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
ANKK1	255239	broad.mit.edu	hg19	11	113270063	113270063	+	Nonsense_Mutation	SNP	G	G	T			TCGA-VD-A8K8-01A-11D-A39W-08	TCGA-VD-A8K8-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68db916e-ad05-47dc-9a78-2ea29d299732	db6a4a82-2ba2-4d1c-92e6-12fd9418c4e6	g.chr11:113270063G>T	ENST00000303941.3	+	8	1466	c.1372G>T	c.(1372-1374)Gaa>Taa	p.E458*		NM_178510.1	NP_848605.1	Q8NFD2	ANKK1_HUMAN	ankyrin repeat and kinase domain containing 1	458				ATP binding|protein serine/threonine kinase activity	NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(14)|ovary(1)|stomach(1)	29		all_cancers(61;1.53e-11)|all_epithelial(67;3e-06)|Melanoma(852;4.04e-05)|all_hematologic(158;0.000315)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0461)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Prostate(24;0.194)		BRCA - Breast invasive adenocarcinoma(274;4.82e-06)|Epithelial(105;5.41e-05)|all cancers(92;0.000442)|OV - Ovarian serous cystadenocarcinoma(223;0.238)	GGATGCCCAGGAACGTGAAGG	0.617	0	19.0	22.0	21.0	11	113270063	2100	4217	6317	SO:0001587	stop_gained	AJ541797	CCDS44734.1	11q23.2	2013-01-10			ENSG00000170209	ENSG00000170209	"""Ankyrin repeat domain containing"""	21027	protein-coding gene	gene with protein product		608774			15146457	Standard	NM_178510	Approved	X-kinase	uc001pny.3	Q8NFD2	OTTHUMG00000167715	ENST00000303941.3:c.1372G>T	11.37:g.113270063G>T	ENSP00000306678:p.Glu458*		ENST00000303941.3	37	CCDS44734.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.978195	0.74360	.	.	ENSG00000170209	ENST00000303941	.	.	.	4.83	4.83	0.62350	.	0.000000	0.64402	D	0.000016	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.42905	T	0.14	-31.0765	17.083	0.86603	0.0:0.0:1.0:0.0	.	.	.	.	X	458	.	ENSP00000306678:E458X	E	+	1	0	ANKK1	112775273	1.000000	0.71417	1.000000	0.80357	0.026000	0.11368	7.465000	0.80898	2.498000	0.84270	0.557000	0.71058	GAA	ANKK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395830.1		11.198050	1	0	10	0	0.014758	1	0.0161635	NM_178510	4	11.222342	5	0.444444
SOX14	8403	broad.mit.edu	hg19	3	137484271	137484271	+	Silent	SNP	C	C	G			TCGA-VD-A8K8-01A-11D-A39W-08	TCGA-VD-A8K8-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68db916e-ad05-47dc-9a78-2ea29d299732	db6a4a82-2ba2-4d1c-92e6-12fd9418c4e6	g.chr3:137484271C>G	ENST00000306087.1	+	1	693	c.645C>G	c.(643-645)ccC>ccG	p.P215P		NM_004189.3	NP_004180.1	O95416	SOX14_HUMAN	SRY (sex determining region Y)-box 14	215		negative regulation of transcription from RNA polymerase II promoter|nervous system development|transcription, DNA-dependent	nucleus	sequence-specific DNA binding	large_intestine(2)|lung(12)	14					TGCAGCCCCCCGTCGCCTACA	0.662	0	45.0	34.0	38.0	3	137484271	2202	4293	6495	SO:0001819	synonymous_variant	AJ006230	CCDS3094.1	3q22-q23	2008-07-18			ENSG00000168875	ENSG00000168875	"""SRY (sex determining region Y)-boxes"""	11193	protein-coding gene	gene with protein product	"""HMG box transcription factor SOX-14"", ""SRY-box 14"""	604747			9925951	Standard	NM_004189	Approved	SOX28	uc003erm.2	O95416	OTTHUMG00000159757	ENST00000306087.1:c.645C>G	3.37:g.137484271C>G		B2RAC0|Q3KPH7	ENST00000306087.1	37	CCDS3094.1																																																																																			SOX14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357182.1		28.978313	0	1	42	0	0	1	0	NM_004189	9	29.229943	5	0.642857
MUC16	94025	broad.mit.edu	hg19	19	9018559	9018559	+	Missense_Mutation	SNP	C	C	A			TCGA-VD-A8K8-01A-11D-A39W-08	TCGA-VD-A8K8-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68db916e-ad05-47dc-9a78-2ea29d299732	db6a4a82-2ba2-4d1c-92e6-12fd9418c4e6	g.chr19:9018559C>A	ENST00000397910.4	-	24	37818	c.37615G>T	c.(37615-37617)Gct>Tct	p.A12539S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	12541	SEA 4.	cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding	NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590					AGAGGGCCAGCAGCTGTAGTG	0.428	0	195.0	167.0	176.0	19	9018559	1923	4138	6061	SO:0001583	missense	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143	"""Mucins"""	15582	protein-coding gene	gene with protein product		606154			11369781	Standard	XM_006722941	Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.37615G>T	19.37:g.9018559C>A	ENSP00000381008:p.Ala12539Ser	Q6ZQW5|Q96RK2	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	.	7.353	0.623202	0.14193	.	.	ENSG00000181143	ENST00000397910	T	0.33438	1.41	2.01	-0.421	0.12332	.	.	.	.	.	T	0.19765	0.0475	L	0.50333	1.59	.	.	.	P	0.35481	0.504	B	0.24394	0.053	T	0.20306	-1.0279	8	0.87932	D	0	.	3.0904	0.06291	0.0:0.4941:0.3105:0.1954	.	12539	B5ME49	.	S	12539	ENSP00000381008:A12539S	ENSP00000381008:A12539S	A	-	1	0	MUC16	8879559	0.000000	0.05858	0.000000	0.03702	0.273000	0.26683	-4.880000	0.00174	-0.025000	0.13918	0.195000	0.17529	GCT	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1		-12.180623	1	-26	129	0	0.014758	1	0.0161635	NM_024690	4	7.808796	86	0.044444
