Table 2 Variants of unknown significance genes for breast PTs identified in the primary tumor of 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

ARHGEF17

c.5020G > A (p.E1674K)

NM_014786.4

VUS

Missense variant

p. E1674K

VUS

1

0.002 Deleterious

0.549 P

34 Deleterious

NR

NR

FCHO1

c.2440 A > T (p.K814*)

NM_015122.3

Likely pathogenic

Stop gained

p.K814*

Pathogenic

1

-

-

47 Deleterious

P. R38W

c.112 C > T

One

case [27]

Be PT

GON4L

c.3970 A > G (p.I1324V)

NM_032292.6

VUS

Missense variant

p. I1324V

VUS

1

0.921Tolerated

0.01 B

0.001Tolerated

NR

NR

KRT27

c.233G > A (p.G78D)

NM_181537.4

VUS

Missense variant

p. G78D

VUS

1

0.001 Deleterious

0.918 P

26.6 Deleterious

NR

NR

TGFB1

c.1043 C > A (p.P348Q)

NM_000660.7

VUS

Missense variant

p. P348Q

VUS

1

0 Deleterious

1 D

32 Deleterious

NR

NR

TTN

c.7721 C > A (p.P2574H)

NM_133378.4

VUS

Missense variant

p. P2574H

VUS

1

0.082 Tolerated

0.74 P

5.255 Tolerated

NR

NR

CFAP57

c.451 A > T (p.T151S)

NM_152498.3

VUS

Missense variant

p. T151S

VUS

2

1 Tolerated

0.013 B

0.2 Tolerated

NR

NR

EMILIN2

c.1880del (p.K627Rfs*3)

NM_032048.3

VUS

Frameshift variant

p. K627Rfs*3

VUS

2

-

-

17.26 Deleterious

NR

NR

F2R

c.280G > A (p.G94R)

NM_001992.5

VUS

Missense variant

p. G94R

VUS

2

0.563 Tolerated

0.01 B

12.59 Tolerated

NR

NR

IGSF9B

c.2255G > A (p.R752H)

NM_001277285.2

VUS

Missense variant

p. R752H

VUS

2

0.194 Tolerated

0.01 B

24Deleterious

NR

NR

LILRB2

c.692 C > T (p.P231L)

NM_001080978.4

VUS

Missense variant

p. P231L

VUS

2

0.023 Deleterious

0.325 B

0.623 Tolerated

NR

NR

LRP12

c.860G > A (p.W287*)

NM_013437.4

VUS

Stop gained

p.W287*

Pathogenic

2

-

-

37 Deleterious

NR

NR

OR5AN1

c.643 A > G (p.I215V)

NM_001004729.1

VUS

Missense variant

p. I215V

VUS

2

0.304 Tolerated

0.012 B

6.505 Tolerated

NR

NR

PCDHA13

c.1279G > A (p.A427T)

NM_018904.3

VUS

Missense variant

p. A427T

VUS

2

0.008 Deleterious

0.972 D

26.2 Deleterious

NR

NR

PKM

c.1516_1525del (p. T506Afs*19)

NM_001206796.3

VUS

Frameshift variant

p. T506Afs*19

Likely pathogenic

2

-

-

34 Deleterious

NR

NR

RELN

c.6904T > A (p.F2302I)

NM_005045.4

VUS

Missense variant

p. F2302I

VUS

2

0.093 Tolerated

0.996 D

24.6 Deleterious

NR

NR

SATB1

c.1953T > G (p.I651M)

NM_001131010.4

VUS

Missense variant

P. I651M

VUS

2

0.002 Deleterious

1 D

22.3 Deleterious

NR

NR

SF3B3

c.2675 C > A (p.A892D)

NM_012426.5

VUS

Missense variant

p. A892D

VUS

2

0.002 Deleterious

0.776 P

32 Deleterious

NR

NR

SYT16

c.1463 C > T (p.A488V)

NM_001367661.1

VUS

Missense variant

p. A488V

VUS

2

0.217 Tolerated

0.022 B

23.2 Deleterious

NR

NR

ZSCAN1

c.1094 A > T

(p.D365V)

NM_182572.4

VUS

Missense variant

p. D365V

VUS

2

0.083 Tolerated

0.137 B

0.063 Tolerated

NR

NR

ZXDB

c.2119G > C

(p.G707R)

NM_007157.3

VUS

Missense variant

p. G707R

VUS

2

0.045 Deleterious

0.002 B

1.576 Tolerated

NR

NR