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	UniProt_AApos	UniProt_Region	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	ref_context	gc_content	COSMIC_n_overlapping_mutations	ESP_AvgAAsampleReadDepth	ESP_AvgEAsampleReadDepth	ESP_AvgSampleReadDepth	ESP_Chromosome	ESP_Position	ESP_TotalAAsamplesCovered	ESP_TotalEAsamplesCovered	ESP_TotalSamplesCovered	Ensembl_so_accession	Ensembl_so_term	HGNC_AccessionNumbers	HGNC_CCDSIDs	HGNC_Chromosome	HGNC_DateModified	HGNC_DateNameChanged	HGNC_DateSymbolChanged	HGNC_EnsemblGeneID	HGNC_EnsemblIDsuppliedbyEnsembl	HGNC_Genefamilydescription	HGNC_HGNCID	HGNC_LocusGroup	HGNC_LocusType	HGNC_NameSynonyms	HGNC_OMIMIDsuppliedbyNCBI	HGNC_PreviousNames	HGNC_PreviousSymbols	HGNC_PubmedIDs	HGNC_RecordType	HGNC_RefSeqsuppliedbyNCBI	HGNC_Status	HGNC_Synonyms	HGNC_UCSCIDsuppliedbyUCSC	HGNC_UniProtIDsuppliedbyUniProt	HGNC_VEGAIDs	HGVS_coding_DNA_change	HGVS_genomic_change	HGVS_protein_change	UniProt_alt_uniprot_accessions	annotation_transcript	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	gencode_transcript_name	gencode_transcript_status	gencode_transcript_tags	gencode_transcript_type	gene_type	havana_transcript	init_n_lod	init_t_lod	isArtifactMode	n_alt_count	n_ref_count	oxoGCut	pox	pox_cutoff	qox	refseq_mrna_id	t_alt_count	t_lod_fstar	t_ref_count	tumor_f
C17orf80	55028	broad.mit.edu	hg19	17	71239111	71239111	+	Silent	SNP	C	C	G			TCGA-V3-A9ZX-01A-11D-A39W-08	TCGA-V3-A9ZX-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f73499c-a4af-4281-b75f-cf8021d1f025	c85f7ffd-e167-4dee-b5d6-b469ef021e55	g.chr17:71239111C>G	ENST00000359042.2	+	5	1892	c.1698C>G	c.(1696-1698)gtC>gtG	p.V566V	C17orf80_ENST00000255557.4_Silent_p.V530V|C17orf80_ENST00000577615.1_Silent_p.V530V|C17orf80_ENST00000535032.2_Silent_p.V566V|C17orf80_ENST00000582793.1_Silent_p.V35V|C17orf80_ENST00000268942.8_Silent_p.V530V|C17orf80_ENST00000426147.2_Silent_p.V566V	NM_017941.4	NP_060411	Q9BSJ5	CQ080_HUMAN	chromosome 17 open reading frame 80	566			integral to membrane		kidney(1)|large_intestine(5)|lung(2)|skin(2)|stomach(2)|urinary_tract(2)	14			LUSC - Lung squamous cell carcinoma(166;0.197)		GATACTTCGTCCTGTGTTGTA	0.468	0	181.0	134.0	150.0	17	71239111	2203	4300	6503	SO:0001819	synonymous_variant	AY163812	CCDS11694.1, CCDS42377.1, CCDS45767.1, CCDS74145.1	17q25.1	2012-02-24	2012-02-24	2012-02-24	ENSG00000141219	ENSG00000141219		29601	protein-coding gene	gene with protein product	"""sperm-expressed protein 1"", ""migration-inducing protein 3"""				12477932	Standard	NM_017941	Approved	HLC-8, MIG3, FLJ20721, SPEP1	uc002jjl.4	Q9BSJ5		ENST00000535032.2:c.1698C>G	17.37:g.71239111C>G		A8K9X3|Q5JB45|Q6YAU3|Q9H0L9|Q9H5E6|Q9NWN5	ENST00000535032.2	37	CCDS11694.1																																																																																			C17orf80-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441893.1		40.699242	0	1	38	0	0	1	0	NM_017941	12	40.707927	13	0.480000
