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
EXPH5	23086	broad.mit.edu	37	11	108382677	108382678	+	Frame_Shift_Ins	INS	-	-	G			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr11:108382677_108382678insG	ENST00000265843.4	-	6	3666_3667	c.3556_3557insC	c.(3556-3558)caafs	p.Q1186fs	EXPH5_ENST00000524840.1_5'Flank|EXPH5_ENST00000443411.1_Frame_Shift_Ins_p.Q998fs|EXPH5_ENST00000428840.1_Frame_Shift_Ins_p.Q1110fs|EXPH5_ENST00000525344.1_Frame_Shift_Ins_p.Q1179fs	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5			91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)			AGTGTATTCTTGGAAGTTTTCC	0.416000																								0							SO:0001589	frameshift_variant			ENST00000265843.4	0	1	hg19	CCDS8341.1																																																																																				TCGA-2J-AAB1-01A-11D-A40W-08	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	1	0	0	76	554	0	91	0	4.117291e-02	0	3	0	91	2	0	0	0	0	0	0		1	1.000000	77	550	0	89	2								-2.841672	1	1	0	0		1	1	2	3	2.042490	0	0.380000	1.940000	0.382347	0.630000	5.000000e-01	0.800000	0.630000	0.645534	0.630000	0	0.560000	0.710000
MBD6	114785	broad.mit.edu	37	12	57919654	57919666	+	Frame_Shift_Del	DEL	GGGGCCCCTGGGA	GGGGCCCCTGGGA	-			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr12:57919654_57919666delGGGGCCCCTGGGA	ENST00000355673.3	+	6	1259_1271	c.903_915delGGGGCCCCTGGGA	c.(901-915)ctggggcccctgggafs	p.LGPLG301fs	MBD6_ENST00000431731.2_Frame_Shift_Del_p.LGPLG301fs	NM_052897.3	NP_443129.3	Q96DN6	MBD6_HUMAN	methyl-CpG binding domain protein 6			31					CCCTGGTCCTGGGGCCCCTGGGAGGGGCCCCCA	0.695000																								0							SO:0001589	frameshift_variant			ENST00000355673.3	0	1	hg19	CCDS8944.1																																																																																				TCGA-2J-AAB1-01A-11D-A40W-08	MBD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407250.1	1	0	0	24	247	0	39	0	9.626537e-01	0	58	0	39	2	0	0	0	0	0	0		2	0.004121	73	292	5	42	59								-2.841673	1	1	0	0		1	0	0	0	1.993904	0	0.380000	1.940000	0.370431	0.460000	3.000000e-01	0.650000	0.460000	0.471682	0.460000	0	0.370000	0.560000
PLEK	5341	broad.mit.edu	37	2	68622834	68622834	+	Frame_Shift_Del	DEL	C	C	-			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr2:68622834delC	ENST00000234313.7	+	9	1118	c.939delC	c.(937-939)aacfs	p.N313fs		NM_002664.2	NP_002655.2	P08567	PLEK_HUMAN	pleckstrin			24		Ovarian(717;0.0129)			AGGAAGAGAACCTTTTTGAGA	0.542000																								0							SO:0001589	frameshift_variant			ENST00000234313.7	1	1	hg19	CCDS1887.1																																																																																				TCGA-2J-AAB1-01A-11D-A40W-08	PLEK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251755.1	1	0	0	86	597	0	121	0	6.824359e-01	0	18	0	121	2	0	0	0	0	0	0		1	0.999916	91	591	5	118	46								-20.000000	1	1	0	0		1	0	0	0	2.015667	0	0.380000	1.940000	0.377635	0.650000	5.300000e-01	0.790000	0.660000	0.664314	0.650000	0	0.590000	0.730000
NT5C2	22978	broad.mit.edu	37	10	104934648	104934648	+	Missense_Mutation	SNP	G	G	A			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr10:104934648G>A	ENST00000404739.3	-	1	91	c.68C>T	c.(67-69)gCc>gTc	p.A23V	NT5C2_ENST00000343289.5_Missense_Mutation_p.A23V|NT5C2_ENST00000369857.4_Intron|NT5C2_ENST00000470299.1_Missense_Mutation_p.A23V			P49902	5NTC_HUMAN	5'-nucleotidase, cytosolic II			16		all_hematologic(284;0.176)|Colorectal(252;0.178)		Adenosine triphosphate(DB00171)|Ribavirin(DB00811)	CTTTTTCAGGGCATGCTTATC	0.378000																								0							SO:0001583	missense			ENST00000404739.3	0	1	hg19	CCDS7544.1	.	.	.	.	.	.	.	.	.	.	G	16.87	3.240896	0.58995	.	.	ENSG00000076685	ENST00000343289;ENST00000404739;ENST00000452156	T;T;T	0.18502	2.21;2.21;2.22	5.39	4.49	0.54785	.	0.159024	0.56097	D	0.000039	T	0.10637	0.0260	N	0.14661	0.345	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.12142	-1.0559	10	0.24483	T	0.36	-2.4411	13.313	0.60390	0.0782:0.0:0.9218:0.0	.	23	P49902	5NTC_HUMAN	V	23	ENSP00000339479:A23V;ENSP00000383960:A23V;ENSP00000396468:A23V	ENSP00000339479:A23V	A	-	2	0	NT5C2	104924638	1.000000	0.71417	0.998000	0.56505	0.984000	0.73092	5.904000	0.69886	1.256000	0.44068	0.650000	0.86243	GCC		TCGA-2J-AAB1-01A-11D-A40W-08	NT5C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050121.1	0	0	0	7	804	0	141	0	1.651182e-01	0	72	0	141	2		0	0	0	0	0	2	1	0.979851	7	795	0	138	2								-2.186632	0	1	0	0		1	1	2	3	2.036995	0	0.380000	1.940000	0.382347	0.040000	1.000000e-02	0.100000	0.040000	0.061253	0.040000	0	0.020000	0.070000
WDR37	22884	broad.mit.edu	37	10	1149626	1149626	+	Missense_Mutation	SNP	C	C	A	rs150728900		TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr10:1149626C>A	ENST00000358220.1	+	10	955	c.811C>A	c.(811-813)Cgc>Agc	p.R271S	WDR37_ENST00000263150.4_Missense_Mutation_p.R271S			Q9Y2I8	WDR37_HUMAN	WD repeat domain 37			17		all_epithelial(10;0.0449)|Colorectal(49;0.142)			CCCCACCATCCGCGTCCCACT	0.622000																								0							SO:0001583	missense			ENST00000358220.1	1	1	hg19	CCDS7057.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.976358	0.74360	.	.	ENSG00000047056	ENST00000358220;ENST00000263150	T;T	0.01265	5.08;5.08	5.95	4.98	0.66077	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.10981	0.0268	M	0.92604	3.325	0.80722	D	1	D;D	0.63046	0.992;0.992	P;D	0.65987	0.9;0.94	T	0.00033	-1.2272	10	0.72032	D	0.01	.	13.835	0.63404	0.2572:0.7428:0.0:0.0	.	272;271	A8K976;Q9Y2I8	.;WDR37_HUMAN	S	271	ENSP00000350954:R271S;ENSP00000263150:R271S	ENSP00000263150:R271S	R	+	1	0	WDR37	1139626	1.000000	0.71417	0.536000	0.28039	0.675000	0.39556	2.057000	0.41365	2.811000	0.96726	0.655000	0.94253	CGC		TCGA-2J-AAB1-01A-11D-A40W-08	WDR37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046418.1	1	0	1	52	246	0	47	1	6.913251e-01	2	11	0	47	2		0	0	0	0	0	2	1	1.000000	52	243	0	46	2								-2.733687	1	1	0	0		1	0	1	1	2.022886	0	0.380000	1.940000	0.378820	0.910000	7.000000e-01	1.000000	1.000000	0.904915	0.910000	1	0.800000	1.000000
NEBL	10529	broad.mit.edu	37	10	21098813	21098813	+	Missense_Mutation	SNP	G	G	A			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr10:21098813G>A	ENST00000377122.4	-	25	2929	c.2533C>T	c.(2533-2535)Cgc>Tgc	p.R845C	NEBL_ENST00000417816.2_Intron|NEBL_ENST00000377159.4_Intron	NM_006393.2	NP_006384.1	O76041	NEBL_HUMAN	nebulette	p.R845C(1)		70					GGATCTGTGCGCCAAACTTTG	0.383000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000377122.4	1	1	hg19	CCDS7134.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.664498	0.88251	.	.	ENSG00000078114	ENST00000377122	T	0.09538	2.97	6.05	6.05	0.98169	.	0.000000	0.85682	D	0.000000	T	0.30759	0.0775	L	0.55990	1.75	0.80722	D	1	D	0.89917	1.0	D	0.66351	0.943	T	0.00069	-1.2136	10	0.62326	D	0.03	.	20.6087	0.99469	0.0:0.0:1.0:0.0	.	845	O76041	NEBL_HUMAN	C	845	ENSP00000366326:R845C	ENSP00000366326:R845C	R	-	1	0	NEBL	21138819	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.001000	0.57046	2.866000	0.98385	0.650000	0.86243	CGC		TCGA-2J-AAB1-01A-11D-A40W-08	NEBL-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047113.1	1	0	1	68	220	0	44		0	0	0	0	44	2		0	0	0	0	0	2	1	1.000000	67	215	0	42	2								-4.142076	1	1	121412	5	36	1	0	1	1	2.022886	0	0.380000	1.940000	0.378820	0.990000	9.900000e-01	1.000000	1.000000	0.998819	0.990000	1	0.990000	1.000000
FDX1	2230	broad.mit.edu	37	11	110327723	110327723	+	Missense_Mutation	SNP	C	C	A			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr11:110327723C>A	ENST00000260270.2	+	3	630	c.392C>A	c.(391-393)aCt>aAt	p.T131N		NM_004109.4	NP_004100.1	P10109	ADX_HUMAN	ferredoxin 1			2		all_cancers(61;1.59e-12)|all_epithelial(67;8.38e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0199)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Mitotane(DB00648)	GATGCAATCACTGATGAGGAG	0.403000																								0							SO:0001583	missense			ENST00000260270.2	0	1	hg19	CCDS8344.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.222520	0.79464	.	.	ENSG00000137714	ENST00000260270	.	.	.	5.46	4.55	0.56014	Beta-grasp fold, ferredoxin-type (1);Ferredoxin (3);	0.049070	0.85682	D	0.000000	T	0.66886	0.2835	L	0.52759	1.655	0.49483	D	0.999795	P	0.41366	0.747	P	0.49301	0.606	T	0.66284	-0.5962	9	0.39692	T	0.17	-2.2088	16.052	0.80772	0.0:0.8654:0.1346:0.0	.	131	P10109	ADX_HUMAN	N	131	.	ENSP00000260270:T131N	T	+	2	0	FDX1	109832933	1.000000	0.71417	0.999000	0.59377	0.837000	0.47467	4.678000	0.61641	1.304000	0.44892	0.561000	0.74099	ACT		TCGA-2J-AAB1-01A-11D-A40W-08	FDX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390590.1	0	0	0	12	691	0	109	1	4.030271e-01	4	72	0	109	2		0	0	0	0	0	2	1	0.999014	12	678	0	107	2								-3.231405	1	1	0	0		1	1	2	3	2.042490	0	0.380000	1.940000	0.382347	0.090000	4.000000e-02	0.170000	0.090000	0.106037	0.090000	0	0.060000	0.130000
UBASH3B	84959	broad.mit.edu	37	11	122659916	122659916	+	Missense_Mutation	SNP	G	G	A			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr11:122659916G>A	ENST00000284273.5	+	6	1255	c.880G>A	c.(880-882)Ggt>Agt	p.G294S		NM_032873.4	NP_116262.2	Q8TF42	UBS3B_HUMAN	ubiquitin associated and SH3 domain containing B			26		Breast(109;0.00254)|Medulloblastoma(222;0.00877)|Lung NSC(97;0.0183)|all_lung(97;0.0186)|all_neural(223;0.0381)|all_hematologic(192;0.104)			CACCAGCGAGGGTTGGATCTA	0.532000																								0							SO:0001583	missense			ENST00000284273.5	1	1	hg19	CCDS31694.1	.	.	.	.	.	.	.	.	.	.	G	36	5.789502	0.96945	.	.	ENSG00000154127	ENST00000284273	T	0.58797	0.31	5.86	5.86	0.93980	Src homology-3 domain (4);	0.000000	0.85682	D	0.000000	T	0.82042	0.4951	M	0.89840	3.065	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.84720	0.0739	10	0.87932	D	0	-7.8749	20.1931	0.98233	0.0:0.0:1.0:0.0	.	294	Q8TF42	UBS3B_HUMAN	S	294	ENSP00000284273:G294S	ENSP00000284273:G294S	G	+	1	0	UBASH3B	122165126	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	9.476000	0.97823	2.771000	0.95319	0.563000	0.77884	GGT		TCGA-2J-AAB1-01A-11D-A40W-08	UBASH3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387499.1	1	0	1	194	820	0	176	1	4.007568e-01	2	5	0	176	2		0	0	0	0	0	2	1	1.000000	191	810	0	172	2								-20.000000	1	1	0	0		1	1	2	3	2.042490	0	0.380000	1.940000	0.382347	0.990000	8.800000e-01	1.000000	1.000000	0.979838	0.990000	1	0.940000	1.000000
UBASH3B	84959	broad.mit.edu	37	11	122667627	122667627	+	Missense_Mutation	SNP	A	A	G			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr11:122667627A>G	ENST00000284273.5	+	9	1618	c.1243A>G	c.(1243-1245)Ata>Gta	p.I415V		NM_032873.4	NP_116262.2	Q8TF42	UBS3B_HUMAN	ubiquitin associated and SH3 domain containing B			26		Breast(109;0.00254)|Medulloblastoma(222;0.00877)|Lung NSC(97;0.0183)|all_lung(97;0.0186)|all_neural(223;0.0381)|all_hematologic(192;0.104)			AGGCCGCTACATACGCACCAA	0.473000																								0							SO:0001583	missense			ENST00000284273.5	1	1	hg19	CCDS31694.1	.	.	.	.	.	.	.	.	.	.	A	8.583	0.882830	0.17467	.	.	ENSG00000154127	ENST00000284273	T	0.04917	3.53	5.94	3.61	0.41365	Histidine phosphatase superfamily, clade-1 (1);	0.337134	0.34110	N	0.004260	T	0.01835	0.0058	N	0.00677	-1.265	0.31402	N	0.676504	B	0.02656	0.0	B	0.01281	0.0	T	0.33343	-0.9872	10	0.15066	T	0.55	-1.7035	9.0924	0.36619	0.6732:0.0:0.3268:0.0	.	415	Q8TF42	UBS3B_HUMAN	V	415	ENSP00000284273:I415V	ENSP00000284273:I415V	I	+	1	0	UBASH3B	122172837	0.980000	0.34600	0.994000	0.49952	0.906000	0.53458	0.760000	0.26475	0.495000	0.27882	0.528000	0.53228	ATA		TCGA-2J-AAB1-01A-11D-A40W-08	UBASH3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387499.1	1	0	0	16	288	0	74	0	1.057222e-01	0	10	0	74	2		0	0	0	0	0	2	1	0.999932	16	284	0	73	2								-18.273270	1	1	0	0		1	1	2	3	2.042490	0	0.380000	1.940000	0.382347	0.280000	1.600000e-01	0.460000	0.280000	0.298889	0.280000	0	0.210000	0.360000
OR51I2	390064	broad.mit.edu	37	11	5475025	5475025	+	Missense_Mutation	SNP	C	C	A			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr11:5475025C>A	ENST00000341449.2	+	1	388	c.307C>A	c.(307-309)Ctt>Att	p.L103I	HBG2_ENST00000380259.2_Intron|AC104389.28_ENST00000415970.1_RNA|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron	NM_001004754.2	NP_001004754.1	Q9H344	O51I2_HUMAN	olfactory receptor, family 51, subfamily I, member 2			29		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)			TCAGATGTTTCTTATTCACTT	0.483000																								0							SO:0001583	missense			ENST00000341449.2	1	1	hg19	CCDS31383.1	.	.	.	.	.	.	.	.	.	.	C	14.77	2.634332	0.47049	.	.	ENSG00000187918	ENST00000341449	T	0.40756	1.02	5.57	0.255	0.15561	GPCR, rhodopsin-like superfamily (1);	0.460534	0.20519	N	0.090739	T	0.22975	0.0555	L	0.28344	0.845	0.25272	N	0.989505	P	0.39665	0.682	B	0.31390	0.129	T	0.13202	-1.0518	10	0.87932	D	0	.	7.8771	0.29599	0.0:0.4244:0.0:0.5756	.	103	Q9H344	O51I2_HUMAN	I	103	ENSP00000341987:L103I	ENSP00000341987:L103I	L	+	1	0	OR51I2	5431601	0.000000	0.05858	0.991000	0.47740	0.981000	0.71138	-0.078000	0.11375	0.162000	0.19483	0.650000	0.86243	CTT		TCGA-2J-AAB1-01A-11D-A40W-08	OR51I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143385.1	1	0	1	95	425	0	100		0	0	0	0	100	2		0	0	0	0	0	2	1	1.000000	93	422	0	100	2								-20.000000	1	1	0	0		1	1	2	3	2.042490	0	0.380000	1.940000	0.382347	0.960000	7.900000e-01	1.000000	1.000000	0.946672	0.960000	1	0.870000	1.000000
OR51I2	390064	broad.mit.edu	37	11	5475027	5475027	+	Silent	SNP	T	T	A			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr11:5475027T>A	ENST00000341449.2	+	1	390	c.309T>A	c.(307-309)ctT>ctA	p.L103L	HBG2_ENST00000380259.2_Intron|AC104389.28_ENST00000415970.1_RNA|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron	NM_001004754.2	NP_001004754.1	Q9H344	O51I2_HUMAN	olfactory receptor, family 51, subfamily I, member 2			29		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)			AGATGTTTCTTATTCACTTCT	0.483000																								0							SO:0001819	synonymous_variant			ENST00000341449.2	1	1	hg19	CCDS31383.1																																																																																				TCGA-2J-AAB1-01A-11D-A40W-08	OR51I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143385.1	1	0	1	92	431	0	101		0	0	0	0	101	2		0	0	0	0	0	2	1	1.000000	91	428	0	101	2								-20.000000	1	1	0	0		1	1	2	3	2.042490	0	0.380000	1.940000	0.382347	0.920000	7.600000e-01	1.000000	1.000000	0.921979	0.920000	1	0.840000	1.000000
OR8J3	81168	broad.mit.edu	37	11	55905125	55905125	+	Missense_Mutation	SNP	G	G	T			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr11:55905125G>T	ENST00000301529.1	-	1	69	c.70C>A	c.(70-72)Cag>Aag	p.Q24K		NM_001004064.1	NP_001004064.1	Q8NGG0	OR8J3_HUMAN	olfactory receptor, family 8, subfamily J, member 3			59	Esophageal squamous(21;0.00693)				AGGGGAATCTGGAGCTCTGGA	0.488000																								0							SO:0001583	missense			ENST00000301529.1	1	1	hg19	CCDS31520.1	.	.	.	.	.	.	.	.	.	.	G	15.62	2.887120	0.52014	.	.	ENSG00000167822	ENST00000301529	T	0.00591	6.35	3.26	3.26	0.37387	.	0.000000	0.64402	D	0.000017	T	0.00998	0.0033	L	0.51422	1.61	0.21782	N	0.999543	P	0.47350	0.894	P	0.49853	0.624	T	0.51834	-0.8655	10	0.48119	T	0.1	.	8.7991	0.34898	0.0:0.1604:0.6748:0.1647	.	24	Q8NGG0	OR8J3_HUMAN	K	24	ENSP00000301529:Q24K	ENSP00000301529:Q24K	Q	-	1	0	OR8J3	55661701	0.879000	0.30193	0.274000	0.24659	0.245000	0.25701	1.766000	0.38491	1.548000	0.49413	0.289000	0.19496	CAG		TCGA-2J-AAB1-01A-11D-A40W-08	OR8J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391542.1	1	0	1	110	441	0	104		0	0	0	0	104	2		0	0	0	0	0	2	1	1.000000	109	430	0	104	2								-3.384226	1	1	0	0		1	1	2	3	2.042490	0	0.380000	1.940000	0.382347	0.990000	8.800000e-01	1.000000	1.000000	0.986273	0.990000	1	0.960000	1.000000
DNAJC4	3338	broad.mit.edu	37	11	63999972	63999972	+	Missense_Mutation	SNP	G	G	A			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr11:63999972G>A	ENST00000321685.3	+	4	716	c.251G>A	c.(250-252)cGt>cAt	p.R84H	RP11-783K16.14_ENST00000539963.1_RNA|VEGFB_ENST00000309422.2_5'Flank|VEGFB_ENST00000426086.2_5'Flank|DNAJC4_ENST00000355040.4_Intron|RP11-783K16.14_ENST00000534988.1_RNA|DNAJC4_ENST00000321460.5_Missense_Mutation_p.R84H	NM_005528.3	NP_005519.2	Q9NNZ3	DNJC4_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 4			3					GAGGCATACCGTGTGCTCAGC	0.632000																								0							SO:0001583	missense			ENST00000321685.3	1	1	hg19	CCDS41666.1	.	.	.	.	.	.	.	.	.	.	G	11.20	1.569823	0.28003	.	.	ENSG00000110011	ENST00000321685;ENST00000321460	T;T	0.29917	1.55;1.55	4.04	-6.62	0.01813	Heat shock protein DnaJ, N-terminal (5);	0.346876	0.25135	N	0.032869	T	0.14614	0.0353	N	0.25890	0.77	0.25398	N	0.98846	P;B	0.38565	0.637;0.029	B;B	0.25506	0.061;0.011	T	0.02220	-1.1193	10	0.59425	D	0.04	-0.004	15.2131	0.73241	0.2268:0.0:0.7732:0.0	.	84;84	Q6PIN0;Q9NNZ3	.;DNJC4_HUMAN	H	84	ENSP00000396896:R84H;ENSP00000320548:R84H	ENSP00000320548:R84H	R	+	2	0	DNAJC4	63756548	0.063000	0.20901	0.002000	0.10522	0.787000	0.44495	0.222000	0.17699	-1.482000	0.01860	-0.448000	0.05591	CGT		TCGA-2J-AAB1-01A-11D-A40W-08	DNAJC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396305.1	1	0	0	7	182	0	35	1	9.383940e-01	7	124	0	35	2		0	0	0	0	0	2	1	0.980095	7	179	0	35	2								-9.110572	1	1	121126	1	26	1	1	2	3	2.042490	0	0.380000	1.940000	0.382347	0.200000	9.000000e-02	0.410000	0.200000	0.227048	0.200000	0	0.140000	0.300000
TMEM116	89894	broad.mit.edu	37	12	112374530	112374530	+	Missense_Mutation	SNP	A	A	T			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr12:112374530A>T	ENST00000550831.3	-	7	646	c.278T>A	c.(277-279)cTg>cAg	p.L93Q	TMEM116_ENST00000552374.2_Missense_Mutation_p.L185Q|TMEM116_ENST00000354825.3_Missense_Mutation_p.L93Q|TMEM116_ENST00000437003.2_Missense_Mutation_p.L93Q|TMEM116_ENST00000549537.2_Intron|TMEM116_ENST00000355445.3_Missense_Mutation_p.L150Q	NM_138341.2	NP_612350.1	Q8NCL8	TM116_HUMAN	transmembrane protein 116			8					AAAGCTGCCCAGGAAAATGGC	0.478000																								0							SO:0001583	missense			ENST00000550831.3	1	1	hg19	CCDS9157.1	.	.	.	.	.	.	.	.	.	.	a	19.40	3.819870	0.71028	.	.	ENSG00000198270	ENST00000355445;ENST00000354825;ENST00000550831;ENST00000437003;ENST00000552374	T;T;T;T;T	0.41758	0.99;0.99;0.99;0.99;0.99	5.12	5.12	0.69794	.	0.000000	0.64402	D	0.000014	T	0.58921	0.2156	L	0.59436	1.845	0.40890	D	0.98406	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.63501	-0.6623	10	0.87932	D	0	-6.5126	11.3186	0.49407	1.0:0.0:0.0:0.0	.	150;185;93	G5E985;G3V1W7;Q8NCL8	.;.;TM116_HUMAN	Q	150;93;93;93;185	ENSP00000347620:L150Q;ENSP00000346883:L93Q;ENSP00000450377:L93Q;ENSP00000395861:L93Q;ENSP00000447731:L185Q	ENSP00000346883:L93Q	L	-	2	0	TMEM116	110858913	1.000000	0.71417	1.000000	0.80357	0.795000	0.44927	4.791000	0.62460	1.939000	0.56221	0.383000	0.25322	CTG		TCGA-2J-AAB1-01A-11D-A40W-08	TMEM116-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405026.3	1	0	1	52	228	0	43	1	7.611682e-01	6	8	0	43	2		0	0	0	0	0	2	1	1.000000	51	224	0	42	2								-20.000000	1	1	0	0		1	0	0	0	1.993904	0	0.380000	1.940000	0.370431	0.950000	7.300000e-01	1.000000	1.000000	0.934309	0.950000	1	0.840000	1.000000
