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Bulletin of the National Research Centre

Table 1 Allele frequencies of the 41 variants observed in GNPTAB, GNPTG, and NAGPA genes among the 79 unrelated persistent stutterers and their comparison with gnomAD database

From: Determination of regulatory motifs and pathogenicity of intronic variants of GNPTAB, GNPTG, and NAGPA genes in individuals with stuttering

Chr

Gene

Variant

rsID

n

%

Allele frequency in this study

Allele frequency South Asian

Allele frequency total

RegulomeDB score

chr12

GNPTAB

c.117+4859_117+4860insATAAC

rs10641124

76

96.20253165

1.853658537

  

4

  

c.3603-1359A>G

rs11110995

30

37.97468354

0.731707317

0.1739

0.1081

1d

  

c.3136-257C>T

rs11111002

32

40.50632911

0.780487805

0.1736

0.1102

1f

  

c.1408+712T>C

rs4764814

52

65.82278481

1.268292683

0.4128

0.457

1f

  

c.2715+427C>G

rs4764813

20

25.3164557

0.487804878

0.2189

0.2622

1f

  

c.771+3179C>G

rs919215

79

100

1.926829268

0.6567

0.6209

5

  

c.771+3153G>A

rs919214

17

21.51898734

0.414634146

0.1542

0.1859

5

  

c.324-340T>A

rs10778150

79

100

1.926829268

0.6443

0.6208

6

  

c.203+609T>C

rs4764654

78

98.73417722

1.902439024

0.6439

0.6021

4

  

c.117+10307A>G

rs10444509

40

50.63291139

0.975609756

0.2218

0.1805

7

  

c.117+4571C>T

rs4764823

69

87.34177215

1.682926829

0.4633

0.2818

4

  

c.203+564A>G

rs10860788

28

35.44303797

0.682926829

0.1617

0.02236

4

  

c.118-7189A>C

rs10860790

45

56.96202532

1.097560976

0.2446

0.1539

7

  

c.3136-295G>A

rs12366292

10

12.65822785

0.243902439

0.05305

0.06437

5

  

c.117+4718G>A

rs7960795

12

15.18987342

0.292682927

  

4

  

c.117+10310T>C

rs80178135

28

35.44303797

0.682926829

0.1611

0.02244

7

  

c.324-457A>G

rs11830792

22

27.84810127

0.536585366

0.2281

0.285

6

  

c.117+10414G>T

rs545549083

2

2.53164557

0.048780488

0.0006211

0.00001971

5

  

c.772-489T>C

rs17725026

5

6.329113924

0.12195122

0.06084

0.03799

3a

  

c.1408+686G>A

rs568797492

1

1.265822785

0.024390244

0.0178

0.0006046

4

  

c.117+10485C>T

rs962073192

1

1.265822785

0.024390244

0

0.000006572

5

  

c.3603-1345T>C

rs75733424

1

1.265822785

0.024390244

0.002276

0.02443

4

chr16

GNPTG

c.178+3230C>T

rs742460

60

75.94936709

1.463414634

0.4372

0.3145

4

  

c.179-1611G>A

rs2887538

66

83.5443038

1.609756098

0.565

0.6081

5

  

c.179-4651G>T

rs8060970

32

40.50632911

0.780487805

0.1592

0.1481

4

  

c.179-4672G>A

rs1008995614

1

1.265822785

0.024390244

0.001241

0.00009197

4

  

c.178+186C>T

rs11865211

12

15.18987342

0.292682927

0.05314

0.06899

2b

  

c.179-1582C>T

rs187809520

1

1.265822785

0.024390244

0

0.00001317

5

  

c.179-4260_179-4259insTTA

rs113850025

2

2.53164557

0.048780488

  

5

  

c.117+4887A>G

rs139670026

1

1.265822785

0.024390244

0.001265

0.00236

5

  

c.178+300G>C

rs572050858

1

1.265822785

0.024390244

0.002698

0.00009201

2b

chr16

NAGPA

c.791+300G>A

rs3743841

59

74.6835443

1.43902439

0.4158

0.3431

4

  

c.791+265G>A

rs3743840

60

75.94936709

1.463414634

0.4125

0.2863

4

  

c.543-404T>A

rs1001171

48

60.75949367

1.170731707

0.4093

0.3341

1f

  

c.543-346A>C

rs1001170

45

56.96202532

1.097560976

  

1f

  

c.920+259G>T

rs62036221

14

17.72151899

0.341463415

  

5

  

c.920+266G>A

rs55936034

6

7.594936709

0.146341463

0.03196

0.008494

5

  

c.791+356A>C

rs571237436

1

1.265822785

0.024390244

0.008506

0.004635

4

  

c.*43C>A

rs1270775930

1

1.265822785

0.024390244

  

4

  

c.920+298G>A

rs12709122

8

10.12658228

0.195121951

  

5

  

c.920+270A>G

rs1307047484

1

1.265822785

0.024390244

0

0.000006576

5

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