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
FLVCR1	28982	broad.mit.edu	37	1	213061902	213061903	+	Frame_Shift_Ins	INS	-	-	TACT			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr1:213061902_213061903insTACT	ENST00000366971.4	+	7	1577_1578	c.1379_1380insTACT	c.(1378-1383)ggtactfs	p.-461fs	FLVCR1_ENST00000483790.1_3'UTR	NM_014053.3	NP_054772.1	Q9Y5Y0	FLVC1_HUMAN	feline leukemia virus subgroup C cellular receptor 1			12					GAATCTGAAGGTACTTCATCTG	0.361000													Esophageal Squamous(199;2235 2952 19233 26256)											0							SO:0001589	frameshift_variant			ENST00000366971.4	0	1	hg19	CCDS1510.1																																																																																				TCGA-3A-A9IU-01A-11D-A397-08	FLVCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089678.2	1	0	0	63	509	0	64	0	4.713168e-01	0	14	0	64	2			0	0	0	0		1	1	75	506	0	64	2	0	0	0	0	0	0		-2.665581	1	1	0	0		1	1	2	3	2.627803	1	0.580000	1.910000	0.672948	0.480000	3.700000e-01	0.630000	0.480000	0.498290	0.480000	0	4.200000e-01	0.550000
ARHGAP21	57584	broad.mit.edu	37	10	24874291	24874291	+	Missense_Mutation	SNP	C	C	T	rs1143061		TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr10:24874291C>T	ENST00000396432.2	-	26	5413	c.4927G>A	c.(4927-4929)Gtg>Atg	p.V1643M		NM_020824.3	NP_065875.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21			78					GTGGGGAACACGGGAAACTCG	0.532000																								0							SO:0001583	missense			ENST00000396432.2	0	1	hg19	CCDS7144.2	.	.	.	.	.	.	.	.	.	.	C	3.155	-0.173447	0.06421	.	.	ENSG00000107863	ENST00000396432;ENST00000447364	T	0.13901	2.55	5.19	-0.0832	0.13695	.	0.329273	0.31797	N	0.007043	T	0.07999	0.0200	L	0.55834	1.745	0.22754	N	0.998774	P	0.39352	0.669	B	0.27076	0.076	T	0.25117	-1.0141	10	0.46703	T	0.11	.	1.9574	0.03379	0.1301:0.4116:0.2524:0.206	rs1143061;rs3206462	1642	Q5T5U3	RHG21_HUMAN	M	1643;1092	ENSP00000379709:V1643M	ENSP00000379709:V1643M	V	-	1	0	ARHGAP21	24914297	0.810000	0.29049	0.000000	0.03702	0.007000	0.05969	1.633000	0.37113	-0.062000	0.13088	-0.974000	0.02594	GTG		TCGA-3A-A9IU-01A-11D-A397-08	ARHGAP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047229.4	0	0	0	9	355	0	64	1	6.638481e-01	3	85	0	64	2		0	0	0	0	0	2	1	9.940669e-01	9	351	0	67	2		0	0	0	0	0	2	-3.200000	1	1	121412	1	30	1	0	1	1	1.504508	1	0.580000	1.910000	0.413244	0.050000	2.000000e-02	0.110000	0.060000	0.067177	0.050000	0	4.000000e-02	0.090000
PTPRJ	5795	broad.mit.edu	37	11	48186036	48186036	+	Missense_Mutation	SNP	G	G	T			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr11:48186036G>T	ENST00000418331.2	+	24	4176	c.3824G>T	c.(3823-3825)cGa>cTa	p.R1275L		NM_002843.3	NP_002834.3	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J			52					TATGACCTTCGAATGCATAGG	0.428000																								0							SO:0001583	missense			ENST00000418331.2	0	1	hg19	CCDS7945.1	.	.	.	.	.	.	.	.	.	.	G	29.1	4.976142	0.92982	.	.	ENSG00000149177	ENST00000418331	D	0.91521	-2.86	4.53	4.53	0.55603	Protein-tyrosine phosphatase, receptor/non-receptor type (4);Protein-tyrosine/Dual-specificity phosphatase (1);	.	.	.	.	D	0.97114	0.9057	H	0.98218	4.175	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98523	1.0624	9	0.87932	D	0	.	15.133	0.72539	0.0:0.0:1.0:0.0	.	1275	Q12913	PTPRJ_HUMAN	L	1275	ENSP00000400010:R1275L	ENSP00000400010:R1275L	R	+	2	0	PTPRJ	48142612	1.000000	0.71417	0.885000	0.34714	0.992000	0.81027	9.735000	0.98825	2.237000	0.73441	0.650000	0.86243	CGA		TCGA-3A-A9IU-01A-11D-A397-08	PTPRJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390525.1	0	0	0	4	259	0	33	0	1.351853e-01	0	33	0	33	2		0	0	0	0	0	2	1	8.777365e-01	4	245	0	32	2		0	0	0	0	0	2	-2.903911	1	1	0	0		1	1	2	3	2.062343	0	0.580000	1.910000	0.581214	0.050000	1.000000e-02	0.130000	0.060000	0.064980	0.050000	0	3.000000e-02	0.090000
ARAP1	116985	broad.mit.edu	37	11	72408662	72408662	+	Missense_Mutation	SNP	C	C	T			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr11:72408662C>T	ENST00000393609.3	-	20	2972	c.2770G>A	c.(2770-2772)Gtg>Atg	p.V924M	ARAP1_ENST00000429686.1_Missense_Mutation_p.V618M|ARAP1_ENST00000426523.1_Missense_Mutation_p.V679M|ARAP1_ENST00000334211.8_Missense_Mutation_p.V679M|ARAP1_ENST00000393605.3_Missense_Mutation_p.V684M|ARAP1-AS2_ENST00000500163.2_RNA|ARAP1_ENST00000455638.2_Missense_Mutation_p.V924M|ARAP1_ENST00000495878.1_5'UTR|ARAP1_ENST00000359373.5_Missense_Mutation_p.V924M	NM_001040118.2	NP_001035207.1	Q96P48	ARAP1_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1			27					TCCACCAGCACCAGCACCTGG	0.637000													Ovarian(102;1198 1520 13195 17913 37529)											0							SO:0001583	missense			ENST00000393609.3	1	1	hg19	CCDS41687.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.694061	0.88735	.	.	ENSG00000186635	ENST00000359373;ENST00000455638;ENST00000393605;ENST00000334211;ENST00000393609;ENST00000426523;ENST00000429686;ENST00000427971;ENST00000452383	T;T;T;T;T;T;T;T;T	0.30448	1.53;1.53;1.53;1.53;1.53;1.53;1.53;1.53;1.53	4.93	4.93	0.64822	Pleckstrin homology domain (1);	0.133016	0.49916	D	0.000132	T	0.48926	0.1527	L	0.54323	1.7	0.41335	D	0.987265	P;D;P;P;P	0.69078	0.843;0.997;0.881;0.843;0.903	P;P;P;P;P	0.61533	0.779;0.845;0.746;0.677;0.89	T	0.52019	-0.8631	10	0.87932	D	0	.	17.0897	0.86618	0.0:1.0:0.0:0.0	.	679;618;924;924;684	E7EU13;B2RTS2;Q96P48-3;Q96P48;Q96P48-1	.;.;.;ARAP1_HUMAN;.	M	924;924;684;679;924;679;618;212;212	ENSP00000352332:V924M;ENSP00000390461:V924M;ENSP00000377230:V684M;ENSP00000335506:V679M;ENSP00000377233:V924M;ENSP00000392264:V679M;ENSP00000403127:V618M;ENSP00000411452:V212M;ENSP00000399118:V212M	ENSP00000335506:V679M	V	-	1	0	ARAP1	72086310	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.823000	0.48081	2.435000	0.82474	0.563000	0.77884	GTG		TCGA-3A-A9IU-01A-11D-A397-08	ARAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347428.1	1	0	1	82	257	0	64	1	1	32	115	0	64	2		0	0	0	0	0	2	1	1	81	255	0	64	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	1	2	3	2.066243	0	0.580000	1.910000	0.581214	0.830000	6.800000e-01	1.000000	0.840000	0.839080	0.830000	0	7.500000e-01	0.920000
TYR	7299	broad.mit.edu	37	11	88924443	88924443	+	Missense_Mutation	SNP	G	G	A	rs148815276	by1000genomes	TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr11:88924443G>A	ENST00000263321.5	+	2	1395	c.893G>A	c.(892-894)cGg>cAg	p.R298Q	TYR_ENST00000526139.1_3'UTR	NM_000372.4	NP_000363.1	P14679	TYRO_HUMAN	tyrosinase			48		Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.0033)		Azelaic Acid(DB00548)|Mimosine(DB01055)|Monobenzone(DB00600)	GGACCTTTACGGCGTAATCCT	0.468000																								0							SO:0001583	missense			ENST00000263321.5	1	1	hg19	CCDS8284.1	.	.	.	.	.	.	.	.	.	.	G	7.767	0.706604	0.15239	2.27E-4	0.0	ENSG00000077498	ENST00000263321	D	0.97114	-4.25	5.59	0.524	0.17066	Tyrosinase (1);Uncharacterised domain, di-copper centre (2);	0.354131	0.29205	N	0.012826	D	0.91576	0.7339	L	0.39020	1.185	0.09310	N	1	P	0.40230	0.708	B	0.33750	0.169	D	0.84793	0.0780	9	.	.	.	.	7.2211	0.25988	0.3203:0.0:0.2284:0.4513	.	298	P14679	TYRO_HUMAN	Q	298	ENSP00000263321:R298Q	.	R	+	2	0	TYR	88564091	0.004000	0.15560	0.033000	0.17914	0.384000	0.30261	1.222000	0.32515	-0.154000	0.11118	-2.213000	0.00299	CGG		TCGA-3A-A9IU-01A-11D-A397-08	TYR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394045.2	1	0	1	150	358	0	37		0	0	0	0	37	2		0	0	0	0	0	2	1	1	148	348	0	36	2		0	0	0	0	0	2	-9.488467	1	1	121400	6	42	1	1	2	3	2.066243	0	0.580000	1.910000	0.581214	0.990000	8.800000e-01	1.000000	1.000000	0.981930	0.990000	1	9.400000e-01	1.000000
PRH2	5555	broad.mit.edu	37	12	11083320	11083320	+	Missense_Mutation	SNP	C	C	G			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr12:11083320C>G	ENST00000396400.3	+	3	198	c.160C>G	c.(160-162)Cag>Gag	p.Q54E	PRH2_ENST00000381847.3_Missense_Mutation_p.Q54E|PRR4_ENST00000536668.1_Intron	NM_001110213.1	NP_001103683.1	P02810	PRPC_HUMAN	proline-rich protein HaeIII subfamily 2			13					TTTGGGAGGACAGCAATCTCA	0.552000																								0							SO:0001583	missense			ENST00000396400.3	0	1	hg19	CCDS8636.1	.	.	.	.	.	.	.	.	.	.	C	0.588	-0.834193	0.02713	.	.	ENSG00000134551	ENST00000381847;ENST00000396400	T;T	0.16457	2.34;2.34	1.11	0.126	0.14722	.	5.544330	0.01935	N	0.041536	T	0.09905	0.0243	N	0.12182	0.205	0.09310	N	1	B	0.24426	0.103	B	0.17722	0.019	T	0.23476	-1.0187	10	0.44086	T	0.13	.	3.5402	0.07808	0.0:0.713:0.0:0.287	.	54	P02810	PRPC_HUMAN	E	54	ENSP00000371271:Q54E;ENSP00000379682:Q54E	ENSP00000371271:Q54E	Q	+	1	0	PRH2	10974587	0.000000	0.05858	0.000000	0.03702	0.051000	0.14879	-1.025000	0.03600	0.041000	0.15688	0.194000	0.17425	CAG		TCGA-3A-A9IU-01A-11D-A397-08	PRH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400231.1	0	0	0	8	564	0	87		0	0	0	0	87	2		0	0	0	0	0	2	1	9.887433e-01	8	554	0	87	2		0	0	0	0	0	2	-2.925302	1	1	0	0		1	0	0	0	2.002191	0	0.580000	1.910000	0.570025	0.040000	1.000000e-02	0.090000	0.050000	0.052834	0.040000	0	2.000000e-02	0.070000
KRAS	3845	broad.mit.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	C	T	rs121913529		TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	KRAS_deep			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr12:25398284C>T	ENST00000256078.4	-	2	98	c.35G>A	c.(34-36)gGt>gAt	p.G12D	KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)		GCCTACGCCACCAGCTCCAAC	0.348000	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		pancreatic, colorectal, lung, thyroid, AML, others				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)			Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		L, E, M, O	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)						SO:0001583	missense	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	ENST00000256078.4	1	1	hg19	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.409094	0.83340	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.85919	0.5809	M	0.91818	3.245	0.80722	D	1	B;P	0.35714	0.385;0.517	B;B	0.41619	0.257;0.361	D	0.87870	0.2670	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	D	12	ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D	ENSP00000256078:G12D	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		TCGA-3A-A9IU-01A-11D-A397-08	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	1	0	1	72	223	0	38	1	9.901401e-01	10	14	0	38	2	1	1	85	245	0	198	2	1	1	71	223	0	38	2	1	1	2786	5228	10	8009	19	-20.000000	1	1	121404	2	44	1	0	0	0	2.002191	0	0.580000	1.910000	0.570025	0.810000	6.600000e-01	0.980000	0.820000	0.825014	0.810000	0	7.300000e-01	0.910000
NELL2	4753	broad.mit.edu	37	12	45105106	45105106	+	Silent	SNP	G	G	T			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr12:45105106G>T	ENST00000429094.2	-	11	1662	c.1158C>A	c.(1156-1158)acC>acA	p.T386T	NELL2_ENST00000437801.2_Silent_p.T436T|NELL2_ENST00000549027.1_Silent_p.T385T|NELL2_ENST00000452445.2_Silent_p.T386T|NELL2_ENST00000395487.2_Silent_p.T385T|NELL2_ENST00000333837.4_Silent_p.T409T|NELL2_ENST00000551601.1_Silent_p.T385T	NM_001145108.1	NP_001138580.1	Q99435	NELL2_HUMAN	NEL-like 2 (chicken)			65	Lung SC(27;0.192)	Lung NSC(34;0.144)			TGTGAGACAAGGTTATCTGAT	0.398000																								0							SO:0001819	synonymous_variant			ENST00000429094.2	1	1	hg19	CCDS8746.1	.	.	.	.	.	.	.	.	.	.	G	8.433	0.849108	0.17034	.	.	ENSG00000184613	ENST00000550313	.	.	.	5.79	-1.97	0.07503	.	.	.	.	.	T	0.39332	0.1074	.	.	.	0.58432	D	0.99999	.	.	.	.	.	.	T	0.31558	-0.9939	4	.	.	.	-8.8524	1.4208	0.02311	0.3427:0.0865:0.3107:0.2601	.	.	.	.	H	130	.	.	P	-	2	0	NELL2	43391373	0.938000	0.31826	0.982000	0.44146	0.983000	0.72400	-0.010000	0.12743	-0.109000	0.12044	-0.126000	0.14955	CCT		TCGA-3A-A9IU-01A-11D-A397-08	NELL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404180.1	1	0	1	65	224	0	30	0	5.168545e-02	0	2	0	30	2		0	0	0	0	0	2	1	1	64	224	0	30	2		0	0	0	0	0	2	-3.583185	1	1	0	0		1	0	0	0	2.002191	0	0.580000	1.910000	0.570025	0.750000	6.000000e-01	0.920000	0.760000	0.761861	0.750000	0	6.700000e-01	0.840000
