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
MAP4K4	9448	broad.mit.edu	37	2	102314997	102314998	+	Frame_Shift_Ins	INS	-	-	A			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr2:102314997_102314998insA	ENST00000347699.4	+	2	120_121	c.120_121insA	c.(121-123)aagfs	p.K41fs	MAP4K4_ENST00000456652.1_Frame_Shift_Ins_p.K41fs|MAP4K4_ENST00000350198.4_Frame_Shift_Ins_p.K41fs|MAP4K4_ENST00000425019.1_Frame_Shift_Ins_p.K41fs|MAP4K4_ENST00000324219.4_Frame_Shift_Ins_p.K41fs|MAP4K4_ENST00000302217.5_Frame_Shift_Ins_p.K41fs|MAP4K4_ENST00000413150.2_Frame_Shift_Ins_p.K41fs	NM_001242559.1|NM_145687.3	NP_001229488.1|NP_663720.1	O95819	M4K4_HUMAN	mitogen-activated protein kinase kinase kinase kinase 4			41					GACAAGTCTATAAGGTCGGTGT	0.515000																								0							SO:0001589	frameshift_variant			ENST00000347699.4	0	1	hg19	CCDS56130.1																																																																																				TCGA-IB-7889-01A-11D-2154-08	MAP4K4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339839.1	1	0	0	63	1187	0	227	0	6.222740e-01	0	41	0	227	2	0	0	0	0	0	0		1	1.000000	64	1166	0	224	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	0	0	0	1.985275	0	0.220000	1.900000	0.202454	0.440000	0.340000	0.560000	0.450000	0.453055	0.440000	0	0.390000	0.510000
GOLGA2	2801	broad.mit.edu	37	9	131022880	131022881	+	Frame_Shift_Ins	INS	-	-	A			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr9:131022880_131022881insA	ENST00000421699.2	-	17	1552_1553	c.1540_1541insT	c.(1540-1542)tggfs	p.W514fs	AL590708.1_ENST00000408370.1_RNA|GOLGA2_ENST00000609374.1_Frame_Shift_Ins_p.W502fs	NM_004486.4	NP_004477.3	Q08379	GOGA2_HUMAN	golgin A2			34					CTGCTCCCCCCAGAGCTCGGCC	0.653000																								0							SO:0001589	frameshift_variant			ENST00000421699.2	0	1	hg19	CCDS6896.2																																																																																				TCGA-IB-7889-01A-11D-2154-08	GOLGA2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054358.2	1	0	0	73	1089	0	171	0	6.252918e-01	0	33	0	171	2	0	0	0	0	0	0		1	1.000000	77	1070	0	171	2	0	0	0	0	0	0		-10.635520	1	1	0	0		1	1	2	3	2.022956	0	0.220000	1.900000	0.221712	0.570000	0.450000	0.730000	0.570000	0.581607	0.570000	0	0.500000	0.640000
PRKG1	5592	broad.mit.edu	37	10	53564378	53564378	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr10:53564378G>A	ENST00000401604.2	+	4	775	c.581G>A	c.(580-582)cGa>cAa	p.R194Q	PRKG1_ENST00000373980.4_Missense_Mutation_p.R209Q|PRKG1_ENST00000373985.1_Missense_Mutation_p.R182Q			Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I			53		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)			GCCATTGATCGACAATGTTTT	0.338000																								0							SO:0001583	missense			ENST00000401604.2	1	1	hg19	CCDS44399.1	.	.	.	.	.	.	.	.	.	.	G	34	5.387931	0.95988	.	.	ENSG00000185532	ENST00000401604;ENST00000373985;ENST00000373980;ENST00000373976	D;D;D;D	0.97378	-4.36;-4.36;-2.08;-2.08	5.42	5.42	0.78866	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (3);	0.000000	0.64402	D	0.000003	D	0.98516	0.9505	M	0.85099	2.735	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	D	0.99327	1.0908	10	0.72032	D	0.01	-5.7115	17.0633	0.86553	0.0:0.0:1.0:0.0	.	209;194	Q13976-2;Q13976	.;KGP1_HUMAN	Q	194;182;209;67	ENSP00000384200:R194Q;ENSP00000363097:R182Q;ENSP00000363092:R209Q;ENSP00000363087:R67Q	ENSP00000363087:R67Q	R	+	2	0	PRKG1	53234384	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	9.386000	0.97228	2.698000	0.92095	0.591000	0.81541	CGA		TCGA-IB-7889-01A-11D-2154-08	PRKG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		1	0	1	31	267	0	43		0	0	0	0	43	2		0	0	0	0	0	2	1	1.000000	31	263	0	43	2		0	0	0	0	43	2	-11.831130	1	1	0	0		1	1	2	3	2.107221	0	0.220000	1.900000	0.238430	0.990000	0.690000	1.000000	1.000000	0.937497	0.990000	1	0.830000	1.000000
MYOZ1	58529	broad.mit.edu	37	10	75391860	75391860	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr10:75391860G>T	ENST00000359322.4	-	6	1092	c.728C>A	c.(727-729)cCc>cAc	p.P243H	RP11-464F9.22_ENST00000609434.1_lincRNA	NM_021245.3	NP_067068.1			myozenin 1			12	Prostate(51;0.0112)				GTCAAACTTGGGCATCTGGAA	0.493000																								0							SO:0001583	missense			ENST00000359322.4	1	1	hg19	CCDS7330.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.170256	0.78452	.	.	ENSG00000177791	ENST00000359322	T	0.70631	-0.5	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	D	0.86104	0.5853	M	0.83384	2.64	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.87452	0.2402	10	0.87932	D	0	-11.7099	19.6772	0.95941	0.0:0.0:1.0:0.0	.	243	Q9NP98	MYOZ1_HUMAN	H	243	ENSP00000352272:P243H	ENSP00000352272:P243H	P	-	2	0	MYOZ1	75061866	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.558000	0.82253	2.656000	0.90262	0.655000	0.94253	CCC		TCGA-IB-7889-01A-11D-2154-08	MYOZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048654.1	0	0	0	14	342	0	49	0	2.513233e-01	0	23	0	49	2		0	0	0	0	0	2	1	0.999749	13	339	0	49	2		0	0	0	0	49	2	-3.125343	1	1	0	0		1	1	2	3	2.107221	0	0.220000	1.900000	0.238430	0.390000	0.210000	1.000000	0.370000	0.486804	0.390000	0	0.290000	1.000000
MYOZ1	58529	broad.mit.edu	37	10	75391861	75391861	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr10:75391861G>T	ENST00000359322.4	-	6	1091	c.727C>A	c.(727-729)Ccc>Acc	p.P243T	RP11-464F9.22_ENST00000609434.1_lincRNA	NM_021245.3	NP_067068.1			myozenin 1			12	Prostate(51;0.0112)				TCAAACTTGGGCATCTGGAAG	0.488000																								0							SO:0001583	missense			ENST00000359322.4	1	1	hg19	CCDS7330.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.136416	0.77662	.	.	ENSG00000177791	ENST00000359322	T	0.70164	-0.46	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	D	0.84065	0.5390	M	0.83384	2.64	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.85787	0.1365	10	0.87932	D	0	-11.7099	19.6772	0.95941	0.0:0.0:1.0:0.0	.	243	Q9NP98	MYOZ1_HUMAN	T	243	ENSP00000352272:P243T	ENSP00000352272:P243T	P	-	1	0	MYOZ1	75061867	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.563000	0.82314	2.656000	0.90262	0.655000	0.94253	CCC		TCGA-IB-7889-01A-11D-2154-08	MYOZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048654.1	0	0	0	14	337	0	48	0	2.407919e-01	0	22	0	48	2		0	0	0	0	0	2	1	0.999749	13	334	0	48	2		0	0	0	0	48	2	-4.170522	1	1	0	0		1	1	2	3	2.107221	0	0.220000	1.900000	0.238430	0.400000	0.220000	1.000000	0.370000	0.491344	0.400000	0	0.290000	1.000000
OR10Q1	219960	broad.mit.edu	37	11	57995470	57995470	+	Missense_Mutation	SNP	A	A	G			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr11:57995470A>G	ENST00000316770.2	-	1	920	c.878T>C	c.(877-879)tTg>tCg	p.L293S		NM_001004471.2	NP_001004471.1	Q8NGQ4	O10Q1_HUMAN	olfactory receptor, family 10, subfamily Q, member 1			35		Breast(21;0.0589)			GCTGTAAAGCAAAGGGTTGAG	0.547000																								0							SO:0001583	missense			ENST00000316770.2	1	1	hg19	CCDS31547.1	.	.	.	.	.	.	.	.	.	.	A	15.25	2.778355	0.49786	.	.	ENSG00000180475	ENST00000316770	T	0.46451	0.87	5.07	5.07	0.68467	GPCR, rhodopsin-like superfamily (1);	0.000000	0.34362	N	0.004034	T	0.62913	0.2467	M	0.79926	2.475	0.32070	N	0.594593	D	0.65815	0.995	P	0.61800	0.894	T	0.74481	-0.3651	10	0.87932	D	0	.	13.8047	0.63223	1.0:0.0:0.0:0.0	.	293	Q8NGQ4	O10Q1_HUMAN	S	293	ENSP00000314324:L293S	ENSP00000314324:L293S	L	-	2	0	OR10Q1	57752046	0.712000	0.27916	0.775000	0.31657	0.195000	0.23768	5.574000	0.67424	2.132000	0.65825	0.528000	0.53228	TTG		TCGA-IB-7889-01A-11D-2154-08	OR10Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394706.1	1	0	0	51	692	0	143		0	0	0	0	143	2		0	0	0	0	0	2	1	1.000000	51	687	0	142	2		0	0	0	0	143	2	-10.818930	1	1	0	0		1	1	2	3	2.035080	0	0.220000	1.900000	0.224267	0.630000	0.470000	1.000000	0.620000	0.648913	0.630000	0	0.540000	0.730000
KRAS	3845	broad.mit.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	C	A	rs121913529		TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08			C	A	C	C		Valid	Somatic	Phase_I	WXS	KRAS_deep			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	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-7889-01A-11D-2154-08	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	1	0	1	13	72	0	17	1	1.279220e-01	3	1	0	17	2	1	9.996229e-01	8	75	0	403	2	1	0.999679	13	72	0	17	2	1	1	1878	6141	0	17	2	-9.865792	1	1	0	0		1	0	3	3	2.089326	1	0.220000	1.900000	0.253660	0.990000	0.870000	1.000000	1.000000	0.992446	0.990000	1	0.990000	1.000000
GPR182	11318	broad.mit.edu	37	12	57389416	57389416	+	Silent	SNP	C	C	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr12:57389416C>T	ENST00000300098.1	+	2	642	c.423C>T	c.(421-423)atC>atT	p.I141I	HBCBP_ENST00000600202.1_5'Flank|RP11-474N8.5_ENST00000556850.1_RNA	NM_007264.3	NP_009195.1	O15218	GP182_HUMAN	G protein-coupled receptor 182			15					ATAGCAGCATCTTCTTCCTGG	0.592000																								0							SO:0001819	synonymous_variant			ENST00000300098.1	1	1	hg19	CCDS8927.1																																																																																				TCGA-IB-7889-01A-11D-2154-08	GPR182-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411212.1	1	0	0	35	320	0	44		0	0	0	0	44	2		0	0	0	0	0	2	1	1.000000	34	317	0	44	2		0	0	0	0	44	2	-20.000000	1	1	0	0		1	1	2	3	2.079019	0	0.220000	1.900000	0.253660	0.990000	0.680000	1.000000	1.000000	0.931965	0.990000	1	0.820000	1.000000
