Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample	pox	qox	pox_cutoff	isArtifactMode	oxoGCut
ADH1C	126	broad.mit.edu	37	4	100266127	100266127	+	RNA	SNP	C	C	G			TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr4:100266127C>G	ENST00000515683.1	-	0	810				ADH1C_ENST00000510055.1_RNA	NM_000669.3	NP_000660.1	P00326	ADH1G_HUMAN	alcohol dehydrogenase 1C (class I), gamma polypeptide						ethanol oxidation|xenobiotic metabolic process	cytosol	alcohol dehydrogenase (NAD) activity|zinc ion binding								OV - Ovarian serous cystadenocarcinoma(123;1.08e-07)	Fomepizole(DB01213)|NADH(DB00157)	CATTCTCATCCACCACTGTGT	0.577000													6	73					0	0	1	0	0
CTR9	9646	broad.mit.edu	37	11	10789666	10789666	+	Missense_Mutation	SNP	C	C	G			TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr11:10789666C>G	ENST00000361367.2	+	15	2344	c.1918C>G	c.(1918-1920)Ctc>Gtc	p.L640V		NM_014633.3	NP_055448.1	Q6PD62	CTR9_HUMAN	CTR9, Paf1/RNA polymerase II complex component	640					histone H2B ubiquitination|histone monoubiquitination	Cdc73/Paf1 complex|nuclear speck				breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(12)|ovary(2)|pancreas(1)|stomach(1)	40				all cancers(16;1.64e-07)|Epithelial(150;2.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.111)		CAAACAAGTACTCAGAAATGA	0.363000													31	40					0	0	1	0	0
KSR1	8844	broad.mit.edu	37	17	25937180	25937180	+	Silent	SNP	G	G	A			TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr17:25937180G>A	ENST00000398988.3	+	19	2413	c.1968G>A	c.(1966-1968)gaG>gaA	p.E656E	KSR1_ENST00000268763.6_Silent_p.E656E|KSR1_ENST00000319524.6_Silent_p.E793E|KSR1_ENST00000582410.1_Silent_p.E7E|KSR1_ENST00000509603.2_Silent_p.E771E	NM_014238.1	NP_055053.1	Q8IVT5	KSR1_HUMAN	kinase suppressor of ras 1	791	Protein kinase.				Ras protein signal transduction	cytoplasm|membrane	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(12)|prostate(2)|urinary_tract(1)	28	Lung NSC(42;0.00836)		BRCA - Breast invasive adenocarcinoma(3;0.00122)	UCEC - Uterine corpus endometrioid carcinoma (53;0.168)		GGAAGGACGAGGATCAGCTGC	0.587000											OREG0024262	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	38	56					0	0	1	0	0
PMS2	5395	broad.mit.edu	37	7	6026444	6026444	+	Missense_Mutation	SNP	T	T	C	rs143844197	by1000genomes	TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr7:6026444T>C	ENST00000265849.7	-	11	2057	c.1952A>G	c.(1951-1953)aAg>aGg	p.K651R	PMS2_ENST00000406569.3_Intron|PMS2_ENST00000382321.4_Intron|PMS2_ENST00000441476.2_Missense_Mutation_p.K545R|PMS2_ENST00000469652.1_Intron	NM_000535.5	NP_000526	P54278	PMS2_HUMAN	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)	651					mismatch repair|reciprocal meiotic recombination|somatic hypermutation of immunoglobulin genes	MutLalpha complex	ATP binding|ATPase activity|endonuclease activity|protein binding|single base insertion or deletion binding			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(6)|kidney(2)|large_intestine(11)|lung(13)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;4.39e-15)		AGGACAAATCTTTGCCCTAAA	0.328000			"""Mis, N, F"""			"""colorectal, endometrial, ovarian, medulloblastoma, glioma"""		Direct reversal of damage;Mismatch excision repair (MMR)	Turcot syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome				4	96					0	0	1	0	0
LRRC37A4P	55073	broad.mit.edu	37	17	43587730	43587730	+	RNA	SNP	A	A	C	rs142536398	by1000genomes	TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr17:43587730A>C	ENST00000253803.2	+	0	267				LRRC37A4P_ENST00000579913.1_RNA																							GTATTGATTCATTTTATTCAT	0.343000													3	47					0	0	1	0	0
SHROOM2	357	broad.mit.edu	37	X	9863274	9863274	+	Missense_Mutation	SNP	C	C	A			TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chrX:9863274C>A	ENST00000380913.3	+	4	1416	c.1326C>A	c.(1324-1326)agC>agA	p.S442R		NM_001649.2	NP_001640.1	Q13796	SHRM2_HUMAN	shroom family member 2	442					apical protein localization|brain development|cell migration|cell morphogenesis|cellular pigment accumulation|ear development|establishment of melanosome localization|eye pigment granule organization|lens morphogenesis in camera-type eye|melanosome organization	apical plasma membrane|cell-cell adherens junction|microtubule|tight junction	actin filament binding|beta-catenin binding|ligand-gated sodium channel activity			breast(4)|central_nervous_system(2)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(13)|ovary(3)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)	57		Hepatocellular(5;0.000888)				GTGCTGACAGCCTTGGGCAGG	0.652000													6	90					0.248553	0.248553	1	1	0
TRBC2	28638	broad.mit.edu	37	7	142499637	142499637	+	RNA	SNP	T	T	C	rs1126990		TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr7:142499637T>C	ENST00000466254.1	+	0	397																											GACTGTGGCTTCACCTCCGGT	0.493000													6	557					0	0	1	0	0
