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
PLSCR2	57047	broad.mit.edu	37	3	146177707	146177707	+	Frame_Shift_Del	DEL	A	A	-			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr3:146177707delA	ENST00000497985.1	-	4	643	c.204delT	c.(202-204)cctfs	p.P68fs	PLSCR2_ENST00000336685.2_5'UTR	NM_001199978.1	NP_001186907.1	Q9NRY7	PLS2_HUMAN	phospholipid scramblase 2			15					GTACCCCTTCAGGTCTACCTG	0.507000																								0							SO:0001589	frameshift_variant			ENST00000497985.1	1	1	hg19	CCDS56284.1																																																																																				TCGA-2L-AAQE-01A-11D-A397-08	PLSCR2-002	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000355264.1	1	0	0	64	321	0	63	0	7.586917e-02	0	3	0	63	2	0	0	0	0	0	0		1	1	65	318	0	62	2	0	0	0	0	0	0		-2.989177	1	1	0	0		1	1	2	3	2.162847	0	0.530000	1.810000	0.536146	0.630000	5.000000e-01	1.000000	0.630000	0.654406	0.630000	0	5.600000e-01	0.720000
EIF3A	8661	broad.mit.edu	37	10	120830492	120830492	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr10:120830492G>A	ENST00000369144.3	-	5	774	c.647C>T	c.(646-648)aCg>aTg	p.T216M	EIF3A_ENST00000541549.1_Missense_Mutation_p.T182M	NM_003750.2	NP_003741.1	P56537	IF6_HUMAN	eukaryotic translation initiation factor 3, subunit A			56		Lung NSC(174;0.094)|all_lung(145;0.123)			ATTGATTGCCGTACTTTGGTT	0.443000																								0							SO:0001583	missense			ENST00000369144.3	0	1	hg19	CCDS7608.1	.	.	.	.	.	.	.	.	.	.	G	17.57	3.422747	0.62733	.	.	ENSG00000107581	ENST00000369144;ENST00000541549	T;T	0.44083	0.93;0.93	5.69	5.69	0.88448	.	0.000000	0.40469	N	0.001098	T	0.63815	0.2543	M	0.61703	1.905	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.58025	-0.7709	10	0.34782	T	0.22	-22.9502	19.813	0.96554	0.0:0.0:1.0:0.0	.	216	Q14152	EIF3A_HUMAN	M	216;182	ENSP00000358140:T216M;ENSP00000438178:T182M	ENSP00000358140:T216M	T	-	2	0	EIF3A	120820482	1.000000	0.71417	0.994000	0.49952	0.993000	0.82548	9.827000	0.99397	2.683000	0.91414	0.591000	0.81541	ACG		TCGA-2L-AAQE-01A-11D-A397-08	EIF3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050634.1	0	0	0	5	273	0	57	0	7.283483e-01	0	136	0	57	2		0	0	0	0	0	2	1	9.375043e-01	5	272	0	56	2		0	0	0	0	0	2	-2.742045	1	1	121412	1	31	1	2	2	4	2.213109	0	0.530000	1.810000	0.553656	0.070000	2.000000e-02	1.000000	0.070000	0.158934	0.070000	0	4.000000e-02	0.140000
INPP5F	22876	broad.mit.edu	37	10	121541192	121541192	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr10:121541192G>A	ENST00000361976.2	+	3	390	c.224G>A	c.(223-225)gGc>gAc	p.G75D	INPP5F_ENST00000369081.1_5'UTR|INPP5F_ENST00000369083.3_Missense_Mutation_p.G75D	NM_014937.3	NP_055752.1	Q01968	OCRL_HUMAN	inositol polyphosphate-5-phosphatase F			42		Lung NSC(174;0.109)|all_lung(145;0.142)			GCATTGGTGGGCAAACTCCCA	0.438000																								0							SO:0001583	missense			ENST00000361976.2	0	1	hg19	CCDS7616.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.655701	0.88056	.	.	ENSG00000198825	ENST00000361976;ENST00000369083	T;T	0.59502	0.26;0.26	5.96	5.04	0.67666	Synaptojanin, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.81009	0.4734	M	0.91768	3.24	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.73380	0.98;0.962	D	0.86073	0.1539	10	0.87932	D	0	-18.5695	16.4613	0.84055	0.0:0.0:0.8678:0.1322	.	75;75	Q9Y2H2;Q9Y2H2-3	SAC2_HUMAN;.	D	75	ENSP00000354519:G75D;ENSP00000358079:G75D	ENSP00000354519:G75D	G	+	2	0	INPP5F	121531182	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.091000	0.94151	1.474000	0.48178	0.655000	0.94253	GGC		TCGA-2L-AAQE-01A-11D-A397-08	INPP5F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050679.1	0	0	0	4	183	0	44	0	9.595635e-02	0	19	0	44	2		0	0	0	0	0	2	1	8.887247e-01	4	181	0	44	2		0	0	0	0	0	2	-2.919370	1	1	0	0		1	2	2	4	2.213109	0	0.530000	1.810000	0.553656	0.090000	2.000000e-02	1.000000	0.090000	0.177086	0.090000	0	5.000000e-02	0.170000
GPR123	84435	broad.mit.edu	37	10	134896361	134896361	+	Splice_Site	SNP	C	C	T			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr10:134896361C>T	ENST00000607359.1	+	7	1373	c.1373C>T	c.(1372-1374)gCg>gTg	p.A458V	RP13-439H18.4_ENST00000444433.1_RNA			Q86SQ6	GP123_HUMAN	G protein-coupled receptor 123			14		all_cancers(35;1.8e-10)|all_epithelial(44;8.95e-09)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Colorectal(31;0.0585)|Melanoma(40;0.123)|Glioma(114;0.203)			AGGCCCTGTGCGGTGAGGCCT	0.662000																								0							SO:0001630	splice_region_variant			ENST00000607359.1	0	1	hg19		.	.	.	.	.	.	.	.	.	.	C	2.107	-0.404715	0.04832	3.21E-4	0.0	ENSG00000197177	ENST00000368577;ENST00000392609	.	.	.	1.64	-3.28	0.05033	.	11.146600	0.01144	U	0.006263	T	0.08626	0.0214	.	.	.	0.21020	N	0.999803	P	0.50272	0.933	B	0.22880	0.042	T	0.31392	-0.9945	7	0.87932	D	0	.	1.3877	0.02243	0.1983:0.2487:0.394:0.159	.	458	Q86SQ6-1	.	V	458	.	ENSP00000357566:A458V	A	+	2	0	GPR123	134746351	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.344000	0.02639	-1.142000	0.02869	0.306000	0.20318	GCG		TCGA-2L-AAQE-01A-11D-A397-08	GPR123-004	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000316904.2	0	0	0	7	33	0	8		0	0	0	0	8	2		0	0	0	0	0	2	1	9.840074e-01	7	33	0	8	2		0	0	0	0	0	2	-15.315740	1	1	117816	5	30	1	1	2	3	2.179679	0	0.530000	1.810000	0.538560	0.710000	3.300000e-01	1.000000	1.000000	0.718482	0.710000	0	4.900000e-01	1.000000
RET	5979	broad.mit.edu	37	10	43622039	43622039	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr10:43622039C>T	ENST00000355710.3	+	19	3288	c.3056C>T	c.(3055-3057)gCg>gTg	p.A1019V	RET_ENST00000340058.5_Missense_Mutation_p.A1019V	NM_020975.4	NP_066124.1	P07949	RET_HUMAN	ret proto-oncogene		CCDC6/RET(4)|KIF5B/RET(79)	607		Ovarian(717;0.0423)		Cabozantinib(DB08875)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)	TTGGACCTTGCGGCGTCCACT	0.557000		1	T, Mis, N, F	H4, PRKAR1A, NCOA4, PCM1, GOLGA5, TRIM33, KTN1, TRIM27, HOOK3, KIF5B, CCDC6	medullary thyroid,  papillary thyroid, pheochromocytoma, NSCLC	medullary thyroid,  papillary thyroid, pheochromocytoma	Hirschsprung disease		Multiple Endocrine Neoplasia, type 2B;Multiple Endocrine Neoplasia, type 2A;Familial Medullary Thyroid Carcinoma				Melanoma(102;360 522 3376 9752 9881 14372 17251 18341 20876 24662 34807 43144 48149)	yes	Dom	yes	Multiple endocrine neoplasia 2A/2B	10	10q11.2	5979	ret proto-oncogene	yes	E, O	0							SO:0001583	missense	Familial Cancer Database	MEN2B, Wagenmann-Froboese s.;MEN2A, Sipple disease, incl MEN2C;FMTC	ENST00000355710.3	0	1	hg19	CCDS7200.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.010130	0.75046	.	.	ENSG00000165731	ENST00000355710;ENST00000340058	T;T	0.80304	-1.24;-1.36	5.09	5.09	0.68999	.	0.000000	0.85682	D	0.000000	D	0.83922	0.5359	N	0.24115	0.695	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.998;0.999	D	0.85682	0.1301	10	0.52906	T	0.07	.	18.5126	0.90923	0.0:1.0:0.0:0.0	.	765;1019;1019	B4DGX8;P07949;P07949-2	.;RET_HUMAN;.	V	1019	ENSP00000347942:A1019V;ENSP00000344798:A1019V	ENSP00000344798:A1019V	A	+	2	0	RET	42942045	1.000000	0.71417	0.735000	0.30896	0.550000	0.35303	7.786000	0.85741	2.374000	0.81015	0.655000	0.94253	GCG		TCGA-2L-AAQE-01A-11D-A397-08	RET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047694.2	0	0	0	8	1098	1	253	0	0	0	1	1	253	2		0	0	0	0	0	2	0	7.157282e-02	8	1090	1	253	16		0	0	0	0	0	2	-1.889802	0	1	0	0		1	1	2	3	2.165270	0	0.530000	1.810000	0.537356	0.020000	0	1.000000	0.020000	0.075259	0.020000	0	1.000000e-02	0.050000
C10orf71	118461	broad.mit.edu	37	10	50532475	50532475	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr10:50532475G>A	ENST00000374144.3	+	3	2173	c.1885G>A	c.(1885-1887)Gga>Aga	p.G629R	C10orf71_ENST00000323868.4_Missense_Mutation_p.G629R			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	p.G629*(1)		1					GGGTCCTGCCGGATCCAGCTG	0.567000																								1	Substitution - Nonsense(1)						SO:0001583	missense			ENST00000374144.3	1	1	hg19	CCDS44387.1	.	.	.	.	.	.	.	.	.	.	G	0.328	-0.958059	0.02267	0.0	1.2E-4	ENSG00000177354	ENST00000323868;ENST00000374144	T;T	0.13196	2.61;3.69	5.74	-0.929	0.10444	.	1.066660	0.07463	N	0.901009	T	0.03434	0.0099	N	0.00538	-1.39	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.42865	-0.9426	10	0.23891	T	0.37	.	6.3022	0.21119	0.5432:0.0:0.34:0.1168	.	629	Q711Q0-3	.	R	629	ENSP00000318713:G629R;ENSP00000363259:G629R	ENSP00000318713:G629R	G	+	1	0	C10orf71	50202481	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	-0.233000	0.09041	-0.118000	0.11851	-1.239000	0.01543	GGA		TCGA-2L-AAQE-01A-11D-A397-08	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	1	0	1	20	60	0	16		0	0	0	0	16	2		0	0	0	0	0	2	1	9.999984e-01	20	60	0	16	2		0	0	0	0	0	2	-20.000000	1	1	120874	5	35	1	2	2	4	2.213109	0	0.530000	1.810000	0.553656	0.990000	6.600000e-01	1.000000	1.000000	0.934301	0.990000	1	8.200000e-01	1.000000
KIAA1377	57562	broad.mit.edu	37	11	101834466	101834466	+	Silent	SNP	G	G	A			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr11:101834466G>A	ENST00000263468.8	+	6	2970	c.2700G>A	c.(2698-2700)cgG>cgA	p.R900R	KIAA1377_ENST00000537689.1_Silent_p.R701R	NM_020802.2	NP_065853.2	Q9P2H0	K1377_HUMAN	KIAA1377			53	all_epithelial(12;0.0104)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00931)			CAGTTGCCCGGCAAGATGCGA	0.413000																								0							SO:0001819	synonymous_variant			ENST00000263468.8	0	1	hg19	CCDS31658.1																																																																																				TCGA-2L-AAQE-01A-11D-A397-08	KIAA1377-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394140.1	0	0	0	5	504	0	144	0	1.865306e-02	0	17	0	144	2		0	0	0	0	0	2	1	9.361954e-01	5	499	0	144	2		0	0	0	0	0	2	-2.300723	0	1	0	0		1	1	2	3	2.185977	0	0.530000	1.810000	0.539757	0.030000	0	1.000000	0.040000	0.106294	0.030000	0	2.000000e-02	0.070000
