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
NFKBIZ	64332	broad.mit.edu	37	3	101575980	101575980	+	Frame_Shift_Del	DEL	C	C	-			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08			C	-	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr3:101575980delC	ENST00000326172.5	+	10	2003	c.1888delC	c.(1888-1890)cgcfs	p.R630fs	NFKBIZ_ENST00000394054.2_Frame_Shift_Del_p.R530fs|NFKBIZ_ENST00000326151.5_Frame_Shift_Del_p.R508fs	NM_031419.3	NP_113607.1	Q9BYH8	IKBZ_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, zeta			24					GGAACTCATTCGCCTCTTTTT	0.463000																								0							SO:0001589	frameshift_variant			ENST00000326172.5	1	1	hg19	CCDS2946.1																																																																																				TCGA-IB-AAUO-01A-12D-A38G-08	NFKBIZ-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353793.1	1	0	0	48	424	0	202	1	9.999883e-01	45	103	0	202	2	0	0	0	0	0	0		1	1.000000	58	431	1	208	10	0	0	0	0	0	0		-15.511920	1	1	0	0		1	0	1	1	1.716026	1	0.380000	1.860000	0.234568	0.420000	0.320000	0.550000	0.430000	0.437665	0.420000	0	0.370000	0.490000
PKD2L1	9033	broad.mit.edu	37	10	102057186	102057186	+	Silent	SNP	G	G	A			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr10:102057186G>A	ENST00000318222.3	-	5	1291	c.909C>T	c.(907-909)atC>atT	p.I303I	PKD2L1_ENST00000353274.3_Silent_p.I303I|PKD2L1_ENST00000338519.3_Intron	NM_001253837.1|NM_016112.2	NP_001240766.1|NP_057196.2	Q9P0L9	PK2L1_HUMAN	polycystic kidney disease 2-like 1			43		Colorectal(252;0.117)			CTGAGAAGTCGATGAACACCA	0.567000																								0							SO:0001819	synonymous_variant			ENST00000318222.3	1	1	hg19	CCDS7492.1																																																																																				TCGA-IB-AAUO-01A-12D-A38G-08	PKD2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049863.2	0	0	1	37	280	1	118		0	0	0	1	118	2		0	0	0	0	0	2	1	0.999979	37	275	1	118	11		0	0	0	1	118	2	-15.167500	1	1	121412	1	35	1	1	2	3	2.064821	0	0.380000	1.860000	0.381176	0.610000	0.440000	0.820000	0.620000	0.624935	0.610000	0	0.520000	0.720000
C10orf82	143379	broad.mit.edu	37	10	118425205	118425205	+	Missense_Mutation	SNP	G	G	C			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr10:118425205G>C	ENST00000369210.3	-	3	242	c.188C>G	c.(187-189)gCc>gGc	p.A63G	C10orf82_ENST00000588184.1_Missense_Mutation_p.A63G	NM_144661.2	NP_653262.1	Q8WW14	CJ082_HUMAN	chromosome 10 open reading frame 82			7					CAGTTTCGGGGCAGTGGCCAC	0.562000																								0							SO:0001583	missense			ENST00000369210.3	1	1	hg19	CCDS7596.1	.	.	.	.	.	.	.	.	.	.	G	16.52	3.146601	0.57044	.	.	ENSG00000165863	ENST00000369210;ENST00000388884	T	0.64260	-0.09	5.16	4.25	0.50352	.	0.715143	0.13142	N	0.410531	T	0.66015	0.2747	M	0.65975	2.015	0.09310	N	1	P;D	0.56521	0.884;0.976	B;P	0.49085	0.42;0.6	T	0.57106	-0.7868	10	0.49607	T	0.09	-4.1516	9.7479	0.40457	0.096:0.0:0.904:0.0	.	63;63	Q8WW14-3;Q8WW14	.;CJ082_HUMAN	G	63	ENSP00000358212:A63G	ENSP00000358212:A63G	A	-	2	0	C10orf82	118415195	0.014000	0.17966	0.010000	0.14722	0.031000	0.12232	1.748000	0.38308	1.161000	0.42604	0.561000	0.74099	GCC		TCGA-IB-AAUO-01A-12D-A38G-08	C10orf82-001	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000050527.1	1	0	1	51	258	0	118		0	0	0	0	118	2		0	0	0	0	0	2	1	1.000000	51	250	0	118	2		0	0	0	0	118	2	-20.000000	1	1	0	0		1	1	2	3	2.064821	0	0.380000	1.860000	0.381176	0.860000	0.660000	1.000000	1.000000	0.868711	0.860000	1	0.760000	0.990000
KIAA1217	56243	broad.mit.edu	37	10	24831899	24831899	+	Nonsense_Mutation	SNP	G	G	T			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr10:24831899G>T	ENST00000376454.3	+	19	3730	c.3700G>T	c.(3700-3702)Gaa>Taa	p.E1234*	KIAA1217_ENST00000307544.6_Intron|KIAA1217_ENST00000376462.1_Intron|KIAA1217_ENST00000396445.1_Intron|KIAA1217_ENST00000376451.2_Nonsense_Mutation_p.E917*|KIAA1217_ENST00000396446.1_Intron|KIAA1217_ENST00000458595.1_Intron|KIAA1217_ENST00000376452.3_Intron	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217			70					AAGAACATCAGAATATAAAAC	0.413000																								0							SO:0001587	stop_gained			ENST00000376454.3	0	1	hg19	CCDS31165.1	.	.	.	.	.	.	.	.	.	.	G	42	9.260198	0.99117	.	.	ENSG00000120549	ENST00000442879;ENST00000376454;ENST00000450158;ENST00000376451	.	.	.	5.42	4.5	0.54988	.	0.360938	0.28062	N	0.016754	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	.	15.1525	0.72713	0.0:0.1417:0.8583:0.0	.	.	.	.	X	917;1234;917;917	.	ENSP00000365634:E917X	E	+	1	0	KIAA1217	24871905	0.993000	0.37304	0.790000	0.31976	0.868000	0.49771	2.681000	0.46926	1.264000	0.44198	0.561000	0.74099	GAA		TCGA-IB-AAUO-01A-12D-A38G-08	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	1	0	1	41	153	0	105	1	7.549167e-01	4	8	0	105	2		0	0	0	0	0	2	1	1.000000	41	150	0	106	2		0	0	0	0	105	2	-20.000000	1	1	0	0		1	0	1	1	1.666965	1	0.380000	1.860000	0.234568	0.850000	0.650000	0.990000	0.890000	0.855220	0.850000	1	0.750000	0.950000
DIP2C	22982	broad.mit.edu	37	10	410376	410376	+	Silent	SNP	G	G	A			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr10:410376G>A	ENST00000280886.6	-	20	2502	c.2415C>T	c.(2413-2415)aaC>aaT	p.N805N	DIP2C_ENST00000381496.3_3'UTR|DIP2C_ENST00000540204.1_Silent_p.N126N	NM_014974.2	NP_055789.1	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C (Drosophila)			81		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)		TGTCGTCGGCGTTGTGCCTGC	0.602000																								0							SO:0001819	synonymous_variant			ENST00000280886.6	1	1	hg19	CCDS7054.1																																																																																				TCGA-IB-AAUO-01A-12D-A38G-08	DIP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046389.1	1	0	1	59	267	1	120	0	2.289787e-01	0	5	1	120	2		0	0	0	0	0	2	1	1.000000	59	262	1	119	11		0	0	0	1	120	2	-20.000000	1	1	121412	18	44	1	0	1	1	2.049863	0	0.380000	1.860000	0.378820	0.940000	0.740000	1.000000	1.000000	0.929680	0.940000	1	0.830000	1.000000
ALOX5	240	broad.mit.edu	37	10	45878098	45878098	+	Silent	SNP	C	C	T	rs150281723	by1000genomes	TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr10:45878098C>T	ENST00000374391.2	+	2	371	c.318C>T	c.(316-318)ggC>ggT	p.G106G	ALOX5_ENST00000542434.1_Silent_p.G106G	NM_000698.3|NM_001256153.1	NP_000689.1|NP_001243082.1	P09917	LOX5_HUMAN	arachidonate 5-lipoxygenase	p.G106G(1)		37		Lung SC(717;0.0257)		Aminosalicylic Acid(DB00233)|Balsalazide(DB01014)|Diclofenac(DB00586)|Diethylcarbamazine(DB00711)|Masoprocol(DB00179)|Meclofenamic acid(DB00939)|Mesalazine(DB00244)|Minocycline(DB01017)|Montelukast(DB00471)|Sulfasalazine(DB00795)|Vitamin E(DB00163)|Zileuton(DB00744)	GGATCACCGGCGATGTCGAGG	0.592000																								1	Substitution - coding silent(1)						SO:0001819	synonymous_variant			ENST00000374391.2	1	1	hg19	CCDS7212.1																																																																																				TCGA-IB-AAUO-01A-12D-A38G-08	ALOX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047780.1	1	0	1	15	94	0	53	1	1	119	191	0	53	2		0	0	0	0	0	2	1	0.999883	13	92	0	53	2		0	0	0	0	53	2	-4.328109	1	1	121412	109	48	1	0	1	1	2.051288	0	0.380000	1.860000	0.378820	0.720000	0.430000	1.000000	1.000000	0.738615	0.720000	0	0.560000	0.910000
C11orf70	85016	broad.mit.edu	37	11	101953816	101953816	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr11:101953816G>A	ENST00000434758.2	+	7	718	c.690G>A	c.(688-690)atG>atA	p.M230I		NM_032930.2	NP_116319.2	Q9BRQ4	CK070_HUMAN	chromosome 11 open reading frame 70			12	all_epithelial(12;0.0137)	Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.0137)	Lung(13;0.245)		CTGCTGGTATGTGCTATCCTT	0.294000																								0							SO:0001583	missense			ENST00000434758.2	1	1	hg19	CCDS8313.2	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	10.29	1.310068	0.23821	0.0	9.3E-4	ENSG00000137691	ENST00000434758;ENST00000423732	.	.	.	5.85	3.99	0.46301	.	0.448291	0.26062	N	0.026578	T	0.46600	0.1401	L	0.50333	1.59	0.80722	D	1	B	0.12013	0.005	B	0.10450	0.005	T	0.36578	-0.9742	9	0.23891	T	0.37	0.0275	7.5577	0.27833	0.1437:0.0:0.7203:0.1361	.	230	Q9BRQ4	CK070_HUMAN	I	230;192	.	ENSP00000392150:M192I	M	+	3	0	C11orf70	101459026	0.991000	0.36638	0.996000	0.52242	0.588000	0.36517	0.758000	0.26447	1.487000	0.48415	0.585000	0.79938	ATG		TCGA-IB-AAUO-01A-12D-A38G-08	C11orf70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394144.1	0	0	0	115	443	0	186	0	1.114614e-01	1	2	0	186	2		0	0	0	0	0	2	1	1.000000	112	435	0	184	2		0	0	0	0	186	2	-2.958174	1	1	121410	50	50	1	1	2	3	2.062376	0	0.380000	1.860000	0.381176	0.990000	0.910000	1.000000	1.000000	0.992752	0.990000	1	0.990000	1.000000
DYNC2H1	79659	broad.mit.edu	37	11	103027117	103027117	+	Splice_Site	SNP	G	G	T			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr11:103027117G>T	ENST00000375735.2	+	26	3889	c.3745G>T	c.(3745-3747)Gat>Tat	p.D1249Y	DYNC2H1_ENST00000334267.7_Intron|DYNC2H1_ENST00000398093.3_Splice_Site_p.D1249Y	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)			TGTTAAATAGGATTTAAATAG	0.284000																								0							SO:0001630	splice_region_variant			ENST00000375735.2	1	0	hg19	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	G	17.09	3.300875	0.60195	.	.	ENSG00000187240	ENST00000375735;ENST00000398093	T;T	0.62639	0.01;0.01	5.27	5.27	0.74061	Dynein heavy chain, domain-2 (1);	0.197764	0.33895	N	0.004459	T	0.76140	0.3946	M	0.88181	2.935	0.80722	D	1	B;B	0.33171	0.4;0.348	B;B	0.43123	0.409;0.301	T	0.76817	-0.2819	9	.	.	.	.	18.8855	0.92376	0.0:0.0:1.0:0.0	.	1249;1249	Q8NCM8;Q8NCM8-2	DYHC2_HUMAN;.	Y	1249	ENSP00000364887:D1249Y;ENSP00000381167:D1249Y	.	D	+	1	0	DYNC2H1	102532327	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.376000	0.79658	2.472000	0.83506	0.563000	0.77884	GAT		TCGA-IB-AAUO-01A-12D-A38G-08	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	1	0	1	21	102	0	54		0	0	0	0	54	2		0	0	0	0	0	2	1	0.999999	20	102	0	53	2		0	0	0	0	54	2	-20.000000	1	1	0	0		1	1	2	3	2.062376	0	0.380000	1.860000	0.381176	0.900000	0.590000	1.000000	1.000000	0.878325	0.900000	1	0.730000	1.000000
ARHGAP20	57569	broad.mit.edu	37	11	110451075	110451075	+	Silent	SNP	T	T	C			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr11:110451075T>C	ENST00000260283.4	-	16	2879	c.2595A>G	c.(2593-2595)tcA>tcG	p.S865S	ARHGAP20_ENST00000528829.1_Silent_p.S829S|ARHGAP20_ENST00000527598.1_Silent_p.S829S|ARHGAP20_ENST00000529591.1_Silent_p.S408S|ARHGAP20_ENST00000533353.1_Silent_p.S839S|ARHGAP20_ENST00000524756.1_Silent_p.S842S|ARHGAP20_ENST00000357139.3_Silent_p.S839S	NM_020809.3	NP_065860.2	Q9P2F6	RHG20_HUMAN	Rho GTPase activating protein 20			60		all_cancers(61;3.26e-12)|all_epithelial(67;6.09e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000484)|Acute lymphoblastic leukemia(157;0.000967)|all_neural(223;0.0199)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)			GTTGTTTCTTTGAATAAATTC	0.493000																								0							SO:0001819	synonymous_variant			ENST00000260283.4	1	1	hg19	CCDS31673.1																																																																																				TCGA-IB-AAUO-01A-12D-A38G-08	ARHGAP20-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390628.1	1	0	1	108	479	0	214	0	0	0	1	0	214	2		0	0	0	0	0	2	1	1.000000	108	468	0	213	2		0	0	0	0	214	2	-20.000000	1	1	0	0		1	1	2	3	2.062376	0	0.380000	1.860000	0.381176	0.960000	0.800000	1.000000	1.000000	0.951003	0.960000	1	0.880000	1.000000
ZBTB16	7704	broad.mit.edu	37	11	114027126	114027126	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr11:114027126C>T	ENST00000335953.4	+	3	1716	c.1336C>T	c.(1336-1338)Cgg>Tgg	p.R446W	ZBTB16_ENST00000392996.2_Missense_Mutation_p.R446W	NM_006006.4	NP_005997.2	Q05516	ZBT16_HUMAN	zinc finger and BTB domain containing 16			6		all_cancers(61;3.79e-18)|all_epithelial(67;2.32e-10)|all_hematologic(158;2.96e-05)|Melanoma(852;0.000362)|Acute lymphoblastic leukemia(157;0.00108)|Breast(348;0.0104)|all_neural(223;0.0294)|Prostate(24;0.0318)|Medulloblastoma(222;0.0438)			GGATAGTTTGCGGCTGAGAAT	0.547000																								0							SO:0001583	missense			ENST00000335953.4	0	1	hg19	CCDS8367.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.389876	0.82902	.	.	ENSG00000109906	ENST00000335953;ENST00000392996;ENST00000310883	T;T	0.15372	2.43;2.43	4.81	4.81	0.61882	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.64402	D	0.000001	T	0.38134	0.1029	M	0.62723	1.935	0.51767	D	0.999937	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.10245	-1.0638	10	0.72032	D	0.01	-2.7332	13.0927	0.59174	0.1603:0.8397:0.0:0.0	.	446;451	Q05516;Q59H43	ZBT16_HUMAN;.	W	446;446;323	ENSP00000338157:R446W;ENSP00000376721:R446W	ENSP00000309507:R323W	R	+	1	2	ZBTB16	113532336	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.419000	0.66435	2.500000	0.84329	0.655000	0.94253	CGG		TCGA-IB-AAUO-01A-12D-A38G-08	ZBTB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398940.1	0	0	0	4	216	0	81	0	6.059872e-04	0	2	0	81	2		0	0	0	0	0	2	1	0.885690	4	211	0	80	2		0	0	0	0	81	2	-2.672181	1	1	0	0		1	1	2	3	2.062376	0	0.380000	1.860000	0.381176	0.100000	0.030000	0.240000	0.100000	0.117887	0.100000	0	0.060000	0.170000
DPAGT1	1798	broad.mit.edu	37	11	118972344	118972344	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr11:118972344G>A	ENST00000409993.2	-	3	1573	c.22C>T	c.(22-24)Ccc>Tcc	p.P8S	DPAGT1_ENST00000432443.2_5'UTR|DPAGT1_ENST00000445653.1_5'UTR|DPAGT1_ENST00000354202.4_Missense_Mutation_p.P8S			Q9H3H5	GPT_HUMAN	dolichyl-phosphate (UDP-N-acetylglucosamine) N-acetylglucosaminephosphotransferase 1 (GlcNAc-1-P transferase)			17	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)			AGCGGCATGGGCAATTCCGAG	0.632000											OREG0021396	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)												0							SO:0001583	missense			ENST00000409993.2	0	1	hg19	CCDS8411.1	.	.	.	.	.	.	.	.	.	.	G	15.61	2.884783	0.51908	.	.	ENSG00000172269	ENST00000409993;ENST00000354202	D;D	0.91011	-2.77;-2.77	4.79	3.87	0.44632	.	0.000000	0.85682	D	0.000000	T	0.80628	0.4659	N	0.19112	0.55	0.80722	D	1	P	0.35174	0.488	B	0.27380	0.079	T	0.78725	-0.2092	10	0.27082	T	0.32	-2.6285	12.3966	0.55389	0.0:0.0:0.8312:0.1688	.	8	Q9H3H5	GPT_HUMAN	S	8	ENSP00000386597:P8S;ENSP00000346142:P8S	ENSP00000346142:P8S	P	-	1	0	DPAGT1	118477554	.	.	0.973000	0.42090	0.691000	0.40173	.	.	1.602000	0.50124	0.655000	0.94253	CCC		TCGA-IB-AAUO-01A-12D-A38G-08	DPAGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331527.2	0	0	0	5	289	0	112	0	2.477637e-01	0	47	0	112	2		0	0	0	0	0	2	1	0.935214	5	284	0	110	2		0	0	0	0	112	2	-2.631334	1	1	0	0		1	1	2	3	2.062376	0	0.380000	1.860000	0.381176	0.090000	0.030000	0.210000	0.090000	0.106304	0.090000	0	0.050000	0.150000
