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	Genome_Change	Annotation_Transcript	Transcript_Strand	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	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	DrugBank	i_ACHILLES_Top_Genes	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	i_CCLE_SEQ_overlapping_mutations	i_CCLE_SEQ_total_mutations_in_gene	MUTSIG_Significant_Genes	OREGANNO_ID	OREGANNO_Values	i_tumor_f	i_init_t_lod	i_t_lod_fstar	i_t_alt_count	i_t_ref_count	i_normal_best_gt	i_failure_reasons	i_judgement	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	dataset	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	type	classification	start	end	gene	chr	ref_allele	tum_allele1	tum_allele2	context_orig	context65	gene_name	newbase	categ	categ_ignoring_null_categ
HSPA12A	259217	broad.mit.edu	36	10	118454682	118454682	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2567-01	TCGA-06-2567-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:118454682G>A	uc001lct.1	-	c.224C>T	c.(223-225)ACC>ATC	p.T75I	HSPA12A_uc001lcu.1_5'UTR	NM_025015	NP_079291	O43301	HS12A_HUMAN	heat shock 70kDa protein 12A	75							ATP binding			ovary(1)	1														0.489362	68.311358	68.316245	23	24	GG		KEEP	---	---	---	---	capture		all cancers(201;0.0158)	Missense_Mutation	SNP	118454682	118454682	7703	10	G	A	A	44	44	HSPA12A	A	2	2
SORL1	6653	broad.mit.edu	36	11	120950209	120950209	+	Silent	SNP	G	A	A			TCGA-06-2567-01	TCGA-06-2567-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:120950209G>A	uc001pxx.2	+	c.3387G>A	c.(3385-3387)GGG>GGA	p.G1129G		NM_003105	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor containing LDLR class	1129	Extracellular (Potential).|LDL-receptor class A 2.				cholesterol metabolic process|lipid transport|receptor-mediated endocytosis	integral to plasma membrane|low-density lipoprotein particle	low-density lipoprotein particle binding|transmembrane receptor activity			ovary(5)|breast(4)|large_intestine(2)|central_nervous_system(1)|pancreas(1)	13		Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113)								937				0.422383	352.432129	353.887214	117	160	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108)	Silent	SNP	120950209	120950209	15434	11	G	A	A	41	41	SORL1	A	2	2
OR5M1	390168	broad.mit.edu	36	11	56136677	56136677	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2567-01	TCGA-06-2567-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:56136677C>T	uc001nja.1	-	c.878G>A	c.(877-879)CGG>CAG	p.R293Q		NM_001004740	NP_001004740	Q8NGP8	OR5M1_HUMAN	olfactory receptor, family 5, subfamily M,	293	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1														0.354396	398.881772	405.678593	129	235	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	56136677	56136677	11582	11	C	T	T	23	23	OR5M1	T	1	1
OR5AR1	219493	broad.mit.edu	36	11	56188438	56188438	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2567-01	TCGA-06-2567-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:56188438G>A	uc001njc.1	+	c.701G>A	c.(700-702)CGC>CAC	p.R234H		NM_001004730	NP_001004730	Q8NGP9	O5AR1_HUMAN	olfactory receptor, family 5, subfamily AR,	234	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.431535	297.168073	298.150312	104	137	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	56188438	56188438	11555	11	G	A	A	38	38	OR5AR1	A	1	1
DNHD1	144132	broad.mit.edu	36	11	6545660	6545660	+	Nonsense_Mutation	SNP	T	G	G			TCGA-06-2567-01	TCGA-06-2567-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr11:6545660T>G	uc001mea.2	+	c.1152T>G	c.(1150-1152)TAT>TAG	p.Y384*	DNHD1_uc001mdw.2_Nonsense_Mutation_p.Y2169*|DNHD1_uc001meb.2_Nonsense_Mutation_p.Y383*|DNHD1_uc001mec.1_Nonsense_Mutation_p.Y383*|DNHD1_uc009yfg.1_5'Flank	NM_144666	NP_653267	Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1 isoform 1	4115					microtubule-based movement	dynein complex	microtubule motor activity			ovary(2)	2		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)												0.375	47.021901	47.567933	15	25	TT		KEEP	---	---	---	---	capture		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)	Nonsense_Mutation	SNP	6545660	6545660	4851	11	T	G	G	50	50	DNHD1	G	5	4
PIWIL1	9271	broad.mit.edu	36	12	129407516	129407516	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2567-01	TCGA-06-2567-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:129407516G>A	uc001uik.1	+	c.1505G>A	c.(1504-1506)CGA>CAA	p.R502Q	PIWIL1_uc001uij.1_Missense_Mutation_p.R502Q	NM_004764	NP_004755	Q96J94	PIWL1_HUMAN	piwi-like 1	502					gene silencing by RNA|meiosis|multicellular organismal development|regulation of translation|spermatid development	chromatoid body|P granule	mRNA binding|piRNA binding|protein binding			ovary(2)	2	all_neural(191;0.101)|Medulloblastoma(191;0.163)													0.313131	81.807516	84.874775	31	68	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(86;3.02e-06)|Epithelial(86;3.85e-05)|all cancers(50;4.65e-05)	Missense_Mutation	SNP	129407516	129407516	12381	12	G	A	A	37	37	PIWIL1	A	1	1
PIP4K2C	79837	broad.mit.edu	36	12	56275238	56275238	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2567-01	TCGA-06-2567-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:56275238G>A	uc001sot.1	+	c.335G>A	c.(334-336)CGT>CAT	p.R112H	PIP4K2C_uc001sou.1_Missense_Mutation_p.R112H	NM_024779	NP_079055	Q8TBX8	PI42C_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type	112	PIPK.					cytoplasm|membrane	1-phosphatidylinositol-5-phosphate 4-kinase activity|ATP binding|identical protein binding			central_nervous_system(2)|lung(1)	3	Melanoma(17;0.122)									258				0.342318	360.872287	368.994334	127	244	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	56275238	56275238	12362	12	G	A	A	40	40	PIP4K2C	A	1	1
KCNC2	3747	broad.mit.edu	36	12	73728229	73728229	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2567-01	TCGA-06-2567-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:73728229G>A	uc001sxg.1	-	c.1751C>T	c.(1750-1752)ACG>ATG	p.T584M	KCNC2_uc009zry.1_Missense_Mutation_p.T584M|KCNC2_uc001sxe.1_Missense_Mutation_p.T584M|KCNC2_uc001sxf.1_Intron	NM_139137	NP_631875	Q96PR1	KCNC2_HUMAN	Shaw-related voltage-gated potassium channel	584	Cytoplasmic (Potential).				energy reserve metabolic process|regulation of insulin secretion	voltage-gated potassium channel complex	voltage-gated potassium channel activity			breast(2)|pancreas(2)|skin(1)|lung(1)	6														0.383459	454.086214	458.835781	153	246	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	73728229	73728229	8320	12	G	A	A	40	40	KCNC2	A	1	1
