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
UBC	7316	broad.mit.edu	37	12	125396390	125396393	+	Frame_Shift_Del	DEL	CCTT	CCTT	-	rs144126075	by1000genomes	TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08			CCTT	-	CCTT	CCTT		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr12:125396390_125396393delCCTT	ENST00000538617.1	-	4	1101_1104	c.785_788delAAGG	c.(784-789)gaaggcfs	p.EG262fs	UBC_ENST00000536661.1_5'Flank|UBC_ENST00000339647.5_Frame_Shift_Del_p.EG642fs|UBC_ENST00000536769.1_Frame_Shift_Del_p.EG642fs|UBC_ENST00000546120.1_Frame_Shift_Del_p.EG566fs			P0CG48	UBC_HUMAN	ubiquitin C			36	all_neural(191;0.101)|Medulloblastoma(191;0.163)				AGGAGGGATGCCTTCCTTATCTTG	0.510000																								0							SO:0001589	frameshift_variant			ENST00000538617.1	1	0	hg19																																																																																					TCGA-S4-A8RM-01A-11D-A377-08	UBC-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000400179.1	1	0	0	188	1089	0	257	1	1	47	7932	0	257	2			0	0	0	0		1	1.000000	227	974	10	266	64	0	0	0	0	0	0		-20.000000	1	0	0	0		1	0	0	0	1.993499	0	0.640000	1.980000	0.637681	0.450000	3.900000e-01	0.520000	0.460000	0.458624	0.450000	0	4.200000e-01	0.490000
SMAD4	4089	broad.mit.edu	37	18	48604715	48604716	+	Frame_Shift_Ins	INS	-	-	A			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08			-	A	-	-		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr18:48604715_48604716insA	ENST00000342988.3	+	12	2075_2076	c.1537_1538insA	c.(1537-1539)tacfs	p.Y513fs	SMAD4_ENST00000588745.1_Frame_Shift_Ins_p.Y417fs|SMAD4_ENST00000586253.1_3'UTR|SMAD4_ENST00000398417.2_Frame_Shift_Ins_p.Y513fs	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	p.0?(36)|p.?(2)		454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)			GGGACCGGATTACCCAAGACAG	0.480000																								38	Whole gene deletion(36)|Unknown(2)						SO:0001589	frameshift_variant			ENST00000342988.3	0	1	hg19	CCDS11950.1																																																																																				TCGA-S4-A8RM-01A-11D-A377-08	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	1	0	0	93	254	0	62	0	1	1	83	0	62	2	1	1	267	660	0	508	2	1	1.000000	93	248	0	61	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	0	1	1	1.440698	1	0.640000	1.980000	0.473068	0.560000	4.700000e-01	0.670000	0.570000	0.573204	0.560000	0	5.100000e-01	0.620000
ZNF468	90333	broad.mit.edu	37	19	53344850	53344850	+	Frame_Shift_Del	DEL	G	G	-			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08			G	-	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr19:53344850delG	ENST00000595646.1	-	4	817	c.697delC	c.(697-699)catfs	p.H233fs	ZNF468_ENST00000396409.4_Frame_Shift_Del_p.H180fs|ZNF468_ENST00000243639.4_3'UTR|ZNF468_ENST00000390651.4_Frame_Shift_Del_p.H180fs|ZNF28_ENST00000594602.1_Intron			Q5VIY5	ZN468_HUMAN	zinc finger protein 468			23					ATTATCTGATGTTTTTTTAAG	0.353000																								0							SO:0001589	frameshift_variant			ENST00000595646.1	1	1	hg19	CCDS33094.1																																																																																				TCGA-S4-A8RM-01A-11D-A377-08	ZNF468-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463098.1	1	0	0	98	379	0	155	1	9.900293e-01	3	27	0	155	2			0	0	0	0		1	1.000000	99	376	1	156	12	0	0	0	0	0	0		-20.000000	1	1	0	0		1	1	2	3	2.032905	0	0.640000	1.980000	0.641148	0.640000	5.300000e-01	0.770000	0.640000	0.647184	0.640000	0	5.800000e-01	0.710000
A4GNT	51146	broad.mit.edu	37	3	137849766	137849767	+	Frame_Shift_Ins	INS	-	-	A			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr3:137849766_137849767insA	ENST00000236709.3	-	2	533_534	c.332_333insT	c.(331-333)atafs	p.I111fs		NM_016161.2	NP_057245.1	Q9UNA3	A4GCT_HUMAN	alpha-1,4-N-acetylglucosaminyltransferase			16					AAACGTTGTCTATTGCTGACAG	0.421000																								0							SO:0001589	frameshift_variant			ENST00000236709.3	0	1	hg19	CCDS3097.1																																																																																				TCGA-S4-A8RM-01A-11D-A377-08	A4GNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357557.1	1	0	0	124	460	0	80	0	9.788509e-01	0	25	0	80	2			0	0	0	0		1	1.000000	127	454	0	80	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	0	0	0	2.015211	0	0.640000	1.980000	0.640000	0.650000	5.500000e-01	0.770000	0.660000	0.665948	0.650000	0	6.000000e-01	0.720000
LMLN	89782	broad.mit.edu	37	3	197687308	197687309	+	Frame_Shift_Del	DEL	TG	TG	-			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr3:197687308_197687309delTG	ENST00000330198.4	+	1	238_239	c.216_217delTG	c.(214-219)actgagfs	p.E73fs	LMLN_ENST00000420910.2_Frame_Shift_Del_p.E73fs|IQCG_ENST00000480302.1_5'Flank|LMLN_ENST00000482695.1_Intron|LMLN_ENST00000332636.5_Intron|IQCG_ENST00000265239.6_5'Flank	NM_033029.3	NP_149018.2	Q96KR4	LMLN_HUMAN	leishmanolysin-like (metallopeptidase M8 family)			25	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)	Lung NSC(153;0.132)	Epithelial(36;9.84e-24)|all cancers(36;3.18e-22)|OV - Ovarian serous cystadenocarcinoma(49;5.35e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)		CCTCTGACACTGAGGTAGGGCG	0.639000																								0							SO:0001589	frameshift_variant			ENST00000330198.4	0	1	hg19	CCDS3332.1																																																																																				TCGA-S4-A8RM-01A-11D-A377-08	LMLN-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339701.1	1	0	0	28	231	0	28	0	9.986996e-02	0	5	0	28	2			0	0	0	0		1	1.000000	30	225	0	28	2	0	0	0	0	0	0		-3.221905	1	1	0	0		1	1	2	3	2.028014	0	0.640000	1.980000	0.641148	0.330000	2.300000e-01	0.480000	0.340000	0.347583	0.330000	0	2.800000e-01	0.410000
SEMA3F	6405	broad.mit.edu	37	3	50222213	50222214	+	In_Frame_Ins	INS	-	-	GACGGGCGT			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr3:50222213_50222214insGACGGGCGT	ENST00000002829.3	+	13	1906_1907	c.1422_1423insGACGGGCGT	c.(1423-1425)gac>GACGGGCGTgac	p.475_475D>DGRD	SEMA3F_ENST00000434342.1_In_Frame_Ins_p.444_444D>DGRD|SEMA3F_ENST00000413852.1_In_Frame_Ins_p.376_376D>DGRD	NM_004186.3	NP_004177.3	Q13275	SEM3F_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F			17					TGGATGCAGCCGACGGGCGCTA	0.673000																								0							SO:0001652	inframe_insertion			ENST00000002829.3	0	1	hg19	CCDS2811.1																																																																																				TCGA-S4-A8RM-01A-11D-A377-08	SEMA3F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345929.1	1	0	0	12	191	0	22	0	4.258142e-01	0	23	0	22	2			0	0	0	0		1	0.999597	33	193	0	23	2	0	0	0	0	0	0		-15.382830	1	1	0	0		1	0	0	0	2.015211	0	0.640000	1.980000	0.640000	0.180000	1.000000e-01	0.300000	0.180000	0.197608	0.180000	0	1.300000e-01	0.250000
SFMBT2	57713	broad.mit.edu	37	10	7218087	7218087	+	Missense_Mutation	SNP	G	G	A			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr10:7218087G>A	ENST00000361972.4	-	17	1939	c.1849C>T	c.(1849-1851)Cgg>Tgg	p.R617W	SFMBT2_ENST00000397167.1_Missense_Mutation_p.R617W	NM_001018039.1	NP_001018049.1	Q5VUG0	SMBT2_HUMAN	Scm-like with four mbt domains 2	p.R617G(1)		99					TCAGATGTCCGTACGATTTTG	0.468000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000361972.4	0	1	hg19	CCDS31138.1	.	.	.	.	.	.	.	.	.	.	G	18.55	3.648095	0.67358	.	.	ENSG00000198879	ENST00000361972;ENST00000397167	T;T	0.47528	0.84;0.84	5.96	5.04	0.67666	.	0.000000	0.85682	D	0.000000	T	0.68522	0.3010	M	0.70275	2.135	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.72868	-0.4162	10	0.72032	D	0.01	.	16.3303	0.83006	0.0:0.0:0.8669:0.1331	.	617	Q5VUG0	SMBT2_HUMAN	W	617	ENSP00000355109:R617W;ENSP00000380353:R617W	ENSP00000355109:R617W	R	-	1	2	SFMBT2	7258093	1.000000	0.71417	0.041000	0.18516	0.283000	0.27025	5.140000	0.64807	1.468000	0.48064	0.655000	0.94253	CGG		TCGA-S4-A8RM-01A-11D-A377-08	SFMBT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046673.1	0	0	0	7	609	0	84	0	1.101637e-03	0	4	0	84	2		0	0	0	0	0	2	1	0.978666	6	593	0	82	2		0	0	0	0	84	2	-2.221656	0	1	121412	1	31	1	1	2	3	2.029876	0	0.640000	1.980000	0.641148	0.030000	0	0.080000	0.040000	0.040412	0.030000	0	1.000000e-02	0.060000
ARHGEF12	23365	broad.mit.edu	37	11	120348235	120348235	+	Splice_Site	SNP	G	G	T			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08			G	T	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr11:120348235G>T	ENST00000397843.2	+	36	3698	c.3532G>T	c.(3532-3534)Gac>Tac	p.D1178Y	ARHGEF12_ENST00000532993.1_Splice_Site_p.D1075Y|ARHGEF12_ENST00000356641.3_Splice_Site_p.D1159Y	NM_015313.2	NP_056128.1	Q9NZN5	ARHGC_HUMAN	Rho guanine nucleotide exchange factor (GEF) 12			61		Breast(109;0.000813)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_hematologic(192;0.107)|all_neural(223;0.112)			GCAGAGTCCAGGTACACTCTT	0.413000			T	MLL	AML										Dom	yes		11	11q23.3	23365	RHO guanine nucleotide exchange factor (GEF) 12 (LARG)		L	0							SO:0001630	splice_region_variant			ENST00000397843.2	1	0	hg19	CCDS41727.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.045601	0.75846	.	.	ENSG00000196914	ENST00000397843;ENST00000356641;ENST00000532993	T;T;T	0.72505	-0.55;-0.66;-0.53	4.85	4.85	0.62838	.	0.141481	0.32357	N	0.006209	T	0.74794	0.3763	L	0.29908	0.895	0.46586	D	0.999111	D;D	0.71674	0.998;0.997	D;P	0.63192	0.912;0.819	T	0.77638	-0.2513	10	0.59425	D	0.04	-5.4223	16.4829	0.84162	0.0:0.0:1.0:0.0	.	1159;1178	Q9NZN5-2;Q9NZN5	.;ARHGC_HUMAN	Y	1178;1159;1075	ENSP00000380942:D1178Y;ENSP00000349056:D1159Y;ENSP00000432984:D1075Y	ENSP00000349056:D1159Y	D	+	1	0	ARHGEF12	119853445	1.000000	0.71417	1.000000	0.80357	0.684000	0.39900	5.638000	0.67861	2.392000	0.81423	0.585000	0.79938	GAC		TCGA-S4-A8RM-01A-11D-A377-08	ARHGEF12-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388052.1	1	0	1	71	165	0	42	1	1	19	84	0	42	2		0	0	0	0	0	2	1	1.000000	70	161	0	42	2		0	0	0	0	42	2	-7.089722	1	1	0	0		1	1	2	3	2.027490	0	0.640000	1.980000	0.641148	0.930000	7.600000e-01	1.000000	1.000000	0.929513	0.930000	1	8.400000e-01	1.000000
NFRKB	4798	broad.mit.edu	37	11	129739654	129739654	+	Missense_Mutation	SNP	C	C	T			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr11:129739654C>T	ENST00000446488.3	-	23	3369	c.3266G>A	c.(3265-3267)cGc>cAc	p.R1089H	NFRKB_ENST00000524746.1_Missense_Mutation_p.R1089H|NFRKB_ENST00000524794.1_Missense_Mutation_p.R1114H|NFRKB_ENST00000304521.5_Missense_Mutation_p.R1089H	NM_001143835.1	NP_001137307.1	Q6P4R8	NFRKB_HUMAN	nuclear factor related to kappaB binding protein			32	all_hematologic(175;0.0537)	Breast(109;0.00526)|Lung NSC(97;0.00901)|all_lung(97;0.018)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)			CTGCACGATGCGGATCGTGGC	0.597000																								0							SO:0001583	missense			ENST00000446488.3	0	1	hg19	CCDS44770.1	.	.	.	.	.	.	.	.	.	.	C	31	5.063126	0.93898	0.0	1.16E-4	ENSG00000170322	ENST00000304521;ENST00000446488;ENST00000524794;ENST00000524746	.	.	.	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	T	0.68540	0.3012	L	0.32530	0.975	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.996;0.998;0.997	T	0.69975	-0.4999	9	0.52906	T	0.07	-11.2341	18.9658	0.92695	0.0:1.0:0.0:0.0	.	1089;1088;1114	Q6P4R8;Q6P4R8-3;Q6P4R8-2	NFRKB_HUMAN;.;.	H	1089;1089;1114;1089	.	ENSP00000303800:R1089H	R	-	2	0	NFRKB	129244864	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.487000	0.81328	2.474000	0.83562	0.655000	0.94253	CGC		TCGA-S4-A8RM-01A-11D-A377-08	NFRKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386063.2	0	0	0	5	522	0	94	0	5.854911e-02	0	33	0	94	2		0	0	0	0	0	2	1	0.935596	5	515	0	94	2		0	0	0	0	94	2	-2.111172	0	1	121412	2	36	1	1	2	3	2.027490	0	0.640000	1.980000	0.641148	0.020000	0	0.070000	0.030000	0.034854	0.020000	0	1.000000e-02	0.050000
KCNA4	3739	broad.mit.edu	37	11	30033579	30033579	+	Missense_Mutation	SNP	C	C	T			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr11:30033579C>T	ENST00000328224.6	-	2	1880	c.647G>A	c.(646-648)cGc>cAc	p.R216H	KCNA4_ENST00000526518.1_5'Flank	NM_002233.3	NP_002224.1	P22459	KCNA4_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 4			78				Dalfampridine(DB06637)	ATACTCATTGCGCAAAGGGTC	0.478000																								0							SO:0001583	missense			ENST00000328224.6	1	1	hg19	CCDS41629.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.410513	0.83340	.	.	ENSG00000182255	ENST00000328224	T	0.77358	-1.09	4.94	4.94	0.65067	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.000000	0.85682	D	0.000000	D	0.84297	0.5441	M	0.84156	2.68	0.80722	D	1	D	0.69078	0.997	P	0.49332	0.607	D	0.87784	0.2614	10	0.72032	D	0.01	.	18.1944	0.89817	0.0:1.0:0.0:0.0	.	216	P22459	KCNA4_HUMAN	H	216	ENSP00000328511:R216H	ENSP00000328511:R216H	R	-	2	0	KCNA4	29990155	1.000000	0.71417	0.981000	0.43875	0.887000	0.51463	7.787000	0.85759	2.297000	0.77311	0.655000	0.94253	CGC		TCGA-S4-A8RM-01A-11D-A377-08	KCNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388074.2	1	0	0	32	434	0	72		0	0	0	0	72	2		0	0	0	0	0	2	1	1.000000	32	429	0	72	2		0	0	0	0	72	2	-8.455999	1	1	0	0		1	1	2	3	2.027490	0	0.640000	1.980000	0.641148	0.210000	1.400000e-01	0.300000	0.220000	0.220793	0.210000	0	1.700000e-01	0.260000
