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
CDH6	1004	broad.mit.edu	hg19	5	31317540	31317540	+	Missense_Mutation	SNP	C	C	T			TCGA-VD-A8KF-01A-11D-A39W-08	TCGA-VD-A8KF-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3c90a47-1079-4c13-b7f6-fbf3e05322e6	5f953c98-fc2c-4be3-a94c-ce5ce67df7e7	g.chr5:31317540C>T	ENST00000265071.2	+	10	1836	c.1571C>T	c.(1570-1572)tCg>tTg	p.S524L	CDH6_ENST00000514738.1_Missense_Mutation_p.S469L	NM_004932.3	NP_004923.1	P55285	CADH6_HUMAN	cadherin 6, type 2, K-cadherin (fetal kidney)	524	Cadherin 5.	adherens junction organization|cell junction assembly|homophilic cell adhesion	cytoplasm|integral to membrane|nucleus|plasma membrane	calcium ion binding	NS(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(42)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	77					CACCAATTTTCGTTTTCCTTG	0.403	0	94.0	90.0	91.0	5	31317540	2203	4300	6503	SO:0001583	missense	D31784	CCDS3894.1	5p13.3	2010-01-26			ENSG00000113361	ENSG00000113361	"""Cadherins / Major cadherins"""	1765	protein-coding gene	gene with protein product	"""K-Cadherin"""	603007			7743525, 10191097	Standard	NM_004932	Approved		uc003jhe.2	P55285	OTTHUMG00000090673	ENST00000265071.2:c.1571C>T	5.37:g.31317540C>T	ENSP00000265071:p.Ser524Leu	A8K5H5|Q9BWS0	ENST00000265071.2	37	CCDS3894.1	.	.	.	.	.	.	.	.	.	.	C	11.03	1.518873	0.27211	.	.	ENSG00000113361	ENST00000514738;ENST00000265071	T;T	0.54071	0.59;0.59	4.75	4.75	0.60458	Cadherin (4);Cadherin-like (1);	0.365840	0.29300	N	0.012543	T	0.48241	0.1489	L	0.49126	1.545	0.49051	D	0.999747	B;B	0.30114	0.269;0.01	B;B	0.26094	0.066;0.008	T	0.43734	-0.9373	10	0.29301	T	0.29	.	18.3208	0.90238	0.0:1.0:0.0:0.0	.	524;524	P55285;P55285-2	CADH6_HUMAN;.	L	469;524	ENSP00000424843:S469L;ENSP00000265071:S524L	ENSP00000265071:S524L	S	+	2	0	CDH6	31353297	0.994000	0.37717	0.871000	0.34182	0.358000	0.29455	3.601000	0.54059	2.621000	0.88768	0.650000	0.86243	TCG	CDH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207355.2		-31.476309	0	3	128	0	0	1	0	NM_004932	4	7.340452	152	0.025641
KIAA2013	90231	broad.mit.edu	hg19	1	11983371	11983371	+	Silent	SNP	C	C	A			TCGA-VD-A8KF-01A-11D-A39W-08	TCGA-VD-A8KF-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3c90a47-1079-4c13-b7f6-fbf3e05322e6	5f953c98-fc2c-4be3-a94c-ce5ce67df7e7	g.chr1:11983371C>A	ENST00000376572.3	-	2	1394	c.1209G>T	c.(1207-1209)ggG>ggT	p.G403G	KIAA2013_ENST00000376576.3_Silent_p.G403G	NM_138346.2	NP_612355.1	Q8IYS2	K2013_HUMAN	KIAA2013	403			integral to membrane		endometrium(1)|lung(3)|ovary(1)|prostate(1)|skin(1)	7	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00149)|all_lung(284;0.00189)|Breast(348;0.00586)|Colorectal(325;0.0062)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0556)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;4.88e-06)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|Kidney(185;0.000722)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)	