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
MLXIP	22877	broad.mit.edu	37	12	122623075	122623075	+	Frame_Shift_Del	DEL	C	C	-			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr12:122623075delC	ENST00000319080.7	+	14	2493	c.2361delC	c.(2359-2361)atcfs	p.I787fs	MLXIP_ENST00000538698.1_Frame_Shift_Del_p.I394fs					MLX interacting protein			20	all_neural(191;0.0837)|Medulloblastoma(191;0.163)	Lung NSC(355;0.0659)			GGGAGGAGATCGAGGAGCTCA	0.632000													Esophageal Squamous(105;787 1493 16200 18566 52466)											0							SO:0001589	frameshift_variant			ENST00000319080.7	0	1	hg19																																																																																					TCGA-XD-AAUI-01A-42D-A40W-08	MLXIP-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000401718.2	1	0	0	14	117	0	24	0	7.643365e-01	0	25	0	24	2	0	0	0	0	0	0		1	0.999811	16	115	0	23	2								-19.970870	1	1	0	0		1	0	0	0	1.988815	0	0.210000	1.910000	0.194781	0.990000	0.580000	1.000000	1.000000	0.912718	0.990000	1	7.700000e-01	1
FRMD4A	55691	broad.mit.edu	37	10	13736001	13736001	+	Silent	SNP	G	G	A			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr10:13736001G>A	ENST00000357447.2	-	15	1382	c.1014C>T	c.(1012-1014)gcC>gcT	p.A338A	FRMD4A_ENST00000378503.1_Silent_p.A338A|FRMD4A_ENST00000358621.4_Silent_p.A323A|FRMD4A_ENST00000492155.1_5'UTR|FRMD4A_ENST00000342409.2_Silent_p.A354A	NM_018027.3	NP_060497.3	Q9P2Q2	FRM4A_HUMAN	FERM domain containing 4A			41					TCAGGTCGATGGCGATCTCAC	0.572000																								0							SO:0001819	synonymous_variant			ENST00000357447.2	1	1	hg19	CCDS7101.1																																																																																				TCGA-XD-AAUI-01A-42D-A40W-08	FRMD4A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046889.1	1	0	1	39	220	0	55	0	6.466338e-01	0	14	0	55	2		0	0	0	0	0	2	1	1.000000	38	217	0	54	2								-20.000000	1	1	0	0		1	0	1	1	1.942227	0	0.210000	1.910000	0.157827	0.990000	0.950000	1.000000	1.000000	0.997077	0.990000	1	9.900000e-01	1
PARD3	56288	broad.mit.edu	37	10	34663857	34663857	+	Missense_Mutation	SNP	C	C	T			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr10:34663857C>T	ENST00000374789.3	-	11	1938	c.1613G>A	c.(1612-1614)gGa>gAa	p.G538E	PARD3_ENST00000374773.1_Missense_Mutation_p.G538E|PARD3_ENST00000545693.1_Missense_Mutation_p.G538E|PARD3_ENST00000545260.1_Missense_Mutation_p.G494E|PARD3_ENST00000374794.3_Missense_Mutation_p.G494E|PARD3_ENST00000374788.3_Missense_Mutation_p.G538E|PARD3_ENST00000544292.1_Missense_Mutation_p.G268E|PARD3_ENST00000374768.1_5'Flank|PARD3_ENST00000374776.1_Missense_Mutation_p.G538E|PARD3_ENST00000346874.4_Missense_Mutation_p.G538E|PARD3_ENST00000374790.3_Missense_Mutation_p.G494E|PARD3_ENST00000350537.4_Missense_Mutation_p.G538E|PARD3_ENST00000340077.5_Missense_Mutation_p.G538E	NM_019619.3	NP_062565.2	Q8TEW0	PARD3_HUMAN	par-3 family cell polarity regulator			63		Breast(68;0.0707)			GCTCACAGTTCCTTCCATCTT	0.438000																								0							SO:0001583	missense			ENST00000374789.3	0	1	hg19	CCDS7178.1	.	.	.	.	.	.	.	.	.	.	c	13.72	2.321178	0.41096	.	.	ENSG00000148498	ENST00000545693;ENST00000545260;ENST00000374789;ENST00000374788;ENST00000346874;ENST00000374794;ENST00000350537;ENST00000374790;ENST00000374776;ENST00000340077;ENST00000374773;ENST00000544292	T;T;T;T;T;T;T;T;T;T;T;T	0.18338	2.22;2.22;2.22;2.22;2.22;2.22;2.22;2.22;2.22;2.22;2.22;2.22	5.82	5.82	0.92795	PDZ/DHR/GLGF (4);	0.000000	0.85682	D	0.000000	T	0.28200	0.0696	L	0.31157	0.91	0.80722	D	1	D;D;D;D;D;D;D;B;B;D;D;B;B;B;B	0.89917	1.0;0.993;0.998;0.997;0.994;0.998;0.997;0.195;0.324;0.997;0.994;0.217;0.008;0.026;0.001	D;P;D;P;D;D;P;B;B;D;D;B;B;B;B	0.80764	0.994;0.709;0.969;0.903;0.934;0.923;0.903;0.096;0.119;0.942;0.963;0.082;0.024;0.018;0.001	T	0.01276	-1.1398	10	0.05351	T	0.99	.	20.088	0.97803	0.0:1.0:0.0:0.0	.	494;494;538;538;538;538;538;538;494;538;538;538;538;538;268	Q8TEW0-5;Q8TEW0-3;Q8TEW0-7;Q8TEW0-6;F5H5T0;Q8TEW0-4;Q8TEW0-2;Q8TEW0;Q5VWV2;Q6IQ47;Q5VWU8;Q8TEW0-8;Q8TEW0-9;Q8TEW0-10;F5GZI3	.;.;.;.;.;.;.;PARD3_HUMAN;.;.;.;.;.;.;.	E	538;494;538;538;538;494;538;494;538;538;538;268	ENSP00000443147:G538E;ENSP00000440857:G494E;ENSP00000363921:G538E;ENSP00000363920:G538E;ENSP00000340591:G538E;ENSP00000363926:G494E;ENSP00000311986:G538E;ENSP00000363922:G494E;ENSP00000363908:G538E;ENSP00000341844:G538E;ENSP00000363905:G538E;ENSP00000444429:G268E	ENSP00000341844:G538E	G	-	2	0	PARD3	34703863	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.451000	0.80668	2.739000	0.93911	0.655000	0.94253	GGA		TCGA-XD-AAUI-01A-42D-A40W-08	PARD3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047527.1	0	0	0	7	531	0	118	0	1.083584e-01	0	37	0	118	2		0	0	0	0	0	2	1	0.979938	7	525	0	118	2								-2.718959	1	1	0	0		1	0	1	1	1.942227	0	0.210000	1.910000	0.157827	0.120000	0.050000	0.230000	0.110000	0.131042	0.120000	0	8.000000e-02	1.700000e-01
CHAT	1103	broad.mit.edu	37	10	50857681	50857681	+	Splice_Site	SNP	C	C	T			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr10:50857681C>T	ENST00000337653.2	+	10	1663	c.1510C>T	c.(1510-1512)Cga>Tga	p.R504*	CHAT_ENST00000455728.2_Splice_Site_p.R386*|CHAT_ENST00000395559.2_Splice_Site_p.R386*|CHAT_ENST00000395562.2_Splice_Site_p.R422*|CHAT_ENST00000339797.1_Splice_Site_p.R386*|CHAT_ENST00000351556.3_Splice_Site_p.R386*	NM_001142929.1|NM_020549.4	NP_001136401.1|NP_065574	P28329	CLAT_HUMAN	choline O-acetyltransferase			56		all_neural(218;0.107)		Choline(DB00122)|Nicotine(DB00184)	AAAACTTCAACGGTAAGGATA	0.602000																								0							SO:0001630	splice_region_variant			ENST00000337653.2	0	0	hg19	CCDS7232.1	.	.	.	.	.	.	.	.	.	.	C	36	5.855479	0.97030	0.0	1.16E-4	ENSG00000070748	ENST00000339797;ENST00000351556;ENST00000395559;ENST00000337653;ENST00000395562;ENST00000455728	.	.	.	4.77	0.0456	0.14231	.	0.156020	0.56097	D	0.000032	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.13470	T	0.59	-5.4337	7.7047	0.28642	0.5652:0.3444:0.0:0.0904	.	.	.	.	X	386;386;386;504;422;386	.	ENSP00000337103:R504X	R	+	1	2	CHAT	50527687	0.999000	0.42202	0.959000	0.39883	0.135000	0.20990	2.130000	0.42064	0.376000	0.24707	0.462000	0.41574	CGA		TCGA-XD-AAUI-01A-42D-A40W-08	CHAT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047997.1	1	0	1	37	264	0	92		0	0	0	0	92	2		0	0	0	0	0	2	1	1.000000	37	261	0	89	2								-20.000000	1	1	121392	2	33	1	0	1	1	1.942227	0	0.210000	1.910000	0.157827	0.990000	0.780000	1.000000	1.000000	0.972845	0.990000	1	9.200000e-01	1
C2CD2L	9854	broad.mit.edu	37	11	118982297	118982297	+	Missense_Mutation	SNP	C	C	A	rs140133210		TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr11:118982297C>A	ENST00000528586.1	+	3	291	c.221C>A	c.(220-222)gCg>gAg	p.A74E	C2CD2L_ENST00000336702.3_Missense_Mutation_p.A326E			O14523	C2C2L_HUMAN	C2CD2-like			13					ACCAAGCCCGCGAGGGCTGGA	0.562000																								0							SO:0001583	missense			ENST00000528586.1	0	1	hg19		.	.	.	.	.	.	.	.	.	.	C	7.519	0.656367	0.14580	.	.	ENSG00000172375	ENST00000336702;ENST00000528586	T;T	0.40225	1.04;1.04	5.54	-11.1	0.00147	C2 calcium/lipid-binding domain, CaLB (1);	1.839290	0.02350	N	0.075789	T	0.24547	0.0595	N	0.14661	0.345	0.09310	N	1	B;B	0.24618	0.107;0.107	B;B	0.27715	0.082;0.082	T	0.48328	-0.9045	10	0.05525	T	0.97	-3.7304	19.4928	0.95059	0.0:0.217:0.0:0.783	.	326;326	O14523;O14523-2	C2C2L_HUMAN;.	E	326;74	ENSP00000338885:A326E;ENSP00000433600:A74E	ENSP00000338885:A326E	A	+	2	0	C2CD2L	118487507	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	-1.299000	0.02754	-2.688000	0.00405	-0.140000	0.14226	GCG		TCGA-XD-AAUI-01A-42D-A40W-08	C2CD2L-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000388199.2	0	0	0	4	155	0	36	0	2.301066e-01	0	29	0	36	2		0	0	0	0	0	2	1	0.880480	3	149	0	35	2								-6.208200	1	0	0	0		1	0	1	1	1.839385	1	0.210000	1.910000	0.117318	0.230000	0.070000	0.480000	0.210000	0.252258	0.230000	0	1.400000e-01	3.500000e-01
NUP98	4928	broad.mit.edu	37	11	3704600	3704600	+	Missense_Mutation	SNP	G	G	A			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr11:3704600G>A	ENST00000324932.7	-	30	5168	c.4748C>T	c.(4747-4749)gCt>gTt	p.A1583V	NUP98_ENST00000355260.3_Missense_Mutation_p.A1509V|NUP98_ENST00000359171.4_Missense_Mutation_p.A1509V	NM_016320.4|NM_139132.3	NP_057404.2|NP_624358.2	P52948	NUP98_HUMAN	nucleoporin 98kDa			66		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)			AGTCTCTTTAGCCCAAGATTC	0.512000			T	HOXA9, NSD1, WHSC1L1, DDX10, TOP1, HOXD13, PMX1, HOXA13, HOXD11, HOXA11, RAP1GDS1, HOXC11	AML										Dom	yes		11	11p15	4928	nucleoporin 98kDa		L	0							SO:0001583	missense			ENST00000324932.7	1	1	hg19	CCDS7746.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.052507	0.75960	.	.	ENSG00000110713	ENST00000324932;ENST00000359171;ENST00000355260	.	.	.	6.02	5.1	0.69264	.	0.131086	0.53938	D	0.000044	T	0.59404	0.2191	M	0.74647	2.275	0.23563	N	0.997403	D;D;P	0.53462	0.96;0.96;0.933	P;P;P	0.51615	0.675;0.6;0.461	T	0.56774	-0.7923	9	0.31617	T	0.26	-18.3788	15.8043	0.78481	0.0:0.0:0.8629:0.1371	.	1509;1583;1497	P52948-2;P52948-5;P52948-6	.;.;.	V	1583;1509;1509	.	ENSP00000316032:A1583V	A	-	2	0	NUP98	3661176	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	3.236000	0.51336	1.552000	0.49463	-0.187000	0.12897	GCT		TCGA-XD-AAUI-01A-42D-A40W-08	NUP98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032766.3	1	0	1	22	349	0	80	1	9.610911e-01	11	76	0	80	2		0	0	0	0	0	2	1	0.999999	22	345	0	80	2								-6.003247	1	1	0	0		1	1	2	3	2.045850	0	0.210000	1.910000	0.217396	0.580000	0.370000	1.000000	0.560000	0.617040	0.580000	0	4.600000e-01	7.500000e-01
FZD10	11211	broad.mit.edu	37	12	130649223	130649223	+	Missense_Mutation	SNP	C	C	A			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr12:130649223C>A	ENST00000229030.4	+	1	2220	c.1736C>A	c.(1735-1737)aCc>aAc	p.T579N	FZD10_ENST00000539839.1_3'UTR|FZD10-AS1_ENST00000505807.2_RNA			Q9ULW2	FZD10_HUMAN	frizzled class receptor 10			35	all_neural(191;0.101)|Medulloblastoma(191;0.163)				CAGTCGCCCACCTGCGTGTGA	0.527000																								0							SO:0001583	missense			ENST00000229030.4	0	1	hg19	CCDS9267.1	.	.	.	.	.	.	.	.	.	.	C	12.03	1.817078	0.32145	.	.	ENSG00000111432	ENST00000229030	T	0.77098	-1.07	4.69	4.69	0.59074	.	0.000000	0.64402	U	0.000001	T	0.70684	0.3252	L	0.27053	0.805	0.53005	D	0.999969	B	0.32968	0.392	B	0.35813	0.211	T	0.74578	-0.3619	10	0.87932	D	0	.	17.6375	0.88127	0.0:1.0:0.0:0.0	.	579	Q9ULW2	FZD10_HUMAN	N	579	ENSP00000229030:T579N	ENSP00000229030:T579N	T	+	2	0	FZD10	129215176	1.000000	0.71417	0.989000	0.46669	0.397000	0.30659	3.619000	0.54196	2.127000	0.65507	0.561000	0.74099	ACC		TCGA-XD-AAUI-01A-42D-A40W-08	FZD10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		0	0	0	4	97	0	30	0	3.514690e-02	0	6	0	30	2		0	0	0	0	0	2	1	0.889477	4	96	0	30	2								-7.556106	1	1	0	0		1	0	0	0	1.988815	0	0.210000	1.910000	0.194781	0.400000	0.130000	0.830000	0.360000	0.434336	0.400000	0	2.400000e-01	6.100000e-01