TPCN1	53373	broad.mit.edu	37	12	113711435	113711435	+	Missense_Mutation	SNP	G	G	A			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr12:113711435G>A	ENST00000335509.6	+	10	1218	c.904G>A	c.(904-906)Gtg>Atg	p.V302M	TPCN1_ENST00000550785.1_Missense_Mutation_p.V374M|TPCN1_ENST00000541517.1_Missense_Mutation_p.V374M|TPCN1_ENST00000392569.4_Missense_Mutation_p.V234M	NM_017901.4	NP_060371.2	Q9ULQ1	TPC1_HUMAN	two pore segment channel 1			40					CTTCTTCATCGTGTACCTCTC	0.557000																								0							SO:0001583	missense			ENST00000335509.6	1	1	hg19	CCDS31908.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.538199	0.85917	.	.	ENSG00000186815	ENST00000335509;ENST00000550785;ENST00000541517;ENST00000392569	D;D;D;D	0.98701	-5.08;-5.08;-5.08;-5.08	5.64	5.64	0.86602	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98576	0.9524	L	0.60845	1.875	0.47214	D	0.999354	D;D;D	0.76494	0.999;0.999;0.998	D;D;P	0.66847	0.947;0.919;0.848	D	0.98287	1.0511	10	0.48119	T	0.1	-26.0173	12.9637	0.58472	0.0742:0.0:0.9258:0.0	.	302;374;302	A5PKY2;Q9ULQ1-3;Q9ULQ1	.;.;TPC1_HUMAN	M	302;374;374;234	ENSP00000335300:V302M;ENSP00000448083:V374M;ENSP00000438125:V374M;ENSP00000376350:V234M	ENSP00000335300:V302M	V	+	1	0	TPCN1	112195818	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.600000	0.82769	2.656000	0.90262	0.655000	0.94253	GTG		TCGA-2J-AAB1-01A-11D-A40W-08	TPCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405156.3	1	0	1	117	609	0	147	1	9.973635e-01	6	42	0	147	2		0	0	0	0	0	2	1	1.000000	115	597	0	143	2								-20.000000	1	1	0	0		1	0	0	0	1.993904	0	0.380000	1.940000	0.370431	0.830000	6.900000e-01	0.970000	0.830000	0.837777	0.830000	0	0.760000	0.910000
RSRC2	65117	broad.mit.edu	37	12	123005948	123005948	+	Missense_Mutation	SNP	C	C	T			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr12:123005948C>T	ENST00000331738.7	-	3	336	c.191G>A	c.(190-192)cGg>cAg	p.R64Q	RSRC2_ENST00000354654.2_Missense_Mutation_p.G9R	NM_023012.5	NP_075388.2	Q7L4I2	RSRC2_HUMAN	arginine/serine-rich coiled-coil 2			24	all_neural(191;0.0837)|Medulloblastoma(191;0.163)				GCTTCTGCTCCGGCTCCTGTG	0.308000																								0							SO:0001583	missense			ENST00000331738.7	0	1	hg19	CCDS31920.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.99|14.99	2.700233|2.700233	0.48307|0.48307	.|.	.|.	ENSG00000111011|ENSG00000111011	ENST00000354654;ENST00000528279|ENST00000331738;ENST00000418773	T|T	0.46063|0.20332	0.88|2.08	5.44|5.44	5.44|5.44	0.79542|0.79542	.|.	.|0.220291	.|0.47852	.|D	.|0.000206	T|T	0.16599|0.16599	0.0399|0.0399	N|N	0.19112|0.19112	0.55|0.55	0.26343|0.26343	N|N	0.977338|0.977338	P|D;D	0.41673|0.56521	0.759|0.976;0.976	B|B;B	0.30495|0.40825	0.116|0.341;0.341	T|T	0.07520|0.07520	-1.0768|-1.0768	9|10	0.41790|0.39692	T|T	0.15|0.17	.|.	19.2639|19.2639	0.93979|0.93979	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	9|64;64	Q7L4I2-2|F5GXM2;Q7L4I2	.|.;RSRC2_HUMAN	R|Q	9|64	ENSP00000346678:G9R|ENSP00000330188:R64Q	ENSP00000346678:G9R|ENSP00000330188:R64Q	G|R	-|-	1|2	0|0	RSRC2|RSRC2	121571901|121571901	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	5.313000|5.313000	0.65798|0.65798	2.541000|2.541000	0.85698|0.85698	0.555000|0.555000	0.69702|0.69702	GGA|CGG		TCGA-2J-AAB1-01A-11D-A40W-08	RSRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395096.3	0	0	0	4	254	0	52	0	7.612298e-01	1	169	0	52	2		0	0	0	0	0	2	1	0.886451	4	249	0	50	2								-2.796904	1	1	121398	1	38	1	0	0	0	1.993904	0	0.380000	1.940000	0.370431	0.080000	2.000000e-02	0.190000	0.080000	0.099011	0.080000	0	0.050000	0.140000
NOC4L	79050	broad.mit.edu	37	12	132635870	132635870	+	Missense_Mutation	SNP	C	C	T			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr12:132635870C>T	ENST00000330579.1	+	11	1071	c.1030C>T	c.(1030-1032)Cgc>Tgc	p.R344C	NOC4L_ENST00000535343.1_3'UTR|NOC4L_ENST00000538784.1_5'UTR	NM_024078.1	NP_076983.1	Q9BVI4	NOC4L_HUMAN	nucleolar complex associated 4 homolog (S. cerevisiae)			14	all_neural(191;0.0982)|Medulloblastoma(191;0.163)				CGTCAAGTACCGCGCCCGCTT	0.652000																								0							SO:0001583	missense			ENST00000330579.1	1	1	hg19	CCDS9277.1	.	.	.	.	.	.	.	.	.	.	C	15.18	2.755773	0.49362	.	.	ENSG00000184967	ENST00000330579	T	0.65178	-0.14	5.2	4.3	0.51218	CCAAT-binding factor (1);	0.000000	0.85682	D	0.000000	D	0.83908	0.5356	M	0.93978	3.48	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.88477	0.3066	10	0.87932	D	0	-22.5329	15.3287	0.74190	0.0:0.8591:0.1409:0.0	.	344	Q9BVI4	NOC4L_HUMAN	C	344	ENSP00000328854:R344C	ENSP00000328854:R344C	R	+	1	0	NOC4L	131201823	1.000000	0.71417	0.489000	0.27452	0.056000	0.15407	2.615000	0.46368	1.165000	0.42670	0.561000	0.74099	CGC		TCGA-2J-AAB1-01A-11D-A40W-08	NOC4L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398999.1	0	0	1	101	486	0	135	1	9.999963e-01	26	61	0	135	2		0	0	0	0	0	2	1	1.000000	99	477	1	129	16								-2.827600	1	1	121290	9	44	1	0	0	0	1.993904	0	0.380000	1.940000	0.370431	0.880000	7.300000e-01	1.000000	1.000000	0.890903	0.880000	1	0.800000	0.970000
KRAS	3845	broad.mit.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	C	T	rs121913529		TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr12:25398284C>T	ENST00000256078.4	-	2	98	c.35G>A	c.(34-36)gGt>gAt	p.G12D	KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D	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	23.4	4.409094	0.83340	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.85919	0.5809	M	0.91818	3.245	0.80722	D	1	B;P	0.35714	0.385;0.517	B;B	0.41619	0.257;0.361	D	0.87870	0.2670	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	D	12	ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D	ENSP00000256078:G12D	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-2J-AAB1-01A-11D-A40W-08	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	1	0	0	8	199	0	53	0	1.537874e-01	1	15	0	53	2	1	9.993325e-01	11	354	0	365	2	1	0.989787	8	199	0	51	2								-4.074507	1	1	121404	2	44	1	0	0	0	1.993904	0	0.380000	1.940000	0.370431	0.200000	9.000000e-02	0.370000	0.200000	0.221373	0.200000	0	0.140000	0.290000
KRAS	3845	broad.mit.edu	37	12	25398285	25398285	+	Missense_Mutation	SNP	C	C	G	rs121913530		TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08			C	G	C	C		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr12:25398285C>G	ENST00000256078.4	-	2	97	c.34G>C	c.(34-36)Ggt>Cgt	p.G12R	KRAS_ENST00000556131.1_Missense_Mutation_p.G12R|KRAS_ENST00000557334.1_Missense_Mutation_p.G12R|KRAS_ENST00000311936.3_Missense_Mutation_p.G12R	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	p.G12C(3001)|p.G12S(1288)|p.G12R(789)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12W(3)|p.A11_G12insGA(2)|p.G12Y(2)|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)		CCTACGCCACCAGCTCCAACT	0.348000	G12C(CALU1_LUNG)|G12C(HCC44_LUNG)|G12C(IALM_LUNG)|G12C(KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12C(KYSE410_OESOPHAGUS)|G12C(LU65_LUNG)|G12C(LU99_LUNG)|G12C(MIAPACA2_PANCREAS)|G12C(NCIH1373_LUNG)|G12C(NCIH1792_LUNG)|G12C(NCIH2030_LUNG)|G12C(NCIH2122_LUNG)|G12C(NCIH23_LUNG)|G12C(NCIH358_LUNG)|G12C(OV56_OVARY)|G12C(SW1463_LARGE_INTESTINE)|G12C(SW1573_LUNG)|G12C(SW837_LARGE_INTESTINE)|G12C(UMUC3_URINARY_TRACT)|G12R(CAL62_THYROID)|G12R(HS274T_BREAST)|G12R(HUPT3_PANCREAS)|G12R(KP2_PANCREAS)|G12R(PSN1_PANCREAS)|G12R(TCCPAN2_PANCREAS)|G12S(A549_LUNG)|G12S(KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12S(LS123_LARGE_INTESTINE)	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	5144	Substitution - Missense(5142)|Insertion - In frame(2)	GRCh37	CM076251	KRAS	M	rs121913530	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	28.6	4.930538	0.92389	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78246	-1.16;-1.16;-1.16;-1.16	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.84893	0.5573	M	0.84082	2.675	0.80722	D	1	P;P	0.43287	0.802;0.741	B;P	0.47941	0.36;0.562	D	0.86658	0.1902	10	0.66056	D	0.02	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	R	12	ENSP00000308495:G12R;ENSP00000452512:G12R;ENSP00000256078:G12R;ENSP00000451856:G12R	ENSP00000256078:G12R	G	-	1	0	KRAS	25289552	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-2J-AAB1-01A-11D-A40W-08	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	1	0	1	26	181	0	55	1	6.511692e-01	10	7	0	55	2	1	1	47	316	0	364	2	1	1.000000	26	181	0	53	2								-12.853510	1	1	0	0		1	0	0	0	1.993904	0	0.380000	1.940000	0.370431	0.650000	4.400000e-01	0.890000	0.640000	0.663868	0.650000	0	0.540000	0.780000
ARNTL2	56938	broad.mit.edu	37	12	27533278	27533278	+	Missense_Mutation	SNP	G	G	A	rs149871988		TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr12:27533278G>A	ENST00000266503.5	+	5	443	c.425G>A	c.(424-426)cGt>cAt	p.R142H	ARNTL2_ENST00000261178.5_Missense_Mutation_p.R94H|ARNTL2_ENST00000395901.2_Missense_Mutation_p.R105H|ARNTL2_ENST00000542388.1_Missense_Mutation_p.R57H|ARNTL2_ENST00000311001.5_Missense_Mutation_p.R128H|ARNTL2_ENST00000544915.1_Missense_Mutation_p.R108H|ARNTL2_ENST00000546179.1_Missense_Mutation_p.R105H			Q8WYA1	BMAL2_HUMAN	aryl hydrocarbon receptor nuclear translocator-like 2			21	Colorectal(261;0.0847)|Lung SC(9;0.184)				CCCATGGCGCGTAAACTGGAC	0.418000																								0							SO:0001583	missense			ENST00000266503.5	0	1	hg19	CCDS8712.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.36|15.36	2.809399|2.809399	0.50421|0.50421	0.0|0.0	1.16E-4|1.16E-4	ENSG00000029153|ENSG00000029153	ENST00000544915;ENST00000395901;ENST00000546179;ENST00000311001;ENST00000261178;ENST00000266503;ENST00000542388|ENST00000457040	D;D;D;D;D;D;D|.	0.98044|.	-4.68;-4.68;-4.68;-4.68;-4.68;-4.68;-4.68|.	3.33|3.33	2.41|2.41	0.29592|0.29592	Helix-loop-helix DNA-binding (5);|.	0.166448|.	0.41294|.	N|.	0.000915|.	T|T	0.52933|0.52933	0.1765|0.1765	L|L	0.43701|0.43701	1.375|1.375	0.45962|0.45962	D|D	0.998786|0.998786	P;P;P;P;P;P|.	0.46578|.	0.507;0.708;0.647;0.647;0.501;0.88|.	B;B;B;B;B;P|.	0.44696|.	0.169;0.329;0.233;0.233;0.109;0.458|.	T|T	0.42932|0.42932	-0.9422|-0.9422	10|5	0.54805|.	T|.	0.06|.	.|.	8.1033|8.1033	0.30870|0.30870	0.1179:0.0:0.8821:0.0|0.1179:0.0:0.8821:0.0	.|.	105;108;105;94;128;142|.	F5H402;Q8WYA1-5;Q8WYA1-3;Q8WYA1-4;Q8WYA1-2;Q8WYA1|.	.;.;.;.;.;BMAL2_HUMAN|.	H|I	108;105;105;128;94;142;57|94	ENSP00000442438:R108H;ENSP00000379238:R105H;ENSP00000438545:R105H;ENSP00000312247:R128H;ENSP00000261178:R94H;ENSP00000266503:R142H;ENSP00000445836:R57H|.	ENSP00000261178:R94H|.	R|V	+|+	2|1	0|0	ARNTL2|ARNTL2	27424545|27424545	0.987000|0.987000	0.35691|0.35691	0.059000|0.059000	0.19551|0.19551	0.969000|0.969000	0.65631|0.65631	6.556000|6.556000	0.73932|0.73932	0.728000|0.728000	0.32382|0.32382	0.655000|0.655000	0.94253|0.94253	CGT|GTA		TCGA-2J-AAB1-01A-11D-A40W-08	ARNTL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403162.1	0	0	0	5	450	0	86	0	2.298764e-02	0	17	0	86	2		0	0	0	0	0	2	1	0.932983	5	437	0	84	2								-2.520841	1	1	121412	4	39	1	0	0	0	1.993904	0	0.380000	1.940000	0.370431	0.050000	1.000000e-02	0.130000	0.060000	0.067790	0.050000	0	0.030000	0.090000
SLC6A15	55117	broad.mit.edu	37	12	85255590	85255590	+	Missense_Mutation	SNP	C	C	T			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr12:85255590C>T	ENST00000266682.5	-	12	2555	c.2014G>A	c.(2014-2016)Gat>Aat	p.D672N	SLC6A15_ENST00000309283.7_3'UTR|SLC6A15_ENST00000552192.1_Missense_Mutation_p.D565N	NM_182767.5	NP_877499.1	Q9H2J7	S6A15_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 15			44					CTTGTATCATCGCCCTCTAAG	0.423000																								0							SO:0001583	missense			ENST00000266682.5	1	1	hg19	CCDS9026.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.699502	0.88830	.	.	ENSG00000072041	ENST00000266682;ENST00000552192;ENST00000548267	T;T	0.77620	-0.93;-1.11	5.85	5.85	0.93711	.	0.182364	0.64402	D	0.000018	D	0.86581	0.5967	L	0.54323	1.7	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.85436	0.1152	10	0.49607	T	0.09	.	20.1649	0.98147	0.0:1.0:0.0:0.0	.	672	Q9H2J7	S6A15_HUMAN	N	672;565;150	ENSP00000266682:D672N;ENSP00000450145:D565N	ENSP00000266682:D672N	D	-	1	0	SLC6A15	83779721	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	5.665000	0.68052	2.753000	0.94483	0.655000	0.94253	GAT		TCGA-2J-AAB1-01A-11D-A40W-08	SLC6A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405678.1	1	0	1	126	511	0	142		0	0	0	0	142	2		0	0	0	0	0	2	1	1.000000	125	506	0	135	2								-20.000000	1	1	0	0		1	0	0	0	1.993904	0	0.380000	1.940000	0.370431	0.990000	8.600000e-01	1.000000	1.000000	0.979447	0.990000	1	0.940000	1.000000
USP44	84101	broad.mit.edu	37	12	95922666	95922666	+	Missense_Mutation	SNP	G	G	A			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr12:95922666G>A	ENST00000258499.3	-	3	1829	c.1541C>T	c.(1540-1542)cCa>cTa	p.P514L	USP44_ENST00000552440.1_Intron|USP44_ENST00000537435.2_Missense_Mutation_p.P514L|USP44_ENST00000393091.2_Missense_Mutation_p.P514L	NM_001278393.1|NM_032147.2	NP_001265322.1|NP_115523.2	Q9H0E7	UBP44_HUMAN	ubiquitin specific peptidase 44			36					AACCAGACATGGCTGGGAAGC	0.393000																								0							SO:0001583	missense			ENST00000258499.3	1	1	hg19	CCDS9053.1	.	.	.	.	.	.	.	.	.	.	G	19.23	3.787659	0.70337	.	.	ENSG00000136014	ENST00000258499;ENST00000393091;ENST00000537435	T;T;T	0.02631	4.22;4.22;4.22	5.94	5.94	0.96194	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.049563	0.85682	D	0.000000	T	0.06050	0.0157	L	0.31371	0.925	0.58432	D	0.999998	P	0.37731	0.607	P	0.45913	0.497	T	0.52845	-0.8521	10	0.35671	T	0.21	.	20.3632	0.98871	0.0:0.0:1.0:0.0	.	514	Q9H0E7	UBP44_HUMAN	L	514	ENSP00000258499:P514L;ENSP00000376806:P514L;ENSP00000442629:P514L	ENSP00000258499:P514L	P	-	2	0	USP44	94446797	1.000000	0.71417	1.000000	0.80357	0.863000	0.49368	6.662000	0.74426	2.826000	0.97356	0.561000	0.74099	CCA		TCGA-2J-AAB1-01A-11D-A40W-08	USP44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408312.1	1	0	1	50	247	0	57	0	1.385372e-01	0	4	0	57	2		0	0	0	0	0	2	1	1.000000	50	244	0	57	2								-20.000000	1	0	0	0		1	0	0	0	1.993904	0	0.380000	1.940000	0.370431	0.860000	6.600000e-01	1.000000	1.000000	0.870168	0.860000	1	0.760000	0.990000
LRCH1	23143	broad.mit.edu	37	13	47266683	47266683	+	Missense_Mutation	SNP	G	G	T			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08			G	T	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr13:47266683G>T	ENST00000389798.3	+	8	1224	c.1027G>T	c.(1027-1029)Gac>Tac	p.D343Y	LRCH1_ENST00000311191.6_Missense_Mutation_p.D343Y|LRCH1_ENST00000389797.3_Missense_Mutation_p.D343Y	NM_015116.2	NP_055931	Q9Y2L9	LRCH1_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 1			26		all_lung(13;5.61e-07)|Lung NSC(96;0.000117)|Breast(56;0.000141)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)		TTCTGACGAAGACACTGTTAG	0.418000																								0							SO:0001583	missense			ENST00000389798.3	1	1	hg19	CCDS31972.1	.	.	.	.	.	.	.	.	.	.	G	19.73	3.882904	0.72410	.	.	ENSG00000136141	ENST00000311191;ENST00000389798;ENST00000389797;ENST00000463929	T;T;T	0.59906	0.35;0.39;0.23	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	T	0.77928	0.4204	M	0.82630	2.6	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.994;0.999;0.999	T	0.73448	-0.3979	10	0.21540	T	0.41	-24.1686	19.122	0.93367	0.0:0.0:1.0:0.0	.	343;343;343;343	Q17R43;Q9Y2L9-2;F8W6F0;Q9Y2L9	.;.;.;LRCH1_HUMAN	Y	343;343;343;89	ENSP00000308493:D343Y;ENSP00000374448:D343Y;ENSP00000374447:D343Y	ENSP00000308493:D343Y	D	+	1	0	LRCH1	46164684	1.000000	0.71417	1.000000	0.80357	0.640000	0.38277	7.924000	0.87555	2.770000	0.95276	0.655000	0.94253	GAC		TCGA-2J-AAB1-01A-11D-A40W-08	LRCH1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044824.2	1	0	1	113	468	0	90	1	9.994734e-01	14	34	0	90	2		0	0	0	0	0	2	1	1.000000	112	467	0	89	2								-20.000000	1	1	0	0		1	0	0	0	2.015661	0	0.380000	1.940000	0.377635	0.990000	8.500000e-01	1.000000	1.000000	0.975856	0.990000	1	0.930000	1.000000
PCDH9	5101	broad.mit.edu	37	13	66878827	66878827	+	Missense_Mutation	SNP	G	G	A			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr13:66878827G>A	ENST00000377865.2	-	4	3808	c.3674C>T	c.(3673-3675)gCa>gTa	p.A1225V	PCDH9-AS1_ENST00000430861.1_RNA|PCDH9_ENST00000328454.5_Missense_Mutation_p.A1191V|PCDH9_ENST00000456367.1_Missense_Mutation_p.A1191V|PCDH9_ENST00000544246.1_Missense_Mutation_p.A1225V			Q9HC56	PCDH9_HUMAN	protocadherin 9	p.A1225E(1)		103		Hepatocellular(98;0.0906)|Breast(118;0.107)			AGCACCTCCTGCTTGCTTATA	0.438000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000377865.2	1	1	hg19	CCDS9444.1	.	.	.	.	.	.	.	.	.	.	G	15.84	2.950604	0.53186	.	.	ENSG00000184226	ENST00000544246;ENST00000377865;ENST00000456367;ENST00000328454	T;T;T;T	0.57907	0.47;0.47;0.37;0.37	6.05	5.2	0.72013	.	0.461993	0.18412	N	0.142037	T	0.38374	0.1038	N	0.19112	0.55	0.32371	N	0.555834	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.46803	-0.9165	10	0.56958	D	0.05	.	11.2657	0.49110	0.1389:0.0:0.8611:0.0	.	1183;1191;1225	B7ZM79;Q9HC56-2;Q9HC56	.;.;PCDH9_HUMAN	V	1225;1225;1191;1191	ENSP00000442186:A1225V;ENSP00000367096:A1225V;ENSP00000401699:A1191V;ENSP00000332060:A1191V	ENSP00000332060:A1191V	A	-	2	0	PCDH9	65776828	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.884000	0.56175	1.561000	0.49584	0.650000	0.86243	GCA		TCGA-2J-AAB1-01A-11D-A40W-08	PCDH9-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276387.1	1	0	1	59	221	0	56	0	1.175597e-01	0	3	0	56	2		0	0	0	0	0	2	1	1.000000	59	218	0	56	2								-20.000000	1	1	0	0		1	0	0	0	2.015661	0	0.380000	1.940000	0.377635	0.990000	8.600000e-01	1.000000	1.000000	0.987129	0.990000	1	0.970000	1.000000
KLHL1	57626	broad.mit.edu	37	13	70535555	70535555	+	Silent	SNP	G	G	A			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr13:70535555G>A	ENST00000377844.4	-	3	1461	c.702C>T	c.(700-702)tcC>tcT	p.S234S	KLHL1_ENST00000545028.1_Silent_p.S41S	NM_020866.2	NP_065917.1	Q9NR64	KLHL1_HUMAN	kelch-like family member 1	p.S234S(1)		84		Breast(118;0.000162)			CAAAATAGTCGGAGACTGAAC	0.453000																								1	Substitution - coding silent(1)						SO:0001819	synonymous_variant			ENST00000377844.4	1	1	hg19	CCDS9445.1																																																																																				TCGA-2J-AAB1-01A-11D-A40W-08	KLHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045231.3	1	0	1	29	204	0	48		0	0	0	0	48	2		0	0	0	0	0	2	1	1.000000	29	200	0	48	2								-2.691054	1	1	121388	2	38	1	0	0	0	2.015661	0	0.380000	1.940000	0.377635	0.650000	4.500000e-01	0.880000	0.640000	0.664462	0.650000	0	0.540000	0.770000
DIO3	1735	broad.mit.edu	37	14	102028329	102028329	+	Missense_Mutation	SNP	G	G	A			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr14:102028329G>A	ENST00000510508.4	+	1	642	c.496G>A	c.(496-498)Ggc>Agc	p.G166S	DIO3_ENST00000359323.3_Missense_Mutation_p.G140S|DIO3OS_ENST00000408206.1_lincRNA			P55073	IOD3_HUMAN	deiodinase, iodothyronine, type III			22		all_neural(303;0.185)			TCTCAATTTCGGCAGCTGCAC	0.627000																								0							SO:0001583	missense			ENST00000510508.4	1	1	hg19	CCDS41992.2	.	.	.	.	.	.	.	.	.	.	G	29.7	5.030514	0.93575	.	.	ENSG00000197406;ENSG00000258865	ENST00000359323;ENST00000510508	T;T	0.57907	0.37;0.37	3.51	3.51	0.40186	Thioredoxin-like fold (1);	0.000000	0.47852	U	0.000217	T	0.75184	0.3815	M	0.91510	3.215	0.46927	D	0.999255	D	0.89917	1.0	D	0.64877	0.93	T	0.82051	-0.0649	10	0.59425	D	0.04	-16.4547	14.2065	0.65737	0.0:0.0:1.0:0.0	.	140	P55073	IOD3_HUMAN	S	140;166	ENSP00000352273:G140S;ENSP00000427336:G166S	ENSP00000352273:G166S	G	+	1	0	DIO3;AL049836.1	101098082	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.515000	0.98015	1.799000	0.52666	0.462000	0.41574	GGC		TCGA-2J-AAB1-01A-11D-A40W-08	DIO3-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS|seleno	protein_coding	protein_coding	OTTHUMT00000361712.4	0	0	0	13	238	0	54	0	3.817580e-01	0	24	0	54	2		0	0	0	0	0	2	1	0.999525	13	234	0	52	2								-3.328041	1	1	0	0		1	0	0	0	2.012091	0	0.380000	1.940000	0.377635	0.270000	1.500000e-01	0.440000	0.270000	0.288239	0.270000	0	0.200000	0.360000
