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
EIF1AX	1964	broad.mit.edu	hg19	X	20156740	20156740	+	Splice_Site	SNP	C	C	T			TCGA-VD-AA8R-01A-11D-A39W-08	TCGA-VD-AA8R-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14b7d726-410a-4847-83d0-ba01ffc3336c	6b99c1ba-83d1-4636-bb8d-b1dccaca6afe	g.chrX:20156740C>T	ENST00000379607.5	-	2	220	c.17G>A	c.(16-18)gGt>gAt	p.G6D	EIF1AX_ENST00000379593.1_Intron	NM_001412.3	NP_001403.1	P47813	IF1AX_HUMAN	eukaryotic translation initiation factor 1A, X-linked	6			cytosol	translation initiation factor activity	endometrium(2)|lung(1)|ovary(1)|prostate(1)	5					ACCTCCTTTACCTGATGGTTT	0.299	0	130.0	120.0	123.0	X	20156740	2203	4300	6503	SO:0001630	splice_region_variant	L18960	CCDS14196.1	Xp22.13	2014-02-19	2002-11-28	2004-05-26	ENSG00000173674	ENSG00000173674		3250	protein-coding gene	gene with protein product		300186	"""eukaryotic translation initiation factor 1A, X chromosome"""	EIF4C, EIF1A	8106356, 9381176	Standard	NM_001412	Approved	eIF-1A, eIF-4C	uc004czt.3	P47813	OTTHUMG00000022704	ENST00000379607.5:c.17-1G>A	X.37:g.20156740C>T		B2R5U5|Q0VGC2|Q5JPS5|Q5JPS6	ENST00000379607.5	37	CCDS14196.1	.	.	.	.	.	.	.	.	.	.	C	18.74	3.689024	0.68271	.	.	ENSG00000173674	ENST00000379607	T	0.45668	0.89	4.84	4.84	0.62591	Nucleic acid-binding, OB-fold-like (1);Nucleic acid-binding, OB-fold (1);	.	.	.	.	T	0.73885	0.3644	H	0.95780	3.72	0.80722	D	1	D	0.55800	0.973	D	0.63703	0.917	D	0.83652	0.0156	9	0.87932	D	0	.	17.4345	0.87547	0.0:1.0:0.0:0.0	.	6	P47813	IF1AX_HUMAN	D	6	ENSP00000368927:G6D	ENSP00000368927:G6D	G	-	2	0	EIF1AX	20066661	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	7.237000	0.78164	2.129000	0.65627	0.600000	0.82982	GGT	EIF1AX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058913.1		115.075213	0	-25	128	0	0	1	0		34	120.959243	4	0.894737
MYH2	4620	broad.mit.edu	hg19	17	10426880	10426880	+	Missense_Mutation	SNP	C	C	T			TCGA-VD-AA8R-01A-11D-A39W-08	TCGA-VD-AA8R-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14b7d726-410a-4847-83d0-ba01ffc3336c	6b99c1ba-83d1-4636-bb8d-b1dccaca6afe	g.chr17:10426880C>T	ENST00000245503.5	-	37	5789	c.5405G>A	c.(5404-5406)cGt>cAt	p.R1802H	MYH2_ENST00000397183.2_Missense_Mutation_p.R1802H|MYH2_ENST00000532183.2_Intron|RP11-799N11.1_ENST00000399342.2_RNA|CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_017534.5	NP_060004.3	Q9UKX2	MYH2_HUMAN	myosin, heavy chain 2, skeletal muscle, adult	1802		muscle filament sliding	muscle myosin complex|myosin filament|sarcomere	actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle	NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(99)|ovary(6)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(4)	176					CTCATCCAGACGGAGCTGCAG	0.572	0	105.0	106.0	105.0	17	10426880	2203	4300	6503	SO:0001583	missense		CCDS11156.1	17p13.1	2014-02-04	2006-09-29		ENSG00000125414	ENSG00000125414	"""Myosins / Myosin superfamily : Class II"""	7572	protein-coding gene	gene with protein product		160740	"""myosin, heavy polypeptide 2, skeletal muscle, adult"", ""inclusion body myopathy 3, autosomal dominant"""	IBM3	7545970, 11889243	Standard	NM_001100112	Approved	MYH2A, MYHSA2, MyHC-IIa, MYHas8, MyHC-2A	uc010coi.3	Q9UKX2	OTTHUMG00000130363	ENST00000245503.5:c.5405G>A	17.37:g.10426880C>T	ENSP00000245503:p.Arg1802His	A0AVL4|Q14322|Q16229|Q567P6|Q86T56	ENST00000245503.5	37	CCDS11156.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.717717	0.89205	.	.	ENSG00000125414	ENST00000245503;ENST00000397183	D;D	0.82526	-1.62;-1.62	5.5	5.5	0.81552	Myosin tail (1);	0.000000	0.40144	U	0.001168	D	0.91576	0.7339	H	0.97940	4.11	0.58432	D	0.999999	P	0.38148	0.62	B	0.41723	0.365	D	0.93510	0.6852	10	0.87932	D	0	.	19.5916	0.95514	0.0:1.0:0.0:0.0	.	1802	Q9UKX2	MYH2_HUMAN	H	1802	ENSP00000245503:R1802H;ENSP00000380367:R1802H	ENSP00000245503:R1802H	R	-	2	0	MYH2	10367605	1.000000	0.71417	0.828000	0.32881	0.757000	0.42996	7.651000	0.83577	2.861000	0.98227	0.655000	0.94253	CGT	MYH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252726.3		143.841722	0	-15	90	0	0	1	0	NM_017534	46	144.015953	55	0.455446
