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
C3	718	broad.mit.edu	hg19	19	6710848	6710848	+	Missense_Mutation	SNP	G	G	T			TCGA-V4-A9F5-01A-11D-A39W-08	TCGA-V4-A9F5-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ae46b873-ecff-4701-a5ed-f1b222f8b37a	44b54082-d4f3-4a61-91dd-0e6ad3ff3a33	g.chr19:6710848G>T	ENST00000245907.6	-	13	1580	c.1488C>A	c.(1486-1488)aaC>aaA	p.N496K		NM_000064.2	NP_000055.2	P01024	CO3_HUMAN	complement component 3	496		complement activation, alternative pathway|complement activation, classical pathway|G-protein coupled receptor protein signaling pathway|inflammatory response|positive regulation vascular endothelial growth factor production	extracellular space	endopeptidase inhibitor activity|receptor binding	breast(5)|endometrium(7)|kidney(6)|large_intestine(18)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)	72				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)	GCCTGCCCTTGTTCATGATCT	0.667	0	35.0	38.0	37.0	19	6710848	2203	4300	6503	SO:0001583	missense	J04763	CCDS32883.1	19p13.3-p13.2	2014-09-17			ENSG00000125730	ENSG00000125730	"""Complement system"", ""Endogenous ligands"""	1318	protein-coding gene	gene with protein product	"""C3a anaphylatoxin"", ""complement component C3a"", ""complement component C3b"", ""prepro-C3"""	120700				Standard	NM_000064	Approved	CPAMD1, ARMD9, C3a, C3b	uc002mfm.3	P01024	OTTHUMG00000150335	ENST00000245907.6:c.1488C>A	19.37:g.6710848G>T	ENSP00000245907:p.Asn496Lys	A7E236	ENST00000245907.6	37	CCDS32883.1	.	.	.	.	.	.	.	.	.	.	G	15.35	2.806118	0.50421	.	.	ENSG00000125730	ENST00000245907	T	0.62639	0.01	5.31	5.31	0.75309	Alpha-2-macroglobulin, N-terminal 2 (1);	0.123057	0.64402	D	0.000001	T	0.78477	0.4289	M	0.83852	2.665	0.31869	N	0.619951	D	0.56746	0.977	D	0.66979	0.948	T	0.83210	-0.0074	10	0.87932	D	0	.	11.957	0.52986	0.0841:0.0:0.9159:0.0	.	496	P01024	CO3_HUMAN	K	496	ENSP00000245907:N496K	ENSP00000245907:N496K	N	-	3	2	C3	6661848	1.000000	0.71417	0.993000	0.49108	0.051000	0.14879	3.236000	0.51336	2.499000	0.84300	0.655000	0.94253	AAC	C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317636.2		48.229842	1	-1	27	0	2.32078e-09	1	2.32078e-09	NM_000064	15	48.448793	10	0.600000
GNA11	2767	broad.mit.edu	hg19	19	3118942	3118942	+	Missense_Mutation	SNP	A	A	T			TCGA-V4-A9F5-01A-11D-A39W-08	TCGA-V4-A9F5-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ae46b873-ecff-4701-a5ed-f1b222f8b37a	44b54082-d4f3-4a61-91dd-0e6ad3ff3a33	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		64.970964	0	-12	69	0	0	1	0	NM_002067	21	65.046538	25	0.456522
WDR3	10885	broad.mit.edu	hg19	1	118477140	118477140	+	Silent	SNP	C	C	T			TCGA-V4-A9F5-01A-11D-A39W-08	TCGA-V4-A9F5-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ae46b873-ecff-4701-a5ed-f1b222f8b37a	44b54082-d4f3-4a61-91dd-0e6ad3ff3a33	g.chr1:118477140C>T	ENST00000349139.5	+	3	263	c.216C>T	c.