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
TACR3	6870	broad.mit.edu	37	4	104577461	104577469	+	In_Frame_Del	DEL	ATGGGAAAC	ATGGGAAAC	-			TCGA-2J-AABR-01A-11D-A40W-08	TCGA-2J-AABR-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	534d051f-0b40-486a-8f77-646bf003d3d0	4c28dd95-5359-4c03-b338-7038de30008f	g.chr4:104577461_104577469delATGGGAAAC	ENST00000304883.2	-	3	910_918	c.770_778delGTTTCCCAT	c.(769-780)tgtttcccattg>ttg	p.CFP257del		NM_001059.2	NP_001050.1	P29371	NK3R_HUMAN	tachykinin receptor 3			51		Hepatocellular(203;0.217)			ATGATGAGCAATGGGAAACAGTACACCAG	0.392000																								0							SO:0001651	inframe_deletion			ENST00000304883.2	1	1	hg19	CCDS3664.1																																																																																				TCGA-2J-AABR-01A-11D-A40W-08	TACR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253804.1	0	0	0	9	516	0	118	0	0	0	0	0	0		0	0	0	0	0	0		1	0.994679	16	517	0	116	2								-7.783322	1	1	0	0		1	1	2	3	2.014557	0	0.090000	1.970000	0.098921	0.430000	0.200000	1.000000	0.370000	0.513428	0.430000	0	0.290000	1.000000
CNNM2	54805	broad.mit.edu	37	10	104678687	104678687	+	Silent	SNP	C	C	T			TCGA-2J-AABR-01A-11D-A40W-08	TCGA-2J-AABR-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	534d051f-0b40-486a-8f77-646bf003d3d0	4c28dd95-5359-4c03-b338-7038de30008f	g.chr10:104678687C>T	ENST00000369878.4	+	1	638	c.450C>T	c.(448-450)tgC>tgT	p.C150C	CNNM2_ENST00000369875.3_Silent_p.C150C|CNNM2_ENST00000433628.2_Silent_p.C150C	NM_017649.4	NP_060119.3	Q9H8M5	CNNM2_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 2			19		Colorectal(252;0.103)|all_hematologic(284;0.152)|Breast(234;0.198)			CCCAGCGATGCGGCATCCGCA	0.687000																								0							SO:0001819	synonymous_variant			ENST00000369878.4	0	1	hg19	CCDS44474.1																																																																																				TCGA-2J-AABR-01A-11D-A40W-08	CNNM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050113.3	0	0	0	8	656	0	144	0	1.185577e-03	0	4	0	144	2		0	0	0	0	0	2	1	0.989023	9	649	0	143	2								-2.095396	0	1	0	0		1	0	0	0	1.941341	0	0.090000	1.970000	0.054251	0.260000	0.120000	0.470000	0.250000	0.281374	0.260000	0	0.180000	0.370000
BCCIP	56647	broad.mit.edu	37	10	127520157	127520157	+	Missense_Mutation	SNP	C	C	T			TCGA-2J-AABR-01A-11D-A40W-08	TCGA-2J-AABR-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	534d051f-0b40-486a-8f77-646bf003d3d0	4c28dd95-5359-4c03-b338-7038de30008f	g.chr10:127520157C>T	ENST00000278100.6	+	5	592	c.580C>T	c.(580-582)Ccc>Tcc	p.P194S	BCCIP_ENST00000368759.5_Missense_Mutation_p.P194S|BCCIP_ENST00000429863.2_Missense_Mutation_p.P164S|BCCIP_ENST00000299130.3_Missense_Mutation_p.P194S	NM_078468.2	NP_510868.1	Q9P287	BCCIP_HUMAN	BRCA2 and CDKN1A interacting protein			8		all_lung(145;0.00751)|Lung NSC(174;0.0115)|Colorectal(57;0.0846)|all_neural(114;0.0936)			GATCGCTCTGCCCATGTACCA	0.383000																								0							SO:0001583	missense			ENST00000278100.6	0	1	hg19	CCDS7651.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.808990	0.90707	.	.	ENSG00000107949	ENST00000278100;ENST00000299130;ENST00000368759;ENST00000429863;ENST00000392718	T;T;T;T	0.51071	0.72;0.72;0.72;0.72	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	T	0.78616	0.4311	H	0.94734	3.575	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.998;1.0;1.0;0.999;1.0	D	0.85215	0.1023	10	0.87932	D	0	-2.8285	18.8517	0.92235	0.0:1.0:0.0:0.0	.	164;194;194;194;194	B4E318;B4DUS0;Q9P287-2;Q9P287-4;Q9P287	.;.;.;.;BCCIP_HUMAN	S	194;194;194;164;194	ENSP00000278100:P194S;ENSP00000299130:P194S;ENSP00000357748:P194S;ENSP00000394758:P164S	ENSP00000278100:P194S	P	+	1	0	BCCIP	127510147	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.470000	0.80973	2.444000	0.82710	0.650000	0.86243	CCC		TCGA-2J-AABR-01A-11D-A40W-08	BCCIP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050941.1	0	0	0	6	325	0	52	1	6.088257e-01	4	101	0	52	2		0	0	0	0	0	2	1	0.964345	6	323	0	52	2								-2.939098	1	1	121412	1	30	1	0	0	0	1.941341	0	0.090000	1.970000	0.054251	0.400000	0.160000	0.750000	0.370000	0.425568	0.400000	0	0.260000	0.570000
PDSS1	23590	broad.mit.edu	37	10	27024505	27024505	+	Silent	SNP	G	G	A			TCGA-2J-AABR-01A-11D-A40W-08	TCGA-2J-AABR-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	534d051f-0b40-486a-8f77-646bf003d3d0	4c28dd95-5359-4c03-b338-7038de30008f	g.chr10:27024505G>A	ENST00000376215.5	+	10	1076	c.1023G>A	c.(1021-1023)caG>caA	p.Q341Q	PDSS1_ENST00000376203.5_Intron|PDSS1_ENST00000470978.1_3'UTR	NM_014317.3	NP_055132.2	Q5T2R2	DPS1_HUMAN	prenyl (decaprenyl) diphosphate synthase, subunit 1			21					TTGCCTGTCAGCAGGTAGGTT	0.498000																								0							SO:0001819	synonymous_variant			ENST00000376215.5	0	1	hg19	CCDS31168.1																																																																																				TCGA-2J-AABR-01A-11D-A40W-08	PDSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047276.1	0	0	0	6	154	0	36	0	1.898360e-02	0	5	0	36	2		0	0	0	0	0	2	1	0.963800	6	151	0	36	2								-8.575297	1	1	0	0		1	1	2	3	2.006452	0	0.090000	1.970000	0.097312	0.930000	0.380000	1.000000	1.000000	0.841811	0.930000	1	0.600000	1.000000
KRAS	3845	broad.mit.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	C	A	rs121913529		TCGA-2J-AABR-01A-11D-A40W-08	TCGA-2J-AABR-10A-01D-A40W-08			C	A	C	C		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	534d051f-0b40-486a-8f77-646bf003d3d0	4c28dd95-5359-4c03-b338-7038de30008f	g.chr12:25398284C>A	ENST00000256078.4	-	2	98	c.35G>T	c.(34-36)gGt>gTt	p.G12V	KRAS_ENST00000556131.1_Missense_Mutation_p.G12V|KRAS_ENST00000557334.1_Missense_Mutation_p.G12V|KRAS_ENST00000311936.3_Missense_Mutation_p.G12V	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)		GCCTACGCCACCAGCTCCAAC	0.348000	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		pancreatic, colorectal, lung, thyroid, AML, others				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)			Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		L, E, M, O	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)						SO:0001583	missense	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	ENST00000256078.4	1	1	hg19	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.808637	0.90707	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90373	0.6987	M	0.90650	3.135	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.72625	0.969;0.978	D	0.91773	0.5429	10	0.72032	D	0.01	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	V	12	ENSP00000308495:G12V;ENSP00000452512:G12V;ENSP00000256078:G12V;ENSP00000451856:G12V	ENSP00000256078:G12V	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		TCGA-2J-AABR-01A-11D-A40W-08	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	0	0	0	8	215	0	67	1	4.051874e-02	2	6	0	67	2	1	9.986014e-01	5	339	0	515	2	1	0.988752	8	210	0	65	2								-3.951907	1	1	0	0		1	0	1	1	1.988592	0	0.090000	1.970000	0.080483	0.790000	0.380000	1.000000	1.000000	0.785590	0.790000	0	0.560000	1.000000
EDNRB	1910	broad.mit.edu	37	13	78477390	78477390	+	Silent	SNP	G	G	T	rs112618428	byFrequency	TCGA-2J-AABR-01A-11D-A40W-08	TCGA-2J-AABR-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	534d051f-0b40-486a-8f77-646bf003d3d0	4c28dd95-5359-4c03-b338-7038de30008f	g.chr13:78477390G>T	ENST00000334286.5	-	3	938	c.702C>A	c.(700-702)gtC>gtA	p.V234V	EDNRB_ENST00000377211.4_Silent_p.V324V|EDNRB_ENST00000446573.1_Silent_p.V234V	NM_000115.3|NM_001122659.2	NP_000106.1|NP_001116131.1	P24530	EDNRB_HUMAN	endothelin receptor type B			42		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.037)		Bosentan(DB00559)|MACITENTAN(DB08932)|Sitaxentan(DB06268)	TGGCTTCAGGGACAGCCAGAA	0.433000																								0							SO:0001819	synonymous_variant			ENST00000334286.5	0	1	hg19	CCDS9461.1																																																																																				TCGA-2J-AABR-01A-11D-A40W-08	EDNRB-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276505.1	0	0	0	13	630	0	121	0	6.544281e-02	0	19	0	121	2		0	0	0	0	0	2	1	0.999497	13	622	0	120	2								-2.597057	1	1	0	0		1	0	0	0	1.952484	0	0.090000	1.970000	0.059529	0.430000	0.240000	0.690000	0.430000	0.455257	0.430000	0	0.330000	0.570000
