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
CLCA2	9635	broad.mit.edu	37	1	86916415	86916415	+	Splice_Site	SNP	C	C	T	rs140158852		TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr1:86916415C>T	ENST00000370565.4	+	12	2316	c.2154C>T	c.(2152-2154)aaC>aaT	p.N718N	CLCA2_ENST00000498802.1_3'UTR	NM_006536.5	NP_006527.1	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2	718					cell adhesion	basal plasma membrane|cell junction|extracellular region|integral to plasma membrane	chloride channel activity	p.N718N(1)		NS(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	42		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)		ACACAGCAAACGGTAAGAACC	0.448													31	203	---	---	---	---
SEMA6C	10500	broad.mit.edu	37	1	151105861	151105861	+	Missense_Mutation	SNP	C	C	T			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr1:151105861C>T	ENST00000341697.3	-	19	3583	c.1892G>A	c.(1891-1893)cGc>cAc	p.R631H				Q9H3T2	SEM6C_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C	631						integral to membrane	receptor activity	p.R631H(1)		central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	28	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			TCGGTGGGCGCGGCGACAAGC	0.716													3	24	---	---	---	---
HMCN1	83872	broad.mit.edu	37	1	185880818	185880818	+	Missense_Mutation	SNP	A	A	C			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr1:185880818A>C	ENST00000271588.4	+	6	1035	c.806A>C	c.(805-807)aAa>aCa	p.K269T	HMCN1_ENST00000367492.2_Missense_Mutation_p.K269T	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	269					response to stimulus|visual perception	basement membrane	calcium ion binding	p.K269T(1)		NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						AAGCTGATAAAAAAGGGATTT	0.393													24	389	---	---	---	---
CPS1	1373	broad.mit.edu	37	2	211421556	211421556	+	Silent	SNP	A	A	G			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr2:211421556A>G	ENST00000233072.5	+	1	295	c.99A>G	c.(97-99)agA>agG	p.R33R	CPS1_ENST00000430249.2_Silent_p.R39R	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	33					carbamoyl phosphate biosynthetic process|citrulline biosynthetic process|glutamine metabolic process|glycogen catabolic process|nitric oxide metabolic process|positive regulation of vasodilation|response to lipopolysaccharide|triglyceride catabolic process|urea cycle	mitochondrial nucleoid	ATP binding|carbamoyl-phosphate synthase (ammonia) activity	p.R33R(1)		breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	142				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)		AATTTTCAAGACCTGGCATCA	0.403													13	235	---	---	---	---
ABCA12	26154	broad.mit.edu	37	2	215914419	215914419	+	Missense_Mutation	SNP	G	G	T			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr2:215914419G>T	ENST00000272895.7	-	6	843	c.624C>A	c.(622-624)aaC>aaA	p.N208K		NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	208					cellular homeostasis|lipid transport	integral to membrane	ATP binding|ATPase activity	p.N208K(1)		NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		GGCAAAATTTGTTAAAAACAT	0.383													28	103	---	---	---	---
LOC101929006	101929006	broad.mit.edu	37	6	29231318	29231318	+	RNA	SNP	G	G	A			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr6:29231318G>A	ENST00000441381.1	+	0	79																		p.S180F(1)									GACCATTGCAGATATTTCACA	0.433													48	118	---	---	---	---
