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
KCNQ2	3785	broad.mit.edu	37	20	62078155	62078158	+	Frame_Shift_Del	DEL	ACAG	ACAG	-			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr20:62078155_62078158delACAG	ENST00000359125.2	-	2	503_506	c.329_332delCTGT	c.(328-333)tctgtgfs	p.SV110fs	KCNQ2_ENST00000370224.1_Frame_Shift_Del_p.SV110fs|RP11-358D14.2_ENST00000436263.1_RNA|KCNQ2_ENST00000357249.2_Frame_Shift_Del_p.SV110fs|KCNQ2_ENST00000360480.3_Frame_Shift_Del_p.SV110fs|KCNQ2_ENST00000344425.5_Frame_Shift_Del_p.SV110fs|KCNQ2_ENST00000354587.3_Frame_Shift_Del_p.SV110fs|KCNQ2_ENST00000344462.4_Frame_Shift_Del_p.SV110fs|KCNQ2_ENST00000359689.1_Frame_Shift_Del_p.SV110fs	NM_172107.2	NP_742105.1	O43526	KCNQ2_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 2			65	all_cancers(38;1.24e-11)		BRCA - Breast invasive adenocarcinoma(10;1.04e-05)	Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	GGTGGAAAACACAGACAGCACGAG	0.632000																								0							SO:0001589	frameshift_variant			ENST00000359125.2	1	0	hg19	CCDS13520.1																																																																																				TCGA-US-A77E-01A-11D-A32N-08	KCNQ2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080353.1	1	0	0	76	793	0	194	0	1.063594e-12	0	1	0	194	2	0	0	0	0	0	0		1	0.272572	124	817	16	205	91	0	0	0	0	0	0		-18.895520	1	0	0	0		1	1	2	3	2.336157	1	0.390000	2.070000	0.487868	0.530000	4.200000e-01	0.680000	0.540000	0.543852	0.530000	0	0.470000	0.600000
BRAF	673	broad.mit.edu	37	7	140477831	140477845	+	In_Frame_Del	DEL	GAGGTGTAGGTGCTG	GAGGTGTAGGTGCTG	-			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr7:140477831_140477845delGAGGTGTAGGTGCTG	ENST00000288602.6	-	12	1523_1537	c.1463_1477delCAGCACCTACACCTC	c.(1462-1479)acagcacctacacctcag>aag	p.488_493TAPTPQ>K		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	p.L485_P490>Y(2)|p.N486_P490del(1)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	27380	Melanoma(164;0.00956)			Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	TGTAACTGCTGAGGTGTAGGTGCTGTCACATTCAA	0.353000		61	Mis, T, O	AKAP9, KIAA1549	melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome				Colon(40;35 892 2973 5743 27438)		Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	3	Complex - deletion inframe(2)|Deletion - In frame(1)						SO:0001651	inframe_deletion	Familial Cancer Database	CFC, CFCS	ENST00000288602.6	0	1	hg19	CCDS5863.1																																																																																				TCGA-US-A77E-01A-11D-A32N-08	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	1	0	0	26	281	0	51	0	2.167422e-01	0	10	0	51	2	0	0	0	0	0	0		1	1.000000	34	283	0	51	2	0	0	0	0	0	0		-2.841673	1	1	0	0		1	1	2	3	2.349308	1	0.390000	2.070000	0.489540	0.520000	3.500000e-01	0.720000	0.510000	0.533661	0.520000	0	0.430000	0.630000
NEBL	10529	broad.mit.edu	37	10	21074742	21074742	+	Silent	SNP	G	G	A	rs139156783	by1000genomes	TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr10:21074742G>A	ENST00000377122.4	-	28	3375	c.2979C>T	c.(2977-2979)taC>taT	p.Y993Y	NEBL_ENST00000417816.2_Silent_p.Y249Y|NEBL_ENST00000377159.4_Silent_p.Y215Y	NM_006393.2	NP_006384.1	O76041	NEBL_HUMAN	nebulette			70					GCACTGTGCCGTACATCCAGC	0.468000																								0							SO:0001819	synonymous_variant			ENST00000377122.4	0	1	hg19	CCDS7134.1																																																																																				TCGA-US-A77E-01A-11D-A32N-08	NEBL-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047113.1	0	0	0	4	248	0	48	0	1.181304e-01	0	29	0	48	2		0	0	0	0	0	2	1	0.887304	4	244	0	47	2	0	0	0	0	0	0		-3.223479	1	1	121412	2	41	1	0	1	1	1.968530	0	0.390000	2.070000	0.388808	0.080000	2.000000e-02	0.190000	0.080000	0.100113	0.080000	0	0.050000	0.140000
MYO3A	53904	broad.mit.edu	37	10	26457784	26457784	+	Silent	SNP	C	C	T	rs35541310	byFrequency	TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr10:26457784C>T	ENST00000265944.5	+	28	3421	c.3255C>T	c.(3253-3255)agC>agT	p.S1085S	MYO3A_ENST00000543632.1_Intron	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA			146					GGAAAGAAAGCGCTATAATAA	0.328000																								0							SO:0001819	synonymous_variant			ENST00000265944.5	1	1	hg19	CCDS7148.1																																																																																				TCGA-US-A77E-01A-11D-A32N-08	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	1	0	1	36	195	0	41	0	0	0	1	0	41	2		0	0	0	0	0	2	1	1.000000	36	192	0	41	2	0	0	0	0	0	0		-20.000000	1	1	121410	16	45	1	0	1	1	1.968530	0	0.390000	2.070000	0.388808	0.790000	5.700000e-01	1.000000	1.000000	0.803464	0.790000	0	0.680000	0.920000
APOA4	337	broad.mit.edu	37	11	116691783	116691783	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08			G	A	G	G		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr11:116691783G>A	ENST00000357780.3	-	3	1105	c.991C>T	c.(991-993)Ccc>Tcc	p.P331S		NM_000482.3	NP_000473.2	P06727	APOA4_HUMAN	apolipoprotein A-IV			20	all_hematologic(175;0.0487)	Breast(348;0.0126)|Medulloblastoma(222;0.0425)|all_hematologic(158;0.0564)|all_neural(223;0.234)			CCCGCATGGGGGCCCAGTTTC	0.592000																								0							SO:0001583	missense			ENST00000357780.3	1	1	hg19	CCDS31681.1	.	.	.	.	.	.	.	.	.	.	G	13.78	2.340577	0.41498	.	.	ENSG00000110244	ENST00000357780	T	0.76316	-1.01	5.39	4.46	0.54185	Apolipoprotein/apolipophorin (1);	0.377447	0.26019	N	0.026825	T	0.73016	0.3533	M	0.64676	1.99	0.29390	N	0.862669	P	0.50272	0.933	P	0.45167	0.472	T	0.69394	-0.5157	10	0.29301	T	0.29	-39.6749	7.0255	0.24938	0.142:0.0:0.7148:0.1432	.	331	P06727	APOA4_HUMAN	S	331	ENSP00000350425:P331S	ENSP00000350425:P331S	P	-	1	0	APOA4	116196993	0.241000	0.23857	0.999000	0.59377	0.626000	0.37791	1.085000	0.30840	2.522000	0.85027	0.557000	0.71058	CCC		TCGA-US-A77E-01A-11D-A32N-08	APOA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106279.2	1	0	1	93	371	0	85	0	1	0	269	0	85	2		0	0	0	0	0	2	1	1.000000	93	369	0	85	2	0	0	0	0	0	0		-3.644587	1	1	0	0		1	1	2	3	1.982548	0	0.390000	2.070000	0.391187	0.990000	8.400000e-01	1.000000	1.000000	0.976487	0.990000	1	0.930000	1.000000
IFT46	56912	broad.mit.edu	37	11	118416522	118416522	+	Missense_Mutation	SNP	A	A	G			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08			A	G	A	A		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr11:118416522A>G	ENST00000264021.3	-	10	1137	c.719T>C	c.(718-720)aTt>aCt	p.I240T	TMEM25_ENST00000442938.2_Intron|IFT46_ENST00000530872.1_Missense_Mutation_p.I291T|IFT46_ENST00000264020.2_Missense_Mutation_p.I291T|TMEM25_ENST00000354284.4_Intron	NM_001168618.1	NP_001162089.1	Q9NQC8	IFT46_HUMAN	intraflagellar transport 46			9					GATCATGTCAATGTACTCTGC	0.507000																								0							SO:0001583	missense			ENST00000264021.3	1	1	hg19	CCDS53718.1	.	.	.	.	.	.	.	.	.	.	A	13.21	2.169425	0.38315	.	.	ENSG00000118096	ENST00000264021;ENST00000264020;ENST00000530872	T;T;T	0.48522	0.82;0.81;0.81	6.03	4.91	0.64330	.	0.364645	0.29335	N	0.012458	T	0.36936	0.0985	L	0.37561	1.115	0.41527	D	0.988432	B;B;B	0.21071	0.01;0.051;0.008	B;B;B	0.17433	0.012;0.018;0.011	T	0.16394	-1.0404	10	0.45353	T	0.12	-8.0521	9.5551	0.39334	0.8583:0.0:0.1417:0.0	.	291;240;291	E9PR06;Q9NQC8;Q9NQC8-2	.;IFT46_HUMAN;.	T	240;291;291	ENSP00000264021:I240T;ENSP00000264020:I291T;ENSP00000432384:I291T	ENSP00000264020:I291T	I	-	2	0	IFT46	117921732	0.998000	0.40836	0.992000	0.48379	0.823000	0.46562	3.755000	0.55197	1.104000	0.41587	0.533000	0.62120	ATT		TCGA-US-A77E-01A-11D-A32N-08	IFT46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389627.1	1	0	1	68	394	0	78	1	9.984372e-01	26	32	0	78	2		0	0	0	0	0	2	1	1.000000	68	389	0	77	2	0	0	0	0	0	0		-20.000000	1	1	121412	4	37	1	1	2	3	1.982548	0	0.390000	2.070000	0.391187	0.750000	5.900000e-01	0.930000	0.750000	0.761391	0.750000	0	0.670000	0.850000
UPK2	7379	broad.mit.edu	37	11	118828843	118828843	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr11:118828843G>A	ENST00000264031.2	+	5	490	c.455G>A	c.(454-456)cGc>cAc	p.R152H	UPK2_ENST00000534788.1_3'UTR	NM_006760.3	NP_006751.1	O00526	UPK2_HUMAN	uroplakin 2			5	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_hematologic(192;0.122)|all_neural(223;0.224)			GGTATGGCCCGCACAGGGGGC	0.617000																								0							SO:0001583	missense			ENST00000264031.2	0	1	hg19	CCDS8404.1	.	.	.	.	.	.	.	.	.	.	g	17.59	3.427814	0.62733	.	.	ENSG00000110375	ENST00000534788;ENST00000264031	T	0.41400	1.0	5.43	4.51	0.55191	.	0.151206	0.31134	N	0.008188	T	0.61311	0.2337	M	0.65975	2.015	0.26235	N	0.978957	D	0.89917	1.0	D	0.87578	0.998	T	0.56908	-0.7901	10	0.46703	T	0.11	-3.4525	13.3218	0.60436	0.0836:0.0:0.9164:0.0	.	152	O00526	UPK2_HUMAN	H	18;152	ENSP00000264031:R152H	ENSP00000264031:R152H	R	+	2	0	UPK2	118334053	1.000000	0.71417	0.969000	0.41365	0.873000	0.50193	3.661000	0.54503	0.802000	0.34089	-0.937000	0.02696	CGC		TCGA-US-A77E-01A-11D-A32N-08	UPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389311.1	0	0	0	5	372	0	84		0	0	0	0	84	2		0	0	0	0	0	2	1	0.937064	5	370	0	83	2	0	0	0	0	0	0		-2.126169	0	1	0	0		1	1	2	3	1.982548	0	0.390000	2.070000	0.391187	0.070000	2.000000e-02	0.160000	0.070000	0.081011	0.070000	0	0.040000	0.110000
ADAMTS8	11095	broad.mit.edu	37	11	130284700	130284700	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr11:130284700G>A	ENST00000257359.6	-	5	1998	c.1292C>T	c.(1291-1293)gCg>gTg	p.A431V		NM_007037.4	NP_008968.4	Q9UP79	ATS8_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 8			10	all_hematologic(175;0.0429)	Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)			GGGCAGGGCCGCAGCAGGGGC	0.652000																								0							SO:0001583	missense			ENST00000257359.6	1	1	hg19	CCDS41732.1	.	.	.	.	.	.	.	.	.	.	G	7.801	0.713736	0.15306	.	.	ENSG00000134917	ENST00000257359;ENST00000414575	T	0.03580	3.88	5.42	4.5	0.54988	.	0.751547	0.12761	N	0.441396	T	0.03564	0.0102	N	0.24115	0.695	0.09310	N	1	B	0.14805	0.011	B	0.10450	0.005	T	0.38329	-0.9666	10	0.59425	D	0.04	.	9.1476	0.36942	0.0:0.119:0.5962:0.2848	.	431	Q9UP79	ATS8_HUMAN	V	431;460	ENSP00000257359:A431V	ENSP00000257359:A431V	A	-	2	0	ADAMTS8	129789910	0.000000	0.05858	0.040000	0.18447	0.079000	0.17450	0.809000	0.27168	1.264000	0.44198	0.655000	0.94253	GCG		TCGA-US-A77E-01A-11D-A32N-08	ADAMTS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385636.1	0	0	0	40	149	1	42	0	1.199467e-01	0	3	1	42	2		0	0	0	0	0	2	1	0.999919	40	146	1	42	15	0	0	0	0	0	0		-20.000000	1	1	120648	3	27	1	1	2	3	1.982548	0	0.390000	2.070000	0.391187	0.990000	8.000000e-01	1.000000	1.000000	0.976490	0.990000	1	0.930000	1.000000
FIBIN	387758	broad.mit.edu	37	11	27016362	27016362	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr11:27016362G>A	ENST00000318627.2	+	1	735	c.289G>A	c.(289-291)Gtg>Atg	p.V97M		NM_203371.1	NP_976249.1	Q8TAL6	FIBIN_HUMAN	fin bud initiation factor homolog (zebrafish)			11					TGCTGGGCGCGTGCTGGAGGG	0.657000																								0							SO:0001583	missense			ENST00000318627.2	1	1	hg19	CCDS7861.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	27.4	4.826858	0.90955	.	.	ENSG00000176971	ENST00000318627	.	.	.	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.68723	0.3032	L	0.32530	0.975	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.70605	-0.4826	9	0.72032	D	0.01	-14.2051	18.3976	0.90504	0.0:0.0:1.0:0.0	.	97	Q8TAL6	FIBIN_HUMAN	M	97	.	ENSP00000321962:V97M	V	+	1	0	FIBIN	26972938	1.000000	0.71417	0.985000	0.45067	0.994000	0.84299	9.245000	0.95431	2.706000	0.92434	0.557000	0.71058	GTG		TCGA-US-A77E-01A-11D-A32N-08	FIBIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387945.1	1	0	1	32	142	0	45	0	9.859475e-01	0	33	0	45	2		0	0	0	0	0	2	1	1.000000	32	142	0	45	2	0	0	0	0	0	0		-20.000000	1	1	121392	2	29	1	1	2	3	1.976461	0	0.390000	2.070000	0.391187	0.940000	6.700000e-01	1.000000	1.000000	0.914454	0.940000	1	0.800000	1.000000
EXT2	2132	broad.mit.edu	37	11	44129401	44129401	+	Missense_Mutation	SNP	C	C	T			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr11:44129401C>T	ENST00000343631.3	+	2	268	c.139C>T	c.(139-141)Ccc>Tcc	p.P47S	EXT2_ENST00000358681.4_Missense_Mutation_p.P47S|EXT2_ENST00000395673.3_Missense_Mutation_p.P80S|EXT2_ENST00000533608.1_Missense_Mutation_p.P47S			Q93063	EXT2_HUMAN	exostosin glycosyltransferase 2			32					TCAGTTTTGGCCCCATTCTAT	0.527000			Mis, N, F, S			exostoses, osteosarcoma			Hereditary Multiple Exostoses					yes	Rec		Multiple Exostoses Type 2	11	11p12-p11	2132	multiple exostoses type 2 gene		M	0							SO:0001583	missense	Familial Cancer Database	HME, Hereditary Exostoses, Multiple Osteochondromatosis, Multiple Cartilaginous Exostoses	ENST00000343631.3	0	1	hg19	CCDS7908.1	.	.	.	.	.	.	.	.	.	.	C	13.85	2.360982	0.41801	.	.	ENSG00000151348	ENST00000533608;ENST00000532479;ENST00000527014;ENST00000358681;ENST00000395673;ENST00000343631	T;T;T;T;T;T	0.47177	0.85;0.85;0.85;0.85;0.85;0.85	5.45	4.52	0.55395	.	0.050514	0.85682	D	0.000000	T	0.56863	0.2014	L	0.29908	0.895	0.80722	D	1	D;D;D;P;B	0.89917	1.0;0.984;0.979;0.956;0.296	D;P;P;P;B	0.83275	0.996;0.786;0.798;0.63;0.027	T	0.57636	-0.7777	10	0.44086	T	0.13	1.5466	15.282	0.73794	0.1413:0.8587:0.0:0.0	.	47;47;47;47;60	Q6NUL1;C9JU51;Q93063-2;Q93063;D3DR24	.;.;.;EXT2_HUMAN;.	S	47;47;47;47;80;47	ENSP00000431173:P47S;ENSP00000433827:P47S;ENSP00000434716:P47S;ENSP00000351509:P47S;ENSP00000379032:P80S;ENSP00000342656:P47S	ENSP00000342656:P47S	P	+	1	0	EXT2	44085977	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.380000	0.79704	1.253000	0.44018	0.650000	0.86243	CCC		TCGA-US-A77E-01A-11D-A32N-08	EXT2-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390074.1	0	0	0	5	420	0	84	0	1.999998e-01	0	58	0	84	2		0	0	0	0	0	2	1	0.936327	5	416	0	83	2	0	0	0	0	0	0		-2.259352	0	1	0	0		1	1	2	3	1.976461	0	0.390000	2.070000	0.391187	0.060000	1.000000e-02	0.140000	0.060000	0.071930	0.060000	0	0.030000	0.100000
CKAP5	9793	broad.mit.edu	37	11	46780946	46780946	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr11:46780946G>A	ENST00000529230.1	-	34	4487	c.4441C>T	c.(4441-4443)Cgc>Tgc	p.R1481C	SNORD67_ENST00000516618.1_RNA|CKAP5_ENST00000312055.5_Missense_Mutation_p.R1481C|CKAP5_ENST00000415402.1_Missense_Mutation_p.R1481C|SNORD67_ENST00000390833.1_RNA|CKAP5_ENST00000354558.3_Missense_Mutation_p.R1481C			Q14008	CKAP5_HUMAN	cytoskeleton associated protein 5			43					AATTCTCGGCGGACCATCTGG	0.483000													Ovarian(4;85 273 2202 4844 13323)											0							SO:0001583	missense			ENST00000529230.1	0	1	hg19	CCDS31477.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.81|19.81	3.896803|3.896803	0.72639|0.72639	.|.	.|.	ENSG00000175216|ENSG00000175216	ENST00000527333|ENST00000529230;ENST00000415402;ENST00000312055;ENST00000354558;ENST00000526876	.|T;T;T;T	.|0.48201	.|0.84;0.85;0.82;0.82	5.53|5.53	5.53|5.53	0.82687|0.82687	.|Armadillo-like helical (1);Armadillo-type fold (1);	.|0.094061	.|0.85682	.|D	.|0.000000	T|T	0.34745|0.34745	0.0908|0.0908	N|N	0.14661|0.14661	0.345|0.345	0.51767|0.51767	D|D	0.999933|0.999933	.|P;P;P	.|0.49447	.|0.924;0.894;0.83	.|B;B;B	.|0.39840	.|0.235;0.311;0.165	T|T	0.23084|0.23084	-1.0198|-1.0198	5|10	.|0.44086	.|T	.|0.13	-9.5534|-9.5534	19.8389|19.8389	0.96675|0.96675	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1481;1481;1481	.|Q14008-3;Q14008-2;Q14008	.|.;.;CKAP5_HUMAN	L|C	37|1481;1481;1481;1481;212	.|ENSP00000432768:R1481C;ENSP00000395302:R1481C;ENSP00000310227:R1481C;ENSP00000346566:R1481C	.|ENSP00000310227:R1481C	P|R	-|-	2|1	0|0	CKAP5|CKAP5	46737522|46737522	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.998000|0.998000	0.95712|0.95712	7.753000|7.753000	0.85153|0.85153	2.755000|2.755000	0.94549|0.94549	0.650000|0.650000	0.86243|0.86243	CCG|CGC		TCGA-US-A77E-01A-11D-A32N-08	CKAP5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390679.1	0	0	0	5	354	0	71	0	3.410767e-01	0	73	0	71	2		0	0	0	0	0	2	1	0.937042	5	352	0	71	2	0	0	0	0	0	0		-2.916531	1	1	121412	1	33	1	1	2	3	1.976461	0	0.390000	2.070000	0.391187	0.070000	2.000000e-02	0.170000	0.070000	0.085034	0.070000	0	0.040000	0.120000
OR4A47	403253	broad.mit.edu	37	11	48510885	48510885	+	Missense_Mutation	SNP	C	C	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr11:48510885C>A	ENST00000446524.1	+	1	617	c.541C>A	c.(541-543)Ccc>Acc	p.P181T		NM_001005512.2	NP_001005512.2	Q6IF82	O4A47_HUMAN	olfactory receptor, family 4, subfamily A, member 47	p.P181A(1)		29					TGACATGTATCCCTTATTGAA	0.443000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000446524.1	1	1	hg19	CCDS31490.1	.	.	.	.	.	.	.	.	.	.	N	7.778	0.708860	0.15239	.	.	ENSG00000237388	ENST00000446524	T	0.00216	8.53	4.84	1.9	0.25705	GPCR, rhodopsin-like superfamily (1);	0.117629	0.38778	N	0.001571	T	0.00666	0.0022	H	0.94658	3.565	0.09310	N	1	D	0.89917	1.0	D	0.97110	1.0	T	0.38045	-0.9679	10	0.72032	D	0.01	.	6.6304	0.22853	0.0:0.6819:0.147:0.171	.	181	Q6IF82	O4A47_HUMAN	T	181	ENSP00000412752:P181T	ENSP00000412752:P181T	P	+	1	0	OR4A47	48467461	0.000000	0.05858	0.219000	0.23793	0.012000	0.07955	0.174000	0.16743	0.105000	0.17753	-0.409000	0.06214	CCC		TCGA-US-A77E-01A-11D-A32N-08	OR4A47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390559.1	0	0	0	25	619	0	154		0	0	0	0	154	2		0	0	0	0	0	2	1	1.000000	25	595	0	157	2	0	0	0	0	0	0		-4.050987	1	1	0	0		1	1	2	3	1.976461	0	0.390000	2.070000	0.391187	0.190000	1.200000e-01	0.290000	0.200000	0.206301	0.190000	0	0.160000	0.250000
OR4S2	219431	broad.mit.edu	37	11	55418776	55418776	+	Missense_Mutation	SNP	A	A	C			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr11:55418776A>C	ENST00000312422.2	+	1	397	c.397A>C	c.(397-399)Atc>Ctc	p.I133L		NM_001004059.2	NP_001004059.2	Q8NH73	OR4S2_HUMAN	olfactory receptor, family 4, subfamily S, member 2			45		all_epithelial(135;0.0748)			TTATATGACCATCATGAACCG	0.428000																								0							SO:0001583	missense			ENST00000312422.2	1	1	hg19	CCDS31505.1	.	.	.	.	.	.	.	.	.	.	A	10.57	1.386439	0.25031	.	.	ENSG00000174982	ENST00000312422	T	0.00940	5.52	5.35	5.35	0.76521	GPCR, rhodopsin-like superfamily (1);	0.243922	0.28453	N	0.015284	T	0.01387	0.0045	L	0.45698	1.435	0.26071	N	0.981224	B	0.14438	0.01	B	0.10450	0.005	T	0.38564	-0.9655	10	0.72032	D	0.01	.	10.9264	0.47193	0.8431:0.1569:0.0:0.0	.	133	Q8NH73	OR4S2_HUMAN	L	133	ENSP00000310337:I133L	ENSP00000310337:I133L	I	+	1	0	OR4S2	55175352	0.008000	0.16893	0.997000	0.53966	0.193000	0.23685	0.647000	0.24812	2.028000	0.59812	0.443000	0.29094	ATC		TCGA-US-A77E-01A-11D-A32N-08	OR4S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391503.1	1	0	0	42	839	0	184		0	0	0	0	184	2		0	0	0	0	0	2	1	1.000000	41	828	0	181	2	0	0	0	0	0	0		-6.012469	1	1	0	0		1	1	2	3	1.976461	0	0.390000	2.070000	0.391187	0.240000	1.700000e-01	0.330000	0.240000	0.249778	0.240000	0	0.200000	0.290000
CHRM1	1128	broad.mit.edu	37	11	62677297	62677297	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr11:62677297G>A	ENST00000306960.3	-	2	1817	c.1276C>T	c.(1276-1278)Cgg>Tgg	p.R426W	AP000438.2_ENST00000543624.1_RNA	NM_000738.2	NP_000729.2	P11229	ACM1_HUMAN	cholinergic receptor, muscarinic 1			9				Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Benzatropine(DB00245)|Biperiden(DB00810)|Brompheniramine(DB00835)|Buclizine(DB00354)|Carbachol(DB00411)|Cevimeline(DB00185)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Citalopram(DB00215)|Clidinium(DB00771)|Clozapine(DB00363)|Cocaine(DB00907)|Cryptenamine(DB00785)|Cyclopentolate(DB00979)|Cycrimine(DB00942)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Dicyclomine(DB00804)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxepin(DB01142)|Doxylamine(DB00366)|Escitalopram(DB01175)|Ethopropazine(DB00392)|Fesoterodine(DB06702)|Flavoxate(DB01148)|Flupentixol(DB00875)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Mepenzolate(DB04843)|Methantheline(DB00940)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Metoclopramide(DB01233)|Minaprine(DB00805)|Molindone(DB01618)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Oxyphenonium(DB00219)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pirenzepine(DB00670)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propantheline(DB00782)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Triflupromazine(DB00508)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Trospium(DB00209)|Ziprasidone(DB00246)	AAGGTGTCCCGGAAGGCTTTG	0.632000																								0							SO:0001583	missense			ENST00000306960.3	0	1	hg19	CCDS8040.1	.	.	.	.	.	.	.	.	.	.	G	15.89	2.966720	0.53507	.	.	ENSG00000168539	ENST00000306960;ENST00000543973	T;T	0.58358	0.34;0.34	3.98	1.97	0.26223	.	0.792889	0.10240	N	0.698549	T	0.64972	0.2647	L	0.57536	1.79	0.39146	D	0.962134	D	0.89917	1.0	D	0.64321	0.924	T	0.62148	-0.6915	10	0.87932	D	0	-13.9234	9.6941	0.40147	0.0:0.0:0.4009:0.5991	.	426	P11229	ACM1_HUMAN	W	426	ENSP00000306490:R426W;ENSP00000441188:R426W	ENSP00000306490:R426W	R	-	1	2	CHRM1	62433873	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.136000	0.64783	0.263000	0.21812	0.561000	0.74099	CGG		TCGA-US-A77E-01A-11D-A32N-08	CHRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396178.1	0	0	0	6	820	0	183		0	0	0	0	183	2		0	0	0	0	0	2	1	0.962859	6	804	0	183	2	0	0	0	0	0	0		-1.903257	0	1	121412	1	33	1	1	2	3	1.982548	0	0.390000	2.070000	0.391187	0.030000	0	0.080000	0.040000	0.043167	0.030000	0	0.020000	0.060000
