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
PRC1	9055	broad.mit.edu	37	15	91527307	91527308	+	Frame_Shift_Ins	INS	-	-	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08			-	T	-	-		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr15:91527307_91527308insT	ENST00000361188.5	-	3	1418_1419	c.207_208insA	c.(205-210)atatccfs	p.S70fs	PRC1-AS1_ENST00000554388.1_RNA|PRC1_ENST00000394249.3_Frame_Shift_Ins_p.S70fs|PRC1_ENST00000361919.3_Frame_Shift_Ins_p.S70fs|PRC1_ENST00000442656.2_Intron|PRC1_ENST00000556129.1_5'UTR					protein regulator of cytokinesis 1			25	Lung NSC(78;0.0987)|all_lung(78;0.175)				TGACAGACGGATATGCTTTTGA	0.490000																								0							SO:0001589	frameshift_variant			ENST00000361188.5	0	1	hg19	CCDS45352.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	PRC1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414760.1	1	0	0	397	1227	0	362	0	9.992689e-01	0	35	0	362	2	0	0	0	0	0	0		1	1.000000	404	1221	0	354	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	2	4	6	2.035251	1	0.550000	3.150000	0.667160	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	9.900000e-01	1
BDP1	55814	broad.mit.edu	37	5	70751780	70751798	+	Frame_Shift_Del	DEL	AATCCCCAGCGTGGACGGG	AATCCCCAGCGTGGACGGG	-	rs3748042		TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr5:70751780_70751798delAATCCCCAGCGTGGACGGG	ENST00000358731.4	+	1	339_357	c.76_94delAATCCCCAGCGTGGACGGG	c.(76-96)aatccccagcgtggacgggagfs	p.NPQRGRE26fs	BDP1_ENST00000380675.2_5'UTR	NM_018429.2	NP_060899.2	A6H8Y1	BDP1_HUMAN	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB			72		Lung NSC(167;0.000422)|Prostate(74;0.00815)|Ovarian(174;0.0176)|Breast(144;0.198)			CACAGCTTCCAATCCCCAGCGTGGACGGGAGTCTCCCAG	0.680000																								0							SO:0001589	frameshift_variant			ENST00000358731.4	0	1	hg19	CCDS43328.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	BDP1-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374681.2	1	0	0	14	104	0	32	0	4.498035e-02	0	3	0	32	2	0	0	0	0	0	0		1	0.699014	17	107	1	33	13	0	0	0	0	0	0		-19.996320	1	1	0	0		1	1	2	3	1.889547	1	0.550000	3.150000	0.646296	0.560000	0.320000	0.870000	0.550000	0.575410	0.560000	0	4.300000e-01	7.100000e-01
HIF1AN	55662	broad.mit.edu	37	10	102296374	102296374	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr10:102296374C>A	ENST00000299163.6	+	2	484	c.384C>A	c.(382-384)ttC>ttA	p.F128L	HIF1AN_ENST00000528044.1_3'UTR	NM_017902.2	NP_060372.2	Q9NWT6	HIF1N_HUMAN	hypoxia inducible factor 1, alpha subunit inhibitor			10		Colorectal(252;0.234)			TTCATGAGTTCGTTGAGAAAC	0.418000																								0							SO:0001583	missense			ENST00000299163.6	1	0	hg19	CCDS7498.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.497411	0.85069	.	.	ENSG00000166135	ENST00000533589;ENST00000299163;ENST00000442724	T;T	0.75589	-0.95;-0.95	5.6	-3.81	0.04294	.	3.236230	0.00682	N	0.000698	D	0.83348	0.5235	L	0.57130	1.785	0.58432	D	0.999997	D	0.89917	1.0	D	0.91635	0.999	T	0.72711	-0.4211	10	0.42905	T	0.14	-26.9035	12.1375	0.53979	0.0:0.3619:0.0:0.6381	.	128	Q9NWT6	HIF1N_HUMAN	L	21;128;161	ENSP00000433360:F21L;ENSP00000299163:F128L	ENSP00000299163:F128L	F	+	3	2	HIF1AN	102286364	1.000000	0.71417	0.931000	0.37212	0.916000	0.54674	1.676000	0.37565	-0.977000	0.03537	-1.154000	0.01816	TTC		TCGA-IB-A7LX-01A-12D-A36O-08	HIF1AN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049865.5	1	0	0	13	375	0	98	0	5.557056e-01	0	53	0	98	2		0	0	0	0	0	2	1	0.999477	13	366	0	97	2		0	0	0	0	98	2	-3.023347	1	1	0	0		1	2	2	4	2.372051	1	0.550000	3.150000	0.709677	0.190000	0.090000	0.310000	0.200000	0.202123	0.190000	0	1.400000e-01	2.500000e-01
DHX32	55760	broad.mit.edu	37	10	127569154	127569154	+	Silent	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr10:127569154G>T	ENST00000284690.3	-	1	730	c.240C>A	c.(238-240)atC>atA	p.I80I	DHX32_ENST00000284688.6_Silent_p.I80I	NM_018180.2	NP_060650.2	Q7L7V1	DHX32_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 32			29		all_lung(145;0.00751)|Lung NSC(174;0.0115)|Colorectal(57;0.0846)|all_neural(114;0.0936)			AAACAATCACGATTTGATTTT	0.318000																								0							SO:0001819	synonymous_variant			ENST00000284690.3	1	0	hg19	CCDS7652.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	DHX32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050945.2	1	0	0	13	325	0	84	0	8.589719e-01	0	90	0	84	2		0	0	0	0	0	2	1	0.999502	13	319	0	83	2		0	0	0	0	84	2	-3.805459	1	1	0	0		1	2	2	4	2.357296	1	0.550000	3.150000	0.709677	0.220000	0.110000	0.360000	0.210000	0.231810	0.220000	0	1.600000e-01	2.900000e-01
GPR158	57512	broad.mit.edu	37	10	25701403	25701403	+	Splice_Site	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr10:25701403G>T	ENST00000376351.3	+	4	1694		c.e4+1			NM_020752.2	NP_065803.2	Q5T848	GP158_HUMAN	G protein-coupled receptor 158			119					CAAAGCAAAGGTAAACCCAGG	0.433000																								0							SO:0001630	splice_region_variant			ENST00000376351.3	1	1	hg19	CCDS31166.1	.	.	.	.	.	.	.	.	.	.	G	29.4	4.999869	0.93227	.	.	ENSG00000151025	ENST00000376351	.	.	.	6.16	6.16	0.99307	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.8598	0.99761	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	GPR158	25741409	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.252000	0.95491	2.937000	0.99478	0.650000	0.86243	.		TCGA-IB-A7LX-01A-12D-A36O-08	GPR158-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047248.2	1	0	0	46	312	0	123		0	0	0	0	123	2		0	0	0	0	0	2	1	1.000000	44	299	0	122	2		0	0	0	0	123	2	-20.000000	1	1	0	0		1	1	2	3	1.868416	1	0.550000	3.150000	0.647059	0.590000	0.440000	0.760000	0.600000	0.604385	0.590000	0	5.100000e-01	6.800000e-01
WAC	51322	broad.mit.edu	37	10	28878735	28878735	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr10:28878735G>T	ENST00000354911.4	+	5	613	c.452G>T	c.(451-453)cGa>cTa	p.R151L	WAC_ENST00000347934.4_Missense_Mutation_p.R151L|WAC_ENST00000375664.4_Missense_Mutation_p.R106L|WAC_ENST00000375646.1_Missense_Mutation_p.R106L|WAC_ENST00000428935.1_Missense_Mutation_p.R106L	NM_016628.4	NP_057712.2	Q9BTA9	WAC_HUMAN	WW domain containing adaptor with coiled-coil			32					TACAATTGTCGAACAGAAGTT	0.318000																								0							SO:0001583	missense			ENST00000354911.4	1	0	hg19	CCDS7159.1	.	.	.	.	.	.	.	.	.	.	G	31	5.081695	0.94050	.	.	ENSG00000095787	ENST00000375664;ENST00000375646;ENST00000347934;ENST00000354911;ENST00000428935;ENST00000420266;ENST00000424454;ENST00000538000;ENST00000442148;ENST00000414108	D;D;D;D;D;D;D;D	0.82255	-1.59;-1.59;-1.59;-1.59;-1.59;-1.59;-1.59;-1.59	5.24	4.33	0.51752	WW/Rsp5/WWP (6);	0.000000	0.85682	D	0.000000	T	0.79009	0.4374	N	0.20304	0.555	0.80722	D	1	P;B;P	0.49447	0.811;0.447;0.924	P;B;P	0.49085	0.464;0.245;0.6	T	0.81284	-0.1002	10	0.52906	T	0.07	-5.4856	16.1738	0.81836	0.0:0.1336:0.8664:0.0	.	106;151;151	Q9BTA9-2;Q9BTA9-5;Q9BTA9	.;.;WAC_HUMAN	L	106;106;151;151;106;106;106;106;106;106	ENSP00000364816:R106L;ENSP00000364797:R106L;ENSP00000311106:R151L;ENSP00000346986:R151L;ENSP00000399706:R106L;ENSP00000404758:R106L;ENSP00000400848:R106L;ENSP00000415645:R106L	ENSP00000311106:R151L	R	+	2	0	WAC	28918741	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.567000	0.98161	1.315000	0.45114	0.563000	0.77884	CGA		TCGA-IB-A7LX-01A-12D-A36O-08	WAC-017	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000047371.1	1	0	0	20	437	0	142	0	9.847569e-01	0	148	0	142	2		0	0	0	0	0	2	1	0.999994	20	426	0	138	2		0	0	0	0	142	2	-3.100219	1	1	0	0		1	1	2	3	1.868416	1	0.550000	3.150000	0.647059	0.200000	0.120000	0.300000	0.210000	0.211863	0.200000	0	1.600000e-01	2.600000e-01
RHOBTB1	9886	broad.mit.edu	37	10	62648097	62648097	+	Missense_Mutation	SNP	G	G	T	rs151278163		TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr10:62648097G>T	ENST00000337910.5	-	6	1666	c.1329C>A	c.(1327-1329)ttC>ttA	p.F443L	RHOBTB1_ENST00000357917.4_Missense_Mutation_p.F443L	NM_001242359.1|NM_014836.4	NP_001229288.1|NP_055651.1	O94844	RHBT1_HUMAN	Rho-related BTB domain containing 1			23	Prostate(12;0.0112)				TCCTCAAATCGAACATCTCGA	0.463000																								0							SO:0001583	missense			ENST00000337910.5	1	0	hg19	CCDS7261.1	.	.	.	.	.	.	.	.	.	.	G	6.234	0.411291	0.11812	.	.	ENSG00000072422	ENST00000357917;ENST00000337910	T;T	0.66460	-0.21;-0.21	5.71	2.11	0.27256	BTB/POZ-like (1);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	T	0.73505	0.3595	M	0.64567	1.98	0.58432	D	0.999993	D	0.89917	1.0	D	0.97110	1.0	T	0.67639	-0.5619	10	0.16896	T	0.51	.	8.601	0.33745	0.7158:0.0:0.2842:0.0	.	443	O94844	RHBT1_HUMAN	L	443	ENSP00000350595:F443L;ENSP00000338671:F443L	ENSP00000338671:F443L	F	-	3	2	RHOBTB1	62318103	1.000000	0.71417	0.993000	0.49108	0.846000	0.48090	2.104000	0.41815	0.115000	0.18071	-0.793000	0.03317	TTC		TCGA-IB-A7LX-01A-12D-A36O-08	RHOBTB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048220.1	1	0	0	18	330	0	80	0	3.159376e-01	0	21	0	80	2		0	0	0	0	0	2	1	0.999982	17	327	0	79	2		0	0	0	0	80	2	-2.919542	1	1	0	0		1	2	2	4	2.372051	1	0.550000	3.150000	0.709677	0.290000	0.170000	0.440000	0.280000	0.305621	0.290000	0	2.300000e-01	3.700000e-01
FAS	355	broad.mit.edu	37	10	90773947	90773947	+	Silent	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr10:90773947C>A	ENST00000355740.2	+	9	968	c.748C>A	c.(748-750)Cga>Aga	p.R250R	FAS_ENST00000355279.2_3'UTR|FAS_ENST00000352159.4_3'UTR|FAS_ENST00000357339.2_Silent_p.R229R|RP11-399O19.9_ENST00000562983.1_RNA	NM_000043.4|NM_152871.2|NM_152872.2	NP_000034.1|NP_690610.1|NP_690611.1	P49327	FAS_HUMAN	Fas cell surface death receptor			18		Colorectal(252;0.0161)		Cerulenin(DB01034)|Orlistat(DB01083)	AGGCTTTGTTCGAAAGAATGG	0.353000																								0		GRCh37	CM961371	FAS	M		SO:0001819	synonymous_variant			ENST00000355740.2	1	0	hg19	CCDS7393.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	FAS-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049274.3	1	0	0	27	596	0	129	0	6.293041e-01	1	47	0	129	2		0	0	0	0	0	2	1	1.000000	26	592	0	129	2		0	0	0	0	129	2	-3.186713	1	1	121412	1	31	1	2	2	4	2.372051	1	0.550000	3.150000	0.709677	0.240000	0.150000	0.350000	0.240000	0.252349	0.240000	0	1.900000e-01	3.000000e-01
TRIM29	23650	broad.mit.edu	37	11	119993732	119993732	+	Silent	SNP	C	C	A	rs137882673		TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08			C	A	C	C		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr11:119993732C>A	ENST00000341846.5	-	5	1786	c.1365G>T	c.(1363-1365)acG>acT	p.T455T	TRIM29_ENST00000528870.1_5'UTR|TRIM29_ENST00000524816.3_Silent_p.T21T|TRIM29_ENST00000541857.1_Silent_p.T188T|TRIM29_ENST00000529044.1_Silent_p.T194T|TRIM29_ENST00000525887.1_5'Flank	NM_012101.3	NP_036233.2	Q14134	TRI29_HUMAN	tripartite motif containing 29			30		Breast(109;0.00117)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)			CGAAGCTGTTCGTGTAGTTGT	0.577000																								0							SO:0001819	synonymous_variant			ENST00000341846.5	1	0	hg19	CCDS8428.1	.	.	.	.	.	.	.	.	.	.	C	4.375	0.069135	0.08436	.	.	ENSG00000137699	ENST00000525327	.	.	.	4.12	-8.25	0.01025	.	.	.	.	.	.	.	.	.	.	.	0.18873	N	0.999985	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.2926	0.21069	0.0942:0.2723:0.4906:0.1429	.	.	.	.	X	48	.	.	E	-	1	0	TRIM29	119498942	0.000000	0.05858	0.001000	0.08648	0.690000	0.40134	-3.482000	0.00456	-4.073000	0.00076	-1.707000	0.00718	GAA		TCGA-IB-A7LX-01A-12D-A36O-08	TRIM29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277108.2	1	0	0	14	340	0	123	0	9.999955e-01	0	572	0	123	2		0	0	0	0	0	2	1	0.999743	15	334	0	121	2		0	0	0	0	123	2	-2.740996	1	1	0	0		1	0	2	2	1.608709	1	0.550000	3.150000	0.550000	0.140000	0.070000	0.230000	0.140000	0.152847	0.140000	0	1.000000e-01	1.900000e-01
RPS13	6207	broad.mit.edu	37	11	17097027	17097027	+	Silent	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08			G	T	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr11:17097027G>T	ENST00000525634.1	-	4	440	c.295C>A	c.(295-297)Cga>Aga	p.R99R	PIK3C2A_ENST00000531428.1_5'Flank|AC116533.1_ENST00000408395.1_RNA|SNORD14B_ENST00000364533.1_RNA|RPS13_ENST00000526895.1_5'UTR|SNORD14A_ENST00000606526.1_RNA|RPS13_ENST00000228140.2_Silent_p.R99R			P62277	RS13_HUMAN	ribosomal protein S13	p.R99*(1)|p.R99G(1)		5					AGATGCTTTCGAACAGCAACT	0.353000																								2	Substitution - Missense(1)|Substitution - Nonsense(1)						SO:0001819	synonymous_variant			ENST00000525634.1	1	0	hg19	CCDS7823.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	RPS13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387320.2	1	0	0	13	276	0	55	1	1	2	5206	0	55	2		0	0	0	0	0	2	1	0.999545	13	274	0	54	2		0	0	0	0	55	2	-2.993735	1	1	0	0		1	2	5	7	2.287299	1	0.550000	3.150000	0.701740	0.270000	0.140000	1.000000	0.250000	0.429577	0.270000	0	1.900000e-01	1
RAPSN	5913	broad.mit.edu	37	11	47469684	47469684	+	Missense_Mutation	SNP	C	C	A	rs150051760		TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr11:47469684C>A	ENST00000298854.2	-	2	424	c.211G>T	c.(211-213)Gac>Tac	p.D71Y	RAPSN_ENST00000352508.3_Missense_Mutation_p.D71Y|RAPSN_ENST00000529341.1_Missense_Mutation_p.D71Y|RAPSN_ENST00000524487.1_Missense_Mutation_p.D71Y	NM_005055.4	NP_005046.2	Q13702	RAPSN_HUMAN	receptor-associated protein of the synapse			12					CGGGCCGTGTCGATCTGGACC	0.622000																								0							SO:0001583	missense			ENST00000298854.2	1	0	hg19	CCDS7936.1	.	.	.	.	.	.	.	.	.	.	C	17.65	3.442798	0.63067	.	.	ENSG00000165917	ENST00000298854;ENST00000352508;ENST00000524487;ENST00000529341	D;D;D;D	0.81739	-1.53;-1.53;-1.53;-1.53	4.72	4.72	0.59763	Tetratricopeptide-like helical (1);Rapsyn, myristoylation/linker region, N-terminal (1);	0.047920	0.85682	D	0.000000	D	0.86772	0.6013	L	0.47716	1.5	0.58432	D	0.99999	P;D;D	0.89917	0.468;0.996;1.0	B;D;D	0.75484	0.339;0.92;0.986	D	0.87824	0.2640	10	0.59425	D	0.04	-53.4394	18.0701	0.89403	0.0:1.0:0.0:0.0	.	71;71;71	E9PK11;Q13702-2;Q13702	.;.;RAPSN_HUMAN	Y	71	ENSP00000298854:D71Y;ENSP00000298853:D71Y;ENSP00000435551:D71Y;ENSP00000431732:D71Y	ENSP00000298854:D71Y	D	-	1	0	RAPSN	47426260	1.000000	0.71417	0.998000	0.56505	0.691000	0.40173	5.569000	0.67391	2.334000	0.79466	0.557000	0.71058	GAC		TCGA-IB-A7LX-01A-12D-A36O-08	RAPSN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391726.1	1	0	0	7	129	0	44		0	0	0	0	44	2		0	0	0	0	0	2	1	0.979399	7	125	0	44	2		0	0	0	0	44	2	-10.377630	1	0	0	0		1	2	6	8	2.128606	1	0.550000	3.150000	0.681416	0.300000	0.120000	1.000000	0.270000	0.422891	0.300000	0	2.000000e-01	1
OR4C15	81309	broad.mit.edu	37	11	55322649	55322649	+	Silent	SNP	T	T	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr11:55322649T>A	ENST00000314644.2	+	1	867	c.867T>A	c.(865-867)gcT>gcA	p.A289A		NM_001001920.1	NP_001001920.1	Q8NGM1	OR4CF_HUMAN	olfactory receptor, family 4, subfamily C, member 15			56					GCTGGAAAGCTCTCTCCACCT	0.438000										HNSCC(20;0.049)														0							SO:0001819	synonymous_variant			ENST00000314644.2	1	1	hg19	CCDS31501.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	OR4C15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391164.1	1	0	1	202	276	0	147		0	0	0	0	147	2		0	0	0	0	0	2	1	1.000000	204	273	0	146	2		0	0	0	0	147	2	-20.000000	1	0	0	0		1						0.550000	3.150000									0	0
OR4C15	81309	broad.mit.edu	37	11	55322650	55322650	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr11:55322650C>A	ENST00000314644.2	+	1	868	c.868C>A	c.(868-870)Ctc>Atc	p.L290I		NM_001001920.1	NP_001001920.1	Q8NGM1	OR4CF_HUMAN	olfactory receptor, family 4, subfamily C, member 15			56					CTGGAAAGCTCTCTCCACCTG	0.433000										HNSCC(20;0.049)														0							SO:0001583	missense			ENST00000314644.2	1	1	hg19	CCDS31501.1	.	.	.	.	.	.	.	.	.	.	C	13.12	2.141818	0.37825	.	.	ENSG00000181939	ENST00000314644	T	0.00137	8.68	5.02	5.02	0.67125	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00300	0.0009	M	0.81682	2.555	0.25891	N	0.983471	P	0.44195	0.828	P	0.48524	0.58	T	0.42965	-0.9420	9	0.87932	D	0	.	9.2831	0.37740	0.0:0.9041:0.0:0.0959	.	236	Q8NGM1	OR4CF_HUMAN	I	290	ENSP00000324958:L290I	ENSP00000324958:L290I	L	+	1	0	OR4C15	55079226	0.000000	0.05858	0.971000	0.41717	0.282000	0.26991	-0.491000	0.06474	2.608000	0.88229	0.385000	0.25706	CTC		TCGA-IB-A7LX-01A-12D-A36O-08	OR4C15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391164.1	1	0	1	203	276	0	149		0	0	0	0	149	2		0	0	0	0	0	2	1	1.000000	205	272	0	148	2		0	0	0	0	149	2	-20.000000	1	1	0	0		1						0.550000	3.150000									0	0
OR8K3	219473	broad.mit.edu	37	11	56086466	56086466	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr11:56086466G>T	ENST00000312711.1	+	1	684	c.684G>T	c.(682-684)atG>atT	p.M228I		NM_001005202.1	NP_001005202.1	Q8NH51	OR8K3_HUMAN	olfactory receptor, family 8, subfamily K, member 3			40	Esophageal squamous(21;0.00448)				TTCTCAGGATGAATTCTGCTG	0.413000																								0							SO:0001583	missense			ENST00000312711.1	1	0	hg19	CCDS31527.1	.	.	.	.	.	.	.	.	.	.	G	0.620	-0.821600	0.02755	.	.	ENSG00000181689	ENST00000312711	T	0.00021	9.03	4.28	2.37	0.29283	GPCR, rhodopsin-like superfamily (1);	0.077917	0.56097	D	0.000035	T	0.00039	0.0001	N	0.02379	-0.575	0.09310	N	0.999998	B	0.19817	0.039	B	0.26969	0.075	T	0.02464	-1.1155	10	0.08599	T	0.76	.	9.6999	0.40180	0.1726:0.0:0.8274:0.0	.	228	Q8NH51	OR8K3_HUMAN	I	228	ENSP00000323555:M228I	ENSP00000323555:M228I	M	+	3	0	OR8K3	55843042	0.001000	0.12720	0.971000	0.41717	0.029000	0.11900	-0.140000	0.10342	0.542000	0.28846	0.471000	0.43371	ATG		TCGA-IB-A7LX-01A-12D-A36O-08	OR8K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391602.1	1	0	0	17	409	0	112		0	0	0	0	112	2		0	0	0	0	0	2	1	0.999963	17	404	0	111	2		0	0	0	0	112	2	-4.239183	1	1	0	0		1	2	5	7	2.095029	1	0.550000	3.150000	0.675090	0.210000	0.120000	1.000000	0.200000	0.364225	0.210000	0	1.600000e-01	1
EML3	256364	broad.mit.edu	37	11	62370095	62370095	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08			G	A	G	G		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr11:62370095G>A	ENST00000394773.2	-	22	2850	c.2543C>T	c.(2542-2544)aCg>aTg	p.T848M	EML3_ENST00000529309.1_Silent_p.H811H|EML3_ENST00000494176.2_Silent_p.H783H|MTA2_ENST00000278823.2_5'Flank|EML3_ENST00000531557.1_Missense_Mutation_p.T631M|EML3_ENST00000278845.4_Missense_Mutation_p.T849M|MTA2_ENST00000527204.1_5'Flank	NM_153265.2	NP_694997.2	Q32P44	EMAL3_HUMAN	echinoderm microtubule associated protein like 3			26					GTCGTCGTGCGTGAATCGGAC	0.746000																								0							SO:0001583	missense			ENST00000394773.2	0	1	hg19	CCDS8023.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.3|21.3	4.126410|4.126410	0.77549|0.77549	.|.	.|.	ENSG00000149499|ENSG00000149499	ENST00000394776|ENST00000439994;ENST00000394773;ENST00000278845;ENST00000531557	.|T;T;T;T	.|0.41400	.|2.28;1.52;1.0;1.0	4.96|4.96	4.96|4.96	0.65561|0.65561	.|WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);	.|0.511488	.|0.19627	.|N	.|0.109775	T|T	0.54191|0.54191	0.1843|0.1843	L|L	0.39397|0.39397	1.21|1.21	0.80722|0.80722	D|D	1|1	.|D;P;D	.|0.76494	.|0.995;0.882;0.999	.|P;B;D	.|0.66351	.|0.832;0.325;0.943	T|T	0.50775|0.50775	-0.8788|-0.8788	5|10	.|0.42905	.|T	.|0.14	-32.5046|-32.5046	16.0654|16.0654	0.80867|0.80867	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|848;631;849	.|Q32P44;G3V195;B7WPE2	.|EMAL3_HUMAN;.;.	C|M	806|89;848;849;631	.|ENSP00000409611:T89M;ENSP00000378254:T848M;ENSP00000278845:T849M;ENSP00000433417:T631M	.|ENSP00000278845:T849M	R|T	-|-	1|2	0|0	EML3|EML3	62126671|62126671	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	3.027000|3.027000	0.49697|0.49697	2.472000|2.472000	0.83506|0.83506	0.462000|0.462000	0.41574|0.41574	CGC|ACG		TCGA-IB-A7LX-01A-12D-A36O-08	EML3-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313432.1	0	0	0	4	36	0	11	0	9.946877e-01	0	113	0	11	2		0	0	0	0	0	2	0	0.859457	1	34	0	10	2		0	0	0	0	11	2	-9.647493	1	0	0	0		1	2	5	7	2.095029	1	0.550000	3.150000	0.675090	0.630000	0.200000	1.000000	1.000000	0.663491	0.630000	0	3.700000e-01	1
DNHD1	144132	broad.mit.edu	37	11	6593035	6593035	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr11:6593035G>A	ENST00000527990.2	+	41	14081	c.14081G>A	c.(14080-14082)aGt>aAt	p.S4694N	DNHD1_ENST00000254579.6_Missense_Mutation_p.S4694N			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1			55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)			CCGGGCACCAGTGACCTGCCA	0.637000																								0							SO:0001583	missense			ENST00000527990.2	1	1	hg19	CCDS44532.1	.	.	.	.	.	.	.	.	.	.	G	1.262	-0.615437	0.03663	.	.	ENSG00000179532	ENST00000254579;ENST00000527990;ENST00000530197	T;T	0.26067	1.76;1.76	4.75	-5.17	0.02849	Dynein heavy chain (1);	1.578020	0.03032	N	0.152237	T	0.11922	0.0290	N	0.08118	0	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.28490	-1.0042	10	0.12103	T	0.63	1.5404	9.9464	0.41611	0.1879:0.1309:0.6813:0.0	.	3782;747;4694	B0I1S4;Q9NSW8;Q96M86	.;.;DNHD1_HUMAN	N	4694;4694;962	ENSP00000254579:S4694N;ENSP00000436180:S4694N	ENSP00000254579:S4694N	S	+	2	0	DNHD1	6549611	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.007000	0.03667	-0.921000	0.03794	-0.165000	0.13383	AGT		TCGA-IB-A7LX-01A-12D-A36O-08	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	1	0	0	46	150	0	66	1	5.963972e-01	3	5	0	66	2		0	0	0	0	0	2	1	1.000000	45	145	0	65	2		0	0	0	0	66	2	-20.000000	1	1	0	0		1	2	5	7	2.287299	1	0.550000	3.150000	0.701740	0.990000	0.990000	1.000000	1.000000	0.998724	0.990000	1	9.900000e-01	1
KDM2A	22992	broad.mit.edu	37	11	67012810	67012810	+	Silent	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr11:67012810C>A	ENST00000529006.2	+	14	2160	c.1714C>A	c.(1714-1716)Cga>Aga	p.R572R	KDM2A_ENST00000308783.5_Silent_p.R30R|KDM2A_ENST00000526258.1_3'UTR|KDM2A_ENST00000530342.1_Silent_p.R133R|KDM2A_ENST00000398645.2_Silent_p.R572R	NM_012308.2	NP_036440.1	Q9Y2K7	KDM2A_HUMAN	lysine (K)-specific demethylase 2A			36					AGTGCGATGTCGAAAATGCAA	0.552000																								0							SO:0001819	synonymous_variant			ENST00000529006.2	1	0	hg19	CCDS44657.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	KDM2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393140.2	1	0	0	11	236	0	75	0	9.606481e-01	0	121	0	75	2		0	0	0	0	0	2	1	0.997992	11	225	0	74	2		0	0	0	0	75	2	-12.880610	1	1	0	0		1	2	5	7	2.095029	1	0.550000	3.150000	0.675090	0.250000	0.120000	1.000000	0.230000	0.388959	0.250000	0	1.700000e-01	1
C11orf30	56946	broad.mit.edu	37	11	76257216	76257216	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr11:76257216G>A	ENST00000529032.1	+	19	3649	c.3649G>A	c.(3649-3651)Gtt>Att	p.V1217I	C11orf30_ENST00000524767.1_Missense_Mutation_p.V1232I|C11orf30_ENST00000334736.3_Missense_Mutation_p.V1217I|C11orf30_ENST00000343878.3_Intron|C11orf30_ENST00000525038.1_Missense_Mutation_p.V1218I|C11orf30_ENST00000524490.1_Missense_Mutation_p.V1119I|C11orf30_ENST00000525919.1_Missense_Mutation_p.V1218I|C11orf30_ENST00000533248.1_Missense_Mutation_p.V1126I			Q7Z589	EMSY_HUMAN	chromosome 11 open reading frame 30			60					TCCATCCACTGTTGGCTCTTC	0.512000																								0							SO:0001583	missense			ENST00000529032.1	1	1	hg19	CCDS8244.1	.	.	.	.	.	.	.	.	.	.	G	9.733	1.162780	0.21538	.	.	ENSG00000158636	ENST00000524490;ENST00000334736;ENST00000393457;ENST00000524767;ENST00000533248;ENST00000525919;ENST00000525038;ENST00000529032	.	.	.	6.06	3.0	0.34707	.	0.499003	0.20569	N	0.089772	T	0.36166	0.0957	N	0.14661	0.345	0.80722	D	1	B;B;B;B;B;B	0.22346	0.068;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.20767	0.031;0.0;0.0;0.0;0.0;0.0	T	0.15150	-1.0447	9	0.27082	T	0.32	-1.8144	9.3812	0.38316	0.1312:0.119:0.7498:0.0	.	1126;1218;1232;1218;1119;1217	B7ZKT8;B7ZKU2;B7ZKU0;Q17RM7;E9PMC9;Q7Z589	.;.;.;.;.;EMSY_HUMAN	I	1119;1217;899;1232;1126;1218;1218;1217	.	ENSP00000334130:V1217I	V	+	1	0	C11orf30	75934864	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	2.038000	0.41184	1.580000	0.49851	0.650000	0.86243	GTT		TCGA-IB-A7LX-01A-12D-A36O-08	C11orf30-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383288.2	1	0	0	15	326	0	95	0	2.058821e-01	0	18	0	95	2		0	0	0	0	0	2	1	0.999866	14	322	0	95	2		0	0	0	0	95	2	-4.221989	1	1	0	0		1	2	5	7	2.111242	1	0.550000	3.150000	0.678284	0.240000	0.130000	1.000000	0.210000	0.387989	0.240000	0	1.800000e-01	1