RYR1	6261	broad.mit.edu	hg19	19	38983214	38983214	+	Missense_Mutation	SNP	G	G	A	rs139775280		TCGA-VD-AA8R-01A-11D-A39W-08	TCGA-VD-AA8R-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14b7d726-410a-4847-83d0-ba01ffc3336c	6b99c1ba-83d1-4636-bb8d-b1dccaca6afe	g.chr19:38983214G>A	ENST00000355481.4	+	38	6343	c.6212G>A	c.(6211-6213)cGg>cAg	p.R2071Q	RYR1_ENST00000359596.3_Missense_Mutation_p.R2071Q|RYR1_ENST00000360985.3_Missense_Mutation_p.R2071Q	NM_000540.2|NM_001042723.1	NP_000531.2|NP_001036188.1	P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	2071	6 X approximate repeats.	muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity	NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		GAGAAAGTGCGGCTGGTGAAG	0.592	1	53.0	50.0	51.0	19	38983214	2203	4300	6503	SO:0001583	missense	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218	"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO	1862346, 16621918	Standard	NM_000540	Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.6212G>A	19.37:g.38983214G>A	ENSP00000352608:p.Arg2071Gln	Q16314|Q16368|Q9NPK1|Q9P1U4	ENST00000359596.3	37	CCDS33011.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	g	14.95	2.687932	0.48097	2.27E-4	0.0	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	T;T;T	0.72282	-0.64;-0.64;-0.64	5.05	2.44	0.29823	.	0.173200	0.32134	U	0.006527	T	0.56366	0.1980	L	0.48642	1.525	0.09310	N	0.999995	B;D	0.53151	0.009;0.958	B;B	0.38296	0.003;0.27	T	0.51164	-0.8740	10	0.30854	T	0.27	.	9.4058	0.38460	0.2693:0.0:0.7307:0.0	.	2071;2071	P21817-2;P21817	.;RYR1_HUMAN	Q	2071	ENSP00000352608:R2071Q;ENSP00000347667:R2071Q;ENSP00000354254:R2071Q	ENSP00000347667:R2071Q	R	+	2	0	RYR1	43675054	0.637000	0.27216	0.997000	0.53966	0.970000	0.65996	1.180000	0.32005	1.089000	0.41292	0.539000	0.68188	CGG	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		36.597635	0	-7	24	0	0	1	0		12	37.134735	21	0.363636
GNA11	2767	broad.mit.edu	hg19	19	3118942	3118942	+	Missense_Mutation	SNP	A	A	T			TCGA-VD-AA8R-01A-11D-A39W-08	TCGA-VD-AA8R-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14b7d726-410a-4847-83d0-ba01ffc3336c	6b99c1ba-83d1-4636-bb8d-b1dccaca6afe	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		76.997732	0	-4	77	0	0	1	0	NM_002067	25	77.031867	28	0.471698
BICC1	80114	broad.mit.edu	hg19	10	60549448	60549448	+	Missense_Mutation	SNP	A	A	G			TCGA-VD-AA8R-01A-11D-A39W-08	TCGA-VD-AA8R-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14b7d726-410a-4847-83d0-ba01ffc3336c	6b99c1ba-83d1-4636-bb8d-b1dccaca6afe	g.chr10:60549448A>G	ENST00000373886.3	+	8	806	c.802A>G	c.(802-804)Act>Gct	p.T268A		NM_001080512.1	NP_001073981.1	Q9H694	BICC1_HUMAN	bicaudal C homolog 1 (Drosophila)	268		multicellular organismal development		RNA binding	breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(22)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	44					TTAGGAAGGAACTGCCATGCT	0.393	0	183.0	175.0	178.0	10	60549448	2203	4300	6503	SO:0001583	missense	AK026129	CCDS31206.1	10q21.3	2014-09-17	2014-02-03		ENSG00000122870	ENSG00000122870	"""Sterile alpha motif (SAM) domain containing"""	19351	protein-coding gene	gene with protein product		614295	"""bicaudal C homolog 1 (Drosophila)"""			Standard	XM_005270166	Approved		uc001jki.1	Q9H694	OTTHUMG00000018271	ENST00000373886.3:c.802A>G	10.37:g.60549448A>G	ENSP00000362993:p.Thr268Ala		ENST00000373886.3	37	CCDS31206.1	.	