Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_position End_position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_file Sequencer dataset type classification start end gene chr ref_allele tum_allele1 tum_allele2 context EXTL1 2134 broad.mit.edu 36 1 26221812 26221812 + Missense_Mutation SNP C C T novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 26221812 26221812 EXTL1 1 C C T 32 MRPS15 64960 broad.mit.edu 36 1 36694499 36694499 + Missense_Mutation SNP C C T novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 36694499 36694499 MRPS15 1 C C T 19 GBP6 163351 broad.mit.edu 36 1 89607795 89607795 + Missense_Mutation SNP C C A novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 89607795 89607795 GBP6 1 C C A 18 ABCA4 24 broad.mit.edu 36 1 94267639 94267639 + Missense_Mutation SNP T T A novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 94267639 94267639 ABCA4 1 T T A 59 LPPR4 9890 broad.mit.edu 36 1 99539933 99539933 + Missense_Mutation SNP T T A novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 99539933 99539933 LPPR4 1 T T A 61 AMIGO1 57463 broad.mit.edu 36 1 109852263 109852263 + Silent SNP C C T novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 109852263 109852263 AMIGO1 1 C C T 29 RBM15 64783 broad.mit.edu 36 1 110684843 110684843 + Silent SNP A A G novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 110684843 110684843 RBM15 1 A A G 4 CTTNBP2NL 55917 broad.mit.edu 36 1 112798625 112798625 + Missense_Mutation SNP G G T novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 112798625 112798625 CTTNBP2NL 1 G G T 39 IGSF3 3321 broad.mit.edu 36 1 116923710 116923710 + Missense_Mutation SNP C C G novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 116923710 116923710 IGSF3 1 C C G 27 TCHH 7062 broad.mit.edu 36 1 150350676 150350676 + Silent SNP C C T novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 150350676 150350676 TCHH 1 C C T 28 GON4L 54856 broad.mit.edu 36 1 154009625 154009625 + Missense_Mutation SNP G G A novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 154009625 154009625 GON4L 1 G G A 38 SELE 6401 broad.mit.edu 36 1 167968549 167968549 + Silent SNP T T A novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 167968549 167968549 SELE 1 T T A 53 ZBTB41 360023 broad.mit.edu 36 1 195435724 195435724 + Missense_Mutation SNP A A C novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 195435724 195435724 ZBTB41 1 A A C 16 ATP2B4 493 broad.mit.edu 36 1 201975442 201975442 + Missense_Mutation SNP A A T novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 201975442 201975442 ATP2B4 1 A A T 11 PIGR 5284 broad.mit.edu 36 1 205173109 205173109 + Missense_Mutation SNP C C A novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 205173109 205173109 PIGR 1 C C A 24 C4BPA 722 broad.mit.edu 36 1 205383942 205383942 + Missense_Mutation SNP A A T novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 205383942 205383942 C4BPA 1 A A T 11 ARHGAP21 57584 broad.mit.edu 36 10 24951666 24951666 + Splice_Site_SNP SNP A A T novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Splice_Site_SNP SNP 24951666 24951666 ARHGAP21 10 A A T 14 SHOC2 8036 broad.mit.edu 36 10 112714797 112714797 + Missense_Mutation SNP C C T novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 112714797 112714797 SHOC2 10 C C T 18 C11orf41 25758 broad.mit.edu 36 11 33546309 33546309 + Missense_Mutation SNP G G A novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 33546309 33546309 C11orf41 11 G G A 39 OR4C13 283092 broad.mit.edu 36 11 49930899 49930899 + Missense_Mutation SNP G G T novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 49930899 49930899 OR4C13 11 G G T 42 AHNAK 79026 broad.mit.edu 36 11 62041330 62041330 + Missense_Mutation SNP A A G novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 62041330 62041330 AHNAK 11 A A G 12 NAALADL1 10004 broad.mit.edu 36 11 64569328 64569328 + Silent SNP A A G novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 64569328 64569328 NAALADL1 11 A A G 7 TBX10 347853 broad.mit.edu 36 11 67159191 67159191 + Missense_Mutation SNP A A G novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 67159191 67159191 TBX10 11 A A