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_alt_allele	validation_method	validation_status	validation_tumor_sample	pox	qox	pox_cutoff	isArtifactMode	oxoGCut
KRTAP4-6	81871	broad.mit.edu	37	17	39296466	39296466	+	Missense_Mutation	SNP	G	G	A	rs35985080	by1000genomes	TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr17:39296466G>A	ENST00000345847.4	-	1	273	c.274C>T	c.(274-276)Ccc>Tcc	p.P92S		NM_030976.1	NP_112238.1	Q9BYQ5	KRA46_HUMAN	keratin associated protein 4-6	88	29 X 5 AA repeats of C-C-[IRQVEL]-[SPTR]- [STVQRCP].					keratin filament				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(1)|prostate(1)|urinary_tract(1)	9						CAGCACTGGGGTCTGCAGCAG	0.657000													6	70					0	0	1	0	0
PTPN11	5781	broad.mit.edu	37	12	112888197	112888197	+	Missense_Mutation	SNP	T	T	A			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr12:112888197T>A	ENST00000351677.2	+	3	411	c.213T>A	c.(211-213)ttT>ttA	p.F71L	PTPN11_ENST00000392597.1_Missense_Mutation_p.F71L	NM_002834.3	NP_002825.3	Q06124	PTN11_HUMAN	protein tyrosine phosphatase, non-receptor type 11	71	SH2 1.		F -> K (in acute myeloid leukemia; requires 2 nucleotide substitutions).|F -> L (in myelodysplastic syndrome).		axon guidance|cell junction assembly|ephrin receptor signaling pathway|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|interferon-gamma-mediated signaling pathway|leukocyte migration|platelet activation|regulation of cell adhesion mediated by integrin|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|T cell costimulation|type I interferon-mediated signaling pathway	cytosol	non-membrane spanning protein tyrosine phosphatase activity|protein binding	p.F71L(5)|p.F71K(1)		NS(1)|autonomic_ganglia(2)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(406)|kidney(2)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(3)|stomach(3)	451						GGGAGAAATTTGCCACTTTGG	0.418000			Mis		"""JMML, AML, MDS"""		Noonan Syndrome		Noonan syndrome				50	97					0	0	1	0	0
DNAH8	1769	broad.mit.edu	37	6	38810444	38810444	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr6:38810444G>A	ENST00000359357.3	+	33	4213	c.3959G>A	c.(3958-3960)cGt>cAt	p.R1320H	DNAH8_ENST00000441566.1_Missense_Mutation_p.R1320H|DNAH8_ENST00000449981.2_Missense_Mutation_p.R1537H					dynein, axonemal, heavy chain 8											NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						GAAAGATGTCGTAAACTTCCA	0.323000													24	67					0	0	1	0	0
APEX2	27301	broad.mit.edu	37	X	55033116	55033116	+	Missense_Mutation	SNP	C	C	T	rs145122391		TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chrX:55033116C>T	ENST00000374987.3	+	6	871	c.805C>T	c.(805-807)Cat>Tat	p.H269Y	APEX2_ENST00000471758.1_3'UTR	NM_014481.2	NP_055296.2	Q9UBZ4	APEX2_HUMAN	APEX nuclease (apurinic/apyrimidinic endonuclease) 2	269			H -> Y (identified in a patient with mtDNA maintenance disorders).		cell cycle|DNA recombination|DNA repair	nucleus	DNA binding|DNA-(apurinic or apyrimidinic site) lyase activity|endonuclease activity|exonuclease activity|zinc ion binding			breast(1)|endometrium(8)|large_intestine(4)|lung(6)|prostate(1)|urinary_tract(1)	21						TGGCGCCCGCCATCTCAACTA	0.597000								Other BER factors					3	22					0	0	1	0	0
SDHAP1	0	broad.mit.edu	37	3	195712586	195712586	+	RNA	SNP	C	C	T			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr3:195712586C>T	ENST00000427841.1	-	0	250					NR_003264.2																						AAATGCAGCTCGCAAAGCCGG	0.493000													4	55					0	0	1	0	0
RIBC1	158787	broad.mit.edu	37	X	53455598	53455598	+	Silent	SNP	C	C	T			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chrX:53455598C>T	ENST00000457095.1	+	5	771	c.567C>T	c.(565-567)gaC>gaT	p.D189D	RIBC1_ENST00000375327.3_Intron|RIBC1_ENST00000490702.1_Intron|RIBC1_ENST00000414955.2_Intron	NM_144968.2	NP_659405.1	Q8N443	RIBC1_HUMAN	RIB43A domain with coiled-coils 1	0										lung(2)	2						GCCCTCCAGACTCAGAGACCT	0.552000													5	19					0	0	1	0	0