BRCA2	675	broad.mit.edu	37	13	32912670	32912670	+	Missense_Mutation	SNP	C	C	T			TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr13:32912670C>T	ENST00000544455.1	+	11	4405	c.4178C>T	c.(4177-4179)gCg>gTg	p.A1393V	BRCA2_ENST00000380152.3_Missense_Mutation_p.A1393V	NM_000059.3	NP_000050	P51587	BRCA2_HUMAN	breast cancer 2, early onset	1393					cell cycle cytokinesis|centrosome duplication|double-strand break repair via homologous recombination|negative regulation of mammary gland epithelial cell proliferation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|regulation of S phase of mitotic cell cycle	BRCA2-MAGE-D1 complex|centrosome|nucleoplasm|stored secretory granule	gamma-tubulin binding|H3 histone acetyltransferase activity|H4 histone acetyltransferase activity|protease binding|single-stranded DNA binding			NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		TTGGAAGTTGCGAAAGCTCAA	0.333000			"""D, Mis, N, F, S"""		"""breast, ovarian, pancreatic"""	"""breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"""		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)			25	37					0	0	1	0	0
NKD2	85409	broad.mit.edu	37	5	1034967	1034967	+	Missense_Mutation	SNP	G	G	A			TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr5:1034967G>A	ENST00000296849.5	+	7	752	c.523G>A	c.(523-525)Gtc>Atc	p.V175I	NKD2_ENST00000537972.1_Missense_Mutation_p.V175I|NKD2_ENST00000274150.4_Missense_Mutation_p.V175I	NM_033120.3	NP_149111.1	Q969F2	NKD2_HUMAN	naked cuticle homolog 2 (Drosophila)	175	Interaction with DVL1, DVL2 and DVL3 (By similarity).				exocytosis|Wnt receptor signaling pathway	cytoplasmic membrane-bounded vesicle|plasma membrane	calcium ion binding|ubiquitin protein ligase binding	p.V175I(1)		breast(1)|central_nervous_system(3)|large_intestine(1)|lung(8)|pancreas(1)	14	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09)		Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165)			GAAGCTAACCGTCAGCCCTGA	0.617000													7	24					0	0	1	0	0
MAGEA11	4110	broad.mit.edu	37	X	148797890	148797890	+	Missense_Mutation	SNP	G	G	C			TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chrX:148797890G>C	ENST00000355220.5	+	5	846	c.744G>C	c.(742-744)atG>atC	p.M248I	MAGEA11_ENST00000333104.4_Missense_Mutation_p.M219I	NM_005366.4	NP_005357.2	P43364	MAGAB_HUMAN	melanoma antigen family A, 11	248	MAGE.					cytoplasm|nucleus	protein binding			cervix(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(2)|skin(1)	9	Acute lymphoblastic leukemia(192;6.56e-05)|Colorectal(9;0.0662)					AGGCAGAAATGCTGGGGAGTG	0.413000													7	165					0	0	1	0	0
F9	2158	broad.mit.edu	37	X	138643011	138643011	+	Missense_Mutation	SNP	G	G	A	rs137852247		TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chrX:138643011G>A	ENST00000218099.2	+	7	842	c.835G>A	c.(835-837)Gca>Aca	p.A279T	F9_ENST00000394090.2_Missense_Mutation_p.A241T	NM_000133.3	NP_000124.1	P00740	FA9_HUMAN	coagulation factor IX	279	Peptidase S1.		A -> T (in HEMB; mild).		blood coagulation, extrinsic pathway|blood coagulation, intrinsic pathway|peptidyl-glutamic acid carboxylation|post-translational protein modification|proteolysis	endoplasmic reticulum lumen|extracellular region|Golgi lumen|plasma membrane	calcium ion binding|serine-type endopeptidase activity			breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(7)|lung(19)|ovary(1)|skin(1)	35	Acute lymphoblastic leukemia(192;0.000127)				Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Heparin(DB01109)|Menadione(DB00170)	TACAGTTGTCGCAGGTAAATA	0.353000													32	98					0	0	1	0	0
RCN3	57333	broad.mit.edu	37	19	50031918	50031918	+	Silent	SNP	A	A	G			TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr19:50031918A>G	ENST00000270645.3	+	2	636	c.189A>G	c.(187-189)gaA>gaG	p.E63E	RCN3_ENST00000593644.1_3'UTR	NM_020650.2	NP_065701.2	Q96D15	RCN3_HUMAN	reticulocalbin 3, EF-hand calcium binding domain	63						endoplasmic reticulum lumen	calcium ion binding|protein binding			endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	12		all_lung(116;7.84e-06)|Lung NSC(112;2.8e-05)|all_neural(266;0.0966)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00295)|GBM - Glioblastoma multiforme(134;0.0159)		TGGGACGGGAAGTGGCCAAGG	0.637000													39	26					0	0	1	0	0
GRIA4	2893	broad.mit.edu	37	11	105845182	105845182	+	Missense_Mutation	SNP	G	G	C			TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr11:105845182G>C	ENST00000393127.2	+	16	3001	c.2555G>C	c.(2554-2556)aGt>aCt	p.S852T	GRIA4_ENST00000525187.1_Missense_Mutation_p.S852T|GRIA4_ENST00000282499.5_Intron|GRIA4_ENST00000530497.1_Intron|GRIA4_ENST00000533094.1_3'UTR	NM_001077243.2	NP_001070711	P48058	GRIA4_HUMAN	glutamate receptor, ionotropic, AMPA 4	852					glutamate signaling pathway|synaptic transmission	cell junction|endocytic vesicle membrane|integral to membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(24)|liver(2)|lung(25)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	82		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)	L-Glutamic Acid(DB00142)	GTGGCAAAGAGTGCACAGACT	0.438000													4	79					0	0	1	0	0
KLHL41	10324	broad.mit.edu	37	2	170367045	170367045	+	Missense_Mutation	SNP	A	A	G			TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr2:170367045A>G	ENST00000284669.1	+	1	834	c.757A>G	c.(757-759)Aaa>Gaa	p.K253E	RP11-724O16.1_ENST00000513963.1_Intron|BBS5_ENST00000554017.1_Intron	NM_006063.2	NP_006054.2			kelch-like family member 41																		GAAAAAAATCAAAGTTCTAAA	0.398000													5	77					0	0	1	0	0
CASZ1	54897	broad.mit.edu	37	1	10710809	10710809	+	Silent	SNP	G	G	A	rs141036792	by1000genomes	TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr1:10710809G>A	ENST00000377022.3	-	13	3137	c.2820C>T	c.(2818-2820)aaC>aaT	p.N940N	RP4-734G22.3_ENST00000606802.1_RNA|CASZ1_ENST00000344008.5_Silent_p.N940N	NM_001079843.2	NP_001073312.1	Q86V15	CASZ1_HUMAN	castor zinc finger 1	940					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)		CATTTGATTCGTTGCTAGAAC	0.597000													27	80					0	0	1	0	0