MICB	4277	broad.mit.edu	37	6	31477560	31477560	+	Splice_Site	SNP	G	G	T			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr6:31477560G>T	ENST00000252229.6	+	6	1105	c.1026G>T	c.(1024-1026)gaG>gaT	p.E342D	MICB_ENST00000538442.1_Splice_Site_p.E310D|MICB_ENST00000399150.3_Splice_Site_p.E299D	NM_005931.3	NP_005922.2	Q29980	MICB_HUMAN	MHC class I polypeptide-related sequence B	342					antigen processing and presentation|cytolysis|gamma-delta T cell activation|immune response|immune response-activating cell surface receptor signaling pathway|interspecies interaction between organisms|negative regulation of defense response to virus by host|response to heat|response to oxidative stress|response to retinoic acid	integral to plasma membrane|MHC class I protein complex	natural killer cell lectin-like receptor binding	p.E342D(1)		NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)	13						CTTCTCCAGAGCTTGTGAGCC	0.522													30	136	---	---	---	---
FAM83B	222584	broad.mit.edu	37	6	54735357	54735357	+	Missense_Mutation	SNP	G	G	A			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr6:54735357G>A	ENST00000306858.7	+	2	429	c.313G>A	c.(313-315)Gac>Aac	p.D105N		NM_001010872.1	NP_001010872.1	Q5T0W9	FA83B_HUMAN	family with sequence similarity 83, member B	105								p.D105N(1)		autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(28)|ovary(6)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	71	Lung NSC(77;0.0178)|Renal(3;0.122)					TCCAAATCTTGACTTAGGCTG	0.463													114	216	---	---	---	---
COL21A1	81578	broad.mit.edu	37	6	56035897	56035897	+	Missense_Mutation	SNP	C	C	A			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr6:56035897C>A	ENST00000244728.5	-	4	1067	c.670G>T	c.(670-672)Gca>Tca	p.A224S	COL21A1_ENST00000370819.1_Missense_Mutation_p.A224S|COL21A1_ENST00000535941.1_Missense_Mutation_p.A224S	NM_030820.3	NP_110447.2	Q96P44	COLA1_HUMAN	collagen, type XXI, alpha 1	224					cell adhesion	collagen|cytoplasm	structural molecule activity	p.A224S(2)		breast(1)|endometrium(1)|kidney(3)|large_intestine(11)|lung(21)|ovary(2)|prostate(2)	41	Lung NSC(77;0.0483)		LUSC - Lung squamous cell carcinoma(124;0.181)			TCACGAGCTGCCACTGGAATT	0.318													36	92	---	---	---	---
TTYH3	80727	broad.mit.edu	37	7	2698620	2698620	+	Missense_Mutation	SNP	C	C	G			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr7:2698620C>G	ENST00000258796.7	+	13	1676	c.1471C>G	c.(1471-1473)Ctc>Gtc	p.L491V	TTYH3_ENST00000407643.1_Missense_Mutation_p.L459V|TTYH3_ENST00000403167.1_Missense_Mutation_p.L320V	NM_025250.2	NP_079526.1	Q9C0H2	TTYH3_HUMAN	tweety family member 3	491						chloride channel complex|plasma membrane	chloride channel activity	p.L491V(1)		kidney(1)|large_intestine(3)|lung(9)|prostate(2)|upper_aerodigestive_tract(2)	17		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;2.04e-14)		GAACACCCCACTCATTGGGCG	0.647													16	175	---	---	---	---
KMT2C	58508	broad.mit.edu	37	7	151845693	151845693	+	Missense_Mutation	SNP	T	T	C			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr7:151845693T>C	ENST00000355193.2	-	53	13708	c.13490A>G	c.(13489-13491)tAt>tGt	p.Y4497C	KMT2C_ENST00000262189.6_Missense_Mutation_p.Y4440C					lysine (K)-specific methyltransferase 2C									p.Y4497C(1)|p.Y4440C(1)									CTGAGTCTCATAGACCTCCGT	0.507													70	195	---	---	---	---
ARHGEF39	84904	broad.mit.edu	37	9	35662634	35662634	+	Missense_Mutation	SNP	G	G	T			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr9:35662634G>T	ENST00000378387.3	-	7	895	c.778C>A	c.(778-780)Cct>Act	p.P260T	ARHGEF39_ENST00000343259.3_Intron|ARHGEF39_ENST00000378395.2_Missense_Mutation_p.P224T|ARHGEF39_ENST00000490970.1_5'UTR	NM_032818.2	NP_116207.2			Rho guanine nucleotide exchange factor (GEF) 39									p.P260T(1)									GGAGGCCGAGGCTTGGCCATG	0.632													21	23	---	---	---	---
