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
MYH7B	57644	broad.mit.edu	37	20	33586211	33586212	+	Frame_Shift_Del	DEL	AC	AC	-			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr20:33586211_33586212delAC	ENST00000262873.7	+	31	4079_4080	c.3987_3988delAC	c.(3985-3990)ctacagfs	p.Q1330fs		NM_020884.3	NP_065935.2	A7E2Y1	MYH7B_HUMAN	myosin, heavy chain 7B, cardiac muscle, beta			54			BRCA - Breast invasive adenocarcinoma(18;0.00691)		GTGGGCGACTACAGACGGAAAG	0.649000																								0							SO:0001589	frameshift_variant			ENST00000262873.7	1	1	hg19	CCDS42869.1																																																																																				TCGA-3A-A9J0-01A-11D-A40W-08	MYH7B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078833.2	1	0	0	66	458	0	97	0	1.255107e-01	0	5	0	97	2	0	0	0	0	0	0		1	0.999997	71	454	2	93	26								-20.000000	1	1	0	0		1	1	3	4	2.263571	1	0.470000	3.280000	0.639456	0.780000	6.100000e-01	0.970000	0.800000	0.795274	0.780000	0		
SLC12A5	57468	broad.mit.edu	37	20	44685140	44685142	+	In_Frame_Del	DEL	AGA	AGA	-			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr20:44685140_44685142delAGA	ENST00000454036.2	+	23	3165_3167	c.3116_3118delAGA	c.(3115-3120)gagaag>gag	p.K1040del	SLC12A5_ENST00000243964.3_In_Frame_Del_p.K1017del	NM_001134771.1	NP_001128243.1	Q9H2X9	S12A5_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 5			80		Myeloproliferative disorder(115;0.0122)		Bumetanide(DB00887)|Potassium Chloride(DB00761)	TCGGTGGCAGAGAAGAATAAGGG	0.635000																								0							SO:0001651	inframe_deletion			ENST00000454036.2	0	1	hg19	CCDS46610.1																																																																																				TCGA-3A-A9J0-01A-11D-A40W-08	SLC12A5-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000471538.1	1	0	0	18	249	0	49			0	0	0	49		0	0	0	0	0	0		1	0.241023	25	251	2	50	24								-19.995170	1	0	0	0		1	1	3	4	2.263571	1	0.470000	3.280000	0.639456	0.420000	2.600000e-01	0.630000	0.430000	0.440905	0.420000	0		
ANKRD50	57182	broad.mit.edu	37	4	125599951	125599952	+	Frame_Shift_Ins	INS	-	-	A			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr4:125599951_125599952insA	ENST00000504087.1	-	3	1658_1659	c.621_622insT	c.(619-624)tctaccfs	p.T208fs	ANKRD50_ENST00000515641.1_Frame_Shift_Ins_p.T29fs	NM_020337.2	NP_065070.1	Q9ULJ7	ANR50_HUMAN	ankyrin repeat domain 50			55					GATAAGCTGGTAGACGTTTGTT	0.475000																								0							SO:0001589	frameshift_variant			ENST00000504087.1	0	1	hg19	CCDS34060.1																																																																																				TCGA-3A-A9J0-01A-11D-A40W-08	ANKRD50-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364775.1	1	0	0	219	735	0	130			0	0	0	130		0	0	0	0	0	0		1	1.000000	220	731	0	127	2								-20.000000	1	1	0	0		1	1	2	3	1.838072	1	0.470000	3.280000	0.566728	0.990000	9.900000e-01	1.000000	1.000000	0.999958	0.990000	1		
CPXM2	119587	broad.mit.edu	37	10	125557591	125557591	+	Missense_Mutation	SNP	C	C	T			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr10:125557591C>T	ENST00000241305.3	-	6	944	c.790G>A	c.(790-792)Gtc>Atc	p.V264I	CPXM2_ENST00000368854.3_5'UTR	NM_198148.2	NP_937791.2	Q8N436	CPXM2_HUMAN	carboxypeptidase X (M14 family), member 2			47		all_lung(145;0.174)|Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)|Lung NSC(174;0.233)			ACCATGGGGACGGGTAGCTCA	0.483000																								0							SO:0001583	missense			ENST00000241305.3	1	1	hg19	CCDS7637.1	.	.	.	.	.	.	.	.	.	.	C	6.854	0.526842	0.13066	.	.	ENSG00000121898	ENST00000241305;ENST00000540123;ENST00000418782	D	0.98164	-4.76	4.46	4.46	0.54185	Coagulation factor 5/8 C-terminal type domain (3);Galactose-binding domain-like (1);	0.450854	0.23631	N	0.046134	D	0.95850	0.8649	L	0.45051	1.395	0.25694	N	0.985655	P	0.41420	0.749	B	0.36534	0.227	D	0.90460	0.4445	10	0.23891	T	0.37	-14.947	17.3109	0.87210	0.0:1.0:0.0:0.0	.	264	Q8N436	CPXM2_HUMAN	I	264;97;264	ENSP00000241305:V264I	ENSP00000241305:V264I	V	-	1	0	CPXM2	125547581	0.000000	0.05858	0.972000	0.41901	0.126000	0.20510	0.687000	0.25407	2.292000	0.77174	0.557000	0.71058	GTC		TCGA-3A-A9J0-01A-11D-A40W-08	CPXM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050853.1	1	0	0	19	240	0	46	0	4.267932e-01	0	19	0	46	2		0	0	0	0	0	2	1	0.999990	19	235	0	43	2								-6.781784	1	1	121412	20	43	1	0	3	3	1.934708	1	0.470000	3.280000	0.570850	0.380000	2.400000e-01	0.570000	0.390000	0.401540	0.380000	0		
ARHGAP21	57584	broad.mit.edu	37	10	24959236	24959236	+	Missense_Mutation	SNP	T	T	G			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr10:24959236T>G	ENST00000396432.2	-	3	640	c.154A>C	c.(154-156)Acg>Ccg	p.T52P		NM_020824.3	NP_065875.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21			78					CTTTTCAACGTAACTGTTTTG	0.343000																								0							SO:0001583	missense			ENST00000396432.2	1	1	hg19	CCDS7144.2	.	.	.	.	.	.	.	.	.	.	T	10.53	1.375711	0.24857	.	.	ENSG00000107863	ENST00000396432;ENST00000447364;ENST00000376410;ENST00000446003;ENST00000416305	T;T;T;T	0.19250	2.16;2.16;2.16;2.16	5.19	-0.861	0.10676	PDZ/DHR/GLGF (2);	0.700803	0.15367	N	0.266050	T	0.19046	0.0457	M	0.63843	1.955	0.09310	N	1	B;B;B	0.15719	0.014;0.011;0.002	B;B;B	0.28638	0.077;0.092;0.039	T	0.29792	-1.0000	10	0.52906	T	0.07	.	3.228	0.06739	0.1417:0.131:0.5257:0.2015	.	52;51;51	F8W9U9;Q5T5U2;Q5T5U3	.;.;RHG21_HUMAN	P	52;51;52;52;41	ENSP00000379709:T52P;ENSP00000365592:T52P;ENSP00000405018:T52P;ENSP00000400566:T41P	ENSP00000365592:T52P	T	-	1	0	ARHGAP21	24999242	0.001000	0.12720	0.006000	0.13384	0.925000	0.55904	0.156000	0.16382	-0.015000	0.14150	-0.321000	0.08615	ACG		TCGA-3A-A9J0-01A-11D-A40W-08	ARHGAP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047229.4	0	0	0	21	323	1	78	1	1.212428e-01	3	16	1	78	3		0	0	0	0	0	2	1	0.873978	20	319	1	78	15								-6.276031	1	1	0	0		1	0	3	3	1.931745	1	0.470000	3.280000	0.570850	0.320000	2.000000e-01	0.470000	0.330000	0.333422	0.320000	0		
IL2RA	3559	broad.mit.edu	37	10	6063598	6063598	+	Silent	SNP	G	G	A			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr10:6063598G>A	ENST00000379959.3	-	4	599	c.426C>T	c.(424-426)ttC>ttT	p.F142F	IL2RA_ENST00000379954.1_Intron|IL2RA_ENST00000256876.6_Silent_p.F142F	NM_000417.2	NP_000408.1	P01589	IL2RA_HUMAN	interleukin 2 receptor, alpha	p.F142F(2)		17				Aldesleukin(DB00041)|Basiliximab(DB00074)|Daclizumab(DB00111)|Denileukin diftitox(DB00004)	GCCCCACCACGAAATGATAAA	0.512000																								2	Substitution - coding silent(2)						SO:0001819	synonymous_variant			ENST00000379959.3	1	1	hg19	CCDS7076.1																																																																																				TCGA-3A-A9J0-01A-11D-A40W-08	IL2RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046627.1	1	0	1	85	303	0	76	0	3.054982e-01	0	5	0	76	2		0	0	0	0	0	2	1	1.000000	84	294	0	74	2								-20.000000	1	1	121412	1	33	1	0	3	3	1.931745	1	0.470000	3.280000	0.570850	0.990000	9.400000e-01	1.000000	1.000000	0.996612	0.990000	1		
MCAM	4162	broad.mit.edu	37	11	119182565	119182565	+	Missense_Mutation	SNP	C	C	T			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr11:119182565C>T	ENST00000264036.4	-	10	1252	c.1238G>A	c.(1237-1239)aGc>aAc	p.S413N	MCAM_ENST00000392814.1_Missense_Mutation_p.S362N	NM_006500.2	NP_006491.2	P43121	MUC18_HUMAN	melanoma cell adhesion molecule			22		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)			GCCGGGTATGCTGGGCACAGA	0.617000																								0							SO:0001583	missense			ENST00000264036.4	0	1	hg19	CCDS31690.1	.	.	.	.	.	.	.	.	.	.	C	14.87	2.664926	0.47572	.	.	ENSG00000076706	ENST00000264036;ENST00000392814	T;T	0.15256	2.44;2.44	4.86	1.75	0.24633	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);	.	.	.	.	T	0.20577	0.0495	M	0.80183	2.485	0.22354	N	0.999179	B	0.20671	0.047	B	0.20577	0.03	T	0.17684	-1.0361	9	0.38643	T	0.18	-5.4	6.2247	0.20701	0.0:0.5299:0.3693:0.1008	.	413	P43121	MUC18_HUMAN	N	413;362	ENSP00000264036:S413N;ENSP00000376561:S362N	ENSP00000264036:S413N	S	-	2	0	MCAM	118687775	0.002000	0.14202	0.803000	0.32268	0.710000	0.40934	-0.056000	0.11787	1.216000	0.43427	0.561000	0.74099	AGC		TCGA-3A-A9J0-01A-11D-A40W-08	MCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388332.2	0	0	0	5	401	0	113	0	3.755845e-01	0	91	0	113	2		0	0	0	0	0	2	1	0.935436	5	395	0	110	2								-2.580035	1	1	0	0		1	1	2	3	1.848552	1	0.470000	3.280000	0.564216	0.070000	1.000000e-02	1.000000	0.060000	0.135251	0.070000	0		
PKNOX2	63876	broad.mit.edu	37	11	125281736	125281736	+	Missense_Mutation	SNP	G	G	A			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr11:125281736G>A	ENST00000298282.9	+	10	1182	c.911G>A	c.(910-912)cGt>cAt	p.R304H	PKNOX2_ENST00000542175.1_Missense_Mutation_p.R240H|PKNOX2_ENST00000530517.1_3'UTR	NM_022062.2	NP_071345.2	Q96KN3	PKNX2_HUMAN	PBX/knotted 1 homeobox 2			29		Breast(109;0.00234)|all_lung(97;0.0191)|Lung NSC(97;0.0196)|Medulloblastoma(222;0.0447)|all_neural(223;0.116)			AATATAATGCGTTCTTGGCTC	0.517000																								0							SO:0001583	missense			ENST00000298282.9	1	1	hg19	CCDS41730.1	.	.	.	.	.	.	.	.	.	.	G	32	5.173199	0.94807	.	.	ENSG00000165495	ENST00000530517;ENST00000531116;ENST00000298282;ENST00000542175;ENST00000535518	D;D;D;D	0.84298	-1.83;-1.83;-1.83;-1.83	5.45	5.45	0.79879	Homeodomain-related (1);Homeobox (2);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.91095	0.7197	L	0.55990	1.75	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.91635	0.999;0.987;0.98	D	0.91504	0.5221	10	0.87932	D	0	-4.6596	19.2404	0.93879	0.0:0.0:1.0:0.0	.	240;275;304	F5GZ15;B7Z3G7;Q96KN3	.;.;PKNX2_HUMAN	H	275;275;304;240;292	ENSP00000434732:R275H;ENSP00000433971:R275H;ENSP00000298282:R304H;ENSP00000441470:R240H	ENSP00000298282:R304H	R	+	2	0	PKNOX2	124786946	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.048000	0.93830	2.714000	0.92807	0.561000	0.74099	CGT		TCGA-3A-A9J0-01A-11D-A40W-08	PKNOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386866.3	1	0	1	87	382	0	129	0	3.522977e-02	0	2	0	129	2		0	0	0	0	0	2	1	1.000000	87	376	0	127	2								-20.000000	1	1	121012	1	33	1	1	2	3	1.859412	1	0.470000	3.280000	0.570032	0.970000	7.900000e-01	1.000000	1.000000	0.950271	0.970000	1		
APLP2	334	broad.mit.edu	37	11	129993656	129993656	+	Missense_Mutation	SNP	G	G	A			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr11:129993656G>A	ENST00000263574.5	+	7	1144	c.1072G>A	c.(1072-1074)Gct>Act	p.A358T	APLP2_ENST00000528499.1_Intron|APLP2_ENST00000543137.1_Missense_Mutation_p.A265T|APLP2_ENST00000345598.5_Intron|APLP2_ENST00000338167.5_Missense_Mutation_p.A358T|APLP2_ENST00000539648.1_Intron|APLP2_ENST00000278756.7_Missense_Mutation_p.A368T	NM_001642.2	NP_001633.1	Q06481	APLP2_HUMAN	amyloid beta (A4) precursor-like protein 2			31	all_hematologic(175;0.0429)	Breast(109;0.00586)|Lung NSC(97;0.00785)|all_lung(97;0.0154)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)			TTATTGTATGGCTGTGTGTAA	0.562000																								0							SO:0001583	missense			ENST00000263574.5	1	1	hg19	CCDS8486.1	.	.	.	.	.	.	.	.	.	.	G	34	5.360245	0.95877	.	.	ENSG00000084234	ENST00000263574;ENST00000338167;ENST00000278756;ENST00000543137	T;T;T;T	0.58060	0.36;0.36;0.36;0.36	5.61	5.61	0.85477	Proteinase inhibitor I2, Kunitz metazoa (6);	0.050804	0.85682	D	0.000000	T	0.66470	0.2792	L	0.42686	1.345	0.80722	D	1	P;D	0.89917	0.91;1.0	P;D	0.87578	0.508;0.998	T	0.61569	-0.7036	10	0.33141	T	0.24	-17.6546	18.621	0.91321	0.0:0.0:1.0:0.0	.	358;358	Q06481;Q06481-3	APLP2_HUMAN;.	T	358;358;368;265	ENSP00000263574:A358T;ENSP00000345444:A358T;ENSP00000278756:A368T;ENSP00000444122:A265T	ENSP00000263574:A358T	A	+	1	0	APLP2	129498866	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.630000	0.83225	2.631000	0.89168	0.650000	0.86243	GCT		TCGA-3A-A9J0-01A-11D-A40W-08	APLP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386109.1	1	0	1	89	380	0	143	1	1	19	119	0	143	2		0	0	0	0	0	2	1	1.000000	87	374	0	139	2								-20.000000	1	1	0	0		1	1	2	3	1.859412	1	0.470000	3.280000	0.570032	0.990000	8.100000e-01	1.000000	1.000000	0.962247	0.990000	1		
FAR1	84188	broad.mit.edu	37	11	13749183	13749183	+	Missense_Mutation	SNP	G	G	T			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr11:13749183G>T	ENST00000354817.3	+	11	1482	c.1338G>T	c.(1336-1338)ttG>ttT	p.L446F	FAR1_ENST00000532502.1_Missense_Mutation_p.L70F	NM_032228.5	NP_115604.1	Q8WVX9	FACR1_HUMAN	fatty acyl CoA reductase 1			13					AGTACGTATTGAATGAAGAAA	0.373000																								0							SO:0001583	missense			ENST00000354817.3	1	1	hg19	CCDS7813.1	.	.	.	.	.	.	.	.	.	.	G	15.93	2.979207	0.53827	.	.	ENSG00000197601	ENST00000354817;ENST00000532502	T	0.28454	1.61	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.50309	0.1608	L	0.55834	1.745	0.51482	D	0.999929	D	0.89917	1.0	D	0.83275	0.996	T	0.23797	-1.0178	10	0.30078	T	0.28	-8.0128	16.1581	0.81680	0.0:0.1335:0.8665:0.0	.	446	Q8WVX9	FACR1_HUMAN	F	446;70	ENSP00000346874:L446F	ENSP00000346874:L446F	L	+	3	2	FAR1	13705759	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	1.970000	0.40520	2.783000	0.95769	0.655000	0.94253	TTG		TCGA-3A-A9J0-01A-11D-A40W-08	FAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385990.2	1	0	1	57	287	0	50	1	9.660403e-01	9	21	0	50	2		0	0	0	0	0	2	1	1.000000	57	286	0	49	2								-3.247996	1	1	0	0		1	1	2	3	1.851246	1	0.470000	3.280000	0.565894	0.860000	6.700000e-01	1.000000	1.000000	0.869408	0.860000	1		
UVRAG	7405	broad.mit.edu	37	11	75851957	75851957	+	Missense_Mutation	SNP	G	G	A			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr11:75851957G>A	ENST00000356136.3	+	15	1841	c.1600G>A	c.(1600-1602)Gtc>Atc	p.V534I	UVRAG_ENST00000531818.1_Missense_Mutation_p.V162I|UVRAG_ENST00000533454.1_Missense_Mutation_p.V162I|UVRAG_ENST00000532130.1_Missense_Mutation_p.V162I|UVRAG_ENST00000539288.1_Missense_Mutation_p.V162I|UVRAG_ENST00000528420.1_Missense_Mutation_p.V433I|UVRAG_ENST00000538870.1_Missense_Mutation_p.V90I	NM_003369.3	NP_003360.2	Q9P2Y5	UVRAG_HUMAN	UV radiation resistance associated			32					TGTGACCACCGTCCCCTCCAT	0.493000																								0							SO:0001583	missense			ENST00000356136.3	1	1	hg19	CCDS8241.1	.	.	.	.	.	.	.	.	.	.	G	0.634	-0.816014	0.02776	.	.	ENSG00000198382	ENST00000356136;ENST00000528420;ENST00000533454;ENST00000531818;ENST00000532130;ENST00000539288;ENST00000538870	T	0.44881	0.91	5.3	-10.6	0.00265	.	1.580430	0.03003	N	0.148498	T	0.18299	0.0439	N	0.03608	-0.345	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.01281	0.0;0.0	T	0.22382	-1.0218	10	0.12766	T	0.61	1.0426	15.3224	0.74132	0.2482:0.0:0.6594:0.0925	.	90;534	B7Z6A0;Q9P2Y5	.;UVRAG_HUMAN	I	534;433;162;162;162;162;90	ENSP00000348455:V534I	ENSP00000348455:V534I	V	+	1	0	UVRAG	75529605	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-0.434000	0.06939	-2.212000	0.00736	-0.768000	0.03414	GTC		TCGA-3A-A9J0-01A-11D-A40W-08	UVRAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383430.1	1	0	1	55	227	0	64	1	9.968574e-01	6	33	0	64	2		0	0	0	0	0	2	1	1.000000	56	222	0	63	2								-3.270213	1	1	0	0		1	1	2	3	1.848552	1	0.470000	3.280000	0.564216	0.990000	7.800000e-01	1.000000	1.000000	0.962392	0.990000	1		
ULK1	8408	broad.mit.edu	37	12	132396530	132396530	+	Missense_Mutation	SNP	C	C	T			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr12:132396530C>T	ENST00000321867.4	+	13	1343	c.992C>T	c.(991-993)cCg>cTg	p.P331L		NM_003565.2	NP_003556	O75385	ULK1_HUMAN	unc-51 like autophagy activating kinase 1			29	all_neural(191;0.0982)|Medulloblastoma(191;0.163)				CTGGCCTCCCCGGCTGACACC	0.632000																								0							SO:0001583	missense			ENST00000321867.4	1	1	hg19	CCDS9274.1	.	.	.	.	.	.	.	.	.	.	C	15.93	2.977274	0.53720	.	.	ENSG00000177169	ENST00000321867	T	0.72394	-0.65	4.87	4.87	0.63330	Protein kinase-like domain (1);	0.141351	0.47852	D	0.000218	D	0.82513	0.5053	M	0.78049	2.395	0.80722	D	1	D	0.76494	0.999	P	0.59546	0.859	D	0.85704	0.1315	10	0.87932	D	0	-38.8868	17.5963	0.88013	0.0:1.0:0.0:0.0	.	331	O75385	ULK1_HUMAN	L	331	ENSP00000324560:P331L	ENSP00000324560:P331L	P	+	2	0	ULK1	130962483	1.000000	0.71417	0.303000	0.25071	0.032000	0.12392	4.382000	0.59594	2.245000	0.73994	0.561000	0.74099	CCG		TCGA-3A-A9J0-01A-11D-A40W-08	ULK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397769.3	1	0	0	92	67	0	43	1	1	15	15	0	43	2		0	0	0	0	0	2	1	1.000000	89	65	0	41	2								-20.000000	1	1	121154	1	35	1	0	3	3	1.895325	1	0.470000	3.280000	0.558241	0.990000	9.900000e-01	1.000000	1.000000	1.000000	0.990000	1		
EP400	57634	broad.mit.edu	37	12	132445272	132445272	+	Silent	SNP	G	G	A			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr12:132445272G>A	ENST00000333577.4	+	2	217	c.108G>A	c.(106-108)ccG>ccA	p.P36P	EP400_ENST00000330386.6_Silent_p.P36P|EP400_ENST00000389562.2_Silent_p.P36P|EP400_ENST00000389561.2_Silent_p.P36P|EP400_ENST00000332482.4_Silent_p.P36P			Q96L91	EP400_HUMAN	E1A binding protein p400			161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)			ACCCACCCCCGTCCCCCGCAG	0.667000																								0							SO:0001819	synonymous_variant			ENST00000333577.4	1	0	hg19																																																																																					TCGA-3A-A9J0-01A-11D-A40W-08	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		1	0	0	21	35	0	24	0	1.382514e-01	1	1	0	24	2		0	0	0	0	0	2	1	0.999999	20	32	0	18	2								-1.203433	0	1	119986	14	35	1	0	3	3	1.895325	1	0.470000	3.280000	0.558241	0.990000	9.900000e-01	1.000000	1.000000	0.999952	0.990000	1		
ZNF605	100289635	broad.mit.edu	37	12	133502024	133502024	+	Missense_Mutation	SNP	C	C	G			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr12:133502024C>G	ENST00000360187.4	-	5	2209	c.1861G>C	c.(1861-1863)Gag>Cag	p.E621Q	ZNF605_ENST00000331711.7_5'Flank|ZNF605_ENST00000392321.3_Missense_Mutation_p.E652Q	NM_183238.3	NP_899061.1	Q86T29	ZN605_HUMAN	zinc finger protein 605			28	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;0.00227)|all_epithelial(31;0.142)			GTCCCACACTCATTGCATCCA	0.383000																								0							SO:0001583	missense			ENST00000360187.4	1	1	hg19	CCDS31938.1	.	.	.	.	.	.	.	.	.	.	C	15.44	2.835555	0.50951	.	.	ENSG00000196458	ENST00000360187;ENST00000392321	T;T	0.52057	0.68;0.68	3.72	1.76	0.24704	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.35451	0.0932	L	0.32530	0.975	0.21984	N	0.999438	B;B	0.16166	0.003;0.016	B;B	0.12156	0.006;0.007	T	0.20571	-1.0271	9	0.22706	T	0.39	.	12.2303	0.54484	0.0:0.656:0.344:0.0	.	652;621	B3KVG4;Q86T29	.;ZN605_HUMAN	Q	621;652	ENSP00000353314:E621Q;ENSP00000376135:E652Q	ENSP00000353314:E621Q	E	-	1	0	ZNF605	132012097	0.000000	0.05858	0.005000	0.12908	0.937000	0.57800	0.278000	0.18753	0.325000	0.23359	0.462000	0.41574	GAG		TCGA-3A-A9J0-01A-11D-A40W-08	ZNF605-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397135.2	1	0	1	129	196	0	104	0	1.587790e-01	0	2	0	104	2		0	0	0	0	0	2	1	1.000000	129	192	0	103	2								-20.000000	1	1	0	0		1	0	3	3	1.895325	1	0.470000	3.280000	0.558241	0.990000	9.900000e-01	1.000000	1.000000	1.000000	0.990000	1		
FGD4	121512	broad.mit.edu	37	12	32754273	32754273	+	Missense_Mutation	SNP	A	A	G			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr12:32754273A>G	ENST00000427716.2	+	6	1176	c.752A>G	c.(751-753)aAt>aGt	p.N251S	FGD4_ENST00000531134.1_Missense_Mutation_p.N336S|FGD4_ENST00000534526.2_Missense_Mutation_p.N388S|FGD4_ENST00000381025.3_Missense_Mutation_p.N3S|FGD4_ENST00000266482.3_Missense_Mutation_p.N3S|FGD4_ENST00000546442.1_Missense_Mutation_p.N158S|FGD4_ENST00000525053.1_Missense_Mutation_p.N363S	NM_139241.2	NP_640334.2	Q96M96	FGD4_HUMAN	FYVE, RhoGEF and PH domain containing 4			27	Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)				GAGATGGTGAATAAAATCTTT	0.348000																								0							SO:0001583	missense			ENST00000427716.2	1	1	hg19	CCDS8727.1	.	.	.	.	.	.	.	.	.	.	A	11.96	1.794476	0.31777	.	.	ENSG00000139132	ENST00000534526;ENST00000531134;ENST00000427716;ENST00000266482;ENST00000546442;ENST00000525053;ENST00000381025	T;T;T;T;T;T;T	0.62941	-0.01;-0.01;-0.01;-0.01;-0.01;-0.01;-0.01	4.86	4.86	0.63082	Dbl homology (DH) domain (5);	0.000000	0.53938	D	0.000056	T	0.64800	0.2631	L	0.31578	0.945	0.42950	D	0.99437	B;B;D;B	0.58970	0.236;0.071;0.984;0.288	B;B;P;B	0.57846	0.18;0.18;0.828;0.095	T	0.67534	-0.5646	10	0.49607	T	0.09	-25.0515	14.6203	0.68579	1.0:0.0:0.0:0.0	.	363;336;251;3	E9PJX4;B7Z493;Q96M96;G3XA97	.;.;FGD4_HUMAN;.	S	388;336;251;3;158;363;3	ENSP00000449273:N388S;ENSP00000431323:N336S;ENSP00000394487:N251S;ENSP00000266482:N3S;ENSP00000446695:N158S;ENSP00000433666:N363S;ENSP00000370413:N3S	ENSP00000266482:N3S	N	+	2	0	FGD4	32645540	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.697000	0.68295	2.037000	0.60232	0.459000	0.35465	AAT		TCGA-3A-A9J0-01A-11D-A40W-08	FGD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268017.1	1	0	1	42	156	0	66	0	0	0	1	0	66	2		0	0	0	0	0	2	1	1.000000	42	155	0	65	2								-20.000000	1	1	0	0		1	0	3	3	1.895325	1	0.470000	3.280000	0.558241	0.990000	8.100000e-01	1.000000	1.000000	0.980028	0.990000	1		