.	.	.	.	.	.	.	.	.	A	18.31	3.594980	0.66219	.	.	ENSG00000122870	ENST00000373886	T	0.40756	1.02	5.88	4.76	0.60689	.	0.042911	0.85682	N	0.000000	T	0.37999	0.1024	L	0.54323	1.7	0.80722	D	1	B	0.09022	0.002	B	0.09377	0.004	T	0.13255	-1.0516	10	0.34782	T	0.22	-12.1964	11.657	0.51324	0.9313:0.0:0.0687:0.0	.	268	Q9H694	BICC1_HUMAN	A	268	ENSP00000362993:T268A	ENSP00000362993:T268A	T	+	1	0	BICC1	60219454	1.000000	0.71417	0.977000	0.42913	0.994000	0.84299	5.306000	0.65756	1.062000	0.40625	0.533000	0.62120	ACT	BICC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048150.2		224.216939	0	-66	145	0	0	1	0	NM_025044	67	224.398032	78	0.462069
SGTA	6449	broad.mit.edu	hg19	19	2759273	2759273	+	Missense_Mutation	SNP	T	T	C			TCGA-VD-AA8R-01A-11D-A39W-08	TCGA-VD-AA8R-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14b7d726-410a-4847-83d0-ba01ffc3336c	6b99c1ba-83d1-4636-bb8d-b1dccaca6afe	g.chr19:2759273T>C	ENST00000221566.2	-	9	880	c.719A>G	c.(718-720)aAt>aGt	p.N240S		NM_003021.3	NP_003012.1	O43765	SGTA_HUMAN	small glutamine-rich tetratricopeptide repeat (TPR)-containing, alpha	240		interspecies interaction between organisms	cytoplasm	protein binding	endometrium(2)|large_intestine(2)|lung(2)|ovary(1)	7		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)	AATCTGGGGATTGTTCATTAG	0.403	0	129.0	137.0	134.0	19	2759273	2203	4300	6503	SO:0001583	missense	AJ223828	CCDS12094.1	19p13	2013-01-10	2003-11-24	2003-11-26		ENSG00000104969	"""Tetratricopeptide (TTC) repeat domain containing"""	10819	protein-coding gene	gene with protein product		603419	"""small glutamine-rich tetratricopeptide repeat (TPR)-containing"""	SGT	9740675, 12735788	Standard	NM_003021	Approved		uc002lwi.1	O43765		ENST00000221566.2:c.719A>G	19.37:g.2759273T>C	ENSP00000221566:p.Asn240Ser	D6W610|Q6FIA9|Q9BTZ9	ENST00000221566.2	37	CCDS12094.1	.	.	.	.	.	.	.	.	.	.	T	7.807	0.714844	0.15306	.	.	ENSG00000104969	ENST00000221566	T	0.39406	1.08	4.05	2.99	0.34606	.	0.097264	0.64402	N	0.000002	T	0.42154	0.1190	M	0.73962	2.25	0.34545	D	0.710736	B	0.10296	0.003	B	0.17979	0.02	T	0.49698	-0.8912	10	0.56958	D	0.05	-23.5309	9.2874	0.37766	0.0:0.0:0.1823:0.8177	.	240	O43765	SGTA_HUMAN	S	240	ENSP00000221566:N240S	ENSP00000221566:N240S	N	-	2	0	SGTA	2710273	0.962000	0.33011	0.247000	0.24249	0.176000	0.22953	1.514000	0.35834	0.406000	0.25560	0.459000	0.35465	AAT	SGTA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451448.2		-38.798252	0	-34	193	0	0	1	0	NM_003021	5	9.796509	190	0.025641
RAI14	26064	broad.mit.edu	hg19	5	34823886	34823886	+	Missense_Mutation	SNP	G	G	A			TCGA-VD-AA8R-01A-11D-A39W-08	TCGA-VD-AA8R-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14b7d726-410a-4847-83d0-ba01ffc3336c	6b99c1ba-83d1-4636-bb8d-b1dccaca6afe	g.chr5:34823886G>A	ENST00000265109.3	+	15	2226	c.1939G>A	c.(1939-1941)Gag>Aag	p.E647K	RAI14_ENST00000506376.1_Missense_Mutation_p.E639K|RAI14_ENST00000512629.1_Missense_Mutation_p.E618K|RAI14_ENST00000503673.1_Missense_Mutation_p.E647K|RAI14_ENST00000397449.1_Missense_Mutation_p.E640K|RAI14_ENST00000428746.2_Missense_Mutation_p.E647K|RAI14_ENST00000515799.1_Missense_Mutation_p.E650K	NM_001145522.1|NM_015577.2	NP_001138994.1|NP_056392.2	Q9P0K7	RAI14_HUMAN	retinoic acid induced 14	647			cell cortex|cytoskeleton	protein binding	breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(19)|lung(22)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(31;0.000191)				ACAGGTGAGCGAGCTGTCACA	0.443	0	77.0	81.0	80.0	