#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
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	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	t_alt_count	t_ref_count
OR51F2	119694	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	4843405	4843405	+	Missense_Mutation	SNP	A	A	G			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr11:4843405A>G	ENST00000322110.5	+	1	855	c.790A>G	c.(790-792)Atc>Gtc	p.I264V	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001004753.1	NP_001004753.1	Q8NH61	O51F2_HUMAN	olfactory receptor, family 51, subfamily F, member 2	264						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|endometrium(4)|large_intestine(3)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|skin(2)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.0778)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)		TGCTGTTTCCATCTTCTACCT	0.478																																																0													277.0	187.0	218.0					11																	4843405		2201	4298	6499	SO:0001583	missense	119694			BK004281	CCDS31361.1	11p15.4	2012-08-09			ENSG00000176925	ENSG00000176925		"""GPCR / Class A : Olfactory receptors"""	15197	protein-coding gene	gene with protein product							Standard	NM_001004753		Approved		uc010qyn.2	Q8NH61	OTTHUMG00000066508	ENST00000322110.5:c.790A>G	11.37:g.4843405A>G	ENSP00000323952:p.Ile264Val		Q6IFI1	Missense_Mutation	SNP	ENST00000322110.5	37	CCDS31361.1	.	.	.	.	.	.	.	.	.	.	A	9.355	1.066443	0.20067	.	.	ENSG00000176925	ENST00000322110	T	0.00107	8.72	4.61	3.44	0.39384	GPCR, rhodopsin-like superfamily (1);	0.405503	0.17786	U	0.162054	T	0.00109	0.0003	L	0.31476	0.935	0.27901	N	0.938984	B	0.27559	0.181	B	0.35114	0.196	T	0.01848	-1.1261	10	0.27082	T	0.32	.	5.1986	0.15252	0.7547:0.0:0.088:0.1573	.	264	Q8NH61	O51F2_HUMAN	V	264	ENSP00000323952:I264V	ENSP00000323952:I264V	I	+	1	0	OR51F2	4799981	0.000000	0.05858	0.999000	0.59377	0.957000	0.61999	-0.282000	0.08445	0.850000	0.35239	0.459000	0.35465	ATC		0.478	OR51F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142181.1	NM_001004753		27	49	27	49
CCDC82	79780	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	96092275	96092275	+	Missense_Mutation	SNP	A	A	T			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr11:96092275A>T	ENST00000278520.5	-	8	1876	c.1448T>A	c.(1447-1449)tTc>tAc	p.F483Y	CCDC82_ENST00000542662.1_Missense_Mutation_p.F483Y|CCDC82_ENST00000423339.2_Missense_Mutation_p.F483Y			Q8N4S0	CCD82_HUMAN	coiled-coil domain containing 82	483										endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)	19		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)		BRCA - Breast invasive adenocarcinoma(274;0.154)		GTATAGTTTGAATTTAAAATG	0.343																																																0													117.0	116.0	117.0					11																	96092275		2201	4297	6498	SO:0001583	missense	79780			AF245436	CCDS8307.1	11q21	2006-03-09			ENSG00000149231	ENSG00000149231			26282	protein-coding gene	gene with protein product						12477932	Standard	NM_024725		Approved	FLJ23518	uc001pfx.4	Q8N4S0	OTTHUMG00000167678	ENST00000278520.5:c.1448T>A	11.37:g.96092275A>T	ENSP00000278520:p.Phe483Tyr		B3KPU7|Q8WV71|Q9H2Q5|Q9H5E3	Missense_Mutation	SNP	ENST00000278520.5	37	CCDS8307.1	.	.	.	.	.	.	.	.	.	.	A	6.439	0.449219	0.12223	.	.	ENSG00000149231	ENST00000278520;ENST00000542662;ENST00000423339	T;T;T	0.10960	2.82;2.82;2.82	5.78	4.53	0.55603	.	0.063418	0.64402	D	0.000005	T	0.04724	0.0128	N	0.11818	0.18	0.32446	N	0.546061	B	0.02656	0.0	B	0.04013	0.001	T	0.23404	-1.0189	10	0.02654	T	1	-11.7999	8.4749	0.33007	0.6789:0.0:0.0:0.3211	.	483	Q8N4S0	CCD82_HUMAN	Y	483	ENSP00000278520:F483Y;ENSP00000444010:F483Y;ENSP00000397156:F483Y	ENSP00000278520:F483Y	F	-	2	0	CCDC82	95731923	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.196000	0.42686	2.333000	0.79357	0.533000	0.62120	TTC		0.343	CCDC82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395542.2	NM_024725		32	81	32	81