KRAS	3845	broad.mit.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	C	A	rs121913529		TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08			C	A	C	C		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	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-XD-AAUI-01A-42D-A40W-08	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	1	0	1	22	155	0	56	0	5.055540e-01	1	5	0	56	2	1	1	41	401	0	361	2	1	0.999999	22	154	0	52	2								-11.597720	1	1	0	0		1	1	2	3	2.030377	0	0.210000	1.910000	0.217396	0.990000	0.790000	1.000000	1.000000	0.981165	0.990000	1	9.800000e-01	1
ITFG2	55846	broad.mit.edu	37	12	2929953	2929953	+	Missense_Mutation	SNP	G	G	T			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr12:2929953G>T	ENST00000228799.2	+	6	749	c.610G>T	c.(610-612)Ggt>Tgt	p.G204C	ITFG2_ENST00000542548.1_Missense_Mutation_p.G92C|ITFG2_ENST00000419778.2_Missense_Mutation_p.G27C	NM_018463.3	NP_060933.3	Q969R8	ITFG2_HUMAN	integrin alpha FG-GAP repeat containing 2			19			OV - Ovarian serous cystadenocarcinoma(31;0.000818)		GTCTCAGCCAGGTTGTGCGTA	0.562000																								0							SO:0001583	missense			ENST00000228799.2	1	1	hg19	CCDS8513.1	.	.	.	.	.	.	.	.	.	.	G	28.2	4.902630	0.92035	.	.	ENSG00000111203	ENST00000228799;ENST00000419778;ENST00000542548	T	0.72942	-0.7	5.08	5.08	0.68730	.	0.000000	0.85682	D	0.000000	D	0.85500	0.5711	M	0.82517	2.595	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87516	0.2443	10	0.87932	D	0	-21.1172	17.6386	0.88129	0.0:0.0:1.0:0.0	.	204	Q969R8	ITFG2_HUMAN	C	204;27;92	ENSP00000228799:G204C	ENSP00000228799:G204C	G	+	1	0	ITFG2	2800214	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.350000	0.97070	2.632000	0.89209	0.655000	0.94253	GGT		TCGA-XD-AAUI-01A-42D-A40W-08	ITFG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253091.1	1	0	0	14	240	0	81	0	9.667885e-02	1	8	0	81	2		0	0	0	0	0	2	1	0.999752	14	236	0	81	2								-3.221883	1	1	0	0		1	1	2	3	2.021246	0	0.210000	1.910000	0.211656	0.530000	0.300000	0.890000	0.520000	0.555264	0.530000	0	4.100000e-01	6.900000e-01
PLXNC1	10154	broad.mit.edu	37	12	94641698	94641698	+	Missense_Mutation	SNP	C	C	T			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr12:94641698C>T	ENST00000258526.4	+	13	2657	c.2408C>T	c.(2407-2409)gCg>gTg	p.A803V		NM_005761.2	NP_005752.1	O60486	PLXC1_HUMAN	plexin C1			64					TATTGTGTGGCGACTTACTGC	0.428000																								0							SO:0001583	missense			ENST00000258526.4	1	1	hg19	CCDS9049.1	.	.	.	.	.	.	.	.	.	.	C	3.557	-0.090472	0.07053	.	.	ENSG00000136040	ENST00000258526	T	0.07114	3.22	6.16	1.83	0.25207	Cell surface receptor IPT/TIG (2);	0.869786	0.10286	N	0.692988	T	0.06096	0.0158	L	0.27053	0.805	0.09310	N	1	P	0.36944	0.574	B	0.31869	0.137	T	0.39461	-0.9613	10	0.27785	T	0.31	.	10.7249	0.46061	0.6283:0.2651:0.1066:0.0	.	803	O60486	PLXC1_HUMAN	V	803	ENSP00000258526:A803V	ENSP00000258526:A803V	A	+	2	0	PLXNC1	93165829	0.000000	0.05858	0.000000	0.03702	0.066000	0.16364	-0.066000	0.11598	0.440000	0.26502	-0.175000	0.13238	GCG		TCGA-XD-AAUI-01A-42D-A40W-08	PLXNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408126.2	1	0	0	26	587	0	149	0	1.123669e-02	0	4	0	149	2		0	0	0	0	0	2	1	1.000000	24	575	0	146	2								-3.903845	1	1	121412	1	31	1	0	0	0	1.988815	0	0.210000	1.910000	0.194781	0.390000	0.260000	0.560000	0.400000	0.407454	0.390000	0	3.200000e-01	4.800000e-01
GPC6	10082	broad.mit.edu	37	13	95034762	95034762	+	Missense_Mutation	SNP	C	C	T			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr13:95034762C>T	ENST00000377047.4	+	7	1862	c.1247C>T	c.(1246-1248)aCg>aTg	p.T416M		NM_005708.3	NP_005699.1	Q9Y625	GPC6_HUMAN	glypican 6			38	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)			ACAGCGGGCACGTCCAACGAG	0.537000																								0							SO:0001583	missense			ENST00000377047.4	1	1	hg19	CCDS9469.1	.	.	.	.	.	.	.	.	.	.	C	15.78	2.935396	0.52866	.	.	ENSG00000183098	ENST00000377047	T	0.51071	0.72	5.74	5.74	0.90152	.	0.262572	0.38720	N	0.001587	T	0.36496	0.0969	L	0.34521	1.04	0.28457	N	0.916084	P	0.48350	0.909	B	0.39379	0.298	T	0.44682	-0.9312	10	0.54805	T	0.06	.	12.4114	0.55469	0.0:0.923:0.0:0.077	.	416	Q9Y625	GPC6_HUMAN	M	416	ENSP00000366246:T416M	ENSP00000366246:T416M	T	+	2	0	GPC6	93832763	0.856000	0.29760	0.999000	0.59377	0.660000	0.38997	2.153000	0.42282	2.708000	0.92522	0.650000	0.86243	ACG		TCGA-XD-AAUI-01A-42D-A40W-08	GPC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045460.4	1	0	0	34	314	0	85	0	1.510796e-01	0	7	0	85	2	0	0	0	1	0	0	2	1	1.000000	34	307	0	84	2								-12.176790	1	1	121412	42	48	1	1	2	3	2.024408	0	0.210000	1.910000	0.213304	0.930000	0.660000	1.000000	1.000000	0.910749	0.930000	1	7.900000e-01	1
PYGL	5836	broad.mit.edu	37	14	51387719	51387719	+	Missense_Mutation	SNP	G	G	A			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr14:51387719G>A	ENST00000216392.7	-	6	1059	c.727C>T	c.(727-729)Cgc>Tgc	p.R243C	PYGL_ENST00000532462.1_Missense_Mutation_p.R243C|PYGL_ENST00000544180.2_Missense_Mutation_p.R209C	NM_002863.4	NP_002854.3	P06737	PYGL_HUMAN	phosphorylase, glycogen, liver			25	all_epithelial(31;0.00825)|Breast(41;0.148)			Adenosine monophosphate(DB00131)	GACCAGAGGCGCATGGTGTTG	0.498000																								0							SO:0001583	missense			ENST00000216392.7	1	1	hg19	CCDS32080.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.547610	0.86022	.	.	ENSG00000100504	ENST00000532462;ENST00000544180;ENST00000216392	D;D;D	0.96232	-3.95;-3.95;-3.95	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	D	0.98704	0.9565	M	0.94101	3.495	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	D	0.99267	1.0892	10	0.87932	D	0	-0.3184	19.3504	0.94381	0.0:0.0:1.0:0.0	.	209;243;243	F5H816;E9PK47;P06737	.;.;PYGL_HUMAN	C	243;209;243	ENSP00000431657:R243C;ENSP00000443787:R209C;ENSP00000216392:R243C	ENSP00000216392:R243C	R	-	1	0	PYGL	50457469	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	2.626000	0.46460	2.885000	0.99019	0.655000	0.94253	CGC		TCGA-XD-AAUI-01A-42D-A40W-08	PYGL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390654.3	1	0	0	15	237	0	60	1	7.880128e-01	4	44	0	60	2		0	0	0	0	0	2	1	0.561145	15	235	1	58	15								-2.965748	1	1	0	0		1	0	0	0	1.997598	0	0.210000	1.910000	0.199919	0.560000	0.330000	0.860000	0.550000	0.582669	0.560000	0	4.300000e-01	7.200000e-01
PLEKHG3	26030	broad.mit.edu	37	14	65210050	65210050	+	Missense_Mutation	SNP	C	C	T			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr14:65210050C>T	ENST00000394691.1	+	17	3436	c.3289C>T	c.(3289-3291)Cgc>Tgc	p.R1097C	PLEKHG3_ENST00000492928.1_Intron|PLEKHG3_ENST00000484731.2_Missense_Mutation_p.R602C|PLEKHG3_ENST00000471182.2_Missense_Mutation_p.R630C|PLEKHG3_ENST00000247226.7_Missense_Mutation_p.R1041C			A1L390	PKHG3_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 3			29					CAGGGTGGGCCGCTGCCGCAG	0.731000																								0							SO:0001583	missense			ENST00000394691.1	1	1	hg19		.	.	.	.	.	.	.	.	.	.	C	13.99	2.401959	0.42613	.	.	ENSG00000126822	ENST00000247226;ENST00000394691;ENST00000471182;ENST00000484731	T;T;T;T	0.62364	0.48;0.03;1.37;1.37	5.22	3.38	0.38709	.	0.348750	0.24999	N	0.033935	T	0.65821	0.2728	L	0.53249	1.67	0.19300	N	0.999974	D;D;D;D	0.76494	0.999;0.998;0.988;0.997	P;P;P;P	0.53861	0.736;0.736;0.533;0.724	T	0.59026	-0.7531	10	0.87932	D	0	.	9.9514	0.41640	0.0:0.8303:0.0:0.1697	.	630;602;1097;1041	A1L390-2;G3V311;A1L390;A1L390-3	.;.;PKHG3_HUMAN;.	C	1041;1097;630;602	ENSP00000247226:R1041C;ENSP00000378183:R1097C;ENSP00000450945:R630C;ENSP00000450973:R602C	ENSP00000247226:R1041C	R	+	1	0	PLEKHG3	64279803	0.003000	0.15002	0.987000	0.45799	0.357000	0.29423	0.011000	0.13264	0.563000	0.29222	0.563000	0.77884	CGC		TCGA-XD-AAUI-01A-42D-A40W-08	PLEKHG3-010	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000412028.1	1	0	0	9	108	0	29	1	9.345033e-01	20	40	0	29	2		0	0	0	0	0	2	1	0.992214	9	98	0	27	2								-14.084520	1	1	120986	3	34	1	1	2	3	2.084678	1	0.210000	1.910000	0.250901	0.900000	0.410000	1.000000	1.000000	0.836278	0.900000	1	6.100000e-01	1
RYR3	6263	broad.mit.edu	37	15	33895400	33895400	+	Missense_Mutation	SNP	G	G	A			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr15:33895400G>A	ENST00000389232.4	+	18	2069	c.1999G>A	c.(1999-2001)Gac>Aac	p.D667N	RYR3_ENST00000415757.3_Missense_Mutation_p.D667N	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3			311		all_lung(180;7.18e-09)			GCTGATTATCGACCAGGTGGA	0.567000																								0							SO:0001583	missense			ENST00000389232.4	1	1	hg19	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	G	31	5.058903	0.93846	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	T;T	0.70516	-0.49;-0.49	5.42	4.5	0.54988	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.85682	D	0.000000	D	0.85392	0.5686	M	0.85299	2.745	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.91635	0.996;0.999	D	0.88122	0.2832	10	0.66056	D	0.02	.	15.8752	0.79156	0.0:0.0:0.8636:0.1364	.	667;667	Q15413-2;Q15413	.;RYR3_HUMAN	N	667	ENSP00000373884:D667N;ENSP00000399610:D667N	ENSP00000354735:D667N	D	+	1	0	RYR3	31682692	1.000000	0.71417	0.994000	0.49952	0.985000	0.73830	9.522000	0.98032	1.529000	0.49120	-0.164000	0.13417	GAC		TCGA-XD-AAUI-01A-42D-A40W-08	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1	0	0	0	37	540	0	146		0	0	0	0	146	2		0	0	0	0	0	2	1	1.000000	37	530	0	142	2								-7.797808	1	1	0	0		1	0	0	0	1.872458	1	0.210000	1.910000	0.145392	0.560000	0.400000	0.740000	0.560000	0.571921	0.560000	0	4.700000e-01	6.600000e-01
RYR3	6263	broad.mit.edu	37	15	34130000	34130000	+	Missense_Mutation	SNP	C	C	A			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr15:34130000C>A	ENST00000389232.4	+	89	11889	c.11819C>A	c.(11818-11820)tCc>tAc	p.S3940Y	RYR3_ENST00000415757.3_Missense_Mutation_p.S3935Y	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3			311		all_lung(180;7.18e-09)			GGAATTATCTCCAAAAAAGAA	0.398000																								0							SO:0001583	missense			ENST00000389232.4	1	1	hg19	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	C	17.85	3.490354	0.64074	.	.	ENSG00000198838	ENST00000389232;ENST00000361728	D	0.85013	-1.93	5.4	5.4	0.78164	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	D	0.93572	0.7948	M	0.86953	2.85	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.91635	0.988;0.999	D	0.93668	0.6987	10	0.59425	D	0.04	.	19.373	0.94498	0.0:1.0:0.0:0.0	.	3935;3940	Q15413-2;Q15413	.;RYR3_HUMAN	Y	3940;3936	ENSP00000373884:S3940Y	ENSP00000354735:S3936Y	S	+	2	0	RYR3	31917292	1.000000	0.71417	1.000000	0.80357	0.819000	0.46315	7.554000	0.82212	2.817000	0.96982	0.551000	0.68910	TCC		TCGA-XD-AAUI-01A-42D-A40W-08	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1	1	0	0	18	221	0	63		0	0	0	0	63	2		0	0	0	0	0	2	1	0.999983	18	218	0	62	2								-2.920913	1	1	0	0		1	0	0	0	1.872458	1	0.210000	1.910000	0.145392	0.660000	0.410000	0.970000	0.650000	0.675355	0.660000	0	5.200000e-01	8.200000e-01
