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Table 2 Mutations in invasive micropapillary carcinomas

From: Polarity gene alterations in pure invasive micropapillary carcinomas of the breast

Gene

Cases,n

(%)

Chr

Mutation

WH seq

MiSeq

Sanger seq

Effect of the mutation

Type of mutation

PolyPhen-2 score

GERP score

RNA-seq expression

TP53

5

(10)

17

GAA>CAA/p.E286Q

X

NA

X

Missense

Transversion

1.00

 

Yes

    

ATG>ACG/p.M246T

X

NA

X

Missense

Transition

1.00

 

Yes

    

GAG>AAG/p.E68K

NA

NA

X

Missense

Transition

0.09

 

ND

    

TAC>TGC/p.Y234C

NA

NA

X

Missense

Transition

0.97

 

ND

    

c.742_743insA

NA

NA

X

Frame shift

Ins/del

 

5.91

ND

DNAH9

4

(8)

17

A>G

X

X

X

Splice intron

Transition

 

4.05

No coverage

    

CGG>CAG/p.R2605Q

X

X

X

Missense

Transition

1.00

 

No coverage

    

ATG>ATA/p.M3430I

NA

X

X

Missense

Transition

0.00

 

ND

    

CAG>TAG/p.Q3082*

NA

X

X

Nonsense

Transition

 

4.05

ND

FBXO38

2

(4)

5

TAT>TGT/p.Y1058C

X

X

X

Missense

Transition

1.00

 

Yes

    

GAA>CAA/p.E20Q

NA

X

X

Missense

Transversion

0.96

 

ND

THSD4

2

(4)

15

GAG>AAG/p.E476K

X

X

X

Missense

Transition

1.00

 

Yes

    

GAG>AAG/p.E652K

NA

X

X

Missense

Transition

0.96

 

ND

TRMT5

2

(4)

14

TTT>CTT/p.F303L

X

X

X

Missense

Transition

0.04

 

Yes

    

GAG>CAG/p.E152Q

NA

X

X

Missense

Transversion

0.03

 

ND

PIK3CA

2

(4)

3

CTC>GTC/p.L540V

NA

NA

X

Missense

Transversion

0.99

 

ND

    

CAG>CCG/p.Q546P

NA

NA

X

Missense

Transversion

1.00

 

ND

FOXO3

1

(2)

6

GCA>ACA/p.A267T

NA

NA

X

Missense

Transition

0.97

 

ND

    

CCT>TCT/p.P292S

NA

NA

X

Missense

Transition

0.34

 

ND

    

TTG>GTG/p.L528V

NA

NA

X

Missense

Transversion

0.03

 

ND

BBS12

1

(2)

4

CGC>TGC/p.R674C

X

X

X

Missense

Transition

1.00

 

Yes

BBS9

1

(2)

7

CCA>TCA/p.P77S

X

X

X

Missense

Transition

1.00

 

No coverage

CASP8AP2

1

(2)

6

GAT>AAT/p.D1420N

X

X

X

Missense

Transition

1.00

 

No coverage

EIF2B5

1

(2)

3

GCA>ACA/p.A406T

X

*

X

Missense

Transition

0.05

 

Yes

FMN2

1

(2)

1

GCT>CCT/p.A659P

X

*

*

Missense

Transversion

0.74

 

No coverage

HSP90B1

1

(2)

12

ACG>ATG/p.T468M

X

 

X

Missense

Transition

0.98

 

Yes

IKBKE

1

(2)

1

GAC>TAC/p.D571Y

X

*

X

Missense

Transversion

0.68

 

Yes

PCF11

1

(2)

11

AAT>AGT/p.N167S

X

X

X

Missense

Transition

0.02

 

Yes

PLCL1

1

(2)

2

AAG>AAT/p.K279N

X

X

X

Missense

Transversion

0.98

 

No coverage

PTPN21

1

(2)

14

CGA>CTA/p.R864L

X

X

X

Missense

Transversion

1.00

 

Yes

SEC63

1

(2)

6

CGC>TGC/p.R217C

NA

X

X

Missense

Transition

1.00

 

ND

SPTLC3

1

(2)

20

G>A

X

X

X

Splice intron

Transition

 

5.91

No coverage

ST7L

1

(2)

1

GAT>GCT/p.D339A

X

X

X

Missense

Transversion

1.00

 

Yes

SYNRG

1

(2)

17

ATG>ATA/pM970I

X

*

X

Missense

Transition

0.45

 

Yes

UBR4

1

(2)

1

AAC>AAA/p.N3400K

X

X

X

Missense

Transversion

0.98

 

Yes

ZFYVE26

1

(2)

14

CAA>CCA/p.Q1582P

X

X

X

Missense

Transversion

0.00

 

Yes

  1. a%, Percentage of mutated cases out of the sequenced cases; *Assessed but not identified with the technique; Chr, Chromosome; GERP, Genomic Evolutionary Rate Profiling; IMPC, Invasive micropapillary carcinoma; NA, Not assessed with this technique; ND, Not determined (that is, no RNA sequence available for that sample); No coverage, Absence of aligned reads at the corresponding genomic position; WH seq, Whole-exome sequencing; X, Assessed and identified with the technique; Yes, Mutated allele is expressed.