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
DIXDC1	85458	broad.mit.edu	37	11	111853203	111853203	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr11:111853203G>A	ENST00000440460.2	+	8	1204	c.907G>A	c.(907-909)Gga>Aga	p.G303R	DIXDC1_ENST00000315253.5_Missense_Mutation_p.G92R|DIXDC1_ENST00000389821.4_3'UTR	NM_001037954.2	NP_001033043.1	Q155Q3	DIXC1_HUMAN	DIX domain containing 1			17		all_cancers(61;7.58e-15)|all_epithelial(67;5.42e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)			AATGATATCAGGACTACAGGT	0.368000																								0							SO:0001583	missense			ENST00000440460.2	0	1	hg19		.	.	.	.	.	.	.	.	.	.	G	18.01	3.528320	0.64860	.	.	ENSG00000150764	ENST00000440460;ENST00000315253	T;T	0.19806	2.12;2.12	6.16	6.16	0.99307	.	0.354131	0.36519	N	0.002544	T	0.43612	0.1255	.	.	.	0.54753	D	0.999988	B;D	0.89917	0.05;1.0	B;D	0.76575	0.048;0.988	T	0.01858	-1.1259	9	0.19590	T	0.45	-10.0595	19.4236	0.94732	0.0:0.0:1.0:0.0	.	92;304	E7EQ17;Q155Q3	.;DIXC1_HUMAN	R	303;92	ENSP00000394352:G303R;ENSP00000314068:G92R	ENSP00000314068:G92R	G	+	1	0	DIXDC1	111358413	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	4.817000	0.62650	2.937000	0.99478	0.650000	0.86243	GGA		TCGA-2L-AAQI-01A-12D-A397-08	DIXDC1-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		0	0	0	6	71	0	21	1	1.918343e-01	2	7	0	21	2		0	0	0	0	0	2	1	0.967009	6	71	0	21	2		0	0	0	0	0	2	-10.626720	1	1	0	0		1	1	2	3	2.070542	0	0.290000	1.810000	0.294094	0.570000	2.400000e-01	1.000000	1.000000	0.602160	0.570000	0	0.380000	0.830000
MRPL16	54948	broad.mit.edu	37	11	59573897	59573897	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr11:59573897G>A	ENST00000300151.4	-	4	892	c.679C>T	c.(679-681)Cgg>Tgg	p.R227W		NM_017840.3	NP_060310.1	Q9NX20	RM16_HUMAN	mitochondrial ribosomal protein L16			11					AGTACTTTCCGTATGCCCAGC	0.468000																								0							SO:0001583	missense			ENST00000300151.4	0	1	hg19	CCDS7976.1	.	.	.	.	.	.	.	.	.	.	G	19.63	3.863130	0.71949	.	.	ENSG00000166902	ENST00000300151	T	0.25912	1.77	6.07	4.02	0.46733	.	0.045846	0.85682	D	0.000000	T	0.47637	0.1456	M	0.74258	2.255	0.80722	D	1	D	0.89917	1.0	D	0.74348	0.983	T	0.50676	-0.8800	10	0.87932	D	0	-22.0244	10.3068	0.43685	0.0:0.1084:0.6643:0.2273	.	227	Q9NX20	RM16_HUMAN	W	227	ENSP00000300151:R227W	ENSP00000300151:R227W	R	-	1	2	MRPL16	59330473	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.383000	0.52471	1.562000	0.49601	0.655000	0.94253	CGG		TCGA-2L-AAQI-01A-12D-A397-08	MRPL16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394521.1	0	0	0	5	648	0	138	0	4.002915e-01	0	155	0	138	2		0	0	0	0	0	2	1	0.937248	6	645	0	138	2		0	0	0	0	0	2	-2.207349	0	1	121412	4	42	1	1	2	3	2.082394	0	0.290000	1.810000	0.296124	0.050000	1.000000e-02	1.000000	0.060000	0.107439	0.050000	0	0.030000	0.100000
CNGA4	1262	broad.mit.edu	37	11	6261751	6261751	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr11:6261751G>A	ENST00000379936.2	+	4	842	c.727G>A	c.(727-729)Gag>Aag	p.E243K	CNGA4_ENST00000533426.1_Intron	NM_001037329.3	NP_001032406.1	Q8IV77	CNGA4_HUMAN	cyclic nucleotide gated channel alpha 4	p.E243K(1)		40		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)			CAGGGAAGAAGAGTACCTCTT	0.552000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000379936.2	1	1	hg19	CCDS31408.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.133543	0.77662	.	.	ENSG00000132259	ENST00000379936	D	0.97731	-4.51	5.3	5.3	0.74995	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99281	0.9749	H	0.98005	4.125	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.77557	0.99;0.982	D	0.98722	1.0709	10	0.87932	D	0	.	17.8807	0.88840	0.0:0.0:1.0:0.0	.	243;203	Q8IV77;Q8IV77-2	CNGA4_HUMAN;.	K	243	ENSP00000369268:E243K	ENSP00000369268:E243K	E	+	1	0	CNGA4	6218327	1.000000	0.71417	1.000000	0.80357	0.186000	0.23388	9.420000	0.97426	2.640000	0.89533	0.561000	0.74099	GAG		TCGA-2L-AAQI-01A-12D-A397-08	CNGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383765.2	1	0	1	56	344	0	76		0	0	0	0	76	2		0	0	0	0	0	2	1	1.000000	54	341	0	76	2		0	0	0	0	0	2	-3.222344	1	1	0	0		1	1	2	3	2.082394	0	0.290000	1.810000	0.296124	0.970000	7.500000e-01	1.000000	1.000000	0.944158	0.970000	1	0.850000	1.000000
NCOR2	9612	broad.mit.edu	37	12	124816902	124816902	+	Missense_Mutation	SNP	C	C	A			TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr12:124816902C>A	ENST00000405201.1	-	43	6867	c.6867G>T	c.(6865-6867)aaG>aaT	p.K2289N	NCOR2_ENST00000356219.3_Missense_Mutation_p.K2296N|NCOR2_ENST00000429285.2_Missense_Mutation_p.K2279N|NCOR2_ENST00000404621.1_Missense_Mutation_p.K2279N|NCOR2_ENST00000397355.1_Missense_Mutation_p.K2280N|NCOR2_ENST00000404121.2_Missense_Mutation_p.K1850N			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2			69	all_neural(191;0.0804)|Medulloblastoma(191;0.163)				TGTTCAGCTTCTTGTTGATCT	0.607000											OREG0022237	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)												0							SO:0001583	missense			ENST00000405201.1	0	1	hg19	CCDS41858.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.73|14.73	2.623667|2.623667	0.46840|0.46840	.|.	.|.	ENSG00000196498|ENSG00000196498	ENST00000405201;ENST00000404621;ENST00000356219;ENST00000397355;ENST00000447011;ENST00000404121;ENST00000447675;ENST00000429285|ENST00000443451;ENST00000440337	T;T;T;T;T;T|.	0.26810|.	1.71;1.99;1.72;1.99;1.73;1.98|.	4.4|4.4	4.4|4.4	0.53042|0.53042	.|.	0.056456|.	0.64402|.	D|.	0.000001|.	T|T	0.63792|0.63792	0.2541|0.2541	M|M	0.64997|0.64997	1.995|1.995	0.47584|0.47584	D|D	0.999463|0.999463	D;D;D|.	0.76494|.	0.999;0.995;0.991|.	D;D;D|.	0.80764|.	0.994;0.98;0.979|.	T|T	0.63292|0.63292	-0.6670|-0.6670	10|5	0.87932|.	D|.	0|.	-35.1737|-35.1737	10.6433|10.6433	0.45604|0.45604	0.0:0.9104:0.0:0.0896|0.0:0.9104:0.0:0.0896	.|.	2280;2289;2300|.	C9J239;C9JFD3;Q9Y618|.	.;.;NCOR2_HUMAN|.	N|I	2289;2279;2296;2280;2288;1850;381;2279|161;80	ENSP00000384018:K2289N;ENSP00000384202:K2279N;ENSP00000348551:K2296N;ENSP00000380513:K2280N;ENSP00000385618:K1850N;ENSP00000400281:K2279N|.	ENSP00000348551:K2296N|.	K|R	-|-	3|2	2|0	NCOR2|NCOR2	123382855|123382855	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.960000|0.960000	0.62799|0.62799	2.101000|2.101000	0.41787|0.41787	1.981000|1.981000	0.57761|0.57761	0.462000|0.462000	0.41574|0.41574	AAG|AGA		TCGA-2L-AAQI-01A-12D-A397-08	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	0	0	0	5	360	0	89	0	8.223016e-01	0	229	0	89	2		0	0	0	0	0	2	1	0.937952	6	359	0	89	2		0	0	0	0	0	2	-3.031984	1	1	0	0		1	0	1	1	1.801923	1	0.290000	1.810000	0.169591	0.080000	2.000000e-02	0.180000	0.080000	0.095104	0.080000	0	0.050000	0.130000
GPR133	283383	broad.mit.edu	37	12	131569149	131569149	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr12:131569149G>A	ENST00000261654.5	+	15	2171	c.1612G>A	c.(1612-1614)Gtc>Atc	p.V538I	GPR133_ENST00000535015.1_Missense_Mutation_p.V570I|GPR133_ENST00000376682.4_Missense_Mutation_p.V224I|GPR133_ENST00000543617.1_Missense_Mutation_p.V57I	NM_198827.3	NP_942122.2	Q6QNK2	GP133_HUMAN	G protein-coupled receptor 133			67	all_neural(191;0.0982)|Medulloblastoma(191;0.163)				CACCTACTCCGTCTGCCGCTG	0.622000																								0							SO:0001583	missense			ENST00000261654.5	1	1	hg19	CCDS9272.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	4.863	0.160432	0.09287	.	.	ENSG00000111452	ENST00000261654;ENST00000535015;ENST00000376682;ENST00000543617	T;T;T;T	0.69175	-0.38;-0.38;-0.38;-0.38	4.99	-6.86	0.01676	GPS domain (3);	1.327960	0.05058	N	0.479422	T	0.45498	0.1345	N	0.13235	0.315	0.09310	N	0.999996	B;B;B	0.15930	0.003;0.012;0.015	B;B;B	0.15870	0.004;0.005;0.014	T	0.47222	-0.9134	10	0.09338	T	0.73	.	15.0568	0.71921	0.6686:0.0:0.3314:0.0	.	570;57;538	B7ZLF7;Q6QNK2-3;Q6QNK2	.;.;GP133_HUMAN	I	538;570;224;57	ENSP00000261654:V538I;ENSP00000444425:V570I;ENSP00000365872:V224I;ENSP00000438021:V57I	ENSP00000261654:V538I	V	+	1	0	GPR133	130135102	0.001000	0.12720	0.002000	0.10522	0.157000	0.22087	-0.217000	0.09253	-1.452000	0.01931	-2.516000	0.00186	GTC		TCGA-2L-AAQI-01A-12D-A397-08	GPR133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399356.1	1	0	1	41	200	0	46	0	3.473397e-01	0	7	0	46	2		0	0	0	0	0	2	1	1.000000	41	199	0	44	2		0	0	0	0	0	2	-3.204582	1	1	121410	6	38	1	0	1	1	1.801923	1	0.290000	1.810000	0.169591	0.900000	7.000000e-01	1.000000	0.980000	0.893778	0.900000	1	0.800000	0.970000
KRAS	3845	broad.mit.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	C	A	rs121913529		TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08			C	A	C	C		Valid	Somatic	Phase_I	WXS	KRAS_deep			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	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-2L-AAQI-01A-12D-A397-08	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	1	0	0	34	272	0	56	1	7.633422e-01	10	14	0	56	2	1	1	43	379	0	173	2	1	1.000000	34	271	0	56	2	1	1	1230	6776	4	8006	12	-13.942770	1	1	0	0		1	1	2	3	2.119234	0	0.290000	1.810000	0.302143	0.790000	5.600000e-01	1.000000	1.000000	0.808335	0.790000	0	0.660000	0.980000
