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 EYA3 2140 broad.mit.edu 36 1 28187735 28187735 + Missense_Mutation SNP G G C novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 28187735 28187735 EYA3 1 G G C 33 SPOCD1 90853 broad.mit.edu 36 1 32052195 32052195 + Missense_Mutation SNP C C G novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 32052195 32052195 SPOCD1 1 C C G 32 CSMD2 114784 broad.mit.edu 36 1 33901272 33901272 + Missense_Mutation SNP A A T novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 33901272 33901272 CSMD2 1 A A T 3 EIF2C4 192670 broad.mit.edu 36 1 36064236 36064236 + Missense_Mutation SNP A A G novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 36064236 36064236 EIF2C4 1 A A G 5 DAB1 1600 broad.mit.edu 36 1 57253676 57253676 + Silent SNP G G A novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 57253676 57253676 DAB1 1 G G A 38 PALMD 54873 broad.mit.edu 36 1 99927002 99927002 + Missense_Mutation SNP G G C novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 99927002 99927002 PALMD 1 G G C 33 SLC16A4 9122 broad.mit.edu 36 1 110723108 110723108 + Missense_Mutation SNP G G C novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 110723108 110723108 SLC16A4 1 G G C 33 RHOC 389 broad.mit.edu 36 1 113047244 113047244 + Missense_Mutation SNP G G T novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 G T G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 113047244 113047244 RHOC 1 G G T 48 CCT3 7203 broad.mit.edu 36 1 154555309 154555309 + Missense_Mutation SNP G G C novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 G C G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 154555309 154555309 CCT3 1 G G C 33 CD1C 911 broad.mit.edu 36 1 156526512 156526512 + Missense_Mutation SNP C C T novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 156526512 156526512 CD1C 1 C C T 32 CD84 8832 broad.mit.edu 36 1 158801956 158801956 + Missense_Mutation SNP G G A novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 158801956 158801956 CD84 1 G G A 40 CD244 51744 broad.mit.edu 36 1 159074894 159074894 + Missense_Mutation SNP C C T novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 159074894 159074894 CD244 1 C C T 17 MPZ 4359 broad.mit.edu 36 1 159542864 159542864 + Missense_Mutation SNP C C T novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 159542864 159542864 MPZ 1 C C T 23 FCGR2A 2212 broad.mit.edu 36 1 159747303 159747303 + Silent SNP G G A novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 159747303 159747303 FCGR2A 1 G G A 37 PFKFB2 5208 broad.mit.edu 36 1 205303127 205303127 + Missense_Mutation SNP G G T novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 205303127 205303127 PFKFB2 1 G G T 42 USH2A 7399 broad.mit.edu 36 1 214564266 214564266 + Missense_Mutation SNP T T A novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 214564266 214564266 USH2A 1 T T A 50 OBSCN 84033 broad.mit.edu 36 1 226471507 226471507 + Missense_Mutation SNP G G T novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 226471507 226471507 OBSCN 1 G G T 43 RYR2 6262 broad.mit.edu 36 1 235869021 235869021 + Missense_Mutation SNP G G C novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 235869021 235869021 RYR2 1 G G C 33 MRC1 4360 broad.mit.edu 36 10 17905243 17905243 + Missense_Mutation SNP G G A novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 17905243 17905243 MRC1 10 G G A 43 DNA2 1763 broad.mit.edu 36 10 69846615 69846615 + Missense_Mutation SNP C C A novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 69846615 69846615 DNA2 10 C C A 21 CDH23 64072 broad.mit.edu 36 10 73228218 73228218 + Missense_Mutation SNP C C T novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 73228218 73228218 CDH23 10 C C T 22 PLAU 5328 broad.mit.edu 36 10 75343489 75343489 + Missense_Mutation SNP C C G novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 75343489 75343489 PLAU 10 C C G 24 DLG5 9231 broad.mit.edu 36 10 79239434 79239434 + Silent SNP G G T novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 79239434 79239434 DLG5 10 G G T 43 CYP2C19 1557 broad.mit.edu 36 10 96592593 96592593 + Missense_Mutation SNP A A G novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 96592593 96592593 CYP2C19 10 A A G 7 SLK 9748 broad.mit.edu 36 10 105758054 105758054 + Nonsense_Mutation SNP G G T novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 G T G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Nonsense_Mutation SNP 105758054 105758054 SLK 10 G G T 33 CUZD1 50624 broad.mit.edu 36 10 124588689 124588689 + Silent SNP G G A novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 124588689 124588689 CUZD1 10 G G A 40 ANO5 203859 broad.mit.edu 36 11 22250961 22250961 + Silent SNP T T A novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 T A T T Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 22250961 22250961 ANO5 11 T T A 62 API5 8539 broad.mit.edu 36 11 43298958 43298958 + Missense_Mutation SNP A A C novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 43298958 43298958 API5 11 A A C 3 B3GAT3 26229 broad.mit.edu 36 11 62141083 62141083 + Silent SNP G G A novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 62141083 62141083 B3GAT3 11 G G A 33 ALG8 79053 broad.mit.edu 36 11 77509759 77509759 + Missense_Mutation SNP G G A novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 77509759 77509759 ALG8 11 G G A 39 MED17 9440 broad.mit.edu 36 11 93166659 93166659 + Missense_Mutation SNP A A G novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 93166659 93166659 MED17 11 A A G 11 TRIM29 23650 broad.mit.edu 36 11 119501780 119501780 + Missense_Mutation SNP A A T novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 119501780 119501780 TRIM29 11 A A T 11 ST14 6768 broad.mit.edu 36 11 129565684 129565684 + Missense_Mutation SNP T T G novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 129565684 129565684 ST14 11 T T G 54 LRTM2 654429 broad.mit.edu 36 12 1814040 1814040 + Silent SNP C C T novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 1814040 1814040 LRTM2 12 C C T 19 VWF 7450 broad.mit.edu 36 12 5971280 5971280 + Missense_Mutation SNP G G C novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 5971280 5971280 VWF 12 G G C 36 PHB2 11331 broad.mit.edu 36 12 6946612 6946612 + Missense_Mutation SNP G G C novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 6946612 6946612 PHB2 12 G G C 47 CD163L1 283316 broad.mit.edu 36 12 7422921 7422921 + Missense_Mutation SNP G G T novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 7422921 7422921 CD163L1 12 G G T 42 DIP2B 57609 broad.mit.edu 36 12 49355378 49355378 + Splice_Site_SNP SNP G G C novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Splice_Site_SNP SNP 49355378 49355378 DIP2B 12 G G C 35 ITGB7 3695 broad.mit.edu 36 12 51877565 51877565 + Missense_Mutation SNP C C T novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 51877565 51877565 ITGB7 12 C C T 20 MARS 4141 broad.mit.edu 36 12 56178523 56178523 + Missense_Mutation SNP A A G novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 56178523 56178523 MARS 12 A A G 16 KITLG 4254 broad.mit.edu 36 12 87436769 87436769 + Missense_Mutation SNP G G A novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 87436769 87436769 KITLG 12 G G A 45 APAF1 317 broad.mit.edu 36 12 97567504 97567504 + Missense_Mutation SNP A A T novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 A T A A Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 97567504 97567504 APAF1 12 A A T 9 CRY1 1407 broad.mit.edu 36 12 105919188 105919188 + Missense_Mutation SNP T T A novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 105919188 105919188 CRY1 12 T T A 56 CMKLR1 1240 broad.mit.edu 36 12 107210540 107210540 + Silent SNP G G C novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 107210540 107210540 CMKLR1 12 G G C 47 MED13L 23389 broad.mit.edu 36 12 114905449 114905449 + Missense_Mutation SNP G G A novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 114905449 114905449 MED13L 12 G G A 33 EFNB2 1948 broad.mit.edu 36 13 105943609 105943609 + Missense_Mutation SNP G G A novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 105943609 105943609 EFNB2 13 G G A 39 CEBPE 1053 broad.mit.edu 36 14 22656582 22656582 + Missense_Mutation SNP A A G novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 