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
SNAP91	9892	broad.mit.edu	hg19	6	84291979	84291979	+	Missense_Mutation	SNP	G	G	A			TCGA-YZ-A983-01A-11D-A39W-08	TCGA-YZ-A983-10B-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	699c8dc5-4c3b-4069-aac9-634da96679d1	fc2a9e37-ddcc-43d4-8d65-815c22a42e3a	g.chr6:84291979G>A	ENST00000428679.2	-	23	2704	c.2111C>T	c.(2110-2112)aCg>aTg	p.T704M	SNAP91_ENST00000369694.2_Missense_Mutation_p.T704M|SNAP91_ENST00000520213.1_Missense_Mutation_p.T397M|SNAP91_ENST00000439399.2_Missense_Mutation_p.T704M|SNAP91_ENST00000195649.6_Missense_Mutation_p.T704M|SNAP91_ENST00000521485.1_Missense_Mutation_p.T704M|SNAP91_ENST00000437520.1_Missense_Mutation_p.T397M|SNAP91_ENST00000520302.1_Missense_Mutation_p.T674M|SNAP91_ENST00000521743.1_Missense_Mutation_p.T704M			O60641	AP180_HUMAN	synaptosomal-associated protein, 91kDa	704		clathrin coat assembly	clathrin coat|coated pit|plasma membrane	1-phosphatidylinositol binding|clathrin binding	breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(22)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;2.91e-07)|all_hematologic(105;0.000337)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0967)	AGTTGAAGGCGTTGTCCCAAA	0.468	0	86.0	88.0	87.0	6	84291979	1979	4179	6158	SO:0001583	missense	AB014556	CCDS47455.1, CCDS56437.1, CCDS56438.1	6q15	2012-12-07	2012-12-07		ENSG00000065609	ENSG00000065609		14986	protein-coding gene	gene with protein product		607923	"""synaptosomal-associated protein, 91 kDa (mouse) homolog"", ""synaptosomal-associated protein, 91kDa homolog (mouse)"""		9734811, 12493563, 10436022	Standard	NM_014841	Approved	KIAA0656, AP180, CALM	uc003pka.3	O60641	OTTHUMG00000015114	ENST00000439399.2:c.2111C>T	6.37:g.84291979G>A	ENSP00000400459:p.Thr704Met	A8K0L7|E5RI02|Q5JX13|Q68DL9|Q6P9D3|Q9NTY7	ENST00000439399.2	37	CCDS47455.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.022845	0.75275	.	.	ENSG00000065609	ENST00000521485;ENST00000369694;ENST00000439399;ENST00000195649;ENST00000428679;ENST00000437520;ENST00000520302;ENST00000521743;ENST00000520213;ENST00000523448;ENST00000521931	T;T;T;T;T;T;T;T;T;T;T	0.29917	1.55;1.55;1.55;1.55;1.55;1.55;1.55;1.55;1.55;1.55;1.55	5.43	5.43	0.79202	.	0.348037	0.30159	N	0.010276	T	0.27629	0.0679	N	0.19112	0.55	0.24748	N	0.992998	P;D;D;D;D	0.89917	0.923;1.0;1.0;1.0;1.0	B;D;D;P;D	0.71870	0.198;0.975;0.964;0.904;0.964	T	0.15723	-1.0427	10	0.87932	D	0	-5.1581	14.1174	0.65164	0.0:0.0:0.8498:0.1502	.	585;397;674;704;702	B7Z2N2;O60641-3;E5RI02;O60641;E1P549	.;.;.;AP180_HUMAN;.	M	704;704;704;704;704;397;674;704;397;45;517	ENSP00000429776:T704M;ENSP00000358708:T704M;ENSP00000400459:T704M;ENSP00000195649:T704M;ENSP00000412492:T704M;ENSP00000413277:T397M;ENSP00000428511:T674M;ENSP00000428215:T704M;ENSP00000428026:T397M;ENSP00000430255:T45M;ENSP00000430071:T517M	ENSP00000195649:T704M	T	-	2	0	SNAP91	84348698	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	5.315000	0.65810	2.564000	0.86499	0.561000	0.74099	ACG	SNAP91-007	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000375296.1		50.465699	0	-24	54	0	0	1	0		17	50.963349	27	0.386364
LRP1B	53353	broad.mit.edu	hg19	2	141092048	141092048	+	Missense_Mutation	SNP	A	A	G			TCGA-YZ-A983-01A-11D-A39W-08	TCGA-YZ-A983-10B-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	699c8dc5-4c3b-4069-aac9-634da96679d1	fc2a9e37-ddcc-43d4-8d65-815c22a42e3a	g.chr2:141092048A>G	ENST00000389484.3	-	79	13168	c.12197T>C	c.(12196-12198)gTa>gCa	p.V4066A		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	4066		protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding	NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)	GTTCTTTTGTACTAAAATCCT	0.403	0	177.0	162.0	167.0	2	141092048	2203	4300	6503	SO:0001583	missense	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702	"""Low density lipoprotein receptors"""	6693	protein-coding gene	gene with protein product	"""LRP-deleted in tumors"""	608766			10766186	Standard	NM_018557	Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.12197T>C	2.37:g.141092048A>G	ENSP00000374135:p.Val4066Ala	Q8WY29|Q8WY30|Q8WY31	ENST00000389484.3	37	CCDS2182.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	27.1|27.1	4.796568|4.796568	0.90453|0.90453	.|.	.|.	ENSG00000168702|ENSG00000168702	ENST00000389484;ENST00000544579|ENST00000437977	D|.	0.96011|.	-3.88|.	6.08|6.08	6.08|6.08	0.98989|0.98989	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);|.	0.381500|.	0.24359|.	N|.	0.039212|.	T|T	0.67477|0.67477	0.2897|0.2897	L|L	0.56769|0.56769	1.78|1.78	0.37120|0.37120	D|D	0.900784|0.900784	P|.	0.39044|.	0.656|.	B|.	0.37550|.	0.253|.	T|T	0.70085|0.70085	-0.4969|-0.4969	10|5	0.36615|.	T|.	0.2|.	.|.	16.6512|16.6512	0.85203|0.85203	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	4066|.	Q9NZR2|.	LRP1B_HUMAN|.	A|H	4066;4004|298	ENSP00000374135:V4066A|.	ENSP00000374135:V4066A|.	V|Y	-|-	2|1	0|0	LRP1B|LRP1B	140808518|140808518	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	8.837000|8.837000	0.92110|0.92110	2.333000|2.333000	0.79357|0.79357	0.482000|0.482000	0.46254|0.46254	GTA|TAC	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2		74.648766	0	4	54	0	0	1	0	NM_018557	22	74.667596	24	0.478261
PTPMT1	114971	broad.mit.edu	hg19	11	47591272	47591272	+	Nonsense_Mutation	SNP	C	C	T			TCGA-YZ-A983-01A-11D-A39W-08	TCGA-YZ-A983-10B-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	699c8dc5-4c3b-4069-aac9-634da96679d1	fc2a9e37-ddcc-43d4-8d65-815c22a42e3a	g.chr11:47591272C>T	ENST00000534775.1	+	2	550	c.385C>T	c.(385-387)Cga>Tga	p.R129*	PTPMT1_ENST00000527079.2_3'UTR|PTPMT1_ENST00000326656.8_Intron|PTPMT1_ENST00000426530.2_Intron|NDUFS3_ENST00000533507.1_Intron|PTPMT1_ENST00000326674.9_Silent_p.V92V			Q8WUK0	PTPM1_HUMAN	protein tyrosine phosphatase, mitochondrial 1	0	Tyrosine-protein phosphatase.	inositol phosphate dephosphorylation	mitochondrial inner membrane	phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	breast(1)|kidney(1)|large_intestine(2)|lung(1)|skin(1)	6					GACTAGGAGTCGAGCAGCTGC	0.522	0	64.0	66.0	65.0	11	47591272	1966	4167	6133	SO:0001587	stop_gained	BC014048	CCDS41643.1, CCDS44593.1	11p11.2	2011-06-09			ENSG00000110536	ENSG00000110536	"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	26965	protein-coding gene	gene with protein product		609538			12477932	Standard	NM_175732	Approved	PLIP, DUSP23, MOSP	uc001nfs.4	Q8WUK0	OTTHUMG00000166892	ENST00000534775.1:c.385C>T	11.37:g.47591272C>T	ENSP00000436160:p.Arg129*	E9PAT8|Q7Z557|Q96CR2|Q9BXV8	ENST00000534775.1	37		.	.	.	.	.	.	.	.	.	.	C	16.39	3.111195	0.56398	.	.	ENSG00000110536	ENST00000534775	.	.	.	5.2	-10.4	0.00318	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-21.8019	5.9036	0.18980	0.1222:0.3998:0.3765:0.1016	.	.	.	.	X	129	.	ENSP00000436160:R129X	R	+	1	2	PTPMT1	47547848	0.007000	0.16637	0.438000	0.26821	0.935000	0.57460	-1.465000	0.02357	-2.418000	0.00566	-0.379000	0.06801	CGA	PTPMT1-004	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000391743.1		28.944805	0	-21	29	0	0	1	0	XM_374879	10	29.163465	15	0.400000