OR4M1	441670	broad.mit.edu	37	14	20248817	20248817	+	Missense_Mutation	SNP	G	G	A			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr14:20248817G>A	ENST00000315957.4	+	1	417	c.336G>A	c.(334-336)atG>atA	p.M112I		NM_001005500.1	NP_001005500.1	Q8NGD0	OR4M1_HUMAN	olfactory receptor, family 4, subfamily M, member 1			42	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)		CTTCGGAGATGTTCTTGCTCA	0.478000																								0							SO:0001583	missense			ENST00000315957.4	1	1	hg19	CCDS32021.1	.	.	.	.	.	.	.	.	.	.	.	1.041	-0.678902	0.03378	.	.	ENSG00000176299	ENST00000315957	T	0.00388	7.59	4.33	4.33	0.51752	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000014	T	0.00210	0.0006	L	0.31207	0.915	0.27921	N	0.938258	B	0.30439	0.279	B	0.27608	0.081	T	0.41945	-0.9480	10	0.05959	T	0.93	-21.4932	14.6986	0.69139	0.0:0.0:1.0:0.0	.	112	Q8NGD0	OR4M1_HUMAN	I	112	ENSP00000319654:M112I	ENSP00000319654:M112I	M	+	3	0	OR4M1	19318657	0.000000	0.05858	1.000000	0.80357	0.945000	0.59286	-0.007000	0.12810	2.407000	0.81776	0.506000	0.49869	ATG		TCGA-2J-AAB1-01A-11D-A40W-08	OR4M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409770.1	0	0	0	130	1897	0	354		0	0	0	0	354	2		0	0	0	0	0	2	1	1.000000	129	1880	0	346	2								-18.041860	1	1	0	0		1	1	2	3	2.350241	1	0.380000	1.940000	0.478992	0.390000	3.300000e-01	0.470000	0.390000	0.404155	0.390000	0	0.360000	0.440000
FBN1	2200	broad.mit.edu	37	15	48704920	48704920	+	Missense_Mutation	SNP	C	C	T			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr15:48704920C>T	ENST00000316623.5	-	65	8527	c.8072G>A	c.(8071-8073)gGc>gAc	p.G2691D	FBN1_ENST00000561429.1_5'UTR	NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1			139		all_lung(180;0.00279)			TCGGCCCATGCCCATTCCAGA	0.502000																								0							SO:0001583	missense			ENST00000316623.5	0	1	hg19	CCDS32232.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.647484	0.87958	.	.	ENSG00000166147	ENST00000316623	D	0.81821	-1.54	5.38	5.38	0.77491	Growth factor, receptor (1);	0.000000	0.85682	D	0.000000	D	0.88599	0.6480	M	0.73598	2.24	0.80722	D	1	D	0.69078	0.997	D	0.66196	0.942	D	0.85789	0.1366	10	0.27785	T	0.31	.	18.926	0.92544	0.0:1.0:0.0:0.0	.	2691	P35555	FBN1_HUMAN	D	2691	ENSP00000325527:G2691D	ENSP00000325527:G2691D	G	-	2	0	FBN1	46492212	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.651000	0.83577	2.793000	0.96121	0.655000	0.94253	GGC		TCGA-2J-AAB1-01A-11D-A40W-08	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1	0	0	0	6	718	0	127	0	4.193274e-01	0	152	0	127	2		0	0	0	0	0	2	1	0.963687	6	709	0	125	2								-1.655459	0	1	0	0		1	1	2	3	2.029824	0	0.380000	1.940000	0.381176	0.040000	0	0.100000	0.040000	0.050708	0.040000	0	0.020000	0.070000
ANPEP	290	broad.mit.edu	37	15	90334315	90334315	+	Silent	SNP	G	G	A			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr15:90334315G>A	ENST00000300060.6	-	19	2851	c.2538C>T	c.(2536-2538)agC>agT	p.S846S		NM_001150.2	NP_001141.2	P15144	AMPN_HUMAN	alanyl (membrane) aminopeptidase			57	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.169)	Ezetimibe(DB00973)|Icatibant(DB06196)	TCAGGGTGTAGCTCAGGTACC	0.532000													NSCLC(30;827 977 2459 19669 26125)											0							SO:0001819	synonymous_variant			ENST00000300060.6	1	1	hg19	CCDS10356.1																																																																																				TCGA-2J-AAB1-01A-11D-A40W-08	ANPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313425.1	0	0	0	13	366	0	80	1	9.447764e-01	2	139	0	80	2		0	0	0	0	0	2	1	0.999529	13	363	0	79	2								-3.816047	1	1	0	0		1	1	2	3	2.029824	0	0.380000	1.940000	0.381176	0.180000	9.000000e-02	0.300000	0.180000	0.192936	0.180000	0	0.130000	0.240000
CACNA1H	8912	broad.mit.edu	37	16	1256207	1256207	+	Missense_Mutation	SNP	C	C	A			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr16:1256207C>A	ENST00000348261.5	+	12	2955	c.2707C>A	c.(2707-2709)Cgc>Agc	p.R903S	CACNA1H_ENST00000565831.1_Missense_Mutation_p.R903S|RP11-616M22.3_ENST00000564700.1_RNA|CACNA1H_ENST00000358590.4_Missense_Mutation_p.R903S	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit			34		Hepatocellular(780;0.00369)		Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	AGCCCTGCGGCGCCAGCTCGT	0.632000																								0							SO:0001583	missense			ENST00000348261.5	1	1	hg19	CCDS45375.1	.	.	.	.	.	.	.	.	.	.	C	19.72	3.880727	0.72294	.	.	ENSG00000196557	ENST00000348261;ENST00000358590	D;D	0.98474	-4.95;-4.95	3.96	3.96	0.45880	Ion transport (1);	0.127635	0.51477	N	0.000098	D	0.98632	0.9542	M	0.71920	2.185	0.35343	D	0.786673	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.99970	1.1986	10	0.87932	D	0	.	15.1886	0.73025	0.0:1.0:0.0:0.0	.	903;903	O95180-2;O95180	.;CAC1H_HUMAN	S	903	ENSP00000334198:R903S;ENSP00000351401:R903S	ENSP00000334198:R903S	R	+	1	0	CACNA1H	1196208	0.986000	0.35501	0.999000	0.59377	0.794000	0.44872	2.180000	0.42537	2.050000	0.60909	0.561000	0.74099	CGC		TCGA-2J-AAB1-01A-11D-A40W-08	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	1	0	1	9	39	0	14	0	3.444169e-01	0	6	0	14	2		0	0	0	0	0	2	1	0.995741	9	39	0	14	2								-17.915760	1	1	0	0		1	1	2	3	2.023473	0	0.380000	1.940000	0.381176	0.990000	5.100000e-01	1.000000	1.000000	0.896701	0.990000	1	0.730000	1.000000
CACNA1H	8912	broad.mit.edu	37	16	1256208	1256208	+	Missense_Mutation	SNP	G	G	A			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr16:1256208G>A	ENST00000348261.5	+	12	2956	c.2708G>A	c.(2707-2709)cGc>cAc	p.R903H	CACNA1H_ENST00000565831.1_Missense_Mutation_p.R903H|RP11-616M22.3_ENST00000564700.1_RNA|CACNA1H_ENST00000358590.4_Missense_Mutation_p.R903H	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit			34		Hepatocellular(780;0.00369)		Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	GCCCTGCGGCGCCAGCTCGTG	0.632000																								0							SO:0001583	missense			ENST00000348261.5	1	1	hg19	CCDS45375.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.982149	0.93044	.	.	ENSG00000196557	ENST00000348261;ENST00000358590	D;D	0.98474	-4.95;-4.95	3.96	3.96	0.45880	Ion transport (1);	0.127635	0.51477	D	0.000098	D	0.98896	0.9626	M	0.85542	2.76	0.40805	D	0.98337	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.99884	1.1119	10	0.87932	D	0	.	15.1886	0.73025	0.0:0.0:1.0:0.0	.	903;903	O95180-2;O95180	.;CAC1H_HUMAN	H	903	ENSP00000334198:R903H;ENSP00000351401:R903H	ENSP00000334198:R903H	R	+	2	0	CACNA1H	1196209	1.000000	0.71417	0.993000	0.49108	0.785000	0.44390	9.153000	0.94687	2.050000	0.60909	0.561000	0.74099	CGC		TCGA-2J-AAB1-01A-11D-A40W-08	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	1	0	1	9	38	0	14	0	4.285151e-01	0	7	0	14	2		0	0	0	0	0	2	1	0.995774	9	38	0	14	2								-17.943830	1	1	0	0		1	1	2	3	2.023473	0	0.380000	1.940000	0.381176	0.990000	5.200000e-01	1.000000	1.000000	0.904532	0.990000	1	0.740000	1.000000
CYLD	1540	broad.mit.edu	37	16	50827516	50827516	+	Missense_Mutation	SNP	G	G	A			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr16:50827516G>A	ENST00000427738.3	+	16	2615	c.2410G>A	c.(2410-2412)Gac>Aac	p.D804N	CYLD_ENST00000398568.2_Missense_Mutation_p.D801N|CYLD_ENST00000566206.1_Missense_Mutation_p.D801N|CYLD_ENST00000568704.2_Missense_Mutation_p.D619N|RP11-327F22.4_ENST00000575917.1_RNA|CYLD_ENST00000564326.1_Missense_Mutation_p.D801N|CYLD_ENST00000540145.1_Missense_Mutation_p.D804N|RP11-327F22.4_ENST00000564510.1_RNA|CYLD_ENST00000569418.1_Missense_Mutation_p.D801N|CYLD_ENST00000311559.9_Missense_Mutation_p.D804N			Q9NQC7	CYLD_HUMAN	cylindromatosis (turban tumor syndrome)			62		all_cancers(37;0.0156)			AGAATGCTACGACGATCCGGA	0.438000			Mis, N, F, S		cylindroma	cylindroma			Multiple Trichoepithelioma, Familial;Familial Cylindromatosis					yes	Rec	yes	Familial cylindromatosis	16	16q12-q13	1540	familial cylindromatosis gene		E	0							SO:0001583	missense	Familial Cancer Database	;FADC, Turban Tumor syndrome, Epithelioma Adenoides Cysticum of Brooke, Hereditary Multiple Benign Cystic Epithelioma, Dermal Eccrine Cylindromatosis, Brooke-Spiegler s.	ENST00000427738.3	0	1	hg19	CCDS45482.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.052407	0.75960	.	.	ENSG00000083799	ENST00000540145;ENST00000311559;ENST00000427738;ENST00000398568	T;T;T	0.74002	-0.8;-0.8;-0.8	5.25	5.25	0.73442	.	0.188320	0.56097	D	0.000035	T	0.62183	0.2407	N	0.14661	0.345	0.58432	D	0.999999	P;P	0.45176	0.852;0.821	B;B	0.40165	0.321;0.215	T	0.67011	-0.5778	10	0.45353	T	0.12	-19.1886	19.2041	0.93723	0.0:0.0:1.0:0.0	.	801;801	A8KAB0;Q9NQC7-2	.;.	N	804;804;801;801	ENSP00000445447:D804N;ENSP00000308928:D804N;ENSP00000381574:D801N	ENSP00000308928:D804N	D	+	1	0	CYLD	49385017	1.000000	0.71417	0.273000	0.24645	0.846000	0.48090	7.522000	0.81844	2.620000	0.88729	0.655000	0.94253	GAC		TCGA-2J-AAB1-01A-11D-A40W-08	CYLD-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422998.2	0	0	0	14	618	0	129	0	4.095970e-01	1	59	0	129	2		0	0	0	0	0	2	1	0.999751	14	616	0	126	2								-2.758398	1	1	0	0		1	1	2	3	2.027735	0	0.380000	1.940000	0.381176	0.110000	6.000000e-02	0.200000	0.120000	0.124440	0.110000	0	0.080000	0.160000
C16orf11	0	broad.mit.edu	37	16	615296	615296	+	Missense_Mutation	SNP	G	G	A			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr16:615296G>A	ENST00000409413.3	+	3	1984	c.1705G>A	c.(1705-1707)Gcc>Acc	p.A569T	NHLRC4_ENST00000424439.2_5'Flank|NHLRC4_ENST00000540585.1_5'Flank|PIGQ_ENST00000409527.2_5'Flank	NM_145270.2	NP_660313.1	P0CG20	PRR35_HUMAN				10					CCCCCAGGGCGCCGAGGTCTG	0.677000																								0							SO:0001583	missense			ENST00000409413.3	1	1	hg19	CCDS45365.1	.	.	.	.	.	.	.	.	.	.	G	13.28	2.189481	0.38707	.	.	ENSG00000161992	ENST00000409413	.	.	.	5.25	1.61	0.23674	.	1.152320	0.06446	N	0.726940	T	0.23766	0.0575	N	0.20986	0.625	0.09310	N	1	B	0.30021	0.265	B	0.20577	0.03	T	0.26573	-1.0099	9	0.87932	D	0	.	6.6076	0.22734	0.1873:0.0:0.6619:0.1507	.	569	P0CG20	CP011_HUMAN	T	569	.	ENSP00000386499:A569T	A	+	1	0	C16orf11	555297	0.000000	0.05858	0.006000	0.13384	0.021000	0.10359	0.126000	0.15769	0.554000	0.29061	0.491000	0.48974	GCC		TCGA-2J-AAB1-01A-11D-A40W-08	C16orf11-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000333913.1	1	0	1	11	37	0	12		0	0	0	0	12	2		0	0	0	0	0	2	1	0.998993	11	37	0	12	2								-19.998620	1	1	117812	5	30	1	1	2	3	2.023473	0	0.380000	1.940000	0.381176	0.990000	6.700000e-01	1.000000	1.000000	0.963165	0.990000	1	0.910000	1.000000
CES3	23491	broad.mit.edu	37	16	67006841	67006841	+	Silent	SNP	C	C	T			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr16:67006841C>T	ENST00000303334.4	+	13	1676	c.1605C>T	c.(1603-1605)gcC>gcT	p.A535A	CES3_ENST00000543856.1_Silent_p.A174A|CES3_ENST00000394037.1_Silent_p.A532A	NM_024922.5	NP_079198.2	Q6UWW8	EST3_HUMAN	carboxylesterase 3			24		Ovarian(137;0.0563)			TGCCACGGGCCGGACAGAAGT	0.582000																								0							SO:0001819	synonymous_variant			ENST00000303334.4	1	1	hg19	CCDS10826.1																																																																																				TCGA-2J-AAB1-01A-11D-A40W-08	CES3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268848.1	1	0	0	18	368	0	63	0	5.348096e-01	1	36	0	63	2		0	0	0	0	0	2	1	0.999978	18	357	0	62	2								-4.545027	1	1	121412	2	34	1	1	2	3	2.027735	0	0.380000	1.940000	0.381176	0.240000	1.500000e-01	0.380000	0.240000	0.257139	0.240000	0	0.190000	0.310000
SMYD4	114826	broad.mit.edu	37	17	1703597	1703597	+	Missense_Mutation	SNP	C	C	T			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr17:1703597C>T	ENST00000305513.7	-	5	1258	c.1091G>A	c.(1090-1092)cGc>cAc	p.R364H		NM_052928.2	NP_443160.2	Q8IYR2	SMYD4_HUMAN	SET and MYND domain containing 4			21					TATGATTTTGCGAACATCCTC	0.453000																								0							SO:0001583	missense			ENST00000305513.7	0	1	hg19	CCDS11013.1	.	.	.	.	.	.	.	.	.	.	C	10.27	1.304550	0.23736	.	.	ENSG00000186532	ENST00000305513	T	0.10099	2.91	6.17	3.9	0.45041	SET domain (2);	0.633514	0.19290	N	0.117933	T	0.06280	0.0162	N	0.08118	0	0.09310	N	1	P	0.40660	0.726	P	0.44860	0.462	T	0.19224	-1.0312	10	0.45353	T	0.12	-4.1382	2.4272	0.04462	0.1423:0.5342:0.1385:0.1849	.	364	Q8IYR2	SMYD4_HUMAN	H	364	ENSP00000304360:R364H	ENSP00000304360:R364H	R	-	2	0	SMYD4	1650347	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	0.710000	0.25748	0.647000	0.30713	0.655000	0.94253	CGC		TCGA-2J-AAB1-01A-11D-A40W-08	SMYD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207108.4	0	0	0	6	365	1	78	0	7.781872e-03	0	7	1	78	2		0	0	0	0	0	2	0	0.023796	6	363	1	78	16								-2.303287	0	1	121412	4	38	1	0	0	0	1.952011	0	0.380000	1.940000	0.355509	0.080000	3.000000e-02	0.170000	0.080000	0.094556	0.080000	0	0.050000	0.130000
RTN4RL1	146760	broad.mit.edu	37	17	1840902	1840902	+	Missense_Mutation	SNP	C	C	T			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr17:1840902C>T	ENST00000331238.6	-	2	693	c.214G>A	c.(214-216)Ggc>Agc	p.G72S		NM_178568.2	NP_848663.1			reticulon 4 receptor-like 1			11					CTGAAGTGGCCGGGCTGGAGG	0.637000													GBM(68;949 1139 14865 32798 38342)											0							SO:0001583	missense			ENST00000331238.6	1	1	hg19	CCDS45569.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.242161	0.79912	.	.	ENSG00000185924	ENST00000331238	T	0.02323	4.34	5.49	5.49	0.81192	.	0.000000	0.40064	N	0.001187	T	0.10895	0.0266	L	0.53780	1.695	0.80722	D	1	D	0.55605	0.972	P	0.59012	0.85	T	0.03051	-1.1078	10	0.38643	T	0.18	.	19.4381	0.94806	0.0:1.0:0.0:0.0	.	72	Q86UN2	R4RL1_HUMAN	S	72	ENSP00000330631:G72S	ENSP00000330631:G72S	G	-	1	0	RTN4RL1	1787652	1.000000	0.71417	0.998000	0.56505	0.576000	0.36127	7.813000	0.86123	2.606000	0.88127	0.650000	0.86243	GGC		TCGA-2J-AAB1-01A-11D-A40W-08	RTN4RL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450155.2	1	0	1	29	139	0	32	0	4.859141e-01	0	9	0	32	2		0	0	0	0	0	2	1	1.000000	23	135	0	31	2								-20.000000	1	1	121282	2	33	1	0	0	0	1.952011	0	0.380000	1.940000	0.355509	0.870000	6.100000e-01	1.000000	1.000000	0.864865	0.870000	1	0.730000	1.000000
MAP2K3	5606	broad.mit.edu	37	17	21208417	21208417	+	Missense_Mutation	SNP	G	G	A	rs150613942	byFrequency	TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08			G	A	G	G		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr17:21208417G>A	ENST00000342679.4	+	9	1000	c.751G>A	c.(751-753)Gtc>Atc	p.V251I	MAP2K3_ENST00000361818.5_Missense_Mutation_p.V222I|MAP2K3_ENST00000316920.6_Missense_Mutation_p.V222I	NM_145109.2	NP_659731.1	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3	p.V255I(1)							CAAGTCCGACGTCTGGAGCCT	0.637000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000342679.4	1	1	hg19	CCDS11217.1	.	.	.	.	.	.	.	.	.	.	G	13.88	2.369435	0.42003	2.27E-4	0.001395	ENSG00000034152	ENST00000342679;ENST00000395491;ENST00000361818;ENST00000316920	T;T	0.40756	1.02;1.02	5.13	5.13	0.70059	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.085299	0.46758	D	0.000277	T	0.19565	0.0470	N	0.02345	-0.59	0.58432	D	0.99999	B	0.10296	0.003	B	0.11329	0.006	T	0.08351	-1.0726	10	0.32370	T	0.25	-49.0281	11.9966	0.53206	0.0796:0.0:0.9204:0.0	.	251	P46734	MP2K3_HUMAN	I	251;222;222;255	ENSP00000345083:V251I;ENSP00000355081:V222I	ENSP00000319139:V255I	V	+	1	0	MAP2K3	21149010	1.000000	0.71417	0.951000	0.38953	0.735000	0.41995	3.362000	0.52314	2.387000	0.81309	0.462000	0.41574	GTC		TCGA-2J-AAB1-01A-11D-A40W-08	MAP2K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259374.2	1	0	0	27	549	0	129	0	9.997718e-01	0	262	0	129	2		0	0	0	0	0	2	1	1.000000	27	537	0	128	2								-2.281329	0	1	121412	273	50	1	1	2	3	2.024650	0	0.380000	1.940000	0.381176	0.240000	1.600000e-01	0.360000	0.240000	0.254729	0.240000	0	0.200000	0.300000
TOP2A	7153	broad.mit.edu	37	17	38564781	38564781	+	Missense_Mutation	SNP	G	G	C			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr17:38564781G>C	ENST00000423485.1	-	11	1463	c.1305C>G	c.(1303-1305)atC>atG	p.I435M		NM_001067.3	NP_001058.2	P11388	TOP2A_HUMAN	topoisomerase (DNA) II alpha 170kDa			39		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00183)	Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385)	GAATTCCCTTGATTCTATTAT	0.338000																								0							SO:0001583	missense			ENST00000423485.1	1	1	hg19	CCDS45672.1	.	.	.	.	.	.	.	.	.	.	G	18.48	3.632601	0.67015	.	.	ENSG00000131747	ENST00000423485;ENST00000269577;ENST00000348049;ENST00000357601	T	0.25250	1.81	5.5	4.51	0.55191	DNA topoisomerase, type IIA, subunit B/N-terminal, alpha-beta (1);DNA topoisomerase, type IIA, central (1);DNA topoisomerase, type IIA, subunit B/N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.38401	0.1039	M	0.73372	2.23	0.58432	D	0.999992	P	0.50443	0.935	P	0.54460	0.753	T	0.14227	-1.0480	10	0.35671	T	0.21	.	8.5579	0.33492	0.232:0.0:0.7679:0.0	.	435	P11388	TOP2A_HUMAN	M	435;515;458;471	ENSP00000411532:I435M	ENSP00000269577:I515M	I	-	3	3	TOP2A	35818307	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.709000	0.54853	1.277000	0.44412	0.591000	0.81541	ATC		TCGA-2J-AAB1-01A-11D-A40W-08	TOP2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338035.1	0	0	0	9	250	0	47	1	1.024245e-01	2	12	0	47	2		0	0	0	0	0	2	1	0.994037	9	246	0	47	2								-3.733343	1	1	0	0		1	1	2	3	2.039392	0	0.380000	1.940000	0.382347	0.190000	9.000000e-02	0.360000	0.180000	0.208987	0.190000	0	0.130000	0.270000
KRT38	8687	broad.mit.edu	37	17	39596894	39596894	+	Missense_Mutation	SNP	C	C	T			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr17:39596894C>T	ENST00000246646.3	-	1	279	c.280G>A	c.(280-282)Gcc>Acc	p.A94T		NM_006771.3	NP_006762.3	O76015	KRT38_HUMAN	keratin 38			29		Breast(137;0.000496)			TCACCATAGGCCCCACAGATT	0.602000																								0							SO:0001583	missense			ENST00000246646.3	1	1	hg19	CCDS11392.1	.	.	.	.	.	.	.	.	.	.	C	10.97	1.500176	0.26861	.	.	ENSG00000171360	ENST00000246646	T	0.81330	-1.48	4.89	-9.78	0.00496	.	1.660260	0.03712	N	0.250436	T	0.55986	0.1955	N	0.11064	0.09	0.09310	N	1	B	0.14438	0.01	B	0.10450	0.005	T	0.48139	-0.9061	10	0.26408	T	0.33	.	4.3812	0.11295	0.2664:0.4535:0.1747:0.1055	.	94	O76015	KRT38_HUMAN	T	94	ENSP00000246646:A94T	ENSP00000246646:A94T	A	-	1	0	KRT38	36850420	0.000000	0.05858	0.000000	0.03702	0.177000	0.22998	-1.774000	0.01784	-2.506000	0.00507	-0.912000	0.02778	GCC		TCGA-2J-AAB1-01A-11D-A40W-08	KRT38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257307.2	1	0	1	70	313	0	62		0	0	0	0	62	2		0	0	0	0	0	2	1	1.000000	68	306	0	60	2								-3.992291	1	1	121412	5	39	1	1	2	3	2.039392	0	0.380000	1.940000	0.382347	0.960000	7.600000e-01	1.000000	1.000000	0.942156	0.960000	1	0.860000	1.000000
DHX58	79132	broad.mit.edu	37	17	40263826	40263826	+	Missense_Mutation	SNP	C	C	T			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr17:40263826C>T	ENST00000251642.3	-	3	307	c.85G>A	c.(85-87)Ggg>Agg	p.G29R		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)			CGGGTCTTCCCGGCACCCGTG	0.592000																								0							SO:0001583	missense			ENST00000251642.3	0	1	hg19	CCDS11416.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.089390	0.76756	0.0	1.16E-4	ENSG00000108771	ENST00000251642;ENST00000423748;ENST00000413196;ENST00000430773	D;D;D	0.95554	-3.23;-3.74;-3.74	4.99	4.02	0.46733	DEAD-like helicase (2);Helicase/UvrB domain (1);	0.000000	0.85682	D	0.000000	D	0.98673	0.9555	H	0.99169	4.455	0.58432	D	0.999993	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98660	1.0683	10	0.87932	D	0	-2.8477	12.3178	0.54966	0.0:0.9172:0.0:0.0828	.	29;29	B7Z455;Q96C10	.;DHX58_HUMAN	R	29	ENSP00000251642:G29R;ENSP00000416389:G29R;ENSP00000404639:G29R	ENSP00000251642:G29R	G	-	1	0	DHX58	37517352	1.000000	0.71417	0.836000	0.33094	0.493000	0.33554	5.333000	0.65917	1.348000	0.45733	0.455000	0.32223	GGG		TCGA-2J-AAB1-01A-11D-A40W-08	DHX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257396.1	0	0	0	6	482	0	93	0	1.308777e-01	0	43	0	93	2		0	0	0	0	1	2	1	0.963816	6	476	0	89	2								-2.414314	0	1	121412	4	40	1	1	2	3	2.039392	0	0.380000	1.940000	0.382347	0.060000	2.000000e-02	0.150000	0.060000	0.084300	0.060000	0	0.040000	0.110000
