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
PRTFDC1	56952	broad.mit.edu	37	10	25226219	25226219	+	Frame_Shift_Del	DEL	C	C	-			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr10:25226219delC	ENST00000320152.6	-	3	261	c.233delG	c.(232-234)ggtfs	p.G78fs	PRTFDC1_ENST00000376376.3_Frame_Shift_Del_p.G78fs|PRTFDC1_ENST00000376378.1_Frame_Shift_Del_p.G78fs	NM_020200.5	NP_064585.1	Q9NRG1	PRDC1_HUMAN	phosphoribosyl transferase domain containing 1			9					GAATTTGTAACCTCCTTTAAG	0.378000																								0							SO:0001589	frameshift_variant			ENST00000320152.6	1	1	hg19	CCDS7145.1																																																																																				TCGA-HZ-A8P0-01A-11D-A36O-08	PRTFDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047243.2	1	0	0	79	312	0	96	1	9.175640e-01	3	16	0	96	2			0	0	0	0		1	1.000000	83	310	2	96	20	0	0	0	0	0	0		-3.323268	1	1	0	0		1	0	1	1	1.612117	1	0.380000	1.960000	0.234568	0.840000	6.900000e-01	0.980000	0.850000	0.850073	0.840000	0	7.600000e-01	9.300000e-01
MUC6	4588	broad.mit.edu	37	11	1025891	1025892	+	Frame_Shift_Ins	INS	-	-	T			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08			-	T	-	-		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr11:1025891_1025892insT	ENST00000421673.2	-	22	2762_2763	c.2712_2713insA	c.(2710-2715)tcacagfs	p.Q905fs		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming			80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)			AAGGTGGGCTGTGAGTCGTTGA	0.658000																								0							SO:0001589	frameshift_variant			ENST00000421673.2	0	1	hg19	CCDS44513.1																																																																																				TCGA-HZ-A8P0-01A-11D-A36O-08	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	1	0	0	15	116	0	31	0	9.999623e-01	0	147	0	31	2			0	0	0	0		1	0.999910	15	117	0	32	2	0	0	0	0	0	0		-19.999290	1	1	0	0		1	1	2	3	2.036293	0	0.380000	1.960000	0.385835	0.620000	3.600000e-01	1.000000	0.600000	0.644657	0.620000	0	4.800000e-01	8.000000e-01
STK11	6794	broad.mit.edu	37	19	1207092	1207092	+	Frame_Shift_Del	DEL	C	C	-			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08			C	-	C	C		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr19:1207092delC	ENST00000326873.7	+	1	1353	c.180delC	c.(178-180)tacfs	p.Y60fs	STK11_ENST00000585748.1_Intron	NM_000455.4	NP_000446.1	Q15831	STK11_HUMAN	serine/threonine kinase 11	p.0?(20)|p.?(3)|p.Y60fs*1(3)|p.Y60*(2)		328		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Renal(1328;0.0183)|Hepatocellular(1079;0.137)			AAGGCTCTTACGGCAAGGTGA	0.622000		14	D, Mis, N, F, S		NSCLC, pancreatic	jejunal harmartoma, ovarian, testicular, pancreatic			Peutz-Jeghers syndrome	TSP Lung(3;<1E-08)				yes	Rec	yes	Peutz-Jeghers syndrome	19	19p13.3	6794	serine/threonine kinase 11 gene (LKB1)		E, M, O	28	Whole gene deletion(20)|Deletion - Frameshift(4)|Substitution - Nonsense(2)|Unknown(2)	GRCh37	CD064644|CM981863|CM991149	STK11	D|M		SO:0001589	frameshift_variant	Familial Cancer Database	PJS, Hamartous Intestinal Polyposis	ENST00000326873.7	1	1	hg19	CCDS45896.1																																																																																				TCGA-HZ-A8P0-01A-11D-A36O-08	STK11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449839.3	1	0	0	52	167	0	37	1	1	21	72	0	37	2	1	1	324	962	0	879	2	1	1.000000	52	162	0	37	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	0	2	2	2.079930	1	0.380000	1.960000	0.380000	0.990000	9.600000e-01	1.000000	1.000000	0.997862	0.990000	1	9.900000e-01	1
ARHGAP22	58504	broad.mit.edu	37	10	49667870	49667870	+	Silent	SNP	C	C	T			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr10:49667870C>T	ENST00000249601.4	-	5	812	c.516G>A	c.(514-516)gcG>gcA	p.A172A	ARHGAP22_ENST00000417247.2_Silent_p.A82A|ARHGAP22_ENST00000435790.2_Silent_p.A178A|ARHGAP22_ENST00000417912.2_Silent_p.A188A|ARHGAP22_ENST00000374172.1_Silent_p.A63A|ARHGAP22_ENST00000374170.1_Silent_p.A82A	NM_001256024.1|NM_021226.3	NP_001242953.1|NP_067049.2	Q7Z5H3	RHG22_HUMAN	Rho GTPase activating protein 22			18					CCAGCAGGGGCGCCAGGCGGG	0.652000																								0							SO:0001819	synonymous_variant			ENST00000249601.4	1	1	hg19	CCDS7227.1																																																																																				TCGA-HZ-A8P0-01A-11D-A36O-08	ARHGAP22-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000358767.1	1	0	1	67	300	0	86	0	4.485014e-01	0	8	0	86	2		0	0	0	0	0	2	1	1.000000	67	292	0	84	2		0	0	0	0	86	2	-20.000000	1	1	0	0		1	0	0	0	1.938979	0	0.380000	1.960000	0.355509	0.910000	7.300000e-01	1.000000	1.000000	0.913408	0.910000	1	8.200000e-01	1
SLC18A3	6572	broad.mit.edu	37	10	50820227	50820227	+	Nonsense_Mutation	SNP	G	G	T	rs144340824		TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr10:50820227G>T	ENST00000374115.3	+	1	1881	c.1441G>T	c.(1441-1443)Gag>Tag	p.E481*	CHAT_ENST00000337653.2_5'Flank|CHAT_ENST00000455728.2_5'Flank|CHAT_ENST00000395559.2_5'Flank|CHAT_ENST00000395562.2_5'Flank|CHAT_ENST00000339797.1_Intron|CHAT_ENST00000351556.3_5'Flank	NM_003055.2	NP_003046.2	Q16572	VACHT_HUMAN	solute carrier family 18 (vesicular acetylcholine transporter), member 3			43					CTCCCGTTCCGAGCGCGATGT	0.657000																								0							SO:0001587	stop_gained			ENST00000374115.3	0	1	hg19	CCDS7231.1	.	.	.	.	.	.	.	.	.	.	G	41	8.864615	0.98982	.	.	ENSG00000187714	ENST00000374115	.	.	.	4.87	4.87	0.63330	.	0.000000	0.85682	U	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.21014	T	0.42	-18.4589	18.0047	0.89207	0.0:0.0:1.0:0.0	.	.	.	.	X	481	.	ENSP00000363229:E481X	E	+	1	0	SLC18A3	50490233	1.000000	0.71417	0.976000	0.42696	0.726000	0.41606	9.869000	0.99810	2.262000	0.75019	0.561000	0.74099	GAG		TCGA-HZ-A8P0-01A-11D-A36O-08	SLC18A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047995.1	0	0	0	5	294	0	63		0	0	0	0	63	2		0	0	0	0	0	2	1	0.936393	4	292	0	63	2		0	0	0	0	63	2	-4.014923	1	0	0	0		1	0	0	0	1.938979	0	0.380000	1.960000	0.355509	0.080000	2.000000e-02	0.190000	0.090000	0.100316	0.080000	0	5.000000e-02	1.400000e-01
WAPAL	23063	broad.mit.edu	37	10	88260206	88260206	+	Missense_Mutation	SNP	T	T	G			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr10:88260206T>G	ENST00000298767.5	-	3	1266	c.794A>C	c.(793-795)gAt>gCt	p.D265A		NM_015045.2	NP_055860.1	Q7Z5K2	WAPL_HUMAN	wings apart-like homolog (Drosophila)			31					AAAATCGTCATCCTTCATCTC	0.363000																								0							SO:0001583	missense			ENST00000298767.5	1	1	hg19	CCDS7375.1	.	.	.	.	.	.	.	.	.	.	T	10.76	1.441746	0.25900	.	.	ENSG00000062650	ENST00000342368;ENST00000298767;ENST00000372076	T	0.47528	0.84	5.77	3.4	0.38934	.	0.535917	0.20186	N	0.097418	T	0.35740	0.0942	L	0.34521	1.04	0.80722	D	1	B;B;B	0.22683	0.043;0.043;0.073	B;B;B	0.21151	0.01;0.01;0.033	T	0.23404	-1.0189	10	0.72032	D	0.01	.	9.4528	0.38736	0.0:0.1534:0.0:0.8466	.	265;265;308	B2RTX8;Q7Z5K2;Q7Z5K2-2	.;WAPL_HUMAN;.	A	350;265;350	ENSP00000298767:D265A	ENSP00000298767:D265A	D	-	2	0	WAPAL	88250186	1.000000	0.71417	1.000000	0.80357	0.852000	0.48524	1.613000	0.36900	0.996000	0.38943	0.528000	0.53228	GAT		TCGA-HZ-A8P0-01A-11D-A36O-08	WAPAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049151.2	1	0	1	81	256	0	82	1	8.817855e-01	5	9	0	82	2		0	0	0	0	0	2	1	1.000000	80	253	0	80	2		0	0	0	0	82	2	-20.000000	1	1	0	0		1	0	1	1	1.619202	1	0.380000	1.960000	0.234568	0.930000	8.000000e-01	1.000000	0.990000	0.933580	0.930000	1	8.700000e-01	9.900000e-01
KDELC2	143888	broad.mit.edu	37	11	108356954	108356954	+	Missense_Mutation	SNP	C	C	T			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr11:108356954C>T	ENST00000323468.5	-	3	679	c.614G>A	c.(613-615)cGg>cAg	p.R205Q	KDELC2_ENST00000532730.1_5'UTR|KDELC2_ENST00000434945.2_Missense_Mutation_p.R149Q|KDELC2_ENST00000375648.1_Missense_Mutation_p.R149Q	NM_153705.4	NP_714916.3	Q7Z4H8	KDEL2_HUMAN	KDEL (Lys-Asp-Glu-Leu) containing 2			13		all_cancers(61;1.38e-11)|all_epithelial(67;3.16e-07)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)			TAAAGATCTCCGGTAAACATG	0.378000																								0							SO:0001583	missense			ENST00000323468.5	1	1	hg19	CCDS41711.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.800251	0.90538	.	.	ENSG00000178202	ENST00000323468;ENST00000434945;ENST00000375648	T;T;T	0.23754	1.89;1.89;1.89	4.68	3.76	0.43208	.	0.000000	0.85682	D	0.000000	T	0.53690	0.1812	M	0.87381	2.88	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.995	T	0.58842	-0.7565	10	0.31617	T	0.26	-17.0817	14.0815	0.64925	0.0:0.926:0.0:0.074	.	205;149	Q7Z4H8;Q7Z4H8-2	KDEL2_HUMAN;.	Q	205;149;149	ENSP00000315386:R205Q;ENSP00000413429:R149Q;ENSP00000364799:R149Q	ENSP00000315386:R205Q	R	-	2	0	KDELC2	107862164	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.543000	0.82106	1.566000	0.49654	0.655000	0.94253	CGG		TCGA-HZ-A8P0-01A-11D-A36O-08	KDELC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390273.1	1	0	1	69	322	0	99	0	9.039388e-01	1	20	0	99	2		0	0	0	0	0	2	1	1.000000	68	316	0	99	2		0	0	0	0	99	2	-2.619481	1	1	120806	4	41	1	0	0	0	1.993013	0	0.380000	1.960000	0.375252	0.910000	7.300000e-01	1.000000	1.000000	0.912199	0.910000	1	8.200000e-01	1
APOA4	337	broad.mit.edu	37	11	116692155	116692155	+	Nonsense_Mutation	SNP	C	C	A	rs145184607		TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr11:116692155C>A	ENST00000357780.3	-	3	733	c.619G>T	c.(619-621)Gaa>Taa	p.E207*		NM_000482.3	NP_000473.2	P06727	APOA4_HUMAN	apolipoprotein A-IV			20	all_hematologic(175;0.0487)	Breast(348;0.0126)|Medulloblastoma(222;0.0425)|all_hematologic(158;0.0564)|all_neural(223;0.234)			ACTTTGAATTCGTCAGCGTAG	0.622000																								0							SO:0001587	stop_gained			ENST00000357780.3	0	1	hg19	CCDS31681.1	.	.	.	.	.	.	.	.	.	.	C	17.55	3.417451	0.62622	.	.	ENSG00000110244	ENST00000357780	.	.	.	5.2	-0.358	0.12575	.	1.439250	0.04140	N	0.319406	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.38643	T	0.18	-6.1119	7.4216	0.27075	0.0:0.4561:0.2494:0.2944	.	.	.	.	X	207	.	ENSP00000350425:E207X	E	-	1	0	APOA4	116197365	0.000000	0.05858	0.009000	0.14445	0.413000	0.31143	0.036000	0.13819	-0.027000	0.13873	0.563000	0.77884	GAA		TCGA-HZ-A8P0-01A-11D-A36O-08	APOA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106279.2	0	0	0	11	1070	1	301	0	4.496430e-03	0	9	1	301	2		0	0	0	0	0	2	1	0.998143	11	1050	0	300	2		0	0	0	1	301	2	-2.287407	0	1	0	0		1	0	0	0	1.993013	0	0.380000	1.960000	0.375252	0.050000	2.000000e-02	0.090000	0.060000	0.057759	0.050000	0	3.000000e-02	8.000000e-02
DSCAML1	57453	broad.mit.edu	37	11	117387332	117387332	+	Silent	SNP	G	G	A			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr11:117387332G>A	ENST00000321322.6	-	8	1814	c.1813C>T	c.(1813-1815)Ctg>Ttg	p.L605L	DSCAML1_ENST00000527706.1_Silent_p.L335L	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1			110	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)			TTGTCTGGCAGCAGCAGGGCA	0.582000																								0							SO:0001819	synonymous_variant			ENST00000321322.6	0	1	hg19	CCDS8384.1																																																																																				TCGA-HZ-A8P0-01A-11D-A36O-08	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	0	0	0	4	191	0	47		0	0	0	0	47	2		0	0	0	0	0	2	1	0.886308	4	187	0	47	2		0	0	0	0	47	2	-5.685554	1	1	0	0		1	0	0	0	1.993013	0	0.380000	1.960000	0.375252	0.110000	3.000000e-02	0.250000	0.100000	0.131439	0.110000	0	6.000000e-02	1.900000e-01
HYOU1	10525	broad.mit.edu	37	11	118919004	118919004	+	Missense_Mutation	SNP	C	C	T			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr11:118919004C>T	ENST00000404233.3	-	20	2456	c.2332G>A	c.(2332-2334)Gca>Aca	p.A778T	HYOU1_ENST00000525859.1_Missense_Mutation_p.A716T|RP11-110I1.6_ENST00000531886.1_RNA|HYOU1_ENST00000529972.1_Missense_Mutation_p.A716T	NM_001130991.1|NM_006389.3	NP_001124463.1|NP_006380.1	Q9Y4L1	HYOU1_HUMAN	hypoxia up-regulated 1			33	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)|all_hematologic(192;0.207)			CAGGTGGATGCGGCGCTGAGC	0.617000																								0							SO:0001583	missense			ENST00000404233.3	0	1	hg19	CCDS8408.1	.	.	.	.	.	.	.	.	.	.	C	6.079	0.382934	0.11524	.	.	ENSG00000149428	ENST00000404233;ENST00000353883;ENST00000529972;ENST00000535579;ENST00000525859;ENST00000544701	T;T;T	0.14022	2.54;2.54;2.54	5.53	-0.593	0.11667	.	0.229106	0.44902	N	0.000409	T	0.08802	0.0218	L	0.37697	1.125	0.09310	N	0.999994	B;D;B;B	0.52996	0.104;0.957;0.023;0.023	B;B;B;B	0.43386	0.021;0.418;0.015;0.015	T	0.35549	-0.9784	10	0.06757	T	0.87	-4.1834	10.1432	0.42747	0.0:0.5981:0.0:0.4019	.	769;760;778;778	B3KXH0;B7Z2N4;Q9Y4L1;A8C1Z0	.;.;HYOU1_HUMAN;.	T	778;769;716;627;716;759	ENSP00000384144:A778T;ENSP00000437313:A716T;ENSP00000433397:A716T	ENSP00000278752:A769T	A	-	1	0	HYOU1	118424214	0.087000	0.21565	0.000000	0.03702	0.044000	0.14063	0.693000	0.25497	-0.257000	0.09459	-0.894000	0.02916	GCA		TCGA-HZ-A8P0-01A-11D-A36O-08	HYOU1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389353.1	0	0	0	7	386	0	85	0	7.364256e-01	0	142	0	85	2		0	0	0	0	0	2	1	0.980471	7	384	0	84	2		0	0	0	0	85	2	-1.996603	0	1	121412	3	37	1	0	0	0	1.993013	0	0.380000	1.960000	0.375252	0.090000	3.000000e-02	0.180000	0.100000	0.105340	0.090000	0	6.000000e-02	1.400000e-01
OR5A1	219982	broad.mit.edu	37	11	59211572	59211572	+	Missense_Mutation	SNP	A	A	G			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr11:59211572A>G	ENST00000302030.2	+	1	956	c.931A>G	c.(931-933)Aag>Gag	p.K311E		NM_001004728.1	NP_001004728.1	Q8NGJ0	OR5A1_HUMAN	olfactory receptor, family 5, subfamily A, member 1			28					GTTGGAAAGGAAGAAAGTGTT	0.438000																								0							SO:0001583	missense			ENST00000302030.2	1	1	hg19	CCDS31561.1	.	.	.	.	.	.	.	.	.	.	A	7.443	0.641062	0.14386	.	.	ENSG00000172320	ENST00000302030	T	0.39406	1.08	5.02	2.68	0.31781	.	0.762345	0.11693	N	0.538628	T	0.25901	0.0631	L	0.28115	0.83	0.09310	N	1	P	0.37122	0.583	B	0.30646	0.118	T	0.09930	-1.0652	10	0.52906	T	0.07	-1.0631	6.7823	0.23652	0.8103:0.0:0.1897:0.0	.	311	Q8NGJ0	OR5A1_HUMAN	E	311	ENSP00000303096:K311E	ENSP00000303096:K311E	K	+	1	0	OR5A1	58968148	0.998000	0.40836	0.001000	0.08648	0.222000	0.24845	4.557000	0.60782	0.351000	0.24027	0.528000	0.53228	AAG		TCGA-HZ-A8P0-01A-11D-A36O-08	OR5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394233.1	1	0	1	101	457	0	132		0	0	0	0	132	2		0	0	0	0	0	2	1	1.000000	100	451	0	131	2		0	0	0	0	132	2	-20.000000	1	1	0	0		1	0	0	0	2.000324	0	0.380000	1.960000	0.375252	0.940000	7.800000e-01	1.000000	1.000000	0.933889	0.940000	1	8.500000e-01	1