ANO3	63982	broad.mit.edu	37	11	26556047	26556047	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr11:26556047G>A	ENST00000256737.3	+	9	1766	c.914G>A	c.(913-915)cGa>cAa	p.R305Q	ANO3_ENST00000531568.1_Missense_Mutation_p.R159Q|ANO3_ENST00000537978.1_Missense_Mutation_p.R289Q|ANO3_ENST00000525139.1_Missense_Mutation_p.R289Q	NM_031418.2	NP_113606.2	Q9BYT9	ANO3_HUMAN	anoctamin 3	p.R305Q(1)		68					AATGCTACTCGAAGCAGAATA	0.348000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000256737.3	1	1	hg19	CCDS31447.1	.	.	.	.	.	.	.	.	.	.	G	32	5.138511	0.94560	.	.	ENSG00000134343	ENST00000537978;ENST00000525139;ENST00000256737;ENST00000538001;ENST00000531568	T;T;T;T	0.69806	-0.43;-0.43;-0.43;-0.43	5.03	5.03	0.67393	.	0.000000	0.85682	D	0.000000	D	0.87120	0.6098	H	0.94183	3.505	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	D	0.90997	0.4839	10	0.87932	D	0	.	17.9596	0.89081	0.0:0.0:1.0:0.0	.	207;305	B7Z7Y6;Q9BYT9	.;ANO3_HUMAN	Q	289;289;305;207;159	ENSP00000440737:R289Q;ENSP00000432576:R289Q;ENSP00000256737:R305Q;ENSP00000432394:R159Q	ENSP00000256737:R305Q	R	+	2	0	ANO3	26512623	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.516000	0.98017	2.349000	0.79799	0.460000	0.39030	CGA		TCGA-2L-AAQE-01A-11D-A397-08	ANO3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387806.1	1	0	1	102	288	1	97		0	0	0	1	97	2		0	0	0	0	0	2	1	1	101	288	1	97	15		0	0	0	0	0	2	-6.159810	1	1	121406	1	36	1	1	2	3	2.185977	0	0.530000	1.810000	0.539757	0.990000	8.400000e-01	1.000000	1.000000	0.972668	0.990000	1	9.200000e-01	1.000000
ELP4	26610	broad.mit.edu	37	11	31541617	31541617	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr11:31541617G>A	ENST00000350638.5	+	2	273	c.238G>A	c.(238-240)Gtt>Att	p.V80I	ELP4_ENST00000395934.2_Missense_Mutation_p.V80I|ELP4_ENST00000379163.5_Missense_Mutation_p.V80I	NM_019040.3	NP_061913.3	Q96EB1	ELP4_HUMAN	elongator acetyltransferase complex subunit 4			20	Lung SC(675;0.225)				AGGTTTAGCCGTTGGAACAGT	0.348000																								0							SO:0001583	missense			ENST00000350638.5	1	1	hg19	CCDS7875.2	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	10.03	1.239257	0.22711	0.0	1.22E-4	ENSG00000109911	ENST00000350638;ENST00000379163;ENST00000395934	T;T;T	0.40756	1.02;1.02;1.02	5.15	4.23	0.50019	.	0.125811	0.53938	N	0.000059	T	0.52837	0.1759	L	0.41710	1.295	0.33585	D	0.600371	D;D;D	0.89917	0.994;1.0;1.0	P;D;D	0.87578	0.869;0.995;0.998	T	0.57957	-0.7721	10	0.15066	T	0.55	-12.2988	15.406	0.74877	0.0731:0.0:0.9269:0.0	.	80;80;80	B4E3W0;G5E9D4;Q96EB1	.;.;ELP4_HUMAN	I	80	ENSP00000298937:V80I;ENSP00000368461:V80I;ENSP00000379267:V80I	ENSP00000298937:V80I	V	+	1	0	ELP4	31498193	1.000000	0.71417	0.922000	0.36590	0.892000	0.51952	4.374000	0.59543	0.692000	0.31613	-1.151000	0.01829	GTT		TCGA-2L-AAQE-01A-11D-A397-08	ELP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286640.1	1	0	1	76	221	0	70	1	9.042740e-01	5	9	0	70	2		0	0	0	0	0	2	1	1	76	220	0	70	2		0	0	0	0	0	2	-5.289739	1	1	120798	22	43	1	1	2	3	2.185977	0	0.530000	1.810000	0.539757	0.990000	8.000000e-01	1.000000	1.000000	0.958488	0.990000	1	8.900000e-01	1.000000
OR5M11	219487	broad.mit.edu	37	11	56310189	56310189	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr11:56310189G>A	ENST00000528616.2	-	1	568	c.545C>T	c.(544-546)cCg>cTg	p.P182L		NM_001005245.1	NP_001005245.1	Q96RB7	OR5MB_HUMAN	olfactory receptor, family 5, subfamily M, member 11			18					CTTAATGAGCGGCGGGTCAGC	0.502000																								0							SO:0001583	missense			ENST00000528616.2	1	1	hg19	CCDS53629.1	.	.	.	.	.	.	.	.	.	.	A	11.09	1.535136	0.27475	0.0	4.74E-4	ENSG00000255223	ENST00000528616	T	0.00224	8.51	4.89	1.97	0.26223	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00496	0.0016	M	0.80422	2.495	0.21445	N	0.99969	D	0.89917	1.0	D	0.74348	0.983	T	0.47032	-0.9148	9	0.72032	D	0.01	.	7.6395	0.28286	0.1337:0.0:0.6314:0.2349	.	182	Q96RB7	OR5MB_HUMAN	L	182	ENSP00000432417:P182L	ENSP00000432417:P182L	P	-	2	0	OR5M11	56066765	0.003000	0.15002	0.493000	0.27502	0.234000	0.25298	1.152000	0.31663	0.040000	0.15660	-1.789000	0.00628	CCG		TCGA-2L-AAQE-01A-11D-A397-08	OR5M11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391608.1	1	0	1	43	131	0	30		0	0	0	0	30	2		0	0	0	0	0	2	1	1	42	121	0	28	2		0	0	0	0	0	2	-2.895511	1	1	121030	32	48	1	1	2	3	2.185977	0	0.530000	1.810000	0.539757	0.960000	7.200000e-01	1.000000	1.000000	0.931059	0.960000	1	8.300000e-01	1.000000
GLYATL1	92292	broad.mit.edu	37	11	58723412	58723412	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr11:58723412G>A	ENST00000317391.4	+	8	1161	c.821G>A	c.(820-822)cGc>cAc	p.R274H	RP11-142C4.6_ENST00000525714.1_RNA|GLYATL1_ENST00000300079.5_Missense_Mutation_p.R305H|RP11-142C4.6_ENST00000533954.1_RNA	NM_001220494.1	NP_001207423.1	Q969I3	GLYL1_HUMAN	glycine-N-acyltransferase-like 1	p.R305H(1)		34				Glycine(DB00145)	GAAGACTCCCGCAGATTTGTG	0.448000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000317391.4	1	1	hg19	CCDS55768.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	.	0.271	-0.993172	0.02145	.	.	ENSG00000166840	ENST00000444580;ENST00000317391;ENST00000300079	T;T	0.18657	2.2;2.2	1.97	-2.28	0.06826	Acyl-CoA N-acyltransferase (2);Glycine N-acyltransferase, C-terminal (1);	0.732987	0.11663	N	0.541605	T	0.06280	0.0162	N	0.04508	-0.205	0.09310	N	1	B;B	0.17465	0.022;0.01	B;B	0.12156	0.004;0.007	T	0.36529	-0.9744	10	0.13853	T	0.58	.	1.8117	0.03092	0.4455:0.0:0.2831:0.2714	.	305;274	Q969I3-2;Q969I3	.;GLYL1_HUMAN	H	251;274;305	ENSP00000322223:R274H;ENSP00000300079:R305H	ENSP00000300079:R305H	R	+	2	0	GLYATL1	58479988	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.478000	0.02329	-0.626000	0.05596	0.411000	0.27672	CGC		TCGA-2L-AAQE-01A-11D-A397-08	GLYATL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393783.1	1	0	1	89	233	0	64	0	0	0	1	0	64	2		0	0	0	0	0	2	1	1	88	229	0	63	2		0	0	0	0	0	2	-6.211773	1	1	121412	4	41	1	1	2	3	2.185977	0	0.530000	1.810000	0.539757	0.990000	8.800000e-01	1.000000	1.000000	0.987679	0.990000	1	9.700000e-01	1.000000
AHNAK	79026	broad.mit.edu	37	11	62287090	62287090	+	Silent	SNP	T	T	C			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr11:62287090T>C	ENST00000378024.4	-	5	15073	c.14799A>G	c.(14797-14799)tcA>tcG	p.S4933S	AHNAK_ENST00000530124.1_Intron|AHNAK_ENST00000525875.1_5'Flank|AHNAK_ENST00000257247.7_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein			268		Melanoma(852;0.155)			ACTTCGGACCTGAAAATCCAA	0.458000																								0							SO:0001819	synonymous_variant			ENST00000378024.4	0	1	hg19	CCDS31584.1																																																																																				TCGA-2L-AAQE-01A-11D-A397-08	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	0	0	0	5	521	0	139	0	9.812960e-01	1	788	0	139	2		0	0	0	0	0	2	1	9.371875e-01	5	519	0	139	2		0	0	0	0	0	2	-2.385043	0	1	0	0		1	1	2	3	2.185977	0	0.530000	1.810000	0.539757	0.030000	0	1.000000	0.040000	0.104887	0.030000	0	1.000000e-02	0.070000
SRRM4	84530	broad.mit.edu	37	12	119568554	119568554	+	Missense_Mutation	SNP	T	T	A			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr12:119568554T>A	ENST00000267260.4	+	8	1074	c.686T>A	c.(685-687)cTc>cAc	p.L229H	SRRM4_ENST00000537597.1_3'UTR	NM_194286.3	NP_919262.2	A7MD48	SRRM4_HUMAN	serine/arginine repetitive matrix 4			24					TCCAAGACCCTCTGCAAGGAC	0.652000																								0							SO:0001583	missense			ENST00000267260.4	1	1	hg19	CCDS44994.1	.	.	.	.	.	.	.	.	.	.	T	14.62	2.590902	0.46214	.	.	ENSG00000139767	ENST00000267260	T	0.23552	1.9	5.07	2.5	0.30297	.	0.407083	0.22564	N	0.058424	T	0.11239	0.0274	N	0.19112	0.55	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.21381	-1.0247	10	0.15066	T	0.55	-8.4824	1.5524	0.02578	0.1784:0.0995:0.1716:0.5504	.	229	A7MD48	SRRM4_HUMAN	H	229	ENSP00000267260:L229H	ENSP00000267260:L229H	L	+	2	0	SRRM4	118052937	0.059000	0.20769	0.996000	0.52242	0.987000	0.75469	0.734000	0.26101	0.734000	0.32515	0.368000	0.22195	CTC		TCGA-2L-AAQE-01A-11D-A397-08	SRRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401640.2	0	0	1	29	71	0	23		0	0	0	0	23	2		0	0	0	0	0	2	1	1	25	65	0	22	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	0	1	1	1.758242	1	0.530000	1.810000	0.378471	0.810000	5.800000e-01	1.000000	1.000000	0.815603	0.810000	0	6.900000e-01	0.940000
KRAS	3845	broad.mit.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	C	T	rs121913529		TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	KRAS_deep			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	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-2L-AAQE-01A-11D-A397-08	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	1	0	1	72	173	0	79	1	9.965879e-01	16	8	0	79	2	1	1	73	264	0	271	2	1	1	72	172	0	79	2	1	1	2983	5037	13	8012	23	-20.000000	1	1	121404	2	44	1	0	2	2	2.090760	1	0.530000	1.810000	0.530000	0.990000	9.000000e-01	1.000000	1.000000	0.993266	0.990000	1	9.900000e-01	1.000000
RND1	27289	broad.mit.edu	37	12	49254866	49254866	+	Missense_Mutation	SNP	T	T	A			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr12:49254866T>A	ENST00000309739.5	-	4	497	c.367A>T	c.(367-369)Att>Ttt	p.I123F		NM_014470.3	NP_055285.1	Q92730	RND1_HUMAN	Rho family GTPase 1			10					TTGCAGCCAATGAGCAAAACG	0.552000																								0							SO:0001583	missense			ENST00000309739.5	1	1	hg19	CCDS8771.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.185328	0.78677	.	.	ENSG00000172602	ENST00000550607;ENST00000309739	T;T	0.79352	-1.26;-1.26	5.66	3.33	0.38152	Small GTP-binding protein domain (1);	0.051099	0.85682	D	0.000000	T	0.74718	0.3753	L	0.61387	1.9	0.58432	D	0.999998	P	0.47962	0.903	B	0.44108	0.441	T	0.76266	-0.3022	10	0.87932	D	0	-22.6091	9.2452	0.37520	0.0:0.1499:0.0:0.8501	.	123	Q92730	RND1_HUMAN	F	17;123	ENSP00000447059:I17F;ENSP00000308461:I123F	ENSP00000308461:I123F	I	-	1	0	RND1	47541133	0.915000	0.31059	0.998000	0.56505	0.935000	0.57460	1.352000	0.34033	1.084000	0.41184	-0.274000	0.10170	ATT		TCGA-2L-AAQE-01A-11D-A397-08	RND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408915.1	1	0	1	118	240	0	75	1	9.685573e-01	6	8	0	75	2		0	0	0	0	0	2	1	1	118	238	0	75	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	0	2	2	2.094693	1	0.530000	1.810000	0.530000	0.990000	9.900000e-01	1.000000	1.000000	0.999929	0.990000	1	9.900000e-01	1.000000