VPS9D1	9605	broad.mit.edu	37	16	89785502	89785502	+	Silent	SNP	G	G	A			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr16:89785502G>A	ENST00000389386.3	-	2	232	c.108C>T	c.(106-108)taC>taT	p.Y36Y	VPS9D1_ENST00000561976.1_5'UTR	NM_004913.2	NP_004904.2			VPS9 domain containing 1																		GGTATTCCGTGTATGCCTCCT	0.552000													17	107					0	0	1	0	0
EXOC4	60412	broad.mit.edu	37	7	133749244	133749244	+	Missense_Mutation	SNP	A	A	G			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr7:133749244A>G	ENST00000253861.4	+	18	2917	c.2888A>G	c.(2887-2889)aAg>aGg	p.K963R	EXOC4_ENST00000539845.1_Missense_Mutation_p.K862R|EXOC4_ENST00000545148.1_Missense_Mutation_p.K573R|EXOC4_ENST00000541309.1_Missense_Mutation_p.K251R	NM_021807.3	NP_068579.3	Q96A65	EXOC4_HUMAN	exocyst complex component 4	963					vesicle docking involved in exocytosis	exocyst	protein N-terminus binding			NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(16)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	50		Esophageal squamous(399;0.129)				GCTGCCATCAAGCAAGCCACC	0.572000													21	68					0	0	1	0	0
KLHL25	64410	broad.mit.edu	37	15	86311637	86311637	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr15:86311637C>T	ENST00000337975.5	-	2	1679	c.1405G>A	c.(1405-1407)Gag>Aag	p.E469K	KLHL25_ENST00000536947.1_Missense_Mutation_p.E469K|KLHL25_ENST00000559131.1_Intron	NM_022480.3	NP_071925.2	Q9H0H3	ENC2_HUMAN	kelch-like family member 25	469						cytoplasm				breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	25						CACCTGTTCTCCGAGGGGTCA	0.602000													18	137					0	0	1	0	0
HMGN2P46	0	broad.mit.edu	37	15	45848224	45848224	+	RNA	SNP	G	G	T			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr15:45848224G>T	ENST00000409454.1	+	0	1219																											TGCAGATTTTGTTTAGCTTTT	0.318000													8	19					1.76689e-08	1.88736e-08	1	1	0
NPAP1	23742	broad.mit.edu	37	15	24921605	24921605	+	Silent	SNP	C	C	T			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr15:24921605C>T	ENST00000329468.2	+	1	1065	c.591C>T	c.(589-591)gaC>gaT	p.D197D		NM_018958.2	NP_061831.2			nuclear pore associated protein 1																		CCCAGGGAGACGTGGCCTCCT	0.592000													6	44					0	0	1	0	0
POU6F2	11281	broad.mit.edu	37	7	39500263	39500263	+	Missense_Mutation	SNP	A	A	C			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr7:39500263A>C	ENST00000518318.2	+	9	1562	c.1520A>C	c.(1519-1521)cAg>cCg	p.Q507P	POU6F2_ENST00000559001.1_Missense_Mutation_p.Q452P|POU6F2_ENST00000403058.1_Missense_Mutation_p.Q507P			P78424	PO6F2_HUMAN	POU class 6 homeobox 2	507	POU-specific.				central nervous system development|ganglion mother cell fate determination|transcription from RNA polymerase II promoter|visual perception		sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	p.Q507L(1)|p.Q507R(1)		NS(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	42						CAGGTGGGACAGGCTCTCAGT	0.602000													6	11					0	0	1	0	0
OR10C1	442194	broad.mit.edu	37	6	29407957	29407957	+	Missense_Mutation	SNP	G	G	T			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr6:29407957G>T	ENST00000444197.2	+	1	875	c.165G>T	c.(163-165)caG>caT	p.Q55H	OR11A1_ENST00000377149.1_Intron	NM_013941.3	NP_039229.3	Q96KK4	O10C1_HUMAN	olfactory receptor, family 10, subfamily C, member 1 (gene/pseudogene)	55					sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			NS(1)|breast(2)|kidney(1)|large_intestine(3)|liver(2)|lung(14)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						CTGCCCTCCAGTCCCCTATGT	0.567000													20	159					5.35267e-07	5.59056e-07	1	1	0