KLHDC2	23588	broad.mit.edu	37	14	50249311	50249311	+	Splice_Site	SNP	C	C	T			TCGA-2J-AABR-01A-11D-A40W-08	TCGA-2J-AABR-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	534d051f-0b40-486a-8f77-646bf003d3d0	4c28dd95-5359-4c03-b338-7038de30008f	g.chr14:50249311C>T	ENST00000298307.5	+	12	1957	c.1096C>T	c.(1096-1098)Cgg>Tgg	p.R366W	NEMF_ENST00000556925.1_5'Flank|KLHDC2_ENST00000554589.1_Intron|KLHDC2_ENST00000557247.1_Intron	NM_014315.2	NP_055130.1	Q9Y2U9	KLDC2_HUMAN	kelch domain containing 2			16	all_epithelial(31;0.000959)|Breast(41;0.0117)				ATCTCTTGTACGGTAAGTAAC	0.308000																								0							SO:0001630	splice_region_variant			ENST00000298307.5	1	0	hg19	CCDS9693.1	.	.	.	.	.	.	.	.	.	.	C	17.83	3.484982	0.63962	.	.	ENSG00000165516	ENST00000298307	T	0.05081	3.5	5.23	3.12	0.35913	.	0.000000	0.85682	D	0.000000	T	0.22126	0.0533	M	0.73962	2.25	0.80722	D	1	D	0.89917	1.0	D	0.75020	0.985	T	0.00440	-1.1738	10	0.87932	D	0	-15.6679	11.6456	0.51259	0.5345:0.4655:0.0:0.0	.	366	Q9Y2U9	KLDC2_HUMAN	W	366	ENSP00000298307:R366W	ENSP00000298307:R366W	R	+	1	2	KLHDC2	49319061	1.000000	0.71417	1.000000	0.80357	0.902000	0.53008	0.984000	0.29565	0.629000	0.30376	0.655000	0.94253	CGG		TCGA-2J-AABR-01A-11D-A40W-08	KLHDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276869.1	1	0	0	8	143	0	44	1	9.617955e-01	5	101	0	44	2		0	0	0	0	0	2	1	0.988815	8	140	0	43	2								-4.409441	1	1	121386	7	33	1	1	2	3	2.014109	0	0.090000	1.970000	0.098921	0.990000	0.590000	1.000000	1.000000	0.952268	0.990000	1	0.880000	1.000000
SLC27A2	11001	broad.mit.edu	37	15	50519366	50519366	+	Missense_Mutation	SNP	A	A	G			TCGA-2J-AABR-01A-11D-A40W-08	TCGA-2J-AABR-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	534d051f-0b40-486a-8f77-646bf003d3d0	4c28dd95-5359-4c03-b338-7038de30008f	g.chr15:50519366A>G	ENST00000267842.5	+	7	1680	c.1448A>G	c.(1447-1449)gAt>gGt	p.D483G	SLC27A2_ENST00000544960.1_Missense_Mutation_p.D248G|SLC27A2_ENST00000380902.4_Missense_Mutation_p.D430G	NM_003645.3	NP_003636.2	O14975	S27A2_HUMAN	solute carrier family 27 (fatty acid transporter), member 2			25		all_lung(180;0.00177)			AGAGTTGGAGATACATTCCGG	0.408000																								0							SO:0001583	missense			ENST00000267842.5	0	1	hg19	CCDS10133.1	.	.	.	.	.	.	.	.	.	.	A	26.0	4.694762	0.88830	.	.	ENSG00000140284	ENST00000380902;ENST00000267842;ENST00000544960	T;T;T	0.59502	0.26;0.26;0.26	5.78	5.78	0.91487	AMP-dependent synthetase/ligase (1);	0.000000	0.85682	D	0.000000	D	0.84620	0.5512	H	0.98111	4.15	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.90026	0.4131	10	0.87932	D	0	.	14.0725	0.64868	1.0:0.0:0.0:0.0	.	430;483	Q6PF09;O14975	.;S27A2_HUMAN	G	430;483;248	ENSP00000370289:D430G;ENSP00000267842:D483G;ENSP00000444549:D248G	ENSP00000267842:D483G	D	+	2	0	SLC27A2	48306658	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.027000	0.93706	2.205000	0.71048	0.533000	0.62120	GAT		TCGA-2J-AABR-01A-11D-A40W-08	SLC27A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254539.2	0	0	0	9	320	0	72	0	3.047758e-02	0	9	0	72	2		0	0	0	0	0	2	1	0.994384	9	320	0	72	2								-3.081625	1	1	121412	13	41	1	1	2	3	2.007232	0	0.090000	1.970000	0.097312	0.670000	0.320000	1.000000	1.000000	0.699133	0.670000	0	0.460000	1.000000
SRRM2	23524	broad.mit.edu	37	16	2814969	2814969	+	Missense_Mutation	SNP	T	T	G			TCGA-2J-AABR-01A-11D-A40W-08	TCGA-2J-AABR-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	534d051f-0b40-486a-8f77-646bf003d3d0	4c28dd95-5359-4c03-b338-7038de30008f	g.chr16:2814969T>G	ENST00000301740.8	+	11	4989	c.4440T>G	c.(4438-4440)tgT>tgG	p.C1480W		NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2			105					GAAGCGAATGTGATTCTTCCC	0.532000																								0							SO:0001583	missense			ENST00000301740.8	1	1	hg19	CCDS32373.1	.	.	.	.	.	.	.	.	.	.	T	8.461	0.855301	0.17106	.	.	ENSG00000167978	ENST00000301740;ENST00000382301;ENST00000544933	T	0.26660	1.72	6.06	2.44	0.29823	.	0.089407	0.49916	D	0.000133	T	0.23688	0.0573	L	0.29908	0.895	0.46774	D	0.999198	D	0.63880	0.993	P	0.53006	0.715	T	0.02991	-1.1085	10	0.62326	D	0.03	-5.977	4.8712	0.13633	0.1664:0.167:0.0:0.6666	.	1480	Q9UQ35	SRRM2_HUMAN	W	1480;1480;732	ENSP00000301740:C1480W	ENSP00000301740:C1480W	C	+	3	2	SRRM2	2754970	0.997000	0.39634	1.000000	0.80357	0.925000	0.55904	0.114000	0.15520	0.530000	0.28619	0.533000	0.62120	TGT		TCGA-2J-AABR-01A-11D-A40W-08	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1	0	0	0	17	643	0	127	1	9.150515e-01	11	152	0	127	2		0	0	0	0	0	2	1	0.999963	17	640	0	121	2								-13.990710	1	1	0	0		1	1	2	3	2.035123	0	0.090000	1.970000	0.103316	0.630000	0.360000	1.000000	0.570000	0.689005	0.630000	0	0.480000	1.000000
FAM86A	196483	broad.mit.edu	37	16	5140142	5140142	+	Missense_Mutation	SNP	C	C	T			TCGA-2J-AABR-01A-11D-A40W-08	TCGA-2J-AABR-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	534d051f-0b40-486a-8f77-646bf003d3d0	4c28dd95-5359-4c03-b338-7038de30008f	g.chr16:5140142C>T	ENST00000427587.4	-	6	753	c.685G>A	c.(685-687)Gac>Aac	p.D229N	FAM86A_ENST00000458008.4_Missense_Mutation_p.D195N|FAM86A_ENST00000587133.1_Missense_Mutation_p.D168N	NM_201400.2	NP_958802.1	Q96G04	FA86A_HUMAN	family with sequence similarity 86, member A			12					GTCGCGACGTCCCAGTCCAGC	0.602000																								0							SO:0001583	missense			ENST00000427587.4	0	1	hg19	CCDS10529.1	.	.	.	.	.	.	.	.	.	.	c	15.70	2.911632	0.52439	.	.	ENSG00000118894	ENST00000458008;ENST00000427587	T;T	0.06687	3.27;3.27	5.02	5.02	0.67125	.	0.452097	0.23549	N	0.046998	T	0.12220	0.0297	L	0.50333	1.59	0.49389	D	0.999781	P;B	0.36392	0.551;0.34	B;B	0.40982	0.345;0.14	T	0.15435	-1.0437	10	0.17832	T	0.49	.	17.1053	0.86660	0.0:1.0:0.0:0.0	.	195;229	Q96G04-2;Q96G04	.;FA86A_HUMAN	N	195;229	ENSP00000389710:D195N;ENSP00000398502:D229N	ENSP00000398502:D229N	D	-	1	0	FAM86A	5080143	1.000000	0.71417	0.997000	0.53966	0.066000	0.16364	3.106000	0.50322	2.620000	0.88729	0.450000	0.29827	GAC		TCGA-2J-AABR-01A-11D-A40W-08	FAM86A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251713.1	0	0	0	6	268	1	71	0	3.081356e-02	0	25	1	71	3		0	0	0	0	0	2	0	0.048814	0	246	1	71	13								-7.145509	1	0	0	0		1	1	2	3	2.035123	0	0.090000	1.970000	0.103316	0.590000	0.230000	1.000000	1.000000	0.646253	0.590000	0	0.370000	1.000000
MMP2	4313	broad.mit.edu	37	16	55519538	55519538	+	Silent	SNP	C	C	T			TCGA-2J-AABR-01A-11D-A40W-08	TCGA-2J-AABR-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	534d051f-0b40-486a-8f77-646bf003d3d0	4c28dd95-5359-4c03-b338-7038de30008f	g.chr16:55519538C>T	ENST00000219070.4	+	5	1190	c.681C>T	c.(679-681)aaC>aaT	p.N227N	MMP2_ENST00000543485.1_Silent_p.N151N|MMP2_ENST00000437642.2_Silent_p.N177N|MMP2_ENST00000570308.1_Silent_p.N151N	NM_004530.4	NP_004521.1	P08253	MMP2_HUMAN	matrix metallopeptidase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase)			58		Renal(780;0.00183)|Breast(268;0.00354)|Hepatocellular(780;0.00826)|all_neural(199;0.0189)		Captopril(DB01197)|Marimastat(DB00786)	AGTATGGGAACGCCGATGGGG	0.542000																								0							SO:0001819	synonymous_variant			ENST00000219070.4	1	1	hg19	CCDS10752.1																																																																																				TCGA-2J-AABR-01A-11D-A40W-08	MMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256913.3	0	0	0	20	572	1	131	0	7.571674e-01	0	497	1	131	14		0	0	0	0	0	2	1	0.786320	20	563	1	127	16								-3.744623	1	1	121412	5	40	1	1	2	3	2.015526	0	0.090000	1.970000	0.099322	0.800000	0.490000	1.000000	1.000000	0.810259	0.800000	0	0.620000	1.000000
MMP15	4324	broad.mit.edu	37	16	58074496	58074496	+	Silent	SNP	G	G	A			TCGA-2J-AABR-01A-11D-A40W-08	TCGA-2J-AABR-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	534d051f-0b40-486a-8f77-646bf003d3d0	4c28dd95-5359-4c03-b338-7038de30008f	g.chr16:58074496G>A	ENST00000219271.3	+	5	1589	c.804G>A	c.(802-804)gaG>gaA	p.E268E		NM_002428.2	NP_002419.1	P51511	MMP15_HUMAN	matrix metallopeptidase 15 (membrane-inserted)			18				Marimastat(DB00786)	TGGGGCTGGAGCACTCCAGCA	0.607000																								0							SO:0001819	synonymous_variant			ENST00000219271.3	1	1	hg19	CCDS10792.1																																																																																				TCGA-2J-AABR-01A-11D-A40W-08	MMP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257342.1	0	0	1	8	282	0	57	1	7.320762e-01	13	78	0	57	2		0	0	0	0	0	2	1	0.989183	9	278	0	55	2								-8.815554	1	1	0	0		1	1	2	3	2.009490	0	0.090000	1.970000	0.097715	0.680000	0.310000	1.000000	1.000000	0.708195	0.680000	0	0.460000	1.000000
