Table 1 Mutation analysis of the CTNNB1gene in melanoma patients.

From: Temporal activation of WNT/β-catenin signaling is sufficient to inhibit SOX10 expression and block melanoma growth

Study

Sample ID

Cancer type

Protein change

Annotation

Functional impact

Mutation type

Copy #

COSMIC

MS

VS

Center

Chromosome

Start Pos

End Pos

Ref

Var

Allele Freq (T)

Allele Freq (N)

Variant reads

Ref reads

Variant reads (N)

Ref reads (N)

# Mut in sample

Skin cutaneous melanoma (TCGA, PanCancer Atlas)

TCGA-D9-A6EG-06

Cutaneous melanoma

S45P

OncoKB: Likely Oncogenic, level NA;CIViC: Diagnostic: 2, Prognostic: 1;MyCancerGenome: present;CancerHotspot: yes;3DHotspot: no

MutationAssessor: impact: medium, score: 2.215;SIFT: impact: deleterious, score: 0;Polyphen-2: impact: probably_damaging, score: 0.939

Missense_Mutation

 

817

–

–

–

3

41266136

41266136

T

C

  

24

55

0

66

65

Skin cutaneous melanoma (TCGA, Provisional)

TCGA-D9-A6EG-06

Cutaneous melanoma

S45P

OncoKB: Likely Oncogenic, level NA;CIViC: Diagnostic: 2, Prognostic: 1;MyCancerGenome: present;CancerHotspot: yes;3DHotspot: no

MutationAssessor: impact: medium, score: 2.215;SIFT: impact: deleterious, score: 0;Polyphen-2: impact: probably_damaging, score: 0.939

Missense_Mutation

 

817

Somatic

NA

broad.mit.edu

3

41266136

41266136

T

C

   

52

−1

−1

74

Skin cutaneous melanoma (TCGA, PanCancer Atlas)

TCGA-ER-A19O-06

Cutaneous melanoma

T41A

OncoKB: Oncogenic, level NA;CIViC: Predictive: 3, Diagnostic: 2, Prognostic: 1;MyCancerGenome: not present;CancerHotspot: yes;3DHotspot: no

MutationAssessor: impact: medium, score: 2.68;SIFT: impact: deleterious, score: 0;Polyphen-2: impact: possibly_damaging, score: 0.844

Missense_Mutation

 

941

–

–

–

3

41266124

41266124

A

G

  

7

14

0

43

213

Skin cutaneous melanoma (TCGA, Provisional)

TCGA-ER-A19O-06

Cutaneous melanoma

T41A

OncoKB: Oncogenic, level NA;CIViC: Predictive: 3, Diagnostic: 2, Prognostic: 1;MyCancerGenome: not present;CancerHotspot: yes;3DHotspot: no

MutationAssessor: impact: medium, score: 2.68;SIFT: impact: deleterious, score: 0;Polyphen-2: impact: possibly_damaging, score: 0.844

Missense_Mutation

 

941

Somatic

NA

broad.mit.edu

3

41266124

41266124

A

G

   

14

−1

−1

155

Skin cutaneous melanoma (TCGA, PanCancer Atlas)

TCGA-WE-A8ZN-06

Cutaneous melanoma

S37F

OncoKB: Likely Oncogenic, level NA;CIViC: NA;MyCancerGenome: present;CancerHotspot: yes;3DHotspot: no

MutationAssessor: impact: medium, score: 2.66;SIFT: impact: deleterious, score: 0;Polyphen-2: impact: probably_damaging, score: 0.962

Missense_Mutation

 

493

–

–

–

3

41266113

41266113

C

T

  

17

34

0

38

135

Skin cutaneous melanoma (TCGA, PanCancer Atlas)

TCGA-FS-A1YY-06

Cutaneous melanoma

S45C

OncoKB: Likely Oncogenic, level NA;CIViC: NA;MyCancerGenome: present;CancerHotspot: yes;3DHotspot: no

MutationAssessor: impact: medium, score: 2.565;SIFT: impact: deleterious, score: 0;Polyphen-2: impact: probably_damaging, score: 0.968

