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
SPPL3	121665	broad.mit.edu	37	12	121221520	121221522	+	In_Frame_Del	DEL	GGA	GGA	-			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08			GGA	-	GGA	GGA		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr12:121221520_121221522delGGA	ENST00000353487.2	-	5	847_849	c.344_346delTCC	c.(343-348)ctcccg>ccg	p.L115del		NM_139015.4	NP_620584.2	Q8TCT6	SPPL3_HUMAN	signal peptide peptidase like 3				all_neural(191;0.0684)|Medulloblastoma(191;0.0922)				TGGCACATCGGGAGGAGAAGAAA	0.325000																								0							SO:0001651	inframe_deletion			ENST00000353487.2	1	1	hg19	CCDS9208.1																																																																																				TCGA-YH-A8SY-01A-11D-A377-08	SPPL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402980.2	1	0	0	59	303	0	59	1	9.999943e-01	17	76	0	59	2	0	0	0	0	0	0		1	0.999972	79	310	2	61	28	0	0	0	0	0	0		-2.119162	0	0	0	0		1	0	3	3	1.842395	1	0.220000	3.360000	0.286694	0.990000	0.990000	1.000000	1.000000	0.999996	0.990000	1	0.990000	1.000000
CANX	821	broad.mit.edu	37	5	179151711	179151728	+	In_Frame_Del	DEL	GAAGGAAGAGGAAGAAGA	GAAGGAAGAGGAAGAAGA	-			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08			GAAGGAAGAGGAAGAAGA	-	GAAGGAAGAGGAAGAAGA	GAAGGAAGAGGAAGAAGA		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr5:179151711_179151728delGAAGGAAGAGGAAGAAGA	ENST00000247461.4	+	13	1772_1789	c.1572_1589delGAAGGAAGAGGAAGAAGA	c.(1570-1590)gtgaaggaagaggaagaagag>gtg	p.KEEEEE525del	CANX_ENST00000415618.2_In_Frame_Del_p.KEEEEE560del|CANX_ENST00000452673.2_In_Frame_Del_p.KEEEEE525del|CANX_ENST00000504734.1_In_Frame_Del_p.KEEEEE525del|CANX_ENST00000512607.2_In_Frame_Del_p.KEEEEE417del	NM_001746.3	NP_001737.1	P27824	CALX_HUMAN	calnexin			22	all_cancers(89;0.000129)|all_epithelial(37;5.59e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0413)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	Antihemophilic Factor(DB00025)|Tenecteplase(DB00031)	AACCGGATGTGAaggaagaggaagaagagaaggaagag	0.413000																								0							SO:0001651	inframe_deletion			ENST00000247461.4	1	1	hg19	CCDS4447.1																																																																																				TCGA-YH-A8SY-01A-11D-A377-08	CANX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253500.2	1	0	0	33	204	0	44	0	1	0	519	0	44	2	0	0	0	0	0	0		2	0.008683	110	281	11	56	85	0	0	0	0	0	0		-20.000000	1	1	0	0		1	1	2	3	1.949770	0	0.220000	3.360000	0.297297	0.990000	0.990000	1.000000	1.000000	0.998528	0.990000	1	0.990000	1.000000
VWA2	340706	broad.mit.edu	37	10	116046089	116046089	+	Silent	SNP	C	C	T			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr10:116046089C>T	ENST00000392982.3	+	11	1639	c.1389C>T	c.(1387-1389)ggC>ggT	p.G463G	VWA2_ENST00000603594.1_Silent_p.G463G			Q5GFL6	VWA2_HUMAN	von Willebrand factor A domain containing 2			26					AGGTTGCGGGCCCAGCGCGTC	0.657000																								0							SO:0001819	synonymous_variant			ENST00000392982.3	1	1	hg19																																																																																					TCGA-YH-A8SY-01A-11D-A377-08	VWA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050456.3	1	0	1	39	257	0	48	0	4.974722e-02	1	2	0	48	2		0	0	0	0	0	2	1	1.000000	39	254	0	48	2		0	0	0	0	48	2	-3.018321	1	1	0	0		1	2	2	4	2.114795	1	0.220000	3.360000	0.360656	0.990000	0.990000	1.000000	1.000000	0.999551	0.990000	1	0.990000	1.000000
OGDHL	55753	broad.mit.edu	37	10	50966564	50966564	+	Silent	SNP	C	C	T	rs149391137		TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr10:50966564C>T	ENST00000374103.4	-	2	160	c.75G>A	c.(73-75)ccG>ccA	p.P25P	OGDHL_ENST00000432695.1_Intron|OGDHL_ENST00000419399.1_Silent_p.P25P	NM_018245.2	NP_060715.2	Q9ULD0	OGDHL_HUMAN	oxoglutarate dehydrogenase-like			61					AGCCAAACACCGGGACGTCAT	0.627000																								0							SO:0001819	synonymous_variant			ENST00000374103.4	1	1	hg19	CCDS7234.1																																																																																				TCGA-YH-A8SY-01A-11D-A377-08	OGDHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048007.1	1	0	1	43	199	0	29		0	0	0	0	29	2		0	0	0	0	0	2	1	1.000000	43	193	0	28	2		0	0	0	0	29	2	-3.323279	1	1	0	0		1	2	2	4	2.110973	1	0.220000	3.360000	0.359501	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	0.990000	1.000000
ITIH2	3698	broad.mit.edu	37	10	7773950	7773950	+	Silent	SNP	G	G	A	rs150260189		TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr10:7773950G>A	ENST00000358415.4	+	13	1804	c.1638G>A	c.(1636-1638)acG>acA	p.T546T	ITIH2_ENST00000379587.4_Silent_p.T535T	NM_002216.2	NP_002207.2	P19823	ITIH2_HUMAN	inter-alpha-trypsin inhibitor heavy chain 2			64					GCGTTATCACGGCGACTTCGG	0.438000																								0							SO:0001819	synonymous_variant			ENST00000358415.4	0	1	hg19	CCDS31141.1																																																																																				TCGA-YH-A8SY-01A-11D-A377-08	ITIH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046678.2	0	0	0	7	413	1	92	0	4.033478e-04	0	2	1	92	2		0	0	0	0	0	2	0	0.040124	7	406	1	91	16		0	0	0	1	92	2	-2.881760	1	1	121408	1	47	1	2	2	4	2.086287	0	0.220000	3.360000	0.351297	0.190000	0.080000	1.000000	0.190000	0.257374	0.190000	0	0.130000	0.300000
PVRL1	5818	broad.mit.edu	37	11	119535865	119535865	+	Silent	SNP	C	C	T			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr11:119535865C>T	ENST00000264025.3	-	6	1676	c.1146G>A	c.(1144-1146)cgG>cgA	p.R382R	PVRL1_ENST00000341398.2_Intron	NM_002855.4	NP_002846.3	Q15223	PVRL1_HUMAN	poliovirus receptor-related 1 (herpesvirus entry mediator C)	p.R382R(1)		27		Breast(348;0.037)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)			TGAAGGTGTGCCGGCGCCGAC	0.657000																								1	Substitution - coding silent(1)						SO:0001819	synonymous_variant			ENST00000264025.3	0	1	hg19	CCDS8426.1																																																																																				TCGA-YH-A8SY-01A-11D-A377-08	PVRL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388231.1	0	0	0	5	385	0	55	0	6.844956e-02	0	27	0	55	2		0	0	0	0	0	2	1	0.933587	5	376	0	54	2		0	0	0	0	55	2	-2.107250	0	1	121410	1	39	1	1	2	3	1.963246	0	0.220000	3.360000	0.297297	0.130000	0.040000	0.280000	0.120000	0.153515	0.130000	0	0.080000	0.210000
MUC5B	727897	broad.mit.edu	37	11	1272055	1272055	+	Missense_Mutation	SNP	G	G	A			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr11:1272055G>A	ENST00000529681.1	+	31	14003	c.13945G>A	c.(13945-13947)Gcc>Acc	p.A4649T	MUC5B_ENST00000447027.1_Missense_Mutation_p.A4652T|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	p.A4649T(1)|p.A4604T(1)		137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)			cacccacaccgccagagtgct	0.612000																								2	Substitution - Missense(2)						SO:0001583	missense			ENST00000529681.1	1	1	hg19	CCDS44515.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	-|-	3.668|3.668	-0.068133|-0.068133	0.07228|0.07228	2.36E-4|2.36E-4	0.0|0.0	ENSG00000117983|ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637|ENST00000535652	T;T|.	0.15834|.	2.39;2.57|.	0.976|0.976	-0.754|-0.754	0.11065|0.11065	.|.	.|.	.|.	.|.	.|.	T|T	0.11623|0.11623	0.0283|0.0283	N|N	0.03608|0.03608	-0.345|-0.345	0.09310|0.09310	N|N	1|1	B|.	0.25235|.	0.121|.	B|.	0.12156|.	0.007|.	T|T	0.18366|0.18366	-1.0339|-1.0339	9|6	0.87932|0.45353	D|T	0|0.12	.|.	4.0397|4.0397	0.09745|0.09745	0.0:0.3403:0.4612:0.1985|0.0:0.3403:0.4612:0.1985	.|.	4652|.	E9PBJ0|.	.|.	T|H	4649;4652;4593|423	ENSP00000436812:A4649T;ENSP00000415793:A4652T|.	ENSP00000343037:A4593T|ENSP00000439776:R423H	A|R	+|+	1|2	0|0	MUC5B|MUC5B	1228631|1228631	0.000000|0.000000	0.05858|0.05858	0.002000|0.002000	0.10522|0.10522	0.014000|0.014000	0.08584|0.08584	-5.897000|-5.897000	0.00092|0.00092	-1.423000|-1.423000	0.02002|0.02002	-1.123000|-1.123000	0.02005|0.02005	GCC|CGC		TCGA-YH-A8SY-01A-11D-A377-08	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	0	0	0	17	123	0	53	1	8.501358e-01	6	21	0	53	2		0	0	0	0	0	2	1	0.999954	10	120	0	52	2		0	0	0	0	53	2	-3.077458	1	1	120990	5	40	1	1	2	3	1.950487	0	0.220000	3.360000	0.297297	0.990000	0.760000	1.000000	1.000000	0.978461	0.990000	1	0.970000	1.000000
KCNC1	3746	broad.mit.edu	37	11	17758047	17758047	+	Silent	SNP	C	C	T			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr11:17758047C>T	ENST00000379472.3	+	1	528	c.498C>T	c.(496-498)ggC>ggT	p.G166G	KCNC1_ENST00000265969.6_Silent_p.G166G	NM_004976.4	NP_004967.1	P48547	KCNC1_HUMAN	potassium voltage-gated channel, Shaw-related subfamily, member 1			33				Dalfampridine(DB06637)	GCCGGCCTGGCGGCTTTTGGC	0.687000																								0							SO:0001819	synonymous_variant			ENST00000379472.3	1	1	hg19	CCDS7827.1																																																																																				TCGA-YH-A8SY-01A-11D-A377-08	KCNC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389389.1	1	0	0	21	72	0	23		0	0	0	0	23	2		0	0	0	0	0	2	1	0.999999	21	71	0	23	2		0	0	0	0	23	2	-20.000000	1	1	0	0		1	1	2	3	1.950487	0	0.220000	3.360000	0.297297	0.990000	0.990000	1.000000	1.000000	0.999990	0.990000	1	0.990000	1.000000
HIPK3	10114	broad.mit.edu	37	11	33373714	33373714	+	Missense_Mutation	SNP	G	G	A			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr11:33373714G>A	ENST00000303296.4	+	16	3379	c.3074G>A	c.(3073-3075)cGa>cAa	p.R1025Q	HIPK3_ENST00000525975.1_Missense_Mutation_p.R1004Q|AL122015.1_ENST00000411202.1_RNA|HIPK3_ENST00000379016.3_Missense_Mutation_p.R1004Q|HIPK3_ENST00000456517.1_Missense_Mutation_p.R1004Q	NM_005734.3	NP_005725.3	Q9H422	HIPK3_HUMAN	homeodomain interacting protein kinase 3			39					ATAAAAGGACGATCTGCCCCT	0.378000																								0							SO:0001583	missense			ENST00000303296.4	0	1	hg19	CCDS7884.1	.	.	.	.	.	.	.	.	.	.	G	12.25	1.880365	0.33162	.	.	ENSG00000110422	ENST00000525975;ENST00000303296;ENST00000379016;ENST00000456517	T;T;T;T	0.50277	0.75;0.75;0.75;0.75	5.62	4.7	0.59300	.	0.145914	0.31872	N	0.006928	T	0.28267	0.0698	N	0.14661	0.345	0.49483	D	0.999795	B;B	0.14805	0.011;0.006	B;B	0.16289	0.015;0.006	T	0.08493	-1.0719	10	0.07325	T	0.83	.	13.6209	0.62136	0.0754:0.0:0.9246:0.0	.	1004;1025	Q9H422-2;Q9H422	.;HIPK3_HUMAN	Q	1004;1025;1004;1004	ENSP00000431710:R1004Q;ENSP00000304226:R1025Q;ENSP00000368301:R1004Q;ENSP00000398241:R1004Q	ENSP00000304226:R1025Q	R	+	2	0	HIPK3	33330290	1.000000	0.71417	0.617000	0.29091	0.818000	0.46254	4.652000	0.61454	1.359000	0.45940	0.655000	0.94253	CGA		TCGA-YH-A8SY-01A-11D-A377-08	HIPK3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255358.1	0	0	0	9	743	0	170	0	6.254984e-02	0	30	0	170	2		0	0	0	0	0	2	1	0.993885	9	734	0	166	2		0	0	0	0	170	2	-2.665725	1	1	0	0		1	1	2	3	1.963246	0	0.220000	3.360000	0.297297	0.120000	0.050000	0.220000	0.120000	0.133401	0.120000	0	0.080000	0.170000
OR51E1	143503	broad.mit.edu	37	11	4674426	4674426	+	Missense_Mutation	SNP	A	A	T			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr11:4674426A>T	ENST00000396952.5	+	2	1320	c.670A>T	c.(670-672)Att>Ttt	p.I224F	OR51E1_ENST00000530215.1_Intron	NM_152430.3	NP_689643.2	Q8TCB6	O51E1_HUMAN	olfactory receptor, family 51, subfamily E, member 1			30		Medulloblastoma(188;0.0025)|Breast(177;0.0101)|all_neural(188;0.0227)			ATATCTGCTTATTCTTAAGAC	0.483000																								0							SO:0001583	missense			ENST00000396952.5	1	1	hg19	CCDS31358.2	.	.	.	.	.	.	.	.	.	.	A	22.6	4.309349	0.81247	.	.	ENSG00000180785	ENST00000396952	T	0.57436	0.4	4.68	4.68	0.58851	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000021	T	0.81870	0.4914	H	0.97829	4.085	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.88235	0.2906	10	0.87932	D	0	.	13.3903	0.60821	1.0:0.0:0.0:0.0	.	223	Q8TCB6	O51E1_HUMAN	F	224	ENSP00000380155:I224F	ENSP00000380155:I224F	I	+	1	0	OR51E1	4631002	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.711000	0.91396	2.105000	0.64084	0.533000	0.62120	ATT		TCGA-YH-A8SY-01A-11D-A377-08	OR51E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347136.2	1	0	0	30	300	0	79		0	0	0	0	79	2		0	0	0	0	0	2	1	1.000000	30	294	0	77	2		0	0	0	0	79	2	-20.000000	1	1	0	0		1	1	2	3	1.950487	0	0.220000	3.360000	0.297297	0.920000	0.630000	1.000000	1.000000	0.897681	0.920000	1	0.770000	1.000000
UTP20	27340	broad.mit.edu	37	12	101755761	101755761	+	Missense_Mutation	SNP	G	G	A	rs76643734	byFrequency	TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr12:101755761G>A	ENST00000261637.4	+	44	5887	c.5713G>A	c.(5713-5715)Gtt>Att	p.V1905I		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)			88					GACTTTCACCGTTCACATGCT	0.413000																								0							SO:0001583	missense			ENST00000261637.4	1	0	hg19	CCDS9081.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	13.14	2.148199	0.37923	0.004993	0.0	ENSG00000120800	ENST00000261637	T	0.40225	1.04	6.03	5.05	0.67936	Armadillo-type fold (1);	0.179437	0.48767	D	0.000171	T	0.24392	0.0591	L	0.39633	1.23	0.48185	D	0.999606	B	0.26935	0.164	B	0.19148	0.024	T	0.03981	-1.0987	10	0.17832	T	0.49	-22.9366	13.7726	0.63036	0.099:0.0:0.901:0.0	.	1905	O75691	UTP20_HUMAN	I	1905	ENSP00000261637:V1905I	ENSP00000261637:V1905I	V	+	1	0	UTP20	100279892	1.000000	0.71417	0.860000	0.33809	0.458000	0.32498	4.835000	0.62781	2.854000	0.98071	0.655000	0.94253	GTT		TCGA-YH-A8SY-01A-11D-A377-08	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	1	0	1	132	416	0	88	1	3.490724e-01	4	1	0	88	2		0	0	0	0	0	2	1	1.000000	131	410	0	87	2		0	0	0	0	88	2	-3.021590	1	1	121412	90	55	1	0	3	3	1.842395	1	0.220000	3.360000	0.286694	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	0.990000	1.000000
PTPN11	5781	broad.mit.edu	37	12	112926259	112926259	+	Silent	SNP	C	C	T			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr12:112926259C>T	ENST00000351677.2	+	12	1590	c.1392C>T	c.(1390-1392)ggC>ggT	p.G464G		NM_002834.3	NP_002825.3	Q06124	PTN11_HUMAN	protein tyrosine phosphatase, non-receptor type 11			451					CTGGAATTGGCCGGACAGGGA	0.443000			Mis		JMML, AML, MDS		Noonan Syndrome		Noonan syndrome						Dom	yes		12	12q24.1	5781	protein tyrosine phosphatase, non-receptor type 11	yes	L	0							SO:0001819	synonymous_variant	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	ENST00000351677.2	0	1	hg19	CCDS9163.1																																																																																				TCGA-YH-A8SY-01A-11D-A377-08	PTPN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259496.2	0	0	0	5	363	1	53	0	5.544371e-03	0	20	1	53	3		0	0	0	0	0	2	0	0.000825	5	354	1	53	21		0	0	0	1	53	2	-1.960411	0	1	0	0		1	0	3	3	1.842395	1	0.220000	3.360000	0.286694	0.150000	0.050000	1.000000	0.140000	0.259874	0.150000	0	0.090000	0.280000
GPR133	283383	broad.mit.edu	37	12	131622750	131622750	+	Silent	SNP	C	C	T	rs34765022		TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr12:131622750C>T	ENST00000261654.5	+	24	3064	c.2505C>T	c.(2503-2505)aaC>aaT	p.N835N	GPR133_ENST00000535015.1_Silent_p.N867N|GPR133_ENST00000540207.1_3'UTR|GPR133_ENST00000376682.4_Silent_p.N521N|GPR133_ENST00000543617.1_Silent_p.N354N	NM_198827.3	NP_942122.2	Q6QNK2	GP133_HUMAN	G protein-coupled receptor 133	p.N835N(1)		67	all_neural(191;0.0982)|Medulloblastoma(191;0.163)				GCACCTCCAACGCGAAGCCCT	0.612000																								1	Substitution - coding silent(1)						SO:0001819	synonymous_variant			ENST00000261654.5	1	1	hg19	CCDS9272.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	3.018	-0.202417	0.06219	0.0	2.33E-4	ENSG00000111452	ENST00000335486	.	.	.	4.46	-0.207	0.13189	.	.	.	.	.	T	0.31979	0.0814	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.30090	-0.9990	4	.	.	.	.	8.0838	0.30760	0.0:0.47:0.0:0.53	rs34765022	.	.	.	M	189	.	.	T	+	2	0	GPR133	130188703	0.201000	0.23410	0.000000	0.03702	0.034000	0.12701	0.158000	0.16422	0.022000	0.15160	-0.254000	0.11334	ACG		TCGA-YH-A8SY-01A-11D-A377-08	GPR133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399356.1	1	0	1	35	140	0	23	0	1.088827e-01	0	3	0	23	2		0	0	0	0	0	2	1	1.000000	33	138	0	23	2		0	0	0	0	23	2	-20.000000	1	1	121412	62	45	1	0	3	3	1.842395	1	0.220000	3.360000	0.286694	0.990000	0.990000	1.000000	1.000000	0.999998	0.990000	1	0.990000	1.000000