ALOX15	246	broad.mit.edu	37	17	4544868	4544868	+	Missense_Mutation	SNP	C	C	G			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr17:4544868C>G	ENST00000570836.1	-	2	175	c.79G>C	c.(79-81)Gtc>Ctc	p.V27L	ALOX15_ENST00000293761.3_Missense_Mutation_p.V27L|ALOX15_ENST00000545513.1_Missense_Mutation_p.V49L|ALOX15_ENST00000574640.1_Missense_Mutation_p.V27L			P16050	LOX15_HUMAN	arachidonate 15-lipoxygenase			20					TGCTGGCCGACCAGCCACAGC	0.687000																								0							SO:0001583	missense			ENST00000570836.1	1	1	hg19	CCDS11049.1	.	.	.	.	.	.	.	.	.	.	C	18.79	3.698666	0.68501	.	.	ENSG00000161905	ENST00000293761;ENST00000545513	T;T	0.65549	-0.16;-0.16	5.33	3.31	0.37934	Lipoxygenase, LH2 (4);Lipase/lipooxygenase, PLAT/LH2 (1);	0.294429	0.26891	N	0.021975	T	0.68979	0.3060	M	0.88906	2.99	0.27340	N	0.956541	B;B;B	0.31859	0.106;0.343;0.129	B;B;B	0.38712	0.169;0.125;0.28	T	0.65940	-0.6046	10	0.66056	D	0.02	-16.6582	9.0593	0.36425	0.0:0.8459:0.0:0.1541	.	49;27;27	F5H0G8;B7ZA11;P16050	.;.;LOX15_HUMAN	L	27;49	ENSP00000293761:V27L;ENSP00000439855:V49L	ENSP00000293761:V27L	V	-	1	0	ALOX15	4491617	1.000000	0.71417	0.921000	0.36526	0.960000	0.62799	2.813000	0.48002	0.607000	0.29982	0.655000	0.94253	GTC		TCGA-2J-AAB1-01A-11D-A40W-08	ALOX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207487.2	1	0	1	36	155	0	32		0	0	0	0	32	2		0	0	0	0	0	2	1	1.000000	36	153	0	32	2								-20.000000	1	1	0	0		1	0	0	0	1.952011	0	0.380000	1.940000	0.355509	0.940000	6.900000e-01	1.000000	1.000000	0.921623	0.940000	1	0.810000	1.000000
ABCA9	10350	broad.mit.edu	37	17	67016614	67016614	+	Missense_Mutation	SNP	C	C	T	rs61740908		TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr17:67016614C>T	ENST00000340001.4	-	19	2726	c.2515G>A	c.(2515-2517)Gtg>Atg	p.V839M	ABCA9_ENST00000370732.2_Missense_Mutation_p.V839M|ABCA9_ENST00000453985.2_Missense_Mutation_p.V839M|ABCA9-AS1_ENST00000458677.1_RNA	NM_080283.3	NP_525022.2	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 9	p.V839M(1)		91	Breast(10;1.47e-12)				CAGAGCGCCACGCCACTGATT	0.443000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000340001.4	0	1	hg19	CCDS11681.1	.	.	.	.	.	.	.	.	.	.	c	0.305	-0.971160	0.02232	.	.	ENSG00000154258	ENST00000340001;ENST00000453985;ENST00000370732;ENST00000453749	T;T	0.75938	-0.98;-0.98	5.08	-4.05	0.03998	.	0.703590	0.12727	N	0.444186	T	0.26593	0.0650	N	0.00413	-1.525	0.22684	N	0.998856	B;B	0.11235	0.004;0.001	B;B	0.08055	0.003;0.001	T	0.45205	-0.9277	10	0.02654	T	1	.	2.4227	0.04452	0.1895:0.1485:0.43:0.232	.	839;839	Q8IUA7-3;Q8IUA7	.;ABCA9_HUMAN	M	839;822;839;834	ENSP00000342216:V839M;ENSP00000359767:V839M	ENSP00000342216:V839M	V	-	1	0	ABCA9	64528209	0.000000	0.05858	0.810000	0.32431	0.644000	0.38419	-0.621000	0.05559	-0.594000	0.05836	-0.464000	0.05259	GTG		TCGA-2J-AAB1-01A-11D-A40W-08	ABCA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277072.2	0	0	0	10	546	0	86	0	4.231827e-04	0	2	0	86	2		0	0	0	0	0	2	1	0.996753	10	540	0	83	2								-3.166621	1	1	121410	6	41	1	0	1	1	2.019142	0	0.380000	1.940000	0.378820	0.090000	4.000000e-02	0.170000	0.100000	0.103253	0.090000	0	0.060000	0.130000
POLR2A	5430	broad.mit.edu	37	17	7401414	7401414	+	Missense_Mutation	SNP	G	G	A	rs141769858	byFrequency	TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr17:7401414G>A	ENST00000322644.6	+	8	1619	c.1220G>A	c.(1219-1221)cGc>cAc	p.R407H	POLR2A_ENST00000572844.1_Missense_Mutation_p.R407H	NM_000937.4	NP_000928	P24928	RPB1_HUMAN	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa			50		Prostate(122;0.173)			GAACTAGTGCGCAGGGGGAAC	0.517000																								0							SO:0001583	missense			ENST00000322644.6	0	1	hg19	CCDS32548.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.969615	0.74246	0.00227	0.0	ENSG00000181222	ENST00000535204;ENST00000322644	T	0.68765	-0.35	5.6	5.6	0.85130	RNA polymerase, alpha subunit (1);RNA polymerase, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.73567	0.3603	M	0.86343	2.81	0.58432	D	0.999999	B;B	0.23490	0.086;0.024	B;B	0.22152	0.038;0.014	T	0.73572	-0.3940	10	0.62326	D	0.03	-11.3406	18.3894	0.90477	0.0:0.0:1.0:0.0	.	407;407	P24928;Q6NX41	RPB1_HUMAN;.	H	363;407	ENSP00000314949:R407H	ENSP00000314949:R407H	R	+	2	0	SLC35G6	7342138	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.828000	0.92047	2.653000	0.90120	0.563000	0.77884	CGC		TCGA-2J-AAB1-01A-11D-A40W-08	POLR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437967.1	0	0	0	5	339	1	51	0	2.325891e-03	0	80	1	51	7		0	0	0	0	0	2	0	0.000960	5	337	1	51	21								-3.238978	1	1	121412	27	45	1	0	0	0	1.959757	0	0.380000	1.940000	0.358045	0.070000	2.000000e-02	0.160000	0.070000	0.087686	0.070000	0	0.040000	0.120000
TP53	7157	broad.mit.edu	37	17	7578406	7578406	+	Missense_Mutation	SNP	C	C	T	rs28934578		TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr17:7578406C>T	ENST00000269305.4	-	5	713	c.524G>A	c.(523-525)cGc>cAc	p.R175H	TP53_ENST00000445888.2_Missense_Mutation_p.R175H|TP53_ENST00000574684.1_5'UTR|TP53_ENST00000455263.2_Missense_Mutation_p.R175H|TP53_ENST00000420246.2_Missense_Mutation_p.R175H|TP53_ENST00000359597.4_Missense_Mutation_p.R175H|TP53_ENST00000413465.2_Missense_Mutation_p.R175H	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	p.R175H(847)|p.R43H(36)|p.R82H(36)|p.R175L(19)|p.0?(8)|p.R175P(6)|p.R174fs*24(3)|p.R175_E180delRCPHHE(3)|p.V173fs*59(2)|p.R174fs*1(2)|p.V157_C176del20(1)|p.V173fs*69(1)|p.E171fs*61(1)|p.V173fs*23(1)|p.R174_H178>S(1)|p.V172_E180delVVRRCPHHE(1)|p.R174_H179delRRCPHH(1)|p.E171fs*1(1)|p.R175_H178>X(1)|p.R175fs*5(1)|p.R42fs*24(1)|p.R174_C176delRRC(1)|p.H168fs*69(1)|p.R174fs*70(1)|p.E171_H179delEVVRRCPHH(1)|p.R81fs*24(1)|p.R174_E180>K(1)|p.R174fs*3(1)		24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		Acetylsalicylic acid(DB00945)	GTGGGGGCAGCGCCTCACAAC	0.652000	R175H(AU565_BREAST)|R175H(CAL33_UPPER_AERODIGESTIVE_TRACT)|R175H(DETROIT562_UPPER_AERODIGESTIVE_TRACT)|R175H(HCC1395_BREAST)|R175H(HUCCT1_BILIARY_TRACT)|R175H(KLE_ENDOMETRIUM)|R175H(KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R175H(LS123_LARGE_INTESTINE)|R175H(NCIH196_LUNG)|R175H(RKN_OVARY)|R175H(SKBR3_BREAST)|R175H(SKUT1_SOFT_TISSUE)|R175H(TYKNU_OVARY)	111	Mis, N, F		breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types	breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		L, E, M, O	980	Substitution - Missense(944)|Deletion - Frameshift(17)|Whole gene deletion(8)|Deletion - In frame(8)|Complex - deletion inframe(3)	GRCh37	CM062017|CM951224	TP53	M	rs28934578	SO:0001583	missense	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	ENST00000269305.4	1	1	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	31	5.079737	0.94050	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99889	-7.55;-7.55;-7.55;-7.55;-7.55;-7.55;-7.55;-7.55	5.41	5.41	0.78517	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.101149	0.64402	D	0.000008	D	0.99908	0.9956	M	0.92784	3.345	0.80722	A	1	D;P;D;D;P;B;D	0.89917	0.999;0.578;1.0;0.998;0.632;0.213;0.999	D;B;D;D;B;B;D	0.91635	0.985;0.26;0.999;0.921;0.378;0.144;0.939	D	0.96278	0.9204	9	0.87932	D	0	-11.8679	17.0767	0.86588	0.0:1.0:0.0:0.0	rs28934578	136;175;175;82;175;175;175	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	H	175;175;175;175;175;175;164;82;43;82;43	ENSP00000410739:R175H;ENSP00000352610:R175H;ENSP00000269305:R175H;ENSP00000398846:R175H;ENSP00000391127:R175H;ENSP00000391478:R175H;ENSP00000425104:R43H;ENSP00000423862:R82H	ENSP00000269305:R175H	R	-	2	0	TP53	7519131	1.000000	0.71417	0.989000	0.46669	0.795000	0.44927	6.042000	0.70996	2.702000	0.92279	0.655000	0.94253	CGC		TCGA-2J-AAB1-01A-11D-A40W-08	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	1	0	0	13	238	0	49	1	8.920237e-01	8	66	0	49	2	1	9.999992e-01	52	1018	1	857	7	1	0.999538	13	235	0	48	2								-3.027011	1	1	121412	1	41	1	0	0	0	1.959757	0	0.380000	1.940000	0.358045	0.260000	1.400000e-01	0.420000	0.260000	0.279280	0.260000	0	0.200000	0.350000
LAMA1	284217	broad.mit.edu	37	18	7023334	7023334	+	Missense_Mutation	SNP	C	C	T			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr18:7023334C>T	ENST00000389658.3	-	19	2623	c.2530G>A	c.(2530-2532)Gaa>Aaa	p.E844K		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1			205		Colorectal(10;0.172)			ACACAAGATTCGCCAGGCACT	0.532000																								0							SO:0001583	missense			ENST00000389658.3	1	1	hg19	CCDS32787.1	.	.	.	.	.	.	.	.	.	.	C	11.87	1.767948	0.31320	0.0	1.16E-4	ENSG00000101680	ENST00000389658	T	0.61392	0.11	5.47	4.61	0.57282	EGF-like, laminin (4);	0.325995	0.26971	N	0.021577	T	0.49440	0.1557	L	0.52573	1.65	0.22745	N	0.99879	B	0.12013	0.005	B	0.10450	0.005	T	0.38478	-0.9659	10	0.31617	T	0.26	.	10.5047	0.44826	0.0:0.753:0.1702:0.0769	.	844	P25391	LAMA1_HUMAN	K	844	ENSP00000374309:E844K	ENSP00000374309:E844K	E	-	1	0	LAMA1	7013334	0.334000	0.24739	0.677000	0.29947	0.127000	0.20565	3.215000	0.51169	1.323000	0.45263	-0.149000	0.13747	GAA		TCGA-2J-AAB1-01A-11D-A40W-08	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	1	0	1	49	171	0	39	0	0	0	1	0	39	2		0	0	0	0	0	2	1	1.000000	48	168	0	38	2								-3.749639	1	1	121412	4	38	1	1	2	3	2.043860	0	0.380000	1.940000	0.384676	0.990000	9.000000e-01	1.000000	1.000000	0.993917	0.990000	1	0.990000	1.000000
C19orf57	79173	broad.mit.edu	37	19	14006194	14006194	+	Missense_Mutation	SNP	G	G	A	rs145142690		TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr19:14006194G>A	ENST00000586783.1	-	2	196	c.197C>T	c.(196-198)gCc>gTc	p.A66V	C19orf57_ENST00000346736.2_Missense_Mutation_p.A66V|C19orf57_ENST00000454313.1_Missense_Mutation_p.A66V|C19orf57_ENST00000591586.1_Missense_Mutation_p.A66V			Q0VDD7	CS057_HUMAN	chromosome 19 open reading frame 57			14			OV - Ovarian serous cystadenocarcinoma(19;2e-21)		CCTGGAGACGGCCTTTCCTGG	0.562000																								0							SO:0001583	missense			ENST00000586783.1	1	1	hg19		.	.	.	.	.	.	.	.	.	.	G	5.727	0.318640	0.10845	2.27E-4	0.0	ENSG00000132016	ENST00000454313;ENST00000346736	T;T	0.35605	1.3;1.3	4.03	-0.708	0.11241	.	0.461071	0.16102	N	0.229524	T	0.15825	0.0381	N	0.12746	0.255	0.09310	N	1	B	0.16603	0.018	B	0.17433	0.018	T	0.12243	-1.0555	10	0.38643	T	0.18	-3.5745	3.3117	0.07018	0.2027:0.0:0.4413:0.356	.	66	Q0VDD7-2	.	V	66	ENSP00000404382:A66V;ENSP00000254336:A66V	ENSP00000254336:A66V	A	-	2	0	C19orf57	13867194	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.281000	0.08456	-0.011000	0.14247	-0.137000	0.14449	GCC		TCGA-2J-AAB1-01A-11D-A40W-08	C19orf57-003	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000457947.1	1	0	1	78	408	0	77	0	2.648429e-02	0	2	0	77	2		0	0	0	0	0	2	1	1.000000	76	401	0	77	2								-20.000000	1	1	121412	2	37	1	1	2	3	2.047246	0	0.380000	1.940000	0.384676	0.850000	6.800000e-01	1.000000	1.000000	0.857597	0.850000	1	0.760000	0.950000
SARS2	54938	broad.mit.edu	37	19	39421234	39421234	+	Missense_Mutation	SNP	G	G	A			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr19:39421234G>A	ENST00000221431.6	-	1	302	c.143C>T	c.(142-144)gCg>gTg	p.A48V	MRPS12_ENST00000308018.4_5'UTR|MRPS12_ENST00000402029.3_5'Flank|SARS2_ENST00000600042.1_Missense_Mutation_p.A48V|SARS2_ENST00000430193.3_Missense_Mutation_p.A48V|MRPS12_ENST00000407800.2_5'Flank|SARS2_ENST00000448145.2_Intron|CTC-360G5.8_ENST00000599996.1_Intron|SARS2_ENST00000594171.1_5'Flank	NM_017827.3	NP_060297.1	Q9NP81	SYSM_HUMAN	seryl-tRNA synthetase 2, mitochondrial			15	all_cancers(60;2.74e-06)|all_epithelial(25;4.36e-06)|Ovarian(47;0.0454)		Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554)		GCCCTCGCGCGCATACTCGTA	0.627000											OREG0025455	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)												0							SO:0001583	missense			ENST00000221431.6	0	1	hg19	CCDS33017.1	.	.	.	.	.	.	.	.	.	.	G	14.36	2.512002	0.44660	.	.	ENSG00000104835	ENST00000430193;ENST00000221431;ENST00000455102	T;T;T	0.55588	0.51;0.51;1.49	5.65	4.57	0.56435	.	0.122893	0.53938	D	0.000045	T	0.40979	0.1139	L	0.43923	1.385	.	.	.	D;B;B	0.56746	0.977;0.206;0.257	B;B;B	0.43623	0.425;0.014;0.007	T	0.44952	-0.9294	9	0.16896	T	0.51	.	8.6175	0.33840	0.1027:0.0:0.8973:0.0	.	48;48;48	B4DJP6;B4DE10;Q9NP81	.;.;SYSM_HUMAN	V	48	ENSP00000406754:A48V;ENSP00000221431:A48V;ENSP00000414954:A48V	ENSP00000221431:A48V	A	-	2	0	FBXO17	44113074	1.000000	0.71417	1.000000	0.80357	0.672000	0.39443	3.764000	0.55264	2.941000	0.99782	0.655000	0.94253	GCG		TCGA-2J-AAB1-01A-11D-A40W-08	SARS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463139.1	0	0	0	6	597	0	129	0	3.925745e-02	0	26	0	129	2		0	0	0	0	0	2	1	0.963070	6	586	0	127	2								-1.740918	0	1	121412	2	37	1	1	2	3	2.030287	0	0.380000	1.940000	0.381176	0.050000	1.000000e-02	0.110000	0.060000	0.060873	0.050000	0	0.030000	0.080000
ZNF404	342908	broad.mit.edu	37	19	44388109	44388109	+	Splice_Site	SNP	C	C	T			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr19:44388109C>T	ENST00000587539.1	-	1	7	c.8G>A	c.(7-9)cGg>cAg	p.R3Q	ZNF404_ENST00000588094.1_5'UTR	NM_001033719.2	NP_001028891.2	Q494X3	ZN404_HUMAN	zinc finger protein 404			17		Prostate(69;0.0352)			TCAACTCACCCGGGCCATGGT	0.388000																								0							SO:0001630	splice_region_variant			ENST00000587539.1	1	0	hg19	CCDS59394.1																																																																																				TCGA-2J-AAB1-01A-11D-A40W-08	ZNF404-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460019.1	0	0	1	41	169	0	40	0	0	0	1	0	40	2		0	0	0	0	0	2	1	1.000000	41	162	0	40	2								-2.534310	1	1	119076	132	49	1	0	0	0	1.990385	0	0.380000	1.940000	0.367992	0.990000	7.400000e-01	1.000000	1.000000	0.951392	0.990000	1	0.860000	1.000000
ZNF227	7770	broad.mit.edu	37	19	44739673	44739673	+	Missense_Mutation	SNP	A	A	T			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr19:44739673A>T	ENST00000313040.7	+	6	1295	c.1090A>T	c.(1090-1092)Agt>Tgt	p.S364C	ZNF227_ENST00000589005.1_Missense_Mutation_p.S313C|ZNF227_ENST00000391961.2_Missense_Mutation_p.S313C	NM_182490.1	NP_872296.1	Q86WZ6	ZN227_HUMAN	zinc finger protein 227			24		Prostate(69;0.0435)			CTTTAGTCAAAGTTCAAATTT	0.423000																								0							SO:0001583	missense			ENST00000313040.7	0	1	hg19	CCDS12636.1	.	.	.	.	.	.	.	.	.	.	A	15.35	2.808701	0.50421	.	.	ENSG00000131115	ENST00000313040;ENST00000328297;ENST00000391961;ENST00000418980;ENST00000377916	T;T	0.16743	2.32;3.13	4.54	4.54	0.55810	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.27027	0.0662	M	0.78285	2.405	0.18873	N	0.999988	B;B;D;B	0.64830	0.238;0.114;0.994;0.114	B;B;P;B	0.47402	0.016;0.023;0.546;0.023	T	0.21484	-1.0244	9	0.52906	T	0.07	.	8.7324	0.34507	0.8306:0.0:0.0:0.1694	.	285;343;316;364	B7Z6M2;Q658S5;Q9NS43;Q86WZ6	.;.;.;ZN227_HUMAN	C	364;321;313;343;65	ENSP00000321049:S364C;ENSP00000375823:S313C	ENSP00000321049:S364C	S	+	1	0	ZNF227	49431513	0.062000	0.20869	0.998000	0.56505	0.993000	0.82548	1.890000	0.39728	1.801000	0.52704	0.460000	0.39030	AGT		TCGA-2J-AAB1-01A-11D-A40W-08	ZNF227-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460720.1	0	0	0	5	327	0	43	0	4.043804e-02	0	17	0	43	2		0	0	0	0	0	2	1	0.935993	4	324	0	43	2								-5.855425	1	0	0	0		1	0	0	0	1.990385	0	0.380000	1.940000	0.367992	0.080000	2.000000e-02	0.170000	0.080000	0.092276	0.080000	0	0.050000	0.130000
ZNF114	163071	broad.mit.edu	37	19	48789674	48789674	+	Missense_Mutation	SNP	A	A	C			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr19:48789674A>C	ENST00000595607.1	+	6	1287	c.793A>C	c.(793-795)Atg>Ctg	p.M265L	ZNF114_ENST00000315849.1_Missense_Mutation_p.M265L|ZNF114_ENST00000597695.1_Missense_Mutation_p.M231L|ZNF114_ENST00000600687.1_Missense_Mutation_p.M265L			Q8NC26	ZN114_HUMAN	zinc finger protein 114			18		all_epithelial(76;8.01e-05)|all_lung(116;0.000112)|Lung NSC(112;0.000192)|Prostate(7;0.0187)|all_neural(266;0.0228)|Ovarian(192;0.113)			AATTCACGCCATGCAGATGCA	0.463000																								0							SO:0001583	missense			ENST00000595607.1	1	1	hg19	CCDS12713.1	.	.	.	.	.	.	.	.	.	.	G	1.280	-0.610640	0.03690	.	.	ENSG00000178150	ENST00000315849	T	0.04502	3.61	2.01	0.895	0.19247	.	.	.	.	.	T	0.02304	0.0071	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48234	-0.9053	9	0.24483	T	0.36	.	4.187	0.10402	0.1438:0.0:0.6304:0.2258	.	265	Q8NC26	ZN114_HUMAN	L	265	ENSP00000318898:M265L	ENSP00000318898:M265L	M	+	1	0	ZNF114	53481486	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.407000	0.07178	0.016000	0.14998	-0.349000	0.07799	ATG		TCGA-2J-AAB1-01A-11D-A40W-08	ZNF114-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465601.1	0	0	0	12	385	1	95		0	0	0	1	95	2		0	0	0	0	0	2	0	0.333234	12	380	1	95	15								-12.119060	1	1	0	0		1	0	0	0	1.990385	0	0.380000	1.940000	0.367992	0.150000	8.000000e-02	0.260000	0.150000	0.167493	0.150000	0	0.110000	0.210000
RPL28	6158	broad.mit.edu	37	19	55899358	55899358	+	Missense_Mutation	SNP	C	C	T	rs150642428		TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr19:55899358C>T	ENST00000344063.2	+	4	895	c.266C>T	c.(265-267)aCg>aTg	p.T89M	RPL28_ENST00000558815.1_Missense_Mutation_p.T89M|RPL28_ENST00000458349.2_Missense_Mutation_p.T89M|RPL28_ENST00000560055.1_Missense_Mutation_p.T89M|RPL28_ENST00000558131.1_Missense_Mutation_p.R83C|RPL28_ENST00000559463.1_Missense_Mutation_p.T89M|RPL28_ENST00000560583.1_Missense_Mutation_p.T89M			P46779	RL28_HUMAN	ribosomal protein L28			6	Breast(117;0.191)	Renal(1328;0.245)	LUSC - Lung squamous cell carcinoma(43;0.13)|BRCA - Breast invasive adenocarcinoma(297;0.209)		GCTCGCGCCACGCTCAGCAGC	0.622000																								0							SO:0001583	missense			ENST00000344063.2	1	1	hg19	CCDS12924.1	.	.	.	.	.	.	.	.	.	.	C	16.19	3.054549	0.55218	.	.	ENSG00000108107	ENST00000344063;ENST00000426763;ENST00000458349	T;T	0.44881	0.91;0.91	3.44	3.44	0.39384	.	0.000000	0.85682	D	0.000000	T	0.51075	0.1653	L	0.53617	1.68	0.58432	D	0.999996	D;D;P	0.65815	0.978;0.995;0.607	P;P;B	0.56042	0.543;0.79;0.427	T	0.54925	-0.8220	10	0.52906	T	0.07	.	13.1887	0.59697	0.0:1.0:0.0:0.0	.	89;89;89	B4DEP9;E9PB24;P46779	.;.;RL28_HUMAN	M	89	ENSP00000342787:T89M;ENSP00000401450:T89M	ENSP00000342787:T89M	T	+	2	0	RPL28	60591170	1.000000	0.71417	1.000000	0.80357	0.651000	0.38670	7.107000	0.77047	1.864000	0.54056	0.462000	0.41574	ACG		TCGA-2J-AAB1-01A-11D-A40W-08	RPL28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416277.2	1	0	0	17	386	0	80	1	1	326	6836	0	80	2		0	0	0	0	0	2	1	0.999960	17	377	0	75	2								-4.410952	1	1	121410	9	41	1	0	0	0	2.014203	0	0.380000	1.940000	0.377635	0.220000	1.300000e-01	0.340000	0.220000	0.232081	0.220000	0	0.170000	0.280000
DCLRE1B	64858	broad.mit.edu	37	1	114454068	114454068	+	Missense_Mutation	SNP	T	T	G			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr1:114454068T>G	ENST00000369563.3	+	4	1300	c.854T>G	c.(853-855)tTt>tGt	p.F285C	DCLRE1B_ENST00000466480.1_3'UTR	NM_022836.3	NP_073747.1	Q9H816	DCR1B_HUMAN	DNA cross-link repair 1B			18	Lung SC(450;0.184)	all_cancers(81;1.46e-05)|all_epithelial(167;2.42e-05)|all_lung(203;0.000353)|Lung NSC(69;0.000518)			CTTCGTGCCTTTGTCGCAGCA	0.567000								Other identified genes with known or suspected DNA repair function																0							SO:0001583	missense			ENST00000369563.3	1	1	hg19	CCDS866.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.298120	0.81025	.	.	ENSG00000118655	ENST00000369563	T	0.61980	0.06	6.02	4.9	0.64082	DNA repair metallo-beta-lactamase (1);	0.000000	0.85682	D	0.000000	T	0.70439	0.3224	M	0.85630	2.765	0.58432	D	0.999998	D	0.63046	0.992	P	0.59357	0.856	T	0.75983	-0.3125	10	0.59425	D	0.04	-9.6429	11.9514	0.52956	0.0:0.0672:0.0:0.9328	.	285	Q9H816	DCR1B_HUMAN	C	285	ENSP00000358576:F285C	ENSP00000358576:F285C	F	+	2	0	DCLRE1B	114255591	1.000000	0.71417	0.988000	0.46212	0.939000	0.58152	7.967000	0.87967	1.116000	0.41820	0.533000	0.62120	TTT		TCGA-2J-AAB1-01A-11D-A40W-08	DCLRE1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033020.2	1	0	1	64	300	0	61	1	6.953711e-01	3	10	0	61	2		0	0	0	0	0	2	1	1.000000	63	292	0	60	2								-20.000000	1	1	0	0		1	1	2	3	2.038935	0	0.380000	1.940000	0.382347	0.920000	7.300000e-01	1.000000	1.000000	0.917342	0.920000	1	0.820000	1.000000