IL26	55801	broad.mit.edu	37	12	68619408	68619408	+	Silent	SNP	G	G	A			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr12:68619408G>A	ENST00000229134.4	-	1	193	c.129C>T	c.(127-129)gaC>gaT	p.D43D	IFNG-AS1_ENST00000536914.1_RNA	NM_018402.1	NP_060872.1	Q9NPH9	IL26_HUMAN	interleukin 26			12			Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.018)		TATAGAGAGCGTCAACAGCTT	0.438000																								0							SO:0001819	synonymous_variant			ENST00000229134.4	0	1	hg19	CCDS8981.1																																																																																				TCGA-3A-A9IU-01A-11D-A397-08	IL26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402302.1	0	0	0	6	741	0	96		0	0	0	0	96	2		0	0	0	0	0	2	1	9.638753e-01	6	733	0	96	2		0	0	0	0	0	2	-2.554088	1	1	121412	2	39	1	0	0	0	2.002191	0	0.580000	1.910000	0.570025	0.020000	0	0.060000	0.020000	0.030569	0.020000	0	1.000000e-02	0.040000
EML1	2009	broad.mit.edu	37	14	100405582	100405582	+	Missense_Mutation	SNP	G	G	A			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr14:100405582G>A	ENST00000262233.6	+	21	2379	c.2240G>A	c.(2239-2241)cGg>cAg	p.R747Q	EML1_ENST00000327921.9_Missense_Mutation_p.R735Q|EML1_ENST00000334192.4_Missense_Mutation_p.R766Q	NM_004434.2	NP_004425.2	O00423	EMAL1_HUMAN	echinoderm microtubule associated protein like 1	p.R766Q(1)		42		Melanoma(154;0.0879)|all_epithelial(191;0.216)			GCCGTCTGTCGGGCCCATGAG	0.552000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000262233.6	0	1	hg19	CCDS32155.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.117755	0.77323	.	.	ENSG00000066629	ENST00000327921;ENST00000262233;ENST00000334192;ENST00000542138	T;T;T	0.17854	2.25;2.25;2.25	4.56	4.56	0.56223	.	0.051684	0.64402	D	0.000001	T	0.47710	0.1460	M	0.90082	3.085	0.80722	D	1	P;D;D	0.71674	0.926;0.998;0.959	B;P;B	0.61397	0.388;0.888;0.293	T	0.62205	-0.6903	10	0.87932	D	0	-22.3911	17.6609	0.88193	0.0:0.0:1.0:0.0	.	735;747;766	F8W717;O00423;O00423-3	.;EMAL1_HUMAN;.	Q	735;747;766;766	ENSP00000327384:R735Q;ENSP00000262233:R747Q;ENSP00000334314:R766Q	ENSP00000262233:R747Q	R	+	2	0	EML1	99475335	1.000000	0.71417	0.997000	0.53966	0.556000	0.35491	7.627000	0.83176	2.240000	0.73641	0.561000	0.74099	CGG		TCGA-3A-A9IU-01A-11D-A397-08	EML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413943.1	0	0	0	5	324	0	58	0	8.043302e-02	1	24	0	58	2		0	0	0	0	0	2	1	9.380017e-01	6	323	0	55	2		0	0	0	0	0	2	-2.900681	1	1	121412	3	36	1	0	0	0	2.059044	0	0.580000	1.910000	0.580000	0.050000	1.000000e-02	0.120000	0.060000	0.062318	0.050000	0	3.000000e-02	0.090000
FANCM	57697	broad.mit.edu	37	14	45665470	45665470	+	Silent	SNP	G	G	A			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr14:45665470G>A	ENST00000267430.5	+	21	5521	c.5436G>A	c.(5434-5436)ccG>ccA	p.P1812P	FANCM_ENST00000542564.2_Silent_p.P1786P	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M			85					TTAGACTTCCGCAGGAAGGAA	0.438000								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia															0							SO:0001819	synonymous_variant	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	ENST00000267430.5	0	1	hg19	CCDS32070.1	.	.	.	.	.	.	.	.	.	.	G	6.510	0.462289	0.12342	2.27E-4	0.0	ENSG00000187790	ENST00000554809	.	.	.	5.27	-1.83	0.07833	.	.	.	.	.	T	0.18800	0.0451	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.25082	-1.0142	4	.	.	.	.	1.3233	0.02121	0.293:0.1242:0.3414:0.2414	.	.	.	.	T	780	.	.	A	+	1	0	FANCM	44735220	0.000000	0.05858	0.008000	0.14137	0.362000	0.29581	-0.041000	0.12084	-0.216000	0.10048	-0.414000	0.06135	GCA		TCGA-3A-A9IU-01A-11D-A397-08	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	0	0	0	6	589	0	78	0	1.522051e-03	0	5	0	78	2		0	0	0	0	0	2	1	9.649367e-01	7	587	0	78	2		0	0	0	0	0	2	-2.373405	0	1	121412	3	40	1	0	0	0	2.059044	0	0.580000	1.910000	0.580000	0.030000	0	0.070000	0.040000	0.040047	0.030000	0	1.000000e-02	0.060000
ATP10A	57194	broad.mit.edu	37	15	25953374	25953374	+	Missense_Mutation	SNP	T	T	G			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr15:25953374T>G	ENST00000356865.6	-	11	2529	c.2418A>C	c.(2416-2418)gaA>gaC	p.E806D		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A			103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)			TGCGCAGGCCTTCCGCCGCAT	0.577000																								0							SO:0001583	missense			ENST00000356865.6	1	1	hg19	CCDS32178.1	.	.	.	.	.	.	.	.	.	.	T	7.022	0.558919	0.13436	.	.	ENSG00000206190	ENST00000356865	D	0.82433	-1.61	4.84	-4.91	0.03085	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.093232	0.64402	N	0.000001	T	0.53578	0.1805	N	0.12920	0.275	0.46317	D	0.998986	B	0.06786	0.001	B	0.15484	0.013	T	0.51764	-0.8664	10	0.02654	T	1	-23.9456	2.2901	0.04136	0.283:0.4025:0.0988:0.2157	.	806	O60312	AT10A_HUMAN	D	806	ENSP00000349325:E806D	ENSP00000349325:E806D	E	-	3	2	ATP10A	23504467	1.000000	0.71417	0.792000	0.32020	0.854000	0.48673	1.151000	0.31651	-0.677000	0.05231	0.533000	0.62120	GAA		TCGA-3A-A9IU-01A-11D-A397-08	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	1	0	1	102	297	0	102	0	8.500320e-01	0	12	0	102	2		0	0	0	0	0	2	1	1	99	293	0	102	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	1	2	3	2.066352	0	0.580000	1.910000	0.581214	0.880000	7.300000e-01	1.000000	1.000000	0.884204	0.880000	1	8.000000e-01	0.960000
VPS33B	26276	broad.mit.edu	37	15	91557033	91557033	+	Splice_Site	SNP	C	C	T			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr15:91557033C>T	ENST00000333371.3	-	5	711		c.e5+1		VPS33B_ENST00000557358.1_Intron|VPS33B_ENST00000535906.1_Splice_Site|VPS33B_ENST00000535843.1_Splice_Site	NM_018668.3	NP_061138.3	Q9H267	VP33B_HUMAN	vacuolar protein sorting 33 homolog B (yeast)			16	Lung NSC(78;0.0987)|all_lung(78;0.175)				TCCAAACTCACCTTTTGAGGG	0.522000																								0							SO:0001630	splice_region_variant			ENST00000333371.3	1	1	hg19	CCDS10369.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.600940	0.87055	.	.	ENSG00000184056	ENST00000333371;ENST00000535906;ENST00000535843;ENST00000537510	.	.	.	5.62	5.62	0.85841	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.2545	0.93940	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	VPS33B	89358037	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	5.902000	0.69869	2.647000	0.89833	0.650000	0.86243	.		TCGA-3A-A9IU-01A-11D-A397-08	VPS33B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313496.1	1	0	1	110	330	0	68	0	6.349141e-02	1	1	0	68	2		0	0	0	0	0	2	1	1	109	327	0	67	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	1	2	3	2.064462	0	0.580000	1.910000	0.581214	0.860000	7.200000e-01	1.000000	0.860000	0.866016	0.860000	1	7.900000e-01	0.940000
SSTR5	6755	broad.mit.edu	37	16	1129924	1129924	+	Silent	SNP	C	C	T			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr16:1129924C>T	ENST00000293897.4	+	1	1144	c.1056C>T	c.(1054-1056)cgC>cgT	p.R352R	SSTR5_ENST00000397547.2_Silent_p.R352R|SSTR5_ENST00000562758.1_Intron|SSTR5-AS1_ENST00000569832.1_RNA	NM_001053.3	NP_001044.1	P35346	SSR5_HUMAN	somatostatin receptor 5			9		Hepatocellular(780;0.00369)		Octreotide(DB00104)|Pasireotide(DB06663)|Vapreotide(DB04894)	CCGCGCACCGCGCCGCAGCCA	0.711000																								0							SO:0001819	synonymous_variant			ENST00000293897.4	0	1	hg19	CCDS10429.1																																																																																				TCGA-3A-A9IU-01A-11D-A397-08	SSTR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420836.1	0	0	0	9	39	0	14		0	0	0	0	14	2		0	0	0	0	0	2	1	9.952899e-01	9	38	0	13	2		0	0	0	0	0	2	-19.995970	1	1	119194	1	29	1	1	2	3	2.102201	0	0.580000	1.910000	0.584816	0.670000	3.400000e-01	1.000000	1.000000	0.690285	0.670000	0	4.900000e-01	0.900000
PKD1	5310	broad.mit.edu	37	16	2156826	2156826	+	Missense_Mutation	SNP	T	T	C			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr16:2156826T>C	ENST00000262304.4	-	17	7397	c.7189A>G	c.(7189-7191)Agc>Ggc	p.S2397G	PKD1_ENST00000561991.1_5'Flank|PKD1_ENST00000423118.1_Missense_Mutation_p.S2397G	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)			72					GAGCCGCTGCTGCAATTGAGG	0.662000																								0							SO:0001583	missense			ENST00000262304.4	0	1	hg19	CCDS32369.1	.	.	.	.	.	.	.	.	.	.	t	2.685	-0.274485	0.05679	.	.	ENSG00000008710	ENST00000262304;ENST00000423118;ENST00000306101;ENST00000382481	T;T	0.69926	-0.44;-0.44	4.22	3.11	0.35812	Egg jelly receptor, REJ-like (1);PKD/REJ-like protein (1);Polycystin cation channel (1);	0.607624	0.18369	N	0.143312	T	0.54679	0.1873	L	0.51422	1.61	0.22754	N	0.998778	B;B	0.18610	0.029;0.016	B;B	0.23852	0.049;0.026	T	0.38672	-0.9650	10	0.19590	T	0.45	.	5.6771	0.17755	0.0:0.1065:0.3359:0.5576	.	2397;2397	P98161-3;P98161	.;PKD1_HUMAN	G	2397;2397;1748;676	ENSP00000262304:S2397G;ENSP00000399501:S2397G	ENSP00000262304:S2397G	S	-	1	0	PKD1	2096827	1.000000	0.71417	0.960000	0.40013	0.494000	0.33585	2.464000	0.45067	0.782000	0.33613	0.445000	0.29226	AGC		TCGA-3A-A9IU-01A-11D-A397-08	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1	0	0	0	7	72	0	14	0	1.174952e-01	1	5	0	14	2		0	0	0	0	0	2	1	7.484324e-01	5	24	0	19	2		0	0	0	0	0	2	-13.122090	1	1	0	0		1	1	2	3	2.102201	0	0.580000	1.910000	0.584816	0.320000	1.400000e-01	1.000000	0.310000	0.360419	0.320000	0	2.200000e-01	0.470000
ADCY9	115	broad.mit.edu	37	16	4016903	4016903	+	Missense_Mutation	SNP	C	C	T			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr16:4016903C>T	ENST00000294016.3	-	11	3473	c.2935G>A	c.(2935-2937)Ggc>Agc	p.G979S		NM_001116.3	NP_001107.2	O60503	ADCY9_HUMAN	adenylate cyclase 9			47					ACCTCCTGGCCGATGAGGCTG	0.582000																								0							SO:0001583	missense			ENST00000294016.3	1	1	hg19	CCDS32382.1	.	.	.	.	.	.	.	.	.	.	C	16.15	3.041963	0.55003	.	.	ENSG00000162104	ENST00000294016	D	0.83250	-1.7	5.48	5.48	0.80851	.	0.149249	0.64402	D	0.000011	D	0.82337	0.5015	N	0.22421	0.69	0.51767	D	0.999931	D	0.76494	0.999	P	0.59115	0.852	T	0.76348	-0.2992	10	0.08837	T	0.75	.	19.7084	0.96083	0.0:1.0:0.0:0.0	.	979	O60503	ADCY9_HUMAN	S	979	ENSP00000294016:G979S	ENSP00000294016:G979S	G	-	1	0	ADCY9	3956904	0.998000	0.40836	0.970000	0.41538	0.455000	0.32408	3.763000	0.55257	2.739000	0.93911	0.561000	0.74099	GGC		TCGA-3A-A9IU-01A-11D-A397-08	ADCY9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438076.1	1	0	1	124	309	0	88	1	9.846138e-01	2	17	0	88	2		0	0	0	0	0	2	1	1	121	304	0	87	2		0	0	0	0	0	2	-7.874103	1	1	121400	2	38	1	1	2	3	2.102201	0	0.580000	1.910000	0.584816	0.990000	8.500000e-01	1.000000	1.000000	0.970957	0.990000	1	9.200000e-01	1.000000
HSDL1	83693	broad.mit.edu	37	16	84164829	84164829	+	Missense_Mutation	SNP	G	G	A	rs143907842		TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr16:84164829G>A	ENST00000219439.4	-	3	274	c.98C>T	c.(97-99)aCg>aTg	p.T33M	HSDL1_ENST00000434463.3_Missense_Mutation_p.T33M	NM_001146051.1|NM_031463.4	NP_001139523.1|NP_113651.4	Q3SXM5	HSDL1_HUMAN	hydroxysteroid dehydrogenase like 1			7					TTTTCTGGCCGTATACCAGGC	0.493000																								0							SO:0001583	missense			ENST00000219439.4	0	1	hg19	CCDS10942.1	.	.	.	.	.	.	.	.	.	.	G	15.61	2.883945	0.51908	0.0	5.81E-4	ENSG00000103160	ENST00000434463;ENST00000219439	T;D	0.83163	-1.11;-1.69	5.84	5.84	0.93424	.	0.185252	0.47852	D	0.000218	T	0.74581	0.3735	N	0.17082	0.46	0.42561	D	0.993148	D;P	0.64830	0.994;0.812	P;B	0.45449	0.481;0.137	T	0.77161	-0.2689	10	0.45353	T	0.12	-18.6731	14.306	0.66384	0.0706:0.0:0.9294:0.0	.	33;33	B4DSL2;Q3SXM5	.;HSDL1_HUMAN	M	33	ENSP00000407437:T33M;ENSP00000219439:T33M	ENSP00000219439:T33M	T	-	2	0	HSDL1	82722330	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	5.371000	0.66150	2.765000	0.95021	0.655000	0.94253	ACG		TCGA-3A-A9IU-01A-11D-A397-08	HSDL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269076.3	0	0	0	6	654	0	122	0	2.889622e-02	0	24	0	122	2		0	0	0	0	0	2	1	9.652566e-01	6	655	0	122	2		0	0	0	0	0	2	-2.208772	0	1	121412	39	50	1	1	2	3	2.108988	0	0.580000	1.910000	0.586003	0.030000	0	1.000000	0.040000	0.072915	0.030000	0	1.000000e-02	0.060000
