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
KBTBD4	55709	broad.mit.edu	37	11	47595092	47595094	+	In_Frame_Del	DEL	CGA	CGA	-			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr11:47595092_47595094delCGA	ENST00000526005.1	-	4	1098_1100	c.945_947delTCG	c.(943-948)cctcgg>ccg	p.R316del	RNU5E-10P_ENST00000363506.1_RNA|NDUFS3_ENST00000533507.1_Intron|KBTBD4_ENST00000430070.2_In_Frame_Del_p.R332del|KBTBD4_ENST00000395288.2_In_Frame_Del_p.R316del|KBTBD4_ENST00000533290.1_In_Frame_Del_p.R341del			Q9NVX7	KBTB4_HUMAN	kelch repeat and BTB (POZ) domain containing 4			24					GAGCCGGTCCCGAGGCAAAGGAG	0.571000																								0							SO:0001651	inframe_deletion			ENST00000526005.1	1	1	hg19	CCDS7940.1																																																																																				TCGA-S4-A8RO-01A-12D-A377-08	KBTBD4-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000391763.1	1	0	0	53	250	0	60	1	9.589791e-01	6	21	0	60	2	0	0	0	0	0	0		1	1	60	253	0	59	2	0	0	0	0	0	0		-2.734738	1	1	0	0		1	1	2	3	2.034398	0	0.680000	2.080000	0.687439	0.530000	4.000000e-01	1.000000	0.520000	0.558403	0.530000	0	4.600000e-01	0.610000
KLF5	688	broad.mit.edu	37	13	73636195	73636195	+	Frame_Shift_Del	DEL	C	C	-			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08			C	-	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr13:73636195delC	ENST00000377687.4	+	2	994	c.458delC	c.(457-459)tccfs	p.S153fs	KLF5_ENST00000477333.1_3'UTR|KLF5_ENST00000539231.1_Frame_Shift_Del_p.S62fs	NM_001730.3	NP_001721.2	Q13887	KLF5_HUMAN	Kruppel-like factor 5 (intestinal)			17		Prostate(6;0.00187)|Breast(118;0.0735)			CTCTACAAATCCCAGAGACCG	0.532000																								0							SO:0001589	frameshift_variant			ENST00000377687.4	1	0	hg19	CCDS9448.1																																																																																				TCGA-S4-A8RO-01A-12D-A377-08	KLF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045263.1	1	0	0	126	413	0	101	1	1	38	205	0	101	2	0	0	0	0	0	0		1	1	141	408	2	100	25	0	0	0	0	0	0		-4.444923	1	1	0	0		1	0	0	0	1.894646	0	0.680000	2.080000	0.671053	0.660000	5.600000e-01	0.770000	0.670000	0.671050	0.660000	0	6.100000e-01	0.720000
GPR125	166647	broad.mit.edu	37	4	22436937	22436938	+	Frame_Shift_Del	DEL	TT	TT	-			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr4:22436937_22436938delTT	ENST00000334304.5	-	10	1708_1709	c.1439_1440delAA	c.(1438-1440)aaafs	p.K480fs	GPR125_ENST00000502482.1_Frame_Shift_Del_p.K480fs|GPR125_ENST00000282943.5_5'UTR|GPR125_ENST00000508133.1_Frame_Shift_Del_p.K254fs	NM_145290.3	NP_660333.2	Q8IWK6	GP125_HUMAN	G protein-coupled receptor 125			56		Breast(46;0.198)			GAAGTACCTCTTTTGATTTTTC	0.337000																								0							SO:0001589	frameshift_variant			ENST00000334304.5	1	0	hg19	CCDS33964.1																																																																																				TCGA-S4-A8RO-01A-12D-A377-08	GPR125-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362960.3	1	0	0	82	302	0	87	0	8.597445e-01	0	15	0	87	2	0	0	0	0	0	0		1	9.999993e-01	87	303	5	88	36	0	0	0	0	0	0		-3.586915	1	1	0	0		1	1	2	3	1.968126	0	0.680000	2.080000	0.681084	0.620000	5.100000e-01	0.760000	0.630000	0.633807	0.620000	0	5.600000e-01	0.700000
SORBS1	10580	broad.mit.edu	37	10	97096368	97096368	+	Silent	SNP	G	G	A			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr10:97096368G>A	ENST00000361941.3	-	28	3575	c.3549C>T	c.(3547-3549)agC>agT	p.S1183S	SORBS1_ENST00000354106.3_Intron|SORBS1_ENST00000371247.2_Silent_p.S1183S|SORBS1_ENST00000393949.1_Intron|SORBS1_ENST00000371239.1_Intron|SORBS1_ENST00000371249.2_Intron|SORBS1_ENST00000371241.1_Intron|SORBS1_ENST00000607232.1_Intron|SORBS1_ENST00000353505.5_Intron|SORBS1_ENST00000277982.5_Silent_p.S1042S|SORBS1_ENST00000347291.4_Intron|SORBS1_ENST00000306402.6_Intron|SORBS1_ENST00000371227.4_Silent_p.S1137S|SORBS1_ENST00000371245.3_Intron|SORBS1_ENST00000371246.2_Silent_p.S1042S	NM_001034954.1	NP_001030126			sorbin and SH3 domain containing 1			42		Colorectal(252;0.0429)			CTGGAAAAGCGCTACCCAGGG	0.617000																								0							SO:0001819	synonymous_variant			ENST00000361941.3	1	1	hg19	CCDS31255.1																																																																																				TCGA-S4-A8RO-01A-12D-A377-08	SORBS1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049517.1	1	0	1	179	144	0	81		0	0	0	0	81	2		0	0	0	0	0	2	1	1	178	142	0	81	2		0	0	0	0	81	2	-20.000000	1	1	0	0		1	0	1	1	1.472099	1	0.680000	2.080000	0.515152	0.970000	9.100000e-01	1.000000	0.990000	0.978554	0.970000	1	9.500000e-01	1.000000
ANGPTL5	253935	broad.mit.edu	37	11	101773403	101773403	+	Silent	SNP	T	T	C			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr11:101773403T>C	ENST00000334289.3	-	6	1084	c.489A>G	c.(487-489)acA>acG	p.T163T		NM_178127.4	NP_835228.2	Q86XS5	ANGL5_HUMAN	angiopoietin-like 5			29		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.043)			AACCACTCGGTGTTTTGGTGA	0.353000																								0							SO:0001819	synonymous_variant			ENST00000334289.3	1	1	hg19	CCDS8312.1																																																																																				TCGA-S4-A8RO-01A-12D-A377-08	ANGPTL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394138.1	1	0	1	112	228	0	64		0	0	0	0	64	2		0	0	0	0	0	2	1	1	109	225	0	64	2		0	0	0	0	64	2	-20.000000	1	1	0	0		1	1	2	3	2.033988	0	0.680000	2.080000	0.687439	0.990000	8.400000e-01	1.000000	1.000000	0.967906	0.990000	1	9.100000e-01	1.000000
PKNOX2	63876	broad.mit.edu	37	11	125299995	125299995	+	Missense_Mutation	SNP	G	G	A			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr11:125299995G>A	ENST00000298282.9	+	12	1421	c.1150G>A	c.(1150-1152)Gtg>Atg	p.V384M	PKNOX2_ENST00000542175.1_Missense_Mutation_p.V320M|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)			CGCTGCGGGGGTGCTGCAGCA	0.622000																								0							SO:0001583	missense			ENST00000298282.9	0	1	hg19	CCDS41730.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.014071	0.75161	.	.	ENSG00000165495	ENST00000530517;ENST00000531116;ENST00000298282;ENST00000542175	D;D;D;D	0.85258	-1.95;-1.95;-1.96;-1.93	4.82	4.82	0.62117	.	0.000000	0.85682	D	0.000000	D	0.90328	0.6974	L	0.53249	1.67	0.80722	D	1	D;D;D	0.71674	0.998;0.989;0.978	D;P;P	0.70487	0.969;0.795;0.496	D	0.90201	0.4257	10	0.46703	T	0.11	-13.6476	18.252	0.90006	0.0:0.0:1.0:0.0	.	320;355;384	F5GZ15;B7Z3G7;Q96KN3	.;.;PKNX2_HUMAN	M	355;355;384;320	ENSP00000434732:V355M;ENSP00000433971:V355M;ENSP00000298282:V384M;ENSP00000441470:V320M	ENSP00000298282:V384M	V	+	1	0	PKNOX2	124805205	1.000000	0.71417	0.995000	0.50966	0.606000	0.37113	9.809000	0.99208	2.399000	0.81585	0.462000	0.41574	GTG		TCGA-S4-A8RO-01A-12D-A377-08	PKNOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386866.3	0	0	0	5	328	0	52	0	3.731343e-04	0	2	0	52	2		0	0	0	0	0	2	1	9.339264e-01	5	320	0	50	2		0	0	0	0	52	2	-5.508372	1	1	0	0		1	0	2	2	1.994209	1	0.680000	2.080000	0.680000	0.040000	0	0.100000	0.040000	0.052475	0.040000	0	2.000000e-02	0.070000
OR51F2	119694	broad.mit.edu	37	11	4843156	4843156	+	Missense_Mutation	SNP	T	T	C			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr11:4843156T>C	ENST00000322110.5	+	1	606	c.541T>C	c.(541-543)Tcc>Ccc	p.S181P	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001004753.1	NP_001004753.1	Q8NH61	O51F2_HUMAN	olfactory receptor, family 51, subfamily F, member 2			33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.0778)			CAAGAGGTTGTCCTTCTGCAG	0.448000																								0							SO:0001583	missense			ENST00000322110.5	0	1	hg19	CCDS31361.1	.	.	.	.	.	.	.	.	.	.	T	2.880	-0.232112	0.05983	.	.	ENSG00000176925	ENST00000322110	T	0.00036	8.86	4.66	2.17	0.27698	GPCR, rhodopsin-like superfamily (1);	0.663319	0.12337	U	0.477833	T	0.00210	0.0006	L	0.35487	1.065	0.09310	N	1	D	0.69078	0.997	D	0.71656	0.974	T	0.32824	-0.9892	10	0.02654	T	1	.	5.3429	0.15994	0.4154:0.0:0.148:0.4366	.	181	Q8NH61	O51F2_HUMAN	P	181	ENSP00000323952:S181P	ENSP00000323952:S181P	S	+	1	0	OR51F2	4799732	0.000000	0.05858	0.977000	0.42913	0.614000	0.37383	-0.787000	0.04618	0.309000	0.22966	0.459000	0.35465	TCC		TCGA-S4-A8RO-01A-12D-A377-08	OR51F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142181.1	0	0	0	9	528	0	201		0	0	0	0	201	2		0	0	0	0	0	2	1	9.942409e-01	9	527	0	199	2		0	0	0	0	201	2	-3.335725	1	1	0	0		1	0	1	1	1.316738	1	0.680000	2.080000	0.515152	0.020000	1.000000e-02	0.060000	0.030000	0.035941	0.020000	0	1.000000e-02	0.050000
OR51G1	79324	broad.mit.edu	37	11	4945382	4945382	+	Missense_Mutation	SNP	T	T	A			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr11:4945382T>A	ENST00000321961.2	-	1	255	c.188A>T	c.(187-189)tAt>tTt	p.Y63F	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001005237.1	NP_001005237.1	Q8NGK1	O51G1_HUMAN	olfactory receptor, family 51, subfamily G, member 1			25		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)			GCCCAAGAAATAGTACATGGG	0.483000																								0							SO:0001583	missense			ENST00000321961.2	1	1	hg19	CCDS31366.1	.	.	.	.	.	.	.	.	.	.	T	14.38	2.517143	0.44763	.	.	ENSG00000176879	ENST00000321961	T	0.01685	4.69	4.2	4.2	0.49525	GPCR, rhodopsin-like superfamily (1);	0.000000	0.35739	U	0.003015	T	0.01592	0.0051	N	0.25060	0.705	0.27676	N	0.946609	B	0.15719	0.014	B	0.15484	0.013	T	0.37934	-0.9684	10	0.66056	D	0.02	.	6.9793	0.24694	0.3172:0.0:0.0:0.6828	.	63	Q8NGK1	O51G1_HUMAN	F	63	ENSP00000322546:Y63F	ENSP00000322546:Y63F	Y	-	2	0	OR51G1	4901958	0.901000	0.30685	1.000000	0.80357	0.963000	0.63663	1.508000	0.35769	1.760000	0.52011	0.455000	0.32223	TAT		TCGA-S4-A8RO-01A-12D-A377-08	OR51G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142345.1	1	0	0	7	92	0	39		0	0	0	0	39	2		0	0	0	0	0	2	1	9.804965e-01	7	90	0	37	2		0	0	0	0	39	2	-11.939750	1	1	0	0		1	0	1	1	1.316738	1	0.680000	2.080000	0.515152	0.140000	6.000000e-02	0.260000	0.140000	0.152302	0.140000	0	9.000000e-02	0.200000
RPS6KB2	6199	broad.mit.edu	37	11	67200423	67200423	+	Splice_Site	SNP	G	G	A			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr11:67200423G>A	ENST00000312629.5	+	8	662	c.617G>A	c.(616-618)gGc>gAc	p.G206D	RPS6KB2_ENST00000539188.1_3'UTR|AP003419.16_ENST00000535922.1_RNA|RPS6KB2_ENST00000524814.1_3'UTR	NM_003952.2	NP_003943.2	Q9UBS0	KS6B2_HUMAN	ribosomal protein S6 kinase, 70kDa, polypeptide 2			25			BRCA - Breast invasive adenocarcinoma(15;3.26e-06)		CCTTCCTCAGGCCACATCAAA	0.612000																								0							SO:0001630	splice_region_variant			ENST00000312629.5	1	0	hg19	CCDS41677.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.69|15.69	2.909408|2.909408	0.52439|0.52439	.|.	.|.	ENSG00000175634|ENSG00000175634	ENST00000524814|ENST00000312629	.|T	.|0.31510	.|1.49	4.76|4.76	4.76|4.76	0.60689|0.60689	.|Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.58308|0.58308	0.2113|0.2113	M|M	0.80422|0.80422	2.495|2.495	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.91635	.|0.999;0.999	T|T	0.61778|0.61778	-0.6993|-0.6993	5|9	.|.	.|.	.|.	.|.	16.6904|16.6904	0.85320|0.85320	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|206;206	.|Q9BRS0;Q9UBS0	.|.;KS6B2_HUMAN	T|D	157|206	.|ENSP00000308413:G206D	.|.	A|G	+|+	1|2	0|0	RPS6KB2|RPS6KB2	66956999|66956999	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.899000|0.899000	0.52679|0.52679	9.087000|9.087000	0.94110|0.94110	2.461000|2.461000	0.83175|0.83175	0.561000|0.561000	0.74099|0.74099	GCC|GGC		TCGA-S4-A8RO-01A-12D-A377-08	RPS6KB2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395508.1	0	0	1	61	175	1	29	1	9.999898e-01	20	158	1	29	18		0	0	0	0	0	2	1	9.999987e-01	61	173	1	29	23		0	0	0	1	29	2	-20.000000	1	1	0	0		1	1	3	4	2.761429	1	0.680000	2.080000	0.768250	0.990000	8.400000e-01	1.000000	1.000000	0.982603	0.990000	1	9.500000e-01	1.000000
OR10A5	144124	broad.mit.edu	37	11	6867677	6867677	+	Missense_Mutation	SNP	C	C	G			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr11:6867677C>G	ENST00000299454.4	+	1	795	c.764C>G	c.(763-765)tCt>tGt	p.S255C	OR10A5_ENST00000379831.2_Missense_Mutation_p.S259C			Q9H207	O10A5_HUMAN	olfactory receptor, family 10, subfamily A, member 5			21		Medulloblastoma(188;0.0523)|all_neural(188;0.236)			TTCTATATATCTTCTAGCCTC	0.433000													Pancreas(44;21 1072 25662 28041 45559)											0							SO:0001583	missense			ENST00000299454.4	0	1	hg19	CCDS7773.1	.	.	.	.	.	.	.	.	.	.	.	7.000	0.554679	0.13436	.	.	ENSG00000166363	ENST00000299454;ENST00000379831	T;T	0.00183	8.6;8.6	3.59	3.59	0.41128	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000018	T	0.00300	0.0009	L	0.29908	0.895	0.09310	N	1	D	0.71674	0.998	D	0.70016	0.967	T	0.68834	-0.5304	10	0.41790	T	0.15	.	13.509	0.61499	0.0:1.0:0.0:0.0	.	255	Q9H207	O10A5_HUMAN	C	255;259	ENSP00000299454:S255C;ENSP00000369159:S259C	ENSP00000299454:S255C	S	+	2	0	OR10A5	6824253	0.000000	0.05858	0.221000	0.23827	0.007000	0.05969	0.600000	0.24104	2.269000	0.75478	0.591000	0.81541	TCT		TCGA-S4-A8RO-01A-12D-A377-08	OR10A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385983.1	0	0	0	7	426	1	195		0	0	0	1	195	2		0	0	0	0	0	2	0	2.990150e-01	7	419	1	194	10		0	0	0	1	195	2	-2.713086	1	1	0	0		1	0	1	1	1.302272	1	0.680000	2.080000	0.515152	0.020000	0	0.060000	0.030000	0.035623	0.020000	0	1.000000e-02	0.050000
NOX4	50507	broad.mit.edu	37	11	89088203	89088203	+	Nonsense_Mutation	SNP	G	G	A			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08			G	A	G	G		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr11:89088203G>A	ENST00000263317.4	-	13	1382	c.1144C>T	c.(1144-1146)Cga>Tga	p.R382*	NOX4_ENST00000535633.1_Nonsense_Mutation_p.R358*|NOX4_ENST00000528341.1_Nonsense_Mutation_p.R357*|NOX4_ENST00000542487.1_Nonsense_Mutation_p.R358*|NOX4_ENST00000534731.1_Nonsense_Mutation_p.R382*|NOX4_ENST00000531342.1_Nonsense_Mutation_p.R75*|NOX4_ENST00000532825.1_Nonsense_Mutation_p.R358*|NOX4_ENST00000527626.1_Nonsense_Mutation_p.R216*|NOX4_ENST00000525196.1_Intron|NOX4_ENST00000527956.1_Nonsense_Mutation_p.R358*|NOX4_ENST00000424319.1_Nonsense_Mutation_p.R358*|NOX4_ENST00000413594.2_Nonsense_Mutation_p.R403*|NOX4_ENST00000343727.5_Nonsense_Mutation_p.R358*|NOX4_ENST00000375979.3_Nonsense_Mutation_p.R75*			Q9NPH5	NOX4_HUMAN	NADPH oxidase 4	p.R382*(1)		44		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.011)			AGTAAATCTCGAAATCGTTCT	0.328000																								1	Substitution - Nonsense(1)						SO:0001587	stop_gained			ENST00000263317.4	0	1	hg19	CCDS8285.1	.	.	.	.	.	.	.	.	.	.	G	32	5.124446	0.94429	0.0	1.16E-4	ENSG00000086991	ENST00000424319;ENST00000535633;ENST00000343727;ENST00000534731;ENST00000263317;ENST00000532825;ENST00000527956;ENST00000542487;ENST00000527626;ENST00000528341;ENST00000413594;ENST00000531342;ENST00000375979	.	.	.	5.31	5.31	0.75309	.	0.325791	0.27060	N	0.021133	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-6.9276	14.4891	0.67639	0.0:0.0:1.0:0.0	.	.	.	.	X	358;358;358;382;382;358;358;358;216;357;403;75;75	.	.	R	-	1	2	NOX4	88727851	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	5.228000	0.65310	2.479000	0.83701	0.563000	0.77884	CGA		TCGA-S4-A8RO-01A-12D-A377-08	NOX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394054.1	1	0	1	126	85	0	27	0	9.952362e-01	0	9	0	27	2		0	0	0	0	0	2	1	1	117	78	0	28	2		0	0	0	0	27	2	-20.000000	1	1	121326	1	38	1	1	3	4	3.157427	1	0.680000	2.080000	0.803150	0.990000	9.900000e-01	1.000000	1.000000	1.000000	0.990000	1	9.900000e-01	1.000000