TGGTGGCGTGCCCGCTGAAGC	0.647	0	52.0	43.0	46.0	1	11983371	2203	4300	6503	SO:0001819	synonymous_variant	AB095933	CCDS141.1	1p36.22	2011-02-09			ENSG00000116685	ENSG00000116685		28513	protein-coding gene	gene with protein product					12477932	Standard	NM_138346	Approved	MGC33867, RP5-1077B9.1	uc001atk.3	Q8IYS2	OTTHUMG00000002391	ENST00000376572.3:c.1209G>T	1.37:g.11983371C>A		Q5JXC1|Q8IVF8|Q8NDI7|Q9BSY1	ENST00000376572.3	37	CCDS141.1																																																																																			KIAA2013-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006858.1		2.904502	1	-19	32	0	0.115264	1	0.115264	NM_138346	3	7.192323	25	0.107143
GNA11	2767	broad.mit.edu	hg19	19	3118942	3118942	+	Missense_Mutation	SNP	A	A	T			TCGA-VD-A8KF-01A-11D-A39W-08	TCGA-VD-A8KF-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3c90a47-1079-4c13-b7f6-fbf3e05322e6	5f953c98-fc2c-4be3-a94c-ce5ce67df7e7	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		53.474156	0	-13	68	0	0	1	0	NM_002067	17	53.480694	16	0.515152
ATAD3A	55210	broad.mit.edu	hg19	1	1463226	1463226	+	Missense_Mutation	SNP	G	G	A			TCGA-VD-A8KF-01A-11D-A39W-08	TCGA-VD-A8KF-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3c90a47-1079-4c13-b7f6-fbf3e05322e6	5f953c98-fc2c-4be3-a94c-ce5ce67df7e7	g.chr1:1463226G>A	ENST00000378755.5	+	14	1727	c.1633G>A	c.(1633-1635)Gcc>Acc	p.A545T	ATAD3A_ENST00000536055.1_Missense_Mutation_p.A418T|ATAD3A_ENST00000378756.3_Missense_Mutation_p.A497T	NM_018188.3	NP_060658.3	Q9NVI7	ATD3A_HUMAN	ATPase family, AAA domain containing 3A	545				ATP binding|nucleoside-triphosphatase activity|protein binding	endometrium(4)|kidney(6)|large_intestine(1)|lung(5)|prostate(1)|skin(2)|urinary_tract(1)	20	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;1.12e-36)|OV - Ovarian serous cystadenocarcinoma(86;2.18e-22)|Colorectal(212;0.000164)|COAD - Colon adenocarcinoma(227;0.000195)|Kidney(185;0.00233)|BRCA - Breast invasive adenocarcinoma(365;0.00469)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0347)|Lung(427;0.147)	TCTTAAGCCGGCCACAGAAGG	0.582	0	93.0	100.0	98.0	1	1463226	2203	4300	6503	SO:0001583	missense	AK025865	CCDS31.1, CCDS53259.1, CCDS53260.1	1p36.33	2010-04-21		2007-02-08	ENSG00000197785	ENSG00000197785	"""ATPases / AAA-type"""	25567	protein-coding gene	gene with protein product		612316			12477932	Standard	NM_018188	Approved	FLJ10709	uc001afz.2	Q9NVI7	OTTHUMG00000000575	ENST00000378756.3:c.1489G>A	1.37:g.1463226G>A	ENSP00000368031:p.Ala497Thr	B3KPB3|D2K8Q1|G3V1I6|Q5SV23|Q8N275|Q96A50	ENST00000378756.3	37	CCDS53259.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	16.34|16.34	3.095164|3.095164	0.56075|0.56075	.|.	.|.	ENSG00000197785|ENSG00000197785	ENST00000378756;ENST00000378755;ENST00000378759;ENST00000536055;ENST00000400830|ENST00000339113	D;D;D|.	0.94650|.	-3.24;-3.11;-3.48|.	4.15|4.15	4.15|4.15	0.48705|0.48705	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.74366|0.74366	0.3707|0.3707	M|M	0.76002|0.76002	2.32|2.32	0.80722|0.80722	D|D	1|1	B;B|.	