QRICH2	84074	broad.mit.edu	37	17	74288916	74288916	+	Missense_Mutation	SNP	G	G	A			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr17:74288916G>A	ENST00000262765.5	-	4	1573	c.1394C>T	c.(1393-1395)gCc>gTc	p.A465V		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2			62					accaggttgggccaaaccaga	0.557000																								0							SO:0001583	missense			ENST00000262765.5	0	1	hg19	CCDS32741.1	.	.	.	.	.	.	.	.	.	.	-	9.875	1.200097	0.22121	.	.	ENSG00000129646	ENST00000262765;ENST00000301613	T	0.08370	3.1	5.38	-5.83	0.02325	.	.	.	.	.	T	0.01730	0.0055	N	0.00621	-1.32	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43734	-0.9373	9	0.27082	T	0.32	-3.7961	2.3937	0.04385	0.3394:0.2868:0.2749:0.0989	.	465;465	B5MD94;Q9H0J4	.;QRIC2_HUMAN	V	465	ENSP00000262765:A465V	ENSP00000262765:A465V	A	-	2	0	QRICH2	71800511	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.107000	0.03316	-0.983000	0.03511	-0.272000	0.10252	GCC		TCGA-3A-A9IU-01A-11D-A397-08	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	0	0	0	4	139	0	11		0	0	0	0	11	2		0	0	0	0	0	2	1	8.881317e-01	4	137	0	11	2		0	0	0	0	0	2	-3.328154	1	1	0	0		1	1	2	3	2.101218	0	0.580000	1.910000	0.584816	0.100000	3.000000e-02	1.000000	0.100000	0.145024	0.100000	0	6.000000e-02	0.180000
TP53	7157	broad.mit.edu	37	17	7579473	7579473	+	Missense_Mutation	SNP	G	G	C			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08			G	C	G	G		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr17:7579473G>C	ENST00000269305.4	-	4	403	c.214C>G	c.(214-216)Ccc>Gcc	p.P72A	TP53_ENST00000445888.2_Missense_Mutation_p.P72A|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.P72A|TP53_ENST00000420246.2_Missense_Mutation_p.P72A|TP53_ENST00000359597.4_Missense_Mutation_p.P72A|TP53_ENST00000413465.2_Missense_Mutation_p.P72A	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.0?(8)|p.G59fs*23(3)|p.R72fs*51(2)|p.R72C(2)|p.E68fs*76(1)|p.D48fs*55(1)|p.P13fs*18(1)|p.R65fs*38(1)|p.D57_A76del20(1)|p.S33fs*23(1)		24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		Acetylsalicylic acid(DB00945)	GGGGCCACGGGGGGAGCAGCC	0.602000		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	21	Whole gene deletion(8)|Deletion - Frameshift(8)|Substitution - Missense(2)|Complex - frameshift(2)|Deletion - In frame(1)						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	0	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	2.042	-0.419843	0.04734	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000508793;ENST00000503591	D;D;D;D;D;D;D;D	0.99287	-5.17;-5.69;-5.4;-5.68;-5.68;-5.4;-4.05;-1.96	3.66	0.238	0.15480	.	2.010640	0.04441	U	0.370853	D	0.95500	0.8538	N	0.03608	-0.345	0.09310	N	1	B;B;B;B;B	0.10296	0.0;0.0;0.0;0.0;0.003	B;B;B;B;B	0.08055	0.0;0.001;0.001;0.0;0.003	D	0.93649	0.6971	10	0.26408	T	0.33	.	7.4166	0.27048	0.1022:0.4057:0.492:0.0	.	72;72;72;72;72	E7EMR6;P04637-2;P04637-3;P04637;E7EQX7	.;.;.;P53_HUMAN;.	A	72	ENSP00000410739:P72A;ENSP00000352610:P72A;ENSP00000269305:P72A;ENSP00000398846:P72A;ENSP00000391127:P72A;ENSP00000391478:P72A;ENSP00000424104:P72A;ENSP00000426252:P72A	ENSP00000269305:P72A	P	-	1	0	TP53	7520198	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.284000	0.08422	0.102000	0.17638	-0.264000	0.10439	CCC		TCGA-3A-A9IU-01A-11D-A397-08	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	1	0	0	194	315	0	135	0	9.998652e-01	0	25	0	135	2	1	1	78	171	0	192	2	1	1	222	291	1	132	14		0	0	0	0	0	2	-19.999790	1	0	121404	1	41	1	0	1	1	1.504503	1	0.580000	1.910000	0.408451	0.920000	8.200000e-01	1.000000	0.930000	0.922150	0.920000	1	8.700000e-01	0.970000
TP53	7157	broad.mit.edu	37	17	7579479	7579479	+	Missense_Mutation	SNP	C	C	T			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr17:7579479C>T	ENST00000269305.4	-	4	397	c.208G>A	c.(208-210)Gct>Act	p.A70T	TP53_ENST00000445888.2_Missense_Mutation_p.A70T|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.A70T|TP53_ENST00000420246.2_Missense_Mutation_p.A70T|TP53_ENST00000359597.4_Missense_Mutation_p.A70T|TP53_ENST00000413465.2_Missense_Mutation_p.A70T	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.0?(8)|p.G59fs*23(3)|p.E68fs*76(1)|p.D48fs*55(1)|p.R65_P71delRMPEAAP(1)|p.A70T(1)|p.P13fs*18(1)|p.R65fs*38(1)|p.D57_A76del20(1)|p.S33fs*23(1)		24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		Acetylsalicylic acid(DB00945)	ACGGGGGGAGCAGCCTCTGGC	0.597000		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	19	Whole gene deletion(8)|Deletion - Frameshift(7)|Deletion - In frame(2)|Substitution - Missense(1)|Complex - frameshift(1)						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	9.093	1.002269	0.19121	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000508793;ENST00000503591	D;D;D;D;D;D;D;D	0.99376	-5.28;-5.79;-5.51;-5.79;-5.79;-5.51;-4.19;-2.14	3.66	-2.27	0.06846	.	4.481350	0.01345	N	0.011694	D	0.95092	0.8410	N	0.08118	0	0.09310	N	1	B;B;B;B;B;B;B	0.27971	0.079;0.049;0.196;0.013;0.031;0.025;0.0	B;B;B;B;B;B;B	0.29785	0.031;0.026;0.107;0.017;0.034;0.022;0.0	D	0.97004	0.9731	10	0.09843	T	0.71	.	1.4508	0.02374	0.1962:0.3205:0.3268:0.1566	.	31;70;70;70;70;70;70	B4E095;E7EMR6;P04637-2;P04637-3;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	T	70	ENSP00000410739:A70T;ENSP00000352610:A70T;ENSP00000269305:A70T;ENSP00000398846:A70T;ENSP00000391127:A70T;ENSP00000391478:A70T;ENSP00000424104:A70T;ENSP00000426252:A70T	ENSP00000269305:A70T	A	-	1	0	TP53	7520204	0.016000	0.18221	0.000000	0.03702	0.001000	0.01503	-0.099000	0.11007	-0.331000	0.08501	-1.242000	0.01536	GCT		TCGA-3A-A9IU-01A-11D-A397-08	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	1	0	1	239	320	0	146	0	9.999616e-01	0	24	0	146	2	1	1	99	192	0	219	2	1	1	242	320	0	144	2		0	0	0	0	0	2	-20.000000	1	0	0	0		1	0	1	1	1.504503	1	0.580000	1.910000	0.408451	0.970000	9.100000e-01	1.000000	0.990000	0.975482	0.970000	1	9.400000e-01	1.000000
NPLOC4	55666	broad.mit.edu	37	17	79556050	79556050	+	Silent	SNP	G	G	A			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr17:79556050G>A	ENST00000331134.6	-	12	1416	c.1201C>T	c.(1201-1203)Ctg>Ttg	p.L401L	NPLOC4_ENST00000374747.5_Silent_p.L401L|NPLOC4_ENST00000539314.1_Silent_p.L240L	NM_017921.2	NP_060391.2	Q8TAT6	NPL4_HUMAN	nuclear protein localization 4 homolog (S. cerevisiae)			11	all_neural(118;0.0878)|Melanoma(429;0.242)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)		TTGCATGGCAGCAAACACTCA	0.498000																								0							SO:0001819	synonymous_variant			ENST00000331134.6	0	1	hg19	CCDS45812.1																																																																																				TCGA-3A-A9IU-01A-11D-A397-08	NPLOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440140.1	0	0	0	5	325	0	54	0	4.603752e-01	0	90	0	54	2		0	0	0	0	0	2	1	9.354747e-01	5	321	0	54	2		0	0	0	0	0	2	-2.459651	0	1	0	0		1	1	2	3	2.101218	0	0.580000	1.910000	0.584816	0.050000	1.000000e-02	1.000000	0.060000	0.089843	0.050000	0	3.000000e-02	0.090000
CELF4	56853	broad.mit.edu	37	18	34901802	34901802	+	Nonsense_Mutation	SNP	G	G	A			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr18:34901802G>A	ENST00000591282.1	-	3	411	c.412C>T	c.(412-414)Cga>Tga	p.R138*	CELF4_ENST00000601019.1_Nonsense_Mutation_p.R138*|CELF4_ENST00000420428.2_Nonsense_Mutation_p.R138*|CELF4_ENST00000334919.5_Nonsense_Mutation_p.R138*|CELF4_ENST00000603232.1_Nonsense_Mutation_p.R138*|CELF4_ENST00000588597.1_Nonsense_Mutation_p.R138*|CELF4_ENST00000361795.5_Nonsense_Mutation_p.R138*|CELF4_ENST00000591287.1_Nonsense_Mutation_p.R138*|CELF4_ENST00000412753.1_Nonsense_Mutation_p.R138*			Q9BZC1	CELF4_HUMAN	CUGBP, Elav-like family member 4			44					CTACCTCCTCGGCTCTCGCTG	0.647000											OREG0024927	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)												0							SO:0001587	stop_gained			ENST00000591282.1	0	1	hg19	CCDS32818.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	41|41	8.838326|8.838326	0.98972|0.98972	.|.	.|.	ENSG00000101489|ENSG00000101489	ENST00000361683|ENST00000361795;ENST00000412753;ENST00000420428;ENST00000334919	.|.	.|.	.|.	5.19|5.19	5.19|5.19	0.71726|0.71726	.|.	.|0.085967	.|0.47455	.|D	.|0.000223	T|.	0.38214|.	0.1032|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.31280|.	-0.9949|.	4|.	0.51188|0.02654	T|T	0.08|1	-2.4113|-2.4113	16.1974|16.1974	0.82040|0.82040	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	L|X	32|138	.|.	ENSP00000355189:P32L|ENSP00000335631:R138X	P|R	-|-	2|1	0|2	CELF4|CELF4	33155800|33155800	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	3.015000|3.015000	0.49599|0.49599	2.413000|2.413000	0.81919|0.81919	0.484000|0.484000	0.47621|0.47621	CCG|CGA		TCGA-3A-A9IU-01A-11D-A397-08	CELF4-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000440892.1	1	0	1	43	83	0	21		0	0	0	0	21	2		0	0	0	0	0	2	1	1	42	81	0	21	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	0	1	1	1.486081	1	0.580000	1.910000	0.410857	0.820000	6.300000e-01	0.980000	0.830000	0.825013	0.820000	0	7.200000e-01	0.920000
DSEL	92126	broad.mit.edu	37	18	65180274	65180274	+	Missense_Mutation	SNP	C	C	A			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr18:65180274C>A	ENST00000310045.7	-	2	3075	c.1602G>T	c.(1600-1602)caG>caT	p.Q534H	CTD-2541J13.2_ENST00000581951.1_RNA|CTD-2541J13.2_ENST00000583493.1_RNA	NM_032160.2	NP_115536.1	Q8IZU8	DSEL_HUMAN	dermatan sulfate epimerase-like			74		Esophageal squamous(42;0.129)			ACTTAAGCCACTGCGCACATT	0.512000																								0							SO:0001583	missense			ENST00000310045.7	1	1	hg19	CCDS11995.1	.	.	.	.	.	.	.	.	.	.	C	18.07	3.541902	0.65198	.	.	ENSG00000171451	ENST00000310045;ENST00000397964	T	0.18810	2.19	5.67	2.89	0.33648	.	0.067597	0.64402	U	0.000016	T	0.32912	0.0845	L	0.51422	1.61	0.45704	D	0.998613	D	0.67145	0.996	P	0.59703	0.862	T	0.04454	-1.0950	10	0.72032	D	0.01	-9.1529	10.5565	0.45121	0.0:0.7858:0.0:0.2142	.	524	Q8IZU8	DSEL_HUMAN	H	534;524	ENSP00000310565:Q534H	ENSP00000310565:Q534H	Q	-	3	2	DSEL	63331254	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.112000	0.50368	0.735000	0.32537	0.563000	0.77884	CAG		TCGA-3A-A9IU-01A-11D-A397-08	DSEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256221.1	1	0	1	118	133	0	78	0	9.126792e-01	0	7	0	78	2		0	0	0	0	0	2	1	1	114	133	0	76	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	0	1	1	1.503831	1	0.580000	1.910000	0.410857	0.980000	9.100000e-01	1.000000	1.000000	0.981811	0.980000	1	9.500000e-01	1.000000
DSEL	92126	broad.mit.edu	37	18	65180275	65180275	+	Missense_Mutation	SNP	T	T	A			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr18:65180275T>A	ENST00000310045.7	-	2	3074	c.1601A>T	c.(1600-1602)cAg>cTg	p.Q534L	CTD-2541J13.2_ENST00000581951.1_RNA|CTD-2541J13.2_ENST00000583493.1_RNA	NM_032160.2	NP_115536.1	Q8IZU8	DSEL_HUMAN	dermatan sulfate epimerase-like			74		Esophageal squamous(42;0.129)			CTTAAGCCACTGCGCACATTC	0.517000																								0							SO:0001583	missense			ENST00000310045.7	1	1	hg19	CCDS11995.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.954048	0.73902	.	.	ENSG00000171451	ENST00000310045;ENST00000397964	T	0.18657	2.2	5.67	5.67	0.87782	.	0.067597	0.64402	U	0.000016	T	0.24774	0.0601	L	0.51422	1.61	0.54753	D	0.999981	D	0.53151	0.958	B	0.42692	0.395	T	0.02526	-1.1146	10	0.87932	D	0	-9.1529	15.578	0.76408	0.0:0.0:0.0:1.0	.	524	Q8IZU8	DSEL_HUMAN	L	534;524	ENSP00000310565:Q534L	ENSP00000310565:Q534L	Q	-	2	0	DSEL	63331255	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.849000	0.86908	2.169000	0.68431	0.460000	0.39030	CAG		TCGA-3A-A9IU-01A-11D-A397-08	DSEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256221.1	1	0	1	119	134	0	75	0	9.128961e-01	0	7	0	75	2		0	0	0	0	0	2	1	1	115	134	0	73	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	0	1	1	1.503831	1	0.580000	1.910000	0.410857	0.980000	9.100000e-01	1.000000	1.000000	0.982048	0.980000	1	9.500000e-01	1.000000
