Table 2.
Results of in-silico analysis for the candidate missense mutations in the patients with developmental delay and/or intellectual disability.
| Patients | 46_S11 | 88_S3 | 47_S3 | 36_S4 | 38_S2 | 108_S9 |
|---|---|---|---|---|---|---|
| Gene | ZDHHC9 | SMARCB1 | CHD8 | CACNA1H | FOXP1 | KCNK18 |
| Accession ID | NM_016032.3 | NM_003073.3 | NM_020920.3 | NM_021098.2 | NM_032682.5 | NM_181840.1 |
| AA Change | p.Arg96Trp | p.Gly11Arg | p.Arg1551Cys | p.Arg1892His | p.Ala52Val | p.Trp101Arg |
| FUNCTIONAL PREDICTIONS | ||||||
| SIFT | D (0) | D (0.001) | D (0) | T (0.12) | T (0.639) | D (0.001) |
| Polyphen2 | D (1) | D (1) | D (1) | P (0.696) | D (0.972) | D (1) |
| LRT | D (0) | N (0) | D (0) | N (0) | N (0.001) | D (0) |
| MutationTaster | D (1) | D (1) | D (1) | N (1) | D (0.743) | D (1) |
| MutationAssessor | H (4.24) | M (2.505) | M (2.7) | N (0.345) | L (0.97) | M (3.07) |
| FATHMM | T (1.69) | D (−3.31) | D (−3.52) | D (−4.02) | D (−2.45) | T (1.3) |
| PROVEAN | D (−7.84) | D (−4.88) | D (−7.46) | N (−0.32) | N (−0.04) | D (−10.64) |
| VEST3 | 0.945 | 0.402 | 0.935 | 0.196 | 0.264 | 0.781 |
| MetaSVM | T (−0.278) | D (0.841) | D (1.045) | D (0.181) | T (−0.07) | T (−0.636) |
| MetaLR | T (0.263) | D (0.862) | D (0.924) | D (0.748) | D (0.561) | T (0.227) |
| M-CAP | D (0.593) | D (0.905) | D (0.513) | D (0.231) | D (0.098) | D (0.042) |
| CADD | 33 | 33 | 33 | 12.32 | 23.7 | 24.8 |
| DANN | 0.999 | 0.999 | 0.999 | 0.997 | 0.999 | 0.994 |
| fathmm-MKL | D (0.924) | D (0.968) | D (0.985) | N (0.059) | D (0.927) | D (0.928) |
| CONSERVATION SCORES | ||||||
| GERP++ | 4.84 | 2.48 | 5.42 | −0.615 | 5.65 | 3.2 |
| phyloP20way | 1.048 | 0.9 | 1.048 | −0.298 | 1.048 | 0.964 |
| phastCons20way | 0.996 | 1 | 1 | 0 | 0.983 | 0.926 |
| SiPhy_29way | 13.641 | 10.434 | 18.15 | 3.374 | 20.078 | 9.937 |
SIFT prediction, D(amaging), T(olerated); Polyphen2 prediction, D (probably damaging), P (possibly damaging); LRT prediction, D(eleterious), N(eutral); MutationTaster prediction, D (disease causing), N (polymorphism); MutationAssessor prediction, functional [H(igh), M(edium)], non-functional [L(ow), N(eutral)]; FATHMM prediction, D(amaging), T(olerated); PROVEAN prediction, D(eleterious), N(eutral); MetaSVM prediction, D(eleterious), T(olerated); MetaLR prediction, D(eleterious), T(olerated); M-CAP prediction, D(eleterious); fathmm-MKL prediction, D(eleterious), N(eutral).