KRAS	3845	broad.mit.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	C	A	rs121913529		TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08			C	A	C	C		Valid	Somatic	Phase_I	WXS	KRAS_deep			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr12:25398284C>A	ENST00000256078.4	-	2	98	c.35G>T	c.(34-36)gGt>gTt	p.G12V	KRAS_ENST00000556131.1_Missense_Mutation_p.G12V|KRAS_ENST00000557334.1_Missense_Mutation_p.G12V|KRAS_ENST00000311936.3_Missense_Mutation_p.G12V	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)		GCCTACGCCACCAGCTCCAAC	0.348000	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		pancreatic, colorectal, lung, thyroid, AML, others				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)			Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		L, E, M, O	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)						SO:0001583	missense	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	ENST00000256078.4	1	1	hg19	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.808637	0.90707	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90373	0.6987	M	0.90650	3.135	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.72625	0.969;0.978	D	0.91773	0.5429	10	0.72032	D	0.01	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	V	12	ENSP00000308495:G12V;ENSP00000452512:G12V;ENSP00000256078:G12V;ENSP00000451856:G12V	ENSP00000256078:G12V	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		TCGA-YH-A8SY-01A-11D-A377-08	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	1	0	1	74	267	0	76	1	8.377904e-01	6	8	0	76	2	1	1	86	314	0	316	2	1	1.000000	74	266	0	75	2	1	1	2275	5743	0	76	2	-20.000000	1	1	0	0		1	3	5	8	2.589570	1	0.220000	3.360000	0.475947	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	0.990000	1.000000
C1RL	51279	broad.mit.edu	37	12	7254566	7254566	+	Missense_Mutation	SNP	G	G	A			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr12:7254566G>A	ENST00000266542.4	-	3	510	c.418C>T	c.(418-420)Cgc>Tgc	p.R140C	C1RL_ENST00000545280.1_Intron|C1RL_ENST00000544702.1_Missense_Mutation_p.R140C|C1RL_ENST00000545337.1_Missense_Mutation_p.R140C	NM_016546.2	NP_057630.2	Q9NZP8	C1RL_HUMAN	complement component 1, r subcomponent-like			16					GGCTGTGTGCGGAAGGTCAGC	0.622000																								0							SO:0001583	missense			ENST00000266542.4	0	1	hg19	CCDS8573.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	5.842|5.842	0.339585|0.339585	0.11069|0.11069	.|.	.|.	ENSG00000139178|ENSG00000139178	ENST00000534950|ENST00000266542;ENST00000396661;ENST00000544702;ENST00000543933;ENST00000545337	.|T;T;T;T	.|0.30448	.|1.53;1.53;1.53;1.53	3.76|3.76	-0.133|-0.133	0.13485|0.13485	.|CUB (5);	.|1.399260	.|0.04433	.|N	.|0.369511	T|T	0.35799|0.35799	0.0944|0.0944	M|M	0.88640|0.88640	2.97|2.97	0.24098|0.24098	N|N	0.995883|0.995883	.|B;B;B	.|0.33919	.|0.432;0.038;0.285	.|B;B;B	.|0.27887	.|0.051;0.007;0.084	T|T	0.30268|0.30268	-0.9984|-0.9984	5|10	.|0.45353	.|T	.|0.12	.|.	3.3529|3.3529	0.07159|0.07159	0.2989:0.0:0.5228:0.1783|0.2989:0.0:0.5228:0.1783	.|.	.|140;140;140	.|F5GWF3;F5H7C8;Q9NZP8	.|.;.;C1RL_HUMAN	L|C	39|140	.|ENSP00000266542:R140C;ENSP00000441885:R140C;ENSP00000437398:R140C;ENSP00000442611:R140C	.|ENSP00000266542:R140C	P|R	-|-	2|1	0|0	C1RL|C1RL	7145842|7145842	0.147000|0.147000	0.22687|0.22687	0.103000|0.103000	0.21229|0.21229	0.289000|0.289000	0.27227|0.27227	0.193000|0.193000	0.17116|0.17116	-0.034000|-0.034000	0.13713|0.13713	-1.529000|-1.529000	0.00923|0.00923	CCG|CGC		TCGA-YH-A8SY-01A-11D-A377-08	C1RL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398367.1	0	0	0	7	793	0	96	0	1.220433e-01	0	59	0	96	2		0	0	0	0	0	2	1	0.979379	6	780	0	95	2		0	0	0	0	96	2	-2.133026	0	1	121412	1	35	1	3	5	8	2.599697	1	0.220000	3.360000	0.480554	0.140000	0.030000	1.000000	0.130000	0.286300	0.140000	0	0.080000	1.000000
NR2C1	7181	broad.mit.edu	37	12	95451597	95451597	+	Missense_Mutation	SNP	G	G	A			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr12:95451597G>A	ENST00000333003.5	-	6	932	c.602C>T	c.(601-603)gCc>gTc	p.A201V	NR2C1_ENST00000330677.7_Missense_Mutation_p.A201V|NR2C1_ENST00000545833.1_5'UTR|NR2C1_ENST00000393101.3_Missense_Mutation_p.A201V	NM_003297.3	NP_003288.2	P13056	NR2C1_HUMAN	nuclear receptor subfamily 2, group C, member 1			13					TGTTGAAGCGGCACAGTTGGA	0.343000																								0							SO:0001583	missense			ENST00000333003.5	0	1	hg19	CCDS9051.1	.	.	.	.	.	.	.	.	.	.	G	28.6	4.934588	0.92458	.	.	ENSG00000120798	ENST00000333003;ENST00000393101;ENST00000330677	D;D;D	0.92149	-2.98;-2.7;-2.7	5.6	5.6	0.85130	Nuclear hormone receptor, ligand-binding (1);	0.000000	0.85682	D	0.000000	D	0.95921	0.8672	M	0.73962	2.25	0.80722	D	1	D;D;D;D	0.89917	0.998;0.998;1.0;0.997	D;D;D;D	0.80764	0.989;0.994;0.989;0.985	D	0.95074	0.8207	10	0.44086	T	0.13	.	19.6188	0.95647	0.0:0.0:1.0:0.0	.	201;201;201;201	B6ZGT7;P13056-3;P13056-2;P13056	.;.;.;NR2C1_HUMAN	V	201	ENSP00000333275:A201V;ENSP00000376813:A201V;ENSP00000328843:A201V	ENSP00000328843:A201V	A	-	2	0	NR2C1	93975728	1.000000	0.71417	0.966000	0.40874	0.889000	0.51656	9.385000	0.97223	2.646000	0.89796	0.655000	0.94253	GCC		TCGA-YH-A8SY-01A-11D-A377-08	NR2C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407565.2	0	0	0	5	594	1	116	0	3.835748e-03	0	28	1	116	3		0	0	0	0	0	2	0	0.004459	5	586	1	115	18		0	0	0	1	116	2	-2.031101	0	1	0	0		1	0	3	3	1.842395	1	0.220000	3.360000	0.286694	0.090000	0.020000	1.000000	0.090000	0.205853	0.090000	0	0.050000	0.180000
ELF1	1997	broad.mit.edu	37	13	41523989	41523989	+	Missense_Mutation	SNP	G	G	A			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr13:41523989G>A	ENST00000239882.3	-	5	796	c.482C>T	c.(481-483)gCa>gTa	p.A161V	ELF1_ENST00000442101.1_Missense_Mutation_p.A137V|ELF1_ENST00000498824.1_5'UTR	NM_172373.3	NP_758961.1	P32519	ELF1_HUMAN	E74-like factor 1 (ets domain transcription factor)			37		Lung NSC(96;8.3e-05)|Prostate(109;0.0233)|Breast(139;0.0296)|Lung SC(185;0.0367)			CGGTGAGTCTGCATATTTTTC	0.473000																								0							SO:0001583	missense			ENST00000239882.3	0	1	hg19	CCDS9374.1	.	.	.	.	.	.	.	.	.	.	G	10.11	1.259936	0.23051	.	.	ENSG00000120690	ENST00000442101;ENST00000239882	T;T	0.20332	2.11;2.08	5.84	-2.05	0.07321	.	0.767917	0.12353	N	0.476371	T	0.07369	0.0186	N	0.08118	0	0.09310	N	1	B;B	0.14012	0.004;0.009	B;B	0.09377	0.003;0.004	T	0.27971	-1.0058	10	0.33940	T	0.23	.	1.3405	0.02153	0.2585:0.0968:0.3523:0.2924	.	137;161	E9PDQ9;P32519	.;ELF1_HUMAN	V	137;161	ENSP00000405580:A137V;ENSP00000239882:A161V	ENSP00000239882:A161V	A	-	2	0	ELF1	40421989	0.001000	0.12720	0.033000	0.17914	0.656000	0.38851	0.096000	0.15147	-0.099000	0.12263	-0.282000	0.10007	GCA		TCGA-YH-A8SY-01A-11D-A377-08	ELF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044654.3	0	0	0	6	791	0	101	0	4.949738e-02	0	39	0	101	2		0	0	0	0	0	2	1	0.963223	7	778	0	100	2		0	0	0	0	101	2	-1.969131	0	1	0	0		1	2	2	4	2.119557	1	0.220000	3.360000	0.360656	0.080000	0.010000	0.180000	0.080000	0.096851	0.080000	0	0.050000	0.130000
PCDH8	5100	broad.mit.edu	37	13	53420520	53420520	+	Silent	SNP	G	G	A			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr13:53420520G>A	ENST00000377942.3	-	1	2255	c.2052C>T	c.(2050-2052)cgC>cgT	p.R684R	PCDH8_ENST00000338862.4_Silent_p.R684R	NM_002590.3	NP_002581.2	O95206	PCDH8_HUMAN	protocadherin 8			36		Lung NSC(96;0.0019)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)			CCCTGAACACGCGACCGGGTG	0.706000													GBM(36;25 841 9273 49207)											0							SO:0001819	synonymous_variant			ENST00000377942.3	1	1	hg19	CCDS9438.1																																																																																				TCGA-YH-A8SY-01A-11D-A377-08	PCDH8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045108.2	1	0	0	26	91	0	18		0	0	0	0	18	2		0	0	0	0	0	2	1	1.000000	26	91	0	18	2		0	0	0	0	18	2	-20.000000	1	1	0	0		1	2	2	4	2.119557	1	0.220000	3.360000	0.360656	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	0.990000	1.000000
PCDH17	27253	broad.mit.edu	37	13	58208913	58208913	+	Missense_Mutation	SNP	G	G	A			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr13:58208913G>A	ENST00000377918.3	+	1	2259	c.2233G>A	c.(2233-2235)Gcc>Acc	p.A745T		NM_001040429.2	NP_001035519.1	O14917	PCD17_HUMAN	protocadherin 17			120		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)			CTGCCGCATCGCCGAGTACAG	0.547000													Melanoma(72;952 1291 1619 12849 33676)											0							SO:0001583	missense			ENST00000377918.3	1	1	hg19	CCDS31986.1	.	.	.	.	.	.	.	.	.	.	G	16.33	3.092421	0.55968	.	.	ENSG00000118946	ENST00000377918	T	0.56444	0.46	5.55	5.55	0.83447	.	0.097709	0.64402	D	0.000001	T	0.58680	0.2139	M	0.69823	2.125	0.53005	D	0.999961	P;P	0.47302	0.835;0.893	B;B	0.43331	0.416;0.285	T	0.60835	-0.7184	9	.	.	.	.	19.5072	0.95124	0.0:0.0:1.0:0.0	.	745;745	O14917-2;O14917	.;PCD17_HUMAN	T	745	ENSP00000367151:A745T	.	A	+	1	0	PCDH17	57106914	1.000000	0.71417	0.992000	0.48379	0.917000	0.54804	7.968000	0.87980	2.607000	0.88179	0.591000	0.81541	GCC		TCGA-YH-A8SY-01A-11D-A377-08	PCDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045139.1	1	0	1	26	170	0	53	0	5.199635e-02	0	3	0	53	2		0	0	0	0	0	2	1	1.000000	26	168	0	52	2		0	0	0	0	53	2	-13.396410	1	0	0	0		1	2	2	4	2.119557	1	0.220000	3.360000	0.360656	0.990000	0.990000	1.000000	1.000000	0.998392	0.990000	1	0.990000	1.000000
RYR3	6263	broad.mit.edu	37	15	34040439	34040439	+	Missense_Mutation	SNP	G	G	T			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr15:34040439G>T	ENST00000389232.4	+	54	8184	c.8114G>T	c.(8113-8115)cGa>cTa	p.R2705L	RYR3_ENST00000415757.3_Missense_Mutation_p.R2705L	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	p.R2705Q(2)		311		all_lung(180;7.18e-09)			GAGAAGCTTCGAAGTGTGTCC	0.577000																								2	Substitution - Missense(2)						SO:0001583	missense			ENST00000389232.4	1	1	hg19	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.410408	0.83340	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	D;D	0.96830	-4.14;-4.14	5.18	5.18	0.71444	.	0.071281	0.56097	D	0.000040	D	0.94155	0.8125	L	0.41492	1.28	0.58432	D	0.999992	B;B	0.32543	0.375;0.009	B;B	0.33392	0.163;0.018	D	0.93169	0.6564	10	0.49607	T	0.09	.	18.8778	0.92345	0.0:0.0:1.0:0.0	.	2705;2705	Q15413-2;Q15413	.;RYR3_HUMAN	L	2705	ENSP00000373884:R2705L;ENSP00000399610:R2705L	ENSP00000354735:R2705L	R	+	2	0	RYR3	31827731	1.000000	0.71417	0.991000	0.47740	0.897000	0.52465	7.158000	0.77470	2.679000	0.91253	0.655000	0.94253	CGA		TCGA-YH-A8SY-01A-11D-A377-08	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1	1	0	0	15	135	0	36		0	0	0	0	36	2		0	0	0	0	0	2	1	0.999883	15	133	0	34	2		0	0	0	0	36	2	-8.165503	1	1	0	0		1	2	3	5	1.937316	0	0.220000	3.360000	0.300762	0.990000	0.630000	1.000000	1.000000	0.942475	0.990000	1	0.830000	1.000000
CHST14	113189	broad.mit.edu	37	15	40764233	40764233	+	Missense_Mutation	SNP	G	G	A			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr15:40764233G>A	ENST00000306243.5	+	1	1074	c.821G>A	c.(820-822)cGc>cAc	p.R274H	CHST14_ENST00000559991.1_Missense_Mutation_p.R249H	NM_130468.3	NP_569735.1	Q8NCH0	CHSTE_HUMAN	carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 14			4		all_cancers(109;2.34e-14)|all_epithelial(112;1.08e-11)|Lung NSC(122;2.95e-09)|all_lung(180;6.03e-08)|Melanoma(134;0.091)|Colorectal(260;0.198)|Ovarian(310;0.243)			GACCCTGAGCGCATGAATGAG	0.587000																								0							SO:0001583	missense			ENST00000306243.5	0	1	hg19	CCDS10059.1	.	.	.	.	.	.	.	.	.	.	G	15.22	2.769808	0.49680	.	.	ENSG00000169105	ENST00000306243	T	0.75260	-0.92	4.92	3.02	0.34903	.	0.133960	0.44097	N	0.000487	T	0.61714	0.2369	L	0.40543	1.245	0.43403	D	0.995531	B	0.09022	0.002	B	0.08055	0.003	T	0.52859	-0.8519	10	0.28530	T	0.3	-11.2791	8.6952	0.34291	0.1901:0.0:0.8099:0.0	.	274	Q8NCH0	CHSTE_HUMAN	H	274	ENSP00000307297:R274H	ENSP00000307297:R274H	R	+	2	0	CHST14	38551525	0.991000	0.36638	0.986000	0.45419	0.982000	0.71751	1.809000	0.38922	0.650000	0.30769	0.655000	0.94253	CGC		TCGA-YH-A8SY-01A-11D-A377-08	CHST14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252251.1	0	0	0	5	507	0	83	0	4.053859e-01	0	123	0	83	2		0	0	0	0	0	2	1	0.935871	5	501	0	83	2		0	0	0	0	83	2	-2.235578	0	1	0	0		1	2	3	5	1.937316	0	0.220000	3.360000	0.300762	0.120000	0.030000	1.000000	0.090000	0.311711	0.120000	0	0.070000	1.000000
CAPN3	825	broad.mit.edu	37	15	42695097	42695097	+	Missense_Mutation	SNP	C	C	T			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr15:42695097C>T	ENST00000397163.3	+	13	1861	c.1642C>T	c.(1642-1644)Cgc>Tgc	p.R548C	CAPN3_ENST00000397204.4_5'Flank|RP11-164J13.1_ENST00000495723.1_RNA|CAPN3_ENST00000569136.1_5'Flank|CAPN3_ENST00000356316.3_Missense_Mutation_p.R461C|CAPN3_ENST00000349748.3_Missense_Mutation_p.R500C|CAPN3_ENST00000337571.4_5'Flank|CAPN3_ENST00000561817.1_5'Flank|CAPN3_ENST00000397200.4_Missense_Mutation_p.R36C|CAPN3_ENST00000318023.7_Missense_Mutation_p.R548C|CAPN3_ENST00000357568.3_Missense_Mutation_p.R548C	NM_000070.2	NP_000061.1	P20807	CAN3_HUMAN	calpain 3, (p94)			47		all_cancers(109;1.65e-16)|all_epithelial(112;8.34e-15)|Lung NSC(122;3.56e-09)|all_lung(180;1.68e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)			CCAGCGCTTCCGCCTGCCTCC	0.592000																								0							SO:0001583	missense			ENST00000397163.3	1	1	hg19	CCDS45245.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.987438	0.74589	0.0	1.16E-4	ENSG00000092529	ENST00000356316;ENST00000337522;ENST00000397163;ENST00000357568;ENST00000349748;ENST00000318023;ENST00000397200	D;D;D;D;D;D	0.88046	-2.33;-2.33;-2.33;-2.33;-2.33;-2.33	4.87	4.87	0.63330	Peptidase C2, calpain, large subunit, domain III (2);Peptidase C2, calpain, domain III (1);	0.000000	0.85682	U	0.000000	D	0.82481	0.5046	L	0.38649	1.16	0.80722	D	1	B;B;B;B;B;B	0.33857	0.102;0.208;0.083;0.206;0.429;0.053	B;B;B;B;B;B	0.31290	0.031;0.077;0.018;0.032;0.127;0.075	T	0.82752	-0.0302	10	0.49607	T	0.09	.	18.1939	0.89814	0.0:1.0:0.0:0.0	.	413;461;500;548;548;461	C6EVS4;C6EVS3;P20807-2;P20807-3;P20807;Q762C8	.;.;.;.;CAN3_HUMAN;.	C	461;36;548;548;500;548;36	ENSP00000348667:R461C;ENSP00000380349:R548C;ENSP00000350181:R548C;ENSP00000183936:R500C;ENSP00000326281:R548C;ENSP00000380384:R36C	ENSP00000326281:R548C	R	+	1	0	CAPN3	40482389	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.733000	0.68571	2.527000	0.85204	0.455000	0.32223	CGC		TCGA-YH-A8SY-01A-11D-A377-08	CAPN3-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421075.1	1	0	1	80	418	0	75	0	1.262146e-01	0	4	0	75	2		0	0	0	0	0	2	1	1.000000	78	415	0	75	2		0	0	0	0	75	2	-2.722726	1	1	121412	1	41	1	2	3	5	1.937316	0	0.220000	3.360000	0.300762	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	0.990000	1.000000
GLCE	26035	broad.mit.edu	37	15	69553616	69553616	+	Silent	SNP	G	G	A			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr15:69553616G>A	ENST00000261858.2	+	4	1005	c.777G>A	c.(775-777)gcG>gcA	p.A259A	GLCE_ENST00000559420.2_Silent_p.A195A|GLCE_ENST00000559500.1_3'UTR	NM_015554.1	NP_056369.1	O94923	GLCE_HUMAN	glucuronic acid epimerase			18					GCTTTATGGCGAATGTGGCTG	0.393000																								0							SO:0001819	synonymous_variant			ENST00000261858.2	0	1	hg19	CCDS32277.1																																																																																				TCGA-YH-A8SY-01A-11D-A377-08	GLCE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		0	0	0	5	555	0	117	0	1.327408e-04	0	2	0	117	2		0	0	0	0	0	2	1	0.933860	5	541	0	116	2		0	0	0	0	117	2	-2.510514	1	1	0	0		1	2	3	5	1.937316	0	0.220000	3.360000	0.300762	0.110000	0.030000	1.000000	0.090000	0.303882	0.110000	0	0.060000	1.000000