NOX4	50507	broad.mit.edu	37	11	89133524	89133524	+	Silent	SNP	A	A	G			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr11:89133524A>G	ENST00000263317.4	-	10	1108	c.870T>C	c.(868-870)ccT>ccC	p.P290P	NOX4_ENST00000535633.1_Silent_p.P266P|NOX4_ENST00000528341.1_Silent_p.P265P|NOX4_ENST00000542487.1_Silent_p.P266P|NOX4_ENST00000534731.1_Silent_p.P290P|NOX4_ENST00000531342.1_Intron|NOX4_ENST00000532825.1_Silent_p.P266P|NOX4_ENST00000527626.1_Silent_p.P124P|NOX4_ENST00000525196.1_Intron|NOX4_ENST00000527956.1_Silent_p.P266P|NOX4_ENST00000424319.1_Silent_p.P266P|NOX4_ENST00000413594.2_Silent_p.P311P|NOX4_ENST00000343727.5_Silent_p.P266P|NOX4_ENST00000375979.3_Intron			Q9NPH5	NOX4_HUMAN	NADPH oxidase 4			44		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.011)			ACAGGCACAAAGGTCCAGAAA	0.398000																								0							SO:0001819	synonymous_variant			ENST00000263317.4	1	1	hg19	CCDS8285.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	NOX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394054.1	1	0	0	11	199	0	78	0	7.448056e-02	0	8	0	78	2		0	0	0	0	0	2	1	0.997876	10	188	0	82	2		0	0	0	0	78	2	-4.718546	1	1	0	0		1	0	2	2	1.592599	1	0.550000	3.150000	0.550000	0.190000	0.100000	0.320000	0.190000	0.205018	0.190000	0	1.400000e-01	2.600000e-01
TAF1D	79101	broad.mit.edu	37	11	93472407	93472407	+	Silent	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08			G	T	G	G		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr11:93472407G>T	ENST00000448108.2	-	2	714	c.64C>A	c.(64-66)Cga>Aga	p.R22R	C11orf54_ENST00000354421.3_5'Flank|C11orf54_ENST00000528288.1_5'Flank|C11orf54_ENST00000528099.1_5'Flank|C11orf54_ENST00000540113.1_5'Flank|C11orf54_ENST00000331239.4_5'Flank	NM_024116.3	NP_077021.1	Q9H5J8	TAF1D_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, D, 41kDa			7					ACTCACCTTCGATTTGCAAGT	0.318000																								0							SO:0001819	synonymous_variant			ENST00000448108.2	1	0	hg19	CCDS8293.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	TAF1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394662.2	1	0	0	12	255	0	81	0	9.973335e-01	0	218	0	81	2		0	0	0	0	0	2	1	0.999053	12	249	0	80	2		0	0	0	0	81	2	-3.261399	1	1	0	0		1	0	2	2	1.608709	1	0.550000	3.150000	0.550000	0.160000	0.080000	0.270000	0.160000	0.175182	0.160000	0	1.200000e-01	2.200000e-01
UHRF1BP1L	23074	broad.mit.edu	37	12	100491190	100491190	+	Silent	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr12:100491190G>T	ENST00000279907.7	-	6	834	c.622C>A	c.(622-624)Cga>Aga	p.R208R	UHRF1BP1L_ENST00000356828.3_Silent_p.R208R	NM_015054.1	NP_055869.1	A0JNW5	UH1BL_HUMAN	UHRF1 binding protein 1-like	p.R208*(2)		50					GTTATTAATCGAACAGGAGCA	0.343000																								2	Substitution - Nonsense(2)						SO:0001819	synonymous_variant			ENST00000279907.7	1	0	hg19	CCDS31882.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	UHRF1BP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407875.1	1	0	0	10	200	0	62	0	6.368889e-02	0	8	0	62	2		0	0	0	0	0	2	1	0.996710	10	196	0	60	2		0	0	0	0	62	2	-3.207791	1	1	0	0		1	0	2	2	1.513293	1	0.550000	3.150000	0.550000	0.170000	0.080000	0.300000	0.180000	0.187931	0.170000	0	1.200000e-01	2.400000e-01
DRAM1	55332	broad.mit.edu	37	12	102295199	102295199	+	Silent	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr12:102295199C>A	ENST00000258534.8	+	3	769	c.330C>A	c.(328-330)gtC>gtA	p.V110V	DRAM1_ENST00000544152.1_Silent_p.V110V	NM_018370.2	NP_060840.2	Q8N682	DRAM1_HUMAN	DNA-damage regulated autophagy modulator 1			12					TGGGCATTGTCGCCAATTTTC	0.428000																								0							SO:0001819	synonymous_variant			ENST00000258534.8	1	0	hg19	CCDS41823.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	DRAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409195.1	1	0	0	9	158	0	78	0	6.905539e-01	0	43	0	78	2		0	0	0	0	0	2	1	0.994147	9	156	0	77	2		0	0	0	0	78	2	-3.299010	1	1	0	0		1	0	2	2	1.513293	1	0.550000	3.150000	0.550000	0.200000	0.090000	0.350000	0.200000	0.214106	0.200000	0	1.400000e-01	2.800000e-01
UBE3B	89910	broad.mit.edu	37	12	109945463	109945463	+	Silent	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr12:109945463G>T	ENST00000342494.3	+	15	2140	c.1545G>T	c.(1543-1545)ctG>ctT	p.L515L	UBE3B_ENST00000535900.1_3'UTR|UBE3B_ENST00000280774.5_Silent_p.L515L|UBE3B_ENST00000434735.2_Silent_p.L515L	NM_130466.3	NP_569733.2	Q7Z3V4	UBE3B_HUMAN	ubiquitin protein ligase E3B			45					TGGAATGCCTGAACAATGACA	0.522000																								0							SO:0001819	synonymous_variant			ENST00000342494.3	1	0	hg19	CCDS9129.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	UBE3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403119.1	1	0	0	20	474	0	152	0	2.081888e-01	0	20	0	152	2		0	0	0	0	0	2	1	0.999995	19	471	0	151	2		0	0	0	0	152	2	-3.064727	1	1	0	0		1	0	2	2	1.513293	1	0.550000	3.150000	0.550000	0.140000	0.080000	0.220000	0.140000	0.153688	0.140000	0	1.100000e-01	1.900000e-01
TBX5	6910	broad.mit.edu	37	12	114841631	114841631	+	Missense_Mutation	SNP	C	C	A	rs148195311		TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr12:114841631C>A	ENST00000310346.4	-	2	739	c.73G>T	c.(73-75)Gat>Tat	p.D25Y	TBX5_ENST00000552726.1_5'UTR|TBX5_ENST00000405440.2_Missense_Mutation_p.D25Y|TBX5_ENST00000349716.5_Intron|TBX5_ENST00000526441.1_Missense_Mutation_p.D25Y	NM_000192.3	NP_000183.2	Q99593	TBX5_HUMAN	T-box 5			56	Medulloblastoma(191;0.163)|all_neural(191;0.178)				GGTTTCGAATCGCAGGGCAGG	0.706000													NSCLC(152;1358 1980 4050 23898 40356)											0							SO:0001583	missense			ENST00000310346.4	1	0	hg19	CCDS9173.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.413796	0.83449	2.27E-4	0.0	ENSG00000089225	ENST00000310346;ENST00000405440;ENST00000526441	D;D;D	0.88201	-2.35;-2.35;-2.31	5.31	5.31	0.75309	.	0.307696	0.35615	N	0.003093	D	0.86764	0.6011	N	0.19112	0.55	0.46701	D	0.999163	P;P	0.49447	0.887;0.924	P;P	0.49012	0.598;0.594	D	0.88669	0.3194	10	0.62326	D	0.03	.	18.988	0.92780	0.0:1.0:0.0:0.0	.	25;25	Q99593-2;Q99593	.;TBX5_HUMAN	Y	25	ENSP00000309913:D25Y;ENSP00000384152:D25Y;ENSP00000433292:D25Y	ENSP00000309913:D25Y	D	-	1	0	TBX5	113326014	0.997000	0.39634	0.575000	0.28536	0.908000	0.53690	3.897000	0.56273	2.476000	0.83614	0.655000	0.94253	GAT		TCGA-IB-A7LX-01A-12D-A36O-08	TBX5-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388297.1	1	0	0	12	166	0	45		0	0	0	0	45	2		0	0	0	0	0	2	1	0.998929	12	157	0	44	2		0	0	0	0	45	2	-15.904110	1	1	121398	1	30	1	0	2	2	1.513293	1	0.550000	3.150000	0.550000	0.240000	0.130000	0.400000	0.240000	0.261411	0.240000	0	1.800000e-01	3.300000e-01
CLIP1	6249	broad.mit.edu	37	12	122839066	122839066	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr12:122839066C>A	ENST00000540338.1	-	6	1282	c.1241G>T	c.(1240-1242)cGa>cTa	p.R414L	CLIP1_ENST00000361654.4_Missense_Mutation_p.R414L|CLIP1_ENST00000545889.1_Missense_Mutation_p.R115L|CLIP1_ENST00000537178.1_Missense_Mutation_p.R414L|CLIP1_ENST00000302528.7_Missense_Mutation_p.R414L|CLIP1_ENST00000358808.2_Missense_Mutation_p.R414L			P30622	CLIP1_HUMAN	CAP-GLY domain containing linker protein 1			60	all_neural(191;0.0837)|Medulloblastoma(191;0.163)				CACCATTGTTCGCAGCTGGTC	0.512000																								0							SO:0001583	missense			ENST00000540338.1	1	0	hg19	CCDS58285.1	.	.	.	.	.	.	.	.	.	.	C	31	5.083510	0.94050	.	.	ENSG00000130779	ENST00000545889;ENST00000302528;ENST00000358808;ENST00000542885;ENST00000537178;ENST00000540338;ENST00000540304;ENST00000537004	T;T;T;T;T;T;T	0.69040	2.38;0.45;0.45;0.44;0.48;-0.11;-0.37	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	T	0.82116	0.4967	M	0.72118	2.19	0.80722	D	1	D;D;D;D;D	0.89917	0.995;1.0;0.996;0.989;0.993	P;D;D;D;P	0.76071	0.878;0.987;0.935;0.935;0.862	T	0.81402	-0.0949	10	0.52906	T	0.07	-7.3582	20.1346	0.98019	0.0:1.0:0.0:0.0	.	348;115;414;414;414	F6VGP8;F5H0N7;P30622-2;P30622-1;P30622	.;.;.;.;CLIP1_HUMAN	L	115;414;414;259;414;414;348;348	ENSP00000438743:R115L;ENSP00000303585:R414L;ENSP00000351665:R414L;ENSP00000445531:R414L;ENSP00000439093:R414L;ENSP00000437786:R348L;ENSP00000441409:R348L	ENSP00000303585:R414L	R	-	2	0	CLIP1	121405019	1.000000	0.71417	0.925000	0.36789	0.973000	0.67179	7.818000	0.86416	2.765000	0.95021	0.655000	0.94253	CGA		TCGA-IB-A7LX-01A-12D-A36O-08	CLIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000401625.1	1	0	0	11	271	0	71	0	6.345548e-01	1	52	0	71	2		0	0	0	0	0	2	1	0.998258	11	266	0	69	2		0	0	0	0	71	2	-3.002067	1	1	0	0		1	0	3	3	1.820111	1	0.550000	3.150000	0.641648	0.180000	0.090000	1.000000	0.180000	0.237578	0.180000	0	1.300000e-01	2.600000e-01
RILPL2	196383	broad.mit.edu	37	12	123907604	123907604	+	Missense_Mutation	SNP	T	T	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr12:123907604T>A	ENST00000280571.8	-	3	888	c.592A>T	c.(592-594)Atc>Ttc	p.I198F		NM_145058.1	NP_659495.1	Q969X0	RIPL2_HUMAN	Rab interacting lysosomal protein-like 2			6	all_neural(191;0.101)|Medulloblastoma(191;0.163)				TTTTTTATGATTGTCTTCTCC	0.507000																								0							SO:0001583	missense			ENST00000280571.8	0	1	hg19	CCDS9248.1	.	.	.	.	.	.	.	.	.	.	T	13.79	2.342477	0.41498	.	.	ENSG00000150977	ENST00000280571	T	0.45668	0.89	5.0	3.85	0.44370	.	0.229969	0.44688	D	0.000439	T	0.32224	0.0822	L	0.29908	0.895	0.38433	D	0.946505	P	0.49961	0.93	P	0.44860	0.462	T	0.14392	-1.0474	10	0.48119	T	0.1	.	8.3232	0.32140	0.0:0.0913:0.0:0.9087	.	198	Q969X0	RIPL2_HUMAN	F	198	ENSP00000280571:I198F	ENSP00000280571:I198F	I	-	1	0	RILPL2	122473557	0.981000	0.34729	0.610000	0.28997	0.063000	0.16089	1.962000	0.40442	0.858000	0.35431	0.533000	0.62120	ATC		TCGA-IB-A7LX-01A-12D-A36O-08	RILPL2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		0	0	0	6	322	0	82	1	5.462801e-01	2	89	0	82	2		0	0	0	0	0	2	1	0.963650	6	317	0	82	2		0	0	0	0	82	2	-6.754241	1	0	0	0		1	0	3	3	1.820111	1	0.550000	3.150000	0.641648	0.090000	0.030000	1.000000	0.090000	0.147092	0.090000	0	5.000000e-02	1.400000e-01
PLEKHA5	54477	broad.mit.edu	37	12	19512436	19512436	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08			C	A	C	C		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr12:19512436C>A	ENST00000299275.6	+	22	2947	c.2941C>A	c.(2941-2943)Caa>Aaa	p.Q981K	PLEKHA5_ENST00000424268.1_Missense_Mutation_p.Q970K|PLEKHA5_ENST00000429027.2_Missense_Mutation_p.Q1147K|PLEKHA5_ENST00000317589.4_Missense_Mutation_p.Q1044K|PLEKHA5_ENST00000543806.1_Missense_Mutation_p.Q963K|PLEKHA5_ENST00000355397.3_Missense_Mutation_p.Q1039K|PLEKHA5_ENST00000539256.1_Missense_Mutation_p.Q739K|PLEKHA5_ENST00000538714.1_Missense_Mutation_p.Q1039K|PLEKHA5_ENST00000359180.3_Missense_Mutation_p.Q925K	NM_019012.5	NP_061885.2	Q9HAU0	PKHA5_HUMAN	pleckstrin homology domain containing, family A member 5			35	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)				AGAAATTGTTCAACTAAAAGA	0.383000													Pancreas(196;329 2193 11246 14234 19524)											0							SO:0001583	missense			ENST00000299275.6	1	0	hg19	CCDS8682.1	.	.	.	.	.	.	.	.	.	.	C	12.07	1.828021	0.32329	.	.	ENSG00000052126	ENST00000317589;ENST00000355397;ENST00000359180;ENST00000542828;ENST00000429027;ENST00000299275;ENST00000539256;ENST00000538714;ENST00000424268;ENST00000543806;ENST00000536974;ENST00000538972	T;T;T;T;T;T;T;T;T;T;T	0.09073	3.02;3.02;3.02;3.02;3.02;3.02;3.02;3.02;3.02;3.02;3.02	4.75	4.75	0.60458	.	1.239000	0.05720	N	0.597588	T	0.07818	0.0196	N	0.24115	0.695	0.09310	N	1	B;B;B;B;B;B;B;B	0.22146	0.065;0.024;0.014;0.011;0.003;0.02;0.014;0.024	B;B;B;B;B;B;B;B	0.18561	0.022;0.018;0.008;0.008;0.006;0.008;0.008;0.018	T	0.11916	-1.0568	10	0.42905	T	0.14	3.8378	9.1527	0.36973	0.0:0.9019:0.0:0.0981	.	1044;963;970;1142;925;1147;981;1039	Q9HAU0-4;F5H0I0;E7EME8;B4DHK5;Q9HAU0-5;E9PHQ3;Q9HAU0;Q9HAU0-2	.;.;.;.;.;.;PKHA5_HUMAN;.	K	1044;1039;925;1143;1147;981;739;1039;970;963;936;262	ENSP00000325155:Q1044K;ENSP00000347560:Q1039K;ENSP00000352104:Q925K;ENSP00000404296:Q1147K;ENSP00000299275:Q981K;ENSP00000440611:Q739K;ENSP00000439673:Q1039K;ENSP00000400411:Q970K;ENSP00000439837:Q963K;ENSP00000440371:Q936K;ENSP00000443553:Q262K	ENSP00000299275:Q981K	Q	+	1	0	PLEKHA5	19403703	0.013000	0.17824	0.005000	0.12908	0.173000	0.22820	2.184000	0.42575	2.627000	0.88993	0.460000	0.39030	CAA		TCGA-IB-A7LX-01A-12D-A36O-08	PLEKHA5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397013.1	1	0	0	17	401	0	63	0	9.999126e-01	0	370	0	63	2		0	0	0	0	0	2	1	0.999960	17	392	0	63	2		0	0	0	0	63	2	-3.260106	1	1	0	0		1	2	4	6	3.113844	1	0.550000	3.150000	0.779951	0.310000	0.170000	1.000000	0.290000	0.344369	0.310000	0	2.300000e-01	4.100000e-01
KRAS	3845	broad.mit.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	C	T	rs121913529		TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	KRAS_deep			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr12:25398284C>T	ENST00000256078.4	-	2	98	c.35G>A	c.(34-36)gGt>gAt	p.G12D	KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)		GCCTACGCCACCAGCTCCAAC	0.348000	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		pancreatic, colorectal, lung, thyroid, AML, others				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)			Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		L, E, M, O	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)						SO:0001583	missense	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	ENST00000256078.4	1	1	hg19	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.409094	0.83340	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.85919	0.5809	M	0.91818	3.245	0.80722	D	1	B;P	0.35714	0.385;0.517	B;B	0.41619	0.257;0.361	D	0.87870	0.2670	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	D	12	ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D	ENSP00000256078:G12D	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		TCGA-IB-A7LX-01A-12D-A36O-08	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	1	0	1	230	222	0	84	1	1	26	20	0	84	2	1	1	210	282	0	767	2	1	1.000000	225	214	0	82	2	1	1	4367	3666	0	84	2	-20.000000	1	1	121404	2	44	1	2	4	6	3.113844	1	0.550000	3.150000	0.779951	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	9.900000e-01	1
STK38L	23012	broad.mit.edu	37	12	27461299	27461299	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08			C	A	C	C		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr12:27461299C>A	ENST00000389032.3	+	4	383	c.214C>A	c.(214-216)Cgc>Agc	p.R72S	STK38L_ENST00000539577.1_Intron	NM_015000.3	NP_055815.1			serine/threonine kinase 38 like			12	Colorectal(261;0.0847)				ACAACACGCTCGCAAAGAAAC	0.368000																								0							SO:0001583	missense			ENST00000389032.3	1	0	hg19	CCDS31761.1	.	.	.	.	.	.	.	.	.	.	C	17.50	3.405421	0.62288	.	.	ENSG00000211455	ENST00000541191;ENST00000389032;ENST00000540996;ENST00000543246;ENST00000544969	T;T;T;T;T	0.49720	0.99;0.77;0.99;0.99;0.99	4.54	4.54	0.55810	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.46639	0.1403	L	0.56199	1.76	0.80722	D	1	B	0.10296	0.003	B	0.12837	0.008	T	0.46331	-0.9199	10	0.51188	T	0.08	.	17.29	0.87153	0.0:1.0:0.0:0.0	.	72	Q9Y2H1	ST38L_HUMAN	S	72	ENSP00000437856:R72S;ENSP00000373684:R72S;ENSP00000443838:R72S;ENSP00000442253:R72S;ENSP00000440279:R72S	ENSP00000373684:R72S	R	+	1	0	STK38L	27352566	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.515000	0.60489	2.257000	0.74773	0.460000	0.39030	CGC		TCGA-IB-A7LX-01A-12D-A36O-08	STK38L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403297.1	1	0	0	36	770	0	144	0	9.916101e-01	0	159	0	144	2		0	0	0	0	0	2	1	1.000000	39	757	0	142	2		0	0	0	0	144	2	-2.488282	0	1	0	0		1	2	4	6	3.113844	1	0.550000	3.150000	0.779951	0.330000	0.220000	1.000000	0.340000	0.365460	0.330000	0	2.700000e-01	4.100000e-01
CNTN1	1272	broad.mit.edu	37	12	41414201	41414201	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr12:41414201C>A	ENST00000551295.2	+	20	2599	c.2482C>A	c.(2482-2484)Cat>Aat	p.H828N	CNTN1_ENST00000347616.1_Missense_Mutation_p.H828N|CNTN1_ENST00000348761.2_Missense_Mutation_p.H817N|CNTN1_ENST00000550305.1_3'UTR	NM_001843.3	NP_001834.2	Q12860	CNTN1_HUMAN	contactin 1	p.H828Y(1)		90	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)			GATATCTGTTCATTGGGAACA	0.294000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000551295.2	1	0	hg19	CCDS8737.1	.	.	.	.	.	.	.	.	.	.	C	11.19	1.566934	0.28003	.	.	ENSG00000018236	ENST00000551295;ENST00000347616;ENST00000348761	T;T;T	0.55760	0.5;0.5;0.5	5.75	3.58	0.41010	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.366663	0.30639	N	0.009186	T	0.26268	0.0641	N	0.08118	0	0.80722	D	1	B;B	0.09022	0.001;0.002	B;B	0.15870	0.008;0.014	T	0.09292	-1.0681	10	0.35671	T	0.21	.	3.1624	0.06524	0.0:0.4877:0.2254:0.2869	.	817;828	Q12860-2;Q12860	.;CNTN1_HUMAN	N	828;828;817	ENSP00000447006:H828N;ENSP00000325660:H828N;ENSP00000261160:H817N	ENSP00000325660:H828N	H	+	1	0	CNTN1	39700468	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.154000	0.42291	1.583000	0.49898	-0.140000	0.14226	CAT		TCGA-IB-A7LX-01A-12D-A36O-08	CNTN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403692.2	1	0	0	17	386	0	86	0	1.883276e-02	0	5	0	86	2		0	0	0	0	0	2	1	0.999963	20	377	0	85	2		0	0	0	0	86	2	-3.010795	1	1	0	0		1	2	2	4	2.117339	1	0.550000	3.150000	0.677650	0.230000	0.120000	1.000000	0.210000	0.375333	0.230000	0	1.700000e-01	1
SOCS2	8835	broad.mit.edu	37	12	93968645	93968645	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr12:93968645G>T	ENST00000340600.2	+	3	885	c.287G>T	c.(286-288)cGa>cTa	p.R96L	SOCS2_ENST00000536696.2_Missense_Mutation_p.R96L|SOCS2_ENST00000548537.1_3'UTR|SOCS2_ENST00000549122.1_Missense_Mutation_p.R96L|SOCS2_ENST00000551556.1_Missense_Mutation_p.R96L|SOCS2_ENST00000549206.1_Missense_Mutation_p.R96L	NM_001270468.1|NM_001270469.1|NM_001270471.1|NM_003877.4	NP_001257397.1|NP_001257398.1|NP_001257400.1|NP_003868.1	O14508	SOCS2_HUMAN	suppressor of cytokine signaling 2	p.R96Q(1)		14					ACTAATCTTCGAATCGAATAC	0.378000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000340600.2	1	0	hg19	CCDS9047.1	.	.	.	.	.	.	.	.	.	.	G	18.78	3.696989	0.68386	.	.	ENSG00000120833	ENST00000340600;ENST00000549206;ENST00000536696;ENST00000539385;ENST00000548091;ENST00000549122;ENST00000549887;ENST00000551556	D;D;D;D;D;D;D	0.89485	-2.52;-2.52;-2.52;-2.52;-2.52;-2.52;-2.52	5.84	5.84	0.93424	SH2 motif (4);	0.055893	0.64402	D	0.000001	D	0.94830	0.8330	M	0.79343	2.45	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.94707	0.7888	10	0.87932	D	0	-0.8535	20.1346	0.98019	0.0:0.0:1.0:0.0	.	96	O14508	SOCS2_HUMAN	L	96;96;96;44;96;96;96;96	ENSP00000339428:R96L;ENSP00000448815:R96L;ENSP00000442898:R96L;ENSP00000447902:R96L;ENSP00000447161:R96L;ENSP00000448611:R96L;ENSP00000449227:R96L	ENSP00000339428:R96L	R	+	2	0	SOCS2	92492776	1.000000	0.71417	0.966000	0.40874	0.239000	0.25481	9.531000	0.98054	2.765000	0.95021	0.655000	0.94253	CGA		TCGA-IB-A7LX-01A-12D-A36O-08	SOCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407731.2	1	0	0	11	234	0	93	0	1.162609e-01	0	12	0	93	2		0	0	0	0	0	2	1	0.998211	11	228	0	93	2		0	0	0	0	93	2	-3.084451	1	1	0	0		1	0	2	2	1.513293	1	0.550000	3.150000	0.550000	0.160000	0.080000	0.280000	0.160000	0.176061	0.160000	0	1.200000e-01	2.200000e-01
CUL4A	8451	broad.mit.edu	37	13	113887578	113887578	+	Silent	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr13:113887578C>A	ENST00000375440.4	+	6	684	c.600C>A	c.(598-600)atC>atA	p.I200I	CUL4A_ENST00000451881.1_Silent_p.I100I|CUL4A_ENST00000326335.4_Silent_p.I100I|CUL4A_ENST00000375441.3_Silent_p.I100I	NM_001008895.1	NP_001008895.1	Q13619	CUL4A_HUMAN	cullin 4A			17	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0482)|all_epithelial(44;0.0148)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.112)		TACTGCTGATCGAGCGCGAGA	0.512000																								0							SO:0001819	synonymous_variant			ENST00000375440.4	1	0	hg19	CCDS41908.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	CUL4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045888.3	1	0	0	13	370	0	83	0	9.257780e-01	0	130	0	83	2		0	0	0	0	0	2	1	0.999512	13	365	0	83	2		0	0	0	0	83	2	-3.216127	1	1	0	0		1	2	2	4	2.350227	1	0.550000	3.150000	0.709677	0.190000	0.100000	0.320000	0.200000	0.204745	0.190000	0	1.400000e-01	2.600000e-01
WASF3	10810	broad.mit.edu	37	13	27239254	27239254	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr13:27239254C>A	ENST00000335327.5	+	4	401	c.223C>A	c.(223-225)Cgc>Agc	p.R75S	WASF3_ENST00000361042.4_Missense_Mutation_p.R75S|WASF3_ENST00000496788.1_3'UTR	NM_006646.5	NP_006637.2	Q9UPY6	WASF3_HUMAN	WAS protein family, member 3			22	Colorectal(5;0.000247)	Lung SC(185;0.0156)|Breast(139;0.147)			CAGAATTGATCGCCTTGCTGT	0.413000																								0							SO:0001583	missense			ENST00000335327.5	1	0	hg19	CCDS9318.1	.	.	.	.	.	.	.	.	.	.	C	28.9	4.956245	0.92726	.	.	ENSG00000132970	ENST00000361042;ENST00000335327	T;T	0.67523	-0.27;-0.27	5.64	5.64	0.86602	.	0.052354	0.85682	D	0.000000	T	0.77343	0.4116	M	0.79805	2.47	0.80722	D	1	P;P	0.50156	0.932;0.498	P;B	0.49387	0.609;0.318	T	0.79259	-0.1877	10	0.51188	T	0.08	-23.1243	19.6999	0.96048	0.0:1.0:0.0:0.0	.	75;75	Q86VQ2;Q9UPY6	.;WASF3_HUMAN	S	75	ENSP00000354325:R75S;ENSP00000335055:R75S	ENSP00000335055:R75S	R	+	1	0	WASF3	26137254	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	7.320000	0.79064	2.659000	0.90383	0.650000	0.86243	CGC		TCGA-IB-A7LX-01A-12D-A36O-08	WASF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044258.1	1	0	0	9	236	0	66	0	3.210462e-02	0	7	0	66	2		0	0	0	0	0	2	1	0.993916	9	231	0	65	2		0	0	0	0	66	2	-3.116152	1	1	0	0		1	2	2	4	2.350227	1	0.550000	3.150000	0.709677	0.210000	0.100000	0.370000	0.200000	0.227817	0.210000	0	1.500000e-01	3.000000e-01
FREM2	341640	broad.mit.edu	37	13	39452994	39452994	+	Silent	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr13:39452994G>T	ENST00000280481.7	+	23	9102	c.8886G>T	c.(8884-8886)gcG>gcT	p.A2962A		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2			148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)			AGACACAAGCGACCAGTTTTG	0.443000																								0							SO:0001819	synonymous_variant			ENST00000280481.7	1	0	hg19	CCDS31960.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	1	0	0	15	439	0	110	0	1.305232e-03	0	2	0	110	2		0	0	0	0	0	2	1	0.999856	15	430	0	110	2		0	0	0	0	110	2	-2.980733	1	1	0	0		1	2	2	4	2.350227	1	0.550000	3.150000	0.709677	0.180000	0.100000	0.300000	0.200000	0.197593	0.180000	0	1.400000e-01	2.500000e-01
NHLRC3	387921	broad.mit.edu	37	13	39616292	39616292	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr13:39616292C>A	ENST00000379600.3	+	4	758	c.436C>A	c.(436-438)Caa>Aaa	p.Q146K	NHLRC3_ENST00000470258.1_5'UTR|NHLRC3_ENST00000379599.2_Intron	NM_001012754.3	NP_001012772.1	Q5JS37	NHLC3_HUMAN	NHL repeat containing 3			11		Lung NSC(96;6.01e-07)|Breast(139;0.00394)|Prostate(109;0.00676)|Lung SC(185;0.0548)|Hepatocellular(188;0.114)			TGATCTTGTTCAAGTCTTGGG	0.338000																								0							SO:0001583	missense			ENST00000379600.3	1	0	hg19	CCDS31961.1	.	.	.	.	.	.	.	.	.	.	C	9.802	1.180739	0.21787	.	.	ENSG00000188811	ENST00000379600	T	0.45276	0.9	5.3	5.3	0.74995	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	T	0.48804	0.1520	L	0.42245	1.32	0.80722	D	1	P;D	0.56521	0.473;0.976	B;P	0.52343	0.056;0.696	T	0.36625	-0.9740	9	.	.	.	-10.6501	17.9281	0.88989	0.0:1.0:0.0:0.0	.	146;146	Q5JS37;B4DRC8	NHLC3_HUMAN;.	K	146	ENSP00000368920:Q146K	.	Q	+	1	0	NHLRC3	38514292	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	3.945000	0.56637	2.457000	0.83068	0.467000	0.42956	CAA		TCGA-IB-A7LX-01A-12D-A36O-08	NHLRC3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044616.2	1	0	0	17	384	0	91	0	4.728714e-01	0	36	0	91	2		0	0	0	0	0	2	1	0.999960	15	377	0	90	2		0	0	0	0	91	2	-4.523921	1	1	0	0		1	2	2	4	2.350227	1	0.550000	3.150000	0.709677	0.240000	0.130000	0.370000	0.240000	0.251497	0.240000	0	1.800000e-01	3.100000e-01
