Table 1 List of the identified HNF1B ASVs in eleven pools of different tissue types.

From: Identification of novel HNF1B mRNA splicing variants and their qualitative and semi-quantitative profile in selected healthy and tumour tissues

Variant name

HGVS description

Functional annotation

Splicing biotype

Endometrioid endometrial carcinoma

Colorectal carcinoma

Healthy colon

Kidney carcinoma

Healthy kidney

Kidney oncocy-toma

Pancreatic carcinoma

Healthy pancreas

Prostate carcinoma

Paired healthy tissue

Prostate hyper-plasia

No. of pools with ASV

Novel (0), known (1)

Δ2

c.345_544 del200

FS

CΔ

255

0

1 454

199

754

259

322

556

0

0

444

8

0

Δ2,3p

c.345_622 del278

FS

CΔ + SDSΔ

0

143

0

127

436

163

64

0

0

136

385

7

0

Δ2_4

c.345_1045 del701

FS

mCΔ

68

0

57

468

166

216

143

91

0

0

0

7

0

Δ2_5

c.345_1206 del862

FS

mCΔ

0

0

0

34

14

0

0

0

0

0

0

2

0

Δ2_6

c.345_1339 del995

FS

mCΔ

0

0

0

770

0

0

0

0

0

0

1 719

3

0

Δ2_7,8p

c.345_1584 del1204

FS

mCΔ + SASΔ

0

0

0

0

117

0

0

0

0

0

0

1

0

Δ2_8

c.345_1653 del1309

FS

mCΔ

0

0

226

951

844

276

433

275

446

0

0

7

0

3p

c.545_622 del78

IF

SASΔ

89 082

166 213

185 492

178 626

179 688

130 503

182 721

163 105

227 604

199 210

273 908

11

1

Δ3_4

c.545_1045 del501

IF

mCΔ

19

138

89

199

237

74

303

221

0

0

0

8

0

Δ3_5

c.545_1206 del662

FS

mCΔ

0

0

0

0

0

5

0

0

0

0

0

1

0

Δ3_5,6p

c.545_1328 del784

FS

mCΔ + SASΔ

0

0

0

132

0

0

0

0

0

0

0

1

0

Δ3_8

c.545_1653 del1109

FS*

mCΔ

0

0

0

0

139

0

0

0

0

0

0

1

0

Δ4_5,3q,6p

c.796_1222 del427

FS

mCΔ + SDSΔ + SASΔ

0

0

0

0

22

0

0

0

0

0

0

1

0

Δ4,3q

c.799_1045 del247

FS

CΔ + SDSΔ

0

0

0

0

0

0

16

0

0

0

0

1

0

Δ4_6,3q,7p

c.804_1359 del556

FS

mCΔ + SDSΔ + SASΔ

8

0

0

0

0

0

0

0

0

0

0

1

0

Δ4

c.810_1045 del236

FS

CΔ

0

0

39

41

54

0

292

116

0

0

0

5

0

Δ5_7,4q,8p

c.1039_1548 del510

IF

mCΔ + SDSΔ + SASΔ

0

0

59

0

0

0

0

0

0

0

0

1

0

Δ5_6,4q,7p

c.1041_1520 del480

FS

mCΔ + SDSΔ + SASΔ

0

0

519

0

0

0

0

0

0

0

0

1

0

Δ5

c.1046_1206 del161

FS

CΔ

135

77

271

674

365

187

884

411

634

694

336

11

0

Δ5,6p

c.1046_1222 del177

IF

CΔ + SASΔ

0

7

0

18

0

46

0

0

0

0

4

4

0

Δ5,6p

c.1046_1225 del180

IF

CΔ + SASΔ

0

0

0

8

0

0

0

0

0

0

0

2

0

Δ5_6

c.1046_1339 del294

IF

mCΔ

0

0

0

158

621

0

0

0

0

0

0

2

0

Δ5_7

c.1046_1534 del489

IF

mCΔ

0

0

0

594

0

0

0

0

0

0

0

1

0

Δ5_8

c.1046_1653 del608

IF*

mCΔ

113

208

866

2 739

2 324

2 145

786

927

0

407

1 064

10

0

Δ6_7,5q

c.1199_1534 del336

IF

mCΔ + SDSΔ

0

0

229

0

5

0

26

0

0

0

0

3

0

Δ6

c.1207_1339 del133

FS

CΔ

191

63

101

269

155

190

240

310

540

0

0

9

0

Δ6_7

c.1207_1534 del328

FS

mCΔ

0

0

0

545

152

411

263

108

0

0

0

5

0

Variant name

                