PPP4R1	9989	broad.mit.edu	37	18	9583116	9583116	+	Splice_Site	SNP	C	C	A			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr18:9583116C>A	ENST00000400556.3	-	9	990	c.917G>T	c.(916-918)tGg>tTg	p.W306L	PPP4R1_ENST00000580583.1_Intron|PPP4R1_ENST00000400555.3_Splice_Site_p.W289L	NM_001042388.2	NP_001035847.1	Q8TF05	PP4R1_HUMAN	protein phosphatase 4, regulatory subunit 1			3					AAACCCTACCCAACGTGAAGG	0.328000													Melanoma(188;1232 2082 5061 11948 35994)											0							SO:0001630	splice_region_variant			ENST00000400556.3	0	1	hg19	CCDS42412.1	.	.	.	.	.	.	.	.	.	.	C	27.7	4.856783	0.91433	.	.	ENSG00000154845	ENST00000400556;ENST00000400555;ENST00000285124	T;T	0.17854	2.25;2.25	5.65	5.65	0.86999	Armadillo-like helical (1);Armadillo-type fold (1);	0.309004	0.33040	N	0.005343	T	0.43743	0.1261	M	0.71206	2.165	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.76575	0.973;0.988	T	0.05305	-1.0893	9	.	.	.	-13.8309	19.5069	0.95121	0.0:1.0:0.0:0.0	.	306;289	Q8TF05;Q8TF05-2	PP4R1_HUMAN;.	L	306;289;217	ENSP00000383402:W306L;ENSP00000383401:W289L	.	W	-	2	0	PPP4R1	9573116	1.000000	0.71417	1.000000	0.80357	0.903000	0.53119	7.294000	0.78760	2.941000	0.99782	0.655000	0.94253	TGG		TCGA-3A-A9IU-01A-11D-A397-08	PPP4R1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268571.1	0	0	0	4	223	0	32	0	3.986485e-01	0	65	0	32	2		0	0	0	0	0	2	1	8.890625e-01	4	221	0	32	2		0	0	0	0	0	2	-3.124691	1	1	0	0		1	0	0	0	2.028010	0	0.580000	1.910000	0.575071	0.060000	1.000000e-02	0.140000	0.060000	0.074128	0.060000	0	3.000000e-02	0.110000
ABHD8	79575	broad.mit.edu	37	19	17405196	17405196	+	Silent	SNP	G	G	A			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr19:17405196G>A	ENST00000247706.3	-	4	1289	c.1050C>T	c.(1048-1050)ggC>ggT	p.G350G	CTD-2278I10.4_ENST00000594077.1_RNA|MRPL34_ENST00000600434.1_Intron|MRPL34_ENST00000595444.1_Intron	NM_024527.4	NP_078803.4	Q96I13	ABHD8_HUMAN	abhydrolase domain containing 8	p.G350G(1)		9					AGACCTCGTCGCCCTCGGGCC	0.612000													Ovarian(156;1368 2543 15275 41187)											1	Substitution - coding silent(1)						SO:0001819	synonymous_variant			ENST00000247706.3	1	1	hg19	CCDS12355.1																																																																																				TCGA-3A-A9IU-01A-11D-A397-08	ABHD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462937.1	1	0	1	122	169	0	98	1	9.999997e-01	15	21	0	98	2		0	0	0	0	0	2	1	1	122	166	0	97	2		0	0	0	0	0	2	-19.854080	1	1	121412	1	27	1	0	1	1	1.500903	1	0.580000	1.910000	0.408451	0.950000	8.500000e-01	1.000000	0.990000	0.954827	0.950000	1	9.100000e-01	0.990000
RASIP1	54922	broad.mit.edu	37	19	49232704	49232704	+	Silent	SNP	G	G	A			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr19:49232704G>A	ENST00000222145.4	-	5	1527	c.1323C>T	c.(1321-1323)cgC>cgT	p.R441R	RASIP1_ENST00000594232.1_5'Flank	NM_017805.2	NP_060275.2	Q5U651	RAIN_HUMAN	Ras interacting protein 1			21		all_lung(116;4.89e-06)|all_epithelial(76;7.04e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)			CAGGGCCCGCGCGCACTGTGC	0.741000																								0							SO:0001819	synonymous_variant			ENST00000222145.4	0	1	hg19	CCDS12731.1																																																																																				TCGA-3A-A9IU-01A-11D-A397-08	RASIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466185.1	1	0	0	5	25	0	8	0	1.006016e-01	0	3	0	8	2		0	0	0	0	0	2	1	9.433425e-01	5	25	0	8	2		0	0	0	0	0	2	-14.364150	1	1	117836	2	33	1	1	2	3	2.708686	1	0.580000	1.910000	0.674419	0.780000	3.200000e-01	1.000000	1.000000	0.765730	0.780000	0	5.100000e-01	1.000000
A1BG	1	broad.mit.edu	37	19	58862886	58862886	+	Missense_Mutation	SNP	G	G	A			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr19:58862886G>A	ENST00000263100.3	-	5	842	c.781C>T	c.(781-783)Cgc>Tgc	p.R261C	CTD-2619J13.8_ENST00000599109.1_RNA|A1BG-AS1_ENST00000594950.1_RNA|A1BG-AS1_ENST00000599728.1_RNA|A1BG-AS1_ENST00000595302.1_RNA|A1BG-AS1_ENST00000593374.1_RNA|A1BG-AS1_ENST00000600379.1_RNA|A1BG-AS1_ENST00000600686.1_RNA|A1BG-AS1_ENST00000593960.1_RNA	NM_130786.3	NP_570602.2	P04217	A1BG_HUMAN	alpha-1-B glycoprotein			15		all_cancers(17;3.04e-16)|all_epithelial(17;7.77e-12)|Lung NSC(17;3.25e-05)|Colorectal(82;5.46e-05)|all_lung(17;0.000129)|all_neural(62;0.0182)|Ovarian(87;0.0443)|Breast(46;0.0889)|Renal(17;0.157)			AAGAAGATGCGATCTGGGCTG	0.637000																								0							SO:0001583	missense			ENST00000263100.3	1	1	hg19	CCDS12976.1	.	.	.	.	.	.	.	.	.	.	G	15.23	2.772683	0.49680	.	.	ENSG00000121410	ENST00000263100;ENST00000453054	T	0.13089	2.62	4.08	0.302	0.15786	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.104360	0.07058	N	0.833228	T	0.37652	0.1011	M	0.77820	2.39	0.09310	N	1	D	0.89917	1.0	D	0.74023	0.982	T	0.28902	-1.0029	10	0.72032	D	0.01	.	11.1079	0.48214	0.0:0.0:0.5207:0.4793	.	261	P04217	A1BG_HUMAN	C	261;139	ENSP00000263100:R261C	ENSP00000263100:R261C	R	-	1	0	A1BG	63554698	0.000000	0.05858	0.000000	0.03702	0.042000	0.13812	0.465000	0.22004	0.042000	0.15717	0.462000	0.41574	CGC		TCGA-3A-A9IU-01A-11D-A397-08	A1BG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466930.1	1	0	1	81	244	0	68	0	6.345566e-02	0	2	0	68	2		0	0	0	0	0	2	1	1	80	242	0	67	2		0	0	0	0	0	2	-20.000000	1	1	121410	1	35	1	1	2	3	2.696253	1	0.580000	1.910000	0.674419	0.990000	9.000000e-01	1.000000	1.000000	0.992676	0.990000	1	9.900000e-01	1.000000
C1orf43	25912	broad.mit.edu	37	1	154192337	154192337	+	Missense_Mutation	SNP	A	A	T			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08			A	T	A	A		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr1:154192337A>T	ENST00000368521.5	-	2	341	c.143T>A	c.(142-144)gTc>gAc	p.V48D	C1orf43_ENST00000350592.3_Intron|UBAP2L_ENST00000271877.7_5'Flank|UBAP2L_ENST00000343815.6_5'Flank|C1orf43_ENST00000362076.4_Intron|UBAP2L_ENST00000428931.1_5'Flank|C1orf43_ENST00000368516.1_Intron|C1orf43_ENST00000368519.1_Missense_Mutation_p.V48D|C1orf43_ENST00000368518.1_Missense_Mutation_p.V48D	NM_001098616.1	NP_001092086.1	Q9BWL3	CA043_HUMAN	chromosome 1 open reading frame 43			10	all_lung(78;1.98e-30)|Lung NSC(65;2.87e-28)|Hepatocellular(266;0.0877)				TCCCACAGGGACATGAGGTCC	0.428000																								0							SO:0001583	missense			ENST00000368521.5	1	1	hg19	CCDS41404.1	.	.	.	.	.	.	.	.	.	.	A	26.4	4.736629	0.89482	.	.	ENSG00000143612	ENST00000368521;ENST00000368519;ENST00000368518	.	.	.	6.17	6.17	0.99709	.	0.054326	0.64402	D	0.000001	T	0.72479	0.3465	M	0.75615	2.305	0.80722	D	1	D;D	0.62365	0.982;0.991	P;P	0.62184	0.682;0.899	T	0.76515	-0.2931	9	0.72032	D	0.01	-18.2699	16.0034	0.80327	1.0:0.0:0.0:0.0	.	48;48	Q9BWL3-5;Q9BWL3	.;CA043_HUMAN	D	48	.	ENSP00000357504:V48D	V	-	2	0	C1orf43	152458961	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.842000	0.69417	2.371000	0.80710	0.533000	0.62120	GTC		TCGA-3A-A9IU-01A-11D-A397-08	C1orf43-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087664.2	1	0	1	82	311	0	65	1	1	121	262	0	65	2		0	0	0	0	0	2	1	1	82	311	0	65	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	1	2	3	2.611330	1	0.580000	1.910000	0.670717	0.920000	7.400000e-01	1.000000	1.000000	0.915880	0.920000	1	8.300000e-01	1.000000
TMEM79	84283	broad.mit.edu	37	1	156256255	156256255	+	Missense_Mutation	SNP	C	C	T			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr1:156256255C>T	ENST00000405535.2	+	3	1133	c.962C>T	c.(961-963)gCc>gTc	p.A321V	TMEM79_ENST00000495881.1_3'UTR|TMEM79_ENST00000295694.5_Missense_Mutation_p.A321V|TMEM79_ENST00000357501.2_Silent_p.C82C	NM_032323.2	NP_115699.1	Q9BSE2	TMM79_HUMAN	transmembrane protein 79			21	Hepatocellular(266;0.158)				GGTCTCTTTGCCGTCTCCCGG	0.562000																								0							SO:0001583	missense			ENST00000405535.2	0	1	hg19	CCDS1138.1	.	.	.	.	.	.	.	.	.	.	C	18.62	3.663832	0.67700	.	.	ENSG00000163472	ENST00000295694;ENST00000405535	T;T	0.50277	0.75;0.75	5.62	5.62	0.85841	.	0.169075	0.52532	D	0.000061	T	0.29684	0.0741	N	0.11427	0.14	0.58432	D	0.999999	P	0.51537	0.946	P	0.52646	0.705	T	0.10989	-1.0606	10	0.30854	T	0.27	-1.5462	16.3903	0.83532	0.0:1.0:0.0:0.0	.	321	Q9BSE2	TMM79_HUMAN	V	321	ENSP00000295694:A321V;ENSP00000384748:A321V	ENSP00000295694:A321V	A	+	2	0	TMEM79	154522879	1.000000	0.71417	0.996000	0.52242	0.971000	0.66376	4.836000	0.62789	2.645000	0.89757	0.462000	0.41574	GCC		TCGA-3A-A9IU-01A-11D-A397-08	TMEM79-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052101.1	0	0	0	6	616	0	73	0	7.890499e-02	0	40	0	73	2		0	0	0	0	0	2	1	9.644004e-01	6	612	0	72	2		0	0	0	0	0	2	-2.140398	0	1	0	0		1	1	2	3	2.611330	1	0.580000	1.910000	0.670717	0.040000	0	1.000000	0.040000	0.084190	0.040000	0	2.000000e-02	0.070000
KCNJ9	3765	broad.mit.edu	37	1	160054516	160054516	+	Silent	SNP	C	C	T			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr1:160054516C>T	ENST00000368088.3	+	2	938	c.696C>T	c.(694-696)ttC>ttT	p.F232F		NM_004983.2	NP_004974.2	Q92806	KCNJ9_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 9			16	all_cancers(52;5.86e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)		GCGTGGGCTTCGACACGGGAG	0.682000																								0							SO:0001819	synonymous_variant			ENST00000368088.3	0	1	hg19	CCDS1194.1																																																																																				TCGA-3A-A9IU-01A-11D-A397-08	KCNJ9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060628.1	0	0	0	3	52	0	10		0	0	0	0	10	2		0	0	0	0	0	2	1	8.125789e-01	3	52	0	10	2		0	0	0	0	0	2	-7.238686	1	1	0	0		1	1	2	3	2.611330	1	0.580000	1.910000	0.670717	0.280000	8.000000e-02	1.000000	0.230000	0.332260	0.280000	0	1.600000e-01	0.480000
DNMT3B	1789	broad.mit.edu	37	20	31388677	31388677	+	Missense_Mutation	SNP	G	G	A			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	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-3A-A9IU-01A-11D-A397-08	DNMT3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078643.2	0	0	0	5	804	1	147	0	6.362132e-05	0	2	1	147	2		0	0	0	0	0	2	0	2.948121e-03	5	799	1	146	19		0	0	0	0	0	2	-1.781598	0	1	0	0		1	0	1	1	2.044812	0	0.580000	1.910000	0.578778	0.010000	0	0.050000	0.020000	0.024952	0.010000	0	0	0.040000
OGFR	11054	broad.mit.edu	37	20	61444872	61444872	+	Silent	SNP	C	C	T			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr20:61444872C>T	ENST00000290291.6	+	7	1930	c.1905C>T	c.(1903-1905)gcC>gcT	p.A635A	OGFR_ENST00000370461.1_Silent_p.A583A	NM_007346.2	NP_031372.2	Q9NZT2	OGFR_HUMAN	opioid growth factor receptor			17	Breast(26;3.65e-08)				ACGAGCCAGCCGAGAGCCCAT	0.736000																								0							SO:0001819	synonymous_variant			ENST00000290291.6	0	1	hg19	CCDS13504.1																																																																																				TCGA-3A-A9IU-01A-11D-A397-08	OGFR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080067.1	0	0	0	4	308	0	60	0	1.213840e-02	0	10	0	60	2		0	0	0	0	0	2		0	0	0	0	0	2		0	0	0	0	0	2	-5.006299	1	0	0	0		1	0	1	1	2.044812	0	0.580000	1.910000	0.578778	0.040000	0	0.110000	0.040000	0.054451	0.040000	0	2.000000e-02	0.080000
GMEB2	26205	broad.mit.edu	37	20	62250746	62250746	+	Missense_Mutation	SNP	G	G	A			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr20:62250746G>A	ENST00000266068.1	-	1	483	c.5C>T	c.(4-6)gCg>gTg	p.A2V	GMEB2_ENST00000370077.1_Missense_Mutation_p.A2V			Q9UKD1	GMEB2_HUMAN	glucocorticoid modulatory element binding protein 2			18	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;4.79e-09)|all cancers(9;2.76e-08)|BRCA - Breast invasive adenocarcinoma(10;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(5;0.0114)		GTCGGGAGTCGCCATGGCTCA	0.632000																								0							SO:0001583	missense			ENST00000266068.1	0	1	hg19	CCDS13528.1	.	.	.	.	.	.	.	.	.	.	G	17.93	3.509854	0.64522	.	.	ENSG00000101216	ENST00000370077;ENST00000266068	T;T	0.67345	-0.26;-0.26	4.57	4.57	0.56435	.	0.150819	0.43260	D	0.000590	T	0.74007	0.3660	L	0.32530	0.975	0.43137	D	0.994882	D	0.76494	0.999	D	0.70716	0.97	T	0.78448	-0.2200	10	0.87932	D	0	-3.3315	17.3087	0.87202	0.0:0.0:1.0:0.0	.	2	Q9UKD1	GMEB2_HUMAN	V	2	ENSP00000359094:A2V;ENSP00000266068:A2V	ENSP00000266068:A2V	A	-	2	0	GMEB2	61721190	1.000000	0.71417	0.970000	0.41538	0.153000	0.21895	6.679000	0.74513	2.239000	0.73571	0.462000	0.41574	GCG		TCGA-3A-A9IU-01A-11D-A397-08	GMEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080166.1	0	0	0	5	202	0	46	0	2.890168e-02	0	9	0	46	2		0	0	0	0	0	2	1	9.367036e-01	5	200	0	45	2		0	0	0	0	0	2	-3.710251	1	1	121412	1	29	1	0	1	1	2.044812	0	0.580000	1.910000	0.578778	0.080000	2.000000e-02	0.180000	0.080000	0.098365	0.080000	0	5.000000e-02	0.140000