5	34823886	2203	4300	6503	SO:0001583	missense	AB037755	CCDS34142.1, CCDS54837.1, CCDS54838.1, CCDS54839.1	5p13.3-p13.2	2013-01-10			ENSG00000039560	ENSG00000039560	"""Ankyrin repeat domain containing"""	14873	protein-coding gene	gene with protein product	"""novel retinal pigment epithelial"""	606586			11042181	Standard	NM_015577	Approved	NORPEG, KIAA1334, RAI13, DKFZp564G013	uc011coj.2	Q9P0K7	OTTHUMG00000162019	ENST00000265109.3:c.1939G>A	5.37:g.34823886G>A	ENSP00000265109:p.Glu647Lys	E9PED3|Q6V1W9|Q7Z5I4|Q7Z733|Q9P2L2|Q9Y3T5	ENST00000265109.3	37	CCDS34142.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.989851	0.93106	.	.	ENSG00000039560	ENST00000265109;ENST00000512629;ENST00000428746;ENST00000503673;ENST00000515799;ENST00000506376;ENST00000397449	T;T;T;T;T;T;T	0.54279	0.75;0.6;0.75;0.75;0.58;0.63;0.62	5.68	5.68	0.88126	.	.	.	.	.	T	0.61874	0.2382	L	0.34521	1.04	0.80722	D	1	D;D;D;D	0.76494	0.995;0.997;0.999;0.997	P;P;P;P	0.60173	0.749;0.678;0.87;0.546	T	0.62158	-0.6913	9	0.54805	T	0.06	-26.0717	19.7964	0.96487	0.0:0.0:1.0:0.0	.	639;618;650;647	Q9P0K7-3;E9PED3;Q9P0K7-2;Q9P0K7	.;.;.;RAI14_HUMAN	K	647;618;647;647;650;639;640	ENSP00000265109:E647K;ENSP00000422377:E618K;ENSP00000388725:E647K;ENSP00000422942:E647K;ENSP00000427123:E650K;ENSP00000423854:E639K;ENSP00000380591:E640K	ENSP00000265109:E647K	E	+	1	0	RAI14	34859643	1.000000	0.71417	0.989000	0.46669	0.974000	0.67602	5.748000	0.68697	2.683000	0.91414	0.555000	0.69702	GAG	RAI14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366786.1		57.922589	0	-9	42	0	0	1	0	NM_015577	19	58.005060	23	0.452381
GLI2	2736	broad.mit.edu	hg19	2	121748132	121748132	+	Nonsense_Mutation	SNP	C	C	T			TCGA-VD-AA8R-01A-11D-A39W-08	TCGA-VD-AA8R-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14b7d726-410a-4847-83d0-ba01ffc3336c	6b99c1ba-83d1-4636-bb8d-b1dccaca6afe	g.chr2:121748132C>T	ENST00000452319.1	+	14	4702	c.4642C>T	c.(4642-4644)Cga>Tga	p.R1548*	GLI2_ENST00000361492.4_Nonsense_Mutation_p.R1548*|GLI2_ENST00000314490.11_Intron			P10070	GLI2_HUMAN	GLI family zinc finger 2	1548		axon guidance|branching morphogenesis of a tube|cell proliferation|cerebellar cortex morphogenesis|developmental growth|embryonic digestive tract development|epidermal cell differentiation|floor plate formation|heart development|hindgut morphogenesis|kidney development|lung development|negative regulation of transcription from RNA polymerase II promoter|odontogenesis of dentine-containing tooth|osteoblast development|osteoblast differentiation|pituitary gland development|positive regulation of DNA replication|positive regulation of T cell differentiation in thymus|positive regulation of transcription from RNA polymerase II promoter|proximal/distal pattern formation|skeletal system development|smoothened signaling pathway involved in ventral spinal cord interneuron specification|spinal cord ventral commissure morphogenesis	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(24)|ovary(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	Renal(3;0.0496)	Prostate(154;0.0623)			CACCACCCCCCGAAACTCCTT	0.617	0	111.0	128.0	122.0	2	121748132	2203	4300	6503	SO:0001587	stop_gained		CCDS33283.1	2q14	2013-01-25	2009-03-05		ENSG00000074047	ENSG00000074047	"""Zinc fingers, C2H2-type"""	4318	protein-coding gene	gene with protein product	"""tax-responsive element-2 holding protein"", ""tax helper protein 1"", ""tax helper protein 2"""	165230	"""GLI-Kruppel family member GLI2"", ""glioma-associated oncogene family zinc finger 2"""		2850480, 9557682	Standard	NM_005270	Approved	THP2, HPE9, THP1	uc010flp.3	P10070	OTTHUMG00000153741	ENST00000452319.1:c.4642C>T	2.37:g.121748132C>T	ENSP00000390436:p.Arg1548*		ENST00000452319.1	37	CCDS33283.1	.	