Table 2.
Filtered variants called by WES in mouse (A), human (B), and translocation breakpoint (C) candidate genes verified by Sanger sequencing
| Gene | Chromosome | Exonic change | Protein change | Reference transcript | CADD score | gnomAD allelic frequency v.2.1.1 | gnomAD allelic frequency v.3 | gnomAD variant ID | #Patients with variant | MRKH type |
|---|---|---|---|---|---|---|---|---|---|---|
| (A) | ||||||||||
| HOXA10 | 7 | missense; exon 1 c.T188C | p.V63A | NM_018951 | 20.2 | 0 | 0 | − | 1 | I |
| LAMC1 | 1 | missense; exon 2 c.C713T | p.P238L | NM_002293 | 26.9 | 3.18E-05 | 1.40E-05 | 1–183072757-C-T | 1 | I |
| LAMC1 | 1 | missense; exon 11 c.T1978C | p.Y660H | NM_002293 | 24.2 | 0 | 0 | − | 1 | I |
| LAMC1 | 1 | missense; exon 16 c.G2854A | p.G952S | NM_002293 | 34.0 | 7.96E–06 | 1.40E–05 | 1–183095307-G-A | 1 | II |
| LAMC1 | 1 | missense; exon 17 c.G3032A | p.R1011H | NM_002293 | 29.6 | 4.35E–04 | 0 | 1–183096448-G-A | 1 | I |
| PAX2 | 10 | missense; exon 3 c.G394A | p.V132I | NM_000278 | 32 | 1.20E–05 | 1.40E-05 | 10–102510632-G-A | 1 | I |
| RARA | 17 | missense; exon 1 c.127 T | p.P43S | NM_001024809 | 20.3 | 3.14E–04 | 2.93E–04 | 17–38499083-C-T | 1 | I |
| RARA | 17 | missense; exon 3 c.A320G | p.Q107R | NM_001145302 | 23.5 | 0 | 0 | − | 1 | I |
| –RARA | 17 | missense; exon 5 c.A611G | p.Q204R | NM_000964 | 24 | 0 | 6.98E–06 | 17–40352051-A-G | 1 | I |
| WNT4 | 1 | missense; exon 5 c.C1015T | p.R339W | NM_030761 | 33 | 3.18E–05 | 1.40E–05 | 1–22446584-G-A | 1 | I |
| WNT4 | 1 | missense; exon 5 c.C829A | p.P277T | NM_030761 | 26.4 | 1.42E–05 | 5.58E–05 | 1–22446770-G-T | 1 | I |
| WNT4 | 1 | missense; exon 5 c.C739T | p.R247C | NM_030761 | 32 | 3.18E–05 | 1.40E–05 | 1–22446860-G-A | 1 | I |
| WNT9B | 17 | missense; exon 3 c.G454A | p.E152K | NM_001320458 | 26.4 | 5.38E–04 | 4.53E–04 | 17–44952586-G-A | 1 | I |
| (B) | ||||||||||
| AMH | 19 | missense; exon 1 c.A236G | p.Y79C | NM_000479 | 23.3 | 0 | 0 | − | 1 | I |
| AMH | 19 | missense; exon 2 c.C451T | p.P151S | NM_000479 | 23.0 | 4.50E–05 | 9.07E–05 | 19–2250374-C-T | 1 | II |
| AMH | 19 | missense; exon 5 c.C864G | p.D288E | NM_000479 | 22.9 | 1.27E–03 | 1.53E–03 | 19–2251137-C-G | 1 | I |
| AMH | 19 | missense; exon 5 c.A974G | p.Q325R | NM_000479 | 22.8 | 5.54E–03 | 9.48E–03 | 19–2251247-A-G | 1 | I |
| CFTR | 7 | stop-gained; exon 15 c.G2491T | p.E831X | NM_000492 | 55 | 0 | 0 | − | 1 | I |
| CFTR | 7 | frameshift; exon 24 c.3903dupA | p.R1301fs | NM_000492 | n/a | 0 | 0 | − | 1 | II |
| CFTR | 7 | missense; exon 2 c.C91T | p.R31C | NM_000492 | 27.3 | 1.64E–03 | 1.19E–03 | 7–117144344-C-T | 1 | I |
| CFTR | 7 | missense; exon 3 c.C220T | p.R74W | NM_000492 | 24 | 1.72E–03 | 4.33E–03 | 7–117149143-C-T | 3 | I |
| CFTR | 7 | missense; exon 4 c.G358A | p.A120T | NM_000492 | 27.1 | 1.38E–04 | 4.19E–05 | 7–117171037-G-A | 1 | I |
| CFTR | 7 | missense; exon 6 c.A650G | p.E217G | NM_000492 | 24.5 | 4.58E–03 | 3.29E–03 | 7–117175372-A-G | 2 | I & II |
| GALT | 9 | missense; exon 4 c.A236G | p.Q79R | NM_001258332 | 25.3 | 0 | 0 | − | 1 | II |
| LRP10 | 14 | missense; exon 3 c.C142T | p.R48W | NM_001329226 | 23.4 | 1.09E–03 | 3.28E–04 | 14–23342582-C-T | 1 | I |
| LRP10 | 14 | missense; exon 5 c.C691T | p.R231W | NM_001329226 | 33.0 | 2.35E–03 | 7.21E–03 | 14–23344848-C-T | 1 | I |