DUSP16	80824	broad.mit.edu	37	12	12639992	12639992	+	Missense_Mutation	SNP	G	G	A			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr12:12639992G>A	ENST00000228862.2	-	5	1292	c.661C>T	c.(661-663)Ccg>Tcg	p.P221S	DUSP16_ENST00000298573.4_3'UTR|DUSP16_ENST00000545864.1_5'UTR|RP11-253I19.3_ENST00000544086.1_lincRNA	NM_030640.2	NP_085143.1	Q9BY84	DUS16_HUMAN	dual specificity phosphatase 16			26		Prostate(47;0.0687)			TCCAACCACGGCAAAATTTTC	0.458000													Ovarian(158;443 1896 15437 36069 46477)											0							SO:0001583	missense			ENST00000228862.2	0	1	hg19	CCDS8650.1	.	.	.	.	.	.	.	.	.	.	G	29.0	4.968201	0.92855	.	.	ENSG00000111266	ENST00000228862	D	0.85339	-1.97	5.27	5.27	0.74061	Dual specificity phosphatase, catalytic domain (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	0.128209	0.53938	D	0.000056	D	0.89525	0.6740	L	0.39326	1.205	0.80722	D	1	D;D	0.63880	0.993;0.966	D;D	0.72338	0.977;0.948	D	0.89322	0.3641	10	0.49607	T	0.09	.	19.2465	0.93904	0.0:0.0:1.0:0.0	.	221;221	Q9BY84;Q96N49	DUS16_HUMAN;.	S	221	ENSP00000228862:P221S	ENSP00000228862:P221S	P	-	1	0	DUSP16	12531259	1.000000	0.71417	0.734000	0.30879	0.975000	0.68041	9.516000	0.98017	2.621000	0.88768	0.561000	0.74099	CCG		TCGA-S4-A8RM-01A-11D-A377-08	DUSP16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400311.1	0	0	0	5	524	0	106	0	1.723071e-01	0	65	0	106	2		0	0	0	0	0	2	1	0.936243	5	519	0	106	2		0	0	0	0	106	2	-1.930126	0	1	0	0		1	1	2	3	2.030759	0	0.640000	1.980000	0.641148	0.020000	0	0.070000	0.030000	0.034714	0.020000	0	1.000000e-02	0.050000
DDX47	51202	broad.mit.edu	37	12	12974195	12974195	+	Missense_Mutation	SNP	G	G	T			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr12:12974195G>T	ENST00000358007.3	+	3	257	c.235G>T	c.(235-237)Gct>Tct	p.A79S	DDX47_ENST00000352940.4_Missense_Mutation_p.A79S|DDX47_ENST00000392155.2_3'UTR	NM_016355.3	NP_057439.2	Q9H0S4	DDX47_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 47			16		Prostate(47;0.0526)			AGGCGCCTTTGCTTTGCCCAT	0.488000																								0							SO:0001583	missense			ENST00000358007.3	0	1	hg19	CCDS8655.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.703195	0.88924	.	.	ENSG00000213782	ENST00000352940;ENST00000358007	T;T	0.44083	0.93;2.57	5.6	4.71	0.59529	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.53077	0.1774	L	0.49571	1.57	0.80722	D	1	B;B;B;B	0.30634	0.134;0.098;0.08;0.288	P;B;B;P	0.49387	0.609;0.326;0.34;0.475	T	0.48980	-0.8986	10	0.25106	T	0.35	-9.5993	14.6773	0.68989	0.0699:0.0:0.93:0.0	.	79;79;79;79	B4DYP6;Q9H4E3;G5E955;Q9H0S4	.;.;.;DDX47_HUMAN	S	79	ENSP00000319578:A79S;ENSP00000350698:A79S	ENSP00000319578:A79S	A	+	1	0	DDX47	12865462	1.000000	0.71417	0.992000	0.48379	0.993000	0.82548	9.201000	0.95017	1.370000	0.46153	0.555000	0.69702	GCT		TCGA-S4-A8RM-01A-11D-A377-08	DDX47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400674.1	0	0	0	10	1049	0	150	0	3.313435e-01	1	114	0	150	2		0	0	0	0	0	2	1	0.996661	9	1036	0	148	2		0	0	0	0	150	2	-2.878864	1	1	0	0		1	1	2	3	2.030759	0	0.640000	1.980000	0.641148	0.020000	0	0.060000	0.040000	0.031808	0.020000	0	1.000000e-02	0.050000
LRMP	4033	broad.mit.edu	37	12	25232195	25232195	+	Silent	SNP	C	C	T	rs114104872	by1000genomes	TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr12:25232195C>T	ENST00000354454.3	+	6	871	c.42C>T	c.(40-42)cgC>cgT	p.R14R	LRMP_ENST00000547044.1_Silent_p.R14R|LRMP_ENST00000548766.1_Silent_p.R14R	NM_006152.3	NP_006143.2	Q12912	LRMP_HUMAN	lymphoid-restricted membrane protein			19	Acute lymphoblastic leukemia(6;0.00112)|all_hematologic(7;0.00152)|Colorectal(261;0.11)				GTGTTGAACGCGTGTGTCCTG	0.373000																								0							SO:0001819	synonymous_variant			ENST00000354454.3	1	1	hg19	CCDS8701.1																																																																																				TCGA-S4-A8RM-01A-11D-A377-08	LRMP-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407870.1	1	0	1	220	564	0	152	1	9.999242e-01	15	23	0	152	2		0	0	0	0	0	2	1	1.000000	217	556	0	150	2		0	0	0	0	152	2	-20.000000	1	1	121412	40	49	1	1	2	3	2.030759	0	0.640000	1.980000	0.641148	0.870000	7.700000e-01	0.980000	0.880000	0.880645	0.870000	1	8.200000e-01	0.930000
KRAS	3845	broad.mit.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	C	A	rs121913529		TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08			C	A	C	C		Valid	Somatic	Phase_I	WXS	KRAS_deep			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr12:25398284C>A	ENST00000256078.4	-	2	98	c.35G>T	c.(34-36)gGt>gTt	p.G12V	KRAS_ENST00000556131.1_Missense_Mutation_p.G12V|KRAS_ENST00000557334.1_Missense_Mutation_p.G12V|KRAS_ENST00000311936.3_Missense_Mutation_p.G12V	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)		GCCTACGCCACCAGCTCCAAC	0.348000	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		pancreatic, colorectal, lung, thyroid, AML, others				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)			Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		L, E, M, O	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)						SO:0001583	missense	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	ENST00000256078.4	1	1	hg19	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.808637	0.90707	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90373	0.6987	M	0.90650	3.135	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.72625	0.969;0.978	D	0.91773	0.5429	10	0.72032	D	0.01	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	V	12	ENSP00000308495:G12V;ENSP00000452512:G12V;ENSP00000256078:G12V;ENSP00000451856:G12V	ENSP00000256078:G12V	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		TCGA-S4-A8RM-01A-11D-A377-08	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	1	0	1	82	228	0	51	1	9.999627e-01	27	18	0	51	2	1	1	111	310	0	247	2	1	1.000000	82	225	0	51	2	1	1	2492	5524	0	51	2	-20.000000	1	1	0	0		1	1	2	3	2.030759	0	0.640000	1.980000	0.641148	0.820000	6.700000e-01	0.990000	0.830000	0.831894	0.820000	0	7.400000e-01	0.910000
STAT6	6778	broad.mit.edu	37	12	57492807	57492807	+	Missense_Mutation	SNP	G	G	A			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr12:57492807G>A	ENST00000300134.3	-	17	2271	c.1946C>T	c.(1945-1947)aCc>aTc	p.T649I	STAT6_ENST00000556155.1_Missense_Mutation_p.T649I|STAT6_ENST00000538913.2_Missense_Mutation_p.T539I|STAT6_ENST00000537215.2_Missense_Mutation_p.T539I|STAT6_ENST00000454075.3_Missense_Mutation_p.T649I|STAT6_ENST00000543873.2_Missense_Mutation_p.T649I	NM_001178078.1|NM_003153.4	NP_001171549.1|NP_003144.3	P42226	STAT6_HUMAN	signal transducer and activator of transcription 6, interleukin-4 induced			28					CCTTTCCACGGTCATCTTGAT	0.532000																								0							SO:0001583	missense			ENST00000300134.3	0	1	hg19	CCDS8931.1	.	.	.	.	.	.	.	.	.	.	G	15.64	2.894701	0.52121	.	.	ENSG00000166888	ENST00000300134;ENST00000535201;ENST00000538913;ENST00000543873;ENST00000556155;ENST00000537215;ENST00000454075;ENST00000542721;ENST00000555318;ENST00000542516	D;D;D;D;D;D;T	0.92048	-2.72;-2.96;-2.72;-2.72;-2.96;-2.72;-1.17	5.77	4.87	0.63330	SH2 motif (1);	0.344421	0.30473	N	0.009541	D	0.86535	0.5956	N	0.19112	0.55	0.36500	D	0.868949	P;P	0.48694	0.914;0.844	B;B	0.43623	0.425;0.313	D	0.89133	0.3511	10	0.51188	T	0.08	-11.3662	12.7493	0.57300	0.0:0.1647:0.8353:0.0	.	649;649	A8K4S9;P42226	.;STAT6_HUMAN	I	649;539;539;649;649;539;649;539;77;649	ENSP00000300134:T649I;ENSP00000445409:T539I;ENSP00000438451:T649I;ENSP00000451742:T649I;ENSP00000444530:T539I;ENSP00000401486:T649I;ENSP00000450428:T77I	ENSP00000300134:T649I	T	-	2	0	STAT6	55779074	0.998000	0.40836	0.998000	0.56505	0.954000	0.61252	3.174000	0.50847	1.417000	0.47077	0.561000	0.74099	ACC		TCGA-S4-A8RM-01A-11D-A377-08	STAT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412248.3	0	0	0	5	620	0	105	0	9.377629e-01	0	624	0	105	2		0	0	0	0	0	2	1	0.935358	5	611	0	104	2		0	0	0	0	105	2	-2.897311	1	1	0	0		1	0	0	0	1.993499	0	0.640000	1.980000	0.637681	0.020000	0	0.060000	0.020000	0.028882	0.020000	0	0	0.040000
B4GALNT1	2583	broad.mit.edu	37	12	58021575	58021575	+	Missense_Mutation	SNP	G	G	T			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr12:58021575G>T	ENST00000341156.4	-	10	1794	c.1210C>A	c.(1210-1212)Ccc>Acc	p.P404T	B4GALNT1_ENST00000418555.2_Missense_Mutation_p.P349T	NM_001478.3	NP_001469.1	Q00973	B4GN1_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 1			20	Melanoma(17;0.122)		BRCA - Breast invasive adenocarcinoma(9;0.109)		GGGGCGCCGGGCTCCACGCTC	0.706000																								0							SO:0001583	missense			ENST00000341156.4	1	1	hg19	CCDS8950.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	10.01|10.01	1.234514|1.234514	0.22626|0.22626	.|.	.|.	ENSG00000135454|ENSG00000135454	ENST00000341156;ENST00000418555|ENST00000547741	T;T|.	0.18338|.	2.22;2.26|.	4.5|4.5	2.54|2.54	0.30619|0.30619	Glycosyl transferase, family 2 (1);|.	0.499457|.	0.21274|.	N|.	0.077269|.	T|T	0.49474|0.49474	0.1559|0.1559	L|L	0.33753|0.33753	1.03|1.03	0.80722|0.80722	D|D	1|1	B;B|.	0.29805|.	0.126;0.257|.	B;B|.	0.28916|.	0.096;0.082|.	T|T	0.36114|0.36114	-0.9761|-0.9761	10|5	0.12430|.	T|.	0.62|.	-7.0386|-7.0386	8.8722|8.8722	0.35323|0.35323	0.0874:0.1505:0.7621:0.0|0.0874:0.1505:0.7621:0.0	.|.	349;404|.	B4DE26;Q00973|.	.;B4GN1_HUMAN|.	T|R	404;349|86	ENSP00000341562:P404T;ENSP00000401601:P349T|.	ENSP00000341562:P404T|.	P|S	-|-	1|3	0|2	B4GALNT1|B4GALNT1	56307842|56307842	0.097000|0.097000	0.21791|0.21791	0.942000|0.942000	0.38095|0.38095	0.968000|0.968000	0.65278|0.65278	0.656000|0.656000	0.24948|0.24948	1.063000|1.063000	0.40649|0.40649	0.462000|0.462000	0.41574|0.41574	CCC|AGC		TCGA-S4-A8RM-01A-11D-A377-08	B4GALNT1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407853.1	1	0	0	20	53	0	12		0	0	0	0	12	2		0	0	0	0	0	2	1	0.999998	20	51	0	11	2		0	0	0	0	12	2	-20.000000	1	1	0	0		1	0	0	0	1.993499	0	0.640000	1.980000	0.637681	0.840000	5.600000e-01	1.000000	1.000000	0.844342	0.840000	0	6.900000e-01	1.000000
TPI1	7167	broad.mit.edu	37	12	6979268	6979268	+	Missense_Mutation	SNP	C	C	T	rs139532537		TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08			C	T	C	C		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr12:6979268C>T	ENST00000229270.4	+	6	1047	c.710C>T	c.(709-711)gCg>gTg	p.A237V	TPI1_ENST00000396705.5_Missense_Mutation_p.A200V|TPI1_ENST00000535434.1_Missense_Mutation_p.A118V|TPI1_ENST00000488464.2_Missense_Mutation_p.A118V	NM_001159287.1	NP_001152759.1	P60174	TPIS_HUMAN	triosephosphate isomerase 1			19					GTCTCTGATGCGGTGGCTCAG	0.552000											OREG0021638	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)												0							SO:0001583	missense			ENST00000229270.4	0	1	hg19	CCDS53740.1	.	.	.	.	.	.	.	.	.	.	C	13.87	2.366735	0.41902	0.0	1.16E-4	ENSG00000111669	ENST00000229270;ENST00000396705;ENST00000535434	D;D;D	0.94330	-3.4;-3.4;-3.4	5.44	3.57	0.40892	Aldolase-type TIM barrel (1);	0.213213	0.38837	U	0.001559	D	0.90748	0.7096	M	0.67569	2.06	0.18873	N	0.999984	B	0.17667	0.023	B	0.12156	0.007	T	0.83227	-0.0065	10	0.56958	D	0.05	.	8.4396	0.32808	0.4046:0.4513:0.144:0.0	.	237	P60174	TPIS_HUMAN	V	237;200;118	ENSP00000229270:A237V;ENSP00000379933:A200V;ENSP00000443599:A118V	ENSP00000229270:A237V	A	+	2	0	TPI1	6849529	0.989000	0.36119	0.048000	0.18961	0.889000	0.51656	2.951000	0.49089	0.626000	0.30322	0.462000	0.41574	GCG		TCGA-S4-A8RM-01A-11D-A377-08	TPI1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258252.1	0	0	0	5	577	0	76	0	9.940087e-01	1	1199	0	76	2		0	0	0	0	0	2	1	0.934302	5	565	0	75	2		0	0	0	0	76	2	-1.931661	0	1	121412	4	39	1	1	2	3	2.031110	0	0.640000	1.980000	0.641148	0.020000	0	0.070000	0.020000	0.031381	0.020000	0	1.000000e-02	0.050000
GDF3	9573	broad.mit.edu	37	12	7843026	7843026	+	Silent	SNP	G	G	A			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr12:7843026G>A	ENST00000329913.3	-	2	590	c.543C>T	c.(541-543)ttC>ttT	p.F181F		NM_020634.1	NP_065685.1	Q9NR23	GDF3_HUMAN	growth differentiation factor 3			28					CCAGCAGGTTGAAGTGAACAG	0.507000																								0							SO:0001819	synonymous_variant			ENST00000329913.3	1	1	hg19	CCDS8581.1																																																																																				TCGA-S4-A8RM-01A-11D-A377-08	GDF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399717.1	1	0	0	137	367	0	79	0	4.137300e-01	0	5	0	79	2		0	0	0	0	0	2	1	1.000000	135	360	0	79	2		0	0	0	0	79	2	-20.000000	1	1	0	0		1	1	2	3	2.031110	0	0.640000	1.980000	0.641148	0.840000	7.200000e-01	0.980000	0.850000	0.853793	0.840000	0	7.800000e-01	0.920000
NAV3	89795	broad.mit.edu	37	12	78604240	78604240	+	Silent	SNP	C	C	T			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr12:78604240C>T	ENST00000397909.2	+	40	7274	c.7101C>T	c.(7099-7101)agC>agT	p.S2367S	NAV3_ENST00000536525.2_Silent_p.S2345S|NAV3_ENST00000228327.6_Silent_p.S2345S|NAV3_ENST00000266692.7_Silent_p.S2168S|NAV3_ENST00000541270.1_Silent_p.S197S			Q8IVL0	NAV3_HUMAN	neuron navigator 3			236					GCTGCGACAGCGAAAGCACCA	0.393000										HNSCC(70;0.22)														0							SO:0001819	synonymous_variant			ENST00000397909.2	1	1	hg19		.	.	.	.	.	.	.	.	.	.	C	0.332	-0.955497	0.02267	.	.	ENSG00000067798	ENST00000552895;ENST00000551162	.	.	.	5.35	-5.24	0.02789	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-5.8606	16.3886	0.83524	0.0:0.3108:0.0:0.6892	.	.	.	.	X	1240;235	.	.	R	+	1	2	NAV3	77128371	0.488000	0.25996	0.415000	0.26534	0.199000	0.23934	-0.262000	0.08682	-0.911000	0.03843	-0.768000	0.03414	CGA		TCGA-S4-A8RM-01A-11D-A377-08	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	1	0	1	110	266	0	62	0	5.646561e-01	1	5	0	62	2		0	0	0	0	0	2	1	1.000000	108	262	0	61	2		0	0	0	0	62	2	-8.416818	1	1	120858	5	39	1	0	0	0	1.993499	0	0.640000	1.980000	0.637681	0.900000	7.600000e-01	1.000000	1.000000	0.906308	0.900000	1	8.300000e-01	0.980000
