Table 2.
Computational pathogenicity prediction scores of the LD candidate variants.
| S. no | Variant | Gene | CADD | FATHMM | MetaLR | MutationTaster | PROVEAN | REVEL |
|---|---|---|---|---|---|---|---|---|
| (1) | rs115805535 | ZC3H12A | 16.06 | 0.22678 | 0.0431 | 0.08975 | 0.30964 | 0.027 |
| (2) | rs116208741 | ZC3H12A | – | – | – | – | – | – |
| (3) | rs150443459 | CPNE7 | – | – | – | – | – | – |
| (4) | rs192716734 | ASXL2 | 14.94 | 0.18248 | 0.025 | 0.25126 | 0.24026 | 0.079 |
| (5) | rs148871144 | EPB42 | 0.135 | 0.78537 | 0.1928 | 0.08975 | 0.23156 | 0.121 |
| (6) | rs75910050 | FAM220A | 0.524 | 0.06931 | 0.0102 | 0.08975 | 0.58248 | 0.049 |
| (7) | rs150322658 | OR10A2 | – | – | – | – | – | – |
| (8) | rs183593116 | TMEM184A | 9.855 | 0.43279 | 0.0355 | 0.08975 | 0.07008 | 0.039 |
| (9) | rs7209106 | MYO1D | 23.2 | 0.88298 | 0.6557 | 0.81001 | 0.80682 | 0.553 |
LD, laterality defect.
CADD: >25 = damaging; <25 = tolerated; FATHMM: >0.5 = damaging; <0.5 = tolerated; MetaLR: > 0.5 = damaging; <0.5 = tolerated; Mutation Tester: >0.5 = damaging; <0.5 = tolerated; PROVEAN: >0.5 = damaging; <0.5 = tolerated; REVEL: >0.5 = damaging; <0.5 = tolerated.