TMEM104	54868	broad.mit.edu	37	17	72832755	72832755	+	Missense_Mutation	SNP	G	G	A			TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr17:72832755G>A	ENST00000335464.5	+	10	1582	c.1420G>A	c.(1420-1422)Gtg>Atg	p.V474M	TMEM104_ENST00000417024.2_Intron|TMEM104_ENST00000582330.1_Missense_Mutation_p.V474M|TMEM104_ENST00000582773.1_Intron	NM_017728.3	NP_060198.3	Q8NE00	TM104_HUMAN	transmembrane protein 104	474						integral to membrane				NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(5)|ovary(1)	19	all_lung(278;0.23)					GGTGGGCTTCGTGCTGCTCTG	0.592000													29	32					0	0	1	0	0
NBPF1	55672	broad.mit.edu	37	1	16918653	16918653	+	Splice_Site	SNP	C	C	T			TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr1:16918653C>T	ENST00000430580.2	-	6	853		c.e6+1			NM_017940.3	NP_060410.2	Q3BBV0	NBPF1_HUMAN	neuroblastoma breakpoint family, member 1							cytoplasm									UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		TCTTAACTTACTGTTGTGAAA	0.418000													6	51					0	0	1	0	0
ST14	6768	broad.mit.edu	37	11	130079712	130079712	+	Silent	SNP	G	G	A			TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr11:130079712G>A	ENST00000278742.5	+	19	2980	c.2562G>A	c.(2560-2562)ggG>ggA	p.G854G		NM_021978.3	NP_068813.1	Q9Y5Y6	ST14_HUMAN	suppression of tumorigenicity 14 (colon carcinoma)	854	Peptidase S1.				proteolysis	integral to plasma membrane	serine-type endopeptidase activity			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(12)|ovary(3)|pancreas(2)|prostate(1)|skin(3)	32	all_hematologic(175;0.0429)	Lung NSC(97;0.000602)|Breast(109;0.000962)|all_lung(97;0.00126)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0183)|Lung(977;0.228)	Urokinase(DB00013)	AGAACACTGGGGTATAGGGGC	0.637000													5	108					0	0	1	0	0
POMT2	29954	broad.mit.edu	37	14	77765887	77765887	+	Silent	SNP	G	G	A			TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr14:77765887G>A	ENST00000261534.4	-	7	1036	c.834C>T	c.(832-834)caC>caT	p.H278H		NM_013382.5	NP_037514.2	Q9UKY4	POMT2_HUMAN	protein-O-mannosyltransferase 2	278					protein O-linked glycosylation	endoplasmic reticulum membrane|integral to membrane	dolichyl-phosphate-mannose-protein mannosyltransferase activity|metal ion binding			breast(2)|endometrium(2)|large_intestine(1)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)	14			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0292)		GAGCAGTCAGGTGTTTTCCCA	0.498000													9	62					0	0	1	0	0
NNT	23530	broad.mit.edu	37	5	43649290	43649290	+	Missense_Mutation	SNP	C	C	G			TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr5:43649290C>G	ENST00000264663.5	+	11	1707	c.1486C>G	c.(1486-1488)Cta>Gta	p.L496V	NNT_ENST00000344920.4_Missense_Mutation_p.L496V|NNT_ENST00000512996.2_Missense_Mutation_p.L365V	NM_012343.3	NP_036475.3	Q13423	NNTM_HUMAN	nicotinamide nucleotide transhydrogenase	496					tricarboxylic acid cycle	integral to membrane|mitochondrial respiratory chain	NAD binding|NAD(P)+ transhydrogenase (AB-specific) activity|NAD(P)+ transhydrogenase (B-specific) activity|NADP binding			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(7)|large_intestine(6)|liver(2)|lung(20)|ovary(3)|prostate(2)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(6;2.58e-06)				NADH(DB00157)	GGCTCCCAATCTAGCCTTTTC	0.498000													109	167					0	0	1	0	0
PTPRC	5788	broad.mit.edu	37	1	198668788	198668788	+	Missense_Mutation	SNP	G	G	A			TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr1:198668788G>A	ENST00000367376.2	+	5	559	c.388G>A	c.(388-390)Gcc>Acc	p.A130T	PTPRC_ENST00000391970.3_3'UTR|PTPRC_ENST00000352140.3_Missense_Mutation_p.A130T|PTPRC_ENST00000594404.1_Intron|PTPRC_ENST00000442510.2_Missense_Mutation_p.A132T|PTPRC_ENST00000348564.6_Intron	NM_002838.4	NP_002829.3	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	130					axon guidance|B cell proliferation|B cell receptor signaling pathway|defense response to virus|immunoglobulin biosynthetic process|negative regulation of cytokine-mediated signaling pathway|negative regulation of protein kinase activity|negative regulation of T cell mediated cytotoxicity|positive regulation of antigen receptor-mediated signaling pathway|positive regulation of B cell proliferation|positive regulation of protein kinase activity|positive regulation of T cell proliferation|regulation of S phase|release of sequestered calcium ion into cytosol|T cell differentiation|T cell receptor signaling pathway	focal adhesion|integral to plasma membrane|membrane raft	protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			breast(7)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(22)|lung(41)|ovary(4)|pancreas(2)|prostate(1)|skin(13)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	111						CGGCTCCGCCGCCAATGCAAA	0.532000											OREG0014061	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	7	203					0	0	1	0	0
UGT2B7	7364	broad.mit.edu	37	4	69962319	69962319	+	Silent	SNP	G	G	T			TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr4:69962319G>T	ENST00000305231.7	+	1	127	c.81G>T	c.(79-81)ctG>ctT	p.L27L	UGT2B7_ENST00000508661.1_Silent_p.L27L|UGT2B7_ENST00000509763.1_Intron	NM_001074.2	NP_001065.2	P16662	UD2B7_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B7	27					lipid metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			autonomic_ganglia(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						GAAAGGTGCTGGTGTGGGCAG	0.433000													11	93					3.07112e-06	3.16861e-06	1	1	0