HSP90AA1	3320	broad.mit.edu	37	14	102551163	102551163	+	Missense_Mutation	SNP	T	T	A	rs55793809	byFrequency	TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08			T	A	T	T		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr14:102551163T>A	ENST00000216281.8	-	5	1041	c.836A>T	c.(835-837)aAg>aTg	p.K279M	HSP90AA1_ENST00000334701.7_Missense_Mutation_p.K401M|HSP90AA1_ENST00000441629.2_Missense_Mutation_p.K100M	NM_005348.3	NP_005339.3	P07900	HS90A_HUMAN	heat shock protein 90kDa alpha (cytosolic), class A member 1			28				Nedocromil(DB00716)|Rifabutin(DB00615)	ttccttaatcttcttcttctt	0.393000																								0							SO:0001583	missense			ENST00000216281.8	1	0	hg19	CCDS9967.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	t	18.27	3.588032	0.66105	0.002043	8.14E-4	ENSG00000080824	ENST00000216281;ENST00000334701;ENST00000441629	T;T;T	0.13538	2.58;2.58;2.58	4.47	4.47	0.54385	.	0.338820	0.24182	U	0.040783	T	0.55305	0.1912	H	0.98701	4.305	0.80722	D	1	D;D;D	0.89917	0.999;1.0;0.999	D;D;D	0.87578	0.996;0.998;0.996	T	0.74372	-0.3687	10	0.87932	D	0	-21.8453	13.7315	0.62789	0.0:0.0:0.0:1.0	rs55793809	100;401;279	Q86U12;P07900-2;P07900	.;.;HS90A_HUMAN	M	279;401;100	ENSP00000216281:K279M;ENSP00000335153:K401M;ENSP00000396189:K100M	ENSP00000216281:K279M	K	-	2	0	HSP90AA1	101620916	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	6.016000	0.70798	1.786000	0.52430	0.533000	0.62120	AAG		TCGA-IB-7889-01A-11D-2154-08	HSP90AA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414952.2	1	0	1	31	175	0	43	1	1	661	437	0	43	2		0	0	0	0	0	2	1	1.000000	29	174	0	42	2		0	0	0	0	43	2	-1.749966	0	1	121306	164	52	1	0	2	2	1.976087	1	0.220000	1.900000	0.220000	0.990000	0.970000	1.000000	1.000000	0.997684	0.990000	1	0.990000	1.000000
FOXA1	3169	broad.mit.edu	37	14	38061592	38061592	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr14:38061592C>T	ENST00000250448.2	-	2	458	c.397G>A	c.(397-399)Gcc>Acc	p.A133T	FOXA1_ENST00000545425.2_5'UTR|FOXA1_ENST00000540786.1_Missense_Mutation_p.A100T	NM_004496.3	NP_004487.2	P55317	FOXA1_HUMAN	forkhead box A1			19	Breast(36;0.0954)|Esophageal squamous(585;0.164)|Hepatocellular(127;0.213)		Lung(238;5.41e-07)|LUAD - Lung adenocarcinoma(48;2.48e-05)|Epithelial(34;0.0454)|LUSC - Lung squamous cell carcinoma(13;0.0917)|all cancers(34;0.0925)|BRCA - Breast invasive adenocarcinoma(188;0.239)		GGGTTCATGGCGGCCGCGTAG	0.736000																								0							SO:0001583	missense			ENST00000250448.2	0	1	hg19	CCDS9665.1	.	.	.	.	.	.	.	.	.	.	C	4.498	0.092298	0.08632	.	.	ENSG00000129514	ENST00000250448;ENST00000540786	T;T	0.18502	2.21;2.21	3.99	1.91	0.25777	Fork-head N-terminal (1);	0.667620	0.14434	N	0.319836	T	0.05868	0.0153	N	0.03608	-0.345	0.22954	N	0.998514	B	0.27997	0.197	B	0.23150	0.044	T	0.40308	-0.9570	10	0.10902	T	0.67	.	8.1718	0.31260	0.4693:0.5307:0.0:0.0	.	133	P55317	FOXA1_HUMAN	T	133;100	ENSP00000250448:A133T;ENSP00000440178:A100T	ENSP00000250448:A133T	A	-	1	0	FOXA1	37131343	0.000000	0.05858	0.991000	0.47740	0.985000	0.73830	-0.572000	0.05881	0.869000	0.35703	0.505000	0.49811	GCC		TCGA-IB-7889-01A-11D-2154-08	FOXA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276735.1	1	0	0	8	121	0	18		0	0	0	0	18	2		0	0	0	0	0	2	1	0.989095	8	118	0	16	2		0	0	0	0	18	2	-12.521950	1	1	0	0		1	0	2	2	1.976087	1	0.220000	1.900000	0.220000	0.610000	0.280000	1.000000	1.000000	0.653599	0.610000	0	0.420000	0.990000
PLA2G4E	123745	broad.mit.edu	37	15	42276761	42276761	+	Silent	SNP	G	G	A			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr15:42276761G>A	ENST00000399518.3	-	19	2745	c.2259C>T	c.(2257-2259)taC>taT	p.Y753Y	CTD-2382E5.1_ENST00000499478.2_RNA|PLA2G4E_ENST00000413860.2_Silent_p.Y724Y	NM_001206670.1	NP_001193599.1	Q3MJ16	PA24E_HUMAN	phospholipase A2, group IVE			16		all_cancers(109;8.09e-13)|all_epithelial(112;2.03e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.0273)			CTGGCAGCTCGTATTTGGGGA	0.522000																								0							SO:0001819	synonymous_variant			ENST00000399518.3	1	1	hg19	CCDS55962.1																																																																																				TCGA-IB-7889-01A-11D-2154-08	PLA2G4E-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252738.2	0	0	0	11	241	0	41		0	0	0	0	41	2		0	0	0	0	0	2	1	0.998330	11	238	0	41	2		0	0	0	0	41	2	-3.229017	1	1	120874	6	38	1	1	2	3	2.104604	0	0.220000	1.900000	0.237611	0.440000	0.220000	1.000000	0.400000	0.523035	0.440000	0	0.320000	0.840000
SECISBP2L	9728	broad.mit.edu	37	15	49288724	49288724	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr15:49288724C>A	ENST00000559471.1	-	17	2726	c.2463G>T	c.(2461-2463)atG>atT	p.M821I	SECISBP2L_ENST00000261847.3_Missense_Mutation_p.M776I|Y_RNA_ENST00000384377.1_RNA	NM_001193489.1	NP_001180418.1	Q93073	SBP2L_HUMAN	SECIS binding protein 2-like			46					TTGCTGCAACCATATCTTTAT	0.408000																								0							SO:0001583	missense			ENST00000559471.1	1	1	hg19	CCDS53942.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.747448	0.89663	.	.	ENSG00000138593	ENST00000261847;ENST00000380927	D	0.91843	-2.92	4.94	4.94	0.65067	.	0.000000	0.85682	D	0.000000	D	0.90109	0.6910	L	0.29908	0.895	0.58432	D	0.999997	D;P	0.54207	0.965;0.94	B;P	0.47402	0.344;0.546	D	0.91643	0.5328	10	0.72032	D	0.01	.	18.3573	0.90362	0.0:1.0:0.0:0.0	.	821;776	Q93073;Q93073-2	SBP2L_HUMAN;.	I	776;821	ENSP00000261847:M776I	ENSP00000261847:M776I	M	-	3	0	SECISBP2L	47076016	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.300000	0.78841	2.569000	0.86673	0.650000	0.86243	ATG		TCGA-IB-7889-01A-11D-2154-08	SECISBP2L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417277.1	1	0	0	42	958	0	165	0	7.920589e-02	1	10	0	165	2		0	0	0	0	0	2	1	1.000000	42	943	0	164	2		0	0	0	0	165	2	-3.858861	1	1	0	0		1	1	2	3	2.104604	0	0.220000	1.900000	0.237611	0.400000	0.280000	1.000000	0.390000	0.492732	0.400000	0	0.330000	0.580000
KIAA1199	0	broad.mit.edu	37	15	81201475	81201475	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr15:81201475C>T	ENST00000394685.3	+	14	2044	c.1625C>T	c.(1624-1626)aCg>aTg	p.T542M	KIAA1199_ENST00000356249.5_Missense_Mutation_p.T542M|RP11-351M8.2_ENST00000560873.1_RNA|RP11-351M8.1_ENST00000560560.1_Intron|KIAA1199_ENST00000220244.3_Missense_Mutation_p.T542M			Q8WUJ3	CEMIP_HUMAN				49					TTGGAGGGCACGGAGCTGAAG	0.552000																								0							SO:0001583	missense			ENST00000394685.3	1	1	hg19	CCDS10315.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	T	10.26	1.302383	0.23736	.	.	ENSG00000103888	ENST00000220244;ENST00000394685;ENST00000356249;ENST00000394683	T;T;T	0.80123	-1.34;-1.34;-1.34	5.09	5.09	0.68999	Pectin lyase fold/virulence factor (1);	0.291065	0.31177	N	0.008117	T	0.60945	0.2308	N	0.03608	-0.345	0.20307	N	0.999913	B	0.02656	0.0	B	0.01281	0.0	T	0.54043	-0.8352	10	0.54805	T	0.06	-9.3098	10.8753	0.46906	0.0:0.0747:0.0:0.9253	.	542	Q8WUJ3	K1199_HUMAN	M	542	ENSP00000220244:T542M;ENSP00000378177:T542M;ENSP00000348583:T542M	ENSP00000220244:T542M	T	+	2	0	KIAA1199	78988530	1.000000	0.71417	0.995000	0.50966	0.215000	0.24574	5.679000	0.68160	0.787000	0.33731	-0.516000	0.04426	ACG		TCGA-IB-7889-01A-11D-2154-08	KIAA1199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291389.1	1	0	0	16	289	0	47	0	2.430141e-01	1	16	0	47	2		0	0	0	0	0	2	1	0.999934	16	286	0	47	2		0	0	0	0	47	2	-3.324015	1	1	121412	3	34	1	1	2	3	2.100873	0	0.220000	1.900000	0.236791	0.520000	0.300000	1.000000	0.490000	0.583472	0.520000	0	0.390000	0.830000
SLC28A1	9154	broad.mit.edu	37	15	85461805	85461805	+	Silent	SNP	C	C	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr15:85461805C>T	ENST00000286749.3	+	9	936	c.846C>T	c.(844-846)caC>caT	p.H282H	SLC28A1_ENST00000537703.1_Silent_p.H204H|SLC28A1_ENST00000537216.1_Silent_p.H282H|SLC28A1_ENST00000394573.1_Silent_p.H282H|SLC28A1_ENST00000538177.1_Silent_p.H282H|SLC28A1_ENST00000537624.1_Silent_p.H282H			O00337	S28A1_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 1			41			BRCA - Breast invasive adenocarcinoma(143;0.0587)	Gemcitabine(DB00441)|Stavudine(DB00649)|Zidovudine(DB00495)	TTCTCTACCACGTGGGCCTCA	0.562000																								0							SO:0001819	synonymous_variant			ENST00000286749.3	1	1	hg19	CCDS10334.1																																																																																				TCGA-IB-7889-01A-11D-2154-08	SLC28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308998.2	1	0	0	41	753	0	120		0	0	0	0	120	2		0	0	0	0	0	2	1	1.000000	41	748	0	119	2		0	0	0	0	120	2	-6.248170	1	1	121412	2	39	1	1	2	3	2.100873	0	0.220000	1.900000	0.236791	0.490000	0.350000	1.000000	0.480000	0.565820	0.490000	0	0.410000	0.670000
ST8SIA2	8128	broad.mit.edu	37	15	92981637	92981637	+	Silent	SNP	A	A	G			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr15:92981637A>G	ENST00000268164.3	+	4	582	c.345A>G	c.(343-345)ggA>ggG	p.G115G	ST8SIA2_ENST00000539113.1_Silent_p.G94G	NM_006011.3	NP_006002.1	Q92186	SIA8B_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 2			20	Lung NSC(78;0.0893)|all_lung(78;0.125)		BRCA - Breast invasive adenocarcinoma(143;0.0355)|OV - Ovarian serous cystadenocarcinoma(32;0.203)		TCCTAAAGGGAACCCTGAAGC	0.473000																								0							SO:0001819	synonymous_variant			ENST00000268164.3	1	1	hg19	CCDS10372.1																																																																																				TCGA-IB-7889-01A-11D-2154-08	ST8SIA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313526.1	1	0	1	131	918	0	162		0	0	0	0	162	2		0	0	0	0	0	2	1	1.000000	130	911	0	159	2		0	0	0	0	162	2	-20.000000	1	1	121412	1	26	1	1	2	3	2.100873	0	0.220000	1.900000	0.236791	0.990000	0.980000	1.000000	1.000000	0.998882	0.990000	1	0.990000	1.000000
TEPP	374739	broad.mit.edu	37	16	58010414	58010414	+	Silent	SNP	G	G	A			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr16:58010414G>A	ENST00000441824.2	+	1	76	c.39G>A	c.(37-39)ctG>ctA	p.L13L	TEPP_ENST00000290871.5_Silent_p.L13L	NM_199456.2	NP_955535.2	Q6URK8	TEPP_HUMAN	testis, prostate and placenta expressed			8					TTATTCTGCTGCTGTCCATAA	0.517000																								0							SO:0001819	synonymous_variant			ENST00000441824.2	1	1	hg19	CCDS45496.1																																																																																				TCGA-IB-7889-01A-11D-2154-08	TEPP-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000431966.1	1	0	0	29	423	0	87		0	0	0	0	87	2		0	0	0	0	0	2	1	1.000000	29	415	0	87	2		0	0	0	0	87	2	-7.293606	1	1	0	0		1	0	0	0	1.971177	0	0.220000	1.900000	0.197035	0.560000	0.380000	0.780000	0.560000	0.578283	0.560000	0	0.470000	0.680000