| LRP10 | 14 | missense; exon 6 c.G1458C | p.E486D | NM_001329226 | 28.1 | 1.13E–04 | 2.37E–04 | 14–23345931-G-C | 1 | II |
| LRP10 | 14 | missense; exon 7 c.G1685A | p.R562H | NM_014045 | 26.6 | 7.02E–03 | 6.01E–03 | 14–23346279-G-A | 2 | I |
| MMP14 | 14 | missense; exon 8 c.G1237A | p.D413N | NM_004995 | 28.5 | 1.59E–05 | 0 | 14–23313925-G-A | 1 | I |
| MMP14 | 14 | missense; exon 10 c.C1484T | p.P495L | NM_004995 | 34.0 | 1.19E–05 | 1.40E–05 | 14–23314983-C-T | 1 | I |
| SHOX | X | missense; exon 5 c.G547A | p.V183I | NM_000451 | 22.8 | 0 | 1.26E–04 | X-641001-G-A | 1 | I |
| SHOX | X | missense; exon 6 c.C698T | p.A233V | NM_000451 | 29.0 | 0 | 9.77E–05 | X-644455-C-T | 1 | II |
| TBX6 | 16 | missense; exon 6 c.G815A | p.R272Q | NM_004608 | 34.0 | 9.61E–04 | 7.68E–04 | 16–30099890-C-T | 1 | II |
| TBX6 | 16 | missense; exon 5 c.C718T | p.R240C | NM_004608 | 24.6 | 2.83E–05 | 4.19E–05 | 16–30100064-G-A | 1 | I |
| TBX6 | 16 | missense; exon 4 c.G484A | p.G162S | NM_004608 | 33.0 | 4.54E–03 | 3.97E–03 | 16–30100401-C-T | 1 | II |
|
| ||||||||||
| (C) CNOT1 |
3 | missense; exon 1 c.C122T | p.S41L | NM_001256742 | 24.3 | 1.77E–03 | 1.86E–03 | 3–32737239-C-T | 1 | I |
| CNOT1 | 3 | missense; exon 12 c.T1586C | p.L529S | NM_001256742 | 28.8 | 1.80E–04 | 1.26E–04 | 3–32776360-T-C | 1 | II |
| CNOT1 | 3 | missense; exon 12 c.C1634T | p.A545V | NM_001256742 | 23.7 | 4.60E–05 | 4.19E–05 | 3–32776408-C-T | 1 | I |
| CNOT1 | 3 | missense; exon 14 c.A1802T | p.Y601F | NM_001256742 | 28.9 | 6.56E–03 | 6.56E–03 | 3–32800976-A-T | 2 | II |
| CRTAP | 3 | missense; exon 2 c.C514G | p.L172V | NM_006371 | 23.9 | 2.14E–05 | 1.19E–04 | 3–33161878-C-G | 1 | II |
| CRTAP | 3 | missense; exon 5 c.C1039T | p.L347F | NM_006371 | 29.0 | 1.99E–03 | 2.44E–03 | 3–33174163-C-T | 1 | I |
| MEFV | 16 | stop-gained; exon 1 c.C202T | p.Q68X | NM_001198536 | 29.3 | 0 | 0 | − | 1 | I |
| MEFV | 16 | missense; exon 9 c.G1777A | p.A593T | NM_001198536 | 21.6 | 3.98E–06 | 0 | 16–3293875-C-T | 1 | I |
| MEFV | 16 | missense; exon 8 c.G1319A | p.R440H | NM_001198536 | 21.6 | 0 | 0 | − | 1 | I |
| OR1F1 | 16 | missense; exon 1 c.C172T | p.P58S | NM_012360 | 25.1 | 7.78E–05 | 4.19E–05 | 16–3254418-C-T | 1 | I |
| OR1F1 | 16 | missense; exon 1 c.G538C | p.D180H | NM_012360 | 24.8 | 2.47E–05 | 2.79E–05 | 16–3254784-G-C | 1 | II |
| TIGD7 | 16 | frameshift; exon 2 c.143delA | p.N48fs | NM_033208 | − | 0 | 0.00E + 0 | 0 | 1 | II |
| TMPPE | 3 | missense; exon 2 c.G628A | p.V210M | NM_001039770 | 25.6 | 1.63E–04 | 1.40E–05 | 3–33135060-C-T | 1 | I |
| TRIM71 | 3 | missense; exon 2 c.G965A | p.R322Q | NM_001039111 | 25.0 | 5.35E–05 | 5.59E–05 | 3–32915422-G-A | 1 | I |
| ZNF200 | 16 | missense; exon 4 c.T347A | p.V116E | NM_001145446 | 21.6 | 3.89E–05 | 2.79E–05 | 16–3282540-A-T | 1 | I |
| ZNF205 | 16 | missense; exon 7 c.C925T | p.R309W | NM_001042428 | 23.1 | 3.28E–05 | 2.09E–05 | 16–3169586-C-T | 1 | I |
| ZNF205 | 16 | missense; exon 7 | p.S517T | NM 001042428 | 23.2 | 2.68E–03 | 2.73E–03 | 16–3170210-T-A | 2 | II |
| C.T1549A | ||||||||||
| ZNF263 | 16 | missense; exon 4 C.G653T | p.S218I | NM_005741 | 24.9 | 3.93E–04 | 1.95E–04 | 16–3336033-G-T | 1 | II |
| ZSCAN10 | 16 | missense; exon 5 C.G568T | p.G190W | NMJXH282415 | 26.5 | 0 | 0 | − | 1 | II |