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
MUC6	4588	broad.mit.edu	37	11	1016412	1016414	+	In_Frame_Del	DEL	GAG	GAG	-			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08			GAG	-	GAG	GAG		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr11:1016412_1016414delGAG	ENST00000421673.2	-	31	6437_6439	c.6387_6389delCTC	c.(6385-6390)tcctca>tca	p.2129_2130SS>S		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	p.S2130delS(1)		80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)			GGGAGAAAATGAGGAGGACAGCT	0.522000																								1	Deletion - In frame(1)						SO:0001651	inframe_deletion			ENST00000421673.2	1	1	hg19	CCDS44513.1																																																																																				TCGA-2L-AAQA-01A-21D-A38G-08	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	1	0	0	57	209	0	58	1	1	16	404	0	58	2			0	0	0	0		1	0.997701	67	210	5	62	35	0	0	0	0	0	0		-20.000000	1	0	0	0		1	0	0	0	2.071255	0	0.600000	1.890000	0.600000	0.710000	5.500000e-01	0.880000	0.720000	0.719562	0.710000	0	6.300000e-01	8.000000e-01
RNF43	54894	broad.mit.edu	37	17	56492904	56492908	+	Frame_Shift_Del	DEL	AGGGC	AGGGC	-			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08			AGGGC	-	AGGGC	AGGGC		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr17:56492904_56492908delAGGGC	ENST00000584437.1	-	1	1986_1990	c.31_35delGCCCT	c.(31-36)gccctcfs	p.AL11fs	RNF43_ENST00000583753.1_Frame_Shift_Del_p.AL11fs|RNF43_ENST00000580014.1_5'Flank|RNF43_ENST00000577716.1_Frame_Shift_Del_p.AL11fs|RNF43_ENST00000500597.2_Frame_Shift_Del_p.AL11fs|BZRAP1-AS1_ENST00000583841.1_RNA|RNF43_ENST00000407977.2_Frame_Shift_Del_p.AL11fs|RNF43_ENST00000581868.1_Intron			Q68DV7	RNF43_HUMAN	ring finger protein 43			60	Medulloblastoma(34;0.127)|all_neural(34;0.237)				CCAGGGCCAGAGGGCAGCCAGCTGC	0.556000																								0							SO:0001589	frameshift_variant			ENST00000584437.1	1	1	hg19	CCDS11607.1																																																																																				TCGA-2L-AAQA-01A-21D-A38G-08	RNF43-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444713.1	1	0	0	38	158	0	103	1	7.845042e-01	4	10	0	103	2	1	1	115	316	0	228	2	1	1.000000	50	165	0	103	2	0	0	0	0	0	0		-20.000000	1	0	0	0		1	0	1	1	1.475023	1	0.600000	1.890000	0.431010	0.450000	3.300000e-01	0.580000	0.450000	0.458472	0.450000	0	3.800000e-01	5.200000e-01
PMEPA1	56937	broad.mit.edu	37	20	56227349	56227349	+	Frame_Shift_Del	DEL	G	G	-			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08			G	-	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr20:56227349delG	ENST00000341744.3	-	4	943	c.624delC	c.(622-624)cccfs	p.P208fs	PMEPA1_ENST00000395814.1_Frame_Shift_Del_p.P158fs|PMEPA1_ENST00000347215.4_Frame_Shift_Del_p.P173fs|PMEPA1_ENST00000265626.4_Frame_Shift_Del_p.P158fs|PMEPA1_ENST00000395816.3_Frame_Shift_Del_p.P158fs	NM_020182.4	NP_064567.2	Q969W9	PMEPA_HUMAN	prostate transmembrane protein, androgen induced 1			16					AGTTACTGCTGGGGGGGCAGG	0.682000																								0							SO:0001589	frameshift_variant			ENST00000341744.3	1	0	hg19	CCDS13463.1																																																																																				TCGA-2L-AAQA-01A-21D-A38G-08	PMEPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079858.2	1	0	0	55	285	0	80	1	1	238	785	0	80	2			0	0	0	0		1	0.976157	77	278	6	80	40	0	0	0	0	0	0		-1.563211	0	1	0	0		1	0	0	0	2.045390	0	0.600000	1.890000	0.597586	0.530000	4.100000e-01	0.670000	0.530000	0.541462	0.530000	0	4.600000e-01	6.100000e-01
ARRDC1	92714	broad.mit.edu	37	9	140507340	140507354	+	Splice_Site	DEL	CTTTGCAGCCATCCG	CTTTGCAGCCATCCG	-	rs147183389	byFrequency	TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08			CTTTGCAGCCATCCG	-	CTTTGCAGCCATCCG	CTTTGCAGCCATCCG		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr9:140507340_140507354delCTTTGCAGCCATCCG	ENST00000371421.4	+	2	182_189	c.118_125delCTTTGCAGCCATCCG	c.(118-126)ctttgcagc>c	p.LCS40del	C9orf37_ENST00000496793.1_5'Flank|ARRDC1_ENST00000491911.1_3'UTR	NM_152285.2	NP_689498.1	Q8N5I2	ARRD1_HUMAN	arrestin domain containing 1			13	all_cancers(76;0.106)				CAGCCATCCCCTTTGCAGCCATCCGGGTGACCTGC	0.633000																								0							SO:0001630	splice_region_variant			ENST00000371421.4	1	1	hg19	CCDS7049.1																																																																																				TCGA-2L-AAQA-01A-21D-A38G-08	ARRDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055358.1	0	0	0	32	157	0	48	0	1	0	437	0	48	2			0	0	0	0		1	1.000000	39	162	0	48	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	0	0	0	2.067674	0	0.600000	1.890000	0.600000	0.560000	4.000000e-01	0.750000	0.560000	0.573886	0.560000	0	4.700000e-01	6.600000e-01
FAM178A	55719	broad.mit.edu	37	10	102672997	102672997	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr10:102672997C>T	ENST00000238961.4	+	1	672	c.130C>T	c.(130-132)Cct>Tct	p.P44S	FAM178A_ENST00000370271.3_Missense_Mutation_p.P44S|FAM178A_ENST00000609386.1_Missense_Mutation_p.P44S|FAM178A_ENST00000370269.3_Missense_Mutation_p.P44S|RP11-179B2.2_ENST00000608554.1_RNA	NM_018121.3	NP_060591.3	Q8IX21	F178A_HUMAN	family with sequence similarity 178, member A								AACAGAGAGTCCTGGGGACAG	0.682000																								0							SO:0001583	missense			ENST00000238961.4	1	1	hg19	CCDS7500.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.545875	0.86022	.	.	ENSG00000119906	ENST00000370271;ENST00000238961;ENST00000370269	T;T;T	0.61392	0.11;0.85;0.81	5.25	5.25	0.73442	.	0.000000	0.53938	D	0.000044	T	0.63745	0.2537	N	0.24115	0.695	0.35168	D	0.771306	D;D;D	0.89917	0.995;0.995;1.0	D;D;D	0.87578	0.919;0.919;0.998	T	0.72204	-0.4361	10	0.72032	D	0.01	-15.2639	14.5237	0.67873	0.0:1.0:0.0:0.0	.	44;44;44	Q8IX21;B1AL17;B1AL16	F178A_HUMAN;.;.	S	44	ENSP00000359294:P44S;ENSP00000238961:P44S;ENSP00000359292:P44S	ENSP00000238961:P44S	P	+	1	0	FAM178A	102662987	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	3.254000	0.51477	2.890000	0.99128	0.585000	0.79938	CCT		TCGA-2L-AAQA-01A-21D-A38G-08	FAM178A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049897.3	1	0	1	16	30	0	19	1	9.857931e-01	11	6	0	19	2		0	0	0	0	0	2	1	0.999973	16	28	0	19	2		0	0	0	0	19	2	-20.000000	1	1	121232	2	25	1	1	2	3	2.117229	0	0.600000	1.890000	0.604743	0.990000	7.500000e-01	1.000000	1.000000	0.974213	0.990000	1	9.400000e-01	1
CRTAC1	55118	broad.mit.edu	37	10	99696061	99696061	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr10:99696061G>A	ENST00000370597.3	-	3	642	c.287C>T	c.(286-288)gCg>gTg	p.A96V	CRTAC1_ENST00000370591.2_Missense_Mutation_p.A96V|CRTAC1_ENST00000298819.4_Missense_Mutation_p.A96V	NM_018058.6	NP_060528.3	Q9NQ79	CRAC1_HUMAN	cartilage acidic protein 1			35		Colorectal(252;0.24)			CTCATCGACCGCGATGTTCAC	0.662000																								0							SO:0001583	missense			ENST00000370597.3	1	1	hg19	CCDS31266.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.184476	0.78677	.	.	ENSG00000095713	ENST00000370597;ENST00000298819;ENST00000309155;ENST00000370591	T;T;T;T	0.20881	2.04;2.04;2.04;2.04	4.76	4.76	0.60689	.	0.000000	0.85682	D	0.000000	T	0.47875	0.1469	M	0.79475	2.455	0.80722	D	1	D;D	0.89917	0.996;1.0	P;D	0.91635	0.704;0.999	T	0.43523	-0.9386	10	0.27785	T	0.31	-10.778	17.7665	0.88480	0.0:0.0:1.0:0.0	.	96;96	Q9NQ79-2;Q9NQ79	.;CRAC1_HUMAN	V	96;96;88;96	ENSP00000359629:A96V;ENSP00000298819:A96V;ENSP00000310810:A88V;ENSP00000359623:A96V	ENSP00000298819:A96V	A	-	2	0	CRTAC1	99686051	1.000000	0.71417	0.892000	0.35008	0.640000	0.38277	9.725000	0.98778	2.204000	0.70986	0.313000	0.20887	GCG		TCGA-2L-AAQA-01A-21D-A38G-08	CRTAC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049754.1	1	0	1	64	206	0	81	0	0	0	1	0	81	2		0	0	0	0	0	2	1	1.000000	63	203	0	81	2		0	0	0	0	81	2	-20.000000	1	1	121408	1	31	1	1	2	3	2.117229	0	0.600000	1.890000	0.604743	0.800000	6.300000e-01	1.000000	0.800000	0.809308	0.800000	0	7.100000e-01	9.000000e-01
HIPK3	10114	broad.mit.edu	37	11	33369721	33369721	+	Missense_Mutation	SNP	G	G	C			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08			G	C	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr11:33369721G>C	ENST00000303296.4	+	12	2621	c.2316G>C	c.(2314-2316)ttG>ttC	p.L772F	HIPK3_ENST00000525975.1_Intron|HIPK3_ENST00000379016.3_Intron|HIPK3_ENST00000456517.1_Intron	NM_005734.3	NP_005725.3	Q9H422	HIPK3_HUMAN	homeodomain interacting protein kinase 3			39					GAGGTATTTTGGTAAAACTAA	0.363000																								0							SO:0001583	missense			ENST00000303296.4	1	1	hg19	CCDS7884.1	.	.	.	.	.	.	.	.	.	.	G	11.03	1.517978	0.27211	.	.	ENSG00000110422	ENST00000303296	T	0.23348	1.91	5.74	5.74	0.90152	.	0.162090	0.29314	N	0.012518	T	0.13713	0.0332	N	0.14661	0.345	0.80722	D	1	P	0.35908	0.527	B	0.33042	0.157	T	0.12066	-1.0562	10	0.09843	T	0.71	.	13.1561	0.59518	0.0728:0.0:0.9272:0.0	.	772	Q9H422	HIPK3_HUMAN	F	772	ENSP00000304226:L772F	ENSP00000304226:L772F	L	+	3	2	HIPK3	33326297	1.000000	0.71417	1.000000	0.80357	0.894000	0.52154	3.785000	0.55424	2.707000	0.92482	0.557000	0.71058	TTG		TCGA-2L-AAQA-01A-21D-A38G-08	HIPK3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255358.1	1	0	1	72	136	0	59	1	9.977588e-01	11	10	0	59	2		0	0	0	0	0	2	1	1.000000	72	134	0	59	2		0	0	0	0	59	2	-9.530416	1	1	0	0		1	0	0	0	2.071255	0	0.600000	1.890000	0.600000	0.990000	9.400000e-01	1.000000	1.000000	0.996524	0.990000	1	9.900000e-01	1
PAMR1	25891	broad.mit.edu	37	11	35513689	35513689	+	Nonsense_Mutation	SNP	G	G	A			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr11:35513689G>A	ENST00000378880.2	-	3	728	c.283C>T	c.(283-285)Cga>Tga	p.R95*	PAMR1_ENST00000532848.1_Nonsense_Mutation_p.R55*|PAMR1_ENST00000378878.3_Nonsense_Mutation_p.R95*|PAMR1_ENST00000278360.3_Nonsense_Mutation_p.R95*|PAMR1_ENST00000534803.1_5'UTR	NM_001001991.1	NP_001001991.1	Q6UXH9	PAMR1_HUMAN	peptidase domain containing associated with muscle regeneration 1			26					GAGCCATTTCGGCAGCTCTTG	0.522000																								0							SO:0001587	stop_gained			ENST00000378880.2	0	1	hg19	CCDS31460.1	.	.	.	.	.	.	.	.	.	.	G	41	9.063677	0.99053	2.27E-4	0.0	ENSG00000149090	ENST00000278360;ENST00000378880;ENST00000378878;ENST00000532848;ENST00000527605;ENST00000529303	.	.	.	5.05	3.08	0.35506	.	0.459441	0.22469	N	0.059650	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	12.6536	0.56776	0.0:0.0:0.5742:0.4258	.	.	.	.	X	95;95;95;55;55;95	.	ENSP00000278360:R95X	R	-	1	2	PAMR1	35470265	1.000000	0.71417	0.978000	0.43139	0.911000	0.54048	3.430000	0.52807	0.471000	0.27319	0.491000	0.48974	CGA		TCGA-2L-AAQA-01A-21D-A38G-08	PAMR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389177.1	1	0	1	301	741	1	362	0	9.244735e-01	0	13	1	362	2		0	0	0	0	0	2	1	1.000000	300	732	1	357	12		0	0	0	1	362	2	-14.292280	1	1	121412	3	43	1	0	0	0	2.071255	0	0.600000	1.890000	0.600000	0.950000	8.600000e-01	1.000000	1.000000	0.957509	0.950000	1	9.100000e-01	1
PEX16	9409	broad.mit.edu	37	11	45936217	45936217	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr11:45936217C>T	ENST00000378750.5	-	6	722	c.479G>A	c.(478-480)gGc>gAc	p.G160D	PEX16_ENST00000532554.1_5'UTR|PEX16_ENST00000241041.3_Missense_Mutation_p.G160D|PEX16_ENST00000532681.1_Missense_Mutation_p.G65D			Q9Y5Y5	PEX16_HUMAN	peroxisomal biogenesis factor 16			7					CTCATGGTTGCCAGGGCTGTG	0.582000																								0							SO:0001583	missense			ENST00000378750.5	1	1	hg19	CCDS31472.1	.	.	.	.	.	.	.	.	.	.	C	3.698	-0.062097	0.07317	.	.	ENSG00000121680	ENST00000241041;ENST00000378750;ENST00000532681;ENST00000533151;ENST00000525192	T;T;T;T;T	0.21361	2.01;2.01;2.01;2.01;2.01	5.85	4.0	0.46444	.	0.670270	0.16493	N	0.212040	T	0.13756	0.0333	L	0.31294	0.92	0.09310	N	1	B;B	0.12630	0.004;0.006	B;B	0.12156	0.007;0.004	T	0.32161	-0.9917	10	0.15952	T	0.53	-5.9846	8.1875	0.31348	0.0:0.7141:0.139:0.1469	.	160;160	Q9Y5Y5;Q9Y5Y5-2	PEX16_HUMAN;.	D	160;160;65;56;65	ENSP00000241041:G160D;ENSP00000368024:G160D;ENSP00000434654:G65D;ENSP00000433045:G56D;ENSP00000431309:G65D	ENSP00000241041:G160D	G	-	2	0	PEX16	45892793	0.123000	0.22298	0.047000	0.18901	0.134000	0.20937	0.876000	0.28092	0.827000	0.34685	-0.291000	0.09656	GGC		TCGA-2L-AAQA-01A-21D-A38G-08	PEX16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392398.1	0	0	1	114	318	1	141	1	1	106	132	1	141	8		0	0	0	0	0	2	1	1.000000	110	308	0	139	2		0	0	0	1	141	2	-20.000000	1	1	0	0		1	0	0	0	2.071255	0	0.600000	1.890000	0.600000	0.870000	7.400000e-01	1.000000	1.000000	0.880302	0.870000	1	8.000000e-01	9.500000e-01