TMC3	342125	broad.mit.edu	37	15	81650502	81650502	+	Missense_Mutation	SNP	A	A	G			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr15:81650502A>G	ENST00000359440.5	-	7	866	c.731T>C	c.(730-732)aTt>aCt	p.I244T	RP11-761I4.3_ENST00000559781.1_RNA|TMC3_ENST00000558726.1_Missense_Mutation_p.I244T|RP11-761I4.3_ENST00000560851.1_RNA	NM_001080532.1	NP_001074001.1			transmembrane channel-like 3			34					TTTTAAAAGAATGATGAAGCT	0.408000																								0							SO:0001583	missense			ENST00000359440.5	0	1	hg19	CCDS45324.1	.	.	.	.	.	.	.	.	.	.	A	11.85	1.763052	0.31228	.	.	ENSG00000188869	ENST00000359440	T	0.50001	0.76	5.59	4.46	0.54185	.	0.478461	0.21754	N	0.069626	T	0.23054	0.0557	N	0.02854	-0.475	0.28128	N	0.930305	B;B	0.14805	0.004;0.011	B;B	0.17098	0.009;0.017	T	0.12863	-1.0531	10	0.39692	T	0.17	-9.4363	8.7012	0.34327	0.8534:0.0:0.1466:0.0	.	244;244	Q7Z5M5-2;Q7Z5M5	.;TMC3_HUMAN	T	244	ENSP00000352413:I244T	ENSP00000352413:I244T	I	-	2	0	TMC3	79437557	1.000000	0.71417	0.465000	0.27155	0.944000	0.59088	5.350000	0.66016	0.971000	0.38288	0.481000	0.45027	ATT		TCGA-XD-AAUI-01A-42D-A40W-08	TMC3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417795.3	1	0	0	5	128	0	33	0	0	0	1	0	33	2		0	0	0	0	0	2	1	0.937519	5	127	0	33	2								-8.136713	1	1	0	0		1	0	0	0	1.877483	1	0.210000	1.910000	0.147329	0.350000	0.130000	0.680000	0.320000	0.375172	0.350000	0	2.200000e-01	5.100000e-01
IFT140	9742	broad.mit.edu	37	16	1633329	1633329	+	Missense_Mutation	SNP	G	G	A			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr16:1633329G>A	ENST00000426508.2	-	12	1781	c.1418C>T	c.(1417-1419)gCg>gTg	p.A473V	IFT140_ENST00000439987.2_5'UTR|LA16c-395F10.2_ENST00000563162.1_RNA	NM_014714.3	NP_055529.2	Q96RY7	IF140_HUMAN	intraflagellar transport 140			53		Hepatocellular(780;0.219)			ACTCCGTATCGCGGCTCCAGA	0.567000																								0							SO:0001583	missense			ENST00000426508.2	0	1	hg19	CCDS10439.1	.	.	.	.	.	.	.	.	.	.	G	5.952	0.359713	0.11239	.	.	ENSG00000187535	ENST00000397417;ENST00000426508;ENST00000439987	T	0.69685	-0.42	5.48	-2.97	0.05530	.	1.408220	0.04710	N	0.417384	T	0.46483	0.1395	N	0.16478	0.41	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.18429	-1.0337	10	0.25106	T	0.35	.	6.8317	0.23913	0.4417:0.0:0.4466:0.1116	.	473;198	Q96RY7;B4DR58	IF140_HUMAN;.	V	473	ENSP00000406012:A473V	ENSP00000380562:A473V	A	-	2	0	IFT140	1573330	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.229000	0.09098	-0.918000	0.03808	-0.797000	0.03246	GCG		TCGA-XD-AAUI-01A-42D-A40W-08	IFT140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250438.2	0	0	0	5	185	0	51	0	5.712201e-02	1	11	0	51	2		0	0	0	0	0	2	1	0.933915	5	180	0	50	2								-6.885066	1	1	121412	2	30	1	0	0	0	1.926961	0	0.210000	1.910000	0.169906	0.250000	0.090000	0.510000	0.230000	0.275999	0.250000	0	1.600000e-01	3.800000e-01
PKD1	5310	broad.mit.edu	37	16	2162878	2162878	+	Silent	SNP	G	G	A			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr16:2162878G>A	ENST00000262304.4	-	13	3280	c.3072C>T	c.(3070-3072)gtC>gtT	p.V1024V	RP11-304L19.4_ENST00000568795.1_RNA|PKD1_ENST00000423118.1_Silent_p.V1024V	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)			72					GCACTGTGGAGACCTGCAGAC	0.642000																								0							SO:0001819	synonymous_variant			ENST00000262304.4	1	1	hg19	CCDS32369.1																																																																																				TCGA-XD-AAUI-01A-42D-A40W-08	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1	1	0	0	12	156	0	59	0	1.504626e-01	0	9	0	59	2		0	0	0	0	0	2	1	0.999136	12	153	0	59	2								-16.376080	1	1	120976	1	34	1	0	0	0	1.926961	0	0.210000	1.910000	0.169906	0.650000	0.360000	1.000000	1.000000	0.668789	0.650000	0	4.900000e-01	8.400000e-01
CHST5	23563	broad.mit.edu	37	16	75564081	75564081	+	Silent	SNP	G	G	A			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr16:75564081G>A	ENST00000336257.3	-	3	1596	c.202C>T	c.(202-204)Ctg>Ttg	p.L68L	RP11-77K12.7_ENST00000460606.1_3'UTR|CHST5_ENST00000541075.1_Silent_p.L74L	NM_024533.4	NP_078809.2	Q9GZS9	CHST5_HUMAN	carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 5			24					CACGAGGACAGCACCAGCACG	0.662000																								0							SO:0001819	synonymous_variant			ENST00000336257.3	0	1	hg19	CCDS10919.1																																																																																				TCGA-XD-AAUI-01A-42D-A40W-08	CHST5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269025.2	0	0	0	5	251	0	51	0	6.337115e-02	0	17	0	51	2		0	0	0	0	0	2	1	0.937505	5	250	0	50	2								-6.337946	1	1	0	0		1						0.210000	1.910000									0	0
IL17C	27189	broad.mit.edu	37	16	88706390	88706390	+	Silent	SNP	G	G	A			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr16:88706390G>A	ENST00000244241.4	+	3	553	c.504G>A	c.(502-504)tcG>tcA	p.S168S		NM_013278.3	NP_037410.1	Q9P0M4	IL17C_HUMAN	interleukin 17C			2					GCGACGGCTCGGGGCTCCCCA	0.716000																								0							SO:0001819	synonymous_variant			ENST00000244241.4	1	1	hg19	CCDS42217.1																																																																																				TCGA-XD-AAUI-01A-42D-A40W-08	IL17C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422575.1	1	0	1	18	288	0	85	1	2.826653e-01	4	13	0	85	2		0	0	0	0	0	2	1	0.999980	18	281	0	82	2								-2.506811	1	1	120554	4	34	1	2	2	4	2.173436	1	0.210000	1.910000	0.268383	0.660000	0.380000	1.000000	0.600000	0.712927	0.660000	0	5.000000e-01	1
DNAH9	1770	broad.mit.edu	37	17	11725368	11725368	+	Nonsense_Mutation	SNP	C	C	T			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr17:11725368C>T	ENST00000262442.4	+	46	8907	c.8839C>T	c.(8839-8841)Cga>Tga	p.R2947*	DNAH9_ENST00000454412.2_Nonsense_Mutation_p.R2947*	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9			290		Breast(5;0.0122)|all_epithelial(5;0.131)			TCGGATCCGGCGACAGCTGAA	0.463000																								0							SO:0001587	stop_gained			ENST00000262442.4	0	1	hg19	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	C	48	14.878058	0.99813	.	.	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703	.	.	.	4.21	-1.36	0.09085	.	0.146107	0.23074	U	0.052233	.	.	.	.	.	.	0.21762	N	0.999553	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.2049	0.59790	0.5135:0.4865:0.0:0.0	.	.	.	.	X	2947;2947;1529	.	ENSP00000262442:R2947X	R	+	1	2	DNAH9	11666093	0.296000	0.24398	0.019000	0.16419	0.046000	0.14306	0.403000	0.20982	0.203000	0.20529	0.467000	0.42956	CGA		TCGA-XD-AAUI-01A-42D-A40W-08	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	1	0	1	17	130	0	36		0	0	0	0	36	2		0	0	0	0	0	2	1	0.999974	17	129	0	36	2								-20.000000	1	1	121412	7	36	1	0	1	1	1.862336	1	0.210000	1.910000	0.123488	0.870000	0.570000	1.000000	1.000000	0.860084	0.870000	1	7.200000e-01	1
LRRC37B	114659	broad.mit.edu	37	17	30374829	30374829	+	Silent	SNP	A	A	G			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr17:30374829A>G	ENST00000341671.7	+	9	2297	c.2292A>G	c.(2290-2292)ttA>ttG	p.L764L	LRRC37B_ENST00000543378.2_Silent_p.L682L|LRRC37B_ENST00000394713.3_Silent_p.L713L|LRRC37B_ENST00000584368.1_Silent_p.L725L|LRRC37B_ENST00000327564.7_Silent_p.L791L	NM_052888.2	NP_443120.2	Q96QE4	LR37B_HUMAN	leucine rich repeat containing 37B			29		Myeloproliferative disorder(56;0.0255)|all_hematologic(16;0.111)|Ovarian(249;0.182)|Breast(31;0.244)			TGAAGATGTTACAAGCCCGGA	0.488000																								0							SO:0001819	synonymous_variant			ENST00000341671.7	1	1	hg19	CCDS32609.1																																																																																				TCGA-XD-AAUI-01A-42D-A40W-08	LRRC37B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446508.1	1	0	1	64	587	0	182	1	8.211094e-01	4	27	0	182	2		0	0	0	0	0	2	1	1.000000	64	577	0	181	2								-20.000000	1	1	0	0		1	2	2	4	2.236854	1	0.210000	1.910000	0.289121	0.990000	0.820000	1.000000	1.000000	0.978822	0.990000	1	9.400000e-01	1
CASC3	22794	broad.mit.edu	37	17	38320039	38320039	+	Missense_Mutation	SNP	C	C	T			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr17:38320039C>T	ENST00000264645.7	+	7	1317	c.1091C>T	c.(1090-1092)cCa>cTa	p.P364L		NM_007359.4	NP_031385.2	O15234	CASC3_HUMAN	cancer susceptibility candidate 3			16					GATCCATCTCCAGAAGCAGAT	0.587000																								0							SO:0001583	missense			ENST00000264645.7	1	1	hg19	CCDS11362.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.426140	0.83667	.	.	ENSG00000108349	ENST00000264645;ENST00000418132;ENST00000394114	.	.	.	5.61	5.61	0.85477	.	0.056403	0.64402	D	0.000001	T	0.73434	0.3586	L	0.36672	1.1	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.75187	-0.3406	9	0.72032	D	0.01	-8.0315	19.2489	0.93914	0.0:1.0:0.0:0.0	.	364;364	B4DKR6;O15234	.;CASC3_HUMAN	L	364	.	ENSP00000264645:P364L	P	+	2	0	CASC3	35573565	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	5.784000	0.68990	2.648000	0.89879	0.563000	0.77884	CCA		TCGA-XD-AAUI-01A-42D-A40W-08	CASC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257127.3	1	0	0	33	736	0	172	1	7.201792e-01	4	54	0	172	2		0	0	0	0	0	2	1	1.000000	33	720	0	170	2								-3.072344	1	1	0	0		1	1	3	4	2.263984	1	0.210000	1.910000	0.315009	0.490000	0.330000	1.000000	0.470000	0.580754	0.490000	0	4.000000e-01	1
DHX58	79132	broad.mit.edu	37	17	40260081	40260081	+	Missense_Mutation	SNP	C	C	A			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr17:40260081C>A	ENST00000251642.3	-	7	946	c.724G>T	c.(724-726)Gac>Tac	p.D242Y		NM_024119.2	NP_077024.2	Q96C10	DHX58_HUMAN	DEXH (Asp-Glu-X-His) box polypeptide 58			16		all_cancers(22;9.73e-07)|all_epithelial(22;3.58e-05)|Breast(137;0.000143)			TCCAGGTGGTCATGGATTTGG	0.557000																								0							SO:0001583	missense			ENST00000251642.3	0	1	hg19	CCDS11416.1	.	.	.	.	.	.	.	.	.	.	C	13.11	2.139297	0.37728	.	.	ENSG00000108771	ENST00000251642;ENST00000423748;ENST00000413196	T;T	0.24350	2.0;1.86	5.08	1.82	0.25136	.	0.408706	0.26991	N	0.021480	T	0.27967	0.0689	M	0.64997	1.995	0.09310	N	0.999996	B;D	0.55385	0.245;0.971	B;P	0.47645	0.08;0.553	T	0.11348	-1.0591	10	0.45353	T	0.12	-12.1084	6.7211	0.23330	0.0:0.5553:0.2787:0.166	.	235;242	B7Z455;Q96C10	.;DHX58_HUMAN	Y	242;205;242	ENSP00000251642:D242Y;ENSP00000416389:D242Y	ENSP00000251642:D242Y	D	-	1	0	DHX58	37513607	0.000000	0.05858	0.515000	0.27774	0.061000	0.15899	0.163000	0.16520	0.117000	0.18138	0.563000	0.77884	GAC		TCGA-XD-AAUI-01A-42D-A40W-08	DHX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257396.1	0	0	0	8	372	0	105	0	8.365598e-02	0	20	0	105	2		0	0	0	0	0	2	1	0.988345	8	362	0	104	2								-2.934218	1	1	0	0		1	1	2	3	2.082176	0	0.210000	1.910000	0.224654	0.220000	0.100000	1.000000	0.200000	0.334120	0.220000	0	1.500000e-01	4.000000e-01