SCYL2	55681	broad.mit.edu	36	12	99235780	99235780	+	Silent	SNP	C	T	T			TCGA-06-2567-01	TCGA-06-2567-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:99235780C>T	uc001thn.1	+	c.1341C>T	c.(1339-1341)AAC>AAT	p.N447N	SCYL2_uc009ztw.1_Silent_p.N274N|SCYL2_uc001thm.1_Silent_p.N447N	NM_017988	NP_060458	Q6P3W7	SCYL2_HUMAN	SCY1-like 2 protein	447	HEAT.				endosome to lysosome transport|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of receptor internalization|protein phosphorylation	clathrin-coated vesicle|endosome membrane|Golgi apparatus|perinuclear region of cytoplasm	ATP binding|protein kinase activity|receptor binding			lung(3)|ovary(2)|skin(1)	6										647				0.379845	136.736365	138.372628	49	80	CC		KEEP	---	---	---	---	capture			Silent	SNP	99235780	99235780	14433	12	C	T	T	17	17	SCYL2	T	2	2
HEATR4	399671	broad.mit.edu	36	14	73044703	73044703	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2567-01	TCGA-06-2567-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:73044703C>T	uc010art.1	-	c.1628G>A	c.(1627-1629)GGT>GAT	p.G543D		NM_203309	NP_976054	Q86WZ0	HEAT4_HUMAN	HEAT repeat containing 4	543							binding				0														0.286624	115.470062	121.848745	45	112	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(234;0.00386)|OV - Ovarian serous cystadenocarcinoma(108;0.0719)	Missense_Mutation	SNP	73044703	73044703	7313	14	C	T	T	18	18	HEATR4	T	2	2
C15orf43	145645	broad.mit.edu	36	15	43036442	43036442	+	Missense_Mutation	SNP	G	C	C			TCGA-06-2567-01	TCGA-06-2567-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:43036442G>C	uc001zuk.1	+	c.121G>C	c.(121-123)GAT>CAT	p.D41H		NM_152448	NP_689661	Q8NHR7	CO043_HUMAN	hypothetical protein LOC145645	41											0		all_cancers(109;3.68e-08)|all_epithelial(112;1.05e-06)|Lung NSC(122;1.42e-05)|all_lung(180;0.000112)|Melanoma(134;0.0192)												0.344444	102.196812	104.120686	31	59	GG		KEEP	---	---	---	---	capture		all cancers(107;7.64e-17)|GBM - Glioblastoma multiforme(94;2.03e-06)	Missense_Mutation	SNP	43036442	43036442	1847	15	G	C	C	45	45	C15orf43	C	3	3
CYP11A1	1583	broad.mit.edu	36	15	72424497	72424497	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2567-01	TCGA-06-2567-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:72424497G>A	uc002axt.2	-	c.566C>T	c.(565-567)GCG>GTG	p.A189V	CYP11A1_uc002axs.2_Missense_Mutation_p.A31V|CYP11A1_uc010bjm.1_Missense_Mutation_p.A31V|CYP11A1_uc010bjn.1_Non-coding_Transcript|CYP11A1_uc010bjo.1_Missense_Mutation_p.A189V|CYP11A1_uc010bjp.1_5'Flank|CYP11A1_uc010bjq.1_Missense_Mutation_p.A189V	NM_000781	NP_001093243	P05108	CP11A_HUMAN	cytochrome P450, subfamily XIA isoform a	189			A -> V (in AICSR; no loss of activity).		C21-steroid hormone biosynthetic process|cholesterol metabolic process|oxidation-reduction process|vitamin D metabolic process|xenobiotic metabolic process	mitochondrial matrix	cholesterol monooxygenase (side-chain-cleaving) activity|electron carrier activity|heme binding			ovary(2)	2					Aminoglutethimide(DB00357)|Cholecalciferol(DB00169)|Cimetidine(DB00501)|Clotrimazole(DB00257)|Digitoxin(DB01396)|Digoxin(DB00390)|Medroxyprogesterone(DB00603)|Ouabain(DB01092)|Progesterone(DB00396)|Testosterone(DB00624)|Trilostane(DB01108)	Esophageal Squamous(87;818 1337 4093 9268 37314)								0.452632	124.72002	124.9038	43	52	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	72424497	72424497	4309	15	G	A	A	38	38	CYP11A1	A	1	1
ORAI3	93129	broad.mit.edu	36	16	30868336	30868336	+	Silent	SNP	C	T	T			TCGA-06-2567-01	TCGA-06-2567-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:30868336C>T	uc002eac.1	+	c.225C>T	c.(223-225)GCC>GCT	p.A75A		NM_152288	NP_689501	Q9BRQ5	ORAI3_HUMAN	ORAI calcium release-activated calcium modulator	75	Helical; (Potential).					integral to membrane	protein binding				0														0.35	18.01745	18.415151	7	13	CC		KEEP	---	---	---	---	capture			Silent	SNP	30868336	30868336	11670	16	C	T	T	21	21	ORAI3	T	2	2
ZNF213	7760	broad.mit.edu	36	16	3127510	3127510	+	Silent	SNP	C	T	T			TCGA-06-2567-01	TCGA-06-2567-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:3127510C>T	uc010btg.1	+	c.228C>T	c.(226-228)CCC>CCT	p.P76P	ZNF213_uc002cud.1_Non-coding_Transcript|ZNF213_uc010btf.1_Silent_p.P76P|ZNF213_uc010bth.1_Silent_p.P76P	NM_004220	NP_004211	O14771	ZN213_HUMAN	zinc finger protein 213	76	SCAN box.				regulation of transcription, DNA-dependent|viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0														0.447917	125.966653	126.182899	43	53	CC		KEEP	---	---	---	---	capture			Silent	SNP	3127510	3127510	18360	16	C	T	T	23	23	ZNF213	T	1	1
MYH13	8735	broad.mit.edu	36	17	10147264	10147264	+	Missense_Mutation	SNP	A	G	G			TCGA-06-2567-01	TCGA-06-2567-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr17:10147264A>G	uc002gmk.1	-	c.5641T>C	c.(5641-5643)TCT>CCT	p.S1881P		NM_003802	NP_003793	Q9UKX3	MYH13_HUMAN	myosin, heavy polypeptide 13, skeletal muscle	1881	Potential.				muscle contraction	muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(4)	4														0.386617	341.656022	344.680324	104	165	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	10147264	10147264	10427	17	A	G	G	10	10	MYH13	G	4	4
HELZ	9931	broad.mit.edu	36	17	62535176	62535176	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2567-01	TCGA-06-2567-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:62535176G>A	uc002jfx.2	-	c.4618C>T	c.(4618-4620)CTC>TTC	p.L1540F	HELZ_uc002jfv.2_Non-coding_Transcript|HELZ_uc010der.1_Missense_Mutation_p.L84F	NM_014877	NP_055692			helicase with zinc finger domain											ovary(1)|pancreas(1)	2	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)													0.39604	122.300684	123.248132	40	61	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	62535176	62535176	7332	17	G	A	A	35	35	HELZ	A	2	2
TP53	7157	broad.mit.edu	36	17	7517852	7517852	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2567-01	TCGA-06-2567-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7517852C>T	uc002gim.2	-	c.811G>A	c.(811-813)GAG>AAG	p.E271K	TP53_uc002gig.1_Intron|TP53_uc002gih.1_Missense_Mutation_p.E271K|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.E139K|TP53_uc010cng.1_Missense_Mutation_p.E139K|TP53_uc002gii.1_Missense_Mutation_p.E139K|TP53_uc010cnh.1_Missense_Mutation_p.E271K|TP53_uc010cni.1_Missense_Mutation_p.E271K|TP53_uc002gij.2_Missense_Mutation_p.E271K	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	271	|Interaction with E4F1.|Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		E -> D (in sporadic cancers; somatic mutation).|E -> G (in sporadic cancers; somatic mutation).|E -> V (in an osteosarcoma with no family history; germline mutation and in sporadic cancers; somatic mutation).|E -> K (in sporadic cancers; somatic mutation).