OPRM1	4988	broad.mit.edu	hg19	6	154411258	154411258	+	Silent	SNP	C	C	T			TCGA-YZ-A983-01A-11D-A39W-08	TCGA-YZ-A983-10B-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	699c8dc5-4c3b-4069-aac9-634da96679d1	fc2a9e37-ddcc-43d4-8d65-815c22a42e3a	g.chr6:154411258C>T	ENST00000414028.2	+	2	638	c.588C>T	c.(586-588)ctC>ctT	p.L196L	OPRM1_ENST00000419506.2_Silent_p.L196L|OPRM1_ENST00000520708.1_Silent_p.L96L|OPRM1_ENST00000229768.5_Silent_p.L196L|OPRM1_ENST00000522555.1_Silent_p.L96L|OPRM1_ENST00000452687.2_Silent_p.L196L|OPRM1_ENST00000428397.2_Silent_p.L196L|OPRM1_ENST00000330432.7_Silent_p.L196L|OPRM1_ENST00000434900.2_Silent_p.L289L|OPRM1_ENST00000337049.4_Silent_p.L196L|OPRM1_ENST00000435918.2_Silent_p.L196L|OPRM1_ENST00000518759.1_Silent_p.L115L|OPRM1_ENST00000522236.1_Silent_p.L96L|OPRM1_ENST00000360422.4_Silent_p.L196L|OPRM1_ENST00000524163.1_Silent_p.L196L	NM_001145284.2	NP_001138756.1	P35372	OPRM_HUMAN	opioid receptor, mu 1	196		behavior|negative regulation of cell proliferation|sensory perception	endoplasmic reticulum|Golgi apparatus|integral to plasma membrane	mu-opioid receptor activity|protein binding	breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(15)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	33		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;9.26e-11)|BRCA - Breast invasive adenocarcinoma(81;0.0154)	ACTGGATCCTCTCTTCAGCCA	0.473	0	138.0	130.0	132.0	6	154411258	2025	4217	6242	SO:0001819	synonymous_variant	L29301	CCDS43517.1, CCDS43518.1, CCDS47503.1, CCDS47504.1, CCDS47505.1, CCDS47506.1, CCDS47507.1, CCDS47508.1, CCDS55071.1, CCDS55068.1, CCDS55069.1, CCDS55070.1	6q24-q25	2012-08-08			ENSG00000112038	ENSG00000112038	"""GPCR / Class A : Opioid receptors"""	8156	protein-coding gene	gene with protein product		600018				Standard	NM_001145285	Approved	MOR1	uc003qpo.1	P35372	OTTHUMG00000015870	ENST00000522236.1:c.288C>T	6.37:g.154411258C>T		B0FXJ1|B2R9S7|B8Q1L7|B8Q1L8|B8Q1L9|E7EWZ3|G8XRH6|G8XRH8|Q12930|Q4VWM1|Q4VWM2|Q4VWM3|Q4VWM4|Q4VWM6|Q4VWX6|Q5TDA1|Q6UPP1|Q6UQ80|Q7Z2D8|Q86V80|Q8IWW3|Q8IWW4|Q9UCZ4|Q9UN57	ENST00000522236.1	37	CCDS55071.1																																																																																			OPRM1-020	PUTATIVE	alternative_5_UTR|basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000375975.1		77.686362	0	14	105	0	0	1	0	NM_000914	25	77.980371	34	0.423729
CACNA2D1	781	broad.mit.edu	hg19	7	81978919	81978919	+	Missense_Mutation	SNP	C	C	T			TCGA-YZ-A983-01A-11D-A39W-08	TCGA-YZ-A983-10B-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	699c8dc5-4c3b-4069-aac9-634da96679d1	fc2a9e37-ddcc-43d4-8d65-815c22a42e3a	g.chr7:81978919C>T	ENST00000356860.3	-	2	480	c.142G>A	c.(142-144)Gca>Aca	p.A48T	CACNA2D1_ENST00000356253.5_Missense_Mutation_p.A48T|CACNA2D1_ENST00000423588.1_Missense_Mutation_p.A48T	NM_000722.2	NP_000713.2	P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 1	48			voltage-gated calcium channel complex	metal ion binding	breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(15)|liver(1)|lung(42)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	81					GCTGTTTTTGCCAGTGTGACA	0.358	2	210.0	194.0	199.0	7	81978919	2203	4300	6503	SO:0001583	missense	M76559	CCDS5598.1	7q21-q22	2014-09-17			ENSG00000153956	ENSG00000153956	"""Calcium channel subunits"""	1399	protein-coding gene	gene with protein product		114204	"""long intergenic non-protein coding RNA 1112"""	CACNL2A, CACNA2, MHS3, LINC01112	8188232	Standard	XM_005250570	Approved	lncRNA-N3	uc003uhr.1	P54289	OTTHUMG00000023622	ENST00000423588.1:c.142G>A	7.37:g.81978919C>T	ENSP00000405395:p.Ala48Thr	Q17R45|Q9UD80|Q9UD81|Q9UD82	ENST00000423588.1	37		.	.	.	.	.	.	.	.	.	.	C	17.05	3.289623	0.59976	.	.	ENSG00000153956	ENST00000356860;ENST00000284088;ENST00000356253;ENST00000423588	T;T;T	0.24908	3.15;3.15;1.83	6.01	6.01	0.97437	.	0.000000	0.64402	D	0.000001	T	0.31765	0.0807	L	0.56769	1.78	0.80722	D	1	B	0.18741	0.03	B	0.17979	0.02	T	0.02751	-1.1115	10	0.51188	T	0.08	-18.9022	19.3532	0.94398	0.0:1.0:0.0:0.0	.	48	P54289-2	.	T	48	ENSP00000349320:A48T;ENSP00000348589:A48T;ENSP00000405395:A48T	ENSP00000284088:A48T	A	-	1	0	CACNA2D1	81816855	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	5.319000	0.65835	2.873000	0.98535	0.644000	0.83932	GCA	CACNA2D1-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000336994.3		-21.711510	0	28	166	0	0	1	0		4	7.655678	119	0.032520
MPP3	4356	broad.mit.edu	hg19	17	41879154	41879154	+	Missense_Mutation	SNP	A	A	C			TCGA-YZ-A983-01A-11D-A39W-08	TCGA-YZ-A983-10B-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	699c8dc5-4c3b-4069-aac9-634da96679d1	fc2a9e37-ddcc-43d4-8d65-815c22a42e3a	g.chr17:41879154A>C	ENST00000398393.1	-	18	2008	c.1748T>G	c.(1747-1749)cTc>cGc	p.L583R	MPP3_ENST00000398389.4_Missense_Mutation_p.L558R			Q13368	MPP3_HUMAN	membrane protein, palmitoylated 3 (MAGUK p55 subfamily member 3)	558		signal transduction	cell surface|integral to plasma membrane	guanylate kinase activity	endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	26		Breast(137;0.00394)		BRCA - Breast invasive adenocarcinoma(366;0.119)	GGCACCCTGGAGATCCTCCTT	0.552	0	111.0	105.0	107.0	17	41879154	1939	4151	6090	SO:0001583	missense		CCDS42344.1	17q12-q21	2008-07-18			ENSG00000161647	ENSG00000161647		7221	protein-coding gene	gene with protein product	"""MAGUK p55 subfamily member 3"", ""discs, large (Drosophila) homolog 3"", ""membrane protein palmitoylated 3"""	601114		DLG3	8824795	Standard	NR_003562	Approved		uc002iei.4	Q13368	OTTHUMG00000133838	ENST00000398389.4:c.1673T>G	17.37:g.41879154A>C	ENSP00000381425:p.Leu558Arg	B2R7N0|D3DX47|Q4GX05|Q6PGR3|Q86SV1	ENST00000398389.4	37	CCDS42344.1	.	.	.	.	.	.	.	.	.	.	A	18.86	3.712694	0.68730	.	.	ENSG00000161647	ENST00000398393;ENST00000398389	T;T	0.55930	0.49;0.49	5.42	5.42	0.78866	Guanylate kinase/L-type calcium channel (1);Guanylate kinase (2);	0.267510	0.37623	N	0.002001	T	0.74794	0.3763	M	0.90870	3.155	0.47994	D	0.999567	D;D	0.53151	0.958;0.958	P;P	0.60345	0.873;0.873	T	0.80928	-0.1163	10	0.87932	D	0	.	13.0831	0.59125	1.0:0.0:0.0:0.0	.	558;583	Q13368;D3DX46	MPP3_HUMAN;.	R	583;558	ENSP00000381430:L583R;ENSP00000381425:L558R	ENSP00000381425:L558R	L	-	2	0	MPP3	39234680	1.000000	0.71417	0.981000	0.43875	0.917000	0.54804	5.137000	0.64789	2.280000	0.76307	0.460000	0.39030	CTC	MPP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258371.1		99.929284	0	-17	102	0	0	1	0	NM_001932	34	100.522527	49	0.409639