CNTN1	1272	broad.mit.edu	37	12	41323657	41323657	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr12:41323657C>T	ENST00000551295.2	+	7	673	c.556C>T	c.(556-558)Cgg>Tgg	p.R186W	CNTN1_ENST00000547849.1_Missense_Mutation_p.R186W|CNTN1_ENST00000347616.1_Missense_Mutation_p.R186W|CNTN1_ENST00000348761.2_Missense_Mutation_p.R175W|CNTN1_ENST00000360099.3_Missense_Mutation_p.R186W|CNTN1_ENST00000547702.1_Missense_Mutation_p.R186W	NM_001843.3	NP_001834.2	Q12860	CNTN1_HUMAN	contactin 1			90	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)			AATGGATAAACGGCGATTTGT	0.378000																								0							SO:0001583	missense			ENST00000551295.2	1	1	hg19	CCDS8737.1	.	.	.	.	.	.	.	.	.	.	C	18.58	3.654902	0.67472	.	.	ENSG00000018236	ENST00000547702;ENST00000551295;ENST00000547849;ENST00000347616;ENST00000360099;ENST00000348761	D;D;D;D;D;D	0.82081	-1.57;-1.57;-1.57;-1.57;-1.57;-1.57	5.17	4.27	0.50696	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.93494	0.7924	H	0.95917	3.74	0.52501	D	0.99995	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.94943	0.8093	10	0.87932	D	0	.	13.2205	0.59885	0.2891:0.7109:0.0:0.0	.	186;175;186	Q12860-3;Q12860-2;Q12860	.;.;CNTN1_HUMAN	W	186;186;186;186;186;175	ENSP00000448004:R186W;ENSP00000447006:R186W;ENSP00000448653:R186W;ENSP00000325660:R186W;ENSP00000353213:R186W;ENSP00000261160:R175W	ENSP00000325660:R186W	R	+	1	2	CNTN1	39609924	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.900000	0.48687	1.308000	0.44962	0.655000	0.94253	CGG		TCGA-2L-AAQI-01A-12D-A397-08	CNTN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403692.2	1	0	1	68	426	0	103	0	3.083668e-01	0	8	0	103	2		0	0	0	0	0	2	1	1.000000	68	421	0	102	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	1	2	3	2.119234	0	0.290000	1.810000	0.302143	0.970000	7.600000e-01	1.000000	1.000000	0.946369	0.970000	1	0.860000	1.000000
KRT6B	3854	broad.mit.edu	37	12	52845384	52845384	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr12:52845384C>T	ENST00000252252.3	-	1	526	c.479G>A	c.(478-480)cGg>cAg	p.R160Q		NM_005555.3	NP_005546.2	P04259	K2C6B_HUMAN	keratin 6B			40					CTCCTCGGCCCGCACCCGCTG	0.597000																								0							SO:0001583	missense			ENST00000252252.3	0	1	hg19	CCDS8828.1	.	.	.	.	.	.	.	.	.	.	C	14.68	2.606483	0.46527	.	.	ENSG00000185479	ENST00000252252;ENST00000544607	D	0.85556	-2.0	3.28	0.429	0.16506	.	0.089287	0.44902	D	0.000418	D	0.88890	0.6560	M	0.94021	3.485	0.32244	N	0.572368	D	0.60160	0.987	P	0.48552	0.581	D	0.88941	0.3380	10	0.87932	D	0	.	8.7904	0.34848	0.0:0.7388:0.0:0.2612	.	160	P04259	K2C6B_HUMAN	Q	160	ENSP00000252252:R160Q	ENSP00000252252:R160Q	R	-	2	0	KRT6B	51131651	0.168000	0.22989	0.024000	0.17045	0.255000	0.26057	0.832000	0.27490	0.094000	0.17404	0.298000	0.19748	CGG		TCGA-2L-AAQI-01A-12D-A397-08	KRT6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404969.1	0	0	0	19	512	0	115	0	0	0	1	0	115	2		0	0	0	0	0	2	1	0.999941	14	418	0	184	2		0	0	0	0	0	2	-2.681262	1	1	121406	2	31	1	1	2	3	2.091128	0	0.290000	1.810000	0.297134	0.250000	1.500000e-01	1.000000	0.250000	0.301491	0.250000	0	0.200000	0.330000
SLITRK5	26050	broad.mit.edu	37	13	88329453	88329453	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	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-2L-AAQI-01A-12D-A397-08	SLITRK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045416.3	0	0	0	7	876	0	182	0	1.336522e-03	0	6	0	182	2		0	0	0	0	0	2	1	0.979983	8	865	0	180	2		0	0	0	0	0	2	-1.756732	0	1	121412	1	37	1	1	2	3	2.086869	0	0.290000	1.810000	0.296124	0.050000	1.000000e-02	1.000000	0.060000	0.106784	0.050000	0	0.030000	0.090000
DLK1	8788	broad.mit.edu	37	14	101200618	101200618	+	Silent	SNP	C	C	T	rs143814604	byFrequency	TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08			C	T	C	C		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr14:101200618C>T	ENST00000341267.4	+	5	779	c.537C>T	c.(535-537)tgC>tgT	p.C179C	DLK1_ENST00000331224.6_Silent_p.C179C	NM_003836.5	NP_003827	P80370	DLK1_HUMAN	delta-like 1 homolog (Drosophila)			29		Melanoma(154;0.155)			CCAACCCATGCGAGAACGACG	0.657000																								0							SO:0001819	synonymous_variant			ENST00000341267.4	1	1	hg19	CCDS9963.1																																																																																				TCGA-2L-AAQI-01A-12D-A397-08	DLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414389.1	0	0	1	49	337	0	69	0	9.999976e-01	0	133	0	69	2		0	0	0	0	0	2	1	1.000000	49	334	0	67	2		0	0	0	0	0	2	-19.752180	1	1	121402	19	45	1	1	2	3	2.098086	0	0.290000	1.810000	0.298142	0.890000	6.700000e-01	1.000000	1.000000	0.888443	0.890000	1	0.770000	1.000000
NAGPA	51172	broad.mit.edu	37	16	5077996	5077996	+	Nonsense_Mutation	SNP	C	C	A			TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr16:5077996C>A	ENST00000312251.3	-	6	1130	c.1111G>T	c.(1111-1113)Gga>Tga	p.G371*	RP11-165E7.1_ENST00000588778.1_RNA|NAGPA_ENST00000381955.3_Nonsense_Mutation_p.G371*	NM_016256.3	NP_057340.2	Q9UK23	NAGPA_HUMAN	N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase			12				N-Acetyl-D-glucosamine(DB00141)	GTGCACAGTCCGTGCTGGCTG	0.687000																								0							SO:0001587	stop_gained			ENST00000312251.3	0	1	hg19	CCDS10527.1	.	.	.	.	.	.	.	.	.	.	C	18.32	3.597193	0.66332	.	.	ENSG00000103174	ENST00000312251;ENST00000381955	.	.	.	4.42	4.42	0.53409	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-29.7837	17.027	0.86450	0.0:1.0:0.0:0.0	.	.	.	.	X	371	.	ENSP00000310998:G371X	G	-	1	0	NAGPA	5017997	1.000000	0.71417	0.351000	0.25721	0.106000	0.19336	7.381000	0.79718	2.002000	0.58637	0.561000	0.74099	GGA		TCGA-2L-AAQI-01A-12D-A397-08	NAGPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207003.1	1	0	1	22	166	0	39	1	7.878343e-01	2	22	0	39	2		0	0	0	0	0	2	1	0.999999	22	165	0	39	2		0	0	0	0	0	2	-3.076474	1	1	0	0		1	1	2	3	2.086316	0	0.290000	1.810000	0.296124	0.820000	5.300000e-01	1.000000	1.000000	0.825569	0.820000	0	0.670000	1.000000
TMEM186	25880	broad.mit.edu	37	16	8890319	8890319	+	Silent	SNP	C	C	T	rs149142450		TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr16:8890319C>T	ENST00000333050.6	-	2	165	c.132G>A	c.(130-132)tcG>tcA	p.S44S	PMM2_ENST00000569958.1_5'Flank|TMEM186_ENST00000564869.1_Intron|PMM2_ENST00000268261.4_5'Flank|PMM2_ENST00000537352.1_5'Flank|PMM2_ENST00000566983.1_Intron|PMM2_ENST00000539622.1_5'Flank	NM_015421.3	NP_056236.2	Q96B77	TM186_HUMAN	transmembrane protein 186			9					GTTTCTCCTTCGAGATGGGTG	0.532000																								0							SO:0001819	synonymous_variant			ENST00000333050.6	1	1	hg19	CCDS10535.1																																																																																				TCGA-2L-AAQI-01A-12D-A397-08	TMEM186-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251903.1	1	0	0	44	415	0	102	0	9.032090e-01	1	39	0	102	2		0	0	0	0	0	2	1	1.000000	44	413	0	102	2		0	0	0	0	0	2	-13.604630	1	1	121412	6	42	1	1	2	3	2.086316	0	0.290000	1.810000	0.296124	0.670000	4.900000e-01	1.000000	0.660000	0.690748	0.670000	0	0.570000	0.790000
TEX2	55852	broad.mit.edu	37	17	62290359	62290359	+	Missense_Mutation	SNP	A	A	C			TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr17:62290359A>C	ENST00000583097.1	-	2	1391	c.1219T>G	c.(1219-1221)Ttg>Gtg	p.L407V	TEX2_ENST00000258991.3_Missense_Mutation_p.L407V|TEX2_ENST00000584379.1_Missense_Mutation_p.L407V			Q8IWB9	TEX2_HUMAN	testis expressed 2			41			BRCA - Breast invasive adenocarcinoma(8;1.33e-10)		AAGGCAGACAAAGAACATTTC	0.448000																								0							SO:0001583	missense			ENST00000583097.1	1	1	hg19		.	.	.	.	.	.	.	.	.	.	A	6.515	0.463155	0.12402	.	.	ENSG00000136478	ENST00000258991	T	0.54866	0.55	6.11	-3.07	0.05363	.	0.241819	0.43260	D	0.000598	T	0.45577	0.1349	L	0.56769	1.78	0.25501	N	0.987551	P;P	0.42827	0.791;0.687	B;B	0.44133	0.442;0.257	T	0.47522	-0.9111	10	0.54805	T	0.06	-10.7897	8.1698	0.31247	0.4215:0.0:0.463:0.1155	.	407;407	Q8IWB9-2;Q8IWB9	.;TEX2_HUMAN	V	407	ENSP00000258991:L407V	ENSP00000258991:L407V	L	-	1	2	TEX2	59644091	0.625000	0.27111	0.126000	0.21872	0.971000	0.66376	1.066000	0.30604	-0.522000	0.06417	-0.250000	0.11733	TTG		TCGA-2L-AAQI-01A-12D-A397-08	TEX2-003	KNOWN	alternative_5_UTR|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000443745.1	1	0	1	88	532	0	130	1	8.989089e-01	3	23	0	130	2		0	0	0	0	0	2	1	1.000000	87	529	0	130	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	1	2	3	2.087263	0	0.290000	1.810000	0.297134	0.990000	8.000000e-01	1.000000	1.000000	0.959778	0.990000	1	0.890000	1.000000
TP53	7157	broad.mit.edu	37	17	7577090	7577090	+	Missense_Mutation	SNP	C	C	G			TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08			C	G	C	C		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr17:7577090C>G	ENST00000269305.4	-	8	1037	c.848G>C	c.(847-849)cGc>cCc	p.R283P	TP53_ENST00000445888.2_Missense_Mutation_p.R283P|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.R283P|TP53_ENST00000420246.2_Missense_Mutation_p.R283P|TP53_ENST00000359597.4_Missense_Mutation_p.R283P|TP53_ENST00000413465.2_Intron	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.R283P(27)|p.R283H(13)|p.0?(8)|p.R283L(4)|p.R283fs*23(2)|p.?(2)|p.R283fs*16(2)|p.A276_R283delACPGRDRR(1)|p.R283del(1)|p.R283fs*22(1)|p.R282_E287delRRTEEE(1)|p.T284_G293del10(1)|p.G279fs*59(1)|p.S269fs*21(1)|p.C275_R283delCACPGRDRR(1)|p.L265_K305del41(1)|p.T284fs*57(1)|p.R283fs*56(1)|p.R283_T284>T(1)|p.V272_K292del21(1)|p.R283fs*59(1)|p.C275fs*20(1)		24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		Acetylsalicylic acid(DB00945)	TTCCTCTGTGCGCCGGTCTCT	0.562000		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	73	Substitution - Missense(44)|Deletion - Frameshift(9)|Whole gene deletion(8)|Deletion - In frame(7)|Insertion - Frameshift(2)|Unknown(2)|Complex - deletion inframe(1)	GRCh37	CM021154	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	18.76	3.692626	0.68271	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99804	-6.83;-6.83;-6.83;-6.83;-6.83;-6.83	4.99	4.02	0.46733	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.056377	0.64402	D	0.000003	D	0.99641	0.9868	M	0.78049	2.395	0.28236	N	0.925907	P;D;D;P	0.76494	0.939;0.999;0.977;0.951	P;D;D;D	0.70016	0.889;0.967;0.933;0.933	D	0.98126	1.0428	10	0.87932	D	0	-4.3612	11.3481	0.49573	0.0:0.9114:0.0:0.0886	.	283;283;283;283	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	P	283;283;283;283;283;272;151	ENSP00000352610:R283P;ENSP00000269305:R283P;ENSP00000398846:R283P;ENSP00000391127:R283P;ENSP00000391478:R283P;ENSP00000425104:R151P	ENSP00000269305:R283P	R	-	2	0	TP53	7517815	0.998000	0.40836	0.015000	0.15790	0.873000	0.50193	3.584000	0.53936	1.318000	0.45170	0.462000	0.41574	CGC		TCGA-2L-AAQI-01A-12D-A397-08	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	1	0	1	29	132	0	39	1	9.999854e-01	46	39	0	39	2	1	1	146	930	0	645	2	1	1.000000	29	132	0	39	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	0	1	1	1.790263	1	0.290000	1.810000	0.169591	0.900000	6.800000e-01	1.000000	0.990000	0.889786	0.900000	1	0.790000	0.970000