DNAH10	196385	broad.mit.edu	37	12	124317833	124317833	+	Missense_Mutation	SNP	C	C	A			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr12:124317833C>A	ENST00000409039.3	+	26	4389	c.4364C>A	c.(4363-4365)cCt>cAt	p.P1455H		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10			52	all_neural(191;0.101)|Medulloblastoma(191;0.163)				TTTGTGGGGCCTTTTCTGCAA	0.433000																								0							SO:0001583	missense			ENST00000409039.3	1	1	hg19	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	C	29.1	4.980145	0.92982	.	.	ENSG00000197653	ENST00000409039	T	0.62105	0.05	5.83	5.83	0.93111	Dynein heavy chain, domain-2 (1);	0.000000	0.64402	U	0.000001	T	0.80742	0.4681	M	0.79123	2.44	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.78600	-0.2141	10	0.40728	T	0.16	.	20.1162	0.97934	0.0:1.0:0.0:0.0	.	1455	Q8IVF4	DYH10_HUMAN	H	1455	ENSP00000386770:P1455H	ENSP00000386770:P1455H	P	+	2	0	DNAH10	122883786	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.818000	0.86416	2.756000	0.94617	0.655000	0.94253	CCT		TCGA-S4-A8RO-01A-12D-A377-08	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3	1	0	1	30	79	0	23	0	0	0	1	0	23	2		0	0	0	0	0	2	1	1	30	78	0	22	2		0	0	0	0	23	2	-20.000000	1	1	0	0		1	1	2	3	1.982775	0	0.680000	2.080000	0.682161	0.810000	5.800000e-01	1.000000	1.000000	0.820021	0.810000	0	6.900000e-01	0.950000
KRAS	3845	broad.mit.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	C	T	rs121913529		TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	KRAS_deep			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr12:25398284C>T	ENST00000256078.4	-	2	98	c.35G>A	c.(34-36)gGt>gAt	p.G12D	KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)		GCCTACGCCACCAGCTCCAAC	0.348000	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		pancreatic, colorectal, lung, thyroid, AML, others				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)			Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		L, E, M, O	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)						SO:0001583	missense	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	ENST00000256078.4	1	1	hg19	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.409094	0.83340	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.85919	0.5809	M	0.91818	3.245	0.80722	D	1	B;P	0.35714	0.385;0.517	B;B	0.41619	0.257;0.361	D	0.87870	0.2670	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	D	12	ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D	ENSP00000256078:G12D	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		TCGA-S4-A8RO-01A-12D-A377-08	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	1	0	1	79	177	0	51	1	9.959214e-01	6	16	0	51	2	1	1	118	342	0	696	2	1	1	78	173	0	51	2	1	1	3068	4964	0	51	2	-20.000000	1	1	121404	2	44	1	1	2	3	2.002208	0	0.680000	2.080000	0.684294	0.910000	7.500000e-01	1.000000	1.000000	0.916249	0.910000	1	8.300000e-01	1.000000
SYT10	341359	broad.mit.edu	37	12	33538128	33538128	+	Silent	SNP	C	C	T			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr12:33538128C>T	ENST00000228567.3	-	4	1472	c.1176G>A	c.(1174-1176)gcG>gcA	p.A392A	SYT10_ENST00000535526.1_Silent_p.A211A	NM_198992.3	NP_945343.1	Q6XYQ8	SYT10_HUMAN	synaptotagmin X			42	Lung NSC(5;8.37e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0334)				TAATATCCATCGCCTTCAGAT	0.413000																								0							SO:0001819	synonymous_variant			ENST00000228567.3	1	1	hg19	CCDS8732.1																																																																																				TCGA-S4-A8RO-01A-12D-A377-08	SYT10-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403222.1	1	0	1	114	277	0	94		0	0	0	0	94	2		0	0	0	0	0	2	1	1	113	273	0	93	2		0	0	0	0	94	2	-8.396578	1	1	121412	1	38	1	1	2	3	1.982775	0	0.680000	2.080000	0.682161	0.860000	7.200000e-01	1.000000	0.860000	0.866062	0.860000	1	7.900000e-01	0.940000
PDZRN4	29951	broad.mit.edu	37	12	41966704	41966704	+	Missense_Mutation	SNP	G	G	A			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr12:41966704G>A	ENST00000402685.2	+	10	2131	c.2123G>A	c.(2122-2124)cGg>cAg	p.R708Q	PDZRN4_ENST00000539469.2_Missense_Mutation_p.R450Q|PDZRN4_ENST00000298919.7_Missense_Mutation_p.R448Q	NM_001164595.1	NP_001158067.1	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing ring finger 4			77	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)			GGAGGATTCCGGAATTATAAC	0.443000																								0							SO:0001583	missense			ENST00000402685.2	1	1	hg19	CCDS53777.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	10.61	1.398179	0.25205	.	.	ENSG00000165966	ENST00000402685;ENST00000539469;ENST00000298919	T;T;T	0.72505	-0.66;3.83;3.83	4.32	3.42	0.39159	.	0.094359	0.43416	D	0.000561	T	0.65565	0.2703	M	0.76838	2.35	0.39920	D	0.974143	B;B;B	0.31503	0.114;0.326;0.043	B;B;B	0.24269	0.003;0.052;0.014	T	0.64892	-0.6300	10	0.34782	T	0.22	-7.5442	9.2356	0.37464	0.0828:0.1469:0.7702:0.0	.	708;448;450	Q6ZMN7;Q6ZMN7-4;Q6ZMN7-2	PZRN4_HUMAN;.;.	Q	708;450;448	ENSP00000384197:R708Q;ENSP00000439990:R450Q;ENSP00000298919:R448Q	ENSP00000298919:R448Q	R	+	2	0	PDZRN4	40252971	1.000000	0.71417	0.981000	0.43875	0.762000	0.43233	2.333000	0.43912	1.124000	0.41980	0.650000	0.86243	CGG		TCGA-S4-A8RO-01A-12D-A377-08	PDZRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403701.1	1	0	1	70	198	0	73		0	0	0	0	73	2		0	0	0	0	0	2	1	1	69	196	0	72	2		0	0	0	0	73	2	-5.095352	1	1	121412	3	38	1	1	2	3	1.982775	0	0.680000	2.080000	0.682161	0.770000	6.200000e-01	0.960000	0.770000	0.779414	0.770000	0	6.900000e-01	0.860000
KCNA5	3741	broad.mit.edu	37	12	5153999	5153999	+	Missense_Mutation	SNP	G	G	A			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr12:5153999G>A	ENST00000252321.3	+	1	915	c.686G>A	c.(685-687)cGc>cAc	p.R229H		NM_002234.3	NP_002225.2	P22460	KCNA5_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 5			52				Dalfampridine(DB06637)	CCCCTGCCCCGCAACGAGTTC	0.607000																								0							SO:0001583	missense			ENST00000252321.3	1	1	hg19	CCDS8536.1	.	.	.	.	.	.	.	.	.	.	G	12.70	2.016133	0.35606	.	.	ENSG00000130037	ENST00000252321	T	0.65549	-0.16	4.77	4.77	0.60923	.	1.183500	0.06286	U	0.698225	T	0.56906	0.2017	L	0.35644	1.08	0.29339	N	0.866187	B	0.13145	0.007	B	0.12837	0.008	T	0.46938	-0.9155	10	0.52906	T	0.07	.	12.4671	0.55764	0.0832:0.0:0.9168:0.0	.	229	P22460	KCNA5_HUMAN	H	229	ENSP00000252321:R229H	ENSP00000252321:R229H	R	+	2	0	KCNA5	5024260	0.000000	0.05858	0.996000	0.52242	0.991000	0.79684	-0.403000	0.07214	2.478000	0.83669	0.561000	0.74099	CGC		TCGA-S4-A8RO-01A-12D-A377-08	KCNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398925.2	1	0	1	136	201	0	76	0	0	0	1	0	76	2		0	0	0	0	0	2	1	1	136	200	0	76	2		0	0	0	0	76	2	-20.000000	1	1	121412	1	36	1	1	2	3	2.038143	0	0.680000	2.080000	0.687439	0.990000	9.900000e-01	1.000000	1.000000	0.999932	0.990000	1	9.900000e-01	1.000000
KRT1	3848	broad.mit.edu	37	12	53069133	53069133	+	Silent	SNP	G	G	A			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr12:53069133G>A	ENST00000252244.3	-	9	1837	c.1779C>T	c.(1777-1779)ggC>ggT	p.G593G		NM_006121.3	NP_006112.3	P04264	K2C1_HUMAN	keratin 1	p.G593G(1)		39					cgccgccgccgcctccagagc	0.721000																								1	Substitution - coding silent(1)						SO:0001819	synonymous_variant			ENST00000252244.3	1	1	hg19	CCDS8836.1																																																																																				TCGA-S4-A8RO-01A-12D-A377-08	KRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405706.1	1	0	0	56	93	0	38		0	0	0	0	38	2		0	0	0	0	0	2	1	1	52	85	0	33	2		0	0	0	0	38	2	-9.192583	1	1	118658	1	30	1	1	2	3	1.982775	0	0.680000	2.080000	0.682161	0.990000	8.800000e-01	1.000000	1.000000	0.990479	0.990000	1	9.900000e-01	1.000000
ATP2B1	490	broad.mit.edu	37	12	90036041	90036041	+	Missense_Mutation	SNP	T	T	A			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr12:90036041T>A	ENST00000428670.3	-	3	756	c.300A>T	c.(298-300)caA>caT	p.Q100H	ATP2B1_ENST00000261173.2_Missense_Mutation_p.Q100H|ATP2B1_ENST00000348959.3_Missense_Mutation_p.Q100H|ATP2B1_ENST00000359142.3_Missense_Mutation_p.Q100H			P20020	AT2B1_HUMAN	ATPase, Ca++ transporting, plasma membrane 1			45					CCCATACTAATTGAAGAAAGG	0.343000																								0							SO:0001583	missense			ENST00000428670.3	1	1	hg19	CCDS9035.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.237947	0.79800	.	.	ENSG00000070961	ENST00000261173;ENST00000348959;ENST00000359142;ENST00000428670	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.76	-5.69	0.02428	.	0.000000	0.85682	D	0.000000	D	0.83275	0.5219	M	0.79805	2.47	0.53005	D	0.99996	D;P	0.63880	0.993;0.5	P;P	0.60682	0.878;0.55	D	0.84356	0.0535	9	.	.	.	-20.2557	15.3162	0.74081	0.0:0.6036:0.0:0.3964	.	100;100	P20020-3;P20020-2	.;.	H	100	ENSP00000261173:Q100H;ENSP00000343599:Q100H;ENSP00000352054:Q100H;ENSP00000392043:Q100H	.	Q	-	3	2	ATP2B1	88560172	0.015000	0.18098	0.906000	0.35671	0.986000	0.74619	-0.835000	0.04386	-0.979000	0.03529	0.379000	0.24179	CAA		TCGA-S4-A8RO-01A-12D-A377-08	ATP2B1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406653.1	1	0	1	449	823	0	322	1	9.411745e-01	2	9	0	322	2		0	0	0	0	0	2	1	1	443	816	0	322	2		0	0	0	0	322	2	-20.000000	1	1	0	0		1	1	2	3	1.982775	0	0.680000	2.080000	0.682161	0.990000	9.600000e-01	1.000000	1.000000	0.997460	0.990000	1	9.900000e-01	1.000000
TUBA3C	7278	broad.mit.edu	37	13	19751734	19751734	+	Missense_Mutation	SNP	G	G	A			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr13:19751734G>A	ENST00000400113.3	-	4	493	c.389C>T	c.(388-390)aCg>aTg	p.T130M		NM_006001.2	NP_005992.1	Q13748	TBA3C_HUMAN	tubulin, alpha 3c			72		all_cancers(29;1.31e-20)|all_epithelial(30;1.59e-20)|all_lung(29;6.91e-20)|Lung NSC(5;9.25e-17)|Hepatocellular(1;0.0207)|Lung SC(185;0.0262)|Ovarian(182;0.162)			CTGCAGTCCCGTGCACAGATC	0.582000																								0							SO:0001583	missense			ENST00000400113.3	1	1	hg19	CCDS9284.1	.	.	.	.	.	.	.	.	.	.	g	9.895	1.205228	0.22205	.	.	ENSG00000198033	ENST00000400113;ENST00000360801	T	0.68624	-0.34	1.19	1.19	0.21007	.	0.000000	0.48286	U	0.000184	T	0.70439	0.3224	.	.	.	0.40500	D	0.980633	.	.	.	.	.	.	T	0.72763	-0.4195	7	0.87932	D	0	.	8.3041	0.32032	0.0:0.0:1.0:0.0	.	.	.	.	M	130	ENSP00000382982:T130M	ENSP00000354037:T130M	T	-	2	0	TUBA3C	18649734	1.000000	0.71417	0.920000	0.36463	0.408000	0.30992	4.910000	0.63321	0.966000	0.38159	0.162000	0.16502	ACG		TCGA-S4-A8RO-01A-12D-A377-08	TUBA3C-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044007.2	1	0	1	61	104	0	47		0	0	0	0	47	2		0	0	0	0	0	2	1	1	58	102	0	48	2		0	0	0	0	47	2	-20.000000	1	1	0	0		1	0	0	0	1.894646	0	0.680000	2.080000	0.671053	0.990000	8.400000e-01	1.000000	1.000000	0.980914	0.990000	1	9.400000e-01	1.000000
PABPC3	5042	broad.mit.edu	37	13	25671262	25671262	+	Missense_Mutation	SNP	G	G	A			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr13:25671262G>A	ENST00000281589.3	+	1	963	c.926G>A	c.(925-927)cGt>cAt	p.R309H		NM_030979.2	NP_112241.2	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3			47		Lung SC(185;0.0225)|Breast(139;0.0602)			GATGATGAACGTCTCCGGAAA	0.408000																								0							SO:0001583	missense			ENST00000281589.3	1	1	hg19	CCDS9311.1	.	.	.	.	.	.	.	.	.	.	G	8.903	0.956849	0.18507	.	.	ENSG00000151846	ENST00000281589	T	0.15952	2.38	0.875	-0.438	0.12268	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.135449	0.32473	N	0.006058	T	0.07007	0.0178	N	0.10685	0.025	0.50632	D	0.999884	P	0.43094	0.799	B	0.38985	0.287	T	0.30880	-0.9963	10	0.62326	D	0.03	.	6.1527	0.20320	0.0:0.3209:0.679:0.0	.	309	Q9H361	PABP3_HUMAN	H	309	ENSP00000281589:R309H	ENSP00000281589:R309H	R	+	2	0	PABPC3	24569262	1.000000	0.71417	0.851000	0.33527	0.226000	0.24999	3.068000	0.50018	-0.161000	0.10983	0.313000	0.20887	CGT		TCGA-S4-A8RO-01A-12D-A377-08	PABPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044220.2	1	0	1	378	755	0	310	0	0	0	1	0	310	2		0	0	0	0	0	2	1	1	376	733	0	309	2		0	0	0	0	310	2	-20.000000	1	0	121412	6	43	1	0	0	0	1.894646	0	0.680000	2.080000	0.671053	0.940000	8.700000e-01	1.000000	1.000000	0.952174	0.940000	1	9.000000e-01	0.990000
PPP2R5C	5527	broad.mit.edu	37	14	102360847	102360847	+	Missense_Mutation	SNP	G	G	A			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr14:102360847G>A	ENST00000334743.5	+	8	850	c.802G>A	c.(802-804)Gca>Aca	p.A268T	PPP2R5C_ENST00000328724.5_Missense_Mutation_p.A323T|PPP2R5C_ENST00000557095.1_Missense_Mutation_p.A268T|PPP2R5C_ENST00000445439.3_Missense_Mutation_p.A268T|PPP2R5C_ENST00000422945.2_Missense_Mutation_p.A299T|PPP2R5C_ENST00000350249.3_Missense_Mutation_p.A268T	NM_002719.3	NP_002710.2	Q13362	2A5G_HUMAN	protein phosphatase 2, regulatory subunit B', gamma			20					TTTTTAGCTGGCATACTGTGT	0.403000																								0							SO:0001583	missense			ENST00000334743.5	0	1	hg19	CCDS9964.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.593023	0.86953	.	.	ENSG00000078304	ENST00000422945;ENST00000328724;ENST00000557268;ENST00000350249;ENST00000334756;ENST00000445439;ENST00000334743;ENST00000557095;ENST00000557716	T;T;T;T;T	0.49720	0.78;0.77;0.77;0.83;0.78	5.63	5.63	0.86233	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.56615	0.1997	L	0.59436	1.845	0.80722	D	1	P;B;P;P;B;P	0.45531	0.831;0.083;0.765;0.86;0.148;0.567	B;B;B;P;B;B	0.48063	0.429;0.122;0.252;0.565;0.074;0.443	T	0.57487	-0.7803	10	0.54805	T	0.06	-6.5997	19.6959	0.96026	0.0:0.0:1.0:0.0	.	299;166;268;268;268;323	F5GWP3;E9PHN5;Q13362-3;Q13362;Q13362-2;Q6ZN33	.;.;.;2A5G_HUMAN;.;.	T	299;323;297;268;166;268;268;268;64	ENSP00000412324:A299T;ENSP00000329009:A323T;ENSP00000450931:A297T;ENSP00000262239:A268T;ENSP00000333905:A268T	ENSP00000329009:A323T	A	+	1	0	PPP2R5C	101430600	1.000000	0.71417	0.999000	0.59377	0.799000	0.45148	9.694000	0.98686	2.659000	0.90383	0.650000	0.86243	GCA		TCGA-S4-A8RO-01A-12D-A377-08	PPP2R5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414373.2	0	0	0	6	403	0	64	0	5.924434e-01	0	125	0	64	2		0	0	0	0	0	2	1	9.633321e-01	6	396	0	62	2		0	0	0	0	64	2	-2.802890	1	1	0	0		1	1	2	3	2.596884	1	0.680000	2.080000	0.761194	0.050000	1.000000e-02	0.120000	0.060000	0.066869	0.050000	0	3.000000e-02	0.090000
