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
PLCE1	51196	broad.mit.edu	37	10	95791760	95791760	+	Frame_Shift_Del	DEL	G	G	-			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr10:95791760delG	ENST00000371380.3	+	1	1192	c.957delG	c.(955-957)aagfs	p.K319fs	PLCE1_ENST00000260766.3_Frame_Shift_Del_p.K319fs			Q9P212	PLCE1_HUMAN	phospholipase C, epsilon 1			8		Colorectal(252;0.0458)			AAAGCAAAAAGGAGCGATCCA	0.388000																								0							SO:0001589	frameshift_variant			ENST00000371380.3	1	1	hg19	CCDS41552.1																																																																																				TCGA-2L-AAQJ-01A-12D-A397-08	PLCE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049469.3	1	0	0	57	448	0	88	0	3.586020e-14	0	1	0	88	2	0	0	0	0	0	0		1	0.997694	66	446	3	89	33	0	0	0	0	0	0		-19.750740	1	1	0	0		1	1	2	3	2.067720	0	0.440000	1.870000	0.441229	0.510000	0.390000	0.650000	0.510000	0.519832	0.510000	0	4.500000e-01	5.800000e-01
SETD1A	9739	broad.mit.edu	37	16	30977566	30977567	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr16:30977566_30977567delAG	ENST00000262519.8	+	8	3050_3051	c.2364_2365delAG	c.(2362-2367)gcaggcfs	p.G789fs		NM_014712.1	NP_055527.1	O15047	SET1A_HUMAN	SET domain containing 1A			59					TCCCGACAGCAGGCACCGTGGG	0.658000																								0							SO:0001589	frameshift_variant			ENST00000262519.8	1	1	hg19	CCDS32435.1																																																																																				TCGA-2L-AAQJ-01A-12D-A397-08	SETD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318244.2	1	0	0	34	145	0	35	1	9.520197e-01	3	21	0	35	2	0	0	0	0	0	0		1	1.000000	35	145	0	35	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	0	0	0	2.044786	0	0.440000	1.870000	0.437525	0.850000	0.620000	1.000000	1.000000	0.856636	0.850000	1	7.300000e-01	1
GAS7	8522	broad.mit.edu	37	17	9923188	9923189	+	Frame_Shift_Ins	INS	-	-	A			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr17:9923188_9923189insA	ENST00000432992.2	-	2	369_370	c.209_210insT	c.(208-210)ccgfs	p.P70fs	GAS7_ENST00000542249.1_Frame_Shift_Ins_p.P6fs|GAS7_ENST00000540214.1_Frame_Shift_Ins_p.P6fs|GAS7_ENST00000585266.1_Frame_Shift_Ins_p.P10fs|GAS7_ENST00000578655.1_5'UTR|GAS7_ENST00000323816.4_Frame_Shift_Ins_p.P10fs|GAS7_ENST00000437099.2_Frame_Shift_Ins_p.P6fs|GAS7_ENST00000579158.1_Frame_Shift_Ins_p.P6fs|GAS7_ENST00000396115.2_Frame_Shift_Ins_p.P6fs	NM_201433.1	NP_958839.1	O60861	GAS7_HUMAN	growth arrest-specific 7			39					TTTCTTCTCCCGGCGGAGGGGG	0.540000			T	MLL	AML*										Dom	yes		17	17p	8522	growth arrest-specific 7		L	0							SO:0001589	frameshift_variant			ENST00000432992.2	0	1	hg19	CCDS11152.1																																																																																				TCGA-2L-AAQJ-01A-12D-A397-08	GAS7-017	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439883.1	1	0	0	66	234	0	38	0	5.564741e-01	0	8	0	38	2	0	0	0	0	0	0		1	1.000000	71	234	0	38	2	0	0	0	0	0	0		-3.071452	1	1	0	0		1	0	1	1	1.685553	1	0.440000	1.870000	0.282051	0.770000	0.610000	0.930000	0.770000	0.778383	0.770000	0	6.900000e-01	8.600000e-01
HSPA12A	259217	broad.mit.edu	37	10	118434408	118434408	+	Missense_Mutation	SNP	C	C	T	rs41284376		TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr10:118434408C>T	ENST00000369209.3	-	12	2016	c.1912G>A	c.(1912-1914)Gcc>Acc	p.A638T	RP11-498B4.5_ENST00000433600.1_RNA	NM_025015.2	NP_079291.2	O43301	HS12A_HUMAN	heat shock 70kDa protein 12A			32					TCCCTCCGGGCGGGCACCGCA	0.577000																								0							SO:0001583	missense			ENST00000369209.3	1	0	hg19	CCDS41569.1	11	0.005036630036630037	0	0.0	2	0.0055248618784530384	0	0.0	9	0.011873350923482849	C	0.572	-0.840640	0.02692	5.07E-4	0.004221	ENSG00000165868	ENST00000369209	T	0.41758	0.99	6.02	-1.03	0.10102	.	0.615275	0.18234	N	0.147479	T	0.11367	0.0277	N	0.08118	0	0.19945	N	0.99994	B	0.02656	0.0	B	0.06405	0.002	T	0.23084	-1.0198	10	0.11485	T	0.65	.	5.9177	0.19063	0.0:0.3231:0.366:0.311	rs41284376	638	O43301	HS12A_HUMAN	T	638	ENSP00000358211:A638T	ENSP00000358211:A638T	A	-	1	0	HSPA12A	118424398	0.006000	0.16342	0.315000	0.25238	0.186000	0.23388	0.029000	0.13666	-0.068000	0.12953	0.655000	0.94253	GCC		TCGA-2L-AAQJ-01A-12D-A397-08	HSPA12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050530.1	1	0	1	62	237	0	68	0	4.435546e-02	1	1	0	68	2		0	0	0	0	0	2	1	1.000000	60	237	0	67	2		0	0	0	0	0	2	-2.305815	0	1	120908	586	59	1	1	2	3	2.067720	0	0.440000	1.870000	0.441229	0.940000	0.740000	1.000000	1.000000	0.927086	0.940000	1	8.300000e-01	1
MYO3A	53904	broad.mit.edu	37	10	26434386	26434386	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr10:26434386G>A	ENST00000265944.5	+	22	2594	c.2428G>A	c.(2428-2430)Ggt>Agt	p.G810S	MYO3A_ENST00000543632.1_Intron	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA			146					AAAATTTGAAGGTAACCTGAA	0.313000																								0							SO:0001583	missense			ENST00000265944.5	1	1	hg19	CCDS7148.1	.	.	.	.	.	.	.	.	.	.	G	17.19	3.325787	0.60743	.	.	ENSG00000095777	ENST00000265944	T	0.70164	-0.46	5.72	3.72	0.42706	Myosin head, motor domain (2);	0.357715	0.33144	N	0.005222	T	0.48223	0.1488	N	0.11023	0.085	0.80722	D	1	B	0.26547	0.152	B	0.32928	0.155	T	0.44205	-0.9343	10	0.34782	T	0.22	.	11.4508	0.50151	0.1574:0.0:0.8426:0.0	.	810	Q8NEV4	MYO3A_HUMAN	S	810	ENSP00000265944:G810S	ENSP00000265944:G810S	G	+	1	0	MYO3A	26474392	1.000000	0.71417	0.957000	0.39632	0.999000	0.98932	5.647000	0.67923	1.276000	0.44395	0.655000	0.94253	GGT		TCGA-2L-AAQJ-01A-12D-A397-08	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	1	0	1	22	127	0	27	0	0	0	1	0	27	2		0	0	0	0	0	2	1	0.999999	22	127	0	27	2		0	0	0	0	0	2	-3.169113	1	1	0	0		1	0	0	0	2.040737	0	0.440000	1.870000	0.435028	0.660000	0.430000	0.930000	0.660000	0.679641	0.660000	0	5.400000e-01	8.000000e-01
KIAA1462	57608	broad.mit.edu	37	10	30336573	30336573	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr10:30336573G>A	ENST00000375377.1	-	2	270	c.169C>T	c.(169-171)Cgt>Tgt	p.R57C		NM_020848.2	NP_065899.1	Q9P266	JCAD_HUMAN	KIAA1462			75					GACGTCTTACGATGTGCGAGG	0.662000																								0							SO:0001583	missense			ENST00000375377.1	1	1	hg19	CCDS41500.1	.	.	.	.	.	.	.	.	.	.	G	14.49	2.551265	0.45383	.	.	ENSG00000165757	ENST00000375377	T	0.12569	2.67	5.06	1.48	0.22813	.	0.673294	0.14424	N	0.320462	T	0.08088	0.0202	N	0.14661	0.345	0.09310	N	1	D	0.56521	0.976	P	0.44696	0.458	T	0.22626	-1.0211	10	0.56958	D	0.05	-6.0436	4.5512	0.12114	0.0:0.1942:0.1909:0.6149	.	57	Q9P266	K1462_HUMAN	C	57	ENSP00000364526:R57C	ENSP00000364526:R57C	R	-	1	0	KIAA1462	30376579	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	0.567000	0.23608	0.069000	0.16605	0.467000	0.42956	CGT		TCGA-2L-AAQJ-01A-12D-A397-08	KIAA1462-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047409.1	1	0	1	55	210	0	71	0	1.145889e-01	0	3	0	71	2		0	0	0	0	0	2	1	1.000000	54	206	0	71	2		0	0	0	0	0	2	-3.668932	1	1	120938	1	31	1	0	0	0	2.040737	0	0.440000	1.870000	0.435028	0.930000	0.720000	1.000000	1.000000	0.918833	0.930000	1	8.200000e-01	1
DYNC2H1	79659	broad.mit.edu	37	11	102980335	102980335	+	Missense_Mutation	SNP	T	T	C			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr11:102980335T>C	ENST00000375735.2	+	1	176	c.32T>C	c.(31-33)cTc>cCc	p.L11P	DYNC2H1_ENST00000334267.7_Missense_Mutation_p.L11P|DYNC2H1_ENST00000398093.3_Missense_Mutation_p.L11P	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1			33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)			GTTCGGAAGCTCTTCATCTTC	0.507000																								0							SO:0001583	missense			ENST00000375735.2	1	1	hg19	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	T	11.60	1.686710	0.29962	.	.	ENSG00000187240	ENST00000375735;ENST00000334267;ENST00000398093	T;T;T	0.30182	1.67;1.54;1.67	5.63	3.2	0.36748	.	0.568065	0.12492	U	0.464170	T	0.26738	0.0654	L	0.36672	1.1	0.24814	N	0.992625	B;B;B	0.29590	0.25;0.082;0.066	B;B;B	0.37091	0.241;0.05;0.079	T	0.15578	-1.0432	10	0.30854	T	0.27	.	8.7491	0.34605	0.1029:0.0:0.2424:0.6546	.	11;11;11	Q8NCM8-3;Q8NCM8;Q8NCM8-2	.;DYHC2_HUMAN;.	P	11	ENSP00000364887:L11P;ENSP00000334021:L11P;ENSP00000381167:L11P	ENSP00000334021:L11P	L	+	2	0	DYNC2H1	102485545	0.140000	0.22579	0.989000	0.46669	0.993000	0.82548	0.695000	0.25527	2.137000	0.66172	0.482000	0.46254	CTC		TCGA-2L-AAQJ-01A-12D-A397-08	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	1	0	0	10	103	0	24		0	0	0	0	24	2		0	0	0	0	0	2	1	0.997309	10	103	0	24	2		0	0	0	0	0	2	-15.664810	1	1	0	0		1	0	0	0	2.041626	0	0.440000	1.870000	0.435028	0.400000	0.210000	0.670000	0.390000	0.426042	0.400000	0	3.000000e-01	5.400000e-01
ADAMTS15	170689	broad.mit.edu	37	11	130343367	130343367	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr11:130343367C>T	ENST00000299164.2	+	8	2504	c.2504C>T	c.(2503-2505)cCg>cTg	p.P835L		NM_139055.2	NP_620686.1	Q8TE58	ATS15_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 15			36	all_hematologic(175;0.0429)	Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)			GTGGAGCAGCCGGACGACAGG	0.697000																								0							SO:0001583	missense			ENST00000299164.2	1	1	hg19	CCDS8488.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	11.83	1.754593	0.31046	.	.	ENSG00000166106	ENST00000299164	T	0.61742	0.08	5.69	4.77	0.60923	.	.	.	.	.	T	0.35393	0.0930	N	0.08118	0	0.37764	D	0.926416	B	0.25105	0.118	B	0.14578	0.011	T	0.24870	-1.0148	9	0.19147	T	0.46	.	14.1591	0.65434	0.1583:0.8417:0.0:0.0	.	835	Q8TE58	ATS15_HUMAN	L	835	ENSP00000299164:P835L	ENSP00000299164:P835L	P	+	2	0	ADAMTS15	129848577	0.000000	0.05858	0.681000	0.30009	0.939000	0.58152	1.050000	0.30404	1.373000	0.46208	0.655000	0.94253	CCG		TCGA-2L-AAQJ-01A-12D-A397-08	ADAMTS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385638.1	0	0	0	112	376	0	117	0	0	0	1	0	117	2		0	0	0	0	0	2	1	1.000000	110	371	0	115	2		0	0	0	0	0	2	-4.375662	1	1	121108	16	45	1	0	0	0	2.059310	0	0.440000	1.870000	0.440000	0.990000	0.870000	1.000000	1.000000	0.983884	0.990000	1	9.500000e-01	1
OR51I1	390063	broad.mit.edu	37	11	5462461	5462461	+	Missense_Mutation	SNP	G	G	A	rs115148889		TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr11:5462461G>A	ENST00000380211.1	-	1	283	c.284C>T	c.(283-285)gCg>gTg	p.A95V	HBG2_ENST00000380259.2_Intron|AC104389.28_ENST00000415970.1_RNA|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron	NM_001005288.2	NP_001005288.1	Q9H343	O51I1_HUMAN	olfactory receptor, family 51, subfamily I, member 1			30		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)			AGCATTAAACGCAACATGGTT	0.458000																								0							SO:0001583	missense			ENST00000380211.1	1	1	hg19	CCDS31382.1	.	.	.	.	.	.	.	.	.	.	C	14.42	2.529926	0.45073	.	.	ENSG00000167359	ENST00000317283;ENST00000321307;ENST00000380211	T	0.37235	1.21	5.78	-2.31	0.06765	GPCR, rhodopsin-like superfamily (1);	0.518492	0.17730	N	0.163931	T	0.19366	0.0465	L	0.39898	1.24	0.09310	N	1	B	0.27700	0.186	B	0.19148	0.024	T	0.12708	-1.0537	10	0.62326	D	0.03	.	0.4262	0.00464	0.2041:0.2902:0.1998:0.3058	.	95	Q9H343	O51I1_HUMAN	V	80;92;95	ENSP00000369559:A95V	ENSP00000348350:A80V	A	-	2	0	OR51I1	5419037	0.000000	0.05858	0.025000	0.17156	0.074000	0.17049	-2.368000	0.01077	-0.628000	0.05582	-0.231000	0.12243	GCG		TCGA-2L-AAQJ-01A-12D-A397-08	OR51I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143399.1	1	0	1	52	153	0	60		0	0	0	0	60	2		0	0	0	0	0	2	1	1.000000	51	151	0	60	2		0	0	0	0	0	2	-20.000000	1	1	121408	3	40	1	0	0	0	2.041626	0	0.440000	1.870000	0.435028	0.990000	0.880000	1.000000	1.000000	0.991182	0.990000	1	9.900000e-01	1
OR5J2	282775	broad.mit.edu	37	11	55944377	55944377	+	Missense_Mutation	SNP	C	C	G			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr11:55944377C>G	ENST00000312298.1	+	1	284	c.284C>G	c.(283-285)tCt>tGt	p.S95C		NM_001005492.1	NP_001005492.1	Q8NH18	OR5J2_HUMAN	olfactory receptor, family 5, subfamily J, member 2			44	Esophageal squamous(21;0.00693)				ATTTCTTTCTCTGCTTGCATG	0.458000																								0							SO:0001583	missense			ENST00000312298.1	0	1	hg19	CCDS31522.1	.	.	.	.	.	.	.	.	.	.	C	13.69	2.311684	0.40895	.	.	ENSG00000174957	ENST00000312298	T	0.00408	7.54	4.67	-0.729	0.11158	GPCR, rhodopsin-like superfamily (1);	0.831860	0.10480	N	0.669723	T	0.00496	0.0016	L	0.46670	1.46	0.09310	N	1	D	0.67145	0.996	P	0.55785	0.784	T	0.53746	-0.8395	10	0.38643	T	0.18	.	6.1701	0.20412	0.1189:0.5225:0.0:0.3586	.	95	Q8NH18	OR5J2_HUMAN	C	95	ENSP00000310788:S95C	ENSP00000310788:S95C	S	+	2	0	OR5J2	55700953	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.352000	0.07701	-0.056000	0.13221	0.584000	0.79450	TCT		TCGA-2L-AAQJ-01A-12D-A397-08	OR5J2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391544.1	0	0	0	9	409	0	56		0	0	0	0	56	2		0	0	0	0	0	2	1	0.994269	9	409	0	56	2		0	0	0	0	0	2	-2.407337	0	1	0	0		1	0	0	0	2.041626	0	0.440000	1.870000	0.435028	0.090000	0.040000	0.180000	0.100000	0.106941	0.090000	0	6.000000e-02	1.400000e-01
SYT12	91683	broad.mit.edu	37	11	66807576	66807576	+	Nonsense_Mutation	SNP	C	C	T			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr11:66807576C>T	ENST00000393946.2	+	7	1685	c.523C>T	c.(523-525)Cag>Tag	p.Q175*	SYT12_ENST00000527043.1_Nonsense_Mutation_p.Q175*|SYT12_ENST00000525457.1_Nonsense_Mutation_p.Q175*|SYT12_ENST00000526281.1_3'UTR			Q8IV01	SYT12_HUMAN	synaptotagmin XII			20					GGCGGTGATGCAGGGCAAGGA	0.632000													Ovarian(65;2862 3307)											0							SO:0001587	stop_gained			ENST00000393946.2	0	1	hg19	CCDS8154.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.273932	0.80580	.	.	ENSG00000173227	ENST00000393946;ENST00000525457;ENST00000527043	.	.	.	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06494	T	0.89	.	17.1708	0.86830	0.0:1.0:0.0:0.0	.	.	.	.	X	175	.	ENSP00000377520:Q175X	Q	+	1	0	SYT12	66564152	1.000000	0.71417	1.000000	0.80357	0.569000	0.35902	7.797000	0.85911	2.655000	0.90218	0.462000	0.41574	CAG		TCGA-2L-AAQJ-01A-12D-A397-08	SYT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393129.1	0	0	0	5	231	0	57	0	2.165887e-03	0	3	0	57	2		0	0	0	0	0	2	1	0.933143	5	224	0	55	2		0	0	0	0	0	2	-3.865519	1	1	0	0		1	0	0	0	2.041626	0	0.440000	1.870000	0.435028	0.100000	0.030000	0.210000	0.100000	0.112963	0.100000	0	6.000000e-02	1.600000e-01
PDE2A	5138	broad.mit.edu	37	11	72295749	72295749	+	Silent	SNP	G	G	A			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr11:72295749G>A	ENST00000334456.5	-	18	1628	c.1383C>T	c.(1381-1383)gcC>gcT	p.A461A	PDE2A_ENST00000418754.2_Silent_p.A346A|PDE2A_ENST00000444035.2_Silent_p.A452A|RP11-169D4.2_ENST00000545254.1_RNA|PDE2A_ENST00000544570.1_Silent_p.A454A|PDE2A_ENST00000540345.1_Silent_p.A452A|PDE2A_ENST00000376450.3_Silent_p.A205A	NM_002599.4	NP_002590.1	O00408	PDE2A_HUMAN	phosphodiesterase 2A, cGMP-stimulated			36			BRCA - Breast invasive adenocarcinoma(5;3.55e-05)	Caffeine(DB00201)|Tofisopam(DB08811)	TGCCCTGATCGGCCGGGATGC	0.622000																								0							SO:0001819	synonymous_variant			ENST00000334456.5	1	1	hg19	CCDS8216.1																																																																																				TCGA-2L-AAQJ-01A-12D-A397-08	PDE2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219839.2	1	0	0	36	135	0	40	0	5.327078e-01	0	8	0	40	2		0	0	0	0	0	2	1	1.000000	34	134	0	40	2		0	0	0	0	0	2	-19.999450	1	1	0	0		1	0	0	0	2.041626	0	0.440000	1.870000	0.435028	0.940000	0.690000	1.000000	1.000000	0.919394	0.940000	1	8.100000e-01	1
USP35	57558	broad.mit.edu	37	11	77907359	77907359	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr11:77907359G>A	ENST00000529308.1	+	2	329	c.68G>A	c.(67-69)cGg>cAg	p.R23Q	USP35_ENST00000530267.1_Intron|USP35_ENST00000441408.2_5'Flank|USP35_ENST00000530535.1_Intron|USP35_ENST00000526425.1_5'Flank	NM_020798.2	NP_065849.1	Q9P2H5	UBP35_HUMAN	ubiquitin specific peptidase 35			23	all_cancers(14;3.77e-18)|all_epithelial(13;6.16e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1.04e-25)		GGGCTGGTTCGGCGCGTGCTG	0.716000																								0							SO:0001583	missense			ENST00000529308.1	1	1	hg19	CCDS41693.1	.	.	.	.	.	.	.	.	.	.	G	14.83	2.652237	0.47362	.	.	ENSG00000118369	ENST00000529308	T	0.05649	3.41	4.31	3.38	0.38709	.	0.000000	0.41823	D	0.000817	T	0.04588	0.0125	L	0.29908	0.895	0.80722	D	1	P	0.35155	0.487	B	0.22152	0.038	T	0.50583	-0.8811	10	0.27785	T	0.31	-28.6736	13.2753	0.60184	0.0:0.0:0.8307:0.1693	.	23	Q9P2H5	UBP35_HUMAN	Q	23	ENSP00000431876:R23Q	ENSP00000431876:R23Q	R	+	2	0	USP35	77585007	1.000000	0.71417	1.000000	0.80357	0.624000	0.37722	6.220000	0.72237	0.989000	0.38761	0.313000	0.20887	CGG		TCGA-2L-AAQJ-01A-12D-A397-08	USP35-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390026.1	1	0	0	59	229	0	46	0	0	1	0	0	46	2		0	0	0	0	0	2	1	1.000000	59	225	0	44	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	0	0	0	2.041626	0	0.440000	1.870000	0.435028	0.910000	0.720000	1.000000	1.000000	0.911448	0.910000	1	8.100000e-01	1
BTBD11	121551	broad.mit.edu	37	12	108051434	108051434	+	Missense_Mutation	SNP	G	G	T			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr12:108051434G>T	ENST00000280758.5	+	17	3782	c.3254G>T	c.(3253-3255)aGg>aTg	p.R1085M	BTBD11_ENST00000420571.2_Missense_Mutation_p.R966M|BTBD11_ENST00000494235.2_Missense_Mutation_p.R164M|BTBD11_ENST00000357167.4_Missense_Mutation_p.R622M	NM_001018072.1	NP_001018082.1	A6QL63	BTBDB_HUMAN	BTB (POZ) domain containing 11			53					GACTTACAGAGGACGTTGGCC	0.493000																								0							SO:0001583	missense			ENST00000280758.5	1	1	hg19	CCDS31893.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.402325	0.83230	.	.	ENSG00000151136	ENST00000280758;ENST00000420571;ENST00000357167;ENST00000494235	T;T;T;T	0.39997	1.26;1.39;1.05;1.17	5.84	5.84	0.93424	.	0.085133	0.85682	D	0.000000	T	0.41026	0.1141	N	0.22421	0.69	0.58432	D	0.999994	D;D	0.56521	0.976;0.976	P;P	0.47744	0.459;0.556	T	0.22103	-1.0226	10	0.48119	T	0.1	.	20.1551	0.98106	0.0:0.0:1.0:0.0	.	622;1085	E9PHS4;A6QL63	.;BTBDB_HUMAN	M	1085;966;622;164	ENSP00000280758:R1085M;ENSP00000413889:R966M;ENSP00000349690:R622M;ENSP00000448322:R164M	ENSP00000280758:R1085M	R	+	2	0	BTBD11	106575564	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.694000	0.68272	2.760000	0.94817	0.655000	0.94253	AGG		TCGA-2L-AAQJ-01A-12D-A397-08	BTBD11-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318003.1	1	0	1	38	184	0	63	1	2.105079e-01	2	3	0	63	2		0	0	0	0	0	2	1	1.000000	38	181	0	63	2		0	0	0	0	0	2	-3.294152	1	1	0	0		1	1	2	3	2.095273	0	0.440000	1.870000	0.446093	0.790000	0.570000	1.000000	1.000000	0.801056	0.790000	0	6.700000e-01	9.300000e-01
PRDM4	11108	broad.mit.edu	37	12	108138409	108138409	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr12:108138409G>A	ENST00000228437.5	-	7	1765	c.1306C>T	c.(1306-1308)Cgg>Tgg	p.R436W	RP11-864J10.4_ENST00000546714.1_RNA	NM_012406.3	NP_036538.3	Q9UKN5	PRDM4_HUMAN	PR domain containing 4			20					AAGCAAGTCCGCACAGGAATG	0.463000																								0							SO:0001583	missense			ENST00000228437.5	0	1	hg19	CCDS9115.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.108122	0.77096	.	.	ENSG00000110851	ENST00000228437;ENST00000550659	T;T	0.41758	0.99;0.99	5.88	4.98	0.66077	SET domain (2);	0.000000	0.85682	D	0.000000	T	0.44746	0.1308	M	0.78049	2.395	0.53688	D	0.999977	D	0.62365	0.991	B	0.43331	0.416	T	0.50980	-0.8763	10	0.54805	T	0.06	-1.7026	8.8668	0.35291	0.0726:0.0:0.6819:0.2455	.	436	Q9UKN5	PRDM4_HUMAN	W	436;188	ENSP00000228437:R436W;ENSP00000449295:R188W	ENSP00000228437:R436W	R	-	1	2	PRDM4	106662539	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.390000	0.52523	1.481000	0.48307	0.655000	0.94253	CGG		TCGA-2L-AAQJ-01A-12D-A397-08	PRDM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406546.1	0	0	0	5	256	0	47	0	3.273736e-02	0	12	0	47	2		0	0	0	0	0	2	1	0.938133	5	256	0	47	2		0	0	0	0	0	2	-2.578033	1	1	121412	3	34	1	1	2	3	2.095273	0	0.440000	1.870000	0.446093	0.090000	0.030000	1.000000	0.090000	0.138354	0.090000	0	5.000000e-02	1.500000e-01
TRPV4	59341	broad.mit.edu	37	12	110221488	110221488	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr12:110221488G>A	ENST00000418703.2	-	15	2648	c.2554C>T	c.(2554-2556)Cgc>Tgc	p.R852C	TRPV4_ENST00000544971.1_Missense_Mutation_p.R745C|TRPV4_ENST00000392719.2_Missense_Mutation_p.R805C|TRPV4_ENST00000541794.1_Missense_Mutation_p.R805C|TRPV4_ENST00000346520.2_Missense_Mutation_p.R792C|TRPV4_ENST00000536838.1_Missense_Mutation_p.R818C|TRPV4_ENST00000537083.1_Missense_Mutation_p.R792C|TRPV4_ENST00000261740.2_Missense_Mutation_p.R852C	NM_001177431.1	NP_001170902.1	Q9HBA0	TRPV4_HUMAN	transient receptor potential cation channel, subfamily V, member 4			35					CCATCGCAGCGGGGGTTCCCC	0.642000																								0							SO:0001583	missense			ENST00000418703.2	1	1	hg19	CCDS9134.1	.	.	.	.	.	.	.	.	.	.	G	12.34	1.909237	0.33721	0.0	1.16E-4	ENSG00000111199	ENST00000418703;ENST00000261740;ENST00000392719;ENST00000346520;ENST00000544971;ENST00000537083;ENST00000541794;ENST00000536838	D;D;D;D;D;D;D;D	0.89343	-2.5;-2.5;-2.29;-2.5;-2.29;-2.5;-2.29;-2.5	5.39	1.7	0.24286	.	0.722577	0.14111	N	0.340695	T	0.72028	0.3410	N	0.08118	0	0.28470	N	0.915481	P;B;P;B;B	0.41546	0.754;0.389;0.584;0.34;0.167	B;B;B;B;B	0.34722	0.188;0.083;0.13;0.097;0.123	T	0.67604	-0.5628	10	0.62326	D	0.03	-0.0455	4.314	0.10984	0.0:0.2373:0.1878:0.5749	.	792;852;745;805;818	Q9HBA0-2;Q9HBA0;Q9HBA0-6;Q9HBA0-4;Q9HBA0-5	.;TRPV4_HUMAN;.;.;.	C	852;852;805;792;745;792;805;818	ENSP00000406191:R852C;ENSP00000261740:R852C;ENSP00000376480:R805C;ENSP00000319003:R792C;ENSP00000443611:R745C;ENSP00000442738:R792C;ENSP00000442167:R805C;ENSP00000444336:R818C	ENSP00000261740:R852C	R	-	1	0	TRPV4	108705871	0.983000	0.35010	0.998000	0.56505	0.533000	0.34776	0.091000	0.15046	0.356000	0.24157	-0.397000	0.06425	CGC		TCGA-2L-AAQJ-01A-12D-A397-08	TRPV4-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403270.1	1	0	1	34	141	0	34	1	9.859692e-01	14	17	0	34	2		0	0	0	0	0	2	1	1.000000	34	140	0	33	2		0	0	0	0	0	2	-3.406252	1	1	121408	3	33	1	1	2	3	2.095273	0	0.440000	1.870000	0.446093	0.890000	0.640000	1.000000	1.000000	0.886737	0.890000	1	7.600000e-01	1