RCOR2	283248	broad.mit.edu	37	11	63680166	63680166	+	Nonsense_Mutation	SNP	G	G	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr11:63680166G>A	ENST00000301459.4	-	10	1396	c.1009C>T	c.(1009-1011)Cag>Tag	p.Q337*	RCOR2_ENST00000473926.2_5'Flank	NM_173587.3	NP_775858.2	Q8IZ40	RCOR2_HUMAN	REST corepressor 2			17					GCCAAAAGCTGCTCATCTGTG	0.532000																								0							SO:0001587	stop_gained			ENST00000301459.4	0	1	hg19	CCDS8052.1	.	.	.	.	.	.	.	.	.	.	G	41	8.641449	0.98897	.	.	ENSG00000167771	ENST00000301459	.	.	.	4.45	4.45	0.53987	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	16.4081	0.83697	0.0:0.0:1.0:0.0	.	.	.	.	X	337	.	ENSP00000301459:Q337X	Q	-	1	0	RCOR2	63436742	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.524000	0.98036	2.479000	0.83701	0.561000	0.74099	CAG		TCGA-US-A77E-01A-11D-A32N-08	RCOR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318233.1	1	0	1	229	656	0	173	0	6.699958e-02	0	2	0	173	2		0	0	0	0	0	2	1	1.000000	228	651	0	171	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	1	2	3	1.982548	0	0.390000	2.070000	0.391187	0.990000	9.900000e-01	1.000000	1.000000	1.000000	0.990000	1	0.990000	1.000000
ESRRA	2101	broad.mit.edu	37	11	64082689	64082689	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr11:64082689G>A	ENST00000405666.1	+	6	1193	c.959G>A	c.(958-960)cGg>cAg	p.R320Q	ESRRA_ENST00000000442.6_Missense_Mutation_p.R320Q|PRDX5_ENST00000265462.4_5'Flank|PRDX5_ENST00000352435.4_5'Flank|PRDX5_ENST00000347941.4_5'Flank|ESRRA_ENST00000406310.1_Missense_Mutation_p.R319Q	NM_001282450.1	NP_001269379.1	P11474	ERR1_HUMAN	estrogen-related receptor alpha			14					CAGGCCCTGCGGCTGGAGCGA	0.627000																								0							SO:0001583	missense			ENST00000405666.1	1	1	hg19	CCDS41667.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.914|9.914	1.210433|1.210433	0.22289|0.22289	0.0|0.0	1.2E-4|1.2E-4	ENSG00000173153|ENSG00000173153	ENST00000545035|ENST00000406310;ENST00000000442;ENST00000405666	.|D;D;D	.|0.96334	.|-3.98;-3.98;-3.98	4.14|4.14	4.14|4.14	0.48551|0.48551	.|Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	.|0.192229	.|0.44483	.|D	.|0.000441	D|D	0.89269|0.89269	0.6667|0.6667	N|N	0.16903|0.16903	0.455|0.455	0.44073|0.44073	D|D	0.996821|0.996821	.|B;P	.|0.51449	.|0.033;0.945	.|B;B	.|0.31547	.|0.0;0.132	D|D	0.90139|0.90139	0.4212|0.4212	5|10	.|0.39692	.|T	.|0.17	.|.	14.3272|14.3272	0.66528|0.66528	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|319;320	.|P11474-2;P11474	.|.;ERR1_HUMAN	S|Q	101|319;320;320	.|ENSP00000385971:R319Q;ENSP00000000442:R320Q;ENSP00000384851:R320Q	.|ENSP00000000442:R320Q	G|R	+|+	1|2	0|0	ESRRA|ESRRA	63839265|63839265	0.082000|0.082000	0.21442|0.21442	0.944000|0.944000	0.38274|0.38274	0.203000|0.203000	0.24098|0.24098	2.216000|2.216000	0.42871|0.42871	2.309000|2.309000	0.77851|0.77851	0.462000|0.462000	0.41574|0.41574	GGC|CGG		TCGA-US-A77E-01A-11D-A32N-08	ESRRA-003	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319304.1	1	0	1	51	174	0	38	1	1	43	124	0	38	2		0	0	0	0	0	2	1	1.000000	49	170	0	38	2	0	0	0	0	0	0		-20.000000	1	1	120840	5	33	1	1	2	3	1.982548	0	0.390000	2.070000	0.391187	0.990000	8.900000e-01	1.000000	1.000000	0.992830	0.990000	1	0.990000	1.000000
FOXN4	121643	broad.mit.edu	37	12	109719343	109719343	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr12:109719343G>A	ENST00000299162.5	-	9	1267	c.1163C>T	c.(1162-1164)cCg>cTg	p.P388L	FOXN4_ENST00000355216.1_Missense_Mutation_p.P208L	NM_213596.2	NP_998761.2	Q96NZ1	FOXN4_HUMAN	forkhead box N4			16					GCTGAGGTCCGGCAGGGCGTG	0.657000																								0							SO:0001583	missense			ENST00000299162.5	1	1	hg19	CCDS9126.2	.	.	.	.	.	.	.	.	.	.	G	17.27	3.347910	0.61183	.	.	ENSG00000139445	ENST00000355216;ENST00000299162	D;D	0.95482	-3.72;-3.4	4.49	3.58	0.41010	.	0.472963	0.19054	N	0.123947	D	0.96901	0.8988	M	0.71581	2.175	0.80722	D	1	D;D	0.89917	1.0;0.981	D;P	0.69654	0.965;0.57	D	0.96418	0.9309	10	0.52906	T	0.07	-12.9682	13.1717	0.59602	0.0:0.0:0.8395:0.1605	.	388;388	A6H901;Q96NZ1	.;FOXN4_HUMAN	L	208;388	ENSP00000347354:P208L;ENSP00000299162:P388L	ENSP00000299162:P388L	P	-	2	0	FOXN4	108203726	1.000000	0.71417	0.819000	0.32651	0.417000	0.31264	4.115000	0.57865	1.212000	0.43366	0.561000	0.74099	CCG		TCGA-US-A77E-01A-11D-A32N-08	FOXN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328306.1	1	0	1	29	105	0	27		0	0	0	0	27	2		0	0	0	0	0	2	1	1.000000	29	100	0	27	2	0	0	0	0	0	0		-20.000000	1	1	121376	1	23	1	1	2	3	1.973903	0	0.390000	2.070000	0.391187	0.990000	7.800000e-01	1.000000	1.000000	0.974490	0.990000	1	0.930000	1.000000
RPH3A	22895	broad.mit.edu	37	12	113266105	113266105	+	Splice_Site	SNP	G	G	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr12:113266105G>A	ENST00000389385.4	+	3	479		c.e3-1		RPH3A_ENST00000543106.2_Splice_Site|RPH3A_ENST00000551052.1_Splice_Site|RPH3A_ENST00000415485.3_Splice_Site|RPH3A_ENST00000548866.1_Splice_Site|RPH3A_ENST00000447659.2_Splice_Site|RPH3A_ENST00000420983.2_5'Flank	NM_001143854.1|NM_014954.3	NP_001137326.1|NP_055769.2	Q9Y2J0	RP3A_HUMAN	rabphilin 3A			47					ATGTTTTCCAGGAGCACTAGA	0.488000																								0							SO:0001630	splice_region_variant			ENST00000389385.4	0	1	hg19	CCDS44979.1																																																																																				TCGA-US-A77E-01A-11D-A32N-08	RPH3A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405561.1	0	0	0	6	313	0	73		0	0	0	0	73	2		0	0	0	0	0	2	1	0.964325	6	310	0	71	2	0	0	0	0	0	0		-2.870380	1	1	0	0		1	1	2	3	1.973903	0	0.390000	2.070000	0.391187	0.100000	3.000000e-02	0.210000	0.100000	0.111507	0.100000	0	0.060000	0.150000
KRT72	140807	broad.mit.edu	37	12	52994910	52994910	+	Silent	SNP	C	C	T			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr12:52994910C>T	ENST00000537672.2	-	1	337	c.327G>A	c.(325-327)ccG>ccA	p.P109P	RP11-641A6.2_ENST00000551089.1_RNA|KRT72_ENST00000398066.3_5'UTR|KRT72_ENST00000354310.4_Silent_p.P109P|KRT72_ENST00000293745.2_Silent_p.P109P	NM_001146225.1	NP_001139697.1	Q14CN4	K2C72_HUMAN	keratin 72	p.P109P(1)		36					CCACGTTGAGCGGGGCCAGGA	0.667000																								1	Substitution - coding silent(1)						SO:0001819	synonymous_variant			ENST00000537672.2	0	1	hg19	CCDS8833.1	.	.	.	.	.	.	.	.	.	.	C	13.45	2.239736	0.39598	.	.	ENSG00000170486	ENST00000549979	.	.	.	4.49	-1.94	0.07571	.	.	.	.	.	T	0.39279	0.1072	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.27123	-1.0083	4	.	.	.	.	1.5914	0.02655	0.2117:0.371:0.1662:0.2511	.	.	.	.	H	95	.	.	R	-	2	0	KRT72	51281177	0.000000	0.05858	0.947000	0.38551	0.805000	0.45488	-2.331000	0.01110	-0.362000	0.08113	-1.083000	0.02208	CGC		TCGA-US-A77E-01A-11D-A32N-08	KRT72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405693.1	0	0	0	6	291	0	63		0	0	0	0	63	2		0	0	0	0	0	2	1	0.963522	6	286	0	62	2	0	0	0	0	0	0		-2.785011	1	1	121412	2	34	1	1	2	3	1.980614	0	0.390000	2.070000	0.391187	0.100000	4.000000e-02	0.220000	0.100000	0.119667	0.100000	0	0.070000	0.160000
SPRYD4	283377	broad.mit.edu	37	12	56863123	56863123	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr12:56863123G>A	ENST00000338146.5	+	2	461	c.386G>A	c.(385-387)cGc>cAc	p.R129H	MIP_ENST00000555551.1_5'Flank	NM_207344.3	NP_997227	Q8WW59	SPRY4_HUMAN	SPRY domain containing 4			7					TATGCCCAGCGCAAGTGGTAC	0.572000																								0							SO:0001583	missense			ENST00000338146.5	0	1	hg19	CCDS8920.1	.	.	.	.	.	.	.	.	.	.	G	35	5.514600	0.96402	.	.	ENSG00000176422	ENST00000338146;ENST00000543121	T	0.61158	0.13	5.46	5.46	0.80206	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.102358	0.64402	D	0.000003	T	0.71796	0.3382	L	0.49126	1.545	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.73380	0.98;0.95	T	0.71101	-0.4690	10	0.51188	T	0.08	-18.1887	18.4593	0.90732	0.0:0.0:1.0:0.0	.	51;129	B4DUC9;Q8WW59	.;SPRY4_HUMAN	H	129;51	ENSP00000338034:R129H	ENSP00000338034:R129H	R	+	2	0	SPRYD4	55149390	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.921000	0.56454	2.735000	0.93741	0.561000	0.74099	CGC		TCGA-US-A77E-01A-11D-A32N-08	SPRYD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		0	0	0	6	626	0	134	0	8.336658e-02	0	42	0	134	2		0	0	0	0	0	2	1	0.963333	6	616	0	134	2	0	0	0	0	0	0		-2.126141	0	1	0	0		1	1	2	3	1.976042	0	0.390000	2.070000	0.391187	0.040000	1.000000e-02	0.110000	0.050000	0.056609	0.040000	0	0.020000	0.080000
LRP1	4035	broad.mit.edu	37	12	57590012	57590012	+	Missense_Mutation	SNP	G	G	T			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr12:57590012G>T	ENST00000243077.3	+	55	9310	c.8844G>T	c.(8842-8844)aaG>aaT	p.K2948N	MIR1228_ENST00000408438.1_RNA	NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1			184				Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	TCAGCCGCAAGCTCAGTGGCT	0.632000																								0							SO:0001583	missense			ENST00000243077.3	0	1	hg19	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	G	13.76	2.334687	0.41297	.	.	ENSG00000123384	ENST00000243077	D	0.89681	-2.55	5.02	2.11	0.27256	Growth factor, receptor (1);EGF-like calcium-binding (1);	0.000000	0.64402	D	0.000001	T	0.80989	0.4730	N	0.02685	-0.53	0.80722	D	1	D	0.61697	0.99	D	0.64776	0.929	T	0.74497	-0.3646	10	0.17832	T	0.49	.	6.2253	0.20703	0.2279:0.1436:0.6285:0.0	.	2948	Q07954	LRP1_HUMAN	N	2948	ENSP00000243077:K2948N	ENSP00000243077:K2948N	K	+	3	2	LRP1	55876279	0.962000	0.33011	1.000000	0.80357	0.982000	0.71751	0.431000	0.21444	0.687000	0.31509	0.655000	0.94253	AAG		TCGA-US-A77E-01A-11D-A32N-08	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	0	0	0	5	149	0	31	0	8.527393e-01	0	105	0	31	2		0	0	0	0	0	2	0	0.928190	0	145	0	31	2	0	0	0	0	0	0		-7.967799	1	0	0	0		1	1	2	3	1.976042	0	0.390000	2.070000	0.391187	0.180000	6.000000e-02	0.380000	0.160000	0.195639	0.180000	0	0.110000	0.270000
C1RL	51279	broad.mit.edu	37	12	7254566	7254566	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr12:7254566G>A	ENST00000266542.4	-	3	510	c.418C>T	c.(418-420)Cgc>Tgc	p.R140C	C1RL_ENST00000545280.1_Intron|C1RL_ENST00000544702.1_Missense_Mutation_p.R140C|C1RL_ENST00000545337.1_Missense_Mutation_p.R140C	NM_016546.2	NP_057630.2	Q9NZP8	C1RL_HUMAN	complement component 1, r subcomponent-like			16					GGCTGTGTGCGGAAGGTCAGC	0.622000																								0							SO:0001583	missense			ENST00000266542.4	0	1	hg19	CCDS8573.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	5.842|5.842	0.339585|0.339585	0.11069|0.11069	.|.	.|.	ENSG00000139178|ENSG00000139178	ENST00000534950|ENST00000266542;ENST00000396661;ENST00000544702;ENST00000543933;ENST00000545337	.|T;T;T;T	.|0.30448	.|1.53;1.53;1.53;1.53	3.76|3.76	-0.133|-0.133	0.13485|0.13485	.|CUB (5);	.|1.399260	.|0.04433	.|N	.|0.369511	T|T	0.35799|0.35799	0.0944|0.0944	M|M	0.88640|0.88640	2.97|2.97	0.24098|0.24098	N|N	0.995883|0.995883	.|B;B;B	.|0.33919	.|0.432;0.038;0.285	.|B;B;B	.|0.27887	.|0.051;0.007;0.084	T|T	0.30268|0.30268	-0.9984|-0.9984	5|10	.|0.45353	.|T	.|0.12	.|.	3.3529|3.3529	0.07159|0.07159	0.2989:0.0:0.5228:0.1783|0.2989:0.0:0.5228:0.1783	.|.	.|140;140;140	.|F5GWF3;F5H7C8;Q9NZP8	.|.;.;C1RL_HUMAN	L|C	39|140	.|ENSP00000266542:R140C;ENSP00000441885:R140C;ENSP00000437398:R140C;ENSP00000442611:R140C	.|ENSP00000266542:R140C	P|R	-|-	2|1	0|0	C1RL|C1RL	7145842|7145842	0.147000|0.147000	0.22687|0.22687	0.103000|0.103000	0.21229|0.21229	0.289000|0.289000	0.27227|0.27227	0.193000|0.193000	0.17116|0.17116	-0.034000|-0.034000	0.13713|0.13713	-1.529000|-1.529000	0.00923|0.00923	CCG|CGC		TCGA-US-A77E-01A-11D-A32N-08	C1RL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398367.1	0	0	0	6	618	0	157	0	2.229390e-01	0	79	0	157	2		0	0	0	0	0	2	1	0.963682	5	611	0	157	2	0	0	0	0	0	0		-2.133321	0	1	121412	1	35	1	1	2	3	1.980614	0	0.390000	2.070000	0.391187	0.050000	1.000000e-02	0.110000	0.050000	0.057333	0.050000	0	0.030000	0.080000
MMP14	4323	broad.mit.edu	37	14	23315041	23315041	+	Silent	SNP	G	G	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08			G	A	G	G		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr14:23315041G>A	ENST00000311852.6	+	10	1803	c.1542G>A	c.(1540-1542)ccG>ccA	p.P514P	MMP14_ENST00000548162.1_Intron	NM_004995.2	NP_004986.1	P50281	MMP14_HUMAN	matrix metallopeptidase 14 (membrane-inserted)			20	all_cancers(95;9.47e-05)			Marimastat(DB00786)	GAGGCCGGCCGGATGAGGGGA	0.637000																								0							SO:0001819	synonymous_variant			ENST00000311852.6	0	1	hg19	CCDS9577.1																																																																																				TCGA-US-A77E-01A-11D-A32N-08	MMP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071660.3	0	0	0	4	240	0	50	0	9.998255e-01	0	1682	0	50	2		0	0	0	0	0	2	1	0.886206	4	235	0	49	2	0	0	0	0	0	0		-2.949559	1	1	121410	2	35	1	1	2	3	1.983148	0	0.390000	2.070000	0.391187	0.090000	2.000000e-02	0.210000	0.080000	0.103761	0.090000	0	0.050000	0.150000
NKX2-8	26257	broad.mit.edu	37	14	37050517	37050517	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr14:37050517G>A	ENST00000258829.5	-	2	527	c.310C>T	c.(310-312)Cgg>Tgg	p.R104W		NM_014360.2	NP_055175.2	O15522	NKX28_HUMAN	NK2 homeobox 8			1	Breast(36;0.143)|Hepatocellular(127;0.158)|Esophageal squamous(585;0.164)		Lung(8;1.12e-09)|LUAD - Lung adenocarcinoma(9;2.16e-07)|Epithelial(34;0.00357)|all cancers(34;0.0113)|LUSC - Lung squamous cell carcinoma(13;0.0189)		CGCTGCTGCCGGAAGCGCCGC	0.662000																								0							SO:0001583	missense			ENST00000258829.5	0	1	hg19	CCDS9660.1	.	.	.	.	.	.	.	.	.	.	G	28.3	4.911256	0.92178	.	.	ENSG00000136327	ENST00000258829	D	0.96459	-4.02	4.25	4.25	0.50352	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.067264	0.64402	D	0.000008	D	0.97920	0.9316	M	0.80028	2.48	0.58432	D	0.999999	D	0.89917	1.0	D	0.80764	0.994	D	0.98869	1.0765	10	0.87932	D	0	.	15.8354	0.78793	0.0:0.0:1.0:0.0	.	104	O15522	NKX28_HUMAN	W	104	ENSP00000258829:R104W	ENSP00000258829:R104W	R	-	1	2	NKX2-8	36120268	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.079000	0.41577	2.186000	0.69663	0.549000	0.68633	CGG		TCGA-US-A77E-01A-11D-A32N-08	NKX2-8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071844.6	0	0	0	3	46	0	10		0	0	0	0	10	2		0	0	0	0	0	2	1	0.806023	3	45	0	10	2	0	0	0	0	0	0		-8.326563	1	1	0	0		1	0	1	1	1.968804	0	0.390000	2.070000	0.388808	0.350000	1.000000e-01	0.780000	0.300000	0.388295	0.350000	0	0.200000	0.560000
BTBD7	55727	broad.mit.edu	37	14	93709084	93709084	+	Silent	SNP	G	G	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr14:93709084G>A	ENST00000334746.5	-	11	3241	c.2934C>T	c.(2932-2934)taC>taT	p.Y978Y	BTBD7_ENST00000554565.1_Silent_p.Y627Y|BTBD7_ENST00000393170.2_Silent_p.Y552Y	NM_001002860.2	NP_001002860.2	Q9P203	BTBD7_HUMAN	BTB (POZ) domain containing 7			35		all_cancers(154;0.08)			TATTGTGGCTGTACAGATCGG	0.483000																								0							SO:0001819	synonymous_variant			ENST00000334746.5	0	1	hg19	CCDS32146.1																																																																																				TCGA-US-A77E-01A-11D-A32N-08	BTBD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412701.1	0	0	0	5	525	0	111	0	2.143140e-02	0	19	0	111	2		0	0	0	0	0	2	1	0.936245	5	520	0	111	2	0	0	0	0	0	0		-2.465566	0	1	121412	1	28	1	0	1	1	1.968804	0	0.390000	2.070000	0.388808	0.040000	1.000000e-02	0.110000	0.050000	0.057496	0.040000	0	0.020000	0.080000
CLMN	79789	broad.mit.edu	37	14	95677190	95677190	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr14:95677190G>A	ENST00000298912.4	-	7	748	c.635C>T	c.(634-636)gCg>gTg	p.A212V		NM_024734.3	NP_079010.2	Q96JQ2	CLMN_HUMAN	calmin (calponin-like, transmembrane)			44					CCAACTGCCCGCAAAGTCCTG	0.567000																								0							SO:0001583	missense			ENST00000298912.4	0	1	hg19	CCDS9933.1	.	.	.	.	.	.	.	.	.	.	G	32	5.119023	0.94385	.	.	ENSG00000165959	ENST00000298912	T	0.59638	0.25	5.93	5.93	0.95920	Calponin homology domain (5);	0.000000	0.39341	N	0.001394	T	0.59797	0.2220	N	0.14661	0.345	0.80722	D	1	D	0.63046	0.992	P	0.57468	0.821	T	0.65113	-0.6247	10	0.72032	D	0.01	.	20.3311	0.98718	0.0:0.0:1.0:0.0	.	212	Q96JQ2	CLMN_HUMAN	V	212	ENSP00000298912:A212V	ENSP00000298912:A212V	A	-	2	0	CLMN	94746943	1.000000	0.71417	0.260000	0.24451	0.983000	0.72400	6.642000	0.74329	2.797000	0.96272	0.655000	0.94253	GCG		TCGA-US-A77E-01A-11D-A32N-08	CLMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414518.2	0	0	0	7	695	0	152	0	1.531691e-01	1	59	0	152	2		0	0	0	0	0	2	1	0.979113	6	681	0	151	2	0	0	0	0	0	0		-1.844680	0	1	121402	4	35	1	0	1	1	1.968804	0	0.390000	2.070000	0.388808	0.050000	1.000000e-02	0.100000	0.060000	0.058093	0.050000	0	0.030000	0.080000
TPM1	7168	broad.mit.edu	37	15	63353068	63353068	+	Splice_Site	SNP	G	G	T			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08			G	T	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr15:63353068G>T	ENST00000403994.3	+	5	573	c.493G>T	c.(493-495)Gtg>Ttg	p.V165L	TPM1_ENST00000317516.7_Splice_Site_p.V129L|TPM1_ENST00000358278.3_Splice_Site_p.V165L|TPM1_ENST00000559397.1_Splice_Site_p.V165L|TPM1_ENST00000560959.1_Splice_Site_p.V129L|TPM1_ENST00000404484.4_Splice_Site_p.V129L|TPM1_ENST00000334895.5_Splice_Site_p.V129L|TPM1_ENST00000357980.4_Splice_Site_p.V207L|TPM1_ENST00000559556.1_Splice_Site_p.V165L|TPM1_ENST00000267996.7_Splice_Site_p.V165L|TPM1_ENST00000288398.6_Splice_Site_p.V165L|TPM1_ENST00000560445.1_Intron|TPM1_ENST00000559281.1_Splice_Site_p.V129L	NM_001018005.1	NP_001018005.1	P09493	TPM1_HUMAN	tropomyosin 1 (alpha)			4					CCTGCTGCAGGTGGCCCGTAA	0.592000																								0							SO:0001630	splice_region_variant			ENST00000403994.3	1	0	hg19	CCDS45273.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.490295	0.84962	.	.	ENSG00000140416	ENST00000288398;ENST00000267996;ENST00000358278;ENST00000403994;ENST00000357980;ENST00000404484;ENST00000334895;ENST00000317516	D;D;D;D;D;D	0.98150	-4.75;-4.75;-4.75;-4.75;-4.75;-4.75	5.58	5.58	0.84498	.	0.000000	0.44902	D	0.000411	D	0.99032	0.9669	M	0.92507	3.315	0.80722	D	1	P;P;D;P;B;B;P;D;D;D;D;P;P;P	0.69078	0.486;0.841;0.997;0.47;0.352;0.314;0.912;0.985;0.966;0.995;0.98;0.848;0.836;0.912	P;P;D;B;B;B;D;D;D;D;D;P;P;D	0.75020	0.622;0.846;0.985;0.337;0.261;0.366;0.919;0.957;0.961;0.965;0.979;0.817;0.87;0.919	D	0.99541	1.0963	9	.	.	.	-30.939	18.5512	0.91065	0.0:0.0:1.0:0.0	.	129;129;165;131;129;129;165;207;165;165;165;165;165;165	B7Z722;B7Z596;P09493-6;F5H7S3;D9YZV7;Q1ZYL5;D9YZV4;Q6ZN40;D9YZV8;D9YZV5;Q9Y427;D9YZV3;D9YZV2;P09493	.;.;.;.;.;.;.;.;.;.;.;.;.;TPM1_HUMAN	L	165;165;165;165;207;187;129;131	ENSP00000288398:V165L;ENSP00000267996:V165L;ENSP00000351022:V165L;ENSP00000385107:V165L;ENSP00000350667:V207L;ENSP00000334624:V129L	.	V	+	1	0	TPM1	61140121	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	9.869000	0.99810	2.628000	0.89032	0.491000	0.48974	GTG		TCGA-US-A77E-01A-11D-A32N-08	TPM1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000417083.2	1	0	1	49	226	0	52	1	1	116	803	0	52	2		0	0	0	0	0	2	1	1.000000	49	223	0	52	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	1	2	3	1.986821	0	0.390000	2.070000	0.392370	0.910000	6.900000e-01	1.000000	1.000000	0.905602	0.910000	1	0.800000	1.000000
HOMER2	9455	broad.mit.edu	37	15	83561566	83561566	+	Silent	SNP	C	C	T			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr15:83561566C>T	ENST00000304231.8	-	2	225	c.33G>A	c.(31-33)gcG>gcA	p.A11A	HOMER2_ENST00000450735.2_Silent_p.A11A|HOMER2_ENST00000399166.2_Silent_p.A11A|HOMER2_ENST00000426485.1_Silent_p.A11A	NM_199330.2	NP_955362.1	Q9NSB8	HOME2_HUMAN	homer homolog 2 (Drosophila)	p.A11A(1)		9					GGAAGACATGCGCTCGGGTGG	0.483000																								1	Substitution - coding silent(1)						SO:0001819	synonymous_variant			ENST00000304231.8	0	1	hg19	CCDS45334.1																																																																																				TCGA-US-A77E-01A-11D-A32N-08	HOMER2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418689.1	0	0	0	5	471	0	98	0	9.568124e-02	0	40	0	98	2		0	0	0	0	0	2	1	0.936101	5	466	0	97	2	0	0	0	0	0	0		-2.272608	0	1	120902	3	39	1	1	2	3	1.986821	0	0.390000	2.070000	0.392370	0.050000	1.000000e-02	0.130000	0.060000	0.073551	0.050000	0	0.030000	0.090000