OR8B4	283162	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	124293908	124293908	+	Missense_Mutation	SNP	G	G	A			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr11:124293908G>A	ENST00000356130.3	-	1	881	c.860C>T	c.(859-861)tCg>tTg	p.S287L		NM_001005196.1	NP_001005196.1	Q96RC9	OR8B4_HUMAN	olfactory receptor, family 8, subfamily B, member 4	287						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(7)|lung(15)|ovary(1)|skin(6)|stomach(1)|urinary_tract(1)	32		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		ACTGTAGATCGAAGGGTTAAG	0.443																																																0													92.0	90.0	91.0					11																	124293908		2201	4299	6500	SO:0001583	missense	283162			AB065831	CCDS31710.1	11q24	2012-08-09		2001-06-29	ENSG00000198657	ENSG00000198657		"""GPCR / Class A : Olfactory receptors"""	8473	protein-coding gene	gene with protein product				OR8B4P			Standard	NM_001005196		Approved		uc010sak.2	Q96RC9	OTTHUMG00000165916	ENST00000356130.3:c.860C>T	11.37:g.124293908G>A	ENSP00000348449:p.Ser287Leu		B2RNF8|Q6IFQ7	Missense_Mutation	SNP	ENST00000356130.3	37	CCDS31710.1	.	.	.	.	.	.	.	.	.	.	a	6.094	0.385610	0.11524	.	.	ENSG00000198657	ENST00000356130	T	0.29142	1.58	4.1	4.1	0.47936	GPCR, rhodopsin-like superfamily (1);	0.189156	0.24633	N	0.036866	T	0.03053	0.0090	N	0.00002	-3.525	0.21984	N	0.999431	B	0.02656	0.0	B	0.01281	0.0	T	0.37056	-0.9722	10	0.02654	T	1	.	10.0234	0.42057	0.9172:0.0:0.0828:0.0	.	287	Q96RC9	OR8B4_HUMAN	L	287	ENSP00000348449:S287L	ENSP00000348449:S287L	S	-	2	0	OR8B4	123799118	0.890000	0.30428	0.996000	0.52242	0.996000	0.88848	6.506000	0.73712	0.922000	0.37019	-0.254000	0.11334	TCG		0.443	OR8B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387055.1	NM_001005196		32	52	32	52
PYROXD1	79912	hgsc.bcm.edu;broad.mit.edu	37	12	21593340	21593340	+	Silent	SNP	A	A	G			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr12:21593340A>G	ENST00000240651.9	+	2	177	c.123A>G	c.(121-123)gtA>gtG	p.V41V	PYROXD1_ENST00000545178.1_Silent_p.V41V|PYROXD1_ENST00000538582.1_5'UTR	NM_024854.3	NP_079130.2	Q8WU10	PYRD1_HUMAN	pyridine nucleotide-disulphide oxidoreductase domain 1	41							oxidoreductase activity (GO:0016491)			endometrium(3)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|skin(2)|soft_tissue(1)	18						TTCTCTTGGTAACAGCTTCTC	0.289																																																0													59.0	66.0	64.0					12																	21593340		2202	4290	6492	SO:0001819	synonymous_variant	79912			AL832441	CCDS31755.1	12p12.1	2014-02-12			ENSG00000121350	ENSG00000121350			26162	protein-coding gene	gene with protein product						12477932	Standard	NM_024854		Approved	DKFZp762G094, FLJ22028	uc001rew.3	Q8WU10	OTTHUMG00000169129	ENST00000240651.9:c.123A>G	12.37:g.21593340A>G			A6NKI6|B3KWN8|Q9H6P1	Silent	SNP	ENST00000240651.9	37	CCDS31755.1																																																																																				0.289	PYROXD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402363.1	NM_024854		10	157	10	157