ZIC2	7546	broad.mit.edu	37	13	100637726	100637726	+	Silent	SNP	G	G	T			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr13:100637726G>T	ENST00000376335.3	+	3	1682	c.1389G>T	c.(1387-1389)gcG>gcT	p.A463A	ZIC2_ENST00000477213.1_3'UTR	NM_007129.3	NP_009060.2	O95409	ZIC2_HUMAN	Zic family member 2			13	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				cggcggcggcggctgcggcgg	0.816000													Pancreas(97;119 1522 31925 44771 48764)											0							SO:0001819	synonymous_variant			ENST00000376335.3	0	1	hg19	CCDS9495.1																																																																																				TCGA-3A-A9J0-01A-11D-A40W-08	ZIC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045618.2	0	0	0	3	25	0	9		0	0	0	0	9	2		0	0	0	0	0	2	0	0.882106	0	36	0	9	2								-4.074491	1	0	0	0		1	2	3	5	2.631542	1	0.470000	3.280000	0.689150	0.880000	2.700000e-01	1.000000	1.000000	0.799445	0.880000	1		
RNF17	56163	broad.mit.edu	37	13	25444786	25444786	+	Silent	SNP	C	C	T			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr13:25444786C>T	ENST00000255324.5	+	32	4408	c.4356C>T	c.(4354-4356)agC>agT	p.S1452S	RNF17_ENST00000339524.3_Silent_p.S462S|RNF17_ENST00000381921.1_Silent_p.S1410S	NM_001184993.1|NM_031277.2	NP_001171922.1|NP_112567.2	Q9BXT8	RNF17_HUMAN	ring finger protein 17			36		Lung SC(185;0.0225)|Breast(139;0.077)			GTGGAGTCAGCGGGGAATCAG	0.438000																								0							SO:0001819	synonymous_variant			ENST00000255324.5	1	1	hg19	CCDS9308.2																																																																																				TCGA-3A-A9J0-01A-11D-A40W-08	RNF17-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044217.1	0	0	1	148	357	1	87		0	0	0	1	87	2		0	0	0	0	0	2	1	1.000000	145	351	1	83	20								-9.594065	1	1	121412	2	36	1	3	3	6	2.641929	1	0.470000	3.280000	0.692540	0.990000	9.900000e-01	1.000000	1.000000	1.000000	0.990000	1		
KL	9365	broad.mit.edu	37	13	33635841	33635841	+	Silent	SNP	C	C	T			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr13:33635841C>T	ENST00000380099.3	+	4	2633	c.2625C>T	c.(2623-2625)atC>atT	p.I875I	KL_ENST00000487852.1_3'UTR	NM_004795.3	NP_004786.2	Q9UEF7	KLOT_HUMAN	klotho			41	all_epithelial(80;0.133)	Ovarian(182;1.78e-06)|Breast(139;4.08e-05)|Hepatocellular(188;0.00886)|Lung SC(185;0.0262)			CCAATGGAATCGATGACGGGC	0.517000																								0							SO:0001819	synonymous_variant			ENST00000380099.3	1	1	hg19	CCDS9347.1																																																																																				TCGA-3A-A9J0-01A-11D-A40W-08	KL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045987.1	1	0	1	207	348	0	115	0	0	0	1	0	115	2		0	0	0	0	0	2	1	1.000000	205	344	0	109	2								-19.999950	1	1	121412	1	31	1	2	3	5	2.606114	1	0.470000	3.280000	0.689150	0.990000	9.900000e-01	1.000000	1.000000	1.000000	0.990000	1		
CPB2	1361	broad.mit.edu	37	13	46638808	46638808	+	Silent	SNP	C	C	T			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr13:46638808C>T	ENST00000181383.4	-	8	787	c.771G>A	c.(769-771)agG>agA	p.R257R	CPB2_ENST00000439329.3_Silent_p.R220R|CPB2-AS1_ENST00000606243.1_RNA|CPB2-AS1_ENST00000606991.1_RNA|CPB2-AS1_ENST00000415033.2_RNA|CPB2-AS1_ENST00000606351.1_RNA	NM_001872.3	NP_001863.3	Q96IY4	CBPB2_HUMAN	carboxypeptidase B2 (plasma)			21		Lung NSC(96;4.21e-05)|Breast(56;0.000118)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)|all_neural(104;0.235)	KIRC - Kidney renal clear cell carcinoma(16;0.234)		AAGCAAAGTTCCTATTCAGGT	0.413000																								0							SO:0001819	synonymous_variant			ENST00000181383.4	0	1	hg19	CCDS9401.1																																																																																				TCGA-3A-A9J0-01A-11D-A40W-08	CPB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044803.2	0	0	0	5	381	1	73		0	0	0	1	73	2		0	0	0	0	0	2	0	0.004268	5	376	1	73	18								-4.637711	1	1	0	0		1	2	3	5	2.631542	1	0.470000	3.280000	0.689150	0.100000	1.000000e-02	0.210000	0.100000	0.111343	0.100000	0		
PCDH8	5100	broad.mit.edu	37	13	53420319	53420319	+	Silent	SNP	G	G	A			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr13:53420319G>A	ENST00000377942.3	-	1	2456	c.2253C>T	c.(2251-2253)atC>atT	p.I751I	PCDH8_ENST00000338862.4_Silent_p.I751I	NM_002590.3	NP_002581.2	O95206	PCDH8_HUMAN	protocadherin 8			36		Lung NSC(96;0.0019)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)			CGATGATGACGATCAGCGGCG	0.701000													GBM(36;25 841 9273 49207)											0							SO:0001819	synonymous_variant			ENST00000377942.3	1	1	hg19	CCDS9438.1																																																																																				TCGA-3A-A9J0-01A-11D-A40W-08	PCDH8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045108.2	1	0	0	31	244	0	74		0	0	0	0	74	2		0	0	0	0	0	2	1	1.000000	29	242	0	72	2								-20.000000	1	1	0	0		1	2	3	5	2.631542	1	0.470000	3.280000	0.689150	0.820000	5.700000e-01	1.000000	1.000000	0.826789	0.820000	0		
SLAIN1	122060	broad.mit.edu	37	13	78293775	78293775	+	Silent	SNP	G	G	A			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr13:78293775G>A	ENST00000466548.1	+	3	695	c.669G>A	c.(667-669)gcG>gcA	p.A223A	SLAIN1_ENST00000418532.1_Silent_p.A4A|SLAIN1_ENST00000267219.8_Silent_p.A4A|SLAIN1_ENST00000488699.1_Silent_p.A81A	NM_001242868.1	NP_001229797.1	Q8ND83	SLAI1_HUMAN	SLAIN motif family, member 1			14		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.037)			TGGAAGCAGCGAGACGTTCCC	0.468000																								0							SO:0001819	synonymous_variant			ENST00000466548.1	1	1	hg19																																																																																					TCGA-3A-A9J0-01A-11D-A40W-08	SLAIN1-009	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000355018.1	1	0	1	110	811	0	116	1	3.415559e-01	4	6	0	116	2		0	0	0	0	0	2	1	1.000000	105	799	0	111	2								-3.017764	1	1	121408	2	30	1	2	3	5	2.631542	1	0.470000	3.280000	0.689150	0.860000	7.100000e-01	1.000000	1.000000	0.869848	0.860000	1		
FERMT2	10979	broad.mit.edu	37	14	53386031	53386031	+	Silent	SNP	C	C	T			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr14:53386031C>T	ENST00000395631.2	-	3	417	c.201G>A	c.(199-201)aaG>aaA	p.K67K	FERMT2_ENST00000553373.1_Silent_p.K67K|FERMT2_ENST00000343279.4_Silent_p.K67K|FERMT2_ENST00000399304.3_Silent_p.K67K|FERMT2_ENST00000341590.3_Silent_p.K67K			Q96AC1	FERM2_HUMAN	fermitin family member 2		ERO1L/FERMT2(2)	20	Breast(41;0.0342)				AAGTTCTCTTCTTTTCCCACC	0.393000																								0							SO:0001819	synonymous_variant			ENST00000395631.2	1	1	hg19	CCDS9713.1																																																																																				TCGA-3A-A9J0-01A-11D-A40W-08	FERMT2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276907.2	1	0	1	109	723	0	127	0	9.252279e-01	0	31	0	127	2		0	0	0	0	0	2	1	1.000000	105	719	0	125	2								-20.000000	1	1	0	0		1	2	3	5	2.541460	1	0.470000	3.280000	0.677134	0.920000	7.500000e-01	1.000000	1.000000	0.918918	0.920000	1		
WDR89	112840	broad.mit.edu	37	14	64066609	64066609	+	Missense_Mutation	SNP	A	A	T			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr14:64066609A>T	ENST00000394942.2	-	2	140	c.52T>A	c.(52-54)Tta>Ata	p.L18I	CTD-2302E22.2_ENST00000553983.1_lincRNA|WDR89_ENST00000267522.3_Missense_Mutation_p.L18I	NM_001008726.2|NM_001258272.1|NM_080666.3	NP_001008726.1|NP_001245201.1|NP_542397.1	Q96FK6	WDR89_HUMAN	WD repeat domain 89			14					TTGGTTCCTAAGGAACATTTA	0.368000																								0							SO:0001583	missense			ENST00000394942.2	1	1	hg19	CCDS9759.1	.	.	.	.	.	.	.	.	.	.	A	3.553	-0.091356	0.07053	.	.	ENSG00000140006	ENST00000394942;ENST00000267522;ENST00000554717	T;T;T	0.67171	-0.25;-0.25;0.96	5.93	3.42	0.39159	.	0.938409	0.09031	N	0.858708	T	0.47040	0.1424	N	0.14661	0.345	0.09310	N	0.999998	B	0.15473	0.013	B	0.09377	0.004	T	0.29579	-1.0007	10	0.20046	T	0.44	.	8.1435	0.31097	0.6475:0.2533:0.0:0.0992	.	18	Q96FK6	WDR89_HUMAN	I	18	ENSP00000378399:L18I;ENSP00000267522:L18I;ENSP00000451702:L18I	ENSP00000267522:L18I	L	-	1	2	WDR89	63136362	0.692000	0.27719	0.971000	0.41717	0.360000	0.29518	0.704000	0.25661	1.055000	0.40461	0.533000	0.62120	TTA		TCGA-3A-A9J0-01A-11D-A40W-08	WDR89-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411879.2	1	0	1	135	385	0	93	1	8.572710e-01	3	9	0	93	2		0	0	0	0	0	2	1	1.000000	131	381	0	89	2								-20.000000	1	1	0	0		1	2	3	5	2.541460	1	0.470000	3.280000	0.677134	0.990000	9.900000e-01	1.000000	1.000000	1.000000	0.990000	1		
RYR3	6263	broad.mit.edu	37	15	34130031	34130031	+	Silent	SNP	G	G	A			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr15:34130031G>A	ENST00000389232.4	+	89	11920	c.11850G>A	c.(11848-11850)ggG>ggA	p.G3950G	RYR3_ENST00000415757.3_Silent_p.G3945G	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	p.G3949G(1)		311		all_lung(180;7.18e-09)			CCATGGAAGGGCAAAAACAGT	0.408000																								1	Substitution - coding silent(1)						SO:0001819	synonymous_variant			ENST00000389232.4	0	1	hg19	CCDS45210.1																																																																																				TCGA-3A-A9J0-01A-11D-A40W-08	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1	0	0	0	5	427	0	61		0	0	0	0	61	2		0	0	0	0	0	2	1	0.934374	5	418	0	60	2								-2.537812	1	1	0	0		1	0	4	4	2.083936	1	0.470000	3.280000	0.621293	0.070000	1.000000e-02	1.000000	0.070000	0.190765	0.070000	0		
MYO5C	55930	broad.mit.edu	37	15	52534277	52534277	+	Nonsense_Mutation	SNP	G	G	A			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr15:52534277G>A	ENST00000261839.7	-	20	2685	c.2524C>T	c.(2524-2526)Cga>Tga	p.R842*	MYO5C_ENST00000443683.2_Intron	NM_018728.3	NP_061198.2	Q9NQX4	MYO5C_HUMAN	myosin VC			66					AGGAATCCTCGGCTGTAGGCC	0.542000																								0							SO:0001587	stop_gained			ENST00000261839.7	0	1	hg19	CCDS42036.1	.	.	.	.	.	.	.	.	.	.	G	39	7.406745	0.98265	.	.	ENSG00000128833	ENST00000261839	.	.	.	5.09	3.11	0.35812	.	0.068470	0.56097	D	0.000024	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.3048	0.60347	0.0:0.0:0.5797:0.4203	.	.	.	.	X	842	.	ENSP00000261839:R842X	R	-	1	2	MYO5C	50321569	0.973000	0.33851	0.975000	0.42487	0.225000	0.24961	1.711000	0.37930	0.653000	0.30826	0.650000	0.86243	CGA		TCGA-3A-A9J0-01A-11D-A40W-08	MYO5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419562.1	1	0	1	341	1028	0	232	1	9.999711e-01	4	43	0	232	2		0	0	0	0	0	2	1	1.000000	337	1016	0	231	2								-8.225900	1	1	0	0		1	2	4	6	2.826299	1	0.470000	3.280000	0.711423	0.990000	9.900000e-01	1.000000	1.000000	1.000000	0.990000	1		
UNC13C	440279	broad.mit.edu	37	15	54825264	54825264	+	Splice_Site	SNP	C	C	T			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr15:54825264C>T	ENST00000260323.11	+	25	5696	c.5696C>T	c.(5695-5697)aCa>aTa	p.T1899I	UNC13C_ENST00000537900.1_Splice_Site_p.T1897I|UNC13C_ENST00000545554.1_Splice_Site_p.T1899I	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)			121					TTGGACAAAACGTAAGTTTTT	0.338000																								0							SO:0001630	splice_region_variant			ENST00000260323.11	0	1	hg19	CCDS45264.1	.	.	.	.	.	.	.	.	.	.	C	12.80	2.047374	0.36085	0.0	1.23E-4	ENSG00000137766	ENST00000260323;ENST00000545554;ENST00000537900	T;T;T	0.15256	2.44;2.44;2.44	5.83	4.91	0.64330	Mammalian uncoordinated homology 13, domain 2 (1);Mammalian uncoordinated homology 13, subgroup, domain 2 (1);	0.104815	0.64402	D	0.000004	T	0.14570	0.0352	L	0.29908	0.895	0.40999	D	0.98491	B	0.16603	0.018	B	0.16722	0.016	T	0.03863	-1.0997	10	0.39692	T	0.17	.	14.2915	0.66281	0.0:0.9288:0.0:0.0712	.	1899	Q8NB66	UN13C_HUMAN	I	1899;1899;1897	ENSP00000260323:T1899I;ENSP00000438156:T1899I;ENSP00000442569:T1897I	ENSP00000260323:T1899I	T	+	2	0	UNC13C	52612556	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	1.303000	0.33470	1.472000	0.48140	0.655000	0.94253	ACA		TCGA-3A-A9J0-01A-11D-A40W-08	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	0	0	0	5	59	0	10		0	0	0	0	10	2		0	0	0	0	0	2	1	0.937584	5	58	0	10	2								-10.057750	1	1	120228	1	21	1	2	4	6	2.826299	1	0.470000	3.280000	0.711423	0.700000	2.600000e-01	1.000000	1.000000	0.707984	0.700000	0		
CIB2	10518	broad.mit.edu	37	15	78401612	78401612	+	Missense_Mutation	SNP	C	C	T			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr15:78401612C>T	ENST00000258930.3	-	4	639	c.311G>A	c.(310-312)cGa>cAa	p.R104Q	CIB2_ENST00000560618.1_Missense_Mutation_p.R61Q|CIB2_ENST00000539011.1_Missense_Mutation_p.R61Q|CIB2_ENST00000557846.1_Missense_Mutation_p.R55Q	NM_006383.2	NP_006374.1	O75838	CIB2_HUMAN	calcium and integrin binding family member 2	p.R104Q(1)		11					CTTGAGCTCTCGGGGAGCCGA	0.552000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000258930.3	0	1	hg19	CCDS10296.1	.	.	.	.	.	.	.	.	.	.	C	32	5.114424	0.94339	0.0	3.49E-4	ENSG00000136425	ENST00000258930;ENST00000539011	T;T	0.67171	-0.25;2.96	4.46	4.46	0.54185	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	T	0.77363	0.4119	L	0.58669	1.825	0.80722	D	1	D;D	0.76494	0.999;0.997	D;D	0.64506	0.926;0.925	T	0.78607	-0.2138	10	0.48119	T	0.1	-16.4882	16.4633	0.84071	0.0:1.0:0.0:0.0	.	104;104	B4DDF0;O75838	.;CIB2_HUMAN	Q	104;61	ENSP00000258930:R104Q;ENSP00000442459:R61Q	ENSP00000258930:R104Q	R	-	2	0	CIB2	76188667	1.000000	0.71417	0.981000	0.43875	0.958000	0.62258	7.617000	0.83032	2.199000	0.70637	0.591000	0.81541	CGA		TCGA-3A-A9J0-01A-11D-A40W-08	CIB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289798.1	0	0	0	5	372	0	53	0	5.945755e-02	0	24	0	53	2		0	0	0	0	0	2	1	0.933436	5	362	0	52	2								-4.339525	1	1	0	0		1	2	3	5	2.668272	1	0.470000	3.280000	0.689150	0.100000	2.000000e-02	0.220000	0.100000	0.114076	0.100000	0		
RGMA	56963	broad.mit.edu	37	15	93588701	93588701	+	Missense_Mutation	SNP	C	C	T			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr15:93588701C>T	ENST00000329082.7	-	4	1151	c.880G>A	c.(880-882)Gtc>Atc	p.V294I	RGMA_ENST00000425933.2_Missense_Mutation_p.V278I|RGMA_ENST00000542321.2_Missense_Mutation_p.V278I|RGMA_ENST00000557301.1_Missense_Mutation_p.V302I|RGMA_ENST00000556658.1_Missense_Mutation_p.V185I|RGMA_ENST00000538818.1_Missense_Mutation_p.V185I|RGMA_ENST00000543599.1_Missense_Mutation_p.V278I|RGMA_ENST00000557420.1_3'UTR	NM_020211.2	NP_064596	Q96B86	RGMA_HUMAN	repulsive guidance molecule family member a			9	Lung NSC(78;0.0542)|all_lung(78;0.0786)		BRCA - Breast invasive adenocarcinoma(143;0.0312)|OV - Ovarian serous cystadenocarcinoma(32;0.108)		GGCATGCGGACGGCAAAGGTC	0.622000																								0							SO:0001583	missense			ENST00000329082.7	0	1	hg19	CCDS45357.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	5.222	0.226549	0.09916	.	.	ENSG00000182175	ENST00000543599;ENST00000425933;ENST00000329082;ENST00000542321;ENST00000538818;ENST00000557301	D;D;D;D;D;D	0.84298	-1.83;-1.83;-1.83;-1.83;-1.83;-1.83	4.76	3.81	0.43845	Repulsive guidance molecule, C-terminal (1);	0.058854	0.64402	N	0.000002	T	0.71417	0.3337	N	0.25825	0.765	0.80722	D	1	B;B	0.18741	0.024;0.03	B;B	0.15052	0.012;0.012	T	0.61491	-0.7052	10	0.02654	T	1	-9.2223	10.6561	0.45675	0.0:0.8974:0.0:0.1026	.	302;294	G3V518;Q96B86	.;RGMA_HUMAN	I	278;278;294;278;185;302	ENSP00000442498:V278I;ENSP00000404442:V278I;ENSP00000330005:V294I;ENSP00000440025:V278I;ENSP00000442546:V185I;ENSP00000452126:V302I	ENSP00000330005:V294I	V	-	1	0	RGMA	91389705	0.999000	0.42202	0.400000	0.26346	0.678000	0.39670	4.046000	0.57376	0.880000	0.35969	0.491000	0.48974	GTC		TCGA-3A-A9J0-01A-11D-A40W-08	RGMA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000415091.1	1	0	1	18	135	0	26	0	4.379888e-01	0	12	0	26	2		0	0	0	0	0	2	1	0.999981	17	129	0	26	2								-20.000000	1	1	121100	13	39	1	2	3	5	2.668272	1	0.470000	3.280000	0.689150	0.860000	5.400000e-01	1.000000	1.000000	0.852002	0.860000	1		
CACNA1H	8912	broad.mit.edu	37	16	1246017	1246017	+	Missense_Mutation	SNP	G	G	A			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr16:1246017G>A	ENST00000348261.5	+	5	885	c.637G>A	c.(637-639)Gtg>Atg	p.V213M	CACNA1H_ENST00000565831.1_Missense_Mutation_p.V213M|CACNA1H_ENST00000358590.4_Missense_Mutation_p.V213M	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit			34		Hepatocellular(780;0.00369)		Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	CATCAACCGCGTGCCTAGTAA	0.652000																								0							SO:0001583	missense			ENST00000348261.5	1	1	hg19	CCDS45375.1	.	.	.	.	.	.	.	.	.	.	G	17.67	3.447525	0.63178	.	.	ENSG00000196557	ENST00000348261;ENST00000358590	D;D	0.98649	-5.05;-5.05	4.23	4.23	0.50019	Ion transport (1);	0.149470	0.44688	N	0.000436	D	0.99080	0.9684	M	0.83774	2.66	0.40988	D	0.984831	D;D	0.89917	1.0;1.0	D;D	0.91635	0.992;0.999	D	0.99875	1.1103	10	0.87932	D	0	.	15.9489	0.79817	0.0:0.0:1.0:0.0	.	213;213	O95180-2;O95180	.;CAC1H_HUMAN	M	213	ENSP00000334198:V213M;ENSP00000351401:V213M	ENSP00000334198:V213M	V	+	1	0	CACNA1H	1186018	1.000000	0.71417	0.923000	0.36655	0.020000	0.10135	9.594000	0.98254	2.061000	0.61500	0.478000	0.44815	GTG		TCGA-3A-A9J0-01A-11D-A40W-08	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	1	0	1	46	258	0	69	0	1.726037e-01	0	5	0	69	2		0	0	0	0	0	2	1	1.000000	45	253	0	67	2								-20.000000	1	1	120908	2	30	1	2	2	4	2.300494	1	0.470000	3.280000	0.639456	0.940000	7.100000e-01	1.000000	1.000000	0.924757	0.940000	1		
USP31	57478	broad.mit.edu	37	16	23119457	23119457	+	Silent	SNP	A	A	G			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr16:23119457A>G	ENST00000219689.7	-	2	680	c.681T>C	c.(679-681)caT>caC	p.H227H		NM_020718.3	NP_065769.3	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 31			57					CCTGGGCATCATGTTGGGAAT	0.478000																								0							SO:0001819	synonymous_variant			ENST00000219689.7	1	1	hg19	CCDS10607.1																																																																																				TCGA-3A-A9J0-01A-11D-A40W-08	USP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211607.1	1	0	1	67	294	0	50	1	2.376766e-01	2	3	0	50	2		0	0	0	0	0	2	1	1.000000	66	286	0	48	2								-20.000000	1	1	0	0		1	2	2	4	2.241091	1	0.470000	3.280000	0.638299	0.990000	9.200000e-01	1.000000	1.000000	0.994906	0.990000	1		
ZKSCAN2	342357	broad.mit.edu	37	16	25251421	25251421	+	Missense_Mutation	SNP	A	A	C			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr16:25251421A>C	ENST00000328086.7	-	7	3423	c.2620T>G	c.(2620-2622)Ttc>Gtc	p.F874V	CTD-2547G23.2_ENST00000569456.1_RNA	NM_001012981.4	NP_001012999.3	Q63HK3	ZKSC2_HUMAN	zinc finger with KRAB and SCAN domains 2			36					TGGGCGCTGAAATGAGAACTG	0.458000																								0							SO:0001583	missense			ENST00000328086.7	1	1	hg19	CCDS32410.1	.	.	.	.	.	.	.	.	.	.	A	16.10	3.026466	0.54683	.	.	ENSG00000155592	ENST00000328086	T	0.18338	2.22	5.53	5.53	0.82687	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.173579	0.41823	D	0.000812	T	0.19886	0.0478	L	0.31120	0.905	0.36356	D	0.860369	P;D	0.53619	0.951;0.961	P;P	0.53224	0.696;0.721	T	0.10451	-1.0629	10	0.66056	D	0.02	-9.4959	8.0971	0.30835	0.913:0.0:0.087:0.0	.	670;874	B4DYF0;Q63HK3	.;ZKSC2_HUMAN	V	874	ENSP00000331626:F874V	ENSP00000331626:F874V	F	-	1	0	ZKSCAN2	25158922	0.820000	0.29190	0.998000	0.56505	0.489000	0.33432	1.465000	0.35299	2.315000	0.78130	0.533000	0.62120	TTC		TCGA-3A-A9J0-01A-11D-A40W-08	ZKSCAN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435739.1	1	0	1	71	431	0	91	0	5.591180e-02	1	2	0	91	2		0	0	0	0	0	2	1	1.000000	68	423	0	91	2								-20.000000	1	1	0	0		1	2	2	4	2.241091	1	0.470000	3.280000	0.638299	0.880000	7.000000e-01	1.000000	1.000000	0.882631	0.880000	1		
