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
UBA2	10054	broad.mit.edu	37	19	34921468	34921485	+	Splice_Site	DEL	TATGCATTTGTAGATTGA	TATGCATTTGTAGATTGA	-	rs146650320	byFrequency	TCGA-3A-A9I7-01A-21D-A38G-08	TCGA-3A-A9I7-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b47f6bb9-23ad-4f47-bb37-b232b97a1ddc	c1a3fec7-91d6-4675-9cc3-398269c967c6	g.chr19:34921468_34921485delTATGCATTTGTAGATTGA	ENST00000246548.4	+	2	208_213	c.138_143delTATGCATTTGTAGATTGA	c.(136-144)cttatgcat>ctt	p.MH47del	CTD-2588C8.8_ENST00000592220.1_RNA|UBA2_ENST00000439527.2_5'UTR	NM_005499.2	NP_005490.1	Q9UBT2	SAE2_HUMAN	ubiquitin-like modifier activating enzyme 2			20	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.211)		ATCTGGGGTTTATGCATTTGTAGATTGATCTGGATACT	0.362000																								0							SO:0001630	splice_region_variant			ENST00000246548.4	1	1	hg19	CCDS12439.1																																																																																				TCGA-3A-A9I7-01A-21D-A38G-08	UBA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459257.3	0	0	0	9	416	0	138	0	4.468751e-01	0	66	0	138	2	0	0	0	0	0	0		0	0.101270	11	406	2	140	16	0	0	0	0	0	0		-8.537428	1	1	0	0		1	0	0	0	1.997096	0	0.190000	1.940000	0.182231	0.220000	0.110000	0.400000	0.210000	0.241604	0.220000	0	0.160000	0.310000
SLC18A3	6572	broad.mit.edu	37	10	50819671	50819671	+	Silent	SNP	C	C	T			TCGA-3A-A9I7-01A-21D-A38G-08	TCGA-3A-A9I7-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b47f6bb9-23ad-4f47-bb37-b232b97a1ddc	c1a3fec7-91d6-4675-9cc3-398269c967c6	g.chr10:50819671C>T	ENST00000374115.3	+	1	1325	c.885C>T	c.(883-885)gcC>gcT	p.A295A	CHAT_ENST00000337653.2_5'Flank|CHAT_ENST00000455728.2_5'Flank|CHAT_ENST00000395559.2_5'Flank|CHAT_ENST00000395562.2_5'Flank|CHAT_ENST00000339797.1_Intron|CHAT_ENST00000351556.3_5'Flank	NM_003055.2	NP_003046.2	Q16572	VACHT_HUMAN	solute carrier family 18 (vesicular acetylcholine transporter), member 3	p.A295A(1)		43					CCGTGGTGGCCGGCGCGCTCA	0.642000																								1	Substitution - coding silent(1)						SO:0001819	synonymous_variant			ENST00000374115.3	0	1	hg19	CCDS7231.1																																																																																				TCGA-3A-A9I7-01A-21D-A38G-08	SLC18A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047995.1	0	0	0	6	317	0	128	0	3.037911e-03	0	4	0	128	2		0	0	0	0	0	2	1	0.962192	6	308	0	124	2		0	0	0	0	128	2	-3.386138	1	1	0	0		1	0	0	0	1.997220	0	0.190000	1.940000	0.182231	0.200000	0.080000	0.390000	0.190000	0.221455	0.200000	0	0.130000	0.300000
OVOL1	5017	broad.mit.edu	37	11	65554913	65554913	+	Silent	SNP	C	C	G			TCGA-3A-A9I7-01A-21D-A38G-08	TCGA-3A-A9I7-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b47f6bb9-23ad-4f47-bb37-b232b97a1ddc	c1a3fec7-91d6-4675-9cc3-398269c967c6	g.chr11:65554913C>G	ENST00000335987.3	+	1	421	c.69C>G	c.(67-69)ccC>ccG	p.P23P	RP11-770G2.4_ENST00000532454.1_RNA|RP11-770G2.4_ENST00000534178.1_RNA|RP11-770G2.4_ENST00000527453.1_RNA	NM_004561.3	NP_004552.2	O14753	OVOL1_HUMAN	ovo-like zinc finger 1			6					GCGAGCTCCCCGACGAGGAGC	0.721000																								0							SO:0001819	synonymous_variant			ENST00000335987.3	0	1	hg19	CCDS8112.1																																																																																				TCGA-3A-A9I7-01A-21D-A38G-08	OVOL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390690.1	0	0	0	5	39	0	13	0	8.959754e-01	0	35	0	13	2		0	0	0	0	0	2	1	0.941401	5	39	0	13	2		0	0	0	0	13	2	-10.609310	1	1	0	0		1	1	2	3	2.017652	0	0.190000	1.940000	0.193829	0.990000	0.480000	1.000000	1.000000	0.924650	0.990000	1	0.780000	1.000000
KRAS	3845	broad.mit.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	C	T	rs121913529		TCGA-3A-A9I7-01A-21D-A38G-08	TCGA-3A-A9I7-10A-01D-A38J-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	KRAS_deep			Illumina GAIIx	b47f6bb9-23ad-4f47-bb37-b232b97a1ddc	c1a3fec7-91d6-4675-9cc3-398269c967c6	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-3A-A9I7-01A-21D-A38G-08	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	1	0	0	23	295	0	111	1	5.773374e-01	4	22	0	111	2	1	9.999999e-01	21	347	0	199	2	1	0.999999	22	285	0	111	2	1	1	643	7367	0	111	2	-7.665470	1	1	121404	2	44	1	0	1	1	2.010853	0	0.190000	1.940000	0.186910	0.750000	0.490000	1.000000	1.000000	0.769312	0.750000	0	0.610000	0.920000
CACNA1C	775	broad.mit.edu	37	12	2797804	2797804	+	Silent	SNP	C	C	T			TCGA-3A-A9I7-01A-21D-A38G-08	TCGA-3A-A9I7-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b47f6bb9-23ad-4f47-bb37-b232b97a1ddc	c1a3fec7-91d6-4675-9cc3-398269c967c6	g.chr12:2797804C>T	ENST00000347598.4	+	48	6120	c.6120C>T	c.(6118-6120)tgC>tgT	p.C2040C	CACNA1C_ENST00000399637.1_Silent_p.C2011C|CACNA1C_ENST00000399644.1_Silent_p.C1992C|CACNA1C_ENST00000399603.1_Silent_p.C1992C|CACNA1C-AS1_ENST00000541673.1_RNA|CACNA1C_ENST00000327702.7_Silent_p.C2027C|CACNA1C_ENST00000399641.1_Silent_p.C1992C|CACNA1C_ENST00000399655.1_Silent_p.C1992C|CACNA1C_ENST00000399597.1_Silent_p.C1992C|CACNA1C_ENST00000399617.1_Silent_p.C2027C|CACNA1C_ENST00000402845.3_Silent_p.C2011C|CACNA1C_ENST00000399638.1_Silent_p.C2020C|CACNA1C_ENST00000399591.1_Silent_p.C2000C|CACNA1C_ENST00000399634.1_Silent_p.C2063C|CACNA1C_ENST00000399629.1_Silent_p.C2009C|CACNA1C_ENST00000399606.1_Silent_p.C2012C|CACNA1C_ENST00000399621.1_Silent_p.C2011C|CACNA1C_ENST00000335762.5_Silent_p.C2017C|CACNA1C-AS1_ENST00000501371.1_RNA|CACNA1C_ENST00000399649.1_Silent_p.C1998C|CACNA1C-AS1_ENST00000544517.1_RNA|CACNA1C_ENST00000344100.3_Silent_p.C2033C|CACNA1C_ENST00000399601.1_Silent_p.C1992C|CACNA1C_ENST00000399595.1_Silent_p.C2000C|CACNA1C_ENST00000406454.3_Silent_p.C2063C	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit			132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	CCATCCACTGCGGCTCCTGGG	0.721000																								0							SO:0001819	synonymous_variant			ENST00000347598.4	0	1	hg19	CCDS44788.1																																																																																				TCGA-3A-A9I7-01A-21D-A38G-08	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	0	0	0	6	456	1	174	0	3.943564e-02	0	46	1	174	3		0	0	0	0	0	2	0	0.148409	6	443	1	173	11		0	0	0	1	174	2	-3.213351	1	1	120860	4	37	1	0	1	1	2.010853	0	0.190000	1.940000	0.186910	0.140000	0.050000	0.280000	0.140000	0.156714	0.140000	0	0.090000	0.210000