ANKS1B	56899	broad.mit.edu	37	12	99898356	99898356	+	Missense_Mutation	SNP	A	A	T			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr12:99898356A>T	ENST00000547776.2	-	10	1335	c.1336T>A	c.(1336-1338)Ttt>Att	p.F446I	ANKS1B_ENST00000329257.7_Missense_Mutation_p.F446I|ANKS1B_ENST00000547010.1_Missense_Mutation_p.F26I	NM_152788.4	NP_690001.3	Q7Z6G8	ANS1B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1B			70		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)			TCTGAAGGAAATGTATCCAGA	0.383000																								0							SO:0001583	missense			ENST00000547776.2	1	1	hg19	CCDS55872.1	.	.	.	.	.	.	.	.	.	.	A	15.63	2.890646	0.52014	.	.	ENSG00000185046	ENST00000547776;ENST00000547010;ENST00000329257;ENST00000538702;ENST00000549866	T;T;T;T	0.61742	0.92;0.08;0.92;0.78	5.68	5.68	0.88126	.	0.136396	0.48767	D	0.000169	T	0.41766	0.1173	L	0.29908	0.895	0.80722	D	1	B;B;B	0.32829	0.386;0.386;0.02	B;B;B	0.27170	0.077;0.077;0.006	T	0.33828	-0.9853	9	.	.	.	-6.2914	11.418	0.49965	0.8382:0.1618:0.0:0.0	.	412;26;446	F8VVQ4;Q7Z6G8-6;Q7Z6G8	.;.;ANS1B_HUMAN	I	446;26;446;25;412	ENSP00000449629:F446I;ENSP00000448512:F26I;ENSP00000331381:F446I;ENSP00000449894:F412I	.	F	-	1	0	ANKS1B	98422487	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.066000	0.50002	2.175000	0.68902	0.528000	0.53228	TTT		TCGA-2L-AAQE-01A-11D-A397-08	ANKS1B-003	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000408421.3	1	0	1	17	48	0	31		0	0	0	0	31	2		0	0	0	0	0	2	1	9.999869e-01	17	48	0	31	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	0	1	1	1.758242	1	0.530000	1.810000	0.378471	0.730000	4.600000e-01	1.000000	1.000000	0.739562	0.730000	0	5.900000e-01	0.880000
LTB4R	1241	broad.mit.edu	37	14	24784967	24784967	+	Missense_Mutation	SNP	G	G	C			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr14:24784967G>C	ENST00000396789.4	+	2	1835	c.110G>C	c.(109-111)aGc>aCc	p.S37T	LTB4R_ENST00000345363.3_Missense_Mutation_p.S37T|LTB4R_ENST00000396782.2_Missense_Mutation_p.S37T	NM_181657.3	NP_858043.1	Q15722	LT4R1_HUMAN	leukotriene B4 receptor			8					CCCGGCAACAGCTTTGTGGTG	0.577000																								0							SO:0001583	missense			ENST00000396789.4	1	1	hg19	CCDS9626.1	.	.	.	.	.	.	.	.	.	.	G	5.085	0.201347	0.09652	.	.	ENSG00000213903	ENST00000553481;ENST00000345363;ENST00000396789;ENST00000396782	T;T;T;T	0.37752	1.18;1.18;1.18;1.18	5.89	0.269	0.15631	GPCR, rhodopsin-like superfamily (1);	0.568969	0.17126	U	0.186005	T	0.19846	0.0477	L	0.28115	0.83	0.18873	N	0.999986	B	0.22003	0.063	B	0.18263	0.021	T	0.28933	-1.0028	10	0.10377	T	0.69	.	8.9335	0.35686	0.0:0.4012:0.3233:0.2755	.	37	Q15722	LT4R1_HUMAN	T	37	ENSP00000450457:S37T;ENSP00000307445:S37T;ENSP00000380008:S37T;ENSP00000380002:S37T	ENSP00000307445:S37T	S	+	2	0	LTB4R	23854807	0.015000	0.18098	0.089000	0.20774	0.999000	0.98932	0.329000	0.19698	0.050000	0.15949	0.655000	0.94253	AGC		TCGA-2L-AAQE-01A-11D-A397-08	LTB4R-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073198.4	1	0	1	170	467	0	131	1	9.620468e-01	5	12	0	131	2		0	0	0	0	0	2	1	1	169	463	0	129	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	1	2	3	2.130831	0	0.530000	1.810000	0.532478	0.990000	8.800000e-01	1.000000	1.000000	0.979970	0.990000	1	9.400000e-01	1.000000
SNRPN	6638	broad.mit.edu	37	15	25223413	25223413	+	Silent	SNP	G	G	A			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr15:25223413G>A	ENST00000400100.1	+	12	1523	c.633G>A	c.(631-633)acG>acA	p.T211T	SNRPN_ENST00000577565.1_Silent_p.T211T|SNRPN_ENST00000444203.2_Silent_p.T215T|SNRPN_ENST00000390687.4_Silent_p.T211T|SNURF_ENST00000551312.2_Intron|SNRPN_ENST00000400098.1_Silent_p.T211T|SNHG14_ENST00000551631.2_RNA|SNURF_ENST00000338094.6_3'UTR|SNRPN_ENST00000400097.1_Silent_p.T211T|SNRPN_ENST00000346403.6_Silent_p.T211T|SNRPN_ENST00000554227.2_Silent_p.T215T	NM_022807.2	NP_073718.1	P63162	RSMN_HUMAN	small nuclear ribonucleoprotein polypeptide N			24		all_cancers(20;9.33e-22)|Breast(32;0.000625)			CTCGAGGGACGCCAATAGGCA	0.557000									Prader-Willi syndrome															0							SO:0001819	synonymous_variant	Familial Cancer Database	Prader-Labhart-Willi syndrome	ENST00000400100.1	1	1	hg19	CCDS10017.1																																																																																				TCGA-2L-AAQE-01A-11D-A397-08	SNRPN-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413849.10	1	0	1	191	499	1	140	1	1	262	143	1	140	12		0	0	0	0	0	2	1	1	185	495	1	136	17		0	0	0	0	0	2	-20.000000	1	1	120858	9	44	1	1	2	3	2.120405	0	0.530000	1.810000	0.531242	0.990000	9.100000e-01	1.000000	1.000000	0.991671	0.990000	1	9.700000e-01	1.000000
ABCC1	4363	broad.mit.edu	37	16	16150130	16150130	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr16:16150130C>T	ENST00000399410.3	+	12	1830	c.1655C>T	c.(1654-1656)aCc>aTc	p.T552I	ABCC1_ENST00000399408.2_Missense_Mutation_p.T552I|ABCC1_ENST00000351154.5_Missense_Mutation_p.T552I|ABCC1_ENST00000349029.5_Missense_Mutation_p.T552I|ABCC1_ENST00000345148.5_Missense_Mutation_p.T552I|ABCC1_ENST00000346370.5_Missense_Mutation_p.T552I	NM_004996.3	NP_004987.2	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 1			56				Abiraterone(DB05812)|Aminohippurate(DB00345)|Amprenavir(DB00701)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Diclofenac(DB00586)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Epirubicin(DB00445)|Erythromycin(DB00199)|Etoposide(DB00773)|Fluorescein(DB00693)|Glutathione(DB00143)|Glyburide(DB01016)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Methotrexate(DB00563)|Mifepristone(DB00834)|Mitoxantrone(DB01204)|Ofloxacin(DB01165)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Probenecid(DB01032)|Progesterone(DB00396)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sulfinpyrazone(DB01138)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Zoledronate(DB00399)	GGCACCTTCACCTGGGTCTGC	0.517000																								0							SO:0001583	missense			ENST00000399410.3	1	1	hg19	CCDS42122.1	.	.	.	.	.	.	.	.	.	.	C	9.579	1.123011	0.20959	.	.	ENSG00000103222	ENST00000399410;ENST00000399408;ENST00000346370;ENST00000351154;ENST00000345148;ENST00000349029;ENST00000536381	D;D;D;D;D;D	0.90069	-2.61;-2.61;-2.61;-2.61;-2.61;-2.61	5.29	4.34	0.51931	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.046759	0.85682	D	0.000000	D	0.88265	0.6390	N	0.21448	0.665	0.49915	D	0.99983	D;D;P;D;D;P;P	0.89917	0.998;0.996;0.821;1.0;0.999;0.806;0.923	D;P;P;D;D;P;P	0.76071	0.923;0.898;0.599;0.987;0.973;0.848;0.764	D	0.83738	0.0202	10	0.09338	T	0.73	-45.3552	13.1912	0.59711	0.0:0.9229:0.0:0.0771	.	552;552;552;552;552;552;552	P33527-6;P33527-5;P33527-4;P33527-3;P33527-2;P33527;P33527-9	.;.;.;.;.;MRP1_HUMAN;.	I	552;552;552;552;552;552;226	ENSP00000382342:T552I;ENSP00000382340:T552I;ENSP00000263019:T552I;ENSP00000263017:T552I;ENSP00000263014:T552I;ENSP00000263016:T552I	ENSP00000263014:T552I	T	+	2	0	ABCC1	16057631	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	7.450000	0.80656	1.216000	0.43427	0.462000	0.41574	ACC		TCGA-2L-AAQE-01A-11D-A397-08	ABCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109701.1	1	0	1	39	162	0	41	1	9.991354e-01	19	29	0	41	2		0	0	0	0	0	2	1	1	39	160	0	41	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	1	2	3	2.189608	0	0.530000	1.810000	0.539757	0.750000	5.500000e-01	1.000000	0.740000	0.771166	0.750000	0	6.400000e-01	0.890000
XYLT1	64131	broad.mit.edu	37	16	17235134	17235134	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr16:17235134G>A	ENST00000261381.6	-	7	1547	c.1463C>T	c.(1462-1464)gCc>gTc	p.A488V	CTD-2576D5.4_ENST00000567344.1_RNA	NM_022166.3	NP_071449.1	Q86Y38	XYLT1_HUMAN	xylosyltransferase I			67					GCCATCCACGGCAATGCCCTC	0.577000																								0							SO:0001583	missense			ENST00000261381.6	0	1	hg19	CCDS10569.1	.	.	.	.	.	.	.	.	.	.	G	8.165	0.790357	0.16258	.	.	ENSG00000103489	ENST00000261381	T	0.11385	2.78	5.92	5.92	0.95590	.	0.342297	0.36374	N	0.002632	T	0.04770	0.0129	N	0.02142	-0.665	0.09310	N	0.999997	P	0.45044	0.849	B	0.40702	0.338	T	0.45527	-0.9255	10	0.20046	T	0.44	-20.7778	14.1696	0.65500	0.0:0.0:0.8505:0.1495	.	488	Q86Y38	XYLT1_HUMAN	V	488	ENSP00000261381:A488V	ENSP00000261381:A488V	A	-	2	0	XYLT1	17142635	0.894000	0.30519	0.015000	0.15790	0.196000	0.23810	4.775000	0.62346	2.797000	0.96272	0.555000	0.69702	GCC		TCGA-2L-AAQE-01A-11D-A397-08	XYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252241.2	0	0	0	5	510	1	129	0	9.182503e-04	0	4	1	129	2		0	0	0	0	0	2	0	1.752358e-02	7	498	1	125	15		0	0	0	0	0	2	-2.495725	0	1	0	0		1	1	2	3	2.189608	0	0.530000	1.810000	0.539757	0.030000	0	1.000000	0.040000	0.105788	0.030000	0	1.000000e-02	0.070000
TMC7	79905	broad.mit.edu	37	16	19067891	19067891	+	Silent	SNP	G	G	A			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr16:19067891G>A	ENST00000304381.5	+	14	2029	c.1899G>A	c.(1897-1899)ccG>ccA	p.P633P	TMC7_ENST00000569532.1_Silent_p.P633P|TMC7_ENST00000421369.3_Silent_p.P523P	NM_024847.3	NP_079123.3	Q7Z402	TMC7_HUMAN	transmembrane channel-like 7			28					CCTGTGGGCCGTTCACCAACT	0.602000																								0							SO:0001819	synonymous_variant			ENST00000304381.5	0	1	hg19	CCDS10573.1																																																																																				TCGA-2L-AAQE-01A-11D-A397-08	TMC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254276.3	0	0	0	5	324	0	78	0	3.182076e-01	0	64	0	78	2		0	0	0	0	0	2	1	9.369998e-01	5	322	0	76	2		0	0	0	0	0	2	-2.835645	1	1	121412	9	42	1	1	2	3	2.189608	0	0.530000	1.810000	0.539757	0.060000	1.000000e-02	1.000000	0.060000	0.129508	0.060000	0	3.000000e-02	0.110000
