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
PMEPA1	56937	broad.mit.edu	37	20	56227291	56227309	+	Frame_Shift_Del	DEL	GCCCCTCCATGCGCCCGCC	GCCCCTCCATGCGCCCGCC	-			TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08			GCCCCTCCATGCGCCCGCC	-	GCCCCTCCATGCGCCCGCC	GCCCCTCCATGCGCCCGCC		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr20:56227291_56227309delGCCCCTCCATGCGCCCGCC	ENST00000341744.3	-	4	983_1001	c.664_682delGGCGGGCGCATGGAGGGGC	c.(664-684)ggcgggcgcatggaggggccgfs	p.GGRMEGP222fs	PMEPA1_ENST00000395814.1_Frame_Shift_Del_p.GGRMEGP172fs|PMEPA1_ENST00000347215.4_Frame_Shift_Del_p.GGRMEGP187fs|PMEPA1_ENST00000265626.4_Frame_Shift_Del_p.GGRMEGP172fs|PMEPA1_ENST00000395816.3_Frame_Shift_Del_p.GGRMEGP172fs	NM_020182.4	NP_064567.2	Q969W9	PMEPA_HUMAN	prostate transmembrane protein, androgen induced 1			16					GTGGGCGGCGGCCCCTCCATGCGCCCGCCGCTGCCGTAG	0.694000																								0							SO:0001589	frameshift_variant			ENST00000341744.3	0	1	hg19	CCDS13463.1																																																																																				TCGA-2J-AABA-01A-21D-A40W-08	PMEPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079858.2	1	0	0	12	121	0	36	0	9.999954e-01	0	265	0	36	2	0	0	0	0	0	0		1	0.999358	18	118	0	34	2								-18.219060	1	1	0	0		1	0	1	1	2.057827	0	0.340000	1.830000	0.338876	0.530000	2.900000e-01	0.850000	0.520000	0.556949	0.530000	0	0.400000	0.700000
GTF3C3	9330	broad.mit.edu	37	2	197636516	197636516	+	Frame_Shift_Del	DEL	T	T	-			TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr2:197636516delT	ENST00000263956.3	-	15	2305	c.2216delA	c.(2215-2217)aatfs	p.N739fs		NM_012086.4	NP_036218.1	Q9Y5Q9	TF3C3_HUMAN	general transcription factor IIIC, polypeptide 3, 102kDa			33					ATTGTGTCCATTTAAGACACA	0.428000																								0							SO:0001589	frameshift_variant			ENST00000263956.3	1	0	hg19	CCDS2316.1																																																																																				TCGA-2J-AABA-01A-21D-A40W-08	GTF3C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256104.1	1	0	0	41	260	0	67	0	7.994480e-01	1	20	0	67	2	0	0	0	0	0	0		1	1.000000	44	257	0	67	2								-20.000000	1	1	0	0		1	0	1	1	2.053808	0	0.340000	1.830000	0.338876	0.790000	5.800000e-01	1.000000	1.000000	0.805588	0.790000	0	0.680000	0.920000
APOB	338	broad.mit.edu	37	2	21225066	21225069	+	Frame_Shift_Del	DEL	GACT	GACT	-			TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr2:21225066_21225069delGACT	ENST00000233242.1	-	29	13352_13355	c.13225_13228delAGTC	c.(13225-13230)agtctgfs	p.SL4409fs	RP11-116D2.1_ENST00000567376.2_lincRNA	NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B			305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				TTCTTGATCAGACTGACTATCTTT	0.373000																								0							SO:0001589	frameshift_variant			ENST00000233242.1	1	0	hg19	CCDS1703.1																																																																																				TCGA-2J-AABA-01A-21D-A40W-08	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1	1	0	0	37	295	0	64	0	2.296132e-01	0	8	0	64	2	0	0	0	0	0	0		1	0.879521	51	304	3	63	31								-14.282990	1	0	0	0		1	0	0	0	2.048860	0	0.340000	1.830000	0.337748	0.650000	4.700000e-01	0.860000	0.650000	0.662996	0.650000	0	0.550000	0.760000
MLLT4	4301	broad.mit.edu	37	6	168299092	168299092	+	Frame_Shift_Del	DEL	G	G	-			TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr6:168299092delG	ENST00000447894.2	+	11	1525	c.1525delG	c.(1525-1527)gcafs	p.A509fs	MLLT4_ENST00000392108.3_Frame_Shift_Del_p.A509fs|MLLT4_ENST00000351017.4_Frame_Shift_Del_p.A509fs|MLLT4_ENST00000392112.1_Frame_Shift_Del_p.A493fs|MLLT4_ENST00000344191.4_Frame_Shift_Del_p.A509fs|MLLT4_ENST00000400822.3_Frame_Shift_Del_p.A508fs|MLLT4_ENST00000366806.2_Frame_Shift_Del_p.A509fs			P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4			65		Breast(66;1.07e-05)|Ovarian(120;0.024)			TCATGCTCTTGCAAAAAGATC	0.438000			T	MLL	AL										Dom	yes		6	6q27	4301	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4 (AF6)		L	0							SO:0001589	frameshift_variant			ENST00000447894.2	0	1	hg19																																																																																					TCGA-2J-AABA-01A-21D-A40W-08	MLLT4-013	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000372077.1	1	0	0	26	202	0	56	0	7.183328e-02	1	3	0	56	2	0	0	0	0	0	0		1	1.000000	27	200	0	55	2								-20.000000	1	1	0	0		1	0	1	1	1.739085	1	0.340000	1.830000	0.206445	0.550000	3.700000e-01	0.760000	0.550000	0.564640	0.550000	0	0.450000	0.660000
NEBL	10529	broad.mit.edu	37	10	21158753	21158753	+	Silent	SNP	G	G	A			TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr10:21158753G>A	ENST00000377122.4	-	6	894	c.498C>T	c.(496-498)gaC>gaT	p.D166D	NEBL_ENST00000417816.2_Intron|NEBL_ENST00000377159.4_Intron|NEBL_ENST00000377119.1_Silent_p.D166D	NM_006393.2	NP_006384.1	O76041	NEBL_HUMAN	nebulette			70					TGTCCTGCACGTCTTTCCTAT	0.358000																								0							SO:0001819	synonymous_variant			ENST00000377122.4	1	1	hg19	CCDS7134.1																																																																																				TCGA-2J-AABA-01A-21D-A40W-08	NEBL-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047113.1	1	0	0	62	256	0	83		0	0	0	0	83	2		0	0	0	0	0	2	1	1.000000	61	252	0	82	2								-20.000000	1	1	121400	6	41	1	0	1	1	1.772244	1	0.340000	1.830000	0.204819	0.900000	7.300000e-01	1.000000	0.940000	0.895666	0.900000	1	0.810000	0.970000
MUC2	4583	broad.mit.edu	37	11	1092201	1092201	+	Silent	SNP	G	G	A			TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr11:1092201G>A	ENST00000441003.2	+	30	4047	c.4020G>A	c.(4018-4020)tcG>tcA	p.S1340S	MUC2_ENST00000359061.5_Silent_p.S1341S|MUC2_ENST00000361558.6_Silent_p.S6S|MUC2_ENST00000333592.6_5'Flank	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming			102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		Pranlukast(DB01411)	AGTGCAGGTCGGTCAAGGATC	0.557000																								0							SO:0001819	synonymous_variant			ENST00000441003.2	1	1	hg19																																																																																					TCGA-2J-AABA-01A-21D-A40W-08	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	1	0	1	19	105	0	21		0	0	0	0	21	2		0	0	0	0	0	2	1	0.999994	19	103	0	20	2								-12.141570	1	1	0	0		1	1	2	3	2.064705	0	0.340000	1.830000	0.341120	0.900000	5.700000e-01	1.000000	1.000000	0.877461	0.900000	1	0.720000	1.000000
STT3A	3703	broad.mit.edu	37	11	125476284	125476284	+	Missense_Mutation	SNP	G	G	A			TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr11:125476284G>A	ENST00000529196.1	+	9	910	c.704G>A	c.(703-705)cGg>cAg	p.R235Q	STT3A_ENST00000392708.4_Missense_Mutation_p.R235Q|STT3A_ENST00000531491.1_Missense_Mutation_p.R143Q			P46977	STT3A_HUMAN	STT3A, subunit of the oligosaccharyltransferase complex (catalytic)			33	all_hematologic(175;0.228)	Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0919)|all_lung(97;0.0994)|all_neural(223;0.224)			TTCTCTCACCGGATCTATGTG	0.493000																								0							SO:0001583	missense			ENST00000529196.1	0	1	hg19	CCDS8458.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	37	6.154801	0.97329	.	.	ENSG00000134910	ENST00000392708;ENST00000529196;ENST00000531491	.	.	.	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	D	0.85243	0.5652	M	0.88775	2.98	0.80722	D	1	D;D;D	0.76494	0.995;0.999;0.999	P;D;D	0.68765	0.74;0.96;0.96	D	0.86443	0.1768	9	0.66056	D	0.02	-15.5244	20.177	0.98182	0.0:0.0:1.0:0.0	.	143;143;235	B4DJ24;E9PNQ1;P46977	.;.;STT3A_HUMAN	Q	235;235;143	.	ENSP00000376472:R235Q	R	+	2	0	STT3A	124981494	1.000000	0.71417	0.998000	0.56505	0.999000	0.98932	7.912000	0.87465	2.854000	0.98071	0.655000	0.94253	CGG		TCGA-2J-AABA-01A-21D-A40W-08	STT3A-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386691.1	0	0	0	7	655	0	185	0	5.101609e-01	0	148	0	185	2		0	0	0	0	0	2	1	0.980255	7	650	0	177	2								-1.947696	0	1	121412	2	39	1	0	1	1	2.057508	0	0.340000	1.830000	0.338876	0.060000	2.000000e-02	0.120000	0.060000	0.070568	0.060000	0	0.030000	0.090000
ACCS	84680	broad.mit.edu	37	11	44089316	44089316	+	Missense_Mutation	SNP	C	C	G			TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr11:44089316C>G	ENST00000263776.8	+	2	573	c.139C>G	c.(139-141)Ctc>Gtc	p.L47V	ACCS_ENST00000432284.2_Missense_Mutation_p.L47V|ACCS_ENST00000533208.1_3'UTR	NM_001127219.1|NM_032592.3	NP_001120691.1|NP_115981.1	Q96QU6	1A1L1_HUMAN	1-aminocyclopropane-1-carboxylate synthase homolog (Arabidopsis)(non-functional)			35					GCTGCCAGAGCTCCGTGGAGT	0.552000													Esophageal Squamous(158;148 1889 8077 23160 41213)											0							SO:0001583	missense			ENST00000263776.8	1	1	hg19	CCDS7907.1	.	.	.	.	.	.	.	.	.	.	C	2.726	-0.265394	0.05754	.	.	ENSG00000110455	ENST00000524990;ENST00000263776;ENST00000432284;ENST00000533404	T;T;T;T	0.60548	1.21;0.18;1.21;0.82	4.94	-0.726	0.11170	.	1.197120	0.05715	N	0.596590	T	0.44095	0.1277	L	0.40543	1.245	0.09310	N	1	B;B	0.32829	0.386;0.099	B;B	0.34242	0.178;0.027	T	0.33727	-0.9857	10	0.38643	T	0.18	-1.6262	1.7604	0.02991	0.1416:0.4323:0.1391:0.287	.	47;47	B4E219;Q96QU6	.;1A1L1_HUMAN	V	47	ENSP00000434156:L47V;ENSP00000263776:L47V;ENSP00000391775:L47V;ENSP00000435919:L47V	ENSP00000263776:L47V	L	+	1	0	ACCS	44045892	0.000000	0.05858	0.001000	0.08648	0.101000	0.19017	-1.526000	0.02229	-0.001000	0.14495	0.655000	0.94253	CTC		TCGA-2J-AABA-01A-21D-A40W-08	ACCS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389721.1	1	0	1	35	206	0	38	0	4.463793e-01	1	9	0	38	2		0	0	0	0	0	2	1	1.000000	35	205	0	38	2								-20.000000	1	1	0	0		1	1	2	3	2.064705	0	0.340000	1.830000	0.341120	0.850000	6.100000e-01	1.000000	1.000000	0.853770	0.850000	1	0.720000	1.000000
