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
SMAD4	4089	broad.mit.edu	37	18	48604742	48604743	+	Frame_Shift_Del	DEL	CC	CC	-			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08			CC	-	CC	CC		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr18:48604742_48604743delCC	ENST00000342988.3	+	12	2102_2103	c.1564_1565delCC	c.(1564-1566)cctfs	p.P522fs	SMAD4_ENST00000588745.1_Frame_Shift_Del_p.P426fs|SMAD4_ENST00000586253.1_3'UTR|SMAD4_ENST00000398417.2_Frame_Shift_Del_p.P522fs	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	p.0?(36)|p.?(2)		454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)			CAAAGAAACACCTTGCTGGATT	0.480000																								38	Whole gene deletion(36)|Unknown(2)	GRCh37	CD000943	SMAD4	D		SO:0001589	frameshift_variant			ENST00000342988.3	1	1	hg19	CCDS11950.1																																																																																				TCGA-US-A77G-01A-11D-A32N-08	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	1	0	0	90	392	0	88	1	9.999994e-01	31	60	0	88	2	1	1	116	413	0	539	2	1	1.000000	93	390	0	87	2	0	0	0	0	0	0		-2.964154	1	1	0	0		1	0	1	1	1.633574	1	0.420000	1.870000	0.265823	0.690000	5.700000e-01	0.830000	0.700000	0.703254	0.690000	0	6.300000e-01	7.700000e-01
SPEF2	79925	broad.mit.edu	37	5	35691186	35691187	+	Frame_Shift_Ins	INS	-	-	CCACCCT			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr5:35691186_35691187insCCACCCT	ENST00000356031.3	+	11	1726_1727	c.1572_1573insCCACCCT	c.(1573-1575)ccafs	p.-527fs	SPEF2_ENST00000440995.2_Frame_Shift_Ins_p.-527fs|CTD-2113L7.1_ENST00000510433.1_RNA|SPEF2_ENST00000509059.1_Frame_Shift_Ins_p.-527fs	NM_024867.3	NP_079143.3	Q9C093	SPEF2_HUMAN	sperm flagellar 2			37	all_lung(31;7.56e-05)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)		TTGACAATTTACCACCCTCCAA	0.396000																								0							SO:0001589	frameshift_variant			ENST00000356031.3	0	1	hg19	CCDS43309.1																																																																																				TCGA-US-A77G-01A-11D-A32N-08	SPEF2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367199.1	1	0	0	28	419	0	68			0	0	0	68				0	0	0	0		1	1.000000	47	424	0	68	2	0	0	0	0	0	0		-6.736745	1	1	0	0		1	0	0	0	2.055894	0	0.420000	1.870000	0.420000	0.290000	2.000000e-01	0.410000	0.300000	0.306600	0.290000	0	2.400000e-01	3.600000e-01
SRPK3	26576	broad.mit.edu	37	X	153050878	153050892	+	In_Frame_Del	DEL	CACAGTTCAGCGCCT	CACAGTTCAGCGCCT	-			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chrX:153050878_153050892delCACAGTTCAGCGCCT	ENST00000370101.3	+	15	1653_1667	c.1607_1621delCACAGTTCAGCGCCT	c.(1606-1623)acacagttcagcgccttt>att	p.536_541TQFSAF>I	SRPK3_ENST00000370104.1_In_Frame_Del_p.535_540TQFSAF>I|SRPK3_ENST00000370108.3_In_Frame_Del_p.503_508TQFSAF>I|IDH3G_ENST00000497043.1_5'Flank|SRPK3_ENST00000393786.3_In_Frame_Del_p.502_507TQFSAF>I|SRPK3_ENST00000489426.1_In_Frame_Del_p.603_608TQFSAF>I|SRPK3_ENST00000370100.1_In_Frame_Del_p.461_466TQFSAF>I	NM_001170760.1|NM_014370.3	NP_001164231.1|NP_055185.2	Q9UPE1	SRPK3_HUMAN	SRSF protein kinase 3			13	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)				GAGCAGGCCACACAGTTCAGCGCCTTTCTGCTGCC	0.628000													Esophageal Squamous(167;766 3400 32156)											0							SO:0001651	inframe_deletion			ENST00000370101.3	1	1	hg19	CCDS35441.1																																																																																				TCGA-US-A77G-01A-11D-A32N-08	SRPK3-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354501.1	0	0	0	89	370	0	91			0	0	0	91				0	0	0	0		1	1.000000	113	382	0	92	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	0	1	1			0.420000	1.870000	0.420000	0.450000	3.700000e-01	0.550000	0.460000	0.463432	0.450000	0	4.100000e-01	5.100000e-01
PKD2L1	9033	broad.mit.edu	37	10	102056026	102056026	+	Silent	SNP	G	G	A			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr10:102056026G>A	ENST00000318222.3	-	7	1591	c.1209C>T	c.(1207-1209)ttC>ttT	p.F403F	PKD2L1_ENST00000353274.3_Silent_p.F403F|PKD2L1_ENST00000338519.3_Silent_p.F328F	NM_001253837.1|NM_016112.2	NP_001240766.1|NP_057196.2	Q9P0L9	PK2L1_HUMAN	polycystic kidney disease 2-like 1			43		Colorectal(252;0.117)			GGAATATGTGGAAGCCCACAG	0.567000																								0							SO:0001819	synonymous_variant			ENST00000318222.3	1	1	hg19	CCDS7492.1																																																																																				TCGA-US-A77G-01A-11D-A32N-08	PKD2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049863.2	1	0	1	51	191	0	55		0	0	0	0	55	2		0	0	0	0	0	2	1	1.000000	51	187	0	55	2		0	0	0	0	55	2	-20.000000	1	1	121412	2	22	1	1	2	3	2.059775	0	0.420000	1.870000	0.421215	0.990000	7.700000e-01	1.000000	1.000000	0.955954	0.990000	1	8.800000e-01	1
TRPC6	7225	broad.mit.edu	37	11	101375398	101375398	+	Missense_Mutation	SNP	C	C	T			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr11:101375398C>T	ENST00000344327.3	-	2	726	c.302G>A	c.(301-303)cGc>cAc	p.R101H	TRPC6_ENST00000348423.4_Missense_Mutation_p.R101H|TRPC6_ENST00000360497.4_Missense_Mutation_p.R101H|TRPC6_ENST00000526713.1_5'Flank|TRPC6_ENST00000532133.1_Missense_Mutation_p.R101H	NM_004621.5	NP_004612.2	Q9Y210	TRPC6_HUMAN	transient receptor potential cation channel, subfamily C, member 6			55		Acute lymphoblastic leukemia(157;0.000918)|all_hematologic(158;0.0162)			ATCCAAAAAGCGTTCCTCCTC	0.483000													Colon(166;1315 1927 11094 12848 34731)											0							SO:0001583	missense			ENST00000344327.3	1	1	hg19	CCDS8311.1	.	.	.	.	.	.	.	.	.	.	C	15.46	2.839593	0.51057	.	.	ENSG00000137672	ENST00000344327;ENST00000532133;ENST00000348423;ENST00000360497	T;T;T;T	0.80393	-1.17;-1.26;-1.09;-1.37	5.87	5.87	0.94306	.	0.096864	0.64402	D	0.000001	D	0.87577	0.6212	L	0.47190	1.495	0.54753	D	0.999989	B;D;B	0.89917	0.37;1.0;0.128	B;D;B	0.91635	0.087;0.999;0.018	D	0.86300	0.1679	10	0.48119	T	0.1	-6.1692	20.206	0.98277	0.0:1.0:0.0:0.0	.	101;101;101	Q9Y210-3;Q9Y210-2;Q9Y210	.;.;TRPC6_HUMAN	H	101	ENSP00000340913:R101H;ENSP00000435574:R101H;ENSP00000343672:R101H;ENSP00000353687:R101H	ENSP00000340913:R101H	R	-	2	0	TRPC6	100880608	1.000000	0.71417	1.000000	0.80357	0.891000	0.51852	3.915000	0.56409	2.785000	0.95823	0.655000	0.94253	CGC		TCGA-US-A77G-01A-11D-A32N-08	TRPC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394770.1	1	0	1	127	533	0	141	0	0	0	1	0	141	2		0	0	0	0	0	2	1	1.000000	125	527	0	139	2		0	0	0	0	141	2	-20.000000	1	1	121402	3	37	1	1	2	3	2.058032	0	0.420000	1.870000	0.421215	0.910000	7.700000e-01	1.000000	1.000000	0.915160	0.910000	1	8.400000e-01	9.900000e-01
DSCAML1	57453	broad.mit.edu	37	11	117651507	117651507	+	Missense_Mutation	SNP	C	C	T			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr11:117651507C>T	ENST00000321322.6	-	2	246	c.245G>A	c.(244-246)gGc>gAc	p.G82D	DSCAML1_ENST00000527706.1_Missense_Mutation_p.G22D	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1			110	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)			GAGGCTGGTGCCAACATCTTC	0.612000																								0							SO:0001583	missense			ENST00000321322.6	1	1	hg19	CCDS8384.1	.	.	.	.	.	.	.	.	.	.	C	13.90	2.374942	0.42105	.	.	ENSG00000177103	ENST00000527706;ENST00000321322	T;T	0.61158	0.13;0.24	5.1	5.1	0.69264	Immunoglobulin-like (1);	.	.	.	.	T	0.38241	0.1033	N	0.08118	0	0.51482	D	0.99992	B	0.26002	0.139	B	0.24701	0.055	T	0.26849	-1.0091	9	0.11182	T	0.66	.	18.9124	0.92491	0.0:1.0:0.0:0.0	.	22	Q8TD84	DSCL1_HUMAN	D	22;82	ENSP00000434335:G22D;ENSP00000315465:G82D	ENSP00000315465:G82D	G	-	2	0	DSCAML1	117156717	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.439000	0.44846	2.536000	0.85505	0.563000	0.77884	GGC		TCGA-US-A77G-01A-11D-A32N-08	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	1	0	0	19	34	0	20		0	0	0	0	20	2		0	0	0	0	0	2	1	0.999998	19	34	0	19	2		0	0	0	0	20	2	-20.000000	1	1	0	0		1	1	2	3	2.058032	0	0.420000	1.870000	0.421215	0.990000	9.900000e-01	1.000000	1.000000	0.999443	0.990000	1	9.900000e-01	1
CHST1	8534	broad.mit.edu	37	11	45671609	45671609	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr11:45671609G>A	ENST00000308064.2	-	4	1535	c.865C>T	c.(865-867)Cgg>Tgg	p.R289W	CHST1_ENST00000533673.1_5'Flank|RP11-495O11.1_ENST00000525563.1_RNA	NM_003654.5	NP_003645.1	O43916	CHST1_HUMAN	carbohydrate (keratan sulfate Gal-6) sulfotransferase 1			42					CACGGGGGCCGCATGAGGCCG	0.617000																								0							SO:0001583	missense			ENST00000308064.2	0	1	hg19	CCDS7913.1	.	.	.	.	.	.	.	.	.	.	G	19.41	3.821565	0.71028	.	.	ENSG00000175264	ENST00000308064	T	0.76316	-1.01	4.89	4.89	0.63831	Sulfotransferase domain (1);	0.062547	0.64402	D	0.000005	D	0.86422	0.5929	M	0.67953	2.075	0.58432	D	0.999998	D	0.89917	1.0	D	0.70935	0.971	D	0.85721	0.1325	10	0.37606	T	0.19	-19.3412	18.0436	0.89326	0.0:0.0:1.0:0.0	.	289	O43916	CHST1_HUMAN	W	289	ENSP00000309270:R289W	ENSP00000309270:R289W	R	-	1	2	CHST1	45628185	1.000000	0.71417	0.850000	0.33497	0.988000	0.76386	5.503000	0.66962	2.252000	0.74401	0.462000	0.41574	CGG		TCGA-US-A77G-01A-11D-A32N-08	CHST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390127.1	0	0	0	5	556	0	127	0	1.743712e-02	0	18	0	127	2		0	0	0	0	0	2	1	0.936315	5	551	0	120	2		0	0	0	0	127	2	-1.780105	0	1	0	0		1	1	2	3	2.058032	0	0.420000	1.870000	0.421215	0.040000	0	0.100000	0.040000	0.050588	0.040000	0	2.000000e-02	7.000000e-02
OR51A7	119687	broad.mit.edu	37	11	4929119	4929119	+	Missense_Mutation	SNP	C	C	T			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr11:4929119C>T	ENST00000359350.4	+	1	520	c.520C>T	c.(520-522)Ctt>Ttt	p.L174F	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001004749.1	NP_001004749.1	Q8NH64	O51A7_HUMAN	olfactory receptor, family 51, subfamily A, member 7			33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)			AAAGAATCTTCTTTCTCACTC	0.388000																								0							SO:0001583	missense			ENST00000359350.4	0	1	hg19	CCDS31364.1	.	.	.	.	.	.	.	.	.	.	C	16.84	3.234429	0.58886	.	.	ENSG00000176895	ENST00000359350;ENST00000545959;ENST00000544684	T	0.38240	1.15	5.02	4.08	0.47627	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42172	D	0.000741	T	0.63010	0.2475	M	0.90922	3.16	0.21604	N	0.999623	D	0.89917	1.0	D	0.97110	1.0	T	0.57900	-0.7731	10	0.87932	D	0	.	7.8969	0.29712	0.1585:0.757:0.0:0.0845	.	174	Q8NH64	O51A7_HUMAN	F	174;174;163	ENSP00000352305:L174F	ENSP00000352305:L174F	L	+	1	0	OR51A7	4885695	0.004000	0.15560	0.995000	0.50966	0.955000	0.61496	0.280000	0.18790	2.596000	0.87737	0.655000	0.94253	CTT		TCGA-US-A77G-01A-11D-A32N-08	OR51A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142175.1	0	0	0	5	388	0	88		0	0	0	0	88	2		0	0	0	0	0	2	1	0.935804	5	383	0	88	2		0	0	0	0	88	2	-3.227376	1	1	0	0		1	1	2	3	2.069199	0	0.420000	1.870000	0.422426	0.060000	1.000000e-02	0.150000	0.060000	0.081463	0.060000	0	3.000000e-02	1.000000e-01
MMP26	56547	broad.mit.edu	37	11	5009493	5009493	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr11:5009493G>A	ENST00000380390.1	+	2	268	c.52G>A	c.(52-54)Gtt>Att	p.V18I	MMP26_ENST00000300762.1_Missense_Mutation_p.V18I|MMP26_ENST00000477339.1_Intron			Q9NRE1	MMP26_HUMAN	matrix metallopeptidase 26			22		Medulloblastoma(188;0.0025)|Breast(177;0.0204)|all_neural(188;0.0227)		Marimastat(DB00786)	GTGTTTCGCCGTTCCAGTGCC	0.493000																								0							SO:0001583	missense			ENST00000380390.1	0	1	hg19	CCDS7752.1	.	.	.	.	.	.	.	.	.	.	g	3.577	-0.086437	0.07097	.	.	ENSG00000167346	ENST00000380390;ENST00000300762	T;T	0.26067	1.76;1.76	3.3	-6.6	0.01824	.	0.975329	0.08322	N	0.963623	T	0.06872	0.0175	N	0.02011	-0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.26710	-1.0095	10	0.35671	T	0.21	0.1393	2.2024	0.03927	0.2392:0.4375:0.1215:0.2018	.	18	Q9NRE1	MMP26_HUMAN	I	18	ENSP00000369753:V18I;ENSP00000300762:V18I	ENSP00000300762:V18I	V	+	1	0	MMP26	4966069	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.164000	0.01275	-2.497000	0.00513	-4.594000	0.00004	GTT		TCGA-US-A77G-01A-11D-A32N-08	MMP26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142058.3	0	0	0	7	683	0	123		0	0	0	0	123	2		0	0	0	0	0	2	1	0.979845	8	674	0	121	2		0	0	0	0	123	2	-2.351227	0	1	121412	5	40	1	1	2	3	2.069199	0	0.420000	1.870000	0.422426	0.040000	1.000000e-02	0.110000	0.050000	0.064504	0.040000	0	3.000000e-02	8.000000e-02
HPX	3263	broad.mit.edu	37	11	6452915	6452915	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr11:6452915G>A	ENST00000265983.3	-	9	1185	c.1085C>T	c.(1084-1086)gCg>gTg	p.A362V		NM_000613.2	NP_000604.1	P02790	HEMO_HUMAN	hemopexin			15		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)			GATAAAGGCCGCATCCACAGA	0.557000																								0							SO:0001583	missense			ENST00000265983.3	0	1	hg19	CCDS7763.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.336128	0.81801	.	.	ENSG00000110169	ENST00000265983	T	0.20200	2.09	5.62	5.62	0.85841	Hemopexin/matrixin (2);	0.000000	0.85682	D	0.000000	T	0.48277	0.1491	M	0.84683	2.71	0.80722	D	1	D	0.89917	1.0	P	0.59221	0.854	T	0.54463	-0.8290	10	0.87932	D	0	-12.4094	17.1339	0.86734	0.0:0.0:1.0:0.0	.	362	P02790	HEMO_HUMAN	V	362	ENSP00000265983:A362V	ENSP00000265983:A362V	A	-	2	0	HPX	6409491	1.000000	0.71417	1.000000	0.80357	0.337000	0.28794	6.271000	0.72569	2.656000	0.90262	0.561000	0.74099	GCG		TCGA-US-A77G-01A-11D-A32N-08	HPX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257256.1	0	0	0	5	526	0	89		0	0	0	0	89	2		0	0	0	0	0	2	1	0.935930	5	520	0	87	2		0	0	0	0	89	2	-2.276699	0	1	121412	1	31	1	1	2	3	2.058032	0	0.420000	1.870000	0.421215	0.040000	0	0.110000	0.040000	0.053477	0.040000	0	2.000000e-02	8.000000e-02
UTP20	27340	broad.mit.edu	37	12	101760468	101760468	+	Silent	SNP	C	C	T	rs112368779		TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr12:101760468C>T	ENST00000261637.4	+	47	6432	c.6258C>T	c.(6256-6258)tcC>tcT	p.S2086S		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)			88					TTATTGAGTCCGGGCTTCGGG	0.458000																								0							SO:0001819	synonymous_variant			ENST00000261637.4	1	1	hg19	CCDS9081.1																																																																																				TCGA-US-A77G-01A-11D-A32N-08	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	0	0	0	14	514	0	105	0	3.863188e-02	0	11	0	105	2		0	0	0	0	0	2	1	0.999732	14	507	0	103	2		0	0	0	0	105	2	-2.416580	0	1	121412	1	35	1	0	1	1	1.616471	1	0.420000	1.870000	0.267769	0.090000	5.000000e-02	0.160000	0.100000	0.106196	0.090000	0	7.000000e-02	1.300000e-01