SPAG17	200162	broad.mit.edu	37	1	118550780	118550780	+	Missense_Mutation	SNP	G	G	A			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr1:118550780G>A	ENST00000336338.5	-	31	4539	c.4474C>T	c.(4474-4476)Cgg>Tgg	p.R1492W		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17			123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)			CTTTCTACCCGCATACACTTC	0.493000																								0							SO:0001583	missense			ENST00000336338.5	1	1	hg19	CCDS899.1	.	.	.	.	.	.	.	.	.	.	G	11.93	1.785810	0.31593	.	.	ENSG00000155761	ENST00000336338	T	0.23348	1.91	5.83	2.83	0.33086	.	0.346719	0.27932	N	0.017261	T	0.26048	0.0635	L	0.41961	1.31	0.30207	N	0.798109	D	0.89917	1.0	D	0.66196	0.942	T	0.11470	-1.0586	10	0.62326	D	0.03	.	14.1367	0.65291	0.0:0.0:0.6081:0.3919	.	1492	Q6Q759	SPG17_HUMAN	W	1492	ENSP00000337804:R1492W	ENSP00000337804:R1492W	R	-	1	2	SPAG17	118352303	0.805000	0.28982	0.998000	0.56505	0.340000	0.28889	1.437000	0.34991	0.326000	0.23384	0.563000	0.77884	CGG		TCGA-2J-AAB1-01A-11D-A40W-08	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	1	0	0	16	197	0	46	0	0	0	1	0	46	2		0	0	0	0	0	2	1	0.999932	15	193	0	46	2								-3.017764	1	1	121402	3	36	1	1	2	3	2.038935	0	0.380000	1.940000	0.382347	0.400000	2.400000e-01	0.650000	0.390000	0.420318	0.400000	0	0.310000	0.510000
SV2A	9900	broad.mit.edu	37	1	149877463	149877463	+	Missense_Mutation	SNP	A	A	C			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr1:149877463A>C	ENST00000369146.3	-	12	2504	c.2014T>G	c.(2014-2016)Ttg>Gtg	p.L672V	SV2A_ENST00000369145.1_Missense_Mutation_p.L672V	NM_001278719.1|NM_014849.3	NP_001265648.1|NP_055664.3	Q7L0J3	SV2A_HUMAN	synaptic vesicle glycoprotein 2A			55	Breast(34;0.00769)|all_hematologic(923;0.127)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247)	Levetiracetam(DB01202)	TCAACAGTCAACACGTCCAGC	0.557000																								0							SO:0001583	missense			ENST00000369146.3	0	1	hg19	CCDS940.1	.	.	.	.	.	.	.	.	.	.	A	2.739	-0.262762	0.05754	.	.	ENSG00000159164	ENST00000369146;ENST00000369145	T;T	0.06371	3.31;3.31	3.89	-0.377	0.12501	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.982908	0.08311	N	0.965306	T	0.00695	0.0023	N	0.02865	-0.47	0.48632	D	0.999689	B;B	0.16802	0.019;0.005	B;B	0.21360	0.034;0.023	T	0.48768	-0.9006	10	0.02654	T	1	-9.4314	8.0509	0.30577	0.3216:0.0:0.6784:0.0	.	124;672	B4E000;Q7L0J3	.;SV2A_HUMAN	V	672	ENSP00000358142:L672V;ENSP00000358141:L672V	ENSP00000358141:L672V	L	-	1	2	SV2A	148144087	0.954000	0.32549	0.999000	0.59377	0.960000	0.62799	0.088000	0.14979	0.030000	0.15379	0.247000	0.18012	TTG		TCGA-2J-AAB1-01A-11D-A40W-08	SV2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033754.1	0	0	0	12	884	0	128	0	5.892605e-03	0	8	0	128	2		0	0	0	0	0	2	1	0.998968	11	863	0	125	2								-8.023559	1	1	0	0		1	1	2	3	2.040103	0	0.380000	1.940000	0.382347	0.070000	3.000000e-02	0.130000	0.070000	0.085386	0.070000	0	0.040000	0.100000
CRNN	49860	broad.mit.edu	37	1	152382863	152382863	+	Missense_Mutation	SNP	G	G	A			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr1:152382863G>A	ENST00000271835.3	-	3	757	c.695C>T	c.(694-696)aCt>aTt	p.T232I	RP1-91G5.3_ENST00000411804.1_RNA	NM_016190.2	NP_057274.1	Q9UBG3	CRNN_HUMAN	cornulin			35	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)		CTGGGTCTGAGTTCCAGATCC	0.572000																								0							SO:0001583	missense			ENST00000271835.3	1	1	hg19	CCDS1010.1	.	.	.	.	.	.	.	.	.	.	G	12.31	1.900907	0.33535	.	.	ENSG00000143536	ENST00000271835	T	0.05025	3.51	4.93	1.99	0.26369	.	0.507715	0.18383	N	0.142896	T	0.01254	0.0041	L	0.43923	1.385	0.09310	N	0.999999	P	0.43431	0.807	B	0.35470	0.203	T	0.46176	-0.9210	10	0.16896	T	0.51	.	4.0875	0.09953	0.1931:0.0:0.6221:0.1848	.	232	Q9UBG3	CRNN_HUMAN	I	232	ENSP00000271835:T232I	ENSP00000271835:T232I	T	-	2	0	CRNN	150649487	0.996000	0.38824	0.242000	0.24170	0.021000	0.10359	2.827000	0.48112	0.255000	0.21593	-0.237000	0.12165	ACT		TCGA-2J-AAB1-01A-11D-A40W-08	CRNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034503.1	1	0	1	186	817	0	194		0	0	0	0	194	2		0	0	0	0	0	2	1	1.000000	185	805	0	191	2								-20.000000	1	1	0	0		1	1	2	3	2.040103	0	0.380000	1.940000	0.382347	0.970000	8.500000e-01	1.000000	1.000000	0.963924	0.970000	1	0.910000	1.000000
S100A8	6279	broad.mit.edu	37	1	153362970	153362970	+	Silent	SNP	G	G	A			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr1:153362970G>A	ENST00000368733.3	-	2	211	c.42C>T	c.(40-42)gaC>gaT	p.D14D	S100A8_ENST00000368732.1_Silent_p.D14D|S100A8_ENST00000477801.1_5'UTR	NM_002964.4	NP_002955.2	P05109	S10A8_HUMAN	S100 calcium binding protein A8			4	all_lung(78;2.81e-33)|Lung NSC(65;9.54e-32)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.171)		TGTGGTAGACGTCGATGATAG	0.507000																								0							SO:0001819	synonymous_variant			ENST00000368733.3	0	1	hg19	CCDS1038.1																																																																																				TCGA-2J-AAB1-01A-11D-A40W-08	S100A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036791.1	0	0	0	11	902	0	169	0	6.464373e-02	0	31	0	169	2		0	0	0	0	0	2	1	0.998115	10	884	0	166	2								-2.744861	1	1	121412	14	45	1	1	2	3	2.040103	0	0.380000	1.940000	0.382347	0.060000	2.000000e-02	0.120000	0.060000	0.078264	0.060000	0	0.040000	0.090000
OLFML2B	25903	broad.mit.edu	37	1	161953983	161953983	+	Missense_Mutation	SNP	G	G	A			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08			G	A	G	G		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr1:161953983G>A	ENST00000294794.3	-	8	2158	c.1735C>T	c.(1735-1737)Cgc>Tgc	p.R579C	OLFML2B_ENST00000367938.1_Missense_Mutation_p.R62C|OLFML2B_ENST00000367940.2_Missense_Mutation_p.R580C	NM_015441.1	NP_056256.1	Q68BL8	OLM2B_HUMAN	olfactomedin-like 2B			48	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.0172)		GTGAAGGCGCGATTGTAGTAG	0.597000																								0							SO:0001583	missense			ENST00000294794.3	1	1	hg19	CCDS1236.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.968748	0.74131	.	.	ENSG00000162745	ENST00000294794;ENST00000367940;ENST00000367938	D;D;D	0.90004	-2.6;-2.6;-2.6	5.06	5.06	0.68205	Olfactomedin-like (3);	.	.	.	.	D	0.92453	0.7604	M	0.77313	2.365	0.46849	D	0.999222	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.977	D	0.93668	0.6987	8	0.87932	D	0	.	11.0657	0.47974	0.0:0.0:0.8145:0.1855	.	580;579	F2Z3N3;Q68BL8	.;OLM2B_HUMAN	C	579;580;62	ENSP00000294794:R579C;ENSP00000356917:R580C;ENSP00000356915:R62C	ENSP00000294794:R579C	R	-	1	0	OLFML2B	160220607	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.692000	0.84203	2.328000	0.79073	0.561000	0.74099	CGC		TCGA-2J-AAB1-01A-11D-A40W-08	OLFML2B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060552.2	1	0	1	60	272	0	57	0	9.999855e-01	0	77	0	57	2		0	0	0	0	0	2	1	1.000000	60	265	0	56	2								-3.417237	1	1	0	0		1	1	2	3	2.040103	0	0.380000	1.940000	0.382347	0.950000	7.400000e-01	1.000000	1.000000	0.933171	0.950000	1	0.840000	1.000000
ELF3	1999	broad.mit.edu	37	1	201981145	201981145	+	Nonsense_Mutation	SNP	G	G	A			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr1:201981145G>A	ENST00000359651.3	+	2	3416	c.224G>A	c.(223-225)tGg>tAg	p.W75*	RP11-510N19.5_ENST00000504773.1_RNA|ELF3_ENST00000367284.5_Nonsense_Mutation_p.W75*|ELF3_ENST00000495848.1_3'UTR|RP11-465N4.4_ENST00000419190.1_RNA|ELF3_ENST00000367283.3_Nonsense_Mutation_p.W75*					E74-like factor 3 (ets domain transcription factor, epithelial-specific )			20					GTTCTGGACTGGATCAGCTAC	0.577000																								0							SO:0001587	stop_gained			ENST00000359651.3	0	1	hg19	CCDS1419.1	.	.	.	.	.	.	.	.	.	.	G	38	6.948324	0.97956	.	.	ENSG00000163435	ENST00000359651;ENST00000367284;ENST00000367283;ENST00000310044;ENST00000446188	.	.	.	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.5332	0.95237	0.0:0.0:1.0:0.0	.	.	.	.	X	75;75;75;75;73	.	ENSP00000311348:W75X	W	+	2	0	ELF3	200247768	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.149000	0.94659	2.608000	0.88229	0.591000	0.81541	TGG		TCGA-2J-AAB1-01A-11D-A40W-08	ELF3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087360.1	1	0	1	123	616	0	131	1	1	465	1498	0	131	2		0	0	0	0	0	2	1	1.000000	117	599	0	128	2								-3.323569	1	1	0	0		1	1	2	3	2.040103	0	0.380000	1.940000	0.382347	0.870000	7.300000e-01	1.000000	1.000000	0.881466	0.870000	1	0.800000	0.960000
OPRD1	4985	broad.mit.edu	37	1	29189523	29189523	+	Missense_Mutation	SNP	G	G	A			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr1:29189523G>A	ENST00000234961.2	+	3	1089	c.847G>A	c.(847-849)Gtc>Atc	p.V283I		NM_000911.3	NP_000902.3	P41143	OPRD_HUMAN	opioid receptor, delta 1			15		Colorectal(325;3.46e-05)|Lung NSC(340;0.000947)|all_lung(284;0.00131)|Renal(390;0.00758)|Breast(348;0.00765)|all_neural(195;0.0199)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Alvimopan(DB06274)|Amitriptyline(DB00321)|Buprenorphine(DB00921)|Butorphanol(DB00611)|Codeine(DB00318)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diphenoxylate(DB01081)|Fentanyl(DB00813)|Heroin(DB01452)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Ketamine(DB01221)|Ketobemidone(DB06738)|Levorphanol(DB00854)|Loperamide(DB00836)|Methadone(DB00333)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Remifentanil(DB00899)|Sufentanil(DB00708)|Tapentadol(DB06204)|Tramadol(DB00193)	CTTCGTCATCGTCTGGACGCT	0.662000																								0							SO:0001583	missense			ENST00000234961.2	0	1	hg19	CCDS329.1	.	.	.	.	.	.	.	.	.	.	G	16.11	3.029141	0.54790	.	.	ENSG00000116329	ENST00000234961;ENST00000536280	T	0.37235	1.21	4.06	4.06	0.47325	GPCR, rhodopsin-like superfamily (1);	0.149246	0.44688	D	0.000439	T	0.28499	0.0705	N	0.25992	0.78	0.80722	D	1	B	0.24768	0.111	B	0.32805	0.153	T	0.07673	-1.0760	10	0.23891	T	0.37	.	13.7884	0.63123	0.0:0.0:1.0:0.0	.	283	P41143	OPRD_HUMAN	I	283;235	ENSP00000234961:V283I	ENSP00000234961:V283I	V	+	1	0	OPRD1	29062110	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.554000	0.73923	2.097000	0.63578	0.462000	0.41574	GTC		TCGA-2J-AAB1-01A-11D-A40W-08	OPRD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010330.1	0	0	0	4	67	0	13		0	0	0	0	13	2		0	0	0	0	0	2	1	0.888999	4	66	0	13	2								-8.354660	1	1	0	0		1	0	1	1	1.664513	1	0.380000	1.940000	0.234568	0.250000	8.000000e-02	0.530000	0.230000	0.278751	0.250000	0	0.150000	0.390000
CSMD2	114784	broad.mit.edu	37	1	34286109	34286109	+	Missense_Mutation	SNP	C	C	T			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr1:34286109C>T	ENST00000373381.4	-	8	1336	c.1160G>A	c.(1159-1161)gGc>gAc	p.G387D		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2			246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)			TTCGGGTATGCCAGGGTCTGG	0.448000																								0							SO:0001583	missense			ENST00000373381.4	0	1	hg19		.	.	.	.	.	.	.	.	.	.	C	31	5.068273	0.93950	.	.	ENSG00000121904	ENST00000373381	T	0.63417	-0.04	5.81	5.81	0.92471	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.85682	D	0.000000	T	0.78194	0.4245	M	0.76938	2.355	0.80722	D	1	D;B	0.57257	0.979;0.07	P;B	0.60473	0.875;0.102	T	0.76310	-0.3006	10	0.38643	T	0.18	.	19.0707	0.93134	0.0:1.0:0.0:0.0	.	347;387	Q7Z408;E7EUA6	CSMD2_HUMAN;.	D	387	ENSP00000362479:G387D	ENSP00000241312:G347D	G	-	2	0	CSMD2	34058696	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.069000	0.71209	2.746000	0.94184	0.655000	0.94253	GGC		TCGA-2J-AAB1-01A-11D-A40W-08	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		0	0	0	7	842	0	148		0	0	0	0	148	2		0	0	0	0	0	2	1	0.978267	7	815	0	144	2								-1.872151	0	1	0	0		1	1	2	3	2.045202	0	0.380000	1.940000	0.384676	0.040000	0	1.000000	0.040000	0.077185	0.040000	0	0.020000	0.070000
RNF207	388591	broad.mit.edu	37	1	6279452	6279452	+	Silent	SNP	G	G	A			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr1:6279452G>A	ENST00000377939.4	+	18	2017	c.1890G>A	c.(1888-1890)agG>agA	p.R630R	RNF207_ENST00000377948.2_3'UTR|ICMT_ENST00000495791.1_5'Flank	NM_207396.2	NP_997279.2	Q6ZRF8	RN207_HUMAN	ring finger protein 207			16	Ovarian(185;0.0634)	all_cancers(23;1.22e-38)|all_epithelial(116;4.25e-22)|all_lung(118;7.95e-08)|Lung NSC(185;1.6e-06)|all_neural(13;3.18e-06)|all_hematologic(16;8.99e-06)|Acute lymphoblastic leukemia(12;0.000365)|Breast(487;0.000496)|Renal(390;0.0007)|Colorectal(325;0.00104)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)|Medulloblastoma(700;0.211)			CCACATGGAGGGAACACCCGA	0.532000																								0							SO:0001819	synonymous_variant			ENST00000377939.4	1	1	hg19	CCDS59.2																																																																																				TCGA-2J-AAB1-01A-11D-A40W-08	RNF207-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003669.2	1	0	1	29	99	0	26	1	9.609944e-01	11	10	0	26	2		0	0	0	0	0	2	1	1.000000	29	98	0	25	2								-20.000000	1	1	0	0		1	1	2	3	2.041574	0	0.380000	1.940000	0.382347	0.990000	8.400000e-01	1.000000	1.000000	0.987780	0.990000	1	0.990000	1.000000
LHX8	431707	broad.mit.edu	37	1	75622617	75622617	+	Missense_Mutation	SNP	G	G	A			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr1:75622617G>A	ENST00000294638.5	+	9	1514	c.850G>A	c.(850-852)Gtc>Atc	p.V284I	LHX8_ENST00000356261.3_Missense_Mutation_p.V274I	NM_001001933.1	NP_001001933.1	Q68G74	LHX8_HUMAN	LIM homeobox 8			30					CAAGAAACACGTCAGTCCTAA	0.502000																								0							SO:0001583	missense			ENST00000294638.5	1	1	hg19	CCDS30756.1	.	.	.	.	.	.	.	.	.	.	G	15.50	2.852331	0.51270	.	.	ENSG00000162624	ENST00000294638;ENST00000356261	D;D	0.86097	-2.07;-2.06	5.12	5.12	0.69794	Homeodomain-related (1);Homeobox (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	T	0.70185	0.3195	L	0.29908	0.895	0.80722	D	1	B	0.22480	0.07	B	0.16722	0.016	T	0.66400	-0.5933	10	0.27785	T	0.31	.	18.9441	0.92615	0.0:0.0:1.0:0.0	.	284	Q68G74	LHX8_HUMAN	I	284;274	ENSP00000294638:V284I;ENSP00000348597:V274I	ENSP00000294638:V284I	V	+	1	0	LHX8	75395205	1.000000	0.71417	0.990000	0.47175	0.940000	0.58332	7.404000	0.79996	2.556000	0.86216	0.455000	0.32223	GTC		TCGA-2J-AAB1-01A-11D-A40W-08	LHX8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026700.1	0	0	0	23	710	0	123		0	0	0	0	123	2		0	0	0	0	0	2	1	0.999999	23	702	0	120	2								-3.184890	1	1	121412	2	36	1	1	2	3	2.045202	0	0.380000	1.940000	0.384676	0.160000	1.000000e-01	1.000000	0.160000	0.196597	0.160000	0	0.130000	0.210000
ABCA4	24	broad.mit.edu	37	1	94497517	94497517	+	Silent	SNP	C	C	T			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr1:94497517C>T	ENST00000370225.3	-	27	4031	c.3945G>A	c.(3943-3945)caG>caA	p.Q1315Q		NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4			147		all_lung(203;0.000757)|Lung NSC(277;0.00335)			CATTGGAGTCCTGGGGTGTCT	0.632000																								0							SO:0001819	synonymous_variant			ENST00000370225.3	1	1	hg19	CCDS747.1																																																																																				TCGA-2J-AAB1-01A-11D-A40W-08	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	1	0	0	19	388	0	62	0	0	0	1	0	62	2		0	0	0	0	0	2	1	0.999989	19	378	0	59	2								-3.308679	1	1	0	0		1	1	2	3	2.045202	0	0.380000	1.940000	0.384676	0.250000	1.500000e-01	1.000000	0.250000	0.279655	0.250000	0	0.190000	0.320000
DPYD	1806	broad.mit.edu	37	1	98205957	98205957	+	Missense_Mutation	SNP	A	A	C			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr1:98205957A>C	ENST00000370192.3	-	4	412	c.312T>G	c.(310-312)atT>atG	p.I104M	DPYD_ENST00000306031.5_Missense_Mutation_p.I104M|DPYD_ENST00000423006.2_Missense_Mutation_p.I67M	NM_000110.3	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase			83		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Capecitabine(DB01101)|Flavin adenine dinucleotide(DB03147)|Fluorouracil(DB00544)	CCTTGTTTGCAATACTTGTGA	0.343000																								0							SO:0001583	missense			ENST00000370192.3	1	1	hg19	CCDS30777.1	.	.	.	.	.	.	.	.	.	.	A	18.70	3.679197	0.68042	.	.	ENSG00000188641	ENST00000370192;ENST00000423006;ENST00000306031	T;T;T	0.76186	-1.0;-1.0;-1.0	5.69	-5.09	0.02920	Fumarate reductase, C-terminal (1);Alpha-helical ferredoxin (1);	0.000000	0.85682	D	0.000000	D	0.83464	0.5260	H	0.96604	3.85	0.54753	D	0.999984	D;D	0.89917	1.0;1.0	D;D	0.91635	0.993;0.999	T	0.82926	-0.0215	10	0.87932	D	0	-18.9959	7.7046	0.28642	0.5443:0.0:0.3574:0.0983	.	104;104	E9PFN1;Q12882	.;DPYD_HUMAN	M	104;67;104	ENSP00000359211:I104M;ENSP00000398884:I67M;ENSP00000307107:I104M	ENSP00000307107:I104M	I	-	3	3	DPYD	97978545	0.973000	0.33851	0.958000	0.39756	0.987000	0.75469	0.190000	0.17057	-0.884000	0.03976	-0.361000	0.07541	ATT		TCGA-2J-AAB1-01A-11D-A40W-08	DPYD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095698.3	1	0	1	72	326	0	89	1	9.786672e-01	2	28	0	89	2		0	0	0	0	0	2	1	1.000000	70	325	0	88	2								-20.000000	1	1	121408	2	32	1	1	2	3	2.045202	0	0.380000	1.940000	0.384676	0.950000	7.600000e-01	1.000000	1.000000	0.940137	0.950000	1	0.850000	1.000000
DHX35	60625	broad.mit.edu	37	20	37653909	37653909	+	Missense_Mutation	SNP	C	C	G			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr20:37653909C>G	ENST00000252011.3	+	18	1741	c.1708C>G	c.(1708-1710)Ctg>Gtg	p.L570V	DHX35_ENST00000373325.2_Missense_Mutation_p.L570V|DHX35_ENST00000373323.4_Missense_Mutation_p.L539V	NM_021931.3	NP_068750.2	Q9H5Z1	DHX35_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 35			40		Myeloproliferative disorder(115;0.00878)			GGAACATTTCCTGAATTACAA	0.418000																								0							SO:0001583	missense			ENST00000252011.3	1	1	hg19	CCDS13310.1	.	.	.	.	.	.	.	.	.	.	C	15.64	2.894638	0.52121	.	.	ENSG00000101452	ENST00000373325;ENST00000252011;ENST00000373323;ENST00000373321;ENST00000449559	T;T;T;T	0.41758	3.7;3.65;3.59;0.99	5.41	4.46	0.54185	.	0.000000	0.85682	D	0.000000	T	0.43545	0.1252	L	0.45228	1.405	0.80722	D	1	P;B	0.40534	0.72;0.429	P;B	0.49752	0.621;0.088	T	0.19778	-1.0295	10	0.25751	T	0.34	.	9.8859	0.41262	0.0:0.834:0.0:0.166	.	539;570	F5GXM6;Q9H5Z1	.;DHX35_HUMAN	V	570;570;539;50;34	ENSP00000362422:L570V;ENSP00000252011:L570V;ENSP00000362420:L539V;ENSP00000397997:L34V	ENSP00000252011:L570V	L	+	1	2	DHX35	37087323	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.399000	0.44495	1.269000	0.44280	0.655000	0.94253	CTG		TCGA-2J-AAB1-01A-11D-A40W-08	DHX35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079212.2	1	0	1	184	782	0	157	1	9.285829e-01	6	15	0	157	2		0	0	0	0	0	2	1	1.000000	181	773	0	155	2								-2.997715	1	1	0	0		1	0	0	0	2.013459	0	0.380000	1.940000	0.377635	0.990000	8.600000e-01	1.000000	1.000000	0.973634	0.990000	1	0.920000	1.000000
CHD6	84181	broad.mit.edu	37	20	40085993	40085993	+	Missense_Mutation	SNP	C	C	T			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr20:40085993C>T	ENST00000373233.3	-	18	2917	c.2740G>A	c.(2740-2742)Gag>Aag	p.E914K	CHD6_ENST00000309279.7_Intron	NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6			129		Myeloproliferative disorder(115;0.00425)			ATCTCGCGCTCGTAGGAATTT	0.542000																								0							SO:0001583	missense			ENST00000373233.3	1	1	hg19	CCDS13317.1	.	.	.	.	.	.	.	.	.	.	C	33	5.210518	0.95069	.	.	ENSG00000124177	ENST00000373233	D	0.85088	-1.94	5.42	5.42	0.78866	Helicase, C-terminal (1);	0.000000	0.56097	D	0.000021	D	0.95449	0.8522	H	0.97077	3.935	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96602	0.9445	10	0.87932	D	0	-28.0288	19.5951	0.95533	0.0:1.0:0.0:0.0	.	914	Q8TD26	CHD6_HUMAN	K	914	ENSP00000362330:E914K	ENSP00000362330:E914K	E	-	1	0	CHD6	39519407	1.000000	0.71417	0.998000	0.56505	0.479000	0.33129	7.729000	0.84864	2.705000	0.92388	0.591000	0.81541	GAG		TCGA-2J-AAB1-01A-11D-A40W-08	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1	1	0	1	58	231	0	44	0	5.026555e-01	0	8	0	44	2		0	0	0	0	0	2	1	1.000000	55	231	0	43	2								-20.000000	1	1	0	0		1	0	0	0	2.013459	0	0.380000	1.940000	0.377635	0.990000	8.200000e-01	1.000000	1.000000	0.974932	0.990000	1	0.920000	1.000000
