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 sequencea | Effect | SNP Linkb | Classificationc |
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.