GNPTG	84572	broad.mit.edu	37	16	1412884	1412884	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr16:1412884G>A	ENST00000204679.4	+	10	843	c.800G>A	c.(799-801)gGc>gAc	p.G267D	LA16c-316G12.2_ENST00000569831.1_RNA	NM_032520.4	NP_115909.1	Q9UJJ9	GNPTG_HUMAN	N-acetylglucosamine-1-phosphate transferase, gamma subunit			7		Hepatocellular(780;0.0893)			ACCCAGCACGGCATCCCCTAC	0.567000																								0							SO:0001583	missense			ENST00000204679.4	0	1	hg19	CCDS10436.1	.	.	.	.	.	.	.	.	.	.	G	16.58	3.161810	0.57368	.	.	ENSG00000090581	ENST00000204679	D	0.88664	-2.41	5.04	4.06	0.47325	.	0.332660	0.35466	N	0.003194	D	0.87325	0.6149	M	0.71581	2.175	0.38684	D	0.952614	P	0.40578	0.722	B	0.39185	0.293	D	0.89026	0.3438	10	0.51188	T	0.08	-35.0628	12.1825	0.54220	0.0896:0.0:0.9104:0.0	.	267	Q9UJJ9	GNPTG_HUMAN	D	267	ENSP00000204679:G267D	ENSP00000204679:G267D	G	+	2	0	GNPTG	1352885	0.997000	0.39634	0.551000	0.28230	0.143000	0.21401	1.542000	0.36137	2.527000	0.85204	0.650000	0.86243	GGC		TCGA-US-A77E-01A-11D-A32N-08	GNPTG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109058.2	0	0	0	6	467	0	110	0	9.488421e-01	1	415	0	110	2		0	0	0	0	0	2	1	0.964259	6	463	0	109	2	0	0	0	0	0	0		-2.183592	0	1	0	0		1	1	2	3	1.983116	0	0.390000	2.070000	0.391187	0.060000	2.000000e-02	0.140000	0.060000	0.075491	0.060000	0	0.040000	0.100000
XYLT1	64131	broad.mit.edu	37	16	17352929	17352929	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr16:17352929G>A	ENST00000261381.6	-	3	913	c.829C>T	c.(829-831)Cgc>Tgc	p.R277C		NM_022166.3	NP_071449.1	Q86Y38	XYLT1_HUMAN	xylosyltransferase I			67					ATCTCCTGGCGGCAGTGCTTG	0.607000																								0							SO:0001583	missense			ENST00000261381.6	1	1	hg19	CCDS10569.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.508056	0.85282	.	.	ENSG00000103489	ENST00000261381	T	0.07444	3.19	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	T	0.32406	0.0828	M	0.79475	2.455	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.03306	-1.1050	10	0.87932	D	0	-31.9029	18.2463	0.89986	0.0:0.0:1.0:0.0	.	277	Q86Y38	XYLT1_HUMAN	C	277	ENSP00000261381:R277C	ENSP00000261381:R277C	R	-	1	0	XYLT1	17260430	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.731000	0.84895	2.547000	0.85894	0.655000	0.94253	CGC		TCGA-US-A77E-01A-11D-A32N-08	XYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252241.2	1	0	1	73	344	0	94	0	9.600882e-01	1	26	0	94	2		0	0	0	0	0	2	1	1.000000	73	343	0	93	2	0	0	0	0	0	0		-3.271079	1	1	121102	4	36	1	1	2	3	1.982829	0	0.390000	2.070000	0.391187	0.890000	7.100000e-01	1.000000	1.000000	0.895581	0.890000	1	0.800000	1.000000
ZNF646	9726	broad.mit.edu	37	16	31090857	31090857	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr16:31090857G>A	ENST00000394979.2	+	1	3635	c.3212G>A	c.(3211-3213)cGc>cAc	p.R1071H	ZNF646_ENST00000300850.5_Missense_Mutation_p.R1071H			O15015	ZN646_HUMAN	zinc finger protein 646			49					GTGAACCACCGCAAGATCCAC	0.617000																								0							SO:0001583	missense			ENST00000394979.2	0	1	hg19		.	.	.	.	.	.	.	.	.	.	G	20.5	4.004264	0.74932	0.0	1.16E-4	ENSG00000167395	ENST00000300850;ENST00000394979	T;T	0.52057	0.68;0.68	5.75	4.78	0.61160	.	.	.	.	.	T	0.33147	0.0853	L	0.31065	0.9	0.33612	D	0.603727	D	0.56521	0.976	B	0.41813	0.367	T	0.51498	-0.8698	9	0.62326	D	0.03	-15.9326	5.5911	0.17301	0.1514:0.0:0.6807:0.1679	.	1071	O15015-2	.	H	1071	ENSP00000300850:R1071H;ENSP00000378429:R1071H	ENSP00000300850:R1071H	R	+	2	0	ZNF646	30998358	0.512000	0.26186	1.000000	0.80357	0.987000	0.75469	1.081000	0.30791	1.389000	0.46526	0.563000	0.77884	CGC		TCGA-US-A77E-01A-11D-A32N-08	ZNF646-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000108510.2	0	0	0	8	1060	0	278	0	1.581895e-02	0	22	0	278	2		0	0	0	0	0	2	1	0.989029	8	1052	0	272	2	0	0	0	0	0	0		-2.188596	0	1	121412	2	38	1	1	2	3	1.982829	0	0.390000	2.070000	0.391187	0.030000	0	0.080000	0.040000	0.043305	0.030000	0	0.020000	0.060000
SLC6A2	6530	broad.mit.edu	37	16	55727937	55727937	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr16:55727937G>A	ENST00000379906.2	+	6	1189	c.934G>A	c.(934-936)Gca>Aca	p.A312T	SLC6A2_ENST00000567238.1_Missense_Mutation_p.A207T|SLC6A2_ENST00000414754.3_Missense_Mutation_p.A312T|SLC6A2_ENST00000219833.8_Missense_Mutation_p.A312T|SLC6A2_ENST00000568943.1_Missense_Mutation_p.A312T|SLC6A2_ENST00000561820.1_Missense_Mutation_p.A312T|SLC6A2_ENST00000566163.1_Missense_Mutation_p.A267T	NM_001043.3	NP_001034.1	P23975	SC6A2_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 2			41				Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Atomoxetine(DB00289)|Bupropion(DB01156)|Chlorphenamine(DB01114)|Citalopram(DB00215)|Clomipramine(DB01242)|Cocaine(DB00907)|Debrisoquin(DB04840)|Desipramine(DB01151)|Desvenlafaxine(DB06700)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Dextromethorphan(DB00514)|Diethylpropion(DB00937)|Dopamine(DB00988)|Doxepin(DB01142)|Droxidopa(DB06262)|Duloxetine(DB00476)|Ephedra(DB01363)|Ephedrine(DB01364)|Ergotamine(DB00696)|Escitalopram(DB01175)|Ginkgo biloba(DB01381)|Guanadrel(DB00226)|Guanethidine(DB01170)|Imipramine(DB00458)|Iobenguane(DB06704)|Ketamine(DB01221)|Levomilnacipran(DB08918)|Levonordefrin(DB06707)|Loxapine(DB00408)|Maprotiline(DB00934)|Mazindol(DB00579)|Methamphetamine(DB01577)|Methylphenidate(DB00422)|Mianserin(DB06148)|Milnacipran(DB04896)|Mirtazapine(DB00370)|Nefazodone(DB01149)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Orphenadrine(DB01173)|Paroxetine(DB00715)|Pethidine(DB00454)|Phendimetrazine(DB01579)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Reboxetine(DB00234)|Sibutramine(DB01105)|Tapentadol(DB06204)|Tramadol(DB00193)|Trimipramine(DB00726)|Venlafaxine(DB00285)	GATTGATGCCGCAACTCAGAT	0.453000																								0							SO:0001583	missense			ENST00000379906.2	0	1	hg19	CCDS10754.1	.	.	.	.	.	.	.	.	.	.	G	14.23	2.474824	0.43942	.	.	ENSG00000103546	ENST00000414754;ENST00000537705;ENST00000379906;ENST00000219833	T;T;T	0.75938	-0.98;-0.98;-0.98	4.74	4.74	0.60224	.	0.000000	0.85682	D	0.000000	D	0.88418	0.6431	M	0.88031	2.925	0.58432	D	0.999998	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.998;0.998;0.998;0.996	D	0.91031	0.4864	10	0.87932	D	0	.	17.3376	0.87286	0.0:0.0:1.0:0.0	.	312;26;207;312	Q96KH8;F5H0T4;B4DX48;P23975	.;.;.;SC6A2_HUMAN	T	312;26;312;312	ENSP00000394956:A312T;ENSP00000369237:A312T;ENSP00000219833:A312T	ENSP00000219833:A312T	A	+	1	0	SLC6A2	54285438	1.000000	0.71417	0.999000	0.59377	0.930000	0.56654	9.501000	0.97979	2.196000	0.70406	0.561000	0.74099	GCA		TCGA-US-A77E-01A-11D-A32N-08	SLC6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256922.2	0	0	0	5	541	0	94		0	0	0	0	94	2		0	0	0	0	0	2	1	0.934726	5	532	0	94	2	0	0	0	0	0	0		-2.187734	0	1	121412	1	34	1	1	2	3	1.982829	0	0.390000	2.070000	0.391187	0.040000	0	0.110000	0.050000	0.056023	0.040000	0	0.020000	0.080000
KIFC3	3801	broad.mit.edu	37	16	57803635	57803635	+	Missense_Mutation	SNP	C	C	T	rs146824728	byFrequency	TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr16:57803635C>T	ENST00000379655.4	-	9	1347	c.1090G>A	c.(1090-1092)Gtc>Atc	p.V364I	KIFC3_ENST00000540079.2_Missense_Mutation_p.V262I|KIFC3_ENST00000543930.1_Missense_Mutation_p.V225I|KIFC3_ENST00000562903.1_Missense_Mutation_p.V225I|KIFC3_ENST00000465878.2_Missense_Mutation_p.V225I|KIFC3_ENST00000566975.1_5'Flank|KIFC3_ENST00000445690.2_Missense_Mutation_p.V364I|KIFC3_ENST00000541240.1_Missense_Mutation_p.V386I|KIFC3_ENST00000539578.1_Missense_Mutation_p.V306I|KIFC3_ENST00000421376.2_Missense_Mutation_p.V225I	NM_005550.3	NP_005541.3	Q9BVG8	KIFC3_HUMAN	kinesin family member C3			23		all_neural(199;0.224)			TTGGTCCGGACGCCTATGGGG	0.667000																								0							SO:0001583	missense			ENST00000379655.4	1	1	hg19	CCDS10789.2	.	.	.	.	.	.	.	.	.	.	C	17.90	3.503117	0.64298	4.55E-4	0.0	ENSG00000140859	ENST00000379655;ENST00000445690;ENST00000421376;ENST00000541240;ENST00000540079;ENST00000543930;ENST00000539578	T;T;T;T;T;T;T	0.74632	-0.82;-0.8;-0.79;-0.81;-0.78;-0.86;-0.79	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	T	0.69504	0.3118	L	0.54323	1.7	0.58432	D	0.999999	B;P;B;B;B;B;P	0.44627	0.4;0.839;0.4;0.133;0.088;0.4;0.495	B;B;B;B;B;B;B	0.36845	0.051;0.234;0.051;0.08;0.04;0.051;0.058	T	0.71024	-0.4712	10	0.35671	T	0.21	.	18.1742	0.89756	0.0:1.0:0.0:0.0	.	386;306;225;262;69;364;225	B7Z484;F5H4I9;B7Z896;F5H3M2;B7Z3I6;Q9BVG8;A8K6S2	.;.;.;.;.;KIFC3_HUMAN;.	I	364;364;225;386;262;225;306	ENSP00000368976:V364I;ENSP00000401696:V364I;ENSP00000396399:V225I;ENSP00000442008:V386I;ENSP00000438805:V262I;ENSP00000444012:V225I;ENSP00000444884:V306I	ENSP00000368976:V364I	V	-	1	0	KIFC3	56361136	1.000000	0.71417	0.987000	0.45799	0.186000	0.23388	5.980000	0.70516	2.624000	0.88883	0.655000	0.94253	GTC		TCGA-US-A77E-01A-11D-A32N-08	KIFC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257329.2	1	0	1	37	151	0	47	1	9.999954e-01	12	70	0	47	2		0	0	0	0	0	2	1	1.000000	37	149	0	45	2	0	0	0	0	0	0		-20.000000	1	1	121404	19	40	1	1	2	3	1.976157	0	0.390000	2.070000	0.391187	0.990000	7.400000e-01	1.000000	1.000000	0.950524	0.990000	1	0.860000	1.000000
CDH11	1009	broad.mit.edu	37	16	65032559	65032559	+	Silent	SNP	C	C	T			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08			C	T	C	C		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr16:65032559C>T	ENST00000268603.4	-	4	1044	c.429G>A	c.(427-429)tcG>tcA	p.S143S	CDH11_ENST00000394156.3_Silent_p.S143S|CDH11_ENST00000566827.1_Silent_p.S17S	NM_001797.2	NP_001788.2	P55287	CAD11_HUMAN	cadherin 11, type 2, OB-cadherin (osteoblast)			88		Ovarian(137;0.0973)			CAATGAATTCCGACGGTGGCT	0.557000			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)					Dom	yes		16	16q22.1	1009	cadherin 11, type 2, OB-cadherin (osteoblast)		M	0							SO:0001819	synonymous_variant			ENST00000268603.4	1	1	hg19	CCDS10803.1	.	.	.	.	.	.	.	.	.	.	C	7.100	0.573882	0.13623	.	.	ENSG00000140937	ENST00000536902	.	.	.	5.77	-11.5	0.00074	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.1085	0.10049	0.127:0.3975:0.2727:0.2028	.	.	.	.	.	-1	.	.	.	-	.	.	CDH11	63590060	0.000000	0.05858	0.005000	0.12908	0.809000	0.45718	-2.084000	0.01363	-3.488000	0.00154	-1.021000	0.02439	.		TCGA-US-A77E-01A-11D-A32N-08	CDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268755.1	1	0	1	56	243	0	68	0	9.999999e-01	0	108	0	68	2		0	0	0	0	0	2	1	1.000000	56	242	1	68	15	0	0	0	0	0	0		-3.179270	1	1	121412	2	35	1	1	2	3	1.976157	0	0.390000	2.070000	0.391187	0.950000	7.400000e-01	1.000000	1.000000	0.935818	0.950000	1	0.840000	1.000000
FHOD1	29109	broad.mit.edu	37	16	67273270	67273270	+	Missense_Mutation	SNP	C	C	T			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr16:67273270C>T	ENST00000258201.4	-	2	536	c.289G>A	c.(289-291)Ggc>Agc	p.G97S		NM_013241.2	NP_037373.2	Q9Y613	FHOD1_HUMAN	formin homology 2 domain containing 1			34		Ovarian(137;0.0563)			TCATAGAAGCCCTCCAGCATC	0.582000																								0							SO:0001583	missense			ENST00000258201.4	1	1	hg19	CCDS10834.1	.	.	.	.	.	.	.	.	.	.	C	14.69	2.610778	0.46527	.	.	ENSG00000135723	ENST00000258201	T	0.20200	2.09	4.85	2.67	0.31697	GTPase-binding/formin homology 3 (1);	0.390655	0.28834	N	0.013983	T	0.15262	0.0368	L	0.41492	1.28	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.07927	-1.0747	10	0.24483	T	0.36	.	8.5697	0.33561	0.0:0.8069:0.0:0.1931	.	97	Q9Y613	FHOD1_HUMAN	S	97	ENSP00000258201:G97S	ENSP00000258201:G97S	G	-	1	0	FHOD1	65830771	0.100000	0.21855	1.000000	0.80357	0.997000	0.91878	0.337000	0.19841	0.516000	0.28340	0.655000	0.94253	GGC		TCGA-US-A77E-01A-11D-A32N-08	FHOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268844.2	1	0	1	42	300	0	87	1	7.246828e-01	3	17	0	87	2		0	0	0	0	0	2	1	1.000000	39	296	0	85	2	0	0	0	0	0	0		-3.318838	1	1	0	0		1	1	2	3	1.976157	0	0.390000	2.070000	0.391187	0.630000	4.600000e-01	0.830000	0.630000	0.639354	0.630000	0	0.540000	0.730000
SLC12A4	6560	broad.mit.edu	37	16	67980419	67980419	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr16:67980419G>A	ENST00000316341.3	-	18	2499	c.2359C>T	c.(2359-2361)Cgg>Tgg	p.R787W	SLC12A4_ENST00000338335.3_Intron|LCAT_ENST00000264005.5_5'Flank|SLC12A4_ENST00000541864.2_Missense_Mutation_p.R756W|SLC12A4_ENST00000572037.1_Missense_Mutation_p.R739W|SLC12A4_ENST00000537830.2_Missense_Mutation_p.R781W|SLC12A4_ENST00000576616.1_Missense_Mutation_p.R787W|CTC-479C5.17_ENST00000590594.1_lincRNA|SLC12A4_ENST00000422611.2_Missense_Mutation_p.R789W	NM_001145961.1|NM_005072.4	NP_001139433.1|NP_005063.1	Q9UP95	S12A4_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 4			29		Ovarian(137;0.192)		Bumetanide(DB00887)|Potassium Chloride(DB00761)	GAGTTATGCCGCATGCCTCCC	0.652000																								0							SO:0001583	missense			ENST00000316341.3	0	1	hg19	CCDS10855.1	.	.	.	.	.	.	.	.	.	.	G	18.93	3.728223	0.69074	0.0	1.16E-4	ENSG00000124067	ENST00000422611;ENST00000541864;ENST00000537830;ENST00000316341	D;D;D;D	0.92595	-3.07;-3.07;-3.07;-3.07	4.57	2.23	0.28157	.	0.048575	0.85682	D	0.000000	D	0.94837	0.8332	M	0.80982	2.52	0.80722	D	1	D;D;D;D;D;D	0.63046	0.989;0.986;0.992;0.992;0.992;0.986	P;P;D;P;P;P	0.63381	0.877;0.582;0.914;0.761;0.828;0.582	D	0.93878	0.7168	10	0.87932	D	0	.	11.329	0.49465	0.0:0.0:0.3051:0.6949	.	789;787;756;781;787;787	F5H3C0;B4DF30;F5H066;F5H0S9;Q9UP95-2;Q9UP95	.;.;.;.;.;S12A4_HUMAN	W	789;756;781;787	ENSP00000395983:R789W;ENSP00000438334:R756W;ENSP00000445962:R781W;ENSP00000318557:R787W	ENSP00000318557:R787W	R	-	1	2	SLC12A4	66537920	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.502000	0.53332	0.220000	0.20860	-0.262000	0.10625	CGG		TCGA-US-A77E-01A-11D-A32N-08	SLC12A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268864.4	0	0	0	6	341	1	86	0	3.981331e-02	0	82	1	86	5		0	0	0	0	0	2	0	0.036408	6	341	1	86	15	0	0	0	0	0	0		-2.414368	0	1	121396	1	32	1	1	2	3	1.976157	0	0.390000	2.070000	0.391187	0.090000	3.000000e-02	0.190000	0.090000	0.102604	0.090000	0	0.050000	0.140000
WWP2	11060	broad.mit.edu	37	16	69832593	69832593	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr16:69832593G>A	ENST00000359154.2	+	3	180	c.79G>A	c.(79-81)Gca>Aca	p.A27T	WWP2_ENST00000356003.2_Missense_Mutation_p.A27T|WWP2_ENST00000448661.1_Missense_Mutation_p.A27T|WWP2_ENST00000569174.1_Missense_Mutation_p.A27T	NM_001270454.1|NM_007014.4	NP_001257383.1|NP_008945.2	O00308	WWP2_HUMAN	WW domain containing E3 ubiquitin protein ligase 2			42					AGTGGTGTCCGCAAAGCCCAA	0.527000											OREG0023909	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)												0							SO:0001583	missense			ENST00000359154.2	0	1	hg19	CCDS10885.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.551721	0.86127	.	.	ENSG00000198373	ENST00000359154;ENST00000448661;ENST00000356003	T;T;T	0.80738	-1.41;-1.41;-1.41	5.76	5.76	0.90799	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.198406	0.45606	D	0.000349	T	0.76054	0.3934	M	0.67397	2.05	0.80722	D	1	P	0.46020	0.871	B	0.32583	0.148	T	0.78339	-0.2242	9	.	.	.	.	16.6952	0.85333	0.0:0.0:1.0:0.0	.	27	O00308	WWP2_HUMAN	T	27	ENSP00000352069:A27T;ENSP00000396871:A27T;ENSP00000348283:A27T	.	A	+	1	0	WWP2	68390094	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	4.778000	0.62368	2.713000	0.92767	0.655000	0.94253	GCA		TCGA-US-A77E-01A-11D-A32N-08	WWP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268954.1	0	0	0	6	490	1	113	0	2.503172e-02	0	41	1	113	3	0	3.173886e-01	1	693	2	360	12	0	0.024402	7	488	1	112	16	0	0	0	0	0	0		-1.705587	0	1	0	0		1	1	2	3	1.976157	0	0.390000	2.070000	0.391187	0.060000	2.000000e-02	0.140000	0.060000	0.072019	0.060000	0	0.030000	0.100000
PLCG2	5336	broad.mit.edu	37	16	81942078	81942078	+	Nonsense_Mutation	SNP	A	A	T			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr16:81942078A>T	ENST00000359376.3	+	17	1829	c.1615A>T	c.(1615-1617)Aag>Tag	p.K539*		NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN	phospholipase C, gamma 2 (phosphatidylinositol-specific)			58					GAAGGTGGAGAAGAGGACGAG	0.547000																								0							SO:0001587	stop_gained			ENST00000359376.3	0	1	hg19	CCDS42204.1	.	.	.	.	.	.	.	.	.	.	A	40	8.275878	0.98737	.	.	ENSG00000197943	ENST00000359376	.	.	.	4.72	4.72	0.59763	.	0.385009	0.29884	N	0.010957	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.27082	T	0.32	.	7.2706	0.26254	0.8622:0.0:0.1378:0.0	.	.	.	.	X	539	.	ENSP00000352336:K539X	K	+	1	0	PLCG2	80499579	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.998000	0.70653	1.770000	0.52166	0.460000	0.39030	AAG		TCGA-US-A77E-01A-11D-A32N-08	PLCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432429.1	1	0	1	45	191	0	44	0	3.243658e-01	0	6	0	44	2		0	0	0	0	0	2	1	1.000000	43	190	0	44	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	1	2	3	1.976157	0	0.390000	2.070000	0.391187	0.970000	7.300000e-01	1.000000	1.000000	0.940789	0.970000	1	0.850000	1.000000
KRT36	8689	broad.mit.edu	37	17	39643660	39643660	+	Silent	SNP	G	G	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr17:39643660G>A	ENST00000328119.6	-	5	929	c.930C>T	c.(928-930)atC>atT	p.I310I	KRT36_ENST00000393986.2_Silent_p.I260I	NM_003771.4	NP_003762.1	O76013	KRT36_HUMAN	keratin 36			17		Breast(137;0.000286)			GTCTCAGCTCGATGATCTCCG	0.627000																								0							SO:0001819	synonymous_variant			ENST00000328119.6	1	1	hg19	CCDS11395.1																																																																																				TCGA-US-A77E-01A-11D-A32N-08	KRT36-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259508.1	1	0	1	20	115	0	32	0	0	0	1	0	32	2		0	0	0	0	0	2	1	0.999997	20	113	0	31	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	1	2	3	1.988334	0	0.390000	2.070000	0.392370	0.760000	4.900000e-01	1.000000	1.000000	0.775080	0.760000	0	0.620000	0.940000
ARMC7	79637	broad.mit.edu	37	17	73124988	73124988	+	Missense_Mutation	SNP	C	C	T			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr17:73124988C>T	ENST00000245543.1	+	3	754	c.452C>T	c.(451-453)tCg>tTg	p.S151L	NT5C_ENST00000579082.1_5'Flank|ARMC7_ENST00000581078.1_3'UTR|ARMC7_ENST00000579096.1_3'UTR	NM_024585.2	NP_078861.1	Q9H6L4	ARMC7_HUMAN	armadillo repeat containing 7			9	all_lung(278;0.14)|Lung NSC(278;0.168)		LUSC - Lung squamous cell carcinoma(166;0.162)|Lung(188;0.235)		TTCTCCCTCTCGGCCAGCGCC	0.701000																								0							SO:0001583	missense			ENST00000245543.1	1	1	hg19	CCDS11714.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.697716	0.88830	.	.	ENSG00000125449	ENST00000245543	T	0.56444	0.46	5.18	5.18	0.71444	Armadillo-like helical (1);Armadillo-type fold (1);	0.071680	0.64402	D	0.000016	T	0.70228	0.3200	M	0.67397	2.05	0.80722	D	1	D	0.89917	1.0	D	0.63033	0.91	T	0.73219	-0.4052	10	0.72032	D	0.01	.	19.0722	0.93143	0.0:1.0:0.0:0.0	.	151	Q9H6L4	ARMC7_HUMAN	L	151	ENSP00000245543:S151L	ENSP00000245543:S151L	S	+	2	0	ARMC7	70636583	1.000000	0.71417	0.977000	0.42913	0.480000	0.33159	7.771000	0.85420	2.595000	0.87683	0.655000	0.94253	TCG		TCGA-US-A77E-01A-11D-A32N-08	ARMC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445846.1	1	0	1	28	98	0	26	1	8.160037e-01	4	9	0	26	2		0	0	0	0	0	2	1	1.000000	28	98	0	26	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	1	2	3	1.988334	0	0.390000	2.070000	0.392370	0.990000	8.000000e-01	1.000000	1.000000	0.979937	0.990000	1	0.960000	1.000000
ZBTB4	57659	broad.mit.edu	37	17	7369754	7369754	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr17:7369754G>A	ENST00000311403.4	-	3	706	c.367C>T	c.(367-369)Ccc>Tcc	p.P123S	ZBTB4_ENST00000380599.4_Missense_Mutation_p.P123S	NM_020899.3	NP_065950.2	Q9P1Z0	ZBTB4_HUMAN	zinc finger and BTB domain containing 4			36		Colorectal(1115;3.46e-05)|Myeloproliferative disorder(207;0.0255)			AGGACCCGGGGTGGGGAAGAA	0.592000																								0							SO:0001583	missense			ENST00000311403.4	0	1	hg19	CCDS11107.1	.	.	.	.	.	.	.	.	.	.	G	12.76	2.034919	0.35893	.	.	ENSG00000174282	ENST00000311403;ENST00000380599	T;T	0.46451	0.87;0.87	4.5	4.5	0.54988	BTB/POZ-like (2);BTB/POZ fold (2);	0.081322	0.48286	N	0.000193	T	0.14485	0.0350	N	0.01464	-0.85	0.34368	D	0.691707	B	0.33413	0.411	B	0.23018	0.043	T	0.16719	-1.0393	10	0.59425	D	0.04	-17.1852	8.349	0.32290	0.1059:0.0:0.8941:0.0	.	123	Q9P1Z0	ZBTB4_HUMAN	S	123	ENSP00000307858:P123S;ENSP00000369973:P123S	ENSP00000307858:P123S	P	-	1	0	ZBTB4	7310478	1.000000	0.71417	0.996000	0.52242	0.860000	0.49131	1.958000	0.40402	2.332000	0.79248	0.462000	0.41574	CCC		TCGA-US-A77E-01A-11D-A32N-08	ZBTB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226940.2	1	0	0	7	83	0	13	1	8.041582e-01	2	36	0	13	2		0	0	0	0	0	2	1	0.981287	7	82	0	13	2	0	0	0	0	0	0		-12.065770	1	1	0	0		1	0	1	1	1.705046	1	0.390000	2.070000	0.283869	0.350000	1.500000e-01	0.620000	0.330000	0.369311	0.350000	0	0.240000	0.490000
