Table 1 Characteristics of patients with pathogenic or likely pathogenic variants
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] |