BPTF	2186	broad.mit.edu	37	17	65925454	65925454	+	Missense_Mutation	SNP	G	G	A			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr17:65925454G>A	ENST00000321892.4	+	19	6440	c.6379G>A	c.(6379-6381)Gtt>Att	p.V2127I	BPTF_ENST00000335221.5_Missense_Mutation_p.V2127I|BPTF_ENST00000424123.3_Missense_Mutation_p.V1988I|BPTF_ENST00000306378.6_Missense_Mutation_p.V2001I			Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor			78	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)		TTTTTAAGGCGTTGTTCAAGT	0.433000																								0							SO:0001583	missense			ENST00000321892.4	1	1	hg19		.	.	.	.	.	.	.	.	.	.	G	10.43	1.348665	0.24426	.	.	ENSG00000171634	ENST00000306378;ENST00000335221;ENST00000321892	T;T;T	0.64803	-0.06;-0.12;-0.09	5.84	4.85	0.62838	.	.	.	.	.	T	0.44808	0.1311	N	0.17082	0.46	0.33129	D	0.542898	P;P	0.47034	0.466;0.889	B;B	0.36922	0.029;0.236	T	0.56786	-0.7921	9	0.34782	T	0.22	-11.045	15.4007	0.74838	0.0676:0.0:0.9324:0.0	.	2001;2127	Q12830-2;Q12830-4	.;.	I	2001;2127;2127	ENSP00000307208:V2001I;ENSP00000334351:V2127I;ENSP00000315454:V2127I	ENSP00000307208:V2001I	V	+	1	0	BPTF	63355916	1.000000	0.71417	0.990000	0.47175	0.981000	0.71138	3.766000	0.55280	1.443000	0.47586	0.650000	0.86243	GTT		TCGA-XD-AAUI-01A-42D-A40W-08	BPTF-201	KNOWN	basic	protein_coding	protein_coding		1	0	0	12	234	0	77	1	3.570716e-01	4	20	0	77	2		0	0	0	0	0	2	1	0.999162	12	233	0	77	2								-13.869140	1	1	121412	15	44	1	0	1	1	1.853394	1	0.210000	1.910000	0.117318	0.410000	0.220000	0.660000	0.400000	0.433162	0.410000	0	3.100000e-01	5.400000e-01
ABCA9	10350	broad.mit.edu	37	17	66979885	66979885	+	Silent	SNP	G	G	A			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr17:66979885G>A	ENST00000340001.4	-	36	4816	c.4605C>T	c.(4603-4605)atC>atT	p.I1535I	ABCA9_ENST00000370732.2_3'UTR|ABCA9_ENST00000482072.1_5'Flank|ABCA9_ENST00000453985.2_Silent_p.I1497I	NM_080283.3	NP_525022.2	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 9			91	Breast(10;1.47e-12)				AAAGCCTCAGGATCTCTGCAT	0.463000																								0							SO:0001819	synonymous_variant			ENST00000340001.4	1	1	hg19	CCDS11681.1																																																																																				TCGA-XD-AAUI-01A-42D-A40W-08	ABCA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277072.2	1	0	1	47	286	0	85	0	4.291758e-01	0	10	0	85	2		0	0	0	0	0	2	1	1.000000	47	284	0	85	2								-19.981730	1	0	0	0		1	0	1	1	1.853394	1	0.210000	1.910000	0.117318	0.940000	0.790000	1.000000	0.990000	0.937043	0.940000	1	8.700000e-01	9.900000e-01
TP53	7157	broad.mit.edu	37	17	7577538	7577538	+	Missense_Mutation	SNP	C	C	T	rs11540652		TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr17:7577538C>T	ENST00000269305.4	-	7	932	c.743G>A	c.(742-744)cGg>cAg	p.R248Q	TP53_ENST00000445888.2_Missense_Mutation_p.R248Q|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.R248Q|TP53_ENST00000420246.2_Missense_Mutation_p.R248Q|TP53_ENST00000359597.4_Missense_Mutation_p.R248Q|TP53_ENST00000413465.2_Missense_Mutation_p.R248Q	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.R248Q(580)|p.R248L(75)|p.R248P(19)|p.R155Q(18)|p.0?(8)|p.?(5)|p.R155L(3)|p.R155P(2)|p.N247_R248delNR(2)|p.R248fs*16(2)|p.M246_P250delMNRRP(2)|p.R248_P250delRRP(1)|p.unknown(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R249fs*96(1)|p.R248fs*>39(1)|p.R248C(1)|p.G245fs*14(1)|p.N247_R248>IP(1)		24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		Acetylsalicylic acid(DB00945)	GATGGGCCTCCGGTTCATGCC	0.572000	R248Q(BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(HCC1143_BREAST)|R248Q(HCC70_BREAST)|R248Q(HEC1A_ENDOMETRIUM)|R248Q(HS683_CENTRAL_NERVOUS_SYSTEM)|R248Q(HSC4_UPPER_AERODIGESTIVE_TRACT)|R248Q(KASUMI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(KYSE150_OESOPHAGUS)|R248Q(MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NAMALWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NB4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NCIH211_LUNG)|R248Q(NCIN87_STOMACH)|R248Q(NIHOVCAR3_OVARY)|R248Q(NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(P12ICHIKAWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(PANC0203_PANCREAS)|R248Q(PC14_LUNG)|R248Q(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(RT112_URINARY_TRACT)|R248Q(SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SF295_CENTRAL_NERVOUS_SYSTEM)|R248Q(SKUT1_SOFT_TISSUE)|R248Q(SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SW1463_LARGE_INTESTINE)|R248Q(WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	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	725	Substitution - Missense(698)|Whole gene deletion(8)|Deletion - In frame(7)|Unknown(6)|Insertion - Frameshift(3)|Deletion - Frameshift(2)|Complex - compound substitution(1)	GRCh37	CM920675	TP53	M	rs11540652	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	27.3	4.822907	0.90873	0.0	1.16E-4	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99864	-7.28;-7.28;-7.28;-7.28;-7.28;-7.28;-7.28;-7.28	4.62	3.65	0.41850	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99840	0.9927	M	0.88640	2.97	0.58432	A	0.999994	D;D;D;D;D;D	0.89917	1.0;0.994;1.0;1.0;1.0;1.0	D;P;D;D;D;D	0.91635	0.996;0.882;0.999;0.995;0.996;0.995	D	0.96819	0.9602	9	0.72032	D	0.01	-9.5643	10.6687	0.45745	0.0:0.9059:0.0:0.0941	rs11540652;rs11540652	248;248;155;248;248;248	P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;P53_HUMAN;.;.	Q	248;248;248;248;248;248;237;155;116;155	ENSP00000410739:R248Q;ENSP00000352610:R248Q;ENSP00000269305:R248Q;ENSP00000398846:R248Q;ENSP00000391127:R248Q;ENSP00000391478:R248Q;ENSP00000425104:R116Q;ENSP00000423862:R155Q	ENSP00000269305:R248Q	R	-	2	0	TP53	7518263	1.000000	0.71417	1.000000	0.80357	0.887000	0.51463	5.884000	0.69729	1.305000	0.44909	0.462000	0.41574	CGG		TCGA-XD-AAUI-01A-42D-A40W-08	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	1	0	1	28	156	0	72	1	9.996647e-01	27	46	0	72	2	1	1	84	845	2	899	8	1	1.000000	28	150	0	72	2								-2.603265	1	1	121412	7	38	1	0	1	1	1.862336	1	0.210000	1.910000	0.123488	0.980000	0.760000	1.000000	1.000000	0.953148	0.980000	1	8.800000e-01	1
DSC1	1823	broad.mit.edu	37	18	28710559	28710559	+	Missense_Mutation	SNP	C	C	G			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr18:28710559C>G	ENST00000257198.5	-	16	2864	c.2603G>C	c.(2602-2604)cGg>cCg	p.R868P	DSC1_ENST00000257197.3_3'UTR|RP11-408H20.3_ENST00000582307.1_RNA|RP11-408H20.2_ENST00000581836.1_RNA	NM_024421.2	NP_077739.1	Q08554	DSC1_HUMAN	desmocollin 1			53			OV - Ovarian serous cystadenocarcinoma(10;0.00778)		TTCTTCCTGCCGATCGCTGCA	0.438000																								0							SO:0001583	missense			ENST00000257198.5	1	1	hg19	CCDS11894.1	.	.	.	.	.	.	.	.	.	.	C	14.19	2.460536	0.43736	.	.	ENSG00000134765	ENST00000257198	T	0.76839	-1.05	6.17	1.38	0.22167	Cadherin, cytoplasmic domain (1);	0.137951	0.33235	N	0.005138	T	0.67878	0.2940	M	0.63843	1.955	0.09310	N	1	B	0.15719	0.014	B	0.20955	0.032	T	0.60383	-0.7274	10	0.59425	D	0.04	.	1.3924	0.02253	0.1426:0.3912:0.1396:0.3265	.	868	Q08554	DSC1_HUMAN	P	868	ENSP00000257198:R868P	ENSP00000257198:R868P	R	-	2	0	DSC1	26964557	0.926000	0.31397	0.445000	0.26908	0.605000	0.37080	0.758000	0.26447	0.492000	0.27815	0.655000	0.94253	CGG		TCGA-XD-AAUI-01A-42D-A40W-08	DSC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254946.1	1	0	0	36	505	0	147		0	0	0	0	147	2		0	0	0	0	0	2	1	1.000000	36	496	0	144	2								-2.879449	1	1	0	0		1	0	0	0	1.913322	0	0.210000	1.910000	0.164375	0.590000	0.420000	0.790000	0.590000	0.607759	0.590000	0	5.000000e-01	7.000000e-01
C19orf57	79173	broad.mit.edu	37	19	14006193	14006193	+	Silent	SNP	G	G	A			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr19:14006193G>A	ENST00000586783.1	-	2	197	c.198C>T	c.(196-198)gcC>gcT	p.A66A	C19orf57_ENST00000346736.2_Silent_p.A66A|C19orf57_ENST00000454313.1_Silent_p.A66A|C19orf57_ENST00000591586.1_Silent_p.A66A			Q0VDD7	CS057_HUMAN	chromosome 19 open reading frame 57			14			OV - Ovarian serous cystadenocarcinoma(19;2e-21)		ACCTGGAGACGGCCTTTCCTG	0.562000																								0							SO:0001819	synonymous_variant			ENST00000586783.1	0	1	hg19																																																																																					TCGA-XD-AAUI-01A-42D-A40W-08	C19orf57-003	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000457947.1	0	0	0	7	377	1	86	0	4.795013e-04	0	2	1	86	2		0	0	0	0	0	2	0	0.041244	7	374	1	86	16								-2.718714	1	1	121412	1	34	1	1	2	3	2.028289	0	0.210000	1.910000	0.214126	0.180000	0.070000	1.000000	0.170000	0.227040	0.180000	0	1.200000e-01	2.800000e-01
LSR	51599	broad.mit.edu	37	19	35753531	35753531	+	Silent	SNP	G	G	A			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr19:35753531G>A	ENST00000361790.3	+	5	1017	c.858G>A	c.(856-858)ccG>ccA	p.P286P	AD000684.2_ENST00000602262.1_RNA|LSR_ENST00000347609.4_Silent_p.P249P|LSR_ENST00000602122.1_Silent_p.P267P|LSR_ENST00000597933.1_3'UTR|LSR_ENST00000427250.1_Intron|LSR_ENST00000354900.3_Silent_p.P267P|LSR_ENST00000360798.3_Intron	NM_205834.3	NP_991403.1	Q86X29	LSR_HUMAN	lipolysis stimulated lipoprotein receptor			13	all_lung(56;3.91e-09)|Lung NSC(56;5.64e-09)|Esophageal squamous(110;0.162)		Epithelial(14;1.33e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.29e-18)|all cancers(14;7.11e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)		AGTGCTGCCCGCACACTTGCT	0.622000																								0							SO:0001819	synonymous_variant			ENST00000361790.3	0	1	hg19	CCDS12450.1																																																																																				TCGA-XD-AAUI-01A-42D-A40W-08	LSR-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465513.2	0	0	0	6	429	0	87	1	9.853121e-01	2	560	0	87	2		0	0	0	0	0	2	1	0.963160	6	421	0	87	2								-2.513202	1	1	121412	4	37	1	1	3	4	2.395528	1	0.210000	1.910000	0.329656	0.170000	0.060000	1.000000	0.150000	0.276476	0.170000	0	1.100000e-01	3.100000e-01
USP29	57663	broad.mit.edu	37	19	57641566	57641566	+	Missense_Mutation	SNP	T	T	A	rs145552693		TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr19:57641566T>A	ENST00000254181.4	+	4	1977	c.1523T>A	c.(1522-1524)aTc>aAc	p.I508N	USP29_ENST00000598197.1_Missense_Mutation_p.I508N	NM_020903.2	NP_065954.1	Q9HBJ7	UBP29_HUMAN	ubiquitin specific peptidase 29			85		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)			AGGGTCCTTATCATTCATCTG	0.368000																								0							SO:0001583	missense			ENST00000254181.4	0	1	hg19	CCDS33124.1	.	.	.	.	.	.	.	.	.	.	T	11.77	1.737455	0.30774	.	.	ENSG00000131864	ENST00000254181	T	0.77229	-1.08	2.69	1.66	0.24008	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.32819	U	0.005605	D	0.84483	0.5482	M	0.78916	2.43	0.31512	N	0.663476	D	0.89917	1.0	D	0.97110	1.0	T	0.81992	-0.0678	10	0.87932	D	0	-10.247	5.9622	0.19305	0.0:0.138:0.0:0.8619	.	508	Q9HBJ7	UBP29_HUMAN	N	508	ENSP00000254181:I508N	ENSP00000254181:I508N	I	+	2	0	USP29	62333378	1.000000	0.71417	0.168000	0.22838	0.221000	0.24807	3.064000	0.49986	0.430000	0.26230	0.482000	0.46254	ATC		TCGA-XD-AAUI-01A-42D-A40W-08	USP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465075.1	0	0	0	5	435	0	103		0	0	0	0	103	2		0	0	0	0	0	2	1	0.936748	5	432	0	103	2								-5.220647	1	1	0	0		1	0	2	2	1.961025	1	0.210000	1.910000	0.210000	0.120000	0.040000	1.000000	0.110000	0.205652	0.120000	0	7.000000e-02	2.100000e-01
