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
TGFBR2	7048	broad.mit.edu	37	3	30713755	30713758	+	Frame_Shift_Del	DEL	CCTC	CCTC	-			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08			CCTC	-	CCTC	CCTC		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr3:30713755_30713758delCCTC	ENST00000295754.5	+	4	1462_1465	c.1080_1083delCCTC	c.(1078-1083)cacctcfs	p.HL360fs	TGFBR2_ENST00000359013.4_Frame_Shift_Del_p.HL385fs	NM_003242.5	NP_003233.4	P37173	TGFR2_HUMAN	transforming growth factor, beta receptor II (70/80kDa)			53					GGATTGCTCACCTCCACAGTGATC	0.608000																								0							SO:0001589	frameshift_variant			ENST00000295754.5	1	1	hg19	CCDS2648.1																																																																																				TCGA-2L-AAQL-01A-11D-A38G-08	TGFBR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252994.2	1	0	0	84	539	1	224	0	5.086617e-02	0	3	1	224	2	1	1	135	554	0	336	2	1	1.000000	103	543	2	218	16	0	0	0	0	0	0		-3.318799	1	1	0	0		1	0	1	1	1.703696	1	0.380000	1.790000	0.234568	0.560000	4.600000e-01	0.690000	0.570000	0.576759	0.560000	0	0.510000	0.630000
FLNC	2318	broad.mit.edu	37	7	128495281	128495282	+	Frame_Shift_Ins	INS	-	-	A			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr7:128495281_128495282insA	ENST00000325888.8	+	43	7425_7426	c.7164_7165insA	c.(7165-7167)gatfs	p.D2389fs	RP11-309L24.2_ENST00000469965.1_RNA|FLNC_ENST00000346177.6_Frame_Shift_Ins_p.D2356fs	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma			128					TCAAGTTCAATGATGAGCACAT	0.624000																								0							SO:0001589	frameshift_variant			ENST00000325888.8	0	1	hg19	CCDS43644.1																																																																																				TCGA-2L-AAQL-01A-11D-A38G-08	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3	1	0	0	59	572	0	196	0	2.442070e-01	0	10	0	196	2			0	0	0	0		1	1.000000	62	561	0	194	2	0	0	0	0	0	0		-16.845870	1	1	0	0		1	1	2	3	2.121637	0	0.380000	1.790000	0.386988	0.490000	3.800000e-01	1.000000	0.500000	0.526627	0.490000	0	0.430000	0.580000
KNDC1	85442	broad.mit.edu	37	10	135009218	135009218	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr10:135009218G>A	ENST00000304613.3	+	10	1648	c.1627G>A	c.(1627-1629)Gtc>Atc	p.V543I	KNDC1_ENST00000368572.2_Missense_Mutation_p.V543I|KNDC1_ENST00000368571.2_Missense_Mutation_p.V478I			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1			60		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)			CAAGTTCAGCGTCCCCCGCAA	0.687000																								0							SO:0001583	missense			ENST00000304613.3	1	1	hg19	CCDS7674.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	1.067	-0.671207	0.03403	2.27E-4	3.49E-4	ENSG00000171798	ENST00000304613;ENST00000368572;ENST00000368571	T;T;T	0.32272	1.46;1.46;1.46	4.63	-5.31	0.02730	KIND (2);	0.976965	0.08346	N	0.960109	T	0.13415	0.0325	N	0.15975	0.35	0.09310	N	1	B;B	0.17465	0.022;0.005	B;B	0.09377	0.004;0.002	T	0.28138	-1.0053	10	0.27082	T	0.32	-20.5636	5.616	0.17432	0.5361:0.0:0.2633:0.2006	.	478;543	Q76NI1-2;Q76NI1	.;VKIND_HUMAN	I	543;543;478	ENSP00000304437:V543I;ENSP00000357561:V543I;ENSP00000357560:V478I	ENSP00000304437:V543I	V	+	1	0	KNDC1	134859208	0.000000	0.05858	0.002000	0.10522	0.026000	0.11368	-0.398000	0.07259	-0.658000	0.05366	-0.692000	0.03713	GTC		TCGA-2L-AAQL-01A-11D-A38G-08	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	1	0	1	26	90	0	42	0	0	0	1	0	42	2		0	0	0	0	0	2	1	1.000000	26	90	0	42	2		0	0	0	0	42	2	-20.000000	1	1	121322	7	40	1	1	2	3	2.117198	0	0.380000	1.790000	0.385835	0.990000	8.200000e-01	1.000000	1.000000	0.985433	0.990000	1	0.990000	1.000000
CUBN	8029	broad.mit.edu	37	10	17169885	17169885	+	Silent	SNP	C	C	A			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr10:17169885C>A	ENST00000377833.4	-	3	356	c.291G>T	c.(289-291)ggG>ggT	p.G97G	CUBN_ENST00000377823.1_Silent_p.G97G	NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)			241				Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	CAATTGCACTCCCTTTTAACT	0.323000																								0							SO:0001819	synonymous_variant			ENST00000377833.4	1	1	hg19	CCDS7113.1																																																																																				TCGA-2L-AAQL-01A-11D-A38G-08	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	1	0	1	101	589	0	212		0	0	0	0	212	2		0	0	0	0	0	2	1	1.000000	99	577	0	208	2		0	0	0	0	212	2	-20.000000	1	1	0	0		1	1	2	3	2.117198	0	0.380000	1.790000	0.385835	0.770000	6.400000e-01	1.000000	0.780000	0.789605	0.770000	0	0.700000	0.860000
TLL2	7093	broad.mit.edu	37	10	98157035	98157035	+	Missense_Mutation	SNP	G	G	A	rs142713663	byFrequency	TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr10:98157035G>A	ENST00000357947.3	-	11	1517	c.1292C>T	c.(1291-1293)cCg>cTg	p.P431L	TLL2_ENST00000469598.1_5'UTR	NM_012465.3	NP_036597.1	Q9Y6L7	TLL2_HUMAN	tolloid-like 2			58		Colorectal(252;0.0846)			GAGGGGCTCCGGGATCTTATC	0.577000																								0							SO:0001583	missense			ENST00000357947.3	1	1	hg19	CCDS7449.1	.	.	.	.	.	.	.	.	.	.	G	19.66	3.868544	0.72065	0.0	0.001047	ENSG00000095587	ENST00000357947	T	0.39406	1.08	5.11	5.11	0.69529	CUB (5);	0.000000	0.45361	D	0.000368	T	0.72590	0.3479	M	0.92268	3.29	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.76716	-0.2857	10	0.40728	T	0.16	.	17.7077	0.88313	0.0:0.0:1.0:0.0	.	431	Q9Y6L7	TLL2_HUMAN	L	431	ENSP00000350630:P431L	ENSP00000350630:P431L	P	-	2	0	TLL2	98147025	1.000000	0.71417	0.486000	0.27416	0.177000	0.22998	9.464000	0.97655	2.654000	0.90174	0.650000	0.86243	CCG		TCGA-2L-AAQL-01A-11D-A38G-08	TLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049608.1	0	0	1	20	166	0	65	0	0	1	0	0	65	2		0	0	0	0	0	2	1	0.999996	20	163	0	65	2		0	0	0	0	65	2	-3.075081	1	1	121412	77	49	1	1	2	3	2.117198	0	0.380000	1.790000	0.385835	0.580000	3.600000e-01	1.000000	0.570000	0.603999	0.580000	0	0.460000	0.730000
NCAM1	4684	broad.mit.edu	37	11	113078701	113078701	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr11:113078701C>T	ENST00000533760.1	+	7	1138	c.539C>T	c.(538-540)gCg>gTg	p.A180V	NCAM1_ENST00000397957.4_3'UTR|NCAM1_ENST00000401611.2_Missense_Mutation_p.A297V|NCAM1_ENST00000316851.7_Missense_Mutation_p.A288V	NM_001242608.1	NP_001229537.1	P13591	NCAM1_HUMAN	neural cell adhesion molecule 1			49		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)			GAGCAGGATGCGACCATCCAC	0.537000																								0							SO:0001583	missense			ENST00000533760.1	1	1	hg19		.	.	.	.	.	.	.	.	.	.	C	21.1	4.105555	0.77096	.	.	ENSG00000149294	ENST00000531044;ENST00000401611;ENST00000316851	T;T	0.69040	-0.37;-0.37	5.71	4.75	0.60458	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.205034	0.50627	D	0.000106	T	0.72293	0.3442	.	.	.	0.80722	D	1	D;D;D;D;D	0.76494	0.999;0.999;0.999;0.999;0.97	P;P;P;P;B	0.51657	0.612;0.612;0.609;0.676;0.329	T	0.75260	-0.3380	9	0.56958	D	0.05	-40.4986	15.5067	0.75745	0.1389:0.8611:0.0:0.0	.	298;298;298;298;298	P13591-5;P13591-1;P13591;P13591-3;P13591-6	.;.;NCAM1_HUMAN;.;.	V	180;297;288	ENSP00000384055:A297V;ENSP00000318472:A288V	ENSP00000318472:A288V	A	+	2	0	NCAM1	112583911	0.996000	0.38824	0.946000	0.38457	0.966000	0.64601	4.470000	0.60175	2.710000	0.92621	0.655000	0.94253	GCG		TCGA-2L-AAQL-01A-11D-A38G-08	NCAM1-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000394068.2	0	0	0	4	60	0	22	0	0	0	1	0	22	2		0	0	0	0	0	2	1	0.892544	4	60	0	21	2		0	0	0	0	22	2	-8.011300	1	1	0	0		1	0	1	1	1.900546	0	0.380000	1.790000	0.324839	0.320000	1.100000e-01	0.670000	0.290000	0.354389	0.320000	0	0.200000	0.500000
OR4D5	219875	broad.mit.edu	37	11	123810974	123810974	+	Silent	SNP	G	G	A			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr11:123810974G>A	ENST00000307033.2	+	1	725	c.651G>A	c.(649-651)tcG>tcA	p.S217S		NM_001001965.1	NP_001001965.1	Q8NGN0	OR4D5_HUMAN	olfactory receptor, family 4, subfamily D, member 5			41		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)			TTCTGGGATCGTACACAGCAC	0.512000																								0							SO:0001819	synonymous_variant			ENST00000307033.2	0	1	hg19	CCDS31699.1																																																																																				TCGA-2L-AAQL-01A-11D-A38G-08	OR4D5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387263.1	0	0	0	8	814	0	324		0	0	0	0	324	2		0	0	0	0	0	2	1	0.988035	8	791	0	321	2		0	0	0	0	324	2	-2.142773	0	1	121412	6	41	1	0	1	1	1.900546	0	0.380000	1.790000	0.324839	0.040000	1.000000e-02	0.090000	0.050000	0.052671	0.040000	0	0.020000	0.070000
OPCML	4978	broad.mit.edu	37	11	132307148	132307148	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr11:132307148G>A	ENST00000331898.7	-	4	1210	c.632C>T	c.(631-633)cCc>cTc	p.P211L	OPCML_ENST00000524381.1_Missense_Mutation_p.P204L|OPCML_ENST00000541867.1_Missense_Mutation_p.P211L|OPCML_ENST00000374778.4_Missense_Mutation_p.P170L|OPCML_ENST00000529038.1_5'UTR	NM_002545.3	NP_002536.1	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion molecule-like			47	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)			CCGCACATCGGGCGCAGCGAC	0.542000																								0							SO:0001583	missense			ENST00000331898.7	1	1	hg19	CCDS8492.1	.	.	.	.	.	.	.	.	.	.	G	19.43	3.825927	0.71143	.	.	ENSG00000183715	ENST00000331898;ENST00000524381;ENST00000374778;ENST00000416724;ENST00000541867	T;T;T;T	0.59224	0.29;0.28;1.19;1.19	5.95	5.95	0.96441	Immunoglobulin-like (1);	0.000000	0.85682	D	0.000000	T	0.77980	0.4212	M	0.75085	2.285	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.999;1.0	D;D;D;D	0.85130	0.997;0.997;0.995;0.997	T	0.78640	-0.2125	10	0.87932	D	0	-13.4278	19.9958	0.97383	0.0:0.0:1.0:0.0	.	211;204;210;211	B7ZLQ1;Q7Z3W6;B7ZLQ0;Q14982	.;.;.;OPCM_HUMAN	L	211;204;170;178;211	ENSP00000330862:P211L;ENSP00000434750:P204L;ENSP00000363910:P170L;ENSP00000445496:P211L	ENSP00000330862:P211L	P	-	2	0	OPCML	131812358	1.000000	0.71417	0.320000	0.25306	0.040000	0.13550	9.476000	0.97823	2.825000	0.97269	0.655000	0.94253	CCC		TCGA-2L-AAQL-01A-11D-A38G-08	OPCML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374689.3	1	0	1	40	295	0	129		0	0	0	0	129	2		0	0	0	0	0	2	1	1.000000	40	287	0	127	2		0	0	0	0	129	2	-3.221909	1	1	0	0		1	0	1	1	1.900546	0	0.380000	1.790000	0.324839	0.570000	4.200000e-01	0.750000	0.570000	0.584373	0.570000	0	0.490000	0.670000
FAT3	120114	broad.mit.edu	37	11	92532543	92532543	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr11:92532543G>A	ENST00000298047.6	+	9	6381	c.6364G>A	c.(6364-6366)Gtc>Atc	p.V2122I	FAT3_ENST00000525166.1_Missense_Mutation_p.V1972I|FAT3_ENST00000409404.2_Missense_Mutation_p.V2122I			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	p.V2122L(2)		85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)			AGTGACCTATGTCCTGCAGGA	0.423000										TCGA Ovarian(4;0.039)														2	Substitution - Missense(2)						SO:0001583	missense			ENST00000298047.6	1	1	hg19		.	.	.	.	.	.	.	.	.	.	G	6.771	0.511125	0.12883	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166	T;T;T	0.01767	4.65;4.65;4.65	5.9	0.248	0.15526	.	.	.	.	.	T	0.00936	0.0031	N	0.12853	0.265	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.53464	-0.8435	9	0.23302	T	0.38	.	0.7489	0.00987	0.2335:0.2878:0.2715:0.2072	.	2122	Q8TDW7-3	.	I	2122;2122;1972	ENSP00000298047:V2122I;ENSP00000387040:V2122I;ENSP00000432586:V1972I	ENSP00000298047:V2122I	V	+	1	0	FAT3	92172191	0.011000	0.17503	0.983000	0.44433	0.964000	0.63967	0.949000	0.29109	0.412000	0.25729	-0.136000	0.14681	GTC		TCGA-2L-AAQL-01A-11D-A38G-08	FAT3-201	KNOWN	basic	protein_coding	protein_coding		1	0	1	23	108	0	42		0	0	0	0	42	2		0	0	0	0	0	2	1	1.000000	23	106	0	42	2		0	0	0	0	42	2	-20.000000	1	1	0	0		1	0	1	1	1.900546	0	0.380000	1.790000	0.324839	0.840000	5.600000e-01	1.000000	1.000000	0.840859	0.840000	0	0.690000	1.000000
KRAS	3845	broad.mit.edu	37	12	25380276	25380276	+	Missense_Mutation	SNP	T	T	C	rs121913240		TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08			T	C	T	T		Valid	Somatic	Phase_I	WXS	KRAS_deep			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr12:25380276T>C	ENST00000256078.4	-	3	245	c.182A>G	c.(181-183)cAa>cGa	p.Q61R	KRAS_ENST00000557334.1_Intron|AC087239.1_ENST00000594112.1_5'Flank|KRAS_ENST00000311936.3_Missense_Mutation_p.Q61R	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	p.Q61L(73)|p.Q61R(56)|p.Q61P(12)	UBE2L3/KRAS(2)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)		GTACTCCTCTTGACCTGCTGT	0.418000	Q61L(NCIH650_LUNG)|Q61L(SW948_LARGE_INTESTINE)|Q61R(PANC0213_PANCREAS)	119	Mis		pancreatic, colorectal, lung, thyroid, AML, others				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)			Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		L, E, M, O	141	Substitution - Missense(141)						SO:0001583	missense	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	ENST00000256078.4	1	1	hg19	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.022613	0.75275	.	.	ENSG00000133703	ENST00000311936;ENST00000256078	D;D	0.83673	-1.75;-1.75	5.77	5.77	0.91146	Small GTP-binding protein domain (1);	0.049057	0.85682	D	0.000000	D	0.88358	0.6415	M	0.92367	3.3	0.80722	D	1	B;B	0.26744	0.158;0.026	B;B	0.32805	0.135;0.153	D	0.87885	0.2680	10	0.66056	D	0.02	.	15.5753	0.76373	0.0:0.0:0.0:1.0	.	61;61	P01116-2;P01116	.;RASK_HUMAN	R	61	ENSP00000308495:Q61R;ENSP00000256078:Q61R	ENSP00000256078:Q61R	Q	-	2	0	KRAS	25271543	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.983000	0.88140	2.326000	0.78906	0.533000	0.62120	CAA		TCGA-2L-AAQL-01A-11D-A38G-08	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	1	0	1	68	298	0	102	0	6.358014e-01	1	10	0	102	2	1	1	107	675	0	451	2	1	1.000000	66	293	0	102	2	1	1	1264	6758	0	102	2	-20.000000	1	1	0	0		1	0	0	0	2.018804	0	0.380000	1.790000	0.358045	0.930000	7.400000e-01	1.000000	1.000000	0.927625	0.930000	1	0.840000	1.000000
AHNAK2	113146	broad.mit.edu	37	14	105413912	105413912	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr14:105413912C>T	ENST00000333244.5	-	7	7995	c.7876G>A	c.(7876-7878)Gat>Aat	p.D2626N	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2			33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)		CGCGCACCATCCAGCTTTGCT	0.592000																								0							SO:0001583	missense			ENST00000333244.5	0	1	hg19	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	c	13.05	2.120665	0.37436	.	.	ENSG00000185567	ENST00000333244	T	0.01629	4.72	2.6	2.6	0.31112	.	.	.	.	.	T	0.02156	0.0067	M	0.70903	2.155	0.09310	N	1	P	0.40834	0.73	B	0.34385	0.181	T	0.42582	-0.9443	9	0.21540	T	0.41	.	4.3944	0.11356	0.0:0.7139:0.0:0.2861	.	2626	Q8IVF2	AHNK2_HUMAN	N	2626	ENSP00000353114:D2626N	ENSP00000353114:D2626N	D	-	1	0	AHNAK2	104484957	0.000000	0.05858	0.005000	0.12908	0.015000	0.08874	-0.581000	0.05820	1.000000	0.39049	0.306000	0.20318	GAT		TCGA-2L-AAQL-01A-11D-A38G-08	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	0	0	0	9	1282	0	583		0	0	0	0	583	2		0	0	0	0	0	2	1	0.992519	9	1211	0	582	2		0	0	0	0	583	2	-2.875356	1	1	0	0		1	0	1	1	1.727848	1	0.380000	1.790000	0.241683	0.020000	0	0.060000	0.030000	0.033207	0.020000	0	0.010000	0.040000
