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
SPEN	23013	broad.mit.edu	hg19	1	16259500	16259500	+	Silent	SNP	G	G	A			TCGA-V4-A9ED-01A-11D-A39W-08	TCGA-V4-A9ED-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e98b1c3c-18b3-4b03-b636-de1b96529d0a	57b12469-3e06-48f7-a3c0-62fc4a316460	g.chr1:16259500G>A	ENST00000375759.3	+	11	6969	c.6765G>A	c.(6763-6765)gcG>gcA	p.A2255A		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	2255	Interaction with MSX2 (By similarity).|RID.	interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway	nucleus	nucleotide binding|protein binding|RNA binding	NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)	GTGCACAGGCGCTGCAGCCTT	0.537	0	83.0	90.0	88.0	1	16259500	2203	4300	6503	SO:0001819	synonymous_variant		CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526	"""RNA binding motif (RRM) containing"""	17575	protein-coding gene	gene with protein product		613484	"""SPEN homolog, transcriptional regulator (Drosophila)"", ""spen homolog, transcriptional regulator (Drosophila)"""		10451362, 11331609	Standard	NM_015001	Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.6765G>A	1.37:g.16259500G>A		Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	ENST00000375759.3	37	CCDS164.1																																																																																			SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1		-25.232431	0	-23	105	0	0	1	0	NM_015001	4	6.924838	129	0.030075
NACA	4666	broad.mit.edu	hg19	12	57113149	57113149	+	Missense_Mutation	SNP	G	G	A			TCGA-V4-A9ED-01A-11D-A39W-08	TCGA-V4-A9ED-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e98b1c3c-18b3-4b03-b636-de1b96529d0a	57b12469-3e06-48f7-a3c0-62fc4a316460	g.chr12:57113149G>A	ENST00000454682.1	-	3	2446	c.2165C>T	c.(2164-2166)gCt>gTt	p.A722V	NACA_ENST00000550952.1_Intron|NACA_ENST00000546392.1_Intron|NACA_ENST00000552540.1_Intron|NACA_ENST00000551793.1_Intron|NACA_ENST00000393891.4_Intron|NACA_ENST00000548563.1_Intron|NACA_ENST00000356769.3_Intron	NM_001113203.2	NP_001106674.2	Q13765	NACA_HUMAN	nascent polypeptide-associated complex alpha subunit	0		interspecies interaction between organisms|protein transport|transcription, DNA-dependent|translation	nascent polypeptide-associated complex|nucleus	DNA binding	breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	10					CACTAAGGTAGCCAGAGGAGC	0.512	0	29.0	27.0	28.0	12	57113149	1568	3582	5150	SO:0001583	missense	X80909	CCDS31837.1, CCDS44925.1, CCDS44925.2	12q23-q24.1	2008-09-05	2007-04-20		ENSG00000196531	ENSG00000196531		7629	protein-coding gene	gene with protein product		601234	"""nascent-polypeptide-associated complex alpha polypeptide"""		8047162	Standard	NM_001113202	Approved	NACA1	uc001sma.2	E9PAV3		ENST00000454682.1:c.2165C>T	12.37:g.57113149G>A	ENSP00000403817:p.Ala722Val		ENST00000454682.1	37		.	.	.	.	.	.	.	.	.	.	G	10.76	1.440380	0.25900	.	.	ENSG00000196531	ENST00000454682	T	0.52983	0.64	3.33	3.33	0.38152	.	.	.	.	.	T	0.30947	0.0781	.	.	.	0.09310	N	1	B	0.30068	0.267	B	0.25291	0.059	T	0.10613	-1.0622	7	.	.	.	.	10.531	0.44977	0.0:0.0:1.0:0.0	.	722	E9PAV3	.	V	722	ENSP00000403817:A722V	.	A	-	2	0	NACA	55399416	0.000000	0.05858	0.002000	0.10522	0.077000	0.17291	0.069000	0.14552	1.578000	0.49821	0.449000	0.29647	GCT	NACA-201	KNOWN	basic	protein_coding	protein_coding			28.677330	0	-7	21	0	0	1	0	NM_005594	9	28.808411	6	0.600000
CYSLTR2	57105	broad.mit.edu	hg19	13	49281339	49281339	+	Missense_Mutation	SNP	T	T	A			TCGA-V4-A9ED-01A-11D-A39W-08	TCGA-V4-A9ED-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e98b1c3c-18b3-4b03-b636-de1b96529d0a	57b12469-3e06-48f7-a3c0-62fc4a316460	g.chr13:49281339T>A	ENST00000282018.3	+	1	389	c.386T>A	c.