LRRC8E	80131	broad.mit.edu	37	19	7965572	7965572	+	Missense_Mutation	SNP	G	G	A			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr19:7965572G>A	ENST00000306708.6	+	3	2266	c.2165G>A	c.(2164-2166)cGc>cAc	p.R722H	RN7SL115P_ENST00000392196.5_RNA|AC010336.1_ENST00000539278.1_5'UTR	NM_001268284.1|NM_001268285.1|NM_025061.4	NP_001255213.1|NP_001255214.1|NP_079337.2	Q6NSJ5	LRC8E_HUMAN	leucine rich repeat containing 8 family, member E			35					TTCTTCTGCCGCAAGCTGCGG	0.657000																								0							SO:0001583	missense			ENST00000306708.6	0	1	hg19	CCDS12189.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	7.848	0.723462	0.15439	.	.	ENSG00000171017	ENST00000306708	T	0.10382	2.88	4.35	2.07	0.26955	.	0.307696	0.29444	N	0.012138	T	0.06826	0.0174	L	0.31578	0.945	0.24912	N	0.992033	B	0.13594	0.008	B	0.10450	0.005	T	0.24693	-1.0153	10	0.40728	T	0.16	.	4.6497	0.12589	0.3968:0.0:0.6032:0.0	.	722	Q6NSJ5	LRC8E_HUMAN	H	722	ENSP00000306524:R722H	ENSP00000306524:R722H	R	+	2	0	LRRC8E	7871572	0.992000	0.36948	0.479000	0.27329	0.045000	0.14185	2.928000	0.48908	1.028000	0.39785	0.585000	0.79938	CGC		TCGA-XD-AAUI-01A-42D-A40W-08	LRRC8E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461354.1	0	0	0	5	250	0	79	0	2.900688e-02	0	11	0	79	2		0	0	0	0	0	2	1	0.934172	5	244	0	78	2								-2.308896	0	1	121410	11	41	1	0	1	1	1.923094	0	0.210000	1.910000	0.153087	0.180000	0.060000	0.370000	0.170000	0.202923	0.180000	0	1.100000e-01	2.800000e-01
MTOR	2475	broad.mit.edu	37	1	11193143	11193143	+	Missense_Mutation	SNP	C	C	G			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr1:11193143C>G	ENST00000361445.4	-	38	5434	c.5358G>C	c.(5356-5358)tgG>tgC	p.W1786C	MTOR_ENST00000495435.1_5'UTR|MTOR_ENST00000376838.1_5'Flank	NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)			149				Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	TCACCTTGTACCAGCTGCGGT	0.577000																								0							SO:0001583	missense			ENST00000361445.4	1	1	hg19	CCDS127.1	.	.	.	.	.	.	.	.	.	.	C	15.58	2.875568	0.51695	.	.	ENSG00000198793	ENST00000361445	T	0.72835	-0.69	5.65	4.74	0.60224	PIK-related kinase (1);PIK-related kinase, FAT (1);Armadillo-like helical (1);	0.059201	0.64402	N	0.000001	T	0.73393	0.3581	M	0.80616	2.505	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.71741	-0.4501	10	0.51188	T	0.08	-12.1729	16.7143	0.85394	0.0:0.8706:0.1294:0.0	.	1786	P42345	MTOR_HUMAN	C	1786	ENSP00000354558:W1786C	ENSP00000354558:W1786C	W	-	3	0	MTOR	11115730	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.456000	0.80751	1.367000	0.46095	0.655000	0.94253	TGG		TCGA-XD-AAUI-01A-42D-A40W-08	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	1	0	0	33	392	0	106	1	3.951495e-01	8	9	0	106	2		0	0	0	0	0	2	1	1.000000	33	387	0	104	2								-9.515631	1	1	0	0		1	1	2	3	2.034459	0	0.210000	1.910000	0.214946	0.750000	0.520000	1.000000	1.000000	0.766159	0.750000	0	6.300000e-01	9.100000e-01
KRTAP24-1	643803	broad.mit.edu	37	21	31654596	31654596	+	Nonsense_Mutation	SNP	G	G	A			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr21:31654596G>A	ENST00000340345.4	-	1	680	c.655C>T	c.(655-657)Cga>Tga	p.R219*		NM_001085455.1	NP_001078924.1	Q3LI83	KR241_HUMAN	keratin associated protein 24-1			14					CTCAGTGGTCGGCAGCTCGTA	0.443000																								0							SO:0001587	stop_gained			ENST00000340345.4	0	1	hg19	CCDS42915.1	.	.	.	.	.	.	.	.	.	.	G	15.89	2.967829	0.53507	.	.	ENSG00000188694	ENST00000340345	.	.	.	4.04	3.15	0.36227	.	1.427210	0.04871	N	0.445896	.	.	.	.	.	.	0.47214	D	0.999352	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	2.7357	8.2674	0.31821	0.1164:0.0:0.8836:0.0	.	.	.	.	X	219	.	ENSP00000339238:R219X	R	-	1	2	KRTAP24-1	30576467	0.010000	0.17322	0.013000	0.15412	0.022000	0.10575	1.624000	0.37018	0.998000	0.38996	-0.251000	0.11542	CGA		TCGA-XD-AAUI-01A-42D-A40W-08	KRTAP24-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246806.2	0	0	0	14	407	0	112		0	0	0	0	112	2		0	0	0	0	0	2	1	0.999738	13	402	0	112	2								-2.621413	1	1	120808	2	34	1	0	0	0	1.978313	0	0.210000	1.910000	0.191319	0.310000	0.170000	0.490000	0.310000	0.326617	0.310000	0	2.300000e-01	4.100000e-01
LRP1B	53353	broad.mit.edu	37	2	141533746	141533746	+	Silent	SNP	G	G	A			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr2:141533746G>A	ENST00000389484.3	-	33	6392	c.5421C>T	c.(5419-5421)gaC>gaT	p.D1807D		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B			606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)			GGTTTCTTCCGTCTCTTTTGC	0.383000										TSP Lung(27;0.18)			Colon(99;50 2074 2507 20106)											0							SO:0001819	synonymous_variant			ENST00000389484.3	1	1	hg19	CCDS2182.1																																																																																				TCGA-XD-AAUI-01A-42D-A40W-08	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	1	0	1	30	203	0	50		0	0	0	0	50	2		0	0	0	0	0	2	1	1.000000	30	201	0	49	2								-14.093960	1	1	121412	6	38	1	1	2	3	2.075048	0	0.210000	1.910000	0.223053	0.990000	0.880000	1.000000	1.000000	0.992440	0.990000	1	9.900000e-01	1
MYCN	4613	broad.mit.edu	37	2	16086019	16086019	+	Missense_Mutation	SNP	T	T	A			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr2:16086019T>A	ENST00000281043.3	+	3	1492	c.1195T>A	c.(1195-1197)Tcc>Acc	p.S399T		NM_005378.4	NP_005369.2	P04198	MYCN_HUMAN	v-myc avian myelocytomatosis viral oncogene neuroblastoma derived homolog			31	all_cancers(1;1.35e-08)|all_neural(1;2.92e-24)|Lung SC(1;3.26e-07)|Medulloblastoma(1;6.9e-06)|all_lung(1;1.26e-05)|Glioma(3;0.135)|Acute lymphoblastic leukemia(172;0.155)|all_epithelial(1;0.169)|all_hematologic(175;0.197)		GBM - Glioblastoma multiforme(3;0.000332)		CGACCTTCGGTCCAGCTTTCT	0.562000			A		neuroblastoma										Dom	yes		2	2p24.1	4613	v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian)		O	0							SO:0001583	missense			ENST00000281043.3	1	1	hg19	CCDS1687.1	.	.	.	.	.	.	.	.	.	.	T	15.43	2.831915	0.50845	.	.	ENSG00000134323	ENST00000281043;ENST00000426211	D	0.98120	-4.73	5.14	3.98	0.46160	Helix-loop-helix DNA-binding (5);	0.000000	0.85682	D	0.000000	D	0.95335	0.8486	N	0.05078	-0.115	0.53688	D	0.999976	D	0.64830	0.994	D	0.64506	0.926	D	0.92718	0.6189	10	0.22109	T	0.4	-18.6908	10.7944	0.46451	0.0:0.0748:0.0:0.9252	.	399	P04198	MYCN_HUMAN	T	399;317	ENSP00000281043:S399T	ENSP00000281043:S399T	S	+	1	0	MYCN	16003470	1.000000	0.71417	0.850000	0.33497	0.991000	0.79684	5.091000	0.64505	0.931000	0.37242	0.496000	0.49642	TCC		TCGA-XD-AAUI-01A-42D-A40W-08	MYCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095469.2	0	0	1	51	449	1	145	0	3.028889e-02	0	3	1	145	2		0	0	0	0	0	2	1	1.000000	50	442	1	145	13								-20.000000	1	1	0	0		1	1	2	3	2.075048	0	0.210000	1.910000	0.223053	0.990000	0.750000	1.000000	1.000000	0.952667	0.990000	1	8.700000e-01	1
SCN9A	6335	broad.mit.edu	37	2	167056341	167056341	+	Missense_Mutation	SNP	A	A	G			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr2:167056341A>G	ENST00000409435.1	-	26	4807	c.4808T>C	c.(4807-4809)tTt>tCt	p.F1603S	AC010127.3_ENST00000447809.2_RNA|SCN9A_ENST00000409672.1_Missense_Mutation_p.F1592S|SCN9A_ENST00000303354.6_Missense_Mutation_p.F1604S|SCN9A_ENST00000375387.4_Missense_Mutation_p.F1604S			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit			108				Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	AGGGGACACAAAATACGTTTC	0.423000																								0							SO:0001583	missense			ENST00000409435.1	1	1	hg19	CCDS46441.1	.	.	.	.	.	.	.	.	.	.	A	19.39	3.817625	0.70912	.	.	ENSG00000169432	ENST00000409672;ENST00000375387;ENST00000303354;ENST00000409435	D;D;D;D	0.98296	-4.85;-4.85;-4.85;-4.85	5.74	5.74	0.90152	.	0.000000	0.64402	D	0.000009	D	0.98425	0.9476	M	0.65498	2.005	0.80722	D	1	D	0.55172	0.97	P	0.58820	0.846	D	0.99548	1.0965	10	0.87932	D	0	.	16.0249	0.80536	1.0:0.0:0.0:0.0	.	1592	E7EUN6	.	S	1592;1604;1604;1603	ENSP00000386306:F1592S;ENSP00000364536:F1604S;ENSP00000304748:F1604S;ENSP00000386330:F1603S	ENSP00000304748:F1604S	F	-	2	0	SCN9A	166764587	1.000000	0.71417	0.998000	0.56505	0.855000	0.48748	9.157000	0.94714	2.181000	0.69327	0.528000	0.53228	TTT		TCGA-XD-AAUI-01A-42D-A40W-08	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	1	0	0	43	373	0	89		0	0	0	0	89	2		0	0	0	0	0	2	1	1.000000	43	364	0	88	2								-20.000000	1	1	0	0		1	1	2	3	2.075048	0	0.210000	1.910000	0.223053	0.990000	0.740000	1.000000	1.000000	0.954575	0.990000	1	8.700000e-01	1
XIRP2	129446	broad.mit.edu	37	2	168103840	168103840	+	Missense_Mutation	SNP	A	A	C			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr2:168103840A>C	ENST00000409195.1	+	9	6027	c.5938A>C	c.(5938-5940)Aag>Cag	p.K1980Q	XIRP2_ENST00000295237.9_Missense_Mutation_p.K1980Q|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.K1758Q|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409756.2_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2			315					TCTTCAGCCAAAGCCAGGTCC	0.468000																								0							SO:0001583	missense			ENST00000409195.1	1	1	hg19	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	A	0.052	-1.247707	0.01469	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.02552	4.25;4.25;4.25	5.73	2.16	0.27623	.	0.674670	0.15536	N	0.257239	T	0.01558	0.0050	N	0.14661	0.345	0.09310	N	1	B;B;B	0.26258	0.09;0.145;0.091	B;B;B	0.24541	0.024;0.054;0.034	T	0.48399	-0.9039	10	0.12766	T	0.61	-1.5086	3.3189	0.07043	0.5633:0.0:0.2707:0.1659	.	1805;1805;1758	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	Q	1980;1980;1758	ENSP00000386840:K1980Q;ENSP00000295237:K1980Q;ENSP00000387255:K1758Q	ENSP00000295237:K1980Q	K	+	1	0	XIRP2	167812086	0.000000	0.05858	0.947000	0.38551	0.012000	0.07955	-0.097000	0.11042	0.465000	0.27167	-0.263000	0.10527	AAG		TCGA-XD-AAUI-01A-42D-A40W-08	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	1	0	0	16	220	0	61		0	0	0	0	61	2		0	0	0	0	0	2	1	0.999938	14	220	0	61	2								-19.894760	1	1	0	0		1	1	2	3	2.075048	0	0.210000	1.910000	0.223053	0.690000	0.400000	1.000000	1.000000	0.719264	0.690000	0	5.300000e-01	9.800000e-01