MS4A3	932	broad.mit.edu	37	11	59837071	59837071	+	Missense_Mutation	SNP	C	C	T			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr11:59837071C>T	ENST00000278865.3	+	6	611	c.538C>T	c.(538-540)Ctc>Ttc	p.L180F	MS4A3_ENST00000534744.1_Missense_Mutation_p.L134F|MS4A3_ENST00000395032.2_Missense_Mutation_p.L57F|MS4A3_ENST00000358152.2_Missense_Mutation_p.L134F	NM_006138.4	NP_006129.4	Q96HJ5	MS4A3_HUMAN	membrane-spanning 4-domains, subfamily A, member 3 (hematopoietic cell-specific)			21		all_epithelial(135;0.245)			ACTGCTGATTCTCACCTTGCT	0.413000																								0							SO:0001583	missense			ENST00000278865.3	0	1	hg19	CCDS31567.1	.	.	.	.	.	.	.	.	.	.	C	7.678	0.688406	0.14973	.	.	ENSG00000149516	ENST00000395032;ENST00000358152;ENST00000278865;ENST00000534744	T;T;T;T	0.02067	4.47;4.47;4.47;4.47	4.75	-0.38	0.12490	.	0.452259	0.22739	N	0.056237	T	0.01489	0.0048	N	0.20986	0.625	0.09310	N	1	B;P	0.38395	0.215;0.629	B;B	0.40199	0.097;0.322	T	0.40021	-0.9585	10	0.02654	T	1	-7.6657	7.4388	0.27171	0.0:0.5146:0.0:0.4854	.	134;180	Q96HJ5-2;Q96HJ5	.;MS4A3_HUMAN	F	57;134;180;134	ENSP00000378473:L57F;ENSP00000350872:L134F;ENSP00000278865:L180F;ENSP00000434117:L134F	ENSP00000278865:L180F	L	+	1	0	MS4A3	59593647	0.108000	0.22018	0.003000	0.11579	0.108000	0.19459	-0.073000	0.11468	-0.246000	0.09611	0.643000	0.83706	CTC		TCGA-HZ-A8P0-01A-11D-A36O-08	MS4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394417.1	0	0	0	14	755	1	148		0	0	0	1	148	2		0	0	0	0	0	2	1	0.999749	14	753	0	145	2		0	0	0	1	148	2	-2.470769	0	1	0	0		1	0	0	0	2.000324	0	0.380000	1.960000	0.375252	0.090000	4.000000e-02	0.150000	0.100000	0.101400	0.090000	0	6.000000e-02	1.300000e-01
BEST1	7439	broad.mit.edu	37	11	61730184	61730184	+	Missense_Mutation	SNP	G	G	A	rs61747600		TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr11:61730184G>A	ENST00000378043.4	+	10	2201	c.1558G>A	c.(1558-1560)Gat>Aat	p.D520N	BEST1_ENST00000534553.1_3'UTR|BEST1_ENST00000301774.9_Missense_Mutation_p.D148N|FTH1_ENST00000529631.1_Intron|FTH1_ENST00000529191.1_Intron|BEST1_ENST00000449131.2_Missense_Mutation_p.D460N|BEST1_ENST00000378042.3_Missense_Mutation_p.D433N	NM_004183.3	NP_004174.1	O76090	BEST1_HUMAN	bestrophin 1			25					CTCAGAGAGCGATGGGGCCTT	0.468000																								0							SO:0001583	missense			ENST00000378043.4	1	1	hg19	CCDS31580.1	.	.	.	.	.	.	.	.	.	.	G	12.98	2.099498	0.37048	.	.	ENSG00000167995	ENST00000378043;ENST00000378042;ENST00000301774;ENST00000449131	D;D;T;D	0.97404	-4.36;-4.1;-0.33;-4.37	5.34	1.03	0.20045	.	1.615380	0.03680	N	0.245331	D	0.90195	0.6935	N	0.14661	0.345	0.09310	N	0.999994	P;B;P	0.38370	0.628;0.355;0.628	B;B;B	0.24848	0.04;0.018;0.056	D	0.86624	0.1881	10	0.23891	T	0.37	-0.3632	4.8606	0.13581	0.2543:0.2983:0.4474:0.0	rs61747600	433;520;460	O76090-4;O76090;O76090-3	.;BEST1_HUMAN;.	N	520;433;148;460	ENSP00000367282:D520N;ENSP00000367281:D433N;ENSP00000301774:D148N;ENSP00000399709:D460N	ENSP00000301774:D148N	D	+	1	0	BEST1	61486760	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	0.302000	0.19192	0.254000	0.21573	0.655000	0.94253	GAT		TCGA-HZ-A8P0-01A-11D-A36O-08	BEST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394715.1	1	0	1	34	183	0	56	0	1.241329e-01	0	4	0	56	2		0	0	0	0	0	2	1	1.000000	34	180	0	53	2		0	0	0	0	56	2	-20.000000	1	1	121412	1	31	1	0	0	0	2.000324	0	0.380000	1.960000	0.375252	0.810000	5.800000e-01	1.000000	1.000000	0.821902	0.810000	0	6.900000e-01	9.500000e-01
STAB2	55576	broad.mit.edu	37	12	104147083	104147083	+	Silent	SNP	C	C	T	rs139125034		TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr12:104147083C>T	ENST00000388887.2	+	61	6870	c.6666C>T	c.(6664-6666)aaC>aaT	p.N2222N	RP11-341G23.4_ENST00000551299.1_RNA	NM_017564.9	NP_060034.9			stabilin 2			174					CCTGTGCCAACGAAGCTGCGA	0.552000																								0							SO:0001819	synonymous_variant			ENST00000388887.2	1	1	hg19	CCDS31888.1																																																																																				TCGA-HZ-A8P0-01A-11D-A36O-08	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1	1	0	1	48	188	0	34	0	1.911326e-01	0	4	0	34	2		0	0	0	0	0	2	1	1.000000	46	185	0	33	2		0	0	0	0	34	2	-3.381505	1	1	121412	31	46	1	0	0	0	1.998835	0	0.380000	1.960000	0.375252	0.990000	8.000000e-01	1.000000	1.000000	0.973909	0.990000	1	9.200000e-01	1
TAS2R20	259295	broad.mit.edu	37	12	11149731	11149731	+	Silent	SNP	C	C	T			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr12:11149731C>T	ENST00000538986.1	-	1	743	c.744G>A	c.(742-744)tcG>tcA	p.S248S	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_176889.2	NP_795370.2	P59543	T2R20_HUMAN	taste receptor, type 2, member 20			13					AATTCCAAAACGATATGATTA	0.378000																								0							SO:0001819	synonymous_variant			ENST00000538986.1	1	1	hg19	CCDS8639.1																																																																																				TCGA-HZ-A8P0-01A-11D-A36O-08	TAS2R20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370130.2	1	0	1	76	355	0	106		0	0	0	0	106	2		0	0	0	0	0	2	1	1.000000	75	353	0	105	2		0	0	0	0	106	2	-20.000000	1	1	121408	11	45	1	0	0	0	1.971689	0	0.380000	1.960000	0.365534	0.900000	7.200000e-01	1.000000	1.000000	0.901639	0.900000	1	8.100000e-01	1
KRAS	3845	broad.mit.edu	37	12	25380275	25380275	+	Missense_Mutation	SNP	T	T	A	rs17851045		TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08			T	A	T	T		Valid	Somatic	Phase_I	WXS	KRAS_deep			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr12:25380275T>A	ENST00000256078.4	-	3	246	c.183A>T	c.(181-183)caA>caT	p.Q61H	KRAS_ENST00000557334.1_Intron|AC087239.1_ENST00000594112.1_5'Flank|KRAS_ENST00000311936.3_Missense_Mutation_p.Q61H	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	p.Q61H(153)	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)		TGTACTCCTCTTGACCTGCTG	0.423000	Q61H(CL11_LARGE_INTESTINE)|Q61H(HS766T_PANCREAS)|Q61H(NCIH1155_LUNG)|Q61H(NCIH460_LUNG)|Q61H(T3M4_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	153	Substitution - Missense(153)						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	.	.	.	.	.	.	.	.	.	.	T	22.1	4.243092	0.79912	.	.	ENSG00000133703	ENST00000311936;ENST00000256078	D;D	0.84146	-1.81;-1.81	5.77	5.77	0.91146	Small GTP-binding protein domain (1);	0.049057	0.85682	D	0.000000	D	0.87265	0.6134	M	0.91140	3.18	0.80722	D	1	B;B	0.33413	0.411;0.09	B;B	0.32724	0.092;0.151	D	0.87829	0.2643	10	0.72032	D	0.01	.	9.9836	0.41828	0.0:0.0752:0.0:0.9248	rs17851045	61;61	P01116-2;P01116	.;RASK_HUMAN	H	61	ENSP00000308495:Q61H;ENSP00000256078:Q61H	ENSP00000256078:Q61H	Q	-	3	2	KRAS	25271542	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.240000	0.43088	2.326000	0.78906	0.533000	0.62120	CAA		TCGA-HZ-A8P0-01A-11D-A36O-08	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	1	0	1	72	280	0	68	1	9.732354e-01	6	19	0	68	2	1	1	197	939	0	931	2	1	1.000000	69	277	0	68	2	1	1	1372	6654	0	68	2	-20.000000	1	1	0	0		1	0	0	0	1.998835	0	0.380000	1.960000	0.375252	0.990000	8.500000e-01	1.000000	1.000000	0.983073	0.990000	1	9.500000e-01	1
ESPL1	9700	broad.mit.edu	37	12	53681786	53681786	+	Missense_Mutation	SNP	G	G	A			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr12:53681786G>A	ENST00000257934.4	+	19	4298	c.4207G>A	c.(4207-4209)Gac>Aac	p.D1403N	ESPL1_ENST00000552462.1_Missense_Mutation_p.D1403N	NM_012291.4	NP_036423.4	Q14674	ESPL1_HUMAN	extra spindle pole bodies homolog 1 (S. cerevisiae)			70					TGACTTGGAAGACCCTGTCTC	0.582000											OREG0021863	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	Colon(53;1069 1201 2587 5382)											0							SO:0001583	missense			ENST00000257934.4	1	1	hg19	CCDS8852.1	.	.	.	.	.	.	.	.	.	.	G	18.53	3.645049	0.67358	.	.	ENSG00000135476	ENST00000257934;ENST00000552671;ENST00000552462	T;T	0.12039	2.72;2.72	5.8	5.8	0.92144	.	0.429106	0.26935	N	0.021758	T	0.19565	0.0470	M	0.67953	2.075	0.38567	D	0.949859	P	0.44734	0.842	B	0.40329	0.326	T	0.02743	-1.1116	10	0.34782	T	0.22	.	16.9805	0.86326	0.0:0.0:1.0:0.0	.	1403	Q14674	ESPL1_HUMAN	N	1403;1078;1403	ENSP00000257934:D1403N;ENSP00000449831:D1403N	ENSP00000257934:D1403N	D	+	1	0	ESPL1	51968053	1.000000	0.71417	1.000000	0.80357	0.868000	0.49771	5.401000	0.66326	2.751000	0.94390	0.650000	0.86243	GAC		TCGA-HZ-A8P0-01A-11D-A36O-08	ESPL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406899.2	1	0	1	73	310	0	104	0	3.734607e-02	0	2	0	104	2		0	0	0	0	0	2	1	1.000000	73	308	0	103	2		0	0	0	0	104	2	-20.000000	1	1	0	0		1	0	0	0	1.998835	0	0.380000	1.960000	0.375252	0.990000	7.900000e-01	1.000000	1.000000	0.958100	0.990000	1	8.800000e-01	1
ATP5B	506	broad.mit.edu	37	12	57037629	57037629	+	Missense_Mutation	SNP	C	C	T			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08			C	T	C	C		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr12:57037629C>T	ENST00000262030.3	-	4	649	c.599G>A	c.(598-600)gGc>gAc	p.G200D	ATP5B_ENST00000552919.1_Missense_Mutation_p.G200D|SNORD59A_ENST00000384304.1_RNA|ATP5B_ENST00000550162.1_5'Flank	NM_001686.3	NP_001677.2	P06576	ATPB_HUMAN	ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptide			19					ACCAATTTTGCCACCCTTGGC	0.418000																								0							SO:0001583	missense			ENST00000262030.3	0	1	hg19	CCDS8924.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	29.3|29.3	4.996446|4.996446	0.93167|0.93167	.|.	.|.	ENSG00000110955|ENSG00000110955	ENST00000262030;ENST00000552919;ENST00000551020|ENST00000552959	D;D;D|.	0.82433|.	-1.61;-1.61;-1.61|.	5.56|5.56	5.56|5.56	0.83823|0.83823	ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain (1);ATPase, AAA+ type, core (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|.	0.88822|.	0.6541|.	H|H	0.97315|0.97315	3.98|3.98	0.80722|0.80722	D|D	1|1	P|.	0.43542|.	0.81|.	P|.	0.60886|.	0.88|.	D|.	0.92479|.	0.5991|.	10|.	0.87932|.	D|.	0|.	-0.5245|-0.5245	18.303|18.303	0.90171|0.90171	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	200|.	P06576|.	ATPB_HUMAN|.	D|X	200;200;139|136	ENSP00000262030:G200D;ENSP00000450297:G200D;ENSP00000446677:G139D|.	ENSP00000262030:G200D|.	G|W	-|-	2|3	0|0	ATP5B|ATP5B	55323896|55323896	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.919000|0.919000	0.55068|0.55068	7.114000|7.114000	0.77103|0.77103	2.627000|2.627000	0.88993|0.88993	0.313000|0.313000	0.20887|0.20887	GGC|TGG		TCGA-HZ-A8P0-01A-11D-A36O-08	ATP5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408380.1	0	0	0	5	427	0	94	0	9.911597e-01	1	804	0	94	2		0	0	0	0	0	2	1	0.936349	5	423	0	93	2		0	0	0	0	94	2	-2.286737	0	1	0	0		1	0	0	0	1.998835	0	0.380000	1.960000	0.375252	0.060000	1.000000e-02	0.130000	0.060000	0.071926	0.060000	0	3.000000e-02	1.000000e-01
POTEG	404785	broad.mit.edu	37	14	19553823	19553823	+	Missense_Mutation	SNP	G	G	A			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr14:19553823G>A	ENST00000409832.3	+	1	459	c.407G>A	c.(406-408)cGt>cAt	p.R136H		NM_001005356.2	NP_001005356.1	Q6S5H5	POTEG_HUMAN	POTE ankyrin domain family, member G	p.R136H(1)		47					TACCACGTCCGTCGAGAAGAT	0.577000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000409832.3	1	1	hg19	CCDS32018.1	.	.	.	.	.	.	.	.	.	.	g	5.784	0.328972	0.10956	.	.	ENSG00000222036	ENST00000409832	T	0.53206	0.63	1.47	-2.95	0.05564	.	.	.	.	.	T	0.34687	0.0906	L	0.50333	1.59	0.09310	N	1	B	0.10296	0.003	B	0.08055	0.003	T	0.24657	-1.0154	9	0.39692	T	0.17	.	4.5394	0.12049	0.0:0.4621:0.3049:0.2331	.	136	Q6S5H5	POTEG_HUMAN	H	136	ENSP00000386971:R136H	ENSP00000386971:R136H	R	+	2	0	POTEG	18623823	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.250000	0.08830	-0.851000	0.04147	-0.715000	0.03620	CGT		TCGA-HZ-A8P0-01A-11D-A36O-08	POTEG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408579.1	1	0	0	45	871	1	258		0	0	0	1	258	2		0	0	0	0	0	2	1	0.999921	22	479	1	382	7		0	0	0	1	258	2	-3.317601	1	1	119144	18	34	1						0.380000	1.960000									0	0
ZNF219	51222	broad.mit.edu	37	14	21561128	21561128	+	Nonsense_Mutation	SNP	C	C	A			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr14:21561128C>A	ENST00000360947.3	-	3	739	c.328G>T	c.(328-330)Gag>Tag	p.E110*	ZNF219_ENST00000421093.2_Nonsense_Mutation_p.E110*|RP11-998D10.7_ENST00000554733.2_lincRNA|ZNF219_ENST00000451119.2_Nonsense_Mutation_p.E110*|ZNF219_ENST00000556101.1_5'Flank	NM_016423.2	NP_057507.2	Q9P2Y4	ZN219_HUMAN	zinc finger protein 219			8	all_cancers(95;0.00185)		OV - Ovarian serous cystadenocarcinoma(11;9.86e-11)|Epithelial(56;1.27e-08)|all cancers(55;6.06e-08)		CGTGGGCGCTCGGGCTGGTGT	0.721000											OREG0022565	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)												0							SO:0001587	stop_gained			ENST00000360947.3	0	1	hg19	CCDS9568.1	.	.	.	.	.	.	.	.	.	.	C	36	5.775484	0.96922	.	.	ENSG00000165804	ENST00000360947;ENST00000451119;ENST00000421093;ENST00000555270;ENST00000554478;ENST00000556174	.	.	.	4.99	4.99	0.66335	.	0.244954	0.34291	N	0.004083	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-18.6504	13.6641	0.62384	0.0:1.0:0.0:0.0	.	.	.	.	X	110;110;110;110;156;110	.	ENSP00000354206:E110X	E	-	1	0	ZNF219	20630968	0.012000	0.17670	0.945000	0.38365	0.486000	0.33341	2.161000	0.42358	2.597000	0.87782	0.655000	0.94253	GAG		TCGA-HZ-A8P0-01A-11D-A36O-08	ZNF219-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073931.2	0	0	0	5	105	0	50	0	2.680743e-01	0	19	0	50	2		0	0	0	0	0	2	1	0.939005	6	104	0	49	2		0	0	0	0	50	2	-8.336414	1	1	0	0		1	0	1	1	2.013854	0	0.380000	1.960000	0.378820	0.250000	9.000000e-02	0.510000	0.240000	0.277262	0.250000	0	1.600000e-01	3.800000e-01