ZBED4	9889	broad.mit.edu	37	22	50279783	50279783	+	Missense_Mutation	SNP	G	G	A			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr22:50279783G>A	ENST00000216268.5	+	2	2950	c.2473G>A	c.(2473-2475)Gtg>Atg	p.V825M		NM_014838.2	NP_055653.2	O75132	ZBED4_HUMAN	zinc finger, BED-type containing 4			44		all_cancers(38;8.58e-10)|all_epithelial(38;1.15e-08)|all_lung(38;0.000109)|Lung NSC(38;0.0018)|Breast(42;0.00191)|Ovarian(80;0.0164)|Lung SC(80;0.164)			GCACTCGAGCGTGCAGTGCTT	0.627000																								0							SO:0001583	missense			ENST00000216268.5	1	1	hg19	CCDS33677.1	.	.	.	.	.	.	.	.	.	.	G	14.69	2.611814	0.46631	.	.	ENSG00000100426	ENST00000216268	T	0.28069	1.63	5.57	4.56	0.56223	Ribonuclease H-like (1);	0.118290	0.53938	D	0.000043	T	0.27866	0.0686	L	0.38175	1.15	0.48087	D	0.999586	D	0.57257	0.979	P	0.44518	0.452	T	0.02144	-1.1206	10	0.31617	T	0.26	-40.5602	14.3766	0.66881	0.071:0.0:0.929:0.0	.	825	O75132	ZBED4_HUMAN	M	825	ENSP00000216268:V825M	ENSP00000216268:V825M	V	+	1	0	ZBED4	48665787	1.000000	0.71417	0.995000	0.50966	0.809000	0.45718	2.802000	0.47916	1.345000	0.45676	0.655000	0.94253	GTG		TCGA-3A-A9IU-01A-11D-A397-08	ZBED4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317408.2	1	0	1	36	55	0	24	1	9.914573e-01	6	9	0	24	2		0	0	0	0	0	2	1	1	36	53	0	24	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	0	1	1	1.534266	1	0.580000	1.910000	0.410857	0.900000	7.000000e-01	1.000000	1.000000	0.895051	0.900000	1	8.000000e-01	0.980000
NMS	129521	broad.mit.edu	37	2	101089991	101089991	+	Missense_Mutation	SNP	G	G	A			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr2:101089991G>A	ENST00000376865.1	+	3	180	c.173G>A	c.(172-174)cGc>cAc	p.R58H		NM_001011717.1	NP_001011717.1	Q5H8A3	NMS_HUMAN	neuromedin S			14					CCTCTTTCTCGCCAACCTAAG	0.343000																								0							SO:0001583	missense			ENST00000376865.1	1	1	hg19	CCDS33259.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	3.177	-0.168837	0.06461	.	.	ENSG00000204640	ENST00000376865	T	0.23754	1.89	3.81	-3.39	0.04868	.	1.207740	0.05936	N	0.636093	T	0.16428	0.0395	L	0.44542	1.39	0.09310	N	1	P	0.46220	0.874	B	0.35971	0.215	T	0.25222	-1.0138	10	0.45353	T	0.12	3.2782	4.8169	0.13371	0.5921:0.0:0.2415:0.1664	.	58	Q5H8A3	NMS_HUMAN	H	58	ENSP00000366061:R58H	ENSP00000366061:R58H	R	+	2	0	NMS	100456423	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-0.190000	0.09615	-0.676000	0.05238	0.650000	0.86243	CGC		TCGA-3A-A9IU-01A-11D-A397-08	NMS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329737.1	1	0	1	39	121	0	15		0	0	0	0	15	2		0	0	0	0	0	2	1	1	39	120	0	15	2		0	0	0	0	0	2	-4.184800	1	1	121220	20	39	1	0	1	1	2.043824	0	0.580000	1.910000	0.578778	0.830000	6.200000e-01	1.000000	1.000000	0.839517	0.830000	0	7.200000e-01	0.960000
ROCK2	9475	broad.mit.edu	37	2	11337396	11337396	+	Missense_Mutation	SNP	G	G	A			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr2:11337396G>A	ENST00000315872.6	-	27	3806	c.3358C>T	c.(3358-3360)Cgg>Tgg	p.R1120W	ROCK2_ENST00000401753.1_Missense_Mutation_p.R877W	NM_004850.3	NP_004841.2	O75116	ROCK2_HUMAN	Rho-associated, coiled-coil containing protein kinase 2			43	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)				AGTTGTGACCGCAGCTGCTCA	0.438000																								0							SO:0001583	missense			ENST00000315872.6	0	1	hg19	CCDS42654.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.302523	0.81136	.	.	ENSG00000134318	ENST00000315872;ENST00000401753;ENST00000399089	T;T	0.64803	-0.12;0.93	5.72	4.85	0.62838	.	0.000000	0.85682	D	0.000000	T	0.77322	0.4113	M	0.71581	2.175	0.58432	D	0.999994	D	0.89917	1.0	D	0.71414	0.973	T	0.80453	-0.1376	10	0.87932	D	0	.	14.8283	0.70130	0.0692:0.0:0.9308:0.0	.	1120	O75116	ROCK2_HUMAN	W	1120;877;478	ENSP00000317985:R1120W;ENSP00000385509:R877W	ENSP00000317985:R1120W	R	-	1	2	ROCK2	11254847	1.000000	0.71417	0.987000	0.45799	0.990000	0.78478	3.726000	0.54977	1.418000	0.47098	0.563000	0.77884	CGG		TCGA-3A-A9IU-01A-11D-A397-08	ROCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313886.3	0	0	0	6	438	0	59	0	9.475727e-02	0	32	0	59	2		0	0	0	0	0	2	1	9.639671e-01	5	434	0	58	2		0	0	0	0	0	2	-2.392674	0	1	0	0		1	0	0	0	2.053432	0	0.580000	1.910000	0.580000	0.040000	1.000000e-02	0.100000	0.040000	0.054021	0.040000	0	2.000000e-02	0.070000
SMPD4	55627	broad.mit.edu	37	2	130910653	130910653	+	Missense_Mutation	SNP	C	C	T			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr2:130910653C>T	ENST00000409031.1	-	19	3382	c.2234G>A	c.(2233-2235)cGc>cAc	p.R745H	SMPD4_ENST00000339679.7_Missense_Mutation_p.R603H|SMPD4_ENST00000443958.2_Missense_Mutation_p.R409H|SMPD4_ENST00000453750.1_Missense_Mutation_p.R494H|SMPD4_ENST00000351288.6_Missense_Mutation_p.R716H|SMPD4_ENST00000426662.2_Missense_Mutation_p.R381H|SMPD4_ENST00000452225.2_Missense_Mutation_p.R486H|SMPD4_ENST00000431183.2_Missense_Mutation_p.R643H|SMPD4_ENST00000473720.1_5'Flank	NM_017951.4	NP_060421.2	Q9NXE4	NSMA3_HUMAN	sphingomyelin phosphodiesterase 4, neutral membrane (neutral sphingomyelinase-3)			29	Colorectal(110;0.1)			Phosphatidylserine(DB00144)	AAAGAGTGTGCGGACCAAGCT	0.582000																								0							SO:0001583	missense			ENST00000409031.1	0	1	hg19	CCDS42751.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	18.14|18.14	3.557063|3.557063	0.65425|0.65425	2.27E-4|2.27E-4	0.0|0.0	ENSG00000136699|ENSG00000136699	ENST00000439886|ENST00000351288;ENST00000409031;ENST00000431183;ENST00000453750;ENST00000443958;ENST00000339679;ENST00000452225;ENST00000426662	.|.	.|.	.|.	4.09|4.09	4.09|4.09	0.47781|0.47781	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.79604|0.79604	0.4474|0.4474	M|M	0.82323|0.82323	2.585|2.585	0.54753|0.54753	D|D	0.99998|0.99998	.|D;D;D;D;D;D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0;1.0;0.997;1.0;1.0;1.0;1.0	.|D;D;D;D;D;D;D;D;D;D	.|0.85130	.|0.984;0.987;0.995;0.989;0.997;0.937;0.959;0.997;0.993;0.984	T|T	0.83285|0.83285	-0.0036|-0.0036	5|9	.|0.72032	.|D	.|0.01	.|.	13.8586|13.8586	0.63545|0.63545	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|381;486;643;603;494;677;706;745;752;277	.|B4E0L6;B4DQ31;E7ESA2;B4E0T5;B4DM23;Q9NXE4-2;Q9NXE4;B1PBA3;Q9NXE4-4;Q9NXE4-5	.|.;.;.;.;.;.;NSMA3_HUMAN;.;.;.	T|H	620|716;745;643;494;409;603;486;381	.|.	.|ENSP00000339721:R603H	A|R	-|-	1|2	0|0	SMPD4|SMPD4	130627123|130627123	1.000000|1.000000	0.71417|0.71417	0.871000|0.871000	0.34182|0.34182	0.066000|0.066000	0.16364|0.16364	7.434000|7.434000	0.80377|0.80377	1.820000|1.820000	0.53075|0.53075	0.549000|0.549000	0.68633|0.68633	GCA|CGC		TCGA-3A-A9IU-01A-11D-A397-08	SMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254516.3	0	0	0	5	431	0	109	0	6.516198e-01	0	179	0	109	2		0	0	0	0	0	2	1	9.371228e-01	5	429	0	108	2		0	0	0	0	0	2	-1.770476	0	1	121412	2	36	1	0	1	1	2.043824	0	0.580000	1.910000	0.578778	0.030000	0	0.090000	0.040000	0.046817	0.030000	0	2.000000e-02	0.070000
ITGA6	3655	broad.mit.edu	37	2	173333951	173333951	+	Missense_Mutation	SNP	G	G	T			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr2:173333951G>T	ENST00000264106.6	+	4	689	c.486G>T	c.(484-486)agG>agT	p.R162S	ITGA6_ENST00000409532.1_Missense_Mutation_p.R48S|ITGA6_ENST00000264107.7_Missense_Mutation_p.R162S|ITGA6_ENST00000409080.1_Missense_Mutation_p.R162S|ITGA6_ENST00000375221.2_Missense_Mutation_p.R162S|ITGA6_ENST00000343713.4_Missense_Mutation_p.R162S			P23229	ITA6_HUMAN	integrin, alpha 6			44			OV - Ovarian serous cystadenocarcinoma(117;0.0979)		AGAATCTCAGGATTGAAGACG	0.473000																								0							SO:0001583	missense			ENST00000264106.6	0	1	hg19		.	.	.	.	.	.	.	.	.	.	G	11.49	1.653589	0.29425	.	.	ENSG00000091409	ENST00000412899;ENST00000409532;ENST00000264107;ENST00000264106;ENST00000375221;ENST00000343713;ENST00000409080;ENST00000442250;ENST00000458358	T;T;T;T;T;T;T;T;T	0.69926	-0.44;-0.44;-0.44;-0.44;-0.44;-0.44;-0.44;-0.44;-0.44	6.17	-0.233	0.13078	.	0.138320	0.64402	D	0.000003	T	0.23370	0.0565	N	0.01152	-0.98	0.36788	D	0.884674	B;B;B	0.06786	0.001;0.001;0.0	B;B;B	0.09377	0.004;0.004;0.004	T	0.18555	-1.0333	10	0.06365	T	0.9	.	0.6097	0.00759	0.3751:0.2013:0.241:0.1826	.	162;162;162	P23229-4;G5E9H1;P23229-2	.;.;.	S	48;48;162;162;162;162;162;162;162	ENSP00000413470:R48S;ENSP00000386614:R48S;ENSP00000264107:R162S;ENSP00000264106:R162S;ENSP00000364369:R162S;ENSP00000341078:R162S;ENSP00000386896:R162S;ENSP00000406694:R162S;ENSP00000394169:R162S	ENSP00000264106:R162S	R	+	3	2	ITGA6	173042197	0.334000	0.24739	1.000000	0.80357	0.995000	0.86356	0.224000	0.17738	0.471000	0.27319	0.655000	0.94253	AGG		TCGA-3A-A9IU-01A-11D-A397-08	ITGA6-201	KNOWN	basic	protein_coding	protein_coding		0	0	0	10	638	0	96	0	4.999536e-01	0	102	0	96	2		0	0	0	0	0	2	1	9.968389e-01	10	635	0	96	2		0	0	0	0	0	2	-2.885254	1	1	0	0		1	0	1	1	2.043824	0	0.580000	1.910000	0.578778	0.050000	2.000000e-02	0.100000	0.060000	0.058132	0.050000	0	3.000000e-02	0.080000
CHRNA1	1134	broad.mit.edu	37	2	175612881	175612881	+	Nonsense_Mutation	SNP	G	G	A			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr2:175612881G>A	ENST00000261007.5	-	10	1486	c.1420C>T	c.(1420-1422)Cga>Tga	p.R474*	CHRNA1_ENST00000409542.1_Nonsense_Mutation_p.R367*|CHRNA1_ENST00000409219.1_Nonsense_Mutation_p.R369*|AC018890.6_ENST00000442996.1_RNA|CHRNA1_ENST00000348749.5_Nonsense_Mutation_p.R449*	NM_001039523.2	NP_001034612.1	P02708	ACHA_HUMAN	cholinergic receptor, nicotinic, alpha 1 (muscle)			37				Galantamine(DB00674)	TCAATGAGTCGACCTGCAAAC	0.502000																								0							SO:0001587	stop_gained			ENST00000261007.5	0	1	hg19	CCDS33331.1	.	.	.	.	.	.	.	.	.	.	G	36	5.913560	0.97099	.	.	ENSG00000138435	ENST00000348749;ENST00000261007;ENST00000409542;ENST00000409219	.	.	.	5.24	5.24	0.73138	.	0.159217	0.56097	D	0.000024	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.33141	T	0.24	.	19.1987	0.93701	0.0:0.0:1.0:0.0	.	.	.	.	X	449;474;367;369	.	ENSP00000261007:R474X	R	-	1	2	CHRNA1	175321127	1.000000	0.71417	0.998000	0.56505	0.989000	0.77384	6.397000	0.73239	2.607000	0.88179	0.655000	0.94253	CGA		TCGA-3A-A9IU-01A-11D-A397-08	CHRNA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000334116.1	0	0	0	4	245	0	25	0	6.607742e-03	0	6	0	25	2		0	0	0	0	0	2	1	8.892017e-01	4	243	0	25	2		0	0	0	0	0	2	-5.306639	1	1	0	0		1	0	1	1	2.043824	0	0.580000	1.910000	0.578778	0.050000	1.000000e-02	0.130000	0.060000	0.068220	0.050000	0	3.000000e-02	0.100000
FOSL2	2355	broad.mit.edu	37	2	28635275	28635275	+	Missense_Mutation	SNP	C	C	T			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr2:28635275C>T	ENST00000264716.4	+	4	1804	c.941C>T	c.(940-942)tCa>tTa	p.S314L	FOSL2_ENST00000379619.1_Missense_Mutation_p.S306L|FOSL2_ENST00000545753.1_Missense_Mutation_p.S275L	NM_005253.3	NP_005244.1	P15408	FOSL2_HUMAN	FOS-like antigen 2			14	Acute lymphoblastic leukemia(172;0.155)				GGGGACCAATCATCAGACTCC	0.622000																								0							SO:0001583	missense			ENST00000264716.4	1	1	hg19	CCDS1766.1	.	.	.	.	.	.	.	.	.	.	C	33	5.217527	0.95104	.	.	ENSG00000075426	ENST00000379619;ENST00000264716;ENST00000545753	D;T;D	0.86497	-2.06;-1.13;-2.13	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	D	0.88518	0.6458	M	0.77616	2.38	0.80722	D	1	P	0.47762	0.9	B	0.40602	0.334	D	0.90308	0.4335	10	0.87932	D	0	-0.9556	19.8481	0.96728	0.0:1.0:0.0:0.0	.	314	P15408	FOSL2_HUMAN	L	306;314;275	ENSP00000368939:S306L;ENSP00000264716:S314L;ENSP00000439303:S275L	ENSP00000264716:S314L	S	+	2	0	FOSL2	28488779	1.000000	0.71417	0.986000	0.45419	0.994000	0.84299	4.804000	0.62554	2.693000	0.91896	0.655000	0.94253	TCA		TCGA-3A-A9IU-01A-11D-A397-08	FOSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215116.2	1	0	1	54	147	0	41	1	1	42	191	0	41	2		0	0	0	0	0	2	1	1	54	146	0	41	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	0	0	0	2.053432	0	0.580000	1.910000	0.580000	0.920000	7.200000e-01	1.000000	1.000000	0.913582	0.920000	1	8.100000e-01	1.000000