NDUFA12	55967	broad.mit.edu	37	12	95397439	95397439	+	Silent	SNP	G	G	T			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr12:95397439G>T	ENST00000327772.2	-	1	107	c.18C>A	c.(16-18)gtC>gtA	p.V6V	NDUFA12_ENST00000547986.1_Silent_p.V6V|NDUFA12_ENST00000547157.1_Silent_p.V6V	NM_018838.4	NP_061326.1	Q9UI09	NDUAC_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 12			6					CGCGTTTCAGGACCTGCACTA	0.647000																								0							SO:0001819	synonymous_variant			ENST00000327772.2	0	1	hg19	CCDS9050.1																																																																																				TCGA-S4-A8RM-01A-11D-A377-08	NDUFA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407245.2	0	0	0	14	489	0	51	1	9.852838e-01	12	233	0	51	2		0	0	0	0	0	2	1	0.999735	14	482	0	51	2		0	0	0	0	51	2	-3.579756	1	1	0	0		1	0	0	0	1.993499	0	0.640000	1.980000	0.637681	0.080000	4.000000e-02	0.140000	0.080000	0.092124	0.080000	0	6.000000e-02	0.120000
CCDC38	120935	broad.mit.edu	37	12	96292480	96292480	+	Silent	SNP	G	G	T			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr12:96292480G>T	ENST00000344280.3	-	6	956	c.399C>A	c.(397-399)atC>atA	p.I133I	SNRPF_ENST00000552085.1_Intron	NM_182496.2	NP_872302.2	Q502W7	CCD38_HUMAN	coiled-coil domain containing 38			18					CAAACTTTTTGATTGTGTTTC	0.373000																								0							SO:0001819	synonymous_variant			ENST00000344280.3	1	1	hg19	CCDS9056.1																																																																																				TCGA-S4-A8RM-01A-11D-A377-08	CCDC38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408634.1	1	0	1	89	222	0	76		0	0	0	0	76	2		0	0	0	0	0	2	1	1.000000	85	217	0	75	2		0	0	0	0	76	2	-20.000000	1	1	121412	1	33	1	0	0	0	1.993499	0	0.640000	1.980000	0.637681	0.880000	7.300000e-01	1.000000	1.000000	0.887777	0.880000	1	8.000000e-01	0.970000
EIF5	1983	broad.mit.edu	37	14	103805083	103805083	+	Missense_Mutation	SNP	G	G	T			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08			G	T	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr14:103805083G>T	ENST00000216554.3	+	8	1273	c.597G>T	c.(595-597)gaG>gaT	p.E199D	EIF5_ENST00000558506.1_Missense_Mutation_p.E199D|SNORA28_ENST00000606769.1_RNA|EIF5_ENST00000392715.2_Missense_Mutation_p.E199D	NM_001969.4	NP_001960.2	P55010	IF5_HUMAN	eukaryotic translation initiation factor 5			18		Melanoma(154;0.155)	Epithelial(46;0.182)		AAGAAGAGGAGGATGATGACT	0.413000																								0							SO:0001583	missense			ENST00000216554.3	1	1	hg19	CCDS9980.1	.	.	.	.	.	.	.	.	.	.	.	1.304	-0.604076	0.03717	.	.	ENSG00000100664	ENST00000216554;ENST00000392715	D;D	0.82433	-1.61;-1.61	5.37	0.862	0.19056	.	0.138874	0.64402	N	0.000008	T	0.57475	0.2056	N	0.16903	0.455	0.38094	D	0.937046	B	0.02656	0.0	B	0.01281	0.0	T	0.49570	-0.8926	10	0.02654	T	1	-4.7689	0.5359	0.00636	0.3386:0.1608:0.2956:0.2049	.	199	P55010	IF5_HUMAN	D	199	ENSP00000216554:E199D;ENSP00000376477:E199D	ENSP00000216554:E199D	E	+	3	2	EIF5	102874836	0.291000	0.24352	0.996000	0.52242	0.657000	0.38888	-0.406000	0.07187	-0.043000	0.13513	-0.259000	0.10710	GAG		TCGA-S4-A8RM-01A-11D-A377-08	EIF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415329.2	1	0	1	113	258	0	65	1	1	107	171	0	65	2		0	0	0	0	0	2	1	1.000000	102	270	0	65	2		0	0	0	0	65	2	-20.000000	1	0	0	0		1	0	0	0	1.995992	0	0.640000	1.980000	0.637681	0.940000	7.900000e-01	1.000000	1.000000	0.936814	0.940000	1	8.600000e-01	1.000000
OR4N2	390429	broad.mit.edu	37	14	20295937	20295937	+	Silent	SNP	G	G	A			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr14:20295937G>A	ENST00000315947.1	+	1	330	c.330G>A	c.(328-330)ggG>ggA	p.G110G	OR4N2_ENST00000568211.1_Silent_p.G110G	NM_001004723.1	NP_001004723.1	Q8NGD1	OR4N2_HUMAN	olfactory receptor, family 4, subfamily N, member 2			52	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)		TTGGAGGAGGGGAGGGATTAC	0.522000																								0							SO:0001819	synonymous_variant			ENST00000315947.1	0	1	hg19	CCDS32022.1																																																																																				TCGA-S4-A8RM-01A-11D-A377-08	OR4N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409821.2	0	0	0	22	866	1	206		0	0	0	1	206	2		0	0	0	0	0	2	1	0.922100	19	786	1	237	13		0	0	0	1	206	2	-2.093702	0	1	121412	2	39	1	0	2	2	1.914286	1	0.640000	1.980000	0.640000	0.080000	4.000000e-02	1.000000	0.080000	0.302127	0.080000	0	6.000000e-02	1.000000
PRMT5	10419	broad.mit.edu	37	14	23391693	23391693	+	Missense_Mutation	SNP	G	G	A			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr14:23391693G>A	ENST00000324366.8	-	15	1878	c.1655C>T	c.(1654-1656)gCc>gTc	p.A552V	PRMT5-AS1_ENST00000587245.2_RNA|PRMT5-AS1_ENST00000590290.1_RNA|PRMT5_ENST00000538452.1_Missense_Mutation_p.A446V|PRMT5_ENST00000553897.1_Missense_Mutation_p.A508V|PRMT5-AS1_ENST00000595662.1_RNA|PRMT5_ENST00000397440.4_Missense_Mutation_p.A381V|PRMT5-AS1_ENST00000424245.2_RNA|PRMT5-AS1_ENST00000599580.2_RNA|PRMT5_ENST00000216350.8_Missense_Mutation_p.A491V|PRMT5_ENST00000397441.2_Missense_Mutation_p.A535V|PRMT5-AS1_ENST00000457443.2_RNA|PRMT5-AS1_ENST00000609885.1_RNA	NM_006109.3	NP_006100.2	O14744	ANM5_HUMAN	protein arginine methyltransferase 5			25	all_cancers(95;2.76e-05)				AAAGTAGCCGGCAAAGCCATG	0.463000																								0							SO:0001583	missense			ENST00000324366.8	0	1	hg19	CCDS9579.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.518793	0.85495	.	.	ENSG00000100462	ENST00000324366;ENST00000397441;ENST00000397440;ENST00000216350;ENST00000555454;ENST00000538452;ENST00000553897	T;T;T;T;T;T;T	0.21191	2.02;2.02;2.02;2.02;2.02;2.02;2.02	5.79	5.79	0.91817	.	0.046588	0.85682	D	0.000000	T	0.44286	0.1286	M	0.87547	2.89	0.80722	D	1	P;B;P;P;P	0.46142	0.694;0.416;0.792;0.832;0.873	B;B;P;B;P	0.48952	0.328;0.285;0.596;0.389;0.457	T	0.49542	-0.8929	10	0.66056	D	0.02	-12.7059	18.796	0.91994	0.0:0.0:1.0:0.0	.	508;491;381;552;535	G3V5W5;B4DX49;A8MTP3;O14744;A8MZ91	.;.;.;ANM5_HUMAN;.	V	552;535;381;491;151;446;508	ENSP00000319169:A552V;ENSP00000380583:A535V;ENSP00000380582:A381V;ENSP00000216350:A491V;ENSP00000451245:A151V;ENSP00000444915:A446V;ENSP00000452555:A508V	ENSP00000216350:A491V	A	-	2	0	PRMT5	22461533	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	8.655000	0.91098	2.750000	0.94351	0.561000	0.74099	GCC		TCGA-S4-A8RM-01A-11D-A377-08	PRMT5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071674.3	0	0	0	9	934	0	160	0	3.208989e-01	0	110	0	160	2		0	0	0	0	0	2	1	0.993996	8	928	0	155	2		0	0	0	0	160	2	-2.094841	0	1	0	0		1	0	0	0	1.995992	0	0.640000	1.980000	0.637681	0.020000	0	0.060000	0.040000	0.032226	0.020000	0	1.000000e-02	0.050000
NID2	22795	broad.mit.edu	37	14	52505475	52505475	+	Silent	SNP	G	G	A			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr14:52505475G>A	ENST00000216286.5	-	9	2246	c.2247C>T	c.(2245-2247)ggC>ggT	p.G749G	NID2_ENST00000541773.1_Silent_p.G696G	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)			87	Breast(41;0.0639)|all_epithelial(31;0.123)				CTTTGACCGGGCCAATTTGAT	0.438000																								0							SO:0001819	synonymous_variant			ENST00000216286.5	0	1	hg19	CCDS9706.1	.	.	.	.	.	.	.	.	.	.	G	0.970	-0.700373	0.03279	.	.	ENSG00000087303	ENST00000556572	.	.	.	6.17	4.27	0.50696	.	.	.	.	.	T	0.55577	0.1929	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53690	-0.8403	4	.	.	.	.	6.2489	0.20835	0.0705:0.2083:0.6002:0.1209	.	.	.	.	S	66	.	.	P	-	1	0	NID2	51575225	0.998000	0.40836	1.000000	0.80357	0.083000	0.17756	0.369000	0.20416	1.636000	0.50526	-0.136000	0.14681	CCC		TCGA-S4-A8RM-01A-11D-A377-08	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1	0	0	0	4	246	0	45	0	3.911369e-02	0	15	0	45	2		0	0	0	0	0	2	1	0.888247	4	243	0	45	2		0	0	0	0	45	2	-2.981512	1	1	0	0		1	0	0	0	1.995992	0	0.640000	1.980000	0.637681	0.050000	0	0.120000	0.050000	0.061362	0.050000	0	2.000000e-02	0.090000
PAPLN	89932	broad.mit.edu	37	14	73733472	73733472	+	Missense_Mutation	SNP	C	C	G			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr14:73733472C>G	ENST00000554301.1	+	24	3596	c.3433C>G	c.(3433-3435)Cca>Gca	p.P1145A	PAPLN_ENST00000340738.5_Missense_Mutation_p.P1118A|PAPLN_ENST00000555445.1_Missense_Mutation_p.P1129A|PAPLN_ENST00000427855.1_Missense_Mutation_p.P1145A|PAPLN_ENST00000381166.3_Intron			O95428	PPN_HUMAN	papilin, proteoglycan-like sulfated glycoprotein			42					TGTGACAGTGCCAGAGGGTGA	0.547000																								0							SO:0001583	missense			ENST00000554301.1	1	1	hg19		.	.	.	.	.	.	.	.	.	.	C	0.066	-1.213152	0.01555	.	.	ENSG00000100767	ENST00000340738;ENST00000427855;ENST00000554301;ENST00000555445	T;T;T;T	0.65178	-0.14;-0.14;-0.14;-0.14	5.07	2.17	0.27698	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.35393	0.0930	N	0.05031	-0.125	0.53005	D	0.999961	B;B;B;B	0.19073	0.001;0.001;0.033;0.002	B;B;B;B	0.19946	0.004;0.008;0.027;0.007	T	0.04065	-1.0980	9	0.30854	T	0.27	.	5.6369	0.17542	0.1071:0.5598:0.2118:0.1213	.	1129;1145;344;1118	O95428-5;O95428;O95428-2;O95428-6	.;PPN_HUMAN;.;.	A	1118;1145;1145;1129	ENSP00000345395:P1118A;ENSP00000403403:P1145A;ENSP00000451803:P1145A;ENSP00000451729:P1129A	ENSP00000345395:P1118A	P	+	1	0	PAPLN	72803225	0.370000	0.25047	0.171000	0.22900	0.001000	0.01503	-0.021000	0.12504	0.030000	0.15379	-1.268000	0.01426	CCA		TCGA-S4-A8RM-01A-11D-A377-08	PAPLN-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000413182.1	1	0	1	34	77	0	23	0	9.623422e-01	0	15	0	23	2		0	0	0	0	0	2	1	1.000000	31	76	0	23	2		0	0	0	0	23	2	-20.000000	1	1	0	0		1	0	0	0	1.995992	0	0.640000	1.980000	0.637681	0.940000	6.900000e-01	1.000000	1.000000	0.921762	0.940000	1	8.100000e-01	1.000000
EML5	161436	broad.mit.edu	37	14	89181392	89181392	+	Silent	SNP	G	G	A			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr14:89181392G>A	ENST00000380664.5	-	9	1334	c.1335C>T	c.(1333-1335)ggC>ggT	p.G445G	EML5_ENST00000352093.5_Silent_p.G445G|EML5_ENST00000554922.1_Silent_p.G445G			Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like 5			50					CCAAACACTCGCCAACTTTTT	0.383000																								0							SO:0001819	synonymous_variant			ENST00000380664.5	1	1	hg19	CCDS45148.1																																																																																				TCGA-S4-A8RM-01A-11D-A377-08	EML5-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410491.1	1	0	1	72	143	0	51		0	0	0	0	51	2		0	0	0	0	0	2	1	1.000000	72	142	0	51	2		0	0	0	0	51	2	-20.000000	1	1	0	0		1	0	0	0	1.995992	0	0.640000	1.980000	0.637681	0.990000	8.400000e-01	1.000000	1.000000	0.978016	0.990000	1	9.300000e-01	1.000000
OCA2	4948	broad.mit.edu	37	15	28263652	28263652	+	Missense_Mutation	SNP	G	G	T			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr15:28263652G>T	ENST00000354638.3	-	7	853	c.698C>A	c.(697-699)gCa>gAa	p.A233E	OCA2_ENST00000382996.2_Missense_Mutation_p.A233E|OCA2_ENST00000353809.5_Missense_Mutation_p.A233E	NM_000275.2	NP_000266.2	Q04671	P_HUMAN	oculocutaneous albinism II			85		all_lung(180;2.93e-12)|Breast(32;0.000315)|Colorectal(260;0.234)			TAGGGCCCCTGCCAGGTCCAC	0.647000									Oculocutaneous Albinism															0							SO:0001583	missense	Familial Cancer Database		ENST00000354638.3	1	1	hg19	CCDS10020.1	.	.	.	.	.	.	.	.	.	.	G	11.17	1.558383	0.27827	.	.	ENSG00000104044	ENST00000354638;ENST00000353809;ENST00000382996;ENST00000431101	T;T;T;T	0.64618	-0.11;-0.11;-0.11;-0.11	5.54	2.47	0.30058	.	0.354079	0.28130	N	0.016485	T	0.47746	0.1462	M	0.61703	1.905	0.24313	N	0.99508	P;B	0.35944	0.529;0.36	B;B	0.36567	0.228;0.09	T	0.41520	-0.9504	10	0.02654	T	1	-4.3929	3.9439	0.09339	0.1888:0.0:0.5739:0.2373	.	233;233	Q04671-2;Q04671	.;P_HUMAN	E	233	ENSP00000346659:A233E;ENSP00000261276:A233E;ENSP00000372457:A233E;ENSP00000415431:A233E	ENSP00000261276:A233E	A	-	2	0	OCA2	25937247	0.795000	0.28851	0.641000	0.29422	0.139000	0.21198	0.946000	0.29069	0.565000	0.29255	-0.136000	0.14681	GCA		TCGA-S4-A8RM-01A-11D-A377-08	OCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250823.1	1	0	1	41	90	0	20	0	1.013354e-01	0	2	0	20	2		0	0	0	0	0	2	1	1.000000	41	90	0	19	2		0	0	0	0	20	2	-20.000000	1	1	0	0		1	1	2	3	2.043679	0	0.640000	1.980000	0.642289	0.980000	7.400000e-01	1.000000	1.000000	0.944432	0.980000	1	8.500000e-01	1.000000
ACAN	176	broad.mit.edu	37	15	89382106	89382106	+	Missense_Mutation	SNP	C	C	T			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr15:89382106C>T	ENST00000561243.1	+	2	283	c.283C>T	c.(283-285)Cgg>Tgg	p.R95W	ACAN_ENST00000559004.1_Missense_Mutation_p.R95W|ACAN_ENST00000558207.1_Missense_Mutation_p.R95W|ACAN_ENST00000352105.7_Missense_Mutation_p.R95W|ACAN_ENST00000439576.2_Missense_Mutation_p.R95W			P16112	PGCA_HUMAN	aggrecan			93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)		AGGGCGCGTGCGGGTCAACAG	0.622000																								0							SO:0001583	missense			ENST00000561243.1	0	1	hg19	CCDS53970.1	.	.	.	.	.	.	.	.	.	.	C	14.01	2.407857	0.42715	.	.	ENSG00000157766	ENST00000439576;ENST00000352105;ENST00000268134	T;T	0.66815	-0.23;-0.23	5.36	1.15	0.20763	.	.	.	.	.	T	0.81074	0.4747	M	0.79011	2.435	0.36546	D	0.871562	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79784	0.987;0.987;0.993	D	0.84991	0.0894	9	0.87932	D	0	-12.5802	16.4177	0.83748	0.4344:0.5656:0.0:0.0	.	95;95;95	E7ENV9;E7EX88;Q6PID9	.;.;.	W	95	ENSP00000387356:R95W;ENSP00000341615:R95W	ENSP00000268134:R95W	R	+	1	2	ACAN	87183110	0.998000	0.40836	0.860000	0.33809	0.768000	0.43524	0.886000	0.28241	-0.170000	0.10816	-1.378000	0.01179	CGG		TCGA-S4-A8RM-01A-11D-A377-08	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	0	0	0	7	614	0	103	0	0	0	1	0	103	2		0	0	0	0	0	2	1	0.980125	7	609	0	103	2		0	0	0	0	103	2	-1.916548	0	1	121178	2	36	1	1	2	3	2.042131	0	0.640000	1.980000	0.642289	0.030000	0	0.080000	0.040000	0.049595	0.030000	0	1.000000e-02	0.060000