TEP1	7011	broad.mit.edu	37	14	20869179	20869179	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr14:20869179G>A	ENST00000262715.5	-	9	1553	c.1513C>T	c.(1513-1515)Cgg>Tgg	p.R505W	TEP1_ENST00000556935.1_Missense_Mutation_p.R397W	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1			96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)		TTGTTCCCCCGTAGGCTCAGC	0.542000																								0							SO:0001583	missense			ENST00000262715.5	0	1	hg19	CCDS9548.1	.	.	.	.	.	.	.	.	.	.	G	15.53	2.860278	0.51482	.	.	ENSG00000129566	ENST00000262715;ENST00000359243;ENST00000556935	T;T	0.15718	2.4;2.4	5.71	2.77	0.32553	TROVE (2);	0.542528	0.20377	N	0.093526	T	0.17789	0.0427	M	0.64997	1.995	0.20307	N	0.999916	B;B	0.22346	0.022;0.068	B;B	0.17722	0.008;0.019	T	0.18335	-1.0340	10	0.87932	D	0	-9.617	8.5605	0.33507	0.0721:0.0:0.4738:0.4541	.	397;505	G3V5X7;Q99973	.;TEP1_HUMAN	W	505;505;397	ENSP00000262715:R505W;ENSP00000452574:R397W	ENSP00000262715:R505W	R	-	1	2	TEP1	19939019	0.002000	0.14202	0.333000	0.25482	0.410000	0.31052	0.233000	0.17911	0.752000	0.32923	0.555000	0.69702	CGG		TCGA-2L-AAQL-01A-11D-A38G-08	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	0	0	0	4	303	0	97	0	0	0	1	0	97	2		0	0	0	0	0	2	1	0.886320	4	297	0	96	2		0	0	0	0	97	2	-2.721050	1	1	121412	4	35	1	1	2	3	2.137626	0	0.380000	1.790000	0.389283	0.070000	2.000000e-02	1.000000	0.070000	0.144784	0.070000	0	0.040000	0.140000
CHD8	57680	broad.mit.edu	37	14	21875121	21875121	+	Missense_Mutation	SNP	C	C	G			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr14:21875121C>G	ENST00000557364.1	-	14	3064	c.2801G>C	c.(2800-2802)tGt>tCt	p.C934S	CHD8_ENST00000430710.3_Missense_Mutation_p.C655S|CHD8_ENST00000399982.2_Missense_Mutation_p.C934S|CHD8_ENST00000555962.1_Intron			Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8			85	all_cancers(95;0.00121)		Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)		AAGCTCAGGACAATCTGACAA	0.438000																								0							SO:0001583	missense			ENST00000557364.1	1	1	hg19	CCDS53885.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.5|24.5	4.542986|4.542986	0.86022|0.86022	.|.	.|.	ENSG00000100888|ENSG00000100888	ENST00000430710;ENST00000399982;ENST00000262707;ENST00000557364|ENST00000555935	D;D;D|.	0.93019|.	-3.15;-3.15;-3.15|.	5.41|5.41	5.41|5.41	0.78517|0.78517	DEAD-like helicase (2);SNF2-related (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.34193|0.34193	0.0889|0.0889	N|N	0.02334|0.02334	-0.595|-0.595	0.80722|0.80722	D|D	1|1	B;P|.	0.36633|.	0.236;0.562|.	B;B|.	0.43950|.	0.345;0.437|.	T|T	0.30357|0.30357	-0.9981|-0.9981	10|5	0.27785|.	T|.	0.31|.	-17.6138|-17.6138	18.1343|18.1343	0.89612|0.89612	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	934;655|.	Q9HCK8;Q9HCK8-2|.	CHD8_HUMAN;.|.	S|F	655;934;654;934|159	ENSP00000406288:C655S;ENSP00000382863:C934S;ENSP00000451601:C934S|.	ENSP00000262707:C654S|.	C|L	-|-	2|3	0|2	CHD8|CHD8	20944961|20944961	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	5.932000|5.932000	0.70121|0.70121	2.816000|2.816000	0.96949|0.96949	0.561000|0.561000	0.74099|0.74099	TGT|TTG		TCGA-2L-AAQL-01A-11D-A38G-08	CHD8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410436.1	1	0	1	16	82	0	32		0	0	0	0	32	2		0	0	0	0	0	2	1	0.999952	16	80	0	32	2		0	0	0	0	32	2	-20.000000	1	1	0	0		1	1	2	3	2.137626	0	0.380000	1.790000	0.389283	0.890000	5.400000e-01	1.000000	1.000000	0.864814	0.890000	1	0.700000	1.000000
SYNE2	23224	broad.mit.edu	37	14	64468799	64468799	+	Splice_Site	SNP	G	G	C			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr14:64468799G>C	ENST00000344113.4	+	29	3998	c.3786G>C	c.(3784-3786)agG>agC	p.R1262S	SYNE2_ENST00000357395.3_5'UTR|SYNE2_ENST00000358025.3_Splice_Site_p.R1262S|SYNE2_ENST00000554584.1_Splice_Site_p.R1262S	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2			224					AACACCTAAGGGTAAGTATAT	0.368000																								0							SO:0001630	splice_region_variant			ENST00000344113.4	1	0	hg19	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	G	12.13	1.844143	0.32606	.	.	ENSG00000054654	ENST00000358025;ENST00000344113;ENST00000554584;ENST00000261678	T;T;T	0.59224	0.66;0.66;0.28	5.41	5.41	0.78517	.	0.323796	0.26446	N	0.024340	T	0.48732	0.1516	L	0.47716	1.5	0.80722	D	1	P;P	0.38504	0.501;0.634	B;B	0.28011	0.039;0.085	T	0.51450	-0.8704	10	0.39692	T	0.17	.	17.3435	0.87304	0.0:0.0:1.0:0.0	.	1262;1262	Q8WXH0;Q8WXH0-2	SYNE2_HUMAN;.	S	1262	ENSP00000350719:R1262S;ENSP00000341781:R1262S;ENSP00000452570:R1262S	ENSP00000261678:R1262S	R	+	3	2	SYNE2	63538552	1.000000	0.71417	0.941000	0.38009	0.045000	0.14185	5.812000	0.69194	2.709000	0.92574	0.655000	0.94253	AGG		TCGA-2L-AAQL-01A-11D-A38G-08	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	1	0	1	80	317	0	168		0	0	0	0	168	2		0	0	0	0	0	2	1	1.000000	78	312	0	166	2		0	0	0	0	168	2	-3.267440	1	1	0	0		1	0	1	1	1.727848	1	0.380000	1.790000	0.241683	0.850000	6.900000e-01	1.000000	0.860000	0.860600	0.850000	1	0.770000	0.940000
SPESP1	246777	broad.mit.edu	37	15	69238112	69238112	+	Missense_Mutation	SNP	A	A	G			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr15:69238112A>G	ENST00000310673.3	+	2	393	c.239A>G	c.(238-240)cAt>cGt	p.H80R	SPESP1_ENST00000560188.1_3'UTR|NOX5_ENST00000260364.5_Intron|NOX5_ENST00000448182.3_Intron|RP11-809H16.2_ENST00000557966.1_RNA|NOX5_ENST00000455873.3_Intron	NM_145658.3	NP_663633.1	Q6UW49	SPESP_HUMAN	sperm equatorial segment protein 1			19					CTAGTTACACATGGAGACGCT	0.403000																								0							SO:0001583	missense			ENST00000310673.3	0	1	hg19	CCDS10230.1	.	.	.	.	.	.	.	.	.	.	A	1.739	-0.492198	0.04322	.	.	ENSG00000258484	ENST00000310673	T	0.20738	2.05	4.62	-1.08	0.09936	.	0.742875	0.11558	N	0.552026	T	0.14614	0.0353	L	0.32530	0.975	0.09310	N	1	B	0.32160	0.358	B	0.33521	0.165	T	0.25779	-1.0122	10	0.41790	T	0.15	-0.9374	7.6284	0.28226	0.3289:0.5445:0.0:0.1265	.	80	Q6UW49	SPESP_HUMAN	R	80	ENSP00000312284:H80R	ENSP00000312284:H80R	H	+	2	0	SPESP1	67025166	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.104000	0.15313	-0.050000	0.13356	-0.313000	0.08912	CAT		TCGA-2L-AAQL-01A-11D-A38G-08	SPESP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257125.1	0	0	0	9	415	0	141	0	8.415348e-03	0	6	0	141	2		0	0	0	0	0	2	1	0.994077	9	411	0	139	2		0	0	0	0	141	2	-3.404401	1	1	0	0		1	0	2	2	2.115839	1	0.380000	1.790000	0.380000	0.110000	5.000000e-02	0.200000	0.110000	0.123056	0.110000	0	0.070000	0.160000
AKAP13	11214	broad.mit.edu	37	15	86124353	86124353	+	Silent	SNP	G	G	A			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr15:86124353G>A	ENST00000394518.2	+	7	3149	c.3054G>A	c.(3052-3054)gtG>gtA	p.V1018V	AKAP13_ENST00000361243.2_Silent_p.V1018V|RP11-815J21.2_ENST00000561409.1_RNA	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13			98					AGAGCCTGGTGCCACCAGGAG	0.572000													Melanoma(94;603 1453 3280 32295 32951)											0							SO:0001819	synonymous_variant			ENST00000394518.2	0	1	hg19	CCDS32319.1																																																																																				TCGA-2L-AAQL-01A-11D-A38G-08	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	0	0	0	5	298	0	121		0	0	0	0	121	2		0	0	0	0	0	2	1	0.932972	5	289	0	119	2		0	0	0	0	121	2	-5.980025	1	1	0	0		1	0	2	2	2.102882	1	0.380000	1.790000	0.380000	0.090000	3.000000e-02	0.190000	0.080000	0.102966	0.090000	0	0.050000	0.140000
IGFALS	3483	broad.mit.edu	37	16	1843655	1843655	+	Translation_Start_Site	SNP	C	C	A			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr16:1843655C>A	ENST00000215539.3	-	0	109				IGFALS_ENST00000568221.1_Intron|IGFALS_ENST00000415638.3_De_novo_Start_InFrame			P35858	ALS_HUMAN	insulin-like growth factor binding protein, acid labile subunit			8					CAGGGCCATCCTGCATGCAGG	0.716000																								0											ENST00000215539.3	0	1	hg19	CCDS10446.1																																																																																				TCGA-2L-AAQL-01A-11D-A38G-08	IGFALS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250509.2	0	0	0	7	32	0	10	0	4.181185e-02	1	1	0	10	2		0	0	0	0	0	2	1	0.982476	7	31	0	10	2		0	0	0	0	10	2	-15.078530	1	1	0	0		1	1	2	3	2.123545	0	0.380000	1.790000	0.386988	0.980000	4.600000e-01	1.000000	1.000000	0.880501	0.980000	1	0.690000	1.000000
TMC5	79838	broad.mit.edu	37	16	19488791	19488791	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr16:19488791G>A	ENST00000396229.2	+	13	2869	c.2120G>A	c.(2119-2121)gGc>gAc	p.G707D	TMC5_ENST00000381414.4_Missense_Mutation_p.G707D|TMC5_ENST00000542583.2_Missense_Mutation_p.G707D|TMC5_ENST00000561503.1_Missense_Mutation_p.G348D|TMC5_ENST00000219821.5_Missense_Mutation_p.G461D|CTA-363E6.6_ENST00000561762.1_RNA|TMC5_ENST00000541464.1_Missense_Mutation_p.G655D|TMC5_ENST00000564959.1_Missense_Mutation_p.G390D	NM_001105248.1	NP_001098718.1	Q6UXY8	TMC5_HUMAN	transmembrane channel-like 5			31					TCAATCATTGGCATTCTTTGT	0.383000																								0							SO:0001583	missense			ENST00000396229.2	1	1	hg19	CCDS45431.1	.	.	.	.	.	.	.	.	.	.	G	18.05	3.537353	0.65085	.	.	ENSG00000103534	ENST00000541464;ENST00000381414;ENST00000396229;ENST00000542583;ENST00000219821;ENST00000440743	T;T;T;T;T	0.69561	-0.41;-0.03;-0.03;-0.03;-0.03	4.33	4.33	0.51752	.	0.193755	0.43579	D	0.000559	T	0.81781	0.4895	M	0.81802	2.56	0.51233	D	0.99991	D;D;D;D;D;D	0.89917	1.0;0.996;0.999;0.998;0.999;1.0	D;D;D;D;D;D	0.81914	0.992;0.954;0.982;0.94;0.981;0.995	T	0.82625	-0.0365	10	0.38643	T	0.18	-14.3434	16.7528	0.85490	0.0:0.0:1.0:0.0	.	655;390;461;461;707;707	F5GYU8;E7EU57;Q6UXY8-3;B3KUQ8;Q6UXY8;Q6UXY8-2	.;.;.;.;TMC5_HUMAN;.	D	655;707;707;707;461;390	ENSP00000441227:G655D;ENSP00000370822:G707D;ENSP00000379531:G707D;ENSP00000446274:G707D;ENSP00000219821:G461D	ENSP00000219821:G461D	G	+	2	0	TMC5	19396292	1.000000	0.71417	0.998000	0.56505	0.422000	0.31414	7.615000	0.83006	2.112000	0.64535	0.655000	0.94253	GGC		TCGA-2L-AAQL-01A-11D-A38G-08	TMC5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435888.1	1	0	1	111	495	0	223	1	9.929468e-01	11	25	0	223	2		0	0	0	0	0	2	1	1.000000	108	482	0	222	2		0	0	0	0	223	2	-20.000000	1	1	0	0		1	1	2	3	2.123545	0	0.380000	1.790000	0.386988	0.970000	8.100000e-01	1.000000	1.000000	0.956426	0.970000	1	0.890000	1.000000
ADCY9	115	broad.mit.edu	37	16	4164208	4164208	+	Silent	SNP	G	G	A	rs73492586	byFrequency	TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr16:4164208G>A	ENST00000294016.3	-	2	1774	c.1236C>T	c.(1234-1236)gcC>gcT	p.A412A		NM_001116.3	NP_001107.2	O60503	ADCY9_HUMAN	adenylate cyclase 9			47					CCAGGGCGTGGGCAGACTTGT	0.512000																								0							SO:0001819	synonymous_variant			ENST00000294016.3	1	0	hg19	CCDS32382.1																																																																																				TCGA-2L-AAQL-01A-11D-A38G-08	ADCY9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438076.1	1	0	1	68	278	0	104	0	0	0	1	0	104	2		0	0	0	0	0	2	1	1.000000	66	268	0	102	2		0	0	0	0	104	2	-2.705214	1	1	121408	217	55	1	1	2	3	2.123545	0	0.380000	1.790000	0.386988	0.990000	8.300000e-01	1.000000	1.000000	0.977301	0.990000	1	0.930000	1.000000
FOXF1	2294	broad.mit.edu	37	16	86544569	86544569	+	Missense_Mutation	SNP	T	T	C			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr16:86544569T>C	ENST00000262426.4	+	1	437	c.394T>C	c.(394-396)Ttc>Ctc	p.F132L	FENDRR_ENST00000595886.1_lincRNA	NM_001451.2	NP_001442.2	Q12946	FOXF1_HUMAN	forkhead box F1			12					CGAGTTCATGTTCGAGGAGGG	0.632000																								0							SO:0001583	missense			ENST00000262426.4	1	1	hg19	CCDS10957.2	.	.	.	.	.	.	.	.	.	.	T	28.1	4.887395	0.91814	.	.	ENSG00000103241	ENST00000262426	T	0.36340	1.26	4.51	4.51	0.55191	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (3);	0.000000	0.85682	D	0.000000	T	0.49915	0.1585	L	0.45285	1.41	0.80722	D	1	D	0.55605	0.972	D	0.66716	0.946	T	0.52563	-0.8559	10	0.87932	D	0	.	12.9875	0.58599	0.0:0.0:0.0:1.0	.	132	Q12946	FOXF1_HUMAN	L	132	ENSP00000262426:F132L	ENSP00000262426:F132L	F	+	1	0	FOXF1	85102070	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.653000	0.83643	1.668000	0.50843	0.528000	0.53228	TTC		TCGA-2L-AAQL-01A-11D-A38G-08	FOXF1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000269103.2	1	0	0	141	450	0	287	0	0	0	1	0	287	2		0	0	0	0	0	2	1	1.000000	140	433	0	281	2		0	0	0	0	287	2	-20.000000	1	1	0	0		1	0	1	1	1.734762	1	0.380000	1.790000	0.241683	0.980000	8.600000e-01	1.000000	1.000000	0.968899	0.980000	1	0.920000	1.000000
ANKRD11	29123	broad.mit.edu	37	16	89350085	89350085	+	Silent	SNP	C	C	A			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr16:89350085C>A	ENST00000301030.4	-	9	3325	c.2865G>T	c.(2863-2865)ctG>ctT	p.L955L	ANKRD11_ENST00000378330.2_Silent_p.L955L	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11			83		all_hematologic(23;0.00824)|Colorectal(91;0.0475)			TGCAGCTCTCCAGGGCGTCCT	0.612000																								0							SO:0001819	synonymous_variant			ENST00000301030.4	1	1	hg19	CCDS32513.1																																																																																				TCGA-2L-AAQL-01A-11D-A38G-08	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430462.3	1	0	1	111	387	0	218	0	5.052295e-02	1	1	0	218	2		0	0	0	0	0	2	1	1.000000	110	373	0	216	2		0	0	0	0	218	2	-20.000000	1	1	0	0		1	0	1	1	1.734762	1	0.380000	1.790000	0.241683	0.930000	7.900000e-01	1.000000	1.000000	0.932835	0.930000	1	0.860000	1.000000
MYH4	4622	broad.mit.edu	37	17	10352050	10352050	+	Missense_Mutation	SNP	C	C	A			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr17:10352050C>A	ENST00000255381.2	-	32	4526	c.4416G>T	c.(4414-4416)gaG>gaT	p.E1472D	RP11-799N11.1_ENST00000399342.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|CTC-297N7.11_ENST00000587182.2_RNA	NM_017533.2	NP_060003.2	Q9Y623	MYH4_HUMAN	myosin, heavy chain 4, skeletal muscle			149					TCTGGGAGGCCTCAAGTTCAG	0.448000																								0							SO:0001583	missense			ENST00000255381.2	0	1	hg19	CCDS11154.1	.	.	.	.	.	.	.	.	.	.	C	14.47	2.545239	0.45280	.	.	ENSG00000141048	ENST00000255381	T	0.77229	-1.08	4.97	0.598	0.17512	Myosin tail (1);	0.000000	0.37577	U	0.002040	T	0.66819	0.2828	L	0.35249	1.045	0.38463	D	0.947264	B	0.28760	0.221	B	0.37015	0.239	T	0.56625	-0.7948	10	0.23302	T	0.38	.	9.7593	0.40522	0.0:0.6205:0.0:0.3795	.	1472	Q9Y623	MYH4_HUMAN	D	1472	ENSP00000255381:E1472D	ENSP00000255381:E1472D	E	-	3	2	MYH4	10292775	0.001000	0.12720	0.997000	0.53966	0.973000	0.67179	-1.559000	0.02162	0.222000	0.20900	0.561000	0.74099	GAG		TCGA-2L-AAQL-01A-11D-A38G-08	MYH4-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252731.1	0	0	0	5	315	0	154		0	0	0	0	154	2		0	0	0	0	0	2	0	0.193994	5	307	1	152	9		0	0	0	0	154	2	-3.015550	1	1	0	0		1	0	1	1	1.732470	1	0.380000	1.790000	0.238142	0.060000	2.000000e-02	0.150000	0.070000	0.079016	0.060000	0	0.040000	0.110000
