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
CASZ1	54897	broad.mit.edu	37	1	10713867	10713867	+	Silent	SNP	C	C	T			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr1:10713867C>T	uc001aro.3	-	10	2567	c.2247G>A	c.(2245-2247)gcG>gcA	p.A749A	CASZ1_uc001arp.1_Silent_p.A749A|CASZ1_uc009vmx.2_Silent_p.A773A	NM_001079843	NP_001073312	Q86V15	CASZ1_HUMAN	Homo sapiens castor zinc finger 1 (CASZ1), transcript variant 1, mRNA.	749					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|large_intestine(13)|lung(18)|ovary(2)|prostate(5)|skin(2)|urinary_tract(1)	54	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)		CAGCCAGGGACGCAGAGGACT	0.667												
GLIS1	148979	broad.mit.edu	37	1	54059816	54059816	+	Nonsense_Mutation	SNP	G	G	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr1:54059816G>A	uc001cvr.1	-	2	1327	c.760C>T	c.(760-762)Cga>Tga	p.R254*		NM_147193	NP_671726	Q8NBF1	GLIS1_HUMAN	Homo sapiens GLIS family zinc finger 1 (GLIS1), mRNA.	254					negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	DNA binding|zinc ion binding			endometrium(3)|kidney(2)|large_intestine(3)|liver(1)|lung(7)|ovary(1)|skin(3)|urinary_tract(4)	24						GAGTGCACTCGCATGTGGATG	0.652												
INADL	10207	broad.mit.edu	37	1	62228837	62228837	+	Frame_Shift_Del	DEL	C	C	-			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr1:62228837delC	uc001dab.3	+	2	289	c.175delC	c.(175-177)caafs	p.Q59fs	INADL_uc009waf.1_Frame_Shift_Del_p.Q59fs|INADL_uc001daa.2_Frame_Shift_Del_p.Q59fs	NM_176877	NP_795352	Q8NI35	INADL_HUMAN	Homo sapiens InaD-like (Drosophila) (INADL), mRNA.	59	L27.				intracellular signal transduction|tight junction assembly	apical plasma membrane|perinuclear region of cytoplasm|tight junction	protein binding			breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						GTCCATCAAGCAACTGAAGGG	0.363												
ITGA10	8515	broad.mit.edu	37	1	145532131	145532131	+	Nonsense_Mutation	SNP	C	C	T			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr1:145532131C>T	uc001eoa.3	+	7	851	c.775C>T	c.(775-777)Cag>Tag	p.Q259*	ITGA10_uc010oyv.2_Nonsense_Mutation_p.Q128*|ITGA10_uc009wiw.3_Nonsense_Mutation_p.Q116*|ITGA10_uc010oyw.2_Nonsense_Mutation_p.Q204*	NM_003637	NP_003628	O75578	ITA10_HUMAN	Homo sapiens integrin, alpha 10 (ITGA10), mRNA.	259	VWFA.				cell-matrix adhesion|integrin-mediated signaling pathway	integrin complex	collagen binding|receptor activity			NS(1)|breast(2)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					AGGGTTCAGTCAGTCCCATGG	0.542												
CRTC2	200186	broad.mit.edu	37	1	153923904	153923904	+	Silent	SNP	G	G	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr1:153923904G>A	uc021pab.1	-	10	1395	c.1236C>T	c.(1234-1236)ggC>ggT	p.G412G	CRTC2_uc001fde.4_Non-coding_Transcript|CRTC2_uc001fdf.4_Intron	NM_181715	NP_859066	Q53ET0	CRTC2_HUMAN	Homo sapiens CREB regulated transcription coactivator 2 (CRTC2), mRNA.	412					interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	protein binding			NS(1)|breast(1)|cervix(2)|endometrium(4)|large_intestine(5)|lung(8)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)	27	all_lung(78;3.05e-32)|Lung NSC(65;3.74e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			AAGAGGGGGCGCCCAAAACAG	0.672												
IBA57	200205	broad.mit.edu	37	1	228362896	228362896	+	Silent	SNP	C	C	T			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr1:228362896C>T	uc001hsl.4	+	2	842	c.753C>T	c.(751-753)aaC>aaT	p.N251N	IBA57_uc010pvw.2_Silent_p.N58N	NM_001010867	NP_001010867	Q5T440	CAF17_HUMAN	Homo sapiens IBA57, iron-sulfur cluster assembly homolog (S. cerevisiae) (IBA57), mRNA.	251					glycine catabolic process|heme biosynthetic process	mitochondrion	aminomethyltransferase activity			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(7)|prostate(1)	11						CCTTCATGAACGGCGTGAGCT	0.647												
ZNF496	84838	broad.mit.edu	37	1	247464120	247464120	+	Missense_Mutation	SNP	C	C	T			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr1:247464120C>T	uc009xgv.3	-	7	1610	c.1573G>A	c.(1573-1575)Gac>Aac	p.D525N	ZNF496_uc001ico.3_Missense_Mutation_p.D489N	NM_032752	NP_116141	Q96IT1	ZN496_HUMAN	Homo sapiens zinc finger protein 496 (ZNF496), mRNA.	489					positive regulation of transcription, DNA-dependent|viral reproduction		DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			NS(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	36	all_cancers(71;0.000136)|all_epithelial(71;2.62e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0607)|Lung NSC(105;0.0661)		OV - Ovarian serous cystadenocarcinoma(106;0.00703)			TGGAGTCTGTCCGGCTGCAGG	0.642												
OR2G6	391211	broad.mit.edu	37	1	248685052	248685052	+	Silent	SNP	C	C	T			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr1:248685052C>T	uc001ien.1	+	0	105	c.105C>T	c.(103-105)taC>taT	p.Y35Y		NM_001013355	NP_001013373	Q5TZ20	OR2G6_HUMAN	Homo sapiens olfactory receptor, family 2, subfamily G, member 6 (OR2G6), mRNA.	35					sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			NS(1)|cervix(1)|endometrium(2)|large_intestine(7)|lung(40)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	61	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0156)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TGTACTTCTACGTCTTGAGCC	0.463												
PTEN	5728	broad.mit.edu	37	10	89720831	89720831	+	Frame_Shift_Del	DEL	G	G	-			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr10:89720831delG	uc001kfb.3	+	7	2014	c.982delG	c.(982-984)gcafs	p.A328fs	PTEN_uc021pvw.1_Non-coding_Transcript	NM_000314	NP_000305	P60484	PTEN_HUMAN	Homo sapiens phosphatase and tensin homolog (PTEN), mRNA.	328	C2 tensin-type.				activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway	cytosol|internal side of plasma membrane|PML body	anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	p.0?(37)|p.R55fs*1(5)|p.T319_K332del(2)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.W274_F341del(2)|p.A328fs*1(2)|p.D326_K342del(2)|p.G165_*404del(1)|p.G165_K342del(1)|p.A328fs*15(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		TCTTGACAAAGCAAATAAAGA	0.333		31	"""D, Mis, N, F, S"""		"""glioma,  prostate, endometrial"""	"""harmartoma, glioma,  prostate, endometrial"""			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)		
Unknown	727897	broad.mit.edu	37	11	1283520	1283520	+	Missense_Mutation	SNP	A	A	C			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr11:1283520A>C								MUC5B (114 upstream) : TOLLIP (12078 downstream)																							GCAGTCCAGGACCCCCAGCAG	0.657												
LRRC32	2615	broad.mit.edu	37	11	76371805	76371805	+	Missense_Mutation	SNP	G	G	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr11:76371805G>A	uc001oxq.4	-	2	1075	c.832C>T	c.(832-834)Cgg>Tgg	p.R278W	LRRC32_uc001oxr.4_Missense_Mutation_p.R278W|LRRC32_uc010rsf.2_Missense_Mutation_p.R278W	NM_005512	NP_005503	Q14392	LRC32_HUMAN	Homo sapiens leucine rich repeat containing 32 (LRRC32), transcript variant 1, mRNA.	278						integral to plasma membrane				endometrium(1)|large_intestine(3)|lung(26)|upper_aerodigestive_tract(1)	31						GTGGGGAGCCGGATGAGGTTG	0.652												
GRAMD1B	57476	broad.mit.edu	37	11	123485469	123485469	+	Silent	SNP	G	G	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr11:123485469G>A	uc001pyw.2	+	16	2165	c.1836G>A	c.(1834-1836)cgG>cgA	p.R612R	GRAMD1B_uc001pyx.2_Silent_p.R605R|GRAMD1B_uc010rzw.2_Silent_p.R565R|GRAMD1B_uc010rzx.1_Silent_p.R565R|GRAMD1B_uc001pyy.2_Silent_p.R296R	NM_020716	NP_065767	Q3KR37	GRM1B_HUMAN	Homo sapiens GRAM domain containing 1B (GRAMD1B), mRNA.	605						integral to membrane				NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(17)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	30		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.32e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0394)		CACAGACGCGGCATATCCCGG	0.537												