KIRREL3	84623	broad.mit.edu	37	11	126432761	126432761	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr11:126432761C>T	ENST00000525144.2	-	2	351	c.102G>A	c.(100-102)atG>atA	p.M34I	KIRREL3_ENST00000533026.2_5'UTR|KIRREL3_ENST00000525704.2_Missense_Mutation_p.M34I|KIRREL3-AS1_ENST00000548204.1_RNA|KIRREL3_ENST00000529097.2_Missense_Mutation_p.M34I	NM_032531.3	NP_115920.1	Q8IZU9	KIRR3_HUMAN	kin of IRRE like 3 (Drosophila)			29	all_hematologic(175;0.145)	Lung NSC(97;0.0484)|all_lung(97;0.0522)|Medulloblastoma(222;0.0523)|Breast(109;0.0949)|all_neural(223;0.224)			TGTCCTTGGCCATGTAGCCCA	0.547000																								0							SO:0001583	missense			ENST00000525144.2	1	1	hg19	CCDS53723.1	.	.	.	.	.	.	.	.	.	.	C	16.07	3.017523	0.54576	.	.	ENSG00000149571	ENST00000525144;ENST00000529097;ENST00000525704	T;T;T	0.70516	-0.49;-0.26;-0.35	5.62	5.62	0.85841	.	0.078542	0.53938	D	0.000046	T	0.54255	0.1847	N	0.08118	0	0.80722	D	1	B;B;B	0.26547	0.048;0.152;0.077	B;B;B	0.26614	0.025;0.071;0.019	T	0.52719	-0.8538	10	0.37606	T	0.19	.	17.8583	0.88773	0.0:1.0:0.0:0.0	.	34;34;34	Q8IZU9-2;E9PRX9;Q8IZU9	.;.;KIRR3_HUMAN	I	34	ENSP00000435466:M34I;ENSP00000434081:M34I;ENSP00000435094:M34I	ENSP00000435466:M34I	M	-	3	0	KIRREL3	125937971	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.770000	0.62309	2.645000	0.89757	0.650000	0.86243	ATG		TCGA-IB-AAUO-01A-12D-A38G-08	KIRREL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386479.2	1	0	1	31	207	0	72	0	0	0	1	0	72	2		0	0	0	0	0	2	1	1.000000	31	203	0	72	2		0	0	0	0	72	2	-3.320078	1	1	0	0		1	1	2	3	2.062376	0	0.380000	1.860000	0.381176	0.680000	0.480000	0.940000	0.680000	0.697943	0.680000	0	0.570000	0.810000
MUC5B	727897	broad.mit.edu	37	11	1268340	1268340	+	Silent	SNP	A	A	T			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr11:1268340A>T	ENST00000529681.1	+	31	10288	c.10230A>T	c.(10228-10230)ccA>ccT	p.P3410P	MUC5B_ENST00000447027.1_Silent_p.P3413P|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming			137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)			cctcaactccagggacaactc	0.637000																								0							SO:0001819	synonymous_variant			ENST00000529681.1	0	1	hg19	CCDS44515.2																																																																																				TCGA-IB-AAUO-01A-12D-A38G-08	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	0	0	0	3	29	0	14	0	4.481793e-02	0	3	0	14	2		0	0	0	0	0	2	1	0.779939	3	26	0	13	2		0	0	0	0	14	2	-0.923199	0	1	114872	183	46	1	0	1	1	2.051225	0	0.380000	1.860000	0.378820	0.540000	0.160000	1.000000	1.000000	0.573597	0.540000	0	0.310000	0.840000
SSH1	54434	broad.mit.edu	37	12	109186420	109186420	+	Missense_Mutation	SNP	C	C	T	rs146699038	by1000genomes	TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr12:109186420C>T	ENST00000326495.5	-	14	1628	c.1535G>A	c.(1534-1536)cGg>cAg	p.R512Q	SSH1_ENST00000551165.1_Missense_Mutation_p.R512Q|SSH1_ENST00000326470.5_Missense_Mutation_p.R523Q|SSH1_ENST00000360239.3_Missense_Mutation_p.R200Q	NM_018984.3	NP_061857.3	Q8WYL5	SSH1_HUMAN	slingshot protein phosphatase 1			38					TGAGAGTCGCCGGAAACAGCA	0.637000																								0							SO:0001583	missense			ENST00000326495.5	0	1	hg19	CCDS9121.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	14.68	2.607225	0.46527	0.001817	0.0	ENSG00000084112	ENST00000360239;ENST00000326495;ENST00000551165;ENST00000326470	T;T;T;T	0.15834	2.39;2.4;2.49;2.46	5.48	4.6	0.57074	.	3.113600	0.01024	N	0.004037	T	0.23054	0.0557	M	0.71581	2.175	0.39015	D	0.959636	P;B;P;P	0.39624	0.681;0.218;0.569;0.681	B;B;B;B	0.26614	0.071;0.016;0.07;0.071	T	0.39563	-0.9608	10	0.37606	T	0.19	-25.6956	12.894	0.58089	0.0:0.9248:0.0:0.0752	.	523;512;512;200	Q8WYL5-5;Q8WYL5-2;Q8WYL5;Q8WYL5-4	.;.;SSH1_HUMAN;.	Q	200;512;512;523	ENSP00000353374:R200Q;ENSP00000315713:R512Q;ENSP00000448824:R512Q;ENSP00000326107:R523Q	ENSP00000326107:R523Q	R	-	2	0	SSH1	107710549	0.990000	0.36364	0.815000	0.32552	0.069000	0.16628	2.653000	0.46691	1.460000	0.47911	-0.136000	0.14681	CGG		TCGA-IB-AAUO-01A-12D-A38G-08	SSH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403724.1	0	0	0	7	256	0	119	0	8.719772e-02	1	15	0	119	2		0	0	0	0	0	2	1	0.979070	7	249	0	117	2		0	0	0	0	119	2	-3.215354	1	1	121338	22	43	1	0	0	0	2.013098	0	0.380000	1.860000	0.365534	0.140000	0.060000	0.270000	0.130000	0.154241	0.140000	0	0.090000	0.200000
GPR133	283383	broad.mit.edu	37	12	131476784	131476784	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr12:131476784G>A	ENST00000261654.5	+	8	1372	c.813G>A	c.(811-813)atG>atA	p.M271I	RP11-76C10.5_ENST00000542980.1_lincRNA|GPR133_ENST00000535015.1_Missense_Mutation_p.M303I	NM_198827.3	NP_942122.2	Q6QNK2	GP133_HUMAN	G protein-coupled receptor 133			67	all_neural(191;0.0982)|Medulloblastoma(191;0.163)				TCTTTCAGATGCCCACAGATG	0.393000																								0							SO:0001583	missense			ENST00000261654.5	1	1	hg19	CCDS9272.1	.	.	.	.	.	.	.	.	.	.	G	2.052	-0.417574	0.04766	.	.	ENSG00000111452	ENST00000261654;ENST00000542091;ENST00000535015;ENST00000537600	T;T	0.38887	1.11;1.11	5.62	2.61	0.31194	.	1.491050	0.03428	N	0.207351	T	0.30727	0.0774	L	0.29908	0.895	0.22081	N	0.999377	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.16512	-1.0400	10	0.27785	T	0.31	.	3.881	0.09079	0.1601:0.1364:0.5778:0.1257	.	303;271	B7ZLF7;Q6QNK2	.;GP133_HUMAN	I	271;211;303;30	ENSP00000261654:M271I;ENSP00000444425:M303I	ENSP00000261654:M271I	M	+	3	0	GPR133	130042737	0.174000	0.23070	0.228000	0.23943	0.043000	0.13939	0.405000	0.21015	1.350000	0.45770	0.655000	0.94253	ATG		TCGA-IB-AAUO-01A-12D-A38G-08	GPR133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399356.1	0	0	0	24	951	0	356		0	0	0	0	356	2		0	0	0	0	0	2	1	1.000000	24	930	0	355	2		0	0	0	0	356	2	-2.688130	1	1	0	0		1	0	0	0	2.013098	0	0.380000	1.860000	0.365534	0.120000	0.070000	0.180000	0.130000	0.131366	0.120000	0	0.090000	0.160000
RECQL	5965	broad.mit.edu	37	12	21644543	21644543	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr12:21644543G>T	ENST00000444129.2	-	3	592	c.124C>A	c.(124-126)Ctg>Atg	p.L42M	RECQL_ENST00000421138.2_Missense_Mutation_p.L42M	NM_002907.3|NM_032941.2	NP_002898.2|NP_116559.1	P46063	RECQ1_HUMAN	RecQ helicase-like			17					TTCTTTGTCAGGACTTTTTTT	0.378000								Other identified genes with known or suspected DNA repair function																0							SO:0001583	missense			ENST00000444129.2	1	0	hg19	CCDS31756.1	.	.	.	.	.	.	.	.	.	.	G	11.66	1.704990	0.30232	.	.	ENSG00000004700	ENST00000444129;ENST00000421138;ENST00000396093;ENST00000314748;ENST00000542432;ENST00000536240;ENST00000536964;ENST00000539672	T;T;T;T;D;D;D;D	0.87256	0.29;0.29;0.55;0.54;-2.23;-2.23;-2.23;-1.68	4.33	3.42	0.39159	.	0.087041	0.48767	D	0.000177	D	0.92195	0.7525	M	0.83953	2.67	0.24809	N	0.992651	D	0.89917	1.0	D	0.73380	0.98	D	0.84614	0.0680	10	0.72032	D	0.01	-4.8901	8.4221	0.32707	0.0843:0.0:0.7589:0.1568	.	42	P46063	RECQ1_HUMAN	M	42	ENSP00000416739:L42M;ENSP00000395449:L42M;ENSP00000379400:L42M;ENSP00000318727:L42M;ENSP00000445555:L42M;ENSP00000439069:L42M;ENSP00000446036:L42M;ENSP00000440700:L42M	ENSP00000318727:L42M	L	-	1	2	RECQL	21535810	0.652000	0.27349	0.372000	0.25991	0.193000	0.23685	0.781000	0.26774	1.123000	0.41961	0.655000	0.94253	CTG		TCGA-IB-AAUO-01A-12D-A38G-08	RECQL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402371.1	1	0	1	69	392	0	174	1	8.603249e-01	5	17	0	174	2		0	0	0	0	0	2	1	1.000000	67	382	0	172	2		0	0	0	0	174	2	-2.922170	1	1	0	0		1	0	0	0	2.013098	0	0.380000	1.860000	0.365534	0.760000	0.600000	0.940000	0.770000	0.774454	0.760000	0	0.680000	0.860000
KRAS	3845	broad.mit.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	C	T	rs121913529		TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	KRAS_deep			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr12:25398284C>T	ENST00000256078.4	-	2	98	c.35G>A	c.(34-36)gGt>gAt	p.G12D	KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)		GCCTACGCCACCAGCTCCAAC	0.348000	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		pancreatic, colorectal, lung, thyroid, AML, others				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)			Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		L, E, M, O	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)						SO:0001583	missense	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	ENST00000256078.4	1	1	hg19	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.409094	0.83340	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.85919	0.5809	M	0.91818	3.245	0.80722	D	1	B;P	0.35714	0.385;0.517	B;B	0.41619	0.257;0.361	D	0.87870	0.2670	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	D	12	ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D	ENSP00000256078:G12D	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		TCGA-IB-AAUO-01A-12D-A38G-08	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	1	0	1	51	227	0	107	1	4.524297e-01	2	6	0	107	2	1	1	59	312	0	333	2	1	1.000000	50	221	0	107	2	1	1	1697	6340	0	107	2	-20.000000	1	1	121404	2	44	1	0	0	0	2.013098	0	0.380000	1.860000	0.365534	0.930000	0.720000	1.000000	1.000000	0.922427	0.930000	1	0.820000	1.000000
ACSM4	341392	broad.mit.edu	37	12	7469871	7469871	+	Silent	SNP	C	C	T			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr12:7469871C>T	ENST00000399422.4	+	4	807	c.759C>T	c.(757-759)tgC>tgT	p.C253C		NM_001080454.1	NP_001073923.1	P0C7M7	ACSM4_HUMAN	acyl-CoA synthetase medium-chain family member 4			21					TCACCCTCTGCGGAAGGTAGG	0.463000																								0							SO:0001819	synonymous_variant			ENST00000399422.4	0	1	hg19	CCDS44825.1																																																																																				TCGA-IB-AAUO-01A-12D-A38G-08	ACSM4-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000337866.2	0	0	0	7	26	0	9		0	0	0	0	9	2		0	0	0	0	0	2	1	0.984761	7	26	0	9	2		0	0	0	0	9	2	-15.874150	1	1	116028	9	32	1	0	0	0	2.013098	0	0.380000	1.860000	0.365534	0.990000	0.520000	1.000000	1.000000	0.916676	0.990000	1	0.760000	1.000000
SEL1L	6400	broad.mit.edu	37	14	81950645	81950645	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr14:81950645G>A	ENST00000336735.4	-	19	2086	c.1970C>T	c.(1969-1971)gCt>gTt	p.A657V		NM_005065.5	NP_005056.3	Q9UBV2	SE1L1_HUMAN	sel-1 suppressor of lin-12-like (C. elegans)			28					CTGCTCAGAAGCCAGACGGTA	0.428000																								0							SO:0001583	missense			ENST00000336735.4	1	1	hg19	CCDS9876.1	.	.	.	.	.	.	.	.	.	.	G	36	5.610409	0.96637	.	.	ENSG00000071537	ENST00000336735;ENST00000261258	T	0.65178	-0.14	5.92	5.92	0.95590	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	D	0.85191	0.5640	M	0.92219	3.285	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87620	0.2509	10	0.87932	D	0	.	20.3167	0.98654	0.0:0.0:1.0:0.0	.	657	Q9UBV2	SE1L1_HUMAN	V	657;18	ENSP00000337053:A657V	ENSP00000261258:A18V	A	-	2	0	SEL1L	81020398	1.000000	0.71417	0.916000	0.36221	0.980000	0.70556	9.335000	0.96500	2.809000	0.96659	0.557000	0.71058	GCT		TCGA-IB-AAUO-01A-12D-A38G-08	SEL1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413325.1	0	0	0	46	1233	0	514	0	6.003873e-02	1	10	0	514	2		0	0	0	0	0	2	1	1.000000	45	1208	0	512	2		0	0	0	0	514	2	-3.687732	1	1	0	0		1	0	0	0	2.033170	0	0.380000	1.860000	0.375252	0.180000	0.130000	0.250000	0.190000	0.191390	0.180000	0	0.150000	0.220000
CHGA	1113	broad.mit.edu	37	14	93396099	93396099	+	Missense_Mutation	SNP	C	C	A	rs150929444	byFrequency	TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr14:93396099C>A	ENST00000216492.5	+	5	574	c.294C>A	c.(292-294)agC>agA	p.S98R	CHGA_ENST00000334654.4_Missense_Mutation_p.S98R|CHGA_ENST00000553866.1_3'UTR	NM_001275.3	NP_001266.1	P10645	CMGA_HUMAN	chromogranin A (parathyroid secretory protein 1)			8		all_cancers(154;0.0843)			AGAAACACAGCGGTTTTGAAG	0.542000													Colon(31;154 822 45066 49155)|NSCLC(28;804 1157 13734 25204)											0							SO:0001583	missense			ENST00000216492.5	1	1	hg19	CCDS9906.1	.	.	.	.	.	.	.	.	.	.	C	8.843	0.942786	0.18281	.	.	ENSG00000100604	ENST00000216492;ENST00000334654	T;T	0.07021	4.56;3.23	4.78	1.53	0.23141	.	0.334049	0.33382	N	0.004968	T	0.09468	0.0233	L	0.53249	1.67	0.09310	N	0.999998	B;P	0.36162	0.057;0.54	B;B	0.40677	0.028;0.337	T	0.14392	-1.0474	10	0.41790	T	0.15	-6.3264	5.9182	0.19067	0.1371:0.545:0.0:0.3179	.	98;98	G5E968;P10645	.;CMGA_HUMAN	R	98	ENSP00000216492:S98R;ENSP00000334023:S98R	ENSP00000216492:S98R	S	+	3	2	CHGA	92465852	0.008000	0.16893	0.012000	0.15200	0.675000	0.39556	0.091000	0.15046	0.466000	0.27193	-0.221000	0.12465	AGC		TCGA-IB-AAUO-01A-12D-A38G-08	CHGA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412411.1	1	0	0	19	197	0	77	0	4.318480e-01	0	16	0	77	2		0	0	0	0	0	2	1	0.999991	19	193	0	77	2		0	0	0	0	77	2	-3.017770	1	1	0	0		1	0	0	0	2.033170	0	0.380000	1.860000	0.375252	0.460000	0.290000	0.670000	0.450000	0.475512	0.460000	0	0.360000	0.570000
PLCB2	5330	broad.mit.edu	37	15	40581489	40581489	+	Missense_Mutation	SNP	C	C	G			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr15:40581489C>G	ENST00000260402.3	-	31	3587	c.3338G>C	c.(3337-3339)cGg>cCg	p.R1113P	PLCB2_ENST00000557821.1_Missense_Mutation_p.R1109P|PLCB2_ENST00000456256.2_Missense_Mutation_p.R1098P	NM_001284297.1|NM_004573.2	NP_001271226.1|NP_004564.2	Q00722	PLCB2_HUMAN	phospholipase C, beta 2			39		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)			TTCCATCTCCCGTATCTGTTC	0.582000																								0							SO:0001583	missense			ENST00000260402.3	1	1	hg19	CCDS42020.1	.	.	.	.	.	.	.	.	.	.	C	15.50	2.852673	0.51270	.	.	ENSG00000137841	ENST00000260402;ENST00000456256	T;T	0.45668	0.89;0.89	5.05	-0.161	0.13371	PLC-beta, C-terminal (1);	0.561271	0.17537	N	0.170673	T	0.33177	0.0854	N	0.22421	0.69	0.80722	D	1	P;B;P	0.37122	0.523;0.451;0.583	P;B;P	0.46299	0.509;0.333;0.511	T	0.06180	-1.0841	10	0.33141	T	0.24	.	8.7765	0.34765	0.0:0.4418:0.0:0.5582	.	1098;1109;1113	B9EGH5;Q00722-2;Q00722	.;.;PLCB2_HUMAN	P	1113;1098	ENSP00000260402:R1113P;ENSP00000411991:R1098P	ENSP00000260402:R1113P	R	-	2	0	PLCB2	38368781	0.889000	0.30405	0.991000	0.47740	0.983000	0.72400	-0.086000	0.11233	-0.207000	0.10187	0.561000	0.74099	CGG		TCGA-IB-AAUO-01A-12D-A38G-08	PLCB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418430.1	0	0	0	12	392	0	173	0	8.674163e-01	0	118	0	173	2		0	0	0	0	0	2	1	0.999005	11	383	0	170	2		0	0	0	0	173	2	-2.211676	0	1	0	0		1	1	2	3	2.055270	0	0.380000	1.860000	0.381176	0.150000	0.080000	0.270000	0.160000	0.168167	0.150000	0	0.110000	0.210000