CSMD1	64478	broad.mit.edu	hg19	8	3263679	3263679	+	Silent	SNP	C	C	T			TCGA-VD-A8K8-01A-11D-A39W-08	TCGA-VD-A8K8-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68db916e-ad05-47dc-9a78-2ea29d299732	db6a4a82-2ba2-4d1c-92e6-12fd9418c4e6	g.chr8:3263679C>T	ENST00000602557.1	-	16	2694	c.2139G>A	c.(2137-2139)agG>agA	p.R713R	CSMD1_ENST00000520002.1_Silent_p.R713R|CSMD1_ENST00000537824.1_Silent_p.R712R|CSMD1_ENST00000602723.1_Silent_p.R713R|CSMD1_ENST00000400186.3_Silent_p.R713R|CSMD1_ENST00000539096.1_Silent_p.R712R|CSMD1_ENST00000542608.1_Silent_p.R712R			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	713	Sushi 4.		integral to membrane		breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)	CGAGTAGAAACCTGTCACCAA	0.453	0	48.0	49.0	49.0	8	3263679	1886	4120	6006	SO:0001819	synonymous_variant			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117	"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14026	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 24"""	608397				Standard	NM_033225	Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.2139G>A	8.37:g.3263679C>T		Q0H0J5|Q96QU9|Q96RM4	ENST00000520002.1	37		.	.	.	.	.	.	.	.	.	.	C	0.402	-0.917671	0.02396	.	.	ENSG00000183117	ENST00000335551	.	.	.	5.46	2.26	0.28386	.	.	.	.	.	T	0.55146	0.1902	.	.	.	0.41946	D	0.990636	.	.	.	.	.	.	T	0.49133	-0.8971	4	.	.	.	.	7.148	0.25593	0.1187:0.6047:0.0:0.2767	.	.	.	.	I	193	.	.	V	-	1	0	CSMD1	3251086	0.217000	0.23597	0.883000	0.34634	0.018000	0.09664	-0.404000	0.07205	0.675000	0.31264	-0.126000	0.14955	GTT	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2		19.115391	0	-3	18	0	0	1	0	NM_033225	5	19.084596	0	1.000000
NMRK2	27231	broad.mit.edu	hg19	19	3941074	3941074	+	Missense_Mutation	SNP	G	G	A			TCGA-VD-A8K8-01A-11D-A39W-08	TCGA-VD-A8K8-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68db916e-ad05-47dc-9a78-2ea29d299732	db6a4a82-2ba2-4d1c-92e6-12fd9418c4e6	g.chr19:3941074G>A	ENST00000168977.2	+	7	691	c.401G>A	c.(400-402)cGc>cAc	p.R134H	NMRK2_ENST00000599576.1_Intron|NMRK2_ENST00000593949.1_Missense_Mutation_p.R139H	NM_170678.2	NP_733778.1			nicotinamide riboside kinase 2												TGCAGTACCCGCAACTACACA	0.577	0	153.0	130.0	138.0	19	3941074	2203	4300	6503	SO:0001583	missense	AF190819	CCDS12115.1, CCDS74259.1	19p13.3	2013-10-28	2012-05-31	2012-05-31	ENSG00000077009	ENSG00000077009		17871	protein-coding gene	gene with protein product	"""muscle-specific beta 1 integrin binding protein"", ""nicotinamide riboside kinase 2"""	608705	"""integrin beta 1 binding protein 3"""	ITGB1BP3	10613898, 15137942	Standard	NM_170678	Approved	MIBP, NRK2	uc002lyz.4	Q9NPI5	OTTHUMG00000181758	ENST00000168977.2:c.401G>A	19.37:g.3941074G>A	ENSP00000168977:p.Arg134His	B7ZKR3|Q52M81|Q9NZK3	ENST00000168977.2	37	CCDS12115.1	.	.	.	.	.	.	.	.	.	.	G	18.40	3.615742	0.66672	.	.	ENSG00000077009	ENST00000168977	T	0.65916	-0.18	3.51	2.47	0.30058	.	0.891815	0.09184	U	0.837061	T	0.80465	0.4628	M	0.92507	3.315	0.48975	D	0.999733	D;D	0.89917	1.0;0.97	P;P	0.61132	0.884;0.502	T	0.76908	-0.2785	10	0.87932	D	0	-20.1072	8.4184	0.32685	0.1197:0.0:0.8803:0.0	.	139;134	B7ZKR3;Q9NPI5	.;NRK2_HUMAN	H	134	ENSP00000168977:R134H	ENSP00000168977:R134H	R	+	2	0	ITGB1BP3	3892074	0.999000	0.42202	0.008000	0.14137	0.001000	0.01503	8.047000	0.89440	0.691000	0.31592	-0.218000	0.12543	CGC	NMRK2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457492.1		-7.654894	0	1	101	0	0	1	0	NM_014446, NM_170678	4	8.408052	72	0.052632
UPK1A	11045	broad.mit.edu	hg19	19	36164371	36164371	+	Missense_Mutation	SNP	A	A	T			TCGA-VD-A8K8-01A-11D-A39W-08	TCGA-VD-A8K8-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68db916e-ad05-47dc-9a78-2ea29d299732	db6a4a82-2ba2-4d1c-92e6-12fd9418c4e6	g.chr19:36164371A>T	ENST00000222275.2	+	4	392	c.392A>T	c.(391-393)cAg>cTg	p.Q131L	UPK1A_ENST00000379013.2_Missense_Mutation_p.Q131L	NM_007000.2	NP_008931.1	O00322	UPK1A_HUMAN	uroplakin 1A	131		epithelial cell differentiation|protein oligomerization	endoplasmic reticulum|integral to membrane	monosaccharide binding|protein homodimerization activity	breast(1)|large_intestine(4)|lung(2)|stomach(2)	9	all_lung(56;2.22e-07)|Lung NSC(56;3.47e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)		ATCACCAAGCAGATGCTGACC	0.662	0	51.0	48.0	49.0	19	36164371	2203	4300	6503	SO:0001583	missense	AF085807	CCDS12470.1, CCDS62640.1	19q13.1	2013-02-14			ENSG00000105668	ENSG00000105668	"""Tetraspanins"""	12577	protein-coding gene	gene with protein product		611557			9846985, 10404304	Standard	NM_007000	Approved	TSPAN21	uc002oaw.3	O00322	OTTHUMG00000048115	ENST00000222275.2:c.392A>T	19.37:g.36164371A>T	ENSP00000222275:p.Gln131Leu	Q3KNU5|Q3KNU6	ENST00000222275.2	37	CCDS12470.1	.	.	.	.	.	.	.	.	.	.	A	27.4	4.828828	0.90955	.	.	ENSG00000105668	ENST00000222275;ENST00000379013	D;D	0.86865	-2.18;-2.18	5.54	5.54	0.83059	Tetraspanin, EC2 domain (1);	0.000000	0.64402	D	0.000001	D	0.90466	0.7014	M	0.65498	2.005	0.51012	D	0.999909	D;P	0.60575	0.988;0.951	P;P	0.56216	0.794;0.708	D	0.91301	0.5067	10	0.66056	D	0.02	0.466	13.6153	0.62103	1.0:0.0:0.0:0.0	.	131;131	O00322-2;O00322	.;UPK1A_HUMAN	L	131	ENSP00000222275:Q131L;ENSP00000368298:Q131L	ENSP00000222275:Q131L	Q	+	2	0	UPK1A	40856211	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	6.345000	0.72995	2.103000	0.63969	0.533000	0.62120	CAG	UPK1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109486.3		42.037790	0	0	51	0	0	1	0		14	42.948310	27	0.341463