ADAMTS18	170692	broad.mit.edu	37	16	77353780	77353780	+	Missense_Mutation	SNP	G	G	A	rs147816593		TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr16:77353780G>A	ENST00000282849.5	-	16	2916	c.2498C>T	c.(2497-2499)gCg>gTg	p.A833V		NM_199355.2	NP_955387.1	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 18			118					GGGCCCTGGCGCGTACAGACG	0.542000																								0							SO:0001583	missense			ENST00000282849.5	1	1	hg19	CCDS10926.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.141924	0.77775	2.27E-4	0.0	ENSG00000140873	ENST00000282849	T	0.56941	0.43	5.54	5.54	0.83059	ADAM-TS Spacer 1 (1);	0.000000	0.85682	D	0.000000	T	0.77336	0.4115	M	0.87038	2.855	0.80722	D	1	D;D	0.89917	0.997;1.0	P;D	0.81914	0.897;0.995	T	0.81191	-0.1045	10	0.87932	D	0	.	18.4764	0.90793	0.0:0.0:1.0:0.0	.	833;833	Q8TE60-2;Q8TE60	.;ATS18_HUMAN	V	833	ENSP00000282849:A833V	ENSP00000282849:A833V	A	-	2	0	ADAMTS18	75911281	1.000000	0.71417	0.242000	0.24170	0.254000	0.26022	9.378000	0.97191	2.618000	0.88619	0.563000	0.77884	GCG		TCGA-IB-7889-01A-11D-2154-08	ADAMTS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269037.1	1	0	0	28	461	0	74		0	0	0	0	74	2		0	0	0	0	0	2	1	1.000000	28	457	0	74	2		0	0	0	0	74	2	-20.000000	1	1	121412	4	36	1	0	0	0	1.971177	0	0.220000	1.900000	0.197035	0.500000	0.340000	0.700000	0.500000	0.517243	0.500000	0	0.410000	0.610000
DRG2	1819	broad.mit.edu	37	17	18003681	18003681	+	Silent	SNP	C	C	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr17:18003681C>T	ENST00000225729.3	+	6	610	c.472C>T	c.(472-474)Ctg>Ttg	p.L158L	DRG2_ENST00000583355.1_Intron|DRG2_ENST00000395726.4_Silent_p.L158L	NM_001388.4	NP_001379.1	P55039	DRG2_HUMAN	developmentally regulated GTP binding protein 2			14	all_neural(463;0.228)				TCCTAGGTCTCTGCTGGAGAA	0.577000																								0							SO:0001819	synonymous_variant			ENST00000225729.3	1	1	hg19	CCDS11191.1																																																																																				TCGA-IB-7889-01A-11D-2154-08	DRG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132075.3	1	0	0	66	703	0	111	1	9.998704e-01	27	110	0	111	2		0	0	0	0	0	2	1	1.000000	66	698	0	110	2		0	0	0	0	111	2	-3.318794	1	1	121412	14	44	1	1	5	6	2.880456	1	0.220000	1.900000	0.443016	0.990000	0.850000	1.000000	1.000000	0.986362	0.990000	1	0.970000	1.000000
NF1	4763	broad.mit.edu	37	17	29576089	29576089	+	Silent	SNP	C	C	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr17:29576089C>T	ENST00000358273.4	+	30	4445	c.4062C>T	c.(4060-4062)tcC>tcT	p.S1354S	NF1_ENST00000356175.3_Silent_p.S1354S	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	p.0?(8)|p.?(4)	NF1/ACCN1(2)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)			TCAGTTCCTCCTCAGAATTCC	0.398000			D, Mis, N, F, S, O		neurofibroma, glioma	neurofibroma, glioma			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)				yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	12	Whole gene deletion(8)|Unknown(4)						SO:0001819	synonymous_variant	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	ENST00000358273.4	1	1	hg19	CCDS42292.1																																																																																				TCGA-IB-7889-01A-11D-2154-08	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	0	0	0	18	580	0	88	0	1.439571e-02	0	6	0	88	2		0	0	0	0	0	2	1	0.999980	18	571	0	88	2		0	0	0	0	88	2	-2.616949	1	1	0	0		1	1	2	3	2.048456	0	0.220000	1.900000	0.226804	0.280000	0.170000	1.000000	0.270000	0.334518	0.280000	0	0.220000	0.370000
BPTF	2186	broad.mit.edu	37	17	65850550	65850550	+	Nonsense_Mutation	SNP	C	C	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr17:65850550C>T	ENST00000321892.4	+	2	1169	c.1108C>T	c.(1108-1110)Cag>Tag	p.Q370*	BPTF_ENST00000335221.5_Nonsense_Mutation_p.Q370*|BPTF_ENST00000424123.3_Nonsense_Mutation_p.Q231*|BPTF_ENST00000306378.6_Nonsense_Mutation_p.Q370*			Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor			78	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)		TCTAGTCGATCAGTTTCTTAC	0.418000																								0							SO:0001587	stop_gained			ENST00000321892.4	0	1	hg19		.	.	.	.	.	.	.	.	.	.	C	32	5.169246	0.94768	.	.	ENSG00000171634	ENST00000544491;ENST00000306378;ENST00000335221;ENST00000321892;ENST00000544778	.	.	.	5.62	5.62	0.85841	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.6584	0.95853	0.0:1.0:0.0:0.0	.	.	.	.	X	275;370;370;370;231	.	ENSP00000307208:Q370X	Q	+	1	0	BPTF	63281012	1.000000	0.71417	0.999000	0.59377	0.406000	0.30931	7.818000	0.86416	2.646000	0.89796	0.655000	0.94253	CAG		TCGA-IB-7889-01A-11D-2154-08	BPTF-201	KNOWN	basic	protein_coding	protein_coding		0	0	1	90	693	0	129	1	3.749916e-02	2	1	0	129	2		0	0	0	0	0	2	1	1.000000	90	686	0	128	2		0	0	0	0	129	2	-20.000000	1	1	0	0		1	1	2	3	2.041252	0	0.220000	1.900000	0.225960	0.990000	0.850000	1.000000	1.000000	0.982510	0.990000	1	0.950000	1.000000
TP53	7157	broad.mit.edu	37	17	7577046	7577046	+	Nonsense_Mutation	SNP	C	C	A			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08			C	A	C	C		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr17:7577046C>A	ENST00000269305.4	-	8	1081	c.892G>T	c.(892-894)Gag>Tag	p.E298*	TP53_ENST00000445888.2_Nonsense_Mutation_p.E298*|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Nonsense_Mutation_p.E298*|TP53_ENST00000420246.2_Nonsense_Mutation_p.E298*|TP53_ENST00000359597.4_Nonsense_Mutation_p.E298*|TP53_ENST00000413465.2_Intron	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.E298*(49)|p.0?(8)|p.?(2)|p.E298K(1)|p.L299fs*2(1)|p.L265_K305del41(1)|p.E298fs*53(1)|p.G293fs*1(1)|p.E298Q(1)|p.E298_P301delELPP(1)|p.H296_S303delHHELPPGS(1)		24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		Acetylsalicylic acid(DB00945)	GGGGGCAGCTCGTGGTGAGGC	0.567000		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	67	Substitution - Nonsense(49)|Whole gene deletion(8)|Deletion - In frame(3)|Unknown(2)|Deletion - Frameshift(2)|Substitution - Missense(2)|Insertion - Frameshift(1)	GRCh37	CM031387	TP53	M		SO:0001587	stop_gained	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	0	1	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	18.34	3.603544	0.66445	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	.	.	.	5.26	-4.03	0.04021	.	0.553557	0.18174	N	0.149346	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.25106	T	0.35	-12.8318	5.9489	0.19234	0.0:0.2155:0.4162:0.3682	.	.	.	.	X	298;298;298;298;298;287;166	.	ENSP00000269305:E298X	E	-	1	0	TP53	7517771	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.837000	0.04377	-0.441000	0.07201	-0.218000	0.12543	GAG		TCGA-IB-7889-01A-11D-2154-08	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	1	0	0	36	340	0	64	1	9.965345e-01	2	82	0	64	2	1	9.998332e-01	26	126	2	1162	3	1	1.000000	34	338	0	63	2		0	0	0	0	64	2	-3.221884	1	1	0	0		1	0	1	1	1.882628	1	0.220000	1.900000	0.147820	0.780000	0.560000	1.000000	1.000000	0.797851	0.780000	0	0.670000	0.920000
SMAD4	4089	broad.mit.edu	37	18	48591918	48591918	+	Missense_Mutation	SNP	C	C	T	rs80338963		TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr18:48591918C>T	ENST00000342988.3	+	9	1619	c.1081C>T	c.(1081-1083)Cgc>Tgc	p.R361C	SMAD4_ENST00000588745.1_Missense_Mutation_p.R265C|SMAD4_ENST00000398417.2_Missense_Mutation_p.R361C	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	p.0?(36)|p.R361C(3)|p.R361S(2)|p.?(2)		454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)			TGGAGGAGATCGCTTTTGTTT	0.413000																								43	Whole gene deletion(36)|Substitution - Missense(5)|Unknown(2)	GRCh37	CM040450|CM041789|CM981228	SMAD4	M	rs80338963	SO:0001583	missense			ENST00000342988.3	1	1	hg19	CCDS11950.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.820743	0.90873	.	.	ENSG00000141646	ENST00000342988;ENST00000544926;ENST00000398417	D;D	0.98164	-4.76;-4.76	5.86	5.86	0.93980	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3);	0.000000	0.85682	D	0.000000	D	0.99275	0.9747	M	0.94021	3.485	0.80722	A	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99157	1.0860	9	0.87932	D	0	.	18.9646	0.92691	0.0:1.0:0.0:0.0	.	361	Q13485	SMAD4_HUMAN	C	361	ENSP00000341551:R361C;ENSP00000381452:R361C	ENSP00000341551:R361C	R	+	1	0	SMAD4	46845916	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.718000	0.61930	2.771000	0.95319	0.563000	0.77884	CGC		TCGA-IB-7889-01A-11D-2154-08	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	1	0	1	35	268	0	50	1	8.172738e-01	6	20	0	50	2	1	9.995530e-01	12	80	1	867	2	1	1.000000	34	267	0	50	2		0	0	0	0	50	2	-3.221909	1	1	0	0		1	0	1	1	1.793076	1	0.220000	1.900000	0.128978	0.880000	0.650000	1.000000	1.000000	0.879974	0.880000	1	0.760000	0.990000
CDH20	28316	broad.mit.edu	37	18	59195270	59195270	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr18:59195270G>A	ENST00000262717.4	+	7	1486	c.1088G>A	c.(1087-1089)cGt>cAt	p.R363H	CDH20_ENST00000538374.1_Missense_Mutation_p.R363H|CDH20_ENST00000536675.2_Missense_Mutation_p.R363H			Q9HBT6	CAD20_HUMAN	cadherin 20, type 2			61		Colorectal(73;0.186)			CTAGAGATGCGTTTTCTGAAC	0.473000																								0							SO:0001583	missense			ENST00000262717.4	1	1	hg19	CCDS11977.1	.	.	.	.	.	.	.	.	.	.	G	15.33	2.800571	0.50315	.	.	ENSG00000101542	ENST00000536675;ENST00000538374;ENST00000262717	T;T;T	0.38401	1.14;1.14;1.14	5.88	5.01	0.66863	Cadherin (4);Cadherin-like (1);	0.352394	0.34110	N	0.004250	T	0.44307	0.1287	M	0.79805	2.47	0.39023	D	0.959782	B	0.21905	0.062	B	0.22601	0.04	T	0.48127	-0.9062	10	0.54805	T	0.06	.	14.9937	0.71412	0.0683:0.0:0.9317:0.0	.	363	Q9HBT6	CAD20_HUMAN	H	363	ENSP00000444767:R363H;ENSP00000442226:R363H;ENSP00000262717:R363H	ENSP00000262717:R363H	R	+	2	0	CDH20	57346250	0.997000	0.39634	1.000000	0.80357	0.991000	0.79684	1.798000	0.38814	1.492000	0.48499	0.650000	0.86243	CGT		TCGA-IB-7889-01A-11D-2154-08	CDH20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256141.2	1	0	0	34	321	0	66		0	0	0	0	66	2		0	0	0	0	0	2	1	1.000000	34	318	0	65	2		0	0	0	0	66	2	-20.000000	1	1	121412	4	36	1	0	1	1	1.793076	1	0.220000	1.900000	0.128978	0.760000	0.540000	0.990000	0.770000	0.775037	0.760000	0	0.650000	0.890000
