Table 3.
Genetic variants in transcription factors, splicing factors, and metal ion transporters
| Gene | Nucleotide Changes | Amino Acid Changes | Gene Type | ExAC EAS/ALL | gnomAD EAS/ALL | dbSNP | PolyPhen-2 | Mutation Taster | SIFT | InterVar | Disease (OMIM) |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Transcription factors | |||||||||||
| AR | c.1369_1377 delGGCGGCGGC |
p.457_459 delGGG |
het | -/- | 0.0366/0.0378 | Uncertain | 313 200|300 068|312 300|300 633|176 807 | ||||
| AR | c.1369_1374 delGGCGGC |
p.457_458 delGG |
hom | -/- | 0.0026/0.0354 | Uncertain | 313 200|300 068|312 300|300 633|176 807 | ||||
| FOXI2 | c.182C > A | p.P61Q | het | -/- | 0.0074/0.0004 | rs118034115 | Benign | Polymorphism | Tolerated | Uncertain | #N/A |
| FOXK2 | c.1899G > C | p.K633N | het | 0.0099/0.0007 | 0.008/0.0005 | rs117690256 | Possibly_damaging | Disease_causing | Damaging | Uncertain | #N/A |
| FOXK2 | c.500C > T | p.A167V | het | 0.0135/0.001 | 0.0167/0.0009 | rs150523977 | Benign | Disease_causing | Tolerated | Uncertain | #N/A |
| FOXO3 | c.1141dupG | p.L382Afs*2 | het | -/- | 0/0 | rs34133353 | Uncertain | #N/A | |||
| FOXO3 | c.184G > A | p.D62N | het | 0.0043/0.0022 | 0.0043/0.0002 | rs532258926 | Benign | Disease_causing | Damaging | Uncertain | #N/A |
| GLI2 | c.3623G > T | p.R1208L | het | -/- | -/- | Benign | Polymorphism | Tolerated | Uncertain | 615 849|610 829 | |
| KLF4 | c.1100-7C > A | het | 0.0115/0.0011 | 0.0123/0.0006 | rs188071068 | Uncertain | #N/A | ||||
| MGA | c.9112C > T | p.R3038W | het | 0.0044/0.0004 | 0.0037/0.0002 | rs117068470 | Possibly_damaging | Disease_causing | Damaging | Uncertain | #N/A |
| NCOR2 | c.1529_1531 delAGC |
p.510delQ | het | 0.0031/0.0036 | -/- | rs753830534 | Uncertain | #N/A | |||
| NCOR2 | c.2033A > C | p.N678T | het | -/- | -/- | Possibly_damaging | Disease_causing | Tolerated | Uncertain | #N/A | |
| NFE2L3 | c.166G > C | p.A56P | het | -/- | 0.0012/0.00 006 525 | rs748882173 | Possibly_damaging | Polymorphism | Damaging | Uncertain | #N/A |
| NR1H2 | c.695C > T | p.A232V | het | 0.0002/0.0002 | -/- | rs201627190 | Benign | Disease_causing | Tolerated | Uncertain | #N/A |
| NR1H2 | c.211C > T | p.R71C | het | 0.0008/0.00 005 957 | 0/0.00 003 234 | rs756403846 | Benign | Disease_causing | Damaging | Uncertain | #N/A |
| PDX1 | c.127_129 delCCG |
p.43delP | het | -/0.0032 | 0.0006/0.00 003 243 | rs752633548 | Uncertain | 606 392|260 370|125 853 | |||
| RUNX2 | c.232_234 delGCG |
p.78delA | het | -/0.0006 | 0/0.00 003 362 | rs756546787 | Uncertain | 119 600|156 510 | |||
| TRPS1 | c.592A > G | p.K198E | het | -/0.000 008 282 | -/- | rs754340524 | Benign | Polymorphism | Damaging | Uncertain | 190 350|190 351 |
| ZC3H6 | c.871C > G | p.Q291E | het | 0.0052/0.0003 | 0.0065/0.0004 | rs375792649 | Benign | Disease_causing | Damaging | Uncertain | #N/A |
| ZFHX2 | c.1108G > T | p.A370S | het | -/- | -/- | Polymorphism | Damaging | Uncertain | 147 430|613 750 | ||
| ZNF23 | c.583C > A | p.P195T | het | 0.0054/0.0004 | 0.0068/0.0004 | rs76530144 | Possibly_damaging | Polymorphism | Damaging | Likely_benign | #N/A |
| ZNF333 | c.452T > C | p.I151T | het | 0.0025/0.0002 | 0.0018/0.00 009 684 | rs141998898 | Benign | Polymorphism | Tolerated | Uncertain | #N/A |
| ZNF438 | c.590G > A | p.G197E | het | 0.0074/0.0006 | 0.0062/0.0003 | rs148252990 | Benign | Polymorphism | Tolerated | Likely_benign | #N/A |
