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Table 3 In silico data obtained for the variants of unknown significance (VUS) identified in our study of familial CRC individuals

From: Identification of genetic variants for clinical management of familial colorectal tumors

Selected variants (VAR)

Reference splice site-dedicated analyses

Cryptic splice site-dedicated analyses

ESR-dedicated analyses

Protein-dedicated analyses

Patient_ID

Genomic position (GRCh37)

Gene

Exon

Nucleotide change (cNomen)

Predicted protein change (pNomen)

Nearest reference

MES scores

SSFL scores

Potential local splice effect

Local MES scores

∆tESRseq

∆Hzei

ΔΨ

splice site

WT

Var

VAR vs WT

WT

Var

VAR vs WT

WT

Var

Distance

Type

∆ (%)

(nt)

(3’ or 5’ss)

Δ (%)

AGVGD

SIFT

MAPP

PolyPhen-2

MutationTaster

3222 & 4932

chr19:15273335 C>T

NOTCH3

32

c.5854G>A

p.V1952M

39

3’

11.5

11.5

0

89.2

89.2

0

-

-

-

-1.78501

-11.15

-0.89

C15

Deleterious

bad

probably damaging

disease causing

3222

 

POLE

25

c.3046G>A

p.V1016M

-15

5’

9.1

9.1

0

82.5

82.5

0

-

-

-

-0.74478

1

-0.43

C0

Deleterious

bad

benign

disease causing

3308

chr8:90965597 A>T

NBN

11

c.1720T>A

p.L574I

-126

5’

8.0

8.0

0

82.4

82.4

0

-

-

-

1.97427

33.38

0.18

C0

Tolerated

good

benign

polymorphism

chr12:133219838 C>T

POLE

35

c.4523G>A

p.R1508H

-29

5’

7.9

7.9

0

73.8

73.8

0

-

-

-

-0.600279

-3.17

-0.08

C0

Tolerated

good

benign

disease causing

4932

chr19:1221318 C>A

STK11

6

c.841C>A

p.P281T

-22

5’

6.0

6.0

0

79.9

79.9

0

-

-

-

-0.17437

7.7

-0.72

C0

Tolerated

good

benign

disease causing

5597

chr5:56177843 C>G

MAP3K1

14

c.2816C>G

p.S939C

447

3’

12.0

12.0

0

100.0

100.0

0

-

-

-

-0.486881

-16.1

0

C0

Deleterious

good

benign

polymorphism

9876

chr17: 40729320 C>T

PSMC3IP

3

c.136G>A

p.V46M

1

3’

12.5

11.7

-6

87.5

83.6

-4

-

-

-

2.0413

74.24

-0.3

C0

Deleterious

-

possibly damaging

disease causing

9876 & 8913

chr14:69061228 G>A

RAD51B

11*

c.1063G>A

p.A355T

27

3’

11.8

11.8

0

80.2

80.2

0

-

-

-

-1.24035

-50.64

-

C0

Deleterious

-

benign

polymorphism

12954

chr1: 45797950_C>T

MUTYH

10

c.812G>A

p.R271Q

33

3’

9.5

9.5

0

86.8

86.8

0

-

-

-

-2.31042

0.88

0.09

C35

Deleterious

bad

possibly damaging

disease causing

chr17:56787304 G>A

RAD51C

5

c.790G>A

p.G264S

-48

5’

8.6

8.6

0

75.4

75.4

0

New Acceptor Site?

0

2.5

-1.71397

-59.31

-0.21

C0

Tolerated

good

benign

disease causing

13072

chr17:41234463 G>A

BRCA1

12

c.4315C>T

p.L1439F

-43

5’

6.6

6.6

0

85.2

85.2

0

-

-

-

-0.261141

8.83

-2.67

C0

Tolerated

good

benign

polymorphism

18843

chr2:48027317 G>A

MSH6

4**

c.2195G>A

p.R732Q

-978

5’

8.9

8.9

0

81.6

81.6

0

-

-

-

-0.805417

-13.15

0

C0

Tolerated

good

benign

disease causing

19673

chr17:63554395 T>C

AXIN2

2

c.344A>G

p.N115S

460

3’

11.1

11.1

0

93.3

93.3

0

New Acceptor Site?

11.1

7.2

-0.162849

-2.19

-0.05

C0

Tolerated

good

benign

disease causing

21368

chr5:56155672 A>G

MAP3K1

3

c.764A>G

p.N255S

-71

5’

7.5

7.5

0

78.5

78.5

0

New Acceptor Site?

