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	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	t_alt_count	t_ref_count	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	pox	qox	pox_cutoff	isArtifactMode	oxoGCut
NBPF1	55672	broad.mit.edu	37	1	16902764	16902764	+	Missense_Mutation	SNP	G	A	A			TCGA-CS-4944-01A-01D-1468-08	TCGA-CS-4944-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	471d39e4-2d0b-4f56-8e98-216f5a1baf5d	c4d192e1-a280-4ca9-963d-dc5efaacb683	g.chr1:16902764G>A	uc009vos.1	-	19	3005	c.2117C>T	c.(2116-2118)CCA>CTA	p.P706L	NBPF1_uc009vot.1_Intron|NBPF1_uc001ayz.1_Missense_Mutation_p.P164L|NBPF1_uc010oce.1_Missense_Mutation_p.P435L	NM_017940	NP_060410	Q3BBV0	NBPF1_HUMAN	hypothetical protein LOC55672	706						cytoplasm					0				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		CACCTTACCTGGGCTGAGCTT	0.537000													15	588					0	0	0.076483	0	0
MST1P2	11209	broad.mit.edu	37	1	16974224	16974224	+	RNA	SNP	C	G	G	rs148702086	by1000genomes	TCGA-CS-4944-01A-01D-1468-08	TCGA-CS-4944-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	471d39e4-2d0b-4f56-8e98-216f5a1baf5d	c4d192e1-a280-4ca9-963d-dc5efaacb683	g.chr1:16974224C>G	uc009vow.2	+	5		c.1034C>G			MST1P2_uc010ocg.1_RNA|MST1P2_uc010och.1_Intron|MST1P2_uc010oci.1_RNA|MST1P2_uc001azk.2_Intron|MST1P2_uc001azl.3_RNA|MST1P2_uc009vox.2_Intron|MST1P2_uc001azm.3_Intron					Homo sapiens cDNA FLJ53774 complete cds, moderately similar to Hepatocyte growth factor-like protein precursor.												0						TTGGTCCCAGCCCCAGAGGGA	0.652000													4	12					0	0	0.021553	0	0
NBPF10	100132406	broad.mit.edu	37	1	145296373	145296373	+	Missense_Mutation	SNP	G	T	T	rs3969711		TCGA-CS-4944-01A-01D-1468-08	TCGA-CS-4944-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	471d39e4-2d0b-4f56-8e98-216f5a1baf5d	c4d192e1-a280-4ca9-963d-dc5efaacb683	g.chr1:145296373G>T	uc001end.3	+	3	330	c.295G>T	c.(295-297)GTT>TTT	p.V99F	NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NBPF10_uc001emp.3_Missense_Mutation_p.V99F|NBPF10_uc001emq.1_Intron	NM_001039703	NP_001034792	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC100132406	99											0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		TAAAGTCCTAGTTCACTCTCA	0.473000													5	89					5.18039e-06	5.88044e-06	0.038147	1	0
CDC42BPA	8476	broad.mit.edu	37	1	227348328	227348328	+	Silent	SNP	T	C	C			TCGA-CS-4944-01A-01D-1468-08	TCGA-CS-4944-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	471d39e4-2d0b-4f56-8e98-216f5a1baf5d	c4d192e1-a280-4ca9-963d-dc5efaacb683	g.chr1:227348328T>C	uc001hqr.2	-	6	1552	c.609A>G	c.(607-609)AAA>AAG	p.K203K	CDC42BPA_uc001hqs.2_Silent_p.K203K|CDC42BPA_uc009xes.2_Silent_p.K203K|CDC42BPA_uc010pvs.1_Silent_p.K203K	NM_003607	NP_003598	Q5VT25	MRCKA_HUMAN	CDC42-binding protein kinase alpha isoform B	203	Protein kinase.				actin cytoskeleton reorganization|intracellular signal transduction	cell leading edge|cell-cell junction|cytoplasm	ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity			lung(6)|breast(2)|stomach(1)|ovary(1)|pancreas(1)	11		all_cancers(173;0.156)|Prostate(94;0.0792)				TATTGTCAGGTTTAATGTCTC	0.284000													50	99					0	0	0.048971	0	0
OR14A16	284532	broad.mit.edu	37	1	247978653	247978653	+	Missense_Mutation	SNP	G	T	T			TCGA-CS-4944-01A-01D-1468-08	TCGA-CS-4944-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	471d39e4-2d0b-4f56-8e98-216f5a1baf5d	c4d192e1-a280-4ca9-963d-dc5efaacb683	g.chr1:247978653G>T	uc001idm.1	-	1	379	c.379C>A	c.(379-381)CCT>ACT	p.P127T		NM_001001966	NP_001001966	Q8NHC5	O14AG_HUMAN	olfactory receptor, family 14, subfamily A,	127	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						TAGTGCAGAGGGTGACATATA	0.512000													55	126					1.14385e-22	1.3345e-22	0.048971	1	0