DDX11	1663	broad.mit.edu	37	12	31236988	31236988	+	Missense_Mutation	SNP	G	G	T			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr12:31236988G>T	uc001rjt.1	+	2	637	c.386G>T	c.(385-387)cGa>cTa	p.R129L	DDX11_uc010sjw.1_Missense_Mutation_p.R129L|DDX11_uc010sjx.1_Non-coding_Transcript|DDX11_uc001rjr.1_Missense_Mutation_p.R129L|DDX11_uc001rjs.1_Missense_Mutation_p.R129L|DDX11_uc001rju.1_5'UTR|DDX11_uc001rjv.1_Missense_Mutation_p.R129L|DDX11_uc001rjw.1_Missense_Mutation_p.R103L	NM_152438	NP_689651	Q96FC9	DDX11_HUMAN	Homo sapiens DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 (DDX11), transcript variant 3, mRNA.	129	Helicase ATP-binding.				G2/M transition of mitotic cell cycle|interspecies interaction between organisms|mitotic sister chromatid segregation|positive regulation of cell proliferation|S phase of mitotic cell cycle|sister chromatid cohesion	midbody|nuclear chromatin|nucleolus|spindle pole	ATP binding|ATP-dependent DNA helicase activity|DNA binding|protein binding|RNA binding			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(11)|large_intestine(5)|lung(23)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	57	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)					CTGGTGGACCGACTAAAGGTG	0.587										Multiple Myeloma(12;0.14)		
PTPN11	5781	broad.mit.edu	37	12	112926909	112926909	+	Missense_Mutation	SNP	A	A	T	rs121918470		TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr12:112926909A>T	uc001ttx.3	+	12	1909	c.1529A>T	c.(1528-1530)cAg>cTg	p.Q510L		NM_002834	NP_002825	Q06124	PTN11_HUMAN	Homo sapiens protein tyrosine phosphatase, non-receptor type 11 (PTPN11), mRNA.	514	Tyrosine-protein phosphatase.		Q -> P (in LEOPARD1).|Q -> R (in NS1).		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.Q510K(2)|p.Q510H(1)|p.Q510L(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						ACAGAAGCACAGTACCGATTT	0.498			Mis		"""JMML, AML, MDS"""		Noonan Syndrome		Noonan syndrome			
DIAPH3	81624	broad.mit.edu	37	13	60686198	60686198	+	Missense_Mutation	SNP	G	G	T			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr13:60686198G>T	uc001vht.3	-	2	555	c.336C>A	c.(334-336)aaC>aaA	p.N112K	DIAPH3_uc001vhw.1_Missense_Mutation_p.N101K|DIAPH3_uc010aed.1_Missense_Mutation_p.N101K|DIAPH3_uc010aee.1_Intron	NM_001042517	NP_001035982	Q9NSV4	DIAP3_HUMAN	Homo sapiens diaphanous homolog 3 (Drosophila) (DIAPH3), transcript variant 1, mRNA.	112					actin cytoskeleton organization		actin binding|Rho GTPase binding			cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|liver(1)|lung(20)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;2.77e-05)		GCTTTGGAAAGTTCTCCATCA	0.403												
MAP3K9	4293	broad.mit.edu	37	14	71205013	71205013	+	Missense_Mutation	SNP	G	G	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr14:71205013G>A	uc001xmm.3	-	7	1793	c.1793C>T	c.(1792-1794)aCg>aTg	p.T598M	MAP3K9_uc010ttk.2_Missense_Mutation_p.T335M|MAP3K9_uc001xmk.3_Missense_Mutation_p.T340M|MAP3K9_uc001xml.3_Missense_Mutation_p.T598M	NM_033141	NP_149132	P80192	M3K9_HUMAN	Homo sapiens mitogen-activated protein kinase kinase kinase 9 (MAP3K9), mRNA.	598					activation of JUN kinase activity|protein autophosphorylation		ATP binding|JUN kinase kinase kinase activity|MAP kinase kinase activity|protein homodimerization activity			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|prostate(1)|skin(3)|stomach(2)	46				all cancers(60;0.00779)|BRCA - Breast invasive adenocarcinoma(234;0.00884)|OV - Ovarian serous cystadenocarcinoma(108;0.08)		TGGCCCCCACGTCCGTCCCTT	0.557												
AHSA1	10598	broad.mit.edu	37	14	77930956	77930956	+	Missense_Mutation	SNP	T	T	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr14:77930956T>A	uc001xtw.3	+	4	648	c.488T>A	c.(487-489)aTg>aAg	p.M163K	AHSA1_uc010tvk.1_Missense_Mutation_p.M163K	NM_012111	NP_036243	O95433	AHSA1_HUMAN	Homo sapiens AHA1, activator of heat shock 90kDa protein ATPase homolog 1 (yeast) (AHSA1), mRNA.	163					protein folding|response to stress	cytosol|endoplasmic reticulum	ATPase activator activity|chaperone binding			endometrium(1)|kidney(3)|large_intestine(1)|prostate(1)|skin(1)|stomach(1)	8			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0281)		ACCCAGGGCATGATCTTACCT	0.468												
AHSA1	10598	broad.mit.edu	37	14	77930997	77930997	+	Missense_Mutation	SNP	G	G	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr14:77930997G>A	uc001xtw.3	+	4	689	c.529G>A	c.(529-531)Ggg>Agg	p.G177R	AHSA1_uc010tvk.1_Missense_Mutation_p.G177R	NM_012111	NP_036243	O95433	AHSA1_HUMAN	Homo sapiens AHA1, activator of heat shock 90kDa protein ATPase homolog 1 (yeast) (AHSA1), mRNA.	177					protein folding|response to stress	cytosol|endoplasmic reticulum	ATPase activator activity|chaperone binding			endometrium(1)|kidney(3)|large_intestine(1)|prostate(1)|skin(1)|stomach(1)	8			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0281)		AGACCCAGTGGGGCAGCCAGC	0.473												
RPS6KA5	9252	broad.mit.edu	37	14	91372576	91372576	+	Missense_Mutation	SNP	G	G	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr14:91372576G>A	uc001xys.2	-	7	1089	c.874C>T	c.(874-876)Cgt>Tgt	p.R292C	RPS6KA5_uc010twi.1_Missense_Mutation_p.R213C|RPS6KA5_uc001xyt.3_Missense_Mutation_p.R292C|RPS6KA5_uc010att.1_Non-coding_Transcript	NM_004755	NP_004746	O75582	KS6A5_HUMAN	Homo sapiens ribosomal protein S6 kinase, 90kDa, polypeptide 5 (RPS6KA5), transcript variant 1, mRNA.	292	Protein kinase 1.				axon guidance|epidermal growth factor receptor signaling pathway|histone phosphorylation|innate immune response|interleukin-1-mediated signaling pathway|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of histone acetylation|positive regulation of histone phosphorylation|positive regulation of transcription from RNA polymerase II promoter|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytoplasm|nucleoplasm	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			endometrium(2)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|skin(2)|urinary_tract(2)	24		all_cancers(154;0.0148)|Melanoma(154;0.099)|all_epithelial(191;0.146)		Epithelial(152;0.182)|BRCA - Breast invasive adenocarcinoma(234;0.201)		ATCAAAAGACGCTGAATTAGG	0.383												
SENP8	123228	broad.mit.edu	37	15	72432087	72432090	+	Frame_Shift_Del	DEL	CAGT	CAGT	-			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr15:72432087_72432090delCAGT	uc021spq.1	+	1	456_459	c.123_126delCAGT	c.(121-126)aacagtfs	p.N41fs	SENP8_uc021spr.1_Frame_Shift_Del_p.N41fs|SENP8_uc021sps.1_Frame_Shift_Del_p.N41fs|SENP8_uc021spt.1_Frame_Shift_Del_p.N41fs|SENP8_uc002atp.3_Frame_Shift_Del_p.N41fs|SENP8_uc021spu.1_Frame_Shift_Del_p.N41fs	NM_001166340	NP_660205	Q96LD8	SENP8_HUMAN	Homo sapiens SUMO/sentrin specific peptidase family member 8 (SENP8), transcript variant 1, mRNA.	41	Protease.				proteolysis		cysteine-type peptidase activity|protein binding			breast(1)|kidney(2)|lung(1)|ovary(1)|skin(1)	6						ACTTTGCCAACAGTCAGTTTCATG	0.475												
RHBDL1	9028	broad.mit.edu	37	16	726867	726867	+	Missense_Mutation	SNP	G	G	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr16:726867G>A	uc002cis.1	+	1	619	c.592G>A	c.(592-594)Gtg>Atg	p.V198M	RHBDL1_uc002cir.1_Missense_Mutation_p.V133M|RHBDL1_uc010uun.1_Missense_Mutation_p.V133M	NM_003961	NP_003952	O75783	RHBL1_HUMAN	Homo sapiens rhomboid, veinlet-like 1 (Drosophila) (RHBDL1), mRNA.	198					proteolysis|signal transduction	integral to plasma membrane|membrane fraction	calcium ion binding|serine-type endopeptidase activity			endometrium(1)|kidney(1)|lung(4)|urinary_tract(3)	9		Hepatocellular(780;0.0218)				CCCACCCCCCGTGTTCATGGC	0.667												
