it is the damaging variant.
Abbreviation: NA, not applicable.