OR5D13	390142	broad.mit.edu	37	11	55541761	55541761	+	Missense_Mutation	SNP	C	C	T	rs140938722	by1000genomes	TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr11:55541761C>T	ENST00000361760.1	+	1	848	c.848C>T	c.(847-849)gCg>gTg	p.A283V		NM_001001967.1	NP_001001967.1	Q8NGL4	OR5DD_HUMAN	olfactory receptor, family 5, subfamily D, member 13			40		all_epithelial(135;0.196)			TACACAGTGGCGATTCCAATG	0.363000																								0							SO:0001583	missense			ENST00000361760.1	1	0	hg19	CCDS31507.1	4	0.0018315018315018315	0	0.0	2	0.0055248618784530384	2	0.0034965034965034965	0	0.0	C	0	-2.801658	0.00075	.	.	ENSG00000198877	ENST00000361760	T	0.00013	9.25	3.68	1.18	0.20946	GPCR, rhodopsin-like superfamily (1);	0.960258	0.08414	N	0.949423	T	0.00012	0.0000	N	0.00006	-3.225	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.49588	-0.8924	10	0.02654	T	1	-3.3382	3.6909	0.08346	0.1898:0.1116:0.0:0.6986	.	283	Q8NGL4	OR5DD_HUMAN	V	283	ENSP00000354800:A283V	ENSP00000354800:A283V	A	+	2	0	OR5D13	55298337	0.002000	0.14202	0.022000	0.16811	0.001000	0.01503	1.319000	0.33655	0.020000	0.15106	-1.495000	0.00966	GCG		TCGA-2L-AAQA-01A-21D-A38G-08	OR5D13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391511.1	1	0	1	135	250	0	110		0	0	0	0	110	2		0	0	0	0	0	2	1	1.000000	134	246	0	110	2		0	0	0	0	110	2	-14.940370	1	1	121378	52	47	1	0	0	0	2.071255	0	0.600000	1.890000	0.600000	0.990000	9.900000e-01	1.000000	1.000000	0.999547	0.990000	1	9.900000e-01	1
FAM181B	220382	broad.mit.edu	37	11	82444594	82444594	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr11:82444594G>A	ENST00000329203.3	-	1	312	c.178C>T	c.(178-180)Cgc>Tgc	p.R60C		NM_175885.3	NP_787081.2	A6NEQ2	F181B_HUMAN	family with sequence similarity 181, member B			4					GTGGCCTCGCGCACGTCCCCT	0.662000																								0							SO:0001583	missense			ENST00000329203.3	0	1	hg19	CCDS31648.1	.	.	.	.	.	.	.	.	.	.	G	12.73	2.025614	0.35701	.	.	ENSG00000182103	ENST00000329203	T	0.34275	1.37	3.79	1.62	0.23740	.	0.378309	0.21245	U	0.077752	T	0.41465	0.1160	L	0.43152	1.355	0.43919	D	0.996568	D	0.76494	0.999	D	0.63113	0.911	T	0.18366	-1.0339	9	.	.	.	.	6.0139	0.19592	0.0:0.1346:0.4145:0.4508	.	60	A6NEQ2	F181B_HUMAN	C	60	ENSP00000365295:R60C	.	R	-	1	0	FAM181B	82122242	1.000000	0.71417	0.998000	0.56505	0.004000	0.04260	2.558000	0.45879	0.771000	0.33359	-0.519000	0.04390	CGC		TCGA-2L-AAQA-01A-21D-A38G-08	FAM181B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391626.1	0	0	0	4	103	0	17	0	2.502085e-03	0	2	0	17	2		0	0	0	0	0	2	1	0.880154	3	99	0	17	2		0	0	0	0	17	2	-7.220390	1	0	0	0		1	0	0	0	2.073547	0	0.600000	1.890000	0.600000	0.130000	4.000000e-02	0.290000	0.120000	0.151943	0.130000	0	8.000000e-02	2.100000e-01
BTBD11	121551	broad.mit.edu	37	12	108013765	108013765	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr12:108013765G>A	ENST00000280758.5	+	11	2983	c.2455G>A	c.(2455-2457)Gtc>Atc	p.V819I	BTBD11_ENST00000490090.2_Missense_Mutation_p.V819I|BTBD11_ENST00000420571.2_Missense_Mutation_p.V700I|BTBD11_ENST00000357167.4_Missense_Mutation_p.V356I|RP11-128P10.1_ENST00000548473.1_RNA	NM_001018072.1	NP_001018082.1	A6QL63	BTBDB_HUMAN	BTB (POZ) domain containing 11			53					CGCTCCAGGCGTCCCGTGGAC	0.587000																								0							SO:0001583	missense			ENST00000280758.5	1	1	hg19	CCDS31893.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.868192	0.91587	2.27E-4	1.16E-4	ENSG00000151136	ENST00000280758;ENST00000420571;ENST00000490090;ENST00000357167	T;T;T;T	0.55052	0.65;0.65;0.67;0.54	5.15	5.15	0.70609	.	0.117935	0.56097	D	0.000021	T	0.72495	0.3467	M	0.70275	2.135	0.80722	D	1	D;P;D;D	0.71674	0.998;0.508;0.987;0.99	D;B;B;P	0.73708	0.981;0.073;0.403;0.496	T	0.75560	-0.3275	10	0.66056	D	0.02	.	18.6524	0.91435	0.0:0.0:1.0:0.0	.	700;356;819;819	A6QL63-2;E9PHS4;A6QL63;A6QL63-3	.;.;BTBDB_HUMAN;.	I	819;700;819;356	ENSP00000280758:V819I;ENSP00000413889:V700I;ENSP00000447319:V819I;ENSP00000349690:V356I	ENSP00000280758:V819I	V	+	1	0	BTBD11	106537895	1.000000	0.71417	1.000000	0.80357	0.727000	0.41649	7.975000	0.88055	2.398000	0.81561	0.650000	0.86243	GTC		TCGA-2L-AAQA-01A-21D-A38G-08	BTBD11-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318003.1	0	0	1	32	101	0	36		0	0	0	0	36	2		0	0	0	0	0	2	1	1.000000	30	101	0	35	2		0	0	0	0	36	2	-3.017664	1	1	121406	35	41	1	0	0	0	2.008629	0	0.600000	1.890000	0.587629	0.770000	5.600000e-01	1.000000	1.000000	0.783994	0.770000	0	6.600000e-01	9.000000e-01
KRAS	3845	broad.mit.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	C	A	rs121913529		TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08			C	A	C	C		Valid	Somatic	Phase_I	WXS	KRAS_deep			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr12:25398284C>A	ENST00000256078.4	-	2	98	c.35G>T	c.(34-36)gGt>gTt	p.G12V	KRAS_ENST00000556131.1_Missense_Mutation_p.G12V|KRAS_ENST00000557334.1_Missense_Mutation_p.G12V|KRAS_ENST00000311936.3_Missense_Mutation_p.G12V	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)		GCCTACGCCACCAGCTCCAAC	0.348000	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		pancreatic, colorectal, lung, thyroid, AML, others				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)			Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		L, E, M, O	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)						SO:0001583	missense	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	ENST00000256078.4	1	1	hg19	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.808637	0.90707	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90373	0.6987	M	0.90650	3.135	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.72625	0.969;0.978	D	0.91773	0.5429	10	0.72032	D	0.01	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	V	12	ENSP00000308495:G12V;ENSP00000452512:G12V;ENSP00000256078:G12V;ENSP00000451856:G12V	ENSP00000256078:G12V	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		TCGA-2L-AAQA-01A-21D-A38G-08	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	1	0	1	101	239	1	129	1	9.999856e-01	28	29	1	129	4	1	1	68	251	0	178	2	1	1.000000	101	236	0	128	2	1	1	2498	5510	1	129	146	-20.000000	1	1	0	0		1	0	0	0	2.008629	0	0.600000	1.890000	0.587629	0.950000	8.000000e-01	1.000000	1.000000	0.945562	0.950000	1	8.700000e-01	1
CPNE8	144402	broad.mit.edu	37	12	39117617	39117617	+	Missense_Mutation	SNP	A	A	T			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr12:39117617A>T	ENST00000331366.5	-	13	967	c.871T>A	c.(871-873)Ttg>Atg	p.L291M	CPNE8_ENST00000360449.3_Missense_Mutation_p.L279M|CPNE8_ENST00000538596.2_5'Flank	NM_153634.2	NP_705898.1	Q86YQ8	CPNE8_HUMAN	copine VIII			21	Esophageal squamous(101;0.187)	Lung NSC(34;0.137)|Melanoma(24;0.152)|all_lung(34;0.157)			GTTTCTACCAAGAAAGAGAGT	0.328000																								0							SO:0001583	missense			ENST00000331366.5	1	1	hg19	CCDS8733.1	.	.	.	.	.	.	.	.	.	.	A	15.26	2.781337	0.49891	.	.	ENSG00000139117	ENST00000331366;ENST00000360449	T;T	0.25085	1.82;1.82	4.51	0.923	0.19413	.	0.174644	0.38720	N	0.001594	T	0.20047	0.0482	L	0.35854	1.095	0.48762	D	0.999705	P	0.37207	0.587	B	0.42882	0.401	T	0.03534	-1.1027	10	0.59425	D	0.04	-5.3906	4.2841	0.10846	0.582:0.1718:0.2463:0.0	.	291	Q86YQ8	CPNE8_HUMAN	M	291;279	ENSP00000329748:L291M;ENSP00000353633:L279M	ENSP00000329748:L291M	L	-	1	2	CPNE8	37403884	0.989000	0.36119	0.997000	0.53966	0.989000	0.77384	0.619000	0.24388	0.317000	0.23160	0.460000	0.39030	TTG		TCGA-2L-AAQA-01A-21D-A38G-08	CPNE8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403856.1	1	0	1	130	388	0	151	1	9.596372e-01	6	12	0	151	2		0	0	0	0	0	2	1	1.000000	130	383	0	149	2		0	0	0	0	151	2	-20.000000	1	1	0	0		1	0	0	0	2.008629	0	0.600000	1.890000	0.587629	0.800000	6.800000e-01	0.930000	0.810000	0.813416	0.800000	0	7.400000e-01	8.700000e-01
KCNA6	3742	broad.mit.edu	37	12	4920011	4920011	+	Silent	SNP	G	G	A			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr12:4920011G>A	ENST00000280684.3	+	1	1670	c.804G>A	c.(802-804)acG>acA	p.T268T	RP11-234B24.4_ENST00000542988.1_lincRNA|KCNA6_ENST00000433855.1_Silent_p.T268T			P17658	KCNA6_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 6			49				Dalfampridine(DB06637)	TGGTGGAGACGCTGTGCATTG	0.562000										HNSCC(72;0.22)														0							SO:0001819	synonymous_variant			ENST00000280684.3	1	1	hg19	CCDS8534.1																																																																																				TCGA-2L-AAQA-01A-21D-A38G-08	KCNA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398909.1	1	0	1	143	324	0	147		0	0	0	0	147	2		0	0	0	0	0	2	1	1.000000	141	322	0	146	2		0	0	0	0	147	2	-20.000000	1	1	0	0		1	0	0	0	2.042440	0	0.600000	1.890000	0.595142	0.990000	8.600000e-01	1.000000	1.000000	0.976558	0.990000	1	9.300000e-01	1
NCKAP5L	57701	broad.mit.edu	37	12	50191075	50191075	+	Missense_Mutation	SNP	T	T	A			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr12:50191075T>A	ENST00000335999.6	-	8	769	c.568A>T	c.(568-570)Att>Ttt	p.I190F		NM_001037806.3	NP_001032895.2	Q9HCH0	NCK5L_HUMAN	NCK-associated protein 5-like			18					ACCTCCAGAATCTGGGCCTTC	0.682000																								0							SO:0001583	missense			ENST00000335999.6	1	1	hg19	CCDS41781.2	.	.	.	.	.	.	.	.	.	.	T	23.9	4.465970	0.84425	.	.	ENSG00000167566	ENST00000335999;ENST00000354423	T	0.63913	-0.07	4.3	4.3	0.51218	.	.	.	.	.	T	0.71204	0.3312	L	0.42245	1.32	0.47153	D	0.999339	D	0.76494	0.999	D	0.87578	0.998	T	0.73372	-0.4003	9	0.59425	D	0.04	-4.9163	12.7587	0.57350	0.0:0.0:0.0:1.0	.	186	E2QRB5	.	F	190;186	ENSP00000337998:I190F	ENSP00000337998:I190F	I	-	1	0	NCKAP5L	48477342	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.480000	0.53172	1.717000	0.51406	0.379000	0.24179	ATT		TCGA-2L-AAQA-01A-21D-A38G-08	NCKAP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346884.2	1	0	1	56	122	0	56	1	9.829473e-01	4	13	0	56	2		0	0	0	0	0	2	1	1.000000	56	122	0	53	2		0	0	0	0	56	2	-20.000000	1	1	0	0		1	0	0	0	2.008629	0	0.600000	1.890000	0.587629	0.990000	8.000000e-01	1.000000	1.000000	0.964849	0.990000	1	9.000000e-01	1
NCAPD2	9918	broad.mit.edu	37	12	6631057	6631057	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr12:6631057C>T	ENST00000315579.5	+	15	2607	c.1808C>T	c.(1807-1809)tCg>tTg	p.S603L	NCAPD2_ENST00000545962.1_Missense_Mutation_p.S558L	NM_014865.3	NP_055680.3	Q15021	CND1_HUMAN	non-SMC condensin I complex, subunit D2			48					CCCAATATGTCGGATCCTGAG	0.483000																								0							SO:0001583	missense			ENST00000315579.5	0	1	hg19	CCDS8548.1	.	.	.	.	.	.	.	.	.	.	C	6.832	0.522777	0.13066	.	.	ENSG00000010292	ENST00000315579;ENST00000382457;ENST00000545962;ENST00000535602	T;T;T	0.31769	2.49;1.48;2.22	4.69	0.379	0.16213	Armadillo-type fold (1);	0.958927	0.08648	N	0.914555	T	0.14917	0.0360	N	0.08118	0	0.09310	N	1	B;B;B	0.12013	0.005;0.0;0.001	B;B;B	0.06405	0.002;0.0;0.001	T	0.30179	-0.9987	10	0.29301	T	0.29	0.0031	7.6424	0.28300	0.1363:0.5837:0.0:0.28	.	558;564;603	F5GZJ1;B3KY03;Q15021	.;.;CND1_HUMAN	L	603;475;558;475	ENSP00000325017:S603L;ENSP00000371895:S475L;ENSP00000444417:S558L	ENSP00000325017:S603L	S	+	2	0	NCAPD2	6501318	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.426000	0.07008	-0.050000	0.13356	-1.736000	0.00690	TCG		TCGA-2L-AAQA-01A-21D-A38G-08	NCAPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399964.1	0	0	0	7	396	1	129	0	4.147525e-02	0	60	1	129	4		0	0	0	0	0	2	0	0.171051	6	394	1	129	12		0	0	0	1	129	2	-3.228614	1	1	0	0		1	0	0	0	2.042440	0	0.600000	1.890000	0.595142	0.050000	2.000000e-02	0.110000	0.060000	0.064975	0.050000	0	3.000000e-02	9.000000e-02