DUOX1	53905	broad.mit.edu	37	15	45433521	45433521	+	Nonsense_Mutation	SNP	C	C	T			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr15:45433521C>T	ENST00000321429.4	+	15	2004	c.1597C>T	c.(1597-1599)Cga>Tga	p.R533*	DUOX1_ENST00000389037.3_Nonsense_Mutation_p.R533*|DUOX1_ENST00000561166.1_Nonsense_Mutation_p.R179*	NM_017434.3	NP_059130.2	Q9NRD9	DUOX1_HUMAN	dual oxidase 1			57		all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)			TGAAGAAATCCGAAATACCAC	0.527000																								0							SO:0001587	stop_gained			ENST00000321429.4	0	1	hg19	CCDS32221.1	.	.	.	.	.	.	.	.	.	.	C	37	6.140306	0.97320	.	.	ENSG00000137857	ENST00000431588;ENST00000321429;ENST00000389037	.	.	.	4.53	2.15	0.27550	.	0.095326	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-15.0907	10.5604	0.45142	0.4411:0.5589:0.0:0.0	.	.	.	.	X	533	.	ENSP00000317997:R533X	R	+	1	2	DUOX1	43220813	1.000000	0.71417	1.000000	0.80357	0.027000	0.11550	2.572000	0.45999	0.336000	0.23639	-0.271000	0.10264	CGA		TCGA-IB-AAUO-01A-12D-A38G-08	DUOX1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416251.1	0	0	0	11	274	0	120	1	7.740379e-02	2	9	0	120	2		0	0	0	0	0	2	1	0.998258	11	269	0	118	2		0	0	0	0	120	2	-2.927638	1	1	121412	3	37	1	1	2	3	2.055270	0	0.380000	1.860000	0.381176	0.200000	0.100000	0.360000	0.200000	0.219229	0.200000	0	0.150000	0.280000
IDH2	3418	broad.mit.edu	37	15	90630448	90630448	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr15:90630448C>A	ENST00000330062.3	-	7	976	c.863G>T	c.(862-864)cGg>cTg	p.R288L	IDH2_ENST00000539790.1_Missense_Mutation_p.R158L|IDH2_ENST00000540499.2_Missense_Mutation_p.R236L|IDH2_ENST00000559482.1_Missense_Mutation_p.R179L	NM_002168.2	NP_002159.2	P48735	IDHP_HUMAN	isocitrate dehydrogenase 2 (NADP+), mitochondrial			1109	Melanoma(11;0.00551)|Lung NSC(78;0.0196)|all_lung(78;0.04)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.106)		ATCAATGAGCCGGTGCTCATA	0.527000			M		GBM						OREG0023466	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)			Dom	yes		15	15q26.1	3418	socitrate dehydrogenase 2 (NADP+), mitochondrial 		M	0							SO:0001583	missense			ENST00000330062.3	0	1	hg19	CCDS10359.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.476860	0.84640	.	.	ENSG00000182054	ENST00000330062;ENST00000539790;ENST00000540499	T;T;T	0.76316	-1.01;-1.01;-1.01	5.73	5.73	0.89815	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.90995	0.7168	M	0.92077	3.27	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.995;1.0	D	0.92661	0.6141	10	0.87932	D	0	.	17.3795	0.87401	0.0:1.0:0.0:0.0	.	288;288	Q53GL5;P48735	.;IDHP_HUMAN	L	288;158;236	ENSP00000331897:R288L;ENSP00000438457:R158L;ENSP00000446147:R236L	ENSP00000331897:R288L	R	-	2	0	IDH2	88431452	1.000000	0.71417	1.000000	0.80357	0.401000	0.30781	7.786000	0.85741	2.709000	0.92574	0.491000	0.48974	CGG		TCGA-IB-AAUO-01A-12D-A38G-08	IDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313426.1	0	0	0	6	235	0	113	1	9.815272e-01	10	281	0	113	2		0	0	0	0	0	2	1	0.964155	6	232	0	113	2		0	0	0	0	113	2	-3.142651	1	1	0	0		1	1	2	3	2.061161	0	0.380000	1.860000	0.381176	0.130000	0.050000	0.280000	0.130000	0.150883	0.130000	0	0.090000	0.210000
WWP2	11060	broad.mit.edu	37	16	69969883	69969883	+	Nonsense_Mutation	SNP	G	G	A			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr16:69969883G>A	ENST00000359154.2	+	18	2071	c.1970G>A	c.(1969-1971)tGg>tAg	p.W657*	MIR140_ENST00000385282.1_RNA|WWP2_ENST00000542271.1_Nonsense_Mutation_p.W541*|WWP2_ENST00000356003.2_Nonsense_Mutation_p.W657*|WWP2_ENST00000568684.1_Nonsense_Mutation_p.W218*|WWP2_ENST00000448661.1_Nonsense_Mutation_p.W657*|WWP2_ENST00000544162.1_3'UTR	NM_001270454.1|NM_007014.4	NP_001257383.1|NP_008945.2	O00308	WWP2_HUMAN	WW domain containing E3 ubiquitin protein ligase 2			42					TCCATTGTCTGGATCAAGTGA	0.542000																								0							SO:0001587	stop_gained			ENST00000359154.2	0	1	hg19	CCDS10885.1	.	.	.	.	.	.	.	.	.	.	G	39	7.554393	0.98355	.	.	ENSG00000198373	ENST00000359154;ENST00000545099;ENST00000448661;ENST00000356003;ENST00000544162;ENST00000542271	.	.	.	5.7	5.7	0.88788	.	0.105878	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.843	0.96697	0.0:0.0:1.0:0.0	.	.	.	.	X	657;218;657;657;544;541	.	.	W	+	2	0	WWP2	68527384	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.869000	0.99810	2.679000	0.91253	0.655000	0.94253	TGG		TCGA-IB-AAUO-01A-12D-A38G-08	WWP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268954.1	1	0	0	82	348	0	157	1	9.988206e-01	7	38	0	157	2	1	1	85	333	0	358	2	1	1.000000	82	344	0	152	2		0	0	0	0	157	2	-2.865302	1	1	0	0		1	1	2	3	2.056115	0	0.380000	1.860000	0.381176	0.990000	0.810000	1.000000	1.000000	0.964804	0.990000	1	0.900000	1.000000
ADAMTS18	170692	broad.mit.edu	37	16	77317969	77317969	+	Splice_Site	SNP	C	C	G			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr16:77317969C>G	ENST00000282849.5	-	23	3969		c.e23-1		RP11-538I12.3_ENST00000561672.1_RNA	NM_199355.2	NP_955387.1	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 18			118					GATGGATCCTCTAAAATAAGA	0.398000																								0							SO:0001630	splice_region_variant			ENST00000282849.5	1	1	hg19	CCDS10926.1	.	.	.	.	.	.	.	.	.	.	C	19.80	3.894540	0.72639	.	.	ENSG00000140873	ENST00000282849	.	.	.	5.93	5.93	0.95920	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.3291	0.94278	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ADAMTS18	75875470	1.000000	0.71417	0.997000	0.53966	0.888000	0.51559	7.188000	0.77739	2.814000	0.96858	0.655000	0.94253	.		TCGA-IB-AAUO-01A-12D-A38G-08	ADAMTS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269037.1	1	0	0	35	238	0	117		0	0	0	0	117	2		0	0	0	0	0	2	1	1.000000	35	236	0	117	2		0	0	0	0	117	2	-2.842164	1	1	121408	1	30	1	1	2	3	2.056115	0	0.380000	1.860000	0.381176	0.670000	0.480000	0.910000	0.670000	0.686066	0.670000	0	0.570000	0.790000
PRPF8	10594	broad.mit.edu	37	17	1564593	1564593	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr17:1564593C>T	ENST00000572621.1	-	26	4575	c.4310G>A	c.(4309-4311)cGt>cAt	p.R1437H	PRPF8_ENST00000304992.6_Missense_Mutation_p.R1437H			Q6P2Q9	PRP8_HUMAN	pre-mRNA processing factor 8			77					AGTTCTGACACGCCAGCCCTT	0.483000																								0							SO:0001583	missense			ENST00000572621.1	1	0	hg19	CCDS11010.1	.	.	.	.	.	.	.	.	.	.	c	29.7	5.028120	0.93518	.	.	ENSG00000174231	ENST00000304992	D	0.85484	-1.99	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	D	0.94971	0.8373	M	0.93283	3.4	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95043	0.8180	10	0.87932	D	0	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	1437	Q6P2Q9	PRP8_HUMAN	H	1437	ENSP00000304350:R1437H	ENSP00000304350:R1437H	R	-	2	0	PRPF8	1511343	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.792000	0.85828	2.941000	0.99782	0.655000	0.94253	CGT		TCGA-IB-AAUO-01A-12D-A38G-08	PRPF8-002	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438412.2	0	0	1	87	473	2	239	0	9.811253e-01	0	47	2	239	3		0	0	0	0	0	2	1	1.000000	87	465	2	239	13		0	0	0	2	239	2	-20.000000	1	0	0	0		1	0	1	1	2.050195	0	0.380000	1.860000	0.378820	0.810000	0.660000	0.970000	0.820000	0.819632	0.810000	0	0.730000	0.900000
SLC47A1	55244	broad.mit.edu	37	17	19458922	19458922	+	Missense_Mutation	SNP	A	A	G			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr17:19458922A>G	ENST00000270570.4	+	8	744	c.658A>G	c.(658-660)Aac>Gac	p.N220D	SLC47A1_ENST00000395585.1_Missense_Mutation_p.N220D|SNORA59B_ENST00000458926.1_RNA|SLC47A1_ENST00000542886.1_Missense_Mutation_p.K187R|SLC47A1_ENST00000457293.1_Missense_Mutation_p.N220D|SLC47A1_ENST00000575023.1_Intron|SLC47A1_ENST00000436810.2_Missense_Mutation_p.N197D|SLC47A1_ENST00000571335.1_Intron	NM_018242.2	NP_060712.2	Q96FL8	S47A1_HUMAN	solute carrier family 47 (multidrug and toxin extrusion), member 1			23	all_cancers(12;2.49e-05)|all_epithelial(12;0.00263)|Hepatocellular(7;0.00345)			Aciclovir(DB00787)|Bromodiphenhydramine(DB01237)|Cephalexin(DB00567)|Cimetidine(DB00501)|Metformin(DB00331)|Sirolimus(DB00877)	TGCACTGGCAAACTTGATTTC	0.527000																								0							SO:0001583	missense			ENST00000270570.4	1	1	hg19	CCDS11209.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.34|14.34	2.506537|2.506537	0.44558|0.44558	.|.	.|.	ENSG00000142494|ENSG00000142494	ENST00000542886|ENST00000436810;ENST00000270570;ENST00000457293;ENST00000395585	.|T;T;T;T	.|0.32272	.|1.51;1.46;1.46;1.46	5.34|5.34	5.34|5.34	0.76211|0.76211	.|.	.|0.082064	.|0.85682	.|D	.|0.000000	T|T	0.50257|0.50257	0.1605|0.1605	H|H	0.95260|0.95260	3.645|3.645	0.32301|0.32301	N|N	0.565074|0.565074	.|B;B;B	.|0.33238	.|0.403;0.059;0.04	.|B;B;B	.|0.34873	.|0.191;0.067;0.078	T|T	0.69109|0.69109	-0.5232|-0.5232	6|10	0.14656|0.66056	T|D	0.56|0.02	-5.1336|-5.1336	14.5405|14.5405	0.67990|0.67990	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|197;220;220	.|E7EX57;Q96FL8;Q96FL8-3	.|.;S47A1_HUMAN;.	R|D	187|197;220;220;220	.|ENSP00000407155:N197D;ENSP00000270570:N220D;ENSP00000415586:N220D;ENSP00000378951:N220D	ENSP00000440435:K187R|ENSP00000270570:N220D	K|N	+|+	2|1	0|0	SLC47A1|SLC47A1	19399514|19399514	1.000000|1.000000	0.71417|0.71417	0.729000|0.729000	0.30791|0.30791	0.302000|0.302000	0.27658|0.27658	6.624000|6.624000	0.74243|0.74243	2.036000|2.036000	0.60181|0.60181	0.529000|0.529000	0.55759|0.55759	AAA|AAC		TCGA-IB-AAUO-01A-12D-A38G-08	SLC47A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132250.1	1	0	1	71	200	0	134		0	0	0	0	134	2		0	0	0	0	0	2	1	1.000000	69	195	0	130	2		0	0	0	0	134	2	-20.000000	1	1	0	0		1	0	1	1	1.676844	1	0.380000	1.860000	0.234568	0.950000	0.820000	1.000000	0.990000	0.948216	0.950000	1	0.890000	0.990000
KRT24	192666	broad.mit.edu	37	17	38857493	38857493	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr17:38857493G>A	ENST00000264651.2	-	3	810	c.754C>T	c.(754-756)Cgg>Tgg	p.R252W		NM_019016.2	NP_061889.2	Q2M2I5	K1C24_HUMAN	keratin 24			29		Breast(137;0.00526)			AGGACTTTCCGCAGGCCATTG	0.547000													GBM(61;380 1051 14702 23642 31441)											0							SO:0001583	missense			ENST00000264651.2	1	1	hg19	CCDS11372.1	.	.	.	.	.	.	.	.	.	.	G	13.59	2.282977	0.40394	.	.	ENSG00000167916	ENST00000264651	D	0.92545	-3.06	5.82	1.51	0.23008	Filament (1);	.	.	.	.	D	0.97145	0.9067	H	0.96175	3.78	0.38355	D	0.944446	D	0.89917	1.0	D	0.78314	0.991	D	0.98696	1.0698	9	0.87932	D	0	.	15.8909	0.79296	0.0:0.0:0.5363:0.4637	.	252	Q2M2I5	K1C24_HUMAN	W	252	ENSP00000264651:R252W	ENSP00000264651:R252W	R	-	1	2	KRT24	36111019	0.000000	0.05858	0.001000	0.08648	0.108000	0.19459	0.336000	0.19823	0.078000	0.16900	-1.227000	0.01581	CGG		TCGA-IB-AAUO-01A-12D-A38G-08	KRT24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257217.1	0	0	0	11	268	0	86		0	0	0	0	86	2		0	0	0	0	0	2	1	0.998221	11	262	0	83	2		0	0	0	0	86	2	-3.186940	1	1	0	0		1	1	2	3	2.100635	0	0.380000	1.860000	0.388138	0.220000	0.110000	1.000000	0.210000	0.269596	0.220000	0	0.160000	0.310000
VPS25	84313	broad.mit.edu	37	17	40925498	40925498	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08			C	A	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr17:40925498C>A	ENST00000253794.2	+	1	45	c.5C>A	c.(4-6)gCg>gAg	p.A2E		NM_032353.2	NP_115729.1	Q9BRG1	VPS25_HUMAN	vacuolar protein sorting 25 homolog (S. cerevisiae)			5		Breast(137;0.00104)			ACTACGATGGCGATGAGTTTC	0.612000																								0							SO:0001583	missense			ENST00000253794.2	1	1	hg19	CCDS11438.1	.	.	.	.	.	.	.	.	.	.	C	17.88	3.496557	0.64186	.	.	ENSG00000131475	ENST00000253794	T	0.47869	0.83	4.95	4.95	0.65309	.	0.067954	0.56097	D	0.000024	T	0.35799	0.0944	N	0.24115	0.695	0.48341	D	0.999631	B	0.11235	0.004	B	0.11329	0.006	T	0.19811	-1.0294	10	0.62326	D	0.03	-16.8888	13.689	0.62533	0.0:1.0:0.0:0.0	.	2	Q9BRG1	VPS25_HUMAN	E	2	ENSP00000253794:A2E	ENSP00000253794:A2E	A	+	2	0	VPS25	38179024	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.300000	0.43620	2.292000	0.77174	0.491000	0.48974	GCG		TCGA-IB-AAUO-01A-12D-A38G-08	VPS25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452383.1	1	0	1	89	554	0	251	1	9.999971e-01	27	86	0	251	2		0	0	0	0	0	2	1	1.000000	86	547	0	249	2		0	0	0	0	251	2	-20.000000	1	1	121412	1	27	1	1	2	3	2.100635	0	0.380000	1.860000	0.388138	0.740000	0.600000	1.000000	0.740000	0.756694	0.740000	0	0.660000	0.830000