GOLGA3	2802	broad.mit.edu	37	12	133381515	133381515	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr12:133381515G>A	ENST00000450791.2	-	6	1567	c.1384C>T	c.(1384-1386)Cgg>Tgg	p.R462W	GOLGA3_ENST00000545875.1_Missense_Mutation_p.R462W|GOLGA3_ENST00000204726.3_Missense_Mutation_p.R462W|GOLGA3_ENST00000456883.2_Missense_Mutation_p.R462W|GOLGA3_ENST00000537452.1_Missense_Mutation_p.R462W			Q08378	GOGA3_HUMAN	golgin A3			64	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)			GAATCCTGCCGCTGCTGGCTG	0.612000																								0							SO:0001583	missense			ENST00000450791.2	0	1	hg19	CCDS9281.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.240122	0.79912	.	.	ENSG00000090615	ENST00000204726;ENST00000450791;ENST00000456883;ENST00000537452;ENST00000545875	D;D;D;D;D	0.82711	-1.64;-1.64;-1.64;-1.64;-1.64	5.45	3.12	0.35913	.	0.357463	0.36167	N	0.002757	T	0.74099	0.3672	N	0.14661	0.345	0.80722	D	1	D;D;D	0.71674	0.995;0.995;0.998	P;B;P	0.50708	0.648;0.431;0.62	T	0.73503	-0.3962	10	0.87932	D	0	.	7.5344	0.27702	0.0:0.0804:0.1589:0.7607	.	462;462;462	Q08378-4;Q08378-2;Q08378	.;.;GOGA3_HUMAN	W	462	ENSP00000204726:R462W;ENSP00000410378:R462W;ENSP00000409303:R462W;ENSP00000442143:R462W;ENSP00000442603:R462W	ENSP00000204726:R462W	R	-	1	2	GOLGA3	131891588	1.000000	0.71417	0.973000	0.42090	0.927000	0.56198	2.687000	0.46976	0.376000	0.24707	0.561000	0.74099	CGG		TCGA-US-A77G-01A-11D-A32N-08	GOLGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397569.2	0	0	0	6	404	0	91	0	1.702012e-01	0	43	0	91	2		0	0	0	0	0	2	1	0.963616	6	398	0	90	2		0	0	0	0	91	2	-2.925938	1	1	121380	1	28	1	0	1	1	2.050329	0	0.420000	1.870000	0.418779	0.070000	2.000000e-02	0.140000	0.070000	0.080478	0.070000	0	4.000000e-02	1.100000e-01
KRAS	3845	broad.mit.edu	37	12	25398285	25398285	+	Missense_Mutation	SNP	C	C	G	rs121913530		TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08			C	G	C	C		Valid	Somatic	Phase_I	WXS	KRAS_deep			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr12:25398285C>G	ENST00000256078.4	-	2	97	c.34G>C	c.(34-36)Ggt>Cgt	p.G12R	KRAS_ENST00000556131.1_Missense_Mutation_p.G12R|KRAS_ENST00000557334.1_Missense_Mutation_p.G12R|KRAS_ENST00000311936.3_Missense_Mutation_p.G12R	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	p.G12C(3001)|p.G12S(1288)|p.G12R(789)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12W(3)|p.A11_G12insGA(2)|p.G12Y(2)|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)		CCTACGCCACCAGCTCCAACT	0.348000	G12C(CALU1_LUNG)|G12C(HCC44_LUNG)|G12C(IALM_LUNG)|G12C(KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12C(KYSE410_OESOPHAGUS)|G12C(LU65_LUNG)|G12C(LU99_LUNG)|G12C(MIAPACA2_PANCREAS)|G12C(NCIH1373_LUNG)|G12C(NCIH1792_LUNG)|G12C(NCIH2030_LUNG)|G12C(NCIH2122_LUNG)|G12C(NCIH23_LUNG)|G12C(NCIH358_LUNG)|G12C(OV56_OVARY)|G12C(SW1463_LARGE_INTESTINE)|G12C(SW1573_LUNG)|G12C(SW837_LARGE_INTESTINE)|G12C(UMUC3_URINARY_TRACT)|G12R(CAL62_THYROID)|G12R(HS274T_BREAST)|G12R(HUPT3_PANCREAS)|G12R(KP2_PANCREAS)|G12R(PSN1_PANCREAS)|G12R(TCCPAN2_PANCREAS)|G12S(A549_LUNG)|G12S(KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12S(LS123_LARGE_INTESTINE)	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	5144	Substitution - Missense(5142)|Insertion - In frame(2)	GRCh37	CM076251	KRAS	M	rs121913530	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	28.6	4.930538	0.92389	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78246	-1.16;-1.16;-1.16;-1.16	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.84893	0.5573	M	0.84082	2.675	0.80722	D	1	P;P	0.43287	0.802;0.741	B;P	0.47941	0.36;0.562	D	0.86658	0.1902	10	0.66056	D	0.02	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	R	12	ENSP00000308495:G12R;ENSP00000452512:G12R;ENSP00000256078:G12R;ENSP00000451856:G12R	ENSP00000256078:G12R	G	-	1	0	KRAS	25289552	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-US-A77G-01A-11D-A32N-08	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	1	0	1	19	93	0	17	1	9.685956e-01	14	17	0	17	2	1	1	56	255	0	340	2	1	0.999995	19	93	0	17	2	1	1	1940	6087	0	17	2	-12.947140	1	1	0	0		1	0	0	0	2.056247	0	0.420000	1.870000	0.420000	0.800000	5.100000e-01	1.000000	1.000000	0.810550	0.800000	0	6.500000e-01	9.800000e-01
SPRYD3	84926	broad.mit.edu	37	12	53462066	53462066	+	Missense_Mutation	SNP	C	C	T			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr12:53462066C>T	ENST00000301463.4	-	7	802	c.716G>A	c.(715-717)gGc>gAc	p.G239D	SPRYD3_ENST00000547837.1_Missense_Mutation_p.G276D	NM_032840.2	NP_116229.1	Q8NCJ5	SPRY3_HUMAN	SPRY domain containing 3			17					GATGCTTTTGCCCTTCCCTAA	0.637000																								0							SO:0001583	missense			ENST00000301463.4	0	1	hg19	CCDS8845.1	.	.	.	.	.	.	.	.	.	.	C	32	5.152619	0.94645	.	.	ENSG00000167778	ENST00000301463;ENST00000547837	.	.	.	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	T	0.67363	0.2885	L	0.36672	1.1	0.80722	D	1	D	0.76494	0.999	D	0.74023	0.982	T	0.67345	-0.5694	9	0.48119	T	0.1	.	16.5377	0.84377	0.0:1.0:0.0:0.0	.	239	Q8NCJ5	SPRY3_HUMAN	D	239;276	.	ENSP00000301463:G239D	G	-	2	0	SPRYD3	51748333	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.218000	0.77991	2.575000	0.86900	0.561000	0.74099	GGC		TCGA-US-A77G-01A-11D-A32N-08	SPRYD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407264.1	0	0	0	6	858	0	176	0	2.611069e-01	1	122	0	176	2		0	0	0	0	0	2	1	0.963354	6	846	0	175	2		0	0	0	0	176	2	-1.980946	0	1	0	0		1	0	1	1	2.052164	0	0.420000	1.870000	0.418779	0.030000	0	0.070000	0.040000	0.037918	0.030000	0	1.000000e-02	5.000000e-02
NCKAP1L	3071	broad.mit.edu	37	12	54917197	54917197	+	Missense_Mutation	SNP	C	C	T			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr12:54917197C>T	ENST00000293373.6	+	19	1977	c.1898C>T	c.(1897-1899)gCc>gTc	p.A633V	NCKAP1L_ENST00000545638.2_Missense_Mutation_p.A583V	NM_005337.4	NP_005328.2	P55160	NCKPL_HUMAN	NCK-associated protein 1-like			80					AAGCACTGTGCCACTACAATC	0.473000																								0							SO:0001583	missense			ENST00000293373.6	0	1	hg19	CCDS31813.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.701576	0.88924	.	.	ENSG00000123338	ENST00000293373;ENST00000545638	T;T	0.39787	1.06;1.06	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	T	0.61999	0.2392	M	0.63843	1.955	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	T	0.57814	-0.7746	10	0.36615	T	0.2	-15.2108	16.9443	0.86226	0.0:1.0:0.0:0.0	.	633	P55160	NCKPL_HUMAN	V	633;583	ENSP00000293373:A633V;ENSP00000445596:A583V	ENSP00000293373:A633V	A	+	2	0	NCKAP1L	53203464	1.000000	0.71417	1.000000	0.80357	0.909000	0.53808	7.491000	0.81471	2.673000	0.90976	0.655000	0.94253	GCC		TCGA-US-A77G-01A-11D-A32N-08	NCKAP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406195.1	0	0	0	6	876	0	147	0	1.042657e-03	0	6	0	147	2		0	0	0	0	0	2	1	0.964280	6	870	0	146	2		0	0	0	0	147	2	-2.087043	0	1	0	0		1	0	1	1	2.052164	0	0.420000	1.870000	0.418779	0.030000	0	0.070000	0.040000	0.037083	0.030000	0	1.000000e-02	5.000000e-02
ARHGAP9	64333	broad.mit.edu	37	12	57868253	57868253	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr12:57868253G>A	ENST00000356411.2	-	15	1931	c.1793C>T	c.(1792-1794)gCg>gTg	p.A598V	ARHGAP9_ENST00000550288.1_Missense_Mutation_p.A658V|ARHGAP9_ENST00000430041.2_Missense_Mutation_p.A395V|ARHGAP9_ENST00000393791.3_Missense_Mutation_p.A579V|ARHGAP9_ENST00000550454.1_5'Flank|ARHGAP9_ENST00000393797.2_Missense_Mutation_p.A669V|ARHGAP9_ENST00000424809.2_Missense_Mutation_p.A579V			Q9BRR9	RHG09_HUMAN	Rho GTPase activating protein 9			30			GBM - Glioblastoma multiforme(3;3.37e-34)		GGAGGTGACCGCACGCTCTGC	0.517000																								0							SO:0001583	missense			ENST00000356411.2	0	1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.68|19.68	3.873016|3.873016	0.72180|0.72180	.|.	.|.	ENSG00000123329|ENSG00000123329	ENST00000393791;ENST00000356411;ENST00000423291;ENST00000424809;ENST00000393797;ENST00000340423;ENST00000430041|ENST00000550399	T;T;T;T;T|.	0.19669|.	2.13;2.13;2.13;2.13;2.13|.	5.08|5.08	5.08|5.08	0.68730|0.68730	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);|.	0.075671|.	0.48286|.	D|.	0.000194|.	T|T	0.61565|0.61565	0.2357|0.2357	L|L	0.43152|0.43152	1.355|1.355	0.58432|0.58432	D|D	0.999992|0.999992	P;P;P;P;D|.	0.59767|.	0.934;0.837;0.758;0.934;0.986|.	P;B;B;P;P|.	0.54965|.	0.457;0.272;0.328;0.535;0.765|.	T|T	0.55854|0.55854	-0.8075|-0.8075	10|5	0.59425|.	D|.	0.04|.	.|.	15.8782|15.8782	0.79182|0.79182	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	658;598;579;579;395|.	Q6ZN13;Q9BRR9;Q9BRR9-2;E9PDX9;B4DVI3|.	.;RHG09_HUMAN;.;.;.|.	V|W	579;598;249;579;669;628;395|49	ENSP00000377380:A579V;ENSP00000348782:A598V;ENSP00000394307:A579V;ENSP00000377386:A669V;ENSP00000397950:A395V|.	ENSP00000344852:A628V|.	A|R	-|-	2|1	0|2	ARHGAP9|ARHGAP9	56154520|56154520	1.000000|1.000000	0.71417|0.71417	0.954000|0.954000	0.39281|0.39281	0.245000|0.245000	0.25701|0.25701	5.408000|5.408000	0.66368|0.66368	2.826000|2.826000	0.97356|0.97356	0.655000|0.655000	0.94253|0.94253	GCG|CGG		TCGA-US-A77G-01A-11D-A32N-08	ARHGAP9-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		0	0	0	4	223	0	54	0	3.081344e-02	0	12	0	54	2		0	0	0	0	0	2	1	0.891148	4	223	0	53	2		0	0	0	0	54	2	-3.171083	1	1	0	0		1	0	1	1	2.052164	0	0.420000	1.870000	0.418779	0.090000	2.000000e-02	0.200000	0.080000	0.103111	0.090000	0	5.000000e-02	1.500000e-01
GNS	2799	broad.mit.edu	37	12	65113959	65113959	+	Missense_Mutation	SNP	A	A	G			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08			A	G	A	A		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr12:65113959A>G	ENST00000258145.3	-	13	1593	c.1423T>C	c.(1423-1425)Ttt>Ctt	p.F475L	GNS_ENST00000543646.1_Missense_Mutation_p.F507L|GNS_ENST00000418919.2_Missense_Mutation_p.F419L|GNS_ENST00000542058.1_Missense_Mutation_p.F455L	NM_002076.3	NP_002067.1	P15586	GNS_HUMAN	glucosamine (N-acetyl)-6-sulfatase			15	Lung NSC(1;7.25e-14)|all_lung(1;1.25e-12)		LUAD - Lung adenocarcinoma(6;0.115)		ACTTCTACAAACACCTAGAGG	0.408000																								0							SO:0001583	missense			ENST00000258145.3	1	1	hg19	CCDS8970.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	33|33	5.208974|5.208974	0.95069|0.95069	.|.	.|.	ENSG00000135677|ENSG00000135677	ENST00000418919;ENST00000258145;ENST00000543646;ENST00000542058;ENST00000539825|ENST00000540196	T;T;T;T|T	0.64991|0.19105	1.84;-0.13;-0.13;-0.13|2.17	5.39|5.39	5.39|5.39	0.77823|0.77823	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.48059|0.48059	0.1479|0.1479	M|M	0.85777|0.85777	2.775|2.775	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.89917|.	0.995;1.0;0.974;1.0|.	D;D;D;D|.	0.91635|.	0.969;0.999;0.949;0.998|.	T|T	0.53344|0.53344	-0.8452|-0.8452	9|6	.|.	.|.	.|.	-20.6884|-20.6884	15.7218|15.7218	0.77718|0.77718	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	455;507;475;419|.	B4DYH8;F6S8M0;P15586;Q7Z3X3|.	.;.;GNS_HUMAN;.|.	L|A	419;475;507;455;392|260	ENSP00000413130:F419L;ENSP00000258145:F475L;ENSP00000438497:F507L;ENSP00000444819:F455L|ENSP00000437782:V260A	.|.	F|V	-|-	1|2	0|0	GNS|GNS	63400226|63400226	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.904000|0.904000	0.53231|0.53231	9.204000|9.204000	0.95041|0.95041	2.180000|2.180000	0.69256|0.69256	0.459000|0.459000	0.35465|0.35465	TTT|GTT		TCGA-US-A77G-01A-11D-A32N-08	GNS-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401195.2	1	0	1	166	578	0	127	1	1	44	56	0	127	2		0	0	0	0	0	2	1	1.000000	163	573	0	125	2		0	0	0	0	127	2	-20.000000	1	1	0	0		1	0	1	1	2.052164	0	0.420000	1.870000	0.418779	0.990000	9.100000e-01	1.000000	1.000000	0.992277	0.990000	1	9.800000e-01	1
SLC46A3	283537	broad.mit.edu	37	13	29284936	29284936	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr13:29284936G>A	ENST00000266943.6	-	4	1474	c.1105C>T	c.(1105-1107)Cgg>Tgg	p.R369W	SLC46A3_ENST00000380814.4_Missense_Mutation_p.R369W	NM_001135919.1|NM_181785.3	NP_001129391.1|NP_861450.1	Q7Z3Q1	S46A3_HUMAN	solute carrier family 46, member 3			15		Lung SC(185;0.0367)			AACATGGACCGTAGAACAGAG	0.398000																								0							SO:0001583	missense			ENST00000266943.6	0	1	hg19	CCDS9332.1	.	.	.	.	.	.	.	.	.	.	G	17.35	3.367312	0.61513	.	.	ENSG00000139508	ENST00000266943;ENST00000380814	T;T	0.80304	-1.36;-1.36	5.87	4.05	0.47172	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.85682	D	0.000000	D	0.89914	0.6853	M	0.82630	2.6	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.91020	0.4856	10	0.87932	D	0	-25.3129	15.0378	0.71764	0.0:0.0:0.7331:0.2669	.	369;369	Q7Z3Q1-2;Q7Z3Q1	.;S46A3_HUMAN	W	369	ENSP00000266943:R369W;ENSP00000370192:R369W	ENSP00000266943:R369W	R	-	1	2	SLC46A3	28182936	1.000000	0.71417	0.662000	0.29724	0.241000	0.25554	3.111000	0.50360	0.837000	0.34925	0.655000	0.94253	CGG		TCGA-US-A77G-01A-11D-A32N-08	SLC46A3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276111.1	0	0	0	5	419	0	67	0	2.783418e-01	0	74	0	67	2		0	0	0	0	0	2	1	0.936324	5	415	0	65	2		0	0	0	0	67	2	-2.523234	1	1	0	0		1	1	2	3	2.146113	0	0.420000	1.870000	0.433095	0.060000	1.000000e-02	1.000000	0.060000	0.151171	0.060000	0	3.000000e-02	1.100000e-01