FES	2242	broad.mit.edu	hg19	15	91433097	91433097	+	Silent	SNP	T	T	G			TCGA-YZ-A983-01A-11D-A39W-08	TCGA-YZ-A983-10B-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	699c8dc5-4c3b-4069-aac9-634da96679d1	fc2a9e37-ddcc-43d4-8d65-815c22a42e3a	g.chr15:91433097T>G	ENST00000328850.3	+	8	1096	c.954T>G	c.(952-954)gcT>gcG	p.A318A	FES_ENST00000414248.2_Silent_p.A260A|FES_ENST00000448367.1_3'UTR|FES_ENST00000394302.1_Silent_p.A260A|FES_ENST00000394300.3_Silent_p.A260A|FES_ENST00000450438.2_Silent_p.A260A|FES_ENST00000444422.2_Silent_p.A318A	NM_002005.3	NP_001996.1	P07332	FES_HUMAN	feline sarcoma oncogene	318		axon guidance|cell proliferation|peptidyl-tyrosine phosphorylation	cytosol	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding	lung(2)|ovary(1)	3	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.229)		ATGAGCTGGCTGTGGCCACCG	0.617	0	108.0	113.0	111.0	15	91433097	2198	4298	6496	SO:0001819	synonymous_variant	X52192	CCDS10365.1, CCDS45349.1, CCDS45350.1, CCDS45351.1	15q26.1	2014-06-26	2014-06-26		ENSG00000182511	ENSG00000182511	"""SH2 domain containing"""	3657	protein-coding gene	gene with protein product	"""Oncogene FES, feline sarcoma virus"", ""c-fes/fps protein"""	190030	"""feline sarcoma (Snyder-Theilen) viral (v-fes)/Fujinami avian sarcoma (PRCII) viral (v-fps) oncogene homolog"", ""feline sarcoma oncogene"""		1870997	Standard	NM_002005	Approved	FPS	uc002bpv.3	P07332	OTTHUMG00000044456	ENST00000328850.3:c.954T>G	15.37:g.91433097T>G		B2R6E6|B4DUD0|E9PC94|E9PC95|Q2VXS7|Q2VXS8|Q2VXT0|Q6GTU5	ENST00000328850.3	37	CCDS10365.1																																																																																			FES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313497.1		-1.456921	0	15	140	0	0	1	0	NM_002005	8	10.883606	70	0.102564
PCDHGB1	0	broad.mit.edu	hg19	5	140730154	140730154	+	Missense_Mutation	SNP	C	C	A			TCGA-YZ-A983-01A-11D-A39W-08	TCGA-YZ-A983-10B-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	699c8dc5-4c3b-4069-aac9-634da96679d1	fc2a9e37-ddcc-43d4-8d65-815c22a42e3a	g.chr5:140730154C>A	ENST00000523390.1	+	1	327	c.327C>A	c.(325-327)aaC>aaA	p.N109K	PCDHGA1_ENST00000517417.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018922.2|NM_032095.1	NP_061745.1|NP_115266.1									central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|prostate(1)	16			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		TCGCTGAAAACCCAATGAATG	0.423	0	65.0	64.0	64.0	5	140730154	1867	4112	5979	SO:0001583	missense	AF152517	CCDS54923.1, CCDS75330.1	5q31	2010-01-26				ENSG00000254221	"""Cadherins / Protocadherins : Clustered"""	8708	other	protocadherin	"""protocadherin gamma subfamily B, 1, isoform 2"""	606299			10380929	Standard	NM_018922	Approved	PCDH-GAMMA-B1		Q9Y5G3		ENST00000523390.1:c.327C>A	5.37:g.140730154C>A	ENSP00000429273:p.Asn109Lys	Q3SY75|Q9Y5C8	ENST00000523390.1	37	CCDS54923.1	.	.	.	.	.	.	.	.	.	.	.	12.32	1.901247	0.33535	.	.	ENSG00000254221	ENST00000523390	T	0.28255	1.62	5.46	-4.25	0.03766	Cadherin, N-terminal (1);Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.31702	0.0805	L	0.55743	1.74	0.24380	N	0.994793	B;B	0.25351	0.124;0.041	B;B	0.33121	0.149;0.158	T	0.44236	-0.9341	9	0.48119	T	0.1	.	14.9572	0.71124	0.0:0.279:0.0:0.721	.	109;109	Q9Y5G3-2;Q9Y5G3	.;PCDGD_HUMAN	K	109	ENSP00000429273:N109K	ENSP00000429273:N109K	N	+	3	2	PCDHGB1	140710338	0.011000	0.17503	0.883000	0.34634	0.771000	0.43674	-1.126000	0.03254	-0.720000	0.04935	-0.251000	0.11542	AAC	PCDHGB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374740.1		3.002575	1	-11	54	0	0.115264	1	0.119106	NM_018922	3	7.543567	26	0.103448
TBX6	6911	broad.mit.edu	hg19	16	30099934	30099934	+	Missense_Mutation	SNP	G	G	C			TCGA-YZ-A983-01A-11D-A39W-08	TCGA-YZ-A983-10B-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	699c8dc5-4c3b-4069-aac9-634da96679d1	fc2a9e37-ddcc-43d4-8d65-815c22a42e3a	g.chr16:30099934G>C	ENST00000553607.1	-	5	1464	c.771C>G	c.(769-771)atC>atG	p.I257M	TBX6_ENST00000395224.2_Missense_Mutation_p.I257M|TBX6_ENST00000279386.2_Missense_Mutation_p.I257M			O95947	TBX6_HUMAN	T-box 6	257		anatomical structure morphogenesis|mesoderm development|multicellular organismal development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity	endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|pancreas(1)	9					TCAGTTGTGTGATCTGGGGAC	0.542	0	144.0	139.0	141.0	16	30099934	2197	4300	6497	SO:0001583	missense	AJ007989	CCDS10670.1	16p11.2	2008-02-05			ENSG00000149922	ENSG00000149922	"""T-boxes"""	11605	protein-coding gene	gene with protein product		602427			9888994, 9933572	Standard	NM_004608	Approved		uc010veh.2	O95947	OTTHUMG00000132115	ENST00000395224.2:c.771C>G	16.37:g.30099934G>C	ENSP00000378650:p.Ile257Met	Q8TAS4|Q9HA44	ENST00000395224.2	37	CCDS10670.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.635402	0.87760	.	.	ENSG00000149922	ENST00000395224;ENST00000279386;ENST00000553607	D;D;D	0.91068	-2.78;-2.78;-2.78	5.95	5.95	0.96441	p53-like transcription factor, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.95850	0.8649	M	0.83603	2.65	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.91635	0.999;0.999	D	0.95770	0.8808	10	0.87932	D	0	.	19.1503	0.93485	0.0:0.0:1.0:0.0	.	257;257	O95947;Q9HA44	TBX6_HUMAN;.	M	257	ENSP00000378650:I257M;ENSP00000279386:I257M;ENSP00000461223:I257M	ENSP00000279386:I257M	I	-	3	3	TBX6	30007435	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.596000	0.67570	2.826000	0.97356	0.563000	0.77884	ATC	TBX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255157.2		134.339667	0	20	146	0	0	1	0	NM_004608, NM_080758	42	134.426820	48	0.466667