ITGAX	3687	broad.mit.edu	37	16	31391078	31391078	+	Splice_Site	SNP	G	G	T			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08			G	T	G	G		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr16:31391078G>T	ENST00000268296.4	+	25	2990	c.2869G>T	c.(2869-2871)Gtc>Ttc	p.V957F	ITGAX_ENST00000562522.1_Splice_Site_p.V957F	NM_000887.3	NP_000878.2	P20702	ITAX_HUMAN	integrin, alpha X (complement component 3 receptor 4 subunit)			77					CTCTGTGCAGGTCAATAACCT	0.627000																								0							SO:0001630	splice_region_variant			ENST00000268296.4	1	0	hg19	CCDS10711.1	.	.	.	.	.	.	.	.	.	.	G	12.97	2.096174	0.36952	.	.	ENSG00000140678	ENST00000268296	T	0.56776	0.44	4.58	4.58	0.56647	Integrin alpha-2 (1);	.	.	.	.	T	0.58206	0.2106	L	0.33485	1.01	0.80722	D	1	D;D	0.67145	0.996;0.992	D;D	0.65573	0.936;0.918	T	0.54043	-0.8352	8	.	.	.	.	13.0477	0.58937	0.0:0.0:1.0:0.0	.	957;142	P20702;Q8TES5	ITAX_HUMAN;.	F	957	ENSP00000268296:V957F	.	V	+	1	0	ITGAX	31298579	1.000000	0.71417	0.998000	0.56505	0.211000	0.24417	2.460000	0.45031	2.535000	0.85469	0.313000	0.20887	GTC		TCGA-2L-AAQE-01A-11D-A397-08	ITGAX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255628.2	1	0	1	34	59	0	18	0	9.947066e-01	0	18	0	18	2		0	0	0	0	0	2	1	1	34	58	0	18	2		0	0	0	0	0	2	-20.000000	1	1	121410	3	36	1	1	2	3	2.189608	0	0.530000	1.810000	0.539757	0.990000	9.900000e-01	1.000000	1.000000	0.999363	0.990000	1	9.900000e-01	1.000000
TEX14	56155	broad.mit.edu	37	17	56659016	56659016	+	Missense_Mutation	SNP	C	C	G			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr17:56659016C>G	ENST00000240361.8	-	20	3350	c.3265G>C	c.(3265-3267)Gaa>Caa	p.E1089Q	TEX14_ENST00000349033.5_Intron|TEX14_ENST00000389934.3_Missense_Mutation_p.E1083Q			Q8IWB6	TEX14_HUMAN	testis expressed 14			81	Medulloblastoma(34;0.127)|all_neural(34;0.237)				TAAAAATATTCACCGTCTGGA	0.368000																								0							SO:0001583	missense			ENST00000240361.8	1	1	hg19	CCDS56042.1	.	.	.	.	.	.	.	.	.	.	C	13.82	2.352360	0.41700	.	.	ENSG00000121101	ENST00000240361;ENST00000389934	T;T	0.80214	-1.35;-1.35	5.34	4.37	0.52481	.	0.200908	0.34603	N	0.003829	T	0.73048	0.3537	L	0.27053	0.805	0.29767	N	0.835083	P;P	0.52061	0.917;0.95	B;P	0.49887	0.421;0.625	T	0.68368	-0.5427	10	0.31617	T	0.26	-4.298	8.9678	0.35887	0.0:0.9008:0.0:0.0992	.	1089;1083	Q8IWB6;Q8IWB6-2	TEX14_HUMAN;.	Q	1089;1083	ENSP00000240361:E1089Q;ENSP00000374584:E1083Q	ENSP00000240361:E1089Q	E	-	1	0	TEX14	54014015	0.751000	0.28327	0.573000	0.28510	0.696000	0.40369	2.632000	0.46511	2.504000	0.84457	0.462000	0.41574	GAA		TCGA-2L-AAQE-01A-11D-A397-08	TEX14-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445446.1	1	0	1	65	234	0	58		0	0	0	0	58	2		0	0	0	0	0	2	1	1	64	230	0	58	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	1	2	3	2.182309	0	0.530000	1.810000	0.546813	0.860000	6.700000e-01	1.000000	1.000000	0.869288	0.860000	1	7.600000e-01	1.000000
TP53	7157	broad.mit.edu	37	17	7579575	7579575	+	Nonsense_Mutation	SNP	G	G	A			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr17:7579575G>A	ENST00000269305.4	-	4	301	c.112C>T	c.(112-114)Caa>Taa	p.Q38*	TP53_ENST00000445888.2_Nonsense_Mutation_p.Q38*|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Nonsense_Mutation_p.Q38*|TP53_ENST00000420246.2_Nonsense_Mutation_p.Q38*|TP53_ENST00000359597.4_Nonsense_Mutation_p.Q38*|TP53_ENST00000413465.2_Nonsense_Mutation_p.Q38*	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.Q38*(8)|p.0?(8)|p.P36fs*4(3)|p.?(1)|p.S33fs*23(1)|p.P13fs*18(1)|p.S37fs*79(1)		24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		Acetylsalicylic acid(DB00945)	TCCATTGCTTGGGACGGCAAG	0.592000		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	23	Substitution - Nonsense(8)|Whole gene deletion(8)|Deletion - Frameshift(6)|Unknown(1)						SO:0001587	stop_gained	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	0	1	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	14.56	2.571091	0.45798	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000508793;ENST00000503591	.	.	.	3.41	-1.11	0.09840	.	3.135740	0.02989	U	0.146625	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09338	T	0.73	0.2222	0.8266	0.01122	0.224:0.1841:0.4032:0.1887	.	.	.	.	X	38	.	ENSP00000269305:Q38X	Q	-	1	0	TP53	7520300	0.000000	0.05858	0.000000	0.03702	0.042000	0.13812	-0.754000	0.04787	-0.145000	0.11294	0.561000	0.74099	CAA		TCGA-2L-AAQE-01A-11D-A397-08	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	1	0	1	245	464	0	204	1	9.999999e-01	30	19	0	204	2	1	1	155	251	0	335	2	1	1	243	460	0	200	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	0	1	1	1.646491	1	0.530000	1.810000	0.369635	0.960000	8.600000e-01	1.000000	1.000000	0.959032	0.960000	1	9.100000e-01	1.000000
DAND5	199699	broad.mit.edu	37	19	13084387	13084387	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr19:13084387G>A	ENST00000317060.2	+	2	688	c.509G>A	c.(508-510)cGt>cAt	p.R170H	DAND5_ENST00000585548.1_3'UTR	NM_152654.2	NP_689867.1	Q8N907	DAND5_HUMAN	DAN domain family member 5, BMP antagonist			6			OV - Ovarian serous cystadenocarcinoma(19;1.87e-18)		TCAGCCTCCCGTCGACGGGTG	0.602000																								0							SO:0001583	missense			ENST00000317060.2	1	1	hg19	CCDS12291.1	.	.	.	.	.	.	.	.	.	.	G	11.08	1.534859	0.27475	2.27E-4	2.33E-4	ENSG00000179284	ENST00000317060	T	0.33654	1.4	5.49	-3.42	0.04825	DAN (1);	0.906086	0.09091	N	0.849807	T	0.23410	0.0566	L	0.40543	1.245	0.09310	N	1	B	0.15141	0.012	B	0.12837	0.008	T	0.29088	-1.0023	10	0.30854	T	0.27	-1.7171	5.2395	0.15464	0.3965:0.2644:0.3391:0.0	.	170	Q8N907	DAND5_HUMAN	H	170	ENSP00000323155:R170H	ENSP00000323155:R170H	R	+	2	0	DAND5	12945387	0.000000	0.05858	0.001000	0.08648	0.059000	0.15707	-0.058000	0.11750	-0.216000	0.10048	-0.136000	0.14681	CGT		TCGA-2L-AAQE-01A-11D-A397-08	DAND5-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452761.1	1	0	1	91	240	0	83	0	0	1	0	0	83	2		0	0	0	0	0	2	1	1	91	238	0	81	2		0	0	0	0	0	2	-6.565702	1	1	121412	6	43	1	1	2	3	2.128114	0	0.530000	1.810000	0.532478	0.990000	8.600000e-01	1.000000	1.000000	0.981746	0.990000	1	9.400000e-01	1.000000
DMKN	93099	broad.mit.edu	37	19	36004243	36004243	+	Silent	SNP	G	G	A	rs113646456		TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr19:36004243G>A	ENST00000339686.3	-	1	311	c.135C>T	c.(133-135)gaC>gaT	p.D45D	DMKN_ENST00000451297.2_Silent_p.D45D|DMKN_ENST00000492341.2_5'Flank|DMKN_ENST00000458071.1_5'Flank|DMKN_ENST00000436012.1_5'Flank|DMKN_ENST00000392206.2_5'Flank|DMKN_ENST00000472252.2_5'Flank|DMKN_ENST00000440396.1_Silent_p.D45D|DMKN_ENST00000419602.1_Silent_p.D45D|DMKN_ENST00000488892.1_5'Flank|DMKN_ENST00000414866.2_5'Flank|DMKN_ENST00000602781.1_5'Flank|DMKN_ENST00000447113.2_Silent_p.D45D|DMKN_ENST00000418261.1_Silent_p.D45D|DMKN_ENST00000424570.2_Silent_p.D45D|DMKN_ENST00000462126.1_5'Flank|DMKN_ENST00000467637.1_5'Flank|DMKN_ENST00000474928.1_5'Flank|DMKN_ENST00000461300.1_5'Flank|DMKN_ENST00000402589.2_5'Flank|DMKN_ENST00000429837.1_Silent_p.D45D|DMKN_ENST00000480502.1_5'Flank|DMKN_ENST00000443640.1_5'Flank	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine			27	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)		CGCTCAGGGCGTCTCCCAGGC	0.642000																								0							SO:0001819	synonymous_variant			ENST00000339686.3	1	1	hg19	CCDS12463.1																																																																																				TCGA-2L-AAQE-01A-11D-A397-08	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	1	0	1	65	270	0	66	0	0	1	0	0	66	2		0	0	0	0	0	2	1	1	65	269	0	63	2		0	0	0	0	0	2	-20.000000	1	1	121412	27	47	1	0	0	0	2.020278	0	0.530000	1.810000	0.509190	0.690000	5.500000e-01	0.850000	0.700000	0.705670	0.690000	0	6.200000e-01	0.780000
ZNF780B	163131	broad.mit.edu	37	19	40541025	40541025	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr19:40541025C>T	ENST00000434248.1	-	5	1806	c.1741G>A	c.(1741-1743)Gga>Aga	p.G581R	ZNF780B_ENST00000221355.6_Missense_Mutation_p.G433R	NM_001005851.2	NP_001005851.1	Q9Y6R6	Z780B_HUMAN	zinc finger protein 780B	p.G581R(1)		23	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)				GGTTTCTTTCCGGTATGAATA	0.388000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000434248.1	1	1	hg19	CCDS46077.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.970459	0.74246	2.27E-4	0.0	ENSG00000128000	ENST00000434248;ENST00000221355	T;T	0.26223	1.75;1.75	2.56	1.45	0.22620	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.43277	0.1240	M	0.69248	2.105	0.31143	N	0.706402	D	0.89917	1.0	D	0.97110	1.0	T	0.42582	-0.9443	9	0.56958	D	0.05	.	6.4082	0.21676	0.0:0.8247:0.0:0.1753	.	581	Q9Y6R6	Z780B_HUMAN	R	581;433	ENSP00000391641:G581R;ENSP00000221355:G433R	ENSP00000221355:G433R	G	-	1	0	ZNF780B	45232865	0.000000	0.05858	0.017000	0.16124	0.602000	0.36980	0.958000	0.29227	0.214000	0.20742	0.462000	0.41574	GGA		TCGA-2L-AAQE-01A-11D-A397-08	ZNF780B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338466.1	1	0	1	70	473	1	113	1	2.805598e-01	3	5	1	113	2		0	0	0	0	0	2	1	1	70	471	1	113	17		0	0	0	0	0	2	-2.920857	1	1	121412	7	41	1	0	0	0	2.020278	0	0.530000	1.810000	0.509190	0.460000	3.600000e-01	0.570000	0.460000	0.469926	0.460000	0	4.100000e-01	0.520000
HIF3A	64344	broad.mit.edu	37	19	46834437	46834437	+	Silent	SNP	C	C	T			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr19:46834437C>T	ENST00000377670.4	+	13	1768	c.1737C>T	c.(1735-1737)gaC>gaT	p.D579D	HIF3A_ENST00000244303.6_Silent_p.D510D|AC007193.10_ENST00000596807.1_RNA|HIF3A_ENST00000472815.1_Intron|HIF3A_ENST00000300862.3_Silent_p.D577D|HIF3A_ENST00000420102.2_Silent_p.D528D|HIF3A_ENST00000600383.1_Silent_p.D510D|HIF3A_ENST00000339613.2_Silent_p.D523D	NM_152795.3	NP_690008.2	Q9Y2N7	HIF3A_HUMAN	hypoxia inducible factor 3, alpha subunit	p.D577D(1)		33		Ovarian(192;0.00965)|all_neural(266;0.0887)			GCTCAGAGGACGAGGACGAGG	0.552000																								1	Substitution - coding silent(1)						SO:0001819	synonymous_variant			ENST00000377670.4	1	1	hg19	CCDS12681.2																																																																																				TCGA-2L-AAQE-01A-11D-A397-08	HIF3A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280556.3	1	0	1	37	150	0	46		0	0	0	0	46	2		0	0	0	0	0	2	1	1	37	148	0	43	2		0	0	0	0	0	2	-20.000000	1	1	121412	2	30	1	1	2	3	2.131241	0	0.530000	1.810000	0.536146	0.760000	5.500000e-01	1.000000	0.750000	0.773132	0.760000	0	6.500000e-01	0.890000