Missense_Mutation

 

817

–

–

–

3

41266137

41266137

C

G

  

15

27

0

54

165

Skin cutaneous melanoma (TCGA, Provisional)

TCGA-FS-A1YY-06

Cutaneous melanoma

S45C

OncoKB: Likely Oncogenic, level NA;CIViC: NA;MyCancerGenome: present;CancerHotspot: yes;3DHotspot: no

MutationAssessor: impact: medium, score: 2.565;SIFT: impact: deleterious, score: 0;Polyphen-2: impact: probably_damaging, score: 0.968

Missense_Mutation

 

817

Somatic

NA

broad.mit.edu

3

41266137

41266137

C

G

   

26

−1

−1

169

Skin cutaneous melanoma (TCGA, PanCancer Atlas)

TCGA-D3-A8GV-06

Cutaneous melanoma

S45del

OncoKB: Likely Oncogenic, level NA;CIViC: NA;MyCancerGenome: present;CancerHotspot: yes;3DHotspot: no

 

In_Frame_Del

 

57

–

–

–

3

41266134

41266136

CTT

–

  

24

32

0

57

339

Skin cutaneous melanoma (TCGA, PanCancer Atlas)

TCGA-EE-A2M6-06

Cutaneous melanoma

S45del

OncoKB: Likely Oncogenic, level NA;CIViC: NA;MyCancerGenome: present;CancerHotspot: yes;3DHotspot: no

 

In_Frame_Del

 

57

–

–

–

3

41266134

41266136

CTT

–

  

15

19

0

41

571

Skin cutaneous melanoma (TCGA, Provisional)

TCGA-EE-A2M6-06

Cutaneous melanoma

S45del

OncoKB: Likely Oncogenic, level NA;CIViC: NA;MyCancerGenome: present;CancerHotspot: yes;3DHotspot: no

 

In_Frame_Del

 

57

Somatic

NA

broad.mit.edu

3

41266134

41266136

CTT

–

   

20

−1

−1

460

Skin cutaneous melanoma (TCGA, PanCancer Atlas)

TCGA-FS-A4F9-06

Cutaneous melanoma

G34R

OncoKB: Likely Oncogenic, level NA;CIViC: NA;MyCancerGenome: not present;CancerHotspot: yes;3DHotspot: no

MutationAssessor: impact: medium, score: 2.66;SIFT: impact: deleterious, score: 0;Polyphen-2: impact: probably_damaging, score: 0.997

Missense_Mutation

 

285

–

–

–

3

41266103

41266103

G

A

  

19

18

0

51

372

Skin cutaneous melanoma (TCGA, Provisional)

TCGA-FS-A4F9-06

Cutaneous melanoma

G34R

OncoKB: Likely Oncogenic, level NA;CIViC: NA;MyCancerGenome: not present;CancerHotspot: yes;3DHotspot: no

MutationAssessor: impact: medium, score: 2.66;SIFT: impact: deleterious, score: 0;Polyphen-2: impact: probably_damaging, score: 0.997

Missense_Mutation

 

285

Somatic

NA

broad.mit.edu

3

41266103

41266103

G

A

   

18

−1

−1

378

Skin cutaneous melanoma (TCGA, PanCancer Atlas)

TCGA-EB-A5SH-06

Cutaneous melanoma

T41N

OncoKB: Likely Oncogenic, level NA;CIViC: NA;MyCancerGenome: not present;CancerHotspot: yes;3DHotspot: no

MutationAssessor: impact: medium, score: 2.335;SIFT: impact: deleterious, score: 0.03;Polyphen-2: impact: probably_damaging, score: 0.95

Missense_Mutation

 

941

–

–

–

3

41266125

41266125

C

A

  

14

39

0

45

88

Skin cutaneous melanoma (TCGA, Provisional)

TCGA-EB-A5SH-06

Cutaneous melanoma

T41N

OncoKB: Likely Oncogenic, level NA;CIViC: NA;MyCancerGenome: not present;CancerHotspot: yes;3DHotspot: no

MutationAssessor: impact: medium, score: 2.335;SIFT: impact: deleterious, score: 0.03;Polyphen-2: impact: probably_damaging, score: 0.95