GP2	2813	broad.mit.edu	37	16	20329591	20329591	+	Missense_Mutation	SNP	C	C	T	rs145287300		TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr16:20329591C>T	ENST00000381362.4	-	8	1254	c.1178G>A	c.(1177-1179)cGg>cAg	p.R393Q	GP2_ENST00000302555.5_Missense_Mutation_p.R390Q|GP2_ENST00000573897.1_5'Flank|GP2_ENST00000381360.5_Missense_Mutation_p.R246Q|GP2_ENST00000341642.5_Missense_Mutation_p.R243Q	NM_001007240.1|NM_001502.2	NP_001007241.2|NP_001493.2	P55259	GP2_HUMAN	glycoprotein 2 (zymogen granule membrane)			48					CAGGTTAAACCGGGAGGTGTC	0.498000																								0							SO:0001583	missense			ENST00000381362.4	1	1	hg19	CCDS42128.1	.	.	.	.	.	.	.	.	.	.	C	9.634	1.137313	0.21123	.	.	ENSG00000169347	ENST00000302555;ENST00000381362;ENST00000381360;ENST00000341642;ENST00000537520	D;D;D;D	0.82344	-1.6;-1.6;-1.6;-1.6	5.8	-0.158	0.13383	Endoglin/CD105 antigen conserved site (1);Endoglin/CD105 antigen subgroup (1);Zona pellucida sperm-binding protein (3);	.	.	.	.	T	0.64560	0.2609	L	0.28192	0.835	0.09310	N	1	B;B;B;B	0.26147	0.012;0.122;0.135;0.143	B;B;B;B	0.23419	0.006;0.044;0.01;0.046	T	0.47433	-0.9118	9	0.11794	T	0.64	-6.5112	1.9729	0.03409	0.1244:0.4067:0.1377:0.3312	.	243;371;390;393	P55259-4;B7Z1G2;P55259-3;P55259	.;.;.;GP2_HUMAN	Q	390;393;246;243;371	ENSP00000304044:R390Q;ENSP00000370767:R393Q;ENSP00000370765:R246Q;ENSP00000343861:R243Q	ENSP00000304044:R390Q	R	-	2	0	GP2	20237092	0.033000	0.19621	0.017000	0.16124	0.778000	0.44026	0.163000	0.16520	0.089000	0.17243	-0.143000	0.13931	CGG		TCGA-S4-A8RM-01A-11D-A377-08	GP2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000436920.1	1	0	1	150	329	0	110	1	1	326	463	0	110	2		0	0	0	0	0	2	1	1.000000	150	327	0	110	2		0	0	0	0	110	2	-11.609830	1	1	121412	6	43	1	1	2	3	2.025948	0	0.640000	1.980000	0.641148	0.970000	8.400000e-01	1.000000	1.000000	0.963986	0.970000	1	9.100000e-01	1.000000
SLC47A1	55244	broad.mit.edu	37	17	19480756	19480756	+	Missense_Mutation	SNP	G	G	A			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr17:19480756G>A	ENST00000270570.4	+	17	1689	c.1603G>A	c.(1603-1605)Gct>Act	p.A535T	SLC47A1_ENST00000395585.1_Missense_Mutation_p.A535T|RP11-1113L8.1_ENST00000574267.1_RNA|AC025627.7_ENST00000420951.1_RNA|SLC47A1_ENST00000457293.1_Missense_Mutation_p.A535T|SLC47A1_ENST00000575023.1_Missense_Mutation_p.A233T|SLC47A1_ENST00000436810.2_3'UTR|SLC47A1_ENST00000571335.1_Missense_Mutation_p.A281T	NM_018242.2	NP_060712.2	Q96FL8	S47A1_HUMAN	solute carrier family 47 (multidrug and toxin extrusion), member 1			23	all_cancers(12;2.49e-05)|all_epithelial(12;0.00263)|Hepatocellular(7;0.00345)			Aciclovir(DB00787)|Bromodiphenhydramine(DB01237)|Cephalexin(DB00567)|Cimetidine(DB00501)|Metformin(DB00331)|Sirolimus(DB00877)	ACAGGACGGCGCTAAATTGTC	0.512000																								0							SO:0001583	missense			ENST00000270570.4	0	1	hg19	CCDS11209.1	.	.	.	.	.	.	.	.	.	.	G	6.205	0.406028	0.11754	.	.	ENSG00000142494	ENST00000270570;ENST00000457293;ENST00000395585;ENST00000455670;ENST00000424755	T;T;T	0.32023	1.49;1.47;1.47	5.16	-10.3	0.00346	.	2.640820	0.01350	N	0.011864	T	0.15219	0.0367	N	0.21448	0.665	0.09310	N	1	B;B;B;B	0.12013	0.0;0.0;0.001;0.005	B;B;B;B	0.09377	0.0;0.0;0.001;0.004	T	0.08597	-1.0714	10	0.15066	T	0.55	-11.0131	6.0981	0.20031	0.1985:0.1763:0.5331:0.0921	.	210;210;535;535	E7ENC3;B4DDH5;Q96FL8;Q96FL8-3	.;.;S47A1_HUMAN;.	T	535;535;535;210;247	ENSP00000270570:A535T;ENSP00000415586:A535T;ENSP00000378951:A535T	ENSP00000270570:A535T	A	+	1	0	SLC47A1	19421348	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.188000	0.01249	-3.020000	0.00270	-0.672000	0.03802	GCT		TCGA-S4-A8RM-01A-11D-A377-08	SLC47A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132250.1	0	0	0	5	523	0	98	0	0	0	1	0	98	2		0	0	0	0	0	2	1	0.935280	5	516	0	96	2		0	0	0	0	98	2	-1.916061	0	1	121412	4	42	1	0	1	1	1.453406	1	0.640000	1.980000	0.473068	0.010000	0	0.050000	0.020000	0.024022	0.010000	0	0	0.030000
P2RX1	5023	broad.mit.edu	37	17	3807664	3807664	+	Silent	SNP	G	G	A			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr17:3807664G>A	ENST00000225538.3	-	4	661	c.387C>T	c.(385-387)gaC>gaT	p.D129D		NM_002558.2	NP_002549.1	P51575	P2RX1_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 1			13					TACAGCCACTGTCTTCCTTGC	0.657000																								0							SO:0001819	synonymous_variant			ENST00000225538.3	1	1	hg19	CCDS11040.1																																																																																				TCGA-S4-A8RM-01A-11D-A377-08	P2RX1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438391.1	1	0	0	9	194	0	48	0	2.604783e-03	0	2	0	48	2		0	0	0	0	0	2	1	0.993869	9	189	0	48	2		0	0	0	0	48	2	-11.617700	1	1	0	0		1	0	1	1	1.433139	1	0.640000	1.980000	0.473068	0.090000	4.000000e-02	0.170000	0.090000	0.103575	0.090000	0	6.000000e-02	0.130000
MAPT	4137	broad.mit.edu	37	17	44073913	44073913	+	Silent	SNP	G	G	A	rs115142761	by1000genomes	TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr17:44073913G>A	ENST00000571987.1	+	9	1656	c.1656G>A	c.(1654-1656)tcG>tcA	p.S552S	MAPT_ENST00000431008.3_Silent_p.S235S|MAPT_ENST00000570299.1_3'UTR|MAPT_ENST00000334239.8_Silent_p.S177S|MAPT_ENST00000351559.5_Silent_p.S235S|MAPT_ENST00000535772.1_Silent_p.S235S|MAPT_ENST00000344290.5_Silent_p.S570S|MAPT_ENST00000574436.1_Silent_p.S235S|MAPT_ENST00000446361.3_Silent_p.S177S|MAPT_ENST00000347967.5_Silent_p.S141S|MAPT_ENST00000340799.5_Silent_p.S206S|MAPT_ENST00000576518.1_Silent_p.S166S|STH_ENST00000537309.1_5'Flank|MAPT_ENST00000420682.2_Silent_p.S206S|MAPT_ENST00000262410.5_Silent_p.S552S|MAPT_ENST00000415613.2_Silent_p.S570S			P10636	TAU_HUMAN	microtubule-associated protein tau			38		Melanoma(429;0.216)		Docetaxel(DB01248)|Paclitaxel(DB01229)	CACCCAAGTCGCCGTCTTCCG	0.662000																								0							SO:0001819	synonymous_variant			ENST00000571987.1	0	1	hg19	CCDS11501.1																																																																																				TCGA-S4-A8RM-01A-11D-A377-08	MAPT-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000440133.1	1	0	0	8	142	0	20	0	3.869969e-03	0	2	0	20	2		0	0	0	0	0	2	1	0.988809	8	138	0	20	2		0	0	0	0	20	2	-11.449430	1	1	121388	5	37	1	1	2	3	2.070324	0	0.640000	1.980000	0.645669	0.170000	8.000000e-02	1.000000	0.170000	0.218171	0.170000	0	1.200000e-01	0.260000
RNF43	54894	broad.mit.edu	37	17	56440757	56440757	+	Missense_Mutation	SNP	G	G	A			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr17:56440757G>A	ENST00000584437.1	-	4	2416	c.461C>T	c.(460-462)cCg>cTg	p.P154L	RNF43_ENST00000407977.2_Missense_Mutation_p.P154L|RNF43_ENST00000583753.1_Missense_Mutation_p.P113L|RNF43_ENST00000500597.2_Missense_Mutation_p.P113L|RNF43_ENST00000581868.1_Missense_Mutation_p.P27L|BZRAP1-AS1_ENST00000583841.1_RNA|RNF43_ENST00000577716.1_Missense_Mutation_p.P154L|RNF43_ENST00000577625.1_Missense_Mutation_p.P27L			Q68DV7	RNF43_HUMAN	ring finger protein 43			60	Medulloblastoma(34;0.127)|all_neural(34;0.237)				CAGCCCCAGCGGCTGCTGCAG	0.577000																								0							SO:0001583	missense			ENST00000584437.1	1	1	hg19	CCDS11607.1	.	.	.	.	.	.	.	.	.	.	G	35	5.475540	0.96291	.	.	ENSG00000108375	ENST00000407977;ENST00000500597	T;T	0.27104	1.69;3.06	5.68	5.68	0.88126	.	0.187766	0.47093	D	0.000257	T	0.30103	0.0754	N	0.19112	0.55	0.80722	D	1	D;D;D	0.69078	0.995;0.993;0.997	P;P;P	0.54140	0.743;0.721;0.551	T	0.01725	-1.1287	10	0.34782	T	0.22	-8.5077	18.7682	0.91881	0.0:0.0:1.0:0.0	.	113;154;154	Q68DV7-2;Q68DV7-4;Q68DV7	.;.;RNF43_HUMAN	L	154;113	ENSP00000385328:P154L;ENSP00000441969:P113L	ENSP00000385328:P154L	P	-	2	0	RNF43	53795756	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	8.661000	0.91125	2.684000	0.91462	0.591000	0.81541	CCG		TCGA-S4-A8RM-01A-11D-A377-08	RNF43-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444713.1	1	0	1	151	353	0	76	1	9.998374e-01	8	25	0	76	2	1	1	274	609	0	497	2	1	1.000000	150	347	0	76	2		0	0	0	0	76	2	-10.307860	1	1	121412	1	37	1	1	2	3	2.070324	0	0.640000	1.980000	0.645669	0.950000	8.200000e-01	1.000000	1.000000	0.945798	0.950000	1	8.800000e-01	1.000000
RNF157	114804	broad.mit.edu	37	17	74148532	74148532	+	Missense_Mutation	SNP	C	C	T			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr17:74148532C>T	ENST00000269391.6	-	18	1957	c.1825G>A	c.(1825-1827)Gca>Aca	p.A609T	RNF157-AS1_ENST00000592748.1_RNA|RNF157_ENST00000319945.6_Missense_Mutation_p.A587T|RNF157-AS1_ENST00000590137.1_RNA|RNF157-AS1_ENST00000586661.1_RNA|RNF157-AS1_ENST00000586627.1_RNA|RNF157-AS1_ENST00000585542.1_RNA	NM_052916.2	NP_443148.1	Q96PX1	RN157_HUMAN	ring finger protein 157			25			LUSC - Lung squamous cell carcinoma(166;0.187)		CCTAGAAATGCGCACGTCCTC	0.458000													GBM(186;507 2120 27388 27773 52994)											0							SO:0001583	missense			ENST00000269391.6	0	1	hg19	CCDS32740.1	.	.	.	.	.	.	.	.	.	.	C	18.55	3.649353	0.67358	.	.	ENSG00000141576	ENST00000269391;ENST00000319945	T;T	0.36699	1.7;1.24	5.71	4.68	0.58851	.	0.088535	0.49305	D	0.000154	T	0.35335	0.0928	L	0.54323	1.7	0.80722	D	1	P;P	0.52170	0.951;0.84	B;B	0.41946	0.371;0.089	T	0.24835	-1.0149	10	0.52906	T	0.07	-1.2912	13.8657	0.63588	0.1522:0.8478:0.0:0.0	.	587;609	Q96PX1-2;Q96PX1	.;RN157_HUMAN	T	609;587	ENSP00000269391:A609T;ENSP00000321837:A587T	ENSP00000269391:A609T	A	-	1	0	RNF157	71660127	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.443000	0.44881	2.684000	0.91462	0.655000	0.94253	GCA		TCGA-S4-A8RM-01A-11D-A377-08	RNF157-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255874.2	0	0	0	6	398	0	67	0	1.001739e-03	0	3	0	67	2		0	0	0	0	0	2	1	0.964435	6	395	0	65	2		0	0	0	0	67	2	-2.576342	1	1	121412	7	43	1	1	2	3	2.070324	0	0.640000	1.980000	0.645669	0.040000	1.000000e-02	1.000000	0.050000	0.090569	0.040000	0	2.000000e-02	0.080000
CHD3	1107	broad.mit.edu	37	17	7807208	7807208	+	Missense_Mutation	SNP	G	G	A			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr17:7807208G>A	ENST00000330494.7	+	24	3943	c.3793G>A	c.(3793-3795)Gac>Aac	p.D1265N	SCARNA21_ENST00000517026.1_RNA|CHD3_ENST00000358181.4_Missense_Mutation_p.D1265N|CHD3_ENST00000380358.4_Missense_Mutation_p.D1324N	NM_001005273.2	NP_001005273.1	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3			65		Prostate(122;0.202)			TCGGCTGTTGGACCGGAACCA	0.517000																								0							SO:0001583	missense			ENST00000330494.7	1	1	hg19	CCDS32554.1	.	.	.	.	.	.	.	.	.	.	G	26.3	4.723272	0.89298	.	.	ENSG00000170004	ENST00000380358;ENST00000358181;ENST00000330494	D;D;D	0.91631	-2.88;-2.81;-2.81	5.12	5.12	0.69794	.	0.000000	0.49305	D	0.000159	D	0.95242	0.8457	L	0.60957	1.885	0.80722	D	1	D;D;D	0.71674	0.998;0.997;0.997	D;D;D	0.81914	0.995;0.989;0.989	D	0.95103	0.8232	10	0.62326	D	0.03	-30.8593	19.1045	0.93287	0.0:0.0:1.0:0.0	.	1265;1265;1324	Q12873-2;Q12873;E9PG89	.;CHD3_HUMAN;.	N	1324;1265;1265	ENSP00000369716:D1324N;ENSP00000350907:D1265N;ENSP00000332628:D1265N	ENSP00000332628:D1265N	D	+	1	0	CHD3	7747933	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.203000	0.95033	2.811000	0.96726	0.655000	0.94253	GAC		TCGA-S4-A8RM-01A-11D-A377-08	CHD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318050.1	1	0	1	106	109	0	39	1	1	124	46	0	39	2		0	0	0	0	0	2	1	1.000000	105	106	0	39	2		0	0	0	0	39	2	-20.000000	1	1	0	0		1	0	1	1	1.433139	1	0.640000	1.980000	0.473068	0.970000	8.700000e-01	1.000000	1.000000	0.966016	0.970000	1	9.200000e-01	1.000000
RNF213	57674	broad.mit.edu	37	17	78321225	78321225	+	Silent	SNP	G	G	A			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr17:78321225G>A	ENST00000582970.1	+	29	9233	c.9090G>A	c.(9088-9090)ccG>ccA	p.P3030P	RNF213_ENST00000508628.2_Silent_p.P3079P|RNF213_ENST00000336301.6_Silent_p.P1103P	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213			130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)		AGAAGGTGCCGGGTGGAGAGC	0.547000																								0							SO:0001819	synonymous_variant			ENST00000582970.1	1	1	hg19	CCDS58606.1																																																																																				TCGA-S4-A8RM-01A-11D-A377-08	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	1	0	1	74	180	0	42	1	9.998978e-01	12	25	0	42	2	1	1	133	254	0	274	2	1	1.000000	74	179	0	42	2		0	0	0	0	42	2	-6.107752	1	1	121412	5	37	1	1	2	3	2.070324	0	0.640000	1.980000	0.645669	0.920000	7.500000e-01	1.000000	1.000000	0.920008	0.920000	1	8.300000e-01	1.000000
ZNF407	55628	broad.mit.edu	37	18	72347373	72347373	+	Silent	SNP	C	C	T			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr18:72347373C>T	ENST00000299687.5	+	1	4398	c.4398C>T	c.(4396-4398)gcC>gcT	p.A1466A	ZNF407_ENST00000309902.6_Silent_p.A1466A|ZNF407_ENST00000582337.1_Silent_p.A1466A|ZNF407_ENST00000577538.1_Silent_p.A1466A	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407			67		Esophageal squamous(42;0.131)|Prostate(75;0.173)			TGGCTAGTGCCGGCCACATGA	0.498000																								0							SO:0001819	synonymous_variant			ENST00000299687.5	1	1	hg19	CCDS45885.1																																																																																				TCGA-S4-A8RM-01A-11D-A377-08	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	1	0	0	5	94	0	31	0	2.201027e-02	0	4	0	31	2		0	0	0	0	0	2	1	0.937535	5	93	0	31	2		0	0	0	0	31	2	-4.411144	1	1	120840	6	38	1	0	1	1	1.440698	1	0.640000	1.980000	0.473068	0.110000	4.000000e-02	0.230000	0.110000	0.125417	0.110000	0	7.000000e-02	0.170000