0.32731|.	0.382;0.382|.	B;B|.	0.35607|.	0.15;0.206|.	T|T	0.76318|0.76318	-0.3003|-0.3003	10|5	0.38643|.	T|.	0.18|.	.|.	15.6717|15.6717	0.77283|0.77283	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	497;545|.	D2K8Q1;Q9NVI7|.	.;ATD3A_HUMAN|.	T|D	497;545;174;418;160|482	ENSP00000368031:A497T;ENSP00000368030:A545T;ENSP00000439290:A418T|.	ENSP00000368030:A545T|.	A|G	+|+	1|2	0|0	ATAD3A|ATAD3A	1453089|1453089	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.939000|0.939000	0.58152|0.58152	9.465000|9.465000	0.97660|0.97660	2.157000|2.157000	0.67596|0.67596	0.556000|0.556000	0.70494|0.70494	GCC|GGC	ATAD3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001363.3		-3.917653	0	-16	75	0	0	1	0	NM_018188	3	6.479106	48	0.058824
PCDH9	5101	broad.mit.edu	hg19	13	67800083	67800083	+	Silent	SNP	G	G	A			TCGA-VD-A8KF-01A-11D-A39W-08	TCGA-VD-A8KF-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3c90a47-1079-4c13-b7f6-fbf3e05322e6	5f953c98-fc2c-4be3-a94c-ce5ce67df7e7	g.chr13:67800083G>A	ENST00000544246.1	-	2	3181	c.2490C>T	c.(2488-2490)atC>atT	p.I830I	PCDH9_ENST00000456367.1_Silent_p.I830I|PCDH9_ENST00000377865.2_Silent_p.I830I|PCDH9_ENST00000377861.3_Silent_p.I830I|PCDH9_ENST00000328454.5_Silent_p.I830I	NM_203487.2	NP_982354.1	Q9HC56	PCDH9_HUMAN	protocadherin 9	830		homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding	breast(2)|central_nervous_system(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(33)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	103		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)	CGGTGACGAAGATCACAACAA	0.507	0	200.0	176.0	184.0	13	67800083	2203	4300	6503	SO:0001819	synonymous_variant	AF169692	CCDS9443.1, CCDS9444.1	13q21.32	2010-02-22			ENSG00000184226	ENSG00000184226	"""Cadherins / Protocadherins : Non-clustered"""	8661	protein-coding gene	gene with protein product		603581			9787079	Standard	NM_020403	Approved		uc001vik.3	Q9HC56	OTTHUMG00000017040	ENST00000377865.2:c.2490C>T	13.37:g.67800083G>A		A2A6U1|Q5VT83|Q7Z3U0|Q8N3K7	ENST00000377865.2	37	CCDS9444.1																																																																																			PCDH9-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276387.1		163.400063	0	-13	90	0	0	1	0	NM_203487	52	163.419333	49	0.514851
LRRC15	131578	broad.mit.edu	hg19	3	194081424	194081424	+	Missense_Mutation	SNP	G	G	T			TCGA-VD-A8KF-01A-11D-A39W-08	TCGA-VD-A8KF-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3c90a47-1079-4c13-b7f6-fbf3e05322e6	5f953c98-fc2c-4be3-a94c-ce5ce67df7e7	g.chr3:194081424G>T	ENST00000347624.3	-	2	434	c.349C>A	c.