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Table 2 Identified non-synonymous and novel sequence alterations

From: Screening for BRCA1, BRCA2, CHEK2, PALB2, BRIP1, RAD50, and CDH1 mutations in high-risk Finnish BRCA1/2-founder mutation-negative breast and/or ovarian cancer individuals

   

Carrier frequency

   

Gene/Nucleotide changea

Effect on protein

rs Numberb

Individuals

Controls

P-values

OR; 95%CI

Status

BRCA1

       

4837A > G

Ser1613Gly

rs1799966

0.634 (52/82)g

na

-

-

Reportedc, d

4883T > C

Met1628Thr

rs4986854

0.049 (4/82)

0.016 (6/367)

0.090

3.09; 0.85-11.19

Reportedc, d

5095C > T

Arg1699Trp

rs55770810

0.012 (1/82)

na

-

-

Reportedc, d

BRCA2

       

68-80insTf

-

-

0.012 (1/82)

na

-

-

Novel

72A > T

Leu24Phe

-

0.012 (1/82)

0 (0/380)

0.177

na

Novel

793 + 34T > G

-

-

0.012 (1/82)

na

-

-

Novel

8182G > A

Val2728Ile

rs28897749

0.012 (1/82)

0.003 (1/378)

0.325

4.65; 0.29-75.19

Reportedc, d

9976A > T

Lys3326Stop

rs11571833

0.012 (1/82)

0.029 (11/378)

0.702

0.41; 0.05-3.24

Reportedc, d

10234A > G

Ile3412Val

rs1801426

0.012 (1/82)

0.021 (8/379)

1.000

0.57; 0.07-4.64

Reportedc, d

CHEK2

       

444 + 85T > A

-

-

0.012 (1/82)

0.005 (2/364)

0.457

2.23; 0.20-24.94

Novel

470T > C

Ile157Thr

-

0.098 (8/81)

0.055 (21/381)

0.203

1.88; 0.80-4.41

Reportede

792 + 39C > T

-

-

0.012 (1/82)

0.021 (8/375)

1.000

0.57; 0.07-4.60

Novel

1100delCf

Fs, stop at codon 381

-

0.037 (3/82)

0.016 (6/380)

0.203

2.37; 0.58-9.67

Reportede

1290T > C

His430His

-

0.951 (77/81)g

0.974 (372/382)

0.281

0.52; 0.16-1.69

Novel

1314T > C

Asp438Asp

-

0.951 (77/81)g

0.974 (372/382)

0.281

0.52; 0.16-1.69

Novel

1363G > A

Val455Ile

-

0.975 (79/81)g

0.976 (373/382)

1.000

0.95; 0.20-4.50

Novel

PALB2

       

814G > A

Glu272Lys

-

0.012 (1/82)

0 (0/372)

0.181

na

Novel

1000T > G

Tyr334Asp

-

0.012 (1/82)

0.011 (4/380)

1.000

1.16; 0.13-10.52

Novel

1010T > C

Leu337Ser

rs45494092

0.073 (6/82)

na

-

-

Reportedc

1676A > G

Gln559Arg

rs152451

0.122 (10/82)

0.173 (64/371)

0.323

0.67; 0.33-1.36

Reportedc

2205A > G

Pro735Pro

-

0.012 (1/82)

na

-

-

Novel

2794G > A

Val932Met

rs45624036

0.037 (3/82)

na

-

-

Reportedc

2993G > A

Gly998Glu

rs45551636

0.012 (1/82)

0.038 (14/372)

0.491

0.32; 0.04-2.44

Reportedc

BRIP1

       

584T > C

Leu195Pro

rs4988347

0.024 (2/82)

na

-

-

Reportedc

2755C > T

Pro919Ser

rs4986764

0.390 (32/82)g

na

-

-

Reportedc

RAD50

       

1544A > G

Asp515Gly

-

0.012 (1/82)

0.010 (4/384)

1.000

1.17; 0.13-10.63

Novel

2398-32A > G

-

-

0.012 (1/82)

na

-

-

Novel

3475 + 33C > G

-

-

0.012 (1/82)

na

-

-

Novel

  1. CI, confidence interval; Fs, frameshift; na, not analyzed; OR, odds ratio. aThe reference nucleotide sequencies were obtained from the UCSC Genome Browser [44] and the accession numbers were following: BRCA1: [UCSC Genome Browser:NM_007295.2], BRCA2: [UCSC Genome Browser:NM_000059.3], CHEK2: [UCSC Genome Browser:NM_007194.3], PALB2: [UCSC Genome Browser:NM_024675.3], BRIP1: [UCSC Genome Browser:NM_032043.1], RAD50: [UCSC Genome Browser:NM_005732.3], and CDH1: [UCSC Genome Browser:NM_004360.3]. The accession numbers for the protein sequencies obtained from the Swiss-Prot Protein knowledgebase [45] were following: BRCA1: [Swiss-Prot:P38398], BRCA2: [Swiss-Prot:P51587], CHEK2: [Swiss-Prot:O96017], PALB2: [Swiss-Prot:Q86YC2], BRIP1: [Swiss-Prot:Q9BX63], RAD50: [Swiss-Prot:Q92878], and CDH1: [Swiss-Prot:P12830]. bThe RefSNP number, obtained from the NCBI Single Nucleotide Polymorphism database (dbSNP) [46]. cThe NCBI dbSNP [46]. dThe Breast Cancer Information Core database [47]. eReported in the Finnish population by Vahteristo et al. [11]. fHeterozygous deletion or insertion.gDue to the high frequency of the variant observed in analyzed individuals, variant is not presented in Table 3.
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Breast Cancer Research

ISSN: 1465-542X

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