Table 2 Genetic variants only identified in Trastuzumab-resistant group

No. 1

chr17:7577559

SNV

TP53

NM_000546.6

Missense

6

p.Ser241Phe

c.722C > T

Likely pathogenic

rs28934573

chr17:7578214

SNV

TP53

NM_000546.6

Synonymous

5

p.Thr211 = 

c.633T > G

Likely benign

rs976434163

chr17:7577035

INDEL

TP53

NM_000546.6

Frameshift

7

p.Gly302ArgfsTer4

c.902_903insC

Pathogenic

rs876660726

chr17:7578523

SNV

TP53

NM_000546.6

Missense

4

p.Gln136Arg

c.407A > G

–

rs1567554216

chr11:108205810

SNV

ATM

NM_000051.4

Missense

54

p.Gly2709Ser

c.8125G > A

Uncertain significance

rs3218680

chr11:108205781

SNV

ATM

NM_000051.4

Missense

54

p.Pro2699Leu

c.8096C > T

Uncertain significance

rs879254209

chr11:108236213

SNV

ATM

NM_000051.4

Missense

62

p.Pro3050Leu

c.9149C > T

Uncertain significance

rs778267979

chr11:108170511

SNV

ATM

NM_000051.4

Missense

33

p.Lys1692Asn

c.5076A > C

Uncertain significance

rs767841041

chr16:68835663

SNV

CDH1

NM_004360.5

Missense

3

p.Val85Ala

c.254T > C

Uncertain significance

rs878854688

No. 2

chr17:7577559

SNV

TP53

NM_000546.6

Missense

6

p.Ser241Phe

c.722C > T

Likely pathogenic

rs28934573

chr17:7578555

Duplication

TP53

NM_000546.6

Splice acceptor

-

p.?

c.376-2dup

Conflicting Interpretation

rs751253294

chr13:48955550

SNV

RB1

NM_000321.3

Nonsense

17

p.Arg556Ter

c.1666C > 

Pathogenic

rs121913304

No. 3

chr20:57484421

SNV

GNAS

NM_000516.7

Missense

8

p.Arg201His

c.602G > A

Pathogenic

rs121913495

chr13:48955550

SNV

RB1

NM_000321.3

Nonsense

17

p.Arg556Ter

c.1666C > T

Pathogenic

rs121913304

chr3:10188263

Delet-ion

VHL

NM_000551.4

Frameshift

2

p.Phe136fs

c.408del

Pathogenic

rs397516442

chr3:37067240

SNV

MLH1

NM_000249.4

Missense

12

p.Val384Asp

c.1151T > A

Benign

rs63750447

No. 4

chr17:7577124

SNV

TP53

NM_000546.6

Missense

7

p.Val272Met

c.814G > A

Pathogenic

rs121912657

chr17:7577128

SNV

TP53

NM_000546.6

Missense

7

p.Phe270Leu

c.810 T > G

Likely Pathogenic

rs1057519987

No. 5

chr7:128850341

SNV

SMO

NM_005631.5

Missense

9

p.Trp535Leu

c.1604G > T

Pathogenic

rs121918347

chr11:108180945

SNV

ATM

NM_000051.4

Missense

38

p.Val1941Leu

c.5821G > C

Conflicting interpretation

rs147187700

No. 6

chr17:7578547

SNV

TP53

NM_000546.6

Missense

4

p.Pro128Leu

c.383C > T

Uncertain Significance

rs1597371657

chr17:7578553

SNV

TP53

NM_000546.6

Missense

4

p.Tyr126Cys

c.377A > G

Uncertain Significance

rs1555526335

chr17:7578555

Duplication

TP53

NM_000546.6

Splice acceptor

-

p.?

c.376-2dup

Conflicting Interpretation

rs751253294

No. 7

chr13:49039164

SNV

RB1

NM_000321.3

Nonsense

22

p.Glu748Ter

c.2242G > T

Pathogenic

rs121913297

chr11:108180945

SNV

ATM

NM_000051.4

Missense

38

p.Val1941Leu

c.5821G > C

Conflicting interpretation

rs147187700

No. 8

chr17:7573996

SNV

TP53

NM_000546.6

Missense

9

p.Leu344Pro

c.1031T > C

Likely Pathogenic

rs121912662

chr17:7574017

SNV

TP53

NM_000546.6

Missense

9

p.Arg337Pro

c.1010G > C

Likely Pathogenic

rs121912664

chr17:7574012

SNV

TP53

NM_000546.6

Missense

9

p.Glu339Gln

c.1015G > C

Likely Benign

rs17882252

chr17:7573931

SNV

TP53

NM_000546.6

Missense

9

p.Ser366Ala

c.1096 T > G

Likely Benign

rs17881470

No.9

chr17:7577521

SNV

TP53

NM_000546.6

Missense

6

p.Ile254Val

c.760A > G

Likely benign

rs746601313

chr17:7577515

INDEL

TP53

NM_000546.6

Indel

6

p.Ile255del

c.761TCA[1]

Likely Pathogenic

rs1064794309

chr17:7577522

dele-tion

TP53

NM_000546.6

Frameshift

6

p.Ile254fs

c.759del

Pathogenic

rs1567549129

chr22:24133967

SNV

SMARCB1

NM_003073.5

Nonsense

2

p.Arg40Ter

c.118C > T

Pathogenic

rs1060503015