CD72	971	broad.mit.edu	37	9	35618218	35618218	+	Splice_Site	SNP	C	C	A			TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr9:35618218C>A	ENST00000396757.1	-	2	247		c.e2+1		CD72_ENST00000378431.1_Splice_Site|CD72_ENST00000490239.1_Intron|CD72_ENST00000259633.4_Splice_Site|CD72_ENST00000378430.3_Splice_Site			P21854	CD72_HUMAN	CD72 molecule						axon guidance|cell adhesion	integral to plasma membrane	receptor binding|sugar binding|transmembrane receptor activity			large_intestine(5)|liver(1)|lung(6)	12			Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			ATCCCCCTTACCCTGTCCTAA	0.567000													26	35					3.65163e-15	3.82832e-15	1	1	0
TP53	7157	broad.mit.edu	37	17	7577539	7577539	+	Missense_Mutation	SNP	G	G	A	rs121912651		TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr17:7577539G>A	ENST00000420246.2	-	7	874	c.742C>T	c.(742-744)Cgg>Tgg	p.R248W	TP53_ENST00000269305.4_Missense_Mutation_p.R248W|TP53_ENST00000359597.4_Missense_Mutation_p.R248W|TP53_ENST00000455263.2_Missense_Mutation_p.R248W|TP53_ENST00000445888.2_Missense_Mutation_p.R248W|TP53_ENST00000413465.2_Missense_Mutation_p.R248W	NM_001126114.2|NM_001276696.1	NP_001119586.1|NP_001263625.1	P04637	P53_HUMAN	tumor protein p53	248	Interaction with AXIN1 (By similarity).|Interaction with HIPK1 (By similarity).|Interacts with the 53BP2 SH3 domain.		NR -> IP (in a sporadic cancer; somatic mutation).|NR -> KW (in sporadic cancers; somatic mutation).|R -> C (in a sporadic cancer; somatic mutation).|R -> G (in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs11540652).|R -> W (in LFS; germline mutation and in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.R248W(544)|p.R155W(28)|p.R248G(12)|p.0?(8)|p.?(5)|p.N247_R248delNR(2)|p.R248fs*16(2)|p.N247_R248>KW(2)|p.M246_P250delMNRRP(2)|p.R248fs*97(2)|p.R248R(2)|p.R248fs*>39(1)|p.R248_P250delRRP(1)|p.unknown(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R248C(1)|p.G245fs*14(1)|p.N247_R248>IP(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		ATGGGCCTCCGGTTCATGCCG	0.577000	R248W(786O_KIDNEY)|R248W(CAS1_CENTRAL_NERVOUS_SYSTEM)|R248W(COLO320_LARGE_INTESTINE)|R248W(COLO680N_OESOPHAGUS)|R248W(DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248W(GCT_SOFT_TISSUE)|R248W(HCC2157_BREAST)|R248W(JIMT1_BREAST)|R248W(KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248W(LUDLU1_LUNG)|R248W(LXF289_LUNG)|R248W(MIAPACA2_PANCREAS)|R248W(RD_SOFT_TISSUE)|R248W(SW837_LARGE_INTESTINE)|R248W(VCAP_PROSTATE)	111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			5	35					0	0	1	0	0
ESX1	80712	broad.mit.edu	37	X	103495451	103495451	+	Missense_Mutation	SNP	G	G	A			TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chrX:103495451G>A	ENST00000372588.4	-	4	762	c.679C>T	c.(679-681)Cct>Tct	p.P227S		NM_153448.3	NP_703149.1	Q8N693	ESX1_HUMAN	ESX homeobox 1	227					negative regulation of transcription, DNA-dependent|regulation of cell cycle	cytoplasm|nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			endometrium(2)|large_intestine(10)|lung(12)|ovary(1)|skin(2)	27						TCCAGAGCAGGAGCAGCATAA	0.552000													14	209					0	0	1	0	0
HOXC4	3221	broad.mit.edu	37	12	54447975	54447975	+	Missense_Mutation	SNP	A	A	C			TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr12:54447975A>C	ENST00000430889.2	+	1	315	c.269A>C	c.(268-270)cAc>cCc	p.H90P	HOXC4_ENST00000609810.1_Missense_Mutation_p.H90P|HOXC4_ENST00000303406.4_Missense_Mutation_p.H90P	NM_153633.2	NP_705897.1	P09017	HXC4_HUMAN	homeobox C4	90						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			cervix(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	13						GGCCACCACCACCCCGAGAAA	0.736000													7	44					0	0	1	0	0
IDH1	3417	broad.mit.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr2:209113112C>T	ENST00000415913.1	-	4	776	c.395G>A	c.(394-396)cGt>cAt	p.R132H	IDH1_ENST00000345146.2_Missense_Mutation_p.R132H|IDH1_ENST00000446179.1_Missense_Mutation_p.R132H	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132			R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate).|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation).|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).		2-oxoglutarate metabolic process|cellular lipid metabolic process|glyoxylate cycle|isocitrate metabolic process|NADPH regeneration|tricarboxylic acid cycle	cytosol|peroxisomal matrix	isocitrate dehydrogenase (NADP+) activity|magnesium ion binding|NAD binding|protein homodimerization activity	p.R132H(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		ATAAGCATGACGACCTATGAT	0.393000			Mis		gliobastoma								18	33					0	0	1	0	0
KIAA1614	57710	broad.mit.edu	37	1	180885464	180885464	+	Silent	SNP	A	A	G			TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr1:180885464A>G	ENST00000367588.4	+	2	280	c.225A>G	c.(223-225)gtA>gtG	p.V75V		NM_020950.1	NP_066001.1	Q5VZ46	K1614_HUMAN	KIAA1614	75										NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(12)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	33						TATGGGGAGTACAGCTCCAGG	0.597000													18	27					0	0	1	0	0
