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	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_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	ACHILLES_Lineage_Results_Top_Genes	CGC_CancerGermlineMut	CGC_CancerMolecularGenetics	CGC_CancerSomaticMut	CGC_CancerSyndrome	CGC_Chr	CGC_ChrBand	CGC_GeneID	CGC_Name	CGC_OtherGermlineMut	CGC_TissueType	COSMIC_n_overlapping_mutations	COSMIC_overlapping_mutation_descriptions	ClinVar_ASSEMBLY	ClinVar_HGMD_ID	ClinVar_SYM	ClinVar_TYPE	ClinVar_rs	Ensembl_so_accession	Ensembl_so_term	Familial_Cancer_Genes_Reference	Familial_Cancer_Genes_Synonym	annotation_transcript	bcgsc	broad	build	ccds_id	dbNSFP_1000Gp1_AC	dbNSFP_1000Gp1_AF	dbNSFP_1000Gp1_AFR_AC	dbNSFP_1000Gp1_AFR_AF	dbNSFP_1000Gp1_AMR_AC	dbNSFP_1000Gp1_AMR_AF	dbNSFP_1000Gp1_ASN_AC	dbNSFP_1000Gp1_ASN_AF	dbNSFP_1000Gp1_EUR_AC	dbNSFP_1000Gp1_EUR_AF	dbNSFP_Ancestral_allele	dbNSFP_CADD_phred	dbNSFP_CADD_raw	dbNSFP_CADD_raw_rankscore	dbNSFP_ESP6500_AA_AF	dbNSFP_ESP6500_EA_AF	dbNSFP_Ensembl_geneid	dbNSFP_Ensembl_transcriptid	dbNSFP_FATHMM_pred	dbNSFP_FATHMM_rankscore	dbNSFP_FATHMM_score	dbNSFP_GERP_NR	dbNSFP_GERP_RS	dbNSFP_GERP_RS_rankscore	dbNSFP_Interpro_domain	dbNSFP_LRT_Omega	dbNSFP_LRT_converted_rankscore	dbNSFP_LRT_pred	dbNSFP_LRT_score	dbNSFP_LR_pred	dbNSFP_LR_rankscore	dbNSFP_LR_score	dbNSFP_MutationAssessor_pred	dbNSFP_MutationAssessor_rankscore	dbNSFP_MutationAssessor_score	dbNSFP_MutationTaster_converted_rankscore	dbNSFP_MutationTaster_pred	dbNSFP_MutationTaster_score	dbNSFP_Polyphen2_HDIV_pred	dbNSFP_Polyphen2_HDIV_rankscore	dbNSFP_Polyphen2_HDIV_score	dbNSFP_Polyphen2_HVAR_pred	dbNSFP_Polyphen2_HVAR_rankscore	dbNSFP_Polyphen2_HVAR_score	dbNSFP_RadialSVM_pred	dbNSFP_RadialSVM_rankscore	dbNSFP_RadialSVM_score	dbNSFP_Reliability_index	dbNSFP_SIFT_converted_rankscore	dbNSFP_SIFT_pred	dbNSFP_SIFT_score	dbNSFP_SLR_test_statistic	dbNSFP_SiPhy_29way_logOdds	dbNSFP_SiPhy_29way_logOdds_rankscore	dbNSFP_SiPhy_29way_pi	dbNSFP_UniSNP_ids	dbNSFP_Uniprot_aapos	dbNSFP_Uniprot_acc	dbNSFP_Uniprot_id	dbNSFP_aaalt	dbNSFP_aapos	dbNSFP_aapos_FATHMM	dbNSFP_aapos_SIFT	dbNSFP_aaref	dbNSFP_cds_strand	dbNSFP_codonpos	dbNSFP_folddegenerate	dbNSFP_genename	dbNSFP_hg18_pos1coor	dbNSFP_phastCons100way_vertebrate	dbNSFP_phastCons100way_vertebrate_rankscore	dbNSFP_phastCons46way_placental	dbNSFP_phastCons46way_placental_rankscore	dbNSFP_phastCons46way_primate	dbNSFP_phastCons46way_primate_rankscore	dbNSFP_phyloP100way_vertebrate	dbNSFP_phyloP100way_vertebrate_rankscore	dbNSFP_phyloP46way_placental	dbNSFP_phyloP46way_placental_rankscore	dbNSFP_phyloP46way_primate	dbNSFP_phyloP46way_primate_rankscore	dbNSFP_refcodon	entrez_gene_id	external_id_capture	gencode_transcript_name	gencode_transcript_status	gencode_transcript_tags	gencode_transcript_type	gene_type	havana_transcript	hgsc	igv_bad	ucsc	t_alt_count	t_ref_count	n_alt_count	n_ref_count	validation_judgement_rna	validation_power_rna	validation_tumor_alt_count_rna	validation_tumor_ref_count_rna	validation_normal_alt_count_rna	validation_normal_ref_count_rna	min_val_count_rna	validation_judgement_targeted	validation_power_targeted	validation_tumor_alt_count_targeted	validation_tumor_ref_count_targeted	validation_normal_alt_count_targeted	validation_normal_ref_count_targeted	min_val_count_targeted	validation_judgement_localAssembly	validation_power_localAssembly	t_alt_count_localAssembly	t_ref_count_localAssembly	n_alt_count_localAssembly	n_ref_count_localAssembly	min_val_count_localAssembly	validation_judgement_KRAS	validation_power_KRAS	t_alt_count_KRAS	t_ref_count_KRAS	n_alt_count_KRAS	n_ref_count_KRAS	min_val_count_KRAS	pon_loglike	pon_pass_loglike	localAssembly_detected	ExAC_AN	ExAC_AC	ExAC_LQ	passExAC	SCNA_NA	SCNA_NB	SCNA_q_hat	SCNA_tau	IS_SCNA	purity	ploidy	dna_fraction_in_tumor	CCF_hat	CCF_CI95_low	CCF_CI95_high	CCF_mode	CCF_mean	CCF_median	clonal	CCF_CI_low	CCF_CI_high
SEC31B	25956	broad.mit.edu	37	10	102262171	102262171	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr10:102262171C>T	ENST00000370345.3	-	11	1347	c.1250G>A	c.(1249-1251)cGc>cAc	p.R417H	SEC31B_ENST00000494350.1_5'Flank|SEC31B_ENST00000451524.1_Missense_Mutation_p.R417H	NM_015490.3	NP_056305.1	Q9NQW1	SC31B_HUMAN	SEC31 homolog B (S. cerevisiae)			36		Colorectal(252;0.117)			GAAGACTAGGCGGGGGCAAGG	0.527000																								0							SO:0001583	missense			ENST00000370345.3	1	1	hg19	CCDS7495.1	.	.	.	.	.	.	.	.	.	.	c	7.417	0.635990	0.14386	2.27E-4	0.0	ENSG00000075826	ENST00000370345;ENST00000451524	T;T	0.59083	0.66;0.29	5.38	-1.01	0.10169	.	0.242628	0.49305	N	0.000156	T	0.39627	0.1085	L	0.31926	0.97	0.80722	D	1	B;B	0.06786	0.001;0.0	B;B	0.10450	0.005;0.002	T	0.16778	-1.0391	10	0.14656	T	0.56	-0.3817	11.439	0.50086	0.0:0.5274:0.0:0.4726	.	416;417	Q9NQW1-5;Q9NQW1	.;SC31B_HUMAN	H	417	ENSP00000359370:R417H;ENSP00000391178:R417H	ENSP00000359370:R417H	R	-	2	0	SEC31B	102252161	0.334000	0.24739	0.219000	0.23793	0.509000	0.34042	-0.023000	0.12456	-0.190000	0.10465	-0.227000	0.12334	CGC		TCGA-IB-7647-01A-11D-2154-08	SEC31B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051198.1	1	0	1	49	328	0	65		0	0	0	0	65	2		0	0	0	0	0	2	1	1.000000	49	327	0	65	2								-2.879556	1	1	121412	3	36	1	1	2	3	2.033932	0	0.240000	1.920000	0.244533	0.990000	0.820000	1.000000	1.000000	0.980343	0.990000	1	0.950000	1.000000
CUBN	8029	broad.mit.edu	37	10	16970247	16970247	+	Silent	SNP	C	C	A			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr10:16970247C>A	ENST00000377833.4	-	41	6245	c.6180G>T	c.(6178-6180)ggG>ggT	p.G2060G		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)			241				Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	ACCGGATGGGCCCAGGGATCT	0.478000																								0							SO:0001819	synonymous_variant			ENST00000377833.4	1	1	hg19	CCDS7113.1																																																																																				TCGA-IB-7647-01A-11D-2154-08	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	0	0	0	9	289	0	81	0	0	0	1	0	81	2		0	0	0	0	0	2	1	0.994409	9	289	0	79	2								-3.318793	1	1	0	0		1	1	2	3	2.033932	0	0.240000	1.920000	0.244533	0.260000	0.120000	1.000000	0.250000	0.304030	0.260000	0	0.180000	0.380000
ST8SIA6	338596	broad.mit.edu	37	10	17363212	17363212	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr10:17363212C>T	ENST00000377602.4	-	8	936	c.862G>A	c.(862-864)Gaa>Aaa	p.E288K		NM_001004470.1	NP_001004470.1	P61647	SIA8F_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 6			37					TTAGACTCTTCGAGCGTGTAG	0.443000																								0							SO:0001583	missense			ENST00000377602.4	1	1	hg19	CCDS31158.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	0.010|0.010	-1.793994|-1.793994	0.00617|0.00617	.|.	.|.	ENSG00000148488|ENSG00000148488	ENST00000377610;ENST00000377602|ENST00000440449	T|.	0.28454|.	1.61|.	5.18|5.18	1.42|1.42	0.22433|0.22433	.|.	0.613081|.	0.19292|.	N|.	0.117871|.	T|T	0.09423|0.09423	0.0232|0.0232	N|N	0.01874|0.01874	-0.695|-0.695	0.09310|0.09310	N|N	1|1	B|.	0.11235|.	0.004|.	B|.	0.04013|.	0.001|.	T|T	0.32025|0.32025	-0.9922|-0.9922	10|5	0.02654|.	T|.	1|.	-14.1943|-14.1943	5.6706|5.6706	0.17721|0.17721	0.0:0.2239:0.2137:0.5624|0.0:0.2239:0.2137:0.5624	.|.	288|.	P61647|.	SIA8F_HUMAN|.	K|Q	118;288|108	ENSP00000366827:E288K|.	ENSP00000366827:E288K|.	E|R	-|-	1|2	0|0	ST8SIA6|ST8SIA6	17403218|17403218	0.060000|0.060000	0.20803|0.20803	0.011000|0.011000	0.14972|0.14972	0.107000|0.107000	0.19398|0.19398	1.102000|1.102000	0.31050|0.31050	0.533000|0.533000	0.28675|0.28675	-0.312000|-0.312000	0.09012|0.09012	GAA|CGA		TCGA-IB-7647-01A-11D-2154-08	ST8SIA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047036.1	0	0	0	28	1142	0	176	0	6.317615e-04	0	2	0	176	2		0	0	0	0	0	2	1	1.000000	29	1130	0	175	2								-2.564368	1	1	121412	8	45	1	1	2	3	2.033932	0	0.240000	1.920000	0.244533	0.200000	0.130000	1.000000	0.200000	0.237006	0.200000	0	0.160000	0.250000
ANK3	288	broad.mit.edu	37	10	61847990	61847990	+	Missense_Mutation	SNP	C	C	G			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr10:61847990C>G	ENST00000280772.2	-	29	3646	c.3455G>C	c.(3454-3456)gGa>gCa	p.G1152A	ANK3_ENST00000355288.2_Missense_Mutation_p.G286A|ANK3_ENST00000373827.2_Missense_Mutation_p.G1146A|ANK3_ENST00000503366.1_Missense_Mutation_p.G1153A	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)			196					GCTCAGAATTCCACCTTCAGG	0.468000																								0							SO:0001583	missense			ENST00000280772.2	1	1	hg19	CCDS7258.1	.	.	.	.	.	.	.	.	.	.	C	34	5.306184	0.95629	.	.	ENSG00000151150	ENST00000280772;ENST00000373827;ENST00000355288;ENST00000423532;ENST00000503366;ENST00000395299;ENST00000373817;ENST00000395293;ENST00000395304;ENST00000544789;ENST00000536348	T;T;T;T	0.26223	1.75;1.75;1.75;1.75	6.17	6.17	0.99709	.	0.000000	0.41500	D	0.000864	T	0.62756	0.2454	M	0.90542	3.125	0.80722	D	1	P;D;D;D;D;D;D	0.89917	0.947;1.0;1.0;1.0;0.999;1.0;0.999	P;D;D;D;D;D;D	0.91635	0.878;0.998;0.999;0.999;0.997;0.997;0.996	T	0.67317	-0.5701	10	0.87932	D	0	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	1153;286;685;1146;1152;387;286	E9PE32;A8KA62;Q59G01;Q5CZH9;Q12955;F5GXK0;B1AQT2	.;.;.;.;ANK3_HUMAN;.;.	A	1152;1146;286;286;1153;1132;387;787;787;285;685	ENSP00000280772:G1152A;ENSP00000362933:G1146A;ENSP00000347436:G286A;ENSP00000425236:G1153A	ENSP00000280772:G1152A	G	-	2	0	ANK3	61517996	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	7.466000	0.80914	2.941000	0.99782	0.655000	0.94253	GGA		TCGA-IB-7647-01A-11D-2154-08	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	1	0	1	69	507	0	136	1	9.863805e-01	20	31	0	136	2		0	0	0	0	0	2	1	1.000000	68	504	0	135	2								-19.999990	1	1	0	0		1	1	2	3	2.033932	0	0.240000	1.920000	0.244533	0.990000	0.790000	1.000000	1.000000	0.961262	0.990000	1	0.890000	1.000000
MUC6	4588	broad.mit.edu	37	11	1031906	1031906	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr11:1031906C>T	ENST00000421673.2	-	3	313	c.263G>A	c.(262-264)cGa>cAa	p.R88Q		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming			80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)			GTCTGGGCCTCGCCGCAGCTG	0.622000																								0							SO:0001583	missense			ENST00000421673.2	1	1	hg19	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.941759	0.73557	.	.	ENSG00000184956	ENST00000421673;ENST00000525923	T;T	0.59638	0.25;0.25	4.03	4.03	0.46877	von Willebrand factor, type D domain (3);	0.000000	0.28016	U	0.016921	T	0.75443	0.3850	M	0.76002	2.32	0.34055	D	0.656646	D	0.89917	1.0	D	0.91635	0.999	D	0.84681	0.0717	10	0.72032	D	0.01	.	16.1414	0.81528	0.0:1.0:0.0:0.0	.	88	Q6W4X9	MUC6_HUMAN	Q	88;112	ENSP00000406861:R88Q;ENSP00000433790:R112Q	ENSP00000406861:R88Q	R	-	2	0	MUC6	1021906	0.828000	0.29307	0.981000	0.43875	0.586000	0.36452	3.799000	0.55529	1.968000	0.57251	0.462000	0.41574	CGA		TCGA-IB-7647-01A-11D-2154-08	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	1	0	0	11	193	0	68	0	0	0	1	0	68	2		0	0	0	0	0	2	1	0.998386	11	191	0	65	2								-3.231474	1	1	121076	3	38	1	1	2	3	2.282413	1	0.240000	1.920000	0.319971	0.520000	0.270000	0.910000	0.500000	0.541109	0.520000	0	0.380000	0.690000
LDLRAD3	143458	broad.mit.edu	37	11	36250849	36250849	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr11:36250849G>A	ENST00000315571.5	+	6	961	c.940G>A	c.(940-942)Gtg>Atg	p.V314M	LDLRAD3_ENST00000524419.1_Missense_Mutation_p.V304M|LDLRAD3_ENST00000528989.1_Missense_Mutation_p.V265M	NM_174902.2	NP_777562.1	Q86YD5	LRAD3_HUMAN	low density lipoprotein receptor class A domain containing 3			28	all_lung(20;0.089)|Lung NSC(22;0.175)|all_epithelial(35;0.177)	all_hematologic(20;0.124)			CCTCCTGAGCGTGGAAGACAC	0.662000																								0							SO:0001583	missense			ENST00000315571.5	0	1	hg19	CCDS31462.1	.	.	.	.	.	.	.	.	.	.	G	9.730	1.161967	0.21538	0.0	1.16E-4	ENSG00000179241	ENST00000528989;ENST00000524419;ENST00000315571	D;D;D	0.94576	-3.46;-3.33;-3.22	5.22	-1.14	0.09741	.	1.345450	0.04918	N	0.454465	D	0.86151	0.5864	N	0.14661	0.345	0.09310	N	1	B;B;B	0.15473	0.013;0.003;0.003	B;B;B	0.08055	0.003;0.0;0.0	T	0.73984	-0.3810	10	0.38643	T	0.18	.	2.0251	0.03517	0.5317:0.1415:0.1838:0.1429	.	304;265;314	E9PR86;B7Z1U3;Q86YD5	.;.;LRAD3_HUMAN	M	265;304;314	ENSP00000433954:V265M;ENSP00000434313:V304M;ENSP00000318607:V314M	ENSP00000318607:V314M	V	+	1	0	LDLRAD3	36207425	0.000000	0.05858	0.031000	0.17742	0.580000	0.36256	-0.821000	0.04452	-0.105000	0.12132	0.563000	0.77884	GTG		TCGA-IB-7647-01A-11D-2154-08	LDLRAD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389085.1	0	0	0	16	941	0	167	0	9.819553e-04	0	3	0	167	2		0	0	0	0	0	2	1	0.999917	16	919	0	159	2								-3.078595	1	1	121390	9	42	1	1	2	3	2.282413	1	0.240000	1.920000	0.319971	0.150000	0.080000	0.260000	0.150000	0.172912	0.150000	0	0.110000	0.210000
LRRC4C	57689	broad.mit.edu	37	11	40137319	40137319	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr11:40137319C>T	ENST00000278198.2	-	2	2487	c.524G>A	c.(523-525)cGc>cAc	p.R175H	LRRC4C_ENST00000530763.1_Missense_Mutation_p.R175H|LRRC4C_ENST00000527150.1_Missense_Mutation_p.R175H|LRRC4C_ENST00000528697.1_Missense_Mutation_p.R175H			Q9HCJ2	LRC4C_HUMAN	leucine rich repeat containing 4C			86		all_lung(304;0.0575)|Lung NSC(402;0.138)			GTCTAGTCGGCGCAAAGAAGG	0.428000																								0							SO:0001583	missense			ENST00000278198.2	0	1	hg19	CCDS31464.1	.	.	.	.	.	.	.	.	.	.	C	17.11	3.305659	0.60305	.	.	ENSG00000148948	ENST00000278198;ENST00000527150;ENST00000528697;ENST00000530763	T;T;T;T	0.05081	3.5;3.5;3.5;3.5	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	T	0.25344	0.0616	M	0.67517	2.055	0.58432	D	0.999998	D	0.89917	1.0	D	0.80764	0.994	T	0.00029	-1.2295	10	0.49607	T	0.09	.	19.0894	0.93221	0.0:1.0:0.0:0.0	.	175	Q9HCJ2	LRC4C_HUMAN	H	175	ENSP00000278198:R175H;ENSP00000436976:R175H;ENSP00000437132:R175H;ENSP00000434761:R175H	ENSP00000278198:R175H	R	-	2	0	LRRC4C	40093895	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.050000	0.71063	2.754000	0.94517	0.650000	0.86243	CGC		TCGA-IB-7647-01A-11D-2154-08	LRRC4C-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389499.1	0	0	0	30	551	1	74	0	1.120463e-01	0	22	1	74	3		0	0	0	0	0	2	1	0.830445	30	550	1	73	24								-5.881021	1	1	121412	3	34	1	1	2	3	2.282413	1	0.240000	1.920000	0.319971	0.480000	0.330000	0.700000	0.480000	0.498374	0.480000	0	0.400000	0.580000
TAS2R31	259290	broad.mit.edu	37	12	11183165	11183165	+	Missense_Mutation	SNP	T	T	C			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr12:11183165T>C	ENST00000390675.2	-	1	841	c.770A>G	c.(769-771)aAc>aGc	p.N257S	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_176885.2	NP_795366.2	P59538	T2R31_HUMAN	taste receptor, type 2, member 31			7					GACAGGTTTGTTTTCCAGACT	0.383000																								0							SO:0001583	missense			ENST00000390675.2	0	1	hg19	CCDS53747.1	.	.	.	.	.	.	.	.	.	.	.	5.489	0.275150	0.10403	.	.	ENSG00000256436	ENST00000390675	T	0.00760	5.73	2.45	-0.013	0.13986	.	.	.	.	.	T	0.00906	0.0030	L	0.42487	1.325	0.09310	N	1	B	0.26672	0.156	B	0.33799	0.17	T	0.46148	-0.9212	9	0.26408	T	0.33	.	4.233	0.10613	0.0:0.3766:0.0:0.6234	.	257	P59538	T2R31_HUMAN	S	257	ENSP00000375093:N257S	ENSP00000375093:N257S	N	-	2	0	TAS2R31	11074432	0.000000	0.05858	0.003000	0.11579	0.023000	0.10783	0.106000	0.15354	0.198000	0.20407	0.163000	0.16589	AAC		TCGA-IB-7647-01A-11D-2154-08	TAS2R31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400233.1	0	0	0	21	1452	0	223	0	0	0	1	0	223	2		0	0	0	0	0	2	1	0.999996	18	1399	0	227	2								-2.774755	1	1	0	0		1	0	0	0	2.006602	0	0.240000	1.920000	0.232633	0.110000	0.060000	0.180000	0.120000	0.122824	0.110000	0	0.090000	0.150000