(385-387)cTg>cAg	p.L129Q		NM_020377.2	NP_065110.1	Q9NS75	CLTR2_HUMAN	cysteinyl leukotriene receptor 2	129		immune response	integral to membrane|plasma membrane		endometrium(2)|large_intestine(4)|lung(12)|skin(2)	20		all_cancers(8;1.66e-53)|all_epithelial(8;1.96e-19)|all_lung(13;9.94e-09)|all_hematologic(8;7.13e-07)|Lung NSC(96;1.72e-06)|Breast(56;1.53e-05)|Acute lymphoblastic leukemia(8;6.86e-05)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0416)|Lung SC(185;0.0787)		GBM - Glioblastoma multiforme(99;1.19e-09)	ATTTATTTCCTGACCGTGCTG	0.468	0	209.0	201.0	204.0	13	49281339	2203	4300	6503	SO:0001583	missense	AB038269	CCDS9412.1	13q14.2	2012-08-10			ENSG00000152207	ENSG00000152207	"""GPCR / Class A : Leukotriene receptors"""	18274	protein-coding gene	gene with protein product		605666			10913337, 1085123	Standard	NM_020377	Approved	CysLT(2), CYSLT2R	uc001vck.2	Q9NS75	OTTHUMG00000016906	ENST00000282018.3:c.386T>A	13.37:g.49281339T>A	ENSP00000282018:p.Leu129Gln	Q9HCQ2	ENST00000282018.3	37	CCDS9412.1	.	.	.	.	.	.	.	.	.	.	T	25.8	4.679001	0.88542	.	.	ENSG00000152207	ENST00000282018	D	0.81579	-1.51	6.08	6.08	0.98989	GPCR, rhodopsin-like superfamily (1);	0.000000	0.52532	D	0.000066	D	0.93756	0.8004	H	0.97783	4.075	0.54753	D	0.999982	D	0.89917	1.0	D	0.85130	0.997	D	0.95820	0.8849	10	0.87932	D	0	.	15.825	0.78698	0.0:0.0:0.0:1.0	.	129	Q9NS75	CLTR2_HUMAN	Q	129	ENSP00000282018:L129Q	ENSP00000282018:L129Q	L	+	2	0	CYSLTR2	48179340	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	8.004000	0.88535	2.333000	0.79357	0.533000	0.62120	CTG	CYSLTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044894.1		257.200558	0	40	193	0	0	1	0		83	258.325435	115	0.419192
ASIC2	40	broad.mit.edu	hg19	17	32483180	32483180	+	Silent	SNP	C	C	T			TCGA-V4-A9ED-01A-11D-A39W-08	TCGA-V4-A9ED-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e98b1c3c-18b3-4b03-b636-de1b96529d0a	57b12469-3e06-48f7-a3c0-62fc4a316460	g.chr17:32483180C>T	ENST00000359872.6	-	1	1133	c.372G>A	c.(370-372)ccG>ccA	p.P124P		NM_001094.4	NP_001085.2	Q16515	ACCN1_HUMAN	acid-sensing (proton-gated) ion channel 2	124		central nervous system development|peripheral nervous system development|synaptic transmission	integral to plasma membrane	ligand-gated sodium channel activity|protein binding							GATGGGGGTCCGGGATCTGCA	0.597	0	81.0	92.0	88.0	17	32483180	2161	4264	6425	SO:0001819	synonymous_variant	AL834182	CCDS11276.1, CCDS42296.1	17q11.2-q12	2012-02-23	2012-02-22	2012-02-22	ENSG00000108684	ENSG00000108684	"""Ion channels / Acid-sensing (proton-gated) ion channels"""	99	protein-coding gene	gene with protein product	"""degenerin"""	601784	"""amiloride-sensitive cation channel 1, neuronal"""	ACCN, ACCN1	8921408	Standard	NM_183377	Approved	ASIC2a, BNC1, BNaC1, hBNaC1, MDEG	uc002hhu.3	Q16515	OTTHUMG00000132885	ENST00000359872.6:c.372G>A	17.37:g.32483180C>T		E9PBX2|Q13553|Q6DJU1|Q8N3E2	ENST00000359872.6	37	CCDS42296.1																																																																																			ASIC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447552.1		93.113109	0	8	88	0	0	1	0	NM_183377, NM_001094	31	93.829402	47	0.397436
CEP164	22897	broad.mit.edu	hg19	11	117267963	117267963	+	Silent	SNP	G	G	A	rs149964584	by1000genomes	TCGA-V4-A9ED-01A-11D-A39W-08	TCGA-V4-A9ED-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e98b1c3c-18b3-4b03-b636-de1b96529d0a	57b12469-3e06-48f7-a3c0-62fc4a316460	g.chr11:117267963G>A	ENST00000278935.3	+	27	3582	c.3435G>A	c.(3433-3435)gcG>gcA	p.A1145A	CEP164_ENST00000533706.1_3'UTR	NM_001271933.1|NM_014956.4	NP_001258862.1|NP_055771.4	Q9UPV0	CE164_HUMAN	centrosomal protein 164kDa	1145		cell division|DNA repair|G2/M transition of mitotic cell cycle|mitosis	centriole|cytosol|nucleus		breast(3)|central_nervous_system(1)|kidney(7)|large_intestine(12)|lung(18)|ovary(3)|prostate(3)	47	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;4e-05)|Epithelial(105;0.0008)	TGGCCAGTGCGCAGGAGGTGG	0.617	0	40.0	38.0	39.0	11	117267963	2201	4296	6497	SO:0001819	synonymous_variant	AB028975	CCDS31683.1	11q23.3	2014-02-20			ENSG00000110274	ENSG00000110274		29182	protein-coding gene	gene with protein product		614848			10470851, 14654843	Standard	NM_014956	Approved	KIAA1052, NPHP15	uc001prc.3	Q9UPV0	OTTHUMG00000167070	ENST00000278935.3:c.3435G>A	11.37:g.117267963G>A		Q6PKH9|Q7Z2X9|Q9NVS0|Q9UFJ6	ENST00000278935.3	37	CCDS31683.1																																																																																			CEP164-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392893.1		-0.505416	0	-15	46	0	0	1	0	NM_014956	3	6.640689	36	0.076923