LGALS3BP	3959	broad.mit.edu	37	17	76968673	76968673	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr17:76968673G>A	ENST00000262776.3	-	6	1051	c.743C>T	c.(742-744)gCc>gTc	p.A248V	LGALS3BP_ENST00000591778.1_Missense_Mutation_p.P164S	NM_005567.3	NP_005558.1	Q08380	LG3BP_HUMAN	lectin, galactoside-binding, soluble, 3 binding protein			17			BRCA - Breast invasive adenocarcinoma(99;0.0677)|OV - Ovarian serous cystadenocarcinoma(97;0.139)		GAGGAGGATGGCAAAGAGGCT	0.617000													GBM(89;1105 1755 18102 21513)											0							SO:0001583	missense			ENST00000262776.3	1	1	hg19	CCDS11759.1	.	.	.	.	.	.	.	.	.	.	G	6.875	0.530901	0.13127	.	.	ENSG00000108679	ENST00000262776;ENST00000536190	T	0.01422	4.91	3.65	0.453	0.16639	BTB/POZ fold (1);	0.197685	0.25183	N	0.032512	T	0.01387	0.0045	L	0.44542	1.39	0.09310	N	0.999999	B	0.15141	0.012	B	0.10450	0.005	T	0.46952	-0.9154	10	0.25751	T	0.34	-24.5418	6.2835	0.21021	0.3254:0.0:0.6746:0.0	.	248	Q08380	LG3BP_HUMAN	V	248;236	ENSP00000262776:A248V	ENSP00000262776:A248V	A	-	2	0	LGALS3BP	74480268	0.743000	0.28239	0.008000	0.14137	0.424000	0.31475	2.722000	0.47269	0.146000	0.19002	0.561000	0.74099	GCC		TCGA-2L-AAQI-01A-12D-A397-08	LGALS3BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437785.3	1	0	1	29	227	0	42	1	1	843	1440	0	42	2		0	0	0	0	0	2	1	1.000000	28	221	0	39	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	1	2	3	2.087263	0	0.290000	1.810000	0.297134	0.800000	5.500000e-01	1.000000	1.000000	0.807942	0.800000	0	0.660000	0.970000
MAST1	22983	broad.mit.edu	37	19	12969441	12969441	+	Missense_Mutation	SNP	G	G	C			TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr19:12969441G>C	ENST00000251472.4	+	12	1293	c.1254G>C	c.(1252-1254)caG>caC	p.Q418H	MAST1_ENST00000591495.1_Missense_Mutation_p.Q414H	NM_014975.2	NP_055790.1			microtubule associated serine/threonine kinase 1			56					AGATCCAGCAGGCCTTTGTGG	0.587000																								0							SO:0001583	missense			ENST00000251472.4	1	1	hg19	CCDS32921.1	.	.	.	.	.	.	.	.	.	.	G	18.17	3.564284	0.65651	.	.	ENSG00000105613	ENST00000251472;ENST00000542153	T	0.66460	-0.21	4.75	3.71	0.42584	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.60248	0.2254	N	0.03071	-0.42	0.58432	D	0.999992	D;B	0.76494	0.999;0.357	D;B	0.87578	0.998;0.237	T	0.69343	-0.5170	10	0.87932	D	0	-32.5112	11.0071	0.47641	0.0928:0.0:0.9072:0.0	.	418;418	Q9Y2H9;F5H2S9	MAST1_HUMAN;.	H	418	ENSP00000251472:Q418H	ENSP00000251472:Q418H	Q	+	3	2	MAST1	12830441	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.809000	0.62591	1.144000	0.42321	0.561000	0.74099	CAG		TCGA-2L-AAQI-01A-12D-A397-08	MAST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451733.2	1	0	0	14	216	0	62		0	0	0	0	62	2		0	0	0	0	0	2	1	0.999768	14	214	0	62	2		0	0	0	0	0	2	-17.659470	1	1	0	0		1	1	2	3	2.076358	0	0.290000	1.810000	0.295110	0.430000	2.400000e-01	1.000000	0.420000	0.465581	0.430000	0	0.330000	0.570000
ATP4A	495	broad.mit.edu	37	19	36051809	36051809	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr19:36051809G>A	ENST00000262623.3	-	5	474	c.446C>T	c.(445-447)gCt>gTt	p.A149V		NM_000704.2	NP_000695.2	P20648	ATP4A_HUMAN	ATPase, H+/K+ exchanging, alpha polypeptide			53	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)	Esomeprazole(DB00736)|Lansoprazole(DB00448)|Omeprazole(DB00338)|Pantoprazole(DB00213)|Rabeprazole(DB01129)	GACAACCACAGCAATGAGAGC	0.587000																								0							SO:0001583	missense			ENST00000262623.3	0	1	hg19	CCDS12467.1	.	.	.	.	.	.	.	.	.	.	g	14.83	2.651116	0.47362	.	.	ENSG00000105675	ENST00000262623	D	0.90563	-2.69	3.22	3.22	0.36961	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.000000	0.64402	D	0.000018	T	0.81735	0.4885	N	0.17838	0.53	0.58432	D	0.999991	B	0.19445	0.036	B	0.27796	0.083	T	0.73704	-0.3899	10	0.10377	T	0.69	.	11.9305	0.52843	0.0:0.0:1.0:0.0	.	149	P20648	ATP4A_HUMAN	V	149	ENSP00000262623:A149V	ENSP00000262623:A149V	A	-	2	0	ATP4A	40743649	0.998000	0.40836	0.990000	0.47175	0.830000	0.47004	4.954000	0.63631	1.620000	0.50308	0.197000	0.17608	GCT		TCGA-2L-AAQI-01A-12D-A397-08	ATP4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109470.2	0	0	0	5	388	0	69		0	0	0	0	69	2		0	0	0	0	0	2	1	0.935372	5	382	0	69	2		0	0	0	0	0	2	-3.219679	1	1	0	0		1	1	2	3	2.076358	0	0.290000	1.810000	0.295110	0.090000	3.000000e-02	1.000000	0.090000	0.138869	0.090000	0	0.050000	0.150000
CCDC8	83987	broad.mit.edu	37	19	46914987	46914987	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr19:46914987C>T	ENST00000307522.3	-	1	1854	c.1081G>A	c.(1081-1083)Gaa>Aaa	p.E361K		NM_032040.4	NP_114429.2	Q9H0W5	CCDC8_HUMAN	coiled-coil domain containing 8			23					GCAGCCTCTTCCCTCTGGTTA	0.597000																								0							SO:0001583	missense			ENST00000307522.3	1	1	hg19	CCDS12685.1	.	.	.	.	.	.	.	.	.	.	C	9.334	1.061247	0.19987	.	.	ENSG00000169515	ENST00000307522	T	0.11495	2.77	3.19	3.19	0.36642	.	0.455403	0.16199	N	0.225029	T	0.07007	0.0178	N	0.19112	0.55	0.21325	N	0.999721	B	0.25169	0.119	B	0.21546	0.035	T	0.31833	-0.9929	10	0.15066	T	0.55	0.0165	12.6394	0.56700	0.0:1.0:0.0:0.0	.	361	Q9H0W5	CCDC8_HUMAN	K	361	ENSP00000303158:E361K	ENSP00000303158:E361K	E	-	1	0	CCDC8	51606827	0.000000	0.05858	0.029000	0.17559	0.042000	0.13812	-0.412000	0.07132	2.093000	0.63338	0.297000	0.19635	GAA		TCGA-2L-AAQI-01A-12D-A397-08	CCDC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368598.1	1	0	1	103	618	0	132	0	9.672482e-01	0	35	0	132	2		0	0	0	0	0	2	1	1.000000	100	609	0	131	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	1	2	3	2.076358	0	0.290000	1.810000	0.295110	0.990000	8.200000e-01	1.000000	1.000000	0.963205	0.990000	1	0.900000	1.000000
PLEKHA4	57664	broad.mit.edu	37	19	49340735	49340735	+	Missense_Mutation	SNP	C	C	G			TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr19:49340735C>G	ENST00000263265.6	-	20	2706	c.2151G>C	c.(2149-2151)gaG>gaC	p.E717D	HSD17B14_ENST00000599157.1_5'Flank|PLEKHA4_ENST00000355496.5_3'UTR|HSD17B14_ENST00000263278.4_5'Flank	NM_020904.2	NP_065955.2	Q9H4M7	PKHA4_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 4			30		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;0.000108)|all_neural(266;0.0506)|Ovarian(192;0.113)			GGGGAGGGGTCTCCTGGCGCG	0.672000																								0							SO:0001583	missense			ENST00000263265.6	0	1	hg19	CCDS12737.1	.	.	.	.	.	.	.	.	.	.	c	12.76	2.035882	0.35893	.	.	ENSG00000105559	ENST00000263265	T	0.08370	3.1	4.1	0.204	0.15199	.	1.664920	0.03742	N	0.255152	T	0.05181	0.0138	N	0.08118	0	0.09310	N	0.999997	B	0.02656	0.0	B	0.01281	0.0	T	0.39583	-0.9607	10	0.39692	T	0.17	.	6.9353	0.24463	0.1931:0.4688:0.3382:0.0	.	717	Q9H4M7	PKHA4_HUMAN	D	717	ENSP00000263265:E717D	ENSP00000263265:E717D	E	-	3	2	PLEKHA4	54032547	0.000000	0.05858	0.000000	0.03702	0.287000	0.27160	-0.065000	0.11617	0.057000	0.16193	0.299000	0.19835	GAG		TCGA-2L-AAQI-01A-12D-A397-08	PLEKHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466216.1	0	0	0	5	324	0	50	0	5.839805e-01	0	117	0	50	2		0	0	0	0	0	2	0	0.933358	0	320	0	49	2		0	0	0	0	0	2	-5.481152	1	0	0	0		1	1	2	3	2.076358	0	0.290000	1.810000	0.295110	0.110000	3.000000e-02	1.000000	0.100000	0.158234	0.110000	0	0.070000	0.180000
RRAS	6237	broad.mit.edu	37	19	50139001	50139001	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr19:50139001G>A	ENST00000246792.3	-	5	664	c.562C>T	c.(562-564)Cgg>Tgg	p.R188W		NM_006270.3	NP_006261.1	P10301	RRAS_HUMAN	related RAS viral (r-ras) oncogene homolog			6					CGGACAGCCCGCACCAGCTGC	0.597000																								0							SO:0001583	missense			ENST00000246792.3	0	1	hg19	CCDS12774.1	.	.	.	.	.	.	.	.	.	.	G	19.01	3.744428	0.69418	.	.	ENSG00000126458	ENST00000246792	T	0.79454	-1.27	4.85	4.85	0.62838	.	0.204104	0.34067	N	0.004286	D	0.90459	0.7012	H	0.96398	3.815	0.58432	D	0.999999	D	0.89917	1.0	D	0.71184	0.972	D	0.92164	0.5738	10	0.87932	D	0	.	10.503	0.44817	0.0:0.0:0.6965:0.3035	.	188	P10301	RRAS_HUMAN	W	188	ENSP00000246792:R188W	ENSP00000246792:R188W	R	-	1	2	RRAS	54830813	0.312000	0.24545	0.994000	0.49952	0.740000	0.42216	2.016000	0.40971	2.509000	0.84616	0.491000	0.48974	CGG		TCGA-2L-AAQI-01A-12D-A397-08	RRAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465791.1	0	0	0	6	454	0	98	0	9.859706e-01	0	602	0	98	2	0	0	0	1	0	0	2	1	0.963752	6	448	0	95	2		0	0	0	0	0	2	-2.244413	0	1	0	0		1	1	2	3	2.076358	0	0.290000	1.810000	0.295110	0.090000	3.000000e-02	1.000000	0.090000	0.138704	0.090000	0	0.060000	0.150000