PAWR	5074	broad.mit.edu	37	12	79990331	79990331	+	Missense_Mutation	SNP	G	G	A			TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr12:79990331G>A	ENST00000328827.4	-	5	1163	c.791C>T	c.(790-792)tCa>tTa	p.S264L		NM_002583.2	NP_002574.2	Q96IZ0	PAWR_HUMAN	PRKC, apoptosis, WT1, regulator			8					TGTGCTACTTGAAACCAGAGT	0.323000																								0							SO:0001583	missense			ENST00000328827.4	1	1	hg19	CCDS31863.1	.	.	.	.	.	.	.	.	.	.	G	15.10	2.732142	0.48939	.	.	ENSG00000177425	ENST00000328827	T	0.17370	2.28	5.21	5.21	0.72293	.	0.977772	0.08368	N	0.956530	T	0.17450	0.0419	L	0.29908	0.895	0.32789	N	0.501387	P	0.36535	0.557	B	0.39258	0.295	T	0.07481	-1.0770	9	.	.	.	-0.0939	13.6695	0.62416	0.0:0.0:0.8453:0.1547	.	264	Q96IZ0	PAWR_HUMAN	L	264	ENSP00000328088:S264L	.	S	-	2	0	PAWR	78514462	1.000000	0.71417	0.985000	0.45067	0.148000	0.21650	4.049000	0.57397	2.601000	0.87937	0.585000	0.79938	TCA		TCGA-2J-AABA-01A-21D-A40W-08	PAWR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407175.1	1	0	1	48	259	0	87	1	9.994344e-01	19	44	0	87	2		0	0	0	0	0	2	1	1.000000	47	254	0	83	2								-3.234357	1	1	0	0		1	0	0	0	2.005386	0	0.340000	1.830000	0.321546	0.890000	6.700000e-01	1.000000	1.000000	0.887011	0.890000	1	0.770000	1.000000
SLITRK5	26050	broad.mit.edu	37	13	88329453	88329453	+	Missense_Mutation	SNP	C	C	T			TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr13:88329453C>T	ENST00000325089.6	+	2	2029	c.1810C>T	c.(1810-1812)Cgc>Tgc	p.R604C	SLITRK5_ENST00000400028.3_Missense_Mutation_p.R363C	NM_015567.1	NP_056382.1	O94991	SLIK5_HUMAN	SLIT and NTRK-like family, member 5	p.R604C(1)		81	all_neural(89;0.101)|Medulloblastoma(90;0.163)				GACCGACATGCGCTCCATTAA	0.567000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000325089.6	0	1	hg19	CCDS9465.1	.	.	.	.	.	.	.	.	.	.	C	16.04	3.011439	0.54468	0.0	1.16E-4	ENSG00000165300	ENST00000325089;ENST00000400028	T;T	0.61158	0.13;0.49	5.47	4.54	0.55810	Cysteine-rich flanking region, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.78033	0.4220	M	0.87971	2.92	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.987;0.993	T	0.81450	-0.0927	9	.	.	.	-15.1954	14.535	0.67953	0.1566:0.8434:0.0:0.0	.	363;604	B4DSH5;O94991	.;SLIK5_HUMAN	C	604;363	ENSP00000366283:R604C;ENSP00000442244:R363C	.	R	+	1	0	SLITRK5	87127454	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	3.167000	0.50793	2.554000	0.86153	0.555000	0.69702	CGC		TCGA-2J-AABA-01A-21D-A40W-08	SLITRK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045416.3	0	0	0	6	851	0	165	0	2.253067e-04	0	3	0	165	2		0	0	0	0	0	2	1	0.962799	7	833	0	158	2								-1.757131	0	1	121412	1	37	1	1	2	3	2.094580	0	0.340000	1.830000	0.346664	0.040000	0	1.000000	0.040000	0.092934	0.040000	0	0.020000	0.070000
PARP6	56965	broad.mit.edu	37	15	72557486	72557486	+	Silent	SNP	G	G	A			TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr15:72557486G>A	ENST00000569795.1	-	7	951	c.264C>T	c.(262-264)gtC>gtT	p.V88V	PARP6_ENST00000287196.9_Silent_p.V88V|PARP6_ENST00000413097.2_5'UTR|PARP6_ENST00000260376.7_Silent_p.V88V			Q2NL67	PARP6_HUMAN	poly (ADP-ribose) polymerase family, member 6			18					CTGTCCGGAGGACCTTCCAGG	0.473000																								0							SO:0001819	synonymous_variant			ENST00000569795.1	0	1	hg19	CCDS10241.2																																																																																				TCGA-2J-AABA-01A-21D-A40W-08	PARP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257315.2	1	0	1	6	117	0	21	1	6.979104e-01	9	38	0	21	2		0	0	0	0	0	2	1	0.963480	6	114	0	20	2								-9.388886	1	1	0	0		1	1	2	3	2.068233	0	0.340000	1.830000	0.342236	0.300000	1.200000e-01	0.630000	0.290000	0.332014	0.300000	0	0.200000	0.450000
NF1	4763	broad.mit.edu	37	17	29559101	29559101	+	Nonsense_Mutation	SNP	C	C	T			TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr17:29559101C>T	ENST00000358273.4	+	25	3591	c.3208C>T	c.(3208-3210)Cag>Tag	p.Q1070*	NF1_ENST00000356175.3_Nonsense_Mutation_p.Q1070*	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	p.0?(8)|p.?(4)	NF1/ACCN1(2)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)			AGATTTGGACCAGGCAAGCAT	0.373000			D, Mis, N, F, S, O		neurofibroma, glioma	neurofibroma, glioma			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)				yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	12	Whole gene deletion(8)|Unknown(4)						SO:0001587	stop_gained	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	ENST00000358273.4	0	1	hg19	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	C	46	12.239175	0.99649	.	.	ENSG00000196712	ENST00000358273;ENST00000356175;ENST00000456735	.	.	.	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.30078	T	0.28	.	19.0592	0.93080	0.0:1.0:0.0:0.0	.	.	.	.	X	1070;1070;736	.	ENSP00000348498:Q1070X	Q	+	1	0	NF1	26583227	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.402000	0.79972	2.499000	0.84300	0.484000	0.47621	CAG		TCGA-2J-AABA-01A-21D-A40W-08	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	0	0	1	12	53	0	12	0	3.994732e-02	1	1	0	12	2		0	0	0	0	0	2	1	0.999300	11	52	0	12	2								-19.996930	1	1	0	0		1	0	1	1	1.721658	1	0.340000	1.830000	0.204819	0.790000	4.700000e-01	0.990000	0.860000	0.784012	0.790000	0	0.630000	0.930000
SMAD4	4089	broad.mit.edu	37	18	48604705	48604705	+	Nonsense_Mutation	SNP	G	G	A			TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr18:48604705G>A	ENST00000342988.3	+	12	2065	c.1527G>A	c.(1525-1527)tgG>tgA	p.W509*	SMAD4_ENST00000588745.1_Nonsense_Mutation_p.W413*|SMAD4_ENST00000586253.1_3'UTR|SMAD4_ENST00000398417.2_Nonsense_Mutation_p.W509*	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	p.0?(36)|p.?(2)|p.W509*(1)		454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)			TGAAAGGCTGGGGACCGGATT	0.473000																								39	Whole gene deletion(36)|Unknown(2)|Substitution - Nonsense(1)	GRCh37	CM086965	SMAD4	M		SO:0001587	stop_gained			ENST00000342988.3	0	1	hg19	CCDS11950.1	.	.	.	.	.	.	.	.	.	.	G	42	9.263344	0.99118	.	.	ENSG00000141646	ENST00000342988;ENST00000398417	.	.	.	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.4362	0.94796	0.0:0.0:1.0:0.0	.	.	.	.	X	509	.	ENSP00000341551:W509X	W	+	3	0	SMAD4	46858703	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.586000	0.98226	2.890000	0.99128	0.655000	0.94253	TGG		TCGA-2J-AABA-01A-21D-A40W-08	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	1	0	1	56	250	0	50	1	9.986344e-01	24	23	0	50	2	1	1	125	607	1	1047	5	1	1.000000	55	250	0	47	2								-2.787374	1	1	0	0		1	0	1	1	1.734443	1	0.340000	1.830000	0.208063	0.870000	6.800000e-01	1.000000	1.000000	0.869917	0.870000	1	0.770000	0.960000
PSMD8	5714	broad.mit.edu	37	19	38874009	38874009	+	Silent	SNP	G	G	A			TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08			G	A	G	G		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr19:38874009G>A	ENST00000215071.4	+	7	1098	c.1032G>A	c.(1030-1032)cgG>cgA	p.R344R	GGN_ENST00000591809.1_5'Flank|AC005789.9_ENST00000585411.1_RNA|PSMD8_ENST00000602911.1_Silent_p.R281R	NM_002812.4	NP_002803.2	P48556	PSMD8_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 8			6	all_cancers(60;3.4e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		AGTATGCCCGGCAGCTGGAGA	0.562000																								0							SO:0001819	synonymous_variant			ENST00000215071.4	0	1	hg19	CCDS12515.2																																																																																				TCGA-2J-AABA-01A-21D-A40W-08	PSMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319627.1	0	0	0	4	148	0	43	0	9.933983e-01	0	410	0	43	2		0	0	0	0	0	2	1	0.885046	4	144	0	42	2								-3.607143	1	1	0	0		1	0	0	0	2.039874	0	0.340000	1.830000	0.335481	0.160000	5.000000e-02	0.360000	0.150000	0.187231	0.160000	0	0.100000	0.260000
ZNF28	7576	broad.mit.edu	37	19	53304471	53304471	+	Missense_Mutation	SNP	G	G	C			TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr19:53304471G>C	ENST00000457749.2	-	4	746	c.627C>G	c.(625-627)caC>caG	p.H209Q	ZNF28_ENST00000414252.2_Missense_Mutation_p.H156Q|ZNF28_ENST00000360272.4_Missense_Mutation_p.H156Q|ZNF28_ENST00000438150.2_Missense_Mutation_p.H156Q	NM_006969.3	NP_008900.3	P17035	ZNF28_HUMAN	zinc finger protein 28			34					TTTCTCTCATGTGTACATTCC	0.333000																								0							SO:0001583	missense			ENST00000457749.2	1	1	hg19	CCDS33093.2	.	.	.	.	.	.	.	.	.	.	-	8.679	0.904585	0.17760	.	.	ENSG00000198538	ENST00000438150;ENST00000457749;ENST00000360272;ENST00000414252;ENST00000391783	T;T;T;T;T	0.41400	1.0;1.0;1.0;1.0;1.0	1.47	0.307	0.15811	.	.	.	.	.	T	0.65863	0.2732	M	0.93720	3.45	0.09310	N	1	P	0.50156	0.932	D	0.63703	0.917	T	0.54629	-0.8265	9	0.87932	D	0	.	5.3957	0.16268	0.2136:0.0:0.7864:0.0	.	209	P17035	ZNF28_HUMAN	Q	156;209;156;156;156	ENSP00000412143:H156Q;ENSP00000397693:H209Q;ENSP00000353410:H156Q;ENSP00000444965:H156Q;ENSP00000375661:H156Q	ENSP00000353410:H156Q	H	-	3	2	ZNF28	57996283	0.009000	0.17119	0.001000	0.08648	0.036000	0.12997	0.142000	0.16096	-0.050000	0.13356	0.186000	0.17326	CAC		TCGA-2J-AABA-01A-21D-A40W-08	ZNF28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336038.2	1	0	1	79	583	0	125	1	1.135772e-01	3	2	0	125	2		0	0	0	0	0	2	1	1.000000	79	575	0	124	2								-20.000000	1	1	0	0		1	0	1	1	2.054197	0	0.340000	1.830000	0.338876	0.690000	5.600000e-01	0.850000	0.700000	0.705427	0.690000	0	0.620000	0.780000