TENC1	23371	broad.mit.edu	hg19	12	53449609	53449609	+	Silent	SNP	C	C	T			TCGA-V3-A9ZX-01A-11D-A39W-08	TCGA-V3-A9ZX-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f73499c-a4af-4281-b75f-cf8021d1f025	c85f7ffd-e167-4dee-b5d6-b469ef021e55	g.chr12:53449609C>T	ENST00000314250.6	+	10	1031	c.741C>T	c.(739-741)caC>caT	p.H247H	TENC1_ENST00000549700.1_Silent_p.H247H|TENC1_ENST00000314276.3_Silent_p.H257H|TENC1_ENST00000552570.1_Silent_p.H247H|TENC1_ENST00000379902.3_Silent_p.H123H|TENC1_ENST00000451358.1_Silent_p.H247H|TENC1_ENST00000546602.1_Silent_p.H247H	NM_170754.2	NP_736610.2	Q63HR2	TENC1_HUMAN	tensin like C1 domain containing phosphatase (tensin 2)	247	Phosphatase tensin-type.	intracellular signal transduction|negative regulation of cell proliferation	focal adhesion	metal ion binding|phosphoprotein phosphatase activity|protein binding	central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(19)|ovary(1)|pancreas(1)|stomach(3)	34					CCTACATGCACTACAGCAAGA	0.597	0	195.0	183.0	187.0	12	53449609	2203	4300	6503	SO:0001819	synonymous_variant	AF518729	CCDS8842.1, CCDS8843.1, CCDS8844.1	12q13.13	2013-02-14	2004-03-05			ENSG00000111077	"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"", ""SH2 domain containing"""	19737	protein-coding gene	gene with protein product	"""tensin 2"""	607717	"""tensin like C1 domain-containing phosphatase"""			Standard	NM_015319	Approved	KIAA1075, C1-TEN, TNS2	uc001sbp.3	Q63HR2	OTTHUMG00000169730	ENST00000546602.1:c.741C>T	12.37:g.53449609C>T		A2VDF2|A2VDF3|A2VDI8|A5PKY4|Q2NL80|Q76MW6|Q7Z5T9|Q8NFF9|Q8NFG0|Q96P25|Q9NT29|Q9UPS7	ENST00000546602.1	37																																																																																				TENC1-008	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000405791.2		123.405672	0	3	181	0	0	1	0	NM_170754	42	125.352791	74	0.362069
hsa-mir-125a	0	broad.mit.edu	hg19	19	52196513	52196513	+	RNA	SNP	T	T	A			TCGA-V3-A9ZX-01A-11D-A39W-08	TCGA-V3-A9ZX-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f73499c-a4af-4281-b75f-cf8021d1f025	c85f7ffd-e167-4dee-b5d6-b469ef021e55	g.chr19:52196513T>A	ENST00000602324.1	-	0	196				MIR125A_ENST00000385273.1_RNA	NR_029482.1|NR_029693.1																ATGTTGCCAGTCTCTAGGTCC	0.577	0	35.0	34.0	35.0	19	52196513	1568	3580	5148																												19.37:g.52196513T>A			ENST00000602324.1	37																																																																																				hsa-mir-125a.1-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000467329.1		8.722913	0	-3	13	0	0	1	0		3	8.832691	5	0.375000
