Table 3.
Pathogenic BRCA1/BRCA2 variants found in breast/ovarian cancer patients (n = 200).
| Variant | Case Freq /Zygosity | Type of cancer | Mutation Database | dbSNP ID | Protein Prediction | MAFgnomAD (%) | Reference | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Exon /Intron | HGVS cDNA | HGVS aa | Variant Effect | ClinVar | BIC | HGMD(Accession #) | SIFT | PolyPhen-2 | Mutation Taster | CONDEL | |||||
| BRCA1: pathogenic variants | |||||||||||||||
| E18 | c.5186C>A | p.Ala1729Glu | Missense | 1 (0.5%) Het | Breast | Pathogenic | CI |
DM CM950153 |
rs28897696 | Deleterious | Probably damaging | Disease causing | Deleterious | 0.0004 | 21 |
| E18 | c.5158C>T | p.Arg1720Trp | Missense | 1 (0.5%) Het | Breast | Pathogenic | CI |
DM |
rs55770810 | Deleterious | Probably damaging | Disease causing | Deleterious | 0.002 | 21 |
| E10 | c.4065_4068delTCAA | p.Asn1355Lysfs*10 | Frameshift | 2 (1%) Het | Breast | Pathogenic | CI |
DM CD941619 |
rs80357508 | – | – | – | – | 0.0008 | 22 |
| E10 | c.1224delA | p.Val409* | Nonsense | 1 (0.5%) Het | Ovarian | Pathogenic | N/A |
DM CD159317 |
rs879255320 | – | – | – | – | N/A | 23 |
| E19 | c.5224C>T | p.Gln1742* | Nonsense | 1 (0.5%) Het | Ovarian | Pathogenic | N/A |
DM CM1211123 |
N/A | – | – | – | – | N/A | 24 |
| E3 | c.121C>T | p.His41Tyr | Missense | 2 (1%)Het | Breast | N/A | N/A |
DM CM1712699 |
N/A | Deleterious | Probably damaging | Disease causing | Deleterious | N/A | 25 |
| BRCA2: pathogenic variants | |||||||||||||||
| E10 | c.2254_2257delGACT | p.Asp752Phefs*19 | Frameshift | 2 (1%) Het | Breast | Pathogenic | CI | DM CD023496 | rs80359326 | – | – | – | – | N/A | 28 |
| E11 | c.5042_5043delTG | p.Val1681Glufs*7 | Frameshift | 1 (0.5%) Het | Breast | Pathogenic | CI |
DM CD082063 |
rs80359478 | – | – | – | – | N/A | 30 |
| E11 | c.5351dupA | p.Asn1784Lysfs*3 | Frameshift | 1 (0.5%) Het | Breast | Pathogenic | CI |
DM |
rs80359508 | – | – | – | – | N/A | 23 |
| E11 | c.6634_6637delTGTT | p.Cys2212Leufs*16 | Frameshift | 2 (1%) Het | Breast | Pathogenic | N/A |
DM CD077812 |
rs397507871 | – | – | – | – | N/A | 24 |
| E11 | c.6224_6225delAA | p.Lys2075Serfs*2 | Frameshift | 1 (0.5%) Het | Ovarian | N/A | N/A | N/A | N/A | – | – | – | – | N/A | Novel |
| E21 | c.8696A>G | p.Gln2899Arg | Missense | 1 (0.5%) Het | Breast | N/A | N/A | N/A | N/A | Deleterious | Probably damaging | Disease causing | Deleterious | N/A | Novel |
BIC Breast Cancer Information Core, HGMD Human Gene Mutation Database, MAF Minor allele frequency, E Exon, Het Heterozygous, Hom Homozygous, CI Clinically Important, DM Disease causing mutation, N/A Not available.