ZNF761	388561	broad.mit.edu	37	19	53960290	53960290	+	RNA	SNP	C	C	T			TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr19:53960290C>T	ENST00000454407.1	+	0	2982							Q86XN6	ZN761_HUMAN	zinc finger protein 761			30					TCGCACCTGGCACAACATGCT	0.438000																								0											ENST00000454407.1	0	1	hg19																																																																																					TCGA-2J-AABA-01A-21D-A40W-08	ZNF761-203	KNOWN	basic	processed_transcript	processed_transcript		0	0	0	10	88	0	9	1	4.902955e-01	7	8	0	9	2		0	0	0	0	0	2	1	0.997085	10	86	0	8	2								-16.562990	1	1	0	0		1	0	1	1	2.054197	0	0.340000	1.830000	0.338876	0.610000	3.200000e-01	0.990000	1.000000	0.630304	0.610000	0	0.450000	0.800000
PSMB4	5692	broad.mit.edu	37	1	151372561	151372561	+	Missense_Mutation	SNP	G	G	A			TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr1:151372561G>A	ENST00000290541.6	+	2	299	c.245G>A	c.(244-246)cGc>cAc	p.R82H		NM_002796.2	NP_002787.2	P28070	PSB4_HUMAN	proteasome (prosome, macropain) subunit, beta type, 4			14	Lung SC(34;0.00471)|Ovarian(49;0.00871)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)		GCTCGTTTCCGCAACATCTCT	0.562000																								0							SO:0001583	missense			ENST00000290541.6	0	1	hg19	CCDS996.1	.	.	.	.	.	.	.	.	.	.	G	36	5.616730	0.96649	.	.	ENSG00000159377	ENST00000290541	T	0.23950	1.88	5.34	5.34	0.76211	Proteasome, beta-type subunit, conserved site (1);	0.000000	0.85682	D	0.000000	T	0.42765	0.1217	M	0.68952	2.095	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.985	T	0.23226	-1.0194	10	0.48119	T	0.1	-10.0508	17.6208	0.88080	0.0:0.0:1.0:0.0	.	82;82	B4DFL3;P28070	.;PSB4_HUMAN	H	82	ENSP00000290541:R82H	ENSP00000290541:R82H	R	+	2	0	PSMB4	149639185	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	9.420000	0.97426	2.502000	0.84385	0.561000	0.74099	CGC		TCGA-2J-AABA-01A-21D-A40W-08	PSMB4-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034885.1	0	0	0	6	815	1	185	0	1.663031e-02	0	418	1	185	10		0	0	0	0	0	2	0	0.021741	6	793	1	178	16								-2.119973	0	1	0	0		1	1	2	3	2.061605	0	0.340000	1.830000	0.341120	0.040000	0	0.100000	0.040000	0.049969	0.040000	0	0.020000	0.070000
PIGM	93183	broad.mit.edu	37	1	160000872	160000872	+	Missense_Mutation	SNP	T	T	C			TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr1:160000872T>C	ENST00000368090.2	-	1	911	c.658A>G	c.(658-660)Aaa>Gaa	p.K220E		NM_145167.2	NP_660150.1	Q9H3S5	PIGM_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class M			17	all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)		CACAGCCTTTTCAGGAGCTCG	0.493000																								0							SO:0001583	missense			ENST00000368090.2	0	1	hg19	CCDS1192.1	.	.	.	.	.	.	.	.	.	.	T	0.284	-0.984168	0.02180	.	.	ENSG00000143315	ENST00000368090	T	0.42513	0.97	5.01	-0.346	0.12620	.	1.434850	0.03898	N	0.279844	T	0.13157	0.0319	L	0.39898	1.24	0.09310	N	1	B	0.02656	0.0	B	0.09377	0.004	T	0.15009	-1.0452	9	.	.	.	-16.8801	5.5481	0.17076	0.0:0.1892:0.4536:0.3572	.	220	Q9H3S5	PIGM_HUMAN	E	220	ENSP00000357069:K220E	.	K	-	1	0	PIGM	158267496	0.000000	0.05858	0.000000	0.03702	0.090000	0.18270	-0.053000	0.11846	0.035000	0.15519	0.379000	0.24179	AAA		TCGA-2J-AABA-01A-21D-A40W-08	PIGM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060643.2	0	0	0	5	555	0	88	0	1.392864e-02	0	16	0	88	2		0	0	0	0	0	2	1	0.935104	4	548	0	87	2								-4.538811	1	0	0	0		1	1	2	3	2.061605	0	0.340000	1.830000	0.341120	0.050000	1.000000e-02	0.120000	0.060000	0.062660	0.050000	0	0.030000	0.090000
KIF21B	23046	broad.mit.edu	37	1	200950209	200950209	+	Silent	SNP	C	C	T			TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr1:200950209C>T	ENST00000422435.2	-	29	4174	c.3858G>A	c.(3856-3858)ccG>ccA	p.P1286P	KIF21B_ENST00000332129.2_Silent_p.P1273P|KIF21B_ENST00000461742.2_Silent_p.P1286P|KIF21B_ENST00000360529.5_Silent_p.P1273P	NM_001252100.1	NP_001239029.1	O75037	KI21B_HUMAN	kinesin family member 21B			83					CTCCTCCAACCGGGGAGATGA	0.637000																								0							SO:0001819	synonymous_variant			ENST00000422435.2	1	1	hg19	CCDS58056.1																																																																																				TCGA-2J-AABA-01A-21D-A40W-08	KIF21B-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382635.1	1	0	1	32	196	0	45	1	1.026975e-01	2	2	0	45	2		0	0	0	0	0	2	1	1.000000	32	191	0	43	2								-2.971653	1	1	121412	6	37	1	1	2	3	2.069687	0	0.340000	1.830000	0.342236	0.830000	5.800000e-01	1.000000	1.000000	0.832285	0.830000	0	0.700000	0.980000
ARID1A	8289	broad.mit.edu	37	1	27101342	27101342	+	Nonsense_Mutation	SNP	G	G	T			TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08			G	T	G	G		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr1:27101342G>T	ENST00000324856.7	+	18	4995	c.4624G>T	c.(4624-4626)Gaa>Taa	p.E1542*	ARID1A_ENST00000374152.2_Nonsense_Mutation_p.E1159*|ARID1A_ENST00000540690.1_Intron|ARID1A_ENST00000457599.2_Intron	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	p.E1542*(1)	ARID1A/MAST2_ENST00000361297(2)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)			GGCCAACCACGAAGGCTCGTG	0.642000			Mis, N, F, S, D		clear cell ovarian carcinoma, RCC										Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	1	Substitution - Nonsense(1)						SO:0001587	stop_gained			ENST00000324856.7	0	1	hg19	CCDS285.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	43|43	10.343878|10.343878	0.99388|0.99388	.|.	.|.	ENSG00000117713|ENSG00000117713	ENST00000324856;ENST00000374152|ENST00000430799	.|.	.|.	.|.	5.41|5.41	5.41|5.41	0.78517|0.78517	.|.	0.045702|.	0.85682|.	D|.	0.000000|.	.|T	.|0.75287	.|0.3829	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.72743	.|-0.4201	.|4	0.42905|.	T|.	0.14|.	-7.5866|-7.5866	19.3941|19.3941	0.94598|0.94598	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|L	1542;1159|438	.|.	ENSP00000320485:E1542X|.	E|R	+|+	1|2	0|0	ARID1A|ARID1A	26973929|26973929	1.000000|1.000000	0.71417|0.71417	0.994000|0.994000	0.49952|0.49952	0.479000|0.479000	0.33129|0.33129	9.144000|9.144000	0.94629|0.94629	2.822000|2.822000	0.97130|0.97130	0.557000|0.557000	0.71058|0.71058	GAA|CGA		TCGA-2J-AABA-01A-21D-A40W-08	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	1	0	1	41	181	0	68	1	7.599884e-01	5	9	0	68	2	1	1	70	223	0	338	2	1	1.000000	40	166	0	64	2								-20.000000	1	1	0	0		1	0	1	1	1.733261	1	0.340000	1.830000	0.206445	0.860000	6.500000e-01	1.000000	1.000000	0.859098	0.860000	1	0.750000	0.960000
MFSD2A	84879	broad.mit.edu	37	1	40421012	40421012	+	Silent	SNP	A	A	G			TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr1:40421012A>G	ENST00000372809.5	+	1	191	c.48A>G	c.(46-48)ctA>ctG	p.L16L	MFSD2A_ENST00000372811.5_Silent_p.L16L|MFSD2A_ENST00000420632.2_5'UTR	NM_001136493.1	NP_001129965.1	Q8NA29	NLS1_HUMAN	major facilitator superfamily domain containing 2A			24					CGGGGCTGCTACCCACCAGCA	0.716000																								0							SO:0001819	synonymous_variant			ENST00000372809.5	0	1	hg19	CCDS44118.1																																																																																				TCGA-2J-AABA-01A-21D-A40W-08	MFSD2A-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000025756.1	0	0	0	4	59	0	12	0	7.068444e-01	0	36	0	12	2		0	0	0	0	0	2	1	0.880764	4	56	0	10	2								-10.096200	1	1	0	0		1	1	2	3	2.071606	0	0.340000	1.830000	0.342236	0.410000	1.400000e-01	0.930000	0.370000	0.445072	0.410000	0	0.250000	0.630000
SGSM1	129049	broad.mit.edu	37	22	25264736	25264736	+	Missense_Mutation	SNP	C	C	T			TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr22:25264736C>T	ENST00000400359.4	+	12	1212	c.1205C>T	c.(1204-1206)gCc>gTc	p.A402V	SGSM1_ENST00000400358.4_Missense_Mutation_p.A402V	NM_001039948.2|NM_133454.2	NP_001035037.1|NP_597711.1	Q2NKQ1	SGSM1_HUMAN	small G protein signaling modulator 1			41					CAGGGTTCTGCCGAGTCCACA	0.512000																								0							SO:0001583	missense			ENST00000400359.4	0	1	hg19	CCDS46674.1	.	.	.	.	.	.	.	.	.	.	C	0.043	-1.275275	0.01410	.	.	ENSG00000167037	ENST00000403206;ENST00000400358;ENST00000400359	T;T	0.31510	1.49;1.49	4.97	2.9	0.33743	.	1.043230	0.07422	N	0.894208	T	0.08935	0.0221	N	0.01729	-0.75	0.09310	N	1	B;B;P;B	0.39665	0.05;0.102;0.682;0.007	B;B;B;B	0.30572	0.017;0.047;0.117;0.011	T	0.07385	-1.0775	10	0.08179	T	0.78	-10.6163	5.5656	0.17168	0.1576:0.6761:0.0:0.1663	.	402;518;535;402	Q2NKQ1-4;C9J7S8;Q2NKQ1-3;Q2NKQ1	.;.;.;SGSM1_HUMAN	V	518;402;402	ENSP00000383211:A402V;ENSP00000383212:A402V	ENSP00000383211:A402V	A	+	2	0	SGSM1	23594736	0.054000	0.20591	0.004000	0.12327	0.018000	0.09664	3.246000	0.51414	0.644000	0.30656	-0.218000	0.12543	GCC		TCGA-2J-AABA-01A-21D-A40W-08	SGSM1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320282.1	0	0	0	6	476	0	99		0	0	0	0	99	2		0	0	0	0	0	2	1	0.962860	6	467	0	98	2								-2.104343	0	1	0	0		1	1	2	3	2.074349	0	0.340000	1.830000	0.342236	0.070000	2.000000e-02	0.170000	0.080000	0.093996	0.070000	0	0.040000	0.120000