HECTD1	25831	broad.mit.edu	37	14	31576215	31576215	+	Missense_Mutation	SNP	T	T	A			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr14:31576215T>A	ENST00000399332.1	-	38	7351	c.6863A>T	c.(6862-6864)tAt>tTt	p.Y2288F	HECTD1_ENST00000553700.1_Missense_Mutation_p.Y2288F	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1			70	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)		TCGTGACTCATAAATCAGTTT	0.368000																								0							SO:0001583	missense			ENST00000399332.1	1	1	hg19	CCDS41939.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.57|11.57	1.677590|1.677590	0.29783|0.29783	.|.	.|.	ENSG00000092148|ENSG00000092148	ENST00000554882|ENST00000553700;ENST00000261312;ENST00000399332	.|T;T	.|0.39406	.|1.08;1.08	5.96|5.96	5.96|5.96	0.96718|0.96718	.|HECT (4);	.|0.085238	.|0.49305	.|U	.|0.000145	T|T	0.38161|0.38161	0.1030|0.1030	N|N	0.03608|0.03608	-0.345|-0.345	0.58432|0.58432	D|D	0.999996|0.999996	.|D	.|0.57257	.|0.979	.|D	.|0.71414	.|0.973	T|T	0.39563|0.39563	-0.9608|-0.9608	5|10	.|0.11794	.|T	.|0.64	-10.4726|-10.4726	15.0049|15.0049	0.71504|0.71504	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|2288	.|Q9ULT8	.|HECD1_HUMAN	L|F	654|2288;2290;2288	.|ENSP00000450697:Y2288F;ENSP00000382269:Y2288F	.|ENSP00000261312:Y2290F	M|Y	-|-	1|2	0|0	HECTD1|HECTD1	30645966|30645966	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	7.694000|7.694000	0.84235|0.84235	2.270000|2.270000	0.75569|0.75569	0.533000|0.533000	0.62120|0.62120	ATG|TAT		TCGA-2L-AAQA-01A-21D-A38G-08	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1	0	0	0	12	537	1	134	0	1.834330e-01	0	123	1	134	5		0	0	0	0	0	2	0	0.345185	12	536	1	132	15		0	0	0	1	134	2	-10.451700	1	1	120808	1	30	1	0	0	0	2.052130	0	0.600000	1.890000	0.597586	0.070000	3.000000e-02	0.120000	0.080000	0.078078	0.070000	0	5.000000e-02	1.000000e-01
MAGEL2	54551	broad.mit.edu	37	15	23890209	23890209	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr15:23890209G>A	ENST00000532292.1	-	1	966	c.872C>T	c.(871-873)gCc>gTc	p.A291V		NM_019066.4	NP_061939.3	Q9UJ55	MAGL2_HUMAN	MAGE-like 2			7		all_cancers(20;1.78e-24)|all_epithelial(15;7.75e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000625)|Colorectal(260;0.14)			GTCCTCTTGGGCTTCCAGATG	0.632000																								0							SO:0001583	missense			ENST00000532292.1	1	1	hg19		.	.	.	.	.	.	.	.	.	.	G	7.175	0.588375	0.13812	.	.	ENSG00000254585	ENST00000532292	.	.	.	4.22	3.3	0.37823	.	.	.	.	.	T	0.18593	0.0446	N	0.08118	0	0.09310	N	1	.	.	.	.	.	.	T	0.19877	-1.0292	5	.	.	.	.	7.8726	0.29576	0.1098:0.0:0.8901:0.0	.	.	.	.	S	323	.	.	P	-	1	0	MAGEL2	21441302	0.001000	0.12720	0.002000	0.10522	0.299000	0.27559	0.810000	0.27183	1.364000	0.46038	0.655000	0.94253	CCC		TCGA-2L-AAQA-01A-21D-A38G-08	MAGEL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395182.2	1	0	0	16	232	0	118	0	0	0	1	0	118	2		0	0	0	0	0	2	1	0.999921	16	223	0	115	2		0	0	0	0	118	2	-19.366610	1	1	0	0		1	0	1	1	1.428970	1	0.600000	1.890000	0.428571	0.140000	8.000000e-02	0.230000	0.150000	0.157810	0.140000	0	1.100000e-01	1.900000e-01
ISLR2	57611	broad.mit.edu	37	15	74425848	74425848	+	Silent	SNP	C	C	T			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr15:74425848C>T	ENST00000361742.3	+	4	1522	c.753C>T	c.(751-753)cgC>cgT	p.R251R	ISLR2_ENST00000453268.2_Silent_p.R251R|ISLR2_ENST00000565540.1_Silent_p.R251R|ISLR2_ENST00000435464.1_Silent_p.R251R|ISLR2_ENST00000561975.1_Intron|ISLR2_ENST00000419208.1_Silent_p.R251R|ISLR2_ENST00000565159.1_Silent_p.R251R|ISLR2_ENST00000445793.1_Silent_p.R251R	NM_001130136.1|NM_020851.2	NP_001123608.1|NP_065902.1	Q6UXK2	ISLR2_HUMAN	immunoglobulin superfamily containing leucine-rich repeat 2			36					CCCCACTGCGCGCAGGACTGG	0.677000																								0							SO:0001819	synonymous_variant			ENST00000361742.3	1	1	hg19	CCDS10259.1																																																																																				TCGA-2L-AAQA-01A-21D-A38G-08	ISLR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269046.1	1	0	1	90	188	0	94	0	2.475146e-01	0	3	0	94	2		0	0	0	0	0	2	1	1.000000	88	185	0	94	2		0	0	0	0	94	2	-20.000000	1	1	0	0		1						0.600000	1.890000									0	0
CCL8	6355	broad.mit.edu	37	17	32647821	32647821	+	Splice_Site	SNP	C	C	T			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr17:32647821C>T	ENST00000394620.1	+	3	661	c.195C>T	c.(193-195)atC>atT	p.I65I		NM_005623.2	NP_005614.2	P80075	CCL8_HUMAN	chemokine (C-C motif) ligand 8			4		Ovarian(249;0.0443)|Breast(31;0.151)			TCCCCCACAGCTTCAAGACCA	0.512000																								0							SO:0001630	splice_region_variant			ENST00000394620.1	1	0	hg19	CCDS11280.1																																																																																				TCGA-2L-AAQA-01A-21D-A38G-08	CCL8-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256376.2	1	0	1	40	78	0	72	0	0	0	1	0	72	2		0	0	0	0	0	2	1	1.000000	39	73	0	70	2		0	0	0	0	72	2	-20.000000	1	1	0	0		1	0	1	1	1.479540	1	0.600000	1.890000	0.431010	0.780000	5.900000e-01	0.960000	0.790000	0.787428	0.780000	0	6.800000e-01	8.800000e-01
RNF43	54894	broad.mit.edu	37	17	56492899	56492899	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr17:56492899G>A	ENST00000584437.1	-	1	1995	c.40C>T	c.(40-42)Ccc>Tcc	p.P14S	RNF43_ENST00000583753.1_Missense_Mutation_p.P14S|RNF43_ENST00000580014.1_5'Flank|RNF43_ENST00000577716.1_Missense_Mutation_p.P14S|RNF43_ENST00000500597.2_Missense_Mutation_p.P14S|BZRAP1-AS1_ENST00000583841.1_RNA|RNF43_ENST00000407977.2_Missense_Mutation_p.P14S|RNF43_ENST00000581868.1_Intron			Q68DV7	RNF43_HUMAN	ring finger protein 43			60	Medulloblastoma(34;0.127)|all_neural(34;0.237)				AGCAGCCAGGGCCAGAGGGCA	0.552000																								0							SO:0001583	missense			ENST00000584437.1	1	0	hg19	CCDS11607.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.492626	0.84962	.	.	ENSG00000108375	ENST00000407977;ENST00000500597	T;T	0.23950	2.6;1.88	5.69	5.69	0.88448	.	0.000000	0.64402	D	0.000008	T	0.37237	0.0996	N	0.14661	0.345	0.52099	D	0.999941	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	T	0.32798	-0.9893	10	0.62326	D	0.03	-25.2822	19.1688	0.93569	0.0:0.0:1.0:0.0	.	14;14	Q68DV7-2;Q68DV7	.;RNF43_HUMAN	S	14	ENSP00000385328:P14S;ENSP00000441969:P14S	ENSP00000385328:P14S	P	-	1	0	RNF43	53847898	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	8.758000	0.91663	2.840000	0.97914	0.655000	0.94253	CCC		TCGA-2L-AAQA-01A-21D-A38G-08	RNF43-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444713.1	1	0	1	51	120	0	107	1	9.466499e-01	14	0	0	107	2	1	1	128	200	0	227	2	1	1.000000	51	119	0	107	2		0	0	0	0	107	2	-20.000000	1	0	0	0		1	0	1	1	1.475023	1	0.600000	1.890000	0.431010	0.690000	5.400000e-01	0.850000	0.690000	0.698904	0.690000	0	6.100000e-01	7.800000e-01
EXOC7	23265	broad.mit.edu	37	17	74097870	74097870	+	Silent	SNP	C	C	T			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr17:74097870C>T	ENST00000335146.7	-	3	254	c.201G>A	c.(199-201)acG>acA	p.T67T	EXOC7_ENST00000467929.2_Silent_p.T26T|EXOC7_ENST00000332065.5_Silent_p.T67T|EXOC7_ENST00000589210.1_Silent_p.T67T|EXOC7_ENST00000405575.4_Silent_p.T67T|EXOC7_ENST00000411744.2_Silent_p.T67T|EXOC7_ENST00000607838.1_Silent_p.T67T|EXOC7_ENST00000406660.3_Silent_p.T67T			Q9UPT5	EXOC7_HUMAN	exocyst complex component 7			14			LUSC - Lung squamous cell carcinoma(166;0.187)		GCAGATTCTCCGTCTGCTTGT	0.522000																								0							SO:0001819	synonymous_variant			ENST00000335146.7	1	1	hg19	CCDS45782.1																																																																																				TCGA-2L-AAQA-01A-21D-A38G-08	EXOC7-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000319768.2	1	0	1	106	124	0	120	1	1	19	21	0	120	2		0	0	0	0	0	2	1	1.000000	103	123	0	118	2		0	0	0	0	120	2	-19.975330	1	1	121412	1	27	1	0	1	1	1.486540	1	0.600000	1.890000	0.431010	0.970000	8.700000e-01	1.000000	1.000000	0.969823	0.970000	1	9.300000e-01	1
TP53	7157	broad.mit.edu	37	17	7578406	7578406	+	Missense_Mutation	SNP	C	C	T	rs28934578		TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr17:7578406C>T	ENST00000269305.4	-	5	713	c.524G>A	c.(523-525)cGc>cAc	p.R175H	TP53_ENST00000445888.2_Missense_Mutation_p.R175H|TP53_ENST00000574684.1_5'UTR|TP53_ENST00000455263.2_Missense_Mutation_p.R175H|TP53_ENST00000420246.2_Missense_Mutation_p.R175H|TP53_ENST00000359597.4_Missense_Mutation_p.R175H|TP53_ENST00000413465.2_Missense_Mutation_p.R175H	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.R175H(847)|p.R43H(36)|p.R82H(36)|p.R175L(19)|p.0?(8)|p.R175P(6)|p.R174fs*24(3)|p.R175_E180delRCPHHE(3)|p.V173fs*59(2)|p.R174fs*1(2)|p.V157_C176del20(1)|p.V173fs*69(1)|p.E171fs*61(1)|p.V173fs*23(1)|p.R174_H178>S(1)|p.V172_E180delVVRRCPHHE(1)|p.R174_H179delRRCPHH(1)|p.E171fs*1(1)|p.R175_H178>X(1)|p.R175fs*5(1)|p.R42fs*24(1)|p.R174_C176delRRC(1)|p.H168fs*69(1)|p.R174fs*70(1)|p.E171_H179delEVVRRCPHH(1)|p.R81fs*24(1)|p.R174_E180>K(1)|p.R174fs*3(1)		24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		Acetylsalicylic acid(DB00945)	GTGGGGGCAGCGCCTCACAAC	0.652000	R175H(AU565_BREAST)|R175H(CAL33_UPPER_AERODIGESTIVE_TRACT)|R175H(DETROIT562_UPPER_AERODIGESTIVE_TRACT)|R175H(HCC1395_BREAST)|R175H(HUCCT1_BILIARY_TRACT)|R175H(KLE_ENDOMETRIUM)|R175H(KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R175H(LS123_LARGE_INTESTINE)|R175H(NCIH196_LUNG)|R175H(RKN_OVARY)|R175H(SKBR3_BREAST)|R175H(SKUT1_SOFT_TISSUE)|R175H(TYKNU_OVARY)	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	980	Substitution - Missense(944)|Deletion - Frameshift(17)|Whole gene deletion(8)|Deletion - In frame(8)|Complex - deletion inframe(3)	GRCh37	CM062017|CM951224	TP53	M	rs28934578	SO:0001583	missense	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	31	5.079737	0.94050	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99889	-7.55;-7.55;-7.55;-7.55;-7.55;-7.55;-7.55;-7.55	5.41	5.41	0.78517	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.101149	0.64402	D	0.000008	D	0.99908	0.9956	M	0.92784	3.345	0.80722	A	1	D;P;D;D;P;B;D	0.89917	0.999;0.578;1.0;0.998;0.632;0.213;0.999	D;B;D;D;B;B;D	0.91635	0.985;0.26;0.999;0.921;0.378;0.144;0.939	D	0.96278	0.9204	9	0.87932	D	0	-11.8679	17.0767	0.86588	0.0:1.0:0.0:0.0	rs28934578	136;175;175;82;175;175;175	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	H	175;175;175;175;175;175;164;82;43;82;43	ENSP00000410739:R175H;ENSP00000352610:R175H;ENSP00000269305:R175H;ENSP00000398846:R175H;ENSP00000391127:R175H;ENSP00000391478:R175H;ENSP00000425104:R43H;ENSP00000423862:R82H	ENSP00000269305:R175H	R	-	2	0	TP53	7519131	1.000000	0.71417	0.989000	0.46669	0.795000	0.44927	6.042000	0.70996	2.702000	0.92279	0.655000	0.94253	CGC		TCGA-2L-AAQA-01A-21D-A38G-08	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	1	0	1	134	159	0	152	1	1	47	15	0	152	2	1	1	330	366	0	514	2	1	1.000000	134	157	0	152	2		0	0	0	0	152	2	-20.000000	1	1	121412	1	41	1	0	1	1	1.491143	1	0.600000	1.890000	0.428571	0.970000	8.800000e-01	1.000000	0.990000	0.967531	0.970000	1	9.300000e-01	1
RAB40B	10966	broad.mit.edu	37	17	80616499	80616499	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr17:80616499C>T	ENST00000571995.1	-	5	564	c.433G>A	c.(433-435)Gcc>Acc	p.A145T	RAB40B_ENST00000571880.1_5'Flank|RAB40B_ENST00000269347.6_5'UTR|RAB40B_ENST00000538809.2_Intron	NM_006822.2	NP_006813.1	Q12829	RB40B_HUMAN	RAB40B, member RAS oncogene family			10	Breast(20;0.00132)|all_neural(118;0.0952)	all_cancers(8;0.072)|all_epithelial(8;0.139)	BRCA - Breast invasive adenocarcinoma(99;0.0262)|OV - Ovarian serous cystadenocarcinoma(97;0.061)		AGGCGCTCGGCGTAGGCCTGG	0.652000																								0							SO:0001583	missense			ENST00000571995.1	1	1	hg19	CCDS11816.1	.	.	.	.	.	.	.	.	.	.	C	34	5.306869	0.95629	.	.	ENSG00000141542	ENST00000269347;ENST00000538809	.	.	.	3.84	3.84	0.44239	Small GTP-binding protein domain (1);	0.000000	0.64402	D	0.000008	D	0.84804	0.5553	M	0.93678	3.445	0.80722	D	1	D	0.71674	0.998	D	0.63597	0.916	D	0.89908	0.4049	9	0.87932	D	0	.	16.2189	0.82244	0.0:1.0:0.0:0.0	.	145	Q12829	RB40B_HUMAN	T	145;179	.	ENSP00000269347:A145T	A	-	1	0	RAB40B	78209788	1.000000	0.71417	0.792000	0.32020	0.907000	0.53573	5.860000	0.69546	2.082000	0.62665	0.591000	0.81541	GCC		TCGA-2L-AAQA-01A-21D-A38G-08	RAB40B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439007.1	1	0	1	78	154	0	100	1	9.985576e-01	16	7	0	100	2		0	0	0	0	0	2	1	1.000000	78	150	0	100	2		0	0	0	0	100	2	-20.000000	1	1	121400	1	29	1	0	1	1	1.486540	1	0.600000	1.890000	0.431010	0.770000	6.400000e-01	0.920000	0.780000	0.786322	0.770000	0	7.000000e-01	8.600000e-01