PRAMEF6	440561	broad.mit.edu	hg19	1	13108945	13108945	+	Missense_Mutation	SNP	C	C	A			TCGA-V3-A9ZX-01A-11D-A39W-08	TCGA-V3-A9ZX-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f73499c-a4af-4281-b75f-cf8021d1f025	c85f7ffd-e167-4dee-b5d6-b469ef021e55	g.chr1:13108945C>A	ENST00000376182.1	-	4	1423	c.1324G>T	c.(1324-1326)Gtg>Ttg	p.V442L	PRAMEF6_ENST00000414205.2_Missense_Mutation_p.V442L|PRAMEF6_ENST00000376192.5_Intron	NM_001282323.1	NP_001269252.1	Q5VXH4	PRAM6_HUMAN	PRAME family member 6	442					NS(1)|kidney(1)|lung(5)|urinary_tract(2)	9	Ovarian(185;0.249)	Lung NSC(185;3.67e-05)|all_lung(284;4.03e-05)|Renal(390;0.000147)|Breast(348;0.000278)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)	AAGTCCCTCACTCTCTTCATC	0.517	0									SO:0001583	missense		CCDS30594.1	1p36.21	2013-01-17				ENSG00000232423	"""-"""	30583	protein-coding gene	gene with protein product						Standard	NM_001010889	Approved		uc001auq.2	Q5VXH4	OTTHUMG00000001984	ENST00000376182.1:c.1324G>T	1.37:g.13108945C>A	ENSP00000365353:p.Val442Leu	A0AUJ9	ENST00000376182.1	37		.	.	.	.	.	.	.	.	.	.	.	0.004	-2.353666	0.00217	.	.	ENSG00000232423	ENST00000376182;ENST00000414205	T;T	0.43688	0.94;0.94	1.21	-2.17	0.07059	.	0.473069	0.18384	N	0.142871	T	0.11196	0.0273	N	0.02973	-0.45	0.09310	N	1	B	0.15930	0.015	B	0.14023	0.01	T	0.25398	-1.0133	10	0.02654	T	1	.	2.8471	0.05547	0.0:0.3133:0.3916:0.2952	.	442	A6NMV5	PRA23_HUMAN	L	442	ENSP00000365353:V442L;ENSP00000393084:V442L	ENSP00000365353:V442L	V	-	1	0	PRAMEF6	13031532	0.000000	0.05858	0.000000	0.03702	0.064000	0.16182	-0.499000	0.06413	-0.512000	0.06505	0.184000	0.17185	GTG	PRAMEF6-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding			6.970345	1	166	166	0	1.49906e-05	1	1.69893e-05	NM_001010889	10	23.468062	92	0.098039
P2RX3	5024	broad.mit.edu	hg19	11	57118298	57118298	+	Nonsense_Mutation	SNP	C	C	A			TCGA-V3-A9ZX-01A-11D-A39W-08	TCGA-V3-A9ZX-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f73499c-a4af-4281-b75f-cf8021d1f025	c85f7ffd-e167-4dee-b5d6-b469ef021e55	g.chr11:57118298C>A	ENST00000263314.2	+	8	802	c.768C>A	c.(766-768)tgC>tgA	p.C256*		NM_002559.3	NP_002550.2	P56373	P2RX3_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 3	256		positive regulation of calcium ion transport into cytosol|positive regulation of calcium-mediated signaling	integral to plasma membrane	ATP binding|extracellular ATP-gated cation channel activity|purinergic nucleotide receptor activity	endometrium(4)|kidney(2)|large_intestine(4)|lung(15)|prostate(1)	26					GGGACCAGTGCATCCCCAAAT	0.582	0	102.0	85.0	91.0	11	57118298	2201	4296	6497	SO:0001587	stop_gained	Y07683	CCDS7953.1	11q12	2012-01-17			ENSG00000109991	ENSG00000109991	"""Purinergic receptors"", ""Ligand-gated ion channels / Purinergic receptors, ionotropic"""	8534	protein-coding gene	gene with protein product		600843			9221902	Standard	NM_002559	Approved	P2X3	uc001nju.3	P56373	OTTHUMG00000167025	ENST00000263314.2:c.768C>A	11.37:g.57118298C>A	ENSP00000263314:p.Cys256*	Q6DK37|Q9UQB6	ENST00000263314.2	37	CCDS7953.