NOD2	64127	broad.mit.edu	37	16	50733737	50733737	+	Missense_Mutation	SNP	C	C	G			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr16:50733737C>G	uc002egm.1	+	1	517	c.412C>G	c.(412-414)Cgg>Ggg	p.R138G	NOD2_uc010cbj.1_Missense_Mutation_p.R111G|NOD2_uc021tia.1_5'UTR|NOD2_uc010cbk.1_Missense_Mutation_p.R111G|NOD2_uc002egl.1_5'UTR	NM_022162	NP_071445	Q9HC29	NOD2_HUMAN	Homo sapiens nucleotide-binding oligomerization domain containing 2 (NOD2), mRNA.	138	CARD 2.				activation of MAPK activity involved in innate immune response|cytokine production involved in immune response|detection of bacterium|detection of muramyl dipeptide|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of macrophage apoptosis|nucleotide-binding oligomerization domain containing 2 signaling pathway|positive regulation of B cell activation|positive regulation of dendritic cell antigen processing and presentation|positive regulation of epithelial cell proliferation|positive regulation of ERK1 and ERK2 cascade|positive regulation of gamma-delta T cell activation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-1 beta secretion|positive regulation of interleukin-10 production|positive regulation of interleukin-17 production|positive regulation of interleukin-6 production|positive regulation of JNK cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of nitric-oxide synthase biosynthetic process|positive regulation of Notch signaling pathway|positive regulation of phosphatidylinositol 3-kinase activity|positive regulation of prostaglandin-E synthase activity|positive regulation of prostaglandin-endoperoxide synthase activity|positive regulation of stress-activated MAPK cascade|positive regulation of tumor necrosis factor production|positive regulation of type 2 immune response|protein oligomerization|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cell surface|cytosol|plasma membrane|vesicle	ATP binding|CARD domain binding|muramyl dipeptide binding|protein kinase binding			cervix(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(30)|ovary(3)|skin(3)	52		all_cancers(37;0.0156)				GCAGAGTCACCGGCCAGCCAT	0.632												
GPR56	9289	broad.mit.edu	37	16	57688009	57688009	+	Silent	SNP	C	C	T			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr16:57688009C>T	uc002emb.2	+	5	1024	c.732C>T	c.(730-732)gcC>gcT	p.A244A	GPR56_uc002elz.1_Silent_p.A74A|GPR56_uc002ema.1_Silent_p.A69A|GPR56_uc002emc.2_Silent_p.A244A|GPR56_uc002emf.2_Silent_p.A244A|GPR56_uc010vhs.1_Silent_p.A244A|GPR56_uc002emd.2_Silent_p.A244A|GPR56_uc002eme.2_Silent_p.A244A|GPR56_uc010vht.1_Silent_p.A249A|GPR56_uc002emg.3_Silent_p.A244A|GPR56_uc010vhu.1_Silent_p.A69A	NM_005682	NP_005673	Q9Y653	GPR56_HUMAN	Homo sapiens G protein-coupled receptor 56 (GPR56), transcript variant 1, mRNA.	244					brain development|cell adhesion|cell-cell signaling|neuropeptide signaling pathway	integral to plasma membrane	G-protein coupled receptor activity			kidney(1)|large_intestine(3)|lung(9)|prostate(1)|skin(1)	15						AGCCCACAGCCGGCCTCCAGG	0.662												
NF1	4763	broad.mit.edu	37	17	29652976	29652979	+	Frame_Shift_Del	DEL	TCTC	TCTC	-			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr17:29652976_29652979delTCTC	uc002hgg.3	+	36	5357_5360	c.4974_4977delTCTC	c.(4972-4977)tttctcfs	p.F1658fs	NF1_uc002hgh.3_Frame_Shift_Del_p.F1637fs|NF1_uc002hgi.1_Frame_Shift_Del_p.F670fs|NF1_uc010cso.3_5'UTR	NM_001042492	NP_001035957	P21359	NF1_HUMAN	Homo sapiens neurofibromin 1 (NF1), transcript variant 1, mRNA.	1658	CRAL-TRIO.				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.?(3)|p.S1660fs*37(2)	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)		AAACAGACTTTCTCTCTAAGTGGT	0.422			"""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)		
KRT35	3886	broad.mit.edu	37	17	39637191	39637191	+	Silent	SNP	T	T	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr17:39637191T>A	uc002hws.3	-	0	202	c.159A>T	c.(157-159)tcA>tcT	p.S53S		NM_002280	NP_002271	Q92764	KRT35_HUMAN	Homo sapiens keratin 35 (KRT35), mRNA.	53	Head.				anatomical structure morphogenesis	intermediate filament	protein binding|structural molecule activity	p.S53L(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	29		Breast(137;0.000286)				CCAGACCCACTGAGCAGGCAG	0.632												
PTPRM	5797	broad.mit.edu	37	18	8244151	8244151	+	Missense_Mutation	SNP	G	G	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr18:8244151G>A	uc002knn.4	+	14	2899	c.2396G>A	c.(2395-2397)gGc>gAc	p.G799D	PTPRM_uc010dkv.3_Missense_Mutation_p.G799D|PTPRM_uc010wzl.2_Missense_Mutation_p.G586D	NM_002845	NP_002836	P28827	PTPRM_HUMAN	Homo sapiens protein tyrosine phosphatase, receptor type, M (PTPRM), transcript variant 2, mRNA.	799					homophilic cell adhesion|negative regulation of angiogenesis|negative regulation of endothelial cell migration|negative regulation of endothelial cell proliferation|response to drug|retina layer formation|retinal ganglion cell axon guidance	cell-cell adherens junction|integral to plasma membrane|lamellipodium|perinuclear region of cytoplasm	cadherin binding|transmembrane receptor protein tyrosine phosphatase activity			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				GCTGAGCAGGGCACAAACTGC	0.483												
PPP4R1	9989	broad.mit.edu	37	18	9570482	9570482	+	Nonsense_Mutation	SNP	G	G	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr18:9570482G>A	uc002koe.1	-	10	1364	c.1246C>T	c.(1246-1248)Cag>Tag	p.Q416*	PPP4R1_uc002kof.2_5'UTR|PPP4R1_uc010wzo.1_Nonsense_Mutation_p.Q262*|PPP4R1_uc002kod.1_Nonsense_Mutation_p.Q399*|PPP4R1_uc010wzp.1_Non-coding_Transcript	NM_001042388	NP_001035847	Q8TF05	PP4R1_HUMAN	Homo sapiens protein phosphatase 4, regulatory subunit 1 (PPP4R1), transcript variant 1, mRNA.	416					protein phosphorylation|signal transduction	protein phosphatase 4 complex	protein binding|protein phosphatase type 4 regulator activity			large_intestine(1)|skin(2)	3						GCTGCTTCCTGGTGAGATTCT	0.443												
NPC1	4864	broad.mit.edu	37	18	21120489	21120489	+	Missense_Mutation	SNP	C	C	T			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr18:21120489C>T	uc002kum.4	-	16	2801	c.2527G>A	c.(2527-2529)Gtg>Atg	p.V843M	NPC1_uc010xaz.2_Missense_Mutation_p.V576M|NPC1_uc010xba.1_Missense_Mutation_p.V688M	NM_000271	NP_000262	O15118	NPC1_HUMAN	Homo sapiens Niemann-Pick disease, type C1 (NPC1), mRNA.	843					autophagy|bile acid metabolic process|cholesterol efflux|cholesterol homeostasis|lysosomal transport	endoplasmic reticulum|integral to plasma membrane|late endosome membrane|lysosomal membrane|nuclear envelope|perinuclear region of cytoplasm	hedgehog receptor activity|protein binding|sterol transporter activity			breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(10)|lung(13)|ovary(2)|stomach(1)	38	all_cancers(21;0.000106)|all_epithelial(16;6.57e-07)|Lung NSC(20;0.00166)|all_lung(20;0.00536)|Colorectal(14;0.0202)|Ovarian(20;0.127)					AGAACACCCACAAATATTGCT	0.363												