|E -> R (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|E -> A (in sporadic cancers; somatic mutation).|E -> Q (in sporadic cancers; somatic mutation).|E -> P (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).		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 gene-specific transcription from RNA polymerase II promoter|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 gene-specific transcription from RNA polymerase II promoter|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	chromatin|cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|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|promoter binding|promoter binding|protease binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|sequence-specific DNA binding transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|ubiquitin protein ligase binding|zinc ion binding	p.E271K(22)|p.E271*(11)|p.0?(6)|p.E271Q(3)|p.G266_E271delGRNSFE(2)|p.F270fs*72(1)|p.?(1)|p.L265_K305del41(1)|p.E271P(1)|p.S269fs*21(1)|p.E258fs*71(1)|p.E271del(1)|p.S269fs*34(1)|p.F270_D281del12(1)|p.E271fs*34(1)|p.E271fs*35(1)|p.E271_R273delEVR(1)		large_intestine(4614)|breast(2344)|upper_aerodigestive_tract(2150)|lung(1958)|ovary(1559)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1212)|stomach(1127)|urinary_tract(1113)|central_nervous_system(1072)|liver(805)|skin(693)|pancreas(370)|biliary_tract(247)|soft_tissue(209)|prostate(192)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(41)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	21904		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)				Pancreas(47;798 1329 9957 10801)		111	p.E271K(HUH28-Tumor)|p.F270fs(EFM192A-Tumor)|p.E271K(J82-Tumor)	690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.26	30.454243	33.060962	13	37	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Missense_Mutation	SNP	7517852	7517852	16923	17	C	T	T	29	29	TP53	T	2	2
TP53	7157	broad.mit.edu	36	17	7518988	7518988	+	Nonsense_Mutation	SNP	G	A	A			TCGA-06-2567-01	TCGA-06-2567-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7518988G>A	uc002gim.2	-	c.586C>T	c.(586-588)CGA>TGA	p.R196*	TP53_uc002gig.1_Nonsense_Mutation_p.R196*|TP53_uc002gih.1_Nonsense_Mutation_p.R196*|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Nonsense_Mutation_p.R64*|TP53_uc010cng.1_Nonsense_Mutation_p.R64*|TP53_uc002gii.1_Nonsense_Mutation_p.R64*|TP53_uc010cnh.1_Nonsense_Mutation_p.R196*|TP53_uc010cni.1_Nonsense_Mutation_p.R196*|TP53_uc002gij.2_Nonsense_Mutation_p.R196*|TP53_uc010cnj.1_Intron|TP53_uc002gin.2_Nonsense_Mutation_p.R103*|TP53_uc002gio.2_Nonsense_Mutation_p.R64*	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	196	Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		R -> L (in sporadic cancers; somatic mutation).|R -> P (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> S (in a sporadic cancer; somatic mutation).|R -> Q (in sporadic cancers; somatic mutation).|R -> G (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 gene-specific transcription from RNA polymerase II promoter|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 gene-specific transcription from RNA polymerase II promoter|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	chromatin|cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|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|promoter binding|promoter binding|protease binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|sequence-specific DNA binding transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|ubiquitin protein ligase binding|zinc ion binding	p.R196*(121)|p.0?(6)|p.R196fs*51(4)|p.A189_V197delAPPQHLIRV(4)|p.I195fs*50(1)|p.P191fs*6(1)|p.I195_G199delIRVEG(1)|p.I195fs*12(1)|p.R196R(1)		large_intestine(4614)|breast(2344)|upper_aerodigestive_tract(2150)|lung(1958)|ovary(1559)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1212)|stomach(1127)|urinary_tract(1113)|central_nervous_system(1072)|liver(805)|skin(693)|pancreas(370)|biliary_tract(247)|soft_tissue(209)|prostate(192)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(41)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	21904		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)				Pancreas(47;798 1329 9957 10801)		111	p.R196*(P31FUJ-Tumor)|p.R196*(CALU6-Tumor)|p.R196*(HUT78-Tumor)|p.H193fs(59M-Tumor)	690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.363636	111.073044	112.692623	36	63	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Nonsense_Mutation	SNP	7518988	7518988	16923	17	G	A	A	39	39	TP53	A	5	1
DSG1	1828	broad.mit.edu	36	18	27188950	27188950	+	Silent	SNP	C	T	T			TCGA-06-2567-01	TCGA-06-2567-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr18:27188950C>T	uc002kwp.1	+	c.2793C>T	c.(2791-2793)TCC>TCT	p.S931S		NM_001942	NP_001933	Q02413	DSG1_HUMAN	desmoglein 1 preproprotein	931	Desmoglein repeat 5.|Cytoplasmic (Potential).				calcium-dependent cell-cell adhesion|cell-cell junction assembly|cellular component disassembly involved in apoptosis|homophilic cell adhesion|protein stabilization	cytosol|desmosome|integral to membrane|internal side of plasma membrane	calcium ion binding|gamma-catenin binding|toxin binding			ovary(2)|central_nervous_system(2)	4														0.368778	494.421263	501.10592	163	279	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(10;0.00559)		Silent	SNP	27188950	27188950	4960	18	C	T	T	23	23	DSG1	T	1	1
FHOD3	80206	broad.mit.edu	36	18	32515473	32515473	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2567-01	TCGA-06-2567-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr18:32515473C>T	uc002kzs.1	+	c.1387C>T	c.(1387-1389)CGG>TGG	p.R463W	FHOD3_uc002kzr.1_Missense_Mutation_p.R463W|FHOD3_uc002kzt.1_Missense_Mutation_p.R463W|FHOD3_uc010dmz.1_Missense_Mutation_p.R178W	NM_025135	NP_079411	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3	463	Potential.				actin cytoskeleton organization	cytoplasm|cytoskeleton	actin binding			large_intestine(2)|breast(2)|ovary(1)	5		all_epithelial(2;0.0181)|Colorectal(2;0.0195)												0.2	24.632489	29.207546	11	44	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	32515473	32515473	6121	18	C	T	T	27	27	FHOD3	T	1	1
ATG4D	84971	broad.mit.edu	36	19	10520590	10520590	+	Silent	SNP	G	A	A			TCGA-06-2567-01	TCGA-06-2567-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:10520590G>A	uc002mov.1	+	c.846G>A	c.(844-846)GCG>GCA	p.A282A	ATG4D_uc010dxh.1_Non-coding_Transcript|ATG4D_uc010dxi.1_Non-coding_Transcript|ATG4D_uc010dxj.1_Intron	NM_032885	NP_116274	Q86TL0	ATG4D_HUMAN	APG4 autophagy 4 homolog D	282					autophagy|protein transport	cytoplasm	cysteine-type endopeptidase activity				0														0.406977	109.910414	110.560271	35	51	GG		KEEP	---	---	---	---	capture	Epithelial(33;9.2e-06)|all cancers(31;3.9e-05)		Silent	SNP	10520590	10520590	1118	19	G	A	A	39	39	ATG4D	A	1	1