GOLGA4	2803	broad.mit.edu	hg19	3	37368986	37368986	+	Missense_Mutation	SNP	A	A	C			TCGA-YZ-A983-01A-11D-A39W-08	TCGA-YZ-A983-10B-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	699c8dc5-4c3b-4069-aac9-634da96679d1	fc2a9e37-ddcc-43d4-8d65-815c22a42e3a	g.chr3:37368986A>C	ENST00000361924.2	+	14	5983	c.5609A>C	c.(5608-5610)cAt>cCt	p.H1870P	GOLGA4_ENST00000444882.1_Intron|GOLGA4_ENST00000356847.4_Missense_Mutation_p.H1892P	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN	golgin A4	1870	Glu-rich.	Golgi to plasma membrane protein transport	Golgi membrane|trans-Golgi network	protein binding	NS(2)|breast(3)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(17)|liver(2)|lung(16)|ovary(4)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	65					AAAGAAGTACATAGAGTTGAA	0.383	0	57.0	59.0	58.0	3	37368986	2203	4299	6502	SO:0001583	missense	U31906	CCDS2666.1, CCDS54564.1	3p22-p21.3	2010-02-12	2010-02-12		ENSG00000144674	ENSG00000144674		4427	protein-coding gene	gene with protein product	"""golgin 245"""	602509	"""golgi autoantigen, golgin subfamily a, 4"""		8626529	Standard	NM_002078	Approved	GOLG, GCP2, p230, golgin-240	uc003cgw.3	Q13439	OTTHUMG00000130799	ENST00000356847.4:c.5675A>C	3.37:g.37368986A>C	ENSP00000349305:p.His1892Pro	F8W8Q7|Q13270|Q13654|Q14436|Q59EW8	ENST00000356847.4	37	CCDS54564.1	.	.	.	.	.	.	.	.	.	.	A	9.519	1.107829	0.20714	.	.	ENSG00000144674	ENST00000361924;ENST00000356847;ENST00000437131	T;T;T	0.23754	1.9;1.89;1.89	5.11	2.58	0.30949	.	0.000000	0.34932	N	0.003568	T	0.22282	0.0537	L	0.57536	1.79	0.09310	N	1	B;B;B;B	0.28820	0.224;0.125;0.063;0.021	B;B;B;B	0.28991	0.097;0.054;0.027;0.007	T	0.09292	-1.0681	10	0.30854	T	0.27	.	8.0355	0.30491	0.672:0.1144:0.0:0.2136	.	1870;1870;1892;1870	Q13439-3;Q13439-4;F8W8Q7;Q13439	.;.;.;GOGA4_HUMAN	P	1870;1892;1741	ENSP00000354486:H1870P;ENSP00000349305:H1892P;ENSP00000405842:H1741P	ENSP00000349305:H1892P	H	+	2	0	GOLGA4	37343990	0.001000	0.12720	0.305000	0.25099	0.963000	0.63663	0.532000	0.23067	1.931000	0.55961	0.448000	0.29417	CAT	GOLGA4-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000342257.2		83.714846	0	-9	59	0	0	1	0	NM_002078	24	85.251639	9	0.727273
TMEM39A	55254	broad.mit.edu	hg19	3	119155786	119155786	+	Missense_Mutation	SNP	G	G	C			TCGA-YZ-A983-01A-11D-A39W-08	TCGA-YZ-A983-10B-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	699c8dc5-4c3b-4069-aac9-634da96679d1	fc2a9e37-ddcc-43d4-8d65-815c22a42e3a	g.chr3:119155786G>C	ENST00000319172.5	-	7	1384	c.964C>G	c.(964-966)Ctc>Gtc	p.L322V		NM_018266.1	NP_060736.1	Q9NV64	TM39A_HUMAN	transmembrane protein 39A	322			integral to membrane		NS(1)|breast(1)|endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|skin(1)	13				GBM - Glioblastoma multiforme(114;0.244)	ACCATAATGAGGTGCTCACAT	0.468	0	241.0	216.0	224.0	3	119155786	2203	4300	6503	SO:0001583	missense	BC021277	CCDS2987.1	3q13.33	2005-01-10			ENSG00000176142	ENSG00000176142		25600	protein-coding gene	gene with protein product					12477932	Standard	NM_018266	Approved	FLJ10902	uc003eck.2	Q9NV64	OTTHUMG00000159361	ENST00000319172.5:c.964C>G	3.37:g.119155786G>C	ENSP00000326063:p.Leu322Val	D3DN80|Q53FN4|Q53GI1|Q6PKB5	ENST00000319172.5	37	CCDS2987.1	.	.	.	.	.	.	.	.	.	.	G	15.21	2.765116	0.49574	.	.	ENSG00000176142	ENST00000319172	T	0.44482	0.92	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	T	0.51398	0.1672	L	0.34521	1.04	0.80722	D	1	D	0.65815	0.995	P	0.61533	0.89	T	0.44050	-0.9353	10	0.39692	T	0.17	-10.2264	17.8168	0.88637	0.0:0.0:1.0:0.0	.	322	Q9NV64	TM39A_HUMAN	V	322	ENSP00000326063:L322V	ENSP00000326063:L322V	L	-	1	0	TMEM39A	120638476	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.171000	0.64996	2.692000	0.91855	0.650000	0.86243	CTC	TMEM39A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354941.3		95.954622	0	38	178	0	0	1	0	NM_018266	33	96.799544	51	0.392857
CD4	920	broad.mit.edu	hg19	12	6923368	6923368	+	Missense_Mutation	SNP	T	T	C			TCGA-YZ-A983-01A-11D-A39W-08	TCGA-YZ-A983-10B-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	699c8dc5-4c3b-4069-aac9-634da96679d1	fc2a9e37-ddcc-43d4-8d65-815c22a42e3a	g.chr12:6923368T>C	ENST00000011653.4	+	4	533	c.275T>C	c.(274-276)tTt>tCt	p.F92S	CD4_ENST00000541982.1_Missense_Mutation_p.F37S|CD4_ENST00000538827.1_3'UTR	NM_000616.4|NM_001195015.2|NM_001195016.2|NM_001195017.2	NP_000607.1|NP_001181944.1|NP_001181945.1|NP_001181946.1	P01730	CD4_HUMAN	CD4 molecule	92	Ig-like V-type.	cell adhesion|entry into host cell|immune response|induction by virus of host cell-cell fusion|initiation of viral infection|maintenance of protein location in cell|positive regulation of interleukin-2 biosynthetic process|positive regulation of protein kinase activity|protein palmitoleylation|regulation of defense response to virus by virus|T cell costimulation|T cell receptor signaling pathway|T cell selection|transmembrane receptor protein tyrosine kinase signaling pathway	early endosome|endoplasmic reticulum membrane|integral to membrane|T cell receptor complex	coreceptor activity|extracellular matrix structural constituent|glycoprotein binding|MHC class II protein binding|protein homodimerization activity|protein kinase binding|transmembrane receptor activity|zinc ion binding	breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)	23		Myeloproliferative disorder(1001;0.0122)			CAAGGAAACTTTCCCCTGATC	0.498	0	141.0	137.0	138.0	12	6923368	2203	4300	6503	SO:0001583	missense	M35160	CCDS8562.1	12p13.31	2013-01-11	2006-03-28		ENSG00000010610	ENSG00000010610	"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"""	1678	protein-coding gene	gene with protein product		186940	"""CD4 antigen (p55)"", ""T-cell surface glycoprotein CD4"""			Standard	NM_000616	Approved		uc001qqv.2	P01730	OTTHUMG00000168514	ENST00000541982.1:c.110T>C	12.37:g.6923368T>C	ENSP00000445167:p.Phe37Ser	B2R737|D3DUS5|Q4ZGK2|Q5U066|Q9UDE5	ENST00000541982.1	37		.	.	.	.	.	.	.	.	.	.	T	14.35	2.510235	0.44660	.	.	ENSG00000010610	ENST00000011653;ENST00000541982	T;T	0.68765	-0.35;-0.35	5.32	5.32	0.75619	Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin V-set, subgroup (1);Immunoglobulin-like fold (1);	0.861493	0.10180	N	0.705942	T	0.79975	0.4539	M	0.64260	1.97	0.37698	D	0.924097	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.77838	-0.2439	10	0.66056	D	0.02	1.5086	11.6738	0.51417	0.0:0.0:0.0:1.0	.	37;92	F5H480;P01730	.;CD4_HUMAN	S	92;37	ENSP00000011653:F92S;ENSP00000445167:F37S	ENSP00000011653:F92S	F	+	2	0	CD4	6793629	0.684000	0.27642	0.077000	0.20336	0.005000	0.04900	1.456000	0.35201	2.012000	0.59069	0.379000	0.24179	TTT	CD4-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000399982.1		124.976002	0	-15	117	0	0	1	0	NM_000616	37	124.976002	37	0.500000