BRCA1	672	broad.mit.edu	37	17	41245612	41245612	+	Missense_Mutation	SNP	T	T	C			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08			T	C	T	T		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr17:41245612T>C	ENST00000357654.3	-	10	2054	c.1936A>G	c.(1936-1938)Agc>Ggc	p.S646G	BRCA1_ENST00000346315.3_Missense_Mutation_p.S646G|BRCA1_ENST00000493795.1_Missense_Mutation_p.S599G|BRCA1_ENST00000468300.1_Intron|BRCA1_ENST00000351666.3_Intron|BRCA1_ENST00000471181.2_Missense_Mutation_p.S646G|BRCA1_ENST00000309486.4_Missense_Mutation_p.S350G|BRCA1_ENST00000591849.1_Intron|BRCA1_ENST00000591534.1_Intron|BRCA1_ENST00000586385.1_Intron|BRCA1_ENST00000352993.3_Intron|BRCA1_ENST00000354071.3_Missense_Mutation_p.S646G|BRCA1_ENST00000491747.2_Intron	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset			120		Breast(137;0.000717)			TCTTCACTGCTAGAACAACTA	0.408000			D, Mis, N, F, S		ovarian	breast, ovarian		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)				yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	familial breast/ovarian cancer gene 1		E	0							SO:0001583	missense	Familial Cancer Database		ENST00000357654.3	1	1	hg19	CCDS11453.1	.	.	.	.	.	.	.	.	.	.	T	14.99	2.701528	0.48307	.	.	ENSG00000012048	ENST00000357654;ENST00000412061;ENST00000354071;ENST00000346315;ENST00000309486;ENST00000471181;ENST00000493795;ENST00000470026;ENST00000477152	D;D;D;D;D;D;D;D	0.99032	-3.64;-3.72;-3.69;-3.57;-3.66;-3.78;-3.99;-5.35	5.15	5.15	0.70609	.	0.000000	0.64402	D	0.000002	D	0.99318	0.9761	M	0.93594	3.435	0.32644	N	0.52031	D;D;P;P;D;P	0.89917	1.0;1.0;0.751;0.849;0.984;0.808	D;D;B;P;P;P	0.71414	0.973;0.973;0.318;0.561;0.799;0.614	D	0.99886	1.1122	10	0.72032	D	0.01	-12.2956	9.02	0.36193	0.0:0.0823:0.0:0.9177	.	646;605;646;646;646;646	E7EMP0;E7ERL4;Q5YLB2;E9PFC7;P38398;P38398-2	.;.;.;.;BRCA1_HUMAN;.	G	646;646;646;646;350;646;599;646;620	ENSP00000350283:S646G;ENSP00000326002:S646G;ENSP00000246907:S646G;ENSP00000310938:S350G;ENSP00000418960:S646G;ENSP00000418775:S599G;ENSP00000419274:S646G;ENSP00000419988:S620G	ENSP00000310938:S350G	S	-	1	0	BRCA1	38499138	1.000000	0.71417	0.987000	0.45799	0.844000	0.47949	3.457000	0.53007	2.170000	0.68504	0.459000	0.35465	AGC		TCGA-IB-AAUO-01A-12D-A38G-08	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348798.2	1	0	1	57	514	0	203	0	0	0	1	0	203	2	1	1	28	295	0	240	2	1	1.000000	56	503	0	202	2		0	0	0	0	203	2	-17.872030	1	1	0	0		1	1	2	3	2.100635	0	0.380000	1.860000	0.388138	0.530000	0.400000	1.000000	0.540000	0.564082	0.530000	0	0.460000	0.620000
EFTUD2	9343	broad.mit.edu	37	17	42928694	42928694	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08			G	T	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr17:42928694G>T	ENST00000426333.2	-	28	3164	c.2867C>A	c.(2866-2868)cCt>cAt	p.P956H	EFTUD2_ENST00000591382.1_Missense_Mutation_p.P956H|EFTUD2_ENST00000402521.3_Missense_Mutation_p.P921H|EFTUD2_ENST00000592576.1_Missense_Mutation_p.P946H	NM_001142605.1|NM_001258354.1|NM_004247.3	NP_001136077.1|NP_001245283.1|NP_004238.3	Q15029	U5S1_HUMAN	elongation factor Tu GTP binding domain containing 2			32		Prostate(33;0.109)			CAGCAACATAGGATCATCGAA	0.522000													Ovarian(10;65 485 10258 29980 30707)											0							SO:0001583	missense			ENST00000426333.2	1	1	hg19	CCDS11489.1	.	.	.	.	.	.	.	.	.	.	G	33	5.195069	0.94960	.	.	ENSG00000108883	ENST00000426333;ENST00000262414;ENST00000402521	T;T	0.71103	-0.53;-0.54	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	D	0.86293	0.5898	M	0.87758	2.905	0.80722	D	1	D;D	0.71674	0.998;0.998	D;D	0.65773	0.938;0.938	D	0.87972	0.2737	10	0.72032	D	0.01	-13.7718	19.7014	0.96054	0.0:0.0:1.0:0.0	.	946;956	B4DMC0;Q15029	.;U5S1_HUMAN	H	956;946;921	ENSP00000392094:P956H;ENSP00000385873:P921H	ENSP00000262414:P946H	P	-	2	0	EFTUD2	40284220	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	9.277000	0.95755	2.660000	0.90430	0.563000	0.77884	CCT		TCGA-IB-AAUO-01A-12D-A38G-08	EFTUD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448672.1	1	0	1	85	520	0	234	1	1	70	262	0	234	2		0	0	0	0	0	2	1	1.000000	85	504	0	231	2		0	0	0	0	234	2	-3.318829	1	1	0	0		1	1	2	3	2.100635	0	0.380000	1.860000	0.388138	0.750000	0.600000	1.000000	0.750000	0.767346	0.750000	0	0.670000	0.850000
LPO	4025	broad.mit.edu	37	17	56345237	56345237	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr17:56345237C>T	ENST00000262290.4	+	13	2337	c.2021C>T	c.(2020-2022)aCc>aTc	p.T674I	LPO_ENST00000543544.1_Missense_Mutation_p.T615I|LPO_ENST00000582328.1_Missense_Mutation_p.T591I|LPO_ENST00000421678.2_Missense_Mutation_p.T591I	NM_006151.2	NP_006142.1	P22079	PERL_HUMAN	lactoperoxidase			30					TGTGACAACACCCGCATCACC	0.557000																								0							SO:0001583	missense			ENST00000262290.4	1	1	hg19	CCDS32689.1	.	.	.	.	.	.	.	.	.	.	C	29.3	4.992253	0.93167	.	.	ENSG00000167419	ENST00000262290;ENST00000421678;ENST00000543544;ENST00000389576	T;T;T	0.71817	-0.6;-0.6;-0.6	5.5	5.5	0.81552	.	0.046101	0.85682	D	0.000000	D	0.86994	0.6067	M	0.88640	2.97	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	D	0.89017	0.3432	10	0.72032	D	0.01	-33.3127	17.9786	0.89133	0.0:1.0:0.0:0.0	.	591;674	E7EMJ3;P22079	.;PERL_HUMAN	I	674;591;615;419	ENSP00000262290:T674I;ENSP00000400245:T591I;ENSP00000445344:T615I	ENSP00000262290:T674I	T	+	2	0	LPO	53700236	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.267000	0.78462	2.591000	0.87537	0.655000	0.94253	ACC		TCGA-IB-AAUO-01A-12D-A38G-08	LPO-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443961.1	1	0	1	68	284	0	148		0	0	0	0	148	2		0	0	0	0	0	2	1	1.000000	66	279	0	147	2		0	0	0	0	148	2	-20.000000	1	1	0	0		1	1	2	3	2.114584	0	0.380000	1.860000	0.389283	0.990000	0.820000	1.000000	1.000000	0.973526	0.990000	1	0.920000	1.000000
WSCD1	23302	broad.mit.edu	37	17	6023840	6023840	+	Silent	SNP	G	G	A			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr17:6023840G>A	ENST00000574946.1	+	9	1977	c.1587G>A	c.(1585-1587)cgG>cgA	p.R529R	WSCD1_ENST00000573634.1_Silent_p.R413R|WSCD1_ENST00000539421.1_Silent_p.R529R|WSCD1_ENST00000317744.5_Silent_p.R529R|WSCD1_ENST00000574232.1_Silent_p.R529R			Q658N2	WSCD1_HUMAN	WSC domain containing 1			35					GCAGCTTCCGGCGGCGCGGCC	0.647000																								0							SO:0001819	synonymous_variant			ENST00000574946.1	1	1	hg19	CCDS32538.1																																																																																				TCGA-IB-AAUO-01A-12D-A38G-08	WSCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438965.4	1	0	1	65	173	0	102		0	0	0	0	102	2		0	0	0	0	0	2	1	1.000000	64	166	0	98	2		0	0	0	0	102	2	-20.000000	1	1	0	0		1	0	1	1	1.701426	1	0.380000	1.860000	0.246933	0.990000	0.870000	1.000000	1.000000	0.982674	0.990000	1	0.950000	1.000000
ENPP7	339221	broad.mit.edu	37	17	77709028	77709028	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr17:77709028G>A	ENST00000328313.5	+	3	807	c.586G>A	c.(586-588)Ggg>Agg	p.G196R		NM_178543.3	NP_848638.3			ectonucleotide pyrophosphatase/phosphodiesterase 7			34			OV - Ovarian serous cystadenocarcinoma(97;0.016)|BRCA - Breast invasive adenocarcinoma(99;0.0224)		ACTCTACTTCGGGGAGCCGGA	0.627000																								0							SO:0001583	missense			ENST00000328313.5	1	1	hg19	CCDS11763.1	.	.	.	.	.	.	.	.	.	.	G	16.64	3.179033	0.57692	.	.	ENSG00000182156	ENST00000328313	T	0.71698	-0.59	4.75	3.76	0.43208	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.058821	0.64402	D	0.000002	T	0.72350	0.3449	L	0.60845	1.875	0.80722	D	1	D	0.58620	0.983	P	0.49451	0.611	T	0.72950	-0.4136	10	0.42905	T	0.14	-33.0178	14.1159	0.65154	0.0:0.0:0.8483:0.1517	.	196	Q6UWV6	ENPP7_HUMAN	R	196	ENSP00000332656:G196R	ENSP00000332656:G196R	G	+	1	0	ENPP7	75323623	1.000000	0.71417	0.978000	0.43139	0.346000	0.29079	7.909000	0.87444	0.962000	0.38057	0.591000	0.81541	GGG		TCGA-IB-AAUO-01A-12D-A38G-08	ENPP7-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437038.1	0	0	0	5	159	0	66		0	0	0	0	66	2		0	0	0	0	0	2	1	0.934398	5	155	0	65	2		0	0	0	0	66	2	-3.522876	1	1	0	0		1	1	2	3	2.114584	0	0.380000	1.860000	0.389283	0.180000	0.060000	1.000000	0.160000	0.243320	0.180000	0	0.110000	0.290000
SERPINB10	5273	broad.mit.edu	37	18	61602106	61602106	+	Missense_Mutation	SNP	A	A	C			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr18:61602106A>C	ENST00000238508.3	+	8	883	c.824A>C	c.(823-825)gAg>gCg	p.E275A	AC009802.1_ENST00000599868.1_Intron	NM_005024.1	NP_005015.1	P48595	SPB10_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 10			24		Esophageal squamous(42;0.131)			AAGCTGAATGAGTGGACCAGT	0.438000																								0							SO:0001583	missense			ENST00000238508.3	1	1	hg19	CCDS11990.1	.	.	.	.	.	.	.	.	.	.	A	4.321	0.059004	0.08339	.	.	ENSG00000242550	ENST00000238508	D	0.84589	-1.87	5.53	3.07	0.35406	Serpin domain (3);	0.291996	0.37623	N	0.002012	T	0.75649	0.3878	L	0.43701	1.375	0.36153	D	0.847574	B	0.28419	0.211	B	0.28465	0.09	T	0.66976	-0.5787	10	0.12766	T	0.61	.	7.9103	0.29787	0.7907:0.1376:0.0717:0.0	.	275	P48595	SPB10_HUMAN	A	275	ENSP00000238508:E275A	ENSP00000238508:E275A	E	+	2	0	SERPINB10	59753086	0.078000	0.21339	0.629000	0.29254	0.699000	0.40488	1.977000	0.40589	0.446000	0.26666	0.533000	0.62120	GAG		TCGA-IB-AAUO-01A-12D-A38G-08	SERPINB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134012.3	1	0	1	52	239	0	120		0	0	0	0	120	2		0	0	0	0	0	2	1	1.000000	51	232	0	120	2		0	0	0	0	120	2	-20.000000	1	1	0	0		1	0	0	0	2.047911	0	0.380000	1.860000	0.377635	0.930000	0.710000	1.000000	1.000000	0.918748	0.930000	1	0.820000	1.000000
ZNF653	115950	broad.mit.edu	37	19	11596490	11596490	+	Silent	SNP	C	C	T			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr19:11596490C>T	ENST00000293771.5	-	7	1687	c.1551G>A	c.(1549-1551)cgG>cgA	p.R517R	CTC-398G3.6_ENST00000585656.1_Intron	NM_138783.3	NP_620138.2	Q96CK0	ZN653_HUMAN	zinc finger protein 653			17					TGATCATGTGCCGCCGCAGGT	0.592000													Pancreas(83;980 1446 4542 6441 43352)											0							SO:0001819	synonymous_variant			ENST00000293771.5	0	1	hg19	CCDS12261.1																																																																																				TCGA-IB-AAUO-01A-12D-A38G-08	ZNF653-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458836.2	0	0	0	6	299	0	133	0	2.334933e-01	0	40	0	133	2		0	0	0	0	0	2	1	0.961623	5	290	0	133	2		0	0	0	0	133	2	-2.527964	1	1	0	0		1	1	2	3	2.086690	0	0.380000	1.860000	0.385835	0.110000	0.040000	1.000000	0.100000	0.153914	0.110000	0	0.070000	0.170000
DAPK3	1613	broad.mit.edu	37	19	3964300	3964300	+	Silent	SNP	C	C	T			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr19:3964300C>T	ENST00000545797.2	-	4	738	c.495G>A	c.(493-495)gcG>gcA	p.A165A	MIR637_ENST00000385000.1_RNA|DAPK3_ENST00000301264.3_Silent_p.A165A			O43293	DAPK3_HUMAN	death-associated protein kinase 3			21		Hepatocellular(1079;0.137)			CGATCTTGTGCGCGATGCCGA	0.622000																								0							SO:0001819	synonymous_variant			ENST00000545797.2	0	1	hg19	CCDS12116.1																																																																																				TCGA-IB-AAUO-01A-12D-A38G-08	DAPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457817.2	0	0	0	4	170	0	49	0	9.785343e-01	1	325	0	49	2		0	0	0	0	0	2	1	0.884336	4	165	0	46	2		0	0	0	0	49	2	-2.691923	1	1	121392	6	30	1	1	2	3	2.086690	0	0.380000	1.860000	0.385835	0.130000	0.040000	1.000000	0.120000	0.181860	0.130000	0	0.080000	0.230000
PSG3	5671	broad.mit.edu	37	19	43237204	43237204	+	Silent	SNP	G	G	T			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr19:43237204G>T	ENST00000327495.5	-	3	625	c.441C>A	c.(439-441)ccC>ccA	p.P147P	PSG3_ENST00000490592.1_5'Flank|PSG3_ENST00000595140.1_Silent_p.P147P	NM_021016.3	NP_066296.2	Q16557	PSG3_HUMAN	pregnancy specific beta-1-glycoprotein 3			36		Prostate(69;0.00682)			TGGAGGGCTTGGGAGTCTCCA	0.522000																								0							SO:0001819	synonymous_variant			ENST00000327495.5	1	1	hg19	CCDS12611.1																																																																																				TCGA-IB-AAUO-01A-12D-A38G-08	PSG3-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321423.2	1	0	0	151	699	0	380		0	0	0	0	380	2		0	0	0	0	0	2	1	1.000000	141	676	0	417	2		0	0	0	0	380	2	-2.689206	1	1	0	0		1	1	2	3	2.077877	0	0.380000	1.860000	0.384676	0.940000	0.800000	1.000000	1.000000	0.937454	0.940000	1	0.870000	1.000000
ZNF667	63934	broad.mit.edu	37	19	56953041	56953041	+	Silent	SNP	T	T	C			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr19:56953041T>C	ENST00000504904.3	-	7	2042	c.1323A>G	c.(1321-1323)aaA>aaG	p.K441K	ZNF667_ENST00000292069.6_Silent_p.K441K|ZNF667_ENST00000342634.3_Silent_p.K569K|ZNF667_ENST00000591790.1_3'UTR			Q5HYK9	ZN667_HUMAN	zinc finger protein 667			38		Colorectal(82;0.000256)|Ovarian(87;0.243)			ATTTGAAAGGTTTCTCTTCAG	0.338000																								0							SO:0001819	synonymous_variant			ENST00000504904.3	1	1	hg19	CCDS12944.1																																																																																				TCGA-IB-AAUO-01A-12D-A38G-08	ZNF667-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458394.1	0	0	0	12	429	0	164		0	0	0	0	164	2		0	0	0	0	0	2	1	0.999026	12	420	0	163	2		0	0	0	0	164	2	-3.468115	1	1	0	0		1	1	2	3	2.081337	0	0.380000	1.860000	0.384676	0.140000	0.070000	1.000000	0.140000	0.179382	0.140000	0	0.100000	0.200000
MBD3L1	85509	broad.mit.edu	37	19	8953738	8953738	+	Silent	SNP	G	G	A			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr19:8953738G>A	ENST00000595891.1	+	3	615	c.384G>A	c.(382-384)gcG>gcA	p.A128A	MBD3L1_ENST00000305625.2_Silent_p.A128A			Q8WWY6	MB3L1_HUMAN	methyl-CpG binding domain protein 3-like 1			12					CTTCAGATGCGGTGGAGATAA	0.522000																								0							SO:0001819	synonymous_variant			ENST00000595891.1	1	1	hg19	CCDS12209.1																																																																																				TCGA-IB-AAUO-01A-12D-A38G-08	MBD3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459973.1	0	0	1	21	122	0	44		0	0	0	0	44	2		0	0	0	0	0	2	1	0.999998	21	119	0	44	2		0	0	0	0	44	2	-3.169665	1	1	121412	1	29	1	1	2	3	2.086690	0	0.380000	1.860000	0.385835	0.790000	0.510000	1.000000	1.000000	0.796399	0.790000	0	0.640000	0.980000
MUC16	94025	broad.mit.edu	37	19	9074660	9074660	+	Silent	SNP	G	G	T			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr19:9074660G>T	ENST00000397910.4	-	3	12989	c.12786C>A	c.(12784-12786)atC>atA	p.I4262I		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated			590					TATGGCCTGGGATAGGAGAAT	0.468000																								0							SO:0001819	synonymous_variant			ENST00000397910.4	0	1	hg19	CCDS54212.1																																																																																				TCGA-IB-AAUO-01A-12D-A38G-08	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	0	0	0	7	258	0	114	0	0	0	1	0	114	2		0	0	0	0	0	2	1	0.979368	7	252	0	113	2		0	0	0	0	114	2	-7.963883	1	1	0	0		1	1	2	3	2.086690	0	0.380000	1.860000	0.385835	0.140000	0.060000	1.000000	0.140000	0.190207	0.140000	0	0.090000	0.220000
