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Table 1 Pathogenic drivers and other genetic alterations shared between brain and abdominal tumors

From: Missense mutation of NRAS is associated with malignant progression in neurocutaneous melanosis

Gene

Chromosome

Variant Classification

HGVSc

HGVSp

Site

Number of mutant reads

Number of normal reads

MAF (%)

Significance (SIFT)

Significance (PolyPhen)

Exon (Intron)

GNAQ

chr9

missense mutation

c.548G > A

p.Arg183Gln

Abdominal tumor

215

47

82.1

deleterious (0.03)

probably damaging (0.958)

4/7

     

Brain tumor

194

23

89.4

   
     

Cerebral cortex

11

207

5

   
     

Normal skin

7

225

3

   

S1PR3

chr9

missense mutation

c.265G > A

p.Gly89Ser

Abdominal tumor

336

117

74.2

deleterious (0.02)

possibly damaging (0.796)

1/1

     

Brain tumor

222

26

89.5

   
     

Cerebral cortex

13

508

2.5

   
     

Normal skin

10

492

2

   

NRAS

chr1

missense mutation

c.35G > T

p.Gly12Val

Abdominal tumor

90

136

39.8

deleterious (0)

possibly damaging (0.454)

2/7

CTC1

chr17

missense mutation

c.1019C > T

p.Ser340Leu

Abdominal tumor

124

341

26.7

tolerated (0.68)

benign (0.158)

6/23

     

Brain tumor

105

116

47.5

   

GIGYF1

chr7

missense mutation

c.1931G > A

p.Arg644His

Abdominal tumor

12

478

2.4

deleterious (0)

benign (0.025)

19/27

     

Brain tumor

93

383

19.5

   

MTUS2

chr13

missense mutation

c.2747G > C

p.Ser916Thr

Abdominal tumor

31

264

10.5

tolerated (0.08)

possibly damaging (0.621)

6/16

     

Brain tumor

53

71

42.7

   

POM121

chr7

missense mutation

c.113G > C

p.Gly38Ala

Abdominal tumor

61

214

22.2

tolerated (0.06)

benign (0.145)

1/13

     

Brain tumor

92

274

25.1

   

PTPN14

chr1

missense mutation

c.1894A > C

p.Lys632Gln

Abdominal tumor

134

1457

8.4

tolerated (0.13)

benign (0.255)

13/19

     

Brain tumor

191

636

23.1

   

SPOPL

chr2

splice site

c.981-2A > T

Abdominal tumor

26

105

19.8

  

(9/10)

     

Brain tumor

36

64

36

   

ZNF208

chr19

missense mutation

c.986T > C

p.Ile329Thr

Brain tumor

11

15

42.3

tolerated (1)

benign (0.003)

4/4

ZNF208

chr19

missense mutation

c.980C > T

p.Thr327IIe

Abdominal tumor

16

44

26.7

tolerated (0.43)

benign (0.015)

4/4

     

Brain tumor

11

21

34.4

   

ZNF208

chr19

missense mutation

c.973G > T

p.Val325Phe

Brain tumor

21

16

56.8

tolerated (0.77)

possibly damaging (0.632)

4/4

  1. Pathogenic/possibly pathogenic alterations are indicated in bold. HGVSc: Human Genome Variation Society coding DNA; HGVSp: Human Genome Variation Society protein; SIFT: Sorting Intolerant From Tolerant MAF: mutant allele frequency
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Acta Neuropathologica Communications

ISSN: 2051-5960

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