.	.	.	.	.	.	.	.	.	C	40	8.520170	0.98848	.	.	ENSG00000074047	ENST00000452319;ENST00000361492	.	.	.	4.98	2.01	0.26516	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.6438	0.62267	0.5689:0.4311:0.0:0.0	.	.	.	.	X	1548	.	ENSP00000354586:R1548X	R	+	1	2	GLI2	121464602	0.914000	0.31030	0.899000	0.35326	0.844000	0.47949	1.864000	0.39469	0.207000	0.20607	-0.410000	0.06199	CGA	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3		172.550726	0	-76	183	0	0	1	0	NM_005270	57	173.679376	84	0.404255
MUC5AC	4586	broad.mit.edu	hg19	11	1162271	1162271	+	Missense_Mutation	SNP	G	G	A			TCGA-VD-AA8R-01A-11D-A39W-08	TCGA-VD-AA8R-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14b7d726-410a-4847-83d0-ba01ffc3336c	6b99c1ba-83d1-4636-bb8d-b1dccaca6afe	g.chr11:1162271G>A	ENST00000356191.2	+	20	1771	c.1771G>A	c.(1771-1773)Gcg>Acg	p.A591T						mucin 5AC, oligomeric mucus/gel-forming						NS(1)|breast(2)|central_nervous_system(7)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(5)|kidney(9)|large_intestine(19)|liver(1)|lung(89)|ovary(7)|prostate(8)|skin(9)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	203		all_cancers(49;2.94e-05)|Breast(177;0.00257)|all_epithelial(84;0.00314)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		BRCA - Breast invasive adenocarcinoma(625;0.00146)|Lung(200;0.0612)|LUSC - Lung squamous cell carcinoma(625;0.0724)	GGCCACCGCTGCGGCCTTCTT	0.622	0	28.0	28.0	28.0	11	1162271	867	1985	2852	SO:0001583	missense	AJ001402, AJ298317		11p15.5	2007-04-23	2006-03-14		ENSG00000215182	ENSG00000215182	"""Mucins"""	7515	protein-coding gene	gene with protein product		158373	"""mucin 5, subtypes A and C, tracheobronchial/gastric"""		7826332, 9588204	Standard	XM_006709945	Approved	MUC5	uc001lsz.3	P98088	OTTHUMG00000154270	ENST00000356191.2:c.1771G>A	11.37:g.1162271G>A	ENSP00000348519:p.Ala591Thr	O60460|O76065|Q13792|Q14425|Q658Q1|Q7M4S5|Q8N4M9|Q8WWQ3|Q8WWQ4|Q8WWQ5	ENST00000356191.2	37		.	.	.	.	.	.	.	.	.	.	g	10.30	1.311558	0.23821	.	.	ENSG00000215182	ENST00000534821;ENST00000356191	T;T	0.18502	2.21;2.24	2.86	2.86	0.33363	.	.	.	.	.	T	0.17365	0.0417	L	0.55017	1.72	.	.	.	P	0.43094	0.799	B	0.40782	0.34	T	0.19582	-1.0301	8	0.54805	T	0.06	.	8.3181	0.32113	0.1131:0.0:0.8869:0.0	.	594	A7Y9J9	.	T	594;591	ENSP00000435591:A594T;ENSP00000348519:A591T	ENSP00000348519:A591T	A	+	1	0	MUC5AC	1152271	0.012000	0.17670	0.063000	0.19743	0.006000	0.05464	1.218000	0.32467	1.618000	0.50286	0.289000	0.19496	GCG	MUC5AC-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding			41.248607	0	-2	23	0	0	1	0	XM_001130382	14	41.248607	14	0.500000
ZNF780A	284323	broad.mit.edu	hg19	19	40581890	40581890	+	Silent	SNP	A	A	G			TCGA-VD-AA8R-01A-11D-A39W-08	TCGA-VD-AA8R-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14b7d726-410a-4847-83d0-ba01ffc3336c	6b99c1ba-83d1-4636-bb8d-b1dccaca6afe	g.chr19:40581890A>G	ENST00000450241.2	-	6	668	c.357T>C	c.(355-357)ccT>ccC	p.P119P	ZNF780A_ENST00000455521.1_Silent_p.P154P|ZNF780A_ENST00000594395.1_Silent_p.P154P|AC005614.5_ENST00000595508.1_RNA|ZNF780A_ENST00000595687.2_Silent_p.P153P|ZNF780A_ENST00000414720.2_Intron|ZNF780A_ENST00000340963.5_Silent_p.P153P			O75290	Z780A_HUMAN	zinc finger protein 780A	153		regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(16)|upper_aerodigestive_tract(3)|urinary_tract(1)	31	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)				GAGAAGCATGAGGAGTATGAG	0.353	0	190.0	163.0	172.0	19	40581890	2203	4300	6503	SO:0001819	synonymous_variant	AK091274	CCDS33026.2, CCDS46078.1, CCDS46079.1	19q13.2	2014-02-12	2006-08-15		ENSG00000197782	ENSG00000197782	"""Zinc fingers, C2H2-type"", ""-"""	27603	protein-coding gene	gene with protein product						Standard	NM_001142577	Approved	ZNF780	uc010xvh.2	O75290	OTTHUMG00000155119	ENST00000594395.1:c.462T>C	19.37:g.40581890A>G		E9PB48|Q6ZN87	ENST00000594395.1	37	CCDS46079.1																																																																																			ZNF780A-008	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462498.2		-4.520298	0	-3	79	0	0	1	0	NM_001010880	3	6.427574	50	0.056604