TTC27	55622	broad.mit.edu	37	2	33003024	33003024	+	Missense_Mutation	SNP	C	C	T			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr2:33003024C>T	ENST00000317907.4	+	14	1987	c.1756C>T	c.(1756-1758)Cgc>Tgc	p.R586C		NM_001193509.1|NM_017735.4	NP_001180438.1|NP_060205.3	Q6P3X3	TTC27_HUMAN	tetratricopeptide repeat domain 27			38					GGCATTTCAGCGCTGTGTGAC	0.438000																								0							SO:0001583	missense			ENST00000317907.4	0	1	hg19	CCDS33176.1	.	.	.	.	.	.	.	.	.	.	C	18.14	3.557601	0.65425	.	.	ENSG00000018699	ENST00000317907	T	0.61859	0.07	5.32	5.32	0.75619	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.049606	0.64402	D	0.000001	D	0.85230	0.5649	H	0.97758	4.07	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.90675	0.4601	10	0.87932	D	0	-9.9189	19.0041	0.92843	0.0:1.0:0.0:0.0	.	586	Q6P3X3	TTC27_HUMAN	C	586	ENSP00000313953:R586C	ENSP00000313953:R586C	R	+	1	0	TTC27	32856528	1.000000	0.71417	1.000000	0.80357	0.532000	0.34746	4.480000	0.60243	2.465000	0.83290	0.557000	0.71058	CGC		TCGA-3A-A9IU-01A-11D-A397-08	TTC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325395.1	0	0	0	4	247	0	42	0	2.125085e-01	0	43	0	42	2		0	0	0	0	0	2	1	8.872906e-01	4	243	0	42	2		0	0	0	0	0	2	-2.975077	1	1	121412	2	36	1	0	0	0	2.053432	0	0.580000	1.910000	0.580000	0.050000	1.000000e-02	0.130000	0.060000	0.067856	0.050000	0	3.000000e-02	0.100000
LMAN2L	81562	broad.mit.edu	37	2	97400208	97400208	+	Missense_Mutation	SNP	C	C	G			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08			C	G	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr2:97400208C>G	ENST00000264963.4	-	3	384	c.362G>C	c.(361-363)gGa>gCa	p.G121A	LMAN2L_ENST00000426463.2_Missense_Mutation_p.E4Q|LMAN2L_ENST00000537039.1_5'UTR|LMAN2L_ENST00000534882.1_Missense_Mutation_p.E4Q|LMAN2L_ENST00000377079.4_Missense_Mutation_p.G121A	NM_030805.3	NP_110432.1	Q9H0V9	LMA2L_HUMAN	lectin, mannose-binding 2-like			7					ATTCTTCTTTCCTTGTCCATG	0.468000																								0							SO:0001583	missense			ENST00000264963.4	1	1	hg19	CCDS2023.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.6|20.6	4.011148|4.011148	0.75046|0.75046	.|.	.|.	ENSG00000114988|ENSG00000114988	ENST00000426463;ENST00000534882|ENST00000264963;ENST00000377079	T;T|T;T	0.78924|0.63255	-1.22;-1.16|-0.03;-0.03	5.95|5.95	5.95|5.95	0.96441|0.96441	.|Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.81828|0.81828	0.4905|0.4905	M|M	0.83223|0.83223	2.63|2.63	0.80722|0.80722	D|D	1|1	B;B|D;D	0.20550|0.89917	0.046;0.046|0.986;1.0	B;B|P;D	0.22386|0.91635	0.039;0.039|0.768;0.999	T|T	0.82348|0.82348	-0.0502|-0.0502	9|10	0.39692|0.56958	T|D	0.17|0.05	.|.	19.1527|19.1527	0.93495|0.93495	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	4;4|121;121	B4DVH1;B4DSH3|Q9H0V9-2;Q9H0V9	.;.|.;LMA2L_HUMAN	Q|A	4|121	ENSP00000396391:E4Q;ENSP00000438501:E4Q|ENSP00000264963:G121A;ENSP00000366280:G121A	ENSP00000396391:E4Q|ENSP00000264963:G121A	E|G	-|-	1|2	0|0	LMAN2L|LMAN2L	96763935|96763935	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.967000|0.967000	0.64934|0.64934	7.468000|7.468000	0.80943|0.80943	2.821000|2.821000	0.97095|0.97095	0.650000|0.650000	0.86243|0.86243	GAA|GGA		TCGA-3A-A9IU-01A-11D-A397-08	LMAN2L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252844.1	1	0	1	85	207	0	64	1	9.995103e-01	9	22	0	64	2		0	0	0	0	0	2	1	1	83	205	0	63	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	0	1	1	2.043824	0	0.580000	1.910000	0.578778	0.990000	8.200000e-01	1.000000	1.000000	0.965253	0.990000	1	9.000000e-01	1.000000
ILDR1	286676	broad.mit.edu	37	3	121720701	121720701	+	Silent	SNP	G	G	A			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr3:121720701G>A	ENST00000344209.5	-	4	516	c.390C>T	c.(388-390)ctC>ctT	p.L130L	ILDR1_ENST00000273691.3_Silent_p.L130L|ILDR1_ENST00000460554.1_5'UTR|ILDR1_ENST00000393631.1_Intron|ILDR1_ENST00000462014.1_Silent_p.L142L	NM_001199799.1	NP_001186728.1	Q86SU0	ILDR1_HUMAN	immunoglobulin-like domain containing receptor 1			25					CATTTATCACGAGATCTGCTC	0.517000																								0							SO:0001819	synonymous_variant			ENST00000344209.5	1	1	hg19	CCDS56271.1																																																																																				TCGA-3A-A9IU-01A-11D-A397-08	ILDR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355666.1	1	0	1	58	151	0	25	1	9.083933e-01	3	10	0	25	2		0	0	0	0	0	2	1	1	58	148	0	25	2		0	0	0	0	0	2	-5.535798	1	1	121412	1	27	1	0	0	0	2.055893	0	0.580000	1.910000	0.580000	0.950000	7.500000e-01	1.000000	1.000000	0.934903	0.950000	1	8.400000e-01	1.000000
TNIK	23043	broad.mit.edu	37	3	170786732	170786732	+	Missense_Mutation	SNP	C	C	T			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr3:170786732C>T	ENST00000436636.2	-	30	3948	c.3604G>A	c.(3604-3606)Ggt>Agt	p.G1202S	TNIK_ENST00000538048.1_Missense_Mutation_p.G1154S|TNIK_ENST00000341852.6_Missense_Mutation_p.G1118S|TNIK_ENST00000470834.1_Missense_Mutation_p.G1165S|TNIK_ENST00000460047.1_Missense_Mutation_p.G1139S|TNIK_ENST00000475336.1_Missense_Mutation_p.G1110S|TNIK_ENST00000369326.5_Missense_Mutation_p.G1180S|TNIK_ENST00000488470.1_Missense_Mutation_p.G1147S|TNIK_ENST00000357327.5_Missense_Mutation_p.G1173S|TNIK_ENST00000284483.8_Missense_Mutation_p.G1194S	NM_015028.2	NP_055843.1	Q9UKE5	TNIK_HUMAN	TRAF2 and NCK interacting kinase			62	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)		AATCTTTGACCTTCTTCTACC	0.388000																								0							SO:0001583	missense			ENST00000436636.2	1	1	hg19	CCDS46956.1	.	.	.	.	.	.	.	.	.	.	C	28.8	4.954878	0.92726	.	.	ENSG00000154310	ENST00000436636;ENST00000369326;ENST00000538048;ENST00000341852;ENST00000284483;ENST00000475336;ENST00000357327;ENST00000460047;ENST00000488470;ENST00000470834	T;T;T;T;T;T;T;T;T;T	0.75154	-0.89;-0.88;-0.9;-0.9;-0.89;-0.89;-0.9;-0.9;-0.91;-0.89	6.06	6.06	0.98353	Citron-like (3);	0.000000	0.85682	D	0.000000	D	0.86108	0.5854	M	0.77616	2.38	0.80722	D	1	D;P;P;P;P;D;P;P;D	0.61080	0.979;0.748;0.863;0.884;0.748;0.986;0.936;0.884;0.989	P;B;B;B;B;P;B;B;P	0.61003	0.882;0.319;0.437;0.41;0.319;0.8;0.437;0.41;0.874	D	0.86263	0.1656	10	0.72032	D	0.01	.	20.6208	0.99490	0.0:1.0:0.0:0.0	.	1154;1110;1165;1139;1118;1194;1173;1147;1202	F5H5M9;Q9UKE5-8;Q9UKE5-6;Q9UKE5-7;Q9UKE5-5;Q9UKE5-4;Q9UKE5-2;Q9UKE5-3;Q9UKE5	.;.;.;.;.;.;.;.;TNIK_HUMAN	S	1202;1180;1154;1118;1194;1110;1173;1139;1147;1165	ENSP00000399511:G1202S;ENSP00000358332:G1180S;ENSP00000443278:G1154S;ENSP00000345352:G1118S;ENSP00000284483:G1194S;ENSP00000418156:G1110S;ENSP00000349880:G1173S;ENSP00000418916:G1139S;ENSP00000418378:G1147S;ENSP00000419990:G1165S	ENSP00000284483:G1194S	G	-	1	0	TNIK	172269426	1.000000	0.71417	1.000000	0.80357	0.756000	0.42949	5.920000	0.70017	2.882000	0.98803	0.655000	0.94253	GGT		TCGA-3A-A9IU-01A-11D-A397-08	TNIK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352973.2	1	0	1	114	303	0	54	1	9.052270e-01	5	8	0	54	2		0	0	0	0	0	2	1	1	113	301	0	54	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	0	0	0	2.055893	0	0.580000	1.910000	0.580000	0.930000	7.900000e-01	1.000000	1.000000	0.934338	0.930000	1	8.600000e-01	1.000000
PCYT1A	5130	broad.mit.edu	37	3	195975170	195975170	+	Missense_Mutation	SNP	G	G	A			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr3:195975170G>A	ENST00000292823.2	-	5	414	c.242C>T	c.(241-243)gCc>gTc	p.A81V	PCYT1A_ENST00000419333.1_Missense_Mutation_p.A81V|RP11-447L10.1_ENST00000431391.1_3'UTR|AC069257.8_ENST00000425275.1_RNA|PCYT1A_ENST00000431016.1_Missense_Mutation_p.A81V|AC069257.8_ENST00000608995.1_RNA|PCYT1A_ENST00000491544.1_5'UTR	NM_005017.2	NP_005008.2	P49585	PCY1A_HUMAN	phosphate cytidylyltransferase 1, choline, alpha			18	all_cancers(143;1.19e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.28e-24)|all cancers(36;1.01e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	Choline(DB00122)|Lamivudine(DB00709)	TATTCCATCGGCATAAACTCT	0.383000																								0							SO:0001583	missense			ENST00000292823.2	0	1	hg19	CCDS3315.1	.	.	.	.	.	.	.	.	.	.	g	26.8	4.769299	0.90020	.	.	ENSG00000161217	ENST00000441879;ENST00000419333;ENST00000292823;ENST00000416798;ENST00000431016;ENST00000411591;ENST00000430755;ENST00000412869;ENST00000443555	D;D;D;D;D;D;D;D	0.96913	-4.17;-4.17;-4.17;-4.17;-4.17;-4.17;-4.17;-4.17	5.67	5.67	0.87782	Cytidylyltransferase (1);Rossmann-like alpha/beta/alpha sandwich fold (1);Cytidyltransferase-related (1);	0.044612	0.85682	D	0.000000	D	0.97334	0.9128	L	0.48260	1.515	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.98016	1.0368	10	0.87932	D	0	-4.6307	18.8171	0.92081	0.0:0.0:1.0:0.0	.	81	P49585	PCY1A_HUMAN	V	81;81;81;42;81;81;15;81;81	ENSP00000392397:A81V;ENSP00000390968:A81V;ENSP00000292823:A81V;ENSP00000394617:A81V;ENSP00000400430:A81V;ENSP00000402283:A15V;ENSP00000402015:A81V;ENSP00000393341:A81V	ENSP00000292823:A81V	A	-	2	0	PCYT1A	197459567	1.000000	0.71417	0.998000	0.56505	0.423000	0.31445	9.472000	0.97709	2.686000	0.91538	0.645000	0.84053	GCC		TCGA-3A-A9IU-01A-11D-A397-08	PCYT1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341147.1	0	0	0	5	347	0	74	0	1.301313e-01	0	36	0	74	2		0	0	0	0	0	2	1	9.365585e-01	5	344	0	73	2		0	0	0	0	0	2	-2.659890	1	1	0	0		1	1	2	3	2.065867	0	0.580000	1.910000	0.581214	0.050000	1.000000e-02	0.110000	0.050000	0.058442	0.050000	0	2.000000e-02	0.080000
GRM2	2912	broad.mit.edu	37	3	51743211	51743211	+	Missense_Mutation	SNP	G	G	A	rs144180122	by1000genomes	TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr3:51743211G>A	ENST00000395052.3	+	2	446	c.212G>A	c.(211-213)cGc>cAc	p.R71H	GRM2_ENST00000442933.2_Missense_Mutation_p.R71H|GRM2_ENST00000475478.1_Intron	NM_000839.3	NP_000830.2	Q14416	GRM2_HUMAN	glutamate receptor, metabotropic 2			33					GCACTGGACCGCATCAACCGT	0.632000																								0							SO:0001583	missense			ENST00000395052.3	0	1	hg19	CCDS2834.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.247197	0.80024	.	.	ENSG00000164082	ENST00000395052;ENST00000442933	D;D	0.86497	-2.13;-2.13	5.28	4.41	0.53225	Extracellular ligand-binding receptor (1);	0.167226	0.46758	D	0.000274	T	0.81093	0.4751	L	0.56199	1.76	0.42153	D	0.991563	B	0.28419	0.211	B	0.21917	0.037	T	0.78252	-0.2276	10	0.62326	D	0.03	.	5.1701	0.15105	0.2123:0.1632:0.6245:0.0	.	71	Q14416	GRM2_HUMAN	H	71	ENSP00000378492:R71H;ENSP00000408906:R71H	ENSP00000296479:R71H	R	+	2	0	GRM2	51718251	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.691000	0.54720	1.245000	0.43885	-0.137000	0.14449	CGC		TCGA-3A-A9IU-01A-11D-A397-08	GRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346542.1	0	0	0	6	671	0	148		0	0	0	0	148	2		0	0	0	0	0	2	1	9.644367e-01	6	667	0	147	2		0	0	0	0	0	2	-1.831932	0	1	0	0		1	0	0	0	2.055893	0	0.580000	1.910000	0.580000	0.020000	0	0.070000	0.040000	0.034823	0.020000	0	1.000000e-02	0.050000
STAB1	23166	broad.mit.edu	37	3	52555958	52555958	+	Missense_Mutation	SNP	G	G	A	rs144247661	byFrequency	TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08			G	A	G	G		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr3:52555958G>A	ENST00000321725.6	+	58	6338	c.6262G>A	c.(6262-6264)Gtg>Atg	p.V2088M		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	p.V2088L(1)		76					GGATGGCCGTGTGTGTACAGG	0.642000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000321725.6	1	1	hg19	CCDS33768.1	.	.	.	.	.	.	.	.	.	.	G	7.022	0.558925	0.13436	6.81E-4	0.0	ENSG00000010327	ENST00000321725	D	0.87571	-2.27	5.75	-2.33	0.06724	Epidermal growth factor-like (1);EGF-like region, conserved site (1);Epidermal growth factor-like, type 3 (1);	1.447070	0.03638	N	0.239087	T	0.71005	0.3289	N	0.08118	0	0.09310	N	1	P	0.38148	0.62	B	0.36885	0.235	T	0.64597	-0.6370	10	0.66056	D	0.02	.	0.7708	0.01024	0.384:0.1181:0.262:0.2359	.	2088	Q9NY15	STAB1_HUMAN	M	2088	ENSP00000312946:V2088M	ENSP00000312946:V2088M	V	+	1	0	STAB1	52530998	0.000000	0.05858	0.003000	0.11579	0.000000	0.00434	0.653000	0.24902	-0.277000	0.09193	-1.130000	0.01982	GTG		TCGA-3A-A9IU-01A-11D-A397-08	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	1	0	1	66	169	0	50	0	9.986905e-01	0	29	0	50	2		0	0	0	0	0	2	1	1	65	167	0	50	2		0	0	0	0	0	2	-20.000000	1	1	121220	24	45	1	0	0	0	2.055893	0	0.580000	1.910000	0.580000	0.960000	7.700000e-01	1.000000	1.000000	0.943979	0.960000	1	8.600000e-01	1.000000