TP53	7157	broad.mit.edu	37	17	7578555	7578555	+	Splice_Site	SNP	C	C	A			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08			C	A	C	C		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr17:7578555C>A	ENST00000269305.4	-	5	565		c.e5-1		TP53_ENST00000445888.2_Splice_Site|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Splice_Site|TP53_ENST00000420246.2_Splice_Site|TP53_ENST00000359597.4_Splice_Site|TP53_ENST00000413465.2_Splice_Site	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	p.?(39)|p.0?(8)|p.V73fs*9(1)|p.Y126fs*11(1)|p.P13fs*18(1)|p.T125_Y126insX(1)		24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		Acetylsalicylic acid(DB00945)	CAGGGGAGTACTGTAGGAAGA	0.552000		111	Mis, N, F		breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types	breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		L, E, M, O	51	Unknown(39)|Whole gene deletion(8)|Deletion - Frameshift(3)|Insertion - In frame(1)						SO:0001630	splice_region_variant	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	ENST00000269305.4	1	1	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	17.36	3.370877	0.61624	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000514944;ENST00000508793;ENST00000503591	.	.	.	4.87	3.9	0.45041	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.4246	0.50003	0.0:0.9094:0.0:0.0906	.	.	.	.	.	-1	.	.	.	-	.	.	TP53	7519280	1.000000	0.71417	0.999000	0.59377	0.918000	0.54935	7.639000	0.83342	1.359000	0.45940	0.655000	0.94253	.		TCGA-2L-AAQL-01A-11D-A38G-08	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	1	0	1	35	80	0	55	0	0	1	0	0	55	2	1	1	319	1076	0	1006	2	1	1.000000	33	73	0	53	2		0	0	0	0	55	2	-20.000000	1	1	0	0		1	0	1	1	1.732470	1	0.380000	1.790000	0.238142	0.960000	8.000000e-01	1.000000	1.000000	0.952497	0.960000	1	0.890000	1.000000
NOTUM	147111	broad.mit.edu	37	17	79914915	79914915	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr17:79914915C>T	ENST00000409678.3	-	7	1114	c.731G>A	c.(730-732)cGt>cAt	p.R244H		NM_178493.5	NP_848588.3	Q6P988	NOTUM_HUMAN	notum pectinacetylesterase homolog (Drosophila)			15	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)		CTCAGCCACACGGTCCACATT	0.662000																								0							SO:0001583	missense			ENST00000409678.3	1	1	hg19	CCDS32771.2	.	.	.	.	.	.	.	.	.	.	C	11.73	1.724700	0.30593	.	.	ENSG00000185269	ENST00000409678;ENST00000425009	.	.	.	4.54	3.56	0.40772	.	0.302720	0.37483	N	0.002071	T	0.43255	0.1239	L	0.39245	1.2	0.43994	D	0.996693	B	0.28258	0.205	B	0.28139	0.086	T	0.44817	-0.9303	9	0.48119	T	0.1	.	5.0317	0.14413	0.1749:0.6566:0.0:0.1686	.	244	Q6P988	NOTUM_HUMAN	H	244	.	ENSP00000387310:R244H	R	-	2	0	NOTUM	77508205	0.958000	0.32768	0.998000	0.56505	0.611000	0.37282	2.080000	0.41586	2.055000	0.61198	0.313000	0.20887	CGT		TCGA-2L-AAQL-01A-11D-A38G-08	NOTUM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335123.2	1	0	1	25	127	0	45		0	0	0	0	45	2		0	0	0	0	0	2	1	1.000000	25	126	0	45	2		0	0	0	0	45	2	-20.000000	1	1	0	0		1	1	2	3	2.111665	0	0.380000	1.790000	0.384676	0.870000	5.900000e-01	1.000000	1.000000	0.866653	0.870000	1	0.720000	1.000000
DSG3	1830	broad.mit.edu	37	18	29049139	29049139	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr18:29049139G>A	ENST00000257189.4	+	12	1807	c.1724G>A	c.(1723-1725)cGg>cAg	p.R575Q		NM_001944.2	NP_001935.2	P32926	DSG3_HUMAN	desmoglein 3			62			OV - Ovarian serous cystadenocarcinoma(10;0.00504)		CAGAACAATCGGTGTGAGATG	0.527000																								0							SO:0001583	missense			ENST00000257189.4	0	1	hg19	CCDS11898.1	.	.	.	.	.	.	.	.	.	.	G	10.84	1.462788	0.26248	.	.	ENSG00000134757	ENST00000257189	T	0.58060	0.36	5.95	-11.9	0.00025	.	1.487420	0.04727	N	0.420484	T	0.23094	0.0558	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.05852	-1.0860	10	0.14252	T	0.57	.	8.0923	0.30807	0.1856:0.0:0.3465:0.4679	.	575	P32926	DSG3_HUMAN	Q	575	ENSP00000257189:R575Q	ENSP00000257189:R575Q	R	+	2	0	DSG3	27303137	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.230000	0.01207	-3.245000	0.00206	-1.911000	0.00521	CGG		TCGA-2L-AAQL-01A-11D-A38G-08	DSG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254949.1	0	0	0	8	514	0	223	0	0	0	1	0	223	2		0	0	0	0	0	2	1	0.988692	8	505	0	223	2		0	0	0	0	223	2	-2.028886	0	1	121412	2	40	1	0	1	1	1.729344	1	0.380000	1.790000	0.238142	0.060000	2.000000e-02	0.120000	0.070000	0.073116	0.060000	0	0.040000	0.100000
ST8SIA5	29906	broad.mit.edu	37	18	44272163	44272163	+	Missense_Mutation	SNP	C	C	A			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr18:44272163C>A	ENST00000315087.7	-	3	940	c.280G>T	c.(280-282)Gcg>Tcg	p.A94S	ST8SIA5_ENST00000538168.1_Missense_Mutation_p.A130S|ST8SIA5_ENST00000590497.1_5'UTR|ST8SIA5_ENST00000536490.1_Missense_Mutation_p.A63S	NM_013305.4	NP_037437.2	O15466	SIA8E_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 5			22					ATGTTCATCGCCCATTTGCAC	0.522000																								0							SO:0001583	missense			ENST00000315087.7	1	1	hg19	CCDS11930.1	.	.	.	.	.	.	.	.	.	.	C	11.40	1.627958	0.28978	.	.	ENSG00000101638	ENST00000315087;ENST00000538168;ENST00000536490	T;T;T	0.43294	0.97;0.95;1.57	4.89	4.02	0.46733	.	0.249281	0.40064	N	0.001183	T	0.30823	0.0777	L	0.29908	0.895	0.34705	D	0.727107	B;B;B;B	0.16166	0.008;0.006;0.001;0.016	B;B;B;B	0.18561	0.017;0.004;0.003;0.022	T	0.32534	-0.9903	10	0.23302	T	0.38	.	13.3123	0.60386	0.0:0.923:0.0:0.077	.	63;130;63;94	F5H8D1;B7Z1K9;B7Z5F7;O15466	.;.;.;SIA8E_HUMAN	S	94;130;63	ENSP00000321343:A94S;ENSP00000445492:A130S;ENSP00000443683:A63S	ENSP00000321343:A94S	A	-	1	0	ST8SIA5	42526161	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	5.591000	0.67536	1.199000	0.43173	0.555000	0.69702	GCG		TCGA-2L-AAQL-01A-11D-A38G-08	ST8SIA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255892.1	1	0	1	57	232	0	131		0	0	0	0	131	2		0	0	0	0	0	2	1	1.000000	57	227	0	129	2		0	0	0	0	131	2	-20.000000	1	1	0	0		1	0	1	1	1.729344	1	0.380000	1.790000	0.238142	0.830000	6.500000e-01	0.990000	0.830000	0.834387	0.830000	0	0.730000	0.930000
MALT1	10892	broad.mit.edu	37	18	56401610	56401610	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr18:56401610C>T	ENST00000348428.3	+	12	1730	c.1472C>T	c.(1471-1473)gCc>gTc	p.A491V	MALT1_ENST00000345724.3_Missense_Mutation_p.A480V|RP11-126O1.4_ENST00000588835.1_RNA	NM_006785.2|NM_173844.1	NP_006776.1|NP_776216.1	Q9UDY8	MALT1_HUMAN	mucosa associated lymphoid tissue lymphoma translocation gene 1			12					TTTGGATATGCCACGTAAGAA	0.403000			T	BIRC3	MALT										Dom	yes		18	18q21	10892	mucosa associated lymphoid tissue lymphoma translocation gene 1		L	0							SO:0001583	missense			ENST00000348428.3	0	1	hg19	CCDS11967.1	.	.	.	.	.	.	.	.	.	.	C	36	5.609673	0.96637	.	.	ENSG00000172175	ENST00000348428;ENST00000345724	T;T	0.56611	0.45;0.45	5.88	5.88	0.94601	Peptidase C14, caspase catalytic (1);	0.046173	0.85682	D	0.000000	T	0.78168	0.4241	M	0.88570	2.965	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.74348	0.971;0.983	T	0.81450	-0.0927	10	0.87932	D	0	.	19.0095	0.92867	0.0:1.0:0.0:0.0	.	480;491	Q9UDY8-2;Q9UDY8	.;MALT1_HUMAN	V	491;480	ENSP00000319279:A491V;ENSP00000304161:A480V	ENSP00000304161:A480V	A	+	2	0	MALT1	54552590	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.487000	0.81328	2.779000	0.95612	0.650000	0.86243	GCC		TCGA-2L-AAQL-01A-11D-A38G-08	MALT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256132.2	0	0	0	4	219	0	81	0	0	0	1	0	81	2		0	0	0	0	0	2	1	0.884668	4	214	0	79	2		0	0	0	0	81	2	-2.777912	1	1	0	0		1	0	1	1	1.729344	1	0.380000	1.790000	0.238142	0.080000	2.000000e-02	0.180000	0.080000	0.093822	0.080000	0	0.040000	0.130000
TMX3	54495	broad.mit.edu	37	18	66377374	66377374	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr18:66377374G>A	ENST00000299608.2	-	4	465	c.149C>T	c.(148-150)gCg>gTg	p.A50V	TMX3_ENST00000562706.1_Missense_Mutation_p.A50V|TMX3_ENST00000443099.2_Missense_Mutation_p.A50V	NM_019022.3	NP_061895.3	Q96JJ7	TMX3_HUMAN	thioredoxin-related transmembrane protein 3			17					ACACCATGGCGCATAAAACTT	0.323000																								0							SO:0001583	missense			ENST00000299608.2	0	1	hg19	CCDS32840.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.916459	0.92249	.	.	ENSG00000166479	ENST00000299608;ENST00000544714;ENST00000443099	T;T;T	0.10192	2.9;2.9;2.9	5.57	5.57	0.84162	Thioredoxin domain (1);Thioredoxin, conserved site (1);Thioredoxin-like fold (3);	0.000000	0.85682	D	0.000000	T	0.47060	0.1425	H	0.94925	3.6	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.61352	-0.7080	10	0.87932	D	0	.	18.1057	0.89519	0.0:0.0:1.0:0.0	.	50;50;50	B4DIE3;Q96JJ7-2;Q96JJ7	.;.;TMX3_HUMAN	V	50	ENSP00000299608:A50V;ENSP00000444954:A50V;ENSP00000402605:A50V	ENSP00000299608:A50V	A	-	2	0	TMX3	64528354	1.000000	0.71417	1.000000	0.80357	0.798000	0.45092	9.738000	0.98835	2.619000	0.88677	0.563000	0.77884	GCG		TCGA-2L-AAQL-01A-11D-A38G-08	TMX3-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420155.1	0	0	0	4	181	0	56	0	4.871187e-03	0	4	0	56	2		0	0	0	0	0	2	1	0.884723	4	176	0	56	2		0	0	0	0	56	2	-3.115087	1	1	121396	5	24	1	0	1	1	1.729344	1	0.380000	1.790000	0.238142	0.090000	3.000000e-02	0.220000	0.090000	0.112553	0.090000	0	0.050000	0.160000
ZNF709	163051	broad.mit.edu	37	19	12576048	12576048	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr19:12576048C>T	ENST00000397732.3	-	4	859	c.688G>A	c.(688-690)Ggg>Agg	p.G230R	ZNF709_ENST00000428311.1_Missense_Mutation_p.G230R|CTD-3105H18.18_ENST00000598753.1_Intron	NM_152601.3	NP_689814.1	Q8N972	ZN709_HUMAN	zinc finger protein 709			6					AACGTTTTCCCGCATTCTTTA	0.403000													GBM(33;565 669 12371 29134 51667)											0							SO:0001583	missense			ENST00000397732.3	1	1	hg19	CCDS42504.1	.	.	.	.	.	.	.	.	.	.	C	17.47	3.397133	0.62177	.	.	ENSG00000242852;ENSG00000196826	ENST00000397732;ENST00000428311	T;T	0.03524	3.9;3.9	2.4	0.0633	0.14348	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.34676	N	0.003765	T	0.12732	0.0309	M	0.77616	2.38	0.30398	N	0.780325	D	0.89917	1.0	D	0.78314	0.991	T	0.01972	-1.1237	10	0.66056	D	0.02	.	6.0058	0.19544	0.0:0.6798:0.1959:0.1243	.	230	Q8N972	ZN709_HUMAN	R	230	ENSP00000380840:G230R;ENSP00000404127:G230R	ENSP00000404127:G230R	G	-	1	0	ZNF709;CTD-2192J16.17	12437048	0.059000	0.20769	0.201000	0.23476	0.396000	0.30629	1.548000	0.36201	0.097000	0.17492	0.313000	0.20887	GGG		TCGA-2L-AAQL-01A-11D-A38G-08	ZNF709-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344088.1	1	0	1	127	568	0	239		0	0	0	0	239	2		0	0	0	0	0	2	1	1.000000	124	557	0	238	2		0	0	0	0	239	2	-2.520565	1	1	121390	2	33	1	1	2	3	2.107045	0	0.380000	1.790000	0.384676	0.960000	8.100000e-01	1.000000	1.000000	0.953869	0.960000	1	0.890000	1.000000
ATP8B3	148229	broad.mit.edu	37	19	1785279	1785279	+	Missense_Mutation	SNP	C	C	A			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr19:1785279C>A	ENST00000310127.6	-	27	3649	c.3411G>T	c.(3409-3411)aaG>aaT	p.K1137N	ATP8B3_ENST00000539485.1_Missense_Mutation_p.K1147N|ATP8B3_ENST00000525591.1_Missense_Mutation_p.K1100N	NM_138813.3	NP_620168.1	O60423	AT8B3_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 3			23		Hepatocellular(1079;0.137)			CGGTCCAGTACTTGATGATAA	0.607000																								0							SO:0001583	missense			ENST00000310127.6	1	1	hg19	CCDS45901.1	.	.	.	.	.	.	.	.	.	.	C	13.80	2.345599	0.41498	.	.	ENSG00000130270	ENST00000310127;ENST00000539485;ENST00000525591	D;D;D	0.88664	-2.41;-2.41;-2.41	4.49	-0.244	0.13031	.	0.488846	0.21162	N	0.079130	D	0.83594	0.5288	L	0.28694	0.88	0.21604	N	0.999627	D;D	0.54964	0.961;0.969	P;P	0.52159	0.617;0.691	T	0.75068	-0.3448	10	0.45353	T	0.12	.	5.2161	0.15344	0.1426:0.6161:0.0:0.2414	.	1137;1100	O60423;Q7Z485	AT8B3_HUMAN;.	N	1137;1147;1100	ENSP00000311336:K1137N;ENSP00000443574:K1147N;ENSP00000437115:K1100N	ENSP00000311336:K1137N	K	-	3	2	ATP8B3	1736279	0.001000	0.12720	0.070000	0.20053	0.053000	0.15095	-0.307000	0.08167	-0.219000	0.10003	-0.136000	0.14681	AAG		TCGA-2L-AAQL-01A-11D-A38G-08	ATP8B3-002	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388279.1	1	0	1	15	77	0	22		0	0	0	0	22	2		0	0	0	0	0	2	1	0.999920	15	77	0	21	2		0	0	0	0	22	2	-20.000000	1	1	0	0		1	1	2	3	2.102412	0	0.380000	1.790000	0.382347	0.860000	5.200000e-01	1.000000	1.000000	0.848274	0.860000	1	0.680000	1.000000
ZNF790	388536	broad.mit.edu	37	19	37310991	37310991	+	Missense_Mutation	SNP	C	C	A			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr19:37310991C>A	ENST00000356725.4	-	5	375	c.255G>T	c.(253-255)aaG>aaT	p.K85N	CTD-2162K18.5_ENST00000588906.1_RNA|CTD-2162K18.5_ENST00000587278.1_RNA	NM_001242802.1|NM_206894.3	NP_001229731.1|NP_996777.2	Q6PG37	ZN790_HUMAN	zinc finger protein 790			32	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)		GTAATAACTTCTTGGTCTGAC	0.323000																								0							SO:0001583	missense			ENST00000356725.4	1	1	hg19	CCDS12496.1	.	.	.	.	.	.	.	.	.	.	C	8.442	0.851037	0.17034	.	.	ENSG00000197863	ENST00000356725;ENST00000528994;ENST00000525288	T;T;T	0.07327	3.2;6.04;5.63	3.08	3.08	0.35506	.	.	.	.	.	T	0.09862	0.0242	L	0.50333	1.59	0.09310	N	1	P	0.41313	0.745	B	0.41202	0.35	T	0.16482	-1.0401	9	0.52906	T	0.07	.	7.5937	0.28035	0.2541:0.7459:0.0:0.0	.	85	Q6PG37	ZN790_HUMAN	N	85	ENSP00000349161:K85N;ENSP00000435944:K85N;ENSP00000433389:K85N	ENSP00000349161:K85N	K	-	3	2	ZNF790	42002831	0.000000	0.05858	0.115000	0.21578	0.254000	0.26022	0.138000	0.16016	1.708000	0.51301	0.484000	0.47621	AAG		TCGA-2L-AAQL-01A-11D-A38G-08	ZNF790-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385341.2	0	0	0	11	354	0	142	0	6.550418e-03	0	4	0	142	2		0	0	0	0	0	2	1	0.998292	11	351	0	141	2		0	0	0	0	142	2	-11.387680	1	1	0	0		1	1	2	3	2.090028	0	0.380000	1.790000	0.381176	0.160000	8.000000e-02	0.280000	0.160000	0.171654	0.160000	0	0.110000	0.220000
EEF2	1938	broad.mit.edu	37	19	3980040	3980040	+	Nonsense_Mutation	SNP	G	G	C			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08			G	C	G	G		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr19:3980040G>C	ENST00000309311.6	-	10	1459	c.1371C>G	c.(1369-1371)taC>taG	p.Y457*	SNORD37_ENST00000384048.1_RNA	NM_001961.3	NP_001952.1	P13639	EF2_HUMAN	eukaryotic translation elongation factor 2			21		Hepatocellular(1079;0.137)			TGGGCTCCACGTAGCGGCCCA	0.627000													Colon(165;1804 1908 4071 6587 18799)											0							SO:0001587	stop_gained			ENST00000309311.6	0	1	hg19	CCDS12117.1	.	.	.	.	.	.	.	.	.	.	G	36	5.611568	0.96637	.	.	ENSG00000167658	ENST00000543343;ENST00000309311	.	.	.	5.45	-4.98	0.03019	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-38.4193	14.8867	0.70575	0.5244:0.0:0.4756:0.0	.	.	.	.	X	457	.	ENSP00000307940:Y457X	Y	-	3	2	EEF2	3931040	0.000000	0.05858	0.873000	0.34254	0.950000	0.60333	-2.827000	0.00746	-0.965000	0.03591	-1.134000	0.01955	TAC		TCGA-2L-AAQL-01A-11D-A38G-08	EEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457615.2	1	0	1	18	111	0	44	1	1	4	777	0	44	2	1	1	142	619	0	473	2	1	0.999987	17	110	0	44	2		0	0	0	0	44	2	-20.000000	1	1	0	0		1	1	2	3	2.102412	0	0.380000	1.790000	0.382347	0.740000	4.600000e-01	1.000000	1.000000	0.753013	0.740000	0	0.590000	0.920000