ACIN1	22985	broad.mit.edu	37	14	23531399	23531399	+	Missense_Mutation	SNP	G	G	A			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr14:23531399G>A	ENST00000262710.1	-	16	3578	c.3251C>T	c.(3250-3252)gCt>gTt	p.A1084V	ACIN1_ENST00000357481.2_Missense_Mutation_p.A326V|ACIN1_ENST00000457657.1_Missense_Mutation_p.A1044V|ACIN1_ENST00000397341.3_Missense_Mutation_p.A326V|ACIN1_ENST00000557515.1_Missense_Mutation_p.A325V|ACIN1_ENST00000338631.6_Missense_Mutation_p.A357V|ACIN1_ENST00000555053.1_Missense_Mutation_p.A1071V|ACIN1_ENST00000605057.1_Missense_Mutation_p.A1026V	NM_001164814.1|NM_014977.3	NP_001158286.1|NP_055792	Q9UKV3	ACINU_HUMAN	apoptotic chromatin condensation inducer 1			37	all_cancers(95;1.36e-05)				GGCATAGTCAGCACAAAGGAA	0.537000																								0							SO:0001583	missense			ENST00000262710.1	0	1	hg19	CCDS9587.1	.	.	.	.	.	.	.	.	.	.	G	9.790	1.177752	0.21787	.	.	ENSG00000100813	ENST00000557515;ENST00000338631;ENST00000357481;ENST00000262710;ENST00000457657;ENST00000397341;ENST00000555053	T;T;T;T;T;T;T	0.18502	2.21;2.21;2.21;2.21;2.21;2.21;2.21	5.19	5.19	0.71726	Nucleotide-binding, alpha-beta plait (1);	0.000000	0.38720	N	0.001589	T	0.04407	0.0121	N	0.00289	-1.7	0.44388	D	0.997291	B;B;B;B;B	0.27013	0.137;0.166;0.084;0.111;0.054	B;B;B;B;B	0.35859	0.135;0.212;0.064;0.016;0.011	T	0.41610	-0.9499	10	0.02654	T	1	-9.2231	11.4006	0.49868	0.0848:0.0:0.9152:0.0	.	1071;1084;1044;357;326	G3V3M7;Q9UKV3;E7EQT4;Q9UKV3-2;Q9UKV3-3	.;ACINU_HUMAN;.;.;.	V	325;357;326;1084;1044;326;1071	ENSP00000451138:A325V;ENSP00000345541:A357V;ENSP00000350073:A326V;ENSP00000262710:A1084V;ENSP00000405677:A1044V;ENSP00000380502:A326V;ENSP00000451328:A1071V	ENSP00000262710:A1084V	A	-	2	0	ACIN1	22601239	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.835000	0.62781	2.578000	0.87016	0.563000	0.77884	GCT		TCGA-S4-A8RO-01A-12D-A377-08	ACIN1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071707.3	0	0	0	5	601	0	90	0	6.780961e-01	0	264	0	90	2		0	0	0	0	0	2	1	9.372288e-01	5	599	0	89	2		0	0	0	0	90	2	-2.446123	0	1	0	0		1	1	2	3	2.617345	1	0.680000	2.080000	0.760587	0.030000	0	0.080000	0.030000	0.037971	0.030000	0	1.000000e-02	0.060000
ZFYVE26	23503	broad.mit.edu	37	14	68238816	68238816	+	Missense_Mutation	SNP	G	G	A			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr14:68238816G>A	ENST00000347230.4	-	28	5570	c.5432C>T	c.(5431-5433)cCg>cTg	p.P1811L	ZFYVE26_ENST00000555452.1_Missense_Mutation_p.P1811L	NM_015346.3	NP_056161.2	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26			94					AGTCTCATCCGGTACCCACTG	0.562000																								0							SO:0001583	missense			ENST00000347230.4	0	1	hg19	CCDS9788.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.269444	0.80469	.	.	ENSG00000072121	ENST00000347230;ENST00000411699;ENST00000555452	T;T	0.49720	0.77;0.77	5.76	5.76	0.90799	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, FYVE-type (2);Zinc finger, FYVE/PHD-type (1);	0.000000	0.85682	D	0.000000	T	0.77260	0.4104	M	0.90870	3.155	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.994;0.996	T	0.81780	-0.0776	10	0.87932	D	0	-14.759	19.9574	0.97228	0.0:0.0:1.0:0.0	.	1811;1811	G3V2D8;Q68DK2	.;ZFY26_HUMAN	L	1811;1790;1811	ENSP00000251119:P1811L;ENSP00000450603:P1811L	ENSP00000251119:P1811L	P	-	2	0	ZFYVE26	67308569	1.000000	0.71417	0.432000	0.26747	0.625000	0.37756	7.804000	0.85993	2.715000	0.92844	0.561000	0.74099	CCG		TCGA-S4-A8RO-01A-12D-A377-08	ZFYVE26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412736.2	1	0	1	50	64	0	14	1	9.680347e-01	6	4	0	14	2		0	0	0	0	0	2	1	1	49	64	0	14	2		0	0	0	0	14	2	-20.000000	1	1	0	0		1	1	2	3	2.577519	1	0.680000	2.080000	0.757502	0.990000	9.900000e-01	1.000000	1.000000	1.000000	0.990000	1	9.900000e-01	1.000000
GALC	2581	broad.mit.edu	37	14	88411975	88411975	+	Missense_Mutation	SNP	C	C	T			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr14:88411975C>T	ENST00000261304.2	-	14	1698	c.1592G>A	c.(1591-1593)cGc>cAc	p.R531H	GALC_ENST00000544807.2_Missense_Mutation_p.R475H|GALC_ENST00000393569.2_Missense_Mutation_p.R505H|GALC_ENST00000393568.4_Missense_Mutation_p.R508H	NM_000153.3|NM_001201401.1	NP_000144.2|NP_001188330.1	P54803	GALC_HUMAN	galactosylceramidase			21					GAGAACTTGGCGTAGCGTGAA	0.408000																								0		GRCh37	CM990620	GALC	M		SO:0001583	missense			ENST00000261304.2	1	1	hg19	CCDS9878.2	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	17.14	3.314547	0.60524	.	.	ENSG00000054983	ENST00000261304;ENST00000544807;ENST00000393569;ENST00000539620;ENST00000393568	D;D;D;D	0.95035	-3.59;-3.59;-3.59;-3.59	5.5	4.61	0.57282	.	0.048176	0.85682	D	0.000000	D	0.97745	0.9260	M	0.91140	3.18	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.997;0.999;0.997;0.999	D	0.98792	1.0736	10	0.87932	D	0	-13.106	15.9398	0.79745	0.1363:0.8637:0.0:0.0	.	475;508;505;531	P54803-5;E7EPA4;P54803-4;P54803	.;.;.;GALC_HUMAN	H	531;475;505;320;508	ENSP00000261304:R531H;ENSP00000437513:R475H;ENSP00000377199:R505H;ENSP00000377198:R508H	ENSP00000261304:R531H	R	-	2	0	GALC	87481728	1.000000	0.71417	0.840000	0.33206	0.012000	0.07955	7.637000	0.83313	1.441000	0.47550	0.585000	0.79938	CGC		TCGA-S4-A8RO-01A-12D-A377-08	GALC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071559.2	1	0	1	117	338	0	76	1	9.999999e-01	17	53	0	76	2		0	0	0	0	0	2	1	1	116	333	0	76	2		0	0	0	0	76	2	-6.177353	1	1	120816	7	43	1	1	2	3	2.596884	1	0.680000	2.080000	0.761194	0.990000	8.500000e-01	1.000000	1.000000	0.975393	0.990000	1	9.300000e-01	1.000000
IFT140	9742	broad.mit.edu	37	16	1612009	1612009	+	Missense_Mutation	SNP	G	G	A			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr16:1612009G>A	ENST00000426508.2	-	18	2539	c.2176C>T	c.(2176-2178)Cct>Tct	p.P726S	IFT140_ENST00000439987.2_5'UTR	NM_014714.3	NP_055529.2	Q96RY7	IF140_HUMAN	intraflagellar transport 140			53		Hepatocellular(780;0.219)			TAGTAATAAGGCACTTCCATC	0.557000																								0							SO:0001583	missense			ENST00000426508.2	1	1	hg19	CCDS10439.1	.	.	.	.	.	.	.	.	.	.	G	18.81	3.702254	0.68501	.	.	ENSG00000187535	ENST00000397417;ENST00000426508;ENST00000439987	T	0.68025	-0.3	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	D	0.84288	0.5439	M	0.84433	2.695	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.86852	0.2024	10	0.87932	D	0	.	18.9059	0.92460	0.0:0.0:1.0:0.0	.	726;451	Q96RY7;B4DR58	IF140_HUMAN;.	S	726	ENSP00000406012:P726S	ENSP00000380562:P726S	P	-	1	0	IFT140	1552010	1.000000	0.71417	0.797000	0.32132	0.084000	0.17831	9.225000	0.95219	2.535000	0.85469	0.563000	0.77884	CCT		TCGA-S4-A8RO-01A-12D-A377-08	IFT140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250438.2	1	0	1	93	86	0	52	1	9.833467e-01	6	3	0	52	2		0	0	0	0	0	2	1	1	92	85	0	50	2		0	0	0	0	52	2	-20.000000	1	1	0	0		1	0	1	1	1.413717	1	0.680000	2.080000	0.515152	0.950000	8.300000e-01	1.000000	0.990000	0.946414	0.950000	1	8.900000e-01	0.990000
NUDT21	11051	broad.mit.edu	37	16	56468701	56468701	+	Missense_Mutation	SNP	T	T	C			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08			T	C	T	T		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr16:56468701T>C	ENST00000300291.5	-	5	684	c.512A>G	c.(511-513)cAt>cGt	p.H171R		NM_007006.2	NP_008937.1	O43809	CPSF5_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 21			7					CAACTTCTTATGTTCCTTAGG	0.303000																								0							SO:0001583	missense			ENST00000300291.5	1	1	hg19	CCDS10760.1	.	.	.	.	.	.	.	.	.	.	T	14.53	2.563365	0.45694	.	.	ENSG00000167005	ENST00000300291	.	.	.	5.34	5.34	0.76211	NUDIX hydrolase domain (1);	0.000000	0.85682	D	0.000000	T	0.62974	0.2472	L	0.42581	1.335	0.80722	D	1	D	0.63046	0.992	P	0.57152	0.814	T	0.58578	-0.7612	9	0.23302	T	0.38	.	15.602	0.76631	0.0:0.0:0.0:1.0	.	171	O43809	CPSF5_HUMAN	R	171	.	ENSP00000300291:H171R	H	-	2	0	NUDT21	55026202	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.582000	0.82546	2.145000	0.66743	0.477000	0.44152	CAT		TCGA-S4-A8RO-01A-12D-A377-08	NUDT21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256980.3	1	0	1	236	453	0	177	1	1	34	83	0	177	2		0	0	0	0	0	2	1	1	232	441	0	176	2		0	0	0	0	177	2	-20.000000	1	1	0	0		1	1	2	3	2.034749	0	0.680000	2.080000	0.687439	0.990000	9.200000e-01	1.000000	1.000000	0.991122	0.990000	1	9.700000e-01	1.000000
NRN1L	123904	broad.mit.edu	37	16	67920029	67920029	+	Missense_Mutation	SNP	G	G	A			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr16:67920029G>A	ENST00000339176.3	+	3	464	c.365G>A	c.(364-366)cGg>cAg	p.R122Q	NRN1L_ENST00000576147.1_Missense_Mutation_p.G49R|CTC-479C5.10_ENST00000572067.1_lincRNA	NM_198443.1	NP_940845.1	Q496H8	NRN1L_HUMAN	neuritin 1-like			7		Ovarian(137;0.192)			GTGCATGTTCGGGAGCGCGGC	0.667000																								0							SO:0001583	missense			ENST00000339176.3	1	1	hg19	CCDS10850.1	.	.	.	.	.	.	.	.	.	.	G	11.31	1.599853	0.28534	0.0	2.33E-4	ENSG00000188038	ENST00000339176	.	.	.	4.86	-3.54	0.04653	.	1.058750	0.07350	N	0.882262	T	0.10508	0.0257	N	0.01109	-1.01	0.09310	N	1	B	0.15719	0.014	B	0.06405	0.002	T	0.29822	-0.9999	9	0.19147	T	0.46	.	6.5616	0.22489	0.4412:0.2124:0.3464:0.0	.	122	Q496H8	NRN1L_HUMAN	Q	122	.	ENSP00000342411:R122Q	R	+	2	0	NRN1L	66477530	0.010000	0.17322	0.049000	0.19019	0.006000	0.05464	0.003000	0.13083	-0.579000	0.05952	-1.417000	0.01113	CGG		TCGA-S4-A8RO-01A-12D-A377-08	NRN1L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268872.2	1	0	1	27	45	0	32	0	3.234139e-01	1	2	0	32	2		0	0	0	0	0	2	1	1	27	45	0	31	2		0	0	0	0	32	2	-6.860764	1	1	121372	13	39	1	1	2	3	2.034749	0	0.680000	2.080000	0.687439	0.990000	8.100000e-01	1.000000	1.000000	0.981270	0.990000	1	9.600000e-01	1.000000
GPR179	440435	broad.mit.edu	37	17	36485458	36485458	+	Missense_Mutation	SNP	A	A	G			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr17:36485458A>G	ENST00000342292.4	-	11	4014	c.3994T>C	c.(3994-3996)Tcc>Ccc	p.S1332P	GPR179_ENST00000584976.1_5'Flank	NM_001004334.2	NP_001004334.2	Q6PRD1	GP179_HUMAN	G protein-coupled receptor 179			60	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)			GACCCAGGGGACAGACCTCCT	0.607000																								0							SO:0001583	missense			ENST00000342292.4	0	1	hg19	CCDS42308.1	.	.	.	.	.	.	.	.	.	.	A	2.564	-0.301204	0.05495	.	.	ENSG00000188888	ENST00000342292	T	0.53206	0.63	4.74	1.23	0.21249	.	0.407814	0.21212	N	0.078287	T	0.32912	0.0845	L	0.44542	1.39	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.14839	-1.0458	10	0.39692	T	0.17	-4.2878	4.6654	0.12662	0.6483:0.1668:0.185:0.0	.	1332	Q6PRD1	GP179_HUMAN	P	1332	ENSP00000345060:S1332P	ENSP00000345060:S1332P	S	-	1	0	GPR179	33738984	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	0.510000	0.22723	0.854000	0.35336	0.374000	0.22700	TCC		TCGA-S4-A8RO-01A-12D-A377-08	GPR179-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255329.2	0	0	0	5	207	0	60	0	9.128450e-04	0	2	0	60	2		0	0	0	0	0	2	1	9.342993e-01	5	202	0	57	2		0	0	0	0	60	2	-6.856036	1	1	0	0		1	2	2	4	2.154984	1	0.680000	2.080000	0.711400	0.080000	2.000000e-02	1.000000	0.070000	0.205533	0.080000	0	5.000000e-02	0.170000
KRTAP4-3	85290	broad.mit.edu	37	17	39324213	39324213	+	Missense_Mutation	SNP	C	C	T			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr17:39324213C>T	ENST00000391356.2	-	1	211	c.212G>A	c.(211-213)cGc>cAc	p.R71H		NM_033187.1	NP_149443.1	Q9BYR4	KRA43_HUMAN	keratin associated protein 4-3			12		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)		gcagctggggcggcagcaggt	0.637000																								0							SO:0001583	missense			ENST00000391356.2	0	1	hg19	CCDS42331.1	.	.	.	.	.	.	.	.	.	.	.	14.27	2.484619	0.44147	.	.	ENSG00000196156	ENST00000391356	T	0.01495	4.83	4.46	1.32	0.21799	.	.	.	.	.	T	0.01870	0.0059	L	0.54908	1.71	0.09310	N	1	P	0.38335	0.627	B	0.23018	0.043	T	0.44667	-0.9313	9	0.66056	D	0.02	.	8.1078	0.30896	0.0:0.721:0.0:0.279	.	71	Q9BYR4	KRA43_HUMAN	H	71	ENSP00000375151:R71H	ENSP00000375151:R71H	R	-	2	0	KRTAP4-3	36577739	0.000000	0.05858	0.174000	0.22961	0.413000	0.31143	-0.095000	0.11077	0.081000	0.16988	0.609000	0.83330	CGC		TCGA-S4-A8RO-01A-12D-A377-08	KRTAP4-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257784.1	1	0	0	12	25	0	9		0	0	0	0	9	2		0	0	0	0	0	2		0	0	0	0	0	2		0	0	0	0	9	2	-4.420187	1	0	0	0		1	2	2	4	2.154984	1	0.680000	2.080000	0.711400	0.990000	6.300000e-01	1.000000	1.000000	0.945630	0.990000	1	8.400000e-01	1.000000
KRT34	3885	broad.mit.edu	37	17	39537409	39537409	+	Missense_Mutation	SNP	G	G	A			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr17:39537409G>A	ENST00000394001.1	-	3	643	c.613C>T	c.(613-615)Cgc>Tgc	p.R205C		NM_021013.3	NP_066293.2	O76011	KRT34_HUMAN	keratin 34			25		Breast(137;0.000496)			AGGATCCTGCGTATGCTGTTG	0.562000																								0							SO:0001583	missense			ENST00000394001.1	1	1	hg19	CCDS11390.1	.	.	.	.	.	.	.	.	.	.	g	17.97	3.519112	0.64634	2.27E-4	0.0	ENSG00000131737	ENST00000394001;ENST00000251648	.	.	.	5.52	5.52	0.82312	Filament (1);	0.000000	0.64402	D	0.000003	T	0.80019	0.4547	M	0.74881	2.28	0.48341	D	0.999631	D	0.89917	1.0	D	0.85130	0.997	T	0.81852	-0.0742	9	0.87932	D	0	.	18.419	0.90582	0.0:0.0:1.0:0.0	.	205	O76011	KRT34_HUMAN	C	163;205	.	ENSP00000251648:R205C	R	-	1	0	KRT34	36790935	0.995000	0.38212	1.000000	0.80357	0.497000	0.33675	2.210000	0.42816	2.606000	0.88127	0.655000	0.94253	CGC		TCGA-S4-A8RO-01A-12D-A377-08	KRT34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257304.3	1	0	1	112	166	0	66		0	0	0	0	66	2		0	0	0	0	0	2	1	1	110	165	0	65	2		0	0	0	0	66	2	-20.000000	1	1	121412	2	39	1	2	2	4	2.154984	1	0.680000	2.080000	0.711400	0.990000	9.900000e-01	1.000000	1.000000	0.999993	0.990000	1	9.900000e-01	1.000000