CDH2	1000	broad.mit.edu	37	18	25570188	25570188	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr18:25570188C>T	ENST00000269141.3	-	10	1894	c.1471G>A	c.(1471-1473)Gta>Ata	p.V491I	CDH2_ENST00000399380.3_Missense_Mutation_p.V460I	NM_001792.3	NP_001783.2	P19022	CADH2_HUMAN	cadherin 2, type 1, N-cadherin (neuronal)	p.V491I(1)		82					TTTTCATTTACGTCAATAACT	0.468000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000269141.3	1	1	hg19	CCDS11891.1	.	.	.	.	.	.	.	.	.	.	C	19.67	3.871347	0.72065	0.0	1.16E-4	ENSG00000170558	ENST00000269141;ENST00000399380	T;T	0.62232	0.04;0.04	6.16	6.16	0.99307	Cadherin (3);Cadherin-like (1);	0.056760	0.64402	D	0.000001	T	0.61476	0.2350	L	0.49699	1.58	0.80722	D	1	B;B	0.17268	0.021;0.007	B;B	0.08055	0.003;0.001	T	0.53961	-0.8364	10	0.49607	T	0.09	.	20.8598	0.99761	0.0:1.0:0.0:0.0	.	460;491	A8MWK3;P19022	.;CADH2_HUMAN	I	491;460	ENSP00000269141:V491I;ENSP00000382312:V460I	ENSP00000269141:V491I	V	-	1	0	CDH2	23824186	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.487000	0.81328	2.937000	0.99478	0.650000	0.86243	GTA		TCGA-2L-AAQA-01A-21D-A38G-08	CDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133246.3	1	0	1	154	181	0	158	0	9.413594e-01	0	8	0	158	2		0	0	0	0	0	2	1	1.000000	150	176	0	158	2		0	0	0	0	158	2	-20.000000	1	1	121412	3	40	1	0	1	1	1.506894	1	0.600000	1.890000	0.431010	0.980000	9.000000e-01	1.000000	1.000000	0.978490	0.980000	1	9.400000e-01	1
ALPK2	115701	broad.mit.edu	37	18	56246544	56246544	+	Missense_Mutation	SNP	A	A	T			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr18:56246544A>T	ENST00000361673.3	-	4	1677	c.1464T>A	c.(1462-1464)gaT>gaA	p.D488E	ALPK2_ENST00000587399.1_5'Flank	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2			84					TTACTGATTCATCCATGTTGA	0.493000											OREG0025011	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)												0							SO:0001583	missense			ENST00000361673.3	1	1	hg19	CCDS11966.2	.	.	.	.	.	.	.	.	.	.	A	10.08	1.251969	0.22880	.	.	ENSG00000198796	ENST00000361673	T	0.54479	0.57	5.34	-0.259	0.12971	.	0.515524	0.15105	N	0.280317	T	0.31231	0.0790	L	0.33485	1.01	0.09310	N	1	B	0.32829	0.386	B	0.24269	0.052	T	0.09122	-1.0689	10	0.35671	T	0.21	-8.4846	4.6008	0.12352	0.3972:0.4204:0.0685:0.1138	.	488	Q86TB3	ALPK2_HUMAN	E	488	ENSP00000354991:D488E	ENSP00000354991:D488E	D	-	3	2	ALPK2	54397524	0.027000	0.19231	0.028000	0.17463	0.004000	0.04260	0.054000	0.14205	-0.291000	0.09012	-0.313000	0.08912	GAT		TCGA-2L-AAQA-01A-21D-A38G-08	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	1	0	1	169	223	0	228		0	0	0	0	228	2		0	0	0	0	0	2	1	1.000000	169	222	0	228	2		0	0	0	0	228	2	-20.000000	1	1	0	0		1	0	1	1	1.506894	1	0.600000	1.890000	0.431010	0.960000	8.700000e-01	1.000000	1.000000	0.964200	0.960000	1	9.200000e-01	1
RASAL3	64926	broad.mit.edu	37	19	15567402	15567402	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr19:15567402G>A	ENST00000343625.7	-	10	1572	c.1487C>T	c.(1486-1488)gCg>gTg	p.A496V	RASAL3_ENST00000608577.1_5'Flank	NM_022904.1	NP_075055.1	Q86YV0	RASL3_HUMAN	RAS protein activator like 3			18					GAACAGCAGCGCCTCACGGCC	0.617000																								0							SO:0001583	missense			ENST00000343625.7	1	1	hg19	CCDS46006.1	.	.	.	.	.	.	.	.	.	.	g	19.47	3.834497	0.71373	.	.	ENSG00000105122	ENST00000343625	T	0.79554	-1.28	4.37	4.37	0.52481	Rho GTPase activation protein (1);Ras GTPase-activating protein (4);	0.212338	0.22735	U	0.056263	T	0.82098	0.4963	L	0.49350	1.555	0.38814	D	0.955492	D	0.56968	0.978	P	0.54312	0.748	T	0.80476	-0.1366	10	0.23302	T	0.38	.	14.8191	0.70059	0.0:0.0:1.0:0.0	.	496	Q86YV0	RASL3_HUMAN	V	496	ENSP00000341905:A496V	ENSP00000341905:A496V	A	-	2	0	RASAL3	15428402	0.007000	0.16637	1.000000	0.80357	0.994000	0.84299	1.074000	0.30703	2.158000	0.67659	0.558000	0.71614	GCG		TCGA-2L-AAQA-01A-21D-A38G-08	RASAL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461331.3	1	0	1	42	106	0	39	0	3.256585e-01	0	4	0	39	2		0	0	0	0	0	2	1	1.000000	43	106	0	38	2		0	0	0	0	39	2	-20.000000	1	1	0	0		1	0	0	0	2.067134	0	0.600000	1.890000	0.600000	0.940000	7.100000e-01	1.000000	1.000000	0.922540	0.940000	1	8.200000e-01	1
PDCD2L	84306	broad.mit.edu	37	19	34912428	34912428	+	Missense_Mutation	SNP	T	T	C			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08			T	C	T	T		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr19:34912428T>C	ENST00000246535.3	+	6	849	c.802T>C	c.(802-804)Tcc>Ccc	p.S268P	PDCD2L_ENST00000587065.2_5'UTR|RN7SL154P_ENST00000578043.1_RNA	NM_032346.1	NP_115722.1	Q9BRP1	PDD2L_HUMAN	programmed cell death 2-like			11	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.211)		TCCTAGGTATTCCTGGAGTGG	0.493000																								0							SO:0001583	missense			ENST00000246535.3	1	1	hg19	CCDS12438.1	.	.	.	.	.	.	.	.	.	.	T	17.84	3.486734	0.63962	.	.	ENSG00000126249	ENST00000246535	.	.	.	5.98	4.94	0.65067	Programmed cell death protein 2, C-terminal (1);	0.144113	0.64402	D	0.000004	T	0.81451	0.4825	M	0.91196	3.185	0.41755	D	0.989686	D	0.76494	0.999	D	0.73708	0.981	D	0.83431	0.0038	9	0.48119	T	0.1	-15.8635	11.5108	0.50492	0.1347:0.0:0.0:0.8653	.	268	Q9BRP1	PDD2L_HUMAN	P	268	.	ENSP00000246535:S268P	S	+	1	0	PDCD2L	39604268	1.000000	0.71417	0.999000	0.59377	0.749000	0.42624	3.088000	0.50175	1.048000	0.40298	0.477000	0.44152	TCC		TCGA-2L-AAQA-01A-21D-A38G-08	PDCD2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459251.3	1	0	1	345	803	0	451	1	9.999897e-01	15	26	0	451	2		0	0	0	0	0	2	1	1.000000	341	785	0	448	2		0	0	0	0	451	2	-20.000000	1	1	0	0		1	0	0	0	2.067134	0	0.600000	1.890000	0.600000	0.990000	9.000000e-01	1.000000	1.000000	0.982919	0.990000	1	9.500000e-01	1
SBK2	646643	broad.mit.edu	37	19	56042597	56042597	+	Silent	SNP	G	G	A			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr19:56042597G>A	ENST00000413299.1	-	3	406	c.369C>T	c.(367-369)taC>taT	p.Y123Y	SBK2_ENST00000344158.3_Silent_p.Y123Y	NM_001101401.2	NP_001094871.2	P0C263	SBK2_HUMAN	SH3 domain binding kinase family, member 2			9					TGCCAATGCCGTAGGCCGTCA	0.642000																								0							SO:0001819	synonymous_variant			ENST00000413299.1	1	1	hg19	CCDS42631.1																																																																																				TCGA-2L-AAQA-01A-21D-A38G-08	SBK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341919.1	1	0	1	57	139	0	65		0	0	0	0	65	2		0	0	0	0	0	2	1	1.000000	56	137	0	65	2		0	0	0	0	65	2	-6.138701	1	1	0	0		1	1	2	3	2.123521	0	0.600000	1.890000	0.605911	0.980000	7.700000e-01	1.000000	1.000000	0.951894	0.980000	1	8.700000e-01	1
ZNF787	126208	broad.mit.edu	37	19	56600294	56600294	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr19:56600294G>A	ENST00000270459.3	-	3	365	c.247C>T	c.(247-249)Cgg>Tgg	p.R83W		NM_001002836.2	NP_001002836	Q6DD87	ZN787_HUMAN	zinc finger protein 787			5		Colorectal(82;3.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)			CGCTGGTGCCGCGTCAGCTTG	0.721000																								0							SO:0001583	missense			ENST00000270459.3	1	1	hg19	CCDS42634.1	.	.	.	.	.	.	.	.	.	.	G	17.51	3.406781	0.62399	.	.	ENSG00000142409	ENST00000270459	T	0.56275	0.47	3.22	3.22	0.36961	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.73860	0.3641	M	0.88377	2.95	0.80722	D	1	D	0.89917	1.0	D	0.72075	0.976	T	0.78902	-0.2021	9	0.59425	D	0.04	-20.4997	12.27	0.54700	0.0:0.0:1.0:0.0	.	83	Q6DD87	ZN787_HUMAN	W	83	ENSP00000270459:R83W	ENSP00000270459:R83W	R	-	1	2	ZNF787	61292106	0.000000	0.05858	0.980000	0.43619	0.978000	0.69477	-0.893000	0.04127	1.812000	0.52913	0.462000	0.41574	CGG		TCGA-2L-AAQA-01A-21D-A38G-08	ZNF787-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457498.1	1	0	0	43	133	0	51	1	9.999788e-01	30	25	0	51	2		0	0	0	0	0	2	1	1.000000	43	132	0	50	2		0	0	0	0	51	2	-20.000000	1	1	0	0		1	1	2	3	2.123521	0	0.600000	1.890000	0.605911	0.830000	6.200000e-01	1.000000	1.000000	0.836174	0.830000	0	7.200000e-01	9.600000e-01
MYO1F	4542	broad.mit.edu	37	19	8595429	8595429	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr19:8595429C>T	ENST00000338257.8	-	20	2339	c.2072G>A	c.(2071-2073)cGa>cAa	p.R691Q		NM_012335.3	NP_036467.2	O00160	MYO1F_HUMAN	myosin IF			42					ATCGAACTTTCGCTCTCGCAC	0.647000																								0							SO:0001583	missense			ENST00000338257.8	1	1	hg19	CCDS42494.1	.	.	.	.	.	.	.	.	.	.	C	36	5.683094	0.96774	.	.	ENSG00000142347	ENST00000305795;ENST00000338257	D	0.95205	-3.64	5.36	5.36	0.76844	Myosin head, motor domain (1);	0.000000	0.85682	D	0.000000	D	0.96259	0.8780	M	0.81942	2.565	0.80722	D	1	D	0.63880	0.993	P	0.54174	0.744	D	0.95729	0.8773	10	0.41790	T	0.15	.	18.1619	0.89710	0.0:1.0:0.0:0.0	.	691	O00160	MYO1F_HUMAN	Q	736;691	ENSP00000344871:R691Q	ENSP00000304899:R736Q	R	-	2	0	MYO1F	8501429	1.000000	0.71417	0.952000	0.39060	0.951000	0.60555	7.748000	0.85085	2.532000	0.85374	0.555000	0.69702	CGA		TCGA-2L-AAQA-01A-21D-A38G-08	MYO1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342716.2	0	0	0	20	669	0	219	0	7.598679e-02	0	15	0	219	2		0	0	0	0	0	2	1	0.999994	20	654	0	218	2		0	0	0	0	219	2	-3.016125	1	1	0	0		1	0	0	0	2.067134	0	0.600000	1.890000	0.600000	0.090000	5.000000e-02	0.150000	0.100000	0.101187	0.090000	0	7.000000e-02	1.200000e-01
AGL	178	broad.mit.edu	37	1	100336383	100336383	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr1:100336383G>A	ENST00000294724.4	+	7	1394	c.916G>A	c.(916-918)Gtc>Atc	p.V306I	AGL_ENST00000370161.2_Missense_Mutation_p.V290I|AGL_ENST00000361522.4_Missense_Mutation_p.V289I|AGL_ENST00000361302.3_Missense_Mutation_p.V290I|AGL_ENST00000370165.3_Missense_Mutation_p.V306I|AGL_ENST00000361915.3_Missense_Mutation_p.V306I|AGL_ENST00000370163.3_Missense_Mutation_p.V306I	NM_000028.2	NP_000019.2	P35573	GDE_HUMAN	amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase			69		all_epithelial(167;2.2e-06)|all_lung(203;0.000295)|Lung NSC(277;0.00131)			CCAAGTAGATGTCAACAAAGC	0.303000																								0							SO:0001583	missense			ENST00000294724.4	1	1	hg19	CCDS759.1	.	.	.	.	.	.	.	.	.	.	g	5.406	0.260007	0.10239	.	.	ENSG00000162688	ENST00000361915;ENST00000370165;ENST00000370163;ENST00000294724;ENST00000361302;ENST00000370161;ENST00000361522	D;D;D;D;D;D;D	0.85171	-1.95;-1.95;-1.95;-1.95;-1.95;-1.95;-1.95	5.34	1.41	0.22369	Glycoside hydrolase, superfamily (1);	0.273612	0.36101	N	0.002797	T	0.60843	0.2300	L	0.39898	1.24	0.09310	N	0.999996	B;B;B	0.06786	0.001;0.001;0.0	B;B;B	0.14578	0.011;0.011;0.007	T	0.53760	-0.8393	10	0.30078	T	0.28	.	9.6993	0.40175	0.2549:0.0:0.7451:0.0	.	289;290;306	P35573-2;P35573-3;P35573	.;.;GDE_HUMAN	I	306;306;306;306;290;290;289	ENSP00000355106:V306I;ENSP00000359184:V306I;ENSP00000359182:V306I;ENSP00000294724:V306I;ENSP00000354971:V290I;ENSP00000359180:V290I;ENSP00000354635:V289I	ENSP00000294724:V306I	V	+	1	0	AGL	100108971	0.990000	0.36364	0.001000	0.08648	0.123000	0.20343	2.092000	0.41700	0.073000	0.16731	-0.796000	0.03273	GTC		TCGA-2L-AAQA-01A-21D-A38G-08	AGL-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029778.1	1	0	1	70	137	0	120	0	1.164730e-01	1	1	0	120	2		0	0	0	0	0	2	1	1.000000	70	136	0	119	2		0	0	0	0	120	2	-20.000000	1	1	121298	1	28	1	0	1	1	1.507771	1	0.600000	1.890000	0.431010	0.780000	6.400000e-01	0.930000	0.790000	0.790369	0.780000	0	7.000000e-01	8.600000e-01
AP4B1	10717	broad.mit.edu	37	1	114445373	114445373	+	Silent	SNP	A	A	G			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08			A	G	A	A		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr1:114445373A>G	ENST00000369569.1	-	2	505	c.225T>C	c.(223-225)taT>taC	p.Y75Y	AP4B1_ENST00000369567.1_Intron|AP4B1_ENST00000369566.3_Silent_p.Y75Y|AP4B1_ENST00000256658.4_Silent_p.Y75Y|AP4B1-AS1_ENST00000419536.1_RNA|DCLRE1B_ENST00000369563.3_5'Flank	NM_001253852.1	NP_001240781.1	Q9Y6B7	AP4B1_HUMAN	adaptor-related protein complex 4, beta 1 subunit			25	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.1e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05)			TCAGGGGAGCATATGTGCACA	0.498000																								0							SO:0001819	synonymous_variant			ENST00000369569.1	1	1	hg19	CCDS865.1																																																																																				TCGA-2L-AAQA-01A-21D-A38G-08	AP4B1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033037.1	1	0	0	135	158	0	149	1	9.999999e-01	33	1	0	149	2		0	0	0	0	0	2	1	1.000000	135	157	0	147	2		0	0	0	0	149	2	-20.000000	1	1	0	0		1	0	1	1	1.474776	1	0.600000	1.890000	0.440559	0.990000	9.200000e-01	1.000000	1.000000	0.990683	0.990000	1	9.700000e-01	1