TRPM4	54795	broad.mit.edu	37	19	49684660	49684660	+	Missense_Mutation	SNP	C	C	T			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr19:49684660C>T	ENST00000252826.5	+	10	1331	c.1205C>T	c.(1204-1206)gCt>gTt	p.A402V	TRPM4_ENST00000427978.2_Missense_Mutation_p.A402V|TRPM4_ENST00000355712.5_Intron|TRPM4_ENST00000601347.1_Intron	NM_017636.3	NP_060106.2	Q8TD43	TRPM4_HUMAN	transient receptor potential cation channel, subfamily M, member 4			49		all_lung(116;8.54e-05)|Lung NSC(112;0.000139)|all_neural(266;0.0506)|Ovarian(192;0.15)			TTGGCTGTGGCTTGGAACCGC	0.617000																								0							SO:0001583	missense			ENST00000252826.5	1	1	hg19	CCDS33073.1	.	.	.	.	.	.	.	.	.	.	C	18.38	3.611107	0.66558	.	.	ENSG00000130529	ENST00000252826;ENST00000427978	T;T	0.67865	-0.29;-0.29	3.92	3.92	0.45320	.	0.070546	0.64402	D	0.000018	T	0.81621	0.4861	M	0.84948	2.725	0.80722	D	1	D;D;D	0.71674	0.987;0.994;0.998	P;D;P	0.64144	0.807;0.922;0.887	D	0.85892	0.1429	10	0.87932	D	0	-11.7547	15.0744	0.72066	0.0:1.0:0.0:0.0	.	228;402;402	Q8TD43-2;Q8TD43-3;Q8TD43	.;.;TRPM4_HUMAN	V	402	ENSP00000252826:A402V;ENSP00000407492:A402V	ENSP00000252826:A402V	A	+	2	0	TRPM4	54376472	1.000000	0.71417	1.000000	0.80357	0.233000	0.25261	6.665000	0.74442	1.899000	0.54978	0.455000	0.32223	GCT		TCGA-S4-A8RM-01A-11D-A377-08	TRPM4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465543.2	1	0	1	93	247	0	34	1	1	83	141	0	34	2		0	0	0	0	0	2	1	1.000000	93	242	0	32	2		0	0	0	0	34	2	-5.227186	1	1	0	0		1	1	2	3	2.032905	0	0.640000	1.980000	0.641148	0.850000	7.100000e-01	1.000000	0.850000	0.859105	0.850000	1	7.700000e-01	0.940000
TNFSF9	8744	broad.mit.edu	37	19	6534843	6534843	+	Silent	SNP	C	C	T			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr19:6534843C>T	ENST00000245817.3	+	3	569	c.531C>T	c.(529-531)gcC>gcT	p.A177A		NM_003811.3	NP_003802.1	P41273	TNFL9_HUMAN	tumor necrosis factor (ligand) superfamily, member 9			5					CTGGGGCCGCCGCCCTGGCTT	0.692000																								0							SO:0001819	synonymous_variant			ENST00000245817.3	1	1	hg19	CCDS12169.1																																																																																				TCGA-S4-A8RM-01A-11D-A377-08	TNFSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457856.1	1	0	0	30	65	0	20	0	3.833312e-01	0	4	0	20	2		0	0	0	0	0	2	1	1.000000	29	64	0	20	2		0	0	0	0	20	2	-20.000000	1	1	120038	1	29	1	1	2	3	2.087110	0	0.640000	1.980000	0.646782	0.990000	7.200000e-01	1.000000	1.000000	0.948828	0.990000	1	8.600000e-01	1.000000
SMG7	9887	broad.mit.edu	37	1	183515464	183515464	+	Missense_Mutation	SNP	C	C	T			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr1:183515464C>T	ENST00000347615.2	+	17	2853	c.2734C>T	c.(2734-2736)Ccg>Tcg	p.P912S	SMG7_ENST00000508461.1_Missense_Mutation_p.P870S|SMG7_ENST00000507469.1_Missense_Mutation_p.P866S|SMG7_ENST00000515829.2_Missense_Mutation_p.P866S|SMG7_ENST00000367537.3_Missense_Mutation_p.P895S|SMG7_ENST00000456731.2_Missense_Mutation_p.P824S	NM_173156.2	NP_775179.1	Q92540	SMG7_HUMAN	SMG7 nonsense mediated mRNA decay factor			46					ACCCAGAATGCCGTTTGAGGT	0.458000																								0							SO:0001583	missense			ENST00000347615.2	0	1	hg19	CCDS1355.1	.	.	.	.	.	.	.	.	.	.	C	14.54	2.565506	0.45694	.	.	ENSG00000116698	ENST00000456731;ENST00000367537;ENST00000508461;ENST00000347615;ENST00000507469;ENST00000515829	T;T;T;T;T;T	0.44482	0.92;0.92;0.92;0.92;0.92;0.92	5.61	5.61	0.85477	.	0.492382	0.20703	N	0.087223	T	0.29556	0.0737	N	0.24115	0.695	0.46458	D	0.99905	B;B;B;B;B;B	0.28713	0.22;0.19;0.084;0.137;0.191;0.19	B;B;B;B;B;B	0.29942	0.054;0.034;0.051;0.109;0.073;0.081	T	0.08722	-1.0708	10	0.27082	T	0.32	-9.5004	11.4831	0.50337	0.1457:0.7286:0.1256:0.0	.	870;895;824;866;912;866	E9PCI0;E9PD50;E9PCE5;Q92540-2;Q92540;E9PEH2	.;.;.;.;SMG7_HUMAN;.	S	824;895;870;912;866;866	ENSP00000407629:P824S;ENSP00000356507:P895S;ENSP00000426915:P870S;ENSP00000340766:P912S;ENSP00000425133:P866S;ENSP00000421358:P866S	ENSP00000340766:P912S	P	+	1	0	SMG7	181782087	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	2.030000	0.41108	2.620000	0.88729	0.655000	0.94253	CCG		TCGA-S4-A8RM-01A-11D-A377-08	SMG7-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000085432.1	0	0	0	6	428	0	50	0	5.031734e-01	0	110	0	50	2		0	0	0	0	0	2	1	0.964463	6	425	0	50	2		0	0	0	0	50	2	-2.742843	1	1	121406	8	39	1	1	2	3	2.680464	1	0.640000	1.980000	0.727273	0.050000	1.000000e-02	0.120000	0.060000	0.065936	0.050000	0	3.000000e-02	0.090000
OBSCN	84033	broad.mit.edu	37	1	228506686	228506686	+	Missense_Mutation	SNP	C	C	T			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr1:228506686C>T	ENST00000422127.1	+	54	14277	c.14233C>T	c.(14233-14235)Cgg>Tgg	p.R4745W	OBSCN_ENST00000284548.11_Missense_Mutation_p.R4745W|OBSCN_ENST00000366707.4_Missense_Mutation_p.R2379W|OBSCN_ENST00000570156.2_Missense_Mutation_p.R5702W|OBSCN_ENST00000366709.4_Missense_Mutation_p.R1864W	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF			223		Prostate(94;0.0405)			GGCCCTGGCTCGGAAACGTCG	0.687000																								0							SO:0001583	missense			ENST00000422127.1	0	1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	C	17.75	3.466374	0.63625	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	T;T;T;T	0.65364	0.26;-0.15;-0.09;0.41	4.03	1.89	0.25635	.	0.207897	0.29139	N	0.013029	T	0.61702	0.2368	N	0.24115	0.695	0.31729	N	0.637237	D;D	0.76494	0.999;0.999	P;D	0.65140	0.857;0.932	T	0.66520	-0.5903	10	0.62326	D	0.03	.	10.3422	0.43884	0.6289:0.3711:0.0:0.0	.	4745;4745	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	W	4745;4745;2379;1864	ENSP00000284548:R4745W;ENSP00000409493:R4745W;ENSP00000355668:R2379W;ENSP00000355670:R1864W	ENSP00000284548:R4745W	R	+	1	2	OBSCN	226573309	1.000000	0.71417	0.998000	0.56505	0.428000	0.31595	5.230000	0.65321	0.882000	0.36016	0.313000	0.20887	CGG		TCGA-S4-A8RM-01A-11D-A377-08	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		1	0	0	9	46	0	9	0	3.534299e-01	1	6	0	9	2		0	0	0	0	0	2	1	0.995547	8	47	0	9	2		0	0	0	0	9	2	-17.537120	1	1	120636	3	24	1	1	2	3	2.685707	1	0.640000	1.980000	0.727273	0.690000	3.500000e-01	1.000000	1.000000	0.707775	0.690000	0	5.000000e-01	0.910000
OR2AK2	391191	broad.mit.edu	37	1	248129097	248129097	+	Missense_Mutation	SNP	T	T	G			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr1:248129097T>G	ENST00000366480.3	+	1	563	c.464T>G	c.(463-465)aTc>aGc	p.I155S	OR2L13_ENST00000366478.2_Intron	NM_001004491.1	NP_001004491.1	Q8NG84	O2AK2_HUMAN	olfactory receptor, family 2, subfamily AK, member 2			36	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0152)		AGCAAGAAGATCTGCTGCCTC	0.438000													Melanoma(45;390 1181 23848 28461 41504)											0							SO:0001583	missense			ENST00000366480.3	0	1	hg19	CCDS31102.1	.	.	.	.	.	.	.	.	.	.	.	12.99	2.103841	0.37145	.	.	ENSG00000187080	ENST00000366480	T	0.00164	8.64	3.03	-3.31	0.04988	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00210	0.0006	L	0.33485	1.01	0.09310	N	1	D	0.56746	0.977	P	0.60541	0.876	T	0.46303	-0.9201	9	0.87932	D	0	.	4.6463	0.12574	0.1485:0.3771:0.0:0.4744	.	155	Q8NG84	O2AK2_HUMAN	S	155	ENSP00000355436:I155S	ENSP00000355436:I155S	I	+	2	0	OR2AK2	246195720	0.001000	0.12720	0.000000	0.03702	0.024000	0.10985	0.382000	0.20635	-0.847000	0.04168	-0.475000	0.04921	ATC		TCGA-S4-A8RM-01A-11D-A377-08	OR2AK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096858.2	0	0	0	9	1127	0	187		0	0	0	0	187	2		0	0	0	0	0	2	1	0.993972	9	1117	0	185	2		0	0	0	0	187	2	-5.786677	1	1	0	0		1	1	2	3	2.685707	1	0.640000	1.980000	0.727273	0.020000	0	0.070000	0.030000	0.033467	0.020000	0	1.000000e-02	0.050000
HCRTR1	3061	broad.mit.edu	37	1	32087188	32087188	+	Missense_Mutation	SNP	C	C	T			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr1:32087188C>T	ENST00000373706.5	+	4	886	c.733C>T	c.(733-735)Cgc>Tgc	p.R245C	HCRTR1_ENST00000403528.2_Missense_Mutation_p.R245C|HCRTR1_ENST00000468521.1_3'UTR|HCRTR1_ENST00000373705.1_Missense_Mutation_p.R245C			O43613	OX1R_HUMAN	hypocretin (orexin) receptor 1			7		Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.116)			GCTCTGGGGCCGCCAGGTGAG	0.597000																								0							SO:0001583	missense			ENST00000373706.5	0	1	hg19	CCDS344.1	.	.	.	.	.	.	.	.	.	.	c	29.2	4.987869	0.93106	.	.	ENSG00000121764	ENST00000403528;ENST00000373706;ENST00000373705	T;T;T	0.38887	1.11;1.11;1.11	5.25	5.25	0.73442	GPCR, rhodopsin-like superfamily (1);	0.129259	0.56097	D	0.000036	T	0.63674	0.2531	M	0.73430	2.235	0.80722	D	1	D;D	0.76494	0.994;0.999	P;D	0.63703	0.846;0.917	T	0.66622	-0.5877	10	0.87932	D	0	.	17.1746	0.86838	0.0:1.0:0.0:0.0	.	245;245	A6NMV7;O43613	.;OX1R_HUMAN	C	245	ENSP00000384387:R245C;ENSP00000362810:R245C;ENSP00000362809:R245C	ENSP00000362809:R245C	R	+	1	0	HCRTR1	31859775	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.354000	0.59417	2.836000	0.97738	0.651000	0.88453	CGC		TCGA-S4-A8RM-01A-11D-A377-08	HCRTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011042.1	0	0	0	7	252	0	48		0	0	0	0	48	2		0	0	0	0	0	2	1	0.979916	7	248	0	47	2		0	0	0	0	48	2	-7.979174	1	1	0	0		1	0	1	1	1.449678	1	0.640000	1.980000	0.475524	0.050000	2.000000e-02	0.110000	0.060000	0.065468	0.050000	0	3.000000e-02	0.090000
BARHL2	343472	broad.mit.edu	37	1	91180182	91180182	+	Missense_Mutation	SNP	G	G	A			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr1:91180182G>A	ENST00000370445.4	-	2	798	c.757C>T	c.(757-759)Cgg>Tgg	p.R253W		NM_020063.1	NP_064447.1	Q9NY43	BARH2_HUMAN	BarH-like homeobox 2			24		all_lung(203;0.0263)|Lung SC(238;0.128)			TACTTCTGCCGCTCAAAGCTA	0.567000													GBM(199;3561 4100 22440)											0							SO:0001583	missense			ENST00000370445.4	0	1	hg19	CCDS730.1	.	.	.	.	.	.	.	.	.	.	G	17.81	3.481732	0.63849	.	.	ENSG00000143032	ENST00000370445	D	0.96427	-4.01	5.48	4.55	0.56014	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.088225	0.53938	D	0.000059	D	0.97763	0.9266	M	0.85299	2.745	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.98465	1.0598	10	0.72032	D	0.01	.	14.0787	0.64907	0.0:0.0:0.848:0.1519	.	253	Q9NY43	BARH2_HUMAN	W	253	ENSP00000359474:R253W	ENSP00000359474:R253W	R	-	1	2	BARHL2	90952770	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.479000	0.35453	1.243000	0.43853	0.655000	0.94253	CGG		TCGA-S4-A8RM-01A-11D-A377-08	BARHL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027728.2	0	0	0	6	532	0	111		0	0	0	0	111	2		0	0	0	0	0	2	1	0.963704	6	526	0	110	2		0	0	0	0	111	2	-2.204897	0	1	0	0		1	0	1	1	1.449678	1	0.640000	1.980000	0.475524	0.020000	0	0.050000	0.020000	0.027753	0.020000	0	1.000000e-02	0.040000
ZSWIM3	140831	broad.mit.edu	37	20	44506675	44506675	+	Missense_Mutation	SNP	G	G	A			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr20:44506675G>A	ENST00000255152.2	+	2	1687	c.1478G>A	c.(1477-1479)gGc>gAc	p.G493D	ZSWIM3_ENST00000454862.2_Missense_Mutation_p.G487D	NM_080752.3	NP_542790.2	Q96MP5	ZSWM3_HUMAN	zinc finger, SWIM-type containing 3			35		Myeloproliferative disorder(115;0.0122)			TCGCAGGTTGGCATGCTGGAC	0.582000																								0							SO:0001583	missense			ENST00000255152.2	0	1	hg19	CCDS13381.1	.	.	.	.	.	.	.	.	.	.	G	0.793	-0.758013	0.03019	.	.	ENSG00000132801	ENST00000255152;ENST00000454862	T;T	0.25414	1.84;1.8	5.65	2.51	0.30379	.	0.603536	0.17459	N	0.173509	T	0.12092	0.0294	N	0.17082	0.46	0.27138	N	0.961732	B;B	0.11235	0.004;0.004	B;B	0.09377	0.004;0.004	T	0.29761	-1.0001	10	0.11794	T	0.64	-12.4254	6.0596	0.19830	0.2499:0.1427:0.6074:0.0	.	487;493	E7ETT6;Q96MP5	.;ZSWM3_HUMAN	D	493;487	ENSP00000255152:G493D;ENSP00000406313:G487D	ENSP00000255152:G493D	G	+	2	0	ZSWIM3	43940082	0.515000	0.26210	0.928000	0.36995	0.504000	0.33889	0.453000	0.21811	0.941000	0.37499	0.655000	0.94253	GGC		TCGA-S4-A8RM-01A-11D-A377-08	ZSWIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079540.1	0	0	0	4	217	1	49	0	3.425885e-03	0	4	1	49	2		0	0	0	0	0	2	0	0.006899	4	212	1	49	15		0	0	0	1	49	2	-5.343423	1	1	0	0		1	0	0	0	2.000980	0	0.640000	1.980000	0.637681	0.050000	1.000000e-02	0.140000	0.060000	0.069377	0.050000	0	3.000000e-02	0.100000
DIDO1	11083	broad.mit.edu	37	20	61511162	61511162	+	Missense_Mutation	SNP	G	G	A			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr20:61511162G>A	ENST00000266070.4	-	16	6471	c.6146C>T	c.(6145-6147)gCg>gTg	p.A2049V	DIDO1_ENST00000395343.1_Missense_Mutation_p.A2049V	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1			99	Breast(26;5.68e-08)				GGAGGAGAGCGCGGAGGGCGG	0.716000													Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)											0							SO:0001583	missense			ENST00000266070.4	1	1	hg19	CCDS33506.1	.	.	.	.	.	.	.	.	.	.	G	6.147	0.395336	0.11638	.	.	ENSG00000101191	ENST00000266070;ENST00000395343	T;T	0.09163	3.01;3.01	3.89	1.76	0.24704	.	1.633200	0.04269	U	0.341785	T	0.07999	0.0200	N	0.22421	0.69	0.09310	N	0.999999	B	0.30211	0.273	B	0.15484	0.013	T	0.34576	-0.9823	10	0.56958	D	0.05	0.4278	6.5979	0.22685	0.088:0.0:0.5951:0.3169	.	2049	Q9BTC0	DIDO1_HUMAN	V	2049	ENSP00000266070:A2049V;ENSP00000378752:A2049V	ENSP00000266070:A2049V	A	-	2	0	DIDO1	60981607	0.027000	0.19231	0.002000	0.10522	0.013000	0.08279	2.240000	0.43088	0.084000	0.17077	0.563000	0.77884	GCG		TCGA-S4-A8RM-01A-11D-A377-08	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	1	0	0	177	419	0	109	1	9.999491e-01	18	19	0	109	2		0	0	0	0	0	2	1	1.000000	173	410	0	106	2		0	0	0	0	109	2	-20.000000	1	1	118202	4	39	1	0	0	0	2.000980	0	0.640000	1.980000	0.637681	0.910000	8.000000e-01	1.000000	1.000000	0.920609	0.910000	1	8.500000e-01	0.980000