(214-216)tgC>tgT	p.C72C	WDR3_ENST00000471680.1_3'UTR|WDR3_ENST00000369441.3_3'UTR	NM_006784.2	NP_006775.1	Q9UNX4	WDR3_HUMAN	WD repeat domain 3				nuclear membrane|nucleolus		breast(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(9)|liver(2)|lung(22)|prostate(2)|upper_aerodigestive_tract(1)	49	Esophageal squamous(2;0.162)	all_cancers(81;2.72e-05)|Acute lymphoblastic leukemia(138;1e-08)|all_epithelial(167;4.4e-07)|all_lung(203;1.7e-06)|Lung NSC(69;1.98e-05)|Prostate(1639;0.00955)|Breast(1374;0.244)		OV - Ovarian serous cystadenocarcinoma(397;1.39e-08)|Epithelial(280;1.82e-07)|all cancers(265;2.04e-05)|Lung(183;0.0525)|BRCA - Breast invasive adenocarcinoma(282;0.0695)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.185)	CTTGCTTATGCCCCTCCCCAG	0.428	1	120.0	116.0	117.0	1	118477140	2203	4300	6503	SO:0001819	synonymous_variant	AF083217	CCDS898.1	1p12	2013-01-09			ENSG00000065183	ENSG00000065183	"""WD repeat domain containing"""	12755	protein-coding gene	gene with protein product		604737			10395803	Standard	NM_006784	Approved	FLJ12796, UTP12, DIP2	uc010oxe.1	Q9UNX4	OTTHUMG00000012197	ENST00000349139.5:c.216C>T	1.37:g.118477140C>T			ENST00000349139.5	37	CCDS898.1																																																																																			WDR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033720.2		-5.087674	0	36	171	0	0	1	0	NM_006784	3	6.380182	52	0.054545
CMYA5	202333	broad.mit.edu	hg19	5	79032425	79032425	+	Missense_Mutation	SNP	A	A	C			TCGA-V4-A9F5-01A-11D-A39W-08	TCGA-V4-A9F5-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ae46b873-ecff-4701-a5ed-f1b222f8b37a	44b54082-d4f3-4a61-91dd-0e6ad3ff3a33	g.chr5:79032425A>C	ENST00000446378.2	+	2	7868	c.7837A>C	c.(7837-7839)Aag>Cag	p.K2613Q		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	2613			perinuclear region of cytoplasm		NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)	CAGAGAAGCAAAGGCAGTAGG	0.418	0	65.0	67.0	66.0	5	79032425	1862	4100	5962	SO:0001583	missense	AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309	"""Tripartite motif containing / Tripartite motif containing"", ""A-kinase anchor proteins"", ""Fibronectin type III domain containing"""	14305	protein-coding gene	gene with protein product	"""genethonin-3"", ""tripartite motif-containing 76"""	612193	"""chromosome 5 open reading frame 10"""	C5orf10	14688250	Standard	NM_153610	Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.7837A>C	5.37:g.79032425A>C	ENSP00000394770:p.Lys2613Gln	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	ENST00000446378.2	37	CCDS47238.1	.	.	.	.	.	.	.	.	.	.	A	15.46	2.838706	0.51057	.	.	ENSG00000164309	ENST00000446378	T	0.28895	1.59	5.14	3.97	0.46021	.	0.341296	0.25419	N	0.030815	T	0.42630	0.1211	L	0.49126	1.545	0.20196	N	0.999921	D	0.76494	0.999	D	0.64144	0.922	T	0.19614	-1.0300	10	0.56958	D	0.05	.	7.5711	0.27909	0.9017:0.0:0.0983:0.0	.	2613	Q8N3K9	CMYA5_HUMAN	Q	2613	ENSP00000394770:K2613Q	ENSP00000394770:K2613Q	K	+	1	0	CMYA5	79068181	0.411000	0.25384	0.989000	0.46669	0.566000	0.35808	1.060000	0.30530	0.800000	0.34041	0.459000	0.35465	AAG	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1		62.220762	0	-5	44	0	0	1	0	NM_153610	19	62.303635	23	0.452381