C3	718	broad.mit.edu	37	19	6694601	6694601	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr19:6694601G>A	ENST00000245907.6	-	24	3087	c.2995C>T	c.(2995-2997)Cgg>Tgg	p.R999W		NM_000064.2	NP_000055.2	P01024	CO3_HUMAN	complement component 3			72				Intravenous Immunoglobulin(DB00028)	TGCTTCAGCCGTTCCGCGTCG	0.622000																								0							SO:0001583	missense			ENST00000245907.6	1	1	hg19	CCDS32883.1	.	.	.	.	.	.	.	.	.	.	G	15.71	2.913948	0.52546	.	.	ENSG00000125730	ENST00000245907	T	0.37584	1.19	5.67	4.61	0.57282	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);	0.519800	0.21650	N	0.071200	T	0.32704	0.0838	N	0.08118	0	0.20926	N	0.999829	D	0.76494	0.999	P	0.58620	0.842	T	0.13683	-1.0500	10	0.72032	D	0.01	.	10.8984	0.47036	0.0:0.0:0.6435:0.3565	.	999	P01024	CO3_HUMAN	W	999	ENSP00000245907:R999W	ENSP00000245907:R999W	R	-	1	2	C3	6645601	0.290000	0.24343	0.988000	0.46212	0.150000	0.21749	1.655000	0.37345	2.693000	0.91896	0.650000	0.86243	CGG		TCGA-2L-AAQL-01A-11D-A38G-08	C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317636.2	1	0	1	29	230	0	99	1	1	2	349	0	99	2		0	0	0	0	0	2	1	1.000000	29	224	0	99	2		0	0	0	0	99	2	-20.000000	1	1	0	0		1	1	2	3	2.107045	0	0.380000	1.790000	0.384676	0.590000	4.100000e-01	1.000000	0.590000	0.617138	0.590000	0	0.490000	0.720000
ACTL9	284382	broad.mit.edu	37	19	8807951	8807951	+	Missense_Mutation	SNP	G	G	C			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr19:8807951G>C	ENST00000324436.3	-	1	1221	c.1101C>G	c.(1099-1101)caC>caG	p.H367Q		NM_178525.3	NP_848620.3	Q8TC94	ACTL9_HUMAN	actin-like 9			36					CCACCACCACGTGGGTCTCGG	0.677000																								0							SO:0001583	missense			ENST00000324436.3	1	1	hg19	CCDS12207.1	.	.	.	.	.	.	.	.	.	.	g	3.006	-0.204896	0.06180	.	.	ENSG00000181786	ENST00000324436	T	0.07444	3.19	4.51	2.29	0.28610	.	0.738936	0.11482	U	0.559628	T	0.05227	0.0139	N	0.17564	0.495	0.09310	N	1	B	0.12630	0.006	B	0.19148	0.024	T	0.38243	-0.9670	10	0.87932	D	0	.	3.6914	0.08347	0.088:0.316:0.4331:0.1629	.	367	Q8TC94	ACTL9_HUMAN	Q	367	ENSP00000316674:H367Q	ENSP00000316674:H367Q	H	-	3	2	ACTL9	8668951	0.001000	0.12720	0.084000	0.20598	0.088000	0.18126	0.676000	0.25247	0.604000	0.29930	-0.482000	0.04802	CAC		TCGA-2L-AAQL-01A-11D-A38G-08	ACTL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459953.1	1	0	1	30	159	0	73		0	0	0	0	73	2		0	0	0	0	0	2	1	1.000000	28	150	0	71	2		0	0	0	0	73	2	-20.000000	1	1	0	0		1	1	2	3	2.107045	0	0.380000	1.790000	0.384676	0.840000	5.900000e-01	1.000000	1.000000	0.845971	0.840000	0	0.710000	1.000000
S1PR1	1901	broad.mit.edu	37	1	101705012	101705012	+	Missense_Mutation	SNP	T	T	G			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr1:101705012T>G	ENST00000305352.6	+	2	847	c.472T>G	c.(472-474)Ttc>Gtc	p.F158V	S1PR1_ENST00000475821.1_3'UTR|RP4-575N6.4_ENST00000432195.1_RNA	NM_001400.4	NP_001391.2	P21453	S1PR1_HUMAN	sphingosine-1-phosphate receptor 1			43					GAGCAATAACTTCCGCCTCTT	0.557000											OREG0013620	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)												0							SO:0001583	missense			ENST00000305352.6	1	1	hg19	CCDS777.1	.	.	.	.	.	.	.	.	.	.	T	6.195	0.404153	0.11754	.	.	ENSG00000170989	ENST00000305352;ENST00000424264	T	0.36699	1.24	5.46	3.01	0.34805	GPCR, rhodopsin-like superfamily (1);	0.270993	0.42964	D	0.000624	T	0.04588	0.0125	N	0.02916	-0.46	0.31924	N	0.613066	B	0.02656	0.0	B	0.06405	0.002	T	0.38067	-0.9678	10	0.17369	T	0.5	.	7.8339	0.29360	0.0:0.0721:0.1384:0.7895	.	158	P21453	S1PR1_HUMAN	V	158	ENSP00000305416:F158V	ENSP00000305416:F158V	F	+	1	0	S1PR1	101477600	1.000000	0.71417	0.972000	0.41901	0.514000	0.34195	3.361000	0.52306	0.918000	0.36919	0.374000	0.22700	TTC		TCGA-2L-AAQL-01A-11D-A38G-08	S1PR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029908.1	0	0	1	71	280	0	147	0	1.877652e-01	0	4	0	147	2		0	0	0	0	0	2	1	1.000000	68	275	0	147	2		0	0	0	0	147	2	-20.000000	1	1	0	0		1	0	1	1	1.731845	1	0.380000	1.790000	0.238142	0.850000	6.800000e-01	1.000000	0.860000	0.855459	0.850000	1	0.760000	0.940000
AMY2A	279	broad.mit.edu	37	1	104160198	104160198	+	Missense_Mutation	SNP	T	T	G			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08			T	G	T	T		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr1:104160198T>G	ENST00000414303.2	+	1	200	c.136T>G	c.(136-138)Tat>Gat	p.Y46D		NM_000699.2	NP_000690.1	P04746	AMYP_HUMAN	amylase, alpha 2A (pancreatic)			22		all_epithelial(167;3.05e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000451)		Acarbose(DB00284)|Icodextrin(DB00702)|Miglitol(DB00491)	ATGTGAGCGATATTTAGCTCC	0.423000																								0							SO:0001583	missense			ENST00000414303.2	1	1	hg19	CCDS783.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|t	15.43|15.43	2.831461|2.831461	0.50845|0.50845	.|.	.|.	ENSG00000243480|ENSG00000243480	ENST00000423678|ENST00000414303;ENST00000393932	.|D	.|0.99663	.|-6.33	3.22|3.22	3.22|3.22	0.36961|0.36961	.|Glycoside hydrolase, subgroup, catalytic domain (1);Glycosyl hydrolase, family 13, catalytic domain (1);Glycoside hydrolase, superfamily (1);Glycosyl hydrolase, family 13, subfamily, catalytic domain (1);	.|0.056220	.|0.64402	.|D	.|0.000001	D|D	0.99462|0.99462	0.9809|0.9809	M|M	0.82132|0.82132	2.575|2.575	0.58432|0.58432	D|D	0.999998|0.999998	.|D;D	.|0.89917	.|1.0;0.999	.|D;D	.|0.97110	.|1.0;0.985	D|D	0.98570|0.98570	1.0645|1.0645	5|10	.|0.87932	.|D	.|0	.|.	11.6147|11.6147	0.51083|0.51083	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|46;46	.|B9EJG1;P04746	.|.;AMYP_HUMAN	R|D	44|46	.|ENSP00000397582:Y46D	.|ENSP00000377509:Y46D	I|Y	+|+	2|1	0|0	AMY2A|AMY2A	103961721|103961721	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.474000|0.474000	0.32979|0.32979	7.267000|7.267000	0.78462|0.78462	1.455000|1.455000	0.47813|0.47813	0.374000|0.374000	0.22700|0.22700	ATA|TAT		TCGA-2L-AAQL-01A-11D-A38G-08	AMY2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030315.1	0	0	1	322	1045	1	625	0	1	0	265	1	625	4		0	0	0	0	0	2	1	1.000000	195	630	2	678	9		0	0	0	1	625	2	-20.000000	1	0	0	0		1	0	1	1	1.731845	1	0.380000	1.790000	0.238142	0.970000	8.900000e-01	1.000000	1.000000	0.975165	0.970000	1	0.940000	1.000000
CLCN6	1185	broad.mit.edu	37	1	11897102	11897102	+	Missense_Mutation	SNP	A	A	G			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr1:11897102A>G	ENST00000346436.6	+	19	2079	c.2027A>G	c.(2026-2028)cAg>cGg	p.Q676R	CLCN6_ENST00000376487.3_Missense_Mutation_p.Q654R|CLCN6_ENST00000312413.6_3'UTR|CLCN6_ENST00000376496.3_Missense_Mutation_p.Q676R	NM_001286.3	NP_001277	P51797	CLCN6_HUMAN	chloride channel, voltage-sensitive 6			36	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)			AAACGGAGCCAGTCCATGAAG	0.602000																								0							SO:0001583	missense			ENST00000346436.6	1	1	hg19	CCDS138.1	.	.	.	.	.	.	.	.	.	.	A	11.52	1.664137	0.29604	.	.	ENSG00000011021	ENST00000346436;ENST00000376487;ENST00000376496	D;D;D	0.91237	-2.8;-2.8;-2.81	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	D	0.85026	0.5603	L	0.34521	1.04	0.80722	D	1	B;B	0.17268	0.021;0.012	B;B	0.12837	0.008;0.004	T	0.80251	-0.1460	10	0.16420	T	0.52	-27.6288	15.1511	0.72700	1.0:0.0:0.0:0.0	.	654;676	F8W9R3;P51797	.;CLCN6_HUMAN	R	676;654;676	ENSP00000234488:Q676R;ENSP00000365670:Q654R;ENSP00000365679:Q676R	ENSP00000234488:Q676R	Q	+	2	0	CLCN6	11819689	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	8.422000	0.90262	2.189000	0.69895	0.459000	0.35465	CAG		TCGA-2L-AAQL-01A-11D-A38G-08	CLCN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006639.2	1	0	1	70	220	0	106	0	0	0	1	0	106	2		0	0	0	0	0	2	1	1.000000	68	216	0	105	2		0	0	0	0	106	2	-20.000000	1	1	0	0		1	1	2	3	2.170676	0	0.380000	1.790000	0.393821	0.990000	9.900000e-01	1.000000	1.000000	0.999678	0.990000	1	0.990000	1.000000
ADAMTS4	9507	broad.mit.edu	37	1	161166670	161166670	+	Splice_Site	SNP	G	G	A			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr1:161166670G>A	ENST00000367996.5	-	2	1062	c.634C>T	c.(634-636)Cgc>Tgc	p.R212C	NDUFS2_ENST00000367993.3_5'Flank|ADAMTS4_ENST00000478394.1_5'Flank|ADAMTS4_ENST00000367995.3_Splice_Site_p.R212C	NM_005099.4	NP_005090.3	O75173	ATS4_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 4			43	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)	Tinzaparin(DB06822)	GAAGCAAAGCGCTGTAGAGAA	0.527000																								0							SO:0001630	splice_region_variant			ENST00000367996.5	1	0	hg19	CCDS1223.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.989431	0.74589	.	.	ENSG00000158859	ENST00000367996;ENST00000367995	T;T	0.76839	-0.51;-1.05	4.64	4.64	0.57946	Metallopeptidase, catalytic domain (1);	0.197716	0.32548	N	0.005951	T	0.75287	0.3829	L	0.27053	0.805	0.54753	D	0.999987	D;D	0.89917	1.0;0.982	D;P	0.83275	0.996;0.75	T	0.79671	-0.1706	10	0.87932	D	0	.	11.7012	0.51571	0.0:0.0:0.823:0.177	.	212;212	Q5VTW1;O75173	.;ATS4_HUMAN	C	212	ENSP00000356975:R212C;ENSP00000356974:R212C	ENSP00000356974:R212C	R	-	1	0	ADAMTS4	159433294	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.564000	0.67359	2.418000	0.82041	0.650000	0.86243	CGC		TCGA-2L-AAQL-01A-11D-A38G-08	ADAMTS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083066.2	1	0	1	164	772	1	282	0	0	0	1	1	282	2		0	0	0	0	0	2	1	1.000000	165	755	1	280	13		0	0	0	1	282	2	-20.000000	1	1	0	0		1	1	2	3	2.499219	1	0.380000	1.790000	0.478992	0.990000	9.400000e-01	1.000000	1.000000	0.996569	0.990000	1	0.990000	1.000000
TRIM67	440730	broad.mit.edu	37	1	231298879	231298879	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr1:231298879C>T	ENST00000366653.5	+	1	164	c.164C>T	c.(163-165)tCg>tTg	p.S55L	TRIM67_ENST00000449018.3_Intron|TRIM67_ENST00000366652.2_Missense_Mutation_p.S55L|TRIM67_ENST00000444294.3_Missense_Mutation_p.S55L			Q6ZTA4	TRI67_HUMAN	tripartite motif containing 67			29	Breast(184;0.0871)	all_cancers(173;0.189)|Prostate(94;0.167)			TCCCGGGGATCGGGGCTGCAG	0.741000																								0							SO:0001583	missense			ENST00000366653.5	0	1	hg19	CCDS44333.1	.	.	.	.	.	.	.	.	.	.	C	9.408	1.079775	0.20309	.	.	ENSG00000119283	ENST00000444294;ENST00000366652;ENST00000366653	T;T;T	0.70516	-0.49;-0.4;-0.49	4.02	4.02	0.46733	Zinc finger, RING-type (1);	2.080550	0.03330	N	0.193199	T	0.55784	0.1942	N	0.08118	0	0.09310	N	1	B	0.22851	0.076	B	0.12156	0.007	T	0.41305	-0.9516	10	0.28530	T	0.3	.	13.4243	0.61015	0.0:1.0:0.0:0.0	.	55	Q6ZTA4	TRI67_HUMAN	L	55	ENSP00000412124:S55L;ENSP00000355612:S55L;ENSP00000355613:S55L	ENSP00000355612:S55L	S	+	2	0	TRIM67	229365502	0.772000	0.28567	0.083000	0.20561	0.114000	0.19823	-0.265000	0.08644	1.949000	0.56562	0.313000	0.20887	TCG		TCGA-2L-AAQL-01A-11D-A38G-08	TRIM67-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092649.3	0	0	0	6	34	0	15		0	0	0	0	15	2		0	0	0	0	0	2	1	0.960448	6	31	0	15	2		0	0	0	0	15	2	-15.775740	1	1	0	0		1	1	2	3	2.508464	1	0.380000	1.790000	0.478992	0.970000	4.300000e-01	1.000000	1.000000	0.870693	0.970000	1	0.660000	1.000000
OR1C1	26188	broad.mit.edu	37	1	247920907	247920907	+	Missense_Mutation	SNP	G	G	T			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr1:247920907G>T	ENST00000408896.2	-	1	1075	c.802C>A	c.(802-804)Cct>Act	p.P268T		NM_012353.2	NP_036485.2	Q15619	OR1C1_HUMAN	olfactory receptor, family 1, subfamily C, member 1			46	all_cancers(71;4.34e-05)|all_epithelial(71;1.13e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0786)|Lung NSC(105;0.0858)	all_cancers(173;0.0247)	OV - Ovarian serous cystadenocarcinoma(106;0.0168)		TCGCTCTCAGGCATATGGGGG	0.517000																								0							SO:0001583	missense			ENST00000408896.2	1	1	hg19	CCDS41481.1	.	.	.	.	.	.	.	.	.	.	G	0.009	-1.835122	0.00579	.	.	ENSG00000221888	ENST00000408896	T	0.00207	8.55	3.22	2.29	0.28610	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00109	0.0003	N	0.11313	0.125	0.09310	N	1	B	0.22800	0.075	B	0.32393	0.145	T	0.09122	-1.0689	9	0.38643	T	0.18	.	5.286	0.15702	0.1055:0.0:0.5646:0.3299	.	268	Q15619	OR1C1_HUMAN	T	268	ENSP00000386138:P268T	ENSP00000386138:P268T	P	-	1	0	OR1C1	245987530	0.000000	0.05858	0.009000	0.14445	0.036000	0.12997	-0.309000	0.08145	0.681000	0.31386	0.591000	0.81541	CCT		TCGA-2L-AAQL-01A-11D-A38G-08	OR1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096855.1	1	0	1	119	280	0	141		0	0	0	0	141	2		0	0	0	0	0	2	1	1.000000	117	275	0	141	2		0	0	0	0	141	2	-20.000000	1	1	0	0		1	1	2	3	2.508464	1	0.380000	1.790000	0.478992	0.990000	9.900000e-01	1.000000	1.000000	1.000000	0.990000	1	0.990000	1.000000
OR2T1	26696	broad.mit.edu	37	1	248569553	248569553	+	Missense_Mutation	SNP	C	C	A			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr1:248569553C>A	ENST00000366474.1	+	1	258	c.258C>A	c.(256-258)ttC>ttA	p.F86L		NM_030904.1	NP_112166.1	O43869	OR2T1_HUMAN	olfactory receptor, family 2, subfamily T, member 1			39	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)		TCATCTTCTTCACCGCACTGA	0.443000																								0							SO:0001583	missense			ENST00000366474.1	1	1	hg19	CCDS31115.1	.	.	.	.	.	.	.	.	.	.	c	1.274	-0.612375	0.03690	.	.	ENSG00000175143	ENST00000366474	T	0.00672	5.89	4.71	-0.642	0.11486	.	0.422262	0.17374	N	0.176578	T	0.00241	0.0007	N	0.00496	-1.435	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.45323	-0.9269	10	0.02654	T	1	.	1.4067	0.02282	0.1474:0.2756:0.1437:0.4333	.	86	O43869	OR2T1_HUMAN	L	86	ENSP00000355430:F86L	ENSP00000355430:F86L	F	+	3	2	OR2T1	246636176	0.000000	0.05858	0.105000	0.21289	0.088000	0.18126	-4.701000	0.00196	0.213000	0.20722	0.557000	0.71058	TTC		TCGA-2L-AAQL-01A-11D-A38G-08	OR2T1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097346.2	1	0	1	133	775	0	298		0	0	0	0	298	2		0	0	0	0	0	2	1	1.000000	129	763	0	296	2		0	0	0	0	298	2	-20.000000	1	1	0	0		1	1	3	4	2.532632	1	0.380000	1.790000	0.496672	0.970000	8.100000e-01	1.000000	1.000000	0.954059	0.970000	1	0.880000	1.000000
LEPR	3953	broad.mit.edu	37	1	66102532	66102532	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr1:66102532C>T	ENST00000349533.6	+	20	3517	c.3332C>T	c.(3331-3333)aCg>aTg	p.T1111M	LEPR_ENST00000406510.3_Missense_Mutation_p.T178M	NM_002303.5	NP_002294.2	O15243	OBRG_HUMAN	leptin receptor			36					TGTTTATTCACGGACATCAGA	0.418000																								0							SO:0001583	missense			ENST00000349533.6	1	1	hg19	CCDS631.1	.	.	.	.	.	.	.	.	.	.	C	9.281	1.048241	0.19827	.	.	ENSG00000116678	ENST00000349533;ENST00000406510	T	0.55760	0.5	5.37	-1.07	0.09968	.	0.746455	0.13820	N	0.360475	T	0.31765	0.0807	L	0.51422	1.61	0.09310	N	1	D	0.56287	0.975	P	0.49999	0.628	T	0.12372	-1.0550	10	0.48119	T	0.1	-4.0534	5.9674	0.19332	0.1701:0.3559:0.402:0.0719	.	1111	P48357	LEPR_HUMAN	M	1111;178	ENSP00000330393:T1111M	ENSP00000330393:T1111M	T	+	2	0	LEPR	65875120	0.038000	0.19896	0.098000	0.21074	0.002000	0.02628	0.224000	0.17738	0.136000	0.18733	-0.237000	0.12165	ACG		TCGA-2L-AAQL-01A-11D-A38G-08	LEPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025275.1	1	0	1	48	177	0	82	0	0	1	0	0	82	2		0	0	0	0	0	2	1	1.000000	48	173	0	80	2		0	0	0	0	82	2	-20.000000	1	1	121412	1	25	1	0	1	1	1.731845	1	0.380000	1.790000	0.238142	0.870000	6.800000e-01	1.000000	1.000000	0.875325	0.870000	1	0.770000	0.970000