TUBG2	27175	broad.mit.edu	37	17	40817827	40817827	+	Silent	SNP	G	G	A			TCGA-2J-AABR-01A-11D-A40W-08	TCGA-2J-AABR-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	534d051f-0b40-486a-8f77-646bf003d3d0	4c28dd95-5359-4c03-b338-7038de30008f	g.chr17:40817827G>A	ENST00000251412.7	+	8	1024	c.825G>A	c.(823-825)ccG>ccA	p.P275P	PLEKHH3_ENST00000456950.2_5'Flank	NM_016437.2	NP_057521.1	Q9NRH3	TBG2_HUMAN	tubulin, gamma 2			15		Breast(137;0.00116)			GCTACACCCCGCTCACTACAG	0.637000																								0							SO:0001819	synonymous_variant			ENST00000251412.7	1	1	hg19	CCDS32658.1																																																																																				TCGA-2J-AABR-01A-11D-A40W-08	TUBG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452326.1	1	0	0	29	594	0	96	1	4.543521e-01	2	30	0	96	2		0	0	0	0	0	2	1	1.000000	29	578	0	88	2								-3.049135	1	1	121412	1	40	1	1	2	3	2.005968	0	0.090000	1.970000	0.096909	0.990000	0.720000	1.000000	1.000000	0.958496	0.990000	1	0.880000	1.000000
TP53	7157	broad.mit.edu	37	17	7578508	7578508	+	Missense_Mutation	SNP	C	C	T			TCGA-2J-AABR-01A-11D-A40W-08	TCGA-2J-AABR-10A-01D-A40W-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	534d051f-0b40-486a-8f77-646bf003d3d0	4c28dd95-5359-4c03-b338-7038de30008f	g.chr17:7578508C>T	ENST00000269305.4	-	5	611	c.422G>A	c.(421-423)tGc>tAc	p.C141Y	TP53_ENST00000445888.2_Missense_Mutation_p.C141Y|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.C141Y|TP53_ENST00000420246.2_Missense_Mutation_p.C141Y|TP53_ENST00000359597.4_Missense_Mutation_p.C141Y|TP53_ENST00000413465.2_Missense_Mutation_p.C141Y	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.C141Y(79)|p.0?(8)|p.C9Y(5)|p.C48Y(5)|p.A138_P142delAKTCP(4)|p.C141F(4)|p.C141S(3)|p.N131fs*27(2)|p.C9S(1)|p.K139_C141>N(1)|p.L137_W146del10(1)|p.C141A(1)|p.A6_P10delAKTCP(1)|p.K139fs*4(1)|p.A45_P49delAKTCP(1)|p.T140fs*28(1)|p.A138_V143delAKTCPV(1)|p.C48S(1)|p.C141fs*5(1)		24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		Acetylsalicylic acid(DB00945)	CTGCACAGGGCAGGTCTTGGC	0.572000		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	121	Substitution - Missense(99)|Whole gene deletion(8)|Deletion - In frame(8)|Deletion - Frameshift(5)|Complex - deletion inframe(1)	GRCh37	CM993216	TP53	M		SO:0001583	missense	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	ENST00000269305.4	1	1	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	15.06	2.720132	0.48728	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315;ENST00000508793	D;D;D;D;D;D;D;D;D	0.99822	-6.94;-6.94;-6.94;-6.94;-6.94;-6.94;-6.94;-6.94;-6.94	5.48	4.5	0.54988	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.046412	0.85682	D	0.000000	D	0.99832	0.9924	M	0.90309	3.105	0.58432	D	0.999998	D;D;D;D;D;D;D	0.89917	1.0;1.0;0.998;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;0.998;0.987;1.0;0.999;1.0;1.0	D	0.96735	0.9542	10	0.87932	D	0	-26.1094	13.743	0.62860	0.1552:0.8448:0.0:0.0	.	102;141;141;48;141;141;141	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	Y	141;141;141;141;141;141;130;48;9;48;9;141	ENSP00000410739:C141Y;ENSP00000352610:C141Y;ENSP00000269305:C141Y;ENSP00000398846:C141Y;ENSP00000391127:C141Y;ENSP00000391478:C141Y;ENSP00000425104:C9Y;ENSP00000423862:C48Y;ENSP00000424104:C141Y	ENSP00000269305:C141Y	C	-	2	0	TP53	7519233	1.000000	0.71417	0.996000	0.52242	0.022000	0.10575	6.016000	0.70798	1.427000	0.47276	-0.182000	0.12963	TGC		TCGA-2J-AABR-01A-11D-A40W-08	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	1	0	1	8	197	0	56	1	7.237210e-01	7	56	0	56	2	1	9.999863e-01	55	1722	3	2018	9	1	0.989584	8	196	0	53	2								-3.302200	1	1	0	0		1	0	0	0	1.979295	0	0.090000	1.970000	0.072470	0.840000	0.400000	1.000000	1.000000	0.816712	0.840000	0	0.600000	1.000000
PSG11	5680	broad.mit.edu	37	19	43528993	43528993	+	Missense_Mutation	SNP	C	C	T			TCGA-2J-AABR-01A-11D-A40W-08	TCGA-2J-AABR-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	534d051f-0b40-486a-8f77-646bf003d3d0	4c28dd95-5359-4c03-b338-7038de30008f	g.chr19:43528993C>T	ENST00000401740.1	-	2	383	c.280G>A	c.(280-282)Gca>Aca	p.A94T	PSG11_ENST00000320078.7_Missense_Mutation_p.A94T|PSG11_ENST00000403486.1_Intron|PSG11_ENST00000306322.7_Intron			Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 11			26		Prostate(69;0.00682)			CCACTGTATGCCGGTCCATAT	0.443000																								0							SO:0001583	missense			ENST00000401740.1	0	1	hg19	CCDS12614.2	.	.	.	.	.	.	.	.	.	.	c	9.498	1.102465	0.20632	.	.	ENSG00000243130	ENST00000320078;ENST00000401740	T;T	0.66280	-0.2;-0.2	0.929	-1.86	0.07760	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.64023	0.2561	M	0.80746	2.51	0.09310	N	1	B	0.25563	0.129	B	0.39904	0.313	T	0.63812	-0.6552	9	0.62326	D	0.03	.	2.5413	0.04726	0.0:0.4411:0.3119:0.247	.	94	Q9UQ72	PSG11_HUMAN	T	94	ENSP00000319140:A94T;ENSP00000384995:A94T	ENSP00000319140:A94T	A	-	1	0	PSG11	48220833	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.352000	0.07701	-0.979000	0.03529	-1.140000	0.01884	GCA		TCGA-2J-AABR-01A-11D-A40W-08	PSG11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323079.1	0	0	0	8	1146	0	234		0	0	0	0	234	2		0	0	0	0	0	2	1	0.988769	8	1131	0	233	2								-1.522631	0	1	0	0		1	1	2	3	2.011089	0	0.090000	1.970000	0.098117	0.170000	0.070000	1.000000	0.160000	0.298524	0.170000	0	0.110000	0.340000
NLRP9	338321	broad.mit.edu	37	19	56244158	56244158	+	Missense_Mutation	SNP	C	C	T			TCGA-2J-AABR-01A-11D-A40W-08	TCGA-2J-AABR-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	534d051f-0b40-486a-8f77-646bf003d3d0	4c28dd95-5359-4c03-b338-7038de30008f	g.chr19:56244158C>T	ENST00000332836.2	-	2	1066	c.1039G>A	c.(1039-1041)Gtg>Atg	p.V347M		NM_176820.2	NP_789790.2	Q7RTR0	NALP9_HUMAN	NLR family, pyrin domain containing 9			74		Colorectal(82;0.000133)|Ovarian(87;0.133)			CTCTGTTTCACACAAGTACAG	0.418000																								0							SO:0001583	missense			ENST00000332836.2	1	1	hg19	CCDS12934.1	.	.	.	.	.	.	.	.	.	.	C	0.863	-0.734758	0.03111	.	.	ENSG00000185792	ENST00000332836;ENST00000333452	D	0.84298	-1.83	2.56	-5.13	0.02884	.	.	.	.	.	T	0.57504	0.2058	N	0.01493	-0.835	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.46512	-0.9186	9	0.59425	D	0.04	.	2.9394	0.05825	0.192:0.1001:0.4605:0.2475	.	347	Q7RTR0	NALP9_HUMAN	M	347	ENSP00000331857:V347M	ENSP00000331857:V347M	V	-	1	0	NLRP9	60935970	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-2.639000	0.00865	-2.030000	0.00929	-0.313000	0.08912	GTG		TCGA-2J-AABR-01A-11D-A40W-08	NLRP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453653.1	0	0	0	20	617	0	121		0	0	0	0	121	2		0	0	0	0	0	2	1	0.999994	20	607	0	118	2								-3.660984	1	1	0	0		1	1	2	3	2.023719	0	0.090000	1.970000	0.100924	0.760000	0.450000	1.000000	1.000000	0.776638	0.760000	0	0.580000	1.000000
NLRP5	126206	broad.mit.edu	37	19	56539375	56539375	+	Silent	SNP	C	C	T			TCGA-2J-AABR-01A-11D-A40W-08	TCGA-2J-AABR-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	534d051f-0b40-486a-8f77-646bf003d3d0	4c28dd95-5359-4c03-b338-7038de30008f	g.chr19:56539375C>T	ENST00000390649.3	+	7	1776	c.1776C>T	c.(1774-1776)gcC>gcT	p.A592A		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5			25		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)			ACTTCTGTGCCGCCTTGTACT	0.532000																								0							SO:0001819	synonymous_variant			ENST00000390649.3	0	1	hg19	CCDS12938.1																																																																																				TCGA-2J-AABR-01A-11D-A40W-08	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	0	0	0	5	137	0	42		0	0	0	0	42	2		0	0	0	0	0	2	1	0.937517	5	136	0	39	2								-3.273354	1	1	120936	5	34	1	1	2	3	2.023719	0	0.090000	1.970000	0.100924	0.930000	0.340000	1.000000	1.000000	0.828862	0.930000	1	0.570000	1.000000
TPR	7175	broad.mit.edu	37	1	186328936	186328936	+	Missense_Mutation	SNP	T	T	C			TCGA-2J-AABR-01A-11D-A40W-08	TCGA-2J-AABR-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	534d051f-0b40-486a-8f77-646bf003d3d0	4c28dd95-5359-4c03-b338-7038de30008f	g.chr1:186328936T>C	ENST00000367478.4	-	12	1680	c.1384A>G	c.(1384-1386)Atg>Gtg	p.M462V	TPR_ENST00000474852.1_5'UTR	NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein			123		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)			CCAACCTTCATAGCTTGTTCA	0.368000			T	NTRK1	papillary thyroid										Dom	yes		1	1q25	7175	translocated promoter region		E	0							SO:0001583	missense			ENST00000367478.4	1	1	hg19	CCDS41446.1	.	.	.	.	.	.	.	.	.	.	T	10.51	1.369874	0.24771	.	.	ENSG00000047410	ENST00000367478	T	0.00940	5.52	5.76	5.76	0.90799	.	0.176337	0.64402	D	0.000009	T	0.00906	0.0030	N	0.16656	0.425	0.45690	D	0.998602	B;B	0.21753	0.06;0.025	B;B	0.22386	0.039;0.008	T	0.61515	-0.7047	10	0.08381	T	0.77	.	16.0697	0.80914	0.0:0.0:0.0:1.0	.	462;462	Q15624;P12270	.;TPR_HUMAN	V	462	ENSP00000356448:M462V	ENSP00000356448:M462V	M	-	1	0	TPR	184595559	0.998000	0.40836	0.993000	0.49108	0.996000	0.88848	2.901000	0.48695	2.194000	0.70268	0.528000	0.53228	ATG		TCGA-2J-AABR-01A-11D-A40W-08	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	0	0	0	15	267	0	67	1	4.469519e-01	2	25	0	67	2		0	0	0	0	0	2	1	0.999880	15	266	0	66	2								-18.044060	1	1	120804	6	35	1	0	1	1	1.993890	0	0.090000	1.970000	0.081736	0.990000	0.680000	1.000000	1.000000	0.961146	0.990000	1	0.890000	1.000000