BCAT2	587	broad.mit.edu	37	19	49300574	49300574	+	Missense_Mutation	SNP	C	C	T	rs139881168		TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr19:49300574C>T	ENST00000316273.6	-	7	724	c.712G>A	c.(712-714)Gtg>Atg	p.V238M	BCAT2_ENST00000402551.1_Missense_Mutation_p.V198M|BCAT2_ENST00000598162.1_Missense_Mutation_p.V238M|BCAT2_ENST00000599246.1_Missense_Mutation_p.V146M|BCAT2_ENST00000597011.1_Missense_Mutation_p.V198M|BCAT2_ENST00000545387.2_Missense_Mutation_p.V146M	NM_001190.3	NP_001181.2	O15382	BCAT2_HUMAN	branched chain amino-acid transaminase 2, mitochondrial			12		all_epithelial(76;7e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		L-Isoleucine(DB00167)|L-Leucine(DB00149)	TGCACTAACACGGTGGGCCCA	0.617000																								0							SO:0001583	missense			ENST00000316273.6	1	1	hg19	CCDS12735.1	.	.	.	.	.	.	.	.	.	.	C	15.76	2.928560	0.52759	0.0	1.16E-4	ENSG00000105552	ENST00000316273;ENST00000545387;ENST00000402551	T;T;T	0.21543	2.0;2.0;2.0	5.06	5.06	0.68205	.	0.061208	0.64402	D	0.000005	T	0.31575	0.0801	L	0.35414	1.06	0.37282	D	0.907881	D;D;D;D	0.89917	0.999;1.0;0.976;1.0	D;D;P;D	0.68483	0.937;0.937;0.458;0.958	T	0.17379	-1.0371	10	0.87932	D	0	-16.3767	9.8608	0.41114	0.0:0.9059:0.0:0.094	.	198;238;146;238	B3KSI3;Q53EW7;O15382-2;O15382	.;.;.;BCAT2_HUMAN	M	238;146;198	ENSP00000322991:V238M;ENSP00000440973:V146M;ENSP00000385161:V198M	ENSP00000322991:V238M	V	-	1	0	BCAT2	53992386	0.991000	0.36638	0.476000	0.27291	0.493000	0.33554	2.602000	0.46257	2.523000	0.85059	0.491000	0.48974	GTG		TCGA-2L-AAQE-01A-11D-A397-08	BCAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466202.1	1	0	1	23	95	0	24	1	9.999561e-01	34	38	0	24	2		0	0	0	0	0	2	1	9.999997e-01	22	95	0	24	2		0	0	0	0	0	2	-3.604268	1	1	121412	3	34	1	1	2	3	2.131241	0	0.530000	1.810000	0.536146	0.750000	5.000000e-01	1.000000	1.000000	0.765225	0.750000	0	6.100000e-01	0.920000
FBN3	84467	broad.mit.edu	37	19	8155007	8155007	+	Missense_Mutation	SNP	C	C	T	rs149936210		TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr19:8155007C>T	ENST00000600128.1	-	49	6574	c.6160G>A	c.(6160-6162)Gaa>Aaa	p.E2054K	FBN3_ENST00000601739.1_Missense_Mutation_p.E2054K|FBN3_ENST00000270509.2_Missense_Mutation_p.E2054K			Q75N90	FBN3_HUMAN	fibrillin 3			132					GGACACAGTTCGCAGGGGTCT	0.612000																								0							SO:0001583	missense			ENST00000600128.1	1	1	hg19	CCDS12196.1	2	9.157509157509158E-4	0	0.0	2	0.0055248618784530384	0	0.0	0	0.0	C	21.7	4.181062	0.78677	2.27E-4	0.0	ENSG00000142449	ENST00000270509	D	0.95885	-3.84	4.13	4.13	0.48395	Matrix fibril-associated (3);TGF-beta binding (1);	0.000000	0.85682	U	0.000000	D	0.95478	0.8531	M	0.82193	2.58	0.80722	D	1	D	0.69078	0.997	P	0.52758	0.708	D	0.94770	0.7944	10	0.51188	T	0.08	.	16.3935	0.83548	0.0:1.0:0.0:0.0	.	2054	Q75N90	FBN3_HUMAN	K	2054	ENSP00000270509:E2054K	ENSP00000270509:E2054K	E	-	1	0	FBN3	8061007	1.000000	0.71417	0.942000	0.38095	0.333000	0.28666	5.572000	0.67411	1.836000	0.53414	0.462000	0.41574	GAA		TCGA-2L-AAQE-01A-11D-A397-08	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	1	0	1	51	136	0	40		0	0	0	0	40	2		0	0	0	0	0	2	1	1	50	133	0	38	2		0	0	0	0	0	2	-20.000000	1	1	121412	3	38	1	1	2	3	2.124373	0	0.530000	1.810000	0.532478	0.990000	8.000000e-01	1.000000	1.000000	0.968762	0.990000	1	9.100000e-01	1.000000
OR7D2	162998	broad.mit.edu	37	19	9296821	9296821	+	Missense_Mutation	SNP	C	C	T	rs150499443		TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr19:9296821C>T	ENST00000344248.2	+	1	543	c.364C>T	c.(364-366)Cgg>Tgg	p.R122W		NM_175883.2	NP_787079.1	Q96RA2	OR7D2_HUMAN	olfactory receptor, family 7, subfamily D, member 2			20					GGCCTATGACCGGTTTGTGGC	0.507000																								0							SO:0001583	missense			ENST00000344248.2	0	1	hg19	CCDS32900.1	.	.	.	.	.	.	.	.	.	.	C	11.95	1.790563	0.31685	4.54E-4	0.0	ENSG00000188000	ENST00000344248	T	0.77620	-1.11	2.21	-0.197	0.13228	GPCR, rhodopsin-like superfamily (1);	0.200776	0.24490	U	0.038067	D	0.82309	0.5009	H	0.98314	4.2	0.22226	N	0.999272	P	0.35684	0.515	B	0.30572	0.117	T	0.77032	-0.2738	10	0.87932	D	0	.	8.8799	0.35367	0.5707:0.4293:0.0:0.0	.	122	Q96RA2	OR7D2_HUMAN	W	122	ENSP00000345563:R122W	ENSP00000345563:R122W	R	+	1	2	OR7D2	9157821	0.418000	0.25440	0.996000	0.52242	0.822000	0.46500	0.150000	0.16263	0.051000	0.15978	0.511000	0.50034	CGG		TCGA-2L-AAQE-01A-11D-A397-08	OR7D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449002.1	0	0	0	9	652	0	137		0	0	0	0	137	2		0	0	0	0	0	2	1	9.938478e-01	9	642	0	136	2		0	0	0	0	0	2	-2.019665	0	1	121412	3	45	1	1	2	3	2.124373	0	0.530000	1.810000	0.532478	0.050000	1.000000e-02	0.110000	0.060000	0.066441	0.050000	0	3.000000e-02	0.080000
FLG	2312	broad.mit.edu	37	1	152286796	152286796	+	Missense_Mutation	SNP	T	T	A			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr1:152286796T>A	ENST00000368799.1	-	3	601	c.566A>T	c.(565-567)gAa>gTa	p.E189V	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin			424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)		TCTAGTATTTTCAGTCTTGTT	0.308000									Ichthyosis															0							SO:0001583	missense	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	ENST00000368799.1	1	1	hg19	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	T	10.59	1.391622	0.25118	.	.	ENSG00000143631	ENST00000368799	T	0.00801	5.68	3.68	-3.27	0.05048	.	.	.	.	.	T	0.00328	0.0010	N	0.08118	0	0.09310	N	1	D	0.53885	0.963	P	0.53035	0.716	T	0.48502	-0.9030	9	0.29301	T	0.29	0.9076	4.776	0.13180	0.0:0.3342:0.3439:0.322	.	189	P20930	FILA_HUMAN	V	189	ENSP00000357789:E189V	ENSP00000357789:E189V	E	-	2	0	FLG	150553420	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.049000	0.03514	-0.583000	0.05921	0.378000	0.23410	GAA		TCGA-2L-AAQE-01A-11D-A397-08	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	1	0	0	10	206	0	76		0	0	0	0	76	2		0	0	0	0	0	2	1	9.970829e-01	10	206	0	76	2		0	0	0	0	0	2	-4.509725	1	1	0	0		1	0	1	1	1.973246	0	0.530000	1.810000	0.489408	0.160000	8.000000e-02	0.280000	0.160000	0.174429	0.160000	0	1.100000e-01	0.220000
TMEM63A	9725	broad.mit.edu	37	1	226037743	226037743	+	Silent	SNP	C	C	T			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr1:226037743C>T	ENST00000366835.3	-	21	2211	c.1941G>A	c.(1939-1941)cgG>cgA	p.R647R		NM_014698.2	NP_055513.2	O94886	CSCL1_HUMAN	transmembrane protein 63A			24	Breast(184;0.197)				AGAGGTTGTGCCGGTCCACCA	0.602000																								0							SO:0001819	synonymous_variant			ENST00000366835.3	0	1	hg19	CCDS31042.1																																																																																				TCGA-2L-AAQE-01A-11D-A397-08	TMEM63A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091154.2	0	0	0	5	422	0	95	0	6.921161e-01	0	192	0	95	2		0	0	0	0	0	2	1	9.367252e-01	5	419	0	95	2		0	0	0	0	0	2	-1.923306	0	1	0	0		1	0	1	1	1.973246	0	0.530000	1.810000	0.489408	0.040000	0	0.090000	0.040000	0.048395	0.040000	0	2.000000e-02	0.070000
OBSCN	84033	broad.mit.edu	37	1	228451984	228451984	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr1:228451984G>A	ENST00000422127.1	+	16	4797	c.4753G>A	c.(4753-4755)Gtg>Atg	p.V1585M	OBSCN_ENST00000359599.6_Missense_Mutation_p.V241M|OBSCN_ENST00000284548.11_Missense_Mutation_p.V1585M|OBSCN_ENST00000570156.2_Missense_Mutation_p.V1769M|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000366709.4_5'UTR	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF			223		Prostate(94;0.0405)			AATGGAGGCCGTGGGCTGCAC	0.662000																								0							SO:0001583	missense			ENST00000422127.1	0	1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	.	9.689	1.151336	0.21371	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000359599	T;T;T	0.67523	-0.27;-0.27;-0.27	4.82	-9.64	0.00541	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	2.685180	0.02136	N	0.056724	T	0.57519	0.2059	L	0.34521	1.04	0.09310	N	0.999999	D;D	0.59767	0.965;0.986	P;P	0.52881	0.712;0.462	T	0.65611	-0.6126	10	0.48119	T	0.1	.	3.3118	0.07020	0.2018:0.2166:0.4408:0.1408	.	1585;1585	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	M	1585;1585;241	ENSP00000284548:V1585M;ENSP00000409493:V1585M;ENSP00000352613:V241M	ENSP00000284548:V1585M	V	+	1	0	OBSCN	226518607	0.002000	0.14202	0.000000	0.03702	0.000000	0.00434	0.071000	0.14594	-2.145000	0.00801	-0.218000	0.12543	GTG		TCGA-2L-AAQE-01A-11D-A397-08	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		0	0	0	5	317	0	89	0	0	0	1	0	89	2		0	0	0	0	0	2	1	9.364698e-01	5	314	0	87	2		0	0	0	0	0	2	-2.778025	1	1	121122	5	41	1	0	1	1	1.973246	0	0.530000	1.810000	0.489408	0.050000	1.000000e-02	0.120000	0.050000	0.064111	0.050000	0	3.000000e-02	0.090000
CHD6	84181	broad.mit.edu	37	20	40052243	40052243	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr20:40052243G>A	ENST00000373233.3	-	30	4621	c.4444C>T	c.(4444-4446)Cgc>Tgc	p.R1482C		NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6			129		Myeloproliferative disorder(115;0.00425)			GAAATGATGCGGAACTGTGTC	0.443000																								0							SO:0001583	missense			ENST00000373233.3	0	1	hg19	CCDS13317.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.928613	0.92389	.	.	ENSG00000124177	ENST00000373233	D	0.94793	-3.52	6.07	6.07	0.98685	SANT domain, DNA binding (1);	0.000000	0.64402	D	0.000007	D	0.97876	0.9302	M	0.89287	3.02	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.97909	1.0307	10	0.87932	D	0	-12.954	20.6439	0.99570	0.0:0.0:1.0:0.0	.	1482	Q8TD26	CHD6_HUMAN	C	1482	ENSP00000362330:R1482C	ENSP00000362330:R1482C	R	-	1	0	CHD6	39485657	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.405000	0.73272	2.884000	0.98904	0.655000	0.94253	CGC		TCGA-2L-AAQE-01A-11D-A397-08	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1	0	0	0	5	787	0	214	0	3.446151e-03	0	11	0	214	2		0	0	0	0	0	2	1	9.372926e-01	5	785	0	212	2		0	0	0	0	0	2	-1.736653	0	1	0	0		1	1	2	3	2.177491	0	0.530000	1.810000	0.538560	0.020000	0	1.000000	0.020000	0.082419	0.020000	0	0	0.050000