LILRB1	10859	broad.mit.edu	37	19	55144109	55144109	+	Missense_Mutation	SNP	C	C	A			TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr19:55144109C>A	ENST00000396331.1	+	7	1213	c.856C>A	c.(856-858)Cct>Act	p.P286T	LILRB1_ENST00000324602.7_Missense_Mutation_p.P286T|LILRB1_ENST00000418536.2_Missense_Mutation_p.P286T|LILRB1_ENST00000396315.1_Missense_Mutation_p.P286T|LILRB1_ENST00000427581.2_Missense_Mutation_p.P322T|LILRB1_ENST00000396321.2_Missense_Mutation_p.P286T|LILRB1_ENST00000434867.2_Missense_Mutation_p.P286T|LILRB1_ENST00000396327.3_Missense_Mutation_p.P286T|LILRB1_ENST00000396317.1_Missense_Mutation_p.P286T|LILRB1_ENST00000396332.4_Missense_Mutation_p.P286T|LILRB1_ENST00000448689.1_Missense_Mutation_p.P286T	NM_006669.3	NP_006660.3	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1			74					CACCCTGGGCCCTGTGAGCCG	0.632000										HNSCC(37;0.09)														0							SO:0001583	missense			ENST00000396331.1	1	1	hg19	CCDS42617.1	.	.	.	.	.	.	.	.	.	.	C	8.074	0.770833	0.15983	.	.	ENSG00000104972	ENST00000396321;ENST00000418536;ENST00000448689;ENST00000396331;ENST00000396327;ENST00000324602;ENST00000434867;ENST00000396332;ENST00000427581;ENST00000396317;ENST00000396315	T;T;T;T;T;T;T;T;T;T;T	0.11495	2.77;2.77;2.77;2.77;2.77;2.77;2.77;2.77;2.77;2.77;2.77	2.03	-1.43	0.08884	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.672928	0.12913	N	0.428831	T	0.31358	0.0794	M	0.91090	3.175	0.09310	N	1	B;D;P;P;D	0.65815	0.387;0.969;0.767;0.83;0.995	B;P;P;P;D	0.67382	0.241;0.868;0.53;0.646;0.951	T	0.07809	-1.0753	10	0.66056	D	0.02	.	4.745	0.13033	0.0:0.4872:0.0:0.5128	.	286;286;286;286;286	A8MVE2;Q8NHL6-3;A2IXV4;Q8NHL6-2;Q8NHL6	.;.;.;.;LIRB1_HUMAN	T	286;286;286;286;286;286;286;286;322;286;286	ENSP00000379614:P286T;ENSP00000391514:P286T;ENSP00000409968:P286T;ENSP00000379622:P286T;ENSP00000379618:P286T;ENSP00000315997:P286T;ENSP00000405243:P286T;ENSP00000379623:P286T;ENSP00000395004:P322T;ENSP00000379610:P286T;ENSP00000379608:P286T	ENSP00000315997:P286T	P	+	1	0	LILRB1	59835921	0.000000	0.05858	0.001000	0.08648	0.067000	0.16453	-1.269000	0.02834	-0.418000	0.07450	0.194000	0.17425	CCT		TCGA-2L-AAQI-01A-12D-A397-08	LILRB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140796.4	1	0	0	26	356	0	76	0	1.457254e-02	0	3	0	76	2		0	0	0	0	0	2	1	1.000000	24	339	0	84	2		0	0	0	0	0	2	-3.142702	1	1	0	0		1	1	2	3	2.063628	0	0.290000	1.810000	0.292053	0.470000	3.100000e-01	0.700000	0.460000	0.488303	0.470000	0	0.380000	0.580000
RFX2	5990	broad.mit.edu	37	19	6013025	6013025	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr19:6013025G>A	ENST00000303657.5	-	8	1020	c.871C>T	c.(871-873)Cgg>Tgg	p.R291W	RFX2_ENST00000592546.1_Missense_Mutation_p.R266W|RFX2_ENST00000359161.3_Missense_Mutation_p.R291W|CTC-232P5.1_ENST00000587836.1_RNA	NM_000635.3	NP_000626.2	P48378	RFX2_HUMAN	regulatory factor X, 2 (influences HLA class II expression)			21					GGCTGCTGCCGCATGGCCATG	0.622000													Colon(38;171 817 19800 47433 48051)											0							SO:0001583	missense			ENST00000303657.5	0	1	hg19	CCDS12157.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.263838	0.80358	.	.	ENSG00000087903	ENST00000303657;ENST00000359161;ENST00000537791	T	0.68903	-0.36	4.99	0.693	0.18056	.	0.000000	0.85682	D	0.000000	T	0.81517	0.4839	M	0.86178	2.8	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.982	D	0.83606	0.0131	10	0.87932	D	0	-48.1749	13.7584	0.62950	0.0:0.0:0.234:0.766	.	266;291	P48378-2;P48378	.;RFX2_HUMAN	W	291;266;78	ENSP00000306335:R291W	ENSP00000306335:R291W	R	-	1	2	RFX2	5964025	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	1.976000	0.40579	0.152000	0.19188	0.557000	0.71058	CGG		TCGA-2L-AAQI-01A-12D-A397-08	RFX2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452687.1	0	0	0	7	870	0	175	0	3.178309e-03	0	9	0	175	2		0	0	0	0	0	2	1	0.980308	7	866	0	172	2		0	0	0	0	0	2	-2.092584	0	1	0	0		1	1	2	3	2.076358	0	0.290000	1.810000	0.295110	0.050000	1.000000e-02	1.000000	0.060000	0.098675	0.050000	0	0.030000	0.090000
NES	10763	broad.mit.edu	37	1	156641485	156641485	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr1:156641485G>A	ENST00000368223.3	-	4	2627	c.2495C>T	c.(2494-2496)gCg>gTg	p.A832V		NM_006617.1	NP_006608.1	P48681	NEST_HUMAN	nestin			64	all_hematologic(923;0.088)|Hepatocellular(266;0.158)				CTCTTGTCCCGCAGACTTCAG	0.413000																								0							SO:0001583	missense			ENST00000368223.3	0	1	hg19	CCDS1151.1	.	.	.	.	.	.	.	.	.	.	G	15.56	2.868932	0.51588	.	.	ENSG00000132688	ENST00000368223	D	0.85955	-2.05	5.68	-1.11	0.09840	.	0.494478	0.15171	N	0.276645	T	0.52208	0.1720	L	0.38838	1.175	0.09310	N	1	B	0.25312	0.123	B	0.12837	0.008	T	0.36040	-0.9764	10	0.35671	T	0.21	.	1.1534	0.01790	0.3298:0.2257:0.3163:0.1282	.	832	P48681	NEST_HUMAN	V	832	ENSP00000357206:A832V	ENSP00000357206:A832V	A	-	2	0	NES	154908109	0.000000	0.05858	0.001000	0.08648	0.305000	0.27757	-0.007000	0.12810	0.332000	0.23536	0.563000	0.77884	GCG		TCGA-2L-AAQI-01A-12D-A397-08	NES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082844.2	0	0	0	8	786	1	160	0	1.418588e-02	0	74	1	160	4		0	0	0	0	0	2	0	0.051478	7	785	1	160	17		0	0	0	0	0	2	-1.951808	0	1	121410	1	39	1	1	2	3	2.111475	0	0.290000	1.810000	0.301147	0.070000	2.000000e-02	1.000000	0.070000	0.160840	0.070000	0	0.040000	0.120000
CTRC	11330	broad.mit.edu	37	1	15769925	15769925	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08			C	T	C	C		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr1:15769925C>T	ENST00000375949.4	+	5	394	c.368C>T	c.(367-369)gCc>gTc	p.A123V	CTRC_ENST00000483406.1_3'UTR|CTRC_ENST00000375943.2_Missense_Mutation_p.P60S	NM_007272.2	NP_009203.2	Q99895	CTRC_HUMAN	chymotrypsin C (caldecrin)			13		Breast(348;0.000207)|all_lung(284;0.00021)|Colorectal(325;0.000257)|Lung NSC(340;0.000269)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)|Hepatocellular(190;0.0634)			AATGATATTGCCCTCATCAAG	0.592000																								0							SO:0001583	missense			ENST00000375949.4	0	1	hg19	CCDS156.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	26.9|26.9	4.783551|4.783551	0.90282|0.90282	.|.	.|.	ENSG00000162438|ENSG00000162438	ENST00000375949|ENST00000375943	D|.	0.97941|.	-4.62|.	4.91|4.91	4.91|4.91	0.64330|0.64330	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.85066|0.85066	0.5612|0.5612	M|M	0.91717|0.91717	3.235|3.235	0.42584|0.42584	D|D	0.993226|0.993226	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.91635|.	0.999;0.999|.	D|D	0.88780|0.88780	0.3270|0.3270	10|6	0.87932|0.87932	D|D	0|0	-50.5833|-50.5833	16.8963|16.8963	0.86101|0.86101	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	123;123|.	A8MTQ9;Q99895|.	.;CTRC_HUMAN|.	V|S	123|60	ENSP00000365116:A123V|.	ENSP00000365116:A123V|ENSP00000365110:P60S	A|P	+|+	2|1	0|0	CTRC|CTRC	15642512|15642512	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.693000|0.693000	0.40251|0.40251	7.562000|7.562000	0.82300|0.82300	2.576000|2.576000	0.86940|0.86940	0.549000|0.549000	0.68633|0.68633	GCC|CCC		TCGA-2L-AAQI-01A-12D-A397-08	CTRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006435.1	0	0	0	7	1218	0	299	0	9.970995e-01	0	1945	0	299	2		0	0	0	0	0	2	1	0.980062	7	1209	0	297	2		0	0	0	0	0	2	-2.555883	1	1	0	0		1	0	1	1	1.832690	1	0.290000	1.810000	0.182075	0.030000	1.000000e-02	0.070000	0.030000	0.038885	0.030000	0	0.010000	0.050000
NHLH1	4807	broad.mit.edu	37	1	160340909	160340909	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr1:160340909G>A	ENST00000302101.5	+	2	834	c.388G>A	c.(388-390)Gtg>Atg	p.V130M		NM_005598.3	NP_005589.1	Q02575	HEN1_HUMAN	nescient helix loop helix 1			7	all_cancers(52;7.11e-19)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)		CCTGAACCACGTGCTGGACGT	0.622000																								0							SO:0001583	missense			ENST00000302101.5	1	1	hg19	CCDS1204.1	.	.	.	.	.	.	.	.	.	.	G	15.52	2.857019	0.51376	.	.	ENSG00000171786	ENST00000302101	D	0.88509	-2.39	3.98	3.98	0.46160	Helix-loop-helix DNA-binding (3);	0.000000	0.49305	D	0.000146	T	0.73713	0.3622	L	0.47190	1.495	0.58432	D	0.999997	P	0.41569	0.755	B	0.21360	0.034	T	0.77838	-0.2439	10	0.33940	T	0.23	-29.3292	15.1633	0.72801	0.0:0.0:1.0:0.0	.	130	Q02575	HEN1_HUMAN	M	130	ENSP00000302189:V130M	ENSP00000302189:V130M	V	+	1	0	NHLH1	158607533	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.477000	0.73591	2.215000	0.71742	0.655000	0.94253	GTG		TCGA-2L-AAQI-01A-12D-A397-08	NHLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080676.1	1	0	1	48	278	0	61		0	0	0	0	61	2		0	0	0	0	0	2	1	1.000000	46	273	0	60	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	1	2	3	2.111475	0	0.290000	1.810000	0.301147	0.990000	7.800000e-01	1.000000	1.000000	0.966656	0.990000	1	0.900000	1.000000
OR2M2	391194	broad.mit.edu	37	1	248344094	248344094	+	Silent	SNP	G	G	A	rs140026971		TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr1:248344094G>A	ENST00000359682.2	+	1	807	c.807G>A	c.(805-807)acG>acA	p.T269T		NM_001004688.1	NP_001004688.1	Q96R28	OR2M2_HUMAN	olfactory receptor, family 2, subfamily M, member 2	p.T269T(1)		70	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)		ACTCCCCAACGCAGGACAAGA	0.502000																								1	Substitution - coding silent(1)						SO:0001819	synonymous_variant			ENST00000359682.2	1	1	hg19	CCDS31106.1																																																																																				TCGA-2L-AAQI-01A-12D-A397-08	OR2M2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097356.2	1	0	1	107	681	0	185		0	0	0	0	185	2		0	0	0	0	0	2	1	1.000000	103	676	0	188	2		0	0	0	0	0	2	-20.000000	1	1	121412	14	48	1	1	2	3	2.111475	0	0.290000	1.810000	0.301147	0.950000	7.900000e-01	1.000000	1.000000	0.943847	0.950000	1	0.860000	1.000000