SORCS2	57537	broad.mit.edu	37	4	7533314	7533314	+	Silent	SNP	C	C	T			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr4:7533314C>T	ENST00000507866.2	+	3	715	c.606C>T	c.(604-606)acC>acT	p.T202T	SORCS2_ENST00000511199.1_3'UTR|SORCS2_ENST00000329016.9_Silent_p.T30T	NM_020777.2	NP_065828.2	Q96PQ0	SORC2_HUMAN	sortilin-related VPS10 domain containing receptor 2			42					GTGTCACCACCGTCATCGACA	0.602000																								0							SO:0001819	synonymous_variant			ENST00000507866.2	1	1	hg19	CCDS47008.1																																																																																				TCGA-3A-A9IU-01A-11D-A397-08	SORCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358685.4	1	0	0	49	127	1	20	0	3.997764e-01	0	8	1	20	3		0	0	0	0	0	2	1	9.997850e-01	49	125	1	20	23		0	0	0	0	0	2	-5.351211	1	1	121052	50	45	1	1	2	3	2.100555	0	0.580000	1.910000	0.584816	0.970000	7.500000e-01	1.000000	1.000000	0.941796	0.970000	1	8.500000e-01	1.000000
ACOT12	134526	broad.mit.edu	37	5	80667586	80667586	+	Missense_Mutation	SNP	A	A	G			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr5:80667586A>G	ENST00000307624.3	-	3	269	c.241T>C	c.(241-243)Ttc>Ctc	p.F81L	ACOT12_ENST00000513751.1_Missense_Mutation_p.F81L	NM_130767.2	NP_570123.1	Q8WYK0	ACO12_HUMAN	acyl-CoA thioesterase 12			23		Lung NSC(167;0.0176)|all_lung(232;0.0205)|Ovarian(174;0.135)			CTTGTGCTGAATGCTCTAGTA	0.393000																								0							SO:0001583	missense			ENST00000307624.3	1	1	hg19	CCDS4055.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.532595	0.85812	.	.	ENSG00000172497	ENST00000307624;ENST00000513751	T;T	0.21734	1.99;1.99	5.8	5.8	0.92144	Thioesterase superfamily (1);	0.000000	0.85682	D	0.000000	T	0.53190	0.1781	M	0.90650	3.135	0.52099	D	0.999946	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.60120	-0.7325	10	0.46703	T	0.11	-10.442	13.6838	0.62504	1.0:0.0:0.0:0.0	.	81;81	Q5FWE9;Q8WYK0	.;ACO12_HUMAN	L	81	ENSP00000303246:F81L;ENSP00000421628:F81L	ENSP00000303246:F81L	F	-	1	0	ACOT12	80703342	1.000000	0.71417	0.982000	0.44146	0.992000	0.81027	5.817000	0.69229	2.227000	0.72691	0.460000	0.39030	TTC		TCGA-3A-A9IU-01A-11D-A397-08	ACOT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254074.1	1	0	1	64	176	0	25		0	0	0	0	25	2		0	0	0	0	0	2	1	1	64	176	0	25	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	1	2	3	2.074995	0	0.580000	1.910000	0.581214	0.910000	7.300000e-01	1.000000	1.000000	0.912756	0.910000	1	8.200000e-01	1.000000
GPR98	84059	broad.mit.edu	37	5	90046453	90046453	+	Missense_Mutation	SNP	G	G	A			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr5:90046453G>A	ENST00000405460.2	+	53	11156	c.11060G>A	c.(11059-11061)cGt>cAt	p.R3687H		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98			269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)			ACATATGGCCGTATAACCATA	0.343000																								0							SO:0001583	missense			ENST00000405460.2	0	1	hg19	CCDS47246.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.95|12.95	2.092138|2.092138	0.36952|0.36952	.|.	.|.	ENSG00000164199|ENSG00000164199	ENST00000405460;ENST00000296619|ENST00000509621	T|.	0.27720|.	1.65|.	5.52|5.52	1.66|1.66	0.24008|0.24008	.|.	0.152878|.	0.64402|.	N|.	0.000017|.	T|T	0.55097|0.55097	0.1899|0.1899	L|L	0.45051|0.45051	1.395|1.395	0.80722|0.80722	D|D	1|1	B;B|.	0.26483|.	0.15;0.101|.	B;B|.	0.18561|.	0.022;0.01|.	T|T	0.43653|0.43653	-0.9378|-0.9378	10|5	0.37606|.	T|.	0.19|.	.|.	11.2443|11.2443	0.48987|0.48987	0.2377:0.0:0.7623:0.0|0.2377:0.0:0.7623:0.0	.|.	3687;3687|.	E7ETI5;Q8WXG9|.	.;GPR98_HUMAN|.	H|I	3687|1253	ENSP00000384582:R3687H|.	ENSP00000296619:R3687H|.	R|V	+|+	2|1	0|0	GPR98|GPR98	90082209|90082209	0.096000|0.096000	0.21769|0.21769	0.050000|0.050000	0.19076|0.19076	0.779000|0.779000	0.44077|0.44077	0.982000|0.982000	0.29539|0.29539	0.028000|0.028000	0.15324|0.15324	-0.123000|-0.123000	0.14984|0.14984	CGT|GTA		TCGA-3A-A9IU-01A-11D-A397-08	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	0	0	0	5	602	0	72		0	0	0	0	72	2		0	0	0	0	0	2	1	9.369563e-01	5	599	0	72	2		0	0	0	0	0	2	-1.922761	0	1	120822	8	41	1	1	2	3	2.074995	0	0.580000	1.910000	0.581214	0.020000	0	0.070000	0.030000	0.033299	0.020000	0	1.000000e-02	0.050000
LNPEP	4012	broad.mit.edu	37	5	96342191	96342191	+	Silent	SNP	A	A	G			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr5:96342191A>G	ENST00000231368.5	+	11	2699	c.2007A>G	c.(2005-2007)caA>caG	p.Q669Q	LNPEP_ENST00000395770.3_Silent_p.Q655Q	NM_005575.2	NP_005566.2	Q9UIQ6	LCAP_HUMAN	leucyl/cystinyl aminopeptidase			34		all_cancers(142;7e-07)|all_epithelial(76;9.52e-10)|all_lung(232;0.00101)|Lung NSC(167;0.00137)|Ovarian(225;0.024)|Colorectal(57;0.0269)|Breast(839;0.244)			CAAAATATCAATCGGTATCAT	0.308000																								0							SO:0001819	synonymous_variant			ENST00000231368.5	1	1	hg19	CCDS4087.1																																																																																				TCGA-3A-A9IU-01A-11D-A397-08	LNPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250624.1	1	0	1	101	271	0	35	1	7.476668e-01	3	6	0	35	2		0	0	0	0	0	2	1	1	100	270	0	34	2		0	0	0	0	0	2	-20.000000	1	1	121386	5	36	1	1	2	3	2.074995	0	0.580000	1.910000	0.581214	0.930000	7.800000e-01	1.000000	1.000000	0.930317	0.930000	1	8.500000e-01	1.000000
ELOVL2	54898	broad.mit.edu	37	6	10984107	10984107	+	Missense_Mutation	SNP	C	C	A			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr6:10984107C>A	ENST00000354666.3	-	8	881	c.798G>T	c.(796-798)atG>atT	p.M266I		NM_017770.3	NP_060240.3	Q9NXB9	ELOV2_HUMAN	ELOVL fatty acid elongase 2			14	Breast(50;0.0418)|Ovarian(93;0.0919)	all_hematologic(90;0.117)	Epithelial(50;0.176)		GTGGCTCTTGCATATCTTTCT	0.353000																								0							SO:0001583	missense			ENST00000354666.3	1	1	hg19	CCDS4518.1	.	.	.	.	.	.	.	.	.	.	C	11.38	1.622984	0.28889	.	.	ENSG00000197977	ENST00000354666	T	0.21191	2.02	5.2	1.35	0.21983	.	.	.	.	.	T	0.02727	0.0082	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.44847	-0.9301	9	0.38643	T	0.18	1.9891	4.5775	0.12241	0.0:0.4456:0.1567:0.3977	.	266	Q9NXB9	ELOV2_HUMAN	I	266	ENSP00000346693:M266I	ENSP00000346693:M266I	M	-	3	0	ELOVL2	11092093	0.000000	0.05858	0.000000	0.03702	0.709000	0.40893	-0.408000	0.07169	0.020000	0.15106	0.650000	0.86243	ATG		TCGA-3A-A9IU-01A-11D-A397-08	ELOVL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039849.1	1	0	1	64	186	0	41	0	1.663651e-01	0	3	0	41	2		0	0	0	0	0	2	1	1	63	183	0	41	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	0	0	0	2.026811	0	0.580000	1.910000	0.575071	0.860000	6.900000e-01	1.000000	1.000000	0.871958	0.860000	1	7.700000e-01	0.970000
ABCA13	154664	broad.mit.edu	37	7	48411864	48411864	+	Missense_Mutation	SNP	G	G	A			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr7:48411864G>A	ENST00000435803.1	+	33	10927	c.10903G>A	c.(10903-10905)Gtt>Att	p.V3635I		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	p.V3635I(1)|p.V3580I(1)		270					TCTGGCCATCGTTCTGAAAAC	0.468000																								2	Substitution - Missense(2)						SO:0001583	missense			ENST00000435803.1	1	1	hg19	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	G	1.351	-0.591282	0.03799	.	.	ENSG00000179869	ENST00000435803	D	0.87491	-2.26	5.77	-1.16	0.09678	.	0.381500	0.22125	N	0.064274	T	0.55114	0.1900	N	0.00801	-1.175	0.49582	D	0.999804	B;B	0.06786	0.0;0.001	B;B	0.06405	0.002;0.002	T	0.54543	-0.8278	10	0.02654	T	1	.	6.8687	0.24108	0.4762:0.128:0.3958:0.0	.	1337;3635	Q86UQ4-3;Q86UQ4	.;ABCAD_HUMAN	I	3635	ENSP00000411096:V3635I	ENSP00000411096:V3635I	V	+	1	0	ABCA13	48382410	0.853000	0.29707	0.008000	0.14137	0.914000	0.54420	0.853000	0.27777	-0.342000	0.08363	-0.294000	0.09567	GTT		TCGA-3A-A9IU-01A-11D-A397-08	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	1	0	1	110	292	0	49	0	0	0	1	0	49	2		0	0	0	0	0	2	1	1	109	291	0	48	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	1	2	3	2.071627	0	0.580000	1.910000	0.581214	0.940000	7.900000e-01	1.000000	1.000000	0.936633	0.940000	1	8.600000e-01	1.000000
TYW1	55253	broad.mit.edu	37	7	66479413	66479413	+	Silent	SNP	T	T	C	rs145686658	by1000genomes	TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr7:66479413T>C	ENST00000359626.5	+	5	599	c.435T>C	c.(433-435)acT>acC	p.T145T		NM_018264.2	NP_060734.2	Q9NV66	TYW1_HUMAN	tRNA-yW synthesizing protein 1 homolog (S. cerevisiae)	p.T145T(1)		46		Lung NSC(55;0.0846)|all_lung(88;0.183)			GCCTACCAACTGAAAGTGCAG	0.428000																								1	Substitution - coding silent(1)						SO:0001819	synonymous_variant			ENST00000359626.5	0	1	hg19	CCDS5538.1																																																																																				TCGA-3A-A9IU-01A-11D-A397-08	TYW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251932.2	0	0	0	7	609	0	101	0	5.418782e-02	0	28	0	101	2		0	0	0	0	0	2	1	9.797682e-01	7	601	0	100	2		0	0	0	0	0	2	-1.820533	0	1	121412	80	43	1	1	2	3	2.071627	0	0.580000	1.910000	0.581214	0.030000	0	0.080000	0.040000	0.044739	0.030000	0	2.000000e-02	0.060000
TG	7038	broad.mit.edu	37	8	133923730	133923730	+	Missense_Mutation	SNP	C	C	T			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr8:133923730C>T	ENST00000220616.4	+	19	4151	c.4111C>T	c.(4111-4113)Cgg>Tgg	p.R1371W	TG_ENST00000377869.1_Missense_Mutation_p.R1371W	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin			168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)		ATGGAAATCACGGCTTGAGGA	0.478000																								0							SO:0001583	missense			ENST00000220616.4	0	1	hg19	CCDS34944.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.209064	0.79240	0.0	1.16E-4	ENSG00000042832	ENST00000377869;ENST00000543313;ENST00000220616	T;T	0.64803	-0.11;-0.12	5.51	5.51	0.81932	.	1.131830	0.06509	N	0.737751	T	0.58495	0.2126	L	0.40543	1.245	0.09310	N	1	D	0.69078	0.997	B	0.40534	0.332	T	0.57774	-0.7753	10	0.72032	D	0.01	.	14.9365	0.70960	0.0:1.0:0.0:0.0	.	1371	P01266	THYG_HUMAN	W	1371;177;1371	ENSP00000367100:R1371W;ENSP00000220616:R1371W	ENSP00000220616:R1371W	R	+	1	2	TG	133992912	0.036000	0.19791	0.006000	0.13384	0.514000	0.34195	3.406000	0.52637	2.582000	0.87167	0.557000	0.71058	CGG		TCGA-3A-A9IU-01A-11D-A397-08	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	0	0	0	9	625	0	71		0	0	0	0	71	2		0	0	0	0	0	2	1	9.937437e-01	9	613	0	70	2		0	0	0	0	0	2	-2.301031	0	1	121412	5	41	1	0	0	0	2.055610	0	0.580000	1.910000	0.580000	0.040000	1.000000e-02	0.090000	0.050000	0.054226	0.040000	0	3.000000e-02	0.070000
RALYL	138046	broad.mit.edu	37	8	85774611	85774611	+	Missense_Mutation	SNP	C	C	T			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr8:85774611C>T	ENST00000521268.1	+	6	1599	c.494C>T	c.(493-495)aCg>aTg	p.T165M	RALYL_ENST00000518566.1_Missense_Mutation_p.T154M|RALYL_ENST00000521376.1_Missense_Mutation_p.T76M|RALYL_ENST00000522455.1_Missense_Mutation_p.T165M|RALYL_ENST00000523850.1_Missense_Mutation_p.T92M|RALYL_ENST00000521695.1_Missense_Mutation_p.T165M|RALYL_ENST00000517638.1_Missense_Mutation_p.T178M	NM_173848.5	NP_776247.3	Q86SE5	RALYL_HUMAN	RALY RNA binding protein-like			24					GCAGTCACAACGACTCGCAGG	0.483000																								0							SO:0001583	missense			ENST00000521268.1	1	1	hg19	CCDS55253.1	.	.	.	.	.	.	.	.	.	.	C	18.00	3.526572	0.64860	.	.	ENSG00000184672	ENST00000522455;ENST00000521695;ENST00000521268;ENST00000518566;ENST00000517638;ENST00000523850;ENST00000521376	T;T;T;T;T;T;T	0.18657	2.83;2.83;2.83;2.85;2.83;2.42;2.2	5.1	5.1	0.69264	.	0.214143	0.49305	D	0.000143	T	0.35941	0.0949	M	0.61703	1.905	0.09310	N	1	P;D;P;P;D	0.60160	0.791;0.987;0.939;0.93;0.987	B;P;B;P;P	0.51016	0.336;0.588;0.337;0.656;0.588	T	0.19192	-1.0313	10	0.62326	D	0.03	-3.4988	18.8851	0.92375	0.0:1.0:0.0:0.0	.	154;165;92;178;165	B3KT61;B3KSX3;Q86SE5-2;G3V129;Q86SE5	.;.;.;.;RALYL_HUMAN	M	165;165;165;154;178;92;76	ENSP00000430394:T165M;ENSP00000428667:T165M;ENSP00000430367:T165M;ENSP00000430065:T154M;ENSP00000430128:T178M;ENSP00000428807:T92M;ENSP00000428310:T76M	ENSP00000430128:T178M	T	+	2	0	RALYL	85937166	0.679000	0.27596	0.011000	0.14972	0.798000	0.45092	5.613000	0.67688	2.511000	0.84671	0.551000	0.68910	ACG		TCGA-3A-A9IU-01A-11D-A397-08	RALYL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379448.1	1	0	1	36	89	0	18		0	0	0	0	18	2		0	0	0	0	0	2	1	1	36	85	0	18	2		0	0	0	0	0	2	-20.000000	1	1	120836	3	28	1	0	0	0	2.055610	0	0.580000	1.910000	0.580000	0.980000	7.300000e-01	1.000000	1.000000	0.944361	0.980000	1	8.500000e-01	1.000000