TET2	54790	broad.mit.edu	37	4	106155166	106155166	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr4:106155166C>T	ENST00000540549.1	+	3	927	c.67C>T	c.(67-69)Ccc>Tcc	p.P23S	TET2_ENST00000394764.1_Missense_Mutation_p.P23S|TET2_ENST00000305737.2_Missense_Mutation_p.P23S|TET2_ENST00000413648.2_Missense_Mutation_p.P23S|TET2_ENST00000380013.4_Missense_Mutation_p.P23S|TET2_ENST00000513237.1_Missense_Mutation_p.P44S|TET2_ENST00000545826.1_Missense_Mutation_p.P23S			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	23					cell cycle|myeloid cell differentiation		metal ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1272)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	1314		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)		ACCATCACCTCCCATTTGCCA	0.527000			"""Mis N, F"""		MDS								11	43					0	0	1	0	0
ABCA4	24	broad.mit.edu	37	1	94528252	94528252	+	Silent	SNP	G	G	T			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr1:94528252G>T	ENST00000370225.3	-	13	1904	c.1818C>A	c.(1816-1818)ggC>ggA	p.G606G	ABCA4_ENST00000535735.1_Silent_p.G606G	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	606					phototransduction, visible light|visual perception	integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of substances			NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	147		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		AGGCAAACCCGCCCCAGATGT	0.562000													10	30					0.000442599	0.000442599	1	1	0
UBR5	51366	broad.mit.edu	37	8	103266680	103266680	+	Silent	SNP	G	G	A			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr8:103266680G>A	ENST00000520539.1	-	59	8856	c.8250C>T	c.(8248-8250)ccC>ccT	p.P2750P	UBR5_ENST00000518205.1_Silent_p.P478P|UBR5_ENST00000220959.4_Silent_p.P2749P|UBR5_ENST00000521922.1_Silent_p.P2743P	NM_015902.5	NP_056986.2	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin 5	2750	HECT.|Pro-rich.				cell proliferation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of protein import into nucleus, translocation|progesterone receptor signaling pathway|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to DNA damage stimulus	nucleus|soluble fraction	protein binding|RNA binding|ubiquitin-ubiquitin ligase activity|zinc ion binding			NS(1)|breast(13)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(19)|liver(1)|lung(51)|ovary(6)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	124	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)			TTGTGATTGAGGGCATAGGCT	0.408000													10	68					0	0	1	0	0
ANKK1	255239	broad.mit.edu	37	11	113267965	113267965	+	Silent	SNP	C	C	T			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr11:113267965C>T	ENST00000303941.3	+	6	952	c.858C>T	c.(856-858)gaC>gaT	p.D286D		NM_178510.1	NP_848605.1	Q8NFD2	ANKK1_HUMAN	ankyrin repeat and kinase domain containing 1	286	Protein kinase.						ATP binding|protein serine/threonine kinase activity			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(14)|ovary(1)|stomach(1)	29		all_cancers(61;1.53e-11)|all_epithelial(67;3e-06)|Melanoma(852;4.04e-05)|all_hematologic(158;0.000315)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0461)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Prostate(24;0.194)		BRCA - Breast invasive adenocarcinoma(274;4.82e-06)|Epithelial(105;5.41e-05)|all cancers(92;0.000442)|OV - Ovarian serous cystadenocarcinoma(223;0.238)		TCGAGACAGACATACTGCTGT	0.582000													10	37					0	0	1	0	0
HERC2P2	0	broad.mit.edu	37	15	23283162	23283162	+	RNA	SNP	T	T	C	rs409694		TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr15:23283162T>C	ENST00000560464.1	-	0	5097																											TCCTGTAGGGTGTGTGATGAG	0.547000													5	12					0	0	1	0	0
AP001347.6	0	broad.mit.edu	37	21	15399864	15399864	+	RNA	SNP	T	T	C	rs2298673	by1000genomes	TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr21:15399864T>C	ENST00000428809.1	+	0	123																											TGTGACCTGCTGGCATTGAAT	0.587000													4	49					0	0	1	0	0