PTRF	284119	broad.mit.edu	37	17	40557353	40557353	+	Silent	SNP	C	C	T			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr17:40557353C>T	ENST00000357037.5	-	2	944	c.525G>A	c.(523-525)tcG>tcA	p.S175S		NM_012232.5	NP_036364.2			polymerase I and transcript release factor	p.S175S(1)		17		all_cancers(22;0.00146)|Breast(137;0.00116)|all_epithelial(22;0.0134)			GCAGCGCCTCCGACTCTTTCA	0.647000																								1	Substitution - coding silent(1)						SO:0001819	synonymous_variant			ENST00000357037.5	1	1	hg19	CCDS11425.1																																																																																				TCGA-S4-A8RO-01A-12D-A377-08	PTRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449938.1	1	0	1	177	367	0	101	1	1	26	173	0	101	2		0	0	0	0	0	2	1	1	174	356	0	97	2		0	0	0	0	101	2	-14.659870	1	1	0	0		1	2	2	4	2.154984	1	0.680000	2.080000	0.711400	0.990000	9.300000e-01	1.000000	1.000000	0.994829	0.990000	1	9.900000e-01	1.000000
PLD2	5338	broad.mit.edu	37	17	4712837	4712837	+	Missense_Mutation	SNP	G	G	A			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr17:4712837G>A	ENST00000263088.6	+	7	736	c.605G>A	c.(604-606)cGc>cAc	p.R202H	RP11-81A22.5_ENST00000571067.1_lincRNA|PLD2_ENST00000572940.1_Missense_Mutation_p.R202H	NM_001243108.1|NM_002663.4	NP_001230037.1|NP_002654.3	O14939	PLD2_HUMAN	phospholipase D2			31				Choline(DB00122)	GACTTGGGCCGCAAAGGACTG	0.567000																								0							SO:0001583	missense			ENST00000263088.6	0	1	hg19	CCDS11057.1	.	.	.	.	.	.	.	.	.	.	G	12.45	1.940910	0.34283	.	.	ENSG00000129219	ENST00000263088	T	0.06449	3.3	5.1	0.825	0.18824	.	0.567307	0.19886	N	0.103853	T	0.02610	0.0079	N	0.04508	-0.205	0.19775	N	0.99996	B;B;B	0.21225	0.053;0.041;0.01	B;B;B	0.12156	0.001;0.007;0.002	T	0.48151	-0.9060	10	0.15499	T	0.54	-1.3847	9.5998	0.39596	0.0:0.495:0.426:0.079	.	59;202;202	B7Z905;O14939-2;O14939	.;.;PLD2_HUMAN	H	202	ENSP00000263088:R202H	ENSP00000263088:R202H	R	+	2	0	PLD2	4659801	0.761000	0.28439	0.852000	0.33557	0.645000	0.38454	1.825000	0.39081	0.056000	0.16144	-0.311000	0.09066	CGC		TCGA-S4-A8RO-01A-12D-A377-08	PLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207561.3	0	0	0	5	258	0	93	0	8.680755e-02	0	21	0	93	2		0	0	0	0	0	2	1	9.362356e-01	5	255	0	93	2		0	0	0	0	93	2	-2.064513	0	1	121412	1	36	1	0	1	1	1.467511	1	0.680000	2.080000	0.515152	0.030000	0	0.080000	0.040000	0.043786	0.030000	0	2.000000e-02	0.060000
TP53	7157	broad.mit.edu	37	17	7577094	7577094	+	Missense_Mutation	SNP	G	G	A	rs28934574		TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr17:7577094G>A	ENST00000269305.4	-	8	1033	c.844C>T	c.(844-846)Cgg>Tgg	p.R282W	TP53_ENST00000445888.2_Missense_Mutation_p.R282W|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.R282W|TP53_ENST00000420246.2_Missense_Mutation_p.R282W|TP53_ENST00000359597.4_Missense_Mutation_p.R282W|TP53_ENST00000413465.2_Intron	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	p.R282W(401)|p.R282G(29)|p.0?(8)|p.R282fs*24(4)|p.R282R(3)|p.?(2)|p.D281fs*63(2)|p.D281_R282>EW(2)|p.A276_R283delACPGRDRR(1)|p.D281_R282insXX(1)|p.C275fs*20(1)|p.R282_E287delRRTEEE(1)|p.L265_K305del41(1)|p.D281_R282delDR(1)|p.G279fs*59(1)|p.R280fs*62(1)|p.S269fs*21(1)|p.R282fs*63(1)|p.V272_K292del21(1)|p.C275_R283delCACPGRDRR(1)		24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		Acetylsalicylic acid(DB00945)	TCTGTGCGCCGGTCTCTCCCA	0.557000		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	463	Substitution - Missense(430)|Whole gene deletion(8)|Deletion - In frame(6)|Deletion - Frameshift(5)|Insertion - Frameshift(4)|Substitution - coding silent(3)|Unknown(2)|Complex - frameshift(2)|Complex - compound substitution(2)|Insertion - In frame(1)	GRCh37	CM056413|CM920678	TP53	M	rs28934574	SO:0001583	missense	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	ENST00000269305.4	1	1	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.057525	0.76074	0.0	2.33E-4	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99869	-7.34;-7.34;-7.34;-7.34;-7.34;-7.34	4.75	1.49	0.22878	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99825	0.9922	M	0.89968	3.075	0.58432	A	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;0.998;1.0;0.999	D	0.97713	1.0192	9	0.87932	D	0	-12.0909	8.7508	0.34613	0.0:0.1376:0.5833:0.2792	rs28934574	282;282;282;282	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	W	282;282;282;282;282;271;150	ENSP00000352610:R282W;ENSP00000269305:R282W;ENSP00000398846:R282W;ENSP00000391127:R282W;ENSP00000391478:R282W;ENSP00000425104:R150W	ENSP00000269305:R282W	R	-	1	2	TP53	7517819	1.000000	0.71417	0.327000	0.25402	0.901000	0.52897	4.477000	0.60223	0.174000	0.19809	0.462000	0.41574	CGG		TCGA-S4-A8RO-01A-12D-A377-08	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	1	0	1	50	35	0	28	1	1	61	16	0	28	2	1	1	524	485	0	1785	2	1	1	50	35	0	28	2		0	0	0	0	28	2	-17.795730	1	1	121412	2	36	1	0	1	1	1.467511	1	0.680000	2.080000	0.515152	0.960000	8.300000e-01	1.000000	0.990000	0.953847	0.960000	1	9.000000e-01	0.990000
DSC3	1825	broad.mit.edu	37	18	28610959	28610959	+	Silent	SNP	G	G	A			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr18:28610959G>A	ENST00000360428.4	-	3	414	c.334C>T	c.(334-336)Ctg>Ttg	p.L112L	DSC3_ENST00000434452.1_Silent_p.L112L	NM_001941.3	NP_001932.2	Q14574	DSC3_HUMAN	desmocollin 3			56			OV - Ovarian serous cystadenocarcinoma(10;0.125)		TGTTCTAGCAGCACAGTAACC	0.338000																								0							SO:0001819	synonymous_variant			ENST00000360428.4	1	1	hg19	CCDS32810.1																																																																																				TCGA-S4-A8RO-01A-12D-A377-08	DSC3-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447384.1	1	0	1	100	231	0	81		0	0	0	0	81	2		0	0	0	0	0	2	1	1	100	229	0	80	2		0	0	0	0	81	2	-20.000000	1	1	0	0		1	1	2	3	2.061145	0	0.680000	2.080000	0.689501	0.910000	7.600000e-01	1.000000	1.000000	0.918646	0.910000	1	8.400000e-01	1.000000
KEAP1	9817	broad.mit.edu	37	19	10610147	10610147	+	Missense_Mutation	SNP	G	G	C			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08			G	C	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr19:10610147G>C	ENST00000171111.5	-	2	1110	c.563C>G	c.(562-564)gCc>gGc	p.A188G	KEAP1_ENST00000393623.2_Missense_Mutation_p.A188G|KEAP1_ENST00000588024.1_5'UTR	NM_203500.1	NP_987096.1	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1			92			OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05)	Dimethyl fumarate(DB08908)	AGCGAAGTTGGCGATGCCGAT	0.597000																								0							SO:0001583	missense			ENST00000171111.5	1	1	hg19	CCDS12239.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.980801	0.74474	.	.	ENSG00000079999	ENST00000171111;ENST00000393623	T;T	0.69306	-0.39;-0.39	4.81	4.81	0.61882	BTB/Kelch-associated (2);	0.053770	0.64402	D	0.000001	T	0.76962	0.4061	L	0.53617	1.68	0.80722	D	1	D	0.67145	0.996	D	0.65573	0.936	T	0.79619	-0.1728	10	0.72032	D	0.01	.	15.3825	0.74669	0.0:0.0:1.0:0.0	.	188	Q14145	KEAP1_HUMAN	G	188	ENSP00000171111:A188G;ENSP00000377245:A188G	ENSP00000171111:A188G	A	-	2	0	KEAP1	10471147	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	4.017000	0.57167	2.232000	0.73038	0.561000	0.74099	GCC		TCGA-S4-A8RO-01A-12D-A377-08	KEAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452000.1	1	0	0	38	82	0	33	1	1	41	66	0	33	2		0	0	0	0	0	2	1	1	38	81	0	32	2		0	0	0	0	33	2	-20.000000	1	1	0	0		1	2	2	4	2.177001	1	0.680000	2.080000	0.714897	0.990000	7.900000e-01	1.000000	1.000000	0.971735	0.990000	1	9.200000e-01	1.000000
UNC13A	23025	broad.mit.edu	37	19	17766751	17766751	+	Silent	SNP	G	G	A			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr19:17766751G>A	ENST00000519716.2	-	10	1223	c.1224C>T	c.(1222-1224)ccC>ccT	p.P408P	UNC13A_ENST00000551649.1_Silent_p.P408P|UNC13A_ENST00000252773.7_Silent_p.P408P|UNC13A_ENST00000552293.1_Silent_p.P408P|UNC13A_ENST00000550896.1_Silent_p.P408P|UNC13A_ENST00000428389.2_Silent_p.P496P	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)			61					GCACCTTGTCGGGCGTGGCTG	0.692000																								0							SO:0001819	synonymous_variant			ENST00000519716.2	1	1	hg19	CCDS46013.2																																																																																				TCGA-S4-A8RO-01A-12D-A377-08	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376169.2	1	0	1	22	53	0	10		0	0	0	0	10	2		0	0	0	0	0	2	1	9.999995e-01	21	51	0	10	2		0	0	0	0	10	2	-4.735589	1	1	120118	10	36	1	1	2	3	2.034048	0	0.680000	2.080000	0.687439	0.890000	6.000000e-01	1.000000	1.000000	0.877317	0.890000	1	7.300000e-01	1.000000
FXYD3	5349	broad.mit.edu	37	19	35613737	35613737	+	Missense_Mutation	SNP	G	G	A			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr19:35613737G>A	ENST00000344013.6	+	6	362	c.166G>A	c.(166-168)Gtc>Atc	p.V56I	FXYD3_ENST00000346446.5_Missense_Mutation_p.V56I|FXYD3_ENST00000604621.1_Missense_Mutation_p.V56I|FXYD3_ENST00000603524.1_Missense_Mutation_p.V85I|FXYD3_ENST00000604404.1_Missense_Mutation_p.V56I|FXYD3_ENST00000406242.3_Missense_Mutation_p.V56I|FXYD3_ENST00000406988.1_Missense_Mutation_p.V56I|LGI4_ENST00000493050.1_5'Flank|FXYD3_ENST00000535103.1_Missense_Mutation_p.V113I|FXYD3_ENST00000603181.1_Missense_Mutation_p.V56I|FXYD3_ENST00000604255.1_Missense_Mutation_p.V113I|FXYD3_ENST00000605677.1_Missense_Mutation_p.V56I|FXYD3_ENST00000604804.1_Missense_Mutation_p.V85I|FXYD3_ENST00000435734.2_Missense_Mutation_p.V56I|FXYD3_ENST00000605550.1_Missense_Mutation_p.V56I			Q14802	FXYD3_HUMAN	FXYD domain containing ion transport regulator 3	p.V56L(1)		4	all_lung(56;5.38e-08)|Lung NSC(56;8.61e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.54e-20)|OV - Ovarian serous cystadenocarcinoma(14;1.33e-18)|all cancers(14;4.27e-17)|LUSC - Lung squamous cell carcinoma(66;0.0849)		CATCATCATCGTCATGAGTGA	0.637000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000344013.6	1	1	hg19	CCDS12442.1	.	.	.	.	.	.	.	.	.	.	G	7.337	0.620212	0.14193	.	.	ENSG00000089356	ENST00000406242;ENST00000435734;ENST00000346446;ENST00000344013;ENST00000406988;ENST00000535103	T;T;T;T;T	0.59083	0.29;0.29;0.29;0.29;0.29	4.97	2.77	0.32553	.	0.160135	0.41294	D	0.000906	T	0.24005	0.0581	N	0.02334	-0.595	0.20821	N	0.999848	B;B;B;B	0.33379	0.389;0.41;0.248;0.16	B;B;B;B	0.22386	0.039;0.036;0.024;0.027	T	0.23547	-1.0185	10	0.09084	T	0.74	-1.8921	11.7292	0.51726	0.0:0.6497:0.3503:0.0	.	113;56;56;56	F5H174;F8WB34;Q14802-2;Q14802	.;.;.;FXYD3_HUMAN	I	56;113;56;56;56;113	ENSP00000385412:V56I;ENSP00000328259:V56I;ENSP00000339499:V56I;ENSP00000385200:V56I;ENSP00000443953:V113I	ENSP00000339499:V56I	V	+	1	0	FXYD3	40305577	0.031000	0.19500	0.271000	0.24616	0.012000	0.07955	0.640000	0.24705	0.485000	0.27652	-0.153000	0.13522	GTC		TCGA-S4-A8RO-01A-12D-A377-08	FXYD3-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000468985.1	1	0	1	108	204	0	45	1	1	1139	1443	0	45	2		0	0	0	0	0	2	1	1	109	202	0	43	2		0	0	0	0	45	2	-20.000000	1	1	0	0		1	1	2	3	2.034048	0	0.680000	2.080000	0.687439	0.990000	8.800000e-01	1.000000	1.000000	0.985950	0.990000	1	9.600000e-01	1.000000
HAUS5	23354	broad.mit.edu	37	19	36105981	36105981	+	Missense_Mutation	SNP	G	G	A			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr19:36105981G>A	ENST00000203166.5	+	5	282	c.257G>A	c.(256-258)cGc>cAc	p.R86H	HAUS5_ENST00000379045.2_Missense_Mutation_p.R86H|AC002115.9_ENST00000589603.1_lincRNA	NM_015302.1	NP_056117.1	O94927	HAUS5_HUMAN	HAUS augmin-like complex, subunit 5			16					GCTGTGACCCGCCTGCGGGCA	0.607000																								0							SO:0001583	missense			ENST00000203166.5	0	1	hg19	CCDS42550.1	.	.	.	.	.	.	.	.	.	.	G	8.109	0.778332	0.16120	.	.	ENSG00000249115	ENST00000203166;ENST00000379045	T;T	0.35421	1.31;1.31	4.94	0.373	0.16178	.	0.501507	0.20263	N	0.095838	T	0.32224	0.0822	M	0.67953	2.075	0.09310	N	1	B	0.18013	0.025	B	0.12837	0.008	T	0.28870	-1.0030	10	0.59425	D	0.04	-19.0807	7.3956	0.26934	0.3627:0.0:0.6373:0.0	.	86	O94927	HAUS5_HUMAN	H	86	ENSP00000439056:R86H;ENSP00000444373:R86H	ENSP00000439056:R86H	R	+	2	0	HAUS5	40797821	0.859000	0.29813	0.931000	0.37212	0.070000	0.16714	0.651000	0.24873	-0.066000	0.12998	-0.234000	0.12200	CGC		TCGA-S4-A8RO-01A-12D-A377-08	HAUS5-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459055.2	1	0	1	12	29	0	12	1	9.634036e-01	6	11	0	12	2		0	0	0	0	0	2	1	9.995117e-01	12	28	0	12	2		0	0	0	0	12	2	-20.000000	1	1	120806	2	26	1	1	2	3	2.034048	0	0.680000	2.080000	0.687439	0.900000	5.200000e-01	1.000000	1.000000	0.864858	0.900000	1	6.900000e-01	1.000000
PSG7	5676	broad.mit.edu	37	19	43433817	43433817	+	RNA	SNP	C	C	T			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr19:43433817C>T	ENST00000406070.2	-	0	582				PSG7_ENST00000446844.3_RNA	NM_002783.2	NP_002774.2	Q13046	PSG7_HUMAN	pregnancy specific beta-1-glycoprotein 7 (gene/pseudogene)					Prostate(69;0.00682)			TCACAGCCTCCGTGGCCTCCC	0.532000																								0											ENST00000406070.2	1	1	hg19																																																																																					TCGA-S4-A8RO-01A-12D-A377-08	PSG7-001	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000321431.2	0	0	0	274	584	0	230		0	0	0	0	230	2		0	0	0	0	0	2	1	1	274	579	0	227	2		0	0	0	0	230	2	-18.962320	1	1	121340	1	33	1	1	2	3	2.047076	0	0.680000	2.080000	0.688474	0.960000	8.600000e-01	1.000000	1.000000	0.961279	0.960000	1	9.100000e-01	1.000000
HIF3A	64344	broad.mit.edu	37	19	46807230	46807230	+	Silent	SNP	G	G	A			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr19:46807230G>A	ENST00000377670.4	+	2	133	c.102G>A	c.(100-102)ctG>ctA	p.L34L	HIF3A_ENST00000244303.6_Missense_Mutation_p.C14Y|HIF3A_ENST00000472815.1_Missense_Mutation_p.C14Y|HIF3A_ENST00000300862.3_Silent_p.L32L|RNU6-924P_ENST00000362926.1_RNA|HIF3A_ENST00000420102.2_Missense_Mutation_p.C32Y|HIF3A_ENST00000600383.1_Missense_Mutation_p.C14Y|HIF3A_ENST00000339613.2_5'UTR	NM_152795.3	NP_690008.2	Q9Y2N7	HIF3A_HUMAN	hypoxia inducible factor 3, alpha subunit			33		Ovarian(192;0.00965)|all_neural(266;0.0887)			CCGAGGTGCTGTACCAGCTGG	0.672000																								0							SO:0001819	synonymous_variant			ENST00000377670.4	0	1	hg19	CCDS12681.2	.	.	.	.	.	.	.	.	.	.	G	18.94	3.729761	0.69074	.	.	ENSG00000124440	ENST00000457865;ENST00000244303;ENST00000533145;ENST00000457771;ENST00000420102	T;T	0.67171	-0.16;-0.25	4.97	2.85	0.33270	.	.	.	.	.	T	0.53433	0.1796	.	.	.	0.80722	D	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.08055	0.003;0.001;0.001	T	0.53287	-0.8460	8	0.87932	D	0	.	4.5387	0.12047	0.1824:0.0:0.6419:0.1757	.	32;14;32	F5H884;B4DNA2;B4DSD9	.;.;.	Y	14;14;14;14;32	ENSP00000244303:C14Y;ENSP00000407771:C32Y	ENSP00000244303:C14Y	C	+	2	0	HIF3A	51499070	0.834000	0.29399	1.000000	0.80357	0.998000	0.95712	-0.000000	0.12993	0.811000	0.34303	0.563000	0.77884	TGT		TCGA-S4-A8RO-01A-12D-A377-08	HIF3A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280556.3	0	0	0	3	51	0	10		0	0	0	0	10	2		0	0	0	0	0	2	1	8.066311e-01	3	50	0	10	2		0	0	0	0	10	2	-7.466402	1	1	0	0		1	2	2	4	2.144197	1	0.680000	2.080000	0.709619	0.220000	6.000000e-02	1.000000	0.180000	0.321265	0.220000	0	1.200000e-01	0.440000