RAP2C	57826	broad.mit.edu	37	X	131348314	131348314	+	Missense_Mutation	SNP	G	G	A			TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chrX:131348314G>A	ENST00000342983.2	-	3	1180	c.434C>T	c.(433-435)aCa>aTa	p.T145I	RAP2C_ENST00000370874.1_Missense_Mutation_p.T145I|RAP2C_ENST00000460462.1_5'UTR	NM_001271187.1|NM_021183.4	NP_001258116.1|NP_067006.3	Q9Y3L5	RAP2C_HUMAN	RAP2C, member of RAS oncogene family	145					negative regulation of cell migration|positive regulation of protein autophosphorylation|Rap protein signal transduction|regulation of protein tyrosine kinase activity	recycling endosome membrane	GTP binding|GTPase activity			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|ovary(1)|upper_aerodigestive_tract(2)	8	Acute lymphoblastic leukemia(192;0.000127)					TTTTGCCGATGTCTCCATGAA	0.443000													25	67					0	0	1	0	0
RANBP2	5903	broad.mit.edu	37	2	109371692	109371692	+	Missense_Mutation	SNP	T	T	C			TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr2:109371692T>C	ENST00000283195.6	+	17	2569	c.2443T>C	c.(2443-2445)Tgc>Cgc	p.C815R		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	815					carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA transport|protein folding|protein import into nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore	peptidyl-prolyl cis-trans isomerase activity|Ran GTPase binding|zinc ion binding		RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						GAAAATGATTTGCCAACAAGT	0.348000													4	163					0	0	1	0	0
KCND2	3751	broad.mit.edu	37	7	119915148	119915148	+	Silent	SNP	C	C	T			TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr7:119915148C>T	ENST00000331113.4	+	1	1427	c.462C>T	c.(460-462)acC>acT	p.T154T		NM_012281.2	NP_036413.1	Q9NZV8	KCND2_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 2	154					regulation of action potential|synaptic transmission	cell surface|dendritic spine	metal ion binding			NS(2)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(35)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	75	all_neural(327;0.117)					ACGCGGATACCGACACCGCTG	0.622000													6	101					0	0	1	0	0
CT47B1	643311	broad.mit.edu	37	X	120009261	120009261	+	Silent	SNP	C	C	T			TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chrX:120009261C>T	ENST00000371311.3	-	1	518	c.264G>A	c.(262-264)ggG>ggA	p.G88G		NM_001145718.1	NP_001139190.1	P0C2W7	CT47B_HUMAN	cancer/testis antigen family 47, member B1	88										breast(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|lung(9)|ovary(1)|skin(1)	22						ccGTCGCGGGCCCGATATCTG	0.721000													10	20					0	0	1	0	0
POLR2A	5430	broad.mit.edu	37	17	7412932	7412932	+	Missense_Mutation	SNP	A	A	T			TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr17:7412932A>T	ENST00000322644.6	+	22	4193	c.3794A>T	c.(3793-3795)gAt>gTt	p.D1265V		NM_000937.4	NP_000928	P24928	RPB1_HUMAN	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	1265					mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of viral transcription|protein phosphorylation|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	DNA-directed RNA polymerase II, core complex	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|RNA-directed RNA polymerase activity|ubiquitin protein ligase binding			breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(17)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	50		Prostate(122;0.173)				ATGAACAGCGATGAGAACAAG	0.458000													13	115					0	0	1	0	0
TCEA2	6919	broad.mit.edu	37	20	62701881	62701881	+	Missense_Mutation	SNP	A	A	T			TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr20:62701881A>T	ENST00000361317.2	+	9	1073	c.631A>T	c.(631-633)Atg>Ttg	p.M211L	TCEA2_ENST00000465111.1_3'UTR|TCEA2_ENST00000343484.5_Missense_Mutation_p.M238L|TCEA2_ENST00000395053.3_3'UTR	NM_198723.1	NP_942016.1	Q15560	TCEA2_HUMAN	transcription elongation factor A (SII), 2	238	TFIIS central.				regulation of transcription elongation, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription elongation, DNA-dependent	transcription elongation factor complex	DNA binding|protein binding|translation elongation factor activity|zinc ion binding			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)	12	all_cancers(38;3.45e-11)|all_epithelial(29;9.12e-13)|Lung NSC(23;2e-09)|all_lung(23;6.77e-09)					CCGTAAGGCCATGACCAAGGA	0.632000													24	40					0	0	1	0	0
MAMDC4	158056	broad.mit.edu	37	9	139752161	139752161	+	Missense_Mutation	SNP	A	A	G			TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr9:139752161A>G	ENST00000445819.1	+	21	2664	c.2614A>G	c.(2614-2616)Acg>Gcg	p.T872A	MAMDC4_ENST00000485732.1_3'UTR|MAMDC4_ENST00000317446.2_Missense_Mutation_p.T793A			Q6UXC1	AEGP_HUMAN	MAM domain containing 4	872	MAM 5.				protein transport	integral to membrane				breast(4)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(4)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	19	all_cancers(76;0.0763)|all_epithelial(76;0.198)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.52e-05)|Epithelial(140;0.000171)		CCGGGGCCAGACGGCCTCCCT	0.677000													3	21					0	0	1	0	0
NT5C1B	93034	broad.mit.edu	37	2	18768782	18768782	+	Missense_Mutation	SNP	C	C	T			TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr2:18768782C>T	ENST00000304081.4	-	2	207	c.107G>A	c.(106-108)cGt>cAt	p.R36H	NT5C1B_ENST00000359846.2_Missense_Mutation_p.R36H|NT5C1B_ENST00000460052.1_5'UTR|NT5C1B_ENST00000600945.1_Missense_Mutation_p.R36H|NT5C1B-RDH14_ENST00000532967.1_Missense_Mutation_p.R36H	NM_033253.3	NP_150278.2			5'-nucleotidase, cytosolic IB											endometrium(2)|kidney(2)|large_intestine(10)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	29	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.177)	Ovarian(717;0.208)				ATTGCTCAGACGAACTCCTGT	0.438000													36	60					0	0	1	0	0