PTHLH	5744	broad.mit.edu	37	12	28116383	28116383	+	Missense_Mutation	SNP	C	C	T			TCGA-3A-A9I7-01A-21D-A38G-08	TCGA-3A-A9I7-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b47f6bb9-23ad-4f47-bb37-b232b97a1ddc	c1a3fec7-91d6-4675-9cc3-398269c967c6	g.chr12:28116383C>T	ENST00000545234.1	-	5	962	c.422G>A	c.(421-423)cGg>cAg	p.R141Q	PTHLH_ENST00000395868.3_Missense_Mutation_p.R141Q|RP11-993B23.3_ENST00000538113.1_RNA|PTHLH_ENST00000201015.4_Missense_Mutation_p.R141Q|PTHLH_ENST00000395872.1_Missense_Mutation_p.R141Q|PTHLH_ENST00000354417.3_Missense_Mutation_p.R141Q|PTHLH_ENST00000535992.1_Missense_Mutation_p.R141Q|PTHLH_ENST00000539239.1_Missense_Mutation_p.R141Q|PTHLH_ENST00000538310.1_Missense_Mutation_p.R141Q			P12272	PTHR_HUMAN	parathyroid hormone-like hormone			10	Lung SC(9;0.184)				GCGAGTTCGCCGTTTTTTCTT	0.542000																								0							SO:0001583	missense			ENST00000545234.1	1	1	hg19	CCDS44853.1	.	.	.	.	.	.	.	.	.	.	C	31	5.072552	0.93950	.	.	ENSG00000087494	ENST00000395872;ENST00000539239;ENST00000545234;ENST00000538310;ENST00000354417;ENST00000201015;ENST00000535992;ENST00000395868;ENST00000542963	D;D;D;D;D;D;D;D;D	0.92199	-2.88;-2.88;-2.88;-2.99;-2.99;-2.87;-2.87;-2.87;-2.85	5.63	5.63	0.86233	.	0.053580	0.64402	D	0.000001	D	0.95589	0.8566	M	0.66939	2.045	0.42178	D	0.991676	D	0.76494	0.999	D	0.72625	0.978	D	0.95866	0.8887	10	0.87932	D	0	-14.8282	18.6479	0.91418	0.0:1.0:0.0:0.0	.	141	P12272	PTHR_HUMAN	Q	141	ENSP00000379213:R141Q;ENSP00000441571:R141Q;ENSP00000441765:R141Q;ENSP00000441890:R141Q;ENSP00000346398:R141Q;ENSP00000201015:R141Q;ENSP00000440613:R141Q;ENSP00000379209:R141Q;ENSP00000444519:R141Q	ENSP00000201015:R141Q	R	-	2	0	PTHLH	28007650	1.000000	0.71417	0.887000	0.34795	0.994000	0.84299	4.979000	0.63806	2.657000	0.90304	0.591000	0.81541	CGG		TCGA-3A-A9I7-01A-21D-A38G-08	PTHLH-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402913.1	1	0	0	27	414	0	146	1	9.156306e-01	4	63	0	146	2		0	0	0	0	0	2	1	1.000000	25	400	0	146	2		0	0	0	0	146	2	-2.774692	1	1	0	0		1	0	1	1	2.010853	0	0.190000	1.940000	0.186910	0.640000	0.430000	0.890000	0.630000	0.656007	0.640000	0	0.530000	0.770000
PDZRN4	29951	broad.mit.edu	37	12	41966629	41966629	+	Missense_Mutation	SNP	T	T	A			TCGA-3A-A9I7-01A-21D-A38G-08	TCGA-3A-A9I7-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b47f6bb9-23ad-4f47-bb37-b232b97a1ddc	c1a3fec7-91d6-4675-9cc3-398269c967c6	g.chr12:41966629T>A	ENST00000402685.2	+	10	2056	c.2048T>A	c.(2047-2049)aTc>aAc	p.I683N	PDZRN4_ENST00000539469.2_Missense_Mutation_p.I425N|PDZRN4_ENST00000298919.7_Missense_Mutation_p.I423N	NM_001164595.1	NP_001158067.1	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing ring finger 4			77	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)			TGTCAGAATATCATGCAGGCT	0.448000																								0							SO:0001583	missense			ENST00000402685.2	0	1	hg19	CCDS53777.1	.	.	.	.	.	.	.	.	.	.	T	18.67	3.672946	0.67928	.	.	ENSG00000165966	ENST00000402685;ENST00000539469;ENST00000298919	D;T;T	0.81499	-1.5;3.01;3.0	4.64	4.64	0.57946	.	0.151474	0.45126	D	0.000400	D	0.88880	0.6557	M	0.76170	2.325	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.87578	0.998;0.997;0.996	D	0.90408	0.4407	10	0.87932	D	0	-34.5847	14.7814	0.69769	0.0:0.0:0.0:1.0	.	683;423;425	Q6ZMN7;Q6ZMN7-4;Q6ZMN7-2	PZRN4_HUMAN;.;.	N	683;425;423	ENSP00000384197:I683N;ENSP00000439990:I425N;ENSP00000298919:I423N	ENSP00000298919:I423N	I	+	2	0	PDZRN4	40252896	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.997000	0.88414	2.049000	0.60858	0.528000	0.53228	ATC		TCGA-3A-A9I7-01A-21D-A38G-08	PDZRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403701.1	1	0	0	8	245	0	103	0	7.808217e-03	0	4	0	103	2		0	0	0	0	0	2	1	0.989521	8	244	0	100	2		0	0	0	0	103	2	-9.891595	1	1	0	0		1	0	1	1	2.010853	0	0.190000	1.940000	0.186910	0.340000	0.160000	0.610000	0.330000	0.363764	0.340000	0	0.240000	0.480000
RAD51AP1	10635	broad.mit.edu	37	12	4653066	4653066	+	Missense_Mutation	SNP	A	A	G			TCGA-3A-A9I7-01A-21D-A38G-08	TCGA-3A-A9I7-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b47f6bb9-23ad-4f47-bb37-b232b97a1ddc	c1a3fec7-91d6-4675-9cc3-398269c967c6	g.chr12:4653066A>G	ENST00000544927.1	+	3	215	c.205A>G	c.(205-207)Aaa>Gaa	p.K69E	RAD51AP1_ENST00000543041.1_5'UTR|RAD51AP1_ENST00000228843.9_Missense_Mutation_p.K69E|RAD51AP1_ENST00000321524.7_Missense_Mutation_p.K69E|RAD51AP1_ENST00000352618.4_Missense_Mutation_p.K69E					RAD51 associated protein 1			13			Colorectal(7;0.00306)|COAD - Colon adenocarcinoma(12;0.0389)		AACCCCTAAAAAAAGGTGAGA	0.353000																								0							SO:0001583	missense			ENST00000544927.1	0	1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	15.02|15.02	2.708549|2.708549	0.48517|0.48517	.|.	.|.	ENSG00000111247|ENSG00000111247	ENST00000321524;ENST00000228843;ENST00000352618;ENST00000544927|ENST00000536117	T;T;T;T|T	0.32988|0.34072	1.43;1.43;1.43;1.43|1.38	5.06|5.06	5.06|5.06	0.68205|0.68205	.|.	0.120167|0.120167	0.51477|0.51477	D|N	0.000083|0.000083	T|T	0.45054|0.45054	0.1323|0.1323	M|M	0.75264|0.75264	2.295|2.295	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.85130|.	0.994;0.997|.	T|T	0.37979|0.37979	-0.9682|-0.9682	10|8	0.52906|0.20046	T|T	0.07|0.44	-19.6144|-19.6144	7.6299|7.6299	0.28232|0.28232	0.9038:0.0:0.0962:0.0|0.9038:0.0:0.0962:0.0	.|.	69;69|.	Q96B01;Q96B01-2|.	R51A1_HUMAN;.|.	E|R	69|63	ENSP00000323750:K69E;ENSP00000228843:K69E;ENSP00000309479:K69E;ENSP00000446296:K69E|ENSP00000444769:K63R	ENSP00000228843:K69E|ENSP00000444769:K63R	K|K	+|+	1|2	0|0	RAD51AP1|RAD51AP1	4523327|4523327	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.964000|0.964000	0.63967|0.63967	3.552000|3.552000	0.53705|0.53705	1.884000|1.884000	0.54569|0.54569	0.477000|0.477000	0.44152|0.44152	AAA|AAA		TCGA-3A-A9I7-01A-21D-A38G-08	RAD51AP1-012	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000399208.1	0	0	0	5	250	0	78	0	8.748650e-03	0	6	0	78	2		0	0	0	0	0	2	1	0.932782	5	242	0	75	2		0	0	0	0	78	2	-7.157501	1	1	0	0		1	0	1	1	2.010853	0	0.190000	1.940000	0.186910	0.220000	0.080000	0.440000	0.200000	0.240657	0.220000	0	0.140000	0.330000