DNMT3B	1789	broad.mit.edu	37	20	31388072	31388072	+	Missense_Mutation	SNP	G	G	A	rs77767360	by1000genomes	TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr20:31388072G>A	ENST00000328111.2	+	17	2194	c.1873G>A	c.(1873-1875)Gtg>Atg	p.V625M	DNMT3B_ENST00000348286.2_Missense_Mutation_p.V605M|DNMT3B_ENST00000353855.2_Missense_Mutation_p.V605M|DNMT3B_ENST00000375623.4_3'UTR|DNMT3B_ENST00000344505.4_Missense_Mutation_p.V605M|DNMT3B_ENST00000456297.2_Missense_Mutation_p.V529M|DNMT3B_ENST00000443239.3_Missense_Mutation_p.V563M|DNMT3B_ENST00000201963.3_Missense_Mutation_p.V617M	NM_006892.3	NP_008823.1	Q9UBC3	DNM3B_HUMAN	DNA (cytosine-5-)-methyltransferase 3 beta			39					TATCAAATACGTGAACGACGT	0.493000																								0							SO:0001583	missense			ENST00000328111.2	1	1	hg19	CCDS13205.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	G	23.1	4.372608	0.82573	.	.	ENSG00000088305	ENST00000328111;ENST00000353855;ENST00000348286;ENST00000443239;ENST00000456297;ENST00000344505;ENST00000201963	T;T;T;T;T;T;T	0.77750	-1.12;-1.12;-1.12;-1.12;-1.12;-1.12;-1.12	5.65	5.65	0.86999	.	0.058115	0.64402	D	0.000002	D	0.83133	0.5188	M	0.66439	2.03	0.80722	D	1	D;P;P;P;B;P;P	0.55800	0.973;0.952;0.909;0.778;0.435;0.491;0.689	P;P;P;B;B;B;P	0.51193	0.523;0.641;0.662;0.322;0.146;0.322;0.554	D	0.84179	0.0438	10	0.59425	D	0.04	-22.0454	19.0797	0.93177	0.0:0.0:1.0:0.0	.	529;563;324;617;605;605;625	E9PBF2;E7EN63;B3KM53;Q9UBC3-6;Q9UBC3-3;Q9UBC3-2;Q9UBC3	.;.;.;.;.;.;DNM3B_HUMAN	M	625;605;605;563;529;605;617	ENSP00000328547:V625M;ENSP00000313397:V605M;ENSP00000337764:V605M;ENSP00000403169:V563M;ENSP00000412305:V529M;ENSP00000345105:V605M;ENSP00000201963:V617M	ENSP00000201963:V617M	V	+	1	0	DNMT3B	30851733	1.000000	0.71417	0.951000	0.38953	0.794000	0.44872	7.973000	0.88032	2.810000	0.96702	0.650000	0.86243	GTG		TCGA-2L-AAQI-01A-12D-A397-08	DNMT3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078643.2	1	0	1	63	407	0	86	1	9.214169e-02	2	2	0	86	2		0	0	0	0	0	2	1	1.000000	63	404	0	85	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	0	0	0	2.025662	0	0.290000	1.810000	0.277427	0.900000	7.100000e-01	1.000000	1.000000	0.900503	0.900000	1	0.800000	1.000000
DNMT3B	1789	broad.mit.edu	37	20	31388677	31388677	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr20:31388677G>A	ENST00000328111.2	+	18	2263	c.1942G>A	c.(1942-1944)Gga>Aga	p.G648R	DNMT3B_ENST00000348286.2_Missense_Mutation_p.G628R|DNMT3B_ENST00000353855.2_Missense_Mutation_p.G628R|DNMT3B_ENST00000375623.4_3'UTR|DNMT3B_ENST00000344505.4_Missense_Mutation_p.G628R|DNMT3B_ENST00000456297.2_Missense_Mutation_p.G552R|DNMT3B_ENST00000443239.3_Missense_Mutation_p.G586R|DNMT3B_ENST00000201963.3_Missense_Mutation_p.G640R	NM_006892.3	NP_008823.1	Q9UBC3	DNM3B_HUMAN	DNA (cytosine-5-)-methyltransferase 3 beta			39					GGTGATTGGCGGAAGCCCATG	0.522000																								0							SO:0001583	missense			ENST00000328111.2	0	1	hg19	CCDS13205.1	.	.	.	.	.	.	.	.	.	.	G	36	5.691842	0.96793	.	.	ENSG00000088305	ENST00000328111;ENST00000353855;ENST00000348286;ENST00000443239;ENST00000456297;ENST00000344505;ENST00000201963	D;D;D;D;D;D;D	0.93547	-3.24;-3.24;-3.24;-3.24;-3.24;-3.24;-3.24	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	D	0.98172	0.9396	H	0.97635	4.045	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.997;1.0;1.0	D;D;D;D;D;D;D	0.97110	0.998;0.996;0.988;1.0;0.997;1.0;1.0	D	0.98850	1.0758	10	0.87932	D	0	-22.4387	19.2231	0.93806	0.0:0.0:1.0:0.0	.	552;586;347;640;628;628;648	E9PBF2;E7EN63;B3KM53;Q9UBC3-6;Q9UBC3-3;Q9UBC3-2;Q9UBC3	.;.;.;.;.;.;DNM3B_HUMAN	R	648;628;628;586;552;628;640	ENSP00000328547:G648R;ENSP00000313397:G628R;ENSP00000337764:G628R;ENSP00000403169:G586R;ENSP00000412305:G552R;ENSP00000345105:G628R;ENSP00000201963:G640R	ENSP00000201963:G640R	G	+	1	0	DNMT3B	30852338	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.779000	0.99018	2.885000	0.99019	0.655000	0.94253	GGA		TCGA-2L-AAQI-01A-12D-A397-08	DNMT3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078643.2	0	0	0	6	886	0	158	0	1.022059e-03	0	6	0	158	2	0	0	0	1	0	0	2	1	0.964161	5	880	0	157	2		0	0	0	0	0	2	-1.778336	0	1	0	0		1	0	0	0	2.025662	0	0.290000	1.810000	0.277427	0.040000	1.000000e-02	0.100000	0.040000	0.052940	0.040000	0	0.020000	0.070000
CDK5RAP1	51654	broad.mit.edu	37	20	31984682	31984682	+	Silent	SNP	C	C	T			TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr20:31984682C>T	ENST00000357886.4	-	2	342	c.189G>A	c.(187-189)ccG>ccA	p.P63P	CDK5RAP1_ENST00000339269.5_Silent_p.P63P|CDK5RAP1_ENST00000544843.1_Silent_p.P63P|CDK5RAP1_ENST00000477105.1_Intron|CDK5RAP1_ENST00000473997.1_5'UTR|CDK5RAP1_ENST00000346416.2_Silent_p.P63P			Q96SZ6	CK5P1_HUMAN	CDK5 regulatory subunit associated protein 1			26					GTTGAAAAGTCGGTCCAGCAG	0.517000																								0							SO:0001819	synonymous_variant			ENST00000357886.4	1	1	hg19																																																																																					TCGA-2L-AAQI-01A-12D-A397-08	CDK5RAP1-011	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000078697.1	1	0	1	65	329	0	76	1	8.959031e-01	6	16	0	76	2		0	0	0	0	0	2	1	1.000000	64	326	0	76	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	0	0	0	2.025662	0	0.290000	1.810000	0.277427	0.990000	8.800000e-01	1.000000	1.000000	0.989801	0.990000	1	0.990000	1.000000
CDH4	1002	broad.mit.edu	37	20	60503309	60503309	+	Silent	SNP	C	C	T			TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr20:60503309C>T	ENST00000360469.5	+	12	1921	c.1833C>T	c.(1831-1833)aaC>aaT	p.N611N	CDH4_ENST00000543233.1_Silent_p.N537N	NM_001794.3	NP_001785.2	P55283	CADH4_HUMAN	cadherin 4, type 1, R-cadherin (retinal)			74			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)		TCAACGACAACGCCCCTGAGC	0.627000																								0							SO:0001819	synonymous_variant			ENST00000360469.5	1	1	hg19	CCDS13488.1																																																																																				TCGA-2L-AAQI-01A-12D-A397-08	CDH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079965.2	0	0	0	110	879	1	204		0	0	0	1	204	2		0	0	0	0	0	2	1	1.000000	109	867	1	202	17		0	0	0	0	0	2	-20.000000	1	1	121404	2	38	1	0	0	0	2.025662	0	0.290000	1.810000	0.277427	0.740000	6.200000e-01	0.880000	0.750000	0.757018	0.740000	0	0.680000	0.820000
IKZF2	22807	broad.mit.edu	37	2	213872107	213872107	+	Nonsense_Mutation	SNP	G	G	A			TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr2:213872107G>A	ENST00000434687.1	-	9	1867	c.1558C>T	c.(1558-1560)Cga>Tga	p.R520*	IKZF2_ENST00000342002.2_Nonsense_Mutation_p.R526*|IKZF2_ENST00000374327.4_Nonsense_Mutation_p.R375*|IKZF2_ENST00000421754.2_Nonsense_Mutation_p.R446*|IKZF2_ENST00000374319.4_Nonsense_Mutation_p.R494*|IKZF2_ENST00000413091.3_3'UTR|AC079610.1_ENST00000415387.1_RNA|IKZF2_ENST00000451136.2_Nonsense_Mutation_p.R448*|IKZF2_ENST00000457361.1_Nonsense_Mutation_p.R520*			Q9UKS7	IKZF2_HUMAN	IKAROS family zinc finger 2 (Helios)			23		Esophageal squamous(248;0.0559)|Renal(323;0.218)			TGCTCCCCTCGAACAATGTGT	0.483000																								0							SO:0001587	stop_gained			ENST00000434687.1	0	1	hg19	CCDS2395.1	.	.	.	.	.	.	.	.	.	.	G	36	5.623235	0.96660	.	.	ENSG00000030419	ENST00000457361;ENST00000342002;ENST00000434687;ENST00000374319;ENST00000451136;ENST00000421754;ENST00000374327;ENST00000542010	.	.	.	5.67	5.67	0.87782	.	0.000000	0.53938	D	0.000060	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.7304	19.7738	0.96383	0.0:0.0:1.0:0.0	.	.	.	.	X	520;526;520;494;448;446;375;224	.	ENSP00000342876:R526X	R	-	1	2	IKZF2	213580352	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.894000	0.87336	2.672000	0.90937	0.655000	0.94253	CGA		TCGA-2L-AAQI-01A-12D-A397-08	IKZF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256593.3	1	0	1	35	269	0	69	1	5.360529e-01	4	11	0	69	2		0	0	0	0	0	2	1	1.000000	33	266	0	69	2		0	0	0	0	0	2	-3.142725	1	1	0	0		1	0	1	1	2.050658	0	0.290000	1.810000	0.287935	0.790000	5.600000e-01	1.000000	1.000000	0.798341	0.790000	0	0.670000	0.920000
UGT1A10	54575	broad.mit.edu	37	2	234545974	234545974	+	Missense_Mutation	SNP	T	T	G			TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr2:234545974T>G	ENST00000344644.5	+	1	875	c.806T>G	c.(805-807)aTg>aGg	p.M269R	UGT1A10_ENST00000373445.1_Missense_Mutation_p.M269R|UGT1A1_ENST00000373450.4_Intron	NM_019075.2	NP_061948.1	Q9HAW8	UD110_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A10			32		Breast(86;0.000766)|all_lung(227;0.00271)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0334)|Lung NSC(271;0.0461)|Lung SC(224;0.128)		Acetaminophen(DB00316)|Etodolac(DB00749)|Losartan(DB00678)|Mycophenolate mofetil(DB00688)|Valproic Acid(DB00313)	ATGCCCAACATGATCTTCATT	0.433000																								0							SO:0001583	missense			ENST00000344644.5	0	1	hg19	CCDS33403.1	.	.	.	.	.	.	.	.	.	.	T	16.17	3.046766	0.55110	.	.	ENSG00000242515	ENST00000344644;ENST00000373445	T;T	0.61859	0.07;0.07	3.56	3.56	0.40772	.	.	.	.	.	T	0.80869	0.4706	H	0.95816	3.725	0.36481	D	0.867853	D;D	0.61697	0.961;0.99	P;D	0.67725	0.908;0.953	D	0.88685	0.3205	9	0.87932	D	0	.	12.6049	0.56516	0.0:0.0:0.0:1.0	.	269;269	Q9HAW8;Q7Z6H8	UD110_HUMAN;.	R	269	ENSP00000343838:M269R;ENSP00000362544:M269R	ENSP00000343838:M269R	M	+	2	0	UGT1A10	234210713	1.000000	0.71417	0.996000	0.52242	0.924000	0.55760	4.888000	0.63164	1.632000	0.50472	0.333000	0.21579	ATG		TCGA-2L-AAQI-01A-12D-A397-08	UGT1A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130986.1	0	0	0	7	1213	0	235	1	6.652814e-01	10	367	0	235	2		0	0	0	0	0	2	1	0.980236	6	1208	0	234	2		0	0	0	0	0	2	-3.294109	1	0	0	0		1	0	1	1	2.050658	0	0.290000	1.810000	0.287935	0.030000	0	0.080000	0.040000	0.044967	0.030000	0	0.020000	0.060000
SLC6A1	6529	broad.mit.edu	37	3	11064024	11064024	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr3:11064024G>A	ENST00000287766.4	+	7	1005	c.584G>A	c.(583-585)cGc>cAc	p.R195H	SLC6A1_ENST00000536032.1_Missense_Mutation_p.R17H	NM_003042.3	NP_003033.3	P30531	SC6A1_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 1			26		Ovarian(110;0.0392)		Clobazam(DB00349)|Tiagabine(DB00906)	TTGACCAGGCGCAACATGCAT	0.597000																								0							SO:0001583	missense			ENST00000287766.4	0	1	hg19	CCDS2603.1	.	.	.	.	.	.	.	.	.	.	G	18.21	3.572459	0.65765	.	.	ENSG00000157103	ENST00000287766;ENST00000536032	T;T	0.77489	-1.1;-1.1	5.02	4.15	0.48705	.	0.074293	0.56097	N	0.000023	T	0.74876	0.3774	M	0.73372	2.23	0.80722	D	1	P	0.39665	0.682	B	0.35859	0.212	T	0.76699	-0.2863	10	0.48119	T	0.1	.	13.6297	0.62188	0.0746:0.0:0.9254:0.0	.	195	P30531	SC6A1_HUMAN	H	195;17	ENSP00000287766:R195H;ENSP00000445171:R17H	ENSP00000287766:R195H	R	+	2	0	SLC6A1	11039024	1.000000	0.71417	0.997000	0.53966	0.888000	0.51559	5.479000	0.66813	1.340000	0.45581	0.561000	0.74099	CGC		TCGA-2L-AAQI-01A-12D-A397-08	SLC6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102767.2	0	0	0	4	119	0	16	0	0	0	1	0	16	2		0	0	0	0	0	2	1	0.889680	4	118	0	16	2		0	0	0	0	0	2	-6.495645	1	1	121412	3	31	1	0	1	1	1.937603	0	0.290000	1.810000	0.239259	0.220000	7.000000e-02	0.480000	0.210000	0.250860	0.220000	0	0.130000	0.350000