NPAS3	64067	broad.mit.edu	37	14	34269465	34269465	+	Missense_Mutation	SNP	A	A	T			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr14:34269465A>T	ENST00000356141.4	+	12	1952	c.1952A>T	c.(1951-1953)gAg>gTg	p.E651V	NPAS3_ENST00000357798.5_Missense_Mutation_p.E638V|NPAS3_ENST00000548645.1_Missense_Mutation_p.E621V|NPAS3_ENST00000551492.1_Missense_Mutation_p.E656V|NPAS3_ENST00000346562.2_Missense_Mutation_p.E619V			Q8IXF0	NPAS3_HUMAN	neuronal PAS domain protein 3			40	Breast(36;0.0102)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00968)		ATCAAGACGGAGATCTCAGAA	0.627000																								0							SO:0001583	missense			ENST00000356141.4	1	1	hg19	CCDS53891.1	.	.	.	.	.	.	.	.	.	.	A	17.33	3.362475	0.61403	.	.	ENSG00000151322	ENST00000551634;ENST00000551492;ENST00000346562;ENST00000548645;ENST00000356141;ENST00000357798	T;T;T;T;T;T	0.72167	-0.63;2.95;2.97;2.97;2.95;2.82	5.07	5.07	0.68467	.	0.135165	0.50627	D	0.000116	T	0.75488	0.3856	L	0.27053	0.805	0.80722	D	1	D;D;D;D	0.76494	0.999;0.998;0.999;0.999	D;D;D;D	0.80764	0.994;0.987;0.994;0.994	T	0.79055	-0.1960	10	0.72032	D	0.01	.	14.8262	0.70113	1.0:0.0:0.0:0.0	.	621;651;619;638	Q8IXF0-2;Q8IXF0;Q8IXF0-4;Q8IXF0-3	.;NPAS3_HUMAN;.;.	V	625;656;619;621;651;638	ENSP00000448373:E625V;ENSP00000450392:E656V;ENSP00000319610:E619V;ENSP00000448916:E621V;ENSP00000348460:E651V;ENSP00000350446:E638V	ENSP00000319610:E619V	E	+	2	0	NPAS3	33339216	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.019000	0.93662	1.887000	0.54652	0.454000	0.30748	GAG		TCGA-HZ-A8P0-01A-11D-A36O-08	NPAS3-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276645.1	1	0	0	36	155	0	52		0	0	0	0	52	2		0	0	0	0	0	2	1	1.000000	35	153	0	51	2		0	0	0	0	52	2	-20.000000	1	1	0	0		1	0	1	1	2.013854	0	0.380000	1.960000	0.378820	0.980000	7.200000e-01	1.000000	1.000000	0.940499	0.980000	1	8.400000e-01	1
BTBD7	55727	broad.mit.edu	37	14	93761248	93761248	+	Nonsense_Mutation	SNP	C	C	A			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr14:93761248C>A	ENST00000334746.5	-	3	425	c.118G>T	c.(118-120)Gaa>Taa	p.E40*	BTBD7_ENST00000554565.1_Intron|BTBD7_ENST00000555525.1_Nonsense_Mutation_p.E40*|BTBD7_ENST00000298896.3_Nonsense_Mutation_p.E40*|BTBD7_ENST00000393170.2_5'Flank	NM_001002860.2	NP_001002860.2	Q9P203	BTBD7_HUMAN	BTB (POZ) domain containing 7			35		all_cancers(154;0.08)			AACTTTGATTCGCAACCATAG	0.348000																								0							SO:0001587	stop_gained			ENST00000334746.5	0	1	hg19	CCDS32146.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.505722	0.85282	.	.	ENSG00000011114	ENST00000334746;ENST00000298896;ENST00000555525;ENST00000554968	.	.	.	5.9	5.9	0.94986	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.39692	T	0.17	.	20.27	0.98469	0.0:1.0:0.0:0.0	.	.	.	.	X	40	.	ENSP00000298896:E40X	E	-	1	0	BTBD7	92831001	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.487000	0.81328	2.804000	0.96469	0.655000	0.94253	GAA		TCGA-HZ-A8P0-01A-11D-A36O-08	BTBD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412701.1	0	0	0	6	442	0	91	0	2.651224e-03	0	5	0	91	2		0	0	0	0	0	2	1	0.964226	6	438	0	90	2		0	0	0	0	91	2	-2.694294	1	1	0	0		1	0	1	1	2.013854	0	0.380000	1.960000	0.378820	0.070000	2.000000e-02	0.150000	0.070000	0.081431	0.070000	0	4.000000e-02	1.100000e-01
DICER1	23405	broad.mit.edu	37	14	95590833	95590833	+	Missense_Mutation	SNP	C	C	T			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr14:95590833C>T	ENST00000526495.1	-	10	1367	c.1076G>A	c.(1075-1077)tGt>tAt	p.C359Y	DICER1_ENST00000343455.3_Missense_Mutation_p.C359Y|DICER1_ENST00000541352.1_Missense_Mutation_p.C359Y|DICER1_ENST00000527414.1_Missense_Mutation_p.C359Y|DICER1_ENST00000393063.1_Missense_Mutation_p.C359Y			Q9UPY3	DICER_HUMAN	dicer 1, ribonuclease type III			75		all_cancers(154;0.0621)|all_epithelial(191;0.223)			GTGCTCTTCACATAGTGCATG	0.373000			Mis F, N		sex cord-stromal tumour, TGCT, embryonal rhadomyosarcoma	pleuropulmonary blastoma			Familial Multinodular Goiter ;DICER 1 syndrome					yes	Rec	yes	Familial Pleuropulmonary Blastoma	14	14q32.13	23405	dicer 1, ribonuclease type III 		E, M, O	0							SO:0001583	missense	Familial Cancer Database	Adolescent Multinodular Goiter, incl. Multinodular Euthyroid Goiter & Non-Medullary Thyroid Cancer;incl. Pleuropulmonary Blastoma, Familial ; Cystic Nephroma, Familial	ENST00000526495.1	1	1	hg19	CCDS9931.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.387947	0.82902	.	.	ENSG00000100697	ENST00000343455;ENST00000526495;ENST00000393063;ENST00000527414;ENST00000541352	T;T;T;T;T	0.39056	1.1;1.1;1.1;1.1;1.1	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.58061	0.2096	M	0.63843	1.955	0.80722	D	1	D	0.60575	0.988	D	0.63192	0.912	T	0.50415	-0.8831	10	0.09338	T	0.73	-18.0875	19.4888	0.95042	0.0:1.0:0.0:0.0	.	359	Q9UPY3	DICER_HUMAN	Y	359	ENSP00000343745:C359Y;ENSP00000437256:C359Y;ENSP00000376783:C359Y;ENSP00000435681:C359Y;ENSP00000444719:C359Y	ENSP00000343745:C359Y	C	-	2	0	DICER1	94660586	1.000000	0.71417	0.987000	0.45799	0.998000	0.95712	7.267000	0.78462	2.607000	0.88179	0.585000	0.79938	TGT		TCGA-HZ-A8P0-01A-11D-A36O-08	DICER1-004	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387997.1	1	0	1	104	431	0	123	1	1.740028e-01	2	2	0	123	2		0	0	0	0	0	2	1	1.000000	102	429	0	121	2		0	0	0	0	123	2	-20.000000	1	1	0	0		1	0	1	1	2.013854	0	0.380000	1.960000	0.378820	0.990000	8.400000e-01	1.000000	1.000000	0.975102	0.990000	1	9.200000e-01	1
LDHAL6B	92483	broad.mit.edu	37	15	59499545	59499545	+	Missense_Mutation	SNP	G	G	A			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr15:59499545G>A	ENST00000307144.4	+	1	504	c.406G>A	c.(406-408)Gca>Aca	p.A136T	MYO1E_ENST00000288235.4_Intron	NM_033195.2	NP_149972.1	Q9BYZ2	LDH6B_HUMAN	lactate dehydrogenase A-like 6B			10					CTTTGTCACAGCAAACTCCAA	0.428000																								0							SO:0001583	missense			ENST00000307144.4	0	1	hg19	CCDS10171.1	.	.	.	.	.	.	.	.	.	.	G	17.91	3.503507	0.64298	.	.	ENSG00000171989	ENST00000307144	D	0.88431	-2.38	1.47	1.47	0.22746	Lactate/malate dehydrogenase, N-terminal (1);NAD(P)-binding domain (1);	0.000000	0.64402	U	0.000005	D	0.87051	0.6081	M	0.79693	2.465	0.53005	D	0.999961	P	0.39311	0.667	B	0.37943	0.261	D	0.85352	0.1102	10	0.62326	D	0.03	.	8.4578	0.32910	0.0:0.0:1.0:0.0	.	136	Q9BYZ2	LDH6B_HUMAN	T	136	ENSP00000302393:A136T	ENSP00000302393:A136T	A	+	1	0	LDHAL6B	57286837	1.000000	0.71417	0.083000	0.20561	0.047000	0.14425	6.111000	0.71541	0.784000	0.33661	0.305000	0.20034	GCA		TCGA-HZ-A8P0-01A-11D-A36O-08	LDHAL6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256015.1	0	0	0	6	617	1	176		0	0	0	1	176	2		0	0	0	0	0	2	0	0.075100	6	605	1	175	13		0	0	0	1	176	2	-2.010238	0	1	0	0		1	0	0	0	1.991875	0	0.380000	1.960000	0.375252	0.050000	1.000000e-02	0.110000	0.050000	0.058366	0.050000	0	3.000000e-02	8.000000e-02
SLCO3A1	28232	broad.mit.edu	37	15	92690367	92690367	+	Missense_Mutation	SNP	C	C	T			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr15:92690367C>T	ENST00000318445.6	+	8	1880	c.1666C>T	c.(1666-1668)Ccc>Tcc	p.P556S	SLCO3A1_ENST00000424469.2_Missense_Mutation_p.P556S|SLCO3A1_ENST00000555549.1_3'UTR|RP11-152L20.3_ENST00000561674.1_RNA	NM_013272.3	NP_037404.2	Q9UIG8	SO3A1_HUMAN	solute carrier organic anion transporter family, member 3A1			25	Lung NSC(78;0.0158)|all_lung(78;0.0255)		BRCA - Breast invasive adenocarcinoma(143;0.0841)	Alprostadil(DB00770)|Aminohippurate(DB00345)|Benzylpenicillin(DB01053)|Conjugated Estrogens(DB00286)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Iloprost(DB01088)|Methotrexate(DB00563)	GGCACAGACACCCTCAGTCAT	0.582000																								0							SO:0001583	missense			ENST00000318445.6	1	1	hg19	CCDS10371.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.978773	0.74360	.	.	ENSG00000176463	ENST00000318445;ENST00000424469;ENST00000555549	T;T	0.42131	0.98;0.98	6.03	6.03	0.97812	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.85682	D	0.000000	T	0.65091	0.2658	M	0.66506	2.035	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.998;0.999	T	0.56798	-0.7919	10	0.31617	T	0.26	.	20.5568	0.99304	0.0:1.0:0.0:0.0	.	498;556;556	Q9UIG8-3;Q9UIG8-2;Q9UIG8	.;.;SO3A1_HUMAN	S	556;556;275	ENSP00000320634:P556S;ENSP00000387846:P556S	ENSP00000320634:P556S	P	+	1	0	SLCO3A1	90491371	1.000000	0.71417	0.972000	0.41901	0.765000	0.43378	7.305000	0.78891	2.861000	0.98227	0.655000	0.94253	CCC		TCGA-HZ-A8P0-01A-11D-A36O-08	SLCO3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313529.1	1	0	1	69	284	0	71	1	9.949985e-01	2	34	0	71	2		0	0	0	0	0	2	1	1.000000	68	280	0	70	2		0	0	0	0	71	2	-20.000000	1	1	0	0		1	0	0	0	1.991875	0	0.380000	1.960000	0.375252	0.990000	8.100000e-01	1.000000	1.000000	0.967863	0.990000	1	9.100000e-01	1
GTF3C1	2975	broad.mit.edu	37	16	27481702	27481702	+	Missense_Mutation	SNP	C	C	A			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr16:27481702C>A	ENST00000356183.4	-	31	4556	c.4541G>T	c.(4540-4542)cGa>cTa	p.R1514L	GTF3C1_ENST00000561623.1_Missense_Mutation_p.R1514L	NM_001520.3	NP_001511.2	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide 1, alpha 220kDa			80					GCTTGGAAATCGCCACGTAAA	0.502000																								0							SO:0001583	missense			ENST00000356183.4	0	1	hg19	CCDS32414.1	.	.	.	.	.	.	.	.	.	.	C	30	5.050089	0.93740	.	.	ENSG00000077235	ENST00000356183;ENST00000388971	T	0.26957	1.7	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.54029	0.1833	M	0.76574	2.34	0.48288	D	0.999624	D;D	0.89917	1.0;1.0	D;D	0.87578	0.997;0.998	T	0.53837	-0.8382	10	0.54805	T	0.06	-10.7008	19.1435	0.93455	0.0:1.0:0.0:0.0	.	1514;1514	Q12789;Q12789-3	TF3C1_HUMAN;.	L	1514;1510	ENSP00000348510:R1514L	ENSP00000348510:R1514L	R	-	2	0	GTF3C1	27389203	1.000000	0.71417	0.982000	0.44146	0.971000	0.66376	6.537000	0.73847	2.614000	0.88457	0.585000	0.79938	CGA		TCGA-HZ-A8P0-01A-11D-A36O-08	GTF3C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433856.1	0	0	0	6	636	0	190	0	8.426084e-02	0	43	0	190	2		0	0	0	0	0	2	1	0.964242	6	631	0	190	2		0	0	0	0	190	2	-2.537684	1	1	0	0		1	1	2	3	2.030199	0	0.380000	1.960000	0.382347	0.050000	1.000000e-02	0.120000	0.050000	0.066536	0.050000	0	3.000000e-02	8.000000e-02
RNF40	9810	broad.mit.edu	37	16	30778186	30778186	+	Missense_Mutation	SNP	A	A	G			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08			A	G	A	A		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr16:30778186A>G	ENST00000324685.6	+	11	1853	c.1418A>G	c.(1417-1419)aAc>aGc	p.N473S	RNF40_ENST00000402121.3_Missense_Mutation_p.N165S|RNF40_ENST00000357890.5_Missense_Mutation_p.N373S|RNF40_ENST00000563683.1_Missense_Mutation_p.N433S	NM_001207033.1|NM_014771.3	NP_001193962.1|NP_055586	O75150	BRE1B_HUMAN	ring finger protein 40, E3 ubiquitin protein ligase			30			Colorectal(24;0.198)		CTGGCGGCCAACGAGCAGGCG	0.602000																								0							SO:0001583	missense			ENST00000324685.6	1	1	hg19	CCDS10691.1	.	.	.	.	.	.	.	.	.	.	A	27.1	4.804399	0.90623	.	.	ENSG00000103549	ENST00000324685;ENST00000357890;ENST00000402121	T;T;T	0.26957	1.7;1.7;1.7	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	T	0.54935	0.1889	M	0.84948	2.725	0.80722	D	1	D;D;D;D	0.71674	0.977;0.998;0.995;0.995	P;D;D;D	0.69654	0.883;0.919;0.965;0.939	T	0.62096	-0.6926	10	0.72032	D	0.01	-18.9766	15.0705	0.72034	1.0:0.0:0.0:0.0	.	165;373;473;473	F8W8Z4;O75150-4;A8K6K1;O75150	.;.;.;BRE1B_HUMAN	S	473;373;165	ENSP00000325677:N473S;ENSP00000350563:N373S;ENSP00000384942:N165S	ENSP00000325677:N473S	N	+	2	0	RNF40	30685687	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	8.711000	0.91396	2.199000	0.70637	0.533000	0.62120	AAC		TCGA-HZ-A8P0-01A-11D-A36O-08	RNF40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255524.2	1	0	1	14	99	0	26	1	9.948492e-01	17	49	0	26	2		0	0	0	0	0	2	1	0.999767	14	95	0	25	2		0	0	0	0	26	2	-20.000000	1	1	0	0		1	1	2	3	2.030199	0	0.380000	1.960000	0.382347	0.660000	3.800000e-01	1.000000	1.000000	0.679717	0.660000	0	5.100000e-01	8.500000e-01
FOXF1	2294	broad.mit.edu	37	16	86544628	86544628	+	Silent	SNP	C	C	A			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr16:86544628C>A	ENST00000262426.4	+	1	496	c.453C>A	c.(451-453)ctC>ctA	p.L151L	FENDRR_ENST00000595886.1_lincRNA	NM_001451.2	NP_001442.2	Q12946	FOXF1_HUMAN	forkhead box F1			12					GCCAGGCGCTCAAGCCCATGT	0.667000																								0							SO:0001819	synonymous_variant			ENST00000262426.4	0	1	hg19	CCDS10957.2																																																																																				TCGA-HZ-A8P0-01A-11D-A36O-08	FOXF1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000269103.2	0	0	0	6	438	0	113	0	3.842601e-02	0	19	0	113	2		0	0	0	0	0	2	1	0.964221	7	433	0	113	2		0	0	0	0	113	2	-2.844498	1	1	0	0		1	1	2	3	2.030831	0	0.380000	1.960000	0.382347	0.070000	2.000000e-02	0.160000	0.070000	0.091615	0.070000	0	4.000000e-02	1.200000e-01
SERPINF2	5345	broad.mit.edu	37	17	1648635	1648635	+	Silent	SNP	C	C	T			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr17:1648635C>T	ENST00000324015.3	+	4	188	c.111C>T	c.(109-111)agC>agT	p.S37S	SERPINF2_ENST00000382061.4_Silent_p.S37S|SERPINF2_ENST00000450523.2_Silent_p.S37S	NM_000934.3	NP_000925.2	P08697	A2AP_HUMAN	serpin peptidase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 2			12				Ocriplasmin(DB08888)	AGCTAACTAGCGGGCCGAACC	0.657000																								0							SO:0001819	synonymous_variant			ENST00000324015.3	1	0	hg19	CCDS11011.1																																																																																				TCGA-HZ-A8P0-01A-11D-A36O-08	SERPINF2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207078.3	1	0	0	38	172	0	41	0	3.454690e-02	1	1	0	41	2		0	0	0	0	0	2	1	1.000000	38	168	0	39	2		0	0	0	0	41	2	-2.990709	1	1	121386	169	51	1	0	0	0	1.987048	0	0.380000	1.960000	0.370431	0.930000	6.800000e-01	1.000000	1.000000	0.913506	0.930000	1	8.000000e-01	1
