Constitutional CHEK2mutations are infrequent in early-onset and familial breast/ovarian cancer patients from Pakistan

Table 2 CHEK2 germ line mutations and nucleotide changes in non- BRCA1/2 -associated early-onset and familial breast/ovarian cancer patients from Pakistan

Location	Coding (c.) DNA sequence^a	Effect	SNP Link^b	Classification^c	Prevalence
					Group 1	Group 2
					Cases (n = 145) n (%)	Cases (n = 229) n (%)	Controls (n = 150) n (%)
Exon 1	c.252A>G (E84E)	Silent	rs1805129	P	13 (8.9)	18 (7.9)	12 (8.0)
Exon 1	c.275C>G (P92R)	Missense	-	M	1 (0.7)	0 (0)	0 (0)
Exon 10	c.1216C>T (R406C)	Missense	-	M	1 (0.7)	0 (0)	0 (0)
Exon 13	c.1501G>A (E501K)	Missense	rs17883172	P	3 (2.1)	1 (0.4)	0 (0)
Intron 1	c.319 +43_319 +44insA	Intronic	rs17879991	P	64 (44.1)	-	47 (31.3)
Intron 3	c.592 +50A>T	Intronic	rs17881298	P	1 (0.7)	-	0 (0)
Intron 4	c.683 +119_683 +122delATTT	Intronic	-	P	2 (1.4)	-	1 (0.7)
Intron 4	c.684 -78_-100dup23	Intronic	-	P	16 (11.0)	-	20 (13.3)
Intron 7	c.908 +48dupA	Intronic	-	VUS	1 (0.7)	-	0 (0)
Intron 13	c.1542 +92dupA	Intronic	-	VUS	1 (0.7)	-	0 (0)

Novel germ line mutations and nucleotide changes are marked in bold.
P, polymorphism; M, mutation; VUS, variant of unknown significance.
^aNomenclature follows Human Genome Variation Society (HGVS) (http://www.hgvs.org). Numbering starts at the first A of the first coding ATG (located in exon 2) of NCBI GenBank Accession NM_007194.
^bLink to NCBI SNP database (http://ncbi.nlm.nih.gov/projects/SNP/).
^cClassification of missense mutations is based on in silico analyses.