| ZNF469 | c.11053C > T | p.R3685C | het | 0.0025/0.00 006 775 | 0.0043/0.0003 | rs748126365 | Benign | Polymorphism | Damaging | Uncertain | 229 200 |
| ZNF469 | c.1663G > A | p.D555N | het | 0.0047/0.0002 | 0.0025/0.0001 | rs749179728 | Possibly_damaging | Polymorphism | Damaging | Uncertain | 229 200 |
| ZNF644 | c.2707G > A | p.G903R | het | -/- | -/- | Probably_damaging | Disease_causing | Damaging | Uncertain | 614 167 | |
| ZNF655 | c.413T > C | p.F138S | het | 0.0156/0.0011 | 0.0167/0.0009 | rs149822831 | Possibly_damaging | Disease_causing | Damaging | Uncertain | #N/A |
| ZNF669 | c.89G > T | p.R30L | het | 0.0157/0.0011 | 0.0111/0.0006 | rs201216518 | Benign | Polymorphism | Tolerated | Likely_benign | #N/A |
| ZSCAN25 | c.307C > T | p.R103W | het | 0.0035/0.0015 | 0.0055/0.0014 | rs145815306 | Benign | Polymorphism | Damaging | Uncertain | #N/A |
| Splicing factors | |||||||||||
| ANKHD1 | c.74C > T | p.P25L | het | 0.0013/0.0001 | 0.0018/0.00 009 718 | rs557072130 | Benign | Disease_causing | Damaging | Uncertain | #N/A |
| RBM45 | c.652A > G | p.R218G | het | 0.0054/0.0004 | 0.008/0.0004 | rs138537367 | Benign | Disease_causing | Tolerated | Uncertain | #N/A |
| Metal ion transporters | |||||||||||
| ABCA10 | c.3103T > C | p.S835P | het | -/- | -/- | Probably_damaging | Disease_causing | Damaging | Uncertain | #N/A | |
| ABCA10 | c.2260C > T | p.R754X | het | 0.0071/0.0005 | 0.0025/0.0001 | rs190646470 | Disease_causing | Uncertain | #N/A | ||
| ATP6V1C2 | c.923G > A | p.G308E | het | 0.0047/0.0004 | 0.0062/0.0003 | rs117054621 | Benign | Disease_causing | Damaging | Uncertain | #N/A |
| CACNA1F | c.3094G > A | p.E1032K | het | -/0.00 006 846 | 0/0.00 004 745 | rs200976011 | Possibly_damaging | Disease_causing | Tolerated | Uncertain | 300 071|300 476|300 600 |
| KCNG4 | c.778T > C | p.Y260H | het | 0.0076/0.0006 | 0.0105/0.0005 | rs117787002 | Benign | Disease_causing | Tolerated | Uncertain | #N/A |
| KCNJ12 | c.139G > A | p.V47I | het | 0.0075/0.0011 | 0.0032/0.0006 | rs201403828 | Possibly_damaging | Disease_causing | Tolerated | Uncertain | #N/A |
| SLCO1A2 | c.1681A > G | p.I561V | het | 0.0106/0.0008 | 0.0117/0.0006 | rs116587731 | Probably_damaging | Disease_causing | Damaging | Uncertain | #N/A |
| SLCO1A2 | c.1736dupG | p.T580Nfs*5 | het | 0.0007/0.00 005 773 | 0.0006/0.00 003 228 | rs3830207 | Uncertain | #N/A | |||
| SLC26A9 | c.2621delC | p.P874Hfs*19 | het | 0.0069/0.0006 | 0.0111/0.0006 | rs536446020 | Uncertain | #N/A | |||
| SLC31A2 | c.86C > T | p.S29L | het | 0.0022/0.0002 | 0.0024/0.0002 | rs200288219 | Probably_damaging | Disease_causing | Damaging | Uncertain | #N/A |
| SLC34A3 | c.473C > T | p.P158L | het | 0.0002/0.00 001 754 | -/- | rs771246525 | Probably_damaging | Disease_causing | Damaging | Uncertain | 241 530 |
| SLC39A4 | c.592G > A | p.A198T | het | 0.0016/0.0002 | 0.0012/0.0001 | rs781818806 | Benign | Polymorphism | Tolerated | Uncertain | 201 100 |
| SLC5A3 | c.1415A > G | p.Y472C | het | 0.0074/0.0006 | 0.0099/0.0005 | rs117638044 | Benign | Disease_causing | Damaging | Uncertain | #N/A |
| SLC7A2 | c.1301A > G | p.Y434C | het | 0.0017/0.0002 | -/- | rs201373242 | Probably_damaging | Disease_causing | Damaging | Uncertain | #N/A |
dbSNP: Database for single nucleotide polymorphisms; EAS: East Asian.