Table 1.
NGS panel for the diagnosis of male infertility
| 1. | NPHP4 | 23. | DAZL | 45. | FKBPL | 67. | DDX25 | 89. | ZMYND15 | 111. | SYCP2 |
| 2. | C1orf167 | 24. | DNAH1 | 46. | PLG | 68. | C1RL | 90. | GP1BA | 112. | CBS |
| 3. | MTHFR | 25. | PROS1 | 47. | ZPBP | 69. | C1RL-AS1 | 91. | KLHL10 | 113. | DNMT3L |
| 4. | CLCA4 | 26. | BOC | 48. | C7orf61 | 70. | DPY19L2 | 92. | ITGB3 | 114. | POFUT2 |
| 5. | BRDT | 27. | CFAP44 | 49. | SERPINE1 | 71. | CHPT1 | 93. | TEX14 | 115. | GP1BB |
| 6. | F3 | 28. | CFAP44-AS1 | 50. | POLR2J3 | 72. | SYCP3 | 94. | ACE | 116. | POLR2F |
| 7. | SPAG17 | 29. | GP9 | 51. | CFTR | 73. | CCDC62 | 95. | PGS1 | 117. | SOX10 |
| 8. | F5 | 30. | SPATA16 | 52. | TEX15 | 74. | PIWIL1 | 96. | DNAH17 | 118. | PICK1 |
| 9. | SERPINC1 | 31. | CCDC39 | 53. | PLAT | 75. | CPB2 | 97. | DNAH17-AS1 | 119. | MEI1 |
| 10. | F13B | 32. | GP5 | 54. | CHD7 | 76. | F7 | 98. | TAF4B | 120. | ADGRG2 |
| 11. | MTR | 33. | CEP135 | 55. | TMEM70 | 77. | F10 | 99. | GGN | 121. | MAGEB4 |
| 12. | LHCGR | 34. | SPINK2 | 56. | CCIN | 78. | TDRD9 | 100. | PLAUR | 122. | MAGEB1 |
| 13. | FSHR | 35. | BMP3 | 57. | NR5A1 | 79. | CATSPER2 | 101. | LHB | 123. | NR0B1 |
| 14. | DNAH6 | 36. | FGB | 58. | ASS1 | 80. | TERB2 | 102. | NLRP7 | 124. | TBC1D25 |
| 15. | NPAS2 | 37. | FGA | 59. | UPF2 | 81. | NME4 | 103. | NLRP2 | 125. | AR |
| 16. | LOC101927142 | 38. | KLKB1 | 60. | CFAP43 | 82. | FAHD1 | 104. | AURKC | 126. | TEX11 |
| 17. | PROC | 39. | F11 | 61. | NANOS1 | 83. | MEIOB | 105. | SIRPG | 127. | USP26 |
| 18. | TFPI | 40. | MTRR | 62. | SYCE1 | 84. | SEPT12 | 106. | SIRPA | 128. | F9 |
| 19. | STRADB | 41. | PRDM9 | 63. | FSHB | 85. | PRM1 | 107. | THBD | 129. | F8 |
| 20. | C2CD6 | 42. | ITGA2 | 64. | F2 | 86. | TERB1 | 108. | SUN5 | 130. | FUNDC2 |
| 21. | LOC100129175 | 43. | F2R | 65. | MAJIN | 87. | SERPINF1 | 109. | E2F1 | 131. | SRY |
| 22. | CFAP65 | 44. | F13A1 | 66. | CATSPER1 | 88. | CXCL16 | 110. | PROCR | 132. | USP9Y |
Table 2.