TRAPPC8	22878	broad.mit.edu	37	18	29487454	29487454	+	Missense_Mutation	SNP	T	T	G			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr18:29487454T>G	uc002kxc.4	-	8	1722	c.1358A>C	c.(1357-1359)gAt>gCt	p.D453A	TRAPPC8_uc002kxb.4_Missense_Mutation_p.D399A|TRAPPC8_uc002kxd.4_Non-coding_Transcript|TRAPPC8_uc021uio.1_Missense_Mutation_p.D453A|TRAPPC8_uc002kxe.2_Missense_Mutation_p.D453A	NM_014939	NP_055754	Q9Y2L5	TPPC8_HUMAN	Homo sapiens trafficking protein particle complex 8 (TRAPPC8), mRNA.	453					ER to Golgi vesicle-mediated transport	cis-Golgi network				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(7)|liver(2)|lung(13)|ovary(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						CATTGCTTGATCATTAAGAAA	0.338												
CREB3L3	84699	broad.mit.edu	37	19	4164609	4164609	+	Missense_Mutation	SNP	C	C	T			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr19:4164609C>T	uc002lzl.3	+	4	802	c.686C>T	c.(685-687)aCc>aTc	p.T229I	CREB3L3_uc002lzm.3_Missense_Mutation_p.T219I|CREB3L3_uc010xib.2_Missense_Mutation_p.T218I|CREB3L3_uc010xic.2_Missense_Mutation_p.T220I	NM_032607	NP_115996	Q68CJ9	CR3L3_HUMAN	Homo sapiens cAMP responsive element binding protein 3-like 3 (CREB3L3), mRNA.	229					response to unfolded protein	endoplasmic reticulum membrane|integral to membrane|nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	p.T229P(1)		breast(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|skin(2)|urinary_tract(3)	24				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0232)|STAD - Stomach adenocarcinoma(1328;0.18)		GAAGGCATCACCCTGCCCACT	0.617												
DNAJB1	3337	broad.mit.edu	37	19	14627500	14627500	+	Silent	SNP	T	T	C	rs143985567	byFrequency	TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr19:14627500T>C	uc002myz.1	-	1	610	c.570A>G	c.(568-570)ctA>ctG	p.L190L	DNAJB1_uc010xnr.1_Silent_p.L90L	NM_006145	NP_006136	P25685	DNJB1_HUMAN	Homo sapiens DnaJ (Hsp40) homolog, subfamily B, member 1 (DNAJB1), mRNA.	190					chaperone cofactor-dependent protein refolding|response to unfolded protein	cytoplasm|nucleolus	heat shock protein binding|unfolded protein binding	p.L190L(2)		NS(1)|breast(1)|cervix(3)|endometrium(1)|kidney(1)|lung(7)|prostate(1)|urinary_tract(1)	16				GBM - Glioblastoma multiforme(1328;0.0476)		CGTCGGGGTTTAGCCGCTTGT	0.483												
LILRB5	10990	broad.mit.edu	37	19	54760357	54760357	+	Missense_Mutation	SNP	G	G	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr19:54760357G>A	uc010yer.1	-	2	461	c.350C>T	c.(349-351)gCg>gTg	p.A117V	LILRB3_uc002qew.2_Intron|LILRB5_uc002qey.3_Missense_Mutation_p.A117V|LILRB5_uc002qez.3_Missense_Mutation_p.A117V|LILRB5_uc002qex.3_Missense_Mutation_p.A117V|LILRB5_uc002qfa.1_Missense_Mutation_p.A107V|LILRB5_uc010yes.1_Non-coding_Transcript			O75023	LIRB5_HUMAN	Homo sapiens leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 5 (LILRB5), transcript variant 1, mRNA.	117	Ig-like C2-type 2.				cell surface receptor linked signaling pathway|defense response	integral to membrane	transmembrane receptor activity	p.A117V(3)		NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	all_cancers(19;0.00681)|all_epithelial(19;0.00368)|all_lung(19;0.016)|Lung NSC(19;0.0296)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		CTCACCTGTCGCCACCAGCTC	0.637												
DPP10	57628	broad.mit.edu	37	2	116593818	116593818	+	Missense_Mutation	SNP	A	A	T			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr2:116593818A>T	uc002tle.3	+	21	2069	c.2048A>T	c.(2047-2049)gAc>gTc	p.D683V	DPP10_uc002tla.2_Missense_Mutation_p.D679V|DPP10_uc002tlb.2_Missense_Mutation_p.D629V|DPP10_uc002tlc.2_Missense_Mutation_p.D675V|DPP10_uc002tlf.2_Missense_Mutation_p.D672V	NM_001178034	NP_001171505	Q8N608	DPP10_HUMAN	Homo sapiens dipeptidyl-peptidase 10 (non-functional) (DPP10), transcript variant 3, mRNA.	679					proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(24)|liver(2)|lung(48)|ovary(6)|prostate(1)|skin(5)|soft_tissue(1)	101						CCTATCACAGACTTGAAATTG	0.368												
WDR33	55339	broad.mit.edu	37	2	128484320	128484320	+	Nonsense_Mutation	SNP	C	C	T			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr2:128484320C>T	uc002tpg.2	-	7	955	c.756G>A	c.(754-756)tgG>tgA	p.W252*		NM_018383	NP_060853	Q9C0J8	WDR33_HUMAN	Homo sapiens WD repeat domain 33 (WDR33), transcript variant 1, mRNA.	252					postreplication repair|spermatogenesis	collagen|nucleus	protein binding			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)		TGGTTGGATGCCAGTCTACAC	0.408												
HOXD10	3236	broad.mit.edu	37	2	176981726	176981726	+	Silent	SNP	G	G	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr2:176981726G>A	uc002ukj.3	+	0	235	c.165G>A	c.(163-165)ccG>ccA	p.P55P		NM_002148	NP_002139	P28358	HXD10_HUMAN	Homo sapiens homeobox D10 (HOXD10), mRNA.	55						nucleus	sequence-specific DNA binding	p.P55P(4)|p.P55T(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	17			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18)	Colorectal(32;0.0226)|READ - Rectum adenocarcinoma(9;0.0556)		GACTGCTCCCGTCTCTGGCCA	0.488												
PLEKHM3	389072	broad.mit.edu	37	2	208841462	208841462	+	Missense_Mutation	SNP	G	G	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr2:208841462G>A	uc002vcl.2	-	2	1949	c.1459C>T	c.(1459-1461)Cgc>Tgc	p.R487C	PLEKHM3_uc002vcm.2_Missense_Mutation_p.R487C	NM_001080475	NP_001073944	Q6ZWE6	PKHM3_HUMAN	Homo sapiens pleckstrin homology domain containing, family M, member 3 (PLEKHM3), mRNA.	487					intracellular signal transduction		metal ion binding			central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						ACAGATTGGCGTTTGTTCTTC	0.478												
CCDC108	255101	broad.mit.edu	37	2	219874081	219874081	+	Missense_Mutation	SNP	G	G	C			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr2:219874081G>C	uc002vjl.1	-	27	4638	c.4554C>G	c.(4552-4554)gaC>gaG	p.D1518E		NM_194302	NP_919278	Q6ZU64	CC108_HUMAN	Homo sapiens coiled-coil domain containing 108 (CCDC108), transcript variant 1, mRNA.	1518						integral to membrane	structural molecule activity			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(1)|lung(34)|ovary(2)|pancreas(1)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Renal(207;0.0915)		Epithelial(149;1.12e-06)|all cancers(144;0.000196)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TGCATACCAGGTCTGCACTGT	0.587												
RBM44	375316	broad.mit.edu	37	2	238738022	238738022	+	Silent	SNP	G	G	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr2:238738022G>A	uc002vxi.4	+	12	2898	c.2766G>A	c.(2764-2766)tcG>tcA	p.S922S		NM_001080504	NP_001073973	Q6ZP01	RBM44_HUMAN	Homo sapiens RNA binding motif protein 44 (RBM44), mRNA.	921							nucleotide binding|RNA binding			breast(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(7)|ovary(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	33		Breast(86;0.0042)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;3.74e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.3e-11)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000118)|Lung(119;0.0112)|LUSC - Lung squamous cell carcinoma(224;0.0266)		GAATTAGTTCGAATAATTTAG	0.388												
NOP56	10528	broad.mit.edu	37	20	2633552	2633552	+	Missense_Mutation	SNP	A	A	T			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr20:2633552A>T	uc002wgh.3	+	1	197	c.68A>T	c.(67-69)gAg>gTg	p.E23V	NOP56_uc010zpy.2_Non-coding_Transcript|NOP56_uc002wgi.3_5'Flank|SNORD110_uc002wgj.3_5'Flank|SNORA51_uc002wgk.1_5'Flank	NM_006392	NP_006383	O00567	NOP56_HUMAN	Homo sapiens NOP56 ribonucleoprotein homolog (yeast) (NOP56), transcript variant 1, mRNA.	23					rRNA processing	box C/D snoRNP complex|pre-snoRNP complex	protein binding|snoRNA binding			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	25						AAGGAAGTGGAGGAGATCAGT	0.677												