ASTN1	460	broad.mit.edu	37	1	176833536	176833536	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr1:176833536C>T	ENST00000367654.3	-	23	4004	c.3793G>A	c.(3793-3795)Gag>Aag	p.E1265K	ASTN1_ENST00000367657.3_Intron|ASTN1_ENST00000361833.2_Missense_Mutation_p.E1257K	NM_004319.1	NP_004310.1	O14525	ASTN1_HUMAN	astrotactin 1			153					GGTTTGATCTCGCTGTAGCGG	0.587000																								0							SO:0001583	missense			ENST00000367654.3	1	1	hg19		.	.	.	.	.	.	.	.	.	.	C	25.1	4.600256	0.87055	.	.	ENSG00000152092	ENST00000361833;ENST00000367654	T;T	0.14022	2.55;2.54	4.61	4.61	0.57282	.	0.047461	0.85682	D	0.000000	T	0.09774	0.0240	L	0.27053	0.805	0.80722	D	1	P	0.50710	0.938	B	0.33454	0.164	T	0.12218	-1.0556	10	0.87932	D	0	-23.1216	17.4153	0.87498	0.0:1.0:0.0:0.0	.	1257	O14525-2	.	K	1257;1265	ENSP00000354536:E1257K;ENSP00000356626:E1265K	ENSP00000354536:E1257K	E	-	1	0	ASTN1	175100159	1.000000	0.71417	0.998000	0.56505	0.974000	0.67602	7.018000	0.76406	2.282000	0.76494	0.555000	0.69702	GAG		TCGA-2L-AAQA-01A-21D-A38G-08	ASTN1-201	KNOWN	basic	protein_coding	protein_coding		1	0	1	93	595	0	168		0	0	0	0	168	2		0	0	0	0	0	2	1	1.000000	92	586	0	164	2		0	0	0	0	168	2	-3.221886	1	1	121412	1	31	1	1	2	3	2.711459	1	0.600000	1.890000	0.692308	0.580000	4.700000e-01	0.700000	0.580000	0.589959	0.580000	0	5.200000e-01	6.500000e-01
COL24A1	255631	broad.mit.edu	37	1	86590761	86590761	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr1:86590761C>T	ENST00000370571.2	-	3	1624	c.1258G>A	c.(1258-1260)Gaa>Aaa	p.E420K	COL24A1_ENST00000436319.1_Missense_Mutation_p.E420K	NM_152890.5	NP_690850.2	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1	p.E420*(1)		101					TCCATGAGTTCGTTAGTGTGT	0.358000																								1	Substitution - Nonsense(1)						SO:0001583	missense			ENST00000370571.2	1	1	hg19	CCDS41353.1	.	.	.	.	.	.	.	.	.	.	C	9.195	1.026954	0.19512	.	.	ENSG00000171502	ENST00000370571;ENST00000436319	T;T	0.11821	2.74;2.74	5.45	3.24	0.37175	.	0.000000	0.40640	N	0.001059	T	0.02418	0.0074	N	0.19112	0.55	0.35766	D	0.820548	B;B	0.27791	0.189;0.046	B;B	0.25506	0.061;0.005	T	0.29119	-1.0022	10	0.07990	T	0.79	.	10.6098	0.45415	0.0:0.8214:0.0:0.1786	.	420;420	F8WDM8;Q17RW2	.;COOA1_HUMAN	K	420	ENSP00000359603:E420K;ENSP00000392531:E420K	ENSP00000359603:E420K	E	-	1	0	COL24A1	86363349	1.000000	0.71417	1.000000	0.80357	0.263000	0.26337	2.119000	0.41958	1.307000	0.44944	0.563000	0.77884	GAA		TCGA-2L-AAQA-01A-21D-A38G-08	COL24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029335.4	1	0	1	127	186	0	130		0	0	0	0	130	2		0	0	0	0	0	2	1	1.000000	126	182	0	130	2		0	0	0	0	130	2	-20.000000	1	1	120786	1	32	1	0	1	1	1.507771	1	0.600000	1.890000	0.431010	0.920000	8.100000e-01	1.000000	1.000000	0.929221	0.920000	1	8.700000e-01	9.800000e-01
TSHZ2	128553	broad.mit.edu	37	20	51871827	51871827	+	Silent	SNP	G	G	A	rs147016688	byFrequency	TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr20:51871827G>A	ENST00000371497.5	+	2	2717	c.1830G>A	c.(1828-1830)gcG>gcA	p.A610A	TSHZ2_ENST00000603338.2_Silent_p.A607A|TSHZ2_ENST00000329613.6_Silent_p.A607A|RP4-678D15.1_ENST00000606932.1_RNA	NM_001193421.1|NM_173485.5	NP_001180350.1|NP_775756.3	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	p.A610A(1)		84			STAD - Stomach adenocarcinoma(23;0.1)		AAGATGAAGCGGTGAAGGAGT	0.502000																								1	Substitution - coding silent(1)						SO:0001819	synonymous_variant			ENST00000371497.5	1	1	hg19	CCDS33490.1																																																																																				TCGA-2L-AAQA-01A-21D-A38G-08	TSHZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080398.6	1	0	1	130	397	0	164	0	3.622207e-01	0	5	0	164	2		0	0	0	0	0	2	1	1.000000	130	395	0	160	2		0	0	0	0	164	2	-5.034111	1	1	121412	9	46	1	0	0	0	2.045390	0	0.600000	1.890000	0.597586	0.810000	6.900000e-01	0.940000	0.810000	0.819403	0.810000	0	7.500000e-01	8.800000e-01
DSCAM	1826	broad.mit.edu	37	21	41385178	41385178	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr21:41385178G>A	ENST00000400454.1	-	33	6299	c.5822C>T	c.(5821-5823)aCg>aTg	p.T1941M		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule			142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)			CTCCAGGACCGTGGGGCGCTT	0.627000													Melanoma(134;970 1778 1785 21664 32388)											0							SO:0001583	missense			ENST00000400454.1	1	1	hg19	CCDS42929.1	.	.	.	.	.	.	.	.	.	.	.	19.61	3.860756	0.71834	.	.	ENSG00000171587	ENST00000400454;ENST00000404019	T;T	0.59638	0.25;0.36	5.29	5.29	0.74685	.	0.345440	0.33180	N	0.005197	T	0.38585	0.1046	N	0.08118	0	0.43073	D	0.994714	P	0.48640	0.913	B	0.36666	0.23	T	0.52931	-0.8509	10	0.72032	D	0.01	.	18.9499	0.92637	0.0:0.0:1.0:0.0	.	1941	O60469	DSCAM_HUMAN	M	1941;1675	ENSP00000383303:T1941M;ENSP00000385342:T1675M	ENSP00000383303:T1941M	T	-	2	0	DSCAM	40307048	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	9.219000	0.95173	2.464000	0.83262	0.557000	0.71058	ACG		TCGA-2L-AAQA-01A-21D-A38G-08	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	0	0	1	87	212	1	99		0	0	0	1	99	2		0	0	0	0	0	2	1	1.000000	87	208	1	97	12		0	0	0	1	99	2	-20.000000	1	1	120890	2	32	1	1	2	3	2.084981	0	0.600000	1.890000	0.601196	0.960000	8.000000e-01	1.000000	1.000000	0.951129	0.960000	1	8.800000e-01	1
TRIOBP	11078	broad.mit.edu	37	22	38153721	38153721	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr22:38153721G>A	ENST00000406386.3	+	16	6044	c.5789G>A	c.(5788-5790)cGg>cAg	p.R1930Q	TRIOBP_ENST00000403663.2_Missense_Mutation_p.R217Q|TRIOBP_ENST00000407319.2_Missense_Mutation_p.R217Q	NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein			12	Melanoma(58;0.0574)				GTCATCAGCCGGGGTGGCCCT	0.701000																								0							SO:0001583	missense			ENST00000406386.3	0	1	hg19	CCDS43015.1	.	.	.	.	.	.	.	.	.	.	G	24.7	4.561208	0.86335	.	.	ENSG00000100106	ENST00000406386;ENST00000407319;ENST00000403663;ENST00000418339;ENST00000417857	T	0.26957	1.7	5.5	5.5	0.81552	.	.	.	.	.	T	0.43055	0.1230	M	0.76574	2.34	0.31902	N	0.615782	D;D;D	0.71674	0.993;0.994;0.998	P;P;P	0.53760	0.713;0.734;0.608	T	0.56505	-0.7968	9	0.66056	D	0.02	.	13.1341	0.59399	0.0828:0.0:0.9172:0.0	.	217;217;1930	F8W6V6;F2Z2W0;Q9H2D6	.;.;TARA_HUMAN	Q	1930;217;217;176;146	ENSP00000384312:R1930Q	ENSP00000386026:R217Q	R	+	2	0	TRIOBP	36483667	0.999000	0.42202	0.997000	0.53966	0.785000	0.44390	3.643000	0.54374	2.580000	0.87095	0.555000	0.69702	CGG		TCGA-2L-AAQA-01A-21D-A38G-08	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2	1	0	1	11	14	0	11	1	1	131	133	0	11	2		0	0	0	0	0	2	1	0.999115	11	12	0	11	2		0	0	0	0	11	2	-20.000000	1	1	119488	4	28	1	1	2	3	2.121955	0	0.600000	1.890000	0.605911	0.990000	8.700000e-01	1.000000	1.000000	0.992558	0.990000	1	9.900000e-01	1
TRIOBP	11078	broad.mit.edu	37	22	38165362	38165362	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr22:38165362C>T	ENST00000406386.3	+	21	7084	c.6829C>T	c.(6829-6831)Cgg>Tgg	p.R2277W	TRIOBP_ENST00000403663.2_Missense_Mutation_p.R564W	NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein			12	Melanoma(58;0.0574)				CAGCAACGAGCGGAGTTCCTG	0.667000																								0							SO:0001583	missense			ENST00000406386.3	1	1	hg19	CCDS43015.1	.	.	.	.	.	.	.	.	.	.	C	16.69	3.193152	0.58017	.	.	ENSG00000100106	ENST00000406386;ENST00000403663	T	0.23950	1.88	4.96	0.994	0.19832	.	.	.	.	.	T	0.44265	0.1285	L	0.53249	1.67	0.44711	D	0.997706	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.79784	0.993;0.971;0.989;0.976	T	0.48305	-0.9047	9	0.87932	D	0	.	14.7584	0.69588	0.5226:0.4774:0.0:0.0	.	2179;266;564;2277	Q9H2D6-2;Q8TCM3;F8W6V6;Q9H2D6	.;.;.;TARA_HUMAN	W	2277;564	ENSP00000384312:R2277W	ENSP00000386026:R564W	R	+	1	2	TRIOBP	36495308	1.000000	0.71417	0.989000	0.46669	0.459000	0.32528	0.925000	0.28791	0.428000	0.26173	0.462000	0.41574	CGG		TCGA-2L-AAQA-01A-21D-A38G-08	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2	1	0	1	10	53	0	19	1	1	181	229	0	19	2		0	0	0	0	0	2	1	0.997463	9	53	0	18	2		0	0	0	0	19	2	-18.667730	1	1	120778	3	35	1	1	2	3	2.121955	0	0.600000	1.890000	0.605911	0.550000	2.900000e-01	1.000000	0.530000	0.582761	0.550000	0	4.100000e-01	7.500000e-01
UXS1	80146	broad.mit.edu	37	2	106710580	106710580	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr2:106710580G>A	ENST00000409501.3	-	15	1222	c.1165C>T	c.(1165-1167)Cac>Tac	p.H389Y	UXS1_ENST00000409032.1_Missense_Mutation_p.H221Y|UXS1_ENST00000283148.7_Missense_Mutation_p.H394Y|UXS1_ENST00000540130.1_Missense_Mutation_p.H332Y			Q8NBZ7	UXS1_HUMAN	UDP-glucuronate decarboxylase 1			17					CGGAAGTAGTGAATTGCTTTG	0.473000																								0							SO:0001583	missense			ENST00000409501.3	1	1	hg19	CCDS46378.1	.	.	.	.	.	.	.	.	.	.	G	17.04	3.287260	0.59867	.	.	ENSG00000115652	ENST00000283148;ENST00000540130;ENST00000409501;ENST00000409032	T;T;T;T	0.60548	0.18;0.18;0.18;0.18	5.68	5.68	0.88126	.	0.046027	0.85682	D	0.000000	T	0.54647	0.1871	L	0.43923	1.385	0.80722	D	1	B;B;B	0.19817	0.039;0.023;0.023	B;B;B	0.14578	0.011;0.005;0.008	T	0.51748	-0.8666	10	0.72032	D	0.01	-10.5314	19.7704	0.96361	0.0:0.0:1.0:0.0	.	394;389;394	Q8NBZ7-2;Q8NBZ7;A8K3Q3	.;UXS1_HUMAN;.	Y	394;332;389;221	ENSP00000283148:H394Y;ENSP00000438265:H332Y;ENSP00000387019:H389Y;ENSP00000387096:H221Y	ENSP00000283148:H394Y	H	-	1	0	UXS1	106077012	1.000000	0.71417	0.981000	0.43875	0.998000	0.95712	9.266000	0.95659	2.670000	0.90874	0.563000	0.77884	CAC		TCGA-2L-AAQA-01A-21D-A38G-08	UXS1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000329778.1	1	0	1	80	217	0	108	1	1	33	80	0	108	2		0	0	0	0	0	2	1	1.000000	80	214	0	108	2		0	0	0	0	108	2	-20.000000	1	1	0	0		1	0	0	0	2.070463	0	0.600000	1.890000	0.600000	0.890000	7.300000e-01	1.000000	1.000000	0.895344	0.890000	1	8.100000e-01	9.800000e-01
INHBB	3625	broad.mit.edu	37	2	121106698	121106698	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr2:121106698C>T	ENST00000295228.3	+	2	518	c.472C>T	c.(472-474)Cgc>Tgc	p.R158C		NM_002193.2	NP_002184.2	P09529	INHBB_HUMAN	inhibin, beta B			15		Prostate(154;0.122)			CTCCCGGGTCCGCCTATACTT	0.557000																								0							SO:0001583	missense			ENST00000295228.3	1	1	hg19	CCDS2132.1	.	.	.	.	.	.	.	.	.	.	C	16.25	3.070536	0.55539	.	.	ENSG00000163083	ENST00000295228	T	0.66995	-0.24	5.09	5.09	0.68999	Transforming growth factor-beta, N-terminal (1);	0.216528	0.39210	N	0.001426	T	0.61751	0.2372	L	0.54323	1.7	0.47698	D	0.999492	B	0.17667	0.023	B	0.12837	0.008	T	0.60667	-0.7218	10	0.59425	D	0.04	-3.9508	12.8184	0.57679	0.1636:0.8364:0.0:0.0	.	158	P09529	INHBB_HUMAN	C	158	ENSP00000295228:R158C	ENSP00000295228:R158C	R	+	1	0	INHBB	120823168	1.000000	0.71417	1.000000	0.80357	0.871000	0.50021	1.726000	0.38085	2.804000	0.96469	0.655000	0.94253	CGC		TCGA-2L-AAQA-01A-21D-A38G-08	INHBB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254234.1	1	0	1	109	283	0	155	0	8.852491e-01	0	12	0	155	2		0	0	0	0	0	2	1	1.000000	109	281	0	153	2		0	0	0	0	155	2	-7.065246	1	1	121410	1	32	1	0	0	0	2.070463	0	0.600000	1.890000	0.600000	0.920000	7.700000e-01	1.000000	1.000000	0.921713	0.920000	1	8.400000e-01	1
TRIB2	28951	broad.mit.edu	37	2	12858610	12858610	+	Silent	SNP	T	T	G			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08			T	G	T	T		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr2:12858610T>G	ENST00000405331.3	+	1	247	c.177T>G	c.(175-177)tcT>tcG	p.S59S	TRIB2_ENST00000155926.4_Silent_p.S59S|TRIB2_ENST00000381465.2_Intron|RP11-333O1.1_ENST00000569860.1_lincRNA					tribbles pseudokinase 2			19	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)				ATTGCGTTTCTTGTATCGGGA	0.567000											OREG0014450	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)												0							SO:0001819	synonymous_variant			ENST00000405331.3	1	1	hg19																																																																																					TCGA-2L-AAQA-01A-21D-A38G-08	TRIB2-004	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000323585.1	1	0	1	146	370	0	151	1	1	26	51	0	151	2		0	0	0	0	0	2	1	1.000000	143	366	0	150	2		0	0	0	0	151	2	-20.000000	1	1	0	0		1	0	0	0	2.066531	0	0.600000	1.890000	0.600000	0.930000	8.100000e-01	1.000000	1.000000	0.937002	0.930000	1	8.700000e-01	1