HBS1L	10767	broad.mit.edu	37	6	135314939	135314939	+	Missense_Mutation	SNP	C	C	T			TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr6:135314939C>T	ENST00000367837.5	-	8	1246	c.1040G>A	c.(1039-1041)gGc>gAc	p.G347D	HBS1L_ENST00000367824.4_Missense_Mutation_p.G183D|HBS1L_ENST00000367826.2_Missense_Mutation_p.G305D|HBS1L_ENST00000445176.2_Missense_Mutation_p.G71D|HBS1L_ENST00000527578.1_Missense_Mutation_p.G183D|HBS1L_ENST00000415177.2_Missense_Mutation_p.G282D	NM_001145158.1|NM_006620.3	NP_001138630.1|NP_006611.1	Q9Y450	HBS1L_HUMAN	HBS1-like (S. cerevisiae)	347					signal transduction		GTP binding|GTPase activity|translation elongation factor activity			NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	20	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.0046)|GBM - Glioblastoma multiforme(68;0.00702)		GTCCTTATGGCCTGGAGCATC	0.368000													3	23					0	0	1	0	0
ZFHX3	463	broad.mit.edu	37	16	72821618	72821618	+	Silent	SNP	A	A	G	rs112443847		TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr16:72821618A>G	ENST00000268489.5	-	10	11229	c.10557T>C	c.(10555-10557)ggT>ggC	p.G3519G	ZFHX3_ENST00000397992.5_Silent_p.G2605G|AC004943.1_ENST00000584072.1_RNA	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	3519	Poly-Gly.				muscle organ development|negative regulation of myoblast differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|positive regulation of myoblast differentiation	transcription factor complex	enzyme binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding|zinc ion binding	p.G3519G(3)		NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				cgccgccgccaccgccgccgc	0.716000													6	42					0	0	1	0	0
RRN3P2	653390	broad.mit.edu	37	16	29110458	29110458	+	RNA	SNP	T	T	C	rs151074589	by1000genomes	TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr16:29110458T>C	ENST00000564580.1	+	0	1131																		p.W375R(25)									GAATTTTGAGTGGATAGTGAT	0.328000													5	31					0	0	1	0	0
ARHGAP33	115703	broad.mit.edu	37	19	36268615	36268615	+	Silent	SNP	G	G	A			TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr19:36268615G>A	ENST00000007510.4	+	2	219	c.75G>A	c.(73-75)ggG>ggA	p.G25G	ARHGAP33_ENST00000221905.1_3'UTR|ARHGAP33_ENST00000314737.5_Silent_p.G25G|ARHGAP33_ENST00000378944.5_Intron			O14559	RHG33_HUMAN	Rho GTPase activating protein 33	25					cell communication|protein transport|signal transduction	intracellular	GTPase activator activity|phosphatidylinositol binding|protein binding			endometrium(7)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	37						CTGCTGGGGGGCCCAGTGTGA	0.642000													3	7					0	0	1	0	0
ADAMTS3	9508	broad.mit.edu	37	4	73169701	73169701	+	Missense_Mutation	SNP	T	T	C			TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr4:73169701T>C	ENST00000286657.4	-	17	2393	c.2357A>G	c.(2356-2358)tAt>tGt	p.Y786C		NM_014243.2	NP_055058.2	O15072	ATS3_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 3	786	Spacer.				collagen catabolic process|collagen fibril organization|proteolysis	proteinaceous extracellular matrix	heparin binding|metalloendopeptidase activity|zinc ion binding			NS(1)|breast(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(33)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	76			Epithelial(6;4.97e-05)|OV - Ovarian serous cystadenocarcinoma(6;5.66e-05)|all cancers(17;0.000486)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			TTCAATGTTATAATCCCACTC	0.413000													5	208					0	0	1	0	0
DCHS1	8642	broad.mit.edu	37	11	6650970	6650970	+	Silent	SNP	G	G	A	rs144759454		TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr11:6650970G>A	ENST00000299441.3	-	11	5379	c.4968C>T	c.(4966-4968)gtC>gtT	p.V1656V		NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	1656	Cadherin 16.				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CACGCAAGAGGACGCTGTACT	0.632000													11	20					0	0	1	0	0
PKHD1	5314	broad.mit.edu	37	6	51512879	51512879	+	Missense_Mutation	SNP	G	G	C			TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr6:51512879G>C	ENST00000371117.3	-	63	11623	c.11348C>G	c.(11347-11349)cCa>cGa	p.P3783R		NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	3783			P -> S (in ARPKD).		cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					AATTGTCCATGGCTCTGAAGG	0.423000													27	60					0	0	1	0	0
C4orf19	55286	broad.mit.edu	37	4	37591775	37591775	+	Missense_Mutation	SNP	T	T	C			TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr4:37591775T>C	ENST00000284437.6	+	3	276	c.98T>C	c.(97-99)cTa>cCa	p.L33P	C4orf19_ENST00000381980.4_Missense_Mutation_p.L33P|C4orf19_ENST00000508175.1_Intron	NM_018302.2	NP_060772.2	Q8IY42	CD019_HUMAN	chromosome 4 open reading frame 19	33										large_intestine(1)|lung(3)|skin(3)|stomach(1)|urinary_tract(1)	9						AGCTGCAAGCTAGATGAAGAC	0.458000													10	369					0	0	1	0	0