CYP4F22	126410	broad.mit.edu	37	19	15662205	15662205	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr19:15662205C>T	ENST00000269703.3	+	14	1718	c.1519C>T	c.(1519-1521)Cgg>Tgg	p.R507W	CYP4F22_ENST00000601005.2_Missense_Mutation_p.R507W	NM_173483.3	NP_775754.2	Q6NT55	CP4FN_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 22			37					GCGCAAGGTGCGGCGGAAGCC	0.672000																								0							SO:0001583	missense			ENST00000269703.3	0	1	hg19	CCDS12331.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.566553	0.86439	.	.	ENSG00000171954	ENST00000269703	T	0.69040	-0.37	4.6	4.6	0.57074	.	0.125575	0.53938	D	0.000052	T	0.82006	0.4943	M	0.82823	2.61	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.82500	-0.0426	10	0.37606	T	0.19	.	15.245	0.73499	0.0:1.0:0.0:0.0	.	507	Q6NT55	CP4FN_HUMAN	W	507	ENSP00000269703:R507W	ENSP00000269703:R507W	R	+	1	2	CYP4F22	15523205	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	6.527000	0.73803	2.247000	0.74100	0.455000	0.32223	CGG		TCGA-IB-7889-01A-11D-2154-08	CYP4F22-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461338.2	1	0	0	5	75	0	14	0	0	0	1	0	14	2		0	0	0	0	0	2	1	0.939603	5	75	0	14	2		0	0	0	0	14	2	-9.210014	1	0	0	0		1	0	0	0	2.005031	0	0.220000	1.900000	0.211325	0.590000	0.230000	1.000000	1.000000	0.615780	0.590000	0	0.380000	0.860000
GRIN2D	2906	broad.mit.edu	37	19	48919318	48919318	+	Silent	SNP	C	C	T	rs148340456	byFrequency	TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr19:48919318C>T	ENST00000263269.3	+	7	1729	c.1641C>T	c.(1639-1641)tcC>tcT	p.S547S		NM_000836.2	NP_000827.2	O15399	NMDE4_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2D			37		all_epithelial(76;1.11e-06)|all_lung(116;5.79e-06)|Lung NSC(112;1.18e-05)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	AGGAGCGCTCCGAGATCGTGG	0.662000																								0							SO:0001819	synonymous_variant			ENST00000263269.3	1	1	hg19	CCDS12719.1																																																																																				TCGA-IB-7889-01A-11D-2154-08	GRIN2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466121.1	1	0	0	26	429	0	86	0	9.648041e-02	0	9	0	86	2		0	0	0	0	0	2	1	1.000000	25	424	0	85	2		0	0	0	0	86	2	-2.690484	1	1	121412	16	50	1	0	1	1	2.013467	0	0.220000	1.900000	0.215686	0.510000	0.340000	0.720000	0.510000	0.529886	0.510000	0	0.420000	0.620000
TPM3P9	147804	broad.mit.edu	37	19	53950474	53950474	+	RNA	SNP	C	C	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr19:53950474C>T	ENST00000424846.3	+	0	2920				ZNF761_ENST00000454407.1_RNA	NR_003148.3				tropomyosin 3 pseudogene 9								ACTCTTGGTACGTGAGGAAGA	0.433000																								0											ENST00000424846.3	0	1	hg19																																																																																					TCGA-IB-7889-01A-11D-2154-08	TPM3P9-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000347070.1	0	0	0	21	341	0	71	0	1.210399e-01	0	10	0	71	2		0	0	0	0	0	2	1	0.999997	19	330	0	69	2		0	0	0	0	71	2	-5.232620	1	1	121408	7	33	1	0	1	1	2.013467	0	0.220000	1.900000	0.215686	0.520000	0.330000	0.760000	0.510000	0.540943	0.520000	0	0.420000	0.650000
MUC16	94025	broad.mit.edu	37	19	9071237	9071237	+	Silent	SNP	C	C	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr19:9071237C>T	ENST00000397910.4	-	3	16412	c.16209G>A	c.(16207-16209)ccG>ccA	p.P5403P		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	p.P5403P(2)|p.P1036P(1)		590					TGTAAGTGGCCGGTCTCTCAT	0.502000																								3	Substitution - coding silent(3)						SO:0001819	synonymous_variant			ENST00000397910.4	1	1	hg19	CCDS54212.1																																																																																				TCGA-IB-7889-01A-11D-2154-08	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	1	0	0	85	1563	0	298	0	7.947024e-03	0	3	0	298	2		0	0	0	0	0	2	1	1.000000	84	1535	0	295	2		0	0	0	0	298	2	-7.962869	1	1	121062	6	44	1	0	0	0	2.005031	0	0.220000	1.900000	0.211325	0.460000	0.360000	0.560000	0.460000	0.467558	0.460000	0	0.410000	0.520000
AMPD1	270	broad.mit.edu	37	1	115216697	115216697	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr1:115216697C>T	ENST00000520113.2	-	14	1921	c.1906G>A	c.(1906-1908)Gtg>Atg	p.V636M	AMPD1_ENST00000353928.6_Missense_Mutation_p.V603M|AMPD1_ENST00000369538.3_Missense_Mutation_p.V632M			P23109	AMPD1_HUMAN	adenosine monophosphate deaminase 1			45	all_epithelial(7;7.83e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Adenosine monophosphate(DB00131)	TACTGTAGCACGGGACTCTGA	0.353000																								0							SO:0001583	missense			ENST00000520113.2	1	1	hg19	CCDS876.2	.	.	.	.	.	.	.	.	.	.	C	25.5	4.647876	0.87958	.	.	ENSG00000116748	ENST00000520113;ENST00000369538;ENST00000353928	D;D;D	0.95554	-3.74;-3.74;-3.74	5.96	5.96	0.96718	Adenosine/AMP deaminase (1);	0.052104	0.85682	D	0.000000	D	0.97923	0.9317	M	0.82923	2.615	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.988;0.996	D	0.98016	1.0368	10	0.87932	D	0	-21.0775	20.4008	0.98991	0.0:1.0:0.0:0.0	.	632;603	Q5TF02;P23109	.;AMPD1_HUMAN	M	636;632;603	ENSP00000430075:V636M;ENSP00000358551:V632M;ENSP00000316520:V603M	ENSP00000316520:V603M	V	-	1	0	AMPD1	115018220	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	7.818000	0.86416	2.826000	0.97356	0.655000	0.94253	GTG		TCGA-IB-7889-01A-11D-2154-08	AMPD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032860.4	1	0	0	9	164	0	37	0	3.113139e-02	0	5	0	37	2		0	0	0	0	0	2	1	0.994302	9	162	0	36	2		0	0	0	0	37	2	-3.318794	1	1	121378	2	34	1	0	0	0	1.888448	1	0.220000	1.900000	0.162910	0.440000	0.220000	0.760000	0.430000	0.469668	0.440000	0	0.320000	0.610000
ADAMTSL4	54507	broad.mit.edu	37	1	150529196	150529196	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr1:150529196G>A	ENST00000369038.2	+	8	1877	c.1676G>A	c.(1675-1677)cGt>cAt	p.R559H	ADAMTSL4_ENST00000369039.5_Missense_Mutation_p.R582H|RP11-54A4.2_ENST00000442435.2_RNA|ADAMTSL4_ENST00000271643.4_Missense_Mutation_p.R559H|ADAMTSL4_ENST00000369041.5_Missense_Mutation_p.R559H			Q6UY14	ATL4_HUMAN	ADAMTS-like 4			32	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;3.18e-23)|all cancers(9;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(6;1.13e-14)|BRCA - Breast invasive adenocarcinoma(12;0.000503)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)		CGATATAACCGTCCTCCCAGG	0.647000																								0							SO:0001583	missense			ENST00000369038.2	1	1	hg19	CCDS955.1	.	.	.	.	.	.	.	.	.	.	G	16.85	3.235869	0.58886	.	.	ENSG00000143382	ENST00000369041;ENST00000271643;ENST00000407995;ENST00000369039;ENST00000369038	T;T;T;T	0.55413	0.52;0.52;0.52;0.52	4.54	4.54	0.55810	ADAM-TS Spacer 1 (1);	.	.	.	.	T	0.65852	0.2731	M	0.85777	2.775	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.83275	0.996;0.995;0.993;0.988	T	0.70992	-0.4721	9	0.72032	D	0.01	.	8.4206	0.32698	0.1047:0.0:0.8953:0.0	.	582;582;559;559	B7ZMJ3;F8WAD0;Q6UY14;Q6UY14-2	.;.;ATL4_HUMAN;.	H	559;559;97;582;559	ENSP00000358037:R559H;ENSP00000271643:R559H;ENSP00000358035:R582H;ENSP00000358034:R559H	ENSP00000271643:R559H	R	+	2	0	ADAMTSL4	148795820	0.988000	0.35896	0.629000	0.29254	0.140000	0.21249	5.061000	0.64319	2.346000	0.79739	0.462000	0.41574	CGT		TCGA-IB-7889-01A-11D-2154-08	ADAMTSL4-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084395.4	1	0	0	51	1047	0	163	0	2.991740e-02	0	6	0	163	2		0	0	0	0	0	2	1	0.999803	48	1032	1	162	22		0	0	0	0	163	2	-5.477019	1	1	121412	1	37	1	0	3	3	2.120537	1	0.220000	1.900000	0.277242	0.470000	0.340000	1.000000	0.460000	0.566720	0.470000	0	0.400000	1.000000
RIT1	6016	broad.mit.edu	37	1	155880296	155880296	+	Splice_Site	SNP	G	G	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08			G	T	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr1:155880296G>T	ENST00000368323.3	-	3	312	c.108C>A	c.(106-108)gcC>gcA	p.A36A	RIT1_ENST00000368322.3_Splice_Site_p.A53A|RIT1_ENST00000539040.1_5'UTR	NM_006912.5	NP_008843.1	Q92963	RIT1_HUMAN	Ras-like without CAAX 1			19	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)		OV - Ovarian serous cystadenocarcinoma(3;1.79e-05)		GCATGGTCATGGCTTCAAAAG	0.393000																								0							SO:0001630	splice_region_variant			ENST00000368323.3	1	0	hg19	CCDS1123.1																																																																																				TCGA-IB-7889-01A-11D-2154-08	RIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039593.1	1	0	1	50	275	0	47	1	9.965648e-01	16	34	0	47	2		0	0	0	0	0	2	1	1.000000	49	274	0	47	2		0	0	0	0	47	2	-3.150828	1	1	0	0		1	0	3	3	2.120537	1	0.220000	1.900000	0.277242	0.990000	0.990000	1.000000	1.000000	0.999941	0.990000	1	0.990000	1.000000