PAX7	5081	broad.mit.edu	hg19	1	19029758	19029758	+	Missense_Mutation	SNP	A	A	C			TCGA-VD-A8K8-01A-11D-A39W-08	TCGA-VD-A8K8-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68db916e-ad05-47dc-9a78-2ea29d299732	db6a4a82-2ba2-4d1c-92e6-12fd9418c4e6	g.chr1:19029758A>C	ENST00000420770.2	+	7	1206	c.1123A>C	c.(1123-1125)Atg>Ctg	p.M375L	PAX7_ENST00000375375.3_Missense_Mutation_p.M375L|PAX7_ENST00000400661.3_Missense_Mutation_p.M373L	NM_001135254.1	NP_001128726.1	P23759	PAX7_HUMAN	paired box 7	375		anti-apoptosis	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(17)|ovary(1)|prostate(1)|skin(2)	31		Colorectal(325;3.46e-05)|all_lung(284;0.000439)|Renal(390;0.000518)|Lung NSC(340;0.000543)|Breast(348;0.00093)|Ovarian(437;0.00768)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00609)|BRCA - Breast invasive adenocarcinoma(304;4.71e-05)|Kidney(64;0.000279)|KIRC - Kidney renal clear cell carcinoma(64;0.00371)|STAD - Stomach adenocarcinoma(196;0.00658)|READ - Rectum adenocarcinoma(331;0.0576)	CTCCAACCACATGAACCCGGT	0.632	0	54.0	55.0	55.0	1	19029758	2203	4300	6503	SO:0001583	missense	X96743	CCDS186.1, CCDS44074.1, CCDS44075.1	1p36.13	2011-06-20	2007-07-12		ENSG00000009709	ENSG00000009709	"""Paired boxes"", ""Homeoboxes / PRD class"""	8621	protein-coding gene	gene with protein product		167410	"""paired box gene 7"""		7981748, 8431641	Standard	NM_001135254	Approved	Hup1	uc001bay.3	P23759	OTTHUMG00000002433	ENST00000420770.2:c.1123A>C	1.37:g.19029758A>C	ENSP00000403389:p.Met375Leu	E9PFV9|Q0VA99|Q2PJS5	ENST00000420770.2	37	CCDS44074.1	.	.	.	.	.	.	.	.	.	.	A	18.88	3.717407	0.68844	.	.	ENSG00000009709	ENST00000375375;ENST00000420770;ENST00000400661	T;T;T	0.80909	-1.43;-1.43;-1.43	5.41	5.41	0.78517	.	2.593350	0.01163	N	0.006697	D	0.83834	0.5340	M	0.65498	2.005	0.58432	D	0.999996	B;B;B	0.32382	0.055;0.134;0.368	B;B;B	0.35114	0.032;0.067;0.196	T	0.61840	-0.6980	10	0.36615	T	0.2	.	14.5614	0.68140	1.0:0.0:0.0:0.0	.	375;373;375	E9PFV9;P23759-2;P23759	.;.;PAX7_HUMAN	L	375;375;373	ENSP00000364524:M375L;ENSP00000403389:M375L;ENSP00000383502:M373L	ENSP00000364524:M375L	M	+	1	0	PAX7	18902345	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	8.713000	0.91408	2.179000	0.69175	0.459000	0.35465	ATG	PAX7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372482.1		38.492012	0	0	88	0	0	1	0	NM_002584	12	39.031532	21	0.363636
WDR75	84128	broad.mit.edu	hg19	2	190331249	190331249	+	Missense_Mutation	SNP	C	C	A			TCGA-VD-A8K8-01A-11D-A39W-08	TCGA-VD-A8K8-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68db916e-ad05-47dc-9a78-2ea29d299732	db6a4a82-2ba2-4d1c-92e6-12fd9418c4e6	g.chr2:190331249C>A	ENST00000314761.4	+	13	1448	c.1388C>A	c.(1387-1389)aCa>aAa	p.T463K		NM_032168.1	NP_115544.1	Q8IWA0	WDR75_HUMAN	WD repeat domain 75	463			nucleolus		breast(1)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)	25			OV - Ovarian serous cystadenocarcinoma(117;0.00105)|Epithelial(96;0.0129)|all cancers(119;0.0456)		ACCTTGGTTACAGCTAGCAAA	0.338	0	108.0	110.0	110.0	2	190331249	2203	4299	6502	SO:0001583	missense	AK091546	CCDS2298.1	2q32.2	2013-01-09			ENSG00000115368	ENSG00000115368	"""WD repeat domain containing"""	25725	protein-coding gene	gene with protein product	"""UTP17, small subunit (SSU) processome component, homolog (yeast)"""				17699751	Standard	NM_032168	Approved	FLJ12519, NET16, UTP17	uc002uql.1	Q8IWA0	OTTHUMG00000132660	ENST00000314761.4:c.1388C>A	2.37:g.190331249C>A	ENSP00000314193:p.Thr463Lys	Q96J10|Q9H8U8|Q9H9U5|Q9H9V8|Q9UIX2	ENST00000314761.4	37	CCDS2298.1	.	.	.	.	.	.	.	.	.	.	C	27.0	4.793383	0.90453	.	.	ENSG00000115368	ENST00000314761	T	0.68181	-0.31	5.29	5.29	0.74685	WD40/YVTN repeat-like-containing domain (1);	0.047591	0.85682	D	0.000000	T	0.82181	0.4981	M	0.75264	2.295	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.75484	0.986;0.986	D	0.83768	0.0218	10	0.87932	D	0	-19.1179	18.7417	0.91775	0.0:1.0:0.0:0.0	.	463;463	A8K330;Q8IWA0	.;WDR75_HUMAN	K	463	ENSP00000314193:T463K	ENSP00000314193:T463K	T	+	2	0	WDR75	190039494	1.000000	0.71417	0.999000	0.59377	0.959000	0.62525	6.531000	0.73820	2.752000	0.94435	0.655000	0.94253	ACA	WDR75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255913.1		-2.915786	1	6	71	0	1	1	1	NM_032168	3	6.660141	45	0.062500