ITGA6	3655	broad.mit.edu	37	2	173333979	173333979	+	Missense_Mutation	SNP	T	T	A			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08			T	A	T	T		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr2:173333979T>A	ENST00000264106.6	+	4	717	c.514T>A	c.(514-516)Tgg>Agg	p.W172R	ITGA6_ENST00000409532.1_Missense_Mutation_p.W58R|ITGA6_ENST00000264107.7_Missense_Mutation_p.W172R|ITGA6_ENST00000409080.1_Missense_Mutation_p.W172R|ITGA6_ENST00000375221.2_Missense_Mutation_p.W172R|ITGA6_ENST00000343713.4_Missense_Mutation_p.W172R			P23229	ITA6_HUMAN	integrin, alpha 6			44			OV - Ovarian serous cystadenocarcinoma(117;0.0979)		TGGGGGAGATTGGAGCTTTTG	0.448000																								0							SO:0001583	missense			ENST00000264106.6	1	1	hg19		.	.	.	.	.	.	.	.	.	.	T	18.32	3.597715	0.66332	.	.	ENSG00000091409	ENST00000412899;ENST00000409532;ENST00000264107;ENST00000264106;ENST00000375221;ENST00000343713;ENST00000409080;ENST00000442250;ENST00000458358	T;T;T;T;T;T;T;T;T	0.54675	0.56;0.56;0.56;0.56;0.56;0.56;0.56;0.56;0.56	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.68943	0.3056	M	0.77406	2.37	0.80722	D	1	B;B;P	0.43578	0.313;0.448;0.811	B;P;P	0.54346	0.279;0.55;0.749	T	0.66748	-0.5845	10	0.33141	T	0.24	.	16.8222	0.85835	0.0:0.0:0.0:1.0	.	172;172;172	P23229-4;G5E9H1;P23229-2	.;.;.	R	58;58;172;172;172;172;172;172;172	ENSP00000413470:W58R;ENSP00000386614:W58R;ENSP00000264107:W172R;ENSP00000264106:W172R;ENSP00000364369:W172R;ENSP00000341078:W172R;ENSP00000386896:W172R;ENSP00000406694:W172R;ENSP00000394169:W172R	ENSP00000264106:W172R	W	+	1	0	ITGA6	173042225	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.040000	0.89188	2.371000	0.80710	0.533000	0.62120	TGG		TCGA-2L-AAQA-01A-21D-A38G-08	ITGA6-201	KNOWN	basic	protein_coding	protein_coding		1	0	1	225	514	0	249	1	1	43	103	0	249	2		0	0	0	0	0	2	1	1.000000	223	501	0	247	2		0	0	0	0	249	2	-14.468880	1	1	0	0		1	0	0	0	2.070463	0	0.600000	1.890000	0.600000	0.990000	9.000000e-01	1.000000	1.000000	0.984398	0.990000	1	9.500000e-01	1
PPM1G	5496	broad.mit.edu	37	2	27607706	27607706	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr2:27607706C>T	ENST00000344034.4	-	5	923	c.659G>A	c.(658-660)cGt>cAt	p.R220H	PPM1G_ENST00000350803.4_Missense_Mutation_p.R220H	NM_177983.2	NP_817092.1	O15355	PPM1G_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1G			19	Acute lymphoblastic leukemia(172;0.155)				CTCAGTCCCACGTTCCGAGTT	0.572000																								0							SO:0001583	missense			ENST00000344034.4	1	1	hg19	CCDS1752.1	.	.	.	.	.	.	.	.	.	.	C	10.38	1.335465	0.24253	.	.	ENSG00000115241	ENST00000344034;ENST00000350803;ENST00000544412	T;T	0.44083	0.93;0.93	5.75	2.95	0.34219	Protein phosphatase 2C-like (3);	0.608394	0.16245	N	0.222966	T	0.27663	0.0680	L	0.36672	1.1	0.27600	N	0.948996	B	0.02656	0.0	B	0.01281	0.0	T	0.21245	-1.0251	10	0.21014	T	0.42	0.2289	5.1636	0.15073	0.0:0.5481:0.1408:0.3111	.	220	O15355	PPM1G_HUMAN	H	220;220;203	ENSP00000342778:R220H;ENSP00000264714:R220H	ENSP00000342778:R220H	R	-	2	0	PPM1G	27461210	0.997000	0.39634	0.997000	0.53966	0.986000	0.74619	1.019000	0.30014	0.348000	0.23949	0.655000	0.94253	CGT		TCGA-2L-AAQA-01A-21D-A38G-08	PPM1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215032.1	1	0	0	16	398	0	113	1	9.996773e-01	11	322	0	113	2		0	0	0	0	0	2	1	0.999922	16	388	0	112	2		0	0	0	0	113	2	-4.127870	1	1	0	0		1	0	0	0	2.066531	0	0.600000	1.890000	0.600000	0.120000	7.000000e-02	0.200000	0.130000	0.135982	0.120000	0	9.000000e-02	1.700000e-01
FANCD2	2177	broad.mit.edu	37	3	10107621	10107621	+	Silent	SNP	C	C	T			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr3:10107621C>T	ENST00000419585.1	+	25	2504	c.2343C>T	c.(2341-2343)ttC>ttT	p.F781F	FANCD2_ENST00000287647.3_Silent_p.F781F|FANCD2_ENST00000383806.1_Silent_p.F781F|FANCD2_ENST00000383807.1_Silent_p.F781F			Q9BXW9	FACD2_HUMAN	Fanconi anemia, complementation group D2			51					AGCGTTCATTCATGTGTTCTC	0.393000			D, Mis, N, F			AML, leukemia		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia					yes	Rec		Fanconi anaemia D2	3	3p26	2177	Fanconi anemia, complementation group D2		L	0							SO:0001819	synonymous_variant	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	ENST00000419585.1	1	1	hg19	CCDS33696.1																																																																																				TCGA-2L-AAQA-01A-21D-A38G-08	FANCD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339873.1	1	0	1	62	218	0	90	1	9.137255e-01	6	11	0	90	2		0	0	0	0	0	2	1	1.000000	60	217	0	90	2		0	0	0	0	90	2	-20.000000	1	1	0	0		1	0	0	0	2.047777	0	0.600000	1.890000	0.597586	0.730000	5.700000e-01	0.890000	0.730000	0.738402	0.730000	0	6.500000e-01	8.200000e-01
GPR156	165829	broad.mit.edu	37	3	119962542	119962542	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr3:119962542C>T	ENST00000464295.1	-	3	623	c.178G>A	c.(178-180)Gga>Aga	p.G60R	GPR156_ENST00000461057.1_Missense_Mutation_p.G60R|GPR156_ENST00000315843.3_Missense_Mutation_p.G60R			Q8NFN8	GP156_HUMAN	G protein-coupled receptor 156			32					AGCAGAAGTCCACAGCTGAGA	0.433000																								0							SO:0001583	missense			ENST00000464295.1	1	1	hg19	CCDS2997.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.949646	0.73787	.	.	ENSG00000175697	ENST00000464295;ENST00000315843;ENST00000461057	D;D;D	0.91945	-2.94;-2.94;-2.94	5.2	4.31	0.51392	GPCR, family 3, C-terminal (2);	0.089971	0.46758	D	0.000261	D	0.95974	0.8689	M	0.88512	2.96	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.75020	0.985;0.985	D	0.95894	0.8909	9	.	.	.	-13.3173	10.9026	0.47059	0.187:0.813:0.0:0.0	.	60;60	E9PFZ4;Q8NFN8	.;GP156_HUMAN	R	60	ENSP00000417261:G60R;ENSP00000324553:G60R;ENSP00000418758:G60R	.	G	-	1	0	GPR156	121445232	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.539000	0.60657	1.385000	0.46445	0.650000	0.86243	GGA		TCGA-2L-AAQA-01A-21D-A38G-08	GPR156-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355139.1	1	0	1	118	273	0	127	0	0	0	1	0	127	2		0	0	0	0	0	2	1	1.000000	118	271	0	122	2		0	0	0	0	127	2	-8.936694	1	1	0	0		1	0	0	0	2.047777	0	0.600000	1.890000	0.597586	0.990000	8.400000e-01	1.000000	1.000000	0.970078	0.990000	1	9.100000e-01	1
PIK3CA	5290	broad.mit.edu	37	3	178936074	178936074	+	Missense_Mutation	SNP	C	C	G	rs121913285		TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08			C	G	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr3:178936074C>G	ENST00000263967.3	+	10	1773	c.1616C>G	c.(1615-1617)cCt>cGt	p.P539R		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	p.P539R(17)		5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)	Caffeine(DB00201)	ACACGAGATCCTCTCTCTGAA	0.328000	P539R(BT20_BREAST)|P539R(MFE296_ENDOMETRIUM)	57	Mis		colorectal, gastric, gliobastoma, breast					HNSCC(19;0.045)|TSP Lung(28;0.18)			Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	phosphoinositide-3-kinase, catalytic, alpha polypeptide		E, O	17	Substitution - Missense(17)						SO:0001583	missense			ENST00000263967.3	1	1	hg19	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	C	29.2	4.987372	0.93106	.	.	ENSG00000121879	ENST00000263967	D	0.89270	-2.49	5.78	5.78	0.91487	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.94466	0.8219	M	0.80332	2.49	0.80722	D	1	D	0.59357	0.985	D	0.63192	0.912	D	0.94197	0.7446	10	0.59425	D	0.04	-26.0829	20.0024	0.97423	0.0:1.0:0.0:0.0	.	539	P42336	PK3CA_HUMAN	R	539	ENSP00000263967:P539R	ENSP00000263967:P539R	P	+	2	0	PIK3CA	180418768	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.487000	0.81328	2.722000	0.93159	0.467000	0.42956	CCT		TCGA-2L-AAQA-01A-21D-A38G-08	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2	1	0	1	87	251	0	103	1	9.932764e-01	9	16	0	103	2		0	0	0	0	0	2	1	1.000000	82	242	0	105	2		0	0	0	0	103	2	-5.078832	1	1	0	0		1	1	2	3	2.084391	0	0.600000	1.890000	0.601196	0.850000	7.000000e-01	1.000000	1.000000	0.862002	0.850000	1	7.700000e-01	9.400000e-01
TOP2B	7155	broad.mit.edu	37	3	25674236	25674236	+	Missense_Mutation	SNP	A	A	G			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr3:25674236A>G	ENST00000264331.4	-	9	1075	c.1076T>C	c.(1075-1077)aTt>aCt	p.I359T	TOP2B_ENST00000435706.2_Missense_Mutation_p.I354T	NM_001068.2	NP_001059.2	Q02880	TOP2B_HUMAN	topoisomerase (DNA) II beta 180kDa			36				Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Etoposide(DB00773)	AACTACTTCAATCAGTTTACC	0.328000																								0							SO:0001583	missense			ENST00000264331.4	0	1	hg19		.	.	.	.	.	.	.	.	.	.	A	17.51	3.408676	0.62399	.	.	ENSG00000077097	ENST00000435706;ENST00000264331;ENST00000424225	T;T	0.46063	0.88;0.88	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	T	0.43233	0.1238	L	0.53561	1.675	0.80722	D	1	B	0.25048	0.117	B	0.29440	0.102	T	0.37337	-0.9710	10	0.54805	T	0.06	-15.1386	15.4062	0.74881	1.0:0.0:0.0:0.0	.	354	Q02880-2	.	T	354;359;354	ENSP00000396704:I354T;ENSP00000264331:I359T	ENSP00000264331:I359T	I	-	2	0	TOP2B	25649240	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.059000	0.93902	2.032000	0.59987	0.528000	0.53228	ATT		TCGA-2L-AAQA-01A-21D-A38G-08	TOP2B-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		0	0	0	11	657	0	209	0	1.635157e-01	0	40	0	209	2		0	0	0	0	0	2	1	0.998218	11	648	0	205	2		0	0	0	0	209	2	-3.327245	1	1	120794	1	34	1	0	0	0	2.047777	0	0.600000	1.890000	0.597586	0.050000	2.000000e-02	0.100000	0.060000	0.059260	0.050000	0	3.000000e-02	8.000000e-02
ITPR1	3708	broad.mit.edu	37	3	4722339	4722339	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr3:4722339G>A	ENST00000443694.2	+	22	3025	c.3025G>A	c.(3025-3027)Gga>Aga	p.G1009R	ITPR1_ENST00000354582.6_Missense_Mutation_p.G1024R|ITPR1_ENST00000357086.4_Missense_Mutation_p.G1015R|ITPR1_ENST00000423119.2_Missense_Mutation_p.G1015R|ITPR1_ENST00000456211.2_Missense_Mutation_p.G1000R|ITPR1_ENST00000302640.8_Missense_Mutation_p.G1009R|ITPR1_ENST00000544951.1_Intron			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1			106				Caffeine(DB00201)	AACATCCTCCGGAAACAGCAG	0.433000																								0							SO:0001583	missense			ENST00000443694.2	1	1	hg19	CCDS54551.1	.	.	.	.	.	.	.	.	.	.	G	14.99	2.700462	0.48307	.	.	ENSG00000150995	ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000357086;ENST00000456211;ENST00000443694	T;T;T;T;T;T	0.54866	0.55;0.55;0.55;0.55;0.55;0.55	5.56	5.56	0.83823	.	0.236966	0.43260	D	0.000598	T	0.50735	0.1633	M	0.69358	2.11	0.80722	D	1	B;B;P	0.36837	0.308;0.311;0.571	B;B;B	0.32090	0.027;0.02;0.14	T	0.50320	-0.8842	10	0.26408	T	0.33	.	17.7004	0.88293	0.0:0.0:1.0:0.0	.	1009;1024;1015	E7EPX7;Q14643;G5E9P1	.;ITPR1_HUMAN;.	R	1024;1009;1024;1015;1015;1000;1009	ENSP00000306253:G1009R;ENSP00000346595:G1024R;ENSP00000405934:G1015R;ENSP00000349597:G1015R;ENSP00000397885:G1000R;ENSP00000401671:G1009R	ENSP00000306253:G1009R	G	+	1	0	ITPR1	4697339	1.000000	0.71417	0.968000	0.41197	0.959000	0.62525	6.688000	0.74557	2.599000	0.87857	0.591000	0.81541	GGA		TCGA-2L-AAQA-01A-21D-A38G-08	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	0	0	1	65	128	1	67	0	1.156986e-01	0	2	1	67	2		0	0	0	0	0	2	1	1.000000	65	126	1	67	11		0	0	0	1	67	2	-20.000000	1	1	0	0		1	0	0	0	2.047777	0	0.600000	1.890000	0.597586	0.990000	8.900000e-01	1.000000	1.000000	0.992010	0.990000	1	9.900000e-01	1
DCHS2	54798	broad.mit.edu	37	4	155156138	155156138	+	Silent	SNP	C	C	T			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr4:155156138C>T	ENST00000357232.4	-	25	8300	c.8301G>A	c.(8299-8301)acG>acA	p.T2767T		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2			176	all_hematologic(180;0.208)	Renal(120;0.0854)			GATCAGAGGTCGTCTGAGTTG	0.418000																								0							SO:0001819	synonymous_variant			ENST00000357232.4	1	1	hg19	CCDS3785.1																																																																																				TCGA-2L-AAQA-01A-21D-A38G-08	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	0	0	0	12	301	0	151		0	0	0	0	151	2		0	0	0	0	0	2	1	0.999129	12	299	0	150	2		0	0	0	0	151	2	-3.831311	1	1	121408	1	36	1	0	1	1	1.574951	1	0.600000	1.890000	0.454297	0.090000	4.000000e-02	0.160000	0.090000	0.100455	0.090000	0	6.000000e-02	1.300000e-01