RPTOR	57521	broad.mit.edu	37	17	78923328	78923328	+	Missense_Mutation	SNP	C	C	G			TCGA-3A-A9I7-01A-21D-A38G-08	TCGA-3A-A9I7-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b47f6bb9-23ad-4f47-bb37-b232b97a1ddc	c1a3fec7-91d6-4675-9cc3-398269c967c6	g.chr17:78923328C>G	ENST00000306801.3	+	28	3713	c.3351C>G	c.(3349-3351)gaC>gaG	p.D1117E	RPTOR_ENST00000575542.1_3'UTR|RPTOR_ENST00000544334.2_Missense_Mutation_p.D959E	NM_020761.2	NP_065812.1	Q8N122	RPTOR_HUMAN	regulatory associated protein of MTOR, complex 1			44					GGCTCTCGGACATGCTGCCAA	0.617000																								0							SO:0001583	missense			ENST00000306801.3	1	1	hg19	CCDS11773.1	.	.	.	.	.	.	.	.	.	.	C	12.19	1.862663	0.32884	.	.	ENSG00000141564	ENST00000306801;ENST00000544334	T;T	0.48836	0.82;0.8	4.73	4.73	0.59995	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.56062	0.1960	L	0.39566	1.225	0.80722	D	1	D;B	0.61697	0.99;0.031	D;B	0.73380	0.98;0.01	T	0.52079	-0.8623	10	0.33940	T	0.23	.	11.2536	0.49041	0.0:0.9153:0.0:0.0847	.	959;1117	F5H7J5;Q8N122	.;RPTOR_HUMAN	E	1117;959	ENSP00000307272:D1117E;ENSP00000442479:D959E	ENSP00000307272:D1117E	D	+	3	2	RPTOR	76537923	1.000000	0.71417	1.000000	0.80357	0.831000	0.47069	4.572000	0.60886	2.182000	0.69389	0.462000	0.41574	GAC		TCGA-3A-A9I7-01A-21D-A38G-08	RPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438125.1	1	0	0	34	637	0	264	1	5.716883e-01	2	35	0	264	2		0	0	0	0	0	2	1	1.000000	34	624	0	260	2		0	0	0	0	264	2	-5.988357	1	1	121412	1	34	1	1	2	3	2.028173	0	0.190000	1.940000	0.196110	0.540000	0.380000	1.000000	0.540000	0.577291	0.540000	0	0.450000	0.670000
APCDD1	147495	broad.mit.edu	37	18	10485496	10485496	+	Missense_Mutation	SNP	A	A	G			TCGA-3A-A9I7-01A-21D-A38G-08	TCGA-3A-A9I7-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b47f6bb9-23ad-4f47-bb37-b232b97a1ddc	c1a3fec7-91d6-4675-9cc3-398269c967c6	g.chr18:10485496A>G	ENST00000355285.5	+	4	1166	c.812A>G	c.(811-813)tAt>tGt	p.Y271C	APCDD1_ENST00000578882.1_Intron	NM_153000.4	NP_694545.1			adenomatosis polyposis coli down-regulated 1			22					CGGATCATCTATCGGTCAGAC	0.602000																								0							SO:0001583	missense			ENST00000355285.5	1	1	hg19	CCDS11849.1	.	.	.	.	.	.	.	.	.	.	A	12.44	1.937161	0.34189	.	.	ENSG00000154856	ENST00000355285;ENST00000423585	T	0.18016	2.24	4.9	2.39	0.29439	.	0.373449	0.31872	N	0.006924	T	0.25865	0.0630	L	0.54323	1.7	0.80722	D	1	P	0.49307	0.922	P	0.54346	0.749	T	0.00719	-1.1595	10	0.48119	T	0.1	-27.5474	9.1807	0.37141	0.5802:0.0:0.0:0.4198	.	271	Q8J025	APCD1_HUMAN	C	271;322	ENSP00000347433:Y271C	ENSP00000347433:Y271C	Y	+	2	0	APCDD1	10475496	1.000000	0.71417	0.991000	0.47740	0.873000	0.50193	2.380000	0.44327	0.314000	0.23086	0.454000	0.30748	TAT		TCGA-3A-A9I7-01A-21D-A38G-08	APCDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254529.2	1	0	0	26	493	0	172	0	9.810225e-01	0	122	0	172	2		0	0	0	0	0	2	1	1.000000	26	479	0	171	2		0	0	0	0	172	2	-20.000000	1	1	121412	8	44	1	0	0	0	1.930840	0	0.190000	1.940000	0.152985	0.500000	0.330000	0.700000	0.500000	0.516116	0.500000	0	0.410000	0.610000
C18orf8	29919	broad.mit.edu	37	18	21110072	21110072	+	Silent	SNP	C	C	T			TCGA-3A-A9I7-01A-21D-A38G-08	TCGA-3A-A9I7-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b47f6bb9-23ad-4f47-bb37-b232b97a1ddc	c1a3fec7-91d6-4675-9cc3-398269c967c6	g.chr18:21110072C>T	ENST00000269221.3	+	17	1685	c.1575C>T	c.(1573-1575)caC>caT	p.H525H	C18orf8_ENST00000590868.1_Silent_p.H477H|C18orf8_ENST00000591367.1_3'UTR	NM_013326.3	NP_037458.3	Q96DM3	MIC1_HUMAN	chromosome 18 open reading frame 8			21	all_cancers(21;0.000122)|all_epithelial(16;8.08e-07)|Lung NSC(20;0.00206)|all_lung(20;0.00659)|Colorectal(14;0.0202)|Ovarian(20;0.127)				TGCAGTACCACGTCCTCAGCG	0.393000																								0							SO:0001819	synonymous_variant			ENST00000269221.3	1	1	hg19	CCDS32803.1																																																																																				TCGA-3A-A9I7-01A-21D-A38G-08	C18orf8-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445386.1	0	0	0	38	1561	0	539	1	7.483041e-01	7	105	0	539	2		0	0	0	0	0	2	1	1.000000	38	1535	0	531	2		0	0	0	0	539	2	-2.914844	1	1	121412	2	36	1	0	0	0	1.930840	0	0.190000	1.940000	0.152985	0.230000	0.160000	0.320000	0.240000	0.244364	0.230000	0	0.200000	0.280000
ZNF521	25925	broad.mit.edu	37	18	22806967	22806967	+	Silent	SNP	G	G	A			TCGA-3A-A9I7-01A-21D-A38G-08	TCGA-3A-A9I7-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b47f6bb9-23ad-4f47-bb37-b232b97a1ddc	c1a3fec7-91d6-4675-9cc3-398269c967c6	g.chr18:22806967G>A	ENST00000361524.3	-	4	1063	c.915C>T	c.(913-915)agC>agT	p.S305S	ZNF521_ENST00000538137.2_Silent_p.S305S|ZNF521_ENST00000579111.1_5'Flank|ZNF521_ENST00000584787.1_Silent_p.S85S	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521			149	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)				TCTTCTCCCCGCTATGCACCT	0.547000			T	PAX5	ALL										Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	0							SO:0001819	synonymous_variant			ENST00000361524.3	1	1	hg19	CCDS32806.1																																																																																				TCGA-3A-A9I7-01A-21D-A38G-08	ZNF521-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446781.2	0	0	0	8	242	0	95	0	1.254137e-01	0	17	0	95	2		0	0	0	0	0	2	1	0.989172	8	240	0	94	2		0	0	0	0	95	2	-3.433661	1	1	121412	3	33	1	0	0	0	1.930840	0	0.190000	1.940000	0.152985	0.330000	0.150000	0.590000	0.320000	0.351580	0.330000	0	0.230000	0.460000
ZNF763	284390	broad.mit.edu	37	19	12088187	12088187	+	Splice_Site	SNP	G	G	A			TCGA-3A-A9I7-01A-21D-A38G-08	TCGA-3A-A9I7-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b47f6bb9-23ad-4f47-bb37-b232b97a1ddc	c1a3fec7-91d6-4675-9cc3-398269c967c6	g.chr19:12088187G>A	ENST00000358987.3	+	3	259	c.132G>A	c.(130-132)ggG>ggA	p.G44G	ZNF763_ENST00000592625.1_Intron|ZNF763_ENST00000343949.5_Splice_Site_p.G47G|ZNF763_ENST00000538752.1_Splice_Site_p.G64G|ZNF763_ENST00000591944.1_Intron|ZNF763_ENST00000545530.1_Intron|ZNF763_ENST00000590798.1_Splice_Site_p.G64G			Q0D2J5	ZN763_HUMAN	zinc finger protein 763			15					GTATTTTAGGGAAAAAGTGGA	0.353000																								0							SO:0001630	splice_region_variant			ENST00000358987.3	0	1	hg19																																																																																					TCGA-3A-A9I7-01A-21D-A38G-08	ZNF763-002	KNOWN	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000344158.1	0	0	0	6	439	0	119	1	5.492939e-03	2	5	0	119	2		0	0	0	0	0	2	1	0.962674	5	430	0	119	2		0	0	0	0	119	2	-2.522364	1	0	121396	3	38	1	0	0	0	1.997096	0	0.190000	1.940000	0.182231	0.140000	0.050000	0.290000	0.140000	0.161630	0.140000	0	0.090000	0.220000