GNAS	2778	broad.mit.edu	37	20	57484421	57484421	+	Missense_Mutation	SNP	G	G	A	rs121913495		TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr20:57484421G>A	ENST00000371085.3	+	8	1026	c.602G>A	c.(601-603)cGt>cAt	p.R201H	GNAS_ENST00000313949.7_3'UTR|GNAS_ENST00000371075.3_3'UTR|GNAS_ENST00000265620.7_Missense_Mutation_p.R186H|GNAS_ENST00000371102.4_Missense_Mutation_p.R830H|GNAS_ENST00000354359.7_Missense_Mutation_p.R202H|GNAS_ENST00000371095.3_Missense_Mutation_p.R187H|GNAS_ENST00000306090.10_Missense_Mutation_p.R187H|GNAS_ENST00000464624.2_3'UTR|GNAS_ENST00000371100.4_Missense_Mutation_p.R844H	NM_000516.4	NP_000507.1	P63092	GNAS2_HUMAN	GNAS complex locus	p.R201H(81)|p.R844H(4)|p.R201L(2)|p.R844L(1)		441	all_lung(29;0.0104)		BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109)		CTTCGCTGCCGTGTCCTGACT	0.423000			Mis		pituitary adenoma		McCune-Albright syndrome; pseudohypoparathyroidism, type IA			TSP Lung(22;0.16)			Colon(117;935 1597 6045 8307 46442)		Dom	yes		20	20q13.2	2778	guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1	yes	E	88	Substitution - Missense(88)						SO:0001583	missense			ENST00000371085.3	0	1	hg19	CCDS13472.1	.	.	.	.	.	.	.	.	.	.	G	35	5.430570	0.96150	.	.	ENSG00000087460	ENST00000371100;ENST00000371102;ENST00000371095;ENST00000371085;ENST00000354359;ENST00000265620;ENST00000306090	D;D;D;D;D;D;D	0.99458	-5.93;-5.93;-5.93;-5.93;-5.93;-2.96;-5.93	5.53	5.53	0.82687	G protein alpha subunit, helical insertion (2);	0.000000	0.85682	D	0.000000	D	0.99799	0.9914	H	0.98965	4.385	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.997;0.994;0.983;1.0	D	0.96812	0.9597	10	0.87932	D	0	.	19.4606	0.94915	0.0:0.0:1.0:0.0	.	201;202;186;844	P63092;A6NI00;P63092-3;Q5JWF2	GNAS2_HUMAN;.;.;GNAS1_HUMAN	H	844;830;187;201;202;186;187	ENSP00000360141:R844H;ENSP00000360143:R830H;ENSP00000360136:R187H;ENSP00000360126:R201H;ENSP00000346328:R202H;ENSP00000265620:R186H;ENSP00000304472:R187H	ENSP00000265620:R186H	R	+	2	0	GNAS	56917816	1.000000	0.71417	0.963000	0.40424	0.936000	0.57629	9.291000	0.96070	2.596000	0.87737	0.563000	0.77884	CGT		TCGA-2J-AAB1-01A-11D-A40W-08	GNAS-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080431.2	0	0	0	5	315	0	50	1	9.999926e-01	24	2779	0	50	2	1	8.695476e-01	6	622	1	545	6	1	0.933250	5	307	0	48	2								-2.938661	1	1	121412	10	32	1	0	0	0	2.013459	0	0.380000	1.940000	0.377635	0.080000	2.000000e-02	0.180000	0.080000	0.097200	0.080000	0	0.050000	0.130000
DIDO1	11083	broad.mit.edu	37	20	61525110	61525110	+	Silent	SNP	C	C	T			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr20:61525110C>T	ENST00000266070.4	-	12	3334	c.3009G>A	c.(3007-3009)ttG>ttA	p.L1003L	DIDO1_ENST00000395340.1_Silent_p.L1003L|DIDO1_ENST00000395335.2_Silent_p.L1003L|DIDO1_ENST00000395343.1_Silent_p.L1003L	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1			99	Breast(26;5.68e-08)				TCACAGAAGTCAAGACAGGCT	0.567000													Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)											0							SO:0001819	synonymous_variant			ENST00000266070.4	0	1	hg19	CCDS33506.1																																																																																				TCGA-2J-AAB1-01A-11D-A40W-08	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	0	0	0	6	482	1	92	0	8.715306e-03	0	27	1	92	3		0	0	0	0	0	2	0	0.009572	6	476	1	92	18								-2.880596	1	1	121412	1	29	1	0	0	0	2.013459	0	0.380000	1.940000	0.377635	0.060000	2.000000e-02	0.130000	0.060000	0.074668	0.060000	0	0.040000	0.100000
CHAF1B	8208	broad.mit.edu	37	21	37783861	37783861	+	Silent	SNP	C	C	T			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr21:37783861C>T	ENST00000314103.5	+	11	1171	c.1020C>T	c.(1018-1020)taC>taT	p.Y340Y		NM_005441.2	NP_005432.1	Q13112	CAF1B_HUMAN	chromatin assembly factor 1, subunit B (p60)			20					CTTTTGGTTACGTGTCTAATA	0.522000																								0							SO:0001819	synonymous_variant			ENST00000314103.5	0	1	hg19	CCDS13644.1																																																																																				TCGA-2J-AAB1-01A-11D-A40W-08	CHAF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194616.2	0	0	0	6	762	1	145	0	5.719412e-03	0	12	1	145	2		0	0	0	0	0	2	0	0.006037	5	751	1	139	19								-2.614970	1	1	121412	1	37	1	0	0	0	2.008296	0	0.380000	1.940000	0.375252	0.040000	0	0.090000	0.040000	0.047333	0.040000	0	0.020000	0.070000
BRWD1	54014	broad.mit.edu	37	21	40578077	40578077	+	Missense_Mutation	SNP	G	G	A			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr21:40578077G>A	ENST00000333229.2	-	37	4648	c.4321C>T	c.(4321-4323)Cgg>Tgg	p.R1441W	BRWD1_ENST00000342449.3_Missense_Mutation_p.R1441W|BRWD1_ENST00000380800.3_Missense_Mutation_p.R1441W	NM_018963.4	NP_061836.2	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1			58		Prostate(19;8.44e-08)|all_epithelial(19;0.223)			CAATTTTGCCGTTGCTTGAAC	0.328000													Melanoma(170;988 1986 4794 16843 39731)											0							SO:0001583	missense			ENST00000333229.2	1	1	hg19	CCDS13662.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.62|14.62	2.589350|2.589350	0.46214|0.46214	.|.	.|.	ENSG00000185658|ENSG00000185658	ENST00000333229;ENST00000342449;ENST00000380800;ENST00000380783|ENST00000424441	T;T;T|.	0.59638|.	0.25;0.28;0.34|.	4.87|4.87	-4.09|-4.09	0.03951|0.03951	.|.	0.173450|.	0.35970|.	N|.	0.002879|.	T|T	0.47432|0.47432	0.1445|0.1445	L|L	0.58101|0.58101	1.795|1.795	0.09310|0.09310	N|N	0.999995|0.999995	D;D;B|.	0.71674|.	0.997;0.998;0.009|.	P;P;B|.	0.56474|.	0.799;0.785;0.003|.	T|T	0.52366|0.52366	-0.8585|-0.8585	10|5	0.87932|.	D|.	0|.	-0.1605|-0.1605	11.4109|11.4109	0.49925|0.49925	0.0715:0.0:0.3738:0.5547|0.0715:0.0:0.3738:0.5547	.|.	1441;1441;1441|.	Q9NSI6-3;Q9NSI6-2;Q9NSI6|.	.;.;BRWD1_HUMAN|.	W|M	1441;1441;1441;397|378	ENSP00000330753:R1441W;ENSP00000344333:R1441W;ENSP00000370178:R1441W|.	ENSP00000330753:R1441W|.	R|T	-|-	1|2	2|0	BRWD1|BRWD1	39499947|39499947	0.044000|0.044000	0.20184|0.20184	0.347000|0.347000	0.25668|0.25668	0.557000|0.557000	0.35523|0.35523	0.106000|0.106000	0.15354|0.15354	-0.524000|-0.524000	0.06400|0.06400	-0.215000|-0.215000	0.12644|0.12644	CGG|ACG		TCGA-2J-AAB1-01A-11D-A40W-08	BRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141398.3	1	0	1	141	661	0	125	0	8.499323e-01	1	17	0	125	2		0	0	0	0	0	2	1	1.000000	138	644	1	124	21								-20.000000	1	1	121412	4	43	1	0	0	0	2.008296	0	0.380000	1.940000	0.375252	0.910000	7.800000e-01	1.000000	1.000000	0.915689	0.910000	1	0.840000	0.990000
DSCAM	1826	broad.mit.edu	37	21	41559185	41559185	+	Splice_Site	SNP	C	C	A			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr21:41559185C>A	ENST00000400454.1	-	14	3129	c.2652G>T	c.(2650-2652)gaG>gaT	p.E884D		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule			142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)			GGTCTGGGGGCTCTGTGCCAT	0.483000													Melanoma(134;970 1778 1785 21664 32388)											0							SO:0001630	splice_region_variant			ENST00000400454.1	0	1	hg19	CCDS42929.1	.	.	.	.	.	.	.	.	.	.	C	13.91	2.378979	0.42207	.	.	ENSG00000171587	ENST00000400454;ENST00000404019	T;T	0.39229	1.09;1.09	5.18	2.29	0.28610	Fibronectin, type III (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.28863	0.0716	N	0.25332	0.735	0.40427	D	0.979904	B	0.17465	0.022	B	0.12156	0.007	T	0.12993	-1.0526	10	0.62326	D	0.03	.	10.457	0.44557	0.0:0.6553:0.0:0.3447	.	884	O60469	DSCAM_HUMAN	D	884;636	ENSP00000383303:E884D;ENSP00000385342:E636D	ENSP00000383303:E884D	E	-	3	2	DSCAM	40481055	0.293000	0.24371	1.000000	0.80357	0.973000	0.67179	-0.338000	0.07842	0.659000	0.30945	0.561000	0.74099	GAG		TCGA-2J-AAB1-01A-11D-A40W-08	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	0	0	0	5	131	0	26		0	0	0	0	26	2		0	0	0	0	0	2	1	0.933734	4	128	0	26	2								-8.004621	1	1	0	0		1	0	0	0	2.008296	0	0.380000	1.940000	0.375252	0.200000	7.000000e-02	0.410000	0.190000	0.224334	0.200000	0	0.130000	0.310000
SEZ6L	23544	broad.mit.edu	37	22	26736580	26736580	+	Missense_Mutation	SNP	T	T	C			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr22:26736580T>C	ENST00000248933.6	+	10	2289	c.2194T>C	c.(2194-2196)Ttt>Ctt	p.F732L	SEZ6L_ENST00000403121.1_Missense_Mutation_p.F505L|SEZ6L_ENST00000360929.3_Missense_Mutation_p.F732L|SEZ6L_ENST00000404234.3_Missense_Mutation_p.F732L|SEZ6L_ENST00000343706.4_Missense_Mutation_p.F732L|SEZ6L_ENST00000529632.2_Missense_Mutation_p.F732L|SEZ6L_ENST00000402979.1_Missense_Mutation_p.F505L			Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like			80					GGGCCAGGGATTTATCATGAA	0.458000																								0							SO:0001583	missense			ENST00000248933.6	1	1	hg19	CCDS13833.1	.	.	.	.	.	.	.	.	.	.	T	17.70	3.455009	0.63290	.	.	ENSG00000100095	ENST00000404234;ENST00000529632;ENST00000360929;ENST00000248933;ENST00000343706;ENST00000403121;ENST00000402979	T;T;T;T;T;T;T	0.66638	-0.22;-0.22;-0.22;-0.22;-0.22;-0.22;-0.22	5.01	5.01	0.66863	CUB (4);	0.000000	0.56097	D	0.000031	T	0.73916	0.3648	M	0.91663	3.23	0.80722	D	1	B;B;B;B;B;B;B	0.22480	0.007;0.07;0.007;0.056;0.05;0.07;0.07	B;B;B;B;B;B;B	0.23574	0.022;0.046;0.024;0.027;0.047;0.046;0.046	T	0.75761	-0.3204	10	0.56958	D	0.05	.	14.0549	0.64761	0.0:0.0:0.0:1.0	.	732;732;505;732;732;732;732	B7ZLJ8;B7ZLJ6;B0QYH4;Q9BYH1-5;Q9BYH1-4;B0QYG3;Q9BYH1	.;.;.;.;.;.;SE6L1_HUMAN	L	732;732;732;732;732;505;505	ENSP00000384772:F732L;ENSP00000437037:F732L;ENSP00000354185:F732L;ENSP00000248933:F732L;ENSP00000342661:F732L;ENSP00000384838:F505L;ENSP00000384733:F505L	ENSP00000248933:F732L	F	+	1	0	SEZ6L	25066580	1.000000	0.71417	0.959000	0.39883	0.971000	0.66376	7.350000	0.79385	2.104000	0.64026	0.260000	0.18958	TTT		TCGA-2J-AAB1-01A-11D-A40W-08	SEZ6L-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320359.3	1	0	1	33	194	0	47	0	0	0	1	0	47	2		0	0	0	0	0	2	1	1.000000	33	192	0	47	2								-17.006960	1	1	0	0		1	1	2	3	2.064369	0	0.380000	1.940000	0.386988	0.780000	5.500000e-01	1.000000	1.000000	0.792180	0.780000	0	0.660000	0.930000
RANGAP1	5905	broad.mit.edu	37	22	41650338	41650338	+	Missense_Mutation	SNP	G	G	A	rs139571477	byFrequency	TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr22:41650338G>A	ENST00000455915.2	-	10	2703	c.1234C>T	c.(1234-1236)Cgg>Tgg	p.R412W	RANGAP1_ENST00000405486.1_Missense_Mutation_p.R412W|RANGAP1_ENST00000356244.3_Missense_Mutation_p.R412W|RANGAP1_ENST00000407260.4_Missense_Mutation_p.R357W			P46060	RAGP1_HUMAN	Ran GTPase activating protein 1			19					AGAATCTTCCGTGAGGGCGTG	0.552000																								0							SO:0001583	missense			ENST00000455915.2	1	0	hg19	CCDS14012.1	.	.	.	.	.	.	.	.	.	.	G	12.98	2.101483	0.37048	2.27E-4	0.001395	ENSG00000100401	ENST00000405486;ENST00000356244;ENST00000405383;ENST00000455915;ENST00000407260	T;T;T;T	0.42131	0.98;0.98;0.98;0.98	4.39	2.17	0.27698	Ran-GTPase activating protein 1, C-terminal (1);	1.014230	0.07853	N	0.965026	T	0.45975	0.1369	L	0.36672	1.1	0.19775	N	0.999959	D;D	0.76494	0.999;0.995	P;P	0.54372	0.711;0.75	T	0.34054	-0.9844	10	0.72032	D	0.01	-21.7601	8.6119	0.33808	0.0:0.0:0.4106:0.5894	.	357;412	F8W7I9;P46060	.;RAGP1_HUMAN	W	412;412;412;412;357	ENSP00000385866:R412W;ENSP00000348577:R412W;ENSP00000401470:R412W;ENSP00000385354:R357W	ENSP00000348577:R412W	R	-	1	2	RANGAP1	39980284	0.792000	0.28813	0.401000	0.26359	0.093000	0.18481	0.893000	0.28336	0.297000	0.22615	-0.521000	0.04368	CGG		TCGA-2J-AAB1-01A-11D-A40W-08	RANGAP1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320606.1	0	0	1	63	253	0	79	1	1	56	157	0	79	2		0	0	0	0	0	2	1	1.000000	63	249	0	77	2								-2.933500	1	1	121412	35	55	1	1	2	3	2.064369	0	0.380000	1.940000	0.386988	0.990000	8.300000e-01	1.000000	1.000000	0.979999	0.990000	1	0.940000	1.000000
MOV10L1	54456	broad.mit.edu	37	22	50538027	50538027	+	Silent	SNP	C	C	T			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr22:50538027C>T	ENST00000262794.5	+	3	521	c.438C>T	c.(436-438)tgC>tgT	p.C146C	MOV10L1_ENST00000540615.1_Silent_p.C126C|MOV10L1_ENST00000395858.3_Silent_p.C146C|MOV10L1_ENST00000395843.1_5'UTR|MOV10L1_ENST00000545383.1_Silent_p.C146C|MOV10L1_ENST00000475190.1_3'UTR	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1			67		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)			AGAGTGTGTGCGAAGGTATGC	0.512000																								0							SO:0001819	synonymous_variant			ENST00000262794.5	1	1	hg19	CCDS14084.1																																																																																				TCGA-2J-AAB1-01A-11D-A40W-08	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	1	0	0	47	229	0	70	0	0	0	1	0	70	2		0	0	0	0	0	2	1	1.000000	46	228	0	68	2								-19.999990	1	1	121412	4	35	1	1	2	3	2.064369	0	0.380000	1.940000	0.386988	0.910000	6.800000e-01	1.000000	1.000000	0.901233	0.910000	1	0.790000	1.000000
GLI2	2736	broad.mit.edu	37	2	121740416	121740416	+	Missense_Mutation	SNP	C	C	T			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr2:121740416C>T	ENST00000452319.1	+	11	1703	c.1643C>T	c.(1642-1644)tCg>tTg	p.S548L	GLI2_ENST00000361492.4_Missense_Mutation_p.S548L|GLI2_ENST00000435313.2_3'UTR|GLI2_ENST00000314490.11_Missense_Mutation_p.S220L					GLI family zinc finger 2			64	Renal(3;0.0496)	Prostate(154;0.0623)			TCCAACGCCTCGGACCGCGCC	0.637000																								0							SO:0001583	missense			ENST00000452319.1	1	1	hg19	CCDS33283.1	.	.	.	.	.	.	.	.	.	.	C	33	5.240212	0.95240	.	.	ENSG00000074047	ENST00000452319;ENST00000361492;ENST00000314490	T;T;T	0.52526	0.66;0.66;0.66	4.59	4.59	0.56863	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.67126	0.2860	M	0.64676	1.99	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.996;0.994;0.998;0.999;0.994	T	0.70967	-0.4728	10	0.87932	D	0	.	17.9271	0.88987	0.0:1.0:0.0:0.0	.	548;531;203;203;220	P10070;Q0VGA0;P10070-2;P10070-4;P10070-3	GLI2_HUMAN;.;.;.;.	L	548;548;220	ENSP00000390436:S548L;ENSP00000354586:S548L;ENSP00000312694:S220L	ENSP00000312694:S220L	S	+	2	0	GLI2	121456886	1.000000	0.71417	0.998000	0.56505	0.850000	0.48378	7.599000	0.82757	2.536000	0.85505	0.484000	0.47621	TCG		TCGA-2J-AAB1-01A-11D-A40W-08	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	1	0	1	50	282	0	51	0	3.510172e-01	0	8	0	51	2		0	0	0	0	0	2	1	1.000000	48	279	0	48	2								-3.022880	1	1	0	0		1	0	0	0	2.015667	0	0.380000	1.940000	0.377635	0.780000	6.000000e-01	0.990000	0.790000	0.795310	0.780000	0	0.680000	0.900000
EPC2	26122	broad.mit.edu	37	2	149542414	149542414	+	Missense_Mutation	SNP	A	A	G			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr2:149542414A>G	ENST00000258484.6	+	13	2229	c.2195A>G	c.(2194-2196)cAc>cGc	p.H732R		NM_015630.3	NP_056445.3	Q52LR7	EPC2_HUMAN	enhancer of polycomb homolog 2 (Drosophila)			13					AATGCAGTGCACCTCAATAAT	0.473000																								0							SO:0001583	missense			ENST00000258484.6	1	1	hg19	CCDS46422.1	.	.	.	.	.	.	.	.	.	.	A	12.37	1.916638	0.33815	.	.	ENSG00000135999	ENST00000258484	.	.	.	5.93	5.93	0.95920	.	0.105505	0.64402	D	0.000005	T	0.68449	0.3002	L	0.44542	1.39	0.80722	D	1	D	0.54772	0.968	D	0.67900	0.954	T	0.65713	-0.6101	9	0.34782	T	0.22	-2.9627	16.3783	0.83418	1.0:0.0:0.0:0.0	.	732	Q52LR7	EPC2_HUMAN	R	732	.	ENSP00000258484:H732R	H	+	2	0	EPC2	149258884	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.746000	0.74866	2.261000	0.74972	0.477000	0.44152	CAC		TCGA-2J-AAB1-01A-11D-A40W-08	EPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332278.1	1	0	1	23	187	0	34	1	9.015453e-01	8	27	0	34	2		0	0	0	0	0	2	1	1.000000	22	186	0	34	2								-10.431350	1	1	0	0		1	0	0	0	2.015667	0	0.380000	1.940000	0.377635	0.570000	3.800000e-01	0.810000	0.570000	0.588896	0.570000	0	0.470000	0.700000
TANC1	85461	broad.mit.edu	37	2	160087288	160087288	+	Missense_Mutation	SNP	C	C	T			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr2:160087288C>T	ENST00000263635.6	+	27	5588	c.5351C>T	c.(5350-5352)aCc>aTc	p.T1784I	TANC1_ENST00000454300.1_Missense_Mutation_p.T1678I	NM_001145909.1|NM_033394.2	NP_001139381.1|NP_203752.2	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1			77					CAAGCCAAAACCTGTTCTGTT	0.498000																								0							SO:0001583	missense			ENST00000263635.6	1	1	hg19	CCDS42766.1	.	.	.	.	.	.	.	.	.	.	C	9.077	0.998461	0.19121	.	.	ENSG00000115183	ENST00000454300;ENST00000263635	T;T	0.69685	-0.42;-0.42	5.96	4.9	0.64082	.	0.635444	0.17407	N	0.175331	T	0.50939	0.1645	N	0.22421	0.69	0.18873	N	0.999989	B	0.15473	0.013	B	0.16289	0.015	T	0.24261	-1.0165	9	.	.	.	.	12.4187	0.55508	0.0:0.8581:0.0:0.1419	.	1784	Q9C0D5	TANC1_HUMAN	I	1678;1784	ENSP00000396339:T1678I;ENSP00000263635:T1784I	.	T	+	2	0	TANC1	159795534	0.992000	0.36948	0.283000	0.24790	0.386000	0.30323	0.906000	0.28517	2.823000	0.97156	0.655000	0.94253	ACC		TCGA-2J-AAB1-01A-11D-A40W-08	TANC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333135.1	1	0	1	40	138	0	26	1	9.994377e-01	18	25	0	26	2		0	0	0	0	0	2	1	1.000000	40	134	0	26	2								-20.000000	1	1	0	0		1	0	0	0	2.015667	0	0.380000	1.940000	0.377635	0.990000	8.700000e-01	1.000000	1.000000	0.990875	0.990000	1	0.990000	1.000000
PDE11A	50940	broad.mit.edu	37	2	178762794	178762794	+	Silent	SNP	G	G	A			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr2:178762794G>A	ENST00000286063.6	-	4	1610	c.1293C>T	c.(1291-1293)atC>atT	p.I431I	PDE11A_ENST00000409504.1_Silent_p.I73I|PDE11A_ENST00000449286.2_Silent_p.I73I|PDE11A_ENST00000497003.1_5'UTR|PDE11A_ENST00000358450.4_Silent_p.I181I	NM_016953.3	NP_058649.3	Q9HCR9	PDE11_HUMAN	phosphodiesterase 11A	p.I431I(2)|p.I181I(2)		58			OV - Ovarian serous cystadenocarcinoma(117;0.00121)|Epithelial(96;0.00455)|all cancers(119;0.02)	Caffeine(DB00201)|Tadalafil(DB00820)	CTGGTGATTCGATGTCCTCTA	0.348000									Primary Pigmented Nodular Adrenocortical Disease, Familial															4	Substitution - coding silent(4)						SO:0001819	synonymous_variant	Familial Cancer Database	iPPNAD, PPNAD1, incl. familial micronodular adrenocortical hyperplasia, PPNAD2	ENST00000286063.6	1	1	hg19	CCDS33334.1	.	.	.	.	.	.	.	.	.	.	G	9.329	1.059928	0.19987	.	.	ENSG00000128655	ENST00000433879	.	.	.	5.89	0.569	0.17340	.	.	.	.	.	T	0.57417	0.2052	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49808	-0.8900	4	.	.	.	.	9.715	0.40270	0.7158:0.0:0.2842:0.0	.	.	.	.	L	70	.	.	S	-	2	0	PDE11A	178471040	0.922000	0.31269	0.995000	0.50966	0.966000	0.64601	0.180000	0.16860	-0.128000	0.11641	-0.302000	0.09304	TCG		TCGA-2J-AAB1-01A-11D-A40W-08	PDE11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334313.2	1	0	1	94	338	0	77	0	4.830764e-02	1	1	0	77	2		0	0	0	0	0	2	1	1.000000	93	336	0	77	2								-3.842923	1	1	121412	2	32	1	0	0	0	2.015667	0	0.380000	1.940000	0.377635	0.990000	9.400000e-01	1.000000	1.000000	0.996523	0.990000	1	0.990000	1.000000
SF3B1	23451	broad.mit.edu	37	2	198267359	198267359	+	Missense_Mutation	SNP	C	C	G			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08			C	G	C	C		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr2:198267359C>G	ENST00000335508.6	-	14	2089	c.1998G>C	c.(1996-1998)aaG>aaC	p.K666N	SNORA4_ENST00000365564.1_RNA|SF3B1_ENST00000462613.1_5'Flank	NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	p.K666N(19)		633			OV - Ovarian serous cystadenocarcinoma(117;0.246)		GTTGTACAATCTTAATACCAG	0.413000			Mis		myelodysplastic syndrome										Dom	yes		2	2q33.1	23451	splicing factor 3b, subunit 1, 155kDa		L	19	Substitution - Missense(19)						SO:0001583	missense			ENST00000335508.6	1	1	hg19	CCDS33356.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.159735	0.78226	0.0	1.16E-4	ENSG00000115524	ENST00000335508	T	0.65732	-0.17	5.68	4.81	0.61882	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.83575	0.5284	H	0.95645	3.7	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	D	0.87121	0.2191	10	0.87932	D	0	.	11.0204	0.47715	0.0:0.8576:0.0:0.1424	.	666	O75533	SF3B1_HUMAN	N	666	ENSP00000335321:K666N	ENSP00000335321:K666N	K	-	3	2	SF3B1	197975604	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.643000	0.46604	1.410000	0.46936	0.561000	0.74099	AAG		TCGA-2J-AAB1-01A-11D-A40W-08	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2	0	0	0	11	319	0	56	1	9.944347e-01	7	253	0	56	2	1	9.999981e-01	15	840	0	794	2	1	0.998349	11	317	0	55	2								-3.187404	1	1	121412	7	39	1	0	0	0	2.015667	0	0.380000	1.940000	0.377635	0.170000	9.000000e-02	0.300000	0.180000	0.188569	0.170000	0	0.130000	0.240000