SOHLH2	54937	broad.mit.edu	37	13	36744911	36744911	+	Silent	SNP	G	G	A			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr13:36744911G>A	ENST00000379881.3	-	10	1102	c.1014C>T	c.(1012-1014)tcC>tcT	p.S338S	SOHLH2_ENST00000554962.1_Silent_p.S415S|CCDC169-SOHLH2_ENST00000511166.1_Silent_p.S415S	NM_017826.2	NP_060296.2	Q9NX45	SOLH2_HUMAN	spermatogenesis and oogenesis specific basic helix-loop-helix 2			26		Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.184)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)		TCTCTGAGGCGGAGCTTGATG	0.388000																								0							SO:0001819	synonymous_variant			ENST00000379881.3	0	1	hg19	CCDS9355.1																																																																																				TCGA-US-A77G-01A-11D-A32N-08	SOHLH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044477.2	0	0	0	6	429	0	73	0	0	0	1	0	73	2		0	0	0	0	0	2	1	0.964207	5	426	0	70	2		0	0	0	0	73	2	-3.061295	1	1	0	0		1	1	2	3	2.146113	0	0.420000	1.870000	0.433095	0.070000	2.000000e-02	1.000000	0.070000	0.159773	0.070000	0	4.000000e-02	1.200000e-01
DIAPH3	81624	broad.mit.edu	37	13	60557994	60557994	+	Silent	SNP	C	C	T			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr13:60557994C>T	ENST00000400324.4	-	13	1609	c.1389G>A	c.(1387-1389)gaG>gaA	p.E463E	DIAPH3_ENST00000400320.1_Silent_p.E417E|DIAPH3_ENST00000267215.4_Silent_p.E463E|DIAPH3_ENST00000465066.1_5'UTR|DIAPH3_ENST00000377908.2_Silent_p.E452E|DIAPH3_ENST00000400319.1_Silent_p.E393E|DIAPH3_ENST00000400330.1_Silent_p.E463E	NM_001042517.1|NM_001258366.1	NP_001035982.1|NP_001245295.1	Q9NSV4	DIAP3_HUMAN	diaphanous-related formin 3			46		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)			GGGATACACACTCATCAATTA	0.313000																								0							SO:0001819	synonymous_variant			ENST00000400324.4	1	1	hg19	CCDS41898.1																																																																																				TCGA-US-A77G-01A-11D-A32N-08	DIAPH3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045166.3	1	0	1	107	428	0	84	1	4.258298e-01	4	3	0	84	2		0	0	0	0	0	2	1	1.000000	107	424	0	84	2		0	0	0	0	84	2	-20.000000	1	1	0	0		1	1	2	3	2.146113	0	0.420000	1.870000	0.433095	0.980000	8.100000e-01	1.000000	1.000000	0.957805	0.980000	1	8.900000e-01	1
C14orf93	60686	broad.mit.edu	37	14	23467783	23467783	+	Silent	SNP	G	G	A			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr14:23467783G>A	ENST00000299088.6	-	2	879	c.450C>T	c.(448-450)agC>agT	p.S150S	C14orf93_ENST00000557513.1_5'Flank|C14orf93_ENST00000397377.1_5'UTR|RP11-298I3.4_ENST00000555294.1_RNA|C14orf93_ENST00000406429.2_Silent_p.S150S|RP11-298I3.4_ENST00000556503.1_RNA|C14orf93_ENST00000397382.4_Silent_p.S150S|C14orf93_ENST00000341470.4_Silent_p.S150S|C14orf93_ENST00000397379.3_Silent_p.S150S	NM_001130708.1|NM_021944.2	NP_001124180.1|NP_068763.2	Q9H972	CN093_HUMAN	chromosome 14 open reading frame 93			17	all_cancers(95;3.3e-05)				CCTGCACGCCGCTGCCCACGC	0.637000																								0							SO:0001819	synonymous_variant			ENST00000299088.6	0	1	hg19	CCDS9583.1																																																																																				TCGA-US-A77G-01A-11D-A32N-08	C14orf93-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071688.5	0	0	0	5	212	0	52	0	1.262221e-01	0	22	0	52	2		0	0	0	0	0	2	1	0.934390	5	208	0	52	2		0	0	0	0	52	2	-3.518828	1	1	121412	1	33	1	0	1	1	1.647296	1	0.420000	1.870000	0.265823	0.090000	3.000000e-02	0.190000	0.090000	0.101752	0.090000	0	5.000000e-02	1.400000e-01
FANCM	57697	broad.mit.edu	37	14	45658329	45658329	+	Missense_Mutation	SNP	G	G	T			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr14:45658329G>T	ENST00000267430.5	+	20	5189	c.5104G>T	c.(5104-5106)Gac>Tac	p.D1702Y	FANCM_ENST00000542564.2_Missense_Mutation_p.D1676Y	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M			85					CAAACAACAGGACCATTGTTT	0.398000								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia															0							SO:0001583	missense	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	ENST00000267430.5	1	1	hg19	CCDS32070.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.75|14.75	2.627860|2.627860	0.46944|0.46944	.|.	.|.	ENSG00000187790|ENSG00000187790	ENST00000267430;ENST00000542564;ENST00000556250|ENST00000554809	T;T;T|.	0.76578|.	-1.03;-1.03;-1.03|.	4.83|4.83	2.99|2.99	0.34606|0.34606	.|.	1.959200|.	0.02691|.	N|.	0.110584|.	T|T	0.40372|0.40372	0.1114|0.1114	L|L	0.50333|0.50333	1.59|1.59	0.09310|0.09310	N|N	1|1	D;D|.	0.56521|.	0.976;0.976|.	P;P|.	0.47744|.	0.556;0.556|.	T|T	0.25047|0.25047	-1.0143|-1.0143	10|5	0.54805|.	T|.	0.06|.	.|.	7.073|7.073	0.25189|0.25189	0.2863:0.0:0.7137:0.0|0.2863:0.0:0.7137:0.0	.|.	1676;1702|.	B2RTQ9;Q8IYD8|.	.;FANCM_HUMAN|.	Y|V	1702;1676;1218|634	ENSP00000267430:D1702Y;ENSP00000442493:D1676Y;ENSP00000452033:D1218Y|.	ENSP00000267430:D1702Y|.	D|G	+|+	1|2	0|0	FANCM|FANCM	44728079|44728079	0.290000|0.290000	0.24343|0.24343	0.001000|0.001000	0.08648|0.08648	0.313000|0.313000	0.28021|0.28021	1.643000|1.643000	0.37217|0.37217	0.565000|0.565000	0.29255|0.29255	0.650000|0.650000	0.86243|0.86243	GAC|GGA		TCGA-US-A77G-01A-11D-A32N-08	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	1	0	1	124	534	0	113	0	3.936267e-01	1	6	0	113	2		0	0	0	0	0	2	1	1.000000	121	525	0	112	2		0	0	0	0	113	2	-20.000000	1	1	0	0		1	0	1	1	2.054670	0	0.420000	1.870000	0.418779	0.890000	7.500000e-01	1.000000	1.000000	0.895139	0.890000	1	8.200000e-01	9.700000e-01
PGBD4	161779	broad.mit.edu	37	15	34396066	34396066	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr15:34396066G>A	ENST00000397766.2	+	1	1793	c.1334G>A	c.(1333-1335)cGc>cAc	p.R445H	EMC7_ENST00000256545.4_5'Flank|EMC7_ENST00000532113.1_5'Flank	NM_152595.4	NP_689808.2	Q96DM1	PGBD4_HUMAN	piggyBac transposable element derived 4			16		all_lung(180;1.76e-08)			CCATCTGAGCGCAAAAGACAC	0.413000																								0							SO:0001583	missense			ENST00000397766.2	0	1	hg19	CCDS10033.1	.	.	.	.	.	.	.	.	.	.	g	17.93	3.508096	0.64410	.	.	ENSG00000182405	ENST00000397766	T	0.19938	2.11	1.02	-1.24	0.09435	.	3.690650	0.02398	N	0.080343	T	0.34106	0.0886	L	0.55481	1.735	0.09310	N	0.99999	D	0.67145	0.996	D	0.68353	0.957	T	0.23511	-1.0186	10	0.25106	T	0.35	.	1.9806	0.03426	0.4088:0.0:0.3294:0.2618	.	445	Q96DM1	PGBD4_HUMAN	H	445	ENSP00000380872:R445H	ENSP00000380872:R445H	R	+	2	0	PGBD4	32183358	0.487000	0.25988	0.009000	0.14445	0.953000	0.61014	0.430000	0.21428	-0.479000	0.06813	0.306000	0.20318	CGC		TCGA-US-A77G-01A-11D-A32N-08	PGBD4-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251522.1	0	0	0	6	377	0	85	0	3.768252e-04	0	2	0	85	2		0	0	0	0	0	2	1	0.964702	6	375	0	85	2		0	0	0	0	85	2	-2.432565	0	1	0	0		1	0	0	0	2.032407	0	0.420000	1.870000	0.415087	0.070000	2.000000e-02	0.150000	0.080000	0.085546	0.070000	0	4.000000e-02	1.200000e-01
TLN2	83660	broad.mit.edu	37	15	63088384	63088384	+	Missense_Mutation	SNP	C	C	A			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr15:63088384C>A	ENST00000561311.1	+	46	6172	c.5942C>A	c.(5941-5943)aCa>aAa	p.T1981K	TLN2_ENST00000306829.6_Missense_Mutation_p.T1981K			Q9Y4G6	TLN2_HUMAN	talin 2			99					GCATGCATTACAGCCGCCACC	0.562000																								0							SO:0001583	missense			ENST00000561311.1	0	1	hg19	CCDS32261.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.317805	0.81469	.	.	ENSG00000171914	ENST00000306829	T	0.69040	-0.37	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.75155	0.3811	M	0.64997	1.995	0.80722	D	1	D	0.67145	0.996	P	0.55303	0.773	T	0.70941	-0.4735	10	0.23302	T	0.38	-17.5484	19.3855	0.94554	0.0:1.0:0.0:0.0	.	1981	Q9Y4G6	TLN2_HUMAN	K	1981	ENSP00000303476:T1981K	ENSP00000303476:T1981K	T	+	2	0	TLN2	60875437	1.000000	0.71417	0.964000	0.40570	0.521000	0.34408	7.776000	0.85560	2.569000	0.86673	0.655000	0.94253	ACA		TCGA-US-A77G-01A-11D-A32N-08	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2	0	0	0	6	402	0	63	0	9.775769e-02	0	30	0	63	2		0	0	0	0	0	2	0	0.963044	1	399	0	62	2		0	0	0	0	63	2	-5.984040	1	0	0	0		1	0	0	0	2.031128	0	0.420000	1.870000	0.415087	0.070000	2.000000e-02	0.140000	0.070000	0.080351	0.070000	0	4.000000e-02	1.100000e-01
KIAA0556	23247	broad.mit.edu	37	16	27640032	27640032	+	Missense_Mutation	SNP	A	A	G			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr16:27640032A>G	ENST00000261588.4	+	4	210	c.191A>G	c.(190-192)cAc>cGc	p.H64R		NM_015202.2	NP_056017.2	O60303	K0556_HUMAN	KIAA0556			76					AGGCTGGAGCACTTGGAGCAA	0.488000																								0							SO:0001583	missense			ENST00000261588.4	1	1	hg19	CCDS32415.1	.	.	.	.	.	.	.	.	.	.	A	12.65	2.000654	0.35320	.	.	ENSG00000047578	ENST00000261588	T	0.39997	1.05	5.21	5.21	0.72293	.	0.237136	0.35349	N	0.003262	T	0.51092	0.1654	L	0.48642	1.525	0.40163	D	0.977085	D	0.61697	0.99	P	0.61592	0.891	T	0.45366	-0.9266	10	0.22109	T	0.4	.	12.6144	0.56567	1.0:0.0:0.0:0.0	.	64	O60303	K0556_HUMAN	R	64	ENSP00000261588:H64R	ENSP00000261588:H64R	H	+	2	0	KIAA0556	27547533	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.096000	0.50243	1.973000	0.57446	0.454000	0.30748	CAC		TCGA-US-A77G-01A-11D-A32N-08	KIAA0556-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433724.1	1	0	0	69	699	0	128	1	1.948003e-01	2	7	0	128	2		0	0	0	0	0	2	1	1.000000	69	688	0	128	2		0	0	0	0	128	2	-18.467950	1	1	0	0		1	0	0	0	2.054990	0	0.420000	1.870000	0.420000	0.420000	3.300000e-01	0.530000	0.420000	0.432112	0.420000	0	3.700000e-01	4.800000e-01
HAS3	3038	broad.mit.edu	37	16	69148721	69148721	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr16:69148721G>A	ENST00000306560.1	+	4	1370	c.1214G>A	c.(1213-1215)cGc>cAc	p.R405H	HAS3_ENST00000569188.1_Missense_Mutation_p.R405H|HAS3_ENST00000219322.3_Intron	NM_005329.2	NP_005320.2	O00219	HYAS3_HUMAN	hyaluronan synthase 3	p.R405H(1)		16		Ovarian(137;0.101)			TACCGGGGCCGCATCTGGAAC	0.542000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000306560.1	0	1	hg19	CCDS10871.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.700380	0.88924	.	.	ENSG00000103044	ENST00000306560	T	0.59364	0.27	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.68869	0.3048	L	0.59436	1.845	0.58432	D	0.999998	D	0.63046	0.992	P	0.54312	0.748	T	0.65899	-0.6056	10	0.44086	T	0.13	-8.402	20.2544	0.98414	0.0:0.0:1.0:0.0	.	405	O00219	HAS3_HUMAN	H	405	ENSP00000304440:R405H	ENSP00000304440:R405H	R	+	2	0	HAS3	67706222	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.749000	0.74883	2.885000	0.99019	0.655000	0.94253	CGC		TCGA-US-A77G-01A-11D-A32N-08	HAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268898.2	0	0	0	6	620	1	124	0	2.440147e-02	0	51	1	124	3		0	0	0	0	0	2	0	0.010155	7	615	1	122	18		0	0	0	1	124	2	-2.015021	0	1	121412	1	31	1	0	0	0	2.054990	0	0.420000	1.870000	0.420000	0.040000	1.000000e-02	0.100000	0.040000	0.052942	0.040000	0	2.000000e-02	7.000000e-02
WDR90	197335	broad.mit.edu	37	16	711075	711075	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr16:711075G>A	ENST00000293879.4	+	29	3416	c.3416G>A	c.(3415-3417)cGc>cAc	p.R1139H	WDR90_ENST00000549091.1_Missense_Mutation_p.R1139H			Q96KV7	WDR90_HUMAN	WD repeat domain 90			37		Hepatocellular(780;0.0218)			ACGTGCGGCCGCCTGGTGGTG	0.746000																								0							SO:0001583	missense			ENST00000293879.4	0	1	hg19	CCDS42092.1	.	.	.	.	.	.	.	.	.	.	G	11.47	1.648178	0.29336	2.62E-4	0.0	ENSG00000161996	ENST00000549091;ENST00000293879	T;T	0.42513	1.55;0.97	4.96	3.0	0.34707	Quinonprotein alcohol dehydrogenase-like (1);	0.436630	0.26072	N	0.026520	T	0.24236	0.0587	N	0.12182	0.205	0.80722	D	1	B;B	0.10296	0.003;0.002	B;B	0.08055	0.003;0.002	T	0.03807	-1.1002	10	0.42905	T	0.14	.	10.5167	0.44894	0.1582:0.0:0.8418:0.0	.	1139;1139	F8VUX9;Q96KV7	.;WDR90_HUMAN	H	1139	ENSP00000448122:R1139H;ENSP00000293879:R1139H	ENSP00000293879:R1139H	R	+	2	0	WDR90	651076	0.817000	0.29147	0.620000	0.29132	0.104000	0.19210	4.351000	0.59398	0.619000	0.30197	-0.671000	0.03813	CGC		TCGA-US-A77G-01A-11D-A32N-08	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	0	0	0	3	47	0	13	0	5.522551e-01	0	25	0	13	2		0	0	0	0	0	2	1	0.812596	3	47	0	12	2		0	0	0	0	13	2	-7.311756	1	1	116534	15	34	1	1	2	3	2.077619	0	0.420000	1.870000	0.422426	0.330000	9.000000e-02	0.810000	0.290000	0.364061	0.330000	0	1.800000e-01	5.300000e-01
JPH3	57338	broad.mit.edu	37	16	87636931	87636931	+	Missense_Mutation	SNP	C	C	A			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr16:87636931C>A	ENST00000284262.2	+	1	421	c.179C>A	c.(178-180)aCg>aAg	p.T60K	RP11-482M8.3_ENST00000602388.1_RNA	NM_020655.2	NP_065706.2	Q8WXH2	JPH3_HUMAN	junctophilin 3			30					AGCGGCAACACGTACCAGGGC	0.677000																								0							SO:0001583	missense			ENST00000284262.2	0	1	hg19	CCDS10962.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.048418	0.75846	.	.	ENSG00000154118	ENST00000301008;ENST00000284262	T	0.55930	0.49	4.07	4.07	0.47477	.	0.177447	0.47852	D	0.000213	T	0.40670	0.1126	N	0.04787	-0.16	0.58432	D	0.999998	B	0.22851	0.076	B	0.39771	0.309	T	0.38520	-0.9657	10	0.30854	T	0.27	.	15.2272	0.73359	0.0:1.0:0.0:0.0	.	60	Q8WXH2	JPH3_HUMAN	K	60	ENSP00000284262:T60K	ENSP00000284262:T60K	T	+	2	0	JPH3	86194432	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	1.759000	0.38420	1.800000	0.52685	0.462000	0.41574	ACG		TCGA-US-A77G-01A-11D-A32N-08	JPH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269108.2	0	0	0	5	163	0	48	0	0	0	1	0	48	2		0	0	0	0	0	2	0	0.931268	0	161	0	48	2		0	0	0	0	48	2	-7.799874	1	0	0	0		1	1	2	3	2.061710	0	0.420000	1.870000	0.421215	0.150000	5.000000e-02	0.320000	0.140000	0.167051	0.150000	0	9.000000e-02	2.300000e-01
MYO1D	4642	broad.mit.edu	37	17	31082528	31082528	+	Silent	SNP	G	G	A			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr17:31082528G>A	ENST00000318217.5	-	11	1753	c.1449C>T	c.(1447-1449)gcC>gcT	p.A483A	MYO1D_ENST00000584232.1_5'UTR|MYO1D_ENST00000394649.4_Silent_p.A395A|MYO1D_ENST00000579584.1_Silent_p.A483A	NM_015194.1	NP_056009.1	O94832	MYO1D_HUMAN	myosin ID			39			BRCA - Breast invasive adenocarcinoma(9;0.0362)		TGGAAAAATGGGCGTGTTTGC	0.393000																								0							SO:0001819	synonymous_variant			ENST00000318217.5	1	1	hg19	CCDS32615.1																																																																																				TCGA-US-A77G-01A-11D-A32N-08	MYO1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447457.1	0	0	0	15	399	0	80	1	9.531356e-01	7	132	0	80	2		0	0	0	0	0	2	1	0.999865	15	394	0	79	2		0	0	0	0	80	2	-3.695217	1	0	0	0		1	1	2	3	2.072926	0	0.420000	1.870000	0.422426	0.170000	9.000000e-02	0.290000	0.180000	0.191313	0.170000	0	1.300000e-01	2.300000e-01