ATXN2L	11273	broad.mit.edu	37	16	28841228	28841228	+	Missense_Mutation	SNP	C	C	T			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr16:28841228C>T	ENST00000336783.4	+	8	1050	c.883C>T	c.(883-885)Cgt>Tgt	p.R295C	ATXN2L_ENST00000325215.6_Missense_Mutation_p.R295C|ATXN2L_ENST00000395547.2_Missense_Mutation_p.R295C|ATXN2L_ENST00000382686.4_Missense_Mutation_p.R295C|RP11-24N18.1_ENST00000563565.1_RNA|ATXN2L_ENST00000564304.1_Missense_Mutation_p.R295C|ATXN2L_ENST00000570200.1_Missense_Mutation_p.R295C|ATXN2L_ENST00000340394.8_Missense_Mutation_p.R295C	NM_007245.3	NP_009176.2	Q8WWM7	ATX2L_HUMAN	ataxin 2-like			36					GCGAGAGCTGCGTGCGGCCCA	0.577000																								0							SO:0001583	missense			ENST00000336783.4	1	1	hg19	CCDS10641.1	.	.	.	.	.	.	.	.	.	.	.	28.0	4.882278	0.91740	.	.	ENSG00000168488	ENST00000340394;ENST00000395547;ENST00000336783;ENST00000359153;ENST00000382686;ENST00000325215	T;T;T;T;T	0.51817	0.7;0.7;0.69;0.7;0.7	5.85	5.85	0.93711	LsmAD domain (1);	0.000000	0.64402	D	0.000001	T	0.67711	0.2922	M	0.72118	2.19	0.80722	D	1	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	D;D;D;D;D;D;D;D	0.87578	0.997;0.998;0.998;0.998;0.997;0.997;0.998;0.997	T	0.69672	-0.5082	10	0.87932	D	0	-9.2431	14.4368	0.67287	0.148:0.8519:0.0:0.0	.	295;295;295;295;295;295;295;295	Q8WWM7-6;Q8WWM7-5;Q63ZY4;Q8WWM7;Q8WWM7-2;Q8WWM7-4;A8K1R6;Q8WWM7-3	.;.;.;ATX2L_HUMAN;.;.;.;.	C	295	ENSP00000341459:R295C;ENSP00000378917:R295C;ENSP00000338718:R295C;ENSP00000372133:R295C;ENSP00000315650:R295C	ENSP00000315650:R295C	R	+	1	0	ATXN2L	28748729	0.953000	0.32496	1.000000	0.80357	0.950000	0.60333	2.191000	0.42640	2.779000	0.95612	0.491000	0.48974	CGT		TCGA-3A-A9J0-01A-11D-A40W-08	ATXN2L-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214139.1	1	0	1	51	221	0	66	1	9.999999e-01	22	87	0	66	2		0	0	0	0	0	2	1	1.000000	51	219	0	62	2								-20.000000	1	1	0	0		1	2	2	4	2.241091	1	0.470000	3.280000	0.638299	0.990000	8.900000e-01	1.000000	1.000000	0.993174	0.990000	1		
KIF22	3835	broad.mit.edu	37	16	29814108	29814108	+	Missense_Mutation	SNP	C	C	A			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr16:29814108C>A	ENST00000160827.4	+	9	1339	c.1299C>A	c.(1297-1299)agC>agA	p.S433R	KIF22_ENST00000400751.5_Missense_Mutation_p.S365R|KIF22_ENST00000569382.2_Missense_Mutation_p.S365R|KIF22_ENST00000561482.1_Missense_Mutation_p.S365R|KIF22_ENST00000400750.2_5'UTR	NM_001256269.1|NM_007317.2	NP_001243198.1|NP_015556.1	Q14807	KIF22_HUMAN	kinesin family member 22			14					AGAAGCTAAGCAGCATGGACC	0.617000																								0							SO:0001583	missense			ENST00000160827.4	0	1	hg19	CCDS10653.1	.	.	.	.	.	.	.	.	.	.	C	14.81	2.646600	0.47258	.	.	ENSG00000079616	ENST00000160827;ENST00000400751	T;T	0.74002	-0.72;-0.8	5.67	-4.09	0.03951	.	.	.	.	.	T	0.50034	0.1592	N	0.14661	0.345	0.25229	N	0.989848	P;P	0.40731	0.483;0.728	B;B	0.37601	0.084;0.254	T	0.46020	-0.9221	9	0.23891	T	0.37	.	8.278	0.31883	0.0:0.5586:0.2028:0.2385	.	365;433	B7Z265;Q14807	.;KIF22_HUMAN	R	433;365	ENSP00000160827:S433R;ENSP00000383562:S365R	ENSP00000160827:S433R	S	+	3	2	KIF22	29721609	0.167000	0.22975	0.935000	0.37517	0.919000	0.55068	-0.212000	0.09319	-0.299000	0.08909	-0.156000	0.13503	AGC		TCGA-3A-A9J0-01A-11D-A40W-08	KIF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215012.2	0	0	0	5	399	0	99	0	4.681834e-01	0	112	0	99	2		0	0	0	0	0	2	1	0.934150	5	390	0	98	2								-2.924628	1	1	0	0		1	2	2	4	2.241091	1	0.470000	3.280000	0.638299	0.080000	1.000000e-02	0.180000	0.080000	0.091559	0.080000	0		
SEPT1	1731	broad.mit.edu	37	16	30393182	30393182	+	Silent	SNP	G	G	A			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr16:30393182G>A	ENST00000571393.1	-	5	390	c.204C>T	c.(202-204)gcC>gcT	p.A68A	SEPT1_ENST00000570039.1_5'Flank|SEPT1_ENST00000605106.1_Silent_p.A73A|SEPT1_ENST00000321367.3_Silent_p.A115A			Q8WYJ6	SEPT1_HUMAN	septin 1			24			Colorectal(24;0.193)		GGCGCTCAATGGCCAGGGTCT	0.562000																								0							SO:0001819	synonymous_variant			ENST00000571393.1	1	1	hg19																																																																																					TCGA-3A-A9J0-01A-11D-A40W-08	SEPT1-201	KNOWN	basic	protein_coding	protein_coding		0	0	0	28	839	1	164	0	3.501273e-02	0	9	1	164	2		0	0	0	0	0	2	1	1.000000	28	813	0	157	2								-2.900864	1	1	0	0		1	2	2	4	2.241091	1	0.470000	3.280000	0.638299	0.200000	1.200000e-01	0.290000	0.200000	0.207946	0.200000	0		
ABCC12	94160	broad.mit.edu	37	16	48174686	48174686	+	Missense_Mutation	SNP	G	G	A			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr16:48174686G>A	ENST00000311303.3	-	4	914	c.569C>T	c.(568-570)aCg>aTg	p.T190M	ABCC12_ENST00000448542.1_Missense_Mutation_p.T190M|ABCC12_ENST00000416054.1_Missense_Mutation_p.T190M	NM_033226.2	NP_150229.2	Q96J65	MRP9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 12			90		all_cancers(37;0.0474)|all_lung(18;0.047)			CCGGATGGCCGTGCGGTAGTT	0.532000																								0							SO:0001583	missense			ENST00000311303.3	0	1	hg19	CCDS10730.1	.	.	.	.	.	.	.	.	.	.	G	14.79	2.641298	0.47153	.	.	ENSG00000140798	ENST00000311303;ENST00000448542;ENST00000449939;ENST00000416054	D;D;D	0.90197	-2.63;-2.63;-2.63	6.07	4.13	0.48395	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.94896	0.8350	M	0.84219	2.685	0.58432	D	0.999996	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.998	D	0.94242	0.7486	10	0.51188	T	0.08	.	12.0291	0.53388	0.1413:0.0:0.8587:0.0	.	190;190	Q96J65-2;Q96J65	.;MRP9_HUMAN	M	190	ENSP00000311030:T190M;ENSP00000401855:T190M;ENSP00000413046:T190M	ENSP00000311030:T190M	T	-	2	0	ABCC12	46732187	1.000000	0.71417	0.755000	0.31263	0.011000	0.07611	5.520000	0.67080	0.900000	0.36469	0.655000	0.94253	ACG		TCGA-3A-A9J0-01A-11D-A40W-08	ABCC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256837.1	0	0	0	6	674	0	110		0	0	0	0	110	2		0	0	0	0	0	2	1	0.964110	6	668	0	110	2								-2.512945	1	1	121412	7	43	1	2	2	4	2.241091	1	0.470000	3.280000	0.638299	0.050000	0	0.130000	0.040000	0.062019	0.050000	0		
SLC12A3	6559	broad.mit.edu	37	16	56904081	56904081	+	Silent	SNP	C	C	T			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr16:56904081C>T	ENST00000563236.1	+	5	700	c.675C>T	c.(673-675)ttC>ttT	p.F225F	SLC12A3_ENST00000262502.5_Silent_p.F224F|SLC12A3_ENST00000438926.2_Silent_p.F225F|SLC12A3_ENST00000566786.1_Silent_p.F224F			P55017	S12A3_HUMAN	solute carrier family 12 (sodium/chloride transporter), member 3			50				Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Diazoxide(DB01119)|Hydrochlorothiazide(DB00999)|Metolazone(DB00524)|Polythiazide(DB01324)|Quinethazone(DB01325)	TTTTCGCTTTCGCCAATGCCG	0.647000																								0							SO:0001819	synonymous_variant			ENST00000563236.1	1	1	hg19	CCDS58464.1																																																																																				TCGA-3A-A9J0-01A-11D-A40W-08	SLC12A3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432337.1	1	0	1	58	299	0	77		0	0	0	0	77	2		0	0	0	0	0	2	1	1.000000	57	297	0	75	2								-3.336150	1	1	121412	8	41	1	2	2	4	2.220512	1	0.470000	3.280000	0.633598	0.990000	7.800000e-01	1.000000	1.000000	0.958304	0.990000	1		
WDR90	197335	broad.mit.edu	37	16	708985	708985	+	Silent	SNP	C	C	G			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr16:708985C>G	ENST00000293879.4	+	24	2985	c.2985C>G	c.(2983-2985)ctC>ctG	p.L995L	WDR90_ENST00000549091.1_Silent_p.L995L|LA16c-349E10.1_ENST00000573609.1_RNA			Q96KV7	WDR90_HUMAN	WD repeat domain 90			37		Hepatocellular(780;0.0218)			CCGTCTTCCTCTGGGATGTCC	0.642000																								0							SO:0001819	synonymous_variant			ENST00000293879.4	1	1	hg19	CCDS42092.1																																																																																				TCGA-3A-A9J0-01A-11D-A40W-08	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	1	0	0	20	423	0	91	1	4.594150e-01	3	30	0	91	2		0	0	0	0	0	2	1	0.999995	20	415	0	88	2								-4.855244	1	1	121024	3	38	1	2	2	4	2.300494	1	0.470000	3.280000	0.639456	0.280000	1.700000e-01	0.420000	0.280000	0.294826	0.280000	0		
DHX38	9785	broad.mit.edu	37	16	72132878	72132878	+	Nonsense_Mutation	SNP	A	A	T			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08			A	T	A	A		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr16:72132878A>T	ENST00000268482.3	+	6	1326	c.817A>T	c.(817-819)Aaa>Taa	p.K273*	DHX38_ENST00000536867.1_Intron	NM_014003.3	NP_054722.2	Q92620	PRP16_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 38			48		Ovarian(137;0.125)			TCCCTCCTACAAATATAACGA	0.592000													Melanoma(97;711 1442 7855 13832 28836)											0							SO:0001587	stop_gained			ENST00000268482.3	0	1	hg19	CCDS10907.1	.	.	.	.	.	.	.	.	.	.	A	41	8.828726	0.98970	.	.	ENSG00000140829	ENST00000268482	.	.	.	4.87	4.87	0.63330	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.7562	0.69567	1.0:0.0:0.0:0.0	.	.	.	.	X	273	.	ENSP00000268482:K273X	K	+	1	0	DHX38	70690379	1.000000	0.71417	1.000000	0.80357	0.741000	0.42261	8.784000	0.91818	1.958000	0.56883	0.460000	0.39030	AAA		TCGA-3A-A9J0-01A-11D-A40W-08	DHX38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269004.3	1	0	1	55	105	0	31	1	9.999941e-01	6	34	0	31	2		0	0	0	0	0	2	1	1.000000	55	102	0	29	2								-20.000000	1	1	0	0		1	2	2	4	2.220512	1	0.470000	3.280000	0.633598	0.990000	9.900000e-01	1.000000	1.000000	1.000000	0.990000	1		
SPATA2L	124044	broad.mit.edu	37	16	89764252	89764252	+	Silent	SNP	C	C	T			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr16:89764252C>T	ENST00000289805.5	-	3	833	c.765G>A	c.(763-765)gcG>gcA	p.A255A	SPATA2L_ENST00000335360.7_Intron	NM_152339.3	NP_689552.2	Q8IUW3	SPA2L_HUMAN	spermatogenesis associated 2-like			6		Lung NSC(15;0.00043)|all_lung(18;0.000665)|all_hematologic(23;0.0355)			AGGCCAGCTCCGCCGGGGGCG	0.701000																								0							SO:0001819	synonymous_variant			ENST00000289805.5	1	1	hg19	CCDS10985.1																																																																																				TCGA-3A-A9J0-01A-11D-A40W-08	SPATA2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269923.1	1	0	1	24	38	0	15	1	9.941312e-01	4	13	0	15	2		0	0	0	0	0	2	1	1.000000	16	34	0	13	2								-20.000000	1	1	121026	3	32	1	2	2	4	2.258548	1	0.470000	3.280000	0.639456	0.990000	9.900000e-01	1.000000	1.000000	1.000000	0.990000	1		
SCARF1	8578	broad.mit.edu	37	17	1538332	1538332	+	Missense_Mutation	SNP	C	C	T	rs147642060	byFrequency	TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr17:1538332C>T	ENST00000263071.4	-	11	2262	c.2213G>A	c.(2212-2214)cGg>cAg	p.R738Q	SCARF1_ENST00000348987.3_Missense_Mutation_p.R652Q|SCARF1_ENST00000571272.1_3'UTR	NM_003693.2|NM_145350.1	NP_003684.2|NP_663325.1	Q14162	SREC_HUMAN	scavenger receptor class F, member 1			20					GCCCTTTTTCCGATTCAGGGC	0.632000																								0							SO:0001583	missense			ENST00000263071.4	1	1	hg19	CCDS11007.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	c	10.85	1.466182	0.26335	0.00227	1.16E-4	ENSG00000074660	ENST00000263071;ENST00000348987	T;T	0.22539	1.95;2.62	4.89	2.46	0.29980	.	0.197318	0.25025	N	0.033728	T	0.17916	0.0430	M	0.63428	1.95	0.22918	N	0.998569	B;B	0.32781	0.384;0.145	B;B	0.26693	0.072;0.024	T	0.14227	-1.0480	10	0.26408	T	0.33	-6.2381	8.5352	0.33360	0.0:0.8531:0.0:0.1469	.	652;738	Q14162-2;Q14162	.;SREC_HUMAN	Q	738;652	ENSP00000263071:R738Q;ENSP00000323964:R652Q	ENSP00000263071:R738Q	R	-	2	0	SCARF1	1485082	0.995000	0.38212	0.865000	0.33974	0.372000	0.29890	0.814000	0.27239	0.257000	0.21650	0.550000	0.68814	CGG		TCGA-3A-A9J0-01A-11D-A40W-08	SCARF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207081.4	1	0	1	18	86	0	51	1	9.437098e-01	2	24	0	51	2		0	0	0	0	0	2	1	0.999989	16	87	0	48	2								-3.634488	1	1	121406	30	44	1	0	2	2	1.636792	1	0.470000	3.280000	0.470000	0.730000	4.600000e-01	1.000000	1.000000	0.749210	0.730000	0		
ERBB2	2064	broad.mit.edu	37	17	37863277	37863277	+	Silent	SNP	T	T	A			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08			T	A	T	T		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr17:37863277T>A	ENST00000269571.5	+	2	267	c.108T>A	c.(106-108)ccT>ccA	p.P36P	ERBB2_ENST00000541774.1_Silent_p.P21P|ERBB2_ENST00000584450.1_Silent_p.P36P|ERBB2_ENST00000540042.1_Silent_p.P6P|ERBB2_ENST00000445658.2_Intron|ERBB2_ENST00000578199.1_Silent_p.P6P|ERBB2_ENST00000584601.1_Silent_p.P6P|ERBB2_ENST00000406381.2_Silent_p.P6P|ERBB2_ENST00000540147.1_Silent_p.P6P			P04626	ERBB2_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2			247	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)	Ovarian(249;0.0547)|Colorectal(1115;0.234)	UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171)	ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Lapatinib(DB01259)|Pertuzumab(DB06366)|Trastuzumab(DB00072)	TGCGGCTCCCTGCCAGTCCCG	0.642000		1	A, Mis, O		breast, ovarian, other tumour types, NSCLC, gastric					TCGA GBM(5;<1E-08)					Dom	yes		17	17q21.1	2064	v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)		E	0							SO:0001819	synonymous_variant			ENST00000269571.5	0	1	hg19	CCDS32642.1																																																																																				TCGA-3A-A9J0-01A-11D-A40W-08	ERBB2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445621.2	0	0	0	51	4703	0	55	1	1	16	2906	0	55	2		0	0	0	0	0	2	1	1.000000	52	4489	0	50	2								-16.205390	1	1	0	0		1	1	15	16	38.437938	1	0.470000	3.280000	0.876457	0.150000	3.000000e-02	0.280000	0.160000	0.160263	0.150000	0		
TTYH2	94015	broad.mit.edu	37	17	72227040	72227040	+	Missense_Mutation	SNP	G	G	A	rs150215307	byFrequency	TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr17:72227040G>A	ENST00000269346.4	+	3	390	c.316G>A	c.(316-318)Gtt>Att	p.V106I	TTYH2_ENST00000529107.1_Missense_Mutation_p.V85I	NM_032646.5	NP_116035.5	Q9BSA4	TTYH2_HUMAN	tweety family member 2			36					TGCGGTGGGCGTTGGTTTCTA	0.483000																								0							SO:0001583	missense			ENST00000269346.4	1	0	hg19	CCDS32717.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	g	8.083	0.772809	0.16051	0.013164	2.33E-4	ENSG00000141540	ENST00000269346;ENST00000529107	T;T	0.12984	2.63;2.63	5.35	3.38	0.38709	.	0.185685	0.46758	N	0.000263	T	0.06234	0.0161	L	0.41961	1.31	0.80722	D	1	B;B	0.33857	0.429;0.092	B;B	0.28305	0.088;0.037	T	0.24870	-1.0148	10	0.13470	T	0.59	-8.4172	7.2697	0.26250	0.3324:0.0:0.6676:0.0	.	85;106	B4DKD1;Q9BSA4	.;TTYH2_HUMAN	I	106;85	ENSP00000269346:V106I;ENSP00000433089:V85I	ENSP00000269346:V106I	V	+	1	0	TTYH2	69738635	0.567000	0.26626	0.943000	0.38184	0.688000	0.40055	1.396000	0.34531	0.658000	0.30925	-0.119000	0.15052	GTT		TCGA-3A-A9J0-01A-11D-A40W-08	TTYH2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387459.1	0	0	1	49	302	0	66	0	3.163420e-01	0	8	0	66	2		0	0	0	0	0	2	1	1.000000	48	299	0	66	2								-3.218233	1	1	121412	205	55	1	1	3	4	2.244625	1	0.470000	3.280000	0.634785	0.860000	6.500000e-01	1.000000	1.000000	0.868288	0.860000	1		
TP53	7157	broad.mit.edu	37	17	7578370	7578370	+	Splice_Site	SNP	C	C	T			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr17:7578370C>T	ENST00000269305.4	-	5	749		c.e5+1		TP53_ENST00000445888.2_Splice_Site|TP53_ENST00000574684.1_Splice_Site|TP53_ENST00000455263.2_Splice_Site|TP53_ENST00000420246.2_Splice_Site|TP53_ENST00000359597.4_Splice_Site|TP53_ENST00000413465.2_Splice_Site	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	p.?(54)|p.0?(8)|p.G187fs*16(2)|p.D186_P191delDGLAPP(1)|p.L188fs*19(1)|p.G187_L188delGL(1)|p.G187fs*22(1)		24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		Acetylsalicylic acid(DB00945)	CAGCTGCTCACCATCGCTATC	0.632000		111	Mis, N, F		breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types	breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		L, E, M, O	68	Unknown(54)|Whole gene deletion(8)|Deletion - Frameshift(3)|Deletion - In frame(2)|Insertion - Frameshift(1)						SO:0001630	splice_region_variant	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	ENST00000269305.4	1	1	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	11.89	1.774230	0.31411	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	.	.	.	4.7	3.7	0.42460	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.0738	0.59075	0.0:0.8363:0.1637:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TP53	7519095	1.000000	0.71417	0.967000	0.41034	0.201000	0.24016	3.085000	0.50151	1.248000	0.43934	0.655000	0.94253	.		TCGA-3A-A9J0-01A-11D-A40W-08	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	1	0	1	74	96	0	60		0	0	0	0	60	2	1	1	400	408	0	681	2	1	1.000000	74	94	0	58	2								-20.000000	1	1	0	0		1	0	2	2	1.636792	1	0.470000	3.280000	0.470000	0.990000	9.900000e-01	1.000000	1.000000	1.000000	0.990000	1		
LIPG	9388	broad.mit.edu	37	18	47110141	47110141	+	Missense_Mutation	SNP	G	G	A			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr18:47110141G>A	ENST00000261292.4	+	8	1651	c.1373G>A	c.(1372-1374)cGg>cAg	p.R458Q	LIPG_ENST00000427224.2_Missense_Mutation_p.R384Q	NM_006033.2	NP_006024.1	Q9Y5X9	LIPE_HUMAN	lipase, endothelial			18					GAAACCCAGCGGAAGTAAGTG	0.562000													Pancreas(126;280 1778 12814 26243 34948)											0							SO:0001583	missense			ENST00000261292.4	0	1	hg19	CCDS11938.1	.	.	.	.	.	.	.	.	.	.	G	13.21	2.168290	0.38315	.	.	ENSG00000101670	ENST00000261292;ENST00000427224	T;T	0.64438	-0.1;-0.1	5.6	-1.19	0.09585	Lipoxygenase, LH2 (3);Lipase/lipooxygenase, PLAT/LH2 (1);	0.314978	0.38381	N	0.001720	T	0.21509	0.0518	N	0.00885	-1.115	0.80722	D	1	B;B	0.20550	0.001;0.046	B;B	0.12837	0.001;0.008	T	0.11131	-1.0600	10	0.09084	T	0.74	-10.3611	7.2214	0.25990	0.6792:0.0:0.1813:0.1396	.	384;458	B4DTR8;Q9Y5X9	.;LIPE_HUMAN	Q	458;384	ENSP00000261292:R458Q;ENSP00000387978:R384Q	ENSP00000261292:R458Q	R	+	2	0	LIPG	45364139	0.664000	0.27457	0.301000	0.25044	0.917000	0.54804	0.558000	0.23469	-0.126000	0.11682	0.561000	0.74099	CGG		TCGA-3A-A9J0-01A-11D-A40W-08	LIPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447546.1	0	0	0	3	43	0	16	0	3.757470e-01	0	16	0	16	2		0	0	0	0	0	2	1	0.798256	3	41	0	16	2								-7.404661	1	1	121394	3	27	1	0	1	1	1.264376	1	0.470000	3.280000	0.321774	0.240000	7.000000e-02	0.530000	0.210000	0.264678	0.240000	0		
TCF4	6925	broad.mit.edu	37	18	52899837	52899837	+	Missense_Mutation	SNP	C	C	T			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08			C	T	C	C		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr18:52899837C>T	ENST00000356073.4	-	17	2163	c.1552G>A	c.(1552-1554)Gag>Aag	p.E518K	TCF4_ENST00000398339.1_Missense_Mutation_p.E620K|TCF4_ENST00000564999.1_Missense_Mutation_p.E518K|TCF4_ENST00000564403.2_Missense_Mutation_p.E524K|TCF4_ENST00000567880.1_Missense_Mutation_p.E458K|TCF4_ENST00000568740.1_Missense_Mutation_p.E493K|TCF4_ENST00000561831.3_Missense_Mutation_p.E358K|TCF4_ENST00000566286.1_Missense_Mutation_p.E515K|TCF4_ENST00000561992.1_Missense_Mutation_p.E388K|TCF4_ENST00000537578.1_Missense_Mutation_p.E494K|TCF4_ENST00000570287.2_Missense_Mutation_p.E358K|TCF4_ENST00000565018.2_Missense_Mutation_p.E518K|TCF4_ENST00000540999.1_Missense_Mutation_p.E494K|TCF4_ENST00000570177.2_Missense_Mutation_p.E388K|TCF4_ENST00000457482.3_Missense_Mutation_p.E358K|TCF4_ENST00000543082.1_Missense_Mutation_p.E476K|TCF4_ENST00000537856.3_Missense_Mutation_p.E388K|TCF4_ENST00000568673.1_Missense_Mutation_p.E494K|TCF4_ENST00000544241.2_Missense_Mutation_p.E447K|TCF4_ENST00000564228.1_Missense_Mutation_p.E447K|TCF4_ENST00000566279.1_Missense_Mutation_p.E458K|TCF4_ENST00000354452.3_Missense_Mutation_p.E518K	NM_003199.2	NP_003190.1	P15884	ITF2_HUMAN	transcription factor 4			41					TCATCACCCTCGTCATCGGAT	0.468000																								0							SO:0001583	missense			ENST00000356073.4	1	1	hg19	CCDS11960.1	.	.	.	.	.	.	.	.	.	.	C	15.14	2.745039	0.49151	.	.	ENSG00000196628	ENST00000354452;ENST00000457482;ENST00000356073;ENST00000543082;ENST00000540999;ENST00000537578;ENST00000544241;ENST00000537856;ENST00000398339	T;T;T;T;T;T;T;T;T	0.18810	2.51;2.22;2.47;2.46;2.48;2.51;2.48;2.19;2.49	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	T	0.35856	0.0946	L	0.49640	1.575	0.80722	D	1	B;B;B;P;D;B;B;D;B	0.65815	0.038;0.172;0.065;0.919;0.992;0.038;0.038;0.995;0.371	B;B;B;B;P;B;B;D;B	0.68192	0.007;0.017;0.025;0.394;0.905;0.007;0.007;0.956;0.095	T	0.06826	-1.0805	10	0.02654	T	1	-15.4116	17.8399	0.88712	0.0:1.0:0.0:0.0	.	494;518;358;620;518;476;447;358;515	B7Z5M6;G0LNT9;G0LNV1;E9PH57;P15884;B3KUC0;B3KT62;G0LNU9;G0LNU5	.;.;.;.;ITF2_HUMAN;.;.;.;.	K	518;358;518;476;494;494;447;388;620	ENSP00000346440:E518K;ENSP00000409447:E358K;ENSP00000348374:E518K;ENSP00000439656:E476K;ENSP00000445202:E494K;ENSP00000440731:E494K;ENSP00000441562:E447K;ENSP00000439827:E388K;ENSP00000381382:E620K	ENSP00000346440:E518K	E	-	1	0	TCF4	51050835	0.998000	0.40836	0.998000	0.56505	0.952000	0.60782	3.845000	0.55880	2.510000	0.84645	0.467000	0.42956	GAG		TCGA-3A-A9J0-01A-11D-A40W-08	TCF4-002	KNOWN	upstream_uORF|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256014.1	1	0	1	49	125	0	64	0	9.968765e-01	1	25	0	64	2		0	0	0	0	0	2	1	1.000000	49	125	0	62	2								-5.456219	1	1	0	0		1	0	1	1	1.249961	1	0.470000	3.280000	0.325828	0.910000	7.100000e-01	1.000000	1.000000	0.909871	0.910000	1		