NLK	51701	broad.mit.edu	37	17	26495642	26495642	+	Missense_Mutation	SNP	G	G	A			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr17:26495642G>A	ENST00000407008.3	+	6	1724	c.1006G>A	c.(1006-1008)Gga>Aga	p.G336R		NM_016231.4	NP_057315.3	Q9UBE8	NLK_HUMAN	nemo-like kinase			14	all_lung(13;0.000343)|Lung NSC(42;0.00184)				AGAACTACTAGGACGAAGAAT	0.413000																								0							SO:0001583	missense			ENST00000407008.3	1	1	hg19	CCDS11224.2	.	.	.	.	.	.	.	.	.	.	G	21.8	4.200775	0.79015	.	.	ENSG00000087095	ENST00000407008	T	0.41758	0.99	6.08	6.08	0.98989	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.36717	0.0977	N	0.12920	0.275	0.80722	D	1	B	0.26081	0.141	B	0.35353	0.201	T	0.22556	-1.0213	10	0.56958	D	0.05	-13.0763	19.6516	0.95815	0.0:0.0:1.0:0.0	.	336	Q9UBE8	NLK_HUMAN	R	336	ENSP00000384625:G336R	ENSP00000384625:G336R	G	+	1	0	NLK	23519769	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.476000	0.97823	2.894000	0.99253	0.655000	0.94253	GGA		TCGA-HZ-A8P0-01A-11D-A36O-08	NLK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255607.3	1	0	1	70	274	0	82	1	6.887126e-01	2	9	0	82	2		0	0	0	0	0	2	1	1.000000	69	271	0	81	2		0	0	0	0	82	2	-3.457728	1	1	0	0		1	1	2	3	2.018854	0	0.380000	1.960000	0.381176	0.990000	8.500000e-01	1.000000	1.000000	0.983682	0.990000	1	9.500000e-01	1
TBC1D3F	84218	broad.mit.edu	37	17	36288204	36288204	+	Missense_Mutation	SNP	G	G	T			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr17:36288204G>T	ENST00000327454.6	+	6	436	c.290G>T	c.(289-291)cGa>cTa	p.R97L	TBC1D3F_ENST00000505415.1_Missense_Mutation_p.R97L|TBC1D3F_ENST00000539424.1_Missense_Mutation_p.R17L|TBC1D3F_ENST00000378174.5_Missense_Mutation_p.R97L	NM_032258.2	NP_115634.2	A6NER0	TBC3F_HUMAN	TBC1 domain family, member 3F	p.R97Q(1)|p.R97L(1)		2					CTCATAGATCGAGCGTACAAG	0.547000																								2	Substitution - Missense(2)						SO:0001583	missense			ENST00000327454.6	0	1	hg19	CCDS45657.1	.	.	.	.	.	.	.	.	.	.	g	10.29	1.309800	0.23821	.	.	ENSG00000185128	ENST00000327454;ENST00000378174;ENST00000505415;ENST00000539424	T;T;T;T	0.03330	3.97;3.97;3.97;3.97	.	.	.	Rab-GAP/TBC domain (2);	0.212784	0.34460	U	0.003960	T	0.05547	0.0146	M	0.79614	2.46	0.39492	D	0.968062	B;B;B;B	0.19935	0.007;0.04;0.001;0.004	B;B;B;B	0.19148	0.024;0.011;0.007;0.002	T	0.15723	-1.0427	9	0.48119	T	0.1	.	5.9051	0.18992	8.0E-4:0.0:0.9992:0.0	.	97;97;97;97	B9A6J9;A6NFD7;P0C7X1;A6NER0	.;.;TBC3H_HUMAN;TBC3F_HUMAN	L	97;97;97;17	ENSP00000329256:R97L;ENSP00000367416:R97L;ENSP00000421962:R97L;ENSP00000443859:R17L	ENSP00000329256:R97L	R	+	2	0	TBC1D3F	33362586	1.000000	0.71417	0.076000	0.20297	0.076000	0.17211	3.336000	0.52113	0.119000	0.18210	0.121000	0.15741	CGA		TCGA-HZ-A8P0-01A-11D-A36O-08	TBC1D3F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256100.3	0	0	0	10	1636	0	505	0	7.108719e-04	0	6	0	505	2		0	0	0	0	0	2	0	0.215910	2	234	1	742	3		0	0	0	0	505	2	-1.920210	0	1	118610	302	46	1	1	2	3	2.018854	0	0.380000	1.960000	0.381176	0.030000	0	0.060000	0.040000	0.035171	0.030000	0	1.000000e-02	5.000000e-02
GPR179	440435	broad.mit.edu	37	17	36485562	36485562	+	Nonsense_Mutation	SNP	G	G	T			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr17:36485562G>T	ENST00000342292.4	-	11	3910	c.3890C>A	c.(3889-3891)tCa>tAa	p.S1297*	GPR179_ENST00000584976.1_5'Flank	NM_001004334.2	NP_001004334.2	Q6PRD1	GP179_HUMAN	G protein-coupled receptor 179			60	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)			TATGGGCTCTGATTTTCCCCG	0.582000																								0							SO:0001587	stop_gained			ENST00000342292.4	0	1	hg19	CCDS42308.1	.	.	.	.	.	.	.	.	.	.	G	38	6.866372	0.97897	.	.	ENSG00000188888	ENST00000342292	.	.	.	4.97	4.97	0.65823	.	1.494310	0.04246	N	0.337834	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.1238	15.2627	0.73637	0.0:0.0:1.0:0.0	.	.	.	.	X	1297	.	ENSP00000345060:S1297X	S	-	2	0	GPR179	33739088	0.000000	0.05858	0.039000	0.18376	0.039000	0.13416	0.770000	0.26618	2.575000	0.86900	0.462000	0.41574	TCA		TCGA-HZ-A8P0-01A-11D-A36O-08	GPR179-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255329.2	0	0	0	5	283	0	64		0	0	0	0	64	2		0	0	0	0	0	2	1	0.937504	5	282	0	62	2		0	0	0	0	64	2	-3.380250	1	1	0	0		1	1	2	3	2.018854	0	0.380000	1.960000	0.381176	0.090000	3.000000e-02	0.210000	0.090000	0.108491	0.090000	0	6.000000e-02	1.500000e-01
PTRF	284119	broad.mit.edu	37	17	40557270	40557270	+	Nonsense_Mutation	SNP	G	G	T			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr17:40557270G>T	ENST00000357037.5	-	2	1027	c.608C>A	c.(607-609)tCg>tAg	p.S203*		NM_012232.5	NP_036364.2			polymerase I and transcript release factor			17		all_cancers(22;0.00146)|Breast(137;0.00116)|all_epithelial(22;0.0134)			CGCCTCGTCCGACGAAAGCTC	0.662000																								0							SO:0001587	stop_gained			ENST00000357037.5	0	1	hg19	CCDS11425.1	.	.	.	.	.	.	.	.	.	.	G	37	5.978629	0.97168	.	.	ENSG00000177469	ENST00000357037;ENST00000357684	.	.	.	5.35	5.35	0.76521	.	0.067530	0.64402	D	0.000009	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.0007	19.0756	0.93159	0.0:0.0:1.0:0.0	.	.	.	.	X	203;158	.	ENSP00000349541:S203X	S	-	2	0	PTRF	37810796	1.000000	0.71417	0.965000	0.40720	0.906000	0.53458	7.396000	0.79891	2.511000	0.84671	0.446000	0.29264	TCG		TCGA-HZ-A8P0-01A-11D-A36O-08	PTRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449938.1	0	0	0	8	657	1	173	0	8.995252e-02	0	255	1	173	7		0	0	0	0	0	2	0	0.131638	7	647	1	172	14		0	0	0	1	173	2	-2.474199	0	1	0	0		1	1	2	3	2.018854	0	0.380000	1.960000	0.381176	0.060000	2.000000e-02	0.130000	0.060000	0.070993	0.060000	0	4.000000e-02	1.000000e-01
NDEL1	81565	broad.mit.edu	37	17	8370257	8370257	+	Silent	SNP	C	C	T	rs138863036	byFrequency	TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr17:8370257C>T	ENST00000334527.7	+	9	1151	c.954C>T	c.(952-954)aaC>aaT	p.N318N	NDEL1_ENST00000585098.1_Intron|NDEL1_ENST00000380025.4_Missense_Mutation_p.R268W|NDEL1_ENST00000299734.7_Intron|NDEL1_ENST00000402554.3_3'UTR	NM_030808.4	NP_110435.1	Q9GZM8	NDEL1_HUMAN	nudE neurodevelopment protein 1-like 1			13					GGGCAGTAAACGGCTTTGACC	0.537000																								0							SO:0001819	synonymous_variant			ENST00000334527.7	1	1	hg19	CCDS11143.1																																																																																				TCGA-HZ-A8P0-01A-11D-A36O-08	NDEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226999.2	0	0	1	50	274	0	78	1	9.999875e-01	15	79	0	78	2		0	0	0	0	0	2	1	1.000000	48	270	0	78	2		0	0	0	0	78	2	-4.780038	1	1	121412	40	50	1	0	0	0	1.987048	0	0.380000	1.960000	0.370431	0.790000	6.000000e-01	1.000000	1.000000	0.804888	0.790000	0	6.900000e-01	9.100000e-01
ZNF181	339318	broad.mit.edu	37	19	35232318	35232318	+	Silent	SNP	T	T	G	rs2607243		TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr19:35232318T>G	ENST00000492450.1	+	4	1121	c.1032T>G	c.(1030-1032)acT>acG	p.T344T	ZNF181_ENST00000392232.3_Silent_p.T388T|ZNF181_ENST00000459757.2_Silent_p.T343T			Q2M3W8	ZN181_HUMAN	zinc finger protein 181			22	all_lung(56;1.13e-07)|Lung NSC(56;1.81e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.138)		GAATTCATACTCAAGAAAAAC	0.388000																								0							SO:0001819	synonymous_variant			ENST00000492450.1	0	1	hg19	CCDS32990.2																																																																																				TCGA-HZ-A8P0-01A-11D-A36O-08	ZNF181-002	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349005.3	0	0	0	7	276	0	47	0	2.704974e-02	0	9	0	47	2		0	0	0	0	0	2	1	0.979704	7	271	0	45	2		0	0	0	0	47	2	-2.557237	1	1	0	0		1	1	2	3	2.047715	0	0.380000	1.960000	0.385835	0.140000	5.000000e-02	1.000000	0.130000	0.180646	0.140000	0	9.000000e-02	2.100000e-01
PLEKHG2	64857	broad.mit.edu	37	19	39908691	39908691	+	Missense_Mutation	SNP	G	G	T			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr19:39908691G>T	ENST00000409794.3	+	9	1879	c.1029G>T	c.(1027-1029)atG>atT	p.M343I	PLEKHG2_ENST00000409797.2_Missense_Mutation_p.M343I|PLEKHG2_ENST00000378550.1_Missense_Mutation_p.M343I|PLEKHG2_ENST00000425673.1_Missense_Mutation_p.M343I|PLEKHG2_ENST00000458508.2_Missense_Mutation_p.M284I	NM_022835.2	NP_073746.2	Q9H7P9	PKHG2_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 2			40	all_cancers(60;3.08e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;6.57e-07)|Ovarian(47;0.0569)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)		TCTCTCGGATGCTGCTGGTGG	0.612000																								0							SO:0001583	missense			ENST00000409794.3	0	1	hg19	CCDS33022.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.10|19.10	3.761628|3.761628	0.69763|0.69763	.|.	.|.	ENSG00000090924|ENSG00000090924	ENST00000205135|ENST00000409794;ENST00000425673;ENST00000378550;ENST00000458508;ENST00000409797	.|D;D;D;D;D	.|0.87412	.|-2.25;-2.25;-2.25;-2.25;-2.25	4.65|4.65	4.65|4.65	0.58169|0.58169	.|Pleckstrin homology-type (1);Pleckstrin homology domain (2);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.88235|0.88235	0.6382|0.6382	L|L	0.52573|0.52573	1.65|1.65	0.49915|0.49915	D|D	0.999832|0.999832	.|B;B;B;B	.|0.31599	.|0.33;0.136;0.222;0.198	.|P;B;B;B	.|0.44897	.|0.463;0.214;0.183;0.343	D|D	0.85506|0.85506	0.1194|0.1194	5|10	.|0.30854	.|T	.|0.27	.|.	16.8319|16.8319	0.85946|0.85946	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|343;343;284;343	.|Q9H7P9-3;Q9H7P9;E7ESZ3;Q9H7P9-2	.|.;PKHG2_HUMAN;.;.	F|I	240|343;343;343;284;343	.|ENSP00000386733:M343I;ENSP00000392906:M343I;ENSP00000367812:M343I;ENSP00000408857:M284I;ENSP00000386492:M343I	.|ENSP00000367812:M343I	C|M	+|+	2|3	0|0	PLEKHG2|PLEKHG2	44600531|44600531	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.688000|0.688000	0.40055|0.40055	3.401000|3.401000	0.52601|0.52601	2.606000|2.606000	0.88127|0.88127	0.556000|0.556000	0.70494|0.70494	TGC|ATG		TCGA-HZ-A8P0-01A-11D-A36O-08	PLEKHG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326802.1	0	0	1	8	64	0	17	0	6.827786e-01	0	20	0	17	2		0	0	0	0	0	2	1	0.990209	8	63	0	17	2		0	0	0	0	17	2	-14.568410	1	1	0	0		1	1	2	3	2.047715	0	0.380000	1.960000	0.385835	0.610000	2.900000e-01	1.000000	1.000000	0.641673	0.610000	0	4.300000e-01	8.600000e-01
MYADM	91663	broad.mit.edu	37	19	54377360	54377360	+	Missense_Mutation	SNP	G	G	T			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr19:54377360G>T	ENST00000391769.2	+	3	857	c.577G>T	c.(577-579)Gac>Tac	p.D193Y	MYADM_ENST00000336967.3_Missense_Mutation_p.D193Y|MYADM_ENST00000391771.1_Missense_Mutation_p.D193Y|MYADM_ENST00000391770.4_Missense_Mutation_p.D193Y|MYADM_ENST00000391768.2_Missense_Mutation_p.D193Y|AC008440.5_ENST00000413496.2_RNA	NM_001020821.1	NP_001018657.1	Q96S97	MYADM_HUMAN	myeloid-associated differentiation marker			12	Ovarian(34;0.19)				GTTCATCAGCGACCCCAACCT	0.642000																								0							SO:0001583	missense			ENST00000391769.2	0	1	hg19	CCDS12866.1	.	.	.	.	.	.	.	.	.	.	G	3.909	-0.020465	0.07634	.	.	ENSG00000179820	ENST00000421337;ENST00000336967;ENST00000391770;ENST00000439000;ENST00000391771;ENST00000415619;ENST00000391769;ENST00000391768	T;T;T;T;T;T;T	0.25085	1.82;1.82;1.82;1.82;1.82;1.82;1.82	4.21	-5.25	0.02781	Marvel (1);MARVEL-like domain (1);	1.023760	0.07811	N	0.958108	T	0.27098	0.0664	L	0.41710	1.295	0.09310	N	1	P	0.42941	0.794	P	0.46076	0.503	T	0.41431	-0.9509	10	0.56958	D	0.05	-2.8128	14.9568	0.71120	0.1028:0.0:0.8972:0.0	.	193	Q96S97	MYADM_HUMAN	Y	193;193;193;193;193;156;193;193	ENSP00000398269:D193Y;ENSP00000337222:D193Y;ENSP00000375650:D193Y;ENSP00000416919:D193Y;ENSP00000375651:D193Y;ENSP00000375649:D193Y;ENSP00000375648:D193Y	ENSP00000337222:D193Y	D	+	1	0	MYADM	59069172	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.121000	0.15667	-1.181000	0.02730	-0.657000	0.03884	GAC		TCGA-HZ-A8P0-01A-11D-A36O-08	MYADM-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134337.1	0	0	0	8	426	0	165	0	7.787326e-01	0	153	0	165	2		0	0	0	0	0	2	1	0.989105	8	423	0	164	2		0	0	0	0	165	2	-2.525760	1	1	0	0		1	0	1	1	1.688809	1	0.380000	1.960000	0.241683	0.070000	3.000000e-02	0.150000	0.080000	0.088182	0.070000	0	5.000000e-02	1.200000e-01
NLRP13	126204	broad.mit.edu	37	19	56416346	56416346	+	Silent	SNP	C	C	T			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr19:56416346C>T	ENST00000342929.3	-	8	2579	c.2580G>A	c.(2578-2580)gcG>gcA	p.A860A	NLRP13_ENST00000588751.1_Silent_p.A860A	NM_176810.2	NP_789780.2	Q86W25	NAL13_HUMAN	NLR family, pyrin domain containing 13			109		Colorectal(82;3.48e-05)|Ovarian(87;0.0481)|Renal(1328;0.218)			GAGTCAGGGCCGCACACAATA	0.468000																								0							SO:0001819	synonymous_variant			ENST00000342929.3	1	1	hg19	CCDS33119.1																																																																																				TCGA-HZ-A8P0-01A-11D-A36O-08	NLRP13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396560.1	1	0	1	31	116	0	39		0	0	0	0	39	2		0	0	0	0	0	2	1	1.000000	31	116	0	39	2		0	0	0	0	39	2	-3.542038	1	1	121412	5	38	1	0	1	1	1.686526	1	0.380000	1.960000	0.238142	0.850000	6.200000e-01	1.000000	1.000000	0.851212	0.850000	1	7.300000e-01	9.600000e-01
PHGDH	26227	broad.mit.edu	37	1	120263916	120263916	+	Missense_Mutation	SNP	G	G	A	rs142988234		TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr1:120263916G>A	ENST00000369409.4	+	2	398	c.262G>A	c.(262-264)Gca>Aca	p.A88T	PHGDH_ENST00000369407.3_Missense_Mutation_p.A54T	NM_006623.3	NP_006614.2	O43175	SERA_HUMAN	phosphoglycerate dehydrogenase			18	all_cancers(5;1.18e-09)|all_epithelial(5;2.16e-10)|Melanoma(3;1.93e-05)|all_neural(166;0.219)	all_lung(203;3.66e-05)|Lung NSC(69;0.000202)|all_epithelial(167;0.0347)			TCTGGAGGCCGCAACAAGGAA	0.587000																								0							SO:0001583	missense			ENST00000369409.4	0	1	hg19	CCDS904.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.748004	0.89663	2.27E-4	0.0	ENSG00000092621	ENST00000369409;ENST00000369407	D;D	0.88586	-2.4;-2.4	5.92	5.92	0.95590	D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.95999	0.8697	M	0.93808	3.46	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	D	0.96332	0.9244	10	0.87932	D	0	-11.8066	18.8845	0.92370	0.0:0.0:1.0:0.0	.	54;88	Q5SZU1;O43175	.;SERA_HUMAN	T	88;54	ENSP00000358417:A88T;ENSP00000358415:A54T	ENSP00000358415:A54T	A	+	1	0	PHGDH	120065439	1.000000	0.71417	0.192000	0.23308	0.339000	0.28857	9.628000	0.98415	2.813000	0.96785	0.561000	0.74099	GCA		TCGA-HZ-A8P0-01A-11D-A36O-08	PHGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033464.1	0	0	0	5	372	0	104	0	1.809369e-01	0	48	0	104	2		0	0	0	0	0	2	1	0.935726	5	367	0	102	2		0	0	0	0	104	2	-1.914139	0	1	121412	3	38	1	0	0	0	1.976828	0	0.380000	1.960000	0.367992	0.070000	2.000000e-02	0.150000	0.070000	0.081371	0.070000	0	4.000000e-02	1.100000e-01