FAT1	2195	broad.mit.edu	hg19	4	187538910	187538910	+	Missense_Mutation	SNP	C	C	T			TCGA-V4-A9F5-01A-11D-A39W-08	TCGA-V4-A9F5-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ae46b873-ecff-4701-a5ed-f1b222f8b37a	44b54082-d4f3-4a61-91dd-0e6ad3ff3a33	g.chr4:187538910C>T	ENST00000441802.2	-	10	9039	c.8830G>A	c.(8830-8832)Gat>Aat	p.D2944N		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2944	Cadherin 27.	actin filament organization|anatomical structure morphogenesis|cell migration|cell-cell signaling|establishment or maintenance of cell polarity|homophilic cell adhesion	cell-cell junction|integral to plasma membrane|nucleus|perinuclear region of cytoplasm	calcium ion binding|protein binding	NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228					GAATCAGCATCCGTGGTACTT	0.388	0	108.0	106.0	107.0	4	187538910	1896	4100	5996	SO:0001583	missense	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857	"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT	8586420	Standard	XM_005262834	Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.8830G>A	4.37:g.187538910C>T	ENSP00000406229:p.Asp2944Asn		ENST00000441802.2	37	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	C	19.16	3.773144	0.69992	.	.	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.78003	-1.14	4.89	4.89	0.63831	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	D	0.92172	0.7518	H	0.99555	4.625	0.80722	D	1	P	0.48350	0.909	P	0.54060	0.741	D	0.95385	0.8476	10	0.87932	D	0	.	18.6013	0.91248	0.0:1.0:0.0:0.0	.	2944	Q14517	FAT1_HUMAN	N	2944;2946	ENSP00000406229:D2944N	ENSP00000260147:D2946N	D	-	1	0	FAT1	187775904	1.000000	0.71417	0.387000	0.26183	0.007000	0.05969	7.574000	0.82434	2.698000	0.92095	0.650000	0.86243	GAT	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3		93.715052	0	-12	80	0	0	1	0	NM_005245	31	93.914295	39	0.442857
EXOC5	10640	broad.mit.edu	hg19	14	57676363	57676363	+	Silent	SNP	T	T	C			TCGA-V4-A9F5-01A-11D-A39W-08	TCGA-V4-A9F5-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ae46b873-ecff-4701-a5ed-f1b222f8b37a	44b54082-d4f3-4a61-91dd-0e6ad3ff3a33	g.chr14:57676363T>C	ENST00000413566.2	-	17	2219	c.1860A>G	c.(1858-1860)caA>caG	p.Q620Q	EXOC5_ENST00000340918.7_Silent_p.Q555Q	NM_006544.3	NP_006535.1	O00471	EXOC5_HUMAN	exocyst complex component 5	620		exocytosis|post-Golgi vesicle-mediated transport|protein transport|vesicle docking	cytoplasm		breast(3)|endometrium(1)|large_intestine(3)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	22					TGTAGGAATATTGTTGAAGAT	0.388	0	118.0	104.0	109.0	14	57676363	1900	4132	6032	SO:0001819	synonymous_variant	U85946	CCDS45111.1	14q22.3	2013-01-22	2005-11-01	2005-11-01	ENSG00000070367	ENSG00000070367		10696	protein-coding gene	gene with protein product		604469	"""SEC10 (S. cerevisiae)-like 1"", ""SEC10-like 1 (S. cerevisiae)"""	SEC10L1	9119050	Standard	XM_005267272	Approved	SEC10, SEC10P	uc001xct.3	O00471	OTTHUMG00000171309	ENST00000413566.2:c.1860A>G	14.37:g.57676363T>C		B2R6C5	ENST00000413566.2	37	CCDS45111.1																																																																																			EXOC5-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412905.1		29.570653	0	0	24	0	0	1	0	NM_006544	9	29.808430	14	0.391304
COL9A1	1297	broad.mit.edu	hg19	6	70964709	70964709	+	Missense_Mutation	SNP	C	C	T			TCGA-V4-A9F5-01A-11D-A39W-08	TCGA-V4-A9F5-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ae46b873-ecff-4701-a5ed-f1b222f8b37a	44b54082-d4f3-4a61-91dd-0e6ad3ff3a33	g.chr6:70964709C>T	ENST00000357250.6	-	24	1780	c.1622G>A	c.(1621-1623)gGt>gAt	p.G541D	COL9A1_ENST00000489611.1_5'UTR|COL9A1_ENST00000370499.4_Missense_Mutation_p.G298D|COL9A1_ENST00000320755.7_Missense_Mutation_p.G298D	NM_001851.4	NP_001842.3	P20849	CO9A1_HUMAN	collagen, type IX, alpha 1	541	Triple-helical region (COL2).	