Table 2 Rare protein truncating variants in the BROCA gene set
Gene | dbSNP ID | Variant type | Ref | Alt | Protein change | ClinVar | ExAC MAF (EUR) | CADD | Phenotype category |
|---|---|---|---|---|---|---|---|---|---|
ATM | Frameshift deletion | A | – | p.K828fs | – | – | 31 | Non-aggressive | |
ATM | rs587779834 | Frameshift deletion | G | – | p.V1268fs | 5 | 4.5×10−5 | 28.3 | Metastatic |
ATM | rs786204751 | Nonsense | C | T | p.Q1839* | 4 | – | 46 | Metastatic |
ATM | rs770641163 | Nonsense | C | T | p.R2993* | 5|4 | 3.0×10−5 | 47 | Metastatic |
ATR | Nonsense | A | T | p.Y1527* | – | – | 42 | Metastatic | |
BRCA2 | rs41293477 | Nonsense | T | G | p.L1053* | 5 | – | 29.2 | Non-aggressive |
BRCA2 | rs80359454 | Frameshift deletion | GAAA | – | p.E1493fs | 5 | – | 29.6 | Metastatic |
BRCA2 | rs80359470 | Frameshift deletion | AA | – | p.N1626fs | 5 | – | 25.5 | Metastatic |
BRCA2 | rs11571658 | Frameshift deletion | TT | – | p.L2092fs | 5 | 1.5×10−5 | 24.6 | Metastatic |
BRCA2 | rs80359752 | Frameshift insertion | – | A | p.T3085fs | 5 | – | 36 | Metastatic |
CHEK2 | rs587781269 | Nonsense | G | A | p.R95* | 5 | 0 | 38 | Non-aggressive |
NBN | rs587780100 | Frameshift deletion | TGTT | – | p.K233fs | 5 | 4.7×10−5 | 35 | Metastatic |
NBN | rs587776650 | Frameshift deletion | TTTGT | – | p.K219fs | 5 | 3.2×10−5 | 35 | Metastatic |
NBN | Frameshift deletion | C | – | p.R89fs | – | – | 8.3 | Metastatic | |
NBN | rs587781891 | Frameshift deletion | G | – | p.I41fs | 5 | – | 28.3 | Metastatic |
PALB2 | rs180177110 | Nonsense | G | A | p.R753* | 5 | 4.5×10−5 | 35 | Metastatic |
PMS2 | Nonsense | G | A | p.Q244* | – | – | 40 | Metastatic | |
PRSS1 | rs766199324 | Frameshift deletion | C | – | p.P164fs | – | 1.5×10−5 | 26 | Metastatic |
RAD51D | rs786202750 | Frameshift deletion | A | – | p.T188fs | 5 | – | 27 | Metastatic |
SLX4 | Frameshift deletion | C | – | p.A1653fs | – | – | 20.5 | Non-aggressive | |
SLX4 | rs767631456 | Frameshift deletion | CT | – | p.S936fs | – | 4.5×10−5 | 24 | Metastatic |
XRCC2 | rs776336749 | Frameshift deletion | T | – | p.H268fs | 3 | 0 | 28.3 | Metastatic |