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.893386	0.91889	.	.	ENSG00000109991	ENST00000439993;ENST00000263314	.	.	.	5.73	4.82	0.62117	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-33.9567	11.758	0.51886	0.0:0.9176:0.0:0.0824	.	.	.	.	X	256	.	ENSP00000263314:C256X	C	+	3	2	P2RX3	56874874	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	0.870000	0.28010	1.428000	0.47296	0.650000	0.86243	TGC	P2RX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392465.1		2.402557	1	0	62	0	0.115264	1	0.122468	NM_002559	3	6.944120	26	0.103448
GNA11	2767	broad.mit.edu	hg19	19	3118942	3118942	+	Missense_Mutation	SNP	A	A	T			TCGA-V3-A9ZX-01A-11D-A39W-08	TCGA-V3-A9ZX-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f73499c-a4af-4281-b75f-cf8021d1f025	c85f7ffd-e167-4dee-b5d6-b469ef021e55	g.chr19:3118942A>T	ENST00000078429.4	+	5	868	c.626A>T	c.(625-627)cAg>cTg	p.Q209L	AC005262.3_ENST00000587701.1_RNA|GNA11_ENST00000586180.1_3'UTR	NM_002067.2	NP_002058.2	P29992	GNA11_HUMAN	guanine nucleotide binding protein (G protein), alpha 11 (Gq class)	209		activation of phospholipase C activity by dopamine receptor signaling pathway|G-protein signaling, coupled to cAMP nucleotide second messenger|platelet activation|protein ADP-ribosylation|regulation of action potential	cytoplasm|heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activity|signal transducer activity	endometrium(2)|eye(132)|kidney(1)|large_intestine(2)|lung(1)|meninges(5)|ovary(1)|prostate(1)|skin(16)	161		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.79e-05)|OV - Ovarian serous cystadenocarcinoma(105;2.68e-113)|Epithelial(107;1.22e-111)|all cancers(105;5.78e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00141)|STAD - Stomach adenocarcinoma(1328;0.181)	GTGGGGGGCCAGCGGTCGGAG	0.612	82	104.0	89.0	94.0	19	3118942	2203	4300	6503	SO:0001583	missense	AF493900	CCDS12103.1	19p13.3	2014-02-04			ENSG00000088256	ENSG00000088256		4379	protein-coding gene	gene with protein product		139313	"""hypocalciuric hypercalcemia 2"""	HHC2	1302014, 23802516	Standard	NM_002067	Approved	FBH, FBH2, FHH2	uc002lxd.3	P29992	OTTHUMG00000180631	ENST00000078429.4:c.626A>T	19.37:g.3118942A>T	ENSP00000078429:p.Gln209Leu	O15109|Q14350|Q6IB00	ENST00000078429.4	37	CCDS12103.1	.	.	.	.	.	.	.	.	.	.	.	15.05	2.718086	0.48622	.	.	ENSG00000088256	ENST00000078429	D	0.91237	-2.81	3.26	3.26	0.37387	.	0.000000	0.64402	U	0.000006	D	0.96950	0.9004	H	0.99357	4.53	0.80722	D	1	D	0.59767	0.986	D	0.68483	0.958	D	0.96823	0.9605	10	0.87932	D	0	.	10.7338	0.46113	1.0:0.0:0.0:0.0	.	209	P29992	GNA11_HUMAN	L	209	ENSP00000078429:Q209L	ENSP00000078429:Q209L	Q	+	2	0	GNA11	3069942	1.000000	0.71417	0.438000	0.26821	0.027000	0.11550	9.104000	0.94239	1.256000	0.44068	0.379000	0.24179	CAG	GNA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452261.2		59.585746	0	-2	79	0	0	1	0	NM_002067	20	59.947947	29	0.408163