axon guidance|cell adhesion|organ morphogenesis	collagen type IX	metal ion binding	breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(44)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)	80					GCCATCCACACCTGGCAAACC	0.453	0	140.0	124.0	129.0	6	70964709	2203	4300	6503	SO:0001583	missense		CCDS4971.1, CCDS47447.1	6q13	2013-05-07			ENSG00000112280	ENSG00000112280	"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"""	2217	protein-coding gene	gene with protein product		120210			1429648	Standard	NM_001851	Approved		uc003pfg.4	P20849	OTTHUMG00000014988	ENST00000357250.6:c.1622G>A	6.37:g.70964709C>T	ENSP00000349790:p.Gly541Asp	Q13699|Q13700|Q5TF52|Q6P467|Q96BM8|Q99225|Q9H151|Q9H152|Q9Y6P2|Q9Y6P3	ENST00000357250.6	37	CCDS4971.1	.	.	.	.	.	.	.	.	.	.	C	18.07	3.541624	0.65085	.	.	ENSG00000112280	ENST00000357250;ENST00000320755;ENST00000370499	D;D;D	0.99619	-5.52;-6.28;-5.77	5.38	5.38	0.77491	.	0.000000	0.85682	D	0.000000	D	0.99873	0.9940	H	0.99454	4.575	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.992;1.0;1.0	D	0.96412	0.9305	10	0.87932	D	0	.	17.6661	0.88203	0.0:1.0:0.0:0.0	.	541;298;114	P20849;P20849-2;B3KWS8	CO9A1_HUMAN;.;.	D	541;298;298	ENSP00000349790:G541D;ENSP00000315252:G298D;ENSP00000359530:G298D	ENSP00000315252:G298D	G	-	2	0	COL9A1	71021430	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	4.634000	0.61325	2.680000	0.91292	0.655000	0.94253	GGT	COL9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041131.2		60.930084	0	-1	48	0	0	1	0		16	60.930069	0	1.000000
ARHGDIA	396	broad.mit.edu	hg19	17	79827106	79827106	+	Nonsense_Mutation	SNP	G	G	A			TCGA-V4-A9F5-01A-11D-A39W-08	TCGA-V4-A9F5-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ae46b873-ecff-4701-a5ed-f1b222f8b37a	44b54082-d4f3-4a61-91dd-0e6ad3ff3a33	g.chr17:79827106G>A	ENST00000269321.7	-	5	493	c.358C>T	c.(358-360)Cga>Tga	p.R120*	ARHGDIA_ENST00000580685.1_Nonsense_Mutation_p.R120*|ARHGDIA_ENST00000541078.2_Nonsense_Mutation_p.R120*|ARHGDIA_ENST00000400721.4_Nonsense_Mutation_p.R120*|ARHGDIA_ENST00000581876.1_Intron|ARHGDIA_ENST00000584461.1_Nonsense_Mutation_p.R120*	NM_001185078.1|NM_004309.4	NP_001172007.1|NP_004300.1	P52565	GDIR1_HUMAN	Rho GDP dissociation inhibitor (GDI) alpha	120		anti-apoptosis|cellular component movement|negative regulation of axonogenesis|negative regulation of cell adhesion|nerve growth factor receptor signaling pathway|positive regulation of axonogenesis|regulation of small GTPase mediated signal transduction|Rho protein signal transduction	cytoskeleton|cytosol	GTPase activator activity|identical protein binding|Rho GDP-dissociation inhibitor activity	endometrium(1)|lung(1)|prostate(1)	3	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.013)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)		ACTATCTCTCGGTTAACCTGC	0.642	0	70.0	68.0	69.0	17	79827106	2203	4300	6503	SO:0001587	stop_gained	BC028333	CCDS11788.1, CCDS58609.1	17q25.3	2005-12-20				ENSG00000141522		678	protein-coding gene	gene with protein product		601925		GDIA1	9186513	Standard	NM_001185077	Approved	RHOGDI	uc002kbq.3	P52565		ENST00000269321.7:c.358C>T	17.37:g.79827106G>A	ENSP00000269321:p.Arg120*	A8MXW0|B2R5X1|B4DDD3|B4DUV9|Q6IBM5	ENST00000269321.7	37	CCDS11788.1	.	