ALS2CR12	130540	broad.mit.edu	37	2	202172323	202172323	+	Silent	SNP	G	G	A			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr2:202172323G>A	ENST00000286190.5	-	10	844	c.798C>T	c.(796-798)ttC>ttT	p.F266F	ALS2CR12_ENST00000392257.3_Silent_p.F266F|ALS2CR12_ENST00000448967.1_5'Flank|ALS2CR12_ENST00000405148.2_Silent_p.F266F|ALS2CR12_ENST00000439709.1_Silent_p.F266F			Q96Q35	AL2SB_HUMAN	amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 12	p.F266F(1)		21					ACTCCATTTCGAATTTTTTGG	0.383000																								1	Substitution - coding silent(1)						SO:0001819	synonymous_variant			ENST00000286190.5	1	1	hg19	CCDS2346.1	.	.	.	.	.	.	.	.	.	.	G	0.508	-0.867740	0.02590	.	.	ENSG00000155749	ENST00000415745	.	.	.	5.53	-0.054	0.13816	.	.	.	.	.	T	0.50888	0.1642	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.35919	-0.9769	4	.	.	.	-8.4115	5.6157	0.17430	0.6368:0.1427:0.2205:0.0	.	.	.	.	L	41	.	.	S	-	2	0	ALS2CR12	201880568	0.992000	0.36948	0.993000	0.49108	0.026000	0.11368	0.295000	0.19065	-0.114000	0.11936	-0.300000	0.09419	TCG		TCGA-XD-AAUI-01A-42D-A40W-08	ALS2CR12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256286.1	1	0	0	26	462	0	137		0	0	0	0	137	2		0	0	0	0	0	2	1	1.000000	26	458	0	137	2								-5.217164	1	1	121404	6	41	1	1	2	3	2.067490	0	0.210000	1.910000	0.221445	0.530000	0.350000	1.000000	0.510000	0.581268	0.530000	0	4.300000e-01	7.000000e-01
SIX2	10736	broad.mit.edu	37	2	45233480	45233480	+	Silent	SNP	C	C	T	rs146943650	byFrequency	TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr2:45233480C>T	ENST00000303077.6	-	2	1024	c.705G>A	c.(703-705)ccG>ccA	p.P235P		NM_016932.4	NP_058628.3	Q9NPC8	SIX2_HUMAN	SIX homeobox 2	p.P235P(1)		22		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)			CAGGGGGCGGCGGGCTGAGGA	0.706000																								1	Substitution - coding silent(1)						SO:0001819	synonymous_variant			ENST00000303077.6	1	1	hg19	CCDS1822.1																																																																																				TCGA-XD-AAUI-01A-42D-A40W-08	SIX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326188.2	0	0	0	16	296	0	106	0	3.947501e-02	1	5	0	106	2		0	0	0	0	0	2	1	0.999921	16	286	0	105	2								-3.317208	1	1	121410	48	49	1	1	2	3	2.075048	0	0.210000	1.910000	0.223053	0.520000	0.300000	1.000000	0.500000	0.578975	0.520000	0	4.000000e-01	7.500000e-01
FBXO11	80204	broad.mit.edu	37	2	48066031	48066031	+	Missense_Mutation	SNP	C	C	T			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr2:48066031C>T	ENST00000403359.3	-	4	626	c.554G>A	c.(553-555)cGc>cAc	p.R185H	FBXO11_ENST00000480038.1_5'UTR|FBXO11_ENST00000402508.1_Missense_Mutation_p.R101H|FBXO11_ENST00000378314.3_Missense_Mutation_p.R67H|FBXO11_ENST00000316377.4_Missense_Mutation_p.R101H	NM_001190274.1	NP_001177203.1	Q86XK2	FBX11_HUMAN	F-box protein 11	p.0?(2)		26		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		TTCACTGAAGCGTTTACATAC	0.363000			Mis, F, D		DLBCL										Rec	yes		2	2p16.3	80204	F-box protein 11		L	2	Whole gene deletion(2)						SO:0001583	missense			ENST00000403359.3	0	1	hg19	CCDS54357.1	.	.	.	.	.	.	.	.	.	.	C	34	5.310469	0.95629	.	.	ENSG00000138081	ENST00000402508;ENST00000403359;ENST00000316377;ENST00000424163;ENST00000378314	T;T;T;T;T	0.51325	0.71;0.71;0.71;0.71;0.71	5.5	5.5	0.81552	F-box domain, cyclin-like (2);F-box domain, Skp2-like (1);	0.000000	0.85682	D	0.000000	T	0.69070	0.3070	M	0.72118	2.19	0.80722	D	1	D	0.76494	0.999	D	0.68621	0.959	T	0.71906	-0.4451	10	0.87932	D	0	-4.1684	19.3886	0.94570	0.0:1.0:0.0:0.0	.	185	Q86XK2	FBX11_HUMAN	H	101;185;101;101;67	ENSP00000385398:R101H;ENSP00000384823:R185H;ENSP00000323822:R101H;ENSP00000392272:R101H;ENSP00000367565:R67H	ENSP00000323822:R101H	R	-	2	0	FBXO11	47919535	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.573000	0.86826	0.563000	0.77884	CGC		TCGA-XD-AAUI-01A-42D-A40W-08	FBXO11-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251181.3	0	0	1	33	227	1	65	1	3.817560e-01	6	11	1	65	3		0	0	0	0	0	2	1	0.998886	32	226	1	65	14								-14.982660	1	1	0	0		1	1	2	3	2.075048	0	0.210000	1.910000	0.223053	0.990000	0.880000	1.000000	1.000000	0.992454	0.990000	1	9.900000e-01	1
BOC	91653	broad.mit.edu	37	3	112998688	112998688	+	Nonsense_Mutation	SNP	C	C	T			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr3:112998688C>T	ENST00000495514.1	+	13	2742	c.2038C>T	c.(2038-2040)Cga>Tga	p.R680*	BOC_ENST00000273395.4_Nonsense_Mutation_p.R681*|BOC_ENST00000355385.3_Nonsense_Mutation_p.R680*			Q9BWV1	BOC_HUMAN	BOC cell adhesion associated, oncogene regulated			68			Epithelial(53;0.227)		CTACAAGTTTCGAGTCCGGGC	0.622000																								0							SO:0001587	stop_gained			ENST00000495514.1	0	1	hg19	CCDS2971.1	.	.	.	.	.	.	.	.	.	.	C	43	10.022862	0.99319	.	.	ENSG00000144857	ENST00000495514;ENST00000273395;ENST00000355385	.	.	.	5.53	5.53	0.82687	.	0.065151	0.64402	D	0.000007	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.4493	0.94860	0.0:1.0:0.0:0.0	.	.	.	.	X	680;681;680	.	ENSP00000273395:R681X	R	+	1	2	BOC	114481378	1.000000	0.71417	1.000000	0.80357	0.725000	0.41563	5.444000	0.66587	2.593000	0.87608	0.563000	0.77884	CGA		TCGA-XD-AAUI-01A-42D-A40W-08	BOC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354485.3	1	0	0	27	433	0	95	0	2.757958e-01	0	17	0	95	2		0	0	0	0	0	2	1	1.000000	24	425	0	91	2								-6.147839	1	1	0	0		1	1	2	3	2.064228	0	0.210000	1.910000	0.220638	0.580000	0.380000	1.000000	0.560000	0.624300	0.580000	0	4.700000e-01	7.500000e-01
DHX36	170506	broad.mit.edu	37	3	154018839	154018839	+	Missense_Mutation	SNP	T	T	A			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr3:154018839T>A	ENST00000496811.1	-	10	1375	c.1295A>T	c.(1294-1296)aAa>aTa	p.K432I	DHX36_ENST00000308361.6_Missense_Mutation_p.K432I|DHX36_ENST00000329463.5_Missense_Mutation_p.K432I|DHX36_ENST00000544526.1_Missense_Mutation_p.K432I	NM_020865.2	NP_065916.2	Q9H2U1	DHX36_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 36			35			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)		TTTTTCTTCTTTTTCTTGTCT	0.353000																								0							SO:0001583	missense			ENST00000496811.1	1	1	hg19	CCDS3171.1	.	.	.	.	.	.	.	.	.	.	T	19.36	3.813041	0.70912	.	.	ENSG00000174953	ENST00000496811;ENST00000308361;ENST00000544526;ENST00000329463;ENST00000481941	T;T;T;T;T	0.03801	3.98;3.9;3.81;3.8;3.99	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.12475	0.0303	L	0.60845	1.875	0.54753	D	0.999989	P;P;B	0.42456	0.78;0.78;0.27	P;P;B	0.48400	0.576;0.576;0.092	T	0.00240	-1.1887	10	0.72032	D	0.01	.	16.0307	0.80574	0.0:0.0:0.0:1.0	.	432;432;432	Q9H2U1-2;Q9H2U1-3;Q9H2U1	.;.;DHX36_HUMAN	I	432;432;432;432;346	ENSP00000417078:K432I;ENSP00000309296:K432I;ENSP00000444247:K432I;ENSP00000330113:K432I;ENSP00000419862:K346I	ENSP00000309296:K432I	K	-	2	0	DHX36	155501533	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	6.502000	0.73695	2.190000	0.69967	0.455000	0.32223	AAA		TCGA-XD-AAUI-01A-42D-A40W-08	DHX36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353349.1	1	0	1	61	402	0	97	1	9.072670e-01	3	26	0	97	2		0	0	0	0	0	2	1	1.000000	60	400	0	97	2								-20.000000	1	0	0	0		1	1	2	3	2.064228	0	0.210000	1.910000	0.220638	0.990000	0.990000	1.000000	1.000000	0.998838	0.990000	1	9.900000e-01	1
DHX36	170506	broad.mit.edu	37	3	154018849	154018849	+	Missense_Mutation	SNP	T	T	C			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr3:154018849T>C	ENST00000496811.1	-	10	1365	c.1285A>G	c.(1285-1287)Aga>Gga	p.R429G	DHX36_ENST00000308361.6_Missense_Mutation_p.R429G|DHX36_ENST00000329463.5_Missense_Mutation_p.R429G|DHX36_ENST00000544526.1_Missense_Mutation_p.R429G	NM_020865.2	NP_065916.2	Q9H2U1	DHX36_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 36			35			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)		TTTTCTTGTCTATTTACATGC	0.343000																								0							SO:0001583	missense			ENST00000496811.1	1	1	hg19	CCDS3171.1	.	.	.	.	.	.	.	.	.	.	T	11.26	1.587020	0.28268	0.0	1.16E-4	ENSG00000174953	ENST00000496811;ENST00000308361;ENST00000544526;ENST00000329463;ENST00000481941	T;T;T;T;T	0.03635	4.04;3.97;3.86;3.86;4.05	5.73	3.31	0.37934	.	0.050847	0.85682	D	0.000000	T	0.05502	0.0145	L	0.60455	1.87	0.42665	D	0.993495	B;P;B	0.47106	0.002;0.89;0.001	B;B;B	0.44224	0.011;0.444;0.004	T	0.48937	-0.8990	10	0.28530	T	0.3	.	8.1451	0.31106	0.1262:0.0:0.2626:0.6112	.	429;429;429	Q9H2U1-2;Q9H2U1-3;Q9H2U1	.;.;DHX36_HUMAN	G	429;429;429;429;343	ENSP00000417078:R429G;ENSP00000309296:R429G;ENSP00000444247:R429G;ENSP00000330113:R429G;ENSP00000419862:R343G	ENSP00000309296:R429G	R	-	1	2	DHX36	155501543	1.000000	0.71417	0.935000	0.37517	0.661000	0.39034	2.751000	0.47508	0.425000	0.26087	-1.580000	0.00857	AGA		TCGA-XD-AAUI-01A-42D-A40W-08	DHX36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353349.1	1	0	1	60	386	0	90	1	9.446982e-01	6	27	0	90	2		0	0	0	0	0	2	1	1.000000	60	384	0	90	2								-6.888420	1	0	121408	18	47	1	1	2	3	2.064228	0	0.210000	1.910000	0.220638	0.990000	0.990000	1.000000	1.000000	0.999196	0.990000	1	9.900000e-01	1
ANKRD28	23243	broad.mit.edu	37	3	15720986	15720986	+	Missense_Mutation	SNP	G	G	A			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr3:15720986G>A	ENST00000399451.2	-	22	2751	c.2384C>T	c.(2383-2385)gCc>gTc	p.A795V	ANKRD28_ENST00000497037.1_5'UTR|ANKRD28_ENST00000383777.1_Missense_Mutation_p.A828V	NM_001195098.1|NM_001195099.1|NM_015199.3	NP_001182027.1|NP_001182028.1|NP_056014.2	O15084	ANR28_HUMAN	ankyrin repeat domain 28			6					TACTTACACGGCACAATGCAA	0.378000																								0							SO:0001583	missense			ENST00000399451.2	0	1	hg19	CCDS46769.1	.	.	.	.	.	.	.	.	.	.	G	36	5.755213	0.96898	.	.	ENSG00000206560	ENST00000399451;ENST00000383777;ENST00000412318	T;T;T	0.79653	-1.29;-1.29;-1.29	6.06	6.06	0.98353	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	D	0.91751	0.7391	M	0.87547	2.89	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.91917	0.5544	10	0.87932	D	0	.	20.6208	0.99490	0.0:0.0:1.0:0.0	.	795	O15084	ANR28_HUMAN	V	795;828;795	ENSP00000382379:A795V;ENSP00000373287:A828V;ENSP00000397341:A795V	ENSP00000373287:A828V	A	-	2	0	ANKRD28	15695990	1.000000	0.71417	0.997000	0.53966	0.919000	0.55068	9.869000	0.99810	2.882000	0.98803	0.655000	0.94253	GCC		TCGA-XD-AAUI-01A-42D-A40W-08	ANKRD28-003	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339758.1	0	0	0	5	182	0	47	0	1.484274e-01	0	21	0	47	2		0	0	0	0	0	2	1	0.935712	5	179	0	47	2								-3.019073	1	1	0	0		1	1	2	3	2.064228	0	0.210000	1.910000	0.220638	0.290000	0.100000	1.000000	0.250000	0.373596	0.290000	0	1.800000e-01	5.000000e-01
TLR9	54106	broad.mit.edu	37	3	52257685	52257685	+	Missense_Mutation	SNP	C	C	T			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr3:52257685C>T	ENST00000360658.2	-	2	1280	c.647G>A	c.(646-648)cGc>cAc	p.R216H	TLR9_ENST00000494383.1_Silent_p.P369P|TLR9_ENST00000597542.1_Missense_Mutation_p.R240H	NM_017442.3	NP_059138.1	Q9NR96	TLR9_HUMAN	toll-like receptor 9	p.R216H(1)		30				Chloroquine(DB00608)|Hydroxychloroquine(DB01611)	AGGCAGGTTGCGGGGCACCAC	0.632000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000360658.2	0	1	hg19	CCDS2848.1	.	.	.	.	.	.	.	.	.	.	C	15.78	2.934649	0.52866	.	.	ENSG00000239732	ENST00000360658	T	0.57273	0.41	5.57	1.0	0.19881	.	0.000000	0.37012	N	0.002294	T	0.45955	0.1368	N	0.11870	0.19	0.09310	N	1	P;D	0.89917	0.476;1.0	B;D	0.76575	0.057;0.988	T	0.23655	-1.0182	10	0.52906	T	0.07	.	3.8792	0.09071	0.3023:0.4532:0.0:0.2445	.	313;216	B4E0A1;Q9NR96	.;TLR9_HUMAN	H	216	ENSP00000353874:R216H	ENSP00000353874:R216H	R	-	2	0	TLR9	52232725	0.000000	0.05858	0.326000	0.25389	0.560000	0.35617	-0.644000	0.05415	0.263000	0.21812	0.655000	0.94253	CGC		TCGA-XD-AAUI-01A-42D-A40W-08	TLR9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000350203.1	1	0	0	6	123	0	32	0	0	0	1	0	32	2		0	0	0	0	0	2	1	0.962635	5	120	0	32	2								-3.149805	1	1	121364	1	23	1	1	2	3	2.064228	0	0.210000	1.910000	0.220638	0.500000	0.200000	1.000000	0.440000	0.552728	0.500000	0	3.200000e-01	8.100000e-01