GNB3	2784	broad.mit.edu	hg19	12	6953033	6953033	+	Missense_Mutation	SNP	A	A	G			TCGA-VD-AA8R-01A-11D-A39W-08	TCGA-VD-AA8R-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14b7d726-410a-4847-83d0-ba01ffc3336c	6b99c1ba-83d1-4636-bb8d-b1dccaca6afe	g.chr12:6953033A>G	ENST00000229264.3	+	9	995	c.590A>G	c.(589-591)aAt>aGt	p.N197S	GNB3_ENST00000435982.2_Missense_Mutation_p.N196S	NM_002075.2	NP_002066.1	P16520	GBB3_HUMAN	guanine nucleotide binding protein (G protein), beta polypeptide 3	197		cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|regulation of blood pressure|synaptic transmission	plasma membrane	GTPase activity|GTPase binding|signal transducer activity	cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(7)|prostate(1)|stomach(1)	20					CCTGACTTCAATCTCTTCATT	0.562	0	134.0	116.0	122.0	12	6953033	2203	4300	6503	SO:0001583	missense		CCDS8564.1, CCDS73427.1	12p13	2013-01-10			ENSG00000111664	ENSG00000111664	"""WD repeat domain containing"""	4400	protein-coding gene	gene with protein product		139130			11770079, 16600389	Standard	XM_005253680	Approved		uc001qrd.3	P16520	OTTHUMG00000168517	ENST00000229264.3:c.590A>G	12.37:g.6953033A>G	ENSP00000229264:p.Asn197Ser	Q96B71|Q9BQC0	ENST00000229264.3	37	CCDS8564.1	.	.	.	.	.	.	.	.	.	.	A	8.347	0.830069	0.16749	.	.	ENSG00000111664	ENST00000229264;ENST00000541257;ENST00000435982	T;T;T	0.60171	0.21;0.21;0.21	5.46	1.79	0.24919	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.273432	0.46758	D	0.000278	T	0.34513	0.0900	N	0.11560	0.145	0.30405	N	0.779626	B;B	0.06786	0.001;0.0	B;B	0.12837	0.008;0.008	T	0.20306	-1.0279	10	0.39692	T	0.17	-11.6507	9.4239	0.38567	0.7957:0.0:0.2043:0.0	.	196;197	E9PCP0;P16520	.;GBB3_HUMAN	S	197;196;196	ENSP00000229264:N197S;ENSP00000442002:N196S;ENSP00000414734:N196S	ENSP00000229264:N197S	N	+	2	0	GNB3	6823294	1.000000	0.71417	0.993000	0.49108	0.002000	0.02628	3.897000	0.56273	0.062000	0.16340	-0.379000	0.06801	AAT	GNB3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400006.1		75.056169	0	-12	58	0	0	1	0	NM_002075	25	75.357224	34	0.423729
GTSE1	51512	broad.mit.edu	hg19	22	46704545	46704545	+	Missense_Mutation	SNP	A	A	C			TCGA-VD-AA8R-01A-11D-A39W-08	TCGA-VD-AA8R-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14b7d726-410a-4847-83d0-ba01ffc3336c	6b99c1ba-83d1-4636-bb8d-b1dccaca6afe	g.chr22:46704545A>C	ENST00000454366.1	+	4	679	c.467A>C	c.(466-468)aAa>aCa	p.K156T		NM_016426.6	NP_057510	Q9NYZ3	GTSE1_HUMAN	G-2 and S-phase expressed 1	137		DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G2 phase of mitotic cell cycle|microtubule-based process	cytoplasmic microtubule		NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	27		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00462)	GAAATGAAGAAAAGCCCCACG	0.532	0	58.0	72.0	67.0	22	46704545	2200	4291	6491	SO:0001583	missense	AF223408	CCDS14074.2	22q13.2-q13.3	2008-06-10			ENSG00000075218	ENSG00000075218		13698	protein-coding gene	gene with protein product		607477			10974554, 10984615, 12750368	Standard	NM_016426	Approved	GTSE-1, B99	uc011aqy.2	Q9NYZ3	OTTHUMG00000150486	ENST00000454366.1:c.467A>C	22.37:g.46704545A>C	ENSP00000415430:p.Lys156Thr	B0QYM3|Q20WK2|Q53GX5|Q5R3I6|Q6DHX4|Q9BRE0|Q9UGZ9|Q9Y557	ENST00000454366.1	37	CCDS14074.2	.	