SFMBT2	57713	broad.mit.edu	37	10	7214050	7214050	+	Missense_Mutation	SNP	C	T	T			TCGA-CS-4944-01A-01D-1468-08	TCGA-CS-4944-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	471d39e4-2d0b-4f56-8e98-216f5a1baf5d	c4d192e1-a280-4ca9-963d-dc5efaacb683	g.chr10:7214050C>T	uc009xio.1	-	19	2313	c.2222G>A	c.(2221-2223)CGG>CAG	p.R741Q	SFMBT2_uc001ijn.1_Missense_Mutation_p.R741Q|SFMBT2_uc010qay.1_Missense_Mutation_p.R576Q	NM_001029880	NP_001025051	Q5VUG0	SMBT2_HUMAN	Scm-like with four mbt domains 2	741					regulation of transcription, DNA-dependent	nucleus				ovary(4)|upper_aerodigestive_tract(2)|large_intestine(1)|central_nervous_system(1)	8						CTGGTCATCCCGGAGCTCGGA	0.692000													9	16					0	0	0.080935	0	0
KIF20B	9585	broad.mit.edu	37	10	91477448	91477448	+	Missense_Mutation	SNP	A	G	G			TCGA-CS-4944-01A-01D-1468-08	TCGA-CS-4944-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	471d39e4-2d0b-4f56-8e98-216f5a1baf5d	c4d192e1-a280-4ca9-963d-dc5efaacb683	g.chr10:91477448A>G	uc001kgs.1	+	11	1312	c.1240A>G	c.(1240-1242)ATT>GTT	p.I414V	KIF20B_uc001kgr.1_Missense_Mutation_p.I414V	NM_016195	NP_057279	Q96Q89	KI20B_HUMAN	M-phase phosphoprotein 1	414					cell cycle arrest|cell division|microtubule-based movement|mitosis|regulation of mitosis	centrosome|microtubule|nucleolus|nucleoplasm|spindle	ATP binding|ATPase activity|microtubule motor activity|WW domain binding			ovary(1)|pancreas(1)|skin(1)	3						GGGAAAGTGTATTAACGTCTT	0.313000													6	194					0	0	0.021553	0	0
C10orf12	26148	broad.mit.edu	37	10	98709000	98709000	+	Missense_Mutation	SNP	C	G	G			TCGA-CS-4944-01A-01D-1468-08	TCGA-CS-4944-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	471d39e4-2d0b-4f56-8e98-216f5a1baf5d	c4d192e1-a280-4ca9-963d-dc5efaacb683	g.chr10:98709000C>G	uc009xvg.1	+	6	707	c.186C>G	c.(184-186)GAC>GAG	p.D62E	LCOR_uc001kmr.2_Missense_Mutation_p.D62E|LCOR_uc001kms.1_Missense_Mutation_p.D62E|LCOR_uc001kmt.1_Missense_Mutation_p.D62E|LCOR_uc001kmu.1_Missense_Mutation_p.D62E	NM_015652	NP_056467	Q8N655	CJ012_HUMAN	hypothetical protein LOC26148	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment										skin(2)	2		Colorectal(252;0.172)		Epithelial(162;6.35e-09)|all cancers(201;3.21e-07)		CTGACCAAGACTCACCTCTGG	0.483000													77	125					0	0	0.048971	0	0
PTPN5	84867	broad.mit.edu	37	11	18754164	18754164	+	Missense_Mutation	SNP	T	C	C			TCGA-CS-4944-01A-01D-1468-08	TCGA-CS-4944-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	471d39e4-2d0b-4f56-8e98-216f5a1baf5d	c4d192e1-a280-4ca9-963d-dc5efaacb683	g.chr11:18754164T>C	uc001mpd.2	-	12	1735	c.1304A>G	c.(1303-1305)TAC>TGC	p.Y435C	PTPN5_uc001mpb.2_Missense_Mutation_p.Y403C|PTPN5_uc001mpc.2_Missense_Mutation_p.Y435C|PTPN5_uc001mpe.2_Missense_Mutation_p.Y403C|PTPN5_uc010rdj.1_Missense_Mutation_p.Y379C|PTPN5_uc001mpf.2_Missense_Mutation_p.Y411C|PTPN5_uc010rdk.1_Missense_Mutation_p.Y380C	NM_006906	NP_008837	P54829	PTN5_HUMAN	protein-tyrosine-phosphatase non-receptor 5	435	Tyrosine-protein phosphatase.					integral to membrane	phosphotyrosine binding|protein tyrosine phosphatase activity			ovary(2)	2						TCGCAGCCGGTAATCCTCCGT	0.592000											OREG0020824	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	6	258					0	0	0.038147	0	0