RYR1	6261	broad.mit.edu	37	19	38958285	38958285	+	Missense_Mutation	SNP	C	C	T			TCGA-3A-A9I7-01A-21D-A38G-08	TCGA-3A-A9I7-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b47f6bb9-23ad-4f47-bb37-b232b97a1ddc	c1a3fec7-91d6-4675-9cc3-398269c967c6	g.chr19:38958285C>T	ENST00000359596.3	+	25	3214	c.3214C>T	c.(3214-3216)Cgc>Tgc	p.R1072C	RYR1_ENST00000360985.3_Missense_Mutation_p.R1072C|RYR1_ENST00000355481.4_Missense_Mutation_p.R1072C			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	p.R1072C(1)		285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)	Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	TGACCGGGTGCGCATCTTCCG	0.572000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000359596.3	1	1	hg19	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	c	11.60	1.686114	0.29962	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.97688	-4.49;-4.49;-4.49	2.92	2.92	0.33932	B30.2/SPRY domain (1);	0.000000	0.64402	U	0.000016	D	0.98604	0.9533	M	0.85462	2.755	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	D	0.99053	1.0828	10	0.87932	D	0	.	14.736	0.69416	0.0:1.0:0.0:0.0	.	1072;1072	P21817-2;P21817	.;RYR1_HUMAN	C	1072	ENSP00000352608:R1072C;ENSP00000347667:R1072C;ENSP00000354254:R1072C	ENSP00000347667:R1072C	R	+	1	0	RYR1	43650125	1.000000	0.71417	1.000000	0.80357	0.604000	0.37047	5.533000	0.67160	1.966000	0.57179	0.154000	0.16183	CGC		TCGA-3A-A9I7-01A-21D-A38G-08	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1	1	0	0	21	505	0	168		0	0	0	0	168	2		0	0	0	0	0	2	1	0.999997	20	495	0	168	2		0	0	0	0	168	2	-3.565176	1	1	0	0		1	0	0	0	1.997096	0	0.190000	1.940000	0.182231	0.410000	0.260000	0.610000	0.410000	0.430731	0.410000	0	0.330000	0.520000
ANKRD24	170961	broad.mit.edu	37	19	4217177	4217177	+	Missense_Mutation	SNP	G	G	A			TCGA-3A-A9I7-01A-21D-A38G-08	TCGA-3A-A9I7-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b47f6bb9-23ad-4f47-bb37-b232b97a1ddc	c1a3fec7-91d6-4675-9cc3-398269c967c6	g.chr19:4217177G>A	ENST00000600132.1	+	18	2296	c.2020G>A	c.(2020-2022)Gcc>Acc	p.A674T	ANKRD24_ENST00000318934.4_Missense_Mutation_p.A674T|ANKRD24_ENST00000262970.5_Missense_Mutation_p.A764T	NM_133475.1	NP_597732.1	Q8TF21	ANR24_HUMAN	ankyrin repeat domain 24			21					AAACATGGAGGCCACGGGCTC	0.612000																								0							SO:0001583	missense			ENST00000600132.1	1	1	hg19	CCDS45925.1	.	.	.	.	.	.	.	.	.	.	g	13.81	2.347909	0.41599	.	.	ENSG00000089847	ENST00000318934;ENST00000262970	T;T	0.39229	1.12;1.09	2.05	0.887	0.19200	.	.	.	.	.	T	0.24353	0.0590	N	0.19112	0.55	0.22975	N	0.998482	P;D	0.53885	0.937;0.963	B;B	0.41174	0.143;0.349	T	0.12091	-1.0561	9	0.24483	T	0.36	.	8.2537	0.31741	0.0:0.0:0.7599:0.2401	.	674;764	Q8TF21;Q8TF21-2	ANR24_HUMAN;.	T	674;764	ENSP00000321731:A674T;ENSP00000262970:A764T	ENSP00000262970:A764T	A	+	1	0	ANKRD24	4168177	0.032000	0.19561	0.033000	0.17914	0.010000	0.07245	0.256000	0.18351	0.156000	0.19299	0.407000	0.27541	GCC		TCGA-3A-A9I7-01A-21D-A38G-08	ANKRD24-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458188.1	1	0	0	6	85	0	43	0	1.800383e-02	0	3	0	43	2		0	0	0	0	0	2	1	0.965491	6	84	0	43	2		0	0	0	0	43	2	-10.653140	1	1	0	0		1	0	0	0	1.998454	0	0.190000	1.940000	0.182231	0.700000	0.300000	1.000000	1.000000	0.715797	0.700000	0	0.470000	1.000000
NAPSA	9476	broad.mit.edu	37	19	50861863	50861863	+	Missense_Mutation	SNP	G	G	A			TCGA-3A-A9I7-01A-21D-A38G-08	TCGA-3A-A9I7-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b47f6bb9-23ad-4f47-bb37-b232b97a1ddc	c1a3fec7-91d6-4675-9cc3-398269c967c6	g.chr19:50861863G>A	ENST00000253719.2	-	9	1418	c.1210C>T	c.(1210-1212)Cgc>Tgc	p.R404C	NR1H2_ENST00000542413.1_Intron|NR1H2_ENST00000600978.1_Intron	NM_004851.1	NP_004842.1	O96009	NAPSA_HUMAN	napsin A aspartic peptidase			12		all_neural(266;0.057)			TCCGCTCCGCGAGTGCGAGCG	0.697000																								0							SO:0001583	missense			ENST00000253719.2	0	1	hg19	CCDS12794.1	.	.	.	.	.	.	.	.	.	.	G	15.62	2.887283	0.52014	.	.	ENSG00000131400	ENST00000253719	T	0.52983	0.64	3.38	2.31	0.28768	.	0.766391	0.11657	N	0.542216	T	0.39886	0.1095	L	0.38175	1.15	0.09310	N	1	D	0.56968	0.978	P	0.44477	0.451	T	0.20672	-1.0268	10	0.72032	D	0.01	.	9.1465	0.36937	0.0:0.2257:0.7743:0.0	.	404	O96009	NAPSA_HUMAN	C	404	ENSP00000253719:R404C	ENSP00000253719:R404C	R	-	1	0	NAPSA	55553675	0.002000	0.14202	0.002000	0.10522	0.002000	0.02628	1.090000	0.30902	0.688000	0.31529	-0.463000	0.05309	CGC		TCGA-3A-A9I7-01A-21D-A38G-08	NAPSA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464714.1	1	0	0	6	102	0	23	0	2.466787e-02	0	4	0	23	2		0	0	0	0	0	2	1	0.966380	6	102	0	23	2		0	0	0	0	23	2	-9.841152	1	1	0	0		1	0	1	1	2.007665	0	0.190000	1.940000	0.186910	0.600000	0.250000	1.000000	1.000000	0.630029	0.600000	0	0.400000	0.860000
HDLBP	3069	broad.mit.edu	37	2	242189325	242189325	+	Silent	SNP	G	G	A			TCGA-3A-A9I7-01A-21D-A38G-08	TCGA-3A-A9I7-10A-01D-A38J-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	b47f6bb9-23ad-4f47-bb37-b232b97a1ddc	c1a3fec7-91d6-4675-9cc3-398269c967c6	g.chr2:242189325G>A	ENST00000391975.1	-	12	1670	c.1443C>T	c.(1441-1443)atC>atT	p.I481I	HDLBP_ENST00000427183.2_Silent_p.I448I|HDLBP_ENST00000310931.4_Silent_p.I481I|HDLBP_ENST00000391976.2_Silent_p.I481I|HDLBP_ENST00000476807.1_5'UTR	NM_203346.3	NP_976221	Q00341	VIGLN_HUMAN	high density lipoprotein binding protein			44		all_cancers(19;7.77e-41)|all_epithelial(40;1.74e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.0121)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)			CCTCGATGCGGATCAAATTGC	0.537000																								0							SO:0001819	synonymous_variant			ENST00000391975.1	1	1	hg19	CCDS2547.1	.	.	.	.	.	.	.	.	.	.	G	11.05	1.524353	0.27299	.	.	ENSG00000115677	ENST00000373292	.	.	.	5.76	1.91	0.25777	.	.	.	.	.	T	0.56992	0.2023	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47947	-0.9077	4	.	.	.	-25.3058	8.197	0.31402	0.1831:0.1146:0.7023:0.0	.	.	.	.	S	290	.	.	P	-	1	0	HDLBP	241837998	1.000000	0.71417	0.846000	0.33378	0.958000	0.62258	3.394000	0.52551	0.140000	0.18849	-0.136000	0.14681	CCG		TCGA-3A-A9I7-01A-21D-A38G-08	HDLBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257245.5	1	0	0	30	503	0	171	1	1	51	462	0	171	2		0	0	0	0	0	2	1	1.000000	29	497	0	170	2		0	0	0	0	171	2	-5.951295	1	1	0	0		1	1	2	3	2.020873	0	0.190000	1.940000	0.194591	0.600000	0.410000	1.000000	0.590000	0.627012	0.600000	0	0.500000	0.740000