PCNT	5116	broad.mit.edu	hg19	21	47845774	47845774	+	Silent	SNP	C	C	T			TCGA-V4-A9ED-01A-11D-A39W-08	TCGA-V4-A9ED-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e98b1c3c-18b3-4b03-b636-de1b96529d0a	57b12469-3e06-48f7-a3c0-62fc4a316460	g.chr21:47845774C>T	ENST00000359568.5	+	33	7316	c.7209C>T	c.(7207-7209)agC>agT	p.S2403S	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	2403		cilium assembly|G2/M transition of mitotic cell cycle	cytosol|microtubule	calmodulin binding	NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)				GTGACGAGAGCCACCAGATCC	0.637	0	82.0	80.0	81.0	21	47845774	2203	4300	6503	SO:0001819	synonymous_variant	AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299		16068	protein-coding gene	gene with protein product	"""kendrin"", ""Seckel syndrome 4"""	605925	"""pericentrin 2 (kendrin)"""	PCNT2	8812505, 9455477	Standard	NM_006031	Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.7209C>T	21.37:g.47845774C>T		O43152|Q7Z7C9	ENST00000359568.5	37	CCDS33592.1																																																																																			PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1		-12.979379	0	-11	94	0	0	1	0	NM_006031	4	7.570087	88	0.043478
RAD54L2	23132	ucsc.edu	hg19	3	51696598	51696598	+	Missense_Mutation	SNP	G	G	T			TCGA-V4-A9ED-01A-11D-A39W-08	TCGA-V4-A9ED-10A-01D-A39Z-08	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	e98b1c3c-18b3-4b03-b636-de1b96529d0a	57b12469-3e06-48f7-a3c0-62fc4a316460																										GCTGCTGCCCGGGAATCCCGT	0.647	0	42.0	47.0	45.0	3	51696598	2203	4300	6503	SO:0001583	missense	AB018352	CCDS33765.2	3p21.2	2006-01-17			ENSG00000164080	ENSG00000164080		29123	protein-coding gene	gene with protein product					9872452	Standard	NM_015106	Approved	KIAA0809, SRISNF2L	uc011bdt.2	Q9Y4B4	OTTHUMG00000152936	ENST00000409535.2:c.3566G>T	3.37:g.51696598G>T	ENSP00000386520:p.Arg1189Leu	Q8TB57|Q9BV54	ENST00000409535.2	37	CCDS33765.2	.	.	.	.	.	.	.	.	.	.	G	16.03	3.005907	0.54254	.	.	ENSG00000164080	ENST00000409535;ENST00000296477	D;D	0.93763	-3.19;-3.28	5.23	5.23	0.72850	.	0.250591	0.33161	N	0.005205	D	0.86590	0.5969	N	0.19112	0.55	0.47737	D	0.999502	P;P	0.44690	0.841;0.662	B;B	0.33196	0.159;0.087	D	0.87934	0.2712	10	0.44086	T	0.13	-14.3883	17.7973	0.88577	0.0:0.0:1.0:0.0	.	1189;778	Q9Y4B4;B3KV54	ARIP4_HUMAN;.	L	1189;883	ENSP00000386520:R1189L;ENSP00000296477:R883L	ENSP00000296477:R883L	R	+	2	0	RAD54L2	51671638	0.937000	0.31787	1.000000	0.80357	0.958000	0.62258	2.785000	0.47782	2.435000	0.82474	0.563000	0.77884	CGG	RAD54L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328700.2				-11	68					NM_015106	4		29	
WDR65	149465	broad.mit.edu	hg19	1	43663300	43663300	+	Missense_Mutation	SNP	G	G	A			TCGA-V4-A9ED-01A-11D-A39W-08	TCGA-V4-A9ED-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e98b1c3c-18b3-4b03-b636-de1b96529d0a	57b12469-3e06-48f7-a3c0-62fc4a316460	g.chr1:43663300G>A	ENST00000372492.4	+	7	1523	c.1199G>A	c.(1198-1200)cGc>cAc	p.R400H	WDR65_ENST00000528956.1_Missense_Mutation_p.R400H	NM_001195831.2	NP_001182760.2	Q96MR6	WDR65_HUMAN	WD repeat domain 65	400					NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)			ACCTGCATCCGCAAACCCCTT	0.458	1	180.0	153.0	162.0	1	43663300	2203	4300	6503	SO:0001583	missense																									ENST00000372492.4:c.1199G>A	1.37:g.43663300G>A	ENSP00000361570:p.Arg400His	A6NKQ3|Q17RI9|Q5TAI0	ENST00000372492.4	37		.	.	.	.	.	.	.	.	.	.	G	35	5.497360	0.96355	0.0	1.16E-4	ENSG00000243710	ENST00000372492;ENST00000528956	T;T	0.39997	1.05;3.58	5.76	5.76	0.90799	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.64907	0.2641	M	0.75085	2.285	0.53005	D	0.999964	D;D	0.89917	1.0;1.0	D;D	0.83275	0.994;0.996	T	0.57400	-0.7818	10	0.15499	T	0.54	.	19.9634	0.97258	0.0:0.0:1.0:0.0	.	400;400	Q96MR6;Q96MR6-2	WDR65_HUMAN;.	H	400	ENSP00000361570:R400H;ENSP00000435310:R400H	ENSP00000361570:R400H	R	+	2	0	WDR65	43435887	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	9.209000	0.95087	2.721000	0.93114	0.563000	0.77884	CGC	WDR65-002	NOVEL	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000384325.1		-20.704491	0	-23	113	0	0	1	0		4	6.948021	113	0.034188