KIAA1468	57614	broad.mit.edu	37	18	59912054	59912054	+	Missense_Mutation	SNP	G	G	A			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr18:59912054G>A	ENST00000398130.2	+	11	1910	c.1678G>A	c.(1678-1680)Gat>Aat	p.D560N	RP11-173A16.2_ENST00000588561.1_RNA|KIAA1468_ENST00000256858.6_Missense_Mutation_p.D560N	NM_020854.3	NP_065905.2	Q9P260	K1468_HUMAN	KIAA1468			47		Colorectal(73;0.186)			TAAAGAGCGAGATCAGCTTCT	0.378000																								0							SO:0001583	missense			ENST00000398130.2	1	1	hg19	CCDS11979.2	.	.	.	.	.	.	.	.	.	.	G	34	5.334181	0.95758	.	.	ENSG00000134444	ENST00000398130;ENST00000256858	T;T	0.39787	1.06;1.06	5.61	5.61	0.85477	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.63236	0.2494	L	0.60845	1.875	0.80722	D	1	D;D;D	0.89917	0.994;0.98;1.0	P;P;D	0.83275	0.895;0.753;0.996	T	0.57969	-0.7719	9	.	.	.	-19.5571	20.0051	0.97433	0.0:0.0:1.0:0.0	.	560;560;204	Q9P260-2;Q9P260;B2RD46	.;K1468_HUMAN;.	N	560	ENSP00000381198:D560N;ENSP00000256858:D560N	.	D	+	1	0	KIAA1468	58063034	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.715000	0.98748	2.799000	0.96334	0.650000	0.86243	GAT		TCGA-3A-A9J0-01A-11D-A40W-08	KIAA1468-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256187.1	1	0	1	60	118	0	28	1	9.709536e-01	9	5	0	28	2		0	0	0	0	0	2	1	1.000000	58	116	0	27	2								-20.000000	1	1	0	0		1	0	1	1	1.255422	1	0.470000	3.280000	0.307190	0.940000	8.100000e-01	1.000000	0.990000	0.941718	0.940000	1		
PHLPP1	23239	broad.mit.edu	37	18	60563163	60563163	+	Missense_Mutation	SNP	T	T	G			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr18:60563163T>G	ENST00000262719.5	+	6	2597	c.2363T>G	c.(2362-2364)cTt>cGt	p.L788R	PHLPP1_ENST00000400316.4_Missense_Mutation_p.L276R			O60346	PHLP1_HUMAN	PH domain and leucine rich repeat protein phosphatase 1			17					GTGGATAAACTTTGTATGTCT	0.383000																								0							SO:0001583	missense			ENST00000262719.5	1	1	hg19	CCDS45881.2	.	.	.	.	.	.	.	.	.	.	T	26.1	4.709037	0.89018	.	.	ENSG00000081913	ENST00000400316;ENST00000262719	T;T	0.59638	0.25;0.25	5.07	5.07	0.68467	.	.	.	.	.	T	0.81250	0.4783	M	0.92317	3.295	0.80722	D	1	D	0.76494	0.999	D	0.91635	0.999	D	0.86211	0.1625	9	0.87932	D	0	-10.6448	15.016	0.71584	0.0:0.0:0.0:1.0	.	788	O60346	PHLP1_HUMAN	R	276;788	ENSP00000383170:L276R;ENSP00000262719:L788R	ENSP00000262719:L788R	L	+	2	0	PHLPP1	58714143	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	7.489000	0.81451	2.146000	0.66826	0.533000	0.62120	CTT		TCGA-3A-A9J0-01A-11D-A40W-08	PHLPP1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319249.2	1	0	1	45	109	0	49	1	6.544192e-01	4	3	0	49	2		0	0	0	0	0	2	1	1.000000	45	108	0	49	2								-20.000000	1	1	0	0		1	0	1	1	1.255422	1	0.470000	3.280000	0.307190	0.890000	7.000000e-01	1.000000	0.940000	0.886424	0.890000	1		
ZNF181	339318	broad.mit.edu	37	19	35232318	35232318	+	Silent	SNP	T	T	G	rs2607243		TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr19:35232318T>G	ENST00000492450.1	+	4	1121	c.1032T>G	c.(1030-1032)acT>acG	p.T344T	ZNF181_ENST00000392232.3_Silent_p.T388T|ZNF181_ENST00000459757.2_Silent_p.T343T			Q2M3W8	ZN181_HUMAN	zinc finger protein 181			22	all_lung(56;1.13e-07)|Lung NSC(56;1.81e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.138)		GAATTCATACTCAAGAAAAAC	0.388000																								0							SO:0001819	synonymous_variant			ENST00000492450.1	0	1	hg19	CCDS32990.2																																																																																				TCGA-3A-A9J0-01A-11D-A40W-08	ZNF181-002	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349005.3	0	0	0	6	307	0	46	0	1.074758e-02	0	7	0	46	2		0	0	0	0	0	2	1	0.965022	6	306	0	46	2								-2.537562	1	1	0	0		1	0	3	3	1.942808	1	0.470000	3.280000	0.570850	0.100000	3.000000e-02	0.210000	0.100000	0.116518	0.100000	0		
KLK15	55554	broad.mit.edu	37	19	51330356	51330356	+	Missense_Mutation	SNP	G	G	A	rs61751959		TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr19:51330356G>A	ENST00000598239.1	-	3	289	c.259C>T	c.(259-261)Cgg>Tgg	p.R87W	KLK15_ENST00000596931.1_Missense_Mutation_p.R86W|KLK15_ENST00000416184.1_Missense_Mutation_p.R87W|KLK15_ENST00000326856.4_Missense_Mutation_p.R86W|KLK15_ENST00000301421.2_Missense_Mutation_p.R87W	NM_017509.2	NP_059979.2	Q9H2R5	KLK15_HUMAN	kallikrein-related peptidase 15			24		all_neural(266;0.057)			GACGTGGTCCGTAGTTGCTCT	0.652000													Pancreas(140;10 2513 7143 9246)											0							SO:0001583	missense			ENST00000598239.1	1	1	hg19	CCDS12805.1	.	.	.	.	.	.	.	.	.	.	g	18.66	3.671049	0.67814	4.54E-4	6.98E-4	ENSG00000174562	ENST00000326856;ENST00000416184;ENST00000301421;ENST00000544946	D;D	0.93712	-3.27;-3.27	4.51	-0.491	0.12045	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.354502	0.20216	N	0.096801	D	0.96519	0.8864	M	0.90814	3.15	0.09310	N	0.999999	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	P;D;D;D	0.70016	0.892;0.93;0.94;0.967	D	0.92113	0.5697	10	0.87932	D	0	.	13.1286	0.59369	0.0:0.0:0.296:0.704	rs61751959	87;86;87;87	Q6UBM2;Q6ISI0;Q9H2R5-4;Q9H2R5	.;.;.;KLK15_HUMAN	W	87	ENSP00000415136:R87W;ENSP00000301421:R87W	ENSP00000301421:R87W	R	-	1	2	KLK15	56022168	0.000000	0.05858	0.000000	0.03702	0.329000	0.28539	0.668000	0.25127	-0.033000	0.13736	-0.268000	0.10319	CGG		TCGA-3A-A9J0-01A-11D-A40W-08	KLK15-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465160.1	1	0	1	79	375	0	155		0	0	0	0	155	2		0	0	0	0	0	2	1	1.000000	79	369	0	151	2								-3.901235	1	1	121346	122	54	1	0	4	4	2.013086	1	0.470000	3.280000	0.609490	0.990000	8.100000e-01	1.000000	1.000000	0.970630	0.990000	1		
LILRA1	11024	broad.mit.edu	37	19	55106342	55106342	+	Missense_Mutation	SNP	C	C	T			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr19:55106342C>T	ENST00000251372.3	+	4	465	c.283C>T	c.(283-285)Cgg>Tgg	p.R95W	LILRA1_ENST00000453777.1_Missense_Mutation_p.R95W|LILRB1_ENST00000418536.2_Intron|LILRB1_ENST00000396321.2_Intron|LILRB1_ENST00000448689.1_Intron|LILRA1_ENST00000473156.1_3'UTR	NM_006863.2	NP_006854.1	O75019	LIRA1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 1			47					ACACACAGGGCGGTATCGCTG	0.572000																								0							SO:0001583	missense			ENST00000251372.3	1	1	hg19	CCDS12901.1	.	.	.	.	.	.	.	.	.	.	C	8.318	0.823541	0.16678	0.0	1.16E-4	ENSG00000104974	ENST00000251372;ENST00000453777	T;T	0.13778	2.56;2.56	1.58	-1.3	0.09259	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.639860	0.04121	N	0.316290	T	0.19604	0.0471	M	0.86740	2.835	0.09310	N	1	B;P	0.38440	0.097;0.631	B;B	0.32805	0.03;0.153	T	0.37842	-0.9688	10	0.72032	D	0.01	.	5.5529	0.17101	0.6042:0.3958:0.0:0.0	.	95;95	O75019-2;O75019	.;LIRA1_HUMAN	W	95	ENSP00000251372:R95W;ENSP00000413715:R95W	ENSP00000251372:R95W	R	+	1	2	LILRA1	59798154	0.000000	0.05858	0.001000	0.08648	0.007000	0.05969	-0.728000	0.04925	-0.245000	0.09625	0.194000	0.17425	CGG		TCGA-3A-A9J0-01A-11D-A40W-08	LILRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140807.2	1	0	0	88	314	0	105	0	0	0	1	0	105	2		0	0	0	0	0	2	1	1.000000	87	307	0	104	2								-20.000000	1	1	121412	14	45	1	0	4	4	2.048062	1	0.470000	3.280000	0.613505	0.990000	9.900000e-01	1.000000	1.000000	0.999800	0.990000	1		
NLRP7	199713	broad.mit.edu	37	19	55450945	55450945	+	Silent	SNP	C	C	T			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr19:55450945C>T	ENST00000590030.1	-	3	1282	c.1242G>A	c.(1240-1242)acG>acA	p.T414T	NLRP7_ENST00000446217.1_Silent_p.T442T|NLRP7_ENST00000588756.1_Silent_p.T414T|NLRP7_ENST00000592784.1_Silent_p.T414T|NLRP7_ENST00000340844.2_Silent_p.T414T|NLRP7_ENST00000328092.5_Silent_p.T414T|NLRP7_ENST00000448121.2_Silent_p.T414T			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7			73					GGAGGCTCAGCGTCCGCAGCG	0.711000																								0							SO:0001819	synonymous_variant			ENST00000590030.1	1	1	hg19	CCDS33109.1																																																																																				TCGA-3A-A9J0-01A-11D-A40W-08	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	1	0	0	39	77	0	38		0	0	0	0	38	2		0	0	0	0	0	2	1	1.000000	36	67	0	52	2								-20.000000	1	1	119984	7	34	1	0	4	4	2.046693	1	0.470000	3.280000	0.612176	0.990000	9.900000e-01	1.000000	1.000000	1.000000	0.990000	1		
SYT5	6861	broad.mit.edu	37	19	55690401	55690401	+	Silent	SNP	C	C	T			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr19:55690401C>T	ENST00000354308.3	-	2	378	c.9G>A	c.(7-9)ccG>ccA	p.P3P	SYT5_ENST00000537500.1_Silent_p.P3P|CTD-2587H24.5_ENST00000591665.1_RNA|SYT5_ENST00000590851.1_Missense_Mutation_p.R58Q	NM_003180.2	NP_003171.2	O00445	SYT5_HUMAN	synaptotagmin V			18			BRCA - Breast invasive adenocarcinoma(297;0.209)		TTGGGGGCTCCGGGAACATGG	0.677000																								0							SO:0001819	synonymous_variant			ENST00000354308.3	0	1	hg19	CCDS12919.1	.	.	.	.	.	.	.	.	.	.	C	8.945	0.966705	0.18659	.	.	ENSG00000129990	ENST00000543844	.	.	.	3.54	1.3	0.21679	.	.	.	.	.	T	0.23649	0.0572	.	.	.	0.80722	D	1	B	0.34372	0.451	B	0.18871	0.023	T	0.05178	-1.0901	7	0.27785	T	0.31	.	3.9386	0.09316	0.2358:0.6379:0.0:0.1263	.	58	B7Z300	.	Q	58	.	ENSP00000441336:R58Q	R	-	2	0	SYT5	60382213	0.974000	0.33945	1.000000	0.80357	0.304000	0.27724	-0.295000	0.08298	0.450000	0.26774	0.558000	0.71614	CGG		TCGA-3A-A9J0-01A-11D-A40W-08	SYT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452501.1	0	0	0	5	51	0	12		0	0	0	0	12	2		0	0	0	0	0	2	1	0.934520	5	49	0	11	2								-3.233199	1	1	0	0		1	0	4	4	2.046693	1	0.470000	3.280000	0.612176	0.620000	2.300000e-01	1.000000	1.000000	0.654928	0.620000	0		
FBN3	84467	broad.mit.edu	37	19	8180474	8180474	+	Missense_Mutation	SNP	C	C	T	rs146523311		TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr19:8180474C>T	ENST00000600128.1	-	30	4177	c.3763G>A	c.(3763-3765)Gag>Aag	p.E1255K	FBN3_ENST00000601739.1_Missense_Mutation_p.E1255K|FBN3_ENST00000270509.2_Missense_Mutation_p.E1255K			Q75N90	FBN3_HUMAN	fibrillin 3			132					TTCGTGTTCTCGCAGTCCCCA	0.607000																								0							SO:0001583	missense			ENST00000600128.1	1	1	hg19	CCDS12196.1	.	.	.	.	.	.	.	.	.	.	C	10.26	1.300009	0.23650	2.27E-4	0.0	ENSG00000142449	ENST00000270509	D	0.87334	-2.24	3.94	1.81	0.25067	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.056825	0.64402	U	0.000002	T	0.76807	0.4039	L	0.37750	1.13	0.53688	D	0.999971	P	0.35050	0.482	B	0.29440	0.102	T	0.68131	-0.5490	10	0.28530	T	0.3	.	9.5212	0.39135	0.0:0.8225:0.0:0.1775	.	1255	Q75N90	FBN3_HUMAN	K	1255	ENSP00000270509:E1255K	ENSP00000270509:E1255K	E	-	1	0	FBN3	8086474	0.991000	0.36638	0.727000	0.30756	0.091000	0.18340	2.896000	0.48656	0.349000	0.23975	-0.254000	0.11334	GAG		TCGA-3A-A9J0-01A-11D-A40W-08	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	1	0	1	32	110	0	45		0	0	0	0	45	2		0	0	0	0	0	2	1	1.000000	32	107	0	44	2								-3.705161	1	1	121412	48	45	1	0	3	3	1.668820	1	0.470000	3.280000	0.545786	0.990000	8.200000e-01	1.000000	1.000000	0.983334	0.990000	1		
OR7G1	125962	broad.mit.edu	37	19	9225729	9225729	+	Silent	SNP	C	C	T	rs138779373	byFrequency	TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr19:9225729C>T	ENST00000541538.1	-	1	710	c.711G>A	c.(709-711)gcG>gcA	p.A237A	OR7G1_ENST00000293614.1_Silent_p.A237A	NM_001005192.2	NP_001005192.2	Q8NGA0	OR7G1_HUMAN	olfactory receptor, family 7, subfamily G, member 1			20					AGGTGGAAAACGCTTTATACT	0.418000																								0							SO:0001819	synonymous_variant			ENST00000541538.1	1	1	hg19	CCDS32898.2																																																																																				TCGA-3A-A9J0-01A-11D-A40W-08	OR7G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397912.1	1	0	1	60	176	0	60		0	0	0	0	60	2		0	0	0	0	0	2	1	1.000000	59	174	0	58	2								-20.000000	1	1	121412	24	46	1	0	3	3	1.668820	1	0.470000	3.280000	0.545786	0.990000	9.900000e-01	1.000000	1.000000	0.999135	0.990000	1		
ZNF562	54811	broad.mit.edu	37	19	9764114	9764114	+	Missense_Mutation	SNP	G	G	T			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr19:9764114G>T	ENST00000448622.1	-	6	954	c.792C>A	c.(790-792)aaC>aaA	p.N264K	ZNF562_ENST00000453792.2_Missense_Mutation_p.N195K|ZNF562_ENST00000537617.1_Missense_Mutation_p.N148K|ZNF562_ENST00000590155.1_Missense_Mutation_p.N263K|ZNF562_ENST00000453372.2_Missense_Mutation_p.N264K|ZNF562_ENST00000293648.4_Missense_Mutation_p.N192K|ZNF562_ENST00000541032.1_Missense_Mutation_p.N227K	NM_001130031.1|NM_001130032.1	NP_001123503.1|NP_001123504.1	Q6V9R5	ZN562_HUMAN	zinc finger protein 562			17					ATTTCCCACAGTTCTTAGTCT	0.378000																								0							SO:0001583	missense			ENST00000448622.1	0	1	hg19	CCDS45956.1	.	.	.	.	.	.	.	.	.	.	G	0.658	-0.806919	0.02819	.	.	ENSG00000171466	ENST00000453372;ENST00000448622;ENST00000293648;ENST00000541032;ENST00000453792;ENST00000537617	T;T;T;T;T;T	0.06768	3.28;3.28;3.35;3.26;3.36;3.38	1.67	-3.33	0.04958	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02571	0.0078	N	0.02412	-0.56	0.09310	N	1	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.001;0.0;0.0;0.0;0.0	T	0.39643	-0.9604	9	0.54805	T	0.06	.	1.739	0.02948	0.1587:0.1235:0.163:0.5548	.	148;263;227;264;192	F5H1B4;B4DMG0;B4DZP9;Q6V9R5;Q6V9R5-2	.;.;.;ZN562_HUMAN;.	K	264;264;192;227;195;148	ENSP00000410734:N264K;ENSP00000411784:N264K;ENSP00000293648:N192K;ENSP00000442614:N227K;ENSP00000440451:N195K;ENSP00000445816:N148K	ENSP00000293648:N192K	N	-	3	2	ZNF562	9625114	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-6.367000	0.00069	-1.457000	0.01919	-3.756000	0.00021	AAC		TCGA-3A-A9J0-01A-11D-A40W-08	ZNF562-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450239.1	1	0	0	20	326	0	82	0	4.780103e-02	0	6	0	82	2		0	0	0	0	0	2	1	0.999995	20	323	0	80	2								-5.810944	1	0	121410	9	41	1	0	3	3	1.668820	1	0.470000	3.280000	0.545786	0.310000	1.800000e-01	1.000000	0.280000	0.437706	0.310000	0		
PLOD1	5351	broad.mit.edu	37	1	12030859	12030859	+	Missense_Mutation	SNP	G	G	A			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr1:12030859G>A	ENST00000196061.4	+	17	1915	c.1888G>A	c.(1888-1890)Ggc>Agc	p.G630S	PLOD1_ENST00000376369.3_Missense_Mutation_p.G677S	NM_000302.3	NP_000293.2	Q02809	PLOD1_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1			29	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		Succinic acid(DB00139)|Vitamin C(DB00126)	GCTCTACCCCGGCTACTACAC	0.607000																								0							SO:0001583	missense			ENST00000196061.4	0	1	hg19	CCDS142.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.864455	0.91511	.	.	ENSG00000083444	ENST00000414311;ENST00000376369;ENST00000196061	T;T	0.65916	-0.18;-0.17	5.94	5.94	0.96194	Prolyl 4-hydroxylase, alpha subunit (1);	0.000000	0.85682	D	0.000000	T	0.70325	0.3211	M	0.89715	3.055	0.80722	D	1	B;B	0.31435	0.323;0.323	B;B	0.23275	0.03;0.045	T	0.73864	-0.3848	10	0.87932	D	0	.	19.3514	0.94389	0.0:0.0:1.0:0.0	.	677;630	B4DR87;Q02809	.;PLOD1_HUMAN	S	294;677;630	ENSP00000365548:G677S;ENSP00000196061:G630S	ENSP00000196061:G630S	G	+	1	0	PLOD1	11953446	1.000000	0.71417	0.986000	0.45419	0.995000	0.86356	9.869000	0.99810	2.826000	0.97356	0.561000	0.74099	GGC		TCGA-3A-A9J0-01A-11D-A40W-08	PLOD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000006865.1	0	0	0	4	159	0	35	0	9.881234e-01	0	369	0	35	2		0	0	0	0	0	2	1	0.886949	4	156	0	35	2								-6.080160	1	1	121386	3	33	1	1	3	4	2.035345	1	0.470000	3.280000	0.598363	0.180000	5.000000e-02	1.000000	0.140000	0.343673	0.180000	0		
HNRNPCL1	343069	broad.mit.edu	37	1	12908073	12908073	+	Missense_Mutation	SNP	T	T	C			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr1:12908073T>C	ENST00000317869.6	-	2	295	c.70A>G	c.(70-72)Aac>Gac	p.N24D		NM_001013631.1|NM_001136561.2|NM_001146181.1	NP_001013653.1|NP_001130033.2|NP_001139653.1	O60812	HNRC1_HUMAN	heterogeneous nuclear ribonucleoprotein C-like 1			29					ACAAGAGTGTTGAGATTCCCA	0.453000																								0							SO:0001583	missense			ENST00000317869.6	1	1	hg19	CCDS30591.1	.	.	.	.	.	.	.	.	.	.	T	18.56	3.650509	0.67472	.	.	ENSG00000179172	ENST00000317869	T	0.40225	1.04	1.09	-0.423	0.12325	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.179946	0.45361	U	0.000369	T	0.24005	0.0581	N	0.17474	0.49	0.42596	D	0.993268	B	0.31931	0.347	B	0.37989	0.262	T	0.03068	-1.1076	10	0.39692	T	0.17	.	4.9313	0.13919	0.0:0.0:0.3116:0.6884	.	24	O60812	HNRCL_HUMAN	D	24	ENSP00000365370:N24D	ENSP00000365370:N24D	N	-	1	0	HNRNPCL1	12830660	1.000000	0.71417	0.489000	0.27452	0.699000	0.40488	5.399000	0.66314	-0.107000	0.12088	0.341000	0.21757	AAC		TCGA-3A-A9J0-01A-11D-A40W-08	HNRNPCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005462.1	0	0	0	59	942	0	202		0	0	0	0	202	2		0	0	0	0	0	2	1	1.000000	59	930	0	199	2								-9.527195	1	1	0	0		1	1	3	4	2.035345	1	0.470000	3.280000	0.598363	0.340000	2.500000e-01	1.000000	0.330000	0.475043	0.340000	0		
S100A3	6274	broad.mit.edu	37	1	153520200	153520200	+	Missense_Mutation	SNP	C	C	A			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr1:153520200C>A	ENST00000368713.3	-	3	460	c.264G>T	c.(262-264)gaG>gaT	p.E88D	S100A3_ENST00000368712.1_Missense_Mutation_p.E88D|S100A4_ENST00000481009.1_5'Flank|S100A4_ENST00000368715.1_5'Flank|S100A4_ENST00000368714.1_Intron|S100A4_ENST00000368716.4_5'Flank|S100A4_ENST00000354332.4_5'Flank	NM_002960.1	NP_002951.1	P33764	S10A3_HUMAN	S100 calcium binding protein A3			3	all_lung(78;5.98e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)		CCTTGAAGTACTCGTGGCAGT	0.597000																								0							SO:0001583	missense			ENST00000368713.3	1	1	hg19	CCDS1043.1	.	.	.	.	.	.	.	.	.	.	C	10.91	1.485114	0.26598	.	.	ENSG00000188015	ENST00000368713;ENST00000368712	T;T	0.15139	2.45;2.45	5.02	-0.489	0.12052	EF-hand-like domain (1);	0.179337	0.47093	N	0.000253	T	0.03220	0.0094	L	0.41632	1.29	0.37075	D	0.898697	B	0.06786	0.001	B	0.06405	0.002	T	0.38779	-0.9645	10	0.08837	T	0.75	.	6.8995	0.24275	0.0:0.4367:0.3951:0.1682	.	88	P33764	S10A3_HUMAN	D	88	ENSP00000357702:E88D;ENSP00000357701:E88D	ENSP00000357701:E88D	E	-	3	2	S100A3	151786824	0.992000	0.36948	0.997000	0.53966	0.958000	0.62258	0.042000	0.13949	-0.037000	0.13646	0.655000	0.94253	GAG		TCGA-3A-A9J0-01A-11D-A40W-08	S100A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037726.1	1	0	0	79	446	0	108	0	2.886893e-01	0	7	0	108	2		0	0	0	0	0	2	1	1.000000	79	440	0	102	2								-20.000000	1	1	0	0		1	3	3	6	2.322612	1	0.470000	3.280000	0.648448	0.990000	7.800000e-01	1.000000	1.000000	0.957669	0.990000	1		
UBQLN4	56893	broad.mit.edu	37	1	156012004	156012004	+	Silent	SNP	G	G	A			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr1:156012004G>A	ENST00000368309.3	-	8	1382	c.1290C>T	c.(1288-1290)ttC>ttT	p.F430F		NM_020131.3	NP_064516.2	Q9NRR5	UBQL4_HUMAN	ubiquilin 4			16	Hepatocellular(266;0.133)|all_neural(408;0.195)				GGTTCCCCGCGAAGAGCGGCA	0.617000																								0							SO:0001819	synonymous_variant			ENST00000368309.3	1	1	hg19	CCDS1127.1																																																																																				TCGA-3A-A9J0-01A-11D-A40W-08	UBQLN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046193.1	1	0	1	46	320	0	66	1	9.993203e-01	15	63	0	66	2		0	0	0	0	0	2	1	0.996464	44	317	2	65	25								-20.000000	1	1	121410	5	39	1	3	3	6	2.322612	1	0.470000	3.280000	0.648448	0.850000	6.100000e-01	1.000000	1.000000	0.859474	0.850000	1		