22656582 22656582 CEBPE 14 A A G 4 TRIP11 9321 broad.mit.edu 36 14 91542457 91542457 + Missense_Mutation SNP T T G novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 T G T T Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 91542457 91542457 TRIP11 14 T T G 62 TRIP11 9321 broad.mit.edu 36 14 91550328 91550328 + Silent SNP T T C novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 T C T T Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 91550328 91550328 TRIP11 14 T T C 57 DYNC1H1 1778 broad.mit.edu 36 14 101574586 101574586 + Missense_Mutation SNP C C G novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 101574586 101574586 DYNC1H1 14 C C G 28 DUOX1 53905 broad.mit.edu 36 15 43235335 43235335 + Nonsense_Mutation SNP T T A novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 43235335 43235335 DUOX1 15 T T A 51 FANCI 55215 broad.mit.edu 36 15 87648148 87648148 + Missense_Mutation SNP G G A novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 87648148 87648148 FANCI 15 G G A 39 C15orf32 145858 broad.mit.edu 36 15 90816584 90816584 + Missense_Mutation SNP C C T novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 90816584 90816584 C15orf32 15 C C T 25 GEMIN4 50628 broad.mit.edu 36 17 597178 597178 + Silent SNP G G A novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 597178 597178 GEMIN4 17 G G A 44 TP53 7157 broad.mit.edu 36 17 7519094 7519094 + Splice_Site_SNP SNP A A C novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Splice_Site_SNP SNP 7519094 7519094 TP53 17 A A C 6 ALDH3A2 224 broad.mit.edu 36 17 19515740 19515740 + Missense_Mutation SNP C C T novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 19515740 19515740 ALDH3A2 17 C C T 24 EFTUD2 9343 broad.mit.edu 36 17 40292851 40292851 + Missense_Mutation SNP A A T novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 40292851 40292851 EFTUD2 17 A A T 8 HOXB4 3214 broad.mit.edu 36 17 44010278 44010278 + Missense_Mutation SNP C C T novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 44010278 44010278 HOXB4 17 C C T 27 MYOM1 8736 broad.mit.edu 36 18 3205130 3205130 + Missense_Mutation SNP C C A novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 3205130 3205130 MYOM1 18 C C A 23 RBBP8 5932 broad.mit.edu 36 18 18831639 18831639 + Missense_Mutation SNP G G A novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 18831639 18831639 RBBP8 18 G G A 36 CLPP 8192 broad.mit.edu 36 19 6315626 6315626 + Silent SNP C C T novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 6315626 6315626 CLPP 19 C C T 30 CDKN2D 1032 broad.mit.edu 36 19 10538786 10538787 + Missense_Mutation DNP CC CC AG novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 CC AG CC CC Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation DNP 10538786 10538787 CDKN2D 19 CC CC AG 22 ZNF823 55552 broad.mit.edu 36 19 11693769 11693769 + Missense_Mutation SNP T T C novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 T C T T Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 11693769 11693769 ZNF823 19 T T C 49 RHPN2 85415 broad.mit.edu 36 19 38174570 38174570 + Missense_Mutation SNP G G A novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 38174570 38174570 RHPN2 19 G G A 37 ZNF222 7673 broad.mit.edu 36 19 49227973 49227973 + Missense_Mutation SNP G G T novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 49227973 49227973 ZNF222 19 G G T 33 IL4I1 259307 broad.mit.edu 36 19 55090198 55090198 + Missense_Mutation SNP G G C novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 55090198 55090198 IL4I1 19 G G C 39 CNOT3 4849 broad.mit.edu 36 19 59343873 59343873 + Missense_Mutation SNP G G T novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 59343873 59343873 CNOT3 19 G G T 36 CNOT3 4849 broad.mit.edu 36 19 59349278 59349278 + Missense_Mutation SNP G G C novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 59349278 59349278 CNOT3 19 G G C 36 TNNT1 7138 broad.mit.edu 36 19 60340308 60340308 + Missense_Mutation SNP C C G novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 60340308 60340308 TNNT1 19 C C G 29 ZNF586 54807 broad.mit.edu 36 19 62982007 62982007 + Silent SNP A A G novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 A G A A Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 62982007 62982007 ZNF586 19 A A G 11 LPIN1 23175 broad.mit.edu 36 2 11860585 11860585 + Missense_Mutation SNP C C A novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 11860585 11860585 LPIN1 2 C C A 20 SLC5A6 8884 broad.mit.edu 36 2 27279631 27279631 + Missense_Mutation SNP C C G novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 27279631 27279631 SLC5A6 2 C C G 23 DYSF 8291 broad.mit.edu 36 2 71739621 71739621 + Missense_Mutation SNP A A G novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 71739621 71739621 DYSF 2 A A G 16 EIF5B 9669 broad.mit.edu 36 2 99373550 99373550 + Missense_Mutation SNP C C A novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 99373550 99373550 EIF5B 2 C C A 29 NEB 4703 broad.mit.edu 36 2 152070318 152070318 + Missense_Mutation SNP C C G novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 152070318 152070318 NEB 2 C C G 30 KIAA1715 80856 broad.mit.edu 36 2 176512585 176512585 + Silent SNP T T C novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 176512585 176512585 KIAA1715 2 T T C 54 PARD3B 117583 broad.mit.edu 36 2 206188590 206188590 + Missense_Mutation SNP C C G novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 206188590 206188590 PARD3B 2 C C G 20 ADAM23 8745 broad.mit.edu 36 2 207146159 207146159 + Missense_Mutation SNP G G A novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 207146159 207146159 ADAM23 2 G G A 47 PIKFYVE 200576 broad.mit.edu 36 2 208926972 208926972 + Nonsense_Mutation SNP C C T novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Nonsense_Mutation SNP 208926972 208926972 PIKFYVE 2 C C T 31 FARSB 10056 broad.mit.edu 36 2 223173002 223173002 + Missense_Mutation SNP T T G novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 223173002 223173002 FARSB 2 T T G 63 NCL 4691 broad.mit.edu 36 2 232033805 232033805 + Silent SNP A A T novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 232033805 232033805 NCL 2 A A T 15 DEFB118 117285 broad.mit.edu 36 20 29424534 29424534 + Missense_Mutation SNP C C A novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 29424534 29424534 DEFB118 20 C C A 17 TTLL9 164395 broad.mit.edu 36 20 29961352 29961352 + Missense_Mutation SNP G G C novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 29961352 29961352 TTLL9 20 G G C 38 GSS 2937 broad.mit.edu 36 20 32994031 32994031 + Missense_Mutation SNP G G C novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 32994031 32994031 GSS 20 G G C 43 ADNP 23394 broad.mit.edu 36 20 48952048 48952048 + Silent SNP A A G novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 48952048 48952048 ADNP 20 A A G 13 CYP24A1 1591 broad.mit.edu 36 20 52215711 52215711 + Missense_Mutation SNP T T A novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 52215711 52215711 CYP24A1 20 T T A 62 TAF4 6874 broad.mit.edu 36 20 60023144 60023144 + Missense_Mutation SNP G G C novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 60023144 60023144 TAF4 20 G G C 39 ZNF385D 79750 broad.mit.edu 36 3 21437843 21437843 + Missense_Mutation SNP C C A novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 21437843 21437843 ZNF385D 3 C C A 20 TOP2B 7155 broad.mit.edu 36 3 25640152 25640152 + Missense_Mutation SNP T T C novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 T C T T Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 25640152 25640152 TOP2B 3 T T C 49 SETD2 29072 broad.mit.edu 36 3 47100875 47100875 + Missense_Mutation SNP A A T novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 A T A A Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 47100875 47100875 SETD2 3 A A T 4 ZNF80 7634 broad.mit.edu 36 3 115438336 115438336 + Silent SNP G G A novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 115438336 115438336 ZNF80 3 G G A 37 ZBTB20 26137 broad.mit.edu 36 3 115552582 115552582 + Missense_Mutation SNP C C G novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 115552582 115552582 ZBTB20 3 C C G 18 GOLGB1 2804 broad.mit.edu 36 3 122893196 122893196 + Nonsense_Mutation SNP C C A novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 122893196 