CLIP1	6249	broad.mit.edu	37	12	122758652	122758652	+	Missense_Mutation	SNP	T	C	C			TCGA-CS-4944-01A-01D-1468-08	TCGA-CS-4944-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	471d39e4-2d0b-4f56-8e98-216f5a1baf5d	c4d192e1-a280-4ca9-963d-dc5efaacb683	g.chr12:122758652T>C	uc001ucg.1	-	24	4130	c.4024A>G	c.(4024-4026)ATG>GTG	p.M1342V	CLIP1_uc001uch.1_Missense_Mutation_p.M1331V|CLIP1_uc001uci.1_Missense_Mutation_p.M1296V|CLIP1_uc001ucf.1_Missense_Mutation_p.M1V	NM_002956	NP_002947	P30622	CLIP1_HUMAN	restin isoform a	1342	Potential.				mitotic prometaphase|positive regulation of microtubule polymerization	centrosome|cytosol|endosome|intermediate filament|kinetochore	nucleic acid binding|protein homodimerization activity|zinc ion binding			ovary(2)|breast(1)	3	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.81e-05)|Epithelial(86;6.85e-05)|BRCA - Breast invasive adenocarcinoma(302;0.226)		TCCACCTTCATCTTGAGGTCT	0.338000													127	197					0	0	0.048971	0	0
SMOC1	64093	broad.mit.edu	37	14	70490099	70490099	+	Missense_Mutation	SNP	A	T	T			TCGA-CS-4944-01A-01D-1468-08	TCGA-CS-4944-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	471d39e4-2d0b-4f56-8e98-216f5a1baf5d	c4d192e1-a280-4ca9-963d-dc5efaacb683	g.chr14:70490099A>T	uc001xls.1	+	11	1479	c.1226A>T	c.(1225-1227)GAC>GTC	p.D409V	SMOC1_uc001xlt.1_Missense_Mutation_p.D409V	NM_022137	NP_071420	Q9H4F8	SMOC1_HUMAN	secreted modular calcium-binding protein 1	409	2 (Potential).|EF-hand 2.				cell differentiation|eye development|limb development|regulation of osteoblast differentiation|signal transduction	basement membrane	calcium ion binding			upper_aerodigestive_tract(1)|pancreas(1)	2				all cancers(60;0.00417)|BRCA - Breast invasive adenocarcinoma(234;0.0119)|OV - Ovarian serous cystadenocarcinoma(108;0.028)		GACTACTGTGACCTGAACAAA	0.522000													5	176					0	0	0.014758	0	0
TSHR	7253	broad.mit.edu	37	14	81610525	81610525	+	Missense_Mutation	SNP	G	T	T			TCGA-CS-4944-01A-01D-1468-08	TCGA-CS-4944-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	471d39e4-2d0b-4f56-8e98-216f5a1baf5d	c4d192e1-a280-4ca9-963d-dc5efaacb683	g.chr14:81610525G>T	uc001xvd.1	+	10	2279	c.2123G>T	c.(2122-2124)GGG>GTG	p.G708V		NM_000369	NP_000360	P16473	TSHR_HUMAN	thyroid stimulating hormone receptor isoform 1	708	Cytoplasmic (Potential).				cell-cell signaling|positive regulation of cell proliferation	integral to plasma membrane	protein binding|thyroid-stimulating hormone receptor activity			thyroid(289)|ovary(5)|lung(3)|kidney(1)|skin(1)	299				BRCA - Breast invasive adenocarcinoma(234;0.0402)	Thyrotropin Alfa(DB00024)	GCATACCGGGGGCAGAGGGTT	0.498000			Mis		toxic thyroid adenoma	thyroid  adenoma	Hereditary nonautoimmune hyperthyroidism; subclinical hypothyroidism 						58	113					1.20869e-33	1.45043e-33	0.048971	1	0
GABRG3	2567	broad.mit.edu	37	15	27574011	27574011	+	Missense_Mutation	SNP	T	C	C			TCGA-CS-4944-01A-01D-1468-08	TCGA-CS-4944-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	471d39e4-2d0b-4f56-8e98-216f5a1baf5d	c4d192e1-a280-4ca9-963d-dc5efaacb683	g.chr15:27574011T>C	uc001zbg.1	+	5	716	c.550T>C	c.(550-552)TCC>CCC	p.S184P	GABRG3_uc001zbf.2_Missense_Mutation_p.S184P	NM_033223	NP_150092	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma	184	Extracellular (Probable).				gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity				0		all_lung(180;4.58e-12)|Breast(32;0.000625)|Colorectal(260;0.235)		all cancers(64;3.15e-07)|Epithelial(43;1.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0261)		GGACGAACACTCCTGCCCGCT	0.557000													14	31					0	0	0.020292	0	0