COL20A1	57642	broad.mit.edu	37	20	61950533	61950533	+	Silent	SNP	C	C	A			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr20:61950533C>A	ENST00000358894.6	+	22	2887	c.2787C>A	c.(2785-2787)ctC>ctA	p.L929L	COL20A1_ENST00000422202.1_Silent_p.L936L|COL20A1_ENST00000435874.1_Silent_p.L936L|COL20A1_ENST00000326996.6_Silent_p.L929L	NM_020882.2	NP_065933.2	Q9P218	COKA1_HUMAN	collagen, type XX, alpha 1			36	all_cancers(38;1.39e-10)				TCCAGCCCCTCCTTGGGGTTC	0.667000																								0							SO:0001819	synonymous_variant			ENST00000358894.6	1	1	hg19	CCDS46628.1																																																																																				TCGA-S4-A8RM-01A-11D-A377-08	COL20A1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000144595.2	1	0	1	38	106	0	12		0	0	0	0	12	2		0	0	0	0	0	2	1	1.000000	38	104	0	10	2		0	0	0	0	12	2	-20.000000	1	1	0	0		1	0	0	0	2.000980	0	0.640000	1.980000	0.637681	0.810000	6.000000e-01	1.000000	1.000000	0.822544	0.810000	0	7.000000e-01	0.930000
IL1RL1	9173	broad.mit.edu	37	2	102957161	102957161	+	Silent	SNP	G	G	A	rs142878092		TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr2:102957161G>A	ENST00000233954.1	+	5	754	c.483G>A	c.(481-483)gcG>gcA	p.A161A	IL1RL1_ENST00000404917.2_Silent_p.A44A|IL1RL1_ENST00000393393.3_Silent_p.A161A|IL1RL1_ENST00000311734.2_Silent_p.A161A|IL1RL1_ENST00000409584.1_Silent_p.A161A	NM_016232.4	NP_057316.3	Q01638	ILRL1_HUMAN	interleukin 1 receptor-like 1			16					GGTACAGGGCGCACAAGTCAT	0.358000																								0							SO:0001819	synonymous_variant			ENST00000233954.1	0	1	hg19	CCDS2057.1																																																																																				TCGA-S4-A8RM-01A-11D-A377-08	IL1RL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253296.1	0	0	0	6	590	0	112	0	4.627791e-04	1	2	0	112	2		0	0	0	0	0	2	1	0.964195	6	585	0	111	2		0	0	0	0	112	2	-2.056157	0	1	121410	8	44	1	0	0	0	2.007309	0	0.640000	1.980000	0.640000	0.030000	0	0.070000	0.040000	0.035947	0.030000	0	1.000000e-02	0.050000
LRP1B	53353	broad.mit.edu	37	2	141571360	141571360	+	Missense_Mutation	SNP	T	T	C			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr2:141571360T>C	ENST00000389484.3	-	32	6196	c.5225A>G	c.(5224-5226)tAt>tGt	p.Y1742C		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B			606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)			GTTTTCCACATAGTCTATCGA	0.348000										TSP Lung(27;0.18)			Colon(99;50 2074 2507 20106)											0							SO:0001583	missense			ENST00000389484.3	0	1	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	T	17.43	3.388112	0.61956	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.91295	-2.82	5.71	5.71	0.89125	Six-bladed beta-propeller, TolB-like (1);	0.164731	0.41938	D	0.000793	D	0.94686	0.8286	M	0.85099	2.735	0.41501	D	0.988284	D	0.69078	0.997	P	0.57283	0.817	D	0.95215	0.8329	10	0.56958	D	0.05	.	15.9781	0.80086	0.0:0.0:0.0:1.0	.	1742	Q9NZR2	LRP1B_HUMAN	C	1742;1680	ENSP00000374135:Y1742C	ENSP00000374135:Y1742C	Y	-	2	0	LRP1B	141287830	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.982000	0.56909	2.171000	0.68590	0.533000	0.62120	TAT		TCGA-S4-A8RM-01A-11D-A377-08	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	0	0	0	4	296	0	62		0	0	0	0	62	2		0	0	0	0	0	2	1	0.889445	4	294	0	61	2		0	0	0	0	62	2	-3.038080	1	1	0	0		1	0	0	0	2.007309	0	0.640000	1.980000	0.640000	0.040000	0	0.100000	0.040000	0.051410	0.040000	0	2.000000e-02	0.070000
SCN9A	6335	broad.mit.edu	37	2	167133600	167133600	+	Missense_Mutation	SNP	C	C	T			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr2:167133600C>T	ENST00000409435.1	-	15	2766	c.2767G>A	c.(2767-2769)Gtg>Atg	p.V923M	AC010127.3_ENST00000447809.2_RNA|SCN9A_ENST00000409672.1_Missense_Mutation_p.V912M|SCN9A_ENST00000303354.6_Missense_Mutation_p.V924M|SCN9A_ENST00000375387.4_Missense_Mutation_p.V924M			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit			108				Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CCACACAGCACGCGGAACACA	0.478000																								0							SO:0001583	missense			ENST00000409435.1	1	1	hg19	CCDS46441.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.703467	0.88924	.	.	ENSG00000169432	ENST00000409672;ENST00000375387;ENST00000303354;ENST00000409435	D;D;D;D	0.98602	-5.02;-5.02;-5.02;-5.02	5.65	5.65	0.86999	.	0.000000	0.64402	D	0.000013	D	0.98620	0.9538	L	0.55834	1.745	0.58432	D	0.999994	D	0.89917	1.0	D	0.81914	0.995	D	0.99865	1.1088	10	0.87932	D	0	.	20.096	0.97843	0.0:1.0:0.0:0.0	.	912	E7EUN6	.	M	912;924;924;923	ENSP00000386306:V912M;ENSP00000364536:V924M;ENSP00000304748:V924M;ENSP00000386330:V923M	ENSP00000304748:V924M	V	-	1	0	SCN9A	166841846	1.000000	0.71417	0.968000	0.41197	0.996000	0.88848	7.715000	0.84713	2.819000	0.97034	0.650000	0.86243	GTG		TCGA-S4-A8RM-01A-11D-A377-08	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	1	0	0	43	688	0	130	0	8.013086e-02	1	7	0	130	2		0	0	0	0	0	2	1	1.000000	41	669	0	152	2		0	0	0	0	130	2	-7.602644	1	1	121406	3	39	1	0	0	0	2.007309	0	0.640000	1.980000	0.640000	0.180000	1.200000e-01	0.240000	0.180000	0.187425	0.180000	0	1.500000e-01	0.210000
COL5A2	1290	broad.mit.edu	37	2	189904090	189904090	+	Missense_Mutation	SNP	T	T	G			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08			T	G	T	T		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr2:189904090T>G	ENST00000374866.3	-	51	4107	c.3833A>C	c.(3832-3834)cAg>cCg	p.Q1278P		NM_000393.3	NP_000384.2	P05997	CO5A2_HUMAN	collagen, type V, alpha 2			95			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.127)		GGTTTCAATCTGACTACTGAG	0.522000																								0							SO:0001583	missense			ENST00000374866.3	1	1	hg19	CCDS33350.1	.	.	.	.	.	.	.	.	.	.	T	19.38	3.817476	0.70912	.	.	ENSG00000204262	ENST00000374866;ENST00000452536	D	0.83914	-1.78	5.28	5.28	0.74379	Fibrillar collagen, C-terminal (2);	0.000000	0.43747	D	0.000537	D	0.91781	0.7400	M	0.90369	3.11	0.80722	D	1	D;D	0.61697	0.99;0.99	D;D	0.70487	0.969;0.969	D	0.91360	0.5111	10	0.27082	T	0.32	.	15.1969	0.73100	0.0:0.0:0.0:1.0	.	918;1278	Q5PR22;P05997	.;CO5A2_HUMAN	P	1278;918	ENSP00000364000:Q1278P	ENSP00000364000:Q1278P	Q	-	2	0	COL5A2	189612335	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.977000	0.88081	1.983000	0.57843	0.533000	0.62120	CAG		TCGA-S4-A8RM-01A-11D-A377-08	COL5A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313523.1	1	0	1	111	248	0	52	0	1	0	139	0	52	2		0	0	0	0	0	2	1	1.000000	109	246	0	51	2		0	0	0	0	52	2	-20.000000	1	1	0	0		1	0	0	0	2.007309	0	0.640000	1.980000	0.640000	0.960000	8.100000e-01	1.000000	1.000000	0.950781	0.960000	1	8.800000e-01	1.000000
HDAC4	9759	broad.mit.edu	37	2	239975284	239975284	+	Silent	SNP	G	G	A			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr2:239975284G>A	ENST00000345617.3	-	26	3878	c.3087C>T	c.(3085-3087)cgC>cgT	p.R1029R	HDAC4_ENST00000543185.1_Silent_p.R613R	NM_006037.3	NP_006028.2	P56524	HDAC4_HUMAN	histone deacetylase 4			62		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)			GCTGCAGGCAGCGCCAGTACT	0.627000																								0							SO:0001819	synonymous_variant			ENST00000345617.3	1	1	hg19	CCDS2529.1	.	.	.	.	.	.	.	.	.	.	G	7.965	0.747822	0.15710	.	.	ENSG00000068024	ENST00000430200	.	.	.	4.38	2.12	0.27331	.	.	.	.	.	T	0.53190	0.1781	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.46105	-0.9215	4	.	.	.	.	6.304	0.21129	0.3473:0.0:0.6527:0.0	.	.	.	.	V	120	.	.	A	-	2	0	HDAC4	239640221	1.000000	0.71417	1.000000	0.80357	0.767000	0.43475	1.786000	0.38694	0.972000	0.38314	-0.142000	0.14014	GCT		TCGA-S4-A8RM-01A-11D-A377-08	HDAC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257174.2	1	0	1	26	79	0	20	0	4.687787e-01	1	5	0	20	2		0	0	0	0	0	2	1	1.000000	26	79	0	20	2		0	0	0	0	20	2	-20.000000	1	1	0	0		1	0	0	0	2.007309	0	0.640000	1.980000	0.640000	0.770000	5.300000e-01	1.000000	1.000000	0.780974	0.770000	0	6.400000e-01	0.910000
NRXN1	9378	broad.mit.edu	37	2	51254893	51254893	+	Silent	SNP	C	C	T			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr2:51254893C>T	ENST00000406316.2	-	2	1995	c.519G>A	c.(517-519)tcG>tcA	p.S173S	NRXN1_ENST00000405581.1_Silent_p.S173S|NRXN1_ENST00000406859.3_Silent_p.S173S|NRXN1_ENST00000404971.1_Silent_p.S173S|NRXN1_ENST00000401669.2_Silent_p.S173S|NRXN1_ENST00000402717.3_Silent_p.S173S|NRXN1_ENST00000405472.3_Silent_p.S173S	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1			58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)		GCTCCCTCACCGAGGCCAGGG	0.672000																								0							SO:0001819	synonymous_variant			ENST00000406316.2	1	1	hg19	CCDS54360.1																																																																																				TCGA-S4-A8RM-01A-11D-A377-08	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2	1	0	0	35	69	0	19	0	0	0	1	0	19	2		0	0	0	0	0	2	1	1.000000	33	67	0	18	2		0	0	0	0	19	2	-20.000000	1	1	0	0		1	0	0	0	2.007309	0	0.640000	1.980000	0.640000	0.990000	7.800000e-01	1.000000	1.000000	0.967091	0.990000	1	9.000000e-01	1.000000
INPP4A	3631	broad.mit.edu	37	2	99163080	99163080	+	Silent	SNP	G	G	A			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr2:99163080G>A	ENST00000523221.1	+	11	1086	c.1086G>A	c.(1084-1086)gcG>gcA	p.A362A	INPP4A_ENST00000545415.1_Silent_p.A362A|INPP4A_ENST00000409851.3_Silent_p.A362A|INPP4A_ENST00000409540.3_Silent_p.A362A|INPP4A_ENST00000409463.1_Intron|INPP4A_ENST00000409016.4_Silent_p.A362A|INPP4A_ENST00000074304.5_Silent_p.A362A			Q96PE3	INP4A_HUMAN	inositol polyphosphate-4-phosphatase, type I, 107kDa			43					CCATTGGGGCGCCAGCAGCAC	0.493000																								0							SO:0001819	synonymous_variant			ENST00000523221.1	0	1	hg19	CCDS46369.1																																																																																				TCGA-S4-A8RM-01A-11D-A377-08	INPP4A-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376095.1	0	0	0	4	236	0	26	0	3.212255e-02	0	12	0	26	2		0	0	0	0	0	2	1	0.886131	4	232	0	26	2		0	0	0	0	26	2	-2.894204	1	1	120882	7	37	1	0	0	0	2.007309	0	0.640000	1.980000	0.640000	0.050000	1.000000e-02	0.130000	0.060000	0.064301	0.050000	0	3.000000e-02	0.090000
CD86	942	broad.mit.edu	37	3	121822548	121822548	+	Missense_Mutation	SNP	G	G	A			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr3:121822548G>A	ENST00000330540.2	+	3	370	c.254G>A	c.(253-255)cGc>cAc	p.R85H	CD86_ENST00000264468.5_Intron|CD86_ENST00000493101.1_Intron|CD86_ENST00000469710.1_Missense_Mutation_p.R3H|CD86_ENST00000393627.2_Missense_Mutation_p.R79H	NM_175862.4	NP_787058	P42081	CD86_HUMAN	CD86 molecule			23				Abatacept(DB01281)|Antithymocyte globulin(DB00098)|Belatacept(DB06681)	TATATGGGCCGCACAAGTTTT	0.423000													GBM(67;1379 1389 36064 39806)											0							SO:0001583	missense			ENST00000330540.2	0	1	hg19	CCDS3009.1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.619268	0.87460	.	.	ENSG00000114013	ENST00000469710;ENST00000330540;ENST00000482356;ENST00000393627	T;T;T;T	0.72505	1.2;-0.66;-0.66;-0.66	5.54	5.54	0.83059	Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin V-set, subgroup (1);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000016	D	0.87414	0.6171	M	0.93106	3.38	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89572	0.3814	10	0.87932	D	0	-18.8448	14.8575	0.70351	0.0:0.0:1.0:0.0	.	85	P42081	CD86_HUMAN	H	3;85;79;79	ENSP00000418988:R3H;ENSP00000332049:R85H;ENSP00000419116:R79H;ENSP00000377248:R79H	ENSP00000332049:R85H	R	+	2	0	CD86	123305238	0.999000	0.42202	0.958000	0.39756	0.915000	0.54546	4.887000	0.63156	2.884000	0.98904	0.655000	0.94253	CGC		TCGA-S4-A8RM-01A-11D-A377-08	CD86-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000355671.1	0	0	0	6	766	1	152	0	1.003833e-02	0	16	1	152	2	0	7.103134e-01	0	1338	1	710	9	0	0.009939	7	756	1	152	18		0	0	0	1	152	2	-1.804410	0	1	0	0		1	0	0	0	2.015211	0	0.640000	1.980000	0.640000	0.020000	0	0.050000	0.020000	0.027051	0.020000	0	0	0.040000
SIAH2	6478	broad.mit.edu	37	3	150460176	150460176	+	Missense_Mutation	SNP	G	G	C			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08			G	C	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr3:150460176G>C	ENST00000312960.3	-	2	1254	c.727C>G	c.(727-729)Cag>Gag	p.Q243E		NM_005067.5	NP_005058.3	O43255	SIAH2_HUMAN	siah E3 ubiquitin protein ligase 2			16			LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)		AAAAACTGCTGGTGGCCTTCG	0.527000																								0							SO:0001583	missense			ENST00000312960.3	1	1	hg19	CCDS3152.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.372610	0.82573	.	.	ENSG00000181788	ENST00000312960	T	0.25749	1.78	5.67	4.79	0.61399	TRAF-type (1);Seven-in-absentia protein, TRAF-like domain (1);TRAF-like (1);	0.000000	0.85682	D	0.000000	T	0.36799	0.0980	M	0.83603	2.65	0.54753	D	0.999986	B	0.27450	0.179	B	0.32805	0.153	T	0.19418	-1.0306	10	0.25106	T	0.35	.	15.8794	0.79193	0.0:0.0:0.8633:0.1367	.	243	O43255	SIAH2_HUMAN	E	243	ENSP00000322457:Q243E	ENSP00000322457:Q243E	Q	-	1	0	SIAH2	151942866	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.848000	0.99507	1.349000	0.45751	0.591000	0.81541	CAG		TCGA-S4-A8RM-01A-11D-A377-08	SIAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357697.1	1	0	1	103	200	0	57	1	1	37	38	0	57	2		0	0	0	0	0	2	1	1.000000	103	198	0	57	2		0	0	0	0	57	2	-11.521760	1	1	0	0		1	0	0	0	2.015211	0	0.640000	1.980000	0.640000	0.990000	8.900000e-01	1.000000	1.000000	0.989100	0.990000	1	9.700000e-01	1.000000