FMO5	2330	broad.mit.edu	37	1	146672844	146672844	+	Missense_Mutation	SNP	G	G	A			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr1:146672844G>A	ENST00000254090.4	-	7	1461	c.1073C>T	c.(1072-1074)cCt>cTt	p.P358L	FMO5_ENST00000441068.2_Missense_Mutation_p.P358L|RP11-337C18.10_ENST00000606856.1_RNA|RP11-337C18.8_ENST00000607149.1_RNA|RP11-337C18.8_ENST00000606757.1_RNA|FMO5_ENST00000369272.3_Intron	NM_001461.2	NP_001452.2	P49326	FMO5_HUMAN	flavin containing monooxygenase 5			25	all_hematologic(923;0.0487)				CAGGTTAGGAGGGAAGACCTT	0.468000																								0							SO:0001583	missense			ENST00000254090.4	0	1	hg19	CCDS926.1	.	.	.	.	.	.	.	.	.	.	.	25.6	4.659505	0.88154	.	.	ENSG00000131781	ENST00000441068;ENST00000254090	T;T	0.66815	-0.23;-0.23	6.17	6.17	0.99709	.	0.097121	0.64402	D	0.000001	T	0.81259	0.4785	M	0.80183	2.485	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.81786	-0.0773	10	0.72032	D	0.01	-16.718	18.3732	0.90420	0.0:0.0:1.0:0.0	.	358;358	P49326;C9JJD1	FMO5_HUMAN;.	L	358	ENSP00000416011:P358L;ENSP00000254090:P358L	ENSP00000254090:P358L	P	-	2	0	FMO5	145139468	1.000000	0.71417	1.000000	0.80357	0.710000	0.40934	9.828000	0.99408	2.941000	0.99782	0.655000	0.94253	CCT		TCGA-HZ-A8P0-01A-11D-A36O-08	FMO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040373.2	0	0	0	11	477	0	74	0	4.712206e-02	0	14	0	74	2		0	0	0	0	0	2	1	0.998272	11	472	0	73	2		0	0	0	0	74	2	-3.257086	1	1	0	0		1	1	3	4	2.706172	1	0.380000	1.960000	0.544453	0.160000	8.000000e-02	1.000000	0.160000	0.206445	0.160000	0	1.100000e-01	2.400000e-01
SV2A	9900	broad.mit.edu	37	1	149882423	149882423	+	Missense_Mutation	SNP	C	C	T			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr1:149882423C>T	ENST00000369146.3	-	4	1400	c.910G>A	c.(910-912)Ggc>Agc	p.G304S	SV2A_ENST00000369145.1_Missense_Mutation_p.G304S	NM_001278719.1|NM_014849.3	NP_001265648.1|NP_055664.3	Q7L0J3	SV2A_HUMAN	synaptic vesicle glycoprotein 2A			55	Breast(34;0.00769)|all_hematologic(923;0.127)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247)	Levetiracetam(DB01202)	GCGTACACGCCACCAATCATC	0.562000																								0							SO:0001583	missense			ENST00000369146.3	1	1	hg19	CCDS940.1	.	.	.	.	.	.	.	.	.	.	C	33	5.232995	0.95207	.	.	ENSG00000159164	ENST00000369146;ENST00000369145	T;T	0.74106	-0.81;-0.81	4.99	4.99	0.66335	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.76608	0.4011	L	0.52905	1.665	0.80722	D	1	D	0.69078	0.997	D	0.71414	0.973	T	0.71613	-0.4540	10	0.19147	T	0.46	-14.7314	15.8174	0.78615	0.0:1.0:0.0:0.0	.	304	Q7L0J3	SV2A_HUMAN	S	304	ENSP00000358142:G304S;ENSP00000358141:G304S	ENSP00000358141:G304S	G	-	1	0	SV2A	148149047	1.000000	0.71417	0.976000	0.42696	0.963000	0.63663	7.651000	0.83577	2.591000	0.87537	0.585000	0.79938	GGC		TCGA-HZ-A8P0-01A-11D-A36O-08	SV2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033754.1	1	0	1	51	228	0	60	0	3.794461e-01	0	7	0	60	2		0	0	0	0	0	2	1	1.000000	49	228	0	60	2		0	0	0	0	60	2	-3.348764	1	1	0	0		1	1	3	4	2.706172	1	0.380000	1.960000	0.544453	0.990000	9.900000e-01	1.000000	1.000000	0.998988	0.990000	1	9.900000e-01	1
GABPB2	126626	broad.mit.edu	37	1	151063024	151063024	+	Missense_Mutation	SNP	C	C	T			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr1:151063024C>T	ENST00000368918.3	+	3	582	c.251C>T	c.(250-252)gCg>gTg	p.A84V	GABPB2_ENST00000368916.1_Missense_Mutation_p.A84V|GABPB2_ENST00000368917.1_Missense_Mutation_p.A84V	NM_144618.2	NP_653219.1	Q8TAK5	GABP2_HUMAN	GA binding protein transcription factor, beta subunit 2			15					GATGGACATGCGCACATCGTG	0.488000																								0							SO:0001583	missense			ENST00000368918.3	0	1	hg19	CCDS983.1	.	.	.	.	.	.	.	.	.	.	C	9.007	0.981617	0.18812	.	.	ENSG00000143458	ENST00000368918;ENST00000368917;ENST00000446567;ENST00000368916	T;T;T	0.62498	0.02;0.02;0.02	5.46	3.31	0.37934	Ankyrin repeat-containing domain (4);	0.357560	0.33144	N	0.005223	T	0.11836	0.0288	N	0.03050	-0.425	0.09310	N	1	P;B	0.39404	0.672;0.126	B;B	0.20184	0.028;0.008	T	0.10428	-1.0630	10	0.33141	T	0.24	6.5452	9.7477	0.40457	0.0:0.8043:0.0:0.1957	.	100;84	B4DXA3;Q8TAK5	.;GABP2_HUMAN	V	84;84;100;84	ENSP00000357914:A84V;ENSP00000357913:A84V;ENSP00000357912:A84V	ENSP00000357912:A84V	A	+	2	0	GABPB2	149329648	0.001000	0.12720	0.005000	0.12908	0.348000	0.29142	1.370000	0.34238	0.664000	0.31047	0.650000	0.86243	GCG		TCGA-HZ-A8P0-01A-11D-A36O-08	GABPB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033700.2	0	0	0	5	558	0	86	0	1.726632e-02	0	18	0	86	2		0	0	0	0	0	2	1	0.935117	5	550	0	86	2		0	0	0	0	86	2	-2.385675	0	1	121412	3	38	1	1	3	4	2.706172	1	0.380000	1.960000	0.544453	0.060000	1.000000e-02	1.000000	0.080000	0.110124	0.060000	0	3.000000e-02	1.200000e-01
HRNR	388697	broad.mit.edu	37	1	152192788	152192788	+	Silent	SNP	G	G	A			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr1:152192788G>A	ENST00000368801.2	-	3	1392	c.1317C>T	c.(1315-1317)tcC>tcT	p.S439S	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin			192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)		CATGTTGGCCGGAGCTGGGAG	0.617000																								0							SO:0001819	synonymous_variant			ENST00000368801.2	0	1	hg19	CCDS30859.1																																																																																				TCGA-HZ-A8P0-01A-11D-A36O-08	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	0	0	0	6	597	0	152		0	0	0	0	152	2		0	0	0	0	0	2	1	0.962874	6	585	0	151	2		0	0	0	0	152	2	-2.168665	0	1	121412	4	41	1	1	3	4	2.706172	1	0.380000	1.960000	0.544453	0.070000	1.000000e-02	1.000000	0.080000	0.117195	0.070000	0	4.000000e-02	1.200000e-01
CCT3	7203	broad.mit.edu	37	1	156280946	156280946	+	Missense_Mutation	SNP	C	C	T			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr1:156280946C>T	ENST00000295688.3	-	12	1476	c.1196G>A	c.(1195-1197)cGc>cAc	p.R399H	CCT3_ENST00000472765.2_Missense_Mutation_p.R354H|CCT3_ENST00000368259.2_Missense_Mutation_p.R361H|CCT3_ENST00000368261.3_Missense_Mutation_p.R354H	NM_005998.4	NP_005989.3	P49368	TCPG_HUMAN	chaperonin containing TCP1, subunit 3 (gamma)			22	Hepatocellular(266;0.158)				GAGAACATTGCGACACACTTG	0.537000																								0							SO:0001583	missense			ENST00000295688.3	1	1	hg19	CCDS1140.2	.	.	.	.	.	.	.	.	.	.	C	33	5.252956	0.95336	.	.	ENSG00000163468	ENST00000295688;ENST00000368259;ENST00000368261;ENST00000472765	T;T;T;T	0.80994	-1.44;-1.44;-1.44;-1.44	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	D	0.92740	0.7692	H	0.96805	3.885	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.73708	0.96;0.981;0.972	D	0.94427	0.7646	10	0.72032	D	0.01	-9.7785	17.4945	0.87713	0.0:1.0:0.0:0.0	.	361;398;399	P49368-2;E9PAQ6;P49368	.;.;TCPG_HUMAN	H	399;361;354;354	ENSP00000295688:R399H;ENSP00000357242:R361H;ENSP00000357244:R354H;ENSP00000431543:R354H	ENSP00000295688:R399H	R	-	2	0	CCT3	154547570	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.441000	0.80485	2.726000	0.93360	0.650000	0.86243	CGC		TCGA-HZ-A8P0-01A-11D-A36O-08	CCT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060602.3	1	0	1	40	342	1	71	1	9.998671e-01	80	425	1	71	22		0	0	0	0	0	2	1	0.999147	41	338	1	71	18		0	0	0	1	71	2	-3.221884	1	1	121412	2	36	1	1	3	4	2.706172	1	0.380000	1.960000	0.544453	0.750000	5.500000e-01	1.000000	0.740000	0.770939	0.750000	0	6.400000e-01	8.900000e-01
PRG4	10216	broad.mit.edu	37	1	186269304	186269304	+	Missense_Mutation	SNP	A	A	C			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr1:186269304A>C	ENST00000445192.2	+	3	203	c.158A>C	c.(157-159)tAc>tCc	p.Y53S	PRG4_ENST00000367485.4_Missense_Mutation_p.Y53S|PRG4_ENST00000367483.4_Intron|PRG4_ENST00000367486.3_Missense_Mutation_p.Y53S|PRG4_ENST00000367484.3_Intron	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4			102					TGTCAACACTACATGGAGTGC	0.483000																								0							SO:0001583	missense			ENST00000445192.2	1	1	hg19	CCDS1369.1	.	.	.	.	.	.	.	.	.	.	A	12.19	1.862154	0.32884	.	.	ENSG00000116690	ENST00000367486;ENST00000367485;ENST00000445192	T;T;T	0.42900	0.96;0.96;0.96	5.57	4.38	0.52667	Somatomedin B domain (4);	0.178558	0.27122	N	0.020830	T	0.59074	0.2167	M	0.66439	2.03	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.988;0.993	T	0.62248	-0.6894	10	0.87932	D	0	-5.8319	9.7406	0.40416	0.7331:0.0:0.0:0.2669	.	53;53	Q92954-3;Q92954	.;PRG4_HUMAN	S	53	ENSP00000356456:Y53S;ENSP00000356455:Y53S;ENSP00000399679:Y53S	ENSP00000356455:Y53S	Y	+	2	0	PRG4	184535927	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.078000	0.41567	2.117000	0.64856	0.528000	0.53228	TAC		TCGA-HZ-A8P0-01A-11D-A36O-08	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	1	0	1	96	724	0	136	0	0	0	1	0	136	2		0	0	0	0	0	2	1	1.000000	96	717	0	135	2		0	0	0	0	136	2	-20.000000	1	1	0	0		1	1	3	4	2.706172	1	0.380000	1.960000	0.544453	0.840000	6.800000e-01	1.000000	0.820000	0.849195	0.840000	0	7.500000e-01	9.400000e-01
MYBPH	4608	broad.mit.edu	37	1	203138179	203138179	+	Silent	SNP	G	G	A			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr1:203138179G>A	ENST00000255416.4	-	9	1329	c.1272C>T	c.(1270-1272)ggC>ggT	p.G424G		NM_004997.2	NP_004988.2	Q13203	MYBPH_HUMAN	myosin binding protein H			20			BRCA - Breast invasive adenocarcinoma(75;0.153)		ATTTGGGGTTGCCCTGGATCT	0.562000													NSCLC(32;174 1025 14462 23899 42933)											0							SO:0001819	synonymous_variant			ENST00000255416.4	1	1	hg19	CCDS30975.1																																																																																				TCGA-HZ-A8P0-01A-11D-A36O-08	MYBPH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100264.1	1	0	1	78	566	0	136		0	0	0	0	136	2		0	0	0	0	0	2	1	1.000000	78	557	0	135	2		0	0	0	0	136	2	-20.000000	1	1	0	0		1	1	3	4	2.728117	1	0.380000	1.960000	0.545721	0.870000	6.900000e-01	1.000000	1.000000	0.876196	0.870000	1	7.800000e-01	9.800000e-01
MYBPH	4608	broad.mit.edu	37	1	203138180	203138180	+	Missense_Mutation	SNP	C	C	T			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr1:203138180C>T	ENST00000255416.4	-	9	1328	c.1271G>A	c.(1270-1272)gGc>gAc	p.G424D		NM_004997.2	NP_004988.2	Q13203	MYBPH_HUMAN	myosin binding protein H			20			BRCA - Breast invasive adenocarcinoma(75;0.153)		TTTGGGGTTGCCCTGGATCTC	0.567000													NSCLC(32;174 1025 14462 23899 42933)											0							SO:0001583	missense			ENST00000255416.4	1	1	hg19	CCDS30975.1	.	.	.	.	.	.	.	.	.	.	C	9.378	1.072135	0.20147	.	.	ENSG00000133055	ENST00000255416	T	0.66099	-0.19	5.36	5.36	0.76844	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.51477	D	0.000083	T	0.33294	0.0858	N	0.04724	-0.175	0.44155	D	0.996955	B	0.23377	0.084	B	0.26614	0.071	T	0.35549	-0.9784	10	0.02654	T	1	.	6.983	0.24713	0.0:0.7879:0.0:0.2121	.	424	Q13203	MYBPH_HUMAN	D	424	ENSP00000255416:G424D	ENSP00000255416:G424D	G	-	2	0	MYBPH	201404803	1.000000	0.71417	0.947000	0.38551	0.879000	0.50718	5.802000	0.69122	2.492000	0.84095	0.655000	0.94253	GGC		TCGA-HZ-A8P0-01A-11D-A36O-08	MYBPH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100264.1	1	0	1	75	557	0	138		0	0	0	0	138	2		0	0	0	0	0	2	1	1.000000	75	548	0	137	2		0	0	0	0	138	2	-20.000000	1	1	0	0		1	1	3	4	2.728117	1	0.380000	1.960000	0.545721	0.850000	6.800000e-01	1.000000	1.000000	0.860739	0.850000	1	7.600000e-01	9.600000e-01
USH2A	7399	broad.mit.edu	37	1	216495296	216495296	+	Missense_Mutation	SNP	C	C	T			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr1:216495296C>T	ENST00000307340.3	-	9	1959	c.1573G>A	c.(1573-1575)Gat>Aat	p.D525N	USH2A_ENST00000366943.2_Missense_Mutation_p.D525N|USH2A_ENST00000366942.3_Missense_Mutation_p.D525N	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)			527					TCGCAGTTATCGGCATGACCA	0.443000										HNSCC(13;0.011)														0							SO:0001583	missense			ENST00000307340.3	1	1	hg19	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	C	11.99	1.803455	0.31869	0.0	1.16E-4	ENSG00000042781	ENST00000307340;ENST00000366943;ENST00000366942	T;T;T	0.63417	-0.04;-0.04;-0.04	5.65	-0.114	0.13564	EGF-like, laminin (3);	0.531595	0.15476	N	0.260375	T	0.42517	0.1206	N	0.22421	0.69	0.09310	N	0.999999	B;B	0.20368	0.021;0.044	B;B	0.14023	0.009;0.01	T	0.24728	-1.0152	10	0.37606	T	0.19	.	8.3498	0.32295	0.0:0.6291:0.1083:0.2626	.	525;525	O75445-2;O75445	.;USH2A_HUMAN	N	525	ENSP00000305941:D525N;ENSP00000355910:D525N;ENSP00000355909:D525N	ENSP00000305941:D525N	D	-	1	0	USH2A	214561919	0.100000	0.21855	0.000000	0.03702	0.160000	0.22226	1.178000	0.31981	0.053000	0.16036	0.557000	0.71058	GAT		TCGA-HZ-A8P0-01A-11D-A36O-08	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	1	0	1	43	343	0	50		0	0	0	0	50	2		0	0	0	0	0	2	1	1.000000	42	338	0	50	2		0	0	0	0	50	2	-3.075756	1	1	121402	7	39	1	1	3	4	2.728117	1	0.380000	1.960000	0.545721	0.800000	5.900000e-01	1.000000	1.000000	0.814860	0.800000	0	6.900000e-01	9.400000e-01
DISP1	84976	broad.mit.edu	37	1	223176847	223176847	+	Missense_Mutation	SNP	G	G	T			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr1:223176847G>T	ENST00000284476.6	+	8	2272	c.2108G>T	c.(2107-2109)cGa>cTa	p.R703L		NM_032890.3	NP_116279.2	Q96F81	DISP1_HUMAN	dispatched homolog 1 (Drosophila)			69					GAAGCATCTCGAATTTTTTTC	0.418000																								0							SO:0001583	missense			ENST00000284476.6	0	1	hg19	CCDS1536.1	.	.	.	.	.	.	.	.	.	.	G	18.85	3.711729	0.68730	.	.	ENSG00000154309	ENST00000284476	D	0.86030	-2.06	5.91	5.91	0.95273	.	0.104774	0.64402	D	0.000005	D	0.91195	0.7226	L	0.59436	1.845	0.54753	D	0.999989	D	0.61697	0.99	D	0.69307	0.963	D	0.90102	0.4185	10	0.49607	T	0.09	-28.8962	20.2983	0.98569	0.0:0.0:1.0:0.0	.	703	Q96F81	DISP1_HUMAN	L	703	ENSP00000284476:R703L	ENSP00000284476:R703L	R	+	2	0	DISP1	221243470	1.000000	0.71417	0.236000	0.24074	0.984000	0.73092	6.665000	0.74442	2.802000	0.96397	0.655000	0.94253	CGA		TCGA-HZ-A8P0-01A-11D-A36O-08	DISP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092512.1	0	0	0	8	864	0	166	0	3.969421e-03	0	9	0	166	2		0	0	0	0	0	2	1	0.988820	8	853	0	165	2		0	0	0	0	166	2	-2.329120	0	1	0	0		1	1	3	4	2.728117	1	0.380000	1.960000	0.545721	0.060000	1.000000e-02	1.000000	0.080000	0.100331	0.060000	0	3.000000e-02	1.100000e-01
