Table 2.
Mutations in invasive micropapillary carcinomas
| 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 |
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.