(349-351)Ccc>Acc	p.P117T	LRRC15_ENST00000428839.1_Missense_Mutation_p.P123T|LRRC15_ENST00000439944.2_Missense_Mutation_p.P123T	NM_130830.4	NP_570843.2	Q8TF66	LRC15_HUMAN	leucine rich repeat containing 15	117			integral to membrane		biliary_tract(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(20)|ovary(4)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.94e-05)	AGGCCGATGGGCAGAACCTGC	0.602	0	53.0	56.0	55.0	3	194081424	2203	4300	6503	SO:0001583	missense	AB071037	CCDS3306.1, CCDS46984.1	3q29	2008-02-05			ENSG00000172061	ENSG00000172061		20818	protein-coding gene	gene with protein product					12923058	Standard	NM_001135057	Approved	LIB	uc003ftu.3	Q8TF66	OTTHUMG00000156048	ENST00000347624.3:c.349C>A	3.37:g.194081424G>T	ENSP00000306276:p.Pro117Thr	Q495Q6|Q7RTN7	ENST00000347624.3	37	CCDS3306.1	.	.	.	.	.	.	.	.	.	.	G	19.64	3.866379	0.72065	.	.	ENSG00000172061	ENST00000347624;ENST00000439944;ENST00000428839	T;T;T	0.59224	0.28;3.06;3.06	4.8	4.8	0.61643	.	0.085123	0.50627	D	0.000109	T	0.78097	0.4230	M	0.81614	2.55	0.54753	D	0.999982	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.984	T	0.80612	-0.1305	10	0.59425	D	0.04	.	18.7514	0.91818	0.0:0.0:1.0:0.0	.	117;123	Q8TF66;Q8TF66-2	LRC15_HUMAN;.	T	117;123;123	ENSP00000306276:P117T;ENSP00000389128:P123T;ENSP00000413707:P123T	ENSP00000306276:P117T	P	-	1	0	LRRC15	195562719	1.000000	0.71417	0.997000	0.53966	0.852000	0.48524	5.249000	0.65427	2.602000	0.87976	0.462000	0.41574	CCC	LRRC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342858.2		65.988172	1	-14	49	0	5.3912e-06	1	6.16138e-06		19	68.036559	1	0.950000
ZFC3H1	196441	broad.mit.edu	hg19	12	72057131	72057131	+	Nonsense_Mutation	SNP	G	G	T			TCGA-VD-A8KF-01A-11D-A39W-08	TCGA-VD-A8KF-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3c90a47-1079-4c13-b7f6-fbf3e05322e6	5f953c98-fc2c-4be3-a94c-ce5ce67df7e7	g.chr12:72057131G>T	ENST00000378743.3	-	1	618	c.260C>A	c.(259-261)tCa>tAa	p.S87*	ZFC3H1_ENST00000552037.1_Nonsense_Mutation_p.S87*|ZFC3H1_ENST00000548100.1_Nonsense_Mutation_p.S87*|ZFC3H1_ENST00000549407.1_5'UTR|THAP2_ENST00000308086.2_5'UTR	NM_144982.4	NP_659419.3	O60293	ZC3H1_HUMAN	zinc finger, C3H1-type containing	87	Ser-rich.	RNA processing	intracellular	metal ion binding	NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(31)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69					CCGCGAGCGTGAGAAATTCCT	0.657	0	59.0	66.0	64.0	12	72057131	1969	4152	6121	SO:0001587	stop_gained	AB011118	CCDS41813.1	12q21.1	2013-01-25	2008-10-01	2008-10-01		ENSG00000133858	"""Zinc finger, C3H1-type containing"""	28328	protein-coding gene	gene with protein product			"""proline/serine-rich coiled-coil 2"", ""coiled-coil domain containing 131"""	PSRC2, CCDC131	9628581	Standard	NM_144982	Approved	MGC23401, KIAA0546	uc001swo.2	O60293	OTTHUMG00000169545	ENST00000552037.1:c.260C>A	12.37:g.72057131G>T	ENSP00000447976:p.Ser87*	Q6GMU1|Q6P2S9|Q6ZV36|Q96BE7	ENST00000552037.1	37		.	.	.	.	.	.	.	.	.	.	G	39	7.359003	0.98235	.	.	ENSG00000133858	ENST00000378743;ENST00000548100;ENST00000552037	.	.	.	4.09	3.18	0.36537	.	0.118844	0.34362	N	0.004034	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.5178	0.56042	0.0:0.168:0.832:0.0	.	.	.	.	X	87	.	ENSP00000368017:S87X	S	-	2	0	ZFC3H1	70343398	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.122000	0.50446	1.048000	0.40298	0.455000	0.32223	TCA	ZFC3H1-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404761.1		122.463607	1	-10	102	0	3.4345e-17	1	4.57933e-17	NM_144982	41	122.657448	50	0.450549