MTMR15	22909	broad.mit.edu	37	15	31202868	31202868	+	Missense_Mutation	SNP	A	G	G			TCGA-CS-4944-01A-01D-1468-08	TCGA-CS-4944-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	471d39e4-2d0b-4f56-8e98-216f5a1baf5d	c4d192e1-a280-4ca9-963d-dc5efaacb683	g.chr15:31202868A>G	uc001zff.2	+	4	1718	c.1427A>G	c.(1426-1428)GAA>GGA	p.E476G	MTMR15_uc001zfc.3_Missense_Mutation_p.E476G|MTMR15_uc010azw.2_Missense_Mutation_p.E476G|MTMR15_uc001zfd.3_Missense_Mutation_p.E476G|MTMR15_uc001zfe.2_Missense_Mutation_p.E81G	NM_014967	NP_055782	Q9Y2M0	FAN1_HUMAN	myotubularin related protein 15 isoform a	476					double-strand break repair via homologous recombination|nucleotide-excision repair, DNA incision	nucleus	5'-3' exonuclease activity|5'-flap endonuclease activity|DNA binding|magnesium ion binding|phosphodiesterase I activity|ubiquitin binding				0		all_lung(180;2.23e-09)		all cancers(64;4.72e-15)|Epithelial(43;5.4e-11)|GBM - Glioblastoma multiforme(186;0.000136)|BRCA - Breast invasive adenocarcinoma(123;0.00402)|Lung(196;0.168)		TCTGCTCCTGAACTAAAATCC	0.398000								Direct_reversal_of_damage|Editing_and_processing_nucleases					6	108					0	0	0.029380	0	0
HPR	3250	broad.mit.edu	37	16	72110680	72110680	+	Silent	SNP	C	T	T			TCGA-CS-4944-01A-01D-1468-08	TCGA-CS-4944-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	471d39e4-2d0b-4f56-8e98-216f5a1baf5d	c4d192e1-a280-4ca9-963d-dc5efaacb683	g.chr16:72110680C>T	uc002fby.2	+	5	777	c.747C>T	c.(745-747)TAC>TAT	p.Y249Y	TXNL4B_uc010cgl.2_Intron	NM_020995	NP_066275	P00739	HPTR_HUMAN	haptoglobin-related protein precursor	249	Peptidase S1.				proteolysis	spherical high-density lipoprotein particle	hemoglobin binding|serine-type endopeptidase activity			central_nervous_system(1)	1		Ovarian(137;0.125)				CTGACCAATACGATTGCATAA	0.507000													35	67					0	0	0.054565	0	0
DMKN	93099	broad.mit.edu	37	19	36002345	36002345	+	Missense_Mutation	SNP	T	C	C			TCGA-CS-4944-01A-01D-1468-08	TCGA-CS-4944-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	471d39e4-2d0b-4f56-8e98-216f5a1baf5d	c4d192e1-a280-4ca9-963d-dc5efaacb683	g.chr19:36002345T>C	uc002nzm.3	-	5	1069	c.886A>G	c.(886-888)AGC>GGC	p.S296G	DMKN_uc002nzj.2_5'Flank|DMKN_uc002nzk.3_5'Flank|DMKN_uc002nzl.3_5'Flank|DMKN_uc002nzo.3_Intron|DMKN_uc002nzn.3_Intron|DMKN_uc002nzw.2_5'Flank|DMKN_uc002nzr.2_5'Flank|DMKN_uc002nzp.2_5'Flank|DMKN_uc002nzq.2_5'Flank|DMKN_uc002nzt.2_5'Flank|DMKN_uc002nzs.2_5'Flank|DMKN_uc002nzu.2_5'Flank|DMKN_uc002nzv.2_5'Flank|DMKN_uc010xsv.1_5'Flank|DMKN_uc010xsw.1_5'Flank|DMKN_uc002nzx.3_5'Flank|DMKN_uc002nzy.3_5'Flank|DMKN_uc002nzz.2_RNA|DMKN_uc002oac.3_Missense_Mutation_p.S296G|DMKN_uc010eeb.2_Missense_Mutation_p.S296G|DMKN_uc002oaa.3_Missense_Mutation_p.S296G|DMKN_uc002oab.3_Missense_Mutation_p.S296G	NM_033317	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine isoform 2 precursor	296	Gly-rich.					extracellular region				large_intestine(1)|ovary(1)|skin(1)	3	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			TCACCTctgctgccaccactg	0.308000													6	4					0	0	0.093190	0	0
MLL4	9757	broad.mit.edu	37	19	36218411	36218411	+	Missense_Mutation	SNP	C	T	T			TCGA-CS-4944-01A-01D-1468-08	TCGA-CS-4944-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	471d39e4-2d0b-4f56-8e98-216f5a1baf5d	c4d192e1-a280-4ca9-963d-dc5efaacb683	g.chr19:36218411C>T	uc010eei.2	+	17	4190	c.4190C>T	c.(4189-4191)GCG>GTG	p.A1397V		NM_014727	NP_055542	Q9UMN6	MLL4_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 4	1397					chromatin-mediated maintenance of transcription		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			central_nervous_system(6)|breast(2)|ovary(1)|kidney(1)|skin(1)	11	all_lung(56;3.33e-07)|Lung NSC(56;5.02e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GCTGGGGCAGCGCAGCCCCGC	0.657000													5	152					0	0	0.029380	0	0