ENGASE	64772	broad.mit.edu	37	17	77081767	77081767	+	Missense_Mutation	SNP	C	C	T			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr17:77081767C>T	ENST00000579016.1	+	13	1766	c.1766C>T	c.(1765-1767)cCg>cTg	p.P589L		NM_001042573.2	NP_001036038.1	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase			25					TCACGGCCGCCGGGTAGTCGG	0.647000																								0							SO:0001583	missense			ENST00000579016.1	1	1	hg19	CCDS42394.1	.	.	.	.	.	.	.	.	.	.	C	4.447	0.082790	0.08533	.	.	ENSG00000167280	ENST00000545583	.	.	.	5.12	-2.66	0.06077	.	0.740232	0.11997	N	0.509178	T	0.22820	0.0551	L	0.36672	1.1	0.09310	N	1	B	0.12630	0.006	B	0.06405	0.002	T	0.17992	-1.0351	9	0.28530	T	0.3	-14.6675	0.6221	0.00780	0.2261:0.2603:0.1292:0.3843	.	589	Q8NFI3	ENASE_HUMAN	L	589	.	ENSP00000438577:P589L	P	+	2	0	ENGASE	74593362	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.211000	0.09332	-0.062000	0.13088	0.462000	0.41574	CCG		TCGA-US-A77E-01A-11D-A32N-08	ENGASE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395807.1	1	0	1	56	228	0	54	1	9.999064e-01	18	41	0	54	2		0	0	0	0	0	2	1	1.000000	55	224	0	52	2	0	0	0	0	0	0		-3.423686	1	1	120930	2	30	1	1	2	3	1.988334	0	0.390000	2.070000	0.392370	0.990000	7.800000e-01	1.000000	1.000000	0.961933	0.990000	1	0.890000	1.000000
GAA	2548	broad.mit.edu	37	17	78085870	78085870	+	Silent	SNP	C	C	T	rs112517802		TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr17:78085870C>T	ENST00000302262.3	+	12	1944	c.1725C>T	c.(1723-1725)taC>taT	p.Y575Y	GAA_ENST00000390015.3_Silent_p.Y575Y	NM_000152.3	NP_000143.2	P10253	LYAG_HUMAN	glucosidase, alpha; acid			21	all_neural(118;0.117)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.139)	Acarbose(DB00284)|Miglitol(DB00491)	ACAACCTCTACGGCCTGACCG	0.657000																								0							SO:0001819	synonymous_variant			ENST00000302262.3	1	1	hg19	CCDS32760.1																																																																																				TCGA-US-A77E-01A-11D-A32N-08	GAA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437441.1	1	0	0	86	345	0	95	1	1	9	126	0	95	2		0	0	0	0	0	2	1	1.000000	85	338	0	94	2	0	0	0	0	0	0		-20.000000	1	1	121412	2	37	1	1	2	3	1.988334	0	0.390000	2.070000	0.392370	0.990000	8.300000e-01	1.000000	1.000000	0.974530	0.990000	1	0.920000	1.000000
CELF4	56853	broad.mit.edu	37	18	34854360	34854360	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr18:34854360G>A	ENST00000591282.1	-	6	714	c.715C>T	c.(715-717)Cgg>Tgg	p.R239W	CELF4_ENST00000601019.1_Missense_Mutation_p.R238W|CELF4_ENST00000420428.2_Missense_Mutation_p.R239W|CELF4_ENST00000334919.5_Missense_Mutation_p.R229W|CELF4_ENST00000603232.1_Missense_Mutation_p.R239W|CELF4_ENST00000588597.1_Missense_Mutation_p.R228W|CELF4_ENST00000361795.5_Missense_Mutation_p.R238W|RP11-797E24.3_ENST00000588766.1_RNA|CELF4_ENST00000591287.1_Missense_Mutation_p.R238W|RP11-797E24.3_ENST00000586610.1_RNA|CELF4_ENST00000412753.1_Missense_Mutation_p.R239W			Q9BZC1	CELF4_HUMAN	CUGBP, Elav-like family member 4	p.R239W(1)		44					TGCATTCGCCGCATCGTGCGC	0.667000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000591282.1	0	1	hg19	CCDS32818.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.159388	0.78226	.	.	ENSG00000101489	ENST00000361795;ENST00000412753;ENST00000420428;ENST00000334919;ENST00000361683	T;T;T	0.06449	3.3;3.31;3.31	4.55	3.59	0.41128	.	0.000000	0.85682	D	0.000000	T	0.29882	0.0747	M	0.91510	3.215	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.999;0.993;1.0;0.999;0.996	T	0.19614	-1.0300	10	0.87932	D	0	-12.5849	12.0837	0.53686	0.0:0.0:0.7247:0.2753	.	238;228;229;238;239	Q9BZC1-3;B4DHA8;Q9BZC1-5;Q9BZC1-2;Q9BZC1	.;.;.;.;CELF4_HUMAN	W	239;239;238;229;122	ENSP00000355089:R239W;ENSP00000406823:R239W;ENSP00000335631:R229W	ENSP00000335631:R229W	R	-	1	2	CELF4	33108358	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.280000	0.43443	2.373000	0.80994	0.561000	0.74099	CGG		TCGA-US-A77E-01A-11D-A32N-08	CELF4-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000440892.1	0	0	0	5	632	1	164		0	0	0	1	164	2		0	0	0	0	0	2	0	0.028245	5	622	1	162	14	0	0	0	0	0	0		-1.778118	0	1	0	0		1	1	2	3	1.976333	0	0.390000	2.070000	0.391187	0.040000	0	0.100000	0.040000	0.047934	0.040000	0	0.020000	0.070000
PGLYRP2	114770	broad.mit.edu	37	19	15586705	15586705	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr19:15586705G>A	ENST00000340880.4	-	2	1256	c.776C>T	c.(775-777)aCg>aTg	p.T259M	PGLYRP2_ENST00000292609.4_Missense_Mutation_p.T259M	NM_052890.3	NP_443122.3	Q96PD5	PGRP2_HUMAN	peptidoglycan recognition protein 2			28					GTCCAAAAGCGTAAAGGTCCG	0.612000																								0							SO:0001583	missense			ENST00000340880.4	0	1	hg19	CCDS12330.2	.	.	.	.	.	.	.	.	.	.	g	3.963	-0.009976	0.07727	.	.	ENSG00000161031	ENST00000340880;ENST00000292609	T;T	0.05025	3.53;3.51	5.31	3.19	0.36642	.	0.237201	0.32901	N	0.005502	T	0.07728	0.0194	M	0.76002	2.32	0.22819	N	0.998691	P;P	0.43431	0.807;0.576	B;B	0.37267	0.245;0.048	T	0.31943	-0.9925	10	0.66056	D	0.02	-22.5225	4.5625	0.12166	0.0828:0.1521:0.6077:0.1574	.	259;259	Q96PD5-2;Q96PD5	.;PGRP2_HUMAN	M	259	ENSP00000345968:T259M;ENSP00000292609:T259M	ENSP00000292609:T259M	T	-	2	0	PGLYRP2	15447705	0.978000	0.34361	0.446000	0.26920	0.000000	0.00434	2.391000	0.44424	0.647000	0.30713	-1.032000	0.02404	ACG		TCGA-US-A77E-01A-11D-A32N-08	PGLYRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319626.1	0	0	0	4	223	0	43		0	0	0	0	43	2		0	0	0	0	0	2	1	0.891148	4	223	0	43	2	0	0	0	0	0	0		-5.363324	1	1	121412	18	42	1	1	2	3	1.994306	0	0.390000	2.070000	0.394721	0.100000	2.000000e-02	1.000000	0.090000	0.137632	0.100000	0	0.050000	0.170000
SHKBP1	92799	broad.mit.edu	37	19	41096643	41096643	+	Silent	SNP	C	C	T			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr19:41096643C>T	ENST00000291842.5	+	17	1825	c.1776C>T	c.(1774-1776)ggC>ggT	p.G592G	SHKBP1_ENST00000600733.1_Silent_p.G567G|LTBP4_ENST00000545697.1_5'Flank|LTBP4_ENST00000204005.9_5'Flank	NM_138392.3	NP_612401.2	Q8TBC3	SHKB1_HUMAN	SH3KBP1 binding protein 1			29			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)		CAGCAGGTGGCCTGACGGAGC	0.662000																								0							SO:0001819	synonymous_variant			ENST00000291842.5	1	1	hg19	CCDS12560.1																																																																																				TCGA-US-A77E-01A-11D-A32N-08	SHKBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462613.2	1	0	1	79	448	0	114	1	1	71	133	0	114	2		0	0	0	0	0	2	1	1.000000	77	443	0	112	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	1	2	3	2.001483	0	0.390000	2.070000	0.395890	0.770000	6.200000e-01	1.000000	0.780000	0.789007	0.770000	0	0.690000	0.870000
PSG6	5675	broad.mit.edu	37	19	43411874	43411874	+	Missense_Mutation	SNP	G	G	A	rs142652144	byFrequency	TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr19:43411874G>A	ENST00000292125.2	-	4	883	c.839C>T	c.(838-840)cCg>cTg	p.P280L	PSG6_ENST00000187910.2_Missense_Mutation_p.P280L|PSG6_ENST00000402603.4_Intron	NM_002782.4	NP_002773.1	Q00889	PSG6_HUMAN	pregnancy specific beta-1-glycoprotein 6			44		Prostate(69;0.00899)			CGGACTGACCGGGAGGCTCTG	0.478000																								0							SO:0001583	missense			ENST00000292125.2	1	1	hg19	CCDS12613.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	N	0.009	-1.803836	0.00611	0.002499	0.0	ENSG00000170848	ENST00000187910;ENST00000292125	T;T	0.13307	2.6;2.6	1.42	-1.33	0.09172	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.21962	0.0529	L	0.52266	1.64	0.09310	N	1	D;B	0.89917	1.0;0.015	D;B	0.97110	1.0;0.038	T	0.16453	-1.0402	9	0.39692	T	0.17	.	1.6928	0.02856	0.2473:0.0:0.4168:0.3359	.	280;280	Q00889;Q00889-2	PSG6_HUMAN;.	L	280	ENSP00000187910:P280L;ENSP00000292125:P280L	ENSP00000187910:P280L	P	-	2	0	PSG6	48103714	0.000000	0.05858	0.005000	0.12908	0.184000	0.23303	0.090000	0.15025	-0.070000	0.12908	0.134000	0.15878	CCG		TCGA-US-A77E-01A-11D-A32N-08	PSG6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321436.1	1	0	1	256	1086	0	274		0	0	0	0	274	2		0	0	0	0	0	2	1	1.000000	253	1042	0	268	2	0	0	0	0	0	0		-2.719552	1	1	121356	23	50	1	1	2	3	2.001483	0	0.390000	2.070000	0.395890	0.980000	8.700000e-01	1.000000	1.000000	0.972773	0.980000	1	0.920000	1.000000
C5AR1	728	broad.mit.edu	37	19	47823129	47823129	+	Missense_Mutation	SNP	C	C	T			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr19:47823129C>T	ENST00000355085.3	+	2	117	c.95C>T	c.(94-96)aCg>aTg	p.T32M		NM_001736.3	NP_001727.1	P21730	C5AR1_HUMAN	complement component 5a receptor 1	p.T32M(1)		20		all_cancers(25;2e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)			ACTTCTAACACGCTGCGTGTT	0.532000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000355085.3	1	1	hg19	CCDS33063.1	.	.	.	.	.	.	.	.	.	.	C	9.210	1.030611	0.19512	.	.	ENSG00000197405	ENST00000355085	T	0.37411	1.2	3.85	-7.7	0.01259	.	0.484862	0.17251	U	0.181174	T	0.10423	0.0255	N	0.08118	0	0.09310	N	1	P	0.51653	0.947	B	0.38296	0.27	T	0.32771	-0.9894	10	0.48119	T	0.1	.	2.3954	0.04388	0.2001:0.3146:0.3273:0.158	.	32	P21730	C5AR_HUMAN	M	32	ENSP00000347197:T32M	ENSP00000347197:T32M	T	+	2	0	C5AR1	52514969	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-3.504000	0.00449	-2.504000	0.00508	-0.792000	0.03331	ACG		TCGA-US-A77E-01A-11D-A32N-08	C5AR1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466925.1	0	0	1	69	286	0	77	0	9.188805e-01	0	20	0	77	2		0	0	0	0	0	2	1	1.000000	69	284	0	76	2	0	0	0	0	0	0		-20.000000	1	1	121412	4	38	1	1	2	3	2.001483	0	0.390000	2.070000	0.395890	0.990000	8.000000e-01	1.000000	1.000000	0.963577	0.990000	1	0.900000	1.000000
NLRP4	147945	broad.mit.edu	37	19	56369561	56369561	+	Missense_Mutation	SNP	A	A	G			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr19:56369561A>G	ENST00000301295.6	+	3	1224	c.802A>G	c.(802-804)Aag>Gag	p.K268E	NLRP4_ENST00000346986.5_Missense_Mutation_p.K268E|NLRP4_ENST00000587891.1_Missense_Mutation_p.K193E	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4			42		Colorectal(82;0.0002)|Ovarian(87;0.221)			GCTGAGGAAGAAGATGCTCCC	0.592000																								0							SO:0001583	missense			ENST00000301295.6	1	1	hg19	CCDS12936.1	.	.	.	.	.	.	.	.	.	.	A	15.58	2.876238	0.51801	.	.	ENSG00000160505	ENST00000301295;ENST00000346986	T;T	0.79653	-1.29;-1.29	4.1	3.05	0.35203	NACHT nucleoside triphosphatase (1);	.	.	.	.	T	0.81640	0.4865	L	0.41079	1.255	0.09310	N	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.78314	0.947;0.984;0.991	T	0.67692	-0.5605	9	0.18276	T	0.48	.	6.9127	0.24344	0.629:0.0:0.0:0.371	.	268;193;268	Q96MN2-2;Q96MN2-3;Q96MN2	.;.;NALP4_HUMAN	E	268	ENSP00000301295:K268E;ENSP00000344787:K268E	ENSP00000301295:K268E	K	+	1	0	NLRP4	61061373	0.000000	0.05858	0.008000	0.14137	0.087000	0.18053	1.126000	0.31344	0.689000	0.31550	0.533000	0.62120	AAG		TCGA-US-A77E-01A-11D-A32N-08	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	1	0	1	77	346	0	96		0	0	0	0	96	2		0	0	0	0	0	2	1	1.000000	76	343	0	96	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	1	2	3	2.011441	0	0.390000	2.070000	0.397054	0.940000	7.600000e-01	1.000000	1.000000	0.933178	0.940000	1	0.840000	1.000000
NLRP8	126205	broad.mit.edu	37	19	56467178	56467178	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr19:56467178G>A	ENST00000291971.3	+	3	1825	c.1754G>A	c.(1753-1755)aGg>aAg	p.R585K	NLRP8_ENST00000590542.1_Missense_Mutation_p.R585K	NM_176811.2	NP_789781.2	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8			35		Colorectal(82;0.000147)|Ovarian(87;0.17)			GGTAATAAGAGGAAACTGCTG	0.498000																								0							SO:0001583	missense			ENST00000291971.3	1	1	hg19	CCDS12937.1	.	.	.	.	.	.	.	.	.	.	G	0.011	-1.716604	0.00706	.	.	ENSG00000179709	ENST00000291971	D	0.88431	-2.38	2.03	-3.26	0.05064	.	.	.	.	.	T	0.70649	0.3248	N	0.08118	0	0.09310	N	1	B;B	0.20780	0.036;0.048	B;B	0.13407	0.007;0.009	T	0.56703	-0.7935	9	0.18710	T	0.47	.	4.4176	0.11465	0.2921:0.221:0.4869:0.0	.	585;585	Q86W28-2;Q86W28	.;NALP8_HUMAN	K	585	ENSP00000291971:R585K	ENSP00000291971:R585K	R	+	2	0	NLRP8	61158990	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-0.103000	0.10940	-1.059000	0.03193	-0.507000	0.04495	AGG		TCGA-US-A77E-01A-11D-A32N-08	NLRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457462.1	1	0	1	31	168	0	45		0	0	0	0	45	2		0	0	0	0	0	2	1	1.000000	31	167	0	45	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	1	2	3	2.011441	0	0.390000	2.070000	0.397054	0.810000	5.700000e-01	1.000000	1.000000	0.821973	0.810000	0	0.680000	0.980000
MED16	10025	broad.mit.edu	37	19	868430	868430	+	Nonsense_Mutation	SNP	C	C	T			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr19:868430C>T	ENST00000589119.1	-	14	2468	c.2469G>A	c.(2467-2469)tgG>tgA	p.W823*	MED16_ENST00000395808.3_Nonsense_Mutation_p.W823*|MED16_ENST00000269814.4_3'UTR|MED16_ENST00000312090.6_Nonsense_Mutation_p.W842*|MED16_ENST00000325464.1_Nonsense_Mutation_p.W823*			Q9Y2X0	MED16_HUMAN	mediator complex subunit 16			21		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)			AGTTCTTGATCCAGCGCTGCT	0.667000																								0							SO:0001587	stop_gained			ENST00000589119.1	0	1	hg19	CCDS12047.1	.	.	.	.	.	.	.	.	.	.	C	40	8.283552	0.98742	.	.	ENSG00000175221	ENST00000325464;ENST00000312090;ENST00000395808	.	.	.	4.27	4.27	0.50696	.	0.000000	0.64402	D	0.000006	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-18.7101	15.6761	0.77326	0.0:1.0:0.0:0.0	.	.	.	.	X	823;842;823	.	ENSP00000308528:W842X	W	-	3	0	MED16	819430	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	7.266000	0.78452	1.941000	0.56285	0.511000	0.50034	TGG		TCGA-US-A77E-01A-11D-A32N-08	MED16-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457902.3	1	0	0	13	147	0	37	1	9.999975e-01	99	204	0	37	2		0	0	0	0	0	2	1	0.999589	13	146	0	37	2	0	0	0	0	0	0		-18.449790	1	1	0	0		1	1	2	3	2.013232	0	0.390000	2.070000	0.397054	0.430000	2.400000e-01	1.000000	0.410000	0.470238	0.430000	0	0.330000	0.580000
NES	10763	broad.mit.edu	37	1	156639754	156639754	+	Missense_Mutation	SNP	G	G	T			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr1:156639754G>T	ENST00000368223.3	-	4	4358	c.4226C>A	c.(4225-4227)tCc>tAc	p.S1409Y		NM_006617.1	NP_006608.1	P48681	NEST_HUMAN	nestin			64	all_hematologic(923;0.088)|Hepatocellular(266;0.158)				AAACCCATCGGACTCCCCATC	0.647000																								0							SO:0001583	missense			ENST00000368223.3	1	1	hg19	CCDS1151.1	.	.	.	.	.	.	.	.	.	.	G	16.79	3.219120	0.58560	.	.	ENSG00000132688	ENST00000368223	D	0.93811	-3.29	4.46	4.46	0.54185	.	0.000000	0.32640	N	0.005837	D	0.94215	0.8143	M	0.66939	2.045	0.26797	N	0.969277	D	0.76494	0.999	D	0.71184	0.972	D	0.89006	0.3425	10	0.87932	D	0	.	11.8552	0.52433	0.0:0.0:0.8245:0.1755	.	1409	P48681	NEST_HUMAN	Y	1409	ENSP00000357206:S1409Y	ENSP00000357206:S1409Y	S	-	2	0	NES	154906378	0.996000	0.38824	1.000000	0.80357	0.933000	0.57130	3.567000	0.53813	2.316000	0.78162	0.557000	0.71058	TCC		TCGA-US-A77E-01A-11D-A32N-08	NES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082844.2	1	0	0	11	176	0	54	0	7.919837e-01	0	49	0	54	2		0	0	0	0	0	2	1	0.998442	11	175	0	53	2	0	0	0	0	0	0		-14.998890	1	1	0	0		1	1	2	3	2.005218	0	0.390000	2.070000	0.395890	0.310000	1.600000e-01	1.000000	0.300000	0.351699	0.310000	0	0.230000	0.430000
GABRD	2563	broad.mit.edu	37	1	1961076	1961076	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr1:1961076G>A	ENST00000378585.4	+	8	1017	c.934G>A	c.(934-936)Gtc>Atc	p.V312I		NM_000815.4	NP_000806.2	O14764	GBRD_HUMAN	gamma-aminobutyric acid (GABA) A receptor, delta			20	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;2.7e-19)|all_lung(118;1.22e-08)|Lung NSC(185;1.24e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	GGCACTGGACGTCTACTTCTG	0.592000																								0							SO:0001583	missense			ENST00000378585.4	1	1	hg19	CCDS36.1	.	.	.	.	.	.	.	.	.	.	G	8.302	0.820039	0.16678	.	.	ENSG00000187730	ENST00000378585	D	0.85773	-2.03	4.0	4.0	0.46444	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.145269	0.46145	D	0.000310	D	0.85969	0.5821	L	0.36672	1.1	0.58432	D	0.999996	D	0.76494	0.999	D	0.79784	0.993	T	0.80984	-0.1138	10	0.02654	T	1	-16.1297	15.6431	0.77025	0.0:0.0:1.0:0.0	.	312	O14764	GBRD_HUMAN	I	312	ENSP00000367848:V312I	ENSP00000367848:V312I	V	+	1	0	GABRD	1950936	1.000000	0.71417	0.994000	0.49952	0.343000	0.28985	9.302000	0.96175	2.239000	0.73571	0.561000	0.74099	GTC		TCGA-US-A77E-01A-11D-A32N-08	GABRD-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098493.1	1	0	1	36	189	0	40	0	3.828524e-01	0	8	0	40	2		0	0	0	0	0	2	1	1.000000	36	189	0	40	2	0	0	0	0	0	0		-20.000000	1	1	121328	17	42	1	1	2	3	2.026464	0	0.390000	2.070000	0.399370	0.840000	6.000000e-01	1.000000	1.000000	0.846143	0.840000	0	0.710000	1.000000
CELA3A	10136	broad.mit.edu	37	1	22329556	22329556	+	Missense_Mutation	SNP	C	C	T			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr1:22329556C>T	ENST00000290122.3	+	2	123	c.104C>T	c.(103-105)gCg>gTg	p.A35V	RN7SL768P_ENST00000584415.1_RNA|CELA3A_ENST00000374663.1_Missense_Mutation_p.A35V	NM_005747.4	NP_005738.4	P09093	CEL3A_HUMAN	chymotrypsin-like elastase family, member 3A	p.A35V(1)		18					GGTGAGGATGCGGTCCCCTAC	0.612000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000290122.3	0	1	hg19	CCDS220.1	.	.	.	.	.	.	.	.	.	.	C	18.75	3.689677	0.68271	.	.	ENSG00000142789	ENST00000290122;ENST00000374663;ENST00000374661	T;D	0.94417	2.07;-3.42	3.47	2.54	0.30619	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	D	0.92639	0.7661	L	0.48260	1.515	0.43756	D	0.996263	D	0.71674	0.998	P	0.52627	0.704	D	0.89403	0.3697	9	0.39692	T	0.17	-25.4813	6.7714	0.23596	0.0:0.8655:0.0:0.1345	.	35	P09093	CEL3A_HUMAN	V	35;35;51	ENSP00000290122:A35V;ENSP00000363795:A35V	ENSP00000290122:A35V	A	+	2	0	CELA3A	22202143	0.996000	0.38824	0.042000	0.18584	0.880000	0.50808	3.389000	0.52516	0.781000	0.33589	0.400000	0.26472	GCG		TCGA-US-A77E-01A-11D-A32N-08	CELA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007791.1	0	0	0	5	444	0	91	0	1.207299e-03	0	4	0	91	2		0	0	0	0	0	2	1	0.931308	5	427	0	91	2	0	0	0	0	0	0		-2.066993	0	1	119974	1	32	1	1	2	3	2.014975	0	0.390000	2.070000	0.397054	0.060000	1.000000e-02	1.000000	0.060000	0.112506	0.060000	0	0.030000	0.100000
CNIH3	149111	broad.mit.edu	37	1	224868727	224868727	+	Splice_Site	SNP	C	C	T			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr1:224868727C>T	ENST00000272133.3	+	2	1031	c.149C>T	c.(148-150)gCg>gTg	p.A50V		NM_152495.1	NP_689708.1	Q8TBE1	CNIH3_HUMAN	cornichon family AMPA receptor auxiliary protein 3			9	Breast(184;0.218)				CCTGTTCATGCGGTAAGTGGC	0.473000																								0							SO:0001630	splice_region_variant			ENST00000272133.3	1	0	hg19	CCDS1544.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.386315	0.82902	.	.	ENSG00000143786	ENST00000272133	.	.	.	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	T	0.67268	0.2875	L	0.29908	0.895	0.53688	D	0.999979	D	0.89917	1.0	D	0.91635	0.999	T	0.69800	-0.5047	9	0.59425	D	0.04	-0.2012	17.7753	0.88505	0.0:1.0:0.0:0.0	.	50	Q8TBE1	CNIH3_HUMAN	V	50	.	ENSP00000272133:A50V	A	+	2	0	CNIH3	222935350	1.000000	0.71417	1.000000	0.80357	0.835000	0.47333	5.322000	0.65852	2.504000	0.84457	0.551000	0.68910	GCG		TCGA-US-A77E-01A-11D-A32N-08	CNIH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091752.2	1	0	1	53	297	1	97	0	4.662368e-01	0	10	1	97	2		0	0	0	0	0	2	1	1.000000	50	291	1	97	13	0	0	0	0	0	0		-3.022584	1	1	121412	3	37	1	1	2	3	1.991274	0	0.390000	2.070000	0.392370	0.770000	5.900000e-01	1.000000	0.780000	0.787582	0.770000	0	0.680000	0.890000
PTCH2	8643	broad.mit.edu	37	1	45294946	45294946	+	Silent	SNP	G	G	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr1:45294946G>A	ENST00000372192.3	-	10	1384	c.1254C>T	c.(1252-1254)tgC>tgT	p.C418C	PTCH2_ENST00000447098.2_Silent_p.C418C	NM_003738.4	NP_003729.3	Q9Y6C5	PTC2_HUMAN	patched 2			50	Acute lymphoblastic leukemia(166;0.155)				GGGACTGGGCGCAGTCCCACC	0.687000									Basal Cell Nevus syndrome															0							SO:0001819	synonymous_variant	Familial Cancer Database	Gorlin syndrome, Gorlin-Golz syndrome, Naevoid Basal Cell Carcinoma syndrome, NBCCS	ENST00000372192.3	0	1	hg19	CCDS516.1																																																																																				TCGA-US-A77E-01A-11D-A32N-08	PTCH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023428.4	0	0	0	5	237	0	54	0	4.035170e-03	0	4	0	54	2		0	0	0	0	0	2	1	0.936124	5	234	0	52	2	0	0	0	0	0	0		-6.115855	1	1	121380	1	28	1	1	2	3	2.014431	0	0.390000	2.070000	0.397054	0.110000	4.000000e-02	1.000000	0.110000	0.167791	0.110000	0	0.070000	0.190000
