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Table 1 Characteristics of patients with pathogenic or likely pathogenic variants

From: Variants of cancer susceptibility genes in Korean BRCA1/2 mutation-negative patients with high risk for hereditary breast cancer

Case number Site/histology of breast cancer Breast cancer subtype Breast cancer stage (AJCC 7th ed) Concomitant cancers Affected gene Nucleotide change Amino acid change dbSNP Variant effect Family cancer history (family member, age) MAF by ExAC (n = 60,704) MAF by ExAC Asian (n = 12,583) MAF by KRGDB(n = 622) Confirmation method Pathogenicity Reference
1 L/IDC ER+/PR+/HER2- IIA TP53 exon2–9 deletion N/A Large deletion Breast ca (mother, 32) N/A N/A N/A MLPA Pathogenic  
2 B/IDC ER+/PR+/HER2- IIA PALB2 c.3267_3268delGT p.Phe1090SerfsTer6 rs587781890 Frameshift Breast ca (aunt, 47),
Colon ca (GF, 60),
Stomach ca (GM, 60)
** ** ** Sanger sequencing Likely pathogenic  
3 R/IDC ER+/PR+/HER2- IIB AoV PALB2 c.2257C > T p.Arg753Ter rs180177110 Nonsense Breast ca (sister, 53) 3.29 × 10−5 ** ** Sanger sequencing Pathogenic  
4* L/poorly differentiated TNBC IA Stomach PALB2 c.695delG p.Gly232ValfsTer6 Frameshift Stomach ca (GF, 90),
Liver ca (uncle, 60)
** ** ** Sanger sequencing Likely pathogenic  
4* L/poorly differentiated TNBC IA Stomach MRE11A c.1773_1774delAA p.Gly593LysfsTer4 Frameshift Stomach ca (GF, 90),
Liver ca (uncle, 60)
** ** ** Sanger sequencing Likely pathogenic  
5† L/mucinous TNBC IA BARD1 c.1345C > T p.Gln449Ter Nonsense Breast ca (sister1, 67; sister2, 47) ** ** ** Sanger sequencing Likely pathogenic  
6† L/IDC ER+/PR-/HER2- IIA BARD1 c.1345C > T p.Gln449Ter Nonsense Breast ca (sister1, 67; sister2, 58) ** ** ** Sanger sequencing Likely pathogenic  
7 L/IDC ER-/PR-/HER2+ IA BRIP1 exon5–6 deletion N/A Largedeletion Ovarian ca (mother, 35) N/A N/A N/A MLPA Pathogenic  
8 R/IDC ER-/PR-/HER2+ IA Cervix uteri BRIP1 c.1066C > T p.Arg356Ter rs730881633 Nonsense Breast ca (sister, 40) ** ** ** Sanger sequencing Likely pathogenic  
9 B/IDC ER-/PR-/HER2+ IIA TP53 c.733G > A p.Gly245Ser rs28934575 Missense Stomach ca (father, 56); Pancreatic ca (father, 73) 8.24 × 10−6 ** ** Sanger sequencing Likely pathogenic (Table S2) [23]
  1. Abbreviation: AJCC, American Joint Committee on Cancer; AoV, ampulla of Vater; B: bilateral; ca: cancer; dbSNP, single nucleotide polymorphism database; DCIS, ductal carcinoma in situ; ER, estrogen receptor; ExAC, Exome Aggregation Consortium; HER2, human epidermal growth factor receptor 2; IDC, invasive ductal carcinoma; KRGDB, Korean Reference Genome database; L, left; N/A, not assessable; MAF, minor allele frequency; MLPA, multiplex ligation-dependent probe amplification; Polyphen, Polymorphism Phenotyping-2; PR, progesterone receptor; R, right; SIFT, Sorting Intolerant From Tolerant; TNBC, triple negative breast cancer
  2. *Case 4 had pathogenic variants in PALB2 and MRE11A. Case 5 and Case 6 are siblings. **There was no case with the relevant variant in the databases with respect to the general population