PTK6	5753	broad.mit.edu	37	20	62166328	62166328	+	Silent	SNP	C	C	T			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr20:62166328C>T	ENST00000217185.2	-	2	342	c.315G>A	c.(313-315)agG>agA	p.R105R	PTK6_ENST00000542869.1_Intron	NM_005975.3	NP_005966.1	Q13882	PTK6_HUMAN	protein tyrosine kinase 6			15	all_cancers(38;2.51e-11)		Epithelial(9;1.5e-08)|all cancers(9;8.67e-08)|BRCA - Breast invasive adenocarcinoma(10;6.43e-06)	Vandetanib(DB05294)	TCTCGCTGACCCTGATCAGGA	0.692000																								0							SO:0001819	synonymous_variant			ENST00000217185.2	1	1	hg19	CCDS13524.1																																																																																				TCGA-2L-AAQE-01A-11D-A397-08	PTK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080313.1	1	0	0	16	77	0	20	1	9.999998e-01	80	87	0	20	2		0	0	0	0	0	2	1	9.999570e-01	16	76	0	20	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	1	2	3	2.177491	0	0.530000	1.810000	0.538560	0.670000	4.100000e-01	1.000000	0.660000	0.697733	0.670000	0	5.300000e-01	0.870000
TIAM1	7074	broad.mit.edu	37	21	32502539	32502539	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr21:32502539G>A	ENST00000286827.3	-	26	4508	c.4037C>T	c.(4036-4038)gCg>gTg	p.A1346V	TIAM1_ENST00000541036.1_Missense_Mutation_p.A1286V	NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1			115					ACCTGCACTCGCCAAAGCTCG	0.473000																								0							SO:0001583	missense			ENST00000286827.3	0	1	hg19	CCDS13609.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.02|14.02	2.411603|2.411603	0.42817|0.42817	.|.	.|.	ENSG00000156299|ENSG00000156299	ENST00000286827;ENST00000541036|ENST00000423206	T;T|.	0.43294|.	0.95;0.96|.	6.03|6.03	6.03|6.03	0.97812|0.97812	Pleckstrin homology-type (1);Pleckstrin homology domain (1);|.	0.249575|.	0.39544|.	N|.	0.001336|.	T|.	0.69495|.	0.3117|.	L|L	0.44542|0.44542	1.39|1.39	0.38497|0.38497	D|D	0.948125|0.948125	B;B;B|.	0.28971|.	0.229;0.016;0.147|.	B;B;B|.	0.27170|.	0.077;0.003;0.035|.	T|.	0.65055|.	-0.6261|.	10|.	0.46703|.	T|.	0.11|.	.|.	20.5666|20.5666	0.99351|0.99351	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1286;1286;1346|.	F5GZ53;B7ZLR6;Q13009|.	.;.;TIAM1_HUMAN|.	V|X	1346;1286|1	ENSP00000286827:A1346V;ENSP00000441570:A1286V|.	ENSP00000286827:A1346V|.	A|R	-|-	2|1	0|2	TIAM1|TIAM1	31424410|31424410	1.000000|1.000000	0.71417|0.71417	0.983000|0.983000	0.44433|0.44433	0.291000|0.291000	0.27294|0.27294	7.077000|7.077000	0.76814|0.76814	2.854000|2.854000	0.98071|0.98071	0.655000|0.655000	0.94253|0.94253	GCG|CGA		TCGA-2L-AAQE-01A-11D-A397-08	TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192552.1	0	0	0	6	733	0	209	0	1.015770e-04	0	2	0	209	2		0	0	0	0	0	2	1	9.632487e-01	6	722	0	209	2		0	0	0	0	0	2	-1.857569	0	1	121412	1	35	1	0	1	1	1.897546	1	0.530000	1.810000	0.463133	0.020000	0	0.060000	0.030000	0.030917	0.020000	0	1.000000e-02	0.040000
DOPEY2	9980	broad.mit.edu	37	21	37609569	37609569	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr21:37609569C>T	ENST00000399151.3	+	16	2717	c.2632C>T	c.(2632-2634)Cgt>Tgt	p.R878C		NM_005128.2	NP_005119.2	Q9Y3R5	DOP2_HUMAN	dopey family member 2			58					GAGGGTGGCTCGTGTGCTTTG	0.587000																								0							SO:0001583	missense			ENST00000399151.3	1	1	hg19	CCDS13643.1	.	.	.	.	.	.	.	.	.	.	C	14.48	2.547731	0.45383	.	.	ENSG00000142197	ENST00000399151	T	0.67523	-0.27	5.3	5.3	0.74995	.	0.368606	0.30076	N	0.010472	T	0.56601	0.1996	L	0.36672	1.1	0.26838	N	0.968431	B	0.18461	0.028	B	0.10450	0.005	T	0.52442	-0.8575	10	0.48119	T	0.1	-8.3965	12.7613	0.57365	0.0:0.9152:0.0:0.0848	.	878	Q9Y3R5	DOP2_HUMAN	C	878	ENSP00000382104:R878C	ENSP00000382104:R878C	R	+	1	0	DOPEY2	36531439	0.604000	0.26932	0.983000	0.44433	0.978000	0.69477	5.633000	0.67825	2.489000	0.83994	0.591000	0.81541	CGT		TCGA-2L-AAQE-01A-11D-A397-08	DOPEY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194636.1	1	0	1	46	261	0	60	0	1.134076e-01	0	4	0	60	2		0	0	0	0	0	2	1	1	46	250	0	59	2		0	0	0	0	0	2	-2.926773	1	1	0	0		1	0	1	1	1.897546	1	0.530000	1.810000	0.463133	0.490000	3.700000e-01	0.630000	0.490000	0.500596	0.490000	0	4.200000e-01	0.570000
ZNF280A	129025	broad.mit.edu	37	22	22869193	22869193	+	Silent	SNP	G	G	A			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr22:22869193G>A	ENST00000302097.3	-	2	1014	c.762C>T	c.(760-762)gaC>gaT	p.D254D	snoU13_ENST00000459485.1_RNA	NM_080740.3	NP_542778.1	P59817	Z280A_HUMAN	zinc finger protein 280A			18	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)			GACTTGAAATGTCTGTCATTG	0.408000																								0							SO:0001819	synonymous_variant			ENST00000302097.3	1	1	hg19	CCDS13800.1																																																																																				TCGA-2L-AAQE-01A-11D-A397-08	ZNF280A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075433.3	1	0	1	181	286	0	142		0	0	0	0	142	2		0	0	0	0	0	2	1	1	176	285	0	141	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	0	1	1	1.751573	1	0.530000	1.810000	0.365122	0.990000	9.100000e-01	1.000000	1.000000	0.984755	0.990000	1	9.500000e-01	1.000000
RGPD2	729857	broad.mit.edu	37	2	88125207	88125207	+	Silent	SNP	C	C	T			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr2:88125207C>T	ENST00000398146.3	-	1	264	c.42G>A	c.(40-42)tcG>tcA	p.S14S	RGPD2_ENST00000420840.2_Intron|RGPD2_ENST00000327544.6_5'UTR			P0DJD1	RGPD2_HUMAN	RANBP2-like and GRIP domain containing 2			2					AGCCCTGCACCGAGGCGAGGT	0.721000																								0							SO:0001819	synonymous_variant			ENST00000398146.3	0	1	hg19	CCDS42710.2																																																																																				TCGA-2L-AAQE-01A-11D-A397-08	RGPD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330534.2	0	0	0	14	40	0	11		0	0	0	0	11	2		0	0	0	0	0	2		0	0	0	0	0	2		0	0	0	0	0	2	-13.483960	1	0	0	0		1	1	2	3	2.159731	0	0.530000	1.810000	0.536146	0.990000	6.000000e-01	1.000000	1.000000	0.919173	0.990000	1	7.800000e-01	1.000000
NCBP2	22916	broad.mit.edu	37	3	196664485	196664485	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr3:196664485G>A	ENST00000321256.5	-	3	388	c.295C>T	c.(295-297)Cgg>Tgg	p.R99W	NCBP2_ENST00000447325.1_Missense_Mutation_p.R29W|NCBP2_ENST00000467803.1_5'UTR|NCBP2_ENST00000452404.2_Missense_Mutation_p.R81W|NCBP2_ENST00000427641.2_Missense_Mutation_p.R46W|NCBP2-AS1_ENST00000447775.1_RNA|NCBP2_ENST00000422610.1_Missense_Mutation_p.R29W	NM_007362.3	NP_031388.2	P52298	NCBP2_HUMAN	nuclear cap binding protein subunit 2, 20kDa	p.R99W(1)		5	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;3.42e-24)|all cancers(36;2.27e-22)|OV - Ovarian serous cystadenocarcinoma(49;4.13e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)		TTTATGTACCGCATGGCGTTT	0.488000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000321256.5	0	1	hg19	CCDS3323.1	.	.	.	.	.	.	.	.	.	.	G	17.74	3.462954	0.63513	.	.	ENSG00000114503	ENST00000447325;ENST00000321256;ENST00000427641;ENST00000452404;ENST00000422610;ENST00000411704	T;T;T;T;T;T	0.75260	-0.92;2.27;-0.92;2.27;-0.92;-0.92	4.96	2.05	0.26809	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.057701	0.64402	D	0.000003	D	0.85248	0.5653	M	0.82823	2.61	0.80722	D	1	P;D;P	0.89917	0.716;1.0;0.844	B;D;B	0.80764	0.138;0.994;0.217	D	0.84961	0.0877	10	0.48119	T	0.1	.	13.3628	0.60665	0.0:0.0:0.4238:0.5762	.	81;46;99	P52298-2;E9PAR5;P52298	.;.;NCBP2_HUMAN	W	29;99;46;81;29;29	ENSP00000413518:R29W;ENSP00000326806:R99W;ENSP00000397619:R46W;ENSP00000412785:R81W;ENSP00000394105:R29W;ENSP00000389315:R29W	ENSP00000326806:R99W	R	-	1	2	NCBP2	198148882	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	0.449000	0.21744	0.323000	0.23307	-0.182000	0.12963	CGG		TCGA-2L-AAQE-01A-11D-A397-08	NCBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340470.2	0	0	0	5	494	1	93	0	5.516925e-03	0	201	1	93	9		0	0	0	0	0	2	0	4.553594e-03	5	490	1	91	18		0	0	0	0	0	2	-2.167731	0	1	0	0		1	1	2	3	2.162847	0	0.530000	1.810000	0.536146	0.030000	0	1.000000	0.040000	0.081679	0.030000	0	2.000000e-02	0.070000
FBXL5	26234	broad.mit.edu	37	4	15628553	15628553	+	Missense_Mutation	SNP	G	G	T			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr4:15628553G>T	ENST00000341285.3	-	8	1191	c.1067C>A	c.(1066-1068)cCt>cAt	p.P356H	FBXL5_ENST00000412094.2_Missense_Mutation_p.P339H|FBXL5_ENST00000382358.4_Missense_Mutation_p.P230H	NM_001193534.1|NM_001193535.1|NM_012161.3	NP_001180463.1|NP_001180464.1|NP_036293.1	Q9UKA1	FBXL5_HUMAN	F-box and leucine-rich repeat protein 5			13					CTCCAGGTTAGGACAAAGCTC	0.328000																								0							SO:0001583	missense			ENST00000341285.3	0	1	hg19	CCDS3415.1	.	.	.	.	.	.	.	.	.	.	G	29.0	4.966766	0.92855	.	.	ENSG00000118564	ENST00000341285;ENST00000412094;ENST00000382358	T;T;T	0.19669	2.13;2.13;2.13	5.98	5.98	0.97165	.	0.000000	0.85682	D	0.000000	T	0.49795	0.1578	M	0.71581	2.175	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.43718	-0.9374	10	0.87932	D	0	-27.9909	20.0624	0.97681	0.0:0.0:1.0:0.0	.	339;356	Q9UKA1-2;Q9UKA1	.;FBXL5_HUMAN	H	356;339;230	ENSP00000344866:P356H;ENSP00000408679:P339H;ENSP00000371795:P230H	ENSP00000344866:P356H	P	-	2	0	FBXL5	15237651	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.230000	0.95299	2.838000	0.97847	0.591000	0.81541	CCT		TCGA-2L-AAQE-01A-11D-A397-08	FBXL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214235.2	0	0	0	5	224	0	52	0	5.886872e-01	0	82	0	52	2		0	0	0	0	0	2	1	9.382227e-01	5	224	0	52	2		0	0	0	0	0	2	-3.095176	1	1	0	0		1	0	1	1	1.907445	0	0.530000	1.810000	0.474273	0.070000	2.000000e-02	0.160000	0.080000	0.087206	0.070000	0	4.000000e-02	0.120000