LILRA1	11024	broad.mit.edu	37	19	55107243	55107243	+	Silent	SNP	G	G	A			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr19:55107243G>A	ENST00000251372.3	+	6	983	c.801G>A	c.(799-801)caG>caA	p.Q267Q	LILRA1_ENST00000453777.1_Intron|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	p.L268I(1)		47					ACTTCCTCCAGCTCCCTGGCC	0.607000																								1	Substitution - Missense(1)						SO:0001819	synonymous_variant			ENST00000251372.3	1	1	hg19	CCDS12901.1																																																																																				TCGA-S4-A8RO-01A-12D-A377-08	LILRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140807.2	1	0	0	143	232	0	68		0	0	0	0	68	2		0	0	0	0	0	2	1	1	142	232	0	68	2		0	0	0	0	68	2	-20.000000	1	1	0	0		1	2	2	4	2.133410	1	0.680000	2.080000	0.707816	0.990000	9.900000e-01	1.000000	1.000000	0.999964	0.990000	1	9.900000e-01	1.000000
ANKRD34A	284615	broad.mit.edu	37	1	145474036	145474036	+	Silent	SNP	C	C	T			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr1:145474036C>T	ENST00000323397.4	+	4	2001	c.708C>T	c.(706-708)cgC>cgT	p.R236R	RP11-315I20.1_ENST00000600340.1_RNA	NM_001039888.2	NP_001034977.1	Q69YU3	AN34A_HUMAN	ankyrin repeat domain 34A			20	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)				AACCACCACGCCATCCCCCAA	0.622000																								0							SO:0001819	synonymous_variant			ENST00000323397.4	1	1	hg19	CCDS30829.1																																																																																				TCGA-S4-A8RO-01A-12D-A377-08	ANKRD34A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038512.1	1	0	1	164	672	0	124	0	3.364621e-01	1	5	0	124	2		0	0	0	0	0	2	1	1	161	644	0	120	2		0	0	0	0	124	2	-20.000000	1	1	0	0		1	1	3	4	2.762408	1	0.680000	2.080000	0.771624	0.820000	7.000000e-01	1.000000	0.800000	0.855398	0.820000	0	7.500000e-01	1.000000
ANKRD35	148741	broad.mit.edu	37	1	145558485	145558485	+	Silent	SNP	C	C	T			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr1:145558485C>T	ENST00000355594.4	+	6	513	c.426C>T	c.(424-426)caC>caT	p.H142H	ANKRD35_ENST00000544626.1_Missense_Mutation_p.T123M	NM_144698.3	NP_653299.4	Q8N283	ANR35_HUMAN	ankyrin repeat domain 35			47	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)				TGTGTGACCACGAAGCCTTCC	0.542000													Melanoma(9;127 754 22988 51047)											0							SO:0001819	synonymous_variant			ENST00000355594.4	1	1	hg19	CCDS919.1	.	.	.	.	.	.	.	.	.	.	C	13.74	2.326612	0.41197	.	.	ENSG00000198483	ENST00000544626	T	0.15603	2.41	5.09	-7.84	0.01196	.	.	.	.	.	T	0.11281	0.0275	.	.	.	0.19575	N	0.999965	.	.	.	.	.	.	T	0.14559	-1.0468	6	0.72032	D	0.01	-16.9738	16.3209	0.82951	0.0:0.2377:0.0:0.7623	.	.	.	.	M	123	ENSP00000442671:T123M	ENSP00000442671:T123M	T	+	2	0	ANKRD35	144269842	0.000000	0.05858	0.525000	0.27900	0.977000	0.68977	-4.830000	0.00180	-1.784000	0.01272	-0.768000	0.03414	ACG		TCGA-S4-A8RO-01A-12D-A377-08	ANKRD35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038515.1	0	0	1	91	290	0	68		0	0	0	0	68	2		0	0	0	0	0	2	1	1	91	283	0	66	2		0	0	0	0	68	2	-20.000000	1	1	0	0		1	1	3	4	2.762408	1	0.680000	2.080000	0.771624	0.990000	8.200000e-01	1.000000	1.000000	0.967891	0.990000	1	9.100000e-01	1.000000
C1orf105	92346	broad.mit.edu	37	1	172437641	172437641	+	Silent	SNP	C	C	T			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr1:172437641C>T	ENST00000367727.4	+	7	657	c.459C>T	c.(457-459)caC>caT	p.H153H	C1orf105_ENST00000367726.1_3'UTR|C1orf105_ENST00000367725.4_Silent_p.H143H	NM_139240.3	NP_640333.3	O95561	CA105_HUMAN	chromosome 1 open reading frame 105			15					CTGTCTTCCACGGATTACTGA	0.478000																								0							SO:0001819	synonymous_variant			ENST00000367727.4	0	1	hg19	CCDS1301.1																																																																																				TCGA-S4-A8RO-01A-12D-A377-08	C1orf105-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084062.2	0	0	0	23	1249	0	187		0	0	0	0	187	2		0	0	0	0	0	2	1	9.999992e-01	23	1229	0	186	2		0	0	0	0	187	2	-2.491726	0	1	121412	25	50	1	1	3	4	2.693787	1	0.680000	2.080000	0.765945	0.070000	3.000000e-02	1.000000	0.060000	0.297416	0.070000	0	5.000000e-02	1.000000
CRB1	23418	broad.mit.edu	37	1	197411423	197411423	+	Splice_Site	SNP	G	G	A			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr1:197411423G>A	ENST00000367400.3	+	11	4140		c.e11+1		RP11-75C23.1_ENST00000422250.1_RNA|CRB1_ENST00000367399.2_Splice_Site|CRB1_ENST00000544212.1_Splice_Site|CRB1_ENST00000535699.1_Splice_Site|CRB1_ENST00000538660.1_Splice_Site|CRB1_ENST00000367397.1_3'UTR	NM_201253.2	NP_957705.1	P82279	CRUM1_HUMAN	crumbs family member 1, photoreceptor morphogenesis associated			132					CGAGGTGGACGTAAGCAGCCT	0.478000																								0		GRCh37	CS040833	CRB1	S		SO:0001630	splice_region_variant			ENST00000367400.3	0	1	hg19	CCDS1390.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.650712	0.87958	.	.	ENSG00000134376	ENST00000535699;ENST00000538660;ENST00000367400;ENST00000367399;ENST00000544212;ENST00000448952	.	.	.	5.6	5.6	0.85130	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.6189	0.95647	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CRB1	195678046	1.000000	0.71417	0.978000	0.43139	0.971000	0.66376	7.916000	0.87491	2.629000	0.89072	0.591000	0.81541	.		TCGA-S4-A8RO-01A-12D-A377-08	CRB1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086565.2	0	0	0	5	585	0	113		0	0	0	0	113	2		0	0	0	0	0	2	1	9.360915e-01	5	580	0	113	2		0	0	0	0	113	2	-2.219277	0	1	0	0		1	1	2	3	2.035892	0	0.680000	2.080000	0.687439	0.020000	0	1.000000	0.020000	0.083759	0.020000	0	1.000000e-02	0.050000
USH2A	7399	broad.mit.edu	37	1	216144042	216144042	+	Silent	SNP	G	G	A	rs147615382		TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr1:216144042G>A	ENST00000307340.3	-	36	7268	c.6882C>T	c.(6880-6882)taC>taT	p.Y2294Y	USH2A_ENST00000366943.2_Silent_p.Y2294Y	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)			527					GAGCAAATCCGTAAGCACGAT	0.418000										HNSCC(13;0.011)														0							SO:0001819	synonymous_variant			ENST00000307340.3	0	1	hg19	CCDS31025.1																																																																																				TCGA-S4-A8RO-01A-12D-A377-08	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	0	0	0	5	632	0	131		0	0	0	0	131	2		0	0	0	0	0	2	1	9.356635e-01	5	624	0	130	2		0	0	0	0	131	2	-2.620824	1	1	121398	11	44	1	1	2	3	2.041515	0	0.680000	2.080000	0.687439	0.020000	0	1.000000	0.020000	0.081753	0.020000	0	0	0.050000
FMN2	56776	broad.mit.edu	37	1	240256586	240256586	+	Missense_Mutation	SNP	G	G	A			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr1:240256586G>A	ENST00000319653.9	+	1	1407	c.1177G>A	c.(1177-1179)Gcg>Acg	p.A393T		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	p.A536T(1)		178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)		TGACGCCCCCGCGGCCGCTTC	0.726000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000319653.9	1	1	hg19	CCDS31069.2	.	.	.	.	.	.	.	.	.	.	G	3.560	-0.089766	0.07053	.	.	ENSG00000155816	ENST00000319653	T	0.28255	1.62	4.15	-0.182	0.13287	.	0.885835	0.09526	N	0.790278	T	0.15435	0.0372	N	0.12182	0.205	0.09310	N	0.999999	B	0.12630	0.006	B	0.06405	0.002	T	0.24476	-1.0159	10	0.46703	T	0.11	.	5.4466	0.16539	0.2993:0.1625:0.5382:0.0	.	393	Q9NZ56	FMN2_HUMAN	T	393	ENSP00000318884:A393T	ENSP00000318884:A393T	A	+	1	0	FMN2	238323209	0.000000	0.05858	0.001000	0.08648	0.023000	0.10783	-0.165000	0.09968	0.085000	0.17107	-0.379000	0.06801	GCG		TCGA-S4-A8RO-01A-12D-A377-08	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	1	0	0	38	62	0	16	0	0	0	1	0	16	2		0	0	0	0	0	2	1	1	37	62	0	16	2		0	0	0	0	16	2	-20.000000	1	1	0	0		1	1	2	3	2.041515	0	0.680000	2.080000	0.687439	0.990000	8.600000e-01	1.000000	1.000000	0.989597	0.990000	1	9.900000e-01	1.000000
PPP1R16B	26051	broad.mit.edu	37	20	37547257	37547257	+	Missense_Mutation	SNP	C	C	G			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr20:37547257C>G	ENST00000299824.1	+	11	1841	c.1652C>G	c.(1651-1653)gCc>gGc	p.A551G	PPP1R16B_ENST00000373331.2_Missense_Mutation_p.A509G	NM_015568.2	NP_056383.1	Q96T49	PP16B_HUMAN	protein phosphatase 1, regulatory subunit 16B			49		Myeloproliferative disorder(115;0.00878)			AAGTTCAAGGCCCCCATAGAG	0.572000																								0							SO:0001583	missense			ENST00000299824.1	1	1	hg19	CCDS13309.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.01|17.01	3.278924|3.278924	0.59758|0.59758	.|.	.|.	ENSG00000101445|ENSG00000101445	ENST00000299824;ENST00000373331|ENST00000438192	T;T|.	0.77229|.	-0.81;-1.08|.	5.35|5.35	5.35|5.35	0.76521|0.76521	.|.	0.188207|.	0.48767|.	D|.	0.000177|.	T|T	0.64438|0.64438	0.2598|0.2598	M|M	0.61703|0.61703	1.905|1.905	0.32685|0.32685	N|N	0.514994|0.514994	D;D|.	0.61080|.	0.989;0.98|.	P;P|.	0.57101|.	0.813;0.813|.	T|T	0.70619|0.70619	-0.4822|-0.4822	10|5	0.59425|.	D|.	0.04|.	.|.	17.2316|17.2316	0.86985|0.86985	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	509;551|.	E9PFS8;Q96T49|.	.;PP16B_HUMAN|.	G|A	551;509|452	ENSP00000299824:A551G;ENSP00000362428:A509G|.	ENSP00000299824:A551G|.	A|P	+|+	2|1	0|0	PPP1R16B|PPP1R16B	36980671|36980671	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	5.088000|5.088000	0.64486|0.64486	2.498000|2.498000	0.84270|0.84270	0.655000|0.655000	0.94253|0.94253	GCC|CCC		TCGA-S4-A8RO-01A-12D-A377-08	PPP1R16B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079220.2	1	0	1	48	123	0	31	0	4.362384e-01	0	5	0	31	2		0	0	0	0	0	2	1	1	48	122	0	30	2		0	0	0	0	31	2	-20.000000	1	1	0	0		1	1	2	3	2.228471	1	0.680000	2.080000	0.718310	0.980000	7.300000e-01	1.000000	1.000000	0.939121	0.980000	1	8.400000e-01	1.000000
RIMS4	140730	broad.mit.edu	37	20	43386349	43386349	+	Missense_Mutation	SNP	C	C	T	rs141614672	byFrequency	TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr20:43386349C>T	ENST00000372851.3	-	4	479	c.413G>A	c.(412-414)cGg>cAg	p.R138Q	RIMS4_ENST00000541604.2_Missense_Mutation_p.R139Q	NM_001205317.1|NM_182970.3	NP_001192246.1|NP_892015.1	Q9H426	RIMS4_HUMAN	regulating synaptic membrane exocytosis 4	p.R138Q(1)		29		Myeloproliferative disorder(115;0.0122)			TGTCAGTCCCCGAGCCTGGAT	0.597000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000372851.3	1	1	hg19	CCDS13338.1	.	.	.	.	.	.	.	.	.	.	C	34	5.371169	0.95923	0.0	2.33E-4	ENSG00000101098	ENST00000372851;ENST00000541604	T;T	0.69806	-0.43;-0.43	5.76	4.82	0.62117	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.82240	0.4994	M	0.83774	2.66	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.70487	0.95;0.969	D	0.85425	0.1145	10	0.87932	D	0	.	14.8657	0.70412	0.0:0.9312:0.0:0.0688	.	139;138	E1P613;Q9H426	.;RIMS4_HUMAN	Q	138;139	ENSP00000361942:R138Q;ENSP00000439287:R139Q	ENSP00000361942:R138Q	R	-	2	0	RIMS4	42819763	1.000000	0.71417	0.813000	0.32504	0.910000	0.53928	6.089000	0.71384	1.457000	0.47850	0.655000	0.94253	CGG		TCGA-S4-A8RO-01A-12D-A377-08	RIMS4-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000101027.2	1	0	1	109	263	0	57		0	0	0	0	57	2		0	0	0	0	0	2	1	1	107	258	0	55	2		0	0	0	0	57	2	-7.457733	1	1	121412	2	38	1	1	2	3	2.228471	1	0.680000	2.080000	0.718310	0.990000	8.300000e-01	1.000000	1.000000	0.968005	0.990000	1	9.100000e-01	1.000000
ZNF831	128611	broad.mit.edu	37	20	57769643	57769643	+	Missense_Mutation	SNP	G	G	A			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr20:57769643G>A	ENST00000371030.2	+	1	3569	c.3569G>A	c.(3568-3570)cGc>cAc	p.R1190H		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831			125	all_lung(29;0.0085)				TGCCTGAGCCGCAGTGTCCCT	0.647000																								0							SO:0001583	missense			ENST00000371030.2	0	1	hg19	CCDS42894.1	.	.	.	.	.	.	.	.	.	.	G	18.84	3.708768	0.68615	.	.	ENSG00000124203	ENST00000371030	T	0.08896	3.04	5.05	5.05	0.67936	.	0.227351	0.29355	N	0.012399	T	0.21921	0.0528	L	0.52573	1.65	0.31710	N	0.639596	D	0.89917	1.0	D	0.71656	0.974	T	0.03112	-1.1071	10	0.87932	D	0	-16.6053	12.8728	0.57975	0.0814:0.0:0.9186:0.0	.	1190	Q5JPB2	ZN831_HUMAN	H	1190	ENSP00000360069:R1190H	ENSP00000360069:R1190H	R	+	2	0	ZNF831	57203038	0.988000	0.35896	1.000000	0.80357	0.678000	0.39670	3.840000	0.55843	2.352000	0.79861	0.609000	0.83330	CGC		TCGA-S4-A8RO-01A-12D-A377-08	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	0	0	0	5	239	0	50		0	0	0	0	50	2		0	0	0	0	0	2	1	9.318401e-01	5	230	0	49	2		0	0	0	0	50	2	-5.985948	1	1	121046	3	34	1	1	2	3	2.271971	1	0.680000	2.080000	0.721642	0.080000	2.000000e-02	1.000000	0.070000	0.301524	0.080000	0	4.000000e-02	1.000000
SLCO4A1	28231	broad.mit.edu	37	20	61300301	61300301	+	Silent	SNP	C	C	T			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr20:61300301C>T	ENST00000370507.1	+	10	1992	c.1896C>T	c.(1894-1896)atC>atT	p.I632I	RP11-93B14.5_ENST00000433126.1_RNA|RP11-93B14.5_ENST00000411824.1_RNA|SLCO4A1_ENST00000470412.1_3'UTR|SLCO4A1_ENST00000217159.1_Silent_p.I632I|RP11-93B14.5_ENST00000451648.1_RNA			Q96BD0	SO4A1_HUMAN	solute carrier organic anion transporter family, member 4A1			21	Breast(26;3.65e-08)		BRCA - Breast invasive adenocarcinoma(19;2.33e-06)	Benzylpenicillin(DB01053)|Conjugated Estrogens(DB00286)|Dextrothyroxine(DB00509)|Digoxin(DB00390)|Dinoprostone(DB00917)|Estradiol(DB00783)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)	CGGGGCCCATCGCCTTCGGCT	0.662000											OREG0026115	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	Pancreas(168;741 2006 10379 40139 45334)											0							SO:0001819	synonymous_variant			ENST00000370507.1	1	1	hg19	CCDS13501.1																																																																																				TCGA-S4-A8RO-01A-12D-A377-08	SLCO4A1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080048.2	1	0	1	91	110	0	30	1	1	30	29	0	30	2		0	0	0	0	0	2	1	1	91	105	0	29	2		0	0	0	0	30	2	-20.000000	1	1	121276	1	34	1	1	2	3	2.271971	1	0.680000	2.080000	0.721642	0.990000	9.900000e-01	1.000000	1.000000	1.000000	0.990000	1	9.900000e-01	1.000000