ADAMTSL4	54507	broad.mit.edu	37	1	150530955	150530955	+	Missense_Mutation	SNP	G	G	A	rs138636937		TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr1:150530955G>A	ENST00000369038.2	+	13	2590	c.2389G>A	c.(2389-2391)Gtg>Atg	p.V797M	ADAMTSL4_ENST00000369039.5_Missense_Mutation_p.V820M|RP11-54A4.2_ENST00000442435.2_RNA|ADAMTSL4_ENST00000271643.4_Missense_Mutation_p.V797M|ADAMTSL4_ENST00000369041.5_Missense_Mutation_p.V797M			Q6UY14	ATL4_HUMAN	ADAMTS-like 4			32	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;3.18e-23)|all cancers(9;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(6;1.13e-14)|BRCA - Breast invasive adenocarcinoma(12;0.000503)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)		TCAGTGCTCCGTGCGGTGCGG	0.647000																								0							SO:0001583	missense			ENST00000369038.2	1	1	hg19	CCDS955.1	.	.	.	.	.	.	.	.	.	.	G	17.96	3.516530	0.64634	0.0	1.16E-4	ENSG00000143382	ENST00000369041;ENST00000271643;ENST00000407995;ENST00000369039;ENST00000369038	T;T;T;T	0.64991	-0.13;-0.13;-0.13;-0.13	4.91	4.91	0.64330	.	.	.	.	.	T	0.79924	0.4530	M	0.90198	3.095	0.58432	D	0.999993	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.85130	0.997;0.996;0.997;0.992	D	0.83613	0.0135	9	0.66056	D	0.02	.	15.633	0.76926	0.0:0.0:1.0:0.0	.	758;820;797;797	B7ZMJ3;F8WAD0;Q6UY14;Q6UY14-2	.;.;ATL4_HUMAN;.	M	797;797;335;820;797	ENSP00000358037:V797M;ENSP00000271643:V797M;ENSP00000358035:V820M;ENSP00000358034:V797M	ENSP00000271643:V797M	V	+	1	0	ADAMTSL4	148797579	1.000000	0.71417	0.776000	0.31678	0.216000	0.24613	9.034000	0.93747	2.549000	0.85964	0.462000	0.41574	GTG		TCGA-IB-AAUO-01A-12D-A38G-08	ADAMTSL4-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084395.4	1	0	1	37	117	0	68	1	9.996079e-01	16	26	0	68	2		0	0	0	0	0	2	1	1.000000	36	109	0	67	2		0	0	0	0	68	2	-20.000000	1	1	121388	7	37	1	0	0	0	2.041409	0	0.380000	1.860000	0.377635	0.990000	0.920000	1.000000	1.000000	0.995769	0.990000	1	0.990000	1.000000
CLCNKB	1188	broad.mit.edu	37	1	16374889	16374889	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr1:16374889C>T	ENST00000375679.4	+	6	661	c.550C>T	c.(550-552)Cgc>Tgc	p.R184C	CLCNKB_ENST00000375667.3_5'Flank	NM_000085.4	NP_000076.2	P51801	CLCKB_HUMAN	chloride channel, voltage-sensitive Kb			21		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)			GGGCCGTGTGCGCACCACGAC	0.662000																								0							SO:0001583	missense			ENST00000375679.4	0	1	hg19	CCDS168.1	.	.	.	.	.	.	.	.	.	.	c	18.37	3.608384	0.66558	.	.	ENSG00000184908	ENST00000375679;ENST00000331579	D	0.92911	-3.13	4.68	3.69	0.42338	Chloride channel, core (2);	0.349083	0.30649	N	0.009166	D	0.86456	0.5937	L	0.38649	1.16	0.80722	D	1	B	0.20052	0.041	B	0.21151	0.033	D	0.84245	0.0474	10	0.87932	D	0	.	8.4362	0.32789	0.2762:0.5817:0.1421:0.0	.	184	P51801	CLCKB_HUMAN	C	184	ENSP00000364831:R184C	ENSP00000332055:R184C	R	+	1	0	CLCNKB	16247476	1.000000	0.71417	0.627000	0.29227	0.928000	0.56348	2.311000	0.43717	2.139000	0.66308	0.655000	0.94253	CGC		TCGA-IB-AAUO-01A-12D-A38G-08	CLCNKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026331.1	0	0	0	4	143	0	84		0	0	0	0	84	2		0	0	0	0	0	2	1	0.883130	4	138	0	96	2		0	0	0	0	84	2	-2.811024	1	1	0	0		1	0	1	1	1.708494	1	0.380000	1.860000	0.236359	0.120000	0.040000	0.270000	0.110000	0.140263	0.120000	0	0.070000	0.200000
TDRD5	163589	broad.mit.edu	37	1	179604922	179604922	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr1:179604922G>T	ENST00000367614.1	+	9	1779	c.1420G>T	c.(1420-1422)Ggg>Tgg	p.G474W	TDRD5_ENST00000294848.8_Missense_Mutation_p.G474W|TDRD5_ENST00000444136.1_Missense_Mutation_p.G474W	NM_001199091.1	NP_001186020.1	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5			77					TTCCCTCATAGGGGTCTTTGT	0.463000																								0							SO:0001583	missense			ENST00000367614.1	1	1	hg19	CCDS1332.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.058568	0.76074	.	.	ENSG00000162782	ENST00000367614;ENST00000294848;ENST00000444136	T;T;T	0.09723	2.95;2.95;2.95	4.94	4.94	0.65067	Maternal tudor protein (1);	0.299142	0.33272	N	0.005083	T	0.28797	0.0714	L	0.52011	1.625	0.46203	D	0.998927	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.01309	-1.1389	10	0.72032	D	0.01	-19.4684	16.7233	0.85415	0.0:0.0:1.0:0.0	.	474;474	Q8NAT2-1;Q8NAT2	.;TDRD5_HUMAN	W	474	ENSP00000356586:G474W;ENSP00000294848:G474W;ENSP00000406052:G474W	ENSP00000294848:G474W	G	+	1	0	TDRD5	177871545	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	6.639000	0.74314	2.279000	0.76181	0.585000	0.79938	GGG		TCGA-IB-AAUO-01A-12D-A38G-08	TDRD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000085295.1	1	0	1	33	247	0	107		0	0	0	0	107	2		0	0	0	0	0	2	1	1.000000	32	242	0	107	2		0	0	0	0	107	2	-2.879535	1	1	0	0		1	1	2	3	2.057212	0	0.380000	1.860000	0.381176	0.620000	0.440000	0.840000	0.620000	0.632074	0.620000	0	0.520000	0.730000
PLXNA2	5362	broad.mit.edu	37	1	208276511	208276511	+	Missense_Mutation	SNP	A	A	G			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr1:208276511A>G	ENST00000367033.3	-	5	2345	c.1588T>C	c.(1588-1590)Tgg>Cgg	p.W530R		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2			80					AGGGCACACCAGCCACAGTGA	0.547000																								0							SO:0001583	missense			ENST00000367033.3	1	1	hg19	CCDS31013.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.220286	0.79464	.	.	ENSG00000076356	ENST00000367033	D	0.92249	-3.0	4.8	4.8	0.61643	.	0.000000	0.85682	D	0.000000	D	0.97263	0.9105	H	0.95917	3.74	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.98485	1.0607	10	0.87932	D	0	.	14.5136	0.67804	1.0:0.0:0.0:0.0	.	530	O75051	PLXA2_HUMAN	R	530	ENSP00000356000:W530R	ENSP00000356000:W530R	W	-	1	0	PLXNA2	206343134	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.798000	0.91888	2.025000	0.59659	0.533000	0.62120	TGG		TCGA-IB-AAUO-01A-12D-A38G-08	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	1	0	1	18	77	0	41	1	6.513763e-01	6	5	0	41	2		0	0	0	0	0	2	1	0.999988	17	75	0	41	2		0	0	0	0	41	2	-20.000000	1	1	0	0		1	1	2	3	2.063294	0	0.380000	1.860000	0.381176	0.990000	0.630000	1.000000	1.000000	0.925065	0.990000	1	0.800000	1.000000
EXTL1	2134	broad.mit.edu	37	1	26359784	26359784	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr1:26359784G>A	ENST00000374280.3	+	8	2363	c.1496G>A	c.(1495-1497)cGc>cAc	p.R499H		NM_004455.2	NP_004446.2	Q92935	EXTL1_HUMAN	exostosin-like glycosyltransferase 1			23		Colorectal(325;3.46e-05)|Lung NSC(340;6.18e-05)|all_lung(284;9.43e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)			CTCGATGCCCGCAGCAGTCTT	0.597000																								0							SO:0001583	missense			ENST00000374280.3	0	1	hg19	CCDS271.1	.	.	.	.	.	.	.	.	.	.	G	14.20	2.464549	0.43736	2.27E-4	0.0	ENSG00000158008	ENST00000374280	T	0.75704	-0.96	5.06	3.93	0.45458	EXTL2, alpha-1,4-N-acetylhexosaminyltransferase (1);	0.323633	0.33092	N	0.005297	T	0.36496	0.0969	N	0.00237	-1.79	0.27362	N	0.955932	B	0.09022	0.002	B	0.09377	0.004	T	0.37686	-0.9695	10	0.51188	T	0.08	-12.2433	7.0466	0.25048	0.8869:0.0:0.1131:0.0	.	499	Q92935	EXTL1_HUMAN	H	499	ENSP00000363398:R499H	ENSP00000363398:R499H	R	+	2	0	EXTL1	26232371	1.000000	0.71417	0.991000	0.47740	0.940000	0.58332	6.140000	0.71738	0.950000	0.37743	0.561000	0.74099	CGC		TCGA-IB-AAUO-01A-12D-A38G-08	EXTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019749.1	0	0	0	4	157	0	87	0	3.271530e-03	0	3	0	87	2		0	0	0	0	0	2	1	0.889902	4	156	0	87	2		0	0	0	0	87	2	-3.108916	1	1	121412	3	38	1	0	1	1	1.713541	1	0.380000	1.860000	0.234568	0.110000	0.030000	0.250000	0.100000	0.128130	0.110000	0	0.060000	0.180000
OPRD1	4985	broad.mit.edu	37	1	29185499	29185499	+	Silent	SNP	C	C	T			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr1:29185499C>T	ENST00000234961.2	+	2	503	c.261C>T	c.(259-261)taC>taT	p.Y87Y		NM_000911.3	NP_000902.3	P41143	OPRD_HUMAN	opioid receptor, delta 1			15		Colorectal(325;3.46e-05)|Lung NSC(340;0.000947)|all_lung(284;0.00131)|Renal(390;0.00758)|Breast(348;0.00765)|all_neural(195;0.0199)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Alvimopan(DB06274)|Amitriptyline(DB00321)|Buprenorphine(DB00921)|Butorphanol(DB00611)|Codeine(DB00318)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diphenoxylate(DB01081)|Fentanyl(DB00813)|Heroin(DB01452)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Ketamine(DB01221)|Ketobemidone(DB06738)|Levorphanol(DB00854)|Loperamide(DB00836)|Methadone(DB00333)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Remifentanil(DB00899)|Sufentanil(DB00708)|Tapentadol(DB06204)|Tramadol(DB00193)	CCAACATCTACATCTTCAACC	0.493000																								0							SO:0001819	synonymous_variant			ENST00000234961.2	0	1	hg19	CCDS329.1																																																																																				TCGA-IB-AAUO-01A-12D-A38G-08	OPRD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010330.1	0	0	0	9	405	0	189		0	0	0	0	189	2		0	0	0	0	0	2	1	0.993805	9	397	0	186	2		0	0	0	0	189	2	-3.115331	1	1	0	0		1	0	1	1	1.713541	1	0.380000	1.860000	0.234568	0.090000	0.040000	0.170000	0.090000	0.101666	0.090000	0	0.060000	0.130000
PATZ1	23598	broad.mit.edu	37	22	31740473	31740473	+	Silent	SNP	C	C	T			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr22:31740473C>T	ENST00000266269.5	-	1	1745	c.1116G>A	c.(1114-1116)cgG>cgA	p.R372R	PATZ1_ENST00000215919.3_Silent_p.R372R|AC005003.1_ENST00000504184.2_5'Flank|PATZ1_ENST00000405309.3_Silent_p.R372R|PATZ1_ENST00000351933.4_Silent_p.R372R	NM_014323.2	NP_055138.2	Q9HBE1	PATZ1_HUMAN	POZ (BTB) and AT hook containing zinc finger 1	p.R372R(2)	EWSR1/PATZ1(2)	12					ACAGCTTGTGCCGGTTAAGAT	0.582000																								2	Substitution - coding silent(2)						SO:0001819	synonymous_variant			ENST00000266269.5	0	1	hg19	CCDS13894.1																																																																																				TCGA-IB-AAUO-01A-12D-A38G-08	PATZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321932.1	0	0	0	5	317	0	143	0	3.387003e-01	0	66	0	143	2		0	0	0	0	0	2	1	0.935946	5	313	0	141	2		0	0	0	0	143	2	-1.974263	0	1	121412	1	32	1	0	1	1	1.836368	1	0.380000	1.860000	0.295695	0.070000	0.020000	0.160000	0.070000	0.085161	0.070000	0	0.040000	0.120000
IL1RL2	8808	broad.mit.edu	37	2	102851439	102851439	+	Silent	SNP	C	C	T			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr2:102851439C>T	ENST00000264257.2	+	11	1506	c.1380C>T	c.(1378-1380)ggC>ggT	p.G460G	IL1RL2_ENST00000481806.1_3'UTR|IL1RL2_ENST00000441515.2_Silent_p.G342G|IL1RL2_ENST00000539491.1_Silent_p.G460G	NM_003854.2	NP_003845.2	Q9HB29	ILRL2_HUMAN	interleukin 1 receptor-like 2			26					TGGGCTTTGGCCTGTTGAAGA	0.488000																								0							SO:0001819	synonymous_variant			ENST00000264257.2	0	1	hg19	CCDS2056.1																																																																																				TCGA-IB-AAUO-01A-12D-A38G-08	IL1RL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253290.1	0	0	0	5	251	0	108	0	3.564281e-03	0	4	0	108	2		0	0	0	0	0	2	1	0.934211	5	246	0	107	2		0	0	0	0	108	2	-2.633924	1	1	0	0		1	1	2	3	2.055032	0	0.380000	1.860000	0.381176	0.110000	0.030000	0.240000	0.100000	0.121860	0.110000	0	0.060000	0.170000
GREB1	9687	broad.mit.edu	37	2	11780565	11780565	+	Silent	SNP	G	G	A			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr2:11780565G>A	ENST00000381486.2	+	33	6135	c.5835G>A	c.(5833-5835)acG>acA	p.T1945T	GREB1_ENST00000234142.5_Silent_p.T1945T|GREB1_ENST00000396123.1_Silent_p.T943T	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1			30	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)				TTTTTCTGACGGGACGACACA	0.607000													Ovarian(39;850 945 2785 23371 33093)											0							SO:0001819	synonymous_variant			ENST00000381486.2	1	1	hg19	CCDS42655.1																																																																																				TCGA-IB-AAUO-01A-12D-A38G-08	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	1	0	0	29	301	0	125	0	0	0	1	0	125	2		0	0	0	0	0	2	1	1.000000	29	296	0	125	2		0	0	0	0	125	2	-2.429492	0	1	120886	14	45	1	0	1	1	2.052975	0	0.380000	1.860000	0.375252	0.450000	0.310000	0.630000	0.450000	0.469598	0.450000	0	0.380000	0.550000
ZDBF2	57683	broad.mit.edu	37	2	207171284	207171284	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr2:207171284G>T	ENST00000374423.3	+	5	2418	c.2032G>T	c.(2032-2034)Gac>Tac	p.D678Y		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2			95					TCAATTAGCTGACCAGTCTCA	0.428000																								0							SO:0001583	missense			ENST00000374423.3	1	1	hg19	CCDS46501.1	.	.	.	.	.	.	.	.	.	.	G	13.61	2.287181	0.40494	.	.	ENSG00000204186	ENST00000374423	T	0.54675	0.56	4.24	3.33	0.38152	.	0.943578	0.08666	N	0.911684	T	0.57330	0.2046	L	0.34521	1.04	0.09310	N	1	D	0.69078	0.997	P	0.58577	0.841	T	0.47156	-0.9139	10	0.66056	D	0.02	.	9.9562	0.41668	0.0:0.2064:0.7936:0.0	.	678	Q9HCK1	ZDBF2_HUMAN	Y	678	ENSP00000363545:D678Y	ENSP00000363545:D678Y	D	+	1	0	ZDBF2	206879529	0.012000	0.17670	0.014000	0.15608	0.007000	0.05969	1.571000	0.36450	1.318000	0.45170	0.655000	0.94253	GAC		TCGA-IB-AAUO-01A-12D-A38G-08	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	1	0	1	30	158	0	54	0	2.733535e-02	0	2	0	54	2		0	0	0	0	0	2	1	1.000000	29	155	0	53	2		0	0	0	0	54	2	-20.000000	1	1	0	0		1	1	2	3	2.055032	0	0.380000	1.860000	0.381176	0.840000	0.590000	1.000000	1.000000	0.841017	0.840000	0	0.700000	0.990000
ASB18	401036	broad.mit.edu	37	2	237172977	237172977	+	Silent	SNP	C	C	T			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr2:237172977C>T	ENST00000409749.3	-	1	11	c.12G>A	c.(10-12)tcG>tcA	p.S4S	AC079135.1_ENST00000415226.1_RNA	NM_212556.2	NP_997721.2	Q6ZVZ8	ASB18_HUMAN	ankyrin repeat and SOCS box containing 18			6		all_hematologic(139;0.00615)|Renal(207;0.00963)|Breast(86;0.0126)|Acute lymphoblastic leukemia(138;0.0815)			GAAGGTAATCCGAGTTGGACA	0.493000																								0							SO:0001819	synonymous_variant			ENST00000409749.3	0	1	hg19	CCDS46548.1																																																																																				TCGA-IB-AAUO-01A-12D-A38G-08	ASB18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329436.1	0	0	0	5	215	0	83		0	0	0	0	83	2		0	0	0	0	0	2	1	0.936751	5	213	0	83	2		0	0	0	0	83	2	-2.769569	1	1	120908	1	37	1	1	2	3	2.084111	0	0.380000	1.860000	0.385835	0.130000	0.040000	1.000000	0.120000	0.175124	0.130000	0	0.080000	0.210000