PCDH17	27253	broad.mit.edu	37	13	58298909	58298909	+	Silent	SNP	C	C	T	rs138830034	byFrequency	TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr13:58298909C>T	ENST00000377918.3	+	4	2987	c.2961C>T	c.(2959-2961)taC>taT	p.Y987Y		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)			CTGAGACTTACGAAACTGTGA	0.413000													Melanoma(72;952 1291 1619 12849 33676)											0							SO:0001819	synonymous_variant			ENST00000377918.3	1	1	hg19	CCDS31986.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	PCDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045139.1	1	0	1	97	203	0	83	0	8.812058e-01	0	10	0	83	2		0	0	0	0	0	2	1	1.000000	96	201	0	83	2		0	0	0	0	83	2	-2.879461	1	1	121410	85	52	1	2	2	4	2.350227	1	0.550000	3.150000	0.709677	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	9.900000e-01	1
OR11H6	122748	broad.mit.edu	37	14	20692623	20692623	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr14:20692623G>T	ENST00000315519.2	+	1	833	c.755G>T	c.(754-756)cGa>cTa	p.R252L		NM_001004480.1	NP_001004480.1	Q8NGC7	O11H6_HUMAN	olfactory receptor, family 11, subfamily H, member 6			29	all_cancers(95;0.00108)		Epithelial(56;1.75e-06)|all cancers(55;1.22e-05)		GGTGCTGGTCGAACTAAAGCT	0.483000																								0							SO:0001583	missense			ENST00000315519.2	1	0	hg19	CCDS32033.1	.	.	.	.	.	.	.	.	.	.	G	17.36	3.369552	0.61624	.	.	ENSG00000176219	ENST00000315519	T	0.00330	8.08	4.78	3.89	0.44902	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41500	D	0.000870	T	0.00666	0.0022	M	0.85462	2.755	0.09310	N	1	P	0.51449	0.945	P	0.56127	0.792	T	0.27673	-1.0067	10	0.72032	D	0.01	.	10.7593	0.46256	0.0939:0.0:0.9061:0.0	.	252	Q8NGC7	O11H6_HUMAN	L	252	ENSP00000319071:R252L	ENSP00000319071:R252L	R	+	2	0	OR11H6	19762463	0.000000	0.05858	0.878000	0.34440	0.949000	0.60115	0.442000	0.21628	1.223000	0.43536	0.471000	0.43371	CGA		TCGA-IB-A7LX-01A-12D-A36O-08	OR11H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410676.1	1	0	0	15	278	0	71		0	0	0	0	71	2		0	0	0	0	0	2	1	0.999866	15	273	0	71	2		0	0	0	0	71	2	-4.686283	1	1	0	0		1	2	2	4	2.243649	1	0.550000	3.150000	0.695637	0.290000	0.160000	1.000000	0.270000	0.365046	0.290000	0	2.100000e-01	4.100000e-01
TEP1	7011	broad.mit.edu	37	14	20841221	20841221	+	Silent	SNP	T	T	C			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08			T	C	T	T		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr14:20841221T>C	ENST00000262715.5	-	48	6940	c.6900A>G	c.(6898-6900)caA>caG	p.Q2300Q	TEP1_ENST00000556935.1_Silent_p.Q2192Q|TEP1_ENST00000545983.1_Silent_p.Q638Q	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1			96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)		GTTCCCCAGCTTGATTTCCAG	0.522000																								0							SO:0001819	synonymous_variant			ENST00000262715.5	1	1	hg19	CCDS9548.1	.	.	.	.	.	.	.	.	.	.	T	8.134	0.783739	0.16189	.	.	ENSG00000129566	ENST00000553984	.	.	.	5.77	0.76	0.18442	.	.	.	.	.	T	0.32041	0.0816	.	.	.	0.21719	N	0.999572	.	.	.	.	.	.	T	0.26849	-1.0091	4	.	.	.	-0.0235	7.2173	0.25967	0.0:0.4669:0.0:0.5331	.	.	.	.	G	7	.	.	S	-	1	0	TEP1	19911061	0.053000	0.20554	0.110000	0.21437	0.973000	0.67179	0.124000	0.15728	0.135000	0.18707	0.533000	0.62120	AGC		TCGA-IB-A7LX-01A-12D-A36O-08	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	1	0	1	91	178	0	69	1	9.999992e-01	21	24	0	69	2		0	0	0	0	0	2	1	1.000000	87	174	0	67	2		0	0	0	0	69	2	-20.000000	1	1	121412	1	34	1	2	2	4	2.243649	1	0.550000	3.150000	0.695637	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	9.900000e-01	1
AKAP6	9472	broad.mit.edu	37	14	33291486	33291486	+	Silent	SNP	C	C	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr14:33291486C>T	ENST00000280979.4	+	13	4637	c.4467C>T	c.(4465-4467)agC>agT	p.S1489S	AKAP6_ENST00000557272.1_Intron	NM_004274.4	NP_004265.3	Q13023	AKAP6_HUMAN	A kinase (PRKA) anchor protein 6			122	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)		AGTCACAAAGCGAAAAAGCGC	0.348000													Melanoma(49;821 1200 7288 13647 42351)											0							SO:0001819	synonymous_variant			ENST00000280979.4	1	1	hg19	CCDS9644.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	AKAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276617.2	1	0	1	86	190	0	73		0	0	0	0	73	2		0	0	0	0	0	2	1	1.000000	86	189	0	73	2		0	0	0	0	73	2	-20.000000	1	1	121390	7	38	1	2	2	4	2.243649	1	0.550000	3.150000	0.695637	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	9.900000e-01	1
ARID4A	5926	broad.mit.edu	37	14	58785281	58785281	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr14:58785281G>T	ENST00000355431.3	+	6	669	c.296G>T	c.(295-297)cGa>cTa	p.R99L	ARID4A_ENST00000431317.2_Missense_Mutation_p.R99L|ARID4A_ENST00000348476.3_Missense_Mutation_p.R99L|ARID4A_ENST00000395168.3_Missense_Mutation_p.R99L	NM_002892.3	NP_002883.3	P29374	ARI4A_HUMAN	AT rich interactive domain 4A (RBP1-like)			60					GGTGATGAGCGAACATTGAGA	0.378000																								0							SO:0001583	missense			ENST00000355431.3	1	0	hg19	CCDS9732.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.610945	0.87258	.	.	ENSG00000032219	ENST00000355431;ENST00000348476;ENST00000395168;ENST00000445108;ENST00000431317	T;T;T;T;T	0.38887	1.11;1.11;1.11;1.11;1.11	5.78	5.78	0.91487	Tudor domain (1);	0.041251	0.85682	D	0.000000	T	0.59622	0.2207	L	0.43923	1.385	0.53688	D	0.999977	D;D;D	0.76494	0.999;0.997;0.998	D;D;D	0.70935	0.971;0.954;0.97	T	0.59883	-0.7370	10	0.87932	D	0	-25.8845	20.0079	0.97439	0.0:0.0:1.0:0.0	.	99;99;99	P29374-3;P29374;P29374-2	.;ARI4A_HUMAN;.	L	99;99;99;62;99	ENSP00000347602:R99L;ENSP00000344556:R99L;ENSP00000378597:R99L;ENSP00000392567:R62L;ENSP00000397368:R99L	ENSP00000344556:R99L	R	+	2	0	ARID4A	57855034	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	6.001000	0.70685	2.722000	0.93159	0.655000	0.94253	CGA		TCGA-IB-A7LX-01A-12D-A36O-08	ARID4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276927.2	1	0	0	14	358	0	73	0	3.222530e-01	0	29	0	73	2		0	0	0	0	0	2	1	0.999733	12	353	0	71	2		0	0	0	0	73	2	-3.158608	1	1	0	0		1	2	2	4	2.243649	1	0.550000	3.150000	0.695637	0.210000	0.110000	1.000000	0.190000	0.297157	0.210000	0	1.500000e-01	3.100000e-01
MAP3K9	4293	broad.mit.edu	37	14	71216711	71216711	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr14:71216711C>A	ENST00000554752.2	-	4	1088	c.1089G>T	c.(1087-1089)atG>atT	p.M363I	MAP3K9_ENST00000553414.1_Missense_Mutation_p.M57I|MAP3K9_ENST00000554146.1_Missense_Mutation_p.M100I|MAP3K9_ENST00000381250.4_Missense_Mutation_p.M363I|MAP3K9_ENST00000555993.2_Missense_Mutation_p.M363I	NM_001284230.1	NP_001271159.1	P80192	M3K9_HUMAN	mitogen-activated protein kinase kinase kinase 9			46					CGAGTTTGTTCATGGCCACTC	0.507000													GBM(114;411 1587 13539 28235 50070)											0							SO:0001583	missense			ENST00000554752.2	1	0	hg19		.	.	.	.	.	.	.	.	.	.	C	21.9	4.221675	0.79464	.	.	ENSG00000006432	ENST00000554752;ENST00000005198;ENST00000553414;ENST00000381250;ENST00000554146;ENST00000542284	D;D;D;D	0.88896	-2.44;-2.44;-2.44;-2.44	5.91	5.02	0.67125	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.81202	0.4773	N	0.05554	-0.025	0.50632	D	0.999885	B;B;B;B	0.29188	0.022;0.236;0.198;0.198	B;B;B;B	0.37989	0.032;0.262;0.113;0.171	T	0.78272	-0.2268	10	0.33141	T	0.24	.	14.5088	0.67769	0.0:0.9302:0.0:0.0698	.	100;363;363;57	G3V4P9;P80192;P80192-4;G3V347	.;M3K9_HUMAN;.;.	I	363;363;57;363;100;91	ENSP00000451612:M363I;ENSP00000451038:M57I;ENSP00000370649:M363I;ENSP00000451921:M100I	ENSP00000005198:M363I	M	-	3	0	MAP3K9	70286464	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.115000	0.31209	2.808000	0.96608	0.655000	0.94253	ATG		TCGA-IB-A7LX-01A-12D-A36O-08	MAP3K9-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412550.2	1	0	0	14	316	0	68	0	1.467250e-01	0	15	0	68	2		0	0	0	0	0	2	1	0.999714	13	308	0	68	2		0	0	0	0	68	2	-3.196010	1	1	0	0		1	2	2	4	2.243649	1	0.550000	3.150000	0.695637	0.240000	0.120000	1.000000	0.220000	0.321530	0.240000	0	1.700000e-01	3.500000e-01
BATF	10538	broad.mit.edu	37	14	75989073	75989073	+	Silent	SNP	T	T	G			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08			T	G	T	T		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr14:75989073T>G	ENST00000286639.6	+	1	306	c.48T>G	c.(46-48)ccT>ccG	p.P16P	BATF_ENST00000555795.1_Intron|BATF_ENST00000555504.1_Silent_p.P16P	NM_006399.3	NP_006390.1	Q16520	BATF_HUMAN	basic leucine zipper transcription factor, ATF-like			3					GCCGCTCTCCTCCCCCTGGCA	0.587000																								0							SO:0001819	synonymous_variant			ENST00000286639.6	1	1	hg19	CCDS9843.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	BATF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413669.1	1	0	1	79	166	0	54	1	1	44	47	0	54	2		0	0	0	0	0	2	1	1.000000	77	164	0	54	2		0	0	0	0	54	2	-8.900294	1	1	0	0		1	2	2	4	2.243649	1	0.550000	3.150000	0.695637	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	9.900000e-01	1
ADAMTSL3	57188	broad.mit.edu	37	15	84683327	84683327	+	Missense_Mutation	SNP	G	G	C			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr15:84683327G>C	ENST00000286744.5	+	24	4231	c.4007G>C	c.(4006-4008)aGa>aCa	p.R1336T	ADAMTSL3_ENST00000567476.1_Missense_Mutation_p.R1336T	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	p.R1336I(1)		130			BRCA - Breast invasive adenocarcinoma(143;0.211)		TGGTTGAAGAGAGGAGGATCT	0.428000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000286744.5	1	1	hg19	CCDS10326.1	.	.	.	.	.	.	.	.	.	.	G	10.69	1.420685	0.25639	.	.	ENSG00000156218	ENST00000286744	T	0.27402	1.67	4.7	1.68	0.24146	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.739929	0.11659	N	0.541996	T	0.15696	0.0378	N	0.17082	0.46	0.26572	N	0.973534	B;B	0.09022	0.001;0.002	B;B	0.12837	0.008;0.007	T	0.31280	-0.9949	10	0.22109	T	0.4	.	4.2489	0.10684	0.4199:0.1664:0.4137:0.0	.	1336;1336	P82987-2;P82987	.;ATL3_HUMAN	T	1336	ENSP00000286744:R1336T	ENSP00000286744:R1336T	R	+	2	0	ADAMTSL3	82474331	1.000000	0.71417	0.999000	0.59377	0.986000	0.74619	0.900000	0.28431	0.048000	0.15891	-0.266000	0.10368	AGA		TCGA-IB-A7LX-01A-12D-A36O-08	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	1	0	0	35	593	0	182	0	4.274176e-02	0	6	0	182	2		0	0	0	0	0	2	1	1.000000	34	581	0	179	2		0	0	0	0	182	2	-5.808365	1	1	0	0		1	2	4	6	2.035251	1	0.550000	3.150000	0.667160	0.280000	0.190000	1.000000	0.270000	0.431600	0.280000	0	2.300000e-01	1
CPD	1362	broad.mit.edu	37	17	28747986	28747986	+	Silent	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr17:28747986C>A	ENST00000225719.4	+	3	1198	c.1122C>A	c.(1120-1122)atC>atA	p.I374I	CPD_ENST00000543464.2_Silent_p.I127I	NM_001304.4	NP_001295.2	O75976	CBPD_HUMAN	carboxypeptidase D			36					AGTCTTTGATCACATTGATTG	0.393000																								0							SO:0001819	synonymous_variant			ENST00000225719.4	1	0	hg19	CCDS11257.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	CPD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256214.3	1	0	0	12	246	0	69	0	9.087127e-01	0	88	0	69	2		0	0	0	0	0	2	1	0.999118	12	243	0	67	2		0	0	0	0	69	2	-3.217508	1	1	0	0		1	2	2	4	2.274668	1	0.550000	3.150000	0.700100	0.260000	0.130000	1.000000	0.260000	0.325280	0.260000	0	1.900000e-01	3.700000e-01
CCL7	6354	broad.mit.edu	37	17	32597292	32597292	+	Translation_Start_Site	SNP	A	A	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr17:32597292A>T	ENST00000378569.2	+	0	53				CCL7_ENST00000394630.3_De_novo_Start_InFrame|CCL7_ENST00000394627.1_De_novo_Start_InFrame|CCL7_ENST00000200307.4_Missense_Mutation_p.M5L	NM_006273.2	NP_006264.2	P80098	CCL7_HUMAN	chemokine (C-C motif) ligand 7			7	Breast(3;0.00224)	Breast(31;0.151)|Ovarian(249;0.17)			GTGGAAGCCCATGCCCTCACC	0.547000																								0											ENST00000378569.2	1	0	hg19	CCDS11278.1	.	.	.	.	.	.	.	.	.	.	A	0.081	-1.184197	0.01620	.	.	ENSG00000108688	ENST00000378569;ENST00000394630;ENST00000394627	.	.	.	3.89	0.269	0.15631	.	10.005000	0.00166	N	0.000004	T	0.18635	0.0447	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.12477	-1.0546	6	0.11182	T	0.66	.	5.9178	0.19065	0.5474:0.0:0.4526:0.0	.	.	.	.	L	5	.	ENSP00000367832:M5L	M	+	1	0	CCL7	29621405	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-2.026000	0.01434	-0.061000	0.13110	0.528000	0.53228	ATG		TCGA-IB-A7LX-01A-12D-A36O-08	CCL7-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256386.2	0	0	1	60	89	0	50		0	0	0	0	50	2		0	0	0	0	0	2	1	1.000000	57	87	0	50	2		0	0	0	0	50	2	-20.000000	1	1	0	0		1	2	2	4	2.274668	1	0.550000	3.150000	0.700100	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	9.900000e-01	1
AP2B1	163	broad.mit.edu	37	17	33954701	33954701	+	Silent	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08			C	A	C	C		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr17:33954701C>A	ENST00000262325.7	+	9	1664	c.1111C>A	c.(1111-1113)Cga>Aga	p.R371R	AP2B1_ENST00000589344.1_Silent_p.R371R|AP2B1_ENST00000538556.1_Silent_p.R314R|AP2B1_ENST00000312678.8_Silent_p.R371R|AP2B1_ENST00000592545.1_Silent_p.R333R|AP2B1_ENST00000545922.2_3'UTR|AP2B1_ENST00000537622.2_Silent_p.R371R	NM_001282.2	NP_001273.1	P63010	AP2B1_HUMAN	adaptor-related protein complex 2, beta 1 subunit	p.R371*(1)		28		Ovarian(249;0.17)			TGACTTTGTTCGAAAAGCTGT	0.443000																								1	Substitution - Nonsense(1)						SO:0001819	synonymous_variant			ENST00000262325.7	1	0	hg19	CCDS32622.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	AP2B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448969.1	1	0	0	13	269	0	65	0	9.989629e-01	0	246	0	65	2		0	0	0	0	0	2	1	0.999535	13	266	0	63	2		0	0	0	0	65	2	-2.806910	1	1	0	0		1	2	2	4	2.274668	1	0.550000	3.150000	0.700100	0.260000	0.140000	1.000000	0.260000	0.321758	0.260000	0	1.900000e-01	3.700000e-01
TOP2A	7153	broad.mit.edu	37	17	38564239	38564239	+	Silent	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr17:38564239G>T	ENST00000423485.1	-	12	1638	c.1480C>A	c.(1480-1482)Cga>Aga	p.R494R		NM_001067.3	NP_001058.2	P11388	TOP2A_HUMAN	topoisomerase (DNA) II alpha 170kDa			39		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00183)	Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385)	GAAGCTTCTCGAACATTGAGT	0.368000																								0							SO:0001819	synonymous_variant			ENST00000423485.1	1	0	hg19	CCDS45672.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	TOP2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338035.1	1	0	0	21	469	0	102	0	8.623733e-01	0	81	0	102	2		0	0	0	0	0	2	1	0.999997	21	466	0	101	2		0	0	0	0	102	2	-3.071207	1	1	0	0		1	2	2	4	2.267005	1	0.550000	3.150000	0.698997	0.240000	0.140000	1.000000	0.230000	0.304127	0.240000	0	1.800000e-01	3.200000e-01
KRT28	162605	broad.mit.edu	37	17	38949428	38949428	+	Missense_Mutation	SNP	T	T	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr17:38949428T>A	ENST00000306658.7	-	7	1296	c.1231A>T	c.(1231-1233)Agc>Tgc	p.S411C		NM_181535.3	NP_853513.2			keratin 28			30		Breast(137;0.000301)			TTCCCAGGGCTTCCTGATCCA	0.313000													Melanoma(19;789 869 15380 26882 39836)											0							SO:0001583	missense			ENST00000306658.7	1	1	hg19	CCDS11376.1	.	.	.	.	.	.	.	.	.	.	T	14.22	2.471242	0.43942	.	.	ENSG00000173908	ENST00000306658	D	0.83419	-1.72	5.35	0.343	0.16001	.	0.768911	0.12060	N	0.503255	T	0.76586	0.4008	L	0.38175	1.15	0.22081	N	0.999376	P	0.35192	0.489	B	0.41299	0.353	T	0.66968	-0.5789	10	0.62326	D	0.03	.	7.4993	0.27509	0.0:0.4287:0.0:0.5713	.	411	Q7Z3Y7	K1C28_HUMAN	C	411	ENSP00000305263:S411C	ENSP00000305263:S411C	S	-	1	0	KRT28	36202954	0.023000	0.18921	0.940000	0.37924	0.992000	0.81027	-0.298000	0.08265	0.108000	0.17862	0.533000	0.62120	AGC		TCGA-IB-A7LX-01A-12D-A36O-08	KRT28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257201.2	1	0	1	55	296	0	77		0	0	0	0	77	2		0	0	0	0	0	2	1	1.000000	54	287	0	77	2		0	0	0	0	77	2	-20.000000	1	1	0	0		1	2	2	4	2.267005	1	0.550000	3.150000	0.698997	0.860000	0.660000	1.000000	1.000000	0.867460	0.860000	1	7.500000e-01	1
HEATR6	63897	broad.mit.edu	37	17	58128258	58128258	+	Silent	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr17:58128258C>A	ENST00000184956.6	-	15	2386	c.2370G>T	c.(2368-2370)gcG>gcT	p.A790A	HEATR6_ENST00000585976.1_Intron	NM_022070.4	NP_071353.4	Q6AI08	HEAT6_HUMAN	HEAT repeat containing 6			44	all_cancers(5;2.25e-13)|Breast(5;4.84e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		BRCA - Breast invasive adenocarcinoma(1;5.93e-19)|Epithelial(12;7.59e-12)|all cancers(12;1.26e-10)		CACAGGCGCTCGCCTGGAGAG	0.532000																								0							SO:0001819	synonymous_variant			ENST00000184956.6	1	0	hg19	CCDS11623.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	HEATR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449165.1	1	0	0	10	235	0	55	0	2.734309e-01	0	22	0	55	2		0	0	0	0	0	2	1	0.996991	10	234	0	53	2		0	0	0	0	55	2	-2.802442	1	1	0	0		1	2	2	4	2.231336	1	0.550000	3.150000	0.694501	0.230000	0.110000	1.000000	0.220000	0.323144	0.230000	0	1.600000e-01	3.600000e-01
CHD3	1107	broad.mit.edu	37	17	7794350	7794350	+	Silent	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08			C	A	C	C		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr17:7794350C>A	ENST00000330494.7	+	4	627	c.477C>A	c.(475-477)ctC>ctA	p.L159L	CHD3_ENST00000358181.4_Silent_p.L159L|CHD3_ENST00000380358.4_Silent_p.L218L	NM_001005273.2	NP_001005273.1	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3			65		Prostate(122;0.202)			ACCACACGCTCACCAACTACA	0.527000																								0							SO:0001819	synonymous_variant			ENST00000330494.7	1	0	hg19	CCDS32554.1	.	.	.	.	.	.	.	.	.	.	C	9.430	1.085307	0.20390	.	.	ENSG00000170004	ENST00000452447	.	.	.	4.54	-3.21	0.05140	.	.	.	.	.	T	0.40222	0.1108	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.34750	-0.9816	4	.	.	.	-15.2706	3.1578	0.06510	0.1046:0.1724:0.1951:0.5278	.	.	.	.	N	34	.	.	H	+	1	0	CHD3	7735075	0.764000	0.28473	0.974000	0.42286	0.988000	0.76386	-0.190000	0.09615	-0.301000	0.08882	-0.259000	0.10710	CAC		TCGA-IB-A7LX-01A-12D-A36O-08	CHD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318050.1	1	0	0	25	535	0	137	0	9.948179e-01	0	176	0	137	2		0	0	0	0	0	2	1	1.000000	24	529	0	133	2		0	0	0	0	137	2	-3.018473	1	1	0	0		1	1	2	3	1.950712	1	0.550000	3.150000	0.647059	0.200000	0.130000	0.300000	0.210000	0.214279	0.200000	0	1.600000e-01	2.500000e-01
MYH10	4628	broad.mit.edu	37	17	8439125	8439125	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr17:8439125C>A	ENST00000269243.4	-	14	1838	c.1700G>T	c.(1699-1701)cGa>cTa	p.R567L	MYH10_ENST00000360416.3_Missense_Mutation_p.R577L|MYH10_ENST00000396239.1_Missense_Mutation_p.R567L|MYH10_ENST00000379980.4_Missense_Mutation_p.R583L	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle			52					TTTTAATTGTCGAGGTTTCTG	0.368000																								0							SO:0001583	missense			ENST00000269243.4	1	0	hg19	CCDS11144.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.182476	0.78677	.	.	ENSG00000133026	ENST00000269243;ENST00000360416;ENST00000396239;ENST00000379980	T;T;D;T	0.88509	-0.74;-0.74;-2.39;-0.74	5.29	5.29	0.74685	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	D	0.94997	0.8381	M	0.90977	3.165	0.58432	D	0.99999	P;P;P	0.51057	0.941;0.928;0.941	P;P;P	0.56751	0.805;0.705;0.805	D	0.95680	0.8731	10	0.87932	D	0	.	19.1238	0.93374	0.0:1.0:0.0:0.0	.	576;577;567	B2RWP9;F8VTL3;P35580	.;.;MYH10_HUMAN	L	567;577;567;583	ENSP00000269243:R567L;ENSP00000353590:R577L;ENSP00000379539:R567L;ENSP00000369315:R583L	ENSP00000269243:R567L	R	-	2	0	MYH10	8379850	0.401000	0.25303	0.999000	0.59377	0.542000	0.35054	3.206000	0.51098	2.752000	0.94435	0.557000	0.71058	CGA		TCGA-IB-A7LX-01A-12D-A36O-08	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2	1	0	0	14	413	0	109	0	5.657491e-02	0	11	0	109	2		0	0	0	0	0	2	1	0.999739	14	407	0	109	2		0	0	0	0	109	2	-3.256806	1	1	0	0		1	1	2	3	1.950712	1	0.550000	3.150000	0.647059	0.150000	0.080000	0.250000	0.150000	0.161897	0.150000	0	1.100000e-01	2.000000e-01
DSG2	1829	broad.mit.edu	37	18	29115333	29115333	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08			C	A	C	C		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr18:29115333C>A	ENST00000261590.8	+	10	1590	c.1381C>A	c.(1381-1383)Caa>Aaa	p.Q461K		NM_001943.3	NP_001934.2	Q14126	DSG2_HUMAN	desmoglein 2			49			OV - Ovarian serous cystadenocarcinoma(10;0.0068)		TAGATATGTTCAAAATGGCAC	0.279000																								0							SO:0001583	missense			ENST00000261590.8	1	0	hg19	CCDS42423.1	.	.	.	.	.	.	.	.	.	.	C	10.63	1.405016	0.25378	.	.	ENSG00000046604	ENST00000261590	T	0.59906	0.23	5.66	2.39	0.29439	Cadherin (4);Cadherin-like (1);	1.115670	0.06754	N	0.780562	T	0.32971	0.0847	N	0.05554	-0.025	0.09310	N	1	B	0.17667	0.023	B	0.15052	0.012	T	0.14839	-1.0458	10	0.02654	T	1	.	8.9226	0.35621	0.4051:0.4015:0.1934:0.0	.	461	Q14126	DSG2_HUMAN	K	461	ENSP00000261590:Q461K	ENSP00000261590:Q461K	Q	+	1	0	DSG2	27369331	0.000000	0.05858	0.955000	0.39395	0.836000	0.47400	-0.080000	0.11339	0.663000	0.31027	0.462000	0.41574	CAA		TCGA-IB-A7LX-01A-12D-A36O-08	DSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447506.1	1	0	0	22	468	0	170	0	9.998950e-01	0	312	0	170	2		0	0	0	0	0	2	1	0.999999	22	461	0	169	2		0	0	0	0	170	2	-3.210889	1	1	0	0		1	0	3	3	1.685847	1	0.550000	3.150000	0.626091	0.200000	0.120000	1.000000	0.190000	0.350999	0.200000	0	1.600000e-01	1
SLC14A2	8170	broad.mit.edu	37	18	43224013	43224013	+	Silent	SNP	G	G	T	rs149835341		TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr18:43224013G>T	ENST00000255226.6	+	10	2055	c.1239G>T	c.(1237-1239)acG>acT	p.T413T	SLC14A2_ENST00000586448.1_Silent_p.T413T|RP11-116O18.1_ENST00000590535.1_RNA	NM_007163.3	NP_009094.3	Q15849	UT2_HUMAN	solute carrier family 14 (urea transporter), member 2			63					TGCTCCTGACGACAAACAACC	0.542000																								0							SO:0001819	synonymous_variant			ENST00000255226.6	1	0	hg19	CCDS11924.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	SLC14A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255858.1	1	0	0	14	373	0	148		0	0	0	0	148	2		0	0	0	0	0	2	1	0.999753	14	370	0	148	2		0	0	0	0	148	2	-2.841885	1	1	0	0		1	0	3	3	1.685847	1	0.550000	3.150000	0.626091	0.170000	0.080000	1.000000	0.160000	0.321760	0.170000	0	1.200000e-01	1
ZNF491	126069	broad.mit.edu	37	19	11918032	11918032	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr19:11918032C>A	ENST00000323169.5	+	3	1595	c.1264C>A	c.(1264-1266)Cgt>Agt	p.R422S	ZNF491_ENST00000492230.1_Intron	NM_152356.3	NP_689569.2	Q8N8L2	ZN491_HUMAN	zinc finger protein 491			26					AGCCTTCATTCGTTCCAGTTA	0.333000																								0							SO:0001583	missense			ENST00000323169.5	1	0	hg19	CCDS12267.1	.	.	.	.	.	.	.	.	.	.	c	0.278	-0.988536	0.02162	.	.	ENSG00000177599	ENST00000323169;ENST00000455048	T	0.60424	0.19	0.737	-0.437	0.12272	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.32071	0.0817	N	0.13003	0.285	0.09310	N	1	B	0.20052	0.041	B	0.10450	0.005	T	0.14062	-1.0486	9	0.32370	T	0.25	.	2.3692	0.04326	0.2684:0.4281:0.0:0.3035	.	422	Q8N8L2	ZN491_HUMAN	S	422;394	ENSP00000313443:R422S	ENSP00000313443:R422S	R	+	1	0	ZNF491	11779032	0.000000	0.05858	0.002000	0.10522	0.085000	0.17905	-0.354000	0.07681	-0.163000	0.10946	-0.451000	0.05528	CGT		TCGA-IB-A7LX-01A-12D-A36O-08	ZNF491-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344518.1	1	0	0	10	244	0	66	0	0	0	1	0	66	2		0	0	0	0	0	2	1	0.996451	9	236	0	66	2		0	0	0	0	66	2	-3.087178	1	1	0	0		1	1	2	3	1.925710	1	0.550000	3.150000	0.647059	0.180000	0.090000	0.320000	0.180000	0.198787	0.180000	0	1.300000e-01	2.600000e-01
PLVAP	83483	broad.mit.edu	37	19	17488061	17488061	+	Silent	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr19:17488061G>T	ENST00000252590.4	-	1	98	c.37C>A	c.(37-39)Cgg>Agg	p.R13R		NM_031310.1	NP_112600.1	Q9BX97	PLVAP_HUMAN	plasmalemma vesicle associated protein			27					CCCCCCGCCCGAGCGTAGGAC	0.652000																								0							SO:0001819	synonymous_variant			ENST00000252590.4	1	0	hg19	CCDS32952.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	PLVAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463655.1	1	0	0	12	316	0	83	0	9.514635e-01	0	138	0	83	2		0	0	0	0	0	2	1	0.999076	12	311	0	83	2		0	0	0	0	83	2	-2.789037	1	1	0	0		1	2	4	6	2.114927	1	0.550000	3.150000	0.677650	0.210000	0.100000	1.000000	0.180000	0.377920	0.210000	0	1.400000e-01	1