SGIP1	84251	broad.mit.edu	37	1	67147855	67147855	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr1:67147855C>T	ENST00000371037.4	+	15	1195	c.1118C>T	c.(1117-1119)cCg>cTg	p.P373L	SGIP1_ENST00000371036.3_Intron|SGIP1_ENST00000237247.6_Missense_Mutation_p.P377L|SGIP1_ENST00000371035.3_Intron|SGIP1_ENST00000371039.1_Intron	NM_032291.2	NP_115667.2	Q9BQI5	SGIP1_HUMAN	SH3-domain GRB2-like (endophilin) interacting protein 1			71					GTACTATCGCCGCTCAATTTA	0.542000																								0							SO:0001583	missense			ENST00000371037.4	1	1	hg19	CCDS30744.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.068566	0.76301	.	.	ENSG00000118473	ENST00000237247;ENST00000371038;ENST00000407289;ENST00000371037	T;T	0.03152	4.03;4.03	5.19	4.26	0.50523	.	0.113033	0.64402	D	0.000010	T	0.07369	0.0186	L	0.47716	1.5	0.80722	D	1	D;B	0.89917	1.0;0.014	D;B	0.79108	0.992;0.005	T	0.13229	-1.0517	10	0.52906	T	0.07	-9.3174	13.4763	0.61310	0.0:0.9243:0.0:0.0757	.	376;373	A6NEV3;Q9BQI5	.;SGIP1_HUMAN	L	377;376;376;373	ENSP00000237247:P377L;ENSP00000360076:P373L	ENSP00000237247:P377L	P	+	2	0	SGIP1	66920443	0.996000	0.38824	1.000000	0.80357	0.965000	0.64279	4.809000	0.62591	2.570000	0.86706	0.455000	0.32223	CCG		TCGA-2L-AAQL-01A-11D-A38G-08	SGIP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000025395.4	1	0	1	119	435	0	232		0	0	0	0	232	2		0	0	0	0	0	2	1	1.000000	117	416	0	231	2		0	0	0	0	232	2	-20.000000	1	1	121412	4	40	1	0	1	1	1.731845	1	0.380000	1.790000	0.238142	0.900000	7.700000e-01	1.000000	1.000000	0.905272	0.900000	1	0.830000	0.970000
SLC2A7	155184	broad.mit.edu	37	1	9085071	9085071	+	Silent	SNP	G	G	A			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr1:9085071G>A	ENST00000400906.1	-	2	113	c.114C>T	c.(112-114)taC>taT	p.Y38Y		NM_207420.2	NP_997303.2	Q6PXP3	GTR7_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 7			24	Ovarian(185;0.112)|all_lung(157;0.185)	all_epithelial(116;1.34e-15)|all_lung(118;9.46e-05)|Lung NSC(185;0.000172)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.00715)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)			GGTTGTAGCCGTACTGGAAGG	0.647000																								0							SO:0001819	synonymous_variant			ENST00000400906.1	1	1	hg19	CCDS98.2																																																																																				TCGA-2L-AAQL-01A-11D-A38G-08	SLC2A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127768.3	1	0	1	45	229	0	119		0	0	0	0	119	2		0	0	0	0	0	2	1	1.000000	45	223	0	117	2		0	0	0	0	119	2	-3.351963	1	1	121410	1	33	1	1	2	3	2.170676	0	0.380000	1.790000	0.393821	0.890000	6.600000e-01	1.000000	1.000000	0.890780	0.890000	1	0.770000	1.000000
C20orf26	0	broad.mit.edu	37	20	20056245	20056245	+	Silent	SNP	C	C	T	rs116838168	byFrequency	TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr20:20056245C>T	ENST00000245957.5	+	6	628	c.552C>T	c.(550-552)caC>caT	p.H184H	C20orf26_ENST00000377306.1_Silent_p.H184H|C20orf26_ENST00000389656.3_5'UTR|C20orf26_ENST00000451767.2_Silent_p.H184H|C20orf26_ENST00000377309.2_5'UTR	NM_015585.3	NP_056400.3	Q8NHU2	CT026_HUMAN				77					CTCAGCTGCACGTTCGCAAAG	0.478000																								0							SO:0001819	synonymous_variant			ENST00000245957.5	1	1	hg19	CCDS33447.1																																																																																				TCGA-2L-AAQL-01A-11D-A38G-08	C20orf26-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078228.3	1	0	0	93	439	0	176		0	0	0	0	176	2		0	0	0	0	0	2	1	1.000000	92	433	0	175	2		0	0	0	0	176	2	-4.339412	1	1	121412	50	50	1	1	2	3	2.108566	0	0.380000	1.790000	0.384676	0.920000	7.600000e-01	1.000000	1.000000	0.921920	0.920000	1	0.840000	1.000000
SIGLEC1	6614	broad.mit.edu	37	20	3687258	3687258	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr20:3687258C>T	ENST00000344754.4	-	2	144	c.145G>A	c.(145-147)Gtg>Atg	p.V49M	SIGLEC1_ENST00000202578.4_Missense_Mutation_p.V49M	NM_023068.3	NP_075556.1	Q9BZZ2	SN_HUMAN	sialic acid binding Ig-like lectin 1, sialoadhesin			70					GGCACCTCCACGTCGGCAGGG	0.672000																								0							SO:0001583	missense			ENST00000344754.4	0	1	hg19	CCDS13060.1	.	.	.	.	.	.	.	.	.	.	C	15.75	2.926139	0.52759	.	.	ENSG00000088827	ENST00000344754;ENST00000202578	T;T	0.22336	1.96;1.96	5.01	1.48	0.22813	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	0.207799	0.24185	N	0.040780	T	0.36908	0.0984	M	0.70595	2.14	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	T	0.09207	-1.0685	10	0.62326	D	0.03	.	3.7683	0.08632	0.0:0.5395:0.1965:0.2641	.	49;49	Q9BZZ2;Q9BZZ2-3	SN_HUMAN;.	M	49	ENSP00000341141:V49M;ENSP00000202578:V49M	ENSP00000202578:V49M	V	-	1	0	SIGLEC1	3635258	0.133000	0.22466	0.002000	0.10522	0.058000	0.15608	0.940000	0.28992	0.416000	0.25844	0.563000	0.77884	GTG		TCGA-2L-AAQL-01A-11D-A38G-08	SIGLEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077761.2	1	0	0	3	66	0	30		0	0	0	0	30	2		0	0	0	0	0	2	1	0.798246	3	63	0	29	2		0	0	0	0	30	2	-6.996989	1	1	121180	1	25	1	1	2	3	2.108566	0	0.380000	1.790000	0.384676	0.270000	7.000000e-02	1.000000	0.230000	0.312303	0.270000	0	0.150000	0.450000
MMP9	4318	broad.mit.edu	37	20	44639630	44639630	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr20:44639630G>A	ENST00000372330.3	+	4	609	c.590G>A	c.(589-591)gGc>gAc	p.G197D	RP11-465L10.10_ENST00000535913.1_RNA	NM_004994.2	NP_004985.2	P14780	MMP9_HUMAN	matrix metallopeptidase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)			46		Myeloproliferative disorder(115;0.0122)		Captopril(DB01197)|Glucosamine(DB01296)|Marimastat(DB00786)|Minocycline(DB01017)	CCTGGCCCCGGCATTCAGGGA	0.602000																								0							SO:0001583	missense			ENST00000372330.3	0	1	hg19	CCDS13390.1	.	.	.	.	.	.	.	.	.	.	G	32	5.125006	0.94429	.	.	ENSG00000100985	ENST00000372330	T	0.23754	1.89	4.62	4.62	0.57501	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.47414	0.1444	M	0.76328	2.33	0.80722	D	1	P	0.40660	0.726	P	0.53649	0.731	T	0.50642	-0.8804	10	0.87932	D	0	.	16.9809	0.86327	0.0:0.0:1.0:0.0	.	197	P14780	MMP9_HUMAN	D	197	ENSP00000361405:G197D	ENSP00000361405:G197D	G	+	2	0	MMP9	44073037	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	9.601000	0.98297	2.553000	0.86117	0.650000	0.86243	GGC		TCGA-2L-AAQL-01A-11D-A38G-08	MMP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080337.1	0	0	0	7	403	1	162	0	8.874123e-02	0	25	1	162	2		0	0	0	0	0	2	0	0.226476	8	396	1	157	11		0	0	0	1	162	2	-2.281619	0	1	0	0		1	1	2	3	2.108566	0	0.380000	1.790000	0.384676	0.090000	3.000000e-02	1.000000	0.090000	0.128405	0.090000	0	0.060000	0.140000
RNF114	55905	broad.mit.edu	37	20	48561946	48561946	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr20:48561946G>A	ENST00000244061.2	+	3	321	c.319G>A	c.(319-321)Gtg>Atg	p.V107M		NM_018683.3	NP_061153.1	Q9Y508	RN114_HUMAN	ring finger protein 114			5					CCGGTCCCACGTGGCTACTTG	0.458000																								0							SO:0001583	missense			ENST00000244061.2	1	1	hg19	CCDS33482.1	.	.	.	.	.	.	.	.	.	.	G	14.31	2.496437	0.44352	.	.	ENSG00000124226	ENST00000449816;ENST00000244061	T	0.81078	-1.45	5.97	5.02	0.67125	.	0.234988	0.44688	D	0.000431	T	0.73984	0.3657	L	0.46157	1.445	0.26976	N	0.965477	P;B	0.52842	0.956;0.282	B;B	0.43508	0.422;0.041	T	0.70263	-0.4920	10	0.42905	T	0.14	-6.465	9.5071	0.39053	0.0741:0.0:0.7856:0.1403	.	107;107	Q9Y508-2;Q9Y508	.;RN114_HUMAN	M	107	ENSP00000244061:V107M	ENSP00000244061:V107M	V	+	1	0	RNF114	47995353	1.000000	0.71417	0.977000	0.42913	0.934000	0.57294	4.718000	0.61930	2.833000	0.97629	0.585000	0.79938	GTG		TCGA-2L-AAQL-01A-11D-A38G-08	RNF114-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079663.1	1	0	1	41	178	0	78	1	9.999998e-01	32	75	0	78	2		0	0	0	0	0	2	1	1.000000	39	175	0	78	2		0	0	0	0	78	2	-19.999960	1	1	121412	2	32	1	1	2	3	2.108566	0	0.380000	1.790000	0.384676	0.990000	7.300000e-01	1.000000	1.000000	0.946522	0.990000	1	0.850000	1.000000
ARFGAP1	55738	broad.mit.edu	37	20	61906986	61906986	+	Missense_Mutation	SNP	G	G	T			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr20:61906986G>T	ENST00000370283.4	+	2	194	c.54G>T	c.(52-54)gaG>gaT	p.E18D	ARFGAP1_ENST00000370275.4_Missense_Mutation_p.E18D|NKAIN4_ENST00000370307.2_5'Flank|ARFGAP1_ENST00000547204.1_5'UTR|ARFGAP1_ENST00000519273.2_5'UTR|ARFGAP1_ENST00000353546.3_Missense_Mutation_p.E18D|ARFGAP1_ENST00000519604.1_Missense_Mutation_p.R2I	NM_018209.2	NP_060679.1	Q8N6T3	ARFG1_HUMAN	ADP-ribosylation factor GTPase activating protein 1			13	all_cancers(38;1.59e-09)				TGCAGGATGAGAACAACGTAA	0.517000																								0							SO:0001583	missense			ENST00000370283.4	0	1	hg19	CCDS13515.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	2.379|2.379	-0.342631|-0.342631	0.05243|0.05243	.|.	.|.	ENSG00000101199|ENSG00000101199	ENST00000370283;ENST00000523114;ENST00000370275;ENST00000353546;ENST00000522403;ENST00000550188|ENST00000519604	T;T;T;T;T;T|T	0.46819|0.46063	0.86;0.86;0.86;0.86;0.86;0.86|0.88	4.78|4.78	0.0115|0.0115	0.14087|0.14087	.|.	0.057039|.	0.64402|.	N|.	0.000002|.	T|T	0.34890|0.34890	0.0913|0.0913	N|N	0.16862|0.16862	0.45|0.45	0.80722|0.80722	D|D	1|1	B;B;B|B	0.10296|0.29955	0.003;0.0;0.0|0.263	B;B;B|P	0.17098|0.46208	0.017;0.009;0.005|0.507	T|T	0.32534|0.32534	-0.9903|-0.9903	10|9	0.21014|0.87932	T|D	0.42|0	-0.3684|-0.3684	5.8773|5.8773	0.18836|0.18836	0.328:0.1544:0.5176:0.0|0.328:0.1544:0.5176:0.0	.|.	18;18;18|2	B7ZBI2;Q8N6T3;Q8N6T3-2|E7EV62	.;ARFG1_HUMAN;.|.	D|I	18|2	ENSP00000359306:E18D;ENSP00000428355:E18D;ENSP00000359298:E18D;ENSP00000314615:E18D;ENSP00000430929:E18D;ENSP00000449515:E18D|ENSP00000430500:R2I	ENSP00000314615:E18D|ENSP00000430500:R2I	E|R	+|+	3|2	2|0	ARFGAP1|ARFGAP1	61377431|61377431	0.998000|0.998000	0.40836|0.40836	0.900000|0.900000	0.35374|0.35374	0.053000|0.053000	0.15095|0.15095	0.412000|0.412000	0.21131|0.21131	-0.161000|-0.161000	0.10983|0.10983	-0.379000|-0.379000	0.06801|0.06801	GAG|AGA		TCGA-2L-AAQL-01A-11D-A38G-08	ARFGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080134.3	0	0	0	4	142	0	60	0	1.755982e-01	0	22	0	60	2		0	0	0	0	0	2	1	0.884808	4	138	0	60	2		0	0	0	0	60	2	-6.515642	1	0	0	0		1	1	2	3	2.108566	0	0.380000	1.790000	0.384676	0.160000	5.000000e-02	1.000000	0.140000	0.200893	0.160000	0	0.090000	0.260000
PLXNB2	23654	broad.mit.edu	37	22	50728171	50728171	+	Silent	SNP	G	G	A			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr22:50728171G>A	ENST00000449103.1	-	3	983	c.843C>T	c.(841-843)gcC>gcT	p.A281A	PLXNB2_ENST00000359337.4_Silent_p.A281A			O15031	PLXB2_HUMAN	plexin B2			66		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)			CCACGGAGGCGGCCAGGCAGG	0.662000																								0							SO:0001819	synonymous_variant			ENST00000449103.1	0	1	hg19	CCDS43035.1																																																																																				TCGA-2L-AAQL-01A-11D-A38G-08	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	0	0	1	24	144	1	75	0	2.183712e-01	1	5	1	75	2	1	1	38	357	0	223	2	1	0.995154	24	136	1	68	10		0	0	0	1	75	2	-20.000000	1	1	120718	7	37	1	0	1	1	1.915113	0	0.380000	1.790000	0.319205	0.680000	4.500000e-01	0.940000	0.680000	0.695196	0.680000	0	0.560000	0.820000
TTN	7273	broad.mit.edu	37	2	179455476	179455476	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr2:179455476C>T	ENST00000591111.1	-	254	56277	c.56053G>A	c.(56053-56055)Gct>Act	p.A18685T	TTN-AS1_ENST00000590743.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.A17758T|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.A11261T|TTN_ENST00000589042.1_Missense_Mutation_p.A20326T|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.A11453T|TTN_ENST00000359218.5_Missense_Mutation_p.A11386T|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin			1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)		TTCAGGTCAGCGATAGGTGTT	0.443000																								0							SO:0001583	missense			ENST00000591111.1	0	1	hg19		.	.	.	.	.	.	.	.	.	.	C	6.198	0.404659	0.11754	0.0	1.21E-4	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.54279	0.58;0.58;0.58;0.58	6.11	0.782	0.18567	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.35158	0.0922	N	0.13352	0.335	0.09310	N	1	B;B;B;B	0.06786	0.001;0.001;0.001;0.001	B;B;B;B	0.06405	0.002;0.002;0.002;0.002	T	0.28396	-1.0045	9	0.87932	D	0	.	11.1443	0.48422	0.0:0.2701:0.5822:0.1477	.	11261;11386;11453;18685	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	T	17758;11261;11453;11386;11259	ENSP00000343764:A17758T;ENSP00000434586:A11261T;ENSP00000340554:A11453T;ENSP00000352154:A11386T	ENSP00000340554:A11453T	A	-	1	0	TTN	179163722	0.086000	0.21541	0.001000	0.08648	0.796000	0.44982	0.327000	0.19663	-0.131000	0.11578	0.655000	0.94253	GCT		TCGA-2L-AAQL-01A-11D-A38G-08	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	0	0	0	8	484	0	188		0	0	0	0	188	2		0	0	0	0	0	2	1	0.988658	7	477	0	188	2		0	0	0	0	188	2	-2.475960	0	1	120840	27	46	1	1	2	3	2.094280	0	0.380000	1.790000	0.382347	0.080000	3.000000e-02	0.180000	0.080000	0.104789	0.080000	0	0.050000	0.130000
ASNSD1	54529	broad.mit.edu	37	2	190535201	190535201	+	Silent	SNP	C	C	T			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr2:190535201C>T	ENST00000260952.4	+	6	2094	c.1681C>T	c.(1681-1683)Cta>Tta	p.L561L	ASNSD1_ENST00000607062.1_Silent_p.L80L	NM_019048.2	NP_061921	Q9NWL6	ASND1_HUMAN	asparagine synthetase domain containing 1			25			OV - Ovarian serous cystadenocarcinoma(117;0.00318)|Epithelial(96;0.0449)|all cancers(119;0.118)		TGTCTCCTTTCTAAATTCTCT	0.353000																								0							SO:0001819	synonymous_variant			ENST00000260952.4	1	1	hg19	CCDS2300.1																																																																																				TCGA-2L-AAQL-01A-11D-A38G-08	ASNSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255919.3	1	0	0	99	411	0	207	1	1	19	105	0	207	2		0	0	0	0	0	2	1	1.000000	96	405	0	205	2		0	0	0	0	207	2	-20.000000	1	1	0	0		1	1	2	3	2.094280	0	0.380000	1.790000	0.382347	0.990000	8.400000e-01	1.000000	1.000000	0.976147	0.990000	1	0.930000	1.000000
PUM2	23369	broad.mit.edu	37	2	20508209	20508209	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr2:20508209G>A	ENST00000361078.2	-	5	677	c.655C>T	c.(655-657)Cct>Tct	p.P219S	PUM2_ENST00000403432.1_Missense_Mutation_p.P219S|PUM2_ENST00000420234.1_5'UTR|PUM2_ENST00000338086.5_Missense_Mutation_p.P219S|PUM2_ENST00000319801.5_Missense_Mutation_p.P219S|PUM2_ENST00000536417.1_Missense_Mutation_p.P163S			Q8TB72	PUM2_HUMAN	pumilio RNA-binding family member 2			42	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				TGAGTTTCAGGATTTGAAAAT	0.448000																								0							SO:0001583	missense			ENST00000361078.2	1	1	hg19		.	.	.	.	.	.	.	.	.	.	G	14.59	2.581242	0.46006	.	.	ENSG00000055917	ENST00000338086;ENST00000361078;ENST00000319801;ENST00000440577;ENST00000403432;ENST00000536417;ENST00000442400	T;T;T;T;T;T	0.18016	2.31;2.58;2.58;2.24;2.31;2.31	6.07	4.22	0.49857	.	0.151121	0.64402	D	0.000008	T	0.08044	0.0201	N	0.08118	0	0.38222	D	0.94079	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.0;0.001	T	0.25882	-1.0119	10	0.21014	T	0.42	-4.9397	8.5974	0.33723	0.0667:0.0:0.5388:0.3945	.	163;219;219	B4E2B6;B7ZL34;Q8TB72-3	.;.;.	S	219;219;219;110;219;163;219	ENSP00000338173:P219S;ENSP00000354370:P219S;ENSP00000326746:P219S;ENSP00000409905:P110S;ENSP00000385992:P219S;ENSP00000440093:P163S	ENSP00000326746:P219S	P	-	1	0	PUM2	20371690	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.825000	0.39081	0.840000	0.34995	0.650000	0.86243	CCT		TCGA-2L-AAQL-01A-11D-A38G-08	PUM2-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		0	0	1	107	525	0	201		0	0	0	0	201	2		0	0	0	0	0	2	1	1.000000	107	516	0	200	2		0	0	0	0	201	2	-20.000000	1	1	0	0		1	1	2	3	2.093014	0	0.380000	1.790000	0.381176	0.880000	7.400000e-01	1.000000	1.000000	0.892137	0.880000	1	0.810000	0.970000