CADM3	57863	broad.mit.edu	37	1	159163257	159163257	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr1:159163257C>T	ENST00000368125.4	+	4	584	c.427C>T	c.(427-429)Cgg>Tgg	p.R143W	CADM3_ENST00000368124.4_Missense_Mutation_p.R177W|CTA-134P22.2_ENST00000415675.2_RNA	NM_001127173.1	NP_001120645.1	Q8N126	CADM3_HUMAN	cell adhesion molecule 3			55	all_hematologic(112;0.0429)				ATCTTCATTACGGGAAAAAGA	0.532000																								0							SO:0001583	missense			ENST00000368125.4	1	1	hg19	CCDS44251.1	.	.	.	.	.	.	.	.	.	.	C	18.15	3.559293	0.65538	.	.	ENSG00000162706	ENST00000368124;ENST00000368125;ENST00000416746	T;T;T	0.76060	-0.99;-0.99;-0.99	5.13	5.13	0.70059	Immunoglobulin subtype (1);CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.372580	0.26514	N	0.023944	T	0.73418	0.3584	L	0.39245	1.2	0.36569	D	0.872888	P;D;D	0.76494	0.863;0.999;0.998	D;D;P	0.66979	0.913;0.948;0.787	T	0.77275	-0.2648	10	0.66056	D	0.02	.	11.0641	0.47966	0.1847:0.8152:0.0:0.0	.	143;143;177	Q8N126-3;Q8N126;Q8N126-2	.;CADM3_HUMAN;.	W	177;143;143	ENSP00000357106:R177W;ENSP00000357107:R143W;ENSP00000387802:R143W	ENSP00000357106:R177W	R	+	1	2	CADM3	157429881	0.004000	0.15560	1.000000	0.80357	0.953000	0.61014	-0.061000	0.11693	2.655000	0.90218	0.655000	0.94253	CGG		TCGA-IB-7889-01A-11D-2154-08	CADM3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090330.1	1	0	1	84	345	0	73	0	2.575212e-01	0	5	0	73	2		0	0	0	0	0	2	1	1.000000	85	341	0	73	2		0	0	0	0	73	2	-3.322064	1	1	0	0		1	0	3	3	2.161655	1	0.220000	1.900000	0.281636	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	0.990000	1.000000
IGSF9	57549	broad.mit.edu	37	1	159900160	159900160	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr1:159900160C>T	ENST00000368094.1	-	15	2080	c.1883G>A	c.(1882-1884)cGg>cAg	p.R628Q	IGSF9_ENST00000361509.3_Missense_Mutation_p.R612Q|IGSF9_ENST00000493195.1_5'UTR	NM_001135050.1	NP_001128522.1	Q9P2J2	TUTLA_HUMAN	immunoglobulin superfamily, member 9	p.R612L(1)		56	all_hematologic(112;0.0597)	Breast(1374;0.000126)	BRCA - Breast invasive adenocarcinoma(70;0.111)		CACCAGACCCCGCGGAGGGGA	0.652000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000368094.1	1	1	hg19	CCDS44254.1	.	.	.	.	.	.	.	.	.	.	C	15.97	2.988769	0.53934	.	.	ENSG00000085552	ENST00000361509;ENST00000368094	T;T	0.53640	0.61;0.61	5.17	5.17	0.71159	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.37012	N	0.002287	T	0.27489	0.0675	L	0.50333	1.59	0.42485	D	0.992879	P	0.41232	0.743	B	0.33750	0.169	T	0.10941	-1.0608	9	.	.	.	-8.1725	16.1513	0.81624	0.0:1.0:0.0:0.0	.	628	Q9P2J2	TUTLA_HUMAN	Q	612;628	ENSP00000355049:R612Q;ENSP00000357073:R628Q	.	R	-	2	0	IGSF9	158166784	0.010000	0.17322	0.694000	0.30210	0.512000	0.34134	1.424000	0.34848	2.396000	0.81511	0.455000	0.32223	CGG		TCGA-IB-7889-01A-11D-2154-08	IGSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059115.1	1	0	1	137	528	0	103	1	9.975707e-01	26	11	0	103	2		0	0	0	0	0	2	1	1.000000	133	520	0	103	2		0	0	0	0	103	2	-2.963670	1	1	0	0		1	0	3	3	2.161655	1	0.220000	1.900000	0.281636	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	0.990000	1.000000
PAPPA2	60676	broad.mit.edu	37	1	176709307	176709307	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr1:176709307G>A	ENST00000367662.3	+	14	5290	c.4126G>A	c.(4126-4128)Gag>Aag	p.E1376K		NM_020318.2	NP_064714.2	Q9BXP8	PAPP2_HUMAN	pappalysin 2			226					CTCAGAGGACGAGGGGCAGAA	0.483000																								0							SO:0001583	missense			ENST00000367662.3	1	1	hg19	CCDS41438.1	.	.	.	.	.	.	.	.	.	.	G	9.393	1.075892	0.20227	.	.	ENSG00000116183	ENST00000367662	T	0.01745	4.66	5.3	-2.21	0.06973	.	0.849038	0.10709	N	0.643103	T	0.01976	0.0062	L	0.49256	1.55	0.24431	N	0.994576	B	0.18461	0.028	B	0.13407	0.009	T	0.39941	-0.9589	10	0.54805	T	0.06	-0.3589	4.9535	0.14027	0.3507:0.2614:0.3879:0.0	.	1376	Q9BXP8	PAPP2_HUMAN	K	1376	ENSP00000356634:E1376K	ENSP00000356634:E1376K	E	+	1	0	PAPPA2	174975930	0.973000	0.33851	0.000000	0.03702	0.021000	0.10359	1.361000	0.34136	-0.798000	0.04444	-0.345000	0.07892	GAG		TCGA-IB-7889-01A-11D-2154-08	PAPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084763.1	1	0	1	29	279	0	38		0	0	0	0	38	2		0	0	0	0	0	2	1	1.000000	28	275	0	37	2		0	0	0	0	38	2	-2.920854	1	1	120896	3	40	1	0	3	3	2.161655	1	0.220000	1.900000	0.281636	0.970000	0.650000	1.000000	1.000000	0.919572	0.970000	1	0.790000	1.000000
H6PD	9563	broad.mit.edu	37	1	9324398	9324398	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr1:9324398C>A	ENST00000377403.2	+	5	2148	c.1846C>A	c.(1846-1848)Ctg>Atg	p.L616M	H6PD_ENST00000602477.1_Missense_Mutation_p.L627M	NM_001282587.1|NM_004285.3	NP_001269516.1|NP_004276.2	O95479	G6PE_HUMAN	hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)			23	all_lung(157;0.23)	all_epithelial(116;1.28e-19)|all_lung(118;5.22e-06)|Lung NSC(185;1.98e-05)|Renal(390;0.000147)|Breast(348;0.00109)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)			CCACACGCACCTGTGGCTGGT	0.682000																								0							SO:0001583	missense			ENST00000377403.2	1	1	hg19	CCDS101.1	.	.	.	.	.	.	.	.	.	.	C	16.77	3.213707	0.58452	.	.	ENSG00000049239	ENST00000377403	T	0.49139	0.79	5.4	5.4	0.78164	Glucosamine/galactosamine-6-phosphate isomerase (1);6-phosphogluconolactonase, DevB-type (1);	0.230625	0.37715	N	0.001970	T	0.66703	0.2816	M	0.88570	2.965	0.39055	D	0.960407	D	0.54397	0.966	P	0.58331	0.837	T	0.74262	-0.3722	10	0.72032	D	0.01	-23.0015	8.9799	0.35959	0.0:0.7713:0.1498:0.0789	.	616	O95479	G6PE_HUMAN	M	616	ENSP00000366620:L616M	ENSP00000366620:L616M	L	+	1	2	H6PD	9246985	0.995000	0.38212	1.000000	0.80357	0.975000	0.68041	0.536000	0.23129	2.536000	0.85505	0.561000	0.74099	CTG		TCGA-IB-7889-01A-11D-2154-08	H6PD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004928.2	1	0	0	7	159	0	30	0	1.463060e-01	1	13	0	30	2		0	0	0	0	0	2	1	0.980043	7	156	0	28	2		0	0	0	0	30	2	-10.008620	1	1	0	0		1	0	0	0	1.905531	0	0.220000	1.900000	0.168798	0.370000	0.160000	0.670000	0.350000	0.394234	0.370000	0	0.250000	0.520000
TSHZ2	128553	broad.mit.edu	37	20	51872260	51872260	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr20:51872260C>T	ENST00000371497.5	+	2	3150	c.2263C>T	c.(2263-2265)Cgc>Tgc	p.R755C	TSHZ2_ENST00000603338.2_Missense_Mutation_p.R752C|TSHZ2_ENST00000329613.6_Missense_Mutation_p.R752C|RP4-678D15.1_ENST00000606932.1_RNA	NM_001193421.1|NM_173485.5	NP_001180350.1|NP_775756.3	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2			84			STAD - Stomach adenocarcinoma(23;0.1)		CGTGTCCAGGCGCTACCTGTT	0.512000																								0							SO:0001583	missense			ENST00000371497.5	1	1	hg19	CCDS33490.1	.	.	.	.	.	.	.	.	.	.	C	12.62	1.992826	0.35131	.	.	ENSG00000182463	ENST00000371497;ENST00000329613;ENST00000450262	T;T	0.50277	0.75;0.75	5.23	5.23	0.72850	.	0.475787	0.23196	N	0.050846	T	0.43144	0.1234	M	0.68317	2.08	0.34997	D	0.755567	P	0.49358	0.923	B	0.34452	0.183	T	0.65709	-0.6102	10	0.87932	D	0	-5.9641	13.7395	0.62838	0.1538:0.8461:0.0:0.0	.	755	Q9NRE2	TSH2_HUMAN	C	755;752;281	ENSP00000360552:R755C;ENSP00000333114:R752C	ENSP00000333114:R752C	R	+	1	0	TSHZ2	51305667	1.000000	0.71417	1.000000	0.80357	0.872000	0.50106	3.499000	0.53310	2.438000	0.82558	0.579000	0.79373	CGC		TCGA-IB-7889-01A-11D-2154-08	TSHZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080398.6	1	0	0	33	462	0	80	1	1.721122e-01	2	9	0	80	2		0	0	0	0	0	2	1	1.000000	33	446	0	78	2		0	0	0	0	80	2	-8.215395	1	1	121410	1	41	1	0	0	0	1.980412	0	0.220000	1.900000	0.200656	0.590000	0.410000	0.790000	0.590000	0.601979	0.590000	0	0.490000	0.700000
TMX4	56255	broad.mit.edu	37	20	7963022	7963022	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr20:7963022C>T	ENST00000246024.2	-	8	1141	c.926G>A	c.(925-927)cGg>cAg	p.R309Q		NM_021156.2	NP_066979.2	Q9H1E5	TMX4_HUMAN	thioredoxin-related transmembrane protein 4			17					TACTTCCTCCCGGGTCACACC	0.582000																								0							SO:0001583	missense			ENST00000246024.2	1	1	hg19	CCDS13101.1	.	.	.	.	.	.	.	.	.	.	C	10.44	1.350863	0.24512	.	.	ENSG00000125827	ENST00000246024	T	0.09350	2.99	5.54	-7.71	0.01254	.	2.465280	0.01182	N	0.007100	T	0.02888	0.0086	N	0.02011	-0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.35276	-0.9795	10	0.23891	T	0.37	2.3619	0.5542	0.00668	0.2156:0.2763:0.232:0.276	.	309	Q9H1E5	TMX4_HUMAN	Q	309	ENSP00000246024:R309Q	ENSP00000246024:R309Q	R	-	2	0	TMX4	7911022	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-1.154000	0.03166	-1.638000	0.01529	-0.455000	0.05494	CGG		TCGA-IB-7889-01A-11D-2154-08	TMX4-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000077928.2	1	0	0	22	456	0	76	1	9.696323e-01	6	114	0	76	2		0	0	0	0	0	2	1	0.999999	21	451	0	73	2		0	0	0	0	76	2	-2.247832	0	1	0	0		1	0	0	0	1.980412	0	0.220000	1.900000	0.200656	0.410000	0.260000	0.590000	0.410000	0.421529	0.410000	0	0.330000	0.500000
NCAM2	4685	broad.mit.edu	37	21	22656721	22656721	+	Splice_Site	SNP	G	G	A			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr21:22656721G>A	ENST00000400546.1	+	3	586		c.e3+1		NCAM2_ENST00000284894.7_Intron|NCAM2_ENST00000535285.1_Splice_Site|NCAM2_ENST00000486367.1_Splice_Site	NM_004540.3	NP_004531.2	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2	p.?(1)		108		Lung NSC(9;0.195)			GAAATTTACCGTAAGTAATGT	0.294000																								1	Unknown(1)						SO:0001630	splice_region_variant			ENST00000400546.1	0	1	hg19	CCDS42910.1	.	.	.	.	.	.	.	.	.	.	G	19.70	3.876114	0.72180	.	.	ENSG00000154654	ENST00000400546;ENST00000535285	.	.	.	5.58	5.58	0.84498	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.134	0.89612	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	NCAM2	21578592	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	8.804000	0.91921	2.632000	0.89209	0.591000	0.81541	.		TCGA-IB-7889-01A-11D-2154-08	NCAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000170915.1	1	0	0	6	121	0	19		0	0	0	0	19	2		0	0	0	0	0	2	1	0.966148	6	121	0	19	2		0	0	0	0	19	2	-3.360477	1	1	0	0		1	0	0	0	1.988257	0	0.220000	1.900000	0.204244	0.440000	0.180000	0.820000	0.410000	0.468309	0.440000	0	0.290000	0.630000