ZNF99	7652	broad.mit.edu	37	19	22940990	22940990	+	Missense_Mutation	SNP	A	A	C			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr19:22940990A>C	ENST00000596209.1	-	4	1811	c.1721T>G	c.(1720-1722)tTt>tGt	p.F574C	ZNF99_ENST00000397104.3_Missense_Mutation_p.F483C	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99			124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)			AGATTGCTTAAAAGCTTTGCC	0.368000																								0							SO:0001583	missense			ENST00000596209.1	1	1	hg19	CCDS59369.1	.	.	.	.	.	.	.	.	.	.	-	10.29	1.308831	0.23821	.	.	ENSG00000213973	ENST00000397104	T	0.45668	0.89	1.44	0.101	0.14517	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.63570	0.2522	M	0.88377	2.95	0.09310	N	1	D	0.89917	1.0	D	0.91635	0.999	T	0.51348	-0.8717	9	0.66056	D	0.02	.	5.428	0.16438	0.7506:0.0:0.0:0.2493	.	483	A8MXY4	ZNF99_HUMAN	C	483	ENSP00000380293:F483C	ENSP00000380293:F483C	F	-	2	0	ZNF99	22732830	0.978000	0.34361	0.001000	0.08648	0.011000	0.07611	4.718000	0.61930	-0.219000	0.10003	0.163000	0.16589	TTT		TCGA-IB-A7LX-01A-12D-A36O-08	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	1	0	1	114	177	0	104		0	0	0	0	104	2		0	0	0	0	0	2	1	1.000000	112	175	0	103	2		0	0	0	0	104	2	-20.000000	1	1	0	0		1	2	4	6	2.027318	1	0.550000	3.150000	0.664430	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	9.900000e-01	1
FCGBP	8857	broad.mit.edu	37	19	40433627	40433627	+	Silent	SNP	G	G	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr19:40433627G>A	ENST00000221347.6	-	2	649	c.642C>T	c.(640-642)gtC>gtT	p.V214V		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein			165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)		TACTAGCTGTGACCTTTGACC	0.562000																								0							SO:0001819	synonymous_variant			ENST00000221347.6	1	1	hg19	CCDS12546.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	1	0	0	18	252	0	83	0	1.446437e-02	0	3	0	83	2		0	0	0	0	0	2	1	0.999982	18	248	0	82	2		0	0	0	0	83	2	-19.989210	1	1	0	0		1	1	2	3	1.979295	1	0.550000	3.150000	0.647059	0.310000	0.180000	0.470000	0.300000	0.323208	0.310000	0	2.400000e-01	3.900000e-01
BLOC1S3	388552	broad.mit.edu	37	19	45682658	45682658	+	Missense_Mutation	SNP	A	A	C			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr19:45682658A>C	ENST00000433642.2	+	2	200	c.104A>C	c.(103-105)gAg>gCg	p.E35A	BLOC1S3_ENST00000587722.1_Missense_Mutation_p.E35A|TRAPPC6A_ENST00000006275.4_5'Flank|TRAPPC6A_ENST00000592647.1_5'Flank|AC005779.2_ENST00000593083.1_5'Flank|TRAPPC6A_ENST00000585934.1_5'Flank|TRAPPC6A_ENST00000588062.1_5'Flank	NM_212550.3	NP_997715.1	Q6QNY0	BL1S3_HUMAN	biogenesis of lysosomal organelles complex-1, subunit 3			2		Ovarian(192;0.0728)|all_neural(266;0.112)			TCCTCGTCGGAGGAGGAGGAG	0.761000									Hermansky-Pudlak syndrome															0							SO:0001583	missense	Familial Cancer Database	HPS, HPS1-8	ENST00000433642.2	0	1	hg19	CCDS12656.1	.	.	.	.	.	.	.	.	.	.	A	13.92	2.381951	0.42207	.	.	ENSG00000189114	ENST00000433642	.	.	.	2.93	1.77	0.24775	.	0.624228	0.12947	N	0.426136	T	0.16642	0.0400	N	0.08118	0	0.26487	N	0.975019	B	0.28128	0.201	B	0.20767	0.031	T	0.13980	-1.0489	9	0.62326	D	0.03	.	6.2471	0.20825	0.7472:0.2528:0.0:0.0	.	35	Q6QNY0	BL1S3_HUMAN	A	35	.	ENSP00000393840:E35A	E	+	2	0	BLOC1S3	50374498	0.697000	0.27767	0.994000	0.49952	0.982000	0.71751	0.657000	0.24963	1.121000	0.41925	0.374000	0.22700	GAG		TCGA-IB-A7LX-01A-12D-A36O-08	BLOC1S3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457559.1	1	0	0	18	23	0	9	1	9.874824e-01	5	8	0	9	2		0	0	0	0	0	2	1	0.999998	18	23	0	8	2		0	0	0	0	9	2	-20.000000	1	1	119586	6	35	1	1	2	3	1.979295	1	0.550000	3.150000	0.647059	0.990000	0.990000	1.000000	1.000000	0.999957	0.990000	1	9.900000e-01	1
ZNF256	10172	broad.mit.edu	37	19	58453311	58453311	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr19:58453311G>T	ENST00000282308.3	-	3	1061	c.865C>A	c.(865-867)Cac>Aac	p.H289N	ZNF256_ENST00000598928.1_3'UTR	NM_005773.2	NP_005764.2	Q9Y2P7	ZN256_HUMAN	zinc finger protein 256			19		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)			ACTCCAGTGTGAATTCTTCGG	0.393000													NSCLC(55;1313 1552 8040 11996)											0							SO:0001583	missense			ENST00000282308.3	1	0	hg19	CCDS12966.1	.	.	.	.	.	.	.	.	.	.	.	23.0	4.368789	0.82463	.	.	ENSG00000152454	ENST00000282308	T	0.67345	-0.26	3.13	2.07	0.26955	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.81795	0.4898	M	0.89287	3.02	0.28223	N	0.926444	D	0.76494	0.999	D	0.73708	0.981	T	0.72047	-0.4408	9	0.87932	D	0	.	9.0328	0.36269	0.1174:0.0:0.8826:0.0	.	289	Q9Y2P7	ZN256_HUMAN	N	289	ENSP00000282308:H289N	ENSP00000282308:H289N	H	-	1	0	ZNF256	63145123	1.000000	0.71417	0.247000	0.24249	0.980000	0.70556	3.300000	0.51834	0.639000	0.30564	0.460000	0.39030	CAC		TCGA-IB-A7LX-01A-12D-A36O-08	ZNF256-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466702.1	1	0	0	17	441	0	153	0	1.477809e-02	0	5	0	153	2		0	0	0	0	0	2	1	0.999964	17	437	0	152	2		0	0	0	0	153	2	-4.132772	1	1	0	0		1	1	2	3	1.990465	1	0.550000	3.150000	0.647059	0.170000	0.090000	0.270000	0.180000	0.181201	0.170000	0	1.300000e-01	2.200000e-01
C19orf18	147685	broad.mit.edu	37	19	58477954	58477954	+	Silent	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr19:58477954C>A	ENST00000314391.3	-	4	416	c.315G>T	c.(313-315)tcG>tcT	p.S105S		NM_152474.4	NP_689687.1	Q8NEA5	CS018_HUMAN	chromosome 19 open reading frame 18			8		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)			AGGCTACGCTCGAAATTAAAA	0.348000																								0							SO:0001819	synonymous_variant			ENST00000314391.3	1	0	hg19	CCDS12967.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	C19orf18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466704.1	1	0	0	12	308	0	72	0	0	0	1	0	72	2		0	0	0	0	0	2	1	0.999094	11	305	0	72	2		0	0	0	0	72	2	-2.803158	1	1	0	0		1	1	2	3	1.990465	1	0.550000	3.150000	0.647059	0.170000	0.090000	0.290000	0.180000	0.186858	0.170000	0	1.300000e-01	2.400000e-01
ZNF606	80095	broad.mit.edu	37	19	58490276	58490276	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr19:58490276G>A	ENST00000341164.4	-	7	2392	c.1772C>T	c.(1771-1773)aCg>aTg	p.T591M	ZNF606_ENST00000536132.1_Missense_Mutation_p.T501M	NM_025027.3	NP_079303.2	Q8WXB4	ZN606_HUMAN	zinc finger protein 606			26		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)			TTTCTCTCCCGTGTGAGTTCT	0.418000																								0							SO:0001583	missense			ENST00000341164.4	1	1	hg19	CCDS12968.1	.	.	.	.	.	.	.	.	.	.	G	14.81	2.647444	0.47258	.	.	ENSG00000166704	ENST00000341164;ENST00000536132	T;T	0.26373	1.74;1.74	4.91	4.91	0.64330	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.134588	0.34676	N	0.003775	T	0.53530	0.1802	M	0.79926	2.475	0.46416	D	0.999034	D	0.89917	1.0	D	0.68765	0.96	T	0.58973	-0.7541	10	0.87932	D	0	.	17.3812	0.87405	0.0:0.0:1.0:0.0	.	591	Q8WXB4	ZN606_HUMAN	M	591;501	ENSP00000343617:T591M;ENSP00000445624:T501M	ENSP00000343617:T591M	T	-	2	0	ZNF606	63182088	0.994000	0.37717	0.995000	0.50966	0.976000	0.68499	2.147000	0.42226	2.706000	0.92434	0.561000	0.74099	ACG		TCGA-IB-A7LX-01A-12D-A36O-08	ZNF606-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405961.1	0	0	0	13	387	1	116	0	1.740299e-02	0	6	1	116	2		0	0	0	0	0	2	1	0.999461	12	377	0	113	2		0	0	0	1	116	2	-2.695491	1	1	121412	1	29	1	1	2	3	1.990465	1	0.550000	3.150000	0.647059	0.150000	0.070000	0.250000	0.150000	0.161239	0.150000	0	1.100000e-01	2.000000e-01
GPSM2	29899	broad.mit.edu	37	1	109428193	109428193	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr1:109428193C>A	ENST00000406462.2	+	3	822	c.49C>A	c.(49-51)Cgt>Agt	p.R17S	AKNAD1_ENST00000357393.4_Intron|GPSM2_ENST00000264126.3_Missense_Mutation_p.R17S			P81274	GPSM2_HUMAN	G-protein signaling modulator 2			14		all_epithelial(167;7.64e-05)|all_lung(203;0.000321)|Lung NSC(277;0.000626)			TTTTCATGTTCGTTACAGGTA	0.294000																								0							SO:0001583	missense			ENST00000406462.2	1	0	hg19	CCDS792.2	.	.	.	.	.	.	.	.	.	.	C	18.06	3.538254	0.65085	.	.	ENSG00000121957	ENST00000406462;ENST00000435987;ENST00000264126;ENST00000435475;ENST00000446797	D;D;D	0.93189	-3.18;-2.38;-3.18	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	T	0.78413	0.4279	N	0.03608	-0.345	0.39307	D	0.965015	P	0.43024	0.798	B	0.34779	0.189	D	0.84184	0.0441	10	0.46703	T	0.11	-5.4334	18.2007	0.89836	0.0:1.0:0.0:0.0	.	17	P81274	GPSM2_HUMAN	S	17	ENSP00000385510:R17S;ENSP00000408664:R17S;ENSP00000264126:R17S	ENSP00000264126:R17S	R	+	1	0	GPSM2	109229716	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.317000	0.65822	2.801000	0.96364	0.650000	0.86243	CGT		TCGA-IB-A7LX-01A-12D-A36O-08	GPSM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032400.3	1	0	0	26	548	0	174	0	2.066676e-01	0	18	0	174	2		0	0	0	0	0	2	1	1.000000	26	547	0	174	2		0	0	0	0	174	2	-3.914346	1	1	0	0		1	0	2	2	1.629647	1	0.550000	3.150000	0.550000	0.160000	0.100000	0.230000	0.160000	0.170195	0.160000	0	1.300000e-01	2.000000e-01
PHTF1	10745	broad.mit.edu	37	1	114280825	114280825	+	Silent	SNP	G	G	T	rs78000844		TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr1:114280825G>T	ENST00000369604.1	-	5	721	c.238C>A	c.(238-240)Cga>Aga	p.R80R	PHTF1_ENST00000393357.2_Silent_p.R80R|PHTF1_ENST00000447664.2_Silent_p.R80R|PHTF1_ENST00000369596.2_Intron|PHTF1_ENST00000357783.2_Silent_p.R80R|PHTF1_ENST00000369598.1_Silent_p.R80R|PHTF1_ENST00000369600.1_Intron			Q9UMS5	PHTF1_HUMAN	putative homeodomain transcription factor 1			27	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05)			AATACAACTCGAACAAGCCCC	0.358000																								0							SO:0001819	synonymous_variant			ENST00000369604.1	1	0	hg19	CCDS861.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	PHTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032666.1	1	0	0	11	207	0	85	0	1.971210e-01	0	15	0	85	2		0	0	0	0	0	2	1	0.998293	11	203	0	85	2		0	0	0	0	85	2	-4.545072	1	1	0	0		1	0	2	2	1.629647	1	0.550000	3.150000	0.550000	0.180000	0.090000	0.310000	0.180000	0.197590	0.180000	0	1.300000e-01	2.500000e-01
PTCHD2	57540	broad.mit.edu	37	1	11561859	11561859	+	Silent	SNP	C	C	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr1:11561859C>T	ENST00000294484.6	+	2	948	c.810C>T	c.(808-810)caC>caT	p.H270H	PTCHD2_ENST00000389575.3_Silent_p.H270H	NM_020780.1	NP_065831.1	Q9P2K9	PTHD2_HUMAN	patched domain containing 2			76	Ovarian(185;0.249)	Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)			CTCAGACGCACGCGCACTGGC	0.677000																								0							SO:0001819	synonymous_variant			ENST00000294484.6	1	1	hg19	CCDS41247.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	PTCHD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000005770.2	1	0	1	49	24	0	20		0	0	0	0	20	2		0	0	0	0	0	2	1	1.000000	47	24	0	19	2		0	0	0	0	20	2	-20.000000	1	1	0	0		1	0	3	3	1.682210	1	0.550000	3.150000	0.625234	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	9.900000e-01	1
SPAG17	200162	broad.mit.edu	37	1	118609502	118609502	+	Silent	SNP	C	C	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr1:118609502C>T	ENST00000336338.5	-	18	2471	c.2406G>A	c.(2404-2406)aaG>aaA	p.K802K		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17			123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)			ACCTATATTGCTTATGGGCTT	0.358000																								0							SO:0001819	synonymous_variant			ENST00000336338.5	1	1	hg19	CCDS899.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	1	0	1	159	130	0	121		0	0	0	0	121	2		0	0	0	0	0	2	1	1.000000	158	129	0	120	2		0	0	0	0	121	2	-20.000000	1	1	0	0		1	0	2	2	1.629647	1	0.550000	3.150000	0.550000	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	9.900000e-01	1
VPS13D	55187	broad.mit.edu	37	1	12383813	12383813	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr1:12383813C>A	ENST00000358136.3	+	35	8096	c.7966C>A	c.(7966-7968)Cgc>Agc	p.R2656S	VPS13D_ENST00000356315.4_Missense_Mutation_p.R2656S	NM_015378.2	NP_056193.2			vacuolar protein sorting 13 homolog D (S. cerevisiae)			130	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)			GGATGATTGTCGCAAAGCTCT	0.383000																								0							SO:0001583	missense			ENST00000358136.3	1	0	hg19	CCDS30588.1	.	.	.	.	.	.	.	.	.	.	C	17.58	3.424276	0.62733	.	.	ENSG00000048707	ENST00000356315;ENST00000358136	T;T	0.25749	1.78;1.78	5.61	5.61	0.85477	Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote (2);Ubiquitin-associated/translation elongation factor EF1B, N-terminal (1);UBA-like (1);	0.073997	0.52532	D	0.000062	T	0.45216	0.1331	M	0.64404	1.975	0.80722	D	1	D;B;B	0.62365	0.991;0.388;0.442	D;B;B	0.64595	0.927;0.088;0.142	T	0.20806	-1.0264	10	0.08179	T	0.78	.	19.6336	0.95721	0.0:1.0:0.0:0.0	.	563;2656;2656	B1AJZ2;Q5THJ4-2;Q5THJ4	.;.;VP13D_HUMAN	S	2656	ENSP00000348666:R2656S;ENSP00000350854:R2656S	ENSP00000348666:R2656S	R	+	1	0	VPS13D	12306400	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.089000	0.64492	2.646000	0.89796	0.637000	0.83480	CGC		TCGA-IB-A7LX-01A-12D-A36O-08	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	1	0	0	18	387	0	125	0	3.254422e-01	0	24	0	125	2		0	0	0	0	0	2	1	0.999981	17	381	0	123	2		0	0	0	0	125	2	-3.658427	1	1	0	0		1	0	3	3	1.682210	1	0.550000	3.150000	0.625234	0.200000	0.110000	1.000000	0.190000	0.354122	0.200000	0	1.500000e-01	1
THBS3	7059	broad.mit.edu	37	1	155170966	155170966	+	Silent	SNP	G	G	A	rs150820199	byFrequency	TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr1:155170966G>A	ENST00000368378.3	-	12	1379	c.1359C>T	c.(1357-1359)aaC>aaT	p.N453N	RP11-263K19.4_ENST00000447623.1_RNA|THBS3_ENST00000541990.1_De_novo_Start_OutOfFrame|THBS3_ENST00000486260.1_5'UTR|RP11-263K19.4_ENST00000422665.1_RNA|THBS3_ENST00000457183.2_Silent_p.N333N|RP11-263K19.4_ENST00000436772.1_RNA|RP11-263K19.4_ENST00000454348.1_RNA|THBS3_ENST00000541576.1_Intron|RP11-263K19.4_ENST00000430312.1_RNA|RP11-263K19.4_ENST00000453136.1_RNA	NM_001252607.1|NM_007112.4	NP_001239536.1|NP_009043.1	P49746	TSP3_HUMAN	thrombospondin 3	p.N453N(1)		48	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)		TCCCACACACGTTCCCATTCC	0.567000																								1	Substitution - coding silent(1)						SO:0001819	synonymous_variant			ENST00000368378.3	0	1	hg19	CCDS1099.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	THBS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086856.1	0	0	0	8	480	0	112	1	5.365262e-01	4	98	0	112	2		0	0	0	0	0	2	1	0.989030	8	475	0	111	2		0	0	0	0	112	2	-2.825541	1	0	121412	11	43	1	0	9	9	2.571479	1	0.550000	3.150000	0.728015	0.110000	0.030000	1.000000	0.090000	0.303379	0.110000	0	7.000000e-02	1
TPR	7175	broad.mit.edu	37	1	186304589	186304589	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr1:186304589G>T	ENST00000367478.4	-	34	5088	c.4792C>A	c.(4792-4794)Cgc>Agc	p.R1598S		NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein			123		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)			GCAGTAATGCGAACATCCAAT	0.423000			T	NTRK1	papillary thyroid										Dom	yes		1	1q25	7175	translocated promoter region		E	0							SO:0001583	missense			ENST00000367478.4	1	0	hg19	CCDS41446.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.989888	0.93106	.	.	ENSG00000047410	ENST00000367478	T	0.26518	1.73	5.14	5.14	0.70334	.	0.000000	0.85682	D	0.000000	T	0.54498	0.1862	M	0.79805	2.47	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.53585	-0.8418	10	0.36615	T	0.2	.	18.9661	0.92697	0.0:0.0:1.0:0.0	.	1598	P12270	TPR_HUMAN	S	1598	ENSP00000356448:R1598S	ENSP00000356448:R1598S	R	-	1	0	TPR	184571212	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	9.065000	0.93941	2.545000	0.85829	0.650000	0.86243	CGC		TCGA-IB-A7LX-01A-12D-A36O-08	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	1	0	0	25	591	0	155	0	8.368645e-01	0	80	0	155	2		0	0	0	0	0	2	1	1.000000	24	583	0	155	2		0	0	0	0	155	2	-2.881965	1	1	0	0		1	0	4	4	2.292661	1	0.550000	3.150000	0.704433	0.220000	0.140000	1.000000	0.230000	0.261896	0.220000	0	1.800000e-01	2.900000e-01
TROVE2	6738	broad.mit.edu	37	1	193046072	193046072	+	Silent	SNP	C	C	A	rs55932617	by1000genomes	TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr1:193046072C>A	ENST00000367446.3	+	5	1188	c.978C>A	c.(976-978)atC>atA	p.I326I	TROVE2_ENST00000367445.3_Silent_p.I326I|TROVE2_ENST00000416058.2_Silent_p.I51I|TROVE2_ENST00000432079.1_Silent_p.I51I|TROVE2_ENST00000400968.2_Silent_p.I326I|TROVE2_ENST00000367444.3_Silent_p.I326I|TROVE2_ENST00000460715.2_3'UTR|TROVE2_ENST00000367441.1_Silent_p.I326I|TROVE2_ENST00000367443.1_Silent_p.I326I	NM_004600.5	NP_004591.2	P10155	RO60_HUMAN	TROVE domain family, member 2			21					ATATTTTGATCGCATTAGAAA	0.338000																								0							SO:0001819	synonymous_variant			ENST00000367446.3	1	0	hg19	CCDS1379.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	TROVE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086688.1	1	0	0	14	312	0	71	0	3.962869e-01	0	30	0	71	2		0	0	0	0	0	2	1	0.999738	14	306	0	71	2		0	0	0	0	71	2	-2.966611	1	1	0	0		1	0	4	4	2.292661	1	0.550000	3.150000	0.704433	0.240000	0.130000	1.000000	0.240000	0.281234	0.240000	0	1.800000e-01	3.300000e-01
CRB1	23418	broad.mit.edu	37	1	197396927	197396927	+	Silent	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr1:197396927C>A	ENST00000367400.3	+	7	2607	c.2472C>A	c.(2470-2472)atC>atA	p.I824I	CRB1_ENST00000367399.2_Silent_p.I712I|CRB1_ENST00000544212.1_Silent_p.I305I|CRB1_ENST00000535699.1_Silent_p.I755I|CRB1_ENST00000538660.1_Intron|CRB1_ENST00000367397.1_Silent_p.I205I	NM_201253.2	NP_957705.1	P82279	CRUM1_HUMAN	crumbs family member 1, photoreceptor morphogenesis associated	p.I824M(1)		132					CGTGGAAAATCGAAAAGGGAG	0.373000																								1	Substitution - Missense(1)						SO:0001819	synonymous_variant			ENST00000367400.3	1	0	hg19	CCDS1390.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	CRB1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086565.2	1	0	0	13	284	0	73		0	0	0	0	73	2		0	0	0	0	0	2	1	0.999534	13	281	0	73	2		0	0	0	0	73	2	-4.390350	1	0	0	0		1	0	4	4	2.292661	1	0.550000	3.150000	0.704433	0.250000	0.130000	1.000000	0.240000	0.287006	0.250000	0	1.800000e-01	3.400000e-01
KDM5B	10765	broad.mit.edu	37	1	202724554	202724554	+	Missense_Mutation	SNP	C	C	A	rs76768289		TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr1:202724554C>A	ENST00000367265.3	-	11	2547	c.1383G>T	c.(1381-1383)ttG>ttT	p.L461F	KDM5B_ENST00000456180.1_5'UTR|KDM5B_ENST00000367264.2_Missense_Mutation_p.L497F	NM_006618.3	NP_006609.3	Q9UGL1	KDM5B_HUMAN	lysine (K)-specific demethylase 5B			6					GCATGTTGTTCAAATTCCAGC	0.378000																								0							SO:0001583	missense			ENST00000367265.3	0	1	hg19	CCDS30974.1	.	.	.	.	.	.	.	.	.	.	C	18.80	3.700822	0.68501	.	.	ENSG00000117139	ENST00000367265;ENST00000538292;ENST00000367264;ENST00000235790	T;T;T	0.72505	-0.66;-0.66;-0.66	5.73	4.82	0.62117	Transcription factor jumonji/aspartyl beta-hydroxylase (2);	0.000000	0.85682	D	0.000000	D	0.86351	0.5912	M	0.93328	3.405	0.58432	D	0.999999	D;D	0.89917	0.999;1.0	D;D	0.91635	0.961;0.999	D	0.88022	0.2769	10	0.87932	D	0	-12.7178	9.1277	0.36826	0.0:0.7688:0.0:0.2312	.	497;461	Q9UGL1-2;Q9UGL1	.;KDM5B_HUMAN	F	461;303;497;303	ENSP00000356234:L461F;ENSP00000356233:L497F;ENSP00000235790:L303F	ENSP00000235790:L303F	L	-	3	2	KDM5B	200991177	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.022000	0.41030	1.425000	0.47237	0.655000	0.94253	TTG		TCGA-IB-A7LX-01A-12D-A36O-08	KDM5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099184.2	0	0	0	18	487	0	127	0	7.712277e-01	1	77	0	127	2		0	0	0	0	0	2	1	0.999976	16	472	0	125	2		0	0	0	0	127	2	-1.828307	0	1	121390	23	41	1	0	4	4	2.292661	1	0.550000	3.150000	0.704433	0.200000	0.110000	1.000000	0.200000	0.237404	0.200000	0	1.500000e-01	2.600000e-01
CNIH3	149111	broad.mit.edu	37	1	224868723	224868723	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr1:224868723C>A	ENST00000272133.3	+	2	1027	c.145C>A	c.(145-147)Cat>Aat	p.H49N		NM_152495.1	NP_689708.1	Q8TBE1	CNIH3_HUMAN	cornichon family AMPA receptor auxiliary protein 3			9	Breast(184;0.218)				CAATCCTGTTCATGCGGTAAG	0.483000																								0							SO:0001583	missense			ENST00000272133.3	1	0	hg19	CCDS1544.1	.	.	.	.	.	.	.	.	.	.	C	7.784	0.710231	0.15239	.	.	ENSG00000143786	ENST00000272133	.	.	.	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	T	0.24851	0.0603	N	0.00554	-1.385	0.80722	D	1	B	0.31705	0.336	B	0.39531	0.302	T	0.43734	-0.9373	9	0.02654	T	1	-24.8564	18.0599	0.89373	0.0:1.0:0.0:0.0	.	49	Q8TBE1	CNIH3_HUMAN	N	49	.	ENSP00000272133:H49N	H	+	1	0	CNIH3	222935346	0.997000	0.39634	0.970000	0.41538	0.845000	0.48019	5.322000	0.65852	2.573000	0.86826	0.643000	0.83706	CAT		TCGA-IB-A7LX-01A-12D-A36O-08	CNIH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091752.2	1	0	0	15	457	0	131	0	3.651894e-01	0	38	0	131	2		0	0	0	0	0	2	1	0.999851	15	445	0	128	2		0	0	0	0	131	2	-3.049391	1	1	0	0		1	0	4	4	2.292661	1	0.550000	3.150000	0.704433	0.180000	0.090000	1.000000	0.190000	0.217597	0.180000	0	1.300000e-01	2.400000e-01
RYR2	6262	broad.mit.edu	37	1	237995882	237995882	+	Missense_Mutation	SNP	A	A	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr1:237995882A>T	ENST00000366574.2	+	105	15156	c.14839A>T	c.(14839-14841)Agg>Tgg	p.R4947W	RYR2_ENST00000542537.1_Missense_Mutation_p.R4931W|RYR2_ENST00000360064.6_Missense_Mutation_p.R4953W	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)			586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)		GTATCAAGAAAGGTGTTGGGA	0.388000																								0							SO:0001583	missense			ENST00000366574.2	1	1	hg19	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	A	17.22	3.333129	0.60853	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	D;D;D	0.97232	-4.3;-4.26;-4.29	5.16	4.0	0.46444	.	0.000000	0.56097	D	0.000025	D	0.98460	0.9487	M	0.89968	3.075	0.80722	D	1	D	0.76494	0.999	D	0.77557	0.99	D	0.98802	1.0740	10	0.87932	D	0	-17.2433	11.8212	0.52238	0.7051:0.2949:0.0:0.0	.	4947	Q92736	RYR2_HUMAN	W	4947;4953;4931	ENSP00000355533:R4947W;ENSP00000353174:R4953W;ENSP00000443798:R4931W	ENSP00000353174:R4953W	R	+	1	2	RYR2	236062505	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.605000	0.46283	0.932000	0.37266	0.533000	0.62120	AGG		TCGA-IB-A7LX-01A-12D-A36O-08	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	0	0	0	8	155	0	33	0	9.424743e-03	0	3	0	33	2		0	0	0	0	0	2	1	0.989669	8	154	0	32	2		0	0	0	0	33	2	-4.539993	1	1	0	0		1	0	4	4	2.292661	1	0.550000	3.150000	0.704433	0.290000	0.130000	1.000000	0.270000	0.327747	0.290000	0	2.000000e-01	4.200000e-01
SDCCAG8	10806	broad.mit.edu	37	1	243507631	243507631	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr1:243507631C>A	ENST00000366541.3	+	12	1589	c.1471C>A	c.(1471-1473)Cag>Aag	p.Q491K	SDCCAG8_ENST00000355875.4_Missense_Mutation_p.Q448K|SDCCAG8_ENST00000343783.6_Missense_Mutation_p.Q346K|MIR4677_ENST00000584153.1_RNA	NM_006642.3	NP_006633.1	Q86SQ7	SDCG8_HUMAN	serologically defined colon cancer antigen 8			29	all_cancers(71;0.000545)|all_epithelial(71;0.000509)|all_lung(81;0.0821)|Ovarian(71;0.0919)|all_neural(11;0.101)|Breast(184;0.218)	all_cancers(173;0.00395)	all cancers(7;1.58e-07)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00392)		AATTAAAGATCAGGTAAGAGA	0.353000																								0							SO:0001583	missense			ENST00000366541.3	1	1	hg19	CCDS31075.1	.	.	.	.	.	.	.	.	.	.	C	16.26	3.072404	0.55646	.	.	ENSG00000054282	ENST00000355875;ENST00000366541;ENST00000343783;ENST00000435549	T;T;T;T	0.57273	0.7;0.66;0.66;0.41	6.07	5.16	0.70880	.	0.129373	0.52532	D	0.000063	T	0.39886	0.1095	L	0.29908	0.895	0.47245	D	0.999362	B;B	0.25441	0.075;0.126	B;B	0.28638	0.092;0.092	T	0.19614	-1.0300	10	0.15499	T	0.54	-7.4048	12.343	0.55105	0.1339:0.7375:0.1286:0.0	.	448;491	E9PFS7;Q86SQ7	.;SDCG8_HUMAN	K	448;491;346;271	ENSP00000348137:Q448K;ENSP00000355499:Q491K;ENSP00000341260:Q346K;ENSP00000410200:Q271K	ENSP00000341260:Q346K	Q	+	1	0	SDCCAG8	241574254	0.998000	0.40836	1.000000	0.80357	0.998000	0.95712	1.247000	0.32815	1.566000	0.49654	0.585000	0.79938	CAG		TCGA-IB-A7LX-01A-12D-A36O-08	SDCCAG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096485.1	1	0	1	32	199	0	53	1	9.703296e-01	9	29	0	53	2		0	0	0	0	0	2	1	1.000000	32	197	0	52	2		0	0	0	0	53	2	-15.859720	1	1	0	0		1	0	4	4	2.225328	1	0.550000	3.150000	0.698997	0.770000	0.530000	1.000000	1.000000	0.785166	0.770000	0	6.400000e-01	9.400000e-01