VASH2	79805	broad.mit.edu	hg19	1	213146004	213146004	+	Missense_Mutation	SNP	G	G	T			TCGA-YZ-A983-01A-11D-A39W-08	TCGA-YZ-A983-10B-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	699c8dc5-4c3b-4069-aac9-634da96679d1	fc2a9e37-ddcc-43d4-8d65-815c22a42e3a	g.chr1:213146004G>T	ENST00000366968.4	+	7	735	c.385G>T	c.(385-387)Gtt>Ttt	p.V129F	VASH2_ENST00000366966.2_Missense_Mutation_p.V129F|VASH2_ENST00000366967.2_Missense_Mutation_p.V90F|VASH2_ENST00000517399.1_Missense_Mutation_p.V194F|VASH2_ENST00000366965.2_Missense_Mutation_p.V150F|VASH2_ENST00000271776.4_3'UTR|VASH2_ENST00000366964.3_Missense_Mutation_p.V52F	NM_001136474.1	NP_001129946.1	Q86V25	VASH2_HUMAN	vasohibin 2	194		positive regulation of angiogenesis|positive regulation of endothelial cell proliferation	cytoplasm		endometrium(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	7				OV - Ovarian serous cystadenocarcinoma(81;0.00479)|all cancers(67;0.00844)|GBM - Glioblastoma multiforme(131;0.0496)|Epithelial(68;0.0986)	CTTTCACCACGTTGTGCTGGG	0.498	0	114.0	106.0	109.0	1	213146004	2203	4300	6503	SO:0001583	missense	AK022567	CCDS1511.1, CCDS44315.1, CCDS44316.1, CCDS73026.1	1q23	2008-02-05			ENSG00000143494	ENSG00000143494		25723	protein-coding gene	gene with protein product		610471			16528006	Standard	XR_247041	Approved	FLJ12505	uc001hjw.3	Q86V25	OTTHUMG00000036925	ENST00000517399.1:c.580G>T	1.37:g.213146004G>T	ENSP00000428324:p.Val194Phe	B4DYZ5|Q2VT46|Q5VTE7|Q5VTE9|Q7Z6E3|Q8IZ24|Q9H9W5	ENST00000517399.1	37	CCDS1511.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.112063	0.77210	.	.	ENSG00000143494	ENST00000366966;ENST00000366964;ENST00000366968;ENST00000366965;ENST00000366967;ENST00000517399	.	.	.	5.26	5.26	0.73747	.	0.064020	0.64402	D	0.000008	T	0.76821	0.4041	L	0.59436	1.845	0.58432	D	0.999997	D;D	0.71674	0.994;0.998	P;D	0.68483	0.889;0.958	T	0.78682	-0.2109	9	0.87932	D	0	-14.1987	19.2409	0.93883	0.0:0.0:1.0:0.0	.	194;150	Q86V25;Q86V25-5	VASH2_HUMAN;.	F	129;52;129;150;90;194	.	ENSP00000355931:V52F	V	+	1	0	VASH2	211212627	1.000000	0.71417	0.438000	0.26821	0.871000	0.50021	5.142000	0.64820	2.620000	0.88729	0.655000	0.94253	GTT	VASH2-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381686.1		80.840821	1	-21	82	0	1.17739e-12	1	1.25859e-12	NM_024749	26	81.130233	35	0.426230
GABBR2	9568	broad.mit.edu	hg19	9	101304173	101304173	+	Silent	SNP	G	G	A	rs142025089		TCGA-YZ-A983-01A-11D-A39W-08	TCGA-YZ-A983-10B-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	699c8dc5-4c3b-4069-aac9-634da96679d1	fc2a9e37-ddcc-43d4-8d65-815c22a42e3a	g.chr9:101304173G>A	ENST00000259455.2	-	3	1071	c.612C>T	c.(610-612)gaC>gaT	p.D204D	GABBR2_ENST00000477471.1_5'UTR	NM_005458.7	NP_005449.5	O75899	GABR2_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 2	204		negative regulation of adenylate cyclase activity|synaptic transmission	cell junction|integral to plasma membrane|postsynaptic membrane	G-protein coupled receptor activity|GABA-B receptor activity	breast(4)|endometrium(4)|large_intestine(12)|lung(21)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	49		Acute lymphoblastic leukemia(62;0.0527)			ACCTCTGAACGTCTTGCGTCA	0.537	0	156.0	111.0	126.0	9	101304173	2203	4300	6503	SO:0001819	synonymous_variant	AF069755	CCDS6736.1	9q22.1-q22.3	2012-08-29	2006-02-16	2006-02-16	ENSG00000136928	ENSG00000136928	"""GABA receptors"", ""GPCR / Class C : GABA(B) receptors"""	4507	protein-coding gene	gene with protein product		607340	"""G protein-coupled receptor 51"""	GPR51	10087195	Standard	NM_005458	Approved	HG20, GABABR2, GPRC3B	uc004ays.3	O75899	OTTHUMG00000020345	ENST00000259455.2:c.612C>T	9.37:g.101304173G>A		O75974|O75975|Q5VXZ2|Q8WX04|Q9P1R2|Q9UNR1|Q9UNS9	ENST00000259455.2	37	CCDS6736.1																																																																																			GABBR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053373.1		34.019960	0	10	44	0	0	1	0		11	34.301050	17	0.392857
PROSER1	80209	broad.mit.edu	hg19	13	39587518	39587518	+	Missense_Mutation	SNP	T	T	C			TCGA-YZ-A983-01A-11D-A39W-08	TCGA-YZ-A983-10B-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	699c8dc5-4c3b-4069-aac9-634da96679d1	fc2a9e37-ddcc-43d4-8d65-815c22a42e3a	g.chr13:39587518T>C	ENST00000352251.3	-	11	2704	c.1871A>G	c.(1870-1872)cAt>cGt	p.H624R	PROSER1_ENST00000484434.3_Intron|PROSER1_ENST00000350125.3_Missense_Mutation_p.H602R	NM_025138.4	NP_079414.3	Q86XN7	CM023_HUMAN	proline and serine rich 1	624	Ser-rich.										ATTCCCAGAATGAGATGGACC	0.473	0	150.0	156.0	154.0	13	39587518	2203	4300	6503	SO:0001583	missense	AK022723	CCDS9368.2	13q13.2	2011-08-09	2011-08-09	2011-08-09	ENSG00000120685	ENSG00000120685		20291	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 23"""	C13orf23		Standard	NM_025138	Approved	bA50D16.2, FLJ12661	uc001uwy.4	Q86XN7	OTTHUMG00000016764	ENST00000352251.3:c.1871A>G	13.37:g.39587518T>C	ENSP00000332034:p.His624Arg	A6NJ97|Q6P2S2|Q7Z3X5|Q8N3D2|Q8N3P1|Q9H9M1	ENST00000352251.3	37	CCDS9368.2	.	.	.	.	.	.	.	.	.	.	T	11.70	1.716919	0.30413	.	.	ENSG00000120685	ENST00000352251;ENST00000350125	T;T	0.44482	0.92;0.92	4.73	2.16	0.27623	.	.	.	.	.	T	0.39572	0.1083	N	0.19112	0.55	0.40546	D	0.98107	D;B	0.67145	0.996;0.42	D;B	0.77557	0.99;0.087	T	0.35992	-0.9766	8	.	.	.	-4.0017	2.5606	0.04771	0.1513:0.0812:0.1584:0.6091	.	602;624	A6NJ97;Q86XN7	.;PRSR1_HUMAN	R	624;602	ENSP00000332034:H624R;ENSP00000339123:H602R	.	H	-	2	0	PROSER1	38485518	0.988000	0.35896	0.080000	0.20451	0.517000	0.34286	2.001000	0.40825	0.231000	0.21079	0.459000	0.35465	CAT	PROSER1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044607.5		136.186620	0	17	127	0	0	1	0	NM_025138	44	136.500214	56	0.440000