GGT1	2678	broad.mit.edu	37	22	25023843	25023843	+	Silent	SNP	G	G	A			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr22:25023843G>A	ENST00000400382.1	+	13	1988	c.1233G>A	c.(1231-1233)ccG>ccA	p.P411P	GGT1_ENST00000403838.1_Silent_p.P67P|GGT1_ENST00000400380.1_Silent_p.P411P|GGT1_ENST00000248923.4_Silent_p.P411P|GGT1_ENST00000401885.1_Silent_p.P67P|GGT1_ENST00000400383.1_Silent_p.P411P|GGT1_ENST00000406383.2_Silent_p.P411P|GGT1_ENST00000404532.1_Silent_p.P67P|GGT1_ENST00000404920.1_Silent_p.P67P|GGT1_ENST00000466310.1_3'UTR|GGT1_ENST00000404223.1_Silent_p.P67P			P19440	GGT1_HUMAN	gamma-glutamyltransferase 1			40				Glutathione(DB00143)	TCCGCTCCCCGGTCAGCGGGA	0.597000																								0							SO:0001819	synonymous_variant			ENST00000400382.1	1	1	hg19	CCDS42992.1																																																																																				TCGA-IB-7889-01A-11D-2154-08	GGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250797.1	1	0	0	15	313	0	56	1	9.119113e-01	9	81	0	56	2		0	0	0	0	0	2	1	0.999838	15	300	0	62	2		0	0	0	0	56	2	-2.647879	1	1	121410	8	41	1	0	1	1	2.000519	0	0.220000	1.900000	0.208684	0.410000	0.240000	0.640000	0.400000	0.429460	0.410000	0	0.320000	0.530000
CSNK1E	1454	broad.mit.edu	37	22	38690455	38690455	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr22:38690455G>A	ENST00000396832.1	-	8	1231	c.971C>T	c.(970-972)gCg>gTg	p.A324V	CSNK1E_ENST00000403904.1_Missense_Mutation_p.A324V|CSNK1E_ENST00000498529.1_5'Flank|CSNK1E_ENST00000400206.2_Missense_Mutation_p.A324V|CSNK1E_ENST00000359867.3_Missense_Mutation_p.A324V	NM_152221.2	NP_689407.1	P49674	KC1E_HUMAN	casein kinase 1, epsilon			22	Melanoma(58;0.045)				GGCTCGGGTCGCGGACCCCCG	0.726000													Esophageal Squamous(119;108 755 9651 12170 13692 17603 24932 28315 37982 41601)											0							SO:0001583	missense			ENST00000396832.1	0	1	hg19	CCDS13970.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.49|16.49	3.138626|3.138626	0.56936|0.56936	.|.	.|.	ENSG00000213923|ENSG00000213923	ENST00000359867;ENST00000396832;ENST00000402865;ENST00000400206;ENST00000403904|ENST00000366216	T;T;T;T|.	0.57107|.	0.42;0.42;0.42;0.42|.	5.56|5.56	4.54|4.54	0.55810|0.55810	.|.	0.436410|.	0.26156|.	N|.	0.026018|.	T|.	0.61553|.	0.2356|.	L|L	0.48642|0.48642	1.525|1.525	0.42079|0.42079	D|D	0.991242|0.991242	B|.	0.13594|.	0.008|.	B|.	0.08055|.	0.003|.	T|.	0.59836|.	-0.7379|.	10|.	0.31617|.	T|.	0.26|.	.|.	14.7935|14.7935	0.69860|0.69860	0.0699:0.0:0.9301:0.0|0.0699:0.0:0.9301:0.0	.|.	324|.	P49674|.	KC1E_HUMAN|.	V|X	324|27	ENSP00000352929:A324V;ENSP00000380044:A324V;ENSP00000383067:A324V;ENSP00000384074:A324V|.	ENSP00000352929:A324V|.	A|R	-|-	2|1	0|2	CSNK1E|CSNK1E	37020401|37020401	1.000000|1.000000	0.71417|0.71417	0.040000|0.040000	0.18447|0.18447	0.110000|0.110000	0.19582|0.19582	5.714000|5.714000	0.68422|0.68422	1.327000|1.327000	0.45338|0.45338	0.650000|0.650000	0.86243|0.86243	GCG|CGA		TCGA-IB-7889-01A-11D-2154-08	CSNK1E-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321462.1	0	0	0	3	27	0	10	1	6.597741e-01	3	17	0	10	2		0	0	0	0	0	2	1	0.812770	3	27	0	9	2		0	0	0	0	10	2	-9.593557	1	1	119040	7	33	1	0	1	1	2.000519	0	0.220000	1.900000	0.208684	0.900000	0.280000	1.000000	1.000000	0.810961	0.900000	1	0.530000	1.000000
LCT	3938	broad.mit.edu	37	2	136564940	136564940	+	Nonsense_Mutation	SNP	G	G	A			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr2:136564940G>A	ENST00000264162.2	-	9	3941	c.3931C>T	c.(3931-3933)Cga>Tga	p.R1311*	Y_RNA_ENST00000363794.1_RNA	NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase			124				Vitamin C(DB00126)	ACATACCCTCGAAGGTCTATA	0.522000																								0							SO:0001587	stop_gained			ENST00000264162.2	0	1	hg19	CCDS2178.1	.	.	.	.	.	.	.	.	.	.	G	38	6.963892	0.97967	.	.	ENSG00000115850	ENST00000264162;ENST00000455227	.	.	.	5.87	4.98	0.66077	.	0.165435	0.53938	D	0.000056	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.877	13.1749	0.59621	0.0:0.0:0.5643:0.4357	.	.	.	.	X	1311;743	.	ENSP00000264162:R1311X	R	-	1	2	LCT	136281410	0.998000	0.40836	1.000000	0.80357	0.748000	0.42578	2.030000	0.41108	1.446000	0.47643	0.655000	0.94253	CGA		TCGA-IB-7889-01A-11D-2154-08	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	1	0	0	36	450	0	96		0	0	0	0	96	2		0	0	0	0	0	2	1	1.000000	36	443	0	95	2		0	0	0	0	96	2	-9.381009	1	1	0	0		1	0	0	0	1.985275	0	0.220000	1.900000	0.202454	0.650000	0.470000	0.870000	0.660000	0.668554	0.650000	0	0.550000	0.770000
CXCR4	7852	broad.mit.edu	37	2	136872710	136872710	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08			G	A	G	G		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr2:136872710G>A	ENST00000241393.3	-	2	892	c.788C>T	c.(787-789)tCc>tTc	p.S263F	CXCR4_ENST00000466288.1_5'UTR|CXCR4_ENST00000409817.1_Missense_Mutation_p.S267F	NM_003467.2	NP_003458.1	P61073	CXCR4_HUMAN	chemokine (C-X-C motif) receptor 4			25				Framycetin(DB00452)|Plerixafor(DB06809)	GAGGATGAAGGAGTCGATGCT	0.517000																								0							SO:0001583	missense			ENST00000241393.3	1	1	hg19	CCDS46420.1	.	.	.	.	.	.	.	.	.	.	G	15.06	2.722563	0.48728	.	.	ENSG00000121966	ENST00000409817;ENST00000241393;ENST00000537957	T;T	0.36699	1.24;1.24	6.17	5.29	0.74685	GPCR, rhodopsin-like superfamily (1);	0.137085	0.64402	D	0.000003	T	0.30634	0.0771	L	0.33189	0.99	0.49483	D	0.99979	P;D	0.57257	0.718;0.979	B;B	0.39503	0.237;0.301	T	0.16719	-1.0393	10	0.87932	D	0	.	17.6818	0.88246	0.0:0.1228:0.8772:0.0	.	263;267	P61073;P61073-2	CXCR4_HUMAN;.	F	267;263;133	ENSP00000386884:S267F;ENSP00000241393:S263F	ENSP00000241393:S263F	S	-	2	0	CXCR4	136589180	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	4.050000	0.57404	1.615000	0.50252	0.655000	0.94253	TCC		TCGA-IB-7889-01A-11D-2154-08	CXCR4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331732.1	0	0	0	13	382	0	76	0	9.999547e-01	1	540	0	76	2		0	0	0	0	0	2	1	0.999504	13	376	0	75	2		0	0	0	0	76	2	-3.592798	1	1	0	0		1	0	0	0	1.985275	0	0.220000	1.900000	0.202454	0.290000	0.160000	0.470000	0.290000	0.310414	0.290000	0	0.220000	0.390000
RNF144A	9781	broad.mit.edu	37	2	7160800	7160800	+	Silent	SNP	C	C	G			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr2:7160800C>G	ENST00000320892.6	+	6	940	c.498C>G	c.(496-498)ccC>ccG	p.P166P	RNF144A_ENST00000467276.1_3'UTR	NM_014746.3	NP_055561.2	P50876	R144A_HUMAN	ring finger protein 144A			25	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)	all_cancers(51;0.226)			CCTTCCTCCCCGGGGAGACCA	0.587000																								0							SO:0001819	synonymous_variant			ENST00000320892.6	1	1	hg19	CCDS1657.1	.	.	.	.	.	.	.	.	.	.	C	7.556	0.663657	0.14710	.	.	ENSG00000151692	ENST00000432850	T	0.30182	1.54	5.42	-5.68	0.02436	.	0.000000	0.85682	D	0.000000	T	0.16938	0.0407	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.17868	-1.0355	7	0.20046	T	0.44	.	2.4736	0.04570	0.3811:0.1371:0.0718:0.41	.	.	.	.	R	162	ENSP00000411616:P162R	ENSP00000411616:P162R	P	+	2	0	RNF144A	7078251	0.025000	0.19082	0.602000	0.28890	0.849000	0.48306	-0.908000	0.04063	-1.362000	0.02166	-0.254000	0.11334	CCG		TCGA-IB-7889-01A-11D-2154-08	RNF144A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206725.2	1	0	1	59	491	0	92	0	6.145692e-02	0	3	0	92	2		0	0	0	0	0	2	1	1.000000	59	485	0	91	2		0	0	0	0	92	2	-2.429492	0	1	0	0		1	0	0	0	1.983751	0	0.220000	1.900000	0.202454	0.940000	0.730000	1.000000	1.000000	0.929858	0.940000	1	0.830000	1.000000
QTRTD1	79691	broad.mit.edu	37	3	113804663	113804663	+	Missense_Mutation	SNP	A	A	G			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr3:113804663A>G	ENST00000493014.1	+	6	910	c.842A>G	c.(841-843)tAc>tGc	p.Y281C	QTRTD1_ENST00000281273.4_Missense_Mutation_p.Y387C|QTRTD1_ENST00000485050.1_Missense_Mutation_p.Y399C|QTRTD1_ENST00000479882.1_Missense_Mutation_p.Y264C	NM_001256836.1	NP_001243765.1			queuine tRNA-ribosyltransferase domain containing 1			10					TTTGAACACTACTTTGGGTTT	0.463000																								0							SO:0001583	missense			ENST00000493014.1	1	1	hg19	CCDS58845.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.524255	0.85600	.	.	ENSG00000151576	ENST00000485050;ENST00000281273;ENST00000479882;ENST00000493014	.	.	.	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	D	0.85004	0.5598	M	0.89785	3.06	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	D	0.87953	0.2725	9	0.87932	D	0	-16.4311	15.2149	0.73258	1.0:0.0:0.0:0.0	.	281;387	B7Z472;Q9H974	.;QTRD1_HUMAN	C	399;387;264;281	.	ENSP00000281273:Y387C	Y	+	2	0	QTRTD1	115287353	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.273000	0.89887	2.333000	0.79357	0.533000	0.62120	TAC		TCGA-IB-7889-01A-11D-2154-08	QTRTD1-004	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000354711.1	1	0	1	30	565	0	97	1	2.395284e-01	8	10	0	97	2		0	0	0	0	0	2	1	1.000000	30	561	0	96	2		0	0	0	0	97	2	-5.601550	1	1	121412	1	21	1	0	0	0	1.985992	0	0.220000	1.900000	0.204244	0.440000	0.300000	0.620000	0.450000	0.459686	0.440000	0	0.370000	0.540000
SYNPO2	171024	broad.mit.edu	37	4	119948009	119948009	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr4:119948009C>T	ENST00000429713.2	+	3	667	c.485C>T	c.(484-486)cCg>cTg	p.P162L	SYNPO2_ENST00000448416.2_Intron|SYNPO2_ENST00000307142.4_Missense_Mutation_p.P162L|SYNPO2_ENST00000434046.2_Missense_Mutation_p.P162L	NM_001128933.1	NP_001122405.1	Q9UMS6	SYNP2_HUMAN	synaptopodin 2			64					GAAACAGGCCCGAGCTACCAA	0.547000																								0							SO:0001583	missense			ENST00000429713.2	1	1	hg19	CCDS47129.1	.	.	.	.	.	.	.	.	.	.	C	0.003	-2.429248	0.00184	.	.	ENSG00000172403	ENST00000307142;ENST00000429713;ENST00000434046	T;T;T	0.06768	3.26;3.26;3.26	4.56	-5.91	0.02269	.	0.414976	0.17348	N	0.177482	T	0.01489	0.0048	N	0.00237	-1.79	0.09310	N	0.999996	B;B;B;B	0.06786	0.001;0.0;0.0;0.0	B;B;B;B	0.04013	0.0;0.001;0.0;0.0	T	0.47774	-0.9091	10	0.31617	T	0.26	0.9506	8.3027	0.32023	0.1979:0.5711:0.0:0.231	.	162;162;162;162	B9EG60;Q9UMS6-2;E9PEM2;Q9UMS6	.;.;.;SYNP2_HUMAN	L	162	ENSP00000306015:P162L;ENSP00000395143:P162L;ENSP00000390965:P162L	ENSP00000306015:P162L	P	+	2	0	SYNPO2	120167457	0.001000	0.12720	0.000000	0.03702	0.014000	0.08584	0.077000	0.14738	-0.619000	0.05648	-1.181000	0.01715	CCG		TCGA-IB-7889-01A-11D-2154-08	SYNPO2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364020.1	1	0	1	38	196	0	42	0	0	0	1	0	42	2		0	0	0	0	0	2	1	1.000000	38	196	0	41	2		0	0	0	0	42	2	-2.957194	1	1	0	0		1	0	0	0	2.008776	0	0.220000	1.900000	0.213075	0.990000	0.990000	1.000000	1.000000	0.999493	0.990000	1	0.990000	1.000000