NUF2	83540	broad.mit.edu	37	1	163317716	163317716	+	Missense_Mutation	SNP	G	G	A			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr1:163317716G>A	ENST00000271452.3	+	12	1391	c.1112G>A	c.(1111-1113)cGc>cAc	p.R371H	NUF2_ENST00000524800.1_Missense_Mutation_p.R324H|NUF2_ENST00000367900.3_Missense_Mutation_p.R371H	NM_145697.2	NP_663735.2	Q9BZD4	NUF2_HUMAN	NUF2, NDC80 kinetochore complex component	p.R371H(1)		35	all_hematologic(923;0.101)				CAATACAAACGCACAGTAATT	0.318000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000271452.3	1	1	hg19	CCDS1245.1	.	.	.	.	.	.	.	.	.	.	G	12.94	2.089136	0.36855	.	.	ENSG00000143228	ENST00000524800;ENST00000367900;ENST00000271452	T;T;T	0.34859	1.45;1.34;1.34	6.03	4.13	0.48395	.	0.220012	0.49916	D	0.000130	T	0.07863	0.0197	N	0.16478	0.41	0.28144	N	0.929683	P;P	0.39352	0.669;0.669	B;B	0.27076	0.076;0.046	T	0.11372	-1.0590	9	0.44086	T	0.13	-6.6183	9.1986	0.37244	0.2248:0.0:0.7752:0.0	.	324;371	E9PQC4;Q9BZD4	.;NUF2_HUMAN	H	324;371;371	ENSP00000436888:R324H;ENSP00000356875:R371H;ENSP00000271452:R371H	ENSP00000271452:R371H	R	+	2	0	NUF2	161584340	0.995000	0.38212	0.857000	0.33713	0.990000	0.78478	1.124000	0.31320	1.521000	0.48983	0.655000	0.94253	CGC		TCGA-3A-A9J0-01A-11D-A40W-08	NUF2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000082812.1	1	0	1	31	183	0	48	1	8.766069e-01	3	21	0	48	2		0	0	0	0	0	2	1	1.000000	31	181	0	47	2								-16.227440	1	1	121412	2	31	1	3	3	6	2.322612	1	0.470000	3.280000	0.648448	0.990000	6.700000e-01	1.000000	1.000000	0.930027	0.990000	1		
HMCN1	83872	broad.mit.edu	37	1	186030997	186030997	+	Missense_Mutation	SNP	C	C	T			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr1:186030997C>T	ENST00000271588.4	+	47	7556	c.7327C>T	c.(7327-7329)Cgg>Tgg	p.R2443W	HMCN1_ENST00000367492.2_Missense_Mutation_p.R2443W	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1			308					CAGGATGCTACGGCTGATGCA	0.398000																								0							SO:0001583	missense			ENST00000271588.4	1	1	hg19	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.274075	0.80580	0.0	1.16E-4	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.36520	1.25;1.25	5.39	4.42	0.53409	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.56529	0.1991	M	0.68317	2.08	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.53906	-0.8372	10	0.37606	T	0.19	.	14.5328	0.67939	0.1471:0.8529:0.0:0.0	.	2443	Q96RW7	HMCN1_HUMAN	W	2443	ENSP00000271588:R2443W;ENSP00000356462:R2443W	ENSP00000271588:R2443W	R	+	1	2	HMCN1	184297620	1.000000	0.71417	0.330000	0.25442	0.846000	0.48090	4.567000	0.60850	2.528000	0.85240	0.591000	0.81541	CGG		TCGA-3A-A9J0-01A-11D-A40W-08	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	1	0	1	48	212	0	13	0	0	0	1	0	13	2		0	0	0	0	0	2	1	1.000000	48	210	0	12	2								-3.289656	1	1	121402	7	40	1	3	3	6	2.360015	1	0.470000	3.280000	0.654903	0.990000	9.300000e-01	1.000000	1.000000	0.996367	0.990000	1		
ASPM	259266	broad.mit.edu	37	1	197072286	197072286	+	Missense_Mutation	SNP	C	C	T	rs149033840		TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr1:197072286C>T	ENST00000367409.4	-	18	6351	c.6095G>A	c.(6094-6096)cGt>cAt	p.R2032H	ASPM_ENST00000294732.7_Intron|ASPM_ENST00000367408.1_Intron	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)			165					TTTCATACCACGATAAGCTGA	0.333000																								0							SO:0001583	missense			ENST00000367409.4	1	1	hg19	CCDS1389.1	.	.	.	.	.	.	.	.	.	.	c	29.9	5.043488	0.93685	0.0	1.16E-4	ENSG00000066279	ENST00000367409	T	0.77098	-1.07	5.57	5.57	0.84162	.	0.000000	0.64402	D	0.000004	D	0.93012	0.7776	H	0.98048	4.135	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95297	0.8400	10	0.87932	D	0	.	18.5928	0.91220	0.0:1.0:0.0:0.0	.	2032	Q8IZT6	ASPM_HUMAN	H	2032	ENSP00000356379:R2032H	ENSP00000356379:R2032H	R	-	2	0	ASPM	195338909	1.000000	0.71417	0.711000	0.30485	0.987000	0.75469	4.754000	0.62191	2.635000	0.89317	0.632000	0.83419	CGT		TCGA-3A-A9J0-01A-11D-A40W-08	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	1	0	1	84	334	0	64	1	1.851841e-01	3	1	0	64	2		0	0	0	0	0	2	1	1.000000	84	332	0	64	2								-20.000000	1	1	121386	1	31	1	0	2	2	1.605430	1	0.470000	3.280000	0.470000	0.850000	6.900000e-01	1.000000	1.000000	0.857003	0.850000	1		
DISP1	84976	broad.mit.edu	37	1	223175862	223175862	+	Missense_Mutation	SNP	G	G	A			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr1:223175862G>A	ENST00000284476.6	+	8	1287	c.1123G>A	c.(1123-1125)Gtt>Att	p.V375I		NM_032890.3	NP_116279.2	Q96F81	DISP1_HUMAN	dispatched homolog 1 (Drosophila)			69					TGAGCGAGACGTTTCTCATAC	0.527000											OREG0014268|OREG0026708	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)												0							SO:0001583	missense			ENST00000284476.6	1	1	hg19	CCDS1536.1	.	.	.	.	.	.	.	.	.	.	G	11.74	1.730061	0.30684	.	.	ENSG00000154309	ENST00000284476	D	0.86164	-2.08	5.25	4.33	0.51752	.	0.114979	0.64402	D	0.000013	D	0.82765	0.5108	L	0.43598	1.365	0.58432	D	0.999992	P	0.43314	0.803	B	0.39935	0.314	T	0.81145	-0.1066	10	0.27785	T	0.31	-17.2678	16.1121	0.81271	0.0:0.1337:0.8663:0.0	.	375	Q96F81	DISP1_HUMAN	I	375	ENSP00000284476:V375I	ENSP00000284476:V375I	V	+	1	0	DISP1	221242485	1.000000	0.71417	0.522000	0.27862	0.672000	0.39443	5.135000	0.64777	1.433000	0.47394	0.655000	0.94253	GTT		TCGA-3A-A9J0-01A-11D-A40W-08	DISP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092512.1	1	0	1	116	240	0	44	1	7.909829e-01	3	5	0	44	2		0	0	0	0	0	2	1	1.000000	113	237	0	44	2								-20.000000	1	1	121412	1	31	1	3	3	6	2.332360	1	0.470000	3.280000	0.650626	0.990000	9.900000e-01	1.000000	1.000000	1.000000	0.990000	1		
CDC42BPA	8476	broad.mit.edu	37	1	227223274	227223274	+	Silent	SNP	G	G	A			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr1:227223274G>A	ENST00000366769.3	-	24	4420	c.3129C>T	c.(3127-3129)aaC>aaT	p.N1043N	CDC42BPA_ENST00000366764.2_Silent_p.N1015N|CDC42BPA_ENST00000366767.3_Silent_p.N962N|CDC42BPA_ENST00000366766.2_Silent_p.N1078N|CDC42BPA_ENST00000334218.5_Silent_p.N1043N|CDC42BPA_ENST00000366765.3_Silent_p.N1056N|CDC42BPA_ENST00000535525.1_Silent_p.N1023N	NM_003607.3	NP_003598.2			CDC42 binding protein kinase alpha (DMPK-like)			77		all_cancers(173;0.156)|Prostate(94;0.0792)			TTGGAGCTTTGTTTACACAAG	0.373000																								0							SO:0001819	synonymous_variant			ENST00000366769.3	1	1	hg19	CCDS1558.1	.	.	.	.	.	.	.	.	.	.	G	9.760	1.169942	0.21621	.	.	ENSG00000143776	ENST00000448940;ENST00000442054;ENST00000441725	.	.	.	5.8	5.8	0.92144	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.051	0.97627	0.0:0.0:1.0:0.0	.	.	.	.	X	246;372;268	.	.	Q	-	1	0	CDC42BPA	225289897	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.833000	0.48159	2.740000	0.93945	0.650000	0.86243	CAA		TCGA-3A-A9J0-01A-11D-A40W-08	CDC42BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091696.1	1	0	0	69	355	0	87	0	9.367419e-01	0	26	0	87	2		0	0	0	0	0	2	1	1.000000	70	350	0	86	2								-20.000000	1	1	0	0		1	3	3	6	2.332360	1	0.470000	3.280000	0.650626	0.990000	8.400000e-01	1.000000	1.000000	0.983121	0.990000	1		
WNT3A	89780	broad.mit.edu	37	1	228246856	228246856	+	Missense_Mutation	SNP	G	G	A			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr1:228246856G>A	ENST00000284523.1	+	4	827	c.749G>A	c.(748-750)cGc>cAc	p.R250H	WNT3A_ENST00000366753.2_Missense_Mutation_p.R250H	NM_033131.3	NP_149122.1	P56704	WNT3A_HUMAN	wingless-type MMTV integration site family, member 3A			12		Prostate(94;0.0405)			CGGGAGTCCCGCGGCTGGGTG	0.657000																								0							SO:0001583	missense			ENST00000284523.1	1	1	hg19	CCDS1564.1	.	.	.	.	.	.	.	.	.	.	G	34	5.345122	0.95807	.	.	ENSG00000154342	ENST00000284523;ENST00000366753	T;T	0.76448	-1.02;-1.02	4.68	4.68	0.58851	.	0.000000	0.85682	D	0.000000	D	0.85283	0.5661	L	0.51914	1.62	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.987;0.993	D	0.86836	0.2014	10	0.66056	D	0.02	.	17.9461	0.89039	0.0:0.0:1.0:0.0	.	250;250	P56704;Q3SY79	WNT3A_HUMAN;.	H	250	ENSP00000284523:R250H;ENSP00000355715:R250H	ENSP00000284523:R250H	R	+	2	0	WNT3A	226313479	1.000000	0.71417	0.999000	0.59377	0.972000	0.66771	9.733000	0.98818	2.300000	0.77407	0.491000	0.48974	CGC		TCGA-3A-A9J0-01A-11D-A40W-08	WNT3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091648.1	1	0	1	39	217	0	58		0	0	0	0	58	2		0	0	0	0	0	2	1	1.000000	38	211	0	58	2								-20.000000	1	1	0	0		1	3	3	6	2.332360	1	0.470000	3.280000	0.650626	0.990000	7.300000e-01	1.000000	1.000000	0.955290	0.990000	1		
OR2M4	26245	broad.mit.edu	37	1	248402386	248402386	+	Missense_Mutation	SNP	G	G	T			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr1:248402386G>T	ENST00000306687.1	+	1	156	c.156G>T	c.(154-156)gaG>gaT	p.E52D		NM_017504.1	NP_059974.1	Q96R27	OR2M4_HUMAN	olfactory receptor, family 2, subfamily M, member 4			50	all_cancers(71;0.000124)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)		TCTACATAGAGAAACAGCTCC	0.478000																								0							SO:0001583	missense			ENST00000306687.1	1	1	hg19	CCDS31108.1	.	.	.	.	.	.	.	.	.	.	g	0.001	-3.029643	0.00041	.	.	ENSG00000171180	ENST00000306687	T	0.02140	4.43	3.08	1.13	0.20643	GPCR, rhodopsin-like superfamily (1);	0.344625	0.20655	N	0.088135	T	0.00468	0.0015	N	0.00140	-2.01	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46735	-0.9170	10	0.02654	T	1	.	2.8665	0.05603	0.1816:0.523:0.1817:0.1137	.	52	Q96R27	OR2M4_HUMAN	D	52	ENSP00000306688:E52D	ENSP00000306688:E52D	E	+	3	2	OR2M4	246469009	0.000000	0.05858	0.096000	0.21009	0.114000	0.19823	-2.414000	0.01037	0.614000	0.30107	-0.268000	0.10319	GAG		TCGA-3A-A9J0-01A-11D-A40W-08	OR2M4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097352.1	1	0	1	98	646	0	89		0	0	0	0	89	2		0	0	0	0	0	2	1	1.000000	98	633	0	85	2								-3.221884	1	1	0	0		1	3	3	6	2.332360	1	0.470000	3.280000	0.650626	0.880000	7.000000e-01	1.000000	0.840000	0.889382	0.880000	1		
CSMD2	114784	broad.mit.edu	37	1	34092119	34092119	+	Missense_Mutation	SNP	C	C	T			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr1:34092119C>T	ENST00000373380.1	-	12	2102	c.1882G>A	c.(1882-1884)Gca>Aca	p.A628T	CSMD2_ENST00000373377.1_5'UTR|CSMD2_ENST00000373388.2_5'UTR|CSMD2_ENST00000373381.4_Missense_Mutation_p.A1755T			Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2			246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)			CTGGCTGGTGCGAGGCCTTTG	0.542000																								0							SO:0001583	missense			ENST00000373380.1	1	1	hg19		.	.	.	.	.	.	.	.	.	.	c	9.717	1.158608	0.21454	.	.	ENSG00000121904	ENST00000373381;ENST00000373380	T;T	0.59083	0.29;0.29	5.87	0.757	0.18427	CUB (5);	0.497844	0.22002	N	0.065989	T	0.26340	0.0643	N	0.03903	-0.33	0.20403	N	0.999907	B;B;B	0.15473	0.002;0.013;0.002	B;B;B	0.15870	0.002;0.008;0.014	T	0.13737	-1.0498	10	0.22706	T	0.39	.	5.2569	0.15552	0.3639:0.4384:0.0:0.1976	.	628;1715;1755	Q7Z408-2;Q7Z408;E7EUA6	.;CSMD2_HUMAN;.	T	1755;628	ENSP00000362479:A1755T;ENSP00000362478:A628T	ENSP00000241312:A1715T	A	-	1	0	CSMD2	33864706	0.019000	0.18553	0.012000	0.15200	0.327000	0.28475	0.209000	0.17435	0.103000	0.17682	-0.713000	0.03633	GCA		TCGA-3A-A9J0-01A-11D-A40W-08	CSMD2-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000030635.4	1	0	1	10	51	0	19	0	0	0	1	0	19	2		0	0	0	0	0	2	1	0.997694	10	51	0	18	2								-18.535100	1	1	121402	6	32	1	1	3	4	1.984023	1	0.470000	3.280000	0.583530	0.990000	5.000000e-01	1.000000	1.000000	0.893702	0.990000	1		
HIVEP3	59269	broad.mit.edu	37	1	41976495	41976495	+	Missense_Mutation	SNP	C	C	T			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr1:41976495C>T	ENST00000372583.1	-	9	7733	c.6848G>A	c.(6847-6849)gGa>gAa	p.G2283E	HIVEP3_ENST00000372584.1_Missense_Mutation_p.G2282E|HIVEP3_ENST00000429157.2_Missense_Mutation_p.G2282E|HIVEP3_ENST00000247584.5_Missense_Mutation_p.G2283E|HIVEP3_ENST00000460604.1_5'UTR	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3			85	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)			GCCCGGGCCTCCGCCGGTCCT	0.682000																								0							SO:0001583	missense			ENST00000372583.1	1	1	hg19	CCDS463.1	.	.	.	.	.	.	.	.	.	.	C	1.034	-0.680791	0.03353	.	.	ENSG00000127124	ENST00000372584;ENST00000372583;ENST00000247584;ENST00000429157	T;T;T;T	0.04917	3.54;3.53;3.53;3.54	5.27	3.27	0.37495	.	0.615288	0.14475	N	0.317317	T	0.02688	0.0081	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.46679	-0.9174	10	0.09843	T	0.71	-1.0496	4.9301	0.13912	0.0:0.6819:0.0:0.3181	.	2282;2283	Q5T1R4-2;Q5T1R4	.;ZEP3_HUMAN	E	2282;2283;2283;2282	ENSP00000361665:G2282E;ENSP00000361664:G2283E;ENSP00000247584:G2283E;ENSP00000410828:G2282E	ENSP00000247584:G2283E	G	-	2	0	HIVEP3	41749082	0.008000	0.16893	0.462000	0.27118	0.101000	0.19017	0.771000	0.26633	1.462000	0.47948	0.561000	0.74099	GGA		TCGA-3A-A9J0-01A-11D-A40W-08	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000016978.1	1	0	0	22	88	0	28	1	5.068464e-01	2	6	0	28	2		0	0	0	0	0	2	1	0.999999	20	88	0	27	2								-20.000000	1	1	0	0		1	1	3	4	1.984023	1	0.470000	3.280000	0.583530	0.990000	7.400000e-01	1.000000	1.000000	0.970960	0.990000	1		
SSX2IP	117178	broad.mit.edu	37	1	85124124	85124124	+	Missense_Mutation	SNP	C	C	T			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr1:85124124C>T	ENST00000342203.3	-	9	1218	c.955G>A	c.(955-957)Ggg>Agg	p.G319R	SSX2IP_ENST00000603677.1_Intron|SSX2IP_ENST00000437941.2_Missense_Mutation_p.G292R|SSX2IP_ENST00000605755.1_Missense_Mutation_p.G292R|SSX2IP_ENST00000370612.4_Missense_Mutation_p.G319R	NM_001166293.1|NM_001166294.1|NM_014021.3	NP_001159765.1|NP_001159766.1|NP_054740.3	Q9Y2D8	ADIP_HUMAN	synovial sarcoma, X breakpoint 2 interacting protein			19					CTTAGTTCCCCGGCATCTTCT	0.438000																								0							SO:0001583	missense			ENST00000342203.3	1	1	hg19	CCDS699.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.325317	0.81580	.	.	ENSG00000117155	ENST00000342203;ENST00000437941;ENST00000544699;ENST00000370612	T;T	0.49720	0.77;0.77	5.76	4.77	0.60923	.	0.455024	0.25037	N	0.033632	T	0.45796	0.1360	L	0.47716	1.5	0.35549	D	0.803693	D;D;D	0.63046	0.99;0.992;0.985	P;P;P	0.53760	0.615;0.734;0.648	T	0.42766	-0.9432	10	0.46703	T	0.11	.	17.5251	0.87798	0.1322:0.8678:0.0:0.0	.	315;319;292	F5H549;Q9Y2D8;B4DFE3	.;ADIP_HUMAN;.	R	319;292;315;319	ENSP00000340279:G319R;ENSP00000412781:G292R	ENSP00000340279:G319R	G	-	1	0	SSX2IP	84896712	0.967000	0.33354	0.993000	0.49108	0.938000	0.57974	4.489000	0.60309	2.732000	0.93576	0.655000	0.94253	GGG		TCGA-3A-A9J0-01A-11D-A40W-08	SSX2IP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027469.1	1	0	0	13	168	0	25	1	6.577031e-01	2	28	0	25	2		0	0	0	0	0	2	1	0.999494	13	162	0	25	2								-2.841579	1	1	0	0		1	1	3	4	1.986928	1	0.470000	3.280000	0.585062	0.440000	2.300000e-01	1.000000	0.380000	0.551462	0.440000	0		
PPP1R16B	26051	broad.mit.edu	37	20	37536753	37536753	+	Missense_Mutation	SNP	C	C	T			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr20:37536753C>T	ENST00000299824.1	+	10	1300	c.1111C>T	c.(1111-1113)Cgg>Tgg	p.R371W	PPP1R16B_ENST00000373331.2_Missense_Mutation_p.R329W	NM_015568.2	NP_056383.1	Q96T49	PP16B_HUMAN	protein phosphatase 1, regulatory subunit 16B			49		Myeloproliferative disorder(115;0.00878)			CCTGTGGCAGCGGAGTGCAGC	0.602000																								0							SO:0001583	missense			ENST00000299824.1	1	1	hg19	CCDS13309.1	.	.	.	.	.	.	.	.	.	.	C	19.37	3.814832	0.70912	.	.	ENSG00000101445	ENST00000299824;ENST00000373331	T;T	0.71103	-0.41;-0.54	5.26	3.2	0.36748	.	0.204892	0.41938	D	0.000796	T	0.66317	0.2777	L	0.36672	1.1	0.27630	N	0.948065	D;D	0.71674	0.998;0.995	P;P	0.51657	0.613;0.676	T	0.61247	-0.7101	10	0.72032	D	0.01	.	8.6451	0.34000	0.3461:0.5789:0.0:0.075	.	329;371	E9PFS8;Q96T49	.;PP16B_HUMAN	W	371;329	ENSP00000299824:R371W;ENSP00000362428:R329W	ENSP00000299824:R371W	R	+	1	2	PPP1R16B	36970167	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	0.866000	0.27954	1.476000	0.48215	0.644000	0.83932	CGG		TCGA-3A-A9J0-01A-11D-A40W-08	PPP1R16B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079220.2	1	0	1	39	231	1	37	0	2.208576e-02	0	2	1	37	2		0	0	0	0	0	2	1	1.000000	39	224	0	35	2								-2.846317	1	1	0	0		1	1	3	4	2.263571	1	0.470000	3.280000	0.639456	0.900000	6.600000e-01	1.000000	1.000000	0.894557	0.900000	1		
ARFGEF2	10564	broad.mit.edu	37	20	47569336	47569336	+	Missense_Mutation	SNP	G	G	A			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr20:47569336G>A	ENST00000371917.4	+	5	518	c.518G>A	c.(517-519)aGc>aAc	p.S173N		NM_006420.2	NP_006411.2	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)			63			BRCA - Breast invasive adenocarcinoma(12;0.00148)|Colorectal(8;0.198)		TATTTGGCCAGCAAAAATCTC	0.443000													Esophageal Squamous(176;1738 1974 26285 33069 35354)											0							SO:0001583	missense			ENST00000371917.4	0	1	hg19	CCDS13411.1	.	.	.	.	.	.	.	.	.	.	G	35	5.522113	0.96416	.	.	ENSG00000124198	ENST00000538445;ENST00000371917	T	0.33654	1.4	6.06	6.06	0.98353	Armadillo-type fold (1);	0.079509	0.85682	D	0.000000	T	0.74366	0.3707	H	0.96208	3.785	0.80722	D	1	D	0.76494	0.999	D	0.72982	0.979	T	0.81656	-0.0834	10	0.87932	D	0	.	20.6208	0.99490	0.0:0.0:1.0:0.0	.	173	Q9Y6D5	BIG2_HUMAN	N	173	ENSP00000360985:S173N	ENSP00000360985:S173N	S	+	2	0	ARFGEF2	47002743	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.857000	0.99534	2.882000	0.98803	0.655000	0.94253	AGC		TCGA-3A-A9J0-01A-11D-A40W-08	ARFGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079627.1	0	0	0	5	557	0	98	0	4.442817e-03	0	9	0	98	2		0	0	0	0	0	2	0	0.002837	5	553	1	96	19								-2.617075	1	1	0	0		1	1	3	4	2.263571	1	0.470000	3.280000	0.639456	0.050000	0	0.130000	0.050000	0.064971	0.050000	0		
DSCAM	1826	broad.mit.edu	37	21	41710288	41710288	+	Missense_Mutation	SNP	C	C	T			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr21:41710288C>T	ENST00000400454.1	-	8	2000	c.1523G>A	c.(1522-1524)cGa>cAa	p.R508Q		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule			142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)			TTTCATTGGTCGAATGCTTGC	0.403000													Melanoma(134;970 1778 1785 21664 32388)											0							SO:0001583	missense			ENST00000400454.1	1	1	hg19	CCDS42929.1	.	.	.	.	.	.	.	.	.	.	C	33	5.256495	0.95336	.	.	ENSG00000171587	ENST00000400454;ENST00000404019	T;T	0.64260	-0.09;-0.09	5.77	5.77	0.91146	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000001	T	0.75042	0.3796	L	0.50847	1.595	0.53688	D	0.999972	D	0.76494	0.999	D	0.68192	0.956	T	0.70963	-0.4729	10	0.35671	T	0.21	.	19.9857	0.97347	0.0:1.0:0.0:0.0	.	508	O60469	DSCAM_HUMAN	Q	508;260	ENSP00000383303:R508Q;ENSP00000385342:R260Q	ENSP00000383303:R508Q	R	-	2	0	DSCAM	40632158	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.656000	0.83736	2.724000	0.93272	0.655000	0.94253	CGA		TCGA-3A-A9J0-01A-11D-A40W-08	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	1	0	1	57	89	0	60		0	0	0	0	60	2		0	0	0	0	0	2	1	1.000000	54	88	0	59	2								-20.000000	1	1	120828	1	35	1	0	2	2	1.590636	1	0.470000	3.280000	0.470000	0.990000	9.900000e-01	1.000000	1.000000	1.000000	0.990000	1		