OR2W5	441932	broad.mit.edu	37	1	247655339	247655339	+	RNA	SNP	A	A	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr1:247655339A>T	ENST00000522351.1	+	0	970							A6NFC9	OR2W5_HUMAN	olfactory receptor, family 2, subfamily W, member 5			39	all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.222)	OV - Ovarian serous cystadenocarcinoma(106;0.0188)		CCATGAAGAAACTTCTGGGGT	0.507000																								0											ENST00000522351.1	1	1	hg19																																																																																					TCGA-IB-A7LX-01A-12D-A36O-08	OR2W5-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000375789.1	0	0	0	123	246	0	97		0	0	0	0	97	2		0	0	0	0	0	2	1	1.000000	124	239	0	96	2		0	0	0	0	97	2	-20.000000	1	1	0	0		1	0	4	4	2.225328	1	0.550000	3.150000	0.698997	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	9.900000e-01	1
CLDN8	9073	broad.mit.edu	37	21	31587596	31587596	+	Silent	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr21:31587596C>A	ENST00000399899.1	-	1	795	c.648G>T	c.(646-648)ccG>ccT	p.P216P	CLDN8_ENST00000286809.1_Silent_p.P216P	NM_199328.2	NP_955360.1	P56748	CLD8_HUMAN	claudin 8			15					AGTAGACGCTCGGTGACTTCT	0.378000																								0							SO:0001819	synonymous_variant			ENST00000399899.1	1	0	hg19	CCDS13587.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	CLDN8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000182260.1	1	0	0	25	478	0	128	0	4.709011e-02	0	7	0	128	2		0	0	0	0	0	2	1	1.000000	24	470	0	126	2		0	0	0	0	128	2	-2.595282	1	1	0	0		1						0.550000	3.150000									0	0
ITSN1	6453	broad.mit.edu	37	21	35147105	35147105	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr21:35147105C>A	ENST00000381318.3	+	13	1666	c.1378C>A	c.(1378-1380)Caa>Aaa	p.Q460K	ITSN1_ENST00000437442.2_Missense_Mutation_p.Q460K|ITSN1_ENST00000399355.2_Missense_Mutation_p.Q460K|AP000304.12_ENST00000429238.1_Intron|ITSN1_ENST00000381291.4_Missense_Mutation_p.Q460K|ITSN1_ENST00000399353.1_Missense_Mutation_p.Q423K|ITSN1_ENST00000399338.4_Missense_Mutation_p.Q460K|ITSN1_ENST00000399352.1_Missense_Mutation_p.Q460K|ITSN1_ENST00000381285.4_Missense_Mutation_p.Q460K|ITSN1_ENST00000399367.3_Missense_Mutation_p.Q460K|ITSN1_ENST00000399326.3_Missense_Mutation_p.Q460K|ITSN1_ENST00000399349.1_Missense_Mutation_p.Q460K|ITSN1_ENST00000379960.5_Missense_Mutation_p.Q460K	NM_003024.2	NP_003015.2	Q15811	ITSN1_HUMAN	intersectin 1 (SH3 domain protein)			67					ACTACTAAATCAAAGAAACAA	0.373000																								0							SO:0001583	missense			ENST00000381318.3	1	0	hg19	CCDS33545.1	.	.	.	.	.	.	.	.	.	.	C	17.68	3.450044	0.63290	.	.	ENSG00000205726	ENST00000399353;ENST00000381318;ENST00000381291;ENST00000381285;ENST00000381288;ENST00000381289;ENST00000399367;ENST00000399352;ENST00000399355;ENST00000399349;ENST00000399338;ENST00000437442;ENST00000399326;ENST00000379960	T;T;T;T;T;T;T;T;T;T;T;T	0.49432	1.61;0.79;0.83;0.78;1.61;1.61;0.82;1.61;1.61;1.61;1.61;1.61	4.64	4.64	0.57946	.	0.120389	0.56097	D	0.000021	T	0.49236	0.1545	M	0.68317	2.08	0.80722	D	1	B;B;B;B;B;P;B;B;B;B	0.34864	0.064;0.064;0.064;0.023;0.106;0.473;0.023;0.023;0.106;0.064	B;B;B;B;B;B;B;B;B;B	0.33121	0.039;0.039;0.039;0.005;0.084;0.158;0.005;0.005;0.084;0.039	T	0.56703	-0.7935	10	0.54805	T	0.06	.	17.8738	0.88818	0.0:1.0:0.0:0.0	.	423;423;423;460;460;460;460;460;460;423	A8D7D0;A7XZY7;A8CTY7;A8CTY3;F8W7U0;E7ERJ1;A8CTX8;Q15811;Q15811-3;E7ERJ0	.;.;.;.;.;.;.;ITSN1_HUMAN;.;.	K	423;460;460;460;460;460;460;460;460;460;460;460;460;460	ENSP00000382290:Q423K;ENSP00000370719:Q460K;ENSP00000370691:Q460K;ENSP00000370685:Q460K;ENSP00000382301:Q460K;ENSP00000382289:Q460K;ENSP00000382292:Q460K;ENSP00000382286:Q460K;ENSP00000382275:Q460K;ENSP00000387377:Q460K;ENSP00000382265:Q460K;ENSP00000369294:Q460K	ENSP00000369294:Q460K	Q	+	1	0	ITSN1	34068975	1.000000	0.71417	0.855000	0.33649	0.948000	0.59901	5.820000	0.69250	2.289000	0.77006	0.655000	0.94253	CAA		TCGA-IB-A7LX-01A-12D-A36O-08	ITSN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000140070.4	1	0	0	13	316	0	82	0	7.013694e-01	0	60	0	82	2		0	0	0	0	0	2	1	0.999492	12	310	0	81	2		0	0	0	0	82	2	-3.920832	1	1	0	0		1	2	3	5	2.266323	1	0.550000	3.150000	0.698997	0.240000	0.120000	1.000000	0.230000	0.408668	0.240000	0	1.700000e-01	1
DSCAM	1826	broad.mit.edu	37	21	41423897	41423897	+	Silent	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr21:41423897G>T	ENST00000400454.1	-	30	5650	c.5173C>A	c.(5173-5175)Cgg>Agg	p.R1725R		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule			142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)			GTTCCCGGCCGAGCGTCTGAA	0.483000													Melanoma(134;970 1778 1785 21664 32388)											0							SO:0001819	synonymous_variant			ENST00000400454.1	1	0	hg19	CCDS42929.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	1	0	0	27	516	0	122		0	0	0	0	122	2		0	0	0	0	0	2	1	1.000000	27	503	0	121	2		0	0	0	0	122	2	-2.870906	1	1	0	0		1	2	3	5	2.266323	1	0.550000	3.150000	0.698997	0.290000	0.180000	1.000000	0.270000	0.446621	0.290000	0	2.200000e-01	1
CACNG2	10369	broad.mit.edu	37	22	37098459	37098459	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr22:37098459C>T	ENST00000300105.6	-	1	1144	c.163G>A	c.(163-165)Gag>Aag	p.E55K	RP1-293L6.1_ENST00000430281.1_RNA	NM_006078.3	NP_006069.1	Q9Y698	CCG2_HUMAN	calcium channel, voltage-dependent, gamma subunit 2			18					ATAACTTCCTCGTTCTTTTTG	0.517000																								0							SO:0001583	missense			ENST00000300105.6	1	1	hg19	CCDS13931.1	.	.	.	.	.	.	.	.	.	.	c	16.52	3.145171	0.57044	.	.	ENSG00000166862	ENST00000300105	T	0.37584	1.19	4.37	4.37	0.52481	.	0.000000	0.85682	D	0.000000	T	0.22820	0.0551	N	0.12746	0.255	0.58432	D	0.999997	D	0.52996	0.957	P	0.44394	0.448	T	0.04281	-1.0963	10	0.06891	T	0.86	-10.3973	17.3494	0.87318	0.0:1.0:0.0:0.0	.	55	Q9Y698	CCG2_HUMAN	K	55	ENSP00000300105:E55K	ENSP00000300105:E55K	E	-	1	0	CACNG2	35428405	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.284000	0.78650	2.134000	0.65973	0.546000	0.68486	GAG		TCGA-IB-A7LX-01A-12D-A36O-08	CACNG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075500.2	1	0	1	113	322	0	133		0	0	0	0	133	2		0	0	0	0	0	2	1	1.000000	112	318	0	130	2		0	0	0	0	133	2	-5.967919	1	1	0	0		1	2	3	5	1.795983	1	0.550000	3.150000	0.619128	0.990000	0.940000	1.000000	1.000000	0.996954	0.990000	1	9.900000e-01	1
LGALS1	3956	broad.mit.edu	37	22	38075643	38075643	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr22:38075643G>A	ENST00000215909.5	+	4	390	c.295G>A	c.(295-297)Gtc>Atc	p.V99I	LGALS1_ENST00000489315.1_3'UTR	NM_002305.3	NP_002296.1	P09382	LEG1_HUMAN	lectin, galactoside-binding, soluble, 1			3	Melanoma(58;0.0574)				CAACCTGACCGTCAAGCTGCC	0.567000													Pancreas(23;406 890 14304 26016)											0							SO:0001583	missense			ENST00000215909.5	1	1	hg19	CCDS13954.1	.	.	.	.	.	.	.	.	.	.	g	0.469	-0.885255	0.02511	0.0	1.16E-4	ENSG00000100097	ENST00000215909	T	0.04360	3.64	6.08	-0.0473	0.13844	Concanavalin A-like lectin/glucanase (1);Galectin, carbohydrate recognition domain (4);Concanavalin A-like lectin/glucanase, subgroup (1);	0.237165	0.42294	N	0.000737	T	0.03695	0.0105	L	0.31120	0.905	0.31764	N	0.632933	B	0.11235	0.004	B	0.19666	0.026	T	0.35051	-0.9804	10	0.19590	T	0.45	-0.9193	10.1288	0.42665	0.4005:0.0:0.5995:0.0	.	99	P09382	LEG1_HUMAN	I	99	ENSP00000215909:V99I	ENSP00000215909:V99I	V	+	1	0	LGALS1	36405589	0.451000	0.25705	0.997000	0.53966	0.127000	0.20565	0.715000	0.25822	-0.043000	0.13513	-1.057000	0.02308	GTC		TCGA-IB-A7LX-01A-12D-A36O-08	LGALS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319482.1	1	0	1	50	159	0	71	1	1	665	2015	0	71	2		0	0	0	0	0	2	1	1.000000	50	155	0	71	2		0	0	0	0	71	2	-4.275326	1	1	121412	7	44	1	2	3	5	1.795983	1	0.550000	3.150000	0.619128	0.990000	0.800000	1.000000	1.000000	0.971288	0.990000	1	9.100000e-01	1
CHST10	9486	broad.mit.edu	37	2	101010109	101010109	+	Silent	SNP	T	T	C			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr2:101010109T>C	ENST00000264249.3	-	7	1054	c.669A>G	c.(667-669)agA>agG	p.R223R	CHST10_ENST00000542617.1_Silent_p.R271R|CHST10_ENST00000409701.1_Silent_p.R223R	NM_004854.4	NP_004845.1	O43529	CHSTA_HUMAN	carbohydrate sulfotransferase 10			16					TCCTGTATTTTCTGATGATGC	0.483000																								0							SO:0001819	synonymous_variant			ENST00000264249.3	1	1	hg19	CCDS2047.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	CHST10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253162.1	1	0	0	68	464	0	150	0	8.442364e-02	0	4	0	150	2		0	0	0	0	0	2	1	1.000000	64	458	0	150	2		0	0	0	0	150	2	-20.000000	1	1	0	0		1	2	4	6	2.189758	1	0.550000	3.150000	0.685094	0.690000	0.530000	1.000000	0.670000	0.746654	0.690000	0	6.000000e-01	1
MYCN	4613	broad.mit.edu	37	2	16086208	16086208	+	Silent	SNP	C	C	A	rs144531796	by1000genomes	TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr2:16086208C>A	ENST00000281043.3	+	3	1681	c.1384C>A	c.(1384-1386)Cgg>Agg	p.R462R		NM_005378.4	NP_005369.2	P04198	MYCN_HUMAN	v-myc avian myelocytomatosis viral oncogene neuroblastoma derived homolog			31	all_cancers(1;1.35e-08)|all_neural(1;2.92e-24)|Lung SC(1;3.26e-07)|Medulloblastoma(1;6.9e-06)|all_lung(1;1.26e-05)|Glioma(3;0.135)|Acute lymphoblastic leukemia(172;0.155)|all_epithelial(1;0.169)|all_hematologic(175;0.197)		GBM - Glioblastoma multiforme(3;0.000332)		TGAACACGCTCGGACTTGCTA	0.428000			A		neuroblastoma										Dom	yes		2	2p24.1	4613	v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian)		O	0							SO:0001819	synonymous_variant			ENST00000281043.3	1	0	hg19	CCDS1687.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	MYCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095469.2	1	0	0	21	411	0	117	0	0	0	1	0	117	2		0	0	0	0	0	2	1	0.999997	22	400	0	117	2		0	0	0	0	117	2	-2.522253	1	1	121406	6	42	1	2	6	8	2.087735	1	0.550000	3.150000	0.673795	0.260000	0.150000	1.000000	0.240000	0.379979	0.260000	0	2.000000e-01	1
FAM49A	81553	broad.mit.edu	37	2	16743285	16743285	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr2:16743285G>T	ENST00000381323.3	-	6	643	c.423C>A	c.(421-423)ttC>ttA	p.F141L	FAM49A_ENST00000355549.2_Missense_Mutation_p.F141L|FAM49A_ENST00000406434.1_Missense_Mutation_p.F141L	NM_030797.3	NP_110424.1	Q9H0Q0	FA49A_HUMAN	family with sequence similarity 49, member A	p.F141F(1)		23	Acute lymphoblastic leukemia(172;0.0734)|all_hematologic(175;0.088)		GBM - Glioblastoma multiforme(3;0.00969)		TCAGCTCATCGAATCGAAGGG	0.453000																								1	Substitution - coding silent(1)						SO:0001583	missense			ENST00000381323.3	1	0	hg19	CCDS1688.1	.	.	.	.	.	.	.	.	.	.	G	17.95	3.513807	0.64522	.	.	ENSG00000197872	ENST00000381323;ENST00000406434;ENST00000355549	T;T;T	0.57595	0.39;0.39;0.39	5.7	-3.83	0.04269	.	0.000000	0.85682	D	0.000000	T	0.71710	0.3372	M	0.90252	3.1	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.74899	-0.3507	10	0.45353	T	0.12	-22.1984	13.5016	0.61459	0.6789:0.0:0.3211:0.0	.	141	Q9H0Q0	FA49A_HUMAN	L	141	ENSP00000370724:F141L;ENSP00000384771:F141L;ENSP00000347744:F141L	ENSP00000347744:F141L	F	-	3	2	FAM49A	16606766	0.005000	0.15991	0.957000	0.39632	0.494000	0.33585	-0.804000	0.04535	-0.587000	0.05890	-0.136000	0.14681	TTC		TCGA-IB-A7LX-01A-12D-A36O-08	FAM49A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207203.2	1	0	0	11	224	0	71	0	7.585464e-02	0	9	0	71	2		0	0	0	0	0	2	1	0.998333	11	221	0	71	2		0	0	0	0	71	2	-3.343013	1	1	0	0		1	2	6	8	2.087735	1	0.550000	3.150000	0.673795	0.260000	0.120000	1.000000	0.240000	0.379540	0.260000	0	1.800000e-01	1
LRP2	4036	broad.mit.edu	37	2	170025143	170025143	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr2:170025143G>T	ENST00000263816.3	-	61	11826	c.11541C>A	c.(11539-11541)ttC>ttA	p.F3847L		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	p.F3847F(1)		315				"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	TTTTGCATTCGAACATAGTAG	0.428000																								1	Substitution - coding silent(1)						SO:0001583	missense			ENST00000263816.3	1	0	hg19	CCDS2232.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.6|25.6	4.656719|4.656719	0.88154|0.88154	.|.	.|.	ENSG00000081479|ENSG00000081479	ENST00000263816|ENST00000536293	D|.	0.98889|.	-5.21|.	5.82|5.82	-6.33|-6.33	0.01988|0.01988	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.79046|.	0.4380|.	M|M	0.85462|0.85462	2.755|2.755	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.87578|.	0.998|.	D|.	0.83997|.	0.0341|.	10|.	0.72032|0.72032	D|D	0.01|0.01	.|.	17.3947|17.3947	0.87442|0.87442	0.8962:0.0:0.1038:0.0|0.8962:0.0:0.1038:0.0	.|.	3847|.	P98164|.	LRP2_HUMAN|.	L|X	3847|512	ENSP00000263816:F3847L|.	ENSP00000263816:F3847L|ENSP00000438157:S512X	F|S	-|-	3|2	2|0	LRP2|LRP2	169733389|169733389	0.971000|0.971000	0.33674|0.33674	0.855000|0.855000	0.33649|0.33649	0.823000|0.823000	0.46562|0.46562	0.340000|0.340000	0.19892|0.19892	-1.073000|-1.073000	0.03137|0.03137	-0.367000|-0.367000	0.07326|0.07326	TTC|TCG		TCGA-IB-A7LX-01A-12D-A36O-08	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	1	0	0	10	223	0	64		0	0	0	0	64	2		0	0	0	0	0	2	1	0.996647	9	218	0	62	2		0	0	0	0	64	2	-4.333398	1	1	0	0		1	2	5	7	2.129539	1	0.550000	3.150000	0.678284	0.240000	0.110000	1.000000	0.210000	0.388524	0.240000	0	1.700000e-01	1
FASTKD1	79675	broad.mit.edu	37	2	170403116	170403116	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr2:170403116C>A	ENST00000453153.2	-	8	1659	c.1313G>T	c.(1312-1314)cGa>cTa	p.R438L	FASTKD1_ENST00000453929.2_Missense_Mutation_p.R438L	NM_024622.3	NP_078898.3	Q53R41	FAKD1_HUMAN	FAST kinase domains 1			37					GGCTTCAATTCGGGATATCCC	0.413000																								0							SO:0001583	missense			ENST00000453153.2	1	0	hg19	CCDS33318.1	.	.	.	.	.	.	.	.	.	.	C	18.33	3.600955	0.66332	.	.	ENSG00000138399	ENST00000453153;ENST00000453929	T;T	0.25414	1.82;1.8	4.44	2.59	0.31030	.	0.265024	0.35772	N	0.002992	T	0.37652	0.1011	L	0.59436	1.845	0.40632	D	0.981862	D;D	0.64830	0.994;0.99	P;P	0.60682	0.878;0.759	T	0.13255	-1.0516	10	0.56958	D	0.05	-29.0924	7.238	0.26079	0.0:0.6022:0.0:0.3978	.	438;438	Q53R41-2;Q53R41	.;FAKD1_HUMAN	L	438	ENSP00000400513:R438L;ENSP00000403229:R438L	ENSP00000400513:R438L	R	-	2	0	FASTKD1	170111362	0.678000	0.27586	0.245000	0.24217	0.899000	0.52679	1.083000	0.30815	0.585000	0.29608	0.563000	0.77884	CGA		TCGA-IB-A7LX-01A-12D-A36O-08	FASTKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337788.2	1	0	0	13	309	0	65	0	3.550350e-01	0	29	0	65	2		0	0	0	0	0	2	1	0.999491	13	302	0	64	2		0	0	0	0	65	2	-3.222233	1	1	0	0		1	2	5	7	2.129539	1	0.550000	3.150000	0.678284	0.220000	0.110000	1.000000	0.210000	0.373971	0.220000	0	1.600000e-01	1
SF3B1	23451	broad.mit.edu	37	2	198265629	198265629	+	Missense_Mutation	SNP	T	T	C			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08			T	C	T	T		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr2:198265629T>C	ENST00000335508.6	-	18	2619	c.2528A>G	c.(2527-2529)aAa>aGa	p.K843R	SF3B1_ENST00000462613.1_5'Flank	NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa			633			OV - Ovarian serous cystadenocarcinoma(117;0.246)		TGCACCTACTTTGTTTGCCAA	0.348000			Mis		myelodysplastic syndrome										Dom	yes		2	2q33.1	23451	splicing factor 3b, subunit 1, 155kDa		L	0							SO:0001583	missense			ENST00000335508.6	1	1	hg19	CCDS33356.1	.	.	.	.	.	.	.	.	.	.	T	18.25	3.581538	0.65992	.	.	ENSG00000115524	ENST00000335508	T	0.65916	-0.18	5.77	5.77	0.91146	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.68412	0.2998	M	0.76433	2.335	0.80722	D	1	B	0.28082	0.2	B	0.36030	0.216	T	0.68447	-0.5406	10	0.52906	T	0.07	.	16.3948	0.83586	0.0:0.0:0.0:1.0	.	843	O75533	SF3B1_HUMAN	R	843	ENSP00000335321:K843R	ENSP00000335321:K843R	K	-	2	0	SF3B1	197973874	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.936000	0.87665	2.326000	0.78906	0.533000	0.62120	AAA		TCGA-IB-A7LX-01A-12D-A36O-08	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2	1	0	1	65	241	0	78	1	1	100	381	0	78	2	1	1	54	255	0	577	2	1	1.000000	65	239	0	78	2		0	0	0	0	78	2	-20.000000	1	1	0	0		1	2	6	8	2.094740	1	0.550000	3.150000	0.677650	0.990000	0.860000	1.000000	1.000000	0.987063	0.990000	1	9.700000e-01	1
SF3B1	23451	broad.mit.edu	37	2	198266713	198266713	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr2:198266713C>T	ENST00000335508.6	-	15	2310	c.2219G>A	c.(2218-2220)gGa>gAa	p.G740E	SNORA4_ENST00000365564.1_RNA|SF3B1_ENST00000462613.1_5'Flank	NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	p.G740E(1)		633			OV - Ovarian serous cystadenocarcinoma(117;0.246)		ATTTACCTTTCCTCTGTGTTG	0.343000			Mis		myelodysplastic syndrome										Dom	yes		2	2q33.1	23451	splicing factor 3b, subunit 1, 155kDa		L	1	Substitution - Missense(1)						SO:0001583	missense			ENST00000335508.6	1	1	hg19	CCDS33356.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.036521	0.93630	.	.	ENSG00000115524	ENST00000335508	T	0.62364	0.03	5.58	5.58	0.84498	Armadillo-like helical (1);Armadillo-type fold (1);	0.107844	0.64402	D	0.000005	T	0.76449	0.3989	M	0.83692	2.655	0.80722	D	1	D	0.55800	0.973	P	0.51974	0.686	T	0.80183	-0.1488	10	0.66056	D	0.02	.	19.5659	0.95393	0.0:1.0:0.0:0.0	.	740	O75533	SF3B1_HUMAN	E	740	ENSP00000335321:G740E	ENSP00000335321:G740E	G	-	2	0	SF3B1	197974958	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	7.359000	0.79477	2.619000	0.88677	0.563000	0.77884	GGA		TCGA-IB-A7LX-01A-12D-A36O-08	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2	1	0	1	76	226	0	76	1	1	157	347	0	76	2	1	1	42	125	0	366	2	1	1.000000	75	219	0	76	2		0	0	0	0	76	2	-20.000000	1	1	0	0		1	2	6	8	2.094740	1	0.550000	3.150000	0.677650	0.990000	0.990000	1.000000	1.000000	0.999697	0.990000	1	9.900000e-01	1
ATIC	471	broad.mit.edu	37	2	216190751	216190751	+	Silent	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08			C	A	C	C		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr2:216190751C>A	ENST00000236959.9	+	6	747	c.421C>A	c.(421-423)Cga>Aga	p.R141R	ATIC_ENST00000540518.1_Silent_p.R82R|ATIC_ENST00000435675.1_Silent_p.R140R	NM_004044.6	NP_004035.2	P31939	PUR9_HUMAN	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	p.R141*(1)	ATIC/ALK(24)	8		Renal(323;0.229)		Methotrexate(DB00563)|Pemetrexed(DB00642)|Tetrahydrofolic acid(DB00116)	AAACCACGCTCGAGTGACAGT	0.483000			T	ALK	ALCL										Dom	yes		2	2q35	471	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase		L	1	Substitution - Nonsense(1)						SO:0001819	synonymous_variant			ENST00000236959.9	1	0	hg19	CCDS2398.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	ATIC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256610.1	1	0	0	11	238	0	70	0	9.953872e-01	1	202	0	70	2		0	0	0	0	0	2	1	0.998213	11	232	0	68	2		0	0	0	0	70	2	-3.221883	1	1	0	0		1	2	6	8	2.094740	1	0.550000	3.150000	0.677650	0.250000	0.120000	1.000000	0.210000	0.374253	0.250000	0	1.700000e-01	1
CPNE4	131034	broad.mit.edu	37	3	131283152	131283152	+	Missense_Mutation	SNP	G	G	C			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr3:131283152G>C	ENST00000512055.1	-	15	3095	c.969C>G	c.(967-969)aaC>aaG	p.N323K	CPNE4_ENST00000512332.1_Missense_Mutation_p.N341K|CPNE4_ENST00000429747.1_Missense_Mutation_p.N323K|CPNE4_ENST00000502818.1_Missense_Mutation_p.N341K|CPNE4_ENST00000511604.1_Missense_Mutation_p.N323K			Q96A23	CPNE4_HUMAN	copine IV			39					AGGAACAGCTGTTCCTGGGGT	0.433000																								0							SO:0001583	missense			ENST00000512055.1	1	1	hg19	CCDS3072.1	.	.	.	.	.	.	.	.	.	.	G	16.88	3.243726	0.58995	.	.	ENSG00000196353	ENST00000512055;ENST00000429747;ENST00000512332;ENST00000511604;ENST00000502818	T;T;T;T;T	0.54071	0.6;0.6;0.59;0.6;0.59	5.52	4.65	0.58169	von Willebrand factor, type A (1);	0.000000	0.85682	D	0.000000	T	0.67173	0.2865	L	0.58510	1.815	0.80722	D	1	D;P	0.76494	0.999;0.81	D;B	0.74023	0.982;0.313	T	0.65994	-0.6033	10	0.35671	T	0.21	-36.7038	14.6356	0.68686	0.07:0.0:0.93:0.0	.	341;323	Q96A23-2;Q96A23	.;CPNE4_HUMAN	K	323;323;341;323;341	ENSP00000421705:N323K;ENSP00000411904:N323K;ENSP00000424853:N341K;ENSP00000423811:N323K;ENSP00000421646:N341K	ENSP00000411904:N323K	N	-	3	2	CPNE4	132765842	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	5.441000	0.66569	1.350000	0.45770	-0.221000	0.12465	AAC		TCGA-IB-A7LX-01A-12D-A36O-08	CPNE4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356583.4	1	0	1	65	287	0	80	0	3.852143e-01	0	7	0	80	2		0	0	0	0	0	2	1	1.000000	64	282	0	79	2		0	0	0	0	80	2	-20.000000	1	1	0	0		1	1	3	4	2.284976	1	0.550000	3.150000	0.707602	0.990000	0.810000	1.000000	1.000000	0.972263	0.990000	1	9.200000e-01	1
GK5	256356	broad.mit.edu	37	3	141900367	141900367	+	Silent	SNP	G	G	T	rs9866012	byFrequency	TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr3:141900367G>T	ENST00000392993.2	-	11	1135	c.984C>A	c.(982-984)gtC>gtA	p.V328V		NM_001039547.2	NP_001034636.1	Q6ZS86	GLPK5_HUMAN	glycerol kinase 5 (putative)			10					CTAAGCATACGACTTCTTGCC	0.383000																								0							SO:0001819	synonymous_variant			ENST00000392993.2	1	0	hg19	CCDS33871.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	GK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353999.1	1	0	0	18	412	0	105	0	4.667193e-01	0	35	0	105	2		0	0	0	0	0	2	1	0.999979	17	403	0	104	2		0	0	0	0	105	2	-2.721274	1	1	0	0		1	1	3	4	2.284976	1	0.550000	3.150000	0.707602	0.230000	0.130000	0.380000	0.240000	0.253288	0.230000	0	1.800000e-01	3.000000e-01
ATR	545	broad.mit.edu	37	3	142188288	142188288	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr3:142188288C>A	ENST00000350721.4	-	38	6564	c.6443G>T	c.(6442-6444)cGa>cTa	p.R2148L	RP11-383G6.3_ENST00000460977.1_RNA|ATR_ENST00000383101.3_Missense_Mutation_p.R2084L	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	p.R2148Q(1)		122					ATGACAAATTCGAGAGATCAA	0.343000								Other conserved DNA damage response genes																1	Substitution - Missense(1)						SO:0001583	missense			ENST00000350721.4	1	0	hg19	CCDS3124.1	.	.	.	.	.	.	.	.	.	.	C	29.5	5.009379	0.93346	.	.	ENSG00000175054	ENST00000350721;ENST00000383101	T;T	0.15256	2.44;2.58	5.15	5.15	0.70609	PIK-related kinase (1);	0.126462	0.52532	D	0.000080	T	0.25494	0.0620	M	0.71871	2.18	0.80722	D	1	B	0.30068	0.267	B	0.28991	0.097	T	0.07404	-1.0774	10	0.87932	D	0	-3.8171	18.5955	0.91228	0.0:1.0:0.0:0.0	.	2148	Q13535	ATR_HUMAN	L	2148;2084	ENSP00000343741:R2148L;ENSP00000372581:R2084L	ENSP00000343741:R2148L	R	-	2	0	ATR	143670978	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	7.805000	0.86005	2.378000	0.81104	0.591000	0.81541	CGA		TCGA-IB-A7LX-01A-12D-A36O-08	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	1	0	0	22	462	0	118	0	5.986506e-01	0	43	0	118	2		0	0	0	0	0	2	1	0.999999	22	461	0	118	2		0	0	0	0	118	2	-4.388978	1	1	0	0		1	1	3	4	2.284976	1	0.550000	3.150000	0.707602	0.250000	0.150000	0.400000	0.240000	0.271826	0.250000	0	2.000000e-01	3.200000e-01
C3orf20	84077	broad.mit.edu	37	3	14769996	14769996	+	Silent	SNP	C	C	A	rs144350421	byFrequency	TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr3:14769996C>A	ENST00000253697.3	+	12	2193	c.1741C>A	c.(1741-1743)Cgg>Agg	p.R581R	C3orf20_ENST00000435614.1_Silent_p.R459R|C3orf20_ENST00000412910.1_Silent_p.R459R	NM_032137.4	NP_115513.4	Q8ND61	CC020_HUMAN	chromosome 3 open reading frame 20			40					AGAATTTGTTCGGTTCAAGAT	0.463000																								0							SO:0001819	synonymous_variant			ENST00000253697.3	1	0	hg19	CCDS33706.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	C3orf20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340586.1	1	0	0	13	204	0	89		0	0	0	0	89	2		0	0	0	0	0	2	1	0.999542	13	201	0	87	2		0	0	0	0	89	2	-2.842149	1	1	0	0		1	1	2	3	1.822614	1	0.550000	3.150000	0.635258	0.280000	0.150000	1.000000	0.260000	0.370845	0.280000	0	2.100000e-01	4.200000e-01