PTPRD	5789	broad.mit.edu	hg19	9	8331704	8331704	+	Silent	SNP	C	C	T			TCGA-YZ-A983-01A-11D-A39W-08	TCGA-YZ-A983-10B-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	699c8dc5-4c3b-4069-aac9-634da96679d1	fc2a9e37-ddcc-43d4-8d65-815c22a42e3a	g.chr9:8331704C>T	ENST00000381196.4	-	41	5955	c.5412G>A	c.(5410-5412)caG>caA	p.Q1804Q	PTPRD_ENST00000358503.5_Silent_p.Q1782Q|PTPRD_ENST00000355233.5_Silent_p.Q1398Q|PTPRD_ENST00000486161.1_Silent_p.Q1397Q|PTPRD_ENST00000360074.4_Silent_p.Q1791Q|PTPRD_ENST00000540109.1_Silent_p.Q1804Q|PTPRD_ENST00000356435.5_Silent_p.Q1804Q|PTPRD_ENST00000397606.3_Silent_p.Q1397Q|PTPRD_ENST00000397617.3_Silent_p.Q1397Q|PTPRD_ENST00000397611.3_Silent_p.Q1394Q|PTPRD_ENST00000537002.1_Silent_p.Q1394Q	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	1804	Tyrosine-protein phosphatase 2.	transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity	NS(1)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(83)|ovary(4)|pancreas(1)|prostate(7)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	168		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)	AGTCAGTGAACTGGAACTGCC	0.512	0	111.0	105.0	107.0	9	8331704	2203	4300	6503	SO:0001819	synonymous_variant	X54133	CCDS6472.1, CCDS43786.1, CCDS6472.2, CCDS55288.1, CCDS55289.1, CCDS55290.1, CCDS75813.1	9p24.1-p23	2013-02-11			ENSG00000153707	ENSG00000153707	"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9668	protein-coding gene	gene with protein product		601598			7896816, 8355697	Standard	NM_002839	Approved	PTPD, HPTP	uc003zkk.3	P23468	OTTHUMG00000021005	ENST00000381196.4:c.5412G>A	9.37:g.8331704C>T		B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	ENST00000381196.4	37	CCDS43786.1																																																																																			PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3		-2.792682	0	20	181	0	0	1	0		8	18.138882	103	0.072072
CDKN2A	1029	broad.mit.edu	hg19	9	21974744	21974744	+	Missense_Mutation	SNP	A	A	C			TCGA-YZ-A983-01A-11D-A39W-08	TCGA-YZ-A983-10B-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	699c8dc5-4c3b-4069-aac9-634da96679d1	fc2a9e37-ddcc-43d4-8d65-815c22a42e3a	g.chr9:21974744A>C	ENST00000304494.5	-	1	353	c.83T>G	c.(82-84)gTg>gGg	p.V28G	CDKN2A_ENST00000498124.1_Missense_Mutation_p.V28G|CDKN2A_ENST00000530628.2_Intron|CDKN2A_ENST00000579755.1_Intron|RP11-145E5.5_ENST00000404796.2_Intron|CDKN2A_ENST00000498628.2_Intron|CDKN2A_ENST00000494262.1_Intron|CDKN2A_ENST00000579122.1_Missense_Mutation_p.V28G|CDKN2A_ENST00000361570.3_Intron|CDKN2A_ENST00000446177.1_Missense_Mutation_p.V28G	NM_000077.4	NP_000068.1	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A	28		cell cycle arrest|cell cycle checkpoint|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of cell-matrix adhesion|negative regulation of cyclin-dependent protein kinase activity|negative regulation of NF-kappaB transcription factor activity|positive regulation of macrophage apoptosis|positive regulation of smooth muscle cell apoptosis|Ras protein signal transduction|replicative senescence	cytosol|nucleus	cyclin-dependent protein kinase inhibitor activity|NF-kappaB binding|protein binding|protein kinase binding	NS(28)|adrenal_gland(6)|autonomic_ganglia(11)|biliary_tract(74)|bone(84)|breast(46)|central_nervous_system(522)|cervix(23)|endometrium(14)|eye(4)|genital_tract(15)|haematopoietic_and_lymphoid_tissue(698)|kidney(39)|large_intestine(11)|liver(92)|lung(365)|meninges(18)|oesophagus(239)|ovary(98)|pancreas(263)|pleura(94)|prostate(13)|salivary_gland(10)|skin(541)|small_intestine(1)|soft_tissue(93)|stomach(48)|thymus(4)|thyroid(24)|upper_aerodigestive_tract(436)|urinary_tract(283)|vulva(2)	4199		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)	CAGCGCCCGCACCTCCTCTAC	0.736	1345	23.0	30.0	28.0	9	21974744	1949	3939	5888	SO:0001583	missense	L27211	CCDS6510.1, CCDS6511.1, CCDS6511.2, CCDS56565.1	9p21	2014-09-17	2012-03-08		ENSG00000147889	ENSG00000147889		1787	protein-coding gene	gene with protein product		600160	"""cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)"""	CDKN2, MLM	8152487, 7606716	Standard	NM_058195	Approved	CDK4I, p16, INK4a, MTS1, CMM2, ARF, p19, p14, INK4, p16INK4a, p19Arf	uc003zpk.3	P42771	OTTHUMG00000019686	ENST00000498124.1:c.83T>G	9.37:g.21974744A>C	ENSP00000418915:p.Val28Gly	A5X2G7|D3DRK1|O95440|Q15191|Q5VVJ5|Q96B52|Q9NP05	ENST00000498124.1	37	CCDS56565.1	.	.	.	.	.	.	.	.	.	.	A	26.8	4.776837	0.90195	.	.	ENSG00000147889	ENST00000304494;ENST00000446177	T;T	0.73152	-0.72;-0.72	4.89	4.89	0.63831	Ankyrin repeat-containing domain (3);	.	.	.	.	D	0.88540	0.6464	H	0.96208	3.785	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.91605	0.5298	9	0.62326	D	0.03	.	13.8927	0.63750	1.0:0.0:0.0:0.0	.	28;28	P42771;G3XAG3	CD2A1_HUMAN;.	G	28	ENSP00000307101:V28G;ENSP00000394932:V28G	ENSP00000307101:V28G	V	-	2	0	CDKN2A	21964744	0.963000	0.33076	1.000000	0.80357	0.918000	0.54935	4.872000	0.63050	2.165000	0.68154	0.533000	0.62120	GTG	CDKN2A-009	KNOWN	NMD_exception|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354927.1		3.736237	0	-8	46	0	0	1	0	NM_000077	6	6.977329	26	0.187500
LMTK2	22853	broad.mit.edu	hg19	7	97821218	97821218	+	Missense_Mutation	SNP	G	G	A	rs144291659		TCGA-YZ-A983-01A-11D-A39W-08	TCGA-YZ-A983-10B-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	699c8dc5-4c3b-4069-aac9-634da96679d1	fc2a9e37-ddcc-43d4-8d65-815c22a42e3a	g.chr7:97821218G>A	ENST00000297293.5	+	11	1734	c.1441G>A	c.(1441-1443)Gct>Act	p.A481T		NM_014916.3	NP_055731.2	Q8IWU2	LMTK2_HUMAN	lemur tyrosine kinase 2	481		early endosome to late endosome transport|endocytic recycling|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|protein autophosphorylation|receptor recycling|transferrin transport	early endosome|Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|recycling endosome	ATP binding|myosin VI binding|protein phosphatase inhibitor activity|protein serine/threonine kinase activity|protein tyrosine kinase activity	NS(2)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(25)|ovary(1)|pancreas(2)|skin(2)|stomach(3)	59	all_cancers(62;3.23e-09)|all_epithelial(64;7.65e-10)|Lung NSC(181;0.00902)|all_lung(186;0.0104)|Esophageal squamous(72;0.0125)				CTGGGAGGCCGCTAAGCACGA	0.587	0	50.0	48.0	49.0	7	97821218	2203	4300	6503	SO:0001583	missense	AB029002	CCDS5654.1	7q22.1	2014-06-12			ENSG00000164715	ENSG00000164715		17880	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 100"""	610989			15005709	Standard	NM_014916	Approved	KIAA1079, KPI2, KPI-2, cprk, LMR2, BREK, AATYK2, PPP1R100	uc003upd.2	Q8IWU2	OTTHUMG00000154256	ENST00000297293.5:c.1441G>A	7.37:g.97821218G>A	ENSP00000297293:p.Ala481Thr	A4D272|Q75MG7|Q9UPS3	ENST00000297293.5	37	CCDS5654.1	.	.	.	.	.	.	.	.	.	.	G	34	5.293719	0.95546	0.0	2.33E-4	ENSG00000164715	ENST00000297293	D	0.85484	-1.99	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	D	0.92401	0.7588	M	0.80183	2.485	0.80722	D	1	D	0.63880	0.993	P	0.62885	0.908	D	0.92507	0.6013	10	0.87932	D	0	.	19.5705	0.95413	0.0:0.0:1.0:0.0	.	481	Q8IWU2	LMTK2_HUMAN	T	481	ENSP00000297293:A481T	ENSP00000297293:A481T	A	+	1	0	LMTK2	97659154	1.000000	0.71417	0.374000	0.26016	0.841000	0.47740	9.420000	0.97426	2.941000	0.99782	0.655000	0.94253	GCT	LMTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334560.1		2.404561	0	-5	45	0	0	1	0	NM_014916	3	7.452564	28	0.096774