Δ6_8

c.1207_1653 del477

IF

mCΔ

566

599

637

3 527

3 155

1 708

899

2 065

647

354

2 629

11

0

Δ7,6q,8p

c.1336_1542 del207

IF

CΔ + SDSΔ + SASΔ

68

5

12

8

24

60

33

25

27

46

17

11

0

Δ7

c.1340_1534 del195

IF

CΔ

13 053

25 843

25 407

31 199

29 225

27 652

34 884

29 461

31 266

25 085

38 698

11

0

Δ7_8

c.1340_1653 del314

IF*

mCΔ

8 541

39 834

38 134

69 676

76 681

84 948

72 312

45 479

24 189

26 958

45 290

11

1

Δ8

c.1535_1653 del119

IF*

CΔ

1 399

4 506

5 749

6 095

6 421

5 017

3 441

3 690

871

1 713

1 098

11

0

▼106bp_i2

c.545-899_549-793 ins106

FS

C▼

64

0

0

0

0

17

0

5

0

0

0

3

0

▼153bp_i4

c.1046-10281_1046-10129 ins153

IF, PTC

C▼

7

7

6

7

7

0

7

19

6

2

0

9

0

▼157bp_i4

c.1046-10281_1046-10125 ins157

FS

C▼

30

26

16

29

17

4

26

24

9

11

6

11

0

▼91 bp_i4

c.1046-10219_1046-10129 ins91

FS

C▼

0

0

0

4

0

0

0

0

0

0

0

1

0

▼94 bp_i4

c.1046-10219_1046-10125 ins94

FS

C▼

0

0

4

0

0

0

2

0

0

0

0

2

0

▼91 bp_i4

c.1046-1421_1046-1331 ins91

FS

C▼

928

216

204

597

462

178

312

460

236

399

251

11

0

▼128bp_i4

c.1046-765_1046-638 ins128

FS

C▼

98

54

44

101

72

24

44

65

32

86

35

11

0

▼99 bp_i4

c.1046-1421_1046-1331 ins91 + c.1046-8_1046-1 ins8

IF

C▼ + SAS▼

24

0

0

0

0

0

2

0

14

0

0

3

0

▼79 bp_i5

c.1206 + 1417_1206 + 1495 ins79

FS

C▼

0

0

14

0

0

2

0

0

0

0

5

3

0

▼148bp_i5

c.1206 + 1417_1206 + 1564 ins148

FS

C▼

368

75

41

231

162

38

108

185

82

107

15

11

0

▼195bp_i6, Δ7_8

c.1339 + 521_1339 + 715 ins195 + c.1340_1653 del314

FS

C▼ + mCΔ

0

0

0

52

0

0

0

0

0

0

0

1

0

▼92 bp_i6

c.1339 + 1620_1339 + 1711 ins92

FS

C▼

0

0

0

0

0

0

8

0

0

0

0

1

0

▼169bp_i6

c.1340-1781_1340-1613 ins169

FS

C▼

34

40

22

109

10

3

58

39

4

5

0

10

0

ASV reads in pool together

115 049

238 054

259 694

298 184

302 328

254 125

298 628

247 635

286 606

255 213

365 903

  

ASV reads in pool together (% of normalized million)

11,5

23,8

26,0

29,8

30,2

25,4

29,9

24,8

28,7

25,5

36,6

  

No. of ASVs in pool

21

18

25

31

28

24

27

22

16

15

17

  
  1. Cells with stated normalized sequencing coverage higher than 1000 are underlined. The “predominant” and the “predominant candidate” variants are in bold. The list includes the variant’s name, presumed HGVS nomenclature, presumed functional annotation (FS = frameshift; IF – in frame; FS* - frameshift in the last exon 9 with alternative STOP codon), splicing event biotype (Δ = deletion; ▼ = insertion; C = cassette/exon; mC = multicasette/multiexon; SDS = splice donor site shift; SAS = splice acceptor site shift).
Back to article page