SGSM1	129049	broad.mit.edu	hg19	22	25246302	25246302	+	Missense_Mutation	SNP	A	A	T			TCGA-VD-A8K8-01A-11D-A39W-08	TCGA-VD-A8K8-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68db916e-ad05-47dc-9a78-2ea29d299732	db6a4a82-2ba2-4d1c-92e6-12fd9418c4e6	g.chr22:25246302A>T	ENST00000400358.4	+	5	415	c.358A>T	c.(358-360)Aac>Tac	p.N120Y	SGSM1_ENST00000400359.4_Missense_Mutation_p.N120Y	NM_001098497.1|NM_001098498.1	NP_001091967.1|NP_001091968.1	Q2NKQ1	SGSM1_HUMAN	small G protein signaling modulator 1	120	RUN.		Golgi apparatus	Rab GTPase activator activity	NS(2)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(14)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	41					GAAGCTGCCCAACTTGTCCCC	0.483	0	70.0	70.0	70.0	22	25246302	1975	4157	6132	SO:0001583	missense	AB075821	CCDS46674.1, CCDS46675.1, CCDS74834.1	22q11.23	2013-07-09	2007-08-14	2007-08-14	ENSG00000167037	ENSG00000167037	"""Small G protein signaling modulators"""	29410	protein-coding gene	gene with protein product		611417	"""RUN and TBC1 domain containing 2"""	RUTBC2	11853319, 17509819, 22637480	Standard	NM_133454	Approved	KIAA1941	uc003abg.2	Q2NKQ1	OTTHUMG00000150837	ENST00000400358.4:c.358A>T	22.37:g.25246302A>T	ENSP00000383211:p.Asn120Tyr	A5LGW1|A8MUT4|B0QYW0|B0QYW1|B5MEG1|B9A6J4|Q5TFL3|Q8TF60	ENST00000400358.4	37	CCDS46675.1	.	.	.	.	.	.	.	.	.	.	A	16.86	3.238923	0.58995	.	.	ENSG00000167037	ENST00000403206;ENST00000400358;ENST00000400359	T;T	0.07800	3.16;3.16	4.83	4.83	0.62350	RUN (2);	0.364205	0.37053	N	0.002268	T	0.17831	0.0428	M	0.63428	1.95	0.48762	D	0.999703	B;B;P;P;D	0.54047	0.226;0.268;0.955;0.484;0.964	B;P;P;P;P	0.54590	0.202;0.459;0.642;0.452;0.756	T	0.06356	-1.0831	10	0.17832	T	0.49	0.9439	13.905	0.63828	1.0:0.0:0.0:0.0	.	120;95;95;120;95	Q2NKQ1-4;C9J7S8;Q2NKQ1-3;Q2NKQ1;B9A6J4	.;.;.;SGSM1_HUMAN;.	Y	95;120;120	ENSP00000383211:N120Y;ENSP00000383212:N120Y	ENSP00000383211:N120Y	N	+	1	0	SGSM1	23576302	1.000000	0.71417	0.995000	0.50966	0.245000	0.25701	7.253000	0.78320	1.949000	0.56562	0.477000	0.44152	AAC	SGSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320279.1		17.947618	0	0	20	0	0	1	0	XM_059318	6	18.009947	8	0.428571
MAPK8IP3	23162	ucsc.edu	hg19	16	1808152	1808152	+	Missense_Mutation	SNP	A	A	G			TCGA-VD-A8K8-01A-11D-A39W-08	TCGA-VD-A8K8-10A-01D-A39Z-08	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	68db916e-ad05-47dc-9a78-2ea29d299732	db6a4a82-2ba2-4d1c-92e6-12fd9418c4e6																										TCGCCAGGGGAGTTCTCAGGT	0.567	0	106.0	111.0	109.0	16	1808152	2025	4170	6195	SO:0001583	missense	AB028989	CCDS10442.2, CCDS45379.1	16p13.3	2009-11-23			ENSG00000138834	ENSG00000138834		6884	protein-coding gene	gene with protein product	"""homolog of Drosophila Sunday driver 2"""	605431			10523642, 10629060	Standard	XM_005255187	Approved	KIAA1066, JSAP1, JIP3, syd	uc002cmk.3	Q9UPT6	OTTHUMG00000128637	ENST00000250894.4:c.1217A>G	16.37:g.1808152A>G	ENSP00000250894:p.Glu406Gly	A2A2B3|A7E2B3|Q96RY4|Q9H4I4|Q9H7P1|Q9NUG0	ENST00000250894.4	37	CCDS10442.2	.	.	.	.	.	.	.	.	.	.	A	15.37	2.814693	0.50527	.	.	ENSG00000138834	ENST00000250894;ENST00000356010	T;T	0.34859	1.34;1.38	5.21	5.21	0.72293	.	.	.	.	.	T	0.29976	0.0750	L	0.33485	1.01	0.54753	D	0.999989	B;B	0.23540	0.005;0.087	B;B	0.26416	0.01;0.069	T	0.06197	-1.0840	9	0.25751	T	0.34	1.3005	14.751	0.69525	1.0:0.0:0.0:0.0	.	407;406	B7ZMF3;Q9UPT6	.;JIP3_HUMAN	G	406	ENSP00000250894:E406G;ENSP00000348290:E406G	ENSP00000250894:E406G	E	+	2	0	MAPK8IP3	1748153	1.000000	0.71417	1.000000	0.80357	0.889000	0.51656	7.218000	0.77991	1.985000	0.57927	0.459000	0.35465	GAG	MAPK8IP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250508.2				-9	38					NM_001040439	4		21	
GNA11	2767	broad.mit.edu	hg19	19	3118942	3118942	+	Missense_Mutation	SNP	A	A	T			TCGA-VD-A8K8-01A-11D-A39W-08	TCGA-VD-A8K8-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68db916e-ad05-47dc-9a78-2ea29d299732	db6a4a82-2ba2-4d1c-92e6-12fd9418c4e6	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		57.660845	0	-9	70	0	0	1	0	NM_002067	20	57.667110	21	0.487805
TRIM4	89122	broad.mit.edu	hg19	7	99489863	99489863	+	Missense_Mutation	SNP	C	C	T			TCGA-VD-A8K8-01A-11D-A39W-08	TCGA-VD-A8K8-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68db916e-ad05-47dc-9a78-2ea29d299732	db6a4a82-2ba2-4d1c-92e6-12fd9418c4e6	g.chr7:99489863C>T	ENST00000355947.2	-	7	1555	c.1426G>A	c.(1426-1428)Gtc>Atc	p.V476I	TRIM4_ENST00000349062.2_Missense_Mutation_p.V450I	NM_033017.3	NP_148977.2	Q9C037	TRIM4_HUMAN	tripartite motif containing 4	476	B30.2/SPRY.	protein trimerization	cytoplasm|plasma membrane	zinc ion binding	breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|skin(1)	17	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)	Ovarian(593;0.238)			AGGCGTGAGACAGAAGAACAA	0.502	0	111.0	105.0	107.0	7	99489863	2203	4300	6503	SO:0001583	missense	AF220023	CCDS5678.1, CCDS5679.1	7q22-q31.1	2013-01-09	2011-01-25		ENSG00000146833	ENSG00000146833	"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16275	protein-coding gene	gene with protein product	"""tripartite motif protein TRIM4"", ""tripartite motif protein 4"""		"""tripartite motif-containing 4"""		11331580	Standard	NM_033017	Approved	RNF87	uc003use.3	Q9C037	OTTHUMG00000156648	ENST00000355947.2:c.1426G>A	7.37:g.99489863C>T	ENSP00000348216:p.Val476Ile	A4D298|Q75MK1|Q96F06|Q9C036	ENST00000355947.2	37	CCDS5679.1	.	