DFNA5	1687	broad.mit.edu	hg19	7	24758768	24758768	+	Missense_Mutation	SNP	C	C	G			TCGA-V3-A9ZX-01A-11D-A39W-08	TCGA-V3-A9ZX-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f73499c-a4af-4281-b75f-cf8021d1f025	c85f7ffd-e167-4dee-b5d6-b469ef021e55	g.chr7:24758768C>G	ENST00000342947.3	-	4	899	c.474G>C	c.(472-474)ttG>ttC	p.L158F	DFNA5_ENST00000545231.1_5'UTR|DFNA5_ENST00000559637.1_5'UTR|DFNA5_ENST00000409775.3_Missense_Mutation_p.L158F|DFNA5_ENST00000419307.1_5'UTR|DFNA5_ENST00000409970.1_5'UTR	NM_004403.2	NP_004394.1	O60443	DFNA5_HUMAN	deafness, autosomal dominant 5	158		sensory perception of sound			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(3)|stomach(1)	19					TCTTCTGTGTCAAAACGCACA	0.502	0	214.0	177.0	189.0	7	24758768	2203	4300	6503	SO:0001583	missense	AF007790	CCDS5389.1, CCDS47563.1	7p15	2011-07-01			ENSG00000105928	ENSG00000105928		2810	protein-coding gene	gene with protein product		608798			8589696, 9450185	Standard	NM_004403	Approved	ICERE-1	uc010kus.1	O60443	OTTHUMG00000023237	ENST00000342947.3:c.474G>C	7.37:g.24758768C>G	ENSP00000339587:p.Leu158Phe	A4D156|B2RAX9|B3KT05|O14590|Q08AQ8|Q9UBV3	ENST00000342947.3	37	CCDS5389.1	.	.	.	.	.	.	.	.	.	.	C	14.84	2.656975	0.47467	.	.	ENSG00000105928	ENST00000342947;ENST00000409775	T;T	0.25912	1.77;1.77	5.08	5.08	0.68730	.	0.074293	0.56097	D	0.000037	T	0.52773	0.1755	M	0.78916	2.43	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.77004	0.989;0.989	T	0.57780	-0.7752	10	0.72032	D	0.01	-13.3118	15.9613	0.79933	0.0:1.0:0.0:0.0	.	158;158	A4FTY0;O60443	.;DFNA5_HUMAN	F	158	ENSP00000339587:L158F;ENSP00000386670:L158F	ENSP00000339587:L158F	L	-	3	2	DFNA5	24725293	1.000000	0.71417	0.808000	0.32385	0.017000	0.09413	4.565000	0.60836	2.369000	0.80426	0.591000	0.81541	TTG	DFNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214060.2		88.981760	0	-3	99	0	0	1	0	NM_004403	28	89.377208	39	0.417910
WDR16	146845	broad.mit.edu	hg19	17	9490111	9490111	+	Missense_Mutation	SNP	G	G	C			TCGA-V3-A9ZX-01A-11D-A39W-08	TCGA-V3-A9ZX-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f73499c-a4af-4281-b75f-cf8021d1f025	c85f7ffd-e167-4dee-b5d6-b469ef021e55	g.chr17:9490111G>C	ENST00000352665.5	+	3	436	c.367G>C	c.(367-369)Gat>Cat	p.D123H	WDR16_ENST00000576499.1_Missense_Mutation_p.M121I|WDR16_ENST00000299764.5_Missense_Mutation_p.D133H|WDR16_ENST00000396219.3_Missense_Mutation_p.D55H	NM_145054.4	NP_659491.4	Q8N1V2	WDR16_HUMAN	WD repeat domain 16	123			cytoplasm|intracellular membrane-bounded organelle	protein binding	NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	31					TTCTCCAAATGATTTGTACTT	0.388	0	77.0	77.0	77.0	17	9490111	2203	4300	6503	SO:0001583	missense	AB065281	CCDS11149.2, CCDS42262.1	17p13.1	2014-08-01			ENSG00000166596	ENSG00000166596	"""WD repeat domain containing"""	16053	protein-coding gene	gene with protein product	"""WD40-repeat protein upregulated in HCC"""	609804			15967112	Standard	NM_001080556	Approved	WDRPUH, FLJ37528	uc002gly.3	Q8N1V2	OTTHUMG00000150149	ENST00000576499.1:c.363G>C	17.37:g.9490111G>C	ENSP00000476293:p.Met121Ile		ENST00000576499.1	37		.	