BCAS1	8537	broad.mit.edu	hg19	20	52570145	52570145	+	Missense_Mutation	SNP	G	G	C			TCGA-V4-A9ED-01A-11D-A39W-08	TCGA-V4-A9ED-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e98b1c3c-18b3-4b03-b636-de1b96529d0a	57b12469-3e06-48f7-a3c0-62fc4a316460	g.chr20:52570145G>C	ENST00000395961.3	-	11	1672	c.1506C>G	c.(1504-1506)gaC>gaG	p.D502E	BCAS1_ENST00000434986.2_Missense_Mutation_p.D168E|BCAS1_ENST00000371440.3_Missense_Mutation_p.D511E|BCAS1_ENST00000371435.2_Missense_Mutation_p.D424E	NM_003657.2	NP_003648.2	O75363	BCAS1_HUMAN	breast carcinoma amplified sequence 1	502			cytoplasm	protein binding	NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(23)|ovary(2)|skin(2)|stomach(1)|urinary_tract(1)	37	Breast(2;9.53e-15)|Lung NSC(4;5.57e-06)|all_lung(4;1.44e-05)		STAD - Stomach adenocarcinoma(23;0.116)|Colorectal(105;0.198)		CTGACTTCTTGTCCTTCGAGG	0.532	0	246.0	189.0	208.0	20	52570145	2203	4300	6503	SO:0001583	missense	AF041260	CCDS13444.1	20q13.2	2006-11-10			ENSG00000064787	ENSG00000064787		974	protein-coding gene	gene with protein product		602968			9671742	Standard	NM_003657	Approved	NABC1, AIBC1	uc002xws.2	O75363	OTTHUMG00000032772	ENST00000395961.3:c.1506C>G	20.37:g.52570145G>C	ENSP00000379290:p.Asp502Glu	A0AVG5|Q68CZ3	ENST00000395961.3	37	CCDS13444.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.53|17.53	3.413451|3.413451	0.62511|0.62511	.|.	.|.	ENSG00000064787|ENSG00000064787	ENST00000448484;ENST00000371440;ENST00000448710;ENST00000395961;ENST00000371435;ENST00000434986|ENST00000422805	T;T;T;T;T|.	0.10763|.	2.84;2.84;2.84;2.84;2.84|.	5.17|5.17	1.85|1.85	0.25348|0.25348	.|.	0.355510|.	0.27181|.	N|.	0.020555|.	T|T	0.69513|0.69513	0.3119|0.3119	M|M	0.66939|0.66939	2.045|2.045	0.80722|0.80722	D|D	1|1	B;D;P;D;D;D|.	0.89917|.	0.369;0.996;0.715;0.996;1.0;1.0|.	B;D;B;D;D;D|.	0.83275|.	0.242;0.99;0.242;0.99;0.996;0.996|.	T|T	0.68542|0.68542	-0.5381|-0.5381	10|5	0.06365|.	T|.	0.9|.	-11.4327|-11.4327	13.9608|13.9608	0.64177|0.64177	0.0:0.4399:0.5601:0.0|0.0:0.4399:0.5601:0.0	.|.	502;168;511;424;502;502|.	B2RCQ5;B4DFL4;O75363-2;G3XAF7;A0AVG7;O75363|.	.;.;.;.;.;BCAS1_HUMAN|.	E|R	373;511;302;502;424;168|165	ENSP00000396361:D373E;ENSP00000360495:D511E;ENSP00000379290:D502E;ENSP00000360490:D424E;ENSP00000409956:D168E|.	ENSP00000360490:D424E|.	D|T	-|-	3|2	2|0	BCAS1|BCAS1	52003552|52003552	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.637000|0.637000	0.38172|0.38172	3.133000|3.133000	0.50531|0.50531	0.507000|0.507000	0.28148|0.28148	0.555000|0.555000	0.69702|0.69702	GAC|ACA	BCAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079766.2		107.068024	0	-15	69	0	0	1	0	NM_003657	33	107.302698	42	0.440000
ETS1	2113	broad.mit.edu	hg19	11	128360370	128360370	+	Nonsense_Mutation	SNP	G	G	A			TCGA-V4-A9ED-01A-11D-A39W-08	TCGA-V4-A9ED-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e98b1c3c-18b3-4b03-b636-de1b96529d0a	57b12469-3e06-48f7-a3c0-62fc4a316460	g.chr11:128360370G>A	ENST00000392668.4	-	4	400	c.316C>T	c.(316-318)Cga>Tga	p.R106*	ETS1_ENST00000319397.6_Nonsense_Mutation_p.R62*|ETS1_ENST00000535549.1_Intron|ETS1_ENST00000526145.2_Nonsense_Mutation_p.R62*|ETS1_ENST00000531611.1_Nonsense_Mutation_p.R62*|ETS1_ENST00000345075.4_Nonsense_Mutation_p.R62*	NM_001143820.1	NP_001137292.1	P14921	ETS1_HUMAN	v-ets avian erythroblastosis virus E26 oncogene homolog 1		PNT.	cell motility|immune response|induction of apoptosis|negative regulation of cell cycle|negative regulation of cell proliferation|PML body organization|positive regulation of cellular component movement|positive regulation of erythrocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|response to antibiotic|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding	breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|pleura(1)|prostate(1)|upper_aerodigestive_tract(3)	35	all_hematologic(175;0.0537)	Lung NSC(97;0.000542)|all_lung(97;0.000665)|Breast(109;0.00765)|all_neural(223;0.0351)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;1.47e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.0174)|LUSC - Lung squamous cell carcinoma(976;0.0815)|Lung(307;0.0833)	ATCCCCAGTCGTTGCTGTTCT	0.438	2	137.0	125.0	129.0	11	128360370	2201	4297	6498	SO:0001587	stop_gained		CCDS8475.1, CCDS44767.1, CCDS53724.1	11q23.3	2013-07-09	2013-07-09		ENSG00000134954	ENSG00000134954		3488	protein-coding gene	gene with protein product	"""Avian erythroblastosis virus E26 (v-ets) oncogene homolog-1"", ""ets protein"""	164720		EWSR2	1522903	Standard	NM_005238	Approved	FLJ10768, ETS-1	uc001qej.2	P14921	OTTHUMG00000165799	ENST00000319397.6:c.184C>T	11.37:g.128360370G>A	ENSP00000324578:p.Arg62*	A9UL17|F5GYX9|Q14278|Q16080|Q6N087|Q96AC5	ENST00000319397.6	37	CCDS8475.1	.	.	.	.	.	.	.	.	.	.	G	38	7.156526	0.98103	.	.	ENSG00000134954	ENST00000345075;ENST00000392668;ENST00000531611;ENST00000319397;ENST00000526145	.	.	.	5.65	1.24	0.21308	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.2744	0.73732	0.0:0.0:0.4534:0.5466	.	.	.	.	X	62;106;62;62;62	.	ENSP00000324578:R62X	R	-	1	2	ETS1	127865580	1.000000	0.71417	0.967000	0.41034	0.971000	0.66376	1.649000	0.37281	-0.047000	0.13423	0.563000	0.77884	CGA	ETS1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386269.2		27.660076	0	12	125	0	0	1	0	NM_005238	15	39.632675	86	0.148515
HSD17B7	51478	broad.mit.edu	hg19	1	162773243	162773243	+	Missense_Mutation	SNP	G	G	C			TCGA-V4-A9ED-01A-11D-A39W-08	TCGA-V4-A9ED-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e98b1c3c-18b3-4b03-b636-de1b96529d0a	57b12469-3e06-48f7-a3c0-62fc4a316460	g.chr1:162773243G>C	ENST00000254521.3	+	6	720	c.665G>C	c.(664-666)tGt>tCt	p.C222S	HSD17B7_ENST00000485405.1_3'UTR|HSD17B7_ENST00000367917.3_Intron	NM_016371.2	NP_057455.1	P56937	DHB7_HUMAN	hydroxysteroid (17-beta) dehydrogenase 7	222		cholesterol biosynthetic process	endoplasmic reticulum membrane|integral to membrane|plasma membrane	3-keto sterol reductase activity|estradiol 17-beta-dehydrogenase activity	endometrium(3)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	9	all_hematologic(112;0.115)				AATGTGGCCTGTCCAGGTACA	0.413	0	84.0	75.0	78.0	1	162773243	2203	4297	6500	SO:0001583	missense	AF098786	CCDS1242.1	1q23	2011-09-14			ENSG00000132196	ENSG00000132196	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	5215	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 37C, member 1"""	606756			10544267, 10419022, 19027726	Standard	NM_016371	Approved	PRAP, SDR37C1	uc001gci.3	P56937	OTTHUMG00000034420	ENST00000254521.3:c.665G>C	1.37:g.162773243G>C	ENSP00000254521:p.Cys222Ser	Q5T246|Q7Z4V9|Q8WWS2|Q9UF00	ENST00000254521.3	37	CCDS1242.1	.	.	.	.	.	.	.	.	.	.	G	10.83	1.460799	0.26248	.	.	ENSG00000132196	ENST00000254521	T	0.76839	-1.05	4.68	4.68	0.58851	NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.83408	0.5248	M	0.80183	2.485	0.38606	D	0.950770	D	0.89917	1.0	D	0.77004	0.989	T	0.80605	-0.1308	9	0.17369	T	0.5	-18.6451	14.7956	0.69876	0.0:0.0:1.0:0.0	.	222	P56937	DHB7_HUMAN	S	222	ENSP00000254521:C222S	ENSP00000254521:C222S	C	+	2	0	HSD17B7	161039867	1.000000	0.71417	0.943000	0.38184	0.088000	0.18126	9.090000	0.94144	2.578000	0.87016	0.650000	0.86243	TGT	HSD17B7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083207.1		63.655355	0	7	64	0	0	1	0	NM_016371	21	65.204516	42	0.333333
LMO7	4008	broad.mit.edu	hg19	13	76379755	76379755	+	Missense_Mutation	SNP	G	G	A			TCGA-V4-A9ED-01A-11D-A39W-08	TCGA-V4-A9ED-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e98b1c3c-18b3-4b03-b636-de1b96529d0a	57b12469-3e06-48f7-a3c0-62fc4a316460	g.chr13:76379755G>A	ENST00000357063.3	+	10	2471	c.1211G>A	c.