TMCC1	23023	broad.mit.edu	37	3	129370592	129370592	+	Missense_Mutation	SNP	T	T	A			TCGA-3A-A9I7-01A-21D-A38G-08	TCGA-3A-A9I7-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b47f6bb9-23ad-4f47-bb37-b232b97a1ddc	c1a3fec7-91d6-4675-9cc3-398269c967c6	g.chr3:129370592T>A	ENST00000393238.3	-	6	2034	c.1694A>T	c.(1693-1695)cAg>cTg	p.Q565L	TMCC1_ENST00000329333.5_Missense_Mutation_p.Q386L|TMCC1_ENST00000426664.2_Missense_Mutation_p.Q451L|TMCC1_ENST00000432054.2_Missense_Mutation_p.Q241L	NM_001017395.3	NP_001017395.2	O94876	TMCC1_HUMAN	transmembrane and coiled-coil domain family 1		PLXND1/TMCC1(4)	25					CTGCTGCTGCTGCAGCTCCAT	0.572000																								0							SO:0001583	missense			ENST00000393238.3	0	1	hg19	CCDS33855.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.009576	0.75046	.	.	ENSG00000172765	ENST00000432054;ENST00000393238;ENST00000426664;ENST00000329333	T;T;T;T	0.50001	0.76;0.76;0.76;0.76	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	T	0.61261	0.2333	L	0.46614	1.455	0.80722	D	1	D;D	0.67145	0.996;0.985	D;D	0.85130	0.997;0.973	T	0.58278	-0.7664	10	0.33940	T	0.23	-18.4911	15.1509	0.72696	0.0:0.0:0.0:1.0	.	386;565	B4DE04;O94876	.;TMCC1_HUMAN	L	241;565;451;386	ENSP00000404711:Q241L;ENSP00000376930:Q565L;ENSP00000389892:Q451L;ENSP00000327349:Q386L	ENSP00000327349:Q386L	Q	-	2	0	TMCC1	130853282	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.735000	0.84939	2.172000	0.68678	0.533000	0.62120	CAG		TCGA-3A-A9I7-01A-21D-A38G-08	TMCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356418.2	0	0	0	5	364	0	103	0	1.053546e-01	0	33	0	103	2		0	0	0	0	0	2	1	0.939690	4	369	0	105	2		0	0	0	0	103	2	-2.086188	0	1	0	0		1	1	2	3	2.021783	0	0.190000	1.940000	0.194591	0.150000	0.050000	1.000000	0.140000	0.208306	0.150000	0	0.090000	0.250000
C3orf20	84077	broad.mit.edu	37	3	14813595	14813595	+	Missense_Mutation	SNP	C	C	A			TCGA-3A-A9I7-01A-21D-A38G-08	TCGA-3A-A9I7-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b47f6bb9-23ad-4f47-bb37-b232b97a1ddc	c1a3fec7-91d6-4675-9cc3-398269c967c6	g.chr3:14813595C>A	ENST00000253697.3	+	16	2969	c.2517C>A	c.(2515-2517)agC>agA	p.S839R	C3orf20_ENST00000435614.1_Missense_Mutation_p.S717R|C3orf20_ENST00000412910.1_Missense_Mutation_p.S717R	NM_032137.4	NP_115513.4	Q8ND61	CC020_HUMAN	chromosome 3 open reading frame 20			40					CTGTCCTGAGCCTGGAGGATT	0.572000																								0							SO:0001583	missense			ENST00000253697.3	0	1	hg19	CCDS33706.1	.	.	.	.	.	.	.	.	.	.	C	10.78	1.445678	0.25987	.	.	ENSG00000131379	ENST00000253697;ENST00000435614;ENST00000412910	T;T;T	0.08546	3.37;3.08;3.08	2.95	2.95	0.34219	.	0.876695	0.09658	N	0.772847	T	0.08044	0.0201	N	0.19112	0.55	0.09310	N	1	P;P	0.39157	0.662;0.662	B;B	0.42422	0.387;0.387	T	0.32613	-0.9900	10	0.51188	T	0.08	-2.1017	9.6058	0.39632	0.0:1.0:0.0:0.0	.	717;839	Q8ND61-2;Q8ND61	.;CC020_HUMAN	R	839;717;717	ENSP00000253697:S839R;ENSP00000402933:S717R;ENSP00000396081:S717R	ENSP00000253697:S839R	S	+	3	2	C3orf20	14788599	0.012000	0.17670	0.029000	0.17559	0.038000	0.13279	1.422000	0.34826	1.957000	0.56846	0.491000	0.48974	AGC		TCGA-3A-A9I7-01A-21D-A38G-08	C3orf20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340586.1	0	0	0	5	198	0	81		0	0	0	0	81	2		0	0	0	0	0	2	1	0.935855	5	195	0	81	2		0	0	0	0	81	2	-6.672548	1	1	0	0		1	0	1	1	1.915776	0	0.190000	1.940000	0.141039	0.260000	0.090000	0.520000	0.240000	0.281852	0.260000	0	0.160000	0.390000
OXSM	54995	broad.mit.edu	37	3	25832597	25832597	+	Missense_Mutation	SNP	G	G	T			TCGA-3A-A9I7-01A-21D-A38G-08	TCGA-3A-A9I7-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b47f6bb9-23ad-4f47-bb37-b232b97a1ddc	c1a3fec7-91d6-4675-9cc3-398269c967c6	g.chr3:25832597G>T	ENST00000280701.3	+	2	185	c.86G>T	c.(85-87)aGg>aTg	p.R29M	OXSM_ENST00000420173.2_Missense_Mutation_p.R29M|OXSM_ENST00000449808.1_3'UTR|NGLY1_ENST00000417874.2_5'Flank	NM_017897.2	NP_060367.1	Q9NWU1	OXSM_HUMAN	3-oxoacyl-ACP synthase, mitochondrial			25					AGAAGTAAAAGGAAGTTTTTC	0.403000																								0							SO:0001583	missense			ENST00000280701.3	1	1	hg19	CCDS2643.1	.	.	.	.	.	.	.	.	.	.	G	2.156	-0.393253	0.04899	.	.	ENSG00000151093	ENST00000452098;ENST00000280701;ENST00000420173;ENST00000428266	.	.	.	3.7	0.885	0.19188	.	1.235100	0.05357	N	0.533001	T	0.19087	0.0458	N	0.08118	0	0.09310	N	1	P;B	0.41848	0.763;0.327	B;B	0.43360	0.417;0.087	T	0.20505	-1.0273	9	0.72032	D	0.01	-0.3908	4.2462	0.10672	0.3102:0.1799:0.5099:0.0	.	29;29	Q9NWU1-2;Q9NWU1	.;OXSM_HUMAN	M	29	.	ENSP00000280701:R29M	R	+	2	0	OXSM	25807601	0.003000	0.15002	0.002000	0.10522	0.296000	0.27459	0.424000	0.21330	0.548000	0.28955	0.561000	0.74099	AGG		TCGA-3A-A9I7-01A-21D-A38G-08	OXSM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252876.2	0	0	0	19	691	0	257	1	1.764381e-01	2	25	0	257	2		0	0	0	0	0	2	1	0.999989	19	679	0	254	2		0	0	0	0	257	2	-2.472598	0	1	0	0		1	0	1	1	1.915776	0	0.190000	1.940000	0.141039	0.260000	0.160000	0.400000	0.260000	0.276440	0.260000	0	0.210000	0.330000
ANK2	287	broad.mit.edu	37	4	114280346	114280346	+	Silent	SNP	C	C	T			TCGA-3A-A9I7-01A-21D-A38G-08	TCGA-3A-A9I7-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b47f6bb9-23ad-4f47-bb37-b232b97a1ddc	c1a3fec7-91d6-4675-9cc3-398269c967c6	g.chr4:114280346C>T	ENST00000357077.4	+	38	10625	c.10572C>T	c.(10570-10572)acC>acT	p.T3524T	ANK2_ENST00000264366.6_Silent_p.T3491T|ANK2_ENST00000509550.1_Intron|ANK2_ENST00000394537.3_Intron|ANK2_ENST00000506722.1_Intron|ANK2_ENST00000510275.2_Intron	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal			248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)			CTGTTGAGACCGAGCACTCAG	0.473000																								0							SO:0001819	synonymous_variant			ENST00000357077.4	0	1	hg19	CCDS3702.1																																																																																				TCGA-3A-A9I7-01A-21D-A38G-08	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	0	0	0	9	453	0	128	0	9.824809e-03	0	7	0	128	2		0	0	0	0	0	2	1	0.993840	10	444	0	127	2		0	0	0	0	128	2	-2.248747	0	1	121410	2	34	1	0	0	0	1.968363	0	0.190000	1.940000	0.169486	0.200000	0.090000	0.360000	0.200000	0.218914	0.200000	0	0.140000	0.280000