.	.	.	.	.	.	.	.	.	A	17.93	3.509736	0.64522	.	.	ENSG00000075218	ENST00000454366;ENST00000361934	T	0.10099	2.91	5.45	2.91	0.33838	.	0.207947	0.50627	D	0.000113	T	0.27524	0.0676	M	0.68952	2.095	0.31633	N	0.648815	D	0.89917	1.0	D	0.73708	0.981	T	0.21314	-1.0249	10	0.87932	D	0	-24.8417	10.6827	0.45823	0.8429:0.0:0.1571:0.0	.	137	Q9NYZ3	GTSE1_HUMAN	T	156;116	ENSP00000415430:K156T	ENSP00000354634:K116T	K	+	2	0	GTSE1	45083209	0.274000	0.24191	0.857000	0.33713	0.915000	0.54546	0.757000	0.26433	0.855000	0.35359	0.533000	0.62120	AAA	GTSE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318360.2		101.294378	0	-7	94	0	0	1	0	NM_016426	32	101.444139	39	0.450704
ATF2	1386	broad.mit.edu	hg19	2	175945425	175945425	+	Silent	SNP	G	G	A			TCGA-VD-AA8R-01A-11D-A39W-08	TCGA-VD-AA8R-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14b7d726-410a-4847-83d0-ba01ffc3336c	6b99c1ba-83d1-4636-bb8d-b1dccaca6afe	g.chr2:175945425G>A	ENST00000264110.2	-	13	1552	c.1254C>T	c.(1252-1254)tgC>tgT	p.C418C	ATF2_ENST00000409437.1_Silent_p.C302C|ATF2_ENST00000392543.2_Silent_p.C39C|ATF2_ENST00000426833.3_Silent_p.C400C|ATF2_ENST00000409499.1_Silent_p.C57C|ATF2_ENST00000487334.2_3'UTR|ATF2_ENST00000345739.5_Silent_p.C360C|ATF2_ENST00000538946.1_3'UTR|ATF2_ENST00000392544.1_Silent_p.C418C|ATF2_ENST00000409635.1_Silent_p.C360C	NM_001256090.1|NM_001256091.1|NM_001880.3	NP_001243019.1|NP_001243020.1|NP_001871.2	P15336	ATF2_HUMAN	activating transcription factor 2	418		innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|regulation of sequence-specific DNA binding transcription factor activity|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	nucleoplasm	protein dimerization activity|sequence-specific DNA binding|transcription coactivator activity|zinc ion binding	breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(6)|pancreas(1)|skin(1)	17			OV - Ovarian serous cystadenocarcinoma(117;0.125)		CGGTTACAGGGCAATCTTTAT	0.443	0	177.0	173.0	174.0	2	175945425	2203	4300	6503	SO:0001819	synonymous_variant	X15875	CCDS2262.1, CCDS58737.1, CCDS58738.1, CCDS58739.1	2q32	2013-01-10			ENSG00000115966	ENSG00000115966	"""basic leucine zipper proteins"""	784	protein-coding gene	gene with protein product		123811	"""cAMP responsive element binding protein 2"""	CREB2	1833307, 1838349	Standard	NM_001880	Approved	TREB7, CRE-BP1, HB16	uc002ujl.4	P15336	OTTHUMG00000132424	ENST00000264110.2:c.1254C>T	2.37:g.175945425G>A		A1L3Z2|A4D7U4|A4D7U5|A4D7V1|D3DPE9|G8JLM5|Q13000|Q3B7B7|Q4ZFU9|Q53RY2|Q8TAR1|Q96JT8	ENST00000264110.2	37	CCDS2262.1																																																																																			ATF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255562.1		-25.623589	0	-47	143	0	0	1	0	NM_001880	4	7.193720	131	0.029630
SZT2	23334	broad.mit.edu	hg19	1	43912793	43912793	+	Silent	SNP	C	C	T			TCGA-VD-AA8R-01A-11D-A39W-08	TCGA-VD-AA8R-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14b7d726-410a-4847-83d0-ba01ffc3336c	6b99c1ba-83d1-4636-bb8d-b1dccaca6afe	g.chr1:43912793C>T	ENST00000562955.1	+	65	9069	c.9069C>T	c.