PLA1A	51365	broad.mit.edu	37	3	119331938	119331938	+	Missense_Mutation	SNP	G	G	A	rs140761557		TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr3:119331938G>A	ENST00000273371.4	+	5	709	c.637G>A	c.(637-639)Gtg>Atg	p.V213M	PLA1A_ENST00000495992.1_Missense_Mutation_p.V197M|PLA1A_ENST00000488919.1_Missense_Mutation_p.V40M|PLA1A_ENST00000494440.1_Missense_Mutation_p.V197M	NM_015900.3	NP_056984.1	Q53H76	PLA1A_HUMAN	phospholipase A1 member A			30					TGCCCTCTTCGTGGAAGCCAT	0.592000																								0							SO:0001583	missense			ENST00000273371.4	0	0	hg19	CCDS2991.1	.	.	.	.	.	.	.	.	.	.	G	28.6	4.935632	0.92458	0.0	2.33E-4	ENSG00000144837	ENST00000273371;ENST00000488919;ENST00000495992;ENST00000494440;ENST00000475963	D;D;D;D;D	0.96104	-3.91;-3.91;-3.91;-3.91;-3.91	5.68	5.68	0.88126	Lipase, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.98729	0.9573	H	0.98133	4.155	0.53688	D	0.999979	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.99564	1.0969	10	0.87932	D	0	-15.9752	17.5869	0.87984	0.0:0.0:1.0:0.0	.	197;213	Q53H76-3;Q53H76	.;PLA1A_HUMAN	M	213;40;197;197;79	ENSP00000273371:V213M;ENSP00000420625:V40M;ENSP00000417326:V197M;ENSP00000418793:V197M;ENSP00000417295:V79M	ENSP00000273371:V213M	V	+	1	0	PLA1A	120814628	1.000000	0.71417	0.991000	0.47740	0.934000	0.57294	8.933000	0.92911	2.696000	0.92011	0.555000	0.69702	GTG		TCGA-2L-AAQI-01A-12D-A397-08	PLA1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355252.2	1	0	1	10	63	0	14	0	7.052286e-01	0	17	0	14	2		0	0	0	0	0	2	1	0.997377	9	63	0	14	2		0	0	0	0	0	2	-17.580930	1	0	121394	3	35	1	0	1	1	1.945308	0	0.290000	1.810000	0.241615	0.870000	4.600000e-01	1.000000	1.000000	0.843801	0.870000	1	0.650000	1.000000
KALRN	8997	broad.mit.edu	37	3	123813627	123813627	+	Translation_Start_Site	SNP	G	G	A			TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr3:123813627G>A	ENST00000240874.3	+	0	100				KALRN_ENST00000460856.1_De_novo_Start_InFrame|KALRN_ENST00000477496.1_3'UTR|KALRN_ENST00000360013.3_De_novo_Start_InFrame	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase			83					TCGAGTCAGCGGTGGTGGGAT	0.602000																								0											ENST00000240874.3	0	1	hg19	CCDS3027.1																																																																																				TCGA-2L-AAQI-01A-12D-A397-08	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	0	0	0	14	94	0	22		0	0	0	0	22	2	1	1	22	291	0	168	2	1	0.999798	13	93	0	21	2		0	0	0	0	0	2	-9.313086	1	1	0	0		1	0	1	1	1.945308	0	0.290000	1.810000	0.241615	0.830000	4.900000e-01	1.000000	1.000000	0.823900	0.830000	0	0.640000	1.000000
C3orf27	23434	broad.mit.edu	37	3	128292432	128292432	+	Silent	SNP	C	C	T			TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr3:128292432C>T	ENST00000356020.2	-	3	1107	c.141G>A	c.(139-141)aaG>aaA	p.K47K		NM_007354.2	NP_031380.1	O15544	GR6_HUMAN	chromosome 3 open reading frame 27			8					TGCCTAGAAGCTTCCAACCAC	0.627000																								0							SO:0001819	synonymous_variant			ENST00000356020.2	1	1	hg19	CCDS3050.1																																																																																				TCGA-2L-AAQI-01A-12D-A397-08	C3orf27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356924.1	1	0	1	35	212	0	43		0	0	0	0	43	2		0	0	0	0	0	2	1	1.000000	34	209	0	42	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	0	1	1	1.945308	0	0.290000	1.810000	0.241615	0.900000	6.500000e-01	1.000000	1.000000	0.894895	0.900000	1	0.770000	1.000000
MED12L	116931	broad.mit.edu	37	3	150908624	150908624	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr3:150908624G>A	ENST00000474524.1	+	13	1912	c.1874G>A	c.(1873-1875)gGa>gAa	p.G625E	RNA5SP145_ENST00000363124.1_RNA|MED12L_ENST00000273432.4_Missense_Mutation_p.G485E|MED12L_ENST00000309237.4_Missense_Mutation_p.G625E|MED12L_ENST00000422248.2_Missense_Mutation_p.G625E	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like			128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)		ATATCTCGAGGAGATTTGTCA	0.488000																								0							SO:0001583	missense			ENST00000474524.1	1	1	hg19	CCDS33876.1	.	.	.	.	.	.	.	.	.	.	G	31	5.068595	0.93950	.	.	ENSG00000144893	ENST00000422248;ENST00000309237;ENST00000474524;ENST00000273432	T;T;T;T	0.62639	0.01;0.01;0.01;0.01	5.57	5.57	0.84162	Mediator complex, subunit Med12, LCEWAV-domain (1);	0.000000	0.85682	D	0.000000	D	0.83408	0.5248	M	0.88775	2.98	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;0.999;0.999	D	0.85845	0.1400	10	0.87932	D	0	-16.4504	19.5175	0.95170	0.0:0.0:1.0:0.0	.	485;625;625;625	F8WAE6;Q86YW9;Q86YW9-2;Q86YW9-3	.;MD12L_HUMAN;.;.	E	625;625;625;485	ENSP00000403308:G625E;ENSP00000310760:G625E;ENSP00000417235:G625E;ENSP00000273432:G485E	ENSP00000273432:G485E	G	+	2	0	MED12L	152391314	1.000000	0.71417	0.793000	0.32043	0.899000	0.52679	8.888000	0.92464	2.780000	0.95670	0.655000	0.94253	GGA		TCGA-2L-AAQI-01A-12D-A397-08	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	1	0	1	29	221	0	45		0	0	0	0	45	2		0	0	0	0	0	2	1	1.000000	29	218	0	44	2		0	0	0	0	0	2	-3.318911	1	1	0	0		1	0	1	1	1.945308	0	0.290000	1.810000	0.241615	0.740000	5.100000e-01	1.000000	1.000000	0.756587	0.740000	0	0.620000	0.880000
FYCO1	79443	broad.mit.edu	37	3	46021250	46021250	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr3:46021250C>T	ENST00000296137.2	-	4	440	c.235G>A	c.(235-237)Gcc>Acc	p.A79T	FYCO1_ENST00000535325.1_Missense_Mutation_p.A79T	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1			54					TTCACCTTGGCCAGGCAGGCA	0.517000																								0							SO:0001583	missense			ENST00000296137.2	0	1	hg19	CCDS2734.1	.	.	.	.	.	.	.	.	.	.	C	31	5.075950	0.94000	.	.	ENSG00000163820	ENST00000296137;ENST00000535325	T;T	0.30182	1.54;1.54	5.6	5.6	0.85130	RUN (2);	0.000000	0.85682	D	0.000000	T	0.53029	0.1771	L	0.53249	1.67	0.53005	D	0.99996	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.996	T	0.52675	-0.8544	10	0.87932	D	0	-20.7471	17.7942	0.88565	0.0:1.0:0.0:0.0	.	79;79	B7ZKT7;Q9BQS8	.;FYCO1_HUMAN	T	79	ENSP00000296137:A79T;ENSP00000441178:A79T	ENSP00000296137:A79T	A	-	1	0	FYCO1	45996254	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.591000	0.61019	2.641000	0.89580	0.585000	0.79938	GCC		TCGA-2L-AAQI-01A-12D-A397-08	FYCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257320.2	0	0	0	5	412	1	76	0	2.130269e-02	0	15	1	76	2		0	0	0	0	0	2	0	0.004414	5	408	1	75	18		0	0	0	0	0	2	-2.380019	0	1	0	0		1	0	1	1	1.937603	0	0.290000	1.810000	0.239259	0.080000	2.000000e-02	0.170000	0.080000	0.091470	0.080000	0	0.040000	0.130000
CACNA2D3	55799	broad.mit.edu	37	3	54604065	54604065	+	Silent	SNP	C	C	T			TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr3:54604065C>T	ENST00000474759.1	+	8	870	c.822C>T	c.(820-822)atC>atT	p.I274I	CACNA2D3_ENST00000490478.1_Silent_p.I180I|CACNA2D3_ENST00000415676.2_Silent_p.I274I|CACNA2D3_ENST00000288197.5_Silent_p.I274I	NM_018398.2	NP_060868.2	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 3			59				Amlodipine(DB00381)|Nilvadipine(DB06712)|Spironolactone(DB00421)	GTCTGACTATCGCGAAGCAAA	0.463000																								0							SO:0001819	synonymous_variant			ENST00000474759.1	1	1	hg19	CCDS54598.1																																																																																				TCGA-2L-AAQI-01A-12D-A397-08	CACNA2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351402.1	1	0	1	91	584	0	136		0	0	0	0	136	2		0	0	0	0	0	2	1	1.000000	90	578	0	133	2		0	0	0	0	0	2	-3.221886	1	1	120940	7	39	1	0	1	1	1.945308	0	0.290000	1.810000	0.241615	0.860000	7.000000e-01	1.000000	1.000000	0.870389	0.860000	1	0.780000	0.950000
DIAPH1	1729	broad.mit.edu	37	5	140908065	140908065	+	Missense_Mutation	SNP	G	G	C			TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08			G	C	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr5:140908065G>C	ENST00000398557.4	-	23	3243	c.3103C>G	c.(3103-3105)Ctc>Gtc	p.L1035V	DIAPH1_ENST00000494967.1_5'Flank|DIAPH1_ENST00000389057.5_Missense_Mutation_p.L1026V|DIAPH1_ENST00000520569.1_Missense_Mutation_p.L978V|DIAPH1_ENST00000389054.3_Missense_Mutation_p.L1032V|DIAPH1_ENST00000398562.2_Missense_Mutation_p.L1011V|DIAPH1_ENST00000253811.6_Missense_Mutation_p.L1036V|DIAPH1_ENST00000518047.1_Missense_Mutation_p.L1023V|DIAPH1_ENST00000398566.3_Missense_Mutation_p.L1027V	NM_005219.4	NP_005210.3	O60610	DIAP1_HUMAN	diaphanous-related formin 1			23			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		GGAAACTTGAGGACATCGGGA	0.502000																								0							SO:0001583	missense			ENST00000398557.4	1	1	hg19	CCDS43374.1	.	.	.	.	.	.	.	.	.	.	G	15.51	2.855978	0.51376	.	.	ENSG00000131504	ENST00000389054;ENST00000520569;ENST00000398562;ENST00000389057;ENST00000398566;ENST00000398557;ENST00000253811;ENST00000518047	T;T;T;T;T;T;T;T	0.66638	-0.22;-0.22;-0.22;-0.22;-0.22;-0.22;-0.22;-0.22	5.66	5.66	0.87406	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.072630	0.56097	D	0.000032	T	0.64821	0.2633	M	0.67625	2.065	0.47183	D	0.999347	P;P;P	0.48503	0.911;0.604;0.604	B;B;B	0.40677	0.337;0.239;0.239	T	0.70927	-0.4739	10	0.72032	D	0.01	.	12.6178	0.56586	0.0798:0.0:0.9202:0.0	.	978;1026;1035	E7ERW8;E9PEZ2;O60610	.;.;DIAP1_HUMAN	V	1032;978;1011;1026;1027;1035;1036;1023	ENSP00000373706:L1032V;ENSP00000429282:L978V;ENSP00000381570:L1011V;ENSP00000373709:L1026V;ENSP00000381572:L1027V;ENSP00000381565:L1035V;ENSP00000253811:L1036V;ENSP00000428268:L1023V	ENSP00000253811:L1036V	L	-	1	0	DIAPH1	140888249	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.449000	0.35123	2.672000	0.90937	0.467000	0.42956	CTC		TCGA-2L-AAQI-01A-12D-A397-08	DIAPH1-203	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		1	0	1	36	216	0	56	1	1	89	161	0	56	2		0	0	0	0	0	2	1	1.000000	34	214	0	56	2		0	0	0	0	0	2	-3.080585	1	1	0	0		1	1	2	3	2.108194	0	0.290000	1.810000	0.300148	0.990000	7.200000e-01	1.000000	1.000000	0.948427	0.990000	1	0.860000	1.000000