FAM179A	165186	broad.mit.edu	37	2	29247207	29247207	+	Missense_Mutation	SNP	G	A	A			TCGA-CS-4944-01A-01D-1468-08	TCGA-CS-4944-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	471d39e4-2d0b-4f56-8e98-216f5a1baf5d	c4d192e1-a280-4ca9-963d-dc5efaacb683	g.chr2:29247207G>A	uc010ezl.2	+	13	2171	c.1820G>A	c.(1819-1821)CGC>CAC	p.R607H	FAM179A_uc010ymm.1_Missense_Mutation_p.R552H|FAM179A_uc002rmr.3_Missense_Mutation_p.R134H	NM_199280	NP_954974	Q6ZUX3	F179A_HUMAN	hypothetical protein LOC165186	607							binding			ovary(3)|skin(1)	4						ACCCTTGCCCGCTCCCTGGTG	0.478000													5	19					0	0	0.021553	0	0
WDR75	84128	broad.mit.edu	37	2	190313123	190313123	+	Silent	SNP	T	C	C			TCGA-CS-4944-01A-01D-1468-08	TCGA-CS-4944-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	471d39e4-2d0b-4f56-8e98-216f5a1baf5d	c4d192e1-a280-4ca9-963d-dc5efaacb683	g.chr2:190313123T>C	uc002uql.1	+	2	165	c.105T>C	c.(103-105)TCT>TCC	p.S35S	WDR75_uc002uqm.1_5'UTR|WDR75_uc002uqn.1_5'UTR	NM_032168	NP_115544	Q8IWA0	WDR75_HUMAN	WD repeat domain 75	35	WD 1.					nucleolus				ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(117;0.00105)|Epithelial(96;0.0129)|all cancers(119;0.0456)			TCTGTGTCTCTGGAGACTTTG	0.294000													33	55					0	0	0.054565	0	0
IDH1	3417	broad.mit.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	T	T	rs121913500		TCGA-CS-4944-01A-01D-1468-08	TCGA-CS-4944-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	471d39e4-2d0b-4f56-8e98-216f5a1baf5d	c4d192e1-a280-4ca9-963d-dc5efaacb683	g.chr2:209113112C>T	uc002vcs.2	-	4	641	c.395G>A	c.(394-396)CGT>CAT	p.R132H	IDH1_uc002vct.2_Missense_Mutation_p.R132H|IDH1_uc002vcu.2_Missense_Mutation_p.R132H	NM_005896	NP_005887	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132		Substrate.	R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation).|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate).		2-oxoglutarate metabolic process|cellular lipid metabolic process|glyoxylate cycle|isocitrate metabolic process|NADPH regeneration|tricarboxylic acid cycle	cytosol|peroxisomal matrix	isocitrate dehydrogenase (NADP+) activity|magnesium ion binding|NAD binding|protein homodimerization activity	p.R132H(2023)|p.R132C(344)|p.R132?(210)|p.R132G(117)|p.R132S(79)|p.R132L(58)|p.R132V(1)|p.G131_R132>VL(1)		central_nervous_system(2156)|haematopoietic_and_lymphoid_tissue(606)|bone(74)|thyroid(22)|large_intestine(4)|skin(2)|prostate(2)|autonomic_ganglia(1)|soft_tissue(1)	2868				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		ATAAGCATGACGACCTATGAT	0.393000			Mis		gliobastoma 								28	63					0	0	0.037714	0	0
COL6A3	1293	broad.mit.edu	37	2	238280668	238280668	+	Missense_Mutation	SNP	C	T	T			TCGA-CS-4944-01A-01D-1468-08	TCGA-CS-4944-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	471d39e4-2d0b-4f56-8e98-216f5a1baf5d	c4d192e1-a280-4ca9-963d-dc5efaacb683	g.chr2:238280668C>T	uc002vwl.2	-	9	4277	c.3992G>A	c.(3991-3993)CGC>CAC	p.R1331H	COL6A3_uc002vwo.2_Missense_Mutation_p.R1125H|COL6A3_uc010znj.1_Missense_Mutation_p.R724H|COL6A3_uc002vwq.2_Missense_Mutation_p.R1125H|COL6A3_uc002vwr.2_Missense_Mutation_p.R924H	NM_004369	NP_004360	P12111	CO6A3_HUMAN	alpha 3 type VI collagen isoform 1 precursor	1331	VWFA 7.|Nonhelical region.				axon guidance|cell adhesion|muscle organ development	collagen type VI|extracellular space	serine-type endopeptidase inhibitor activity			ovary(8)|central_nervous_system(6)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	18		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		CTCTTCAATGCGGCTCCCCAG	0.632000													28	39					0	0	0.108266	0	0