4.7

8.8

-1.18661

6.7

-0.04

C0

Tolerated

good

benign

polymorphism

24447

chr22:29130636 A>G

CHEK2

2

c.74T>C

p.V25A

80

3’

1.7

1.7

0

85.5

85.5

0

-

-

 

-0.166788

36.67

-0.07

C0

Tolerated

good

benign

polymorphism

11705

chr11:108160467 G>A

ATM

29

c.4375G>A

p.G1459R

-62

5’

8.9

8.9

0

87.5

87.5

0

-

-

 

0.552026

-27.26

-0.09

C15

Deleterious

bad

probably damaging

disease causing

chr2:47672694 C>G

MSH2

8

c.1284C>G

p.H428Q

8

3’

10.1

10.1

0

87.3

87.3

0

-

-

 

0.703136

22.05

0.05

C0

Tolerated

good

possibly damaging

disease causing

13393 & 25167

chr:8_90983460 G>A

NBN

6

c.643C>T

p.R215W

59

3’

6.2

6.2

0

86.8

86.8

0

-

-

 

-1.00071

-16.87

-0.09

C0

Tolerated

good

probably damaging

polymorphism

14963

chr16:23647635 C>T

PALB2

4**

c.232G>A

p.V78I

21

3’

10.0

10.0

0

90.3

90.3

0

-

-

 

-0.783039

-29.17

0.8

C0

Tolerated

good

benign

polymorphism

22953

chr19:15278214 C>G

NOTCH3

29

c.5208G>C

p.E1736D

9

3’

7.8

7.8

0

84.2

84.2

0

-

-

 

0.0501789

-10.44

0.22

C35

Deleterious

bad

benign

disease causing

chr2:47630458 A>G

MSH2

1*

c.128A>G

p.Y43C

-84

5’

10.1

10.1

0

90.6

90.6

0

New Donor Site?

0

1.2

1.50425

4.7

2.11

C55

Deleterious

bad

probably damaging

disease causing

chr14:68352648 T>G

RAD51B

6

c.515T>G

p.L172W

-58

5’

9.5

9.5

0

83.7

83.7

0

-

-

 

1.62772

67.77

1.31

C0

Deleterious

bad

possibly damaging

polymorphism

24789

chr5:112175625 C>T

APC

15*

c.4334C>T

p.T1445I

2376

3’

7.5

7.5

0

93.6

93.6

0

-

-

 

-1.61023

-90.13

-

C0

Tolerated

good

benign

polymorphism

chr16:23646617 G>T

PALB2

4**

c.1250C>A

p.S417Y

-435

5’

8.9

8.9

0

87.5

87.5

0

-

-

 

-0.551724

-22.83

0.05

C0

Deleterious

bad

probably damaging

disease causing

8913

chr2:47601029 G>C

EPCAM

3

c.267G>C

p.Q89H

83

3’

7.0

7.0

0

90.1

90.1

0

-

-

 

-0.40237

-28.93

0

C0

Tolerated

bad

possibly damaging

disease causing

  1. In order to predict the biological impact of the 25 VUS, RNA splicing- and protein-dedicated bioinformatics analyses were performed as described under Materials and Methods. The stars indicate exons that could not be tested in our minigene assay, either because of their terminal position (*, 1st or last exons) or because of their large size (**). Results shown in bold were considered as predictive of a potential variant-induced negative biological effect. MES, MaxEntScan; SSFL, Splice Site Finder-Like; nt, nucleotide; 3’ or 5’ss, 3’ splice site or 5’ splice site; ESR, exonic splicing regulators; AGVGD, align-GVGD (C0, C15, C25, C35, C.45, C55, or C65 with C65 most likely to interfere with function and C0 least likely), SIFT, Sorting Intolerant From Tolerant (tolerated or deleterious), MAPP, Multivariate Analysis of Protein Polymorphism (good or bad), PolyPhen-2, Polymorphism Phenotyping v2 (benign, possibly damaging or probably damaging), MutationTaster (polymorphism or disease causing), CRC: colorectal cancer.
  2. In order to predict the biological impact of the 25 VUS, RNA splicing- and protein-dedicated bioinformatics analyses were performed as described under Materials and Methods. The stars indicate exons that could not be tested in our minigene assay, either because of their terminal position (*, 1st or last exons) or because of their large size (**). Results shown in bold were considered as predictive of a potential variant-induced negative biological effect. MES, MaxEntScan; SSFL, Splice Site Finder-Like; nt, nucleotide; 3′ or 5’ss, 3′ splice site or 5′ splice site; ESR, exonic splicing regulators; AGVGD, align-GVGD (C0, C15, C25, C35, C.45, C55, or C65 with C65 most likely to interfere with function and C0 least likely), SIFT, Sorting Intolerant From Tolerant (tolerated or deleterious), MAPP, Multivariate Analysis of Protein Polymorphism (good or bad), PolyPhen-2, Polymorphism Phenotyping v2 (benign, possibly damaging or probably damaging), MutationTaster (polymorphism or disease causing), CRC: colorectal cancer
  3. In order to predict their biological impact, RNA splicing- and protein-dedicated bioinformatics analyses were performed as described under Materials and Methods. Results shown in bold were considered as predictive of a potential variant-induced negative biological effect. MES, MaxEntScan; SSFL, Splice Site Finder-Like; nt, nucleotide; 3′ or 5’ss, 3′ splice site or 5′ splice site; ESR, exonic splicing regulators; AGVGD, align-GVGD (C0, C15, C25, C35, C.45, C55, or C65 with C65 most likely to interfere with function and C0 least likely), SIFT, Sorting Intolerant From Tolerant (tolerated or deleterious), MAPP, Multivariate Analysis of Protein Polymorphism (good or bad), PolyPhen-2, Polymorphism Phenotyping v2 (benign, possibly damaging or probably damaging), MutationTaster (polymorphism or disease causing)