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Next-Generation Sequencing Infertility Panel in Turkey: First Results

E Ikbal Atli

E Ikbal Atli

Trakya University, Faculty of Medicine, Department of Medical GeneticsEdirne, Turkey
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Ikbal Atli, E
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S Yalcintepe

S Yalcintepe

Trakya University, Faculty of Medicine, Department of Medical GeneticsEdirne, Turkey
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Yalcintepe, S
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E Atli

E Atli

Trakya University, Faculty of Medicine, Department of Medical GeneticsEdirne, Turkey
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Atli, E
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S Demir

S Demir

Trakya University, Faculty of Medicine, Department of Medical GeneticsEdirne, Turkey
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Demir, S
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H Gurkan

H Gurkan

Trakya University, Faculty of Medicine, Department of Medical GeneticsEdirne, Turkey
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Gurkan, H
  
Mar 06, 2025
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Article Category: ORIGINAL ARTICLE
Published Online: Mar 06, 2025
Page range: 49 - 57
DOI: https://doi.org/10.2478/bjmg-2024-0019
Keywords
© 2024 Ikbal Atli E et al., published by Sciendo
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

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>CNP_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

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
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