122893196 GOLGB1 3 C C A 30 ACAD9 28976 broad.mit.edu 36 3 130100986 130100986 + Missense_Mutation SNP G G T novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 130100986 130100986 ACAD9 3 G G T 42 PLSCR1 5359 broad.mit.edu 36 3 147716578 147716578 + Missense_Mutation SNP C C G novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 147716578 147716578 PLSCR1 3 C C G 30 CLNK 116449 broad.mit.edu 36 4 10182479 10182479 + Missense_Mutation SNP T T C novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 10182479 10182479 CLNK 4 T T C 56 HERC5 51191 broad.mit.edu 36 4 89634439 89634439 + Missense_Mutation SNP T T G novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 89634439 89634439 HERC5 4 T T G 64 DDX60 55601 broad.mit.edu 36 4 169443135 169443135 + Silent SNP A A G novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 169443135 169443135 DDX60 4 A A G 1 SLC45A2 51151 broad.mit.edu 36 5 33999763 33999763 + Silent SNP G G A novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 33999763 33999763 SLC45A2 5 G G A 45 GPR98 84059 broad.mit.edu 36 5 90026254 90026254 + Missense_Mutation SNP A A T novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 90026254 90026254 GPR98 5 A A T 11 LNPEP 4012 broad.mit.edu 36 5 96359496 96359496 + Missense_Mutation SNP G G T novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 96359496 96359496 LNPEP 5 G G T 37 SLCO6A1 133482 broad.mit.edu 36 5 101783449 101783449 + Silent SNP C C T novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 101783449 101783449 SLCO6A1 5 C C T 30 ITK 3702 broad.mit.edu 36 5 156601293 156601293 + Missense_Mutation SNP G G T novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 G T G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 156601293 156601293 ITK 5 G G T 34 ODZ2 57451 broad.mit.edu 36 5 167585814 167585814 + Missense_Mutation SNP C C A novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 167585814 167585814 ODZ2 5 C C A 32 DDX41 51428 broad.mit.edu 36 5 176875735 176875735 + Missense_Mutation SNP C C T novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 176875735 176875735 DDX41 5 C C T 31 RMND5B 64777 broad.mit.edu 36 5 177503619 177503619 + Missense_Mutation SNP C C G novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 177503619 177503619 RMND5B 5 C C G 25 CLK4 57396 broad.mit.edu 36 5 177983020 177983020 + Missense_Mutation SNP G G A novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 177983020 177983020 CLK4 5 G G A 38 ZNF354B 117608 broad.mit.edu 36 5 178243672 178243672 + Missense_Mutation SNP T T A novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 178243672 178243672 ZNF354B 5 T T A 49 BAT1 7919 broad.mit.edu 36 6 31616213 31616213 + Missense_Mutation SNP C C T novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 31616213 31616213 BAT1 6 C C T 21 TBX18 9096 broad.mit.edu 36 6 85503762 85503762 + Missense_Mutation SNP C C A novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 85503762 85503762 TBX18 6 C C A 25 EPHA7 2045 broad.mit.edu 36 6 94038740 94038740 + Missense_Mutation SNP C C A novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 C A C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 94038740 94038740 EPHA7 6 C C A 32 MCHR2 84539 broad.mit.edu 36 6 100475619 100475619 + Missense_Mutation SNP T T C novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 100475619 100475619 MCHR2 6 T T C 55 LAMA4 3910 broad.mit.edu 36 6 112613197 112613197 + Nonsense_Mutation SNP G G A novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 112613197 112613197 LAMA4 6 G G A 48 SP4 6671 broad.mit.edu 36 7 21436472 21436472 + Missense_Mutation SNP T T A novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 21436472 21436472 SP4 7 T T A 50 HERPUD2 64224 broad.mit.edu 36 7 35641447 35641447 + Missense_Mutation SNP T T C novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 35641447 35641447 HERPUD2 7 T T C 54 PKD1L1 168507 broad.mit.edu 36 7 47818010 47818010 + Nonsense_Mutation SNP G G T novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 47818010 47818010 PKD1L1 7 G G T 45 SEMA3E 9723 broad.mit.edu 36 7 82957428 82957428 + Missense_Mutation SNP C C G novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 82957428 82957428 SEMA3E 7 C C G 19 ZNF804B 219578 broad.mit.edu 36 7 88802287 88802287 + Silent SNP C C A novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 88802287 88802287 ZNF804B 7 C C A 21 MUC17 140453 broad.mit.edu 36 7 100468359 100468359 + Silent SNP T T A novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 100468359 100468359 MUC17 7 T T A 55 MOGAT3 346606 broad.mit.edu 36 7 100630814 100630814 + Missense_Mutation SNP T T G novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 100630814 100630814 MOGAT3 7 T T G 64 CUX1 1523 broad.mit.edu 36 7 101657399 101657399 + Missense_Mutation SNP C C A novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 101657399 101657399 CUX1 7 C C A 22 CCDC136 64753 broad.mit.edu 36 7 128240009 128240009 + Missense_Mutation SNP A A T novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 128240009 128240009 CCDC136 7 A A T 1 CNTNAP2 26047 broad.mit.edu 36 7 147231700 147231700 + Missense_Mutation SNP A A T novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 147231700 147231700 CNTNAP2 7 A A T 6 PDIA4 9601 broad.mit.edu 36 7 148347173 148347173 + Missense_Mutation SNP T T C novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 148347173 148347173 PDIA4 7 T T C 51 CHPF2 54480 broad.mit.edu 36 7 150562189 150562189 + Missense_Mutation SNP G G C novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 150562189 150562189 CHPF2 7 G G C 33 LZTS1 11178 broad.mit.edu 36 8 20154709 20154709 + Missense_Mutation SNP A A T novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 20154709 20154709 LZTS1 8 A A T 3 MPDZ 8777 broad.mit.edu 36 9 13214467 13214467 + Missense_Mutation SNP C C A novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 13214467 13214467 MPDZ 9 C C A 22 FAM75A3 727830 broad.mit.edu 36 9 40694225 40694225 + Missense_Mutation SNP G G A novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 40694225 40694225 FAM75A3 9 G G A 41 SH2D3C 10044 broad.mit.edu 36 9 129551356 129551356 + Missense_Mutation SNP C C A novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 129551356 129551356 SH2D3C 9 C C A 22 FUBP3 8939 broad.mit.edu 36 9 132495968 132495968 + Missense_Mutation SNP C C A novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 132495968 132495968 FUBP3 9 C C A 26 GRPR 2925 broad.mit.edu 36 X 16078664 16078664 + Missense_Mutation SNP T T A novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 T A T T Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 16078664 16078664 GRPR 23 T T A 50 GPR173 54328 broad.mit.edu 36 X 53122750 53122750 + Silent SNP C C T novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 53122750 53122750 GPR173 23 C C T 32 HTR2C 3358 broad.mit.edu 36 X 114047420 114047420 + Missense_Mutation SNP C C T novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 114047420 114047420 HTR2C 23 C C T 24 GLUD2 2747 broad.mit.edu 36 X 120010098 120010098 + Silent SNP A A G novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 120010098 120010098 GLUD2 23 A A G 15 GRIA3 2892 broad.mit.edu 36 X 122360239 122360239 + Silent SNP A A G novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 122360239 122360239 GRIA3 23 A A G 11 ZIC3 7547 broad.mit.edu 36 X 136478821 136478821 + Silent SNP C C T novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 136478821 136478821 ZIC3 23 C C T 17 NBEA 26960 broad.mit.edu 36 13 34636551 34636567 + Frame_Shift_Del DEL CATAACACAATTCACCT - CATAACACAATTCACCT novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 34636551 34636567 NBEA 13 CATAACACAATTCACCT - CATAACACAATTCACCT 17 PTPRG 5793 broad.mit.edu 36 3 61523076 61523097 + Splice_Site_Del DEL GTGCTTCCCCGGTGAGTGCCGG - GTGCTTCCCCGGTGAGTGCCGG novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Splice_Site_Del DEL 61523076 61523097 PTPRG 3 GTGCTTCCCCGGTGAGTGCCGG - GTGCTTCCCCGGTGAGTGCCGG 48 PHKA2 5256 broad.mit.edu 36 X 18879229 18879248 + Frame_Shift_Del DEL GTGCCACAGGTGGCGGTGTT - GTGCCACAGGTGGCGGTGTT novel Unknown TCGA-13-0923-01 TCGA-13-0923-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 18879229 18879248 PHKA2 23 GTGCCACAGGTGGCGGTGTT - GTGCCACAGGTGGCGGTGTT 40