TBX5	6910	broad.mit.edu	37	12	114836449	114836449	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr12:114836449G>T	ENST00000310346.4	-	5	1105	c.439C>A	c.(439-441)Cat>Aat	p.H147N	TBX5_ENST00000552726.1_5'UTR|TBX5_ENST00000405440.2_Missense_Mutation_p.H147N|TBX5_ENST00000349716.5_Missense_Mutation_p.H97N|TBX5_ENST00000526441.1_Missense_Mutation_p.H147N	NM_000192.3	NP_000183.2	Q99593	TBX5_HUMAN	T-box 5			56	Medulloblastoma(191;0.163)|all_neural(191;0.178)				CTCATCCAATGCGCCCCGGTG	0.612000													NSCLC(152;1358 1980 4050 23898 40356)											0							SO:0001583	missense			ENST00000310346.4	0	1	hg19	CCDS9173.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.143320	0.77888	.	.	ENSG00000089225	ENST00000349716;ENST00000310346;ENST00000448888;ENST00000405440;ENST00000526441	D;D;D;D	0.87887	-2.31;-2.31;-2.31;-2.31	4.35	4.35	0.52113	Transcription factor, T-box, conserved site (1);p53-like transcription factor, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.92971	0.7763	M	0.77103	2.36	0.80722	D	1	D;D	0.65815	0.995;0.988	D;D	0.66979	0.948;0.947	D	0.93955	0.7235	10	0.72032	D	0.01	.	17.429	0.87534	0.0:0.0:1.0:0.0	.	147;147	Q99593-2;Q99593	.;TBX5_HUMAN	N	97;147;44;147;147	ENSP00000337723:H97N;ENSP00000309913:H147N;ENSP00000384152:H147N;ENSP00000433292:H147N	ENSP00000309913:H147N	H	-	1	0	TBX5	113320832	1.000000	0.71417	0.733000	0.30861	0.486000	0.33341	9.581000	0.98210	2.392000	0.81423	0.655000	0.94253	CAT		TCGA-IB-7647-01A-11D-2154-08	TBX5-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388297.1	1	0	1	15	85	0	22		0	0	0	0	22	2		0	0	0	0	0	2	1	0.999893	13	85	0	22	2								-19.999990	1	1	0	0		1	0	1	1	2.015391	0	0.240000	1.920000	0.238172	0.990000	0.740000	1.000000	1.000000	0.976400	0.990000	1	0.970000	1.000000
KRAS	3845	broad.mit.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	C	A	rs121913529		TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08			C	A	C	C		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr12:25398284C>A	ENST00000256078.4	-	2	98	c.35G>T	c.(34-36)gGt>gTt	p.G12V	KRAS_ENST00000556131.1_Missense_Mutation_p.G12V|KRAS_ENST00000557334.1_Missense_Mutation_p.G12V|KRAS_ENST00000311936.3_Missense_Mutation_p.G12V	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)		GCCTACGCCACCAGCTCCAAC	0.348000	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		pancreatic, colorectal, lung, thyroid, AML, others				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)			Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		L, E, M, O	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)						SO:0001583	missense	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	ENST00000256078.4	1	1	hg19	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.808637	0.90707	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90373	0.6987	M	0.90650	3.135	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.72625	0.969;0.978	D	0.91773	0.5429	10	0.72032	D	0.01	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	V	12	ENSP00000308495:G12V;ENSP00000452512:G12V;ENSP00000256078:G12V;ENSP00000451856:G12V	ENSP00000256078:G12V	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		TCGA-IB-7647-01A-11D-2154-08	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	1	0	0	9	94	0	25	1	9.830912e-01	25	53	0	25	2	1	1	57	534	0	389	2	1	0.994669	9	93	0	25	2								-6.245686	1	1	0	0		1	0	0	0	2.006602	0	0.240000	1.920000	0.232633	0.730000	0.370000	1.000000	1.000000	0.739733	0.730000	0	0.530000	0.980000
NELL2	4753	broad.mit.edu	37	12	44917143	44917143	+	Missense_Mutation	SNP	A	A	T			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr12:44917143A>T	ENST00000429094.2	-	17	2433	c.1929T>A	c.(1927-1929)gaT>gaA	p.D643E	NELL2_ENST00000437801.2_Missense_Mutation_p.D693E|NELL2_ENST00000549027.1_Missense_Mutation_p.D642E|NELL2_ENST00000452445.2_Missense_Mutation_p.D643E|NELL2_ENST00000395487.2_Missense_Mutation_p.D642E|NELL2_ENST00000333837.4_Missense_Mutation_p.D666E|NELL2_ENST00000551601.1_Missense_Mutation_p.D595E	NM_001145108.1	NP_001138580.1	Q99435	NELL2_HUMAN	NEL-like 2 (chicken)			65	Lung SC(27;0.192)	Lung NSC(34;0.144)			TAACTTTTCCATCATGGATGC	0.413000																								0							SO:0001583	missense			ENST00000429094.2	1	1	hg19	CCDS8746.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	6.402|6.402	0.442294|0.442294	0.12164|0.12164	.|.	.|.	ENSG00000184613|ENSG00000184613	ENST00000395487;ENST00000429094;ENST00000551601;ENST00000452445;ENST00000549027;ENST00000333837;ENST00000437801|ENST00000550139	T;T;T;T;T;T;D|.	0.81739|.	-1.47;-1.46;-1.13;-1.46;-1.47;-1.4;-1.53|.	5.82|5.82	-1.94|-1.94	0.07571|0.07571	von Willebrand factor, type C (2);|.	0.336601|.	0.33753|.	N|.	0.004596|.	T|T	0.12902|0.12902	0.0313|0.0313	N|N	0.10629|0.10629	0.01|0.01	0.29822|0.29822	N|N	0.830744|0.830744	B;B;B;B;B|.	0.06786|.	0.0;0.0;0.001;0.0;0.0|.	B;B;B;B;B|.	0.08055|.	0.001;0.001;0.003;0.001;0.001|.	T|T	0.26780|0.26780	-1.0093|-1.0093	10|5	0.02654|.	T|.	1|.	-8.98|-8.98	0.8838|0.8838	0.01240|0.01240	0.3152:0.0985:0.2528:0.3335|0.3152:0.0985:0.2528:0.3335	.|.	666;693;595;643;642|.	B7Z2U7;B7Z9U3;F8VVB6;Q99435;Q96JS2|.	.;.;.;NELL2_HUMAN;.|.	E|R	642;643;595;643;642;666;693|56	ENSP00000378866:D642E;ENSP00000390680:D643E;ENSP00000449332:D595E;ENSP00000394612:D643E;ENSP00000447927:D642E;ENSP00000327988:D666E;ENSP00000416341:D693E|.	ENSP00000327988:D666E|.	D|W	-|-	3|1	2|0	NELL2|NELL2	43203410|43203410	0.983000|0.983000	0.35010|0.35010	0.406000|0.406000	0.26421|0.26421	0.961000|0.961000	0.63080|0.63080	0.473000|0.473000	0.22132|0.22132	-0.594000|-0.594000	0.05836|0.05836	0.523000|0.523000	0.50628|0.50628	GAT|TGG		TCGA-IB-7647-01A-11D-2154-08	NELL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404180.1	1	0	1	83	701	0	114	0	8.391413e-01	0	30	0	114	2		0	0	0	0	0	2	1	1.000000	83	696	0	112	2								-20.000000	1	1	0	0		1	0	1	1	2.015391	0	0.240000	1.920000	0.238172	0.870000	0.700000	1.000000	1.000000	0.879691	0.870000	1	0.780000	0.970000
TUBA1A	7846	broad.mit.edu	37	12	49580155	49580155	+	Nonsense_Mutation	SNP	G	G	A			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08			G	A	G	G		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr12:49580155G>A	ENST00000295766.5	-	3	792	c.313C>T	c.(313-315)Cga>Tga	p.R105*	TUBA1A_ENST00000550767.1_Nonsense_Mutation_p.R70*|TUBA1A_ENST00000546918.1_Silent_p.P155P|TUBA1A_ENST00000301071.7_Nonsense_Mutation_p.R105*	NM_001270399.1	NP_001257328.1	Q71U36	TBA1A_HUMAN	tubulin, alpha 1a			2				Albendazole(DB00518)|Mebendazole(DB00643)|Vinblastine(DB00570)	TAGTGCCCTCGGGCATAGTTA	0.468000													Pancreas(111;782 2307 24613 44561)|NSCLC(165;1667 2752 9496 39006)|Ovarian(19;24 776 10875 37451)											0							SO:0001587	stop_gained			ENST00000295766.5	0	1	hg19	CCDS58227.1	.	.	.	.	.	.	.	.	.	.	G	26.2	4.716103	0.89205	.	.	ENSG00000167552	ENST00000301071;ENST00000295766;ENST00000550767;ENST00000547939;ENST00000552924	.	.	.	5.22	5.22	0.72569	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.5677	0.61828	0.0:0.0:0.8438:0.1562	.	.	.	.	X	105;105;70;70;70	.	ENSP00000439020:R105X	R	-	1	2	TUBA1A	47866422	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	7.541000	0.82084	2.605000	0.88082	0.561000	0.74099	CGA		TCGA-IB-7647-01A-11D-2154-08	TUBA1A-002	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000404547.2	0	0	0	34	956	0	180	0	1	1	1406	0	180	2		0	0	0	0	0	2	1	1.000000	34	946	0	183	2								-2.222362	0	1	0	0		1	0	1	1	2.015391	0	0.240000	1.920000	0.238172	0.280000	0.190000	0.390000	0.280000	0.292366	0.280000	0	0.230000	0.340000
KCNA5	3741	broad.mit.edu	37	12	5153781	5153781	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr12:5153781C>A	ENST00000252321.3	+	1	697	c.468C>A	c.(466-468)ttC>ttA	p.F156L		NM_002234.3	NP_002225.2	P22460	KCNA5_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 5			52				Dalfampridine(DB06637)	TGCGCTACTTCGACCCCCTGA	0.652000																								0							SO:0001583	missense			ENST00000252321.3	0	1	hg19	CCDS8536.1	.	.	.	.	.	.	.	.	.	.	C	16.79	3.219176	0.58560	.	.	ENSG00000130037	ENST00000252321	T	0.75821	-0.97	4.7	1.64	0.23874	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.000000	0.85682	U	0.000000	D	0.82342	0.5016	M	0.71036	2.16	0.50632	D	0.999888	D	0.76494	0.999	D	0.79784	0.993	T	0.82074	-0.0637	10	0.87932	D	0	.	9.7379	0.40399	0.0:0.676:0.0:0.324	.	156	P22460	KCNA5_HUMAN	L	156	ENSP00000252321:F156L	ENSP00000252321:F156L	F	+	3	2	KCNA5	5024042	0.971000	0.33674	1.000000	0.80357	0.994000	0.84299	0.197000	0.17197	0.598000	0.29829	0.511000	0.50034	TTC		TCGA-IB-7647-01A-11D-2154-08	KCNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398925.2	0	0	0	7	305	0	84	0	4.185718e-03	0	4	0	84	2		0	0	0	0	0	2	1	0.980472	7	303	0	83	2								-7.322644	1	1	0	0		1	1	2	3	2.022387	0	0.240000	1.920000	0.241820	0.190000	0.080000	0.400000	0.180000	0.218423	0.190000	0	0.130000	0.290000
CAPS2	84698	broad.mit.edu	37	12	75687069	75687069	+	Nonsense_Mutation	SNP	G	G	A			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr12:75687069G>A	ENST00000409445.3	-	13	1376	c.1180C>T	c.(1180-1182)Cga>Tga	p.R394*	CAPS2_ENST00000393284.3_Nonsense_Mutation_p.R162*|RP11-560G2.1_ENST00000534648.2_RNA|CAPS2_ENST00000409799.1_Nonsense_Mutation_p.R312*|CAPS2_ENST00000409004.1_5'UTR|RP11-560G2.1_ENST00000549953.1_RNA|CAPS2_ENST00000442339.2_5'UTR	NM_032606.3	NP_115995.2	Q9BXY5	CAYP2_HUMAN	calcyphosine 2			10					TTTGTGATTCGGAGTTTAAGT	0.318000																								0							SO:0001587	stop_gained			ENST00000409445.3	0	1	hg19	CCDS9008.2	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	21.2	4.110650	0.77210	.	.	ENSG00000180881	ENST00000409799;ENST00000409445;ENST00000378703;ENST00000393284	.	.	.	4.6	4.6	0.57074	.	0.130292	0.34245	N	0.004139	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.0574	8.339	0.32232	0.0819:0.0:0.7645:0.1536	.	.	.	.	X	312;394;130;162	.	ENSP00000367975:R130X	R	-	1	2	CAPS2	73973336	1.000000	0.71417	0.988000	0.46212	0.091000	0.18340	3.286000	0.51724	2.282000	0.76494	0.446000	0.29264	CGA		TCGA-IB-7647-01A-11D-2154-08	CAPS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000327880.2	1	0	0	11	250	0	45	0	2.246803e-03	1	1	0	45	2		0	0	0	0	0	2	1	0.998329	11	247	0	45	2								-2.557264	1	1	121410	9	41	1	0	1	1	2.015391	0	0.240000	1.920000	0.238172	0.350000	0.190000	0.590000	0.340000	0.374684	0.350000	0	0.260000	0.470000
EXOSC8	11340	broad.mit.edu	37	13	37576427	37576427	+	Missense_Mutation	SNP	A	A	G			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr13:37576427A>G	ENST00000389704.3	+	2	300	c.35A>G	c.(34-36)gAg>gGg	p.E12G	ALG5_ENST00000443765.1_5'Flank|EXOSC8_ENST00000489088.1_3'UTR|ALG5_ENST00000413537.2_5'Flank|ALG5_ENST00000496689.1_5'Flank|ALG5_ENST00000239891.3_5'Flank	NM_181503.2	NP_852480.1	Q96B26	EXOS8_HUMAN	exosome component 8			7		Lung NSC(96;6.57e-05)|Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.184)			GAACCTCTGGAGTATTACAGG	0.323000																								0							SO:0001583	missense			ENST00000389704.3	1	1	hg19	CCDS31958.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.943943	0.73672	.	.	ENSG00000120699	ENST00000389704;ENST00000379809	T	0.45276	0.9	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	T	0.43743	0.1261	M	0.75615	2.305	0.80722	D	1	B;P	0.35139	0.219;0.486	B;B	0.28465	0.072;0.09	T	0.48468	-0.9033	10	0.52906	T	0.07	-14.8925	15.5547	0.76184	1.0:0.0:0.0:0.0	.	12;12	Q5JXM0;Q96B26	.;EXOS8_HUMAN	G	12	ENSP00000374354:E12G	ENSP00000369137:E12G	E	+	2	0	EXOSC8	36474427	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.767000	0.74975	2.088000	0.63022	0.528000	0.53228	GAG		TCGA-IB-7647-01A-11D-2154-08	EXOSC8-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044535.2	0	0	0	14	486	0	73	0	9.285532e-01	1	158	0	73	2		0	0	0	0	0	2	1	0.999742	14	481	0	71	2								-3.490276	1	1	0	0		1	1	2	3	2.183870	1	0.240000	1.920000	0.294991	0.280000	0.140000	1.000000	0.250000	0.428207	0.280000	0	0.200000	1.000000
AKAP11	11215	broad.mit.edu	37	13	42873717	42873717	+	Missense_Mutation	SNP	A	A	T			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr13:42873717A>T	ENST00000025301.2	+	8	1010	c.835A>T	c.(835-837)Agg>Tgg	p.R279W		NM_016248.3	NP_057332.1	Q9UKA4	AKA11_HUMAN	A kinase (PRKA) anchor protein 11			56		Lung NSC(96;1.86e-05)|Prostate(109;0.0165)|Lung SC(185;0.0262)|Breast(139;0.0707)|Hepatocellular(98;0.114)			TTGGACCCAAAGGAGTTTCTA	0.393000																								0							SO:0001583	missense			ENST00000025301.2	1	1	hg19	CCDS9383.1	.	.	.	.	.	.	.	.	.	.	A	17.48	3.399892	0.62177	.	.	ENSG00000023516	ENST00000025301	T	0.54675	0.56	5.43	5.43	0.79202	.	0.257696	0.42548	D	0.000687	T	0.49575	0.1565	L	0.51422	1.61	0.29627	N	0.845705	B	0.24426	0.103	B	0.21917	0.037	T	0.53229	-0.8468	10	0.54805	T	0.06	.	15.787	0.78315	1.0:0.0:0.0:0.0	.	279	Q9UKA4	AKA11_HUMAN	W	279	ENSP00000025301:R279W	ENSP00000025301:R279W	R	+	1	2	AKAP11	41771717	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	4.323000	0.59221	2.197000	0.70478	0.533000	0.62120	AGG		TCGA-IB-7647-01A-11D-2154-08	AKAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044700.2	0	0	0	16	672	0	101	1	6.627483e-01	4	91	0	101	2		0	0	0	0	0	2	1	0.999931	16	670	0	100	2								-12.642810	1	1	0	0		1	1	2	3	2.183870	1	0.240000	1.920000	0.294991	0.230000	0.120000	1.000000	0.210000	0.391861	0.230000	0	0.170000	1.000000
KLHL1	57626	broad.mit.edu	37	13	70281775	70281775	+	Silent	SNP	T	T	C			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr13:70281775T>C	ENST00000377844.4	-	10	2928	c.2169A>G	c.(2167-2169)caA>caG	p.Q723Q	KLHL1_ENST00000545028.1_Silent_p.Q530Q	NM_020866.2	NP_065917.1	Q9NR64	KLHL1_HUMAN	kelch-like family member 1			84		Breast(118;0.000162)			ACTCATTAGTTTGTGGGTCAT	0.413000																								0							SO:0001819	synonymous_variant			ENST00000377844.4	0	1	hg19	CCDS9445.1																																																																																				TCGA-IB-7647-01A-11D-2154-08	KLHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045231.3	0	0	0	8	356	0	69		0	0	0	0	69	2		0	0	0	0	0	2	1	0.989198	8	353	0	69	2								-8.438654	1	1	0	0		1	1	2	3	2.050432	0	0.240000	1.920000	0.248120	0.190000	0.080000	1.000000	0.190000	0.263195	0.190000	0	0.130000	0.300000