ITIH3	3699	broad.mit.edu	37	3	52829637	52829637	+	Missense_Mutation	SNP	G	G	A			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr3:52829637G>A	ENST00000449956.2	+	2	118	c.112G>A	c.(112-114)Ggg>Agg	p.G38R	ITIH3_ENST00000416872.2_Missense_Mutation_p.G38R	NM_002217.3	NP_002208.3	Q06033	ITIH3_HUMAN	inter-alpha-trypsin inhibitor heavy chain 3			25					CCTCCCGGAAGGGGTAAGAAC	0.567000																								0							SO:0001583	missense			ENST00000449956.2	1	1	hg19	CCDS46845.1	.	.	.	.	.	.	.	.	.	.	G	9.970	1.225261	0.22457	.	.	ENSG00000162267	ENST00000398670;ENST00000536431;ENST00000273291;ENST00000416872;ENST00000449956	T;T	0.02631	4.22;4.88	4.17	2.37	0.29283	Vault protein inter-alpha-trypsin (1);Vault protein inter-alpha-trypsin, metazoa (1);	0.950075	0.08821	N	0.888844	T	0.01489	0.0048	N	0.03608	-0.345	0.34715	D	0.728176	B;B	0.09022	0.002;0.0	B;B	0.06405	0.002;0.001	T	0.40327	-0.9569	10	0.16420	T	0.52	-9.1591	6.4221	0.21750	0.2186:0.0:0.7814:0.0	.	38;38	E7ET33;Q06033	.;ITIH3_HUMAN	R	38;38;33;38;38	ENSP00000413922:G38R;ENSP00000415769:G38R	ENSP00000273291:G33R	G	+	1	0	ITIH3	52804677	0.984000	0.35163	0.991000	0.47740	0.958000	0.62258	0.768000	0.26590	0.716000	0.32124	0.591000	0.81541	GGG		TCGA-XD-AAUI-01A-42D-A40W-08	ITIH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352668.2	1	0	1	12	56	0	16	0	7.369483e-01	0	14	0	16	2		0	0	0	0	0	2	1	0.999354	12	55	0	15	2								-19.991840	1	1	0	0		1	1	2	3	2.064228	0	0.210000	1.910000	0.220638	0.990000	0.950000	1.000000	1.000000	0.996052	0.990000	1	9.900000e-01	1
CDH18	1016	broad.mit.edu	37	5	19838947	19838947	+	Missense_Mutation	SNP	C	C	T			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr5:19838947C>T	ENST00000507958.1	-	5	1139	c.149G>A	c.(148-150)cGt>cAt	p.R50H	CDH18_ENST00000506372.1_Missense_Mutation_p.R50H|CDH18_ENST00000274170.4_Missense_Mutation_p.R50H|CDH18_ENST00000382275.1_Missense_Mutation_p.R50H|CDH18_ENST00000511273.1_Missense_Mutation_p.R50H|CDH18_ENST00000502796.1_Missense_Mutation_p.R50H			Q13634	CAD18_HUMAN	cadherin 18, type 2			138	Lung NSC(1;0.00734)|all_lung(1;0.0197)				CCTTTTGGGACGATGATGGAC	0.418000																								0							SO:0001583	missense			ENST00000507958.1	1	1	hg19	CCDS3889.1	.	.	.	.	.	.	.	.	.	.	C	33	5.262701	0.95399	.	.	ENSG00000145526	ENST00000382275;ENST00000507958;ENST00000542864;ENST00000274170;ENST00000506372;ENST00000502796;ENST00000511273	T;T;T;T;T;T	0.00585	6.39;6.39;6.39;6.39;6.39;6.39	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.04003	0.0112	M	0.87900	2.915	0.49582	D	0.999802	D;D	0.89917	1.0;1.0	D;D	0.91635	0.987;0.999	T	0.23013	-1.0200	9	.	.	.	.	18.9006	0.92440	0.0:1.0:0.0:0.0	.	50;50	B4DHG6;Q13634	.;CAD18_HUMAN	H	50	ENSP00000371710:R50H;ENSP00000425093:R50H;ENSP00000274170:R50H;ENSP00000424931:R50H;ENSP00000422138:R50H;ENSP00000425854:R50H	.	R	-	2	0	CDH18	19874704	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.452000	0.80683	2.805000	0.96524	0.655000	0.94253	CGT		TCGA-XD-AAUI-01A-42D-A40W-08	CDH18-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366747.1	1	0	0	24	285	0	99		0	0	0	0	99	2		0	0	0	0	0	2	1	1.000000	24	282	0	99	2								-8.080602	1	1	0	0		1	0	0	0	1.939433	0	0.210000	1.910000	0.175365	0.700000	0.460000	0.990000	1.000000	0.720265	0.700000	0	5.700000e-01	8.500000e-01
DDX43	55510	broad.mit.edu	37	6	74104815	74104815	+	Missense_Mutation	SNP	G	G	A			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr6:74104815G>A	ENST00000370336.4	+	1	345	c.187G>A	c.(187-189)Gct>Act	p.A63T	OOEP_ENST00000370363.1_5'UTR|snoU13_ENST00000459178.1_RNA|DDX43_ENST00000539829.1_Missense_Mutation_p.A63T	NM_018665.2	NP_061135.2	Q9NXZ2	DDX43_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 43			24					GGCCGTGGCCGCTGGTCACGA	0.617000											OREG0003900	type=REGULATORY REGION|Gene=BC024931|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay												0							SO:0001583	missense			ENST00000370336.4	0	1	hg19	CCDS4977.1	.	.	.	.	.	.	.	.	.	.	G	10.38	1.335280	0.24253	.	.	ENSG00000080007	ENST00000370336;ENST00000539829	T;T	0.47528	2.45;0.84	3.78	-0.215	0.13157	.	1.510900	0.04111	N	0.314678	T	0.14013	0.0339	L	0.50333	1.59	0.09310	N	1	P	0.41420	0.749	B	0.28385	0.089	T	0.15150	-1.0447	10	0.48119	T	0.1	.	1.0278	0.01531	0.2122:0.1786:0.4258:0.1834	.	63	Q9NXZ2	DDX43_HUMAN	T	63	ENSP00000359361:A63T;ENSP00000441636:A63T	ENSP00000359361:A63T	A	+	1	0	DDX43	74161536	0.000000	0.05858	0.000000	0.03702	0.070000	0.16714	0.092000	0.15066	-0.064000	0.13043	-0.391000	0.06502	GCT		TCGA-XD-AAUI-01A-42D-A40W-08	DDX43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041219.3	0	0	0	11	185	1	40		0	0	0	1	40	2		0	0	0	0	0	2	1	0.997904	10	174	0	40	2								-13.957130	1	1	0	0		1	0	0	0	1.974494	0	0.210000	1.910000	0.189577	0.530000	0.280000	0.860000	0.520000	0.549996	0.530000	0	3.900000e-01	7.000000e-01
TRRAP	8295	broad.mit.edu	37	7	98533290	98533290	+	Missense_Mutation	SNP	C	C	T			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr7:98533290C>T	ENST00000359863.4	+	28	4312	c.4103C>T	c.(4102-4104)gCg>gTg	p.A1368V	TRRAP_ENST00000446306.3_Missense_Mutation_p.A1367V|TRRAP_ENST00000355540.3_Missense_Mutation_p.A1368V	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein			176	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)		TTACGAATTGCGGCATTAAGT	0.393000																								0							SO:0001583	missense			ENST00000359863.4	0	1	hg19	CCDS59066.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.2|24.2	4.501952|4.501952	0.85176|0.85176	.|.	.|.	ENSG00000196367|ENSG00000196367	ENST00000359863;ENST00000355540;ENST00000446306|ENST00000456197	T;T|.	0.66280|.	-0.2;-0.2|.	6.17|6.17	6.17|6.17	0.99709|0.99709	Armadillo-type fold (1);|.	0.051888|.	0.85682|.	D|.	0.000000|.	T|T	0.43166|0.43166	0.1235|0.1235	N|N	0.02751|0.02751	-0.505|-0.505	0.80722|0.80722	D|D	1|1	D;D;D|.	0.62365|.	0.991;0.975;0.987|.	P;B;P|.	0.48654|.	0.585;0.335;0.461|.	T|T	0.40831|0.40831	-0.9542|-0.9542	10|5	0.32370|.	T|.	0.25|.	.|.	20.8794|20.8794	0.99867|0.99867	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1368;1082;1368|.	Q9Y4A5-2;Q59FH1;Q9Y4A5|.	.;.;TRRAP_HUMAN|.	V|W	1368;1368;1366|1083	ENSP00000352925:A1368V;ENSP00000347733:A1368V|.	ENSP00000347733:A1368V|.	A|R	+|+	2|1	0|2	TRRAP|TRRAP	98371226|98371226	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.393000|0.393000	0.30537|0.30537	7.622000|7.622000	0.83099|0.83099	2.941000|2.941000	0.99782|0.99782	0.655000|0.655000	0.94253|0.94253	GCG|CGG		TCGA-XD-AAUI-01A-42D-A40W-08	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1	0	0	0	5	229	0	70	0	4.306397e-03	0	4	0	70	2		0	0	0	0	0	2	1	0.935348	5	225	0	70	2								-2.972344	1	1	121410	3	25	1	1	2	3	2.061193	0	0.210000	1.910000	0.220638	0.230000	0.080000	1.000000	0.210000	0.320778	0.230000	0	1.400000e-01	4.100000e-01
COL14A1	7373	broad.mit.edu	37	8	121243763	121243763	+	Missense_Mutation	SNP	G	G	A			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr8:121243763G>A	ENST00000297848.3	+	19	2525	c.2255G>A	c.(2254-2256)cGg>cAg	p.R752Q	COL14A1_ENST00000537875.1_3'UTR|COL14A1_ENST00000247781.3_Missense_Mutation_p.R657Q|COL14A1_ENST00000309791.4_Missense_Mutation_p.R752Q|COL14A1_ENST00000432943.2_3'UTR	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1			119	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)		TCTAGCCTGCGGGTAAAATGG	0.438000																								0							SO:0001583	missense			ENST00000297848.3	1	1	hg19	CCDS34938.1	.	.	.	.	.	.	.	.	.	.	G	11.43	1.636123	0.29068	.	.	ENSG00000187955	ENST00000309791;ENST00000297848;ENST00000247781;ENST00000434620	T;T;T;T	0.56444	0.46;0.46;0.46;0.46	5.55	4.68	0.58851	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.400288	0.24985	N	0.034030	T	0.43322	0.1242	L	0.33093	0.98	0.80722	D	1	B;P	0.40794	0.189;0.729	B;B	0.42798	0.03;0.398	T	0.25467	-1.0131	10	0.31617	T	0.26	.	9.6977	0.40167	0.1605:0.0:0.8395:0.0	.	752;752	Q05707-2;Q05707	.;COEA1_HUMAN	Q	752;752;657;565	ENSP00000311809:R752Q;ENSP00000297848:R752Q;ENSP00000247781:R657Q;ENSP00000409461:R565Q	ENSP00000247781:R657Q	R	+	2	0	COL14A1	121312944	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.599000	0.46231	1.365000	0.46057	0.561000	0.74099	CGG		TCGA-XD-AAUI-01A-42D-A40W-08	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	1	0	0	11	241	0	54	0	8.081325e-01	0	69	0	54	2		0	0	0	0	0	2	1	0.998330	11	238	0	54	2								-2.558700	1	1	121410	3	32	1	0	0	0	1.976688	0	0.210000	1.910000	0.191319	0.410000	0.220000	0.680000	0.400000	0.432199	0.410000	0	3.000000e-01	5.500000e-01
KIAA1045	23349	broad.mit.edu	37	9	34971545	34971545	+	Missense_Mutation	SNP	G	G	A			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chr9:34971545G>A	ENST00000242315.3	+	2	332	c.250G>A	c.(250-252)Gat>Aat	p.D84N	KIAA1045_ENST00000544237.1_Missense_Mutation_p.D84N|KIAA1045_ENST00000476115.2_Intron	NM_015297.1	NP_056112.1	Q9UPV7	K1045_HUMAN	KIAA1045			19			LUSC - Lung squamous cell carcinoma(32;0.00575)		GCGGCTCCGAGATGGGCGCGG	0.632000																								0							SO:0001583	missense			ENST00000242315.3	1	1	hg19	CCDS43796.1	.	.	.	.	.	.	.	.	.	.	g	36	5.915546	0.97099	.	.	ENSG00000122733	ENST00000544237;ENST00000242315	.	.	.	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	T	0.78240	0.4252	M	0.64997	1.995	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.75127	-0.3427	8	.	.	.	-3.6405	19.545	0.95291	0.0:0.0:1.0:0.0	.	84	Q9UPV7	K1045_HUMAN	N	84	.	.	D	+	1	0	KIAA1045	34961545	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	9.258000	0.95555	2.861000	0.98227	0.655000	0.94253	GAT		TCGA-XD-AAUI-01A-42D-A40W-08	KIAA1045-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052256.2	1	0	0	27	452	0	137		0	0	0	0	137	2		0	0	0	0	0	2	1	1.000000	25	436	0	136	2								-20.000000	1	1	0	0		1	0	1	1	1.878350	1	0.210000	1.910000	0.117318	0.470000	0.320000	0.660000	0.470000	0.488410	0.470000	0	3.900000e-01	5.700000e-01