PCDHB7	56129	broad.mit.edu	37	5	140553506	140553506	+	Missense_Mutation	SNP	G	G	A			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr5:140553506G>A	ENST00000231137.3	+	1	1264	c.1090G>A	c.(1090-1092)Gtc>Atc	p.V364I		NM_018940.2	NP_061763.1	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7			119			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)		ACCCGAGACAGTCGTGGCTGT	0.473000																								0							SO:0001583	missense			ENST00000231137.3	1	1	hg19	CCDS4249.1	.	.	.	.	.	.	.	.	.	.	G	11.86	1.765245	0.31228	.	.	ENSG00000113212	ENST00000231137;ENST00000543636	T	0.51817	0.69	4.61	3.73	0.42828	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.40979	0.1139	L	0.60845	1.875	0.09310	N	1	B	0.17038	0.02	B	0.20384	0.029	T	0.35475	-0.9787	9	0.41790	T	0.15	.	4.5756	0.12232	0.0834:0.1519:0.6079:0.1567	.	364	Q9Y5E2	PCDB7_HUMAN	I	364;147	ENSP00000231137:V364I	ENSP00000231137:V364I	V	+	1	0	PCDHB7	140533690	0.027000	0.19231	0.079000	0.20413	0.449000	0.32228	1.974000	0.40559	1.038000	0.40049	0.650000	0.86243	GTC		TCGA-S4-A8RM-01A-11D-A377-08	PCDHB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251803.2	1	0	1	82	150	0	54	0	5.788988e-01	0	5	0	54	2		0	0	0	0	0	2	1	1.000000	81	145	0	52	2		0	0	0	0	54	2	-20.000000	1	1	0	0		1	1	2	3	2.024827	0	0.640000	1.980000	0.641148	0.990000	9.100000e-01	1.000000	1.000000	0.993822	0.990000	1	9.900000e-01	1.000000
FAM153B	202134	broad.mit.edu	37	5	175528575	175528575	+	Missense_Mutation	SNP	C	C	G			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08			C	G	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr5:175528575C>G	ENST00000253490.4	+	12	712	c.655C>G	c.(655-657)Ctg>Gtg	p.L219V	FAM153B_ENST00000515817.1_Missense_Mutation_p.L142V|FAM153B_ENST00000512862.1_Intron|FAM153B_ENST00000510151.1_Missense_Mutation_p.L142V			P0C7A2	F153B_HUMAN	family with sequence similarity 153, member B			16	all_cancers(89;0.00406)|Renal(175;0.000269)|Lung NSC(126;0.0103)|all_lung(126;0.0164)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)		CCCAGACACACTGGCCGAACG	0.453000																								0							SO:0001583	missense			ENST00000253490.4	1	1	hg19		.	.	.	.	.	.	.	.	.	.	C	6.823	0.520995	0.13005	.	.	ENSG00000182230	ENST00000515817;ENST00000253490	.	.	.	0.607	-1.05	0.10036	.	.	.	.	.	T	0.20333	0.0489	N	0.19112	0.55	0.09310	N	1	P	0.45594	0.862	P	0.46110	0.504	T	0.13361	-1.0512	7	0.46703	T	0.11	.	.	.	.	.	219	P0C7A2	F153B_HUMAN	V	142;219	.	ENSP00000253490:L219V	L	+	1	2	FAM153B	175461181	0.007000	0.16637	0.000000	0.03702	0.008000	0.06430	-0.346000	0.07760	-0.368000	0.08040	0.173000	0.16961	CTG		TCGA-S4-A8RM-01A-11D-A377-08	FAM153B-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		1	0	1	92	256	0	61	1	9.999978e-01	15	41	0	61	2		0	0	0	0	0	2	1	1.000000	90	254	0	61	2		0	0	0	0	61	2	-20.000000	1	0	0	0		1	1	2	3	2.024827	0	0.640000	1.980000	0.641148	0.820000	6.800000e-01	0.980000	0.830000	0.831287	0.820000	0	7.500000e-01	0.910000
MAK	4117	broad.mit.edu	37	6	10802169	10802169	+	Missense_Mutation	SNP	C	C	T			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr6:10802169C>T	ENST00000313243.2	-	8	1169	c.787G>A	c.(787-789)Gaa>Aaa	p.E263K	MAK_ENST00000538030.1_Missense_Mutation_p.E263K|SYCP2L_ENST00000543878.1_Intron|MAK_ENST00000536370.1_Missense_Mutation_p.E263K|MAK_ENST00000474039.1_Missense_Mutation_p.E263K|MAK_ENST00000354489.2_Missense_Mutation_p.E263K|RP11-637O19.3_ENST00000480294.1_Intron			P20794	MAK_HUMAN	male germ cell-associated kinase			22	Breast(50;0.107)|Ovarian(93;0.107)	all_hematologic(90;0.117)			TTCAACATTTCGGTCATGAGC	0.408000											OREG0017187	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)												0							SO:0001583	missense			ENST00000313243.2	1	1	hg19	CCDS4516.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.710536	0.89112	2.27E-4	4.65E-4	ENSG00000111837	ENST00000313243;ENST00000354489;ENST00000538030;ENST00000536370	T;T;T;T	0.63580	-0.05;-0.05;-0.05;-0.05	5.42	5.42	0.78866	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.146778	0.64402	D	0.000016	T	0.18923	0.0454	N	0.00399	-1.545	0.80722	D	1	B	0.20368	0.044	B	0.23419	0.046	T	0.19386	-1.0307	10	0.29301	T	0.29	.	19.6002	0.95559	0.0:1.0:0.0:0.0	.	263	P20794	MAK_HUMAN	K	263	ENSP00000313021:E263K;ENSP00000346484:E263K;ENSP00000442250:E263K;ENSP00000442221:E263K	ENSP00000313021:E263K	E	-	1	0	MAK	10910155	1.000000	0.71417	0.927000	0.36925	0.966000	0.64601	4.566000	0.60843	2.691000	0.91804	0.655000	0.94253	GAA		TCGA-S4-A8RM-01A-11D-A377-08	MAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039841.1	0	0	0	10	328	1	97	0	3.329006e-03	0	3	1	97	2		0	0	0	0	0	2	0	0.328179	10	326	1	97	13		0	0	0	1	97	2	-2.817017	1	1	121412	26	46	1	0	1	1	1.396540	1	0.640000	1.980000	0.480370	0.060000	2.000000e-02	0.110000	0.060000	0.069816	0.060000	0	4.000000e-02	0.090000
RPS6KA2	6196	broad.mit.edu	37	6	166844030	166844030	+	Missense_Mutation	SNP	T	T	G			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr6:166844030T>G	ENST00000265678.4	-	16	1715	c.1492A>C	c.(1492-1494)Atc>Ctc	p.I498L	RPS6KA2_ENST00000481261.2_Missense_Mutation_p.I409L|RPS6KA2_ENST00000405189.3_Missense_Mutation_p.I409L|RPS6KA2_ENST00000503859.1_Missense_Mutation_p.I506L|RPS6KA2_ENST00000510118.1_Missense_Mutation_p.I523L	NM_021135.4	NP_066958.2	Q15349	KS6A2_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 2			45		Breast(66;2.04e-05)|Ovarian(120;0.0652)|Prostate(117;0.105)			TGCCGGAGGATGCGGTCCAGG	0.587000																								0							SO:0001583	missense			ENST00000265678.4	1	1	hg19	CCDS5294.1	.	.	.	.	.	.	.	.	.	.	T	14.06	2.422481	0.43020	.	.	ENSG00000071242	ENST00000265678;ENST00000510118;ENST00000503859;ENST00000481261;ENST00000405189	T;T;T;T;T	0.62788	0.0;0.0;0.0;0.0;0.0	3.63	3.63	0.41609	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.128885	0.50627	D	0.000112	T	0.53818	0.1820	N	0.25031	0.7	0.80722	D	1	B;B;B	0.31989	0.052;0.042;0.35	B;B;P	0.55545	0.413;0.166;0.778	T	0.58657	-0.7598	10	0.33940	T	0.23	.	11.8701	0.52515	0.0:0.0:0.0:1.0	.	523;506;498	F2Z2J1;Q15349-3;Q15349	.;.;KS6A2_HUMAN	L	498;523;506;409;409	ENSP00000265678:I498L;ENSP00000422435:I523L;ENSP00000427015:I506L;ENSP00000422484:I409L;ENSP00000386050:I409L	ENSP00000265678:I498L	I	-	1	0	RPS6KA2	166764020	1.000000	0.71417	0.998000	0.56505	0.526000	0.34562	7.272000	0.78516	1.661000	0.50771	0.402000	0.26972	ATC		TCGA-S4-A8RM-01A-11D-A377-08	RPS6KA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043075.3	1	0	0	11	174	0	40	0	5.099499e-01	0	27	0	40	2		0	0	0	0	0	2	1	0.998395	10	173	0	40	2		0	0	0	0	40	2	-14.966800	1	1	0	0		1	0	1	1	1.429478	1	0.640000	1.980000	0.480370	0.120000	6.000000e-02	0.220000	0.130000	0.138123	0.120000	0	9.000000e-02	0.170000
SLC17A3	10786	broad.mit.edu	37	6	25845701	25845701	+	Missense_Mutation	SNP	G	G	A			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr6:25845701G>A	ENST00000360657.3	-	11	1457	c.1172C>T	c.(1171-1173)gCc>gTc	p.A391V	SLC17A3_ENST00000397060.4_Missense_Mutation_p.A469V|SLC17A3_ENST00000361703.6_Missense_Mutation_p.A391V			O00476	NPT4_HUMAN	solute carrier family 17 (organic anion transporter), member 3			20					CAGGTTAACGGCAAACAGCAA	0.413000																								0							SO:0001583	missense			ENST00000360657.3	0	1	hg19	CCDS4566.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.73|17.73	3.460762|3.460762	0.63513|0.63513	.|.	.|.	ENSG00000124564|ENSG00000124564	ENST00000505420;ENST00000397060;ENST00000360657;ENST00000361703|ENST00000481949	T;T;T;T|.	0.58940|.	0.38;0.3;0.3;0.3|.	4.78|4.78	3.91|3.91	0.45181|0.45181	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);|.	0.141196|.	0.32533|.	N|.	0.005969|.	T|T	0.36880|0.36880	0.0983|0.0983	L|L	0.46741|0.46741	1.465|1.465	0.36016|0.36016	D|D	0.838379|0.838379	B;P|.	0.43973|.	0.165;0.823|.	B;P|.	0.48089|.	0.081;0.566|.	T|T	0.24119|0.24119	-1.0169|-1.0169	10|5	0.48119|.	T|.	0.1|.	.|.	9.3173|9.3173	0.37941|0.37941	0.1012:0.0:0.8988:0.0|0.1012:0.0:0.8988:0.0	.|.	469;391|.	B7Z511;O00476|.	.;NPT4_HUMAN|.	V|S	22;469;391;391|70	ENSP00000424027:A22V;ENSP00000380250:A469V;ENSP00000353873:A391V;ENSP00000355307:A391V|.	ENSP00000353873:A391V|.	A|P	-|-	2|1	0|0	SLC17A3|SLC17A3	25953680|25953680	0.135000|0.135000	0.22499|0.22499	0.305000|0.305000	0.25099|0.25099	0.036000|0.036000	0.12997|0.12997	1.724000|1.724000	0.38064|0.38064	1.130000|1.130000	0.42092|0.42092	0.591000|0.591000	0.81541|0.81541	GCC|CCG		TCGA-S4-A8RM-01A-11D-A377-08	SLC17A3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040070.2	0	0	0	6	405	0	66		0	0	0	0	66	2		0	0	0	0	0	2	1	0.963896	6	400	0	65	2		0	0	0	0	66	2	-2.430920	0	1	0	0		1	0	0	0	1.994505	0	0.640000	1.980000	0.637681	0.040000	1.000000e-02	0.100000	0.040000	0.052561	0.040000	0	2.000000e-02	0.070000
SLC44A4	80736	broad.mit.edu	37	6	31832445	31832445	+	Silent	SNP	C	C	T	rs146889731		TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr6:31832445C>T	ENST00000229729.6	-	20	2015	c.1995G>A	c.(1993-1995)acG>acA	p.T665T	SLC44A4_ENST00000544672.1_Silent_p.T589T|NEU1_ENST00000375631.4_5'Flank|SLC44A4_ENST00000375562.4_Silent_p.T623T	NM_025257.2	NP_079533.2	Q53GD3	CTL4_HUMAN	solute carrier family 44, member 4			35				Choline(DB00122)	AGAGGAAGAGCGTGTCCACAC	0.522000																								0							SO:0001819	synonymous_variant			ENST00000229729.6	1	1	hg19	CCDS4724.2																																																																																				TCGA-S4-A8RM-01A-11D-A377-08	SLC44A4-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076234.3	1	0	1	93	305	0	69	1	1	687	818	0	69	2		0	0	0	0	0	2	1	1.000000	92	300	0	68	2		0	0	0	0	69	2	-20.000000	1	1	121408	1	35	1	0	0	0	1.994505	0	0.640000	1.980000	0.637681	0.720000	5.900000e-01	0.850000	0.720000	0.728635	0.720000	0	6.500000e-01	0.790000
CYP21A2	1589	broad.mit.edu	37	6	32008351	32008351	+	Missense_Mutation	SNP	C	C	T			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr6:32008351C>T	ENST00000418967.2	+	8	1266	c.1108C>T	c.(1108-1110)Cgg>Tgg	p.R370W	CYP21A2_ENST00000435122.2_Missense_Mutation_p.R340W	NM_000500.7	NP_000491.4	P08686	CP21A_HUMAN	cytochrome P450, family 21, subfamily A, polypeptide 2			11				Ketoconazole(DB01026)	CCGCACCACACGGCCCAGCAG	0.667000													Melanoma(174;1669 1998 3915 34700 46447)											0							SO:0001583	missense			ENST00000418967.2	1	1	hg19	CCDS4735.1	.	.	.	.	.	.	.	.	.	.	c	15.70	2.911619	0.52439	.	.	ENSG00000231852	ENST00000418967;ENST00000435122	T;T	0.80123	-1.34;-1.34	4.75	2.87	0.33458	.	0.508711	0.16495	N	0.211913	D	0.83940	0.5363	M	0.80847	2.515	0.09310	N	0.999998	D;D	0.89917	1.0;1.0	D;D	0.83275	0.986;0.996	T	0.75297	-0.3367	10	0.66056	D	0.02	.	9.7965	0.40737	0.3896:0.6104:0.0:0.0	.	340;370	Q5ST44;Q16874	.;.	W	370;340	ENSP00000408860:R370W;ENSP00000415043:R340W	ENSP00000408860:R370W	R	+	1	2	CYP21A2	32116330	0.000000	0.05858	0.073000	0.20177	0.715000	0.41141	0.215000	0.17562	0.656000	0.30886	0.651000	0.88453	CGG		TCGA-S4-A8RM-01A-11D-A377-08	CYP21A2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268768.2	0	0	0	37	255	0	44		0	0	0	0	44	2		0	0	0	0	0	2	1	1.000000	36	218	0	50	2		0	0	0	0	44	2	-16.178910	1	1	121070	2	34	1	1	2	3	2.578348	1	0.640000	1.980000	0.719801	0.510000	3.700000e-01	1.000000	0.510000	0.561059	0.510000	0	4.300000e-01	0.630000
SLC35A1	10559	broad.mit.edu	37	6	88216129	88216129	+	Silent	SNP	C	C	T			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr6:88216129C>T	ENST00000369552.4	+	5	564	c.537C>T	c.(535-537)ggC>ggT	p.G179G	SLC35A1_ENST00000369556.3_Silent_p.G179G|SLC35A1_ENST00000544441.1_Silent_p.G45G|C6orf165_ENST00000506888.1_3'UTR|SLC35A1_ENST00000464978.1_Intron|SLC35A1_ENST00000369557.5_Intron	NM_006416.4	NP_006407.1	P78382	S35A1_HUMAN	solute carrier family 35 (CMP-sialic acid transporter), member A1			9		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)			TAGGGTTTGGCGCTATAGCTA	0.313000													NSCLC(183;214 2117 17033 22638 44782)|Ovarian(87;1008 1343 9644 42916 50932)											0							SO:0001819	synonymous_variant			ENST00000369552.4	0	1	hg19	CCDS5010.1																																																																																				TCGA-S4-A8RM-01A-11D-A377-08	SLC35A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041446.1	0	0	0	5	359	0	89	0	4.128829e-01	0	89	0	89	2		0	0	0	0	0	2	1	0.937048	5	357	0	89	2		0	0	0	0	89	2	-2.180427	0	1	0	0		1	0	1	1	1.396305	1	0.640000	1.980000	0.473068	0.020000	0	0.070000	0.030000	0.034891	0.020000	0	1.000000e-02	0.050000
TMEM176A	55365	broad.mit.edu	37	7	150498695	150498695	+	Silent	SNP	C	C	A			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08			C	A	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr7:150498695C>A	ENST00000484928.1	+	2	638	c.57C>A	c.(55-57)atC>atA	p.I19I	TMEM176B_ENST00000492607.1_5'Flank|TMEM176A_ENST00000004103.3_Silent_p.I19I|TMEM176B_ENST00000450753.2_5'Flank|TMEM176B_ENST00000326442.5_5'Flank|TMEM176B_ENST00000447204.2_5'Flank|TMEM176B_ENST00000434545.1_5'Flank|TMEM176A_ENST00000461345.1_Intron			Q96HP8	T176A_HUMAN	transmembrane protein 176A			12			OV - Ovarian serous cystadenocarcinoma(82;0.0121)		ACACCCACATCGATGTGCACA	0.657000																								0							SO:0001819	synonymous_variant			ENST00000484928.1	1	1	hg19	CCDS5909.1																																																																																				TCGA-S4-A8RM-01A-11D-A377-08	TMEM176A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350222.1	1	0	1	57	260	0	31	1	1	253	1218	0	31	2		0	0	0	0	0	2	1	1.000000	57	254	0	30	2		0	0	0	0	31	2	-3.414216	1	1	0	0		1	1	2	3	2.628128	1	0.640000	1.980000	0.725944	0.730000	5.700000e-01	0.950000	0.740000	0.747855	0.730000	0	6.500000e-01	0.840000