(1210-1212)cGc>cAc	p.R404H	LMO7_ENST00000465261.2_Missense_Mutation_p.R119H|LMO7_ENST00000377534.3_Missense_Mutation_p.R404H|LMO7_ENST00000341547.4_Intron|RP11-29G8.3_ENST00000563635.1_RNA|LMO7_ENST00000526202.1_Intron|LMO7_ENST00000321797.8_Missense_Mutation_p.R119H			Q8WWI1	LMO7_HUMAN	LIM domain 7	404			cytoplasm|nucleus|ubiquitin ligase complex	ubiquitin-protein ligase activity|zinc ion binding	NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(20)|lung(15)|ovary(2)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)	CTTTATGTGCGCAAGCTCAGT	0.413	0	322.0	289.0	299.0	13	76379755	1568	3582	5150	SO:0001583	missense	AF092557	CCDS9454.1, CCDS53876.1	13q22.2	2008-02-05	2004-06-15		ENSG00000136153	ENSG00000136153		6646	protein-coding gene	gene with protein product	"""F-box only protein 20"""	604362	"""LIM domain only 7"""	FBXO20	9826547, 10531035	Standard	NM_005358	Approved	FBX20, KIAA0858	uc021rkq.1	Q8WWI1	OTTHUMG00000017093	ENST00000321797.8:c.356G>A	13.37:g.76379755G>A	ENSP00000317802:p.Arg119His	E9PLH4|O15462|O95346|Q5TBK6|Q9UKC1|Q9UQM5|Q9Y6A7	ENST00000321797.8	37		.	.	.	.	.	.	.	.	.	.	G	25.7	4.668026	0.88348	.	.	ENSG00000136153	ENST00000357063;ENST00000377534;ENST00000321797;ENST00000465261;ENST00000526371	T;T;T;T;T	0.61158	0.13;0.13;0.13;0.13;0.13	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.78117	0.4233	M	0.73962	2.25	0.58432	D	0.999992	D	0.89917	1.0	D	0.87578	0.998	T	0.78763	-0.2077	10	0.87932	D	0	-11.2894	20.3363	0.98740	0.0:0.0:1.0:0.0	.	119	E9PLH4	.	H	404;404;119;119;119	ENSP00000349571:R404H;ENSP00000366757:R404H;ENSP00000317802:R119H;ENSP00000433352:R119H;ENSP00000432269:R119H	ENSP00000317802:R119H	R	+	2	0	LMO7	75277756	1.000000	0.71417	1.000000	0.80357	0.846000	0.48090	8.765000	0.91724	2.814000	0.96858	0.563000	0.77884	CGC	LMO7-005	PUTATIVE	alternative_5_UTR|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000045301.3		-46.975137	0	-5	190	0	0	1	0	NM_005358	4	6.456836	202	0.019417
AMER3	205147	broad.mit.edu	hg19	2	131520173	131520173	+	Silent	SNP	G	G	A			TCGA-V4-A9ED-01A-11D-A39W-08	TCGA-V4-A9ED-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e98b1c3c-18b3-4b03-b636-de1b96529d0a	57b12469-3e06-48f7-a3c0-62fc4a316460	g.chr2:131520173G>A	ENST00000423981.1	+	2	638	c.528G>A	c.(526-528)tcG>tcA	p.S176S	AMER3_ENST00000321420.4_Silent_p.S176S	NM_001105193.1|NM_001105194.1|NM_001105195.1|NM_152698.2	NP_001098663.1|NP_001098664.1|NP_001098665.1|NP_689911.2			APC membrane recruitment protein 3												ACTTGGCCTCGCTGGCGGCCG	0.642	0	45.0	50.0	49.0	2	131520173	2201	4294	6495	SO:0001819	synonymous_variant	AK095696	CCDS2164.1	2q21.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000178171	ENSG00000178171	"""-"""	26771	protein-coding gene	gene with protein product			"""family with sequence similarity 123C"""	FAM123C	20843316	Standard	NM_001105195	Approved	FLJ38377	uc002trw.2	Q8N944	OTTHUMG00000131637	ENST00000423981.1:c.528G>A	2.37:g.131520173G>A		B7ZLH6	ENST00000423981.1	37	CCDS2164.1																																																																																			AMER3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254531.3		61.834739	0	-6	77	0	0	1	0	NM_152698	22	62.772327	38	0.366667
DTL	51514	broad.mit.edu	hg19	1	212220678	212220678	+	Missense_Mutation	SNP	G	G	A			TCGA-V4-A9ED-01A-11D-A39W-08	TCGA-V4-A9ED-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e98b1c3c-18b3-4b03-b636-de1b96529d0a	57b12469-3e06-48f7-a3c0-62fc4a316460	g.chr1:212220678G>A	ENST00000366991.4	+	5	693	c.379G>A	c.(379-381)Gta>Ata	p.V127I	DTL_ENST00000475419.1_3'UTR|DTL_ENST00000542077.1_Missense_Mutation_p.V85I	NM_016448.2	NP_057532.2	Q9NZJ0	DTL_HUMAN	denticleless E3 ubiquitin protein ligase homolog (Drosophila)	127		DNA replication|G2/M transition DNA damage checkpoint|protein monoubiquitination|protein polyubiquitination|response to UV|translesion synthesis|ubiquitin-dependent protein catabolic process	centrosome|Cul4A-RING ubiquitin ligase complex|Cul4B-RING ubiquitin ligase complex|nuclear membrane	protein binding	breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|lung(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23				OV - Ovarian serous cystadenocarcinoma(81;0.00796)|all cancers(67;0.0385)|Epithelial(68;0.102)	ATTTTGGGACGTAAAAGCTGG	0.388	0	210.0	204.0	206.0	1	212220678	2203	4300	6503	SO:0001583	missense	AF195765	CCDS1502.1, CCDS65778.1	1q32	2013-01-10	2012-02-23		ENSG00000143476	ENSG00000143476	"""DDB1 and CUL4 associated factors"", ""WD repeat domain containing"""	30288	protein-coding gene	gene with protein product	"""RA regulated nuclear matrix associated protein"", ""DDB1 and CUL4 associated factor 2"""	610617	"""denticleless homolog (Drosophila)"""		11278750	Standard	NM_001286229	Approved	RAMP, L2DTL, DCAF2	uc009xdc.3	Q9NZJ0	OTTHUMG00000037133	ENST00000366991.4:c.379G>A	1.37:g.212220678G>A	ENSP00000355958:p.Val127Ile	A8K8H8|D3DT98|Q5VT77|Q96SN0|Q9NW03|Q9NW34|Q9NWM5	ENST00000366991.4	37	CCDS1502.