KRTAP3-1	83896	broad.mit.edu	37	17	39165249	39165249	+	Silent	SNP	G	G	A			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr17:39165249G>A	ENST00000391588.1	-	1	117	c.78C>T	c.(76-78)tgC>tgT	p.C26C	KRTAP3-1_ENST00000581033.1_5'UTR	NM_031958.1	NP_114164.1	Q9BYR8	KRA31_HUMAN	keratin associated protein 3-1			8		Breast(137;0.00043)			CTCCACAGCGGCAGCTTTTAT	0.592000																								0							SO:0001819	synonymous_variant			ENST00000391588.1	0	1	hg19	CCDS32645.1																																																																																				TCGA-US-A77G-01A-11D-A32N-08	KRTAP3-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257699.1	0	0	0	5	539	0	102		0	0	0	0	102	2		0	0	0	0	0	2	1	0.933107	5	524	0	100	2		0	0	0	0	102	2	-3.103783	1	1	0	0		1	1	2	3	2.072926	0	0.420000	1.870000	0.422426	0.040000	0	0.110000	0.040000	0.061580	0.040000	0	2.000000e-02	8.000000e-02
DHX8	1659	broad.mit.edu	37	17	41601211	41601211	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr17:41601211G>A	ENST00000262415.3	+	23	3731	c.3659G>A	c.(3658-3660)cGc>cAc	p.R1220H	DHX8_ENST00000540306.1_Intron	NM_004941.1	NP_004932.1	Q14562	DHX8_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 8			42		Breast(137;0.00908)			TTCCGACGGCGCTGAAAGGCA	0.517000													NSCLC(56;1548 1661 49258 49987)											0							SO:0001583	missense			ENST00000262415.3	0	1	hg19	CCDS11464.1	.	.	.	.	.	.	.	.	.	.	G	19.20	3.780753	0.70222	.	.	ENSG00000067596	ENST00000262415	T	0.03801	3.8	6.16	5.2	0.72013	.	0.000000	0.85682	D	0.000000	T	0.09686	0.0238	L	0.36672	1.1	0.58432	D	0.999999	D	0.71674	0.998	P	0.52481	0.7	T	0.03423	-1.1038	10	0.87932	D	0	.	14.6997	0.69147	0.0688:0.0:0.9312:0.0	.	1220	Q14562	DHX8_HUMAN	H	1220	ENSP00000262415:R1220H	ENSP00000262415:R1220H	R	+	2	0	DHX8	38956737	1.000000	0.71417	1.000000	0.80357	0.037000	0.13140	9.841000	0.99482	1.628000	0.50416	-0.145000	0.13849	CGC		TCGA-US-A77G-01A-11D-A32N-08	DHX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453485.1	0	0	0	4	208	0	42	0	5.900968e-01	0	93	0	42	2		0	0	0	0	0	2	1	0.888951	4	206	0	41	2		0	0	0	0	42	2	-3.290682	1	1	121412	1	28	1	1	2	3	2.072926	0	0.420000	1.870000	0.422426	0.090000	2.000000e-02	0.240000	0.090000	0.119707	0.090000	0	5.000000e-02	1.600000e-01
USP43	124739	broad.mit.edu	37	17	9631939	9631939	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr17:9631939G>A	ENST00000285199.7	+	15	3100	c.3004G>A	c.(3004-3006)Gtg>Atg	p.V1002M	USP43_ENST00000570827.2_3'UTR|USP43_ENST00000570475.1_Missense_Mutation_p.V997M	NM_001267576.1|NM_153210.4	NP_001254505.1|NP_694942.3	Q70EL4	UBP43_HUMAN	ubiquitin specific peptidase 43			26					TCTGAGGTCCGTGTTTCGGAA	0.602000																								0							SO:0001583	missense			ENST00000285199.7	0	1	hg19	CCDS45610.1	.	.	.	.	.	.	.	.	.	.	G	6.121	0.390479	0.11581	.	.	ENSG00000154914	ENST00000285199	T	0.10192	2.9	5.24	-0.892	0.10570	.	7.908350	0.00166	N	0.000002	T	0.10723	0.0262	L	0.57536	1.79	0.18873	N	0.999985	B;P;B;P	0.42757	0.297;0.668;0.297;0.789	B;B;B;B	0.27500	0.023;0.055;0.023;0.08	T	0.46162	-0.9211	10	0.51188	T	0.08	-12.3583	8.6472	0.34013	0.4535:0.0:0.5465:0.0	.	997;691;1002;514	B7ZVX5;Q70EL4-3;Q70EL4;Q70EL4-2	.;.;UBP43_HUMAN;.	M	1002	ENSP00000285199:V1002M	ENSP00000285199:V1002M	V	+	1	0	USP43	9572664	0.014000	0.17966	0.378000	0.26068	0.003000	0.03518	0.017000	0.13399	-0.027000	0.13873	-0.768000	0.03414	GTG		TCGA-US-A77G-01A-11D-A32N-08	USP43-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439855.3	0	0	0	4	195	0	61	0	5.136861e-02	0	14	0	61	2		0	0	0	0	0	2	1	0.891223	4	195	0	61	2		0	0	0	0	61	2	-3.861965	1	1	0	0		1	0	1	1	1.648062	1	0.420000	1.870000	0.265823	0.080000	2.000000e-02	0.180000	0.080000	0.092279	0.080000	0	4.000000e-02	1.300000e-01
PSG7	5676	broad.mit.edu	37	19	43433639	43433639	+	RNA	SNP	G	G	T			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr19:43433639G>T	ENST00000406070.2	-	0	760				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)			GCACTCACTGGGTTCCGTATT	0.507000																								0											ENST00000406070.2	1	1	hg19																																																																																					TCGA-US-A77G-01A-11D-A32N-08	PSG7-001	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000321431.2	0	0	0	380	1508	0	429		0	0	0	0	429	2		0	0	0	0	0	2	1	1.000000	366	1427	0	439	2		0	0	0	0	429	2	-20.000000	1	1	121348	1	40	1	1	2	3	2.102128	0	0.420000	1.870000	0.427217	0.960000	8.700000e-01	1.000000	1.000000	0.965739	0.960000	1	9.200000e-01	1
KCNA7	3743	broad.mit.edu	37	19	49573549	49573549	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr19:49573549G>A	ENST00000221444.1	-	2	1497	c.1142C>T	c.(1141-1143)gCg>gTg	p.A381V		NM_031886.2	NP_114092.2	Q96RP8	KCNA7_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 7			11		all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_epithelial(76;3.83e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		Dalfampridine(DB06637)	CAGCACGCCCGCAATGGCACA	0.557000													Colon(74;686 1235 3793 23366 48562)											0							SO:0001583	missense			ENST00000221444.1	0	1	hg19	CCDS12755.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.862088	0.91511	.	.	ENSG00000104848	ENST00000221444	D	0.98313	-4.86	4.65	4.65	0.58169	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.97096	0.9051	L	0.48260	1.515	0.80722	D	1	D	0.60575	0.988	P	0.47251	0.542	D	0.97729	1.0201	10	0.72032	D	0.01	.	16.6617	0.85242	0.0:0.0:1.0:0.0	.	381	Q96RP8	KCNA7_HUMAN	V	381	ENSP00000221444:A381V	ENSP00000221444:A381V	A	-	2	0	KCNA7	54265361	1.000000	0.71417	0.982000	0.44146	0.872000	0.50106	9.860000	0.99555	2.321000	0.78463	0.491000	0.48974	GCG		TCGA-US-A77G-01A-11D-A32N-08	KCNA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466263.1	0	0	0	4	197	0	57		0	0	0	0	57	2		0	0	0	0	0	2	1	0.891217	4	197	0	56	2		0	0	0	0	57	2	-3.365417	1	1	121412	1	31	1	0	1	1	1.714791	1	0.420000	1.870000	0.265823	0.080000	2.000000e-02	0.180000	0.070000	0.091382	0.080000	0	4.000000e-02	1.300000e-01
C3	718	broad.mit.edu	37	19	6719298	6719298	+	Missense_Mutation	SNP	C	C	T			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr19:6719298C>T	ENST00000245907.6	-	2	283	c.191G>A	c.(190-192)gGc>gAc	p.G64D		NM_000064.2	NP_000055.2	P01024	CO3_HUMAN	complement component 3			72				Intravenous Immunoglobulin(DB00028)	TAGTTTTTTGCCTGGGAAGTC	0.592000																								0							SO:0001583	missense			ENST00000245907.6	0	1	hg19	CCDS32883.1	.	.	.	.	.	.	.	.	.	.	C	7.629	0.678519	0.14841	.	.	ENSG00000125730	ENST00000245907	T	0.79845	-1.31	4.87	-9.75	0.00506	.	2.754490	0.01396	N	0.013408	T	0.60209	0.2251	N	0.22421	0.69	0.09310	N	1	B	0.26318	0.146	B	0.28709	0.093	T	0.51957	-0.8639	10	0.11794	T	0.64	.	3.9794	0.09489	0.0806:0.3674:0.1424:0.4095	.	64	P01024	CO3_HUMAN	D	64	ENSP00000245907:G64D	ENSP00000245907:G64D	G	-	2	0	C3	6670298	0.000000	0.05858	0.001000	0.08648	0.154000	0.21943	-1.181000	0.03085	-1.444000	0.01950	0.305000	0.20034	GGC		TCGA-US-A77G-01A-11D-A32N-08	C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317636.2	0	0	0	6	687	0	132	0	4.766381e-01	0	166	0	132	2		0	0	0	0	0	2	1	0.964606	6	684	0	131	2		0	0	0	0	132	2	-2.381119	0	1	0	0		1	1	2	3	2.100189	0	0.420000	1.870000	0.427217	0.040000	0	1.000000	0.040000	0.093086	0.040000	0	2.000000e-02	7.000000e-02
ANKRD34A	284615	broad.mit.edu	37	1	145474624	145474624	+	Silent	SNP	C	C	A			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr1:145474624C>A	ENST00000323397.4	+	4	2589	c.1296C>A	c.(1294-1296)ccC>ccA	p.P432P	LIX1L_ENST00000369308.3_5'Flank|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)				ACGTCAGTCCCCACCCTCCCA	0.687000																								0							SO:0001819	synonymous_variant			ENST00000323397.4	0	1	hg19	CCDS30829.1																																																																																				TCGA-US-A77G-01A-11D-A32N-08	ANKRD34A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038512.1	0	0	0	4	210	0	28	0	1.879019e-03	0	3	0	28	2		0	0	0	0	0	2	1	0.883199	4	203	0	28	2		0	0	0	0	28	2	-3.564516	1	1	0	0		1	0	2	2	2.236663	1	0.420000	1.870000	0.420000	0.090000	2.000000e-02	0.210000	0.090000	0.109494	0.090000	0	5.000000e-02	1.500000e-01
PADI3	51702	broad.mit.edu	37	1	17593248	17593248	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr1:17593248G>A	ENST00000375460.3	+	5	483	c.443G>A	c.(442-444)gGc>gAc	p.G148D		NM_016233.2	NP_057317.2	Q9ULW8	PADI3_HUMAN	peptidyl arginine deiminase, type III			32		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		L-Citrulline(DB00155)	GGGTATGGCGGCATCTTGCTG	0.597000																								0							SO:0001583	missense			ENST00000375460.3	0	1	hg19	CCDS179.1	.	.	.	.	.	.	.	.	.	.	G	17.32	3.359635	0.61403	.	.	ENSG00000142619	ENST00000375460	T	0.14266	2.52	5.15	4.23	0.50019	Protein-arginine deiminase (PAD), central domain (2);	0.052990	0.85682	D	0.000000	T	0.10423	0.0255	N	0.08118	0	0.38404	D	0.945756	P	0.38335	0.627	B	0.42112	0.376	T	0.27226	-1.0080	10	0.87932	D	0	-23.3232	14.4617	0.67453	0.0:0.8491:0.1509:0.0	.	148	Q9ULW8	PADI3_HUMAN	D	148	ENSP00000364609:G148D	ENSP00000364609:G148D	G	+	2	0	PADI3	17465835	1.000000	0.71417	0.661000	0.29709	0.848000	0.48234	5.229000	0.65316	1.169000	0.42739	-0.270000	0.10280	GGC		TCGA-US-A77G-01A-11D-A32N-08	PADI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006805.1	0	0	0	5	478	0	120		0	0	0	0	120	2		0	0	0	0	0	2	1	0.934712	5	470	0	119	2		0	0	0	0	120	2	-2.498435	0	1	0	0		1	1	2	3	2.073686	0	0.420000	1.870000	0.422426	0.050000	1.000000e-02	0.120000	0.050000	0.068156	0.050000	0	2.000000e-02	8.000000e-02
TRIM67	440730	broad.mit.edu	37	1	231339743	231339743	+	Silent	SNP	C	C	T			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr1:231339743C>T	ENST00000366653.5	+	6	1665	c.1665C>T	c.(1663-1665)gcC>gcT	p.A555A	TRIM67_ENST00000449018.3_Silent_p.A493A|TRIM67_ENST00000366652.2_Silent_p.A555A|TRIM67_ENST00000444294.3_Silent_p.A553A			Q6ZTA4	TRI67_HUMAN	tripartite motif containing 67			29	Breast(184;0.0871)	all_cancers(173;0.189)|Prostate(94;0.167)			ACGACGGTGCCGGGGGACAGT	0.627000																								0							SO:0001819	synonymous_variant			ENST00000366653.5	1	1	hg19	CCDS44333.1																																																																																				TCGA-US-A77G-01A-11D-A32N-08	TRIM67-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092649.3	1	0	1	32	241	0	56		0	0	0	0	56	2		0	0	0	0	0	2	1	1.000000	32	240	0	56	2		0	0	0	0	56	2	-3.142781	1	1	120994	6	38	1	1	2	3	2.247887	1	0.420000	1.870000	0.467010	0.650000	4.300000e-01	1.000000	0.600000	0.709099	0.650000	0	5.300000e-01	1
ACOT7	11332	broad.mit.edu	37	1	6409894	6409894	+	Missense_Mutation	SNP	C	C	T			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr1:6409894C>T	ENST00000377855.2	-	2	352	c.206G>A	c.(205-207)gGc>gAc	p.G69D	ACOT7_ENST00000545482.1_Intron|ACOT7_ENST00000377842.3_Missense_Mutation_p.G18D|ACOT7_ENST00000608083.1_Missense_Mutation_p.G27D|ACOT7_ENST00000361521.4_Missense_Mutation_p.G59D|ACOT7_ENST00000377845.3_Missense_Mutation_p.G39D|ACOT7_ENST00000541130.1_Missense_Mutation_p.G39D	NM_181864.2	NP_863654.1	O00154	BACH_HUMAN	acyl-CoA thioesterase 7			16	Ovarian(185;0.0634)|all_lung(157;0.175)	all_cancers(23;1.42e-38)|all_epithelial(116;3.96e-23)|all_lung(118;3.69e-08)|Lung NSC(185;8.52e-07)|all_hematologic(16;6.92e-06)|Colorectal(325;4.53e-05)|Acute lymphoblastic leukemia(12;5e-05)|all_neural(13;0.000164)|Breast(487;0.000688)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0393)|Medulloblastoma(700;0.211)			GTGGACATTGCCGGCCACGTT	0.592000													GBM(74;673 1226 4974 11850 13190)											0							SO:0001583	missense			ENST00000377855.2	0	1	hg19	CCDS65.1	.	.	.	.	.	.	.	.	.	.	C	29.3	4.993767	0.93167	.	.	ENSG00000097021	ENST00000377855;ENST00000377845;ENST00000377842;ENST00000361521;ENST00000541130	T;T;T;T;T	0.51817	0.69;0.69;0.69;0.69;0.69	4.48	4.48	0.54585	Thioesterase superfamily (1);	0.000000	0.85682	D	0.000000	T	0.67896	0.2942	M	0.75085	2.285	0.53688	D	0.999974	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.995;0.991;1.0;0.987	T	0.72327	-0.4327	10	0.72032	D	0.01	.	14.7432	0.69472	0.0:1.0:0.0:0.0	.	59;69;39;18	B3KQ12;O00154;O00154-5;O00154-6	.;BACH_HUMAN;.;.	D	69;39;18;59;39	ENSP00000367086:G69D;ENSP00000367076:G39D;ENSP00000367073:G18D;ENSP00000354615:G59D;ENSP00000441872:G39D	ENSP00000354615:G59D	G	-	2	0	ACOT7	6332481	1.000000	0.71417	0.985000	0.45067	0.996000	0.88848	7.065000	0.76727	2.349000	0.79799	0.650000	0.86243	GGC		TCGA-US-A77G-01A-11D-A32N-08	ACOT7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000003773.1	0	0	0	5	259	0	57	0	5.332093e-01	0	84	0	57	2		0	0	0	0	0	2	1	0.936240	5	256	0	57	2		0	0	0	0	57	2	-3.555150	1	1	0	0		1	1	2	3	2.088200	0	0.420000	1.870000	0.424831	0.090000	3.000000e-02	1.000000	0.090000	0.133444	0.090000	0	6.000000e-02	1.600000e-01
PREX1	57580	broad.mit.edu	37	20	47247332	47247332	+	Splice_Site	SNP	C	C	A			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr20:47247332C>A	ENST00000371941.3	-	36	4549	c.4527G>T	c.(4525-4527)agG>agT	p.R1509S	PREX1_ENST00000396220.1_Splice_Site_p.G1544V	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1			110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)		GGTAAAATGCCCTGCGAGAGA	0.622000																								0							SO:0001630	splice_region_variant			ENST00000371941.3	1	0	hg19	CCDS13410.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.592|9.592	1.126450|1.126450	0.20959|0.20959	.|.	.|.	ENSG00000124126|ENSG00000124126	ENST00000396220|ENST00000371941	T|T	0.62941|0.65732	-0.01|-0.17	4.32|4.32	4.32|4.32	0.51571|0.51571	.|.	.|0.000000	.|0.64402	.|U	.|0.000010	T|T	0.71643|0.71643	0.3364|0.3364	M|M	0.71581|0.71581	2.175|2.175	0.48040|0.48040	D|D	0.999579|0.999579	.|D;D	.|0.58620	.|0.971;0.983	.|P;P	.|0.57324	.|0.78;0.818	T|T	0.75428|0.75428	-0.3321|-0.3321	7|10	0.87932|0.87932	D|D	0|0	.|.	10.5481|10.5481	0.45072|0.45072	0.0:0.9103:0.0:0.0897|0.0:0.9103:0.0:0.0897	.|.	.|1509;806	.|Q8TCU6;Q8TCU6-2	.|PREX1_HUMAN;.	V|S	1544|1509	ENSP00000379522:G1544V|ENSP00000361009:R1509S	ENSP00000379522:G1544V|ENSP00000361009:R1509S	G|R	-|-	2|3	0|2	PREX1|PREX1	46680739|46680739	1.000000|1.000000	0.71417|0.71417	0.974000|0.974000	0.42286|0.42286	0.439000|0.439000	0.31926|0.31926	3.607000|3.607000	0.54102|0.54102	1.974000|1.974000	0.57490|0.57490	0.558000|0.558000	0.71614|0.71614	GGG|AGG		TCGA-US-A77G-01A-11D-A32N-08	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	1	0	1	70	227	0	59	0	7.219600e-01	0	10	0	59	2		0	0	0	0	0	2	1	1.000000	70	222	0	59	2		0	0	0	0	59	2	-4.544402	1	1	0	0		1	0	0	0	2.025145	0	0.420000	1.870000	0.410090	0.990000	8.800000e-01	1.000000	1.000000	0.989745	0.990000	1	9.800000e-01	1
