Table 3.
Putative predispositions in familial breast cancer families and probands
| |
Gene |
Description |
Position |
Nucleotide |
Amino acid |
Type |
PolyPhen2* |
Cancer-affected member |
Frequency |
|||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Score prediction | ||||||||||||||||
| Family 1 |
|
|
|
|
|
|
|
|
1 |
2 |
3 |
4 |
6 |
7 |
8 |
|
| |
GPRIN1 |
G protein regulated inducer of neurite outgrowth 1 |
chr5:176026123 |
c.T713C |
p.L238S |
Exonic |
0.91 |
D |
- |
+ |
+ |
+ |
+ |
+ |
- |
5 |
| |
PINK1 |
PTEN induced putative kinase 1 |
chr1:20972051 |
c.960-2A > G |
|
Splicing |
NA |
NA |
- |
- |
+ |
+ |
- |
- |
- |
2 |
| |
POLK |
Polymerase (DNA directed) kappa |
chr5:74892737 |
c.A2219G |
p.H740R |
Exonic |
0.62 |
P |
- |
- |
- |
+ |
- |
- |
- |
1 |
| Family 2 |
|
|
|
|
|
|
|
|
1 |
2 |
3 |
4 |
5 |
6 |
|
|
| |
KAT6B |
K(lysine) acetyltransferase 6B |
chr10:76789128 |
c.G4546T |
p.D1516Y |
Exonic |
0.95 |
D |
- |
+ |
+ |
+ |
+ |
+ |
|
5 |
| |
KAT6B |
K(lysine) acetyltransferase 6B |
chr10:76789311 |
c.C4729T |
p.R1577C |
Exonic |
0.96 |
D |
- |
+ |
+ |
+ |
+ |
+ |
|
5 |
| |
NOTCH2 |
Notch 2 |
chr1:120459167 |
c.C6178T |
p.R2060C |
Exonic |
0.99 |
D |
- |
- |
+ |
- |
- |
+ |
|
2 |
| Family 3 |
|
|
|
|
|
|
|
|
1 |
2 |
4 |
5 |
6 |
|
|
|
| |
NANP |
N-acetylneuraminic acid phosphatase |
chr20:25596725 |
c.A583G |
p.I195V |
Exonic |
0.98 |
D |
+ |
- |
+ |
- |
- |
|
|
2 |
| |
PHKB |
phosphorylase kinase, beta |
chr16:47628126 |
c.1204 + 1G > T |
|
Splicing |
NA |
NA |
- |
+ |
- |
+ |
- |
|
|
2 |
| Proband |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
JAKMIP3 |
Janus kinase and microtubule interacting protein 3 |
chr10:133955524 |
c.G1574C |
p.G525A |
Exonic |
1.00 |
D |
|
|
|
|
|
|
|
|
| 2 |
POLQ |
Polymerase (DNA directed), theta |
chr3:121207798 |
c.A3980C |
p.Q1327P |
Exonic |
1.00 |
D |
|
|
|
|
|
|
|
|
| 3 |
DUX2 |
Double homeobox 2 |
chr10:135494906 |
|
|
Splicing |
NA |
NA |
|
|
|
|
|
|
|
|
| 4 |
UBE2L3 |
Ubiquitin-conjugating enzyme E2L 3 |
chr22:21975938 |
c.G349A |
p.E117K |
Exonic |
0.96 |
D |
. |
. |
|
|
|
|
|
|
| 5 |
RAD23B |
RAD23 homolog B (S. cerevisiae) |
chr9:110087260 |
c.C1028T |
p.P343L |
Exonic |
0.99 |
D |
. |
. |
|
|
|
|
|
|
| 7 |
GATA3 |
GATA binding protein 3 |
chr10:8100630 |
c.C604T |
p.R202C |
Exonic |
0.92 |
D |
|
|
|
|
|
|
|
|
| 8 |
KAT6B |
K(lysine) acetyltransferase 6B |
chr10:76744854 |
c.G2390A |
p.S797N |
Exonic |
0.98 |
D |
|
|
|
|
|
|
|
|
| 9 |
LIG1 |
Ligase I, DNA, ATP-dependent |
chr19:48637322 |
c.G1525A |
p.E509K |
Exonic |
0.95 |
D |
. |
. |
|
|
|
|
|
|
| 10 |
LIG4 |
Ligase IV, DNA, ATP-dependent |
chr13:108862463 |
c.G1154A |
p.R385K |
Exonic |
1.00 |
D |
|
|
|
|
|
|
|
|
| 14 |
NOTCH2 |
Notch 2 |
chr1:120529603 |
c.G854A |
p.R285H |
Exonic |
1.00 |
D |
|
|
|
|
|
|
|
|
| 15 |
ABL1 |
c-abl oncogene 1, non-receptor tyrosine kinase |
chr9:133729493 |
c.G122A |
p.G41D |
Exonic |
0.92 |
D |
|
|
|
|
|
|
|
|
| 16 |
TNK2 |
Tyrosine kinase, non-receptor, 2 |
chr3:195596385 |
c.C1760T |
p.P587L |
Exonic |
1.00 |
D |
|
|
|
|
|
|
|
|
| 17 |
NFRKB |
Nuclear factor related to kappaB binding protein |
chr11:129755398 |
c.G611A |
p.R204H |
Exonic |
1.00 |
D |
|
|
|
|
|
|
|
|
| 18 |
NFKBIZ |
Nuclear factor of kappa light polypeptide gene enhancer |
chr3:101576029 |
|
|
Splicing |
NA |
NA |
|
|
|
|
|
|
|
|
| 19 |
SMG1 |
SMG1 phosphatidylinositol 3-kinase-related kinase |
chr16:18879624 |
c.C3083T |
p.T1028M |
Exonic |
0.99 |
D |
|
|
|
|
|
|
|
|
| 20 |
PRKCQ |
Protein kinase C, theta |
chr10:6528042 |
c.G855C |
p.Q285H |
Exonic |
1.00 |
D |
|
|
|
|
|
|
|
|
| 21 |
ADRA2A |
Adrenoceptor alpha 2A |
chr10:112838117 |
c.C363G |
p.C121W |
Exonic |
1.00 |
D |
|
|
|
|
|
|
|
|
| 22 | PPFIA4 | Protein tyrosine phosphatase, receptor type | chr1:203025582 | c.C668T | p.T223M | Exonic | 0.92 | D | ||||||||
D: Probably damaging (score: 0.909-1); P: Possibly damaging (score: 0.447 - 0.908).