COL6A2	1292	broad.mit.edu	37	21	47545822	47545822	+	Missense_Mutation	SNP	C	C	T			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr21:47545822C>T	ENST00000300527.4	+	26	2197	c.2093C>T	c.(2092-2094)gCg>gTg	p.A698V	COL6A2_ENST00000357838.4_Missense_Mutation_p.A698V|COL6A2_ENST00000397763.1_Missense_Mutation_p.A698V|COL6A2_ENST00000310645.5_Missense_Mutation_p.A698V|COL6A2_ENST00000409416.1_Missense_Mutation_p.A698V	NM_001849.3	NP_001840.3	P12110	CO6A2_HUMAN	collagen, type VI, alpha 2			43	Breast(49;0.245)				GAGTGGATTGCGGGCGGCACC	0.602000																								0							SO:0001583	missense			ENST00000300527.4	1	1	hg19	CCDS13728.1	.	.	.	.	.	.	.	.	.	.	C	18.15	3.559002	0.65538	.	.	ENSG00000142173	ENST00000300527;ENST00000357838;ENST00000310645;ENST00000409416;ENST00000397763	T;T;T;T;T	0.78481	-1.18;-1.18;-1.18;-1.18;-1.18	4.21	4.21	0.49690	von Willebrand factor, type A (3);	0.000000	0.85682	D	0.000000	D	0.87120	0.6098	M	0.72118	2.19	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.998;0.998	D	0.89107	0.3493	10	0.72032	D	0.01	-18.7532	16.5536	0.84479	0.0:1.0:0.0:0.0	.	698;698;698	P12110;P12110-2;P12110-3	CO6A2_HUMAN;.;.	V	698	ENSP00000300527:A698V;ENSP00000350497:A698V;ENSP00000312529:A698V;ENSP00000387115:A698V;ENSP00000380870:A698V	ENSP00000300527:A698V	A	+	2	0	COL6A2	46370250	1.000000	0.71417	0.030000	0.17652	0.733000	0.41908	7.562000	0.82300	1.889000	0.54706	0.491000	0.48974	GCG		TCGA-3A-A9J0-01A-11D-A40W-08	COL6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206971.1	1	0	1	37	108	0	49	1	1	2	2304	0	49	2		0	0	0	0	0	2	1	1.000000	37	105	0	46	2								-20.000000	1	1	0	0		1	0	2	2	1.590636	1	0.470000	3.280000	0.470000	0.990000	8.000000e-01	1.000000	1.000000	0.975379	0.990000	1		
PPM1F	9647	broad.mit.edu	37	22	22277807	22277807	+	Silent	SNP	G	G	A			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr22:22277807G>A	ENST00000263212.5	-	8	1128	c.1023C>T	c.(1021-1023)gcC>gcT	p.A341A	PPM1F_ENST00000407142.1_Silent_p.A173A|PPM1F_ENST00000538191.1_Silent_p.A237A	NM_014634.3	NP_055449.1	P49593	PPM1F_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1F			12	Colorectal(54;0.105)				AAGCTGCATCGGCCTCCCCAG	0.632000																								0							SO:0001819	synonymous_variant			ENST00000263212.5	1	1	hg19	CCDS13796.1																																																																																				TCGA-3A-A9J0-01A-11D-A40W-08	PPM1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320267.2	1	0	1	46	151	0	52	0	7.650780e-01	1	10	0	52	2		0	0	0	0	0	2	1	1.000000	46	148	0	50	2								-4.271238	1	1	121408	1	28	1	0	3	3	1.990590	1	0.470000	3.280000	0.570850	0.990000	9.300000e-01	1.000000	1.000000	0.996304	0.990000	1		
TBC1D10A	83874	broad.mit.edu	37	22	30722767	30722767	+	Missense_Mutation	SNP	G	G	A			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr22:30722767G>A	ENST00000215790.7	-	1	268	c.104C>T	c.(103-105)aCc>aTc	p.T35I	TBC1D10A_ENST00000490449.1_5'UTR|TBC1D10A_ENST00000403477.3_Missense_Mutation_p.T35I	NM_031937.2	NP_114143.1	Q9BXI6	TB10A_HUMAN	TBC1 domain family, member 10A			23					GAGTTCGTCGGTGGTTGCGGC	0.711000																								0							SO:0001583	missense			ENST00000215790.7	1	1	hg19	CCDS13874.1	.	.	.	.	.	.	.	.	.	.	G	14.44	2.535300	0.45176	.	.	ENSG00000099992	ENST00000215790;ENST00000403477	T;T	0.18174	2.23;3.53	4.13	3.1	0.35709	.	0.783594	0.11519	N	0.555865	T	0.09730	0.0239	N	0.14661	0.345	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.12682	-1.0538	10	0.38643	T	0.18	.	6.2359	0.20762	0.1066:0.1878:0.7056:0.0	.	35;35;35	Q20WK7;B3KXT8;Q9BXI6	.;.;TB10A_HUMAN	I	35	ENSP00000215790:T35I;ENSP00000384996:T35I	ENSP00000215790:T35I	T	-	2	0	TBC1D10A	29052767	0.815000	0.29118	0.337000	0.25536	0.754000	0.42855	1.587000	0.36622	0.843000	0.35070	0.430000	0.28490	ACC		TCGA-3A-A9J0-01A-11D-A40W-08	TBC1D10A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000320550.1	1	0	0	44	258	0	61	1	9.968197e-01	8	46	0	61	2		0	0	0	0	0	2	1	1.000000	42	245	0	58	2								-20.000000	1	1	0	0		1	0	6	6	2.712028	1	0.470000	3.280000	0.703844	0.990000	8.300000e-01	1.000000	1.000000	0.984948	0.990000	1		
GCC2	9648	broad.mit.edu	37	2	109092224	109092224	+	Missense_Mutation	SNP	A	A	G			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08			A	G	A	A		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr2:109092224A>G	ENST00000309863.6	+	9	3692	c.2978A>G	c.(2977-2979)gAa>gGa	p.E993G		NM_181453.3	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain containing 2			54					ACTGTGAAGGAAGAACTTGAA	0.313000																								0							SO:0001583	missense			ENST00000309863.6	1	1	hg19	CCDS33268.1	.	.	.	.	.	.	.	.	.	.	A	18.16	3.561512	0.65538	.	.	ENSG00000135968	ENST00000309863	T	0.37752	1.18	5.69	4.47	0.54385	.	0.060927	0.64402	D	0.000005	T	0.36193	0.0958	M	0.65975	2.015	0.43719	D	0.996197	D	0.53619	0.961	P	0.44597	0.454	T	0.14643	-1.0465	10	0.35671	T	0.21	.	8.0869	0.30777	0.7272:0.1393:0.0:0.1335	.	993	Q8IWJ2	GCC2_HUMAN	G	993	ENSP00000307939:E993G	ENSP00000307939:E993G	E	+	2	0	GCC2	108458656	1.000000	0.71417	1.000000	0.80357	0.552000	0.35366	4.657000	0.61490	2.296000	0.77279	0.533000	0.62120	GAA		TCGA-3A-A9J0-01A-11D-A40W-08	GCC2-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358516.3	1	0	1	107	286	0	73	1	9.985026e-01	9	20	0	73	2		0	0	0	0	0	2	1	1.000000	105	282	0	71	2								-20.000000	1	1	0	0		1	2	2	4	2.183810	1	0.470000	3.280000	0.627547	0.990000	9.900000e-01	1.000000	1.000000	1.000000	0.990000	1		
CKAP2L	150468	broad.mit.edu	37	2	113514074	113514074	+	Missense_Mutation	SNP	A	A	G			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr2:113514074A>G	ENST00000302450.6	-	4	952	c.874T>C	c.(874-876)Tca>Cca	p.S292P	CKAP2L_ENST00000541405.1_Missense_Mutation_p.S127P|CKAP2L_ENST00000481732.1_5'Flank	NM_152515.3	NP_689728.3	Q8IYA6	CKP2L_HUMAN	cytoskeleton associated protein 2-like			28					GGTTTCTTTGATGACTGAACT	0.403000																								0							SO:0001583	missense			ENST00000302450.6	1	1	hg19	CCDS2100.1	.	.	.	.	.	.	.	.	.	.	A	5.274	0.235997	0.10023	.	.	ENSG00000169607	ENST00000541405;ENST00000302450	T;T	0.18657	2.2;2.87	4.69	-2.55	0.06288	.	0.644272	0.13672	N	0.370817	T	0.10723	0.0262	L	0.33485	1.01	0.09310	N	1	B	0.14012	0.009	B	0.16722	0.016	T	0.27123	-1.0083	10	0.33141	T	0.24	-0.2642	0.2847	0.00249	0.3956:0.1484:0.1686:0.2874	.	292	Q8IYA6	CKP2L_HUMAN	P	127;292	ENSP00000438763:S127P;ENSP00000305204:S292P	ENSP00000305204:S292P	S	-	1	0	CKAP2L	113230545	0.527000	0.26306	0.001000	0.08648	0.091000	0.18340	0.044000	0.13992	-0.386000	0.07821	0.477000	0.44152	TCA		TCGA-3A-A9J0-01A-11D-A40W-08	CKAP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254082.2	0	0	1	154	374	0	113	1	7.263466e-01	4	4	0	113	2		0	0	0	0	0	2	1	1.000000	153	371	0	110	2								-20.000000	1	1	0	0		1	2	2	4	2.183810	1	0.470000	3.280000	0.627547	0.990000	9.900000e-01	1.000000	1.000000	1.000000	0.990000	1		
GPR39	2863	broad.mit.edu	37	2	133402714	133402714	+	Missense_Mutation	SNP	C	C	G			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08			C	G	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr2:133402714C>G	ENST00000329321.3	+	2	1366	c.897C>G	c.(895-897)aaC>aaG	p.N299K	GPR39_ENST00000470071.1_3'UTR|LYPD1_ENST00000397463.2_3'UTR	NM_001508.2	NP_001499.1	O43194	GPR39_HUMAN	G protein-coupled receptor 39			22					GGATGCCCAACCAGATTCGGA	0.547000																								0							SO:0001583	missense			ENST00000329321.3	1	1	hg19	CCDS2170.1	.	.	.	.	.	.	.	.	.	.	C	15.31	2.795528	0.50208	.	.	ENSG00000183840	ENST00000329321	T	0.71817	-0.6	5.3	3.48	0.39840	GPCR, rhodopsin-like superfamily (1);	0.108898	0.64402	D	0.000010	T	0.78104	0.4231	L	0.57536	1.79	0.80722	D	1	D	0.63046	0.992	D	0.66847	0.947	T	0.77531	-0.2553	10	0.62326	D	0.03	.	9.5552	0.39334	0.0:0.7715:0.0:0.2285	.	299	O43194	GPR39_HUMAN	K	299	ENSP00000327417:N299K	ENSP00000327417:N299K	N	+	3	2	GPR39	133119184	0.998000	0.40836	1.000000	0.80357	0.995000	0.86356	0.664000	0.25068	0.799000	0.34018	0.650000	0.86243	AAC		TCGA-3A-A9J0-01A-11D-A40W-08	GPR39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254582.1	1	0	1	81	251	0	87	1	9.999954e-01	27	32	0	87	2		0	0	0	0	0	2	1	1.000000	80	250	0	87	2								-20.000000	1	1	0	0		1	2	2	4	2.183810	1	0.470000	3.280000	0.627547	0.990000	9.900000e-01	1.000000	1.000000	0.999997	0.990000	1		
ABCB6	10058	broad.mit.edu	37	2	220080843	220080843	+	Missense_Mutation	SNP	G	G	A			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr2:220080843G>A	ENST00000265316.3	-	5	1346	c.1030C>T	c.(1030-1032)Cgg>Tgg	p.R344W	ABCB6_ENST00000439002.2_Missense_Mutation_p.R298W	NM_005689.2	NP_005680.1	Q9NP58	ABCB6_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 6 (Langereis blood group)			34		Renal(207;0.0474)			AGCTCCACCCGCCGAGACGTG	0.687000																								0							SO:0001583	missense			ENST00000265316.3	0	1	hg19	CCDS2436.1	.	.	.	.	.	.	.	.	.	.	G	13.59	2.282959	0.40394	.	.	ENSG00000115657	ENST00000265316;ENST00000439002	D;D	0.94376	-2.67;-3.41	5.07	2.06	0.26882	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.770646	0.12487	N	0.464574	D	0.94686	0.8286	M	0.71206	2.165	0.18873	N	0.999982	D;D	0.56746	0.975;0.977	P;P	0.55303	0.663;0.773	D	0.87676	0.2544	10	0.72032	D	0.01	-1.3565	12.0339	0.53415	0.0:0.4794:0.3877:0.1328	.	298;344	Q9NP58-4;Q9NP58	.;ABCB6_HUMAN	W	344;298	ENSP00000265316:R344W;ENSP00000394333:R298W	ENSP00000265316:R344W	R	-	1	2	ABCB6	219789087	0.000000	0.05858	0.000000	0.03702	0.031000	0.12232	1.031000	0.30165	0.306000	0.22856	0.650000	0.86243	CGG		TCGA-3A-A9J0-01A-11D-A40W-08	ABCB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256820.2	1	0	0	12	63	0	10	1	9.742557e-01	6	30	0	10	2		0	0	0	0	0	2	1	0.997207	11	47	0	9	2								-19.980230	1	1	0	0		1	2	2	4	2.143198	1	0.470000	3.280000	0.620017	0.990000	5.600000e-01	1.000000	1.000000	0.910020	0.990000	1		
COL4A4	1286	broad.mit.edu	37	2	227920747	227920747	+	Missense_Mutation	SNP	C	C	T	rs150979437	by1000genomes	TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr2:227920747C>T	ENST00000396625.3	-	30	2837	c.2630G>A	c.(2629-2631)cGg>cAg	p.R877Q	COL4A4_ENST00000329662.7_Missense_Mutation_p.R877Q	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4			98		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)			TGCCCCAGGCCGTCCTGGGAG	0.627000																								0							SO:0001583	missense			ENST00000396625.3	1	0	hg19	CCDS42828.1	224	0.10256410256410256	71	0.1443089430894309	23	0.06353591160220995	44	0.07692307692307693	86	0.11345646437994723	C	3.151	-0.174203	0.06421	0.001093	0.003314	ENSG00000081052	ENST00000396625;ENST00000329662	D;D	0.93307	-3.2;-3.2	5.63	-1.9	0.07665	.	.	.	.	.	T	0.02533	0.0077	N	0.16743	0.435	0.09310	N	1	B	0.13145	0.007	B	0.09377	0.004	T	0.40701	-0.9549	9	0.13470	T	0.59	.	2.2257	0.03983	0.2432:0.4338:0.1032:0.2199	.	877	P53420	CO4A4_HUMAN	Q	877	ENSP00000379866:R877Q;ENSP00000328553:R877Q	ENSP00000328553:R877Q	R	-	2	0	COL4A4	227628991	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.006000	0.13152	-0.756000	0.04703	-0.271000	0.10264	CGG		TCGA-3A-A9J0-01A-11D-A40W-08	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313770.1	0	0	1	29	186	0	37	1	1.453389e-01	3	2	0	37	2		0	0	0	0	0	2	1	1.000000	29	183	0	35	2								-2.989699	1	1	120794	502	58	1	2	2	4	2.143198	1	0.470000	3.280000	0.620017	0.830000	5.600000e-01	1.000000	1.000000	0.834406	0.830000	0		
LRRFIP1	9208	broad.mit.edu	37	2	238671269	238671269	+	Missense_Mutation	SNP	A	A	G			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr2:238671269A>G	ENST00000392000.4	+	11	1030	c.913A>G	c.(913-915)Aaa>Gaa	p.K305E	LRRFIP1_ENST00000244815.5_Missense_Mutation_p.K281E|LRRFIP1_ENST00000289175.6_Missense_Mutation_p.K249E|LRRFIP1_ENST00000308482.9_Intron	NM_001137552.1	NP_001131024.1	Q32MZ4	LRRF1_HUMAN	leucine rich repeat (in FLII) interacting protein 1			29		Breast(86;0.00257)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)			AGTGGAGGTGAAAAATGAAAT	0.433000																								0							SO:0001583	missense			ENST00000392000.4	0	1	hg19	CCDS46552.1	.	.	.	.	.	.	.	.	.	.	A	18.59	3.655875	0.67586	.	.	ENSG00000124831	ENST00000289175;ENST00000244815;ENST00000392000	T;T;T	0.47528	0.84;0.84;0.84	5.69	0.0731	0.14389	.	0.837827	0.10426	N	0.676077	T	0.37785	0.1016	L	0.51422	1.61	0.21445	N	0.999689	B;B;B	0.27882	0.192;0.046;0.1	B;B;B	0.25759	0.063;0.046;0.027	T	0.29640	-1.0005	10	0.45353	T	0.12	-15.096	6.5329	0.22336	0.6466:0.1247:0.2287:0.0	.	249;305;281	Q32MZ4-3;Q32MZ4;Q32MZ4-2	.;LRRF1_HUMAN;.	E	249;281;305	ENSP00000289175:K249E;ENSP00000244815:K281E;ENSP00000375857:K305E	ENSP00000244815:K281E	K	+	1	0	LRRFIP1	238336008	0.972000	0.33761	0.276000	0.24689	0.948000	0.59901	0.407000	0.21049	0.095000	0.17434	0.528000	0.53228	AAA		TCGA-3A-A9J0-01A-11D-A40W-08	LRRFIP1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317198.1	0	0	0	4	215	0	37	0	8.366742e-01	0	179	0	37	2		0	0	0	0	0	2	1	0.883376	4	208	0	37	2								-3.118740	1	1	121412	1	27	1	2	2	4	2.137730	1	0.470000	3.280000	0.620017	0.130000	3.000000e-02	1.000000	0.110000	0.242719	0.130000	0		
KIF1A	547	broad.mit.edu	37	2	241697827	241697827	+	Silent	SNP	G	G	A			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr2:241697827G>A	ENST00000320389.7	-	25	2663	c.2505C>T	c.(2503-2505)acC>acT	p.T835T	KIF1A_ENST00000498729.2_Silent_p.T844T	NM_004321.6	NP_004312.2	Q12756	KIF1A_HUMAN	kinesin family member 1A	p.T835T(1)		66		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)			GGTCTCCGCCGGTCACCACGT	0.637000																								1	Substitution - coding silent(1)						SO:0001819	synonymous_variant			ENST00000320389.7	1	1	hg19	CCDS46561.1																																																																																				TCGA-3A-A9J0-01A-11D-A40W-08	KIF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324536.3	1	0	1	12	95	0	29		0	0	0	0	29	2		0	0	0	0	0	2	1	0.999005	12	89	0	28	2								-18.801000	1	1	121188	4	35	1	2	2	4	2.137730	1	0.470000	3.280000	0.620017	0.710000	3.800000e-01	1.000000	1.000000	0.735511	0.710000	0		
PASK	23178	broad.mit.edu	37	2	242065640	242065640	+	Missense_Mutation	SNP	C	C	T			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr2:242065640C>T	ENST00000405260.1	-	10	3388	c.2690G>A	c.(2689-2691)aGc>aAc	p.S897N	PASK_ENST00000403638.3_Missense_Mutation_p.S897N|PASK_ENST00000544142.1_Missense_Mutation_p.S711N|PASK_ENST00000539818.1_Missense_Mutation_p.S681N|PASK_ENST00000358649.4_Missense_Mutation_p.S897N|PASK_ENST00000234040.4_Missense_Mutation_p.S897N	NM_001252120.1	NP_001239049.1	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase			53		all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)			ATGGTAGCAGCTCCCGGAGTA	0.647000																								0							SO:0001583	missense			ENST00000405260.1	1	1	hg19	CCDS2545.1	.	.	.	.	.	.	.	.	.	.	C	8.379	0.837154	0.16891	.	.	ENSG00000115687	ENST00000234040;ENST00000544142;ENST00000405260;ENST00000358649;ENST00000539818;ENST00000403638	T;T;T;T;T;T	0.69175	-0.38;-0.38;-0.38;-0.34;-0.37;0.58	4.94	3.07	0.35406	.	0.267711	0.32357	N	0.006217	T	0.68943	0.3056	L	0.53249	1.67	0.26862	N	0.967935	B;B;B;D;B	0.65815	0.245;0.36;0.2;0.995;0.245	B;B;B;P;B	0.61477	0.052;0.112;0.069;0.889;0.052	T	0.57602	-0.7783	10	0.28530	T	0.3	.	5.2403	0.15467	0.0:0.644:0.1701:0.1859	.	862;711;897;897;897	B7Z7R6;F5GYW7;Q96RG2-2;G5E9F1;Q96RG2	.;.;.;.;PASK_HUMAN	N	897;711;897;897;681;897	ENSP00000234040:S897N;ENSP00000441374:S711N;ENSP00000384016:S897N;ENSP00000351475:S897N;ENSP00000443083:S681N;ENSP00000384438:S897N	ENSP00000234040:S897N	S	-	2	0	PASK	241714313	0.998000	0.40836	0.992000	0.48379	0.111000	0.19643	0.836000	0.27545	1.084000	0.41184	0.561000	0.74099	AGC		TCGA-3A-A9J0-01A-11D-A40W-08	PASK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000323753.1	1	0	1	55	129	0	39	1	8.428958e-01	3	7	0	39	2		0	0	0	0	0	2	1	1.000000	54	123	0	37	2								-20.000000	1	1	0	0		1	2	2	4	2.137730	1	0.470000	3.280000	0.620017	0.990000	9.900000e-01	1.000000	1.000000	1.000000	0.990000	1		
MYH15	22989	broad.mit.edu	37	3	108172884	108172884	+	Nonsense_Mutation	SNP	G	G	A			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr3:108172884G>A	ENST00000273353.3	-	22	2484	c.2428C>T	c.(2428-2430)Cga>Tga	p.R810*	MYH15_ENST00000495753.2_5'Flank	NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15			105					AATTTGATTCGCATCAGTTTG	0.448000																								0							SO:0001587	stop_gained			ENST00000273353.3	0	1	hg19	CCDS43127.1	.	.	.	.	.	.	.	.	.	.	G	38	6.993775	0.97987	2.61E-4	1.21E-4	ENSG00000144821	ENST00000273353	.	.	.	5.51	-4.68	0.03309	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.4871	0.16755	0.2937:0.0:0.3652:0.3411	.	.	.	.	X	810	.	ENSP00000273353:R810X	R	-	1	2	MYH15	109655574	0.146000	0.22672	0.000000	0.03702	0.931000	0.56810	-0.349000	0.07731	-0.540000	0.06265	-0.897000	0.02905	CGA		TCGA-3A-A9J0-01A-11D-A40W-08	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	1	0	1	34	225	0	46		0	0	0	0	46	2		0	0	0	0	0	2	1	1.000000	33	225	0	45	2								-15.432470	1	1	120838	3	34	1	2	2	4	2.249909	1	0.470000	3.280000	0.638299	0.820000	5.800000e-01	1.000000	1.000000	0.826477	0.820000	0		
TBCCD1	55171	broad.mit.edu	37	3	186276243	186276243	+	Missense_Mutation	SNP	G	G	A			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr3:186276243G>A	ENST00000424280.1	-	3	934	c.455C>T	c.(454-456)tCt>tTt	p.S152F	TBCCD1_ENST00000446782.1_Missense_Mutation_p.S56F|TBCCD1_ENST00000338733.5_Missense_Mutation_p.S152F	NM_001134415.1	NP_001127887.1	Q9NVR7	TBCC1_HUMAN	TBCC domain containing 1			17	all_cancers(143;3.75e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;4.3e-21)		CAGGTCAGGAGACTGAGATTT	0.403000																								0							SO:0001583	missense			ENST00000424280.1	1	1	hg19	CCDS3276.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.933597	0.73442	.	.	ENSG00000113838	ENST00000424280;ENST00000338733;ENST00000446782;ENST00000413695;ENST00000430560	T;T;T;T;T	0.73789	-0.78;-0.78;-0.78;-0.78;0.7	5.24	5.24	0.73138	.	0.207799	0.43747	D	0.000530	T	0.77579	0.4151	M	0.61703	1.905	0.43930	D	0.996586	P;P	0.50819	0.939;0.807	P;B	0.53490	0.727;0.401	T	0.75482	-0.3302	10	0.33940	T	0.23	-19.0802	10.1928	0.43037	0.0911:0.0:0.9089:0.0	.	56;152	G5E9J4;Q9NVR7	.;TBCC1_HUMAN	F	152;152;56;152;136	ENSP00000411253:S152F;ENSP00000341652:S152F;ENSP00000397091:S56F;ENSP00000391109:S152F;ENSP00000407506:S136F	ENSP00000341652:S152F	S	-	2	0	TBCCD1	187758937	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	7.081000	0.76844	2.607000	0.88179	0.655000	0.94253	TCT		TCGA-3A-A9J0-01A-11D-A40W-08	TBCCD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344774.1	1	0	1	197	479	0	113	1	9.683370e-01	8	8	0	113	2		0	0	0	0	0	2	1	1.000000	195	469	0	108	2								-20.000000	1	1	0	0		1	2	2	4	2.249909	1	0.470000	3.280000	0.638299	0.990000	9.900000e-01	1.000000	1.000000	1.000000	0.990000	1		
RFC4	5984	broad.mit.edu	37	3	186518951	186518951	+	Silent	SNP	C	C	T			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr3:186518951C>T	ENST00000392481.2	-	3	446	c.165G>A	c.(163-165)caG>caA	p.Q55Q	RFC4_ENST00000296273.2_Silent_p.Q55Q|RFC4_ENST00000433496.1_Silent_p.Q55Q	NM_181573.2	NP_853551.1	P35249	RFC4_HUMAN	replication factor C (activator 1) 4, 37kDa			26	all_cancers(143;2.92e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)		CCACTTCTTCCTGGAAAGCAA	0.383000																								0							SO:0001819	synonymous_variant			ENST00000392481.2	1	1	hg19	CCDS3283.1																																																																																				TCGA-3A-A9J0-01A-11D-A40W-08	RFC4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344471.1	1	0	1	95	475	0	106	1	9.998127e-01	12	52	0	106	2		0	0	0	0	0	2	1	1.000000	94	470	0	103	2								-2.851936	1	1	0	0		1	2	2	4	2.249909	1	0.470000	3.280000	0.638299	0.990000	8.500000e-01	1.000000	1.000000	0.979696	0.990000	1		
STAC	6769	broad.mit.edu	37	3	36547239	36547239	+	Splice_Site	SNP	G	G	A			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr3:36547239G>A	ENST00000273183.3	+	8	1133	c.833G>A	c.(832-834)gGa>gAa	p.G278E	STAC_ENST00000457375.2_Splice_Site_p.G217E|STAC_ENST00000476388.1_3'UTR	NM_003149.1	NP_003140.1	Q99469	STAC_HUMAN	SH3 and cysteine rich domain			32					ctctttcAGGGATCTCTTTCC	0.338000																								0							SO:0001630	splice_region_variant			ENST00000273183.3	1	0	hg19	CCDS2662.1	.	.	.	.	.	.	.	.	.	.	G	8.374	0.835918	0.16820	.	.	ENSG00000144681	ENST00000273183;ENST00000457375;ENST00000544687;ENST00000434649	T;T;T	0.75367	-0.93;1.09;1.57	5.21	-0.896	0.10557	Src homology-3 domain (1);	0.496999	0.22073	N	0.065008	T	0.48572	0.1507	N	0.24115	0.695	0.39959	D	0.974646	B;B	0.06786	0.0;0.001	B;B	0.06405	0.002;0.001	T	0.44081	-0.9351	10	0.02654	T	1	.	6.0123	0.19582	0.3402:0.1237:0.5361:0.0	.	217;278	E9PEA7;Q99469	.;STAC_HUMAN	E	278;217;210;206	ENSP00000273183:G278E;ENSP00000393713:G217E;ENSP00000398403:G206E	ENSP00000273183:G278E	G	+	2	0	STAC	36522243	0.996000	0.38824	0.975000	0.42487	0.667000	0.39255	0.231000	0.17872	-0.428000	0.07339	-0.145000	0.13849	GGA		TCGA-3A-A9J0-01A-11D-A40W-08	STAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253338.2	1	0	1	47	104	0	23	1	6.009984e-01	3	3	0	23	2		0	0	0	0	0	2	1	1.000000	47	100	0	22	2								-20.000000	1	1	0	0		1	2	2	4	2.249909	1	0.470000	3.280000	0.638299	0.990000	9.900000e-01	1.000000	1.000000	1.000000	0.990000	1		