MC3R	4159	broad.mit.edu	37	20	54824819	54824819	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr20:54824819G>A	ENST00000243911.2	+	1	1032	c.920G>A	c.(919-921)cGc>cAc	p.R307H		NM_019888.3	NP_063941.3	P41968	MC3R_HUMAN	melanocortin 3 receptor			26			Colorectal(105;0.202)		CTGGAATTGCGCAACACCTTT	0.517000																								0							SO:0001583	missense			ENST00000243911.2	0	1	hg19	CCDS13449.2	.	.	.	.	.	.	.	.	.	.	G	17.98	3.520625	0.64747	.	.	ENSG00000124089	ENST00000243911	T	0.58358	0.34	5.09	5.09	0.68999	.	0.000000	0.64402	D	0.000014	D	0.82917	0.5141	H	0.97440	4.005	0.51767	D	0.99993	D	0.89917	1.0	D	0.83275	0.996	D	0.89536	0.3789	10	0.87932	D	0	.	18.1096	0.89530	0.0:0.0:1.0:0.0	.	344	P41968	MC3R_HUMAN	H	307	ENSP00000243911:R307H	ENSP00000243911:R307H	R	+	2	0	MC3R	54258226	1.000000	0.71417	0.990000	0.47175	0.182000	0.23217	9.731000	0.98807	2.362000	0.80069	0.555000	0.69702	CGC		TCGA-US-A77G-01A-11D-A32N-08	MC3R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079786.2	0	0	0	7	810	0	152		0	0	0	0	152	2		0	0	0	0	0	2	1	0.980208	7	805	0	152	2		0	0	0	0	152	2	-1.752984	0	1	0	0		1	0	0	0	2.025145	0	0.420000	1.870000	0.410090	0.030000	0	0.080000	0.040000	0.045718	0.030000	0	2.000000e-02	6.000000e-02
PATZ1	23598	broad.mit.edu	37	22	31740473	31740473	+	Silent	SNP	C	C	T			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr22:31740473C>T	ENST00000266269.5	-	1	1745	c.1116G>A	c.(1114-1116)cgG>cgA	p.R372R	PATZ1_ENST00000215919.3_Silent_p.R372R|AC005003.1_ENST00000504184.2_5'Flank|PATZ1_ENST00000405309.3_Silent_p.R372R|PATZ1_ENST00000351933.4_Silent_p.R372R	NM_014323.2	NP_055138.2	Q9HBE1	PATZ1_HUMAN	POZ (BTB) and AT hook containing zinc finger 1	p.R372R(2)	EWSR1/PATZ1(2)	12					ACAGCTTGTGCCGGTTAAGAT	0.582000																								2	Substitution - coding silent(2)						SO:0001819	synonymous_variant			ENST00000266269.5	0	1	hg19	CCDS13894.1																																																																																				TCGA-US-A77G-01A-11D-A32N-08	PATZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321932.1	0	0	0	7	577	1	120	0	2.022992e-02	0	68	1	120	4		0	0	0	0	0	2	0	0.028322	7	569	1	117	17		0	0	0	1	120	2	-1.944095	0	1	121412	1	32	1	0	0	0	2.045565	0	0.420000	1.870000	0.417554	0.050000	2.000000e-02	0.110000	0.060000	0.064621	0.050000	0	3.000000e-02	9.000000e-02
CYTH4	27128	broad.mit.edu	37	22	37707094	37707094	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr22:37707094G>A	ENST00000248901.6	+	10	1061	c.874G>A	c.(874-876)Gag>Aag	p.E292K		NM_013385.3	NP_037517.1	Q9UIA0	CYH4_HUMAN	cytohesin 4			15					CTACTACTTCGAGTTCACCAC	0.612000																								0							SO:0001583	missense			ENST00000248901.6	1	1	hg19	CCDS13946.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.46|16.46	3.130571|3.130571	0.56828|0.56828	.|.	.|.	ENSG00000100055|ENSG00000100055	ENST00000248901|ENST00000446506	T|.	0.72725|.	-0.68|.	4.7|4.7	4.7|4.7	0.59300|0.59300	Pleckstrin homology-type (1);Pleckstrin homology domain (3);|.	0.054141|.	0.64402|.	D|.	0.000001|.	T|T	0.46092|0.46092	0.1375|0.1375	N|N	0.10972|0.10972	0.075|0.075	0.80722|0.80722	D|D	1|1	P|.	0.40211|.	0.707|.	B|.	0.32583|.	0.148|.	T|T	0.41680|0.41680	-0.9495|-0.9495	10|5	0.31617|.	T|.	0.26|.	.|.	16.7637|16.7637	0.85519|0.85519	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	292|.	Q9UIA0|.	CYH4_HUMAN|.	K|Q	292|44	ENSP00000248901:E292K|.	ENSP00000248901:E292K|.	E|R	+|+	1|2	0|0	CYTH4|CYTH4	36037040|36037040	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.962000|0.962000	0.63368|0.63368	7.751000|7.751000	0.85126|0.85126	2.309000|2.309000	0.77851|0.77851	0.655000|0.655000	0.94253|0.94253	GAG|CGA		TCGA-US-A77G-01A-11D-A32N-08	CYTH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318917.1	1	0	1	140	462	0	140	0	2.345171e-01	0	4	0	140	2		0	0	0	0	0	2	1	1.000000	135	458	0	138	2		0	0	0	0	140	2	-4.446789	1	1	121412	1	34	1	0	0	0	2.045565	0	0.420000	1.870000	0.417554	0.990000	9.400000e-01	1.000000	1.000000	0.996423	0.990000	1	9.900000e-01	1
ATG9A	79065	broad.mit.edu	37	2	220089227	220089227	+	Missense_Mutation	SNP	C	C	T			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr2:220089227C>T	ENST00000409618.1	-	8	1305	c.866G>A	c.(865-867)cGc>cAc	p.R289H	ATG9A_ENST00000488833.1_5'Flank|ATG9A_ENST00000396761.2_Missense_Mutation_p.R289H|AC068946.1_ENST00000408417.1_RNA|ATG9A_ENST00000409422.1_Missense_Mutation_p.R228H|ATG9A_ENST00000361242.4_Missense_Mutation_p.R289H			Q7Z3C6	ATG9A_HUMAN	autophagy related 9A			13		Renal(207;0.0474)			CCACAGGATGCGGTTGCTGAG	0.567000																								0							SO:0001583	missense			ENST00000409618.1	1	1	hg19	CCDS42820.1	.	.	.	.	.	.	.	.	.	.	C	15.15	2.749084	0.49257	.	.	ENSG00000198925	ENST00000396761;ENST00000409618;ENST00000361242;ENST00000409422	T;T;T;T	0.39592	1.51;1.51;1.51;1.07	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	T	0.58581	0.2132	L	0.46885	1.475	0.50632	D	0.999889	D	0.89917	1.0	D	0.68353	0.957	T	0.55915	-0.8065	10	0.42905	T	0.14	.	18.9912	0.92793	0.0:1.0:0.0:0.0	.	289	Q7Z3C6	ATG9A_HUMAN	H	289;289;289;228	ENSP00000379983:R289H;ENSP00000386710:R289H;ENSP00000355173:R289H;ENSP00000386535:R228H	ENSP00000355173:R289H	R	-	2	0	ATG9A	219797471	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.953000	0.70290	2.481000	0.83766	0.655000	0.94253	CGC		TCGA-US-A77G-01A-11D-A32N-08	ATG9A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335930.1	1	0	1	32	118	0	31	1	9.999971e-01	26	54	0	31	2		0	0	0	0	0	2	1	1.000000	32	118	0	30	2		0	0	0	0	31	2	-20.000000	1	1	121004	1	28	1	0	0	0	2.036806	0	0.420000	1.870000	0.415087	0.990000	7.200000e-01	1.000000	1.000000	0.945515	0.990000	1	8.500000e-01	1
GMPPA	29926	broad.mit.edu	37	2	220366590	220366590	+	Missense_Mutation	SNP	C	C	T			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr2:220366590C>T	ENST00000358215.3	+	5	629	c.260C>T	c.(259-261)gCc>gTc	p.A87V	GMPPA_ENST00000313597.5_Missense_Mutation_p.A87V|GMPPA_ENST00000373917.3_Missense_Mutation_p.A87V|GMPPA_ENST00000341142.3_Missense_Mutation_p.A87V|AC053503.11_ENST00000429882.1_RNA|GMPPA_ENST00000373908.1_Missense_Mutation_p.A87V	NM_205847.2	NP_995319.1	Q96IJ6	GMPPA_HUMAN	GDP-mannose pyrophosphorylase A			20		Renal(207;0.0183)			CAGGAATTTGCCCCCCTAGGC	0.592000																								0							SO:0001583	missense			ENST00000358215.3	0	1	hg19	CCDS2441.1	.	.	.	.	.	.	.	.	.	.	C	17.03	3.284479	0.59867	.	.	ENSG00000144591	ENST00000313597;ENST00000373917;ENST00000358215;ENST00000373908;ENST00000455657;ENST00000435316;ENST00000341142	D;D;D;D;T;T;D	0.93906	-3.31;-3.31;-3.31;-3.31;-0.7;-0.7;-3.31	4.68	3.8	0.43715	Nucleotidyl transferase (1);	0.270854	0.34338	N	0.004044	D	0.88548	0.6466	L	0.33093	0.98	0.40974	D	0.984729	B;P	0.37276	0.001;0.589	B;B	0.35727	0.008;0.209	D	0.87535	0.2455	10	0.54805	T	0.06	-29.327	12.5741	0.56354	0.0:0.9176:0.0:0.0824	.	87;87	Q96IJ6-2;Q96IJ6	.;GMPPA_HUMAN	V	87;87;87;87;87;52;87	ENSP00000315925:A87V;ENSP00000363027:A87V;ENSP00000350949:A87V;ENSP00000363016:A87V;ENSP00000392465:A87V;ENSP00000411060:A52V;ENSP00000340760:A87V	ENSP00000315925:A87V	A	+	2	0	GMPPA	220074834	1.000000	0.71417	0.984000	0.44739	0.993000	0.82548	5.950000	0.70265	0.967000	0.38186	0.561000	0.74099	GCC		TCGA-US-A77G-01A-11D-A32N-08	GMPPA-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130230.1	0	0	0	6	381	1	82	0	1.863027e-02	0	98	1	82	6		0	0	0	0	0	2	0	0.023214	6	379	1	82	16		0	0	0	1	82	2	-2.162292	0	1	0	0		1	0	0	0	2.036806	0	0.420000	1.870000	0.415087	0.070000	2.000000e-02	0.150000	0.080000	0.084670	0.070000	0	4.000000e-02	1.200000e-01
EFHD1	80303	broad.mit.edu	37	2	233546356	233546356	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr2:233546356G>A	ENST00000264059.3	+	4	1124	c.647G>A	c.(646-648)cGg>cAg	p.R216Q	snoU13_ENST00000459149.1_RNA|EFHD1_ENST00000409708.1_Missense_Mutation_p.R104Q|EFHD1_ENST00000409613.1_Missense_Mutation_p.R120Q|EFHD1_ENST00000410095.1_Missense_Mutation_p.R104Q	NM_025202.3	NP_079478.1	Q9BUP0	EFHD1_HUMAN	EF-hand domain family, member D1			7		all_hematologic(139;0.0123)|Acute lymphoblastic leukemia(138;0.0182)|Breast(86;0.0199)|Renal(207;0.025)			CAAGATGAGCGGAAGCGGGAG	0.542000																								0							SO:0001583	missense			ENST00000264059.3	0	1	hg19	CCDS2497.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.827702	0.90955	.	.	ENSG00000115468	ENST00000409613;ENST00000264059;ENST00000540187;ENST00000409708;ENST00000410095	T;T;T;T	0.38560	1.13;1.13;1.13;1.13	5.65	3.7	0.42460	.	0.332624	0.29715	N	0.011387	T	0.37376	0.1001	L	0.58302	1.8	0.58432	D	0.999998	P;P	0.44006	0.824;0.824	B;B	0.38156	0.121;0.266	T	0.34104	-0.9842	10	0.52906	T	0.07	-5.5142	11.0327	0.47783	0.0:0.14:0.7149:0.1451	.	120;216	E9PFH3;Q9BUP0	.;EFHD1_HUMAN	Q	120;216;119;104;104	ENSP00000386556:R120Q;ENSP00000264059:R216Q;ENSP00000386243:R104Q;ENSP00000386685:R104Q	ENSP00000264059:R216Q	R	+	2	0	EFHD1	233254600	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	1.562000	0.36353	1.362000	0.46000	0.586000	0.80456	CGG		TCGA-US-A77G-01A-11D-A32N-08	EFHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257040.2	0	0	0	5	557	1	122	0	1.924871e-02	0	19	1	122	2		0	0	0	0	0	2	0	0.011331	6	547	1	122	16		0	0	0	1	122	2	-2.455305	0	1	121412	3	40	1	0	0	0	2.031970	0	0.420000	1.870000	0.415087	0.040000	0	0.090000	0.040000	0.049979	0.040000	0	2.000000e-02	7.000000e-02
DNMT3A	1788	broad.mit.edu	37	2	25471001	25471001	+	Missense_Mutation	SNP	C	C	T	rs146110707	by1000genomes	TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr2:25471001C>T	ENST00000264709.3	-	7	1097	c.760G>A	c.(760-762)Gca>Aca	p.A254T	DNMT3A_ENST00000380746.4_Missense_Mutation_p.A65T|DNMT3A_ENST00000402667.1_Missense_Mutation_p.A31T|DNMT3A_ENST00000321117.5_Missense_Mutation_p.A254T	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha			1021	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				GTGGGGGATGCGGGGTCAGTG	0.627000			Mis, F, N, S		AML										Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	0							SO:0001583	missense			ENST00000264709.3	0	1	hg19	CCDS33157.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	28.5	4.928743	0.92389	.	.	ENSG00000119772	ENST00000380746;ENST00000321117;ENST00000264709;ENST00000402667	D;D;D;D	0.93366	-3.21;-3.2;-3.2;-3.21	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	D	0.90242	0.6949	N	0.24115	0.695	0.80722	D	1	P;D	0.61080	0.846;0.989	B;P	0.46917	0.071;0.531	D	0.89436	0.3720	10	0.31617	T	0.26	-4.9539	18.2356	0.89948	0.0:1.0:0.0:0.0	.	254;65	Q9Y6K1;E9PEB8	DNM3A_HUMAN;.	T	65;254;254;31	ENSP00000370122:A65T;ENSP00000324375:A254T;ENSP00000264709:A254T;ENSP00000384237:A31T	ENSP00000264709:A254T	A	-	1	0	DNMT3A	25324505	1.000000	0.71417	0.319000	0.25293	0.901000	0.52897	7.054000	0.76649	2.653000	0.90120	0.563000	0.77884	GCA		TCGA-US-A77G-01A-11D-A32N-08	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000211587.1	0	0	0	8	505	0	108	0	2.263251e-02	0	13	0	108	2		0	0	0	0	0	2	1	0.989041	8	500	0	106	2		0	0	0	0	108	2	-2.001916	0	1	121412	1	28	1	0	0	0	2.044086	0	0.420000	1.870000	0.417554	0.070000	2.000000e-02	0.140000	0.080000	0.082646	0.070000	0	4.000000e-02	1.100000e-01
ASPRV1	151516	broad.mit.edu	37	2	70187919	70187919	+	Missense_Mutation	SNP	C	C	T			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr2:70187919C>T	ENST00000320256.4	-	1	1478	c.902G>A	c.(901-903)cGc>cAc	p.R301H	PCBP1-AS1_ENST00000457076.1_RNA|PCBP1-AS1_ENST00000419542.1_RNA|PCBP1-AS1_ENST00000596259.1_RNA|PCBP1-AS1_ENST00000435880.2_RNA|PCBP1-AS1_ENST00000413436.1_RNA|PCBP1-AS1_ENST00000418564.1_RNA	NM_152792.2	NP_690005.2			aspartic peptidase, retroviral-like 1			14					GGTGCATGTGCGGTGCTCAAA	0.557000																								0							SO:0001583	missense			ENST00000320256.4	0	1	hg19	CCDS1897.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.418130	0.83449	.	.	ENSG00000244617	ENST00000320256	T	0.51071	0.72	5.38	5.38	0.77491	.	0.000000	0.43110	D	0.000601	T	0.55130	0.1901	N	0.24115	0.695	0.38945	D	0.958225	D	0.89917	1.0	D	0.83275	0.996	T	0.60500	-0.7251	10	0.59425	D	0.04	-16.4374	14.6246	0.68611	0.0:1.0:0.0:0.0	.	301	Q53RT3	APRV1_HUMAN	H	301	ENSP00000315383:R301H	ENSP00000315383:R301H	R	-	2	0	ASPRV1	70041423	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	3.858000	0.55979	2.530000	0.85305	0.655000	0.94253	CGC		TCGA-US-A77G-01A-11D-A32N-08	ASPRV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334161.1	0	0	0	8	832	1	162	0	3.370029e-03	0	8	1	162	2		0	0	0	0	0	2	0	0.033767	8	821	1	162	18		0	0	0	1	162	2	-2.114061	0	1	121412	1	31	1	0	0	0	2.044086	0	0.420000	1.870000	0.417554	0.040000	1.000000e-02	0.090000	0.040000	0.050736	0.040000	0	2.000000e-02	7.000000e-02
ATP2B2	491	broad.mit.edu	37	3	10417285	10417285	+	Silent	SNP	G	G	A			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr3:10417285G>A	ENST00000352432.4	-	10	1314	c.1245C>T	c.(1243-1245)taC>taT	p.Y415Y	ATP2B2_ENST00000397077.1_Silent_p.Y370Y|ATP2B2_ENST00000383800.4_Silent_p.Y370Y|ATP2B2_ENST00000360273.2_Silent_p.Y415Y|ATP2B2_ENST00000343816.4_Silent_p.Y401Y			Q01814	AT2B2_HUMAN	ATPase, Ca++ transporting, plasma membrane 2			74					CCACAGTGAAGTAGAGCACCA	0.557000													Ovarian(125;1619 1709 15675 19819 38835)											0							SO:0001819	synonymous_variant			ENST00000352432.4	1	1	hg19	CCDS33701.1																																																																																				TCGA-US-A77G-01A-11D-A32N-08	ATP2B2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250576.2	1	0	1	54	173	0	53		0	0	0	0	53	2		0	0	0	0	0	2	1	1.000000	54	171	0	53	2		0	0	0	0	53	2	-20.000000	1	1	0	0		1	0	0	0	2.047916	0	0.420000	1.870000	0.417554	0.990000	8.700000e-01	1.000000	1.000000	0.989672	0.990000	1	9.900000e-01	1