MRPS18C	51023	broad.mit.edu	hg19	4	84377254	84377254	+	Silent	SNP	C	C	T	rs141532727	byFrequency	TCGA-VD-A8KF-01A-11D-A39W-08	TCGA-VD-A8KF-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3c90a47-1079-4c13-b7f6-fbf3e05322e6	5f953c98-fc2c-4be3-a94c-ce5ce67df7e7	g.chr4:84377254C>T	ENST00000295491.4	+	1	137	c.24C>T	c.(22-24)tgC>tgT	p.C8C	MRPS18C_ENST00000507349.1_Silent_p.C8C|MRPS18C_ENST00000507019.1_Silent_p.C8C	NM_016067.2	NP_057151.1	Q9Y3D5	RT18C_HUMAN	mitochondrial ribosomal protein S18C	8		translation	mitochondrial small ribosomal subunit	structural constituent of ribosome	endometrium(1)|kidney(1)|large_intestine(2)|lung(1)	5		Hepatocellular(203;0.114)			TTGCTGTTTGCGGTGGTCTAG	0.552	0	190.0	195.0	193.0	4	84377254	2203	4300	6503	SO:0001819	synonymous_variant		CCDS3604.1, CCDS75159.1	4q21.21-q21.23	2012-09-13			ENSG00000163319	ENSG00000163319	"""Mitochondrial ribosomal proteins / small subunits"""	16633	protein-coding gene	gene with protein product		611983			11279123, 10810093	Standard	XM_005263043	Approved	MRPS18-1, CGI-134, FLJ11146, FLJ22967	uc003hor.4	Q9Y3D5	OTTHUMG00000130430	ENST00000295491.4:c.24C>T	4.37:g.84377254C>T			ENST00000295491.4	37	CCDS3604.1	.	.	.	.	.	.	.	.	.	.	C	5.334	0.246952	0.10130	9.08E-4	0.0	ENSG00000163319	ENST00000509970	.	.	.	4.72	-0.0422	0.13864	.	.	.	.	.	T	0.23451	0.0567	.	.	.	0.19775	N	0.999951	.	.	.	.	.	.	T	0.25537	-1.0129	4	.	.	.	0.0289	4.1526	0.10245	0.0:0.4496:0.1685:0.3819	.	.	.	.	W	7	.	.	R	+	1	2	MRPS18C	84596278	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.225000	0.02956	0.037000	0.15575	-0.137000	0.14449	CGG	MRPS18C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252820.2		-35.147103	0	-38	178	0	0	1	0		4	7.209012	164	0.023810
SAMD15	161394	broad.mit.edu	hg19	14	77857522	77857522	+	Missense_Mutation	SNP	C	C	A			TCGA-VD-A8KF-01A-11D-A39W-08	TCGA-VD-A8KF-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3c90a47-1079-4c13-b7f6-fbf3e05322e6	5f953c98-fc2c-4be3-a94c-ce5ce67df7e7	g.chr14:77857522C>A	ENST00000216471.4	+	3	2246	c.1960C>A	c.(1960-1962)Cag>Aag	p.Q654K	SAMD15_ENST00000533095.2_Missense_Mutation_p.Q68K	NM_001010860.1	NP_001010860.1	Q9P1V8	SAM15_HUMAN	sterile alpha motif domain containing 15	654					breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|pancreas(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28					AGCAGGATTACAGGATTATGC	0.388	0	82.0	82.0	82.0	14	77857522	2203	4300	6503	SO:0001583	missense	AK093282	CCDS32126.1	14q24.3	2013-01-10	2010-10-20	2010-10-20	ENSG00000100583	ENSG00000100583	"""Sterile alpha motif (SAM) domain containing"""	18631	protein-coding gene	gene with protein product			"""family with sequence similarity 15, member A"", ""chromosome 14 open reading frame 174"""	FAM15A, C14orf174		Standard	XM_006720069	Approved	FLJ35963	uc001xtq.1	Q9P1V8		ENST00000216471.4:c.1960C>A	14.37:g.77857522C>A	ENSP00000216471:p.Gln654Lys	Q2M3P3	ENST00000216471.4	37	CCDS32126.1	.	