ARHGEF39	84904	broad.mit.edu	37	9	35662635	35662635	+	Silent	SNP	C	C	T			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr9:35662635C>T	ENST00000378387.3	-	7	894	c.777G>A	c.(775-777)aaG>aaA	p.K259K	ARHGEF39_ENST00000343259.3_Intron|ARHGEF39_ENST00000378395.2_Silent_p.K223K|ARHGEF39_ENST00000490970.1_5'UTR	NM_032818.2	NP_116207.2			Rho guanine nucleotide exchange factor (GEF) 39									p.K259K(1)									GAGGCCGAGGCTTGGCCATGA	0.632													20	23	---	---	---	---
ROR2	4920	broad.mit.edu	37	9	94486051	94486051	+	Missense_Mutation	SNP	C	C	T			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr9:94486051C>T	ENST00000375708.3	-	9	2923	c.2725G>A	c.(2725-2727)Gtg>Atg	p.V909M	ROR2_ENST00000550066.1_5'UTR|ROR2_ENST00000375715.1_Intron	NM_004560.3	NP_004551.2	Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2	909					negative regulation of cell proliferation|positive regulation of cell migration|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding	p.V909M(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						GCTTCCTGCACGGTGCTCTGG	0.637													39	185	---	---	---	---
TTLL11	158135	broad.mit.edu	37	9	124752018	124752018	+	Missense_Mutation	SNP	C	C	A			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr9:124752018C>A	ENST00000321582.5	-	4	1182	c.995G>T	c.(994-996)tGg>tTg	p.W332L	TTLL11_ENST00000373776.3_Missense_Mutation_p.W332L|TTLL11_ENST00000474723.1_5'UTR	NM_001139442.1	NP_001132914.1	Q8NHH1	TTL11_HUMAN	tubulin tyrosine ligase-like family, member 11	332	TTL.				protein modification process	cilium|microtubule basal body	tubulin-tyrosine ligase activity	p.W332L(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|prostate(3)|skin(1)	18						AGTGGGCTTCCAGGAGGGGTC	0.512													66	240	---	---	---	---
MKI67	4288	broad.mit.edu	37	10	129900972	129900972	+	Silent	SNP	G	G	C			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr10:129900972G>C	ENST00000368654.3	-	13	9507	c.9132C>G	c.(9130-9132)ccC>ccG	p.P3044P	MKI67_ENST00000368653.3_Silent_p.P2684P	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	3044					cell proliferation	nucleolus	ATP binding|protein C-terminus binding	p.P3044P(1)		NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				TGATGACCACGGGTTCGGATG	0.517													10	296	---	---	---	---
EED	8726	broad.mit.edu	37	11	85968564	85968564	+	Missense_Mutation	SNP	T	T	G			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr11:85968564T>G	ENST00000263360.6	+	6	1246	c.560T>G	c.(559-561)gTt>gGt	p.V187G	EED_ENST00000351625.6_Missense_Mutation_p.V187G|EED_ENST00000528180.1_Missense_Mutation_p.V187G|EED_ENST00000327320.4_Missense_Mutation_p.V187G	NM_003797.3	NP_003788.2	O75530	EED_HUMAN	embryonic ectoderm development	187	Interaction with EZH2 (By similarity).|Required for interaction with the matrix protein MA of HIV-1.				negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	ESC/E(Z) complex	histone methyltransferase activity|identical protein binding	p.V187G(1)		haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	21		Acute lymphoblastic leukemia(157;7.24e-07)|all_hematologic(158;0.00092)				TAGCACTATGTTGGCCATGGA	0.303													4	90	---	---	---	---
PKP2	5318	broad.mit.edu	37	12	32975445	32975445	+	Missense_Mutation	SNP	T	T	C			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr12:32975445T>C	ENST00000340811.4	-	8	1903	c.1795A>G	c.(1795-1797)Aaa>Gaa	p.K599E	PKP2_ENST00000070846.6_Missense_Mutation_p.K643E	NM_001005242.2	NP_001005242.2	Q99959	PKP2_HUMAN	plakophilin 2	643					cell-cell adhesion	desmosome|integral to membrane|nucleus	binding	p.K643E(1)		NS(1)|breast(2)|endometrium(1)|kidney(9)|large_intestine(8)|lung(21)|ovary(1)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	50	Lung NSC(5;9.35e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)					CCAATACTTTTGTTGTTGTCA	0.403													11	125	---	---	---	---