NDST1	3340	broad.mit.edu	37	5	149907823	149907823	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr5:149907823G>A	ENST00000261797.6	+	3	1473	c.971G>A	c.(970-972)gGc>gAc	p.G324D	NDST1_ENST00000523767.1_Missense_Mutation_p.G324D	NM_001543.4	NP_001534.1	P52848	NDST1_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1			34		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		ATCTTCGTGGGCAAGGAGGGC	0.612000																								0							SO:0001583	missense			ENST00000261797.6	0	1	hg19	CCDS34277.1	.	.	.	.	.	.	.	.	.	.	G	28.9	4.956426	0.92726	.	.	ENSG00000070614	ENST00000523767;ENST00000261797	T;T	0.56103	0.48;0.75	5.04	5.04	0.67666	.	0.000000	0.85682	D	0.000000	T	0.79997	0.4543	M	0.92367	3.3	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.85347	0.1099	10	0.87932	D	0	.	18.7565	0.91835	0.0:0.0:1.0:0.0	.	324;324;324	E7EVJ3;P52848-2;P52848	.;.;NDST1_HUMAN	D	324	ENSP00000428604:G324D;ENSP00000261797:G324D	ENSP00000261797:G324D	G	+	2	0	NDST1	149888016	1.000000	0.71417	1.000000	0.80357	0.875000	0.50365	9.676000	0.98643	2.494000	0.84150	0.555000	0.69702	GGC		TCGA-2L-AAQI-01A-12D-A397-08	NDST1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374314.2	0	0	0	5	346	0	77	0	1.535150e-01	0	40	0	77	2		0	0	0	0	0	2	1	0.936556	6	342	0	76	2		0	0	0	0	0	2	-3.238259	1	1	0	0		1	1	2	3	2.108194	0	0.290000	1.810000	0.300148	0.110000	3.000000e-02	1.000000	0.100000	0.189479	0.110000	0	0.060000	0.190000
ADAMTS12	81792	broad.mit.edu	37	5	33683131	33683131	+	Nonsense_Mutation	SNP	C	C	A			TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr5:33683131C>A	ENST00000504830.1	-	5	1242	c.907G>T	c.(907-909)Gaa>Taa	p.E303*	ADAMTS12_ENST00000352040.3_Nonsense_Mutation_p.E303*|ADAMTS12_ENST00000504582.1_5'UTR	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12			216					ACCTCTTCTTCTTCGAGTAGA	0.428000										HNSCC(64;0.19)														0							SO:0001587	stop_gained			ENST00000504830.1	0	1	hg19	CCDS34140.1	.	.	.	.	.	.	.	.	.	.	C	42	9.642714	0.99227	.	.	ENSG00000151388	ENST00000504830;ENST00000352040	.	.	.	5.56	5.56	0.83823	.	0.050809	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.30854	T	0.27	.	19.5316	0.95231	0.0:1.0:0.0:0.0	.	.	.	.	X	303	.	ENSP00000344847:E303X	E	-	1	0	ADAMTS12	33718888	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	4.574000	0.60900	2.615000	0.88500	0.637000	0.83480	GAA		TCGA-2L-AAQI-01A-12D-A397-08	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	1	0	1	23	152	0	52	0	2.448155e-01	0	7	0	52	2		0	0	0	0	0	2	1	1.000000	23	150	0	52	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	0	1	1	1.801161	1	0.290000	1.810000	0.172398	0.750000	5.000000e-01	0.980000	0.760000	0.760823	0.750000	0	0.620000	0.890000
KDM1B	221656	broad.mit.edu	37	6	18171668	18171668	+	Silent	SNP	C	C	T			TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr6:18171668C>T	ENST00000297792.5	+	7	669	c.492C>T	c.(490-492)gcC>gcT	p.A164A	KDM1B_ENST00000397244.1_Silent_p.A164A|KDM1B_ENST00000388870.2_Silent_p.A164A|KDM1B_ENST00000546309.2_Intron			Q8NB78	KDM1B_HUMAN	lysine (K)-specific demethylase 1B			25					CACAGATAGCCAAGACTTATC	0.363000																								0							SO:0001819	synonymous_variant			ENST00000297792.5	1	1	hg19	CCDS34343.1																																																																																				TCGA-2L-AAQI-01A-12D-A397-08	KDM1B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277080.1	1	0	0	14	287	0	60	0	1.360359e-01	1	12	0	60	2		0	0	0	0	0	2	1	0.999773	14	287	0	60	2		0	0	0	0	0	2	-4.463510	1	1	121412	1	30	1	0	0	0	1.793805	1	0.290000	1.810000	0.183439	0.280000	1.600000e-01	0.440000	0.270000	0.292483	0.280000	0	0.210000	0.360000
RNF39	80352	broad.mit.edu	37	6	30043491	30043491	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr6:30043491C>T	ENST00000244360.6	-	1	173	c.76G>A	c.(76-78)Gca>Aca	p.A26T	RNF39_ENST00000376751.3_Missense_Mutation_p.A26T	NM_025236.3	NP_079512.2	Q9H2S5	RNF39_HUMAN	ring finger protein 39								TTAACTTTTGCCGCTTTCCGC	0.602000													NSCLC(8;188 360 1520 20207 31481)											0							SO:0001583	missense			ENST00000244360.6	0	1	hg19	CCDS4673.1	.	.	.	.	.	.	.	.	.	.	c	17.05	3.290422	0.59976	.	.	ENSG00000204618	ENST00000376751;ENST00000244360;ENST00000376746	T;T	0.70749	-0.03;-0.51	3.51	0.223	0.15292	.	.	.	.	.	T	0.23492	0.0568	N	0.08118	0	0.09310	N	1	B;B	0.10296	0.002;0.003	B;B	0.09377	0.002;0.004	T	0.17137	-1.0379	9	0.66056	D	0.02	.	2.3362	0.04248	0.1257:0.4139:0.293:0.1674	.	26;26	Q9H2S5;Q9H2S5-2	RNF39_HUMAN;.	T	26	ENSP00000365942:A26T;ENSP00000244360:A26T	ENSP00000244360:A26T	A	-	1	0	RNF39	30151470	0.000000	0.05858	0.000000	0.03702	0.834000	0.47266	-0.148000	0.10219	0.251000	0.21505	0.436000	0.28706	GCA		TCGA-2L-AAQI-01A-12D-A397-08	RNF39-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076625.3	0	0	0	5	395	1	76	0	5.794897e-03	0	22	1	76	3		0	0	0	0	0	2	0	0.004537	5	393	1	76	18		0	0	0	0	0	2	-2.298958	0	1	0	0		1	0	0	0	1.966235	0	0.290000	1.810000	0.255453	0.080000	2.000000e-02	0.180000	0.080000	0.097446	0.080000	0	0.050000	0.130000
KHDRBS2	202559	broad.mit.edu	37	6	62887161	62887161	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr6:62887161G>A	ENST00000281156.4	-	2	426	c.148C>T	c.(148-150)Ctt>Ttt	p.L50F		NM_152688.2	NP_689901.2	Q5VWX1	KHDR2_HUMAN	KH domain containing, RNA binding, signal transduction associated 2			49					ATGACATCAAGATACTTCTTT	0.338000																								0							SO:0001583	missense			ENST00000281156.4	1	1	hg19	CCDS4963.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.174934	0.78564	.	.	ENSG00000112232	ENST00000281156;ENST00000539571	T	0.16324	2.35	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	T	0.16938	0.0407	L	0.56769	1.78	0.80722	D	1	P	0.52842	0.956	P	0.50754	0.649	T	0.00708	-1.1600	10	0.62326	D	0.03	-4.1269	11.3289	0.49465	0.0836:0.0:0.9164:0.0	.	50	Q5VWX1	KHDR2_HUMAN	F	50	ENSP00000281156:L50F	ENSP00000281156:L50F	L	-	1	0	KHDRBS2	62945120	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	6.320000	0.72876	2.447000	0.82792	0.460000	0.39030	CTT		TCGA-2L-AAQI-01A-12D-A397-08	KHDRBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041066.2	1	0	0	17	163	0	29		0	0	0	0	29	2		0	0	0	0	0	2	1	0.999972	17	163	0	29	2		0	0	0	0	0	2	-19.999940	1	1	0	0		1	0	0	0	1.804514	1	0.290000	1.810000	0.188850	0.560000	3.400000e-01	0.840000	0.560000	0.582659	0.560000	0	0.440000	0.710000
MOSPD3	64598	broad.mit.edu	37	7	100212491	100212491	+	Splice_Site	SNP	C	C	T			TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr7:100212491C>T	ENST00000393950.2	+	4	795	c.513C>T	c.(511-513)caC>caT	p.H171H	MOSPD3_ENST00000223054.4_Splice_Site_p.H171H|MOSPD3_ENST00000379527.2_Splice_Site_p.H171H|MOSPD3_ENST00000424091.2_Splice_Site_p.H161H	NM_023948.4	NP_076438.1	O75425	MSPD3_HUMAN	motile sperm domain containing 3			16	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)				GTTTCTCAGACCCCCGCCAGC	0.577000																								0							SO:0001630	splice_region_variant			ENST00000393950.2	1	0	hg19	CCDS5701.1																																																																																				TCGA-2L-AAQI-01A-12D-A397-08	MOSPD3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356395.1	0	0	1	27	191	0	37	1	9.997950e-01	19	78	0	37	2		0	0	0	0	0	2	1	1.000000	28	189	0	35	2		0	0	0	0	0	2	-13.122940	1	1	0	0		1	1	2	3	2.088405	0	0.290000	1.810000	0.297134	0.870000	5.900000e-01	1.000000	1.000000	0.864698	0.870000	1	0.720000	1.000000
SLC13A1	6561	broad.mit.edu	37	7	122821122	122821122	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr7:122821122C>T	ENST00000194130.2	-	2	172	c.133G>A	c.(133-135)Gcc>Acc	p.A45T	SLC13A1_ENST00000539873.1_5'UTR	NM_022444.3	NP_071889.2	Q9BZW2	S13A1_HUMAN	solute carrier family 13 (sodium/sulfate symporter), member 1			45				Succinic acid(DB00139)	CAAAATGTGGCGACCACAAAG	0.428000																								0							SO:0001583	missense			ENST00000194130.2	0	1	hg19	CCDS5786.1	2	9.157509157509158E-4	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	0	0.0	C	21.0	4.089751	0.76756	.	.	ENSG00000081800	ENST00000194130	T	0.03212	4.01	6.16	6.16	0.99307	.	0.047300	0.85682	D	0.000000	T	0.25344	0.0616	M	0.92169	3.28	0.80722	D	1	D	0.76494	0.999	P	0.61658	0.892	T	0.02226	-1.1192	10	0.59425	D	0.04	.	19.848	0.96722	0.0:1.0:0.0:0.0	.	45	Q9BZW2	S13A1_HUMAN	T	45	ENSP00000194130:A45T	ENSP00000194130:A45T	A	-	1	0	SLC13A1	122608358	1.000000	0.71417	0.094000	0.20943	0.191000	0.23601	7.258000	0.78371	2.937000	0.99478	0.650000	0.86243	GCC		TCGA-2L-AAQI-01A-12D-A397-08	SLC13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347404.1	0	0	0	4	196	1	30		0	0	0	1	30	2		0	0	0	0	0	2	0	0.000534	4	196	1	30	20		0	0	0	0	0	2	-3.140462	1	1	121406	66	48	1	1	2	3	2.088405	0	0.290000	1.810000	0.297134	0.160000	5.000000e-02	1.000000	0.140000	0.216659	0.160000	0	0.090000	0.270000
DGKI	9162	broad.mit.edu	37	7	137148251	137148251	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr7:137148251G>A	ENST00000288490.5	-	28	2743	c.2743C>T	c.(2743-2745)Cac>Tac	p.H915Y	DGKI_ENST00000424189.2_Missense_Mutation_p.H928Y|DGKI_ENST00000446122.1_Missense_Mutation_p.H897Y|DGKI_ENST00000453654.2_Intron	NM_004717.2	NP_004708.1	O75912	DGKI_HUMAN	diacylglycerol kinase, iota			84					ACGCGGGAGTGGCTGAGATCT	0.537000																								0							SO:0001583	missense			ENST00000288490.5	1	1	hg19	CCDS5845.1	.	.	.	.	.	.	.	.	.	.	G	14.71	2.617440	0.46736	.	.	ENSG00000157680	ENST00000424189;ENST00000288490;ENST00000446122	T;T	0.34472	1.36;1.56	5.91	5.91	0.95273	.	1.734970	0.02527	N	0.093160	T	0.28300	0.0699	N	0.08118	0	0.42635	D	0.993395	B	0.27882	0.192	B	0.19666	0.026	T	0.07635	-1.0762	10	0.23302	T	0.38	.	18.4769	0.90797	0.0:0.0:1.0:0.0	.	915	O75912	DGKI_HUMAN	Y	918;915;897	ENSP00000288490:H915Y;ENSP00000399131:H897Y	ENSP00000288490:H915Y	H	-	1	0	DGKI	136798791	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.461000	0.60115	2.813000	0.96785	0.655000	0.94253	CAC		TCGA-2L-AAQI-01A-12D-A397-08	DGKI-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341286.3	0	0	1	46	226	0	47	0	0	0	1	0	47	2		0	0	0	0	0	2	1	1.000000	46	226	0	46	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	1	2	3	2.088405	0	0.290000	1.810000	0.297134	0.990000	8.900000e-01	1.000000	1.000000	0.992536	0.990000	1	0.990000	1.000000