PREPL	9581	broad.mit.edu	37	2	44586652	44586652	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr2:44586652C>T	ENST00000409936.1	-	2	640	c.203G>A	c.(202-204)cGg>cAg	p.R68Q	CAMKMT_ENST00000403853.3_5'Flank|PREPL_ENST00000410081.1_Missense_Mutation_p.R68Q|PREPL_ENST00000540817.1_Intron|PREPL_ENST00000260648.6_Missense_Mutation_p.R68Q|PREPL_ENST00000541738.1_Intron|CAMKMT_ENST00000402247.1_5'Flank|PREPL_ENST00000378520.3_Missense_Mutation_p.R68Q|CAMKMT_ENST00000407131.1_5'Flank|PREPL_ENST00000409411.1_Intron|PREPL_ENST00000409957.1_Intron|PREPL_ENST00000409272.1_Missense_Mutation_p.R68Q|PREPL_ENST00000378511.3_Missense_Mutation_p.R68Q|CAMKMT_ENST00000378494.3_5'Flank	NM_001171606.1	NP_001165077.1	Q4J6C6	PPCEL_HUMAN	prolyl endopeptidase-like			33		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)			TGAGAAGCTCCGACTTGGGAT	0.308000																								0							SO:0001583	missense			ENST00000409936.1	1	1	hg19	CCDS33190.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.400937	0.83120	.	.	ENSG00000138078	ENST00000409936;ENST00000260648;ENST00000409272;ENST00000410081;ENST00000378520;ENST00000378511;ENST00000438314	.	.	.	5.27	4.38	0.52667	.	0.251803	0.28409	N	0.015459	T	0.48370	0.1496	N	0.08118	0	0.80722	D	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;P	0.77557	0.975;0.99;0.846	T	0.42085	-0.9472	9	0.30854	T	0.27	-13.6207	10.0499	0.42210	0.0:0.907:0.0:0.093	.	68;68;68	Q4J6C6-3;Q4J6C6-2;Q4J6C6	.;.;PPCEL_HUMAN	Q	68	.	ENSP00000260648:R68Q	R	-	2	0	PREPL	44440156	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.885000	0.39678	2.735000	0.93741	0.655000	0.94253	CGG		TCGA-IB-AAUO-01A-12D-A38G-08	PREPL-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327900.1	1	0	1	110	575	0	254	0	4.378813e-01	0	9	0	254	2		0	0	0	0	0	2	1	1.000000	108	565	0	253	2		0	0	0	0	254	2	-2.808899	1	1	121412	1	34	1	1	2	3	2.055032	0	0.380000	1.860000	0.381176	0.840000	0.700000	1.000000	0.840000	0.849203	0.840000	0	0.770000	0.920000
BCL11A	53335	broad.mit.edu	37	2	60688929	60688929	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr2:60688929G>A	ENST00000335712.6	-	4	1345	c.1118C>T	c.(1117-1119)cCg>cTg	p.P373L	BCL11A_ENST00000538214.1_Missense_Mutation_p.P339L|BCL11A_ENST00000537768.1_Intron|BCL11A_ENST00000359629.5_Intron|BCL11A_ENST00000358510.4_Missense_Mutation_p.P339L|BCL11A_ENST00000477659.1_5'UTR|BCL11A_ENST00000356842.4_Missense_Mutation_p.P373L	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)		GGACTTGACCGGGGGCTGGGA	0.627000			T	IGH@	B-CLL										Dom	yes		2	2p13	53335	B-cell CLL/lymphoma 11A		L	0							SO:0001583	missense			ENST00000335712.6	1	1	hg19	CCDS1862.1	.	.	.	.	.	.	.	.	.	.	G	11.92	1.783620	0.31593	.	.	ENSG00000119866	ENST00000356842;ENST00000378117;ENST00000538214;ENST00000335712;ENST00000358510	T;T;T;T	0.10288	2.89;3.11;3.12;3.03	5.74	4.84	0.62591	.	0.186906	0.46442	D	0.000293	T	0.16471	0.0396	M	0.61703	1.905	0.80722	D	1	B;D;B;P	0.56746	0.334;0.977;0.226;0.652	B;B;B;B	0.43194	0.063;0.411;0.017;0.044	T	0.02126	-1.1209	10	0.54805	T	0.06	-1.7699	16.5742	0.84633	0.0:0.1305:0.8695:0.0	.	339;339;373;373	F5H2Y4;Q9H165-6;Q9H165;D9YZV9	.;.;BC11A_HUMAN;.	L	373;409;339;373;339	ENSP00000349300:P373L;ENSP00000438303:P339L;ENSP00000338774:P373L;ENSP00000351307:P339L	ENSP00000338774:P373L	P	-	2	0	BCL11A	60542433	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.309000	0.65774	1.392000	0.46585	0.655000	0.94253	CCG		TCGA-IB-AAUO-01A-12D-A38G-08	BCL11A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251579.2	1	0	1	47	222	1	99		0	0	0	1	99	2		0	0	0	0	0	2	1	1.000000	44	208	1	96	11		0	0	0	1	99	2	-2.492123	0	1	121362	1	32	1	1	2	3	2.055032	0	0.380000	1.860000	0.381176	0.910000	0.690000	1.000000	1.000000	0.906756	0.910000	1	0.800000	1.000000
DYSF	8291	broad.mit.edu	37	2	71742844	71742844	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr2:71742844C>T	ENST00000258104.3	+	7	1032	c.755C>T	c.(754-756)aCg>aTg	p.T252M	DYSF_ENST00000429174.2_Missense_Mutation_p.T252M|DYSF_ENST00000410020.3_Missense_Mutation_p.T284M|DYSF_ENST00000413539.2_Missense_Mutation_p.T283M|DYSF_ENST00000409762.1_Missense_Mutation_p.T283M|DYSF_ENST00000409651.1_Missense_Mutation_p.T284M|DYSF_ENST00000409744.1_Missense_Mutation_p.T253M|DYSF_ENST00000409582.3_Missense_Mutation_p.T283M|DYSF_ENST00000409366.1_Missense_Mutation_p.T253M|DYSF_ENST00000394120.2_Missense_Mutation_p.T253M|DYSF_ENST00000410041.1_Missense_Mutation_p.T284M	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin			111					ACCAAGCGGACGCGGATCCAC	0.612000																								0							SO:0001583	missense			ENST00000258104.3	1	1	hg19	CCDS1918.1	.	.	.	.	.	.	.	.	.	.	C	19.83	3.899610	0.72754	.	.	ENSG00000135636	ENST00000413539;ENST00000409762;ENST00000409582;ENST00000429174;ENST00000258104;ENST00000409651;ENST00000394120;ENST00000409744;ENST00000409366;ENST00000410020;ENST00000410041	D;D;D;D;D;D;D;D;D;D;D	0.94966	-3.57;-3.57;-3.57;-3.57;-3.57;-3.57;-3.57;-3.57;-3.57;-3.57;-3.57	5.0	5.0	0.66597	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	D	0.98086	0.9369	H	0.95470	3.675	0.53688	D	0.99997	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0;1.0;0.999;1.0;0.999;1.0;1.0;1.0;1.0	D	0.99274	1.0894	10	0.87932	D	0	-14.9292	16.1703	0.81808	0.0:1.0:0.0:0.0	.	284;284;253;253;284;253;283;252;283;283;252;252;253;252	O75923-8;O75923-13;O75923-10;O75923-9;O75923-11;O75923-12;O75923-5;O75923-6;O75923-2;O75923-7;O75923-4;O75923-3;O75923-14;O75923	.;.;.;.;.;.;.;.;.;.;.;.;.;DYSF_HUMAN	M	283;283;283;252;252;284;253;253;253;284;284	ENSP00000407046:T283M;ENSP00000387137:T283M;ENSP00000386547:T283M;ENSP00000398305:T252M;ENSP00000258104:T252M;ENSP00000386683:T284M;ENSP00000377678:T253M;ENSP00000386285:T253M;ENSP00000386512:T253M;ENSP00000386881:T284M;ENSP00000386617:T284M	ENSP00000258104:T252M	T	+	2	0	DYSF	71596352	1.000000	0.71417	0.934000	0.37439	0.374000	0.29953	7.351000	0.79395	2.475000	0.83589	0.549000	0.68633	ACG		TCGA-IB-AAUO-01A-12D-A38G-08	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	1	0	0	11	242	0	112	0	1.331951e-02	0	4	0	112	2		0	0	0	0	0	2	1	0.998292	11	238	0	111	2		0	0	0	0	112	2	-12.760410	1	1	0	0		1	1	2	3	2.055032	0	0.380000	1.860000	0.381176	0.230000	0.120000	0.400000	0.220000	0.246563	0.230000	0	0.170000	0.320000
CTNNA2	1496	broad.mit.edu	37	2	79971679	79971679	+	Missense_Mutation	SNP	T	T	G			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr2:79971679T>G	ENST00000402739.4	+	2	274	c.269T>G	c.(268-270)gTg>gGg	p.V90G	CTNNA2_ENST00000496558.1_Missense_Mutation_p.V90G|CTNNA2_ENST00000466387.1_Missense_Mutation_p.V90G|CTNNA2_ENST00000361291.4_Missense_Mutation_p.V124G|CTNNA2_ENST00000540488.1_Missense_Mutation_p.V90G|CTNNA2_ENST00000541047.1_Missense_Mutation_p.V90G	NM_001282597.1	NP_001269526.1	P26232	CTNA2_HUMAN	catenin (cadherin-associated protein), alpha 2			78					GAAGAGTTGGTGGCTGCTGTA	0.443000																								0							SO:0001583	missense			ENST00000402739.4	0	1	hg19		.	.	.	.	.	.	.	.	.	.	T	16.78	3.219037	0.58560	.	.	ENSG00000066032	ENST00000466387;ENST00000496558;ENST00000409971;ENST00000361291;ENST00000402739;ENST00000541047;ENST00000540488	T;T;T;T;T;T;T	0.37915	1.17;1.17;1.17;1.17;1.17;1.17;1.17	5.5	5.5	0.81552	.	0.140504	0.47852	D	0.000201	T	0.19406	0.0466	N	0.08118	0	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.001	T	0.10497	-1.0627	10	0.15066	T	0.55	.	13.5514	0.61734	0.0:0.0:0.0:1.0	.	90;90;90	P26232;P26232-3;P26232-2	CTNA2_HUMAN;.;.	G	90;90;90;124;90;90;90	ENSP00000418191:V90G;ENSP00000419295:V90G;ENSP00000387073:V90G;ENSP00000355398:V124G;ENSP00000384638:V90G;ENSP00000444675:V90G;ENSP00000441705:V90G	ENSP00000355398:V124G	V	+	2	0	CTNNA2	79825187	1.000000	0.71417	0.964000	0.40570	0.951000	0.60555	6.280000	0.72626	2.091000	0.63221	0.383000	0.25322	GTG		TCGA-IB-AAUO-01A-12D-A38G-08	CTNNA2-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000328511.4	0	0	0	5	162	0	71		0	0	0	0	71	2		0	0	0	0	0	2	1	0.932324	5	156	0	71	2		0	0	0	0	71	2	-7.333867	1	1	0	0		1	1	2	3	2.055032	0	0.380000	1.860000	0.381176	0.170000	0.060000	0.360000	0.160000	0.185404	0.170000	0	0.100000	0.260000
PHLDB2	90102	broad.mit.edu	37	3	111603672	111603672	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr3:111603672G>A	ENST00000431670.2	+	2	1159	c.748G>A	c.(748-750)Gga>Aga	p.G250R	PHLDB2_ENST00000481953.1_Missense_Mutation_p.G250R|PHLDB2_ENST00000393923.3_Missense_Mutation_p.G277R|PHLDB2_ENST00000393925.3_Missense_Mutation_p.G250R|PHLDB2_ENST00000478922.1_Missense_Mutation_p.G250R|PHLDB2_ENST00000477695.1_Missense_Mutation_p.G250R|PHLDB2_ENST00000412622.1_Missense_Mutation_p.G250R	NM_001134438.1	NP_001127910.1	Q86SQ0	PHLB2_HUMAN	pleckstrin homology-like domain, family B, member 2			55					GAGTCACATGGGAGCCTACAG	0.507000																								0							SO:0001583	missense			ENST00000431670.2	1	1	hg19	CCDS46886.1	.	.	.	.	.	.	.	.	.	.	G	19.37	3.815029	0.70912	.	.	ENSG00000144824	ENST00000359729;ENST00000393923;ENST00000431670;ENST00000412622;ENST00000498699;ENST00000478922;ENST00000477695;ENST00000393925;ENST00000481953	T;T;T;T;T;T	0.57273	0.44;0.62;0.46;0.41;0.62;0.46	5.4	5.4	0.78164	.	0.241259	0.41823	D	0.000803	T	0.67988	0.2952	L	0.51422	1.61	0.48185	D	0.999601	D;D;D;D;D	0.89917	0.999;1.0;1.0;0.998;1.0	D;D;D;D;D	0.97110	0.942;1.0;1.0;0.962;0.995	T	0.69320	-0.5176	10	0.72032	D	0.01	.	16.4564	0.84019	0.0:0.0:1.0:0.0	.	250;250;250;250;277	Q86SQ0;G5E9V3;E9PDY7;Q86SQ0-2;Q86SQ0-3	PHLB2_HUMAN;.;.;.;.	R	277;277;250;250;250;250;250;250;250	ENSP00000377500:G277R;ENSP00000405405:G250R;ENSP00000405292:G250R;ENSP00000418296:G250R;ENSP00000377502:G250R;ENSP00000418319:G250R	ENSP00000352764:G277R	G	+	1	0	PHLDB2	113086362	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.291000	0.65667	2.703000	0.92315	0.655000	0.94253	GGA		TCGA-IB-AAUO-01A-12D-A38G-08	PHLDB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354337.1	1	0	1	152	269	0	113	1	9.227752e-01	5	5	0	113	2		0	0	0	0	0	2	1	1.000000	150	265	0	112	2		0	0	0	0	113	2	-17.212780	1	1	0	0		1	1	3	4	2.744515	1	0.380000	1.860000	0.530018	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	0.990000	1.000000
MBD4	8930	broad.mit.edu	37	3	129151965	129151965	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr3:129151965C>T	ENST00000249910.1	-	6	1712	c.1537G>A	c.(1537-1539)Gca>Aca	p.A513T	MBD4_ENST00000507208.1_Missense_Mutation_p.A513T|MBD4_ENST00000429544.2_Missense_Mutation_p.A507T|MBD4_ENST00000503197.1_Missense_Mutation_p.A513T|MBD4_ENST00000509587.1_5'Flank|MBD4_ENST00000393278.2_Missense_Mutation_p.A195T	NM_003925.1	NP_003916.1	O95243	MBD4_HUMAN	methyl-CpG binding domain protein 4			22					ATGGTTTTTGCCCGAAGATCG	0.403000								Base excision repair (BER), DNA glycosylases																0							SO:0001583	missense			ENST00000249910.1	0	1	hg19	CCDS3058.1	.	.	.	.	.	.	.	.	.	.	C	33	5.273592	0.95459	.	.	ENSG00000129071	ENST00000429544;ENST00000249910;ENST00000503197;ENST00000393278;ENST00000507208	T;T;T;T;T	0.62498	0.02;0.02;0.02;0.02;0.02	6.14	6.14	0.99180	HhH-GPD domain (1);DNA glycosylase (2);	0.000000	0.85682	D	0.000000	T	0.81293	0.4792	M	0.79123	2.44	0.80722	D	1	D;D;D;D;D	0.89917	0.996;0.994;0.995;1.0;0.998	D;D;D;D;D	0.91635	0.968;0.945;0.945;0.999;0.98	T	0.80353	-0.1418	10	0.56958	D	0.05	-21.0242	20.4701	0.99162	0.0:1.0:0.0:0.0	.	513;195;507;513;513	E9PEE4;Q2MD36;O95243-2;O95243-3;O95243	.;.;.;.;MBD4_HUMAN	T	507;513;513;195;513	ENSP00000394080:A507T;ENSP00000249910:A513T;ENSP00000424873:A513T;ENSP00000376959:A195T;ENSP00000422327:A513T	ENSP00000249910:A513T	A	-	1	0	MBD4	130634655	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.291000	0.78721	2.937000	0.99478	0.650000	0.86243	GCA		TCGA-IB-AAUO-01A-12D-A38G-08	MBD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355529.1	0	0	0	7	567	0	153	0	7.789249e-01	1	229	0	153	2		0	0	0	0	0	2	1	0.979063	7	554	0	152	2		0	0	0	0	153	2	-2.231298	0	1	0	0		1	1	3	4	2.765071	1	0.380000	1.860000	0.531368	0.090000	0.020000	1.000000	0.080000	0.203991	0.090000	0	0.050000	0.160000
TRIM42	287015	broad.mit.edu	37	3	140407107	140407107	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr3:140407107G>A	ENST00000286349.3	+	3	1774	c.1583G>A	c.(1582-1584)gGc>gAc	p.G528D		NM_152616.4	NP_689829.3	Q8IWZ5	TRI42_HUMAN	tripartite motif containing 42			69					CACAGCCTCGGCAACCAGCAC	0.577000																								0							SO:0001583	missense			ENST00000286349.3	0	1	hg19	CCDS3113.1	.	.	.	.	.	.	.	.	.	.	G	6.665	0.491250	0.12702	.	.	ENSG00000155890	ENST00000286349	T	0.36699	1.24	5.52	-4.17	0.03857	.	0.998540	0.08106	N	0.996959	T	0.15998	0.0385	N	0.24115	0.695	0.09310	N	0.999991	B	0.02656	0.0	B	0.04013	0.001	T	0.30736	-0.9968	10	0.10111	T	0.7	-11.6821	1.9929	0.03450	0.3788:0.1671:0.3411:0.113	.	528	Q8IWZ5	TRI42_HUMAN	D	528	ENSP00000286349:G528D	ENSP00000286349:G528D	G	+	2	0	TRIM42	141889797	0.000000	0.05858	0.007000	0.13788	0.846000	0.48090	-0.386000	0.07370	-0.646000	0.05452	0.655000	0.94253	GGC		TCGA-IB-AAUO-01A-12D-A38G-08	TRIM42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359531.2	0	0	0	6	429	1	157		0	0	0	1	157	2	1	9.996380e-01	19	1294	0	892	2	0	0.156637	6	424	1	156	11		0	0	0	1	157	2	-2.975212	1	1	0	0		1	1	3	4	2.765071	1	0.380000	1.860000	0.531368	0.100000	0.030000	1.000000	0.110000	0.216902	0.100000	0	0.060000	0.190000
WDR48	57599	broad.mit.edu	37	3	39118643	39118643	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr3:39118643G>A	ENST00000302313.5	+	9	939	c.911G>A	c.(910-912)aGa>aAa	p.R304K	WDR48_ENST00000418020.1_5'UTR|WDR48_ENST00000396258.3_Missense_Mutation_p.R222K|WDR48_ENST00000544962.1_Missense_Mutation_p.R96K	NM_020839.2	NP_065890.1	Q8TAF3	WDR48_HUMAN	WD repeat domain 48			15					GAGCTTGATAGATCAGCTGAT	0.373000																								0							SO:0001583	missense			ENST00000302313.5	1	1	hg19	CCDS33738.1	.	.	.	.	.	.	.	.	.	.	G	15.83	2.948961	0.53186	.	.	ENSG00000114742	ENST00000302313;ENST00000544962;ENST00000396258	T;D;T	0.87809	2.28;-2.3;2.25	6.16	6.16	0.99307	WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.88489	0.6450	N	0.22421	0.69	0.80722	D	1	P;B;B;B	0.47910	0.902;0.046;0.003;0.024	P;B;B;B	0.60173	0.87;0.007;0.001;0.002	D	0.84664	0.0708	10	0.22706	T	0.39	-0.2443	20.8598	0.99761	0.0:0.0:1.0:0.0	.	96;222;295;304	Q8TAF3-5;Q8TAF3-4;Q8TAF3-3;Q8TAF3	.;.;.;WDR48_HUMAN	K	304;96;222	ENSP00000307491:R304K;ENSP00000445187:R96K;ENSP00000379557:R222K	ENSP00000307491:R304K	R	+	2	0	WDR48	39093647	1.000000	0.71417	0.998000	0.56505	0.985000	0.73830	9.771000	0.98977	2.937000	0.99478	0.650000	0.86243	AGA		TCGA-IB-AAUO-01A-12D-A38G-08	WDR48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342529.1	0	0	1	60	324	1	122	1	5.352718e-01	4	7	1	122	2		0	0	0	0	0	2	1	1.000000	59	318	1	122	12		0	0	0	1	122	2	-20.000000	1	1	0	0		1	1	2	3	2.099036	0	0.380000	1.860000	0.388138	0.830000	0.650000	1.000000	1.000000	0.845776	0.830000	0	0.730000	0.960000