NCKAP5	344148	broad.mit.edu	37	2	133541374	133541374	+	Missense_Mutation	SNP	T	T	C			TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr2:133541374T>C	ENST00000409261.1	-	14	3383	c.3010A>G	c.(3010-3012)Atc>Gtc	p.I1004V	NCKAP5_ENST00000317721.6_Missense_Mutation_p.I1004V|NCKAP5_ENST00000405974.3_Intron|NCKAP5_ENST00000409213.1_Intron|NCKAP5_ENST00000473859.1_5'Flank	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5			118					TGAGTGAAGATAGGCTTTTTG	0.537000																								0							SO:0001583	missense			ENST00000409261.1	1	1	hg19	CCDS46418.1	.	.	.	.	.	.	.	.	.	.	T	0.015	-1.544604	0.00934	.	.	ENSG00000176771	ENST00000409261;ENST00000317721	T;T	0.08458	3.09;3.09	5.07	-8.15	0.01065	.	1.865620	0.03556	N	0.226266	T	0.04092	0.0114	N	0.12182	0.205	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.34304	-0.9834	10	0.22706	T	0.39	.	7.2862	0.26340	0.0:0.3572:0.1999:0.4429	.	1004	O14513	NCKP5_HUMAN	V	1004	ENSP00000387128:I1004V;ENSP00000380603:I1004V	ENSP00000380603:I1004V	I	-	1	0	NCKAP5	133257844	0.000000	0.05858	0.000000	0.03702	0.692000	0.40212	-2.258000	0.01179	-2.146000	0.00800	-0.798000	0.03219	ATC		TCGA-2J-AABA-01A-21D-A40W-08	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	1	0	1	20	111	0	29	0	2.592302e-02	0	2	0	29	2		0	0	0	0	0	2	1	0.999996	20	107	0	29	2								-20.000000	1	1	120480	1	24	1	0	1	1	2.053808	0	0.340000	1.830000	0.338876	0.890000	5.800000e-01	1.000000	1.000000	0.874564	0.890000	1	0.720000	1.000000
TTN	7273	broad.mit.edu	37	2	179431867	179431867	+	Missense_Mutation	SNP	C	C	T			TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr2:179431867C>T	ENST00000591111.1	-	276	74293	c.74069G>A	c.(74068-74070)cGa>cAa	p.R24690Q	TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R23763Q|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.R17266Q|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R26331Q|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.R17458Q|TTN_ENST00000359218.5_Missense_Mutation_p.R17391Q|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000592600.1_RNA			Q8WZ42	TITIN_HUMAN	titin			1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)		CCAGGCAAGTCGACTGGTTTC	0.413000																								0							SO:0001583	missense			ENST00000591111.1	1	1	hg19		.	.	.	.	.	.	.	.	.	.	C	16.16	3.045692	0.55110	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.56776	0.44;0.44;0.44;0.44	5.52	5.52	0.82312	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.74344	0.3704	M	0.76328	2.33	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.998;0.998;0.998;0.998	T	0.76844	-0.2809	9	0.87932	D	0	.	19.4392	0.94811	0.0:1.0:0.0:0.0	.	17266;17391;17458;24690	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	Q	23763;17266;17458;17391;17264	ENSP00000343764:R23763Q;ENSP00000434586:R17266Q;ENSP00000340554:R17458Q;ENSP00000352154:R17391Q	ENSP00000340554:R17458Q	R	-	2	0	TTN	179140113	1.000000	0.71417	0.994000	0.49952	0.981000	0.71138	7.770000	0.85390	2.580000	0.87095	0.462000	0.41574	CGA		TCGA-2J-AABA-01A-21D-A40W-08	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	0	0	1	95	395	1	96		0	0	0	1	96	2		0	0	0	0	0	2	1	1.000000	95	389	1	95	17								-20.000000	1	1	120842	5	40	1	0	1	1	2.053808	0	0.340000	1.830000	0.338876	0.990000	9.300000e-01	1.000000	1.000000	0.996259	0.990000	1	0.990000	1.000000
DNMT3A	1788	broad.mit.edu	37	2	25459873	25459873	+	Splice_Site	SNP	G	G	A	rs35824014		TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr2:25459873G>A	ENST00000264709.3	-	21	2747	c.2410C>T	c.(2410-2412)Ccg>Tcg	p.P804S	DNMT3A_ENST00000474887.1_Intron|DNMT3A_ENST00000380746.4_Splice_Site_p.P615S|DNMT3A_ENST00000402667.1_Splice_Site_p.P581S|DNMT3A_ENST00000321117.5_Splice_Site_p.P804S	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	p.R803fs*5(3)|p.P804S(2)|p.P615S(2)		1021	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				GATGCCAACGGCCTAGGAGGC	0.582000			Mis, F, N, S		AML										Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	7	Substitution - Missense(4)|Deletion - Frameshift(3)						SO:0001630	splice_region_variant			ENST00000264709.3	1	0	hg19	CCDS33157.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.511478	0.85389	.	.	ENSG00000119772	ENST00000380746;ENST00000321117;ENST00000264709;ENST00000402667	D;D;D;D	0.97232	-4.3;-4.3;-4.3;-4.3	5.62	4.72	0.59763	.	0.047584	0.85682	D	0.000000	D	0.98391	0.9465	M	0.86651	2.83	0.80722	D	1	P;D	0.89917	0.729;1.0	B;D	0.75020	0.274;0.985	D	0.98630	1.0671	10	0.49607	T	0.09	-7.2591	14.0893	0.64980	0.0:0.1518:0.8482:0.0	.	804;615	Q9Y6K1;E9PEB8	DNM3A_HUMAN;.	S	615;804;804;581	ENSP00000370122:P615S;ENSP00000324375:P804S;ENSP00000264709:P804S;ENSP00000384237:P581S	ENSP00000264709:P804S	P	-	1	0	DNMT3A	25313377	1.000000	0.71417	0.997000	0.53966	0.995000	0.86356	9.624000	0.98398	1.325000	0.45301	0.655000	0.94253	CCG		TCGA-2J-AABA-01A-21D-A40W-08	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000211587.1	1	0	1	19	95	0	30	1	7.407874e-01	5	10	0	30	2		0	0	0	0	0	2	1	0.999993	18	93	0	30	2								-20.000000	1	1	0	0		1	0	0	0	2.048860	0	0.340000	1.830000	0.337748	0.970000	6.200000e-01	1.000000	1.000000	0.916529	0.970000	1	0.780000	1.000000
SLC8A1	6546	broad.mit.edu	37	2	40405540	40405540	+	Missense_Mutation	SNP	C	C	A			TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr2:40405540C>A	ENST00000403092.1	-	3	1935	c.1902G>T	c.(1900-1902)atG>atT	p.M634I	SLC8A1-AS1_ENST00000599740.1_RNA|SLC8A1-AS1_ENST00000598247.1_RNA|SLC8A1_ENST00000542024.1_Intron|SLC8A1_ENST00000406391.2_Intron|SLC8A1-AS1_ENST00000593878.1_RNA|SLC8A1_ENST00000542756.1_Missense_Mutation_p.M634I|SLC8A1_ENST00000332839.4_Missense_Mutation_p.M634I|SLC8A1_ENST00000402441.1_Intron|SLC8A1-AS1_ENST00000444629.1_RNA|SLC8A1-AS1_ENST00000435515.1_RNA|SLC8A1-AS1_ENST00000599268.1_RNA|SLC8A1_ENST00000405269.1_Intron|SLC8A1-AS1_ENST00000596532.1_RNA|SLC8A1-AS1_ENST00000593848.1_RNA|SLC8A1-AS1_ENST00000601679.1_RNA|SLC8A1_ENST00000408028.2_Intron|SLC8A1-AS1_ENST00000599956.1_RNA|SLC8A1-AS1_ENST00000597170.1_RNA|SLC8A1-AS1_ENST00000597385.1_RNA|SLC8A1_ENST00000405901.3_Missense_Mutation_p.M634I|SLC8A1_ENST00000406785.2_Intron			P32418	NAC1_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 1			100				Alpha-Linolenic Acid(DB00132)|Icosapent(DB00159)	TCTTCTCACTCATCTCCACCA	0.507000																								0							SO:0001583	missense			ENST00000403092.1	0	1	hg19	CCDS1806.1	.	.	.	.	.	.	.	.	.	.	C	9.553	1.116372	0.20795	.	.	ENSG00000183023	ENST00000378715;ENST00000542756;ENST00000403092;ENST00000405901;ENST00000332839	T;T;T;T	0.25749	1.78;1.79;1.78;1.79	5.39	5.39	0.77823	.	0.176546	0.50627	D	0.000106	T	0.24661	0.0598	L	0.40543	1.245	0.80722	D	1	B;B	0.13594	0.008;0.005	B;B	0.17979	0.02;0.007	T	0.02257	-1.1187	10	0.34782	T	0.22	.	16.6407	0.85098	0.0:1.0:0.0:0.0	.	634;634	F6VPY9;P32418	.;NAC1_HUMAN	I	634	ENSP00000440727:M634I;ENSP00000384763:M634I;ENSP00000385678:M634I;ENSP00000332931:M634I	ENSP00000332931:M634I	M	-	3	0	SLC8A1	40259044	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.616000	0.67709	2.506000	0.84524	0.591000	0.81541	ATG		TCGA-2J-AABA-01A-21D-A40W-08	SLC8A1-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326065.1	0	0	0	13	670	0	174		0	0	0	0	174	2		0	0	0	0	0	2	1	0.999467	13	656	0	169	2								-2.211063	0	1	0	0		1	0	0	0	2.048860	0	0.340000	1.830000	0.337748	0.110000	5.000000e-02	0.180000	0.110000	0.119468	0.110000	0	0.080000	0.150000
SLC3A1	6519	broad.mit.edu	37	2	44531289	44531289	+	Missense_Mutation	SNP	G	G	A			TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr2:44531289G>A	ENST00000260649.6	+	7	1220	c.1144G>A	c.(1144-1146)Ggg>Agg	p.G382R	SLC3A1_ENST00000409740.3_Missense_Mutation_p.G13R|SLC3A1_ENST00000409387.1_Missense_Mutation_p.G382R|SLC3A1_ENST00000409294.1_Missense_Mutation_p.G2R|SLC3A1_ENST00000409741.1_Missense_Mutation_p.G382R|SLC3A1_ENST00000409380.1_Missense_Mutation_p.G104R|SLC3A1_ENST00000409229.3_Missense_Mutation_p.G382R	NM_000341.3	NP_000332.2	Q07837	SLC31_HUMAN	solute carrier family 3 (amino acid transporter heavy chain), member 1			26		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)		L-Cystine(DB00138)	TAGGTTCATGGGGACTGAAGC	0.458000																								0							SO:0001583	missense			ENST00000260649.6	0	1	hg19	CCDS1819.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.213359	0.79352	.	.	ENSG00000138079	ENST00000260649;ENST00000409387;ENST00000540334;ENST00000409741;ENST00000409229;ENST00000541289;ENST00000409380;ENST00000409294;ENST00000409740	D;D;D;D;D;D;D	0.99474	-5.97;-5.97;-5.97;-5.97;-5.97;-4.58;-5.97	5.14	5.14	0.70334	Glycoside hydrolase, subgroup, catalytic domain (1);Glycosyl hydrolase, family 13, catalytic domain (1);Glycoside hydrolase, superfamily (1);Glycosyl hydrolase, family 13, subfamily, catalytic domain (1);	0.054269	0.64402	D	0.000001	D	0.99336	0.9767	L	0.60455	1.87	0.80722	D	1	D;D;D;D	0.76494	0.996;0.991;0.999;0.999	D;D;D;D	0.77004	0.959;0.959;0.989;0.98	D	0.99346	1.0913	10	0.66056	D	0.02	-16.9982	17.398	0.87451	0.0:0.0:1.0:0.0	.	382;382;382;382	Q07837;B8ZZK1;Q4J6B5;Q4J6B6	SLC31_HUMAN;.;.;.	R	382;382;318;382;382;382;104;2;13	ENSP00000260649:G382R;ENSP00000387308:G382R;ENSP00000386954:G382R;ENSP00000386620:G382R;ENSP00000386709:G104R;ENSP00000386852:G2R;ENSP00000386677:G13R	ENSP00000260649:G382R	G	+	1	0	SLC3A1	44384793	1.000000	0.71417	0.997000	0.53966	0.595000	0.36748	8.753000	0.91637	2.393000	0.81446	0.455000	0.32223	GGG		TCGA-2J-AABA-01A-21D-A40W-08	SLC3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250676.1	0	0	0	12	456	0	120	0	4.596796e-01	1	56	0	120	2		0	0	0	0	0	2	1	0.999067	12	450	0	115	2								-2.388793	0	1	0	0		1	0	0	0	2.048860	0	0.340000	1.830000	0.337748	0.150000	7.000000e-02	0.250000	0.150000	0.161472	0.150000	0	0.110000	0.200000