.	.	.	.	.	.	.	.	.	C	12.29	1.892353	0.33442	.	.	ENSG00000100583	ENST00000533095;ENST00000216471	T	0.19250	2.16	5.64	-3.32	0.04973	.	.	.	.	.	T	0.14830	0.0358	L	0.36672	1.1	0.09310	N	1	P	0.44734	0.842	B	0.35114	0.196	T	0.25745	-1.0123	9	0.59425	D	0.04	-5.6079	14.7721	0.69688	0.0:0.291:0.6408:0.0682	.	654	Q9P1V8	SAM15_HUMAN	K	68;654	ENSP00000216471:Q654K	ENSP00000216471:Q654K	Q	+	1	0	SAMD15	76927275	0.947000	0.32204	0.928000	0.36995	0.702000	0.40608	-0.176000	0.09811	-0.206000	0.10203	-0.182000	0.12963	CAG	SAMD15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394587.2		77.801269	1	-18	47	0	9.57634e-11	1	1.17863e-10	NM_001010860	24	77.820117	22	0.521739
LGALS9	3965	broad.mit.edu	hg19	17	25974373	25974373	+	Missense_Mutation	SNP	G	G	A	rs149003631		TCGA-VD-A8KF-01A-11D-A39W-08	TCGA-VD-A8KF-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3c90a47-1079-4c13-b7f6-fbf3e05322e6	5f953c98-fc2c-4be3-a94c-ce5ce67df7e7	g.chr17:25974373G>A	ENST00000395473.2	+	10	2304	c.836G>A	c.(835-837)cGc>cAc	p.R279H	LGALS9_ENST00000413914.2_Intron|LGALS9_ENST00000313648.6_Intron|LGALS9_ENST00000310394.5_Missense_Mutation_p.R235H|LGALS9_ENST00000302228.5_Missense_Mutation_p.R247H	NM_009587.2	NP_033665.1	O00182	LEG9_HUMAN	lectin, galactoside-binding, soluble, 9	279	Galectin 2.	positive regulation of I-kappaB kinase/NF-kappaB cascade	cytoplasm|extracellular region	galactose binding|signal transducer activity	endometrium(3)|large_intestine(2)|lung(12)|skin(1)	18	Lung NSC(42;0.0103)		BRCA - Breast invasive adenocarcinoma(3;0.0141)	UCEC - Uterine corpus endometrioid carcinoma (53;0.155)	GCTGTGGTCCGCAACACCCAG	0.587	0	92.0	87.0	88.0	17	25974373	2203	4300	6503	SO:0001583	missense	AB006782	CCDS11222.1, CCDS32592.1	17q11.2	2013-03-28	2008-07-25		ENSG00000168961	ENSG00000168961	"""Lectins, galactoside-binding"""	6570	protein-coding gene	gene with protein product	"""galectin 9"""	601879			9045665	Standard	NM_009587	Approved	LGALS9A	uc002gzp.3	O00182	OTTHUMG00000179831	ENST00000302228.5:c.740G>A	17.37:g.25974373G>A	ENSP00000306228:p.Arg247His	A7VJG6|O14532|O75028|Q3B8N1|Q53FQ0|Q9NQ58	ENST00000302228.5	37	CCDS32592.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.268327	0.80469	0.0	2.33E-4	ENSG00000168961	ENST00000395473;ENST00000302228;ENST00000310394	T;T;T	0.14144	2.53;2.53;2.53	4.36	3.38	0.38709	Concanavalin A-like lectin/glucanase (1);Galectin, carbohydrate recognition domain (4);Concanavalin A-like lectin/glucanase, subgroup (1);	0.000000	0.85682	D	0.000000	T	0.48786	0.1519	H	0.97131	3.945	0.80722	D	1	D;D;D	0.89917	1.0;0.993;0.996	D;P;P	0.75484	0.986;0.878;0.894	T	0.63102	-0.6712	10	0.72032	D	0.01	.	