Missense_Mutation

 

941

Somatic

NA

broad.mit.edu

3

41266125

41266125

C

A

   

39

−1

−1

97

Skin cutaneous melanoma (TCGA, PanCancer Atlas)

TCGA-D9-A149-06

Cutaneous melanoma

T41I

OncoKB: Likely Oncogenic, level NA;CIViC: NA;MyCancerGenome: not present;CancerHotspot: yes;3DHotspot: no

MutationAssessor: impact: medium, score: 2.68;SIFT: impact: deleterious, score: 0;Polyphen-2: impact: probably_damaging, score: 0.931

Missense_Mutation

 

941

–

–

–

3

41266125

41266125

C

T

  

12

26

0

57

710

Skin cutaneous melanoma (TCGA, Provisional)

TCGA-D9-A149-06

Cutaneous melanoma

T41I

OncoKB: Likely Oncogenic, level NA;CIViC: NA;MyCancerGenome: not present;CancerHotspot: yes;3DHotspot: no

MutationAssessor: impact: medium, score: 2.68;SIFT: impact: deleterious, score: 0;Polyphen-2: impact: probably_damaging, score: 0.931

Missense_Mutation

 

941

Somatic

NA

broad.mit.edu

3

41266125

41266125

C

T

   

25

−1

−1

202

Skin cutaneous melanoma (TCGA, PanCancer Atlas)

TCGA-D3-A8GS-06

Cutaneous melanoma

W383G

OncoKB: Likely Oncogenic, level NA;CIViC: NA;MyCancerGenome: not present;CancerHotspot: yes;3DHotspot: no

MutationAssessor: impact: medium, score: 3.02;SIFT: impact: deleterious, score: 0;Polyphen-2: impact: possibly_damaging, score: 0.745

Missense_Mutation

 

6

–

–

–

3

41274897

41274897

T

G

  

13

112

0

110

172

Skin cutaneous melanoma (TCGA, PanCancer Atlas)

TCGA-EE-A180-06

Cutaneous melanoma

K292E

OncoKB: Predicted Oncogenic, level NA;CIViC: NA;MyCancerGenome: not present;CancerHotspot: yes;3DHotspot: no

MutationAssessor: impact: medium, score: 2.81;SIFT: impact: deleterious, score: 0;Polyphen-2: impact: probably_damaging, score: 0.912

Missense_Mutation

 

2

–

–

–

3

41267290

41267290

A

G

  

22

48

0

61

439

Skin cutaneous melanoma (TCGA, Provisional)

TCGA-EE-A180-06

Cutaneous melanoma

K292E

OncoKB: Predicted Oncogenic, level NA;CIViC: NA;MyCancerGenome: not present;CancerHotspot: yes;3DHotspot: no

MutationAssessor: impact: medium, score: 2.81;SIFT: impact: deleterious, score: 0;Polyphen-2: impact: probably_damaging, score: 0.912

Missense_Mutation

 

2

Somatic

NA

broad.mit.edu

3

41267290

41267290

A

G

   

39

−1

−1

458

Skin cutaneous melanoma (TCGA, PanCancer Atlas)

TCGA-EE-A181-06

Cutaneous melanoma

P714L

OncoKB: Unknown, level NA;CIViC: NA;MyCancerGenome: not present;CancerHotspot: no;3DHotspot: no

MutationAssessor: impact: medium, score: 2.285;SIFT: impact: tolerated_low_confidence, score: 0.07;Polyphen-2: impact: benign, score: 0.075

Missense_Mutation

 

1

–

–

–

3

41280628

41280628

C

T

  

12

32

0

80

4469

Skin cutaneous melanoma (TCGA, Provisional)

TCGA-EE-A181-06

Cutaneous melanoma

P714L

OncoKB: Unknown, level NA;CIViC: NA;MyCancerGenome: not present;CancerHotspot: no;3DHotspot: no

MutationAssessor: impact: medium, score: 2.285;SIFT: impact: tolerated_low_confidence, score: 0.07;Polyphen-2: impact: benign, score: 0.075