TPTE	7179	broad.mit.edu	37	21	10942745	10942745	+	Missense_Mutation	SNP	C	C	A			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr21:10942745C>A	ENST00000361285.4	-	13	1025	c.696G>T	c.(694-696)agG>agT	p.R232S	TPTE_ENST00000298232.7_Missense_Mutation_p.R214S|TPTE_ENST00000342420.5_Missense_Mutation_p.R194S|TPTE_ENST00000415664.2_5'UTR	NM_199261.2	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology			130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)		CAAATCCATCCCTTGTGTATC	0.308000																								0							SO:0001583	missense			ENST00000361285.4	1	1	hg19	CCDS13560.2	.	.	.	.	.	.	.	.	.	.	.	10.06	1.246943	0.22796	.	.	ENSG00000166157	ENST00000298232;ENST00000361285;ENST00000342420	T;T;T	0.29142	1.58;1.58;1.58	2.07	0.162	0.14981	Phosphatase tensin type (1);	0.162065	0.52532	U	0.000067	T	0.24890	0.0604	L	0.46157	1.445	0.26087	N	0.981001	B;B;B	0.33345	0.409;0.409;0.012	B;B;B	0.37422	0.196;0.249;0.008	T	0.16188	-1.0411	10	0.66056	D	0.02	-10.1256	6.055	0.19807	0.0:0.6974:0.0:0.3026	.	194;214;232	P56180-3;P56180-2;P56180	.;.;TPTE_HUMAN	S	214;232;194	ENSP00000298232:R214S;ENSP00000355208:R232S;ENSP00000344441:R194S	ENSP00000298232:R214S	R	-	3	2	TPTE	9964616	0.996000	0.38824	0.396000	0.26296	0.598000	0.36846	0.311000	0.19380	0.028000	0.15324	0.194000	0.17425	AGG		TCGA-S4-A8RO-01A-12D-A377-08	TPTE-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000157413.1	0	0	0	144	740	1	282		0	0	0	1	282	2		0	0	0	0	0	2	1	1	142	727	0	281	2		0	0	0	1	282	2	-3.319936	1	1	121412	1	31	1	0	2	2	1.636674	1	0.680000	2.080000	0.680000	0.470000	4.000000e-01	0.550000	0.480000	0.481077	0.470000	0	4.300000e-01	0.520000
LRP1B	53353	broad.mit.edu	37	2	141264372	141264372	+	Silent	SNP	C	C	T	rs139084384	byFrequency	TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr2:141264372C>T	ENST00000389484.3	-	53	9485	c.8514G>A	c.(8512-8514)ccG>ccA	p.P2838P		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B			606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)			TACCACACTGCGGTGACTCAT	0.383000										TSP Lung(27;0.18)			Colon(99;50 2074 2507 20106)											0							SO:0001819	synonymous_variant			ENST00000389484.3	1	0	hg19	CCDS2182.1																																																																																				TCGA-S4-A8RO-01A-12D-A377-08	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	1	0	1	184	517	0	176		0	0	0	0	176	2		0	0	0	0	0	2	1	1	180	510	0	176	2		0	0	0	0	176	2	-2.598642	1	1	121412	152	56	1	1	2	3	2.024125	0	0.680000	2.080000	0.686397	0.780000	6.800000e-01	1.000000	0.790000	0.799164	0.780000	0	7.300000e-01	0.850000
MYT1L	23040	broad.mit.edu	37	2	1983497	1983497	+	Missense_Mutation	SNP	C	C	A			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr2:1983497C>A	ENST00000399161.2	-	6	800	c.53G>T	c.(52-54)cGa>cTa	p.R18L	MYT1L_ENST00000428368.2_Missense_Mutation_p.R18L	NM_015025.2	NP_055840.2	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like			97	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)			GGACATACCTCGAACCCCTTT	0.582000																								0							SO:0001583	missense			ENST00000399161.2	1	1	hg19		.	.	.	.	.	.	.	.	.	.	C	22.7	4.324853	0.81580	.	.	ENSG00000186487	ENST00000399161;ENST00000295067;ENST00000428368	T;T	0.56444	0.46;0.46	5.1	5.1	0.69264	.	0.000000	0.47852	D	0.000207	T	0.69251	0.3090	L	0.54323	1.7	0.58432	D	0.999995	D;D	0.63046	0.987;0.992	D;D	0.70487	0.931;0.969	T	0.71656	-0.4527	10	0.72032	D	0.01	-19.3941	18.8902	0.92397	0.0:1.0:0.0:0.0	.	18;18	Q9UL68;Q9UL68-4	MYT1L_HUMAN;.	L	18	ENSP00000382114:R18L;ENSP00000396103:R18L	ENSP00000295067:R18L	R	-	2	0	MYT1L	1962504	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	6.591000	0.74090	2.539000	0.85634	0.591000	0.81541	CGA		TCGA-S4-A8RO-01A-12D-A377-08	MYT1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000322493.1	1	0	1	37	115	0	26	0	0	0	1	0	26	2		0	0	0	0	0	2	1	1	37	114	0	26	2		0	0	0	0	26	2	-20.000000	1	1	0	0		1	1	2	3	2.047543	0	0.680000	2.080000	0.688474	0.740000	5.400000e-01	1.000000	0.740000	0.759420	0.740000	0	6.300000e-01	0.880000
WNT6	7475	broad.mit.edu	37	2	219735855	219735855	+	Missense_Mutation	SNP	G	G	A			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr2:219735855G>A	ENST00000233948.3	+	2	404	c.187G>A	c.(187-189)Gca>Aca	p.A63T	WNT6_ENST00000486233.1_Intron	NM_006522.3	NP_006513.1	Q9Y6F9	WNT6_HUMAN	wingless-type MMTV integration site family, member 6			4		Renal(207;0.0474)			GGAAGTGGTGGCAGAGCTAGC	0.682000																								0							SO:0001583	missense			ENST00000233948.3	1	1	hg19	CCDS2425.1	.	.	.	.	.	.	.	.	.	.	g	12.69	2.013700	0.35511	.	.	ENSG00000115596	ENST00000233948	T	0.76448	-1.02	5.17	5.17	0.71159	.	0.451424	0.24781	N	0.035645	T	0.63581	0.2523	L	0.31926	0.97	0.24988	N	0.991557	B	0.16396	0.017	B	0.19391	0.025	T	0.46386	-0.9195	10	0.14252	T	0.57	.	7.7483	0.28881	0.0881:0.1792:0.7326:0.0	.	63	Q9Y6F9	WNT6_HUMAN	T	63	ENSP00000233948:A63T	ENSP00000233948:A63T	A	+	1	0	WNT6	219444099	0.948000	0.32251	0.996000	0.52242	0.887000	0.51463	1.737000	0.38197	2.407000	0.81776	0.586000	0.80456	GCA		TCGA-S4-A8RO-01A-12D-A377-08	WNT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256727.2	1	0	1	302	298	0	66		0	0	0	0	66	2		0	0	0	0	0	2	1	1	300	294	0	62	2		0	0	0	0	66	2	-20.000000	1	1	0	0		1	1	2	3	2.532077	1	0.680000	2.080000	0.750429	0.990000	9.900000e-01	1.000000	1.000000	1.000000	0.990000	1	9.900000e-01	1.000000
AGXT	189	broad.mit.edu	37	2	241817502	241817502	+	Missense_Mutation	SNP	G	G	A			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr2:241817502G>A	ENST00000307503.3	+	10	1393	c.1006G>A	c.(1006-1008)Gtc>Atc	p.V336I		NM_000030.2	NP_000021.1	P21549	SPYA_HUMAN	alanine-glyoxylate aminotransferase	p.V336I(1)		18		all_epithelial(40;1.61e-15)|Breast(86;2.35e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|Lung NSC(271;0.094)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Glycine(DB00145)|L-Alanine(DB00160)|L-Serine(DB00133)	GAGAGACATCGTCAGCTACGT	0.617000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000307503.3	1	1	hg19	CCDS2543.1	.	.	.	.	.	.	.	.	.	.	G	3.824	-0.037151	0.07497	.	.	ENSG00000172482	ENST00000307503	D	0.93547	-3.24	4.02	1.11	0.20524	Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);Aminotransferase, class V/Cysteine desulfurase (1);	0.923809	0.09133	N	0.844131	D	0.86460	0.5938	L	0.41573	1.285	0.09310	N	1	B;B	0.32338	0.365;0.109	B;B	0.22386	0.039;0.018	T	0.72487	-0.4278	10	0.19147	T	0.46	-28.2281	6.537	0.22359	0.4922:0.0:0.5077:0.0	.	214;336	Q9UJX1;P21549	.;SPYA_HUMAN	I	336	ENSP00000302620:V336I	ENSP00000302620:V336I	V	+	1	0	AGXT	241466175	0.000000	0.05858	0.445000	0.26908	0.097000	0.18754	0.572000	0.23684	0.294000	0.22547	0.563000	0.77884	GTC		TCGA-S4-A8RO-01A-12D-A377-08	AGXT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257186.1	1	0	1	53	48	0	23	0	0	1	0	0	23	2		0	0	0	0	0	2	1	1	52	47	0	23	2		0	0	0	0	23	2	-20.000000	1	1	121410	3	36	1	0	1	1	1.295188	1	0.680000	2.080000	0.515152	0.930000	7.900000e-01	1.000000	0.990000	0.930125	0.930000	1	8.600000e-01	0.990000
CRIM1	51232	broad.mit.edu	37	2	36704145	36704145	+	Missense_Mutation	SNP	G	G	A			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr2:36704145G>A	ENST00000280527.2	+	6	1472	c.1105G>A	c.(1105-1107)Gcc>Acc	p.A369T		NM_016441.2	NP_057525.1	Q9NZV1	CRIM1_HUMAN	cysteine rich transmembrane BMP regulator 1 (chordin-like)			45		all_hematologic(82;0.131)|Acute lymphoblastic leukemia(82;0.154)			CTGCTTCACCGCCCAGTGTGG	0.483000																								0							SO:0001583	missense			ENST00000280527.2	0	1	hg19	CCDS1783.1	.	.	.	.	.	.	.	.	.	.	G	32	5.175054	0.94807	.	.	ENSG00000150938	ENST00000280527	T	0.71579	-0.58	5.93	5.93	0.95920	von Willebrand factor, type C (4);	0.000000	0.85682	D	0.000000	T	0.72558	0.3475	N	0.14661	0.345	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.67169	-0.5738	10	0.14656	T	0.56	-18.4323	19.3421	0.94347	0.0:0.0:1.0:0.0	.	369	Q9NZV1	CRIM1_HUMAN	T	369	ENSP00000280527:A369T	ENSP00000280527:A369T	A	+	1	0	CRIM1	36557649	1.000000	0.71417	0.982000	0.44146	0.988000	0.76386	9.714000	0.98744	2.826000	0.97356	0.655000	0.94253	GCC		TCGA-S4-A8RO-01A-12D-A377-08	CRIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216878.2	0	0	0	5	338	0	81	0	5.081038e-02	0	20	0	81	2		0	0	0	0	0	2	1	9.350545e-01	6	331	0	79	2		0	0	0	0	81	2	-2.829005	1	1	121412	1	28	1	1	2	3	2.047543	0	0.680000	2.080000	0.688474	0.040000	0	1.000000	0.040000	0.113295	0.040000	0	2.000000e-02	0.080000
GFPT1	2673	broad.mit.edu	37	2	69556893	69556893	+	Missense_Mutation	SNP	G	G	A			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr2:69556893G>A	ENST00000357308.4	-	16	1698	c.1520C>T	c.(1519-1521)gCc>gTc	p.A507V	GFPT1_ENST00000361060.5_Missense_Mutation_p.A489V	NM_001244710.1	NP_001231639.1	Q06210	GFPT1_HUMAN	glutamine--fructose-6-phosphate transaminase 1			12					CATCATAAGGGCAAACATCAC	0.408000																								0							SO:0001583	missense			ENST00000357308.4	0	1	hg19	CCDS58713.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.875075	0.91664	.	.	ENSG00000198380	ENST00000357308;ENST00000361060	T;T	0.62941	-0.01;-0.01	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	T	0.79673	0.4486	M	0.86268	2.805	0.80722	D	1	D	0.65815	0.995	P	0.59761	0.863	T	0.82959	-0.0198	10	0.87932	D	0	-11.8633	18.081	0.89441	0.0:0.0:1.0:0.0	.	489	Q06210-2	.	V	507;489	ENSP00000349860:A507V;ENSP00000354347:A489V	ENSP00000349860:A507V	A	-	2	0	GFPT1	69410397	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.388000	0.59633	2.758000	0.94735	0.563000	0.77884	GCC		TCGA-S4-A8RO-01A-12D-A377-08	GFPT1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		0	0	0	4	186	0	43	0	3.043414e-01	0	43	0	43	2		0	0	0	0	0	2	1	8.887550e-01	4	184	0	42	2		0	0	0	0	43	2	-2.831103	1	1	0	0		1	0	1	1	1.369433	1	0.680000	2.080000	0.515152	0.040000	1.000000e-02	0.100000	0.040000	0.050286	0.040000	0	2.000000e-02	0.070000
MED12L	116931	broad.mit.edu	37	3	151075109	151075109	+	Missense_Mutation	SNP	C	C	T			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr3:151075109C>T	ENST00000474524.1	+	18	2703	c.2665C>T	c.(2665-2667)Cgc>Tgc	p.R889C	MED12L_ENST00000273432.4_Missense_Mutation_p.R749C|P2RY12_ENST00000302632.3_Intron	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like			128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)		TGTTCTCAGGCGCTATCACAG	0.453000																								0							SO:0001583	missense			ENST00000474524.1	1	1	hg19	CCDS33876.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.953030	0.73902	2.27E-4	0.0	ENSG00000144893	ENST00000474524;ENST00000273432	T;T	0.79454	-1.27;-1.27	5.3	4.42	0.53409	.	0.000000	0.85682	D	0.000000	D	0.85418	0.5692	L	0.60455	1.87	0.80722	D	1	D;D;D	0.89917	1.0;0.997;0.995	D;P;P	0.72982	0.979;0.616;0.635	D	0.86975	0.2100	10	0.72032	D	0.01	-26.0088	15.3411	0.74296	0.141:0.859:0.0:0.0	.	749;889;889	F8WAE6;Q86YW9-4;Q86YW9	.;.;MD12L_HUMAN	C	889;749	ENSP00000417235:R889C;ENSP00000273432:R749C	ENSP00000273432:R749C	R	+	1	0	MED12L	152557799	1.000000	0.71417	0.866000	0.34008	0.957000	0.61999	2.622000	0.46427	1.336000	0.45506	-0.169000	0.13324	CGC		TCGA-S4-A8RO-01A-12D-A377-08	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	1	0	1	145	308	0	88		0	0	0	0	88	2		0	0	0	0	0	2	1	1	145	303	0	88	2		0	0	0	0	88	2	-20.000000	1	1	121412	1	36	1	1	2	3	1.966254	0	0.680000	2.080000	0.681084	0.940000	8.100000e-01	1.000000	1.000000	0.938448	0.940000	1	8.700000e-01	1.000000
PROS1	5627	broad.mit.edu	37	3	93611912	93611912	+	Nonsense_Mutation	SNP	G	G	C			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08			G	C	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr3:93611912G>C	ENST00000394236.3	-	10	1336	c.1020C>G	c.(1018-1020)taC>taG	p.Y340*	PROS1_ENST00000407433.1_Nonsense_Mutation_p.Y209*	NM_000313.3	NP_000304.2	P07225	PROS_HUMAN	protein S (alpha)			46				Drotrecogin alfa(DB00055)|Menadione(DB00170)|Sodium Tetradecyl Sulfate(DB00464)	TAGATTCTGCGTACAGTATCA	0.393000																								0							SO:0001587	stop_gained			ENST00000394236.3	0	1	hg19	CCDS2923.1	.	.	.	.	.	.	.	.	.	.	G	36	5.885622	0.97068	.	.	ENSG00000184500	ENST00000394236;ENST00000407433	.	.	.	4.47	2.05	0.26809	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.4211	0.27073	0.7526:0.0:0.2474:0.0	.	.	.	.	X	340;209	.	ENSP00000377783:Y340X	Y	-	3	2	PROS1	95094602	1.000000	0.71417	0.997000	0.53966	0.557000	0.35523	0.858000	0.27845	0.263000	0.21812	-0.324000	0.08512	TAC		TCGA-S4-A8RO-01A-12D-A377-08	PROS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317762.1	1	0	1	60	113	0	46	1	9.999993e-01	2	44	0	46	2		0	0	0	0	0	2	1	1	59	110	0	46	2		0	0	0	0	46	2	-20.000000	1	1	0	0		1	1	2	3	1.966254	0	0.680000	2.080000	0.681084	0.990000	8.100000e-01	1.000000	1.000000	0.969547	0.990000	1	9.100000e-01	1.000000
OR5H1	26341	broad.mit.edu	37	3	97852022	97852022	+	Nonsense_Mutation	SNP	G	G	T			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr3:97852022G>T	ENST00000354565.2	+	1	481	c.481G>T	c.(481-483)Gga>Tga	p.G161*	RP11-343D2.11_ENST00000508964.1_RNA	NM_001005338.1	NP_001005338.1	A6NKK0	OR5H1_HUMAN	olfactory receptor, family 5, subfamily H, member 1			34					AATCCATGAAGGATTTTTATT	0.358000																								0							SO:0001587	stop_gained			ENST00000354565.2	0	1	hg19	CCDS33797.1	.	.	.	.	.	.	.	.	.	.	G	7.459	0.644345	0.14451	.	.	ENSG00000231192	ENST00000354565	.	.	.	3.57	2.68	0.31781	.	0.626401	0.13894	N	0.355411	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.34782	T	0.22	.	8.4928	0.33110	0.121:0.0:0.879:0.0	.	.	.	.	X	161	.	ENSP00000346575:G161X	G	+	1	0	OR5H1	99334712	0.000000	0.05858	0.005000	0.12908	0.014000	0.08584	-0.384000	0.07389	0.683000	0.31428	0.195000	0.17529	GGA		TCGA-S4-A8RO-01A-12D-A377-08	OR5H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359100.2	0	0	0	39	385	0	177		0	0	0	0	177	2		0	0	0	0	0	2	1	1	30	332	0	227	2		0	0	0	0	177	2	-3.318794	1	1	0	0		1	1	2	3	1.966254	0	0.680000	2.080000	0.681084	0.270000	1.900000e-01	0.360000	0.270000	0.276802	0.270000	0	2.200000e-01	0.320000
OR5H14	403273	broad.mit.edu	37	3	97868710	97868710	+	Nonsense_Mutation	SNP	G	G	T			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr3:97868710G>T	ENST00000437310.1	+	1	541	c.481G>T	c.(481-483)Gga>Tga	p.G161*	RP11-343D2.11_ENST00000508964.1_RNA	NM_001005514.1	NP_001005514.1	A6NHG9	O5H14_HUMAN	olfactory receptor, family 5, subfamily H, member 14			31					AATCCATGAAGGATTTTTATT	0.353000																								0							SO:0001587	stop_gained			ENST00000437310.1	0	1	hg19	CCDS33798.1	.	.	.	.	.	.	.	.	.	.	g	10.51	1.369165	0.24771	.	.	ENSG00000236032	ENST00000437310	.	.	.	2.49	-4.97	0.03029	.	0.899723	0.09201	N	0.834639	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.31617	T	0.26	.	1.2356	0.01952	0.3199:0.1452:0.3874:0.1475	.	.	.	.	X	161	.	ENSP00000401706:G161X	G	+	1	0	OR5H14	99351400	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.434000	0.01021	-1.909000	0.01085	-1.051000	0.02340	GGA		TCGA-S4-A8RO-01A-12D-A377-08	OR5H14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359112.1	0	0	0	9	814	0	260		0	0	0	0	260	2		0	0	0	0	0	2	1	9.937334e-01	9	799	0	260	2		0	0	0	0	260	2	-2.213149	0	1	0	0		1	1	2	3	1.966254	0	0.680000	2.080000	0.681084	0.030000	0	0.070000	0.040000	0.035617	0.030000	0	1.000000e-02	0.050000