MOGS	7841	broad.mit.edu	37	2	74688883	74688883	+	Missense_Mutation	SNP	C	C	T			TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr2:74688883C>T	ENST00000233616.4	-	4	2195	c.2033G>A	c.(2032-2034)cGg>cAg	p.R678Q	MOGS_ENST00000462443.1_5'Flank|MOGS_ENST00000409065.1_3'UTR|MOGS_ENST00000452063.2_Missense_Mutation_p.R572Q	NM_006302.2	NP_006293.2	Q13724	MOGS_HUMAN	mannosyl-oligosaccharide glucosidase			23					AGGTTGGGGCCGACCCACCAC	0.597000																								0							SO:0001583	missense			ENST00000233616.4	1	1	hg19	CCDS42700.1	.	.	.	.	.	.	.	.	.	.	C	6.851	0.526345	0.13066	.	.	ENSG00000115275	ENST00000233616;ENST00000452063	T;T	0.38240	1.15;1.15	5.01	5.01	0.66863	Six-hairpin glycosidase-like (1);	0.118143	0.52532	D	0.000072	T	0.39937	0.1097	L	0.31420	0.93	0.80722	D	1	D	0.89917	1.0	D	0.68353	0.957	T	0.09250	-1.0683	10	0.12430	T	0.62	-11.998	9.2712	0.37673	0.0:0.9044:0.0:0.0956	.	678	Q13724	MOGS_HUMAN	Q	678;572	ENSP00000233616:R678Q;ENSP00000388201:R572Q	ENSP00000233616:R678Q	R	-	2	0	MOGS	74542391	0.992000	0.36948	0.983000	0.44433	0.156000	0.22039	1.923000	0.40055	2.618000	0.88619	0.462000	0.41574	CGG		TCGA-2J-AABA-01A-21D-A40W-08	MOGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328382.1	1	0	1	54	319	0	84	1	9.999990e-01	42	80	0	84	2		0	0	0	0	0	2	1	1.000000	53	311	0	83	2								-19.999970	1	1	120878	1	35	1	0	0	0	2.048860	0	0.340000	1.830000	0.337748	0.840000	6.500000e-01	1.000000	1.000000	0.850258	0.840000	0	0.740000	0.960000
KIDINS220	57498	broad.mit.edu	37	2	8891668	8891668	+	Missense_Mutation	SNP	C	C	A			TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr2:8891668C>A	ENST00000256707.3	-	23	3299	c.3118G>T	c.(3118-3120)Gtg>Ttg	p.V1040L	KIDINS220_ENST00000418530.1_Missense_Mutation_p.V998L|KIDINS220_ENST00000427284.1_Missense_Mutation_p.V1040L|KIDINS220_ENST00000473731.1_Missense_Mutation_p.V1040L	NM_020738.2	NP_065789.1	Q9ULH0	KDIS_HUMAN	kinase D-interacting substrate, 220kDa			60	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)				TCTCGAGCCACAAGAACTGGG	0.353000																								0							SO:0001583	missense			ENST00000256707.3	1	1	hg19	CCDS42650.1	.	.	.	.	.	.	.	.	.	.	C	5.843	0.339815	0.11069	.	.	ENSG00000134313	ENST00000496383;ENST00000541927;ENST00000256707;ENST00000427284;ENST00000418530;ENST00000473731;ENST00000489024;ENST00000459813	T;T;T;T;T;T	0.64803	1.03;-0.12;-0.08;-0.02;-0.08;-0.06	5.07	5.07	0.68467	.	0.215268	0.42821	D	0.000645	T	0.41880	0.1178	N	0.12887	0.27	0.39550	D	0.968969	B;B;B;B;B	0.29552	0.012;0.001;0.058;0.165;0.248	B;B;B;B;B	0.34931	0.01;0.003;0.094;0.192;0.064	T	0.36648	-0.9739	10	0.06494	T	0.89	.	12.2106	0.54377	0.0:0.9213:0.0:0.0787	.	1041;1041;724;998;1040	B4DK94;E9PH70;B4DGY1;Q9ULH0-2;Q9ULH0	.;.;.;.;KDIS_HUMAN	L	787;724;1040;1040;998;1040;1041;49	ENSP00000420364:V787L;ENSP00000256707:V1040L;ENSP00000411849:V1040L;ENSP00000414923:V998L;ENSP00000418974:V1040L;ENSP00000419964:V1041L	ENSP00000256707:V1040L	V	-	1	0	KIDINS220	8809119	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.970000	0.40520	2.509000	0.84616	0.563000	0.77884	GTG		TCGA-2J-AABA-01A-21D-A40W-08	KIDINS220-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323408.2	1	0	1	53	320	0	70	1	7.478136e-01	4	14	0	70	2		0	0	0	0	0	2	1	1.000000	52	284	0	60	2								-19.999930	1	1	0	0		1	0	0	0	2.048860	0	0.340000	1.830000	0.337748	0.820000	6.300000e-01	1.000000	1.000000	0.836070	0.820000	0	0.720000	0.940000
NCAPH	23397	broad.mit.edu	37	2	97019996	97019996	+	Missense_Mutation	SNP	G	G	T			TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr2:97019996G>T	ENST00000240423.4	+	9	1121	c.1078G>T	c.(1078-1080)Gac>Tac	p.D360Y	NCAPH_ENST00000455200.1_Missense_Mutation_p.D349Y|NCAPH_ENST00000427946.1_Missense_Mutation_p.D224Y	NM_001281710.1|NM_001281711.1|NM_015341.3	NP_001268639.1|NP_001268640.1|NP_056156.2	Q15003	CND2_HUMAN	non-SMC condensin I complex, subunit H			28		Ovarian(717;0.0221)			TGACGAGAGTGACTGTGGAGA	0.512000																								0							SO:0001583	missense			ENST00000240423.4	1	1	hg19	CCDS2021.1	.	.	.	.	.	.	.	.	.	.	G	10.56	1.384455	0.25031	.	.	ENSG00000121152	ENST00000240423;ENST00000427946;ENST00000435975;ENST00000455200	T;T;T;T	0.53857	0.67;0.68;0.6;0.67	5.38	4.48	0.54585	.	0.274240	0.42053	N	0.000768	T	0.51346	0.1669	M	0.78049	2.395	0.21064	N	0.999798	B;B;P;B	0.38148	0.19;0.19;0.62;0.19	B;B;B;B	0.39617	0.172;0.172;0.305;0.172	T	0.49588	-0.8924	10	0.06625	T	0.88	-9.4799	12.9558	0.58427	0.0:0.0:0.8368:0.1632	.	336;349;349;360	B4DRG7;E9PHA2;C9J470;Q15003	.;.;.;CND2_HUMAN	Y	360;224;349;349	ENSP00000240423:D360Y;ENSP00000400774:D224Y;ENSP00000405237:D349Y;ENSP00000407308:D349Y	ENSP00000240423:D360Y	D	+	1	0	NCAPH	96383723	1.000000	0.71417	0.003000	0.11579	0.320000	0.28249	5.587000	0.67510	1.215000	0.43411	0.561000	0.74099	GAC		TCGA-2J-AABA-01A-21D-A40W-08	NCAPH-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252842.2	1	0	1	92	584	0	121	0	9.358672e-02	1	3	0	121	2		0	0	0	0	0	2	1	1.000000	91	579	0	119	2								-20.000000	1	1	0	0		1	0	1	1	2.053808	0	0.340000	1.830000	0.338876	0.790000	6.500000e-01	0.950000	0.800000	0.802945	0.790000	0	0.720000	0.880000
ZBED2	79413	broad.mit.edu	37	3	111312977	111312977	+	Silent	SNP	C	C	T	rs145211272		TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr3:111312977C>T	ENST00000317012.4	-	2	1080	c.72G>A	c.(70-72)gaG>gaA	p.E24E	CD96_ENST00000438817.2_Intron|CD96_ENST00000352690.4_Intron|CD96_ENST00000283285.5_Intron	NM_024508.4	NP_078784.2	Q9BTP6	ZBED2_HUMAN	zinc finger, BED-type containing 2			6					TCTCTTCCTCCTCCTTCATCT	0.507000																								0							SO:0001819	synonymous_variant			ENST00000317012.4	1	1	hg19	CCDS2960.2																																																																																				TCGA-2J-AABA-01A-21D-A40W-08	ZBED2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157228.2	0	0	0	9	296	0	57	0	2.447040e-01	1	28	0	57	2		0	0	0	0	0	2	1	0.993678	9	288	0	53	2								-3.581752	1	1	0	0		1	1	2	3	2.059806	0	0.340000	1.830000	0.341120	0.170000	8.000000e-02	0.320000	0.180000	0.190721	0.170000	0	0.120000	0.250000
KLHL24	54800	broad.mit.edu	37	3	183368717	183368717	+	Silent	SNP	G	G	A			TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr3:183368717G>A	ENST00000454652.2	+	4	959	c.573G>A	c.(571-573)gcG>gcA	p.A191A	KLHL24_ENST00000242810.6_Silent_p.A191A|KLHL24_ENST00000476808.1_Silent_p.A191A	NM_017644.3	NP_060114.2	Q6TFL4	KLH24_HUMAN	kelch-like family member 24			27	all_cancers(143;2.88e-10)|Ovarian(172;0.0303)		all cancers(12;1.43e-42)|Epithelial(37;1.73e-36)|OV - Ovarian serous cystadenocarcinoma(80;8.75e-22)		AAAATTTTGCGTTACAGACTT	0.368000																								0							SO:0001819	synonymous_variant			ENST00000454652.2	0	1	hg19	CCDS3246.1																																																																																				TCGA-2J-AABA-01A-21D-A40W-08	KLHL24-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346586.2	0	0	0	8	391	1	84	0	2.610030e-02	0	11	1	84	2		0	0	0	0	0	2	0	0.048487	9	387	1	83	17								-2.787841	1	1	0	0		1	1	2	3	2.059806	0	0.340000	1.830000	0.341120	0.120000	5.000000e-02	0.230000	0.120000	0.131609	0.120000	0	0.080000	0.170000
ZNF35	7584	broad.mit.edu	37	3	44700479	44700479	+	Silent	SNP	C	C	T			TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr3:44700479C>T	ENST00000396056.2	+	4	859	c.624C>T	c.(622-624)ggC>ggT	p.G208G	ZNF35_ENST00000542250.1_Silent_p.G48G|ZNF35_ENST00000296092.3_3'UTR|RP11-944L7.4_ENST00000457331.1_RNA	NM_003420.3	NP_003411.3	P13682	ZNF35_HUMAN	zinc finger protein 35	p.G208G(1)		12		Ovarian(412;0.0228)			TTAATTCTGGCGCTGTTAAAA	0.413000																								1	Substitution - coding silent(1)						SO:0001819	synonymous_variant			ENST00000396056.2	0	1	hg19	CCDS2718.2																																																																																				TCGA-2J-AABA-01A-21D-A40W-08	ZNF35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256749.4	0	0	0	7	652	0	116	0	8.222551e-03	0	11	0	116	2		0	0	0	0	0	2	1	0.980146	7	648	0	113	2								-2.149243	0	1	121412	1	36	1	0	1	1	2.059351	0	0.340000	1.830000	0.338876	0.060000	2.000000e-02	0.120000	0.060000	0.070886	0.060000	0	0.040000	0.100000