Missense_Mutation

 

1

Somatic

NA

broad.mit.edu

3

41280628

41280628

C

T

   

29

−1

−1

2503

Skin cutaneous melanoma (TCGA, PanCancer Atlas)

TCGA-D3-A1Q5-06

Cutaneous melanoma

C429G

OncoKB: Unknown, level NA;CIViC: NA;MyCancerGenome: not present;CancerHotspot: no;3DHotspot: no

MutationAssessor: impact: medium, score: 2.94;SIFT: impact: deleterious, score: 0;Polyphen-2: impact: probably_damaging, score: 0.994

Missense_Mutation

 

2

–

–

–

3

41275119

41275119

T

G

  

35

40

0

95

295

Skin cutaneous melanoma (TCGA, Provisional)

TCGA-D3-A1Q5-06

Cutaneous melanoma

C429G

OncoKB: Unknown, level NA;CIViC: NA;MyCancerGenome: not present;CancerHotspot: no;3DHotspot: no

MutationAssessor: impact: medium, score: 2.94;SIFT: impact: deleterious, score: 0;Polyphen-2: impact: probably_damaging, score: 0.994

Missense_Mutation

 

2

Somatic

NA

broad.mit.edu

3

41275119

41275119

T

G

   

39

−1

−1

306

Skin cutaneous melanoma (TCGA, PanCancer Atlas)

TCGA-D3-A2JN-06

Cutaneous melanoma

P687S

OncoKB: Unknown, level NA;CIViC: NA;MyCancerGenome: not present;CancerHotspot: no;3DHotspot: no

MutationAssessor: impact: low, score: 1.59;SIFT: impact: tolerated, score: 0.32;Polyphen-2: impact: benign, score: 0

Missense_Mutation

  

–

–

–

3

41278183

41278183

C

T

  

34

87

0

99

721

Skin cutaneous melanoma (TCGA, Provisional)

TCGA-D3-A2JN-06

Cutaneous melanoma

P687S

OncoKB: Unknown, level NA;CIViC: NA;MyCancerGenome: not present;CancerHotspot: no;3DHotspot: no

MutationAssessor: impact: low, score: 1.59;SIFT: impact: tolerated, score: 0.32;Polyphen-2: impact: benign, score: 0

Missense_Mutation

  

Somatic

NA

broad.mit.edu

3

41278183

41278183

C

T

   

80

−1

−1

292

Skin cutaneous melanoma (TCGA, PanCancer Atlas)

TCGA-D3-A2JN-06

Cutaneous melanoma

P687L

OncoKB: Unknown, level NA;CIViC: NA;MyCancerGenome: not present;CancerHotspot: no;3DHotspot: no

MutationAssessor: impact: medium, score: 2.14;SIFT: impact: deleterious, score: 0.03;Polyphen-2: impact: benign, score: 0.066

Missense_Mutation

  

–

–

–

3

41278184

41278184

C

T

  

34

89

0

100

721

Skin cutaneous melanoma (TCGA, Provisional)

TCGA-D3-A2JN-06

Cutaneous melanoma

P687L

OncoKB: Unknown, level NA;CIViC: NA;MyCancerGenome: not present;CancerHotspot: no;3DHotspot: no

MutationAssessor: impact: medium, score: 2.14;SIFT: impact: deleterious, score: 0.03;Polyphen-2: impact: benign, score: 0.066

Missense_Mutation

  

Somatic

NA

broad.mit.edu

3

41278184

41278184

C

T

   

81

−1

−1

292

Skin cutaneous melanoma (TCGA, PanCancer Atlas)

TCGA-EE-A3AC-06

Cutaneous melanoma

Q545*

OncoKB: Unknown, level NA;CIViC: NA;MyCancerGenome: not present;CancerHotspot: no;3DHotspot: no

 

Nonsense_Mutation

 

1

–

–

–

3

41275738

41275738

C

T

  

18

27

0

80

1834

Skin cutaneous melanoma (TCGA, Provisional)