NLRP3	114548	broad.mit.edu	37	1	247597507	247597507	+	Silent	SNP	C	C	T	rs147154764		TCGA-2J-AABR-01A-11D-A40W-08	TCGA-2J-AABR-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	534d051f-0b40-486a-8f77-646bf003d3d0	4c28dd95-5359-4c03-b338-7038de30008f	g.chr1:247597507C>T	ENST00000336119.3	+	5	3176	c.2430C>T	c.(2428-2430)ctC>ctT	p.L810L	NLRP3_ENST00000391827.2_Silent_p.L753L|NLRP3_ENST00000348069.2_Silent_p.L753L|NLRP3_ENST00000391828.3_Silent_p.L810L|NLRP3_ENST00000366496.2_Silent_p.L810L|NLRP3_ENST00000366497.2_Silent_p.L810L	NM_001127462.2|NM_001243133.1|NM_004895.4	NP_001120934.1|NP_001230062.1|NP_004886.3	Q96P20	NALP3_HUMAN	NLR family, pyrin domain containing 3			142	all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0172)	OV - Ovarian serous cystadenocarcinoma(106;0.0141)		ACAACGCCCTCGGTGACTTCG	0.567000																								0							SO:0001819	synonymous_variant			ENST00000336119.3	0	1	hg19	CCDS1632.1																																																																																				TCGA-2J-AABR-01A-11D-A40W-08	NLRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097740.1	0	0	0	6	434	0	81	0	2.848522e-02	0	16	0	81	2		0	0	0	0	0	2	1	0.963701	6	428	0	79	2								-2.560650	1	1	121412	10	46	1	0	1	1	1.993890	0	0.090000	1.970000	0.081736	0.310000	0.130000	0.600000	0.290000	0.339876	0.310000	0	0.210000	0.460000
HIVEP3	59269	broad.mit.edu	37	1	42046110	42046110	+	Silent	SNP	C	C	T			TCGA-2J-AABR-01A-11D-A40W-08	TCGA-2J-AABR-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	534d051f-0b40-486a-8f77-646bf003d3d0	4c28dd95-5359-4c03-b338-7038de30008f	g.chr1:42046110C>T	ENST00000372583.1	-	4	5244	c.4359G>A	c.(4357-4359)gaG>gaA	p.E1453E	HIVEP3_ENST00000372584.1_Silent_p.E1453E|HIVEP3_ENST00000429157.2_Silent_p.E1453E|HIVEP3_ENST00000247584.5_Silent_p.E1453E|HIVEP3_ENST00000460604.1_5'Flank	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3			85	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)			TGGAAGCCTCCTCCTCCTTCA	0.512000																								0							SO:0001819	synonymous_variant			ENST00000372583.1	1	1	hg19	CCDS463.1																																																																																				TCGA-2J-AABR-01A-11D-A40W-08	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000016978.1	0	0	0	19	685	0	167	0	0	0	1	0	167	2		0	0	0	0	0	2	1	0.999989	19	678	0	161	2								-2.865752	1	1	0	0		1	0	1	1	1.993890	0	0.090000	1.970000	0.081736	0.590000	0.370000	0.880000	0.590000	0.613537	0.590000	0	0.470000	0.740000
ZSWIM5	57643	broad.mit.edu	37	1	45484833	45484833	+	Missense_Mutation	SNP	G	G	A			TCGA-2J-AABR-01A-11D-A40W-08	TCGA-2J-AABR-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	534d051f-0b40-486a-8f77-646bf003d3d0	4c28dd95-5359-4c03-b338-7038de30008f	g.chr1:45484833G>A	ENST00000359600.5	-	14	3056	c.2851C>T	c.(2851-2853)Cgc>Tgc	p.R951C		NM_020883.1	NP_065934.1	Q9P217	ZSWM5_HUMAN	zinc finger, SWIM-type containing 5			28	Acute lymphoblastic leukemia(166;0.155)				GCCAGTGTGCGAGCACAGCTA	0.542000											OREG0013450	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)												0							SO:0001583	missense			ENST00000359600.5	0	1	hg19	CCDS41319.1	.	.	.	.	.	.	.	.	.	.	G	15.57	2.871440	0.51695	.	.	ENSG00000162415	ENST00000359600	T	0.52295	0.67	4.74	4.74	0.60224	.	0.000000	0.85682	D	0.000000	T	0.66096	0.2755	M	0.69823	2.125	0.80722	D	1	D	0.76494	0.999	P	0.61275	0.886	T	0.68693	-0.5341	10	0.52906	T	0.07	-7.752	18.6023	0.91253	0.0:0.0:1.0:0.0	.	951	Q9P217	ZSWM5_HUMAN	C	951	ENSP00000352614:R951C	ENSP00000352614:R951C	R	-	1	0	ZSWIM5	45257420	1.000000	0.71417	1.000000	0.80357	0.865000	0.49528	4.475000	0.60210	2.558000	0.86282	0.555000	0.69702	CGC		TCGA-2J-AABR-01A-11D-A40W-08	ZSWIM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024823.2	0	0	0	4	213	0	35	0	1.828550e-03	0	3	0	35	2		0	0	0	0	0	2	1	0.885619	4	208	0	35	2								-3.250930	1	1	120956	2	33	1	0	1	1	1.993890	0	0.090000	1.970000	0.081736	0.440000	0.150000	0.920000	0.390000	0.474505	0.440000	0	0.260000	0.670000
AKR1A1	10327	broad.mit.edu	37	1	46032622	46032622	+	Missense_Mutation	SNP	C	C	T			TCGA-2J-AABR-01A-11D-A40W-08	TCGA-2J-AABR-10A-01D-A40W-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	534d051f-0b40-486a-8f77-646bf003d3d0	4c28dd95-5359-4c03-b338-7038de30008f	g.chr1:46032622C>T	ENST00000372070.3	+	5	1033	c.286C>T	c.(286-288)Cgg>Tgg	p.R96W	AKR1A1_ENST00000471651.1_Missense_Mutation_p.R96W|AKR1A1_ENST00000351829.4_Missense_Mutation_p.R96W	NM_001202413.1|NM_001202414.1|NM_006066.3	NP_001189342.1|NP_001189343.1|NP_006057.1	P14550	AK1A1_HUMAN	aldo-keto reductase family 1, member A1 (aldehyde reductase)			5	Acute lymphoblastic leukemia(166;0.155)			Doxorubicin(DB00997)	GCCTGCCCTCCGGAAGACTCT	0.607000																								0							SO:0001583	missense			ENST00000372070.3	1	1	hg19	CCDS523.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	14.21	2.468661	0.43839	.	.	ENSG00000117448	ENST00000372070;ENST00000434299;ENST00000351829	T;T;T	0.31510	1.49;1.49;1.49	6.01	2.85	0.33270	NADP-dependent oxidoreductase domain (3);	0.201358	0.43260	D	0.000588	T	0.44477	0.1295	L	0.56769	1.78	0.45272	D	0.998272	D	0.76494	0.999	D	0.64877	0.93	T	0.36383	-0.9750	10	0.87932	D	0	.	7.8215	0.29290	0.528:0.3896:0.0:0.0824	.	96	P14550	AK1A1_HUMAN	W	96	ENSP00000361140:R96W;ENSP00000398414:R96W;ENSP00000312606:R96W	ENSP00000312606:R96W	R	+	1	2	AKR1A1	45805209	0.997000	0.39634	0.988000	0.46212	0.032000	0.12392	3.428000	0.52792	0.863000	0.35553	-0.151000	0.13558	CGG		TCGA-2J-AABR-01A-11D-A40W-08	AKR1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020851.1	1	0	0	12	247	0	45	1	9.995491e-01	26	260	0	45	2		0	0	0	0	0	2	1	0.999006	12	240	0	44	2								-2.713547	1	1	121412	4	36	1	0	1	1	1.993890	0	0.090000	1.970000	0.081736	0.990000	0.560000	1.000000	1.000000	0.912728	0.990000	1	0.760000	1.000000
CHD6	84181	broad.mit.edu	37	20	40052243	40052243	+	Missense_Mutation	SNP	G	G	A			TCGA-2J-AABR-01A-11D-A40W-08	TCGA-2J-AABR-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	534d051f-0b40-486a-8f77-646bf003d3d0	4c28dd95-5359-4c03-b338-7038de30008f	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-2J-AABR-01A-11D-A40W-08	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1	0	0	0	6	844	1	173	0	4.731315e-03	0	12	1	173	2		0	0	0	0	0	2	0	0.015487	6	835	1	170	17								-1.734834	0	1	0	0		1	1	2	3	2.009716	0	0.090000	1.970000	0.097715	0.180000	0.060000	1.000000	0.160000	0.301090	0.180000	0	0.110000	0.360000
PREX1	57580	broad.mit.edu	37	20	47309283	47309283	+	Silent	SNP	G	G	A			TCGA-2J-AABR-01A-11D-A40W-08	TCGA-2J-AABR-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	534d051f-0b40-486a-8f77-646bf003d3d0	4c28dd95-5359-4c03-b338-7038de30008f	g.chr20:47309283G>A	ENST00000371941.3	-	8	985	c.963C>T	c.(961-963)aaC>aaT	p.N321N	PREX1_ENST00000396220.1_Silent_p.N321N	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1			110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)		AGAGGGAGCCGTTGATGGATT	0.552000																								0							SO:0001819	synonymous_variant			ENST00000371941.3	0	1	hg19	CCDS13410.1																																																																																				TCGA-2J-AABR-01A-11D-A40W-08	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	0	0	0	11	418	0	77	0	1.368641e-01	0	23	0	77	2		0	0	0	0	0	2	1	0.998199	11	410	0	77	2								-3.035764	1	1	121412	28	46	1	1	2	3	2.009716	0	0.090000	1.970000	0.097715	0.620000	0.320000	1.000000	1.000000	0.665409	0.620000	0	0.450000	1.000000
FAM65C	140876	broad.mit.edu	37	20	49218732	49218732	+	Silent	SNP	C	C	A			TCGA-2J-AABR-01A-11D-A40W-08	TCGA-2J-AABR-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	534d051f-0b40-486a-8f77-646bf003d3d0	4c28dd95-5359-4c03-b338-7038de30008f	g.chr20:49218732C>A	ENST00000327979.2	-	13	1935	c.1524G>T	c.(1522-1524)ggG>ggT	p.G508G	FAM65C_ENST00000535356.1_Silent_p.G512G|FAM65C_ENST00000045083.2_Silent_p.G508G			Q96MK2	FA65C_HUMAN	family with sequence similarity 65, member C			29					CCACGCCAGGCCCGTCCTCTC	0.697000																								0							SO:0001819	synonymous_variant			ENST00000327979.2	0	1	hg19	CCDS13431.2																																																																																				TCGA-2J-AABR-01A-11D-A40W-08	FAM65C-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257962.1	0	0	0	5	169	0	34	0	1.348228e-03	0	2	0	34	2		0	0	0	0	0	2	1	0.933571	5	164	0	31	2								-7.333112	1	1	0	0		1	1	2	3	2.009716	0	0.090000	1.970000	0.097715	0.740000	0.270000	1.000000	1.000000	0.735669	0.740000	0	0.460000	1.000000