INSM1	3642	broad.mit.edu	37	20	20350394	20350394	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr20:20350394G>A	ENST00000310227.1	+	1	1630	c.1483G>A	c.(1483-1485)Gaa>Aaa	p.E495K		NM_002196.2	NP_002187.1	Q01101	INSM1_HUMAN	insulinoma-associated 1			6					CCACCCATCCGAAAACAGACA	0.672000																								0							SO:0001583	missense			ENST00000310227.1	1	1	hg19	CCDS13143.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.524404	0.85600	.	.	ENSG00000173404	ENST00000310227	T	0.00856	5.61	5.41	5.41	0.78517	Zinc finger, C2H2 (1);	0.000000	0.64402	U	0.000001	T	0.01661	0.0053	M	0.61703	1.905	0.51482	D	0.999923	D	0.58620	0.983	B	0.39660	0.306	T	0.61589	-0.7032	10	0.87932	D	0	-11.8587	14.4248	0.67207	0.0729:0.0:0.9271:0.0	.	495	Q01101	INSM1_HUMAN	K	495	ENSP00000312631:E495K	ENSP00000312631:E495K	E	+	1	0	INSM1	20298394	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.963000	0.87922	2.522000	0.85027	0.650000	0.86243	GAA		TCGA-US-A77E-01A-11D-A32N-08	INSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078223.1	1	0	1	31	186	0	37	0	2.191781e-02	0	2	0	37	2		0	0	0	0	0	2	1	1.000000	31	183	0	36	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	1	2	3	2.336157	1	0.390000	2.070000	0.487868	0.870000	6.100000e-01	1.000000	1.000000	0.869705	0.870000	1	0.730000	1.000000
NNAT	4826	broad.mit.edu	37	20	36149750	36149750	+	Missense_Mutation	SNP	C	C	G			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr20:36149750C>G	ENST00000062104.2	+	1	134	c.17C>G	c.(16-18)gCg>gGg	p.A6G	BLCAP_ENST00000397131.1_Intron|BLCAP_ENST00000397135.1_Intron|BLCAP_ENST00000373537.2_Intron|BLCAP_ENST00000414542.2_5'UTR|NNAT_ENST00000346199.2_Missense_Mutation_p.A6G|BLCAP_ENST00000397137.1_Intron|BLCAP_ENST00000397134.1_5'Flank	NM_005386.2	NP_005377.1	Q16517	NNAT_HUMAN	neuronatin			3		Myeloproliferative disorder(115;0.00878)			GCAGTGGCGGCGGCCTCGGCT	0.627000																								0							SO:0001583	missense			ENST00000062104.2	1	1	hg19	CCDS13296.1	.	.	.	.	.	.	.	.	.	.	C	16.19	3.052781	0.55218	.	.	ENSG00000053438	ENST00000062104;ENST00000346199	.	.	.	4.59	4.59	0.56863	.	0.000000	0.48767	D	0.000176	T	0.71600	0.3359	.	.	.	0.33830	D	0.630072	D;D	0.61080	0.989;0.989	D;D	0.64237	0.923;0.923	T	0.80132	-0.1510	8	0.87932	D	0	-8.0572	13.2076	0.59807	0.0:1.0:0.0:0.0	.	6;6	Q16517-2;Q16517	.;NNAT_HUMAN	G	6	.	ENSP00000062104:A6G	A	+	2	0	NNAT	35583164	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	2.991000	0.49409	2.836000	0.97738	0.655000	0.94253	GCG		TCGA-US-A77E-01A-11D-A32N-08	NNAT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079116.2	0	0	0	34	1244	0	283	0	1.065260e-02	1	5	0	283	2		0	0	0	0	0	2	1	1.000000	31	1207	0	281	2	0	0	0	0	0	0		-1.905460	0	1	0	0		1	1	2	3	2.336157	1	0.390000	2.070000	0.487868	0.160000	1.000000e-01	0.240000	0.160000	0.175047	0.160000	0	0.130000	0.200000
PREX1	57580	broad.mit.edu	37	20	47324917	47324917	+	Missense_Mutation	SNP	C	C	T			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr20:47324917C>T	ENST00000371941.3	-	6	686	c.664G>A	c.(664-666)Gcg>Acg	p.A222T	PREX1_ENST00000396220.1_Missense_Mutation_p.A222T	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1			110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)		CTCTGGACCGCGGGGTGGTCT	0.582000																								0							SO:0001583	missense			ENST00000371941.3	1	1	hg19	CCDS13410.1	.	.	.	.	.	.	.	.	.	.	C	15.89	2.965570	0.53507	.	.	ENSG00000124126	ENST00000371941;ENST00000396220	T;T	0.64085	-0.08;-0.08	5.64	5.64	0.86602	Dbl homology (DH) domain (5);	0.000000	0.53938	U	0.000049	T	0.65575	0.2704	L	0.40543	1.245	0.41921	D	0.990515	D	0.55800	0.973	P	0.51777	0.679	T	0.61337	-0.7083	10	0.29301	T	0.29	.	19.7013	0.96054	0.0:1.0:0.0:0.0	.	222	Q8TCU6	PREX1_HUMAN	T	222	ENSP00000361009:A222T;ENSP00000379522:A222T	ENSP00000361009:A222T	A	-	1	0	PREX1	46758324	1.000000	0.71417	0.163000	0.22734	0.196000	0.23810	4.780000	0.62382	2.657000	0.90304	0.655000	0.94253	GCG		TCGA-US-A77E-01A-11D-A32N-08	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	1	0	1	176	1040	0	233	0	3.275801e-01	0	8	0	233	2		0	0	0	0	0	2	1	1.000000	174	1017	0	227	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	1	2	3	2.336157	1	0.390000	2.070000	0.487868	0.880000	7.600000e-01	1.000000	0.890000	0.886949	0.880000	1	0.810000	0.950000
GNAS	2778	broad.mit.edu	37	20	57484421	57484421	+	Missense_Mutation	SNP	G	G	A	rs121913495		TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr20:57484421G>A	ENST00000371085.3	+	8	1026	c.602G>A	c.(601-603)cGt>cAt	p.R201H	GNAS_ENST00000313949.7_3'UTR|GNAS_ENST00000371075.3_3'UTR|GNAS_ENST00000265620.7_Missense_Mutation_p.R186H|GNAS_ENST00000371102.4_Missense_Mutation_p.R830H|GNAS_ENST00000354359.7_Missense_Mutation_p.R202H|GNAS_ENST00000371095.3_Missense_Mutation_p.R187H|GNAS_ENST00000306090.10_Missense_Mutation_p.R187H|GNAS_ENST00000464624.2_3'UTR|GNAS_ENST00000371100.4_Missense_Mutation_p.R844H	NM_000516.4	NP_000507.1	P63092	GNAS2_HUMAN	GNAS complex locus	p.R201H(81)|p.R844H(4)|p.R201L(2)|p.R844L(1)		441	all_lung(29;0.0104)		BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109)		CTTCGCTGCCGTGTCCTGACT	0.423000			Mis		pituitary adenoma		McCune-Albright syndrome; pseudohypoparathyroidism, type IA			TSP Lung(22;0.16)			Colon(117;935 1597 6045 8307 46442)		Dom	yes		20	20q13.2	2778	guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1	yes	E	88	Substitution - Missense(88)						SO:0001583	missense			ENST00000371085.3	1	1	hg19	CCDS13472.1	.	.	.	.	.	.	.	.	.	.	G	35	5.430570	0.96150	.	.	ENSG00000087460	ENST00000371100;ENST00000371102;ENST00000371095;ENST00000371085;ENST00000354359;ENST00000265620;ENST00000306090	D;D;D;D;D;D;D	0.99458	-5.93;-5.93;-5.93;-5.93;-5.93;-2.96;-5.93	5.53	5.53	0.82687	G protein alpha subunit, helical insertion (2);	0.000000	0.85682	D	0.000000	D	0.99799	0.9914	H	0.98965	4.385	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.997;0.994;0.983;1.0	D	0.96812	0.9597	10	0.87932	D	0	.	19.4606	0.94915	0.0:0.0:1.0:0.0	.	201;202;186;844	P63092;A6NI00;P63092-3;Q5JWF2	GNAS2_HUMAN;.;.;GNAS1_HUMAN	H	844;830;187;201;202;186;187	ENSP00000360141:R844H;ENSP00000360143:R830H;ENSP00000360136:R187H;ENSP00000360126:R201H;ENSP00000346328:R202H;ENSP00000265620:R186H;ENSP00000304472:R187H	ENSP00000265620:R186H	R	+	2	0	GNAS	56917816	1.000000	0.71417	0.963000	0.40424	0.936000	0.57629	9.291000	0.96070	2.596000	0.87737	0.563000	0.77884	CGT		TCGA-US-A77E-01A-11D-A32N-08	GNAS-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080431.2	1	0	1	113	255	0	51	1	1	1287	1966	0	51	2	1	1	229	556	0	408	2	1	1.000000	111	252	0	50	2	0	0	0	0	0	0		-9.037880	1	1	121412	10	32	1	1	2	3	2.336157	1	0.390000	2.070000	0.487868	0.990000	9.900000e-01	1.000000	1.000000	1.000000	0.990000	1	0.990000	1.000000
U2AF1	7307	broad.mit.edu	37	21	44524456	44524456	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr21:44524456G>A	ENST00000291552.4	-	2	193	c.101C>T	c.(100-102)tCt>tTt	p.S34F	U2AF1_ENST00000459639.1_5'UTR|U2AF1_ENST00000398137.1_5'UTR|U2AF1_ENST00000486519.1_5'UTR|U2AF1_ENST00000380276.2_Missense_Mutation_p.S34F	NM_006758.2	NP_006749.1	Q01081	U2AF1_HUMAN	U2 small nuclear RNA auxiliary factor 1	p.S34F(45)|p.S34Y(12)		126					GTGCAACCGAGAGCACCTGTC	0.358000			Mis		CLL, MDS										Dom	yes		21	21q22.3	7307	U2 small nuclear RNA auxiliary factor 1		L	57	Substitution - Missense(57)						SO:0001583	missense			ENST00000291552.4	1	1	hg19	CCDS13694.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.025187	0.93518	2.27E-4	0.0	ENSG00000160201	ENST00000380276;ENST00000291552	T;T	0.46063	0.88;0.88	5.47	5.47	0.80525	Zinc finger, CCCH-type (3);	0.000000	0.85682	D	0.000000	T	0.77239	0.4101	H	0.96430	3.82	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.997;0.997	D	0.84864	0.0821	10	0.87932	D	0	-15.7954	19.3169	0.94218	0.0:0.0:1.0:0.0	.	34;34;34	Q69YM7;Q01081;Q701P4	.;U2AF1_HUMAN;.	F	34	ENSP00000369629:S34F;ENSP00000291552:S34F	ENSP00000291552:S34F	S	-	2	0	U2AF1	43397525	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.864000	0.92294	2.560000	0.86352	0.563000	0.77884	TCT		TCGA-US-A77E-01A-11D-A32N-08	U2AF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195541.1	1	0	1	32	166	0	43	1	1	85	202	0	43	2	1	1	102	444	0	283	2	1	1.000000	31	164	0	43	2	0	0	0	0	0	0		-3.186309	1	1	121412	5	36	1	1	2	3	1.980002	0	0.390000	2.070000	0.391187	0.830000	5.900000e-01	1.000000	1.000000	0.832257	0.830000	0	0.700000	0.970000
COL6A2	1292	broad.mit.edu	37	21	47552344	47552344	+	Missense_Mutation	SNP	G	G	A	rs140020002		TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08			G	A	G	G		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr21:47552344G>A	ENST00000300527.4	+	28	3042	c.2938G>A	c.(2938-2940)Gtg>Atg	p.V980M		NM_001849.3	NP_001840.3	P12110	CO6A2_HUMAN	collagen, type VI, alpha 2			43	Breast(49;0.245)				GGGCAGCGACGTGGACATGGA	0.662000																								0							SO:0001583	missense			ENST00000300527.4	1	1	hg19	CCDS13728.1	.	.	.	.	.	.	.	.	.	.	G	11.70	1.717812	0.30413	4.54E-4	0.0	ENSG00000142173	ENST00000300527	T	0.80393	-1.37	4.4	4.4	0.53042	von Willebrand factor, type A (3);	0.388276	0.26069	N	0.026522	D	0.86887	0.6041	M	0.68317	2.08	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	D	0.87150	0.2208	10	0.56958	D	0.05	-16.4704	10.6536	0.45663	0.0893:0.0:0.9107:0.0	.	980	P12110	CO6A2_HUMAN	M	980	ENSP00000300527:V980M	ENSP00000300527:V980M	V	+	1	0	COL6A2	46376772	1.000000	0.71417	0.994000	0.49952	0.290000	0.27261	5.117000	0.64667	2.001000	0.58596	0.297000	0.19635	GTG		TCGA-US-A77E-01A-11D-A32N-08	COL6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206971.1	1	0	1	37	120	0	48	0	1	1	3128	0	48	2		0	0	0	0	0	2	1	1.000000	37	118	0	47	2	0	0	0	0	0	0		-20.000000	1	1	121176	9	40	1	1	2	3	1.980002	0	0.390000	2.070000	0.391187	0.990000	8.900000e-01	1.000000	1.000000	0.992813	0.990000	1	0.990000	1.000000
MCM3AP	8888	broad.mit.edu	37	21	47664991	47664991	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr21:47664991G>A	ENST00000397708.1	-	24	5022	c.4768C>T	c.(4768-4770)Cat>Tat	p.H1590Y	MCM3AP-AS1_ENST00000444998.1_RNA|MCM3AP-AS1_ENST00000432735.1_RNA|MCM3AP-AS1_ENST00000591223.1_RNA|MCM3AP-AS1_ENST00000455567.1_RNA|MCM3AP-AS1_ENST00000421927.1_RNA|MCM3AP_ENST00000291688.1_Missense_Mutation_p.H1590Y|MCM3AP-AS1_ENST00000588753.1_RNA|AP001469.7_ENST00000444966.1_RNA|MCM3AP_ENST00000467026.1_5'UTR|MCM3AP-AS1_ENST00000414659.1_RNA|MCM3AP-AS1_ENST00000590829.1_RNA			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein			72	Breast(49;0.112)				CTTCTGTCATGGAAAAAGCGG	0.552000																								0							SO:0001583	missense			ENST00000397708.1	1	1	hg19	CCDS13734.1	.	.	.	.	.	.	.	.	.	.	G	8.432	0.848790	0.17034	.	.	ENSG00000160294	ENST00000397708;ENST00000291688;ENST00000539647	T;T	0.03272	3.99;3.99	5.45	4.37	0.52481	.	0.551176	0.21218	N	0.078193	T	0.04182	0.0116	L	0.31294	0.92	0.31865	N	0.620481	B;B	0.06786	0.001;0.001	B;B	0.10450	0.001;0.005	T	0.06789	-1.0807	10	0.39692	T	0.17	-10.1882	15.096	0.72235	0.0801:0.0:0.9199:0.0	.	1590;85	O60318;B3KT88	MCM3A_HUMAN;.	Y	1590;1590;85	ENSP00000380820:H1590Y;ENSP00000291688:H1590Y	ENSP00000291688:H1590Y	H	-	1	0	MCM3AP	46489419	0.996000	0.38824	0.984000	0.44739	0.846000	0.48090	2.460000	0.45031	2.545000	0.85829	0.655000	0.94253	CAT		TCGA-US-A77E-01A-11D-A32N-08	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1	1	0	1	53	262	0	52	1	9.999926e-01	28	61	0	52	2		0	0	0	0	0	2	1	1.000000	53	258	0	50	2	0	0	0	0	0	0		-3.055940	1	1	0	0		1	1	2	3	1.980002	0	0.390000	2.070000	0.391187	0.860000	6.600000e-01	1.000000	1.000000	0.864055	0.860000	1	0.750000	0.980000
ST6GAL2	84620	broad.mit.edu	37	2	107450522	107450522	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr2:107450522G>A	ENST00000409382.3	-	3	1634	c.1024C>T	c.(1024-1026)Cgc>Tgc	p.R342C	ST6GAL2_ENST00000409087.3_Missense_Mutation_p.R342C|AC016994.2_ENST00000425419.1_RNA|ST6GAL2_ENST00000361686.4_Missense_Mutation_p.R342C	NM_001142351.1	NP_001135823.1	Q96JF0	SIAT2_HUMAN	ST6 beta-galactosamide alpha-2,6-sialyltranferase 2	p.R342C(1)		65					TTAATGATGCGTATGGTGGTT	0.393000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000409382.3	1	1	hg19	CCDS2073.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.606524	0.87157	.	.	ENSG00000144057	ENST00000361686;ENST00000409382;ENST00000409087	T;T;T	0.78924	-1.22;-1.22;-1.22	6.03	6.03	0.97812	Glycoside hydrolase/deacetylase, beta/alpha-barrel (1);	0.000000	0.85682	D	0.000000	D	0.92740	0.7692	H	0.96604	3.85	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.94296	0.7533	10	0.87932	D	0	-37.1524	19.545	0.95291	0.0:0.0:1.0:0.0	.	342;342	Q96JF0-2;Q96JF0	.;SIAT2_HUMAN	C	342	ENSP00000355273:R342C;ENSP00000386942:R342C;ENSP00000387332:R342C	ENSP00000355273:R342C	R	-	1	0	ST6GAL2	106816954	1.000000	0.71417	0.990000	0.47175	0.813000	0.45954	9.869000	0.99810	2.861000	0.98227	0.655000	0.94253	CGC		TCGA-US-A77E-01A-11D-A32N-08	ST6GAL2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330065.1	1	0	1	67	327	0	64	0	0	0	1	0	64	2		0	0	0	0	0	2	1	1.000000	66	319	0	63	2	0	0	0	0	0	0		-20.000000	1	1	121412	2	40	1	1	2	3	1.974951	0	0.390000	2.070000	0.391187	0.870000	6.900000e-01	1.000000	1.000000	0.873282	0.870000	1	0.770000	0.980000
POLR1B	84172	broad.mit.edu	37	2	113322044	113322044	+	Missense_Mutation	SNP	C	C	T			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr2:113322044C>T	ENST00000263331.5	+	10	2294	c.1714C>T	c.(1714-1716)Cca>Tca	p.P572S	POLR1B_ENST00000537335.1_Missense_Mutation_p.P361S|POLR1B_ENST00000541869.1_Missense_Mutation_p.P610S|POLR1B_ENST00000409894.3_Intron|POLR1B_ENST00000417433.2_Missense_Mutation_p.P516S	NM_019014.4	NP_061887.2	Q9H9Y6	RPA2_HUMAN	polymerase (RNA) I polypeptide B, 128kDa			42					GGATCTTGCTCCAGGCATCGC	0.498000													Ovarian(16;256 576 9537 23969 41147)											0							SO:0001583	missense			ENST00000263331.5	1	1	hg19	CCDS2097.1	.	.	.	.	.	.	.	.	.	.	C	8.254	0.809758	0.16537	.	.	ENSG00000125630	ENST00000263331;ENST00000541869;ENST00000537335;ENST00000417433;ENST00000458012	T;T;T;T;T	0.75477	-0.94;-0.94;-0.94;-0.94;-0.51	5.83	3.97	0.46021	RNA polymerase I, Rpa2 specific (1);	0.150076	0.64402	D	0.000009	T	0.68274	0.2983	L	0.43152	1.355	0.58432	D	0.999992	B;B;B	0.25105	0.118;0.0;0.094	B;B;B	0.33254	0.108;0.003;0.16	T	0.59306	-0.7479	10	0.12766	T	0.61	-13.5536	15.3557	0.74425	0.0:0.7349:0.265:0.0	.	610;516;572	F5GZX4;Q9H9Y6-2;Q9H9Y6	.;.;RPA2_HUMAN	S	572;610;361;516;36	ENSP00000263331:P572S;ENSP00000444136:P610S;ENSP00000437914:P361S;ENSP00000405358:P516S;ENSP00000394408:P36S	ENSP00000263331:P572S	P	+	1	0	POLR1B	113038515	1.000000	0.71417	0.534000	0.28014	0.274000	0.26718	3.052000	0.49893	0.738000	0.32606	0.650000	0.86243	CCA		TCGA-US-A77E-01A-11D-A32N-08	POLR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254083.1	1	0	1	92	458	0	107	1	8.025777e-01	4	13	0	107	2		0	0	0	0	0	2	1	1.000000	91	452	0	104	2	0	0	0	0	0	0		-3.087977	1	1	0	0		1	1	2	3	1.974951	0	0.390000	2.070000	0.391187	0.850000	7.000000e-01	1.000000	1.000000	0.861290	0.850000	1	0.770000	0.940000
ZEB2	9839	broad.mit.edu	37	2	145162490	145162490	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr2:145162490G>A	ENST00000558170.2	-	5	1689	c.505C>T	c.(505-507)Cgc>Tgc	p.R169C	ZEB2_ENST00000303660.4_Missense_Mutation_p.R169C|ZEB2_ENST00000409487.3_Missense_Mutation_p.R169C|ZEB2_ENST00000539609.3_Missense_Mutation_p.R145C	NM_014795.3	NP_055610.1	O60315	ZEB2_HUMAN	zinc finger E-box binding homeobox 2			107					GTGTCACTGCGCTGAAGGTAC	0.493000													Melanoma(33;1235 1264 5755 16332)											0							SO:0001583	missense			ENST00000558170.2	1	1	hg19	CCDS2186.1	.	.	.	.	.	.	.	.	.	.	G	17.85	3.489988	0.64074	.	.	ENSG00000169554	ENST00000392860;ENST00000539609;ENST00000303660;ENST00000409487;ENST00000427902;ENST00000392861	T;T;T;T;T	0.77358	-1.09;-1.09;-1.09;-1.09;-1.09	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	D	0.86560	0.5962	L	0.54323	1.7	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.77004	0.989;0.948;0.948;0.948	D	0.86852	0.2024	10	0.87932	D	0	-8.3326	20.0114	0.97452	0.0:0.0:1.0:0.0	.	145;34;168;169	F5H814;Q53TD9;A0JP08;O60315	.;.;.;ZEB2_HUMAN	C	164;145;169;169;169;169	ENSP00000443792:R145C;ENSP00000302501:R169C;ENSP00000386854:R169C;ENSP00000395496:R169C;ENSP00000376601:R169C	ENSP00000302501:R169C	R	-	1	0	ZEB2	144878960	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.820000	0.86633	2.795000	0.96236	0.655000	0.94253	CGC		TCGA-US-A77E-01A-11D-A32N-08	ZEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254778.5	1	0	1	31	154	0	44	0	6.696461e-01	0	13	0	44	2		0	0	0	0	0	2	1	1.000000	31	152	0	44	2	0	0	0	0	0	0		-20.000000	1	1	121412	1	26	1	1	2	3	1.974951	0	0.390000	2.070000	0.391187	0.860000	6.000000e-01	1.000000	1.000000	0.856880	0.860000	1	0.720000	1.000000
TTN	7273	broad.mit.edu	37	2	179466769	179466769	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr2:179466769G>A	ENST00000591111.1	-	234	50530	c.50306C>T	c.(50305-50307)tCa>tTa	p.S16769L	TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.S15842L|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.S9345L|TTN_ENST00000589042.1_Missense_Mutation_p.S18410L|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.S9537L|TTN_ENST00000359218.5_Missense_Mutation_p.S9470L|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin			1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)		TTCCCAAGATGATTTTGGTGT	0.403000																								0							SO:0001583	missense			ENST00000591111.1	1	1	hg19		.	.	.	.	.	.	.	.	.	.	G	14.36	2.512432	0.44660	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.64618	-0.11;-0.11;-0.11;-0.11	6.07	6.07	0.98685	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.50803	0.1637	N	0.11789	0.175	0.34748	D	0.731475	B;B;B;B	0.28128	0.101;0.101;0.201;0.101	B;B;B;B	0.28385	0.089;0.089;0.089;0.089	T	0.59778	-0.7390	9	0.87932	D	0	.	20.6593	0.99626	0.0:0.0:1.0:0.0	.	9345;9470;9537;16769	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	L	15842;9345;9537;9470;9345	ENSP00000343764:S15842L;ENSP00000434586:S9345L;ENSP00000340554:S9537L;ENSP00000352154:S9470L	ENSP00000340554:S9537L	S	-	2	0	TTN	179175014	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.331000	0.79192	2.885000	0.99019	0.655000	0.94253	TCA		TCGA-US-A77E-01A-11D-A32N-08	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	1	0	1	85	363	0	84		0	0	0	0	84	2		0	0	0	0	0	2	1	1.000000	82	361	0	84	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	1	2	3	1.974951	0	0.390000	2.070000	0.391187	0.970000	7.900000e-01	1.000000	1.000000	0.950199	0.970000	1	0.870000	1.000000
COL5A2	1290	broad.mit.edu	37	2	189929337	189929337	+	Silent	SNP	T	T	C			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08			T	C	T	T		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr2:189929337T>C	ENST00000374866.3	-	25	1936	c.1662A>G	c.(1660-1662)aaA>aaG	p.K554K		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)		CCTGGCTTCCTTTGGGTCCTG	0.507000																								0							SO:0001819	synonymous_variant			ENST00000374866.3	1	1	hg19	CCDS33350.1																																																																																				TCGA-US-A77E-01A-11D-A32N-08	COL5A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313523.1	1	0	0	46	300	0	63	0	1	0	283	0	63	2		0	0	0	0	0	2	1	1.000000	46	295	0	63	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	1	2	3	1.974951	0	0.390000	2.070000	0.391187	0.680000	5.100000e-01	0.880000	0.680000	0.690797	0.680000	0	0.590000	0.780000
DOCK10	55619	broad.mit.edu	37	2	225651759	225651759	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr2:225651759G>A	ENST00000258390.7	-	50	5702	c.5635C>T	c.(5635-5637)Cgt>Tgt	p.R1879C	DOCK10_ENST00000409592.3_Missense_Mutation_p.R1873C	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10			87		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)			AATGCCACACGATAGTAGCGA	0.433000																								0							SO:0001583	missense			ENST00000258390.7	1	1	hg19	CCDS46528.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	22.1|22.1	4.238466|4.238466	0.79800|0.79800	.|.	.|.	ENSG00000135905|ENSG00000135905	ENST00000409592;ENST00000258390;ENST00000373702|ENST00000535663	T;T|.	0.32988|.	1.43;1.43|.	5.99|5.99	5.09|5.09	0.68999|0.68999	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.85483|0.85483	0.5707|0.5707	M|M	0.93507|0.93507	3.425|3.425	0.58432|0.58432	D|D	0.999999|0.999999	D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0|.	D;D;D;D|.	0.97110|.	0.994;1.0;0.991;0.997|.	D|D	0.89507|0.89507	0.3768|0.3768	10|5	0.87932|.	D|.	0|.	.|.	15.2244|15.2244	0.73339|0.73339	0.0:0.0:0.7376:0.2624|0.0:0.0:0.7376:0.2624	.|.	1879;700;1873;541|.	Q96BY6;B4DF07;B3FL70;B4DEY4|.	DOC10_HUMAN;.;.;.|.	C|L	1873;1879;384|26	ENSP00000386694:R1873C;ENSP00000258390:R1879C|.	ENSP00000258390:R1879C|.	R|S	-|-	1|2	0|0	DOCK10|DOCK10	225360003|225360003	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.996000|0.996000	0.88848|0.88848	4.329000|4.329000	0.59260|0.59260	1.477000|1.477000	0.48234|0.48234	0.655000|0.655000	0.94253|0.94253	CGT|TCG		TCGA-US-A77E-01A-11D-A32N-08	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1	1	0	1	69	359	0	83	0	3.826724e-01	0	8	0	83	2		0	0	0	0	0	2	1	1.000000	69	353	0	83	2	0	0	0	0	0	0		-3.328643	1	1	0	0		1	1	2	3	1.974951	0	0.390000	2.070000	0.391187	0.820000	6.500000e-01	1.000000	0.830000	0.831826	0.820000	0	0.730000	0.920000