DCLK3	85443	broad.mit.edu	37	3	36779648	36779648	+	Missense_Mutation	SNP	T	T	C			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr3:36779648T>C	ENST00000416516.2	-	2	993	c.503A>G	c.(502-504)aAg>aGg	p.K168R		NM_033403.1	NP_208382.1	Q9C098	DCLK3_HUMAN	doublecortin-like kinase 3			48					CATTGGGCCCTTCCCCATATC	0.567000																								0							SO:0001583	missense			ENST00000416516.2	1	1	hg19	CCDS43064.1	.	.	.	.	.	.	.	.	.	.	T	5.009	0.187282	0.09547	.	.	ENSG00000163673	ENST00000416516	T	0.67171	-0.25	4.7	-2.05	0.07321	.	0.350599	0.17768	N	0.162674	T	0.34832	0.0911	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.23797	-1.0178	10	0.10377	T	0.69	.	6.1062	0.20075	0.2212:0.4608:0.0:0.318	.	168	Q9C098	DCLK3_HUMAN	R	168	ENSP00000394484:K168R	ENSP00000394484:K168R	K	-	2	0	DCLK3	36754652	0.000000	0.05858	0.001000	0.08648	0.834000	0.47266	-0.855000	0.04295	-0.571000	0.06014	0.533000	0.62120	AAG		TCGA-3A-A9J0-01A-11D-A40W-08	DCLK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341727.1	1	0	1	173	362	0	94		0	0	0	0	94	2		0	0	0	0	0	2	1	1.000000	168	358	0	88	2								-20.000000	1	1	0	0		1	2	2	4	2.249909	1	0.470000	3.280000	0.638299	0.990000	9.900000e-01	1.000000	1.000000	1.000000	0.990000	1		
CTNNB1	1499	broad.mit.edu	37	3	41266136	41266136	+	Missense_Mutation	SNP	T	T	C	rs121913407		TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08			T	C	T	T		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr3:41266136T>C	ENST00000349496.5	+	3	413	c.133T>C	c.(133-135)Tct>Cct	p.S45P	CTNNB1_ENST00000405570.1_Missense_Mutation_p.S45P|CTNNB1_ENST00000396183.3_Missense_Mutation_p.S45P|CTNNB1_ENST00000453024.1_Missense_Mutation_p.S38P|CTNNB1_ENST00000396185.3_Missense_Mutation_p.S45P	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	p.S45P(168)|p.A5_A80del(53)|p.S45del(50)|p.S45A(11)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T3_A126del(2)|p.D32_S47del(2)|p.P44_S45del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.S45_G48del(1)|p.Q28_Q61del(1)|p.T41_N51del(1)|p.M1_A87del(1)|p.S45_L46del(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.P44_N51del(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.T42_G48del(1)|p.S45_D58del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.T40_L46del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.S45E(1)|p.M8_A80del(1)|p.A5_E54del(1)|p.S45T(1)|p.A21_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.A20_S111del(1)|p.T42_K49>Q(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	3893					CACAGCTCCTTCTCTGAGTGG	0.502000		15	H, Mis, T	PLAG1	colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma				Pilomatrixoma, Familial Clustering of				Colon(6;3 56 14213 18255)		Dom	yes		3	3p22-p21.3	1499	catenin (cadherin-associated protein), beta 1		E, M, O	355	Substitution - Missense(181)|Deletion - In frame(149)|Complex - deletion inframe(18)|Unknown(7)						SO:0001583	missense	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	ENST00000349496.5	1	1	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.440246	0.83993	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.52295	0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.65903	0.2736	M	0.65677	2.01	0.80722	D	1	D	0.60575	0.988	P	0.62649	0.905	T	0.69083	-0.5239	10	0.87932	D	0	-13.6823	16.3453	0.83126	0.0:0.0:0.0:1.0	.	45	P35222	CTNB1_HUMAN	P	38;45;45;45;45;38;45;45;45	ENSP00000400508:S38P;ENSP00000385604:S45P;ENSP00000412219:S45P;ENSP00000379486:S45P;ENSP00000344456:S45P;ENSP00000411226:S38P;ENSP00000379488:S45P;ENSP00000409302:S45P;ENSP00000401599:S45P	ENSP00000344456:S45P	S	+	1	0	CTNNB1	41241140	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.261000	0.74972	0.533000	0.62120	TCT		TCGA-3A-A9J0-01A-11D-A40W-08	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	1	0	1	82	174	0	35	1	1	201	318	0	35	2		0	0	0	0	0	2	1	1.000000	81	173	0	35	2								-20.000000	1	1	0	0		1	2	2	4	2.249909	1	0.470000	3.280000	0.638299	0.990000	9.900000e-01	1.000000	1.000000	1.000000	0.990000	1		
ALS2CL	259173	broad.mit.edu	37	3	46728567	46728567	+	Missense_Mutation	SNP	C	C	T			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr3:46728567C>T	ENST00000318962.4	-	5	523	c.440G>A	c.(439-441)gGc>gAc	p.G147D	ALS2CL_ENST00000415953.1_Missense_Mutation_p.G147D	NM_147129.3	NP_667340.2	Q60I27	AL2CL_HUMAN	ALS2 C-terminal like			29					CAGCGATGCGCCCACCGAGCC	0.677000																								0							SO:0001583	missense			ENST00000318962.4	1	1	hg19	CCDS2743.1	.	.	.	.	.	.	.	.	.	.	C	9.379	1.072447	0.20147	.	.	ENSG00000178038	ENST00000318962;ENST00000415953	T;T	0.17528	2.27;2.27	4.18	2.22	0.28083	Dbl homology (DH) domain (1);	0.498524	0.18254	N	0.146852	T	0.10208	0.0250	L	0.29908	0.895	0.09310	N	1	B	0.15141	0.012	B	0.13407	0.009	T	0.18871	-1.0323	10	0.35671	T	0.21	.	3.9061	0.09183	0.0:0.5781:0.2013:0.2207	.	147	Q60I27	AL2CL_HUMAN	D	147	ENSP00000313670:G147D;ENSP00000413223:G147D	ENSP00000313670:G147D	G	-	2	0	ALS2CL	46703571	0.005000	0.15991	0.015000	0.15790	0.001000	0.01503	0.589000	0.23939	1.103000	0.41568	0.591000	0.81541	GGC		TCGA-3A-A9J0-01A-11D-A40W-08	ALS2CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250567.3	1	0	1	14	40	0	14	1	9.998274e-01	18	33	0	14	2		0	0	0	0	0	2	1	0.999850	14	38	0	14	2								-20.000000	1	1	0	0		1	2	2	4	2.249909	1	0.470000	3.280000	0.638299	0.990000	9.900000e-01	1.000000	1.000000	0.997352	0.990000	1		
ITPR1	3708	broad.mit.edu	37	3	4718357	4718357	+	Missense_Mutation	SNP	C	C	T			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr3:4718357C>T	ENST00000443694.2	+	21	2794	c.2794C>T	c.(2794-2796)Cgg>Tgg	p.R932W	ITPR1_ENST00000354582.6_Missense_Mutation_p.R947W|ITPR1_ENST00000357086.4_Missense_Mutation_p.R938W|ITPR1_ENST00000423119.2_Missense_Mutation_p.R938W|ITPR1_ENST00000456211.2_Missense_Mutation_p.R923W|ITPR1_ENST00000302640.8_Missense_Mutation_p.R932W|ITPR1_ENST00000544951.1_Intron			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1			106				Caffeine(DB00201)	GGTGGTGCTCCGGGGAGGAGG	0.562000																								0							SO:0001583	missense			ENST00000443694.2	1	1	hg19	CCDS54551.1	.	.	.	.	.	.	.	.	.	.	C	17.48	3.400893	0.62177	.	.	ENSG00000150995	ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000357086;ENST00000456211;ENST00000443694	D;D;D;D;D;D	0.91351	-2.83;-2.83;-2.83;-2.83;-2.83;-2.83	4.1	3.14	0.36123	.	0.000000	0.85682	D	0.000000	D	0.91723	0.7383	L	0.47716	1.5	0.80722	D	1	D;D;D	0.76494	0.998;0.997;0.999	P;P;D	0.63283	0.821;0.895;0.913	D	0.91805	0.5455	10	0.72032	D	0.01	.	11.6166	0.51094	0.252:0.748:0.0:0.0	.	932;947;938	E7EPX7;Q14643;G5E9P1	.;ITPR1_HUMAN;.	W	947;932;947;938;938;923;932	ENSP00000306253:R932W;ENSP00000346595:R947W;ENSP00000405934:R938W;ENSP00000349597:R938W;ENSP00000397885:R923W;ENSP00000401671:R932W	ENSP00000306253:R932W	R	+	1	2	ITPR1	4693357	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	2.115000	0.41921	2.280000	0.76307	0.313000	0.20887	CGG		TCGA-3A-A9J0-01A-11D-A40W-08	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	1	0	1	35	105	0	26	0	0	0	1	0	26	2		0	0	0	0	0	2	1	1.000000	34	104	0	24	2								-3.960281	1	1	121000	1	27	1	2	2	4	2.249909	1	0.470000	3.280000	0.638299	0.990000	9.900000e-01	1.000000	1.000000	0.999850	0.990000	1		
DCLK2	166614	broad.mit.edu	37	4	151160950	151160950	+	Silent	SNP	G	G	A			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr4:151160950G>A	ENST00000296550.7	+	11	2377	c.1623G>A	c.(1621-1623)gcG>gcA	p.A541A	DCLK2_ENST00000506325.1_Silent_p.A540A|DCLK2_ENST00000302176.8_Silent_p.A558A	NM_001040260.3	NP_001035350.2	Q8N568	DCLK2_HUMAN	doublecortin-like kinase 2			26	all_hematologic(180;0.151)				TTGGGCTTGCGACTGTGGTAG	0.458000													GBM(195;186 2215 13375 16801 37459)											0							SO:0001819	synonymous_variant			ENST00000296550.7	1	1	hg19	CCDS34076.1																																																																																				TCGA-3A-A9J0-01A-11D-A40W-08	DCLK2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364952.1	1	0	0	27	422	0	95	0	4.997810e-02	0	6	0	95	2		0	0	0	0	0	2	1	1.000000	27	419	0	91	2								-6.418375	1	1	121412	11	42	1	1	2	3	1.838072	1	0.470000	3.280000	0.566728	0.310000	2.100000e-01	1.000000	0.320000	0.348333	0.310000	0		
HSD17B13	345275	broad.mit.edu	37	4	88243945	88243945	+	Missense_Mutation	SNP	A	A	G			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr4:88243945A>G	ENST00000328546.4	-	1	113	c.49T>C	c.(49-51)Tcc>Ccc	p.S17P	RP11-529H2.2_ENST00000508163.1_RNA|HSD17B13_ENST00000302219.6_Missense_Mutation_p.S17P	NM_178135.3	NP_835236.2	Q7Z5P4	DHB13_HUMAN	hydroxysteroid (17-beta) dehydrogenase 13			8		Acute lymphoblastic leukemia(40;0.244)|all_hematologic(202;0.248)			TCCAAGTAGGAGTAGATGATG	0.468000																								0							SO:0001583	missense			ENST00000328546.4	1	1	hg19	CCDS3618.1	.	.	.	.	.	.	.	.	.	.	A	14.50	2.553115	0.45487	.	.	ENSG00000170509	ENST00000302219;ENST00000328546	D;D	0.90133	-2.62;-1.97	4.81	3.6	0.41247	.	0.194975	0.35436	N	0.003214	D	0.92473	0.7610	M	0.79258	2.445	0.33675	D	0.611372	P;P	0.48503	0.911;0.856	P;P	0.53102	0.718;0.526	D	0.93413	0.6770	10	0.37606	T	0.19	.	11.291	0.49250	0.8469:0.1531:0.0:0.0	.	17;17	Q7Z5P4-2;Q7Z5P4	.;DHB13_HUMAN	P	17	ENSP00000305438:S17P;ENSP00000333300:S17P	ENSP00000305438:S17P	S	-	1	0	HSD17B13	88462969	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	3.554000	0.53720	0.824000	0.34613	0.477000	0.44152	TCC		TCGA-3A-A9J0-01A-11D-A40W-08	HSD17B13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253052.1	1	0	1	42	179	0	44		0	0	0	0	44	2		0	0	0	0	0	2	1	1.000000	40	177	0	42	2								-20.000000	1	1	0	0		1	1	2	3	1.838065	1	0.470000	3.280000	0.566728	0.990000	7.400000e-01	1.000000	1.000000	0.947465	0.990000	1		
ADAMTS19	171019	broad.mit.edu	37	5	128863477	128863477	+	Nonsense_Mutation	SNP	C	C	T			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr5:128863477C>T	ENST00000274487.4	+	5	1250	c.1105C>T	c.(1105-1107)Cag>Tag	p.Q369*	CTC-575N7.1_ENST00000503616.1_RNA	NM_133638.3	NP_598377.3	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 19			91		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		TCTGAGTGTGCAGGTCAATCT	0.299000																								0							SO:0001587	stop_gained			ENST00000274487.4	0	1	hg19	CCDS4146.1	.	.	.	.	.	.	.	.	.	.	C	35	5.444548	0.96187	.	.	ENSG00000145808	ENST00000274487	.	.	.	4.41	4.41	0.53225	.	0.085473	0.47455	D	0.000231	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.326	0.90254	0.0:1.0:0.0:0.0	.	.	.	.	X	369	.	.	Q	+	1	0	ADAMTS19	128891376	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.856000	0.48341	2.737000	0.93849	0.563000	0.77884	CAG		TCGA-3A-A9J0-01A-11D-A40W-08	ADAMTS19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250979.2	1	0	1	276	220	0	63		0	0	0	0	63	2		0	0	0	0	0	2	1	1.000000	273	219	0	60	2								-20.000000	1	1	0	0		1	0	3	3	1.941373	1	0.470000	3.280000	0.570850	0.990000	9.900000e-01	1.000000	1.000000	1.000000	0.990000	1		
PCDHB7	56129	broad.mit.edu	37	5	140552501	140552501	+	Missense_Mutation	SNP	G	G	A			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr5:140552501G>A	ENST00000231137.3	+	1	259	c.85G>A	c.(85-87)Gaa>Aaa	p.E29K		NM_018940.2	NP_061763.1	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7			119			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)		GGCTGGCGCCGAACCGCTTCG	0.517000																								0							SO:0001583	missense			ENST00000231137.3	1	1	hg19	CCDS4249.1	.	.	.	.	.	.	.	.	.	.	G	12.37	1.918636	0.33908	.	.	ENSG00000113212	ENST00000231137	T	0.48836	0.8	4.78	4.78	0.61160	.	.	.	.	.	T	0.57533	0.2060	M	0.88377	2.95	0.22017	N	0.999413	B	0.25312	0.123	B	0.21708	0.036	T	0.54029	-0.8354	9	0.40728	T	0.16	.	16.7421	0.85462	0.0:0.0:1.0:0.0	.	29	Q9Y5E2	PCDB7_HUMAN	K	29	ENSP00000231137:E29K	ENSP00000231137:E29K	E	+	1	0	PCDHB7	140532685	0.877000	0.30153	0.510000	0.27712	0.294000	0.27393	5.150000	0.64869	2.353000	0.79882	0.650000	0.86243	GAA		TCGA-3A-A9J0-01A-11D-A40W-08	PCDHB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251803.2	1	0	1	82	334	0	113	0	4.897161e-01	0	8	0	113	2		0	0	0	0	0	2	1	1.000000	80	326	0	112	2								-20.000000	1	1	121412	1	31	1	0	3	3	1.941373	1	0.470000	3.280000	0.570850	0.990000	8.400000e-01	1.000000	1.000000	0.976823	0.990000	1		
MAP1B	4131	broad.mit.edu	37	5	71494871	71494871	+	Missense_Mutation	SNP	C	C	T			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr5:71494871C>T	ENST00000296755.7	+	5	5987	c.5689C>T	c.(5689-5691)Cgg>Tgg	p.R1897W		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B			104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)			GAAGACCACCCGGACCTCAGA	0.453000													Melanoma(17;367 822 11631 31730 47712)											0							SO:0001583	missense			ENST00000296755.7	1	1	hg19	CCDS4012.1	.	.	.	.	.	.	.	.	.	.	C	3.470	-0.108223	0.06924	.	.	ENSG00000131711	ENST00000296755	T	0.03524	3.9	5.52	3.67	0.42095	.	0.220565	0.30658	N	0.009152	T	0.05044	0.0135	N	0.08118	0	0.09310	N	1	D;D	0.65815	0.995;0.995	P;P	0.56823	0.807;0.714	T	0.31696	-0.9934	10	0.87932	D	0	-2.6404	11.924	0.52808	0.4852:0.5148:0.0:0.0	.	1771;1897	A2BDK6;P46821	.;MAP1B_HUMAN	W	1897	ENSP00000296755:R1897W	ENSP00000296755:R1897W	R	+	1	2	MAP1B	71530627	0.001000	0.12720	0.011000	0.14972	0.113000	0.19764	0.695000	0.25527	0.645000	0.30675	0.551000	0.68910	CGG		TCGA-3A-A9J0-01A-11D-A40W-08	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	1	0	1	180	120	0	60	0	8.185223e-01	0	4	0	60	2		0	0	0	0	0	2	1	1.000000	181	119	0	59	2								-20.000000	1	1	121412	3	36	1	0	3	3	1.932771	1	0.470000	3.280000	0.570850	0.990000	9.900000e-01	1.000000	1.000000	1.000000	0.990000	1		
MAP1B	4131	broad.mit.edu	37	5	71495084	71495084	+	Missense_Mutation	SNP	G	G	A			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr5:71495084G>A	ENST00000296755.7	+	5	6200	c.5902G>A	c.(5902-5904)Gaa>Aaa	p.E1968K		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B			104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)			CAGCCCCCCCGAAGTGAGTGG	0.478000													Melanoma(17;367 822 11631 31730 47712)											0							SO:0001583	missense			ENST00000296755.7	1	1	hg19	CCDS4012.1	.	.	.	.	.	.	.	.	.	.	G	12.11	1.840480	0.32513	.	.	ENSG00000131711	ENST00000296755	T	0.03524	3.9	5.11	5.11	0.69529	.	0.436414	0.21672	N	0.070842	T	0.04679	0.0127	N	0.08118	0	0.36942	D	0.892433	D;P	0.58268	0.982;0.512	P;B	0.50825	0.651;0.14	T	0.57791	-0.7750	10	0.49607	T	0.09	-6.4359	16.7322	0.85438	0.0:0.0:1.0:0.0	.	1842;1968	A2BDK6;P46821	.;MAP1B_HUMAN	K	1968	ENSP00000296755:E1968K	ENSP00000296755:E1968K	E	+	1	0	MAP1B	71530840	0.787000	0.28750	0.992000	0.48379	0.246000	0.25737	4.449000	0.60034	2.381000	0.81170	0.551000	0.68910	GAA		TCGA-3A-A9J0-01A-11D-A40W-08	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	1	0	1	81	372	0	69	0	4.364138e-01	0	8	0	69	2		0	0	0	0	0	2	1	1.000000	81	364	0	65	2								-20.000000	1	1	0	0		1	0	3	3	1.932771	1	0.470000	3.280000	0.570850	0.930000	7.600000e-01	1.000000	1.000000	0.928299	0.930000	1		
LAMA4	3910	broad.mit.edu	37	6	112496518	112496518	+	Missense_Mutation	SNP	C	C	T			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08			C	T	C	C		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr6:112496518C>T	ENST00000230538.7	-	11	1751	c.1354G>A	c.(1354-1356)Gaa>Aaa	p.E452K	LAMA4_ENST00000522006.1_Missense_Mutation_p.E445K|LAMA4_ENST00000424408.2_Missense_Mutation_p.E445K|LAMA4_ENST00000389463.4_Missense_Mutation_p.E445K	NM_001105206.2	NP_001098676.2	Q16363	LAMA4_HUMAN	laminin, alpha 4			100		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)			CACCTACGTTCGTAAGCCTCA	0.483000																								0							SO:0001583	missense			ENST00000230538.7	1	1	hg19	CCDS43491.1	.	.	.	.	.	.	.	.	.	.	C	14.97	2.694350	0.48202	.	.	ENSG00000112769	ENST00000230538;ENST00000522006;ENST00000389463;ENST00000424408	T;T;T;T	0.09163	3.01;3.01;3.01;3.01	5.91	5.91	0.95273	Laminin I (1);	0.213635	0.48767	D	0.000165	T	0.12433	0.0302	L	0.47716	1.5	0.80722	D	1	D;D	0.67145	0.996;0.995	P;P	0.58391	0.838;0.749	T	0.10683	-1.0619	10	0.11182	T	0.66	.	18.0694	0.89400	0.0:1.0:0.0:0.0	.	452;445	Q16363;Q16363-2	LAMA4_HUMAN;.	K	452;445;445;445	ENSP00000230538:E452K;ENSP00000429488:E445K;ENSP00000374114:E445K;ENSP00000416470:E445K	ENSP00000230538:E452K	E	-	1	0	LAMA4	112603211	0.981000	0.34729	0.343000	0.25615	0.031000	0.12232	2.957000	0.49137	2.813000	0.96785	0.655000	0.94253	GAA		TCGA-3A-A9J0-01A-11D-A40W-08	LAMA4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041876.2	1	0	1	163	233	0	86	0	1	0	41	0	86	2		0	0	0	0	0	2	1	1.000000	158	230	0	84	2								-19.999980	1	1	0	0		1	1	2	3	1.945845	1	0.470000	3.280000	0.570850	0.990000	9.900000e-01	1.000000	1.000000	1.000000	0.990000	1		
IFNGR1	3459	broad.mit.edu	37	6	137524778	137524778	+	Missense_Mutation	SNP	C	C	A			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08			C	A	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr6:137524778C>A	ENST00000367739.4	-	5	712	c.591G>T	c.(589-591)gaG>gaT	p.E197D	IFNGR1_ENST00000367735.2_3'UTR|IFNGR1_ENST00000478333.1_5'Flank|IFNGR1_ENST00000543628.1_Missense_Mutation_p.E169D	NM_000416.2	NP_000407.1	P15260	INGR1_HUMAN	interferon gamma receptor 1			18	Colorectal(23;0.24)			Interferon gamma-1b(DB00033)	GGCACTGAATCTCGTCACAAT	0.378000																								0							SO:0001583	missense			ENST00000367739.4	1	1	hg19	CCDS5185.1	.	.	.	.	.	.	.	.	.	.	C	12.20	1.866633	0.32977	.	.	ENSG00000027697	ENST00000367739;ENST00000418947;ENST00000543628;ENST00000458076	T;T;T	0.45276	0.9;0.9;0.9	5.34	-3.11	0.05299	Interferon gamma receptor, poxvirus/mammal (1);Fibronectin, type III (1);Immunoglobulin-like fold (1);	0.212273	0.23342	N	0.049224	T	0.13628	0.0330	M	0.71581	2.175	0.09310	N	1	B;B	0.09022	0.001;0.002	B;B	0.14578	0.007;0.011	T	0.18713	-1.0328	10	0.30078	T	0.28	-11.59	2.1319	0.03752	0.1234:0.2775:0.3634:0.2358	.	169;197	F5H5M7;P15260	.;INGR1_HUMAN	D	197;197;169;163	ENSP00000356713:E197D;ENSP00000443282:E169D;ENSP00000389249:E163D	ENSP00000356713:E197D	E	-	3	2	IFNGR1	137566471	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.316000	0.02710	-0.289000	0.09038	-0.305000	0.09177	GAG		TCGA-3A-A9J0-01A-11D-A40W-08	IFNGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042401.1	1	0	1	86	172	0	64	1	1	119	132	0	64	2		0	0	0	0	0	2	1	1.000000	86	171	0	62	2								-20.000000	1	1	0	0		1	1	2	3	1.945845	1	0.470000	3.280000	0.570850	0.990000	9.900000e-01	1.000000	1.000000	1.000000	0.990000	1		
LPA	4018	broad.mit.edu	37	6	161006101	161006101	+	Silent	SNP	C	C	T			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr6:161006101C>T	ENST00000316300.5	-	26	4310	c.4266G>A	c.(4264-4266)agG>agA	p.R1422R	LPA_ENST00000447678.1_Silent_p.R1422R			P08519	APOA_HUMAN	lipoprotein, Lp(a)	p.R1422S(1)		107		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		Aminocaproic Acid(DB00513)	ATAATGGGATCCTCCGATGCC	0.443000																								1	Substitution - Missense(1)						SO:0001819	synonymous_variant			ENST00000316300.5	1	1	hg19	CCDS43523.1																																																																																				TCGA-3A-A9J0-01A-11D-A40W-08	LPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042957.1	1	0	1	288	550	0	105		0	0	0	0	105	2		0	0	0	0	0	2	1	1.000000	285	545	1	103	25								-20.000000	1	1	0	0		1	1	2	3	1.945845	1	0.470000	3.280000	0.570850	0.990000	9.900000e-01	1.000000	1.000000	1.000000	0.990000	1		