VDAC1	7416	broad.mit.edu	37	5	133316519	133316519	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08			G	A	G	G		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr5:133316519G>A	ENST00000265333.3	-	6	696	c.452C>T	c.(451-453)gCc>gTc	p.A151V	VDAC1_ENST00000395044.3_Missense_Mutation_p.A151V|VDAC1_ENST00000395047.2_Missense_Mutation_p.A151V	NM_003374.2	NP_003365.1	P21796	VDAC1_HUMAN	voltage-dependent anion channel 1			4			KIRC - Kidney renal clear cell carcinoma(527;0.00806)|Kidney(363;0.02)	Dihydroxyaluminium(DB01375)	CTGGTAGCCGGCCAGCCAGCC	0.527000													NSCLC(127;1776 1806 35523 41489 48154)											0							SO:0001583	missense			ENST00000265333.3	0	1	hg19	CCDS4168.1	.	.	.	.	.	.	.	.	.	.	G	35	5.499741	0.96355	.	.	ENSG00000213585	ENST00000265333;ENST00000395044;ENST00000395047;ENST00000425992	T;T;T;T	0.39997	1.05;1.05;1.05;1.05	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.51770	0.1694	L	0.52573	1.65	0.80722	D	1	P	0.48089	0.905	P	0.51079	0.658	T	0.49476	-0.8936	10	0.48119	T	0.1	.	19.2582	0.93955	0.0:0.0:1.0:0.0	.	151	P21796	VDAC1_HUMAN	V	151	ENSP00000265333:A151V;ENSP00000378484:A151V;ENSP00000378487:A151V;ENSP00000390129:A151V	ENSP00000265333:A151V	A	-	2	0	VDAC1	133344418	1.000000	0.71417	0.978000	0.43139	0.973000	0.67179	7.885000	0.87282	2.622000	0.88805	0.655000	0.94253	GCC		TCGA-2L-AAQE-01A-11D-A397-08	VDAC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259208.1	0	0	0	5	324	0	50	0	9.949625e-01	1	710	0	50	2		0	0	0	0	0	2	1	9.369998e-01	5	322	0	49	2		0	0	0	0	0	2	-3.132440	1	1	0	0		1	1	2	3	2.173791	0	0.530000	1.810000	0.537356	0.060000	1.000000e-02	1.000000	0.060000	0.113003	0.060000	0	3.000000e-02	0.100000
SPOCK1	6695	broad.mit.edu	37	5	136315143	136315143	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr5:136315143C>T	ENST00000394945.1	-	10	1176	c.1007G>A	c.(1006-1008)cGg>cAg	p.R336Q	SPOCK1_ENST00000509978.1_5'UTR|SPOCK1_ENST00000282223.7_Missense_Mutation_p.R336Q	NM_004598.3	NP_004589.1	Q08629	TICN1_HUMAN	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 1			18			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)		CTCATTACACCGAGGTATGAA	0.542000																								0							SO:0001583	missense			ENST00000394945.1	1	1	hg19	CCDS4191.1	.	.	.	.	.	.	.	.	.	.	C	15.13	2.743313	0.49151	.	.	ENSG00000152377	ENST00000394945;ENST00000282223	T;T	0.61040	0.14;0.14	4.95	4.95	0.65309	Thyroglobulin type-1 (6);	0.000000	0.85682	D	0.000000	T	0.48642	0.1511	N	0.02334	-0.595	0.51767	D	0.999933	D	0.89917	1.0	D	0.85130	0.997	T	0.51639	-0.8680	10	0.16896	T	0.51	.	12.3181	0.54969	0.169:0.831:0.0:0.0	.	336	Q08629	TICN1_HUMAN	Q	336	ENSP00000378401:R336Q;ENSP00000282223:R336Q	ENSP00000282223:R336Q	R	-	2	0	SPOCK1	136343042	0.998000	0.40836	0.996000	0.52242	0.927000	0.56198	3.885000	0.56182	2.277000	0.76020	0.650000	0.86243	CGG		TCGA-2L-AAQE-01A-11D-A397-08	SPOCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251222.1	1	0	1	64	194	0	51	0	5.526920e-01	0	7	0	51	2		0	0	0	0	0	2	1	1	63	191	0	50	2		0	0	0	0	0	2	-4.153474	1	1	121412	2	30	1	1	2	3	2.173791	0	0.530000	1.810000	0.537356	0.950000	7.500000e-01	1.000000	1.000000	0.935591	0.950000	1	8.500000e-01	1.000000
PCDHA7	56141	broad.mit.edu	37	5	140216036	140216036	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr5:140216036G>A	ENST00000525929.1	+	1	2068	c.2068G>A	c.(2068-2070)Gag>Aag	p.E690K	PCDHA3_ENST00000522353.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA7_ENST00000378125.3_Missense_Mutation_p.E690K|PCDHA1_ENST00000394633.3_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529619.1_Intron	NM_018910.2	NP_061733.1	Q9UN72	PCDA7_HUMAN	protocadherin alpha 7			63			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		TGCAGGCCCAGAGACCGAGCT	0.637000													NSCLC(160;258 2013 5070 22440 28951)											0							SO:0001583	missense			ENST00000525929.1	1	1	hg19	CCDS54918.1	.	.	.	.	.	.	.	.	.	.	G	9.958	1.222045	0.22457	.	.	ENSG00000204963	ENST00000525929;ENST00000378125	T;T	0.52754	0.65;0.66	3.57	1.55	0.23275	.	3.216130	0.05786	U	0.609423	T	0.50188	0.1601	M	0.82132	2.575	0.09310	N	1	B;B	0.09022	0.002;0.001	B;B	0.15052	0.012;0.005	T	0.41822	-0.9487	10	0.33940	T	0.23	.	7.687	0.28546	0.0:0.2711:0.5139:0.215	.	690;690	Q9UN72-2;Q9UN72	.;PCDA7_HUMAN	K	690	ENSP00000436426:E690K;ENSP00000367365:E690K	ENSP00000367365:E690K	E	+	1	0	PCDHA7	140196220	0.000000	0.05858	0.002000	0.10522	0.003000	0.03518	0.072000	0.14617	0.812000	0.34326	-0.467000	0.05162	GAG		TCGA-2L-AAQE-01A-11D-A397-08	PCDHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372887.2	1	0	1	54	416	0	76		0	0	0	0	76	2		0	0	0	0	0	2	1	1	53	411	0	74	2		0	0	0	0	0	2	-19.689040	1	1	0	0		1	1	2	3	2.173791	0	0.530000	1.810000	0.537356	0.440000	3.300000e-01	1.000000	0.440000	0.471915	0.440000	0	3.800000e-01	0.510000
POU4F3	5459	broad.mit.edu	37	5	145719822	145719822	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr5:145719822C>T	ENST00000230732.4	+	2	921	c.832C>T	c.(832-834)Cgc>Tgc	p.R278C	CTC-359M8.1_ENST00000515598.1_RNA	NM_002700.2	NP_002691.1	Q15319	PO4F3_HUMAN	POU class 4 homeobox 3			17			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		GAAGCGCAAACGCACGTCCAT	0.612000																								0							SO:0001583	missense			ENST00000230732.4	1	1	hg19	CCDS4281.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.004800	0.74932	.	.	ENSG00000091010	ENST00000230732	D	0.99186	-5.53	4.62	4.62	0.57501	Homeodomain-related (1);Homeobox (3);POU (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.99638	0.9867	H	0.99130	4.44	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97244	0.9893	10	0.87932	D	0	.	16.3979	0.83621	0.0:1.0:0.0:0.0	.	278	Q15319	PO4F3_HUMAN	C	278	ENSP00000230732:R278C	ENSP00000230732:R278C	R	+	1	0	POU4F3	145700015	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.629000	0.83207	2.372000	0.80975	0.462000	0.41574	CGC		TCGA-2L-AAQE-01A-11D-A397-08	POU4F3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251887.2	1	0	1	56	218	1	55		0	0	0	1	55	2		0	0	0	0	0	2	1	9.999998e-01	55	218	1	55	17		0	0	0	0	0	2	-20.000000	1	1	0	0		1	1	2	3	2.173791	0	0.530000	1.810000	0.537356	0.780000	6.100000e-01	1.000000	0.780000	0.798587	0.780000	0	6.900000e-01	0.900000
UGT3A2	167127	broad.mit.edu	37	5	36049023	36049023	+	Missense_Mutation	SNP	A	A	T			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr5:36049023A>T	ENST00000282507.3	-	4	912	c.811T>A	c.(811-813)Ttg>Atg	p.L271M	UGT3A2_ENST00000504954.1_Intron|UGT3A2_ENST00000513300.1_Missense_Mutation_p.L237M|UGT3A2_ENST00000545528.1_Intron	NM_174914.3	NP_777574.2	Q3SY77	UD3A2_HUMAN	UDP glycosyltransferase 3 family, polypeptide A2			43	all_lung(31;0.000179)		Lung(74;0.111)|Epithelial(62;0.113)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)		TTTTCCATCAAGCCTCCAACA	0.453000																								0							SO:0001583	missense			ENST00000282507.3	1	1	hg19	CCDS3914.1	.	.	.	.	.	.	.	.	.	.	A	16.16	3.044979	0.55110	.	.	ENSG00000168671	ENST00000282507;ENST00000513300	T;T	0.63580	-0.05;-0.05	3.45	0.914	0.19360	.	0.107344	0.38492	N	0.001677	T	0.67050	0.2852	L	0.60067	1.865	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.80764	0.987;0.994	T	0.64398	-0.6417	10	0.72032	D	0.01	.	1.5646	0.02602	0.5509:0.1761:0.1021:0.171	.	237;271	E9PFK7;Q3SY77	.;UD3A2_HUMAN	M	271;237	ENSP00000282507:L271M;ENSP00000427404:L237M	ENSP00000282507:L271M	L	-	1	2	UGT3A2	36084780	0.139000	0.22563	0.911000	0.35937	0.961000	0.63080	0.431000	0.21444	0.186000	0.20125	0.533000	0.62120	TTG		TCGA-2L-AAQE-01A-11D-A397-08	UGT3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253771.2	1	0	1	40	274	0	70		0	0	0	0	70	2		0	0	0	0	0	2	1	1	40	270	0	70	2		0	0	0	0	0	2	-17.383150	1	1	0	0		1	1	2	3	2.173791	0	0.530000	1.810000	0.537356	0.490000	3.500000e-01	1.000000	0.490000	0.519704	0.490000	0	4.200000e-01	0.580000
BCLAF1	9774	broad.mit.edu	37	6	136599814	136599814	+	Nonsense_Mutation	SNP	G	G	A			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr6:136599814G>A	ENST00000531224.1	-	4	457	c.205C>T	c.(205-207)Cga>Tga	p.R69*	BCLAF1_ENST00000527536.1_Nonsense_Mutation_p.R69*|BCLAF1_ENST00000353331.4_Nonsense_Mutation_p.R67*|BCLAF1_ENST00000527759.1_Nonsense_Mutation_p.R67*|BCLAF1_ENST00000530767.1_Nonsense_Mutation_p.R69*|BCLAF1_ENST00000392348.2_Nonsense_Mutation_p.R67*	NM_001077441.1|NM_014739.2	NP_001070909.1|NP_055554.1	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1			9	Colorectal(23;0.24)				CCATAAGGTCGTCTCATTCCT	0.433000													Colon(142;1534 1789 5427 7063 28491)											0							SO:0001587	stop_gained			ENST00000531224.1	0	1	hg19	CCDS5177.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.201669	0.79015	.	.	ENSG00000029363	ENST00000531224;ENST00000353331;ENST00000527536;ENST00000530767;ENST00000527759;ENST00000392348;ENST00000529826	.	.	.	5.64	3.59	0.41128	.	0.000000	0.52532	D	0.000064	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.5909	16.2474	0.82450	0.0:0.0:0.7701:0.2299	.	.	.	.	X	69;67;69;69;67;67;69	.	ENSP00000229446:R67X	R	-	1	2	BCLAF1	136641507	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.151000	0.58105	1.318000	0.45170	0.557000	0.71058	CGA		TCGA-2L-AAQE-01A-11D-A397-08	BCLAF1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042375.2	1	0	0	45	332	0	123	0	8.155079e-01	0	25	0	123	2		0	0	0	0	0	2	1	1	39	329	0	120	2		0	0	0	0	0	2	-17.769040	1	1	121406	18	38	1	0	1	1	1.603364	1	0.530000	1.810000	0.360544	0.320000	2.400000e-01	0.420000	0.330000	0.335053	0.320000	0	2.800000e-01	0.380000
ABRA	137735	broad.mit.edu	37	8	107782214	107782214	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr8:107782214G>A	ENST00000311955.3	-	1	259	c.205C>T	c.(205-207)Cct>Tct	p.P69S		NM_139166.4	NP_631905.1			actin-binding Rho activating protein			27			OV - Ovarian serous cystadenocarcinoma(57;3.83e-09)		TGTGAAGTAGGGGGTGTGATT	0.592000																								0							SO:0001583	missense			ENST00000311955.3	1	1	hg19	CCDS6305.1	.	.	.	.	.	.	.	.	.	.	G	3.421	-0.118071	0.06838	.	.	ENSG00000174429	ENST00000311955	D	0.92446	-3.04	5.07	0.834	0.18880	.	0.373311	0.30020	N	0.010608	D	0.82926	0.5143	N	0.25647	0.755	0.09310	N	1	B	0.26809	0.16	B	0.24701	0.055	T	0.66452	-0.5920	10	0.10902	T	0.67	.	10.6755	0.45783	0.0:0.3894:0.4775:0.1331	.	69	Q8N0Z2	ABRA_HUMAN	S	69	ENSP00000311436:P69S	ENSP00000311436:P69S	P	-	1	0	ABRA	107851390	0.103000	0.21917	0.000000	0.03702	0.001000	0.01503	0.268000	0.18571	0.341000	0.23771	0.655000	0.94253	CCT		TCGA-2L-AAQE-01A-11D-A397-08	ABRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380416.1	1	0	1	61	501	0	95		0	0	0	0	95	2		0	0	0	0	0	2	1	1	58	500	0	94	2		0	0	0	0	0	2	-2.879461	1	1	0	0		1	1	2	3	2.648027	1	0.530000	1.810000	0.626895	0.510000	3.900000e-01	0.670000	0.510000	0.526688	0.510000	0	4.500000e-01	0.590000