CLIP1	6249	broad.mit.edu	37	12	122825945	122825945	+	Silent	SNP	G	G	A			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr12:122825945G>A	ENST00000540338.1	-	10	1847	c.1806C>T	c.(1804-1806)aaC>aaT	p.N602N	CLIP1_ENST00000361654.4_Silent_p.N556N|CLIP1_ENST00000545889.1_Silent_p.N292N|CLIP1_ENST00000537178.1_Silent_p.N556N|CLIP1_ENST00000302528.7_Silent_p.N591N|CLIP1_ENST00000358808.2_Silent_p.N591N			P30622	CLIP1_HUMAN	CAP-GLY domain containing linker protein 1			60	all_neural(191;0.0837)|Medulloblastoma(191;0.163)				TCAATGACTCGTTCTCTTTGG	0.468000																								0							SO:0001819	synonymous_variant			ENST00000540338.1	1	1	hg19	CCDS58285.1																																																																																				TCGA-2L-AAQJ-01A-12D-A397-08	CLIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000401625.1	0	0	1	103	603	0	115	1	9.991301e-01	11	51	0	115	2		0	0	0	0	0	2	1	1.000000	102	601	0	114	2		0	0	0	0	0	2	-20.000000	1	1	121412	27	49	1	1	2	3	2.095273	0	0.440000	1.870000	0.446093	0.670000	0.550000	1.000000	0.670000	0.686238	0.670000	0	6.000000e-01	7.400000e-01
KRAS	3845	broad.mit.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	C	T	rs121913529		TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	KRAS_deep			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	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-2L-AAQJ-01A-12D-A397-08	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	1	0	1	55	181	0	58	1	9.792503e-01	22	1	0	58	2	1	1	56	211	0	208	2	1	1.000000	55	181	0	57	2	1	1	2326	5689	14	7988	25	-20.000000	1	1	121404	2	44	1	0	1	1	1.726764	1	0.440000	1.870000	0.282051	0.810000	0.630000	0.970000	0.820000	0.816580	0.810000	0	7.200000e-01	9.100000e-01
VWF	7450	broad.mit.edu	37	12	6138548	6138548	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08			C	T	C	C		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr12:6138548C>T	ENST00000261405.5	-	22	3181	c.2927G>A	c.(2926-2928)cGc>cAc	p.R976H		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor			129				Antihemophilic Factor(DB00025)	GCTCAGGTGGCGGTCCCAGAC	0.557000																								0							SO:0001583	missense			ENST00000261405.5	1	1	hg19	CCDS8539.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	4.964	0.178991	0.09443	.	.	ENSG00000110799	ENST00000261405	T	0.59364	0.27	4.58	-4.91	0.03085	von Willebrand factor, type D domain (3);	1.340220	0.05412	N	0.542595	T	0.42471	0.1204	L	0.31578	0.945	0.09310	N	0.999998	B	0.14012	0.009	B	0.10450	0.005	T	0.30268	-0.9984	10	0.32370	T	0.25	.	10.1299	0.42672	0.111:0.1943:0.0:0.6948	.	976	P04275	VWF_HUMAN	H	976	ENSP00000261405:R976H	ENSP00000261405:R976H	R	-	2	0	VWF	6008809	0.000000	0.05858	0.141000	0.22245	0.187000	0.23431	-0.956000	0.03865	-1.024000	0.03338	-0.347000	0.07816	CGC		TCGA-2L-AAQJ-01A-12D-A397-08	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	1	0	1	76	247	0	90	0	9.999972e-01	0	64	0	90	2		0	0	0	0	0	2	1	1.000000	76	240	0	90	2		0	0	0	0	0	2	-20.000000	1	1	121412	3	41	1	0	1	1	1.630284	1	0.440000	1.870000	0.282051	0.820000	0.670000	0.970000	0.830000	0.828196	0.820000	0	7.400000e-01	9.100000e-01
IRAK3	11213	broad.mit.edu	37	12	66641598	66641598	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08			G	A	G	G		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr12:66641598G>A	ENST00000261233.4	+	12	1859	c.1438G>A	c.(1438-1440)Gaa>Aaa	p.E480K	IRAK3_ENST00000457197.2_Missense_Mutation_p.E419K	NM_007199.2	NP_009130.2			interleukin-1 receptor-associated kinase 3			36					TATTCCAGTGGAAGATGATGA	0.428000																								0							SO:0001583	missense			ENST00000261233.4	1	1	hg19	CCDS8975.1	.	.	.	.	.	.	.	.	.	.	G	28.8	4.955128	0.92726	.	.	ENSG00000090376	ENST00000261233;ENST00000457197	T;T	0.73258	-0.69;-0.73	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	T	0.77458	0.4133	L	0.36672	1.1	0.40471	D	0.980346	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.994	T	0.75628	-0.3252	9	.	.	.	-27.7703	15.4984	0.75677	0.0:0.0:1.0:0.0	.	419;480	Q9Y616-2;Q9Y616	.;IRAK3_HUMAN	K	480;419	ENSP00000261233:E480K;ENSP00000409852:E419K	.	E	+	1	0	IRAK3	64927865	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	4.853000	0.62911	2.724000	0.93272	0.561000	0.74099	GAA		TCGA-2L-AAQJ-01A-12D-A397-08	IRAK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401908.1	1	0	1	65	210	0	42	0	9.901520e-01	1	25	0	42	2		0	0	0	0	0	2	1	1.000000	65	208	0	42	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	1	2	3	2.095273	0	0.440000	1.870000	0.446093	0.990000	0.860000	1.000000	1.000000	0.986344	0.990000	1	9.700000e-01	1
CAND1	55832	broad.mit.edu	37	12	67691335	67691335	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr12:67691335C>T	ENST00000545606.1	+	5	1077	c.640C>T	c.(640-642)Ctt>Ttt	p.L214F		NM_018448.3	NP_060918.2	Q86VP6	CAND1_HUMAN	cullin-associated and neddylation-dissociated 1			35			GBM - Glioblastoma multiforme(1;1.13e-10)|Lung(24;0.000342)|LUSC - Lung squamous cell carcinoma(43;0.196)		TTTTGTAGATCTTATTGAACA	0.403000																								0							SO:0001583	missense			ENST00000545606.1	1	1	hg19	CCDS8977.1	.	.	.	.	.	.	.	.	.	.	C	28.9	4.963385	0.92791	.	.	ENSG00000111530	ENST00000545606;ENST00000299218;ENST00000540047	T	0.67865	-0.29	5.61	5.61	0.85477	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.79575	0.4469	L	0.55834	1.745	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.76940	-0.2773	9	.	.	.	-12.9708	19.6379	0.95744	0.0:1.0:0.0:0.0	.	214	Q86VP6	CAND1_HUMAN	F	214;214;56	ENSP00000442318:L214F	.	L	+	1	0	CAND1	65977602	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.657000	0.90304	0.655000	0.94253	CTT		TCGA-2L-AAQJ-01A-12D-A397-08	CAND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402105.1	0	0	1	87	291	1	69	1	8.890906e-01	5	16	1	69	3		0	0	0	0	0	2	1	1.000000	86	288	1	68	18		0	0	0	0	0	2	-20.000000	1	1	0	0		1	1	2	3	2.095273	0	0.440000	1.870000	0.446093	0.990000	0.860000	1.000000	1.000000	0.984623	0.990000	1	9.500000e-01	1
LPCAT3	10162	broad.mit.edu	37	12	7086376	7086376	+	Missense_Mutation	SNP	G	G	C			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08			G	C	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr12:7086376G>C	ENST00000261407.4	-	12	1481	c.1396C>G	c.(1396-1398)Cta>Gta	p.L466V	U47924.30_ENST00000606112.1_lincRNA|LPCAT3_ENST00000535021.1_5'UTR	NM_005768.5	NP_005759.4	Q6P1A2	MBOA5_HUMAN	lysophosphatidylcholine acyltransferase 3			17					AATATGAATAGTAGGCTCAGG	0.418000																								0							SO:0001583	missense			ENST00000261407.4	1	1	hg19	CCDS8572.1	.	.	.	.	.	.	.	.	.	.	G	10.54	1.379121	0.24944	.	.	ENSG00000111684	ENST00000261407	T	0.73897	-0.79	4.77	2.95	0.34219	.	0.147474	0.46758	D	0.000278	T	0.63698	0.2533	L	0.39898	1.24	0.48696	D	0.999699	P	0.49090	0.919	B	0.42087	0.375	T	0.58994	-0.7537	10	0.32370	T	0.25	-13.8297	10.1817	0.42972	0.2237:0.0:0.7763:0.0	.	466	Q6P1A2	MBOA5_HUMAN	V	466	ENSP00000261407:L466V	ENSP00000261407:L466V	L	-	1	2	LPCAT3	6956637	0.980000	0.34600	0.277000	0.24703	0.895000	0.52256	1.816000	0.38992	0.627000	0.30340	-0.258000	0.10820	CTA		TCGA-2L-AAQJ-01A-12D-A397-08	LPCAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401812.1	1	0	1	62	158	0	44	1	1	57	29	0	44	2		0	0	0	0	0	2	1	1.000000	62	157	0	44	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	0	1	1	1.630284	1	0.440000	1.870000	0.282051	0.920000	0.760000	1.000000	0.990000	0.917278	0.920000	1	8.400000e-01	9.800000e-01
SACS	26278	broad.mit.edu	37	13	23912096	23912096	+	Missense_Mutation	SNP	T	T	G			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr13:23912096T>G	ENST00000382292.3	-	9	6192	c.5919A>C	c.(5917-5919)aaA>aaC	p.K1973N	SACS_ENST00000402364.1_Missense_Mutation_p.K1223N|SACS_ENST00000382298.3_Missense_Mutation_p.K1973N			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone			189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)			TGGTCAGTTCTTTCCCTTTTC	0.363000																								0							SO:0001583	missense			ENST00000382292.3	1	1	hg19	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	T	6.072	0.381555	0.11524	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.88354	-2.22;-2.37;-2.22	5.93	-1.21	0.09524	.	0.145938	0.64402	D	0.000008	T	0.78817	0.4343	N	0.25647	0.755	0.30667	N	0.753783	B	0.13594	0.008	B	0.11329	0.006	T	0.66048	-0.6020	10	0.33940	T	0.23	.	10.3333	0.43835	0.0:0.4088:0.0:0.5912	.	1973	Q9NZJ4	SACS_HUMAN	N	1973;1223;1973	ENSP00000371729:K1973N;ENSP00000385844:K1223N;ENSP00000371735:K1973N	ENSP00000371729:K1973N	K	-	3	2	SACS	22810096	1.000000	0.71417	0.742000	0.31022	0.119000	0.20118	0.854000	0.27791	-0.412000	0.07519	-0.353000	0.07706	AAA		TCGA-2L-AAQJ-01A-12D-A397-08	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	1	0	1	39	222	0	41	0	2.362023e-02	1	1	0	41	2		0	0	0	0	0	2	1	1.000000	39	219	0	41	2		0	0	0	0	0	2	-19.408850	1	1	0	0		1	0	1	1	1.931512	0	0.440000	1.870000	0.406025	0.630000	0.460000	0.830000	0.640000	0.648128	0.630000	0	5.400000e-01	7.400000e-01
FREM2	341640	broad.mit.edu	37	13	39262875	39262875	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr13:39262875C>T	ENST00000280481.7	+	1	1610	c.1394C>T	c.(1393-1395)cCg>cTg	p.P465L		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	p.P465L(1)		148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)			GGCAGTGGTCCGCAAAACTTG	0.582000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000280481.7	1	1	hg19	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	C	3.698	-0.062202	0.07317	.	.	ENSG00000150893	ENST00000280481	T	0.18174	2.23	5.6	2.0	0.26442	.	0.505278	0.18484	N	0.139857	T	0.13756	0.0333	L	0.43152	1.355	0.09310	N	0.999998	B	0.13145	0.007	B	0.06405	0.002	T	0.21621	-1.0240	10	0.34782	T	0.22	.	8.9993	0.36072	0.0:0.6923:0.0:0.3077	.	465	Q5SZK8	FREM2_HUMAN	L	465	ENSP00000280481:P465L	ENSP00000280481:P465L	P	+	2	0	FREM2	38160875	0.000000	0.05858	0.001000	0.08648	0.248000	0.25809	0.505000	0.22642	0.063000	0.16370	-1.036000	0.02392	CCG		TCGA-2L-AAQJ-01A-12D-A397-08	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	1	0	1	24	168	0	49		0	0	0	0	49	2		0	0	0	0	0	2	1	1.000000	24	167	0	49	2		0	0	0	0	0	2	-2.968319	1	1	121412	3	35	1						0.440000	1.870000									0	0
SIAH3	283514	broad.mit.edu	37	13	46357678	46357678	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr13:46357678G>A	ENST00000400405.2	-	2	756	c.650C>T	c.(649-651)aCg>aTg	p.T217M		NM_198849.2	NP_942146.2	Q8IW03	SIAH3_HUMAN	siah E3 ubiquitin protein ligase family member 3			12					AGACCGGGGCGTGGCCTCCCA	0.612000																								0							SO:0001583	missense			ENST00000400405.2	1	1	hg19	CCDS41883.1	.	.	.	.	.	.	.	.	.	.	G	19.04	3.748952	0.69533	.	.	ENSG00000215475	ENST00000400405	T	0.27256	1.68	5.07	5.07	0.68467	TRAF-type (1);Seven-in-absentia protein, TRAF-like domain (1);TRAF-like (1);	0.000000	0.85682	U	0.000000	T	0.44767	0.1309	L	0.44542	1.39	0.51482	D	0.999923	D	0.89917	1.0	D	0.91635	0.999	T	0.31223	-0.9951	10	0.51188	T	0.08	-19.0347	17.4324	0.87543	0.0:0.0:1.0:0.0	.	217	Q8IW03	SIAH3_HUMAN	M	217	ENSP00000383256:T217M	ENSP00000383256:T217M	T	-	2	0	SIAH3	45255679	1.000000	0.71417	0.987000	0.45799	0.493000	0.33554	9.719000	0.98760	2.369000	0.80426	0.561000	0.74099	ACG		TCGA-2L-AAQJ-01A-12D-A397-08	SIAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044788.2	1	0	1	37	168	0	38		0	0	0	0	38	2		0	0	0	0	0	2	1	1.000000	37	168	0	36	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	2	2	4	2.196026	1	0.440000	1.870000	0.474672	0.890000	0.640000	1.000000	1.000000	0.885740	0.890000	1	7.600000e-01	1
DIO3	1735	broad.mit.edu	37	14	102028119	102028119	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr14:102028119G>A	ENST00000510508.4	+	1	432	c.286G>A	c.(286-288)Gat>Aat	p.D96N	DIO3_ENST00000359323.3_Missense_Mutation_p.D70N|DIO3OS_ENST00000408206.1_lincRNA			P55073	IOD3_HUMAN	deiodinase, iodothyronine, type III			22		all_neural(303;0.185)			GGTGCCTCCCGATGACCCGCC	0.642000																								0							SO:0001583	missense			ENST00000510508.4	1	1	hg19	CCDS41992.2	.	.	.	.	.	.	.	.	.	.	g	18.36	3.607744	0.66558	.	.	ENSG00000197406;ENSG00000258865	ENST00000359323;ENST00000510508	T;T	0.35236	1.37;1.32	3.21	3.21	0.36854	.	0.000000	0.40302	U	0.001121	T	0.54565	0.1866	M	0.80028	2.48	0.28273	N	0.924327	D	0.89917	1.0	D	0.70227	0.968	T	0.46679	-0.9174	10	0.34782	T	0.22	.	7.8692	0.29556	0.124:0.0:0.876:0.0	.	70	P55073	IOD3_HUMAN	N	70;96	ENSP00000352273:D70N;ENSP00000427336:D96N	ENSP00000352273:D96N	D	+	1	0	DIO3;AL049836.1	101097872	1.000000	0.71417	1.000000	0.80357	0.815000	0.46073	6.208000	0.72165	1.608000	0.50180	0.457000	0.33378	GAT		TCGA-2L-AAQJ-01A-12D-A397-08	DIO3-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS|seleno	protein_coding	protein_coding	OTTHUMT00000361712.4	0	0	0	53	271	0	84	0	2.786064e-02	1	1	0	84	2		0	0	0	0	0	2	1	1.000000	52	267	0	82	2		0	0	0	0	0	2	-3.342333	1	1	0	0		1	0	0	0	2.042068	0	0.440000	1.870000	0.437525	0.730000	0.560000	0.920000	0.740000	0.746465	0.730000	0	6.400000e-01	8.400000e-01
KIF26A	26153	broad.mit.edu	37	14	104618363	104618363	+	Silent	SNP	C	C	A			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr14:104618363C>A	ENST00000423312.2	+	3	300	c.300C>A	c.(298-300)ctC>ctA	p.L100L	KIF26A_ENST00000315264.7_5'UTR	NM_015656.1	NP_056471.1	Q9ULI4	KI26A_HUMAN	kinesin family member 26A			21		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0767)	Epithelial(46;0.152)		ATCCTTGCCTCTCTGCCCTGC	0.672000																								0							SO:0001819	synonymous_variant			ENST00000423312.2	1	1	hg19	CCDS45171.1																																																																																				TCGA-2L-AAQJ-01A-12D-A397-08	KIF26A-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414356.1	1	0	1	55	172	0	50	0	1.501976e-01	0	3	0	50	2		0	0	0	0	0	2	1	1.000000	55	170	0	50	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	0	0	0	2.042068	0	0.440000	1.870000	0.437525	0.990000	0.850000	1.000000	1.000000	0.985077	0.990000	1	9.600000e-01	1
ARHGAP5	394	broad.mit.edu	37	14	32623887	32623887	+	Nonsense_Mutation	SNP	G	G	A			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr14:32623887G>A	ENST00000345122.3	+	7	4557	c.4242G>A	c.(4240-4242)tgG>tgA	p.W1414*	ARHGAP5_ENST00000396582.2_Nonsense_Mutation_p.W149*|ARHGAP5_ENST00000432921.1_Nonsense_Mutation_p.W1413*|ARHGAP5_ENST00000539826.2_Nonsense_Mutation_p.W1414*|ARHGAP5_ENST00000433497.1_Nonsense_Mutation_p.W153*|ARHGAP5_ENST00000556611.1_Nonsense_Mutation_p.W1413*	NM_001030055.1	NP_001025226.1	Q13017	RHG05_HUMAN	Rho GTPase activating protein 5			55	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.186)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0952)|STAD - Stomach adenocarcinoma(7;0.173)		TCTGTTTTTGGCCAACCTTGA	0.338000													NSCLC(9;77 350 3443 29227 41353)											0							SO:0001587	stop_gained			ENST00000345122.3	0	1	hg19	CCDS32062.1	.	.	.	.	.	.	.	.	.	.	G	45	11.775769	0.99601	.	.	ENSG00000100852	ENST00000556611;ENST00000539826;ENST00000396582;ENST00000345122;ENST00000432921;ENST00000433497	.	.	.	4.93	4.93	0.64822	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.5752	0.91153	0.0:0.0:1.0:0.0	.	.	.	.	X	1413;1414;149;1414;1413;153	.	ENSP00000371897:W1414X	W	+	3	0	ARHGAP5	31693638	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	9.748000	0.98867	2.475000	0.83589	0.549000	0.68633	TGG		TCGA-2L-AAQJ-01A-12D-A397-08	ARHGAP5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409735.1	1	0	1	84	279	0	79	1	9.999999e-01	54	30	0	79	2		0	0	0	0	0	2	1	1.000000	83	277	0	78	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	0	0	0	2.042068	0	0.440000	1.870000	0.437525	0.990000	0.850000	1.000000	1.000000	0.980703	0.990000	1	9.400000e-01	1
AKAP6	9472	broad.mit.edu	37	14	33291973	33291973	+	Nonsense_Mutation	SNP	C	C	T			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr14:33291973C>T	ENST00000280979.4	+	13	5124	c.4954C>T	c.(4954-4956)Cga>Tga	p.R1652*	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)		AAAGATAAAACGAAGTGTTTC	0.418000													Melanoma(49;821 1200 7288 13647 42351)											0							SO:0001587	stop_gained			ENST00000280979.4	0	1	hg19	CCDS9644.1	.	.	.	.	.	.	.	.	.	.	C	44	10.633637	0.99441	.	.	ENSG00000151320	ENST00000280979	.	.	.	5.98	3.08	0.35506	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.6398	15.1411	0.72612	0.3707:0.6293:0.0:0.0	.	.	.	.	X	1652	.	ENSP00000280979:R1652X	R	+	1	2	AKAP6	32361724	1.000000	0.71417	0.998000	0.56505	0.979000	0.70002	4.452000	0.60054	0.371000	0.24564	-0.188000	0.12872	CGA		TCGA-2L-AAQJ-01A-12D-A397-08	AKAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276617.2	1	0	1	55	216	0	51		0	0	0	0	51	2		0	0	0	0	0	2	1	1.000000	55	213	0	51	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	0	0	0	2.042068	0	0.440000	1.870000	0.437525	0.910000	0.710000	1.000000	1.000000	0.907275	0.910000	1	8.000000e-01	1
VPS39	23339	broad.mit.edu	37	15	42457994	42457994	+	Silent	SNP	C	C	T			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr15:42457994C>T	ENST00000348544.4	-	18	1733	c.1734G>A	c.(1732-1734)ccG>ccA	p.P578P	VPS39_ENST00000318006.5_Silent_p.P567P			Q96JC1	VPS39_HUMAN	vacuolar protein sorting 39 homolog (S. cerevisiae)			28		all_cancers(109;6.78e-16)|all_epithelial(112;1.81e-14)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)			ACTCCACTTCCGGGAGATCTT	0.473000																								0							SO:0001819	synonymous_variant			ENST00000348544.4	0	1	hg19	CCDS10083.1																																																																																				TCGA-2L-AAQJ-01A-12D-A397-08	VPS39-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000420472.1	0	0	0	4	287	0	65	0	1.844012e-01	0	45	0	65	2		0	0	0	0	0	2	1	0.889409	4	285	0	65	2		0	0	0	0	0	2	-3.166510	1	1	121412	2	31	1	0	0	0	2.049200	0	0.440000	1.870000	0.437525	0.060000	0.010000	0.150000	0.060000	0.076844	0.060000	0	3.000000e-02	1.100000e-01
MORF4L1	10933	broad.mit.edu	37	15	79186408	79186408	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08			C	T	C	C		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr15:79186408C>T	ENST00000331268.5	+	11	959	c.755C>T	c.(754-756)gCg>gTg	p.A252V	MORF4L1_ENST00000559345.1_Missense_Mutation_p.A125V|MORF4L1_ENST00000561171.1_Intron|MORF4L1_ENST00000558502.1_Missense_Mutation_p.A125V|MORF4L1_ENST00000426013.2_Missense_Mutation_p.A213V|MORF4L1_ENST00000558746.1_Missense_Mutation_p.A186V|MORF4L1_ENST00000379535.4_Missense_Mutation_p.A238V	NM_206839.2	NP_996670.1	Q9UBU8	MO4L1_HUMAN	mortality factor 4 like 1			10					AGGGAGTATGCGGTTAATGAA	0.333000																								0							SO:0001583	missense			ENST00000331268.5	0	1	hg19	CCDS10307.1	.	.	.	.	.	.	.	.	.	.	C	19.10	3.761130	0.69763	.	.	ENSG00000185787	ENST00000379535;ENST00000426013;ENST00000331268	T;T;T	0.08458	3.09;3.09;3.09	4.36	4.36	0.52297	.	0.000000	0.85682	D	0.000000	T	0.11580	0.0282	L	0.48174	1.505	0.80722	D	1	D;D	0.67145	0.996;0.978	P;B	0.48840	0.592;0.366	T	0.20107	-1.0285	10	0.09590	T	0.72	-22.9863	15.8341	0.78787	0.0:1.0:0.0:0.0	.	213;252	Q9UBU8-2;Q9UBU8	.;MO4L1_HUMAN	V	238;213;252	ENSP00000368850:A238V;ENSP00000408880:A213V;ENSP00000331310:A252V	ENSP00000331310:A252V	A	+	2	0	MORF4L1	76973463	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.604000	0.82830	2.123000	0.65237	0.650000	0.86243	GCG		TCGA-2L-AAQJ-01A-12D-A397-08	MORF4L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000290131.4	0	0	0	7	522	0	95	0	9.977517e-01	0	886	0	95	2		0	0	0	0	0	2	1	0.975966	7	490	0	94	2		0	0	0	0	0	2	-1.807614	0	1	0	0		1	0	0	0	2.049200	0	0.440000	1.870000	0.437525	0.060000	0.020000	0.120000	0.060000	0.068044	0.060000	0	3.000000e-02	9.000000e-02
ADAMTSL3	57188	broad.mit.edu	37	15	84705713	84705713	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr15:84705713G>A	ENST00000286744.5	+	29	5167	c.4943G>A	c.(4942-4944)cGg>cAg	p.R1648Q	ADAMTSL3_ENST00000567476.1_Missense_Mutation_p.R1648Q	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3			130			BRCA - Breast invasive adenocarcinoma(143;0.211)		ATTTCCTGGCGGCACTGTCTT	0.527000																								0							SO:0001583	missense			ENST00000286744.5	1	1	hg19	CCDS10326.1	.	.	.	.	.	.	.	.	.	.	G	6.948	0.544751	0.13312	.	.	ENSG00000156218	ENST00000286744	T	0.61274	0.12	5.19	2.26	0.28386	.	1.096740	0.07323	N	0.878014	T	0.31888	0.0811	N	0.11364	0.135	0.27026	N	0.964354	B;B	0.21452	0.033;0.056	B;B	0.10450	0.005;0.002	T	0.22661	-1.0210	10	0.02654	T	1	.	7.0906	0.25282	0.4565:0.0:0.5435:0.0	.	1648;1648	P82987-2;P82987	.;ATL3_HUMAN	Q	1648	ENSP00000286744:R1648Q	ENSP00000286744:R1648Q	R	+	2	0	ADAMTSL3	82496717	1.000000	0.71417	0.966000	0.40874	0.998000	0.95712	1.780000	0.38634	0.701000	0.31803	0.655000	0.94253	CGG		TCGA-2L-AAQJ-01A-12D-A397-08	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	1	0	1	47	164	0	37	0	0	0	1	0	37	2		0	0	0	0	0	2	1	1.000000	47	159	0	36	2		0	0	0	0	0	2	-4.041260	1	1	121410	2	32	1	0	0	0	2.049200	0	0.440000	1.870000	0.437525	0.990000	0.760000	1.000000	1.000000	0.955385	0.990000	1	8.700000e-01	1
DNAH3	55567	broad.mit.edu	37	16	21080832	21080832	+	Silent	SNP	T	T	A			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr16:21080832T>A	ENST00000261383.3	-	23	3284	c.3285A>T	c.(3283-3285)ccA>ccT	p.P1095P	DNAH3_ENST00000415178.1_Silent_p.P1095P	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3			202					AACTGAAGATTGGTTCCAGGT	0.433000																								0							SO:0001819	synonymous_variant			ENST00000261383.3	0	1	hg19	CCDS10594.1																																																																																				TCGA-2L-AAQJ-01A-12D-A397-08	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	0	0	0	9	628	0	129		0	0	0	0	129	2		0	0	0	0	0	2	1	0.993969	9	621	0	128	2		0	0	0	0	0	2	-3.225134	1	1	0	0		1	0	0	0	2.042094	0	0.440000	1.870000	0.437525	0.060000	0.020000	0.120000	0.060000	0.070680	0.060000	0	4.000000e-02	9.000000e-02
PRSS36	146547	broad.mit.edu	37	16	31152793	31152793	+	Missense_Mutation	SNP	A	A	G			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr16:31152793A>G	ENST00000268281.4	-	12	1956	c.1898T>C	c.(1897-1899)cTc>cCc	p.L633P	PRSS36_ENST00000418068.2_Missense_Mutation_p.L633P|PRSS36_ENST00000569305.1_Missense_Mutation_p.L628P	NM_001258290.1|NM_173502.4	NP_001245219.1|NP_775773.2	Q5K4E3	POLS2_HUMAN	protease, serine, 36			17					GACCCACCTGAGGACACAGTG	0.547000																								0							SO:0001583	missense			ENST00000268281.4	0	1	hg19	CCDS32436.1	.	.	.	.	.	.	.	.	.	.	A	16.81	3.225929	0.58668	.	.	ENSG00000178226	ENST00000268281;ENST00000418068	D;D	0.88818	-2.43;-1.57	5.29	3.99	0.46301	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	D	0.85435	0.5696	N	0.05554	-0.025	0.53005	D	0.999966	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.87578	0.998;0.985;0.985	T	0.82182	-0.0584	9	0.27785	T	0.31	.	7.6216	0.28189	0.8891:0.0:0.1109:0.0	.	633;628;633	E7EX56;B7ZMK8;Q5K4E3	.;.;POLS2_HUMAN	P	633	ENSP00000268281:L633P;ENSP00000407160:L633P	ENSP00000268281:L633P	L	-	2	0	PRSS36	31060294	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	2.959000	0.49153	1.996000	0.58369	0.374000	0.22700	CTC		TCGA-2L-AAQJ-01A-12D-A397-08	PRSS36-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000433542.1	0	0	0	6	464	0	91	0	7.429741e-04	0	3	0	91	2		0	0	0	0	0	2	1	0.964016	6	459	0	90	2		0	0	0	0	0	2	-5.813833	1	1	0	0		1	0	0	0	2.044786	0	0.440000	1.870000	0.437525	0.050000	0.010000	0.120000	0.060000	0.066957	0.050000	0	3.000000e-02	9.000000e-02