CASKIN1	57524	broad.mit.edu	37	16	2228602	2228602	+	Silent	SNP	G	G	A			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr16:2228602G>A	ENST00000343516.6	-	20	4337	c.4245C>T	c.(4243-4245)atC>atT	p.I1415I		NM_020764.3	NP_065815.1	Q8WXD9	CSKI1_HUMAN	CASK interacting protein 1			28					ACATGCTGCCGATGTCGTCCA	0.741000																								0							SO:0001819	synonymous_variant			ENST00000343516.6	0	1	hg19	CCDS42103.1																																																																																				TCGA-YH-A8SY-01A-11D-A377-08	CASKIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435055.1	1	0	0	12	153	0	14		0	0	0	0	14	2		0	0	0	0	0	2	1	0.999169	12	151	0	13	2		0	0	0	0	14	2	-3.319498	1	1	0	0		1	1	2	3	1.978101	0	0.220000	3.360000	0.297297	0.750000	0.410000	1.000000	1.000000	0.756480	0.750000	0	0.560000	0.970000
CREBBP	1387	broad.mit.edu	37	16	3823809	3823809	+	Silent	SNP	G	G	A			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr16:3823809G>A	ENST00000262367.5	-	13	3215	c.2406C>T	c.(2404-2406)tcC>tcT	p.S802S	CREBBP_ENST00000382070.3_Silent_p.S764S	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein			295		Ovarian(90;0.0266)			TCGCCCCGCTGGATGACGGGA	0.607000			T, N, F, Mis, O	MLL, MORF, RUNXBP2	ALL, AML, DLBCL, B-NHL 		Rubinstein-Taybi syndrome								Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	0							SO:0001819	synonymous_variant			ENST00000262367.5	1	1	hg19	CCDS10509.1																																																																																				TCGA-YH-A8SY-01A-11D-A377-08	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	1	0	1	55	214	0	49	1	9.046553e-01	6	12	0	49	2		0	0	0	0	0	2	1	1.000000	55	209	0	48	2		0	0	0	0	49	2	-3.411199	1	1	121406	1	33	1	1	2	3	1.978101	0	0.220000	3.360000	0.297297	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	0.990000	1.000000
GPT2	84706	broad.mit.edu	37	16	46943627	46943627	+	Missense_Mutation	SNP	G	G	A			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr16:46943627G>A	ENST00000340124.4	+	6	720	c.608G>A	c.(607-609)gGc>gAc	p.G203D	GPT2_ENST00000440783.2_Missense_Mutation_p.G103D	NM_133443.2	NP_597700.1	Q8TD30	ALAT2_HUMAN	glutamic pyruvate transaminase (alanine aminotransferase) 2			23		all_cancers(37;0.0276)|all_epithelial(9;0.0498)|all_lung(18;0.0522)		L-Alanine(DB00160)|Phenelzine(DB00780)	TCCGGGGGCGGCAAGTCACGG	0.537000																								0							SO:0001583	missense			ENST00000340124.4	0	1	hg19	CCDS10725.1	.	.	.	.	.	.	.	.	.	.	G	11.78	1.740372	0.30865	.	.	ENSG00000166123	ENST00000340124;ENST00000440783	T;T	0.22134	1.97;2.87	5.12	5.12	0.69794	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.052137	0.85682	D	0.000000	T	0.15565	0.0375	N	0.21448	0.665	0.80722	D	1	B	0.15141	0.012	B	0.20767	0.031	T	0.06770	-1.0808	10	0.07813	T	0.8	.	18.7502	0.91810	0.0:0.0:1.0:0.0	.	203	Q8TD30	ALAT2_HUMAN	D	203;103	ENSP00000345282:G203D;ENSP00000413804:G103D	ENSP00000345282:G203D	G	+	2	0	GPT2	45501128	1.000000	0.71417	0.998000	0.56505	0.298000	0.27526	6.049000	0.71053	2.664000	0.90586	0.655000	0.94253	GGC		TCGA-YH-A8SY-01A-11D-A377-08	GPT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255741.2	0	0	0	4	275	0	53	0	7.272195e-03	0	7	0	53	2		0	0	0	0	0	2	1	0.887642	4	272	0	53	2		0	0	0	0	53	2	-2.670567	1	1	0	0		1	1	2	3	1.978101	0	0.220000	3.360000	0.297297	0.160000	0.040000	0.350000	0.150000	0.178021	0.160000	0	0.090000	0.250000
CIRH1A	84916	broad.mit.edu	37	16	69197063	69197063	+	Silent	SNP	C	C	T			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr16:69197063C>T	ENST00000314423.7	+	14	1806	c.1629C>T	c.(1627-1629)atC>atT	p.I543I	CIRH1A_ENST00000563094.1_Silent_p.I543I|CIRH1A_ENST00000352319.4_Silent_p.I428I			Q969X6	CIR1A_HUMAN	cirrhosis, autosomal recessive 1A (cirhin)			16					ACCTTGTCATCGCTCATTCGG	0.498000													Melanoma(69;1156 1278 4951 8715 52012)											0							SO:0001819	synonymous_variant			ENST00000314423.7	1	1	hg19	CCDS10872.1																																																																																				TCGA-YH-A8SY-01A-11D-A377-08	CIRH1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268950.2	1	0	0	57	551	0	126	1	9.998553e-01	25	100	0	126	2		0	0	0	0	0	2	1	1.000000	57	546	0	126	2		0	0	0	0	126	2	-16.039560	1	1	121412	12	47	1	1	2	3	1.980475	0	0.220000	3.360000	0.288126	0.950000	0.720000	1.000000	1.000000	0.926942	0.950000	1	0.820000	1.000000
MTSS1L	92154	broad.mit.edu	37	16	70713713	70713713	+	Nonsense_Mutation	SNP	G	G	A			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr16:70713713G>A	ENST00000338779.6	-	5	632	c.358C>T	c.(358-360)Cag>Tag	p.Q120*		NM_138383.2	NP_612392.1	Q765P7	MTSSL_HUMAN	metastasis suppressor 1-like			7					TTGTCCAGCTGGTTGGCCGCC	0.697000																								0							SO:0001587	stop_gained			ENST00000338779.6	0	1	hg19	CCDS32476.1	.	.	.	.	.	.	.	.	.	.	G	34	5.394476	0.96009	.	.	ENSG00000132613	ENST00000254951;ENST00000338779	.	.	.	4.84	4.84	0.62591	.	0.250943	0.41294	D	0.000908	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07175	T	0.84	-5.8949	12.979	0.58554	0.0:0.0:0.8383:0.1617	.	.	.	.	X	120	.	ENSP00000254951:Q120X	Q	-	1	0	MTSS1L	69271214	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.575000	0.82447	2.250000	0.74265	0.393000	0.25936	CAG		TCGA-YH-A8SY-01A-11D-A377-08	MTSS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434927.3	1	0	0	12	77	0	10	1	9.929075e-01	5	53	0	10	2		0	0	0	0	0	2	1	0.999185	12	74	0	10	2		0	0	0	0	10	2	-19.766950	1	1	0	0		1	1	2	3	1.980475	0	0.220000	3.360000	0.288126	0.990000	0.770000	1.000000	1.000000	0.983669	0.990000	1	0.990000	1.000000
ANKRD11	29123	broad.mit.edu	37	16	89347349	89347349	+	Silent	SNP	G	G	A			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr16:89347349G>A	ENST00000301030.4	-	9	6061	c.5601C>T	c.(5599-5601)tgC>tgT	p.C1867C	ANKRD11_ENST00000378330.2_Silent_p.C1867C	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11			83		all_hematologic(23;0.00824)|Colorectal(91;0.0475)			CAGCCGGTGGGCAGTGCAAAG	0.622000																								0							SO:0001819	synonymous_variant			ENST00000301030.4	1	1	hg19	CCDS32513.1																																																																																				TCGA-YH-A8SY-01A-11D-A377-08	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430462.3	1	0	0	21	235	0	39	1	8.797368e-01	6	38	0	39	2		0	0	0	0	0	2	1	0.999998	20	235	0	39	2		0	0	0	0	39	2	-20.000000	1	1	121362	1	29	1	1	2	3	1.965588	0	0.220000	3.360000	0.297297	0.830000	0.530000	1.000000	1.000000	0.831076	0.830000	0	0.670000	1.000000
HOXB5	3215	broad.mit.edu	37	17	46670813	46670813	+	Missense_Mutation	SNP	C	C	T			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr17:46670813C>T	ENST00000239151.5	-	1	510	c.232G>A	c.(232-234)Gcg>Acg	p.A78T	HOXB-AS3_ENST00000429755.4_RNA|HOXB-AS3_ENST00000465846.2_RNA|HOXB-AS3_ENST00000474324.1_RNA|HOXB-AS3_ENST00000487849.3_RNA|HOXB-AS3_ENST00000460041.1_RNA|HOXB-AS3_ENST00000480872.1_RNA|HOXB-AS3_ENST00000466037.2_RNA|HOXB-AS3_ENST00000476204.1_RNA|HOXB-AS3_ENST00000474040.1_RNA|HOXB3_ENST00000552000.2_Intron|HOXB-AS3_ENST00000492897.3_RNA|HOXB-AS3_ENST00000481995.1_RNA|HOXB-AS3_ENST00000477144.1_RNA|HOXB-AS3_ENST00000467155.2_RNA	NM_002147.3	NP_002138.1	P09067	HXB5_HUMAN	homeobox B5			3					TGGGCGGGCGCGGGGAAGGCG	0.687000																								0							SO:0001583	missense			ENST00000239151.5	0	1	hg19	CCDS11530.1	.	.	.	.	.	.	.	.	.	.	C	11.07	1.530435	0.27387	.	.	ENSG00000120075	ENST00000239151	D	0.92299	-3.01	5.44	0.916	0.19373	.	0.579461	0.18522	N	0.138741	D	0.82545	0.5060	N	0.21282	0.65	0.29926	N	0.822337	B	0.15930	0.015	B	0.06405	0.002	T	0.72811	-0.4180	10	0.32370	T	0.25	.	6.425	0.21764	0.2685:0.5605:0.0977:0.0732	.	78	P09067	HXB5_HUMAN	T	78	ENSP00000239151:A78T	ENSP00000239151:A78T	A	-	1	0	HOXB5	44025812	0.126000	0.22350	0.998000	0.56505	0.904000	0.53231	0.035000	0.13797	0.663000	0.31027	-0.300000	0.09419	GCG		TCGA-YH-A8SY-01A-11D-A377-08	HOXB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358148.2	1	0	0	13	92	0	18	1	8.680183e-01	3	25	0	18	2		0	0	0	0	0	2	1	0.999547	13	88	0	18	2		0	0	0	0	18	2	-19.984010	1	1	0	0		1	3	3	6	2.173455	1	0.220000	3.360000	0.376399	0.990000	0.850000	1.000000	1.000000	0.991403	0.990000	1	0.990000	1.000000
TP53	7157	broad.mit.edu	37	17	7578406	7578406	+	Missense_Mutation	SNP	C	C	T	rs28934578		TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr17:7578406C>T	ENST00000269305.4	-	5	713	c.524G>A	c.(523-525)cGc>cAc	p.R175H	TP53_ENST00000445888.2_Missense_Mutation_p.R175H|TP53_ENST00000574684.1_5'UTR|TP53_ENST00000455263.2_Missense_Mutation_p.R175H|TP53_ENST00000420246.2_Missense_Mutation_p.R175H|TP53_ENST00000359597.4_Missense_Mutation_p.R175H|TP53_ENST00000413465.2_Missense_Mutation_p.R175H	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.R175H(847)|p.R43H(36)|p.R82H(36)|p.R175L(19)|p.0?(8)|p.R175P(6)|p.R174fs*24(3)|p.R175_E180delRCPHHE(3)|p.V173fs*59(2)|p.R174fs*1(2)|p.V157_C176del20(1)|p.V173fs*69(1)|p.E171fs*61(1)|p.V173fs*23(1)|p.R174_H178>S(1)|p.V172_E180delVVRRCPHHE(1)|p.R174_H179delRRCPHH(1)|p.E171fs*1(1)|p.R175_H178>X(1)|p.R175fs*5(1)|p.R42fs*24(1)|p.R174_C176delRRC(1)|p.H168fs*69(1)|p.R174fs*70(1)|p.E171_H179delEVVRRCPHH(1)|p.R81fs*24(1)|p.R174_E180>K(1)|p.R174fs*3(1)		24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		Acetylsalicylic acid(DB00945)	GTGGGGGCAGCGCCTCACAAC	0.652000	R175H(AU565_BREAST)|R175H(CAL33_UPPER_AERODIGESTIVE_TRACT)|R175H(DETROIT562_UPPER_AERODIGESTIVE_TRACT)|R175H(HCC1395_BREAST)|R175H(HUCCT1_BILIARY_TRACT)|R175H(KLE_ENDOMETRIUM)|R175H(KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R175H(LS123_LARGE_INTESTINE)|R175H(NCIH196_LUNG)|R175H(RKN_OVARY)|R175H(SKBR3_BREAST)|R175H(SKUT1_SOFT_TISSUE)|R175H(TYKNU_OVARY)	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	980	Substitution - Missense(944)|Deletion - Frameshift(17)|Whole gene deletion(8)|Deletion - In frame(8)|Complex - deletion inframe(3)	GRCh37	CM062017|CM951224	TP53	M	rs28934578	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	31	5.079737	0.94050	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99889	-7.55;-7.55;-7.55;-7.55;-7.55;-7.55;-7.55;-7.55	5.41	5.41	0.78517	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.101149	0.64402	D	0.000008	D	0.99908	0.9956	M	0.92784	3.345	0.80722	A	1	D;P;D;D;P;B;D	0.89917	0.999;0.578;1.0;0.998;0.632;0.213;0.999	D;B;D;D;B;B;D	0.91635	0.985;0.26;0.999;0.921;0.378;0.144;0.939	D	0.96278	0.9204	9	0.87932	D	0	-11.8679	17.0767	0.86588	0.0:1.0:0.0:0.0	rs28934578	136;175;175;82;175;175;175	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	H	175;175;175;175;175;175;164;82;43;82;43	ENSP00000410739:R175H;ENSP00000352610:R175H;ENSP00000269305:R175H;ENSP00000398846:R175H;ENSP00000391127:R175H;ENSP00000391478:R175H;ENSP00000425104:R43H;ENSP00000423862:R82H	ENSP00000269305:R175H	R	-	2	0	TP53	7519131	1.000000	0.71417	0.989000	0.46669	0.795000	0.44927	6.042000	0.70996	2.702000	0.92279	0.655000	0.94253	CGC		TCGA-YH-A8SY-01A-11D-A377-08	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	1	0	1	56	251	0	32	1	9.977413e-01	17	27	0	32	2	1	1	197	637	2	779	8	1	1.000000	56	249	0	31	2		0	0	0	0	32	2	-3.134589	1	1	121412	1	41	1	0	2	2	1.769858	1	0.220000	3.360000	0.220000	0.990000	0.990000	1.000000	1.000000	0.999997	0.990000	1	0.990000	1.000000
MALT1	10892	broad.mit.edu	37	18	56409220	56409220	+	Missense_Mutation	SNP	G	G	A			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr18:56409220G>A	ENST00000348428.3	+	14	1985	c.1727G>A	c.(1726-1728)cGg>cAg	p.R576Q	MALT1_ENST00000345724.3_Missense_Mutation_p.R565Q|RP11-126O1.4_ENST00000588835.1_RNA	NM_006785.2|NM_173844.1	NP_006776.1|NP_776216.1	Q9UDY8	MALT1_HUMAN	mucosa associated lymphoid tissue lymphoma translocation gene 1			12					TCTCTTGTGCGGAATCTACAG	0.378000			T	BIRC3	MALT										Dom	yes		18	18q21	10892	mucosa associated lymphoid tissue lymphoma translocation gene 1		L	0							SO:0001583	missense			ENST00000348428.3	0	1	hg19	CCDS11967.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.587606	0.86851	.	.	ENSG00000172175	ENST00000348428;ENST00000345724	T;T	0.14144	2.54;2.53	5.53	5.53	0.82687	.	0.112546	0.64402	D	0.000012	T	0.35128	0.0921	L	0.59436	1.845	0.34914	D	0.747776	D;D	0.89917	1.0;0.999	D;P	0.67725	0.953;0.899	T	0.34551	-0.9824	10	0.62326	D	0.03	-17.4564	19.053	0.93053	0.0:0.0:1.0:0.0	.	565;576	Q9UDY8-2;Q9UDY8	.;MALT1_HUMAN	Q	576;565	ENSP00000319279:R576Q;ENSP00000304161:R565Q	ENSP00000304161:R565Q	R	+	2	0	MALT1	54560200	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	4.500000	0.60387	2.600000	0.87896	0.446000	0.29264	CGG		TCGA-YH-A8SY-01A-11D-A377-08	MALT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256132.2	0	0	0	4	273	0	83	0	4.992063e-02	0	19	0	83	2		0	0	0	0	0	2	1	0.888482	4	270	0	83	2		0	0	0	0	83	2	-2.516217	1	1	0	0		1	0	1	1	1.564562	1	0.220000	3.360000	0.130047	0.120000	0.040000	0.280000	0.120000	0.142560	0.120000	0	0.070000	0.200000
ATP1A3	478	broad.mit.edu	37	19	42471441	42471441	+	Silent	SNP	G	G	A			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr19:42471441G>A	ENST00000302102.5	-	22	3123	c.2973C>T	c.(2971-2973)taC>taT	p.Y991Y	ATP1A3_ENST00000602133.1_Silent_p.Y961Y|ATP1A3_ENST00000545399.1_Silent_p.Y1004Y|ATP1A3_ENST00000543770.1_Silent_p.Y1002Y	NM_152296.4	NP_689509.1	P13637	AT1A3_HUMAN	ATPase, Na+/K+ transporting, alpha 3 polypeptide			52					GGATTTCGTCGTAGACGAAGA	0.652000																								0							SO:0001819	synonymous_variant			ENST00000302102.5	1	1	hg19	CCDS12594.1																																																																																				TCGA-YH-A8SY-01A-11D-A377-08	ATP1A3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268107.1	1	0	1	37	154	0	20	1	3.958122e-02	2	0	0	20	2		0	0	0	0	0	2	1	1.000000	37	152	0	20	2		0	0	0	0	20	2	-20.000000	1	1	121406	5	37	1	2	2	4	2.150199	1	0.220000	3.360000	0.360656	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	0.990000	1.000000
WDR77	79084	broad.mit.edu	37	1	111991320	111991320	+	Silent	SNP	G	G	A			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr1:111991320G>A	ENST00000235090.5	-	2	428	c.222C>T	c.(220-222)tcC>tcT	p.S74S	ATP5F1_ENST00000483994.1_5'Flank|Y_RNA_ENST00000363020.1_RNA|ATP5F1_ENST00000369722.3_5'Flank|WDR77_ENST00000411751.2_Silent_p.S74S|WDR77_ENST00000497278.1_5'Flank	NM_024102.2	NP_077007.1	Q9BQA1	MEP50_HUMAN	WD repeat domain 77			10		all_cancers(81;0.000902)|all_epithelial(167;0.00056)|all_lung(203;0.00277)|Lung NSC(277;0.0043)			GGACTCCGGCGGAGCAGAAGC	0.622000																								0							SO:0001819	synonymous_variant			ENST00000235090.5	0	1	hg19	CCDS835.1	.	.	.	.	.	.	.	.	.	.	G	12.25	1.880414	0.33255	.	.	ENSG00000116455	ENST00000449340	.	.	.	5.73	-1.3	0.09259	.	.	.	.	.	T	0.22898	0.0553	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.30679	-0.9970	4	.	.	.	-18.7416	1.0705	0.01620	0.3009:0.1646:0.3524:0.1822	.	.	.	.	L	11	.	.	P	-	2	0	WDR77	111792843	0.818000	0.29161	0.995000	0.50966	0.991000	0.79684	-0.097000	0.11042	0.077000	0.16863	0.561000	0.74099	CCG		TCGA-YH-A8SY-01A-11D-A377-08	WDR77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032465.1	0	0	0	4	174	0	33	0	2.260210e-01	0	32	0	33	2		0	0	0	0	0	2	1	0.875641	3	164	0	32	2		0	0	0	0	33	2	-5.907009	1	0	0	0		1	1	2	3	1.963322	0	0.220000	3.360000	0.295902	0.250000	0.080000	0.600000	0.230000	0.283117	0.250000	0	0.150000	0.400000
NGF	4803	broad.mit.edu	37	1	115829176	115829176	+	Nonsense_Mutation	SNP	G	G	A			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr1:115829176G>A	ENST00000369512.2	-	3	409	c.241C>T	c.(241-243)Cga>Tga	p.R81*	RP4-663N10.1_ENST00000425449.1_RNA	NM_002506.2	NP_002497.2	P01138	NGF_HUMAN	nerve growth factor (beta polypeptide)			13	Lung SC(450;0.211)	all_cancers(81;1.07e-06)|all_epithelial(167;4.43e-06)|all_lung(203;2.86e-05)|Lung NSC(69;4.99e-05)		Clenbuterol(DB01407)	GAACGGAGTCGCCGCTTTTTA	0.642000																								0							SO:0001587	stop_gained			ENST00000369512.2	0	1	hg19	CCDS882.1	.	.	.	.	.	.	.	.	.	.	G	25.5	4.640906	0.87859	.	.	ENSG00000134259	ENST00000369512	.	.	.	5.06	3.05	0.35203	.	0.058013	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.0674	11.9013	0.52685	0.0:0.0:0.5284:0.4716	.	.	.	.	X	81	.	ENSP00000358525:R81X	R	-	1	2	NGF	115630699	0.998000	0.40836	0.836000	0.33094	0.748000	0.42578	3.935000	0.56560	0.536000	0.28733	0.467000	0.42956	CGA		TCGA-YH-A8SY-01A-11D-A377-08	NGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032832.1	1	0	1	23	144	0	30	0	2.088409e-02	1	1	0	30	2		0	0	0	0	0	2	1	1.000000	22	141	0	29	2		0	0	0	0	30	2	-3.328489	1	1	0	0		1	1	2	3	1.963322	0	0.220000	3.360000	0.295902	0.990000	0.920000	1.000000	1.000000	0.995616	0.990000	1	0.990000	1.000000
