Mutation analysis and characterization of ATR sequence variants in breast cancer cases from high-risk French Canadian breast/ovarian cancer families

Durocher, Francine; Labrie, Yvan; Soucy, Penny; Sinilnikova, Olga; Labuda, Damian; Bessette, Paul; Chiquette, Jocelyne; Laframboise, Rachel; Lépine, Jean; Lespérance, Bernard; Ouellette, Geneviève; Pichette, Roxane; Plante, Marie; Tavtigian, Sean V; Simard, Jacques

doi:10.1186/1471-2407-6-230

Table 1 Observed coding and intronic sequence variants and genotype frequencies in familial breast cancer cases

From: Mutation analysis and characterization of ATR sequence variants in breast cancer cases from high-risk French Canadian breast/ovarian cancer families

SNP Designation					Genotype Frequency
SNP	SNP ID¹	dbSNP ID	Amino acid change	Location	Common homozygote (expected)²	Heterozygote (expected)²	Rare homozygote (expected)²	MAF
1	c.160-179deIT	N/A	-	Intron 1	0.94 (0.91)	0.02 (0.09)	0.04 (0.00)	0.046
2	c.60-51A>T	N/A	-	Intron 1	0.81 (0.82)	0.19 (0.17)	0.00 (0.01)	0.093
3	c. 293-43G>A	N/A	-	Intron 3	0.94 (0.90)	0.02 (0.10)	0.04 (0.00)	0.049
4	c. 293-19C>T	N/A	-	Intron 3	0.94 (0.94)	0.06 (0.06)	0.00 (0.00)	0.029
5*	c.632C>T	rs2227928	Thr211Met	Exon 4	0.42 (0.38)	0.38 (0.47)	0.19 (0.15)	0.385
6	c. 946G>A	rs28897764	Va131611e	Exon 4	0.94 (0.90)	0.02 (0.10)	0.04 (0.00)	0.047
7	c. 1326A>G	rs28897765	Lys442Lys	Exon 5	0.94 (0.91)	0.02 (0.09)	0.04 (0.00)	0.046
8	c. 1488C>T	N/A	Val496Val	Exon 6	0.98 (0.98)	0.02 (0.02)	0.00 (0.00)	0.010
9	c. 1732+I66A>G	N/A	-	Intron 7	0.98 (0.98)	0.02 (0.02)	0.00 (0.00)	0.009
10	c. 1732+279A>G	N/A	-	Intorn 7	0.94 (0.94)	0.06 (0.06)	0.00 (0.00)	0.028
11	c. 1776A>T	rs2227930	Gly592Gly	Exon 8	0.40 (0.34)	0.38 (0.49)	0.23 (0.17)	0.415
12	c. 1815T>C	rs2227929	Asp605Asp	Exon 8	0.40 (0.35)	0.40 (0.48)	0.21 (0.17)	0.406
13	c. 1950G>A	rs28910270	Glu650Glu	Exon 9	0.94 (0.91)	0.02 (0.09)	0.04 (0.00)	0.047
14	c.2290A>G	N/A	Lys764Glu	Exon 10	0.98 (0.98)	0.02 (0.10)	0.00 (0.00)	0.010
15	c. 2634-74T>C	rs9869842	-	Inton 12	0.39 (0.34)	0.39 (0.49)	0.22 (0.17)	0.417
16	c. 2875G>A	rs28910271	Val959Met	Exon 14	0.94 (0.90)	0.02 (0.10)	0.04 (0.00)	0.052
17	c. 2977-97T>C	N/A	-	Intron 14	0.94 (0.91)	0.02 (0.09)	0.04 (0.00)	0.048
18	c. 3120G>A	rs28910272	Leu1040Leu	Exon 15	0.94 (0.91)	0.02 (0.09)	0.04 (0.00)	0.048
19	c.3172-26T>A	N/A	-	Intron 15	0.94 (0.91)	0.02 10.09)	0.04 (0.00)	0.046
20	c.3357+128G>A	rs13091637	-	Intron 16	0.50 (0.51)	0.43 (0.41)	0.07 (0.08)	0.287
21	c. 3725+51T>G	N/A	-	Intron 19	0.98 (0.98)	0.02 (0.02)	0.00 (0.00)	0.009
22	c. 3726-47A>G	N/A	-	Intron 19	0.76 (0.74)	0.20 (0.24)	0.04 (0.02)	0.139
23	c.3945+171C>T	N/A	-	Intron 21	0.96 (0.93)	0.00 (0.07)	0.04 (0.00)	0.038
24	c. 3946-48C>A	N/A	-	Intron 21	0.94 (0.91)	0.02 (0.09)	0.04 (0.00)	0.046
25	c. 4383-232T>G	rs9855919	-	Intron 24	0.43 (0.38)	0.36 (0.47)	0.21 (0.15)	0.387
26	c.4383-177C>T	rs10804682	-	Intron 24	0.72 (0.74)	0.28 (0.24)	0.00 (0.02)	0.139
27	c. 5208T>C	rs2227931	Tyr1736Tyr	Exon 30	0.38 (0.32)	0.37 (0.49)	0.25 (0.19)	0.441
28	c. 5288+130G>A	rs11916455	-	Intron 30	0.44 (0.26)	0.31 (0.48)	0.25 (0.16)	0.403
29	c. 5380+121C>A	rs11927681	-	Intron 31	0.87 (0.87)	0.13 (0.13)	0.00 (0.00)	0.065
30	c. 5460T>C	rs2227932	Tyr1820Tyr	Exon 32	0.79 (0.78)	0.19 (0.21)	0.02 (0.01)	0.115
31	c. 5558+119C>T	N/A	-	Intron 32	0.96 (0.92)	0.00 (0.08)	0.04 (0.00)	0.038
32	c. 5739-4dc19+T	N/A	-	Intron 33	0.94 (0.91)	0.02 (0.09)	0.04 (0.00)	0.046
33	c.5868C>T	N/A	Tyr1956Tyr	Exon 34	0.96 (0.93)	0.00 (0.07)	0.04 (0.00)	0.038
34	c. 6394T>G	rs28910273	Tyr2132Asp	Exon 38	0.98 (0.98)	0.02 (0.02)	0.00 (0.00)	0.009
35	c. 6553-45C>G	N/A	-	Intron 38	0.98 (0.98)	0.02 (0.02)	0.00 (0.00)	0.010
36	c. 6897+88A>G	N/A	-	Intron 40	0 98 (0 98)	0.02 (0.02)	0.00 (0.00)	0.009
37	c. 7041+8G>A	N/A	-	Intron 41	0.98 (0.98)	0.02 (0.02)	0.00 (0.00)	0.009
38	c. 7041+55T>A	N/A	-	Intron 41	0.98 (0.98)	0.02 (0.02)	0.00 (0.00)	0.009
39	c. 7274G>A	rs2229032	Arg2425Gln	Exon 43	0.75 (0.73)	0.02 (0.25)	0.04 (0.02)	0.147
40	c. 7875A>G	rs1802904	Gln2625Gln	Exon 47	0.80 (0.77)	0.16 (0.22)	0.04 (0.01)	0.120
41	c. 7932+104T>C	rs10935463	-	Intron 47	0.39 (0.33)	0.37 (0.49)	0.24 (0.18)	0.422

¹According to the nomenclature of the Human Genome Variation Society
²As expected under Hardy-Weinberg equilibrium
N/A: Information not available for this SNP (not reported in dbSNP)
T allele is considered as the common allele according to the reference sequence NM_001184
MAF : Minor Allele Frequency

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