KCTD8	386617	broad.mit.edu	37	4	44177058	44177058	+	Missense_Mutation	SNP	G	G	A			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr4:44177058G>A	ENST00000360029.3	-	2	1454	c.1171C>T	c.(1171-1173)Cgc>Tgc	p.R391C		NM_198353.2	NP_938167.1	Q6ZWB6	KCTD8_HUMAN	potassium channel tetramerization domain containing 8			41					TTAGAGGGGCGATCCAATGTT	0.507000										HNSCC(17;0.042)														0							SO:0001583	missense			ENST00000360029.3	0	1	hg19	CCDS3467.1	.	.	.	.	.	.	.	.	.	.	G	11.87	1.768485	0.31320	.	.	ENSG00000183783	ENST00000360029	T	0.44083	0.93	4.56	3.68	0.42216	.	0.000000	0.46758	D	0.000275	T	0.50939	0.1645	L	0.36672	1.1	0.49582	D	0.999805	D	0.89917	1.0	D	0.64595	0.927	T	0.54655	-0.8261	10	0.87932	D	0	.	12.9862	0.58594	0.0:0.0:0.8317:0.1682	.	391	Q6ZWB6	KCTD8_HUMAN	C	391	ENSP00000353129:R391C	ENSP00000353129:R391C	R	-	1	0	KCTD8	43871815	1.000000	0.71417	0.995000	0.50966	0.196000	0.23810	3.014000	0.49590	1.202000	0.43218	0.650000	0.86243	CGC		TCGA-S4-A8RO-01A-12D-A377-08	KCTD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216868.1	0	0	0	6	515	0	162		0	0	0	0	162	2		0	0	0	0	0	2	1	9.632236e-01	6	506	0	159	2		0	0	0	0	162	2	-2.390467	0	1	121412	4	40	1	1	2	3	1.968126	0	0.680000	2.080000	0.681084	0.030000	0	0.080000	0.040000	0.039083	0.030000	0	1.000000e-02	0.060000
PCDHB7	56129	broad.mit.edu	37	5	140553979	140553979	+	Silent	SNP	C	C	T			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr5:140553979C>T	ENST00000231137.3	+	1	1737	c.1563C>T	c.(1561-1563)taC>taT	p.Y521Y		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)		CCCTGGACTACGAGGCCCTGC	0.711000																								0							SO:0001819	synonymous_variant			ENST00000231137.3	1	1	hg19	CCDS4249.1																																																																																				TCGA-S4-A8RO-01A-12D-A377-08	PCDHB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251803.2	1	0	1	47	388	0	91	0	1.346715e-01	0	6	0	91	2		0	0	0	0	0	2	1	1	44	373	0	90	2		0	0	0	0	91	2	-16.516610	1	1	121412	1	34	1	1	2	3	1.999080	0	0.680000	2.080000	0.684294	0.320000	2.300000e-01	1.000000	0.320000	0.346475	0.320000	0	2.700000e-01	0.380000
PCDH1	5097	broad.mit.edu	37	5	141248263	141248263	+	Silent	SNP	G	G	A			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr5:141248263G>A	ENST00000394536.3	-	2	913	c.774C>T	c.(772-774)ccC>ccT	p.P258P	PCDH1_ENST00000503492.1_Silent_p.P258P|PCDH1_ENST00000511044.1_5'Flank|PCDH1_ENST00000456271.1_Silent_p.P246P|PCDH1_ENST00000287008.3_Silent_p.P258P|PCDH1_ENST00000536585.1_Silent_p.P236P	NM_001278613.1|NM_001278615.1	NP_001265542.1|NP_001265544.1	Q08174	PCDH1_HUMAN	protocadherin 1			51		Lung NSC(810;0.027)|all_lung(500;0.0321)|all_hematologic(541;0.0433)|Prostate(461;0.0453)|Breast(839;0.128)|Lung SC(612;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		TGGCGCGTGGGGGGCTGCCGC	0.607000													Ovarian(132;1609 1739 4190 14731 45037)											0							SO:0001819	synonymous_variant			ENST00000394536.3	1	1	hg19	CCDS43375.1																																																																																				TCGA-S4-A8RO-01A-12D-A377-08	PCDH1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251862.1	1	0	1	46	101	0	41	1	9.999999e-01	24	37	0	41	2		0	0	0	0	0	2	1	1	45	100	0	40	2		0	0	0	0	41	2	-6.450983	1	1	0	0		1	1	2	3	1.999080	0	0.680000	2.080000	0.684294	0.930000	7.100000e-01	1.000000	1.000000	0.918823	0.930000	1	8.200000e-01	1.000000
IRX2	153572	broad.mit.edu	37	5	2749835	2749835	+	Missense_Mutation	SNP	C	C	T			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr5:2749835C>T	ENST00000382611.6	-	2	564	c.316G>A	c.(316-318)Gcg>Acg	p.A106T	C5orf38_ENST00000505778.1_5'Flank|C5orf38_ENST00000334000.3_5'Flank|IRX2_ENST00000302057.5_Missense_Mutation_p.A106T|C5orf38_ENST00000457752.2_5'Flank|C5orf38_ENST00000397835.4_5'Flank|IRX2_ENST00000502957.1_5'UTR|C5orf38_ENST00000515640.1_5'Flank	NM_001134222.1	NP_001127694.1	Q9BZI1	IRX2_HUMAN	iroquois homeobox 2			26					GGGTAGGCCGCGCTGCCGTAC	0.662000																								0							SO:0001583	missense			ENST00000382611.6	1	1	hg19	CCDS3868.1	.	.	.	.	.	.	.	.	.	.	C	17.75	3.467539	0.63625	.	.	ENSG00000170561	ENST00000382611;ENST00000302057;ENST00000502957	T;T;T	0.66280	-0.2;-0.2;-0.15	4.85	3.96	0.45880	Homeodomain-like (1);	0.108027	0.64402	D	0.000004	T	0.40448	0.1117	N	0.17474	0.49	0.42845	D	0.994069	B	0.32382	0.368	B	0.20184	0.028	T	0.35968	-0.9767	10	0.21540	T	0.41	-22.7679	13.2911	0.60272	0.0:0.7288:0.2712:0.0	.	106	Q9BZI1	IRX2_HUMAN	T	106;106;13	ENSP00000372056:A106T;ENSP00000307006:A106T;ENSP00000426151:A13T	ENSP00000307006:A106T	A	-	1	0	IRX2	2802835	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.500000	0.60387	2.239000	0.73571	0.655000	0.94253	GCG		TCGA-S4-A8RO-01A-12D-A377-08	IRX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206749.2	1	0	1	85	160	0	52	0	2.800953e-01	0	3	0	52	2		0	0	0	0	0	2	1	1	83	159	0	52	2		0	0	0	0	52	2	-20.000000	1	1	0	0		1	1	2	3	1.969744	0	0.680000	2.080000	0.681084	0.990000	8.400000e-01	1.000000	1.000000	0.975774	0.990000	1	9.300000e-01	1.000000
AP3B1	8546	broad.mit.edu	37	5	77436974	77436974	+	Missense_Mutation	SNP	G	G	C			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08			G	C	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr5:77436974G>C	ENST00000255194.6	-	15	1818	c.1643C>G	c.(1642-1644)tCc>tGc	p.S548C	AP3B1_ENST00000519295.1_Missense_Mutation_p.S499C	NM_001271769.1	NP_001258698.1	O00203	AP3B1_HUMAN	adaptor-related protein complex 3, beta 1 subunit			39		all_lung(232;0.000397)|Lung NSC(167;0.00106)|Ovarian(174;0.0105)|Prostate(461;0.215)			CACCTGTTTGGAGTTGGTTAA	0.408000									Hermansky-Pudlak syndrome															0							SO:0001583	missense	Familial Cancer Database	HPS, HPS1-8	ENST00000255194.6	1	1	hg19	CCDS4041.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.686301	0.88639	.	.	ENSG00000132842	ENST00000255194;ENST00000519295;ENST00000535760;ENST00000535667	T;T	0.14266	2.52;2.52	5.63	5.63	0.86233	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.41926	0.1180	M	0.79258	2.445	0.80722	D	1	D	0.76494	0.999	D	0.74023	0.982	T	0.29579	-1.0007	10	0.87932	D	0	-8.1557	19.6633	0.95882	0.0:0.0:1.0:0.0	.	548	O00203	AP3B1_HUMAN	C	548;499;548;452	ENSP00000255194:S548C;ENSP00000430597:S499C	ENSP00000255194:S548C	S	-	2	0	AP3B1	77472730	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.864000	0.99589	2.638000	0.89438	0.655000	0.94253	TCC		TCGA-S4-A8RO-01A-12D-A377-08	AP3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000225548.2	1	0	1	89	235	0	93	1	9.997728e-01	15	21	0	93	2		0	0	0	0	0	2	1	1	89	232	0	91	2		0	0	0	0	93	2	-6.497701	1	1	121410	1	35	1	1	2	3	1.969744	0	0.680000	2.080000	0.681084	0.800000	6.600000e-01	0.960000	0.810000	0.813388	0.800000	0	7.300000e-01	0.890000
SYCP2L	221711	broad.mit.edu	37	6	10894138	10894138	+	Silent	SNP	A	A	T			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr6:10894138A>T	ENST00000283141.6	+	3	413	c.117A>T	c.(115-117)ggA>ggT	p.G39G	SYCP2L_ENST00000543878.1_5'UTR|RP11-637O19.3_ENST00000480294.1_3'UTR	NM_001040274.2	NP_001035364.2	Q5T4T6	SYC2L_HUMAN	synaptonemal complex protein 2-like			36	Breast(50;0.0838)|Ovarian(93;0.107)	all_hematologic(90;0.135)	Epithelial(50;0.239)		ATGATAAAGGATTTCAGAAAA	0.299000																								0							SO:0001819	synonymous_variant			ENST00000283141.6	1	1	hg19	CCDS43423.1																																																																																				TCGA-S4-A8RO-01A-12D-A377-08	SYCP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039845.3	1	0	1	47	73	0	56		0	0	0	0	56	2		0	0	0	0	0	2	1	1	47	72	0	54	2		0	0	0	0	56	2	-20.000000	1	1	0	0		1	1	2	3	2.028779	0	0.680000	2.080000	0.686397	0.990000	9.200000e-01	1.000000	1.000000	0.995110	0.990000	1	9.900000e-01	1.000000
IGF2R	3482	broad.mit.edu	37	6	160465585	160465585	+	Missense_Mutation	SNP	C	C	T			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr6:160465585C>T	ENST00000356956.1	+	13	1809	c.1661C>T	c.(1660-1662)tCt>tTt	p.S554F		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor			95		Breast(66;0.000777)|Ovarian(120;0.0305)		Mecasermin(DB01277)	TTTATTTCCTCTCCCATGAAA	0.348000																								0							SO:0001583	missense			ENST00000356956.1	0	1	hg19	CCDS5273.1	.	.	.	.	.	.	.	.	.	.	C	18.83	3.706258	0.68615	.	.	ENSG00000197081	ENST00000356956	T	0.02656	4.21	5.91	5.91	0.95273	Mannose-6-phosphate receptor, binding (1);	0.210963	0.51477	D	0.000082	T	0.12008	0.0292	M	0.82517	2.595	0.53688	D	0.999974	D	0.58620	0.983	P	0.62649	0.905	T	0.00583	-1.1659	10	0.66056	D	0.02	-9.3461	20.2985	0.98592	0.0:1.0:0.0:0.0	.	554	P11717	MPRI_HUMAN	F	554	ENSP00000349437:S554F	ENSP00000349437:S554F	S	+	2	0	IGF2R	160385575	1.000000	0.71417	0.927000	0.36925	0.330000	0.28571	5.766000	0.68843	2.793000	0.96121	0.655000	0.94253	TCT		TCGA-S4-A8RO-01A-12D-A377-08	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	0	0	0	6	209	0	61	0	1.624572e-01	1	21	0	61	2		0	0	0	0	0	2	1	9.645928e-01	6	207	0	59	2		0	0	0	0	61	2	-3.645305	1	1	0	0		1	1	2	3	1.997743	0	0.680000	2.080000	0.684294	0.080000	3.000000e-02	1.000000	0.080000	0.121988	0.080000	0	5.000000e-02	0.140000
C6orf118	168090	broad.mit.edu	37	6	165715133	165715133	+	Silent	SNP	G	G	A			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr6:165715133G>A	ENST00000230301.8	-	2	698	c.678C>T	c.(676-678)ctC>ctT	p.L226L	C6orf118_ENST00000543069.1_Silent_p.L122L	NM_144980.3	NP_659417.2	Q5T5N4	CF118_HUMAN	chromosome 6 open reading frame 118			40		Breast(66;6.27e-05)|Ovarian(120;0.0228)|Prostate(117;0.0906)|all_neural(5;0.157)			CTTGCTTGGCGAGCACTTCCT	0.622000																								0							SO:0001819	synonymous_variant			ENST00000230301.8	1	1	hg19	CCDS5288.1																																																																																				TCGA-S4-A8RO-01A-12D-A377-08	C6orf118-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043026.1	1	0	1	73	191	0	53		0	0	0	0	53	2		0	0	0	0	0	2	1	1	73	190	0	53	2		0	0	0	0	53	2	-6.139397	1	1	0	0		1	1	2	3	1.997743	0	0.680000	2.080000	0.684294	0.820000	6.600000e-01	1.000000	0.820000	0.832202	0.820000	0	7.400000e-01	0.920000
RBM24	221662	broad.mit.edu	37	6	17283114	17283114	+	Missense_Mutation	SNP	G	G	A			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr6:17283114G>A	ENST00000379052.5	+	2	483	c.247G>A	c.(247-249)Gtg>Atg	p.V83M	RBM24_ENST00000318204.5_Missense_Mutation_p.V38M|RBM24_ENST00000425446.2_Missense_Mutation_p.V25M	NM_001143942.1	NP_001137414.1	Q9BX46	RBM24_HUMAN	RNA binding motif protein 24			13	Breast(50;0.0615)|Ovarian(93;0.0733)	all_hematologic(90;0.062)	all cancers(50;0.131)|Epithelial(50;0.15)		AAAGGCCAACGTGAACCTGGC	0.537000																								0							SO:0001583	missense			ENST00000379052.5	0	1	hg19	CCDS47378.1	.	.	.	.	.	.	.	.	.	.	G	28.1	4.889107	0.91814	.	.	ENSG00000112183	ENST00000379052;ENST00000509686;ENST00000425446;ENST00000318204	T;D;T;T	0.84298	2.72;-1.83;1.47;2.72	4.8	4.8	0.61643	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	0.135582	0.48767	D	0.000169	D	0.93936	0.8059	H	0.95437	3.67	0.80722	D	1	D;P;P	0.65815	0.995;0.652;0.652	D;P;P	0.66084	0.941;0.459;0.459	D	0.95757	0.8797	10	0.87932	D	0	-12.3307	17.9074	0.88923	0.0:0.0:1.0:0.0	.	38;83;83	Q9BX46-2;Q9BX46;A8KAI7	.;RBM24_HUMAN;.	M	83;42;25;38	ENSP00000368341:V83M;ENSP00000426222:V42M;ENSP00000396898:V25M;ENSP00000319551:V38M	ENSP00000319551:V38M	V	+	1	0	RBM24	17391093	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	9.547000	0.98100	2.222000	0.72286	0.650000	0.86243	GTG		TCGA-S4-A8RO-01A-12D-A377-08	RBM24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039946.2	1	0	1	19	152	0	25		0	0	0	0	25	2		0	0	0	0	0	2	1	9.999935e-01	19	152	0	25	2		0	0	0	0	25	2	-20.000000	1	1	0	0		1	1	2	3	2.028779	0	0.680000	2.080000	0.686397	0.340000	2.100000e-01	1.000000	0.330000	0.376748	0.340000	0	2.700000e-01	0.430000
RGL2	5863	broad.mit.edu	37	6	33263940	33263940	+	Silent	SNP	G	G	A			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr6:33263940G>A	ENST00000497454.1	-	6	1128	c.633C>T	c.(631-633)ctC>ctT	p.L211L	RGL2_ENST00000437840.2_5'UTR|PFDN6_ENST00000463584.1_Intron|RGL2_ENST00000444031.2_Silent_p.L129L	NM_001243738.1|NM_004761.4	NP_001230667.1|NP_004752.1	O15211	RGL2_HUMAN	ral guanine nucleotide dissociation stimulator-like 2			34					CCCGGGACCGGAGATTGCGGA	0.662000																								0							SO:0001819	synonymous_variant			ENST00000497454.1	0	1	hg19	CCDS4774.1																																																																																				TCGA-S4-A8RO-01A-12D-A377-08	RGL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076098.2	0	0	0	6	646	0	113	0	1.088041e-01	0	51	0	113	2		0	0	0	0	0	2	1	9.628481e-01	6	633	0	112	2		0	0	0	0	113	2	-2.576665	1	1	0	0		1	1	2	3	2.028779	0	0.680000	2.080000	0.686397	0.020000	0	1.000000	0.020000	0.076529	0.020000	0	1.000000e-02	0.050000
DAAM2	23500	broad.mit.edu	37	6	39845988	39845988	+	Silent	SNP	C	C	T			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr6:39845988C>T	ENST00000398904.2	+	12	1493	c.1311C>T	c.(1309-1311)aaC>aaT	p.N437N	DAAM2_ENST00000274867.4_Silent_p.N437N|DAAM2_ENST00000538976.1_Silent_p.N437N			Q86T65	DAAM2_HUMAN	dishevelled associated activator of morphogenesis 2			49	Ovarian(28;0.0355)|Colorectal(47;0.196)				GGCTCATCAACGAGAATGAAG	0.547000																								0							SO:0001819	synonymous_variant			ENST00000398904.2	1	1	hg19	CCDS56426.1																																																																																				TCGA-S4-A8RO-01A-12D-A377-08	DAAM2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280648.1	1	0	1	52	123	0	32	0	7.960949e-01	0	9	0	32	2		0	0	0	0	0	2	1	1	52	122	0	32	2		0	0	0	0	32	2	-20.000000	1	1	121022	1	34	1	1	2	3	1.997743	0	0.680000	2.080000	0.684294	0.880000	6.900000e-01	1.000000	1.000000	0.885767	0.880000	1	7.800000e-01	1.000000