G 11 GDF3 9573 broad.mit.edu 36 12 7739588 7739588 + Missense_Mutation SNP G G T novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 7739588 7739588 GDF3 12 G G T 34 PKP2 5318 broad.mit.edu 36 12 32922444 32922444 + Missense_Mutation SNP G G A novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 32922444 32922444 PKP2 12 G G A 47 LRRK2 120892 broad.mit.edu 36 12 38982936 38982936 + Missense_Mutation SNP T T C novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 38982936 38982936 LRRK2 12 T T C 52 SHMT2 6472 broad.mit.edu 36 12 55913664 55913664 + Missense_Mutation SNP C C T novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 55913664 55913664 SHMT2 12 C C T 31 TMTC2 160335 broad.mit.edu 36 12 81883627 81883627 + Missense_Mutation SNP G G T novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 81883627 81883627 TMTC2 12 G G T 34 SCYL2 55681 broad.mit.edu 36 12 99244535 99244535 + Missense_Mutation SNP G G A novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 99244535 99244535 SCYL2 12 G G A 40 SSH1 54434 broad.mit.edu 36 12 107729204 107729204 + Missense_Mutation SNP C C T novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 107729204 107729204 SSH1 12 C C T 31 TBX3 6926 broad.mit.edu 36 12 113605310 113605310 + Missense_Mutation SNP C C A novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 113605310 113605310 TBX3 12 C C A 30 NBEA 26960 broad.mit.edu 36 13 34668278 34668278 + Silent SNP T T C novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 34668278 34668278 NBEA 13 T T C 61 REC8 9985 broad.mit.edu 36 14 23716581 23716581 + Missense_Mutation SNP C C A novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 23716581 23716581 REC8 14 C C A 20 LRFN5 145581 broad.mit.edu 36 14 41430889 41430889 + Missense_Mutation SNP C C T novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 41430889 41430889 LRFN5 14 C C T 19 DIO3 1735 broad.mit.edu 36 14 101098382 101098382 + Missense_Mutation SNP A A G novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 101098382 101098382 DIO3 14 A A G 11 RYR3 6263 broad.mit.edu 36 15 31775970 31775970 + Missense_Mutation SNP G G T novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 31775970 31775970 RYR3 15 G G T 45 EHD4 30844 broad.mit.edu 36 15 39980247 39980247 + Missense_Mutation SNP G G A novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 39980247 39980247 EHD4 15 G G A 38 FBN1 2200 broad.mit.edu 36 15 46536234 46536234 + Missense_Mutation SNP C C T novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 46536234 46536234 FBN1 15 C C T 30 RASL12 51285 broad.mit.edu 36 15 63138788 63138789 + Missense_Mutation DNP TC TC AA novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation DNP 63138788 63138789 RASL12 15 TC TC AA 54 CORO2B 10391 broad.mit.edu 36 15 66798128 66798128 + Missense_Mutation SNP C C G novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 66798128 66798128 CORO2B 15 C C G 27 POLG 5428 broad.mit.edu 36 15 87666204 87666204 + Missense_Mutation SNP C C T novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 87666204 87666204 POLG 15 C C T 17 SYNM 23336 broad.mit.edu 36 15 97471387 97471387 + Silent SNP C C T novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 97471387 97471387 SYNM 15 C C T 20 MSLNL 401827 broad.mit.edu 36 16 762928 762928 + Missense_Mutation SNP A A T novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 762928 762928 MSLNL 16 A A T 7 POLR3E 55718 broad.mit.edu 36 16 22235495 22235495 + Missense_Mutation SNP G G C novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 22235495 22235495 POLR3E 16 G G C 40 PRDM7 11105 broad.mit.edu 36 16 88655922 88655922 + Missense_Mutation SNP C C A novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 88655922 88655922 PRDM7 16 C C A 26 PER1 5187 broad.mit.edu 36 17 7990083 7990083 + Silent SNP C C A novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 7990083 7990083 PER1 17 C C A 23 MYO15A 51168 broad.mit.edu 36 17 17990024 17990024 + Silent SNP A A T novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 17990024 17990024 MYO15A 17 A A T 6 MYO15A 51168 broad.mit.edu 36 17 18004036 18004036 + Silent SNP A A C novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 