TTC13	79573	broad.mit.edu	37	1	231044752	231044752	+	Missense_Mutation	SNP	G	G	A			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr1:231044752G>A	ENST00000366661.4	-	21	2331	c.2324C>T	c.(2323-2325)tCg>tTg	p.S775L	TTC13_ENST00000366662.4_Missense_Mutation_p.S721L|TTC13_ENST00000414259.1_Missense_Mutation_p.S722L	NM_024525.4	NP_078801.3	Q8NBP0	TTC13_HUMAN	tetratricopeptide repeat domain 13			39	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)			CACGATGACCGAGTAAGCAAT	0.423000																								0							SO:0001583	missense			ENST00000366661.4	1	1	hg19	CCDS1588.1	.	.	.	.	.	.	.	.	.	.	G	16.95	3.262382	0.59431	.	.	ENSG00000143643	ENST00000366661;ENST00000366662;ENST00000414259	T;T;T	0.42900	0.96;1.0;1.0	5.53	5.53	0.82687	.	0.063181	0.64402	D	0.000003	T	0.30324	0.0761	N	0.25647	0.755	0.80722	D	1	B;P;P;P	0.50066	0.343;0.76;0.846;0.931	B;B;B;B	0.34652	0.009;0.122;0.187;0.184	T	0.11372	-1.0590	10	0.40728	T	0.16	-11.9623	19.4529	0.94875	0.0:0.0:1.0:0.0	.	700;722;721;775	Q69YR0;E9PGV4;Q8NBP0-2;Q8NBP0	.;.;.;TTC13_HUMAN	L	775;721;722	ENSP00000355621:S775L;ENSP00000355622:S721L;ENSP00000416631:S722L	ENSP00000355621:S775L	S	-	2	0	TTC13	229111375	1.000000	0.71417	0.972000	0.41901	0.954000	0.61252	8.920000	0.92779	2.595000	0.87683	0.655000	0.94253	TCG		TCGA-HZ-A8P0-01A-11D-A36O-08	TTC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092229.2	1	0	1	75	581	0	122	1	9.765735e-01	9	39	0	122	2		0	0	0	0	0	2	1	1.000000	74	573	0	122	2		0	0	0	0	122	2	-3.017764	1	1	121412	1	31	1	1	3	4	2.740950	1	0.380000	1.960000	0.548237	0.820000	6.500000e-01	1.000000	0.830000	0.833296	0.820000	0	7.300000e-01	9.300000e-01
OR2M5	127059	broad.mit.edu	37	1	248309316	248309316	+	Silent	SNP	C	C	A			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr1:248309316C>A	ENST00000366476.1	+	1	867	c.867C>A	c.(865-867)atC>atA	p.I289I		NM_001004690.1	NP_001004690.1	A3KFT3	OR2M5_HUMAN	olfactory receptor, family 2, subfamily M, member 5			49	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0388)		ATCCCCTCATCTACAGCCTCC	0.493000																								0							SO:0001819	synonymous_variant			ENST00000366476.1	1	1	hg19	CCDS31105.1																																																																																				TCGA-HZ-A8P0-01A-11D-A36O-08	OR2M5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097343.1	1	0	0	99	612	0	135		0	0	0	0	135	2		0	0	0	0	0	2	1	1.000000	98	602	0	133	2		0	0	0	0	135	2	-20.000000	1	1	0	0		1	1	3	4	2.740950	1	0.380000	1.960000	0.548237	0.990000	8.200000e-01	1.000000	1.000000	0.968151	0.990000	1	9.100000e-01	1
SLC6A9	6536	broad.mit.edu	37	1	44463406	44463406	+	Missense_Mutation	SNP	C	C	A			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr1:44463406C>A	ENST00000360584.2	-	14	2123	c.1932G>T	c.(1930-1932)ttG>ttT	p.L644F	SLC6A9_ENST00000475075.2_Missense_Mutation_p.L460F|SLC6A9_ENST00000357730.2_Missense_Mutation_p.L590F|SLC6A9_ENST00000372306.3_Intron|SLC6A9_ENST00000372310.3_Missense_Mutation_p.L571F|SLC6A9_ENST00000372307.3_Intron	NM_201649.3	NP_964012.2	P48067	SC6A9_HUMAN	solute carrier family 6 (neurotransmitter transporter, glycine), member 9			22	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0511)		Glycine(DB00145)	TGGCATTTTTCAAACGCTGCA	0.647000																								0							SO:0001583	missense			ENST00000360584.2	0	1	hg19	CCDS41317.1	.	.	.	.	.	.	.	.	.	.	C	14.48	2.547710	0.45383	.	.	ENSG00000196517	ENST00000372310;ENST00000475075;ENST00000360584;ENST00000357730	T;T;T;T	0.75821	-0.9;-0.95;-0.97;-0.93	4.92	4.92	0.64577	.	0.000000	0.64402	D	0.000001	T	0.75817	0.3901	L	0.40543	1.245	0.80722	D	1	D;B;B;D	0.65815	0.986;0.251;0.063;0.995	P;B;B;P	0.57425	0.655;0.098;0.073;0.82	T	0.75975	-0.3128	10	0.49607	T	0.09	.	11.4173	0.49960	0.0:0.9164:0.0:0.0836	.	575;571;590;644	B7Z3W8;P48067-2;P48067-3;P48067	.;.;.;SC6A9_HUMAN	F	571;460;644;590	ENSP00000361384:L571F;ENSP00000434460:L460F;ENSP00000353791:L644F;ENSP00000350362:L590F	ENSP00000350362:L590F	L	-	3	2	SLC6A9	44235993	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.373000	0.59537	2.553000	0.86117	0.609000	0.83330	TTG		TCGA-HZ-A8P0-01A-11D-A36O-08	SLC6A9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000022825.2	0	0	0	7	597	0	140	0	3.891117e-03	0	7	0	140	2		0	0	0	0	0	2	1	0.979996	7	591	0	139	2		0	0	0	0	140	2	-2.879119	1	1	0	0		1	0	0	0	2.007290	0	0.380000	1.960000	0.377635	0.060000	2.000000e-02	0.120000	0.060000	0.069056	0.060000	0	3.000000e-02	9.000000e-02
CXCR4	7852	broad.mit.edu	37	2	136873279	136873279	+	Silent	SNP	C	C	T			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr2:136873279C>T	ENST00000241393.3	-	2	323	c.219G>A	c.(217-219)acG>acA	p.T73T	CXCR4_ENST00000466288.1_5'UTR|CXCR4_ENST00000409817.1_Silent_p.T77T	NM_003467.2	NP_003458.1	P61073	CXCR4_HUMAN	chemokine (C-X-C motif) receptor 4	p.T77T(1)		25				Framycetin(DB00452)|Plerixafor(DB06809)	TGTACTTGTCCGTCATGCTTC	0.517000																								1	Substitution - coding silent(1)						SO:0001819	synonymous_variant			ENST00000241393.3	1	1	hg19	CCDS46420.1																																																																																				TCGA-HZ-A8P0-01A-11D-A36O-08	CXCR4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331732.1	1	0	1	76	346	0	110	1	1	10	156	0	110	2		0	0	0	0	0	2	1	1.000000	76	341	0	110	2		0	0	0	0	110	2	-2.675627	1	1	0	0		1	0	0	0	1.995583	0	0.380000	1.960000	0.375252	0.930000	7.500000e-01	1.000000	1.000000	0.926951	0.930000	1	8.400000e-01	1
NEB	4703	broad.mit.edu	37	2	152466350	152466350	+	Silent	SNP	T	T	C			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr2:152466350T>C	ENST00000172853.10	-	77	11721	c.11574A>G	c.(11572-11574)gcA>gcG	p.A3858A	NEB_ENST00000603639.1_Silent_p.A4101A|NEB_ENST00000409198.1_Silent_p.A3858A|NEB_ENST00000427231.2_Silent_p.A4101A|NEB_ENST00000604864.1_Silent_p.A4101A|NEB_ENST00000397345.3_Silent_p.A4101A			P20929	NEBU_HUMAN	nebulin			301					AGGCCTTTTTTGCTTGGATAA	0.448000																								0							SO:0001819	synonymous_variant			ENST00000172853.10	1	1	hg19																																																																																					TCGA-HZ-A8P0-01A-11D-A36O-08	NEB-201	KNOWN	basic	protein_coding	protein_coding		1	0	1	116	506	0	166		0	0	0	0	166	2		0	0	0	0	0	2	1	1.000000	113	499	0	161	2		0	0	0	0	166	2	-20.000000	1	1	0	0		1	0	0	0	1.995583	0	0.380000	1.960000	0.375252	0.960000	8.100000e-01	1.000000	1.000000	0.954296	0.960000	1	8.800000e-01	1
SCN1A	6323	broad.mit.edu	37	2	166911170	166911170	+	Missense_Mutation	SNP	C	C	A	rs121917935		TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr2:166911170C>A	ENST00000303395.4	-	4	579	c.580G>T	c.(580-582)Gat>Tat	p.D194Y	AC010127.3_ENST00000595647.1_RNA|SCN1A_ENST00000375405.3_Missense_Mutation_p.D194Y|SCN1A_ENST00000409050.1_Missense_Mutation_p.D194Y|SCN1A_ENST00000423058.2_Missense_Mutation_p.D194Y|AC010127.3_ENST00000599041.1_RNA|AC010127.3_ENST00000595268.1_RNA			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit			200				Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	ACAGTGAAATCGAGCCAGTTC	0.338000																								0		GRCh37	CM067004	SCN1A	M	rs121917935	SO:0001583	missense			ENST00000303395.4	0	1	hg19	CCDS54413.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.620307	0.87460	.	.	ENSG00000144285	ENST00000423058;ENST00000303395;ENST00000375405;ENST00000409050	D;D;D;D	0.99399	-5.83;-5.83;-5.83;-5.83	5.24	5.24	0.73138	Ion transport (1);	0.000000	0.64402	D	0.000002	D	0.99837	0.9926	H	0.99855	4.85	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.989;1.0;0.999	D	0.96333	0.9245	10	0.87932	D	0	.	19.1745	0.93599	0.0:1.0:0.0:0.0	.	194;194;194	P35498-2;E9PG49;P35498	.;.;SCN1A_HUMAN	Y	194	ENSP00000407030:D194Y;ENSP00000303540:D194Y;ENSP00000364554:D194Y;ENSP00000386312:D194Y	ENSP00000303540:D194Y	D	-	1	0	SCN1A	166619416	1.000000	0.71417	0.998000	0.56505	0.989000	0.77384	7.726000	0.84824	2.597000	0.87782	0.561000	0.74099	GAT		TCGA-HZ-A8P0-01A-11D-A36O-08	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	0	0	0	5	271	0	60		0	0	0	0	60	2		0	0	0	0	0	2	1	0.934433	5	265	0	60	2		0	0	0	0	60	2	-2.719573	1	1	0	0		1	0	0	0	1.995583	0	0.380000	1.960000	0.375252	0.100000	3.000000e-02	0.210000	0.100000	0.112055	0.100000	0	6.000000e-02	1.500000e-01
ITGAV	3685	broad.mit.edu	37	2	187506230	187506230	+	Silent	SNP	G	G	T			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr2:187506230G>T	ENST00000261023.3	+	12	1348	c.1074G>T	c.(1072-1074)acG>acT	p.T358T	ITGAV_ENST00000374907.3_Silent_p.T322T|ITGAV_ENST00000433736.2_Silent_p.T312T|AC017101.10_ENST00000453665.1_RNA	NM_002210.3	NP_002201	P06756	ITAV_HUMAN	integrin, alpha V			47			OV - Ovarian serous cystadenocarcinoma(117;0.0185)|Epithelial(96;0.072)|all cancers(119;0.189)	Antithymocyte globulin(DB00098)	ACTTCCAGACGACAAAGCTGA	0.498000													Melanoma(58;108 1995 6081)											0							SO:0001819	synonymous_variant			ENST00000261023.3	0	1	hg19	CCDS2292.1																																																																																				TCGA-HZ-A8P0-01A-11D-A36O-08	ITGAV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255882.2	0	0	0	7	818	0	209	0	5.568517e-02	0	38	0	209	2		0	0	0	0	0	2	1	0.980384	8	814	0	209	2		0	0	0	0	209	2	-2.213597	0	1	0	0		1	0	0	0	1.995583	0	0.380000	1.960000	0.375252	0.040000	1.000000e-02	0.090000	0.040000	0.050504	0.040000	0	2.000000e-02	7.000000e-02
SPHKAP	80309	broad.mit.edu	37	2	228860288	228860288	+	Missense_Mutation	SNP	G	G	A			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr2:228860288G>A	ENST00000392056.3	-	8	4617	c.4571C>T	c.(4570-4572)gCc>gTc	p.A1524V	SPHKAP_ENST00000344657.5_Missense_Mutation_p.A1524V	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing			185		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)			TTCCTCATTGGCAAGCTGGGT	0.572000																								0							SO:0001583	missense			ENST00000392056.3	0	1	hg19	CCDS46537.1	.	.	.	.	.	.	.	.	.	.	G	14.87	2.664572	0.47572	.	.	ENSG00000153820	ENST00000392056;ENST00000344657	T;T	0.13901	2.55;2.56	6.06	4.04	0.47022	.	0.287377	0.39020	N	0.001482	T	0.14227	0.0344	L	0.49126	1.545	0.43292	D	0.995273	B;P	0.42908	0.18;0.793	B;B	0.39971	0.044;0.315	T	0.02596	-1.1136	10	0.48119	T	0.1	.	11.0015	0.47609	0.1936:0.0:0.8064:0.0	.	1524;1524	Q2M3C7;Q2M3C7-2	SPKAP_HUMAN;.	V	1524	ENSP00000375909:A1524V;ENSP00000339886:A1524V	ENSP00000339886:A1524V	A	-	2	0	SPHKAP	228568532	1.000000	0.71417	0.908000	0.35775	0.542000	0.35054	2.352000	0.44080	1.570000	0.49709	0.655000	0.94253	GCC		TCGA-HZ-A8P0-01A-11D-A36O-08	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	0	0	0	7	582	1	159		0	0	0	1	159	2		0	0	0	0	0	2	0	0.087473	9	573	1	157	14		0	0	0	1	159	2	-2.642522	1	1	0	0		1	0	0	0	1.995583	0	0.380000	1.960000	0.375252	0.060000	2.000000e-02	0.120000	0.060000	0.070522	0.060000	0	3.000000e-02	9.000000e-02
CD207	50489	broad.mit.edu	37	2	71060828	71060828	+	Missense_Mutation	SNP	G	G	A			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr2:71060828G>A	ENST00000410009.3	-	3	559	c.514C>T	c.(514-516)Cgg>Tgg	p.R172W		NM_015717.3	NP_056532	Q9UJ71	CLC4K_HUMAN	CD207 molecule, langerin			20					TGGAGTGCCCGGATCTTTGTA	0.428000																								0							SO:0001583	missense			ENST00000410009.3	1	1	hg19		.	.	.	.	.	.	.	.	.	.	G	6.526	0.465360	0.12402	0.0	1.22E-4	ENSG00000116031	ENST00000410009	T	0.29917	1.55	4.12	4.12	0.48240	.	1.382280	0.04510	N	0.382668	T	0.25568	0.0622	L	0.27053	0.805	0.09310	N	1	D	0.67145	0.996	B	0.39590	0.304	T	0.32719	-0.9896	10	0.59425	D	0.04	.	12.1703	0.54155	0.0:0.0:1.0:0.0	.	172	Q9UJ71	CLC4K_HUMAN	W	172	ENSP00000386378:R172W	ENSP00000386378:R172W	R	-	1	2	CD207	70914336	0.043000	0.20138	0.029000	0.17559	0.004000	0.04260	1.111000	0.31159	2.568000	0.86640	0.655000	0.94253	CGG		TCGA-HZ-A8P0-01A-11D-A36O-08	CD207-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000329959.4	1	0	1	45	196	0	58	0	0	0	1	0	58	2		0	0	0	0	0	2	1	1.000000	45	193	0	58	2		0	0	0	0	58	2	-3.489613	1	1	120810	2	35	1	0	0	0	2.001662	0	0.380000	1.960000	0.375252	0.970000	7.300000e-01	1.000000	1.000000	0.938314	0.970000	1	8.400000e-01	1
GAR1	54433	broad.mit.edu	37	4	110740164	110740164	+	Nonsense_Mutation	SNP	C	C	A			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr4:110740164C>A	ENST00000226796.6	+	4	641	c.377C>A	c.(376-378)tCa>tAa	p.S126*	GAR1_ENST00000394631.3_Nonsense_Mutation_p.S126*	NM_018983.3	NP_061856.1	Q9NY12	GAR1_HUMAN	GAR1 ribonucleoprotein			9					TAGTATTTTTCAGTTAAGTTG	0.299000																								0							SO:0001587	stop_gained			ENST00000226796.6	0	1	hg19	CCDS34050.1	.	.	.	.	.	.	.	.	.	.	C	38	7.040121	0.98021	.	.	ENSG00000109534	ENST00000394631;ENST00000226796	.	.	.	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.9407	0.92604	0.0:1.0:0.0:0.0	.	.	.	.	X	126	.	ENSP00000226796:S126X	S	+	2	0	GAR1	110959613	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.681000	0.74523	2.573000	0.86826	0.591000	0.81541	TCA		TCGA-HZ-A8P0-01A-11D-A36O-08	GAR1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363810.2	0	0	0	10	404	0	85	0	4.445618e-01	0	58	0	85	2		0	0	0	0	0	2	1	0.996846	10	401	0	84	2		0	0	0	0	85	2	-2.995502	1	1	0	0		1	1	2	3	2.016802	0	0.380000	1.960000	0.381176	0.130000	6.000000e-02	0.230000	0.120000	0.138889	0.130000	0	9.000000e-02	1.800000e-01