11.312	0.49368	0.0:0.0:0.8163:0.1837	.	190;247;279	B4DJD7;Q3B8N1;O00182	.;.;LEG9_HUMAN	H	279;247;235	ENSP00000378856:R279H;ENSP00000306228:R247H;ENSP00000312259:R235H	ENSP00000306228:R247H	R	+	2	0	LGALS9	22998500	0.998000	0.40836	1.000000	0.80357	0.880000	0.50808	5.359000	0.66074	1.036000	0.39998	0.467000	0.42956	CGC	LGALS9-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255584.1		-4.517596	0	-21	78	0	0	1	0	NM_009587	3	6.427790	50	0.056604
FAM86HP	0	broad.mit.edu	hg19	3	129823181	129823181	+	RNA	DEL	A	A	-			TCGA-VD-A8KF-01A-11D-A39W-08	TCGA-VD-A8KF-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3c90a47-1079-4c13-b7f6-fbf3e05322e6	5f953c98-fc2c-4be3-a94c-ce5ce67df7e7	g.chr3:129823181delA	ENST00000500074.2	-	0	257																					CAGCAATCAGAAAACAAGTGG	0.522	0													3q22.1	2011-07-01			ENSG00000253540	ENSG00000253540		42359	pseudogene	pseudogene						Standard	NR_024252	Approved		uc011ble.1		OTTHUMG00000159796		3.37:g.129823181delA			ENST00000500074.2	37																																																																																				FAM86HP-002	PUTATIVE	basic	processed_transcript	pseudogene	OTTHUMT00000358348.1	.	.		-1	4						2		4	0.33
ITGB4	3691	broad.mit.edu	hg19	17	73749891	73749891	+	Frame_Shift_Del	DEL	T	T	-			TCGA-VD-A8KF-01A-11D-A39W-08	TCGA-VD-A8KF-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3c90a47-1079-4c13-b7f6-fbf3e05322e6	5f953c98-fc2c-4be3-a94c-ce5ce67df7e7	g.chr17:73749891delT	ENST00000200181.3	+	33	4341	c.4154delT	c.(4153-4155)ctgfs	p.L1385fs	ITGB4_ENST00000579662.1_Intron|ITGB4_ENST00000450894.3_Intron|ITGB4_ENST00000449880.2_Intron|ITGB4_ENST00000339591.3_Intron|GALK1_ENST00000225614.2_Intron	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	integrin, beta 4	1385		cell communication|cell motility|cell-matrix adhesion|hemidesmosome assembly|integrin-mediated signaling pathway|multicellular organismal development|response to wounding	cell leading edge|cell surface|hemidesmosome|integrin complex	protein binding|receptor activity	breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(1)|lung(25)|skin(1)|urinary_tract(1)	43	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)		GAGCTGGACCTGCGGCGCGTC	0.776	0	8.0	10.0	9.0	17	73749891	2169	4252	6421	SO:0001589	frameshift_variant		CCDS11727.1, CCDS32736.1, CCDS58599.1	17q25.1	2013-09-19			ENSG00000132470	ENSG00000132470	"""CD molecules"", ""Integrins"", ""Fibronectin type III domain containing"""	6158	protein-coding gene	gene with protein product		147557			2070796	Standard	XM_005257309	Approved	CD104	uc002jpg.3	P16144	OTTHUMG00000179814	ENST00000200181.3:c.4154delT	17.37:g.73749891delT	ENSP00000200181:p.Leu1385fs	A0AVL6|O14690|O14691|O15339|O15340|O15341|Q0VF97|Q9UIQ4	ENST00000200181.3	37	CCDS11727.1																																																																																			ITGB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448334.1	.	.		-1	7						2		4	0.33
