Table 3. Selected variants with scores of amino acid damage from 5 predictors and variant frequency in ExAC, by patient.
| Patient ID | Variant DNA level | Gene | Consequence | Non-neutral scores | Representation in ExAC (European non-Finnish) | |
|---|---|---|---|---|---|---|
| Allele count | Allele number | |||||
| 112940 | 9:32989766 G/A | APTX | NP_001182178.1 p.R56X | 5† | 0 | 66736 |
| 17:41246481 T/C | BRCA1 | NP_009225.1 p.Q356R | 4 | 4198 | 66734 | |
| 4:178274801 T/G | NEIL3 | NP_060718.2 p.F460C | 3 | 10 | 66730 | |
| 117197 | 22:43933284 CCT/C | EFCAB6 | NP_073622.2 p.Q1340Rfs*43 | 5† | 606 | 66684 |
| 2:38301879 T/A | CYP1B1 | NP_000095.2 p.D218V | 5 | 15 | 41314 | |
| 10:89503283 C/T | PAPSS2 | NP_004661.2 p.P454L | 5 | 0 | 66732 | |
| 17:41246481 T/C | BRCA1 | NP_009225.1 p.Q356R | 4 | 4198 | 66734 | |
| 9:135779052 G/A | TSC1 | NP_000359.1 p.H732Y | 4 | 350 | 66706 | |
| 117939 | 1:156212872 T/A | BGLAP | NP_954642.1 p.C74X | 5† | 8 | 66696 |
| 2:58386928 G/GTAAT | FANCL | NP_060532.2 p.T367Nfs*13 | 5† | 232 | 65648 | |
| 5:80109533 T/C | MSH3 | NP_002430.2 p.I929T | 5 | 0 | 66740 | |
| 12:124209215 G > T | ATP6V0A2 | NP_036595.2 p.K103N | 5 | 15 | 66734 | |
| 3:51673972 A/T | RAD54L2 | NP_055921.2 p.I730F | 4 | − | − | |
| 21:16340242 T/C | NRIP1 | NP_003480.2 p.E91G | 4 | − | − | |
| 2:149226489 C/T | MBD5 | NP_060798.2 p.A326V | 3 | − | − | |
| 123136 | 4:1206089 G/A | CTBP1 | NP_001319.1 p.421L | 4 | 28 | 14670 |
| 3:38888684 A/T | SCN11A | NP_054858.2 p.F1626Y | 3 | − | − | |
| 1:63876815 A/G | ALG6 | Splice acceptor (−2) | − | − | − | |
| 1:120056817 T/TGCA | HSD3B1 | NP_000853.1 p.V224_Y225insH | − | 2 | 66708 | |
| 4:153332604 TCTC/T | FBXW7 | NP_361014.1 p.E117del | − | 35 | 66114 | |
| 124604 | 16:23634293 C/T | PALB2 | NP_078951.2 p.G998E | 5 | 1430 | 66736 |
| 16:89815152 G/A | FANCA | NP_000126.2 p.S1088F | 4 | 4798 | 65430 | |
| 15:91326099 C/T | BLM | NP_000048.1 p.P868L | 4 | 4239 | 66162 | |
| 6:49700908 G/A | CRISP3 | NP_006052.1 p.A197V** | 2 | 0 | 66362 | |
| 124853 | 18:3452067 G/A | TGIF1 | NP_733796.2 p.W30X | 5† | 33 | 66002 |
| 4:55955969 C/T | KDR | NP_002244.1 p.A1065T** | 5 | 52 | 66726 | |
| 17:12901781 A/C | ELAC2 | NP_060597.4 p.S490A | 5 | 39 | 66734 | |
| 19:50766628 C/T | MYH14 | NP_001139281.1 p.A882V | 3 | 23 | 27644 | |
| X:110973633 TGAA/T | ALG13 | NP_001093392.1 p.E795del | − | 33 | 41558 | |
| 4:103747794 C/T | UBE2D3 | Splice acceptor (−1) | − | − | − | |
| 125671 | 9:35707745 G/C | TLN1 | NP_006280.3 p.L1539V | 4 | 13 | 66734 |
| 1:145578236 C/T | PIAS3 | NP_006090.2 p.R67W | 3 | 13 | 66740 | |
| 10:5014483 T/A | AKR1C1 | NP_001344.2 p.S221N | 3 | 119 | 66712 | |
| 10:5014484 C/A | AKR1C1 | 119 | 66712 | |||
| 11:47237894 CAGA/C | DDB2 | NP_000098.1 p.R47del | − | − | − | |
| 126002 | 17:35564593 G/A | ACACA | NP_942134.1 p.R1182W | 5 | 16 | 66612 |