TCGA-EE-A3AC-06

Cutaneous melanoma

Q545*

OncoKB: Unknown, level NA;CIViC: NA;MyCancerGenome: not present;CancerHotspot: no;3DHotspot: no

 

Nonsense_Mutation

 

1

Somatic

NA

broad.mit.edu

3

41275738

41275738

C

T

   

25

−1

−1

844

Skin cutaneous melanoma (TCGA, PanCancer Atlas)

TCGA-D9-A6E9-06

Cutaneous melanoma

D390E

OncoKB: Unknown, level NA;CIViC: NA;MyCancerGenome: not present;CancerHotspot: no;3DHotspot: no

MutationAssessor: impact: medium, score: 3.12;SIFT: impact: deleterious, score: 0;Polyphen-2: impact: probably_damaging, score: 0.982

Missense_Mutation

  

–

–

–

3

41274920

41274920

T

G

  

18

31

0

55

155

Skin cutaneous melanoma (TCGA, Provisional)

TCGA-D9-A6E9-06

Cutaneous melanoma

D390E

OncoKB: Unknown, level NA;CIViC: NA;MyCancerGenome: not present;CancerHotspot: no;3DHotspot: no

MutationAssessor: impact: medium, score: 3.12;SIFT: impact: deleterious, score: 0;Polyphen-2: impact: probably_damaging, score: 0.982

Missense_Mutation

  

Somatic

NA

broad.mit.edu

3

41274920

41274920

T

G

   

31

−1

−1

168

Skin cutaneous melanoma (TCGA, PanCancer Atlas)

TCGA-D9-A6EC-06

Cutaneous melanoma

L762P

OncoKB: Unknown, level NA;CIViC: NA;MyCancerGenome: not present;CancerHotspot: no;3DHotspot: no

MutationAssessor: impact: low, score: 1.215;SIFT: impact: tolerated_low_confidence, score: 0.14;Polyphen-2: impact: benign, score: 0.003

Missense_Mutation

  

–

–

–

3

41280772

41280772

T

C

  

10

27

0

45

3621

Skin cutaneous melanoma (TCGA, Provisional)

TCGA-D9-A6EC-06

Cutaneous melanoma

L762P

OncoKB: Unknown, level NA;CIViC: NA;MyCancerGenome: not present;CancerHotspot: no;3DHotspot: no

MutationAssessor: impact: low, score: 1.215;SIFT: impact: tolerated_low_confidence, score: 0.14;Polyphen-2: impact: benign, score: 0.003

Missense_Mutation

  

Somatic

NA

broad.mit.edu

3

41280772

41280772

T

C

   

26

−1

−1

3905

Skin cutaneous melanoma (TCGA, PanCancer Atlas)

TCGA-EE-A29A-06

Cutaneous melanoma

P606L

OncoKB: Unknown, level NA;CIViC: NA;MyCancerGenome: not present;CancerHotspot: no;3DHotspot: no

MutationAssessor: impact: low, score: 1.7;SIFT: impact: tolerated, score: 0.11;Polyphen-2: impact: benign, score: 0.408

Missense_Mutation

 

1

–

–

–

3

41277853

41277853

C

T

  

68

95

0

214

210

Skin cutaneous melanoma (TCGA, Provisional)

TCGA-EE-A29A-06

Cutaneous melanoma

P606L

OncoKB: Unknown, level NA;CIViC: NA;MyCancerGenome: not present;CancerHotspot: no;3DHotspot: no

MutationAssessor: impact: low, score: 1.7;SIFT: impact: tolerated, score: 0.11;Polyphen-2: impact: benign, score: 0.408

Missense_Mutation

 

1

Somatic

NA

broad.mit.edu

3

41277853

41277853

C

T

   

88

−1

−1

215

Skin cutaneous melanoma (TCGA, PanCancer Atlas)

TCGA-D3-A2JC-06

Cutaneous melanoma

P100H

OncoKB: Unknown, level NA;CIViC: NA;MyCancerGenome: not present;CancerHotspot: no;3DHotspot: no

MutationAssessor: impact: medium, score: 2.735;SIFT: impact: deleterious, score: 0;Polyphen-2: impact: probably_damaging, score: 0.987

