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

From: Constitutional CHEK2mutations are infrequent in 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)
  1. Novel germ line mutations and nucleotide changes are marked in bold.
  2. P, polymorphism; M, mutation; VUS, variant of unknown significance.
  3. 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.
  4. bLink to NCBI SNP database (http://ncbi.nlm.nih.gov/projects/SNP/).
  5. cClassification of missense mutations is based on in silico analyses.