DNAH10	196385	broad.mit.edu	37	12	124395093	124395093	+	Silent	SNP	G	G	A			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr12:124395093G>A	ENST00000409039.3	+	58	9679	c.9654G>A	c.(9652-9654)aaG>aaA	p.K3218K		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	3218	Stalk (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity	p.K1810K(1)|p.K3218K(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		GCCTCTTGAAGACTCTTAATA	0.388													12	219	---	---	---	---
TYRO3	7301	broad.mit.edu	37	15	41860444	41860444	+	Missense_Mutation	SNP	G	G	A			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr15:41860444G>A	ENST00000263798.3	+	8	1215	c.991G>A	c.(991-993)Gcc>Acc	p.A331T	TYRO3_ENST00000559066.1_Missense_Mutation_p.A286T	NM_006293.3	NP_006284.2	Q06418	TYRO3_HUMAN	TYRO3 protein tyrosine kinase	331	Fibronectin type-III 2.					integral to plasma membrane	ATP binding|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity	p.A331T(1)|p.A323T(1)		central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(26)|ovary(3)|prostate(1)	43		all_cancers(109;7.33e-15)|all_epithelial(112;2.8e-12)|Lung NSC(122;3.48e-08)|all_lung(180;1.71e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.31e-18)|GBM - Glioblastoma multiforme(113;9.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.117)		AAACCTCCATGCCATCCGCAC	0.572													17	74	---	---	---	---
SMAD3	4088	broad.mit.edu	37	15	67477178	67477178	+	Missense_Mutation	SNP	G	G	T			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr15:67477178G>T	ENST00000327367.4	+	7	1295	c.985G>T	c.(985-987)Gcc>Tcc	p.A329S	SMAD3_ENST00000540846.2_Missense_Mutation_p.A224S|SMAD3_ENST00000537194.2_Missense_Mutation_p.A134S|SMAD3_ENST00000439724.3_Missense_Mutation_p.A285S	NM_005902.3	NP_005893.1	P84022	SMAD3_HUMAN	SMAD family member 3	329	MH2.				activation of caspase activity|cell cycle arrest|cell-cell junction organization|evasion of host defenses by virus|immune response|induction of apoptosis|negative regulation of cell growth|negative regulation of mitotic cell cycle|negative regulation of protein catabolic process|negative regulation of protein phosphorylation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription factor import into nucleus|positive regulation of transcription from RNA polymerase II promoter|primary miRNA processing|protein stabilization|regulation of transforming growth factor beta receptor signaling pathway|regulation of transforming growth factor-beta2 production|response to hypoxia|SMAD protein complex assembly|transforming growth factor beta receptor signaling pathway|transport|wound healing	cytosol|nuclear inner membrane|receptor complex	beta-catenin binding|co-SMAD binding|metal ion binding|protein homodimerization activity|protein kinase binding|R-SMAD binding|RNA polymerase II activating transcription factor binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transforming growth factor beta receptor binding|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity|ubiquitin protein ligase binding	p.A329S(1)		autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|large_intestine(11)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31				Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(7;0.125)		CTGGCACCCGGCCACCGTCTG	0.597													7	36	---	---	---	---