CRYBB1	1414	broad.mit.edu	37	22	27008105	27008105	+	Missense_Mutation	SNP	G	G	A			TCGA-2J-AABR-01A-11D-A40W-08	TCGA-2J-AABR-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	534d051f-0b40-486a-8f77-646bf003d3d0	4c28dd95-5359-4c03-b338-7038de30008f	g.chr22:27008105G>A	ENST00000215939.2	-	3	360	c.230C>T	c.(229-231)tCg>tTg	p.S77L		NM_001887.3	NP_001878.1	P53674	CRBB1_HUMAN	crystallin, beta B1	p.S77L(1)		31					GCACTCCCCCGAGAATTCTGC	0.612000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000215939.2	1	1	hg19	CCDS13840.1	.	.	.	.	.	.	.	.	.	.	G	10.30	1.312232	0.23908	.	.	ENSG00000100122	ENST00000215939	T	0.77489	-1.1	3.85	3.85	0.44370	Beta/gamma crystallin (4);Gamma-crystallin-related (1);	0.811995	0.11262	N	0.582484	T	0.71213	0.3313	L	0.54863	1.705	0.33899	D	0.638222	B	0.31209	0.313	B	0.27887	0.084	T	0.76088	-0.3087	10	0.51188	T	0.08	.	8.8646	0.35278	0.1045:0.0:0.8955:0.0	.	77	P53674	CRBB1_HUMAN	L	77	ENSP00000215939:S77L	ENSP00000215939:S77L	S	-	2	0	CRYBB1	25338105	0.935000	0.31712	0.999000	0.59377	0.438000	0.31896	1.500000	0.35682	1.961000	0.56991	0.491000	0.48974	TCG		TCGA-2J-AABR-01A-11D-A40W-08	CRYBB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320767.1	1	0	0	19	378	0	74	0	3.405871e-02	0	6	0	74	2		0	0	0	0	0	2	1	0.999986	14	364	0	72	2								-2.774725	1	1	121412	1	36	1	0	1	1	1.990456	0	0.090000	1.970000	0.080901	0.990000	0.650000	1.000000	1.000000	0.940938	0.990000	1	0.830000	1.000000
MICALL1	85377	broad.mit.edu	37	22	38323617	38323617	+	Silent	SNP	T	T	A			TCGA-2J-AABR-01A-11D-A40W-08	TCGA-2J-AABR-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	534d051f-0b40-486a-8f77-646bf003d3d0	4c28dd95-5359-4c03-b338-7038de30008f	g.chr22:38323617T>A	ENST00000215957.6	+	9	1791	c.1665T>A	c.(1663-1665)tcT>tcA	p.S555S	MICALL1_ENST00000402631.1_3'UTR	NM_033386.3	NP_203744.1	Q8N3F8	MILK1_HUMAN	MICAL-like 1			24	Melanoma(58;0.045)				TCAGCCTCTCTACCAACTCCT	0.632000																								0							SO:0001819	synonymous_variant			ENST00000215957.6	0	1	hg19	CCDS13961.1	.	.	.	.	.	.	.	.	.	.	T	0.550	-0.849771	0.02651	.	.	ENSG00000100139	ENST00000454685	.	.	.	5.14	-10.3	0.00346	.	.	.	.	.	T	0.46229	0.1382	.	.	.	0.53688	D	0.999975	.	.	.	.	.	.	T	0.57394	-0.7819	4	.	.	.	.	8.7087	0.34371	0.1652:0.5937:0.0749:0.1661	.	.	.	.	N	133	.	.	Y	+	1	0	MICALL1	36653563	0.000000	0.05858	0.020000	0.16555	0.047000	0.14425	-3.105000	0.00602	-2.558000	0.00475	0.454000	0.30748	TAC		TCGA-2J-AABR-01A-11D-A40W-08	MICALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319545.4	0	0	0	17	689	0	132	1	1.514673e-01	3	24	0	132	2		0	0	0	0	0	2	1	0.999954	17	666	0	130	2								-3.178041	1	1	0	0		1	0	1	1	1.990456	0	0.090000	1.970000	0.080901	0.530000	0.320000	0.800000	0.520000	0.550302	0.530000	0	0.410000	0.670000
L3MBTL2	83746	broad.mit.edu	37	22	41609955	41609955	+	Silent	SNP	G	G	A			TCGA-2J-AABR-01A-11D-A40W-08	TCGA-2J-AABR-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	534d051f-0b40-486a-8f77-646bf003d3d0	4c28dd95-5359-4c03-b338-7038de30008f	g.chr22:41609955G>A	ENST00000216237.5	+	3	479	c.321G>A	c.(319-321)aaG>aaA	p.K107K	RP4-756G23.5_ENST00000451176.1_RNA|RP4-756G23.5_ENST00000441316.1_RNA|L3MBTL2_ENST00000489136.1_3'UTR	NM_031488.4	NP_113676.2	Q969R5	LMBL2_HUMAN	l(3)mbt-like 2 (Drosophila)	p.K107N(1)		24					CCAAGACCAAGAGGTTCTGCA	0.512000																								1	Substitution - Missense(1)						SO:0001819	synonymous_variant			ENST00000216237.5	1	1	hg19	CCDS14011.1																																																																																				TCGA-2J-AABR-01A-11D-A40W-08	L3MBTL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320613.1	0	0	0	15	520	0	83	0	2.151038e-01	1	28	0	83	2		0	0	0	0	0	2	1	0.999859	15	512	0	83	2								-3.584154	1	1	0	0		1	1	5	6	2.261650	1	0.090000	1.970000	0.210755	0.770000	0.430000	1.000000	1.000000	0.776363	0.770000	0	0.580000	1.000000
PKDREJ	10343	broad.mit.edu	37	22	46653425	46653425	+	Missense_Mutation	SNP	G	G	A			TCGA-2J-AABR-01A-11D-A40W-08	TCGA-2J-AABR-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	534d051f-0b40-486a-8f77-646bf003d3d0	4c28dd95-5359-4c03-b338-7038de30008f	g.chr22:46653425G>A	ENST00000253255.5	-	1	5794	c.5795C>T	c.(5794-5796)tCg>tTg	p.S1932L		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly			73		Ovarian(80;0.00965)|all_neural(38;0.0416)			AAATATGACCGAAATGCTACA	0.373000																								0							SO:0001583	missense			ENST00000253255.5	0	1	hg19	CCDS14073.1	.	.	.	.	.	.	.	.	.	.	G	11.51	1.660688	0.29515	.	.	ENSG00000130943	ENST00000253255	T	0.71461	-0.57	5.55	4.52	0.55395	Polycystin cation channel, PKD1/PKD2 (1);	0.000000	0.53938	D	0.000059	T	0.77916	0.4202	L	0.47716	1.5	0.20563	N	0.99989	D	0.89917	1.0	D	0.91635	0.999	T	0.68236	-0.5462	10	0.59425	D	0.04	-21.0782	11.7598	0.51896	0.084:0.0:0.916:0.0	.	1932	Q9NTG1	PKDRE_HUMAN	L	1932	ENSP00000253255:S1932L	ENSP00000253255:S1932L	S	-	2	0	PKDREJ	45032089	0.914000	0.31030	0.108000	0.21378	0.096000	0.18686	2.674000	0.46867	2.618000	0.88619	0.455000	0.32223	TCG		TCGA-2J-AABR-01A-11D-A40W-08	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	0	0	0	6	276	0	36		0	0	0	0	36	2		0	0	0	0	0	2	1	0.964652	5	275	0	35	2								-3.091551	1	1	121412	2	33	1	0	0	0	1.906408	0	0.090000	1.970000	0.037139	0.430000	0.180000	0.720000	0.410000	0.449980	0.430000	0	0.290000	0.600000
IL18RAP	8807	broad.mit.edu	37	2	103063588	103063588	+	Silent	SNP	G	G	C			TCGA-2J-AABR-01A-11D-A40W-08	TCGA-2J-AABR-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	534d051f-0b40-486a-8f77-646bf003d3d0	4c28dd95-5359-4c03-b338-7038de30008f	g.chr2:103063588G>C	ENST00000264260.2	+	10	1720	c.1131G>C	c.(1129-1131)gcG>gcC	p.A377A	IL18RAP_ENST00000409369.1_Silent_p.A235A	NM_003853.2	NP_003844.1	O95256	I18RA_HUMAN	interleukin 18 receptor accessory protein			37					TGCTGGCGGCGAGTGCCCTCC	0.582000																								0							SO:0001819	synonymous_variant			ENST00000264260.2	0	1	hg19	CCDS2061.1																																																																																				TCGA-2J-AABR-01A-11D-A40W-08	IL18RAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253291.2	0	0	0	6	907	1	169	0	6.681461e-05	0	2	1	169	2		0	0	0	0	0	2	0	0.006225	6	893	1	165	19								-2.200819	0	1	0	0		1	1	2	3	2.011385	0	0.090000	1.970000	0.098117	0.170000	0.060000	1.000000	0.150000	0.295668	0.170000	0	0.100000	0.350000
NEB	4703	broad.mit.edu	37	2	152552104	152552104	+	Silent	SNP	A	A	G			TCGA-2J-AABR-01A-11D-A40W-08	TCGA-2J-AABR-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	534d051f-0b40-486a-8f77-646bf003d3d0	4c28dd95-5359-4c03-b338-7038de30008f	g.chr2:152552104A>G	ENST00000172853.10	-	18	1809	c.1662T>C	c.(1660-1662)taT>taC	p.Y554Y	NEB_ENST00000603639.1_Silent_p.Y554Y|NEB_ENST00000409198.1_Silent_p.Y554Y|NEB_ENST00000427231.2_Silent_p.Y554Y|NEB_ENST00000604864.1_Silent_p.Y554Y|NEB_ENST00000397345.3_Silent_p.Y554Y			P20929	NEBU_HUMAN	nebulin			301					CACTCAAGTTATAGGCATTGA	0.373000																								0							SO:0001819	synonymous_variant			ENST00000172853.10	1	1	hg19																																																																																					TCGA-2J-AABR-01A-11D-A40W-08	NEB-201	KNOWN	basic	protein_coding	protein_coding		0	0	0	5	105	0	25		0	0	0	0	25	2		0	0	0	0	0	2	1	0.939019	5	105	0	25	2								-8.516195	1	1	0	0		1	1	2	3	2.011385	0	0.090000	1.970000	0.098117	0.990000	0.420000	1.000000	1.000000	0.898829	0.990000	1	0.710000	1.000000