Variants detected in the patient group as a result of NGS
| Patient n. | VUS - inheritance | Likely pathogenic-inheritance | Pathogenic-inheritance |
|---|---|---|---|
| 1. | NM_000130.5(F5):c.1128G>T p.R376S (PP3) (AD,AR) NM_001370.2(DNAH6):c.8422G>A (p.V2808I) (PP3) (n/a) | ||
| 2. | NM_000313.4(PROS1): c.1021G>T (p.A341S) (PM1,PM2,PP3) (AD) | NM_000492.4(CFTR):c.1516A>G (p.Ile506Val) (PM1,PM2,PM3,PP3,BP6) (AR) | |
| 3. | NM_015512.5(DNAH1):c.8885A>C (p.Lys2962Thr) (PP3) (AR) | ||
| 4. | NM_000492.4(CFTR):c.443T>C (p.Ile148Thr) (PS3,M1,PM2,PM3,PP3,BS2,BS3,BP2,BP6) (AR) | ||
| 5. | NM_000492.4(CFTR):c.2981T>G (p.Phe994Cys) (PM1,PM2,PP3) (AR) | NM_000128.4(F11):c.1556G>A (p.Trp519Ter) (PVS1,PS4,PM2,PM3,PP5) NM_000128.4(F11):c.403G>T (p.Glu135Ter) (PA1,PVS1,PS3,PS4,PM3,PP5,BS1,BS2) (AD,AR) | |
| 6. | NM_001242805.2 (BRDT):c.163C>T (p.Pro55Ser) (PP3) (AR) | ||
| 7. | NM_001350162.2 (TEX15):c.2580_2583del (p.Asp860GlufsTer15) (PS3,PP3) (AR) | NM_000173.7(GP1BA): c.1235_1298delAGCCCAC… (p.E412fs*39) (PVS1,PM2) (AD,AR) | |
| 8. | NM_000789.4(ACE):c.2299G>A (p.Glu767Lys) (PM2,PP3) (AR) | ||
| 9. | NM_000312.4(PROC):c.982C>T (p.Arg328Cys) (PM1,PM2,PP3,PP5) (AD,AR) | NM_002203.4(ITGA2):c.981_985del (p.Lys327AsnfsTer6) (PVS1,PM2) (n/a) | |
| 10. | NM_000492.4 (CFTR):c.2491G>T (p.Glu831Ter) (PVS1,PS3,PS4,PM2) (AR) | ||
| 11. | NM_000492.3(CFTR):c.1521_1523del (p.Phe508del) (PA2,PS3,PM1,PM4,PP3,BS3, BS4,BP2,BP5) (AR) | ||
| 12. | NM_000492.4(CFTR):c.1210-11T>G (PA2,PS3,PM3,PP5,BS1,BS2,BP2) (AR) | ||
| 13. | NM_000492.4(CFTR):c.2991G>C (p.Leu997Phe) (PS1,PM1,PM2,PM3,PP3,BS2,BP2,BP6) (AR) | ||
| 14. | NM_054012.4(ASS1):c.535T>C (p.Trp179Arg) (PS3,PS4,PM1,PM2,PM3,PP3,PP5) (AR) | ||
| 15. | NM_144605.4(SEPT12): c.208T>C (p.Phe70Leu) (PM2,PP3) | NM_000492.4(CFTR): c.1397C>T (p.S466L) (PM1,PM2,PM3,PP3) (AR) | |
| 16. | NM_000492.4(CFTR):c.2973A>G (p.Ile991Met) (PM1,PM2) (AR) | ||
| 17. | NM_015512.5(DNAH1):c.10164G>T (p.K3388N)(PP3) (AR) | ||
| 18. | NM_015102.5(NPHP4):c.224G>A (p.Trp75Ter) (AR) | ||
| 19. | NM_000492.4(CFTR): c.1043T>A (p.M348K) (PM1,PM2,PM3,PP3,BP2,BP6) (AR) NM_012128.4 (CLCA4): c.760dupA (p.T254fs*3) (PVS1) (n/a) | NM_000492.4 (CFTR) : c.3038C>T (p.P1013L) (PM1,PM2,PM3,PP3) | |