DNASE1	1773	broad.mit.edu	37	16	3706107	3706107	+	Missense_Mutation	SNP	G	G	A	rs140530129	by1000genomes	TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr16:3706107G>A	ENST00000246949.5	+	4	3450	c.241G>A	c.(241-243)Gca>Aca	p.A81T	DNASE1_ENST00000414110.2_Start_Codon_SNP_p.M1I|DNASE1_ENST00000407479.1_Missense_Mutation_p.A81T	NM_005223.3	NP_005214.2	P24855	DNAS1_HUMAN	deoxyribonuclease I			1		Ovarian(90;0.0261)			ATCCAGGGATGCACCAGACAC	0.597000																								0							SO:0001583	missense			ENST00000246949.5	0	1	hg19	CCDS10507.1	2|2	9.157509157509158E-4|9.157509157509158E-4	2|2	0.0040650406504065045|0.0040650406504065045	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	G|G	12.44|12.44	1.938101|1.938101	0.34189|0.34189	.|.	.|.	ENSG00000213918|ENSG00000213918	ENST00000407479;ENST00000246949|ENST00000414110	T;T|T	0.51071|0.40476	0.72;0.72|1.03	5.06|5.06	-0.503|-0.503	0.12000|0.12000	Endonuclease/exonuclease/phosphatase (2);|.	1.806170|.	0.02552|.	N|.	0.095796|.	T|T	0.23806|0.23806	0.0576|0.0576	N|N	0.12182|0.12182	0.205|0.205	0.09310|0.09310	N|N	1|1	B|.	0.14438|.	0.01|.	B|.	0.12837|.	0.008|.	T|T	0.29027|0.29027	-1.0025|-1.0025	10|7	0.42905|0.87932	T|D	0.14|0	-7.8118|-7.8118	4.4516|4.4516	0.11623|0.11623	0.3473:0.0:0.4251:0.2276|0.3473:0.0:0.4251:0.2276	.|.	81|.	P24855|.	DNAS1_HUMAN|.	T|I	81|1	ENSP00000385905:A81T;ENSP00000246949:A81T|ENSP00000416699:M1I	ENSP00000246949:A81T|ENSP00000416699:M1I	A|M	+|+	1|3	0|0	DNASE1|DNASE1	3646108|3646108	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.028000|0.028000	0.11728|0.11728	-0.075000|-0.075000	0.11431|0.11431	0.527000|0.527000	0.28560|0.28560	-0.291000|-0.291000	0.09656|0.09656	GCA|ATG		TCGA-2L-AAQJ-01A-12D-A397-08	DNASE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251585.2	1	0	1	57	241	0	49	1	4.752164e-01	3	5	0	49	2		0	0	0	0	0	2	1	1.000000	57	239	0	49	2		0	0	0	0	0	2	-20.000000	1	1	121412	3	33	1	0	0	0	2.042094	0	0.440000	1.870000	0.437525	0.860000	0.670000	1.000000	1.000000	0.865328	0.860000	1	7.600000e-01	9.700000e-01
ZNF423	23090	broad.mit.edu	37	16	49671084	49671084	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr16:49671084C>T	ENST00000561648.1	-	4	2032	c.1979G>A	c.(1978-1980)cGg>cAg	p.R660Q	ZNF423_ENST00000562871.1_Missense_Mutation_p.R600Q|ZNF423_ENST00000562520.1_Missense_Mutation_p.R600Q|ZNF423_ENST00000567169.1_Missense_Mutation_p.R543Q|ZNF423_ENST00000262383.2_Missense_Mutation_p.R660Q|ZNF423_ENST00000563137.2_Missense_Mutation_p.R600Q|ZNF423_ENST00000535559.1_Missense_Mutation_p.R543Q	NM_001271620.1	NP_001258549.1	Q2M1K9	ZN423_HUMAN	zinc finger protein 423			89		all_cancers(37;0.0155)			CGCTTGCTTCCGCAGCAGCAG	0.552000																								0							SO:0001583	missense			ENST00000561648.1	1	1	hg19	CCDS32445.1	.	.	.	.	.	.	.	.	.	.	C	16.81	3.225160	0.58668	.	.	ENSG00000102935	ENST00000262383;ENST00000535559	T;T	0.30714	1.52;1.52	4.86	4.86	0.63082	.	0.000000	0.85682	D	0.000000	T	0.27313	0.0670	L	0.42529	1.33	0.48830	D	0.999718	B	0.29862	0.259	B	0.23150	0.044	T	0.04454	-1.0950	9	.	.	.	.	18.0121	0.89227	0.0:1.0:0.0:0.0	.	660	Q2M1K9	ZN423_HUMAN	Q	660;543	ENSP00000262383:R660Q;ENSP00000442321:R543Q	.	R	-	2	0	ZNF423	48228585	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	4.679000	0.61649	2.250000	0.74265	0.462000	0.41574	CGG		TCGA-2L-AAQJ-01A-12D-A397-08	ZNF423-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000423258.1	1	0	1	37	177	0	51	0	2.156132e-01	0	4	0	51	2		0	0	0	0	0	2	1	1.000000	37	172	0	50	2		0	0	0	0	0	2	-3.004217	1	1	121412	3	37	1	0	0	0	2.044786	0	0.440000	1.870000	0.437525	0.780000	0.570000	1.000000	1.000000	0.789052	0.780000	0	6.600000e-01	9.000000e-01
ABAT	18	broad.mit.edu	37	16	8858595	8858595	+	Splice_Site	SNP	G	G	T			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr16:8858595G>T	ENST00000396600.2	+	8	1386	c.448G>T	c.(448-450)Gtg>Ttg	p.V150L	ABAT_ENST00000425191.2_Splice_Site_p.V150L|ABAT_ENST00000567812.1_Splice_Site_p.V165L|ABAT_ENST00000569156.1_Splice_Site_p.V150L|ABAT_ENST00000268251.8_Splice_Site_p.V150L	NM_000663.4	NP_000654.2	P80404	GABT_HUMAN	4-aminobutyrate aminotransferase			26				L-Alanine(DB00160)|Phenelzine(DB00780)|Pyruvic acid(DB00119)|Valproic Acid(DB00313)|Vigabatrin(DB01080)	CTCCCCACAGGTGGCTCCCAA	0.597000																								0							SO:0001630	splice_region_variant			ENST00000396600.2	0	1	hg19	CCDS10534.1	.	.	.	.	.	.	.	.	.	.	G	19.06	3.754306	0.69648	.	.	ENSG00000183044	ENST00000268251;ENST00000396600;ENST00000425191	T;T;T	0.74315	-0.83;-0.83;-0.83	5.63	5.63	0.86233	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.057206	0.64402	D	0.000001	T	0.76485	0.3994	L	0.60455	1.87	0.80722	D	1	B	0.17268	0.021	B	0.35182	0.197	T	0.69964	-0.5002	9	.	.	.	-19.9755	18.7245	0.91710	0.0:0.0:1.0:0.0	.	150	P80404	GABT_HUMAN	L	150	ENSP00000268251:V150L;ENSP00000379845:V150L;ENSP00000411916:V150L	.	V	+	1	0	ABAT	8766096	1.000000	0.71417	1.000000	0.80357	0.815000	0.46073	6.063000	0.71162	2.661000	0.90470	0.650000	0.86243	GTG		TCGA-2L-AAQJ-01A-12D-A397-08	ABAT-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433620.2	0	0	0	8	276	0	62	0	1.015284e-02	0	5	0	62	2		0	0	0	0	0	2	1	0.989023	6	274	0	61	2		0	0	0	0	0	2	-9.039571	1	1	0	0		1	0	0	0	2.042094	0	0.440000	1.870000	0.437525	0.130000	0.050000	0.240000	0.130000	0.141766	0.130000	0	9.000000e-02	1.900000e-01
MYO15A	51168	broad.mit.edu	37	17	18043920	18043920	+	Silent	SNP	G	G	A			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr17:18043920G>A	ENST00000205890.5	+	20	5639	c.5301G>A	c.(5299-5301)gcG>gcA	p.A1767A	MYO15A_ENST00000412324.1_3'UTR	NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA			99	all_neural(463;0.228)				TCTACAAGGCGCACACTGTGG	0.662000											OREG0024223	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)												0							SO:0001819	synonymous_variant			ENST00000205890.5	0	1	hg19	CCDS42271.1																																																																																				TCGA-2L-AAQJ-01A-12D-A397-08	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	0	0	0	6	413	0	131		0	0	0	0	131	2		0	0	0	0	0	2	1	0.963093	6	405	0	131	2		0	0	0	0	0	2	-2.400880	0	1	120914	6	43	1	0	1	1	1.685553	1	0.440000	1.870000	0.282051	0.050000	0.010000	0.100000	0.050000	0.058585	0.050000	0	3.000000e-02	8.000000e-02
TIAF1	9220	broad.mit.edu	37	17	27401145	27401145	+	Missense_Mutation	SNP	G	G	A	rs151013388		TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr17:27401145G>A	ENST00000359450.6	-	1	4730	c.73C>T	c.(73-75)Cgg>Tgg	p.R25W	MYO18A_ENST00000527372.1_3'UTR|MYO18A_ENST00000533112.1_3'UTR|MYO18A_ENST00000529578.1_5'UTR|MYO18A_ENST00000531253.1_3'UTR|MYO18A_ENST00000354329.4_3'UTR|TIAF1_ENST00000408971.2_Missense_Mutation_p.R25W	NM_004740.3	NP_004731.2	O95411	TIAF1_HUMAN	TGFB1-induced anti-apoptotic factor 1			3	Lung NSC(42;0.015)		Epithelial(11;1.19e-05)|all cancers(11;6.57e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000153)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)		ACCTGGACCCGGCTCTCCTCA	0.592000																								0							SO:0001583	missense			ENST00000359450.6	1	1	hg19	CCDS32599.1	.	.	.	.	.	.	.	.	.	.	G	4.088	0.014265	0.07959	2.27E-4	0.0	ENSG00000221995	ENST00000408971;ENST00000511177	.	.	.	5.99	-10.5	0.00291	.	.	.	.	.	T	0.18215	0.0437	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.42068	-0.9473	8	0.87932	D	0	.	9.1113	0.36730	0.3327:0.2671:0.4002:0.0	.	25	O95411	TIAF1_HUMAN	W	25	.	ENSP00000386130:R25W	R	-	1	2	TIAF1	24425271	0.001000	0.12720	0.001000	0.08648	0.008000	0.06430	-0.869000	0.04232	-1.616000	0.01572	-1.595000	0.00837	CGG		TCGA-2L-AAQJ-01A-12D-A397-08	TIAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372394.2	1	0	1	39	248	0	47	1	1	86	209	0	47	2		0	0	0	0	0	2	1	1.000000	39	245	0	47	2		0	0	0	0	0	2	-3.076960	1	1	121412	2	38	1	1	2	3	2.152119	0	0.440000	1.870000	0.453232	0.640000	0.460000	1.000000	0.630000	0.673497	0.640000	0	5.400000e-01	7.800000e-01
AP2B1	163	broad.mit.edu	37	17	33954713	33954713	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr17:33954713C>T	ENST00000262325.7	+	9	1676	c.1123C>T	c.(1123-1125)Cgg>Tgg	p.R375W	AP2B1_ENST00000589344.1_Missense_Mutation_p.R375W|AP2B1_ENST00000538556.1_Missense_Mutation_p.R318W|AP2B1_ENST00000312678.8_Missense_Mutation_p.R375W|AP2B1_ENST00000592545.1_Missense_Mutation_p.R337W|AP2B1_ENST00000545922.2_3'UTR|AP2B1_ENST00000537622.2_Missense_Mutation_p.R375W	NM_001282.2	NP_001273.1	P63010	AP2B1_HUMAN	adaptor-related protein complex 2, beta 1 subunit			28		Ovarian(249;0.17)			AAAAGCTGTGCGGGCCATTGG	0.438000																								0							SO:0001583	missense			ENST00000262325.7	0	1	hg19	CCDS32622.1	.	.	.	.	.	.	.	.	.	.	C	17.82	3.483673	0.63962	.	.	ENSG00000006125	ENST00000262325;ENST00000312678;ENST00000538556;ENST00000537622;ENST00000545922	T;T;T;T	0.27402	1.67;1.67;1.67;1.67	5.74	2.04	0.26737	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.67420	0.2891	H	0.97158	3.95	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.998;0.999;1.0;0.996	T	0.77787	-0.2457	10	0.87932	D	0	-0.402	14.3775	0.66889	0.4861:0.5139:0.0:0.0	.	112;337;375;375	F5GYG9;B4DWG4;P63010;P63010-2	.;.;AP2B1_HUMAN;.	W	375;375;318;375;112	ENSP00000262325:R375W;ENSP00000314414:R375W;ENSP00000440563:R318W;ENSP00000437413:R375W	ENSP00000262325:R375W	R	+	1	2	AP2B1	30978826	0.999000	0.42202	1.000000	0.80357	0.992000	0.81027	1.241000	0.32743	0.128000	0.18479	-1.036000	0.02392	CGG		TCGA-2L-AAQJ-01A-12D-A397-08	AP2B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448969.1	0	0	0	4	278	0	60	0	7.505153e-01	1	179	0	60	2		0	0	0	0	0	2	1	0.890211	4	277	0	60	2		0	0	0	0	0	2	-2.364776	0	1	0	0		1	1	2	3	2.152119	0	0.440000	1.870000	0.453232	0.070000	0.010000	1.000000	0.070000	0.163183	0.070000	0	4.000000e-02	1.400000e-01
BECN1	8678	broad.mit.edu	37	17	40967986	40967986	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr17:40967986G>A	ENST00000361523.4	-	8	902	c.770C>T	c.(769-771)gCc>gTc	p.A257V	BECN1_ENST00000438274.3_Missense_Mutation_p.A181V|BECN1_ENST00000590099.1_Missense_Mutation_p.A257V	NM_003766.3	NP_003757.1	Q14457	BECN1_HUMAN	beclin 1, autophagy related			13		Breast(137;0.00104)			CTGCGTCTGGGCATAACGCAT	0.463000																								0							SO:0001583	missense			ENST00000361523.4	0	1	hg19	CCDS11441.1	.	.	.	.	.	.	.	.	.	.	G	15.43	2.830695	0.50845	.	.	ENSG00000126581	ENST00000361523;ENST00000438274;ENST00000543382	T;T	0.46451	0.87;2.55	5.95	5.95	0.96441	.	0.171847	0.52532	D	0.000064	T	0.34978	0.0916	L	0.33339	1.005	0.58432	D	0.999994	B;B	0.32188	0.359;0.024	B;B	0.29663	0.105;0.094	T	0.07083	-1.0791	10	0.18710	T	0.47	.	20.3931	0.98965	0.0:0.0:1.0:0.0	.	181;257	E7EV84;Q14457	.;BECN1_HUMAN	V	257;181;170	ENSP00000355231:A257V;ENSP00000416173:A181V	ENSP00000355231:A257V	A	-	2	0	BECN1	38221512	1.000000	0.71417	1.000000	0.80357	0.144000	0.21451	6.847000	0.75404	2.824000	0.97209	0.655000	0.94253	GCC		TCGA-2L-AAQJ-01A-12D-A397-08	BECN1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452405.1	0	0	0	7	376	0	92	0	6.875938e-01	0	124	0	92	2		0	0	0	0	0	2	1	0.981016	8	376	0	92	2		0	0	0	0	0	2	-1.737995	0	1	0	0		1	0	1	1	1.664854	1	0.440000	1.870000	0.282051	0.060000	0.020000	0.130000	0.060000	0.073175	0.060000	0	4.000000e-02	1.000000e-01
AMZ2	51321	broad.mit.edu	37	17	66253070	66253070	+	Missense_Mutation	SNP	A	A	C			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08			A	C	A	A		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr17:66253070A>C	ENST00000359904.3	+	7	2175	c.1043A>C	c.(1042-1044)aAa>aCa	p.K348T	ARSG_ENST00000448504.2_5'Flank|AMZ2_ENST00000359783.4_Missense_Mutation_p.K290T|AMZ2_ENST00000580753.1_Missense_Mutation_p.K348T|AMZ2_ENST00000577273.1_3'UTR|AMZ2_ENST00000392720.2_Missense_Mutation_p.K348T|AMZ2_ENST00000577866.1_Missense_Mutation_p.K348T|AMZ2_ENST00000577985.1_Missense_Mutation_p.K348T	NM_016627.4	NP_057711.3	Q86W34	AMZ2_HUMAN	archaelysin family metallopeptidase 2			9	all_cancers(12;1.12e-09)		BRCA - Breast invasive adenocarcinoma(8;3.17e-08)|LUSC - Lung squamous cell carcinoma(166;0.24)		AAGGAATGGAAAGAGTGGATA	0.398000																								0							SO:0001583	missense			ENST00000359904.3	1	1	hg19	CCDS11674.1	.	.	.	.	.	.	.	.	.	.	A	6.893	0.534347	0.13188	.	.	ENSG00000196704	ENST00000359904;ENST00000359783;ENST00000392720	T;T;T	0.33865	1.39;1.39;1.39	3.42	-3.74	0.04385	.	0.527164	0.15835	N	0.242322	T	0.28928	0.0718	L	0.54323	1.7	0.40767	D	0.983057	B;B	0.32245	0.181;0.361	B;B	0.31686	0.134;0.134	T	0.06110	-1.0845	10	0.51188	T	0.08	-21.1054	10.9082	0.47092	0.2793:0.0:0.7207:0.0	.	290;348	A6NLD9;Q86W34	.;AMZ2_HUMAN	T	348;290;348	ENSP00000352976:K348T;ENSP00000352831:K290T;ENSP00000376481:K348T	ENSP00000352831:K290T	K	+	2	0	AMZ2	63764665	0.719000	0.27986	0.392000	0.26245	0.101000	0.19017	0.235000	0.17948	-0.834000	0.04239	-0.353000	0.07706	AAA		TCGA-2L-AAQJ-01A-12D-A397-08	AMZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448261.1	1	0	1	57	418	0	85	1	9.999999e-01	27	152	0	85	2		0	0	0	0	0	2	1	1.000000	57	412	0	85	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	2	5	7	2.566464	1	0.440000	1.870000	0.553073	0.700000	0.530000	1.000000	0.690000	0.743462	0.700000	0	6.100000e-01	1
GPR142	350383	broad.mit.edu	37	17	72363648	72363648	+	Missense_Mutation	SNP	A	A	T			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr17:72363648A>T	ENST00000335666.4	+	1	52	c.4A>T	c.(4-6)Agt>Tgt	p.S2C		NM_181790.1	NP_861455.1	Q7Z601	GP142_HUMAN	G protein-coupled receptor 142			35					GTTAGCAATGAGTATTATGAT	0.527000																								0							SO:0001583	missense			ENST00000335666.4	1	1	hg19	CCDS11698.1	.	.	.	.	.	.	.	.	.	.	A	10.68	1.417868	0.25552	.	.	ENSG00000257008	ENST00000335666	T	0.71817	-0.6	2.61	1.45	0.22620	.	.	.	.	.	T	0.46776	0.1410	N	0.08118	0	0.27124	N	0.962078	P	0.51653	0.947	B	0.40741	0.339	T	0.42032	-0.9475	9	0.87932	D	0	.	6.1442	0.20276	0.773:0.0:0.0:0.227	.	2	Q7Z601	GP142_HUMAN	C	2	ENSP00000335158:S2C	ENSP00000335158:S2C	S	+	1	0	GPR142	69875243	1.000000	0.71417	0.001000	0.08648	0.000000	0.00434	4.243000	0.58721	0.062000	0.16340	-0.343000	0.07986	AGT		TCGA-2L-AAQJ-01A-12D-A397-08	GPR142-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442545.1	1	0	1	51	324	0	68		0	0	0	0	68	2		0	0	0	0	0	2	1	1.000000	51	320	0	67	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	2	5	7	2.566464	1	0.440000	1.870000	0.553073	0.800000	0.590000	1.000000	0.780000	0.819603	0.800000	0	6.800000e-01	1
TP53	7157	broad.mit.edu	37	17	7577141	7577141	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr17:7577141C>T	ENST00000269305.4	-	8	986	c.797G>A	c.(796-798)gGa>gAa	p.G266E	TP53_ENST00000445888.2_Missense_Mutation_p.G266E|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.G266E|TP53_ENST00000420246.2_Missense_Mutation_p.G266E|TP53_ENST00000359597.4_Missense_Mutation_p.G266E|TP53_ENST00000413465.2_Intron	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	p.G266E(50)|p.G266V(42)|p.0?(8)|p.?(3)|p.G266fs*79(3)|p.G262_F270delGNLLGRNSF(2)|p.G266A(2)|p.G266_E271delGRNSFE(2)|p.G262_S269delGNLLGRNS(2)|p.G266fs*4(1)|p.G266T(1)|p.L265_K305del41(1)|p.E258fs*71(1)|p.L265_R267delLGR(1)|p.G266_N268delGRN(1)|p.G262fs*2(1)		24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		Acetylsalicylic acid(DB00945)	GCTGTTCCGTCCCAGTAGATT	0.517000		111	Mis, N, F		breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types	breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		L, E, M, O	121	Substitution - Missense(95)|Deletion - In frame(9)|Whole gene deletion(8)|Deletion - Frameshift(6)|Unknown(3)						SO:0001583	missense	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	ENST00000269305.4	0	1	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.614795	0.87359	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99898	-7.61;-7.61;-7.61;-7.61;-7.61;-7.61	5.13	5.13	0.70059	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99906	0.9955	M	0.92367	3.3	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;1.0;0.999;0.998	D	0.96190	0.9137	10	0.87932	D	0	-13.0798	16.1198	0.81342	0.0:1.0:0.0:0.0	.	266;266;266;266	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	E	266;266;266;266;266;255;134	ENSP00000352610:G266E;ENSP00000269305:G266E;ENSP00000398846:G266E;ENSP00000391127:G266E;ENSP00000391478:G266E;ENSP00000425104:G134E	ENSP00000269305:G266E	G	-	2	0	TP53	7517866	1.000000	0.71417	0.996000	0.52242	0.744000	0.42396	7.587000	0.82613	2.667000	0.90743	0.462000	0.41574	GGA		TCGA-2L-AAQJ-01A-12D-A397-08	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	1	0	0	15	43	0	13	1	9.996204e-01	33	12	0	13	2	1	1	271	512	0	468	2	1	0.999936	14	43	0	13	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	0	1	1	1.685553	1	0.440000	1.870000	0.282051	0.820000	0.530000	0.990000	0.880000	0.810034	0.820000	0	6.700000e-01	9.400000e-01
AFMID	125061	broad.mit.edu	37	17	76187132	76187132	+	Nonsense_Mutation	SNP	G	G	T			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr17:76187132G>T	ENST00000586731.1	+	2	115	c.94G>T	c.(94-96)Gga>Tga	p.G32*	AFMID_ENST00000589256.1_Nonsense_Mutation_p.G49*|AFMID_ENST00000327898.5_Nonsense_Mutation_p.G49*|AFMID_ENST00000588800.1_Nonsense_Mutation_p.G49*|AFMID_ENST00000409257.5_Nonsense_Mutation_p.G49*|AFMID_ENST00000591952.1_Nonsense_Mutation_p.G49*					arylformamidase			19			BRCA - Breast invasive adenocarcinoma(99;0.00269)|OV - Ovarian serous cystadenocarcinoma(97;0.134)		CTCACAGATAGGAATTGAAGG	0.557000																								0							SO:0001587	stop_gained			ENST00000586731.1	0	1	hg19		.	.	.	.	.	.	.	.	.	.	G	34	5.309732	0.95629	.	.	ENSG00000183077	ENST00000409257;ENST00000409431;ENST00000409722;ENST00000392388;ENST00000327898	.	.	.	4.9	3.86	0.44501	.	0.483859	0.21363	N	0.075763	.	.	.	.	.	.	0.38453	D	0.947022	.	.	.	.	.	.	.	.	.	.	0.25751	T	0.34	-12.3045	4.8598	0.13577	0.1436:0.2108:0.6456:0.0	.	.	.	.	X	49	.	ENSP00000328938:G49X	G	+	1	0	AFMID	73698727	0.755000	0.28372	0.050000	0.19076	0.691000	0.40173	1.557000	0.36299	2.224000	0.72417	0.609000	0.83330	GGA		TCGA-2L-AAQJ-01A-12D-A397-08	AFMID-015	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000438866.1	0	0	0	6	184	0	21	1	9.167167e-01	4	135	0	21	2		0	0	0	0	0	2	1	0.965142	6	183	0	20	2		0	0	0	0	0	2	-8.053794	1	1	0	0		1	2	5	7	2.566464	1	0.440000	1.870000	0.553073	0.210000	0.070000	1.000000	0.190000	0.340724	0.210000	0	1.300000e-01	1
DNAH17	8632	broad.mit.edu	37	17	76567670	76567670	+	Splice_Site	SNP	A	A	T			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr17:76567670A>T	ENST00000585328.1	-	4	857		c.e4+1		DNAH17_ENST00000389840.5_Splice_Site	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17			116			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)		AGGAGGCCGTACCTGTTCATG	0.667000																								0							SO:0001630	splice_region_variant			ENST00000585328.1	1	0	hg19		.	.	.	.	.	.	.	.	.	.	A	16.21	3.058575	0.55325	.	.	ENSG00000187775	ENST00000300671;ENST00000389840	.	.	.	5.13	5.13	0.70059	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.1577	0.59527	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	DNAH17	74079265	1.000000	0.71417	0.965000	0.40720	0.502000	0.33828	7.753000	0.85153	1.922000	0.55676	0.459000	0.35465	.		TCGA-2L-AAQJ-01A-12D-A397-08	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	1	0	0	113	218	0	56		0	0	0	0	56	2		0	0	0	0	0	2	1	1.000000	112	217	0	54	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	2	5	7	2.566464	1	0.440000	1.870000	0.553073	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	9.900000e-01	1
PIK3R5	23533	broad.mit.edu	37	17	8791989	8791989	+	Missense_Mutation	SNP	G	G	C			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr17:8791989G>C	ENST00000447110.1	-	10	1239	c.1115C>G	c.(1114-1116)tCg>tGg	p.S372W	PIK3R5_ENST00000584803.1_Missense_Mutation_p.S372W|PIK3R5_ENST00000581552.1_Missense_Mutation_p.S372W	NM_001142633.2|NM_001251851.1|NM_001251852.1|NM_001251853.1|NM_001251855.1	NP_001136105.1|NP_001238780.1|NP_001238781.1|NP_001238782.1|NP_001238784.1	Q8WYR1	PI3R5_HUMAN	phosphoinositide-3-kinase, regulatory subunit 5			34					CAGATGGCGCGAGAGGGCCGG	0.632000													NSCLC(18;589 615 7696 20311 50332)											0							SO:0001583	missense			ENST00000447110.1	1	1	hg19	CCDS11147.1	.	.	.	.	.	.	.	.	.	.	G	4.122	0.020770	0.08006	.	.	ENSG00000141506	ENST00000269300;ENST00000447110	T	0.80304	-1.36	5.51	4.53	0.55603	.	0.440169	0.25296	N	0.031685	T	0.81664	0.4870	N	0.24115	0.695	0.48452	D	0.99965	D	0.61697	0.99	P	0.61275	0.886	D	0.84368	0.0542	10	0.87932	D	0	-10.1214	15.3433	0.74314	0.0:0.0:0.8589:0.141	.	372	Q8WYR1	PI3R5_HUMAN	W	372	ENSP00000392812:S372W	ENSP00000269300:S372W	S	-	2	0	PIK3R5	8732714	0.943000	0.32029	0.003000	0.11579	0.023000	0.10783	2.226000	0.42963	1.312000	0.45043	0.650000	0.86243	TCG		TCGA-2L-AAQJ-01A-12D-A397-08	PIK3R5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000227003.2	1	0	1	18	121	0	40	0	9.285503e-02	0	4	0	40	2		0	0	0	0	0	2	1	0.999987	18	120	0	38	2		0	0	0	0	0	2	-3.326904	1	1	0	0		1	0	1	1	1.685553	1	0.440000	1.870000	0.282051	0.450000	0.280000	0.660000	0.450000	0.469066	0.450000	0	3.600000e-01	5.600000e-01
DLGAP1	9229	broad.mit.edu	37	18	3879329	3879329	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr18:3879329G>A	ENST00000315677.3	-	4	1335	c.740C>T	c.(739-741)gCg>gTg	p.A247V	DLGAP1-AS3_ENST00000577649.1_RNA|DLGAP1_ENST00000515196.2_Missense_Mutation_p.A247V|DLGAP1_ENST00000581527.1_Missense_Mutation_p.A247V|DLGAP1_ENST00000584874.1_Missense_Mutation_p.A247V	NM_004746.3	NP_004737.2	O14490	DLGP1_HUMAN	discs, large (Drosophila) homolog-associated protein 1			56		Colorectal(8;0.0257)			GGCCTTCACCGCCTGCTCGCT	0.657000																								0							SO:0001583	missense			ENST00000315677.3	1	1	hg19	CCDS11836.1	.	.	.	.	.	.	.	.	.	.	G	18.74	3.688161	0.68271	.	.	ENSG00000170579	ENST00000315677;ENST00000515196	T;T	0.16597	2.33;2.33	5.51	5.51	0.81932	.	0.118257	0.64402	D	0.000017	T	0.16642	0.0400	L	0.40543	1.245	0.53688	D	0.999975	B;P;B	0.40931	0.384;0.733;0.181	B;B;B	0.33339	0.038;0.162;0.069	T	0.01993	-1.1233	10	0.62326	D	0.03	-12.462	19.4162	0.94700	0.0:0.0:1.0:0.0	.	247;247;247	B7Z9Y4;Q6IS01;O14490	.;.;DLGP1_HUMAN	V	247	ENSP00000316377:A247V;ENSP00000445973:A247V	ENSP00000316377:A247V	A	-	2	0	DLGAP1	3869329	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	7.431000	0.80335	2.605000	0.88082	0.655000	0.94253	GCG		TCGA-2L-AAQJ-01A-12D-A397-08	DLGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254394.4	1	0	1	68	260	0	69		0	0	0	0	69	2		0	0	0	0	0	2	1	1.000000	68	258	0	68	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	1	2	3	2.061695	0	0.440000	1.870000	0.441229	0.940000	0.750000	1.000000	1.000000	0.928370	0.940000	1	8.400000e-01	1