LBP	3929	broad.mit.edu	37	20	36992652	36992652	+	Missense_Mutation	SNP	G	G	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr20:36992652G>A	uc002xic.1	+	6	711	c.676G>A	c.(676-678)Gcc>Acc	p.A226T		NM_004139	NP_004130	P18428	LBP_HUMAN	Homo sapiens lipopolysaccharide binding protein (LBP), mRNA.	226					acute-phase response|cellular defense response|cellular response to lipoteichoic acid|defense response to Gram-negative bacterium|defense response to Gram-positive bacterium|detection of molecule of bacterial origin|innate immune response|lipid transport|lipopolysaccharide transport|lipopolysaccharide-mediated signaling pathway|macrophage activation involved in immune response|negative regulation of tumor necrosis factor production|opsonization|positive regulation of interleukin-6 production|positive regulation of interleukin-8 production|positive regulation of macrophage activation|positive regulation of respiratory burst involved in inflammatory response|positive regulation of toll-like receptor 4 signaling pathway|positive regulation of tumor necrosis factor production|Toll signaling pathway	extracellular space	Gram-negative bacterial cell surface binding|Gram-positive bacterial cell surface binding|lipid binding|lipopolysaccharide binding|lipoteichoic acid binding|receptor binding			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(16)|ovary(2)|prostate(1)|urinary_tract(1)	28		Myeloproliferative disorder(115;0.00878)				TGACAGTTTCGCCGACATTGA	0.562												
WFDC9	259240	broad.mit.edu	37	20	44237357	44237357	+	Missense_Mutation	SNP	G	G	A	rs139643257	byFrequency	TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr20:44237357G>A	uc002xoy.3	-	3	402	c.184C>T	c.(184-186)Cgt>Tgt	p.R62C		NM_147198	NP_671731	Q8NEX5	WFDC9_HUMAN	Homo sapiens WAP four-disulfide core domain 9 (WFDC9), mRNA.	62						extracellular region				breast(1)|large_intestine(1)|liver(1)|lung(1)|prostate(1)|stomach(1)	6		Myeloproliferative disorder(115;0.0122)				TGATTTGGACGTACACAAGTC	0.453												
TP53RK	112858	broad.mit.edu	37	20	45315631	45315631	+	Nonsense_Mutation	SNP	C	C	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr20:45315631C>A	uc002xsk.3	-	1	746	c.523G>T	c.(523-525)Gaa>Taa	p.E175*	SLC13A3_uc002xsg.2_5'Flank|SLC13A3_uc010gho.2_5'Flank|TP53RK_uc002xsj.3_3'UTR	NM_033550	NP_291028	Q96S44	PRPK_HUMAN	Homo sapiens TP53 regulating kinase (TP53RK), mRNA.	175	Protein kinase.				lipopolysaccharide biosynthetic process	membrane|nucleus	ATP binding|p53 binding|protein serine/threonine kinase activity|protein tyrosine kinase activity	p.L174fs*23(1)		kidney(1)|large_intestine(1)|lung(4)|skin(1)	7		Myeloproliferative disorder(115;0.0122)				TTCAGCTGTTCCAGGGGGGGT	0.498												
SCAF4	57466	broad.mit.edu	37	21	33074598	33074598	+	Missense_Mutation	SNP	C	C	T			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr21:33074598C>T	uc002ypd.2	-	4	842	c.416G>A	c.(415-417)aGt>aAt	p.S139N	SCAF4_uc002ype.2_Missense_Mutation_p.S139N|SCAF4_uc010glu.2_Missense_Mutation_p.S124N|SCAF4_uc002ypf.1_5'Flank|SCAF4_uc002ypg.2_Missense_Mutation_p.S139N	NM_020706	NP_065757	O95104	SFR15_HUMAN	Homo sapiens SR-related CTD-associated factor 4 (SCAF4), transcript variant 1, mRNA.	139	CID.					nucleus	nucleotide binding|RNA binding			NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(11)|lung(15)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	54						GGCTGCATTACTGGTTCCCGC	0.388												
CAND2	23066	broad.mit.edu	37	3	12858462	12858462	+	Silent	SNP	C	C	T			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr3:12858462C>T	uc003bxk.2	+	9	2080	c.2031C>T	c.(2029-2031)gaC>gaT	p.D677D	CAND2_uc003bxj.2_Silent_p.D584D	NM_001162499	NP_001155971	O75155	CAND2_HUMAN	Homo sapiens cullin-associated and neddylation-dissociated 2 (putative) (CAND2), transcript variant 1, mRNA.	677					positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding	p.D584D(2)		breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(8)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						CAGCCCTGGACGCCCTGGCCC	0.662												
ZIC4	84107	broad.mit.edu	37	3	147113783	147113783	+	Missense_Mutation	SNP	C	C	G			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr3:147113783C>G	uc011bno.2	-	2	880	c.694G>C	c.(694-696)Gga>Cga	p.G232R	ZIC4_uc003ewc.2_Missense_Mutation_p.G112R|ZIC4_uc021xff.1_Missense_Mutation_p.G220R|ZIC4_uc003ewd.2_Missense_Mutation_p.G182R|ZIC4_uc021xfg.1_Intron	NM_001168378	NP_115529	Q8N9L1	ZIC4_HUMAN	Homo sapiens Zic family member 4 (ZIC4), transcript variant 1, mRNA.	182						nucleus	DNA binding|zinc ion binding			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(34)|upper_aerodigestive_tract(4)	57						AAGGGCTTTCCCTGGCGCGGA	0.597												
MECOM	2122	broad.mit.edu	37	3	168834185	168834185	+	Missense_Mutation	SNP	G	G	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr3:168834185G>A	uc011bpj.1	-	7	1878	c.1475C>T	c.(1474-1476)cCt>cTt	p.P492L	MECOM_uc010hwk.1_Missense_Mutation_p.P327L|MECOM_uc003ffj.3_Missense_Mutation_p.P369L|MECOM_uc003ffi.3_Missense_Mutation_p.P304L|MECOM_uc011bpi.1_Missense_Mutation_p.P305L|MECOM_uc003ffn.3_Missense_Mutation_p.P304L|MECOM_uc003ffk.2_Missense_Mutation_p.P304L|MECOM_uc003ffl.2_Missense_Mutation_p.P464L|MECOM_uc011bpk.1_Missense_Mutation_p.P304L|MECOM_uc010hwn.2_Missense_Mutation_p.P492L	NM_004991	NP_004982	Q13465	MDS1_HUMAN	Homo sapiens MDS1 and EVI1 complex locus (MECOM), transcript variant 4, mRNA.	0							sequence-specific DNA binding transcription factor activity			NS(1)|breast(4)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(13)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	85						AAACAGACCAGGGAAGCTAAA	0.473												
NAALADL2	254827	broad.mit.edu	37	3	174951839	174951839	+	Missense_Mutation	SNP	G	G	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr3:174951839G>A	uc003fit.3	+	2	751	c.664G>A	c.(664-666)Gat>Aat	p.D222N	NAALADL2_uc003fiu.1_Missense_Mutation_p.D215N|NAALADL2_uc010hwy.1_Missense_Mutation_p.D44N	NM_207015	NP_996898	Q58DX5	NADL2_HUMAN	Homo sapiens N-acetylated alpha-linked acidic dipeptidase-like 2 (NAALADL2), mRNA.	222					proteolysis	integral to membrane	peptidase activity			central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(20)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)	49	Ovarian(172;0.0102)	all_cancers(1;0.0272)|all_epithelial(1;0.0553)	OV - Ovarian serous cystadenocarcinoma(80;9.26e-28)	Colorectal(1;1.66e-10)|COAD - Colon adenocarcinoma(1;2.1e-07)|STAD - Stomach adenocarcinoma(1;0.00261)|READ - Rectum adenocarcinoma(3;0.0284)		TGTGCTGCTTGATCTGCCAGG	0.443												
GNRHR	2798	broad.mit.edu	37	4	68606377	68606377	+	Missense_Mutation	SNP	C	C	T			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr4:68606377C>T	uc003hdn.3	-	2	2559	c.808G>A	c.(808-810)Gtt>Att	p.V270I	LOC550112_uc003hdl.4_Intron|GNRHR_uc003hdm.3_Missense_Mutation_p.G227D|BC045560_uc003hdo.1_5'Flank	NM_000406	NP_000397	P30968	GNRHR_HUMAN	Homo sapiens gonadotropin-releasing hormone receptor (GNRHR), transcript variant 1, mRNA.	270					multicellular organismal development	integral to plasma membrane	gonadotropin-releasing hormone receptor activity	p.T269T(1)		endometrium(2)|large_intestine(4)|liver(1)|lung(4)|ovary(1)|urinary_tract(1)	13					Abarelix(DB00106)|Cetrorelix(DB00050)|Danazol(DB01406)|Gonadorelin(DB00644)|Leuprolide(DB00007)|Nafarelin(DB00666)	GCAAATGCAACCGTCATTTTT	0.408												