ZNF676	163223	broad.mit.edu	36	19	22155016	22155016	+	Missense_Mutation	SNP	G	T	T			TCGA-06-2567-01	TCGA-06-2567-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:22155016G>T	uc002nqs.1	-	c.1343C>A	c.(1342-1344)CCC>CAC	p.P448H		NM_001001411	NP_001001411	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	448					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.114)												0.384937	266.473641	269.236246	92	147	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	22155016	22155016	18678	19	G	T	T	43	43	ZNF676	T	3	3
TMPRSS9	360200	broad.mit.edu	36	19	2347618	2347618	+	Missense_Mutation	SNP	A	G	G			TCGA-06-2567-01	TCGA-06-2567-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr19:2347618A>G	uc002lvw.1	+	c.224A>G	c.(223-225)GAG>GGG	p.E75G	TMPRSS9_uc002lvv.1_Missense_Mutation_p.E75G	NM_182973	NP_892018	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9	75	Extracellular (Potential).				proteolysis	integral to plasma membrane	serine-type endopeptidase activity			ovary(1)	1														0.333333	6.585904	6.886169	4	8	AA		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)	Missense_Mutation	SNP	2347618	2347618	16794	19	A	G	G	11	11	TMPRSS9	G	4	4
GRIK5	2901	broad.mit.edu	36	19	47250342	47250342	+	Silent	SNP	G	A	A			TCGA-06-2567-01	TCGA-06-2567-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:47250342G>A	uc002osj.1	-	c.1026C>T	c.(1024-1026)CAC>CAT	p.H342H	GRIK5_uc010eib.1_Silent_p.H274H	NM_002088	NP_002079	Q16478	GRIK5_HUMAN	glutamate receptor KA2 precursor	342	Extracellular (Potential).					cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity				0		Prostate(69;0.059)			L-Glutamic Acid(DB00142)									0.33913	100.714287	103.333995	39	76	GG		KEEP	---	---	---	---	capture			Silent	SNP	47250342	47250342	7056	19	G	A	A	40	40	GRIK5	A	1	1
CACNG8	59283	broad.mit.edu	36	19	59158331	59158331	+	Silent	SNP	T	G	G			TCGA-06-2567-01	TCGA-06-2567-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:59158331T>G	uc002qcs.1	+	c.123T>G	c.(121-123)ACT>ACG	p.T41T		NM_031895	NP_114101	Q8WXS5	CCG8_HUMAN	voltage-dependent calcium channel gamma-8	41					regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|endocytic vesicle membrane|postsynaptic density|voltage-gated calcium channel complex	voltage-gated calcium channel activity				0	all_cancers(19;0.0385)|all_epithelial(19;0.0207)|all_lung(19;0.145)|Lung NSC(19;0.168)|Ovarian(34;0.19)													0.307692	30.483982	31.770656	12	27	TT		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(134;0.162)	Silent	SNP	59158331	59158331	2679	19	T	G	G	55	55	CACNG8	G	4	4
NLRP4	147945	broad.mit.edu	36	19	61062396	61062396	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2567-01	TCGA-06-2567-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:61062396G>A	uc002qmd.2	+	c.1825G>A	c.(1825-1827)GTC>ATC	p.V609I	NLRP4_uc002qme.1_Missense_Mutation_p.V609I|NLRP4_uc002qmf.1_Missense_Mutation_p.V534I|NLRP4_uc010etf.1_Missense_Mutation_p.V440I	NM_134444	NP_604393	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	609							ATP binding	p.V609F(1)		ovary(5)|lung(3)|kidney(1)|pancreas(1)	10		Colorectal(82;0.0002)|Ovarian(87;0.221)												0.324324	121.235408	125.296481	48	100	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(193;0.0606)	Missense_Mutation	SNP	61062396	61062396	10882	19	G	A	A	48	48	NLRP4	A	2	2
TCHH	7062	broad.mit.edu	36	1	150349384	150349384	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2567-01	TCGA-06-2567-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:150349384G>A	uc001ezp.2	-	c.2933C>T	c.(2932-2934)CCG>CTG	p.P978L	TCHH_uc009wne.1_Missense_Mutation_p.P978L	NM_007113	NP_009044	Q07283	TRHY_HUMAN	trichohyalin	978	10 X 30 AA tandem repeats.|4-3.				keratinization	cytoskeleton	calcium ion binding			ovary(3)|kidney(1)|central_nervous_system(1)	5	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)													0.174312	109.069467	141.832066	57	270	GG		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.206)		Missense_Mutation	SNP	150349384	150349384	16226	1	G	A	A	39	39	TCHH	A	1	1
OR2M3	127062	broad.mit.edu	36	1	246433695	246433695	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2567-01	TCGA-06-2567-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:246433695C>T	uc001ieb.1	+	c.703C>T	c.(703-705)CGC>TGC	p.R235C		NM_001004689	NP_001004689	Q8NG83	OR2M3_HUMAN	olfactory receptor, family 2, subfamily M,	235	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)													0.370093	568.920901	576.84977	198	337	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(106;0.0245)		Missense_Mutation	SNP	246433695	246433695	11417	1	C	T	T	31	31	OR2M3	T	1	1
GBP4	115361	broad.mit.edu	36	1	89428417	89428417	+	Silent	SNP	C	T	T			TCGA-06-2567-01	TCGA-06-2567-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:89428417C>T	uc001dnb.1	-	c.1089G>A	c.(1087-1089)ACG>ACA	p.T363T		NM_052941	NP_443173	Q96PP9	GBP4_HUMAN	guanylate binding protein 4	363						cytoplasm	GTP binding|GTPase activity				0														0.384615	98.706022	99.766855	35	56	CC		KEEP	---	---	---	---	capture		all cancers(265;0.00723)|Epithelial(280;0.0291)	Silent	SNP	89428417	89428417	6542	1	C	T	T	27	27	GBP4	T	1	1
DYNLRB1	83658	broad.mit.edu	36	20	32586244	32586244	+	Missense_Mutation	SNP	A	T	T			TCGA-06-2567-01	TCGA-06-2567-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr20:32586244A>T	uc002xal.1	+	c.231A>T	c.(229-231)GAA>GAT	p.E77D	DYNLRB1_uc002xam.1_Non-coding_Transcript|DYNLRB1_uc002xan.1_Non-coding_Transcript	NM_014183	NP_054902	Q9NP97	DLRB1_HUMAN	Roadblock-1	77					microtubule-based movement|transport|visual behavior	cytoplasmic dynein complex|microtubule	microtubule motor activity				0														0.269841	40.344119	43.35756	17	46	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	32586244	32586244	5036	20	A	T	T	1	1	DYNLRB1	T	4	4
C21orf91	54149	broad.mit.edu	36	21	18090883	18090883	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2567-01	TCGA-06-2567-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr21:18090883C>T	uc002yko.2	-	c.551G>A	c.(550-552)CGT>CAT	p.R184H	C21orf91_uc002ykq.2_Missense_Mutation_p.R184H|C21orf91_uc002ykp.2_Missense_Mutation_p.R184H	NM_001100420	NP_001093890	Q9NYK6	EURL_HUMAN	early undifferentiated retina and lens isoform	184										ovary(1)	1														0.300813	301.772149	314.799282	111	258	CC		KEEP	---	---	---	---	capture		Epithelial(23;8.76e-05)|all cancers(11;0.000422)|OV - Ovarian serous cystadenocarcinoma(11;0.0107)|Lung(58;0.0129)|COAD - Colon adenocarcinoma(22;0.0303)|LUSC - Lung squamous cell carcinoma(23;0.0381)|Colorectal(24;0.0929)	Missense_Mutation	SNP	18090883	18090883	2214	21	C	T	T	19	19	C21orf91	T	1	1