(9067-9069)gcC>gcT	p.A3023A	SZT2_ENST00000372442.1_Silent_p.A2181A	NM_015284.3	NP_056099.3	Q5T011	SZT2_HUMAN	seizure threshold 2 homolog (mouse)	3080			peroxisome		NS(2)|breast(9)|central_nervous_system(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(39)|ovary(4)|pancreas(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	113					ACTTCCTGGCCCACCACCCTG	0.592	0	127.0	89.0	102.0	1	43912793	2203	4300	6503	SO:0001819	synonymous_variant	AB007936	CCDS30694.1, CCDS30694.2	1p34.2	2012-11-19	2011-06-10	2011-06-10	ENSG00000198198	ENSG00000198198		29040	protein-coding gene	gene with protein product	"""seizure threshold 2 homolog A (mouse)"", ""seizure threshold 2 homolog B (mouse)"""	615463	"""chromosome 1 open reading frame 84"", ""KIAA0467"""	C1orf84, KIAA0467	9455484	Standard	NM_015284	Approved	FLJ10387, SZT2B, RP11-506B15.1, FLJ34502, SZT2A	uc001cjk.3	Q5T011	OTTHUMG00000007423	ENST00000562955.1:c.9069C>T	1.37:g.43912793C>T		A0PJK5|A7E2X4|O75055|Q5JUY7|Q5T012|Q5XKC7|Q6ZNI8|Q6ZT24|Q7Z636|Q8NAY9|Q9H5H7|Q9UFQ8	ENST00000562955.1	37	CCDS30694.2																																																																																			SZT2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019517.3		41.975046	0	-20	15	0	0	1	0	NM_015284	13	41.975046	13	0.500000
KNDC1	85442	broad.mit.edu	hg19	10	135020364	135020364	+	Silent	SNP	C	C	T			TCGA-VD-AA8R-01A-11D-A39W-08	TCGA-VD-AA8R-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14b7d726-410a-4847-83d0-ba01ffc3336c	6b99c1ba-83d1-4636-bb8d-b1dccaca6afe	g.chr10:135020364C>T	ENST00000304613.3	+	19	3507	c.3486C>T	c.(3484-3486)tcC>tcT	p.S1162S	KNDC1_ENST00000368572.2_Silent_p.S1164S|KNDC1_ENST00000368571.2_Silent_p.S1097S			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	1162		regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction			NS(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(27)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	60		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)	CCACAGGTTCCGACGTCAAGA	0.567	0	101.0	109.0	106.0	10	135020364	2203	4300	6503	SO:0001819	synonymous_variant	AK074179	CCDS7674.1	10q26.3	2004-09-14	2004-04-07		ENSG00000171798	ENSG00000171798		29374	protein-coding gene	gene with protein product			"""RasGEF domain family, member 2"""	RASGEF2, C10orf23	11214970	Standard	NM_152643	Approved	KIAA1768, bB439H18.3, FLJ25027	uc001llz.1	Q76NI1	OTTHUMG00000019303	ENST00000304613.3:c.3486C>T	10.37:g.135020364C>T		B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	ENST00000304613.3	37	CCDS7674.1																																																																																			KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3		-1.729267	0	-43	87	0	0	1	0	NM_152643	7	16.259641	89	0.072917
RRNAD1	51093	broad.mit.edu	hg19	1	156704256	156704257	+	Frame_Shift_Del	DEL	CC	CC	-			TCGA-VD-AA8R-01A-11D-A39W-08	TCGA-VD-AA8R-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14b7d726-410a-4847-83d0-ba01ffc3336c	6b99c1ba-83d1-4636-bb8d-b1dccaca6afe	g.chr1:156704256_156704257delCC	ENST00000368216.4	+	6	1722_1723	c.1092_1093delCC	c.(1090-1095)atccccfs	p.P365fs	RRNAD1_ENST00000476229.1_Intron|RRNAD1_ENST00000368218.4_Intron	NM_015997.3	NP_057081.3	Q96FB5	RRNAD_HUMAN	ribosomal RNA adenine dimethylase domain containing 1	365			integral to membrane	rRNA (adenine-N6,N6-)-dimethyltransferase activity	NS(1)|breast(1)|kidney(1)|large_intestine(3)|lung(3)	9					TGCAGGGTATCCCCAGGGTCCA	0.599	0									SO:0001589	frameshift_variant	BC011382	CCDS1154.1, CCDS44246.1	1q23.1	2011-01-28	2011-01-28	2011-01-28	ENSG00000143303	ENSG00000143303		24273	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 66"""	C1orf66	10810093, 310876	Standard	NM_015997	Approved	CGI-41	uc001fpu.3	Q96FB5	OTTHUMG00000041302	ENST00000368216.4:c.1092_1093delCC	1.37:g.156704258_156704259delCC	ENSP00000357199:p.Pro365fs	D3DVC7|Q4VX71|Q5SZ03|Q9Y358	ENST00000368216.4	37	CCDS1154.1																																																																																			RRNAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098973.1	.	.		4	7					NM_015997	2		4	0.33