CCRN4L	25819	broad.mit.edu	37	4	139966043	139966043	+	Silent	SNP	C	C	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr4:139966043C>T	ENST00000280614.2	+	3	904	c.711C>T	c.(709-711)gcC>gcT	p.A237A	ELF2_ENST00000515489.1_Intron	NM_012118.2	NP_036250.2	Q9UK39	NOCT_HUMAN	CCR4 carbon catabolite repression 4-like (S. cerevisiae)			9	all_hematologic(180;0.162)				ATGGTTGTGCCTTATTTTTTC	0.463000													Ovarian(144;566 1842 19130 21379 22209)											0							SO:0001819	synonymous_variant			ENST00000280614.2	1	1	hg19	CCDS3743.1																																																																																				TCGA-IB-7889-01A-11D-2154-08	CCRN4L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257231.3	0	0	0	30	387	0	74	1	2.500807e-01	4	9	0	74	2		0	0	0	0	0	2	1	1.000000	27	384	0	72	2		0	0	0	0	74	2	-2.920856	1	1	0	0		1	0	0	0	2.008776	0	0.220000	1.900000	0.213075	0.640000	0.440000	0.880000	0.640000	0.660609	0.640000	0	0.540000	0.770000
PCDHB13	56123	broad.mit.edu	37	5	140595561	140595561	+	Silent	SNP	C	C	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr5:140595561C>T	ENST00000341948.4	+	1	2053	c.1866C>T	c.(1864-1866)ggC>ggT	p.G622G		NM_018933.2	NP_061756.1	Q9Y5F0	PCDBD_HUMAN	protocadherin beta 13			66			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)		CGCACAATGGCGAGGTGCGCA	0.701000																								0							SO:0001819	synonymous_variant			ENST00000341948.4	1	0	hg19	CCDS4255.1																																																																																				TCGA-IB-7889-01A-11D-2154-08	PCDHB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251810.1	1	0	0	20	268	0	61		0	0	0	0	61	2		0	0	0	0	0	2	1	0.999934	13	201	0	121	2		0	0	0	0	61	2	-19.999950	1	1	0	0		1	0	0	0	1.998860	0	0.220000	1.900000	0.207800	0.620000	0.390000	0.900000	0.610000	0.639125	0.620000	0	0.500000	0.770000
FOXQ1	94234	broad.mit.edu	37	6	1313384	1313384	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr6:1313384C>T	ENST00000296839.2	+	1	710	c.445C>T	c.(445-447)Ctc>Ttc	p.L149F		NM_033260.3	NP_150285.3	Q9C009	FOXQ1_HUMAN	forkhead box Q1			2	Ovarian(93;0.0733)	Breast(5;0.052)|all_lung(73;0.0713)|all_hematologic(90;0.0895)			CAACGAGTACCTCATGGGCAA	0.657000																								0							SO:0001583	missense			ENST00000296839.2	1	1	hg19	CCDS4471.1	.	.	.	.	.	.	.	.	.	.	C	15.40	2.821825	0.50633	.	.	ENSG00000164379	ENST00000296839	D	0.96011	-3.88	3.87	1.9	0.25705	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (4);	0.093430	0.44483	N	0.000458	D	0.91415	0.7291	N	0.25426	0.745	0.45822	D	0.998695	D	0.57571	0.98	P	0.59761	0.863	D	0.90412	0.4410	10	0.66056	D	0.02	.	6.7197	0.23323	0.1739:0.7262:0.0:0.1	.	149	Q9C009	FOXQ1_HUMAN	F	149	ENSP00000296839:L149F	ENSP00000296839:L149F	L	+	1	0	FOXQ1	1258384	0.969000	0.33509	0.955000	0.39395	0.340000	0.28889	0.219000	0.17641	0.643000	0.30638	-1.206000	0.01644	CTC		TCGA-IB-7889-01A-11D-2154-08	FOXQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043410.1	1	0	0	14	264	0	61	1	4.565631e-01	2	27	0	61	2		0	0	0	0	0	2	1	0.999769	14	263	0	61	2		0	0	0	0	61	2	-16.454680	1	1	0	0		1	0	0	0	1.871651	1	0.220000	1.900000	0.154930	0.420000	0.240000	0.660000	0.420000	0.440724	0.420000	0	0.320000	0.550000
ZAN	7455	broad.mit.edu	37	7	100377265	100377265	+	RNA	SNP	A	A	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr7:100377265A>T	ENST00000348028.3	+	0	6679				ZAN_ENST00000546292.1_RNA|ZAN_ENST00000421100.1_RNA|ZAN_ENST00000546213.1_RNA|ZAN_ENST00000349350.6_RNA|ZAN_ENST00000449052.1_RNA|ZAN_ENST00000542585.1_RNA|ZAN_ENST00000427578.1_RNA|ZAN_ENST00000443370.1_RNA|ZAN_ENST00000538115.1_RNA			Q9Y493	ZAN_HUMAN	zonadhesin (gene/pseudogene)			139	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)		ACCCTCTGTGAGTTCGGAGGT	0.652000																								0											ENST00000348028.3	0	1	hg19		.	.	.	.	.	.	.	.	.	.	A	8.808	0.934469	0.18206	.	.	ENSG00000146839	ENST00000546292;ENST00000538115;ENST00000542585	T;T;T	0.77877	-1.13;-1.13;-1.13	4.17	1.81	0.25067	Uncharacterised domain, cysteine-rich (2);	1.310930	0.05416	N	0.543352	D	0.83667	0.5304	.	.	.	0.34357	D	0.690562	D;D	0.63046	0.99;0.992	P;D	0.63283	0.858;0.913	T	0.73940	-0.3824	9	0.46703	T	0.11	.	5.6012	0.17355	0.7788:0.0:0.2212:0.0	.	2171;2172	F5H0T8;Q9Y493	.;ZAN_HUMAN	V	2171	ENSP00000445943:E2171V;ENSP00000445091:E2171V;ENSP00000444427:E2171V	ENSP00000445091:E2171V	E	+	2	0	ZAN	100215201	0.412000	0.25392	0.247000	0.24249	0.095000	0.18619	0.900000	0.28431	0.419000	0.25927	0.456000	0.33151	GAG		TCGA-IB-7889-01A-11D-2154-08	ZAN-006	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000347214.1	0	0	0	7	43	0	12		0	0	0	0	12	2		0	0	0	0	0	2	1	0.983297	7	43	0	12	2		0	0	0	0	12	2	-14.445940	1	1	0	0		1	1	2	3	2.094265	0	0.220000	1.900000	0.235968	0.990000	0.620000	1.000000	1.000000	0.962772	0.990000	1	0.940000	1.000000
SPAM1	6677	broad.mit.edu	37	7	123599604	123599604	+	Silent	SNP	C	C	T	rs146075363		TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr7:123599604C>T	ENST00000439500.1	+	6	1724	c.1111C>T	c.(1111-1113)Cta>Tta	p.L371L	SPAM1_ENST00000223028.7_Silent_p.L371L|SPAM1_ENST00000460182.1_Silent_p.L371L|SPAM1_ENST00000340011.5_Silent_p.L371L|SPAM1_ENST00000402183.2_Silent_p.L371L	NM_001174045.1|NM_001174046.1	NP_001167516.1|NP_001167517.1	P38567	HYALP_HUMAN	sperm adhesion molecule 1 (PH-20 hyaluronidase, zona pellucida binding)			46					CAACGTCACACTAGCAGCCAA	0.378000																								0							SO:0001819	synonymous_variant			ENST00000439500.1	1	1	hg19	CCDS5791.1																																																																																				TCGA-IB-7889-01A-11D-2154-08	SPAM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000348309.1	1	0	1	37	305	0	56		0	0	0	0	56	2		0	0	0	0	0	2	1	1.000000	37	302	0	56	2		0	0	0	0	56	2	-14.405540	1	1	121354	1	25	1	1	2	3	2.094265	0	0.220000	1.900000	0.235968	0.990000	0.730000	1.000000	1.000000	0.953776	0.990000	1	0.870000	1.000000
BBS9	27241	broad.mit.edu	37	7	33407475	33407475	+	Splice_Site	SNP	G	G	A			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr7:33407475G>A	ENST00000242067.6	+	17	2310		c.e17+1		BBS9_ENST00000355070.2_Splice_Site|BBS9_ENST00000350941.3_Splice_Site|BBS9_ENST00000354265.4_Splice_Site|BBS9_ENST00000396127.2_Splice_Site	NM_198428.2	NP_940820.1	Q3SYG4	PTHB1_HUMAN	Bardet-Biedl syndrome 9		BBS9/PKD1L1(2)	50			GBM - Glioblastoma multiforme(11;0.0894)		AAAACTTCTCGTAAGTAAAAC	0.373000									Bardet-Biedl syndrome															0		GRCh37	CS055613	BBS9	S		SO:0001630	splice_region_variant	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	ENST00000242067.6	1	1	hg19	CCDS43566.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.496770	0.85069	.	.	ENSG00000122507	ENST00000242067;ENST00000350941;ENST00000396127;ENST00000355070;ENST00000354265;ENST00000396132;ENST00000434373	.	.	.	5.48	5.48	0.80851	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.9484	0.92630	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	BBS9	33374000	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.787000	0.75099	2.572000	0.86782	0.655000	0.94253	.		TCGA-IB-7889-01A-11D-2154-08	BBS9-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000329064.1	1	0	0	14	266	0	49		0	0	0	0	49	2		0	0	0	0	0	2	1	0.999769	14	265	0	49	2		0	0	0	0	49	2	-4.463742	1	1	0	0		1	1	3	4	2.330104	1	0.220000	1.900000	0.309612	0.580000	0.310000	1.000000	0.510000	0.649202	0.580000	0	0.420000	1.000000
PRKAR1B	5575	broad.mit.edu	37	7	720280	720280	+	Silent	SNP	C	C	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr7:720280C>T	ENST00000406797.1	-	3	435	c.261G>A	c.(259-261)ccG>ccA	p.P87P	PRKAR1B_ENST00000403562.1_Silent_p.P87P|PRKAR1B_ENST00000360274.4_Silent_p.P87P|PRKAR1B_ENST00000537384.1_Silent_p.P87P|PRKAR1B_ENST00000544935.1_Silent_p.P87P	NM_001164761.1	NP_001158233.1	P31321	KAP1_HUMAN	protein kinase, cAMP-dependent, regulatory, type I, beta			17		Ovarian(82;0.0779)			CCACAGGGTTCGGGGGGGTGG	0.622000																								0							SO:0001819	synonymous_variant			ENST00000406797.1	1	0	hg19	CCDS34579.1																																																																																				TCGA-IB-7889-01A-11D-2154-08	PRKAR1B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322525.1	1	0	1	52	431	0	45	0	3.824771e-01	1	11	0	45	2		0	0	0	0	0	2	1	1.000000	52	423	0	42	2		0	0	0	0	45	2	-1.639820	0	1	0	0		1	1	3	4	2.330104	1	0.220000	1.900000	0.309612	0.990000	0.850000	1.000000	1.000000	0.987826	0.990000	1	0.990000	1.000000
RGS22	26166	broad.mit.edu	37	8	101076206	101076206	+	Missense_Mutation	SNP	A	A	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr8:101076206A>T	ENST00000360863.6	-	8	984	c.790T>A	c.(790-792)Ttg>Atg	p.L264M	RGS22_ENST00000523287.1_Missense_Mutation_p.L83M|RGS22_ENST00000523437.1_Missense_Mutation_p.L252M	NM_015668.3	NP_056483.3	Q8NE09	RGS22_HUMAN	regulator of G-protein signaling 22		RGS22/SYCP1(2)	68			Epithelial(11;6.71e-08)|all cancers(13;4.19e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169)		TCAGAAATCAATTTGTTGGTT	0.343000																								0							SO:0001583	missense			ENST00000360863.6	1	1	hg19	CCDS43758.1	.	.	.	.	.	.	.	.	.	.	A	14.54	2.564891	0.45694	.	.	ENSG00000132554	ENST00000360863;ENST00000427793;ENST00000523287;ENST00000523437	T;T;T	0.32988	1.45;1.44;1.43	5.45	0.102	0.14522	.	2.260420	0.01579	N	0.020975	T	0.30386	0.0763	L	0.60455	1.87	0.09310	N	1	P;P;B	0.37864	0.61;0.61;0.065	B;B;B	0.39185	0.293;0.293;0.037	T	0.09509	-1.0671	10	0.39692	T	0.17	.	1.6829	0.02835	0.4861:0.1481:0.0809:0.2849	.	252;264;83	A8K944;Q8NE09;G3V112	.;RGS22_HUMAN;.	M	264;252;83;252	ENSP00000354109:L264M;ENSP00000429382:L83M;ENSP00000428212:L252M	ENSP00000354109:L264M	L	-	1	2	RGS22	101145382	0.000000	0.05858	0.000000	0.03702	0.337000	0.28794	-0.768000	0.04715	-0.138000	0.11434	0.528000	0.53228	TTG		TCGA-IB-7889-01A-11D-2154-08	RGS22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380365.1	1	0	0	51	870	0	109	0	0	0	1	0	109	2		0	0	0	0	0	2	1	1.000000	50	858	0	109	2		0	0	0	0	109	2	-20.000000	1	1	0	0		1	1	3	4	2.338081	1	0.220000	1.900000	0.324090	0.600000	0.440000	1.000000	0.580000	0.672623	0.600000	0	0.510000	1.000000