.	.	.	.	.	.	.	.	.	G	20.2	3.948229	0.73787	.	.	ENSG00000166596	ENST00000352665;ENST00000396219;ENST00000299764	T;D;T	0.90385	0.93;-2.66;4.95	5.69	3.6	0.41247	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.127271	0.64402	D	0.000001	D	0.95033	0.8392	M	0.90019	3.08	0.58432	D	0.999995	D;D;D	0.69078	0.994;0.989;0.997	D;P;D	0.69307	0.91;0.86;0.963	D	0.94116	0.7375	10	0.48119	T	0.1	-28.085	10.7048	0.45948	0.0743:0.0:0.7913:0.1344	.	133;55;123	Q8N1V2-2;Q8N1V2-3;Q8N1V2	.;.;WDR16_HUMAN	H	123;55;133	ENSP00000339449:D123H;ENSP00000379521:D55H;ENSP00000299764:D133H	ENSP00000299764:D133H	D	+	1	0	WDR16	9430836	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	4.934000	0.63491	2.690000	0.91761	0.455000	0.32223	GAT	WDR16-009	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000439850.2		133.520659	0	-12	97	0	0	1	0	NM_145054	39	133.613706	45	0.464286
PLEKHF2	79666	broad.mit.edu	hg19	8	96166799	96166799	+	Missense_Mutation	SNP	G	G	A			TCGA-V3-A9ZX-01A-11D-A39W-08	TCGA-V3-A9ZX-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f73499c-a4af-4281-b75f-cf8021d1f025	c85f7ffd-e167-4dee-b5d6-b469ef021e55	g.chr8:96166799G>A	ENST00000315367.3	+	2	768	c.527G>A	c.(526-528)cGc>cAc	p.R176H	PLEKHF2_ENST00000519516.1_Missense_Mutation_p.R176H	NM_024613.3	NP_078889.1	Q9H8W4	PKHF2_HUMAN	pleckstrin homology domain containing, family F (with FYVE domain) member 2	176			transport vesicle	metal ion binding|protein binding	breast(1)|large_intestine(1)|lung(1)|ovary(2)	5	Breast(36;3.18e-05)				CACCATTGCCGCAAATGTGGT	0.478	0	99.0	91.0	94.0	8	96166799	2203	4300	6503	SO:0001583	missense	AF434819	CCDS6267.1	8q22.1	2013-01-10				ENSG00000175895	"""Zinc fingers, FYVE domain containing"", ""Pleckstrin homology (PH) domain containing"""	20757	protein-coding gene	gene with protein product		615208				Standard	NM_024613	Approved	ZFYVE18, PHAFIN2, FLJ13187	uc003yhn.2	Q9H8W4		ENST00000315367.3:c.527G>A	8.37:g.96166799G>A	ENSP00000322373:p.Arg176His		ENST00000315367.3	37	CCDS6267.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.745385	0.89663	.	.	ENSG00000175895	ENST00000315367;ENST00000519516	T;T	0.81247	-1.47;-1.47	6.07	6.07	0.98685	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, FYVE-type (2);Zinc finger, FYVE-related (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.85682	D	0.000000	D	0.94026	0.8086	H	0.97214	3.96	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94345	0.7574	10	0.49607	T	0.09	-12.2797	20.6525	0.99598	0.0:0.0:1.0:0.0	.	176	Q9H8W4	PKHF2_HUMAN	H	176	ENSP00000322373:R176H;ENSP00000427792:R176H	ENSP00000322373:R176H	R	+	2	0	PLEKHF2	96235975	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.361000	0.97122	2.890000	0.99128	0.585000	0.79938	CGC	PLEKHF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379666.1		-38.689581	0	21	108	0	0	1	0	NM_024613	5	9.033150	187	0.026042