ADAM30	11085	broad.mit.edu	37	1	120436918	120436918	+	Missense_Mutation	SNP	G	G	A	rs115551394	byFrequency	TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr1:120436918G>A	ENST00000369400.1	-	1	2200	c.2042C>T	c.(2041-2043)gCg>gTg	p.A681V		NM_021794.3	NP_068566.2	Q9UKF2	ADA30_HUMAN	ADAM metallopeptidase domain 30			38	all_cancers(5;7.07e-10)|all_epithelial(5;1.62e-10)|all_neural(166;0.153)|Breast(55;0.234)	all_lung(203;1.55e-06)|Lung NSC(69;1.04e-05)|all_epithelial(167;0.00138)			CGAGGGAATCGCCCCTCTGAG	0.473000																								0							SO:0001583	missense			ENST00000369400.1	1	0	hg19	CCDS907.1	4	0.0018315018315018315	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	0	0.0	G	8.508	0.865747	0.17250	0.005447	9.3E-4	ENSG00000134249	ENST00000369400;ENST00000543066	T	0.01178	5.22	5.05	-5.85	0.02311	.	0.692560	0.11763	U	0.531905	T	0.00144	0.0004	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.41787	-0.9489	10	0.29301	T	0.29	.	0.2119	0.00157	0.2303:0.2226:0.2471:0.3	.	681	Q9UKF2	ADA30_HUMAN	V	681	ENSP00000358407:A681V	ENSP00000358407:A681V	A	-	2	0	ADAM30	120238441	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.486000	0.06513	-1.165000	0.02786	-2.744000	0.00126	GCG		TCGA-YH-A8SY-01A-11D-A377-08	ADAM30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033678.1	1	0	1	60	246	0	103		0	0	0	0	103	2		0	0	0	0	0	2	1	1.000000	58	245	0	103	2		0	0	0	0	103	2	-2.865375	1	1	121412	189	55	1	1	2	3	1.963322	0	0.220000	3.360000	0.295902	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	0.990000	1.000000
KLHDC7A	127707	broad.mit.edu	37	1	18809344	18809344	+	Silent	SNP	C	C	T			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr1:18809344C>T	ENST00000400664.1	+	1	1921	c.1869C>T	c.(1867-1869)ttC>ttT	p.F623F		NM_152375.2	NP_689588.2	Q5VTJ3	KLD7A_HUMAN	kelch domain containing 7A			22		Colorectal(325;3.46e-05)|all_lung(284;0.000152)|Lung NSC(340;0.000185)|Breast(348;0.00046)|Renal(390;0.000518)|Ovarian(437;0.0014)|Myeloproliferative disorder(586;0.0255)			GTGACACGTTCGCCCTGGCGC	0.667000																								0							SO:0001819	synonymous_variant			ENST00000400664.1	1	1	hg19	CCDS185.2																																																																																				TCGA-YH-A8SY-01A-11D-A377-08	KLHDC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006923.3	1	0	1	13	101	0	28		0	0	0	0	28	2		0	0	0	0	0	2	1	0.999452	11	96	0	24	2		0	0	0	0	28	2	-19.863460	1	1	0	0		1	1	2	3	1.984081	0	0.220000	3.360000	0.297297	0.990000	0.660000	1.000000	1.000000	0.958633	0.990000	1	0.890000	1.000000
SYT2	127833	broad.mit.edu	37	1	202568444	202568444	+	Missense_Mutation	SNP	T	T	G			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr1:202568444T>G	ENST00000367267.1	-	8	1147	c.955A>C	c.(955-957)Aag>Cag	p.K319Q	SYT2_ENST00000367268.4_Missense_Mutation_p.K319Q	NM_001136504.1	NP_001129976.1	Q8N9I0	SYT2_HUMAN	synaptotagmin II			29			BRCA - Breast invasive adenocarcinoma(75;0.169)	Botulinum Toxin Type B(DB00042)	TTGAGCCTCTTGCCATTCTGC	0.532000																								0							SO:0001583	missense			ENST00000367267.1	1	1	hg19	CCDS1427.1	.	.	.	.	.	.	.	.	.	.	T	28.0	4.881455	0.91740	.	.	ENSG00000143858	ENST00000367268;ENST00000367267	T;T	0.72835	-0.69;-0.69	5.21	5.21	0.72293	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.102327	0.64402	D	0.000003	T	0.72977	0.3528	N	0.25060	0.705	0.80722	D	1	D	0.60575	0.988	D	0.63192	0.912	T	0.76971	-0.2761	10	0.66056	D	0.02	.	14.7397	0.69445	0.0:0.0:0.0:1.0	.	319	Q8N9I0	SYT2_HUMAN	Q	319	ENSP00000356237:K319Q;ENSP00000356236:K319Q	ENSP00000356236:K319Q	K	-	1	0	SYT2	200835067	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.897000	0.87356	1.957000	0.56846	0.460000	0.39030	AAG		TCGA-YH-A8SY-01A-11D-A377-08	SYT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099157.1	1	0	1	58	429	0	108		0	0	0	0	108	2		0	0	0	0	0	2	1	1.000000	58	425	0	107	2		0	0	0	0	108	2	-19.993890	1	1	0	0		1	3	3	6	2.322195	1	0.220000	3.360000	0.417389	0.990000	0.990000	1.000000	1.000000	0.999919	0.990000	1	0.990000	1.000000
USH2A	7399	broad.mit.edu	37	1	215987140	215987140	+	Missense_Mutation	SNP	C	C	T			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr1:215987140C>T	ENST00000307340.3	-	49	10063	c.9677G>A	c.(9676-9678)cGa>cAa	p.R3226Q	USH2A_ENST00000366943.2_Missense_Mutation_p.R3226Q	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)			527					CTCCTGTATTCGGCCACCACA	0.453000										HNSCC(13;0.011)														0							SO:0001583	missense			ENST00000307340.3	1	1	hg19	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	C	14.84	2.656431	0.47467	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.12255	2.71;2.7	5.8	1.02	0.19986	Fibronectin, type III (2);	0.228496	0.22457	U	0.059807	T	0.04318	0.0119	N	0.21240	0.645	0.09310	N	1	P	0.48503	0.911	B	0.31946	0.138	T	0.30621	-0.9972	10	0.08599	T	0.76	.	2.9934	0.05990	0.3129:0.3248:0.0:0.3623	.	3226	O75445	USH2A_HUMAN	Q	3226	ENSP00000305941:R3226Q;ENSP00000355910:R3226Q	ENSP00000305941:R3226Q	R	-	2	0	USH2A	214053763	0.340000	0.24792	0.341000	0.25589	0.810000	0.45777	0.862000	0.27899	0.596000	0.29794	-0.282000	0.10007	CGA		TCGA-YH-A8SY-01A-11D-A377-08	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	1	0	1	105	374	0	68		0	0	0	0	68	2		0	0	0	0	0	2	1	1.000000	103	368	0	67	2		0	0	0	0	68	2	-3.997968	1	1	0	0		1	2	3	5	2.302493	1	0.220000	3.360000	0.412075	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	0.990000	1.000000
MECR	51102	broad.mit.edu	37	1	29543100	29543100	+	Splice_Site	SNP	C	C	A			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr1:29543100C>A	ENST00000263702.6	-	2	299	c.274G>T	c.(274-276)Gga>Tga	p.G92*	MECR_ENST00000373791.3_Splice_Site_p.G16*|MECR_ENST00000489248.1_5'UTR			Q9BV79	MECR_HUMAN	mitochondrial trans-2-enoyl-CoA reductase			11		Colorectal(325;0.000389)|Breast(348;0.00765)|Lung NSC(340;0.0081)|all_lung(284;0.00914)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)			CCAAGGTTACCTTGGATCATA	0.458000																								0							SO:0001630	splice_region_variant			ENST00000263702.6	0	1	hg19	CCDS30659.1	.	.	.	.	.	.	.	.	.	.	C	38	7.283297	0.98186	.	.	ENSG00000116353	ENST00000373791;ENST00000263702;ENST00000373792	.	.	.	5.38	5.38	0.77491	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.5119	0.67794	0.0:1.0:0.0:0.0	.	.	.	.	X	16;92;4	.	.	G	-	1	0	MECR	29415687	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.673000	0.74482	2.802000	0.96397	0.655000	0.94253	GGA		TCGA-YH-A8SY-01A-11D-A377-08	MECR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130740.1	0	0	0	169	710	0	144	0	9.796430e-01	0	28	0	144	2		0	0	0	0	0	2	1	1.000000	166	704	0	144	2		0	0	0	0	144	2	-3.293877	1	1	0	0		1	1	2	3	1.963322	0	0.220000	3.360000	0.295902	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	0.990000	1.000000
STK40	83931	broad.mit.edu	37	1	36807372	36807372	+	Missense_Mutation	SNP	C	C	T			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr1:36807372C>T	ENST00000373129.3	-	12	1698	c.1292G>A	c.(1291-1293)cGc>cAc	p.R431H	STK40_ENST00000373130.3_Missense_Mutation_p.R436H|STK40_ENST00000373132.3_Missense_Mutation_p.R431H|STK40_ENST00000359297.2_3'UTR	NM_032017.1	NP_114406.1	Q8N2I9	STK40_HUMAN	serine/threonine kinase 40			13		Myeloproliferative disorder(586;0.0393)			CCGCAGGTAGCGCTGCGCCAG	0.672000																								0							SO:0001583	missense			ENST00000373129.3	1	1	hg19	CCDS407.1	.	.	.	.	.	.	.	.	.	.	C	17.60	3.431035	0.62844	0.0	1.16E-4	ENSG00000196182	ENST00000373129;ENST00000373130;ENST00000373132	T;T;T	0.68765	-0.34;-0.35;-0.34	5.18	4.26	0.50523	.	0.000000	0.85682	D	0.000000	T	0.70579	0.3240	L	0.27053	0.805	0.49051	D	0.999748	D;D	0.76494	0.999;0.998	D;D	0.74674	0.984;0.964	T	0.73895	-0.3838	10	0.87932	D	0	-21.1861	12.6841	0.56938	0.0:0.9199:0.0:0.0801	.	436;431	Q8N2I9-4;Q8N2I9	.;STK40_HUMAN	H	431;436;431	ENSP00000362221:R431H;ENSP00000362222:R436H;ENSP00000362224:R431H	ENSP00000362221:R431H	R	-	2	0	STK40	36579959	1.000000	0.71417	1.000000	0.80357	0.143000	0.21401	7.378000	0.79679	1.177000	0.42855	0.563000	0.77884	CGC		TCGA-YH-A8SY-01A-11D-A377-08	STK40-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022592.1	1	0	1	56	222	0	41	1	9.997914e-01	10	43	0	41	2		0	0	0	0	0	2	1	1.000000	54	218	0	40	2		0	0	0	0	41	2	-3.362224	1	1	121390	2	34	1	1	2	3	1.963322	0	0.220000	3.360000	0.295902	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	0.990000	1.000000
PTCH2	8643	broad.mit.edu	37	1	45288266	45288266	+	Missense_Mutation	SNP	C	C	T			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr1:45288266C>T	ENST00000372192.3	-	22	3563	c.3433G>A	c.(3433-3435)Gca>Aca	p.A1145T	PTCH2_ENST00000447098.2_Intron|RNU5E-6P_ENST00000365574.1_RNA	NM_003738.4	NP_003729.3	Q9Y6C5	PTC2_HUMAN	patched 2			50	Acute lymphoblastic leukemia(166;0.155)				GAGGAGGATGCCCCCCACCTA	0.627000									Basal Cell Nevus syndrome															0							SO:0001583	missense	Familial Cancer Database	Gorlin syndrome, Gorlin-Golz syndrome, Naevoid Basal Cell Carcinoma syndrome, NBCCS	ENST00000372192.3	0	1	hg19	CCDS516.1	.	.	.	.	.	.	.	.	.	.	c	9.847	1.192670	0.21954	.	.	ENSG00000117425	ENST00000372192	D	0.92299	-3.01	3.92	-7.85	0.01192	.	3.801910	0.00674	N	0.000646	T	0.76371	0.3978	N	0.08118	0	0.19945	N	0.999941	B	0.06786	0.001	B	0.08055	0.003	T	0.72782	-0.4189	10	0.13470	T	0.59	6.7686	0.1418	0.00084	0.2555:0.2463:0.2154:0.2828	.	1145	Q9Y6C5	PTC2_HUMAN	T	1145	ENSP00000361266:A1145T	ENSP00000361266:A1145T	A	-	1	0	PTCH2	45060853	0.000000	0.05858	0.000000	0.03702	0.355000	0.29361	-3.348000	0.00503	-2.059000	0.00894	-0.921000	0.02739	GCA		TCGA-YH-A8SY-01A-11D-A377-08	PTCH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023428.4	0	0	0	5	450	1	67	0	5.949946e-04	0	3	1	67	2		0	0	0	0	0	2	0	0.000968	5	445	1	66	21		0	0	0	1	67	2	-1.947876	0	1	0	0		1	1	2	3	1.963322	0	0.220000	3.360000	0.295902	0.120000	0.030000	0.270000	0.120000	0.140044	0.120000	0	0.070000	0.190000
ELAVL4	1996	broad.mit.edu	37	1	50642759	50642759	+	Splice_Site	SNP	A	A	G			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr1:50642759A>G	ENST00000371823.4	+	3	474		c.e3-1		ELAVL4_ENST00000357083.4_Splice_Site|ELAVL4_ENST00000371821.1_Splice_Site|ELAVL4_ENST00000371824.1_Splice_Site|ELAVL4_ENST00000371819.1_Splice_Site|RP11-567C20.2_ENST00000442477.1_RNA|ELAVL4_ENST00000492299.1_Splice_Site|ELAVL4_ENST00000371827.1_Splice_Site|ELAVL4_ENST00000448907.2_Splice_Site	NM_001144774.1|NM_021952.3	NP_001138246.1|NP_068771.2	P26378	ELAV4_HUMAN	ELAV like neuron-specific RNA binding protein 4			32					ATATTTCCACAGGACAGAGTT	0.403000																								0							SO:0001630	splice_region_variant			ENST00000371823.4	1	1	hg19	CCDS553.1	.	.	.	.	.	.	.	.	.	.	A	17.24	3.339651	0.60963	.	.	ENSG00000162374	ENST00000448907;ENST00000371827;ENST00000357083;ENST00000371824;ENST00000371823;ENST00000371821;ENST00000371819	.	.	.	5.5	5.5	0.81552	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.7759	0.78214	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ELAVL4	50415346	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.703000	0.91344	2.308000	0.77769	0.533000	0.62120	.		TCGA-YH-A8SY-01A-11D-A377-08	ELAVL4-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000021712.1	1	0	1	20	178	0	34		0	0	0	0	34	2		0	0	0	0	0	2	1	0.999995	20	171	0	33	2		0	0	0	0	34	2	-9.262255	1	1	0	0		1	1	2	3	1.963322	0	0.220000	3.360000	0.295902	0.990000	0.650000	1.000000	1.000000	0.936548	0.990000	1	0.820000	1.000000
HFM1	164045	broad.mit.edu	37	1	91739306	91739306	+	Silent	SNP	T	T	A			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr1:91739306T>A	ENST00000370425.3	-	34	3833	c.3735A>T	c.(3733-3735)ggA>ggT	p.G1245G	HFM1_ENST00000462405.1_5'UTR|HFM1_ENST00000294696.5_Silent_p.G477G|HFM1_ENST00000370424.3_Silent_p.G924G	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)			75		all_lung(203;0.00961)|Lung NSC(277;0.0351)			GTCTAACTTTTCCATAGATTT	0.313000																								0							SO:0001819	synonymous_variant			ENST00000370425.3	1	1	hg19	CCDS30769.2	.	.	.	.	.	.	.	.	.	.	T	2.695	-0.272273	0.05716	.	.	ENSG00000162669	ENST00000430465	.	.	.	5.75	2.13	0.27403	.	.	.	.	.	T	0.10680	0.0261	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.33007	-0.9885	4	.	.	.	.	4.7459	0.13036	0.0:0.1688:0.1611:0.6701	.	.	.	.	V	457	.	.	E	-	2	0	HFM1	91511894	0.000000	0.05858	0.000000	0.03702	0.490000	0.33462	0.682000	0.25335	0.105000	0.17753	0.533000	0.62120	GAA		TCGA-YH-A8SY-01A-11D-A377-08	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316716.2	1	0	0	55	587	0	129		0	0	0	0	129	2		0	0	0	0	0	2	1	1.000000	55	580	0	129	2		0	0	0	0	129	2	-14.863670	1	1	0	0		1	1	2	3	1.963322	0	0.220000	3.360000	0.295902	0.860000	0.660000	1.000000	1.000000	0.865749	0.860000	1	0.750000	0.990000
HFM1	164045	broad.mit.edu	37	1	91846537	91846537	+	Missense_Mutation	SNP	C	C	T			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr1:91846537C>T	ENST00000370425.3	-	7	903	c.805G>A	c.(805-807)Gca>Aca	p.A269T	HFM1_ENST00000294696.5_5'UTR|HFM1_ENST00000370424.3_Intron	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	p.A269T(1)		75		all_lung(203;0.00961)|Lung NSC(277;0.0351)			CTAAATTTTGCCGCTTACAAT	0.219000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000370425.3	0	1	hg19	CCDS30769.2	.	.	.	.	.	.	.	.	.	.	C	9.307	1.054465	0.19907	.	.	ENSG00000162669	ENST00000370425;ENST00000541820;ENST00000448819	T	0.58797	0.31	5.81	2.87	0.33458	.	0.000000	0.45606	U	0.000360	T	0.29093	0.0723	L	0.54323	1.7	0.80722	D	1	B;B	0.15719	0.014;0.002	B;B	0.08055	0.003;0.003	T	0.09100	-1.0690	10	0.23891	T	0.37	.	8.468	0.32969	0.0:0.5885:0.0:0.4115	.	269;269	B7ZM16;A2PYH4	.;HFM1_HUMAN	T	269;302;128	ENSP00000359454:A269T	ENSP00000359454:A269T	A	-	1	0	HFM1	91619125	0.079000	0.21365	0.903000	0.35520	0.987000	0.75469	0.529000	0.23019	0.339000	0.23719	-0.136000	0.14681	GCA		TCGA-YH-A8SY-01A-11D-A377-08	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316716.2	0	0	0	5	410	0	102		0	0	0	0	102	2		0	0	0	0	0	2	1	0.936302	5	407	0	101	2		0	0	0	0	102	2	-1.974416	0	1	121328	2	31	1	1	2	3	1.963322	0	0.220000	3.360000	0.295902	0.130000	0.040000	0.300000	0.120000	0.152466	0.130000	0	0.080000	0.200000
NINL	22981	broad.mit.edu	37	20	25442226	25442226	+	Nonsense_Mutation	SNP	G	G	A			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr20:25442226G>A	ENST00000278886.6	-	21	3701	c.3628C>T	c.(3628-3630)Cag>Tag	p.Q1210*	NINL_ENST00000464285.1_5'Flank|NINL_ENST00000422516.1_Nonsense_Mutation_p.Q861*	NM_025176.4	NP_079452.3	Q9Y2I6	NINL_HUMAN	ninein-like			57					TGATGTTCCTGATTCAGGCAT	0.468000																								0							SO:0001587	stop_gained			ENST00000278886.6	0	1	hg19	CCDS33452.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.593669	0.86953	.	.	ENSG00000101004	ENST00000278886;ENST00000422516	.	.	.	4.69	0.163	0.14986	.	0.257192	0.31673	N	0.007250	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.41790	T	0.15	-2.2951	7.9115	0.29793	0.0:0.2925:0.4189:0.2885	.	.	.	.	X	1210;861	.	ENSP00000278886:Q1210X	Q	-	1	0	NINL	25390226	0.990000	0.36364	0.013000	0.15412	0.104000	0.19210	0.957000	0.29215	-0.084000	0.12595	0.555000	0.69702	CAG		TCGA-YH-A8SY-01A-11D-A377-08	NINL-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078445.3	1	0	1	63	267	0	57	0	5.985598e-01	0	10	0	57	2		0	0	0	0	0	2	1	1.000000	63	263	0	56	2		0	0	0	0	57	2	-3.512475	1	1	121412	2	38	1	2	2	4	2.126355	1	0.220000	3.360000	0.360656	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	0.990000	1.000000