OXNAD1	92106	broad.mit.edu	37	3	16312479	16312479	+	Missense_Mutation	SNP	T	T	G			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08			T	G	T	T		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr3:16312479T>G	ENST00000285083.5	+	3	485	c.20T>G	c.(19-21)aTg>aGg	p.M7R	OXNAD1_ENST00000435829.2_Missense_Mutation_p.M25R|OXNAD1_ENST00000544043.1_Missense_Mutation_p.M25R|OXNAD1_ENST00000605932.1_Missense_Mutation_p.M7R|OXNAD1_ENST00000606098.1_Missense_Mutation_p.M7R	NM_138381.3	NP_612390.1	Q96HP4	OXND1_HUMAN	oxidoreductase NAD-binding domain containing 1			13					GCTGCTGTTATGATTCCTGGG	0.458000																								0							SO:0001583	missense			ENST00000285083.5	1	1	hg19	CCDS2630.1	.	.	.	.	.	.	.	.	.	.	T	10.50	1.366861	0.24771	.	.	ENSG00000154814	ENST00000285083;ENST00000435829;ENST00000544043	T;T;T	0.22134	2.29;1.97;2.25	5.07	2.62	0.31277	.	1.342610	0.04581	N	0.394909	T	0.21590	0.0520	L	0.36672	1.1	0.09310	N	1	B;B	0.22683	0.073;0.044	B;B	0.25405	0.06;0.027	T	0.36456	-0.9747	10	0.72032	D	0.01	-16.2189	9.2363	0.37468	0.0:0.0:0.3581:0.6419	.	25;7	F5H620;Q96HP4	.;OXND1_HUMAN	R	7;7;25	ENSP00000285083:M7R;ENSP00000389872:M7R;ENSP00000437967:M25R	ENSP00000285083:M7R	M	+	2	0	OXNAD1	16287483	0.009000	0.17119	0.002000	0.10522	0.181000	0.23173	0.823000	0.27366	0.377000	0.24735	-0.313000	0.08912	ATG		TCGA-US-A77G-01A-11D-A32N-08	OXNAD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252109.1	1	0	1	155	587	0	134	1	9.914238e-01	15	15	0	134	2		0	0	0	0	0	2	1	1.000000	154	576	0	133	2		0	0	0	0	134	2	-20.000000	1	1	121412	1	36	1	0	0	0	2.047916	0	0.420000	1.870000	0.417554	0.980000	8.500000e-01	1.000000	1.000000	0.967673	0.980000	1	9.100000e-01	1
SCN5A	6331	broad.mit.edu	37	3	38639417	38639417	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr3:38639417G>A	ENST00000333535.4	-	14	2214	c.2065C>T	c.(2065-2067)Cgt>Tgt	p.R689C	SCN5A_ENST00000450102.2_Missense_Mutation_p.R689C|SCN5A_ENST00000451551.2_Missense_Mutation_p.R689C|SCN5A_ENST00000413689.1_Missense_Mutation_p.R689C|SCN5A_ENST00000423572.2_Missense_Mutation_p.R689C|SCN5A_ENST00000455624.2_Missense_Mutation_p.R689C|SCN5A_ENST00000443581.1_Missense_Mutation_p.R689C|SCN5A_ENST00000425664.1_Missense_Mutation_p.R689C|SCN5A_ENST00000449557.2_Missense_Mutation_p.R689C|SCN5A_ENST00000414099.2_Missense_Mutation_p.R689C			Q14524	SCN5A_HUMAN	sodium channel, voltage-gated, type V, alpha subunit			107	Medulloblastoma(35;0.163)			Ajmaline(DB01426)|Aprindine(DB01429)|Benzonatate(DB00868)|Carbamazepine(DB00564)|Cinchocaine(DB00527)|Cocaine(DB00907)|Disopyramide(DB00280)|Encainide(DB01228)|Ethotoin(DB00754)|Flecainide(DB01195)|Fosphenytoin(DB01320)|Hexylcaine(DB00473)|Indecainide(DB00192)|Lidocaine(DB00281)|Mexiletine(DB00379)|Moricizine(DB00680)|Oxcarbazepine(DB00776)|Phenytoin(DB00252)|Prilocaine(DB00750)|Procainamide(DB01035)|Propafenone(DB01182)|Quinidine barbiturate(DB01346)|Quinidine(DB00908)|Ranolazine(DB00243)|Riluzole(DB00740)|Tocainide(DB01056)|Valproic Acid(DB00313)|Verapamil(DB00661)|Zonisamide(DB00909)	TGGGCGAGACGGTTCCAGCAT	0.532000																								0							SO:0001583	missense			ENST00000333535.4	1	1	hg19	CCDS46796.1	.	.	.	.	.	.	.	.	.	.	G	13.66	2.304276	0.40795	.	.	ENSG00000183873	ENST00000414099;ENST00000423572;ENST00000413689;ENST00000451551;ENST00000443581;ENST00000425664;ENST00000333535;ENST00000455624;ENST00000450102;ENST00000449557	D;D;D;D;D;D;D;D;D;D	0.96300	-3.88;-3.91;-3.91;-3.91;-3.91;-3.88;-3.91;-3.97;-3.91;-3.91	4.9	4.9	0.64082	.	1.137170	0.06183	N	0.679836	D	0.97785	0.9273	M	0.80183	2.485	0.44603	D	0.997576	D;D;D;D;D;D;D	0.71674	0.978;0.991;0.987;0.978;0.978;0.998;0.987	B;B;P;B;B;P;P	0.52710	0.328;0.328;0.528;0.328;0.328;0.707;0.528	D	0.94661	0.7848	10	0.87932	D	0	.	18.2549	0.90016	0.0:0.0:1.0:0.0	.	689;689;689;689;689;689;689	E9PEF3;E9PHB6;Q14524-6;E9PG18;Q14524;Q14524-2;E9PEK2	.;.;.;.;SCN5A_HUMAN;.;.	C	689	ENSP00000398962:R689C;ENSP00000398266:R689C;ENSP00000410257:R689C;ENSP00000388797:R689C;ENSP00000397915:R689C;ENSP00000416634:R689C;ENSP00000328968:R689C;ENSP00000399524:R689C;ENSP00000403355:R689C;ENSP00000413996:R689C	ENSP00000328968:R689C	R	-	1	0	SCN5A	38614421	0.134000	0.22483	0.982000	0.44146	0.405000	0.30901	1.004000	0.29822	2.563000	0.86464	0.491000	0.48974	CGT		TCGA-US-A77G-01A-11D-A32N-08	SCN5A-014	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377958.1	1	0	1	68	318	0	91		0	0	0	0	91	2		0	0	0	0	0	2	1	1.000000	68	315	0	91	2		0	0	0	0	91	2	-2.980424	1	1	121132	2	34	1	0	0	0	2.047916	0	0.420000	1.870000	0.417554	0.830000	6.600000e-01	1.000000	1.000000	0.838319	0.830000	0	7.400000e-01	9.300000e-01
PTPN23	25930	broad.mit.edu	37	3	47452686	47452686	+	Missense_Mutation	SNP	C	C	T			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr3:47452686C>T	ENST00000265562.4	+	20	3475	c.3398C>T	c.(3397-3399)tCt>tTt	p.S1133F	PTPN23_ENST00000431726.1_Missense_Mutation_p.S1007F	NM_015466.2	NP_056281.1	Q9H3S7	PTN23_HUMAN	protein tyrosine phosphatase, non-receptor type 23			23					GGCACTCAGTCTCCTGGGGGT	0.711000																								0							SO:0001583	missense			ENST00000265562.4	1	1	hg19	CCDS2754.1	.	.	.	.	.	.	.	.	.	.	C	13.01	2.109780	0.37242	.	.	ENSG00000076201	ENST00000265562	T	0.02631	4.22	5.3	4.37	0.52481	.	0.135690	0.49916	D	0.000126	T	0.02083	0.0065	N	0.08118	0	0.22701	N	0.998834	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.48736	-0.9009	10	0.33141	T	0.24	-6.0248	14.322	0.66491	0.0:0.8504:0.1496:0.0	.	1007;1133	B4DST5;Q9H3S7	.;PTN23_HUMAN	F	1133	ENSP00000265562:S1133F	ENSP00000265562:S1133F	S	+	2	0	PTPN23	47427690	1.000000	0.71417	1.000000	0.80357	0.774000	0.43823	2.033000	0.41136	2.468000	0.83385	0.563000	0.77884	TCT		TCGA-US-A77G-01A-11D-A32N-08	PTPN23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257492.2	1	0	0	23	80	0	30	1	9.999977e-01	31	54	0	30	2		0	0	0	0	0	2	1	1.000000	23	80	0	29	2		0	0	0	0	30	2	-20.000000	1	1	0	0		1	0	0	0	2.047916	0	0.420000	1.870000	0.417554	0.990000	7.100000e-01	1.000000	1.000000	0.954746	0.990000	1	8.700000e-01	1
DNAH1	25981	broad.mit.edu	37	3	52383089	52383089	+	Silent	SNP	C	C	T			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr3:52383089C>T	ENST00000420323.2	+	13	2553	c.2292C>T	c.(2290-2292)tcC>tcT	p.S764S		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1			62					ACATTGCCTCCTTTCTCAAGT	0.577000																								0							SO:0001819	synonymous_variant			ENST00000420323.2	1	1	hg19	CCDS46842.1																																																																																				TCGA-US-A77G-01A-11D-A32N-08	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	1	0	1	52	190	0	55	1	2.988486e-01	4	1	0	55	2		0	0	0	0	0	2	1	1.000000	52	189	0	54	2		0	0	0	0	55	2	-3.802473	1	1	0	0		1	0	0	0	2.047916	0	0.420000	1.870000	0.417554	0.990000	7.800000e-01	1.000000	1.000000	0.961789	0.990000	1	8.900000e-01	1
PCDH18	54510	broad.mit.edu	37	4	138449640	138449640	+	Missense_Mutation	SNP	A	A	T			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr4:138449640A>T	ENST00000344876.4	-	3	3118	c.2732T>A	c.(2731-2733)aTt>aAt	p.I911N	PCDH18_ENST00000507846.1_Missense_Mutation_p.I690N|PCDH18_ENST00000511115.1_Missense_Mutation_p.I91N|PCDH18_ENST00000412923.2_Missense_Mutation_p.I910N|PCDH18_ENST00000510305.1_Missense_Mutation_p.I122N	NM_019035.3	NP_061908.1	Q9HCL0	PCD18_HUMAN	protocadherin 18			86	all_hematologic(180;0.24)				ACCTGCTGGAATTCTTCCATC	0.403000																								0							SO:0001583	missense			ENST00000344876.4	1	1	hg19	CCDS34064.1	.	.	.	.	.	.	.	.	.	.	A	14.02	2.410409	0.42715	.	.	ENSG00000189184	ENST00000344876;ENST00000412923;ENST00000507846;ENST00000510305;ENST00000511115	T;T;T;T;T	0.52754	0.74;0.74;0.65;1.57;1.57	5.56	4.38	0.52667	.	0.000000	0.43747	D	0.000521	T	0.37571	0.1008	L	0.40543	1.245	0.34420	D	0.697313	B;B;B;B	0.10296	0.003;0.0;0.001;0.001	B;B;B;B	0.08055	0.003;0.0;0.001;0.0	T	0.42327	-0.9458	10	0.28530	T	0.3	.	11.4281	0.50022	0.9295:0.0:0.0705:0.0	.	91;690;910;911	B4DLR6;D6RIG4;Q9HCL0-2;Q9HCL0	.;.;.;PCD18_HUMAN	N	911;910;690;122;91	ENSP00000355082:I911N;ENSP00000390688:I910N;ENSP00000425903:I690N;ENSP00000424269:I122N;ENSP00000425647:I91N	ENSP00000355082:I911N	I	-	2	0	PCDH18	138669090	1.000000	0.71417	0.993000	0.49108	0.987000	0.75469	6.178000	0.71968	0.943000	0.37553	0.533000	0.62120	ATT		TCGA-US-A77G-01A-11D-A32N-08	PCDH18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364614.1	1	0	1	191	730	0	171	0	3.642832e-01	0	6	0	171	2		0	0	0	0	0	2	1	1.000000	186	715	0	170	2		0	0	0	0	171	2	-20.000000	1	1	0	0		1	1	2	3	2.070103	0	0.420000	1.870000	0.422426	0.980000	8.600000e-01	1.000000	1.000000	0.971106	0.980000	1	9.200000e-01	1
TLR1	7096	broad.mit.edu	37	4	38799732	38799732	+	Nonsense_Mutation	SNP	G	G	A			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr4:38799732G>A	ENST00000502213.2	-	3	950	c.721C>T	c.(721-723)Caa>Taa	p.Q241*	TLR1_ENST00000308979.2_Nonsense_Mutation_p.Q241*			Q15399	TLR1_HUMAN	toll-like receptor 1			28					GGATTTGTTTGAAGTTTCGCC	0.348000													GBM(5;216 373 40795 46382)											0							SO:0001587	stop_gained			ENST00000502213.2	0	1	hg19	CCDS33973.1	.	.	.	.	.	.	.	.	.	.	G	19.29	3.798266	0.70567	.	.	ENSG00000174125	ENST00000308979;ENST00000502213	.	.	.	4.69	0.633	0.17712	.	1.133800	0.06641	N	0.761075	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.28530	T	0.3	.	9.2911	0.37786	0.0:0.11:0.2678:0.6222	.	.	.	.	X	241	.	ENSP00000354932:Q241X	Q	-	1	0	TLR1	38476127	0.050000	0.20438	0.077000	0.20336	0.001000	0.01503	0.818000	0.27295	0.259000	0.21709	-0.169000	0.13324	CAA		TCGA-US-A77G-01A-11D-A32N-08	TLR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360510.3	1	0	1	49	164	0	36	1	3.307641e-01	2	3	0	36	2		0	0	0	0	0	2	1	1.000000	48	162	0	36	2		0	0	0	0	36	2	-20.000000	1	1	0	0		1	0	0	0	2.055408	0	0.420000	1.870000	0.420000	0.990000	8.300000e-01	1.000000	1.000000	0.982638	0.990000	1	9.500000e-01	1
TMPRSS11E	28983	broad.mit.edu	37	4	69337338	69337338	+	Missense_Mutation	SNP	A	A	G			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr4:69337338A>G	ENST00000305363.4	+	5	551	c.487A>G	c.(487-489)Aaa>Gaa	p.K163E		NM_014058.3	NP_054777.2	Q9UL52	TM11E_HUMAN	transmembrane protease, serine 11E			24					AGTTAAAATTAAAAGTAAGTT	0.308000																								0							SO:0001583	missense			ENST00000305363.4	1	1	hg19	CCDS33993.1	.	.	.	.	.	.	.	.	.	.	A	8.476	0.858592	0.17178	.	.	ENSG00000087128	ENST00000305363	T	0.31769	1.48	5.83	5.83	0.93111	.	0.391906	0.21879	N	0.067776	T	0.19765	0.0475	L	0.27053	0.805	0.31370	N	0.680243	P	0.37781	0.608	B	0.35413	0.202	T	0.09662	-1.0664	10	0.10111	T	0.7	.	12.5838	0.56406	1.0:0.0:0.0:0.0	.	163	Q9UL52	TM11E_HUMAN	E	163	ENSP00000307519:K163E	ENSP00000307519:K163E	K	+	1	0	TMPRSS11E	69019933	1.000000	0.71417	1.000000	0.80357	0.021000	0.10359	3.137000	0.50562	2.229000	0.72834	0.482000	0.46254	AAA		TCGA-US-A77G-01A-11D-A32N-08	TMPRSS11E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360584.1	1	0	1	102	468	0	77		0	0	0	0	77	2		0	0	0	0	0	2	1	1.000000	101	462	0	77	2		0	0	0	0	77	2	-20.000000	1	1	0	0		1	0	0	0	2.055408	0	0.420000	1.870000	0.420000	0.840000	7.000000e-01	1.000000	0.850000	0.854301	0.840000	0	7.700000e-01	9.300000e-01
SLC6A18	348932	broad.mit.edu	37	5	1244416	1244416	+	Missense_Mutation	SNP	C	C	T			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr5:1244416C>T	ENST00000324642.3	+	10	1547	c.1424C>T	c.(1423-1425)gCc>gTc	p.A475V	SLC6A18_ENST00000296821.4_Missense_Mutation_p.A373V	NM_182632.2	NP_872438.2	Q96N87	S6A18_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 18			34	all_cancers(3;2.99e-16)|Lung NSC(6;8.55e-15)|all_lung(6;7.2e-14)|all_epithelial(6;1.76e-10)		Epithelial(17;0.000356)|all cancers(22;0.00124)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)		GACAATTTTGCCGCTTCCCCG	0.582000																								0							SO:0001583	missense			ENST00000324642.3	0	1	hg19	CCDS3860.1	.	.	.	.	.	.	.	.	.	.	C	12.56	1.975383	0.34848	.	.	ENSG00000164363	ENST00000324642;ENST00000296821	T;T	0.76578	-1.03;-1.03	4.87	-1.66	0.08265	.	0.373560	0.27126	N	0.020814	T	0.58177	0.2104	N	0.21617	0.685	0.09310	N	1	B	0.16802	0.019	B	0.15052	0.012	T	0.49341	-0.8950	10	0.87932	D	0	.	5.9492	0.19235	0.0:0.3423:0.141:0.5167	.	475	Q96N87	S6A18_HUMAN	V	475;373	ENSP00000323549:A475V;ENSP00000296821:A373V	ENSP00000296821:A373V	A	+	2	0	SLC6A18	1297416	0.226000	0.23696	0.000000	0.03702	0.001000	0.01503	0.643000	0.24750	-0.361000	0.08125	-1.036000	0.02392	GCC		TCGA-US-A77G-01A-11D-A32N-08	SLC6A18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206728.3	0	0	0	6	677	0	112		0	0	0	0	112	2		0	0	0	0	0	2	1	0.963618	6	668	0	111	2		0	0	0	0	112	2	-1.823947	0	1	0	0		1	0	0	0	2.055894	0	0.420000	1.870000	0.420000	0.040000	0	0.090000	0.040000	0.048496	0.040000	0	2.000000e-02	7.000000e-02
CHSY3	337876	broad.mit.edu	37	5	129520070	129520070	+	Missense_Mutation	SNP	G	G	A	rs140992502		TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr5:129520070G>A	ENST00000305031.4	+	3	1593	c.1235G>A	c.(1234-1236)cGc>cAc	p.R412H	CHSY3_ENST00000507545.1_3'UTR	NM_175856.4	NP_787052.3	Q70JA7	CHSS3_HUMAN	chondroitin sulfate synthase 3			28		all_cancers(142;0.0227)|Breast(839;0.198)|Prostate(80;0.215)|Lung NSC(810;0.239)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		ATGCTCAGCCGCAAAATTTCT	0.478000																								0							SO:0001583	missense			ENST00000305031.4	0	1	hg19	CCDS34223.1	.	.	.	.	.	.	.	.	.	.	G	25.5	4.647807	0.87958	0.0	2.33E-4	ENSG00000198108	ENST00000305031	T	0.15834	2.39	4.5	4.5	0.54988	.	0.000000	0.64402	D	0.000016	T	0.27241	0.0668	M	0.65975	2.015	0.80722	D	1	P	0.48998	0.918	P	0.45998	0.5	T	0.03017	-1.1082	9	.	.	.	-2.8659	18.5119	0.90920	0.0:0.0:1.0:0.0	.	412	Q70JA7	CHSS3_HUMAN	H	412	ENSP00000302629:R412H	.	R	+	2	0	CHSY3	129547969	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.601000	0.98297	2.779000	0.95612	0.650000	0.86243	CGC		TCGA-US-A77G-01A-11D-A32N-08	CHSY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371453.1	0	0	0	6	365	0	64	0	0	0	1	0	64	2		0	0	0	0	0	2	0	0.006403	7	364	1	64	19		0	0	0	0	64	2	-2.305597	0	1	121412	22	45	1	0	0	0	2.055894	0	0.420000	1.870000	0.420000	0.070000	2.000000e-02	0.160000	0.080000	0.089023	0.070000	0	5.000000e-02	1.200000e-01