| 20. | NM_000071.3(CBS):c.833T>C (p.Ile278Thr) (PS3,PS4,PM1,PM2,PM3,PM5,PP3) (AR) | ||
| 21. | NM_000128.4(F11):c.325G>A (p.Ala109Thr) (AD,AR) (PS3,PS4,PM1,PM2,PM3,PP3,PP5) NM_000492.4(CFTR):c.1516A>G (p.Ile506Val) (PM1,PM2,PM3,PP3,BP6) (AR) | ||
| 22. | NM_173812.5(DPY19L2): c.247C>T (p.Q83*) (PVS1,PM2) (AR) | NM_000492.4(CFTR):c.1521_1523delCTT (p.F508del) (PA2,PS3,PS4,PM1,PM3,PM4, PP3,PP5,BS1,BS2,BS4,BP2) (AR) | |
| 23. | NM_000492.3(CFTR):c.3872A>G (p.Q1291R) (PM1,PM2,PM3,PM5,PP3,PP5) (AR) | ||
| 24. | NM_000071.3(CBS):c.833T>C (p.I278T) (PS3,PS4,PM1,PM2,PM3,PM5,PP3) (AR) | ||
| 25. | NM_000492.4(CFTR):c.3256A>G (p.Thr1086Ala)(PP3) (AR) | ||
| 26. | NM_000894.2 (LHB):c.169T>C NP_000885.1:p.Tyr57His (PM2,PP3) (AR) | ||
| 27. | NM_000301.5(PLG):c.2384G>A (p.Arg795His) (PS4,PM2,PP3) (AD,AR) | ||
| 28. | NNM_000789.4(ACE): c.3490G>A (p.G1164R) (PM2,PP3) (AR) | ||
| 29. | NM_000492.4(CFTR): c.350G>A (p.R117H) (PA2,PS3,PM1,PM2,PM3,PM5,PP1,PP3, PP5,BS2,BS4,BP2) (AR) | ||
| 30. | NM_015512.5 (DNAH1): c.8976C>G p.F2992L(PP3) (AR) | ||
| 31. | NM_000131.4 (F7): c.805+3_805+6delGGGT (-) (PVS1,PM2) (AR) | ||
| 32. | NM_001994.3(F13B): c.209A>C (p.Q70P) (PM2,PP3) (AR) | NM_000492.4 (CFTR) : c.1521_1523delCTT (p.F508del) (PA2,PS3,PM1,PM3,PM4,PP3,PP5,BS1,BS2,BS3,BS4,BP2) (AR) | |
| 33. | NM_017780.4 (CHD7) :c.5995G>A (p.A1999T)(PS4,PM2,PP2,PP3) (AD) | ||
| 34. | NM_012128.3 (CLCA4):c.575C>A NP_036260.2:p.Ser192Cys (PP3) (n/a) | ||
| 35. | NM_015512.5(DNAH1): c.9495G>A (p.Thr3165) (PM2,PP3) (AR) NM_152467.5 (KLHL10): c.1226A>G (p.E409G) (PM2,PP3) (AD) NM_144605.4 (SEPTIN12) :c.611G>T (p.Arg204Leu) (PP3) (AD) | ||
| 36. | NM_001330438.2 (DDX25): c.110C>T (p.Ala37Val) (PP3) (n/a) | ||
| 37. | NM_000071.3(CBS):c.833T>C (p.Ile278Thr) (PS3,PM1,PM5,PP3) | ||
| 38. | NM_001312675.1 (F10):c.202C>T NP_001299604.1:p.Arg68Cys (PM2,PP3) (AR) NM_000212.2 (ITGB3):c.1576G>C NP_000203.2:p.Glu526Lys (PP3) (AD,AR) NM_015512.5 (DNAH1): c.4642C>G (p.L1548V) (PM2,PP3) (AR) | ||
| 39. | NM_000301.5(PLG):c.2134G>A (p.Gly712Arg) (PP3) (AD,AR) | ||
| 40. | NM_000492.4(CFTR):c.890G>A (p.Arg297Gln) (PS3,PM1,PP3,BS3,BS6) (AR) NM_173812.5(DPY19L2): c.2221C>A (p.P741T) (PM2,PP3) (AR) | ||
| 41. | NM_173628.3(DNAH17):c.7752+2T>A (PVS1) (AR) | ||
| Total | 32 | 11 | 15 |