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.947507	0.73672	.	.	ENSG00000143476	ENST00000366991;ENST00000542077	T;T	0.19105	2.17;2.17	5.18	4.28	0.50868	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.26882	0.0658	N	0.25426	0.745	0.80722	D	1	D;D	0.67145	0.996;0.989	P;P	0.56514	0.8;0.636	T	0.02244	-1.1189	10	0.44086	T	0.13	-16.7073	14.264	0.66104	0.0722:0.0:0.9278:0.0	.	85;127	F5GZ90;Q9NZJ0	.;DTL_HUMAN	I	127;85	ENSP00000355958:V127I;ENSP00000443870:V85I	ENSP00000355958:V127I	V	+	1	0	DTL	210287301	1.000000	0.71417	0.719000	0.30619	0.586000	0.36452	7.058000	0.76676	1.342000	0.45619	-0.119000	0.15052	GTA	DTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090182.1		-32.471394	0	10	171	0	0	1	0	NM_016448	5	8.903745	165	0.029412
PLXND1	23129	broad.mit.edu	hg19	3	129303286	129303286	+	Missense_Mutation	SNP	C	C	A			TCGA-V4-A9ED-01A-11D-A39W-08	TCGA-V4-A9ED-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e98b1c3c-18b3-4b03-b636-de1b96529d0a	57b12469-3e06-48f7-a3c0-62fc4a316460	g.chr3:129303286C>A	ENST00000393239.1	-	6	2149	c.1971G>T	c.(1969-1971)caG>caT	p.Q657H	PLXND1_ENST00000324093.4_Missense_Mutation_p.Q657H			Q9Y4D7	PLXD1_HUMAN	plexin D1	657		axon guidance	integral to membrane|intracellular|plasma membrane		NS(1)|breast(1)|endometrium(4)|kidney(5)|large_intestine(17)|lung(28)|prostate(10)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	72					AGTAGGCAATCTGGTGACCAA	0.637	0	73.0	68.0	70.0	3	129303286	2203	4300	6503	SO:0001583	missense	AY116661	CCDS33854.1	3q21.3	2007-05-16			ENSG00000004399	ENSG00000004399	"""Plexins"""	9107	protein-coding gene	gene with protein product		604282			12412018	Standard	NM_015103	Approved	KIAA0620	uc003emx.2	Q9Y4D7	OTTHUMG00000159547	ENST00000324093.4:c.1971G>T	3.37:g.129303286C>A	ENSP00000317128:p.Gln657His	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	ENST00000324093.4	37	CCDS33854.1	.	.	.	.	.	.	.	.	.	.	C	15.28	2.787986	0.49997	.	.	ENSG00000004399	ENST00000324093;ENST00000393239	T;T	0.36520	1.29;1.25	4.77	3.89	0.44902	.	0.070478	0.56097	D	0.000021	T	0.29355	0.0731	L	0.50333	1.59	0.49915	D	0.999839	B	0.20671	0.047	B	0.17433	0.018	T	0.09314	-1.0680	10	0.39692	T	0.17	.	6.9542	0.24562	0.0:0.7501:0.0:0.2499	.	657	Q9Y4D7	PLXD1_HUMAN	H	657	ENSP00000317128:Q657H;ENSP00000376931:Q657H	ENSP00000317128:Q657H	Q	-	3	2	PLXND1	130785976	1.000000	0.71417	1.000000	0.80357	0.844000	0.47949	0.383000	0.20651	1.134000	0.42165	0.561000	0.74099	CAG	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4		0.565294	1	-6	81	0	0.00909568	1	0.00909568	NM_015103	4	7.741114	39	0.093023
SBNO2	22904	broad.mit.edu	hg19	19	1122978	1122978	+	Frame_Shift_Del	DEL	G	G	-			TCGA-V4-A9ED-01A-11D-A39W-08	TCGA-V4-A9ED-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e98b1c3c-18b3-4b03-b636-de1b96529d0a	57b12469-3e06-48f7-a3c0-62fc4a316460	g.chr19:1122978delG	ENST00000361757.3	-	8	932	c.695delC	c.(694-696)ccafs	p.P232fs	SBNO2_ENST00000587024.1_Frame_Shift_Del_p.P232fs|SBNO2_ENST00000438103.2_Frame_Shift_Del_p.P175fs	NM_014963.2	NP_055778.2	Q9Y2G9	SBNO2_HUMAN	strawberry notch homolog 2 (Drosophila)	232		macrophage activation involved in immune response|negative regulation of transcription, DNA-dependent|regulation of inflammatory response|transcription, DNA-dependent			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)	GGTGATGTCTGGGGGTGGGAC	0.662	0	48.0	50.0	49.0	19	1122978	2172	4259	6431	SO:0001589	frameshift_variant	AK074102	CCDS45894.1, CCDS45895.1	19p13.3	2008-02-05	2006-10-06	2006-10-06		ENSG00000064932		29158	protein-coding gene	gene with protein product		615729	"""KIAA0963"""	KIAA0963	10231032	Standard	NM_014963	Approved	FLJ00173, Stno, Sno	uc002lrk.4	Q9Y2G9		ENST00000587024.1:c.695delC	19.37:g.1122978delG	ENSP00000468520:p.Pro232fs	A8K8P2|B3KWJ1|O75257|Q3KQX0|Q8TEM0	ENST00000587024.1	37																																																																																				SBNO2-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000458060.1	.	.		-7	4					NM_014963	3		6	0.33