DSCAM	1826	broad.mit.edu	36	21	40387535	40387535	+	Missense_Mutation	SNP	A	C	C			TCGA-06-2567-01	TCGA-06-2567-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr21:40387535A>C	uc002yyq.1	-	c.3833T>G	c.(3832-3834)GTC>GGC	p.V1278G	DSCAM_uc002yyr.1_Non-coding_Transcript	NM_001389	NP_001380	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule isoform	1278	Fibronectin type-III 4.|Extracellular (Potential).				cell adhesion|dendrite self-avoidance|negative regulation of cell adhesion|positive regulation of axon extension involved in axon guidance|positive regulation of phosphorylation	axon|extracellular region|growth cone|integral to plasma membrane|membrane fraction	protein binding			ovary(6)	6		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				Melanoma(134;970 1778 1785 21664 32388)								0.162162	8.530396	12.550906	6	31	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	40387535	40387535	4952	21	A	C	C	10	10	DSCAM	C	4	4
WDR4	10785	broad.mit.edu	36	21	43169934	43169934	+	Silent	SNP	G	A	A			TCGA-06-2567-01	TCGA-06-2567-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr21:43169934G>A	uc002zci.1	-	c.102C>T	c.(100-102)AGC>AGT	p.S34S	WDR4_uc002zck.1_Silent_p.S34S|WDR4_uc010gpg.1_Silent_p.S34S|WDR4_uc002zcl.1_5'UTR|WDR4_uc010gph.1_5'UTR	NM_033661	NP_387510	P57081	WDR4_HUMAN	WD repeat domain 4 protein	34					tRNA modification	cytoplasm|nucleoplasm	protein binding			ovary(1)	1														0.344828	83.755455	85.590519	30	57	GG		KEEP	---	---	---	---	capture		Colorectal(79;0.0165)|Lung(125;0.0484)|STAD - Stomach adenocarcinoma(101;0.0624)|COAD - Colon adenocarcinoma(84;0.128)|LUSC - Lung squamous cell carcinoma(216;0.244)	Silent	SNP	43169934	43169934	17866	21	G	A	A	42	42	WDR4	A	2	2
SBF1	6305	broad.mit.edu	36	22	49241950	49241950	+	Missense_Mutation	SNP	C	A	A			TCGA-06-2567-01	TCGA-06-2567-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr22:49241950C>A	uc003blh.1	-	c.3923G>T	c.(3922-3924)CGG>CTG	p.R1308L	SBF1_uc003ble.1_5'Flank|SBF1_uc003blf.1_5'Flank|SBF1_uc003blg.1_Missense_Mutation_p.R1282L	NM_002972	NP_002963	O95248	MTMR5_HUMAN	SET binding factor 1 isoform a	1282	Myotubularin phosphatase.				protein dephosphorylation	integral to membrane|nucleus	protein tyrosine/serine/threonine phosphatase activity				0		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)												0.4	6.549199	6.592872	2	3	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(115;0.206)|LUAD - Lung adenocarcinoma(64;0.247)	Missense_Mutation	SNP	49241950	49241950	14339	22	C	A	A	23	23	SBF1	A	3	3
SPEG	10290	broad.mit.edu	36	2	220057510	220057510	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2567-01	TCGA-06-2567-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:220057510G>A	uc010fwg.1	+	c.7081G>A	c.(7081-7083)GGC>AGC	p.G2361S		NM_005876	NP_005867	Q15772	SPEG_HUMAN	SPEG complex locus	2361	Arg-rich.				muscle organ development|negative regulation of cell proliferation|protein phosphorylation	nucleus	ATP binding|protein serine/threonine kinase activity			ovary(4)|stomach(2)|central_nervous_system(1)	7		Renal(207;0.0183)								482				0.333333	17.344339	17.786981	6	12	GG		KEEP	---	---	---	---	capture		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)	Missense_Mutation	SNP	220057510	220057510	15548	2	G	A	A	39	39	SPEG	A	1	1
IQCA1	79781	broad.mit.edu	36	2	237038942	237038942	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2567-01	TCGA-06-2567-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:237038942C>T	uc002vvz.1	-	c.871G>A	c.(871-873)GTG>ATG	p.V291M	IQCA1_uc002vwa.1_Non-coding_Transcript|IQCA1_uc002vwb.1_Missense_Mutation_p.V298M	NM_024726	NP_079002	Q86XH1	IQCA1_HUMAN	IQ motif containing with AAA domain 1	291							ATP binding			ovary(1)	1														0.416667	117.781972	118.364165	40	56	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	237038942	237038942	8103	2	C	T	T	19	19	IQCA1	T	1	1
SLC15A2	6565	broad.mit.edu	36	3	123130044	123130044	+	Silent	SNP	G	T	T			TCGA-06-2567-01	TCGA-06-2567-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:123130044G>T	uc003eep.1	+	c.1293G>T	c.(1291-1293)GTG>GTT	p.V431V		NM_021082	NP_066568	Q16348	S15A2_HUMAN	solute carrier family 15 (H+/peptide	431					protein transport	integral to plasma membrane	peptide:hydrogen symporter activity|protein binding				0					Cefadroxil(DB01140)									0.393258	312.722524	315.383875	105	162	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(114;0.0967)	Silent	SNP	123130044	123130044	14894	3	G	T	T	47	47	SLC15A2	T	3	3
EPHB1	2047	broad.mit.edu	36	3	136152923	136152923	+	Nonsense_Mutation	SNP	C	A	A			TCGA-06-2567-01	TCGA-06-2567-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:136152923C>A	uc003eqt.1	+	c.144C>A	c.(142-144)TAC>TAA	p.Y48*	EPHB1_uc010htz.1_Non-coding_Transcript	NM_004441	NP_004432	P54762	EPHB1_HUMAN	ephrin receptor EphB1 precursor	48	Extracellular (Potential).				transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding			lung(7)|ovary(4)|stomach(3)|central_nervous_system(2)|large_intestine(1)|pancreas(1)	18										376				0.266667	7.285684	8.032909	4	11	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	136152923	136152923	5367	3	C	A	A	19	19	EPHB1	A	5	3
COPB2	9276	broad.mit.edu	36	3	140580700	140580700	+	Silent	SNP	G	A	A			TCGA-06-2567-01	TCGA-06-2567-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:140580700G>A	uc003etf.2	-	c.234C>T	c.(232-234)GAC>GAT	p.D78D	COPB2_uc010hui.1_Silent_p.D49D	NM_004766	NP_004757	P35606	COPB2_HUMAN	coatomer protein complex, subunit beta 2 (beta	78	WD 2.				COPI coating of Golgi vesicle|intra-Golgi vesicle-mediated transport|intracellular protein transport|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat|cytosol	protein binding|structural molecule activity			ovary(2)	2														0.269841	43.04445	46.057252	17	46	GG		KEEP	---	---	---	---	capture			Silent	SNP	140580700	140580700	3867	3	G	A	A	48	48	COPB2	A	2	2
CSPG5	10675	broad.mit.edu	36	3	47594244	47594244	+	Silent	SNP	C	T	T			TCGA-06-2567-01	TCGA-06-2567-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:47594244C>T	uc003crp.2	-	c.276G>A	c.(274-276)TCG>TCA	p.S92S	CSPG5_uc003crn.1_5'UTR|CSPG5_uc003cro.2_Silent_p.S92S	NM_006574	NP_006565	O95196	CSPG5_HUMAN	chondroitin sulfate proteoglycan 5 (neuroglycan	92	Extracellular (Potential).				cell differentiation|intracellular transport|nervous system development|regulation of growth	endoplasmic reticulum membrane|Golgi-associated vesicle membrane|integral to plasma membrane|membrane fraction	growth factor activity			ovary(1)|central_nervous_system(1)	2														0.352273	87.298058	88.991818	31	57	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(193;0.000266)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)	Silent	SNP	47594244	47594244	4102	3	C	T	T	23	23	CSPG5	T	1	1