Missense_Mutation

  

–

–

–

3

41266502

41266502

C

A

  

4

24

0

56

3091

Skin cutaneous melanoma (TCGA, PanCancer Atlas)

TCGA-D3-A8GI-06

Cutaneous melanoma

T595I

OncoKB: Unknown, level NA;CIViC: NA;MyCancerGenome: not present;CancerHotspot: no;3DHotspot: no

MutationAssessor: impact: low, score: 1.15;SIFT: impact: tolerated, score: 0.43;Polyphen-2: impact: benign, score: 0.393

Missense_Mutation

  

–

–

–

3

41277315

41277315

C

T

  

58

104

0

148

4217

Skin cutaneous melanoma (TCGA, PanCancer Atlas)

TCGA-EE-A20F-06

Cutaneous melanoma

R93S

OncoKB: Unknown, level NA;CIViC: NA;MyCancerGenome: not present;CancerHotspot: no;3DHotspot: no

MutationAssessor: impact: medium, score: 2.69;SIFT: impact: deleterious, score: 0.03;Polyphen-2: impact: possibly_damaging, score: 0.677

Missense_Mutation

  

–

–

–

3

41266482

41266482

G

T

  

6

57

0

179

1819

Skin Cutaneous Melanoma (TCGA, PanCancer Atlas)

TCGA-EE-A29P-06

Cutaneous melanoma

E55*

OncoKB: Unknown, level NA;CIViC: NA;MyCancerGenome: not present;CancerHotspot: no;3DHotspot: no

 

Nonsense_Mutation

  

–

–

–

3

41266166

41266166

G

T

  

3

33

0

84

409

Skin cutaneous melanoma (TCGA, PanCancer Atlas)

TCGA-ER-A19J-06

Cutaneous melanoma

L46M

OncoKB: Unknown, level NA;CIViC: NA;MyCancerGenome: not present;CancerHotspot: no;3DHotspot: no

MutationAssessor: impact: low, score: 1.665;SIFT: impact: tolerated, score: 0.09;Polyphen-2: impact: possibly_damaging, score: 0.635

Missense_Mutation

 

4

–

–

–

3

41266139

41266139

C

A

  

3

32

0

53

182

Skin cutaneous melanoma (TCGA, PanCancer Atlas)

TCGA-GN-A262-06

Cutaneous melanoma

X509_splice

OncoKB: Unknown, level NA;CIViC: NA;MyCancerGenome: not present;CancerHotspot: no;3DHotspot: no

 

Splice_Site

  

–

–

–

3

41275629

41275629

G

T

  

3

33

0

68

949

Skin cutaneous melanoma (TCGA, PanCancer Atlas)

TCGA-GN-A26D-06

Cutaneous melanoma

M398I

OncoKB: Unknown, level NA;CIViC: NA;MyCancerGenome: not present;CancerHotspot: no;3DHotspot: no

MutationAssessor: impact: low, score: 0.935;SIFT: impact: tolerated, score: 0.2;Polyphen-2: impact: benign, score: 0.003

Missense_Mutation

  

–

–

–

3

41275028

41275028

G

T

  

4

34

1

97

618

Skin cutaneous melanoma (TCGA, PanCancer Atlas)

TCGA-W3-AA1V-06

Cutaneous melanoma

A532V

OncoKB: Unknown, level NA;CIViC: NA;MyCancerGenome: not present;CancerHotspot: no;3DHotspot: no

MutationAssessor: impact: low, score: 0.975;SIFT: impact: tolerated, score: 0.68;Polyphen-2: impact: benign, score: 0.01

Missense_Mutation

  

–

–

–

3

41275700

41275700

C

T

  

7

43

0

47

4472

Skin cutaneous melanoma (TCGA, Provisional)

TCGA-EE-A182-06

Cutaneous melanoma

W25*

OncoKB: Unknown, level NA;CIViC: NA;MyCancerGenome: not present;CancerHotspot: no;3DHotspot: no

 

Nonsense_Mutation

 

3

Somatic

NA

broad.mit.edu

3

41266077

41266077

G

A

   

23

−1

−1

1198

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