.	.	.	.	.	.	.	.	.	C	5.143	0.211907	0.09757	.	.	ENSG00000146833	ENST00000355947;ENST00000349062;ENST00000542799	T;T	0.60672	0.17;0.17	2.64	-1.47	0.08772	Concanavalin A-like lectin/glucanase (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	.	.	.	.	T	0.28863	0.0716	N	0.04203	-0.255	0.09310	N	1	B;B	0.09022	0.002;0.002	B;B	0.10450	0.003;0.005	T	0.13361	-1.0512	9	0.41790	T	0.15	.	4.0111	0.09623	0.0:0.3024:0.1947:0.5028	.	450;476	Q9C037-2;Q9C037	.;TRIM4_HUMAN	I	476;450;306	ENSP00000348216:V476I;ENSP00000275736:V450I	ENSP00000275736:V450I	V	-	1	0	TRIM4	99327799	0.000000	0.05858	0.000000	0.03702	0.398000	0.30690	-0.272000	0.08560	-0.378000	0.07918	-0.136000	0.14681	GTC	TRIM4-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345050.1		47.928694	0	13	93	0	0	1	0	NM_033017	18	49.515616	38	0.321429
PDP1	54704	broad.mit.edu	hg19	8	94935040	94935040	+	Silent	SNP	G	G	A	rs138553326		TCGA-VD-A8K8-01A-11D-A39W-08	TCGA-VD-A8K8-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68db916e-ad05-47dc-9a78-2ea29d299732	db6a4a82-2ba2-4d1c-92e6-12fd9418c4e6	g.chr8:94935040G>A	ENST00000396200.3	+	3	1104	c.828G>A	c.(826-828)gcG>gcA	p.A276A	PDP1_ENST00000297598.4_Silent_p.A251A|PDP1_ENST00000520728.1_Silent_p.A251A|PDP1_ENST00000517764.1_Silent_p.A251A	NM_001161779.1	NP_001155251.1	Q9P0J1	PDP1_HUMAN	pyruvate dehyrogenase phosphatase catalytic subunit 1	251		pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix|protein serine/threonine phosphatase complex	[pyruvate dehydrogenase (lipoamide)] phosphatase activity	breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|liver(1)|lung(5)|ovary(1)|pancreas(1)|skin(2)	18					CCTTGGAGGCGCAAGTTGGTG	0.463	0	124.0	125.0	124.0	8	94935040	2203	4300	6503	SO:0001819	synonymous_variant	AF155661	CCDS6259.1, CCDS55262.1	8q22.1	2012-04-17	2009-06-12	2009-06-12	ENSG00000164951	ENSG00000164951	"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"""	9279	protein-coding gene	gene with protein product		605993	"""protein phosphatase 2C, magnesium-dependent, catalytic subunit"""	PPM2C	8396421	Standard	NM_001161779	Approved	PDP, PDH	uc003ygf.3	Q9P0J1		ENST00000297598.4:c.753G>A	8.37:g.94935040G>A		B3KX71|J3KPU0|Q5U5K1	ENST00000297598.4	37	CCDS6259.1																																																																																			PDP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000378415.2		-56.406475	0	0	133	0	0	1	0	NM_018444	4	6.597551	235	0.016736
GRIN2B	2904	broad.mit.edu	hg19	12	13717090	13717090	+	Missense_Mutation	SNP	G	G	A			TCGA-VD-A8K8-01A-11D-A39W-08	TCGA-VD-A8K8-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68db916e-ad05-47dc-9a78-2ea29d299732	db6a4a82-2ba2-4d1c-92e6-12fd9418c4e6	g.chr12:13717090G>A	ENST00000609686.1	-	13	3291	c.3082C>T	c.(3082-3084)Ccc>Tcc	p.P1028S		NM_000834.3	NP_000825.2	Q13224	NMDE2_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2B			response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	glycine binding|N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding	NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(12)|liver(1)|lung(70)|ovary(4)|prostate(6)|skin(10)|upper_aerodigestive_tract(5)|urinary_tract(1)	143					TTGGAGGAGGGGAGGCCGATG	0.597	0	90.0	70.0	77.0	12	13717090	2203	4300	6503	SO:0001583	missense		CCDS8662.1	12p13.1	2014-07-16			ENSG00000273079		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4586	protein-coding gene	gene with protein product		138252		NMDAR2B	1350383	Standard	NM_000834	Approved	GluN2B	uc001rbt.2	Q13224	OTTHUMG00000137373	ENST00000609686.1:c.3082C>T	12.37:g.13717090G>A	ENSP00000477455:p.Pro1028Ser	Q12919|Q13220|Q13225|Q14CU4|Q9UM56	ENST00000609686.1	37	CCDS8662.1	.	.	.	.	.	.	.	.	.	.	G	16.60	3.169345	0.57584	.	.	ENSG00000150086	ENST00000279593	T	0.11930	2.73	5.57	4.68	0.58851	Glutamate [NMDA] receptor, epsilon subunit, C-terminal (1);	0.250220	0.41097	D	0.000952	T	0.09992	0.0245	N	0.25647	0.755	0.53688	D	0.999974	B	0.33448	0.412	B	0.26310	0.068	T	0.11084	-1.0602	10	0.52906	T	0.07	.	12.9157	0.58205	0.0755:0.0:0.9245:0.0	.	1028	Q13224	NMDE2_HUMAN	S	1028	ENSP00000279593:P1028S	ENSP00000279593:P1028S	P	-	1	0	GRIN2B	13608357	1.000000	0.71417	0.860000	0.33809	0.986000	0.74619	4.750000	0.62162	1.363000	0.46019	0.650000	0.86243	CCC	GRIN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268014.2		43.344087	0	2	38	0	0	1	0		14	43.575210	20	0.411765