ZDBF2	57683	broad.mit.edu	37	2	207175041	207175041	+	Missense_Mutation	SNP	A	A	G			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr2:207175041A>G	ENST00000374423.3	+	5	6175	c.5789A>G	c.(5788-5790)aAg>aGg	p.K1930R		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2			95					CCTAAGCAAAAGGGGCGTGTG	0.428000																								0							SO:0001583	missense			ENST00000374423.3	0	1	hg19	CCDS46501.1	.	.	.	.	.	.	.	.	.	.	A	4.060	0.008959	0.07912	.	.	ENSG00000204186	ENST00000374423	T	0.44482	0.92	5.64	-2.84	0.05751	.	.	.	.	.	T	0.19525	0.0469	N	0.22421	0.69	0.09310	N	1	P	0.40144	0.704	B	0.33799	0.17	T	0.22556	-1.0213	9	0.16896	T	0.51	.	5.9471	0.19225	0.1465:0.6094:0.0829:0.1612	.	1930	Q9HCK1	ZDBF2_HUMAN	R	1930	ENSP00000363545:K1930R	ENSP00000363545:K1930R	K	+	2	0	ZDBF2	206883286	0.023000	0.18921	0.000000	0.03702	0.003000	0.03518	0.647000	0.24812	-0.083000	0.12618	0.456000	0.33151	AAG		TCGA-2J-AAB1-01A-11D-A40W-08	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	0	0	0	4	360	0	52		0	0	0	0	52	2		0	0	0	0	0	2	1	0.876406	4	339	0	52	2								-3.207332	1	1	0	0		1	0	0	0	2.015667	0	0.380000	1.940000	0.377635	0.060000	1.000000e-02	0.140000	0.060000	0.071245	0.060000	0	0.030000	0.100000
ACADL	33	broad.mit.edu	37	2	211070474	211070474	+	Missense_Mutation	SNP	G	G	A			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr2:211070474G>A	ENST00000233710.3	-	6	877	c.650C>T	c.(649-651)gCg>gTg	p.A217V	AC006994.2_ENST00000412065.1_RNA	NM_001608.3	NP_001599.1	P28330	ACADL_HUMAN	acyl-CoA dehydrogenase, long chain			14		Renal(323;0.202)			ATTTGTGACCGCAACTACAAT	0.398000																								0							SO:0001583	missense			ENST00000233710.3	0	1	hg19	CCDS2389.1	.	.	.	.	.	.	.	.	.	.	G	11.41	1.630025	0.28978	.	.	ENSG00000115361	ENST00000233710	D	0.97505	-4.41	5.28	4.41	0.53225	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA oxidase/dehydrogenase, central domain (2);	0.208411	0.49305	D	0.000151	D	0.95500	0.8538	L	0.46885	1.475	0.43141	D	0.994895	P	0.45594	0.862	P	0.44772	0.46	D	0.94867	0.8027	10	0.51188	T	0.08	.	14.1005	0.65051	0.0727:0.0:0.9273:0.0	.	217	P28330	ACADL_HUMAN	V	217	ENSP00000233710:A217V	ENSP00000233710:A217V	A	-	2	0	ACADL	210778719	1.000000	0.71417	0.009000	0.14445	0.008000	0.06430	7.334000	0.79224	1.240000	0.43803	-0.137000	0.14449	GCG		TCGA-2J-AAB1-01A-11D-A40W-08	ACADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256561.2	0	0	0	6	349	0	65		0	0	0	0	65	2		0	0	0	0	0	2	1	0.964691	6	347	0	64	2								-2.517377	1	1	121400	3	38	1	0	0	0	2.015667	0	0.380000	1.940000	0.377635	0.090000	3.000000e-02	0.180000	0.090000	0.102334	0.090000	0	0.050000	0.140000
DNPEP	23549	broad.mit.edu	37	2	220239025	220239025	+	Missense_Mutation	SNP	A	A	C			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08			A	C	A	A		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr2:220239025A>C	ENST00000273075.4	-	15	1667	c.1447T>G	c.(1447-1449)Tta>Gta	p.L483V	DNPEP_ENST00000490371.1_5'UTR|DNPEP_ENST00000523282.1_Missense_Mutation_p.L491V|DNPEP_ENST00000373972.1_Missense_Mutation_p.L408V	NM_012100.2	NP_036232	Q9ULA0	DNPEP_HUMAN	aspartyl aminopeptidase			17		Renal(207;0.0474)			CAATCCACTAAGAGATTATGG	0.473000																								0							SO:0001583	missense			ENST00000273075.4	1	1	hg19	CCDS42823.1	.	.	.	.	.	.	.	.	.	.	A	2.901	-0.227412	0.06022	.	.	ENSG00000123992	ENST00000273075;ENST00000373972;ENST00000523282;ENST00000535056	.	.	.	5.44	-10.9	0.00192	.	1.368830	0.04681	N	0.412341	T	0.11495	0.0280	N	0.11023	0.085	0.09310	N	0.999999	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.001;0.0;0.001	T	0.13388	-1.0511	9	0.13470	T	0.59	1.4126	0.5348	0.00635	0.2362:0.1861:0.301:0.2768	.	491;491;473;483	E7ETB3;B7Z7F0;Q9ULA0;Q53SB6	.;.;DNPEP_HUMAN;.	V	483;408;491;376	.	ENSP00000273075:L483V	L	-	1	2	DNPEP	219947269	0.000000	0.05858	0.016000	0.15963	0.364000	0.29643	-1.670000	0.01956	-1.757000	0.01316	-0.333000	0.08304	TTA		TCGA-2J-AAB1-01A-11D-A40W-08	DNPEP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000130212.1	1	0	1	51	256	0	50	1	1	75	140	0	50	2		0	0	0	0	0	2	1	1.000000	51	254	0	49	2								-20.000000	1	1	0	0		1	0	0	0	2.015667	0	0.380000	1.940000	0.377635	0.860000	6.600000e-01	1.000000	1.000000	0.869195	0.860000	1	0.760000	0.980000
TBC1D23	55773	broad.mit.edu	37	3	100016873	100016873	+	Missense_Mutation	SNP	C	C	T			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr3:100016873C>T	ENST00000394144.4	+	9	990	c.983C>T	c.(982-984)gCg>gTg	p.A328V	TBC1D23_ENST00000475134.1_Missense_Mutation_p.A191V|TBC1D23_ENST00000344949.5_Missense_Mutation_p.A328V|TBC1D23_ENST00000486274.1_3'UTR	NM_001199198.2	NP_001186127.1	Q9NUY8	TBC23_HUMAN	TBC1 domain family, member 23			25					ATCCTTCAAGCGAATCAGCTA	0.443000																								0							SO:0001583	missense			ENST00000394144.4	0	1	hg19	CCDS56265.1	.	.	.	.	.	.	.	.	.	.	C	34	5.350043	0.95830	2.27E-4	0.0	ENSG00000036054	ENST00000344949;ENST00000394144;ENST00000475134	T;T;T	0.32988	1.43;1.43;1.43	5.76	5.76	0.90799	Rhodanese-like (2);	0.000000	0.85682	D	0.000000	T	0.41282	0.1152	N	0.22421	0.69	0.80722	D	1	D;D	0.71674	0.998;0.997	P;P	0.62885	0.908;0.851	T	0.09058	-1.0692	9	.	.	.	.	19.9533	0.97211	0.0:1.0:0.0:0.0	.	328;328	Q9NUY8;Q9NUY8-2	TBC23_HUMAN;.	V	328;328;191	ENSP00000340693:A328V;ENSP00000377700:A328V;ENSP00000418059:A191V	.	A	+	2	0	TBC1D23	101499563	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	7.086000	0.76885	2.725000	0.93324	0.585000	0.79938	GCG		TCGA-2J-AAB1-01A-11D-A40W-08	TBC1D23-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353150.1	0	0	0	8	184	0	32	0	4.577688e-01	1	33	0	32	2		0	0	0	0	0	2	1	0.988665	8	179	0	29	2								-3.966471	1	1	121410	3	33	1	0	1	1	2.022971	0	0.380000	1.940000	0.378820	0.220000	1.000000e-01	0.400000	0.220000	0.241633	0.220000	0	0.150000	0.320000
EIF2B5	8893	broad.mit.edu	37	3	183855998	183855998	+	Silent	SNP	T	T	C			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr3:183855998T>C	ENST00000273783.3	+	5	851	c.729T>C	c.(727-729)gaT>gaC	p.D243D	RP11-778D9.12_ENST00000608135.1_RNA|EIF2B5_ENST00000444495.1_Silent_p.D243D	NM_003907.2	NP_003898.2	Q13144	EI2BE_HUMAN	eukaryotic translation initiation factor 2B, subunit 5 epsilon, 82kDa			27	all_cancers(143;7.59e-11)|Ovarian(172;0.0303)		Epithelial(37;7.06e-36)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)		TTCGATATGATTTACTGGATT	0.478000																								0							SO:0001819	synonymous_variant			ENST00000273783.3	1	1	hg19	CCDS3252.1																																																																																				TCGA-2J-AAB1-01A-11D-A40W-08	EIF2B5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346168.1	1	0	0	20	441	0	76	1	5.750939e-01	4	39	0	76	2		0	0	0	0	0	2	1	0.999995	20	436	0	76	2								-19.700530	1	1	0	0		1	0	1	1	2.022971	0	0.380000	1.940000	0.378820	0.220000	1.400000e-01	0.340000	0.220000	0.237419	0.220000	0	0.180000	0.290000
TGFBR2	7048	broad.mit.edu	37	3	30732957	30732957	+	Missense_Mutation	SNP	G	G	T			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08			G	T	G	G		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr3:30732957G>T	ENST00000295754.5	+	7	1952	c.1570G>T	c.(1570-1572)Gac>Tac	p.D524Y	TGFBR2_ENST00000359013.4_Missense_Mutation_p.D549Y	NM_003242.5	NP_003233.4	P37173	TGFR2_HUMAN	transforming growth factor, beta receptor II (70/80kDa)	p.D524N(1)|p.D524Y(1)		53					CTGGGACCACGACCCAGAGGC	0.607000																								2	Substitution - Missense(2)	GRCh37	CM064328	TGFBR2	M		SO:0001583	missense			ENST00000295754.5	1	1	hg19	CCDS2648.1	.	.	.	.	.	.	.	.	.	.	G	29.4	5.005083	0.93287	.	.	ENSG00000163513	ENST00000295754;ENST00000359013;ENST00000439925	D;D	0.95103	-3.61;-3.61	5.91	5.91	0.95273	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.98018	0.9347	M	0.91663	3.23	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98294	1.0515	10	0.87932	D	0	.	20.3052	0.98627	0.0:0.0:1.0:0.0	.	524;549	P37173;D2JYI1	TGFR2_HUMAN;.	Y	524;549;354	ENSP00000295754:D524Y;ENSP00000351905:D549Y	ENSP00000295754:D524Y	D	+	1	0	TGFBR2	30707961	1.000000	0.71417	0.974000	0.42286	0.985000	0.73830	9.869000	0.99810	2.808000	0.96608	0.655000	0.94253	GAC		TCGA-2J-AAB1-01A-11D-A40W-08	TGFBR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252994.2	1	0	1	107	174	0	57	1	1	103	153	0	57	2	1	1	286	423	0	575	2	1	1.000000	105	168	0	56	2								-20.000000	1	1	0	0		1	0	2	2	2.018562	1	0.380000	1.940000	0.380000	0.990000	9.900000e-01	1.000000	1.000000	1.000000	0.990000	1	0.990000	1.000000
DOCK3	1795	broad.mit.edu	37	3	51400102	51400102	+	Nonsense_Mutation	SNP	C	C	T			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr3:51400102C>T	ENST00000266037.9	+	49	5313	c.5290C>T	c.(5290-5292)Cga>Tga	p.R1764*		NM_004947.4	NP_004938.1	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3			45					TTCCAGTGCCCGAGGTAAGGA	0.562000																								0							SO:0001587	stop_gained			ENST00000266037.9	0	1	hg19	CCDS46835.1	.	.	.	.	.	.	.	.	.	.	C	44	10.689336	0.99450	.	.	ENSG00000088538	ENST00000266037;ENST00000402669	.	.	.	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10377	T	0.69	.	15.6164	0.76769	0.1379:0.862:0.0:0.0	.	.	.	.	X	1764;560	.	ENSP00000266037:R1764X	R	+	1	2	DOCK3	51375142	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.049000	0.49869	2.605000	0.88082	0.563000	0.77884	CGA		TCGA-2J-AAB1-01A-11D-A40W-08	DOCK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346478.5	1	0	1	26	50	0	16	0	0	0	1	0	16	2	1	1	185	678	0	739	2	1	1.000000	26	50	0	15	2								-6.053581	1	1	0	0		1	0	1	1	2.022556	0	0.380000	1.940000	0.378820	0.990000	9.900000e-01	1.000000	1.000000	0.999933	0.990000	1	0.990000	1.000000
GABRA4	2557	broad.mit.edu	37	4	46979145	46979145	+	Silent	SNP	C	C	T			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr4:46979145C>T	ENST00000264318.3	-	5	1492	c.510G>A	c.(508-510)gcG>gcA	p.A170A		NM_000809.3|NM_001204266.1|NM_001204267.1	NP_000800.2|NP_001191195.1|NP_001191196.1	P48169	GBRA4_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 4			45				Acamprosate(DB00659)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)	TGGGACACTCCGCACTTATGG	0.343000													Ovarian(6;283 369 8234 12290 33402)											0							SO:0001819	synonymous_variant			ENST00000264318.3	1	1	hg19	CCDS3473.1																																																																																				TCGA-2J-AAB1-01A-11D-A40W-08	GABRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216893.1	0	0	1	33	183	1	38		0	0	0	1	38	2		0	0	0	0	0	2	1	0.989151	32	179	1	38	18								-2.684716	1	1	121372	4	36	1	0	1	1	2.022977	0	0.380000	1.940000	0.378820	0.800000	5.700000e-01	1.000000	1.000000	0.807961	0.800000	0	0.680000	0.940000
TMPRSS11D	9407	broad.mit.edu	37	4	68699089	68699089	+	Silent	SNP	G	G	A			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr4:68699089G>A	ENST00000283916.6	-	7	623	c.525C>T	c.(523-525)gcC>gcT	p.A175A	TMPRSS11D_ENST00000545541.1_Silent_p.A58A|TMPRSS11D_ENST00000509584.1_5'UTR|UBA6-AS1_ENST00000500538.2_RNA	NM_004262.2	NP_004253.1	O60235	TM11D_HUMAN	transmembrane protease, serine 11D			23					GGTCTGGACCGGCCCCACATT	0.463000																								0							SO:0001819	synonymous_variant			ENST00000283916.6	0	1	hg19	CCDS3518.1																																																																																				TCGA-2J-AAB1-01A-11D-A40W-08	TMPRSS11D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251430.3	0	0	0	22	697	0	115		0	0	0	0	115	2		0	0	0	0	0	2	1	0.999999	21	686	0	115	2								-2.764799	1	1	121340	9	44	1	0	1	1	2.022977	0	0.380000	1.940000	0.378820	0.150000	9.000000e-02	0.240000	0.160000	0.167193	0.150000	0	0.120000	0.200000
APC	324	broad.mit.edu	37	5	112176765	112176765	+	Missense_Mutation	SNP	A	A	G			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr5:112176765A>G	ENST00000457016.1	+	16	5854	c.5474A>G	c.(5473-5475)gAt>gGt	p.D1825G	APC_ENST00000508376.2_Missense_Mutation_p.D1825G|APC_ENST00000257430.4_Missense_Mutation_p.D1825G|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	p.K1192fs*3(1)|p.?(1)		3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)			GTCTTCAATGATAAGCTCCCA	0.333000		12	D, Mis, N, F, S		colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS	colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)			NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		E, M, O	2	Unknown(1)|Deletion - Frameshift(1)						SO:0001583	missense	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	ENST00000457016.1	1	1	hg19	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	A	11.59	1.683218	0.29872	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	D;D;D	0.90197	-2.63;-2.63;-2.63	6.07	6.07	0.98685	.	0.322819	0.37955	N	0.001867	D	0.84822	0.5557	L	0.27053	0.805	0.39105	D	0.961357	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.80569	-0.1324	9	.	.	.	-12.6701	16.6277	0.84984	1.0:0.0:0.0:0.0	.	1827;1825	Q4LE70;P25054	.;APC_HUMAN	G	1825	ENSP00000413133:D1825G;ENSP00000257430:D1825G;ENSP00000427089:D1825G	.	D	+	2	0	APC	112204664	1.000000	0.71417	0.582000	0.28627	0.778000	0.44026	7.395000	0.79876	2.330000	0.79161	0.528000	0.53228	GAT		TCGA-2J-AAB1-01A-11D-A40W-08	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	1	0	1	49	203	0	37	0	1.771917e-01	1	3	0	37	2		0	0	0	0	0	2	1	1.000000	47	200	0	35	2								-20.000000	1	1	0	0		1	1	2	3	2.028143	0	0.380000	1.940000	0.381176	0.990000	7.800000e-01	1.000000	1.000000	0.962495	0.990000	1	0.890000	1.000000
ETF1	2107	broad.mit.edu	37	5	137844426	137844426	+	Missense_Mutation	SNP	G	G	A			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr5:137844426G>A	ENST00000360541.5	-	10	1384	c.1163C>T	c.(1162-1164)aCg>aTg	p.T388M	ETF1_ENST00000499810.2_Missense_Mutation_p.T355M|ETF1_ENST00000503014.1_Missense_Mutation_p.T374M	NM_004730.3	NP_004721.1	P62495	ERF1_HUMAN	eukaryotic translation termination factor 1			18			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)		AATTTCCAACGTAGCTCCAAA	0.413000																								0							SO:0001583	missense			ENST00000360541.5	0	1	hg19	CCDS4207.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.150639	0.78001	.	.	ENSG00000120705	ENST00000499810;ENST00000360541;ENST00000503014	.	.	.	6.17	6.17	0.99709	eRF1 domain 3 (1);	0.000000	0.85682	D	0.000000	D	0.83229	0.5209	M	0.88640	2.97	0.80722	D	1	D;P	0.64830	0.994;0.607	P;B	0.57324	0.818;0.087	D	0.83814	0.0243	9	0.51188	T	0.08	-6.0305	20.4745	0.99168	0.0:0.0:1.0:0.0	.	374;388	B7Z7P8;P62495	.;ERF1_HUMAN	M	355;388;374	.	ENSP00000353741:T388M	T	-	2	0	ETF1	137872325	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.857000	0.99534	2.941000	0.99782	0.655000	0.94253	ACG		TCGA-2J-AAB1-01A-11D-A40W-08	ETF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251276.2	0	0	0	6	878	0	162	0	2.975263e-01	0	139	0	162	2		0	0	0	0	0	2	1	0.964533	6	874	0	162	2								-2.489483	0	1	0	0		1	1	2	3	2.028143	0	0.380000	1.940000	0.381176	0.030000	0	0.080000	0.040000	0.041317	0.030000	0	0.010000	0.060000
PCDHA9	9752	broad.mit.edu	37	5	140229874	140229874	+	Silent	SNP	C	C	T			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr5:140229874C>T	ENST00000532602.1	+	1	2827	c.1794C>T	c.(1792-1794)gaC>gaT	p.D598D	PCDHA3_ENST00000522353.2_Intron|PCDHA9_ENST00000378122.3_Silent_p.D598D|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA8_ENST00000531613.1_Intron	NM_031857.1	NP_114063.1	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9			59			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		GCGCAGTGGACGCCGACTCGG	0.672000													Melanoma(55;1800 1972 14909)											0							SO:0001819	synonymous_variant			ENST00000532602.1	1	1	hg19	CCDS54920.1																																																																																				TCGA-2J-AAB1-01A-11D-A40W-08	PCDHA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372896.2	1	0	1	76	318	0	73		0	0	0	0	73	2		0	0	0	0	0	2	1	1.000000	74	312	0	73	2								-20.000000	1	1	120728	1	17	1	1	2	3	2.028143	0	0.380000	1.940000	0.381176	0.990000	8.100000e-01	1.000000	1.000000	0.968228	0.990000	1	0.910000	1.000000
PCDHA9	9752	broad.mit.edu	37	5	140230003	140230003	+	Silent	SNP	C	C	T			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr5:140230003C>T	ENST00000532602.1	+	1	2956	c.1923C>T	c.(1921-1923)gaC>gaT	p.D641D	PCDHA3_ENST00000522353.2_Intron|PCDHA9_ENST00000378122.3_Silent_p.D641D|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA8_ENST00000531613.1_Intron	NM_031857.1	NP_114063.1	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9			59			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		ACGAAACGGACGCACCGCGCC	0.682000													Melanoma(55;1800 1972 14909)											0							SO:0001819	synonymous_variant			ENST00000532602.1	1	1	hg19	CCDS54920.1																																																																																				TCGA-2J-AAB1-01A-11D-A40W-08	PCDHA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372896.2	1	0	1	53	325	0	91		0	0	0	0	91	2		0	0	0	0	0	2	1	1.000000	53	321	0	90	2								-19.999890	1	1	0	0		1	1	2	3	2.028143	0	0.380000	1.940000	0.381176	0.730000	5.600000e-01	0.940000	0.740000	0.745922	0.730000	0	0.640000	0.840000
GLRA1	2741	broad.mit.edu	37	5	151271898	151271898	+	Missense_Mutation	SNP	T	T	A			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr5:151271898T>A	ENST00000455880.2	-	2	444	c.158A>T	c.(157-159)gAt>gTt	p.D53V	GLRA1_ENST00000545569.1_Intron|GLRA1_ENST00000471351.2_5'UTR|GLRA1_ENST00000274576.4_Missense_Mutation_p.D53V			P23415	GLRA1_HUMAN	glycine receptor, alpha 1			23		all_hematologic(541;0.0341)|Medulloblastoma(196;0.0912)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)	Desflurane(DB01189)|Enflurane(DB00228)|Ethanol(DB00898)|Ginkgo biloba(DB01381)|Glycine(DB00145)|Halothane(DB01159)|Isoflurane(DB00753)|Lindane(DB00431)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	GATCCTGGCATCATATCCGGA	0.498000																								0							SO:0001583	missense			ENST00000455880.2	1	1	hg19	CCDS54942.1	.	.	.	.	.	.	.	.	.	.	T	25.0	4.590090	0.86851	.	.	ENSG00000145888	ENST00000274576;ENST00000455880	T;T	0.81415	-1.49;-1.49	5.48	5.48	0.80851	Neurotransmitter-gated ion-channel ligand-binding (3);	0.116646	0.56097	D	0.000030	D	0.91506	0.7318	M	0.91612	3.225	0.80722	D	1	D;D	0.69078	0.996;0.997	D;D	0.72982	0.979;0.964	D	0.93395	0.6755	10	0.87932	D	0	.	15.5709	0.76337	0.0:0.0:0.0:1.0	.	53;53	P23415;P23415-2	GLRA1_HUMAN;.	V	53	ENSP00000274576:D53V;ENSP00000411593:D53V	ENSP00000274576:D53V	D	-	2	0	GLRA1	151252091	1.000000	0.71417	0.993000	0.49108	0.943000	0.58893	7.516000	0.81772	2.089000	0.63090	0.482000	0.46254	GAT		TCGA-2J-AAB1-01A-11D-A40W-08	GLRA1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000373959.1	0	0	0	14	369	0	63		0	0	0	0	63	2		0	0	0	0	0	2	1	0.999753	14	366	0	59	2								-3.703570	1	1	0	0		1	1	2	3	2.028143	0	0.380000	1.940000	0.381176	0.190000	1.000000e-01	0.320000	0.200000	0.204579	0.190000	0	0.140000	0.260000