MC3R	4159	broad.mit.edu	37	20	54824819	54824819	+	Missense_Mutation	SNP	G	G	A			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr20:54824819G>A	ENST00000243911.2	+	1	1032	c.920G>A	c.(919-921)cGc>cAc	p.R307H		NM_019888.3	NP_063941.3	P41968	MC3R_HUMAN	melanocortin 3 receptor			26			Colorectal(105;0.202)		CTGGAATTGCGCAACACCTTT	0.517000																								0							SO:0001583	missense			ENST00000243911.2	0	1	hg19	CCDS13449.2	.	.	.	.	.	.	.	.	.	.	G	17.98	3.520625	0.64747	.	.	ENSG00000124089	ENST00000243911	T	0.58358	0.34	5.09	5.09	0.68999	.	0.000000	0.64402	D	0.000014	D	0.82917	0.5141	H	0.97440	4.005	0.51767	D	0.99993	D	0.89917	1.0	D	0.83275	0.996	D	0.89536	0.3789	10	0.87932	D	0	.	18.1096	0.89530	0.0:0.0:1.0:0.0	.	344	P41968	MC3R_HUMAN	H	307	ENSP00000243911:R307H	ENSP00000243911:R307H	R	+	2	0	MC3R	54258226	1.000000	0.71417	0.990000	0.47175	0.182000	0.23217	9.731000	0.98807	2.362000	0.80069	0.555000	0.69702	CGC		TCGA-YH-A8SY-01A-11D-A377-08	MC3R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079786.2	0	0	0	5	671	0	93		0	0	0	0	93	2		0	0	0	0	0	2	1	0.934759	4	660	0	92	2		0	0	0	0	93	2	-1.750945	0	1	0	0		1	2	2	4	2.126355	1	0.220000	3.360000	0.360656	0.080000	0.010000	0.190000	0.080000	0.097547	0.080000	0	0.050000	0.140000
KRTAP8-1	337879	broad.mit.edu	37	21	32185365	32185365	+	Silent	SNP	C	C	T			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr21:32185365C>T	ENST00000329621.4	-	1	205	c.174G>A	c.(172-174)tcG>tcA	p.S58S		NM_175857.3	NP_787053.1	Q8IUC2	KRA81_HUMAN	keratin associated protein 8-1			6					GAGCAAATGGCGAGTATCTCC	0.562000																								0							SO:0001819	synonymous_variant			ENST00000329621.4	1	1	hg19	CCDS13607.1																																																																																				TCGA-YH-A8SY-01A-11D-A377-08	KRTAP8-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128223.1	1	0	1	70	355	0	74		0	0	0	0	74	2		0	0	0	0	0	2	1	1.000000	69	347	0	74	2		0	0	0	0	74	2	-20.000000	1	1	121412	1	36	1	2	2	4	2.110881	1	0.220000	3.360000	0.359501	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	0.990000	1.000000
KRTAP11-1	337880	broad.mit.edu	37	21	32253572	32253572	+	Missense_Mutation	SNP	C	C	A			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr21:32253572C>A	ENST00000332378.4	-	1	302	c.272G>T	c.(271-273)tGt>tTt	p.C91F		NM_175858.2	NP_787054.1	Q8IUC1	KR111_HUMAN	keratin associated protein 11-1			18					GTTGGAAATACAGGTAGTTTG	0.567000																								0							SO:0001583	missense			ENST00000332378.4	1	1	hg19	CCDS13608.1	.	.	.	.	.	.	.	.	.	.	C	14.59	2.579810	0.46006	.	.	ENSG00000182591	ENST00000332378	T	0.03065	4.06	5.17	4.27	0.50696	.	0.222920	0.39020	N	0.001497	T	0.16128	0.0388	M	0.79258	2.445	0.37098	D	0.899749	D	0.76494	0.999	D	0.74348	0.983	T	0.00907	-1.1519	10	0.49607	T	0.09	-6.145	12.4326	0.55583	0.0:0.9123:0.0:0.0877	.	91	Q8IUC1	KR111_HUMAN	F	91	ENSP00000330720:C91F	ENSP00000330720:C91F	C	-	2	0	KRTAP11-1	31175443	1.000000	0.71417	0.996000	0.52242	0.624000	0.37722	3.372000	0.52387	2.608000	0.88229	0.650000	0.86243	TGT		TCGA-YH-A8SY-01A-11D-A377-08	KRTAP11-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128225.1	1	0	1	37	215	0	53		0	0	0	0	53	2		0	0	0	0	0	2	1	1.000000	37	209	0	53	2		0	0	0	0	53	2	-20.000000	1	1	0	0		1	2	2	4	2.110881	1	0.220000	3.360000	0.359501	0.990000	0.990000	1.000000	1.000000	0.999918	0.990000	1	0.990000	1.000000
DOPEY2	9980	broad.mit.edu	37	21	37603002	37603002	+	Missense_Mutation	SNP	G	G	T			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr21:37603002G>T	ENST00000399151.3	+	14	2005	c.1920G>T	c.(1918-1920)aaG>aaT	p.K640N		NM_005128.2	NP_005119.2	Q9Y3R5	DOP2_HUMAN	dopey family member 2			58					TTGCCAGCAAGAACATTTTTG	0.547000																								0							SO:0001583	missense			ENST00000399151.3	1	1	hg19	CCDS13643.1	.	.	.	.	.	.	.	.	.	.	G	15.93	2.977714	0.53720	.	.	ENSG00000142197	ENST00000399151	T	0.14144	2.53	5.43	4.55	0.56014	.	0.403370	0.29676	N	0.011497	T	0.24509	0.0594	M	0.63843	1.955	0.37959	D	0.932892	D;D	0.67145	0.996;0.992	D;P	0.65573	0.936;0.864	T	0.30679	-0.9970	10	0.09338	T	0.73	.	6.928	0.24426	0.296:0.0:0.704:0.0	.	640;640	Q9Y3R5-2;Q9Y3R5	.;DOP2_HUMAN	N	640	ENSP00000382104:K640N	ENSP00000382104:K640N	K	+	3	2	DOPEY2	36524872	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	2.513000	0.45494	1.436000	0.47453	0.491000	0.48974	AAG		TCGA-YH-A8SY-01A-11D-A377-08	DOPEY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194636.1	1	0	1	60	270	0	80	1	4.467231e-01	4	4	0	80	2		0	0	0	0	0	2	1	1.000000	59	267	0	78	2		0	0	0	0	80	2	-20.000000	1	1	0	0		1	2	2	4	2.110881	1	0.220000	3.360000	0.359501	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	0.990000	1.000000
AFF3	3899	broad.mit.edu	37	2	100210257	100210257	+	Silent	SNP	C	C	T			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr2:100210257C>T	ENST00000409236.2	-	13	1978	c.1866G>A	c.(1864-1866)ccG>ccA	p.P622P	AFF3_ENST00000356421.2_Silent_p.P647P|AFF3_ENST00000409579.1_Silent_p.P647P|AFF3_ENST00000317233.4_Silent_p.P622P			P51826	AFF3_HUMAN	AF4/FMR2 family, member 3			86					TGGTGGGCTCCGGGGGGACCA	0.736000																								0							SO:0001819	synonymous_variant			ENST00000409236.2	1	1	hg19	CCDS42723.1																																																																																				TCGA-YH-A8SY-01A-11D-A377-08	AFF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328982.3	1	0	0	9	167	0	31		0	0	0	0	31	2		0	0	0	0	0	2	1	0.994146	9	164	0	31	2		0	0	0	0	31	2	-2.939472	1	1	121154	1	20	1	2	2	4	2.140913	1	0.220000	3.360000	0.360656	0.590000	0.290000	1.000000	1.000000	0.613214	0.590000	0	0.420000	0.800000
STEAP3	55240	broad.mit.edu	37	2	120005557	120005557	+	Silent	SNP	G	G	A			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr2:120005557G>A	ENST00000354888.5	+	4	1299	c.795G>A	c.(793-795)gtG>gtA	p.V265V	STEAP3_ENST00000409811.1_Silent_p.V265V|STEAP3_ENST00000393106.2_Silent_p.V265V|STEAP3_ENST00000393107.2_Silent_p.V265V|STEAP3_ENST00000425223.2_Silent_p.V265V|STEAP3-AS1_ENST00000454260.1_RNA|STEAP3_ENST00000450943.2_Silent_p.V265V|STEAP3_ENST00000393110.2_Silent_p.V275V|STEAP3_ENST00000393108.2_Silent_p.V265V	NM_182915.2	NP_878919.2	Q658P3	STEA3_HUMAN	STEAP family member 3, metalloreductase			17					TGGCCTACGTGCTGCTGTCAC	0.647000																								0							SO:0001819	synonymous_variant			ENST00000354888.5	0	1	hg19	CCDS2125.1																																																																																				TCGA-YH-A8SY-01A-11D-A377-08	STEAP3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254193.1	0	0	0	8	385	0	59	0	6.593735e-02	1	17	0	59	2		0	0	0	0	0	2	1	0.988857	7	380	0	59	2		0	0	0	0	59	2	-7.693234	1	1	0	0		1	2	2	4	2.138506	1	0.220000	3.360000	0.360656	0.230000	0.100000	0.420000	0.240000	0.251572	0.230000	0	0.160000	0.330000
PXDN	7837	broad.mit.edu	37	2	1643096	1643096	+	Missense_Mutation	SNP	T	T	A			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08			T	A	T	T		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr2:1643096T>A	ENST00000252804.4	-	20	4101	c.4051A>T	c.(4051-4053)Aca>Tca	p.T1351S		NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)			112	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)			CGTGGTCTTGTTTTCTTGGTC	0.562000																								0							SO:0001583	missense			ENST00000252804.4	0	1	hg19	CCDS46221.1	.	.	.	.	.	.	.	.	.	.	T	6.749	0.507109	0.12883	.	.	ENSG00000130508	ENST00000252804	T	0.59772	0.24	5.49	-5.44	0.02624	.	2.195000	0.01825	N	0.034285	T	0.28764	0.0713	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48636	-0.9018	10	0.02654	T	1	-4.7808	10.6794	0.45804	0.1126:0.5895:0.0:0.2979	.	1351	Q92626	PXDN_HUMAN	S	1351	ENSP00000252804:T1351S	ENSP00000252804:T1351S	T	-	1	0	PXDN	1622103	0.000000	0.05858	0.000000	0.03702	0.414000	0.31173	-1.513000	0.02256	-1.322000	0.02278	0.383000	0.25322	ACA		TCGA-YH-A8SY-01A-11D-A377-08	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	0	0	0	6	124	0	35	0	9.977962e-01	0	266	0	35	2		0	0	0	0	0	2	1	0.963555	5	122	0	34	2		0	0	0	0	35	2	-4.220467	1	1	0	0		1	0	2	2	1.757869	1	0.220000	3.360000	0.220000	0.440000	0.180000	0.820000	0.410000	0.468508	0.440000	0	0.290000	0.630000
DPYSL5	56896	broad.mit.edu	37	2	27150261	27150261	+	Silent	SNP	C	C	T			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr2:27150261C>T	ENST00000288699.6	+	4	719	c.561C>T	c.(559-561)atC>atT	p.I187I	DPYSL5_ENST00000401478.1_Silent_p.I187I	NM_001253724.1|NM_020134.3	NP_001240653.1|NP_064519.2	Q9BPU6	DPYL5_HUMAN	dihydropyrimidinase-like 5			27	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				TTGGGGCAATCGCCCGCGTCC	0.527000																								0							SO:0001819	synonymous_variant			ENST00000288699.6	1	1	hg19	CCDS1730.1																																																																																				TCGA-YH-A8SY-01A-11D-A377-08	DPYSL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214187.2	1	0	1	53	163	0	42		0	0	0	0	42	2		0	0	0	0	0	2	1	1.000000	53	162	0	41	2		0	0	0	0	42	2	-4.656197	1	1	121412	1	32	1	0	2	2	1.757869	1	0.220000	3.360000	0.220000	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	0.990000	1.000000
TLX2	3196	broad.mit.edu	37	2	74742813	74742813	+	Missense_Mutation	SNP	C	C	T			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr2:74742813C>T	ENST00000233638.7	+	2	777	c.454C>T	c.(454-456)Cgg>Tgg	p.R152W		NM_016170.4	NP_057254.1	O43763	TLX2_HUMAN	T-cell leukemia homeobox 2			2					CTACCAAAACCGGACCCCTCC	0.657000													Esophageal Squamous(7;240 533 18610 24312)											0							SO:0001583	missense			ENST00000233638.7	1	1	hg19	CCDS1947.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.191186	0.78902	.	.	ENSG00000115297	ENST00000233638	D	0.95756	-3.8	4.29	3.41	0.39046	Homeodomain-related (1);Homeodomain-like (1);	0.000000	0.47093	D	0.000253	D	0.97204	0.9086	M	0.80982	2.52	0.54753	D	0.999983	D	0.89917	1.0	D	0.76575	0.988	D	0.97145	0.9827	10	0.87932	D	0	.	11.3327	0.49485	0.1828:0.8172:0.0:0.0	.	152	O43763	TLX2_HUMAN	W	152	ENSP00000233638:R152W	ENSP00000233638:R152W	R	+	1	2	TLX2	74596321	1.000000	0.71417	1.000000	0.80357	0.871000	0.50021	4.778000	0.62368	1.015000	0.39444	-0.152000	0.13540	CGG		TCGA-YH-A8SY-01A-11D-A377-08	TLX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252224.3	1	0	1	55	303	0	38		0	0	0	0	38	2		0	0	0	0	0	2	1	1.000000	54	300	0	37	2		0	0	0	0	38	2	-20.000000	1	1	121408	1	29	1	2	2	4	2.134063	1	0.220000	3.360000	0.360656	0.990000	0.990000	1.000000	1.000000	0.999998	0.990000	1	0.990000	1.000000
UPK1B	7348	broad.mit.edu	37	3	118913171	118913171	+	Missense_Mutation	SNP	G	G	T			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08			G	T	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr3:118913171G>T	ENST00000264234.3	+	6	723	c.574G>T	c.(574-576)Gtt>Ttt	p.V192F	UPK1B_ENST00000497685.1_Missense_Mutation_p.V112F|UPK1B_ENST00000460625.1_Missense_Mutation_p.V184F	NM_006952.3	NP_008883.2	O75841	UPK1B_HUMAN	uroplakin 1B			14					TCAATGCTGTGTTATGAACAA	0.463000																								0							SO:0001583	missense			ENST00000264234.3	1	1	hg19	CCDS2985.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.391863	0.83011	.	.	ENSG00000114638	ENST00000497685;ENST00000264234;ENST00000460625	D;D;D	0.87179	-2.22;-2.22;-2.22	5.92	5.04	0.67666	Tetraspanin, EC2 domain (1);	0.270923	0.31847	N	0.006975	D	0.87676	0.6237	L	0.43152	1.355	0.41114	D	0.985767	P;P	0.50369	0.934;0.846	P;P	0.53593	0.73;0.452	D	0.86504	0.1805	10	0.39692	T	0.17	-20.5718	14.2934	0.66295	0.0733:0.0:0.9267:0.0	.	184;192	C9J9M7;O75841	.;UPK1B_HUMAN	F	112;192;184	ENSP00000418972:V112F;ENSP00000264234:V192F;ENSP00000418116:V184F	ENSP00000264234:V192F	V	+	1	0	UPK1B	120395861	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	4.124000	0.57924	2.809000	0.96659	0.467000	0.42956	GTT		TCGA-YH-A8SY-01A-11D-A377-08	UPK1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354883.2	1	0	1	71	367	0	76	1	1	222	153	0	76	2		0	0	0	0	0	2	1	1.000000	71	363	0	74	2		0	0	0	0	76	2	-20.000000	1	1	0	0		1	2	2	4	2.127073	1	0.220000	3.360000	0.360656	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	0.990000	1.000000
CLSTN2	64084	broad.mit.edu	37	3	140277663	140277663	+	Missense_Mutation	SNP	G	G	A	rs137889465		TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr3:140277663G>A	ENST00000458420.3	+	12	2195	c.2005G>A	c.(2005-2007)Gcc>Acc	p.A669T		NM_022131.2	NP_071414.2	Q9H4D0	CSTN2_HUMAN	calsyntenin 2	p.A669T(1)		87					GAGCACCTTCGCCAAAACCGA	0.532000										HNSCC(16;0.037)			GBM(45;858 913 3709 36904 37282)											1	Substitution - Missense(1)						SO:0001583	missense			ENST00000458420.3	1	1	hg19	CCDS3112.1	.	.	.	.	.	.	.	.	.	.	G	0.030	-1.341445	0.01277	4.54E-4	0.0	ENSG00000158258	ENST00000458420	T	0.29397	1.57	5.41	2.5	0.30297	.	0.215482	0.46442	N	0.000281	T	0.08802	0.0218	N	0.01219	-0.95	0.23376	N	0.9978	B	0.09022	0.002	B	0.04013	0.001	T	0.33163	-0.9879	9	.	.	.	-0.0386	6.6275	0.22839	0.3845:0.0:0.6155:0.0	.	669	Q9H4D0	CSTN2_HUMAN	T	669	ENSP00000402460:A669T	.	A	+	1	0	CLSTN2	141760353	0.921000	0.31238	0.031000	0.17742	0.075000	0.17131	2.120000	0.41968	0.587000	0.29643	0.650000	0.86243	GCC		TCGA-YH-A8SY-01A-11D-A377-08	CLSTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359393.3	1	0	1	43	193	0	48	0	1.593831e-01	0	4	0	48	2		0	0	0	0	0	2	1	1.000000	42	192	0	48	2		0	0	0	0	48	2	-3.152367	1	1	121412	3	36	1	2	2	4	2.127073	1	0.220000	3.360000	0.360656	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	0.990000	1.000000
ATP11B	23200	broad.mit.edu	37	3	182591715	182591715	+	Missense_Mutation	SNP	C	C	T			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr3:182591715C>T	ENST00000323116.5	+	19	2424	c.2164C>T	c.(2164-2166)Cat>Tat	p.H722Y		NM_014616.2	NP_055431.1	Q9Y2G3	AT11B_HUMAN	ATPase, class VI, type 11B			41	all_cancers(143;9.04e-15)|Ovarian(172;0.0355)		all cancers(12;1.2e-42)|Epithelial(37;2.77e-36)|LUSC - Lung squamous cell carcinoma(7;7.58e-24)|Lung(8;4.66e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.35e-20)		ATCATGTGGCCATTTTCATAG	0.398000																								0							SO:0001583	missense			ENST00000323116.5	1	1	hg19	CCDS33896.1	.	.	.	.	.	.	.	.	.	.	C	28.0	4.883120	0.91740	.	.	ENSG00000058063	ENST00000323116	T	0.62639	0.01	5.78	5.78	0.91487	HAD-like domain (2);	0.000000	0.85682	D	0.000000	D	0.84124	0.5403	M	0.89904	3.07	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.85130	0.997;0.985	D	0.86566	0.1844	10	0.87932	D	0	.	19.9991	0.97403	0.0:1.0:0.0:0.0	.	296;722	B3KSJ2;Q9Y2G3	.;AT11B_HUMAN	Y	722	ENSP00000321195:H722Y	ENSP00000321195:H722Y	H	+	1	0	ATP11B	184074409	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.440000	0.80464	2.724000	0.93272	0.655000	0.94253	CAT		TCGA-YH-A8SY-01A-11D-A377-08	ATP11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350598.1	1	0	1	54	283	0	72	1	9.412088e-01	4	23	0	72	2		0	0	0	0	0	2	1	1.000000	51	281	0	72	2		0	0	0	0	72	2	-20.000000	1	1	0	0		1	2	2	4	2.127073	1	0.220000	3.360000	0.360656	0.990000	0.990000	1.000000	1.000000	0.999999	0.990000	1	0.990000	1.000000