FAT1	2195	broad.mit.edu	37	4	187510153	187510153	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr4:187510153C>T	ENST00000441802.2	-	27	13569	c.13360G>A	c.(13360-13362)Gaa>Aaa	p.E4454K		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	p.E4454K(1)		228					TTGCTGAATTCGGGCGGTAAC	0.527000										HNSCC(5;0.00058)			Colon(197;1040 2055 4143 4984 49344)											1	Substitution - Missense(1)						SO:0001583	missense			ENST00000441802.2	1	1	hg19	CCDS47177.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.74|18.74	3.688735|3.688735	0.68271|0.68271	0.0|0.0	1.21E-4|1.21E-4	ENSG00000083857|ENSG00000083857	ENST00000441802;ENST00000260147|ENST00000512772;ENST00000507105	T|.	0.41400|.	1.0|.	5.37|5.37	5.37|5.37	0.77165|0.77165	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.74107|0.74107	0.3673|0.3673	M|M	0.63428|0.63428	1.95|1.95	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.80764|.	0.994|.	T|T	0.70999|0.70999	-0.4719|-0.4719	10|5	0.42905|.	T|.	0.14|.	.|.	19.3098|19.3098	0.94182|0.94182	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	4454|.	Q14517|.	FAT1_HUMAN|.	K|Q	4454;4456|233;221	ENSP00000406229:E4454K|.	ENSP00000260147:E4456K|.	E|R	-|-	1|2	0|0	FAT1|FAT1	187747147|187747147	1.000000|1.000000	0.71417|0.71417	0.163000|0.163000	0.22734|0.22734	0.033000|0.033000	0.12548|0.12548	7.111000|7.111000	0.77077|0.77077	2.800000|2.800000	0.96347|0.96347	0.455000|0.455000	0.32223|0.32223	GAA|CGA		TCGA-IB-AAUO-01A-12D-A38G-08	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	0	0	0	26	908	0	438	1	9.994895e-01	29	375	0	438	2		0	0	0	0	0	2	1	1.000000	25	883	0	434	2		0	0	0	0	438	2	-2.092925	0	1	120870	1	31	1	0	1	1	1.887815	1	0.380000	1.860000	0.301723	0.120000	0.080000	0.190000	0.130000	0.134470	0.120000	0	0.100000	0.160000
PPARGC1A	10891	broad.mit.edu	37	4	23830129	23830129	+	Silent	SNP	G	G	A			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr4:23830129G>A	ENST00000264867.2	-	5	770	c.651C>T	c.(649-651)aaC>aaT	p.N217N	PPARGC1A_ENST00000509702.1_5'UTR	NM_013261.3	NP_037393.1	Q9UBK2	PRGC1_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 alpha			51		Breast(46;0.0503)			GAGGGTCATCGTTTGTGGTCA	0.468000													Esophageal Squamous(29;694 744 13796 34866 44181)											0							SO:0001819	synonymous_variant			ENST00000264867.2	1	1	hg19	CCDS3429.1																																																																																				TCGA-IB-AAUO-01A-12D-A38G-08	PPARGC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214976.1	0	0	0	12	556	0	234		0	0	0	0	234	2		0	0	0	0	0	2	1	0.999008	12	544	0	232	2		0	0	0	0	234	2	-2.701458	1	1	121412	1	41	1	0	1	1	1.801955	1	0.380000	1.860000	0.292641	0.090000	0.040000	0.160000	0.100000	0.104767	0.090000	0	0.070000	0.130000
GRID2	2895	broad.mit.edu	37	4	94376915	94376915	+	Nonsense_Mutation	SNP	C	C	T			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr4:94376915C>T	ENST00000282020.4	+	11	1906	c.1648C>T	c.(1648-1650)Cga>Tga	p.R550*	GRID2_ENST00000510992.1_Nonsense_Mutation_p.R455*	NM_001510.2	NP_001501.2	O43424	GRID2_HUMAN	glutamate receptor, ionotropic, delta 2			100		Hepatocellular(203;0.114)|all_hematologic(202;0.177)			GGTACTACTTCGAAGGGCTGA	0.478000																								0							SO:0001587	stop_gained			ENST00000282020.4	0	1	hg19	CCDS3637.1	.	.	.	.	.	.	.	.	.	.	C	41	9.088102	0.99061	.	.	ENSG00000152208	ENST00000282020;ENST00000510992	.	.	.	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.1877	0.73016	0.1408:0.8592:0.0:0.0	.	.	.	.	X	550;455	.	ENSP00000282020:R550X	R	+	1	2	GRID2	94595938	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.461000	0.53035	2.836000	0.97738	0.655000	0.94253	CGA		TCGA-IB-AAUO-01A-12D-A38G-08	GRID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253588.2	0	0	0	13	376	0	189		0	0	0	0	189	2		0	0	0	0	0	2	1	0.999468	12	367	0	188	2		0	0	0	0	189	2	-2.960591	1	1	0	0		1	0	1	1	1.819567	1	0.380000	1.860000	0.294171	0.150000	0.080000	0.250000	0.150000	0.164518	0.150000	0	0.110000	0.210000
GRID2	2895	broad.mit.edu	37	4	94547520	94547520	+	Missense_Mutation	SNP	T	T	G			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr4:94547520T>G	ENST00000282020.4	+	14	2552	c.2294T>G	c.(2293-2295)gTt>gGt	p.V765G	GRID2_ENST00000510992.1_Missense_Mutation_p.V670G	NM_001510.2	NP_001501.2	O43424	GRID2_HUMAN	glutamate receptor, ionotropic, delta 2			100		Hepatocellular(203;0.114)|all_hematologic(202;0.177)			GGAAATACTGTTGCTGATCGG	0.388000																								0							SO:0001583	missense			ENST00000282020.4	1	1	hg19	CCDS3637.1	.	.	.	.	.	.	.	.	.	.	T	15.69	2.906796	0.52333	.	.	ENSG00000152208	ENST00000282020;ENST00000510992	T;T	0.11604	2.76;2.76	5.13	5.13	0.70059	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (2);	0.109275	0.64402	D	0.000006	T	0.11281	0.0275	L	0.34521	1.04	0.80722	D	1	B;B	0.20459	0.045;0.045	B;B	0.21917	0.037;0.037	T	0.05305	-1.0893	10	0.87932	D	0	.	15.2141	0.73250	0.0:0.0:0.0:1.0	.	670;765	E9PH24;O43424	.;GRID2_HUMAN	G	765;670	ENSP00000282020:V765G;ENSP00000421257:V670G	ENSP00000282020:V765G	V	+	2	0	GRID2	94766543	1.000000	0.71417	0.996000	0.52242	0.975000	0.68041	4.456000	0.60081	2.055000	0.61198	0.397000	0.26171	GTT		TCGA-IB-AAUO-01A-12D-A38G-08	GRID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253588.2	0	0	0	20	513	1	224	0	0	0	1	1	224	2		0	0	0	0	0	2	1	0.999994	20	502	0	223	2		0	0	0	1	224	2	-3.854210	1	1	0	0		1	0	1	1	1.819567	1	0.380000	1.860000	0.294171	0.170000	0.100000	0.260000	0.170000	0.180657	0.170000	0	0.130000	0.220000
SGCD	6444	broad.mit.edu	37	5	155771593	155771593	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr5:155771593G>A	ENST00000435422.3	+	2	582	c.95G>A	c.(94-96)cGa>cAa	p.R32Q	SGCD_ENST00000447401.1_Missense_Mutation_p.R33Q|SGCD_ENST00000517913.1_Missense_Mutation_p.R33Q|SGCD_ENST00000337851.4_Missense_Mutation_p.R33Q	NM_001128209.1	NP_001121681.1	Q92629	SGCD_HUMAN	sarcoglycan, delta (35kDa dystrophin-associated glycoprotein)			24	Renal(175;0.00488)	Medulloblastoma(196;0.0378)|all_neural(177;0.106)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)		TGGCGGAAACGATGCCTGTAT	0.483000																								0							SO:0001583	missense			ENST00000435422.3	1	1	hg19	CCDS47327.1	.	.	.	.	.	.	.	.	.	.	G	36	5.719233	0.96839	.	.	ENSG00000170624	ENST00000517913;ENST00000435422;ENST00000337851;ENST00000447401	D;D;D;D	0.95035	-3.59;-3.59;-3.59;-3.59	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	D	0.96981	0.9014	M	0.73962	2.25	0.80722	D	1	D;D;D	0.89917	0.998;0.998;1.0	D;D;D	0.83275	0.992;0.986;0.996	D	0.95484	0.8563	10	0.25751	T	0.34	-9.9405	19.6056	0.95580	0.0:0.0:1.0:0.0	.	32;33;33	Q92629;Q92629-2;Q92629-3	SGCD_HUMAN;.;.	Q	33;32;33;33	ENSP00000429378:R33Q;ENSP00000403003:R32Q;ENSP00000338343:R33Q;ENSP00000408324:R33Q	ENSP00000338343:R33Q	R	+	2	0	SGCD	155704171	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.731000	0.98807	2.625000	0.88918	0.655000	0.94253	CGA		TCGA-IB-AAUO-01A-12D-A38G-08	SGCD-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000373469.3	1	0	1	40	240	0	95	0	5.781092e-02	0	3	0	95	2		0	0	0	0	0	2	1	1.000000	40	238	0	94	2		0	0	0	0	95	2	-3.322178	1	1	0	0		1	0	1	1	2.049852	0	0.380000	1.860000	0.378820	0.740000	0.550000	0.970000	0.750000	0.758394	0.740000	0	0.640000	0.860000
ADAMTS12	81792	broad.mit.edu	37	5	33596156	33596156	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr5:33596156C>T	ENST00000504830.1	-	17	2872	c.2537G>A	c.(2536-2538)cGc>cAc	p.R846H	ADAMTS12_ENST00000352040.3_Missense_Mutation_p.R761H|ADAMTS12_ENST00000504582.1_5'UTR	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	p.R846H(1)		216					GGCAGTTTGGCGGCGGATACC	0.517000										HNSCC(64;0.19)														1	Substitution - Missense(1)						SO:0001583	missense			ENST00000504830.1	1	1	hg19	CCDS34140.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.010730	0.75046	.	.	ENSG00000151388	ENST00000504830;ENST00000352040	T;T	0.52983	0.64;0.64	5.77	4.9	0.64082	.	0.196715	0.50627	D	0.000112	T	0.49541	0.1563	L	0.55990	1.75	0.80722	D	1	P;P	0.52577	0.463;0.954	B;P	0.48552	0.067;0.581	T	0.43442	-0.9391	10	0.16420	T	0.52	.	15.3406	0.74293	0.0:0.9327:0.0:0.0673	.	761;846	P58397-3;P58397	.;ATS12_HUMAN	H	846;761	ENSP00000422554:R846H;ENSP00000344847:R761H	ENSP00000344847:R761H	R	-	2	0	ADAMTS12	33631913	0.994000	0.37717	0.987000	0.45799	0.998000	0.95712	2.459000	0.45023	1.582000	0.49881	0.585000	0.79938	CGC		TCGA-IB-AAUO-01A-12D-A38G-08	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	1	0	1	52	337	0	133	0	1.867269e-02	0	2	0	133	2		0	0	0	0	0	2	1	1.000000	52	329	0	131	2		0	0	0	0	133	2	-3.222046	1	1	121412	2	36	1	0	1	1	2.053532	0	0.380000	1.860000	0.378820	0.690000	0.530000	0.880000	0.700000	0.709020	0.690000	0	0.610000	0.800000
TIAM2	26230	broad.mit.edu	37	6	155451469	155451469	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr6:155451469C>T	ENST00000461783.3	+	6	2385	c.1112C>T	c.(1111-1113)gCg>gTg	p.A371V	TIAM2_ENST00000360366.4_Missense_Mutation_p.A371V|TIAM2_ENST00000367174.2_5'UTR|TIAM2_ENST00000318981.5_Missense_Mutation_p.A371V|TIAM2_ENST00000456144.1_Missense_Mutation_p.A371V|TIAM2_ENST00000529824.2_Missense_Mutation_p.A371V			Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2			65		Ovarian(120;0.196)			GAGGATACTGCGAAGAAGGAC	0.547000																								0							SO:0001583	missense			ENST00000461783.3	1	1	hg19	CCDS34558.1	.	.	.	.	.	.	.	.	.	.	C	13.07	2.126396	0.37533	.	.	ENSG00000146426	ENST00000461783;ENST00000528928;ENST00000528535;ENST00000456144;ENST00000318981;ENST00000360366;ENST00000529824	T;T;T;T;T;T	0.05382	3.57;3.45;3.51;3.57;3.57;3.51	5.29	5.29	0.74685	.	0.813614	0.11671	N	0.540830	T	0.03608	0.0103	L	0.40543	1.245	0.47407	D	0.999411	B	0.29909	0.261	B	0.19148	0.024	T	0.35276	-0.9795	10	0.59425	D	0.04	.	17.1487	0.86773	0.0:1.0:0.0:0.0	.	371	Q8IVF5	TIAM2_HUMAN	V	371;617;371;371;371;371;371	ENSP00000437188:A371V;ENSP00000434901:A371V;ENSP00000407746:A371V;ENSP00000327315:A371V;ENSP00000353528:A371V;ENSP00000433348:A371V	ENSP00000327315:A371V	A	+	2	0	TIAM2	155493161	0.002000	0.14202	0.364000	0.25888	0.430000	0.31655	1.419000	0.34793	2.489000	0.83994	0.655000	0.94253	GCG		TCGA-IB-AAUO-01A-12D-A38G-08	TIAM2-005	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000387980.2	0	0	0	12	201	1	91		0	0	0	1	91	2		0	0	0	0	0	2	1	0.713298	11	195	1	91	10		0	0	0	1	91	2	-4.756731	1	1	121412	5	40	1	0	1	1	1.683475	1	0.380000	1.860000	0.234568	0.240000	0.130000	0.390000	0.240000	0.253837	0.240000	0	0.180000	0.320000
HIST1H2BF	8343	broad.mit.edu	37	6	26199947	26199947	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr6:26199947G>A	ENST00000359985.1	+	1	200	c.161G>A	c.(160-162)gGc>gAc	p.G54D	HIST1H2AD_ENST00000341023.1_5'Flank|HIST1H3D_ENST00000377831.5_5'Flank|HIST1H3D_ENST00000356476.2_5'Flank	NM_003522.3	NP_003513.1	P62807	H2B1C_HUMAN	histone cluster 1, H2bf			17		all_hematologic(11;0.196)			CCCGACACCGGCATCTCATCC	0.567000																								0							SO:0001583	missense			ENST00000359985.1	0	1	hg19	CCDS4592.1	.	.	.	.	.	.	.	.	.	.	.	16.80	3.222980	0.58668	.	.	ENSG00000197846	ENST00000359985	T	0.69435	-0.4	3.89	3.89	0.44902	.	0.000000	0.42172	D	0.000755	T	0.73442	0.3587	.	.	.	0.41511	D	0.988346	.	.	.	.	.	.	T	0.78807	-0.2059	7	0.87932	D	0	.	15.7145	0.77658	0.0:0.0:1.0:0.0	.	.	.	.	D	54	ENSP00000353074:G54D	ENSP00000353074:G54D	G	+	2	0	HIST1H2BF	26307926	1.000000	0.71417	0.996000	0.52242	0.014000	0.08584	9.518000	0.98022	2.102000	0.63906	0.650000	0.86243	GGC		TCGA-IB-AAUO-01A-12D-A38G-08	HIST1H2BF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040108.1	0	0	0	7	861	0	446	0	5.811399e-03	0	12	0	446	2		0	0	0	0	0	2	1	0.979120	7	843	0	442	2		0	0	0	0	446	2	-1.773335	0	1	0	0		1	0	1	1	1.735691	1	0.380000	1.860000	0.258905	0.030000	0.010000	0.070000	0.040000	0.040361	0.030000	0	0.020000	0.050000
NCR2	9436	broad.mit.edu	37	6	41318497	41318497	+	Silent	SNP	G	G	A			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr6:41318497G>A	ENST00000373089.5	+	5	814	c.726G>A	c.(724-726)acG>acA	p.T242T	NCR2_ENST00000373086.3_3'UTR|NCR2_ENST00000373083.4_3'UTR	NM_004828.3	NP_004819.2	O95944	NCTR2_HUMAN	natural cytotoxicity triggering receptor 2			14	Ovarian(28;0.0327)|Colorectal(47;0.196)				aacaggtcacggaccttccct	0.478000																								0							SO:0001819	synonymous_variant			ENST00000373089.5	0	1	hg19	CCDS4855.1																																																																																				TCGA-IB-AAUO-01A-12D-A38G-08	NCR2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040511.3	0	0	0	7	206	0	115		0	0	0	0	115	2		0	0	0	0	0	2	1	0.980475	7	204	0	112	2		0	0	0	0	115	2	-3.239604	1	1	0	0		1	0	1	1	1.719762	1	0.380000	1.860000	0.257218	0.140000	0.060000	0.280000	0.140000	0.161258	0.140000	0	0.100000	0.210000
COQ3	51805	broad.mit.edu	37	6	99831606	99831606	+	Silent	SNP	G	G	A			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr6:99831606G>A	ENST00000254759.3	-	2	225	c.201C>T	c.(199-201)atC>atT	p.I67I	COQ3_ENST00000369242.1_5'UTR|COQ3_ENST00000479163.1_5'UTR	NM_017421.3	NP_059117.3	Q9NZJ6	COQ3_HUMAN	coenzyme Q3 methyltransferase			8		all_cancers(76;1.24e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.00716)|Colorectal(196;0.0691)|Lung NSC(302;0.186)			AACAGGAAAAGATCGTCCTGT	0.338000																								0							SO:0001819	synonymous_variant			ENST00000254759.3	1	1	hg19	CCDS5042.1																																																																																				TCGA-IB-AAUO-01A-12D-A38G-08	COQ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041602.1	0	0	0	23	726	0	352	0	5.578315e-02	1	11	0	352	2		0	0	0	0	0	2	1	0.999999	23	712	0	353	2		0	0	0	0	352	2	-18.621690	1	1	0	0		1	0	1	1	1.719762	1	0.380000	1.860000	0.257218	0.130000	0.080000	0.200000	0.130000	0.139851	0.130000	0	0.100000	0.170000