COL18A1	80781	broad.mit.edu	37	21	46925852	46925852	+	Missense_Mutation	SNP	G	A	A			TCGA-CS-4944-01A-01D-1468-08	TCGA-CS-4944-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	471d39e4-2d0b-4f56-8e98-216f5a1baf5d	c4d192e1-a280-4ca9-963d-dc5efaacb683	g.chr21:46925852G>A	uc011afs.1	+	37	4445	c.4424G>A	c.(4423-4425)CGC>CAC	p.R1475H	COL18A1_uc002zhg.2_Missense_Mutation_p.R1060H|COL18A1_uc002zhi.2_Missense_Mutation_p.R1240H|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_Missense_Mutation_p.R41H|COL18A1_uc002zhk.2_5'Flank	NM_130444	NP_569711	P39060	COIA1_HUMAN	alpha 1 type XVIII collagen isoform 3 precursor	1478	Nonhelical region 11 (NC11).				cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception	collagen|extracellular space	extracellular matrix structural constituent|metal ion binding|protein binding			central_nervous_system(1)	1				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		CTCTACGTCCGCGTGCAGAAC	0.667000													41	91					0	0	0.111260	0	0
KIF9	64147	broad.mit.edu	37	3	47312946	47312946	+	Silent	SNP	A	G	G			TCGA-CS-4944-01A-01D-1468-08	TCGA-CS-4944-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	471d39e4-2d0b-4f56-8e98-216f5a1baf5d	c4d192e1-a280-4ca9-963d-dc5efaacb683	g.chr3:47312946A>G	uc010hjp.2	-	6	976	c.372T>C	c.(370-372)TTT>TTC	p.F124F	KIF9_uc003cqx.2_Silent_p.F124F|KIF9_uc003cqy.2_Silent_p.F124F|KIF9_uc011bat.1_RNA|KIF9_uc011bau.1_RNA	NM_001134878	NP_001128350	Q9HAQ2	KIF9_HUMAN	kinesin family member 9 isoform 2	124	Kinesin-motor.				blood coagulation|microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(1)	1		Acute lymphoblastic leukemia(5;0.164)		BRCA - Breast invasive adenocarcinoma(193;0.000284)|KIRC - Kidney renal clear cell carcinoma(197;0.00609)|Kidney(197;0.007)		CGATCATCCTAAAAACCTAGA	0.483000													3	114					0	0	0.009096	0	0
SLC25A36	55186	broad.mit.edu	37	3	140682063	140682063	+	Missense_Mutation	SNP	A	G	G			TCGA-CS-4944-01A-01D-1468-08	TCGA-CS-4944-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	471d39e4-2d0b-4f56-8e98-216f5a1baf5d	c4d192e1-a280-4ca9-963d-dc5efaacb683	g.chr3:140682063A>G	uc003etr.2	+	4	614	c.379A>G	c.(379-381)ATG>GTG	p.M127V	SLC25A36_uc003etp.2_Missense_Mutation_p.M127V|SLC25A36_uc003ets.2_Missense_Mutation_p.M127V|SLC25A36_uc003etq.2_5'UTR|SLC25A36_uc011bmz.1_Missense_Mutation_p.M101V	NM_001104647	NP_001098117	Q96CQ1	S2536_HUMAN	solute carrier family 25, member 36 isoform a	127	Helical; Name=3; (Potential).|Solcar 2.				response to estradiol stimulus|transmembrane transport	integral to membrane|mitochondrial inner membrane	binding				0						TTCAGCTGCAATGGCAGGTAT	0.289000													45	85					0	0	0.104719	0	0
MUC4	4585	broad.mit.edu	37	3	195505813	195505814	+	Missense_Mutation	DNP	TC	CT	CT			TCGA-CS-4944-01A-01D-1468-08	TCGA-CS-4944-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	471d39e4-2d0b-4f56-8e98-216f5a1baf5d	c4d192e1-a280-4ca9-963d-dc5efaacb683	g.chr3:195505813_195505814TC>CT	uc011bto.1	-	3	12713_12714	c.12253_12254GA>AG	c.(12253-12255)GAC>AGC	p.D4085S	MUC4_uc003fva.2_5'Flank|MUC4_uc003fvb.2_5'Flank|MUC4_uc003fvc.2_5'Flank|MUC4_uc003fvd.2_5'Flank|MUC4_uc003fve.2_5'Flank|MUC4_uc010hzr.2_5'Flank|MUC4_uc011btf.1_Intron|MUC4_uc011btg.1_Intron|MUC4_uc011bth.1_Intron|MUC4_uc011bti.1_Intron|MUC4_uc011btj.1_Intron|MUC4_uc011btk.1_Intron|MUC4_uc011btl.1_Intron|MUC4_uc011btm.1_Intron|MUC4_uc011btn.1_Intron|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGAGGAAGTGTCGGTGACAGGA	0.594000													2	3					0	0	0.004672	0	0
