The candidate pathogenic variants of known genes
| ID | HGVS (Human Genome Variation Society) | Gene,Chr | Pred |
| U106 | NC_000023.11:g.130028727G>A;NP_001171701.1:p.(G1391R) | BCORL1 | 6 |
| U37 | NC_000023.11:g.130028727G>A;NP_001171701.1:p.(G1391R) | BCORL1 | 6 |
| U50 | NC_000023.11:g.130028727G>A;NP_001171701.1:p.(G1391R) | BCORL1 | 6 |
| U9 | NC_000023.11:g.130028727G>A;NP_001171701.1:p.(G1391R) | BCORL1 | 6 |
| U60 | NC_000023.11:g.45069958A>C;NP_001278345.1:p.(K775T) | KDM6A | 5 |
| U58 | NC_000023.11:g.45110152A>G;NP_001278344.1:p.(D1412G) | KDM6A | 6 |
| U51 | NC_000023.11:g.47212835A>T;NP_003325.2:p.(Y873F) | UBA1 | 11 |
| U60 | NC_000023.11:g.47214843G>C;NP_695012.1:p.(V1031L) | UBA1 | 5 |
| U49 | NC_000024.10:g.12722148G>A;NP_004645.2:p.(E96K) | USP9Y | 6 |
| U50 | NC_000024.10:g.12722148G>A;NP_004645.2:p.(E96K) | USP9Y | 7 |
| U109 | NC_000024.10:g.12739592C>G;NP_004645.2:p.(S462C) | USP9Y | 5 |
| U73 | NC_000024.10:g.12739592C>G;NP_004645.2:p.(S462C) | USP9Y | 5 |
| U13 | NC_000024.10:g.12739592C>G;NP_004645.2:p.(S462C) | USP9Y | 5 |
| U71 | NC_000024.10:g.12739592C>G;NP_004645.2:p.(S462C) | USP9Y | 5 |
‘B’ and ‘U’ in the ID column are ‘bilateral cryptorchidism’ and ‘unilateral cryptorchidism’, respectively. The ‘Pred’ column shows the number of prediction methods that support deleterious effects of the variants (see online supplemental table 3 for specific methods). Note: USP9Y (underlined) is a Y chromosome gene, while all other genes reside on the X chromosome.