CTNND2	1501	broad.mit.edu	37	5	10973809	10973809	+	Missense_Mutation	SNP	A	A	C			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr5:10973809A>C	ENST00000304623.8	-	22	3623	c.3434T>G	c.(3433-3435)gTc>gGc	p.V1145G	CTNND2_ENST00000503622.1_Missense_Mutation_p.V808G|CTNND2_ENST00000458100.2_Missense_Mutation_p.V712G|CTNND2_ENST00000511377.1_Missense_Mutation_p.V1054G|CTNND2_ENST00000359640.2_Missense_Mutation_p.V1087G|CTNND2_ENST00000495388.2_5'UTR	NM_001332.2	NP_001323.1	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2			136					CTCCTGTGGGACTGGCTGTGC	0.522000																								0							SO:0001583	missense			ENST00000304623.8	1	1	hg19	CCDS3881.1	.	.	.	.	.	.	.	.	.	.	A	6.986	0.551943	0.13374	.	.	ENSG00000169862	ENST00000304623;ENST00000359640;ENST00000511377;ENST00000538638;ENST00000458100;ENST00000503622	T;T;T;T;T	0.78595	-1.08;-1.15;-1.07;-1.19;-1.19	5.93	2.29	0.28610	.	0.757929	0.12479	N	0.465306	T	0.57021	0.2025	N	0.08118	0	0.80722	D	1	B;B;B	0.26318	0.002;0.035;0.146	B;B;B	0.24974	0.004;0.012;0.057	T	0.35943	-0.9768	10	0.26408	T	0.33	-15.0539	9.4259	0.38578	0.8:0.0:0.2:0.0	.	808;737;1145	B4DRK2;B4DG58;Q9UQB3	.;.;CTND2_HUMAN	G	1145;1087;1054;240;712;808	ENSP00000307134:V1145G;ENSP00000352661:V1087G;ENSP00000426510:V1054G;ENSP00000391155:V712G;ENSP00000426887:V808G	ENSP00000307134:V1145G	V	-	2	0	CTNND2	11026809	1.000000	0.71417	0.990000	0.47175	0.996000	0.88848	4.062000	0.57492	0.162000	0.19483	0.533000	0.62120	GTC		TCGA-2L-AAQA-01A-21D-A38G-08	CTNND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206999.1	0	0	1	85	209	0	111		0	0	0	0	111	2		0	0	0	0	0	2	1	1.000000	83	206	0	110	2		0	0	0	0	111	2	-20.000000	1	1	0	0		1	0	1	1	2.058923	0	0.600000	1.890000	0.598796	0.950000	7.900000e-01	1.000000	1.000000	0.943457	0.950000	1	8.700000e-01	1
SRFBP1	153443	broad.mit.edu	37	5	121362757	121362757	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr5:121362757G>A	ENST00000339397.4	+	8	1298	c.1226G>A	c.(1225-1227)aGg>aAg	p.R409K	SRFBP1_ENST00000504881.1_Intron	NM_152546.2	NP_689759.2			serum response factor binding protein 1			15		all_cancers(142;0.0124)|Prostate(80;0.0322)	KIRC - Kidney renal clear cell carcinoma(527;0.206)		GCAAGCAGAAGGCGAAAAGAA	0.368000																								0							SO:0001583	missense			ENST00000339397.4	1	1	hg19	CCDS43354.1	.	.	.	.	.	.	.	.	.	.	G	11.20	1.569176	0.28003	.	.	ENSG00000151304	ENST00000339397	.	.	.	5.76	-0.243	0.13035	Bud-site selection protein, BUD22 (1);	0.337294	0.36303	N	0.002678	T	0.30479	0.0766	N	0.16368	0.405	0.34634	D	0.719936	B	0.17038	0.02	B	0.17433	0.018	T	0.29366	-1.0014	9	0.13853	T	0.58	-6.0429	11.318	0.49403	0.5482:0.0:0.4518:0.0	.	409	Q8NEF9	SRFB1_HUMAN	K	409	.	ENSP00000341324:R409K	R	+	2	0	SRFBP1	121390656	1.000000	0.71417	0.984000	0.44739	0.962000	0.63368	1.433000	0.34947	0.003000	0.14656	0.655000	0.94253	AGG		TCGA-2L-AAQA-01A-21D-A38G-08	SRFBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371200.1	1	0	1	130	228	0	121	1	9.999987e-01	27	12	0	121	2		0	0	0	0	0	2	1	1.000000	129	222	0	120	2		0	0	0	0	121	2	-20.000000	1	1	0	0		1	0	1	1	2.058923	0	0.600000	1.890000	0.598796	0.990000	9.900000e-01	1.000000	1.000000	0.999849	0.990000	1	9.900000e-01	1
DND1	373863	broad.mit.edu	37	5	140052939	140052939	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr5:140052939G>A	ENST00000542735.1	-	2	102	c.59C>T	c.(58-60)gCg>gTg	p.A20V	HARS_ENST00000504156.1_3'UTR	NM_194249.2	NP_919225.1	Q8IYX4	DND1_HUMAN	DND microRNA-mediated repression inhibitor 1			5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		CTCCAGCGCCGCCTTGTTCTC	0.642000																								0							SO:0001583	missense			ENST00000542735.1	1	1	hg19	CCDS4236.1	.	.	.	.	.	.	.	.	.	.	G	13.62	2.290610	0.40494	.	.	ENSG00000256453	ENST00000542735	T	0.34859	1.34	4.58	4.58	0.56647	.	0.209202	0.33457	N	0.004895	T	0.20333	0.0489	N	0.20574	0.59	0.80722	D	1	P	0.35401	0.499	B	0.23716	0.048	T	0.06516	-1.0822	10	0.37606	T	0.19	-6.6743	12.0698	0.53609	0.0868:0.0:0.9132:0.0	.	20	Q8IYX4	DND1_HUMAN	V	20	ENSP00000445366:A20V	ENSP00000445366:A20V	A	-	2	0	DND1	140033123	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	2.251000	0.43187	2.358000	0.79984	0.462000	0.41574	GCG		TCGA-2L-AAQA-01A-21D-A38G-08	DND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251669.2	1	0	0	86	331	0	125	1	9.943920e-01	12	21	0	125	2		0	0	0	0	0	2	1	1.000000	84	327	0	122	2		0	0	0	0	125	2	-20.000000	1	1	0	0		1	0	1	1	2.058923	0	0.600000	1.890000	0.598796	0.680000	5.500000e-01	0.810000	0.680000	0.688942	0.680000	0	6.100000e-01	7.500000e-01
PCDHGA5	56110	broad.mit.edu	37	5	140745619	140745619	+	Silent	SNP	C	C	T			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr5:140745619C>T	ENST00000518069.1	+	1	1722	c.1722C>T	c.(1720-1722)ggC>ggT	p.G574G	PCDHGA4_ENST00000571252.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018918.2|NM_032054.1	NP_061741.1|NP_114443.1	Q9Y5G8	PCDG5_HUMAN	protocadherin gamma subfamily A, 5			18			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		GTTCCACGGGCGTGGAGCTGG	0.622000																								0							SO:0001819	synonymous_variant			ENST00000518069.1	1	1	hg19	CCDS54925.1																																																																																				TCGA-2L-AAQA-01A-21D-A38G-08	PCDHGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374742.1	1	0	1	286	609	0	295	0	6.197435e-01	1	5	0	295	2		0	0	0	0	0	2	1	1.000000	283	598	0	293	2		0	0	0	0	295	2	-20.000000	1	1	0	0		1	0	1	1	2.058923	0	0.600000	1.890000	0.598796	0.990000	9.500000e-01	1.000000	1.000000	0.997153	0.990000	1	9.900000e-01	1
FAT2	2196	broad.mit.edu	37	5	150885588	150885588	+	Silent	SNP	G	G	A			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr5:150885588G>A	ENST00000261800.5	-	23	12600	c.12588C>T	c.(12586-12588)tcC>tcT	p.S4196S		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2			196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		GAGTCACTTCGGAGTGGGGGT	0.622000																								0							SO:0001819	synonymous_variant			ENST00000261800.5	1	1	hg19	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	G	0.702	-0.790312	0.02884	.	.	ENSG00000086570	ENST00000520200	.	.	.	5.02	-5.86	0.02304	.	.	.	.	.	.	.	.	.	.	.	0.29771	N	0.83475	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.4588	0.27283	0.3167:0.2335:0.4498:0.0	.	.	.	.	X	969	.	.	R	-	1	2	FAT2	150865781	0.000000	0.05858	0.001000	0.08648	0.120000	0.20174	-2.499000	0.00968	-0.718000	0.04949	-0.459000	0.05422	CGA		TCGA-2L-AAQA-01A-21D-A38G-08	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	1	0	1	162	409	0	249	0	0	0	1	0	249	2		0	0	0	0	0	2	1	1.000000	161	399	0	248	2		0	0	0	0	249	2	-9.212538	1	1	0	0		1	0	1	1	2.058923	0	0.600000	1.890000	0.598796	0.930000	8.100000e-01	1.000000	1.000000	0.937584	0.930000	1	8.700000e-01	1
FAT2	2196	broad.mit.edu	37	5	150923873	150923873	+	Missense_Mutation	SNP	A	A	G			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr5:150923873A>G	ENST00000261800.5	-	9	6827	c.6815T>C	c.(6814-6816)tTt>tCt	p.F2272S		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2			196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		CAATTGGGAAAAAGTGGGAGG	0.517000																								0							SO:0001583	missense			ENST00000261800.5	0	1	hg19	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	A	17.95	3.513047	0.64522	.	.	ENSG00000086570	ENST00000261800	T	0.32023	1.47	5.68	5.68	0.88126	Cadherin (2);Cadherin-like (1);	0.000000	0.64402	D	0.000002	T	0.69860	0.3158	H	0.96604	3.85	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.81348	-0.0973	10	0.87932	D	0	.	15.938	0.79729	1.0:0.0:0.0:0.0	.	2272	Q9NYQ8	FAT2_HUMAN	S	2272	ENSP00000261800:F2272S	ENSP00000261800:F2272S	F	-	2	0	FAT2	150904066	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	9.252000	0.95491	2.167000	0.68274	0.459000	0.35465	TTT		TCGA-2L-AAQA-01A-21D-A38G-08	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	0	0	0	9	430	1	137	0	0	0	1	1	137	2		0	0	0	0	0	2	0	0.314426	8	424	1	136	12		0	0	0	1	137	2	-8.826884	1	1	0	0		1	0	1	1	2.058923	0	0.600000	1.890000	0.598796	0.060000	2.000000e-02	0.130000	0.070000	0.075243	0.060000	0	4.000000e-02	1.000000e-01
SGCD	6444	broad.mit.edu	37	5	155771526	155771526	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr5:155771526C>T	ENST00000435422.3	+	2	515	c.28C>T	c.(28-30)Cgg>Tgg	p.R10W	SGCD_ENST00000447401.1_Missense_Mutation_p.R11W|SGCD_ENST00000517913.1_Missense_Mutation_p.R11W|SGCD_ENST00000337851.4_Missense_Mutation_p.R11W	NM_001128209.1	NP_001121681.1	Q92629	SGCD_HUMAN	sarcoglycan, delta (35kDa dystrophin-associated glycoprotein)			24	Renal(175;0.00488)	Medulloblastoma(196;0.0378)|all_neural(177;0.106)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)		CACTCACCACCGGAGCACCAT	0.478000																								0							SO:0001583	missense			ENST00000435422.3	1	1	hg19	CCDS47327.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.212095	0.79240	.	.	ENSG00000170624	ENST00000517913;ENST00000435422;ENST00000337851;ENST00000447401	T;D;D;T	0.86694	1.41;-2.15;-2.16;1.41	5.59	2.34	0.29019	.	0.051785	0.64402	D	0.000001	D	0.91297	0.7256	L	0.60455	1.87	0.58432	D	0.999998	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.99;0.996;0.999	D	0.91387	0.5132	10	0.72032	D	0.01	0.2039	14.2572	0.66060	0.5847:0.4153:0.0:0.0	.	10;11;11	Q92629;Q92629-2;Q92629-3	SGCD_HUMAN;.;.	W	11;10;11;11	ENSP00000429378:R11W;ENSP00000403003:R10W;ENSP00000338343:R11W;ENSP00000408324:R11W	ENSP00000338343:R11W	R	+	1	2	SGCD	155704104	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	1.486000	0.35530	0.624000	0.30286	0.655000	0.94253	CGG		TCGA-2L-AAQA-01A-21D-A38G-08	SGCD-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000373469.3	1	0	1	83	231	0	132	0	5.914051e-01	0	7	0	132	2		0	0	0	0	0	2	1	1.000000	83	225	0	132	2		0	0	0	0	132	2	-5.335612	1	1	120894	5	37	1	0	1	1	2.058923	0	0.600000	1.890000	0.598796	0.870000	7.100000e-01	1.000000	1.000000	0.878408	0.870000	1	7.900000e-01	9.600000e-01
HK3	3101	broad.mit.edu	37	5	176318141	176318141	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr5:176318141C>T	ENST00000292432.5	-	4	402	c.311G>A	c.(310-312)cGt>cAt	p.R104H		NM_002115.2	NP_002106.2	P52790	HXK3_HUMAN	hexokinase 3 (white cell)			47	all_cancers(89;0.000104)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		CCACAAAACACGCAGTGAGGC	0.602000																								0							SO:0001583	missense			ENST00000292432.5	1	1	hg19	CCDS4407.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.504410	0.85176	.	.	ENSG00000160883	ENST00000292432	D	0.99724	-6.54	4.96	4.96	0.65561	Hexokinase, N-terminal (1);	0.000000	0.51477	D	0.000081	D	0.99664	0.9875	M	0.87900	2.915	0.32374	N	0.55541	D	0.71674	0.998	D	0.62955	0.909	D	0.97938	1.0324	10	0.62326	D	0.03	-7.6649	17.1545	0.86787	0.0:1.0:0.0:0.0	.	104	P52790	HXK3_HUMAN	H	104	ENSP00000292432:R104H	ENSP00000292432:R104H	R	-	2	0	HK3	176250747	0.996000	0.38824	0.984000	0.44739	0.870000	0.49936	4.152000	0.58111	2.460000	0.83146	0.561000	0.74099	CGT		TCGA-2L-AAQA-01A-21D-A38G-08	HK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253428.1	1	0	1	103	254	0	95	0	6.460933e-01	0	7	0	95	2		0	0	0	0	0	2	1	1.000000	102	249	0	94	2		0	0	0	0	95	2	-20.000000	1	1	121410	7	39	1	0	1	1	2.058923	0	0.600000	1.890000	0.598796	0.950000	8.000000e-01	1.000000	1.000000	0.944724	0.950000	1	8.700000e-01	1
OR2Y1	134083	broad.mit.edu	37	5	180166545	180166545	+	Nonsense_Mutation	SNP	G	G	A			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr5:180166545G>A	ENST00000307832.2	-	1	554	c.514C>T	c.(514-516)Cga>Tga	p.R172*		NM_001001657.1	NP_001001657.1	Q8NGV0	OR2Y1_HUMAN	olfactory receptor, family 2, subfamily Y, member 1			20	all_cancers(89;1.25e-05)|all_epithelial(37;4.36e-06)|Renal(175;0.000159)|Lung NSC(126;0.00317)|all_lung(126;0.0041)|Breast(19;0.114)	all_cancers(40;0.0834)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		TGATTCAGTCGATGGCCACAG	0.542000																								0							SO:0001587	stop_gained			ENST00000307832.2	0	1	hg19	CCDS34323.1	.	.	.	.	.	.	.	.	.	.	g	17.19	3.327676	0.60743	0.0	1.16E-4	ENSG00000174339	ENST00000307832	.	.	.	4.41	2.59	0.31030	.	3.529880	0.00714	N	0.000849	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.0741	0.25195	0.0936:0.0:0.7351:0.1713	.	.	.	.	X	172	.	ENSP00000312403:R172X	R	-	1	2	OR2Y1	180099151	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.967000	0.01508	0.572000	0.29383	0.511000	0.50034	CGA		TCGA-2L-AAQA-01A-21D-A38G-08	OR2Y1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368059.2	1	0	1	79	147	0	80		0	0	0	0	80	2		0	0	0	0	0	2	1	1.000000	79	146	0	80	2		0	0	0	0	80	2	-20.000000	1	1	121412	1	28	1	0	1	1	2.058923	0	0.600000	1.890000	0.598796	0.990000	9.500000e-01	1.000000	1.000000	0.997567	0.990000	1	9.900000e-01	1