COL22A1	169044	broad.mit.edu	37	8	139820045	139820045	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr8:139820045C>T	ENST00000303045.6	-	10	1906	c.1460G>A	c.(1459-1461)gGa>gAa	p.G487E	COL22A1_ENST00000435777.1_Missense_Mutation_p.G487E	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1			211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)		GCCAGCAACTCCCATTTCACC	0.443000										HNSCC(7;0.00092)														0							SO:0001583	missense			ENST00000303045.6	1	1	hg19	CCDS6376.1	.	.	.	.	.	.	.	.	.	.	C	14.78	2.636991	0.47049	.	.	ENSG00000169436	ENST00000303045;ENST00000435777	D;D	0.94184	-3.37;-3.37	4.61	4.61	0.57282	.	0.000000	0.46758	U	0.000262	D	0.96537	0.8870	H	0.96833	3.89	0.38814	D	0.955498	D	0.60160	0.987	P	0.50352	0.638	D	0.98256	1.0496	9	.	.	.	.	13.7328	0.62799	0.0:1.0:0.0:0.0	.	487	Q8NFW1	COMA1_HUMAN	E	487	ENSP00000303153:G487E;ENSP00000387655:G487E	.	G	-	2	0	COL22A1	139889227	0.715000	0.27946	0.317000	0.25265	0.125000	0.20455	3.700000	0.54786	2.520000	0.84964	0.644000	0.83932	GGA		TCGA-2L-AAQE-01A-11D-A397-08	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	1	0	0	50	673	0	115	0	3.890634e-01	1	18	0	115	2		0	0	0	0	0	2	1	1	50	667	0	115	2		0	0	0	0	0	2	-9.797079	1	1	0	0		1	1	3	4	2.724615	1	0.530000	1.810000	0.634582	0.350000	2.500000e-01	1.000000	0.340000	0.499856	0.350000	0	2.900000e-01	1.000000
ANK1	286	broad.mit.edu	37	8	41572577	41572577	+	Silent	SNP	G	G	A			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr8:41572577G>A	ENST00000347528.4	-	15	1701	c.1618C>T	c.(1618-1620)Ctg>Ttg	p.L540L	ANK1_ENST00000396945.1_Silent_p.L540L|ANK1_ENST00000289734.7_Silent_p.L540L|ANK1_ENST00000396942.1_Silent_p.L540L|ANK1_ENST00000379758.2_Silent_p.L540L|ANK1_ENST00000352337.4_Silent_p.L540L|ANK1_ENST00000265709.8_Silent_p.L573L	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic			122	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)		GCCACGTGCAGAGGGGTAAAT	0.622000																								0							SO:0001819	synonymous_variant			ENST00000347528.4	1	1	hg19	CCDS6119.1																																																																																				TCGA-2L-AAQE-01A-11D-A397-08	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317297.1	1	0	1	191	180	0	54		0	0	0	0	54	2		0	0	0	0	0	2	1	1	189	178	0	53	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	1	4	5	3.201363	1	0.530000	1.810000	0.705560	0.990000	9.900000e-01	1.000000	1.000000	1.000000	0.990000	1	9.900000e-01	1.000000
ZNF189	7743	broad.mit.edu	37	9	104170526	104170526	+	Missense_Mutation	SNP	G	G	A	rs146668775		TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr9:104170526G>A	ENST00000339664.2	+	3	605	c.476G>A	c.(475-477)cGc>cAc	p.R159H	ZNF189_ENST00000374861.3_Missense_Mutation_p.R145H|ZNF189_ENST00000259395.4_Missense_Mutation_p.R117H	NM_001278240.1	NP_001265169.1	O75820	ZN189_HUMAN	zinc finger protein 189			26		Acute lymphoblastic leukemia(62;0.0559)			GGTTTTGTCCGCAAGGCCCAT	0.383000																								0							SO:0001583	missense			ENST00000339664.2	0	1	hg19	CCDS6754.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	3.003	-0.205670	0.06180	0.0	2.33E-4	ENSG00000136870	ENST00000374861;ENST00000339664;ENST00000259395	T;T;T	0.15718	2.4;2.4;2.4	4.66	4.66	0.58398	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.49916	D	0.000138	T	0.10809	0.0264	L	0.28776	0.89	0.32692	N	0.513987	B;B;B	0.26902	0.033;0.163;0.163	B;B;B	0.15870	0.003;0.014;0.003	T	0.09250	-1.0683	10	0.16896	T	0.51	.	10.5539	0.45105	0.0:0.0:0.8078:0.1922	.	144;145;159	B7ZLK9;Q5T7D8;O75820	.;.;ZN189_HUMAN	H	145;159;117	ENSP00000363995:R145H;ENSP00000342019:R159H;ENSP00000259395:R117H	ENSP00000259395:R117H	R	+	2	0	ZNF189	103210347	0.000000	0.05858	1.000000	0.80357	0.998000	0.95712	0.052000	0.14163	2.873000	0.98535	0.563000	0.77884	CGC		TCGA-2L-AAQE-01A-11D-A397-08	ZNF189-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053447.1	0	0	0	5	277	0	77	0	2.013852e-02	0	10	0	77	2		0	0	0	0	0	2	1	9.380859e-01	5	277	0	76	2		0	0	0	0	0	2	-2.314507	0	1	121410	6	41	1	0	1	1	1.895776	1	0.530000	1.810000	0.469556	0.060000	1.000000e-02	0.130000	0.060000	0.070354	0.060000	0	3.000000e-02	0.100000
SMC2	10592	broad.mit.edu	37	9	106864325	106864325	+	Silent	SNP	C	C	T			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr9:106864325C>T	ENST00000286398.7	+	8	1009	c.721C>T	c.(721-723)Ctg>Ttg	p.L241L	SMC2_ENST00000303219.8_Silent_p.L241L|SMC2_ENST00000374793.3_Silent_p.L241L|SMC2_ENST00000374787.3_Silent_p.L241L	NM_001042551.1|NM_001265602.1|NM_006444.2	NP_001036016.1|NP_001252531.1|NP_006435.2	O95347	SMC2_HUMAN	structural maintenance of chromosomes 2			48					TCAGTTTTTGCTGGCTGAAGA	0.333000																								0							SO:0001819	synonymous_variant			ENST00000286398.7	0	1	hg19	CCDS35086.1																																																																																				TCGA-2L-AAQE-01A-11D-A397-08	SMC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053470.1	0	0	0	6	427	1	115	0	5.789190e-03	0	7	1	115	2		0	0	0	0	0	2	0	5.381804e-02	6	425	1	115	14		0	0	0	0	0	2	-2.129470	0	1	0	0		1	0	1	1	1.895776	1	0.530000	1.810000	0.469556	0.040000	1.000000e-02	0.100000	0.050000	0.053677	0.040000	0	2.000000e-02	0.070000
GTF3C5	9328	broad.mit.edu	37	9	135917536	135917536	+	Silent	SNP	C	C	T			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chr9:135917536C>T	ENST00000372097.5	+	2	539	c.216C>T	c.(214-216)caC>caT	p.H72H	GTF3C5_ENST00000372108.5_Silent_p.H72H|GTF3C5_ENST00000372099.6_Silent_p.H63H|GTF3C5_ENST00000372095.5_Intron|GTF3C5_ENST00000485692.1_Intron|GTF3C5_ENST00000342018.8_Silent_p.H72H	NM_012087.3	NP_036219.2	Q9Y5Q8	TF3C5_HUMAN	general transcription factor IIIC, polypeptide 5, 63kDa			21					CATACTGCCACCCAGTGTGCG	0.612000																								0							SO:0001819	synonymous_variant			ENST00000372097.5	1	1	hg19	CCDS6958.1																																																																																				TCGA-2L-AAQE-01A-11D-A397-08	GTF3C5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054826.1	1	0	0	51	287	0	90	1	9.997530e-01	25	47	0	90	2		0	0	0	0	0	2	1	1	50	286	0	88	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	0	1	1	1.908518	0	0.530000	1.810000	0.472710	0.500000	3.800000e-01	0.640000	0.510000	0.512738	0.500000	0	4.400000e-01	0.580000
CDKN2A	1029	broad.mit.edu	37	9	21971111	21971111	+	Missense_Mutation	SNP	G	G	A	rs121913385		TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	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-2L-AAQE-01A-11D-A397-08	CDKN2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000051915.1	1	0	0	16	51	0	23	1	1	351	2	0	23	2	1	9.999996e-01	28	76	0	111	2	1	9.998878e-01	14	43	0	18	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	0	0	0	1.326982	1	0.530000	1.810000	0.252782	0.490000	3.200000e-01	0.600000	0.550000	0.495243	0.490000	0	4.100000e-01	0.570000
MAGEB2	4113	broad.mit.edu	37	X	30237553	30237553	+	Missense_Mutation	SNP	A	A	T			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chrX:30237553A>T	ENST00000378988.4	+	2	957	c.856A>T	c.(856-858)Atg>Ttg	p.M286L		NM_002364.4	NP_002355.2	O15479	MAGB2_HUMAN	melanoma antigen family B, 2			23					AACCAGCAAGATGAAAGTCCT	0.507000																								0							SO:0001583	missense			ENST00000378988.4	1	1	hg19	CCDS14219.1	.	.	.	.	.	.	.	.	.	.	A	19.14	3.768852	0.69878	.	.	ENSG00000099399	ENST00000378988	T	0.05025	3.51	3.27	-0.453	0.12201	.	0.242459	0.43579	D	0.000556	T	0.11922	0.0290	M	0.80183	2.485	0.09310	N	1	P	0.35982	0.531	P	0.44422	0.449	T	0.09796	-1.0658	10	0.66056	D	0.02	.	5.7074	0.17915	0.5317:0.0:0.4683:0.0	.	286	O15479	MAGB2_HUMAN	L	286	ENSP00000368273:M286L	ENSP00000368273:M286L	M	+	1	0	MAGEB2	30147474	0.001000	0.12720	0.000000	0.03702	0.922000	0.55478	0.354000	0.20146	-0.185000	0.10550	0.356000	0.21956	ATG		TCGA-2L-AAQE-01A-11D-A397-08	MAGEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056157.1	1	0	1	20	71	0	19		0	0	0	0	19	2		0	0	0	0	0	2	1	9.999981e-01	20	71	0	19	2		0	0	0	0	0	2	-15.736300	1	1	121402	2	31	1	0	1	1			0.530000	1.810000	0.530000	0.410000	2.600000e-01	0.580000	0.410000	0.421942	0.410000	0	3.300000e-01	0.500000
MAGEE2	139599	broad.mit.edu	37	X	75004114	75004114	+	Missense_Mutation	SNP	T	T	C			TCGA-2L-AAQE-01A-11D-A397-08	TCGA-2L-AAQE-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d57069ad-4f07-4f3d-93a2-16b0c4a51325	43d83c90-8211-4c2a-92c4-eee9c092680e	g.chrX:75004114T>C	ENST00000373359.2	-	1	965	c.773A>G	c.(772-774)cAc>cGc	p.H258R		NM_138703.4	NP_619648.1	Q8TD90	MAGE2_HUMAN	melanoma antigen family E, 2			34					GATTTCCCTGTGGGCTCTAGA	0.498000																								0							SO:0001583	missense			ENST00000373359.2	1	1	hg19	CCDS14431.1	.	.	.	.	.	.	.	.	.	.	T	8.525	0.869554	0.17322	.	.	ENSG00000186675	ENST00000373359	T	0.04654	3.58	3.1	0.589	0.17452	.	.	.	.	.	T	0.05227	0.0139	L	0.60455	1.87	0.09310	N	1	B	0.25850	0.136	B	0.27262	0.078	T	0.41716	-0.9493	9	0.33940	T	0.23	.	2.0976	0.03672	0.2592:0.1513:0.0:0.5895	.	258	Q8TD90	MAGE2_HUMAN	R	258	ENSP00000362457:H258R	ENSP00000362457:H258R	H	-	2	0	MAGEE2	74920839	0.685000	0.27652	0.009000	0.14445	0.688000	0.40055	0.561000	0.23515	0.015000	0.14971	0.345000	0.21793	CAC		TCGA-2L-AAQE-01A-11D-A397-08	MAGEE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057288.1	1	0	1	49	173	0	53		0	0	0	0	53	2		0	0	0	0	0	2	1	1	49	172	0	53	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	0	1	1			0.530000	1.810000	0.530000	0.410000	3.100000e-01	0.520000	0.410000	0.419483	0.410000	0	3.600000e-01	0.470000