IRS1	3667	broad.mit.edu	37	2	227660111	227660111	+	Missense_Mutation	SNP	T	T	C			TCGA-2J-AABR-01A-11D-A40W-08	TCGA-2J-AABR-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	534d051f-0b40-486a-8f77-646bf003d3d0	4c28dd95-5359-4c03-b338-7038de30008f	g.chr2:227660111T>C	ENST00000305123.5	-	1	4364	c.3344A>G	c.(3343-3345)aAc>aGc	p.N1115S	IRS1_ENST00000498335.1_5'Flank	NM_005544.2	NP_005535.1	P35568	IRS1_HUMAN	insulin receptor substrate 1			69		Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23)			GGGCACTGTGTTGCCCACCCG	0.617000																								0							SO:0001583	missense			ENST00000305123.5	1	1	hg19	CCDS2463.1	.	.	.	.	.	.	.	.	.	.	T	5.525	0.281845	0.10458	.	.	ENSG00000169047	ENST00000305123	T	0.56275	0.47	5.81	5.81	0.92471	.	0.174974	0.34268	N	0.004120	T	0.25382	0.0617	N	0.11064	0.09	0.27707	N	0.945585	B	0.31581	0.329	B	0.28849	0.095	T	0.32613	-0.9900	10	0.05436	T	0.98	-25.738	6.918	0.24371	0.0:0.1629:0.0:0.8371	.	1115	P35568	IRS1_HUMAN	S	1115	ENSP00000304895:N1115S	ENSP00000304895:N1115S	N	-	2	0	IRS1	227368355	0.000000	0.05858	0.965000	0.40720	0.245000	0.25701	-0.476000	0.06591	2.206000	0.71126	0.533000	0.62120	AAC		TCGA-2J-AABR-01A-11D-A40W-08	IRS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256886.3	0	0	0	12	353	0	82	1	3.860067e-01	4	33	0	82	2		0	0	0	0	0	2	1	0.999046	12	346	0	81	2								-12.531370	1	1	0	0		1	1	2	3	2.010203	0	0.090000	1.970000	0.098117	0.790000	0.420000	1.000000	1.000000	0.792332	0.790000	0	0.580000	1.000000
PER2	8864	broad.mit.edu	37	2	239185809	239185809	+	Missense_Mutation	SNP	C	C	T			TCGA-2J-AABR-01A-11D-A40W-08	TCGA-2J-AABR-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	534d051f-0b40-486a-8f77-646bf003d3d0	4c28dd95-5359-4c03-b338-7038de30008f	g.chr2:239185809C>T	ENST00000254657.3	-	3	535	c.256G>A	c.(256-258)Gca>Aca	p.A86T	PER2_ENST00000254658.3_Missense_Mutation_p.A86T|PER2_ENST00000440245.1_Missense_Mutation_p.A86T|PER2_ENST00000355768.2_Missense_Mutation_p.A86T	NM_022817.2	NP_073728.1	O15055	PER2_HUMAN	period circadian clock 2	p.A86T(1)		37		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0423)|all_lung(227;0.114)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Lung NSC(271;0.223)|Hepatocellular(293;0.244)			TCAGATTTTGCCATCATCAGG	0.383000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000254657.3	0	1	hg19	CCDS2528.1	.	.	.	.	.	.	.	.	.	.	C	0.421	-0.908299	0.02434	.	.	ENSG00000132326	ENST00000254657;ENST00000254658;ENST00000440245;ENST00000355768;ENST00000431832	T;T;T;T;T	0.53423	2.72;0.68;1.71;0.68;0.62	4.96	2.12	0.27331	.	0.345872	0.34110	N	0.004259	T	0.34308	0.0893	L	0.34521	1.04	0.20074	N	0.999938	B;B;B;B	0.10296	0.003;0.0;0.001;0.0	B;B;B;B	0.12837	0.008;0.001;0.005;0.001	T	0.18053	-1.0349	10	0.31617	T	0.26	-1.2378	11.0032	0.47618	0.0:0.7639:0.0:0.2361	.	86;86;86;86	F5GYD5;B4DH14;O15055-2;O15055	.;.;.;PER2_HUMAN	T	86	ENSP00000254657:A86T;ENSP00000254658:A86T;ENSP00000397516:A86T;ENSP00000348013:A86T;ENSP00000405891:A86T	ENSP00000254657:A86T	A	-	1	0	PER2	238850548	0.693000	0.27728	0.002000	0.10522	0.041000	0.13682	0.717000	0.25851	-0.004000	0.14419	-0.797000	0.03246	GCA		TCGA-2J-AABR-01A-11D-A40W-08	PER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257167.1	0	0	0	7	1384	1	321	0	8.469510e-03	0	23	1	321	2		0	0	0	0	0	2	0	0.043278	7	1369	1	318	16								-1.735477	0	1	0	0		1	1	2	3	2.010203	0	0.090000	1.970000	0.098117	0.120000	0.040000	1.000000	0.110000	0.260129	0.120000	0	0.080000	0.260000
ARAP2	116984	broad.mit.edu	37	4	36189102	36189102	+	Missense_Mutation	SNP	C	C	A			TCGA-2J-AABR-01A-11D-A40W-08	TCGA-2J-AABR-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	534d051f-0b40-486a-8f77-646bf003d3d0	4c28dd95-5359-4c03-b338-7038de30008f	g.chr4:36189102C>A	ENST00000303965.4	-	8	2138	c.1649G>T	c.(1648-1650)aGa>aTa	p.R550I		NM_015230.3	NP_056045.2	Q8WZ64	ARAP2_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2			82					AACAAAAGTTCTTTGTGTTGT	0.299000																								0							SO:0001583	missense			ENST00000303965.4	0	1	hg19	CCDS3441.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	28.9	4.962860	0.92791	0.0	1.16E-4	ENSG00000047365	ENST00000303965	T	0.18338	2.22	5.91	5.91	0.95273	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	T	0.54127	0.1839	M	0.91090	3.175	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.87578	0.998;0.998	T	0.62492	-0.6843	10	0.87932	D	0	.	19.8836	0.96906	0.0:1.0:0.0:0.0	.	480;550	A7E2A5;Q8WZ64	.;ARAP2_HUMAN	I	550	ENSP00000302895:R550I	ENSP00000302895:R550I	R	-	2	0	ARAP2	35865497	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.860000	0.69546	2.791000	0.96007	0.650000	0.86243	AGA		TCGA-2J-AABR-01A-11D-A40W-08	ARAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215074.2	0	0	0	11	301	0	48	0	6.667203e-02	1	10	0	48	2		0	0	0	0	0	2	1	0.998292	11	297	0	48	2								-11.968510	1	1	0	0		1	1	2	3	2.014557	0	0.090000	1.970000	0.098921	0.860000	0.440000	1.000000	1.000000	0.829332	0.860000	1	0.620000	1.000000
TSPAN5	10098	broad.mit.edu	37	4	99407920	99407920	+	Missense_Mutation	SNP	G	G	A			TCGA-2J-AABR-01A-11D-A40W-08	TCGA-2J-AABR-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	534d051f-0b40-486a-8f77-646bf003d3d0	4c28dd95-5359-4c03-b338-7038de30008f	g.chr4:99407920G>A	ENST00000305798.3	-	3	650	c.248C>T	c.(247-249)gCg>gTg	p.A83V	TSPAN5_ENST00000509168.1_5'UTR|TSPAN5_ENST00000505184.1_Missense_Mutation_p.A12V	NM_005723.3	NP_005714.2	P62079	TSN5_HUMAN	tetraspanin 5			14					TTCCCGTAGCGCTCCAATGCA	0.478000																								0							SO:0001583	missense			ENST00000305798.3	1	1	hg19	CCDS3646.1	.	.	.	.	.	.	.	.	.	.	G	18.26	3.584361	0.65992	.	.	ENSG00000168785	ENST00000305798;ENST00000505184;ENST00000515287;ENST00000511651	D;D;D;D	0.83837	-1.77;-1.77;-1.77;-1.77	5.51	5.51	0.81932	Tetraspanin, conserved site (1);	0.096844	0.64402	D	0.000001	D	0.93203	0.7835	M	0.92026	3.265	0.80722	D	1	D	0.89917	1.0	D	0.72982	0.979	D	0.93958	0.7238	10	0.87932	D	0	.	19.614	0.95622	0.0:0.0:1.0:0.0	.	83	P62079	TSN5_HUMAN	V	83;12;12;12	ENSP00000307701:A83V;ENSP00000423916:A12V;ENSP00000423504:A12V;ENSP00000426248:A12V	ENSP00000307701:A83V	A	-	2	0	TSPAN5	99626943	1.000000	0.71417	0.973000	0.42090	0.986000	0.74619	9.454000	0.97621	2.873000	0.98535	0.561000	0.74099	GCG		TCGA-2J-AABR-01A-11D-A40W-08	TSPAN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253641.2	0	0	0	18	581	0	102	1	2.558038e-02	3	5	0	102	2		0	0	0	0	0	2	1	0.999980	16	575	0	100	2								-3.238237	1	1	0	0		1	1	2	3	2.014557	0	0.090000	1.970000	0.098921	0.720000	0.420000	1.000000	1.000000	0.745266	0.720000	0	0.550000	1.000000
CHSY3	337876	broad.mit.edu	37	5	129519959	129519959	+	Missense_Mutation	SNP	G	G	A			TCGA-2J-AABR-01A-11D-A40W-08	TCGA-2J-AABR-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	534d051f-0b40-486a-8f77-646bf003d3d0	4c28dd95-5359-4c03-b338-7038de30008f	g.chr5:129519959G>A	ENST00000305031.4	+	3	1482	c.1124G>A	c.(1123-1125)cGg>cAg	p.R375Q	CHSY3_ENST00000507545.1_3'UTR	NM_175856.4	NP_787052.3	Q70JA7	CHSS3_HUMAN	chondroitin sulfate synthase 3			28		all_cancers(142;0.0227)|Breast(839;0.198)|Prostate(80;0.215)|Lung NSC(810;0.239)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		GAACACAATCGGAAGGGTTAC	0.343000																								0							SO:0001583	missense			ENST00000305031.4	1	1	hg19	CCDS34223.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.168044	0.78339	.	.	ENSG00000198108	ENST00000305031	T	0.16196	2.36	4.46	3.59	0.41128	.	0.455483	0.18240	N	0.147272	T	0.19644	0.0472	L	0.43152	1.355	0.36257	D	0.854274	D	0.54047	0.964	P	0.46796	0.527	T	0.19582	-1.0301	9	.	.	.	0.1414	13.2683	0.60146	0.0779:0.0:0.9221:0.0	.	375	Q70JA7	CHSS3_HUMAN	Q	375	ENSP00000302629:R375Q	.	R	+	2	0	CHSY3	129547858	0.973000	0.33851	0.789000	0.31954	0.998000	0.95712	3.393000	0.52544	1.477000	0.48234	0.644000	0.83932	CGG		TCGA-2J-AABR-01A-11D-A40W-08	CHSY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371453.1	0	0	0	16	396	0	59	0	1.004716e-02	0	4	0	59	2		0	0	0	0	0	2	1	0.999931	17	391	0	56	2								-2.494159	0	1	0	0		1	1	2	3	2.010253	0	0.090000	1.970000	0.098117	0.920000	0.530000	1.000000	1.000000	0.875938	0.920000	1	0.700000	1.000000
FAT2	2196	broad.mit.edu	37	5	150911532	150911532	+	Splice_Site	SNP	C	C	T			TCGA-2J-AABR-01A-11D-A40W-08	TCGA-2J-AABR-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	534d051f-0b40-486a-8f77-646bf003d3d0	4c28dd95-5359-4c03-b338-7038de30008f	g.chr5:150911532C>T	ENST00000261800.5	-	13	9440		c.e13-1			NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2			196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		GCATTGGCGCCTGGCAGGGAG	0.652000																								0							SO:0001630	splice_region_variant			ENST00000261800.5	1	1	hg19	CCDS4317.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.87|12.87	2.067656|2.067656	0.36470|0.36470	.|.	.|.	ENSG00000086570|ENSG00000086570	ENST00000261800|ENST00000520200	.|.	.|.	.|.	5.43|5.43	5.43|5.43	0.79202|0.79202	.|.	.|.	.|.	.|.	.|.	.|T	.|0.73760	.|0.3628	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.72337	.|-0.4324	.|4	.|.	.|.	.|.	.|.	17.4335|17.4335	0.87545|0.87545	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	.|K	-1|1	.|.	.|.	.|R	-|-	.|2	.|0	FAT2|FAT2	150891725|150891725	1.000000|1.000000	0.71417|0.71417	0.897000|0.897000	0.35233|0.35233	0.240000|0.240000	0.25518|0.25518	5.591000|5.591000	0.67536|0.67536	2.557000|2.557000	0.86248|0.86248	0.557000|0.557000	0.71058|0.71058	.|AGG		TCGA-2J-AABR-01A-11D-A40W-08	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	1	0	0	20	362	0	63		0	0	0	0	63	2		0	0	0	0	0	2	1	0.999996	20	361	0	60	2								-5.402922	1	1	0	0		1	1	2	3	2.010253	0	0.090000	1.970000	0.098117	0.990000	0.750000	1.000000	1.000000	0.976844	0.990000	1	0.960000	1.000000