RP11-731F5.1	0	broad.mit.edu	hg19	14	106067994	106067994	+	RNA	SNP	G	G	A			TCGA-VD-A8K8-01A-11D-A39W-08	TCGA-VD-A8K8-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68db916e-ad05-47dc-9a78-2ea29d299732	db6a4a82-2ba2-4d1c-92e6-12fd9418c4e6	g.chr14:106067994G>A	ENST00000390540.2	-	0	391																					CCAGAGTCACGGAGGTGGCAT	0.607	0	98.0	112.0	108.0	14	106067994	2131	4232	6363																												14.37:g.106067994G>A			ENST00000390540.2	37																																																																																				RP11-731F5.1-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000380286.1		36.326958	0	-4	27	0	0	1	0		11	36.326958	11	0.500000
ANO10	55129	ucsc.edu	hg19	3	43596927	43596927	+	Missense_Mutation	SNP	T	T	C			TCGA-VD-A8K8-01A-11D-A39W-08	TCGA-VD-A8K8-10A-01D-A39Z-08	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	68db916e-ad05-47dc-9a78-2ea29d299732	db6a4a82-2ba2-4d1c-92e6-12fd9418c4e6																										ATAACCAAACTGCAGGAATAA	0.343	0	90.0	88.0	89.0	3	43596927	2203	4300	6503	SO:0001583	missense	AL832508	CCDS2710.2, CCDS56247.1, CCDS56248.1, CCDS56249.1, CCDS56250.1	3p22.1-p21.33	2014-04-09	2008-08-28	2008-08-28	ENSG00000160746	ENSG00000160746	"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	25519	protein-coding gene	gene with protein product		613726	"""transmembrane protein 16K"""	TMEM16K	12477932, 24692353	Standard	NM_001204831	Approved	FLJ10375, MGC47890, SCAR10	uc003cmv.3	Q9NW15	OTTHUMG00000133044	ENST00000414522.2:c.1511A>G	3.37:g.43596927T>C	ENSP00000396990:p.Gln504Arg	A8K8K3|A8MV74|B3KTZ1|B3KY93|B4DJ83|B4DNK2|B7WP12|C9JHS1|Q8IXX9	ENST00000414522.2	37	CCDS56250.1	.	.	.	.	.	.	.	.	.	.	T	18.05	3.536127	0.64972	.	.	ENSG00000160746	ENST00000292246;ENST00000350459;ENST00000396091;ENST00000414522;ENST00000451430	T;T;T;T;T	0.71579	-0.58;-0.58;-0.58;-0.58;-0.58	5.24	5.24	0.73138	.	0.067852	0.64402	D	0.000010	D	0.84844	0.5562	M	0.88377	2.95	0.37000	D	0.895229	D;D;D;D;D	0.89917	0.995;0.999;1.0;0.995;0.996	D;D;D;D;D	0.76575	0.959;0.988;0.986;0.972;0.984	D	0.89198	0.3555	10	0.87932	D	0	.	10.4237	0.44365	0.1454:0.0:0.0:0.8545	.	393;504;314;438;504	Q9NW15-4;C9JHS1;Q9NW15-2;Q9NW15-3;Q9NW15	.;.;.;.;ANO10_HUMAN	R	504;314;438;504;393	ENSP00000292246:Q504R;ENSP00000327767:Q314R;ENSP00000379398:Q438R;ENSP00000396990:Q504R;ENSP00000394119:Q393R	ENSP00000292246:Q504R	Q	-	2	0	ANO10	43571931	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.466000	0.53071	1.990000	0.58119	0.533000	0.62120	CAG	ANO10-004	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000344332.2				9	50					NM_018075	4		19	
SYNE1	23345	ucsc.edu	hg19	6	152631012	152631012	+	Silent	SNP	G	G	A			TCGA-VD-A8K8-01A-11D-A39W-08	TCGA-VD-A8K8-10A-01D-A39Z-08	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	68db916e-ad05-47dc-9a78-2ea29d299732	db6a4a82-2ba2-4d1c-92e6-12fd9418c4e6																										GCTGCAGCCGGCTGGCCTCTT	0.582	0	61.0	57.0	58.0	6	152631012	2203	4300	6503	SO:0001819	synonymous_variant	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018		17089	protein-coding gene	gene with protein product	"""myocyte nuclear envelope protein 1"", ""nuclear envelope spectrin repeat-1"""	608441	"""chromosome 6 open reading frame 98"""	C6orf98	9872452, 10878022	Standard	NM_182961	Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.17160C>T	6.37:g.152631012G>A		E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	ENST00000367255.5	37	CCDS5236.2																																																																																			SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2				-8	33					NM_182961	4		35	
OR10G4	390264	broad.mit.edu	hg19	11	123886874	123886874	+	Missense_Mutation	SNP	T	T	C			TCGA-VD-A8K8-01A-11D-A39W-08	TCGA-VD-A8K8-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68db916e-ad05-47dc-9a78-2ea29d299732	db6a4a82-2ba2-4d1c-92e6-12fd9418c4e6	g.chr11:123886874T>C	ENST00000320891.4	+	1	593	c.593T>C	c.(592-594)aTc>aCc	p.I198T		NM_001004462.1	NP_001004462.1	Q8NGN3	O10G4_HUMAN	olfactory receptor, family 10, subfamily G, member 4	198		sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	NS(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(1)|skin(4)|stomach(6)|upper_aerodigestive_tract(1)	48		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0401)	GTGATGGTCATCTTTGTGGAC	0.547	0	268.0	217.0	234.0	11	123886874	2201	4299	6500	SO:0001583	missense	AB065757	CCDS31702.1	11q24.1	2012-08-09			ENSG00000254737	ENSG00000254737	"""GPCR / Class A : Olfactory receptors"""	14809	protein-coding gene	gene with protein product						Standard	NM_001004462	Approved		uc010sac.2	Q8NGN3	OTTHUMG00000165966	ENST00000320891.4:c.593T>C	11.37:g.123886874T>C	ENSP00000325076:p.Ile198Thr	Q6IEW0	ENST00000320891.4	37	CCDS31702.1	.	.	.	.	.	.	.	.	.	.	t	6.532	0.466481	0.12402	.	.	ENSG00000254737	ENST00000320891	T	0.00145	8.67	3.33	3.33	0.38152	GPCR, rhodopsin-like superfamily (1);	0.141128	0.32444	N	0.006091	T	0.00178	0.0005	N	0.20445	0.575	0.29292	N	0.869291	D	0.59767	0.986	D	0.63113	0.911	T	0.62421	-0.6858	10	0.33940	T	0.23	.	8.0035	0.30310	0.0:0.1052:0.0:0.8948	.	198	Q8NGN3	O10G4_HUMAN	T	198	ENSP00000325076:I198T	ENSP00000325076:I198T	I	+	2	0	OR10G4	123392084	0.000000	0.05858	0.936000	0.37596	0.063000	0.16089	0.075000	0.14686	1.529000	0.49120	0.473000	0.43528	ATC	OR10G4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387268.1		150.552488	0	13	125	0	0	1	0	NM_001004462	46	150.562175	44	0.511111