ERMARD	55780	broad.mit.edu	hg19	6	170176103	170176103	+	Missense_Mutation	SNP	C	C	T			TCGA-YZ-A983-01A-11D-A39W-08	TCGA-YZ-A983-10B-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	699c8dc5-4c3b-4069-aac9-634da96679d1	fc2a9e37-ddcc-43d4-8d65-815c22a42e3a	g.chr6:170176103C>T	ENST00000588451.1	+	14	1567	c.1054C>T	c.(1054-1056)Cac>Tac	p.H352Y	ERMARD_ENST00000392095.4_Missense_Mutation_p.H362Y|ERMARD_ENST00000366773.3_Missense_Mutation_p.H488Y|ERMARD_ENST00000418781.3_Missense_Mutation_p.H488Y|ERMARD_ENST00000366772.2_Missense_Mutation_p.H488Y					ER membrane-associated RNA degradation	488											TGAGCTGTATCACCATATGCC	0.378	0	154.0	129.0	137.0	6	170176103	2203	4300	6503	SO:0001583	missense	AK002014	CCDS34576.1, CCDS64572.1, CCDS64573.1, CCDS64574.1	6q27	2013-08-28	2013-08-28	2013-08-28	ENSG00000130023	ENSG00000130023		21056	protein-coding gene	gene with protein product		615532	"""chromosome 6 open reading frame 70"""	C6orf70	23768067	Standard	NM_018341	Approved	FLJ11152, dJ266L20.3	uc003qxg.1	Q5T6L9	OTTHUMG00000016067	ENST00000588451.1:c.1054C>T	6.37:g.170176103C>T	ENSP00000468240:p.His352Tyr	B4DFH0|F8WAF1|Q3ZCS8|Q5T6L8|Q9NUT5|Q9NVU2	ENST00000588451.1	37		.	.	.	.	.	.	.	.	.	.	.	3.195	-0.165006	0.06502	.	.	ENSG00000130023	ENST00000366773;ENST00000366772;ENST00000418781;ENST00000392095;ENST00000366771	T;T	0.44482	0.93;0.92	5.27	2.37	0.29283	.	1.069390	0.07104	N	0.841062	T	0.14830	0.0358	L	0.53249	1.67	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.08055	0.003;0.003;0.0	T	0.33929	-0.9849	10	0.10636	T	0.68	.	7.6556	0.28373	0.0:0.6445:0.0:0.3555	.	488;488;488	Q5T6L9-3;Q5T6L9-2;Q5T6L9	.;.;CF070_HUMAN	Y	488;488;488;362;136	ENSP00000355735:H488Y;ENSP00000375945:H362Y	ENSP00000355733:H136Y	H	+	1	0	C6orf70	169918028	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-0.580000	0.05827	0.669000	0.31146	0.558000	0.71614	CAC	ERMARD-007	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000451451.1		65.543138	0	-26	77	0	0	1	0	NM_018341	22	65.654343	27	0.448980
PCK2	5106	broad.mit.edu	hg19	14	24569263	24569263	+	Missense_Mutation	SNP	G	G	A			TCGA-YZ-A983-01A-11D-A39W-08	TCGA-YZ-A983-10B-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	699c8dc5-4c3b-4069-aac9-634da96679d1	fc2a9e37-ddcc-43d4-8d65-815c22a42e3a	g.chr14:24569263G>A	ENST00000545054.2	+	7	1591	c.673G>A	c.(673-675)Gcc>Acc	p.A225T	PCK2_ENST00000396973.4_Missense_Mutation_p.A359T|PCK2_ENST00000216780.4_Missense_Mutation_p.A359T|PCK2_ENST00000561286.1_Missense_Mutation_p.A225T|PCK2_ENST00000558096.1_Missense_Mutation_p.A225T|NRL_ENST00000561028.1_Intron|PCK2_ENST00000559250.1_Missense_Mutation_p.A371T			Q16822	PCKGM_HUMAN	phosphoenolpyruvate carboxykinase 2 (mitochondrial)	359		gluconeogenesis	mitochondrial matrix	GTP binding|metal ion binding|phosphoenolpyruvate carboxykinase (GTP) activity	breast(2)|endometrium(2)|kidney(3)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	18				GBM - Glioblastoma multiforme(265;0.0184)	TGGTACCTCTGCCACCACCAA	0.522	0	115.0	117.0	116.0	14	24569263	2203	4300	6503	SO:0001583	missense	AK129934	CCDS9609.1, CCDS41928.1	14q12	2006-06-09			ENSG00000100889	ENSG00000100889		8725	protein-coding gene	gene with protein product		614095			8645161, 9657976	Standard	XM_005267726	Approved	PEPCK, PEPCK2	uc001wlt.3	Q16822	OTTHUMG00000028791	ENST00000561286.1:c.673G>A	14.37:g.24569263G>A	ENSP00000454011:p.Ala225Thr	O43253|Q86U01|Q9BV62	ENST00000561286.1	37		.	.	.	.	.	.	.	.	.	.	G	14.21	2.467635	0.43839	.	.	ENSG00000100889	ENST00000216780;ENST00000396973;ENST00000545054	T;T;T	0.04317	3.65;3.65;3.65	5.49	5.49	0.81192	.	0.289751	0.42053	D	0.000771	T	0.04815	0.0130	N	0.21142	0.635	0.38824	D	0.955709	B;B;B;B	0.15473	0.001;0.007;0.013;0.007	B;B;B;B	0.17979	0.014;0.017;0.02;0.017	T	0.49466	-0.8937	10	0.20046	T	0.44	-16.065	16.8589	0.86013	0.0:0.0:1.0:0.0	.	225;359;359;359	B4DW73;Q16822;Q16822-2;Q6IB91	.;PCKGM_HUMAN;.;.	T	359;359;225	ENSP00000216780:A359T;ENSP00000380171:A359T;ENSP00000441826:A225T	ENSP00000216780:A359T	A	+	1	0	PCK2	23639103	0.751000	0.28327	1.000000	0.80357	0.967000	0.64934	2.457000	0.45005	2.579000	0.87056	0.655000	0.94253	GCC	PCK2-005	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000416426.1		93.692302	0	-52	110	0	0	1	0	NM_001018073	32	93.695751	33	0.492308
PRRC2B	84726	broad.mit.edu	hg19	9	134350898	134350898	+	Missense_Mutation	SNP	C	C	T			TCGA-YZ-A983-01A-11D-A39W-08	TCGA-YZ-A983-10B-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	699c8dc5-4c3b-4069-aac9-634da96679d1	fc2a9e37-ddcc-43d4-8d65-815c22a42e3a	g.chr9:134350898C>T	ENST00000357304.4	+	15	3437	c.3382C>T	c.(3382-3384)Cgg>Tgg	p.R1128W	PRRC2B_ENST00000405995.1_Intron|PRRC2B_ENST00000372249.1_5'UTR|PRRC2B_ENST00000458550.1_Intron	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	1128				protein binding	cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(20)|ovary(2)	44					CAAGCCCCGACGGAGAGTTGC	0.672	0	12.0	14.0	13.0	9	134350898	1905	4081	5986	SO:0001583	missense	AB011087	CCDS48044.1	9q34.13	2010-12-09	2010-12-09	2010-12-09	ENSG00000130723	ENSG00000130723		28121	protein-coding gene	gene with protein product			"""KIAA0515"", ""HLA-B associated transcript 2-like"", ""HLA-B associated transcript 2-like 1"""	KIAA0515, BAT2L, BAT2L1	9628581	Standard	NM_013318	Approved	MGC10526, LQFBS-1	uc004can.4	Q5JSZ5	OTTHUMG00000020827	ENST00000357304.4:c.3382C>T	9.37:g.134350898C>T	ENSP00000349856:p.Arg1128Trp	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	ENST00000357304.4	37	CCDS48044.1	.	.	.	.	.	.	.	.	.	.	C	15.03	2.711147	0.48517	.	.	ENSG00000130723	ENST00000357304;ENST00000418650	T	0.28895	1.59	5.82	5.82	0.92795	.	.	.	.	.	T	0.50956	0.1646	L	0.59436	1.845	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.39643	-0.9604	8	.	.	.	.	13.9723	0.64250	0.1514:0.8486:0.0:0.0	.	424;1128	Q5H9R5;Q5JSZ5	.;PRC2B_HUMAN	W	1128;424	ENSP00000349856:R1128W	.	R	+	1	2	PRRC2B	133340719	0.994000	0.37717	0.997000	0.53966	0.276000	0.26787	0.882000	0.28186	2.756000	0.94617	0.561000	0.74099	CGG	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			9.592395	0	1	23	0	0	1	0		4	10.501447	12	0.250000