LRFN5	145581	broad.mit.edu	37	14	42356419	42356419	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr14:42356419G>A	ENST00000298119.4	+	3	1780	c.591G>A	c.(589-591)atG>atA	p.M197I	LRFN5_ENST00000554171.1_Missense_Mutation_p.M197I|LRFN5_ENST00000554120.1_Missense_Mutation_p.M197I	NM_152447.3	NP_689660.2	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III domain containing 5			120			LUAD - Lung adenocarcinoma(50;0.0223)|Lung(238;0.0728)		TGCACAAGATGACTCGGTTAG	0.443000										HNSCC(30;0.082)														0							SO:0001583	missense			ENST00000298119.4	1	1	hg19	CCDS9678.1	.	.	.	.	.	.	.	.	.	.	G	12.01	1.809997	0.31961	.	.	ENSG00000165379	ENST00000298119;ENST00000554120;ENST00000554171	T;T;T	0.49139	0.79;0.79;0.79	5.56	5.56	0.83823	.	0.000000	0.64402	D	0.000002	T	0.23289	0.0563	N	0.01771	-0.73	0.42698	D	0.993608	B;B	0.16396	0.001;0.017	B;B	0.19666	0.009;0.026	T	0.11916	-1.0568	10	0.66056	D	0.02	.	10.4503	0.44518	0.0879:0.0:0.9121:0.0	.	197;197	G3V364;Q96NI6	.;LRFN5_HUMAN	I	197	ENSP00000298119:M197I;ENSP00000451897:M197I;ENSP00000451067:M197I	ENSP00000298119:M197I	M	+	3	0	LRFN5	41426169	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.040000	0.41203	2.595000	0.87683	0.650000	0.86243	ATG		TCGA-IB-7647-01A-11D-2154-08	LRFN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276786.1	1	0	1	41	258	0	57	0	0	0	1	0	57	2		0	0	0	0	0	2	1	1.000000	40	254	0	55	2								-20.000000	1	1	0	0		1	0	0	0	1.926440	0	0.240000	1.920000	0.201681	0.990000	0.790000	1.000000	1.000000	0.974723	0.990000	1	0.930000	1.000000
MAGEL2	54551	broad.mit.edu	37	15	23890566	23890566	+	Missense_Mutation	SNP	T	T	C			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr15:23890566T>C	ENST00000532292.1	-	1	609	c.515A>G	c.(514-516)aAc>aGc	p.N172S		NM_019066.4	NP_061939.3	Q9UJ55	MAGL2_HUMAN	MAGE-like 2			7		all_cancers(20;1.78e-24)|all_epithelial(15;7.75e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000625)|Colorectal(260;0.14)			GGCAGGCAGGTTTTTCCAGGC	0.587000																								0							SO:0001583	missense			ENST00000532292.1	0	1	hg19		.	.	.	.	.	.	.	.	.	.	T	1.611	-0.523921	0.04141	.	.	ENSG00000254585	ENST00000532292	.	.	.	4.08	-6.12	0.02124	.	.	.	.	.	T	0.23649	0.0572	N	0.24115	0.695	0.09310	N	1	.	.	.	.	.	.	T	0.28776	-1.0033	5	.	.	.	.	6.4455	0.21873	0.0:0.3177:0.3652:0.317	.	.	.	.	A	204	.	.	T	-	1	0	MAGEL2	21441659	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.962000	0.03841	-1.381000	0.02112	-1.151000	0.01829	ACC		TCGA-IB-7647-01A-11D-2154-08	MAGEL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395182.2	0	0	0	7	218	0	60	0	1.252798e-02	0	5	0	60	2		0	0	0	0	0	2	1	0.979509	6	214	0	54	2								-1.629323	0	1	0	0		1	0	0	0	1.976255	0	0.240000	1.920000	0.221311	0.260000	0.110000	0.480000	0.250000	0.282175	0.260000	0	0.180000	0.370000
GDE1	51573	broad.mit.edu	37	16	19528371	19528371	+	Silent	SNP	A	A	T			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08			A	T	A	A		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr16:19528371A>T	ENST00000353258.3	-	2	582	c.402T>A	c.(400-402)atT>atA	p.I134I		NM_016641.3	NP_057725.1	Q9NZC3	GDE1_HUMAN	glycerophosphodiester phosphodiesterase 1			13					TCAGCTTCCTAATTTGTTCAA	0.408000																								0							SO:0001819	synonymous_variant			ENST00000353258.3	1	1	hg19	CCDS10578.1																																																																																				TCGA-IB-7647-01A-11D-2154-08	GDE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254274.2	1	0	1	70	578	0	99	1	1	82	228	0	99	2		0	0	0	0	0	2	1	1.000000	70	575	0	96	2								-19.999400	1	1	0	0		1	1	2	3	2.033166	0	0.240000	1.920000	0.244533	0.900000	0.710000	1.000000	1.000000	0.903514	0.900000	1	0.800000	1.000000
GDE1	51573	broad.mit.edu	37	16	19528372	19528372	+	Missense_Mutation	SNP	A	A	T			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08			A	T	A	A		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr16:19528372A>T	ENST00000353258.3	-	2	581	c.401T>A	c.(400-402)aTt>aAt	p.I134N		NM_016641.3	NP_057725.1	Q9NZC3	GDE1_HUMAN	glycerophosphodiester phosphodiesterase 1			13					CAGCTTCCTAATTTGTTCAAA	0.408000																								0							SO:0001583	missense			ENST00000353258.3	1	1	hg19	CCDS10578.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.443829	0.83993	.	.	ENSG00000006007	ENST00000353258	T	0.14893	2.47	5.56	5.56	0.83823	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);	0.404440	0.27189	N	0.020509	T	0.43389	0.1245	M	0.84683	2.71	0.42041	D	0.991079	P	0.46457	0.878	P	0.57204	0.815	T	0.49011	-0.8983	10	0.87932	D	0	-2.948	15.7008	0.77541	1.0:0.0:0.0:0.0	.	134	Q9NZC3	GDE1_HUMAN	N	134	ENSP00000261386:I134N	ENSP00000261386:I134N	I	-	2	0	GDE1	19435873	0.993000	0.37304	1.000000	0.80357	0.995000	0.86356	8.900000	0.92551	2.124000	0.65301	0.460000	0.39030	ATT		TCGA-IB-7647-01A-11D-2154-08	GDE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254274.2	1	0	1	71	576	0	100	1	1	82	226	0	100	2		0	0	0	0	0	2	1	1.000000	71	573	0	97	2								-20.000000	1	1	0	0		1	1	2	3	2.033166	0	0.240000	1.920000	0.244533	0.920000	0.720000	1.000000	1.000000	0.914132	0.920000	1	0.820000	1.000000
UQCRC2	7385	broad.mit.edu	37	16	21974207	21974207	+	Splice_Site	SNP	G	G	T			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr16:21974207G>T	ENST00000268379.4	+	6	1278		c.e6+1		UQCRC2_ENST00000561553.1_Splice_Site	NM_003366.2	NP_003357.2	P22695	QCR2_HUMAN	ubiquinol-cytochrome c reductase core protein II			15					CCGCAGACTCGTAAGTACATT	0.363000													Colon(123;450 1645 12841 25393 45623)											0							SO:0001630	splice_region_variant			ENST00000268379.4	1	1	hg19	CCDS10601.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.208992	0.79240	.	.	ENSG00000140740	ENST00000268379	.	.	.	4.88	4.88	0.63580	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.9872	0.86342	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	UQCRC2	21881708	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.328000	0.96403	2.411000	0.81874	0.563000	0.77884	.		TCGA-IB-7647-01A-11D-2154-08	UQCRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254466.1	1	0	0	32	283	0	56	1	3.076204e-02	3	0	0	56	2		0	0	0	0	0	2	1	1.000000	32	281	0	56	2								-20.000000	1	1	0	0		1	1	2	3	2.033166	0	0.240000	1.920000	0.244533	0.850000	0.600000	1.000000	1.000000	0.855447	0.850000	1	0.720000	1.000000
ABCC11	85320	broad.mit.edu	37	16	48209224	48209224	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr16:48209224G>A	ENST00000394747.1	-	25	3992	c.3643C>T	c.(3643-3645)Cgg>Tgg	p.R1215W	ABCC11_ENST00000353782.5_Missense_Mutation_p.R1215W|ABCC11_ENST00000394748.1_Missense_Mutation_p.R1215W|ABCC11_ENST00000356608.2_Missense_Mutation_p.R1215W|ABCC11_ENST00000565329.1_5'UTR	NM_033151.3	NP_149163.2	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 11			83		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)		Conjugated Estrogens(DB00286)|Folic Acid(DB00158)|Indomethacin(DB00328)|Methotrexate(DB00563)|Probenecid(DB01032)	AGCTTGGACCGCAAGTCCTCC	0.622000																								0							SO:0001583	missense			ENST00000394747.1	0	1	hg19	CCDS10732.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.998707	0.74818	.	.	ENSG00000121270	ENST00000353782;ENST00000356608;ENST00000394748;ENST00000394747	D;D;D;D	0.94966	-3.57;-3.57;-3.57;-3.57	4.99	2.72	0.32119	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.85682	D	0.000000	D	0.96904	0.8989	M	0.91196	3.185	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.977;1.0	D	0.94753	0.7929	10	0.87932	D	0	-11.4901	4.5859	0.12282	0.1267:0.0:0.5176:0.3557	.	1215;1215	Q96J66-2;Q96J66	.;ABCCB_HUMAN	W	1215	ENSP00000311326:R1215W;ENSP00000349017:R1215W;ENSP00000378231:R1215W;ENSP00000378230:R1215W	ENSP00000311326:R1215W	R	-	1	2	ABCC11	46766725	1.000000	0.71417	0.310000	0.25168	0.990000	0.78478	2.368000	0.44222	0.342000	0.23796	0.591000	0.81541	CGG		TCGA-IB-7647-01A-11D-2154-08	ABCC11-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429984.1	0	0	0	5	189	0	56	0	0	0	1	0	56	2		0	0	0	0	0	2	1	0.937509	5	188	0	56	2								-2.791385	1	1	0	0		1	1	2	3	2.033166	0	0.240000	1.920000	0.244533	0.230000	0.080000	1.000000	0.210000	0.280950	0.230000	0	0.150000	0.370000
NLRC5	84166	broad.mit.edu	37	16	57060803	57060803	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr16:57060803G>A	ENST00000262510.6	+	6	2173	c.1948G>A	c.(1948-1950)Gac>Aac	p.D650N	NLRC5_ENST00000539144.1_Missense_Mutation_p.D650N|NLRC5_ENST00000308149.7_Missense_Mutation_p.D650N|NLRC5_ENST00000436936.1_Missense_Mutation_p.D650N	NM_032206.4	NP_115582.4	Q86WI3	NLRC5_HUMAN	NLR family, CARD domain containing 5			75		all_neural(199;0.225)			GACCTGCACCGACCTGGCCAC	0.602000																								0							SO:0001583	missense			ENST00000262510.6	1	1	hg19	CCDS10773.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.20|16.20	3.055616|3.055616	0.55325|0.55325	.|.	.|.	ENSG00000140853|ENSG00000140853	ENST00000262510;ENST00000308149;ENST00000436936;ENST00000327982;ENST00000539144;ENST00000538110;ENST00000543030|ENST00000538805	T;T;T;T;T;T|.	0.54675|.	0.56;0.56;0.56;0.56;0.56;0.56|.	5.52|5.52	4.57|4.57	0.56435|0.56435	.|.	0.000000|.	0.36591|.	N|.	0.002501|.	T|T	0.70011|0.70011	0.3175|0.3175	M|M	0.79475|0.79475	2.455|2.455	0.33435|0.33435	D|D	0.581619|0.581619	D;D;D;D|.	0.89917|.	1.0;1.0;0.993;0.992|.	D;D;P;D|.	0.97110|.	1.0;1.0;0.88;0.915|.	T|T	0.79398|0.79398	-0.1820|-0.1820	10|5	0.41790|.	T|.	0.15|.	.|.	13.374|13.374	0.60728|0.60728	0.0759:0.0:0.9241:0.0|0.0759:0.0:0.9241:0.0	.|.	650;650;650;650|.	Q86WI3-5;Q86WI3-4;Q86WI3-6;Q86WI3|.	.;.;.;NLRC5_HUMAN|.	N|Q	650;650;650;124;650;157;5|402	ENSP00000262510:D650N;ENSP00000308886:D650N;ENSP00000389739:D650N;ENSP00000441727:D650N;ENSP00000441597:D157N;ENSP00000440153:D5N|.	ENSP00000262510:D650N|.	D|R	+|+	1|2	0|0	NLRC5|NLRC5	55618304|55618304	1.000000|1.000000	0.71417|0.71417	0.861000|0.861000	0.33841|0.33841	0.050000|0.050000	0.14768|0.14768	6.066000|6.066000	0.71185|0.71185	1.338000|1.338000	0.45544|0.45544	0.561000|0.561000	0.74099|0.74099	GAC|CGA		TCGA-IB-7647-01A-11D-2154-08	NLRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257346.1	1	0	0	20	416	0	129	1	8.538147e-01	6	68	0	129	2		0	0	0	0	0	2	1	0.999995	19	412	0	126	2								-4.442301	1	1	0	0		1	1	2	3	2.033166	0	0.240000	1.920000	0.244533	0.390000	0.240000	1.000000	0.380000	0.421919	0.390000	0	0.310000	0.500000
RTN4RL1	146760	broad.mit.edu	37	17	1840990	1840990	+	Silent	SNP	C	C	T			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr17:1840990C>T	ENST00000331238.6	-	2	605	c.126G>A	c.(124-126)gcG>gcA	p.A42A		NM_178568.2	NP_848663.1			reticulon 4 receptor-like 1			11					CAAAGTTGTGCGCCTGGCAGC	0.672000													GBM(68;949 1139 14865 32798 38342)											0							SO:0001819	synonymous_variant			ENST00000331238.6	1	1	hg19	CCDS45569.1																																																																																				TCGA-IB-7647-01A-11D-2154-08	RTN4RL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450155.2	1	0	1	18	88	0	32	0	3.227999e-02	1	1	0	32	2		0	0	0	0	0	2	1	0.999990	18	88	0	31	2								-20.000000	1	1	121148	15	39	1	0	1	1	1.815224	1	0.240000	1.920000	0.144529	0.950000	0.670000	1.000000	1.000000	0.924934	0.950000	1	0.820000	1.000000
CDK12	51755	broad.mit.edu	37	17	37687333	37687333	+	Missense_Mutation	SNP	C	C	G			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr17:37687333C>G	ENST00000447079.4	+	14	4270	c.4237C>G	c.(4237-4239)Cac>Gac	p.H1413D	CDK12_ENST00000430627.2_Missense_Mutation_p.H1404D	NM_015083.1|NM_016507.2	NP_055898.1|NP_057591.2	Q9NYV4	CDK12_HUMAN	cyclin-dependent kinase 12			70					CTTAGCGTTACACCCGGTGGT	0.582000			Mis, N, F		serous ovarian					TCGA Ovarian(9;0.13)					Rec	yes		17	17q12	51755	cyclin-dependent kinase 12		E	0							SO:0001583	missense			ENST00000447079.4	0	1	hg19	CCDS11337.1	.	.	.	.	.	.	.	.	.	.	C	13.10	2.136315	0.37728	.	.	ENSG00000167258	ENST00000430627;ENST00000447079	T;T	0.69435	-0.37;-0.4	5.34	5.34	0.76211	.	0.124406	0.36665	N	0.002461	T	0.50922	0.1644	N	0.08118	0	0.42641	D	0.99341	P;P	0.40476	0.596;0.718	B;B	0.38803	0.146;0.282	T	0.61143	-0.7122	10	0.62326	D	0.03	-4.3884	18.8418	0.92188	0.0:1.0:0.0:0.0	.	1413;1404	Q9NYV4;Q9NYV4-2	CDK12_HUMAN;.	D	1404;1413	ENSP00000407720:H1404D;ENSP00000398880:H1413D	ENSP00000407720:H1404D	H	+	1	0	CDK12	34940859	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.938000	0.48987	2.775000	0.95449	0.650000	0.86243	CAC		TCGA-IB-7647-01A-11D-2154-08	CDK12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256941.4	0	0	0	8	351	0	78	1	6.865565e-01	4	98	0	78	2		0	0	0	0	0	2	1	0.989198	8	348	0	77	2								-8.065260	1	1	0	0		1	1	2	3	2.046166	0	0.240000	1.920000	0.247227	0.200000	0.090000	1.000000	0.190000	0.258934	0.200000	0	0.130000	0.300000
KIF18B	146909	broad.mit.edu	37	17	43011628	43011628	+	Silent	SNP	G	G	A			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr17:43011628G>A	ENST00000593135.1	-	6	955	c.858C>T	c.(856-858)aaC>aaT	p.N286N	KIF18B_ENST00000590129.1_Silent_p.N295N|KIF18B_ENST00000438933.2_Silent_p.N286N|KIF18B_ENST00000587309.1_Silent_p.N286N|KIF18B_ENST00000339151.4_Silent_p.N286N	NM_001265577.1	NP_001252506.1	Q86Y91	KI18B_HUMAN	kinesin family member 18B			21		Prostate(33;0.155)			CATTGAGGACGTTGATGAGCG	0.617000																								0							SO:0001819	synonymous_variant			ENST00000593135.1	1	1	hg19	CCDS45709.2																																																																																				TCGA-IB-7647-01A-11D-2154-08	KIF18B-001	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000448724.1	0	0	0	4	101	0	29	0	2.903272e-01	1	22	0	29	2		0	0	0	0	0	2	1	0.891773	4	101	0	29	2								-7.196137	1	1	121048	2	29	1	1	2	3	2.046166	0	0.240000	1.920000	0.247227	0.360000	0.120000	1.000000	0.310000	0.421424	0.360000	0	0.220000	0.600000