PPWD1	23398	broad.mit.edu	37	5	64868000	64868000	+	Missense_Mutation	SNP	G	G	A	rs150307628		TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr5:64868000G>A	ENST00000261308.5	+	5	928	c.856G>A	c.(856-858)Gta>Ata	p.V286I	PPWD1_ENST00000535264.1_Missense_Mutation_p.V256I|PPWD1_ENST00000538977.1_Missense_Mutation_p.V130I	NM_015342.3	NP_056157.1	Q96BP3	PPWD1_HUMAN	peptidylprolyl isomerase domain and WD repeat containing 1			19		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)			TCCAACCAGCGTATGTTTTTC	0.348000																								0							SO:0001583	missense			ENST00000261308.5	1	1	hg19	CCDS3985.1	.	.	.	.	.	.	.	.	.	.	A	8.826	0.938643	0.18206	2.27E-4	3.49E-4	ENSG00000113593	ENST00000261308;ENST00000535264;ENST00000538977;ENST00000505380	T;T;T;T	0.61040	0.14;0.14;0.14;0.14	5.59	5.59	0.84812	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.098404	0.64402	N	0.000003	T	0.44095	0.1277	L	0.38838	1.175	0.09310	N	0.999997	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.28808	-1.0032	10	0.09338	T	0.73	.	11.6254	0.51142	0.9304:0.0:0.0695:0.0	.	256;286	F5H7P7;Q96BP3	.;PPWD1_HUMAN	I	286;256;130;205	ENSP00000261308:V286I;ENSP00000442371:V256I;ENSP00000444496:V130I;ENSP00000423234:V205I	ENSP00000261308:V286I	V	+	1	0	PPWD1	64903756	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.661000	0.61518	0.955000	0.37878	-0.361000	0.07541	GTA		TCGA-2L-AAQA-01A-21D-A38G-08	PPWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253970.2	0	0	1	156	414	1	204	1	9.989898e-01	7	23	1	204	2		0	0	0	0	0	2	1	1.000000	155	412	1	202	12		0	0	0	1	204	2	-20.000000	1	1	0	0		1	0	1	1	2.058923	0	0.600000	1.890000	0.598796	0.900000	7.800000e-01	1.000000	1.000000	0.908774	0.900000	1	8.400000e-01	9.700000e-01
TNPO1	3842	broad.mit.edu	37	5	72195908	72195908	+	Splice_Site	SNP	G	G	A			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08			G	A	G	G		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr5:72195908G>A	ENST00000337273.5	+	21	2840	c.2414G>A	c.(2413-2415)tGg>tAg	p.W805*	TNPO1_ENST00000454282.1_Splice_Site_p.W755*|TNPO1_ENST00000523768.1_Splice_Site_p.W755*|TNPO1_ENST00000506351.2_Splice_Site_p.W797*	NM_002270.3	NP_002261.3	Q92973	TNPO1_HUMAN	transportin 1	p.W797*(1)|p.W797L(1)		36		Lung NSC(167;0.0053)|Ovarian(174;0.0175)			ATAAGACCCTGGTGTGTATTA	0.348000																								2	Substitution - Nonsense(1)|Substitution - Missense(1)						SO:0001630	splice_region_variant			ENST00000337273.5	0	0	hg19	CCDS43329.1	.	.	.	.	.	.	.	.	.	.	G	38	6.879768	0.97904	.	.	ENSG00000083312	ENST00000337273;ENST00000454282;ENST00000523768;ENST00000506351;ENST00000519220	.	.	.	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.5419	19.1767	0.93605	0.0:0.0:1.0:0.0	.	.	.	.	X	805;755;755;797;316	.	ENSP00000336712:W805X	W	+	2	0	TNPO1	72231664	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.476000	0.97823	2.619000	0.88677	0.467000	0.42956	TGG		TCGA-2L-AAQA-01A-21D-A38G-08	TNPO1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000218577.3	1	0	1	166	364	0	206	0	1	1	59	0	206	2		0	0	0	0	0	2	1	1.000000	163	359	0	205	2		0	0	0	0	206	2	-12.030340	1	1	0	0		1	0	1	1	2.058923	0	0.600000	1.890000	0.598796	0.990000	9.000000e-01	1.000000	1.000000	0.989269	0.990000	1	9.600000e-01	1
PHF1	5252	broad.mit.edu	37	6	33382134	33382134	+	Silent	SNP	C	C	A			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08			C	A	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr6:33382134C>A	ENST00000374516.3	+	9	1138	c.867C>A	c.(865-867)ctC>ctA	p.L289L	PHF1_ENST00000374512.3_Silent_p.L289L	NM_024165.2	NP_077084.1	O43189	PHF1_HUMAN	PHD finger protein 1			19		Ovarian(999;0.0443)			ACAGTTTGCTCCTGGGGGAGG	0.498000											OREG0017346	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)												0							SO:0001819	synonymous_variant			ENST00000374516.3	1	1	hg19	CCDS4777.1																																																																																				TCGA-2L-AAQA-01A-21D-A38G-08	PHF1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076175.3	1	0	1	139	261	0	131	1	1	39	66	0	131	2		0	0	0	0	0	2	1	1.000000	136	256	0	130	2		0	0	0	0	131	2	-14.824100	1	1	0	0		1	0	0	0	1.902920	0	0.600000	1.890000	0.563319	0.990000	9.100000e-01	1.000000	1.000000	0.992118	0.990000	1	9.800000e-01	1
CBLL1	79872	broad.mit.edu	37	7	107398626	107398626	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr7:107398626G>A	ENST00000440859.3	+	6	946	c.479G>A	c.(478-480)cGa>cAa	p.R160Q	CBLL1_ENST00000415884.2_3'UTR|CBLL1_ENST00000222597.2_Missense_Mutation_p.R159Q	NM_001284291.1|NM_024814.2	NP_001271220.1|NP_079090.2	Q75N03	HAKAI_HUMAN	Cbl proto-oncogene-like 1, E3 ubiquitin protein ligase			21					CAGTGTACACGAGGTTCTCTC	0.378000																								0							SO:0001583	missense			ENST00000440859.3	1	1	hg19	CCDS5747.1	.	.	.	.	.	.	.	.	.	.	G	19.61	3.860457	0.71834	.	.	ENSG00000105879	ENST00000440859;ENST00000535365;ENST00000222597;ENST00000420796;ENST00000417616	T;T;T	0.32753	1.45;1.44;1.48	5.14	4.24	0.50183	.	0.000000	0.85682	D	0.000000	T	0.48241	0.1489	L	0.52759	1.655	0.80722	D	1	D;D	0.89917	1.0;0.996	D;P	0.77004	0.989;0.755	T	0.36432	-0.9748	10	0.28530	T	0.3	-2.0467	15.7175	0.77681	0.0:0.1374:0.8626:0.0	.	159;160	B7ZM03;Q75N03	.;HAKAI_HUMAN	Q	160;39;159;110;106	ENSP00000401277:R160Q;ENSP00000222597:R159Q;ENSP00000410615:R110Q	ENSP00000222597:R159Q	R	+	2	0	CBLL1	107185862	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.543000	0.98089	1.259000	0.44117	0.655000	0.94253	CGA		TCGA-2L-AAQA-01A-21D-A38G-08	CBLL1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337156.2	1	0	1	124	295	0	160	1	9.995125e-01	14	16	0	160	2		0	0	0	0	0	2	1	1.000000	123	291	0	158	2		0	0	0	0	160	2	-8.710860	1	1	121412	6	39	1	0	1	1	2.061758	0	0.600000	1.890000	0.598796	0.970000	8.300000e-01	1.000000	1.000000	0.962309	0.970000	1	9.000000e-01	1
FIGNL1	63979	broad.mit.edu	37	7	50513641	50513641	+	Missense_Mutation	SNP	G	G	T			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr7:50513641G>T	ENST00000419119.1	-	2	2898	c.1345C>A	c.(1345-1347)Cta>Ata	p.L449I	FIGNL1_ENST00000395556.2_Missense_Mutation_p.L449I|FIGNL1_ENST00000356889.4_Missense_Mutation_p.L449I|FIGNL1_ENST00000433017.1_Missense_Mutation_p.L449I			Q6PIW4	FIGL1_HUMAN	fidgetin-like 1	p.L449L(1)		29	Glioma(55;0.08)|all_neural(89;0.245)	Acute lymphoblastic leukemia(4;3.73e-08)|all_hematologic(4;7.51e-06)			TTGCCAATTAGAGTTTTACCA	0.458000																								1	Substitution - coding silent(1)						SO:0001583	missense			ENST00000419119.1	0	1	hg19	CCDS5510.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.031312	0.75504	.	.	ENSG00000132436	ENST00000356889;ENST00000395556;ENST00000433017;ENST00000419119	D;D;D;D	0.95342	-3.68;-3.68;-3.68;-3.68	5.99	4.18	0.49190	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.000000	0.64402	D	0.000001	D	0.97573	0.9205	M	0.92970	3.365	0.80722	D	1	D	0.64830	0.994	D	0.76071	0.987	D	0.98137	1.0434	10	0.72032	D	0.01	-9.5128	12.3571	0.55182	0.1376:0.0:0.8624:0.0	.	449	Q6PIW4	FIGL1_HUMAN	I	449	ENSP00000349356:L449I;ENSP00000378924:L449I;ENSP00000399997:L449I;ENSP00000410811:L449I	ENSP00000349356:L449I	L	-	1	2	FIGNL1	50481135	1.000000	0.71417	0.899000	0.35326	0.997000	0.91878	6.779000	0.75057	1.538000	0.49270	0.655000	0.94253	CTA		TCGA-2L-AAQA-01A-21D-A38G-08	FIGNL1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342579.1	0	0	0	5	377	0	118	0	7.323079e-03	0	8	0	118	2		0	0	0	0	0	2	1	0.934399	5	369	0	118	2		0	0	0	0	118	2	-5.581852	1	1	0	0		1	0	1	1	2.061758	0	0.600000	1.890000	0.598796	0.040000	0	0.100000	0.040000	0.051722	0.040000	0	2.000000e-02	7.000000e-02
ZNF3	7551	broad.mit.edu	37	7	99669508	99669508	+	Missense_Mutation	SNP	T	T	C			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08			T	C	T	T		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr7:99669508T>C	ENST00000424697.1	-	6	905	c.599A>G	c.(598-600)cAt>cGt	p.H200R	ZNF3_ENST00000303915.6_Missense_Mutation_p.H200R|ZNF3_ENST00000299667.4_Missense_Mutation_p.H200R|ZNF3_ENST00000413658.2_Intron	NM_001278284.1|NM_001278287.1|NM_001278290.1|NM_001278291.1|NM_001278292.1|NM_032924.3	NP_001265213.1|NP_001265216.1|NP_001265219.1|NP_001265220.1|NP_001265221.1|NP_116313.3	P17036	ZNF3_HUMAN	zinc finger protein 3			25	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)	Ovarian(593;2.06e-05)|Myeloproliferative disorder(862;0.0122)|Breast(660;0.029)	STAD - Stomach adenocarcinoma(171;0.129)		ATCACACTTATGGGGTCTGTC	0.433000																								0							SO:0001583	missense			ENST00000424697.1	1	1	hg19	CCDS43619.1	.	.	.	.	.	.	.	.	.	.	T	16.68	3.189385	0.57909	.	.	ENSG00000166526	ENST00000424697;ENST00000303915;ENST00000299667	T;T;T	0.35421	1.31;1.31;1.31	4.6	4.6	0.57074	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.53938	D	0.000041	T	0.51584	0.1683	L	0.60845	1.875	0.37016	D	0.895972	D;D	0.63880	0.993;0.982	P;P	0.62491	0.824;0.903	T	0.61783	-0.6992	10	0.87932	D	0	-15.5748	12.2643	0.54668	0.0:0.0:0.0:1.0	.	183;200	B3KRP4;P17036	.;ZNF3_HUMAN	R	200	ENSP00000415358:H200R;ENSP00000306372:H200R;ENSP00000299667:H200R	ENSP00000299667:H200R	H	-	2	0	ZNF3	99507444	0.001000	0.12720	1.000000	0.80357	0.998000	0.95712	0.261000	0.18442	2.075000	0.62263	0.533000	0.62120	CAT		TCGA-2L-AAQA-01A-21D-A38G-08	ZNF3-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336247.3	1	0	1	153	379	0	183	1	9.996521e-01	12	20	0	183	2		0	0	0	0	0	2	1	1.000000	152	376	0	183	2		0	0	0	0	183	2	-20.000000	1	1	121164	5	39	1	0	1	1	2.061758	0	0.600000	1.890000	0.598796	0.950000	8.200000e-01	1.000000	1.000000	0.946925	0.950000	1	8.800000e-01	1
GPSM1	26086	broad.mit.edu	37	9	139228944	139228944	+	Missense_Mutation	SNP	C	C	T	rs140085951		TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr9:139228944C>T	ENST00000440944.1	+	2	329	c.109C>T	c.(109-111)Cgt>Tgt	p.R37C	GPSM1_ENST00000392945.3_Missense_Mutation_p.R37C	NM_001145638.1	NP_001139110	Q86YR5	GPSM1_HUMAN	G-protein signaling modulator 1			9		Myeloproliferative disorder(178;0.0821)			GGAGGGCGAGCGTCTGTGCAA	0.652000																								0							SO:0001583	missense			ENST00000440944.1	1	1	hg19	CCDS48055.1	.	.	.	.	.	.	.	.	.	.	c	19.82	3.899125	0.72754	.	.	ENSG00000160360	ENST00000392945;ENST00000440944;ENST00000354753	T;T;T	0.75477	-0.94;-0.94;-0.0	4.66	3.65	0.41850	.	0.000000	0.64402	U	0.000001	D	0.84397	0.5463	M	0.69523	2.12	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.86778	0.1977	10	0.87932	D	0	-12.3547	14.5162	0.67821	0.1569:0.8431:0.0:0.0	.	37;37	Q86YR5;Q86YR5-3	GPSM1_HUMAN;.	C	37;37;14	ENSP00000376674:R37C;ENSP00000392828:R37C;ENSP00000346797:R14C	ENSP00000346797:R14C	R	+	1	0	GPSM1	138348765	1.000000	0.71417	0.996000	0.52242	0.939000	0.58152	1.805000	0.38883	2.113000	0.64589	0.556000	0.70494	CGT		TCGA-2L-AAQA-01A-21D-A38G-08	GPSM1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		1	0	1	24	100	0	39	1	3.407763e-01	2	4	0	39	2		0	0	0	0	0	2	1	1.000000	24	98	0	39	2		0	0	0	0	39	2	-20.000000	1	1	121256	1	35	1	0	0	0	2.067674	0	0.600000	1.890000	0.600000	0.640000	4.300000e-01	0.880000	0.640000	0.657670	0.640000	0	5.300000e-01	7.700000e-01
KIF24	347240	broad.mit.edu	37	9	34256761	34256761	+	Silent	SNP	A	A	G			TCGA-2L-AAQA-01A-21D-A38G-08	TCGA-2L-AAQA-11A-11D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33208690-91c9-4811-8043-6659815440e9	a7d7a9e6-4f0e-464f-83fe-8c93b30c1da8	g.chr9:34256761A>G	ENST00000402558.2	-	10	2868	c.2844T>C	c.(2842-2844)taT>taC	p.Y948Y	KIF24_ENST00000345050.2_Silent_p.Y814Y|KIF24_ENST00000379166.2_Silent_p.Y948Y|KIF24_ENST00000379174.3_Silent_p.Y814Y			Q5T7B8	KIF24_HUMAN	kinesin family member 24			32			LUSC - Lung squamous cell carcinoma(29;0.0107)		TTTCCTGTCTATATATGAAAT	0.527000																								0							SO:0001819	synonymous_variant			ENST00000402558.2	1	1	hg19	CCDS6551.2																																																																																				TCGA-2L-AAQA-01A-21D-A38G-08	KIF24-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052150.5	1	0	1	140	315	0	136	1	2.273725e-01	2	1	0	136	2		0	0	0	0	0	2	1	1.000000	136	306	0	134	2		0	0	0	0	136	2	-20.000000	1	1	0	0		1	0	1	1	2.060315	0	0.600000	1.890000	0.598796	0.990000	8.800000e-01	1.000000	1.000000	0.981744	0.990000	1	9.400000e-01	1