C2orf54	79919	broad.mit.edu	37	2	241827790	241827790	+	Silent	SNP	G	G	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr2:241827790G>A	ENST00000388934.4	-	4	1328	c.1170C>T	c.(1168-1170)tcC>tcT	p.S390S	C2orf54_ENST00000402775.2_Silent_p.S222S|C2orf54_ENST00000307486.8_Silent_p.S241S	NM_001085437.1	NP_001078906	Q08AI8	CB054_HUMAN	chromosome 2 open reading frame 54			6		all_epithelial(40;3.99e-16)|Breast(86;2.35e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|Lung NSC(271;0.094)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)			CCTTGAGCCCGGAGCCGATGC	0.721000																								0							SO:0001819	synonymous_variant			ENST00000388934.4	1	1	hg19	CCDS42839.1																																																																																				TCGA-US-A77E-01A-11D-A32N-08	C2orf54-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000324353.1	1	0	0	10	44	0	16	0	0	1	0	0	16	2		0	0	0	0	0	2	1	0.997028	10	41	0	15	2	0	0	0	0	0	0		-19.487670	1	1	115602	22	36	1	0	1	1	1.972134	0	0.390000	2.070000	0.388808	0.950000	5.100000e-01	1.000000	1.000000	0.883321	0.950000	1	0.710000	1.000000
ITSN2	50618	broad.mit.edu	37	2	24531532	24531532	+	Silent	SNP	C	C	T			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr2:24531532C>T	ENST00000355123.4	-	8	1190	c.747G>A	c.(745-747)cgG>cgA	p.R249R	ITSN2_ENST00000406921.3_Silent_p.R249R|ITSN2_ENST00000361999.3_Silent_p.R249R|ITSN2_ENST00000407704.1_5'Flank	NM_006277.2	NP_006268.2	Q9NZM3	ITSN2_HUMAN	intersectin 2			61	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				TAAATTTTTGCCGATATTTTA	0.428000																								0							SO:0001819	synonymous_variant			ENST00000355123.4	0	1	hg19	CCDS1710.2																																																																																				TCGA-US-A77E-01A-11D-A32N-08	ITSN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207620.2	0	0	0	5	422	0	88	0	9.243794e-03	0	10	0	88	2		0	0	0	0	0	2	1	0.937885	5	422	0	87	2	0	0	0	0	0	0		-2.321241	0	1	0	0		1	1	2	3	1.974951	0	0.390000	2.070000	0.391187	0.060000	1.000000e-02	0.140000	0.060000	0.071595	0.060000	0	0.030000	0.100000
POMC	5443	broad.mit.edu	37	2	25384178	25384178	+	Silent	SNP	G	G	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr2:25384178G>A	ENST00000405623.1	-	3	1031	c.576C>T	c.(574-576)gaC>gaT	p.D192D	POMC_ENST00000264708.3_Silent_p.D192D|RP11-509E16.1_ENST00000567599.1_lincRNA|POMC_ENST00000395826.2_Silent_p.D192D|POMC_ENST00000380794.1_Silent_p.D192D			P01189	COLI_HUMAN	proopiomelanocortin			12	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)			Loperamide(DB00836)	CGGCAGGGCCGTCGGGGCCAT	0.697000													Colon(110;1515 1566 8452 10082 43216)											0							SO:0001819	synonymous_variant			ENST00000405623.1	1	1	hg19	CCDS1717.1																																																																																				TCGA-US-A77E-01A-11D-A32N-08	POMC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211573.3	1	0	0	19	73	0	22	0	4.542598e-01	0	7	0	22	2		0	0	0	0	0	2	1	0.999993	17	70	0	21	2	0	0	0	0	0	0		-20.000000	1	1	121012	1	26	1	1	2	3	1.974951	0	0.390000	2.070000	0.391187	0.990000	6.800000e-01	1.000000	1.000000	0.949142	0.990000	1	0.850000	1.000000
NRXN1	9378	broad.mit.edu	37	2	50765563	50765563	+	Silent	SNP	C	C	T			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr2:50765563C>T	ENST00000406316.2	-	10	3447	c.1971G>A	c.(1969-1971)cgG>cgA	p.R657R	NRXN1_ENST00000406859.3_Silent_p.R657R|NRXN1_ENST00000404971.1_Silent_p.R697R|NRXN1_ENST00000331040.5_5'UTR|NRXN1_ENST00000401669.2_Silent_p.R657R|NRXN1_ENST00000402717.3_Silent_p.R649R|NRXN1_ENST00000405472.3_Silent_p.R649R	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)		CAGCCATTTGCCGGATATCTT	0.502000																								0							SO:0001819	synonymous_variant			ENST00000406316.2	0	1	hg19	CCDS54360.1																																																																																				TCGA-US-A77E-01A-11D-A32N-08	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2	0	0	0	7	1303	1	303		0	0	0	1	303	2		0	0	0	0	0	2	0	0.043074	7	1288	1	299	16	0	0	0	0	0	0		-2.349706	0	1	0	0		1	1	2	3	1.974951	0	0.390000	2.070000	0.391187	0.020000	0	0.060000	0.020000	0.030122	0.020000	0	0.010000	0.050000
PVRL3	25945	broad.mit.edu	37	3	110852707	110852707	+	Missense_Mutation	SNP	G	G	A	rs15611	by1000genomes	TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr3:110852707G>A	ENST00000485303.1	+	6	1570	c.1295G>A	c.(1294-1296)cGg>cAg	p.R432Q	PVRL3_ENST00000493615.1_Intron|PVRL3_ENST00000319792.3_3'UTR	NM_001243286.1|NM_015480.2	NP_001230215.1|NP_056295.1	Q9NQS3	PVRL3_HUMAN	poliovirus receptor-related 3			19					AGGAGAAGACGGACGTTTCGT	0.413000																								0							SO:0001583	missense			ENST00000485303.1	1	1	hg19	CCDS2957.1	.	.	.	.	.	.	.	.	.	.	G	13.25	2.181044	0.38511	.	.	ENSG00000177707	ENST00000485303	T	0.15834	2.39	5.87	5.87	0.94306	Cytochrome c1, transmembrane anchor, C-terminal (1);	0.064498	0.64402	D	0.000010	T	0.08714	0.0216	N	0.21097	0.63	0.80722	D	1	P	0.48503	0.911	B	0.28991	0.097	T	0.16660	-1.0395	10	0.33940	T	0.23	.	11.0918	0.48121	0.0834:0.0:0.9166:0.0	.	432	Q9NQS3	PVRL3_HUMAN	Q	432	ENSP00000418070:R432Q	ENSP00000418070:R432Q	R	+	2	0	PVRL3	112335397	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	5.640000	0.67875	2.801000	0.96364	0.454000	0.30748	CGG		TCGA-US-A77E-01A-11D-A32N-08	PVRL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354045.1	1	0	1	98	383	0	123	1	9.984107e-01	7	33	0	123	2		0	0	0	0	0	2	1	1.000000	97	379	0	123	2	0	0	0	0	0	0		-3.618345	1	1	121412	2	40	1	1	2	3	1.977426	0	0.390000	2.070000	0.391187	0.990000	8.600000e-01	1.000000	1.000000	0.982550	0.990000	1	0.950000	1.000000
ATP2C1	27032	broad.mit.edu	37	3	130718462	130718462	+	Missense_Mutation	SNP	C	C	G			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08			C	G	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr3:130718462C>G	ENST00000510168.1	+	27	3138	c.2588C>G	c.(2587-2589)cCg>cGg	p.P863R	ATP2C1_ENST00000504381.1_Missense_Mutation_p.P808R|ATP2C1_ENST00000428331.2_Missense_Mutation_p.P863R|ATP2C1_ENST00000328560.8_Missense_Mutation_p.P863R|ATP2C1_ENST00000359644.3_Missense_Mutation_p.P863R|ATP2C1_ENST00000507488.2_Missense_Mutation_p.P847R|ATP2C1_ENST00000504948.1_Missense_Mutation_p.P847R|ATP2C1_ENST00000513801.1_Missense_Mutation_p.P847R|ATP2C1_ENST00000505330.1_Missense_Mutation_p.P847R|ATP2C1_ENST00000508532.1_Missense_Mutation_p.P863R|ATP2C1_ENST00000393221.4_Missense_Mutation_p.P897R|ATP2C1_ENST00000422190.2_Missense_Mutation_p.P863R|ATP2C1_ENST00000533801.2_Missense_Mutation_p.P858R			P98194	AT2C1_HUMAN	ATPase, Ca++ transporting, type 2C, member 1			39				Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	TACTTTCCTCCGCTTCAGAAG	0.343000									Hailey-Hailey disease				Esophageal Squamous(99;456 1443 27647 34099 42636)											0							SO:0001583	missense	Familial Cancer Database	HHD, Familial Benign Chronic Pemphigus, Benign Familial Pemphigus	ENST00000510168.1	1	1	hg19	CCDS46914.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.8|25.8	4.678165|4.678165	0.88542|0.88542	.|.	.|.	ENSG00000017260|ENSG00000017260	ENST00000505330;ENST00000504381;ENST00000507488;ENST00000393221;ENST00000533801;ENST00000510168;ENST00000508532;ENST00000504948;ENST00000513801;ENST00000328560;ENST00000428331;ENST00000359644;ENST00000422190;ENST00000347421|ENST00000504612	D;D;D;D;D;D;D;D;D;D;D;D;D|.	0.89123|.	-2.47;-2.47;-2.47;-2.47;-2.47;-2.47;-2.47;-2.47;-2.47;-2.47;-2.47;-2.47;-2.47|.	5.91|5.91	5.91|5.91	0.95273|0.95273	ATPase, P-type cation-transporter, C-terminal (1);ATPase, P-type,  transmembrane domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.87107|0.87107	0.6095|0.6095	M|M	0.92833|0.92833	3.35|3.35	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;1.0;1.0;1.0|.	D;D;D;D;D;D;D|.	0.91635|.	0.999;0.999;0.996;0.999;0.996;0.999;0.999|.	D|D	0.89107|0.89107	0.3493|0.3493	10|5	0.41790|.	T|.	0.15|.	.|.	20.2985|20.2985	0.98592|0.98592	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	897;858;897;863;897;863;863|.	G3XAH8;B4DSW3;B4E2Q0;P98194-5;B7Z3X9;P98194-2;P98194|.	.;.;.;.;.;.;AT2C1_HUMAN|.	R|G	847;808;847;897;858;863;863;847;847;863;863;863;863;862|817	ENSP00000423774:P847R;ENSP00000425320:P808R;ENSP00000421326:P847R;ENSP00000376914:P897R;ENSP00000432956:P858R;ENSP00000427461:P863R;ENSP00000424783:P863R;ENSP00000423330:P847R;ENSP00000422872:P847R;ENSP00000329664:P863R;ENSP00000395809:P863R;ENSP00000352665:P863R;ENSP00000402677:P863R|.	ENSP00000329664:P863R|.	P|R	+|+	2|1	0|0	ATP2C1|ATP2C1	132201152|132201152	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.925000|0.925000	0.55904|0.55904	7.812000|7.812000	0.86109|0.86109	2.793000|2.793000	0.96121|0.96121	0.655000|0.655000	0.94253|0.94253	CCG|CGC		TCGA-US-A77E-01A-11D-A32N-08	ATP2C1-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356648.2	1	0	1	39	200	0	41	1	1	80	159	0	41	2		0	0	0	0	0	2	1	1.000000	37	198	0	41	2	0	0	0	0	0	0		-2.679540	1	1	0	0		1	1	2	3	1.977426	0	0.390000	2.070000	0.391187	0.830000	6.100000e-01	1.000000	1.000000	0.840070	0.830000	0	0.720000	0.970000
DNAJC13	23317	broad.mit.edu	37	3	132175223	132175223	+	Silent	SNP	C	C	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr3:132175223C>A	ENST00000260818.6	+	10	1325	c.1077C>A	c.(1075-1077)ctC>ctA	p.L359L	DNAJC13_ENST00000486798.1_3'UTR	NM_015268.3	NP_056083.3	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13			34					GCCTTCACCTCAGGTTCTTAG	0.378000																								0							SO:0001819	synonymous_variant			ENST00000260818.6	1	1	hg19	CCDS33857.1																																																																																				TCGA-US-A77E-01A-11D-A32N-08	DNAJC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356807.2	1	0	1	47	211	0	45	1	7.860263e-01	5	10	0	45	2		0	0	0	0	0	2	1	1.000000	47	207	0	45	2	0	0	0	0	0	0		-2.844505	1	1	0	0		1	1	2	3	1.977426	0	0.390000	2.070000	0.391187	0.930000	7.000000e-01	1.000000	1.000000	0.916596	0.930000	1	0.810000	1.000000
FBLN2	2199	broad.mit.edu	37	3	13672892	13672892	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr3:13672892G>A	ENST00000295760.7	+	15	3077	c.3008G>A	c.(3007-3009)gGg>gAg	p.G1003E	FBLN2_ENST00000492059.1_Missense_Mutation_p.G1050E|FBLN2_ENST00000404922.3_Missense_Mutation_p.G1050E|FBLN2_ENST00000535798.1_Missense_Mutation_p.G1029E	NM_001998.2	NP_001989.2	P98095	FBLN2_HUMAN	fibulin 2			24			UCEC - Uterine corpus endometrioid carcinoma (1;0.00416)		AACGTGCCAGGGAGCTACCAG	0.637000																								0							SO:0001583	missense			ENST00000295760.7	0	1	hg19	CCDS46762.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	33|33	5.288281|5.288281	0.95517|0.95517	.|.	.|.	ENSG00000163520|ENSG00000163520	ENST00000535798;ENST00000404922;ENST00000295760;ENST00000492059|ENST00000295761	D;D;D;D|D	0.90504|0.99557	-2.56;-2.56;-2.68;-2.56|-6.16	5.39|5.39	5.39|5.39	0.77823|0.77823	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (1);|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	D|D	0.99775|0.99775	0.9907|0.9907	H|H	0.95294|0.95294	3.65|3.65	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.97110|.	1.0;1.0;1.0|.	D|D	0.97158|0.97158	0.9836|0.9836	10|8	0.87932|0.87932	D|D	0|0	.|.	19.1574|19.1574	0.93517|0.93517	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1003;1050;1029|.	P98095;P98095-2;F5H1F3|.	FBLN2_HUMAN;.;.|.	E|R	1029;1050;1003;1050|22	ENSP00000445705:G1029E;ENSP00000384169:G1050E;ENSP00000295760:G1003E;ENSP00000420042:G1050E|ENSP00000295761:G22R	ENSP00000295760:G1003E|ENSP00000295761:G22R	G|G	+|+	2|1	0|0	FBLN2|FBLN2	13647893|13647893	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.977000|0.977000	0.68977|0.68977	9.839000|9.839000	0.99476|0.99476	2.525000|2.525000	0.85131|0.85131	0.655000|0.655000	0.94253|0.94253	GGG|GGA		TCGA-US-A77E-01A-11D-A32N-08	FBLN2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000340083.3	1	0	1	26	45	0	11	0	1	1	322	0	11	2	1	1	530	1085	0	1028	2	1	1.000000	26	45	0	10	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	0	2	2	1.968864	1	0.390000	2.070000	0.390000	0.990000	9.900000e-01	1.000000	1.000000	0.999968	0.990000	1	0.990000	1.000000
CPA3	1359	broad.mit.edu	37	3	148599357	148599357	+	Nonsense_Mutation	SNP	C	C	T	rs141357361	byFrequency	TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr3:148599357C>T	ENST00000296046.3	+	7	677	c.625C>T	c.(625-627)Cga>Tga	p.R209*	RP11-680B3.2_ENST00000488190.1_RNA	NM_001870.2	NP_001861.2	P15088	CBPA3_HUMAN	carboxypeptidase A3 (mast cell)	p.R209R(1)		35			LUSC - Lung squamous cell carcinoma(72;0.0934)|Lung(72;0.115)		ACTCTTGGACCGAATGAATTT	0.343000																								1	Substitution - coding silent(1)						SO:0001587	stop_gained			ENST00000296046.3	0	1	hg19	CCDS3138.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.071142	0.76301	.	.	ENSG00000163751	ENST00000296046	.	.	.	5.06	3.09	0.35607	.	0.546116	0.18299	N	0.145492	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.14656	T	0.56	.	10.9886	0.47537	0.5206:0.4794:0.0:0.0	.	.	.	.	X	209	.	ENSP00000296046:R209X	R	+	1	2	CPA3	150082047	0.162000	0.22906	0.643000	0.29450	0.200000	0.23975	1.401000	0.34589	1.325000	0.45301	-0.182000	0.12963	CGA		TCGA-US-A77E-01A-11D-A32N-08	CPA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355974.1	1	0	1	32	222	0	67	0	2.765583e-01	0	8	0	67	2		0	0	0	0	0	2	1	1.000000	31	219	0	67	2	0	0	0	0	0	0		-3.142530	1	1	121408	60	50	1	1	2	3	1.977426	0	0.390000	2.070000	0.391187	0.640000	4.500000e-01	0.880000	0.640000	0.658225	0.640000	0	0.540000	0.760000
ALS2CL	259173	broad.mit.edu	37	3	46729748	46729748	+	Missense_Mutation	SNP	G	G	A	rs143519761		TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr3:46729748G>A	ENST00000318962.4	-	3	225	c.142C>T	c.(142-144)Cgg>Tgg	p.R48W	ALS2CL_ENST00000415953.1_Missense_Mutation_p.R48W	NM_147129.3	NP_667340.2	Q60I27	AL2CL_HUMAN	ALS2 C-terminal like			29					TGCAAGAGCCGCAGGCACTCT	0.612000																								0							SO:0001583	missense			ENST00000318962.4	1	1	hg19	CCDS2743.1	.	.	.	.	.	.	.	.	.	.	G	9.542	1.113617	0.20795	0.0	1.16E-4	ENSG00000178038	ENST00000318962;ENST00000415953	T;T	0.17691	2.26;2.26	4.15	2.19	0.27852	.	0.879668	0.09620	N	0.777724	T	0.11196	0.0273	L	0.29908	0.895	0.19300	N	0.999979	D	0.56968	0.978	B	0.36504	0.226	T	0.20338	-1.0278	10	0.72032	D	0.01	.	8.7355	0.34525	0.0:0.0:0.5869:0.4131	.	48	Q60I27	AL2CL_HUMAN	W	48	ENSP00000313670:R48W;ENSP00000413223:R48W	ENSP00000313670:R48W	R	-	1	2	ALS2CL	46704752	0.003000	0.15002	0.255000	0.24374	0.221000	0.24807	0.312000	0.19397	1.098000	0.41479	-0.196000	0.12772	CGG		TCGA-US-A77E-01A-11D-A32N-08	ALS2CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250567.3	1	0	1	32	176	0	50	1	9.912157e-01	22	22	0	50	2		0	0	0	0	0	2	1	1.000000	32	175	0	50	2	0	0	0	0	0	0		-20.000000	1	1	121358	9	38	1	1	2	3	1.977426	0	0.390000	2.070000	0.391187	0.790000	5.600000e-01	1.000000	1.000000	0.797108	0.790000	0	0.660000	0.930000
DNAH1	25981	broad.mit.edu	37	3	52392752	52392752	+	Splice_Site	SNP	C	C	T			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr3:52392752C>T	ENST00000420323.2	+	25	4526	c.4265C>T	c.(4264-4266)aCg>aTg	p.T1422M		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1			62					GCCTACCCCACGGTGAGCCGC	0.672000																								0							SO:0001630	splice_region_variant			ENST00000420323.2	1	0	hg19	CCDS46842.1	.	.	.	.	.	.	.	.	.	.	c	14.44	2.535864	0.45176	.	.	ENSG00000114841	ENST00000420323	T	0.57752	0.38	5.4	-1.98	0.07480	.	1.606480	0.03543	N	0.224331	T	0.55353	0.1915	M	0.85197	2.74	0.09310	N	1	P	0.38767	0.646	B	0.36989	0.238	T	0.52223	-0.8604	10	0.52906	T	0.07	.	6.2438	0.20805	0.4428:0.3398:0.0:0.2173	.	1422	C9JXH6	.	M	1422	ENSP00000401514:T1422M	ENSP00000401514:T1422M	T	+	2	0	DNAH1	52367792	0.000000	0.05858	0.032000	0.17829	0.425000	0.31504	0.412000	0.21131	-0.236000	0.09753	-0.119000	0.15052	ACG		TCGA-US-A77E-01A-11D-A32N-08	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	1	0	1	21	171	0	55	1	1.040082e-01	3	2	0	55	2		0	0	0	0	0	2	1	0.999998	21	170	0	55	2	0	0	0	0	0	0		-20.000000	1	1	121158	5	34	1	1	2	3	1.977426	0	0.390000	2.070000	0.391187	0.560000	3.600000e-01	0.820000	0.560000	0.577949	0.560000	0	0.450000	0.690000
OR5H1	26341	broad.mit.edu	37	3	97852400	97852400	+	Missense_Mutation	SNP	C	C	T			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr3:97852400C>T	ENST00000354565.2	+	1	859	c.859C>T	c.(859-861)Cct>Tct	p.P287S	RP11-343D2.11_ENST00000508964.1_RNA	NM_001005338.1	NP_001005338.1	A6NKK0	OR5H1_HUMAN	olfactory receptor, family 5, subfamily H, member 1			34					TTTGTTAAATCCTATCATCTA	0.363000																								0							SO:0001583	missense			ENST00000354565.2	1	1	hg19	CCDS33797.1	.	.	.	.	.	.	.	.	.	.	C	9.923	1.212625	0.22289	.	.	ENSG00000231192	ENST00000354565	T	0.63417	-0.04	3.38	3.38	0.38709	GPCR, rhodopsin-like superfamily (1);	0.000000	0.46758	D	0.000271	T	0.68833	0.3044	M	0.88842	2.985	0.35061	D	0.761587	B	0.33238	0.403	B	0.37239	0.244	T	0.81182	-0.1049	10	0.87932	D	0	.	12.2602	0.54647	0.0:1.0:0.0:0.0	.	287	A6NKK0	OR5H1_HUMAN	S	287	ENSP00000346575:P287S	ENSP00000346575:P287S	P	+	1	0	OR5H1	99335090	1.000000	0.71417	0.685000	0.30070	0.005000	0.04900	6.901000	0.75693	1.712000	0.51347	0.195000	0.17529	CCT		TCGA-US-A77E-01A-11D-A32N-08	OR5H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359100.2	1	0	1	66	302	0	67		0	0	0	0	67	2		0	0	0	0	0	2	1	1.000000	65	301	0	66	2	0	0	0	0	0	0		-3.224316	1	1	0	0		1	1	2	3	1.977426	0	0.390000	2.070000	0.391187	0.910000	7.200000e-01	1.000000	1.000000	0.911651	0.910000	1	0.810000	1.000000
TBC1D9	23158	broad.mit.edu	37	4	141622724	141622724	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr4:141622724G>A	ENST00000442267.2	-	2	249	c.175C>T	c.(175-177)Cgg>Tgg	p.R59W	Y_RNA_ENST00000384426.1_RNA	NM_015130.2	NP_055945.2	Q6ZT07	TBCD9_HUMAN	TBC1 domain family, member 9 (with GRAM domain)			31	all_hematologic(180;0.162)	Medulloblastoma(177;0.00498)			GGAGCGACCCGGGCGCTGGAG	0.517000																								0							SO:0001583	missense			ENST00000442267.2	1	1	hg19	CCDS47136.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.148616	0.78001	.	.	ENSG00000109436	ENST00000442267	T	0.23552	1.9	5.39	4.45	0.53987	.	0.000000	0.85682	D	0.000000	T	0.48822	0.1521	M	0.74258	2.255	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.51403	-0.8710	10	0.87932	D	0	-4.7968	10.5771	0.45233	0.0:0.0:0.4702:0.5298	.	59	Q6ZT07	TBCD9_HUMAN	W	59	ENSP00000411197:R59W	ENSP00000411197:R59W	R	-	1	2	TBC1D9	141842174	1.000000	0.71417	0.998000	0.56505	0.930000	0.56654	4.245000	0.58734	1.314000	0.45095	0.655000	0.94253	CGG		TCGA-US-A77E-01A-11D-A32N-08	TBC1D9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364806.1	1	0	1	31	161	0	26	0	3.887059e-01	0	8	0	26	2		0	0	0	0	0	2	1	1.000000	31	157	0	26	2	0	0	0	0	0	0		-2.924440	1	1	120842	1	28	1	1	2	3	1.996179	0	0.390000	2.070000	0.394721	0.830000	5.900000e-01	1.000000	1.000000	0.840335	0.830000	0	0.700000	1.000000
GBA3	57733	broad.mit.edu	37	4	22749669	22749669	+	RNA	SNP	T	T	G			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr4:22749669T>G	ENST00000503442.1	+	0	377				GBA3_ENST00000508166.1_RNA|GBA3_ENST00000511446.2_RNA	NM_001128432.2	NP_001121904.1	Q9H227	GBA3_HUMAN	glucosidase, beta, acid 3 (gene/pseudogene)			33					GTGGATTGGATCTACGTGGTA	0.383000																								0											ENST00000503442.1	0	1	hg19																																																																																					TCGA-US-A77E-01A-11D-A32N-08	GBA3-003	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000360620.2	0	0	0	12	63	0	24	0	2.042507e-01	0	5	0	24	2		0	0	0	0	0	2	1	0.999331	12	62	0	23	2	0	0	0	0	0	0		-19.983290	1	1	0	0		1	1	2	3	1.996179	0	0.390000	2.070000	0.394721	0.840000	4.700000e-01	1.000000	1.000000	0.825446	0.840000	0	0.640000	1.000000