MYL3	4634	broad.mit.edu	37	3	46902285	46902285	+	Missense_Mutation	SNP	C	C	T	rs139354105		TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr3:46902285C>T	ENST00000395869.1	-	3	239	c.188G>A	c.(187-189)cGc>cAc	p.R63H	MYL3_ENST00000292327.4_Missense_Mutation_p.R63H			P08590	MYL3_HUMAN	myosin, light chain 3, alkali; ventricular, skeletal, slow			3					CTTGGGTGTGCGGTCGAACAG	0.622000													Melanoma(166;130 1949 2249 18977 46142)											0							SO:0001583	missense			ENST00000395869.1	0	1	hg19	CCDS2746.1	.	.	.	.	.	.	.	.	.	.	C	32	5.108683	0.94292	0.0	1.16E-4	ENSG00000160808	ENST00000395869;ENST00000292327	D;D	0.85861	-2.04;-2.04	4.36	4.36	0.52297	EF-hand-like domain (1);	0.000000	0.64402	D	0.000002	D	0.91341	0.7269	M	0.82323	2.585	0.80722	D	1	D	0.89917	1.0	P	0.60541	0.876	D	0.92718	0.6189	10	0.87932	D	0	-17.4592	14.7939	0.69863	0.0:1.0:0.0:0.0	.	63	P08590	MYL3_HUMAN	H	63	ENSP00000379210:R63H;ENSP00000292327:R63H	ENSP00000292327:R63H	R	-	2	0	MYL3	46877289	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.879000	0.69690	2.415000	0.81967	0.563000	0.77884	CGC		TCGA-2J-AABA-01A-21D-A40W-08	MYL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259165.2	0	0	0	5	557	0	97	0	7.759968e-04	0	4	0	97	2		0	0	0	0	0	2	1	0.936018	5	551	0	95	2								-1.860039	0	1	121412	3	38	1	0	1	1	2.059351	0	0.340000	1.830000	0.338876	0.050000	1.000000e-02	0.120000	0.060000	0.062225	0.050000	0	0.030000	0.090000
IQCF2	389123	broad.mit.edu	37	3	51897313	51897313	+	Missense_Mutation	SNP	G	G	A			TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr3:51897313G>A	ENST00000333127.3	+	3	451	c.422G>A	c.(421-423)tGc>tAc	p.C141Y	IQCF2_ENST00000429548.1_3'UTR	NM_203424.1	NP_982248.1	Q8IXL9	IQCF2_HUMAN	IQ motif containing F2			10					TGCCAGACCTGCGCTCTCCTC	0.567000																								0							SO:0001583	missense			ENST00000333127.3	1	1	hg19	CCDS2835.1	.	.	.	.	.	.	.	.	.	.	G	16.90	3.250045	0.59212	.	.	ENSG00000184345	ENST00000333127	T	0.30448	1.53	5.22	5.22	0.72569	.	0.101398	0.44902	D	0.000401	T	0.44138	0.1279	L	0.36672	1.1	0.18873	N	0.999981	D	0.89917	1.0	D	0.68765	0.96	T	0.24119	-1.0169	10	0.54805	T	0.06	-19.2161	14.4799	0.67573	0.0:0.0:1.0:0.0	.	141	Q8IXL9	IQCF2_HUMAN	Y	141	ENSP00000329904:C141Y	ENSP00000329904:C141Y	C	+	2	0	IQCF2	51872353	0.948000	0.32251	0.293000	0.24932	0.943000	0.58893	2.580000	0.46068	2.866000	0.98385	0.650000	0.86243	TGC		TCGA-2J-AABA-01A-21D-A40W-08	IQCF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346594.1	1	0	1	61	428	0	74		0	0	0	0	74	2		0	0	0	0	0	2	1	1.000000	61	425	0	73	2								-19.999890	1	1	0	0		1	1	2	3	2.059806	0	0.340000	1.830000	0.341120	0.730000	5.700000e-01	0.920000	0.740000	0.741010	0.730000	0	0.640000	0.830000
QRFPR	84109	broad.mit.edu	37	4	122258001	122258001	+	Silent	SNP	G	G	A			TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr4:122258001G>A	ENST00000394427.2	-	3	933	c.522C>T	c.(520-522)gtC>gtT	p.V174V	QRFPR_ENST00000334383.5_Silent_p.V174V	NM_198179.2	NP_937822.2	Q96P65	QRFPR_HUMAN	pyroglutamylated RFamide peptide receptor			28					ATCCTACGATGACTGCCACCA	0.413000																								0							SO:0001819	synonymous_variant			ENST00000394427.2	1	1	hg19	CCDS3719.1																																																																																				TCGA-2J-AABA-01A-21D-A40W-08	QRFPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256641.2	1	0	1	152	724	0	147		0	0	0	0	147	2		0	0	0	0	0	2	1	1.000000	150	709	0	143	2								-20.000000	1	1	0	0		1	1	2	3	2.063727	0	0.340000	1.830000	0.341120	0.990000	8.700000e-01	1.000000	1.000000	0.980720	0.990000	1	0.940000	1.000000
FBXW7	55294	broad.mit.edu	37	4	153244139	153244139	+	Nonsense_Mutation	SNP	C	C	T			TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr4:153244139C>T	ENST00000281708.4	-	12	3247	c.2018G>A	c.(2017-2019)tGg>tAg	p.W673*	FBXW7_ENST00000296555.5_Nonsense_Mutation_p.W555*|FBXW7_ENST00000263981.5_Nonsense_Mutation_p.W593*|FBXW7_ENST00000603841.1_Nonsense_Mutation_p.W673*|FBXW7_ENST00000393956.3_Nonsense_Mutation_p.W497*|FBXW7_ENST00000603548.1_Nonsense_Mutation_p.W673*|RP11-461L13.3_ENST00000603766.1_lincRNA	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	p.?(1)		462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)			TCTGATCCGCCACACAACTCC	0.498000			Mis, N, D, F		colorectal, endometrial, T-ALL										Rec	yes		4	4q31.3	55294	F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)		E, L	1	Unknown(1)						SO:0001587	stop_gained			ENST00000281708.4	0	1	hg19	CCDS3777.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.827871	0.90955	.	.	ENSG00000109670	ENST00000281708;ENST00000296555;ENST00000263981;ENST00000393956	.	.	.	5.67	5.67	0.87782	.	0.119994	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.4663	19.7667	0.96346	0.0:1.0:0.0:0.0	.	.	.	.	X	673;555;593;497	.	ENSP00000263981:W593X	W	-	2	0	FBXW7	153463589	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.794000	0.85869	2.681000	0.91329	0.655000	0.94253	TGG		TCGA-2J-AABA-01A-21D-A40W-08	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1	1	0	0	89	624	0	113	1	6.466035e-01	4	13	0	113	2	1	1	129	584	0	759	2	1	1.000000	87	613	0	110	2								-20.000000	1	1	0	0		1	1	2	3	2.063727	0	0.340000	1.830000	0.341120	0.730000	5.900000e-01	0.890000	0.740000	0.739678	0.730000	0	0.660000	0.810000
JAKMIP1	152789	broad.mit.edu	37	4	6107417	6107417	+	Missense_Mutation	SNP	G	G	A			TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr4:6107417G>A	ENST00000282924.5	-	3	892	c.407C>T	c.(406-408)gCg>gTg	p.A136V	JAKMIP1_ENST00000410077.2_Intron|JAKMIP1_ENST00000409831.1_Missense_Mutation_p.A136V|JAKMIP1_ENST00000409021.3_Missense_Mutation_p.A136V|JAKMIP1_ENST00000457227.2_Intron|JAKMIP1_ENST00000409371.3_Intron	NM_144720.3	NP_653321.1	Q96N16	JKIP1_HUMAN	janus kinase and microtubule interacting protein 1			42					CTCCTCGCGCGCCTCGGTCAG	0.706000																								0							SO:0001583	missense			ENST00000282924.5	1	1	hg19	CCDS3385.1	.	.	.	.	.	.	.	.	.	.	G	17.64	3.438645	0.62955	.	.	ENSG00000152969	ENST00000409021;ENST00000418227;ENST00000425341;ENST00000282924;ENST00000409831	T;T;T	0.06687	3.27;3.27;3.27	4.6	3.74	0.42951	.	0.081594	0.51477	D	0.000100	T	0.09598	0.0236	L	0.54323	1.7	0.80722	D	1	B;B;B	0.28850	0.225;0.01;0.225	B;B;B	0.20767	0.031;0.005;0.031	T	0.07731	-1.0757	10	0.72032	D	0.01	.	12.6579	0.56797	0.0865:0.0:0.9135:0.0	.	136;136;136	F2Z2K5;Q96N16-2;Q96N16	.;.;JKIP1_HUMAN	V	136	ENSP00000386711:A136V;ENSP00000282924:A136V;ENSP00000386925:A136V	ENSP00000282924:A136V	A	-	2	0	JAKMIP1	6158318	1.000000	0.71417	0.981000	0.43875	0.781000	0.44180	6.134000	0.71689	2.259000	0.74868	0.484000	0.47621	GCG		TCGA-2J-AABA-01A-21D-A40W-08	JAKMIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246816.2	1	0	1	15	62	0	14		0	0	0	0	14	2		0	0	0	0	0	2	1	0.999903	15	59	0	13	2								-20.000000	1	1	0	0		1	1	2	3	2.063727	0	0.340000	1.830000	0.341120	0.990000	6.900000e-01	1.000000	1.000000	0.962237	0.990000	1	0.900000	1.000000
DMP1	1758	broad.mit.edu	37	4	88583927	88583927	+	Missense_Mutation	SNP	G	G	A	rs147275271	byFrequency	TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr4:88583927G>A	ENST00000339673.6	+	6	1096	c.997G>A	c.(997-999)Gta>Ata	p.V333I	RP11-742B18.1_ENST00000507894.1_RNA|DMP1_ENST00000282479.7_Missense_Mutation_p.V317I|RP11-742B18.1_ENST00000506814.1_RNA|RP11-742B18.1_ENST00000506480.1_RNA	NM_004407.3	NP_004398.1	Q13316	DMP1_HUMAN	dentin matrix acidic phosphoprotein 1			32		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.227)			GAGCCAAAACGTAGATGGTCC	0.547000																								0							SO:0001583	missense			ENST00000339673.6	1	1	hg19	CCDS3623.1	.	.	.	.	.	.	.	.	.	.	G	3.132	-0.178230	0.06380	0.002043	1.16E-4	ENSG00000152592	ENST00000339673;ENST00000282479	T;T	0.51325	0.71;0.71	5.11	-4.38	0.03622	.	2.186990	0.01837	N	0.035040	T	0.25791	0.0628	L	0.27053	0.805	0.09310	N	1	B;P	0.34662	0.407;0.462	B;B	0.29785	0.065;0.107	T	0.05954	-1.0854	10	0.21540	T	0.41	1.4837	0.1494	0.00091	0.3024:0.2321:0.2291:0.2365	.	317;333	Q13316-2;Q13316	.;DMP1_HUMAN	I	333;317	ENSP00000340935:V333I;ENSP00000282479:V317I	ENSP00000282479:V317I	V	+	1	0	DMP1	88802951	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.407000	0.07178	-0.887000	0.03961	-1.724000	0.00704	GTA		TCGA-2J-AABA-01A-21D-A40W-08	DMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253047.1	1	0	1	33	235	0	38		0	0	0	0	38	2		0	0	0	0	0	2	1	1.000000	33	234	0	38	2								-6.470585	1	1	121412	31	48	1	1	2	3	2.063727	0	0.340000	1.830000	0.341120	0.720000	5.100000e-01	0.980000	0.720000	0.735711	0.720000	0	0.610000	0.850000