CACNA1G	8913	broad.mit.edu	37	17	48650006	48650006	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr17:48650006C>T	ENST00000359106.5	+	6	838	c.838C>T	c.(838-840)Cgg>Tgg	p.R280W	CACNA1G_ENST00000515411.1_Missense_Mutation_p.R280W|CACNA1G_ENST00000354983.4_Missense_Mutation_p.R280W|CACNA1G_ENST00000507896.1_Missense_Mutation_p.R280W|CACNA1G_ENST00000513689.2_Missense_Mutation_p.R280W|CACNA1G_ENST00000352832.5_Missense_Mutation_p.R280W|CACNA1G_ENST00000515765.1_Missense_Mutation_p.R280W|CACNA1G_ENST00000514717.1_Missense_Mutation_p.R280W|CACNA1G_ENST00000429973.2_Missense_Mutation_p.R280W|CACNA1G_ENST00000507336.1_Missense_Mutation_p.R280W|CACNA1G_ENST00000505165.1_Missense_Mutation_p.R280W|CACNA1G_ENST00000510115.1_Missense_Mutation_p.R280W|CACNA1G_ENST00000514079.1_Missense_Mutation_p.R280W|CACNA1G_ENST00000512389.1_Missense_Mutation_p.R280W|CACNA1G_ENST00000514181.1_Missense_Mutation_p.R280W|CACNA1G_ENST00000507609.1_Missense_Mutation_p.R280W|CACNA1G_ENST00000360761.4_Missense_Mutation_p.R280W|CACNA1G_ENST00000515165.1_Missense_Mutation_p.R280W|CACNA1G_ENST00000416767.4_Missense_Mutation_p.R280W|CACNA1G_ENST00000510366.1_Missense_Mutation_p.R280W|CACNA1G_ENST00000502264.1_Missense_Mutation_p.R280W|CACNA1G_ENST00000507510.2_Missense_Mutation_p.R280W|CACNA1G_ENST00000358244.5_Missense_Mutation_p.R280W|CACNA1G_ENST00000503485.1_Missense_Mutation_p.R280W|CACNA1G_ENST00000442258.2_Missense_Mutation_p.R280W|CACNA1G_ENST00000513964.1_Missense_Mutation_p.R280W	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit			47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)	Cinnarizine(DB00568)|Ethosuximide(DB00593)|Flunarizine(DB04841)|Methsuximide(DB05246)|Spironolactone(DB00421)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	GAACGGCATGCGGTCCTGCAG	0.647000																								0							SO:0001583	missense			ENST00000359106.5	0	1	hg19	CCDS45730.1	.	.	.	.	.	.	.	.	.	.	c	21.5	4.154466	0.78114	.	.	ENSG00000006283	ENST00000360761;ENST00000352832;ENST00000416767;ENST00000354983;ENST00000442258;ENST00000502264;ENST00000512389;ENST00000513964;ENST00000514717;ENST00000510366;ENST00000503485;ENST00000507510;ENST00000507336;ENST00000513689;ENST00000507609;ENST00000510115;ENST00000515165;ENST00000514181;ENST00000515765;ENST00000514079;ENST00000358244;ENST00000359106;ENST00000429973;ENST00000515411;ENST00000505165;ENST00000507896	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97066	-4.09;-4.09;-4.23;-4.04;-4.09;-4.08;-4.11;-4.18;-4.15;-4.16;-4.17;-4.04;-4.06;-4.12;-4.07;-4.03;-4.11;-4.07;-4.05;-4.11;-4.09;-4.06;-4.1;-4.05;-4.11;-4.11	5.36	4.38	0.52667	Ion transport (1);	0.332930	0.22063	N	0.065148	D	0.98021	0.9348	M	0.65498	2.005	0.54753	D	0.99998	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97110	0.998;0.993;0.997;0.997;0.999;0.986;0.999;1.0;0.999;0.981;1.0;0.975;0.993;0.998;0.999;0.993;0.991;0.984;1.0;0.987;0.993;0.993;0.999;0.99;0.981;0.985	D	0.98545	1.0634	10	0.66056	D	0.02	.	15.6493	0.77078	0.138:0.862:0.0:0.0	.	280;280;280;280;280;280;280;280;280;280;280;280;280;280;280;280;280;280;280;280;280;280;280;280;280;280	Q19QZ5;Q19QZ1;Q19QZ4;Q19R07;Q19QY8;Q19R10;Q19QZ6;Q19QZ3;Q19R06;Q19R00;Q19R04;O43497-10;Q19QZ9;Q19QZ7;Q19R08;Q19QZ8;Q19R03;O43497-4;Q19R02;Q19R12;Q19R17;Q19R11;Q2TAC4;O43497;Q19R13;O43497-11	.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;CAC1G_HUMAN;.;.	W	280	ENSP00000353990:R280W;ENSP00000339302:R280W;ENSP00000392390:R280W;ENSP00000347078:R280W;ENSP00000409759:R280W;ENSP00000425522:R280W;ENSP00000426261:R280W;ENSP00000425451:R280W;ENSP00000422407:R280W;ENSP00000426814:R280W;ENSP00000427238:R280W;ENSP00000423112:R280W;ENSP00000420918:R280W;ENSP00000426172:R280W;ENSP00000423045:R280W;ENSP00000427173:R280W;ENSP00000426098:R280W;ENSP00000425698:R280W;ENSP00000426232:R280W;ENSP00000423317:R280W;ENSP00000350979:R280W;ENSP00000352011:R280W;ENSP00000414388:R280W;ENSP00000423155:R280W;ENSP00000422268:R280W;ENSP00000421518:R280W	ENSP00000339302:R280W	R	+	1	2	CACNA1G	46005005	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	2.314000	0.43743	1.259000	0.44117	0.505000	0.49811	CGG		TCGA-IB-7647-01A-11D-2154-08	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1	0	0	0	3	53	0	23		0	0	0	0	23	2		0	0	0	0	0	2	1	0.801111	3	51	0	21	2								-6.777303	1	0	0	0		1	1	2	3	2.076965	0	0.240000	1.920000	0.252557	0.550000	0.150000	1.000000	1.000000	0.594085	0.550000	0	0.300000	1.000000
LUC7L3	51747	broad.mit.edu	37	17	48821167	48821167	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr17:48821167C>T	ENST00000505658.1	+	6	716	c.527C>T	c.(526-528)aCg>aTg	p.T176M	LUC7L3_ENST00000393227.2_Missense_Mutation_p.T176M|LUC7L3_ENST00000240304.1_Missense_Mutation_p.T176M|LUC7L3_ENST00000544170.1_Missense_Mutation_p.T100M			O95232	LC7L3_HUMAN	LUC7-like 3 (S. cerevisiae)			12					AGGTCCACAACGTCGGTGAGT	0.368000																								0							SO:0001583	missense			ENST00000505658.1	1	1	hg19	CCDS11573.1	.	.	.	.	.	.	.	.	.	.	C	12.55	1.970220	0.34754	.	.	ENSG00000108848	ENST00000505658;ENST00000393227;ENST00000240304;ENST00000542316;ENST00000544170	T;T;T;T	0.30448	1.53;1.53;1.53;1.53	5.48	5.48	0.80851	.	0.097706	0.64402	D	0.000001	T	0.37489	0.1005	N	0.16478	0.41	0.53005	D	0.99996	P;D;D	0.67145	0.629;0.988;0.996	B;P;P	0.58928	0.091;0.761;0.848	T	0.13282	-1.0515	10	0.38643	T	0.18	-7.8056	19.7073	0.96079	0.0:1.0:0.0:0.0	.	100;176;176	B4DJ96;O95232;A8K3C5	.;LC7L3_HUMAN;.	M	176;176;176;176;100	ENSP00000425092:T176M;ENSP00000376919:T176M;ENSP00000240304:T176M;ENSP00000444253:T100M	ENSP00000240304:T176M	T	+	2	0	LUC7L3	46176166	1.000000	0.71417	0.963000	0.40424	0.042000	0.13812	5.910000	0.69931	2.722000	0.93159	0.557000	0.71058	ACG		TCGA-IB-7647-01A-11D-2154-08	LUC7L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368205.2	1	0	1	36	246	0	64	1	1	85	188	0	64	2		0	0	0	0	0	2	1	1.000000	36	245	0	63	2								-16.138760	1	1	0	0		1	1	2	3	2.088520	0	0.240000	1.920000	0.254317	0.990000	0.790000	1.000000	1.000000	0.975263	0.990000	1	0.930000	1.000000
TP53	7157	broad.mit.edu	37	17	7577539	7577539	+	Missense_Mutation	SNP	G	G	A	rs121912651		TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr17:7577539G>A	ENST00000269305.4	-	7	931	c.742C>T	c.(742-744)Cgg>Tgg	p.R248W	TP53_ENST00000445888.2_Missense_Mutation_p.R248W|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.R248W|TP53_ENST00000420246.2_Missense_Mutation_p.R248W|TP53_ENST00000359597.4_Missense_Mutation_p.R248W|TP53_ENST00000413465.2_Missense_Mutation_p.R248W	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	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)		24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		Acetylsalicylic acid(DB00945)	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)			Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		L, E, M, O	617	Substitution - Missense(585)|Whole gene deletion(8)|Deletion - In frame(7)|Unknown(6)|Insertion - Frameshift(3)|Deletion - Frameshift(3)|Complex - compound substitution(3)|Substitution - coding silent(2)	GRCh37	CM010465|CM900211	TP53	M	rs121912651	SO:0001583	missense	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	ENST00000269305.4	1	1	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	18.84	3.710019	0.68730	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99869	-7.34;-7.34;-7.34;-7.34;-7.34;-7.34;-7.34;-7.34	4.62	2.56	0.30785	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99843	0.9928	M	0.92507	3.315	0.58432	A	0.999997	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0	D	0.97208	0.9869	9	0.87932	D	0	-9.5643	7.568	0.27890	0.0893:0.0:0.7471:0.1636	.	248;248;155;248;248;248	P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;P53_HUMAN;.;.	W	248;248;248;248;248;248;237;155;116;155	ENSP00000410739:R248W;ENSP00000352610:R248W;ENSP00000269305:R248W;ENSP00000398846:R248W;ENSP00000391127:R248W;ENSP00000391478:R248W;ENSP00000425104:R116W;ENSP00000423862:R155W	ENSP00000269305:R248W	R	-	1	2	TP53	7518264	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	1.447000	0.35101	0.644000	0.30656	0.462000	0.41574	CGG		TCGA-IB-7647-01A-11D-2154-08	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	1	0	1	37	216	0	71	1	1	95	99	0	71	2	1	1	107	905	0	942	2	1	1.000000	36	214	0	71	2								-2.605585	1	1	121412	1	37	1	0	1	1	1.820921	1	0.240000	1.920000	0.136364	0.910000	0.710000	1.000000	0.990000	0.904389	0.910000	1	0.820000	0.980000
RAB40B	10966	broad.mit.edu	37	17	80615798	80615798	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr17:80615798C>T	ENST00000571995.1	-	6	909	c.778G>A	c.(778-780)Gtc>Atc	p.V260I	RAB40B_ENST00000571880.1_5'Flank|RAB40B_ENST00000269347.6_Missense_Mutation_p.V81I|RAB40B_ENST00000538809.2_3'UTR	NM_006822.2	NP_006813.1	Q12829	RB40B_HUMAN	RAB40B, member RAS oncogene family			10	Breast(20;0.00132)|all_neural(118;0.0952)	all_cancers(8;0.072)|all_epithelial(8;0.139)	BRCA - Breast invasive adenocarcinoma(99;0.0262)|OV - Ovarian serous cystadenocarcinoma(97;0.061)		GGGGGGCGGACGAGCTTCACT	0.572000																								0							SO:0001583	missense			ENST00000571995.1	0	1	hg19	CCDS11816.1	.	.	.	.	.	.	.	.	.	.	C	2.276	-0.365935	0.05069	.	.	ENSG00000141542	ENST00000269347;ENST00000538809	.	.	.	4.79	-9.58	0.00559	.	2.176640	0.02755	N	0.117936	T	0.05868	0.0153	N	0.00308	-1.67	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.13683	-1.0500	9	0.02654	T	1	.	7.8491	0.29444	0.0702:0.0823:0.1585:0.6889	.	260	Q12829	RB40B_HUMAN	I	260;294	.	ENSP00000269347:V260I	V	-	1	0	RAB40B	78209087	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-0.991000	0.03728	-3.220000	0.00212	-0.244000	0.11960	GTC		TCGA-IB-7647-01A-11D-2154-08	RAB40B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439007.1	0	0	0	16	847	1	184	1	1.813240e-01	12	135	1	184	5		0	0	0	0	0	2	0	0.309789	14	712	1	153	17								-2.386141	0	0	0	0		1	0	1	1	1.963353	0	0.240000	1.920000	0.214551	0.140000	0.080000	0.230000	0.150000	0.157809	0.140000	0	0.110000	0.190000
TECR	9524	broad.mit.edu	37	19	14674472	14674472	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr19:14674472C>T	ENST00000215567.5	+	4	258	c.121C>T	c.(121-123)Ccg>Tcg	p.P41S	TECR_ENST00000600083.1_5'UTR|TECR_ENST00000596164.1_3'UTR|TECR_ENST00000436007.2_Missense_Mutation_p.P56S|TECR_ENST00000596073.1_5'UTR	NM_138501.5	NP_612510.1	Q9NZ01	TECR_HUMAN	trans-2,3-enoyl-CoA reductase			3					CCCCGCAGATCCGCAGTGGTA	0.697000																								0							SO:0001583	missense			ENST00000215567.5	1	1	hg19	CCDS12313.1	.	.	.	.	.	.	.	.	.	.	C	17.52	3.409144	0.62399	.	.	ENSG00000099797	ENST00000215567;ENST00000436007	T;T	0.46451	0.87;0.87	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	T	0.58206	0.2106	L	0.48218	1.51	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.998;0.998	T	0.56335	-0.7996	10	0.45353	T	0.12	-10.426	16.3276	0.82990	0.0:1.0:0.0:0.0	.	41;56;41	B3KM97;B3KSQ1;Q9NZ01	.;.;TECR_HUMAN	S	41;56	ENSP00000215567:P41S;ENSP00000397206:P56S	ENSP00000215567:P41S	P	+	1	0	TECR	14535472	1.000000	0.71417	0.989000	0.46669	0.027000	0.11550	4.298000	0.59067	2.462000	0.83206	0.561000	0.74099	CCG		TCGA-IB-7647-01A-11D-2154-08	TECR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466000.1	1	0	0	12	203	0	48	1	9.999992e-01	90	442	0	48	2		0	0	0	0	0	2	1	0.999045	12	197	0	47	2								-15.968060	1	0	121354	3	34	1	0	1	1	1.952177	0	0.240000	1.920000	0.204688	0.450000	0.240000	0.720000	0.440000	0.468466	0.450000	0	0.330000	0.590000
NOTCH3	4854	broad.mit.edu	37	19	15271507	15271507	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr19:15271507G>A	ENST00000263388.2	-	33	7007	c.6932C>T	c.(6931-6933)cCg>cTg	p.P2311L		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3			93			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)		GGTAACTTCCGGCTGGGGCCC	0.627000																								0							SO:0001583	missense			ENST00000263388.2	1	1	hg19	CCDS12326.1	.	.	.	.	.	.	.	.	.	.	G	10.58	1.390466	0.25118	.	.	ENSG00000074181	ENST00000263388	T	0.81247	-1.47	3.99	3.99	0.46301	.	.	.	.	.	T	0.59390	0.2190	N	0.08118	0	0.21105	N	0.999789	P	0.34587	0.458	B	0.19391	0.025	T	0.55685	-0.8102	9	0.87932	D	0	.	9.199	0.37246	0.1056:0.0:0.8944:0.0	.	2311	Q9UM47	NOTC3_HUMAN	L	2311	ENSP00000263388:P2311L	ENSP00000263388:P2311L	P	-	2	0	NOTCH3	15132507	0.858000	0.29795	0.387000	0.26183	0.565000	0.35776	2.105000	0.41825	1.948000	0.56530	0.591000	0.81541	CCG		TCGA-IB-7647-01A-11D-2154-08	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	1	0	1	48	371	0	89	1	1	56	481	0	89	2		0	0	0	0	0	2	1	1.000000	47	366	0	88	2								-3.075756	1	1	121400	1	26	1	0	1	1	1.952177	0	0.240000	1.920000	0.204688	0.900000	0.680000	1.000000	1.000000	0.898655	0.900000	1	0.790000	1.000000
RYR1	6261	broad.mit.edu	37	19	38976522	38976522	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr19:38976522G>A	ENST00000359596.3	+	34	5227	c.5227G>A	c.(5227-5229)Gcc>Acc	p.A1743T	RYR1_ENST00000360985.3_Missense_Mutation_p.A1743T|RYR1_ENST00000355481.4_Missense_Mutation_p.A1743T			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)			285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)	Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	TGAGACCCGCGCCATCACGCT	0.622000																								0							SO:0001583	missense			ENST00000359596.3	1	1	hg19	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	G	13.64	2.297479	0.40694	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	T;T;T	0.72615	-0.67;-0.67;-0.67	3.77	1.49	0.22878	.	0.137822	0.45126	U	0.000388	T	0.41581	0.1165	N	0.14661	0.345	0.29121	N	0.880273	B;B	0.33940	0.433;0.274	B;B	0.26614	0.071;0.056	T	0.23368	-1.0190	10	0.19590	T	0.45	.	4.2144	0.10528	0.5402:0.0:0.4598:0.0	.	1743;1743	P21817-2;P21817	.;RYR1_HUMAN	T	1743	ENSP00000352608:A1743T;ENSP00000347667:A1743T;ENSP00000354254:A1743T	ENSP00000347667:A1743T	A	+	1	0	RYR1	43668362	0.108000	0.22018	1.000000	0.80357	0.613000	0.37349	0.876000	0.28092	0.796000	0.33947	-0.225000	0.12378	GCC		TCGA-IB-7647-01A-11D-2154-08	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1	1	0	1	50	366	0	120		0	0	0	0	120	2		0	0	0	0	0	2	1	1.000000	50	360	0	117	2								-19.044860	1	1	0	0		1	1	2	3	2.062989	0	0.240000	1.920000	0.249901	0.990000	0.770000	1.000000	1.000000	0.961260	0.990000	1	0.890000	1.000000
BCKDHA	593	broad.mit.edu	37	19	41928085	41928085	+	Silent	SNP	C	C	T	rs151227241		TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr19:41928085C>T	ENST00000269980.2	+	6	1031	c.663C>T	c.(661-663)taC>taT	p.Y221Y	BCKDHA_ENST00000457836.2_Silent_p.Y199Y|CTC-435M10.3_ENST00000540732.1_Silent_p.Y255Y|BCKDHA_ENST00000595085.1_Silent_p.Y255Y|BCKDHA_ENST00000535632.1_3'UTR	NM_000709.3|NM_001164783.1	NP_000700.1|NP_001158255.1	P12694	ODBA_HUMAN	branched chain keto acid dehydrogenase E1, alpha polypeptide			10					GGGCGGCGTACGCAGCCAAGC	0.637000																								0							SO:0001819	synonymous_variant			ENST00000269980.2	1	1	hg19	CCDS12581.1	.	.	.	.	.	.	.	.	.	.	C	1.529	-0.544937	0.04024	0.0	1.16E-4	ENSG00000248098	ENST00000541315	.	.	.	4.85	-8.87	0.00792	.	.	.	.	.	T	0.64461	0.2600	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.72304	-0.4333	4	.	.	.	-19.325	17.7578	0.88455	0.0:0.1167:0.0:0.8833	.	.	.	.	M	188	.	.	T	+	2	0	BCKDHA	46619925	0.000000	0.05858	0.295000	0.24960	0.242000	0.25591	-2.269000	0.01168	-1.955000	0.01023	-1.202000	0.01658	ACG		TCGA-IB-7647-01A-11D-2154-08	BCKDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398313.3	0	0	0	7	183	0	38	1	9.727769e-01	11	160	0	38	2		0	0	0	0	0	2	1	0.980097	7	180	0	37	2								-9.434995	1	1	121412	9	40	1	2	3	5	2.327642	1	0.240000	1.920000	0.343923	0.430000	0.170000	1.000000	0.360000	0.541928	0.430000	0	0.270000	1.000000
KLC3	147700	broad.mit.edu	37	19	45853603	45853603	+	Nonsense_Mutation	SNP	C	C	G			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr19:45853603C>G	ENST00000391946.2	+	9	1250	c.1148C>G	c.(1147-1149)tCa>tGa	p.S383*	ERCC2_ENST00000391945.4_3'UTR|KLC3_ENST00000585434.1_Nonsense_Mutation_p.S382*|KLC3_ENST00000470402.1_Nonsense_Mutation_p.S397*	NM_177417.2	NP_803136.2	Q6P597	KLC3_HUMAN	kinesin light chain 3			8		Ovarian(192;0.0728)|all_neural(266;0.112)			CCGCAGGCCTCAGCCTACCTG	0.532000																								0							SO:0001587	stop_gained			ENST00000391946.2	0	1	hg19	CCDS12660.2	.	.	.	.	.	.	.	.	.	.	C	33	5.269984	0.95429	.	.	ENSG00000104892	ENST00000391946;ENST00000470402	.	.	.	3.74	3.74	0.42951	.	0.094375	0.44285	D	0.000478	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	1.0098	13.0785	0.59100	0.0:1.0:0.0:0.0	.	.	.	.	X	383;397	.	ENSP00000375810:S383X	S	+	2	0	KLC3	50545443	1.000000	0.71417	0.980000	0.43619	0.644000	0.38419	7.541000	0.82084	1.913000	0.55393	0.462000	0.41574	TCA		TCGA-IB-7647-01A-11D-2154-08	KLC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289776.1	1	0	1	21	272	0	65	1	5.967317e-01	5	22	0	65	2		0	0	0	0	0	2	1	0.999998	21	270	0	65	2								-20.000000	1	0	0	0		1	1	2	3	2.335259	1	0.240000	1.920000	0.321429	0.670000	0.430000	0.970000	0.660000	0.689497	0.670000	0	0.540000	0.830000