UGT2A3	79799	broad.mit.edu	37	4	69795535	69795535	+	Missense_Mutation	SNP	T	C	C			TCGA-CS-4944-01A-01D-1468-08	TCGA-CS-4944-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	471d39e4-2d0b-4f56-8e98-216f5a1baf5d	c4d192e1-a280-4ca9-963d-dc5efaacb683	g.chr4:69795535T>C	uc003hef.2	-	6	1611	c.1580A>G	c.(1579-1581)GAA>GGA	p.E527G	UGT2A3_uc010ihp.1_RNA	NM_024743	NP_079019	Q6UWM9	UD2A3_HUMAN	UDP glucuronosyltransferase 2 family,	527	Cytoplasmic (Potential).					integral to membrane	glucuronosyltransferase activity			ovary(1)|skin(1)	2						AAAGATCTATTCCCTCTTTTC	0.328000													35	67					0	0	0.059317	0	0
ZNF12	7559	broad.mit.edu	37	7	6737039	6737039	+	Missense_Mutation	SNP	T	A	A			TCGA-CS-4944-01A-01D-1468-08	TCGA-CS-4944-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	471d39e4-2d0b-4f56-8e98-216f5a1baf5d	c4d192e1-a280-4ca9-963d-dc5efaacb683	g.chr7:6737039T>A	uc003sqt.1	-	4	723	c.169A>T	c.(169-171)ATC>TTC	p.I57F	ZNF12_uc011jxa.1_5'UTR|ZNF12_uc003sqs.1_Missense_Mutation_p.I57F	NM_016265	NP_057349	P17014	ZNF12_HUMAN	zinc finger protein 12 isoform a	57	KRAB.				negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Ovarian(82;0.0776)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0231)		AACTTGCTGATAACATCCGGT	0.463000													10	14					0	0	0.105934	0	0
LOC442308	442308	broad.mit.edu	37	7	55713317	55713317	+	RNA	SNP	A	C	C	rs62455728	by1000genomes	TCGA-CS-4944-01A-01D-1468-08	TCGA-CS-4944-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	471d39e4-2d0b-4f56-8e98-216f5a1baf5d	c4d192e1-a280-4ca9-963d-dc5efaacb683	g.chr7:55713317A>C	uc010kzj.2	+	1		c.6A>C				NR_003598				Homo sapiens similar to tubulin, beta 5 (LOC442308), non-coding RNA.												0						TTAACCATGAAGGAAATTGTG	0.428000													5	20					0	0	0.021553	0	0
DLX5	1749	broad.mit.edu	37	7	96651642	96651642	+	Missense_Mutation	SNP	C	A	A			TCGA-CS-4944-01A-01D-1468-08	TCGA-CS-4944-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	471d39e4-2d0b-4f56-8e98-216f5a1baf5d	c4d192e1-a280-4ca9-963d-dc5efaacb683	g.chr7:96651642C>A	uc003uon.2	-	2	603	c.395G>T	c.(394-396)GGC>GTC	p.G132V	DLX5_uc011kim.1_Missense_Mutation_p.G132V	NM_005221	NP_005212	P56178	DLX5_HUMAN	distal-less homeobox 5	132					cell proliferation|endochondral ossification|osteoblast differentiation|positive regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			ovary(1)	1	all_cancers(62;9.56e-09)|all_epithelial(64;7.38e-09)|Esophageal squamous(72;0.0125)|all_lung(186;0.0855)|Lung NSC(181;0.0858)					CTTTGGTTTGCCATTCACCAT	0.463000													53	89					7.91745e-34	9.78038e-34	0.048971	1	0
FAM83H	286077	broad.mit.edu	37	8	144808629	144808629	+	Missense_Mutation	SNP	C	T	T			TCGA-CS-4944-01A-01D-1468-08	TCGA-CS-4944-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	471d39e4-2d0b-4f56-8e98-216f5a1baf5d	c4d192e1-a280-4ca9-963d-dc5efaacb683	g.chr8:144808629C>T	uc003yzk.2	-	5	3071	c.3002G>A	c.(3001-3003)CGT>CAT	p.R1001H	FAM83H_uc010mfk.1_RNA	NM_198488	NP_940890	Q6ZRV2	FA83H_HUMAN	FAM83H	1001					biomineral tissue development					lung(1)|central_nervous_system(1)|pancreas(1)	3	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			CAGTGACAGACGCCGCGGGCT	0.697000													6	8					0	0	0.029380	0	0