PITX2	5308	broad.mit.edu	37	4	111539460	111539460	+	Missense_Mutation	SNP	T	T	C			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr4:111539460T>C	uc003iaf.3	-	6	2598	c.775A>G	c.(775-777)Acg>Gcg	p.T259A	PITX2_uc003iac.3_Missense_Mutation_p.T266A|PITX2_uc003iad.3_Missense_Mutation_p.T259A|PITX2_uc021xqr.1_Missense_Mutation_p.T259A|PITX2_uc003iae.3_Missense_Mutation_p.T213A|PITX2_uc021xqs.1_Missense_Mutation_p.T213A	NM_001204397	NP_001191326	Q99697	PITX2_HUMAN	Homo sapiens paired-like homeodomain 2 (PITX2), transcript variant 4, mRNA.	259					determination of left/right symmetry|organ morphogenesis	transcription factor complex	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding			breast(1)|endometrium(3)|large_intestine(1)|lung(5)	10		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00222)		CAGGCAGGCGTCGGCACCGCG	0.592												
SLC22A4	6583	broad.mit.edu	37	5	131676327	131676327	+	Frame_Shift_Del	DEL	T	T	-	rs72552721		TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr5:131676327delT	uc003kwq.3	+	8	1679	c.1514delT	c.(1513-1515)cttfs	p.L505fs	LOC553103_uc021ydj.1_Intron	NM_003059	NP_003050	Q9H015	S22A4_HUMAN	Homo sapiens solute carrier family 22 (organic cation/ergothioneine transporter), member 4 (SLC22A4), mRNA.	505					body fluid secretion|sodium ion transport	apical plasma membrane|integral to plasma membrane|mitochondrion	ATP binding|carnitine transporter activity|cation:cation antiporter activity|PDZ domain binding|secondary active organic cation transmembrane transporter activity|symporter activity	p.E509fs*1(1)		endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|urinary_tract(1)	16		all_cancers(142;0.0752)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		L-Carnitine(DB00583)	ATCCTCACCCTTTTTTTCCCT	0.418												
PCDHGC5	56104	broad.mit.edu	37	5	140730012	140730012	+	Missense_Mutation	SNP	G	G	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr5:140730012G>A	uc003ljo.2	+	0	185	c.185G>A	c.(184-186)cGa>cAa	p.R62Q	PCDHGC5_uc003lji.2_Intron|PCDHGC5_uc003ljk.2_Intron|PCDHGC5_uc003ljm.2_Intron|PCDHGC5_uc011daq.2_Missense_Mutation_p.R62Q	NM_018922	NP_061745	Q9Y5F6	PCDGM_HUMAN	Homo sapiens protocadherin gamma subfamily B, 1 (PCDHGB1), transcript variant 1, mRNA.	62	Cadherin 1.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			breast(2)|central_nervous_system(2)|endometrium(6)|kidney(4)|large_intestine(4)|lung(10)|ovary(4)|prostate(1)|urinary_tract(2)	35			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTGCCAACTCGAAAACTGCGG	0.522											OREG0016856	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)
MFAP3	4238	broad.mit.edu	37	5	153432941	153432941	+	Missense_Mutation	SNP	G	G	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr5:153432941G>A	uc010jib.2	+	2	976	c.757G>A	c.(757-759)Gag>Aag	p.E253K	MFAP3_uc011ddb.1_Missense_Mutation_p.E107K|MFAP3_uc003lvf.2_Missense_Mutation_p.E253K|MFAP3_uc021ygf.1_Missense_Mutation_p.E107K	NM_005927	NP_001128509	P55082	MFAP3_HUMAN	Homo sapiens microfibrillar-associated protein 3 (MFAP3), transcript variant 1, mRNA.	253						integral to membrane|plasma membrane				breast(1)|kidney(2)|large_intestine(1)|lung(2)|pancreas(1)	7	Renal(175;0.00488)	Lung NSC(249;0.00145)|all_lung(500;0.00226)|all_neural(177;0.122)|Breast(839;0.14)	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)	OV - Ovarian serous cystadenocarcinoma(192;9.69e-06)|GBM - Glioblastoma multiforme(465;0.0201)		AGCCTTTGTTGAGGAGATGTT	0.453												
EBF1	1879	broad.mit.edu	37	5	158140123	158140123	+	Silent	SNP	G	G	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr5:158140123G>A	uc010jip.3	-	12	1526	c.1224C>T	c.(1222-1224)gcC>gcT	p.A408A	EBF1_uc011ddw.2_Silent_p.A276A|EBF1_uc011ddx.2_Silent_p.A409A|EBF1_uc003lxl.4_Silent_p.A377A	NM_024007	NP_076870	Q9UH73	COE1_HUMAN	Homo sapiens early B-cell factor 1 (EBF1), mRNA.	408					multicellular organismal development	nucleus	DNA binding|metal ion binding		HMGA2/EBF1(2)	breast(3)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(18)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	42	Renal(175;0.00196)	Acute lymphoblastic leukemia(3;2.99e-06)|all_hematologic(3;0.000772)|Medulloblastoma(196;0.037)|all_neural(177;0.143)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			ACAGGGCCTCGGCAATGTCGG	0.527			T	HMGA2	lipoma							
BTNL3	10917	broad.mit.edu	37	5	180432547	180432547	+	Missense_Mutation	SNP	G	G	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr5:180432547G>A	uc003mmr.3	+	7	1260	c.1076G>A	c.(1075-1077)cGg>cAg	p.R359Q	BTNL3_uc010jlp.3_Missense_Mutation_p.R144Q	NM_197975	NP_932079	Q6UXE8	BTNL3_HUMAN	Homo sapiens butyrophilin-like 3 (BTNL3), mRNA.	359	B30.2/SPRY.				lipid metabolic process	integral to membrane				NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(1)|lung(10)|prostate(2)|skin(1)	25	all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.00336)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)|all_lung(500;0.248)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000272)			GGAGTGTGTCGGGATGACGTA	0.478												
ROS1	6098	broad.mit.edu	37	6	117679033	117679033	+	Missense_Mutation	SNP	G	G	T			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr6:117679033G>T	uc003pxp.1	-	23	3987	c.3788C>A	c.(3787-3789)cCc>cAc	p.P1263H	ROS1_uc011ebi.1_Non-coding_Transcript|ROS1_uc003pxq.1_Intron	NM_002944	NP_002935	P08922	ROS_HUMAN	Homo sapiens c-ros oncogene 1 , receptor tyrosine kinase (ROS1), mRNA.	1263					transmembrane receptor protein tyrosine kinase signaling pathway	membrane fraction|sodium:potassium-exchanging ATPase complex	ATP binding|transmembrane receptor protein tyrosine kinase activity	p.P1263F(2)|p.P1263P(1)	TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	162		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		CACCTCTCTGGGATATTTCAC	0.318			T	"""GOPC, SDC4, SLC34A2, EZR, LRIG3"""	"""glioblastoma, NSCLC"""							
CRHR2	1395	broad.mit.edu	37	7	30693212	30693212	+	Missense_Mutation	SNP	C	C	T			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr7:30693212C>T	uc003tbn.3	-	11	1345	c.1100G>A	c.(1099-1101)cGc>cAc	p.R367H	CRHR2_uc010kvw.2_3'UTR|CRHR2_uc010kvx.2_Missense_Mutation_p.R366H|CRHR2_uc022abg.1_Non-coding_Transcript|CRHR2_uc010kvy.2_Missense_Mutation_p.R203H|CRHR2_uc003tbo.3_Missense_Mutation_p.R353H|CRHR2_uc003tbp.3_Missense_Mutation_p.R394H	NM_001883	NP_001874	Q13324	CRFR2_HUMAN	Homo sapiens corticotropin releasing hormone receptor 2 (CRHR2), transcript variant 1, mRNA.	367					G-protein signaling, coupled to cAMP nucleotide second messenger	integral to plasma membrane	corticotrophin-releasing factor receptor activity|protein binding	p.R367H(2)		breast(2)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						CACGGCTGAGCGCACCTGTGG	0.642												
DDX56	54606	broad.mit.edu	37	7	44611162	44611162	+	Silent	SNP	C	C	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr7:44611162C>A	uc003tlg.3	-	5	1462	c.819G>T	c.(817-819)cgG>cgT	p.R273R	DDX56_uc003tlh.3_Non-coding_Transcript|DDX56_uc010kyg.3_Silent_p.R273R|DDX56_uc010kyh.1_Non-coding_Transcript	NM_019082	NP_061955	Q9NY93	DDX56_HUMAN	Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 56 (DDX56), mRNA.	273	Helicase C-terminal.				rRNA processing	nucleolus	ATP binding|ATP-dependent RNA helicase activity|identical protein binding|RNA binding			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(5)|upper_aerodigestive_tract(1)	16						ACAGGCGTAGCCGGTAACTCC	0.522												
GTF2IRD2	84163	broad.mit.edu	37	7	74212399	74212399	+	Silent	SNP	C	C	T			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr7:74212399C>T	uc003ubd.1	-	15	1636	c.1452G>A	c.(1450-1452)gaG>gaA	p.E484E	GTF2IRD2_uc010lbt.1_Silent_p.E31E	NM_173537	NP_775808	Q86UP8	GTD2A_HUMAN	Homo sapiens GTF2I repeat domain containing 2 (GTF2IRD2), mRNA.	484					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(1)|endometrium(3)|large_intestine(2)|lung(2)|ovary(2)|skin(1)	11						cgtgaagcttctcgtcacgca	0.443												