SLC4A7	9497	broad.mit.edu	37	3	27431523	27431523	+	Missense_Mutation	SNP	G	G	A			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr3:27431523G>A	ENST00000295736.5	-	22	3302	c.3232C>T	c.(3232-3234)Ccg>Tcg	p.P1078S	SLC4A7_ENST00000425128.2_3'UTR|SLC4A7_ENST00000428386.1_Missense_Mutation_p.P954S|SLC4A7_ENST00000437179.1_Missense_Mutation_p.P959S|SLC4A7_ENST00000445684.1_Missense_Mutation_p.P1074S|SLC4A7_ENST00000435667.2_Missense_Mutation_p.P963S|SLC4A7_ENST00000454389.1_Missense_Mutation_p.P1087S|SLC4A7_ENST00000440156.1_Missense_Mutation_p.P1074S|SLC4A7_ENST00000455077.1_Missense_Mutation_p.P959S|SLC4A7_ENST00000446700.1_Missense_Mutation_p.P1070S|SLC4A7_ENST00000388777.4_Missense_Mutation_p.P628S	NM_003615.4	NP_003606.3	Q9Y6M7	S4A7_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 7			38				Sodium bicarbonate(DB01390)	TTCCAGAGCGGCACATAACGG	0.373000																								0							SO:0001583	missense			ENST00000295736.5	0	1	hg19	CCDS33721.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.790461	0.90367	.	.	ENSG00000033867	ENST00000419036;ENST00000295736;ENST00000428386;ENST00000454389;ENST00000440156;ENST00000437179;ENST00000446700;ENST00000455077;ENST00000445684;ENST00000435667;ENST00000388777;ENST00000428179	T;T;T;T;T;T;T;T;T;T;T;T	0.78816	-1.21;-1.21;-1.21;-1.21;-1.21;-1.21;-1.21;-1.21;-1.21;-1.21;-1.21;-1.21	5.31	5.31	0.75309	Bicarbonate transporter, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.87892	0.6292	M	0.72624	2.21	0.80722	D	1	D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;0.998;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;0.982;1.0;1.0;1.0	D	0.88424	0.3030	10	0.59425	D	0.04	.	18.9786	0.92747	0.0:0.0:1.0:0.0	.	1074;959;1070;1074;1087;628;954;1078;959	E9PFN4;B5M452;E9PGC1;B5M453;E9PDL9;F8W7E6;Q9Y6M7-2;Q9Y6M7;B2CI53	.;.;.;.;.;.;.;S4A7_HUMAN;.	S	629;1078;954;1087;1074;959;1070;959;1074;963;628;974	ENSP00000411031:P629S;ENSP00000295736:P1078S;ENSP00000416368:P954S;ENSP00000390394:P1087S;ENSP00000414797:P1074S;ENSP00000394252:P959S;ENSP00000406605:P1070S;ENSP00000407382:P959S;ENSP00000406804:P1074S;ENSP00000395336:P963S;ENSP00000373429:P628S;ENSP00000388703:P974S	ENSP00000295736:P1078S	P	-	1	0	SLC4A7	27406527	1.000000	0.71417	0.995000	0.50966	0.770000	0.43624	9.869000	0.99810	2.479000	0.83701	0.650000	0.86243	CCG		TCGA-YH-A8SY-01A-11D-A377-08	SLC4A7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341230.2	0	0	0	6	654	0	125	0	7.517827e-04	0	4	0	125	2		0	0	0	0	0	2	1	0.964087	6	648	0	124	2		0	0	0	0	125	2	-1.875789	0	1	0	0		1	0	2	2	1.759364	1	0.220000	3.360000	0.220000	0.080000	0.030000	0.170000	0.080000	0.095599	0.080000	0	0.050000	0.130000
FBXL2	25827	broad.mit.edu	37	3	33400492	33400492	+	Silent	SNP	C	C	T			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr3:33400492C>T	ENST00000484457.1	+	3	190	c.99C>T	c.(97-99)tgC>tgT	p.C33C	FBXL2_ENST00000507198.1_Silent_p.C33C|FBXL2_ENST00000538892.1_Silent_p.C33C|FBXL2_ENST00000542085.1_5'UTR|FBXL2_ENST00000538181.1_Intron|FBXL2_ENST00000446237.3_5'UTR|FBXL2_ENST00000283627.6_Intron	NM_012157.3	NP_036289.3			F-box and leucine-rich repeat protein 2	p.C33C(2)		15					TAACTTTGTGCCGATGTGCAC	0.289000																								2	Substitution - coding silent(2)						SO:0001819	synonymous_variant			ENST00000484457.1	0	1	hg19	CCDS2658.1																																																																																				TCGA-YH-A8SY-01A-11D-A377-08	FBXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253245.2	0	0	0	5	372	0	57	0	7.471398e-03	0	8	0	57	2		0	0	0	0	0	2	1	0.936624	5	370	0	57	2		0	0	0	0	57	2	-2.572614	1	1	121374	9	19	1	0	2	2	1.759364	1	0.220000	3.360000	0.220000	0.120000	0.040000	0.260000	0.120000	0.142553	0.120000	0	0.080000	0.200000
CACNA1D	776	broad.mit.edu	37	3	53810001	53810001	+	Nonsense_Mutation	SNP	G	G	T			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr3:53810001G>T	ENST00000350061.5	+	35	4802	c.4291G>T	c.(4291-4293)Gag>Tag	p.E1431*	CACNA1D_ENST00000288139.4_Nonsense_Mutation_p.E1451*|CACNA1D_ENST00000540742.1_Nonsense_Mutation_p.E323*|CACNA1D_ENST00000422281.2_Nonsense_Mutation_p.E1416*	NM_001128840.1	NP_001122312.1	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type, alpha 1D subunit			90				Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	CAACCCCGGGGAGGAGTATAC	0.507000																								0							SO:0001587	stop_gained			ENST00000350061.5	0	1	hg19	CCDS46848.1	.	.	.	.	.	.	.	.	.	.	G	45	11.508490	0.99570	.	.	ENSG00000157388	ENST00000350061;ENST00000288139;ENST00000422281;ENST00000481478;ENST00000540742	.	.	.	5.06	5.06	0.68205	.	0.136428	0.46758	D	0.000261	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.48119	T	0.1	.	18.6072	0.91271	0.0:0.0:1.0:0.0	.	.	.	.	X	1431;1451;1416;1124;323	.	ENSP00000288139:E1451X	E	+	1	0	CACNA1D	53785041	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	9.657000	0.98554	2.624000	0.88883	0.650000	0.86243	GAG		TCGA-YH-A8SY-01A-11D-A377-08	CACNA1D-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350557.1	0	0	0	23	559	0	123		0	0	0	0	123	2		0	0	0	0	0	2	1	0.999999	22	550	0	123	2		0	0	0	0	123	2	-3.442191	1	1	0	0		1	0	2	2	1.759364	1	0.220000	3.360000	0.220000	0.360000	0.230000	0.520000	0.360000	0.371314	0.360000	0	0.290000	0.440000
WNT5A	7474	broad.mit.edu	37	3	55504434	55504434	+	Missense_Mutation	SNP	G	G	A			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr3:55504434G>A	ENST00000474267.1	-	6	1350	c.829C>T	c.(829-831)Cgg>Tgg	p.R277W	WNT5A_ENST00000264634.4_Missense_Mutation_p.R277W|WNT5A_ENST00000497027.1_Missense_Mutation_p.R262W|WNT5A_ENST00000493406.1_5'Flank			P41221	WNT5A_HUMAN	wingless-type MMTV integration site family, member 5A			13					CTGTTGAGCCGCATGGCCGCC	0.612000																								0							SO:0001583	missense			ENST00000474267.1	0	1	hg19	CCDS46850.1	.	.	.	.	.	.	.	.	.	.	G	19.24	3.789736	0.70337	.	.	ENSG00000114251	ENST00000474267;ENST00000264634;ENST00000536765;ENST00000497027	T;T;T	0.76709	-1.04;-1.04;-1.04	5.82	2.59	0.31030	.	0.138509	0.49916	D	0.000133	D	0.89121	0.6625	M	0.90542	3.125	0.49915	D	0.999835	D	0.65815	0.995	D	0.76575	0.988	D	0.90846	0.4727	10	0.87932	D	0	.	13.8804	0.63678	0.0:0.0:0.465:0.535	.	277	P41221	WNT5A_HUMAN	W	277;277;188;262	ENSP00000417310:R277W;ENSP00000264634:R277W;ENSP00000420104:R262W	ENSP00000264634:R277W	R	-	1	2	WNT5A	55479474	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.813000	0.38962	0.716000	0.32124	0.655000	0.94253	CGG		TCGA-YH-A8SY-01A-11D-A377-08	WNT5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350793.3	0	0	0	4	113	0	28	0	5.085514e-01	0	43	0	28	2		0	0	0	0	0	2	1	0.889632	4	112	0	25	2		0	0	0	0	28	2	-6.472079	1	1	0	0		1	0	2	2	1.759364	1	0.220000	3.360000	0.220000	0.340000	0.110000	0.710000	0.300000	0.370328	0.340000	0	0.200000	0.520000
TIGD4	201798	broad.mit.edu	37	4	153691293	153691293	+	Silent	SNP	C	C	T			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr4:153691293C>T	ENST00000304337.2	-	2	1684	c.864G>A	c.(862-864)gaG>gaA	p.E288E		NM_145720.3	NP_663772.1	Q8IY51	TIGD4_HUMAN	tigger transposable element derived 4			26	all_hematologic(180;0.093)				CTGGAAAAGACTCAACAAAAA	0.398000																								0							SO:0001819	synonymous_variant			ENST00000304337.2	1	1	hg19	CCDS34079.1																																																																																				TCGA-YH-A8SY-01A-11D-A377-08	TIGD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365028.1	1	0	0	92	472	0	128		0	0	0	0	128	2		0	0	0	0	0	2	1	1.000000	91	466	0	125	2		0	0	0	0	128	2	-20.000000	1	1	0	0		1	2	2	4	2.089236	0	0.220000	3.360000	0.352482	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	0.990000	1.000000
EPHA5	2044	broad.mit.edu	37	4	66230893	66230893	+	Missense_Mutation	SNP	C	C	T			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr4:66230893C>T	ENST00000273854.3	-	12	2678	c.2078G>A	c.(2077-2079)cGt>cAt	p.R693H	EPHA5_ENST00000511294.1_Missense_Mutation_p.R694H|EPHA5_ENST00000354839.4_Missense_Mutation_p.R671H|EPHA5_ENST00000432638.2_Missense_Mutation_p.R530H	NM_001281765.1|NM_004439.5	NP_001268694.1|NP_004430.4	P54756	EPHA5_HUMAN	EPH receptor A5	p.R693H(2)		142					TAGTTTCAAACGTCCACTACA	0.358000										TSP Lung(17;0.13)														2	Substitution - Missense(2)						SO:0001583	missense			ENST00000273854.3	1	1	hg19	CCDS3513.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.722513	0.89298	.	.	ENSG00000145242	ENST00000273854;ENST00000432638;ENST00000354839;ENST00000511294	T;T;T;T	0.63744	-0.06;-0.06;-0.06;-0.06	5.97	5.97	0.96955	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000017	T	0.71609	0.3360	L	0.35341	1.055	0.53688	D	0.999971	D;B;D;D	0.89917	0.996;0.033;0.995;1.0	D;B;P;D	0.66497	0.942;0.047;0.903;0.944	T	0.70364	-0.4892	10	0.49607	T	0.09	.	20.4238	0.99064	0.0:1.0:0.0:0.0	.	672;694;671;693	B7ZKW7;B7ZKJ3;P54756-2;P54756	.;.;.;EPHA5_HUMAN	H	693;530;671;694	ENSP00000273854:R693H;ENSP00000389208:R530H;ENSP00000346899:R671H;ENSP00000427638:R694H	ENSP00000273854:R693H	R	-	2	0	EPHA5	65913488	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.308000	0.51896	2.834000	0.97654	0.650000	0.86243	CGT		TCGA-YH-A8SY-01A-11D-A377-08	EPHA5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251388.2	1	0	1	57	347	0	88		0	0	0	0	88	2		0	0	0	0	0	2	1	1.000000	56	345	0	86	2		0	0	0	0	88	2	-19.999990	1	1	121406	2	36	1	2	2	4	2.089236	0	0.220000	3.360000	0.352482	0.990000	0.990000	1.000000	1.000000	0.999981	0.990000	1	0.990000	1.000000
THAP9	79725	broad.mit.edu	37	4	83827666	83827666	+	Missense_Mutation	SNP	G	G	A			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr4:83827666G>A	ENST00000302236.5	+	3	517	c.466G>A	c.(466-468)Gta>Ata	p.V156I		NM_024672.4	NP_078948.3	Q9H5L6	THAP9_HUMAN	THAP domain containing 9			33		Hepatocellular(203;0.114)			ACTTATCTCCGTAAAGAACTA	0.388000																								0							SO:0001583	missense			ENST00000302236.5	0	1	hg19	CCDS3598.1	.	.	.	.	.	.	.	.	.	.	G	7.115	0.576724	0.13686	.	.	ENSG00000168152	ENST00000302236;ENST00000536314	T	0.35605	1.3	3.87	2.05	0.26809	.	1.248910	0.05868	N	0.624116	T	0.18841	0.0452	N	0.08118	0	0.09310	N	1	B	0.23806	0.091	B	0.17433	0.018	T	0.24584	-1.0156	10	0.21540	T	0.41	-1.8827	6.5895	0.22639	0.0:0.2004:0.5924:0.2072	.	156	Q9H5L6	THAP9_HUMAN	I	156	ENSP00000305533:V156I	ENSP00000305533:V156I	V	+	1	0	THAP9	84046690	0.002000	0.14202	0.015000	0.15790	0.903000	0.53119	0.939000	0.28978	0.556000	0.29098	0.591000	0.81541	GTA		TCGA-YH-A8SY-01A-11D-A377-08	THAP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252633.1	0	0	0	6	564	0	131	0	1.708588e-04	0	2	0	131	2		0	0	0	0	0	2	1	0.964163	6	559	0	131	2		0	0	0	0	131	2	-2.456386	0	1	121410	1	39	1	2	2	4	2.089236	0	0.220000	3.360000	0.352482	0.120000	0.040000	1.000000	0.120000	0.181925	0.120000	0	0.070000	0.200000
PCDHB3	56132	broad.mit.edu	37	5	140481563	140481563	+	Missense_Mutation	SNP	G	G	A			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr5:140481563G>A	ENST00000231130.2	+	1	1330	c.1330G>A	c.(1330-1332)Gtc>Atc	p.V444I	AC005754.7_ENST00000607216.1_RNA	NM_018937.2	NP_061760.1	Q9Y5E6	PCDB3_HUMAN	protocadherin beta 3			72			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)		GGTCTCCGACGTCAATGACAA	0.562000																								0							SO:0001583	missense			ENST00000231130.2	1	1	hg19	CCDS4245.1	.	.	.	.	.	.	.	.	.	.	G	8.241	0.806788	0.16467	.	.	ENSG00000113205	ENST00000231130	T	0.01258	5.09	4.39	1.49	0.22878	Cadherin (3);Cadherin conserved site (1);Cadherin-like (1);	.	.	.	.	T	0.01061	0.0035	N	0.21324	0.655	0.26614	N	0.972776	B	0.20459	0.045	B	0.17098	0.017	T	0.45877	-0.9231	9	0.06625	T	0.88	.	7.9304	0.29899	0.1567:0.1339:0.7094:0.0	.	444	Q9Y5E6	PCDB3_HUMAN	I	444	ENSP00000231130:V444I	ENSP00000231130:V444I	V	+	1	0	PCDHB3	140461747	0.948000	0.32251	0.995000	0.50966	0.908000	0.53690	1.507000	0.35758	0.397000	0.25310	0.655000	0.94253	GTC		TCGA-YH-A8SY-01A-11D-A377-08	PCDHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251817.2	1	0	0	34	467	0	112	0	6.094947e-02	0	6	0	112	2		0	0	0	0	0	2	1	1.000000	34	438	0	112	2		0	0	0	0	112	2	-8.119044	1	1	121412	1	37	1	1	2	3	1.953850	0	0.220000	3.360000	0.297297	0.680000	0.480000	0.920000	0.690000	0.698457	0.680000	0	0.570000	0.810000
PCDHGA1	56114	broad.mit.edu	37	5	140712177	140712177	+	Silent	SNP	C	C	T			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr5:140712177C>T	ENST00000517417.1	+	1	1926	c.1926C>T	c.(1924-1926)ctC>ctT	p.L642L	PCDHGA1_ENST00000378105.3_Silent_p.L642L	NM_018912.2	NP_061735.1	Q9Y5H4	PCDG1_HUMAN	protocadherin gamma subfamily A, 1			78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		AGCAGAGTCTCGTGGTGGCCG	0.701000																								0							SO:0001819	synonymous_variant			ENST00000517417.1	1	1	hg19	CCDS54922.1																																																																																				TCGA-YH-A8SY-01A-11D-A377-08	PCDHGA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374737.1	1	0	1	28	282	0	77		0	0	0	0	77	2		0	0	0	0	0	2	1	1.000000	19	256	0	79	2		0	0	0	0	77	2	-3.221884	1	1	0	0		1	1	2	3	1.953850	0	0.220000	3.360000	0.297297	0.910000	0.620000	1.000000	1.000000	0.892797	0.910000	1	0.760000	1.000000
MYOZ3	91977	broad.mit.edu	37	5	150050154	150050154	+	Missense_Mutation	SNP	G	G	A			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr5:150050154G>A	ENST00000297130.4	+	3	369	c.170G>A	c.(169-171)cGc>cAc	p.R57H	CTC-345K18.2_ENST00000511626.2_RNA|MYOZ3_ENST00000517768.1_Missense_Mutation_p.R57H|MYOZ3_ENST00000520112.1_5'Flank	NM_001122853.2|NM_133371.4	NP_001116325.1|NP_588612.2			myozenin 3			5		Medulloblastoma(196;0.134)|all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		AAGAGGCAGCGCCGTGTGCAG	0.582000																								0							SO:0001583	missense			ENST00000297130.4	0	1	hg19	CCDS4309.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.300097	0.81136	0.0	1.16E-4	ENSG00000164591	ENST00000517768;ENST00000297130	T;T	0.66099	-0.19;-0.19	4.89	4.0	0.46444	.	0.165666	0.29185	N	0.012897	T	0.74504	0.3725	M	0.76574	2.34	0.80722	D	1	D	0.89917	1.0	D	0.73380	0.98	T	0.76187	-0.3051	10	0.72032	D	0.01	-8.5437	8.1756	0.31281	0.1697:0.0:0.8303:0.0	.	57	Q8TDC0	MYOZ3_HUMAN	H	57	ENSP00000428815:R57H;ENSP00000297130:R57H	ENSP00000297130:R57H	R	+	2	0	MYOZ3	150030347	0.991000	0.36638	1.000000	0.80357	0.985000	0.73830	1.895000	0.39778	2.416000	0.81992	0.555000	0.69702	CGC		TCGA-YH-A8SY-01A-11D-A377-08	MYOZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252369.1	1	0	1	11	72	0	12		0	0	0	0	12	2		0	0	0	0	0	2	1	0.998420	11	69	0	12	2		0	0	0	0	12	2	-19.033250	1	1	121406	1	28	1	1	2	3	1.949770	0	0.220000	3.360000	0.297297	0.990000	0.740000	1.000000	1.000000	0.979165	0.990000	1	0.990000	1.000000
ZNF622	90441	broad.mit.edu	37	5	16453182	16453182	+	Missense_Mutation	SNP	G	G	A			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr5:16453182G>A	ENST00000308683.2	-	5	1372	c.1246C>T	c.(1246-1248)Cgg>Tgg	p.R416W		NM_033414.2	NP_219482.1	Q969S3	ZN622_HUMAN	zinc finger protein 622			25					ACGGCCTTCCGATTTTTGGCA	0.498000																								0							SO:0001583	missense			ENST00000308683.2	0	1	hg19	CCDS3886.1	.	.	.	.	.	.	.	.	.	.	G	18.99	3.739888	0.69304	.	.	ENSG00000173545	ENST00000308683	.	.	.	5.7	3.8	0.43715	.	0.533295	0.20075	N	0.099768	T	0.41236	0.1150	M	0.63843	1.955	0.24481	N	0.994344	D	0.56968	0.978	B	0.40410	0.328	T	0.44329	-0.9335	9	0.72032	D	0.01	-6.7854	14.3331	0.66572	0.0:0.0:0.5622:0.4378	.	416	Q969S3	ZN622_HUMAN	W	416	.	ENSP00000310042:R416W	R	-	1	2	ZNF622	16506182	1.000000	0.71417	0.795000	0.32087	0.980000	0.70556	2.028000	0.41088	1.336000	0.45506	0.655000	0.94253	CGG		TCGA-YH-A8SY-01A-11D-A377-08	ZNF622-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207105.1	0	0	0	9	510	0	92	0	7.071678e-01	1	137	0	92	2		0	0	0	0	0	2	1	0.993983	9	505	0	91	2		0	0	0	0	92	2	-2.780967	1	1	0	0		1	1	4	5	2.326018	1	0.220000	3.360000	0.413534	0.210000	0.090000	0.380000	0.200000	0.231388	0.210000	0	0.150000	0.300000