CTDSP1	58190	broad.mit.edu	37	2	219266400	219266400	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr2:219266400C>T	ENST00000273062.2	+	2	517	c.181C>T	c.(181-183)Ccc>Tcc	p.P61S	MIR26B_ENST00000362251.2_RNA|CTDSP1_ENST00000443891.1_Missense_Mutation_p.P61S|RP11-378A13.2_ENST00000608367.1_RNA|CTDSP1_ENST00000488627.1_3'UTR	NM_021198.2|NM_182642.2	NP_067021.1|NP_872580.1	Q9GZU7	CTDS1_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 1			8		Renal(207;0.0915)			CAGCGGGGCGCCCCTGCTTGT	0.667000																								0							SO:0001583	missense			ENST00000273062.2	1	1	hg19	CCDS2416.1	.	.	.	.	.	.	.	.	.	.	C	18.16	3.561410	0.65538	.	.	ENSG00000144579	ENST00000443891;ENST00000273062	T;T	0.14144	2.53;2.55	5.08	4.19	0.49359	.	0.061117	0.64402	D	0.000003	T	0.19725	0.0474	M	0.74467	2.265	0.58432	D	0.999999	B;B	0.17852	0.024;0.024	B;B	0.26202	0.024;0.067	T	0.03060	-1.1077	10	0.44086	T	0.13	-16.6294	12.6141	0.56567	0.0:0.9192:0.0:0.0807	.	61;61	Q9GZU7;C9IYG0	CTDS1_HUMAN;.	S	61	ENSP00000392248:P61S;ENSP00000273062:P61S	ENSP00000273062:P61S	P	+	1	0	CTDSP1	218974644	0.543000	0.26434	0.924000	0.36721	0.734000	0.41952	3.105000	0.50314	2.362000	0.80069	0.655000	0.94253	CCC		TCGA-2L-AAQL-01A-11D-A38G-08	CTDSP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256774.1	1	0	1	36	127	0	56	1	1	31	79	0	56	2		0	0	0	0	0	2	1	1.000000	35	124	0	54	2		0	0	0	0	56	2	-20.000000	1	1	0	0		1	1	2	3	2.094280	0	0.380000	1.790000	0.382347	0.990000	8.500000e-01	1.000000	1.000000	0.988070	0.990000	1	0.990000	1.000000
ACTG2	72	broad.mit.edu	37	2	74146664	74146664	+	Nonsense_Mutation	SNP	G	G	T			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr2:74146664G>T	ENST00000409624.1	+	10	1736	c.1093G>T	c.(1093-1095)Gag>Tag	p.E365*	ACTG2_ENST00000345517.3_Nonsense_Mutation_p.E365*|ACTG2_ENST00000409731.3_Nonsense_Mutation_p.E322*			P63267	ACTH_HUMAN	actin, gamma 2, smooth muscle, enteric			18					TGAGTATGATGAGGCAGGGCC	0.532000																								0							SO:0001587	stop_gained			ENST00000409624.1	0	1	hg19	CCDS1930.1	.	.	.	.	.	.	.	.	.	.	G	36	5.762352	0.96906	.	.	ENSG00000163017	ENST00000409731;ENST00000345517;ENST00000409624	.	.	.	4.8	4.8	0.61643	.	0.502454	0.17436	N	0.174289	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	17.1435	0.86760	0.0:0.0:1.0:0.0	.	.	.	.	X	322;365;365	.	ENSP00000295137:E365X	E	+	1	0	ACTG2	74000172	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	9.601000	0.98297	2.651000	0.90000	0.591000	0.81541	GAG		TCGA-2L-AAQL-01A-11D-A38G-08	ACTG2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328086.1	0	0	0	6	302	0	92	0	8.615652e-01	0	181	0	92	2		0	0	0	0	0	2	1	0.961260	5	292	0	91	2		0	0	0	0	92	2	-6.500245	1	0	0	0		1	1	2	3	2.100867	0	0.380000	1.790000	0.382347	0.100000	4.000000e-02	0.230000	0.100000	0.127306	0.100000	0	0.070000	0.160000
NPHP3	27031	broad.mit.edu	37	3	132415576	132415576	+	Splice_Site	SNP	G	G	A			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr3:132415576G>A	ENST00000337331.5	-	15	2256	c.2170C>T	c.(2170-2172)Cgt>Tgt	p.R724C	NPHP3_ENST00000326682.8_Intron	NM_153240.4	NP_694972.3	Q7Z494	NPHP3_HUMAN	nephronophthisis 3 (adolescent)			42					ACCACTCACCGCGCGATCATT	0.458000																								0							SO:0001630	splice_region_variant			ENST00000337331.5	1	0	hg19	CCDS3078.1	.	.	.	.	.	.	.	.	.	.	G	9.374	1.071278	0.20147	.	.	ENSG00000113971	ENST00000337331	T	0.64085	-0.08	5.9	-3.65	0.04502	.	0.566832	0.22573	N	0.058315	T	0.30448	0.0765	N	0.02539	-0.55	0.35234	D	0.777212	B	0.02656	0.0	B	0.01281	0.0	T	0.04373	-1.0956	10	0.45353	T	0.12	-0.0351	11.0565	0.47922	0.6313:0.0:0.2772:0.0916	.	724	Q7Z494	NPHP3_HUMAN	C	724	ENSP00000338766:R724C	ENSP00000338766:R724C	R	-	1	0	NPHP3	133898266	0.000000	0.05858	0.002000	0.10522	0.043000	0.13939	-0.361000	0.07612	-0.584000	0.05913	0.650000	0.86243	CGT		TCGA-2L-AAQL-01A-11D-A38G-08	NPHP3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357020.2	1	0	1	204	860	0	352		0	0	0	0	352	2		0	0	0	0	0	2	1	1.000000	200	841	0	349	2		0	0	0	0	352	2	-20.000000	1	1	0	0		1	1	2	3	2.103567	0	0.380000	1.790000	0.382347	0.990000	8.800000e-01	1.000000	1.000000	0.981278	0.990000	1	0.940000	1.000000
TTC21A	199223	broad.mit.edu	37	3	39177931	39177931	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr3:39177931G>A	ENST00000431162.2	+	23	3183	c.3049G>A	c.(3049-3051)Gcc>Acc	p.A1017T	TTC21A_ENST00000440121.1_Missense_Mutation_p.A969T|TTC21A_ENST00000301819.6_Missense_Mutation_p.A1018T|TTC21A_ENST00000493856.1_3'UTR			Q8NDW8	TT21A_HUMAN	tetratricopeptide repeat domain 21A			50					CTTTGAATTGGCCAAGAAGGT	0.438000																								0							SO:0001583	missense			ENST00000431162.2	0	1	hg19	CCDS46800.1	.	.	.	.	.	.	.	.	.	.	G	13.23	2.175489	0.38413	.	.	ENSG00000168026	ENST00000301819;ENST00000424305;ENST00000431162;ENST00000440121	T;T;T	0.54479	0.57;0.57;0.57	4.79	2.7	0.31948	Tetratricopeptide repeat-containing (1);	0.648196	0.14838	N	0.295467	T	0.57095	0.2030	M	0.73430	2.235	0.09310	N	1	B;B;B	0.27416	0.178;0.005;0.003	B;B;B	0.33960	0.173;0.015;0.006	T	0.57370	-0.7823	10	0.66056	D	0.02	-5.5503	13.7973	0.63180	0.0:0.0:0.7115:0.2885	.	969;1018;1017	Q8NDW8-6;Q8NDW8-7;Q8NDW8	.;.;TT21A_HUMAN	T	1018;1000;1017;969	ENSP00000301819:A1018T;ENSP00000398211:A1017T;ENSP00000410882:A969T	ENSP00000301819:A1018T	A	+	1	0	TTC21A	39152935	1.000000	0.71417	0.027000	0.17364	0.857000	0.48899	1.702000	0.37836	0.990000	0.38787	0.462000	0.41574	GCC		TCGA-2L-AAQL-01A-11D-A38G-08	TTC21A-021	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377829.1	0	0	0	7	441	0	204	0	1.703103e-02	1	10	0	204	2		0	0	0	0	0	2	1	0.979332	6	433	0	201	2		0	0	0	0	204	2	-2.558218	1	1	0	0		1	0	1	1	1.703696	1	0.380000	1.790000	0.234568	0.060000	2.000000e-02	0.130000	0.070000	0.075230	0.060000	0	0.040000	0.100000
CELSR3	1951	broad.mit.edu	37	3	48696487	48696487	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr3:48696487C>T	ENST00000164024.4	-	1	3861	c.3581G>A	c.(3580-3582)cGc>cAc	p.R1194H	CELSR3_ENST00000544264.1_Missense_Mutation_p.R1194H	NM_001407.2	NP_001398.2	Q9NYQ7	CELR3_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 3			83					AGCTGGGATGCGCCCAATAAT	0.537000																								0							SO:0001583	missense			ENST00000164024.4	0	1	hg19	CCDS2775.1	.	.	.	.	.	.	.	.	.	.	C	16.18	3.049277	0.55218	.	.	ENSG00000008300	ENST00000164024;ENST00000544264	T;T	0.39406	1.08;1.08	5.44	4.56	0.56223	Cadherin (1);Cadherin-like (1);	.	.	.	.	T	0.59797	0.2220	M	0.82056	2.57	0.46437	D	0.999045	D;D	0.89917	1.0;0.999	D;P	0.63488	0.915;0.869	T	0.63545	-0.6613	9	0.72032	D	0.01	.	7.936	0.29931	0.0:0.7749:0.0:0.2251	.	1194;1264	Q9NYQ7;Q5Y190	CELR3_HUMAN;.	H	1194	ENSP00000164024:R1194H;ENSP00000445694:R1194H	ENSP00000164024:R1194H	R	-	2	0	CELSR3	48671491	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.728000	0.47319	2.561000	0.86390	0.561000	0.74099	CGC		TCGA-2L-AAQL-01A-11D-A38G-08	CELSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257523.1	0	0	0	5	229	1	119		0	0	0	1	119	2	0	9.186729e-01	0	211	0	157	2	0	0.192128	5	224	1	119	9		0	0	0	1	119	2	-2.718182	1	1	121412	4	39	1	0	1	1	1.703696	1	0.380000	1.790000	0.234568	0.090000	3.000000e-02	0.200000	0.090000	0.106873	0.090000	0	0.050000	0.150000
DNAH1	25981	broad.mit.edu	37	3	52387151	52387151	+	Missense_Mutation	SNP	C	C	G			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr3:52387151C>G	ENST00000420323.2	+	19	3321	c.3060C>G	c.(3058-3060)ttC>ttG	p.F1020L		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1			62					TGAAGGAGTTCCAACCCTACC	0.602000																								0							SO:0001583	missense			ENST00000420323.2	0	1	hg19	CCDS46842.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.499784	0.85176	.	.	ENSG00000114841	ENST00000420323	T	0.58940	0.3	5.54	4.66	0.58398	.	0.000000	0.56097	D	0.000031	T	0.60907	0.2305	L	0.42632	1.34	0.51012	D	0.999902	D;P	0.76494	0.999;0.931	D;D	0.75484	0.986;0.936	T	0.57171	-0.7857	10	0.05833	T	0.94	.	10.0759	0.42360	0.0:0.8508:0.0:0.1492	.	1020;1020	C9JXH6;Q9P2D7-3	.;.	L	1020	ENSP00000401514:F1020L	ENSP00000401514:F1020L	F	+	3	2	DNAH1	52362191	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.810000	0.47979	2.626000	0.88956	0.650000	0.86243	TTC		TCGA-2L-AAQL-01A-11D-A38G-08	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	0	0	0	6	139	0	74		0	0	0	0	74	2		0	0	0	0	0	2	1	0.962064	4	136	0	74	2		0	0	0	0	74	2	-8.784785	1	1	0	0		1	0	1	1	1.703696	1	0.380000	1.790000	0.234568	0.180000	7.000000e-02	0.350000	0.170000	0.198464	0.180000	0	0.120000	0.270000
ANAPC4	29945	broad.mit.edu	37	4	25395511	25395511	+	Nonsense_Mutation	SNP	C	C	T			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr4:25395511C>T	ENST00000315368.3	+	11	1016	c.874C>T	c.(874-876)Cag>Tag	p.Q292*	ANAPC4_ENST00000510092.1_Nonsense_Mutation_p.Q292*	NM_013367.2	NP_037499.2	Q9UJX5	APC4_HUMAN	anaphase promoting complex subunit 4	p.Q292*(1)		27		Breast(46;0.0503)			CAAGTTTGTGCAGGTAAAGCA	0.353000																								1	Substitution - Nonsense(1)						SO:0001587	stop_gained			ENST00000315368.3	0	1	hg19	CCDS3434.1	.	.	.	.	.	.	.	.	.	.	C	39	7.341870	0.98224	.	.	ENSG00000053900	ENST00000315368;ENST00000510092	.	.	.	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.21540	T	0.41	-20.3366	20.394	0.98981	0.0:1.0:0.0:0.0	.	.	.	.	X	292	.	ENSP00000318775:Q292X	Q	+	1	0	ANAPC4	25004609	1.000000	0.71417	1.000000	0.80357	0.852000	0.48524	7.162000	0.77515	2.830000	0.97506	0.585000	0.79938	CAG		TCGA-2L-AAQL-01A-11D-A38G-08	ANAPC4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214986.1	0	0	0	4	200	0	82	0	2.167323e-02	0	9	0	82	2		0	0	0	0	0	2	1	0.884062	4	194	0	81	2		0	0	0	0	82	2	-3.072895	1	1	0	0		1	0	1	1	1.917799	0	0.380000	1.790000	0.319205	0.100000	3.000000e-02	0.220000	0.090000	0.115125	0.100000	0	0.060000	0.160000
CHRNA9	55584	broad.mit.edu	37	4	40339267	40339267	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr4:40339267G>A	ENST00000310169.2	+	3	390	c.251G>A	c.(250-252)cGc>cAc	p.R84H		NM_017581.3	NP_060051.2	Q9UGM1	ACHA9_HUMAN	cholinergic receptor, nicotinic, alpha 9 (neuronal)	p.R84H(1)		33				Galantamine(DB00674)|Nicotine(DB00184)	TTGTGGATCCGCCAAATCTGG	0.483000													Esophageal Squamous(115;1297 1602 22235 25158 43327)											1	Substitution - Missense(1)						SO:0001583	missense			ENST00000310169.2	0	1	hg19	CCDS3459.1	.	.	.	.	.	.	.	.	.	.	G	29.9	5.045322	0.93685	.	.	ENSG00000174343	ENST00000310169	T	0.80214	-1.35	5.83	5.83	0.93111	Neurotransmitter-gated ion-channel ligand-binding (3);	0.046822	0.85682	D	0.000000	D	0.90937	0.7151	M	0.83603	2.65	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.91105	0.4917	10	0.66056	D	0.02	.	20.1174	0.97942	0.0:0.0:1.0:0.0	.	84	Q9UGM1	ACHA9_HUMAN	H	84	ENSP00000312663:R84H	ENSP00000312663:R84H	R	+	2	0	CHRNA9	40034024	1.000000	0.71417	1.000000	0.80357	0.656000	0.38851	9.476000	0.97823	2.771000	0.95319	0.591000	0.81541	CGC		TCGA-2L-AAQL-01A-11D-A38G-08	CHRNA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216822.1	0	0	0	5	150	0	59		0	0	0	0	59	2		0	0	0	0	0	2	1	0.933067	5	145	0	59	2		0	0	0	0	59	2	-3.055836	1	1	0	0		1	0	1	1	1.917799	0	0.380000	1.790000	0.319205	0.160000	6.000000e-02	0.330000	0.150000	0.180673	0.160000	0	0.100000	0.250000
SLC12A7	10723	broad.mit.edu	37	5	1074737	1074737	+	Missense_Mutation	SNP	C	C	A			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08			C	A	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr5:1074737C>A	ENST00000264930.5	-	16	2060	c.2017G>T	c.(2017-2019)Gcc>Tcc	p.A673S		NM_006598.2	NP_006589.2	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 7			32	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)		Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)	Potassium Chloride(DB00761)	GCGTAGCGGGCGGCGTTCAGG	0.672000																								0							SO:0001583	missense			ENST00000264930.5	1	1	hg19	CCDS34129.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	18.40|18.40	3.616049|3.616049	0.66672|0.66672	.|.	.|.	ENSG00000113504|ENSG00000113504	ENST00000264930|ENST00000513223	D|.	0.98862|.	-5.19|.	4.11|4.11	4.11|4.11	0.48088|0.48088	Amino acid permease domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.84097|0.84097	0.5397|0.5397	M|M	0.92459|0.92459	3.31|3.31	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.91635|.	0.999|.	D|D	0.88363|0.88363	0.2989|0.2989	10|5	0.87932|.	D|.	0|.	.|.	14.1738|14.1738	0.65527|0.65527	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	673|.	Q9Y666|.	S12A7_HUMAN|.	S|L	673|30	ENSP00000264930:A673S|.	ENSP00000264930:A673S|.	A|R	-|-	1|2	0|0	SLC12A7|SLC12A7	1127737|1127737	1.000000|1.000000	0.71417|0.71417	0.979000|0.979000	0.43373|0.43373	0.045000|0.045000	0.14185|0.14185	6.881000|6.881000	0.75584|0.75584	1.996000|1.996000	0.58369|0.58369	0.313000|0.313000	0.20887|0.20887	GCC|CGC		TCGA-2L-AAQL-01A-11D-A38G-08	SLC12A7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366446.2	1	0	1	38	166	0	83	1	9.980570e-01	9	36	0	83	2		0	0	0	0	0	2	1	1.000000	38	159	0	81	2		0	0	0	0	83	2	-3.144754	1	1	0	0		1	0	1	1	1.909116	0	0.380000	1.790000	0.317782	0.880000	6.500000e-01	1.000000	1.000000	0.879766	0.880000	1	0.760000	1.000000
DDX46	9879	broad.mit.edu	37	5	134130654	134130654	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr5:134130654G>A	ENST00000354283.4	+	14	1876	c.1741G>A	c.(1741-1743)Gta>Ata	p.V581I	DDX46_ENST00000509178.1_3'UTR|DDX46_ENST00000452510.2_Missense_Mutation_p.V581I			Q7L014	DDX46_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 46			30			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)		ACCTATTGAAGTACAAGTTGG	0.468000													Colon(13;391 453 4901 21675 24897)											0							SO:0001583	missense			ENST00000354283.4	1	1	hg19	CCDS34240.1	.	.	.	.	.	.	.	.	.	.	G	12.22	1.872519	0.33069	.	.	ENSG00000145833	ENST00000452510;ENST00000354283	D;D	0.92149	-2.98;-2.98	5.42	5.42	0.78866	DEAD-like helicase (2);	0.000000	0.85682	D	0.000000	T	0.81673	0.4872	N	0.04335	-0.225	0.80722	D	1	B	0.12630	0.006	B	0.16289	0.015	T	0.77138	-0.2698	10	0.02654	T	1	-15.5181	19.5998	0.95557	0.0:0.0:1.0:0.0	.	581	Q7L014	DDX46_HUMAN	I	581	ENSP00000416534:V581I;ENSP00000346236:V581I	ENSP00000346236:V581I	V	+	1	0	DDX46	134158553	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.887000	0.87295	2.717000	0.92951	0.655000	0.94253	GTA		TCGA-2L-AAQL-01A-11D-A38G-08	DDX46-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371584.1	1	0	1	147	487	0	311	1	9.128506e-01	7	9	0	311	2		0	0	0	0	0	2	1	1.000000	145	470	0	309	2		0	0	0	0	311	2	-20.000000	1	1	0	0		1	0	1	1	1.923135	0	0.380000	1.790000	0.324839	0.990000	9.600000e-01	1.000000	1.000000	0.997887	0.990000	1	0.990000	1.000000