SETBP1	26040	broad.mit.edu	37	18	42530405	42530405	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr18:42530405G>A	ENST00000282030.5	+	4	1396	c.1100G>A	c.(1099-1101)gGg>gAg	p.G367E		NM_015559.2	NP_056374.2	Q9Y6X0	SETBP_HUMAN	SET binding protein 1			104					AATACAGAAGGGAAAAGGGAA	0.448000									Schinzel-Giedion syndrome															0							SO:0001583	missense	Familial Cancer Database	SGC, Schinzel-Giedion Midface Retraction syndrome	ENST00000282030.5	1	1	hg19	CCDS11923.2	.	.	.	.	.	.	.	.	.	.	G	15.00	2.702158	0.48307	.	.	ENSG00000152217	ENST00000282030	T	0.37058	1.22	5.78	5.78	0.91487	.	0.166529	0.53938	D	0.000041	T	0.31358	0.0794	L	0.27053	0.805	0.36681	D	0.87903	P	0.38597	0.639	B	0.35655	0.207	T	0.34551	-0.9824	10	0.87932	D	0	.	20.3668	0.98882	0.0:0.0:1.0:0.0	.	367	Q9Y6X0	SETBP_HUMAN	E	367	ENSP00000282030:G367E	ENSP00000282030:G367E	G	+	2	0	SETBP1	40784403	1.000000	0.71417	1.000000	0.80357	0.678000	0.39670	3.539000	0.53604	2.894000	0.99253	0.655000	0.94253	GGG		TCGA-2L-AAQJ-01A-12D-A397-08	SETBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255854.4	1	0	1	61	173	0	45	0	3.937572e-01	0	5	0	45	2		0	0	0	0	0	2	1	1.000000	60	172	0	44	2		0	0	0	0	0	2	-4.890624	1	1	0	0		1	0	1	1	1.704625	1	0.440000	1.870000	0.323998	0.960000	0.770000	1.000000	1.000000	0.946051	0.960000	1	8.600000e-01	1
MBD2	8932	broad.mit.edu	37	18	51691000	51691000	+	Silent	SNP	C	C	A			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr18:51691000C>A	ENST00000256429.3	-	5	1230	c.1002G>T	c.(1000-1002)gcG>gcT	p.A334A		NM_003927.4	NP_003918.1	Q9UBB5	MBD2_HUMAN	methyl-CpG binding domain protein 2			8					CTGTGATTGGCGCAGAGCTTG	0.473000																								0							SO:0001819	synonymous_variant			ENST00000256429.3	0	1	hg19	CCDS11953.1																																																																																				TCGA-2L-AAQJ-01A-12D-A397-08	MBD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256003.2	0	0	0	4	217	0	41	0	8.811227e-01	0	212	0	41	2		0	0	0	0	0	2	1	0.889020	4	215	0	41	2		0	0	0	0	0	2	-3.112260	1	1	121412	1	33	1	0	1	1	1.704625	1	0.440000	1.870000	0.323998	0.070000	0.020000	0.160000	0.070000	0.083634	0.070000	0	4.000000e-02	1.200000e-01
GPI	2821	broad.mit.edu	37	19	34884838	34884838	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr19:34884838C>T	ENST00000356487.5	+	12	1170	c.929C>T	c.(928-930)aCg>aTg	p.T310M	GPI_ENST00000415930.3_Missense_Mutation_p.T321M|GPI_ENST00000586425.1_Missense_Mutation_p.T310M	NM_000175.3	NP_000166.2	P06744	G6PI_HUMAN	glucose-6-phosphate isomerase			25	Esophageal squamous(110;0.162)				TTCCGCACGACGCCCCTGGAG	0.627000																								0							SO:0001583	missense			ENST00000356487.5	1	1	hg19	CCDS12437.1	.	.	.	.	.	.	.	.	.	.	C	13.96	2.394367	0.42410	.	.	ENSG00000105220	ENST00000415930;ENST00000356487	D;D	0.93763	-3.28;-3.28	5.65	4.6	0.57074	.	0.386357	0.32868	N	0.005554	D	0.96030	0.8707	M	0.75085	2.285	0.44454	D	0.997381	B;D;B;B	0.56746	0.05;0.977;0.299;0.286	B;D;B;B	0.64144	0.094;0.922;0.094;0.157	D	0.96395	0.9292	10	0.72032	D	0.01	-0.4064	15.9577	0.79898	0.1361:0.8639:0.0:0.0	.	282;321;283;310	B4DE36;B4DG39;B4DVJ0;P06744	.;.;.;G6PI_HUMAN	M	321;310	ENSP00000405573:T321M;ENSP00000348877:T310M	ENSP00000348877:T310M	T	+	2	0	GPI	39576678	0.815000	0.29118	0.084000	0.20598	0.007000	0.05969	7.487000	0.81328	1.371000	0.46172	-0.188000	0.12872	ACG		TCGA-2L-AAQJ-01A-12D-A397-08	GPI-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451693.3	1	0	1	147	636	0	165	1	1	173	393	0	165	2		0	0	0	0	0	2	1	1.000000	148	621	0	162	2		0	0	0	0	0	2	-20.000000	1	1	121410	3	37	1	0	0	0	2.024636	0	0.440000	1.870000	0.429967	0.830000	0.710000	0.960000	0.840000	0.840314	0.830000	0	7.700000e-01	9.000000e-01
HPN	3249	broad.mit.edu	37	19	35556925	35556925	+	Missense_Mutation	SNP	C	C	G			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr19:35556925C>G	ENST00000262626.2	+	12	2029	c.1204C>G	c.(1204-1206)Cag>Gag	p.Q402E	HPN_ENST00000392226.1_Missense_Mutation_p.Q402E|HPN-AS1_ENST00000392227.2_RNA|HPN_ENST00000597419.1_Missense_Mutation_p.Q244E	NM_182983.2	NP_892028.1	P05981	HEPS_HUMAN	hepsin			19	all_lung(56;5.38e-08)|Lung NSC(56;8.61e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)	Coagulation factor VIIa(DB00036)	GTGGATCTTCCAGGCCATAAA	0.562000																								0							SO:0001583	missense			ENST00000262626.2	0	1	hg19	CCDS32993.1	.	.	.	.	.	.	.	.	.	.	C	11.21	1.570793	0.28003	.	.	ENSG00000105707	ENST00000262626;ENST00000392226;ENST00000541345	D;D	0.87887	-2.31;-2.31	4.86	3.81	0.43845	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (1);	0.194075	0.40908	D	0.000999	T	0.62575	0.2439	N	0.01656	-0.775	0.80722	D	1	B;B;B	0.23249	0.024;0.067;0.082	B;B;B	0.13407	0.003;0.006;0.009	T	0.62558	-0.6829	10	0.02654	T	1	.	10.3731	0.44066	0.3539:0.6461:0.0:0.0	.	374;402;402	B7Z1L4;B2ZDQ2;P05981	.;.;HEPS_HUMAN	E	402;402;374	ENSP00000262626:Q402E;ENSP00000376060:Q402E	ENSP00000262626:Q402E	Q	+	1	0	HPN	40248765	0.966000	0.33281	1.000000	0.80357	0.970000	0.65996	1.161000	0.31773	1.252000	0.44001	0.455000	0.32223	CAG		TCGA-2L-AAQJ-01A-12D-A397-08	HPN-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461573.1	0	0	0	11	615	0	145	1	3.861395e-02	2	14	0	145	2		0	0	0	0	0	2	1	0.998276	11	610	0	145	2		0	0	0	0	0	2	-2.290691	0	1	0	0		1	0	0	0	2.024636	0	0.440000	1.870000	0.429967	0.070000	0.030000	0.140000	0.080000	0.085148	0.070000	0	5.000000e-02	1.100000e-01
PLEKHG2	64857	broad.mit.edu	37	19	39914871	39914871	+	Nonsense_Mutation	SNP	C	C	G			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr19:39914871C>G	ENST00000409794.3	+	19	3948	c.3098C>G	c.(3097-3099)tCa>tGa	p.S1033*	PLEKHG2_ENST00000409797.2_Intron|PLEKHG2_ENST00000378550.1_Intron|PLEKHG2_ENST00000425673.1_Nonsense_Mutation_p.S1004*|PLEKHG2_ENST00000458508.2_Nonsense_Mutation_p.S974*|CTB-60E11.4_ENST00000601124.1_lincRNA	NM_022835.2	NP_073746.2	Q9H7P9	PKHG2_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 2			40	all_cancers(60;3.08e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;6.57e-07)|Ovarian(47;0.0569)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)		TTCACAGTTTCAGTCACCACC	0.547000																								0							SO:0001587	stop_gained			ENST00000409794.3	0	1	hg19	CCDS33022.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	37|37	6.087494|6.087494	0.97271|0.97271	.|.	.|.	ENSG00000090924|ENSG00000090924	ENST00000205135|ENST00000409794;ENST00000425673;ENST00000458508	.|.	.|.	.|.	3.08|3.08	-3.41|-3.41	0.04839|0.04839	.|.	.|1.788450	.|0.03467	.|N	.|0.213043	T|.	0.31513|.	0.0799|.	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.26538|.	-1.0100|.	4|.	.|0.28530	.|T	.|0.3	.|.	9.007|9.007	0.36117|0.36117	0.0:0.6787:0.0:0.3213|0.0:0.6787:0.0:0.3213	.|.	.|.	.|.	.|.	E|X	901|1033;1004;974	.|.	.|ENSP00000386733:S1033X	Q|S	+|+	1|2	0|0	PLEKHG2|PLEKHG2	44606711|44606711	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.725000|0.725000	0.41563|0.41563	-0.142000|-0.142000	0.10311|0.10311	-0.739000|-0.739000	0.04809|0.04809	0.491000|0.491000	0.48974|0.48974	CAG|TCA		TCGA-2L-AAQJ-01A-12D-A397-08	PLEKHG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326802.1	1	0	1	69	286	0	66	1	9.710426e-01	3	23	0	66	2		0	0	0	0	0	2	1	1.000000	69	283	0	65	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	0	0	0	2.024636	0	0.440000	1.870000	0.429967	0.860000	0.690000	1.000000	1.000000	0.868087	0.860000	1	7.700000e-01	9.600000e-01
PSG6	5675	broad.mit.edu	37	19	43411814	43411814	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr19:43411814G>A	ENST00000292125.2	-	4	943	c.899C>T	c.(898-900)aCg>aTg	p.T300M	PSG6_ENST00000187910.2_Missense_Mutation_p.T300M|PSG6_ENST00000402603.4_Intron	NM_002782.4	NP_002773.1	Q00889	PSG6_HUMAN	pregnancy specific beta-1-glycoprotein 6			44		Prostate(69;0.00899)			TTCATTTCTCGTGACACTGGG	0.488000																								0							SO:0001583	missense			ENST00000292125.2	1	1	hg19	CCDS12613.1	.	.	.	.	.	.	.	.	.	.	N	8.993	0.978199	0.18812	.	.	ENSG00000170848	ENST00000187910;ENST00000292125	T;T	0.15603	2.41;2.41	1.42	-0.067	0.13762	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.30665	0.0772	H	0.95745	3.715	0.09310	N	0.999998	B;P	0.39520	0.331;0.676	B;B	0.40864	0.146;0.342	T	0.33523	-0.9865	9	0.72032	D	0.01	.	4.8586	0.13571	0.0:0.397:0.603:0.0	.	300;300	Q00889;Q00889-2	PSG6_HUMAN;.	M	300	ENSP00000187910:T300M;ENSP00000292125:T300M	ENSP00000187910:T300M	T	-	2	0	PSG6	48103654	0.000000	0.05858	0.347000	0.25668	0.098000	0.18820	-0.625000	0.05534	0.792000	0.33850	0.134000	0.15878	ACG		TCGA-2L-AAQJ-01A-12D-A397-08	PSG6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321436.1	1	0	1	199	650	0	178		0	0	0	0	178	2		0	0	0	0	0	2	1	1.000000	187	606	0	183	2		0	0	0	0	0	2	-20.000000	1	1	121350	1	34	1	0	0	0	2.024636	0	0.440000	1.870000	0.429967	0.990000	0.910000	1.000000	1.000000	0.991422	0.990000	1	9.700000e-01	1
FPR2	2358	broad.mit.edu	37	19	52272706	52272706	+	Silent	SNP	C	C	T			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr19:52272706C>T	ENST00000598776.1	+	2	1567	c.795C>T	c.(793-795)acC>acT	p.T265T	FPR2_ENST00000598953.1_Silent_p.T265T|FPR2_ENST00000340023.6_Silent_p.T265T	NM_001462.3	NP_001453.1	P25090	FPR2_HUMAN	formyl peptide receptor 2			33					TTCTGGGCACCGTCTGGCTCA	0.502000																								0							SO:0001819	synonymous_variant			ENST00000598776.1	1	1	hg19	CCDS12840.1																																																																																				TCGA-2L-AAQJ-01A-12D-A397-08	FPR2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466912.2	1	0	1	45	160	0	28	0	1.275764e-01	0	3	0	28	2		0	0	0	0	0	2	1	1.000000	45	159	0	27	2		0	0	0	0	0	2	-3.870410	1	1	0	0		1	0	0	0	2.024636	0	0.440000	1.870000	0.429967	0.970000	0.740000	1.000000	1.000000	0.941424	0.970000	1	8.500000e-01	1
PTPRS	5802	broad.mit.edu	37	19	5244288	5244288	+	Silent	SNP	G	G	A	rs144956737		TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr19:5244288G>A	ENST00000587303.1	-	10	1293	c.1194C>T	c.(1192-1194)taC>taT	p.Y398Y	PTPRS_ENST00000348075.2_Silent_p.Y385Y|PTPRS_ENST00000372412.4_Silent_p.Y399Y|PTPRS_ENST00000592099.1_Silent_p.Y385Y|PTPRS_ENST00000357368.4_Silent_p.Y398Y|PTPRS_ENST00000353284.2_Silent_p.Y385Y|PTPRS_ENST00000588552.1_5'UTR|PTPRS_ENST00000588012.1_Silent_p.Y385Y|PTPRS_ENST00000262963.6_Silent_p.Y394Y			Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type, S			61				Alendronate(DB00630)|Etidronic acid(DB01077)	CCCAGATCTCGTACTCCGAGT	0.637000																								0							SO:0001819	synonymous_variant			ENST00000587303.1	1	1	hg19	CCDS45930.1																																																																																				TCGA-2L-AAQJ-01A-12D-A397-08	PTPRS-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450762.2	1	0	1	64	205	0	54	0	1.460317e-01	0	3	0	54	2		0	0	0	0	0	2	1	1.000000	63	202	0	53	2		0	0	0	0	0	2	-20.000000	1	1	121410	3	34	1	0	0	0	2.031251	0	0.440000	1.870000	0.435028	0.990000	0.850000	1.000000	1.000000	0.982518	0.990000	1	9.500000e-01	1
ZNF835	90485	broad.mit.edu	37	19	57175831	57175831	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr19:57175831C>T	ENST00000537055.2	-	2	967	c.736G>A	c.(736-738)Ggt>Agt	p.G246S		NM_001005850.2	NP_001005850.2	Q9Y2P0	ZN835_HUMAN	zinc finger protein 835			47					GGCTTCTCACCGGTGTGGATG	0.692000																								0							SO:0001583	missense			ENST00000537055.2	1	1	hg19	CCDS56105.1	.	.	.	.	.	.	.	.	.	.	C	33	5.267381	0.95399	.	.	ENSG00000127903	ENST00000342088;ENST00000537055	T	0.25085	1.82	2.12	2.12	0.27331	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.39963	0.1098	L	0.43152	1.355	0.31918	N	0.61385	D	0.89917	1.0	D	0.83275	0.996	T	0.46857	-0.9161	9	0.87932	D	0	.	10.2869	0.43573	0.0:1.0:0.0:0.0	.	268	Q9Y2P0	ZN835_HUMAN	S	268;246	ENSP00000444747:G246S	ENSP00000341756:G268S	G	-	1	0	ZNF835	61867643	0.002000	0.14202	0.005000	0.12908	0.717000	0.41224	1.681000	0.37618	1.506000	0.48736	0.561000	0.74099	GGT		TCGA-2L-AAQJ-01A-12D-A397-08	ZNF835-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459800.1	1	0	1	16	123	0	25	0	0	0	1	0	25	2		0	0	0	0	0	2	1	0.999949	16	122	0	25	2		0	0	0	0	0	2	-3.321058	1	1	121392	2	28	1	0	0	0	2.024636	0	0.440000	1.870000	0.429967	0.510000	0.310000	0.770000	0.500000	0.533266	0.510000	0	4.000000e-01	6.500000e-01
ATP5F1	515	broad.mit.edu	37	1	111992194	111992194	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr1:111992194G>A	ENST00000369722.3	+	1	637	c.31G>A	c.(31-33)Gcc>Acc	p.A11T	ATP5F1_ENST00000483994.1_Missense_Mutation_p.A11T|Y_RNA_ENST00000363020.1_RNA|ATP5F1_ENST00000369721.4_3'UTR|WDR77_ENST00000411751.2_5'Flank|WDR77_ENST00000497278.1_5'Flank|WDR77_ENST00000235090.5_5'Flank	NM_001688.4	NP_001679.2	P24539	AT5F1_HUMAN	ATP synthase, H+ transporting, mitochondrial Fo complex, subunit B1			8		all_cancers(81;8.16e-06)|all_epithelial(167;5.63e-06)|all_lung(203;0.000152)|Lung NSC(277;0.000301)			TTCCGCCGCCGCCACAGCGGG	0.577000																								0							SO:0001583	missense			ENST00000369722.3	0	1	hg19	CCDS836.1	.	.	.	.	.	.	.	.	.	.	G	19.52	3.843991	0.71488	.	.	ENSG00000116459	ENST00000369722;ENST00000483994	T;T	0.31510	1.49;1.51	5.73	4.82	0.62117	.	0.250346	0.33650	N	0.004681	T	0.09202	0.0227	L	0.54323	1.7	0.20074	N	0.999938	P;P	0.48640	0.913;0.913	B;B	0.28385	0.089;0.089	T	0.11817	-1.0572	10	0.24483	T	0.36	.	11.2813	0.49197	0.0844:0.0:0.9156:0.0	.	11;11	Q08ET0;P24539	.;AT5F1_HUMAN	T	11	ENSP00000358737:A11T;ENSP00000420366:A11T	ENSP00000358737:A11T	A	+	1	0	ATP5F1	111793717	0.986000	0.35501	1.000000	0.80357	0.867000	0.49689	2.836000	0.48183	1.562000	0.49601	0.655000	0.94253	GCC		TCGA-2L-AAQJ-01A-12D-A397-08	ATP5F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032455.1	0	0	0	6	454	0	105	1	9.088540e-01	2	324	0	105	2		0	0	0	0	0	2	1	0.964964	5	454	0	105	2		0	0	0	0	0	2	-2.421037	0	0	0	0		1	0	1	1	1.798735	1	0.440000	1.870000	0.338061	0.050000	0.010000	0.100000	0.050000	0.058021	0.050000	0	3.000000e-02	8.000000e-02
KPRP	448834	broad.mit.edu	37	1	152733552	152733552	+	Silent	SNP	C	C	A			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr1:152733552C>A	ENST00000606109.1	+	1	1516	c.1488C>A	c.(1486-1488)cgC>cgA	p.R496R	KPRP_ENST00000368773.1_Silent_p.R496R			Q5T749	KPRP_HUMAN	keratinocyte proline-rich protein			60	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)		AGACTTGGCGCAGCCCCAGCC	0.647000																								0							SO:0001819	synonymous_variant			ENST00000606109.1	0	1	hg19	CCDS30862.1																																																																																				TCGA-2L-AAQJ-01A-12D-A397-08	KPRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034522.2	0	0	0	9	296	0	52		0	0	0	0	52	2		0	0	0	0	0	2	1	0.994053	9	292	0	52	2		0	0	0	0	0	2	-9.944246	1	1	0	0		1	2	2	4	2.219696	1	0.440000	1.870000	0.481097	0.150000	0.070000	1.000000	0.140000	0.276156	0.150000	0	1.000000e-01	2.700000e-01
FDPS	2224	broad.mit.edu	37	1	155289625	155289625	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr1:155289625G>A	ENST00000356657.6	+	10	1127	c.965G>A	c.(964-966)gGc>gAc	p.G322D	RUSC1-AS1_ENST00000450199.1_RNA|RUSC1_ENST00000368352.5_5'Flank|FDPS_ENST00000368356.4_Missense_Mutation_p.G322D|FDPS_ENST00000447866.1_Missense_Mutation_p.G256D|RUSC1-AS1_ENST00000543656.1_RNA|RUSC1-AS1_ENST00000446880.1_RNA|RUSC1-AS1_ENST00000443642.1_RNA|RUSC1_ENST00000368354.3_5'Flank	NM_001135821.1	NP_001129293.1	P14324	FPPS_HUMAN	farnesyl diphosphate synthase			10	Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		Epithelial(20;2.03e-10)|all cancers(21;5.23e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000549)|LUSC - Lung squamous cell carcinoma(543;0.127)	Alendronate(DB00630)|Ibandronate(DB00710)|Pamidronate(DB00282)|Risedronate(DB00884)|Zoledronate(DB00399)	AGTGTGACCGGCAAAATTGGC	0.567000																								0							SO:0001583	missense			ENST00000356657.6	0	1	hg19	CCDS1110.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.143251	0.77888	.	.	ENSG00000160752	ENST00000447866;ENST00000368356;ENST00000356657	T;T;T	0.73681	-0.77;-0.77;-0.77	4.28	4.28	0.50868	Terpenoid synthase (2);	0.000000	0.44688	D	0.000439	D	0.88250	0.6386	H	0.94698	3.57	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.90597	0.4541	10	0.87932	D	0	-1.7784	14.6536	0.68817	0.0:0.0:1.0:0.0	.	322	P14324	FPPS_HUMAN	D	256;322;322	ENSP00000391755:G256D;ENSP00000357340:G322D;ENSP00000349078:G322D	ENSP00000349078:G322D	G	+	2	0	FDPS	153556249	1.000000	0.71417	0.997000	0.53966	0.488000	0.33401	9.276000	0.95745	2.673000	0.90976	0.561000	0.74099	GGC		TCGA-2L-AAQJ-01A-12D-A397-08	FDPS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039053.1	0	0	0	7	586	1	114	0	2.698581e-02	2	947	1	114	26		0	0	0	0	0	2	0	0.018526	7	577	1	111	18		0	0	0	0	0	2	-1.788477	0	1	0	0		1	2	2	4	2.219696	1	0.440000	1.870000	0.481097	0.060000	0.020000	1.000000	0.060000	0.195827	0.060000	0	3.000000e-02	1.200000e-01
BCAN	63827	broad.mit.edu	37	1	156621427	156621427	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr1:156621427G>A	ENST00000329117.5	+	7	1579	c.1243G>A	c.(1243-1245)Gga>Aga	p.G415R	RP11-284F21.7_ENST00000448869.1_RNA|BCAN_ENST00000361588.5_Missense_Mutation_p.G415R	NM_021948.4	NP_068767.3	Q96GW7	PGCB_HUMAN	brevican			55	all_hematologic(923;0.088)|Hepatocellular(266;0.158)				GGAGGACGGAGGAGGTGGAAG	0.557000																								0							SO:0001583	missense			ENST00000329117.5	1	1	hg19	CCDS1149.1	.	.	.	.	.	.	.	.	.	.	G	10.23	1.292944	0.23564	.	.	ENSG00000132692	ENST00000255029;ENST00000329117;ENST00000361588	T;T	0.13196	2.61;3.33	5.17	3.16	0.36331	.	0.777525	0.10979	N	0.612889	T	0.02193	0.0068	N	0.11201	0.11	0.09310	N	1	B;B	0.15473	0.006;0.013	B;B	0.14578	0.005;0.011	T	0.43940	-0.9360	10	0.15066	T	0.55	-0.351	11.1054	0.48199	0.1755:0.0:0.8245:0.0	.	415;415	Q96GW7;Q96GW7-2	PGCB_HUMAN;.	R	354;415;415	ENSP00000331210:G415R;ENSP00000354925:G415R	ENSP00000255029:G354R	G	+	1	0	BCAN	154888051	0.011000	0.17503	0.672000	0.29872	0.985000	0.73830	1.976000	0.40579	1.418000	0.47098	0.655000	0.94253	GGA		TCGA-2L-AAQJ-01A-12D-A397-08	BCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081844.2	1	0	1	88	438	0	84		0	0	0	0	84	2		0	0	0	0	0	2	1	1.000000	88	434	0	84	2		0	0	0	0	0	2	-20.000000	1	1	121410	7	41	1	2	2	4	2.219696	1	0.440000	1.870000	0.481097	0.830000	0.670000	1.000000	0.820000	0.848985	0.830000	0	7.400000e-01	9.900000e-01
TNN	63923	broad.mit.edu	37	1	175105027	175105027	+	Missense_Mutation	SNP	G	G	T			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr1:175105027G>T	ENST00000239462.4	+	16	3490	c.3377G>T	c.(3376-3378)tGg>tTg	p.W1126L		NM_022093.1	NP_071376.1	Q9UQP3	TENN_HUMAN	tenascin N	p.W1126*(1)		156		Breast(1374;0.000962)			TTCAAGCGATGGAGGAGCTAT	0.537000																								1	Substitution - Nonsense(1)						SO:0001583	missense			ENST00000239462.4	1	1	hg19	CCDS30943.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.912742	0.92178	.	.	ENSG00000120332	ENST00000239462;ENST00000539081	D	0.86865	-2.18	5.5	5.5	0.81552	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	0.115488	0.64402	D	0.000005	D	0.96614	0.8895	H	0.98818	4.34	0.80722	D	1	D	0.76494	0.999	D	0.75484	0.986	D	0.98254	1.0495	10	0.87932	D	0	.	19.003	0.92841	0.0:0.0:1.0:0.0	.	1126	Q9UQP3	TENN_HUMAN	L	1126;949	ENSP00000239462:W1126L	ENSP00000239462:W1126L	W	+	2	0	TNN	173371650	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	9.420000	0.97426	2.555000	0.86185	0.655000	0.94253	TGG		TCGA-2L-AAQJ-01A-12D-A397-08	TNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084422.1	1	0	1	106	395	0	97		0	0	0	0	97	2		0	0	0	0	0	2	1	1.000000	104	389	0	97	2		0	0	0	0	0	2	-3.575378	1	1	0	0		1	2	2	4	2.219696	1	0.440000	1.870000	0.481097	0.990000	0.870000	1.000000	1.000000	0.984020	0.990000	1	9.500000e-01	1
TNR	7143	broad.mit.edu	37	1	175365862	175365862	+	Missense_Mutation	SNP	G	G	A	rs138654492		TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr1:175365862G>A	ENST00000367674.2	-	5	1766	c.1058C>T	c.(1057-1059)aCg>aTg	p.T353M	TNR_ENST00000263525.2_Missense_Mutation_p.T353M			Q92752	TENR_HUMAN	tenascin R			177	Renal(580;0.146)				CACATATTCCGTCACTGCCAT	0.617000																								0							SO:0001583	missense			ENST00000367674.2	0	1	hg19	CCDS1318.1	.	.	.	.	.	.	.	.	.	.	G	28.3	4.905250	0.92035	2.27E-4	0.0	ENSG00000116147	ENST00000367674;ENST00000263525;ENST00000367673	T;T	0.60171	0.21;0.21	5.96	5.96	0.96718	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.055941	0.64402	D	0.000001	T	0.77805	0.4185	M	0.78344	2.41	0.80722	D	1	D	0.89917	1.0	D	0.72075	0.976	T	0.76277	-0.3018	10	0.46703	T	0.11	.	19.9958	0.97383	0.0:0.0:1.0:0.0	.	353	Q92752	TENR_HUMAN	M	353	ENSP00000356646:T353M;ENSP00000263525:T353M	ENSP00000263525:T353M	T	-	2	0	TNR	173632485	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.328000	0.96403	2.826000	0.97356	0.655000	0.94253	ACG		TCGA-2L-AAQJ-01A-12D-A397-08	TNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084414.4	0	0	0	7	540	0	86		0	0	0	0	86	2		0	0	0	0	0	2	1	0.979406	7	529	0	86	2		0	0	0	0	0	2	-5.621657	1	1	121412	7	42	1	2	2	4	2.219696	1	0.440000	1.870000	0.481097	0.060000	0.020000	1.000000	0.070000	0.200547	0.060000	0	4.000000e-02	1.300000e-01