TNKS	8658	broad.mit.edu	37	8	9609296	9609296	+	Missense_Mutation	SNP	G	G	A			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr8:9609296G>A	ENST00000310430.6	+	19	3036	c.3010G>A	c.(3010-3012)Gta>Ata	p.V1004I	TNKS_ENST00000518281.1_Missense_Mutation_p.V767I	NM_003747.2	NP_003738.2	O95271	TNKS1_HUMAN	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase			49					AGAGTTGGCCGTAGGAGGAGC	0.542000																								0							SO:0001583	missense			ENST00000310430.6	0	1	hg19	CCDS5974.1	.	.	.	.	.	.	.	.	.	.	G	9.102	1.004279	0.19199	0.0	1.16E-4	ENSG00000173273	ENST00000310430;ENST00000518281	T;T	0.61859	0.07;0.14	5.73	5.73	0.89815	.	0.331114	0.32055	N	0.006645	T	0.45034	0.1322	N	0.19112	0.55	0.54753	D	0.999982	B	0.16396	0.017	B	0.09377	0.004	T	0.29941	-0.9995	10	0.18276	T	0.48	.	19.9054	0.97006	0.0:0.0:1.0:0.0	.	1004	O95271	TNKS1_HUMAN	I	1004;767	ENSP00000311579:V1004I;ENSP00000429890:V767I	ENSP00000311579:V1004I	V	+	1	0	TNKS	9646706	1.000000	0.71417	0.901000	0.35422	0.191000	0.23601	6.449000	0.73473	2.698000	0.92095	0.655000	0.94253	GTA		TCGA-3A-A9IU-01A-11D-A397-08	TNKS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206935.1	0	0	0	6	526	0	75	0	1.353191e-02	0	13	0	75	2		0	0	0	0	0	2	1	9.632581e-01	6	517	0	74	2		0	0	0	0	0	2	-2.164740	0	1	121412	3	37	1	0	0	0	2.055610	0	0.580000	1.910000	0.580000	0.030000	0	0.080000	0.040000	0.045001	0.030000	0	2.000000e-02	0.060000
TNC	3371	broad.mit.edu	37	9	117848514	117848514	+	Missense_Mutation	SNP	C	C	T			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr9:117848514C>T	ENST00000350763.4	-	3	1907	c.1496G>A	c.(1495-1497)cGc>cAc	p.R499H	TNC_ENST00000535648.1_Missense_Mutation_p.R499H|TNC_ENST00000346706.3_Missense_Mutation_p.R499H|TNC_ENST00000345230.3_Missense_Mutation_p.R499H|TNC_ENST00000423613.2_Missense_Mutation_p.R499H|TNC_ENST00000340094.3_Missense_Mutation_p.R499H|TNC_ENST00000341037.4_Missense_Mutation_p.R499H|TNC_ENST00000542877.1_Missense_Mutation_p.R499H|TNC_ENST00000537320.1_Missense_Mutation_p.R499H	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	p.R499H(1)		120					GGGGCATTGGCGATCCCGGCA	0.597000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000350763.4	0	1	hg19	CCDS6811.1	.	.	.	.	.	.	.	.	.	.	C	8.572	0.880360	0.17467	.	.	ENSG00000041982	ENST00000340094;ENST00000535648;ENST00000346706;ENST00000345230;ENST00000350763;ENST00000442945;ENST00000341037;ENST00000423613;ENST00000537320;ENST00000542877	T;T;T;T;T;T;T;T;T	0.03524	3.9;3.9;3.9;3.9;3.9;3.9;3.9;3.9;3.9	5.82	-2.57	0.06248	.	0.783888	0.11926	N	0.516193	T	0.03959	0.0111	L	0.59436	1.845	0.09310	N	1	B;B	0.15719	0.014;0.001	B;B	0.08055	0.003;0.001	T	0.37407	-0.9707	10	0.59425	D	0.04	.	4.1099	0.10053	0.5463:0.2293:0.0677:0.1566	.	499;499	E9PC84;P24821	.;TENA_HUMAN	H	499	ENSP00000344400:R499H;ENSP00000438152:R499H;ENSP00000344555:R499H;ENSP00000345861:R499H;ENSP00000265131:R499H;ENSP00000339553:R499H;ENSP00000411406:R499H;ENSP00000443478:R499H;ENSP00000442242:R499H	ENSP00000344400:R499H	R	-	2	0	TNC	116888335	0.000000	0.05858	0.001000	0.08648	0.323000	0.28346	-0.002000	0.12924	-0.330000	0.08514	0.462000	0.41574	CGC		TCGA-3A-A9IU-01A-11D-A397-08	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	0	0	0	6	564	0	101	0	7.643824e-02	0	35	0	101	2	0	2.951098e-01	2	702	1	279	11	1	9.645545e-01	6	561	0	98	2		0	0	0	0	0	2	-2.068723	0	1	121412	2	38	1	0	0	0	2.054451	0	0.580000	1.910000	0.580000	0.030000	0	0.080000	0.040000	0.041898	0.030000	0	1.000000e-02	0.060000
CERCAM	51148	broad.mit.edu	37	9	131193524	131193524	+	Missense_Mutation	SNP	G	G	A			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr9:131193524G>A	ENST00000372838.4	+	9	1543	c.1145G>A	c.(1144-1146)cGc>cAc	p.R382H	RP11-339B21.10_ENST00000610052.1_RNA|CERCAM_ENST00000372842.1_Missense_Mutation_p.R304H	NM_016174.4	NP_057258.3	Q5T4B2	GT253_HUMAN	cerebral endothelial cell adhesion molecule			20					TACTCGGGCCGCACTCTGACC	0.627000																								0							SO:0001583	missense			ENST00000372838.4	0	1	hg19	CCDS6901.2	.	.	.	.	.	.	.	.	.	.	G	19.24	3.789219	0.70337	.	.	ENSG00000167123	ENST00000372842;ENST00000372838;ENST00000413863	T;T	0.80653	-1.37;-1.4	5.02	4.1	0.47936	.	0.055960	0.64402	N	0.000001	D	0.86293	0.5898	M	0.74546	2.27	0.80722	D	1	D	0.59767	0.986	P	0.57679	0.825	D	0.87600	0.2496	10	0.72032	D	0.01	-20.9121	12.8845	0.58036	0.0818:0.0:0.9182:0.0	.	382	Q5T4B2	GT253_HUMAN	H	304;382;335	ENSP00000361933:R304H;ENSP00000361929:R382H	ENSP00000361929:R382H	R	+	2	0	CERCAM	130233345	1.000000	0.71417	1.000000	0.80357	0.715000	0.41141	7.668000	0.83897	1.197000	0.43143	0.491000	0.48974	CGC		TCGA-3A-A9IU-01A-11D-A397-08	CERCAM-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054435.2	0	0	0	6	406	0	71	0	8.631611e-01	0	244	0	71	2		0	0	0	0	0	2	1	9.649787e-01	6	405	0	70	2		0	0	0	0	0	2	-2.041438	0	1	0	0		1	0	0	0	2.054451	0	0.580000	1.910000	0.580000	0.050000	1.000000e-02	0.110000	0.050000	0.058204	0.050000	0	3.000000e-02	0.080000
CDKN2A	1029	broad.mit.edu	37	9	21971000	21971000	+	Nonsense_Mutation	SNP	C	C	A			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08			C	A	C	C		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr9:21971000C>A	ENST00000304494.5	-	2	628	c.358G>T	c.(358-360)Gag>Tag	p.E120*	CDKN2A_ENST00000530628.2_3'UTR|CDKN2A_ENST00000498124.1_Nonsense_Mutation_p.E120*|CDKN2A_ENST00000579755.1_3'UTR|CDKN2A_ENST00000494262.1_Nonsense_Mutation_p.E69*|CDKN2A_ENST00000497750.1_Nonsense_Mutation_p.E69*|CDKN2A_ENST00000578845.2_Nonsense_Mutation_p.E69*|CDKN2A_ENST00000446177.1_Nonsense_Mutation_p.E120*|CDKN2A_ENST00000361570.3_3'UTR|CDKN2A_ENST00000498628.2_Nonsense_Mutation_p.E69*|CDKN2A_ENST00000579122.1_Nonsense_Mutation_p.E120*|RP11-145E5.5_ENST00000404796.2_Intron|CDKN2A_ENST00000479692.2_Nonsense_Mutation_p.E69*	NM_000077.4	NP_000068.1	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A	p.0?(1315)|p.?(13)|p.E120*(9)|p.E120K(4)|p.0(1)|p.A118fs*10(1)		4199		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)			TGGCCCAGCTCCTCAGCCAGG	0.726000		17								HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)														1343	Whole gene deletion(1316)|Unknown(13)|Substitution - Nonsense(9)|Substitution - Missense(4)|Deletion - Frameshift(1)	GRCh37	CD972119	CDKN2A	D		SO:0001587	stop_gained			ENST00000304494.5	0	1	hg19	CCDS6510.1	.	.	.	.	.	.	.	.	.	.	C	37	6.320898	0.97471	.	.	ENSG00000147889	ENST00000304494;ENST00000446177	.	.	.	5.93	5.03	0.67393	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	-15.0988	14.364	0.66792	0.0:0.8518:0.1482:0.0	.	.	.	.	X	120	.	ENSP00000307101:E120X	E	-	1	0	CDKN2A	21961000	0.585000	0.26774	1.000000	0.80357	0.613000	0.37349	1.323000	0.33701	1.489000	0.48450	0.655000	0.94253	GAG		TCGA-3A-A9IU-01A-11D-A397-08	CDKN2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000051915.1	1	0	0	51	81	0	55	1	1	81	14	0	55	2	1	1	84	151	0	269	2	1	1	51	79	0	55	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	0	1	1	1.459422	1	0.580000	1.910000	0.408451	0.890000	7.200000e-01	1.000000	0.940000	0.894260	0.890000	1	8.100000e-01	0.970000
KDM4C	23081	broad.mit.edu	37	9	7049110	7049110	+	Silent	SNP	C	C	T			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr9:7049110C>T	ENST00000381309.3	+	17	2899	c.2334C>T	c.(2332-2334)tgC>tgT	p.C778C	KDM4C_ENST00000536108.1_Intron|KDM4C_ENST00000442236.2_Silent_p.C523C|KDM4C_ENST00000381306.3_Silent_p.C778C|KDM4C_ENST00000535193.1_Silent_p.C800C|KDM4C_ENST00000543771.1_Silent_p.C778C|KDM4C_ENST00000428870.2_Silent_p.C465C	NM_015061.3	NP_055876.2	Q9H3R0	KDM4C_HUMAN	lysine (K)-specific demethylase 4C			43					ATGTCATGTGCGCCGTTGCGG	0.433000																								0							SO:0001819	synonymous_variant			ENST00000381309.3	1	1	hg19	CCDS6471.1																																																																																				TCGA-3A-A9IU-01A-11D-A397-08	KDM4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051692.1	1	0	1	71	124	0	32	1	9.985734e-01	11	10	0	32	2		0	0	0	0	0	2	1	1	69	124	0	32	2		0	0	0	0	0	2	-10.332930	1	1	121410	3	34	1	0	1	1	1.459422	1	0.580000	1.910000	0.408451	0.870000	7.200000e-01	0.990000	0.890000	0.873098	0.870000	1	7.900000e-01	0.950000
RORB	6096	broad.mit.edu	37	9	77282784	77282784	+	Missense_Mutation	SNP	G	G	A			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chr9:77282784G>A	ENST00000396204.2	+	8	1111	c.1111G>A	c.(1111-1113)Gct>Act	p.A371T	RORB_ENST00000376896.3_Missense_Mutation_p.A360T			Q92753	RORB_HUMAN	RAR-related orphan receptor B			12				Melatonin(DB01065)	GGAGGAGATCGCTTTGTTCTC	0.388000																								0							SO:0001583	missense			ENST00000396204.2	1	1	hg19		.	.	.	.	.	.	.	.	.	.	G	36	5.715486	0.96830	.	.	ENSG00000198963	ENST00000376896;ENST00000396204	D;D	0.97575	-4.44;-4.44	6.17	6.17	0.99709	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.092611	0.64402	D	0.000001	D	0.98689	0.9560	M	0.86178	2.8	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.995;0.997	D	0.98965	1.0799	10	0.87932	D	0	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	371;360	Q92753;Q58EY0	RORB_HUMAN;.	T	360;371	ENSP00000366093:A360T;ENSP00000379507:A371T	ENSP00000366093:A360T	A	+	1	0	RORB	76472604	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	9.775000	0.98995	2.941000	0.99782	0.655000	0.94253	GCT		TCGA-3A-A9IU-01A-11D-A397-08	RORB-201	KNOWN	basic	protein_coding	protein_coding		1	0	1	150	379	0	59		0	0	0	0	59	2		0	0	0	0	0	2	1	1	148	376	0	58	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	0	0	0	2.054451	0	0.580000	1.910000	0.580000	0.970000	8.400000e-01	1.000000	1.000000	0.961213	0.970000	1	9.000000e-01	1.000000
GPR112	139378	broad.mit.edu	37	X	135429875	135429875	+	Missense_Mutation	SNP	C	C	A			TCGA-3A-A9IU-01A-11D-A397-08	TCGA-3A-A9IU-10A-01D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	912bafe3-1218-44c3-ba4e-16aeac4f598e	c7a38788-c7eb-42b3-a1f2-75d82c600d91	g.chrX:135429875C>A	ENST00000394143.1	+	6	4301	c.4010C>A	c.(4009-4011)aCa>aAa	p.T1337K	GPR112_ENST00000412101.1_Missense_Mutation_p.T1132K|GPR112_ENST00000370652.1_Missense_Mutation_p.T1337K|GPR112_ENST00000394141.1_Missense_Mutation_p.T1132K|GPR112_ENST00000287534.4_Missense_Mutation_p.T1274K	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112			199	Acute lymphoblastic leukemia(192;0.000127)				TCTGGAAGCACACAGATTACA	0.463000																								0							SO:0001583	missense			ENST00000394143.1	1	1	hg19	CCDS35409.1	.	.	.	.	.	.	.	.	.	.	c	3.929	-0.016606	0.07681	.	.	ENSG00000156920	ENST00000394143;ENST00000370652;ENST00000412101;ENST00000287534;ENST00000394141	T;T;T;T;T	0.31510	1.53;1.53;1.49;1.62;1.49	2.81	-0.405	0.12392	.	.	.	.	.	T	0.16811	0.0404	L	0.29908	0.895	0.09310	N	1	P;P;B	0.45827	0.867;0.642;0.421	B;B;B	0.38020	0.263;0.26;0.081	T	0.12066	-1.0562	9	0.54805	T	0.06	.	3.1011	0.06327	0.2101:0.5296:0.0:0.2603	.	1274;1132;1337	Q8IZF6-2;Q8IZF6-3;Q8IZF6	.;.;GP112_HUMAN	K	1337;1337;1132;1274;1132	ENSP00000377699:T1337K;ENSP00000359686:T1337K;ENSP00000416526:T1132K;ENSP00000287534:T1274K;ENSP00000377697:T1132K	ENSP00000287534:T1274K	T	+	2	0	GPR112	135257541	0.001000	0.12720	0.001000	0.08648	0.070000	0.16714	0.046000	0.14035	-0.387000	0.07809	0.525000	0.51046	ACA		TCGA-3A-A9IU-01A-11D-A397-08	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1	1	0	1	121	105	0	24		0	0	0	0	24	2		0	0	0	0	0	2	1	1	121	105	0	24	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	0	1	1			0.580000	1.910000	0.580000	0.900000	8.000000e-01	0.990000	0.920000	0.911088	0.900000	1	8.500000e-01	0.960000