SQSTM1	8878	broad.mit.edu	37	5	179247944	179247944	+	Missense_Mutation	SNP	C	C	T			TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr5:179247944C>T	ENST00000389805.4	+	1	186	c.8C>T	c.(7-9)tCg>tTg	p.S3L	SQSTM1_ENST00000360718.5_5'Flank|SQSTM1_ENST00000402874.3_5'UTR|SQSTM1_ENST00000376929.3_Intron|SQSTM1_ENST00000510187.1_Missense_Mutation_p.S3L	NM_003900.4	NP_003891.1	Q13501	SQSTM_HUMAN	sequestosome 1		SQSTM1/ALK(2)	13	all_cancers(89;0.000205)|all_epithelial(37;7.15e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0395)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		GCTATGGCGTCGCTCACCGTG	0.711000																								0							SO:0001583	missense			ENST00000389805.4	1	1	hg19	CCDS34317.1	.	.	.	.	.	.	.	.	.	.	C	19.75	3.885955	0.72410	.	.	ENSG00000161011	ENST00000389805;ENST00000504627;ENST00000510187	D;T;T	0.84944	-1.92;1.3;2.08	4.57	0.299	0.15771	Phox/Bem1p (1);	0.320727	0.25402	U	0.030926	T	0.72479	0.3465	L	0.58101	1.795	0.80722	D	1	P;B	0.51351	0.944;0.065	B;B	0.30179	0.112;0.004	T	0.68078	-0.5504	10	0.72032	D	0.01	-10.7097	4.5537	0.12126	0.1172:0.5961:0.1275:0.1592	.	3;3	Q13501;E7EMC7	SQSTM_HUMAN;.	L	3	ENSP00000374455:S3L;ENSP00000425957:S3L;ENSP00000424477:S3L	ENSP00000374455:S3L	S	+	2	0	SQSTM1	179180550	1.000000	0.71417	0.428000	0.26697	0.461000	0.32589	2.655000	0.46707	0.309000	0.22966	0.462000	0.41574	TCG		TCGA-2J-AABA-01A-21D-A40W-08	SQSTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319344.1	1	0	0	7	83	0	23	1	9.999971e-01	171	298	0	23	2		0	0	0	0	0	2	1	0.981287	6	83	0	22	2								-12.156160	1	1	118576	2	29	1	1	2	3	2.127722	0	0.340000	1.830000	0.352115	0.500000	2.200000e-01	1.000000	0.460000	0.553409	0.500000	0	0.340000	0.770000
CMYA5	202333	broad.mit.edu	37	5	79029066	79029066	+	Missense_Mutation	SNP	A	A	G			TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr5:79029066A>G	ENST00000446378.2	+	2	4509	c.4478A>G	c.(4477-4479)gAc>gGc	p.D1493G		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5			128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)			AGGGTAGAAGACAAACAAGAT	0.398000																								0							SO:0001583	missense			ENST00000446378.2	1	1	hg19	CCDS47238.1	.	.	.	.	.	.	.	.	.	.	A	0.115	-1.132640	0.01756	.	.	ENSG00000164309	ENST00000446378	T	0.44881	0.91	5.32	2.9	0.33743	.	0.493610	0.17051	N	0.188919	T	0.21347	0.0514	N	0.14661	0.345	0.09310	N	1	B	0.10296	0.003	B	0.08055	0.003	T	0.17592	-1.0364	10	0.15952	T	0.53	.	6.9254	0.24412	0.8161:0.0:0.1839:0.0	.	1493	Q8N3K9	CMYA5_HUMAN	G	1493	ENSP00000394770:D1493G	ENSP00000394770:D1493G	D	+	2	0	CMYA5	79064822	0.000000	0.05858	0.042000	0.18584	0.034000	0.12701	0.586000	0.23894	1.058000	0.40530	0.533000	0.62120	GAC		TCGA-2J-AABA-01A-21D-A40W-08	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	1	0	1	79	532	0	128		0	0	0	0	128	2		0	0	0	0	0	2	1	1.000000	79	526	0	125	2								-20.000000	1	1	0	0		1	1	2	3	2.127722	0	0.340000	1.830000	0.352115	0.780000	6.200000e-01	1.000000	0.780000	0.799112	0.780000	0	0.690000	0.900000
RNF8	9025	broad.mit.edu	37	6	37349011	37349011	+	Missense_Mutation	SNP	G	G	A			TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr6:37349011G>A	ENST00000373479.4	+	7	1515	c.1322G>A	c.(1321-1323)cGg>cAg	p.R441Q	RNF8_ENST00000469731.1_Intron	NM_003958.3|NM_183078.2	NP_003949.1|NP_898901.1	O76064	RNF8_HUMAN	ring finger protein 8, E3 ubiquitin protein ligase			13					CCCATTTGTCGGAAGGACATT	0.413000																								0							SO:0001583	missense			ENST00000373479.4	0	1	hg19	CCDS4834.1	.	.	.	.	.	.	.	.	.	.	G	35	5.473197	0.96274	.	.	ENSG00000112130	ENST00000373479	T	0.60797	0.16	6.08	6.08	0.98989	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (1);	0.068846	0.64402	D	0.000015	T	0.78136	0.4236	M	0.87180	2.865	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.79631	-0.1723	10	0.66056	D	0.02	-13.1243	19.6603	0.95864	0.0:0.0:1.0:0.0	.	441	O76064	RNF8_HUMAN	Q	441	ENSP00000362578:R441Q	ENSP00000362578:R441Q	R	+	2	0	RNF8	37456989	1.000000	0.71417	1.000000	0.80357	0.803000	0.45373	9.869000	0.99810	2.894000	0.99253	0.591000	0.81541	CGG		TCGA-2J-AABA-01A-21D-A40W-08	RNF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040403.2	0	0	0	5	428	1	95	0	1.003162e-02	0	29	1	95	3		0	0	0	0	0	2	0	0.012078	5	427	1	92	16								-2.516899	1	1	121412	1	39	1	0	0	0	1.970790	0	0.340000	1.830000	0.309479	0.060000	2.000000e-02	0.140000	0.070000	0.077150	0.060000	0	0.040000	0.110000
GUCA1B	2979	broad.mit.edu	37	6	42152645	42152645	+	Missense_Mutation	SNP	G	G	T			TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr6:42152645G>T	ENST00000230361.3	-	4	606	c.511C>A	c.(511-513)Cgt>Agt	p.R171S		NM_002098.5	NP_002089.4	Q9UMX6	GUC1B_HUMAN	guanylate cyclase activator 1B (retina)			8	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|Epithelial(12;0.00154)|STAD - Stomach adenocarcinoma(11;0.00177)		TTGTCCCGACGGGCACCTTCA	0.577000																								0							SO:0001583	missense			ENST00000230361.3	0	1	hg19	CCDS4865.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.425131	0.83667	.	.	ENSG00000112599	ENST00000230361;ENST00000372949	T	0.54866	0.55	4.12	4.12	0.48240	EF-hand-like domain (1);	0.052845	0.85682	D	0.000000	T	0.38026	0.1025	L	0.46157	1.445	0.80722	D	1	P	0.50369	0.934	B	0.43194	0.411	T	0.48958	-0.8988	10	0.87932	D	0	.	14.6554	0.68828	0.0:0.0:1.0:0.0	.	171	Q9UMX6	GUC1B_HUMAN	S	171;163	ENSP00000230361:R171S	ENSP00000230361:R171S	R	-	1	0	GUCA1B	42260623	1.000000	0.71417	0.998000	0.56505	0.980000	0.70556	4.425000	0.59875	2.243000	0.73865	0.655000	0.94253	CGT		TCGA-2J-AABA-01A-21D-A40W-08	GUCA1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040550.1	0	0	0	5	301	0	58	0	2.557718e-03	0	4	0	58	2		0	0	0	0	0	2	1	0.933599	5	293	0	58	2								-2.782677	1	1	0	0		1	0	0	0	1.970790	0	0.340000	1.830000	0.309479	0.090000	3.000000e-02	0.200000	0.090000	0.108731	0.090000	0	0.060000	0.150000
LY86	9450	broad.mit.edu	37	6	6589102	6589102	+	Splice_Site	SNP	C	C	T			TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr6:6589102C>T	ENST00000379953.2	+	2	487	c.135C>T	c.(133-135)tgC>tgT	p.C45C	LY86-AS1_ENST00000429345.1_RNA|LY86_ENST00000230568.4_Splice_Site_p.C45C|LY86-AS1_ENST00000447858.1_RNA|LY86-AS1_ENST00000435641.1_RNA			O95711	LY86_HUMAN	lymphocyte antigen 86			8	Ovarian(93;0.0377)				ACCAGAGTTGCGGTAAGCCCT	0.587000																								0							SO:0001630	splice_region_variant			ENST00000379953.2	1	0	hg19	CCDS4498.1																																																																																				TCGA-2J-AABA-01A-21D-A40W-08	LY86-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039762.2	1	0	1	50	184	0	56	0	5.399564e-01	0	8	0	56	2		0	0	0	0	0	2	1	1.000000	50	179	0	54	2								-3.627983	1	1	121412	55	47	1	0	1	1	1.713140	1	0.340000	1.830000	0.204819	0.920000	7.500000e-01	1.000000	0.990000	0.916664	0.920000	1	0.840000	0.980000
RREB1	6239	broad.mit.edu	37	6	7230223	7230223	+	Missense_Mutation	SNP	G	G	A			TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr6:7230223G>A	ENST00000349384.6	+	10	2205	c.1891G>A	c.(1891-1893)Ggc>Agc	p.G631S	RREB1_ENST00000379938.2_Missense_Mutation_p.G631S|RREB1_ENST00000334984.6_Missense_Mutation_p.G631S|RREB1_ENST00000379933.3_Missense_Mutation_p.G631S	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1			58	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)			GACAGCGCCCGGCGGCAAGAA	0.637000																								0							SO:0001583	missense			ENST00000349384.6	0	1	hg19	CCDS34336.1	.	.	.	.	.	.	.	.	.	.	A	0.003	-2.475359	0.00167	.	.	ENSG00000124782	ENST00000379933;ENST00000379938;ENST00000349384;ENST00000334984;ENST00000483150	T;T;T;T;T	0.11604	2.97;2.94;2.97;2.76;2.86	5.13	0.216	0.15258	.	0.747822	0.12041	N	0.505003	T	0.01800	0.0057	N	0.16478	0.41	0.09310	N	1	B;B;B	0.29188	0.236;0.039;0.007	B;B;B	0.19148	0.024;0.005;0.006	T	0.42515	-0.9447	10	0.33141	T	0.24	-14.9214	10.9984	0.47591	0.4186:0.0:0.5814:0.0	.	631;631;631	Q92766-3;Q92766;Q92766-2	.;RREB1_HUMAN;.	S	631	ENSP00000369265:G631S;ENSP00000369270:G631S;ENSP00000305560:G631S;ENSP00000335574:G631S;ENSP00000419511:G631S	ENSP00000335574:G631S	G	+	1	0	RREB1	7175222	0.000000	0.05858	0.002000	0.10522	0.012000	0.07955	-0.002000	0.12924	-0.418000	0.07450	-0.977000	0.02584	GGC		TCGA-2J-AABA-01A-21D-A40W-08	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1	0	0	0	4	110	0	15	0	1.961137e-02	0	5	0	15	2		0	0	0	0	0	2	1	0.889606	4	109	0	13	2								-7.045847	1	1	0	0		1	0	1	1	1.713140	1	0.340000	1.830000	0.204819	0.180000	6.000000e-02	0.390000	0.170000	0.203336	0.180000	0	0.110000	0.290000
EPHA7	2045	broad.mit.edu	37	6	93967819	93967819	+	Missense_Mutation	SNP	C	C	T			TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr6:93967819C>T	ENST00000369303.4	-	11	2292	c.2108G>A	c.(2107-2109)aGa>aAa	p.R703K		NM_004440.3	NP_004431.1	Q15375	EPHA7_HUMAN	EPH receptor A7			112		all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142)			ATATCTACCTCTTGTAACAAC	0.343000																								0							SO:0001583	missense			ENST00000369303.4	1	1	hg19	CCDS5031.1	.	.	.	.	.	.	.	.	.	.	C	13.52	2.260255	0.39995	.	.	ENSG00000135333	ENST00000369303	D	0.81659	-1.52	6.06	6.06	0.98353	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.72503	0.3468	N	0.17723	0.515	0.80722	D	1	P;D;D	0.62365	0.747;0.989;0.991	P;P;P	0.62089	0.778;0.837;0.898	T	0.68172	-0.5479	10	0.02654	T	1	.	20.6314	0.99525	0.0:1.0:0.0:0.0	.	699;698;703	Q15375-4;Q15375-2;Q15375	.;.;EPHA7_HUMAN	K	703	ENSP00000358309:R703K	ENSP00000358309:R703K	R	-	2	0	EPHA7	94024540	1.000000	0.71417	1.000000	0.80357	0.580000	0.36256	6.063000	0.71162	2.885000	0.99019	0.579000	0.79373	AGA		TCGA-2J-AABA-01A-21D-A40W-08	EPHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041545.1	1	0	1	44	183	0	59	1	1.019112e-01	3	0	0	59	2		0	0	0	0	0	2	1	1.000000	43	178	0	57	2								-3.323014	1	1	0	0		1	0	1	1	1.714906	1	0.340000	1.830000	0.204819	0.880000	6.800000e-01	1.000000	0.930000	0.878528	0.880000	1	0.780000	0.960000