TRPS1	7227	broad.mit.edu	37	8	116616325	116616325	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr8:116616325C>T	ENST00000220888.5	-	3	1991	c.1832G>A	c.(1831-1833)cGa>cAa	p.R611Q	TRPS1_ENST00000520276.1_Missense_Mutation_p.R615Q|TRPS1_ENST00000519076.1_Intron|TRPS1_ENST00000519674.1_Missense_Mutation_p.R611Q|TRPS1_ENST00000395715.3_Missense_Mutation_p.R624Q			Q9UHF7	TRPS1_HUMAN	trichorhinophalangeal syndrome I			111	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)		ATGTTTGACTCGCGAGCTTCC	0.478000									Langer-Giedion syndrome															0							SO:0001583	missense	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II	ENST00000220888.5	1	1	hg19		.	.	.	.	.	.	.	.	.	.	C	15.09	2.729920	0.48833	.	.	ENSG00000104447	ENST00000395715;ENST00000220888;ENST00000520276;ENST00000519674	T;T;T;T	0.10960	2.82;2.82;2.82;2.82	5.87	5.87	0.94306	.	0.183848	0.49305	D	0.000160	T	0.23886	0.0578	L	0.27053	0.805	0.40856	D	0.983791	D;D;D	0.69078	0.991;0.994;0.997	P;D;D	0.69479	0.563;0.921;0.964	T	0.00717	-1.1596	10	0.72032	D	0.01	.	20.5827	0.99408	0.0:1.0:0.0:0.0	.	615;611;624	Q9UHF7-3;Q9UHF7;Q9UHF7-2	.;TRPS1_HUMAN;.	Q	624;611;615;611	ENSP00000379065:R624Q;ENSP00000220888:R611Q;ENSP00000428680:R615Q;ENSP00000429174:R611Q	ENSP00000220888:R611Q	R	-	2	0	TRPS1	116685500	1.000000	0.71417	0.587000	0.28692	0.015000	0.08874	5.682000	0.68182	2.941000	0.99782	0.655000	0.94253	CGA		TCGA-IB-7889-01A-11D-2154-08	TRPS1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000286436.3	1	0	1	56	308	0	46	0	0	0	1	0	46	2		0	0	0	0	0	2	1	1.000000	55	305	0	45	2		0	0	0	0	46	2	-2.926725	1	1	120940	1	30	1	2	2	4	2.208572	1	0.220000	1.900000	0.287411	0.990000	0.990000	1.000000	1.000000	0.999979	0.990000	1	0.990000	1.000000
ASH2L	9070	broad.mit.edu	37	8	37964684	37964684	+	Splice_Site	SNP	C	C	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr8:37964684C>T	ENST00000343823.6	+	3	710	c.401C>T	c.(400-402)tCa>tTa	p.S134L	ASH2L_ENST00000428278.2_Splice_Site_p.S40L|ASH2L_ENST00000545394.1_Intron|ASH2L_ENST00000250635.7_Splice_Site_p.S40L|ASH2L_ENST00000521652.1_Splice_Site_p.S40L	NM_004674.4	NP_004665.2	Q9UBL3	ASH2L_HUMAN	ash2 (absent, small, or homeotic)-like (Drosophila)			19	Colorectal(12;0.000501)	Lung NSC(58;0.0295)|all_lung(54;0.0413)			ATAGATACCTCGTGAGTACTT	0.408000																								0							SO:0001630	splice_region_variant			ENST00000343823.6	1	0	hg19	CCDS6101.1	.	.	.	.	.	.	.	.	.	.	C	18.82	3.705343	0.68615	.	.	ENSG00000129691	ENST00000343823;ENST00000250635;ENST00000517719;ENST00000428278;ENST00000521652	T;T;T;T;T	0.19806	2.12;2.12;2.12;2.12;2.12	4.82	4.82	0.62117	.	0.114028	0.64402	D	0.000014	T	0.16214	0.0390	N	0.19112	0.55	0.80722	D	1	B;B	0.27732	0.187;0.061	B;B	0.21151	0.033;0.005	T	0.05468	-1.0883	10	0.62326	D	0.03	.	17.9105	0.88932	0.0:1.0:0.0:0.0	.	40;134	Q9UBL3-2;Q9UBL3	.;ASH2L_HUMAN	L	134;40;148;40;40	ENSP00000340896:S134L;ENSP00000250635:S40L;ENSP00000428877:S148L;ENSP00000395310:S40L;ENSP00000430259:S40L	ENSP00000250635:S40L	S	+	2	0	ASH2L	38083841	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	2.090000	0.41682	2.223000	0.72356	0.557000	0.71058	TCA		TCGA-IB-7889-01A-11D-2154-08	ASH2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376749.4	1	0	0	33	454	0	60	1	8.169225e-01	2	43	0	60	2		0	0	0	0	0	2	1	1.000000	33	450	0	60	2		0	0	0	0	60	2	-2.744761	1	1	0	0		1	2	2	4	2.146007	1	0.220000	1.900000	0.268293	0.690000	0.470000	1.000000	0.650000	0.736590	0.690000	0	0.570000	1.000000
WHSC1L1	54904	broad.mit.edu	37	8	38187221	38187221	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr8:38187221G>T	ENST00000317025.8	-	6	1773	c.1256C>A	c.(1255-1257)aCc>aAc	p.T419N	WHSC1L1_ENST00000316985.3_Missense_Mutation_p.T419N|WHSC1L1_ENST00000527502.1_Missense_Mutation_p.T419N|WHSC1L1_ENST00000433384.2_Missense_Mutation_p.T419N	NM_023034.1	NP_075447.1	Q9BZ95	NSD3_HUMAN	Wolf-Hirschhorn syndrome candidate 1-like 1			24	Colorectal(12;0.000442)|Esophageal squamous(3;0.0725)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065)	Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511)		TGGTCGTCGGGTTTTTTTAAC	0.433000			T	NUP98	AML										Dom	yes		8	8p12	54904	Wolf-Hirschhorn syndrome candidate 1-like 1 (NSD3)		L	0							SO:0001583	missense			ENST00000317025.8	1	1	hg19	CCDS43729.1	.	.	.	.	.	.	.	.	.	.	G	8.652	0.898580	0.17686	.	.	ENSG00000147548	ENST00000433384;ENST00000317025;ENST00000446459;ENST00000527502;ENST00000316985	D;D;D;T	0.95137	-3.62;-3.62;-3.62;-0.48	5.6	4.65	0.58169	.	0.608282	0.13904	U	0.354722	D	0.82870	0.5131	N	0.02011	-0.69	0.25889	N	0.983491	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.0;0.0;0.001;0.0	T	0.68580	-0.5371	10	0.12103	T	0.63	.	11.164	0.48533	0.0:0.0:0.5948:0.4052	.	419;419;419;419	B7ZL11;Q9BZ95-2;Q9BZ95-3;Q9BZ95	.;.;.;NSD3_HUMAN	N	419;419;356;419;419	ENSP00000393284:T419N;ENSP00000313983:T419N;ENSP00000434730:T419N;ENSP00000313410:T419N	ENSP00000313410:T419N	T	-	2	0	WHSC1L1	38306378	0.785000	0.28726	0.870000	0.34147	0.989000	0.77384	1.199000	0.32235	2.634000	0.89283	0.650000	0.86243	ACC		TCGA-IB-7889-01A-11D-2154-08	WHSC1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381924.3	1	0	0	19	429	0	65	1	8.856142e-01	7	81	0	65	2		0	0	0	0	0	2	1	0.999989	19	421	0	63	2		0	0	0	0	65	2	-3.210257	1	1	0	0		1	2	2	4	2.146007	1	0.220000	1.900000	0.268293	0.440000	0.260000	1.000000	0.420000	0.543674	0.440000	0	0.340000	1.000000
PKN3	29941	broad.mit.edu	37	9	131477728	131477728	+	Silent	SNP	C	C	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr9:131477728C>T	ENST00000291906.4	+	15	2190	c.1797C>T	c.(1795-1797)gaC>gaT	p.D599D	PKN3_ENST00000485301.1_Intron	NM_013355.3	NP_037487.2	Q6P5Z2	PKN3_HUMAN	protein kinase N3	p.D599D(1)		24					TCAGCCGGGACGAGATAGAGA	0.612000																								1	Substitution - coding silent(1)						SO:0001819	synonymous_variant			ENST00000291906.4	1	1	hg19	CCDS6908.1																																																																																				TCGA-IB-7889-01A-11D-2154-08	PKN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054487.1	1	0	0	13	255	0	56	1	8.674753e-01	7	66	0	56	2		0	0	0	0	0	2	1	0.999547	12	254	0	56	2		0	0	0	0	56	2	-15.209500	1	1	0	0		1	1	2	3	2.022956	0	0.220000	1.900000	0.221712	0.450000	0.250000	0.760000	0.440000	0.471469	0.450000	0	0.340000	0.590000
CDKN2A	1029	broad.mit.edu	37	9	21971120	21971120	+	Nonsense_Mutation	SNP	G	G	A	rs121913388		TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr9:21971120G>A	ENST00000304494.5	-	2	508	c.238C>T	c.(238-240)Cga>Tga	p.R80*	CDKN2A_ENST00000530628.2_Missense_Mutation_p.P94L|CDKN2A_ENST00000498124.1_Nonsense_Mutation_p.R80*|CDKN2A_ENST00000579755.1_Missense_Mutation_p.P94L|CDKN2A_ENST00000494262.1_Nonsense_Mutation_p.R29*|CDKN2A_ENST00000497750.1_Nonsense_Mutation_p.R29*|CDKN2A_ENST00000578845.2_Nonsense_Mutation_p.R29*|CDKN2A_ENST00000446177.1_Nonsense_Mutation_p.R80*|CDKN2A_ENST00000361570.3_Missense_Mutation_p.P135L|CDKN2A_ENST00000498628.2_Nonsense_Mutation_p.R29*|CDKN2A_ENST00000579122.1_Nonsense_Mutation_p.R80*|RP11-145E5.5_ENST00000404796.2_Intron|CDKN2A_ENST00000479692.2_Nonsense_Mutation_p.R29*	NM_000077.4	NP_000068.1	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A	p.0?(1315)|p.R80*(100)|p.?(44)|p.P135L(7)|p.L65fs*38(1)|p.T79fs*37(1)|p.0(1)|p.A76fs*64(1)|p.T79fs*65(1)|p.E61_L94del(1)|p.A68fs*3(1)|p.R80fs*34(1)		4199		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)			TGCACGGGTCGGGTGAGAGTG	0.726000	R80*(HSC4_UPPER_AERODIGESTIVE_TRACT)|R80*(MEWO_SKIN)	17								HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)														1474	Whole gene deletion(1316)|Substitution - Nonsense(100)|Unknown(44)|Substitution - Missense(7)|Deletion - Frameshift(6)|Deletion - In frame(1)	GRCh37	CM014695	CDKN2A	M	rs121913388	SO:0001587	stop_gained			ENST00000304494.5	0	1	hg19	CCDS6510.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	39|39	7.328457|7.328457	0.98214|0.98214	.|.	.|.	ENSG00000147889|ENSG00000147889	ENST00000361570;ENST00000530628|ENST00000304494;ENST00000446177	D;D|.	0.86497|.	-2.13;-2.02|.	5.93|5.93	5.01|5.01	0.66863|0.66863	.|.	0.000000|.	0.37136|.	N|.	0.002233|.	T|.	0.44561|.	0.1299|.	L|L	0.36672|0.36672	1.1|1.1	0.47511|0.47511	D|D	0.999443|0.999443	D|.	0.59357|.	0.985|.	B|.	0.40602|.	0.334|.	T|.	0.34825|.	-0.9813|.	10|.	0.13108|0.02654	T|T	0.6|1	-2.989|-2.989	8.7197|8.7197	0.34434|0.34434	0.0759:0.0:0.7715:0.1526|0.0759:0.0:0.7715:0.1526	.|.	135|.	Q8N726|.	CD2A2_HUMAN|.	L|X	135;94|80	ENSP00000355153:P135L;ENSP00000432664:P94L|.	ENSP00000355153:P135L|ENSP00000307101:R80X	P|R	-|-	2|1	0|2	CDKN2A|CDKN2A	21961120|21961120	0.995000|0.995000	0.38212|0.38212	1.000000|1.000000	0.80357|0.80357	0.899000|0.899000	0.52679|0.52679	2.363000|2.363000	0.44178|0.44178	1.464000|1.464000	0.47987|0.47987	0.650000|0.650000	0.86243|0.86243	CCG|CGA		TCGA-IB-7889-01A-11D-2154-08	CDKN2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000051915.1	1	0	0	16	117	0	24		0	0	0	0	24	2	1	7.398962e-01	5	16	0	141	2	1	0.999630	14	88	0	21	2		0	0	0	0	24	2	-2.749063	1	1	0	0		1	0	1	1	1.860055	1	0.220000	1.900000	0.134295	0.880000	0.560000	1.000000	1.000000	0.866427	0.880000	1	0.720000	1.000000