FAM194A	0	broad.mit.edu	37	3	150391782	150391782	+	Missense_Mutation	SNP	T	T	G			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr3:150391782T>G	ENST00000295910.6	-	11	1356	c.1304A>C	c.(1303-1305)aAg>aCg	p.K435T	FAM194A_ENST00000491361.1_Missense_Mutation_p.K289T	NM_152394.3	NP_689607.2						38					AGTCAGAAACTTGCTCCCATG	0.333000																								0							SO:0001583	missense			ENST00000295910.6	1	1	hg19	CCDS3151.2	.	.	.	.	.	.	.	.	.	.	T	17.11	3.306745	0.60305	.	.	ENSG00000163645	ENST00000295910;ENST00000491361;ENST00000313811	T;T	0.12984	2.63;2.63	4.94	4.94	0.65067	.	0.220254	0.31461	N	0.007604	T	0.25457	0.0619	L	0.45228	1.405	0.30174	N	0.801058	D	0.76494	0.999	D	0.79784	0.993	T	0.05131	-1.0904	10	0.46703	T	0.11	-12.9558	8.3833	0.32486	0.0:0.0893:0.0:0.9107	.	435	Q7L0X2	F194A_HUMAN	T	435;289;393	ENSP00000295910:K435T;ENSP00000419366:K289T	ENSP00000295910:K435T	K	-	2	0	FAM194A	151874472	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	3.661000	0.54503	2.053000	0.61076	0.533000	0.62120	AAG		TCGA-IB-A7LX-01A-12D-A36O-08	FAM194A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257666.1	0	0	1	53	371	0	114		0	0	0	0	114	2		0	0	0	0	0	2	1	1.000000	52	363	0	111	2		0	0	0	0	114	2	-20.000000	1	1	0	0		1	1	3	4	2.284976	1	0.550000	3.150000	0.707602	0.700000	0.530000	0.920000	0.710000	0.711508	0.700000	0	6.100000e-01	8.000000e-01
IFT80	57560	broad.mit.edu	37	3	159998536	159998536	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr3:159998536C>A	ENST00000326448.7	-	15	2015	c.1583G>T	c.(1582-1584)cGa>cTa	p.R528L	RP11-432B6.3_ENST00000483754.1_Missense_Mutation_p.R699L|IFT80_ENST00000496589.1_Missense_Mutation_p.R391L|IFT80_ENST00000483465.1_Missense_Mutation_p.R391L	NM_020800.2	NP_065851.1	Q9P2H3	IFT80_HUMAN	intraflagellar transport 80			36			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)		CACTATAAATCGAGTATCTTG	0.348000																								0							SO:0001583	missense			ENST00000326448.7	1	0	hg19	CCDS3188.1	.	.	.	.	.	.	.	.	.	.	C	15.47	2.843076	0.51057	.	.	ENSG00000068885	ENST00000326448;ENST00000483465;ENST00000496589	T;T;T	0.70164	2.32;-0.46;-0.46	5.59	5.59	0.84812	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.281880	0.24645	U	0.036780	T	0.64283	0.2584	M	0.65975	2.015	0.47659	D	0.999489	B	0.09022	0.002	B	0.06405	0.002	T	0.59511	-0.7441	10	0.33940	T	0.23	.	13.3036	0.60338	0.0:0.9182:0.0:0.0818	.	528	Q9P2H3	IFT80_HUMAN	L	528;391;391	ENSP00000312778:R528L;ENSP00000418196:R391L;ENSP00000420646:R391L	ENSP00000312778:R528L	R	-	2	0	IFT80	161481230	0.960000	0.32886	0.970000	0.41538	0.974000	0.67602	1.262000	0.32992	2.635000	0.89317	0.460000	0.39030	CGA		TCGA-IB-A7LX-01A-12D-A36O-08	IFT80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352651.2	1	0	0	13	334	0	80	0	5.624329e-01	0	48	0	80	2		0	0	0	0	0	2	1	0.999521	13	330	0	80	2		0	0	0	0	80	2	-3.096837	1	1	0	0		1	1	3	4	2.284976	1	0.550000	3.150000	0.707602	0.210000	0.110000	0.370000	0.200000	0.231830	0.210000	0	1.500000e-01	2.900000e-01
SMC4	10051	broad.mit.edu	37	3	160132228	160132228	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr3:160132228C>A	ENST00000357388.3	+	9	1646	c.1195C>A	c.(1195-1197)Caa>Aaa	p.Q399K	SMC4_ENST00000462787.1_Missense_Mutation_p.Q399K|SMC4_ENST00000469762.1_Missense_Mutation_p.Q374K|RP11-432B6.3_ENST00000483754.1_Intron|SMC4_ENST00000344722.5_Missense_Mutation_p.Q399K|SMC4_ENST00000360111.2_Missense_Mutation_p.Q399K	NM_001002800.1	NP_001002800.1	Q9NTJ3	SMC4_HUMAN	structural maintenance of chromosomes 4			48			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)		GGAAGATGTTCAAGTTAGAGA	0.289000																								0							SO:0001583	missense			ENST00000357388.3	1	0	hg19	CCDS3189.1	.	.	.	.	.	.	.	.	.	.	C	6.676	0.493216	0.12702	.	.	ENSG00000113810	ENST00000357388;ENST00000360111;ENST00000392788;ENST00000469762;ENST00000489573;ENST00000462787;ENST00000344722	T;T;T;T;T;T	0.73152	-0.69;-0.72;-0.7;0.41;-0.72;-0.69	5.49	5.49	0.81192	RecF/RecN/SMC (1);	0.163089	0.53938	D	0.000045	T	0.41282	0.1152	N	0.02765	-0.5	0.35709	D	0.816222	B;B;B;B	0.12013	0.0;0.001;0.0;0.005	B;B;B;B	0.14023	0.002;0.002;0.001;0.01	T	0.48399	-0.9039	10	0.05833	T	0.94	-13.6609	10.8952	0.47019	0.1516:0.7182:0.1301:0.0	.	399;374;374;399	Q9NTJ3-2;B3KXX5;E9PD53;Q9NTJ3	.;.;.;SMC4_HUMAN	K	399;399;399;374;399;399;399	ENSP00000349961:Q399K;ENSP00000353225:Q399K;ENSP00000417964:Q374K;ENSP00000420121:Q399K;ENSP00000420734:Q399K;ENSP00000341382:Q399K	ENSP00000341382:Q399K	Q	+	1	0	SMC4	161614922	1.000000	0.71417	1.000000	0.80357	0.487000	0.33371	3.146000	0.50631	2.583000	0.87209	0.650000	0.86243	CAA		TCGA-IB-A7LX-01A-12D-A36O-08	SMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352862.1	1	0	0	15	358	0	84	0	7.318526e-01	0	63	0	84	2		0	0	0	0	0	2	1	0.999866	15	353	0	84	2		0	0	0	0	84	2	-3.221883	1	1	0	0		1	1	3	4	2.284976	1	0.550000	3.150000	0.707602	0.230000	0.120000	0.380000	0.230000	0.245974	0.230000	0	1.700000e-01	3.000000e-01
MFN1	55669	broad.mit.edu	37	3	179069714	179069714	+	Silent	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr3:179069714C>A	ENST00000471841.1	+	3	265	c.139C>A	c.(139-141)Cga>Aga	p.R47R	MFN1_ENST00000263969.5_Silent_p.R47R|MFN1_ENST00000280653.7_Silent_p.R47R	NM_033540.2	NP_284941	Q8IWA4	MFN1_HUMAN	mitofusin 1	p.R47*(1)		31	all_cancers(143;1.67e-16)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.00225)|BRCA - Breast invasive adenocarcinoma(182;0.0923)		GGAACTTGATCGAATAGCCAC	0.353000																								1	Substitution - Nonsense(1)						SO:0001819	synonymous_variant			ENST00000471841.1	1	0	hg19	CCDS3228.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	MFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348654.2	1	0	0	18	479	0	117	0	6.098508e-01	0	54	0	117	2		0	0	0	0	0	2	1	0.999979	18	470	0	117	2		0	0	0	0	117	2	-3.302474	1	1	0	0		1	1	3	4	2.284976	1	0.550000	3.150000	0.707602	0.200000	0.110000	0.330000	0.200000	0.220622	0.200000	0	1.500000e-01	2.600000e-01
ACTL6A	86	broad.mit.edu	37	3	179291168	179291168	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr3:179291168G>A	ENST00000429709.2	+	4	502	c.289G>A	c.(289-291)Gat>Aat	p.D97N	ACTL6A_ENST00000392662.1_Missense_Mutation_p.D55N|ACTL6A_ENST00000450518.2_Missense_Mutation_p.D55N	NM_004301.3	NP_004292.1	O96019	ACL6A_HUMAN	actin-like 6A			21	all_cancers(143;3.94e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.98e-26)|GBM - Glioblastoma multiforme(14;0.0169)		TGAAGACTGGGATAGTTTCCA	0.353000																								0							SO:0001583	missense			ENST00000429709.2	0	1	hg19	CCDS3231.1	.	.	.	.	.	.	.	.	.	.	G	34	5.398826	0.96030	.	.	ENSG00000136518	ENST00000429709;ENST00000450518;ENST00000392662	D;D;D	0.95853	-3.83;-3.83;-3.83	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	D	0.96439	0.8838	M	0.64260	1.97	0.80722	D	1	D	0.52996	0.957	P	0.53954	0.738	D	0.96821	0.9604	10	0.87932	D	0	.	19.2768	0.94034	0.0:0.0:1.0:0.0	.	97	O96019	ACL6A_HUMAN	N	97;55;55	ENSP00000397552:D97N;ENSP00000394014:D55N;ENSP00000376430:D55N	ENSP00000376430:D55N	D	+	1	0	ACTL6A	180773862	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.686000	0.98664	2.625000	0.88918	0.555000	0.69702	GAT		TCGA-IB-A7LX-01A-12D-A36O-08	ACTL6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349599.1	0	0	0	13	607	0	144	1	8.162320e-01	4	144	0	144	2		0	0	0	0	0	2	1	0.999457	13	593	0	143	2		0	0	0	0	144	2	-3.068190	1	0	121412	1	27	1	1	3	4	2.284976	1	0.550000	3.150000	0.707602	0.110000	0.050000	0.210000	0.120000	0.134363	0.110000	0	8.000000e-02	1.600000e-01
MCF2L2	23101	broad.mit.edu	37	3	182923997	182923997	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr3:182923997C>A	ENST00000328913.3	-	24	3015	c.2718G>T	c.(2716-2718)atG>atT	p.M906I	MCF2L2_ENST00000468976.1_5'UTR|MCF2L2_ENST00000473233.1_Missense_Mutation_p.M906I	NM_015078.2	NP_055893	Q86YR7	MF2L2_HUMAN	MCF.2 cell line derived transforming sequence-like 2			72	all_cancers(143;1.26e-12)|Ovarian(172;0.0355)		all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)		TTGAAAGTGTCATCAGCTATT	0.408000																								0							SO:0001583	missense			ENST00000328913.3	1	0	hg19	CCDS3243.1	.	.	.	.	.	.	.	.	.	.	C	4.420	0.077657	0.08485	.	.	ENSG00000053524	ENST00000328913;ENST00000473233	T;T	0.11063	2.81;2.81	4.28	1.25	0.21368	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	1.050980	0.07506	N	0.908130	T	0.08179	0.0204	L	0.29908	0.895	0.20975	N	0.999815	B	0.06786	0.001	B	0.04013	0.001	T	0.38112	-0.9676	10	0.56958	D	0.05	.	3.9497	0.09363	0.0:0.5782:0.1998:0.222	.	906	Q86YR7	MF2L2_HUMAN	I	906	ENSP00000328118:M906I;ENSP00000420070:M906I	ENSP00000328118:M906I	M	-	3	0	MCF2L2	184406691	0.023000	0.18921	0.360000	0.25837	0.118000	0.20060	0.077000	0.14738	0.553000	0.29044	0.563000	0.77884	ATG		TCGA-IB-A7LX-01A-12D-A36O-08	MCF2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350868.1	1	0	0	16	367	0	79		0	0	0	0	79	2		0	0	0	0	0	2	1	0.999930	16	362	0	79	2		0	0	0	0	79	2	-4.050431	1	1	0	0		1	1	3	4	2.284976	1	0.550000	3.150000	0.707602	0.230000	0.130000	0.390000	0.240000	0.254224	0.230000	0	1.800000e-01	3.100000e-01
TP63	8626	broad.mit.edu	37	3	189612250	189612250	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr3:189612250C>A	ENST00000264731.3	+	14	2091	c.2002C>A	c.(2002-2004)Cgc>Agc	p.R668S	TP63_ENST00000440651.2_Missense_Mutation_p.R664S|TP63_ENST00000449992.1_Missense_Mutation_p.R489S|TP63_ENST00000456148.1_Missense_Mutation_p.R570S|TP63_ENST00000382063.4_Missense_Mutation_p.R583S|TP63_ENST00000320472.5_3'UTR|TP63_ENST00000354600.5_Missense_Mutation_p.R574S	NM_001114978.1|NM_003722.4	NP_001108450.1|NP_003713.3	Q9H3D4	P63_HUMAN	tumor protein p63			61	all_cancers(143;3.35e-10)|Ovarian(172;0.0925)		Lung(62;3.33e-05)		CATGGATGCTCGCCGCAATAA	0.542000										HNSCC(45;0.13)														0							SO:0001583	missense			ENST00000264731.3	1	0	hg19	CCDS3293.1	.	.	.	.	.	.	.	.	.	.	C	16.73	3.202877	0.58234	.	.	ENSG00000073282	ENST00000264731;ENST00000440651;ENST00000382063;ENST00000354600;ENST00000449992;ENST00000456148	D;D;D;D;D;D	0.90133	-2.62;-2.62;-2.62;-2.62;-2.62;-2.62	5.91	5.91	0.95273	.	0.108147	0.64402	D	0.000006	D	0.84701	0.5530	N	0.19112	0.55	0.80722	D	1	B;B;B	0.18968	0.028;0.028;0.032	B;B;B	0.20955	0.032;0.032;0.026	T	0.78620	-0.2133	9	.	.	.	-11.7075	19.2867	0.94077	0.0:1.0:0.0:0.0	.	489;574;668	Q9H3D4-10;Q9H3D4-2;Q9H3D4	.;.;P63_HUMAN	S	668;664;583;574;489;570	ENSP00000264731:R668S;ENSP00000394337:R664S;ENSP00000371495:R583S;ENSP00000346614:R574S;ENSP00000387839:R489S;ENSP00000389485:R570S	.	R	+	1	0	TP63	191094944	1.000000	0.71417	0.990000	0.47175	0.746000	0.42486	5.598000	0.67585	2.793000	0.96121	0.655000	0.94253	CGC		TCGA-IB-A7LX-01A-12D-A36O-08	TP63-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000343865.1	1	0	0	13	263	0	59	0	1.400073e-01	0	13	0	59	2		0	0	0	0	0	2	1	0.999462	13	254	0	58	2		0	0	0	0	59	2	-3.094281	1	1	0	0		1	1	3	4	2.284976	1	0.550000	3.150000	0.707602	0.270000	0.140000	0.460000	0.270000	0.288450	0.270000	0	2.000000e-01	3.600000e-01
RPL35A	6165	broad.mit.edu	37	3	197680900	197680900	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08			C	A	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr3:197680900C>A	ENST00000464167.1	+	4	458	c.191C>A	c.(190-192)cCa>cAa	p.P64Q	RPL35A_ENST00000329092.8_3'UTR|IQCG_ENST00000480302.1_Intron|IQCG_ENST00000265239.6_Intron|RPL35A_ENST00000448864.1_Missense_Mutation_p.P64Q	NM_000996.2	NP_000987.2	P18077	RL35A_HUMAN	ribosomal protein L35a			3	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)	Lung NSC(153;0.132)	Epithelial(36;1.04e-23)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)		GGCGGCAAACCAAACAAAACC	0.453000																								0							SO:0001583	missense			ENST00000464167.1	1	0	hg19	CCDS33930.1	.	.	.	.	.	.	.	.	.	.	C	16.31	3.087892	0.55968	.	.	ENSG00000182899	ENST00000464167;ENST00000448864;ENST00000442341	.	.	.	5.35	5.35	0.76521	Translation elongation/initiation factor/Ribosomal, beta-barrel (1);	0.000000	0.85682	D	0.000000	T	0.71367	0.3331	M	0.80616	2.505	0.80722	D	1	B	0.12630	0.006	B	0.24269	0.052	T	0.67906	-0.5549	9	0.31617	T	0.26	-21.202	19.1227	0.93369	0.0:1.0:0.0:0.0	.	64	P18077	RL35A_HUMAN	Q	64	.	ENSP00000387688:P64Q	P	+	2	0	RPL35A	199165297	1.000000	0.71417	0.997000	0.53966	0.982000	0.71751	7.755000	0.85180	2.530000	0.85305	0.558000	0.71614	CCA		TCGA-IB-A7LX-01A-12D-A36O-08	RPL35A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339788.1	1	0	0	8	214	0	45	1	1	3	7282	0	45	2		0	0	0	0	0	2	1	0.989940	8	215	0	44	2		0	0	0	0	45	2	-3.079547	1	0	0	0		1	1	3	4	2.284976	1	0.550000	3.150000	0.707602	0.210000	0.090000	0.410000	0.200000	0.232034	0.210000	0	1.400000e-01	3.000000e-01
JAGN1	84522	broad.mit.edu	37	3	9934901	9934901	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr3:9934901G>A	ENST00000307768.4	+	2	561	c.392G>A	c.(391-393)cGc>cAc	p.R131H		NM_032492.3	NP_115881.3			jagunal homolog 1 (Drosophila)			10	Medulloblastoma(99;0.227)				CAGCTCTACCGCCATGGCAAG	0.527000																								0							SO:0001583	missense			ENST00000307768.4	1	1	hg19	CCDS2588.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.6|20.6	4.014448|4.014448	0.75161|0.75161	.|.	.|.	ENSG00000171135|ENSG00000171135	ENST00000543379|ENST00000307768	.|.	.|.	.|.	5.73|5.73	3.76|3.76	0.43208|0.43208	.|.	.|0.054409	.|0.64402	.|D	.|0.000001	T|T	0.74099|0.74099	0.3672|0.3672	M|M	0.84082|0.84082	2.675|2.675	0.53005|0.53005	D|D	0.999963|0.999963	.|D	.|0.63880	.|0.993	.|P	.|0.55713	.|0.782	T|T	0.78671|0.78671	-0.2113|-0.2113	6|9	0.13853|0.66056	T|D	0.58|0.02	-22.0269|-22.0269	11.9619|11.9619	0.53013|0.53013	0.071:0.0:0.7989:0.13|0.071:0.0:0.7989:0.13	.|.	.|131	.|Q8N5M9	.|JAGN1_HUMAN	T|H	130|131	.|.	ENSP00000442889:A130T|ENSP00000306106:R131H	A|R	+|+	1|2	0|0	JAGN1|JAGN1	9909901|9909901	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.933000|0.933000	0.57130|0.57130	7.496000|7.496000	0.81526|0.81526	1.434000|1.434000	0.47414|0.47414	-0.339000|-0.339000	0.08088|0.08088	GCC|CGC		TCGA-IB-A7LX-01A-12D-A36O-08	JAGN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250335.1	0	0	0	16	386	1	130	1	7.515957e-01	17	317	1	130	11		0	0	0	0	0	2	1	0.817874	16	379	1	130	12		0	0	0	1	130	2	-3.461198	1	1	121412	8	40	1	1	2	3	1.822614	1	0.550000	3.150000	0.635258	0.180000	0.100000	1.000000	0.170000	0.284895	0.180000	0	1.400000e-01	2.700000e-01
SPATA5	166378	broad.mit.edu	37	4	123859326	123859326	+	Silent	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr4:123859326G>T	ENST00000274008.4	+	8	1449	c.1380G>T	c.(1378-1380)ccG>ccT	p.P460P	SPATA5_ENST00000422835.2_3'UTR	NM_145207.2	NP_660208.2	Q8NB90	SPAT5_HUMAN	spermatogenesis associated 5			24					CACTTTGTCCGAAAAGAGAGG	0.353000																								0							SO:0001819	synonymous_variant			ENST00000274008.4	1	0	hg19	CCDS3730.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	SPATA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256714.2	1	0	0	14	367	0	116	0	1.492716e-02	0	5	0	116	2		0	0	0	0	0	2	1	0.999743	14	362	0	114	2		0	0	0	0	116	2	-3.056472	1	1	0	0		1	2	3	5	1.795702	1	0.550000	3.150000	0.621769	0.170000	0.080000	1.000000	0.160000	0.309474	0.170000	0	1.200000e-01	1
FAT4	79633	broad.mit.edu	37	4	126411862	126411862	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr4:126411862G>A	ENST00000394329.3	+	17	13898	c.13885G>A	c.(13885-13887)Gcc>Acc	p.A4629T	FAT4_ENST00000335110.5_Missense_Mutation_p.A2870T	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4			355					CAGCAGCATCGCCCCTTCGGA	0.512000																								0							SO:0001583	missense			ENST00000394329.3	1	1	hg19	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	G	17.86	3.493760	0.64186	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	D;D	0.91945	-2.94;-2.39	4.95	4.95	0.65309	.	0.000000	0.34110	U	0.004241	D	0.94807	0.8323	L	0.54323	1.7	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.995;0.998	D	0.94547	0.7750	10	0.45353	T	0.12	.	17.186	0.86867	0.0:0.0:1.0:0.0	.	2870;4629;4628	Q6V0I7-2;Q6V0I7;Q6V0I7-3	.;FAT4_HUMAN;.	T	4629;2870	ENSP00000377862:A4629T;ENSP00000335169:A2870T	ENSP00000335169:A2870T	A	+	1	0	FAT4	126631312	1.000000	0.71417	1.000000	0.80357	0.694000	0.40290	9.440000	0.97547	2.275000	0.75901	0.561000	0.74099	GCC		TCGA-IB-A7LX-01A-12D-A36O-08	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	1	0	0	11	163	0	64	0	4.268310e-02	0	5	0	64	2		0	0	0	0	0	2	1	0.998503	11	163	0	64	2		0	0	0	0	64	2	-3.318043	1	1	121412	1	29	1	2	3	5	1.795702	1	0.550000	3.150000	0.621769	0.300000	0.150000	1.000000	0.270000	0.413185	0.300000	0	2.100000e-01	1
RPS3A	6189	broad.mit.edu	37	4	152021718	152021718	+	Silent	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08			C	A	C	C		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr4:152021718C>A	ENST00000274065.4	+	2	224	c.144C>A	c.(142-144)ctC>ctA	p.L48L	RPS3A_ENST00000322686.6_Silent_p.L35L|SNORD73_ENST00000364394.1_RNA|RPS3A_ENST00000506126.1_Silent_p.L11L|RPS3A_ENST00000512690.1_Silent_p.L48L|RPS3A_ENST00000509736.1_Intron|RPS3A_ENST00000514682.1_Silent_p.L11L	NM_001006.4	NP_000997.1			ribosomal protein S3A			4	all_hematologic(180;0.093)				GAAAGACGCTCGTCACCAGGA	0.393000																								0							SO:0001819	synonymous_variant			ENST00000274065.4	1	0	hg19	CCDS3775.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	RPS3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364957.1	1	0	0	14	214	0	79	0	1	0	3517	0	79	2		0	0	0	0	0	2	1	0.999768	14	212	0	79	2		0	0	0	0	79	2	-3.076017	1	1	0	0		1	2	3	5	1.795702	1	0.550000	3.150000	0.621769	0.280000	0.150000	1.000000	0.270000	0.402755	0.280000	0	2.100000e-01	1
GPR125	166647	broad.mit.edu	37	4	22389706	22389706	+	Silent	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr4:22389706C>A	ENST00000334304.5	-	19	3857	c.3588G>T	c.(3586-3588)acG>acT	p.T1196T	GPR125_ENST00000282943.5_5'UTR	NM_145290.3	NP_660333.2	Q8IWK6	GP125_HUMAN	G protein-coupled receptor 125			56		Breast(46;0.198)			CTTCCACGCTCGTTGGGACAT	0.517000																								0							SO:0001819	synonymous_variant			ENST00000334304.5	1	0	hg19	CCDS33964.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	GPR125-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362960.3	1	0	0	25	534	0	188	0	9.846938e-01	0	144	0	188	2		0	0	0	0	0	2	1	1.000000	25	528	0	185	2		0	0	0	0	188	2	-2.774725	1	1	0	0		1	1	3	4	2.081941	1	0.550000	3.150000	0.664430	0.230000	0.140000	1.000000	0.220000	0.402285	0.230000	0	1.800000e-01	1
NOP14	8602	broad.mit.edu	37	4	2958537	2958537	+	Splice_Site	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr4:2958537C>A	ENST00000314262.6	-	3	380	c.332G>T	c.(331-333)cGa>cTa	p.R111L	NOP14_ENST00000416614.2_Splice_Site_p.R111L|NOP14_ENST00000398071.4_Splice_Site_p.R111L|NOP14_ENST00000502735.1_Splice_Site_p.R111L|NOP14-AS1_ENST00000503709.1_RNA	NM_003703.1	NP_003694.1	P78316	NOP14_HUMAN	NOP14 nucleolar protein			30					CTCATGATGTCGCTGACAGAA	0.313000																								0							SO:0001630	splice_region_variant			ENST00000314262.6	1	0	hg19	CCDS33945.1	.	.	.	.	.	.	.	.	.	.	C	19.99	3.927925	0.73327	.	.	ENSG00000087269	ENST00000416614;ENST00000314262;ENST00000502735;ENST00000398071;ENST00000546137	T;T;T;T	0.35973	1.28;1.28;1.28;1.28	5.41	4.53	0.55603	.	0.227351	0.39615	N	0.001308	T	0.54481	0.1861	M	0.80982	2.52	0.80722	D	1	P;P	0.51057	0.897;0.941	P;P	0.61658	0.892;0.856	T	0.57682	-0.7769	10	0.87932	D	0	-6.5327	6.3695	0.21473	0.0:0.6616:0.0:0.3384	.	111;111	E9PFK5;P78316	.;NOP14_HUMAN	L	111;111;111;111;10	ENSP00000405068:R111L;ENSP00000315674:R111L;ENSP00000427415:R111L;ENSP00000381146:R111L	ENSP00000315674:R111L	R	-	2	0	NOP14	2928335	0.999000	0.42202	1.000000	0.80357	0.995000	0.86356	2.917000	0.48821	1.199000	0.43173	0.655000	0.94253	CGA		TCGA-IB-A7LX-01A-12D-A36O-08	NOP14-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000358135.2	1	0	0	8	164	0	46	0	7.497036e-01	0	56	0	46	2		0	0	0	0	0	2	1	0.989394	8	162	0	45	2		0	0	0	0	46	2	-10.603720	1	1	0	0		1	1	3	4	2.081941	1	0.550000	3.150000	0.664430	0.270000	0.110000	1.000000	0.230000	0.422119	0.270000	0	1.700000e-01	1
TBC1D1	23216	broad.mit.edu	37	4	38134830	38134830	+	Silent	SNP	C	C	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr4:38134830C>T	ENST00000261439.4	+	19	3613	c.3258C>T	c.(3256-3258)acC>acT	p.T1086T	TBC1D1_ENST00000508802.1_Silent_p.T1077T|TBC1D1_ENST00000407365.1_3'UTR	NM_001253914.1|NM_001253915.1|NM_015173.3	NP_001240843.1|NP_001240844.1|NP_055988.2	Q86TI0	TBCD1_HUMAN	TBC1 (tre-2/USP6, BUB2, cdc16) domain family, member 1			36					TAGAGAAAACCAACAGCAGCT	0.393000																								0							SO:0001819	synonymous_variant			ENST00000261439.4	1	1	hg19	CCDS33972.1	.	.	.	.	.	.	.	.	.	.	C	9.867	1.197786	0.22037	.	.	ENSG00000065882	ENST00000510573	.	.	.	4.97	4.13	0.48395	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-27.4575	6.939	0.24483	0.2837:0.6293:0.0:0.087	.	.	.	.	X	774	.	.	Q	+	1	0	TBC1D1	37811225	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	2.306000	0.43673	1.445000	0.47624	0.655000	0.94253	CAA		TCGA-IB-A7LX-01A-12D-A36O-08	TBC1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317443.2	0	0	0	15	222	0	81	1	9.802797e-01	9	91	0	81	2		0	0	0	0	0	2	1	0.999880	15	220	0	81	2		0	0	0	0	81	2	-3.017629	1	0	121412	1	28	1	2	2	4	1.763541	1	0.550000	3.150000	0.613734	0.290000	0.160000	1.000000	0.260000	0.427790	0.290000	0	2.100000e-01	1
FRYL	285527	broad.mit.edu	37	4	48584630	48584630	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr4:48584630G>T	ENST00000503238.1	-	17	1869	c.1870C>A	c.(1870-1872)Cgt>Agt	p.R624S	FRYL_ENST00000506685.1_Missense_Mutation_p.R330S|FRYL_ENST00000507711.1_Missense_Mutation_p.R624S|FRYL_ENST00000537810.1_Missense_Mutation_p.R624S|FRYL_ENST00000264319.7_5'UTR|FRYL_ENST00000358350.4_Missense_Mutation_p.R624S			O94915	FRYL_HUMAN	FRY-like			91					GTCACTTCACGAACAATAAAA	0.398000																								0							SO:0001583	missense			ENST00000503238.1	1	0	hg19	CCDS43227.1	.	.	.	.	.	.	.	.	.	.	G	16.54	3.151439	0.57151	.	.	ENSG00000075539	ENST00000503238;ENST00000358350;ENST00000537810;ENST00000507711;ENST00000506685	T;T;T;T;T	0.64260	3.64;3.64;3.64;3.64;-0.09	5.63	5.63	0.86233	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.64402	U	0.000001	T	0.75459	0.3852	L	0.51422	1.61	0.80722	D	1	D;P	0.64830	0.994;0.869	D;P	0.74023	0.982;0.724	T	0.70872	-0.4754	10	0.34782	T	0.22	.	20.0499	0.97621	0.0:0.0:1.0:0.0	.	624;624	F2Z2S2;O94915	.;FRYL_HUMAN	S	624;624;624;624;330	ENSP00000426064:R624S;ENSP00000351113:R624S;ENSP00000441114:R624S;ENSP00000421584:R624S;ENSP00000425592:R330S	ENSP00000351113:R624S	R	-	1	0	FRYL	48279387	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.926000	0.63433	2.798000	0.96311	0.655000	0.94253	CGT		TCGA-IB-A7LX-01A-12D-A36O-08	FRYL-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369265.2	1	0	0	9	206	0	77	0	1.064061e-01	0	12	0	77	2		0	0	0	0	0	2	1	0.994144	9	203	0	76	2		0	0	0	0	77	2	-3.808958	1	1	0	0		1	2	2	4	1.763541	1	0.550000	3.150000	0.613734	0.200000	0.090000	1.000000	0.180000	0.357415	0.200000	0	1.300000e-01	1
TMPRSS11D	9407	broad.mit.edu	37	4	68725370	68725370	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr4:68725370C>T	ENST00000283916.6	-	2	133	c.35G>A	c.(34-36)aGa>aAa	p.R12K	TMPRSS11D_ENST00000545541.1_Intron|TMPRSS11D_ENST00000509584.1_Intron|UBA6-AS1_ENST00000500538.2_RNA	NM_004262.2	NP_004253.1	O60235	TM11D_HUMAN	transmembrane protease, serine 11D			23					ATTCAGAAATCTTGAAGTCGA	0.388000																								0							SO:0001583	missense			ENST00000283916.6	1	1	hg19	CCDS3518.1	.	.	.	.	.	.	.	.	.	.	C	19.86	3.905995	0.72868	.	.	ENSG00000153802	ENST00000283916	D	0.88046	-2.33	5.19	5.19	0.71726	.	0.000000	0.64402	D	0.000010	D	0.89529	0.6741	L	0.61387	1.9	0.80722	D	1	D	0.67145	0.996	P	0.54759	0.76	D	0.88677	0.3199	10	0.41790	T	0.15	.	14.0925	0.65000	0.0:1.0:0.0:0.0	.	12	O60235	TM11D_HUMAN	K	12	ENSP00000283916:R12K	ENSP00000283916:R12K	R	-	2	0	TMPRSS11D	68407965	1.000000	0.71417	0.997000	0.53966	0.591000	0.36615	1.993000	0.40747	2.704000	0.92352	0.563000	0.77884	AGA		TCGA-IB-A7LX-01A-12D-A36O-08	TMPRSS11D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251430.3	1	0	1	66	188	0	67		0	0	0	0	67	2		0	0	0	0	0	2	1	1.000000	66	186	0	66	2		0	0	0	0	67	2	-20.000000	1	1	0	0		1	2	2	4	1.763541	1	0.550000	3.150000	0.613734	0.990000	0.890000	1.000000	1.000000	0.991382	0.990000	1	9.900000e-01	1