CHD2	1106	broad.mit.edu	37	15	93524064	93524064	+	Missense_Mutation	SNP	G	G	C			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr15:93524064G>C	ENST00000394196.4	+	23	3964	c.2896G>C	c.(2896-2898)Gaa>Caa	p.E966Q	CHD2_ENST00000557381.1_Missense_Mutation_p.E966Q	NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	966	Glu-rich.				regulation of transcription from RNA polymerase II promoter	nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding	p.E966Q(2)		breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	47	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)			TTTTAATAAAGAAGAGCTGAC	0.368													12	105	---	---	---	---
SMARCE1	6605	broad.mit.edu	37	17	38792754	38792754	+	Missense_Mutation	SNP	T	T	C			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr17:38792754T>C	ENST00000348513.6	-	6	1042	c.262A>G	c.(262-264)Aac>Gac	p.N88D	SMARCE1_ENST00000400122.3_Missense_Mutation_p.N18D|SMARCE1_ENST00000578044.1_Missense_Mutation_p.N18D|SMARCE1_ENST00000431889.2_Missense_Mutation_p.N70D|KRT222_ENST00000476049.1_3'UTR|SMARCE1_ENST00000580419.1_Missense_Mutation_p.N53D|SMARCE1_ENST00000377808.4_Missense_Mutation_p.N53D|SMARCE1_ENST00000544009.1_Missense_Mutation_p.N18D	NM_003079.4	NP_003070.3	Q969G3	SMCE1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1	88					chromatin modification|negative regulation of transcription, DNA-dependent|nervous system development|nucleosome disassembly|regulation of transcription from RNA polymerase II promoter	nBAF complex|npBAF complex|nuclear chromosome|SWI/SNF complex|transcriptional repressor complex	chromatin binding|DNA binding|N-acetyltransferase activity|protein binding|protein N-terminus binding|transcription coactivator activity	p.N88D(1)		large_intestine(1)	1		Breast(137;0.000812)				AGGTCAGGGTTGGAAGCCTTT	0.363													68	179	---	---	---	---
NAGS	162417	broad.mit.edu	37	17	42085837	42085837	+	Silent	SNP	C	C	T			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr17:42085837C>T	ENST00000293404.3	+	7	1591	c.1473C>T	c.(1471-1473)ggC>ggT	p.G491G		NM_153006.2	NP_694551.1	Q8N159	NAGS_HUMAN	N-acetylglutamate synthase	491	N-acetyltransferase.				arginine biosynthetic process|urea cycle	mitochondrial matrix	acetyl-CoA:L-glutamate N-acetyltransferase activity	p.G491G(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	8		Breast(137;0.00536)|Prostate(33;0.0724)		BRCA - Breast invasive adenocarcinoma(366;0.113)	L-Glutamic Acid(DB00142)	ACAGTGATGGCAGCTTCTCCA	0.498													27	320	---	---	---	---
DDX42	11325	broad.mit.edu	37	17	61864525	61864525	+	Missense_Mutation	SNP	T	T	C			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr17:61864525T>C	ENST00000578681.1	+	3	717	c.116T>C	c.(115-117)tTt>tCt	p.F39S	DDX42_ENST00000457800.2_Missense_Mutation_p.F39S|DDX42_ENST00000389924.2_Missense_Mutation_p.F39S|DDX42_ENST00000583590.1_Missense_Mutation_p.F39S|DDX42_ENST00000359353.5_Intron	NM_007372.2	NP_031398.2	Q86XP3	DDX42_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 42	39					protein localization|regulation of anti-apoptosis	Cajal body|cytoplasm|nuclear speck	ATP binding|ATP-dependent helicase activity|protein binding|RNA binding	p.F39S(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(3)	46						CACAGTGCCTTTGGGGCAACC	0.502													15	222	---	---	---	---