TRPC3	7222	broad.mit.edu	37	4	122835976	122835976	+	Missense_Mutation	SNP	G	G	T			TCGA-3A-A9I7-01A-21D-A38G-08	TCGA-3A-A9I7-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b47f6bb9-23ad-4f47-bb37-b232b97a1ddc	c1a3fec7-91d6-4675-9cc3-398269c967c6	g.chr4:122835976G>T	ENST00000379645.3	-	4	1373	c.1300C>A	c.(1300-1302)Cca>Aca	p.P434T	TRPC3_ENST00000264811.5_Missense_Mutation_p.P361T|TRPC3_ENST00000513531.1_Intron	NM_001130698.1	NP_001124170.1	Q13507	TRPC3_HUMAN	transient receptor potential cation channel, subfamily C, member 3			51					GCCAGGAATGGAAGGCCCAGG	0.522000																								0							SO:0001583	missense			ENST00000379645.3	0	1	hg19	CCDS47130.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.778659	0.90195	.	.	ENSG00000138741	ENST00000264811;ENST00000379645	T;T	0.76578	-1.03;-1.03	5.5	5.5	0.81552	.	0.000000	0.64402	D	0.000001	D	0.91432	0.7296	M	0.93638	3.44	0.80722	D	1	D;D	0.69078	0.996;0.997	D;D	0.72982	0.979;0.964	D	0.93272	0.6652	10	0.87932	D	0	-29.0106	19.3937	0.94596	0.0:0.0:1.0:0.0	.	349;434	Q13507;Q5G1L5	TRPC3_HUMAN;.	T	361;434	ENSP00000264811:P361T;ENSP00000368966:P434T	ENSP00000264811:P361T	P	-	1	0	TRPC3	123055426	1.000000	0.71417	0.939000	0.37840	0.922000	0.55478	9.753000	0.98904	2.586000	0.87340	0.655000	0.94253	CCA		TCGA-3A-A9I7-01A-21D-A38G-08	TRPC3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364252.1	0	0	0	4	193	0	71	0	0	0	1	0	71	2		0	0	0	0	0	2	1	0.890033	4	192	0	71	2		0	0	0	0	71	2	-6.000074	1	1	0	0		1	0	0	0	1.968363	0	0.190000	1.940000	0.169486	0.220000	0.070000	0.480000	0.210000	0.251563	0.220000	0	0.130000	0.350000
DDX60	55601	broad.mit.edu	37	4	169206628	169206628	+	Missense_Mutation	SNP	G	G	C			TCGA-3A-A9I7-01A-21D-A38G-08	TCGA-3A-A9I7-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b47f6bb9-23ad-4f47-bb37-b232b97a1ddc	c1a3fec7-91d6-4675-9cc3-398269c967c6	g.chr4:169206628G>C	ENST00000393743.3	-	11	1652	c.1361C>G	c.(1360-1362)cCc>cGc	p.P454R		NM_017631.5	NP_060101.3	Q8IY21	DDX60_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60			63		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)			ACCCAAATTGGGCACCATTTC	0.318000																								0							SO:0001583	missense			ENST00000393743.3	1	1	hg19	CCDS34097.1	.	.	.	.	.	.	.	.	.	.	G	10.77	1.443929	0.25987	.	.	ENSG00000137628	ENST00000393743	T	0.19394	2.15	4.53	3.66	0.41972	.	0.430135	0.22084	N	0.064857	T	0.41534	0.1163	M	0.77820	2.39	0.19300	N	0.999977	D	0.71674	0.998	D	0.65684	0.937	T	0.19128	-1.0315	10	0.56958	D	0.05	.	8.3075	0.32051	0.0845:0.0:0.7589:0.1567	.	454	Q8IY21	DDX60_HUMAN	R	454	ENSP00000377344:P454R	ENSP00000377344:P454R	P	-	2	0	DDX60	169443203	0.330000	0.24705	0.051000	0.19133	0.249000	0.25844	2.143000	0.42187	0.972000	0.38314	0.557000	0.71058	CCC		TCGA-3A-A9I7-01A-21D-A38G-08	DDX60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364622.1	0	0	0	13	379	0	112	1	2.239919e-01	4	21	0	112	2		0	0	0	0	0	2	1	0.999478	13	370	0	111	2		0	0	0	0	112	2	-3.227303	1	1	0	0		1	0	0	0	1.968363	0	0.190000	1.940000	0.169486	0.340000	0.190000	0.550000	0.330000	0.360245	0.340000	0	0.260000	0.450000
SLC27A6	28965	broad.mit.edu	37	5	128326140	128326140	+	Missense_Mutation	SNP	C	C	T			TCGA-3A-A9I7-01A-21D-A38G-08	TCGA-3A-A9I7-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b47f6bb9-23ad-4f47-bb37-b232b97a1ddc	c1a3fec7-91d6-4675-9cc3-398269c967c6	g.chr5:128326140C>T	ENST00000262462.4	+	4	1962	c.952C>T	c.(952-954)Ctt>Ttt	p.L318F	SLC27A6_ENST00000506176.1_Missense_Mutation_p.L318F|SLC27A6_ENST00000395266.1_Missense_Mutation_p.L318F			Q9Y2P4	S27A6_HUMAN	solute carrier family 27 (fatty acid transporter), member 6			44		all_cancers(142;0.0483)|Prostate(80;0.055)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		TTGTCGCTACCTTTGCAAACA	0.318000																								0							SO:0001583	missense			ENST00000262462.4	0	1	hg19	CCDS4145.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.001462	0.74818	.	.	ENSG00000113396	ENST00000508645;ENST00000262462;ENST00000395266;ENST00000506176	T;T;T;T	0.56103	0.48;0.48;0.48;0.48	4.59	4.59	0.56863	AMP-dependent synthetase/ligase (1);	0.000000	0.85682	D	0.000000	T	0.81800	0.4899	H	0.98426	4.23	0.54753	D	0.999985	D	0.89917	1.0	D	0.97110	1.0	D	0.86944	0.2081	9	.	.	.	-0.0674	12.1173	0.53872	0.0:0.9204:0.0:0.0796	.	318	Q9Y2P4	S27A6_HUMAN	F	137;318;318;318	ENSP00000421759:L137F;ENSP00000262462:L318F;ENSP00000378684:L318F;ENSP00000421024:L318F	.	L	+	1	0	SLC27A6	128354039	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.144000	0.42197	2.835000	0.97688	0.650000	0.86243	CTT		TCGA-3A-A9I7-01A-21D-A38G-08	SLC27A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250980.1	0	0	0	8	202	1	84	0	1.115611e-02	0	4	1	84	2		0	0	0	0	0	2	0	0.389000	8	199	1	82	10		0	0	0	1	84	2	-3.170455	1	1	0	0		1	0	0	0	1.968272	0	0.190000	1.940000	0.169486	0.400000	0.190000	0.710000	0.380000	0.425672	0.400000	0	0.280000	0.560000
CDHR2	54825	broad.mit.edu	37	5	176003131	176003131	+	Missense_Mutation	SNP	C	C	T			TCGA-3A-A9I7-01A-21D-A38G-08	TCGA-3A-A9I7-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b47f6bb9-23ad-4f47-bb37-b232b97a1ddc	c1a3fec7-91d6-4675-9cc3-398269c967c6	g.chr5:176003131C>T	ENST00000510636.1	+	12	1413	c.1139C>T	c.(1138-1140)gCc>gTc	p.A380V	CDHR2_ENST00000506348.1_Missense_Mutation_p.A380V|CDHR2_ENST00000261944.5_Missense_Mutation_p.A380V	NM_001171976.1	NP_001165447.1	Q9BYE9	CDHR2_HUMAN	cadherin-related family member 2			56					GACGAGCATGCCTCCCCCCGC	0.632000																								0							SO:0001583	missense			ENST00000510636.1	0	1	hg19	CCDS34297.1	.	.	.	.	.	.	.	.	.	.	C	9.075	0.997877	0.19043	.	.	ENSG00000074276	ENST00000510636;ENST00000261944;ENST00000506348	T;T;T	0.61392	0.11;0.11;0.11	4.54	3.68	0.42216	Cadherin (2);Cadherin-like (1);	.	.	.	.	T	0.49898	0.1584	L	0.56124	1.755	0.19945	N	0.999946	B	0.10296	0.003	B	0.10450	0.005	T	0.36335	-0.9752	9	0.18276	T	0.48	-16.43	10.4136	0.44307	0.0:0.9088:0.0:0.0912	.	380	Q9BYE9	CDHR2_HUMAN	V	380	ENSP00000424565:A380V;ENSP00000261944:A380V;ENSP00000421078:A380V	ENSP00000261944:A380V	A	+	2	0	CDHR2	175935737	0.673000	0.27539	0.192000	0.23308	0.160000	0.22226	1.965000	0.40471	1.136000	0.42199	0.549000	0.68633	GCC		TCGA-3A-A9I7-01A-21D-A38G-08	CDHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372201.1	0	0	0	5	296	0	111	0	9.891107e-01	1	527	0	111	2		0	0	0	0	0	2	1	0.935835	5	292	0	111	2		0	0	0	0	111	2	-4.018525	1	0	121412	1	26	1	0	0	0	1.958322	0	0.190000	1.940000	0.164604	0.180000	0.060000	0.370000	0.170000	0.198709	0.180000	0	0.110000	0.270000