ZP2	7783	broad.mit.edu	37	16	21212828	21212828	+	Missense_Mutation	SNP	A	A	G			TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr16:21212828A>G	ENST00000574002.1	-	15	2038	c.1556T>C	c.(1555-1557)tTc>tCc	p.F519S	ZP2_ENST00000574091.1_Missense_Mutation_p.F510S|ZP2_ENST00000219593.4_Missense_Mutation_p.F519S|AF001550.7_ENST00000572747.1_RNA			Q05996	ZP2_HUMAN	zona pellucida glycoprotein 2 (sperm receptor)	519	ZP.				binding of sperm to zona pellucida|intracellular protein transport	endoplasmic reticulum|Golgi apparatus|integral to membrane|multivesicular body|plasma membrane|proteinaceous extracellular matrix|stored secretory granule	acrosin binding|coreceptor activity			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(16)|ovary(1)|prostate(1)|stomach(1)	41				GBM - Glioblastoma multiforme(48;0.0573)		TTGGCGGAGGAATCTCACTAG	0.448000													6	117					0	0	1	0	0
AP4B1	10717	broad.mit.edu	37	1	114438891	114438891	+	Missense_Mutation	SNP	T	T	A			TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr1:114438891T>A	ENST00000369569.1	-	8	1779	c.1499A>T	c.(1498-1500)tAt>tTt	p.Y500F	AP4B1-AS1_ENST00000419536.1_RNA|AP4B1_ENST00000462591.1_5'UTR|AP4B1_ENST00000256658.4_Missense_Mutation_p.Y500F|AP4B1_ENST00000369567.1_Missense_Mutation_p.Y332F	NM_001253852.1	NP_001240781.1	Q9Y6B7	AP4B1_HUMAN	adaptor-related protein complex 4, beta 1 subunit	500					intracellular protein transport|vesicle-mediated transport	clathrin adaptor complex|soluble fraction|trans-Golgi network	protein binding|protein transporter activity			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(9)|ovary(3)|prostate(3)	25	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.1e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TATGCAGTAATACAACAAACG	0.448000													6	123					0	0	1	0	0
TMPRSS11F	389208	broad.mit.edu	37	4	68938111	68938111	+	Silent	SNP	C	C	T			TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr4:68938111C>T	ENST00000356291.2	-	5	503	c.444G>A	c.(442-444)aaG>aaA	p.K148K	UBA6-AS1_ENST00000511571.1_RNA|UBA6-AS1_ENST00000499180.2_RNA|UBA6-AS1_ENST00000500538.2_RNA	NM_207407.2	NP_997290.2	Q6ZWK6	TM11F_HUMAN	transmembrane protease, serine 11F	148	SEA.				proteolysis	extracellular region|integral to plasma membrane	serine-type endopeptidase activity			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(4)	39						GATATAAAGCCTTTTCAATTT	0.323000													11	56					0	0	1	0	0
LRRC37A4P	55073	broad.mit.edu	37	17	43587576	43587576	+	RNA	SNP	A	A	G	rs145439557	by1000genomes	TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr17:43587576A>G	ENST00000253803.2	+	0	267				LRRC37A4P_ENST00000579913.1_RNA																							tctgaaaagaaaagaaaaaaa	0.428000													5	52					0	0	1	0	0
CBX4	8535	broad.mit.edu	37	17	77808940	77808940	+	Missense_Mutation	SNP	T	T	A			TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr17:77808940T>A	ENST00000269397.4	-	5	678	c.501A>T	c.(499-501)aaA>aaT	p.K167N	CBX4_ENST00000448310.1_3'UTR	NM_003655.2	NP_003646.2	O00257	CBX4_HUMAN	chromobox homolog 4	167	Interaction with BMI1.				anti-apoptosis|chromatin modification|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	Golgi apparatus|PcG protein complex	enzyme binding|transcription corepressor activity			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(3)|skin(2)|urinary_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(97;0.0102)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			GGTCGTACATTTTGGGGTCGG	0.687000											OREG0024799	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	107					0	0	1	0	0
MRGPRD	116512	broad.mit.edu	37	11	68747597	68747597	+	Silent	SNP	G	G	A			TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr11:68747597G>A	ENST00000309106.3	-	1	858	c.859C>T	c.(859-861)Ctg>Ttg	p.L287L		NM_198923.2	NP_944605.2	Q8TDS7	MRGRD_HUMAN	MAS-related GPR, member D	287						integral to membrane|plasma membrane	G-protein coupled receptor activity			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(7)|pancreas(1)|prostate(2)	22			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			CTGGTGGGCAGCCTGTGGCTC	0.662000													16	76					0	0	1	0	0
LRRC37A4P	55073	broad.mit.edu	37	17	43587569	43587569	+	RNA	SNP	G	G	C	rs149697015	by1000genomes	TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr17:43587569G>C	ENST00000253803.2	+	0	267				LRRC37A4P_ENST00000579913.1_RNA																							aactccgtctgaaaagaaaag	0.443000													4	39					0	0	1	0	0
CUL4B	8450	broad.mit.edu	37	X	119674329	119674329	+	Missense_Mutation	SNP	A	A	T			TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chrX:119674329A>T	ENST00000371322.5	-	11	1593	c.1532T>A	c.(1531-1533)aTa>aAa	p.I511K	CUL4B_ENST00000404115.3_Missense_Mutation_p.I529K|CUL4B_ENST00000336592.6_Missense_Mutation_p.I516K	NM_001079872.1	NP_001073341.1	Q13620	CUL4B_HUMAN	cullin 4B	529					cell cycle|DNA repair|ubiquitin-dependent protein catabolic process	Cul4B-RING ubiquitin ligase complex|nucleus	protein binding|ubiquitin protein ligase binding			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						GATATCAATTATATGGTCAAC	0.308000													4	64					0	0	1	0	0
GPC6	10082	broad.mit.edu	37	13	93879733	93879733	+	Silent	SNP	G	G	T			TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr13:93879733G>T	ENST00000377047.4	+	1	639	c.24G>T	c.(22-24)gtG>gtT	p.V8V		NM_005708.3	NP_005699.1	Q9Y625	GPC6_HUMAN	glypican 6	8						anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(13)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	38	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)				TCGGGGCTGTGATTCTTCCCC	0.642000											OREG0022460	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	12	88					0.0167234	0.0169847	1	1	0