GTPBP2	54676	broad.mit.edu	37	6	43593543	43593543	+	Missense_Mutation	SNP	G	G	A			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr6:43593543G>A	ENST00000307126.5	-	4	456	c.457C>T	c.(457-459)Ccc>Tcc	p.P153S	GTPBP2_ENST00000476510.1_5'UTR|GTPBP2_ENST00000307114.7_Missense_Mutation_p.P65S	NM_019096.3	NP_061969.3			GTP binding protein 2			18	all_cancers(18;9.36e-06)|Lung NSC(15;0.00161)|all_lung(25;0.004)		all cancers(41;0.000501)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.0826)|OV - Ovarian serous cystadenocarcinoma(102;0.167)		ATCTTCCGGGGCATGTCGCTA	0.552000													GBM(116;405 1620 28302 32150 44768)											0							SO:0001583	missense			ENST00000307126.5	0	1	hg19	CCDS4903.1	.	.	.	.	.	.	.	.	.	.	G	10.62	1.400940	0.25291	.	.	ENSG00000172432	ENST00000307126;ENST00000307114;ENST00000452781	T;T;T	0.42513	1.56;1.59;0.97	4.78	4.78	0.61160	.	0.114076	0.64402	D	0.000013	T	0.11965	0.0291	N	0.05574	-0.02	0.50467	D	0.999875	B;B	0.09022	0.002;0.0	B;B	0.09377	0.004;0.001	T	0.09164	-1.0687	10	0.12766	T	0.61	-15.4253	17.9977	0.89189	0.0:0.0:1.0:0.0	.	145;153	Q9BX10-4;Q9BX10	.;GTPB2_HUMAN	S	153;65;145	ENSP00000303997:P153S;ENSP00000304893:P65S;ENSP00000410676:P145S	ENSP00000304893:P65S	P	-	1	0	GTPBP2	43701521	1.000000	0.71417	0.980000	0.43619	0.797000	0.45037	4.912000	0.63335	2.480000	0.83734	0.561000	0.74099	CCC		TCGA-S4-A8RO-01A-12D-A377-08	GTPBP2-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040679.1	0	0	0	5	355	0	72	0	2.620823e-01	0	60	0	72	2		0	0	0	0	0	2	1	9.365796e-01	5	352	0	71	2		0	0	0	0	72	2	-2.179393	0	1	121412	1	31	1	1	2	3	1.997743	0	0.680000	2.080000	0.684294	0.040000	0	1.000000	0.040000	0.076536	0.040000	0	2.000000e-02	0.070000
RAMP3	10268	broad.mit.edu	37	7	45222846	45222846	+	Silent	SNP	C	C	T	rs138821752		TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08			C	T	C	C		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr7:45222846C>T	ENST00000242249.4	+	3	320	c.282C>T	c.(280-282)acC>acT	p.T94T	RAMP3_ENST00000481345.1_Silent_p.T94T|RAMP3_ENST00000496212.1_Silent_p.T94T	NM_005856.2	NP_005847.1	O60896	RAMP3_HUMAN	receptor (G protein-coupled) activity modifying protein 3			11				Pramlintide(DB01278)	GCTTCATCACCGGCATCCACA	0.592000																								0							SO:0001819	synonymous_variant			ENST00000242249.4	1	1	hg19	CCDS5503.1																																																																																				TCGA-S4-A8RO-01A-12D-A377-08	RAMP3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251343.1	1	0	1	116	229	0	85	0	1	0	80	0	85	2		0	0	0	0	0	2	1	1	115	225	0	85	2		0	0	0	0	85	2	-11.636590	1	1	121412	36	48	1	1	2	3	2.042212	0	0.680000	2.080000	0.687439	0.990000	8.600000e-01	1.000000	1.000000	0.977301	0.990000	1	9.300000e-01	1.000000
SQLE	6713	broad.mit.edu	37	8	126030321	126030321	+	Missense_Mutation	SNP	G	G	A			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr8:126030321G>A	ENST00000265896.5	+	8	2123	c.1225G>A	c.(1225-1227)Gca>Aca	p.A409T	SQLE_ENST00000523430.1_Missense_Mutation_p.A314T	NM_003129.3	NP_003120.2	Q14534	ERG1_HUMAN	squalene epoxidase			14	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205)	Butenafine(DB01091)|Naftifine(DB00735)|Terbinafine(DB00857)	TTTGGGAGACGCATATAATAT	0.353000																								0							SO:0001583	missense			ENST00000265896.5	0	1	hg19	CCDS47918.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.039032	0.75617	.	.	ENSG00000104549	ENST00000523430;ENST00000265896;ENST00000541193;ENST00000518931	T;T;T	0.75050	-0.9;-0.9;-0.9	5.48	5.48	0.80851	Aromatic-ring hydroxylase-like (1);Squalene epoxidase (1);	0.000000	0.85682	D	0.000000	D	0.89639	0.6773	M	0.91872	3.25	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91448	0.5179	10	0.72032	D	0.01	-14.8692	19.3542	0.94404	0.0:0.0:1.0:0.0	.	409	Q14534	ERG1_HUMAN	T	314;409;214;61	ENSP00000430331:A314T;ENSP00000265896:A409T;ENSP00000429916:A61T	ENSP00000265896:A409T	A	+	1	0	SQLE	126099503	1.000000	0.71417	0.950000	0.38849	0.012000	0.07955	9.609000	0.98334	2.575000	0.86900	0.655000	0.94253	GCA		TCGA-S4-A8RO-01A-12D-A377-08	SQLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381362.1	0	0	0	5	436	0	73	0	7.877531e-01	0	251	0	73	2		0	0	0	0	0	2	1	9.363703e-01	5	432	0	73	2		0	0	0	0	73	2	-2.534913	1	1	120800	3	34	1	2	2	4	3.161472	1	0.680000	2.080000	0.803150	0.050000	0	1.000000	0.050000	0.123574	0.050000	0	2.000000e-02	0.100000
LOXL2	4017	broad.mit.edu	37	8	23155589	23155589	+	Silent	SNP	G	G	A			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08			G	A	G	G		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr8:23155589G>A	ENST00000389131.3	-	14	2661	c.2292C>T	c.(2290-2292)agC>agT	p.S764S		NM_002318.2	NP_002309.1	Q9Y4K0	LOXL2_HUMAN	lysyl oxidase-like 2			35		Prostate(55;0.0453)|Breast(100;0.143)			TTAAGAGCCCGCTGAAGTGCT	0.532000																								0							SO:0001819	synonymous_variant			ENST00000389131.3	1	1	hg19	CCDS34864.1																																																																																				TCGA-S4-A8RO-01A-12D-A377-08	LOXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375603.1	1	0	1	61	120	0	23	0	1	1	140	0	23	2		0	0	0	0	0	2	1	1	61	118	0	23	2		0	0	0	0	23	2	-20.000000	1	1	121412	1	35	1	1	3	4	2.732590	1	0.680000	2.080000	0.768250	0.990000	9.900000e-01	1.000000	1.000000	0.999917	0.990000	1	9.900000e-01	1.000000
OR13C3	138803	broad.mit.edu	37	9	107298219	107298219	+	Silent	SNP	C	C	T	rs145221004		TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chr9:107298219C>T	ENST00000374781.2	-	1	918	c.876G>A	c.(874-876)ccG>ccA	p.P292P		NM_001001961.1	NP_001001961.1	Q8NGS6	O13C3_HUMAN	olfactory receptor, family 13, subfamily C, member 3			19					CTTGAGACTTCGGTTTCGCAT	0.438000													GBM(86;1248 1274 14222 15028 46219)											0							SO:0001819	synonymous_variant			ENST00000374781.2	1	1	hg19	CCDS35089.1																																																																																				TCGA-S4-A8RO-01A-12D-A377-08	OR13C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053477.2	1	0	1	162	279	0	126		0	0	0	0	126	2		0	0	0	0	0	2	1	1	161	277	0	125	2		0	0	0	0	126	2	-18.816990	1	1	121412	114	53	1	1	2	3	1.980807	0	0.680000	2.080000	0.682161	0.990000	9.500000e-01	1.000000	1.000000	0.997045	0.990000	1	9.900000e-01	1.000000
COL4A5	1287	broad.mit.edu	37	X	107909779	107909779	+	Missense_Mutation	SNP	G	G	A	rs104886237		TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chrX:107909779G>A	ENST00000361603.2	+	39	3752	c.3508G>A	c.(3508-3510)Ggt>Agt	p.G1170S	COL4A5_ENST00000328300.6_Missense_Mutation_p.G1170S	NM_000495.4	NP_000486.1	P29400	CO4A5_HUMAN	collagen, type IV, alpha 5			99					AGGCAAACCCGGTCAAGATGG	0.443000									Alport syndrome with Diffuse Leiomyomatosis															0		GRCh37	CM993122	COL4A5	M	rs104886237	SO:0001583	missense	Familial Cancer Database		ENST00000361603.2	1	0	hg19	CCDS14543.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.146532	0.77888	.	.	ENSG00000188153	ENST00000328300;ENST00000361603;ENST00000508186	D;D	0.99329	-5.75;-5.75	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	D	0.99729	0.9894	H	0.98965	4.385	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.96983	0.9716	10	0.87932	D	0	.	18.4199	0.90587	0.0:0.0:1.0:0.0	.	1170;1170	E7EVY4;P29400	.;CO4A5_HUMAN	S	1170	ENSP00000331902:G1170S;ENSP00000354505:G1170S	ENSP00000331902:G1170S	G	+	1	0	COL4A5	107796435	1.000000	0.71417	0.969000	0.41365	0.927000	0.56198	8.265000	0.89869	2.290000	0.77057	0.600000	0.82982	GGT		TCGA-S4-A8RO-01A-12D-A377-08	COL4A5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057880.2	1	0	1	46	58	0	18	0	9.248327e-01	0	8	0	18	2		0	0	0	0	0	2	1	1	44	58	0	18	2		0	0	0	0	18	2	-11.387680	1	0	121274	1	31	1	0	1	1			0.680000	2.080000	0.680000	0.990000	9.900000e-01	1.000000	1.000000	0.999274	0.990000	1	9.900000e-01	1.000000
DCX	1641	broad.mit.edu	37	X	110644391	110644391	+	Missense_Mutation	SNP	G	G	A			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chrX:110644391G>A	ENST00000338081.3	-	3	946	c.775C>T	c.(775-777)Cgc>Tgc	p.R259C	DCX_ENST00000488120.1_Missense_Mutation_p.R178C|DCX_ENST00000371993.2_Missense_Mutation_p.R178C|DCX_ENST00000356915.2_Missense_Mutation_p.R178C|DCX_ENST00000496551.1_5'UTR|DCX_ENST00000356220.3_Missense_Mutation_p.R178C	NM_000555.3	NP_000546.2	O43602	DCX_HUMAN	doublecortin	p.R178C(1)|p.R259C(1)		41					AGCTTGGGGCGCACAAAGTCC	0.537000																								2	Substitution - Missense(2)	GRCh37	CM023910	DCX	M		SO:0001583	missense			ENST00000338081.3	0	1	hg19	CCDS14556.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.679772	0.88542	.	.	ENSG00000077279	ENST00000356915;ENST00000371993;ENST00000338081;ENST00000356220;ENST00000488120	D;D;D;D;D	0.93953	-3.32;-3.32;-3.32;-3.32;-3.32	4.74	4.74	0.60224	Doublecortin domain (3);	0.131721	0.50627	D	0.000104	D	0.95592	0.8567	L	0.59436	1.845	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.66351	0.943;0.917	D	0.96124	0.9087	10	0.72032	D	0.01	.	17.6068	0.88040	0.0:0.0:1.0:0.0	.	247;259	B4DM53;O43602	.;DCX_HUMAN	C	178;178;259;178;178	ENSP00000349385:R178C;ENSP00000361061:R178C;ENSP00000337697:R259C;ENSP00000348553:R178C;ENSP00000419861:R178C	ENSP00000337697:R259C	R	-	1	0	DCX	110531047	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.624000	0.74243	2.283000	0.76528	0.600000	0.82982	CGC		TCGA-S4-A8RO-01A-12D-A377-08	DCX-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357058.1	0	0	0	5	442	1	95		0	0	0	1	95	2		0	0	0	0	0	2	0	7.473249e-03	5	440	1	94	17		0	0	0	1	95	2	-2.153610	0	1	0	0		1	0	1	1			0.680000	2.080000	0.680000	0.030000	0	0.070000	0.040000	0.038764	0.030000	0	1.000000e-02	0.060000
BCORL1	63035	broad.mit.edu	37	X	129190051	129190051	+	Silent	SNP	C	C	T			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chrX:129190051C>T	ENST00000218147.7	+	13	5273	c.5076C>T	c.(5074-5076)taC>taT	p.Y1692Y	BCORL1_ENST00000359304.2_Silent_p.Y1562Y|BCORL1_ENST00000303743.5_Silent_p.Y1766Y|BCORL1_ENST00000540052.1_Silent_p.Y1692Y			Q5H9F3	BCORL_HUMAN	BCL6 corepressor-like 1			75					TGGTGCGGTACGAGCCAGACC	0.607000																								0							SO:0001819	synonymous_variant			ENST00000218147.7	1	1	hg19	CCDS14616.1																																																																																				TCGA-S4-A8RO-01A-12D-A377-08	BCORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058223.1	1	0	0	95	195	0	73	0	9.996660e-01	0	27	0	73	2	1	1	303	896	0	1064	2	1	1	92	185	0	71	2		0	0	0	0	73	2	-20.000000	1	1	121394	6	38	1	0	1	1			0.680000	2.080000	0.680000	0.950000	8.000000e-01	1.000000	1.000000	0.947312	0.950000	1	8.700000e-01	1.000000
GDI1	2664	broad.mit.edu	37	X	153670920	153670920	+	Silent	SNP	C	C	T	rs76578139		TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08			C	T	C	C		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chrX:153670920C>T	ENST00000447750.2	+	11	1580	c.1245C>T	c.(1243-1245)aaC>aaT	p.N415N	FAM50A_ENST00000393600.3_5'Flank|GDI1_ENST00000465640.1_3'UTR	NM_001493.2	NP_001484.1	P31150	GDIA_HUMAN	GDP dissociation inhibitor 1			16	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)				CAACCTGCAACGACATCAAAG	0.522000																								0							SO:0001819	synonymous_variant			ENST00000447750.2	1	1	hg19	CCDS35452.1																																																																																				TCGA-S4-A8RO-01A-12D-A377-08	GDI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081649.2	1	0	0	304	259	0	98	0	1	0	332	0	98	2		0	0	0	0	0	2	1	1	300	257	0	98	2		0	0	0	0	98	2	-20.000000	1	1	121410	4	40	1	0	1	1			0.680000	2.080000	0.680000	0.990000	9.900000e-01	1.000000	1.000000	1.000000	0.990000	1	9.900000e-01	1.000000
NAP1L2	4674	broad.mit.edu	37	X	72434324	72434324	+	Missense_Mutation	SNP	G	G	A			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chrX:72434324G>A	ENST00000373517.3	-	1	360	c.5C>T	c.(4-6)gCc>gTc	p.A2V	NAP1L2_ENST00000536638.1_Intron	NM_021963.3	NP_068798.1	Q9ULW6	NP1L2_HUMAN	nucleosome assembly protein 1-like 2			29	Renal(35;0.156)				CTCTGACTCGGCCATTTTTCA	0.532000																								0							SO:0001583	missense			ENST00000373517.3	0	1	hg19	CCDS14423.1	.	.	.	.	.	.	.	.	.	.	g	16.18	3.049801	0.55218	.	.	ENSG00000186462	ENST00000373517	T	0.37584	1.19	3.03	2.16	0.27623	.	0.517494	0.18149	U	0.150154	T	0.20740	0.0499	N	0.19112	0.55	0.80722	D	1	B	0.19445	0.036	B	0.12837	0.008	T	0.06881	-1.0802	10	0.87932	D	0	-3.1541	5.4474	0.16544	0.1624:0.0:0.8376:0.0	.	2	Q9ULW6	NP1L2_HUMAN	V	2	ENSP00000362616:A2V	ENSP00000362616:A2V	A	-	2	0	NAP1L2	72351049	1.000000	0.71417	1.000000	0.80357	0.756000	0.42949	2.935000	0.48963	0.660000	0.30964	-0.208000	0.12717	GCC		TCGA-S4-A8RO-01A-12D-A377-08	NAP1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057225.1	0	0	0	6	352	0	54	0	4.099149e-03	0	5	0	54	2		0	0	0	0	0	2	1	9.627839e-01	5	345	0	53	2		0	0	0	0	54	2	-2.669227	1	1	0	0		1	0	1	1			0.680000	2.080000	0.680000	0.040000	1.000000e-02	0.100000	0.050000	0.057114	0.040000	0	2.000000e-02	0.080000
FAM133A	286499	broad.mit.edu	37	X	92964906	92964906	+	Nonsense_Mutation	SNP	C	C	G			TCGA-S4-A8RO-01A-12D-A377-08	TCGA-S4-A8RO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e046033-4c1a-4a72-9345-ffaf332048d3	0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a	g.chrX:92964906C>G	ENST00000355813.5	+	4	1014	c.488C>G	c.(487-489)tCa>tGa	p.S163*	FAM133A_ENST00000538690.1_Nonsense_Mutation_p.S163*|FAM133A_ENST00000322139.4_Nonsense_Mutation_p.S163*|FAM133A_ENST00000332647.4_Nonsense_Mutation_p.S163*	NM_001171109.1|NM_173698.2	NP_001164580.1|NP_775969.1	Q8N9E0	F133A_HUMAN	family with sequence similarity 133, member A			20					AAAAAGAAGTCAAAGGATGAA	0.363000																								0							SO:0001587	stop_gained			ENST00000355813.5	0	1	hg19	CCDS14466.1	.	.	.	.	.	.	.	.	.	.	c	38	6.748977	0.97809	.	.	ENSG00000179083	ENST00000538690;ENST00000355813;ENST00000322139;ENST00000332647	.	.	.	3.0	2.13	0.27403	.	0.239763	0.36409	U	0.002607	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.51188	T	0.08	-0.0917	5.3653	0.16111	0.0:0.8372:0.0:0.1628	.	.	.	.	X	163	.	ENSP00000318974:S163X	S	+	2	0	FAM133A	92851562	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	0.909000	0.28558	0.668000	0.31126	0.597000	0.82753	TCA		TCGA-S4-A8RO-01A-12D-A377-08	FAM133A-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057452.1	1	0	1	25	96	0	48		0	0	0	0	48	2		0	0	0	0	0	2	1	9.999999e-01	25	95	0	47	2		0	0	0	0	48	2	-20.000000	1	1	0	0		1	0	1	1			0.680000	2.080000	0.680000	0.600000	4.100000e-01	0.820000	0.600000	0.619281	0.600000	0	5.000000e-01	0.720000