PTPRN2	5799	broad.mit.edu	37	7	157929382	157929382	+	Missense_Mutation	SNP	C	C	T	rs144837405		TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr7:157929382C>T	ENST00000389418.4	-	8	1147	c.1138G>A	c.(1138-1140)Gga>Aga	p.G380R	PTPRN2_ENST00000389413.3_Missense_Mutation_p.G380R|PTPRN2_ENST00000409483.1_Missense_Mutation_p.G342R|PTPRN2_ENST00000404321.2_Missense_Mutation_p.G403R|PTPRN2_ENST00000389416.4_Missense_Mutation_p.G363R	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2			86	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)		TCCTGCACTCCGTCATCTGTA	0.448000																								0							SO:0001583	missense			ENST00000389418.4	1	1	hg19	CCDS5947.1	.	.	.	.	.	.	.	.	.	.	C	5.514	0.279739	0.10458	0.0	2.33E-4	ENSG00000155093	ENST00000409483;ENST00000389413;ENST00000389416;ENST00000389418;ENST00000404321	T;T;T;T;T	0.02656	4.21;4.22;4.24;4.23;4.23	4.54	-4.67	0.03319	.	.	.	.	.	T	0.01156	0.0038	N	0.03608	-0.345	0.09310	N	1	B;B;B;B;B	0.06786	0.001;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.001;0.0;0.001;0.0;0.0	T	0.49428	-0.8941	9	0.12430	T	0.62	.	6.5936	0.22659	0.0:0.4711:0.1567:0.3722	.	403;342;380;363;380	Q92932-3;E7EM83;Q92932-2;E9PC57;Q92932	.;.;.;.;PTPR2_HUMAN	R	342;380;363;380;403	ENSP00000387114:G342R;ENSP00000374064:G380R;ENSP00000374067:G363R;ENSP00000374069:G380R;ENSP00000385464:G403R	ENSP00000374064:G380R	G	-	1	0	PTPRN2	157622143	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.284000	0.02793	-0.743000	0.04784	-1.056000	0.02311	GGA		TCGA-S4-A8RM-01A-11D-A377-08	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1	1	0	1	80	524	0	83	1	9.999986e-01	24	101	0	83	2		0	0	0	0	0	2	1	1.000000	80	514	0	83	2		0	0	0	0	83	2	-2.443736	0	1	121412	6	39	1	1	2	3	2.628128	1	0.640000	1.980000	0.725944	0.540000	4.300000e-01	0.680000	0.540000	0.552771	0.540000	0	4.800000e-01	0.610000
PURB	5814	broad.mit.edu	37	7	44924053	44924053	+	Missense_Mutation	SNP	C	C	T			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr7:44924053C>T	ENST00000395699.2	-	1	907	c.895G>A	c.(895-897)Ggc>Agc	p.G299S	MIR4657_ENST00000578157.1_RNA|RP4-673M15.1_ENST00000608450.1_RNA	NM_033224.3	NP_150093.1	Q96QR8	PURB_HUMAN	purine-rich element binding protein B			7					TCGCCGCCGCCGCTGCCCCCA	0.587000																								0							SO:0001583	missense			ENST00000395699.2	0	1	hg19	CCDS5499.1	.	.	.	.	.	.	.	.	.	.	C	15.74	2.923148	0.52653	.	.	ENSG00000146676	ENST00000395699	T	0.29655	1.56	3.06	3.06	0.35304	.	0.137657	0.27549	U	0.018864	T	0.31104	0.0786	N	0.14661	0.345	0.35690	D	0.81476	D	0.89917	1.0	D	0.65684	0.937	T	0.19063	-1.0317	10	0.16896	T	0.51	.	12.3432	0.55105	0.0:1.0:0.0:0.0	.	299	Q96QR8	PURB_HUMAN	S	299	ENSP00000379051:G299S	ENSP00000379051:G299S	G	-	1	0	PURB	44890578	0.980000	0.34600	0.998000	0.56505	0.984000	0.73092	3.212000	0.51145	1.998000	0.58463	0.591000	0.81541	GGC		TCGA-S4-A8RM-01A-11D-A377-08	PURB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251332.2	0	0	0	5	704	0	84	1	8.693792e-02	2	54	0	84	2		0	0	0	0	0	2	1	0.937268	5	702	0	83	2		0	0	0	0	84	2	-1.955223	0	0	0	0		1	1	2	3	2.612313	1	0.640000	1.980000	0.724602	0.020000	0	1.000000	0.030000	0.062338	0.020000	0	1.000000e-02	0.050000
SEMA3E	9723	broad.mit.edu	37	7	83014659	83014659	+	Missense_Mutation	SNP	G	G	A			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr7:83014659G>A	ENST00000307792.3	-	16	2293	c.1826C>T	c.(1825-1827)gCg>gTg	p.A609V	SEMA3E_ENST00000427262.1_Missense_Mutation_p.A549V	NM_012431.2	NP_036563.1	O15041	SEM3E_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E			51		Medulloblastoma(109;0.109)			GATAACTTTCGCTTGTAAAGA	0.398000																								0							SO:0001583	missense			ENST00000307792.3	0	1	hg19	CCDS34674.1	.	.	.	.	.	.	.	.	.	.	G	35	5.430525	0.96150	.	.	ENSG00000170381	ENST00000307792;ENST00000427262;ENST00000541514	T;T	0.19394	2.15;2.15	5.54	5.54	0.83059	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.49440	0.1557	M	0.76838	2.35	0.80722	D	1	D	0.76494	0.999	D	0.68039	0.955	T	0.49854	-0.8895	10	0.59425	D	0.04	.	19.4854	0.95027	0.0:0.0:1.0:0.0	.	609	O15041	SEM3E_HUMAN	V	609;549;609	ENSP00000303212:A609V;ENSP00000405052:A549V	ENSP00000303212:A609V	A	-	2	0	SEMA3E	82852595	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	9.255000	0.95524	2.597000	0.87782	0.650000	0.86243	GCG		TCGA-S4-A8RM-01A-11D-A377-08	SEMA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336606.1	0	0	0	8	803	0	111	0	2.407403e-02	1	20	0	111	2		0	0	0	0	0	2	1	0.988671	8	791	0	110	2		0	0	0	0	111	2	-2.488768	0	1	121410	2	37	1	1	2	3	2.612313	1	0.640000	1.980000	0.724602	0.030000	0	1.000000	0.030000	0.070787	0.030000	0	1.000000e-02	0.070000
CYP3A43	64816	broad.mit.edu	37	7	99454485	99454485	+	Silent	SNP	C	C	A			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr7:99454485C>A	ENST00000354829.2	+	9	931	c.828C>A	c.(826-828)atC>atA	p.I276I	CYP3A43_ENST00000222382.5_Silent_p.I276I|CYP3A43_ENST00000417625.1_Silent_p.I166I|CYP3A43_ENST00000342499.4_Silent_p.I136I|CYP3A43_ENST00000415413.1_Silent_p.I65I|CYP3A43_ENST00000312017.5_Silent_p.I276I|CYP3A43_ENST00000477658.1_3'UTR|CYP3A43_ENST00000444905.1_Silent_p.I23I	NM_022820.3|NM_057095.1	NP_073731.1|NP_476436.1	Q9HB55	CP343_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 43			19	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)			Dexamethasone(DB01234)|Dolutegravir(DB08930)|Ethosuximide(DB00593)|Oxazepam(DB00842)|Phenelzine(DB00780)|Praziquantel(DB01058)|Rifampicin(DB01045)|Rifapentine(DB01201)|Testosterone(DB00624)|Troleandomycin(DB01361)|Zalcitabine(DB00943)	AACAGATGATCGACTCCCAGA	0.433000																								0							SO:0001819	synonymous_variant			ENST00000354829.2	1	1	hg19	CCDS5676.1																																																																																				TCGA-S4-A8RM-01A-11D-A377-08	CYP3A43-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000344379.1	1	0	0	50	1068	0	147	0	0	0	1	0	147	2		0	0	0	0	0	2	1	1.000000	50	1061	0	147	2		0	0	0	0	147	2	-4.878029	1	1	0	0		1	1	2	3	2.612313	1	0.640000	1.980000	0.724602	0.180000	1.200000e-01	1.000000	0.180000	0.209381	0.180000	0	1.500000e-01	0.220000
VPS13B	157680	broad.mit.edu	37	8	100493941	100493941	+	Missense_Mutation	SNP	C	C	A			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr8:100493941C>A	ENST00000358544.2	+	25	3892	c.3781C>A	c.(3781-3783)Cct>Act	p.P1261T	VPS13B_ENST00000357162.2_Missense_Mutation_p.P1261T|VPS13B_ENST00000395996.1_Missense_Mutation_p.P1261T	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)			193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)		AGGGCCTGTTCCTACTTCTCC	0.468000													Colon(161;2205 2542 7338 31318)											0							SO:0001583	missense			ENST00000358544.2	1	1	hg19	CCDS6280.1	.	.	.	.	.	.	.	.	.	.	C	18.16	3.562912	0.65538	.	.	ENSG00000132549	ENST00000357162;ENST00000358544;ENST00000395996	T;T;T	0.64260	-0.09;-0.09;-0.09	5.08	5.08	0.68730	.	0.060752	0.64402	D	0.000004	T	0.77054	0.4074	M	0.63843	1.955	0.54753	D	0.999983	D;D;D;P	0.76494	0.994;0.999;0.998;0.669	D;D;P;B	0.83275	0.991;0.996;0.863;0.264	T	0.75001	-0.3471	10	0.33940	T	0.23	.	18.4942	0.90858	0.0:1.0:0.0:0.0	.	1260;1261;1261;1261	Q7Z7G8-6;Q7Z7G8-2;Q7Z7G8;Q7Z7G8-3	.;.;VP13B_HUMAN;.	T	1261	ENSP00000349685:P1261T;ENSP00000351346:P1261T;ENSP00000379318:P1261T	ENSP00000349685:P1261T	P	+	1	0	VPS13B	100563117	1.000000	0.71417	0.778000	0.31720	0.391000	0.30476	6.906000	0.75719	2.365000	0.80145	0.655000	0.94253	CCT		TCGA-S4-A8RM-01A-11D-A377-08	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	0	0	0	15	462	0	79	0	6.097650e-02	0	12	0	79	2		0	0	0	0	0	2	1	0.999869	15	459	0	79	2		0	0	0	0	79	2	-3.582072	1	1	0	0		1	2	2	4	2.124784	0	0.640000	1.980000	0.659607	0.100000	5.000000e-02	1.000000	0.110000	0.174982	0.100000	0	7.000000e-02	0.150000
CSMD3	114788	broad.mit.edu	37	8	113277800	113277800	+	Silent	SNP	T	T	A			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr8:113277800T>A	ENST00000297405.5	-	60	9772	c.9528A>T	c.(9526-9528)ccA>ccT	p.P3176P	CSMD3_ENST00000352409.3_Silent_p.P3106P|CSMD3_ENST00000455883.2_Silent_p.P3007P|CSMD3_ENST00000343508.3_Silent_p.P3136P	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3			646					CTGGTATACCTGGGTCTCCAC	0.418000										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)														0							SO:0001819	synonymous_variant			ENST00000297405.5	1	1	hg19	CCDS6315.1																																																																																				TCGA-S4-A8RM-01A-11D-A377-08	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	1	0	1	133	371	0	83	0	0	0	1	0	83	2		0	0	0	0	0	2	1	1.000000	133	367	0	82	2		0	0	0	0	83	2	-20.000000	1	1	0	0		1	2	2	4	2.124784	0	0.640000	1.980000	0.659607	0.870000	7.400000e-01	1.000000	0.870000	0.882745	0.870000	1	8.000000e-01	0.960000
SCARA5	286133	broad.mit.edu	37	8	27824044	27824044	+	Missense_Mutation	SNP	C	C	T			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr8:27824044C>T	ENST00000354914.3	-	3	613	c.128G>A	c.(127-129)cGg>cAg	p.R43Q	SCARA5_ENST00000524352.1_Missense_Mutation_p.R43Q|SCARA5_ENST00000380385.2_Missense_Mutation_p.R43Q|SCARA5_ENST00000518030.1_Intron|SCARA5_ENST00000301906.4_Intron	NM_173833.5	NP_776194.2	Q6ZMJ2	SCAR5_HUMAN	scavenger receptor class A, member 5			18		Ovarian(32;0.0218)			GCTTGCCCGCCGTTTGTGACA	0.522000																								0							SO:0001583	missense			ENST00000354914.3	0	1	hg19	CCDS6064.1	.	.	.	.	.	.	.	.	.	.	C	18.12	3.554049	0.65425	.	.	ENSG00000168079	ENST00000354914;ENST00000380385;ENST00000524352	D;D;D	0.92299	-2.56;-2.5;-3.01	5.93	5.93	0.95920	.	0.128700	0.49305	D	0.000152	D	0.91043	0.7182	M	0.62723	1.935	0.80722	D	1	P;D;P	0.61697	0.927;0.99;0.949	P;P;B	0.44359	0.447;0.447;0.261	D	0.89580	0.3820	10	0.30078	T	0.28	.	15.8364	0.78801	0.0:1.0:0.0:0.0	.	43;43;43	Q6ZMJ2-4;Q6ZMJ2-2;Q6ZMJ2	.;.;SCAR5_HUMAN	Q	43	ENSP00000346990:R43Q;ENSP00000369746:R43Q;ENSP00000428663:R43Q	ENSP00000346990:R43Q	R	-	2	0	SCARA5	27879963	0.312000	0.24545	0.847000	0.33407	0.982000	0.71751	1.699000	0.37804	2.814000	0.96858	0.563000	0.77884	CGG		TCGA-S4-A8RM-01A-11D-A377-08	SCARA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255223.2	0	0	0	5	582	0	86	0	1.176250e-03	0	5	0	86	2		0	0	0	0	0	2	1	0.934033	6	568	0	81	2		0	0	0	0	86	2	-2.302391	0	1	121412	3	41	1	2	2	4	2.124784	0	0.640000	1.980000	0.659607	0.020000	0	1.000000	0.020000	0.103069	0.020000	0	1.000000e-02	0.060000
ADAMTSL1	92949	broad.mit.edu	37	9	18706844	18706844	+	Silent	SNP	C	C	T			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chr9:18706844C>T	ENST00000380548.4	+	14	2013	c.1674C>T	c.(1672-1674)tcC>tcT	p.S558S	ADAMTSL1_ENST00000276935.6_Silent_p.S558S	NM_001040272.5	NP_001035362.3	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1			42					TCTCTCAGTCCGTGGCTGACC	0.602000																								0							SO:0001819	synonymous_variant			ENST00000380548.4	1	1	hg19	CCDS47954.1																																																																																				TCGA-S4-A8RM-01A-11D-A377-08	ADAMTSL1-012	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401206.1	1	0	1	34	77	0	17	0	2.304935e-01	0	3	0	17	2		0	0	0	0	0	2	1	1.000000	35	76	0	16	2		0	0	0	0	17	2	-20.000000	1	1	121408	2	34	1	0	1	1	2.001361	1	0.640000	1.980000	0.470588	0.640000	4.700000e-01	0.820000	0.640000	0.651522	0.640000	0	5.500000e-01	0.740000
FOXR2	139628	broad.mit.edu	37	X	55650498	55650498	+	Silent	SNP	A	A	G			TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chrX:55650498A>G	ENST00000339140.3	+	1	666	c.354A>G	c.(352-354)gaA>gaG	p.E118E		NM_198451.3	NP_940853.1	Q6PJQ5	FOXR2_HUMAN	forkhead box R2			19					AAAAAGACGAAGGGTCTAACT	0.527000																								0							SO:0001819	synonymous_variant			ENST00000339140.3	1	1	hg19	CCDS35308.1																																																																																				TCGA-S4-A8RM-01A-11D-A377-08	FOXR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056877.2	1	0	1	92	60	0	27		0	0	0	0	27	2		0	0	0	0	0	2	1	1.000000	91	60	0	27	2		0	0	0	0	27	2	-20.000000	1	1	0	0		1	0	1	1			0.640000	1.980000	0.640000	0.920000	8.000000e-01	1.000000	0.940000	0.923310	0.920000	1	8.600000e-01	0.970000
KLHL4	56062	broad.mit.edu	37	X	86887279	86887279	+	Missense_Mutation	SNP	G	G	A	rs146910003		TCGA-S4-A8RM-01A-11D-A377-08	TCGA-S4-A8RM-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af1fa9c9-fb3e-4ffb-b79d-9f79f2adbe3a	f9ea46fe-0a5b-46ab-a347-8fa786bdea4b	g.chrX:86887279G>A	ENST00000373119.4	+	7	1539	c.1394G>A	c.(1393-1395)cGt>cAt	p.R465H	KLHL4_ENST00000373114.4_Missense_Mutation_p.R465H	NM_019117.4	NP_061990.2	Q9C0H6	KLHL4_HUMAN	kelch-like family member 4	p.R465H(1)		67					ATGAATGGCCGTAGGCTTCAA	0.388000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000373119.4	1	1	hg19	CCDS14457.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.165472	0.78339	2.61E-4	0.0	ENSG00000102271	ENST00000373119;ENST00000373114	T;T	0.66815	-0.23;-0.23	5.32	3.55	0.40652	Galactose oxidase, beta-propeller (1);	0.059533	0.64402	N	0.000005	T	0.65365	0.2684	M	0.69358	2.11	0.58432	D	0.999997	P;D	0.55605	0.692;0.972	B;P	0.44860	0.344;0.462	T	0.66396	-0.5934	10	0.87932	D	0	.	10.0307	0.42099	0.1676:0.0:0.8324:0.0	.	465;465	Q9C0H6;Q9C0H6-2	KLHL4_HUMAN;.	H	465	ENSP00000362211:R465H;ENSP00000362206:R465H	ENSP00000362206:R465H	R	+	2	0	KLHL4	86773935	1.000000	0.71417	0.760000	0.31359	0.976000	0.68499	6.184000	0.72008	0.448000	0.26722	0.506000	0.49869	CGT		TCGA-S4-A8RM-01A-11D-A377-08	KLHL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057413.1	1	0	1	108	73	0	31		0	0	0	0	31	2		0	0	0	0	0	2	1	1.000000	108	72	0	30	2		0	0	0	0	31	2	-20.000000	1	1	121404	3	40	1	0	1	1			0.640000	1.980000	0.640000	0.910000	8.000000e-01	1.000000	0.930000	0.917623	0.910000	1	8.600000e-01	0.970000