PM20D1	148811	broad.mit.edu	37	1	205819140	205819140	+	Missense_Mutation	SNP	T	T	G			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr1:205819140T>G	ENST00000367136.4	-	1	105	c.61A>C	c.(61-63)Acc>Ccc	p.T21P	PM20D1_ENST00000460624.1_5'UTR	NM_152491.4	NP_689704.4	Q6GTS8	P20D1_HUMAN	peptidase M20 domain containing 1			28	Breast(84;0.201)		BRCA - Breast invasive adenocarcinoma(75;0.0252)		CTGGAGACGGTAGGGAAAACT	0.602000																								0							SO:0001583	missense			ENST00000367136.4	1	1	hg19	CCDS1460.1	.	.	.	.	.	.	.	.	.	.	T	12.71	2.018274	0.35606	.	.	ENSG00000162877	ENST00000367136	T	0.07327	3.2	5.44	0.353	0.16058	.	0.566255	0.20291	N	0.095250	T	0.08714	0.0216	L	0.59436	1.845	0.09310	N	1	P	0.49961	0.93	P	0.44860	0.462	T	0.20874	-1.0262	10	0.36615	T	0.2	.	3.7543	0.08579	0.1477:0.2187:0.0:0.6336	.	21	Q6GTS8	P20D1_HUMAN	P	21	ENSP00000356104:T21P	ENSP00000356104:T21P	T	-	1	0	PM20D1	204085763	0.961000	0.32948	0.001000	0.08648	0.039000	0.13416	0.604000	0.24164	-0.105000	0.12132	0.533000	0.62120	ACC		TCGA-2L-AAQJ-01A-12D-A397-08	PM20D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087736.1	1	0	1	28	245	0	58	0	0	0	1	0	58	2		0	0	0	0	0	2	1	1.000000	27	245	0	57	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	2	2	4	2.219696	1	0.440000	1.870000	0.481097	0.520000	0.350000	1.000000	0.500000	0.582681	0.520000	0	4.200000e-01	7.100000e-01
KIAA1522	57648	broad.mit.edu	37	1	33237860	33237860	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr1:33237860G>A	ENST00000373480.1	+	6	3006	c.2903G>A	c.(2902-2904)cGc>cAc	p.R968H	YARS_ENST00000469100.1_5'Flank|KIAA1522_ENST00000401073.2_Missense_Mutation_p.R1027H|KIAA1522_ENST00000373481.3_Missense_Mutation_p.R979H|KIAA1522_ENST00000294521.3_Intron	NM_001198972.1	NP_001185901.1	Q9P206	K1522_HUMAN	KIAA1522			24		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)			CCTGTGGCCCGCAAGCCGTCT	0.662000																								0							SO:0001583	missense			ENST00000373480.1	0	1	hg19	CCDS55588.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.043295	0.75732	.	.	ENSG00000162522	ENST00000401073;ENST00000373481;ENST00000373480	T;T;T	0.16597	2.33;2.34;2.35	5.05	4.14	0.48551	.	0.086750	0.45867	D	0.000333	T	0.20941	0.0504	M	0.61703	1.905	0.30845	N	0.73524	D;D;D	0.57257	0.979;0.979;0.979	P;P;P	0.46049	0.502;0.502;0.502	T	0.16541	-1.0399	10	0.46703	T	0.11	-11.6125	8.9717	0.35910	0.2107:0.0:0.7892:0.0	.	979;968;1027	Q9P206-3;Q9P206;Q9P206-2	.;K1522_HUMAN;.	H	1027;979;968	ENSP00000383851:R1027H;ENSP00000362580:R979H;ENSP00000362579:R968H	ENSP00000362579:R968H	R	+	2	0	KIAA1522	33010447	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	3.416000	0.52707	1.503000	0.48686	0.650000	0.86243	CGC		TCGA-2L-AAQJ-01A-12D-A397-08	KIAA1522-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022130.1	0	0	0	4	182	1	56	0	3.529645e-02	0	168	1	56	11		0	0	0	0	0	2	0	0.031157	4	178	1	55	12		0	0	0	0	0	2	-2.521368	1	1	120800	4	33	1	0	1	1	1.756461	1	0.440000	1.870000	0.323998	0.080000	0.020000	0.190000	0.080000	0.099028	0.080000	0	5.000000e-02	1.400000e-01
ENO1	2023	broad.mit.edu	37	1	8926458	8926458	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08			G	A	G	G		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr1:8926458G>A	ENST00000234590.4	-	7	666	c.547C>T	c.(547-549)Cgc>Tgc	p.R183C		NM_001428.3	NP_001419.1	P06733	ENOA_HUMAN	enolase 1, (alpha)			10	Ovarian(185;0.0661)|all_lung(157;0.127)	all_epithelial(116;2.54e-20)|all_lung(118;2.99e-06)|Lung NSC(185;6.25e-06)|Renal(390;0.000147)|Breast(348;0.00086)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)			GCTCCAATGCGCATGGCTTCC	0.512000													Esophageal Squamous(21;302 608 19946 22210 33560)											0							SO:0001583	missense			ENST00000234590.4	0	1	hg19	CCDS97.1	.	.	.	.	.	.	.	.	.	.	G	19.56	3.849934	0.71603	.	.	ENSG00000074800	ENST00000234590	T	0.58358	0.34	5.33	5.33	0.75918	Enolase, C-terminal (1);	0.052249	0.85682	N	0.000000	T	0.63792	0.2541	M	0.87097	2.86	0.80722	D	1	B;B;B;B;B	0.31769	0.194;0.238;0.339;0.161;0.194	B;B;B;B;B	0.34991	0.102;0.123;0.193;0.061;0.102	T	0.69720	-0.5069	10	0.87932	D	0	-2.9305	18.013	0.89230	0.0:0.0:1.0:0.0	.	87;150;21;90;183	E2DRY6;A4UCS8;Q9BT62;P06733-2;P06733	.;.;.;.;ENOA_HUMAN	C	183	ENSP00000234590:R183C	ENSP00000234590:R183C	R	-	1	0	ENO1	8849045	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	7.984000	0.88150	2.492000	0.84095	0.563000	0.77884	CGC		TCGA-2L-AAQJ-01A-12D-A397-08	ENO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004945.1	0	0	0	6	452	0	104	0	9.994856e-01	0	1288	0	104	2		0	0	0	0	0	2	1	0.964240	6	448	0	103	2		0	0	0	0	0	2	-2.202556	0	1	121412	2	37	1	0	1	1	1.797343	1	0.440000	1.870000	0.343186	0.050000	0.010000	0.110000	0.050000	0.058738	0.050000	0	3.000000e-02	8.000000e-02
RBM12	10137	broad.mit.edu	37	20	34240896	34240896	+	Silent	SNP	C	C	T			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr20:34240896C>T	ENST00000374114.3	-	3	2612	c.2349G>A	c.(2347-2349)tcG>tcA	p.S783S	CPNE1_ENST00000397442.1_Intron|CPNE1_ENST00000317619.3_Intron|CPNE1_ENST00000397446.1_Intron|CPNE1_ENST00000317677.5_Intron|CPNE1_ENST00000352393.4_Intron|CPNE1_ENST00000397443.1_Intron|RP1-309K20.6_ENST00000541176.2_Intron|RBM12_ENST00000374104.3_Silent_p.S783S|RBM12_ENST00000359646.1_Silent_p.S783S|CPNE1_ENST00000397445.1_Intron	NM_001198838.1|NM_001198840.1|NM_006047.5	NP_001185767.1|NP_001185769.1|NP_006038.2	Q9NTZ6	RBM12_HUMAN	RNA binding motif protein 12			36	Lung NSC(9;0.00608)|all_lung(11;0.00918)		BRCA - Breast invasive adenocarcinoma(18;0.00953)		CTCCAAATCCCGATGGCCCAC	0.562000																								0							SO:0001819	synonymous_variant			ENST00000374114.3	1	1	hg19	CCDS13261.1																																																																																				TCGA-2L-AAQJ-01A-12D-A397-08	RBM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078894.1	1	0	0	79	246	0	67	1	9.999997e-01	29	42	0	67	2		0	0	0	0	0	2	1	1.000000	77	245	0	66	2		0	0	0	0	0	2	-4.091664	1	1	0	0		1	0	0	0	2.020317	0	0.440000	1.870000	0.427403	0.990000	0.870000	1.000000	1.000000	0.987650	0.990000	1	9.700000e-01	1
SIGLEC1	6614	broad.mit.edu	37	20	3673686	3673686	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr20:3673686C>T	ENST00000344754.4	-	14	3600	c.3601G>A	c.(3601-3603)Gcc>Acc	p.A1201T	SIGLEC1_ENST00000202578.4_Missense_Mutation_p.A1201T	NM_023068.3	NP_075556.1	Q9BZZ2	SN_HUMAN	sialic acid binding Ig-like lectin 1, sialoadhesin			70					GCCAGCTGGGCGGGCGGGCGG	0.721000																								0							SO:0001583	missense			ENST00000344754.4	1	1	hg19	CCDS13060.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.66|17.66	3.443368|3.443368	0.63067|0.63067	.|.	.|.	ENSG00000088827|ENSG00000088827	ENST00000344754;ENST00000202578|ENST00000419548	T;T|.	0.75154|.	-0.91;-0.91|.	4.74|4.74	4.74|4.74	0.60224|0.60224	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);|.	0.000000|.	0.39615|.	N|.	0.001309|.	T|T	0.73992|0.73992	0.3658|0.3658	M|M	0.78223|0.78223	2.4|2.4	0.36727|0.36727	D|D	0.88151|0.88151	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.75484|.	0.986;0.966|.	T|T	0.79339|0.79339	-0.1844|-0.1844	10|5	0.30078|.	T|.	0.28|.	.|.	13.088|13.088	0.59153|0.59153	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1201;1201|.	Q9BZZ2;Q9BZZ2-3|.	SN_HUMAN;.|.	T|H	1201|14	ENSP00000341141:A1201T;ENSP00000202578:A1201T|.	ENSP00000202578:A1201T|.	A|R	-|-	1|2	0|0	SIGLEC1|SIGLEC1	3621686|3621686	0.045000|0.045000	0.20229|0.20229	0.979000|0.979000	0.43373|0.43373	0.294000|0.294000	0.27393|0.27393	0.222000|0.222000	0.17699|0.17699	2.477000|2.477000	0.83638|0.83638	0.655000|0.655000	0.94253|0.94253	GCC|CGC		TCGA-2L-AAQJ-01A-12D-A397-08	SIGLEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077761.2	1	0	0	48	104	0	22	0	0	0	1	0	22	2		0	0	0	0	0	2	1	1.000000	48	103	0	21	2		0	0	0	0	0	2	-6.835376	1	1	119828	1	27	1	0	1	1	1.597628	1	0.440000	1.870000	0.282051	0.940000	0.780000	1.000000	0.990000	0.934704	0.940000	1	8.700000e-01	9.900000e-01
BAGE2	85319	broad.mit.edu	37	21	11098773	11098773	+	RNA	SNP	G	G	A	rs77771067		TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr21:11098773G>A	ENST00000470054.1	-	0	152							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2						Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)		cgctcaggccgccctcctaac	0.627000																								0											ENST00000470054.1	1	1	hg19																																																																																					TCGA-2L-AAQJ-01A-12D-A397-08	BAGE2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000157417.3	0	0	0	54	747	0	183		0	0	0	0	183	2		0	0	0	0	0	2	1	1.000000	51	677	0	177	2		0	0	0	0	0	2	-2.966611	1	1	121250	21	43	1	0	0	0	2.026235	0	0.440000	1.870000	0.429967	0.290000	0.220000	0.380000	0.300000	0.305350	0.290000	0	2.500000e-01	3.400000e-01
ADARB1	104	broad.mit.edu	37	21	46596475	46596475	+	Missense_Mutation	SNP	C	C	T	rs142476560		TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr21:46596475C>T	ENST00000360697.3	+	2	874	c.859C>T	c.(859-861)Cgg>Tgg	p.R287W	ADARB1_ENST00000389863.4_Missense_Mutation_p.R287W|ADARB1_ENST00000539173.1_Missense_Mutation_p.R287W|ADARB1_ENST00000348831.4_Missense_Mutation_p.R287W|ADARB1_ENST00000437626.1_Intron			P78563	RED1_HUMAN	adenosine deaminase, RNA-specific, B1			17					TGCCAAGGCCCGGGCTGCGCA	0.572000																								0							SO:0001583	missense			ENST00000360697.3	1	1	hg19	CCDS33589.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.077779	0.76528	.	.	ENSG00000197381	ENST00000539173;ENST00000539917;ENST00000389863;ENST00000348831;ENST00000360697	T;T;T;T	0.77750	-1.12;-1.12;-1.12;-1.12	5.14	5.14	0.70334	Double-stranded RNA-binding (3);Double-stranded RNA-binding-like (1);	0.061314	0.64402	D	0.000003	D	0.86727	0.6002	M	0.77486	2.375	0.80722	D	1	D;D;D;D;D	0.89917	0.999;1.0;0.999;0.998;0.998	D;D;D;D;D	0.77004	0.957;0.989;0.975;0.957;0.957	D	0.87690	0.2553	10	0.72032	D	0.01	-46.512	11.5532	0.50733	0.1787:0.8213:0.0:0.0	.	314;287;287;315;287	P78563-4;P78563;Q4AE77;G5E9B4;P78563-3	.;RED1_HUMAN;.;.;.	W	287	ENSP00000441897:R287W;ENSP00000374513:R287W;ENSP00000015877:R287W;ENSP00000353920:R287W	ENSP00000015877:R287W	R	+	1	2	ADARB1	45420903	0.994000	0.37717	1.000000	0.80357	0.976000	0.68499	2.697000	0.47060	2.552000	0.86080	0.655000	0.94253	CGG		TCGA-2L-AAQJ-01A-12D-A397-08	ADARB1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206648.2	1	0	1	87	230	0	57	0	1.861163e-01	0	3	0	57	2		0	0	0	0	0	2	1	1.000000	86	229	0	57	2		0	0	0	0	0	2	-5.924463	1	1	0	0		1	0	0	0	2.026235	0	0.440000	1.870000	0.429967	0.990000	0.990000	1.000000	1.000000	0.999360	0.990000	1	9.900000e-01	1
CECR2	27443	broad.mit.edu	37	22	18021889	18021889	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr22:18021889C>T	ENST00000400585.2	+	16	2006	c.1568C>T	c.(1567-1569)aCa>aTa	p.T523I	CECR2_ENST00000400573.5_Missense_Mutation_p.T664I|CECR2_ENST00000262608.8_Missense_Mutation_p.T665I			Q9BXF3	CECR2_HUMAN	cat eye syndrome chromosome region, candidate 2			59		all_epithelial(15;0.139)			AGGCTAGGCACACCAGAGGAG	0.547000																								0							SO:0001583	missense			ENST00000400585.2	0	1	hg19		.	.	.	.	.	.	.	.	.	.	C	4.046	0.006138	0.07866	.	.	ENSG00000099954	ENST00000400585;ENST00000400573;ENST00000262608	T;T;T	0.26223	1.88;1.87;1.75	5.28	3.1	0.35709	.	1.079560	0.07208	N	0.858745	T	0.25195	0.0612	L	0.51422	1.61	0.09310	N	1	B;B;B	0.23442	0.085;0.049;0.029	B;B;B	0.14023	0.01;0.01;0.01	T	0.17684	-1.0361	10	0.29301	T	0.29	-0.0068	10.7002	0.45922	0.0:0.7801:0.0:0.2199	.	706;523;664	Q9BXF3;B7WPH3;E2QRE6	CECR2_HUMAN;.;.	I	523;664;665	ENSP00000383428:T523I;ENSP00000383417:T664I;ENSP00000262608:T665I	ENSP00000262608:T665I	T	+	2	0	CECR2	16401889	0.000000	0.05858	0.002000	0.10522	0.005000	0.04900	0.558000	0.23469	1.467000	0.48044	0.655000	0.94253	ACA		TCGA-2L-AAQJ-01A-12D-A397-08	CECR2-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000316226.2	0	0	0	9	77	0	21	0	0	0	1	0	21	2		0	0	0	0	0	2	1	0.994775	9	76	0	20	2		0	0	0	0	0	2	-15.383410	1	1	0	0		1	1	2	3	2.062546	0	0.440000	1.870000	0.441229	0.490000	0.240000	0.840000	0.470000	0.509919	0.490000	0	3.500000e-01	6.600000e-01
TRMU	55687	broad.mit.edu	37	22	46742405	46742405	+	Missense_Mutation	SNP	G	G	A	rs34012206	byFrequency	TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr22:46742405G>A	ENST00000290846.4	+	4	782	c.442G>A	c.(442-444)Gaa>Aaa	p.E148K	TRMU_ENST00000424260.2_Missense_Mutation_p.E113K|TRMU_ENST00000381019.3_Missense_Mutation_p.E148K	NM_018006.4	NP_060476.2	O75648	MTU1_HUMAN	tRNA 5-methylaminomethyl-2-thiouridylate methyltransferase	p.E148K(1)		10		Ovarian(80;0.00965)|Breast(42;0.0194)|all_neural(38;0.0416)			TAAGAAGCCCGAAGGGCTTTT	0.443000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000290846.4	1	0	hg19	CCDS14075.1	35	0.016025641025641024	34	0.06910569105691057	1	0.0027624309392265192	0	0.0	0	0.0	g	11.94	1.787630	0.31593	0.047208	4.65E-4	ENSG00000100416	ENST00000290846;ENST00000381019;ENST00000424260	T;T;T	0.74106	-0.49;-0.81;0.01	5.41	0.554	0.17241	Rossmann-like alpha/beta/alpha sandwich fold (1);	0.611098	0.17383	N	0.176250	T	0.06962	0.0177	N	0.08118	0	0.09310	N	1	B;B;B	0.10296	0.002;0.003;0.002	B;B;B	0.06405	0.002;0.001;0.001	T	0.10359	-1.0633	10	0.38643	T	0.18	-16.2804	10.4278	0.44389	0.1212:0.5516:0.3271:0.0	rs34012206	148;148;148	B4DHM1;O75648-2;O75648	.;.;MTU1_HUMAN	K	148;148;113	ENSP00000290846:E148K;ENSP00000370407:E148K;ENSP00000406038:E113K	ENSP00000290846:E148K	E	+	1	0	TRMU	45121069	0.055000	0.20627	0.331000	0.25455	0.916000	0.54674	0.716000	0.25836	0.616000	0.30141	0.651000	0.88453	GAA		TCGA-2L-AAQJ-01A-12D-A397-08	TRMU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318042.2	0	0	1	93	319	0	87	1	9.710165e-01	2	20	0	87	2		0	0	0	0	0	2	1	1.000000	93	318	0	86	2		0	0	0	0	0	2	-2.046559	0	1	121412	561	60	1	0	1	1	2.056367	0	0.440000	1.870000	0.438765	0.990000	0.840000	1.000000	1.000000	0.974810	0.990000	1	9.200000e-01	1
APOB	338	broad.mit.edu	37	2	21231133	21231133	+	Silent	SNP	A	A	G			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr2:21231133A>G	ENST00000233242.1	-	26	8734	c.8607T>C	c.(8605-8607)ctT>ctC	p.L2869L		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B			305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				CTCCATTACTAAGCTCCAGTG	0.393000																								0							SO:0001819	synonymous_variant			ENST00000233242.1	0	1	hg19	CCDS1703.1																																																																																				TCGA-2L-AAQJ-01A-12D-A397-08	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1	0	0	0	9	686	0	112		0	0	0	0	112	2		0	0	0	0	0	2	1	0.994141	8	684	0	112	2		0	0	0	0	0	2	-6.972063	1	1	0	0		1	0	0	0	2.058326	0	0.440000	1.870000	0.440000	0.050000	0.020000	0.110000	0.060000	0.065084	0.050000	0	3.000000e-02	9.000000e-02
GLB1L	79411	broad.mit.edu	37	2	220101856	220101856	+	Missense_Mutation	SNP	T	T	C			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08			T	C	T	T		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr2:220101856T>C	ENST00000295759.7	-	17	2216	c.1903A>G	c.(1903-1905)Atc>Gtc	p.I635V	GLB1L_ENST00000356283.3_Missense_Mutation_p.I545V|GLB1L_ENST00000409640.1_Missense_Mutation_p.I545V|GLB1L_ENST00000392089.2_Missense_Mutation_p.I635V|GLB1L_ENST00000497855.1_5'UTR			Q6UWU2	GLB1L_HUMAN	galactosidase, beta 1-like			22		all_lung(227;1.19e-05)|Lung NSC(271;2.76e-05)|Medulloblastoma(418;0.0208)|Esophageal squamous(248;0.0559)			AGGGAATTGATATGTGTCCTG	0.468000																								0							SO:0001583	missense			ENST00000295759.7	1	1	hg19	CCDS2437.1	.	.	.	.	.	.	.	.	.	.	T	4.871	0.161916	0.09287	.	.	ENSG00000163521	ENST00000295759;ENST00000409640;ENST00000392089;ENST00000356283	D;D;D;D	0.96992	-4.2;-3.93;-4.2;-3.93	4.93	-9.86	0.00473	Galactose-binding domain-like (1);	3.089320	0.00575	N	0.000313	D	0.86112	0.5855	N	0.04959	-0.14	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.81204	-0.1039	10	0.21540	T	0.41	0.3857	2.6931	0.05126	0.1812:0.3995:0.1959:0.2234	.	545;635	Q6UWU2-2;Q6UWU2	.;GLB1L_HUMAN	V	635;545;635;545	ENSP00000295759:I635V;ENSP00000386354:I545V;ENSP00000375939:I635V;ENSP00000348628:I545V	ENSP00000295759:I635V	I	-	1	0	GLB1L	219810100	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-1.053000	0.03500	-2.213000	0.00735	-0.256000	0.11100	ATC		TCGA-2L-AAQJ-01A-12D-A397-08	GLB1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256822.2	1	0	1	99	398	0	107	1	9.999935e-01	20	51	0	107	2		0	0	0	0	0	2	1	1.000000	98	394	0	106	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	0	0	0	2.022512	0	0.440000	1.870000	0.429967	0.880000	0.730000	1.000000	1.000000	0.888803	0.880000	1	8.000000e-01	9.700000e-01
ITSN2	50618	broad.mit.edu	37	2	24533237	24533237	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr2:24533237C>T	ENST00000355123.4	-	7	1012	c.569G>A	c.(568-570)gGg>gAg	p.G190E	ITSN2_ENST00000406921.3_Missense_Mutation_p.G190E|ITSN2_ENST00000361999.3_Missense_Mutation_p.G190E|ITSN2_ENST00000407704.1_5'Flank	NM_006277.2	NP_006268.2	Q9NZM3	ITSN2_HUMAN	intersectin 2			61	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				ATAAGATGACCCATGAGGCAA	0.343000																								0							SO:0001583	missense			ENST00000355123.4	1	1	hg19	CCDS1710.2	.	.	.	.	.	.	.	.	.	.	C	12.21	1.868542	0.32977	.	.	ENSG00000198399	ENST00000361999;ENST00000355123;ENST00000380868;ENST00000445614;ENST00000406921;ENST00000412011;ENST00000443927	T;T;T;T;T;T	0.59906	0.25;0.23;0.25;0.65;0.74;1.57	4.98	4.1	0.47936	.	0.809232	0.09677	U	0.770329	T	0.49779	0.1577	N	0.14661	0.345	0.24743	N	0.993024	B;B;B;P	0.40050	0.131;0.131;0.314;0.7	B;B;B;P	0.44477	0.028;0.028;0.041;0.451	T	0.48410	-0.9038	10	0.56958	D	0.05	.	13.9001	0.63797	0.0:0.1599:0.8401:0.0	.	190;190;190;190	Q9NZM3-4;Q9NZM3-3;Q9NZM3-2;Q9NZM3	.;.;.;ITSN2_HUMAN	E	190;190;190;189;190;190;176	ENSP00000354561:G190E;ENSP00000347244:G190E;ENSP00000370250:G190E;ENSP00000384499:G190E;ENSP00000391224:G190E;ENSP00000391715:G176E	ENSP00000347244:G190E	G	-	2	0	ITSN2	24386741	1.000000	0.71417	0.889000	0.34880	0.766000	0.43426	3.658000	0.54482	1.218000	0.43458	-0.499000	0.04595	GGG		TCGA-2L-AAQJ-01A-12D-A397-08	ITSN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207620.2	1	0	1	123	844	0	166	1	6.229116e-01	4	12	0	166	2		0	0	0	0	0	2	1	1.000000	123	838	0	165	2		0	0	0	0	0	2	-3.142702	1	1	121412	1	36	1	0	0	0	2.058326	0	0.440000	1.870000	0.440000	0.570000	0.480000	0.670000	0.580000	0.580895	0.570000	0	5.200000e-01	6.300000e-01
BCL11A	53335	broad.mit.edu	37	2	60688782	60688782	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr2:60688782C>T	ENST00000335712.6	-	4	1492	c.1265G>A	c.(1264-1266)cGc>cAc	p.R422H	BCL11A_ENST00000538214.1_Missense_Mutation_p.R388H|BCL11A_ENST00000537768.1_Missense_Mutation_p.R91H|BCL11A_ENST00000359629.5_Intron|BCL11A_ENST00000358510.4_Missense_Mutation_p.R388H|BCL11A_ENST00000477659.1_5'UTR|BCL11A_ENST00000356842.4_Missense_Mutation_p.R422H	NM_022893.3	NP_075044.2	Q9H165	BC11A_HUMAN	B-cell CLL/lymphoma 11A (zinc finger protein)			59			LUSC - Lung squamous cell carcinoma(5;9.29e-08)|Lung(5;1.34e-06)|Epithelial(17;0.0562)|all cancers(80;0.199)		CTTCATGTGGCGCTTCAGCTT	0.647000			T	IGH@	B-CLL										Dom	yes		2	2p13	53335	B-cell CLL/lymphoma 11A		L	0							SO:0001583	missense			ENST00000335712.6	0	1	hg19	CCDS1862.1	.	.	.	.	.	.	.	.	.	.	C	13.62	2.291279	0.40494	.	.	ENSG00000119866	ENST00000356842;ENST00000378117;ENST00000538214;ENST00000537768;ENST00000335712;ENST00000358510	T;T;T;T;T	0.16743	3.17;3.17;2.32;5.19;5.19	5.27	4.37	0.52481	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.062434	0.64402	D	0.000010	T	0.41396	0.1157	M	0.73217	2.22	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.999;1.0;1.0;1.0	D;D;D;D;D	0.87578	0.998;0.98;0.997;0.998;0.997	T	0.34153	-0.9840	10	0.56958	D	0.05	-2.2443	15.0016	0.71476	0.1436:0.8564:0.0:0.0	.	388;91;388;422;422	F5H2Y4;B4DT16;Q9H165-6;Q9H165;D9YZV9	.;.;.;BC11A_HUMAN;.	H	422;458;388;91;422;388	ENSP00000349300:R422H;ENSP00000438303:R388H;ENSP00000443712:R91H;ENSP00000338774:R422H;ENSP00000351307:R388H	ENSP00000338774:R422H	R	-	2	0	BCL11A	60542286	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.818000	0.86416	1.173000	0.42796	0.655000	0.94253	CGC		TCGA-2L-AAQJ-01A-12D-A397-08	BCL11A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251579.2	0	0	0	8	421	0	85	0	0	0	1	0	85	2		0	0	0	0	0	2	1	0.988998	8	416	0	84	2		0	0	0	0	0	2	-2.615840	1	1	0	0		1	0	0	0	2.046845	0	0.440000	1.870000	0.437525	0.080000	0.030000	0.160000	0.080000	0.094216	0.080000	0	5.000000e-02	1.200000e-01
ADCY5	111	broad.mit.edu	37	3	123021980	123021980	+	Silent	SNP	C	C	T	rs148384901		TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr3:123021980C>T	ENST00000462833.1	-	14	3858	c.2646G>A	c.(2644-2646)gcG>gcA	p.A882A	ADCY5_ENST00000309879.5_Silent_p.A532A|ADCY5_ENST00000491190.1_Silent_p.A515A	NM_183357.2	NP_899200.1	O95622	ADCY5_HUMAN	adenylate cyclase 5			60					CGGCCGACTCCGCCACGTGAC	0.652000																								0							SO:0001819	synonymous_variant			ENST00000462833.1	1	1	hg19	CCDS3022.1																																																																																				TCGA-2L-AAQJ-01A-12D-A397-08	ADCY5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355889.4	1	0	1	43	169	0	44	0	4.371882e-01	0	7	0	44	2		0	0	0	0	0	2	1	1.000000	43	166	0	42	2		0	0	0	0	0	2	-3.683136	1	1	121410	3	37	1	1	2	3	2.071607	0	0.440000	1.870000	0.441229	0.920000	0.690000	1.000000	1.000000	0.907529	0.920000	1	8.000000e-01	1
TGFBR2	7048	broad.mit.edu	37	3	30713171	30713171	+	Nonsense_Mutation	SNP	C	C	T			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr3:30713171C>T	ENST00000295754.5	+	4	878	c.496C>T	c.(496-498)Caa>Taa	p.Q166*	TGFBR2_ENST00000359013.4_Nonsense_Mutation_p.Q191*	NM_003242.5	NP_003233.4	P37173	TGFR2_HUMAN	transforming growth factor, beta receptor II (70/80kDa)			53					AGTCATATTTCAAGTGACAGG	0.473000																								0							SO:0001587	stop_gained			ENST00000295754.5	0	1	hg19	CCDS2648.1	.	.	.	.	.	.	.	.	.	.	C	38	6.940423	0.97952	.	.	ENSG00000163513	ENST00000295754;ENST00000359013;ENST00000383765;ENST00000439925	.	.	.	4.86	3.91	0.45181	.	0.557577	0.20898	N	0.083695	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07325	T	0.83	.	12.5905	0.56439	0.231:0.769:0.0:0.0	.	.	.	.	X	166;191;68;32	.	ENSP00000295754:Q166X	Q	+	1	0	TGFBR2	30688175	1.000000	0.71417	0.989000	0.46669	0.920000	0.55202	2.769000	0.47654	2.508000	0.84585	0.655000	0.94253	CAA		TCGA-2L-AAQJ-01A-12D-A397-08	TGFBR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252994.2	1	0	1	50	148	0	49	1	9.999827e-01	6	47	0	49	2	1	1	76	223	0	191	2	1	1.000000	49	148	0	49	2		0	0	0	0	0	2	-4.720671	1	1	0	0		1	0	1	1	1.610984	1	0.440000	1.870000	0.282051	0.860000	0.670000	0.990000	0.880000	0.861450	0.860000	1	7.600000e-01	9.500000e-01