GGA2	23062	broad.mit.edu	hg19	16	23481415	23481415	+	Missense_Mutation	SNP	C	C	T			TCGA-V3-A9ZX-01A-11D-A39W-08	TCGA-V3-A9ZX-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f73499c-a4af-4281-b75f-cf8021d1f025	c85f7ffd-e167-4dee-b5d6-b469ef021e55	g.chr16:23481415C>T	ENST00000309859.4	-	15	1604	c.1522G>A	c.(1522-1524)Gcc>Acc	p.A508T	GGA2_ENST00000567468.1_Intron	NM_015044.4	NP_055859.1	Q9UJY4	GGA2_HUMAN	golgi-associated, gamma adaptin ear containing, ARF binding protein 2	508	GAE.	intracellular protein transport|vesicle-mediated transport	clathrin adaptor complex|clathrin-coated vesicle|endosome membrane|trans-Golgi network	ADP-ribosylation factor binding	NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(4)|ovary(1)	21				GBM - Glioblastoma multiforme(48;0.0386)	TGCCCAGGGGCTCCCGTCTGG	0.552	0	74.0	75.0	75.0	16	23481415	2197	4300	6497	SO:0001583	missense	AF190863	CCDS10611.1	16p12	2010-02-12	2010-02-12		ENSG00000103365	ENSG00000103365		16064	protein-coding gene	gene with protein product		606005			10747088, 10749927	Standard	NM_015044	Approved	VEAR, KIAA1080	uc002dlq.3	Q9UJY4	OTTHUMG00000096957	ENST00000309859.4:c.1522G>A	16.37:g.23481415C>T	ENSP00000311962:p.Ala508Thr	D3DWF0|O14564|Q9NYN2|Q9UPS2	ENST00000309859.4	37	CCDS10611.1	.	.	.	.	.	.	.	.	.	.	C	17.18	3.324671	0.60634	.	.	ENSG00000103365	ENST00000309859	T	0.29397	1.57	4.93	4.93	0.64822	Coatomer/clathrin adaptor appendage, Ig-like subdomain (1);Clathrin adaptor, gamma-adaptin, appendage (2);Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain (2);	0.272836	0.35708	N	0.003039	T	0.28566	0.0707	L	0.29908	0.895	0.80722	D	1	P	0.42010	0.768	P	0.48627	0.584	T	0.01988	-1.1234	10	0.14252	T	0.57	-14.3517	11.8415	0.52357	0.0:0.823:0.177:0.0	.	508	Q9UJY4	GGA2_HUMAN	T	508	ENSP00000311962:A508T	ENSP00000311962:A508T	A	-	1	0	GGA2	23388916	0.991000	0.36638	0.871000	0.34182	0.833000	0.47200	2.508000	0.45450	2.418000	0.82041	0.561000	0.74099	GCC	GGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214019.1		38.004902	0	-25	66	0	0	1	0		15	40.245485	38	0.283019
CNTN5	53942	broad.mit.edu	hg19	11	100179204	100179204	+	Nonstop_Mutation	SNP	T	T	C			TCGA-V3-A9ZX-01A-11D-A39W-08	TCGA-V3-A9ZX-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f73499c-a4af-4281-b75f-cf8021d1f025	c85f7ffd-e167-4dee-b5d6-b469ef021e55	g.chr11:100179204T>C	ENST00000527185.1	+	21	3073	c.2734T>C	c.(2734-2736)Tga>Cga	p.*912R	CNTN5_ENST00000528682.1_Intron|CNTN5_ENST00000524871.1_Intron|CNTN5_ENST00000524560.1_Intron|CNTN5_ENST00000279463.3_Intron|CNTN5_ENST00000418526.2_Intron	NM_001243271.1	NP_001230200.1	O94779	CNTN5_HUMAN	contactin 5	0	Fibronectin type-III 3.	