KCNMB1	3779	broad.mit.edu	37	5	169812420	169812420	+	Missense_Mutation	SNP	C	C	T			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr5:169812420C>T	ENST00000274629.4	-	2	474	c.32G>A	c.(31-33)cGg>cAg	p.R11Q	KCNMB1_ENST00000521859.1_Missense_Mutation_p.R11Q|KCNIP1_ENST00000377360.4_Intron|KCNIP1_ENST00000518527.1_Intron	NM_004137.3	NP_004128.1	Q16558	KCMB1_HUMAN	potassium large conductance calcium-activated channel, subfamily M, beta member 1			11	Renal(175;0.000159)|Lung NSC(126;0.0165)|all_lung(126;0.026)	Medulloblastoma(196;0.0109)|all_neural(177;0.0146)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	Miconazole(DB01110)|Procaine(DB00721)	TGTCTCTCCCCGCTTCTGGGC	0.537000																								0							SO:0001583	missense			ENST00000274629.4	1	1	hg19	CCDS4373.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	20.7	4.030060	0.75504	4.54E-4	0.001047	ENSG00000145936	ENST00000274629;ENST00000521859	T;T	0.09630	2.96;2.96	5.14	5.14	0.70334	.	0.193157	0.46145	D	0.000307	T	0.28665	0.0710	L	0.57536	1.79	0.35602	D	0.807915	D;D	0.89917	1.0;1.0	D;D	0.87578	0.997;0.998	T	0.11991	-1.0565	9	.	.	.	.	14.4764	0.67548	0.0:1.0:0.0:0.0	.	11;11	Q16558-2;Q16558	.;KCMB1_HUMAN	Q	11	ENSP00000274629:R11Q;ENSP00000427940:R11Q	.	R	-	2	0	KCNMB1	169744998	1.000000	0.71417	0.998000	0.56505	0.652000	0.38707	2.535000	0.45685	2.545000	0.85829	0.655000	0.94253	CGG		TCGA-YH-A8SY-01A-11D-A377-08	KCNMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252830.3	1	0	1	67	293	0	61	0	5.817372e-01	0	10	0	61	2		0	0	0	0	0	2	1	1.000000	66	288	0	60	2		0	0	0	0	61	2	-2.525824	1	1	121412	80	50	1	1	2	3	1.949770	0	0.220000	3.360000	0.297297	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	0.990000	1.000000
HK3	3101	broad.mit.edu	37	5	176308805	176308805	+	Missense_Mutation	SNP	G	G	A			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr5:176308805G>A	ENST00000292432.5	-	17	2372	c.2281C>T	c.(2281-2283)Cgc>Tgc	p.R761C		NM_002115.2	NP_002106.2	P52790	HXK3_HUMAN	hexokinase 3 (white cell)			47	all_cancers(89;0.000104)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		AGGATGTGGCGGACGATCTCC	0.562000																								0							SO:0001583	missense			ENST00000292432.5	1	1	hg19	CCDS4407.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	17.39	3.377756	0.61735	.	.	ENSG00000160883	ENST00000292432	D	0.98987	-5.3	4.82	3.95	0.45737	Hexokinase, C-terminal (1);	0.000000	0.53938	D	0.000048	D	0.99597	0.9854	H	0.99090	4.425	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97583	1.0112	10	0.87932	D	0	.	13.13	0.59375	0.0786:0.0:0.9214:0.0	.	761	P52790	HXK3_HUMAN	C	761	ENSP00000292432:R761C	ENSP00000292432:R761C	R	-	1	0	HK3	176241411	1.000000	0.71417	0.996000	0.52242	0.628000	0.37860	2.855000	0.48333	1.389000	0.46526	0.561000	0.74099	CGC		TCGA-YH-A8SY-01A-11D-A377-08	HK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253428.1	1	0	1	46	374	0	79	0	5.054404e-01	0	15	0	79	2		0	0	0	0	0	2	1	1.000000	45	370	0	77	2		0	0	0	0	79	2	-3.142702	1	1	121412	3	36	1	1	2	3	1.949770	0	0.220000	3.360000	0.297297	0.990000	0.820000	1.000000	1.000000	0.981769	0.990000	1	0.950000	1.000000
GFPT2	9945	broad.mit.edu	37	5	179763567	179763567	+	Missense_Mutation	SNP	G	G	C			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08			G	C	G	G		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr5:179763567G>C	ENST00000253778.8	-	3	295	c.126C>G	c.(124-126)atC>atG	p.I42M		NM_005110.2	NP_005101.1	O94808	GFPT2_HUMAN	glutamine-fructose-6-phosphate transaminase 2			34	all_cancers(89;4.97e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	Medulloblastoma(196;0.0392)|all_neural(177;0.0529)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	L-Glutamine(DB00130)	TATTCCCATCGATCGCCACAC	0.473000																								0							SO:0001583	missense			ENST00000253778.8	1	1	hg19	CCDS43411.1	.	.	.	.	.	.	.	.	.	.	G	12.34	1.910022	0.33721	.	.	ENSG00000131459	ENST00000253778	T	0.77489	-1.1	6.17	-5.21	0.02815	Glutamine amidotransferase, type II (1);Glutamine amidotransferase, class-II (1);	0.051024	0.85682	D	0.000000	D	0.83147	0.5191	M	0.79011	2.435	0.40542	D	0.981037	P	0.51449	0.945	P	0.57324	0.818	D	0.83771	0.0220	9	.	.	.	-28.7535	18.0332	0.89291	0.7778:0.0:0.2222:0.0	.	42	O94808	GFPT2_HUMAN	M	42	ENSP00000253778:I42M	.	I	-	3	3	GFPT2	179696173	0.002000	0.14202	0.243000	0.24186	0.061000	0.15899	-1.368000	0.02580	-1.095000	0.03050	-0.150000	0.13652	ATC		TCGA-YH-A8SY-01A-11D-A377-08	GFPT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373444.4	1	0	1	180	758	0	201	0	9.986316e-01	0	43	0	201	2		0	0	0	0	0	2	1	1.000000	179	751	0	200	2		0	0	0	0	201	2	-3.459961	1	1	0	0		1	1	2	3	1.949770	0	0.220000	3.360000	0.297297	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	0.990000	1.000000
HTR1A	3350	broad.mit.edu	37	5	63257304	63257304	+	Silent	SNP	G	G	A			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr5:63257304G>A	ENST00000323865.3	-	1	476	c.243C>T	c.(241-243)acC>acT	p.T81T	RP11-158J3.2_ENST00000502882.1_RNA	NM_000524.3	NP_000515.2	P08908	5HT1A_HUMAN	5-hydroxytryptamine (serotonin) receptor 1A, G protein-coupled			56		Lung NSC(810;3.55e-06)|Prostate(74;0.0352)|Ovarian(174;0.0545)|Breast(144;0.0575)|Colorectal(97;0.234)		Acepromazine(DB01614)|Alprenolol(DB00866)|Alverine(DB01616)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bopindolol(DB08807)|Bromocriptine(DB01200)|Buspirone(DB00490)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Cinitapride(DB08810)|Clozapine(DB00363)|Desipramine(DB01151)|Dopamine(DB00988)|Doxepin(DB01142)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Iloperidone(DB04946)|Imipramine(DB00458)|Ketamine(DB01221)|Lisuride(DB00589)|Loxapine(DB00408)|Lurasidone(DB08815)|Methysergide(DB00247)|Mianserin(DB06148)|Molindone(DB01618)|Naratriptan(DB00952)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Ondansetron(DB00904)|Paliperidone(DB01267)|Penbutolol(DB01359)|Pergolide(DB01186)|Pindolol(DB00960)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Propranolol(DB00571)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Sumatriptan(DB00669)|Thioproperazine(DB01622)|Trazodone(DB00656)|Trimipramine(DB00726)|Vilazodone(DB06684)|Yohimbine(DB01392)|Ziprasidone(DB00246)|Zolmitriptan(DB00315)	CCATGAGGTCGGTGACCGCCA	0.612000																								0							SO:0001819	synonymous_variant			ENST00000323865.3	1	1	hg19	CCDS34168.1																																																																																				TCGA-YH-A8SY-01A-11D-A377-08	HTR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368397.1	1	0	1	26	87	0	34		0	0	0	0	34	2		0	0	0	0	0	2	1	1.000000	26	84	0	33	2		0	0	0	0	34	2	-20.000000	1	1	121408	1	29	1	1	2	3	1.953850	0	0.220000	3.360000	0.297297	0.990000	0.990000	1.000000	1.000000	0.999999	0.990000	1	0.990000	1.000000
RASA1	5921	broad.mit.edu	37	5	86672813	86672813	+	Nonsense_Mutation	SNP	C	C	A			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr5:86672813C>A	ENST00000274376.6	+	17	2864	c.2300C>A	c.(2299-2301)tCg>tAg	p.S767*	RASA1_ENST00000512763.1_Nonsense_Mutation_p.S600*|RASA1_ENST00000456692.2_Nonsense_Mutation_p.S590*|RASA1_ENST00000506290.1_Nonsense_Mutation_p.S601*|CTC-428H11.2_ENST00000607486.1_RNA	NM_002890.2	NP_002881.1	P20936	RASA1_HUMAN	RAS p21 protein activator (GTPase activating protein) 1			48		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)			AAGCTTGAATCGTTGTTGTTA	0.383000																								0							SO:0001587	stop_gained			ENST00000274376.6	0	1	hg19	CCDS34200.1	.	.	.	.	.	.	.	.	.	.	C	39	7.861260	0.98531	.	.	ENSG00000145715	ENST00000274376;ENST00000534133;ENST00000456692;ENST00000512763;ENST00000506290	.	.	.	5.52	5.52	0.82312	.	0.056401	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05525	T	0.97	.	19.8119	0.96549	0.0:1.0:0.0:0.0	.	.	.	.	X	767;800;590;600;601	.	ENSP00000274376:S767X	S	+	2	0	RASA1	86708569	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	6.050000	0.71063	2.756000	0.94617	0.563000	0.77884	TCG		TCGA-YH-A8SY-01A-11D-A377-08	RASA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369729.1	1	0	1	61	360	0	103	1	9.250679e-01	5	23	0	103	2		0	0	0	0	0	2	1	1.000000	61	352	0	102	2		0	0	0	0	103	2	-3.143560	1	1	0	0		1	1	2	3	1.953850	0	0.220000	3.360000	0.297297	0.990000	0.990000	1.000000	1.000000	0.999946	0.990000	1	0.990000	1.000000
COL11A2	1302	broad.mit.edu	37	6	33143391	33143391	+	Missense_Mutation	SNP	G	G	A	rs150877886	byFrequency	TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr6:33143391G>A	ENST00000374708.4	-	28	2336	c.2078C>T	c.(2077-2079)cCg>cTg	p.P693L	COL11A2_ENST00000341947.2_Missense_Mutation_p.P779L|COL11A2_ENST00000374712.1_Missense_Mutation_p.P698L|COL11A2_ENST00000374714.1_Missense_Mutation_p.P753L|COL11A2_ENST00000395197.1_Missense_Mutation_p.P719L|COL11A2_ENST00000361917.1_Missense_Mutation_p.P672L|COL11A2_ENST00000477772.1_Intron|COL11A2_ENST00000374713.1_Missense_Mutation_p.P732L|COL11A2_ENST00000357486.1_Missense_Mutation_p.P758L	NM_080681.2	NP_542412.2	P13942	COBA2_HUMAN	collagen, type XI, alpha 2			68					GTCTCCAGTCGGTCCAGTGCG	0.647000													Melanoma(1;90 116 3946 5341 17093)											0							SO:0001583	missense			ENST00000374708.4	1	0	hg19	CCDS43452.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	14.05	2.418368	0.42918	6.62E-4	0.001846	ENSG00000204248	ENST00000374708;ENST00000341947;ENST00000357486;ENST00000374714;ENST00000374713;ENST00000395197;ENST00000374712;ENST00000361917	D;D;D;D;D;D;D;D	0.93426	-3.22;-3.22;-3.22;-3.22;-3.22;-3.22;-3.22;-3.22	4.3	3.44	0.39384	.	0.067235	0.64402	D	0.000012	D	0.83936	0.5362	L	0.37466	1.105	0.80722	D	1	P;P;P	0.50443	0.87;0.758;0.935	B;B;B	0.43867	0.434;0.307;0.334	T	0.81760	-0.0785	10	0.26408	T	0.33	.	10.4953	0.44775	0.0961:0.0:0.9039:0.0	.	672;693;779	P13942-8;P13942-6;P13942	.;.;COBA2_HUMAN	L	693;779;758;753;732;719;698;672	ENSP00000363840:P693L;ENSP00000339915:P779L;ENSP00000350079:P758L;ENSP00000363846:P753L;ENSP00000363845:P732L;ENSP00000378623:P719L;ENSP00000363844:P698L;ENSP00000355123:P672L	ENSP00000339915:P779L	P	-	2	0	COL11A2	33251369	0.999000	0.42202	0.992000	0.48379	0.889000	0.51656	3.017000	0.49615	1.201000	0.43203	-0.350000	0.07774	CCG		TCGA-YH-A8SY-01A-11D-A377-08	COL11A2-001	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076032.2	1	0	1	50	164	0	25	0	5.657962e-02	0	2	0	25	2		0	0	0	0	0	2	1	1.000000	50	161	0	25	2		0	0	0	0	25	2	-2.441409	0	1	118344	359	58	1	1	2	3	1.971587	0	0.220000	3.360000	0.297297	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	0.990000	1.000000
ACHE	43	broad.mit.edu	37	7	100491685	100491685	+	Missense_Mutation	SNP	C	C	T	rs17234982	byFrequency	TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr7:100491685C>T	ENST00000412389.1	-	1	324	c.169G>A	c.(169-171)Ggg>Agg	p.G57R	ACHE_ENST00000497647.1_5'Flank|ACHE_ENST00000241069.5_Missense_Mutation_p.G57R|ACHE_ENST00000411582.1_Missense_Mutation_p.G57R|ACHE_ENST00000428317.1_Missense_Mutation_p.G57R|ACHE_ENST00000302913.4_Missense_Mutation_p.G57R|ACHE_ENST00000419336.2_Missense_Mutation_p.G57R			P22303	ACES_HUMAN	acetylcholinesterase (Yt blood group)			16	Lung NSC(181;0.041)|all_lung(186;0.0581)			Ambenonium(DB01122)|Choline(DB00122)|Decamethonium(DB01245)|Demecarium(DB00944)|Dipivefrin(DB00449)|Donepezil(DB00843)|Edrophonium(DB01010)|Ephedrine(DB01364)|Galantamine(DB00674)|Gallamine Triethiodide(DB00483)|Isoflurophate(DB00677)|Mefloquine(DB00358)|Minaprine(DB00805)|Neostigmine(DB01400)|Physostigmine(DB00981)|Pralidoxime(DB00733)|Pyridostigmine(DB00545)|Rivastigmine(DB00989)|Tubocurarine(DB01199)	ACAGGGCCCCCGGGGGTCTTC	0.701000																								0							SO:0001583	missense			ENST00000412389.1	1	1	hg19	CCDS5709.1	3	0.0013736263736263737	2	0.0040650406504065045	0	0.0	1	0.0017482517482517483	0	0.0	c	9.302	1.053449	0.19907	0.0	2.33E-4	ENSG00000087085	ENST00000419336;ENST00000241069;ENST00000428317;ENST00000302913;ENST00000412389;ENST00000426415;ENST00000430554;ENST00000411582;ENST00000422451;ENST00000441605	T;T;T;T;T;T;T;T;T	0.67865	1.8;1.8;1.8;1.8;1.8;1.8;1.8;1.8;-0.29	4.85	3.97	0.46021	Carboxylesterase, type B (1);	0.245457	0.40222	N	0.001147	T	0.57902	0.2085	M	0.63169	1.94	0.34490	D	0.704821	B;B;B;B	0.28552	0.02;0.215;0.028;0.002	B;B;B;B	0.17433	0.004;0.018;0.004;0.003	T	0.66400	-0.5933	10	0.66056	D	0.02	.	6.5296	0.22320	0.1779:0.7276:0.0:0.0944	rs17234982	57;57;57;57	B7WPI6;P22303-3;P22303-2;P22303	.;.;.;ACES_HUMAN	R	57	ENSP00000403474:G57R;ENSP00000241069:G57R;ENSP00000414858:G57R;ENSP00000303211:G57R;ENSP00000394976:G57R;ENSP00000397143:G57R;ENSP00000399725:G57R;ENSP00000404865:G57R;ENSP00000396360:G57R	ENSP00000241069:G57R	G	-	1	0	ACHE	100329621	0.005000	0.15991	0.042000	0.18584	0.166000	0.22503	0.103000	0.15292	1.162000	0.42619	0.556000	0.70494	GGG		TCGA-YH-A8SY-01A-11D-A377-08	ACHE-013	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347201.1	1	0	1	19	79	0	22	1	2.606560e-01	2	3	0	22	2		0	0	0	0	0	2	1	0.999994	18	77	0	22	2		0	0	0	0	22	2	-3.080742	1	1	120996	239	48	1	2	2	4	2.136248	1	0.220000	3.360000	0.360656	0.990000	0.990000	1.000000	1.000000	0.999957	0.990000	1	0.990000	1.000000
WEE2	494551	broad.mit.edu	37	7	141418884	141418884	+	Nonsense_Mutation	SNP	C	C	T			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr7:141418884C>T	ENST00000397541.2	+	4	1004	c.598C>T	c.(598-600)Cga>Tga	p.R200*	WEE2-AS1_ENST00000471512.1_RNA|WEE2-AS1_ENST00000465110.1_RNA|WEE2-AS1_ENST00000462383.1_RNA|WEE2-AS1_ENST00000459753.1_RNA|WEE2-AS1_ENST00000484172.1_RNA|WEE2-AS1_ENST00000478332.1_RNA|WEE2-AS1_ENST00000495800.1_RNA|WEE2-AS1_ENST00000488785.1_RNA	NM_001105558.1	NP_001099028.1	P0C1S8	WEE2_HUMAN	WEE1 homolog 2 (S. pombe)			31	Melanoma(164;0.0171)				ATGTGTTTTACGAGAAACCAA	0.343000																								0							SO:0001587	stop_gained			ENST00000397541.2	0	1	hg19	CCDS43660.1	.	.	.	.	.	.	.	.	.	.	C	40	8.074404	0.98640	.	.	ENSG00000214102	ENST00000397541	.	.	.	5.52	4.53E-4	0.14042	.	0.719074	0.11076	U	0.602382	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.8902	0.58068	0.3292:0.5127:0.1582:0.0	.	.	.	.	X	200	.	ENSP00000380675:R200X	R	+	1	2	WEE2	141065353	0.837000	0.29446	0.491000	0.27477	0.937000	0.57800	0.581000	0.23819	0.007000	0.14760	-1.367000	0.01198	CGA		TCGA-YH-A8SY-01A-11D-A377-08	WEE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349091.1	1	0	1	116	529	0	132		0	0	0	0	132	2		0	0	0	0	0	2	1	1.000000	115	524	0	131	2		0	0	0	0	132	2	-20.000000	1	1	120776	3	37	1	2	2	4	2.136248	1	0.220000	3.360000	0.360656	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	0.990000	1.000000
GARS	2617	broad.mit.edu	37	7	30656770	30656770	+	Missense_Mutation	SNP	G	G	A			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr7:30656770G>A	ENST00000389266.3	+	10	1476	c.1235G>A	c.(1234-1236)cGc>cAc	p.R412H		NM_002047.2	NP_002038.2	P41250	SYG_HUMAN	glycyl-tRNA synthetase	p.R412H(1)		24				Glycine(DB00145)	TTCATTGGCCGCATCTACCTC	0.433000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000389266.3	0	1	hg19	CCDS43564.1	.	.	.	.	.	.	.	.	.	.	G	34	5.303525	0.95601	.	.	ENSG00000106105	ENST00000389266	T	0.79247	-1.25	5.22	5.22	0.72569	Aminoacyl-tRNA synthetase, class II (1);Aminoacyl-tRNA synthetase, class II (G/ H/ P/ S), conserved domain (1);	0.000000	0.85682	D	0.000000	D	0.89525	0.6740	M	0.87180	2.865	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91138	0.4943	10	0.87932	D	0	-10.2399	16.6573	0.85232	0.0:0.0:1.0:0.0	.	412	P41250	SYG_HUMAN	H	412	ENSP00000373918:R412H	ENSP00000373918:R412H	R	+	2	0	GARS	30623295	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.827000	0.99397	2.603000	0.88011	0.557000	0.71058	CGC		TCGA-YH-A8SY-01A-11D-A377-08	GARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327735.1	0	0	0	6	568	0	109	0	4.950395e-01	0	143	0	109	2		0	0	0	0	0	2	1	0.964168	5	564	0	108	2		0	0	0	0	109	2	-1.956203	0	1	0	0		1	2	2	4	2.129864	1	0.220000	3.360000	0.360656	0.120000	0.040000	0.240000	0.120000	0.134416	0.120000	0	0.070000	0.180000
COL28A1	340267	broad.mit.edu	37	7	7570984	7570984	+	Missense_Mutation	SNP	G	G	A			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr7:7570984G>A	ENST00000399429.3	-	3	816	c.676C>T	c.(676-678)Cgt>Tgt	p.R226C		NM_001037763.2	NP_001032852.2	Q2UY09	COSA1_HUMAN	collagen, type XXVIII, alpha 1			42		Ovarian(82;0.0789)			CCTACCAGACGATCTTGAATT	0.373000																								0							SO:0001583	missense			ENST00000399429.3	1	1	hg19	CCDS43553.1	.	.	.	.	.	.	.	.	.	.	G	10.03	1.239447	0.22711	.	.	ENSG00000215018	ENST00000399429;ENST00000399419;ENST00000448652	T	0.55760	0.5	3.88	3.88	0.44766	von Willebrand factor, type A (2);	0.303428	0.24176	U	0.040860	T	0.43366	0.1244	N	0.08118	0	0.18873	N	0.999983	D	0.64830	0.994	P	0.54965	0.765	T	0.30592	-0.9973	10	0.59425	D	0.04	-0.8455	10.5423	0.45039	0.0:0.0:0.8065:0.1935	.	226	Q2UY09	COSA1_HUMAN	C	226	ENSP00000382356:R226C	ENSP00000382347:R226C	R	-	1	0	COL28A1	7537509	0.326000	0.24669	0.825000	0.32803	0.038000	0.13279	0.862000	0.27899	2.183000	0.69458	0.655000	0.94253	CGT		TCGA-YH-A8SY-01A-11D-A377-08	COL28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315899.1	1	0	1	41	217	0	56		0	0	0	0	56	2		0	0	0	0	0	2	1	1.000000	41	213	0	56	2		0	0	0	0	56	2	-20.000000	1	1	120684	2	28	1	2	2	4	2.129864	1	0.220000	3.360000	0.360656	0.990000	0.990000	1.000000	1.000000	0.999992	0.990000	1	0.990000	1.000000