PCDHA5	56143	broad.mit.edu	37	5	140201497	140201497	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr5:140201497G>A	ENST00000529859.1	+	1	137	c.137G>A	c.(136-138)cGc>cAc	p.R46H	PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000378126.3_Missense_Mutation_p.R46H|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA5_ENST00000529619.1_Missense_Mutation_p.R46H	NM_018908.2	NP_061731.1	Q9Y5H7	PCDA5_HUMAN	protocadherin alpha 5	p.R46H(2)		60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		TTCGTTGGCCGCATCGCGCAG	0.657000																								2	Substitution - Missense(2)						SO:0001583	missense			ENST00000529859.1	0	1	hg19	CCDS54917.1	.	.	.	.	.	.	.	.	.	.	G	17.07	3.294143	0.60086	.	.	ENSG00000204965	ENST00000529619;ENST00000529859;ENST00000378126	T;T;T	0.27256	1.68;1.68;1.68	3.87	2.98	0.34508	Cadherin, N-terminal (1);Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.25827	0.0629	M	0.63428	1.95	0.25612	N	0.986495	P;P;P	0.46987	0.848;0.888;0.609	B;B;B	0.38803	0.282;0.253;0.185	T	0.11275	-1.0594	9	0.72032	D	0.01	.	10.3243	0.43783	0.1721:0.0:0.8279:0.0	.	46;46;46	Q9Y5H7;Q9Y5H7-3;Q9Y5H7-2	PCDA5_HUMAN;.;.	H	46	ENSP00000433416:R46H;ENSP00000436557:R46H;ENSP00000367366:R46H	ENSP00000367366:R46H	R	+	2	0	PCDHA5	140181681	0.004000	0.15560	1.000000	0.80357	0.960000	0.62799	1.772000	0.38552	0.719000	0.32188	0.585000	0.79938	CGC		TCGA-US-A77E-01A-11D-A32N-08	PCDHA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372883.2	0	0	0	7	479	0	115		0	0	0	0	115	2		0	0	0	0	0	2	1	0.980177	7	475	0	115	2	0	0	0	0	0	0		-2.229413	0	1	0	0		1	1	2	3	1.991597	0	0.390000	2.070000	0.392370	0.070000	2.000000e-02	0.160000	0.080000	0.093106	0.070000	0	0.040000	0.120000
FOXI1	2299	broad.mit.edu	37	5	169533243	169533243	+	Silent	SNP	G	G	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr5:169533243G>A	ENST00000306268.6	+	1	343	c.282G>A	c.(280-282)ccG>ccA	p.P94P	FOXI1_ENST00000449804.2_Silent_p.P94P			Q12951	FOXI1_HUMAN	forkhead box I1			35	Renal(175;0.000159)|Lung NSC(126;0.0267)|all_lung(126;0.04)	Medulloblastoma(196;0.0109)|all_neural(177;0.0298)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		TGCAGAGGCCGCTGCTGCCCA	0.697000									Pendred syndrome															0							SO:0001819	synonymous_variant	Familial Cancer Database	Goiter-Deafness syndrome	ENST00000306268.6	1	1	hg19	CCDS4372.1																																																																																				TCGA-US-A77E-01A-11D-A32N-08	FOXI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252827.2	1	0	0	9	37	0	17	0	0	0	1	0	17	2		0	0	0	0	0	2	1	0.995341	9	36	0	17	2	0	0	0	0	0	0		-18.510660	1	1	0	0		1	1	2	3	1.991597	0	0.390000	2.070000	0.392370	0.990000	5.300000e-01	1.000000	1.000000	0.904822	0.990000	1	0.740000	1.000000
STC2	8614	broad.mit.edu	37	5	172744926	172744926	+	Missense_Mutation	SNP	C	C	T	rs145310530		TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08			C	T	C	C		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr5:172744926C>T	ENST00000265087.4	-	4	2142	c.833G>A	c.(832-834)gGc>gAc	p.G278D	STC2_ENST00000520593.1_5'Flank	NM_003714.2	NP_003705.1	O76061	STC2_HUMAN	stanniocalcin 2			25	Renal(175;0.000159)|Lung NSC(126;0.00229)|all_lung(126;0.004)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|Ovarian(839;0.223)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)		AGCCCCAAGGCCCCCGACTCT	0.612000																								0							SO:0001583	missense			ENST00000265087.4	1	1	hg19	CCDS4388.1	.	.	.	.	.	.	.	.	.	.	C	12.57	1.978009	0.34942	.	.	ENSG00000113739	ENST00000265087	.	.	.	5.31	1.1	0.20463	.	0.502817	0.22661	N	0.057194	T	0.22205	0.0535	N	0.24115	0.695	0.09310	N	0.999996	B	0.10296	0.003	B	0.09377	0.004	T	0.10064	-1.0646	9	0.38643	T	0.18	-5.3352	2.7467	0.05268	0.2356:0.2927:0.3461:0.1256	.	278	O76061	STC2_HUMAN	D	278	.	ENSP00000265087:G278D	G	-	2	0	STC2	172677532	0.000000	0.05858	0.000000	0.03702	0.913000	0.54294	-0.238000	0.08977	0.181000	0.19994	0.650000	0.86243	GGC		TCGA-US-A77E-01A-11D-A32N-08	STC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252965.1	0	0	1	125	498	0	151	0	9.946677e-01	0	33	0	151	2		0	0	0	0	0	2	1	1.000000	123	490	0	148	2	0	0	0	0	0	0		-20.000000	1	1	121412	1	33	1	1	2	3	1.991597	0	0.390000	2.070000	0.392370	0.990000	8.700000e-01	1.000000	1.000000	0.982136	0.990000	1	0.940000	1.000000
C7	730	broad.mit.edu	37	5	40981607	40981607	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08			G	A	G	G		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr5:40981607G>A	ENST00000313164.9	+	18	2823	c.2464G>A	c.(2464-2466)Gct>Act	p.A822T		NM_000587.2	NP_000578.2	P10643	CO7_HUMAN	complement component 7					Ovarian(839;0.0112)			TGAGGCGGGCGCTCTGAGATG	0.567000																								0							SO:0001583	missense			ENST00000313164.9	1	1	hg19	CCDS47201.1	.	.	.	.	.	.	.	.	.	.	G	4.186	0.033170	0.08101	.	.	ENSG00000112936	ENST00000313164	T	0.65364	-0.15	5.83	-0.108	0.13588	Factor I / membrane attack complex (1);	1.811360	0.02513	N	0.091774	T	0.48857	0.1523	L	0.37850	1.14	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.10200	-1.0640	10	0.27082	T	0.32	0.8429	2.9604	0.05890	0.462:0.1118:0.3117:0.1144	.	822	P10643	CO7_HUMAN	T	822	ENSP00000322061:A822T	ENSP00000322061:A822T	A	+	1	0	C7	41017364	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.255000	0.08769	-0.082000	0.12640	-0.992000	0.02543	GCT		TCGA-US-A77E-01A-11D-A32N-08	C7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317680.1	1	0	1	24	101	0	17	0	1	1	171	0	17	2		0	0	0	0	0	2	1	1.000000	24	99	0	16	2	0	0	0	0	0	0		-20.000000	1	1	121058	5	34	1	1	2	3	1.991597	0	0.390000	2.070000	0.392370	0.990000	6.700000e-01	1.000000	1.000000	0.929971	0.990000	1	0.810000	1.000000
VCAN	1462	broad.mit.edu	37	5	82876174	82876174	+	Missense_Mutation	SNP	C	C	T			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08			C	T	C	C		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr5:82876174C>T	ENST00000265077.3	+	15	10677	c.10112C>T	c.(10111-10113)tCa>tTa	p.S3371L	VCAN_ENST00000513016.1_3'UTR|VCAN_ENST00000342785.4_Missense_Mutation_p.S1617L|VCAN-AS1_ENST00000513899.1_RNA|VCAN_ENST00000343200.5_Missense_Mutation_p.S2384L|VCAN_ENST00000512590.2_Missense_Mutation_p.S1569L|VCAN_ENST00000502527.2_Missense_Mutation_p.S630L	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican			190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		Hyaluronan(DB08818)	AAAAATTCCTCATCAGCAAAG	0.393000																								0							SO:0001583	missense			ENST00000265077.3	1	1	hg19	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	C	15.86	2.957027	0.53293	.	.	ENSG00000038427	ENST00000265077;ENST00000343200;ENST00000342785;ENST00000512590;ENST00000502527	D;D;D;D;D	0.87029	-2.19;-2.2;-1.94;-1.94;-1.85	5.8	5.8	0.92144	.	0.000000	0.44483	D	0.000456	D	0.89750	0.6805	N	0.24115	0.695	0.38290	D	0.942687	D;B;P;D	0.89917	0.999;0.386;0.502;1.0	D;B;B;D	0.74023	0.964;0.23;0.403;0.982	D	0.91528	0.5240	10	0.72032	D	0.01	.	20.0706	0.97721	0.0:1.0:0.0:0.0	.	1617;630;2384;3371	P13611-3;P13611-4;P13611-2;P13611	.;.;.;CSPG2_HUMAN	L	3371;2384;1617;1569;630	ENSP00000265077:S3371L;ENSP00000340062:S2384L;ENSP00000342768:S1617L;ENSP00000425959:S1569L;ENSP00000421362:S630L	ENSP00000265077:S3371L	S	+	2	0	VCAN	82911930	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	4.512000	0.60469	2.744000	0.94065	0.655000	0.94253	TCA		TCGA-US-A77E-01A-11D-A32N-08	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	1	0	1	59	186	0	56	0	1	0	550	0	56	2		0	0	0	0	0	2	1	1.000000	59	184	0	56	2	0	0	0	0	0	0		-4.083793	1	1	0	0		1	1	2	3	1.991597	0	0.390000	2.070000	0.392370	0.990000	9.700000e-01	1.000000	1.000000	0.998263	0.990000	1	0.990000	1.000000
SERINC1	57515	broad.mit.edu	37	6	122773086	122773086	+	Missense_Mutation	SNP	T	T	C			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08			T	C	T	T		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr6:122773086T>C	ENST00000339697.4	-	6	790	c.706A>G	c.(706-708)Aac>Gac	p.N236D		NM_020755.2	NP_065806.1	Q9NRX5	SERC1_HUMAN	serine incorporator 1			13					AGGAGCATGTTGACACTGATG	0.393000																								0							SO:0001583	missense			ENST00000339697.4	1	1	hg19	CCDS5125.1	.	.	.	.	.	.	.	.	.	.	T	32	5.185893	0.94885	.	.	ENSG00000111897	ENST00000339697;ENST00000368454	T;T	0.20069	2.1;2.1	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.53899	0.1825	H	0.95917	3.74	0.80722	D	1	D	0.58268	0.982	D	0.72075	0.976	T	0.70699	-0.4800	10	0.87932	D	0	-14.7994	15.9701	0.80008	0.0:0.0:0.0:1.0	.	236	Q9NRX5	SERC1_HUMAN	D	236	ENSP00000342962:N236D;ENSP00000357439:N236D	ENSP00000342962:N236D	N	-	1	0	SERINC1	122814785	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.040000	0.89188	2.166000	0.68216	0.528000	0.53228	AAC		TCGA-US-A77E-01A-11D-A32N-08	SERINC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042031.2	1	0	1	53	198	0	49	1	1	82	183	0	49	2		0	0	0	0	0	2	1	1.000000	53	194	0	49	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	1	2	3	1.979114	0	0.390000	2.070000	0.391187	0.990000	8.300000e-01	1.000000	1.000000	0.981579	0.990000	1	0.950000	1.000000
TRDN	10345	broad.mit.edu	37	6	123539785	123539785	+	Silent	SNP	A	A	G			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr6:123539785A>G	ENST00000398178.3	-	41	2172	c.2151T>C	c.(2149-2151)ggT>ggC	p.G717G	TRDN_ENST00000334268.4_Silent_p.G709G	NM_006073.3	NP_006064.2	Q13061	TRDN_HUMAN	triadin			41					AATTTGCTTGACCAGAGCTCT	0.438000																								0							SO:0001819	synonymous_variant			ENST00000398178.3	0	1	hg19	CCDS55053.1																																																																																				TCGA-US-A77E-01A-11D-A32N-08	TRDN-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		1	0	1	18	97	0	15		0	0	0	0	15	2		0	0	0	0	0	2	1	0.999989	18	96	0	15	2	0	0	0	0	0	0		-11.907530	1	1	0	0		1	1	2	3	1.979114	0	0.390000	2.070000	0.391187	0.800000	5.000000e-01	1.000000	1.000000	0.807459	0.800000	0	0.640000	0.990000
PHACTR1	221692	broad.mit.edu	37	6	13206098	13206098	+	Missense_Mutation	SNP	C	C	T			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr6:13206098C>T	ENST00000379350.1	+	7	845	c.716C>T	c.(715-717)cCg>cTg	p.P239L	PHACTR1_ENST00000379345.2_Intron|PHACTR1_ENST00000332995.7_Missense_Mutation_p.P239L|PHACTR1_ENST00000457702.2_Missense_Mutation_p.P94L			Q9C0D0	PHAR1_HUMAN	phosphatase and actin regulator 1			26	Breast(50;0.0427)|Ovarian(93;0.12)	all_hematologic(90;0.122)|Lung SC(78;0.195)	Epithelial(50;0.146)|BRCA - Breast invasive adenocarcinoma(129;0.239)		CTGTCGCCTCCGCTACCTCCA	0.587000																								0							SO:0001583	missense			ENST00000379350.1	0	1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.1|25.1	4.605951|4.605951	0.87157|0.87157	.|.	.|.	ENSG00000112137|ENSG00000112137	ENST00000379350;ENST00000332995;ENST00000432934;ENST00000457702|ENST00000415087	T;T;T|.	0.44482|.	0.92;1.13;1.25|.	5.15|5.15	5.15|5.15	0.70609|0.70609	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.44871|0.44871	0.1314|0.1314	L|L	0.27053|0.27053	0.805|0.805	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.87578|.	0.992;0.997;0.998|.	T|T	0.34502|0.34502	-0.9826|-0.9826	10|5	0.72032|.	D|.	0.01|.	-16.0863|-16.0863	17.7928|17.7928	0.88561|0.88561	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	308;239;239|.	E7ESR5;Q9C0D0;Q9C0D0-2|.	.;PHAR1_HUMAN;.|.	L|C	239;239;308;94|74	ENSP00000368655:P239L;ENSP00000329880:P239L;ENSP00000397669:P94L|.	ENSP00000329880:P239L|.	P|R	+|+	2|1	0|0	PHACTR1|PHACTR1	13314077|13314077	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	7.012000|7.012000	0.76366|0.76366	2.665000|2.665000	0.90641|0.90641	0.561000|0.561000	0.74099|0.74099	CCG|CGC		TCGA-US-A77E-01A-11D-A32N-08	PHACTR1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039876.1	0	0	0	5	356	0	96		0	0	0	0	96	2		0	0	0	0	0	2	1	0.935646	5	351	0	95	2	0	0	0	0	0	0		-2.029818	0	1	120926	1	30	1	1	2	3	1.996224	0	0.390000	2.070000	0.394721	0.070000	2.000000e-02	1.000000	0.070000	0.111398	0.070000	0	0.040000	0.120000
NUP153	9972	broad.mit.edu	37	6	17706578	17706578	+	Missense_Mutation	SNP	C	C	T			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr6:17706578C>T	ENST00000262077.2	-	1	40	c.41G>A	c.(40-42)gGc>gAc	p.G14D	NUP153_ENST00000537253.1_Missense_Mutation_p.G14D|RP11-500C11.3_ENST00000606771.1_RNA	NM_005124.2	NP_005115.2	P49790	NU153_HUMAN	nucleoporin 153kDa			53	Breast(50;0.0259)|Ovarian(93;0.0584)	all_hematologic(90;0.125)	all cancers(50;0.0981)|Epithelial(50;0.112)		CCGGATCTTGCCGCCACCGCC	0.726000																								0							SO:0001583	missense			ENST00000262077.2	0	1	hg19	CCDS4541.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.008788	0.75046	.	.	ENSG00000124789	ENST00000262077;ENST00000430136;ENST00000537253	T;T	0.35048	1.33;1.43	3.12	3.12	0.35913	.	0.000000	0.35525	N	0.003147	T	0.40015	0.1100	L	0.46157	1.445	0.42084	D	0.991265	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.998	T	0.33548	-0.9864	10	0.87932	D	0	-8.5848	10.0092	0.41975	0.0:1.0:0.0:0.0	.	14;36;14	F6QR24;Q4LE47;P49790	.;.;NU153_HUMAN	D	14;36;14	ENSP00000262077:G14D;ENSP00000444029:G14D	ENSP00000262077:G14D	G	-	2	0	NUP153	17814557	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.110000	0.50352	2.085000	0.62840	0.591000	0.81541	GGC		TCGA-US-A77E-01A-11D-A32N-08	NUP153-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039953.1	0	0	0	6	258	0	52	0	4.173195e-02	0	12	0	52	2		0	0	0	0	0	2	1	0.963787	6	254	0	51	2	0	0	0	0	0	0		-3.085488	1	1	0	0		1	1	2	3	1.996224	0	0.390000	2.070000	0.394721	0.120000	4.000000e-02	1.000000	0.120000	0.160111	0.120000	0	0.080000	0.190000
TNXB	7148	broad.mit.edu	37	6	32046862	32046862	+	Silent	SNP	G	G	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr6:32046862G>A	ENST00000375244.3	-	11	4524	c.4323C>T	c.(4321-4323)taC>taT	p.Y1441Y	TNXB_ENST00000375247.2_Silent_p.Y1441Y|RNA5SP206_ENST00000516703.1_RNA			P22105	TENX_HUMAN	tenascin XB			8					CGTGGAGGCCGTACAGGTGCA	0.697000																								0							SO:0001819	synonymous_variant			ENST00000375244.3	0	1	hg19																																																																																					TCGA-US-A77E-01A-11D-A32N-08	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	0	0	0	5	377	0	105	0	2.725191e-03	0	5	0	105	2		0	0	0	0	0	2	1	0.936193	5	373	0	102	2	0	0	0	0	0	0		-2.602696	1	1	120864	5	39	1	1	2	3	1.996224	0	0.390000	2.070000	0.394721	0.070000	2.000000e-02	1.000000	0.070000	0.106896	0.070000	0	0.040000	0.120000
DST	667	broad.mit.edu	37	6	56492887	56492887	+	Nonsense_Mutation	SNP	C	C	T	rs149154059		TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr6:56492887C>T	ENST00000361203.3	-	29	3922	c.3915G>A	c.(3913-3915)tgG>tgA	p.W1305*	DST_ENST00000370788.2_Nonsense_Mutation_p.W1305*|DST_ENST00000421834.2_Nonsense_Mutation_p.W1305*|DST_ENST00000370754.5_Nonsense_Mutation_p.W1483*|DST_ENST00000446842.2_Nonsense_Mutation_p.W979*|DST_ENST00000370765.6_Nonsense_Mutation_p.W979*|DST_ENST00000312431.6_Nonsense_Mutation_p.W1305*|DST_ENST00000518935.1_Nonsense_Mutation_p.W979*|DST_ENST00000244364.6_Nonsense_Mutation_p.W979*|DST_ENST00000370769.4_Nonsense_Mutation_p.W1305*			Q03001	DYST_HUMAN	dystonin			105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)		CCTGCTGGATCCAATCATCTA	0.403000																								0							SO:0001587	stop_gained			ENST00000361203.3	0	1	hg19		.	.	.	.	.	.	.	.	.	.	C	42	9.322677	0.99137	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000312431;ENST00000370788;ENST00000361203;ENST00000439203;ENST00000520645;ENST00000370765;ENST00000518935	.	.	.	5.45	5.45	0.79879	.	0.000000	0.49305	D	0.000156	.	.	.	.	.	.	0.80722	A	1.000000	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.6695	0.95905	0.0:1.0:0.0:0.0	.	.	.	.	X	979;1483;1305;1305;979;1305;1305;1305;979;1345;979;979	.	ENSP00000244364:W979X	W	-	3	0	DST	56600846	1.000000	0.71417	1.000000	0.80357	0.893000	0.52053	5.880000	0.69698	2.701000	0.92244	0.650000	0.86243	TGG		TCGA-US-A77E-01A-11D-A32N-08	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	1	0	0	15	252	0	52	0	3.123456e-01	1	18	0	52	2		0	0	0	0	0	2	1	0.999881	16	250	0	52	2	0	0	0	0	0	0		-17.959750	1	0	0	0		1	1	2	3	1.979114	0	0.390000	2.070000	0.391187	0.290000	1.700000e-01	0.460000	0.280000	0.303844	0.290000	0	0.220000	0.380000
COL12A1	1303	broad.mit.edu	37	6	75901461	75901461	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr6:75901461G>A	ENST00000322507.8	-	5	659	c.350C>T	c.(349-351)tCg>tTg	p.S117L	COL12A1_ENST00000416123.2_Missense_Mutation_p.S117L|COL12A1_ENST00000345356.6_Intron|COL12A1_ENST00000483888.2_Missense_Mutation_p.S117L	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1			169					TGGCTTTGTCGAACTACCTGT	0.299000																								0							SO:0001583	missense			ENST00000322507.8	1	1	hg19	CCDS43482.1	.	.	.	.	.	.	.	.	.	.	G	12.54	1.967274	0.34754	.	.	ENSG00000111799	ENST00000322507;ENST00000432784;ENST00000416123;ENST00000483888	D;D;D	0.86769	-2.17;-2.16;-2.15	5.97	5.97	0.96955	Fibronectin, type III (1);Immunoglobulin-like fold (1);	0.488510	0.20737	N	0.086602	T	0.56232	0.1971	N	0.08118	0	0.21579	N	0.99963	B	0.02656	0.0	B	0.01281	0.0	T	0.30822	-0.9965	10	0.22706	T	0.39	.	8.1231	0.30982	0.0784:0.0:0.7627:0.1589	.	117	Q99715	COCA1_HUMAN	L	117	ENSP00000325146:S117L;ENSP00000412864:S117L;ENSP00000421216:S117L	ENSP00000325146:S117L	S	-	2	0	COL12A1	75958181	0.123000	0.22298	0.822000	0.32727	0.868000	0.49771	1.943000	0.40253	2.833000	0.97629	0.585000	0.79938	TCG		TCGA-US-A77E-01A-11D-A32N-08	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	1	0	1	47	306	0	65	0	9.726732e-01	0	39	0	65	2		0	0	0	0	0	2	1	1.000000	47	303	0	64	2	0	0	0	0	0	0		-19.461560	1	1	120760	3	39	1	1	2	3	1.979114	0	0.390000	2.070000	0.391187	0.680000	5.100000e-01	0.880000	0.680000	0.691649	0.680000	0	0.590000	0.780000
KIAA1549	57670	broad.mit.edu	37	7	138566147	138566147	+	Missense_Mutation	SNP	G	G	C			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr7:138566147G>C	ENST00000422774.1	-	11	4264	c.4216C>G	c.(4216-4218)Cgt>Ggt	p.R1406G	KIAA1549_ENST00000242365.4_Missense_Mutation_p.R1356G|KIAA1549_ENST00000440172.1_Missense_Mutation_p.R1406G			Q9HCM3	K1549_HUMAN	KIAA1549		KIAA1549/BRAF(703)	7					CCTCTGTGACGAACATTCTTG	0.502000			O	BRAF	pilocytic astrocytoma								NSCLC(119;1534 1718 44213 46230 50068)		Dom	yes		7	7q34	57670	KIAA1549		O	0							SO:0001583	missense			ENST00000422774.1	1	1	hg19	CCDS56513.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.221722	0.79464	.	.	ENSG00000122778	ENST00000440172;ENST00000242365;ENST00000422774	T;T;T	0.27557	1.66;1.66;1.68	5.23	5.23	0.72850	.	0.101100	0.64402	D	0.000003	T	0.55242	0.1908	M	0.65975	2.015	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;0.999	D;D;D;D	0.81914	0.995;0.965;0.991;0.965	T	0.56547	-0.7961	10	0.72032	D	0.01	.	17.5362	0.87832	0.0:0.0:1.0:0.0	.	1406;190;1406;190	Q9HCM3;Q9HCM3-4;Q9HCM3-2;Q9HCM3-3	K1549_HUMAN;.;.;.	G	1406;1356;1406	ENSP00000406661:R1406G;ENSP00000242365:R1356G;ENSP00000416040:R1406G	ENSP00000242365:R1356G	R	-	1	0	KIAA1549	138216687	1.000000	0.71417	0.942000	0.38095	0.793000	0.44817	5.140000	0.64807	2.716000	0.92895	0.655000	0.94253	CGT		TCGA-US-A77E-01A-11D-A32N-08	KIAA1549-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348092.1	1	0	1	68	385	0	79	1	5.601395e-01	5	7	0	79	2		0	0	0	0	0	2	1	1.000000	66	380	0	79	2	0	0	0	0	0	0		-2.880992	1	1	0	0		1	1	2	3	2.349308	1	0.390000	2.070000	0.489540	0.910000	7.200000e-01	1.000000	1.000000	0.911890	0.910000	1	0.810000	1.000000
ZNF212	7988	broad.mit.edu	37	7	148951330	148951330	+	Missense_Mutation	SNP	C	C	T			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr7:148951330C>T	ENST00000335870.2	+	5	1440	c.1312C>T	c.(1312-1314)Cac>Tac	p.H438Y		NM_012256.3	NP_036388.2	Q9UDV6	ZN212_HUMAN	zinc finger protein 212			9	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00171)		GAGCTTCAGTCACCCATCTGA	0.587000																								0							SO:0001583	missense			ENST00000335870.2	1	1	hg19	CCDS5896.1	.	.	.	.	.	.	.	.	.	.	C	19.24	3.789182	0.70337	.	.	ENSG00000170260	ENST00000335870	T	0.06528	3.29	5.1	5.1	0.69264	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.53938	D	0.000051	T	0.10895	0.0266	N	0.19112	0.55	0.37851	D	0.92938	D	0.67145	0.996	D	0.65010	0.931	T	0.43147	-0.9409	10	0.16420	T	0.52	-15.4352	14.3872	0.66953	0.0:1.0:0.0:0.0	.	438	Q9UDV6	ZN212_HUMAN	Y	438	ENSP00000338572:H438Y	ENSP00000338572:H438Y	H	+	1	0	ZNF212	148582263	0.000000	0.05858	1.000000	0.80357	0.932000	0.56968	0.028000	0.13644	2.536000	0.85505	0.561000	0.74099	CAC		TCGA-US-A77E-01A-11D-A32N-08	ZNF212-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352710.1	1	0	1	59	287	0	61	1	9.923151e-01	14	25	0	61	2		0	0	0	0	0	2	1	1.000000	59	287	0	60	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	1	2	3	2.349308	1	0.390000	2.070000	0.489540	0.990000	8.100000e-01	1.000000	1.000000	0.973299	0.990000	1	0.920000	1.000000