NAA15	80155	broad.mit.edu	37	4	140262069	140262069	+	Nonsense_Mutation	SNP	G	G	A			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr4:140262069G>A	ENST00000296543.5	+	4	571	c.248G>A	c.(247-249)tGg>tAg	p.W83*	NAA15_ENST00000480277.2_3'UTR|NAA15_ENST00000398947.1_Nonsense_Mutation_p.W83*	NM_057175.3	NP_476516.1	Q9BXJ9	NAA15_HUMAN	N(alpha)-acetyltransferase 15, NatA auxiliary subunit	83					angiogenesis|cell differentiation|N-terminal protein amino acid acetylation|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|transcription factor complex	protein binding			NS(1)|endometrium(3)|large_intestine(7)|liver(2)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29						TCTTTAGGTTGGCACGTTTAT	0.363000													26	51					0	0	1	0	0
DUSP22	56940	broad.mit.edu	37	6	348272	348272	+	Nonsense_Mutation	SNP	C	C	T			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr6:348272C>T	ENST00000604971.1	+	3	1237	c.124C>T	c.(124-126)Cag>Tag	p.Q42*	DUSP22_ENST00000344450.5_Nonsense_Mutation_p.Q145*|DUSP22_ENST00000605315.1_Nonsense_Mutation_p.Q42*|DUSP22_ENST00000603453.1_Nonsense_Mutation_p.Q42*|DUSP22_ENST00000419235.2_Nonsense_Mutation_p.Q145*|DUSP22_ENST00000605035.1_Nonsense_Mutation_p.Q42*|DUSP22_ENST00000605863.1_Nonsense_Mutation_p.Q42*			Q9NRW4	DUS22_HUMAN	dual specificity phosphatase 22	145					apoptosis|cell proliferation|inactivation of MAPK activity|multicellular organismal development|positive regulation of JNK cascade|regulation of cell proliferation|transforming growth factor beta receptor signaling pathway	cytoplasm|nucleus	protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|skin(2)	26	all_hematologic(77;0.228)	Breast(5;0.0249)|all_hematologic(90;0.0489)		OV - Ovarian serous cystadenocarcinoma(45;0.0277)|BRCA - Breast invasive adenocarcinoma(62;0.0669)		TGAGGTCCATCAGGTAAGCAG	0.577000													14	132					0	0	1	0	0
FMNL3	91010	broad.mit.edu	37	12	50043069	50043069	+	Silent	SNP	A	A	G			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr12:50043069A>G	ENST00000335154.5	-	20	2591	c.2358T>C	c.(2356-2358)taT>taC	p.Y786Y	FMNL3_ENST00000550488.1_Silent_p.Y786Y|FMNL3_ENST00000352151.5_Silent_p.Y735Y|FMNL3_ENST00000293590.5_Silent_p.Y786Y	NM_175736.4	NP_783863.4	Q8IVF7	FMNL3_HUMAN	formin-like 3	786	FH2.				actin cytoskeleton organization		actin binding|Rho GTPase binding			breast(4)|endometrium(7)|kidney(2)|large_intestine(6)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(2)|stomach(1)	39						GCTTGAAGCCATACACAGCTC	0.572000													14	94					0	0	1	0	0
EMC10	284361	broad.mit.edu	37	19	50981247	50981247	+	Nonsense_Mutation	SNP	C	C	G			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr19:50981247C>G	ENST00000376918.3	+	2	222	c.176C>G	c.(175-177)tCa>tGa	p.S59*	EMC10_ENST00000334976.6_Nonsense_Mutation_p.S59*|EMC10_ENST00000598585.1_Nonsense_Mutation_p.S59*	NM_175063.4	NP_778233.4			ER membrane protein complex subunit 10																		CTGGAGCACTCATTTGAGATC	0.607000													3	34					0	0	1	0	0
NF1	4763	broad.mit.edu	37	17	29576001	29576001	+	Splice_Site	SNP	G	G	A			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr17:29576001G>A	ENST00000358273.4	+	30	4357		c.e30-1		NF1_ENST00000356175.3_Splice_Site	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1						actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity	p.0?(8)|p.?(4)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		TTTTTTTGTAGGTTAGAACCA	0.368000			"""D, Mis, N, F, S, O"""		"""neurofibroma, glioma"""	"""neurofibroma, glioma"""			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			48	36					0	0	1	0	0