PLRG1	5356	broad.mit.edu	37	4	155458483	155458483	+	Silent	SNP	A	A	C			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08			A	C	A	A		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr4:155458483A>C	ENST00000499023.2	-	14	1566	c.1440T>G	c.(1438-1440)gcT>gcG	p.A480A	PLRG1_ENST00000302078.5_Silent_p.A471A|PLRG1_ENST00000393905.2_Silent_p.A480A	NM_001201564.1|NM_002669.3	NP_001188493.1|NP_002660.1	O43660	PLRG1_HUMAN	pleiotropic regulator 1			22	all_hematologic(180;0.215)	Renal(120;0.0854)			TATCAGCTTCAGCTGTTAGTA	0.408000																								0							SO:0001819	synonymous_variant			ENST00000499023.2	1	1	hg19	CCDS34083.1																																																																																				TCGA-HZ-A8P0-01A-11D-A36O-08	PLRG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364824.1	1	0	1	52	265	0	65	1	9.999927e-01	21	71	0	65	2		0	0	0	0	0	2	1	1.000000	51	263	0	65	2		0	0	0	0	65	2	-20.000000	1	1	121402	6	38	1	1	2	3	2.016802	0	0.380000	1.960000	0.381176	0.860000	6.600000e-01	1.000000	1.000000	0.864340	0.860000	1	7.500000e-01	9.800000e-01
SORBS2	8470	broad.mit.edu	37	4	186544436	186544436	+	Nonsense_Mutation	SNP	G	G	T			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr4:186544436G>T	ENST00000284776.7	-	13	2644	c.2135C>A	c.(2134-2136)tCg>tAg	p.S712*	SORBS2_ENST00000437304.2_Intron|SORBS2_ENST00000448662.2_Intron|SORBS2_ENST00000431808.1_Nonsense_Mutation_p.S712*|SORBS2_ENST00000319471.9_Intron|SORBS2_ENST00000418609.1_Nonsense_Mutation_p.S616*|SORBS2_ENST00000498125.1_Intron|SORBS2_ENST00000355634.5_Nonsense_Mutation_p.S812*|SORBS2_ENST00000449407.2_Intron|SORBS2_ENST00000393528.3_Intron	NM_021069.4	NP_066547.1	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2			53		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)			CTTAGGAGCCGAATTTTTTTT	0.448000													Esophageal Squamous(153;41 2433 9491 36028)											0							SO:0001587	stop_gained			ENST00000284776.7	0	1	hg19	CCDS3845.1	.	.	.	.	.	.	.	.	.	.	G	36	5.837571	0.97009	.	.	ENSG00000154556	ENST00000284776;ENST00000431808;ENST00000418609;ENST00000355634	.	.	.	5.88	5.0	0.66597	.	0.741300	0.13760	N	0.364655	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.1252	11.2173	0.48833	0.0951:0.0:0.9049:0.0	.	.	.	.	X	712;712;616;812	.	ENSP00000284776:S712X	S	-	2	0	SORBS2	186781430	0.872000	0.30054	0.002000	0.10522	0.045000	0.14185	4.786000	0.62425	1.371000	0.46172	0.561000	0.74099	TCG		TCGA-HZ-A8P0-01A-11D-A36O-08	SORBS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347944.3	0	0	0	7	769	1	237		0	0	0	1	237	2		0	0	0	0	0	2	0	0.125135	7	763	1	233	13		0	0	0	1	237	2	-2.135062	0	1	0	0		1	1	2	3	2.016802	0	0.380000	1.960000	0.381176	0.040000	1.000000e-02	0.100000	0.050000	0.054186	0.040000	0	2.000000e-02	7.000000e-02
ST8SIA4	7903	broad.mit.edu	37	5	100191950	100191950	+	Silent	SNP	C	C	A			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr5:100191950C>A	ENST00000231461.5	-	4	964	c.654G>T	c.(652-654)ctG>ctT	p.L218L		NM_005668.4	NP_005659.1	Q92187	SIA8D_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4			25		all_cancers(142;1.5e-07)|all_epithelial(76;1.43e-10)|Prostate(80;0.000644)|Lung NSC(167;0.0059)|all_lung(232;0.00914)|Ovarian(225;0.024)|Colorectal(57;0.09)|Breast(839;0.203)			CACTGTCATTCAGCATGGAAA	0.398000																								0							SO:0001819	synonymous_variant			ENST00000231461.5	0	1	hg19	CCDS4091.1																																																																																				TCGA-HZ-A8P0-01A-11D-A36O-08	ST8SIA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250632.3	0	0	0	6	435	0	99	0	2.733852e-03	0	5	0	99	2		0	0	0	0	0	2	1	0.962386	6	424	0	98	2		0	0	0	0	99	2	-2.647119	1	1	0	0		1	0	0	0	2.008297	0	0.380000	1.960000	0.377635	0.070000	2.000000e-02	0.150000	0.080000	0.082552	0.070000	0	4.000000e-02	1.100000e-01
FAT2	2196	broad.mit.edu	37	5	150947407	150947407	+	Missense_Mutation	SNP	G	G	T			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr5:150947407G>T	ENST00000261800.5	-	1	1098	c.1086C>A	c.(1084-1086)ttC>ttA	p.F362L		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2			196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		CAGCCTTCTCGAATTTGAGGG	0.547000																								0							SO:0001583	missense			ENST00000261800.5	0	1	hg19	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	G	16.35	3.097914	0.56075	.	.	ENSG00000086570	ENST00000261800	T	0.65178	-0.14	5.49	-3.3	0.05003	Cadherin (1);Cadherin-like (1);	0.000000	0.64402	D	0.000005	T	0.73697	0.3620	M	0.79123	2.44	0.49915	D	0.999835	D	0.76494	0.999	D	0.79108	0.992	T	0.73636	-0.3920	10	0.54805	T	0.06	.	12.1639	0.54119	0.6671:0.0:0.3329:0.0	.	362	Q9NYQ8	FAT2_HUMAN	L	362	ENSP00000261800:F362L	ENSP00000261800:F362L	F	-	3	2	FAT2	150927600	0.783000	0.28701	0.420000	0.26596	0.667000	0.39255	0.121000	0.15667	-0.646000	0.05452	-0.997000	0.02515	TTC		TCGA-HZ-A8P0-01A-11D-A36O-08	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	0	0	0	6	466	0	83		0	0	0	0	83	2		0	0	0	0	0	2	1	0.964259	6	462	0	82	2		0	0	0	0	83	2	-3.015943	1	1	0	0		1	0	0	0	2.008297	0	0.380000	1.960000	0.377635	0.060000	2.000000e-02	0.140000	0.060000	0.077177	0.060000	0	4.000000e-02	1.100000e-01
PTPRK	5796	broad.mit.edu	37	6	128294292	128294292	+	Missense_Mutation	SNP	C	C	A			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr6:128294292C>A	ENST00000368215.3	-	29	4140	c.4141G>T	c.(4141-4143)Ggg>Tgg	p.G1381W	PTPRK_ENST00000368227.3_Missense_Mutation_p.G1399W|PTPRK_ENST00000368226.4_Missense_Mutation_p.G1382W|PTPRK_ENST00000532331.1_Missense_Mutation_p.G1404W|PTPRK_ENST00000368213.5_Missense_Mutation_p.G1388W|PTPRK_ENST00000368207.3_Missense_Mutation_p.G1414W|PTPRK_ENST00000368210.3_Missense_Mutation_p.G1400W			Q15262	PTPRK_HUMAN	protein tyrosine phosphatase, receptor type, K		PTPRK/RSPO3(10)	72					CCACTTCGCCCGCCACCATTT	0.428000																								0							SO:0001583	missense			ENST00000368215.3	0	1	hg19		.	.	.	.	.	.	.	.	.	.	C	24.3	4.517548	0.85495	.	.	ENSG00000152894	ENST00000368226;ENST00000368227;ENST00000532331;ENST00000368213;ENST00000368210;ENST00000368215;ENST00000368207	T;T;T;T;T;T;T	0.30182	1.54;1.54;1.54;1.54;1.54;1.54;1.54	5.52	5.52	0.82312	Protein-tyrosine phosphatase, receptor/non-receptor type (3);Protein-tyrosine/Dual-specificity phosphatase (1);	0.000000	0.85682	D	0.000000	T	0.71434	0.3339	H	0.98936	4.375	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.83626	0.0142	10	0.87932	D	0	.	19.7822	0.96420	0.0:1.0:0.0:0.0	.	1404;1388;1381;1382	B7ZMG0;Q15262-3;Q15262;Q15262-2	.;.;PTPRK_HUMAN;.	W	1382;1399;1404;1388;1400;1381;1414	ENSP00000357209:G1382W;ENSP00000357210:G1399W;ENSP00000432973:G1404W;ENSP00000357196:G1388W;ENSP00000357193:G1400W;ENSP00000357198:G1381W;ENSP00000357190:G1414W	ENSP00000357190:G1414W	G	-	1	0	PTPRK	128335985	1.000000	0.71417	0.945000	0.38365	0.728000	0.41692	7.776000	0.85560	2.750000	0.94351	0.655000	0.94253	GGG		TCGA-HZ-A8P0-01A-11D-A36O-08	PTPRK-005	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000042163.1	0	0	0	6	467	0	131	0	3.920894e-01	0	94	0	131	2		0	0	0	0	0	2	1	0.897156	6	313	0	97	2		0	0	0	0	131	2	-1.822784	0	1	0	0		1	0	0	0	1.981112	0	0.380000	1.960000	0.367992	0.060000	2.000000e-02	0.140000	0.060000	0.075828	0.060000	0	4.000000e-02	1.000000e-01
TNFAIP3	7128	broad.mit.edu	37	6	138199962	138199962	+	Silent	SNP	C	C	T			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr6:138199962C>T	ENST00000237289.4	+	7	1446	c.1380C>T	c.(1378-1380)gcC>gcT	p.A460A		NM_001270507.1|NM_001270508.1|NM_006290.3	NP_001257436.1|NP_001257437.1|NP_006281.1	P21580	TNAP3_HUMAN	tumor necrosis factor, alpha-induced protein 3	p.0?(25)|p.P450fs*21(1)		225	Breast(32;0.135)|Colorectal(23;0.24)				CTCATTCGGCCCCACCGACAG	0.642000			D, N, F		marginal zone B-cell lymphomas, Hodgkin's lymphoma, primary mediastinal B cell lymphoma								GBM(130;153 1739 22295 28918 47987)		Rec	yes		6	6q23	7128	tumor necrosis factor, alpha-induced protein 3		L	26	Whole gene deletion(25)|Deletion - Frameshift(1)						SO:0001819	synonymous_variant			ENST00000237289.4	1	1	hg19	CCDS5187.1																																																																																				TCGA-HZ-A8P0-01A-11D-A36O-08	TNFAIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042414.1	1	0	1	28	171	0	40	1	9.121458e-01	2	25	0	40	2		0	0	0	0	0	2	1	1.000000	28	167	0	39	2		0	0	0	0	40	2	-20.000000	1	1	0	0		1	0	0	0	1.981112	0	0.380000	1.960000	0.367992	0.720000	5.000000e-01	0.980000	0.720000	0.737023	0.720000	0	6.000000e-01	8.600000e-01
BRD2	6046	broad.mit.edu	37	6	32945220	32945220	+	Splice_Site	SNP	G	G	A			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr6:32945220G>A	ENST00000374825.4	+	8	2903	c.1202G>A	c.(1201-1203)cGg>cAg	p.R401Q	BRD2_ENST00000395289.2_Splice_Site_p.R401Q|BRD2_ENST00000374831.4_Splice_Site_p.R401Q|BRD2_ENST00000443797.2_Splice_Site_p.R281Q|BRD2_ENST00000449085.2_Splice_Site_p.R354Q|BRD2_ENST00000395287.1_Splice_Site_p.R401Q	NM_005104.3	NP_005095.1	P25440	BRD2_HUMAN	bromodomain containing 2			5					CTTCTGCAGCGGAAGATGGAG	0.527000																								0							SO:0001630	splice_region_variant			ENST00000374825.4	0	1	hg19	CCDS4762.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.70|16.70	3.196084|3.196084	0.58126|0.58126	.|.	.|.	ENSG00000204256|ENSG00000204256	ENST00000449025|ENST00000374825;ENST00000374831;ENST00000395289;ENST00000443797;ENST00000395287;ENST00000449085	.|T;T;T;T;T;T	.|0.27402	.|1.67;1.67;1.67;1.67;1.67;1.67	5.25|5.25	5.25|5.25	0.73442|0.73442	.|Bromodomain (5);Bromodomain, conserved site (1);	.|0.000000	.|0.45606	.|D	.|0.000343	T|T	0.06735|0.06735	0.0172|0.0172	N|N	0.16790|0.16790	0.44|0.44	0.58432|0.58432	D|D	0.999994|0.999994	.|P;B	.|0.38992	.|0.653;0.185	.|B;B	.|0.21708	.|0.036;0.012	T|T	0.13202|0.13202	-1.0518|-1.0518	5|10	.|0.33141	.|T	.|0.24	-13.4946|-13.4946	9.6958|9.6958	0.40156|0.40156	0.0911:0.0:0.9089:0.0|0.0911:0.0:0.9089:0.0	.|.	.|401;401	.|A2AAU0;P25440	.|.;BRD2_HUMAN	R|Q	407|401;401;401;281;401;354	.|ENSP00000363958:R401Q;ENSP00000363964:R401Q;ENSP00000378704:R401Q;ENSP00000413495:R281Q;ENSP00000378702:R401Q;ENSP00000409145:R354Q	.|ENSP00000363958:R401Q	G|R	+|+	1|2	0|0	BRD2|BRD2	33053198|33053198	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	1.760000|1.760000	0.38430|0.38430	2.730000|2.730000	0.93505|0.93505	0.643000|0.643000	0.83706|0.83706	GGA|CGG		TCGA-HZ-A8P0-01A-11D-A36O-08	BRD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076503.2	0	0	0	5	585	0	163	0	6.299104e-01	0	231	0	163	2		0	0	0	0	0	2	1	0.936940	5	582	0	162	2		0	0	0	0	163	2	-2.025574	0	1	0	0		1	0	0	0	1.972772	0	0.380000	1.960000	0.365534	0.040000	0	0.100000	0.040000	0.051917	0.040000	0	2.000000e-02	7.000000e-02
KLHL31	401265	broad.mit.edu	37	6	53519025	53519025	+	Missense_Mutation	SNP	G	G	A			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr6:53519025G>A	ENST00000407079.1	-	1	1045	c.1046C>T	c.(1045-1047)aCg>aTg	p.T349M	KLHL31_ENST00000370905.3_Missense_Mutation_p.T349M			Q9H511	KLH31_HUMAN	kelch-like family member 31			20	Lung NSC(77;0.0158)				TGGCATTTCCGTAAGCTTGCT	0.483000																								0							SO:0001583	missense			ENST00000407079.1	0	1	hg19	CCDS34478.1	.	.	.	.	.	.	.	.	.	.	G	17.70	3.453374	0.63290	.	.	ENSG00000124743	ENST00000370905;ENST00000407079	T;T	0.68025	-0.3;-0.3	5.25	5.25	0.73442	Galactose oxidase, beta-propeller (1);	0.095468	0.64402	D	0.000001	T	0.75852	0.3906	M	0.82716	2.605	0.58432	D	0.999994	D	0.76494	0.999	P	0.57283	0.817	T	0.80621	-0.1301	10	0.87932	D	0	.	15.4902	0.75600	0.0:0.1482:0.8518:0.0	.	349	Q9H511	KLH31_HUMAN	M	349	ENSP00000359942:T349M;ENSP00000384644:T349M	ENSP00000359942:T349M	T	-	2	0	KLHL31	53626984	1.000000	0.71417	0.994000	0.49952	0.980000	0.70556	7.818000	0.86416	2.467000	0.83353	0.561000	0.74099	ACG		TCGA-HZ-A8P0-01A-11D-A36O-08	KLHL31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040965.1	0	0	0	6	421	0	101	0	3.035724e-04	0	2	0	101	2		0	0	0	0	1	2	1	0.964195	6	417	0	99	2		0	0	0	0	101	2	-2.509507	1	1	0	0		1	0	0	0	1.981112	0	0.380000	1.960000	0.367992	0.070000	2.000000e-02	0.150000	0.070000	0.083919	0.070000	0	4.000000e-02	1.100000e-01
RIMS2	9699	broad.mit.edu	37	8	105026833	105026833	+	Silent	SNP	G	G	A			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr8:105026833G>A	ENST00000436393.2	+	17	2785	c.2544G>A	c.(2542-2544)acG>acA	p.T848T	RIMS2_ENST00000507740.1_Silent_p.T922T|RIMS2_ENST00000406091.3_Silent_p.T1108T|RIMS2_ENST00000262231.10_Silent_p.T947T			Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2			144			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)		CAAAGGGAACGTTGGATAGAA	0.438000										HNSCC(12;0.0054)														0							SO:0001819	synonymous_variant			ENST00000436393.2	1	1	hg19																																																																																					TCGA-HZ-A8P0-01A-11D-A36O-08	RIMS2-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000367217.1	1	0	0	48	186	0	48		0	0	0	0	48	2		0	0	0	0	0	2	1	1.000000	48	184	0	48	2		0	0	0	0	48	2	-20.000000	1	1	0	0		1	1	2	3	2.024273	0	0.380000	1.960000	0.381176	0.990000	8.200000e-01	1.000000	1.000000	0.978832	0.990000	1	9.400000e-01	1
FAM83H	286077	broad.mit.edu	37	8	144812372	144812372	+	Silent	SNP	C	C	T			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr8:144812372C>T	ENST00000388913.3	-	2	506	c.381G>A	c.(379-381)caG>caA	p.Q127Q	MIR4664_ENST00000583819.1_RNA	NM_198488.3	NP_940890	Q6ZRV2	FA83H_HUMAN	family with sequence similarity 83, member H			21	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)		GGGGCGGTGGCTGCACCAAGG	0.642000																								0							SO:0001819	synonymous_variant			ENST00000388913.3	1	1	hg19	CCDS6410.2																																																																																				TCGA-HZ-A8P0-01A-11D-A36O-08	FAM83H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257632.2	1	0	1	39	126	0	44	1	9.997998e-01	18	28	0	44	2		0	0	0	0	0	2	1	1.000000	38	125	0	43	2		0	0	0	0	44	2	-20.000000	1	1	0	0		1	1	2	3	2.024273	0	0.380000	1.960000	0.381176	0.990000	9.200000e-01	1.000000	1.000000	0.995601	0.990000	1	9.900000e-01	1