CDH18	1016	broad.mit.edu	37	5	19612555	19612555	+	Missense_Mutation	SNP	G	G	A			TCGA-3A-A9I7-01A-21D-A38G-08	TCGA-3A-A9I7-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b47f6bb9-23ad-4f47-bb37-b232b97a1ddc	c1a3fec7-91d6-4675-9cc3-398269c967c6	g.chr5:19612555G>A	ENST00000507958.1	-	8	1789	c.799C>T	c.(799-801)Cgc>Tgc	p.R267C	CDH18_ENST00000506372.1_Missense_Mutation_p.R267C|CDH18_ENST00000274170.4_Missense_Mutation_p.R267C|CDH18_ENST00000382275.1_Missense_Mutation_p.R267C|CDH18_ENST00000511273.1_Missense_Mutation_p.R267C|CDH18_ENST00000502796.1_Missense_Mutation_p.R267C			Q13634	CAD18_HUMAN	cadherin 18, type 2			138	Lung NSC(1;0.00734)|all_lung(1;0.0197)				TGAGGAAAGCGTGGTGGGTTG	0.378000																								0							SO:0001583	missense			ENST00000507958.1	1	1	hg19	CCDS3889.1	.	.	.	.	.	.	.	.	.	.	G	13.49	2.252883	0.39797	.	.	ENSG00000145526	ENST00000382275;ENST00000507958;ENST00000542864;ENST00000274170;ENST00000506372;ENST00000502796;ENST00000515257;ENST00000511273	T;T;T;T;T;T;T	0.39229	1.09;1.09;1.09;1.09;1.09;1.09;1.09	5.95	0.216	0.15258	Cadherin (3);Cadherin-like (1);	0.101818	0.64402	D	0.000006	T	0.52597	0.1744	L	0.52573	1.65	0.22017	N	0.99941	D;P	0.76494	0.999;0.591	P;B	0.61275	0.886;0.109	T	0.55477	-0.8135	9	.	.	.	.	16.4031	0.83649	0.0:0.0:0.3577:0.6423	.	267;267	B4DHG6;Q13634	.;CAD18_HUMAN	C	267;267;267;267;267;267;213;267	ENSP00000371710:R267C;ENSP00000425093:R267C;ENSP00000274170:R267C;ENSP00000424931:R267C;ENSP00000422138:R267C;ENSP00000427383:R213C;ENSP00000425854:R267C	.	R	-	1	0	CDH18	19648312	0.325000	0.24660	0.889000	0.34880	0.102000	0.19082	1.230000	0.32612	0.088000	0.17205	0.563000	0.77884	CGC		TCGA-3A-A9I7-01A-21D-A38G-08	CDH18-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366747.1	0	0	0	10	331	0	156		0	0	0	0	156	2		0	0	0	0	0	2	1	0.996552	10	322	0	153	2		0	0	0	0	156	2	-3.665638	1	1	0	0		1	0	0	0	1.963604	0	0.190000	1.940000	0.167865	0.300000	0.150000	0.520000	0.300000	0.323836	0.300000	0	0.220000	0.410000
HLA-DMB	3109	broad.mit.edu	37	6	32906460	32906460	+	Splice_Site	SNP	C	C	T			TCGA-3A-A9I7-01A-21D-A38G-08	TCGA-3A-A9I7-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b47f6bb9-23ad-4f47-bb37-b232b97a1ddc	c1a3fec7-91d6-4675-9cc3-398269c967c6	g.chr6:32906460C>T	ENST00000418107.2	-	2	600		c.e2+1		AL645941.1_ENST00000390777.1_RNA|XXbac-BPG181M17.5_ENST00000429234.1_Splice_Site|HLA-DMB_ENST00000416244.2_Splice_Site	NM_002118.4	NP_002109.2	P28068	DMB_HUMAN	major histocompatibility complex, class II, DM beta			13					TCTCTCCTCACGTGTCCTGTT	0.582000																								0							SO:0001630	splice_region_variant			ENST00000418107.2	0	1	hg19	CCDS4760.1	.	.	.	.	.	.	.	.	.	.	C	16.60	3.169133	0.57584	.	.	ENSG00000242574;ENSG00000242574;ENSG00000242574;ENSG00000242574;ENSG00000248993	ENST00000414017;ENST00000446948;ENST00000418107;ENST00000416244;ENST00000429234	.	.	.	5.07	5.07	0.68467	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.823	0.63333	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	XXbac-BPG181M17.5;HLA-DMB	33014438	1.000000	0.71417	0.998000	0.56505	0.876000	0.50452	2.081000	0.41596	2.631000	0.89168	0.637000	0.83480	.		TCGA-3A-A9I7-01A-21D-A38G-08	HLA-DMB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076340.2	0	0	0	7	287	1	122	0	7.655348e-03	0	5	1	122	2		0	0	0	0	0	2	1	0.979983	7	283	0	119	2		0	0	0	1	122	2	-3.197101	1	1	0	0		1	0	0	0	1.956820	0	0.190000	1.940000	0.164604	0.250000	0.110000	0.460000	0.240000	0.271101	0.250000	0	0.170000	0.360000
ZNF318	24149	broad.mit.edu	37	6	43307934	43307934	+	Missense_Mutation	SNP	G	G	C			TCGA-3A-A9I7-01A-21D-A38G-08	TCGA-3A-A9I7-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b47f6bb9-23ad-4f47-bb37-b232b97a1ddc	c1a3fec7-91d6-4675-9cc3-398269c967c6	g.chr6:43307934G>C	ENST00000361428.2	-	10	3879	c.3802C>G	c.(3802-3804)Cca>Gca	p.P1268A	ZNF318_ENST00000318149.3_Intron	NM_014345.2	NP_055160.2	Q5VUA4	ZN318_HUMAN	zinc finger protein 318			61			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0171)|OV - Ovarian serous cystadenocarcinoma(102;0.0579)		GATGATGTTGGTGATTCCTTC	0.403000																								0							SO:0001583	missense			ENST00000361428.2	1	1	hg19	CCDS4895.2	.	.	.	.	.	.	.	.	.	.	G	9.057	0.993512	0.19043	.	.	ENSG00000171467	ENST00000361428	T	0.46063	0.88	5.16	3.37	0.38596	.	0.468764	0.19877	N	0.104057	T	0.12305	0.0299	N	0.19112	0.55	0.19300	N	0.999976	B	0.33171	0.4	B	0.33960	0.173	T	0.07654	-1.0761	10	0.56958	D	0.05	-0.0185	8.6041	0.33762	0.1777:0.0:0.8223:0.0	.	1268	Q5VUA4	ZN318_HUMAN	A	1268	ENSP00000354964:P1268A	ENSP00000354964:P1268A	P	-	1	0	ZNF318	43415912	0.336000	0.24757	0.270000	0.24601	0.907000	0.53573	0.707000	0.25704	0.740000	0.32651	0.655000	0.94253	CCA		TCGA-3A-A9I7-01A-21D-A38G-08	ZNF318-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040601.2	0	0	0	20	820	0	285	0	1.634064e-02	0	8	0	285	2		0	0	0	0	0	2	1	0.999994	19	806	0	284	2		0	0	0	0	285	2	-15.061600	1	1	0	0		1	0	0	0	1.956820	0	0.190000	1.940000	0.164604	0.240000	0.150000	0.360000	0.240000	0.253016	0.240000	0	0.190000	0.310000
DENND2A	27147	broad.mit.edu	37	7	140301961	140301961	+	Silent	SNP	C	C	T			TCGA-3A-A9I7-01A-21D-A38G-08	TCGA-3A-A9I7-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b47f6bb9-23ad-4f47-bb37-b232b97a1ddc	c1a3fec7-91d6-4675-9cc3-398269c967c6	g.chr7:140301961C>T	ENST00000275884.6	-	2	654	c.237G>A	c.(235-237)acG>acA	p.T79T	DENND2A_ENST00000492720.1_Silent_p.T79T|DENND2A_ENST00000496613.1_Silent_p.T79T|DENND2A_ENST00000537639.1_Silent_p.T79T			Q9ULE3	DEN2A_HUMAN	DENN/MADD domain containing 2A			49	Melanoma(164;0.00956)				TCCTCTCCACCGTAGAGGACG	0.522000																								0							SO:0001819	synonymous_variant			ENST00000275884.6	1	1	hg19	CCDS43659.1																																																																																				TCGA-3A-A9I7-01A-21D-A38G-08	DENND2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348742.1	1	0	0	38	543	0	188	0	3.960872e-02	0	5	0	188	2		0	0	0	0	1	2	1	1.000000	38	533	0	183	2		0	0	0	0	188	2	-2.619822	1	1	0	0		1	2	3	5	2.201802	1	0.190000	1.940000	0.257698	0.790000	0.550000	1.000000	0.740000	0.812610	0.790000	0	0.650000	1.000000
RADIL	55698	broad.mit.edu	37	7	4917411	4917411	+	Silent	SNP	G	G	A			TCGA-3A-A9I7-01A-21D-A38G-08	TCGA-3A-A9I7-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b47f6bb9-23ad-4f47-bb37-b232b97a1ddc	c1a3fec7-91d6-4675-9cc3-398269c967c6	g.chr7:4917411G>A	ENST00000399583.3	-	2	547	c.360C>T	c.(358-360)ggC>ggT	p.G120G	RADIL_ENST00000536091.1_Silent_p.G120G	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains			41		Ovarian(82;0.0175)			GCCCAGCATCGCCGGCTTGGC	0.647000																								0							SO:0001819	synonymous_variant			ENST00000399583.3	1	1	hg19	CCDS43544.1																																																																																				TCGA-3A-A9I7-01A-21D-A38G-08	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	1	0	0	21	364	0	156	0	3.369829e-03	0	2	0	156	2		0	0	0	0	0	2	1	0.999997	20	357	0	154	2		0	0	0	0	156	2	-5.527357	1	1	120946	3	38	1	1	2	3	2.051472	0	0.190000	1.940000	0.200632	0.600000	0.370000	1.000000	0.580000	0.644606	0.600000	0	0.480000	0.810000