MYOF	26509	broad.mit.edu	hg19	10	95111448	95111448	+	Missense_Mutation	SNP	T	T	A			TCGA-VD-A8K8-01A-11D-A39W-08	TCGA-VD-A8K8-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68db916e-ad05-47dc-9a78-2ea29d299732	db6a4a82-2ba2-4d1c-92e6-12fd9418c4e6	g.chr10:95111448T>A	ENST00000371501.4	-	33	3759	c.3637A>T	c.(3637-3639)Atg>Ttg	p.M1213L	MYOF_ENST00000359263.4_Missense_Mutation_p.M1213L|MYOF_ENST00000358334.5_Missense_Mutation_p.M1200L|MYOF_ENST00000371502.4_Missense_Mutation_p.M1213L			Q9NZM1	MYOF_HUMAN	myoferlin	1213	C2 4.	blood circulation|muscle contraction|plasma membrane repair	caveola|cytoplasmic vesicle membrane|integral to membrane|nuclear membrane	phospholipid binding|protein binding	NS(2)|autonomic_ganglia(1)|breast(3)|endometrium(7)|kidney(7)|large_intestine(15)|lung(14)|ovary(4)|prostate(4)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	67					AAAAGTTCCATGATAACTTTG	0.403	0	119.0	116.0	117.0	10	95111448	1812	4082	5894	SO:0001583	missense	AB033033	CCDS41550.1, CCDS41551.1	10q24	2014-06-27	2008-11-26	2008-11-26	ENSG00000138119	ENSG00000138119		3656	protein-coding gene	gene with protein product	"""fer-1-like family member 3"""	604603	"""fer-1 (C.elegans)-like 3 (myoferlin)"", ""fer-1-like 3, myoferlin (C. elegans)"""	FER1L3	10607832, 10995573, 17702744	Standard	NM_013451	Approved	KIAA1207	uc001kin.3	Q9NZM1	OTTHUMG00000018772	ENST00000359263.4:c.3637A>T	10.37:g.95111448T>A	ENSP00000352208:p.Met1213Leu	B3KQN5|Q5VWW2|Q5VWW3|Q5VWW4|Q5VWW5|Q7Z642|Q8IWH0|Q9HBU3|Q9NZM0|Q9ULL3|Q9Y4U4	ENST00000359263.4	37	CCDS41551.1	.	.	.	.	.	.	.	.	.	.	T	0.882	-0.728473	0.03135	.	.	ENSG00000138119	ENST00000358334;ENST00000359263;ENST00000371501;ENST00000371502	T;T;T;T	0.61040	0.14;0.14;0.14;0.14	5.77	3.44	0.39384	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.384015	0.30602	N	0.009262	T	0.22589	0.0545	N	0.00873	-1.125	0.19575	N	0.999969	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.21999	-1.0229	10	0.13853	T	0.58	-3.3848	9.1397	0.36897	0.0:0.2068:0.0:0.7932	.	1200;1213	Q9NZM1-6;Q9NZM1	.;MYOF_HUMAN	L	1200;1213;1213;1213	ENSP00000351094:M1200L;ENSP00000352208:M1213L;ENSP00000360556:M1213L;ENSP00000360557:M1213L	ENSP00000351094:M1200L	M	-	1	0	MYOF	95101438	0.999000	0.42202	0.039000	0.18376	0.239000	0.25481	0.708000	0.25719	0.458000	0.26988	-0.297000	0.09499	ATG	MYOF-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049423.2		75.958055	0	7	98	0	0	1	0	NM_013451	25	76.629234	39	0.390625
SYNGAP1	8831	broad.mit.edu	hg19	6	33403335	33403335	+	Missense_Mutation	SNP	C	C	T			TCGA-VD-A8K8-01A-11D-A39W-08	TCGA-VD-A8K8-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68db916e-ad05-47dc-9a78-2ea29d299732	db6a4a82-2ba2-4d1c-92e6-12fd9418c4e6	g.chr6:33403335C>T	ENST00000418600.2	+	7	808	c.707C>T	c.(706-708)gCg>gTg	p.A236V	SYNGAP1_ENST00000496374.1_3'UTR|SYNGAP1_ENST00000428982.2_Missense_Mutation_p.A177V|SYNGAP1_ENST00000293748.5_Missense_Mutation_p.A236V	NM_006772.2	NP_006763.2	Q96PV0	SYGP1_HUMAN	synaptic Ras GTPase activating protein 1	236	PH.	negative regulation of Ras protein signal transduction|signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	Ras GTPase activator activity|SH3 domain binding	breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(15)|ovary(7)|pancreas(1)|stomach(1)|urinary_tract(1)	43					TGTCGGTCTGCGGCCGAAAGA	0.507	0	178.0	163.0	168.0	6	33403335	2203	4300	6503	SO:0001583	missense	AB067525	CCDS34434.2	6p21.3	2010-06-25	2010-06-25		ENSG00000197283	ENSG00000197283		11497	protein-coding gene	gene with protein product		603384	"""synaptic Ras GTPase activating protein 1 homolog (rat)"""		9581761, 18323856	Standard	NM_006772	Approved	SYNGAP, RASA5, KIAA1938	uc011dri.2	Q96PV0	OTTHUMG00000031096	ENST00000418600.2:c.707C>T	6.37:g.33403335C>T	ENSP00000403636:p.Ala236Val	A2AB17|A2BEL6|A2BEL7|A8MQC4|Q8TCS2|Q9UGE2	ENST00000418600.2	37	CCDS34434.2	.	.	.	.	.	.	.	.	.	.	C	33	5.223162	0.95139	.	.	ENSG00000197283	ENST00000293748;ENST00000418600;ENST00000449372;ENST00000428982	D;D;D	0.93366	-3.21;-3.21;-3.21	4.62	4.62	0.57501	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.000000	0.85682	D	0.000000	D	0.94489	0.8226	M	0.80746	2.51	0.80722	D	1	D;D;D	0.61080	0.981;0.989;0.979	B;P;P	0.53689	0.446;0.648;0.732	D	0.95111	0.8238	10	0.87932	D	0	.	15.0065	0.71516	0.0:1.0:0.0:0.0	.	236;236;236	Q96PV0;Q96PV0-4;B7ZCA0	SYGP1_HUMAN;.;.	V	236;236;236;177	ENSP00000293748:A236V;ENSP00000403636:A236V;ENSP00000412475:A177V	ENSP00000293748:A236V	A	+	2	0	SYNGAP1	33511313	1.000000	0.71417	0.958000	0.39756	0.962000	0.63368	7.651000	0.83577	2.391000	0.81399	0.591000	0.81541	GCG	SYNGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076151.4		-23.911289	0	-8	174	0	0	1	0	XM_166407	4	6.896118	124	0.031250