PCDHA7	56141	broad.mit.edu	37	5	140216008	140216008	+	Silent	SNP	G	G	A			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr5:140216008G>A	ENST00000525929.1	+	1	2040	c.2040G>A	c.(2038-2040)tcG>tcA	p.S680S	PCDHA3_ENST00000522353.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA7_ENST00000378125.3_Silent_p.S680S|PCDHA1_ENST00000394633.3_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529619.1_Intron	NM_018910.2	NP_061733.1	Q9UN72	PCDA7_HUMAN	protocadherin alpha 7			63			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		AGGCGTCGTCGCGGGCATCGT	0.622000													NSCLC(160;258 2013 5070 22440 28951)											0							SO:0001819	synonymous_variant			ENST00000525929.1	1	1	hg19	CCDS54918.1																																																																																				TCGA-US-A77G-01A-11D-A32N-08	PCDHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372887.2	1	0	1	89	388	0	107		0	0	0	0	107	2		0	0	0	0	0	2	1	1.000000	88	381	0	105	2		0	0	0	0	107	2	-20.000000	1	1	0	0		1	0	0	0	2.055894	0	0.420000	1.870000	0.420000	0.880000	7.200000e-01	1.000000	1.000000	0.887558	0.880000	1	8.000000e-01	9.700000e-01
PCDHA8	56140	broad.mit.edu	37	5	140221029	140221029	+	Silent	SNP	C	C	T			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr5:140221029C>T	ENST00000531613.1	+	1	123	c.123C>T	c.(121-123)caC>caT	p.H41H	PCDHA3_ENST00000522353.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA8_ENST00000378123.3_Silent_p.H41H|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529619.1_Intron	NM_018911.2	NP_061734.1	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8			78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		AGGCCAAACACGGCACCTTCG	0.672000																								0							SO:0001819	synonymous_variant			ENST00000531613.1	1	1	hg19	CCDS54919.1																																																																																				TCGA-US-A77G-01A-11D-A32N-08	PCDHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372830.2	1	0	1	43	400	0	109		0	0	0	0	109	2		0	0	0	0	0	2	1	1.000000	40	387	0	127	2		0	0	0	0	109	2	-20.000000	1	1	0	0		1	0	0	0	2.055894	0	0.420000	1.870000	0.420000	0.460000	3.300000e-01	0.600000	0.460000	0.469365	0.460000	0	3.900000e-01	5.300000e-01
PCDHGA8	9708	broad.mit.edu	37	5	140773877	140773877	+	Silent	SNP	G	G	A			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr5:140773877G>A	ENST00000398604.2	+	1	1497	c.1497G>A	c.(1495-1497)gcG>gcA	p.A499A	PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron	NM_032088.1	NP_114477.1	Q9Y5G5	PCDG8_HUMAN	protocadherin gamma subfamily A, 8			51			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		TGCAGGGGGCGCCCCTGTCCT	0.562000																								0							SO:0001819	synonymous_variant			ENST00000398604.2	1	1	hg19	CCDS47291.1																																																																																				TCGA-US-A77G-01A-11D-A32N-08	PCDHGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376972.1	1	0	1	47	178	0	44	0	0	1	0	0	44	2		0	0	0	0	0	2	1	1.000000	46	178	0	43	2		0	0	0	0	44	2	-20.000000	1	1	0	0		1	0	0	0	2.055894	0	0.420000	1.870000	0.420000	0.990000	7.500000e-01	1.000000	1.000000	0.949281	0.990000	1	8.600000e-01	1
FAM71B	153745	broad.mit.edu	37	5	156589868	156589868	+	Missense_Mutation	SNP	C	C	T	rs138175460		TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr5:156589868C>T	ENST00000302938.4	-	2	1503	c.1408G>A	c.(1408-1410)Gca>Aca	p.A470T		NM_130899.2	NP_570969.2	Q8TC56	FA71B_HUMAN	family with sequence similarity 71, member B			68	Renal(175;0.00212)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)		TGGCCAGATGCGGACCGGTGG	0.532000																								0							SO:0001583	missense			ENST00000302938.4	0	1	hg19	CCDS4335.1	.	.	.	.	.	.	.	.	.	.	C	9.219	1.032795	0.19590	.	.	ENSG00000170613	ENST00000302938	T	0.19806	2.12	4.64	-9.28	0.00656	.	1.737350	0.03907	N	0.281301	T	0.06735	0.0172	N	0.03608	-0.345	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.22906	-1.0203	10	0.23302	T	0.38	0.0025	4.3119	0.10974	0.1338:0.5568:0.1468:0.1627	.	470	Q8TC56	FA71B_HUMAN	T	470	ENSP00000305596:A470T	ENSP00000305596:A470T	A	-	1	0	FAM71B	156522446	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.937000	0.01547	-2.061000	0.00892	-1.268000	0.01426	GCA		TCGA-US-A77G-01A-11D-A32N-08	FAM71B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252570.2	0	0	0	6	731	0	153		0	0	0	0	153	2		0	0	0	0	0	2	1	0.963244	6	719	0	152	2		0	0	0	0	153	2	-2.015480	0	1	121412	1	34	1	0	0	0	2.055894	0	0.420000	1.870000	0.420000	0.030000	0	0.080000	0.040000	0.044875	0.030000	0	2.000000e-02	6.000000e-02
FGFR4	2264	broad.mit.edu	37	5	176520430	176520430	+	Silent	SNP	C	C	T			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr5:176520430C>T	ENST00000292408.4	+	10	1520	c.1275C>T	c.(1273-1275)tcC>tcT	p.S425S	FGFR4_ENST00000393637.1_Silent_p.S385S|FGFR4_ENST00000393648.2_Missense_Mutation_p.P374L|FGFR4_ENST00000292410.3_Silent_p.S385S|FGFR4_ENST00000502906.1_Silent_p.S425S	NM_002011.3|NM_213647.1	NP_002002.3|NP_998812.1	P22455	FGFR4_HUMAN	fibroblast growth factor receptor 4			34	all_cancers(89;5.93e-05)|Renal(175;0.000269)|Lung NSC(126;0.0088)|all_lung(126;0.0142)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	Palifermin(DB00039)|Ponatinib(DB08901)	CAGGCTCTTCCGGCAAGTCAA	0.622000										TSP Lung(9;0.080)														0							SO:0001819	synonymous_variant			ENST00000292408.4	1	1	hg19	CCDS4410.1	2|2	9.157509157509158E-4|9.157509157509158E-4	0|0	0.0|0.0	0|0	0.0|0.0	2|2	0.0034965034965034965|0.0034965034965034965	0|0	0.0|0.0	C|C	10.16|10.16	1.274249|1.274249	0.23221|0.23221	.|.	.|.	ENSG00000160867|ENSG00000160867	ENST00000393648|ENST00000511076	T|.	0.78481|.	-1.18|.	4.76|4.76	-9.52|-9.52	0.00578|0.00578	.|.	.|.	.|.	.|.	.|.	T|T	0.43743|0.43743	0.1261|0.1261	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.52480|0.52480	-0.8570|-0.8570	8|4	0.44086|.	T|.	0.13|.	.|.	5.7567|5.7567	0.18176|0.18176	0.1148:0.0898:0.4839:0.3115|0.1148:0.0898:0.4839:0.3115	.|.	374|.	B4DVP5|.	.|.	L|W	374|57	ENSP00000377259:P374L|.	ENSP00000377259:P374L|.	P|R	+|+	2|1	0|2	FGFR4|FGFR4	176453036|176453036	0.000000|0.000000	0.05858|0.05858	0.212000|0.212000	0.23672|0.23672	0.653000|0.653000	0.38743|0.38743	-7.064000|-7.064000	0.00045|0.00045	-3.096000|-3.096000	0.00246|0.00246	-0.315000|-0.315000	0.08773|0.08773	CCG|CGG		TCGA-US-A77G-01A-11D-A32N-08	FGFR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253410.1	0	0	1	132	533	0	158	1	9.993709e-01	8	38	0	158	2		0	0	0	0	0	2	1	1.000000	130	529	0	155	2		0	0	0	0	158	2	-2.912873	1	1	121410	47	51	1	0	0	0	2.055894	0	0.420000	1.870000	0.420000	0.940000	8.000000e-01	1.000000	1.000000	0.936883	0.940000	1	8.600000e-01	1
ENC1	8507	broad.mit.edu	37	5	73931388	73931388	+	Missense_Mutation	SNP	T	T	A			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08			T	A	T	T		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr5:73931388T>A	ENST00000302351.4	-	2	2053	c.923A>T	c.(922-924)gAc>gTc	p.D308V	ENC1_ENST00000537006.1_Missense_Mutation_p.D308V|ENC1_ENST00000510316.1_Missense_Mutation_p.D235V	NM_003633.3	NP_003624.1	O14682	ENC1_HUMAN	ectodermal-neural cortex 1 (with BTB domain)			20		all_lung(232;0.0154)|Lung NSC(167;0.0331)|Ovarian(174;0.0798)			ATACAACTTGTCACACATGAA	0.498000																								0							SO:0001583	missense			ENST00000302351.4	1	1	hg19	CCDS4021.1	.	.	.	.	.	.	.	.	.	.	T	19.63	3.863395	0.71949	.	.	ENSG00000171617	ENST00000302351;ENST00000510316;ENST00000537006	T;T;T	0.66280	-0.2;-0.2;-0.2	6.04	6.04	0.98038	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	T	0.68732	0.3033	L	0.55990	1.75	0.80722	D	1	P	0.51351	0.944	P	0.52343	0.696	T	0.66548	-0.5896	10	0.33940	T	0.23	.	16.5763	0.84648	0.0:0.0:0.0:1.0	.	308	O14682	ENC1_HUMAN	V	308;235;308	ENSP00000306356:D308V;ENSP00000423804:D235V;ENSP00000446289:D308V	ENSP00000306356:D308V	D	-	2	0	ENC1	73967144	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.040000	0.89188	2.317000	0.78254	0.459000	0.35465	GAC		TCGA-US-A77G-01A-11D-A32N-08	ENC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219862.2	1	0	1	65	290	0	69	1	9.999827e-01	36	38	0	69	2		0	0	0	0	0	2	1	1.000000	65	290	0	68	2		0	0	0	0	69	2	-20.000000	1	1	0	0		1	0	0	0	2.055894	0	0.420000	1.870000	0.420000	0.860000	6.800000e-01	1.000000	1.000000	0.871506	0.860000	1	7.700000e-01	9.700000e-01
MSH3	4437	broad.mit.edu	37	5	79974874	79974874	+	Silent	SNP	G	G	A			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr5:79974874G>A	ENST00000265081.6	+	8	1382	c.1302G>A	c.(1300-1302)gaG>gaA	p.E434E		NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3			29		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)			CCTTGTCCGAGCAAACAGAGG	0.478000								Mismatch excision repair (MMR)					Melanoma(88;1010 1399 13793 26548 36275)											0							SO:0001819	synonymous_variant			ENST00000265081.6	0	1	hg19	CCDS34195.1																																																																																				TCGA-US-A77G-01A-11D-A32N-08	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369471.1	0	0	0	7	870	0	158	0	2.352844e-02	0	25	0	158	2		0	0	0	0	0	2	1	0.980226	7	865	0	157	2		0	0	0	0	158	2	-2.659744	1	1	0	0		1	0	0	0	2.055894	0	0.420000	1.870000	0.420000	0.030000	0	0.080000	0.040000	0.043238	0.030000	0	2.000000e-02	6.000000e-02
HLA-A	3105	broad.mit.edu	37	6	29910558	29910558	+	Missense_Mutation	SNP	T	T	C	rs76217816	byFrequency	TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08			T	C	T	T		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr6:29910558T>C	ENST00000396634.1	+	4	439	c.98T>C	c.(97-99)tTc>tCc	p.F33S	HLA-A_ENST00000376802.2_Missense_Mutation_p.F33S|HLA-A_ENST00000376806.5_Missense_Mutation_p.F33S|HLA-A_ENST00000376809.5_Missense_Mutation_p.F33S			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	p.F33S(1)		30					AGGTATTTCTTCACATCCGTG	0.726000									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)														1	Substitution - Missense(1)						SO:0001583	missense	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	ENST00000396634.1	1	0	hg19	CCDS34373.1	983	0.4500915750915751	280	0.5691056910569106	184	0.5082872928176796	317	0.5541958041958042	202	0.26649076517150394	.	2.038	-0.420810	0.04734	0.515596	0.264244	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00010	9.43;9.43;9.43;9.43	3.72	-2.31	0.06765	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	20.031000	0.00447	N	0.000090	T	0.00039	0.0001	L	0.38953	1.18	0.80722	P	0.0	B;B;B	0.14012	0.009;0.009;0.008	B;B;B	0.26864	0.074;0.04;0.04	T	0.15065	-1.0450	9	0.33141	T	0.24	.	5.7818	0.18310	0.2651:0.4571:0.0:0.2778	rs2075684;rs3179175;rs17423951;rs41542415	33;33;33	Q5SRN7;Q5SRN5;P04439	.;.;1A03_HUMAN	S	33	ENSP00000379873:F33S;ENSP00000366002:F33S;ENSP00000366005:F33S;ENSP00000365998:F33S	ENSP00000348012:F33S	F	+	2	0	HLA-A	30018537	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-6.129000	0.00079	-0.931000	0.03746	-4.308000	0.00007	TTC		TCGA-US-A77G-01A-11D-A32N-08	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	0	0	1	35	159	0	41	1	1	213	1939	0	41	2		0	0	0	0	0	2	1	0.998461	16	156	1	41	14		0	0	0	0	41	2	-0.670151	0	0	120802	34584	77	1						0.420000	1.870000									0	0
HLA-A	3105	broad.mit.edu	37	6	29910572	29910572	+	Missense_Mutation	SNP	C	C	T	rs76382288	byFrequency	TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr6:29910572C>T	ENST00000396634.1	+	4	453	c.112C>T	c.(112-114)Cgg>Tgg	p.R38W	HLA-A_ENST00000376802.2_Missense_Mutation_p.R38W|HLA-A_ENST00000376806.5_Missense_Mutation_p.R38W|HLA-A_ENST00000376809.5_Missense_Mutation_p.R38W			P16189	1A31_HUMAN	major histocompatibility complex, class I, A			30					ATCCGTGTCCCGGCCCGGCCG	0.706000									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)														0							SO:0001583	missense	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	ENST00000396634.1	1	0	hg19	CCDS34373.1	81	0.03708791208791209	31	0.06300813008130081	21	0.058011049723756904	4	0.006993006993006993	25	0.032981530343007916	.	13.15	2.151849	0.38021	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00922	5.54;5.54;5.54;5.54	3.72	1.87	0.25490	MHC class I, alpha chain, alpha1/alpha2 (3);MHC classes I/II-like antigen recognition protein (3);MHC class I-like antigen recognition (3);	0.758419	0.10308	U	0.690295	T	0.02848	0.0085	H	0.94462	3.54	0.25023	N	0.991328	D;D;D;D;D	0.89917	1.0;0.998;1.0;0.999;1.0	D;P;D;D;D	0.73380	0.976;0.896;0.98;0.96;0.98	T	0.31475	-0.9942	10	0.87932	D	0	.	5.3229	0.15891	0.0:0.6744:0.2073:0.1183	rs45569434	38;38;38;38;38	P13746;Q5SRN7;P16188;Q5SRN5;P04439	1A11_HUMAN;.;1A30_HUMAN;.;1A03_HUMAN	W	38	ENSP00000379873:R38W;ENSP00000366002:R38W;ENSP00000366005:R38W;ENSP00000365998:R38W	ENSP00000348012:R38W	R	+	1	2	HLA-A	30018551	0.163000	0.22920	0.991000	0.47740	0.427000	0.31564	0.209000	0.17435	0.363000	0.24346	0.478000	0.44815	CGG		TCGA-US-A77G-01A-11D-A32N-08	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	0	0	1	34	153	0	40	1	1	284	2200	0	40	2		0	0	0	0	0	2	1	0.998070	19	149	1	40	14		0	0	0	0	40	2	-1.006282	0	0	121162	7513	61	1						0.420000	1.870000									0	0