PCDHA1	56147	broad.mit.edu	37	5	140167336	140167336	+	Silent	SNP	C	C	T			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr5:140167336C>T	ENST00000504120.2	+	1	1461	c.1461C>T	c.(1459-1461)aaC>aaT	p.N487N	PCDHA1_ENST00000378133.3_Silent_p.N487N|PCDHA1_ENST00000394633.3_Silent_p.N487N	NM_018900.2	NP_061723.1	Q9Y5I3	PCDA1_HUMAN	protocadherin alpha 1	p.N487K(2)		70			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		CGCAGGAGAACGCGCTGGTGT	0.657000																								2	Substitution - Missense(2)						SO:0001819	synonymous_variant			ENST00000504120.2	1	1	hg19	CCDS54913.1																																																																																				TCGA-2L-AAQL-01A-11D-A38G-08	PCDHA1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389127.1	1	0	1	112	403	1	184		0	0	0	1	184	2		0	0	0	0	0	2	1	1.000000	106	363	1	174	11		0	0	0	1	184	2	-20.000000	1	1	0	0		1	0	1	1	1.912484	0	0.380000	1.790000	0.322034	0.990000	8.700000e-01	1.000000	1.000000	0.984339	0.990000	1	0.950000	1.000000
FBXL7	23194	broad.mit.edu	37	5	15928366	15928366	+	Silent	SNP	C	C	T			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr5:15928366C>T	ENST00000504595.1	+	3	976	c.495C>T	c.(493-495)aaC>aaT	p.N165N	FBXL7_ENST00000329673.7_Silent_p.N153N|FBXL7_ENST00000510662.1_Silent_p.N118N	NM_001278317.1|NM_012304.3	NP_001265246.1|NP_036436.1	Q9UJT9	FBXL7_HUMAN	F-box and leucine-rich repeat protein 7			60					AGACCATCAACGTGGACCGCG	0.667000																								0							SO:0001819	synonymous_variant			ENST00000504595.1	1	1	hg19	CCDS54833.1																																																																																				TCGA-2L-AAQL-01A-11D-A38G-08	FBXL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366117.1	1	0	1	19	75	0	42		0	0	0	0	42	2		0	0	0	0	0	2	1	0.999995	19	73	0	41	2		0	0	0	0	42	2	-20.000000	1	1	0	0		1	0	1	1	1.909116	0	0.380000	1.790000	0.317782	0.950000	6.100000e-01	1.000000	1.000000	0.908901	0.950000	1	0.770000	1.000000
ADAMTS2	9509	broad.mit.edu	37	5	178541162	178541162	+	Silent	SNP	G	G	A	rs79606317		TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr5:178541162G>A	ENST00000251582.7	-	22	3443	c.3342C>T	c.(3340-3342)aaC>aaT	p.N1114N		NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	p.N1114N(1)		72	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		CGTCAATGTCGTTGTGCTTCC	0.587000																								1	Substitution - coding silent(1)						SO:0001819	synonymous_variant			ENST00000251582.7	1	1	hg19	CCDS4444.1																																																																																				TCGA-2L-AAQL-01A-11D-A38G-08	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1	1	0	0	13	248	0	89	0	8.056376e-01	0	60	0	89	2		0	0	0	0	0	2	1	0.999525	13	244	0	87	2		0	0	0	0	89	2	-4.772792	1	1	121412	30	48	1	0	1	1	1.912484	0	0.380000	1.790000	0.322034	0.240000	1.300000e-01	0.390000	0.240000	0.254155	0.240000	0	0.180000	0.320000
LIN28B	389421	broad.mit.edu	37	6	105474175	105474175	+	Missense_Mutation	SNP	C	C	A			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr6:105474175C>A	ENST00000345080.4	+	3	404	c.201C>A	c.(199-201)agC>agA	p.S67R		NM_001004317.3	NP_001004317.1	Q6ZN17	LN28B_HUMAN	lin-28 homolog B (C. elegans)			12		all_cancers(87;0.00346)|Acute lymphoblastic leukemia(125;2.26e-08)|all_hematologic(75;2.79e-06)|all_epithelial(87;0.204)			CTTTACAGAGCAAACTATTCA	0.338000																								0							SO:0001583	missense			ENST00000345080.4	1	1	hg19	CCDS34504.1	.	.	.	.	.	.	.	.	.	.	C	19.21	3.783141	0.70222	.	.	ENSG00000187772	ENST00000345080	.	.	.	5.92	5.05	0.67936	Cold shock protein (1);Nucleic acid-binding, OB-fold-like (1);Cold-shock protein, DNA-binding (1);Nucleic acid-binding, OB-fold (1);	0.074367	0.85682	D	0.000000	T	0.61160	0.2325	L	0.49640	1.575	0.80722	D	1	D;D	0.76494	0.991;0.999	P;D	0.66497	0.818;0.944	T	0.65302	-0.6201	9	0.52906	T	0.07	-13.7426	14.9456	0.71029	0.0:0.9318:0.0:0.0682	.	44;67	A7E2T3;Q6ZN17	.;LN28B_HUMAN	R	67	.	ENSP00000344401:S67R	S	+	3	2	LIN28B	105580868	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.128000	0.50492	1.499000	0.48617	0.650000	0.86243	AGC		TCGA-2L-AAQL-01A-11D-A38G-08	LIN28B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041646.2	1	0	1	77	351	0	132		0	0	0	0	132	2		0	0	0	0	0	2	1	1.000000	76	344	0	132	2		0	0	0	0	132	2	-20.000000	1	1	121384	1	35	1	0	1	1	1.892103	1	0.380000	1.790000	0.319205	0.850000	6.900000e-01	1.000000	1.000000	0.862233	0.850000	1	0.770000	0.950000
PKHD1	5314	broad.mit.edu	37	6	51944795	51944795	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr6:51944795G>A	ENST00000371117.3	-	5	568	c.293C>T	c.(292-294)tCt>tTt	p.S98F	PKHD1_ENST00000340994.4_Missense_Mutation_p.S98F	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)			304	Lung NSC(77;0.0605)				ATGTGCTTCAGACAGCACAGA	0.473000																								0							SO:0001583	missense			ENST00000371117.3	1	1	hg19	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	G	13.80	2.345983	0.41599	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	D;D	0.88124	-2.13;-2.34	5.31	3.41	0.39046	.	0.768295	0.12007	N	0.508240	T	0.74951	0.3784	L	0.46157	1.445	0.09310	N	1	P;P	0.45474	0.859;0.779	B;B	0.40444	0.329;0.177	T	0.67452	-0.5667	10	0.62326	D	0.03	.	9.7386	0.40404	0.0:0.1492:0.6976:0.1532	.	98;98	P08F94-2;P08F94	.;PKHD1_HUMAN	F	98	ENSP00000360158:S98F;ENSP00000341097:S98F	ENSP00000341097:S98F	S	-	2	0	PKHD1	52052754	0.010000	0.17322	0.008000	0.14137	0.776000	0.43924	1.556000	0.36288	2.631000	0.89168	0.655000	0.94253	TCT		TCGA-2L-AAQL-01A-11D-A38G-08	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	1	0	0	90	296	0	155	0	0	0	1	0	155	2		0	0	0	0	0	2	1	1.000000	89	293	0	155	2		0	0	0	0	155	2	-20.000000	1	1	0	0		1	0	1	1	1.935087	0	0.380000	1.790000	0.319205	0.990000	9.100000e-01	1.000000	1.000000	0.994192	0.990000	1	0.990000	1.000000
GRM8	2918	broad.mit.edu	37	7	126173853	126173853	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr7:126173853G>A	ENST00000339582.2	-	9	2391	c.1583C>T	c.(1582-1584)aCg>aTg	p.T528M	GRM8_ENST00000358373.3_Missense_Mutation_p.T528M|GRM8_ENST00000444921.2_Missense_Mutation_p.T528M|GRM8_ENST00000480995.1_Intron			O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8			125		Prostate(267;0.186)			CCCTTTCACCGTTTTCTTCCT	0.542000										HNSCC(24;0.065)														0							SO:0001583	missense			ENST00000339582.2	1	1	hg19	CCDS5794.1	.	.	.	.	.	.	.	.	.	.	G	1.717	-0.497514	0.04291	.	.	ENSG00000179603	ENST00000339582;ENST00000444921;ENST00000358373	D;D;D	0.89617	-2.54;-2.54;-2.54	5.8	4.92	0.64577	GPCR, family 3, nine cysteines domain (1);	0.100013	0.64402	D	0.000001	T	0.74261	0.3693	N	0.03999	-0.3	0.80722	D	1	B;B	0.16166	0.013;0.016	B;B	0.22880	0.002;0.042	T	0.69075	-0.5241	10	0.02654	T	1	.	14.0626	0.64808	0.0721:0.0:0.9279:0.0	.	528;528	O00222-2;O00222	.;GRM8_HUMAN	M	528	ENSP00000344173:T528M;ENSP00000409790:T528M;ENSP00000351142:T528M	ENSP00000344173:T528M	T	-	2	0	GRM8	125961089	0.754000	0.28360	0.709000	0.30452	0.984000	0.73092	1.180000	0.32005	1.468000	0.48064	0.643000	0.83706	ACG		TCGA-2L-AAQL-01A-11D-A38G-08	GRM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059209.4	1	0	1	55	365	0	154		0	0	0	0	154	2		0	0	0	0	0	2	1	1.000000	54	363	0	154	2		0	0	0	0	154	2	-2.920908	1	1	121412	4	38	1	1	2	3	2.121637	0	0.380000	1.790000	0.386988	0.700000	5.300000e-01	1.000000	0.690000	0.717619	0.700000	0	0.610000	0.810000
FLNC	2318	broad.mit.edu	37	7	128495282	128495282	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr7:128495282G>A	ENST00000325888.8	+	43	7426	c.7165G>A	c.(7165-7167)Gat>Aat	p.D2389N	RP11-309L24.2_ENST00000469965.1_RNA|FLNC_ENST00000346177.6_Missense_Mutation_p.D2356N	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma			128					CAAGTTCAATGATGAGCACAT	0.622000																								0							SO:0001583	missense			ENST00000325888.8	1	0	hg19	CCDS43644.1	.	.	.	.	.	.	.	.	.	.	G	16.66	3.184039	0.57800	.	.	ENSG00000128591	ENST00000325888;ENST00000346177	D;D	0.92249	-3.0;-3.0	5.29	5.29	0.74685	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.053142	0.64402	D	0.000001	D	0.90007	0.6880	L	0.46567	1.45	0.48452	D	0.999652	B;B	0.21071	0.008;0.051	B;B	0.24394	0.013;0.053	D	0.86013	0.1502	10	0.33940	T	0.23	.	18.9397	0.92600	0.0:0.0:1.0:0.0	.	2356;2389	Q14315-2;Q14315	.;FLNC_HUMAN	N	2389;2356	ENSP00000327145:D2389N;ENSP00000344002:D2356N	ENSP00000327145:D2389N	D	+	1	0	FLNC	128282518	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.797000	0.62503	2.470000	0.83445	0.462000	0.41574	GAT		TCGA-2L-AAQL-01A-11D-A38G-08	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3	1	0	0	62	417	0	169	0	3.834085e-01	0	10	0	169	2		0	0	0	0	0	2	1	1.000000	62	409	0	168	2		0	0	0	0	169	2	-19.999990	1	1	0	0		1	1	2	3	2.121637	0	0.380000	1.790000	0.386988	0.690000	5.300000e-01	1.000000	0.680000	0.709231	0.690000	0	0.610000	0.790000
KEL	3792	broad.mit.edu	37	7	142655036	142655036	+	Missense_Mutation	SNP	T	T	G			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr7:142655036T>G	ENST00000355265.2	-	6	1024	c.550A>C	c.(550-552)Aaa>Caa	p.K184Q	KEL_ENST00000479768.2_5'UTR	NM_000420.2	NP_000411.1	P23276	KELL_HUMAN	Kell blood group, metallo-endopeptidase			60	Melanoma(164;0.059)				GAAGTCCATTTACCAGAGATG	0.517000																								0							SO:0001583	missense			ENST00000355265.2	1	1	hg19	CCDS34766.1	.	.	.	.	.	.	.	.	.	.	T	8.336	0.827505	0.16749	.	.	ENSG00000197993	ENST00000355265;ENST00000467543	T;T	0.73363	-0.74;-0.74	5.8	3.26	0.37387	Peptidase M13 (1);	0.316302	0.26719	N	0.022860	T	0.49677	0.1571	N	0.14661	0.345	0.09310	N	1	B	0.32010	0.351	B	0.29663	0.105	T	0.30416	-0.9979	10	0.16896	T	0.51	-4.6538	5.6937	0.17843	0.0:0.0867:0.1694:0.744	.	184	P23276	KELL_HUMAN	Q	184;165	ENSP00000347409:K184Q;ENSP00000420011:K165Q	ENSP00000347409:K184Q	K	-	1	0	KEL	142365158	0.003000	0.15002	0.096000	0.21009	0.846000	0.48090	0.398000	0.20899	0.992000	0.38840	0.528000	0.53228	AAA		TCGA-2L-AAQL-01A-11D-A38G-08	KEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347671.2	1	0	1	38	165	0	70		0	0	0	0	70	2		0	0	0	0	0	2	1	1.000000	36	160	0	68	2		0	0	0	0	70	2	-20.000000	1	1	0	0		1	1	2	3	2.121637	0	0.380000	1.790000	0.386988	0.990000	7.300000e-01	1.000000	1.000000	0.947411	0.990000	1	0.860000	1.000000
DNAH11	8701	broad.mit.edu	37	7	21640427	21640427	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr7:21640427G>A	ENST00000409508.3	+	16	3165	c.3134G>A	c.(3133-3135)cGa>cAa	p.R1045Q	DNAH11_ENST00000328843.6_Missense_Mutation_p.R1045Q	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11			230					GTGGATGATCGAGCTGAGTTT	0.448000									Kartagener syndrome															0							SO:0001583	missense	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	ENST00000409508.3	1	1	hg19		.	.	.	.	.	.	.	.	.	.	G	19.10	3.762115	0.69763	.	.	ENSG00000105877	ENST00000328843	T	0.23348	1.91	5.23	5.23	0.72850	.	0.280795	0.30639	N	0.009182	T	0.35537	0.0935	.	.	.	0.46317	D	0.998987	D	0.76494	0.999	P	0.55615	0.78	T	0.02320	-1.1177	9	0.23891	T	0.37	.	13.1616	0.59547	0.0791:0.0:0.9209:0.0	.	1045	Q96DT5	DYH11_HUMAN	Q	1045	ENSP00000330671:R1045Q	ENSP00000330671:R1045Q	R	+	2	0	DNAH11	21606952	1.000000	0.71417	0.965000	0.40720	0.921000	0.55340	4.241000	0.58707	2.452000	0.82932	0.551000	0.68910	CGA		TCGA-2L-AAQL-01A-11D-A38G-08	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	0	0	1	136	769	0	321		0	0	0	0	321	2		0	0	0	0	0	2	1	1.000000	133	756	0	318	2		0	0	0	0	321	2	-20.000000	1	1	120870	3	38	1	1	2	3	2.120206	0	0.380000	1.790000	0.385835	0.790000	6.700000e-01	1.000000	0.800000	0.808651	0.790000	0	0.730000	0.870000
HECW1	23072	broad.mit.edu	37	7	43351452	43351452	+	Nonsense_Mutation	SNP	C	C	T			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr7:43351452C>T	ENST00000395891.2	+	4	723	c.118C>T	c.(118-120)Cga>Tga	p.R40*	HECW1_ENST00000453890.1_Nonsense_Mutation_p.R40*	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1			125					GGAGCCGCTCCGATACAGCTA	0.617000																								0							SO:0001587	stop_gained			ENST00000395891.2	0	1	hg19	CCDS5469.2	.	.	.	.	.	.	.	.	.	.	C	27.5	4.838602	0.91117	.	.	ENSG00000002746	ENST00000395891;ENST00000453890;ENST00000265522	.	.	.	5.96	5.05	0.67936	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.103	0.65070	0.3056:0.6944:0.0:0.0	.	.	.	.	X	40;40;39	.	ENSP00000265522:R39X	R	+	1	2	HECW1	43317977	0.992000	0.36948	0.995000	0.50966	0.246000	0.25737	2.924000	0.48876	2.813000	0.96785	0.655000	0.94253	CGA		TCGA-2L-AAQL-01A-11D-A38G-08	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	1	0	1	55	243	0	100		0	0	0	0	100	2		0	0	0	0	0	2	1	1.000000	55	234	0	97	2		0	0	0	0	100	2	-3.016166	1	1	0	0		1	1	2	3	2.120206	0	0.380000	1.790000	0.385835	0.980000	7.600000e-01	1.000000	1.000000	0.947448	0.980000	1	0.860000	1.000000
STYXL1	51657	broad.mit.edu	37	7	75634627	75634627	+	Silent	SNP	C	C	T			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr7:75634627C>T	ENST00000248600.1	-	6	891	c.549G>A	c.(547-549)aaG>aaA	p.K183K	STYXL1_ENST00000359697.3_Silent_p.K183K|STYXL1_ENST00000431581.1_Silent_p.K183K|STYXL1_ENST00000360591.3_3'UTR|STYXL1_ENST00000340062.5_Silent_p.K87K|STYXL1_ENST00000451157.1_Silent_p.K183K	NM_016086.2	NP_057170.1	Q9Y6J8	STYL1_HUMAN	serine/threonine/tyrosine interacting-like 1			10					TTTTCAAGTCCTTCTGAATCT	0.398000																								0							SO:0001819	synonymous_variant			ENST00000248600.1	1	1	hg19	CCDS5580.1																																																																																				TCGA-2L-AAQL-01A-11D-A38G-08	STYXL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344825.1	1	0	0	55	300	0	144	1	1	33	133	0	144	2		0	0	0	0	0	2	1	1.000000	55	298	0	144	2		0	0	0	0	144	2	-2.848931	1	0	0	0		1	1	2	3	2.119452	0	0.380000	1.790000	0.385835	0.820000	6.300000e-01	1.000000	1.000000	0.833725	0.820000	0	0.720000	0.950000