ABCA11P	0	broad.mit.edu	37	4	419639	419639	+	RNA	SNP	T	T	C	rs7681990	by1000genomes	TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr4:419639T>C	ENST00000451020.2	-	0	1399					NR_002451.2																						CTTTACAGAGTTCTAAGAACA	0.438000													4	41					0	0	1	0	0
AC226119.5	0	broad.mit.edu	37	4	3948570	3948570	+	RNA	SNP	G	G	A			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr4:3948570G>A	ENST00000281228.8	-	0	815				FAM86EP_ENST00000313946.8_RNA																							GGAGCCCGCTGGTGCTCCCGG	0.622000													4	53					0	0	1	0	0
RP11-119F19.2	0	broad.mit.edu	37	10	81444193	81444193	+	RNA	SNP	T	T	C			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr10:81444193T>C	ENST00000600376.1	-	0	54				RP11-119F19.2_ENST00000596088.1_RNA																							ACGACAAGCTTCAGGGCCTGG	0.627000													2	12					0	0	1	0	0
FUCA1	2517	broad.mit.edu	37	1	24194728	24194728	+	Missense_Mutation	SNP	G	G	C			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr1:24194728G>C	ENST00000374479.3	-	1	56	c.49C>G	c.(49-51)Ctg>Gtg	p.L17V		NM_000147.4	NP_000138.2	P04066	FUCO_HUMAN	fucosidase, alpha-L- 1, tissue	17					fucose metabolic process|glycosaminoglycan catabolic process	lysosome	alpha-L-fucosidase activity|cation binding			breast(1)|endometrium(1)|large_intestine(3)|lung(3)	8		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Ovarian(437;0.00348)|Breast(348;0.00957)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.11e-24)|Colorectal(126;5.69e-08)|COAD - Colon adenocarcinoma(152;3.15e-06)|GBM - Glioblastoma multiforme(114;9.04e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000986)|KIRC - Kidney renal clear cell carcinoma(1967;0.00342)|STAD - Stomach adenocarcinoma(196;0.0128)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.144)		AGCAGCAGCAGCAACAGCGCG	0.746000													2	2					0	0	1	0	0
APOC1P1	0	broad.mit.edu	37	19	45430280	45430280	+	RNA	SNP	C	C	G	rs5112	by1000genomes	TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr19:45430280C>G	ENST00000574565.1	+	0	71					NR_028412.1																						TTCTGTCGATCGTCTTGGAAG	0.607000													3	13					0	0	1	0	0
LINC00610	0	broad.mit.edu	37	11	36293264	36293264	+	RNA	SNP	G	G	A			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr11:36293264G>A	ENST00000355500.1	-	0	307																											CAGGTACCAAGATTTTCTCAT	0.498000													9	36					0	0	1	0	0
PSME4	23198	broad.mit.edu	37	2	54148047	54148049	+	In_Frame_Del	DEL	AGG	AGG	-			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr2:54148047_54148049delAGG	ENST00000404125.1	-	18	2294_2296	c.2239_2241delCCT	c.(2239-2241)del	p.P747del	PSME4_ENST00000421748.2_Intron	NM_014614.2	NP_055429.2	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator subunit 4	747					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|M/G1 transition of mitotic cell cycle|mRNA metabolic process|multicellular organismal development|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|spermatogenesis|viral reproduction	nuclear speck|proteasome complex	binding			breast(5)|endometrium(8)|kidney(1)|large_intestine(11)|lung(26)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(2)	60			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			AGTATTCAGAAGGAGGCTTGTCA	0.374													22	75	---	---	---	---					
ANKRD20A8P	0	broad.mit.edu	37	2	95513688	95513689	+	RNA	INS	-	-	TA			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr2:95513688_95513689insTA	ENST00000432432.2	-	0	850					NR_040113.1																						CTCACCTAATGTATAAGATGGA	0.327													8	192	---	---	---	---					
C4orf17	84103	broad.mit.edu	37	4	100443784	100443785	+	Frame_Shift_Ins	INS	-	-	G	rs36110345	byFrequency	TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr4:100443784_100443785insG	ENST00000514652.1	+	3	609_610	c.255_256insG	c.(253-258)tcgcacfs	p.H86fs	C4orf17_ENST00000503257.1_3'UTR|C4orf17_ENST00000326581.4_Frame_Shift_Ins_p.H86fs			Q53FE4	CD017_HUMAN	chromosome 4 open reading frame 17	86										central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|prostate(1)|urinary_tract(3)	18				OV - Ovarian serous cystadenocarcinoma(123;2.08e-08)		GTTACCCCTCCAGCACTGCAGT	0.500													7	93	---	---	---	---					