CCL24	6369	broad.mit.edu	37	7	75442664	75442664	+	Missense_Mutation	SNP	G	G	C			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr7:75442664G>C	uc011kga.2	-	1	210	c.151C>G	c.(151-153)Cag>Gag	p.Q51E		NM_002991	NP_002982	O00175	CCL24_HUMAN	Homo sapiens chemokine (C-C motif) ligand 24 (CCL24), mRNA.	51					cell-cell signaling|chemotaxis|immune response|inflammatory response|positive regulation of actin filament polymerization|positive regulation of cell migration|positive regulation of endothelial cell proliferation|positive regulation of Rac GTPase activity|signal transduction	extracellular space	chemokine activity			endometrium(1)|lung(2)	3						CTGGACAGCTGGTAGCTGACC	0.562												
CDHR3	222256	broad.mit.edu	37	7	105660961	105660961	+	Missense_Mutation	SNP	C	C	T			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr7:105660961C>T	uc003vdl.4	+	12	1904	c.1796C>T	c.(1795-1797)cCc>cTc	p.P599L	CDHR3_uc003vdk.3_Intron|CDHR3_uc003vdm.4_Missense_Mutation_p.P586L|CDHR3_uc011klt.2_Missense_Mutation_p.P511L|CDHR3_uc003vdn.3_Intron	NM_152750	NP_689963	Q6ZTQ4	CDHR3_HUMAN	Homo sapiens cadherin-related family member 3 (CDHR3), mRNA.	599	Cadherin 6.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			breast(1)|cervix(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(15)|ovary(1)	23						GATTCCAGCCCCAGATCTTTC	0.488												
SND1	27044	broad.mit.edu	37	7	127334947	127334948	+	Frame_Shift_Ins	INS	-	-	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr7:127334947_127334948insA	uc003vmi.3	+	2	520_521	c.294_295insA	c.(292-297)acgatafs	p.T98fs		NM_014390	NP_055205	Q7KZF4	SND1_HUMAN	Homo sapiens staphylococcal nuclease and tudor domain containing 1 (SND1), mRNA.	98	TNase-like 1.				gene silencing by RNA|interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	melanosome|nucleus|RNA-induced silencing complex	nuclease activity|nucleic acid binding|protein binding|transcription cofactor activity			central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	41						TCTGTTTCACGATAGAAAACAA	0.465												
KEL	3792	broad.mit.edu	37	7	142643377	142643377	+	Missense_Mutation	SNP	C	C	T			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr7:142643377C>T	uc003wcb.3	-	10	1441	c.1231G>A	c.(1231-1233)Gtg>Atg	p.V411M		NM_000420	NP_000411	P23276	KELL_HUMAN	Homo sapiens Kell blood group, metallo-endopeptidase (KEL), mRNA.	411					proteolysis|vasoconstriction	integral to membrane|plasma membrane	metal ion binding|metalloendopeptidase activity|protein binding			central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(11)|lung(34)|ovary(3)|prostate(2)|skin(1)	60	Melanoma(164;0.059)					GTCTCCTCCACGCACTTCATC	0.567												
SOX7	83595	broad.mit.edu	37	8	10583649	10583649	+	Missense_Mutation	SNP	G	G	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr8:10583649G>A	uc011kwz.2	-	5	955	c.922C>T	c.(922-924)Ccc>Tcc	p.P308S	SOX7_uc003wtf.3_Missense_Mutation_p.P256S	NM_031439	NP_113627	Q9BT81	SOX7_HUMAN	Homo sapiens SRY (sex determining region Y)-box 7 (SOX7), mRNA.	256	Sox C-terminal.				endoderm formation|negative regulation of cell proliferation|negative regulation of transcription, DNA-dependent|positive regulation of caspase activity|regulation of canonical Wnt receptor signaling pathway	cytoplasm|nucleus	transcription regulatory region DNA binding			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	20				COAD - Colon adenocarcinoma(149;0.0732)		GAGCCCAGGGGGTGGCTACAG	0.692												
HGSNAT	138050	broad.mit.edu	37	8	43048945	43048945	+	Missense_Mutation	SNP	G	G	C			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr8:43048945G>C	uc003xpx.4	+	13	1471	c.1423G>C	c.(1423-1425)Ggc>Cgc	p.G475R		NM_152419	NP_689632	Q68CP4	HGNAT_HUMAN	Homo sapiens heparan-alpha-glucosaminide N-acetyltransferase (HGSNAT), mRNA.	503					lysosomal transport|protein oligomerization	integral to membrane|lysosomal membrane	heparan-alpha-glucosaminide N-acetyltransferase activity			cervix(1)|endometrium(2)|large_intestine(4)|lung(6)	13	Prostate(17;0.0119)|Ovarian(28;0.0172)|Lung SC(25;0.184)	all_cancers(86;0.000223)|all_epithelial(80;1.61e-07)|all_lung(54;0.00021)|Lung NSC(58;0.000778)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.0777)|LUSC - Lung squamous cell carcinoma(45;0.17)			GGGCATCCTGGGCACCATCAA	0.428												
ENPP2	5168	broad.mit.edu	37	8	120628516	120628516	+	Missense_Mutation	SNP	C	C	T			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr8:120628516C>T	uc003yos.2	-	7	852	c.766G>A	c.(766-768)Gga>Aga	p.G256R	ENPP2_uc010mdd.2_Missense_Mutation_p.G256R|ENPP2_uc003yot.2_Missense_Mutation_p.G256R	NM_006209	NP_006200	Q13822	ENPP2_HUMAN	Homo sapiens ectonucleotide pyrophosphatase/phosphodiesterase 2 (ENPP2), transcript variant 1, mRNA.	256					cellular component movement|chemotaxis|G-protein coupled receptor protein signaling pathway|immune response|phosphate metabolic process|phosphatidylcholine catabolic process|regulation of cell migration	extracellular space|integral to plasma membrane	alkylglycerophosphoethanolamine phosphodiesterase activity|calcium ion binding|lysophospholipase activity|nucleic acid binding|nucleotide diphosphatase activity|phosphodiesterase I activity|polysaccharide binding|scavenger receptor activity|transcription factor binding|zinc ion binding			breast(1)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(30)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)	69	Lung NSC(37;5.03e-06)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			GGTTGACCTCCCCACCATCTA	0.378												
HAS2	3037	broad.mit.edu	37	8	122626452	122626452	+	Missense_Mutation	SNP	T	T	C			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr8:122626452T>C	uc003yph.2	-	3	2094	c.1556A>G	c.(1555-1557)tAt>tGt	p.Y519C		NM_005328	NP_005319	Q92819	HAS2_HUMAN	Homo sapiens hyaluronan synthase 2 (HAS2), mRNA.	519						integral to plasma membrane	hyaluronan synthase activity	p.L518F(1)	HAS2/PLAG1(10)	breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|lung(19)|ovary(5)|skin(1)	38	Lung NSC(37;3.12e-08)|Ovarian(258;0.0254)|Hepatocellular(40;0.0997)|all_neural(195;0.142)		STAD - Stomach adenocarcinoma(47;0.00503)			ATAGCATGCATAGAGCAACGT	0.418												
FAM49B	51571	broad.mit.edu	37	8	130866513	130866513	+	Missense_Mutation	SNP	G	G	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr8:130866513G>A	uc003yss.3	-	10	1065	c.516_splice	c.e10+1	p.P172_splice	FAM49B_uc003yst.3_Splice_Site_p.P172_splice|FAM49B_uc003ysu.3_Splice_Site_p.P172_splice|FAM49B_uc003ysw.3_Splice_Site_p.P172_splice|FAM49B_uc003ysx.3_Splice_Site_p.P172_splice|FAM49B_uc003ysy.1_Splice_Site_p.P172_splice	NM_016623	NP_057707	Q9NUQ9	FA49B_HUMAN	Homo sapiens family with sequence similarity 49, member B (FAM49B), mRNA.	172										kidney(1)|large_intestine(6)|lung(4)|prostate(1)	12	Ovarian(5;0.000567)|Esophageal squamous(12;0.00693)|Acute lymphoblastic leukemia(118;0.155)		LUAD - Lung adenocarcinoma(14;0.0989)			TTAACTTACCGGTACATTGTT	0.348												
GSN	2934	broad.mit.edu	37	9	124062285	124062285	+	Splice_Site	SNP	T	T	G			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr9:124062285T>G	uc004blf.1	+	1	205	c.144_splice	c.e1+2	p.R48_splice	GSN_uc004bld.1_Intron|GSN_uc010mvr.1_Intron|GSN_uc010mvq.1_Intron|GSN_uc010mvu.1_Intron|GSN_uc010mvt.1_Intron|GSN_uc010mvs.1_Intron|GSN_uc004ble.1_Intron|GSN_uc010mvv.1_Intron|GSN_uc011lyh.1_Intron|GSN_uc011lyi.1_Intron|GSN_uc011lyj.1_5'Flank	NM_000177	NP_000168	P06396	GELS_HUMAN	Homo sapiens gelsolin (GSN), transcript variant 1, mRNA.	48					actin filament polymerization|actin filament severing|barbed-end actin filament capping|cellular component disassembly involved in apoptosis|cilium morphogenesis	actin cytoskeleton|cytosol	actin binding|calcium ion binding|protein binding			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)	21						gaggcgcgggtgagtgcccgg	0.697												