VPRBP	9730	broad.mit.edu	36	3	51431319	51431319	+	Silent	SNP	G	A	A			TCGA-06-2567-01	TCGA-06-2567-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:51431319G>A	uc003dbe.1	-	c.3288C>T	c.(3286-3288)TTC>TTT	p.F1096F	VPRBP_uc003dbf.1_Silent_p.F372F	NM_014703	NP_055518	Q9Y4B6	VPRBP_HUMAN	HIV-1 Vpr binding protein	1096	WD 1.|WD repeat-like region.				interspecies interaction between organisms	cytoplasm|nucleus	protein binding			ovary(1)|skin(1)	2														0.208333	6.674954	8.692778	5	19	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(193;0.000272)|Kidney(197;0.000729)|KIRC - Kidney renal clear cell carcinoma(197;0.000875)	Silent	SNP	51431319	51431319	17752	3	G	A	A	45	45	VPRBP	A	2	2
OR5K1	26339	broad.mit.edu	36	3	99671353	99671353	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2567-01	TCGA-06-2567-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:99671353G>A	uc003dsm.1	+	c.243G>A	c.(241-243)ATG>ATA	p.M81I		NM_001004736	NP_001004736	Q8NHB7	OR5K1_HUMAN	olfactory receptor, family 5, subfamily K,	81	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			large_intestine(1)	1														0.364286	415.229597	422.04705	153	267	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	99671353	99671353	11576	3	G	A	A	48	48	OR5K1	A	2	2
GNRHR	2798	broad.mit.edu	36	4	68292882	68292882	+	Silent	SNP	G	A	A			TCGA-06-2567-01	TCGA-06-2567-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:68292882G>A	uc003hdn.1	-	c.741C>T	c.(739-741)CAC>CAT	p.H247H	LOC550112_uc003hdl.2_Intron|GNRHR_uc003hdm.1_Nonsense_Mutation_p.R205*	NM_000406	NP_000397	P30968	GNRHR_HUMAN	gonadotropin-releasing hormone receptor isoform	247	Cytoplasmic (Potential).			H -> T (in Ref. 8; CAB17082).	multicellular organismal development	integral to plasma membrane	gonadotropin-releasing hormone receptor activity			ovary(1)	1					Abarelix(DB00106)|Cetrorelix(DB00050)|Danazol(DB01406)|Gonadorelin(DB00644)|Leuprolide(DB00007)|Nafarelin(DB00666)									0.433333	121.515961	121.863729	39	51	GG		KEEP	---	---	---	---	capture			Silent	SNP	68292882	68292882	6818	4	G	A	A	40	40	GNRHR	A	1	1
AREG	374	broad.mit.edu	36	4	75531162	75531162	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2567-01	TCGA-06-2567-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:75531162C>T	uc003hif.1	+	c.109C>T	c.(109-111)CGT>TGT	p.R37C		NM_001657	NP_001648	P15514	AREG_HUMAN	amphiregulin preproprotein	37					cell proliferation|cell-cell signaling|epidermal growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|positive regulation of DNA replication	cell surface|extracellular space|integral to membrane	cytokine activity|growth factor activity				0														0.719424	336.86502	342.893833	100	39	CC		KEEP	---	---	---	---	capture	Lung(101;0.196)		Missense_Mutation	SNP	75531162	75531162	854	4	C	T	T	27	27	AREG	T	1	1
ITGA1	3672	broad.mit.edu	36	5	52219541	52219541	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2567-01	TCGA-06-2567-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:52219541G>A	uc003jou.1	+	c.911G>A	c.(910-912)CGG>CAG	p.R304Q	ITGA1_uc003jov.1_Non-coding_Transcript	NM_181501	NP_852478	P56199	ITA1_HUMAN	integrin, alpha 1 precursor	304	Extracellular (Potential).|VWFA.				axon guidance|cell-matrix adhesion|integrin-mediated signaling pathway|muscle contraction	integrin complex	collagen binding|receptor activity			ovary(1)|lung(1)	2		Lung NSC(810;5.05e-05)|Breast(144;0.0851)												0.373134	155.12797	157.017298	50	84	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	52219541	52219541	8176	5	G	A	A	39	39	ITGA1	A	1	1
ASCC3	10973	broad.mit.edu	36	6	101161450	101161450	+	Missense_Mutation	SNP	A	G	G			TCGA-06-2567-01	TCGA-06-2567-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr6:101161450A>G	uc003pqk.1	-	c.4931T>C	c.(4930-4932)ATT>ACT	p.I1644T		NM_006828	NP_006819	Q8N3C0	HELC1_HUMAN	activating signal cointegrator 1 complex subunit	1644	Helicase C-terminal 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|microtubule cytoskeleton	ATP binding|ATP-dependent helicase activity|nucleic acid binding			ovary(5)	5		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)												0.365385	125.62692	127.282608	38	66	AA		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)	Missense_Mutation	SNP	101161450	101161450	1051	6	A	G	G	4	4	ASCC3	G	4	4
CITED2	10370	broad.mit.edu	36	6	139736640	139736640	+	Silent	SNP	C	T	T			TCGA-06-2567-01	TCGA-06-2567-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:139736640C>T	uc003qip.1	-	c.135G>A	c.(133-135)CAG>CAA	p.Q45Q	CITED2_uc010khb.1_Silent_p.Q45Q	NM_006079	NP_006070	Q99967	CITE2_HUMAN	Cbp/p300-interacting transactivator, with	45	His-rich.				anti-apoptosis|cell proliferation|determination of left/right symmetry|heart development|liver development|negative regulation of cell migration|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell cycle|positive regulation of cell-cell adhesion|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of peroxisome proliferator activated receptor signaling pathway|positive regulation of transcription regulator activity|positive regulation of transforming growth factor beta receptor signaling pathway|response to estrogen stimulus|response to fluid shear stress|response to hypoxia	cytoplasm|nuclear chromatin|nucleus	LBD domain binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription activator activity|transcription coactivator activity|transcription corepressor activity|transcription repressor activity				0	Breast(32;0.226)					NSCLC(98;1219 1550 33720 43229 49330)								0.384615	56.498029	57.101057	20	32	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(68;0.000171)|OV - Ovarian serous cystadenocarcinoma(155;0.00134)	Silent	SNP	139736640	139736640	3575	6	C	T	T	28	28	CITED2	T	2	2
COL11A2	1302	broad.mit.edu	36	6	33261475	33261475	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2567-01	TCGA-06-2567-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:33261475C>T	uc003ocx.1	-	c.857G>A	c.(856-858)GGG>GAG	p.G286E	COL11A2_uc003ocy.1_Intron|COL11A2_uc003ocz.1_Intron	NM_080680	NP_542411	P13942	COBA2_HUMAN	collagen, type XI, alpha 2 isoform 1	286	Nonhelical region.				cartilage development|cell adhesion|collagen fibril organization|sensory perception of sound|soft palate development	collagen type XI	extracellular matrix structural constituent conferring tensile strength|protein binding, bridging			ovary(3)|skin(1)	4						Melanoma(1;90 116 3946 5341 17093)								0.405797	87.405296	87.93466	28	41	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	33261475	33261475	3806	6	C	T	T	22	22	COL11A2	T	2	2