KRT6C	286887	hgsc.bcm.edu;broad.mit.edu	37	12	52865067	52865067	+	Missense_Mutation	SNP	A	A	G			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr12:52865067A>G	ENST00000252250.6	-	5	973	c.926T>C	c.(925-927)aTg>aCg	p.M309T		NM_173086.4	NP_775109.2	P48668	K2C6C_HUMAN	keratin 6C	309	Coil 1B.|Rod.				intermediate filament cytoskeleton organization (GO:0045104)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(3)|prostate(2)|skin(2)	23				BRCA - Breast invasive adenocarcinoma(357;0.0828)		GTGGGTCTGCATCTGGGACAG	0.507																																																0													117.0	110.0	112.0					12																	52865067		2203	4298	6501	SO:0001583	missense	286887			L42611	CCDS8829.1	12q13.13	2013-01-16	2006-07-17	2006-07-17	ENSG00000170465	ENSG00000170465		"""-"", ""Intermediate filaments type II, keratins (basic)"""	20406	protein-coding gene	gene with protein product		612315	"""keratin 6E"""	KRT6E		7543104, 16831889	Standard	NM_173086		Approved		uc001sal.4	P48668	OTTHUMG00000169596	ENST00000252250.6:c.926T>C	12.37:g.52865067A>G	ENSP00000252250:p.Met309Thr		A1L4L5|P48666|Q2TAZ9|Q7RTN9	Missense_Mutation	SNP	ENST00000252250.6	37	CCDS8829.1	.	.	.	.	.	.	.	.	.	.	A	15.07	2.722880	0.48728	.	.	ENSG00000170465	ENST00000252250;ENST00000411979	D	0.88354	-2.37	3.5	3.5	0.40072	Filament (1);	0.000000	0.64402	D	0.000001	D	0.89543	0.6745	M	0.85041	2.73	0.41884	D	0.990339	P	0.37423	0.594	B	0.37943	0.261	D	0.91094	0.4909	10	0.87932	D	0	.	12.4636	0.55745	1.0:0.0:0.0:0.0	.	309	P48668	K2C6C_HUMAN	T	309;294	ENSP00000252250:M309T	ENSP00000252250:M309T	M	-	2	0	KRT6C	51151334	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	8.918000	0.92759	1.575000	0.49775	0.368000	0.22195	ATG		0.507	KRT6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404976.1	NM_173086		51	105	51	105
THBS1	7057	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	15	39883403	39883403	+	Silent	SNP	A	A	G			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr15:39883403A>G	ENST00000260356.5	+	15	2430	c.2265A>G	c.(2263-2265)ccA>ccG	p.P755P	CTD-2033D15.1_ENST00000560769.1_RNA	NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	755					activation of MAPK activity (GO:0000187)|behavioral response to pain (GO:0048266)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to tumor necrosis factor (GO:0071356)|chronic inflammatory response (GO:0002544)|endocardial cushion development (GO:0003197)|engulfment of apoptotic cell (GO:0043652)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|immune response (GO:0006955)|negative regulation of angiogenesis (GO:0016525)|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002581)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cGMP-mediated signaling (GO:0010754)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell antigen processing and presentation (GO:0002605)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of plasminogen activation (GO:0010757)|outflow tract morphogenesis (GO:0003151)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of translation (GO:0045727)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to magnesium ion (GO:0032026)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to unfolded protein (GO:0006986)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|sarcoplasmic reticulum (GO:0016529)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|collagen V binding (GO:0070052)|fibrinogen binding (GO:0070051)|fibroblast growth factor binding (GO:0017134)|fibronectin binding (GO:0001968)|glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|proteoglycan binding (GO:0043394)|transforming growth factor beta binding (GO:0050431)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(5)|large_intestine(15)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	53		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)		ACAACTGTCCATTCCATTACA	0.448																																																0													142.0	137.0	139.0					15																	39883403		2200	4297	6497	SO:0001819	synonymous_variant	7057				CCDS32194.1	15q15	