PTPN12	5782	broad.mit.edu	37	7	77212936	77212936	+	Missense_Mutation	SNP	T	T	G			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr7:77212936T>G	ENST00000248594.6	+	4	622	c.350T>G	c.(349-351)tTt>tGt	p.F117C	PTPN12_ENST00000435495.2_Intron|PTPN12_ENST00000415482.2_5'UTR	NM_002835.3	NP_002826.3	Q05209	PTN12_HUMAN	protein tyrosine phosphatase, non-receptor type 12			39					GTAATAGATTTTTGGAGGATG	0.299000																								0							SO:0001583	missense			ENST00000248594.6	1	1	hg19	CCDS5592.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.31|18.31	3.594923|3.594923	0.66219|0.66219	.|.	.|.	ENSG00000127947|ENSG00000127947	ENST00000248594|ENST00000522115	T|.	0.39997|.	1.05|.	5.65|5.65	5.65|5.65	0.86999|0.86999	Protein-tyrosine phosphatase, receptor/non-receptor type (4);|.	0.051905|0.051905	0.85682|0.85682	D|D	0.000000|0.000000	D|D	0.89339|0.89339	0.6687|0.6687	H|H	0.99626|0.99626	4.665|4.665	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.91635|.	0.999|.	D|D	0.92460|0.92460	0.5977|0.5977	10|7	0.87932|0.87932	D|D	0|0	.|.	10.7297|10.7297	0.46089|0.46089	0.1422:0.0:0.0:0.8578|0.1422:0.0:0.0:0.8578	.|.	117|.	Q05209|.	PTN12_HUMAN|.	C|V	117|80	ENSP00000248594:F117C|.	ENSP00000248594:F117C|ENSP00000430726:F80V	F|F	+|+	2|1	0|0	PTPN12|PTPN12	77050872|77050872	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	4.753000|4.753000	0.62183|0.62183	2.140000|2.140000	0.66376|0.66376	0.482000|0.482000	0.46254|0.46254	TTT|TTT		TCGA-2L-AAQL-01A-11D-A38G-08	PTPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253183.3	1	0	1	58	278	0	116	1	2.827759e-01	2	4	0	116	2		0	0	0	0	0	2	1	1.000000	56	270	0	115	2		0	0	0	0	116	2	-20.000000	1	1	0	0		1	1	2	3	2.119452	0	0.380000	1.790000	0.385835	0.920000	7.100000e-01	1.000000	1.000000	0.910397	0.920000	1	0.810000	1.000000
NEIL2	252969	broad.mit.edu	37	8	11637109	11637109	+	Silent	SNP	C	C	G			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr8:11637109C>G	ENST00000284503.6	+	3	740	c.141C>G	c.(139-141)gtC>gtG	p.V47V	NEIL2_ENST00000436750.3_Silent_p.V47V|NEIL2_ENST00000403422.3_5'UTR|NEIL2_ENST00000528323.1_Intron|NEIL2_ENST00000455213.2_Silent_p.V47V	NM_145043.2	NP_659480.1	Q969S2	NEIL2_HUMAN	nei endonuclease VIII-like 2 (E. coli)			10	all_epithelial(15;0.103)		STAD - Stomach adenocarcinoma(15;0.00225)		TTTTCTAGGTCCATGGAAAGA	0.468000								Base excision repair (BER), DNA glycosylases																0							SO:0001819	synonymous_variant			ENST00000284503.6	1	1	hg19	CCDS5984.1																																																																																				TCGA-2L-AAQL-01A-11D-A38G-08	NEIL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207583.3	1	0	1	136	438	0	249	0	1.428475e-01	1	2	0	249	2		0	0	0	0	0	2	1	1.000000	135	430	0	249	2		0	0	0	0	249	2	-20.000000	1	1	0	0		1	0	2	2	1.952558	1	0.380000	1.790000	0.380000	0.990000	9.900000e-01	1.000000	1.000000	0.999940	0.990000	1	0.990000	1.000000
LGI3	203190	broad.mit.edu	37	8	22006465	22006465	+	Silent	SNP	C	C	T			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr8:22006465C>T	ENST00000306317.2	-	8	1144	c.855G>A	c.(853-855)ccG>ccA	p.P285P	LGI3_ENST00000424267.2_Silent_p.P261P	NM_139278.2	NP_644807.1	Q8N145	LGI3_HUMAN	leucine-rich repeat LGI family, member 3			17					CCACCACCATCGGCTTGCAGT	0.637000																								0							SO:0001819	synonymous_variant			ENST00000306317.2	1	1	hg19	CCDS6025.1																																																																																				TCGA-2L-AAQL-01A-11D-A38G-08	LGI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254482.1	1	0	1	41	82	0	47	0	1.146667e-01	0	2	0	47	2		0	0	0	0	0	2	1	1.000000	40	81	0	46	2		0	0	0	0	47	2	-6.901602	1	1	121408	29	41	1	0	2	2	1.910041	1	0.380000	1.790000	0.380000	0.990000	9.900000e-01	1.000000	1.000000	0.999997	0.990000	1	0.990000	1.000000
ATP6V1H	51606	broad.mit.edu	37	8	54684564	54684564	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr8:54684564C>T	ENST00000359530.2	-	10	1297	c.1034G>A	c.(1033-1035)aGt>aAt	p.S345N	ATP6V1H_ENST00000520188.1_Missense_Mutation_p.S305N|ATP6V1H_ENST00000523899.1_5'Flank|ATP6V1H_ENST00000355221.3_Missense_Mutation_p.S327N|ATP6V1H_ENST00000396774.2_Missense_Mutation_p.S345N	NM_015941.3	NP_057025.2	Q9UI12	VATH_HUMAN	ATPase, H+ transporting, lysosomal 50/57kDa, V1 subunit H			18		all_epithelial(80;0.0487)|Lung NSC(129;0.109)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;2.79e-06)|Epithelial(17;0.000629)|all cancers(17;0.00359)		GTCCTGGACACTCTCTCCAAG	0.373000																								0							SO:0001583	missense			ENST00000359530.2	1	1	hg19	CCDS6153.1	.	.	.	.	.	.	.	.	.	.	C	19.48	3.835276	0.71373	.	.	ENSG00000047249	ENST00000355221;ENST00000520188;ENST00000359530;ENST00000396774	.	.	.	5.31	5.31	0.75309	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.58264	0.2110	L	0.46567	1.45	0.80722	D	1	P;P	0.40360	0.68;0.714	P;B	0.44946	0.465;0.414	T	0.50800	-0.8785	9	0.15952	T	0.53	-20.9211	19.3551	0.94408	0.0:1.0:0.0:0.0	.	327;345	Q9UI12-2;Q9UI12	.;VATH_HUMAN	N	327;305;345;345	.	ENSP00000347359:S327N	S	-	2	0	ATP6V1H	54847117	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.776000	0.85560	2.639000	0.89480	0.609000	0.83330	AGT		TCGA-2L-AAQL-01A-11D-A38G-08	ATP6V1H-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377865.1	1	0	1	127	315	0	182	1	1	58	82	0	182	2		0	0	0	0	0	2	1	1.000000	125	303	0	180	2		0	0	0	0	182	2	-20.000000	1	1	0	0		1	0	2	2	1.910041	1	0.380000	1.790000	0.380000	0.990000	9.900000e-01	1.000000	1.000000	1.000000	0.990000	1	0.990000	1.000000
DMRT2	10655	broad.mit.edu	37	9	1056510	1056510	+	Missense_Mutation	SNP	A	A	G			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr9:1056510A>G	ENST00000358146.2	+	3	923	c.923A>G	c.(922-924)gAt>gGt	p.D308G	DMRT2_ENST00000259622.6_3'UTR|DMRT2_ENST00000382251.3_Missense_Mutation_p.D308G|DMRT2_ENST00000302441.6_Missense_Mutation_p.D308G|DMRT2_ENST00000382255.3_3'UTR			Q9Y5R5	DMRT2_HUMAN	doublesex and mab-3 related transcription factor 2			4		all_lung(10;1.49e-09)|Lung NSC(10;1.86e-09)			ACCTGCCTTGATTTAACCATG	0.458000																								0							SO:0001583	missense			ENST00000358146.2	1	1	hg19	CCDS6444.1	.	.	.	.	.	.	.	.	.	.	A	19.06	3.753973	0.69648	.	.	ENSG00000173253	ENST00000382251;ENST00000302441;ENST00000358146	T;T;T	0.34275	1.37;1.37;1.37	5.62	5.62	0.85841	.	0.289079	0.38663	N	0.001609	T	0.57755	0.2075	M	0.64404	1.975	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.74674	0.965;0.984	T	0.61108	-0.7129	10	0.87932	D	0	-21.4324	15.5071	0.75748	1.0:0.0:0.0:0.0	.	308;152	Q9Y5R5;Q5HYK2	DMRT2_HUMAN;.	G	308	ENSP00000371686:D308G;ENSP00000305785:D308G;ENSP00000350865:D308G	ENSP00000305785:D308G	D	+	2	0	DMRT2	1046510	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.730000	0.91510	2.153000	0.67306	0.528000	0.53228	GAT		TCGA-2L-AAQL-01A-11D-A38G-08	DMRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051492.1	1	0	1	51	245	0	113	0	0	1	0	0	113	2		0	0	0	0	0	2	1	1.000000	51	239	0	112	2		0	0	0	0	113	2	-20.000000	1	1	0	0		1	0	1	1	1.689498	1	0.380000	1.790000	0.234568	0.720000	5.500000e-01	0.910000	0.730000	0.734629	0.720000	0	0.630000	0.820000
COL5A1	1289	broad.mit.edu	37	9	137593107	137593107	+	Silent	SNP	C	C	T			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr9:137593107C>T	ENST00000371817.3	+	4	996	c.582C>T	c.(580-582)agC>agT	p.S194S	COL5A1_ENST00000464187.1_3'UTR	NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1			115		Myeloproliferative disorder(178;0.0341)			TCGACCGCAGCGACCACCCCA	0.522000																								0							SO:0001819	synonymous_variant			ENST00000371817.3	1	1	hg19	CCDS6982.1																																																																																				TCGA-2L-AAQL-01A-11D-A38G-08	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	1	0	1	38	147	0	64	0	8.123676e-01	0	14	0	64	2		0	0	0	0	0	2	1	1.000000	36	144	0	63	2		0	0	0	0	64	2	-3.541542	1	1	121364	3	32	1	1	2	3	2.113077	0	0.380000	1.790000	0.385835	0.990000	8.000000e-01	1.000000	1.000000	0.977072	0.990000	1	0.940000	1.000000
PLAA	9373	broad.mit.edu	37	9	26919394	26919394	+	Missense_Mutation	SNP	A	A	G			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr9:26919394A>G	ENST00000397292.3	-	9	1748	c.1331T>C	c.(1330-1332)cTg>cCg	p.L444P	PLAA_ENST00000520641.1_5'UTR|PLAA_ENST00000520884.1_Missense_Mutation_p.L444P	NM_001031689.2	NP_001026859.1	Q9Y263	PLAP_HUMAN	phospholipase A2-activating protein			17		all_neural(3;3.53e-10)|Glioma(3;2.71e-09)			TACTTGATCCAGAAACATAGG	0.353000													Melanoma(175;2670 2735 14091 35526)											0							SO:0001583	missense			ENST00000397292.3	1	1	hg19	CCDS35000.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.212242	0.79240	.	.	ENSG00000137055	ENST00000397292;ENST00000520884	T;T	0.61627	0.09;0.23	5.53	5.53	0.82687	PLAA family ubiquitin binding, PFU (2);	0.000000	0.85682	D	0.000000	T	0.81108	0.4754	M	0.91140	3.18	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.85613	0.1259	10	0.72032	D	0.01	-5.71	15.6677	0.77242	1.0:0.0:0.0:0.0	.	444;444	E5RIM3;Q9Y263	.;PLAP_HUMAN	P	444	ENSP00000380460:L444P;ENSP00000429372:L444P	ENSP00000380460:L444P	L	-	2	0	PLAA	26909394	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.059000	0.76684	2.092000	0.63282	0.482000	0.46254	CTG		TCGA-2L-AAQL-01A-11D-A38G-08	PLAA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051958.2	0	0	0	16	590	0	270	0	5.877833e-02	0	14	0	270	2		0	0	0	0	0	2	1	0.999920	16	576	0	267	2		0	0	0	0	270	2	-3.411513	1	1	0	0		1	0	1	1	1.703823	1	0.380000	1.790000	0.238142	0.110000	6.000000e-02	0.180000	0.110000	0.119129	0.110000	0	0.080000	0.150000
GLIS3	169792	broad.mit.edu	37	9	4118378	4118378	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chr9:4118378C>T	ENST00000324333.10	-	3	828	c.635G>A	c.(634-636)gGc>gAc	p.G212D	GLIS3_ENST00000381971.3_Missense_Mutation_p.G367D	NM_152629.3	NP_689842.3	Q8NEA6	GLIS3_HUMAN	GLIS family zinc finger 3			26		Acute lymphoblastic leukemia(2;0.00464)|Breast(48;0.148)			CTTCTGGCTGCCGGGCACCGG	0.736000																								0							SO:0001583	missense			ENST00000324333.10	1	1	hg19	CCDS6451.1	.	.	.	.	.	.	.	.	.	.	C	4.448	0.083027	0.08533	.	.	ENSG00000107249	ENST00000324333;ENST00000381971	T;T	0.10573	2.87;2.86	5.63	4.73	0.59995	.	0.314417	0.25622	N	0.029409	T	0.06005	0.0156	N	0.19112	0.55	0.09310	N	1	B;B	0.17667	0.023;0.006	B;B	0.18561	0.022;0.01	T	0.40117	-0.9580	10	0.15066	T	0.55	.	5.5169	0.16912	0.0:0.6111:0.1599:0.229	.	367;212	Q8NEA6-2;Q8NEA6	.;GLIS3_HUMAN	D	212;367	ENSP00000325494:G212D;ENSP00000371398:G367D	ENSP00000325494:G212D	G	-	2	0	GLIS3	4108378	0.000000	0.05858	0.016000	0.15963	0.060000	0.15804	0.091000	0.15046	1.372000	0.46190	0.655000	0.94253	GGC		TCGA-2L-AAQL-01A-11D-A38G-08	GLIS3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051559.1	1	0	0	20	44	0	22	0	0	0	1	0	22	2		0	0	0	0	0	2	1	0.999999	20	44	0	22	2		0	0	0	0	22	2	-20.000000	1	1	0	0		1	0	1	1	1.689498	1	0.380000	1.790000	0.234568	0.920000	7.000000e-01	1.000000	0.990000	0.909478	0.920000	1	0.820000	0.980000
ACTRT1	139741	broad.mit.edu	37	X	127185417	127185417	+	Nonsense_Mutation	SNP	G	G	A			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chrX:127185417G>A	ENST00000371124.3	-	1	965	c.769C>T	c.(769-771)Caa>Taa	p.Q257*		NM_138289.3	NP_612146.1	Q8TDG2	ACTT1_HUMAN	actin-related protein T1			34					TCGGGCACTTGGTACAGCTCA	0.542000																								0							SO:0001587	stop_gained			ENST00000371124.3	0	1	hg19	CCDS14611.1	.	.	.	.	.	.	.	.	.	.	G	15.36	2.811660	0.50527	.	.	ENSG00000123165	ENST00000371124	.	.	.	3.58	0.589	0.17452	.	0.537891	0.16370	N	0.217347	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	9.9033	0.41362	0.0:0.0:0.4788:0.5212	.	.	.	.	X	257	.	ENSP00000360165:Q257X	Q	-	1	0	ACTRT1	127013098	1.000000	0.71417	0.001000	0.08648	0.023000	0.10783	1.058000	0.30504	0.001000	0.14605	0.600000	0.82982	CAA		TCGA-2L-AAQL-01A-11D-A38G-08	ACTRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058192.1	0	0	0	6	419	0	133		0	0	0	0	133	2		0	0	0	0	0	2	1	0.962845	6	410	0	133	2		0	0	0	0	133	2	-2.606201	1	1	0	0		1	0	1	1			0.380000	1.790000	0.380000	0.030000	1.000000e-02	0.080000	0.040000	0.042971	0.030000	0	0.020000	0.060000
BCORL1	63035	broad.mit.edu	37	X	129185988	129185988	+	Missense_Mutation	SNP	G	G	A	rs143047034		TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chrX:129185988G>A	ENST00000218147.7	+	12	5047	c.4850G>A	c.(4849-4851)cGc>cAc	p.R1617H	BCORL1_ENST00000359304.2_Missense_Mutation_p.R1487H|BCORL1_ENST00000303743.5_Missense_Mutation_p.R1691H|BCORL1_ENST00000540052.1_Missense_Mutation_p.R1617H			Q5H9F3	BCORL_HUMAN	BCL6 corepressor-like 1			75					TCAGTGTCCCGCGGGTAAGTG	0.527000																								0							SO:0001583	missense			ENST00000218147.7	1	1	hg19	CCDS14616.1	.	.	.	.	.	.	.	.	.	.	G	11.97	1.798032	0.31777	.	.	ENSG00000085185	ENST00000218147;ENST00000303743;ENST00000359304;ENST00000540052;ENST00000456822	T;T;T;T;T	0.40476	1.03;1.32;1.04;1.03;1.37	5.53	2.58	0.30949	.	0.759301	0.10829	N	0.629586	T	0.36220	0.0959	L	0.47716	1.5	0.32970	D	0.522206	B;B	0.24651	0.108;0.023	B;B	0.18871	0.023;0.006	T	0.42310	-0.9459	10	0.66056	D	0.02	-3.2989	9.7559	0.40502	0.2547:0.0:0.7453:0.0	.	1691;1617	Q5H9F3-3;Q5H9F3	.;BCORL_HUMAN	H	1617;1691;1487;1617;1291	ENSP00000218147:R1617H;ENSP00000307541:R1691H;ENSP00000352253:R1487H;ENSP00000437775:R1617H;ENSP00000399483:R1291H	ENSP00000218147:R1617H	R	+	2	0	BCORL1	129013669	0.988000	0.35896	0.628000	0.29241	0.404000	0.30871	2.792000	0.47837	0.420000	0.25954	0.513000	0.50165	CGC		TCGA-2L-AAQL-01A-11D-A38G-08	BCORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058223.1	1	0	1	61	234	0	95	1	8.454529e-01	3	12	0	95	2	1	1	46	212	0	107	2	1	1.000000	61	223	0	94	2		0	0	0	0	95	2	-3.757349	1	1	121322	3	38	1	0	1	1			0.380000	1.790000	0.380000	0.530000	4.200000e-01	0.660000	0.540000	0.546326	0.530000	0	0.470000	0.610000
CNKSR2	22866	broad.mit.edu	37	X	21627423	21627423	+	Missense_Mutation	SNP	T	T	C			TCGA-2L-AAQL-01A-11D-A38G-08	TCGA-2L-AAQL-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac8948c6-17c3-4cc4-b432-8f66595f2769	8145a789-a66e-4b2d-ae0e-2784364aff45	g.chrX:21627423T>C	ENST00000379510.3	+	20	2416	c.2380T>C	c.(2380-2382)Ttc>Ctc	p.F794L	CNKSR2_ENST00000543067.1_Missense_Mutation_p.F745L|CNKSR2_ENST00000279451.4_Missense_Mutation_p.F794L|CNKSR2_ENST00000425654.2_Missense_Mutation_p.F764L	NM_014927.3	NP_055742.2	Q8WXI2	CNKR2_HUMAN	connector enhancer of kinase suppressor of Ras 2			61					GGATTCTGTCTTCTCTGACTC	0.567000																								0							SO:0001583	missense			ENST00000379510.3	0	1	hg19	CCDS14198.1	.	.	.	.	.	.	.	.	.	.	T	11.23	1.577480	0.28180	.	.	ENSG00000149970	ENST00000425654;ENST00000543067;ENST00000279451;ENST00000379510	T;T;T;T	0.17691	2.52;2.26;2.27;2.55	5.51	5.51	0.81932	.	0.161421	0.56097	D	0.000028	T	0.17619	0.0423	L	0.60455	1.87	0.47037	D	0.999295	B;B;B;B	0.18610	0.0;0.0;0.008;0.029	B;B;B;B	0.16289	0.002;0.001;0.015;0.008	T	0.06006	-1.0851	10	0.08599	T	0.76	-27.16	14.6111	0.68517	0.0:0.0:0.0:1.0	.	764;745;386;794	B7ZLJ1;B4DGR4;B3KPN2;Q8WXI2	.;.;.;CNKR2_HUMAN	L	764;745;794;794	ENSP00000397906:F764L;ENSP00000444633:F745L;ENSP00000279451:F794L;ENSP00000368824:F794L	ENSP00000279451:F794L	F	+	1	0	CNKSR2	21537344	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	4.187000	0.58344	1.831000	0.53308	0.417000	0.27973	TTC		TCGA-2L-AAQL-01A-11D-A38G-08	CNKSR2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056019.1	0	0	0	5	202	0	85		0	0	0	0	85	2		0	0	0	0	0	2	1	0.935072	5	198	0	84	2		0	0	0	0	85	2	-6.828703	1	0	0	0		1	0	1	1			0.380000	1.790000	0.380000	0.060000	2.000000e-02	0.140000	0.060000	0.074947	0.060000	0	0.040000	0.100000