GNAQ	2776	broad.mit.edu	hg19	9	80409488	80409488	+	Missense_Mutation	SNP	T	T	G	rs121913492		TCGA-YZ-A983-01A-11D-A39W-08	TCGA-YZ-A983-10B-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	699c8dc5-4c3b-4069-aac9-634da96679d1	fc2a9e37-ddcc-43d4-8d65-815c22a42e3a	g.chr9:80409488T>G	ENST00000286548.4	-	5	848	c.626A>C	c.(625-627)cAa>cCa	p.Q209P	GNAQ_ENST00000397476.3_Missense_Mutation_p.Q7P	NM_002072.3	NP_002063.2	P50148	GNAQ_HUMAN	guanine nucleotide binding protein (G protein), q polypeptide	209		activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity by dopamine receptor signaling pathway|glutamate signaling pathway|negative regulation of protein kinase activity|platelet activation|protein ADP-ribosylation|protein stabilization|regulation of action potential|regulation of catenin import into nucleus	cytoplasm|heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activator activity|GTPase activity|signal transducer activity	NS(1)|endometrium(3)|eye(229)|kidney(1)|large_intestine(4)|lung(6)|meninges(11)|ovary(1)|prostate(1)|skin(44)|upper_aerodigestive_tract(1)	302					CTCTGACCTTTGGCCCCCTAC	0.348	153	108.0	105.0	106.0	9	80409488	2203	4300	6503	SO:0001583	missense		CCDS6658.1	9q21	2010-03-17			ENSG00000156052	ENSG00000156052		4390	protein-coding gene	gene with protein product		600998			8825633	Standard	NM_002072	Approved	G-ALPHA-q, GAQ	uc004akw.3	P50148	OTTHUMG00000020059	ENST00000286548.4:c.626A>C	9.37:g.80409488T>G	ENSP00000286548:p.Gln209Pro	O15108|Q13462|Q6NT27|Q92471|Q9BZB9	ENST00000286548.4	37	CCDS6658.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.614273	0.87359	.	.	ENSG00000156052	ENST00000286548;ENST00000397476	D;D	0.91237	-2.81;-2.81	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	D	0.97164	0.9073	H	0.97291	3.975	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.98607	1.0661	10	0.87932	D	0	.	15.9502	0.79827	0.0:0.0:0.0:1.0	.	209	P50148	GNAQ_HUMAN	P	209;7	ENSP00000286548:Q209P;ENSP00000443197:Q7P	ENSP00000286548:Q209P	Q	-	2	0	GNAQ	79599308	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	8.040000	0.89188	2.167000	0.68274	0.460000	0.39030	CAA	GNAQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052761.1		80.866073	0	-20	92	0	0	1	0	NM_002072	25	81.229505	35	0.416667
KRT79	338785	broad.mit.edu	hg19	12	53216887	53216887	+	Missense_Mutation	SNP	C	C	T			TCGA-YZ-A983-01A-11D-A39W-08	TCGA-YZ-A983-10B-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	699c8dc5-4c3b-4069-aac9-634da96679d1	fc2a9e37-ddcc-43d4-8d65-815c22a42e3a	g.chr12:53216887C>T	ENST00000330553.5	-	7	1314	c.1280G>A	c.(1279-1281)cGt>cAt	p.R427H		NM_175834.2	NP_787028.1	Q5XKE5	K2C79_HUMAN	keratin 79	427	Coil 2.|Rod.		keratin filament	structural molecule activity	endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30					CTGGTAGTCACGCAGCAGCCG	0.617	0	95.0	87.0	89.0	12	53216887	2203	4300	6503	SO:0001583	missense	AJ564105	CCDS8839.1	12q13.13	2014-02-12	2007-07-03		ENSG00000185640	ENSG00000185640	"""-"", ""Intermediate filaments type II, keratins (basic)"""	28930	protein-coding gene	gene with protein product	"""keratin 6-like"""	611160			11683385	Standard	NM_175834	Approved	K6L, KRT6L	uc001sbb.3	Q5XKE5	OTTHUMG00000169878	ENST00000330553.5:c.1280G>A	12.37:g.53216887C>T	ENSP00000328358:p.Arg427His	Q6P465|Q7Z793	ENST00000330553.5	37	CCDS8839.1	.	.	.	.	.	.	.	.	.	.	C	13.25	2.182379	0.38511	.	.	ENSG00000185640	ENST00000330553;ENST00000549255	D;D	0.89810	-2.57;-2.57	3.92	2.1	0.27182	Filament (1);	0.000000	0.44902	D	0.000418	D	0.85737	0.5766	M	0.75150	2.29	0.34666	D	0.723239	P	0.38148	0.62	B	0.37387	0.248	D	0.85802	0.1374	10	0.72032	D	0.01	.	5.2249	0.15389	0.1628:0.6584:0.0:0.1788	.	427	Q5XKE5	K2C79_HUMAN	H	427;13	ENSP00000328358:R427H;ENSP00000449159:R13H	ENSP00000328358:R427H	R	-	2	0	KRT79	51503154	0.002000	0.14202	0.072000	0.20136	0.078000	0.17371	1.184000	0.32053	0.623000	0.30267	-0.263000	0.10527	CGT	KRT79-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406376.1		40.772292	0	4	103	0	0	1	0	NM_175834	13	40.888158	17	0.433333
RP11-571L19.7	0	broad.mit.edu	hg19	4	99877173	99877173	+	RNA	DEL	A	A	-			TCGA-YZ-A983-01A-11D-A39W-08	TCGA-YZ-A983-10B-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	699c8dc5-4c3b-4069-aac9-634da96679d1	fc2a9e37-ddcc-43d4-8d65-815c22a42e3a	g.chr4:99877173delA	ENST00000583654.1	+	0	237																					AGAGGCTTTGAAAATGTAGAA	0.398	0																																				4.37:g.99877173delA			ENST00000583654.1	37																																																																																				RP11-571L19.7-001	KNOWN	non_canonical_other|not_organism_supported|basic	antisense	antisense	OTTHUMT00000441787.1	.	.		-7	13						2		4	0.33
PLEKHG2	64857	broad.mit.edu	hg19	19	39905669	39905669	+	Frame_Shift_Del	DEL	T	T	-			TCGA-YZ-A983-01A-11D-A39W-08	TCGA-YZ-A983-10B-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	699c8dc5-4c3b-4069-aac9-634da96679d1	fc2a9e37-ddcc-43d4-8d65-815c22a42e3a	g.chr19:39905669delT	ENST00000425673.1	+	3	472	c.147delT	c.(145-147)tctfs	p.S49fs	PLEKHG2_ENST00000409797.2_Frame_Shift_Del_p.S49fs|PLEKHG2_ENST00000458508.2_Intron|PLEKHG2_ENST00000378550.1_Frame_Shift_Del_p.S49fs|PLEKHG2_ENST00000409794.3_Frame_Shift_Del_p.S49fs			Q9H7P9	PKHG2_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	49		apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity	breast(3)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(2)|liver(1)|lung(13)|pancreas(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	40	all_cancers(60;3.08e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;6.57e-07)|Ovarian(47;0.0569)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)		CCCGAGGTTCTGGGAGCTCCA	0.662	0	9.0	9.0	9.0	19	39905669	2187	4277	6464	SO:0001589	frameshift_variant	AK024429	CCDS33022.2	19q13.2	2013-01-11			ENSG00000090924	ENSG00000090924	"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	29515	protein-coding gene	gene with protein product		611893			11839748, 18045877	Standard	NM_022835	Approved	CLG, FLJ00018, ARHGEF42	uc010xuz.2	Q9H7P9	OTTHUMG00000152570	ENST00000409794.3:c.147delT	19.37:g.39905669delT	ENSP00000386733:p.Ser49fs	B8ZZK6|C9J0Y4|Q6DHV6|Q96BU2|Q96D18|Q9H699	ENST00000409794.3	37	CCDS33022.2																																																																																			PLEKHG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326802.1	.	.		-13	6					NM_022835	2		4	0.33