LRRC2	79442	broad.mit.edu	37	3	46563080	46563080	+	Missense_Mutation	SNP	C	C	G			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr3:46563080C>G	ENST00000395905.3	-	8	1390	c.998G>C	c.(997-999)aGt>aCt	p.S333T	LRRC2_ENST00000296144.3_Missense_Mutation_p.S333T	NM_024512.4	NP_078788.2	Q9BYS8	LRRC2_HUMAN	leucine rich repeat containing 2			17		Ovarian(412;0.0563)			ATCCCGTTCACTTTCCATTAT	0.328000																								0							SO:0001583	missense			ENST00000395905.3	0	1	hg19	CCDS2741.1	.	.	.	.	.	.	.	.	.	.	C	11.15	1.554666	0.27739	.	.	ENSG00000163827	ENST00000395905;ENST00000296144	T;T	0.17854	2.25;2.25	4.56	3.67	0.42095	.	0.161627	0.41097	N	0.000942	T	0.13457	0.0326	L	0.40543	1.245	0.32701	N	0.512847	B	0.06786	0.001	B	0.08055	0.003	T	0.13845	-1.0494	10	0.14656	T	0.56	.	12.2733	0.54719	0.0:0.8089:0.1911:0.0	.	333	Q9BYS8	LRRC2_HUMAN	T	333	ENSP00000379241:S333T;ENSP00000296144:S333T	ENSP00000296144:S333T	S	-	2	0	LRRC2	46538084	0.998000	0.40836	0.863000	0.33907	0.897000	0.52465	0.599000	0.24089	1.245000	0.43885	0.591000	0.81541	AGT		TCGA-2L-AAQJ-01A-12D-A397-08	LRRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257375.2	0	0	0	5	189	0	45	0	0	0	1	0	45	2		0	0	0	0	0	2	1	0.937509	5	188	0	45	2		0	0	0	0	0	2	-7.000087	1	1	0	0		1	0	1	1	1.610984	1	0.440000	1.870000	0.282051	0.090000	0.030000	0.200000	0.090000	0.107110	0.090000	0	5.000000e-02	1.500000e-01
DOCK3	1795	broad.mit.edu	37	3	51378785	51378785	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr3:51378785G>A	ENST00000266037.9	+	38	3907	c.3884G>A	c.(3883-3885)cGg>cAg	p.R1295Q		NM_004947.4	NP_004938.1	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3			45					GGACTGTGCCGGAAGATCATT	0.532000																								0							SO:0001583	missense			ENST00000266037.9	0	1	hg19	CCDS46835.1	.	.	.	.	.	.	.	.	.	.	G	15.93	2.977405	0.53720	.	.	ENSG00000088538	ENST00000266037;ENST00000402669	T	0.04603	3.59	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.08891	0.0220	N	0.20766	0.605	0.58432	D	0.999999	D	0.67145	0.996	P	0.55087	0.768	T	0.47032	-0.9148	10	0.28530	T	0.3	.	19.4028	0.94637	0.0:0.0:1.0:0.0	.	1295	Q8IZD9	DOCK3_HUMAN	Q	1295;91	ENSP00000266037:R1295Q	ENSP00000266037:R1295Q	R	+	2	0	DOCK3	51353825	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.863000	0.87023	2.574000	0.86865	0.655000	0.94253	CGG		TCGA-2L-AAQJ-01A-12D-A397-08	DOCK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346478.5	0	0	0	5	117	0	23		0	0	0	0	23	2	0	9.898736e-01	4	773	2	543	10	1	0.937523	5	116	0	22	2		0	0	0	0	0	2	-3.045236	1	1	121008	3	31	1	0	1	1	1.610984	1	0.440000	1.870000	0.282051	0.150000	0.050000	0.310000	0.140000	0.167997	0.150000	0	9.000000e-02	2.300000e-01
CACNA1D	776	broad.mit.edu	37	3	53752385	53752385	+	Missense_Mutation	SNP	G	G	T			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr3:53752385G>T	ENST00000350061.5	+	10	1959	c.1448G>T	c.(1447-1449)gGc>gTc	p.G483V	CACNA1D_ENST00000288139.4_Missense_Mutation_p.G483V|CACNA1D_ENST00000422281.2_Missense_Mutation_p.G483V	NM_001128840.1	NP_001122312.1	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type, alpha 1D subunit			90				Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	AGCGGTGAAGGCGAGAACCGA	0.592000																								0							SO:0001583	missense			ENST00000350061.5	1	1	hg19	CCDS46848.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	10.02|10.02	1.235118|1.235118	0.22626|0.22626	.|.	.|.	ENSG00000157388|ENSG00000157388	ENST00000481085|ENST00000350061;ENST00000288139;ENST00000422281;ENST00000481478	.|D;D;D;D	.|0.93712	.|-3.27;-3.27;-3.27;-3.27	5.44|5.44	4.57|4.57	0.56435|0.56435	.|.	.|153.860000	.|0.00166	.|N	.|0.000000	D|D	0.89853|0.89853	0.6835|0.6835	N|N	0.19112|0.19112	0.55|0.55	0.80722|0.80722	D|D	1|1	.|B;B;B;B	.|0.25486	.|0.01;0.001;0.002;0.127	.|B;B;B;B	.|0.28305	.|0.01;0.002;0.008;0.088	T|T	0.69544|0.69544	-0.5117|-0.5117	5|10	.|0.39692	.|T	.|0.17	.|.	10.5212|10.5212	0.44920|0.44920	0.0:0.1448:0.7048:0.1504|0.0:0.1448:0.7048:0.1504	.|.	.|483;156;483;483	.|B0FYA3;Q59GD8;Q01668;Q01668-2	.|.;.;CAC1D_HUMAN;.	S|V	197|483;483;483;156	.|ENSP00000288133:G483V;ENSP00000288139:G483V;ENSP00000409174:G483V;ENSP00000418014:G156V	.|ENSP00000288139:G483V	A|G	+|+	1|2	0|0	CACNA1D|CACNA1D	53727425|53727425	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.433000|0.433000	0.31745|0.31745	3.391000|3.391000	0.52530|0.52530	1.292000|1.292000	0.44672|0.44672	-0.150000|-0.150000	0.13652|0.13652	GCG|GGC		TCGA-2L-AAQJ-01A-12D-A397-08	CACNA1D-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350557.1	1	0	1	76	236	0	96	0	0	1	0	0	96	2		0	0	0	0	0	2	1	1.000000	75	233	0	93	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	0	1	1	1.610984	1	0.440000	1.870000	0.282051	0.840000	0.690000	0.980000	0.860000	0.851812	0.840000	0	7.600000e-01	9.300000e-01
OXTR	5021	broad.mit.edu	37	3	8794835	8794835	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr3:8794835G>A	ENST00000316793.3	-	4	1622	c.998C>T	c.(997-999)aCg>aTg	p.T333M	CAV3_ENST00000472766.1_Intron	NM_000916.3	NP_000907.2	P30559	OXYR_HUMAN	oxytocin receptor			13				Carbetocin(DB01282)|Oxytocin(DB00107)	GAGGTGGCCCGTGAACAGCAT	0.617000																								0							SO:0001583	missense			ENST00000316793.3	1	1	hg19	CCDS2570.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	23.0	4.366953	0.82463	2.27E-4	1.16E-4	ENSG00000180914	ENST00000316793	T	0.38560	1.13	5.13	4.23	0.50019	.	0.052718	0.85682	D	0.000000	T	0.55449	0.1921	M	0.63428	1.95	0.41902	D	0.990422	D	0.71674	0.998	P	0.57204	0.815	T	0.62158	-0.6913	10	0.87932	D	0	-32.9382	14.1848	0.65598	0.0:0.1509:0.8491:0.0	.	333	P30559	OXYR_HUMAN	M	333	ENSP00000324270:T333M	ENSP00000324270:T333M	T	-	2	0	OXTR	8769835	1.000000	0.71417	0.845000	0.33349	0.985000	0.73830	5.333000	0.65917	1.330000	0.45394	0.655000	0.94253	ACG		TCGA-2L-AAQJ-01A-12D-A397-08	OXTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207061.2	0	0	0	61	152	1	47	1	3.283906e-01	2	2	1	47	2		0	0	0	0	0	2	1	1.000000	61	150	1	46	15		0	0	0	0	0	2	-6.283823	1	1	121412	4	35	1	0	1	1	1.610984	1	0.440000	1.870000	0.282051	0.920000	0.770000	1.000000	0.990000	0.921743	0.920000	1	8.500000e-01	9.800000e-01
LDB2	9079	broad.mit.edu	37	4	16504411	16504411	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr4:16504411G>A	ENST00000304523.5	-	8	1300	c.977C>T	c.(976-978)aCg>aTg	p.T326M	LDB2_ENST00000441778.2_3'UTR|LDB2_ENST00000515064.1_Missense_Mutation_p.T324M|LDB2_ENST00000502640.1_3'UTR|RP11-446J8.1_ENST00000512370.1_RNA	NM_001290.3	NP_001281.1	O43679	LDB2_HUMAN	LIM domain binding 2			33					ATCATATTGCGTGTTTTCTAA	0.537000																								0							SO:0001583	missense			ENST00000304523.5	1	1	hg19	CCDS3420.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.11|16.11	3.030178|3.030178	0.54790|0.54790	.|.	.|.	ENSG00000169744|ENSG00000169744	ENST00000507464|ENST00000515064;ENST00000304523	.|T;T	.|0.26810	.|1.71;1.71	5.48|5.48	5.48|5.48	0.80851|0.80851	.|.	.|0.000000	.|0.64402	.|D	.|0.000002	T|T	0.50531|0.50531	0.1621|0.1621	M|M	0.68952|0.68952	2.095|2.095	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.89917	.|1.0;0.998;1.0;1.0	.|D;P;P;D	.|0.75020	.|0.985;0.899;0.891;0.949	T|T	0.43491|0.43491	-0.9388|-0.9388	5|10	.|0.45353	.|T	.|0.12	-13.6093|-13.6093	18.3199|18.3199	0.90234|0.90234	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|290;324;326;300	.|B7Z6D0;G5E9Y7;O43679;O43679-3	.|.;.;LDB2_HUMAN;.	C|M	247|324;326	.|ENSP00000422552:T324M;ENSP00000306772:T326M	.|ENSP00000306772:T326M	R|T	-|-	1|2	0|0	LDB2|LDB2	16113509|16113509	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.869000|9.869000	0.99810|0.99810	2.558000|2.558000	0.86282|0.86282	0.655000|0.655000	0.94253|0.94253	CGC|ACG		TCGA-2L-AAQJ-01A-12D-A397-08	LDB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250321.2	1	0	1	126	513	1	131	0	9.571750e-01	0	31	1	131	3		0	0	0	0	0	2	1	1.000000	125	504	1	130	17		0	0	0	0	0	2	-20.000000	1	1	121412	1	35	1	0	1	1	2.055782	0	0.440000	1.870000	0.438765	0.880000	0.750000	1.000000	1.000000	0.894130	0.880000	1	8.200000e-01	9.700000e-01
COX7B2	170712	broad.mit.edu	37	4	46737152	46737152	+	Missense_Mutation	SNP	G	G	C			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr4:46737152G>C	ENST00000396533.1	-	4	308	c.58C>G	c.(58-60)Caa>Gaa	p.Q20E	COX7B2_ENST00000355591.3_Missense_Mutation_p.Q20E|COX7B2_ENST00000543208.1_Missense_Mutation_p.Q19E|COX7B2_ENST00000302930.5_Missense_Mutation_p.Q20E			Q8TF08	CX7B2_HUMAN	cytochrome c oxidase subunit VIIb2			5					GCCATGCTTTGCAGAATGCTT	0.423000																								0							SO:0001583	missense			ENST00000396533.1	0	1	hg19	CCDS3472.2	.	.	.	.	.	.	.	.	.	.	G	5.784	0.329026	0.10956	.	.	ENSG00000170516	ENST00000355591;ENST00000396533;ENST00000302930;ENST00000543208;ENST00000505102	T;T;T;T;T	0.45276	0.9;0.9;0.9;0.9;0.9	4.22	1.33	0.21861	.	0.393840	0.25771	N	0.028415	T	0.29256	0.0728	.	.	.	0.09310	N	1	B	0.14438	0.01	B	0.14023	0.01	T	0.24368	-1.0162	9	0.72032	D	0.01	-8.2035	6.926	0.24416	0.0:0.3509:0.4531:0.1959	.	20	Q8TF08	CX7B2_HUMAN	E	20;20;20;19;20	ENSP00000347799:Q20E;ENSP00000379784:Q20E;ENSP00000305964:Q20E;ENSP00000437439:Q19E;ENSP00000423519:Q20E	ENSP00000305964:Q20E	Q	-	1	0	COX7B2	46431909	0.003000	0.15002	0.019000	0.16419	0.193000	0.23685	1.002000	0.29796	0.255000	0.21593	0.585000	0.79938	CAA		TCGA-2L-AAQJ-01A-12D-A397-08	COX7B2-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313899.1	0	0	0	5	397	0	71		0	0	0	0	71	2		0	0	0	0	0	2	1	0.936259	5	393	0	71	2		0	0	0	0	0	2	-3.317288	1	1	0	0		1	0	1	1	2.055782	0	0.440000	1.870000	0.438765	0.050000	0.010000	0.130000	0.060000	0.067131	0.050000	0	3.000000e-02	9.000000e-02
CEP135	9662	broad.mit.edu	37	4	56877620	56877620	+	Nonsense_Mutation	SNP	G	G	T			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr4:56877620G>T	ENST00000257287.4	+	20	2672	c.2548G>T	c.(2548-2550)Gaa>Taa	p.E850*		NM_025009.4	NP_079285.2	Q66GS9	CP135_HUMAN	centrosomal protein 135kDa			50	Glioma(25;0.08)|all_neural(26;0.101)				AGAAAAAGAAGAAATGAAGAG	0.333000																								0							SO:0001587	stop_gained			ENST00000257287.4	0	1	hg19	CCDS33986.1	.	.	.	.	.	.	.	.	.	.	G	41	8.869519	0.98984	.	.	ENSG00000174799	ENST00000257287	.	.	.	5.11	5.11	0.69529	.	0.046328	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.27785	T	0.31	.	18.5341	0.91002	0.0:0.0:1.0:0.0	.	.	.	.	X	850	.	ENSP00000257287:E850X	E	+	1	0	CEP135	56572377	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.811000	0.86092	2.373000	0.80994	0.591000	0.81541	GAA		TCGA-2L-AAQJ-01A-12D-A397-08	CEP135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362092.2	1	0	1	38	178	0	37	0	4.945258e-01	1	8	0	37	2		0	0	0	0	0	2	1	1.000000	38	175	0	37	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	0	1	1	2.055782	0	0.440000	1.870000	0.438765	0.790000	0.580000	1.000000	1.000000	0.803493	0.790000	0	6.800000e-01	9.200000e-01
NAA11	84779	broad.mit.edu	37	4	80246531	80246531	+	Silent	SNP	G	G	A			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr4:80246531G>A	ENST00000286794.4	-	1	673	c.501C>T	c.(499-501)ggC>ggT	p.G167G	NAA11_ENST00000513733.1_5'UTR	NM_032693.2	NP_116082.1	Q9BSU3	NAA11_HUMAN	N(alpha)-acetyltransferase 11, NatA catalytic subunit			23					CCACATACCCGCCCTTCTTCA	0.532000																								0							SO:0001819	synonymous_variant			ENST00000286794.4	1	1	hg19	CCDS47084.1																																																																																				TCGA-2L-AAQJ-01A-12D-A397-08	NAA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362922.1	1	0	1	42	127	0	31		0	0	0	0	31	2		0	0	0	0	0	2	1	1.000000	41	126	0	31	2		0	0	0	0	0	2	-4.581958	1	1	0	0		1	0	1	1	2.055782	0	0.440000	1.870000	0.438765	0.990000	0.840000	1.000000	1.000000	0.985715	0.990000	1	9.700000e-01	1
PDHA2	5161	broad.mit.edu	37	4	96762066	96762066	+	Missense_Mutation	SNP	G	G	T			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr4:96762066G>T	ENST00000295266.4	+	1	828	c.765G>T	c.(763-765)atG>atT	p.M255I		NM_005390.4	NP_005381.1	P29803	ODPAT_HUMAN	pyruvate dehydrogenase (lipoamide) alpha 2			46		Hepatocellular(203;0.114)			TCGATGGAATGGATGTTCTGT	0.463000																								0							SO:0001583	missense			ENST00000295266.4	1	1	hg19	CCDS3644.1	.	.	.	.	.	.	.	.	.	.	G	17.34	3.365331	0.61513	.	.	ENSG00000163114	ENST00000295266	D	0.97209	-4.29	4.91	4.91	0.64330	Dehydrogenase, E1 component (1);	0.000000	0.85682	D	0.000000	D	0.98848	0.9611	H	0.94264	3.515	0.80722	D	1	D	0.76494	0.999	D	0.91635	0.999	D	0.99282	1.0896	10	0.87932	D	0	-26.8691	16.0034	0.80327	0.0:0.0:1.0:0.0	.	255	P29803	ODPAT_HUMAN	I	255	ENSP00000295266:M255I	ENSP00000295266:M255I	M	+	3	0	PDHA2	96981089	1.000000	0.71417	0.992000	0.48379	0.523000	0.34469	4.138000	0.58017	2.733000	0.93635	0.467000	0.42956	ATG		TCGA-2L-AAQJ-01A-12D-A397-08	PDHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253608.1	1	0	1	48	171	0	38		0	0	0	0	38	2		0	0	0	0	0	2	1	1.000000	48	171	0	38	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	0	1	1	2.055782	0	0.440000	1.870000	0.438765	0.980000	0.750000	1.000000	1.000000	0.949661	0.980000	1	8.600000e-01	1
TCERG1	10915	broad.mit.edu	37	5	145886749	145886749	+	Silent	SNP	A	A	G			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08			A	G	A	A		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr5:145886749A>G	ENST00000296702.5	+	19	2927	c.2889A>G	c.(2887-2889)caA>caG	p.Q963Q	TCERG1_ENST00000394421.2_Silent_p.Q942Q	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)		ACTTTAGGCAACTTCTGGATG	0.338000																								0							SO:0001819	synonymous_variant			ENST00000296702.5	1	1	hg19	CCDS4282.1																																																																																				TCGA-2L-AAQJ-01A-12D-A397-08	TCERG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251886.1	1	0	1	72	265	0	72	1	1	31	63	0	72	2		0	0	0	0	0	2	1	1.000000	71	264	0	72	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	1	2	3	2.075514	0	0.440000	1.870000	0.442453	0.970000	0.780000	1.000000	1.000000	0.948660	0.970000	1	8.700000e-01	1
STK32A	202374	broad.mit.edu	37	5	146750320	146750320	+	Nonsense_Mutation	SNP	C	C	A			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr5:146750320C>A	ENST00000397936.3	+	9	1097	c.764C>A	c.(763-765)tCa>tAa	p.S255*	STK32A_ENST00000398523.3_Nonsense_Mutation_p.S255*	NM_001112724.1	NP_001106195.1	Q8WU08	ST32A_HUMAN	serine/threonine kinase 32A			13			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		GAAATGGTGTCACTTCTTAAA	0.418000																								0							SO:0001587	stop_gained			ENST00000397936.3	0	1	hg19	CCDS47299.1	.	.	.	.	.	.	.	.	.	.	C	38	6.721010	0.97788	.	.	ENSG00000169302	ENST00000397936;ENST00000398523	.	.	.	5.52	5.52	0.82312	.	0.191964	0.25885	N	0.027664	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.563	0.91107	0.0:1.0:0.0:0.0	.	.	.	.	X	255	.	ENSP00000381030:S255X	S	+	2	0	STK32A	146730513	0.999000	0.42202	1.000000	0.80357	0.977000	0.68977	4.191000	0.58372	2.761000	0.94854	0.655000	0.94253	TCA		TCGA-2L-AAQJ-01A-12D-A397-08	STK32A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373306.1	1	0	0	70	309	0	68	0	0	0	1	0	68	2		0	0	0	0	0	2	1	1.000000	70	304	0	68	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	1	2	3	2.075514	0	0.440000	1.870000	0.442453	0.840000	0.670000	1.000000	1.000000	0.847287	0.840000	0	7.500000e-01	9.400000e-01
GM2A	2760	broad.mit.edu	37	5	150639359	150639359	+	Missense_Mutation	SNP	G	G	C			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr5:150639359G>C	ENST00000357164.3	+	2	450	c.125G>C	c.(124-126)gGg>gCg	p.G42A		NM_000405.4|NM_001167607.1	NP_000396.2|NP_001161079.1	P17900	SAP3_HUMAN	GM2 ganglioside activator			8		Medulloblastoma(196;0.091)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		TGTGATGAAGGGAAGGACCCT	0.527000																								0							SO:0001583	missense			ENST00000357164.3	0	1	hg19	CCDS4313.1	.	.	.	.	.	.	.	.	.	.	G	2.987	-0.209025	0.06140	.	.	ENSG00000196743	ENST00000523466;ENST00000357164	T;T	0.71579	-0.58;-0.58	4.96	2.14	0.27477	MD-2-related lipid-recognition (1);	0.306608	0.35772	N	0.002992	T	0.57417	0.2052	L	0.47716	1.5	0.09310	N	1	P;P	0.46142	0.797;0.873	B;B	0.39027	0.117;0.288	T	0.48570	-0.9024	10	0.29301	T	0.29	-7.8707	8.4518	0.32875	0.0857:0.4541:0.4602:0.0	.	42;42	B4DQM5;P17900	.;SAP3_HUMAN	A	57;42	ENSP00000429100:G57A;ENSP00000349687:G42A	ENSP00000349687:G42A	G	+	2	0	GM2A	150619552	0.006000	0.16342	0.021000	0.16686	0.165000	0.22458	0.193000	0.17116	0.140000	0.18849	-0.136000	0.14681	GGG		TCGA-2L-AAQJ-01A-12D-A397-08	GM2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252432.1	0	0	0	4	176	0	28	0	4.868203e-01	1	62	0	28	2		0	0	0	0	0	2	1	0.888650	4	174	0	28	2		0	0	0	0	0	2	-3.315606	1	1	0	0		1	1	2	3	2.075514	0	0.440000	1.870000	0.442453	0.110000	0.030000	0.270000	0.100000	0.133120	0.110000	0	6.000000e-02	1.800000e-01
FAM71B	153745	broad.mit.edu	37	5	156590194	156590194	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr5:156590194G>A	ENST00000302938.4	-	2	1177	c.1082C>T	c.(1081-1083)gCg>gTg	p.A361V		NM_130899.2	NP_570969.2	Q8TC56	FA71B_HUMAN	family with sequence similarity 71, member B			68	Renal(175;0.00212)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)		GGCGGCCCCCGCCATCGAGGT	0.567000																								0							SO:0001583	missense			ENST00000302938.4	1	1	hg19	CCDS4335.1	.	.	.	.	.	.	.	.	.	.	G	8.201	0.798141	0.16397	.	.	ENSG00000170613	ENST00000302938	T	0.04156	3.69	3.83	-0.0601	0.13790	.	2.284610	0.01796	N	0.032639	T	0.01695	0.0054	N	0.08118	0	0.09310	N	1	P	0.35628	0.513	B	0.14023	0.01	T	0.32929	-0.9888	10	0.02654	T	1	0.1287	1.1705	0.01824	0.2063:0.1729:0.4431:0.1777	.	361	Q8TC56	FA71B_HUMAN	V	361	ENSP00000305596:A361V	ENSP00000305596:A361V	A	-	2	0	FAM71B	156522772	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.879000	0.04188	-0.036000	0.13669	-0.224000	0.12420	GCG		TCGA-2L-AAQJ-01A-12D-A397-08	FAM71B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252570.2	1	0	1	49	201	0	59		0	0	0	0	59	2		0	0	0	0	0	2	1	1.000000	49	198	0	57	2		0	0	0	0	0	2	-2.671760	1	1	121412	4	34	1	1	2	3	2.075514	0	0.440000	1.870000	0.442453	0.890000	0.680000	1.000000	1.000000	0.889361	0.890000	1	7.800000e-01	1
TPD52L1	7164	broad.mit.edu	37	6	125541274	125541274	+	Missense_Mutation	SNP	A	A	T			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr6:125541274A>T	ENST00000534000.1	+	2	366	c.70A>T	c.(70-72)Agt>Tgt	p.S24C	TPD52L1_ENST00000368402.5_Missense_Mutation_p.S24C|TPD52L1_ENST00000304877.13_Missense_Mutation_p.S24C|TPD52L1_ENST00000368388.2_Missense_Mutation_p.S24C|TPD52L1_ENST00000532429.1_5'UTR|TPD52L1_ENST00000528193.1_Missense_Mutation_p.S24C|HDDC2_ENST00000608456.1_5'UTR|TPD52L1_ENST00000392482.2_5'UTR|TPD52L1_ENST00000524679.1_5'UTR|TPD52L1_ENST00000534199.1_5'UTR|TPD52L1_ENST00000527711.1_Missense_Mutation_p.S24C	NM_003287.2	NP_003278.1	Q16890	TPD53_HUMAN	tumor protein D52-like 1			5			LUSC - Lung squamous cell carcinoma(4;0.0263)|Lung(4;0.0828)		TGCAGTAGCCAGTGCTGACTT	0.378000																								0							SO:0001583	missense			ENST00000534000.1	0	1	hg19	CCDS5130.1	.	.	.	.	.	.	.	.	.	.	A	16.93	3.258538	0.59321	.	.	ENSG00000111907	ENST00000304877;ENST00000534000;ENST00000368402;ENST00000368388;ENST00000527711;ENST00000528193;ENST00000392484	T;T;T;T;T;T	0.26518	1.73;1.73;1.73;1.73;1.73;1.73	5.26	-0.253	0.12996	.	0.282976	0.43919	D	0.000514	T	0.12263	0.0298	L	0.38175	1.15	0.38267	D	0.942041	P;P;P	0.51537	0.844;0.844;0.946	B;B;P	0.50590	0.416;0.416;0.645	T	0.06058	-1.0848	10	0.56958	D	0.05	-0.967	5.6478	0.17598	0.4559:0.1515:0.3926:0.0	.	24;24;24	Q16890-3;Q16890-2;Q16890	.;.;TPD53_HUMAN	C	24	ENSP00000306285:S24C;ENSP00000434142:S24C;ENSP00000357387:S24C;ENSP00000357373:S24C;ENSP00000436953:S24C;ENSP00000434743:S24C	ENSP00000306285:S24C	S	+	1	0	TPD52L1	125582973	0.999000	0.42202	0.993000	0.49108	0.840000	0.47671	1.953000	0.40352	0.087000	0.17167	-0.250000	0.11733	AGT		TCGA-2L-AAQJ-01A-12D-A397-08	TPD52L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042065.2	0	0	0	4	288	0	54	0	2.010071e-01	0	48	0	54	2		0	0	0	0	0	2	1	0.890225	4	287	0	54	2		0	0	0	0	0	2	-5.096504	1	0	0	0		1	0	0	0	2.005955	0	0.440000	1.870000	0.424815	0.060000	0.010000	0.150000	0.060000	0.074888	0.060000	0	3.000000e-02	1.100000e-01
KIAA0408	9729	broad.mit.edu	37	6	127771349	127771349	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr6:127771349G>A	ENST00000483725.3	-	3	620	c.284C>T	c.(283-285)aCg>aTg	p.T95M	SOGA3_ENST00000368268.2_3'UTR|SOGA3_ENST00000556132.1_3'UTR|SOGA3_ENST00000481848.2_3'UTR	NM_014702.4	NP_055517.3	Q6ZU52	K0408_HUMAN	KIAA0408	p.T95M(1)		28					TTTGTGATTCGTCCTTATAAA	0.358000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000483725.3	0	1	hg19	CCDS34531.1	.	.	.	.	.	.	.	.	.	.	G	0.313	-0.966787	0.02232	.	.	ENSG00000189367	ENST00000483725;ENST00000487331	T;T	0.43294	0.95;0.95	5.7	3.22	0.36961	.	0.603786	0.12642	N	0.451213	T	0.04952	0.0133	N	0.00926	-1.1	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.38628	-0.9652	10	0.30078	T	0.28	0.4989	7.4927	0.27471	0.766:0.0:0.234:0.0	.	95	Q6ZU52	K0408_HUMAN	M	95;107	ENSP00000435150:T95M;ENSP00000434384:T107M	ENSP00000435150:T95M	T	-	2	0	KIAA0408	127813042	0.001000	0.12720	0.008000	0.14137	0.002000	0.02628	0.957000	0.29215	0.978000	0.38470	-0.300000	0.09419	ACG		TCGA-2L-AAQJ-01A-12D-A397-08	KIAA0408-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042145.3	0	0	0	6	430	0	68		0	0	0	0	68	2		0	0	0	0	0	2	1	0.965221	6	430	0	68	2		0	0	0	0	0	2	-2.781143	1	1	121406	6	42	1	0	0	0	2.005955	0	0.440000	1.870000	0.424815	0.060000	0.020000	0.130000	0.060000	0.070535	0.060000	0	3.000000e-02	1.000000e-01
NOTCH4	4855	broad.mit.edu	37	6	32168996	32168996	+	Missense_Mutation	SNP	C	C	T	rs116359968	byFrequency	TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr6:32168996C>T	ENST00000375023.3	-	22	4175	c.4037G>A	c.(4036-4038)cGg>cAg	p.R1346Q		NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4			100					TTCTTCAGCCCGGGCCCCAGG	0.617000																								0							SO:0001583	missense			ENST00000375023.3	1	0	hg19	CCDS34420.1	.	.	.	.	.	.	.	.	.	.	C	10.61	1.397977	0.25205	.	.	ENSG00000204301	ENST00000375023	T	0.80824	-1.42	4.37	1.09	0.20402	.	0.581966	0.13081	N	0.415340	T	0.35098	0.0920	N	0.03608	-0.345	0.80722	D	1	B;B	0.18741	0.03;0.001	B;B	0.17979	0.02;0.0	T	0.08534	-1.0717	10	0.25106	T	0.35	.	5.443	0.16519	0.0:0.4431:0.0:0.5569	.	1346;1345	Q99466;B0S882	NOTC4_HUMAN;.	Q	1346	ENSP00000364163:R1346Q	ENSP00000364163:R1346Q	R	-	2	0	NOTCH4	32276974	0.999000	0.42202	0.990000	0.47175	0.931000	0.56810	1.224000	0.32539	0.052000	0.16007	0.456000	0.33151	CGG		TCGA-2L-AAQJ-01A-12D-A397-08	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2	1	0	0	19	338	0	54	0	4.943782e-01	0	30	0	54	2		0	0	0	0	0	2	1	0.999990	19	332	0	54	2		0	0	0	0	0	2	-2.484114	0	1	0	0		1	0	0	0	2.030214	0	0.440000	1.870000	0.435028	0.240000	0.140000	0.360000	0.240000	0.250089	0.240000	0	1.900000e-01	3.000000e-01