DSP	1832	broad.mit.edu	36	6	7514485	7514485	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2567-01	TCGA-06-2567-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:7514485C>T	uc003mxp.1	+	c.1487C>T	c.(1486-1488)ACG>ATG	p.T496M	DSP_uc003mxq.1_Missense_Mutation_p.T496M	NM_004415	NP_004406	P15924	DESP_HUMAN	desmoplakin isoform I	496	Globular 1.|Interacts with plakophilin 1 and junction plakoglobin.				cellular component disassembly involved in apoptosis|keratinocyte differentiation|peptide cross-linking	cornified envelope|cytoplasm|desmosome	protein binding, bridging|structural constituent of cytoskeleton			central_nervous_system(6)|ovary(2)	8	Ovarian(93;0.0584)	all_hematologic(90;0.236)												0.36129	155.995138	158.603661	56	99	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(45;0.000508)	Missense_Mutation	SNP	7514485	7514485	4965	6	C	T	T	19	19	DSP	T	1	1
SLC26A5	375611	broad.mit.edu	36	7	102838166	102838166	+	Missense_Mutation	SNP	A	T	T			TCGA-06-2567-01	TCGA-06-2567-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr7:102838166A>T	uc003vbz.1	-	c.637T>A	c.(637-639)TTT>ATT	p.F213I	SLC26A5_uc003vbt.1_Missense_Mutation_p.F213I|SLC26A5_uc003vbu.1_Missense_Mutation_p.F213I|SLC26A5_uc003vbv.1_Missense_Mutation_p.F213I|SLC26A5_uc003vbw.1_Non-coding_Transcript|SLC26A5_uc003vbx.1_Missense_Mutation_p.F213I|SLC26A5_uc003vby.1_Non-coding_Transcript|SLC26A5_uc010liy.1_Non-coding_Transcript	NM_198999	NP_945350	P58743	S26A5_HUMAN	prestin isoform a	213	Helical; Name=5; (Potential).				regulation of cell shape|sensory perception of sound	integral to membrane	motor activity|secondary active sulfate transmembrane transporter activity			ovary(1)	1														0.285714	85.376085	90.299741	34	85	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	102838166	102838166	15017	7	A	T	T	2	2	SLC26A5	T	4	4
COPG2	26958	broad.mit.edu	36	7	129947607	129947607	+	Missense_Mutation	SNP	T	C	C			TCGA-06-2567-01	TCGA-06-2567-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:129947607T>C	uc003vqh.1	-	c.532A>G	c.(532-534)ATC>GTC	p.I178V		NM_012133	NP_036265	Q9UBF2	COPG2_HUMAN	coatomer protein complex, subunit gamma 2	178					intra-Golgi vesicle-mediated transport|intracellular protein transport|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat	protein binding|structural molecule activity				0	Melanoma(18;0.0435)													0.310345	87.416369	90.190892	27	60	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	129947607	129947607	3870	7	T	C	C	50	50	COPG2	C	4	4
HOXA6	3203	broad.mit.edu	36	7	27151907	27151907	+	Missense_Mutation	SNP	G	C	C			TCGA-06-2567-01	TCGA-06-2567-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:27151907G>C	uc003syo.1	-	c.597C>G	c.(595-597)ATC>ATG	p.I199M	HOXA5_uc003syn.1_5'Flank	NM_024014	NP_076919	P31267	HXA6_HUMAN	homeobox A6	199	Homeobox.				regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity			ovary(1)|central_nervous_system(1)	2														0.222222	206.897671	231.786649	78	273	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	27151907	27151907	7588	7	G	C	C	45	45	HOXA6	C	3	3
TXNDC3	51314	broad.mit.edu	36	7	37900667	37900667	+	Nonsense_Mutation	SNP	C	T	T			TCGA-06-2567-01	TCGA-06-2567-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:37900667C>T	uc003tfn.1	+	c.1474C>T	c.(1474-1476)CAA>TAA	p.Q492*		NM_016616	NP_057700	Q8N427	TXND3_HUMAN	thioredoxin domain containing 3	492	NDK 3.				cell differentiation|cell redox homeostasis|CTP biosynthetic process|GTP biosynthetic process|multicellular organismal development|spermatogenesis|UTP biosynthetic process	cytoplasm|microtubule cytoskeleton	ATP binding|nucleoside diphosphate kinase activity			ovary(1)|breast(1)|central_nervous_system(1)	3						Ovarian(108;903 1537 27096 29907 47400)								0.322835	107.122459	110.666127	41	86	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	37900667	37900667	17354	7	C	T	T	25	25	TXNDC3	T	5	2
COBL	23242	broad.mit.edu	36	7	51064229	51064229	+	Silent	SNP	T	C	C			TCGA-06-2567-01	TCGA-06-2567-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:51064229T>C	uc003tpr.2	-	c.2058A>G	c.(2056-2058)ACA>ACG	p.T686T	COBL_uc003tpp.2_Silent_p.T472T|COBL_uc003tpq.2_Silent_p.T627T|COBL_uc003tps.1_Silent_p.T659T|COBL_uc003tpo.2_Silent_p.T228T	NM_015198	NP_056013	O75128	COBL_HUMAN	cordon-bleu homolog	686										ovary(2)|skin(1)	3	Glioma(55;0.08)					NSCLC(189;2119 2138 12223 30818 34679)								0.266393	181.077617	193.098133	65	179	TT		KEEP	---	---	---	---	capture			Silent	SNP	51064229	51064229	3791	7	T	C	C	51	51	COBL	C	4	4
POM121L12	285877	broad.mit.edu	36	7	53071578	53071578	+	Silent	SNP	C	T	T			TCGA-06-2567-01	TCGA-06-2567-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:53071578C>T	uc003tpz.1	+	c.720C>T	c.(718-720)CTC>CTT	p.L240L		NM_182595	NP_872401	Q8N7R1	P1L12_HUMAN	hypothetical protein LOC285877	240											0														0.422414	141.471903	142.075877	49	67	CC		KEEP	---	---	---	---	capture			Silent	SNP	53071578	53071578	12669	7	C	T	T	31	31	POM121L12	T	1	1
CALN1	83698	broad.mit.edu	36	7	71209086	71209086	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2567-01	TCGA-06-2567-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:71209086C>T	uc003twb.2	-	c.374G>A	c.(373-375)CGC>CAC	p.R125H	CALN1_uc003twa.2_Missense_Mutation_p.R83H|CALN1_uc003twc.2_Missense_Mutation_p.R83H	NM_031468	NP_113656	Q9BXU9	CABP8_HUMAN	calneuron 1 isoform 1	83	EF-hand 2.|Cytoplasmic (Potential).					Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|plasma membrane	calcium ion binding				0		all_cancers(73;0.069)|Lung NSC(55;0.0658)|all_lung(88;0.0912)|all_epithelial(88;0.161)												0.222222	32.415611	36.888478	14	49	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	71209086	71209086	2708	7	C	T	T	27	27	CALN1	T	1	1
CSMD3	114788	broad.mit.edu	36	8	113598550	113598550	+	Missense_Mutation	SNP	T	A	A			TCGA-06-2567-01	TCGA-06-2567-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr8:113598550T>A	uc003ynu.1	-	c.4645A>T	c.(4645-4647)ACT>TCT	p.T1549S	CSMD3_uc003ynt.1_Missense_Mutation_p.T1509S|CSMD3_uc003ynv.1_Missense_Mutation_p.T1408S|CSMD3_uc003yns.1_Missense_Mutation_p.T821S	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	1549	Extracellular (Potential).|Sushi 8.					integral to membrane|plasma membrane				ovary(20)|lung(11)|kidney(8)|large_intestine(6)|skin(3)|central_nervous_system(2)|urinary_tract(1)|breast(1)	52										2888	TCGA Ovarian(7;0.080)			0.379085	176.91462	178.876632	58	95	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	113598550	113598550	4087	8	T	A	A	59	59	CSMD3	A	4	4