GEMIN5	25929	broad.mit.edu	37	5	154292538	154292538	+	Missense_Mutation	SNP	G	G	A			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr5:154292538G>A	ENST00000285873.7	-	14	1991	c.1916C>T	c.(1915-1917)aCg>aTg	p.T639M		NM_001252156.1|NM_015465.4	NP_001239085.1|NP_056280.2	Q8TEQ6	GEMI5_HUMAN	gem (nuclear organelle) associated protein 5			38	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)		AATCTTGGCCGTATGCCCTGA	0.522000																								0							SO:0001583	missense			ENST00000285873.7	0	1	hg19	CCDS4330.1	.	.	.	.	.	.	.	.	.	.	G	19.12	3.766113	0.69878	.	.	ENSG00000082516	ENST00000285873	T	0.65549	-0.16	5.37	5.37	0.77165	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.80742	0.4681	M	0.78637	2.42	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.82647	-0.0354	10	0.87932	D	0	-17.564	19.0919	0.93229	0.0:0.0:1.0:0.0	.	638;639	B7ZLC9;Q8TEQ6	.;GEMI5_HUMAN	M	639	ENSP00000285873:T639M	ENSP00000285873:T639M	T	-	2	0	GEMIN5	154272731	1.000000	0.71417	1.000000	0.80357	0.298000	0.27526	8.881000	0.92415	2.667000	0.90743	0.561000	0.74099	ACG		TCGA-2J-AAB1-01A-11D-A40W-08	GEMIN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252507.1	0	0	0	5	319	0	60	0	1.266467e-02	0	9	0	60	2		0	0	0	0	0	2	1	0.934364	5	312	0	59	2								-2.742171	1	1	121412	5	34	1	1	2	3	2.028143	0	0.380000	1.940000	0.381176	0.080000	2.000000e-02	0.190000	0.080000	0.096572	0.080000	0	0.050000	0.140000
GRM6	2916	broad.mit.edu	37	5	178413623	178413623	+	Silent	SNP	G	G	A	rs139758482		TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr5:178413623G>A	ENST00000517717.1	-	9	1670	c.1632C>T	c.(1630-1632)gaC>gaT	p.D544D	RP11-281O15.4_ENST00000519491.1_RNA|GRM6_ENST00000231188.5_Silent_p.D544D			O15303	GRM6_HUMAN	glutamate receptor, metabotropic 6			55	all_cancers(89;0.000828)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.0156)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		AGCGGTACCCGTCACAGGCCT	0.682000																								0							SO:0001819	synonymous_variant			ENST00000517717.1	0	1	hg19	CCDS4442.1																																																																																				TCGA-2J-AAB1-01A-11D-A40W-08	GRM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253474.2	0	0	0	8	245	1	44		0	0	0	1	44	2		0	0	0	0	0	2	0	0.031009	8	242	1	43	18								-9.201594	1	1	121358	41	47	1	1	2	3	2.028143	0	0.380000	1.940000	0.381176	0.170000	7.000000e-02	0.320000	0.160000	0.184922	0.170000	0	0.120000	0.240000
ADAMTS16	170690	broad.mit.edu	37	5	5242275	5242275	+	Missense_Mutation	SNP	G	G	A			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr5:5242275G>A	ENST00000274181.7	+	17	2771	c.2633G>A	c.(2632-2634)cGc>cAc	p.R878H		NM_139056.2	NP_620687.2	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 16			107					GCCATCGTGCGCTCTGAGTGC	0.642000																								0							SO:0001583	missense			ENST00000274181.7	1	1	hg19	CCDS43299.1	.	.	.	.	.	.	.	.	.	.	G	10.82	1.458019	0.26161	.	.	ENSG00000145536	ENST00000274181;ENST00000536857	T	0.61274	0.12	5.73	2.91	0.33838	.	0.432157	0.23055	N	0.052451	T	0.45796	0.1360	L	0.52759	1.655	0.42913	D	0.994269	B;B	0.20550	0.046;0.021	B;B	0.12837	0.006;0.008	T	0.35351	-0.9792	10	0.49607	T	0.09	.	4.6802	0.12731	0.3127:0.152:0.5352:0.0	.	878;878	Q8TE57;Q8TE57-2	ATS16_HUMAN;.	H	878	ENSP00000274181:R878H	ENSP00000274181:R878H	R	+	2	0	ADAMTS16	5295275	0.049000	0.20398	0.169000	0.22859	0.931000	0.56810	1.271000	0.33098	0.328000	0.23435	0.644000	0.83932	CGC		TCGA-2J-AAB1-01A-11D-A40W-08	ADAMTS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365657.1	0	0	1	30	173	0	49	0	0	0	1	0	49	2		0	0	0	0	0	2	1	1.000000	29	170	0	49	2								-20.000000	1	1	121060	1	31	1	1	2	3	2.028143	0	0.380000	1.940000	0.381176	0.780000	5.400000e-01	1.000000	1.000000	0.786994	0.780000	0	0.650000	0.920000
SEMA5A	9037	broad.mit.edu	37	5	9197372	9197372	+	Missense_Mutation	SNP	C	C	T			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr5:9197372C>T	ENST00000382496.5	-	10	1641	c.976G>A	c.(976-978)Gcc>Acc	p.A326T		NM_003966.2	NP_003957.2	Q13591	SEM5A_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A			81					TGCGCGATGGCGCTCAGGTTG	0.597000																								0							SO:0001583	missense			ENST00000382496.5	1	1	hg19	CCDS3875.1	.	.	.	.	.	.	.	.	.	.	C	19.89	3.910739	0.72983	0.0	1.16E-4	ENSG00000112902	ENST00000382496	T	0.22539	1.95	5.35	4.48	0.54585	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.049884	0.85682	N	0.000000	T	0.34978	0.0916	L	0.43701	1.375	0.58432	D	0.999998	D	0.89917	1.0	D	0.73708	0.981	T	0.03017	-1.1082	10	0.34782	T	0.22	.	11.7948	0.52093	0.0:0.9145:0.0:0.0855	.	326	Q13591	SEM5A_HUMAN	T	326	ENSP00000371936:A326T	ENSP00000371936:A326T	A	-	1	0	SEMA5A	9250372	1.000000	0.71417	0.971000	0.41717	0.171000	0.22731	4.769000	0.62300	1.385000	0.46445	0.650000	0.86243	GCC		TCGA-2J-AAB1-01A-11D-A40W-08	SEMA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206989.2	1	0	1	55	391	0	97		0	0	0	0	97	2		0	0	0	0	0	2	1	1.000000	55	386	0	92	2								-19.983910	1	1	121412	1	35	1	1	2	3	2.028143	0	0.380000	1.940000	0.381176	0.640000	4.900000e-01	0.830000	0.640000	0.656748	0.640000	0	0.560000	0.740000
T	6862	broad.mit.edu	37	6	166574388	166574388	+	Missense_Mutation	SNP	C	C	A			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr6:166574388C>A	ENST00000296946.2	-	8	1439	c.971G>T	c.(970-972)gGa>gTa	p.G324V	T_ENST00000366871.3_Missense_Mutation_p.G266V	NM_003181.3	NP_003172.1	O15178	BRAC_HUMAN	T, brachyury homolog (mouse)			39		Prostate(117;4.48e-07)|Ovarian(120;1.78e-06)|Breast(66;2.54e-06)|Lung SC(201;0.0225)|Esophageal squamous(34;0.0559)			GGCAGGCATTCCAAGGCTGGA	0.522000									Chordoma, Familial Clustering of															0							SO:0001583	missense	Familial Cancer Database		ENST00000296946.2	0	1	hg19	CCDS5290.1	.	.	.	.	.	.	.	.	.	.	C	8.205	0.798999	0.16397	.	.	ENSG00000164458	ENST00000366876;ENST00000296946;ENST00000366871	D;D	0.83837	-1.75;-1.77	4.88	4.88	0.63580	.	0.142303	0.47852	D	0.000214	T	0.72179	0.3428	M	0.64997	1.995	0.58432	D	0.999998	P;P;P	0.37914	0.611;0.57;0.565	B;B;B	0.38106	0.265;0.142;0.146	T	0.73341	-0.4013	10	0.33141	T	0.24	.	10.9779	0.47478	0.0:0.9145:0.0:0.0855	.	266;324;266	E7ERD6;O15178;Q4KMP4	.;BRAC_HUMAN;.	V	324;324;266	ENSP00000296946:G324V;ENSP00000355836:G266V	ENSP00000296946:G324V	G	-	2	0	T	166494378	0.999000	0.42202	0.077000	0.20336	0.013000	0.08279	3.928000	0.56506	2.409000	0.81822	0.655000	0.94253	GGA		TCGA-2J-AAB1-01A-11D-A40W-08	T-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043037.2	0	0	0	9	313	0	52		0	0	0	0	52	2		0	0	0	0	0	2	1	0.994142	9	310	0	51	2								-2.858768	1	1	0	0		1	0	1	1	1.673221	1	0.380000	1.940000	0.252111	0.120000	5.000000e-02	0.220000	0.120000	0.133428	0.120000	0	0.080000	0.170000
EEF1A1	1915	broad.mit.edu	37	6	74227973	74227973	+	Missense_Mutation	SNP	G	G	T			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08			G	T	G	G		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr6:74227973G>T	ENST00000316292.9	-	6	2035	c.1044C>A	c.(1042-1044)aaC>aaA	p.N348K	EEF1A1_ENST00000331523.2_Missense_Mutation_p.N348K|EEF1A1_ENST00000309268.6_Missense_Mutation_p.N348K|EEF1A1_ENST00000491404.1_Intron	NM_001402.5	NP_001393.1	P68104	EF1A1_HUMAN	eukaryotic translation elongation factor 1 alpha 1			18					GGCCTGGATGGTTCAGGATAA	0.423000																								0							SO:0001583	missense			ENST00000316292.9	1	0	hg19	CCDS4980.1	.	.	.	.	.	.	.	.	.	.	G	13.71	2.319688	0.41096	.	.	ENSG00000156508	ENST00000316292;ENST00000358190;ENST00000309268;ENST00000331523;ENST00000391977	T;T;T	0.43688	0.94;0.94;0.94	4.71	3.84	0.44239	Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal (2);Translation elongation factor EFTu/EF1A, C-terminal (2);	0.000000	0.85682	U	0.000000	T	0.52354	0.1729	H	0.98866	4.355	0.80722	D	1	B;B;B	0.26483	0.027;0.027;0.15	B;B;B	0.30316	0.074;0.074;0.114	T	0.65533	-0.6145	10	0.87932	D	0	.	13.2814	0.60216	0.0779:0.0:0.9221:0.0	.	348;348;348	P68104;Q6IPS9;Q5VTE0	EF1A1_HUMAN;.;EF1A3_HUMAN	K	348;346;348;348;327	ENSP00000339063:N348K;ENSP00000339053:N348K;ENSP00000330054:N348K	ENSP00000339053:N348K	N	-	3	2	EEF1A1	74284694	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.738000	0.55067	1.107000	0.41642	0.556000	0.70494	AAC		TCGA-2J-AAB1-01A-11D-A40W-08	EEF1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041210.2	0	0	1	30	189	0	38	0	1	0	3972	0	38	2		0	0	0	0	0	2	1	1.000000	27	189	0	36	2								-1.194063	0	1	121368	961	47	1	0	1	1	1.673221	1	0.380000	1.940000	0.252111	0.590000	4.100000e-01	0.800000	0.590000	0.603762	0.590000	0	0.490000	0.700000
KCND2	3751	broad.mit.edu	37	7	119914985	119914985	+	Missense_Mutation	SNP	G	G	A			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr7:119914985G>A	ENST00000331113.4	+	1	1264	c.299G>A	c.(298-300)cGc>cAc	p.R100H		NM_012281.2	NP_036413.1	Q9NZV8	KCND2_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 2			75	all_neural(327;0.117)			Amitriptyline(DB00321)|Dalfampridine(DB06637)|Disopyramide(DB00280)|Imipramine(DB00458)	AATTTCTACCGCACTGGGAAG	0.522000																								0							SO:0001583	missense			ENST00000331113.4	0	1	hg19	CCDS5776.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.840334	0.91117	.	.	ENSG00000184408	ENST00000331113	T	0.55760	0.5	5.71	5.71	0.89125	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.000000	0.85682	D	0.000000	T	0.81669	0.4871	H	0.94808	3.585	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.86200	0.1618	9	.	.	.	.	19.8677	0.96824	0.0:0.0:1.0:0.0	.	100	Q9NZV8	KCND2_HUMAN	H	100	ENSP00000333496:R100H	.	R	+	2	0	KCND2	119702221	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	8.062000	0.89475	2.709000	0.92574	0.655000	0.94253	CGC		TCGA-2J-AAB1-01A-11D-A40W-08	KCND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346996.1	0	0	0	19	899	0	177	0	4.946053e-04	0	2	0	177	2		0	0	0	0	0	2	1	0.999988	20	878	0	172	2								-2.188806	0	1	0	0		1	1	2	3	2.111304	0	0.380000	1.940000	0.393821	0.110000	6.000000e-02	1.000000	0.110000	0.202197	0.110000	0	0.080000	0.160000
SSPO	23145	broad.mit.edu	37	7	149513539	149513539	+	RNA	SNP	G	G	A			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr7:149513539G>A	ENST00000378016.2	+	0	11160							A2VEC9	SSPO_HUMAN	SCO-spondin				Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)		CCCACGTCACGCAGCAGGTGG	0.692000																								0											ENST00000378016.2	0	1	hg19																																																																																					TCGA-2J-AAB1-01A-11D-A40W-08	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript		0	0	0	8	45	0	17	0	0	0	1	0	17	2		0	0	0	0	0	2	1	0.989769	8	43	0	17	2								-15.999350	1	1	117776	2	20	1	1	2	3	2.111304	0	0.380000	1.940000	0.393821	0.860000	4.100000e-01	1.000000	1.000000	0.824554	0.860000	1	0.600000	1.000000
USP42	84132	broad.mit.edu	37	7	6185257	6185257	+	Silent	SNP	C	C	T			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr7:6185257C>T	ENST00000306177.5	+	10	1259	c.1101C>T	c.(1099-1101)tgC>tgT	p.C367C		NM_032172.2	NP_115548.1	Q9H9J4	UBP42_HUMAN	ubiquitin specific peptidase 42			35		Ovarian(82;0.0423)			GTTTTAATTGCCATGCTGGCC	0.423000																								0							SO:0001819	synonymous_variant			ENST00000306177.5	0	1	hg19	CCDS47535.1																																																																																				TCGA-2J-AAB1-01A-11D-A40W-08	USP42-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324262.3	0	0	0	4	155	0	37	0	1.520467e-02	0	6	0	37	2		0	0	0	0	0	2	1	0.882168	4	150	0	36	2								-3.500347	1	1	120832	2	31	1	1	2	3	2.111304	0	0.380000	1.940000	0.393821	0.160000	4.000000e-02	1.000000	0.130000	0.246221	0.160000	0	0.090000	0.280000
EPB41L4B	54566	broad.mit.edu	37	9	111970268	111970268	+	Missense_Mutation	SNP	G	G	A			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr9:111970268G>A	ENST00000374566.3	-	18	2331	c.1814C>T	c.(1813-1815)gCg>gTg	p.A605V		NM_019114.3	NP_061987.3	Q9H329	E41LB_HUMAN	erythrocyte membrane protein band 4.1 like 4B			39					CACATGATCCGCAACAGGGGA	0.423000																								0							SO:0001583	missense			ENST00000374566.3	0	1	hg19	CCDS43859.1	.	.	.	.	.	.	.	.	.	.	G	15.03	2.711206	0.48517	0.0	4.86E-4	ENSG00000095203	ENST00000262536;ENST00000374566	D	0.84516	-1.86	5.49	5.49	0.81192	.	0.000000	0.39834	N	0.001248	T	0.78130	0.4235	N	0.22421	0.69	0.80722	D	1	B	0.22541	0.071	B	0.12156	0.007	T	0.75255	-0.3382	10	0.87932	D	0	.	16.9032	0.86118	0.0:0.0:1.0:0.0	.	605	Q9H329	E41LB_HUMAN	V	290;605	ENSP00000363694:A605V	ENSP00000262536:A290V	A	-	2	0	EPB41L4B	111010089	0.984000	0.35163	0.130000	0.21974	0.350000	0.29205	4.611000	0.61162	2.583000	0.87209	0.561000	0.74099	GCG		TCGA-2J-AAB1-01A-11D-A40W-08	EPB41L4B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053592.1	0	0	0	5	536	0	89		0	0	0	0	89	2		0	0	0	0	0	2	1	0.935959	5	530	0	89	2								-1.952813	0	1	120806	18	46	1	0	0	0	2.014026	0	0.380000	1.940000	0.377635	0.040000	1.000000e-02	0.110000	0.050000	0.057708	0.040000	0	0.020000	0.080000
KIF24	347240	broad.mit.edu	37	9	34256356	34256356	+	Missense_Mutation	SNP	C	C	G			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chr9:34256356C>G	ENST00000402558.2	-	10	3273	c.3249G>C	c.(3247-3249)gaG>gaC	p.E1083D	KIF24_ENST00000345050.2_Missense_Mutation_p.E949D|KIF24_ENST00000379166.2_Missense_Mutation_p.E1083D|KIF24_ENST00000379174.3_Missense_Mutation_p.E949D			Q5T7B8	KIF24_HUMAN	kinesin family member 24			32			LUSC - Lung squamous cell carcinoma(29;0.0107)		CCCCTGTGCTCTCTGCCACTA	0.602000																								0							SO:0001583	missense			ENST00000402558.2	1	1	hg19	CCDS6551.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.10|12.10	1.837588|1.837588	0.32513|0.32513	.|.	.|.	ENSG00000186638|ENSG00000186638	ENST00000402558;ENST00000379174;ENST00000379166;ENST00000345050;ENST00000420188|ENST00000443226	T;T;T;T|.	0.73152|.	-0.5;-0.72;-0.5;-0.72|.	4.71|4.71	-2.5|-2.5	0.06384|0.06384	.|.	0.770342|0.770342	0.11063|0.11063	N|N	0.603757|0.603757	T|T	0.30135|0.30135	0.0755|0.0755	L|L	0.39898|0.39898	1.24|1.24	0.09310|0.09310	N|N	1|1	B|.	0.06786|.	0.001|.	B|.	0.06405|.	0.002|.	T|T	0.34527|0.34527	-0.9825|-0.9825	10|7	0.40728|0.20046	T|T	0.16|0.44	.|.	6.1763|6.1763	0.20444|0.20444	0.123:0.3985:0.0:0.4785|0.123:0.3985:0.0:0.4785	.|.	1083|.	Q5T7B8|.	KIF24_HUMAN|.	D|Q	1083;949;1083;949;1083|129	ENSP00000384433:E1083D;ENSP00000368472:E949D;ENSP00000368464:E1083D;ENSP00000340179:E949D|.	ENSP00000340179:E949D|ENSP00000414628:E129Q	E|E	-|-	3|1	2|0	KIF24|KIF24	34246356|34246356	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.120000|0.120000	0.20174|0.20174	-0.917000|-0.917000	0.04025|0.04025	-0.108000|-0.108000	0.12066|0.12066	0.563000|0.563000	0.77884|0.77884	GAG|GAG		TCGA-2J-AAB1-01A-11D-A40W-08	KIF24-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052150.5	1	0	0	13	195	0	45	0	4.739336e-03	0	2	0	45	2		0	0	0	0	0	2	1	0.999558	13	193	0	45	2								-16.899190	1	1	0	0		1	0	2	2	2.027475	1	0.380000	1.940000	0.380000	0.330000	1.800000e-01	0.530000	0.320000	0.348125	0.330000	0	0.250000	0.430000
CUL4B	8450	broad.mit.edu	37	X	119674244	119674244	+	Missense_Mutation	SNP	A	A	C			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08			A	C	A	A		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chrX:119674244A>C	ENST00000404115.3	-	13	2072	c.1671T>G	c.(1669-1671)aaT>aaG	p.N557K	CUL4B_ENST00000336592.6_Missense_Mutation_p.N544K|CUL4B_ENST00000371322.5_Missense_Mutation_p.N539K	NM_003588.3	NP_003579.3	Q13620	CUL4B_HUMAN	cullin 4B			36					CAGCTGGTTTATTTGGTCTTT	0.308000																								0							SO:0001583	missense			ENST00000404115.3	1	1	hg19	CCDS35379.1	.	.	.	.	.	.	.	.	.	.	A	11.67	1.707788	0.30322	.	.	ENSG00000158290	ENST00000371322;ENST00000336592;ENST00000404115	T;T;T	0.73363	-0.74;-0.74;-0.74	5.6	2.54	0.30619	Cullin, N-terminal (1);Cullin repeat-like-containing domain (1);Cullin homology (1);	0.000000	0.85682	D	0.000000	D	0.84088	0.5395	M	0.83118	2.625	0.58432	D	0.999999	P;D;D	0.89917	0.535;1.0;1.0	B;D;D	0.83275	0.398;0.996;0.993	T	0.82067	-0.0641	9	.	.	.	-17.2501	7.9584	0.30057	0.5235:0.0:0.4765:0.0	.	361;557;539	Q13620-3;Q13620;Q13620-1	.;CUL4B_HUMAN;.	K	539;544;557	ENSP00000360373:N539K;ENSP00000338919:N544K;ENSP00000384109:N557K	.	N	-	3	2	CUL4B	119558272	1.000000	0.71417	1.000000	0.80357	0.233000	0.25261	1.401000	0.34589	0.413000	0.25759	-0.509000	0.04479	AAT		TCGA-2J-AAB1-01A-11D-A40W-08	CUL4B-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058103.1	1	0	1	44	87	0	14	1	9.999798e-01	23	15	0	14	2		0	0	0	0	0	2	1	1.000000	44	86	0	14	2								-20.000000	1	1	0	0		1	0	1	1			0.380000	1.940000	0.380000	0.850000	6.600000e-01	0.990000	0.870000	0.853511	0.850000	1	0.750000	0.940000
BMX	660	broad.mit.edu	37	X	15526493	15526493	+	Missense_Mutation	SNP	T	T	C			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chrX:15526493T>C	ENST00000357607.2	+	2	205	c.17T>C	c.(16-18)aTt>aCt	p.I6T	BMX_ENST00000463891.1_Intron|BMX_ENST00000342014.6_Missense_Mutation_p.I6T|BMX_ENST00000348343.6_Missense_Mutation_p.I6T			P51813	BMX_HUMAN	BMX non-receptor tyrosine kinase			30	Hepatocellular(33;0.183)				ACAAAATCTATTCTAGAAGAA	0.294000																								0							SO:0001583	missense			ENST00000357607.2	0	1	hg19	CCDS14168.1	.	.	.	.	.	.	.	.	.	.	T	18.97	3.735041	0.69189	.	.	ENSG00000102010	ENST00000357607;ENST00000348343;ENST00000342014	D;D;D	0.94232	-3.38;-3.38;-3.38	5.67	5.67	0.87782	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.097450	0.44483	D	0.000449	D	0.95169	0.8434	M	0.79926	2.475	0.37061	D	0.89808	P	0.50819	0.939	P	0.53988	0.739	D	0.96917	0.9671	10	0.87932	D	0	.	11.1504	0.48455	0.0:0.0:0.0:1.0	.	6	P51813	BMX_HUMAN	T	6	ENSP00000350224:I6T;ENSP00000308774:I6T;ENSP00000340082:I6T	ENSP00000340082:I6T	I	+	2	0	BMX	15436414	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	5.182000	0.65059	1.904000	0.55121	0.486000	0.48141	ATT		TCGA-2J-AAB1-01A-11D-A40W-08	BMX-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055877.1	0	0	0	6	236	0	38	0	1.741371e-02	0	7	0	38	2		0	0	0	0	0	2	1	0.962730	6	230	0	38	2								-7.588117	1	1	0	0		1	0	1	1			0.380000	1.940000	0.380000	0.060000	2.000000e-02	0.130000	0.070000	0.074981	0.060000	0	0.040000	0.100000
OGT	8473	broad.mit.edu	37	X	70757810	70757810	+	Missense_Mutation	SNP	G	G	A			TCGA-2J-AAB1-01A-11D-A40W-08	TCGA-2J-AAB1-10A-01D-A40W-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	3654586b-e1d2-42e7-8560-b339bd5e3488	8a1fecb6-04f4-413a-bed8-63fce4ac7072	g.chrX:70757810G>A	ENST00000373719.3	+	3	567	c.350G>A	c.(349-351)cGt>cAt	p.R117H	OGT_ENST00000373701.3_Missense_Mutation_p.R107H|OGT_ENST00000498566.1_3'UTR	NM_181672.2|NM_181673.2	NP_858058.1|NP_858059.1	O15294	OGT1_HUMAN	O-linked N-acetylglucosamine (GlcNAc) transferase	p.R117H(1)|p.R107H(1)		43	Renal(35;0.156)				CATGCATTGCGTCTCAAACCT	0.493000																								2	Substitution - Missense(2)						SO:0001583	missense			ENST00000373719.3	1	1	hg19	CCDS14414.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	20.1|20.1	3.937205|3.937205	0.73557|0.73557	.|.	.|.	ENSG00000147162|ENSG00000147162	ENST00000373719;ENST00000373701;ENST00000444774|ENST00000455587	T;T;T|.	0.60920|.	0.15;0.15;0.15|.	4.86|4.86	4.86|4.86	0.63082|0.63082	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);|.	0.105470|.	0.64402|.	D|.	0.000011|.	T|T	0.73297|0.73297	0.3569|0.3569	M|M	0.66560|0.66560	2.04|2.04	0.80722|0.80722	D|D	1|1	D;D;B|.	0.71674|.	0.998;0.997;0.369|.	D;P;B|.	0.64042|.	0.921;0.832;0.045|.	T|T	0.73275|0.73275	-0.4034|-0.4034	10|5	0.46703|.	T|.	0.11|.	-19.0221|-19.0221	17.2684|17.2684	0.87093|0.87093	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	117;107;117|.	B4DTL6;O15294-3;O15294|.	.;.;OGT1_HUMAN|.	H|I	117;107;100|77	ENSP00000362824:R117H;ENSP00000362805:R107H;ENSP00000399729:R100H|.	ENSP00000362805:R107H|.	R|V	+|+	2|1	0|0	OGT|OGT	70674535|70674535	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	9.502000|9.502000	0.97981|0.97981	2.259000|2.259000	0.74868|0.74868	0.525000|0.525000	0.51046|0.51046	CGT|GTC		TCGA-2J-AAB1-01A-11D-A40W-08	OGT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000081829.3	1	0	1	75	106	0	30	1	9.999572e-01	11	15	0	30	2		0	0	0	0	0	2	1	1.000000	74	105	0	29	2								-20.000000	1	1	0	0		1	0	1	1			0.380000	1.940000	0.380000	0.950000	8.400000e-01	1.000000	0.990000	0.952522	0.950000	1	0.900000	0.990000