NRK	203447	broad.mit.edu	37	X	105150491	105150491	+	Missense_Mutation	SNP	C	C	G			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chrX:105150491C>G	ENST00000243300.9	+	11	1233	c.930C>G	c.(928-930)caC>caG	p.H310Q	NRK_ENST00000428173.2_Missense_Mutation_p.H310Q	NM_198465.2	NP_940867.2	Q7Z2Y5	NRK_HUMAN	Nik related kinase			76					TGCTTCAACACCCATTTGTTC	0.343000										HNSCC(51;0.14)														0							SO:0001583	missense			ENST00000243300.9	0	1	hg19		.	.	.	.	.	.	.	.	.	.	C	12.96	2.093751	0.36952	.	.	ENSG00000123572	ENST00000243300;ENST00000428173	T;T	0.34275	1.37;1.37	5.27	-2.09	0.07232	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.45126	D	0.000386	T	0.57961	0.2089	M	0.86268	2.805	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.61734	-0.7002	10	0.87932	D	0	.	11.5948	0.50966	0.0:0.2133:0.0:0.7867	.	310	Q7Z2Y5	NRK_HUMAN	Q	310	ENSP00000434830:H310Q;ENSP00000438378:H310Q	ENSP00000434830:H310Q	H	+	3	2	NRK	105037147	0.998000	0.40836	0.981000	0.43875	0.125000	0.20455	0.774000	0.26675	-0.459000	0.07013	-0.192000	0.12808	CAC		TCGA-XD-AAUI-01A-42D-A40W-08	NRK-001	KNOWN	non_canonical_conserved|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000106480.6	0	0	0	6	83	0	19		0	0	0	0	19	2		0	0	0	0	0	2	1	0.966713	6	83	0	19	2								-10.721740	1	1	0	0		1	0	1	1			0.210000	1.910000	0.210000	0.660000	0.280000	1.000000	1.000000	0.681621	0.660000	0	4.400000e-01	9.400000e-01
MORC4	79710	broad.mit.edu	37	X	106229348	106229348	+	Missense_Mutation	SNP	G	G	A			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chrX:106229348G>A	ENST00000355610.4	-	4	665	c.391C>T	c.(391-393)Cgg>Tgg	p.R131W	MORC4_ENST00000535534.1_Intron|MORC4_ENST00000255495.7_Missense_Mutation_p.R131W	NM_001085354.2|NM_024657.4	NP_001078823.1|NP_078933.3	Q8TE76	MORC4_HUMAN	MORC family CW-type zinc finger 4			28					TTTCCTAGCCGCATGGAGCCT	0.473000																								0							SO:0001583	missense			ENST00000355610.4	0	1	hg19	CCDS14525.2	.	.	.	.	.	.	.	.	.	.	G	27.5	4.835024	0.91117	.	.	ENSG00000133131	ENST00000355610;ENST00000255495	T;T	0.74315	-0.83;-0.83	5.35	5.35	0.76521	ATPase-like, ATP-binding domain (3);	0.000000	0.85682	D	0.000000	D	0.87834	0.6277	M	0.87381	2.88	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.89717	0.3916	10	0.87932	D	0	-9.9831	15.875	0.79154	0.0:0.0:1.0:0.0	.	131;131	A1YR23;Q8TE76	.;MORC4_HUMAN	W	131	ENSP00000347821:R131W;ENSP00000255495:R131W	ENSP00000255495:R131W	R	-	1	2	MORC4	106116004	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.562000	0.82300	2.565000	0.86533	0.600000	0.82982	CGG		TCGA-XD-AAUI-01A-42D-A40W-08	MORC4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057816.3	0	0	0	11	673	0	163	0	6.494867e-03	0	7	0	163	2		0	0	0	0	0	2	1	0.998175	11	661	0	159	2								-2.046025	0	1	0	0		1	0	1	1			0.210000	1.910000	0.210000	0.150000	0.070000	0.260000	0.160000	0.165666	0.150000	0	1.100000e-01	2.100000e-01
FRMPD4	9758	broad.mit.edu	37	X	12704277	12704277	+	Missense_Mutation	SNP	A	A	G			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chrX:12704277A>G	ENST00000380682.1	+	7	1141	c.635A>G	c.(634-636)aAt>aGt	p.N212S		NM_014728.3	NP_055543.2	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4			22					TATCTGGAAAATGGGCAGACC	0.398000																								0							SO:0001583	missense			ENST00000380682.1	0	1	hg19	CCDS35201.1	.	.	.	.	.	.	.	.	.	.	A	22.8	4.335472	0.81801	.	.	ENSG00000169933	ENST00000380682;ENST00000429478;ENST00000304087	T	0.76060	-0.99	5.33	5.33	0.75918	Band 4.1 domain (1);FERM domain (1);	0.000000	0.85682	D	0.000000	D	0.85106	0.5621	M	0.78456	2.415	0.47905	D	0.999546	P;P	0.51537	0.946;0.869	D;P	0.64506	0.926;0.805	D	0.86474	0.1787	10	0.56958	D	0.05	.	14.4062	0.67083	1.0:0.0:0.0:0.0	.	204;212	B7ZLE1;Q14CM0	.;FRPD4_HUMAN	S	212;203;201	ENSP00000370057:N212S	ENSP00000304583:N201S	N	+	2	0	FRMPD4	12614198	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.850000	0.92190	1.781000	0.52344	0.486000	0.48141	AAT		TCGA-XD-AAUI-01A-42D-A40W-08	FRMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055771.1	0	0	0	10	367	0	72		0	0	0	0	72	2		0	0	0	0	0	2	1	0.996672	10	361	0	72	2								-3.456681	1	1	0	0		1	0	1	1			0.210000	1.910000	0.210000	0.250000	0.130000	0.440000	0.250000	0.273651	0.250000	0	1.800000e-01	3.500000e-01
F8	2157	broad.mit.edu	37	X	154134766	154134766	+	Missense_Mutation	SNP	G	G	A			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chrX:154134766G>A	ENST00000360256.4	-	15	5502	c.5302C>T	c.(5302-5304)Cgt>Tgt	p.R1768C		NM_000132.3	NP_000123.1	P00451	FA8_HUMAN	coagulation factor VIII, procoagulant component			120	all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)			Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)	AGTTCTCCACGGTATAAGGGC	0.423000																								0		GRCh37	CM055192	F8	M		SO:0001583	missense			ENST00000360256.4	1	1	hg19	CCDS35457.1	.	.	.	.	.	.	.	.	.	.	G	19.82	3.899120	0.72754	.	.	ENSG00000185010	ENST00000360256	D	0.99287	-5.69	5.6	5.6	0.85130	Cupredoxin (2);	0.161419	0.53938	D	0.000042	D	0.99471	0.9812	M	0.87971	2.92	0.58432	D	0.999999	D	0.89917	1.0	D	0.83275	0.996	D	0.98619	1.0666	10	0.87932	D	0	-8.5673	17.091	0.86622	0.0:0.0:1.0:0.0	.	1768	P00451	FA8_HUMAN	C	1768	ENSP00000353393:R1768C	ENSP00000353393:R1768C	R	-	1	0	F8	153787960	0.963000	0.33076	1.000000	0.80357	0.988000	0.76386	3.384000	0.52478	2.350000	0.79820	0.600000	0.82982	CGT		TCGA-XD-AAUI-01A-42D-A40W-08	F8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058869.4	1	0	0	33	567	0	138		0	0	0	0	138	2		0	0	0	0	0	2	1	1.000000	33	558	0	136	2								-2.239660	0	1	0	0		1	0	1	1			0.210000	1.910000	0.210000	0.520000	0.360000	0.710000	0.520000	0.534513	0.520000	0	4.400000e-01	6.200000e-01
TMLHE	55217	broad.mit.edu	37	X	154741370	154741370	+	Missense_Mutation	SNP	C	C	T			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chrX:154741370C>T	ENST00000334398.3	-	5	867	c.722G>A	c.(721-723)cGg>cAg	p.R241Q	TMLHE-AS1_ENST00000452506.1_RNA|TMLHE_ENST00000369439.4_Missense_Mutation_p.R241Q	NM_018196.3	NP_060666.1	Q9NVH6	TMLH_HUMAN	trimethyllysine hydroxylase, epsilon			20	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)			Succinic acid(DB00139)|Vitamin C(DB00126)	GTCAGTGTGCCGATCCAGAGC	0.413000																								0							SO:0001583	missense			ENST00000334398.3	0	1	hg19	CCDS14768.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	17.79	3.476247	0.63737	0.0	4.46E-4	ENSG00000185973	ENST00000334398;ENST00000369439	D;D	0.82081	-1.57;-1.57	3.64	2.77	0.32553	.	0.125013	0.53938	N	0.000049	D	0.82318	0.5011	L	0.44542	1.39	0.47949	D	0.999558	D;D;D	0.71674	0.997;0.998;0.998	P;P;P	0.57960	0.756;0.83;0.778	T	0.77275	-0.2648	10	0.29301	T	0.29	-7.3997	8.53	0.33329	0.0:0.8754:0.0:0.1246	.	241;241;241	Q9NVH6-2;A8K6M9;Q9NVH6	.;.;TMLH_HUMAN	Q	241	ENSP00000335261:R241Q;ENSP00000358447:R241Q	ENSP00000335261:R241Q	R	-	2	0	TMLHE	154394564	0.999000	0.42202	0.989000	0.46669	0.855000	0.48748	4.043000	0.57354	0.507000	0.28148	-0.322000	0.08575	CGG		TCGA-XD-AAUI-01A-42D-A40W-08	TMLHE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058817.1	0	0	0	7	527	0	94	0	1.542070e-01	0	46	0	94	2		0	0	0	0	0	2	1	0.979521	7	518	0	93	2								-2.391118	0	1	121384	25	48	1	0	1	1			0.210000	1.910000	0.210000	0.130000	0.050000	0.240000	0.120000	0.141130	0.130000	0	8.000000e-02	1.900000e-01
USP9X	8239	broad.mit.edu	37	X	41029282	41029282	+	Nonsense_Mutation	SNP	C	C	T			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chrX:41029282C>T	ENST00000324545.8	+	19	3304	c.2671C>T	c.(2671-2673)Cga>Tga	p.R891*	USP9X_ENST00000378308.2_Nonsense_Mutation_p.R891*	NM_001039590.2|NM_001039591.2	NP_001034679.2|NP_001034680.2	Q93008	USP9X_HUMAN	ubiquitin specific peptidase 9, X-linked			87					TTTTGTAGTTCGATTTCCAAA	0.408000													Ovarian(172;1807 2695 35459 49286)											0							SO:0001587	stop_gained			ENST00000324545.8	0	1	hg19	CCDS43930.1	.	.	.	.	.	.	.	.	.	.	c	41	8.770551	0.98948	.	.	ENSG00000124486	ENST00000378308;ENST00000324545	.	.	.	5.85	4.05	0.47172	.	0.104565	0.64402	D	0.000005	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.21	0.31478	0.2778:0.6494:0.0:0.0728	.	.	.	.	X	891	.	ENSP00000316357:R891X	R	+	1	2	USP9X	40914226	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	3.205000	0.51090	0.575000	0.29434	-0.178000	0.13098	CGA		TCGA-XD-AAUI-01A-42D-A40W-08	USP9X-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056250.4	1	0	0	39	550	0	127	0	1.690497e-01	0	11	0	127	2		0	0	0	0	0	2	1	1.000000	39	537	0	126	2								-3.142698	1	1	0	0		1	0	1	1			0.210000	1.910000	0.210000	0.620000	0.450000	0.830000	0.620000	0.640451	0.620000	0	5.300000e-01	7.300000e-01
CYSLTR1	10800	broad.mit.edu	37	X	77528527	77528527	+	Silent	SNP	G	G	T			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chrX:77528527G>T	ENST00000373304.3	-	3	1009	c.717C>A	c.(715-717)acC>acA	p.T239T		NM_001282187.1|NM_001282188.1|NM_006639.3	NP_001269116.1|NP_001269117.1|NP_006630.1	Q9Y271	CLTR1_HUMAN	cysteinyl leukotriene receptor 1			14				Cinalukast(DB00587)|Montelukast(DB00471)|Nedocromil(DB00716)|Pranlukast(DB01411)|Zafirlukast(DB00549)	AAAAGGCAGCGGTCACGACCA	0.338000																								0							SO:0001819	synonymous_variant			ENST00000373304.3	1	1	hg19	CCDS14439.1																																																																																				TCGA-XD-AAUI-01A-42D-A40W-08	CYSLTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057315.1	0	0	0	12	321	0	63	0	9.083371e-03	0	4	0	63	2		0	0	0	0	0	2	1	0.999042	12	314	0	62	2								-2.695737	1	1	0	0		1	0	1	1			0.210000	1.910000	0.210000	0.350000	0.190000	0.560000	0.340000	0.365405	0.350000	0	2.600000e-01	4.600000e-01
PCDH19	57526	broad.mit.edu	37	X	99551638	99551638	+	Missense_Mutation	SNP	C	C	G			TCGA-XD-AAUI-01A-42D-A40W-08	TCGA-XD-AAUI-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8c4cafb-cf40-4343-9fab-78b2e1914ad1	768e3081-1fbc-418f-9000-9721e854cc35	g.chrX:99551638C>G	ENST00000373034.4	-	6	4759	c.3084G>C	c.(3082-3084)gaG>gaC	p.E1028D	PCDH19_ENST00000255531.7_Missense_Mutation_p.E981D|PCDH19_ENST00000420881.2_Missense_Mutation_p.E980D|PCDH19_ENST00000464981.1_5'Flank	NM_001184880.1	NP_001171809.1	Q8TAB3	PCD19_HUMAN	protocadherin 19			68					TAGGCCTCTCCTCAGCCGGGT	0.577000																								0							SO:0001583	missense			ENST00000373034.4	1	1	hg19	CCDS55462.1	.	.	.	.	.	.	.	.	.	.	C	4.652	0.121262	0.08881	.	.	ENSG00000165194	ENST00000420881;ENST00000373034;ENST00000255531	T;T;T	0.54071	0.59;0.64;0.6	5.73	3.95	0.45737	.	0.115763	0.56097	D	0.000025	T	0.34279	0.0892	L	0.34521	1.04	0.47862	D	0.999531	B;B;B	0.09022	0.002;0.002;0.001	B;B;B	0.09377	0.003;0.004;0.002	T	0.10382	-1.0632	10	0.14656	T	0.56	.	5.4949	0.16797	0.14:0.6354:0.0:0.2245	.	1028;981;980	Q8TAB3;Q8TAB3-2;E9PAM6	PCD19_HUMAN;.;.	D	980;1028;981	ENSP00000400327:E980D;ENSP00000362125:E1028D;ENSP00000255531:E981D	ENSP00000255531:E981D	E	-	3	2	PCDH19	99438294	0.998000	0.40836	1.000000	0.80357	0.996000	0.88848	0.647000	0.24812	1.181000	0.42912	0.600000	0.82982	GAG		TCGA-XD-AAUI-01A-42D-A40W-08	PCDH19-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057479.2	1	0	0	10	234	0	45		0	0	0	0	45	2		0	0	0	0	0	2	1	0.996862	9	232	0	44	2								-3.199164	1	1	0	0		1	0	1	1			0.210000	1.910000	0.210000	0.400000	0.200000	0.670000	0.380000	0.419303	0.400000	0	2.900000e-01	5.400000e-01