.	.	.	.	.	.	.	.	.	T	39	7.431408	0.98279	.	.	ENSG00000141522	ENST00000269321;ENST00000541078;ENST00000400721	.	.	.	4.45	-0.408	0.12381	.	0.288011	0.33161	N	0.005205	.	.	.	.	.	.	0.46078	D	0.998853	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.8482	6.1098	0.20094	0.1016:0.0757:0.5587:0.264	.	.	.	.	X	120	.	ENSP00000269321:R120X	R	-	1	2	ARHGDIA	77420395	0.992000	0.36948	0.092000	0.20876	0.353000	0.29299	1.520000	0.35899	-0.565000	0.06061	-0.520000	0.04383	CGA	ARHGDIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441679.2		51.858239	0	6	54	0	0	1	0	NM_004309	17	51.883246	19	0.472222
KTN1	0	broad.mit.edu	hg19	14	56094706	56094706	+	Missense_Mutation	SNP	A	A	G			TCGA-V4-A9F5-01A-11D-A39W-08	TCGA-V4-A9F5-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ae46b873-ecff-4701-a5ed-f1b222f8b37a	44b54082-d4f3-4a61-91dd-0e6ad3ff3a33	g.chr14:56094706A>G	ENST00000416613.1	+	5	1112	c.1040A>G	c.(1039-1041)gAt>gGt	p.D347G	KTN1_ENST00000395309.3_Missense_Mutation_p.D347G|KTN1_ENST00000438792.2_Missense_Mutation_p.D347G|KTN1_ENST00000413890.2_Missense_Mutation_p.D347G|KTN1_ENST00000395314.3_Missense_Mutation_p.D347G|KTN1_ENST00000395308.1_Missense_Mutation_p.D347G|KTN1_ENST00000395311.1_Missense_Mutation_p.D347G			Q86UP2	KTN1_HUMAN	kinectin 1 (kinesin receptor)	347		microtubule-based movement	endoplasmic reticulum membrane|integral to plasma membrane|membrane fraction		breast(4)|central_nervous_system(1)|large_intestine(8)|lung(1)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	19					GTGAAGGAAGATGCTGCTGCT	0.413	0	119.0	101.0	107.0	14	56094706	2203	4300	6503	SO:0001583	missense		CCDS41957.1, CCDS41958.1, CCDS41959.1	14q22.1	2008-05-02			ENSG00000126777	ENSG00000126777		6467	protein-coding gene	gene with protein product		600381			9605849	Standard	NM_001079521	Approved	KIAA0004, CG1	uc001xcc.3	Q86UP2	OTTHUMG00000140312	ENST00000395314.3:c.1040A>G	14.37:g.56094706A>G	ENSP00000378725:p.Asp347Gly	B4DZ88|Q13999|Q14707|Q15387|Q17RZ5|Q5GGW3|Q86W57	ENST00000395314.3	37	CCDS41957.1	.	.	.	.	.	.	.	.	.	.	A	27.5	4.839734	0.91117	.	.	ENSG00000126777	ENST00000413890;ENST00000395309;ENST00000438792;ENST00000395314;ENST00000395308;ENST00000395311;ENST00000416613	T;T;T;T;T;T;T	0.52754	0.65;0.65;0.65;0.65;0.65;0.65;0.65	5.8	5.8	0.92144	.	0.104646	0.42053	D	0.000780	T	0.66567	0.2802	M	0.62723	1.935	0.40129	D	0.97669	D;D;P;D	0.76494	0.975;0.999;0.923;0.975	P;D;P;P	0.87578	0.775;0.998;0.753;0.775	T	0.68648	-0.5353	10	0.52906	T	0.07	-14.6423	15.8076	0.78527	1.0:0.0:0.0:0.0	.	347;347;347;347	B4DZ88;Q86UP2-2;Q17RZ5;Q86UP2	.;.;.;KTN1_HUMAN	G	347	ENSP00000394992:D347G;ENSP00000378720:D347G;ENSP00000391964:D347G;ENSP00000378725:D347G;ENSP00000378719:D347G;ENSP00000378722:D347G;ENSP00000388807:D347G	ENSP00000378719:D347G	D	+	2	0	KTN1	55164459	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	6.714000	0.74692	2.219000	0.72066	0.533000	0.62120	GAT	KTN1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276912.2		55.662827	0	6	41	0	0	1	0		18	55.662827	18	0.500000