PGC	5225	broad.mit.edu	37	6	41704646	41704646	+	Missense_Mutation	SNP	A	A	G			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08			A	G	A	A		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr6:41704646A>G	ENST00000373025.3	-	9	1173	c.1111T>C	c.(1111-1113)Tac>Cac	p.Y371H	TFEB_ENST00000230323.4_5'Flank|TFEB_ENST00000420312.1_5'Flank|TFEB_ENST00000403298.4_5'Flank|TFEB_ENST00000373033.1_5'Flank|TFEB_ENST00000358871.2_5'Flank|RP11-298J23.5_ENST00000438967.1_RNA	NM_002630.3	NP_002621.1	P20142	PEPC_HUMAN	progastricsin (pepsinogen C)			16	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;0.000132)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00507)		ACGGAATAGTAGGACCTGAGG	0.602000																								0							SO:0001583	missense			ENST00000373025.3	1	1	hg19	CCDS4859.1	.	.	.	.	.	.	.	.	.	.	A	14.87	2.663054	0.47572	.	.	ENSG00000096088	ENST00000373025	T	0.34275	1.37	4.82	4.82	0.62117	Peptidase aspartic (1);Peptidase aspartic, catalytic (1);	0.000000	0.64402	D	0.000001	T	0.64136	0.2571	H	0.94620	3.56	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.76091	-0.3086	10	0.87932	D	0	.	14.2156	0.65790	1.0:0.0:0.0:0.0	.	371	P20142	PEPC_HUMAN	H	371	ENSP00000362116:Y371H	ENSP00000362116:Y371H	Y	-	1	0	PGC	41812624	1.000000	0.71417	0.967000	0.41034	0.048000	0.14542	6.504000	0.73704	2.013000	0.59113	0.459000	0.35465	TAC		TCGA-2L-AAQJ-01A-12D-A397-08	PGC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040521.2	1	0	0	10	198	0	39	1	1	11	1109	0	39	2		0	0	0	0	0	2	1	0.997020	10	197	0	39	2		0	0	0	0	0	2	-12.524860	1	1	0	0		1	0	0	0	2.005955	0	0.440000	1.870000	0.424815	0.210000	0.110000	0.370000	0.210000	0.230305	0.210000	0	1.500000e-01	2.900000e-01
DOCK4	9732	broad.mit.edu	37	7	111368508	111368508	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr7:111368508C>T	ENST00000437633.1	-	52	5979	c.5723G>A	c.(5722-5724)cGg>cAg	p.R1908Q	DOCK4_ENST00000428084.1_Missense_Mutation_p.R1917Q|DOCK4_ENST00000494651.2_Missense_Mutation_p.R791Q	NM_014705.3	NP_055520.3	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4			72		Acute lymphoblastic leukemia(1;0.0441)			CCGCAGAGTCCGCTCGTAGAC	0.731000																								0							SO:0001583	missense			ENST00000437633.1	1	1	hg19	CCDS47688.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	36|36	5.850010|5.850010	0.97023|0.97023	0.0|0.0	1.2E-4|1.2E-4	ENSG00000128512|ENSG00000128512	ENST00000423057;ENST00000445943|ENST00000352877;ENST00000428084;ENST00000494651;ENST00000437633;ENST00000342288	.|T;T;T	.|0.32753	.|1.44;1.44;1.44	5.59|5.59	5.59|5.59	0.84812|0.84812	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.53706|0.53706	0.1813|0.1813	L|L	0.57536|0.57536	1.79|1.79	0.46927|0.46927	D|D	0.999258|0.999258	.|D;P;D;D;D;D	.|0.89917	.|0.994;0.951;0.981;0.994;0.997;1.0	.|D;B;B;D;D;D	.|0.85130	.|0.921;0.404;0.391;0.921;0.964;0.997	T|T	0.40515|0.40515	-0.9559|-0.9559	5|10	.|0.33141	.|T	.|0.24	.|.	19.5919|19.5919	0.95518|0.95518	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|777;791;1953;1908;1879;221	.|B7Z2K9;F5GXW1;Q149N5;Q8N1I0;Q8N1I0-2;Q8N1I0-4	.|.;.;.;DOCK4_HUMAN;.;.	R|Q	1331;1941|1896;1917;791;1908;1867	.|ENSP00000410746:R1917Q;ENSP00000440944:R791Q;ENSP00000404179:R1908Q	.|ENSP00000345432:R1867Q	G|R	-|-	1|2	0|0	DOCK4|DOCK4	111155744|111155744	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	5.513000|5.513000	0.67037|0.67037	2.640000|2.640000	0.89533|0.89533	0.655000|0.655000	0.94253|0.94253	GGA|CGG		TCGA-2L-AAQJ-01A-12D-A397-08	DOCK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338369.4	1	0	0	62	201	0	62	0	8.112629e-01	1	11	0	62	2		0	0	0	0	0	2	1	1.000000	62	198	0	59	2		0	0	0	0	0	2	-4.473540	1	1	120600	9	39	1	0	0	0	2.040935	0	0.440000	1.870000	0.435028	0.990000	0.830000	1.000000	1.000000	0.979552	0.990000	1	9.400000e-01	1
FAM71F1	84691	broad.mit.edu	37	7	128363345	128363345	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr7:128363345C>T	ENST00000315184.5	+	4	835	c.782C>T	c.(781-783)gCc>gTc	p.A261V	FAM71F1_ENST00000485070.1_Missense_Mutation_p.A162V|FAM71F1_ENST00000469348.1_3'UTR	NM_001282788.1|NM_032599.2	NP_001269717.1|NP_115988.1	Q96KD3	F71F1_HUMAN	family with sequence similarity 71, member F1	p.A261V(1)		18					CAGATTTTTGCCGACTTACAC	0.502000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000315184.5	0	1	hg19	CCDS5804.1	.	.	.	.	.	.	.	.	.	.	C	15.05	2.717581	0.48622	.	.	ENSG00000135248	ENST00000485070;ENST00000315184;ENST00000466842	T;T;T	0.24151	1.87;3.23;1.92	5.2	3.36	0.38483	.	0.643829	0.14692	N	0.304119	T	0.17365	0.0417	L	0.33485	1.01	0.26152	N	0.980124	B;B;B;B;B	0.18310	0.011;0.01;0.003;0.002;0.027	B;B;B;B;B	0.15052	0.012;0.006;0.004;0.002;0.006	T	0.17992	-1.0351	10	0.30854	T	0.27	-2.5683	6.5261	0.22303	0.1782:0.7313:0.0:0.0905	.	153;261;261;261;162	B4DY15;F8WC62;Q96KD3-2;Q96KD3;Q8NA48	.;.;.;F71F1_HUMAN;.	V	162;261;117	ENSP00000418192:A162V;ENSP00000326652:A261V;ENSP00000417930:A117V	ENSP00000326652:A261V	A	+	2	0	FAM71F1	128150581	0.133000	0.22466	0.998000	0.56505	0.995000	0.86356	0.071000	0.14594	0.862000	0.35528	0.555000	0.69702	GCC		TCGA-2L-AAQJ-01A-12D-A397-08	FAM71F1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350544.2	0	0	0	6	412	0	81		0	0	0	0	81	2		0	0	0	0	0	2	1	0.964714	6	410	0	80	2		0	0	0	0	0	2	-1.790619	0	1	121412	5	39	1	0	0	0	2.040935	0	0.440000	1.870000	0.435028	0.060000	0.020000	0.130000	0.060000	0.074872	0.060000	0	4.000000e-02	1.000000e-01
PTPRN2	5799	broad.mit.edu	37	7	157926586	157926586	+	Missense_Mutation	SNP	C	C	T	rs142388788		TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr7:157926586C>T	ENST00000389418.4	-	9	1348	c.1339G>A	c.(1339-1341)Gtc>Atc	p.V447I	PTPRN2_ENST00000389413.3_Missense_Mutation_p.V447I|PTPRN2_ENST00000409483.1_Missense_Mutation_p.V409I|PTPRN2_ENST00000404321.2_Missense_Mutation_p.V470I|PTPRN2_ENST00000389416.4_Missense_Mutation_p.V430I	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2			86	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)		TGGCTCTTGACGTTCTCCACT	0.612000																								0							SO:0001583	missense			ENST00000389418.4	1	1	hg19	CCDS5947.1	.	.	.	.	.	.	.	.	.	.	C	12.64	1.997688	0.35226	0.0	1.16E-4	ENSG00000155093	ENST00000409483;ENST00000389413;ENST00000389416;ENST00000389418;ENST00000404321	T;T;T;T;T	0.07327	3.29;3.2;3.26;3.29;3.25	3.78	2.88	0.33553	.	0.310886	0.20844	U	0.084645	T	0.05181	0.0138	L	0.32530	0.975	0.26315	N	0.977769	P;P;P;P;P	0.45902	0.868;0.792;0.868;0.792;0.792	B;B;B;B;B	0.30572	0.117;0.055;0.117;0.055;0.055	T	0.32214	-0.9915	10	0.56958	D	0.05	.	9.1024	0.36676	0.0:0.89:0.0:0.11	.	470;409;447;430;447	Q92932-3;E7EM83;Q92932-2;E9PC57;Q92932	.;.;.;.;PTPR2_HUMAN	I	409;447;430;447;470	ENSP00000387114:V409I;ENSP00000374064:V447I;ENSP00000374067:V430I;ENSP00000374069:V447I;ENSP00000385464:V470I	ENSP00000374064:V447I	V	-	1	0	PTPRN2	157619347	0.443000	0.25641	0.048000	0.18961	0.043000	0.13939	1.614000	0.36911	0.681000	0.31386	0.585000	0.79938	GTC		TCGA-2L-AAQJ-01A-12D-A397-08	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1	1	0	1	123	487	0	122	1	9.999559e-01	36	23	0	122	2		0	0	0	0	0	2	1	1.000000	121	482	0	122	2		0	0	0	0	0	2	-20.000000	1	1	121412	1	36	1	0	0	0	2.040935	0	0.440000	1.870000	0.435028	0.900000	0.760000	1.000000	1.000000	0.906609	0.900000	1	8.300000e-01	9.800000e-01
CDK13	8621	broad.mit.edu	37	7	40027359	40027359	+	Missense_Mutation	SNP	A	A	C			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr7:40027359A>C	ENST00000181839.4	+	2	1978	c.1373A>C	c.(1372-1374)aAa>aCa	p.K458T	CDK13_ENST00000340829.5_Missense_Mutation_p.K458T	NM_003718.4|NM_031267.3	NP_003709.3|NP_112557.2	Q14004	CDK13_HUMAN	cyclin-dependent kinase 13			49					AAGAATAAAAAagcacgagca	0.488000																								0							SO:0001583	missense			ENST00000181839.4	0	1	hg19	CCDS5461.1	.	.	.	.	.	.	.	.	.	.	A	17.32	3.358737	0.61403	.	.	ENSG00000065883	ENST00000181839;ENST00000340829	T;T	0.66638	-0.22;-0.22	5.95	5.95	0.96441	.	.	.	.	.	T	0.79924	0.4530	M	0.61703	1.905	0.58432	D	0.999998	D;D	0.89917	1.0;0.999	D;D	0.85130	0.997;0.994	T	0.79212	-0.1896	8	.	.	.	-13.8654	16.4101	0.83708	1.0:0.0:0.0:0.0	.	458;458	Q14004-2;Q14004	.;CDK13_HUMAN	T	458	ENSP00000181839:K458T;ENSP00000340557:K458T	.	K	+	2	0	CDK13	39993884	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.281000	0.72632	2.280000	0.76307	0.460000	0.39030	AAA		TCGA-2L-AAQJ-01A-12D-A397-08	CDK13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250726.2	0	0	0	4	226	0	48	0	3.325394e-01	1	55	0	48	2		0	0	0	0	0	2	1	0.891141	4	226	0	47	2		0	0	0	0	0	2	-7.210621	1	1	0	0		1	0	0	0	2.040935	0	0.440000	1.870000	0.435028	0.080000	0.020000	0.190000	0.080000	0.096540	0.080000	0	4.000000e-02	1.400000e-01
SDK1	221935	broad.mit.edu	37	7	4188979	4188979	+	Silent	SNP	C	C	T			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr7:4188979C>T	ENST00000404826.2	+	30	4648	c.4509C>T	c.(4507-4509)agC>agT	p.S1503S	SDK1_ENST00000389531.3_Silent_p.S1503S	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1			153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)			TCCCGGGCAGCGACGGGGCCT	0.677000																								0							SO:0001819	synonymous_variant			ENST00000404826.2	1	1	hg19	CCDS34590.1																																																																																				TCGA-2L-AAQJ-01A-12D-A397-08	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	1	0	1	10	50	0	17	0	3.588710e-01	0	7	0	17	2		0	0	0	0	0	2	1	0.997708	10	50	0	17	2		0	0	0	0	0	2	-19.021370	1	1	121250	1	26	1	0	0	0	2.040935	0	0.440000	1.870000	0.435028	0.750000	0.400000	1.000000	1.000000	0.762280	0.750000	0	5.600000e-01	9.800000e-01
GLI3	2737	broad.mit.edu	37	7	42005299	42005299	+	Silent	SNP	G	G	A			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr7:42005299G>A	ENST00000395925.3	-	15	3456	c.3372C>T	c.(3370-3372)caC>caT	p.H1124H	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3			112					CACCGGGCCCGTGGGGCACTT	0.657000									Pallister-Hall syndrome;Greig Cephalopolysyndactyly															0							SO:0001819	synonymous_variant	Familial Cancer Database	;	ENST00000395925.3	1	1	hg19	CCDS5465.1																																																																																				TCGA-2L-AAQJ-01A-12D-A397-08	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	1	0	1	97	372	0	109	0	4.364137e-02	0	2	0	109	2		0	0	0	0	0	2	1	1.000000	96	366	0	109	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	0	0	0	2.040935	0	0.440000	1.870000	0.435028	0.920000	0.760000	1.000000	1.000000	0.923828	0.920000	1	8.400000e-01	1
OGDH	4967	broad.mit.edu	37	7	44715672	44715672	+	Missense_Mutation	SNP	T	T	C			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08			T	C	T	T		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr7:44715672T>C	ENST00000222673.5	+	9	1172	c.1130T>C	c.(1129-1131)cTt>cCt	p.L377P	OGDH_ENST00000449767.1_Missense_Mutation_p.L373P|OGDH_ENST00000444676.1_Missense_Mutation_p.L392P|OGDH_ENST00000443864.2_Missense_Mutation_p.L377P|OGDH_ENST00000439616.2_Missense_Mutation_p.L227P|OGDH_ENST00000543843.1_Missense_Mutation_p.L328P|OGDH_ENST00000447398.1_Missense_Mutation_p.L388P	NM_002541.3	NP_002532.2	Q02218	ODO1_HUMAN	oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)			36				Valproic Acid(DB00313)	CCTTCCCACCTTGAGGCCGCT	0.557000																								0							SO:0001583	missense			ENST00000222673.5	1	1	hg19	CCDS34627.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.306757	0.81247	.	.	ENSG00000105953	ENST00000439616;ENST00000443864;ENST00000449767;ENST00000447398;ENST00000444676;ENST00000222673;ENST00000543843	D;T;D;D;D;D;D	0.95788	-3.81;2.0;-3.81;-3.81;-3.81;-3.81;-3.81	5.14	5.14	0.70334	Dehydrogenase, E1 component (1);	0.000000	0.85682	D	0.000000	D	0.98738	0.9576	H	0.98996	4.395	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D	0.99521	1.0958	10	0.87932	D	0	-27.6918	14.9242	0.70862	0.0:0.0:0.0:1.0	.	172;227;373;388;279;377;377	B4E3E9;E9PFG7;E9PBM1;E9PDF2;A2VCT2;Q02218;Q96DD3	.;.;.;.;.;ODO1_HUMAN;.	P	227;377;373;388;392;377;328	ENSP00000398576:L227P;ENSP00000388084:L377P;ENSP00000392878:L373P;ENSP00000388183:L388P;ENSP00000414662:L392P;ENSP00000222673:L377P;ENSP00000443821:L328P	ENSP00000222673:L377P	L	+	2	0	OGDH	44682197	1.000000	0.71417	0.987000	0.45799	0.892000	0.51952	7.788000	0.85771	2.063000	0.61619	0.379000	0.24179	CTT		TCGA-2L-AAQJ-01A-12D-A397-08	OGDH-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339391.1	1	0	1	71	413	0	106	1	9.999272e-01	21	60	0	106	2		0	0	0	0	0	2	1	1.000000	71	408	0	106	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	0	0	0	2.040935	0	0.440000	1.870000	0.435028	0.650000	0.520000	0.800000	0.660000	0.665688	0.650000	0	5.800000e-01	7.400000e-01
C7orf57	136288	broad.mit.edu	37	7	48080979	48080979	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr7:48080979C>T	ENST00000348904.3	+	3	316	c.104C>T	c.(103-105)gCc>gTc	p.A35V	C7orf57_ENST00000430738.1_Missense_Mutation_p.A80V|C7orf57_ENST00000539619.1_Missense_Mutation_p.A35V|C7orf57_ENST00000420324.1_Missense_Mutation_p.A80V|C7orf57_ENST00000435376.1_5'UTR	NM_001100159.2	NP_001093629.1	Q8NEG2	CG057_HUMAN	chromosome 7 open reading frame 57			9					GCCGTGGATGCCCCACCAGCG	0.567000																								0							SO:0001583	missense			ENST00000348904.3	0	1	hg19	CCDS47583.1	.	.	.	.	.	.	.	.	.	.	C	0.418	-0.909812	0.02434	.	.	ENSG00000164746	ENST00000420324;ENST00000430738;ENST00000348904;ENST00000539619	T;T;T;T	0.54675	0.56;0.56;0.56;0.56	5.69	-1.12	0.09808	.	0.758231	0.12566	N	0.457767	T	0.29491	0.0735	N	0.11698	0.16	0.09310	N	1	B	0.14438	0.01	B	0.16722	0.016	T	0.22765	-1.0207	10	0.18710	T	0.47	-42.8651	9.8678	0.41154	0.0:0.4479:0.0:0.5521	.	35	Q8NEG2	CG057_HUMAN	V	80;80;35;35	ENSP00000394648:A80V;ENSP00000410944:A80V;ENSP00000335500:A35V;ENSP00000442474:A35V	ENSP00000335500:A35V	A	+	2	0	C7orf57	48047504	0.000000	0.05858	0.005000	0.12908	0.037000	0.13140	-0.525000	0.06214	-0.112000	0.11979	-0.251000	0.11542	GCC		TCGA-2L-AAQJ-01A-12D-A397-08	C7orf57-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341745.1	0	0	0	4	206	0	48		0	0	0	0	48	2		0	0	0	0	0	2	1	0.888935	4	204	0	48	2		0	0	0	0	0	2	-2.863991	1	1	0	0		1	0	0	0	2.040935	0	0.440000	1.870000	0.435028	0.090000	0.020000	0.200000	0.080000	0.105597	0.090000	0	5.000000e-02	1.500000e-01
WIPI2	26100	broad.mit.edu	37	7	5232787	5232787	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr7:5232787G>A	ENST00000288828.4	+	2	345	c.113G>A	c.(112-114)cGt>cAt	p.R38H	WIPI2_ENST00000382384.2_Intron|WIPI2_ENST00000404704.3_Missense_Mutation_p.R38H|WIPI2_ENST00000485854.1_Intron|WIPI2_ENST00000401525.3_Intron	NM_001033518.1|NM_001278299.1|NM_015610.3	NP_001028690.1|NP_001265228.1|NP_056425.1	Q9Y4P8	WIPI2_HUMAN	WD repeat domain, phosphoinositide interacting 2			16		Ovarian(82;0.0175)			GGTCTTGGCCGTCGCGCTGTT	0.388000																								0							SO:0001583	missense			ENST00000288828.4	1	1	hg19	CCDS5339.1	.	.	.	.	.	.	.	.	.	.	G	7.818	0.717084	0.15372	.	.	ENSG00000157954	ENST00000288828;ENST00000404704	T;T	0.35973	1.28;1.28	3.42	-6.11	0.02131	.	608.758000	0.01314	U	0.010739	T	0.15782	0.0380	N	0.03608	-0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.18967	-1.0320	10	0.40728	T	0.16	.	6.7201	0.23325	0.3457:0.1644:0.4899:0.0	.	38;38	Q9Y4P8-6;Q9Y4P8	.;WIPI2_HUMAN	H	38	ENSP00000288828:R38H;ENSP00000385297:R38H	ENSP00000288828:R38H	R	+	2	0	WIPI2	5199313	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.087000	0.01360	-1.161000	0.02800	-1.223000	0.01593	CGT		TCGA-2L-AAQJ-01A-12D-A397-08	WIPI2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000241669.2	0	0	1	97	377	1	86	1	9.065020e-01	7	11	1	86	2		0	0	0	0	0	2	1	1.000000	96	373	1	83	19		0	0	0	0	0	2	-20.000000	1	1	121412	1	35	1	0	0	0	2.040935	0	0.440000	1.870000	0.435028	0.910000	0.760000	1.000000	1.000000	0.916210	0.910000	1	8.300000e-01	1
FSCN1	6624	broad.mit.edu	37	7	5644983	5644983	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr7:5644983G>A	ENST00000382361.3	+	5	1474	c.1360G>A	c.(1360-1362)Gag>Aag	p.E454K	FSCN1_ENST00000340250.6_Missense_Mutation_p.E433K	NM_003088.3	NP_003079.1	Q16658	FSCN1_HUMAN	fascin actin-bundling protein 1			9		Ovarian(82;0.0694)			CTTCTTCTTCGAGTTCTGCGA	0.617000																								0							SO:0001583	missense			ENST00000382361.3	1	1	hg19	CCDS5342.1	.	.	.	.	.	.	.	.	.	.	G	31	5.060521	0.93846	.	.	ENSG00000075618	ENST00000340250;ENST00000382361;ENST00000535097	T;T	0.52057	0.68;0.68	4.0	4.0	0.46444	Fascin domain (1);Actin cross-linking (1);	0.062034	0.64402	D	0.000007	T	0.45377	0.1339	M	0.62209	1.925	0.80722	D	1	P	0.50443	0.935	B	0.39068	0.289	T	0.59069	-0.7523	10	0.87932	D	0	-0.2446	15.5031	0.75716	0.0:0.0:1.0:0.0	.	454	Q16658	FSCN1_HUMAN	K	433;454;176	ENSP00000339729:E433K;ENSP00000371798:E454K	ENSP00000339729:E433K	E	+	1	0	FSCN1	5611509	1.000000	0.71417	0.998000	0.56505	0.878000	0.50629	9.420000	0.97426	1.944000	0.56390	0.549000	0.68633	GAG		TCGA-2L-AAQJ-01A-12D-A397-08	FSCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207153.3	1	0	1	46	157	0	46	1	1	84	182	0	46	2		0	0	0	0	0	2	1	1.000000	45	156	0	44	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	0	0	0	2.040935	0	0.440000	1.870000	0.435028	0.990000	0.770000	1.000000	1.000000	0.960091	0.990000	1	8.800000e-01	1
MAGI2	9863	broad.mit.edu	37	7	77885649	77885649	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr7:77885649C>T	ENST00000354212.4	-	10	1911	c.1658G>A	c.(1657-1659)cGg>cAg	p.R553Q	MAGI2_ENST00000419488.1_Missense_Mutation_p.R553Q|MAGI2_ENST00000536571.1_Missense_Mutation_p.R385Q|MAGI2_ENST00000522391.1_Missense_Mutation_p.R553Q|MAGI2_ENST00000535697.1_Missense_Mutation_p.R390Q	NM_012301.3	NP_036433.2	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 2			84		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)			CTGTGAGGTCCGAGAAATGTA	0.512000																								0							SO:0001583	missense			ENST00000354212.4	1	1	hg19	CCDS5594.1	.	.	.	.	.	.	.	.	.	.	C	14.28	2.488783	0.44249	.	.	ENSG00000187391	ENST00000419488;ENST00000354212;ENST00000536298;ENST00000522391;ENST00000536571;ENST00000535697	T;T;T;T;T	0.10382	2.97;2.98;2.88;3.82;3.83	5.94	5.06	0.68205	.	0.000000	0.33253	U	0.005115	T	0.12220	0.0297	N	0.16790	0.44	0.49130	D	0.999757	D;B;D;D;B;D	0.76494	0.988;0.145;0.998;0.998;0.376;0.999	P;B;P;P;B;P	0.55011	0.507;0.018;0.652;0.652;0.068;0.766	T	0.23940	-1.0174	10	0.11485	T	0.65	.	14.5211	0.67851	0.0:0.9297:0.0:0.0703	.	390;385;553;553;553;553	F5GWH1;F5GWK7;B7Z4H4;E7EWI0;Q86UL8-2;Q86UL8	.;.;.;.;.;MAGI2_HUMAN	Q	553;553;553;553;385;390	ENSP00000405766:R553Q;ENSP00000346151:R553Q;ENSP00000428389:R553Q;ENSP00000441584:R385Q;ENSP00000441603:R390Q	ENSP00000346151:R553Q	R	-	2	0	MAGI2	77723585	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.243000	0.51392	1.519000	0.48950	0.561000	0.74099	CGG		TCGA-2L-AAQJ-01A-12D-A397-08	MAGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253197.3	1	0	1	38	163	0	38		0	0	0	0	38	2		0	0	0	0	0	2	1	1.000000	38	161	0	38	2		0	0	0	0	0	2	-2.948967	1	1	121408	3	36	1	0	0	0	2.040935	0	0.440000	1.870000	0.435028	0.840000	0.620000	1.000000	1.000000	0.851045	0.840000	0	7.300000e-01	9.800000e-01
COL14A1	7373	broad.mit.edu	37	8	121160087	121160087	+	Missense_Mutation	SNP	G	G	T			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr8:121160087G>T	ENST00000297848.3	+	2	276	c.6G>T	c.(4-6)aaG>aaT	p.K2N	COL14A1_ENST00000537875.1_Missense_Mutation_p.K2N|COL14A1_ENST00000247781.3_Missense_Mutation_p.K2N|COL14A1_ENST00000309791.4_Missense_Mutation_p.K2N|COL14A1_ENST00000432943.2_3'UTR	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1			119	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)		ATAAAATGAAGATTTTCCAGC	0.383000																								0							SO:0001583	missense			ENST00000297848.3	1	1	hg19	CCDS34938.1	.	.	.	.	.	.	.	.	.	.	G	11.64	1.697656	0.30142	.	.	ENSG00000187955	ENST00000537875;ENST00000309791;ENST00000297848;ENST00000247781	T;D;D;D	0.87966	0.45;-2.14;-2.16;-2.32	5.92	5.92	0.95590	.	0.536026	0.19314	N	0.117330	T	0.78214	0.4248	N	0.14661	0.345	0.26614	N	0.972785	B	0.19583	0.037	B	0.17098	0.017	T	0.64296	-0.6441	10	0.27082	T	0.32	.	15.8249	0.78690	0.0:0.0:1.0:0.0	.	2	Q05707	COEA1_HUMAN	N	2	ENSP00000443974:K2N;ENSP00000311809:K2N;ENSP00000297848:K2N;ENSP00000247781:K2N	ENSP00000247781:K2N	K	+	3	2	COL14A1	121229268	1.000000	0.71417	0.513000	0.27749	0.105000	0.19272	2.807000	0.47955	2.818000	0.97014	0.655000	0.94253	AAG		TCGA-2L-AAQJ-01A-12D-A397-08	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	1	0	1	26	223	0	43	0	2.523345e-01	0	9	0	43	2		0	0	0	0	0	2	1	1.000000	27	222	0	43	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	1	2	3	2.477001	1	0.440000	1.870000	0.537649	0.580000	0.390000	1.000000	0.570000	0.601961	0.580000	0	4.800000e-01	7.100000e-01
ENTPD4	9583	broad.mit.edu	37	8	23294452	23294452	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr8:23294452C>T	ENST00000358689.4	-	10	1604	c.1369G>A	c.(1369-1371)Gca>Aca	p.A457T	ENTPD4_ENST00000417069.2_Missense_Mutation_p.A449T|ENTPD4_ENST00000521321.1_5'UTR|ENTPD4_ENST00000356206.6_Missense_Mutation_p.A449T	NM_001128930.2|NM_004901.4	NP_001122402.1|NP_004892.1	Q9Y227	ENTP4_HUMAN	ectonucleoside triphosphate diphosphohydrolase 4			25		Prostate(55;0.114)			GGTACCTTTGCAGCTTTAGTA	0.483000																								0							SO:0001583	missense			ENST00000358689.4	1	1	hg19	CCDS6041.1	.	.	.	.	.	.	.	.	.	.	C	32	5.132882	0.94517	.	.	ENSG00000197217	ENST00000518471;ENST00000356206;ENST00000358689;ENST00000417069	T;T;T;T	0.11930	2.73;2.73;2.73;2.73	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.30759	0.0775	L	0.56340	1.77	0.80722	D	1	D;D;D	0.56521	0.976;0.97;0.976	P;P;P	0.61070	0.883;0.857;0.883	T	0.00236	-1.1891	10	0.35671	T	0.21	-17.3279	18.1443	0.89651	0.0:1.0:0.0:0.0	.	449;449;457	Q8NE73;Q9Y227-2;Q9Y227	.;.;ENTP4_HUMAN	T	52;449;457;449	ENSP00000430579:A52T;ENSP00000348536:A449T;ENSP00000351520:A457T;ENSP00000408573:A449T	ENSP00000348536:A449T	A	-	1	0	ENTPD4	23350397	1.000000	0.71417	0.998000	0.56505	0.955000	0.61496	7.818000	0.86416	2.631000	0.89168	0.462000	0.41574	GCA		TCGA-2L-AAQJ-01A-12D-A397-08	ENTPD4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215142.1	1	0	1	99	433	0	98	1	9.998515e-01	17	41	0	98	2		0	0	0	0	0	2	1	1.000000	98	427	0	98	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	0	0	0	2.039724	0	0.440000	1.870000	0.435028	0.830000	0.690000	0.980000	0.840000	0.840971	0.830000	0	7.600000e-01	9.100000e-01