KLC3	147700	broad.mit.edu	37	19	45853629	45853629	+	Nonsense_Mutation	SNP	C	C	T			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr19:45853629C>T	ENST00000391946.2	+	9	1276	c.1174C>T	c.(1174-1176)Caa>Taa	p.Q392*	ERCC2_ENST00000391945.4_3'UTR|KLC3_ENST00000585434.1_Nonsense_Mutation_p.Q391*|KLC3_ENST00000470402.1_Nonsense_Mutation_p.Q406*	NM_177417.2	NP_803136.2	Q6P597	KLC3_HUMAN	kinesin light chain 3			8		Ovarian(192;0.0728)|all_neural(266;0.112)			GAACAAGTATCAACAAGCGGA	0.567000																								0							SO:0001587	stop_gained			ENST00000391946.2	0	1	hg19	CCDS12660.2	.	.	.	.	.	.	.	.	.	.	C	27.3	4.816862	0.90790	.	.	ENSG00000104892	ENST00000391946;ENST00000470402	.	.	.	3.93	-1.34	0.09143	.	0.172476	0.38436	N	0.001693	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	12.5559	7.0831	0.25241	0.2875:0.2665:0.446:0.0	.	.	.	.	X	392;406	.	ENSP00000375810:Q392X	Q	+	1	0	KLC3	50545469	0.571000	0.26659	0.999000	0.59377	0.813000	0.45954	0.192000	0.17096	0.256000	0.21614	0.462000	0.41574	CAA		TCGA-IB-7647-01A-11D-2154-08	KLC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289776.1	1	0	0	32	302	0	79	1	5.890675e-01	4	16	0	79	2		0	0	0	0	0	2	1	1.000000	32	301	0	79	2								-20.000000	1	0	0	0		1	1	2	3	2.335259	1	0.240000	1.920000	0.321429	0.890000	0.630000	1.000000	1.000000	0.883752	0.890000	1	0.750000	1.000000
ERCC2	2068	broad.mit.edu	37	19	45854888	45854888	+	Nonstop_Mutation	SNP	C	C	G			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr19:45854888C>G	ENST00000391945.4	-	23	2359	c.2282G>C	c.(2281-2283)tGa>tCa	p.*761S	ERCC2_ENST00000391944.3_Nonstop_Mutation_p.*683S	NM_000400.3	NP_000391.1	P18074	ERCC2_HUMAN	excision repair cross-complementation group 2			9		Ovarian(192;0.0728)|all_neural(266;0.112)			CCGCCCCACTCAGAGCTGCTG	0.592000			Mis, N, F, S			skin basal cell, skin squamous cell, melanoma		Nucleotide excision repair (NER)	Xeroderma Pigmentosum					yes	Rec		Xeroderma pigmentosum (D)	19	19q13.2-q13.3	2068	excision repair cross-complementing rodent repair deficiency, complementation group 2 (xeroderma pigmentosum D)		E	0							SO:0001578	stop_lost	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	ENST00000391945.4	0	1	hg19	CCDS33049.1	.	.	.	.	.	.	.	.	.	.	C	9.890	1.203909	0.22121	.	.	ENSG00000104884	ENST00000391941;ENST00000391942;ENST00000391945;ENST00000391944	.	.	.	4.29	3.26	0.37387	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.3154	0.21188	0.0:0.8316:0.0:0.1684	.	.	.	.	S	711;737;761;683	.	.	X	-	2	2	ERCC2	50546728	1.000000	0.71417	0.948000	0.38648	0.024000	0.10985	3.262000	0.51538	0.932000	0.37266	0.561000	0.74099	TGA		TCGA-IB-7647-01A-11D-2154-08	ERCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109626.2	0	0	0	98	1089	0	291	1	8.424976e-01	7	32	0	291	2		0	0	0	0	0	2	1	1.000000	97	1070	0	286	2								-19.928260	1	0	0	0		1	1	2	3	2.335259	1	0.240000	1.920000	0.321429	0.760000	0.620000	0.920000	0.780000	0.775677	0.760000	0	0.690000	0.850000
ERCC2	2068	broad.mit.edu	37	19	45854979	45854979	+	Splice_Site	SNP	C	C	G			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr19:45854979C>G	ENST00000391945.4	-	23	2268	c.2191G>C	c.(2191-2193)Gag>Cag	p.E731Q	ERCC2_ENST00000391944.3_Splice_Site_p.E653Q	NM_000400.3	NP_000391.1	P18074	ERCC2_HUMAN	excision repair cross-complementation group 2			9		Ovarian(192;0.0728)|all_neural(266;0.112)			AGCTGATCCTCCTGCAGAGAA	0.627000			Mis, N, F, S			skin basal cell, skin squamous cell, melanoma		Nucleotide excision repair (NER)	Xeroderma Pigmentosum					yes	Rec		Xeroderma pigmentosum (D)	19	19q13.2-q13.3	2068	excision repair cross-complementing rodent repair deficiency, complementation group 2 (xeroderma pigmentosum D)		E	0							SO:0001630	splice_region_variant	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	ENST00000391945.4	1	0	hg19	CCDS33049.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.056286	0.76074	.	.	ENSG00000104884	ENST00000391941;ENST00000391942;ENST00000391945;ENST00000391944	T;D	0.82893	-1.44;-1.66	4.13	4.13	0.48395	.	0.058002	0.64402	D	0.000002	D	0.90205	0.6938	M	0.79805	2.47	0.80722	D	1	B;B;D	0.63880	0.066;0.114;0.993	B;B;D	0.72982	0.109;0.04;0.979	D	0.90111	0.4192	10	0.41790	T	0.15	-29.0483	13.9463	0.64086	0.0:1.0:0.0:0.0	.	653;731;424	E7EVE9;P18074;Q6ZNQ5	.;ERCC2_HUMAN;.	Q	681;707;731;653	ENSP00000375809:E731Q;ENSP00000375808:E653Q	ENSP00000375805:E681Q	E	-	1	0	ERCC2	50546819	1.000000	0.71417	1.000000	0.80357	0.869000	0.49853	6.925000	0.75829	2.153000	0.67306	0.561000	0.74099	GAG		TCGA-IB-7647-01A-11D-2154-08	ERCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109626.2	1	0	0	51	504	0	131	1	9.181251e-01	3	41	0	131	2		0	0	0	0	0	2	1	1.000000	50	501	0	131	2								-3.017764	1	0	0	0		1	1	2	3	2.335259	1	0.240000	1.920000	0.321429	0.850000	0.640000	1.000000	1.000000	0.859816	0.850000	1	0.740000	0.980000
ZNF671	79891	broad.mit.edu	37	19	58232832	58232832	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr19:58232832C>T	ENST00000317398.6	-	4	717	c.622G>A	c.(622-624)Gac>Aac	p.D208N	ZNF671_ENST00000594803.1_5'Flank|ZNF671_ENST00000335820.3_Missense_Mutation_p.D110N|AC003006.7_ENST00000599221.1_Intron|AC003006.7_ENST00000594684.1_Intron	NM_024833.2	NP_079109.2	Q8TAW3	ZN671_HUMAN	zinc finger protein 671			22		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)			TGGTGCTGGTCAAAGTCTGTA	0.502000																								0							SO:0001583	missense			ENST00000317398.6	1	1	hg19	CCDS12961.1	.	.	.	.	.	.	.	.	.	.	C	13.37	2.218275	0.39201	.	.	ENSG00000083814	ENST00000317398;ENST00000335820	T;T	0.27402	1.67;1.67	2.45	-2.07	0.07276	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.10895	0.0266	N	0.04297	-0.235	0.09310	N	1	B	0.17038	0.02	B	0.19391	0.025	T	0.37314	-0.9711	9	0.13108	T	0.6	.	4.9308	0.13916	0.0:0.5176:0.2982:0.1842	.	208	Q8TAW3	ZN671_HUMAN	N	208;110	ENSP00000321848:D208N;ENSP00000338670:D110N	ENSP00000321848:D208N	D	-	1	0	ZNF671	62924644	0.000000	0.05858	0.006000	0.13384	0.365000	0.29674	-2.416000	0.01035	-0.084000	0.12595	0.467000	0.42956	GAC		TCGA-IB-7647-01A-11D-2154-08	ZNF671-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466817.1	1	0	0	31	540	0	131	0	4.824536e-01	0	29	0	131	2		0	0	0	0	0	2	1	1.000000	31	536	0	130	2								-6.069153	1	1	0	0		1	0	3	3	2.098921	1	0.240000	1.920000	0.301984	0.520000	0.340000	1.000000	0.490000	0.595968	0.520000	0	0.420000	1.000000
MUC16	94025	broad.mit.edu	37	19	9074001	9074001	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr19:9074001G>A	ENST00000397910.4	-	3	13648	c.13445C>T	c.(13444-13446)gCg>gTg	p.A4482V		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated			590					AACTGAAGTCGCAGAAACAGG	0.463000																								0							SO:0001583	missense			ENST00000397910.4	1	1	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	a	1.841	-0.467526	0.04476	4.95E-4	1.2E-4	ENSG00000181143	ENST00000397910	T	0.15603	2.41	2.22	-4.44	0.03557	.	.	.	.	.	T	0.03564	0.0102	N	0.00368	-1.59	.	.	.	B	0.02656	0.0	B	0.04013	0.001	T	0.44667	-0.9313	8	0.87932	D	0	.	5.0828	0.14666	0.4495:0.0:0.4123:0.1382	.	4482	B5ME49	.	V	4482	ENSP00000381008:A4482V	ENSP00000381008:A4482V	A	-	2	0	MUC16	8935001	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-2.514000	0.00956	-2.395000	0.00582	-2.024000	0.00429	GCG		TCGA-IB-7647-01A-11D-2154-08	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	1	0	0	34	465	0	110	0	5.009901e-03	0	2	0	110	2	0	0	0	1	0	0	2	1	1.000000	34	458	0	109	2								-7.773385	1	1	120972	3	41	1	0	1	1	1.952177	0	0.240000	1.920000	0.204688	0.540000	0.380000	0.730000	0.540000	0.551997	0.540000	0	0.450000	0.640000
EPHA2	1969	broad.mit.edu	37	1	16455955	16455955	+	Silent	SNP	G	G	A			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr1:16455955G>A	ENST00000358432.5	-	16	2953	c.2799C>T	c.(2797-2799)atC>atT	p.I933I		NM_004431.3	NP_004422.2	P29317	EPHA2_HUMAN	EPH receptor A2			42		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		Dasatinib(DB01254)|Regorafenib(DB08896)	CCACCTTCTCGATGGCAGTGT	0.652000																								0							SO:0001819	synonymous_variant			ENST00000358432.5	1	1	hg19	CCDS169.1																																																																																				TCGA-IB-7647-01A-11D-2154-08	EPHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026322.1	0	0	0	14	398	0	107	1	9.973017e-01	17	262	0	107	2		0	0	0	0	0	2	1	0.999725	13	390	0	106	2								-13.482850	1	1	121412	9	44	1	1	2	3	2.028492	0	0.240000	1.920000	0.243631	0.290000	0.160000	1.000000	0.280000	0.321218	0.290000	0	0.220000	0.390000
CACNA1E	777	broad.mit.edu	37	1	181732595	181732595	+	Silent	SNP	C	C	T			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr1:181732595C>T	ENST00000367573.2	+	34	4743	c.4743C>T	c.(4741-4743)gcC>gcT	p.A1581A	CACNA1E_ENST00000367567.4_Silent_p.A1188A|CACNA1E_ENST00000526775.1_Silent_p.A1562A|CACNA1E_ENST00000360108.3_Silent_p.A1562A|CACNA1E_ENST00000358338.5_Silent_p.A1513A|CACNA1E_ENST00000357570.5_Silent_p.A1532A|CACNA1E_ENST00000367570.1_Silent_p.A1581A	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit			204					TCCGAGCTGCCCGCCTCATAA	0.463000																								0							SO:0001819	synonymous_variant			ENST00000367573.2	1	1	hg19	CCDS55664.1																																																																																				TCGA-IB-7647-01A-11D-2154-08	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	0	0	0	8	281	0	38	0	1.962366e-02	0	7	0	38	2		0	0	0	0	0	2	1	0.989183	8	278	0	37	2								-3.614931	1	1	0	0		1	0	1	1	2.016410	0	0.240000	1.920000	0.235412	0.230000	0.110000	0.420000	0.230000	0.253315	0.230000	0	0.160000	0.330000
TMCC2	9911	broad.mit.edu	37	1	205241064	205241064	+	Missense_Mutation	SNP	A	A	G			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr1:205241064A>G	ENST00000358024.3	+	5	2331	c.1942A>G	c.(1942-1944)Aac>Gac	p.N648D	TMCC2_ENST00000329800.7_Missense_Mutation_p.N408D|TMCC2_ENST00000330675.7_Missense_Mutation_p.N423D|TMCC2_ENST00000495538.1_3'UTR|TMCC2_ENST00000545499.1_Missense_Mutation_p.N570D	NM_014858.3	NP_055673.2	O75069	TMCC2_HUMAN	transmembrane and coiled-coil domain family 2			20	Breast(84;0.0871)		BRCA - Breast invasive adenocarcinoma(75;0.117)		CAAGTTCATCAACGTGATCCT	0.627000																								0							SO:0001583	missense			ENST00000358024.3	1	1	hg19	CCDS30984.1	.	.	.	.	.	.	.	.	.	.	A	32	5.136024	0.94517	.	.	ENSG00000133069	ENST00000358024;ENST00000545499;ENST00000330675;ENST00000329800	T;T;T;T	0.56444	0.46;0.46;0.46;0.46	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	T	0.75831	0.3903	M	0.88181	2.935	0.80722	D	1	D;D;D	0.76494	0.998;0.999;0.999	D;D;D	0.69479	0.94;0.964;0.964	T	0.81191	-0.1045	10	0.72032	D	0.01	.	15.1067	0.72326	1.0:0.0:0.0:0.0	.	408;423;648	G5E963;B2RAX5;O75069	.;.;TMCC2_HUMAN	D	648;570;423;408	ENSP00000350718:N648D;ENSP00000437943:N570D;ENSP00000331842:N423D;ENSP00000329436:N408D	ENSP00000329436:N408D	N	+	1	0	TMCC2	203507687	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.139000	0.94554	2.233000	0.73108	0.533000	0.62120	AAC		TCGA-IB-7647-01A-11D-2154-08	TMCC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090383.1	1	0	1	70	516	0	162	0	2.971353e-01	1	8	0	162	2		0	0	0	0	0	2	1	1.000000	70	509	0	160	2								-20.000000	1	1	0	0		1	1	2	3	2.024286	0	0.240000	1.920000	0.248120	0.990000	0.790000	1.000000	1.000000	0.963737	0.990000	1	0.900000	1.000000
OBSCN	84033	broad.mit.edu	37	1	228494661	228494661	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr1:228494661G>A	ENST00000422127.1	+	45	12030	c.11986G>A	c.(11986-11988)Gca>Aca	p.A3996T	OBSCN_ENST00000284548.11_Missense_Mutation_p.A3996T|OBSCN_ENST00000366707.4_Missense_Mutation_p.A1630T|OBSCN_ENST00000570156.2_Missense_Mutation_p.A4953T|OBSCN_ENST00000366709.4_Missense_Mutation_p.A1115T	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF			223		Prostate(94;0.0405)			GGGAGGCACCGCACACTTATG	0.662000																								0							SO:0001583	missense			ENST00000422127.1	0	1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	G	16.84	3.234904	0.58886	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	T;T;T;T	0.05996	3.36;3.36;3.36;3.36	5.75	4.83	0.62350	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.080615	0.51477	D	0.000084	T	0.23806	0.0576	M	0.76433	2.335	0.09310	N	1	D;P	0.89917	1.0;0.945	D;P	0.91635	0.999;0.465	T	0.02450	-1.1157	10	0.35671	T	0.21	.	15.1731	0.72891	0.069:0.0:0.931:0.0	.	3996;3996	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	T	3996;3996;1630;1115	ENSP00000284548:A3996T;ENSP00000409493:A3996T;ENSP00000355668:A1630T;ENSP00000355670:A1115T	ENSP00000284548:A3996T	A	+	1	0	OBSCN	226561284	0.393000	0.25237	0.150000	0.22450	0.002000	0.02628	3.437000	0.52863	2.722000	0.93159	0.462000	0.41574	GCA		TCGA-IB-7647-01A-11D-2154-08	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		0	0	0	3	44	0	13		0	0	0	0	13	2		0	0	0	0	0	2	1	0.812608	3	44	0	13	2								-7.313587	1	1	0	0		1	1	2	3	2.024286	0	0.240000	1.920000	0.248120	0.620000	0.180000	1.000000	1.000000	0.645483	0.620000	0	0.350000	1.000000
ACTA1	58	broad.mit.edu	37	1	229568336	229568336	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr1:229568336C>T	ENST00000366684.3	-	3	523	c.421G>A	c.(421-423)Gtg>Atg	p.V141M	ACTA1_ENST00000366683.2_Intron	NM_001100.3	NP_001091.1	P68133	ACTS_HUMAN	actin, alpha 1, skeletal muscle			28	Breast(184;0.0858)|Ovarian(103;0.103)	Prostate(94;0.167)			AGGGACAGCACGGCCTGGATG	0.706000																								0							SO:0001583	missense			ENST00000366684.3	1	1	hg19	CCDS1578.1	.	.	.	.	.	.	.	.	.	.	C	14.13	2.444060	0.43429	.	.	ENSG00000143632	ENST00000366684;ENST00000366682;ENST00000342787	D	0.96136	-3.92	4.54	4.54	0.55810	.	0.000000	0.64402	D	0.000001	D	0.97838	0.9290	H	0.96111	3.77	0.80722	D	1	P	0.41475	0.751	P	0.49332	0.607	D	0.99867	1.1091	10	0.87932	D	0	.	17.4768	0.87661	0.0:1.0:0.0:0.0	.	141	P68133	ACTS_HUMAN	M	141;106;141	ENSP00000355645:V141M	ENSP00000344142:V141M	V	-	1	0	ACTA1	227634959	1.000000	0.71417	0.998000	0.56505	0.419000	0.31324	7.620000	0.83070	2.360000	0.80028	0.655000	0.94253	GTG		TCGA-IB-7647-01A-11D-2154-08	ACTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092781.1	1	0	0	75	367	0	103		0	0	0	0	103	2		0	0	0	0	0	2	1	1.000000	74	360	0	100	2								-20.000000	1	1	0	0		1	1	2	3	2.024286	0	0.240000	1.920000	0.248120	0.990000	0.990000	1.000000	1.000000	0.999975	0.990000	1	0.990000	1.000000