CDHR3	222256	broad.mit.edu	37	7	105673026	105673026	+	Silent	SNP	G	G	A			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr7:105673026G>A	ENST00000317716.9	+	19	2621	c.2541G>A	c.(2539-2541)gcG>gcA	p.A847A	CDHR3_ENST00000478080.1_Silent_p.A759A|CDHR3_ENST00000343407.5_3'UTR|CDHR3_ENST00000542731.1_Silent_p.A847A	NM_152750.4	NP_689963.2	Q6ZTQ4	CDHR3_HUMAN	cadherin-related family member 3			23					GTGGCAAAGCGTGGGCTGAGG	0.577000																								0							SO:0001819	synonymous_variant			ENST00000317716.9	1	1	hg19	CCDS47684.1																																																																																				TCGA-IB-AAUO-01A-12D-A38G-08	CDHR3-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349025.2	1	0	0	9	163	0	76	0	3.612479e-03	0	2	0	76	2		0	0	0	0	0	2	1	0.994603	9	162	0	75	2		0	0	0	0	76	2	-4.752440	1	1	0	0		1	0	0	0	2.043431	0	0.380000	1.860000	0.377635	0.280000	0.130000	0.480000	0.280000	0.298461	0.280000	0	0.200000	0.380000
FLNC	2318	broad.mit.edu	37	7	128480725	128480725	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr7:128480725G>A	ENST00000325888.8	+	10	1934	c.1673G>A	c.(1672-1674)cGc>cAc	p.R558H	FLNC_ENST00000346177.6_Missense_Mutation_p.R558H	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma			128					GCCATCCCTCGCAGGTGAGTA	0.637000																								0							SO:0001583	missense			ENST00000325888.8	1	1	hg19	CCDS43644.1	.	.	.	.	.	.	.	.	.	.	G	18.84	3.708659	0.68615	.	.	ENSG00000128591	ENST00000325888;ENST00000346177	D;D	0.91894	-2.93;-2.93	5.02	5.02	0.67125	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.059561	0.64402	D	0.000004	D	0.94345	0.8182	L	0.53249	1.67	0.47183	D	0.999344	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.953	D	0.94549	0.7752	10	0.87932	D	0	.	12.2416	0.54546	0.0893:0.0:0.9107:0.0	.	558;558	Q14315-2;Q14315	.;FLNC_HUMAN	H	558	ENSP00000327145:R558H;ENSP00000344002:R558H	ENSP00000327145:R558H	R	+	2	0	FLNC	128267961	0.981000	0.34729	1.000000	0.80357	0.037000	0.13140	4.138000	0.58017	2.327000	0.79052	0.491000	0.48974	CGC		TCGA-IB-AAUO-01A-12D-A38G-08	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3	1	0	1	44	345	0	158	0	1.350540e-02	1	1	0	158	2		0	0	0	0	0	2	1	1.000000	41	336	0	158	2		0	0	0	0	158	2	-16.205010	1	1	121074	5	41	1	0	0	0	2.043431	0	0.380000	1.860000	0.377635	0.590000	0.430000	0.760000	0.590000	0.600882	0.590000	0	0.510000	0.680000
MRPS33	51650	broad.mit.edu	37	7	140710243	140710243	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr7:140710243G>A	ENST00000393008.3	-	2	346	c.191C>T	c.(190-192)aCg>aTg	p.T64M	MRPS33_ENST00000467334.1_Missense_Mutation_p.T54M|MRPS33_ENST00000324787.5_Missense_Mutation_p.T64M|MRPS33_ENST00000472343.1_5'Flank|MRPS33_ENST00000496958.1_Missense_Mutation_p.T64M|MRPS33_ENST00000469351.1_Missense_Mutation_p.T64M	NM_016071.3	NP_057155.1	Q9Y291	RT33_HUMAN	mitochondrial ribosomal protein S33			4	Melanoma(164;0.00956)				AAATCGGAGCGTCTGCATGAG	0.413000																								0							SO:0001583	missense			ENST00000393008.3	1	1	hg19	CCDS5864.1	.	.	.	.	.	.	.	.	.	.	G	9.817	1.184686	0.21870	0.0	2.33E-4	ENSG00000090263	ENST00000544013;ENST00000393008;ENST00000324787;ENST00000496958;ENST00000469351;ENST00000467334	.	.	.	5.1	-4.84	0.03151	.	0.517024	0.23549	N	0.046999	T	0.20780	0.0500	N	0.16368	0.405	0.09310	N	0.999996	D	0.69078	0.997	P	0.56514	0.8	T	0.25363	-1.0134	9	0.28530	T	0.3	-2.3832	5.3	0.15773	0.4111:0.0:0.2195:0.3694	.	64	Q9Y291	RT33_HUMAN	M	64;64;64;64;64;54	.	ENSP00000320567:T64M	T	-	2	0	MRPS33	140356712	0.093000	0.21703	0.010000	0.14722	0.057000	0.15508	0.429000	0.21412	-0.574000	0.05990	0.467000	0.42956	ACG		TCGA-IB-AAUO-01A-12D-A38G-08	MRPS33-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348878.1	1	0	1	61	309	0	124	1	1	56	151	0	124	2		0	0	0	0	0	2	1	1.000000	61	301	0	124	2		0	0	0	0	124	2	-20.000000	1	1	121412	11	43	1	0	0	0	2.043431	0	0.380000	1.860000	0.377635	0.860000	0.670000	1.000000	1.000000	0.864594	0.860000	1	0.760000	0.970000
LIMK1	3984	broad.mit.edu	37	7	73511508	73511508	+	Silent	SNP	C	C	A			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr7:73511508C>A	ENST00000336180.2	+	4	441	c.390C>A	c.(388-390)tcC>tcA	p.S130S	LIMK1_ENST00000418310.1_Silent_p.S160S|LIMK1_ENST00000538333.3_Silent_p.S96S|LIMK1_ENST00000491052.1_3'UTR	NM_002314.3	NP_002305.1	P53667	LIMK1_HUMAN	LIM domain kinase 1			21		Lung NSC(55;0.137)		Dabrafenib(DB08912)	TGGAGCACTCCAAGCTGTACT	0.617000																								0							SO:0001819	synonymous_variant			ENST00000336180.2	1	0	hg19	CCDS5563.1																																																																																				TCGA-IB-AAUO-01A-12D-A38G-08	LIMK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252335.2	1	0	0	4	86	0	40	0	6.813097e-01	0	49	0	40	2		0	0	0	0	0	2	1	0.883922	3	84	0	40	2		0	0	0	0	40	2	-7.787154	1	0	0	0		1	0	0	0	2.043431	0	0.380000	1.860000	0.377635	0.250000	0.080000	0.530000	0.230000	0.279792	0.250000	0	0.150000	0.390000
ZHX2	22882	broad.mit.edu	37	8	123965170	123965170	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr8:123965170G>A	ENST00000314393.4	+	3	2255	c.1420G>A	c.(1420-1422)Gag>Aag	p.E474K		NM_014943.3	NP_055758.1	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2			45	Lung NSC(37;2e-09)|Ovarian(258;0.0205)|Hepatocellular(40;0.105)		STAD - Stomach adenocarcinoma(47;0.00527)		CCGGCTCATCGAGGTGACTGG	0.557000													Esophageal Squamous(94;1056 1388 11767 13799 49639)											0							SO:0001583	missense			ENST00000314393.4	0	1	hg19	CCDS6336.1	.	.	.	.	.	.	.	.	.	.	G	11.86	1.765980	0.31228	2.27E-4	0.0	ENSG00000178764	ENST00000314393	D	0.95949	-3.86	5.94	5.07	0.68467	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.102570	0.64402	D	0.000003	D	0.90106	0.6909	N	0.21448	0.665	0.80722	D	1	B	0.24043	0.096	B	0.20577	0.03	D	0.86463	0.1780	10	0.09843	T	0.71	-24.8951	15.4187	0.74995	0.0667:0.0:0.9333:0.0	.	474	Q9Y6X8	ZHX2_HUMAN	K	474	ENSP00000314709:E474K	ENSP00000314709:E474K	E	+	1	0	ZHX2	124034351	1.000000	0.71417	1.000000	0.80357	0.468000	0.32798	7.641000	0.83368	1.531000	0.49152	0.561000	0.74099	GAG		TCGA-IB-AAUO-01A-12D-A38G-08	ZHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381709.1	0	0	0	6	176	0	69	0	1.405705e-01	0	17	0	69	2		0	0	0	0	0	2	1	0.961326	5	170	0	68	2		0	0	0	0	69	2	-7.954317	1	1	121412	2	36	1	0	0	0	2.045321	0	0.380000	1.860000	0.377635	0.180000	0.070000	0.350000	0.170000	0.197672	0.180000	0	0.120000	0.270000
BAI1	575	broad.mit.edu	37	8	143618425	143618425	+	Silent	SNP	C	C	T			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr8:143618425C>T	ENST00000517894.1	+	26	4542	c.3648C>T	c.(3646-3648)aaC>aaT	p.N1216N	BAI1_ENST00000323289.5_Silent_p.N1216N			O14514	BAI1_HUMAN	brain-specific angiogenesis inhibitor 1			57	all_cancers(97;2.84e-12)|all_epithelial(106;5.91e-09)|Lung NSC(106;0.000322)|all_lung(105;0.000616)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)				CCTTCCAGAACGGCCACGCCC	0.692000																								0							SO:0001819	synonymous_variant			ENST00000517894.1	0	1	hg19																																																																																					TCGA-IB-AAUO-01A-12D-A38G-08	BAI1-001	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000379963.3	0	0	0	4	47	0	25	0	0	1	0	0	25	2		0	0	0	0	0	2	1	0.888377	4	46	0	25	2		0	0	0	0	25	2	-8.885540	1	1	120508	2	22	1	0	0	0	2.045321	0	0.380000	1.860000	0.377635	0.440000	0.150000	0.900000	0.400000	0.477273	0.440000	0	0.270000	0.670000
COL5A1	1289	broad.mit.edu	37	9	137709638	137709638	+	Silent	SNP	C	C	T			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr9:137709638C>T	ENST00000371817.3	+	54	4605	c.4191C>T	c.(4189-4191)ccC>ccT	p.P1397P		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1			115		Myeloproliferative disorder(178;0.0341)			CCCCAGGCCCCGCAGGCCCCG	0.657000																								0							SO:0001819	synonymous_variant			ENST00000371817.3	1	1	hg19	CCDS6982.1																																																																																				TCGA-IB-AAUO-01A-12D-A38G-08	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	1	0	1	11	46	0	24	1	9.999994e-01	15	144	0	24	2		0	0	0	0	0	2	1	0.998775	11	45	0	24	2		0	0	0	0	24	2	-19.894380	1	1	0	0		1	0	1	1	2.053346	0	0.380000	1.860000	0.378820	0.990000	0.560000	1.000000	1.000000	0.913558	0.990000	1	0.760000	1.000000
SNAPC4	6621	broad.mit.edu	37	9	139289824	139289824	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr9:139289824C>T	ENST00000298532.2	-	4	765	c.397G>A	c.(397-399)Ggc>Agc	p.G133S		NM_003086.2	NP_003077.2			small nuclear RNA activating complex, polypeptide 4, 190kDa			33		Myeloproliferative disorder(178;0.0511)			AGGCTTTTGCCATCTTTCACC	0.567000																								0							SO:0001583	missense			ENST00000298532.2	1	1	hg19	CCDS6998.1	.	.	.	.	.	.	.	.	.	.	C	6.565	0.472500	0.12461	.	.	ENSG00000165684	ENST00000298532	T	0.28255	1.62	5.35	-2.81	0.05805	.	1.072810	0.07153	N	0.849409	T	0.25791	0.0628	L	0.48362	1.52	0.09310	N	0.999994	B	0.28378	0.209	B	0.22880	0.042	T	0.25012	-1.0144	10	0.52906	T	0.07	-3.3704	10.5123	0.44868	0.0:0.4466:0.0:0.5534	.	133	Q5SXM2	SNPC4_HUMAN	S	133	ENSP00000298532:G133S	ENSP00000298532:G133S	G	-	1	0	SNAPC4	138409645	0.003000	0.15002	0.000000	0.03702	0.004000	0.04260	-0.062000	0.11674	-0.992000	0.03472	-1.074000	0.02243	GGC		TCGA-IB-AAUO-01A-12D-A38G-08	SNAPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055071.1	0	0	0	9	275	0	103	0	6.684777e-02	0	12	0	103	2		0	0	0	0	0	2	1	0.993849	9	269	0	103	2		0	0	0	0	103	2	-3.002049	1	1	121380	1	29	1	0	1	1	2.053346	0	0.380000	1.860000	0.378820	0.170000	0.080000	0.300000	0.160000	0.182619	0.170000	0	0.120000	0.240000
ARID3C	138715	broad.mit.edu	37	9	34622033	34622033	+	Silent	SNP	G	G	A			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr9:34622033G>A	ENST00000378909.2	-	6	1214	c.1122C>T	c.(1120-1122)aaC>aaT	p.N374N	DCTN3_ENST00000259632.7_5'Flank|DCTN3_ENST00000477738.2_5'Flank|DCTN3_ENST00000378916.4_5'Flank|DCTN3_ENST00000341694.2_5'Flank|DCTN3_ENST00000447983.2_5'Flank|DCTN3_ENST00000378913.2_5'Flank	NM_001017363.1	NP_001017363.1	A6NKF2	ARI3C_HUMAN	AT rich interactive domain 3C (BRIGHT-like)			14	all_epithelial(49;0.102)		STAD - Stomach adenocarcinoma(86;0.178)		AGACCACCCCGTTGATCTCTA	0.552000																								0							SO:0001819	synonymous_variant			ENST00000378909.2	1	1	hg19	CCDS35006.1																																																																																				TCGA-IB-AAUO-01A-12D-A38G-08	ARID3C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348265.1	1	0	1	42	302	0	126		0	0	0	0	126	2		0	0	0	0	0	2	1	1.000000	42	293	0	125	2		0	0	0	0	126	2	-3.221920	1	1	121412	3	41	1	0	0	0	2.022799	0	0.380000	1.860000	0.370431	0.630000	0.460000	0.820000	0.630000	0.640969	0.630000	0	0.540000	0.730000
TRPM6	140803	broad.mit.edu	37	9	77390934	77390934	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chr9:77390934G>A	ENST00000360774.1	-	24	3505	c.3268C>T	c.(3268-3270)Cgc>Tgc	p.R1090C	TRPM6_ENST00000451710.3_Missense_Mutation_p.R1090C|TRPM6_ENST00000376871.3_Intron|TRPM6_ENST00000376864.4_Missense_Mutation_p.R1090C|TRPM6_ENST00000361255.3_Missense_Mutation_p.R1085C|TRPM6_ENST00000376872.3_Intron|TRPM6_ENST00000449912.2_Missense_Mutation_p.R1085C	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6			126					ATGATGTAGCGATAGCGGTTG	0.493000																								0							SO:0001583	missense			ENST00000360774.1	1	1	hg19	CCDS6647.1	.	.	.	.	.	.	.	.	.	.	G	32	5.120843	0.94385	.	.	ENSG00000119121	ENST00000360774;ENST00000451710;ENST00000449912;ENST00000361255;ENST00000376864;ENST00000312449;ENST00000448641	T;T;T;T;T	0.55588	0.6;0.6;0.6;0.6;0.51	5.76	5.76	0.90799	.	0.046412	0.85682	D	0.000000	T	0.72779	0.3503	M	0.72894	2.215	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.67900	0.932;0.931;0.954	T	0.74426	-0.3669	10	0.87932	D	0	.	19.9561	0.97218	0.0:0.0:1.0:0.0	.	1090;1085;1085	Q9BX84;Q9BX84-3;Q9BX84-2	TRPM6_HUMAN;.;.	C	1090;1090;1085;1085;1090;753;753	ENSP00000354006:R1090C;ENSP00000407341:R1090C;ENSP00000396672:R1085C;ENSP00000354962:R1085C;ENSP00000366060:R1090C	ENSP00000309693:R753C	R	-	1	0	TRPM6	76580754	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	7.827000	0.86722	2.725000	0.93324	0.591000	0.81541	CGC		TCGA-IB-AAUO-01A-12D-A38G-08	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	0	0	0	12	424	0	147		0	0	0	0	147	2		0	0	0	0	0	2	1	0.999078	12	419	0	143	2		0	0	0	0	147	2	-2.818145	1	1	0	0		1	0	0	0	2.022799	0	0.380000	1.860000	0.370431	0.140000	0.070000	0.240000	0.140000	0.153237	0.140000	0	0.100000	0.190000
DMD	1756	broad.mit.edu	37	X	32663260	32663260	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-AAUO-01A-12D-A38G-08	TCGA-IB-AAUO-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fea1f02f-d937-4ce1-99cc-b1253242f1cf	84813019-93c1-4f1c-8103-a43c6b33b120	g.chrX:32663260C>T	ENST00000357033.4	-	10	1176	c.970G>A	c.(970-972)Gct>Act	p.A324T	DMD_ENST00000288447.4_Missense_Mutation_p.A316T|DMD_ENST00000378677.2_Missense_Mutation_p.A320T	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin			77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)			TCTTCAGGAGCTTCCAAATGC	0.348000																								0							SO:0001583	missense			ENST00000357033.4	0	1	hg19	CCDS14233.1	.	.	.	.	.	.	.	.	.	.	C	3.513	-0.099324	0.07010	.	.	ENSG00000198947	ENST00000534884;ENST00000378677;ENST00000357033;ENST00000542849;ENST00000535280;ENST00000288447	T;T;T	0.72615	0.16;0.16;-0.67	5.67	2.85	0.33270	.	0.197530	0.24231	U	0.040342	T	0.40815	0.1132	N	0.05078	-0.115	0.80722	D	1	B;B;B;B;B	0.10296	0.0;0.0;0.002;0.003;0.001	B;B;B;B;B	0.10450	0.0;0.0;0.005;0.002;0.002	T	0.32188	-0.9916	10	0.02654	T	1	.	7.4854	0.27429	0.0:0.574:0.0:0.426	.	320;316;316;324;320	B1AK23;Q4G0X0;P11532-4;P11532;E9PDN5	.;.;.;DMD_HUMAN;.	T	316;320;324;324;201;316	ENSP00000367948:A320T;ENSP00000354923:A324T;ENSP00000288447:A316T	ENSP00000288447:A316T	A	-	1	0	DMD	32573181	0.963000	0.33076	1.000000	0.80357	0.984000	0.73092	-0.020000	0.12525	0.611000	0.30052	0.600000	0.82982	GCT		TCGA-IB-AAUO-01A-12D-A38G-08	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	0	0	0	8	439	1	205		0	0	0	1	205	2		0	0	0	0	0	2	0	0.387457	8	430	1	202	10		0	0	0	1	205	2	-7.139841	1	1	0	0		1	0	1	1			0.380000	1.860000	0.380000	0.090000	0.040000	0.180000	0.100000	0.105095	0.090000	0	0.060000	0.140000