INTS1	26173	broad.mit.edu	37	7	1522220	1522220	+	Missense_Mutation	SNP	C	C	T			TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr7:1522220C>T	ENST00000404767.3	-	27	3750	c.3665G>A	c.(3664-3666)cGc>cAc	p.R1222H	INTS1_ENST00000389470.4_Missense_Mutation_p.R1384H	NM_001080453.2	NP_001073922.2	Q8N201	INT1_HUMAN	integrator complex subunit 1			62		Ovarian(82;0.0253)			ACGGATCATGCGCAGCTTCAG	0.667000																								0							SO:0001583	missense			ENST00000404767.3	1	1	hg19	CCDS47526.1	.	.	.	.	.	.	.	.	.	.	C	35	5.597216	0.96602	2.36E-4	0.0	ENSG00000164880	ENST00000404767;ENST00000389470	T;T	0.59502	0.26;0.39	4.67	4.67	0.58626	.	0.000000	0.45606	U	0.000346	T	0.70824	0.3268	M	0.69823	2.125	0.58432	D	0.999999	D	0.69078	0.997	P	0.56042	0.79	T	0.76599	-0.2900	10	0.87932	D	0	.	17.5786	0.87958	0.0:1.0:0.0:0.0	.	1222	Q8N201	INT1_HUMAN	H	1222;1384	ENSP00000385722:R1222H;ENSP00000374121:R1384H	ENSP00000374121:R1384H	R	-	2	0	INTS1	1488746	1.000000	0.71417	0.999000	0.59377	0.968000	0.65278	7.540000	0.82074	2.154000	0.67381	0.561000	0.74099	CGC		TCGA-2J-AABA-01A-21D-A40W-08	INTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323683.1	1	0	0	64	241	1	44	1	9.258303e-01	12	27	1	44	5		0	0	0	0	0	2	1	1.000000	63	235	1	42	21								-20.000000	1	1	121046	2	32	1	1	2	3	2.088232	0	0.340000	1.830000	0.345563	0.990000	9.800000e-01	1.000000	1.000000	0.998649	0.990000	1	0.990000	1.000000
HOXA4	3201	broad.mit.edu	37	7	27169037	27169037	+	Missense_Mutation	SNP	C	C	T			TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr7:27169037C>T	ENST00000360046.5	-	2	835	c.770G>A	c.(769-771)cGc>cAc	p.R257H	HOXA3_ENST00000317201.2_5'Flank|HOXA4_ENST00000428284.2_Missense_Mutation_p.R257H|HOXA-AS2_ENST00000521687.1_RNA|RP1-170O19.22_ENST00000467897.2_RNA|HOXA-AS2_ENST00000521159.1_RNA|HOXA3_ENST00000521401.1_Intron|HOXA-AS3_ENST00000518848.1_RNA|HOXA-AS2_ENST00000517550.1_RNA	NM_002141.4	NP_002132.3	Q00056	HXA4_HUMAN	homeobox A4			12					CTTGACCTGGCGCTCAGACAA	0.572000																								0							SO:0001583	missense			ENST00000360046.5	1	1	hg19	CCDS5405.1	.	.	.	.	.	.	.	.	.	.	C	27.5	4.837480	0.91117	0.0	1.16E-4	ENSG00000197576	ENST00000360046;ENST00000428284	D;D	0.96802	-4.13;-4.13	5.29	5.29	0.74685	Homeobox, eukaryotic (1);Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1);	0.000000	0.64402	D	0.000011	D	0.98438	0.9480	M	0.88775	2.98	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.99494	1.0951	10	0.87932	D	0	.	18.9816	0.92757	0.0:1.0:0.0:0.0	.	257	Q00056	HXA4_HUMAN	H	257	ENSP00000353151:R257H;ENSP00000408845:R257H	ENSP00000353151:R257H	R	-	2	0	HOXA4	27135562	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.728000	0.84847	2.485000	0.83878	0.555000	0.69702	CGC		TCGA-2J-AABA-01A-21D-A40W-08	HOXA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059534.4	1	0	1	83	416	0	110	0	7.997745e-01	1	16	0	110	2		0	0	0	0	0	2	1	1.000000	83	413	0	107	2								-3.156128	1	1	121412	16	46	1	1	2	3	2.088232	0	0.340000	1.830000	0.345563	0.980000	8.000000e-01	1.000000	1.000000	0.957452	0.980000	1	0.880000	1.000000
HECW1	23072	broad.mit.edu	37	7	43590047	43590047	+	Missense_Mutation	SNP	A	A	G			TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr7:43590047A>G	ENST00000395891.2	+	27	4857	c.4252A>G	c.(4252-4254)Acg>Gcg	p.T1418A	HECW1_ENST00000453890.1_Missense_Mutation_p.T1384A	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1			125					CTACAAGGTCACGGAAAGGGA	0.507000																								0							SO:0001583	missense			ENST00000395891.2	0	1	hg19	CCDS5469.2	.	.	.	.	.	.	.	.	.	.	A	24.0	4.487153	0.84854	.	.	ENSG00000002746	ENST00000395891;ENST00000453890;ENST00000265522	T;T	0.57273	0.41;0.41	5.62	5.62	0.85841	HECT (4);	0.000000	0.85682	D	0.000000	T	0.60715	0.2290	L	0.31926	0.97	0.80722	D	1	D;B	0.55605	0.972;0.048	D;B	0.67231	0.95;0.027	T	0.56432	-0.7980	10	0.25751	T	0.34	.	15.8276	0.78727	1.0:0.0:0.0:0.0	.	1384;1418	B4DH42;Q76N89	.;HECW1_HUMAN	A	1418;1384;1418	ENSP00000379228:T1418A;ENSP00000407774:T1384A	ENSP00000265522:T1418A	T	+	1	0	HECW1	43556572	1.000000	0.71417	0.986000	0.45419	0.929000	0.56500	8.962000	0.93254	2.122000	0.65172	0.533000	0.62120	ACG		TCGA-2J-AABA-01A-21D-A40W-08	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	0	0	0	5	105	0	19	0	2.879528e-02	0	5	0	19	2		0	0	0	0	0	2	1	0.939019	5	105	0	19	2								-8.669340	1	1	0	0		1	1	2	3	2.088232	0	0.340000	1.830000	0.345563	0.290000	1.100000e-01	1.000000	0.270000	0.338492	0.290000	0	0.180000	0.460000
BLVRA	644	broad.mit.edu	37	7	43810766	43810766	+	Silent	SNP	A	A	T			TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08			A	T	A	A		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr7:43810766A>T	ENST00000402924.1	+	3	172	c.9A>T	c.(7-9)gcA>gcT	p.A3A	BLVRA_ENST00000265523.4_Silent_p.A3A	NM_001253823.1	NP_001240752.1	P53004	BIEA_HUMAN	biliverdin reductase A			12					AGATGAATGCAGAGGTGAGTT	0.463000																								0							SO:0001819	synonymous_variant			ENST00000402924.1	1	1	hg19	CCDS5472.1																																																																																				TCGA-2J-AABA-01A-21D-A40W-08	BLVRA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339006.1	1	0	1	43	199	0	61	1	9.997526e-01	14	47	0	61	2		0	0	0	0	0	2	1	1.000000	42	196	0	61	2								-19.999950	1	1	0	0		1	1	2	3	2.088232	0	0.340000	1.830000	0.345563	0.990000	7.900000e-01	1.000000	1.000000	0.969903	0.990000	1	0.910000	1.000000
RIMS2	9699	broad.mit.edu	37	8	105263381	105263381	+	Missense_Mutation	SNP	A	A	C			TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr8:105263381A>C	ENST00000436393.2	+	27	4116	c.3875A>C	c.(3874-3876)aAa>aCa	p.K1292T	RIMS2_ENST00000507740.1_Missense_Mutation_p.K1088T|RIMS2_ENST00000406091.3_Missense_Mutation_p.K1274T|RIMS2_ENST00000339750.2_Missense_Mutation_p.K210T|RIMS2_ENST00000262231.10_Missense_Mutation_p.K1113T			Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2			144			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)		CCACAAGGAAAAGTTTTACAG	0.368000										HNSCC(12;0.0054)														0							SO:0001583	missense			ENST00000436393.2	0	1	hg19		.	.	.	.	.	.	.	.	.	.	A	20.2	3.951323	0.73787	.	.	ENSG00000176406	ENST00000329869;ENST00000406091;ENST00000402998;ENST00000262231;ENST00000507740;ENST00000436393;ENST00000523362;ENST00000339750	T;T;T;T;T;T	0.68903	-0.36;-0.36;-0.36;-0.36;-0.36;-0.36	5.24	4.03	0.46877	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	.	.	.	.	T	0.79143	0.4396	M	0.72624	2.21	0.58432	D	0.999998	D;P;P;D;D	0.76494	0.994;0.787;0.933;0.999;0.999	D;P;D;D;D	0.85130	0.994;0.69;0.963;0.997;0.997	T	0.79811	-0.1646	9	0.66056	D	0.02	.	11.4916	0.50383	0.9278:0.0:0.0722:0.0	.	1336;1292;1113;1088;1274	Q9UQ26;D6RA03;Q9UQ26-1;Q9UQ26-3;F8WD47	RIMS2_HUMAN;.;.;.;.	T	1311;1274;1336;1113;1088;1292;210;210	ENSP00000384892:K1274T;ENSP00000262231:K1113T;ENSP00000423559:K1088T;ENSP00000390665:K1292T;ENSP00000428478:K210T;ENSP00000342051:K210T	ENSP00000262231:K1113T	K	+	2	0	RIMS2	105332557	1.000000	0.71417	0.904000	0.35570	0.985000	0.73830	7.451000	0.80668	0.889000	0.36185	0.477000	0.44152	AAA		TCGA-2J-AABA-01A-21D-A40W-08	RIMS2-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000367217.1	1	0	1	13	67	0	12		0	0	0	0	12	2		0	0	0	0	0	2	1	0.999688	13	67	0	12	2								-19.999850	1	1	0	0		1	0	1	1	2.053834	0	0.340000	1.830000	0.338876	0.950000	5.500000e-01	1.000000	1.000000	0.894287	0.950000	1	0.730000	1.000000
WRN	7486	broad.mit.edu	37	8	30924630	30924630	+	Missense_Mutation	SNP	C	C	T			TCGA-2J-AABA-01A-21D-A40W-08	TCGA-2J-AABA-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61e9c5f2-e782-404f-92f1-ecc78d28b285	702e85b0-5c6e-4945-a20a-37568587f243	g.chr8:30924630C>T	ENST00000298139.5	+	6	835	c.586C>T	c.(586-588)Cgc>Tgc	p.R196C		NM_000553.4	NP_000544.2	Q14191	WRN_HUMAN	Werner syndrome, RecQ helicase-like			60		Breast(100;0.195)			CAAGTCTATCCGCTGTAGCAA	0.413000			Mis, N, F, S			osteosarcoma, meningioma, others		Genes defective in diseases associated with sensitivity to DNA damaging agents	Werner syndrome				Ovarian(18;161 598 2706 14834 27543)	yes	Rec		Werner Syndrome	8	8p12-p11.2	7486	Werner syndrome (RECQL2)		L, E, M, O	0							SO:0001583	missense	Familial Cancer Database	WS, Adult Progeria	ENST00000298139.5	1	1	hg19	CCDS6082.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.886939	0.91814	2.27E-4	0.0	ENSG00000165392	ENST00000298139	T	0.63913	-0.07	5.82	5.82	0.92795	-5&apos (2);Ribonuclease H-like (1); exonuclease (2);3&apos (2);	0.056461	0.64402	N	0.000001	D	0.85444	0.5698	M	0.93638	3.44	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.88398	0.3013	10	0.87932	D	0	-10.7416	19.6956	0.96023	0.0:1.0:0.0:0.0	.	196	Q14191	WRN_HUMAN	C	196	ENSP00000298139:R196C	ENSP00000298139:R196C	R	+	1	0	WRN	31044172	1.000000	0.71417	0.992000	0.48379	0.966000	0.64601	6.162000	0.71874	2.757000	0.94681	0.561000	0.74099	CGC		TCGA-2J-AABA-01A-21D-A40W-08	WRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376248.1	1	0	1	48	274	0	66	0	2.326686e-02	1	1	0	66	2		0	0	0	0	0	2	1	1.000000	48	272	0	66	2								-2.527547	1	1	121412	1	29	1	0	1	1	2.053834	0	0.340000	1.830000	0.338876	0.870000	6.600000e-01	1.000000	1.000000	0.872277	0.870000	1	0.760000	0.990000
