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Table 3 Putative predispositions in familial breast cancer families and probands

From: Family-specific, novel, deleterious germline variants provide a rich resource to identify genetic predispositions for BRCAx familial breast cancer

  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         
  1. D: Probably damaging (score: 0.909-1); P: Possibly damaging (score: 0.447 - 0.908).