SEMA3E	9723	broad.mit.edu	37	7	83029563	83029563	+	Missense_Mutation	SNP	C	C	T			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr7:83029563C>T	ENST00000307792.3	-	11	1614	c.1147G>A	c.(1147-1149)Gcc>Acc	p.A383T	SEMA3E_ENST00000427262.1_Missense_Mutation_p.A323T	NM_012431.2	NP_036563.1	O15041	SEM3E_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E			51		Medulloblastoma(109;0.109)			ACTTTGCTGGCACACTGAAAA	0.373000																								0							SO:0001583	missense			ENST00000307792.3	1	1	hg19	CCDS34674.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.038932	0.75617	.	.	ENSG00000170381	ENST00000307792;ENST00000427262;ENST00000541514	T;T	0.22945	1.93;1.93	5.52	4.62	0.57501	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.85682	D	0.000000	T	0.42899	0.1223	L	0.58354	1.805	0.58432	D	0.999999	P	0.50617	0.937	P	0.56865	0.808	T	0.32693	-0.9897	10	0.49607	T	0.09	.	16.1726	0.81828	0.0:0.8664:0.1336:0.0	.	383	O15041	SEM3E_HUMAN	T	383;323;383	ENSP00000303212:A383T;ENSP00000405052:A323T	ENSP00000303212:A383T	A	-	1	0	SEMA3E	82867499	1.000000	0.71417	1.000000	0.80357	0.767000	0.43475	2.836000	0.48183	1.282000	0.44496	0.585000	0.79938	GCC		TCGA-YH-A8SY-01A-11D-A377-08	SEMA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336606.1	1	0	0	54	300	0	115		0	0	0	0	115	2		0	0	0	0	0	2	1	1.000000	54	298	0	114	2		0	0	0	0	115	2	-20.000000	1	1	0	0		1	2	2	4	2.129864	1	0.220000	3.360000	0.360656	0.990000	0.990000	1.000000	1.000000	0.999997	0.990000	1	0.990000	1.000000
PLEC	5339	broad.mit.edu	37	8	144994097	144994097	+	Missense_Mutation	SNP	G	G	T			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08			G	T	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr8:144994097G>T	ENST00000322810.4	-	32	10472	c.10303C>A	c.(10303-10305)Ctg>Atg	p.L3435M	PLEC_ENST00000436759.2_Missense_Mutation_p.L3325M|PLEC_ENST00000354589.3_Missense_Mutation_p.L3298M|PLEC_ENST00000527096.1_Missense_Mutation_p.L3321M|PLEC_ENST00000357649.2_Missense_Mutation_p.L3302M|PLEC_ENST00000354958.2_Missense_Mutation_p.L3276M|PLEC_ENST00000345136.3_Missense_Mutation_p.L3298M|PLEC_ENST00000356346.3_Missense_Mutation_p.L3284M|PLEC_ENST00000398774.2_Missense_Mutation_p.L3266M	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin			137					TCCTGCCGCAGGGTCTCCACC	0.637000																								0							SO:0001583	missense			ENST00000322810.4	1	1	hg19	CCDS43772.1	.	.	.	.	.	.	.	.	.	.	G	8.254	0.809766	0.16537	.	.	ENSG00000178209	ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096	T;T;T;T;T;T;T;T;T	0.76968	-1.02;-1.02;-1.06;-1.05;-1.04;-1.02;-1.02;-1.02;-1.02	4.81	-4.87	0.03123	.	1.138360	0.06912	U	0.807848	T	0.57636	0.2067	N	0.08118	0	0.09310	N	1	B;B;B;B;B;B;B;B	0.23591	0.088;0.088;0.088;0.053;0.088;0.088;0.088;0.088	B;B;B;B;B;B;B;B	0.29598	0.086;0.104;0.104;0.039;0.104;0.086;0.086;0.086	T	0.52200	-0.8607	10	0.52906	T	0.07	.	8.9149	0.35576	0.0:0.121:0.2943:0.5847	.	3325;3284;3276;3435;3266;3298;3302;3298	Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4	.;.;.;PLEC_HUMAN;.;.;.;.	M	3298;3302;3298;3266;3435;3276;3284;3325;3321	ENSP00000344848:L3298M;ENSP00000350277:L3302M;ENSP00000346602:L3298M;ENSP00000381756:L3266M;ENSP00000323856:L3435M;ENSP00000347044:L3276M;ENSP00000348702:L3284M;ENSP00000388180:L3325M;ENSP00000434583:L3321M	ENSP00000323856:L3435M	L	-	1	2	PLEC	145066085	0.000000	0.05858	0.000000	0.03702	0.944000	0.59088	0.834000	0.27518	-0.457000	0.07033	0.448000	0.29417	CTG		TCGA-YH-A8SY-01A-11D-A377-08	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	1	0	1	78	320	0	64	1	1	98	242	0	64	2		0	0	0	0	0	2	1	1.000000	77	317	0	64	2		0	0	0	0	64	2	-3.394676	1	1	0	0		1	2	2	4	2.169004	1	0.220000	3.360000	0.360656	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	0.990000	1.000000
ZFHX4	79776	broad.mit.edu	37	8	77617904	77617904	+	Silent	SNP	G	G	A			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr8:77617904G>A	ENST00000521891.2	+	2	2029	c.1581G>A	c.(1579-1581)gcG>gcA	p.A527A	ZFHX4_ENST00000518282.1_Silent_p.A527A|ZFHX4_ENST00000517683.1_Intron|ZFHX4_ENST00000050961.6_Silent_p.A527A|ZFHX4_ENST00000455469.2_Silent_p.A527A	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4			432			BRCA - Breast invasive adenocarcinoma(89;0.0895)		CCTCCTCGGCGACTGTTTCTG	0.433000										HNSCC(33;0.089)														0							SO:0001819	synonymous_variant			ENST00000521891.2	1	1	hg19	CCDS47878.2																																																																																				TCGA-YH-A8SY-01A-11D-A377-08	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	1	0	1	27	225	0	45		0	0	0	0	45	2		0	0	0	0	0	2	1	1.000000	27	222	0	45	2		0	0	0	0	45	2	-3.142725	1	1	0	0		1	2	2	4	2.150082	1	0.220000	3.360000	0.360656	0.990000	0.810000	1.000000	1.000000	0.984429	0.990000	1	0.990000	1.000000
PHF19	26147	broad.mit.edu	37	9	123636876	123636876	+	Silent	SNP	G	G	A			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr9:123636876G>A	ENST00000373896.3	-	2	396	c.144C>T	c.(142-144)tgC>tgT	p.C48C	PHF19_ENST00000312189.6_Silent_p.C48C	NM_015651.1	NP_056466.1	Q5T6S3	PHF19_HUMAN	PHD finger protein 19			19					CTGTCCACCGGCACAGCACAT	0.557000																								0							SO:0001819	synonymous_variant			ENST00000373896.3	0	1	hg19	CCDS35116.1																																																																																				TCGA-YH-A8SY-01A-11D-A377-08	PHF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053838.3	0	0	0	5	362	0	79	0	1.768193e-01	0	46	0	79	2		0	0	0	0	0	2	1	0.934742	5	355	0	76	2		0	0	0	0	79	2	-2.550046	1	1	0	0		1	0	2	2	1.772823	1	0.220000	3.360000	0.220000	0.130000	0.040000	0.270000	0.120000	0.146379	0.130000	0	0.080000	0.200000
CD72	971	broad.mit.edu	37	9	35616044	35616044	+	Missense_Mutation	SNP	G	G	A			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chr9:35616044G>A	ENST00000396757.1	-	6	748	c.584C>T	c.(583-585)aCg>aTg	p.T195M	CD72_ENST00000259633.4_Missense_Mutation_p.T195M|CD72_ENST00000490239.1_5'UTR			P21854	CD72_HUMAN	CD72 molecule			12			Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)		GGTCTCCTTCGTCTTCTGTCT	0.577000																								0							SO:0001583	missense			ENST00000396757.1	0	1	hg19	CCDS6581.1	.	.	.	.	.	.	.	.	.	.	G	15.02	2.709706	0.48517	.	.	ENSG00000137101	ENST00000396757;ENST00000396759;ENST00000259633	T;T	0.61627	0.09;0.09	5.14	2.28	0.28536	.	0.467428	0.19886	N	0.103850	T	0.68357	0.2992	M	0.69823	2.125	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.68765	0.96;0.96	T	0.56511	-0.7967	10	0.59425	D	0.04	-5.2731	6.2975	0.21095	0.3715:0.0:0.6285:0.0	.	195;195	Q5TLG3;P21854	.;CD72_HUMAN	M	195	ENSP00000379980:T195M;ENSP00000259633:T195M	ENSP00000259633:T195M	T	-	2	0	CD72	35606044	0.001000	0.12720	0.056000	0.19401	0.029000	0.11900	0.385000	0.20685	0.569000	0.29329	0.491000	0.48974	ACG		TCGA-YH-A8SY-01A-11D-A377-08	CD72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052336.1	0	0	0	5	487	0	96	0	1.662923e-03	0	5	0	96	2		0	0	0	0	0	2	1	0.935803	5	481	0	94	2		0	0	0	0	96	2	-2.799745	1	1	121412	3	40	1	0	2	2	1.772823	1	0.220000	3.360000	0.220000	0.090000	0.030000	0.200000	0.100000	0.109606	0.090000	0	0.060000	0.150000
AMOT	154796	broad.mit.edu	37	X	112048243	112048243	+	Nonsense_Mutation	SNP	G	G	A			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chrX:112048243G>A	ENST00000524145.1	-	6	1782	c.1708C>T	c.(1708-1710)Cga>Tga	p.R570*	AMOT_ENST00000304758.1_Nonsense_Mutation_p.R161*|AMOT_ENST00000371962.1_Nonsense_Mutation_p.R338*|AMOT_ENST00000371959.3_Nonsense_Mutation_p.R570*|AMOT_ENST00000371958.1_Nonsense_Mutation_p.R338*			Q4VCS5	AMOT_HUMAN	angiomotin			43					TCGATGTGTCGTCTTTGGTCC	0.512000																								0							SO:0001587	stop_gained			ENST00000524145.1	0	1	hg19	CCDS48154.1	.	.	.	.	.	.	.	.	.	.	g	39	7.434134	0.98282	.	.	ENSG00000126016	ENST00000304758;ENST00000371959;ENST00000371962;ENST00000524145;ENST00000371958	.	.	.	5.96	4.17	0.49024	.	0.054811	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.5027	12.9983	0.58660	0.0:0.0:0.4395:0.5605	.	.	.	.	X	161;570;338;570;338	.	ENSP00000305557:R161X	R	-	1	2	AMOT	111934899	0.999000	0.42202	0.985000	0.45067	0.996000	0.88848	2.872000	0.48467	0.623000	0.30267	0.597000	0.82753	CGA		TCGA-YH-A8SY-01A-11D-A377-08	AMOT-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378570.1	1	0	0	167	881	0	150	0	1.229260e-01	0	4	0	150	2		0	0	0	0	0	2	1	1.000000	165	870	0	148	2		0	0	0	0	150	2	-20.000000	1	1	0	0		1	0	1	1			0.220000	3.360000	0.220000	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	0.990000	1.000000
NKRF	55922	broad.mit.edu	37	X	118725258	118725258	+	Nonsense_Mutation	SNP	T	T	A			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chrX:118725258T>A	ENST00000371527.1	-	2	782	c.130A>T	c.(130-132)Aaa>Taa	p.K44*	NKRF_ENST00000542113.1_Nonsense_Mutation_p.K59*|NKRF_ENST00000487600.1_5'UTR|NKRF_ENST00000304449.5_Nonsense_Mutation_p.K44*	NM_001173488.1	NP_001166959.1	O15226	NKRF_HUMAN	NFKB repressing factor			30					GCTTGCTTTTTAGGAGGATTT	0.353000																								0							SO:0001587	stop_gained			ENST00000371527.1	0	1	hg19	CCDS35375.1	.	.	.	.	.	.	.	.	.	.	T	38	6.702982	0.97776	.	.	ENSG00000186416	ENST00000371527;ENST00000304449;ENST00000542113	.	.	.	5.41	5.41	0.78517	.	0.288673	0.39020	N	0.001490	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-17.1562	12.1414	0.54000	0.0:0.0:0.0:1.0	.	.	.	.	X	44;44;59	.	ENSP00000304803:K44X	K	-	1	0	NKRF	118609286	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.298000	0.59067	1.800000	0.52685	0.486000	0.48141	AAA		TCGA-YH-A8SY-01A-11D-A377-08	NKRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058044.1	1	0	1	100	497	0	133	0	6.673818e-01	0	13	0	133	2		0	0	0	0	0	2	1	1.000000	98	489	0	129	2		0	0	0	0	133	2	-20.000000	1	1	0	0		1	0	1	1			0.220000	3.360000	0.220000	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	0.990000	1.000000
FRMPD4	9758	broad.mit.edu	37	X	12516909	12516909	+	Missense_Mutation	SNP	T	T	C			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chrX:12516909T>C	ENST00000380682.1	+	2	658	c.152T>C	c.(151-153)tTc>tCc	p.F51S		NM_014728.3	NP_055543.2	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4			22					CGAGACTACTTCATCAAGTAG	0.488000																								0							SO:0001583	missense			ENST00000380682.1	1	1	hg19	CCDS35201.1	.	.	.	.	.	.	.	.	.	.	T	15.94	2.981669	0.53827	.	.	ENSG00000169933	ENST00000380682;ENST00000429478;ENST00000304087	T	0.13657	2.57	5.13	5.13	0.70059	WW/Rsp5/WWP (2);PDZ/DHR/GLGF (1);	0.281292	0.34200	N	0.004165	T	0.25865	0.0630	M	0.89287	3.02	0.42617	D	0.993335	B;B	0.18013	0.025;0.025	B;B	0.18561	0.022;0.022	T	0.10451	-1.0629	10	0.87932	D	0	.	14.3389	0.66611	0.0:0.0:0.0:1.0	.	43;51	B7ZLE1;Q14CM0	.;FRPD4_HUMAN	S	51;42;40	ENSP00000370057:F51S	ENSP00000304583:F40S	F	+	2	0	FRMPD4	12426830	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.718000	0.54919	1.834000	0.53371	0.486000	0.48141	TTC		TCGA-YH-A8SY-01A-11D-A377-08	FRMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055771.1	1	0	1	42	249	0	30		0	0	0	0	30	2		0	0	0	0	0	2	1	1.000000	42	247	0	30	2		0	0	0	0	30	2	-20.000000	1	1	0	0		1	0	1	1			0.220000	3.360000	0.220000	0.990000	0.970000	1.000000	1.000000	0.997869	0.990000	1	0.990000	1.000000
TFDP3	51270	broad.mit.edu	37	X	132351883	132351883	+	Silent	SNP	G	G	A			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chrX:132351883G>A	ENST00000310125.4	-	1	493	c.405C>T	c.(403-405)ggC>ggT	p.G135G		NM_016521.2	NP_057605.3	Q5H9I0	TFDP3_HUMAN	transcription factor Dp family, member 3	p.G135G(1)|p.G75G(1)		19	Acute lymphoblastic leukemia(192;0.000127)				CGACCAGCTCGCCCACCACTT	0.552000																								2	Substitution - coding silent(2)						SO:0001819	synonymous_variant			ENST00000310125.4	1	1	hg19	CCDS14636.2																																																																																				TCGA-YH-A8SY-01A-11D-A377-08	TFDP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058337.1	1	0	1	75	354	0	70		0	0	0	0	70	2		0	0	0	0	0	2	1	1.000000	74	336	0	68	2		0	0	0	0	70	2	-20.000000	1	1	121394	2	36	1	0	1	1			0.220000	3.360000	0.220000	0.990000	0.990000	1.000000	1.000000	0.999999	0.990000	1	0.990000	1.000000
DUSP9	1852	broad.mit.edu	37	X	152915638	152915638	+	Missense_Mutation	SNP	C	C	T			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chrX:152915638C>T	ENST00000342782.3	+	4	1298	c.1033C>T	c.(1033-1035)Cgg>Tgg	p.R345W	DUSP9_ENST00000370167.4_Missense_Mutation_p.R345W			Q99956	DUS9_HUMAN	dual specificity phosphatase 9			16	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)				GCGCAGCTTGCGGCTGGAGGA	0.612000																								0							SO:0001583	missense			ENST00000342782.3	0	1	hg19	CCDS14724.1	.	.	.	.	.	.	.	.	.	.	c	13.51	2.258205	0.39896	.	.	ENSG00000130829	ENST00000370167;ENST00000342782	T;T	0.61274	0.12;0.12	4.53	2.62	0.31277	Dual specificity phosphatase, subgroup, catalytic domain (1);	1.080270	0.07212	N	0.859447	T	0.55705	0.1937	M	0.73319	2.225	0.40260	D	0.978167	D	0.58268	0.982	B	0.41412	0.356	T	0.55192	-0.8179	10	0.66056	D	0.02	.	5.9303	0.19134	0.4195:0.3277:0.2528:0.0	.	345	Q99956	DUS9_HUMAN	W	345	ENSP00000359186:R345W;ENSP00000345853:R345W	ENSP00000345853:R345W	R	+	1	2	DUSP9	152568832	1.000000	0.71417	0.272000	0.24630	0.422000	0.31414	2.428000	0.44749	0.422000	0.26005	-0.263000	0.10527	CGG		TCGA-YH-A8SY-01A-11D-A377-08	DUSP9-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061022.3	0	0	0	7	892	0	136	0	2.373203e-03	0	8	0	136	2		0	0	0	0	0	2	1	0.979502	7	878	0	131	2		0	0	0	0	136	2	-2.041577	0	1	0	0		1	0	1	1			0.220000	3.360000	0.220000	0.070000	0.020000	0.140000	0.070000	0.080391	0.070000	0	0.040000	0.110000
FLNA	2316	broad.mit.edu	37	X	153593084	153593084	+	Missense_Mutation	SNP	A	A	G			TCGA-YH-A8SY-01A-11D-A377-08	TCGA-YH-A8SY-10A-01D-A37A-08			A	G	A	A		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75	20866917-ab2f-4c68-9874-ea8be01bd72b	g.chrX:153593084A>G	ENST00000369850.3	-	13	2068	c.1832T>C	c.(1831-1833)tTc>tCc	p.F611S	FLNA_ENST00000422373.1_Missense_Mutation_p.F611S|FLNA_ENST00000344736.4_Missense_Mutation_p.F611S|FLNA_ENST00000360319.4_Missense_Mutation_p.F611S	NM_001110556.1	NP_001104026.1	P21333	FLNA_HUMAN	filamin A, alpha			6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)				TTCCACCGAGAAGCCTGACAA	0.642000																								0							SO:0001583	missense			ENST00000369850.3	1	1	hg19	CCDS48194.1	.	.	.	.	.	.	.	.	.	.	A	19.04	3.750803	0.69533	.	.	ENSG00000196924	ENST00000360319;ENST00000369852;ENST00000422373;ENST00000369850;ENST00000344736	D;D;D;D	0.91843	-1.86;-1.86;-2.92;-2.92	4.86	4.86	0.63082	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	U	0.000000	D	0.96519	0.8864	M	0.90252	3.1	0.80722	D	1	D;D	0.89917	1.0;0.991	D;D	0.97110	1.0;0.955	D	0.97193	0.9859	10	0.87932	D	0	.	13.6752	0.62449	1.0:0.0:0.0:0.0	.	611;611	P21333-2;P21333	.;FLNA_HUMAN	S	611;584;611;611;611	ENSP00000353467:F611S;ENSP00000416926:F611S;ENSP00000358866:F611S;ENSP00000358863:F611S	ENSP00000358863:F611S	F	-	2	0	FLNA	153246278	1.000000	0.71417	1.000000	0.80357	0.611000	0.37282	9.336000	0.96533	1.602000	0.50124	0.427000	0.28365	TTC		TCGA-YH-A8SY-01A-11D-A377-08	FLNA-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058942.3	1	0	1	65	379	0	100	0	1	0	323	0	100	2		0	0	0	0	0	2	1	1.000000	65	372	0	98	2		0	0	0	0	100	2	-20.000000	1	1	0	0		1	0	1	1			0.220000	3.360000	0.220000	0.990000	0.990000	1.000000	1.000000	0.999610	0.990000	1	0.990000	1.000000