DOCK5	80005	broad.mit.edu	37	8	25193885	25193885	+	Silent	SNP	T	T	C			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr8:25193885T>C	ENST00000276440.7	+	22	2367	c.2323T>C	c.(2323-2325)Ttg>Ctg	p.L775L		NM_024940.6	NP_079216.4	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5			72		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)			AGTGCTCTACTTGAGGTAATG	0.448000													Pancreas(145;34 1887 3271 10937 30165)											0							SO:0001819	synonymous_variant			ENST00000276440.7	1	1	hg19	CCDS6047.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	T	9.240	1.038124	0.19669	.	.	ENSG00000147459	ENST00000444569	.	.	.	5.76	-4.24	0.03777	.	0.000000	0.64402	D	0.000001	T	0.64875	0.2638	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.65348	-0.6190	5	.	.	.	.	15.9667	0.79979	0.0:0.7662:0.0:0.2338	.	.	.	.	P	546	.	.	L	+	2	0	DOCK5	25249802	0.795000	0.28851	0.949000	0.38748	0.803000	0.45373	-0.041000	0.12084	-0.567000	0.06046	-0.263000	0.10527	CTT		TCGA-2L-AAQJ-01A-12D-A397-08	DOCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254955.2	0	0	1	19	94	0	30	1	5.841187e-01	4	7	0	30	2		0	0	0	0	0	2	1	0.999994	18	93	0	30	2		0	0	0	0	0	2	-12.972770	1	1	121410	8	38	1	0	0	0	2.039724	0	0.440000	1.870000	0.435028	0.750000	0.480000	1.000000	1.000000	0.767735	0.750000	0	6.100000e-01	9.200000e-01
CSMD1	64478	broad.mit.edu	37	8	3216706	3216706	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr8:3216706C>T	ENST00000520002.1	-	22	3830	c.3275G>A	c.(3274-3276)cGt>cAt	p.R1092H	CSMD1_ENST00000542608.1_Missense_Mutation_p.R1091H|CSMD1_ENST00000602557.1_Missense_Mutation_p.R1092H|CSMD1_ENST00000537824.1_Missense_Mutation_p.R1091H|CSMD1_ENST00000400186.3_Missense_Mutation_p.R1092H|CSMD1_ENST00000602723.1_Missense_Mutation_p.R1092H|CSMD1_ENST00000539096.1_Missense_Mutation_p.R1091H			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1			25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)			ACTCCACACACGGCGGCCCCC	0.562000																								0							SO:0001583	missense			ENST00000520002.1	0	1	hg19		.	.	.	.	.	.	.	.	.	.	c	36	5.695321	0.96793	.	.	ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608;ENST00000539096	T;T;T;T;T	0.64803	-0.12;-0.12;-0.12;-0.12;-0.12	5.34	5.34	0.76211	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.64402	D	0.000001	D	0.84483	0.5482	M	0.92268	3.29	0.80722	D	1	D;D;D	0.89917	1.0;0.995;0.994	D;D;P	0.85130	0.997;0.957;0.837	D	0.87265	0.2282	10	0.52906	T	0.07	.	19.067	0.93116	0.0:1.0:0.0:0.0	.	1092;1092;1092	E5RIG2;Q96PZ7;Q96PZ7-4	.;CSMD1_HUMAN;.	H	1092;1092;954;1091;1091;1091	ENSP00000383047:R1092H;ENSP00000430733:R1092H;ENSP00000441462:R1091H;ENSP00000446243:R1091H;ENSP00000441675:R1091H	ENSP00000320445:R954H	R	-	2	0	CSMD1	3204113	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.762000	0.62250	2.489000	0.83994	0.550000	0.68814	CGT		TCGA-2L-AAQJ-01A-12D-A397-08	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	0	0	0	7	319	0	64		0	0	0	0	64	2		0	0	0	0	0	2	1	0.978882	7	310	0	61	2		0	0	0	0	0	2	-3.082203	1	1	121412	4	35	1	0	0	0	2.027595	0	0.440000	1.870000	0.429967	0.090000	0.040000	0.190000	0.100000	0.108472	0.090000	0	6.000000e-02	1.400000e-01
PAG1	55824	broad.mit.edu	37	8	81888976	81888976	+	Missense_Mutation	SNP	T	T	G			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr8:81888976T>G	ENST00000220597.4	-	9	1812	c.1102A>C	c.(1102-1104)Act>Cct	p.T368P	PAG1_ENST00000523463.1_5'Flank	NM_018440.3	NP_060910.3	Q9NWQ8	PHAG1_HUMAN	phosphoprotein membrane anchor with glycosphingolipid microdomains 1			11	Lung NSC(7;5.76e-06)|all_lung(9;2e-05)		BRCA - Breast invasive adenocarcinoma(6;0.0567)|Epithelial(68;0.0634)|all cancers(69;0.197)		CTGTTTGGAGTTTTTTCGAAG	0.512000																								0							SO:0001583	missense			ENST00000220597.4	1	1	hg19	CCDS6227.1	.	.	.	.	.	.	.	.	.	.	T	3.651	-0.071468	0.07228	.	.	ENSG00000076641	ENST00000220597	.	.	.	5.05	-2.76	0.05896	.	0.702006	0.14361	N	0.324452	T	0.34687	0.0906	L	0.51422	1.61	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.26815	-1.0092	9	0.45353	T	0.12	-1.9998	6.671	0.23068	0.0:0.1378:0.3656:0.4965	.	368	Q9NWQ8	PAG1_HUMAN	P	368	.	ENSP00000220597:T368P	T	-	1	0	PAG1	82051531	0.005000	0.15991	0.027000	0.17364	0.026000	0.11368	0.003000	0.13083	-0.242000	0.09667	-1.106000	0.02097	ACT		TCGA-2L-AAQJ-01A-12D-A397-08	PAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379352.3	1	0	0	30	269	0	39	1	1.587105e-01	4	3	0	39	2		0	0	0	0	0	2	1	1.000000	30	264	0	38	2		0	0	0	0	0	2	-11.301750	1	1	0	0		1	1	2	3	2.471346	1	0.440000	1.870000	0.540984	0.550000	0.380000	0.760000	0.550000	0.569510	0.550000	0	4.600000e-01	6.600000e-01
SH2D3C	10044	broad.mit.edu	37	9	130511512	130511512	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr9:130511512G>A	ENST00000314830.8	-	5	1230	c.1117C>T	c.(1117-1119)Cgc>Tgc	p.R373C	SH2D3C_ENST00000429553.1_Missense_Mutation_p.R19C|SH2D3C_ENST00000471939.1_Intron|SH2D3C_ENST00000373274.3_Missense_Mutation_p.R213C|SH2D3C_ENST00000420366.1_Missense_Mutation_p.R215C|SH2D3C_ENST00000373277.4_Missense_Mutation_p.R216C|SH2D3C_ENST00000373276.3_Missense_Mutation_p.R305C	NM_170600.2	NP_733745.1	Q8N5H7	SH2D3_HUMAN	SH2 domain containing 3C	p.R373S(2)		28					CCATCGCTGCGGGTGACCTTG	0.617000																								2	Substitution - Missense(2)						SO:0001583	missense			ENST00000314830.8	1	1	hg19	CCDS6877.1	.	.	.	.	.	.	.	.	.	.	G	12.60	1.986440	0.35036	.	.	ENSG00000095370	ENST00000373277;ENST00000420366;ENST00000373276;ENST00000373274;ENST00000429553;ENST00000314830;ENST00000414380	T;T;T;T;T;T;T	0.38722	2.55;2.56;2.3;2.56;1.68;2.51;1.12	5.37	3.42	0.39159	.	0.469026	0.24884	N	0.034822	T	0.33469	0.0864	L	0.51422	1.61	0.47123	D	0.999322	B;B;B;B;B	0.21821	0.007;0.061;0.033;0.007;0.005	B;B;B;B;B	0.14578	0.003;0.011;0.005;0.007;0.004	T	0.15867	-1.0422	10	0.38643	T	0.18	-28.0923	7.986	0.30212	0.0869:0.0:0.6601:0.253	.	213;373;305;216;215	E9PG48;Q8N5H7;E7EUN5;Q8N5H7-2;Q8N5H7-5	.;SH2D3_HUMAN;.;.;.	C	216;215;305;213;19;373;190	ENSP00000362374:R216C;ENSP00000388536:R215C;ENSP00000362373:R305C;ENSP00000362371:R213C;ENSP00000394632:R19C;ENSP00000317817:R373C;ENSP00000413760:R190C	ENSP00000317817:R373C	R	-	1	0	SH2D3C	129551333	1.000000	0.71417	0.993000	0.49108	0.615000	0.37417	2.677000	0.46892	1.413000	0.46997	0.561000	0.74099	CGC		TCGA-2L-AAQJ-01A-12D-A397-08	SH2D3C-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054264.1	1	0	1	59	337	0	84	0	9.225326e-01	0	27	0	84	2		0	0	0	0	0	2	1	1.000000	58	333	0	83	2		0	0	0	0	0	2	-2.475894	0	1	0	0		1	0	0	0	2.034520	0	0.440000	1.870000	0.435028	0.660000	0.520000	0.830000	0.670000	0.676990	0.660000	0	5.900000e-01	7.500000e-01
LRRC8A	56262	broad.mit.edu	37	9	131669884	131669884	+	Silent	SNP	G	G	A			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr9:131669884G>A	ENST00000259324.5	+	3	964	c.441G>A	c.(439-441)ccG>ccA	p.P147P	LRRC8A_ENST00000372600.4_Silent_p.P147P|LRRC8A_ENST00000372599.3_Silent_p.P147P	NM_001127244.1	NP_001120716.1	Q8IWT6	LRC8A_HUMAN	leucine rich repeat containing 8 family, member A			28					TCAAATTCCCGCGCACCAGCT	0.572000																								0							SO:0001819	synonymous_variant			ENST00000259324.5	1	1	hg19	CCDS35155.1																																																																																				TCGA-2L-AAQJ-01A-12D-A397-08	LRRC8A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054516.2	1	0	1	43	159	0	51	1	1	80	147	0	51	2		0	0	0	0	0	2	1	1.000000	42	158	0	51	2		0	0	0	0	0	2	-3.840315	1	1	121412	1	31	1	0	0	0	2.034520	0	0.440000	1.870000	0.435028	0.950000	0.710000	1.000000	1.000000	0.929177	0.950000	1	8.300000e-01	1
ENTPD2	954	broad.mit.edu	37	9	139944888	139944888	+	Missense_Mutation	SNP	A	A	T			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08			A	T	A	A		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chr9:139944888A>T	ENST00000355097.2	-	6	924	c.877T>A	c.(877-879)Ttc>Atc	p.F293I	ENTPD2_ENST00000312665.5_Missense_Mutation_p.F293I|RP11-229P13.15_ENST00000439076.1_RNA|ENTPD2_ENST00000460614.1_5'Flank	NM_001246.3|NM_203468.2	NP_001237.1|NP_982293.1	Q9Y5L3	ENTP2_HUMAN	ectonucleoside triphosphate diphosphohydrolase 2			12	all_cancers(76;0.0926)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)		CTGCTGTTGAAGTTCTGGGGC	0.632000											OREG0019627	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)												0							SO:0001583	missense			ENST00000355097.2	1	1	hg19	CCDS7026.1	.	.	.	.	.	.	.	.	.	.	A	13.54	2.267428	0.40095	.	.	ENSG00000054179	ENST00000355097;ENST00000312665	T;T	0.11277	2.8;2.79	4.95	1.35	0.21983	.	0.427784	0.23684	N	0.045587	T	0.09905	0.0243	L	0.59436	1.845	0.09310	N	1	B;B	0.22541	0.058;0.071	B;B	0.24006	0.03;0.05	T	0.23261	-1.0193	10	0.42905	T	0.14	-9.6179	4.0512	0.09796	0.5803:0.0:0.262:0.1576	.	293;293	Q9Y5L3-2;Q9Y5L3	.;ENTP2_HUMAN	I	293	ENSP00000347213:F293I;ENSP00000312494:F293I	ENSP00000312494:F293I	F	-	1	0	ENTPD2	139064709	0.411000	0.25384	0.155000	0.22561	0.030000	0.12068	0.623000	0.24447	0.244000	0.21351	0.459000	0.35465	TTC		TCGA-2L-AAQJ-01A-12D-A397-08	ENTPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055169.1	1	0	1	40	141	0	35	1	9.999377e-01	30	26	0	35	2		0	0	0	0	0	2	1	1.000000	39	141	0	35	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	0	0	0	2.034520	0	0.440000	1.870000	0.435028	0.990000	0.740000	1.000000	1.000000	0.946237	0.990000	1	8.500000e-01	1
VSIG1	340547	broad.mit.edu	37	X	107316507	107316507	+	Missense_Mutation	SNP	G	G	A			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chrX:107316507G>A	ENST00000217957.5	+	5	713	c.596G>A	c.(595-597)gGa>gAa	p.G199E	VSIG1_ENST00000415430.3_Missense_Mutation_p.G235E	NM_182607.4	NP_872413.1	Q86XK7	VSIG1_HUMAN	V-set and immunoglobulin domain containing 1			17					TTGGTCATTGGAAATCTGACA	0.418000																								0							SO:0001583	missense			ENST00000217957.5	1	1	hg19	CCDS14535.1	.	.	.	.	.	.	.	.	.	.	G	19.23	3.786560	0.70337	.	.	ENSG00000101842	ENST00000415430;ENST00000217957	T;T	0.11495	2.77;2.77	5.27	4.41	0.53225	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.207594	0.40908	D	0.000995	T	0.12944	0.0314	N	0.16790	0.44	0.42936	D	0.99433	D;D	0.89917	1.0;1.0	D;D	0.77557	0.99;0.985	T	0.13845	-1.0494	10	0.02654	T	1	.	9.9443	0.41600	0.0969:0.0:0.9031:0.0	.	235;199	C9J4P2;Q86XK7	.;VSIG1_HUMAN	E	235;199	ENSP00000402219:G235E;ENSP00000217957:G199E	ENSP00000217957:G199E	G	+	2	0	VSIG1	107203163	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	3.976000	0.56867	1.198000	0.43158	0.513000	0.50165	GGA		TCGA-2L-AAQJ-01A-12D-A397-08	VSIG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057858.1	1	0	1	195	1012	0	282	1	1	8	425	0	282	2		0	0	0	0	0	2	1	1.000000	193	1004	0	280	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	0	1	1			0.440000	1.870000	0.440000	0.720000	0.630000	0.830000	0.740000	0.736116	0.720000	0	6.800000e-01	7.800000e-01
ARHGAP36	158763	broad.mit.edu	37	X	130218925	130218925	+	Missense_Mutation	SNP	T	T	C			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chrX:130218925T>C	ENST00000276211.5	+	7	1187	c.842T>C	c.(841-843)cTg>cCg	p.L281P	ARHGAP36_ENST00000370921.1_Missense_Mutation_p.L145P|ARHGAP36_ENST00000370922.1_Missense_Mutation_p.L269P	NM_144967.3	NP_659404.2	Q6ZRI8	RHG36_HUMAN	Rho GTPase activating protein 36			71					GATGTAGTGCTGGATGACAAT	0.488000																								0							SO:0001583	missense			ENST00000276211.5	1	1	hg19	CCDS14628.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.378294	0.82682	.	.	ENSG00000147256	ENST00000276211;ENST00000370922;ENST00000412432;ENST00000370921	T;T;T;T	0.46451	0.87;0.87;0.87;0.87	5.16	5.16	0.70880	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.187606	0.26397	N	0.024602	T	0.65186	0.2667	M	0.85630	2.765	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.76575	0.988;0.988;0.987	T	0.68876	-0.5293	10	0.52906	T	0.07	.	10.0987	0.42491	0.0:0.0:0.0:1.0	.	250;269;281	Q6ZRI8-2;Q6ZRI8-4;Q6ZRI8	.;.;RHG36_HUMAN	P	281;269;250;145	ENSP00000276211:L281P;ENSP00000359960:L269P;ENSP00000408515:L250P;ENSP00000359959:L145P	ENSP00000276211:L281P	L	+	2	0	ARHGAP36	130046606	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	6.818000	0.75257	1.909000	0.55274	0.356000	0.21956	CTG		TCGA-2L-AAQJ-01A-12D-A397-08	ARHGAP36-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355073.1	1	0	1	113	548	0	134	0	0	0	1	0	134	2		0	0	0	0	0	2	1	1.000000	113	547	0	134	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	0	1	1			0.440000	1.870000	0.440000	0.770000	0.640000	0.900000	0.780000	0.780044	0.770000	0	7.000000e-01	8.400000e-01
ARHGEF6	9459	broad.mit.edu	37	X	135789073	135789073	+	Missense_Mutation	SNP	T	T	A			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chrX:135789073T>A	ENST00000250617.6	-	9	2245	c.1040A>T	c.(1039-1041)cAg>cTg	p.Q347L	ARHGEF6_ENST00000370620.1_Missense_Mutation_p.Q193L|ARHGEF6_ENST00000535227.1_Missense_Mutation_p.Q220L|ARHGEF6_ENST00000370622.1_Missense_Mutation_p.Q193L	NM_004840.2	NP_004831.1	Q15052	ARHG6_HUMAN	Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6			38	Acute lymphoblastic leukemia(192;0.000127)				TTACCTGTGCTGAGTGAGCAC	0.408000																								0							SO:0001583	missense			ENST00000250617.6	0	1	hg19	CCDS14660.1	.	.	.	.	.	.	.	.	.	.	T	17.07	3.295049	0.60086	.	.	ENSG00000129675	ENST00000250617;ENST00000370620;ENST00000370622;ENST00000535736;ENST00000535227	T;T;T;T	0.63744	-0.06;-0.06;-0.06;-0.06	5.15	5.15	0.70609	Dbl homology (DH) domain (5);	0.210007	0.49916	D	0.000125	T	0.70718	0.3256	M	0.81802	2.56	0.42510	D	0.992962	P;P	0.43352	0.629;0.804	B;P	0.47346	0.326;0.544	T	0.76280	-0.3017	10	0.72032	D	0.01	.	13.1422	0.59440	0.0:0.0:0.0:1.0	.	220;347	B7Z3C7;Q15052	.;ARHG6_HUMAN	L	347;193;193;193;220	ENSP00000250617:Q347L;ENSP00000359654:Q193L;ENSP00000359656:Q193L;ENSP00000439483:Q220L	ENSP00000250617:Q347L	Q	-	2	0	ARHGEF6	135616739	1.000000	0.71417	0.995000	0.50966	0.557000	0.35523	7.138000	0.77305	1.813000	0.52934	0.486000	0.48141	CAG		TCGA-2L-AAQJ-01A-12D-A397-08	ARHGEF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058511.2	0	0	0	7	629	0	122	0	7.314050e-03	0	10	0	122	2		0	0	0	0	0	2	1	0.979906	5	624	0	122	2		0	0	0	0	0	2	-5.715155	1	0	0	0		1	0	1	1			0.440000	1.870000	0.440000	0.040000	0.010000	0.100000	0.050000	0.056928	0.040000	0	3.000000e-02	8.000000e-02
NR0B1	190	broad.mit.edu	37	X	30326930	30326930	+	Missense_Mutation	SNP	T	T	G			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chrX:30326930T>G	ENST00000378970.4	-	1	785	c.551A>C	c.(550-552)aAa>aCa	p.K184T	NR0B1_ENST00000453287.1_Missense_Mutation_p.K184T|NR0B1_ENST00000378963.1_5'Flank	NM_000475.4	NP_000466.2	P51843	NR0B1_HUMAN	nuclear receptor subfamily 0, group B, member 1			24				Dexamethasone(DB01234)|Tretinoin(DB00755)	TAGCGCCTCTTTACCCCCTGG	0.692000											OREG0019719	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)												0							SO:0001583	missense			ENST00000378970.4	1	1	hg19	CCDS14223.1	.	.	.	.	.	.	.	.	.	.	T	2.662	-0.279477	0.05642	.	.	ENSG00000169297	ENST00000378970;ENST00000453287	D;D	0.97752	-3.63;-4.52	4.32	0.238	0.15480	.	1.525170	0.04086	N	0.310508	D	0.91597	0.7345	N	0.03608	-0.345	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	D	0.85206	0.1018	10	0.52906	T	0.07	0.6249	4.5457	0.12079	0.0:0.422:0.3572:0.2207	.	184	P51843	NR0B1_HUMAN	T	184	ENSP00000368253:K184T;ENSP00000396403:K184T	ENSP00000368253:K184T	K	-	2	0	NR0B1	30236851	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-0.356000	0.07661	-0.201000	0.10284	-0.402000	0.06365	AAA		TCGA-2L-AAQJ-01A-12D-A397-08	NR0B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056161.1	1	0	1	14	44	0	23		0	0	0	0	23	2		0	0	0	0	0	2	1	0.999843	14	42	0	22	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	0	1	1			0.440000	1.870000	0.440000	0.990000	0.660000	1.000000	1.000000	0.949802	0.990000	1	8.500000e-01	1
NR0B1	190	broad.mit.edu	37	X	30327066	30327066	+	Missense_Mutation	SNP	G	G	C			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chrX:30327066G>C	ENST00000378970.4	-	1	649	c.415C>G	c.(415-417)Cac>Gac	p.H139D	NR0B1_ENST00000453287.1_Missense_Mutation_p.H139D|NR0B1_ENST00000378963.1_5'Flank	NM_000475.4	NP_000466.2	P51843	NR0B1_HUMAN	nuclear receptor subfamily 0, group B, member 1			24				Dexamethasone(DB01234)|Tretinoin(DB00755)	TGCCGCGGGTGGTCTTCACCA	0.692000											OREG0019719	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)												0							SO:0001583	missense			ENST00000378970.4	1	1	hg19	CCDS14223.1	.	.	.	.	.	.	.	.	.	.	G	17.92	3.507718	0.64410	.	.	ENSG00000169297	ENST00000378970;ENST00000453287	D;D	0.98164	-3.9;-4.76	3.96	3.96	0.45880	.	0.000000	0.42053	D	0.000762	D	0.98397	0.9467	M	0.66939	2.045	0.40318	D	0.978796	D	0.69078	0.997	D	0.69142	0.962	D	0.99107	1.0845	10	0.87932	D	0	-5.5412	12.706	0.57061	0.0:0.0:1.0:0.0	.	139	P51843	NR0B1_HUMAN	D	139	ENSP00000368253:H139D;ENSP00000396403:H139D	ENSP00000368253:H139D	H	-	1	0	NR0B1	30236987	1.000000	0.71417	0.998000	0.56505	0.979000	0.70002	3.474000	0.53129	2.222000	0.72286	0.513000	0.50165	CAC		TCGA-2L-AAQJ-01A-12D-A397-08	NR0B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056161.1	1	0	1	42	137	0	41		0	0	0	0	41	2		0	0	0	0	0	2	1	1.000000	41	136	0	39	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	0	1	1			0.440000	1.870000	0.440000	0.990000	0.800000	1.000000	1.000000	0.972910	0.990000	1	9.200000e-01	1
FAM47A	158724	broad.mit.edu	37	X	34148936	34148936	+	Missense_Mutation	SNP	C	C	T			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chrX:34148936C>T	ENST00000346193.3	-	1	1511	c.1460G>A	c.(1459-1461)cGg>cAg	p.R487Q		NM_203408.3	NP_981953.2	Q5JRC9	FA47A_HUMAN	family with sequence similarity 47, member A	p.R487Q(1)		97					ACTGGACCTCCGACGTGTCTT	0.642000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000346193.3	1	1	hg19	CCDS43926.1	.	.	.	.	.	.	.	.	.	.	c	9.489	1.100058	0.20552	.	.	ENSG00000185448	ENST00000346193	T	0.16196	2.36	0.446	0.446	0.16602	.	.	.	.	.	T	0.10380	0.0254	N	0.24115	0.695	0.09310	N	1	D	0.62365	0.991	P	0.44811	0.461	T	0.23762	-1.0179	8	0.13470	T	0.59	.	.	.	.	.	487	Q5JRC9	FA47A_HUMAN	Q	487	ENSP00000345029:R487Q	ENSP00000345029:R487Q	R	-	2	0	FAM47A	34058857	0.022000	0.18835	0.006000	0.13384	0.016000	0.09150	0.010000	0.13242	0.435000	0.26365	0.183000	0.17082	CGG		TCGA-2L-AAQJ-01A-12D-A397-08	FAM47A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056205.1	1	0	1	76	304	0	85		0	0	0	0	85	2		0	0	0	0	0	2	1	1.000000	76	299	0	82	2		0	0	0	0	0	2	-3.239998	1	1	0	0		1	0	1	1			0.440000	1.870000	0.440000	0.900000	0.730000	1.000000	1.000000	0.903808	0.900000	1	8.100000e-01	1
MED14	9282	broad.mit.edu	37	X	40526067	40526067	+	Missense_Mutation	SNP	A	A	C			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08			A	C	A	A		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chrX:40526067A>C	ENST00000324817.1	-	24	3288	c.3170T>G	c.(3169-3171)tTg>tGg	p.L1057W		NM_004229.3	NP_004220.2	O60244	MED14_HUMAN	mediator complex subunit 14			39					TGGGGCTCTCAAAGCCCCACT	0.493000																								0							SO:0001583	missense			ENST00000324817.1	0	1	hg19	CCDS14254.1	.	.	.	.	.	.	.	.	.	.	A	22.8	4.337558	0.81911	.	.	ENSG00000180182	ENST00000324817	.	.	.	5.64	5.64	0.86602	.	0.000000	0.64402	D	0.000001	T	0.75155	0.3811	L	0.53249	1.67	0.58432	D	0.999991	D	0.76494	0.999	D	0.77557	0.99	T	0.77587	-0.2532	9	0.72032	D	0.01	.	14.8838	0.70553	1.0:0.0:0.0:0.0	.	1057	O60244	MED14_HUMAN	W	1057	.	ENSP00000323720:L1057W	L	-	2	0	MED14	40411011	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	8.721000	0.91446	1.896000	0.54893	0.402000	0.26972	TTG		TCGA-2L-AAQJ-01A-12D-A397-08	MED14-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060692.1	0	0	0	31	66	0	18	1	9.989050e-01	2	25	0	18	2		0	0	0	0	0	2	1	1.000000	30	65	0	18	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	0	1	1			0.440000	1.870000	0.440000	0.990000	0.990000	1.000000	1.000000	0.999291	0.990000	1	9.900000e-01	1
KCND1	3750	broad.mit.edu	37	X	48819916	48819916	+	Missense_Mutation	SNP	C	C	T	rs145016539		TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chrX:48819916C>T	ENST00000218176.3	-	6	3167	c.1870G>A	c.(1870-1872)Ggc>Agc	p.G624S	KCND1_ENST00000376477.1_Missense_Mutation_p.G247S	NM_004979.4	NP_004970.3	Q9NSA2	KCND1_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 1			24				Dalfampridine(DB06637)	AGGGTGCTGCCGGCCCTGCCA	0.632000																								0							SO:0001583	missense			ENST00000218176.3	1	1	hg19	CCDS14314.1	.	.	.	.	.	.	.	.	.	.	c	1.827	-0.470870	0.04445	7.82E-4	0.0	ENSG00000102057	ENST00000376477;ENST00000218176	D;D	0.95918	-3.34;-3.85	5.32	-0.965	0.10323	.	1.211090	0.05587	N	0.573947	D	0.88919	0.6568	L	0.36672	1.1	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.77501	-0.2564	10	0.02654	T	1	.	3.4758	0.07583	0.197:0.4041:0.0:0.3989	.	624	Q9NSA2	KCND1_HUMAN	S	247;624	ENSP00000365660:G247S;ENSP00000218176:G624S	ENSP00000218176:G624S	G	-	1	0	KCND1	48704860	0.959000	0.32827	0.014000	0.15608	0.107000	0.19398	1.496000	0.35638	0.195000	0.20347	-0.743000	0.03520	GGC		TCGA-2L-AAQJ-01A-12D-A397-08	KCND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060774.1	1	0	1	24	84	0	25	0	4.925881e-01	0	7	0	25	2		0	0	0	0	0	2	1	1.000000	23	83	0	24	2		0	0	0	0	0	2	-20.000000	1	1	121348	33	41	1	0	1	1			0.440000	1.870000	0.440000	0.990000	0.680000	1.000000	1.000000	0.939084	0.990000	1	8.300000e-01	1
HDX	139324	broad.mit.edu	37	X	83724365	83724365	+	Silent	SNP	T	T	A			TCGA-2L-AAQJ-01A-12D-A397-08	TCGA-2L-AAQJ-11A-11D-A39A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de369dbb-736e-4970-998d-a0470029653f	cb472e98-8801-40f4-9c2c-6ebb03b41c40	g.chrX:83724365T>A	ENST00000297977.5	-	3	477	c.366A>T	c.(364-366)acA>acT	p.T122T	HDX_ENST00000373177.2_Silent_p.T122T|HDX_ENST00000506585.2_Silent_p.T64T	NM_001177479.1|NM_144657.4	NP_001170950.1|NP_653258.2	Q7Z353	HDX_HUMAN	highly divergent homeobox			48					TATGTTTGTTTGTTCCTTGCC	0.403000													Pancreas(53;231 1169 36156 43751 51139)											0							SO:0001819	synonymous_variant			ENST00000297977.5	1	1	hg19	CCDS35342.1																																																																																				TCGA-2L-AAQJ-01A-12D-A397-08	HDX-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057379.2	1	0	1	66	376	0	84	0	6.204219e-02	0	3	0	84	2		0	0	0	0	0	2	1	1.000000	66	373	0	83	2		0	0	0	0	0	2	-20.000000	1	1	0	0		1	0	1	1			0.440000	1.870000	0.440000	0.670000	0.530000	0.830000	0.680000	0.683934	0.670000	0	6.000000e-01	7.600000e-01