OR2W5	441932	broad.mit.edu	37	1	247655201	247655201	+	RNA	SNP	C	C	T			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr1:247655201C>T	ENST00000522351.1	+	0	832							A6NFC9	OR2W5_HUMAN	olfactory receptor, family 2, subfamily W, member 5			39	all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.222)	OV - Ovarian serous cystadenocarcinoma(106;0.0188)		CCATCATCTACGTGTACCTGA	0.532000																								0											ENST00000522351.1	1	1	hg19																																																																																					TCGA-IB-7647-01A-11D-2154-08	OR2W5-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000375789.1	0	0	0	25	603	0	123		0	0	0	0	123	2		0	0	0	0	0	2	1	1.000000	24	601	0	121	2								-4.257193	1	1	0	0		1	1	2	3	2.024286	0	0.240000	1.920000	0.248120	0.340000	0.220000	1.000000	0.330000	0.393516	0.340000	0	0.270000	0.440000
OR2L13	284521	broad.mit.edu	37	1	248262826	248262826	+	Missense_Mutation	SNP	T	T	G			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr1:248262826T>G	ENST00000358120.2	+	2	294	c.149T>G	c.(148-150)gTg>gGg	p.V50G	OR2L13_ENST00000366478.2_Missense_Mutation_p.V50G			Q8N349	OR2LD_HUMAN	olfactory receptor, family 2, subfamily L, member 13			59	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)		OV - Ovarian serous cystadenocarcinoma(106;0.0132)		CTCATCCACGTGGATCCTCGT	0.502000																								0							SO:0001583	missense			ENST00000358120.2	1	1	hg19	CCDS1637.1	.	.	.	.	.	.	.	.	.	.	T	8.900	0.956010	0.18507	.	.	ENSG00000196071	ENST00000366478;ENST00000358120	T;T	0.03004	4.08;4.08	4.07	2.92	0.33932	GPCR, rhodopsin-like superfamily (1);	0.615698	0.13314	N	0.397234	T	0.02807	0.0084	L	0.28014	0.82	0.09310	N	1	B	0.24258	0.1	B	0.21708	0.036	T	0.44697	-0.9311	10	0.54805	T	0.06	.	2.5302	0.04701	0.2215:0.1561:0.0:0.6224	.	50	Q8N349	OR2LD_HUMAN	G	50	ENSP00000355434:V50G;ENSP00000350836:V50G	ENSP00000350836:V50G	V	+	2	0	OR2L13	246329449	0.000000	0.05858	0.003000	0.11579	0.019000	0.09904	-3.499000	0.00450	0.580000	0.29522	0.528000	0.53228	GTG		TCGA-IB-7647-01A-11D-2154-08	OR2L13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097342.1	0	0	0	29	734	0	169		0	0	0	0	169	2		0	0	0	0	0	2	1	1.000000	29	723	0	167	2								-20.000000	1	1	0	0		1	1	2	3	2.024286	0	0.240000	1.920000	0.248120	0.320000	0.210000	1.000000	0.320000	0.377809	0.320000	0	0.260000	0.410000
ACOT11	26027	broad.mit.edu	37	1	55062956	55062956	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr1:55062956G>A	ENST00000371316.3	+	7	714	c.632G>A	c.(631-633)cGc>cAc	p.R211H	ACOT11_ENST00000343744.2_Missense_Mutation_p.R211H|ACOT11_ENST00000481208.1_3'UTR	NM_015547.3	NP_056362.1	Q8WXI4	ACO11_HUMAN	acyl-CoA thioesterase 11	p.R211H(2)		17					GACTGTAGCCGCATGGTGCCG	0.627000													Ovarian(148;1440 1861 22015 32453 51933)											2	Substitution - Missense(2)						SO:0001583	missense			ENST00000371316.3	1	1	hg19	CCDS592.1	.	.	.	.	.	.	.	.	.	.	G	10.16	1.273318	0.23221	.	.	ENSG00000162390	ENST00000343744;ENST00000371316	T;T	0.10573	2.88;2.86	4.93	-7.81	0.01210	.	1.969230	0.02401	N	0.080685	T	0.06872	0.0175	L	0.34521	1.04	0.09310	N	1	B;B	0.09022	0.002;0.0	B;B	0.09377	0.004;0.003	T	0.27606	-1.0069	10	0.44086	T	0.13	-24.5333	2.1472	0.03790	0.4433:0.0829:0.2566:0.2172	.	211;211	Q8WXI4;Q8WXI4-2	ACO11_HUMAN;.	H	211	ENSP00000340260:R211H;ENSP00000360366:R211H	ENSP00000340260:R211H	R	+	2	0	ACOT11	54835544	0.000000	0.05858	0.016000	0.15963	0.557000	0.35523	-2.496000	0.00970	-1.568000	0.01670	-1.808000	0.00615	CGC		TCGA-IB-7647-01A-11D-2154-08	ACOT11-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000027356.1	0	0	0	6	173	0	53	0	2.935509e-01	0	28	0	53	2		0	0	0	0	0	2	1	0.965767	6	173	0	52	2								-3.471743	1	1	0	0		1	0	0	0	2.004852	0	0.240000	1.920000	0.232633	0.290000	0.120000	0.550000	0.270000	0.313339	0.290000	0	0.190000	0.420000
HOOK1	51361	broad.mit.edu	37	1	60330911	60330911	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr1:60330911C>A	ENST00000371208.3	+	18	1995	c.1738C>A	c.(1738-1740)Caa>Aaa	p.Q580K	HOOK1_ENST00000395561.2_Missense_Mutation_p.Q538K|HOOK1_ENST00000465876.1_Intron	NM_015888.4	NP_056972.1	Q9UJC3	HOOK1_HUMAN	hook microtubule-tethering protein 1			29	all_cancers(7;0.000129)				AGATATAAATCAAAATGGTAG	0.363000																								0							SO:0001583	missense			ENST00000371208.3	0	1	hg19	CCDS612.1	.	.	.	.	.	.	.	.	.	.	C	12.53	1.965749	0.34659	.	.	ENSG00000134709	ENST00000371208;ENST00000395561	T;T	0.17213	2.29;2.29	6.03	6.03	0.97812	.	0.156942	0.56097	D	0.000022	T	0.19005	0.0456	L	0.45581	1.43	0.58432	D	0.999999	B	0.11235	0.004	B	0.16722	0.016	T	0.13202	-1.0518	10	0.10377	T	0.69	.	20.6398	0.99548	0.0:1.0:0.0:0.0	.	580	Q9UJC3	HOOK1_HUMAN	K	580;538	ENSP00000360252:Q580K;ENSP00000378928:Q538K	ENSP00000360252:Q580K	Q	+	1	0	HOOK1	60103499	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.497000	0.73674	2.881000	0.98747	0.650000	0.86243	CAA		TCGA-IB-7647-01A-11D-2154-08	HOOK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024934.1	0	0	0	9	237	0	47	1	6.083853e-01	9	44	0	47	2		0	0	0	0	0	2	1	0.994360	9	236	0	47	2								-3.995250	1	1	0	0		1	0	0	0	2.004852	0	0.240000	1.920000	0.232633	0.310000	0.150000	0.530000	0.300000	0.328351	0.310000	0	0.220000	0.420000
NKX2-2	4821	broad.mit.edu	37	20	21492879	21492879	+	Silent	SNP	C	C	T			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr20:21492879C>T	ENST00000377142.4	-	2	860	c.504G>A	c.(502-504)acG>acA	p.T168T	NKX2-2-AS1_ENST00000549659.1_RNA	NM_002509.3	NP_002500.1	O95096	NKX22_HUMAN	NK2 homeobox 2			21					CCTGCGTGGGCGTGAGGCGGA	0.677000																								0							SO:0001819	synonymous_variant			ENST00000377142.4	1	1	hg19	CCDS13145.1																																																																																				TCGA-IB-7647-01A-11D-2154-08	NKX2-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078278.9	1	0	1	23	167	0	50	0	1.685971e-01	0	6	0	50	2		0	0	0	0	0	2	1	1.000000	22	165	0	49	2								-20.000000	1	1	0	0		1	0	1	1	1.927046	0	0.240000	1.920000	0.194574	0.940000	0.620000	1.000000	1.000000	0.905623	0.940000	1	0.770000	1.000000
NFATC2	4773	broad.mit.edu	37	20	50140613	50140613	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr20:50140613G>A	ENST00000396009.3	-	2	386	c.167C>T	c.(166-168)tCc>tTc	p.S56F	NFATC2_ENST00000414705.1_Missense_Mutation_p.S36F|NFATC2_ENST00000609943.1_Missense_Mutation_p.S36F|NFATC2_ENST00000610033.1_Intron|NFATC2_ENST00000609507.1_Intron|NFATC2_ENST00000371564.3_Missense_Mutation_p.S56F	NM_001258297.1|NM_173091.3	NP_001245226.1|NP_775114.1	Q13469	NFAC2_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2		EWSR1/NFATC2(9)	53	Hepatocellular(150;0.248)				TGCGGGTCCGGAGGGTGGGCT	0.597000																								0							SO:0001583	missense			ENST00000396009.3	1	1	hg19	CCDS13437.1	.	.	.	.	.	.	.	.	.	.	G	18.23	3.577607	0.65878	.	.	ENSG00000101096	ENST00000371564;ENST00000396009;ENST00000414705	T;T;T	0.18016	2.26;2.26;2.24	5.13	5.13	0.70059	.	0.428509	0.25903	N	0.027548	T	0.30479	0.0766	N	0.22421	0.69	0.50039	D	0.999842	D;D;D;D	0.71674	0.997;0.998;0.998;0.998	P;D;D;D	0.78314	0.897;0.991;0.943;0.987	T	0.07501	-1.0769	10	0.54805	T	0.06	-28.7684	18.9234	0.92536	0.0:0.0:1.0:0.0	.	36;36;56;56	B5B2N9;B5B2P2;Q13469;B5B2N8	.;.;NFAC2_HUMAN;.	F	56;56;36	ENSP00000360619:S56F;ENSP00000379330:S56F;ENSP00000396471:S36F	ENSP00000360619:S56F	S	-	2	0	NFATC2	49574020	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.705000	0.91357	2.550000	0.86006	0.313000	0.20887	TCC		TCGA-IB-7647-01A-11D-2154-08	NFATC2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079730.2	1	0	0	20	393	0	93	0	3.061662e-01	0	22	0	93	2		0	0	0	0	0	2	1	0.999995	20	385	0	91	2								-5.147189	1	1	0	0		1	1	2	3	2.049961	0	0.240000	1.920000	0.247227	0.410000	0.260000	1.000000	0.410000	0.459752	0.410000	0	0.330000	0.540000
MYT1	4661	broad.mit.edu	37	20	62851191	62851191	+	Silent	SNP	C	C	T	rs117853857	by1000genomes	TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr20:62851191C>T	ENST00000328439.1	+	13	2461	c.2097C>T	c.(2095-2097)gaC>gaT	p.D699D	MYT1_ENST00000536311.1_Silent_p.D726D|MYT1_ENST00000360149.4_Silent_p.D401D	NM_004535.2	NP_004526.1	Q99640	PMYT1_HUMAN	myelin transcription factor 1			55	all_cancers(38;1.82e-11)|all_epithelial(29;3.3e-13)|Lung NSC(23;5.21e-10)|all_lung(23;1.92e-09)				AGTCTCCCGACGCCTCCCAGC	0.657000													GBM(59;481 1041 20555 21139 33705)											0							SO:0001819	synonymous_variant			ENST00000328439.1	1	1	hg19	CCDS13558.1																																																																																				TCGA-IB-7647-01A-11D-2154-08	MYT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080297.1	1	0	0	8	83	0	32	0	0	0	1	0	32	2		0	0	0	0	0	2	1	0.989531	8	81	0	32	2								-5.894015	1	1	121286	33	41	1	0	1	1	1.770176	1	0.240000	1.920000	0.136364	0.620000	0.300000	0.950000	0.610000	0.632616	0.620000	0	0.440000	0.810000
SLC37A1	54020	broad.mit.edu	37	21	43999848	43999848	+	Silent	SNP	C	C	T			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr21:43999848C>T	ENST00000352133.2	+	19	2506	c.1524C>T	c.(1522-1524)ttC>ttT	p.F508F	SLC37A1_ENST00000398341.3_Silent_p.F508F			P57057	GLPT_HUMAN	solute carrier family 37 (glucose-6-phosphate transporter), member 1			15					TGGTGCAGTTCCTGATCCGCC	0.647000																								0							SO:0001819	synonymous_variant			ENST00000352133.2	1	1	hg19	CCDS13689.1																																																																																				TCGA-IB-7647-01A-11D-2154-08	SLC37A1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195377.1	1	0	0	17	144	0	35	1	9.998573e-01	44	86	0	35	2		0	0	0	0	0	2	1	0.999973	17	143	0	35	2								-19.999980	1	1	0	0		1	0	0	0	1.959383	0	0.240000	1.920000	0.215524	0.850000	0.520000	1.000000	1.000000	0.840128	0.850000	1	0.670000	1.000000
OR11H1	81061	broad.mit.edu	37	22	16449649	16449649	+	Silent	SNP	C	C	T			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr22:16449649C>T	ENST00000252835.4	-	1	156	c.156G>A	c.(154-156)ctG>ctA	p.L52L		NM_001005239.1	NP_001005239.1	Q8NG94	O11H1_HUMAN	olfactory receptor, family 11, subfamily H, member 1			11	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.208)			CTGTTATAGTCAGTGCATATG	0.418000																								0							SO:0001819	synonymous_variant			ENST00000252835.4	1	1	hg19	CCDS33594.1																																																																																				TCGA-IB-7647-01A-11D-2154-08	OR11H1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074923.2	0	0	0	42	1003	0	189		0	0	0	0	189	2		0	0	0	0	0	2	1	1.000000	23	570	0	333	2								-4.182016	1	1	0	0		1	1	2	3	2.027205	0	0.240000	1.920000	0.243631	0.330000	0.240000	1.000000	0.340000	0.361786	0.330000	0	0.280000	0.400000
GPR45	11250	broad.mit.edu	37	2	105858390	105858390	+	Silent	SNP	G	G	A			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr2:105858390G>A	ENST00000258456.1	+	1	191	c.75G>A	c.(73-75)ggG>ggA	p.G25G		NM_007227.3	NP_009158.3	Q9Y5Y3	GPR45_HUMAN	G protein-coupled receptor 45			28					CAGACTCGGGGTCCACCCAGT	0.602000																								0							SO:0001819	synonymous_variant			ENST00000258456.1	1	1	hg19	CCDS2066.1																																																																																				TCGA-IB-7647-01A-11D-2154-08	GPR45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253348.1	1	0	0	26	407	0	111		0	0	0	0	111	2		0	0	0	0	0	2	1	1.000000	26	404	0	109	2								-6.753744	1	1	0	0		1	1	2	3	2.055490	0	0.240000	1.920000	0.249012	0.520000	0.340000	1.000000	0.500000	0.558657	0.520000	0	0.420000	0.660000
TTN	7273	broad.mit.edu	37	2	179464316	179464316	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr2:179464316C>A	ENST00000591111.1	-	239	51613	c.51389G>T	c.(51388-51390)gGa>gTa	p.G17130V	TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.G16203V|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.G9706V|TTN_ENST00000589042.1_Missense_Mutation_p.G18771V|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.G9898V|TTN_ENST00000359218.5_Missense_Mutation_p.G9831V|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin			1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)		TGATGCTGTTCCCAGATTATT	0.388000																								0							SO:0001583	missense			ENST00000591111.1	1	1	hg19		.	.	.	.	.	.	.	.	.	.	C	14.85	2.657649	0.47467	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.75050	-0.9;-0.9;-0.9;-0.9	5.55	5.55	0.83447	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.91219	0.7233	H	0.96175	3.78	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.93592	0.6922	9	0.87932	D	0	.	19.5067	0.95121	0.0:1.0:0.0:0.0	.	9706;9831;9898;17130	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	V	16203;9706;9898;9831;9704	ENSP00000343764:G16203V;ENSP00000434586:G9706V;ENSP00000340554:G9898V;ENSP00000352154:G9831V	ENSP00000340554:G9898V	G	-	2	0	TTN	179172561	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.760000	0.85248	2.609000	0.88269	0.650000	0.86243	GGA		TCGA-IB-7647-01A-11D-2154-08	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	1	0	0	74	1376	0	254		0	0	0	0	254	2		0	0	0	0	0	2	1	1.000000	73	1365	0	254	2								-7.614373	1	1	0	0		1	1	2	3	2.037028	0	0.240000	1.920000	0.245433	0.420000	0.330000	1.000000	0.430000	0.459265	0.420000	0	0.380000	0.490000
TTN	7273	broad.mit.edu	37	2	179641506	179641506	+	Silent	SNP	A	A	G			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr2:179641506A>G	ENST00000591111.1	-	28	5309	c.5085T>C	c.(5083-5085)taT>taC	p.Y1695Y	TTN_ENST00000360870.5_Silent_p.Y1695Y|RP11-88L24.4_ENST00000582038.2_RNA|TTN-AS1_ENST00000610005.1_RNA|TTN_ENST00000342992.6_Silent_p.Y1695Y|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Silent_p.Y1649Y|TTN_ENST00000589042.1_Silent_p.Y1695Y|TTN_ENST00000342175.6_Silent_p.Y1649Y|TTN_ENST00000359218.5_Silent_p.Y1649Y|TTN-AS1_ENST00000584485.1_RNA			Q8WZ42	TITIN_HUMAN	titin			1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)		TCTCTTTGTCATAGAGATCAC	0.473000																								0							SO:0001819	synonymous_variant			ENST00000591111.1	1	1	hg19																																																																																					TCGA-IB-7647-01A-11D-2154-08	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	1	0	1	54	331	0	53		0	0	0	0	53	2		0	0	0	0	0	2	1	1.000000	54	330	0	52	2								-19.999890	1	1	0	0		1	1	2	3	2.037028	0	0.240000	1.920000	0.245433	0.990000	0.900000	1.000000	1.000000	0.993917	0.990000	1	0.990000	1.000000
OTOF	9381	broad.mit.edu	37	2	26702178	26702178	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr2:26702178C>T	ENST00000272371.2	-	18	2294	c.2168G>A	c.(2167-2169)cGc>cAc	p.R723H	OTOF_ENST00000402415.3_5'Flank|OTOF_ENST00000339598.3_5'Flank|OTOF_ENST00000338581.6_5'Flank|OTOF_ENST00000403946.3_Missense_Mutation_p.R723H	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin			106	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				GTAGAGGCGGCGGCGCTGGTC	0.652000													GBM(102;732 1451 20652 24062 31372)											0							SO:0001583	missense			ENST00000272371.2	0	1	hg19	CCDS1725.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.888835	0.91814	.	.	ENSG00000115155	ENST00000272371;ENST00000403946	T;T	0.80123	-1.34;-1.34	4.54	4.54	0.55810	.	0.051541	0.64402	D	0.000001	D	0.84215	0.5423	M	0.82056	2.57	0.54753	D	0.999985	D	0.54397	0.966	P	0.50231	0.635	T	0.82952	-0.0202	10	0.15066	T	0.55	-18.8365	15.9074	0.79442	0.0:1.0:0.0:0.0	.	723	Q9HC10	OTOF_HUMAN	H	723	ENSP00000272371:R723H;ENSP00000385255:R723H	ENSP00000272371:R723H	R	-	2	0	OTOF	26555682	0.983000	0.35010	0.997000	0.53966	0.970000	0.65996	5.961000	0.70356	2.074000	0.62210	0.555000	0.69702	CGC		TCGA-IB-7647-01A-11D-2154-08	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3	1	0	1	14	93	0	20		0	0	0	0	20	2		0	0	0	0	0	2	1	0.999799	14	91	0	19	2								-2.659288	1	1	120760	12	37	1	1	2	3	2.055490	0	0.240000	1.920000	0.249012	0.990000	0.650000	1.000000	1.000000	0.952634	0.990000	1	0.870000	1.000000
