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Table 3 Germline alterations in genes identified in Patient 1 and Patient 2

From: Genomic characteristics of two breast malignant phyllodes tumors during pregnancy and lactation identified through whole-exome sequencing

Gene

coding(c.) nomenclature

RefSeq NM

franklin

Type of alteration

Patient

Prediction of functional consequence

    

General

classification

Details

Inter Var Class

  

SIFT. pred

PolyPhen. pred

CADD. phred

ABCC2

c.1457 C > T

NM_000392.5

Likely benign

Missense variant

p.T486I

Likely benign

1

 

0.011 Deleterious

0.063 B

12.73 Tolerated

CYLD

c.98 A > G

NM_001042355.2

VUS

Missense variant

p.K33R

VUS

1

 

0.321 Tolerated

0.024 B

20.3 Deleterious

EWSR1

c.1493 C > T

NM_005243.4

VUS

Missense variant

p.P498L

VUS

1

 

0.01 Deleterious

0.001 B

17.89 Deleterious

FOXO3

c.184G > A

NM_001455.4

VUS

Missense variant

p.D62N

VUS

1

 

0.031 Deleterious

0.229 B

19.65 Deleterious

GRM8

c.1012 A > G

NM_000845.3

VUS

Missense variant

p.I338V

VUS

1

 

0.916 Tolerated

0.013 B

6.229 Tolerated

LZTR1

c.1766T > C

NM_006767.4

VUS

Missense variant

p.L589P

VUS

1

 

0.152 Tolerated

0.999 D

25.5 Deleterious

MPL

c.173 C > T

NM_005373.3

Likely benign

Missense variant

p.A58V

VUS

1

 

0.045 Deleterious

0.533 P

17.63

Deleterious

   

Likely benign

 

p.A58V

VUS

 

2

0.045 Deleterious

0.533 P

17.63

Deleterious

RCC1

c.1123T > C

NM_001269.5

VUS

Missense variant

p.Y375H

VUS

1

 

0.57

Tolerated

0.021 B

18.18 Deleterious

TET2

c.4229 C > T

NM_001127208.2

VUS

Missense variant

p.P1410L

VUS

1

 

0.001 Deleterious

1 D

33

Deleterious

ATM

c.125 A > G

NM_000051.3

Likely benign

Missense variant

p.H42R

VUS

 

2

0.353 Tolerated

0.057

B

8.953

Tolerated

ERBB3

c.1981G > A

NM_001982.3

VUS

Missense variant

p.G661S

VUS

 

2

0.323 Tolerated

0 B

7.111

Tolerated

FANCF

c.1009_1014del

NM_022725.4

VUS

inframe_deletion

p.G337_D338del

VUS

 

2

-

-

22.4

Deleterious

FGFR1

c.103G > A

NM_023110.3

VUS

missense_variant

p.G35R

VUS

 

2

0.674

Tolerated

0.022 B

21.3

Tolerated

GSTP1

c.439G > T

NM_000852.4

VUS

missense_variant

p.D147Y

Likely benign

 

2

0.002

Deleterious

0.428

B

23.3

Deleterious

MTRR

c.362G > A

NM_001364440.2

VUS

missense_variant

p.R121Q

VUS

 

2

0.752 Tolerated

0.003

B

9.307

Tolerated

NOTCH1

c.6788G > A

NM_017617.5

Likely benign

missense_variant

p.R2263Q

VUS

 

2

0.351

Tolerated

0.011

B

15.29

Deleterious

PALB2

c.2474G > C

NM_024675.4

Likely benign

missense_variant

p.R825T

VUS

 

2

0.043

Tolerated

0.026

B

6.958

Tolerated

PRF1

c.65del

NM_005041.5

Likely Pathogenic

inframe_deletion

p.P22Rfs*29

Likely pathogenic

 

2

-

-

23.4

Deleterious

  1. D: probably damaging; P: possibly damaging; B: benign; VUS: variants of Uncertain significance
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Orphanet Journal of Rare Diseases

ISSN: 1750-1172