TANC2	26115	broad.mit.edu	hg19	17	61498656	61498656	+	Silent	SNP	G	G	A			TCGA-V4-A9F5-01A-11D-A39W-08	TCGA-V4-A9F5-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ae46b873-ecff-4701-a5ed-f1b222f8b37a	44b54082-d4f3-4a61-91dd-0e6ad3ff3a33	g.chr17:61498656G>A	ENST00000424789.2	+	25	5317	c.5313G>A	c.(5311-5313)ccG>ccA	p.P1771P	RP11-269G24.3_ENST00000583552.1_RNA|TANC2_ENST00000389520.4_Silent_p.P1781P	NM_025185.3	NP_079461.2	Q9HCD6	TANC2_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2	1771				binding	breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|upper_aerodigestive_tract(3)	44					CTCCCAGGCCGTTGCTGCATT	0.522	0									SO:0001819	synonymous_variant	AB032974	CCDS45754.1	17q23.3	2013-01-11				ENSG00000170921	"""Ankyrin repeat domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	30212	protein-coding gene	gene with protein product	"""rolling pebbles homolog B (Drosophila)"""	615047				Standard	NM_025185	Approved	DKFZP564D166, FLJ10215, FLJ11824, KIAA1148, KIAA1636, rols, ROLSA	uc002jal.4	Q9HCD6		ENST00000424789.2:c.5313G>A	17.37:g.61498656G>A		Q9HAC3|Q9NW88|Q9NXY9|Q9ULS2	ENST00000424789.2	37	CCDS45754.1																																																																																			TANC2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444765.1		-7.127507	0	-9	88	0	0	1	0		3	6.318111	59	0.048387
CYFIP1	23191	broad.mit.edu	hg19	15	22926017	22926017	+	Silent	SNP	T	T	A			TCGA-V4-A9F5-01A-11D-A39W-08	TCGA-V4-A9F5-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ae46b873-ecff-4701-a5ed-f1b222f8b37a	44b54082-d4f3-4a61-91dd-0e6ad3ff3a33	g.chr15:22926017T>A	ENST00000313077.7	+	3	284	c.159T>A	c.(157-159)gtT>gtA	p.V53V	CYFIP1_ENST00000560848.1_Silent_p.V53V	NM_014608.2	NP_055423.1	Q7L576	CYFP1_HUMAN	cytoplasmic FMR1 interacting protein 1	53		axon extension|lamellipodium assembly|regulation of cell shape|ruffle organization	cell junction|lamellipodium|mRNA cap binding complex|perinuclear region of cytoplasm|ruffle|synapse|synaptosome	actin filament binding|Rac GTPase binding	endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|liver(1)|lung(14)|ovary(4)|pancreas(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	40		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.22e-06)|Epithelial(43;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00101)	ATGCATTTGTTACTGGCATCG	0.463	0	154.0	136.0	142.0	15	22926017	2203	4300	6503	SO:0001819	synonymous_variant	D38549	CCDS73695.1, CCDS73696.1	15q11	2008-07-18			ENSG00000068793	ENSG00000273749		13759	protein-coding gene	gene with protein product	"""selective hybridizing clone"", ""cytoplasmic FMRP interacting protein 1"""	606322			11438699	Standard	XM_005272543	Approved	KIAA0068, P140SRA-1, SHYC	uc001yus.3	Q7L576	OTTHUMG00000129100	ENST00000313077.7:c.159T>A	15.37:g.22926017T>A			ENST00000313077.7	37	CCDS10009.1																																																																																			CYFIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251136.2		-19.496976	0	16	159	0	0	1	0	NM_014608	4	6.733701	108	0.035714