2009-04-08			ENSG00000137801	ENSG00000137801			11785	protein-coding gene	gene with protein product	"""thrombospondin-1p180"""	188060				2341158, 2335352	Standard	NM_003246		Approved	TSP1, THBS, TSP, THBS-1, TSP-1	uc001zkh.3	P07996	OTTHUMG00000133665	ENST00000260356.5:c.2265A>G	15.37:g.39883403A>G			A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Silent	SNP	ENST00000260356.5	37	CCDS32194.1																																																																																				0.448	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246		64	126	64	126
IGSF6	10261	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	16	21658638	21658638	+	Missense_Mutation	SNP	G	G	T	rs1454374	byFrequency	TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr16:21658638G>T	ENST00000268389.4	-	2	304	c.243C>A	c.(241-243)gaC>gaA	p.D81E	METTL9_ENST00000396014.4_Intron|METTL9_ENST00000358154.3_Intron	NM_005849.3	NP_005840.2	O95976	IGSF6_HUMAN	immunoglobulin superfamily, member 6	81	Ig-like C2-type.				cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)	integral component of plasma membrane (GO:0005887)	transmembrane signaling receptor activity (GO:0004888)			endometrium(1)|large_intestine(1)|lung(4)|urinary_tract(1)	7				GBM - Glioblastoma multiforme(48;0.066)		TTTTGCACCCGTCCAAGCACA	0.512																																																0													108.0	90.0	96.0					16																	21658638		2199	4300	6499	SO:0001583	missense	10261			AJ223183	CCDS10599.1	16p12.2	2013-01-11			ENSG00000140749	ENSG00000140749		"""Immunoglobulin superfamily / V-set domain containing"""	5953	protein-coding gene	gene with protein product		606222				9809579	Standard	NM_005849		Approved	DORA	uc002djg.2	O95976	OTTHUMG00000090709	ENST00000268389.4:c.243C>A	16.37:g.21658638G>T	ENSP00000268389:p.Asp81Glu		Q8WWD8	Missense_Mutation	SNP	ENST00000268389.4	37	CCDS10599.1	.	.	.	.	.	.	.	.	.	.	G	11.28	1.591456	0.28357	.	.	ENSG00000140749	ENST00000268389	T	0.64260	-0.09	4.85	-9.71	0.00518	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.262060	0.05222	N	0.508761	T	0.51601	0.1684	L	0.51422	1.61	0.09310	N	1	B	0.12630	0.006	B	0.15484	0.013	T	0.39461	-0.9613	10	0.32370	T	0.25	-15.0955	12.7412	0.57253	0.1602:0.0:0.647:0.1928	.	81	O95976	IGSF6_HUMAN	E	81	ENSP00000268389:D81E	ENSP00000268389:D81E	D	-	3	2	IGSF6	21566139	0.000000	0.05858	0.000000	0.03702	0.028000	0.11728	-2.048000	0.01406	-2.967000	0.00288	-0.827000	0.03088	GAC		0.512	IGSF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207400.1			53	68	53	68
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	7577532	7577532	+	Missense_Mutation	SNP	G	G	A			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr17:7577532G>A	ENST00000269305.4	-	7	938	c.749C>T	c.(748-750)cCc>cTc	p.P250L	TP53_ENST00000420246.2_Missense_Mutation_p.P250L|TP53_ENST00000445888.2_Missense_Mutation_p.P250L|TP53_ENST00000359597.4_Missense_Mutation_p.P250L|TP53_ENST00000455263.2_Missense_Mutation_p.P250L|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_Missense_Mutation_p.P250L	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	250	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		P -> A (in sporadic cancers; somatic mutation).|P -> F (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|P -> H (in sporadic cancers; somatic mutation).|P -> L (in sporadic cancers; somatic mutation).|P -> N (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|P -> Q (in sporadic cancers; somatic mutation).|P -> S (in sporadic cancers; somatic mutation).|P -> T (in sporadic cancers; somatic mutation).|RP -> SA (in a sporadic cancer; somatic mutation).|RP -> SS (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.P250L(45)|p.0?