DPP6	1804	broad.mit.edu	37	7	154667694	154667694	+	Silent	SNP	C	C	T			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr7:154667694C>T	ENST00000377770.3	+	20	2103	c.1962C>T	c.(1960-1962)ggC>ggT	p.G654G	DPP6_ENST00000427557.1_Silent_p.G547G|DPP6_ENST00000332007.3_Silent_p.G592G|DPP6_ENST00000404039.1_Silent_p.G590G			P42658	DPP6_HUMAN	dipeptidyl-peptidase 6			71	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)		GCAGCCACGGCGCGGTGGTGG	0.647000													NSCLC(125;1384 1783 2490 7422 34254)											0							SO:0001819	synonymous_variant			ENST00000377770.3	1	1	hg19																																																																																					TCGA-US-A77E-01A-11D-A32N-08	DPP6-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000322932.1	1	0	0	10	129	0	26	0	1.857956e-02	0	3	0	26	2		0	0	0	0	0	2	1	0.997221	10	129	0	26	2	0	0	0	0	0	0		-14.490230	1	1	0	0		1	1	2	3	2.349308	1	0.390000	2.070000	0.489540	0.450000	2.300000e-01	0.750000	0.450000	0.474469	0.450000	0	0.330000	0.600000
CARD11	84433	broad.mit.edu	37	7	2984085	2984085	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr7:2984085G>A	ENST00000396946.4	-	5	848	c.445C>T	c.(445-447)Cgc>Tgc	p.R149C	AC004906.3_ENST00000423194.1_RNA	NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11			150		Ovarian(82;0.0115)			AGCTCGCAGCGTTGCAGGTCC	0.607000			Mis		DLBCL										Dom	yes		7	7p22	84433	caspase recruitment domain family, member 11		L	0							SO:0001583	missense			ENST00000396946.4	1	1	hg19	CCDS5336.2	.	.	.	.	.	.	.	.	.	.	G	16.44	3.124918	0.56613	.	.	ENSG00000198286	ENST00000396946	T	0.35048	1.33	4.38	4.38	0.52667	.	0.370990	0.28766	N	0.014207	T	0.44265	0.1285	L	0.43152	1.355	0.58432	D	0.999992	D	0.76494	0.999	P	0.55871	0.786	T	0.42799	-0.9430	10	0.72032	D	0.01	-31.7767	12.44	0.55619	0.0:0.0:0.8323:0.1677	.	149	Q9BXL7	CAR11_HUMAN	C	149	ENSP00000380150:R149C	ENSP00000380150:R149C	R	-	1	0	CARD11	2950611	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	4.048000	0.57390	2.153000	0.67306	0.655000	0.94253	CGC		TCGA-US-A77E-01A-11D-A32N-08	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	1	0	1	87	466	0	118	1	9.456846e-01	9	19	0	118	2		0	0	0	0	0	2	1	1.000000	85	460	0	118	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	1	2	3	2.339105	1	0.390000	2.070000	0.480210	0.950000	7.700000e-01	1.000000	1.000000	0.939554	0.950000	1	0.850000	1.000000
TECPR1	25851	broad.mit.edu	37	7	97858456	97858456	+	Missense_Mutation	SNP	G	G	T			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr7:97858456G>T	ENST00000447648.2	-	16	2604	c.2305C>A	c.(2305-2307)Cac>Aac	p.H769N	TECPR1_ENST00000542604.1_Missense_Mutation_p.H699N|TECPR1_ENST00000479975.1_5'Flank|TECPR1_ENST00000379795.3_Missense_Mutation_p.H770N			Q7Z6L1	TCPR1_HUMAN	tectonin beta-propeller repeat containing 1			26					ATCCGCAGGTGGCCTCCCATC	0.642000																								0							SO:0001583	missense			ENST00000447648.2	0	1	hg19	CCDS47648.1	.	.	.	.	.	.	.	.	.	.	G	33	5.208596	0.95069	.	.	ENSG00000205356	ENST00000447648;ENST00000379795;ENST00000542604	T;T;T	0.49432	1.02;1.02;0.78	5.12	5.12	0.69794	.	0.051894	0.85682	D	0.000000	T	0.68449	0.3002	M	0.76002	2.32	0.50171	D	0.999851	D;D	0.58970	0.984;0.979	D;P	0.66084	0.941;0.761	T	0.72577	-0.4251	10	0.72032	D	0.01	-30.3075	17.6109	0.88053	0.0:0.0:1.0:0.0	.	699;769	F5GX57;Q7Z6L1	.;TCPR1_HUMAN	N	769;770;699	ENSP00000404923:H769N;ENSP00000369121:H770N;ENSP00000441121:H699N	ENSP00000369121:H770N	H	-	1	0	TECPR1	97696392	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.830000	0.99415	2.389000	0.81357	0.549000	0.68633	CAC		TCGA-US-A77E-01A-11D-A32N-08	TECPR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000334661.1	1	0	1	7	27	0	10	1	9.828066e-01	6	27	0	10	2		0	0	0	0	0	2	1	0.982807	7	26	0	10	2	0	0	0	0	0	0		-15.917780	1	1	0	0		1	1	2	3	2.348736	1	0.390000	2.070000	0.489540	0.990000	6.100000e-01	1.000000	1.000000	0.958050	0.990000	1	0.900000	1.000000
DGAT1	8694	broad.mit.edu	37	8	145541605	145541605	+	Missense_Mutation	SNP	C	C	T			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr8:145541605C>T	ENST00000332324.4	-	9	1100	c.827G>A	c.(826-828)cGc>cAc	p.R276H	GS1-393G12.12_ENST00000525023.1_RNA|DGAT1_ENST00000531896.1_Silent_p.A306A|DGAT1_ENST00000527438.1_5'Flank	NM_012079.4	NP_036211.2	O75907	DGAT1_HUMAN	diacylglycerol O-acyltransferase 1			9	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.94e-40)|Epithelial(56;7.67e-40)|all cancers(56;7.88e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0441)|Colorectal(110;0.055)		CAGCAGAAAGCGCTTCCGGAT	0.622000																								0							SO:0001583	missense			ENST00000332324.4	0	1	hg19	CCDS6420.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.213109	0.79352	.	.	ENSG00000185000	ENST00000332324	T	0.72942	-0.7	4.77	4.77	0.60923	.	0.000000	0.85682	D	0.000000	T	0.66336	0.2779	M	0.66439	2.03	0.80722	D	1	P	0.46457	0.878	B	0.36845	0.234	T	0.71457	-0.4587	10	0.42905	T	0.14	-15.1045	15.3179	0.74095	0.0:1.0:0.0:0.0	.	276	O75907	DGAT1_HUMAN	H	276	ENSP00000332258:R276H	ENSP00000332258:R276H	R	-	2	0	DGAT1	145512413	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	7.047000	0.76599	2.481000	0.83766	0.555000	0.69702	CGC		TCGA-US-A77E-01A-11D-A32N-08	DGAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382059.3	0	0	0	8	205	0	46	1	9.948823e-01	14	235	0	46	2		0	0	0	0	0	2	1	0.989158	8	202	0	45	2	0	0	0	0	0	0		-9.903371	1	1	0	0		1	0	1	1	1.967067	0	0.390000	2.070000	0.388808	0.190000	9.000000e-02	0.350000	0.190000	0.212676	0.190000	0	0.130000	0.280000
IDO1	3620	broad.mit.edu	37	8	39775725	39775725	+	Splice_Site	SNP	A	A	T			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr8:39775725A>T	ENST00000518237.1	+	3	941	c.302A>T	c.(301-303)aAg>aTg	p.K101M	RP11-44K6.4_ENST00000522970.1_RNA|IDO1_ENST00000522495.1_Splice_Site_p.K101M|RP11-44K6.2_ENST00000520185.1_RNA|RP11-44K6.3_ENST00000517623.1_RNA	NM_002164.5	NP_002155.1	P14902	I23O1_HUMAN	indoleamine 2,3-dioxygenase 1			12				L-Tryptophan(DB00150)|Melatonin(DB01065)	GATGTCCGTAAGGTTTGGAGA	0.398000																								0							SO:0001630	splice_region_variant			ENST00000518237.1	1	0	hg19	CCDS47847.1	.	.	.	.	.	.	.	.	.	.	A	16.87	3.243130	0.58995	.	.	ENSG00000131203	ENST00000519154;ENST00000522495;ENST00000518237	T;T;T	0.50277	0.75;0.75;0.75	5.65	5.65	0.86999	.	0.166139	0.38605	N	0.001628	T	0.67767	0.2928	M	0.83953	2.67	0.41481	D	0.98816	D	0.65815	0.995	D	0.64144	0.922	T	0.72384	-0.4310	9	.	.	.	-19.5956	12.2669	0.54683	1.0:0.0:0.0:0.0	.	101	P14902	I23O1_HUMAN	M	101	ENSP00000428716:K101M;ENSP00000430505:K101M;ENSP00000430950:K101M	.	K	+	2	0	IDO1	39894882	0.998000	0.40836	0.974000	0.42286	0.281000	0.26958	4.977000	0.63792	2.154000	0.67381	0.477000	0.44152	AAG		TCGA-US-A77E-01A-11D-A32N-08	IDO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376987.1	1	0	1	76	270	0	63	0	3.070964e-01	1	4	0	63	2		0	0	0	0	0	2	1	1.000000	74	267	0	60	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	0	1	1	1.967067	0	0.390000	2.070000	0.388808	0.990000	9.000000e-01	1.000000	1.000000	0.993234	0.990000	1	0.990000	1.000000
SOX17	64321	broad.mit.edu	37	8	55372148	55372148	+	Missense_Mutation	SNP	G	G	T			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr8:55372148G>T	ENST00000297316.4	+	2	1042	c.838G>T	c.(838-840)Ggt>Tgt	p.G280C		NM_022454.3	NP_071899.1	Q9H6I2	SOX17_HUMAN	SRY (sex determining region Y)-box 17			18		Lung NSC(129;0.109)|all_epithelial(80;0.176)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;1.9e-07)|Epithelial(17;1.7e-05)|all cancers(17;0.000159)		AGAGCCCGCGGGTCCCTCGAT	0.761000																								0							SO:0001583	missense			ENST00000297316.4	0	1	hg19	CCDS6159.1	.	.	.	.	.	.	.	.	.	.	G	6.286	0.420879	0.11928	.	.	ENSG00000164736	ENST00000297316	T	0.77620	-1.11	4.44	3.49	0.39957	.	0.789630	0.11802	N	0.527999	T	0.73583	0.3605	M	0.63843	1.955	0.25014	N	0.99138	B	0.33345	0.409	B	0.34489	0.184	T	0.64394	-0.6418	10	0.37606	T	0.19	.	9.5602	0.39364	0.0:0.153:0.6895:0.1574	.	280	Q9H6I2	SOX17_HUMAN	C	280	ENSP00000297316:G280C	ENSP00000297316:G280C	G	+	1	0	SOX17	55534701	0.009000	0.17119	0.185000	0.23176	0.085000	0.17905	1.627000	0.37050	2.006000	0.58801	0.455000	0.32223	GGT		TCGA-US-A77E-01A-11D-A32N-08	SOX17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378526.2	1	0	0	7	12	0	8	0	3.320158e-01	0	3	0	8	2		0	0	0	0	0	2	1	0.985060	7	11	0	8	2	0	0	0	0	0	0		-19.982810	1	1	0	0		1	0	1	1	1.967067	0	0.390000	2.070000	0.388808	0.990000	8.400000e-01	1.000000	1.000000	0.990877	0.990000	1	0.990000	1.000000
LAPTM4B	55353	broad.mit.edu	37	8	98817579	98817579	+	Splice_Site	SNP	A	A	T	rs149932386		TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr8:98817579A>T	ENST00000521545.2	+	2	333		c.e2-1		LAPTM4B_ENST00000445593.2_Splice_Site			Q86VI4	LAP4B_HUMAN	lysosomal protein transmembrane 4 beta			10	Breast(36;1.59e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.149)		TTCTTGTTGCAGATCATCAAT	0.388000																								0							SO:0001630	splice_region_variant			ENST00000521545.2	1	0	hg19		.	.	.	.	.	.	.	.	.	.	A	19.74	3.884628	0.72410	.	.	ENSG00000104341	ENST00000445593;ENST00000378722;ENST00000517924;ENST00000521545	.	.	.	5.07	5.07	0.68467	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.653	0.56772	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	LAPTM4B	98886755	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	7.723000	0.84788	2.036000	0.60181	0.533000	0.62120	.		TCGA-US-A77E-01A-11D-A32N-08	LAPTM4B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000380016.2	1	0	0	22	483	0	95		0	0	0	0	95	2		0	0	0	0	0	2	1	0.999998	12	461	0	93	2	0	0	0	0	0	0		-1.522542	0	1	0	0		1	0	1	1	1.967067	0	0.390000	2.070000	0.388808	0.220000	1.400000e-01	0.320000	0.220000	0.231466	0.220000	0	0.170000	0.280000
KLF4	9314	broad.mit.edu	37	9	110249341	110249341	+	Missense_Mutation	SNP	G	G	T			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08			G	T	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr9:110249341G>T	ENST00000374672.4	-	4	1705	c.1232C>A	c.(1231-1233)tCc>tAc	p.S411Y		NM_004235.4	NP_004226.3	O43474	KLF4_HUMAN	Kruppel-like factor 4 (gut)			16					CTTGAGATGGGAACTCTTTGT	0.592000																								0							SO:0001583	missense			ENST00000374672.4	1	1	hg19	CCDS6770.2	.	.	.	.	.	.	.	.	.	.	G	24.9	4.579183	0.86645	.	.	ENSG00000136826	ENST00000374672	T	0.35605	1.3	5.57	4.68	0.58851	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.347798	0.21123	N	0.079795	T	0.66208	0.2766	M	0.89601	3.045	0.80722	D	1	D;D	0.76494	0.989;0.999	P;D	0.72625	0.641;0.978	T	0.74041	-0.3792	10	0.87932	D	0	.	14.0741	0.64880	0.0732:0.0:0.9268:0.0	.	445;411	O43474;O43474-1	KLF4_HUMAN;.	Y	411	ENSP00000363804:S411Y	ENSP00000363804:S411Y	S	-	2	0	KLF4	109289162	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	9.824000	0.99380	1.358000	0.45922	-0.136000	0.14681	TCC		TCGA-US-A77E-01A-11D-A32N-08	KLF4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053556.2	1	0	1	125	651	0	191	1	1	63	70	0	191	2		0	0	0	0	0	2	1	1.000000	122	642	0	190	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	0	1	1	1.968358	0	0.390000	2.070000	0.388808	0.810000	6.900000e-01	0.950000	0.820000	0.827054	0.810000	0	0.750000	0.890000
ELAVL2	1993	broad.mit.edu	37	9	23692693	23692693	+	Missense_Mutation	SNP	A	A	C			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr9:23692693A>C	ENST00000397312.2	-	7	1216	c.942T>G	c.(940-942)aaT>aaG	p.N314K	ELAVL2_ENST00000223951.6_Missense_Mutation_p.N301K|ELAVL2_ENST00000544538.1_Missense_Mutation_p.N314K|ELAVL2_ENST00000380117.1_Missense_Mutation_p.N314K|ELAVL2_ENST00000380110.4_Missense_Mutation_p.N344K	NM_004432.3	NP_004423.2	Q12926	ELAV2_HUMAN	ELAV like neuron-specific RNA binding protein 2			39					CTTTGCATTTATTGGTGTTAA	0.473000																								0							SO:0001583	missense			ENST00000397312.2	1	1	hg19	CCDS6515.1	.	.	.	.	.	.	.	.	.	.	A	12.36	1.913291	0.33815	.	.	ENSG00000107105	ENST00000223951;ENST00000397312;ENST00000544538;ENST00000380110;ENST00000380117;ENST00000359598	T;T;T;T	0.05996	3.36;3.36;3.36;3.36	5.94	4.81	0.61882	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.12178	0.0296	L	0.28740	0.885	0.80722	D	1	P;D	0.61080	0.776;0.989	B;D	0.66497	0.377;0.944	T	0.05435	-1.0885	10	0.51188	T	0.08	.	8.3434	0.32258	0.7382:0.0:0.2618:0.0	.	314;301	Q12926;Q12926-2	ELAV2_HUMAN;.	K	301;314;314;301;314;342	ENSP00000223951:N301K;ENSP00000380479:N314K;ENSP00000440998:N314K;ENSP00000369460:N314K	ENSP00000223951:N301K	N	-	3	2	ELAVL2	23682693	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.183000	0.58317	1.074000	0.40909	0.528000	0.53228	AAT		TCGA-US-A77E-01A-11D-A32N-08	ELAVL2-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051943.2	1	0	0	20	465	0	111		0	0	0	0	111	2		0	0	0	0	0	2	1	0.999995	20	458	0	110	2	0	0	0	0	0	0		-19.576970	1	1	0	0		1	0	2	2	1.971494	1	0.390000	2.070000	0.390000	0.210000	1.300000e-01	0.310000	0.210000	0.220407	0.210000	0	0.160000	0.270000
TRPM3	80036	broad.mit.edu	37	9	73442926	73442926	+	Silent	SNP	C	C	T			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr9:73442926C>T	ENST00000377111.2	-	6	1053	c.810G>A	c.(808-810)cgG>cgA	p.R270R	TRPM3_ENST00000360823.2_Silent_p.R117R|TRPM3_ENST00000396283.1_Silent_p.R117R|TRPM3_ENST00000361823.5_Silent_p.R117R|TRPM3_ENST00000396285.1_Silent_p.R117R|TRPM3_ENST00000423814.3_Silent_p.R272R|TRPM3_ENST00000396292.4_Silent_p.R117R|TRPM3_ENST00000377105.1_Silent_p.R117R|TRPM3_ENST00000358082.3_Silent_p.R117R|TRPM3_ENST00000377101.1_Silent_p.R117R|TRPM3_ENST00000377110.3_Silent_p.R270R|TRPM3_ENST00000408909.2_Silent_p.R117R|TRPM3_ENST00000396280.5_Silent_p.R117R|TRPM3_ENST00000377106.1_Silent_p.R117R|TRPM3_ENST00000357533.2_Silent_p.R272R	NM_001007471.2	NP_001007472.2	Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3			95					TCTGGTATGGCCGGACAACCT	0.458000																								0							SO:0001819	synonymous_variant			ENST00000377111.2	0	1	hg19		.	.	.	.	.	.	.	.	.	.	C	9.804	1.181369	0.21787	0.0	1.16E-4	ENSG00000083067	ENST00000396280	.	.	.	5.83	1.69	0.24217	.	.	.	.	.	T	0.46502	0.1396	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.27365	-1.0076	4	.	.	.	-20.7328	4.1127	0.10067	0.2451:0.4474:0.0:0.3075	.	.	.	.	T	117	.	.	A	-	1	0	TRPM3	72632746	0.626000	0.27120	0.998000	0.56505	0.980000	0.70556	-0.166000	0.09954	0.371000	0.24564	0.650000	0.86243	GCC		TCGA-US-A77E-01A-11D-A32N-08	TRPM3-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000214157.5	0	0	0	5	523	0	128		0	0	0	0	128	2		0	0	0	0	0	2	1	0.936874	5	520	0	126	2	0	0	0	0	0	0		-2.167190	0	1	121410	2	35	1	0	1	1	1.968358	0	0.390000	2.070000	0.388808	0.040000	1.000000e-02	0.110000	0.050000	0.057714	0.040000	0	0.020000	0.080000
KIF27	55582	broad.mit.edu	37	9	86504131	86504131	+	Missense_Mutation	SNP	A	A	C			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chr9:86504131A>C	ENST00000297814.2	-	7	1990	c.1847T>G	c.(1846-1848)aTa>aGa	p.I616R	KIF27_ENST00000334204.2_Missense_Mutation_p.I616R|KIF27_ENST00000413982.1_Missense_Mutation_p.I616R|KIF27_ENST00000376347.1_Missense_Mutation_p.I7R	NM_017576.1	NP_060046.1	Q86VH2	KIF27_HUMAN	kinesin family member 27			43					TCCAGCAAATATTCGATCCAG	0.403000																								0							SO:0001583	missense			ENST00000297814.2	1	1	hg19	CCDS6665.1	.	.	.	.	.	.	.	.	.	.	A	17.75	3.465512	0.63513	.	.	ENSG00000165115	ENST00000297814;ENST00000413982;ENST00000334204;ENST00000376347	T;T;T;T	0.53206	0.63;0.63;0.63;0.63	4.85	3.62	0.41486	.	0.461427	0.16718	U	0.202373	T	0.30448	0.0765	N	0.08118	0	0.38420	D	0.946164	P;P;B	0.42993	0.467;0.797;0.337	B;P;B	0.44359	0.133;0.447;0.054	T	0.11446	-1.0587	10	0.29301	T	0.29	.	10.6689	0.45747	0.8568:0.0:0.0:0.1432	.	616;616;616	Q86VH2-3;Q86VH2-2;Q86VH2	.;.;KIF27_HUMAN	R	616;616;616;7	ENSP00000297814:I616R;ENSP00000401688:I616R;ENSP00000333928:I616R;ENSP00000365525:I7R	ENSP00000297814:I616R	I	-	2	0	KIF27	85693951	1.000000	0.71417	0.999000	0.59377	0.826000	0.46750	5.222000	0.65277	1.949000	0.56562	0.455000	0.32223	ATA		TCGA-US-A77E-01A-11D-A32N-08	KIF27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052861.1	0	0	0	32	714	0	118	0	0	0	1	0	118	2		0	0	0	0	0	2	1	1.000000	31	700	0	118	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	0	1	1	1.968358	0	0.390000	2.070000	0.388808	0.210000	1.400000e-01	0.300000	0.220000	0.225328	0.210000	0	0.180000	0.260000
DRP2	1821	broad.mit.edu	37	X	100500426	100500426	+	Missense_Mutation	SNP	T	T	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chrX:100500426T>A	ENST00000395209.3	+	11	1692	c.1165T>A	c.(1165-1167)Tac>Aac	p.Y389N	DRP2_ENST00000541709.1_Missense_Mutation_p.Y311N|DRP2_ENST00000538510.1_Missense_Mutation_p.Y389N|DRP2_ENST00000402866.1_Missense_Mutation_p.Y389N	NM_001939.2	NP_001930.2	Q13474	DRP2_HUMAN	dystrophin related protein 2			31					GACAGAGTTATACCAAACCCT	0.468000																								0							SO:0001583	missense			ENST00000395209.3	0	1	hg19	CCDS14480.2	.	.	.	.	.	.	.	.	.	.	T	27.7	4.854763	0.91355	.	.	ENSG00000102385	ENST00000402866;ENST00000395209;ENST00000541709;ENST00000538510	T;T;T;T	0.63913	-0.07;-0.07;-0.07;-0.07	5.84	5.84	0.93424	EF-hand domain, type 1 (1);	0.059046	0.64402	D	0.000001	T	0.77485	0.4137	M	0.73962	2.25	0.80722	D	1	D	0.76494	0.999	D	0.63793	0.918	T	0.80616	-0.1303	10	0.87932	D	0	-13.6727	15.1354	0.72562	0.0:0.0:0.0:1.0	.	389	Q13474	DRP2_HUMAN	N	389;389;311;389	ENSP00000385038:Y389N;ENSP00000378635:Y389N;ENSP00000444752:Y311N;ENSP00000441051:Y389N	ENSP00000378635:Y389N	Y	+	1	0	DRP2	100387082	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	1.957000	0.56846	0.486000	0.48141	TAC		TCGA-US-A77E-01A-11D-A32N-08	DRP2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057522.3	0	0	0	3	44	0	8		0	0	0	0	8	2		0	0	0	0	0	2	1	0.805743	2	44	0	8	2	0	0	0	0	0	0		-7.624812	1	0	0	0		1	0	1	1			0.390000	2.070000	0.390000	0.180000	5.000000e-02	0.400000	0.160000	0.202488	0.180000	0	0.100000	0.290000
KIF4A	24137	broad.mit.edu	37	X	69521814	69521814	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chrX:69521814G>A	ENST00000374403.3	+	6	663	c.581G>A	c.(580-582)gGc>gAc	p.G194D	KIF4A_ENST00000374388.3_Missense_Mutation_p.G194D	NM_012310.4	NP_036442.3	O95239	KIF4A_HUMAN	kinesin family member 4A			51					TTGGAACAGGGCAACAACTCT	0.438000																								0							SO:0001583	missense			ENST00000374403.3	0	1	hg19	CCDS14401.1	.	.	.	.	.	.	.	.	.	.	G	25.5	4.645442	0.87859	.	.	ENSG00000090889	ENST00000374388;ENST00000374403	D;D	0.83837	-1.77;-1.77	5.1	5.1	0.69264	Kinesin, motor domain (4);	0.000000	0.53938	D	0.000051	D	0.95214	0.8448	H	0.99357	4.53	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.995	D	0.97585	1.0113	10	0.87932	D	0	.	16.5735	0.84631	0.0:0.0:1.0:0.0	.	194;194	O95239;O95239-2	KIF4A_HUMAN;.	D	194	ENSP00000363509:G194D;ENSP00000363524:G194D	ENSP00000363509:G194D	G	+	2	0	KIF4A	69438539	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	9.316000	0.96319	2.115000	0.64714	0.538000	0.68166	GGC		TCGA-US-A77E-01A-11D-A32N-08	KIF4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057068.1	0	0	0	4	220	0	47	0	1.718410e-03	0	3	0	47	2		0	0	0	0	0	2	1	0.886880	4	216	0	46	2	0	0	0	0	0	0		-2.733447	1	1	0	0		1	0	1	1			0.390000	2.070000	0.390000	0.040000	1.000000e-02	0.110000	0.050000	0.056321	0.040000	0	0.020000	0.080000
ATP7A	538	broad.mit.edu	37	X	77244909	77244909	+	Missense_Mutation	SNP	A	A	T			TCGA-US-A77E-01A-11D-A32N-08	TCGA-US-A77E-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41e7b7ba-2ad3-461e-b034-9012b11b0ac6	d4212d5b-eb9c-4720-a339-23763029e0e2	g.chrX:77244909A>T	ENST00000341514.6	+	4	946	c.791A>T	c.(790-792)gAa>gTa	p.E264V	ATP7A_ENST00000350425.4_Intron|ATP7A_ENST00000343533.5_Missense_Mutation_p.E264V	NM_000052.5	NP_000043.4	Q04656	ATP7A_HUMAN	ATPase, Cu++ transporting, alpha polypeptide			53				Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	AAATCCTCAGAAGGGTCACAG	0.403000																								0							SO:0001583	missense			ENST00000341514.6	1	1	hg19	CCDS35339.1	.	.	.	.	.	.	.	.	.	.	A	3.798	-0.042338	0.07452	.	.	ENSG00000165240	ENST00000343533;ENST00000341514;ENST00000400860;ENST00000355691	D;D	0.96334	-3.98;-3.98	4.78	2.24	0.28232	.	0.471910	0.20943	N	0.082889	D	0.95519	0.8544	M	0.88450	2.955	0.80722	D	1	B;B	0.28783	0.002;0.222	B;B	0.35688	0.007;0.208	D	0.91217	0.5003	10	0.30078	T	0.28	-11.1068	4.7038	0.12839	0.5353:0.2948:0.1699:0.0	.	264;274	Q04656;Q59HD1	ATP7A_HUMAN;.	V	264;264;264;274	ENSP00000343026:E264V;ENSP00000345728:E264V	ENSP00000345728:E264V	E	+	2	0	ATP7A	77131565	0.959000	0.32827	0.899000	0.35326	0.225000	0.24961	1.880000	0.39628	0.694000	0.31654	0.422000	0.28245	GAA		TCGA-US-A77E-01A-11D-A32N-08	ATP7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057306.1	1	0	1	114	222	0	83	0	2.691430e-01	1	2	0	83	2		0	0	0	0	0	2	1	1.000000	113	222	0	82	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	0	1	1			0.390000	2.070000	0.390000	0.860000	7.300000e-01	0.980000	0.870000	0.864439	0.860000	1	0.790000	0.930000