NUP155	9631	broad.mit.edu	37	5	37370977	37370977	+	Missense_Mutation	SNP	G	G	C			TCGA-2J-AABR-01A-11D-A40W-08	TCGA-2J-AABR-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	534d051f-0b40-486a-8f77-646bf003d3d0	4c28dd95-5359-4c03-b338-7038de30008f	g.chr5:37370977G>C	ENST00000231498.3	-	1	306	c.103C>G	c.(103-105)Caa>Gaa	p.Q35E	NUP155_ENST00000381843.2_5'Flank|NUP155_ENST00000513532.1_Missense_Mutation_p.Q35E	NM_153485.1	NP_705618.1	O75694	NU155_HUMAN	nucleoporin 155kDa			62	all_lung(31;0.000137)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)		CGGTCCTCTTGCAACTGACGG	0.582000																								0							SO:0001583	missense			ENST00000231498.3	1	1	hg19	CCDS3921.1	.	.	.	.	.	.	.	.	.	.	G	13.87	2.366755	0.41902	.	.	ENSG00000113569	ENST00000231498;ENST00000513532	T;T	0.77877	-1.12;-1.13	4.28	3.38	0.38709	.	0.056570	0.64402	N	0.000001	T	0.69975	0.3171	L	0.57536	1.79	0.50039	D	0.999841	B;B	0.30146	0.0;0.27	B;B	0.31442	0.0;0.13	T	0.63959	-0.6519	10	0.02654	T	1	.	14.0155	0.64521	0.0:0.1524:0.8476:0.0	.	35;35	E9PF10;O75694	.;NU155_HUMAN	E	35	ENSP00000231498:Q35E;ENSP00000422019:Q35E	ENSP00000231498:Q35E	Q	-	1	0	NUP155	37406734	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	5.782000	0.68973	0.985000	0.38656	0.650000	0.86243	CAA		TCGA-2J-AABR-01A-11D-A40W-08	NUP155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207593.2	0	0	0	17	512	0	84	0	6.905859e-03	0	4	0	84	2		0	0	0	0	0	2	1	0.999961	17	504	0	81	2								-3.703665	1	1	0	0		1	1	2	3	2.018212	0	0.090000	1.970000	0.099723	0.770000	0.450000	1.000000	1.000000	0.785584	0.770000	0	0.590000	1.000000
BVES	11149	broad.mit.edu	37	6	105573335	105573335	+	Missense_Mutation	SNP	T	T	C			TCGA-2J-AABR-01A-11D-A40W-08	TCGA-2J-AABR-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	534d051f-0b40-486a-8f77-646bf003d3d0	4c28dd95-5359-4c03-b338-7038de30008f	g.chr6:105573335T>C	ENST00000314641.5	-	4	686	c.470A>G	c.(469-471)aAg>aGg	p.K157R	BVES_ENST00000446408.2_Missense_Mutation_p.K157R|BVES_ENST00000336775.5_Missense_Mutation_p.K157R	NM_001199563.1	NP_001186492.1	Q8NE79	POPD1_HUMAN	blood vessel epicardial substance	p.K157R(1)		21		all_cancers(87;2.83e-05)|Acute lymphoblastic leukemia(125;1.95e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0101)|Colorectal(196;0.204)|Lung NSC(302;0.238)			AGTTTGGCCCTTTTTCAAGGT	0.438000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000314641.5	0	1	hg19	CCDS5051.1	.	.	.	.	.	.	.	.	.	.	T	11.10	1.540510	0.27563	0.0	1.16E-4	ENSG00000112276	ENST00000314641;ENST00000336775;ENST00000446408	T;T;T	0.31510	1.49;1.49;1.49	5.76	3.34	0.38264	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);	0.130282	0.64402	N	0.000002	T	0.07638	0.0192	L	0.31845	0.965	0.39124	D	0.961725	B	0.14438	0.01	B	0.13407	0.009	T	0.12528	-1.0544	10	0.13470	T	0.59	-15.0112	6.8871	0.24208	0.0:0.148:0.1607:0.6914	.	157	Q8NE79	POPD1_HUMAN	R	157	ENSP00000313172:K157R;ENSP00000337259:K157R;ENSP00000397310:K157R	ENSP00000313172:K157R	K	-	2	0	BVES	105680028	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.676000	0.46883	1.016000	0.39470	0.533000	0.62120	AAG		TCGA-2J-AABR-01A-11D-A40W-08	BVES-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406075.1	0	0	0	6	844	1	159	0	4.558606e-04	0	4	1	159	2		0	0	0	0	0	2	0	0.000334	6	831	2	155	25								-1.630380	0	1	121412	4	44	1	1	2	3	2.009004	0	0.090000	1.970000	0.097715	0.180000	0.060000	1.000000	0.160000	0.301090	0.180000	0	0.110000	0.360000
KCNH2	3757	broad.mit.edu	37	7	150656780	150656780	+	Nonsense_Mutation	SNP	C	C	A			TCGA-2J-AABR-01A-11D-A40W-08	TCGA-2J-AABR-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	534d051f-0b40-486a-8f77-646bf003d3d0	4c28dd95-5359-4c03-b338-7038de30008f	g.chr7:150656780C>A	ENST00000262186.5	-	3	753	c.352G>T	c.(352-354)Gag>Tag	p.E118*	KCNH2_ENST00000392968.2_Nonsense_Mutation_p.E22*|KCNH2_ENST00000430723.3_Nonsense_Mutation_p.E118*	NM_000238.3	NP_000229.1	Q12809	KCNH2_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 2			42	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	Alfuzosin(DB00346)|Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Cisapride(DB00604)|Dofetilide(DB00204)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Halofantrine(DB01218)|Ibutilide(DB00308)|Imipramine(DB00458)|Miconazole(DB01110)|Pimozide(DB01100)|Prazosin(DB00457)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terazosin(DB01162)|Thioridazine(DB00679)|Verapamil(DB00661)	GCCCCATCCTCGTTCTTCACG	0.597000													GBM(137;110 1844 13671 20123 45161)											0							SO:0001587	stop_gained			ENST00000262186.5	0	1	hg19	CCDS5910.1	.	.	.	.	.	.	.	.	.	.	c	42	9.256142	0.99117	.	.	ENSG00000055118	ENST00000392968;ENST00000262186;ENST00000430723	.	.	.	4.71	4.71	0.59529	.	0.000000	0.64402	D	0.000012	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	15.2258	0.73352	0.0:1.0:0.0:0.0	.	.	.	.	X	22;118;118	.	ENSP00000262186:E118X	E	-	1	0	KCNH2	150287713	1.000000	0.71417	0.995000	0.50966	0.995000	0.86356	7.258000	0.78371	2.183000	0.69458	0.436000	0.28706	GAG		TCGA-2J-AABR-01A-11D-A40W-08	KCNH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350741.2	0	0	0	4	259	0	42	0	0	0	1	0	42	2		0	0	0	0	0	2	1	0.889278	4	257	0	40	2								-4.063491	1	1	0	0		1	1	2	3	2.016032	0	0.090000	1.970000	0.099322	0.420000	0.130000	1.000000	0.320000	0.508372	0.420000	0	0.240000	1.000000
TAF6	6878	broad.mit.edu	37	7	99707631	99707631	+	Silent	SNP	G	G	A	rs148894017		TCGA-2J-AABR-01A-11D-A40W-08	TCGA-2J-AABR-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	534d051f-0b40-486a-8f77-646bf003d3d0	4c28dd95-5359-4c03-b338-7038de30008f	g.chr7:99707631G>A	ENST00000344095.4	-	12	1749	c.1224C>T	c.(1222-1224)gaC>gaT	p.D408D	TAF6_ENST00000437822.2_Silent_p.D445D|AP4M1_ENST00000421755.1_Intron|TAF6_ENST00000453269.2_Silent_p.D408D|TAF6_ENST00000472509.1_Silent_p.D465D|TAF6_ENST00000452041.1_Silent_p.D408D|TAF6_ENST00000418432.2_Silent_p.D332D	NM_005641.3	NP_005632.1	P49848	TAF6_HUMAN	TAF6 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 80kDa			26	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)				GCACAGGGCCGTCCAGCACAC	0.587000																								0							SO:0001819	synonymous_variant			ENST00000344095.4	0	1	hg19	CCDS5686.1																																																																																				TCGA-2J-AABR-01A-11D-A40W-08	TAF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337024.2	0	0	0	5	349	0	40	0	5.510637e-01	0	117	0	40	2		0	0	0	0	0	2	1	0.934638	5	342	0	40	2								-2.651826	1	1	121412	2	39	1	1	2	3	2.016796	0	0.090000	1.970000	0.099322	0.380000	0.130000	1.000000	0.320000	0.475282	0.380000	0	0.230000	1.000000
SPATC1	375686	broad.mit.edu	37	8	145094826	145094826	+	Silent	SNP	G	G	A			TCGA-2J-AABR-01A-11D-A40W-08	TCGA-2J-AABR-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	534d051f-0b40-486a-8f77-646bf003d3d0	4c28dd95-5359-4c03-b338-7038de30008f	g.chr8:145094826G>A	ENST00000377470.3	+	2	330	c.228G>A	c.(226-228)ccG>ccA	p.P76P	SPATC1_ENST00000447830.2_Silent_p.P76P	NM_198572.2	NP_940974.2	Q76KD6	SPERI_HUMAN	spermatogenesis and centriole associated 1			15	all_cancers(97;8.2e-11)|all_epithelial(106;1.1e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;3.67e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)		TCCTGCCCCCGTCCCCAGCAG	0.632000																								0							SO:0001819	synonymous_variant			ENST00000377470.3	0	1	hg19	CCDS6413.2																																																																																				TCGA-2J-AABR-01A-11D-A40W-08	SPATC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346926.1	0	0	0	10	438	0	79	0	6.504065e-04	0	2	0	79	2		0	0	0	0	0	2	1	0.996697	10	431	0	77	2								-3.022936	1	1	121412	5	39	1	1	2	3	2.017190	0	0.090000	1.970000	0.099322	0.550000	0.270000	1.000000	0.500000	0.615312	0.550000	0	0.390000	1.000000