cell adhesion	anchored to membrane|plasma membrane	protein binding	NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(12)|lung(38)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	81		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)	ATTTGAGGTATGAACAGAATG	0.393	0	59.0	58.0	58.0	11	100179204	1862	4096	5958	SO:0001578	stop_lost	AB013802	CCDS53696.1, CCDS53697.1, CCDS58168.1	11q22.1	2013-02-11			ENSG00000149972	ENSG00000149972	"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2175	protein-coding gene	gene with protein product		607219				Standard	NM_014361	Approved	NB-2, hNB-2	uc021qpb.1	O94779	OTTHUMG00000167579	ENST00000527185.1:c.2734T>C	11.37:g.100179204T>C	ENSP00000433575:p.*912Argext*3	A1L4P0|B7ZM07|E9PKE8|O94780|Q49AF3	ENST00000527185.1	37	CCDS58168.1	.	.	.	.	.	.	.	.	.	.	T	14.29	2.490807	0.44249	.	.	ENSG00000149972	ENST00000527185	.	.	.	5.49	3.02	0.34903	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.8452	0.52381	0.0:0.0:0.4309:0.5691	.	.	.	.	R	912	.	.	X	+	1	0	CNTN5	99684414	1.000000	0.71417	0.998000	0.56505	0.959000	0.62525	1.738000	0.38207	0.393000	0.25203	0.482000	0.46254	TGA	CNTN5-003	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395147.2		27.440209	0	20	36	0	0	1	0	NM_014361	10	28.057334	19	0.344828
BAP1	8314	broad.mit.edu	hg19	3	52441394	52441446	+	Splice_Site	DEL	GCTCCCACAGCTCCCACACACCTGGCATGGCTATTATGGGCCTTGGCCAACTC	GCTCCCACAGCTCCCACACACCTGGCATGGCTATTATGGGCCTTGGCCAACTC	-	rs67706685		TCGA-V3-A9ZX-01A-11D-A39W-08	TCGA-V3-A9ZX-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f73499c-a4af-4281-b75f-cf8021d1f025	c85f7ffd-e167-4dee-b5d6-b469ef021e55	g.chr3:52441394_52441446delGCTCCCACAGCTCCCACACACCTGGCATGGCTATTATGGGCCTTGGCCAACTC	ENST00000460680.1	-	6	877_909	c.406_438delGAGTTGGCCAAGGCCCATAATAGCCATGCCAGGTGTGTGGGAGCTGTGGGAGC	c.(406-438)gagttggccaaggcccataatagccatgccaggdel	p.ELAKAHNSHAR136fs	BAP1_ENST00000296288.5_Splice_Site_p.ELAKAHNSHAR136fs	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0	Interaction with HIP2.	anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)	CCCCACATCAGCTCCCACAGCTCCCACACACCTGGCATGGCTATTATGGGCCTTGGCCAACTCCGGGGCATTG	0.545	6									SO:0001630	splice_region_variant	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930		950	protein-coding gene	gene with protein product		603089			9528852	Standard	NM_004656	Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.437+1GAGTTGGCCAAGGCCCATAATAGCCATGCCAGGTGTGTGGGAGCTGTGGGAGC>-	3:g.52441394_52441446delGCTCCCACAGCTCCCACACACCTGGCATGGCTATTATGGGCCTTGGCCAACTC		B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	ENST00000460680.1		CCDS2853.1																																																																																			BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1	6.178000e+01	2.391000e+01		14	119						8		28	2.220000e-01