MCC	4163	broad.mit.edu	37	5	112720776	112720776	+	Silent	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr5:112720776G>T	ENST00000408903.3	-	2	719	c.304C>A	c.(304-306)Cga>Aga	p.R102R	CTD-2201G3.1_ENST00000416046.2_RNA	NM_001085377.1	NP_001078846	P23508	CRCM_HUMAN	mutated in colorectal cancers			42		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)			CTAATTTCTCGAACAAGCTGC	0.458000																								0							SO:0001819	synonymous_variant			ENST00000408903.3	1	0	hg19	CCDS43351.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	MCC-003	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370839.1	1	0	0	14	374	0	116	0	3.704771e-02	0	8	0	116	2		0	0	0	0	0	2	1	0.999738	14	368	0	116	2		0	0	0	0	116	2	-3.267031	1	1	0	0		1	1	2	3	1.889547	1	0.550000	3.150000	0.646296	0.160000	0.090000	0.280000	0.170000	0.177686	0.160000	0	1.200000e-01	2.200000e-01
MYOT	9499	broad.mit.edu	37	5	137219194	137219194	+	Missense_Mutation	SNP	T	T	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr5:137219194T>A	ENST00000239926.4	+	7	1312	c.938T>A	c.(937-939)gTc>gAc	p.V313D	MYOT_ENST00000509812.1_Intron|RP11-381K20.2_ENST00000514616.1_RNA|MYOT_ENST00000515645.1_Missense_Mutation_p.V198D|MYOT_ENST00000421631.2_Missense_Mutation_p.V129D|RP11-381K20.2_ENST00000508281.2_RNA	NM_006790.2	NP_006781	Q9UBF9	MYOTI_HUMAN	myotilin			23			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)		TTTGAAGTAGTCAGAGCTTCA	0.443000																								0							SO:0001583	missense			ENST00000239926.4	1	1	hg19	CCDS4194.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.221755	0.79464	.	.	ENSG00000120729	ENST00000239926;ENST00000421631;ENST00000515645	T;T;T	0.72505	-0.66;-0.66;-0.66	5.08	5.08	0.68730	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.56097	D	0.000032	D	0.88276	0.6393	H	0.95816	3.725	0.80722	D	1	D	0.76494	0.999	D	0.71184	0.972	D	0.91887	0.5520	10	0.87932	D	0	.	15.1564	0.72746	0.0:0.0:0.0:1.0	.	313	Q9UBF9	MYOTI_HUMAN	D	313;129;198	ENSP00000239926:V313D;ENSP00000391185:V129D;ENSP00000426281:V198D	ENSP00000239926:V313D	V	+	2	0	MYOT	137247093	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	6.191000	0.72063	2.021000	0.59480	0.533000	0.62120	GTC		TCGA-IB-A7LX-01A-12D-A36O-08	MYOT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251219.2	1	0	1	45	242	0	85		0	0	0	0	85	2		0	0	0	0	0	2	1	1.000000	44	235	0	85	2		0	0	0	0	85	2	-19.998670	1	1	0	0		1	1	2	3	1.889547	1	0.550000	3.150000	0.646296	0.720000	0.540000	0.940000	0.720000	0.734723	0.720000	0	6.300000e-01	8.300000e-01
PCDHB14	56122	broad.mit.edu	37	5	140603942	140603942	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr5:140603942C>A	ENST00000239449.4	+	1	865	c.865C>A	c.(865-867)Cgt>Agt	p.R289S	PCDHB14_ENST00000515856.2_Missense_Mutation_p.R136S	NM_018934.2	NP_061757.1	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14			49			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)		AGAAGATATTCGTAAAACATT	0.378000													Ovarian(141;50 1831 27899 33809 37648)											0							SO:0001583	missense			ENST00000239449.4	1	0	hg19	CCDS4256.1	.	.	.	.	.	.	.	.	.	.	-	6.356	0.433698	0.12045	.	.	ENSG00000120327	ENST00000515856;ENST00000239449	T;T	0.50001	0.76;0.76	4.75	0.286	0.15710	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.22282	0.0537	N	0.16602	0.42	0.09310	N	1	B	0.15141	0.012	B	0.15052	0.012	T	0.28396	-1.0045	9	0.02654	T	1	.	4.3959	0.11363	0.2528:0.4394:0.2343:0.0735	.	289	Q9Y5E9	PCDBE_HUMAN	S	136;289	ENSP00000444518:R136S;ENSP00000239449:R289S	ENSP00000239449:R289S	R	+	1	0	PCDHB14	140584126	0.000000	0.05858	0.078000	0.20375	0.873000	0.50193	-0.821000	0.04452	0.109000	0.17891	0.655000	0.94253	CGT		TCGA-IB-A7LX-01A-12D-A36O-08	PCDHB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251814.2	1	0	0	11	240	0	66	0	3.963645e-01	0	29	0	66	2		0	0	0	0	0	2	1	0.998331	11	237	0	66	2		0	0	0	0	66	2	-12.871820	1	0	121402	1	31	1	1	2	3	1.889547	1	0.550000	3.150000	0.646296	0.200000	0.100000	0.360000	0.210000	0.218956	0.200000	0	1.500000e-01	2.800000e-01
TCERG1	10915	broad.mit.edu	37	5	145859431	145859431	+	Silent	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr5:145859431G>T	ENST00000296702.5	+	11	1814	c.1776G>T	c.(1774-1776)ccG>ccT	p.P592P	TCERG1_ENST00000394421.2_Silent_p.P571P	NM_006706.3	NP_006697.2	O14776	TCRG1_HUMAN	transcription elongation regulator 1			46		Lung NSC(249;0.00188)|all_lung(500;0.00307)|all_neural(839;0.0424)|Breast(839;0.0743)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		ACCCAACTCCGACAATGCTGT	0.323000																								0							SO:0001819	synonymous_variant			ENST00000296702.5	1	0	hg19	CCDS4282.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	TCERG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251886.1	1	0	0	10	232	0	51	0	5.719337e-01	0	44	0	51	2		0	0	0	0	0	2	1	0.996725	10	227	0	51	2		0	0	0	0	51	2	-3.110063	1	1	0	0		1	1	2	3	1.889547	1	0.550000	3.150000	0.646296	0.190000	0.090000	0.350000	0.180000	0.208096	0.190000	0	1.400000e-01	2.700000e-01
SLU7	10569	broad.mit.edu	37	5	159839519	159839519	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr5:159839519C>A	ENST00000297151.4	-	6	965	c.578G>T	c.(577-579)cGa>cTa	p.R193L		NM_006425.4	NP_006416.3	O95391	SLU7_HUMAN	SLU7 splicing factor homolog (S. cerevisiae)			20	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		TTTCAATGTTCGTTTTGCCTT	0.274000																								0							SO:0001583	missense			ENST00000297151.4	1	0	hg19	CCDS4352.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.554570	0.86231	.	.	ENSG00000164609	ENST00000297151	T	0.45668	0.89	5.68	4.81	0.61882	Pre-mRNA splicing Prp18-interacting factor (1);	0.051383	0.85682	D	0.000000	T	0.57651	0.2068	M	0.75150	2.29	0.80722	D	1	P	0.51147	0.942	P	0.54140	0.743	T	0.64071	-0.6493	10	0.87932	D	0	-28.4394	14.4844	0.67606	0.0:0.9296:0.0:0.0704	.	193	O95391	SLU7_HUMAN	L	193	ENSP00000297151:R193L	ENSP00000297151:R193L	R	-	2	0	SLU7	159772097	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.749000	0.74883	1.403000	0.46800	0.650000	0.86243	CGA		TCGA-IB-A7LX-01A-12D-A36O-08	SLU7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252673.1	1	0	0	13	318	0	79	0	8.083668e-01	0	78	0	79	2		0	0	0	0	0	2	1	0.999404	13	307	0	76	2		0	0	0	0	79	2	-2.920853	1	1	0	0		1	1	2	3	1.889547	1	0.550000	3.150000	0.646296	0.180000	0.090000	0.310000	0.180000	0.194181	0.180000	0	1.300000e-01	2.500000e-01
TSPAN17	26262	broad.mit.edu	37	5	176084641	176084641	+	Missense_Mutation	SNP	G	G	T	rs141018454		TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr5:176084641G>T	ENST00000503045.1	+	9	927	c.872G>T	c.(871-873)cGa>cTa	p.R291L	TSPAN17_ENST00000405525.2_3'UTR|TSPAN17_ENST00000515708.1_3'UTR|TSPAN17_ENST00000310032.8_Missense_Mutation_p.R314L|TSPAN17_ENST00000298564.10_3'UTR|TSPAN17_ENST00000508164.1_Missense_Mutation_p.R311L			Q96FV3	TSN17_HUMAN	tetraspanin 17			13	all_cancers(89;0.00141)|Renal(175;0.000269)|Lung NSC(126;0.00814)|all_lung(126;0.0133)	Medulloblastoma(196;0.00498)|all_neural(177;0.0212)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		ccacccagccgacatgttttc	0.537000																								0							SO:0001583	missense			ENST00000503045.1	1	0	hg19		.	.	.	.	.	.	.	.	.	.	G	13.99	2.403196	0.42613	.	.	ENSG00000048140	ENST00000310032;ENST00000508164;ENST00000503045	T;T;T	0.17528	3.13;3.14;2.27	2.8	-5.59	0.02505	.	.	.	.	.	T	0.06142	0.0159	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.33317	-0.9873	9	0.87932	D	0	.	0.7854	0.01047	0.235:0.3522:0.1684:0.2445	.	311	Q96FV3-4	.	L	314;311;291	ENSP00000309036:R314L;ENSP00000422053:R311L;ENSP00000425212:R291L	ENSP00000309036:R314L	R	+	2	0	TSPAN17	176017247	0.000000	0.05858	0.000000	0.03702	0.121000	0.20230	-1.876000	0.01633	-1.978000	0.00993	-0.339000	0.08088	CGA		TCGA-IB-A7LX-01A-12D-A36O-08	TSPAN17-008	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000372215.1	1	0	0	9	211	0	54	0	7.700399e-01	0	67	0	54	2		0	0	0	0	0	2	1	0.994019	9	207	0	54	2		0	0	0	0	54	2	-3.282755	1	1	121404	12	41	1	1	2	3	1.889547	1	0.550000	3.150000	0.646296	0.190000	0.090000	0.350000	0.180000	0.207878	0.190000	0	1.300000e-01	2.700000e-01
RUFY1	80230	broad.mit.edu	37	5	178994482	178994482	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr5:178994482G>T	ENST00000319449.4	+	4	635	c.623G>T	c.(622-624)cGa>cTa	p.R208L	RUFY1_ENST00000393438.2_Missense_Mutation_p.R100L|RUFY1_ENST00000377001.2_Missense_Mutation_p.R208L|RUFY1_ENST00000437570.2_Missense_Mutation_p.R100L	NM_025158.4	NP_079434.3	Q96T51	RUFY1_HUMAN	RUN and FYVE domain containing 1			26	all_cancers(89;0.00018)|all_epithelial(37;8.37e-05)|Renal(175;0.000159)|Lung NSC(126;0.00108)|all_lung(126;0.00195)	all_cancers(40;0.0322)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		GGAAGAGGCCGAGCGTGGCTT	0.403000										HNSCC(44;0.11)														0							SO:0001583	missense			ENST00000319449.4	1	0	hg19	CCDS4445.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	33|33	5.271432|5.271432	0.95429|0.95429	.|.	.|.	ENSG00000176783|ENSG00000176783	ENST00000502984;ENST00000508609|ENST00000319449;ENST00000377001;ENST00000437570;ENST00000393438	.|T;T;T;T	.|0.19105	.|2.17;2.17;2.17;2.17	5.43|5.43	5.43|5.43	0.79202|0.79202	.|RUN (3);	.|0.000000	.|0.85682	.|D	.|0.000000	.|T	.|0.56171	.|0.1967	M|M	0.88241|0.88241	2.94|2.94	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.97110	.|1.0	.|T	.|0.63769	.|-0.6562	.|10	.|0.87932	.|D	.|0	-15.4094|-15.4094	19.6173|19.6173	0.95639|0.95639	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|208	.|Q96T51	.|RUFY1_HUMAN	X|L	166;19|208;208;100;100	.|ENSP00000325594:R208L;ENSP00000366200:R208L;ENSP00000390025:R100L;ENSP00000377087:R100L	.|ENSP00000325594:R208L	E|R	+|+	1|2	0|0	RUFY1|RUFY1	178927088|178927088	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.876000|0.876000	0.50452|0.50452	9.481000|9.481000	0.97933|0.97933	2.712000|2.712000	0.92718|0.92718	0.557000|0.557000	0.71058|0.71058	GAG|CGA		TCGA-IB-A7LX-01A-12D-A36O-08	RUFY1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253505.2	1	0	0	9	215	0	68	0	8.642011e-01	0	88	0	68	2		0	0	0	0	0	2	1	0.994264	9	213	0	68	2		0	0	0	0	68	2	-2.896596	1	1	0	0		1	1	2	3	1.889547	1	0.550000	3.150000	0.646296	0.190000	0.090000	0.350000	0.180000	0.204208	0.190000	0	1.300000e-01	2.700000e-01
SKIV2L2	23517	broad.mit.edu	37	5	54718748	54718748	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr5:54718748G>T	ENST00000230640.5	+	26	3268	c.3014G>T	c.(3013-3015)cGa>cTa	p.R1005L	SKIV2L2_ENST00000545714.1_Missense_Mutation_p.R904L	NM_015360.4	NP_056175.3	P42285	SK2L2_HUMAN	superkiller viralicidic activity 2-like 2 (S. cerevisiae)			41		Lung NSC(810;0.000744)|Breast(144;0.181)|Prostate(74;0.194)			GAATTGCTTCGACAAATGTGT	0.383000													Melanoma(2;92 134 23744 29976 33782)											0							SO:0001583	missense			ENST00000230640.5	1	0	hg19	CCDS3967.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.694671	0.88830	.	.	ENSG00000039123	ENST00000230640;ENST00000545714	T;T	0.26373	1.74;1.74	5.79	5.79	0.91817	DSH, C-terminal (1);	0.062767	0.64402	D	0.000008	T	0.69079	0.3071	H	0.97983	4.12	0.80722	D	1	D;D	0.71674	0.998;0.984	D;D	0.71414	0.973;0.921	T	0.81202	-0.1040	10	0.87932	D	0	-10.8717	20.0281	0.97530	0.0:0.0:1.0:0.0	.	904;1005	F5H7E2;P42285	.;SK2L2_HUMAN	L	1005;904	ENSP00000230640:R1005L;ENSP00000442583:R904L	ENSP00000230640:R1005L	R	+	2	0	SKIV2L2	54754505	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.434000	0.97515	2.727000	0.93392	0.655000	0.94253	CGA		TCGA-IB-A7LX-01A-12D-A36O-08	SKIV2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214108.1	1	0	0	13	321	0	79	0	9.695676e-01	0	147	0	79	2		0	0	0	0	0	2	1	0.999531	13	318	0	79	2		0	0	0	0	79	2	-2.975620	1	1	0	0		1	1	2	3	1.889547	1	0.550000	3.150000	0.646296	0.180000	0.090000	0.300000	0.180000	0.192450	0.180000	0	1.300000e-01	2.400000e-01
AIM1	202	broad.mit.edu	37	6	106968971	106968971	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr6:106968971G>T	ENST00000369066.3	+	2	3151	c.2664G>T	c.(2662-2664)ttG>ttT	p.L888F		NM_001624.2	NP_001615	Q9UMX9	S45A2_HUMAN	absent in melanoma 1			69	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)		CCTGTGGTTTGAACAAAGAAC	0.478000																								0							SO:0001583	missense			ENST00000369066.3	1	0	hg19	CCDS34506.1	.	.	.	.	.	.	.	.	.	.	G	11.12	1.546580	0.27652	.	.	ENSG00000112297	ENST00000285105;ENST00000369066	T	0.72051	-0.62	5.99	0.198	0.15168	.	1.843970	0.02402	N	0.080812	T	0.29256	0.0728	N	0.22421	0.69	0.18873	N	0.999986	B	0.31931	0.347	B	0.25759	0.063	T	0.25187	-1.0139	10	0.52906	T	0.07	.	0.6497	0.00824	0.4479:0.1681:0.2214:0.1625	.	888	Q9Y4K1	AIM1_HUMAN	F	1296;888	ENSP00000358062:L888F	ENSP00000285105:L1296F	L	+	3	2	AIM1	107075664	0.970000	0.33590	0.009000	0.14445	0.980000	0.70556	0.373000	0.20484	0.078000	0.16900	-0.345000	0.07892	TTG		TCGA-IB-A7LX-01A-12D-A36O-08	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1	1	0	0	15	264	0	119	0	2.318775e-01	0	16	0	119	2		0	0	0	0	0	2	1	0.999863	15	257	0	119	2		0	0	0	0	119	2	-4.788704	1	1	0	0		1	0	2	2	1.365333	1	0.550000	3.150000	0.550000	0.210000	0.110000	1.000000	0.200000	0.336034	0.210000	0	1.500000e-01	1
RTN4IP1	84816	broad.mit.edu	37	6	107070789	107070789	+	Silent	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr6:107070789G>T	ENST00000369063.3	-	2	795	c.330C>A	c.(328-330)atC>atA	p.I110I	RTN4IP1_ENST00000539449.1_Silent_p.I110I	NM_032730.4	NP_116119.2	Q8WWV3	RT4I1_HUMAN	reticulon 4 interacting protein 1			13	Breast(9;0.0107)|all_epithelial(6;0.14)	all_cancers(87;9.45e-05)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.0144)	Epithelial(6;0.000873)|all cancers(7;0.00363)|BRCA - Breast invasive adenocarcinoma(8;0.00721)|OV - Ovarian serous cystadenocarcinoma(5;0.0394)		CTTCTCCTTTGATTTTCACGT	0.413000																								0							SO:0001819	synonymous_variant			ENST00000369063.3	1	0	hg19	CCDS5056.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	RTN4IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041673.1	1	0	0	16	237	0	93	0	4.033831e-02	0	5	0	93	2		0	0	0	0	0	2	1	0.999935	15	235	0	93	2		0	0	0	0	93	2	-5.935248	1	1	0	0		1	0	2	2	1.365333	1	0.550000	3.150000	0.550000	0.240000	0.130000	1.000000	0.230000	0.365482	0.240000	0	1.800000e-01	1
ROS1	6098	broad.mit.edu	37	6	117710875	117710875	+	Missense_Mutation	SNP	C	C	A	rs140178288	byFrequency	TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr6:117710875C>A	ENST00000368508.3	-	12	1595	c.1397G>T	c.(1396-1398)cGa>cTa	p.R466L	ROS1_ENST00000368507.3_Missense_Mutation_p.R475L|GOPC_ENST00000467125.1_Intron	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase		TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	162		all_cancers(87;0.00846)|all_epithelial(87;0.0242)			GTAAATGATTCGCTTGGCTTG	0.493000			T	GOPC, SDC4, SLC34A2, EZR, LRIG3	glioblastoma, NSCLC										Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		O, E	0							SO:0001583	missense			ENST00000368508.3	1	0	hg19	CCDS5116.1	.	.	.	.	.	.	.	.	.	.	C	19.56	3.850642	0.71719	.	.	ENSG00000047936	ENST00000368508;ENST00000368507	D;D	0.91631	-2.88;-2.88	5.82	4.94	0.65067	.	0.112377	0.37348	N	0.002123	D	0.90253	0.6952	L	0.32530	0.975	0.80722	D	1	D	0.76494	0.999	D	0.65684	0.937	D	0.88337	0.2972	10	0.31617	T	0.26	.	11.6854	0.51483	0.0:0.9193:0.0:0.0807	.	466	P08922	ROS1_HUMAN	L	466;475	ENSP00000357494:R466L;ENSP00000357493:R475L	ENSP00000357493:R475L	R	-	2	0	ROS1	117817568	1.000000	0.71417	0.976000	0.42696	0.482000	0.33219	4.212000	0.58514	2.755000	0.94549	0.561000	0.74099	CGA		TCGA-IB-A7LX-01A-12D-A36O-08	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1	1	0	0	8	121	0	31	0	1.475323e-02	0	3	0	31	2		0	0	0	0	0	2	1	0.985806	8	110	0	31	2		0	0	0	0	31	2	-3.326195	1	1	0	0		1	0	2	2	1.365333	1	0.550000	3.150000	0.550000	0.250000	0.110000	1.000000	0.220000	0.371014	0.250000	0	1.700000e-01	1
MAP3K5	4217	broad.mit.edu	37	6	137113237	137113237	+	Missense_Mutation	SNP	C	C	G			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08			C	G	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr6:137113237C>G	ENST00000359015.4	-	1	419	c.59G>C	c.(58-60)gGc>gCc	p.G20A		NM_005923.3	NP_005914.1	Q99683	M3K5_HUMAN	mitogen-activated protein kinase kinase kinase 5			58	Colorectal(23;0.24)				GGTGCAGAAGCCCGAGGGGGC	0.751000																								0							SO:0001583	missense			ENST00000359015.4	0	1	hg19	CCDS5179.1	.	.	.	.	.	.	.	.	.	.	C	9.984	1.228890	0.22542	.	.	ENSG00000197442	ENST00000359015;ENST00000367768	T	0.68624	-0.34	3.56	1.67	0.24075	.	0.634408	0.14920	N	0.290736	T	0.20170	0.0485	N	0.14661	0.345	0.18873	N	0.999985	B	0.13594	0.008	B	0.11329	0.006	T	0.29792	-1.0000	10	0.12103	T	0.63	.	7.361	0.26745	0.1664:0.7407:0.0:0.0929	.	20	Q99683	M3K5_HUMAN	A	20;100	ENSP00000351908:G20A	ENSP00000351908:G20A	G	-	2	0	MAP3K5	137154930	0.535000	0.26370	0.016000	0.15963	0.025000	0.11179	2.498000	0.45363	0.287000	0.22375	0.573000	0.79308	GGC		TCGA-IB-A7LX-01A-12D-A36O-08	MAP3K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042383.1	1	0	0	36	34	0	11	1	9.999725e-01	14	8	0	11	2		0	0	0	0	0	2	1	1.000000	34	34	0	11	2		0	0	0	0	11	2	-20.000000	1	1	0	0		1	2	8	10	4.331302	1	0.550000	3.150000	0.844398	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	9.900000e-01	1
UTRN	7402	broad.mit.edu	37	6	144768443	144768443	+	Silent	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr6:144768443C>A	ENST00000367545.3	+	14	1711	c.1711C>A	c.(1711-1713)Cga>Aga	p.R571R		NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	p.R571*(2)		148		Ovarian(120;0.218)			TGTCAGTGTTCGACGTCTGGC	0.383000																								2	Substitution - Nonsense(2)						SO:0001819	synonymous_variant			ENST00000367545.3	1	0	hg19	CCDS34547.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1	1	0	0	8	174	0	52	0	1.025800e-01	0	11	0	52	2		0	0	0	0	0	2	1	0.989141	8	171	0	52	2		0	0	0	0	52	2	-4.312080	1	1	0	0		1	3	4	7	2.292266	1	0.550000	3.150000	0.701740	0.280000	0.120000	1.000000	0.230000	0.432807	0.280000	0	1.800000e-01	1
MAP3K4	4216	broad.mit.edu	37	6	161514029	161514029	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr6:161514029G>T	ENST00000392142.4	+	14	3437	c.3289G>T	c.(3289-3291)Gat>Tat	p.D1097Y	MAP3K4_ENST00000366919.2_Missense_Mutation_p.D1097Y|MAP3K4_ENST00000366920.2_Missense_Mutation_p.D1097Y|MAP3K4_ENST00000348824.7_Missense_Mutation_p.D1097Y	NM_005922.2	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4			77		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)			TCAAGGATTTGATTTTCTACA	0.348000																								0							SO:0001583	missense			ENST00000392142.4	1	0	hg19	CCDS34565.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.421880	0.83559	.	.	ENSG00000085511	ENST00000366919;ENST00000392142;ENST00000540111;ENST00000366920;ENST00000348824	T;T;T;T	0.72167	-0.63;-0.61;-0.61;-0.63	5.84	4.97	0.65823	.	0.000000	0.85682	D	0.000000	T	0.76062	0.3935	L	0.51422	1.61	0.80722	D	1	D;D;D;D	0.89917	1.0;0.998;1.0;1.0	D;P;D;D	0.91635	0.998;0.898;0.999;0.999	T	0.80400	-0.1398	10	0.87932	D	0	-38.942	16.2904	0.82747	0.0:0.0:0.8664:0.1336	.	1097;87;1097;1097	F5H538;Q9P1M2;Q9Y6R4-2;Q9Y6R4	.;.;.;M3K4_HUMAN	Y	1097	ENSP00000355886:D1097Y;ENSP00000375986:D1097Y;ENSP00000355887:D1097Y;ENSP00000297332:D1097Y	ENSP00000297332:D1097Y	D	+	1	0	MAP3K4	161434019	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.476000	0.97823	1.461000	0.47929	0.655000	0.94253	GAT		TCGA-IB-A7LX-01A-12D-A36O-08	MAP3K4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042988.3	1	0	0	13	284	0	104	0	3.591268e-01	0	27	0	104	2		0	0	0	0	0	2	1	0.999523	13	279	0	103	2		0	0	0	0	104	2	-3.193374	1	1	0	0		1	0	2	2	1.366277	1	0.550000	3.150000	0.550000	0.170000	0.080000	1.000000	0.160000	0.290527	0.170000	0	1.200000e-01	2.800000e-01
IMPG1	3617	broad.mit.edu	37	6	76751711	76751711	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr6:76751711C>A	ENST00000369950.3	-	2	389	c.200G>T	c.(199-201)cGa>cTa	p.R67L	IMPG1_ENST00000369963.3_Intron	NM_001282368.1|NM_001563.2	NP_001269297.1|NP_001554.2			interphotoreceptor matrix proteoglycan 1			63		Acute lymphoblastic leukemia(125;0.0418)|all_hematologic(105;0.222)			TCTTTTTGTTCGATGCTTTGC	0.363000													Pancreas(37;839 1141 2599 26037)											0							SO:0001583	missense			ENST00000369950.3	1	0	hg19	CCDS4985.1	.	.	.	.	.	.	.	.	.	.	C	26.8	4.768403	0.90020	.	.	ENSG00000112706	ENST00000369950	T	0.79940	-1.32	6.07	5.21	0.72293	.	0.125602	0.36591	N	0.002519	D	0.87877	0.6288	M	0.82323	2.585	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	D	0.89118	0.3501	9	.	.	.	.	15.5075	0.75753	0.0:0.9339:0.0:0.0661	.	67	Q17R60	IMPG1_HUMAN	L	67	ENSP00000358966:R67L	.	R	-	2	0	IMPG1	76808431	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.573000	0.53856	1.581000	0.49865	0.655000	0.94253	CGA		TCGA-IB-A7LX-01A-12D-A36O-08	IMPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041288.1	1	0	0	12	290	0	131		0	0	0	0	131	2		0	0	0	0	0	2	1	0.999037	12	283	0	131	2		0	0	0	0	131	2	-3.065444	1	1	0	0		1	0	2	2	1.369231	1	0.550000	3.150000	0.550000	0.150000	0.070000	1.000000	0.140000	0.277952	0.150000	0	1.100000e-01	2.600000e-01
PMPCB	9512	broad.mit.edu	37	7	102950912	102950912	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr7:102950912C>A	ENST00000249269.4	+	9	1182	c.1144C>A	c.(1144-1146)Caa>Aaa	p.Q382K	PMPCB_ENST00000420236.2_Missense_Mutation_p.Q277K|PMPCB_ENST00000428154.1_Missense_Mutation_p.Q382K	NM_004279.2	NP_004270.2	O75439	MPPB_HUMAN	peptidase (mitochondrial processing) beta			21					ACATGTTGTTCAAAAAGAATG	0.308000																								0							SO:0001583	missense			ENST00000249269.4	1	0	hg19	CCDS5730.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.556733	0.86231	.	.	ENSG00000105819	ENST00000249269;ENST00000428154;ENST00000420236	T;T;T	0.06608	3.28;3.28;3.28	5.71	4.83	0.62350	Peptidase M16, C-terminal (1);Peptidase M16, core (1);Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.000000	0.85682	D	0.000000	T	0.30166	0.0756	M	0.89287	3.02	0.80722	D	1	P;D;D;D;D;D	0.89917	0.937;1.0;1.0;1.0;1.0;1.0	P;D;D;D;D;D	0.76071	0.839;0.985;0.985;0.985;0.985;0.987	T	0.18147	-1.0346	10	0.51188	T	0.08	.	14.8943	0.70633	0.0:0.931:0.0:0.069	.	277;277;382;373;382;382	E7ERZ4;B4DM90;A8K1E9;Q96CP5;O75439;G3V0E4	.;.;.;.;MPPB_HUMAN;.	K	382;382;277	ENSP00000249269:Q382K;ENSP00000390035:Q382K;ENSP00000410393:Q277K	ENSP00000249269:Q382K	Q	+	1	0	PMPCB	102738148	1.000000	0.71417	0.992000	0.48379	0.963000	0.63663	6.026000	0.70873	1.423000	0.47198	0.585000	0.79938	CAA		TCGA-IB-A7LX-01A-12D-A36O-08	PMPCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347913.1	1	0	0	14	267	0	101	0	9.813653e-01	0	129	0	101	2		0	0	0	0	0	2	1	0.782532	14	265	1	99	11		0	0	0	0	101	2	-4.627886	1	1	0	0		1	0	3	3	1.672992	1	0.550000	3.150000	0.627792	0.230000	0.120000	1.000000	0.220000	0.366243	0.230000	0	1.700000e-01	1
LAMB4	22798	broad.mit.edu	37	7	107743496	107743496	+	Silent	SNP	C	C	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr7:107743496C>T	ENST00000388781.3	-	10	1256	c.1173G>A	c.(1171-1173)gcG>gcA	p.A391A	LAMB4_ENST00000414450.2_Silent_p.A391A|LAMB4_ENST00000205386.4_Silent_p.A391A|LAMB4_ENST00000388780.3_Silent_p.A391A|LAMB4_ENST00000418464.1_Silent_p.A391A	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4			97					CACGAATGCACGCGTAGGGAT	0.577000																								0							SO:0001819	synonymous_variant			ENST00000388781.3	1	1	hg19	CCDS34732.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	1	0	1	22	78	0	34		0	0	0	0	34	2		0	0	0	0	0	2	1	0.999999	22	75	0	34	2		0	0	0	0	34	2	-20.000000	1	1	121408	1	33	1	0	3	3	1.672992	1	0.550000	3.150000	0.627792	0.990000	0.660000	1.000000	1.000000	0.934200	0.990000	1	8.200000e-01	1
TSPAN33	340348	broad.mit.edu	37	7	128801559	128801559	+	Silent	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr7:128801559C>A	ENST00000289407.4	+	2	251	c.142C>A	c.(142-144)Cgg>Agg	p.R48R		NM_178562.3	NP_848657.1	Q86UF1	TSN33_HUMAN	tetraspanin 33			14					TGTCTACGCTCGGCTAATGAA	0.582000																								0							SO:0001819	synonymous_variant			ENST00000289407.4	1	0	hg19	CCDS5810.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	TSPAN33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350983.1	1	0	0	13	275	0	92	0	7.192633e-03	0	3	0	92	2		0	0	0	0	0	2	1	0.999523	13	271	0	91	2		0	0	0	0	92	2	-2.890505	1	1	0	0		1	0	3	3	1.672992	1	0.550000	3.150000	0.627792	0.210000	0.110000	1.000000	0.200000	0.349124	0.210000	0	1.500000e-01	1