| 17:41246481 T/C | BRCA1 | NP_009225.1 p.Q356R | 4 | 4198 | 66734 | |
| 7:18633593 A/G | HDAC9 | NP_001191074.1 p.Y199C | 3 | 0 | 66702 | |
| 129413 | 14:50088465 T/G | MGAT2 | NP_002399.1 p.I160S | 5 | 610 | 66402 |
| 17:41246481 T/C | BRCA1 | NP_009225.1 p.Q356R | 4 | 4198 | 66734 | |
| 15:43762077 TGGGATA/T | TP53BP1 | NP_001135451.1 p.I455_P456del | − | − | − | |
| 129547 | 2:38298287 T/TGGTGGCATCA | CYP1B1 | NP_000095.2 p.T404Sfs*30 | 5† | *** | |
| 10:94297192 C/T | IDE | NP_004960.2 p.G72S | 5 | 8 | 66724 | |
| 12:124824917 C/T | NCOR2 | NP_001070729.2 p.R1794Q | 3 | 2 | 65378 | |
| 21:16337279 C/A | NRIP1 | NP_003480.2 p.V1079F | 3 | 44 | 66670 | |
| 129748 | 16:23632788 TTTTC/T | PALB2 | NP_078951.2 p.E1002Tfs*4 | 5† | − | − |
| 6:52657698 C/T | GSTA1 | NP_665683.1 p.E168K | 4 | 1 | 66738 | |
| 8:48973252 G/A | UBE2V2 | NP_003341.1 p.R101Q | 4 | 1 | 65850 | |
| 20:31021718 C/T | ASXL1 | NP_056153.2 p.R573W** | 4 | 4 | 63434 | |
| 12:53776449 G/C | SP1 | NP_612482.2 p.G240R | 3 | 26 | 66738 | |
| 11:62388048 G/C | B3GAT3 | NP_036332.2 p.R60G | 3 | 1 | 60290 | |
| 131534 | 9:131709581 A/AT | DOLK | NP_055723.1 p.M1? | 5† | 823 | 63350 |
| 13:28592620 T/C | FLT3 | NP_004110.2.Y842C | 5 | 2 | 66710 | |
| 10:94274700 A/G | IDE | NP_004960.2 p.M254T | 5 | 11 | 66698 | |
| 4:70723282 C/G | SULT1E1 | NP_005411.1 p.W27C | 4 | − | − | |
| 1:120478125 A/C | NOTCH2 | NP_001186930.1 p.F1209V | 4 | 306 | 66726 | |
| 17:33430313 T/C | RAD51D | NP_001136043.1 p.E223G | 4 | 874 | 51128 | |
| 1:182555767 C/T | RNASEL | NP_066956.1 p.G59S | 4 | 379 | 66514 | |
Nicolas et al., Table 3
score given to variant creating stop gain or frameshift;
variant causing missense and located in splice site;
this variant has been described in patients with congenital glaucoma, an autosomal recessive trait usually recognized during the first year of life (Sena, et al., 2004). The mutation is not listed in ExAC as it excludes mutations associated with severe pediatric diseases. In the representation in the ExAC column, (−) denotes that the variant was not found in the database while (0) denotes that the variant was absent in European non-Finnish but detected in other ethnicities, as listed in Supp Table 4. This Table also lists damaging variants in genes shown to be clearly tumor-promoting in some inherited or somatic forms of other cancers, although not currently well validated for prostate, including FLT3, ASXL1, KDR, NOTCH2 (e.g. (Kindler, et al., 2005; Sallmyr, et al., 2008; Antonescu, et al., 2009)); as well as genes which are identified by the candidate criteria noted in Table 2, but for which limited information is available based on functional characterization to date (e.g., the AR-interacting protein IDE interacts directly with AR (Kupfer, et al., 1994)).