MUC21	394263	broad.mit.edu	37	6	30955236	30955236	+	Silent	SNP	C	C	T			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr6:30955236C>T	ENST00000376296.3	+	2	1525	c.1284C>T	c.(1282-1284)acC>acT	p.T428T	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated			42					CCAGCACAACCTCCAGTGGGG	0.597000																								0							SO:0001819	synonymous_variant			ENST00000376296.3	1	0	hg19	CCDS34388.1																																																																																				TCGA-3A-A9J0-01A-11D-A40W-08	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	1	0	1	91	550	0	128		0	0	0	0	128	2		0	0	0	0	0	2	1	1.000000	86	530	0	125	2								-20.000000	1	1	0	0		1	1	2	3	1.954404	1	0.470000	3.280000	0.570850	0.740000	6.000000e-01	0.890000	0.750000	0.751034	0.740000	0		
TNXB	7148	broad.mit.edu	37	6	32063700	32063700	+	Missense_Mutation	SNP	C	C	T			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr6:32063700C>T	ENST00000479795.1	-	3	2070	c.1930G>A	c.(1930-1932)Ggc>Agc	p.G644S	TNXB_ENST00000375247.2_Missense_Mutation_p.G644S|TNXB_ENST00000375244.3_Missense_Mutation_p.G644S			P22105	TENX_HUMAN	tenascin XB			8					CAGGTAGGGCCGGTGTAGCCT	0.687000																								0							SO:0001583	missense			ENST00000479795.1	1	1	hg19		.	.	.	.	.	.	.	.	.	.	C	14.90	2.673033	0.47781	.	.	ENSG00000168477	ENST00000375244;ENST00000375247;ENST00000479795	T;T;D	0.85013	1.81;1.81;-1.93	4.25	4.25	0.50352	.	0.000000	0.43416	D	0.000580	D	0.92773	0.7702	M	0.91561	3.22	0.40214	D	0.977668	D	0.89917	1.0	D	0.97110	1.0	D	0.93982	0.7259	10	0.59425	D	0.04	.	15.6045	0.76652	0.0:1.0:0.0:0.0	.	644	P22105-3	.	S	644	ENSP00000364393:G644S;ENSP00000364396:G644S;ENSP00000418248:G644S	ENSP00000364393:G644S	G	-	1	0	TNXB	32171678	.	.	0.189000	0.23252	0.058000	0.15608	.	.	2.198000	0.70561	0.563000	0.77884	GGC		TCGA-3A-A9J0-01A-11D-A40W-08	TNXB-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000357059.1	1	0	1	24	82	0	32	0	5.521577e-02	0	2	0	32	2		0	0	0	0	0	2	1	1.000000	21	79	0	32	2								-20.000000	1	1	120958	2	38	1	1	2	3	1.954404	1	0.470000	3.280000	0.570850	0.990000	8.100000e-01	1.000000	1.000000	0.984096	0.990000	1		
PRSS35	167681	broad.mit.edu	37	6	84233890	84233890	+	Missense_Mutation	SNP	G	G	A			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr6:84233890G>A	ENST00000369700.3	+	2	907	c.730G>A	c.(730-732)Gaa>Aaa	p.E244K	PRSS35_ENST00000536636.1_Missense_Mutation_p.E244K	NM_153362.2	NP_699193.2	Q8N3Z0	PRS35_HUMAN	protease, serine, 35			32		all_cancers(76;0.000113)|Acute lymphoblastic leukemia(125;1.09e-08)|all_hematologic(105;3.12e-05)|all_epithelial(107;0.0575)			GAGGATTGCCGAAGGGAGGCC	0.567000																								0							SO:0001583	missense			ENST00000369700.3	1	1	hg19	CCDS4999.1	.	.	.	.	.	.	.	.	.	.	G	10.19	1.281627	0.23392	.	.	ENSG00000146250	ENST00000536636;ENST00000369700	T;T	0.43294	0.95;0.95	5.65	4.76	0.60689	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (1);	0.988869	0.08242	N	0.975900	T	0.09512	0.0234	N	0.04508	-0.205	0.28907	N	0.892957	B	0.28801	0.223	B	0.16722	0.016	T	0.22312	-1.0220	10	0.17832	T	0.49	-10.6501	16.2336	0.82360	0.0:0.1375:0.8625:0.0	.	244	Q8N3Z0	PRS35_HUMAN	K	244	ENSP00000440870:E244K;ENSP00000358714:E244K	ENSP00000358714:E244K	E	+	1	0	PRSS35	84290609	0.017000	0.18338	0.008000	0.14137	0.110000	0.19582	1.679000	0.37597	1.349000	0.45751	0.462000	0.41574	GAA		TCGA-3A-A9J0-01A-11D-A40W-08	PRSS35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041352.1	1	0	1	35	152	0	33	0	0	0	1	0	33	2		0	0	0	0	0	2	1	1.000000	35	146	0	33	2								-3.267408	1	1	121412	2	32	1	1	2	3	1.945845	1	0.470000	3.280000	0.570850	0.980000	7.100000e-01	1.000000	1.000000	0.938784	0.980000	1		
EPHA7	2045	broad.mit.edu	37	6	93956606	93956606	+	Missense_Mutation	SNP	C	C	T			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr6:93956606C>T	ENST00000369303.4	-	15	2814	c.2630G>A	c.(2629-2631)cGt>cAt	p.R877H		NM_004440.3	NP_004431.1	Q15375	EPHA7_HUMAN	EPH receptor A7	p.R877L(1)		112		all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142)			CCTTTCAGCACGCTCCTTTTG	0.423000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000369303.4	1	1	hg19	CCDS5031.1	.	.	.	.	.	.	.	.	.	.	C	35	5.526893	0.96431	.	.	ENSG00000135333	ENST00000369303	T	0.62364	0.03	5.74	5.74	0.90152	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.63177	0.2489	N	0.20445	0.575	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.70716	0.97;0.942;0.966	T	0.69213	-0.5204	10	0.87932	D	0	.	19.9265	0.97104	0.0:1.0:0.0:0.0	.	873;872;877	Q15375-4;Q15375-2;Q15375	.;.;EPHA7_HUMAN	H	877	ENSP00000358309:R877H	ENSP00000358309:R877H	R	-	2	0	EPHA7	94013327	1.000000	0.71417	0.870000	0.34147	0.995000	0.86356	7.726000	0.84824	2.723000	0.93209	0.591000	0.81541	CGT		TCGA-3A-A9J0-01A-11D-A40W-08	EPHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041545.1	1	0	1	115	241	0	64		0	0	0	0	64	2		0	0	0	0	0	2	1	1.000000	116	238	0	63	2								-20.000000	1	1	121412	4	38	1	1	2	3	1.945845	1	0.470000	3.280000	0.570850	0.990000	9.900000e-01	1.000000	1.000000	1.000000	0.990000	1		
OR2A14	135941	broad.mit.edu	37	7	143826573	143826573	+	Missense_Mutation	SNP	C	C	T			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr7:143826573C>T	ENST00000408899.2	+	1	423	c.368C>T	c.(367-369)gCg>gTg	p.A123V		NM_001001659.1	NP_001001659.1	Q96R47	O2A14_HUMAN	olfactory receptor, family 2, subfamily A, member 14			22	Melanoma(164;0.0783)				GATCGCTATGCGGACATCTGC	0.493000																								0							SO:0001583	missense			ENST00000408899.2	0	1	hg19	CCDS43672.1	.	.	.	.	.	.	.	.	.	.	C	0.009	-1.806132	0.00606	.	.	ENSG00000221938	ENST00000408899	T	0.00402	7.56	4.18	3.02	0.34903	GPCR, rhodopsin-like superfamily (1);	0.677608	0.11236	N	0.585087	T	0.00073	0.0002	N	0.00121	-2.07	0.22684	N	0.998858	B	0.02656	0.0	B	0.01281	0.0	T	0.23261	-1.0193	10	0.02654	T	1	-8.6728	8.1672	0.31233	0.0:0.099:0.0:0.901	.	123	Q96R47	O2A14_HUMAN	V	123	ENSP00000386137:A123V	ENSP00000386137:A123V	A	+	2	0	OR2A14	143457506	0.128000	0.22383	0.910000	0.35882	0.018000	0.09664	2.090000	0.41682	0.732000	0.32470	-0.415000	0.06103	GCG		TCGA-3A-A9J0-01A-11D-A40W-08	OR2A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349980.1	0	0	0	7	729	0	135		0	0	0	0	135	2		0	0	0	0	0	2	1	0.979983	8	721	0	135	2								-1.816548	0	1	121204	4	35	1	2	2	4	2.315457	1	0.470000	3.280000	0.639456	0.060000	0	0.120000	0.080000	0.066212	0.060000	0		
NUB1	51667	broad.mit.edu	37	7	151072988	151072988	+	Missense_Mutation	SNP	G	G	A			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr7:151072988G>A	ENST00000355851.4	+	13	1527	c.1450G>A	c.(1450-1452)Gac>Aac	p.D484N	NUB1_ENST00000568733.1_Missense_Mutation_p.D508N|NUB1_ENST00000413040.2_Missense_Mutation_p.D494N|NUB1_ENST00000566856.1_Missense_Mutation_p.D470N|WDR86_ENST00000463000.1_5'Flank	NM_001243351.1	NP_001230280.1	Q9Y5A7	NUB1_HUMAN	negative regulator of ubiquitin-like proteins 1			11			OV - Ovarian serous cystadenocarcinoma(82;0.00569)		TCCTGAAACCGACAACCGTCA	0.493000																								0							SO:0001583	missense			ENST00000355851.4	0	1	hg19		.	.	.	.	.	.	.	.	.	.	G	0.012	-1.671641	0.00758	.	.	ENSG00000013374	ENST00000413040;ENST00000355851	T	0.42513	0.97	5.29	1.42	0.22433	UBA-like (1);	0.997169	0.08136	N	0.992432	T	0.13329	0.0323	N	0.02011	-0.69	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.30475	-0.9977	10	0.02654	T	1	-13.5194	3.5859	0.07970	0.6533:0.1362:0.0787:0.1318	.	484;470	Q9Y5A7;Q9Y5A7-2	NUB1_HUMAN;.	N	470;484	ENSP00000348110:D484N	ENSP00000348110:D484N	D	+	1	0	NUB1	150703921	0.001000	0.12720	0.000000	0.03702	0.077000	0.17291	1.025000	0.30090	0.109000	0.17891	-1.421000	0.01109	GAC		TCGA-3A-A9J0-01A-11D-A40W-08	NUB1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		0	0	0	6	756	0	148	0	2.272615e-01	0	98	0	148	2		0	0	0	0	0	2	1	0.962387	6	739	0	142	2								-2.138169	0	1	120878	1	36	1	2	2	4	2.315457	1	0.470000	3.280000	0.639456	0.040000	0	0.110000	0.040000	0.054933	0.040000	0		
LMBR1	64327	broad.mit.edu	37	7	156520649	156520649	+	Missense_Mutation	SNP	T	T	C			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr7:156520649T>C	ENST00000353442.5	-	12	1204	c.968A>G	c.(967-969)gAa>gGa	p.E323G	LMBR1_ENST00000354505.4_Missense_Mutation_p.E364G|LMBR1_ENST00000359422.4_Missense_Mutation_p.E171G|LMBR1_ENST00000540390.1_Missense_Mutation_p.E302G	NM_022458.3	NP_071903.2	Q8WVP7	LMBR1_HUMAN	limb development membrane protein 1			18	Ovarian(565;0.218)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00231)		CATTGCTGTTTCATCAACCAA	0.363000																								0							SO:0001583	missense			ENST00000353442.5	0	1	hg19	CCDS5945.1	.	.	.	.	.	.	.	.	.	.	T	19.26	3.793587	0.70452	.	.	ENSG00000105983	ENST00000353442;ENST00000359422;ENST00000415428;ENST00000354505;ENST00000540390	T;T;T;T;T	0.32023	1.47;1.47;1.47;1.47;1.47	4.66	4.66	0.58398	LMBR1-like membrane protein (1);	0.000000	0.85682	D	0.000000	T	0.40423	0.1116	L	0.31752	0.955	0.80722	D	1	D;B;D	0.89917	0.999;0.084;1.0	D;B;D	0.83275	0.995;0.042;0.996	T	0.11275	-1.0594	10	0.18276	T	0.48	-11.8648	13.7733	0.63038	0.0:0.0:0.0:1.0	.	302;364;323	B7Z633;Q8WVP7-3;Q8WVP7	.;.;LMBR1_HUMAN	G	323;171;362;364;302	ENSP00000326604:E323G;ENSP00000352392:E171G;ENSP00000408256:E362G;ENSP00000346500:E364G;ENSP00000445509:E302G	ENSP00000326604:E323G	E	-	2	0	LMBR1	156213410	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.084000	0.76866	1.750000	0.51863	0.383000	0.25322	GAA		TCGA-3A-A9J0-01A-11D-A40W-08	LMBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347939.3	0	0	0	7	294	0	57	0	4.811309e-02	0	13	0	57	2		0	0	0	0	0	2	1	0.980472	7	292	0	56	2								-3.482006	1	1	0	0		1	2	2	4	2.315457	1	0.470000	3.280000	0.639456	0.150000	5.000000e-02	0.290000	0.160000	0.164866	0.150000	0		
GLI3	2737	broad.mit.edu	37	7	42018305	42018305	+	Missense_Mutation	SNP	C	C	T	rs148502119		TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr7:42018305C>T	ENST00000395925.3	-	11	1624	c.1540G>A	c.(1540-1542)Gtg>Atg	p.V514M	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3			112					CACCTGCACACGAACTCCTTC	0.443000									Pallister-Hall syndrome;Greig Cephalopolysyndactyly															0							SO:0001583	missense	Familial Cancer Database	;	ENST00000395925.3	1	1	hg19	CCDS5465.1	.	.	.	.	.	.	.	.	.	.	C	32	5.177605	0.94846	4.54E-4	0.0	ENSG00000106571	ENST00000395925	D	0.93811	-3.29	5.84	5.84	0.93424	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.97564	0.9202	M	0.92604	3.325	0.80722	D	1	D	0.89917	1.0	D	0.66979	0.948	D	0.97919	1.0313	10	0.87932	D	0	.	20.1381	0.98040	0.0:1.0:0.0:0.0	.	514	P10071	GLI3_HUMAN	M	514	ENSP00000379258:V514M	ENSP00000379258:V514M	V	-	1	0	GLI3	41984830	1.000000	0.71417	0.989000	0.46669	0.984000	0.73092	7.770000	0.85390	2.763000	0.94921	0.650000	0.86243	GTG		TCGA-3A-A9J0-01A-11D-A40W-08	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	1	0	1	125	279	0	106	0	0	0	1	0	106	2		0	0	0	0	0	2	1	1.000000	124	276	0	104	2								-20.000000	1	1	121412	2	33	1	2	2	4	2.285665	1	0.470000	3.280000	0.639456	0.990000	9.900000e-01	1.000000	1.000000	1.000000	0.990000	1		
ADCY1	107	broad.mit.edu	37	7	45699701	45699701	+	Silent	SNP	G	G	A	rs149589767		TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr7:45699701G>A	ENST00000297323.7	+	7	1390	c.1368G>A	c.(1366-1368)ccG>ccA	p.P456P	ADCY1_ENST00000432715.1_Silent_p.P231P	NM_021116.2	NP_066939.1	Q08828	ADCY1_HUMAN	adenylate cyclase 1 (brain)			71				Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	AGGTAGAACCGGGTTACGGAC	0.507000																								0							SO:0001819	synonymous_variant			ENST00000297323.7	1	1	hg19	CCDS34631.1																																																																																				TCGA-3A-A9J0-01A-11D-A40W-08	ADCY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340055.2	0	0	1	138	286	1	124		0	0	0	1	124	2		0	0	0	0	0	2	1	1.000000	137	281	1	121	13								-11.776190	1	1	121412	2	37	1	2	2	4	2.285665	1	0.470000	3.280000	0.639456	0.990000	9.900000e-01	1.000000	1.000000	1.000000	0.990000	1		
WBSCR17	64409	broad.mit.edu	37	7	71142270	71142270	+	Silent	SNP	G	G	A	rs145007893		TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr7:71142270G>A	ENST00000333538.5	+	9	2113	c.1479G>A	c.(1477-1479)ccG>ccA	p.P493P	WBSCR17_ENST00000498380.2_3'UTR	NM_022479.1	NP_071924.1	Q6IS24	GLTL3_HUMAN	Williams-Beuren syndrome chromosome region 17			100		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)			TATTGTATCCGTGCCATGGCT	0.537000																								0							SO:0001819	synonymous_variant			ENST00000333538.5	0	1	hg19	CCDS5540.1																																																																																				TCGA-3A-A9J0-01A-11D-A40W-08	WBSCR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252006.1	0	0	0	23	952	0	139	0	3.635603e-03	0	4	0	139	2		0	0	0	0	0	2	1	0.999999	23	941	0	136	2								-2.623359	1	1	121412	3	44	1	2	2	4	2.285665	1	0.470000	3.280000	0.639456	0.140000	8.000000e-02	0.220000	0.160000	0.153534	0.140000	0		
LZTS1	11178	broad.mit.edu	37	8	20107374	20107374	+	Silent	SNP	G	G	A			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr8:20107374G>A	ENST00000381569.1	-	4	2007	c.1650C>T	c.(1648-1650)taC>taT	p.Y550Y	LZTS1_ENST00000265801.6_Silent_p.Y550Y|LZTS1_ENST00000522290.1_Silent_p.Y491Y			Q9Y250	LZTS1_HUMAN	leucine zipper, putative tumor suppressor 1			29					ACATGGCCACGTAGCTCTGCT	0.627000																								0							SO:0001819	synonymous_variant			ENST00000381569.1	1	1	hg19	CCDS6015.1																																																																																				TCGA-3A-A9J0-01A-11D-A40W-08	LZTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214122.1	1	0	0	102	343	0	161	0	5.790849e-01	0	8	0	161	2	1	7.545493e-01	7	4	0	4	2	1	1.000000	100	340	0	155	2								-20.000000	1	1	121410	2	35	1	1	2	3	1.601012	0	0.470000	3.280000	0.482169	0.990000	8.300000e-01	1.000000	1.000000	0.968710	0.990000	1		
TEK	7010	broad.mit.edu	37	9	27158047	27158047	+	Nonsense_Mutation	SNP	G	G	T			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr9:27158047G>T	ENST00000380036.4	+	2	713	c.271G>T	c.(271-273)Gaa>Taa	p.E91*	TEK_ENST00000406359.4_Nonsense_Mutation_p.E91*|TEK_ENST00000519097.1_Intron	NM_000459.3	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial			15		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)		Ponatinib(DB08901)|Regorafenib(DB08896)|Vandetanib(DB05294)	TTGGAAGAGAGAAAAGGCTAG	0.448000																								0							SO:0001587	stop_gained			ENST00000380036.4	0	1	hg19	CCDS6519.1	.	.	.	.	.	.	.	.	.	.	G	38	7.144543	0.98092	.	.	ENSG00000120156	ENST00000380036;ENST00000346448;ENST00000406359	.	.	.	5.92	5.92	0.95590	.	0.000000	0.52532	D	0.000066	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	.	20.3206	0.98668	0.0:0.0:1.0:0.0	.	.	.	.	X	91	.	ENSP00000343716:E91X	E	+	1	0	TEK	27148047	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.664000	0.74437	2.809000	0.96659	0.655000	0.94253	GAA		TCGA-3A-A9J0-01A-11D-A40W-08	TEK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051965.3	1	0	1	62	189	0	47	0	6.274315e-02	0	2	0	47	2		0	0	0	0	0	2	1	1.000000	59	186	0	45	2								-20.000000	1	1	0	0		1	0	2	2	1.594592	1	0.470000	3.280000	0.470000	0.990000	8.300000e-01	1.000000	1.000000	0.976859	0.990000	1		
TRPM6	140803	broad.mit.edu	37	9	77376995	77376995	+	Missense_Mutation	SNP	C	C	T			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr9:77376995C>T	ENST00000360774.1	-	26	4829	c.4592G>A	c.(4591-4593)cGc>cAc	p.R1531H	TRPM6_ENST00000451710.3_Missense_Mutation_p.R1531H|TRPM6_ENST00000376871.3_Intron|TRPM6_ENST00000376864.4_Missense_Mutation_p.R1531H|TRPM6_ENST00000361255.3_Missense_Mutation_p.R1526H|TRPM6_ENST00000376872.3_Intron|TRPM6_ENST00000449912.2_Missense_Mutation_p.R1526H	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6			126					CCTGTATCTGCGGAGAGGATT	0.418000																								0							SO:0001583	missense			ENST00000360774.1	1	1	hg19	CCDS6647.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	1.535|1.535	-0.543353|-0.543353	0.04053|0.04053	.|.	.|.	ENSG00000119121|ENSG00000119121	ENST00000448641|ENST00000360774;ENST00000451710;ENST00000449912;ENST00000361255;ENST00000376864;ENST00000312449	.|T;T;T;T;T	.|0.54279	.|0.68;0.68;0.68;0.68;0.58	5.33|5.33	-5.55|-5.55	0.02536|0.02536	.|.	.|1.118960	.|0.06509	.|N	.|0.737619	.|T	.|0.28599	.|0.0708	N|N	0.05383|0.05383	-0.06|-0.06	0.09310|0.09310	N|N	1|1	.|B;B;B	.|0.10296	.|0.002;0.003;0.003	.|B;B;B	.|0.06405	.|0.001;0.002;0.002	.|T	.|0.27226	.|-1.0080	.|10	.|0.54805	.|T	.|0.06	.|.	7.9227|7.9227	0.29857|0.29857	0.1046:0.3691:0.0:0.5263|0.1046:0.3691:0.0:0.5263	.|.	.|1531;1526;1526	.|Q9BX84;Q9BX84-3;Q9BX84-2	.|TRPM6_HUMAN;.;.	.|H	-1|1531;1531;1526;1526;1531;1104	.|ENSP00000354006:R1531H;ENSP00000407341:R1531H;ENSP00000396672:R1526H;ENSP00000354962:R1526H;ENSP00000366060:R1531H	.|ENSP00000309693:R1104H	.|R	-|-	.|2	.|0	TRPM6|TRPM6	76566815|76566815	0.085000|0.085000	0.21516|0.21516	0.000000|0.000000	0.03702|0.03702	0.005000|0.005000	0.04900|0.04900	-0.050000|-0.050000	0.11904|0.11904	-1.668000|-1.668000	0.01471|0.01471	-0.290000|-0.290000	0.09829|0.09829	.|CGC		TCGA-3A-A9J0-01A-11D-A40W-08	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	1	0	1	56	212	0	57		0	0	0	0	57	2		0	0	0	0	0	2	1	1.000000	55	212	0	56	2								-3.695870	1	1	121412	5	39	1	0	2	2	1.594592	1	0.470000	3.280000	0.470000	0.880000	6.900000e-01	1.000000	1.000000	0.885130	0.880000	1		
C9orf89	84270	broad.mit.edu	37	9	95869990	95869990	+	Silent	SNP	G	G	A			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chr9:95869990G>A	ENST00000375464.2	+	2	170	c.42G>A	c.(40-42)acG>acA	p.T14T		NM_032310.3	NP_115686.3	Q96LW7	BINCA_HUMAN	chromosome 9 open reading frame 89			7					TGCAGGACACGCCTTTCCTGA	0.562000																								0							SO:0001819	synonymous_variant			ENST00000375464.2	1	1	hg19	CCDS6702.2																																																																																				TCGA-3A-A9J0-01A-11D-A40W-08	C9orf89-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053128.1	1	0	1	50	67	0	30	1	1	44	37	0	30	2		0	0	0	0	0	2	1	1.000000	49	65	0	30	2								-20.000000	1	1	121412	5	37	1	0	2	2	1.567572	1	0.470000	3.280000	0.470000	0.990000	9.900000e-01	1.000000	1.000000	1.000000	0.990000	1		
TMEM47	83604	broad.mit.edu	37	X	34657384	34657384	+	Missense_Mutation	SNP	G	G	A			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chrX:34657384G>A	ENST00000275954.3	-	2	605	c.347C>T	c.(346-348)gCg>gTg	p.A116V		NM_031442.3	NP_113630.1	Q9BQJ4	TMM47_HUMAN	transmembrane protein 47			9					AAGCATGACCGCAACAGGTCT	0.443000																								0							SO:0001583	missense			ENST00000275954.3	0	1	hg19	CCDS14235.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.638349	0.87760	.	.	ENSG00000147027	ENST00000275954	T	0.69926	-0.44	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.81049	0.4742	M	0.65975	2.015	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.82625	-0.0365	10	0.66056	D	0.02	-7.661	17.3961	0.87445	0.0:0.0:1.0:0.0	.	116	Q9BQJ4	TMM47_HUMAN	V	116	ENSP00000275954:A116V	ENSP00000275954:A116V	A	-	2	0	TMEM47	34567305	1.000000	0.71417	0.997000	0.53966	0.862000	0.49288	9.476000	0.97823	2.321000	0.78463	0.538000	0.68166	GCG		TCGA-3A-A9J0-01A-11D-A40W-08	TMEM47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056209.1	0	0	0	3	27	0	8	0	5.883815e-01	0	17	0	8	2		0	0	0	0	0	2	1	0.801814	2	27	0	8	2								-4.892002	1	0	120388	5	33	1	0	1	1			0.470000	3.280000	0.470000	0.230000	6.000000e-02	0.500000	0.210000	0.256276	0.230000	0		
PCDH11Y	83259	broad.mit.edu	37	Y	4968431	4968431	+	Missense_Mutation	SNP	G	G	C			TCGA-3A-A9J0-01A-11D-A40W-08	TCGA-3A-A9J0-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9a6c492b-d3dc-4d8e-bb91-fef812140b6e	36b866cd-0189-43dc-8ebb-5839e55f48e1	g.chrY:4968431G>C	ENST00000333703.4	+	5	3292	c.2779G>C	c.(2779-2781)Gac>Cac	p.D927H	PCDH11Y_ENST00000215473.6_Missense_Mutation_p.D938H|PCDH11Y_ENST00000362095.5_Missense_Mutation_p.D938H	NM_001278619.1|NM_032971.2	NP_001265548.1|NP_116753.1	Q9BZA8	PC11Y_HUMAN	protocadherin 11 Y-linked			27					AGTCACACTAGACCTTCCTAT	0.428000																								0							SO:0001583	missense			ENST00000333703.4	0	1	hg19	CCDS14776.1																																																																																				TCGA-3A-A9J0-01A-11D-A40W-08	PCDH11Y-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084979.2	1	0	0	71	86	0	45		0	0	0	0	45	2		0	0	0	0	0	2	1	1.000000	47	61	0	55	2								-20.000000	1	1	0	0		1						0.470000	3.280000										