GPAA1	8733	broad.mit.edu	hg19	8	145138937	145138937	+	Missense_Mutation	SNP	G	G	C			TCGA-V4-A9F5-01A-11D-A39W-08	TCGA-V4-A9F5-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ae46b873-ecff-4701-a5ed-f1b222f8b37a	44b54082-d4f3-4a61-91dd-0e6ad3ff3a33	g.chr8:145138937G>C	ENST00000355091.4	+	5	731	c.610G>C	c.(610-612)Gtc>Ctc	p.V204L	GPAA1_ENST00000527144.1_3'UTR|GPAA1_ENST00000361036.6_Missense_Mutation_p.V144L	NM_003801.3	NP_003792.1	O43292	GPAA1_HUMAN	glycosylphosphatidylinositol anchor attachment 1	204		attachment of GPI anchor to protein|C-terminal protein lipidation|protein complex assembly|protein retention in ER lumen	GPI-anchor transamidase complex	tubulin binding	breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(10)|upper_aerodigestive_tract(2)	19	all_cancers(97;2.87e-11)|all_epithelial(106;2.16e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.02e-40)|all cancers(56;2.11e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)		CGATGTCAATGTCACTGGTAG	0.532	0	87.0	92.0	91.0	8	145138937	2158	4256	6414	SO:0001583	missense	AB006969	CCDS43776.1	8q24.3	2012-12-10	2012-12-10		ENSG00000197858	ENSG00000197858		4446	protein-coding gene	gene with protein product	"""GPI transamidase subunit"""	603048	"""anchor attachment protein 1 (Gaa1p, yeast) homolog"", ""GPAA1P anchor attachment protein 1 homolog (yeast)"", ""glycosylphosphatidylinositol anchor attachment protein 1 homolog (yeast)"""		9828142	Standard	NM_003801	Approved	GAA1, hGAA1	uc003zax.3	O43292	OTTHUMG00000165438	ENST00000355091.4:c.610G>C	8.37:g.145138937G>C	ENSP00000347206:p.Val204Leu	Q9NSS0|Q9UQ31	ENST00000355091.4	37	CCDS43776.1	.	.	.	.	.	.	.	.	.	.	G	10.60	1.394711	0.25205	.	.	ENSG00000197858	ENST00000355091;ENST00000525087;ENST00000361036;ENST00000524418	.	.	.	5.47	-0.0141	0.13982	.	0.544817	0.20464	N	0.091823	T	0.21186	0.0510	N	0.14661	0.345	0.09310	N	1	B;B	0.18166	0.02;0.026	B;B	0.23716	0.047;0.048	T	0.28839	-1.0031	9	0.09338	T	0.73	-22.8332	10.121	0.42621	0.4187:0.0:0.5813:0.0	.	204;144	O43292;O43292-2	GPAA1_HUMAN;.	L	204;132;144;190	.	ENSP00000347206:V204L	V	+	1	0	GPAA1	145210925	0.734000	0.28142	0.357000	0.25798	0.941000	0.58515	0.750000	0.26334	0.044000	0.15775	0.561000	0.74099	GTC	GPAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384070.1		-17.399770	0	-26	56	0	0	1	0	NM_003801	4	8.817880	108	0.035714
MAPKAPK5	8550	broad.mit.edu	hg19	12	112306587	112306587	+	Frame_Shift_Del	DEL	G	G	-			TCGA-V4-A9F5-01A-11D-A39W-08	TCGA-V4-A9F5-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ae46b873-ecff-4701-a5ed-f1b222f8b37a	44b54082-d4f3-4a61-91dd-0e6ad3ff3a33	g.chr12:112306587delG	ENST00000550735.2	+	5	1071	c.315delG	c.(313-315)atgfs	p.M105fs	MAPKAPK5_ENST00000546394.1_Intron|MAPKAPK5_ENST00000551404.2_Frame_Shift_Del_p.M105fs	NM_003668.2|NM_139078.1	NP_003659.2|NP_620777.1	Q8IW41	MAPK5_HUMAN	mitogen-activated protein kinase-activated protein kinase 5	105	Protein kinase.	signal transduction	cytoplasm|nucleus	ATP binding|MAP kinase kinase activity|protein binding|protein serine/threonine kinase activity	endometrium(1)|lung(11)|ovary(1)	13					TGGAGATGATGGAAGGGGGAG	0.403	0	25.0	23.0	23.0	12	112306587	1879	4099	5978	SO:0001589	frameshift_variant	AF032437	CCDS44975.1, CCDS44976.1	12q24.13	2012-05-30			ENSG00000089022	ENSG00000089022		6889	protein-coding gene	gene with protein product		606723			9628874	Standard	NM_003668	Approved	PRAK	uc001tta.4	Q8IW41	OTTHUMG00000169605	ENST00000551404.2:c.315delG	12.37:g.112306587delG	ENSP00000449381:p.Met105fs	B3KVA5|O60491|Q86X46|Q9BVX9|Q9UG86	ENST00000551404.2	37	CCDS44975.1																																																																																			MAPKAPK5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405019.2	.	.		1	4					NM_139078	2		4	0.33