RP11-370A5.1	0	broad.mit.edu	hg19	18	20480579	20480579	+	RNA	DEL	T	T	-			TCGA-V4-A9ED-01A-11D-A39W-08	TCGA-V4-A9ED-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e98b1c3c-18b3-4b03-b636-de1b96529d0a	57b12469-3e06-48f7-a3c0-62fc4a316460	g.chr18:20480579delT	ENST00000583086.1	-	0	84				RP11-739L10.1_ENST00000578831.1_RNA																	TAGCAGGCTGTGGATGGAGTG	0.463	0																																				18.37:g.20480579delT			ENST00000583086.1	37																																																																																				RP11-370A5.1-001	KNOWN	basic	antisense	antisense	OTTHUMT00000446416.1	.	.		2	7						2		4	0.33
FOXD3	27022	broad.mit.edu	hg19	1	63790123	63790123	+	Frame_Shift_Del	DEL	C	C	-			TCGA-V4-A9ED-01A-11D-A39W-08	TCGA-V4-A9ED-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e98b1c3c-18b3-4b03-b636-de1b96529d0a	57b12469-3e06-48f7-a3c0-62fc4a316460	g.chr1:63790123delC	ENST00000371116.2	+	1	1394	c.1394delC	c.(1393-1395)gccfs	p.A471fs		NM_012183.2	NP_036315.1	Q9UJU5	FOXD3_HUMAN	forkhead box D3	471	Poly-Ala.	axon extension involved in axon guidance|branching involved in ureteric bud morphogenesis|cartilage development|embryonic placenta development|enteric nervous system development|iridophore differentiation|kidney development|lateral line nerve glial cell development|melanocyte differentiation|negative regulation of transcription from RNA polymerase II promoter|neural crest cell migration|pattern specification process|peripheral nervous system development|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity|sympathetic nervous system development|trophectodermal cell differentiation	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding	breast(1)|cervix(1)|lung(2)|upper_aerodigestive_tract(1)	5					tcggccgccgccgctgctgcg	0.697	0	2.0	2.0	2.0	1	63790123	1146	2571	3717	SO:0001589	frameshift_variant	AF197560	CCDS624.1	1p31.3	2008-04-10			ENSG00000187140	ENSG00000187140	"""Forkhead boxes"""	3804	protein-coding gene	gene with protein product		611539			8499623	Standard	NM_012183	Approved	Genesis, HFH2	uc001dax.2	Q9UJU5	OTTHUMG00000009141	ENST00000371116.2:c.1394delC	1.37:g.63790123delC	ENSP00000360157:p.Ala471fs	Q9BYM2|Q9UDD1	ENST00000371116.2	37	CCDS624.1																																																																																			FOXD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025331.1	.	.		2	3						2		4	0.33
BAP1	8314	broad.mit.edu	hg19	3	52443758	52443831	+	Splice_Site	DEL	GCCTGGGTGGGGCGACAAGAGGAGGGGGTGATGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCC	GCCTGGGTGGGGCGACAAGAGGAGGGGGTGATGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCC	-			TCGA-V4-A9ED-01A-11D-A39W-08	TCGA-V4-A9ED-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e98b1c3c-18b3-4b03-b636-de1b96529d0a	57b12469-3e06-48f7-a3c0-62fc4a316460	g.chr3:52443758_52443831delGCCTGGGTGGGGCGACAAGAGGAGGGGGTGATGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCC	ENST00000460680.1	-	2	509_510	c.38_39delGGCTGGGGAGGCCGGATGGGCCCGGGACGCGCCTGCCTGACCATCACCCCCTCCTCTTGTCGCCCCACCCAGGC	c.(37-39)ggg>g	p.G13fs	PHF7_ENST00000347025.2_5'Flank|PHF7_ENST00000327906.3_5'Flank|BAP1_ENST00000296288.5_Splice_Site_p.G13fs	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)	GGGTGAAGAGGCCTGGGTGGGGCGACAAGAGGAGGGGGTGATGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTC	0.701	3									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.38-1GGCTGGGGAGGCCGGATGGGCCCGGGACGCGCCTGCCTGACCATCACCCCCTCCTCTTGTCGCCCCACCCAGGC>-	3:g.52443758_52443831delGCCTGGGTGGGGCGACAAGAGGAGGGGGTGATGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCC		B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	ENST00000460680.1		CCDS2853.1																																																																																			BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1	1.045000e+01	2.821000e+01		-4	28						10		6	6.430000e-01