TCF7L1	83439	broad.mit.edu	37	2	85533483	85533483	+	Nonsense_Mutation	SNP	A	A	T			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr2:85533483A>T	ENST00000282111.3	+	9	1419	c.1144A>T	c.(1144-1146)Aga>Tga	p.R382*		NM_031283.2	NP_112573.1	Q9HCS4	TF7L1_HUMAN	transcription factor 7-like 1 (T-cell specific, HMG-box)			18					GATCCTTGGAAGAAAGGTAAG	0.567000																								0							SO:0001587	stop_gained			ENST00000282111.3	0	1	hg19	CCDS1971.1	.	.	.	.	.	.	.	.	.	.	A	25.5	4.644390	0.87859	.	.	ENSG00000152284	ENST00000282111	.	.	.	5.17	2.67	0.31697	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.7191	0.46030	0.5148:0.4852:0.0:0.0	.	.	.	.	X	382	.	ENSP00000282111:R382X	R	+	1	2	TCF7L1	85386994	0.082000	0.21442	0.979000	0.43373	0.034000	0.12701	0.726000	0.25984	0.257000	0.21650	-0.435000	0.05868	AGA		TCGA-IB-7647-01A-11D-2154-08	TCF7L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252301.2	0	0	0	11	273	0	64	0	2.809593e-01	0	25	0	64	2		0	0	0	0	0	2	1	0.998326	11	270	0	65	2								-3.959755	1	1	0	0		1	1	2	3	2.055490	0	0.240000	1.920000	0.249012	0.340000	0.170000	1.000000	0.320000	0.402678	0.340000	0	0.250000	0.490000
PARP14	54625	broad.mit.edu	37	3	122422822	122422822	+	Silent	SNP	C	C	T			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr3:122422822C>T	ENST00000474629.2	+	7	3581	c.3315C>T	c.(3313-3315)ctC>ctT	p.L1105L		NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14			50					CATCTTCACTCAAGGTTGGGC	0.483000																								0							SO:0001819	synonymous_variant			ENST00000474629.2	0	1	hg19	CCDS46894.1																																																																																				TCGA-IB-7647-01A-11D-2154-08	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	0	0	0	8	444	0	73	1	8.402633e-01	3	184	0	73	2		0	0	0	0	0	2	1	0.988910	8	438	0	73	2								-2.854990	1	1	0	0		1	1	2	3	2.200593	1	0.240000	1.920000	0.294991	0.180000	0.070000	1.000000	0.160000	0.357987	0.180000	0	0.120000	1.000000
IGSF10	285313	broad.mit.edu	37	3	151155325	151155325	+	Missense_Mutation	SNP	G	G	C			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr3:151155325G>C	ENST00000282466.3	-	6	7023	c.7024C>G	c.(7024-7026)Cca>Gca	p.P2342A	IGSF10_ENST00000495443.1_5'UTR	NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10			116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)		TCATTAAATGGATTTCTAAAT	0.423000																								0							SO:0001583	missense			ENST00000282466.3	1	1	hg19	CCDS3160.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.173936	0.78452	.	.	ENSG00000152580	ENST00000282466	T	0.66815	-0.23	5.77	5.77	0.91146	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.46442	D	0.000299	T	0.82254	0.4997	M	0.73217	2.22	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.82118	-0.0615	10	0.56958	D	0.05	.	19.9792	0.97320	0.0:0.0:1.0:0.0	.	2342;369	Q6WRI0;Q6WRI0-2	IGS10_HUMAN;.	A	2342	ENSP00000282466:P2342A	ENSP00000282466:P2342A	P	-	1	0	IGSF10	152638015	1.000000	0.71417	0.549000	0.28204	0.904000	0.53231	9.414000	0.97362	2.727000	0.93392	0.591000	0.81541	CCA		TCGA-IB-7647-01A-11D-2154-08	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	0	0	0	30	883	0	108	0	1.178419e-03	0	2	0	108	2		0	0	0	0	0	2	1	1.000000	30	879	0	107	2								-3.588511	1	1	0	0		1	1	2	3	2.200593	1	0.240000	1.920000	0.294991	0.310000	0.200000	1.000000	0.290000	0.456618	0.310000	0	0.250000	1.000000
PIK3CA	5290	broad.mit.edu	37	3	178948163	178948163	+	Splice_Site	SNP	A	A	G			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08			A	G	A	A		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr3:178948163A>G	ENST00000263967.3	+	20	3092	c.2935A>G	c.(2935-2937)Agg>Ggg	p.R979G		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha			5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)	Caffeine(DB00201)	AGAATTTGAGAGGTGAGCTCG	0.338000		57	Mis		colorectal, gastric, gliobastoma, breast					HNSCC(19;0.045)|TSP Lung(28;0.18)			Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	phosphoinositide-3-kinase, catalytic, alpha polypeptide		E, O	0							SO:0001630	splice_region_variant			ENST00000263967.3	1	0	hg19	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	A	18.36	3.606615	0.66558	.	.	ENSG00000121879	ENST00000263967	T	0.75938	-0.98	4.99	4.99	0.66335	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (4);	0.000000	0.85682	D	0.000000	T	0.73590	0.3606	L	0.55213	1.73	0.80722	D	1	P	0.45827	0.867	P	0.45071	0.468	T	0.75297	-0.3367	10	0.44086	T	0.13	-11.9936	14.9656	0.71188	1.0:0.0:0.0:0.0	.	979	P42336	PK3CA_HUMAN	G	979	ENSP00000263967:R979G	ENSP00000263967:R979G	R	+	1	2	PIK3CA	180430857	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	6.842000	0.75379	1.990000	0.58119	0.477000	0.44152	AGG		TCGA-IB-7647-01A-11D-2154-08	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2	1	0	1	63	427	0	68	1	9.999911e-01	4	111	0	68	2		0	0	0	0	0	2	1	1.000000	62	423	0	66	2								-19.999990	1	1	0	0		1	1	2	3	2.200593	1	0.240000	1.920000	0.294991	0.990000	0.910000	1.000000	1.000000	0.994887	0.990000	1	0.990000	1.000000
LMLN	89782	broad.mit.edu	37	3	197707289	197707289	+	Silent	SNP	C	C	T	rs146220433		TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr3:197707289C>T	ENST00000330198.4	+	6	664	c.642C>T	c.(640-642)taC>taT	p.Y214Y	LMLN_ENST00000420910.2_Silent_p.Y214Y|LMLN_ENST00000482695.1_Silent_p.Y162Y|LMLN_ENST00000332636.5_Silent_p.Y162Y	NM_033029.3	NP_149018.2	Q96KR4	LMLN_HUMAN	leishmanolysin-like (metallopeptidase M8 family)			25	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)	Lung NSC(153;0.132)	Epithelial(36;9.84e-24)|all cancers(36;3.18e-22)|OV - Ovarian serous cystadenocarcinoma(49;5.35e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)		TTGTTCTTTACGTTGGTGCTC	0.527000																								0							SO:0001819	synonymous_variant			ENST00000330198.4	1	1	hg19	CCDS3332.1																																																																																				TCGA-IB-7647-01A-11D-2154-08	LMLN-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339701.1	0	0	0	25	785	1	120	0	6.458159e-02	1	12	1	120	2		0	0	0	0	0	2	1	0.706700	24	776	1	120	22								-3.247122	1	1	121412	4	41	1	1	2	3	2.316141	1	0.240000	1.920000	0.319971	0.280000	0.180000	0.440000	0.290000	0.304312	0.280000	0	0.230000	0.360000
CELSR3	1951	broad.mit.edu	37	3	48677669	48677669	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr3:48677669G>A	ENST00000164024.4	-	34	9629	c.9349C>T	c.(9349-9351)Cgg>Tgg	p.R3117W	CELSR3_ENST00000544264.1_Missense_Mutation_p.R3122W	NM_001407.2	NP_001398.2	Q9NYQ7	CELR3_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 3			83					GTGCTGCCCCGATCTTTGGGC	0.682000																								0							SO:0001583	missense			ENST00000164024.4	1	1	hg19	CCDS2775.1	.	.	.	.	.	.	.	.	.	.	G	16.74	3.207667	0.58343	.	.	ENSG00000008300	ENST00000164024;ENST00000544264	T;T	0.72167	-0.63;-0.62	4.72	2.78	0.32641	.	.	.	.	.	T	0.71065	0.3296	N	0.19112	0.55	0.29159	N	0.877919	D;D;D	0.89917	0.999;0.999;1.0	P;P;P	0.62885	0.9;0.798;0.908	T	0.67534	-0.5646	9	0.72032	D	0.01	.	12.7798	0.57471	0.0:0.0:0.6916:0.3084	.	3122;3117;3215	Q9NYQ7-2;Q9NYQ7;Q5Y190	.;CELR3_HUMAN;.	W	3117;3122	ENSP00000164024:R3117W;ENSP00000445694:R3122W	ENSP00000164024:R3117W	R	-	1	2	CELSR3	48652673	0.936000	0.31750	0.981000	0.43875	0.483000	0.33249	1.494000	0.35616	0.333000	0.23563	0.484000	0.47621	CGG		TCGA-IB-7647-01A-11D-2154-08	CELSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257523.1	1	0	1	37	228	0	81	1	5.218463e-01	6	6	0	81	2	1	1	137	795	0	865	2	1	1.000000	36	226	0	80	2								-17.797470	1	1	0	0		1	0	1	1	1.793368	1	0.240000	1.920000	0.136364	0.900000	0.690000	1.000000	0.990000	0.892557	0.900000	1	0.800000	0.970000
ADH1A	124	broad.mit.edu	37	4	100205883	100205883	+	Silent	SNP	A	A	G			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr4:100205883A>G	ENST00000209668.2	-	4	450	c.337T>C	c.(337-339)Ttg>Ctg	p.L113L	RP11-696N14.1_ENST00000500358.2_RNA|ADH1A_ENST00000511656.1_5'Flank	NM_000667.3	NP_000658.1	P07327	ADH1A_HUMAN	alcohol dehydrogenase 1A (class I), alpha polypeptide			25				Ethanol(DB00898)|Fomepizole(DB01213)	TCGTTTTTCAAGCAGTAGTTG	0.433000																								0							SO:0001819	synonymous_variant			ENST00000209668.2	1	1	hg19	CCDS3648.1																																																																																				TCGA-IB-7647-01A-11D-2154-08	ADH1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253669.1	1	0	1	52	293	0	49		0	0	0	0	49	2		0	0	0	0	0	2	1	1.000000	52	289	0	49	2								-20.000000	1	1	0	0		1	1	2	3	2.040586	0	0.240000	1.920000	0.246331	0.990000	0.970000	1.000000	1.000000	0.998027	0.990000	1	0.990000	1.000000
COX7B2	170712	broad.mit.edu	37	4	46736995	46736995	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr4:46736995C>T	ENST00000396533.1	-	4	465	c.215G>A	c.(214-216)aGa>aAa	p.R72K	COX7B2_ENST00000355591.3_Missense_Mutation_p.R72K|COX7B2_ENST00000543208.1_Missense_Mutation_p.R71K|COX7B2_ENST00000302930.5_Missense_Mutation_p.R72K			Q8TF08	CX7B2_HUMAN	cytochrome c oxidase subunit VIIb2	p.R71I(1)		5					TGGGGTAACTCTGCCAACAGG	0.428000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000396533.1	0	1	hg19	CCDS3472.2	.	.	.	.	.	.	.	.	.	.	C	18.21	3.574133	0.65765	.	.	ENSG00000170516	ENST00000355591;ENST00000396533;ENST00000302930;ENST00000543208	T;T;T;T	0.45276	0.9;0.9;0.9;0.9	4.57	4.57	0.56435	Cytochrome C oxidase, subunit VIIB, domain (2);	0.057494	0.64402	D	0.000001	T	0.56031	0.1958	.	.	.	0.28946	N	0.890717	D	0.76494	0.999	D	0.85130	0.997	T	0.46555	-0.9183	9	0.24483	T	0.36	-8.9049	13.1628	0.59554	0.0:1.0:0.0:0.0	.	72	Q8TF08	CX7B2_HUMAN	K	72;72;72;71	ENSP00000347799:R72K;ENSP00000379784:R72K;ENSP00000305964:R72K;ENSP00000437439:R71K	ENSP00000305964:R72K	R	-	2	0	COX7B2	46431752	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	0.933000	0.28897	2.830000	0.97506	0.585000	0.79938	AGA		TCGA-IB-7647-01A-11D-2154-08	COX7B2-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313899.1	0	0	0	9	395	0	76		0	0	0	0	76	2		0	0	0	0	0	2	1	0.994208	9	393	0	75	2								-3.868727	1	1	0	0		1	1	2	3	2.040586	0	0.240000	1.920000	0.246331	0.190000	0.090000	1.000000	0.190000	0.249716	0.190000	0	0.130000	0.290000
PCDHA2	56146	broad.mit.edu	37	5	140176361	140176361	+	Silent	SNP	C	C	T			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr5:140176361C>T	ENST00000526136.1	+	1	1812	c.1812C>T	c.(1810-1812)aaC>aaT	p.N604N	PCDHA2_ENST00000520672.2_Silent_p.N604N|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000378132.1_Silent_p.N604N|PCDHA1_ENST00000394633.3_Intron	NM_018905.2	NP_061728.1	Q9Y5H9	PCDA2_HUMAN	protocadherin alpha 2	p.N604N(2)		71			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		CAGGCTACAACGCGTGGCTTT	0.657000																								2	Substitution - coding silent(2)						SO:0001819	synonymous_variant			ENST00000526136.1	1	1	hg19	CCDS54914.1																																																																																				TCGA-IB-7647-01A-11D-2154-08	PCDHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372877.3	1	0	0	27	384	0	130	0	2.582454e-02	0	4	0	130	2		0	0	0	0	0	2	1	1.000000	27	382	0	129	2								-7.190530	1	1	0	0		1	0	0	0	1.994106	0	0.240000	1.920000	0.228896	0.540000	0.360000	0.750000	0.530000	0.552279	0.540000	0	0.440000	0.650000
LMBRD1	55788	broad.mit.edu	37	6	70428941	70428941	+	Silent	SNP	C	C	T			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08			C	T	C	C		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr6:70428941C>T	ENST00000370577.3	-	8	898	c.669G>A	c.(667-669)ctG>ctA	p.L223L	LMBRD1_ENST00000370570.1_Silent_p.L150L	NM_018368.3	NP_060838.3	Q9NUN5	LMBD1_HUMAN	LMBR1 domain containing 1			31					TGCCTTTTATCAGATTTAAAG	0.313000																								0							SO:0001819	synonymous_variant			ENST00000370577.3	0	1	hg19	CCDS4969.1																																																																																				TCGA-IB-7647-01A-11D-2154-08	LMBRD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041124.1	1	0	0	8	188	0	27	0	9.989937e-01	0	320	0	27	2		0	0	0	0	0	2	1	0.988433	4	186	0	26	2								-4.171414	1	0	0	0		1	0	1	1	1.794209	1	0.240000	1.920000	0.136364	0.300000	0.140000	0.530000	0.290000	0.322612	0.300000	0	0.210000	0.420000
ZNF777	27153	broad.mit.edu	37	7	149129516	149129516	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr7:149129516G>A	ENST00000247930.4	-	6	2170	c.1847C>T	c.(1846-1848)gCg>gTg	p.A616V		NM_015694.2	NP_056509.2	Q9ULD5	ZN777_HUMAN	zinc finger protein 777			26	Melanoma(164;0.165)		OV - Ovarian serous cystadenocarcinoma(82;0.00358)		CGGCTTGAGCGCGTGCTTGGG	0.672000																								0							SO:0001583	missense			ENST00000247930.4	1	1	hg19	CCDS43675.1	.	.	.	.	.	.	.	.	.	.	G	13.37	2.216935	0.39201	.	.	ENSG00000196453	ENST00000247930;ENST00000314683	T	0.05319	3.46	5.02	5.02	0.67125	.	1.524830	0.03983	N	0.293589	T	0.07458	0.0188	N	0.25144	0.715	0.30708	N	0.749545	B	0.28971	0.229	B	0.24269	0.052	T	0.30621	-0.9972	10	0.24483	T	0.36	-3.7701	15.8456	0.78887	0.0:0.0:1.0:0.0	.	616	Q9ULD5-2	.	V	616;359	ENSP00000247930:A616V	ENSP00000247930:A616V	A	-	2	0	ZNF777	148760449	0.825000	0.29262	0.934000	0.37439	0.724000	0.41520	3.866000	0.56040	2.328000	0.79073	0.460000	0.39030	GCG		TCGA-IB-7647-01A-11D-2154-08	ZNF777-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352708.1	1	0	1	92	604	0	141	1	8.882131e-02	2	2	0	141	2		0	0	0	0	0	2	1	1.000000	93	590	0	138	2								-20.000000	1	1	121190	2	36	1	1	2	3	2.022996	0	0.240000	1.920000	0.241820	0.990000	0.900000	1.000000	1.000000	0.992020	0.990000	1	0.990000	1.000000