Unknown	0	broad.mit.edu	37	9	74622941	74622941	+	RNA	SNP	G	T	T	rs11143055	by1000genomes	TCGA-CS-4944-01A-01D-1468-08	TCGA-CS-4944-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	471d39e4-2d0b-4f56-8e98-216f5a1baf5d	c4d192e1-a280-4ca9-963d-dc5efaacb683	g.chr9:74622941G>T	uc011lsc.1	-	1		c.112C>A				NR_024392				Homo sapiens heat shock 27kDa protein-like 2 pseudogene (HSPBL2), non-coding RNA.																		TGCCCTCAGGGGACAGGGAGG	0.647000													3	18					0.004672	0.00516379	0.004672	1	0
SLC7A3	84889	broad.mit.edu	37	X	70148834	70148834	+	Missense_Mutation	SNP	C	A	A			TCGA-CS-4944-01A-01D-1468-08	TCGA-CS-4944-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	471d39e4-2d0b-4f56-8e98-216f5a1baf5d	c4d192e1-a280-4ca9-963d-dc5efaacb683	g.chrX:70148834C>A	uc004dyn.2	-	3	547	c.389G>T	c.(388-390)CGG>CTG	p.R130L	SLC7A3_uc004dyo.2_Missense_Mutation_p.R130L	NM_032803	NP_116192	Q8WY07	CTR3_HUMAN	solute carrier family 7 (cationic amino acid	130	Extracellular (Potential).				cellular nitrogen compound metabolic process	integral to membrane|plasma membrane				ovary(1)|kidney(1)	2	Renal(35;0.156)				L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)	GCTCCAGGCCCGGGCCACACT	0.547000													3	46					0.00909568	0.00979535	0.009096	1	0
PIK3R1	5295	broad.mit.edu	37	5	67522794	67522795	+	Frame_Shift_Ins	INS	-	G	G			TCGA-CS-4944-01A-01D-1468-08	TCGA-CS-4944-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	471d39e4-2d0b-4f56-8e98-216f5a1baf5d	c4d192e1-a280-4ca9-963d-dc5efaacb683	g.chr5:67522794_67522795insG	uc003jva.2	+	2	851_852	c.291_292insG	c.(289-294)GTTGCAfs	p.V97fs	PIK3R1_uc003jvb.2_Frame_Shift_Ins_p.V97fs	NM_181523	NP_852664	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1	97_98					epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|growth hormone receptor signaling pathway|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|interspecies interaction between organisms|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol phosphorylation|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|T cell costimulation|T cell receptor signaling pathway	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex	1-phosphatidylinositol binding|ErbB-3 class receptor binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase regulator activity|protein phosphatase binding			endometrium(34)|central_nervous_system(27)|large_intestine(20)|breast(7)|ovary(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|urinary_tract(1)|skin(1)|pancreas(1)	101		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoproterenol(DB01064)	CTCTTCCTGTTGCACCAGGTTC	0.455			Mis|F|O		gliobastoma|ovarian|colorectal					TCGA GBM(4;<1E-08)			36	98	---	---	---	---					
KDM4C	23081	broad.mit.edu	37	9	7128074	7128075	+	Frame_Shift_Del	DEL	GG	-	-			TCGA-CS-4944-01A-01D-1468-08	TCGA-CS-4944-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	471d39e4-2d0b-4f56-8e98-216f5a1baf5d	c4d192e1-a280-4ca9-963d-dc5efaacb683	g.chr9:7128074_7128075delGG	uc003zkh.2	+	19	3199_3200	c.2619_2620delGG	c.(2617-2622)AAGGCTfs	p.K873fs	KDM4C_uc011lmj.1_RNA|KDM4C_uc003zkg.2_Frame_Shift_Del_p.K873fs|KDM4C_uc011lmk.1_Frame_Shift_Del_p.K618fs|KDM4C_uc011lml.1_Frame_Shift_Del_p.K560fs	NM_015061	NP_055876	Q9H3R0	KDM4C_HUMAN	jumonji domain containing 2C isoform 1	873_874					positive regulation of cell proliferation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription, DNA-dependent	nuclear chromatin	androgen receptor binding|enzyme binding|histone demethylase activity (H3-K9 specific)|nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1						AGAAGTCCAAGGCTTGCGAGAA	0.317													34	79	---	---	---	---					