CTC-338M12.9	0	broad.mit.edu	37	5	180708697	180708698	+	RNA	INS	-	-	A	rs1815381		TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr5:180708697_180708698insA	ENST00000412295.2	+	0	238																											ggggcggtaggcgggggctgga	0.718													3	3	---	---	---	---					
RP11-440G9.1	0	broad.mit.edu	37	6	142860298	142860299	+	RNA	INS	-	-	T	rs143051118	by1000genomes	TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr6:142860298_142860299insT	ENST00000447311.1	-	0	364					NR_027312.1																						ttaggccagtatttttttttta	0.470													4	3	---	---	---	---					
ST8SIA6	338596	broad.mit.edu	37	10	17495614	17495614	+	Frame_Shift_Del	DEL	G	G	-			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr10:17495614delG	ENST00000377602.4	-	2	218	c.144delC	c.(142-144)ccfs	p.P48fs		NM_001004470.1	NP_001004470.1	P61647	SIA8F_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 6	48					post-translational protein modification|protein N-linked glycosylation via asparagine	integral to Golgi membrane	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity			endometrium(3)|kidney(3)|large_intestine(4)|liver(1)|lung(24)|ovary(1)|skin(1)	37						TCAGCGCTGCGGGGGTGCCGT	0.697													2	4	---	---	---	---					
RP11-597A11.1	0	broad.mit.edu	37	14	20138373	20138374	+	RNA	INS	-	-	AAG	rs150133272		TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr14:20138373_20138374insAAG	ENST00000548261.1	+	0	391																											GAAACAaaagaaagaaagaaag	0.396													4	4	---	---	---	---					
RP11-44F14.1	0	broad.mit.edu	37	16	53403273	53403273	+	RNA	DEL	A	A	-			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr16:53403273delA	ENST00000565421.1	-	0	1344																											actccatctcaaaaaaaaaag	0.438													3	5	---	---	---	---					
PLA2G15	23659	broad.mit.edu	37	16	68293167	68293171	+	Frame_Shift_Del	DEL	CGTGC	CGTGC	-	rs142263893		TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr16:68293167_68293171delCGTGC	ENST00000219345.5	+	6	929_933	c.846_850delCGTGC	c.(844-852)ttagfs	p.FVQ282fs	PLA2G15_ENST00000566188.1_3'UTR|PLA2G15_ENST00000444212.2_Frame_Shift_Del_p.FVQ82fs|RP11-96D1.7_ENST00000563175.1_RNA|PLA2G15_ENST00000413021.2_Frame_Shift_Del_p.FVQ188fs	NM_012320.3	NP_036452.1	Q8NCC3	PAG15_HUMAN	phospholipase A2, group XV	282					fatty acid catabolic process	extracellular region|lysosome	lysophospholipase activity|phosphatidylcholine-sterol O-acyltransferase activity|phospholipid binding			kidney(2)|large_intestine(2)|lung(2)|ovary(2)|prostate(3)|skin(1)	12						AGAAGGTGTTCGTGCAGACACCCAC	0.580													16	67	---	---	---	---					
ATRX	546	broad.mit.edu	37	X	76814303	76814306	+	Frame_Shift_Del	DEL	ATAA	ATAA	-			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chrX:76814303_76814306delATAA	ENST00000373344.5	-	29	6552_6555	c.6338_6341delTTAT	c.(6337-6342)tcfs	p.FI2113fs	ATRX_ENST00000395603.3_Frame_Shift_Del_p.FI2075fs|ATRX_ENST00000480283.1_5'UTR	NM_000489.3	NP_000480.2	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	2113	Helicase C-terminal.				DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent	nuclear heterochromatin	ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding	p.F2113fs*9(1)|p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145					Phosphatidylserine(DB00144)	AGTAGAAATGATAAATAATCGTCC	0.289			"""Mis, F, N"""		"""Pancreatic neuroendocrine tumors, paediatric GBM"""		ATR-X (alpha thalassemia/mental retardation) syndrome						18	68	---	---	---	---					