ZC3HC1	51530	broad.mit.edu	37	7	129658541	129658541	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr7:129658541C>A	ENST00000358303.4	-	10	1556	c.1472G>T	c.(1471-1473)cGa>cTa	p.R491L	RP11-306G20.1_ENST00000480018.1_RNA|ZC3HC1_ENST00000360708.5_Missense_Mutation_p.R420L|ZC3HC1_ENST00000311873.5_Missense_Mutation_p.R470L|ZC3HC1_ENST00000481503.1_Missense_Mutation_p.R448L|RP11-306G20.1_ENST00000587038.1_RNA	NM_016478.3	NP_057562.3	Q86WB0	NIPA_HUMAN	zinc finger, C3HC-type containing 1	p.R491Q(1)		22	Melanoma(18;0.0435)				CCGAAATATTCGGAATACTTT	0.393000													Melanoma(115;540 1606 16325 28853 48167)											1	Substitution - Missense(1)						SO:0001583	missense			ENST00000358303.4	1	0	hg19	CCDS34753.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.081950	0.76528	.	.	ENSG00000091732	ENST00000358303;ENST00000360708;ENST00000311873;ENST00000481503	T;T;T;T	0.54675	1.21;0.62;1.24;0.56	6.17	6.17	0.99709	.	0.237648	0.36628	N	0.002486	T	0.71099	0.3300	M	0.62723	1.935	0.47737	D	0.9995	D;D;D	0.89917	1.0;0.974;0.987	D;P;P	0.77004	0.989;0.576;0.698	T	0.70651	-0.4813	10	0.66056	D	0.02	-8.1694	17.5987	0.88020	0.0:1.0:0.0:0.0	.	420;491;448	Q86WB0-3;Q86WB0;C9J0I9	.;NIPA_HUMAN;.	L	491;420;470;448	ENSP00000351052:R491L;ENSP00000353933:R420L;ENSP00000309301:R470L;ENSP00000418533:R448L	ENSP00000309301:R470L	R	-	2	0	ZC3HC1	129445777	1.000000	0.71417	1.000000	0.80357	0.384000	0.30261	3.871000	0.56077	2.941000	0.99782	0.655000	0.94253	CGA		TCGA-IB-A7LX-01A-12D-A36O-08	ZC3HC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349316.1	1	0	0	13	304	0	88	0	2.680249e-01	0	23	0	88	2		0	0	0	0	0	2	1	0.999502	12	299	0	86	2		0	0	0	0	88	2	-3.027710	1	1	0	0		1	0	3	3	1.672992	1	0.550000	3.150000	0.627792	0.190000	0.100000	1.000000	0.190000	0.333253	0.190000	0	1.400000e-01	1
UBE3C	9690	broad.mit.edu	37	7	156961790	156961790	+	Silent	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr7:156961790C>A	ENST00000348165.5	+	3	529	c.169C>A	c.(169-171)Cga>Aga	p.R57R	UBE3C_ENST00000389103.4_Intron	NM_014671.2	NP_055486.2	Q15386	UBE3C_HUMAN	ubiquitin protein ligase E3C			63		all_hematologic(28;0.0185)|all_epithelial(9;0.0664)	OV - Ovarian serous cystadenocarcinoma(82;0.00448)		GTCATTTATTCGAGGCTATAG	0.363000																								0							SO:0001819	synonymous_variant			ENST00000348165.5	1	0	hg19	CCDS34789.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	UBE3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348108.1	1	0	0	12	238	0	65	0	6.664925e-01	0	46	0	65	2		0	0	0	0	0	2	1	0.999140	12	236	0	65	2		0	0	0	0	65	2	-2.926263	1	1	0	0		1	0	3	3	1.671923	1	0.550000	3.150000	0.626943	0.230000	0.110000	1.000000	0.210000	0.364627	0.230000	0	1.600000e-01	1
UBE2D4	51619	broad.mit.edu	37	7	43990227	43990227	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr7:43990227G>T	ENST00000222402.3	+	6	423	c.334G>T	c.(334-336)Gac>Tac	p.D112Y	RP5-1165K10.2_ENST00000454572.1_RNA|POLR2J4_ENST00000427076.1_RNA|UBE2D4_ENST00000394798.4_Missense_Mutation_p.D74Y	NM_015983.3	NP_057067.1	Q9Y2X8	UB2D4_HUMAN	ubiquitin-conjugating enzyme E2D 4 (putative)			5					GCTGCTCTGCGACCCCAACCC	0.562000													Esophageal Squamous(27;401 815 16344 30604)											0							SO:0001583	missense			ENST00000222402.3	1	0	hg19	CCDS5474.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.025689	0.75390	.	.	ENSG00000078967	ENST00000222402;ENST00000394798	T;T	0.73789	-0.78;-0.78	4.49	3.61	0.41365	Ubiquitin-conjugating enzyme, E2 (2);Ubiquitin-conjugating enzyme/RWD-like (2);	0.055533	0.64402	D	0.000002	D	0.86834	0.6028	M	0.90369	3.11	0.58432	D	0.999999	D;D	0.89917	0.999;1.0	D;D	0.77557	0.976;0.99	D	0.87620	0.2509	10	0.87932	D	0	.	10.2569	0.43403	0.0996:0.0:0.9004:0.0	.	74;112	Q9UQL0;Q9Y2X8	.;UB2D4_HUMAN	Y	112;74	ENSP00000222402:D112Y;ENSP00000378277:D74Y	ENSP00000222402:D112Y	D	+	1	0	UBE2D4	43956752	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	8.286000	0.89916	0.885000	0.36088	0.655000	0.94253	GAC		TCGA-IB-A7LX-01A-12D-A36O-08	UBE2D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250958.2	1	0	0	11	185	0	41	0	6.120975e-01	0	35	0	41	2		0	0	0	0	0	2	1	0.998390	11	183	0	39	2		0	0	0	0	41	2	-3.220448	1	1	0	0		1	2	4	6	2.227293	1	0.550000	3.150000	0.694501	0.340000	0.160000	1.000000	0.300000	0.484510	0.340000	0	2.400000e-01	1
DYNC1I1	1780	broad.mit.edu	37	7	95665004	95665004	+	Missense_Mutation	SNP	T	T	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr7:95665004T>A	ENST00000324972.6	+	13	1548	c.1355T>A	c.(1354-1356)gTc>gAc	p.V452D	DYNC1I1_ENST00000537881.1_Missense_Mutation_p.V415D|DYNC1I1_ENST00000437599.1_Missense_Mutation_p.V432D|DYNC1I1_ENST00000457059.1_Missense_Mutation_p.V435D|DYNC1I1_ENST00000447467.2_Missense_Mutation_p.V435D|DYNC1I1_ENST00000497626.1_3'UTR|DYNC1I1_ENST00000359388.4_Missense_Mutation_p.V415D	NM_004411.4	NP_004402.1	O14576	DC1I1_HUMAN	dynein, cytoplasmic 1, intermediate chain 1			54	all_cancers(62;9.39e-10)|all_epithelial(64;2.28e-09)|Lung NSC(181;0.165)|all_lung(186;0.191)		STAD - Stomach adenocarcinoma(171;0.0957)		ACGGGAGACGTCAATAACTTC	0.463000																								0							SO:0001583	missense			ENST00000324972.6	1	1	hg19	CCDS5644.1	.	.	.	.	.	.	.	.	.	.	T	16.60	3.168707	0.57584	.	.	ENSG00000158560	ENST00000447467;ENST00000324972;ENST00000537881;ENST00000437599;ENST00000359388;ENST00000457059	T;T;T;T;T;T	0.77098	-1.07;-1.07;-1.07;-1.07;-1.07;-1.07	5.1	5.1	0.69264	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.85673	0.5751	M	0.74546	2.27	0.80722	D	1	D;D;D;D;D	0.76494	0.999;0.999;0.999;0.997;0.996	D;D;D;D;D	0.78314	0.979;0.991;0.991;0.969;0.923	T	0.82631	-0.0362	10	0.11182	T	0.66	0.0118	15.3616	0.74478	0.0:0.0:0.0:1.0	.	435;432;435;452;415	Q7Z6M0;G5E9K1;O14576-2;O14576;O14576-3	.;.;.;DC1I1_HUMAN;.	D	435;452;415;432;415;435	ENSP00000392337:V435D;ENSP00000320130:V452D;ENSP00000438377:V415D;ENSP00000398118:V432D;ENSP00000352348:V415D;ENSP00000412444:V435D	ENSP00000320130:V452D	V	+	2	0	DYNC1I1	95502940	1.000000	0.71417	1.000000	0.80357	0.120000	0.20174	7.868000	0.87116	2.283000	0.76528	0.477000	0.44152	GTC		TCGA-IB-A7LX-01A-12D-A36O-08	DYNC1I1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333432.1	1	0	0	103	1111	0	231	0	0	0	1	0	231	2		0	0	0	0	0	2	1	1.000000	102	1092	0	227	2		0	0	0	0	231	2	-19.999790	1	1	0	0		1	3	6	9	3.443848	1	0.550000	3.150000	0.801806	0.720000	0.570000	1.000000	0.730000	0.769685	0.720000	0	6.400000e-01	1
CSMD3	114788	broad.mit.edu	37	8	113599442	113599442	+	Silent	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr8:113599442C>A	ENST00000297405.5	-	23	3982	c.3738G>T	c.(3736-3738)acG>acT	p.T1246T	CSMD3_ENST00000352409.3_Silent_p.T1246T|CSMD3_ENST00000455883.2_Silent_p.T1142T|CSMD3_ENST00000343508.3_Silent_p.T1206T	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3			646					CTTCATTATTCGTTGCAGATG	0.353000										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)														0							SO:0001819	synonymous_variant			ENST00000297405.5	1	0	hg19	CCDS6315.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	1	0	0	25	628	0	124		0	0	0	0	124	2		0	0	0	0	0	2	1	0.885077	24	622	1	124	18		0	0	0	0	124	2	-3.079016	1	1	0	0		1	2	4	6	3.192915	1	0.550000	3.150000	0.785714	0.290000	0.180000	0.420000	0.300000	0.302985	0.290000	0	2.300000e-01	3.600000e-01
KCTD9	54793	broad.mit.edu	37	8	25296876	25296876	+	Silent	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr8:25296876G>T	ENST00000221200.4	-	6	638	c.418C>A	c.(418-420)Cga>Aga	p.R140R	KCTD9_ENST00000518067.1_5'UTR	NM_017634.3	NP_060104.2	Q7L273	KCTD9_HUMAN	potassium channel tetramerization domain containing 9			12		all_cancers(63;0.0164)|Ovarian(32;0.000878)|all_epithelial(46;0.00542)|Breast(100;0.0164)|Hepatocellular(4;0.114)|Prostate(55;0.191)			TCAGGACTTCGGTCAATTAAG	0.368000																								0							SO:0001819	synonymous_variant			ENST00000221200.4	1	1	hg19	CCDS6048.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	KCTD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216890.1	1	0	0	6	206	0	73	0	2.118032e-01	0	26	0	73	2		0	0	0	0	0	2	1	0.962974	6	201	0	73	2		0	0	0	0	73	2	-2.614836	1	1	0	0		1	0	2	2	1.555864	1	0.550000	3.150000	0.550000	0.100000	0.040000	0.210000	0.100000	0.118473	0.100000	0	6.000000e-02	1.600000e-01
PREX2	80243	broad.mit.edu	37	8	68981315	68981315	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr8:68981315C>T	ENST00000288368.4	+	12	1664	c.1387C>T	c.(1387-1389)Cgc>Tgc	p.R463C	PREX2_ENST00000529398.1_3'UTR	NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	p.R463C(2)		178					ATATAGATTTCGCTATGATGA	0.348000																								2	Substitution - Missense(2)						SO:0001583	missense			ENST00000288368.4	1	1	hg19	CCDS6201.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.751767	0.89753	.	.	ENSG00000046889	ENST00000288368;ENST00000396539;ENST00000354677	T	0.14391	2.51	5.72	4.84	0.62591	DEP domain (2);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.34193	0.0889	L	0.60904	1.88	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.997;0.991;0.996	T	0.08576	-1.0715	10	0.87932	D	0	.	15.0201	0.71624	0.0:0.9317:0.0:0.0683	.	463;463;463	Q70Z35-2;Q70Z35;Q70Z35-3	.;PREX2_HUMAN;.	C	463	ENSP00000288368:R463C	ENSP00000288368:R463C	R	+	1	0	PREX2	69143869	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	7.566000	0.82347	1.559000	0.49555	0.650000	0.86243	CGC		TCGA-IB-A7LX-01A-12D-A36O-08	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	1	0	1	74	122	0	51	0	4.872542e-01	0	4	0	51	2		0	0	0	0	0	2	1	1.000000	74	122	0	50	2		0	0	0	0	51	2	-11.491400	1	1	0	0		1	1	2	3	1.925306	1	0.550000	3.150000	0.641648	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	9.900000e-01	1
JPH1	56704	broad.mit.edu	37	8	75227735	75227735	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr8:75227735C>T	ENST00000342232.4	-	2	540	c.500G>A	c.(499-501)cGc>cAc	p.R167H		NM_020647.2	NP_065698.1	Q9HDC5	JPH1_HUMAN	junctophilin 1			24	Breast(64;0.00576)		BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.0728)|all cancers(69;0.176)		CTGCTCGCTGCGCAGCGAGGC	0.721000																								0							SO:0001583	missense			ENST00000342232.4	1	1	hg19	CCDS6217.1	.	.	.	.	.	.	.	.	.	.	C	33	5.214836	0.95104	.	.	ENSG00000104369	ENST00000342232	T	0.63913	-0.07	4.43	4.43	0.53597	.	0.000000	0.85682	D	0.000000	T	0.80428	0.4621	M	0.82193	2.58	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.82824	-0.0266	10	0.49607	T	0.09	.	17.2378	0.87004	0.0:1.0:0.0:0.0	.	167	Q9HDC5	JPH1_HUMAN	H	167	ENSP00000344488:R167H	ENSP00000344488:R167H	R	-	2	0	JPH1	75390290	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.489000	0.81451	2.284000	0.76573	0.655000	0.94253	CGC		TCGA-IB-A7LX-01A-12D-A36O-08	JPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379102.1	1	0	0	7	79	0	27	0	1.332411e-01	1	6	0	27	2		0	0	0	0	0	2	1	0.977793	7	74	0	27	2		0	0	0	0	27	2	-12.727030	1	1	0	0		1	1	2	3	1.925306	1	0.550000	3.150000	0.641648	0.400000	0.170000	1.000000	0.380000	0.445188	0.400000	0	2.700000e-01	5.900000e-01
PPP1R3B	79660	broad.mit.edu	37	8	8998916	8998916	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr8:8998916G>T	ENST00000310455.3	-	2	396	c.246C>A	c.(244-246)ttC>ttA	p.F82L	RP11-10A14.3_ENST00000520017.1_RNA|RP11-10A14.3_ENST00000522057.1_RNA|PPP1R3B_ENST00000519699.1_Missense_Mutation_p.F82L	NM_001201329.1|NM_024607.3	NP_001188258.1|NP_078883.2	Q86XI6	PPR3B_HUMAN	protein phosphatase 1, regulatory subunit 3B			12					GCGGGTCATCGAATTCCGAGA	0.532000																								0							SO:0001583	missense			ENST00000310455.3	1	0	hg19	CCDS5973.1	.	.	.	.	.	.	.	.	.	.	G	12.70	2.017814	0.35606	.	.	ENSG00000173281	ENST00000310455;ENST00000519699	T;T	0.43688	0.94;0.94	5.68	-8.12	0.01078	.	0.097783	0.64402	D	0.000001	T	0.30792	0.0776	L	0.51914	1.62	0.35771	D	0.820934	D	0.57571	0.98	P	0.46543	0.52	T	0.62464	-0.6849	10	0.09590	T	0.72	-25.5449	13.8132	0.63276	0.6793:0.0811:0.2396:0.0	.	82	Q86XI6	PPR3B_HUMAN	L	82	ENSP00000308318:F82L;ENSP00000428642:F82L	ENSP00000308318:F82L	F	-	3	2	PPP1R3B	9036326	0.005000	0.15991	0.630000	0.29268	0.844000	0.47949	-0.829000	0.04415	-1.404000	0.02050	-0.254000	0.11334	TTC		TCGA-IB-A7LX-01A-12D-A36O-08	PPP1R3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251472.1	1	0	0	11	306	1	117	0	1.171865e-01	0	31	1	117	3		0	0	0	0	0	2	1	0.573693	11	303	1	117	11		0	0	0	1	117	2	-3.046002	1	1	0	0		1	0	2	2	1.565375	1	0.550000	3.150000	0.550000	0.120000	0.060000	0.220000	0.120000	0.136422	0.120000	0	9.000000e-02	1.700000e-01
IKBKAP	8518	broad.mit.edu	37	9	111679935	111679935	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr9:111679935C>A	ENST00000374647.5	-	9	1063	c.756G>T	c.(754-756)ttG>ttT	p.L252F	IKBKAP_ENST00000537196.1_5'UTR	NM_003640.3	NP_003631.2	O95163	ELP1_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein			53					TAGATGCAATCAAACTGCCTG	0.373000																								0							SO:0001583	missense			ENST00000374647.5	1	0	hg19	CCDS6773.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.081679	0.76528	.	.	ENSG00000070061	ENST00000374647	T	0.37752	1.18	5.29	5.29	0.74685	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	T	0.61350	0.2340	M	0.85859	2.78	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.65150	-0.6238	10	0.59425	D	0.04	-0.7514	10.2761	0.43510	0.0:0.9096:0.0:0.0904	.	252	O95163	ELP1_HUMAN	F	252	ENSP00000363779:L252F	ENSP00000363779:L252F	L	-	3	2	IKBKAP	110719756	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.861000	0.48380	2.642000	0.89623	0.561000	0.74099	TTG		TCGA-IB-A7LX-01A-12D-A36O-08	IKBKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053574.1	1	0	0	22	491	0	159	0	8.563759e-02	0	11	0	159	2		0	0	0	0	0	2	1	0.999999	22	483	0	158	2		0	0	0	0	159	2	-3.959990	1	1	0	0		1	0	2	2	1.589671	1	0.550000	3.150000	0.550000	0.150000	0.090000	0.230000	0.160000	0.162125	0.150000	0	1.200000e-01	1.900000e-01
SLC24A2	25769	broad.mit.edu	37	9	19516253	19516253	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr9:19516253C>A	ENST00000341998.2	-	10	1945	c.1884G>T	c.(1882-1884)atG>atT	p.M628I	SLC24A2_ENST00000286344.3_Missense_Mutation_p.M611I	NM_001193288.2|NM_020344.3	NP_001180217.1|NP_065077.1	Q9UI40	NCKX2_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 2			33					GGATTTTGTTCATTCGCCACT	0.502000																								0							SO:0001583	missense			ENST00000341998.2	1	0	hg19	CCDS6493.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.710039	0.89018	.	.	ENSG00000155886	ENST00000341998;ENST00000286344	T;T	0.59502	0.26;0.26	5.07	5.07	0.68467	Sodium/calcium exchanger membrane region (1);	0.000000	0.85682	D	0.000000	T	0.67392	0.2888	L	0.33753	1.03	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.985;1.0	T	0.65492	-0.6155	9	.	.	.	.	18.4603	0.90736	0.0:1.0:0.0:0.0	.	611;628	Q9UI40-2;Q9UI40	.;NCKX2_HUMAN	I	628;611	ENSP00000344801:M628I;ENSP00000286344:M611I	.	M	-	3	0	SLC24A2	19506253	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.771000	0.85420	2.351000	0.79841	0.655000	0.94253	ATG		TCGA-IB-A7LX-01A-12D-A36O-08	SLC24A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051866.2	1	0	0	17	400	0	152	0	1.943403e-03	0	2	0	152	2		0	0	0	0	0	2	1	0.999965	17	397	0	152	2		0	0	0	0	152	2	-3.036471	1	1	0	0		1	0	3	3	1.727980	1	0.550000	3.150000	0.629477	0.190000	0.100000	1.000000	0.170000	0.321835	0.190000	0	1.400000e-01	1
SLC9A6	10479	broad.mit.edu	37	X	135076969	135076969	+	Missense_Mutation	SNP	G	G	T	rs146114052		TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chrX:135076969G>T	ENST00000370698.3	+	2	385	c.350G>T	c.(349-351)cGg>cTg	p.R117L	SLC9A6_ENST00000370695.4_Missense_Mutation_p.R117L|SLC9A6_ENST00000370701.1_Missense_Mutation_p.R65L	NM_006359.2	NP_006350.1	Q92581	SL9A6_HUMAN	solute carrier family 9, subfamily A (NHE6, cation proton antiporter 6), member 6			33	Acute lymphoblastic leukemia(192;0.000127)				CTTGTGCTTCGGTATGGCATT	0.428000																								0							SO:0001583	missense			ENST00000370698.3	1	0	hg19	CCDS14654.1	.	.	.	.	.	.	.	.	.	.	G	29.9	5.048396	0.93740	.	.	ENSG00000198689	ENST00000370701;ENST00000370698;ENST00000370695	T;T;T	0.09817	2.94;2.94;2.94	5.07	5.07	0.68467	Cation/H+ exchanger (1);	0.658813	0.16648	N	0.205338	T	0.20210	0.0486	L	0.39692	1.235	0.80722	D	1	P;P;P	0.50443	0.871;0.701;0.935	P;P;P	0.53809	0.667;0.462;0.735	T	0.00728	-1.1591	10	0.66056	D	0.02	.	16.6984	0.85342	0.0:0.0:1.0:0.0	.	65;117;117	B4DU30;Q92581-2;Q92581	.;.;SL9A6_HUMAN	L	65;117;117	ENSP00000359735:R65L;ENSP00000359732:R117L;ENSP00000359729:R117L	ENSP00000359729:R117L	R	+	2	0	SLC9A6	134904635	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.361000	0.97122	2.234000	0.73211	0.544000	0.68410	CGG		TCGA-IB-A7LX-01A-12D-A36O-08	SLC9A6-001	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058450.1	1	0	0	14	399	0	78	0	1.269711e-01	0	17	0	78	2		0	0	0	0	0	2	1	0.999752	14	396	0	77	2		0	0	0	0	78	2	-2.220510	0	1	0	0		1	0	1	1			0.550000	3.150000	0.550000	0.050000	0.030000	0.100000	0.060000	0.065579	0.050000	0	4.000000e-02	8.000000e-02
EGFL6	25975	broad.mit.edu	37	X	13645269	13645269	+	Silent	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chrX:13645269C>A	ENST00000361306.1	+	11	1682	c.1425C>A	c.(1423-1425)gtC>gtA	p.V475V	EGFL6_ENST00000380602.3_Silent_p.V476V	NM_001167890.1|NM_015507.3	NP_001161362.1|NP_056322.2	Q8IUX8	EGFL6_HUMAN	EGF-like-domain, multiple 6			23					GAGACAAAGTCGGGAAACTTC	0.468000																								0							SO:0001819	synonymous_variant			ENST00000361306.1	1	0	hg19	CCDS14155.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	EGFL6-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055800.1	1	0	0	12	180	0	76	0	9.920691e-02	0	8	0	76	2		0	0	0	0	0	2	1	0.999130	12	176	0	74	2		0	0	0	0	76	2	-2.917043	1	1	0	0		1	0	1	1			0.550000	3.150000	0.550000	0.110000	0.060000	0.190000	0.110000	0.121313	0.110000	0	8.000000e-02	1.500000e-01
GABRE	2564	broad.mit.edu	37	X	151124313	151124313	+	Silent	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08			C	A	C	C		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chrX:151124313C>A	ENST00000370328.3	-	7	857	c.804G>T	c.(802-804)acG>acT	p.T268T	AF274855.1_ENST00000582865.1_RNA|GABRE_ENST00000370325.1_Silent_p.T268T|GABRE_ENST00000483564.1_5'UTR|MIR224_ENST00000384889.1_RNA	NM_004961.3	NP_004952.2	P78334	GBRE_HUMAN	gamma-aminobutyric acid (GABA) A receptor, epsilon			27	Acute lymphoblastic leukemia(192;6.56e-05)			Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	TGAAGAAAATCGTCATGACCA	0.478000																								0							SO:0001819	synonymous_variant			ENST00000370328.3	1	0	hg19	CCDS14703.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	GABRE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060903.1	1	0	0	15	348	0	73	0	9.958631e-01	0	211	0	73	2		0	0	0	0	0	2	1	0.999877	16	346	0	73	2		0	0	0	0	73	2	-3.911315	1	1	0	0		1	0	1	1			0.550000	3.150000	0.550000	0.070000	0.030000	0.120000	0.080000	0.079514	0.070000	0	5.000000e-02	1.000000e-01
CD99	4267	broad.mit.edu	37	X	2632474	2632474	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08			G	T	G	G		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chrX:2632474G>T	ENST00000381192.3	+	2	261	c.79G>T	c.(79-81)Gat>Tat	p.D27Y	CD99_ENST00000381187.3_Missense_Mutation_p.D27Y|CD99_ENST00000381184.1_Missense_Mutation_p.D27Y|CD99_ENST00000482405.2_3'UTR	NM_001277710.1|NM_002414.3	NP_001264639.1|NP_002405.1	P14209	CD99_HUMAN	CD99 molecule			11					TGGTGGTTTCGATTTATCCGA	0.294000																								0							SO:0001583	missense			ENST00000381192.3	1	0	hg19	CCDS14119.1	.	.	.	.	.	.	.	.	.	.	g	9.633	1.136817	0.21123	.	.	ENSG00000002586	ENST00000381192;ENST00000381187;ENST00000381184;ENST00000449611	T;T;T;T	0.49432	1.28;0.78;1.28;1.28	1.14	1.14	0.20703	.	0.162784	0.36932	U	0.002338	T	0.56499	0.1989	L	0.59436	1.845	0.09310	N	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79784	0.993;0.993;0.993	T	0.37663	-0.9696	10	0.72032	D	0.01	.	5.2921	0.15733	0.0:0.0:1.0:0.0	.	27;27;27	A6NIW1;B2R932;P14209	.;.;CD99_HUMAN	Y	27;27;27;70	ENSP00000370588:D27Y;ENSP00000370582:D27Y;ENSP00000370579:D27Y;ENSP00000405544:D70Y	ENSP00000370579:D27Y	D	+	1	0	CD99	2642474	0.069000	0.21087	0.025000	0.17156	0.016000	0.09150	1.398000	0.34554	0.857000	0.35407	0.429000	0.28392	GAT		TCGA-IB-A7LX-01A-12D-A36O-08	CD99-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055624.1	1	0	0	25	577	0	296	0	1	0	866	0	296	2		0	0	0	0	0	2	1	1.000000	24	567	0	295	2		0	0	0	0	296	2	-3.651936	1	1	0	0		1	0	1	1			0.550000	3.150000	0.550000	0.070000	0.040000	0.110000	0.080000	0.078151	0.070000	0	5.000000e-02	9.000000e-02
CXorf21	80231	broad.mit.edu	37	X	30577624	30577624	+	Silent	SNP	A	A	G			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chrX:30577624A>G	ENST00000378962.3	-	3	1171	c.849T>C	c.(847-849)atT>atC	p.I283I		NM_025159.2	NP_079435.1	Q9HAI6	CX021_HUMAN	chromosome X open reading frame 21			20					TAATTTCAGTAATTTCAGTTG	0.378000																								0							SO:0001819	synonymous_variant			ENST00000378962.3	0	1	hg19	CCDS14224.1																																																																																				TCGA-IB-A7LX-01A-12D-A36O-08	CXorf21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056164.1	0	0	0	4	124	0	53	0	5.097955e-03	0	3	0	53	2		0	0	0	0	0	2	1	0.885915	4	121	0	53	2		0	0	0	0	53	2	-7.304968	1	0	0	0		1	0	1	1			0.550000	3.150000	0.550000	0.050000	0.010000	0.130000	0.060000	0.069476	0.050000	0	3.000000e-02	1.000000e-01
BRWD3	254065	broad.mit.edu	37	X	79939559	79939559	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chrX:79939559G>T	ENST00000373275.4	-	37	4399	c.4183C>A	c.(4183-4185)Cgc>Agc	p.R1395S	BRWD3_ENST00000473691.1_Intron	NM_153252.4	NP_694984	Q6RI45	BRWD3_HUMAN	bromodomain and WD repeat domain containing 3			87					AATATTTGGCGAACATCCTTA	0.348000																								0							SO:0001583	missense			ENST00000373275.4	1	0	hg19	CCDS14447.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.596937	0.87055	.	.	ENSG00000165288	ENST00000373275	T	0.29142	1.58	4.66	4.66	0.58398	Bromodomain (6);	0.051438	0.85682	D	0.000000	T	0.64571	0.2610	M	0.91459	3.21	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	T	0.74671	-0.3587	9	.	.	.	0.4745	16.8308	0.85944	0.0:0.0:1.0:0.0	.	1395	Q6RI45	BRWD3_HUMAN	S	1395	ENSP00000362372:R1395S	.	R	-	1	0	BRWD3	79826215	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.298000	0.78815	2.149000	0.67028	0.502000	0.49764	CGC		TCGA-IB-A7LX-01A-12D-A36O-08	BRWD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057344.1	1	0	0	11	242	0	37	0	2.091063e-01	0	17	0	37	2		0	0	0	0	0	2	1	0.998438	12	241	0	35	2		0	0	0	0	37	2	-4.155208	1	1	0	0		1	0	1	1			0.550000	3.150000	0.550000	0.070000	0.030000	0.130000	0.080000	0.085278	0.070000	0	5.000000e-02	1.100000e-01
NAP1L3	4675	broad.mit.edu	37	X	92926869	92926869	+	Missense_Mutation	SNP	T	T	C			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chrX:92926869T>C	ENST00000373079.3	-	1	1698	c.1435A>G	c.(1435-1437)Aaa>Gaa	p.K479E	FAM133A_ENST00000538690.1_5'Flank|NAP1L3_ENST00000475430.2_Missense_Mutation_p.K472E|FAM133A_ENST00000355813.5_5'Flank|FAM133A_ENST00000322139.4_5'Flank|FAM133A_ENST00000332647.4_5'Flank	NM_004538.5	NP_004529.2	Q99457	NP1L3_HUMAN	nucleosome assembly protein 1-like 3			34					TAGATTGATTTCAGGATGACA	0.363000																								0							SO:0001583	missense			ENST00000373079.3	0	1	hg19	CCDS14465.1	.	.	.	.	.	.	.	.	.	.	T	12.32	1.902300	0.33628	.	.	ENSG00000186310	ENST00000373079;ENST00000543136	T	0.25912	1.77	3.42	3.42	0.39159	.	0.053033	0.64402	D	0.000001	T	0.34774	0.0909	L	0.46947	1.48	0.09310	N	1	D	0.63046	0.992	D	0.64410	0.925	T	0.07385	-1.0775	10	0.62326	D	0.03	.	4.6798	0.12729	0.0:0.1434:0.0:0.8566	.	479	Q99457	NP1L3_HUMAN	E	479;472	ENSP00000362171:K479E	ENSP00000362171:K479E	K	-	1	0	NAP1L3	92813525	0.998000	0.40836	0.715000	0.30552	0.719000	0.41307	1.448000	0.35112	1.588000	0.49971	0.430000	0.28490	AAA		TCGA-IB-A7LX-01A-12D-A36O-08	NAP1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057449.1	0	0	0	5	132	0	22	0	1.199328e-02	0	4	0	22	2		0	0	0	0	0	2	1	0.937518	5	131	0	22	2		0	0	0	0	22	2	-8.153669	1	1	0	0		1	0	1	1			0.550000	3.150000	0.550000	0.060000	0.020000	0.140000	0.070000	0.078009	0.060000	0	4.000000e-02	1.100000e-01