ZNF7	7553	broad.mit.edu	37	8	146067242	146067242	+	Silent	SNP	C	C	T			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr8:146067242C>T	ENST00000528372.1	+	5	990	c.750C>T	c.(748-750)taC>taT	p.Y250Y	ZNF7_ENST00000446747.2_Silent_p.Y261Y|ZNF7_ENST00000325241.6_Silent_p.Y250Y|ZNF7_ENST00000325217.5_Intron|ZNF7_ENST00000544249.1_Silent_p.Y154Y|ZNF7_ENST00000529819.1_3'UTR|ZNF7_ENST00000525266.1_Intron			P17097	ZNF7_HUMAN	zinc finger protein 7			25	all_cancers(97;1.03e-11)|all_epithelial(106;6.69e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)	Breast(495;0.0812)|Ovarian(118;0.0822)|Acute lymphoblastic leukemia(644;0.143)	Epithelial(56;8.75e-39)|OV - Ovarian serous cystadenocarcinoma(54;1.13e-38)|all cancers(56;8.48e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)		AGAAGCCGTACGAATGTGCAG	0.438000																								0							SO:0001819	synonymous_variant			ENST00000528372.1	1	1	hg19	CCDS6435.1																																																																																				TCGA-HZ-A8P0-01A-11D-A36O-08	ZNF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382660.1	1	0	0	81	328	0	91	1	9.782079e-01	3	24	0	91	2		0	0	0	0	0	2	1	1.000000	81	326	0	91	2		0	0	0	0	91	2	-20.000000	1	1	121412	3	38	1	1	2	3	2.068953	0	0.380000	1.960000	0.389283	0.990000	8.600000e-01	1.000000	1.000000	0.983633	0.990000	1	9.500000e-01	1
ZDHHC2	51201	broad.mit.edu	37	8	17067927	17067927	+	Silent	SNP	C	C	T			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr8:17067927C>T	ENST00000262096.8	+	10	1583	c.888C>T	c.(886-888)tgC>tgT	p.C296C		NM_016353.4	NP_057437.1	Q9UIJ5	ZDHC2_HUMAN	zinc finger, DHHC-type containing 2			8					TTCCAACTTGCCTTGTTAACC	0.368000																								0							SO:0001819	synonymous_variant			ENST00000262096.8	0	1	hg19	CCDS47810.1																																																																																				TCGA-HZ-A8P0-01A-11D-A36O-08	ZDHHC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376014.2	0	0	0	4	162	0	46	0	6.644295e-01	0	85	0	46	2		0	0	0	0	0	2	1	0.889923	4	161	0	46	2		0	0	0	0	46	2	-3.214261	1	1	0	0		1	1	2	3	2.024273	0	0.380000	1.960000	0.381176	0.140000	4.000000e-02	0.310000	0.120000	0.155412	0.140000	0	8.000000e-02	2.200000e-01
FOXD4	2298	broad.mit.edu	37	9	117739	117739	+	Silent	SNP	G	G	T			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr9:117739G>T	ENST00000382500.2	-	1	678	c.381C>A	c.(379-381)ctC>ctA	p.L127L		NM_207305.4	NP_997188.2	Q12950	FOXD4_HUMAN	forkhead box D4			14	all_lung(41;0.218)	all_cancers(5;0.0395)|Acute lymphoblastic leukemia(5;1.91e-07)|all_hematologic(5;1.95e-06)	Kidney(42;0.112)|KIRC - Kidney renal clear cell carcinoma(5;0.157)		AGATGCCGCTGAGCGTGAGGC	0.637000																								0							SO:0001819	synonymous_variant			ENST00000382500.2	0	1	hg19	CCDS34975.1																																																																																				TCGA-HZ-A8P0-01A-11D-A36O-08	FOXD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055433.1	0	0	0	9	858	0	365		0	0	0	0	365	2		0	0	0	0	0	2	1	0.982023	8	655	0	406	2		0	0	0	0	365	2	-2.352727	0	1	0	0		1						0.380000	1.960000									0	0
TNC	3371	broad.mit.edu	37	9	117846677	117846677	+	Missense_Mutation	SNP	G	G	A	rs149181557	by1000genomes	TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr9:117846677G>A	ENST00000350763.4	-	4	2353	c.1942C>T	c.(1942-1944)Cgg>Tgg	p.R648W	TNC_ENST00000535648.1_Missense_Mutation_p.R648W|TNC_ENST00000346706.3_Missense_Mutation_p.R648W|TNC_ENST00000345230.3_Missense_Mutation_p.R648W|TNC_ENST00000423613.2_Missense_Mutation_p.R648W|TNC_ENST00000340094.3_Missense_Mutation_p.R648W|TNC_ENST00000341037.4_Missense_Mutation_p.R648W|TNC_ENST00000542877.1_Missense_Mutation_p.R648W|TNC_ENST00000537320.1_Missense_Mutation_p.R648W	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C			120					TCTGTGACCCGCATCTCATTG	0.562000																								0							SO:0001583	missense			ENST00000350763.4	1	1	hg19	CCDS6811.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	19.75	3.885200	0.72410	0.0	2.33E-4	ENSG00000041982	ENST00000340094;ENST00000535648;ENST00000346706;ENST00000345230;ENST00000350763;ENST00000442945;ENST00000341037;ENST00000423613;ENST00000537320;ENST00000542877	T;T;T;T;T;T;T;T;T	0.57595	3.61;0.39;3.61;0.39;0.39;0.39;0.39;0.39;0.39	5.93	3.91	0.45181	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.343669	0.29459	N	0.012097	T	0.67420	0.2891	M	0.64404	1.975	0.38978	D	0.958897	D;D	0.89917	1.0;1.0	D;D	0.79784	0.987;0.993	T	0.72228	-0.4354	10	0.66056	D	0.02	.	12.0794	0.53662	0.0:0.1008:0.6328:0.2664	.	648;648	E9PC84;P24821	.;TENA_HUMAN	W	648	ENSP00000344400:R648W;ENSP00000438152:R648W;ENSP00000344555:R648W;ENSP00000345861:R648W;ENSP00000265131:R648W;ENSP00000339553:R648W;ENSP00000411406:R648W;ENSP00000443478:R648W;ENSP00000442242:R648W	ENSP00000344400:R648W	R	-	1	2	TNC	116886498	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	1.409000	0.34680	1.470000	0.48102	0.655000	0.94253	CGG		TCGA-HZ-A8P0-01A-11D-A36O-08	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	1	0	1	63	270	0	104	0	8.570096e-01	0	17	0	104	2	1	1	199	1153	1	1206	6	1	1.000000	62	267	0	104	2		0	0	0	0	104	2	-3.094673	1	1	121412	11	45	1	1	2	3	2.017164	0	0.380000	1.960000	0.381176	0.990000	7.800000e-01	1.000000	1.000000	0.956309	0.990000	1	8.800000e-01	1
OR1J2	26740	broad.mit.edu	37	9	125273336	125273336	+	Missense_Mutation	SNP	C	C	T			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr9:125273336C>T	ENST00000335302.5	+	1	256	c.256C>T	c.(256-258)Cgg>Tgg	p.R86W		NM_054107.1	NP_473448.1	Q8NGS2	OR1J2_HUMAN	olfactory receptor, family 1, subfamily J, member 2			26					GATGGACATGCGGACTAAGTA	0.428000																								0							SO:0001583	missense			ENST00000335302.5	0	1	hg19	CCDS35121.1	.	.	.	.	.	.	.	.	.	.	C	11.47	1.649512	0.29336	.	.	ENSG00000197233	ENST00000335302;ENST00000444856	T	0.01963	4.53	4.71	2.82	0.32997	GPCR, rhodopsin-like superfamily (1);	0.410669	0.17409	U	0.175258	T	0.01254	0.0041	N	0.02830	-0.485	0.20821	N	0.999849	B	0.02656	0.0	B	0.04013	0.001	T	0.46978	-0.9152	10	0.54805	T	0.06	.	8.7949	0.34874	0.0:0.7496:0.0:0.2504	.	86	Q8NGS2	OR1J2_HUMAN	W	86	ENSP00000335575:R86W	ENSP00000335575:R86W	R	+	1	2	OR1J2	124313157	0.000000	0.05858	0.273000	0.24645	0.016000	0.09150	-1.634000	0.02020	1.232000	0.43678	0.650000	0.86243	CGG		TCGA-HZ-A8P0-01A-11D-A36O-08	OR1J2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053932.1	0	0	0	6	529	1	135		0	0	0	1	135	2		0	0	0	0	0	2	0	0.035303	6	524	1	135	15		0	0	0	1	135	2	-2.002432	0	1	121374	1	20	1	1	2	3	2.017164	0	0.380000	1.960000	0.381176	0.060000	1.000000e-02	0.130000	0.060000	0.068554	0.060000	0	3.000000e-02	9.000000e-02
USP20	10868	broad.mit.edu	37	9	132623286	132623286	+	Nonsense_Mutation	SNP	C	C	A			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr9:132623286C>A	ENST00000315480.4	+	7	559	c.401C>A	c.(400-402)tCa>tAa	p.S134*	USP20_ENST00000372429.3_Nonsense_Mutation_p.S134*|USP20_ENST00000358355.1_Nonsense_Mutation_p.S134*			Q9Y2K6	UBP20_HUMAN	ubiquitin specific peptidase 20			11		Ovarian(14;0.00556)			GAGTCTGAGTCAGAGGACGAT	0.577000																								0							SO:0001587	stop_gained			ENST00000315480.4	0	1	hg19	CCDS43892.1	.	.	.	.	.	.	.	.	.	.	C	38	6.955403	0.97960	.	.	ENSG00000136878	ENST00000372429;ENST00000315480;ENST00000358355	.	.	.	5.66	5.66	0.87406	.	0.893214	0.09824	N	0.751070	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05721	T	0.95	.	14.3494	0.66691	0.0:0.8522:0.1478:0.0	.	.	.	.	X	134	.	ENSP00000313811:S134X	S	+	2	0	USP20	131663107	1.000000	0.71417	0.996000	0.52242	0.842000	0.47809	4.459000	0.60102	2.665000	0.90641	0.561000	0.74099	TCA		TCGA-HZ-A8P0-01A-11D-A36O-08	USP20-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054604.2	0	0	0	7	596	0	174	0	1.162114e-02	0	12	0	174	2		0	0	0	0	0	2	1	0.979995	7	590	0	174	2		0	0	0	0	174	2	-2.745178	1	1	0	0		1	1	2	3	2.017164	0	0.380000	1.960000	0.381176	0.060000	2.000000e-02	0.130000	0.060000	0.069569	0.060000	0	3.000000e-02	9.000000e-02
CACNA1B	774	broad.mit.edu	37	9	140968501	140968501	+	Missense_Mutation	SNP	G	G	A			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr9:140968501G>A	ENST00000371372.1	+	34	4985	c.4840G>A	c.(4840-4842)Gcc>Acc	p.A1614T	CACNA1B_ENST00000371365.2_5'Flank|CACNA1B_ENST00000277551.2_Missense_Mutation_p.A1614T|CACNA1B_ENST00000277549.5_Missense_Mutation_p.A808T|CACNA1B_ENST00000371355.4_Missense_Mutation_p.A1615T|CACNA1B_ENST00000371363.1_Missense_Mutation_p.A1612T|CACNA1B_ENST00000371357.1_Missense_Mutation_p.A1613T	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	p.A1614S(1)		80	all_cancers(76;0.166)			Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	CTTCATCTACGCCATCATCGG	0.622000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000371372.1	1	1	hg19	CCDS59522.1	.	.	.	.	.	.	.	.	.	.	G	36	5.943318	0.97128	.	.	ENSG00000148408	ENST00000371372;ENST00000277551;ENST00000277549;ENST00000371363;ENST00000371357;ENST00000371355	D;D;D;D;D;D	0.98400	-4.91;-4.91;-4.91;-4.91;-4.91;-4.91	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	D	0.99251	0.9739	M	0.93462	3.42	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79108	0.992;0.992	D	0.99084	1.0838	10	0.87932	D	0	.	19.0507	0.93043	0.0:0.0:1.0:0.0	.	1613;1612	B1AQK7;B1AQK6	.;.	T	1614;1614;808;1612;1613;1615	ENSP00000360423:A1614T;ENSP00000277551:A1614T;ENSP00000277549:A808T;ENSP00000360414:A1612T;ENSP00000360408:A1613T;ENSP00000360406:A1615T	ENSP00000277549:A808T	A	+	1	0	CACNA1B	140088322	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.624000	0.98398	2.584000	0.87258	0.561000	0.74099	GCC		TCGA-HZ-A8P0-01A-11D-A36O-08	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	1	0	1	84	406	0	158		0	0	0	0	158	2		0	0	0	0	0	2	1	1.000000	83	402	0	155	2		0	0	0	0	158	2	-3.345227	1	1	121378	1	33	1	1	2	3	2.017164	0	0.380000	1.960000	0.381176	0.900000	7.300000e-01	1.000000	1.000000	0.900328	0.900000	1	8.100000e-01	1
CDKN2A	1029	broad.mit.edu	37	9	21971186	21971186	+	Nonsense_Mutation	SNP	G	G	A	rs121913387		TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr9:21971186G>A	ENST00000304494.5	-	2	442	c.172C>T	c.(172-174)Cga>Tga	p.R58*	CDKN2A_ENST00000530628.2_Missense_Mutation_p.P72L|CDKN2A_ENST00000498124.1_Nonsense_Mutation_p.R58*|CDKN2A_ENST00000579755.1_Missense_Mutation_p.P72L|CDKN2A_ENST00000494262.1_Nonsense_Mutation_p.R7*|CDKN2A_ENST00000497750.1_Nonsense_Mutation_p.R7*|CDKN2A_ENST00000578845.2_Nonsense_Mutation_p.R7*|CDKN2A_ENST00000446177.1_Nonsense_Mutation_p.R58*|CDKN2A_ENST00000361570.3_Missense_Mutation_p.P113L|CDKN2A_ENST00000498628.2_Nonsense_Mutation_p.R7*|CDKN2A_ENST00000579122.1_Nonsense_Mutation_p.R58*|RP11-145E5.5_ENST00000404796.2_Intron|CDKN2A_ENST00000479692.2_Nonsense_Mutation_p.R7*	NM_000077.4	NP_000068.1	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A	p.0?(1315)|p.R58*(78)|p.?(45)|p.M53_R58del(3)|p.P113L(3)|p.R58fs*59(2)|p.M54fs*61(2)|p.R58fs*88(2)|p.0(1)|p.V28_V51del(1)|p.A57_R58>V*(1)|p.P113fs*>61(1)|p.R58fs*62(1)|p.R58fs*61(1)|p.G55fs*86(1)|p.R58R(1)|p.A57fs*85(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)			TCCGCCACTCGGGCGCTGCCC	0.677000		17								HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)														1459	Whole gene deletion(1316)|Substitution - Nonsense(78)|Unknown(45)|Deletion - Frameshift(10)|Deletion - In frame(4)|Substitution - Missense(3)|Insertion - Frameshift(1)|Substitution - coding silent(1)|Complex - compound substitution(1)	GRCh37	CM940227	CDKN2A	M	rs121913387	SO:0001587	stop_gained			ENST00000304494.5	0	1	hg19	CCDS6510.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	28.1|28.1	4.893482|4.893482	0.91889|0.91889	.|.	.|.	ENSG00000147889|ENSG00000147889	ENST00000361570;ENST00000530628|ENST00000304494;ENST00000446177	T;T|.	0.75367|.	-0.93;-0.89|.	5.79|5.79	2.71|2.71	0.32032|0.32032	.|.	0.409080|.	0.18162|.	N|.	0.149742|.	T|.	0.29288|.	0.0729|.	L|L	0.27053|0.27053	0.805|0.805	0.09310|0.09310	N|N	1|1	P|.	0.44006|.	0.824|.	B|.	0.33121|.	0.158|.	T|.	0.21381|.	-1.0247|.	10|.	0.72032|0.13470	D|T	0.01|0.59	-3.0019|-3.0019	9.6681|9.6681	0.39996|0.39996	0.0:0.1288:0.474:0.3972|0.0:0.1288:0.474:0.3972	.|.	113|.	Q8N726|.	CD2A2_HUMAN|.	L|X	113;72|58	ENSP00000355153:P113L;ENSP00000432664:P72L|.	ENSP00000355153:P113L|ENSP00000307101:R58X	P|R	-|-	2|1	0|2	CDKN2A|CDKN2A	21961186|21961186	0.000000|0.000000	0.05858|0.05858	0.002000|0.002000	0.10522|0.10522	0.277000|0.277000	0.26821|0.26821	0.096000|0.096000	0.15147|0.15147	0.738000|0.738000	0.32606|0.32606	0.555000|0.555000	0.69702|0.69702	CCG|CGA		TCGA-HZ-A8P0-01A-11D-A36O-08	CDKN2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000051915.1	1	0	0	7	52	0	11	1	7.373807e-01	19	2	0	11	2	1	7.759876e-01	9	14	0	17	2	1	0.982864	7	52	0	11	2		0	0	0	0	11	2	-2.996906	1	1	0	0		1	0	1	1	1.661914	1	0.380000	1.960000	0.234568	0.500000	2.300000e-01	0.850000	0.480000	0.524357	0.500000	0	3.500000e-01	6.900000e-01
SPTLC1	10558	broad.mit.edu	37	9	94812277	94812277	+	Missense_Mutation	SNP	G	G	T			TCGA-HZ-A8P0-01A-11D-A36O-08	TCGA-HZ-A8P0-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	df4c13c2-bf8e-4723-8a7c-341a512c02b7	041a6dc6-65d1-43d9-adb2-89c69d4b3e65	g.chr9:94812277G>T	ENST00000262554.2	-	9	858	c.853C>A	c.(853-855)Cat>Aat	p.H285N		NM_006415.2	NP_006406.1	O15269	SPTC1_HUMAN	serine palmitoyltransferase, long chain base subunit 1			14				L-Serine(DB00133)	CCTCGGCCATGCTCTCCTAGG	0.383000																								0							SO:0001583	missense			ENST00000262554.2	0	1	hg19	CCDS6692.1	.	.	.	.	.	.	.	.	.	.	G	4.415	0.076812	0.08485	.	.	ENSG00000090054	ENST00000262554	D	0.94687	-3.49	4.66	3.73	0.42828	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.104209	0.64402	D	0.000004	D	0.89181	0.6642	L	0.31120	0.905	0.80722	D	1	B;B	0.06786	0.0;0.001	B;B	0.12837	0.006;0.008	D	0.84518	0.0626	10	0.20519	T	0.43	-8.1887	13.3483	0.60587	0.0782:0.0:0.9218:0.0	.	285;285	Q6NUL7;O15269	.;SPTC1_HUMAN	N	285	ENSP00000262554:H285N	ENSP00000262554:H285N	H	-	1	0	SPTLC1	93852098	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.383000	0.59600	2.411000	0.81874	0.551000	0.68910	CAT		TCGA-HZ-A8P0-01A-11D-A36O-08	SPTLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055553.1	0	0	0	7	639	0	138	0	1.819409e-01	0	62	0	138	2		0	0	0	0	0	2	1	0.980027	7	633	0	136	2		0	0	0	0	138	2	-2.664656	1	1	0	0		1	0	0	0	2.008917	0	0.380000	1.960000	0.377635	0.050000	2.000000e-02	0.110000	0.060000	0.064605	0.050000	0	3.000000e-02	9.000000e-02