ARHGEF10	9639	broad.mit.edu	37	8	1841800	1841800	+	Silent	SNP	G	G	A			TCGA-3A-A9I7-01A-21D-A38G-08	TCGA-3A-A9I7-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b47f6bb9-23ad-4f47-bb37-b232b97a1ddc	c1a3fec7-91d6-4675-9cc3-398269c967c6	g.chr8:1841800G>A	ENST00000398564.1	+	12	1323	c.1323G>A	c.(1321-1323)aaG>aaA	p.K441K	ARHGEF10_ENST00000520359.1_Silent_p.K378K|ARHGEF10_ENST00000518288.1_Silent_p.K441K|ARHGEF10_ENST00000349830.3_Silent_p.K416K|ARHGEF10_ENST00000398560.1_Silent_p.K402K|ARHGEF10_ENST00000262112.6_Silent_p.K441K			O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10			35		Colorectal(14;3.46e-05)|Renal(68;0.000518)|Ovarian(12;0.00409)|Myeloproliferative disorder(644;0.0255)|Hepatocellular(245;0.0834)			ATGCTCTTAAGAGGATTTTGG	0.313000																								0							SO:0001819	synonymous_variant			ENST00000398564.1	1	1	hg19																																																																																					TCGA-3A-A9I7-01A-21D-A38G-08	ARHGEF10-203	KNOWN	basic	protein_coding	protein_coding		1	0	0	19	321	0	89	0	3.268954e-01	1	19	0	89	2		0	0	0	0	0	2	1	0.999990	19	316	0	88	2		0	0	0	0	89	2	-3.223548	1	1	0	0		1	1	2	3	2.024692	0	0.190000	1.940000	0.195351	0.600000	0.370000	1.000000	0.590000	0.633517	0.600000	0	0.480000	0.780000
DDHD2	23259	broad.mit.edu	37	8	38110300	38110300	+	Missense_Mutation	SNP	A	A	G			TCGA-3A-A9I7-01A-21D-A38G-08	TCGA-3A-A9I7-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b47f6bb9-23ad-4f47-bb37-b232b97a1ddc	c1a3fec7-91d6-4675-9cc3-398269c967c6	g.chr8:38110300A>G	ENST00000397166.2	+	14	2203	c.1678A>G	c.(1678-1680)Atg>Gtg	p.M560V	DDHD2_ENST00000517385.1_Missense_Mutation_p.M179V|DDHD2_ENST00000529845.1_Missense_Mutation_p.M11V|DDHD2_ENST00000520272.2_Missense_Mutation_p.M560V	NM_015214.2	NP_056029.2	O94830	DDHD2_HUMAN	DDHD domain containing 2			28	Colorectal(12;0.000442)	all_lung(54;0.0657)|Lung NSC(58;0.175)	BRCA - Breast invasive adenocarcinoma(5;3.76e-25)|COAD - Colon adenocarcinoma(9;0.0977)		ATTTGAGCCAATGCTGATCCC	0.453000																								0							SO:0001583	missense			ENST00000397166.2	1	1	hg19	CCDS34883.1	.	.	.	.	.	.	.	.	.	.	A	5.136	0.210761	0.09757	.	.	ENSG00000085788	ENST00000397166;ENST00000520272;ENST00000517385;ENST00000529845	T;T	0.24908	1.83;1.83	5.34	5.34	0.76211	DDHD (2);	0.038953	0.85682	D	0.000000	T	0.12902	0.0313	N	0.11000	0.08	0.50813	D	0.999897	B	0.14012	0.009	B	0.15052	0.012	T	0.07065	-1.0792	10	0.02654	T	1	-27.1583	14.7906	0.69841	1.0:0.0:0.0:0.0	.	560	O94830	DDHD2_HUMAN	V	560;560;179;11	ENSP00000380352:M560V;ENSP00000429932:M560V	ENSP00000380352:M560V	M	+	1	0	DDHD2	38229457	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	5.405000	0.66351	2.143000	0.66587	0.260000	0.18958	ATG		TCGA-3A-A9I7-01A-21D-A38G-08	DDHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377251.2	1	0	1	23	267	0	98	1	9.493398e-01	6	54	0	98	2		0	0	0	0	0	2	1	0.999999	23	261	0	98	2		0	0	0	0	98	2	-20.000000	1	1	121412	3	33	1	1	2	3	2.024692	0	0.190000	1.940000	0.195351	0.850000	0.550000	1.000000	1.000000	0.846914	0.850000	1	0.690000	1.000000
CDKN2A	1029	broad.mit.edu	37	9	21971111	21971111	+	Missense_Mutation	SNP	G	G	A	rs121913385		TCGA-3A-A9I7-01A-21D-A38G-08	TCGA-3A-A9I7-10A-01D-A38J-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	b47f6bb9-23ad-4f47-bb37-b232b97a1ddc	c1a3fec7-91d6-4675-9cc3-398269c967c6	g.chr9:21971111G>A	ENST00000304494.5	-	2	517	c.247C>T	c.(247-249)Cac>Tac	p.H83Y	CDKN2A_ENST00000530628.2_Missense_Mutation_p.A97V|CDKN2A_ENST00000498124.1_Missense_Mutation_p.H83Y|CDKN2A_ENST00000579755.1_Missense_Mutation_p.A97V|CDKN2A_ENST00000494262.1_Missense_Mutation_p.H32Y|CDKN2A_ENST00000497750.1_Missense_Mutation_p.H32Y|CDKN2A_ENST00000578845.2_Missense_Mutation_p.H32Y|CDKN2A_ENST00000446177.1_Missense_Mutation_p.H83Y|CDKN2A_ENST00000361570.3_Missense_Mutation_p.A138V|CDKN2A_ENST00000498628.2_Missense_Mutation_p.H32Y|CDKN2A_ENST00000579122.1_Missense_Mutation_p.H83Y|RP11-145E5.5_ENST00000404796.2_Intron|CDKN2A_ENST00000479692.2_Missense_Mutation_p.H32Y	NM_000077.4	NP_000068.1	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A	p.0?(1315)|p.?(44)|p.H83Y(30)|p.A138V(2)|p.H83fs*2(2)|p.H83N(1)|p.V82fs*62(1)|p.0(1)|p.V82_G89>G(1)|p.E61_L94del(1)|p.R137fs*48(1)|p.A68fs*3(1)|p.P81_A85del(1)|p.R80fs*34(1)|p.V82_E88del(1)		4199		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)			GCAGCGTCGTGCACGGGTCGG	0.741000	H83Y(CALU3_LUNG)|H83Y(HS944T_SKIN)|H83Y(JHH2_LIVER)|H83Y(OPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|H83Y(SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	17								HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)														1403	Whole gene deletion(1316)|Unknown(44)|Substitution - Missense(33)|Deletion - Frameshift(6)|Deletion - In frame(3)|Complex - deletion inframe(1)	GRCh37	CM053801|CM056557	CDKN2A	M	rs121913385	SO:0001583	missense			ENST00000304494.5	1	1	hg19	CCDS6510.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	26.7|26.7	4.762523|4.762523	0.89932|0.89932	.|.	.|.	ENSG00000147889|ENSG00000147889	ENST00000361570;ENST00000530628|ENST00000304494;ENST00000446177	T;T|T;T	0.80393|0.71222	-1.37;-1.31|-0.55;-0.55	5.93|5.93	5.93|5.93	0.95920|0.95920	.|Ankyrin repeat-containing domain (4);	0.000000|.	0.37261|.	N|.	0.002164|.	T|T	0.77579|0.77579	0.4151|0.4151	L|L	0.27053|0.27053	0.805|0.805	0.46521|0.46521	D|D	0.999085|0.999085	P|D	0.47191|0.76494	0.891|0.999	B|D	0.44044|0.75484	0.439|0.986	T|T	0.79024|0.79024	-0.1972|-0.1972	10|9	0.62326|0.66056	D|D	0.03|0.02	-15.192|-15.192	19.1026|19.1026	0.93279|0.93279	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	138|83	Q8N726|P42771	CD2A2_HUMAN|CD2A1_HUMAN	V|Y	138;97|83	ENSP00000355153:A138V;ENSP00000432664:A97V|ENSP00000307101:H83Y;ENSP00000394932:H83Y	ENSP00000355153:A138V|ENSP00000307101:H83Y	A|H	-|-	2|1	0|0	CDKN2A|CDKN2A	21961111|21961111	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.915000|0.915000	0.54546|0.54546	8.665000|8.665000	0.91144|0.91144	2.803000|2.803000	0.96430|0.96430	0.650000|0.650000	0.86243|0.86243	GCA|CAC		TCGA-3A-A9I7-01A-21D-A38G-08	CDKN2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000051915.1	0	0	0	7	97	0	42	1	9.999527e-01	340	10	0	42	2	1	9.968348e-01	9	150	0	74	2	1	0.966250	6	81	0	34	2		0	0	0	0	42	2	-11.491640	1	1	0	0		1	0	1	1	1.917149	0	0.190000	1.940000	0.137564	0.660000	0.300000	1.000000	1.000000	0.683413	0.660000	0	0.460000	0.920000