HLA-A	3105	broad.mit.edu	37	6	29910604	29910604	+	Silent	SNP	C	C	A	rs113699656	by1000genomes	TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08			C	A	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr6:29910604C>A	ENST00000396634.1	+	4	485	c.144C>A	c.(142-144)gcC>gcA	p.A48A	HLA-A_ENST00000376802.2_Silent_p.A48A|HLA-A_ENST00000376806.5_Silent_p.A48A|HLA-A_ENST00000376809.5_Silent_p.A48A			P16189	1A31_HUMAN	major histocompatibility complex, class I, A			30					GCTTCATCGCCGTGGGCTACG	0.701000									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)														0							SO:0001819	synonymous_variant	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	ENST00000396634.1	1	0	hg19	CCDS34373.1																																																																																				TCGA-US-A77G-01A-11D-A32N-08	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	0	0	1	32	175	0	38	1	1	281	3709	0	38	2		0	0	0	0	0	2	1	0.987747	18	169	1	38	16		0	0	0	0	38	2	-0.791091	0	0	121308	43954	75	1						0.420000	1.870000									0	0
GLI3	2737	broad.mit.edu	37	7	42005520	42005520	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr7:42005520G>A	ENST00000395925.3	-	15	3235	c.3151C>T	c.(3151-3153)Cgg>Tgg	p.R1051W	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3			112					CCCTCGGGCCGCGTGTAATTC	0.662000									Pallister-Hall syndrome;Greig Cephalopolysyndactyly															0							SO:0001583	missense	Familial Cancer Database	;	ENST00000395925.3	1	1	hg19	CCDS5465.1	.	.	.	.	.	.	.	.	.	.	G	18.76	3.693058	0.68271	.	.	ENSG00000106571	ENST00000395925	T	0.15834	2.39	5.47	5.47	0.80525	.	0.100400	0.64402	D	0.000001	T	0.31513	0.0799	M	0.66939	2.045	0.80722	D	1	D	0.69078	0.997	P	0.51657	0.676	T	0.01516	-1.1335	10	0.36615	T	0.2	.	17.5184	0.87780	0.0:0.0:1.0:0.0	.	1051	P10071	GLI3_HUMAN	W	1051	ENSP00000379258:R1051W	ENSP00000379258:R1051W	R	-	1	2	GLI3	41972045	1.000000	0.71417	0.926000	0.36857	0.689000	0.40095	7.435000	0.80391	2.561000	0.86390	0.563000	0.77884	CGG		TCGA-US-A77G-01A-11D-A32N-08	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	1	0	1	71	223	0	64		0	0	0	0	64	2		0	0	0	0	0	2	1	1.000000	71	221	0	63	2		0	0	0	0	64	2	-20.000000	1	1	121412	1	26	1	0	0	0	2.057159	0	0.420000	1.870000	0.420000	0.990000	9.200000e-01	1.000000	1.000000	0.995179	0.990000	1	9.900000e-01	1
ZMIZ2	83637	broad.mit.edu	37	7	44805162	44805162	+	Missense_Mutation	SNP	C	C	G			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08			C	G	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr7:44805162C>G	ENST00000309315.4	+	16	2349	c.2226C>G	c.(2224-2226)agC>agG	p.S742R	ZMIZ2_ENST00000441627.1_Missense_Mutation_p.S742R|ZMIZ2_ENST00000413916.1_Missense_Mutation_p.S684R|ZMIZ2_ENST00000265346.7_Missense_Mutation_p.S716R|ZMIZ2_ENST00000433667.1_Missense_Mutation_p.S710R	NM_031449.3	NP_113637.3	Q8NF64	ZMIZ2_HUMAN	zinc finger, MIZ-type containing 2			35					CTGCCCCCAGCGACTACCCTG	0.657000													NSCLC(20;604 852 1948 16908 50522)											0							SO:0001583	missense			ENST00000309315.4	1	1	hg19	CCDS43576.1	.	.	.	.	.	.	.	.	.	.	C	13.54	2.266217	0.40095	.	.	ENSG00000122515	ENST00000413916;ENST00000309315;ENST00000441627;ENST00000433667;ENST00000265346;ENST00000414051	T;T;T;T;T	0.33865	1.4;1.39;1.39;1.39;1.41	5.14	-0.476	0.12100	.	0.724500	0.13304	N	0.398004	T	0.29914	0.0748	L	0.59436	1.845	0.32588	N	0.527618	B;P;B	0.37141	0.009;0.584;0.409	B;B;B	0.37833	0.017;0.259;0.203	T	0.36237	-0.9756	10	0.39692	T	0.17	-2.9204	5.127	0.14890	0.1374:0.4536:0.0:0.409	.	716;742;684	Q8NF64-2;Q8NF64;Q8NF64-3	.;ZMIZ2_HUMAN;.	R	684;742;742;710;716;745	ENSP00000409648:S684R;ENSP00000311778:S742R;ENSP00000414723:S742R;ENSP00000396601:S710R;ENSP00000265346:S716R	ENSP00000265346:S716R	S	+	3	2	ZMIZ2	44771687	0.000000	0.05858	0.735000	0.30896	0.987000	0.75469	-2.469000	0.00992	0.016000	0.14998	0.561000	0.74099	AGC		TCGA-US-A77G-01A-11D-A32N-08	ZMIZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341790.1	1	0	0	20	101	0	26	1	9.999964e-01	52	65	0	26	2		0	0	0	0	0	2	1	0.999997	20	98	0	26	2		0	0	0	0	26	2	-20.000000	1	1	0	0		1	0	0	0	2.057159	0	0.420000	1.870000	0.420000	0.780000	5.100000e-01	1.000000	1.000000	0.793675	0.780000	0	6.300000e-01	9.600000e-01
SCRIB	23513	broad.mit.edu	37	8	144896264	144896264	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr8:144896264G>A	ENST00000320476.3	-	2	190	c.184C>T	c.(184-186)Cgc>Tgc	p.R62C	SCRIB_ENST00000356994.2_Missense_Mutation_p.R62C|MIR937_ENST00000401271.1_RNA|PUF60_ENST00000524570.1_5'Flank|SCRIB_ENST00000377533.3_5'UTR	NM_015356.4	NP_056171	Q14160	SCRIB_HUMAN	scribbled planar cell polarity protein			42	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;1.12e-34)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)		CCCAGCTTGCGCAAGTTCAGC	0.617000													Pancreas(51;966 1133 10533 14576 29674)											0							SO:0001583	missense			ENST00000320476.3	0	1	hg19	CCDS6411.1	.	.	.	.	.	.	.	.	.	.	G	15.57	2.873069	0.51695	.	.	ENSG00000180900	ENST00000356994;ENST00000320476	T;T	0.58940	0.3;0.3	4.49	-0.207	0.13189	.	.	.	.	.	T	0.74222	0.3688	M	0.80422	2.495	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.77180	-0.2682	9	0.87932	D	0	.	13.3897	0.60816	0.0:0.0:0.392:0.608	.	62;62	Q14160;Q14160-3	SCRIB_HUMAN;.	C	62	ENSP00000349486:R62C;ENSP00000322938:R62C	ENSP00000322938:R62C	R	-	1	0	SCRIB	144968252	1.000000	0.71417	0.263000	0.24496	0.577000	0.36160	2.833000	0.48159	0.094000	0.17404	-0.182000	0.12963	CGC		TCGA-US-A77G-01A-11D-A32N-08	SCRIB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000382215.1	1	0	0	8	26	0	9	1	9.997887e-01	38	30	0	9	2		0	0	0	0	0	2	1	0.992400	8	26	0	9	2		0	0	0	0	9	2	-17.505890	1	1	0	0		1	0	1	1	2.050966	0	0.420000	1.870000	0.418779	0.990000	5.600000e-01	1.000000	1.000000	0.932276	0.990000	1	8.100000e-01	1
LHX2	9355	broad.mit.edu	37	9	126776246	126776246	+	Missense_Mutation	SNP	C	C	T			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr9:126776246C>T	ENST00000373615.4	+	2	866	c.127C>T	c.(127-129)Ccg>Tcg	p.P43S	RP11-85O21.4_ENST00000421041.1_RNA	NM_004789.3	NP_004780.3	P50458	LHX2_HUMAN	LIM homeobox 2			10					GCAGACCATGCCGTCCATCAG	0.701000																								0							SO:0001583	missense			ENST00000373615.4	0	1	hg19	CCDS6853.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	34|34	5.325460|5.325460	0.95708|0.95708	.|.	.|.	ENSG00000106689|ENSG00000106689	ENST00000446480|ENST00000373615	.|D	.|0.83914	.|-1.78	5.91|5.91	5.91|5.91	0.95273|0.95273	.|.	.|0.116041	.|0.64402	.|D	.|0.000015	D|D	0.84160|0.84160	0.5411|0.5411	M|M	0.73598|0.73598	2.24|2.24	0.54753|0.54753	D|D	0.999984|0.999984	.|B;B	.|0.24721	.|0.11;0.029	.|B;B	.|0.25884	.|0.064;0.016	T|T	0.80181|0.80181	-0.1489|-0.1489	5|10	.|0.42905	.|T	.|0.14	.|.	18.8766|18.8766	0.92338|0.92338	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|43;43	.|B3KNJ5;P50458	.|.;LHX2_HUMAN	V|S	40|43	.|ENSP00000362717:P43S	.|ENSP00000362717:P43S	A|P	+|+	2|1	0|0	LHX2|LHX2	125816067|125816067	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	7.803000|7.803000	0.85983|0.85983	2.793000|2.793000	0.96121|0.96121	0.655000|0.655000	0.94253|0.94253	GCC|CCG		TCGA-US-A77G-01A-11D-A32N-08	LHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054010.2	0	0	0	5	267	0	59		0	0	0	0	59	2		0	0	0	0	0	2	1	0.937504	5	266	0	59	2		0	0	0	0	59	2	-3.012480	1	1	0	0		1	1	2	3	2.063944	0	0.420000	1.870000	0.421215	0.090000	3.000000e-02	0.200000	0.090000	0.103973	0.090000	0	5.000000e-02	1.500000e-01
TJP2	9414	broad.mit.edu	37	9	71866162	71866162	+	Missense_Mutation	SNP	G	G	C			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chr9:71866162G>C	ENST00000377245.4	+	21	3411	c.3203G>C	c.(3202-3204)aGt>aCt	p.S1068T	TJP2_ENST00000535702.1_Missense_Mutation_p.S1035T|TJP2_ENST00000453658.2_Intron|TJP2_ENST00000348208.4_Intron|TJP2_ENST00000539225.1_Missense_Mutation_p.S1099T	NM_004817.3	NP_004808.2	Q9UDY2	ZO2_HUMAN	tight junction protein 2			35					GGAGAGAGCAGTGAGGAGCAA	0.512000																								0							SO:0001583	missense			ENST00000377245.4	0	1	hg19	CCDS6627.1	.	.	.	.	.	.	.	.	.	.	G	3.985	-0.005558	0.07773	.	.	ENSG00000119139	ENST00000377245;ENST00000535702;ENST00000539225	T;T;T	0.08634	3.08;3.07;3.13	6.17	-1.69	0.08186	.	0.777732	0.12506	N	0.462854	T	0.02418	0.0074	N	0.03608	-0.345	0.09310	N	1	B;B;B	0.09022	0.001;0.002;0.001	B;B;B	0.06405	0.002;0.002;0.001	T	0.43048	-0.9415	10	0.22109	T	0.4	.	0.2337	0.00183	0.244:0.2391:0.234:0.2829	.	1099;1035;1068	F5H301;F5H886;Q9UDY2	.;.;ZO2_HUMAN	T	1068;1035;1099	ENSP00000366453:S1068T;ENSP00000442090:S1035T;ENSP00000438262:S1099T	ENSP00000366453:S1068T	S	+	2	0	TJP2	71055982	0.000000	0.05858	0.003000	0.11579	0.337000	0.28794	-0.333000	0.07894	-0.348000	0.08286	-0.176000	0.13171	AGT		TCGA-US-A77G-01A-11D-A32N-08	TJP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052572.2	0	0	0	4	294	0	57	0	8.886348e-01	0	294	0	57	2		0	0	0	0	0	2	0	0.886186	0	292	0	57	2		0	0	0	0	57	2	-5.443505	1	0	0	0		1	0	0	0	2.056560	0	0.420000	1.870000	0.420000	0.060000	1.000000e-02	0.150000	0.060000	0.078938	0.060000	0	3.000000e-02	1.100000e-01
WDR44	54521	broad.mit.edu	37	X	117527019	117527019	+	Missense_Mutation	SNP	C	C	T			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chrX:117527019C>T	ENST00000254029.3	+	4	1006	c.611C>T	c.(610-612)gCc>gTc	p.A204V	WDR44_ENST00000371822.5_Missense_Mutation_p.A179V|WDR44_ENST00000371825.3_Missense_Mutation_p.A204V|WDR44_ENST00000493448.1_3'UTR	NM_019045.4	NP_061918.3	Q5JSH3	WDR44_HUMAN	WD repeat domain 44	p.A204G(2)		33					AAAGATTTTGCCGCTGTGGAA	0.488000																								2	Substitution - Missense(2)						SO:0001583	missense			ENST00000254029.3	0	1	hg19	CCDS14572.1	.	.	.	.	.	.	.	.	.	.	C	7.626	0.677788	0.14841	.	.	ENSG00000131725	ENST00000371822;ENST00000254029;ENST00000371825	T;T;T	0.73152	-0.72;-0.14;-0.02	5.69	2.87	0.33458	.	0.693990	0.14300	N	0.328333	T	0.50497	0.1619	N	0.19112	0.55	0.21473	N	0.999679	B;B;B	0.18166	0.026;0.01;0.007	B;B;B	0.23419	0.046;0.022;0.015	T	0.36962	-0.9726	10	0.33940	T	0.23	-0.7721	2.9206	0.05767	0.1398:0.5526:0.1462:0.1614	.	179;204;204	F8W913;Q5JSH3-2;Q5JSH3	.;.;WDR44_HUMAN	V	179;204;204	ENSP00000360887:A179V;ENSP00000254029:A204V;ENSP00000360890:A204V	ENSP00000254029:A204V	A	+	2	0	WDR44	117411047	0.995000	0.38212	0.182000	0.23118	0.191000	0.23601	0.769000	0.26604	0.153000	0.19213	-0.253000	0.11424	GCC		TCGA-US-A77G-01A-11D-A32N-08	WDR44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058001.1	0	0	0	5	416	0	61	0	5.309212e-02	0	25	0	61	2		0	0	0	0	0	2	1	0.935915	5	411	0	61	2		0	0	0	0	61	2	-2.079381	0	1	0	0		1	0	1	1			0.420000	1.870000	0.420000	0.020000	0	0.060000	0.030000	0.033644	0.020000	0	1.000000e-02	5.000000e-02
MAGEC3	139081	broad.mit.edu	37	X	140985098	140985098	+	Silent	SNP	C	C	T			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chrX:140985098C>T	ENST00000298296.1	+	7	1554	c.1554C>T	c.(1552-1554)ccC>ccT	p.P518P	MAGEC3_ENST00000443323.2_Silent_p.P140P|MAGEC3_ENST00000536088.1_Silent_p.P220P|MAGEC3_ENST00000409007.1_Silent_p.P220P|MAGEC3_ENST00000544766.1_Silent_p.P220P	NM_138702.1	NP_619647.1	Q8TD91	MAGC3_HUMAN	melanoma antigen family C, 3			69	Acute lymphoblastic leukemia(192;6.56e-05)				ATATGGACCCCGACAACCACT	0.448000																								0							SO:0001819	synonymous_variant			ENST00000298296.1	0	1	hg19	CCDS14676.1																																																																																				TCGA-US-A77G-01A-11D-A32N-08	MAGEC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058606.1	0	0	0	9	511	0	105		0	0	0	0	105	2		0	0	0	0	0	2	1	0.993766	8	502	0	102	2		0	0	0	0	105	2	-1.874510	0	1	121408	17	45	1	0	1	1			0.420000	1.870000	0.420000	0.030000	1.000000e-02	0.080000	0.040000	0.045481	0.030000	0	2.000000e-02	6.000000e-02
IL3RA	3563	broad.mit.edu	37	X	1497572	1497572	+	Missense_Mutation	SNP	G	G	A			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chrX:1497572G>A	ENST00000331035.4	+	10	1244	c.895G>A	c.(895-897)Gca>Aca	p.A299T	IL3RA_ENST00000381469.2_Missense_Mutation_p.A221T	NM_001267713.1|NM_002183.3	NP_001254642.1|NP_002174.1	P26951	IL3RA_HUMAN	interleukin 3 receptor, alpha (low affinity)			3		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)		Sargramostim(DB00020)	GGAGGAGGGCGCAAACACACG	0.672000																								0							SO:0001583	missense			ENST00000331035.4	0	1	hg19	CCDS14113.1	.	.	.	.	.	.	.	.	.	.	.	0.030	-1.340363	0.01277	.	.	ENSG00000185291	ENST00000331035;ENST00000381469	T;D	0.95918	1.53;-3.85	0.798	-1.59	0.08453	.	113.382000	0.00775	N	0.001236	D	0.86834	0.6028	N	0.08118	0	0.09310	N	1	B;B	0.14438	0.01;0.003	B;B	0.09377	0.004;0.0	T	0.80405	-0.1396	9	0.14252	T	0.57	.	.	.	.	.	220;299	P26951-2;P26951	.;IL3RA_HUMAN	T	299;221	ENSP00000327890:A299T;ENSP00000370878:A221T	ENSP00000327890:A299T	A	+	1	0	IL3RA	1457572	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-3.867000	0.00346	-0.741000	0.04797	-0.510000	0.04470	GCA		TCGA-US-A77G-01A-11D-A32N-08	IL3RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055600.3	0	0	0	4	188	0	38	0	1.860800e-01	0	30	0	38	2		0	0	0	0	0	2	1	0.890018	4	187	0	38	2		0	0	0	0	38	2	-3.187799	1	1	121148	28	43	1	0	1	1			0.420000	1.870000	0.420000	0.050000	1.000000e-02	0.120000	0.050000	0.060914	0.050000	0	2.000000e-02	9.000000e-02
PRRG3	79057	broad.mit.edu	37	X	150869406	150869406	+	Silent	SNP	G	G	A			TCGA-US-A77G-01A-11D-A32N-08	TCGA-US-A77G-11A-11D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1c1ef67-68f6-45f8-a296-7bd9201465b8	f15f5b8d-5e60-4946-9975-3fbff641efea	g.chrX:150869406G>A	ENST00000370353.3	+	4	987	c.597G>A	c.(595-597)gcG>gcA	p.A199A	PRRG3_ENST00000538575.1_Silent_p.A199A			Q9BZD7	TMG3_HUMAN	proline rich Gla (G-carboxyglutamic acid) 3 (transmembrane)			24	Acute lymphoblastic leukemia(192;6.56e-05)				AGGTGACTGCGCCCCAAGAGA	0.622000																								0							SO:0001819	synonymous_variant			ENST00000370353.3	1	1	hg19	CCDS14699.1																																																																																				TCGA-US-A77G-01A-11D-A32N-08	PRRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060880.1	1	0	1	120	127	0	39		0	0	0	0	39	2		0	0	0	0	0	2	1	1.000000	118	125	0	39	2		0	0	0	0	39	2	-20.000000	1	1	121392	8	40	1	0	1	1			0.420000	1.870000	0.420000	0.970000	9.000000e-01	1.000000	0.990000	0.976447	0.970000	1	9.400000e-01	1