NOP9	161424	broad.mit.edu	hg19	14	24769766	24769766	+	Missense_Mutation	SNP	C	C	T	rs148747544		TCGA-VD-A8K8-01A-11D-A39W-08	TCGA-VD-A8K8-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68db916e-ad05-47dc-9a78-2ea29d299732	db6a4a82-2ba2-4d1c-92e6-12fd9418c4e6	g.chr14:24769766C>T	ENST00000267425.3	+	2	493	c.400C>T	c.(400-402)Cgc>Tgc	p.R134C	NOP9_ENST00000396802.3_Missense_Mutation_p.R134C	NM_174913.1	NP_777573.1			NOP9 nucleolar protein												CTCTAACTTGCGCACTGTGGC	0.572	0	212.0	185.0	194.0	14	24769766	2203	4300	6503	SO:0001583	missense		CCDS9624.1, CCDS66616.1	14q12	2012-12-10	2012-12-10	2012-06-06	ENSG00000196943	ENSG00000196943		19826	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 21"", ""NOP9 nucleolar protein homolog (yeast)"""	C14orf21	21653694	Standard	XM_005267385	Approved		uc001wol.1	Q86U38	OTTHUMG00000029342	ENST00000267425.3:c.400C>T	14.37:g.24769766C>T	ENSP00000267425:p.Arg134Cys	A8MY76|Q8IVF0|Q8TBS6	ENST00000267425.3	37	CCDS9624.1	.	.	.	.	.	.	.	.	.	.	C	18.33	3.600058	0.66332	2.27E-4	0.0	ENSG00000196943	ENST00000267425;ENST00000396802	T;T	0.14144	2.53;2.53	4.96	4.96	0.65561	Armadillo-like helical (1);Armadillo-type fold (1);	0.301944	0.31963	N	0.006784	T	0.31009	0.0783	M	0.68593	2.085	0.21822	N	0.999527	D	0.76494	0.999	P	0.57960	0.83	T	0.06481	-1.0824	10	0.38643	T	0.18	-12.0003	17.1191	0.86697	0.0:1.0:0.0:0.0	.	134	Q86U38	CN021_HUMAN	C	134	ENSP00000267425:R134C;ENSP00000380020:R134C	ENSP00000267425:R134C	R	+	1	0	C14orf21	23839606	0.790000	0.28787	0.106000	0.21319	0.538000	0.34931	4.099000	0.57755	2.558000	0.86282	0.655000	0.94253	CGC	NOP9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073186.2		-57.411262	0	-4	279	0	0	1	0		4	6.573211	238	0.016529
CDRT15L2	256223	broad.mit.edu	hg19	17	20483993	20483993	+	Frame_Shift_Del	DEL	G	G	-			TCGA-VD-A8K8-01A-11D-A39W-08	TCGA-VD-A8K8-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68db916e-ad05-47dc-9a78-2ea29d299732	db6a4a82-2ba2-4d1c-92e6-12fd9418c4e6	g.chr17:20483993delG	ENST00000399044.1	+	2	817	c.797delG	c.(796-798)tggfs	p.W266fs		NM_001190790.1	NP_001177719.1	A8MXV6	CD15L_HUMAN	CMT1A duplicated region transcript 15-like 2	266			integral to membrane		central_nervous_system(1)	1					GTCTGCAACTGGGCATCCAGG	0.567	0									SO:0001589	frameshift_variant		CCDS54096.1	17p11.2	2008-10-30			ENSG00000214819	ENSG00000214819		34075	protein-coding gene	gene with protein product						Standard	NM_001190790	Approved		uc021tsn.1	A8MXV6	OTTHUMG00000059557	ENST00000399044.1:c.797delG	17.37:g.20483993delG	ENSP00000382000:p.Trp266fs		ENST00000399044.1	37	CCDS54096.1																																																																																			CDRT15L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132432.3	.	.		-5	3					XM_170840	2		4	0.33
DROSHA	29102	broad.mit.edu	hg19	5	31526492	31526492	+	Frame_Shift_Del	DEL	T	T	-			TCGA-VD-A8K8-01A-11D-A39W-08	TCGA-VD-A8K8-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68db916e-ad05-47dc-9a78-2ea29d299732	db6a4a82-2ba2-4d1c-92e6-12fd9418c4e6	g.chr5:31526492delT	ENST00000511367.2	-	4	792	c.548delA	c.(547-549)aatfs	p.N183fs	DROSHA_ENST00000513349.1_Frame_Shift_Del_p.N183fs|DROSHA_ENST00000442743.1_Frame_Shift_Del_p.N183fs|DROSHA_ENST00000344624.3_Frame_Shift_Del_p.N183fs	NM_013235.4	NP_037367.3	Q9NRR4	RNC_HUMAN	drosha, ribonuclease type III	183	Pro-rich.	gene silencing by RNA|ribosome biogenesis|RNA processing	nucleolus|nucleoplasm	double-stranded RNA binding|metal ion binding|protein binding|ribonuclease III activity	breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(19)|lung(33)|ovary(2)|skin(1)	66					CTGGAAACTATTAAAACTGGG	0.522	0	69.0	69.0	69.0	5	31526492	1872	4115	5987	SO:0001589	frameshift_variant	AF116910	CCDS47194.1, CCDS47195.1	5q11.2	2010-11-17	2010-10-28	2010-10-28	ENSG00000113360	ENSG00000113360		17904	protein-coding gene	gene with protein product	"""drosha, ribonuclease type III"", ""drosha, double-stranded RNA-specific endoribonuclease"""	608828	"""ribonuclease type III, nuclear"""	RNASEN	10713462, 10948199	Standard	NM_013235	Approved	RNASE3L, Etohi2, HSA242976, RN3	uc003jhg.2	Q9NRR4	OTTHUMG00000161976	ENST00000511367.2:c.548delA	5.37:g.31526492delT	ENSP00000425979:p.Asn183fs	E7EMP9|Q7Z5V2|Q86YH0|Q9NW73|Q9Y2V9|Q9Y4Y0	ENST00000511367.2	37	CCDS47195.1																																																																																			DROSHA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366561.3	.	.		-3	59					NM_013235	26		28	0.48