PPP1R9A	55607	broad.mit.edu	37	7	94740662	94740662	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr7:94740662G>A	ENST00000433881.1	+	3	2019	c.1487G>A	c.(1486-1488)cGt>cAt	p.R496H	PPP1R9A_ENST00000456331.2_Missense_Mutation_p.R496H|PPP1R9A_ENST00000424654.1_Missense_Mutation_p.R496H|PPP1R9A_ENST00000289495.5_Missense_Mutation_p.R496H|PPP1R9A_ENST00000340694.4_Missense_Mutation_p.R496H|PPP1R9A_ENST00000433360.1_Missense_Mutation_p.R496H			Q9ULJ8	NEB1_HUMAN	protein phosphatase 1, regulatory subunit 9A			71	all_cancers(62;9.12e-11)|all_epithelial(64;4.34e-09)		STAD - Stomach adenocarcinoma(171;0.0031)		CTTGAAAAACGTGTAGAAAAG	0.383000										HNSCC(28;0.073)														0							SO:0001583	missense			ENST00000433881.1	1	1	hg19	CCDS34683.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	19.83	3.899587	0.72754	.	.	ENSG00000158528	ENST00000433360;ENST00000340694;ENST00000424654;ENST00000433881;ENST00000289495;ENST00000456331	T;T;T;T;T;T	0.39229	1.09;1.09;1.09;1.09;1.09;1.09	4.98	4.98	0.66077	PDZ/DHR/GLGF (1);	0.000000	0.85682	D	0.000000	T	0.67951	0.2948	M	0.80616	2.505	0.80722	D	1	D;D;D;D;D	0.89917	0.981;0.987;0.989;1.0;1.0	P;P;P;D;D	0.79784	0.59;0.767;0.819;0.988;0.993	T	0.72268	-0.4343	10	0.87932	D	0	.	18.8349	0.92157	0.0:0.0:1.0:0.0	.	496;496;496;496;496	B7ZLX4;F8W7J9;E9PDX1;E9PCK6;Q9ULJ8	.;.;.;.;NEB1_HUMAN	H	496	ENSP00000405514:R496H;ENSP00000344524:R496H;ENSP00000411342:R496H;ENSP00000398870:R496H;ENSP00000289495:R496H;ENSP00000402893:R496H	ENSP00000289495:R496H	R	+	2	0	PPP1R9A	94578598	1.000000	0.71417	1.000000	0.80357	0.083000	0.17756	9.587000	0.98229	2.755000	0.94549	0.650000	0.86243	CGT		TCGA-IB-7647-01A-11D-2154-08	PPP1R9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340662.1	1	0	0	16	294	0	45	0	2.771978e-02	0	5	0	45	2		0	0	0	0	0	2	1	0.999936	16	292	0	45	2								-17.873090	1	1	121402	1	31	1	1	2	3	2.022996	0	0.240000	1.920000	0.241820	0.430000	0.260000	0.710000	0.420000	0.455942	0.430000	0	0.340000	0.560000
ADCY8	114	broad.mit.edu	37	8	132051844	132051844	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr8:132051844C>T	ENST00000286355.5	-	1	2828	c.736G>A	c.(736-738)Ggc>Agc	p.G246S	ADCY8_ENST00000377928.3_Missense_Mutation_p.G246S	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)			134	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)		GTGACCACGCCGCTGTACTGC	0.637000										HNSCC(32;0.087)														0							SO:0001583	missense			ENST00000286355.5	1	1	hg19	CCDS6363.1	.	.	.	.	.	.	.	.	.	.	C	16.19	3.052698	0.55218	.	.	ENSG00000155897	ENST00000286355;ENST00000377928	T;T	0.39406	1.08;1.08	5.46	5.46	0.80206	.	0.131197	0.52532	D	0.000067	T	0.29652	0.0740	N	0.21545	0.675	0.41736	D	0.989582	B;B	0.19817	0.011;0.039	B;B	0.12156	0.004;0.007	T	0.12451	-1.0547	10	0.08179	T	0.78	.	18.2863	0.90115	0.0:1.0:0.0:0.0	.	246;246	E7EVL1;P40145	.;ADCY8_HUMAN	S	246	ENSP00000286355:G246S;ENSP00000367161:G246S	ENSP00000286355:G246S	G	-	1	0	ADCY8	132121026	1.000000	0.71417	0.889000	0.34880	0.907000	0.53573	5.747000	0.68689	2.580000	0.87095	0.455000	0.32223	GGC		TCGA-IB-7647-01A-11D-2154-08	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1	1	0	0	13	216	0	36		0	0	0	0	36	2		0	0	0	0	0	2	1	0.999553	13	214	0	35	2								-16.078160	1	1	0	0		1	1	4	5	2.610665	1	0.240000	1.920000	0.404948	0.660000	0.350000	1.000000	1.000000	0.699734	0.660000	0	0.480000	1.000000
TSTA3	7264	broad.mit.edu	37	8	144698284	144698284	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr8:144698284C>T	ENST00000425753.2	-	3	356	c.253G>A	c.(253-255)Gac>Aac	p.D85N	TSTA3_ENST00000529064.1_Missense_Mutation_p.D85N	NM_003313.3	NP_003304.1	Q13630	FCL_HUMAN	tissue specific transplantation antigen P35B			9	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.17e-38)|Epithelial(56;7.17e-37)|all cancers(56;2.46e-32)|Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.239)		ACCCAGAAGTCCAAATTGTAT	0.562000																								0							SO:0001583	missense			ENST00000425753.2	1	1	hg19	CCDS6408.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	35|35	5.477638|5.477638	0.96291|0.96291	.|.	.|.	ENSG00000104522|ENSG00000104522	ENST00000529064;ENST00000425753;ENST00000529048;ENST00000533817;ENST00000526290|ENST00000527006	D;D;D;D;D|.	0.94138|.	-3.36;-3.36;-3.36;-3.36;-3.36|.	4.75|4.75	4.75|4.75	0.60458|0.60458	NAD-dependent epimerase/dehydratase (1);NAD(P)-binding domain (1);|.	0.266244|.	0.39759|.	N|.	0.001266|.	D|.	0.85173|.	0.5636|.	M|M	0.93283|0.93283	3.4|3.4	0.80722|0.80722	D|D	1|1	D;D|.	0.56035|.	0.974;0.958|.	P;P|.	0.62382|.	0.901;0.77|.	D|.	0.89272|.	0.3605|.	10|.	0.87932|.	D|.	0|.	-33.5833|-33.5833	14.467|14.467	0.67490|0.67490	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	85;85|.	B4DZW9;Q13630|.	.;FCL_HUMAN|.	N|X	85|117	ENSP00000435386:D85N;ENSP00000398803:D85N;ENSP00000431587:D85N;ENSP00000437012:D85N;ENSP00000433331:D85N|.	ENSP00000398803:D85N|.	D|W	-|-	1|3	0|0	TSTA3|TSTA3	144769427|144769427	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.997000|0.997000	0.91878|0.91878	5.485000|5.485000	0.66850|0.66850	2.158000|2.158000	0.67659|0.67659	0.655000|0.655000	0.94253|0.94253	GAC|TGG		TCGA-IB-7647-01A-11D-2154-08	TSTA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382263.1	1	0	1	90	494	0	90	1	1	467	909	0	90	2		0	0	0	0	0	2	1	1.000000	88	488	0	90	2								-20.000000	1	1	0	0		1	1	4	5	2.610665	1	0.240000	1.920000	0.404948	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	0.990000	1.000000
LRRCC1	85444	broad.mit.edu	37	8	86027446	86027446	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr8:86027446G>A	ENST00000360375.3	+	5	805	c.656G>A	c.(655-657)tGc>tAc	p.C219Y	LRRCC1_ENST00000414626.2_Missense_Mutation_p.C199Y	NM_033402.4	NP_208325.3	Q9C099	LRCC1_HUMAN	leucine rich repeat and coiled-coil centrosomal protein 1			43					CAGCTGCAGTGCCTAGAAGGT	0.323000																								0							SO:0001583	missense			ENST00000360375.3	1	1	hg19	CCDS43750.1	.	.	.	.	.	.	.	.	.	.	G	11.80	1.747158	0.30955	.	.	ENSG00000133739	ENST00000426019;ENST00000360375;ENST00000414626	T;T	0.32272	1.46;1.47	5.52	4.63	0.57726	.	0.000000	0.42420	D	0.000701	T	0.31575	0.0801	L	0.59436	1.845	0.38194	D	0.940008	B;B;B	0.18610	0.016;0.029;0.005	B;B;B	0.25614	0.062;0.037;0.014	T	0.18023	-1.0350	10	0.42905	T	0.14	-1.709	12.0541	0.53524	0.0795:0.0:0.9205:0.0	.	199;126;219	Q9C099-2;E9PE41;Q9C099	.;.;LRCC1_HUMAN	Y	126;219;199	ENSP00000353538:C219Y;ENSP00000394695:C199Y	ENSP00000353538:C219Y	C	+	2	0	LRRCC1	86214698	1.000000	0.71417	0.998000	0.56505	0.666000	0.39218	6.269000	0.72558	2.585000	0.87301	0.460000	0.39030	TGC		TCGA-IB-7647-01A-11D-2154-08	LRRCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380267.1	1	0	1	82	579	0	75	1	9.846473e-01	11	37	0	75	2		0	0	0	0	0	2	1	1.000000	82	577	0	74	2								-20.000000	1	1	0	0		1	1	2	3	2.244964	1	0.240000	1.920000	0.316301	0.990000	0.920000	1.000000	1.000000	0.995710	0.990000	1	0.990000	1.000000
FPGS	2356	broad.mit.edu	37	9	130575756	130575756	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr9:130575756C>T	ENST00000373247.2	+	15	1687	c.1637C>T	c.(1636-1638)aCc>aTc	p.T546I	FPGS_ENST00000373245.1_3'UTR|FPGS_ENST00000460181.1_3'UTR|FPGS_ENST00000393706.2_Missense_Mutation_p.T520I|RP11-228B15.4_ENST00000439298.1_RNA|FPGS_ENST00000373225.3_Missense_Mutation_p.T496I	NM_004957.4	NP_004948.4	Q05932	FOLC_HUMAN	folylpolyglutamate synthase			7				Methotrexate(DB00563)|Pralatrexate(DB06813)|Raltitrexed(DB00293)	GGCCTCCTCACCCACCCTGTG	0.607000																								0							SO:0001583	missense			ENST00000373247.2	1	1	hg19	CCDS35148.1	.	.	.	.	.	.	.	.	.	.	C	5.750	0.322762	0.10900	.	.	ENSG00000136877	ENST00000373247;ENST00000393706;ENST00000373225	T;T;T	0.14144	2.94;2.94;2.53	5.16	3.12	0.35913	.	0.920751	0.09423	N	0.804181	T	0.09598	0.0236	N	0.14661	0.345	0.80722	D	1	B;B	0.22003	0.063;0.063	B;B	0.20577	0.03;0.03	T	0.13764	-1.0497	10	0.33940	T	0.23	-4.02	11.7357	0.51763	0.4523:0.5477:0.0:0.0	.	520;546	Q05932-4;Q05932	.;FOLC_HUMAN	I	546;520;496	ENSP00000362344:T546I;ENSP00000377309:T520I;ENSP00000362322:T496I	ENSP00000362322:T496I	T	+	2	0	FPGS	129615577	0.211000	0.23529	0.692000	0.30179	0.023000	0.10783	0.343000	0.19944	1.103000	0.41568	0.650000	0.86243	ACC		TCGA-IB-7647-01A-11D-2154-08	FPGS-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054251.1	1	0	1	61	540	0	181	1	1	71	161	0	181	2		0	0	0	0	0	2	1	1.000000	61	533	0	178	2								-20.000000	1	1	0	0		1	1	2	3	2.053842	0	0.240000	1.920000	0.248120	0.860000	0.660000	1.000000	1.000000	0.866966	0.860000	1	0.750000	1.000000
DDX31	64794	broad.mit.edu	37	9	135537950	135537950	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr9:135537950C>T	ENST00000372159.3	-	2	674	c.523G>A	c.(523-525)Gca>Aca	p.A175T	DDX31_ENST00000480876.1_5'UTR|DDX31_ENST00000438527.3_Missense_Mutation_p.A46T|DDX31_ENST00000544003.1_Missense_Mutation_p.A79T|DDX31_ENST00000372153.1_Missense_Mutation_p.A175T|DDX31_ENST00000310532.2_Missense_Mutation_p.A175T	NM_022779.7	NP_073616.6	Q9H8H2	DDX31_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 31			27					ATTTTTTGTGCGTTCCCCTTA	0.428000																								0							SO:0001583	missense			ENST00000372159.3	1	1	hg19	CCDS6951.1	.	.	.	.	.	.	.	.	.	.	c	3.149	-0.174630	0.06421	0.0	1.16E-4	ENSG00000125485	ENST00000372159;ENST00000372155;ENST00000372153;ENST00000438527;ENST00000310532;ENST00000544003	T;T;T;T;T	0.47869	4.37;3.92;4.34;3.5;0.83	5.6	-7.73	0.01245	.	1.174590	0.05861	N	0.622977	T	0.15998	0.0385	N	0.08118	0	0.09310	N	1	B;B;B	0.23891	0.093;0.003;0.002	B;B;B	0.14578	0.011;0.003;0.0	T	0.18871	-1.0323	10	0.09843	T	0.71	0.329	0.3822	0.00396	0.2246:0.2316:0.2547:0.2891	.	175;175;175	Q9H8H2-2;Q9H8H2-3;Q9H8H2	.;.;DDX31_HUMAN	T	175;175;175;46;175;79	ENSP00000361232:A175T;ENSP00000361226:A175T;ENSP00000387730:A46T;ENSP00000310539:A175T;ENSP00000442425:A79T	ENSP00000310539:A175T	A	-	1	0	DDX31	134527771	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-0.965000	0.03829	-0.997000	0.03450	-0.285000	0.09966	GCA		TCGA-IB-7647-01A-11D-2154-08	DDX31-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054794.1	1	0	1	85	660	0	95	1	9.686397e-01	8	37	0	95	2		0	0	0	0	0	2	1	1.000000	85	650	0	94	2								-20.000000	1	1	121412	3	39	1	1	2	3	2.049767	0	0.240000	1.920000	0.247227	0.960000	0.770000	1.000000	1.000000	0.944172	0.960000	1	0.860000	1.000000
ADAMTSL1	92949	broad.mit.edu	37	9	18777015	18777015	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chr9:18777015G>A	ENST00000380548.4	+	19	3127	c.2788G>A	c.(2788-2790)Ggc>Agc	p.G930S		NM_001040272.5	NP_001035362.3	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1			42					GGCCCCCTTCGGCTATCTCAA	0.667000																								0							SO:0001583	missense			ENST00000380548.4	1	1	hg19	CCDS47954.1	.	.	.	.	.	.	.	.	.	.	g	17.01	3.279858	0.59758	.	.	ENSG00000178031	ENST00000380548	T	0.73469	-0.75	5.53	4.64	0.57946	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.719030	0.08080	U	1.000000	D	0.85630	0.5741	M	0.73319	2.225	0.80722	D	1	D	0.89917	1.0	D	0.64877	0.93	T	0.79303	-0.1859	10	0.62326	D	0.03	.	14.6057	0.68478	0.0701:0.0:0.9299:0.0	.	930	Q8N6G6	ATL1_HUMAN	S	930	ENSP00000369921:G930S	ENSP00000369921:G930S	G	+	1	0	ADAMTSL1	18767015	1.000000	0.71417	0.881000	0.34555	0.031000	0.12232	9.551000	0.98112	1.350000	0.45770	-0.355000	0.07637	GGC		TCGA-IB-7647-01A-11D-2154-08	ADAMTSL1-012	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401206.1	1	0	1	43	276	0	89	0	9.429832e-02	0	4	0	89	2		0	0	0	0	0	2	1	1.000000	42	271	0	89	2								-2.775340	1	1	120966	6	37	1	0	1	1	1.797798	1	0.240000	1.920000	0.136364	0.890000	0.700000	1.000000	0.970000	0.889925	0.890000	1	0.800000	0.970000
GPR112	139378	broad.mit.edu	37	X	135432097	135432097	+	Missense_Mutation	SNP	G	G	C			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chrX:135432097G>C	ENST00000394143.1	+	6	6523	c.6232G>C	c.(6232-6234)Ggt>Cgt	p.G2078R	GPR112_ENST00000412101.1_Missense_Mutation_p.G1873R|GPR112_ENST00000370652.1_Missense_Mutation_p.G2078R|GPR112_ENST00000394141.1_Missense_Mutation_p.G1873R|GPR112_ENST00000287534.4_Missense_Mutation_p.G2015R	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112			199	Acute lymphoblastic leukemia(192;0.000127)				ACCTACACTGGGTGGTATCAC	0.468000																								0							SO:0001583	missense			ENST00000394143.1	1	1	hg19	CCDS35409.1	.	.	.	.	.	.	.	.	.	.	g	13.55	2.270870	0.40194	.	.	ENSG00000156920	ENST00000394143;ENST00000370652;ENST00000412101;ENST00000287534;ENST00000394141	T;T;T;T;T	0.30981	1.55;1.55;1.51;1.54;1.51	4.04	2.04	0.26737	.	.	.	.	.	T	0.32346	0.0826	L	0.29908	0.895	0.09310	N	1	D;P;D	0.64830	0.982;0.926;0.994	P;P;P	0.59221	0.763;0.45;0.854	T	0.09907	-1.0653	9	0.59425	D	0.04	.	3.828	0.08863	0.1358:0.0:0.6268:0.2374	.	2015;1873;2078	Q8IZF6-2;Q8IZF6-3;Q8IZF6	.;.;GP112_HUMAN	R	2078;2078;1873;2015;1873	ENSP00000377699:G2078R;ENSP00000359686:G2078R;ENSP00000416526:G1873R;ENSP00000287534:G2015R;ENSP00000377697:G1873R	ENSP00000287534:G2015R	G	+	1	0	GPR112	135259763	0.000000	0.05858	0.001000	0.08648	0.135000	0.20990	-0.243000	0.08915	0.646000	0.30693	0.509000	0.49947	GGT		TCGA-IB-7647-01A-11D-2154-08	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1	1	0	0	26	396	0	60		0	0	0	0	60	2		0	0	0	0	0	2	1	1.000000	26	388	0	59	2								-2.598543	1	1	0	0		1	0	1	1			0.240000	1.920000	0.240000	0.250000	0.170000	0.360000	0.250000	0.263339	0.250000	0	0.200000	0.310000
MAGEB16	139604	broad.mit.edu	37	X	35820358	35820358	+	Silent	SNP	C	C	T			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chrX:35820358C>T	ENST00000399989.1	+	2	324	c.45C>T	c.(43-45)caC>caT	p.H15H	MAGEB16_ENST00000399988.1_Silent_p.H15H|MAGEB16_ENST00000399985.1_Silent_p.H15H|MAGEB16_ENST00000399987.1_Silent_p.H15H|MAGEB16_ENST00000399992.1_Silent_p.H47H	NM_001099921.1	NP_001093391.1	A2A368	MAGBG_HUMAN	melanoma antigen family B, 16			31					ATGATCAGCACCTTCAGACCT	0.572000																								0							SO:0001819	synonymous_variant			ENST00000399989.1	1	1	hg19	CCDS43927.1																																																																																				TCGA-IB-7647-01A-11D-2154-08	MAGEB16-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251034.1	1	0	1	23	116	0	24		0	0	0	0	24	2		0	0	0	0	0	2	1	1.000000	22	116	0	23	2								-20.000000	1	1	0	0		1	0	1	1			0.240000	1.920000	0.240000	0.670000	0.450000	0.920000	0.670000	0.688523	0.670000	0	0.550000	0.810000
CXorf22	170063	broad.mit.edu	37	X	35974224	35974224	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-7647-01A-11D-2154-08	TCGA-IB-7647-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d2579415-7e40-48ba-a59c-e5543b8097dc	fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880	g.chrX:35974224G>A	ENST00000297866.5	+	8	1387	c.1321G>A	c.(1321-1323)Gaa>Aaa	p.E441K		NM_152632.3	NP_689845.2	Q6ZTR5	CX022_HUMAN	chromosome X open reading frame 22	p.E441K(2)		44					AAATCAATGCGAATTACTTCC	0.358000																								2	Substitution - Missense(2)						SO:0001583	missense			ENST00000297866.5	1	1	hg19	CCDS14237.2	.	.	.	.	.	.	.	.	.	.	G	0.006	-2.057199	0.00390	.	.	ENSG00000165164	ENST00000297866	T	0.53640	0.61	5.2	-5.28	0.02755	.	1.251890	0.05007	N	0.470268	T	0.16257	0.0391	N	0.03324	-0.35	0.09310	N	1	B	0.13594	0.008	B	0.06405	0.002	T	0.21999	-1.0229	10	0.05959	T	0.93	-31.1423	3.3027	0.06989	0.2448:0.3051:0.3491:0.101	.	441	Q6ZTR5	CX022_HUMAN	K	441	ENSP00000297866:E441K	ENSP00000297866:E441K	E	+	1	0	CXorf22	35884145	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.269000	0.08596	-0.677000	0.05231	-1.184000	0.01707	GAA		TCGA-IB-7647-01A-11D-2154-08	CXorf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056216.2	1	0	0	21	227	0	47		0	0	0	0	47	2		0	0	0	0	0	2	1	0.999998	21	226	0	47	2								-8.067526	1	1	121408	4	33	1	0	1	1			0.240000	1.920000	0.240000	0.350000	0.220000	0.510000	0.350000	0.362001	0.350000	0	0.280000	0.430000