SAMD12	401474	broad.mit.edu	36	8	119461110	119461110	+	Silent	SNP	C	T	T			TCGA-06-2567-01	TCGA-06-2567-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:119461110C>T	uc003yom.2	-	c.333G>A	c.(331-333)CTG>CTA	p.L111L	SAMD12_uc010mda.1_Silent_p.L111L|SAMD12_uc010mdb.1_Non-coding_Transcript	NM_207506	NP_997389	Q8N8I0	SAM12_HUMAN	sterile alpha motif domain containing 12 isoform	111	SAM.									ovary(1)	1	all_cancers(13;3.91e-25)|Lung NSC(37;1.13e-07)|Ovarian(258;0.0249)													0.340278	130.929264	134.177226	49	95	CC		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(47;0.00391)		Silent	SNP	119461110	119461110	14297	8	C	T	T	25	25	SAMD12	T	2	2
SH2D4A	63898	broad.mit.edu	36	8	19221361	19221361	+	Missense_Mutation	SNP	A	G	G			TCGA-06-2567-01	TCGA-06-2567-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr8:19221361A>G	uc003wzb.1	+	c.23A>G	c.(22-24)GAG>GGG	p.E8G	SH2D4A_uc003wzc.1_Missense_Mutation_p.E8G	NM_022071	NP_071354	Q9H788	SH24A_HUMAN	SH2 domain containing 4A	8						cytoplasm|nucleus	protein binding				0														0.3625	99.159531	100.487932	29	51	AA		KEEP	---	---	---	---	capture		Colorectal(111;0.0732)	Missense_Mutation	SNP	19221361	19221361	14726	8	A	G	G	11	11	SH2D4A	G	4	4
PREX2	80243	broad.mit.edu	36	8	69193393	69193393	+	Missense_Mutation	SNP	C	A	A			TCGA-06-2567-01	TCGA-06-2567-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:69193393C>A	uc003xxv.1	+	c.3381C>A	c.(3379-3381)AGC>AGA	p.S1127R		NM_024870	NP_079146	Q70Z35	PREX2_HUMAN	DEP domain containing 2 isoform a	1127					G-protein coupled receptor protein signaling pathway|intracellular signal transduction	intracellular	protein binding|Rac GTPase activator activity|Rac guanyl-nucleotide exchange factor activity			large_intestine(4)|pancreas(3)|lung(2)|skin(2)|ovary(1)|kidney(1)	13										1011				0.445255	182.768901	183.124219	61	76	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	69193393	69193393	12920	8	C	A	A	26	26	PREX2	A	3	3
WWC3	55841	broad.mit.edu	36	X	10056666	10056666	+	Nonsense_Mutation	SNP	G	T	T			TCGA-06-2567-01	TCGA-06-2567-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:10056666G>T	uc004csx.2	+	c.2350G>T	c.(2350-2352)GAG>TAG	p.E784*	WWC3_uc010nds.1_Nonsense_Mutation_p.E448*|WWC3_uc010ndt.1_Non-coding_Transcript	NM_015691	NP_056506	Q9ULE0	WWC3_HUMAN	WWC family member 3	784	Potential.									ovary(4)	4														0.785714	31.926339	32.979195	11	3	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	10056666	10056666	17987	23	G	T	T	41	41	WWC3	T	5	3
HUWE1	10075	broad.mit.edu	36	X	53689118	53689118	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2567-01	TCGA-06-2567-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:53689118G>A	uc004dso.1	-	c.374C>T	c.(373-375)TCC>TTC	p.S125F	HUWE1_uc004dsp.1_Missense_Mutation_p.S125F	NM_031407	NP_113584	Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1	125					base-excision repair|cell differentiation|histone ubiquitination|protein monoubiquitination|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	DNA binding|protein binding|ubiquitin-protein ligase activity			ovary(8)|large_intestine(4)|breast(4)|kidney(1)	17														0.236842	7.268897	9.993933	9	29	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	53689118	53689118	7761	23	G	A	A	41	41	HUWE1	A	2	2
B2M	567	broad.mit.edu	36	15	42795090	42795093	+	Frame_Shift_Del	DEL	TCTA	-	-			TCGA-06-2567-01	TCGA-06-2567-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:42795090_42795093delTCTA	uc001zuc.1	+	c.245_248delTCTA	c.(244-249)TTCTATfs	p.F82fs	B2M_uc010bdx.1_Intron	NM_004048	NP_004039	P61769	B2MG_HUMAN	beta-2-microglobulin precursor	82_83	Ig-like C1-type.				antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|regulation of defense response to virus by virus|viral reproduction	early endosome membrane|Golgi membrane|MHC class I protein complex	protein binding			ovary(2)	2		all_cancers(109;1.88e-13)|all_epithelial(112;2.13e-11)|Lung NSC(122;2.22e-07)|all_lung(180;1.81e-06)|Melanoma(134;0.0122)		all cancers(107;4.16e-21)|GBM - Glioblastoma multiforme(94;8.97e-07)|COAD - Colon adenocarcinoma(120;0.0357)|Colorectal(105;0.0377)|Lung(196;0.0903)|LUSC - Lung squamous cell carcinoma(244;0.192)										0.35			91	169				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	42795090	42795093	1265	15	TCTA	-	-	62	62	B2M	-	5	5
CNTNAP3	79937	broad.mit.edu	36	9	39068395	39068396	+	Frame_Shift_Del	DEL	AG	-	-			TCGA-06-2567-01	TCGA-06-2567-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:39068395_39068396delAG	uc004abi.1	-	c.3731_3732delCT	c.(3730-3732)TCTfs	p.S1244fs	CNTNAP3_uc004abj.1_Frame_Shift_Del_p.S1163fs	NM_033655	NP_387504	Q9BZ76	CNTP3_HUMAN	cell recognition molecule CASPR3	1244	Extracellular (Potential).				cell adhesion|cell recognition|signal transduction	extracellular region|integral to membrane|plasma membrane	receptor binding			ovary(1)	1				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)										0.32			13	28				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	39068395	39068396	3786	9	AG	-	-	7	7	CNTNAP3	-	5	5
DMRT1	1761	broad.mit.edu	36	9	832164	832164	+	Frame_Shift_Del	DEL	C	-	-			TCGA-06-2567-01	TCGA-06-2567-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:832164_832164delC	uc003zgv.1	+	c.326_326delC	c.(325-327)GCCfs	p.A109fs	DMRT1_uc003zgu.1_Frame_Shift_Del_p.A109fs	NM_021951	NP_068770	Q9Y5R6	DMRT1_HUMAN	doublesex and mab-3 related transcription factor	109	DM.				cell differentiation|male gonad development|regulation of transcription, DNA-dependent|sex determination	nucleus	DNA binding|metal ion binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		all_lung(10;2.66e-10)|Lung NSC(10;2.82e-10)|Breast(48;0.232)		Lung(218;0.037)										0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	832164	832164	4765	9	C	-	-	26	26	DMRT1	-	5	5
MSL3	10943	broad.mit.edu	36	X	11690875	11690878	+	Splice_Site_Del	DEL	AGTT	-	-			TCGA-06-2567-01	TCGA-06-2567-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:11690875_11690878delAGTT	uc004cuw.1	+	c.e7_splice_site			MSL3_uc004cuv.1_Splice_Site_Del|MSL3_uc004cux.1_Splice_Site_Del|MSL3_uc004cuy.1_Splice_Site_Del	NM_078629	NP_006791			male-specific lethal 3-like 1 isoform a						chromatin assembly or disassembly|histone H4-K16 acetylation|multicellular organismal development|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	chromatin|MSL complex	chromatin binding|DNA binding|methylated histone residue binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1														0.69			55	25				---	---	---	---	capture_indel			Splice_Site_Del	DEL	11690875	11690878	10272	23	AGTT	-	-	7	7	MSL3	-	5	5
