Table 1 Somatic alterations in oncogenes or tumor suppressor genes identified in Patient 1 and Patient 2

General

classification

Details

Inter Var Class

12

SIFT. pred

PolyPhen. pred

CADD. phred

Specific alteration

Other alterations

Type of tissue

ATM

NM_000051.3

+

Missense variant

p. P2901T

Uncertain significance

1

0 Deleterious

1 D

32 Deleterious

VUS

One case, non-

syn. SNV [29]

NR

M PT

AXIN2

NM_004655.4

+

Missense variant

p. T227N

Uncertain significance

1

0.003 Deleterious

0.989 D

25.1 Deleterious

VUS

NR

NR

BAP1

NM_004656.4

+

Missense

variant

p. D107E

Uncertain significance

1

0.459 Tolerated

0.015 B

10.98

Tolerated

VUS

NR

NR

NOTCH1

NM_017617.5

+

+

Missense

variant

p. A1418T

Uncertain significance

1

0.248 Tolerated

0.014 B

15.54 Deleterious

VUS

NR

NR

TP53

NM_000546.5

+

Stop

gained

p.E180*

Pathogenic

1

-

-

38 Deleterious

pathogenic

NR, c.747G > C

High frequency

[22, 23, 26, 27, 29,30,31,32,33,34]

Be,

Bo, P, R, DM

mostly M PT

Stop

gained

p.C141*

Pathogenic

2

-

-

35 Deleterious

NR, c.747G > C

High frequency

[22, 23, 26, 27, 29,30,31,32,33,34]

Be, Bo P, R, DM

mostly M PT

RB1

NM_000321.2

+

Fusion

RB1: exon3~

CORO2B: exon4

-

1

-

-

-

NA

NR, deletion

Several cases [22, 23, 26,27,28,29,30,31,32,33,34]

Be, Bo, P, R, DM

mostly M PT

FLT1

NM_002019.4

+

Missense variant

p. D1140N

Uncertain significance

2

0.277 Tolerated

0.01 B

23.6 Deleterious

VUS

NR

NR

PTEN

NM_000314.8

+

Missense variant

p. D92G

Likely pathogenic

2

0 Deleterious

0.999 P

27 Deleterious

Likely pathogenic

NR

Several cases [23, 26,27,28]

Be, Bo,

mostly M PT