WDR7	23335	broad.mit.edu	37	18	54591238	54591238	+	Silent	SNP	G	G	A	rs149456946	byFrequency	TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr18:54591238G>A	ENST00000254442.3	+	22	3823	c.3612G>A	c.(3610-3612)ctG>ctA	p.L1204L	WDR7_ENST00000589935.1_Intron|WDR7_ENST00000357574.3_Silent_p.L1171L	NM_015285.2	NP_056100.2	Q9Y4E6	WDR7_HUMAN	WD repeat domain 7	1204								p.L1204L(1)		NS(1)|breast(5)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|lung(37)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)	78				Lung(128;0.0238)|Colorectal(16;0.0296)		CCATTGATCTGATTGGACGTG	0.498													10	122	---	---	---	---
MUC16	94025	broad.mit.edu	37	19	9056757	9056757	+	Missense_Mutation	SNP	G	G	T			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr19:9056757G>T	ENST00000397910.4	-	3	30892	c.30689C>A	c.(30688-30690)cCc>cAc	p.P10230H		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	10232	Ser-rich.|Thr-rich.				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding	p.P5863H(1)|p.P10230H(1)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AGCATTAAAGGGGGTGATTAT	0.448													10	94	---	---	---	---
GPR112	139378	broad.mit.edu	37	X	135431329	135431329	+	Missense_Mutation	SNP	C	C	A			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chrX:135431329C>A	ENST00000394143.1	+	6	5755	c.5464C>A	c.(5464-5466)Cca>Aca	p.P1822T	GPR112_ENST00000412101.1_Missense_Mutation_p.P1617T|GPR112_ENST00000370652.1_Missense_Mutation_p.P1822T|GPR112_ENST00000394141.1_Missense_Mutation_p.P1617T|GPR112_ENST00000287534.4_Missense_Mutation_p.P1759T	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	1822					neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity	p.P1822T(1)		NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					TTCATACCCTCCATGGACCCC	0.408													15	143	---	---	---	---
PLAU	5328	broad.mit.edu	37	10	75673298	75673298	+	Splice_Site	DEL	A	A	-			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr10:75673298delA	ENST00000446342.1	+	6	893	c.411delA	c.(409-411)gga>gg	p.G137fs	PLAU_ENST00000372764.3_Splice_Site_p.G154fs|C10orf55_ENST00000412307.2_Intron|C10orf55_ENST00000409178.1_Intron|PLAU_ENST00000372762.4_Splice_Site_p.G118fs|PLAU_ENST00000494287.1_3'UTR	NM_001145031.1	NP_001138503	P00749	UROK_HUMAN	plasminogen activator, urokinase	154	Kringle.				blood coagulation|chemotaxis|fibrinolysis|proteolysis|regulation of cell adhesion mediated by integrin|regulation of receptor activity|regulation of smooth muscle cell migration|regulation of smooth muscle cell-matrix adhesion|signal transduction	cell surface|extracellular space|plasma membrane	serine-type endopeptidase activity			cervix(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(3)|ovary(2)	16	Prostate(51;0.0112)				Amiloride(DB00594)|Urokinase(DB00013)	GTCCTCCAGGAAAAAAGCCCT	0.517													7	790	---	---	---	---
ARHGAP11A	9824	broad.mit.edu	37	15	32920998	32921007	+	Splice_Site	DEL	GAATTGGTAG	GAATTGGTAG	-			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr15:32920998_32921007delGAATTGGTAG	ENST00000361627.3	+	7	1654_1659	c.932_937delGAATTGGTAG	c.(931-939)agaattggt>agt	p.RIG311fs	ARHGAP11A_ENST00000565905.1_Splice_Site_p.RIG122fs|ARHGAP11A_ENST00000543522.1_Splice_Site_p.RIG122fs|ARHGAP11A_ENST00000563864.1_Splice_Site_p.RIG311fs|ARHGAP11A_ENST00000567348.1_Splice_Site_p.RIG311fs	NM_014783.3	NP_055598.1	Q6P4F7	RHGBA_HUMAN	Rho GTPase activating protein 11A	311					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity	p.A313P(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	31		all_lung(180;1.3e-11)		all cancers(64;3.34e-21)|Epithelial(43;2.64e-15)|GBM - Glioblastoma multiforme(186;5.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.00112)|Lung(196;0.227)		CAAGAAGAAAGAATTGGTAGGTATTTATTA	0.238													13	141	---	---	---	---