18004036 18004036 MYO15A 17 A A C 7 RHBDL3 162494 broad.mit.edu 36 17 27656501 27656501 + Missense_Mutation SNP G G A novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 27656501 27656501 RHBDL3 17 G G A 45 SLFN13 146857 broad.mit.edu 36 17 30795017 30795017 + Nonsense_Mutation SNP G G A novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 30795017 30795017 SLFN13 17 G G A 45 CARD14 79092 broad.mit.edu 36 17 75786892 75786892 + Silent SNP C C T novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 75786892 75786892 CARD14 17 C C T 31 ONECUT2 9480 broad.mit.edu 36 18 53294750 53294750 + Missense_Mutation SNP C C T novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 53294750 53294750 ONECUT2 18 C C T 19 SERPINB4 6318 broad.mit.edu 36 18 59461637 59461637 + Missense_Mutation SNP T T G novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 59461637 59461637 SERPINB4 18 T T G 63 MUC16 94025 broad.mit.edu 36 19 8938660 8938660 + Silent SNP C C A novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 8938660 8938660 MUC16 19 C C A 25 ZNF208 7757 broad.mit.edu 36 19 21946280 21946280 + Missense_Mutation SNP C C A novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 21946280 21946280 ZNF208 19 C C A 24 PEPD 5184 broad.mit.edu 36 19 38672798 38672798 + Silent SNP G G A novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 38672798 38672798 PEPD 19 G G A 38 ZNF527 84503 broad.mit.edu 36 19 42571651 42571651 + Missense_Mutation SNP C C T novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 42571651 42571651 ZNF527 19 C C T 29 SLC8A2 6543 broad.mit.edu 36 19 52627435 52627435 + Silent SNP C C T novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 52627435 52627435 SLC8A2 19 C C T 23 ZNF584 201514 broad.mit.edu 36 19 63618803 63618803 + Missense_Mutation SNP A A C novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 63618803 63618803 ZNF584 19 A A C 3 CLEC4F 165530 broad.mit.edu 36 2 70896853 70896853 + Missense_Mutation SNP T T C novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 70896853 70896853 CLEC4F 2 T T C 50 POLR1A 25885 broad.mit.edu 36 2 86111964 86111964 + Silent SNP C C T novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 86111964 86111964 POLR1A 2 C C T 24 IL1F8 27177 broad.mit.edu 36 2 113500251 113500251 + Silent SNP C C T novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 113500251 113500251 IL1F8 2 C C T 24 SCN1A 6323 broad.mit.edu 36 2 166556278 166556278 + Missense_Mutation SNP G G C novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 166556278 166556278 SCN1A 2 G G C 33 XIRP2 129446 broad.mit.edu 36 2 167813873 167813873 + Missense_Mutation SNP C C A novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 167813873 167813873 XIRP2 2 C C A 26 DLX2 1746 broad.mit.edu 36 2 172675253 172675253 + Missense_Mutation SNP A A T novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 172675253 172675253 DLX2 2 A A T 8 TTN 7273 broad.mit.edu 36 2 179162150 179162150 + Missense_Mutation SNP C C T novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 179162150 179162150 TTN 2 C C T 26 CCDC141 285025 broad.mit.edu 36 2 179410667 179410667 + Missense_Mutation SNP T T G novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 179410667 179410667 CCDC141 2 T T G 54 SLC4A3 6508 broad.mit.edu 36 2 220205295 220205295 + Missense_Mutation SNP G G A novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 220205295 220205295 SLC4A3 2 G G A 38 ACSL3 2181 broad.mit.edu 36 2 223507617 223507617 + Missense_Mutation SNP T T C novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 223507617 223507617 ACSL3 2 T T C 57 UGT1A4 54657 broad.mit.edu 36 2 234292325 234292325 + Silent SNP C C G novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 234292325 234292325 UGT1A4 2 C C G 24 ARL4C 10123 broad.mit.edu 36 2 235069407 235069407 + Missense_Mutation SNP T T G novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 235069407 235069407 ARL4C 2 T T G 55 RBM39 9584 broad.mit.edu 36 20 33773163 33773163 + Silent SNP A A G novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 33773163 33773163 RBM39 20 A A G 6 KIAA1755 85449 broad.mit.edu 36 20 36303401 36303401 + Silent SNP G G A novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 36303401 36303401 KIAA1755 20 G G A 47 TOX2 84969 broad.mit.edu 36 20 42008055 42008055 + Missense_Mutation SNP C C A novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 42008055 42008055 TOX2 20 C C A 25 ZFP64 55734 broad.mit.edu 36 20 50203113 50203113 + Missense_Mutation SNP G G T novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 50203113 50203113 ZFP64 20 G G T 35 TSHZ2 128553 broad.mit.edu 36 20 51306065 51306065 + Missense_Mutation SNP G G T novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 51306065 51306065 TSHZ2 20 G G T 36 COL20A1 57642 broad.mit.edu 36 20 61399771 61399771 + Silent SNP G G A novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 61399771 61399771 COL20A1 20 G G A 39 COL18A1 80781 broad.mit.edu 36 21 45713004 45713004 + Missense_Mutation SNP T T C novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 45713004 45713004 COL18A1 21 T T C 54 SLC4A7 9497 broad.mit.edu 36 3 27414817 27414817 + Missense_Mutation SNP C C G novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 27414817 27414817 SLC4A7 3 C C G 22 ZNF589 51385 broad.mit.edu 36 3 48285204 48285204 + Missense_Mutation SNP G G T novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 48285204 48285204 ZNF589 3 G G T 42 PDZRN3 23024 broad.mit.edu 36 3 73515603 73515603 + Missense_Mutation SNP T T C novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 73515603 73515603 PDZRN3 3 T T C 56 RYK 6259 broad.mit.edu 36 3 135390446 135390446 + Missense_Mutation SNP G G A novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 135390446 135390446 RYK 3 G G A 38 CHST2 9435 broad.mit.edu 36 3 144323925 144323925 + Missense_Mutation SNP G G T novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 144323925 144323925 CHST2 3 G G T 39 ATP11B 23200 broad.mit.edu 36 3 184085261 184085261 + Missense_Mutation SNP G G T novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 184085261 184085261 ATP11B 3 G G T 42 HTR3C 170572 broad.mit.edu 36 3 185256761 185256761 + Missense_Mutation SNP G G A novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 185256761 185256761 HTR3C 3 G G A 40 BCL6 604 broad.mit.edu 36 3 188930009 188930009 + Missense_Mutation SNP T T A novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 188930009 188930009 BCL6 3 T T A 57 FRAS1 80144 broad.mit.edu 36 4 79606527 79606527 + Missense_Mutation SNP G G A novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 79606527 79606527 FRAS1 4 G G A 39 MTTP 4547 broad.mit.edu 36 4 100746944 100746944 + Missense_Mutation SNP A A G novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 100746944 100746944 MTTP 4 A A G 3 WDR17 116966 broad.mit.edu 36 4 177326792 177326792 + Splice_Site_SNP SNP G G T novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Splice_Site_SNP SNP 177326792 177326792 WDR17 4 G G T 36 KIAA0947 23379 broad.mit.edu 36 5 5517525 5517525 + Missense_Mutation SNP C C G novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 5517525 5517525 KIAA0947 5 C C G 24 SLC45A2 51151 broad.mit.edu 36 5 33990231 33990231 + Missense_Mutation SNP T T A novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 33990231 33990231 SLC45A2 5 T T A 51 VCAN 1462 broad.mit.edu 36 5 82872631 82872631 + Missense_Mutation SNP G G A rs59948995 Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 82872631 82872631 VCAN 5 G G A 40 PPARGC1B 133522 broad.mit.edu 36 5 149186536 149186536 + Silent SNP C C T novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 149186536 149186536 PPARGC1B 5 C C T 19 CYFIP2 26999 broad.mit.edu 36 5 156674022 156674022 + Silent SNP C C T novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 156674022 156674022 CYFIP2 5 C C T 21 IMPG1 3617 broad.mit.edu 36 6 76785218 76785218 + Silent SNP C C T novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 76785218 76785218 IMPG1 6 C C T 24 ZBTB24 9841 broad.mit.edu 36 6 109903334 109903334 + Missense_Mutation SNP C C A novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 109903334 109903334 ZBTB24 6 C C A 30 LAMA2 3908 broad.mit.edu 36 6 129683414 129683414 + Missense_Mutation SNP G G T novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 129683414 129683414 LAMA2 6 G G T 40 SGK1 6446 broad.mit.edu 36 6 134533197 134533197 + Missense_Mutation SNP T T C novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 134533197 134533197 SGK1 6 T T C 63 INMT 11185 broad.mit.edu 36 7 30761858 30761858 + Nonsense_Mutation SNP G G T novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 30761858 30761858 INMT 7 G G T 41 AKAP9 10142 broad.mit.edu 36 7 91550881 91550881 + Silent SNP G G A novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 91550881 91550881 AKAP9 7 G G A 45 CBLL1 79872 broad.mit.edu 36 7 107186218 107186218 + Nonsense_Mutation SNP C C T novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 107186218 107186218 CBLL1 7 C C T 29 PLXNA4 91584 broad.mit.edu 36 7 131476006 131476006 + Missense_Mutation SNP G G A novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 131476006 131476006 PLXNA4 7 G G A 44 DENND2A 27147 broad.mit.edu 36 7 139915941 139915941 + Nonsense_Mutation SNP G G A novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 139915941 139915941 DENND2A 7 G G A 47 ZFHX4 79776 broad.mit.edu 36 8 77781037 77781037 + Nonsense_Mutation SNP C C A novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 77781037 77781037 ZFHX4 8 C C A 31 NUDCD1 84955 broad.mit.edu 36 8 110362554 110362554 + Missense_Mutation SNP T T A novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 110362554 110362554 NUDCD1 8 T T A 58 CYP11B1 1584 broad.mit.edu 36 8 143957520 143957520 + Missense_Mutation SNP G G T novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 143957520 143957520 CYP11B1 8 G G T 47 PARP10 84875 broad.mit.edu 36 8 145132235 145132235 + Missense_Mutation SNP C C T novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 145132235 145132235 PARP10 8 C C T 19 IFNA13 3447 broad.mit.edu 36 9 21357973 21357973 + Missense_Mutation SNP C C A novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 21357973 21357973 IFNA13 9 C C A 18 RGP1 9827 broad.mit.edu 36 9 35741705 35741705 + Missense_Mutation SNP T T C novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 35741705 35741705 RGP1 9 T T C 59 FRMPD1 22844 broad.mit.edu 36 9 37723549 37723549 + Missense_Mutation SNP A A G novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 37723549 37723549 FRMPD1 9 A A G 15 CEP78 84131 broad.mit.edu 36 9 80071219 80071219 + Silent SNP C C T novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 80071219 80071219 CEP78 9 C C T 31 C9orf89 84270 broad.mit.edu 36 9 94912803 94912803 + Missense_Mutation SNP C C G novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 94912803 94912803 C9orf89 9 C C G 24 SPTAN1 6709 broad.mit.edu 36 9 130368968 130368968 + Missense_Mutation SNP C C T novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 130368968 130368968 SPTAN1 9 C C T 30 ADAMTS13 11093 broad.mit.edu 36 9 135293271 135293271 + Missense_Mutation SNP C C T novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 135293271 135293271 ADAMTS13 9 C C T 22 NOTCH1 4851 broad.mit.edu 36 9 138511033 138511033 + Missense_Mutation SNP G G A novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 138511033 138511033 NOTCH1 9 G G A 38 UBA1 7317 broad.mit.edu 36 X 46950616 46950616 + Silent SNP C C G novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 46950616 46950616 UBA1 23 C C G 32 ARMCX3 51566 broad.mit.edu 36 X 100766912 100766912 + Missense_Mutation SNP C C G novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 100766912 100766912 ARMCX3 23 C C G 26 PHF6 84295 broad.mit.edu 36 X 133376711 133376711 + Splice_Site_SNP SNP G G C novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Splice_Site_SNP SNP 133376711 133376711 PHF6 23 G G C 36 TKTL1 8277 broad.mit.edu 36 X 153177534 153177534 + Missense_Mutation SNP G G A novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 153177534 153177534 TKTL1 23 G G A 34 MYO7A 4647 broad.mit.edu 36 11 76573419 76573440 + Nonstop_Mutation DEL GGAGGCGGGGACACCAGGGCCT - GGAGGCGGGGACACCAGGGCCT novel Unknown TCGA-61-2012-01 TCGA-61-2012-11 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Nonstop_Mutation DEL 76573419 76573440 MYO7A 11 GGAGGCGGGGACACCAGGGCCT - GGAGGCGGGGACACCAGGGCCT 43