RNF20	56254	broad.mit.edu	37	9	104324559	104324559	+	Missense_Mutation	SNP	G	G	A			TCGA-2J-AABR-01A-11D-A40W-08	TCGA-2J-AABR-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	534d051f-0b40-486a-8f77-646bf003d3d0	4c28dd95-5359-4c03-b338-7038de30008f	g.chr9:104324559G>A	ENST00000389120.3	+	20	2873	c.2783G>A	c.(2782-2784)cGt>cAt	p.R928H		NM_019592.5	NP_062538.5	Q5VTR2	BRE1A_HUMAN	ring finger protein 20, E3 ubiquitin protein ligase			54		all_hematologic(171;8.99e-06)|Acute lymphoblastic leukemia(62;0.000365)|Myeloproliferative disorder(762;0.0255)			TGTAACATGCGTAAAAAGGAT	0.418000																								0							SO:0001583	missense			ENST00000389120.3	0	1	hg19	CCDS35084.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.027440	0.75390	.	.	ENSG00000155827	ENST00000389120	D	0.86297	-2.1	5.87	4.98	0.66077	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.000000	0.85682	D	0.000000	D	0.90249	0.6951	L	0.56340	1.77	0.80722	D	1	D	0.62365	0.991	P	0.58620	0.842	D	0.91247	0.5026	10	0.72032	D	0.01	-9.7351	15.166	0.72825	0.0684:0.0:0.9316:0.0	.	928	Q5VTR2	BRE1A_HUMAN	H	928	ENSP00000373772:R928H	ENSP00000373772:R928H	R	+	2	0	RNF20	103364380	1.000000	0.71417	1.000000	0.80357	0.583000	0.36354	7.601000	0.82783	1.628000	0.50416	-0.150000	0.13652	CGT		TCGA-2J-AABR-01A-11D-A40W-08	RNF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356402.1	0	0	0	5	471	0	85	0	8.045950e-02	0	36	0	85	2		0	0	0	0	0	2	1	0.936454	5	467	0	82	2								-2.554803	1	1	0	0		1	0	1	1	2.002265	0	0.090000	1.970000	0.055576	0.230000	0.090000	0.480000	0.220000	0.259197	0.230000	0	0.150000	0.360000
ANAPC2	29882	broad.mit.edu	37	9	140080689	140080689	+	Missense_Mutation	SNP	C	C	T			TCGA-2J-AABR-01A-11D-A40W-08	TCGA-2J-AABR-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	534d051f-0b40-486a-8f77-646bf003d3d0	4c28dd95-5359-4c03-b338-7038de30008f	g.chr9:140080689C>T	ENST00000323927.2	-	3	864	c.860G>A	c.(859-861)cGt>cAt	p.R287H	SSNA1_ENST00000322310.5_5'Flank	NM_013366.3	NP_037498.1	Q9UJX6	ANC2_HUMAN	anaphase promoting complex subunit 2			15	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)		GTGGAACTCACGCAGGAAGGA	0.642000																								0							SO:0001583	missense			ENST00000323927.2	0	1	hg19	CCDS7033.1	.	.	.	.	.	.	.	.	.	.	C	11.01	1.512989	0.27123	0.0	1.16E-4	ENSG00000176248	ENST00000323927	T	0.03181	4.02	3.7	2.7	0.31948	.	0.867499	0.10426	N	0.676110	T	0.02807	0.0084	N	0.12182	0.205	0.09310	N	1	B;B	0.22851	0.046;0.076	B;B	0.17433	0.008;0.018	T	0.38564	-0.9655	10	0.48119	T	0.1	-16.0898	10.9309	0.47217	0.0:0.8075:0.1925:0.0	.	287;287	Q9UJX6;Q9UJX6-2	ANC2_HUMAN;.	H	287	ENSP00000314004:R287H	ENSP00000314004:R287H	R	-	2	0	ANAPC2	139200510	0.002000	0.14202	0.973000	0.42090	0.917000	0.54804	0.301000	0.19174	2.059000	0.61396	0.555000	0.69702	CGT		TCGA-2J-AABR-01A-11D-A40W-08	ANAPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055315.1	0	0	0	4	182	0	32	0	1.762531e-01	0	28	0	32	2		0	0	0	0	0	2	1	0.888714	4	180	0	31	2								-3.317274	1	1	121340	17	41	1	1	2	3	2.005350	0	0.090000	1.970000	0.127684	0.560000	0.190000	1.000000	1.000000	0.592863	0.560000	0	0.340000	0.880000
BEX2	84707	broad.mit.edu	37	X	102564580	102564580	+	Missense_Mutation	SNP	G	G	A			TCGA-2J-AABR-01A-11D-A40W-08	TCGA-2J-AABR-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	534d051f-0b40-486a-8f77-646bf003d3d0	4c28dd95-5359-4c03-b338-7038de30008f	g.chrX:102564580G>A	ENST00000372677.3	-	3	592	c.325C>T	c.(325-327)Cgg>Tgg	p.R109W	BEX2_ENST00000372674.1_Missense_Mutation_p.R109W|BEX2_ENST00000536889.1_Missense_Mutation_p.R141W	NM_032621.3	NP_116010.1	Q9BXY8	BEX2_HUMAN	brain expressed X-linked 2			3					CTGACTGCCCGCAAACTATGA	0.507000																								0							SO:0001583	missense			ENST00000372677.3	0	1	hg19	CCDS14505.1	.	.	.	.	.	.	.	.	.	.	G	14.93	2.681005	0.47886	.	.	ENSG00000133134	ENST00000372677;ENST00000536889;ENST00000372674	T;T;T	0.15952	2.42;2.38;2.42	4.29	2.44	0.29823	.	0.162857	0.29253	N	0.012700	T	0.38161	0.1030	M	0.83953	2.67	0.28106	N	0.931193	D;D	0.89917	0.999;1.0	D;D	0.68483	0.91;0.958	T	0.15780	-1.0425	10	0.44086	T	0.13	.	8.329	0.32175	0.0:0.0:0.5702:0.4298	.	109;141	Q9BXY8;F5H7H5	BEX2_HUMAN;.	W	109;141;109	ENSP00000361762:R109W;ENSP00000442521:R141W;ENSP00000361759:R109W	ENSP00000361759:R109W	R	-	1	2	BEX2	102451236	0.638000	0.27225	0.551000	0.28230	0.784000	0.44337	0.741000	0.26202	0.518000	0.28383	0.600000	0.82982	CGG		TCGA-2J-AABR-01A-11D-A40W-08	BEX2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057702.1	0	0	0	9	820	0	161	0	1.374317e-01	0	53	0	161	2		0	0	0	0	0	2	1	0.993736	9	805	0	155	2								-1.947661	0	1	0	0		1	0	1	1			0.090000	1.970000	0.090000	0.240000	0.120000	0.430000	0.240000	0.264143	0.240000	0	0.170000	0.340000
IGSF1	3547	broad.mit.edu	37	X	130416639	130416639	+	Missense_Mutation	SNP	C	C	T			TCGA-2J-AABR-01A-11D-A40W-08	TCGA-2J-AABR-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	534d051f-0b40-486a-8f77-646bf003d3d0	4c28dd95-5359-4c03-b338-7038de30008f	g.chrX:130416639C>T	ENST00000361420.3	-	7	1104	c.1025G>A	c.(1024-1026)cGg>cAg	p.R342Q	IGSF1_ENST00000370903.3_Missense_Mutation_p.R342Q|IGSF1_ENST00000370904.1_Missense_Mutation_p.R333Q|IGSF1_ENST00000370910.1_Missense_Mutation_p.R333Q			Q8N6C5	IGSF1_HUMAN	immunoglobulin superfamily, member 1			78					TCCTCGACACCGTAGGCTCAC	0.498000																								0							SO:0001583	missense			ENST00000361420.3	1	1	hg19	CCDS14629.1	.	.	.	.	.	.	.	.	.	.	C	1.457	-0.563461	0.03939	.	.	ENSG00000147255	ENST00000370910;ENST00000361420;ENST00000370904;ENST00000370903	T;T;T;T	0.12774	2.65;2.65;2.65;2.65	4.78	-0.153	0.13403	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	1.769840	0.02967	N	0.143897	T	0.07954	0.0199	N	0.17872	0.535	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.001	T	0.26985	-1.0087	10	0.21014	T	0.42	.	0.7403	0.00972	0.1686:0.3668:0.1618:0.3028	.	333;342	Q8N6C5-2;Q8N6C5	.;IGSF1_HUMAN	Q	333;342;333;342	ENSP00000359947:R333Q;ENSP00000355010:R342Q;ENSP00000359941:R333Q;ENSP00000359940:R342Q	ENSP00000355010:R342Q	R	-	2	0	IGSF1	130244320	0.000000	0.05858	0.000000	0.03702	0.047000	0.14425	-0.077000	0.11394	-0.295000	0.08960	0.594000	0.82650	CGG		TCGA-2J-AABR-01A-11D-A40W-08	IGSF1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058288.1	0	0	0	13	381	0	71	0	0	0	1	0	71	2		0	0	0	0	0	2	1	0.999512	13	376	0	67	2								-2.555299	1	1	121410	5	38	1	0	1	1			0.090000	1.970000	0.090000	0.740000	0.410000	1.000000	1.000000	0.750082	0.740000	0	0.560000	0.950000
PLXNB3	5365	broad.mit.edu	37	X	153036266	153036266	+	Silent	SNP	A	A	T			TCGA-2J-AABR-01A-11D-A40W-08	TCGA-2J-AABR-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	534d051f-0b40-486a-8f77-646bf003d3d0	4c28dd95-5359-4c03-b338-7038de30008f	g.chrX:153036266A>T	ENST00000361971.5	+	11	2178	c.2064A>T	c.(2062-2064)gcA>gcT	p.A688A	PLXNB3_ENST00000538282.1_Silent_p.A298A|PLXNB3_ENST00000538776.1_Silent_p.A341A|PLXNB3_ENST00000538543.1_Intron|PLXNB3_ENST00000538966.1_Silent_p.A711A	NM_005393.2	NP_005384.2	Q9ULL4	PLXB3_HUMAN	plexin B3			32	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)				AAGGCCTGGCAGGTCCCCACC	0.622000																								0							SO:0001819	synonymous_variant			ENST00000361971.5	0	1	hg19	CCDS14729.1																																																																																				TCGA-2J-AABR-01A-11D-A40W-08	PLXNB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061063.1	0	0	0	6	271	0	44	1	9.802928e-03	4	2	0	44	2		0	0	0	0	0	2	1	0.961730	6	262	0	43	2								-7.081947	1	1	0	0		1	0	1	1			0.090000	1.970000	0.090000	0.500000	0.210000	0.950000	1.000000	0.534601	0.500000	0	0.330000	0.720000
PGAM4	441531	broad.mit.edu	37	X	77224488	77224488	+	Silent	SNP	G	G	A			TCGA-2J-AABR-01A-11D-A40W-08	TCGA-2J-AABR-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	534d051f-0b40-486a-8f77-646bf003d3d0	4c28dd95-5359-4c03-b338-7038de30008f	g.chrX:77224488G>A	ENST00000458128.1	-	1	647	c.648C>T	c.(646-648)atC>atT	p.I216I	ATP7A_ENST00000350425.4_Intron|ATP7A_ENST00000343533.5_Intron|ATP7A_ENST00000341514.6_Intron	NM_001029891.2	NP_001025062.1	Q8N0Y7	PGAM4_HUMAN	phosphoglycerate mutase family member 4			6					ATTCATAGACGATGGGAATAC	0.537000																								0							SO:0001819	synonymous_variant			ENST00000458128.1	0	1	hg19	CCDS35338.1																																																																																				TCGA-2J-AABR-01A-11D-A40W-08	PGAM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128371.2	0	0	0	7	745	0	176		0	0	0	0	176	2		0	0	0	0	0	2	1	0.974229	7	688	0	177	2								-2.114288	0	1	0	0		1	0	1	1			0.090000	1.970000	0.090000	0.210000	0.090000	0.400000	0.200000	0.232598	0.210000	0	0.140000	0.310000