ABL1	25	broad.mit.edu	37	9	133760582	133760582	+	Missense_Mutation	SNP	G	G	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr9:133760582G>A	uc004bzw.3	+	10	2908	c.2905G>A	c.(2905-2907)Gcc>Acc	p.A969T	ABL1_uc004bzv.3_Missense_Mutation_p.A988T	NM_005157	NP_005148	P00519	ABL1_HUMAN	Homo sapiens c-abl oncogene 1, non-receptor tyrosine kinase (ABL1), transcript variant a, mRNA.	969	F-actin-binding.|Pro-rich.				actin cytoskeleton organization|axon guidance|blood coagulation|cell adhesion|DNA damage induced protein phosphorylation|DNA damage response, signal transduction resulting in induction of apoptosis|mismatch repair|muscle cell differentiation|negative regulation of protein serine/threonine kinase activity|peptidyl-tyrosine phosphorylation|positive regulation of muscle cell differentiation|positive regulation of oxidoreductase activity|regulation of transcription involved in S phase of mitotic cell cycle	cytoskeleton|cytosol|nuclear membrane|nucleolus|perinuclear region of cytoplasm	ATP binding|DNA binding|magnesium ion binding|manganese ion binding|mitogen-activated protein kinase binding|non-membrane spanning protein tyrosine kinase activity|proline-rich region binding|protein C-terminus binding|SH3 domain binding			breast(3)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1149)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	1195		all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.4e-05)	Adenosine triphosphate(DB00171)|Dasatinib(DB01254)|Imatinib(DB00619)	GCCACAGTCCGCCAAGCCGTC	0.667			"""T, Mis"""	"""BCR, ETV6, NUP214"""	"""CML, ALL, T-ALL"""							
RXRA	6256	broad.mit.edu	37	9	137300840	137300840	+	Missense_Mutation	SNP	C	C	T			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr9:137300840C>T	uc004cfb.2	+	3	647	c.485C>T	c.(484-486)aCg>aTg	p.T162M	RXRA_uc004cfc.1_Missense_Mutation_p.T65M	NM_002957	NP_002948	P19793	RXRA_HUMAN	Homo sapiens retinoid X receptor, alpha (RXRA), mRNA.	162					cellular lipid metabolic process|cholesterol metabolic process|interspecies interaction between organisms|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to retinoic acid|vitamin metabolic process	nuclear chromatin|nucleoplasm	enzyme binding|ligand-regulated transcription factor activity|protein heterodimerization activity|retinoic acid-responsive element binding|retinoid-X receptor activity|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|transcription coactivator activity|vitamin D receptor binding|zinc ion binding			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19				OV - Ovarian serous cystadenocarcinoma(145;4.66e-08)|Epithelial(140;6.72e-08)|all cancers(34;2.22e-07)	Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926)	TTCAAGCGGACGGTGCGCAAG	0.647												
VCX3B	425054	broad.mit.edu	37	X	8433593	8433593	+	Missense_Mutation	SNP	G	G	C			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chrX:8433593G>C	uc011mht.2	+	2	409	c.102_splice	c.e2+1	p.K34_splice	VCX3B_uc004csd.1_Splice_Site_p.K34_splice|VCX3B_uc022bsj.1_5'Flank	NM_001001888	NP_001001888	Q9H321	VCX3B_HUMAN	Homo sapiens variable charge, X-linked 3B (VCX3B), mRNA.	34						nucleolus				NS(1)|large_intestine(1)|lung(2)|prostate(1)|skin(3)|urinary_tract(3)	11						CGAAGAAGAAGGTGAGTGACC	0.632												
USP9X	8239	broad.mit.edu	37	X	41075424	41075424	+	Silent	SNP	G	G	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chrX:41075424G>A	uc004dfb.3	+	34	6237	c.5604G>A	c.(5602-5604)gtG>gtA	p.V1868V	USP9X_uc004dfc.3_Silent_p.V1868V	NM_001039590	NP_001034679	Q93008	USP9X_HUMAN	Homo sapiens ubiquitin specific peptidase 9, X-linked (USP9X), transcript variant 3, mRNA.	1868					BMP signaling pathway|cell division|chromosome segregation|female gamete generation|mitosis|protein deubiquitination|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent protein catabolic process	cytoplasm	co-SMAD binding|cysteine-type endopeptidase activity|ubiquitin thiolesterase activity			NS(3)|breast(6)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(16)|lung(29)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87						TTGTGGGTGTGCTCGTACACA	0.448												
TEX11	56159	broad.mit.edu	37	X	69902635	69902635	+	Missense_Mutation	SNP	G	G	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chrX:69902635G>A	uc004dyl.3	-	14	1252	c.1090C>T	c.(1090-1092)Cgt>Tgt	p.R364C	TEX11_uc004dyk.3_Missense_Mutation_p.R39C|TEX11_uc004dym.3_Missense_Mutation_p.R349C	NM_001003811	NP_001003811	Q8IYF3	TEX11_HUMAN	Homo sapiens testis expressed 11 (TEX11), transcript variant 1, mRNA.	364							protein binding			breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(13)|ovary(3)|prostate(3)|skin(3)	48	Renal(35;0.156)					GACTTAAAACGTTCATGAATA	0.358												
FHL1	2273	broad.mit.edu	37	X	135291466	135291466	+	Silent	SNP	C	C	T			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chrX:135291466C>T	uc004ezo.3	+	6	1082	c.753C>T	c.(751-753)caC>caT	p.H251H	FHL1_uc010nrz.2_Intron|FHL1_uc004ezq.2_Intron|FHL1_uc004ezm.2_Intron|FHL1_uc004ezl.2_Intron|FHL1_uc011mvy.1_Intron|FHL1_uc004ezn.2_Intron|FHL1_uc022ceu.1_Intron|FHL1_uc011mwa.1_Intron|FHL1_uc011mwb.1_Intron|FHL1_uc004ezp.2_Intron|FHL1_uc004ezr.2_Intron	NM_001159702	NP_001153174	Q13642	FHL1_HUMAN	Homo sapiens four and a half LIM domains 1 (FHL1), transcript variant 1, mRNA.	251					cell differentiation|cell growth|muscle organ development|organ morphogenesis	cytosol|nucleus|plasma membrane	protein binding|zinc ion binding			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	19	Acute lymphoblastic leukemia(192;0.000127)					CAGTGTGCCACGGGAAACGCT	0.552											OREG0019943	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)
SLITRK2	84631	broad.mit.edu	37	X	144905002	144905002	+	Silent	SNP	T	T	C			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chrX:144905002T>C	uc022cfn.1	+	0	1059	c.1059T>C	c.(1057-1059)aaT>aaC	p.N353N	SLITRK2_uc004fcd.3_Silent_p.N353N|SLITRK2_uc010nsp.3_Silent_p.N353N|SLITRK2_uc010nso.3_Silent_p.N353N|SLITRK2_uc011mwq.2_Silent_p.N353N|SLITRK2_uc011mwr.2_Silent_p.N353N|SLITRK2_uc011mws.2_Silent_p.N353N|SLITRK2_uc004fcg.3_Silent_p.N353N|SLITRK2_uc011mwt.2_Silent_p.N353N	NM_032539	NP_115928	Q9H156	SLIK2_HUMAN	Homo sapiens SLIT and NTRK-like family, member 2 (SLITRK2), transcript variant 1, mRNA.	353	LRRNT.					integral to membrane				NS(1)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(17)|lung(40)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	86	Acute lymphoblastic leukemia(192;6.56e-05)					GCTCAGACAATGGTCTGAATG	0.493												
PLXNA3	55558	broad.mit.edu	37	X	153689599	153689599	+	Missense_Mutation	SNP	C	C	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chrX:153689599C>A	uc004flm.3	+	2	928	c.755C>A	c.(754-756)aCa>aAa	p.T252K		NM_017514	NP_059984	P51805	PLXA3_HUMAN	Homo sapiens plexin A3 (PLXNA3), mRNA.	252	Sema.				axon guidance	integral to membrane|intracellular|plasma membrane	transmembrane receptor activity			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(26)|ovary(2)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	48	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					CTGTTGGACACAGCGGGCGAG	0.567