POM121L12	285877	broad.mit.edu	37	7	53103442	53103442	+	Silent	SNP	C	C	T			TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr7:53103442C>T	ENST00000408890.4	+	1	94	c.78C>T	c.(76-78)ccC>ccT	p.P26P		NM_182595.3	NP_872401.3	Q8N7R1	P1L12_HUMAN	POM121 transmembrane nucleoporin-like 12			61					TGCAAGGCCCCGACGCCCTGG	0.706000																								0							SO:0001819	synonymous_variant			ENST00000408890.4	1	1	hg19	CCDS43584.1																																																																																				TCGA-2L-AAQI-01A-12D-A397-08	POM121L12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342656.1	1	0	1	20	118	0	24		0	0	0	0	24	2		0	0	0	0	0	2	1	0.999996	19	116	0	23	2		0	0	0	0	0	2	-20.000000	1	1	120836	3	32	1	1	2	3	2.087798	0	0.290000	1.810000	0.297134	0.990000	6.500000e-01	1.000000	1.000000	0.935408	0.990000	1	0.820000	1.000000
RP1L1	94137	broad.mit.edu	37	8	10470671	10470671	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr8:10470671C>T	ENST00000382483.3	-	4	1160	c.937G>A	c.(937-939)Gtc>Atc	p.V313I		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1			148					TTCATGCGGACCTTCTTCTTC	0.657000																								0							SO:0001583	missense			ENST00000382483.3	1	1	hg19	CCDS43708.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.611972	0.87258	.	.	ENSG00000183638	ENST00000382483	T	0.08008	3.14	4.82	3.95	0.45737	.	0.000000	0.30611	U	0.009248	T	0.16599	0.0399	L	0.28504	0.86	0.38893	D	0.957152	D	0.76494	0.999	D	0.78314	0.991	T	0.03453	-1.1035	10	0.44086	T	0.13	-19.7106	12.3052	0.54898	0.0:0.9179:0.0:0.0821	.	313	A6NKC6	.	I	313	ENSP00000371923:V313I	ENSP00000371923:V313I	V	-	1	0	RP1L1	10508081	1.000000	0.71417	0.907000	0.35723	0.945000	0.59286	3.069000	0.50026	1.254000	0.44035	0.591000	0.81541	GTC		TCGA-2L-AAQI-01A-12D-A397-08	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1	0	0	1	80	472	0	145		0	0	0	0	145	2		0	0	0	0	0	2	1	1.000000	80	467	0	144	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	0	1	1	1.834669	1	0.290000	1.810000	0.176573	0.850000	6.900000e-01	1.000000	1.000000	0.856498	0.850000	1	0.760000	0.940000
COL22A1	169044	broad.mit.edu	37	8	139890170	139890170	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr8:139890170C>T	ENST00000303045.6	-	3	927	c.481G>A	c.(481-483)Gcc>Acc	p.A161T	COL22A1_ENST00000435777.1_Missense_Mutation_p.A161T	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1			211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)		GCCGCCGCGGCGTCCAGCACC	0.716000										HNSCC(7;0.00092)														0							SO:0001583	missense			ENST00000303045.6	0	1	hg19	CCDS6376.1	.	.	.	.	.	.	.	.	.	.	C	19.66	3.868949	0.72065	.	.	ENSG00000169436	ENST00000303045;ENST00000435777;ENST00000545577	T;T	0.80214	-1.35;-1.35	5.3	5.3	0.74995	von Willebrand factor, type A (3);	0.283582	0.24727	N	0.036088	D	0.86863	0.6035	M	0.79693	2.465	0.26563	N	0.973692	D	0.67145	0.996	P	0.55965	0.788	T	0.82043	-0.0653	9	.	.	.	.	13.0527	0.58964	0.0:0.727:0.273:0.0	.	161	Q8NFW1	COMA1_HUMAN	T	161	ENSP00000303153:A161T;ENSP00000387655:A161T	.	A	-	1	0	COL22A1	139959352	0.996000	0.38824	0.927000	0.36925	0.876000	0.50452	2.403000	0.44530	2.446000	0.82766	0.655000	0.94253	GCC		TCGA-2L-AAQI-01A-12D-A397-08	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	1	0	0	11	72	0	13	0	0	0	1	0	13	2		0	0	0	0	0	2	1	0.998720	11	72	0	12	2		0	0	0	0	0	2	-19.199840	1	1	0	0		1	0	1	1	2.050710	0	0.290000	1.810000	0.287935	0.910000	5.000000e-01	1.000000	1.000000	0.867553	0.910000	1	0.680000	1.000000
OPLAH	26873	broad.mit.edu	37	8	145109606	145109606	+	Silent	SNP	G	G	A			TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr8:145109606G>A	ENST00000426825.1	-	19	2625	c.2544C>T	c.(2542-2544)ttC>ttT	p.F848F	OPLAH_ENST00000534424.1_5'UTR	NM_017570.3	NP_060040.1	O14841	OPLA_HUMAN	5-oxoprolinase (ATP-hydrolysing)			20	all_cancers(97;1.06e-10)|all_epithelial(106;1.5e-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;2.24e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)		TGGCCACATAGAACACAGGCC	0.667000																								0							SO:0001819	synonymous_variant			ENST00000426825.1	0	1	hg19																																																																																					TCGA-2L-AAQI-01A-12D-A397-08	OPLAH-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		1	0	0	29	203	0	63	1	8.745939e-01	9	19	0	63	2		0	0	0	0	0	2	1	1.000000	29	199	0	61	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	0	1	1	2.050710	0	0.290000	1.810000	0.287935	0.850000	5.900000e-01	1.000000	1.000000	0.854686	0.850000	1	0.710000	1.000000
OR1L4	254973	broad.mit.edu	37	9	125486817	125486817	+	Missense_Mutation	SNP	G	G	T			TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr9:125486817G>T	ENST00000259466.1	+	1	549	c.549G>T	c.(547-549)caG>caT	p.Q183H		NM_001005235.1	NP_001005235.1	Q8NGR5	OR1L4_HUMAN	olfactory receptor, family 1, subfamily L, member 4			20					GTGACACCCAGCCTGTGCTAA	0.512000																								0							SO:0001583	missense			ENST00000259466.1	0	1	hg19	CCDS35129.1	.	.	.	.	.	.	.	.	.	.	.	4.362	0.066629	0.08388	.	.	ENSG00000136939	ENST00000259466	T	0.00107	8.72	4.01	1.57	0.23409	GPCR, rhodopsin-like superfamily (1);	0.301605	0.24571	N	0.037392	T	0.00073	0.0002	N	0.02685	-0.53	0.29480	N	0.856427	B	0.16802	0.019	B	0.19666	0.026	T	0.03957	-1.0989	10	0.52906	T	0.07	-5.0755	6.7183	0.23316	0.4843:0.0:0.5157:0.0	.	183	Q8NGR5	OR1L4_HUMAN	H	183	ENSP00000259466:Q183H	ENSP00000259466:Q183H	Q	+	3	2	OR1L4	124526638	0.000000	0.05858	1.000000	0.80357	0.932000	0.56968	-2.347000	0.01095	0.279000	0.22186	0.298000	0.19748	CAG		TCGA-2L-AAQI-01A-12D-A397-08	OR1L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053951.1	0	0	0	7	841	0	226		0	0	0	0	226	2		0	0	0	0	0	2	1	0.969928	7	740	0	303	2		0	0	0	0	0	2	-3.016504	1	1	0	0		1	0	1	1	1.786389	1	0.290000	1.810000	0.169591	0.040000	1.000000e-02	0.100000	0.050000	0.055168	0.040000	0	0.030000	0.070000
SLC34A3	142680	broad.mit.edu	37	9	140130438	140130438	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chr9:140130438G>A	ENST00000538474.1	+	13	1594	c.1370G>A	c.(1369-1371)gGc>gAc	p.G457D	SLC34A3_ENST00000361134.2_Missense_Mutation_p.G457D	NM_001177316.1|NM_001177317.1	NP_001170787|NP_001170788	Q8N130	NPT2C_HUMAN	solute carrier family 34 (type II sodium/phosphate contransporter), member 3			13	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)		AACCTGGCCGGCATCCTGCTG	0.711000											OREG0019630	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)												0							SO:0001583	missense			ENST00000538474.1	0	1	hg19	CCDS7038.1	.	.	.	.	.	.	.	.	.	.	G	19.82	3.898756	0.72639	.	.	ENSG00000198569	ENST00000538474;ENST00000361134	D;D	0.92858	-3.12;-3.12	4.11	4.11	0.48088	.	0.101834	0.41097	D	0.000960	D	0.96706	0.8925	M	0.92412	3.305	0.51482	D	0.999923	D	0.89917	1.0	D	0.83275	0.996	D	0.97453	1.0029	10	0.87932	D	0	-19.2077	14.2126	0.65773	0.0:0.0:1.0:0.0	.	457	Q8N130	NPT2C_HUMAN	D	457	ENSP00000442397:G457D;ENSP00000355353:G457D	ENSP00000355353:G457D	G	+	2	0	SLC34A3	139250259	1.000000	0.71417	0.991000	0.47740	0.656000	0.38851	7.332000	0.79203	2.304000	0.77564	0.407000	0.27541	GGC		TCGA-2L-AAQI-01A-12D-A397-08	SLC34A3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254712.1	0	0	0	5	489	0	105	0	0	0	1	0	105	2		0	0	0	0	0	2	1	0.934066	5	478	0	101	2		0	0	0	0	0	2	-2.174522	0	1	0	0		1	0	1	1	1.786389	1	0.290000	1.810000	0.169591	0.060000	2.000000e-02	0.130000	0.060000	0.070616	0.060000	0	0.030000	0.100000
KDM6A	7403	broad.mit.edu	37	X	44879977	44879977	+	Splice_Site	SNP	T	T	A			TCGA-2L-AAQI-01A-12D-A397-08	TCGA-2L-AAQI-11A-11D-A39A-08			T	A	T	T		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	bc207a75-c45b-4259-9ab1-568b3669cba7	37e90c67-83cb-401d-aca4-4500866ffa52	g.chrX:44879977T>A	ENST00000377967.4	+	6	605		c.e6+2		KDM6A_ENST00000536777.1_Splice_Site|KDM6A_ENST00000382899.4_Splice_Site|KDM6A_ENST00000543216.1_Splice_Site	NM_021140.2	NP_066963.2	O15550	KDM6A_HUMAN	lysine (K)-specific demethylase 6A	p.0(12)|p.0?(6)|p.?(1)		170					AGTTTAAAGGTAGGTTGTTGG	0.318000			D, N, F, S		renal, oesophageal SCC, MM								Colon(129;1273 1667 15230 27352 52914)		Rec	yes		X	Xp11.2	7403	lysine (K)-specific demethylase 6A, UTX		E, L	19	No detectable mRNA/protein(12)|Whole gene deletion(6)|Unknown(1)						SO:0001630	splice_region_variant			ENST00000377967.4	1	1	hg19	CCDS14265.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.145474	0.77888	.	.	ENSG00000147050	ENST00000377967;ENST00000536777;ENST00000382899;ENST00000543216;ENST00000542299	.	.	.	5.58	5.58	0.84498	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.9212	0.70838	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	KDM6A	44764921	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.392000	0.66272	1.973000	0.57446	0.486000	0.48141	.		TCGA-2L-AAQI-01A-12D-A397-08	KDM6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056324.1	1	0	1	85	281	0	78		0	0	0	0	78	2	1	1	33	118	0	68	2	1	1.000000	84	278	0	78	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	0	1	1			0.290000	1.810000	0.290000	0.790000	6.500000e-01	0.940000	0.800000	0.799209	0.790000	0	0.710000	0.870000
