Next-Generation Sequencing Infertility Panel in Turkey: First Results

Next-Generation Sequencing Infertility Panel in Turkey: First Results

Balkan Journal of Medical Genetics

Volume 27 (2024): Issue 2 (December 2024)

By:

E Ikbal Atli

, S Yalcintepe, E Atli, S Demir and H Gurkan

Open Access

|Mar 2025

Figures & Tables

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.E412fs39) (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.T254fs3) (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

DOI: https://doi.org/10.2478/bjmg-2024-0019 | Journal eISSN: 2199-5761

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Language: English

Page range: 49 - 57

Published on: Mar 6, 2025

Published by: Macedonian Academy of Sciences and Arts

In partnership with: Paradigm Publishing Services

Publication frequency: 2 times per year

Keywords:

Male infertility,

NGS diagnosis,

Genetic causes of male infertility

Related subjects:

Medicine,

Basic medical science,

Basic medical science, other

© 2025 E Ikbal Atli, S Yalcintepe, E Atli, S Demir, H Gurkan, published by Macedonian Academy of Sciences and Arts
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

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