EMC3-AS1	442075	broad.mit.edu	37	3	10035779	10035783	+	RNA	DEL	AGTCT	AGTCT	-	rs35714562		TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr3:10035779_10035783delAGTCT	ENST00000326237.3	+	0	354																											GGGGAAGAGAAGTCTGATCTGACAT	0.380													10	40	---	---	---	---					
SFRP1	6422	broad.mit.edu	37	8	41166638	41166640	+	In_Frame_Del	DEL	GCT	GCT	-	rs3055861		TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr8:41166638_41166640delGCT	ENST00000220772.3	-	1	376_378	c.39_41delAGC	c.(37-42)gcagcc>gcc	p.13_14AA>A		NM_003012.4	NP_003003.3	Q8N474	SFRP1_HUMAN	secreted frizzled-related protein 1	13					brain development|canonical Wnt receptor signaling pathway|cellular response to BMP stimulus|cellular response to estradiol stimulus|cellular response to fibroblast growth factor stimulus|cellular response to heparin|cellular response to hypoxia|cellular response to interleukin-1|cellular response to prostaglandin E stimulus|cellular response to starvation|cellular response to transforming growth factor beta stimulus|cellular response to tumor necrosis factor|cellular response to vitamin D|DNA fragmentation involved in apoptotic nuclear change|dorsal/ventral axis specification|hemopoietic progenitor cell differentiation|hemopoietic stem cell differentiation|menstrual cycle phase|negative regulation of androgen receptor signaling pathway|negative regulation of B cell differentiation|negative regulation of bone remodeling|negative regulation of canonical Wnt receptor signaling pathway involved in controlling type B pancreatic cell proliferation|negative regulation of cell growth|negative regulation of cell migration|negative regulation of cysteine-type endopeptidase activity|negative regulation of epithelial cell proliferation|negative regulation of epithelial to mesenchymal transition|negative regulation of fibroblast apoptosis|negative regulation of fibroblast proliferation|negative regulation of insulin secretion|negative regulation of ossification|negative regulation of osteoblast proliferation|negative regulation of peptidyl-tyrosine phosphorylation|negative regulation of transcription, DNA-dependent|negative regulation of Wnt receptor signaling pathway involved in dorsal/ventral axis specification|osteoblast differentiation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell growth|positive regulation of epithelial cell proliferation|positive regulation of fat cell differentiation|positive regulation of fibroblast apoptosis|positive regulation of focal adhesion assembly|positive regulation of non-canonical Wnt receptor signaling pathway|positive regulation of Rac GTPase activity|positive regulation of smoothened signaling pathway|positive regulation of stress fiber assembly|positive regulation of transcription, DNA-dependent|regulation of angiogenesis|regulation of cell cycle process|response to drug|response to organic cyclic compound|vasculature development	cell surface|cytosol|extracellular space|plasma membrane|proteinaceous extracellular matrix	cysteine-type endopeptidase activity|drug binding|frizzled binding|heparin binding|identical protein binding|PDZ domain binding|Wnt receptor activity|Wnt-protein binding			breast(1)|central_nervous_system(1)|large_intestine(2)|liver(1)|lung(1)|skin(1)	7	Breast(1;9.19e-13)|Ovarian(28;0.00769)|Colorectal(14;0.0305)|Lung SC(25;0.211)	all_lung(54;0.0034)|Lung NSC(58;0.0134)|Hepatocellular(245;0.023)|Esophageal squamous(32;0.0559)	BRCA - Breast invasive adenocarcinoma(1;1.11e-10)|LUSC - Lung squamous cell carcinoma(45;0.00894)|COAD - Colon adenocarcinoma(11;0.0174)			CACGCCCAGGGCTGCCCCGCGGC	0.764													3	6	---	---	---	---					
IRF2BPL	64207	broad.mit.edu	37	14	77493648	77493650	+	In_Frame_Del	DEL	GCG	GCG	-			TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr14:77493648_77493650delGCG	ENST00000238647.3	-	1	1384_1386	c.486_488delCGC	c.(484-489)gccgct>gct	p.162_163AA>A		NM_024496.3	NP_078772.1	Q9H1B7	I2BPL_HUMAN	interferon regulatory factor 2 binding protein-like	162	Poly-Ala.					nucleus				endometrium(2)|kidney(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	11						TTCCACCgcagcggcggcggcgg	0.749													8	8	---	---	---	---					
TCF12	6938	broad.mit.edu	37	15	57523394	57523394	+	Frame_Shift_Del	DEL	T	T	-			TCGA-S9-A6TZ-01A-21D-A32B-08	TCGA-S9-A6TZ-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b34ce7c2-7592-4123-8c4e-50c80b01c9dd	18964457-ef9a-436c-8d75-b11c6c918e6e	g.chr15:57523394delT	ENST00000267811.5	+	9	928	c.624delT	c.(622-624)tctfs	p.S208fs	TCF12_ENST00000560764.1_3'UTR|TCF12_ENST00000543579.1_Frame_Shift_Del_p.S38fs|TCF12_ENST00000333725.5_Frame_Shift_Del_p.S208fs|TCF12_ENST00000557843.1_Frame_Shift_Del_p.S208fs|TCF12_ENST00000438423.2_Frame_Shift_Del_p.S208fs|TCF12_ENST00000452095.2_Frame_Shift_Del_p.S204fs|TCF12_ENST00000537840.1_Frame_Shift_Del_p.L20fs|TCF12_ENST00000343827.3_Frame_Shift_Del_p.S38fs	NM_003205.3|NM_207038.1	NP_003196.1|NP_996921.1	Q99081	HTF4_HUMAN	transcription factor 12	208					immune response|muscle organ development|regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity		TCF12/NR4A3(2)	breast(2)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(1)|lung(13)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	36		Colorectal(260;0.0907)		all cancers(107;0.000313)|GBM - Glioblastoma multiforme(80;0.00878)|STAD - Stomach adenocarcinoma(283;0.239)		ACCGTGAATCTCCTAGTTATC	0.353			T	TEC	extraskeletal myxoid chondrosarcoma								45	106	---	---	---	---					