(8)|p.?(5)|p.P250H(4)|p.P250F(3)|p.P250N(2)|p.M246_P250delMNRRP(2)|p.P250_L252delPIL(2)|p.P250Q(2)|p.R248_P250delRRP(1)|p.P250_T253delPILT(1)|p.N247_P250delNRRP(1)|p.R249_P250delRP(1)|p.R249_T256delRPILTIIT(1)|p.I251fs*94(1)|p.R249_I251delRPI(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GGTGAGGATGGGCCTCCGGTT	0.577		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	80	Substitution - Missense(56)|Deletion - In frame(10)|Whole gene deletion(8)|Unknown(5)|Deletion - Frameshift(1)	large_intestine(14)|lung(10)|breast(10)|upper_aerodigestive_tract(5)|biliary_tract(5)|skin(5)|ovary(5)|stomach(4)|central_nervous_system(4)|haematopoietic_and_lymphoid_tissue(4)|bone(4)|oesophagus(3)|liver(2)|urinary_tract(1)|eye(1)|peritoneum(1)|pancreas(1)|thyroid(1)	GRCh37	CM973401	TP53	M							154.0	112.0	126.0					17																	7577532		2203	4300	6503	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.749C>T	17.37:g.7577532G>A	ENSP00000269305:p.Pro250Leu		Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.504438	0.85176	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D;D	0.99885	-7.5;-7.5;-7.5;-7.5;-7.5;-7.5;-7.5	4.62	4.62	0.57501	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99898	0.9951	M	0.91406	3.205	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.997;0.996;0.998;0.998;1.0	D	0.96045	0.9027	10	0.87932	D	0	-1.5308	15.3618	0.74483	0.0:0.0:1.0:0.0	.	250;250;250;250;250	P04637-2;P04637-3;P04637;Q1MSW8;E7EQX7	.;.;P53_HUMAN;.;.	L	250;250;250;250;250;250;239;118	ENSP00000410739:P250L;ENSP00000352610:P250L;ENSP00000269305:P250L;ENSP00000398846:P250L;ENSP00000391127:P250L;ENSP00000391478:P250L;ENSP00000425104:P118L	ENSP00000269305:P250L	P	-	2	0	TP53	7518257	1.000000	0.71417	1.000000	0.80357	0.724000	0.41520	9.601000	0.98297	2.564000	0.86499	0.462000	0.41574	CCC		0.577	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		40	17	40	17
SMARCA4	6597	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	11132435	11132435	+	Missense_Mutation	SNP	A	A	G			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr19:11132435A>G	ENST00000429416.3	+	20	2932	c.2651A>G	c.(2650-2652)cAc>cGc	p.H884R	SMARCA4_ENST00000344626.4_Missense_Mutation_p.H884R|SMARCA4_ENST00000541122.2_Missense_Mutation_p.H884R|SMARCA4_ENST00000444061.3_Missense_Mutation_p.H884R|SMARCA4_ENST00000358026.2_Missense_Mutation_p.H884R|SMARCA4_ENST00000590574.1_Missense_Mutation_p.H884R|SMARCA4_ENST00000589677.1_Missense_Mutation_p.H884R|SMARCA4_ENST00000450717.3_Missense_Mutation_p.H884R|SMARCA4_ENST00000413806.3_Missense_Mutation_p.H884R	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	884	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.H884P(1)|p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				GACGAAGGTCACCGCATGAAG	0.622			"""F, N, Mis"""		NSCLC																																		Rec	yes		19	19p13.2	6597	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"""		E	2	Substitution - Missense(1)|Unknown(1)	lung(1)|central_nervous_system(1)											82.0	64.0	70.0					19																	11132435		2202	4300	6502	SO:0001583	missense	6597			D26156	CCDS12253.1, CCDS45972.1, CCDS45973.1, CCDS54217.1, CCDS54218.1	19p13.3	2014-09-17	2006-11-09		ENSG00000127616	ENSG00000127616			11100	protein-coding gene	gene with protein product	"""SNF2-like 4"", ""global transcription activator homologous sequence"", ""sucrose nonfermenting-like 4"", ""mitotic growth and transcription activator"", ""BRM/SWI2-related gene 1"", ""homeotic gene regulator"", ""nuclear protein GRB1"", ""brahma protein-like 1"", ""ATP-dependent helicase SMARCA4"""	603254		SNF2L4		8208605	Standard	NM_003072		Approved	hSNF2b, BRG1, BAF190, SNF2, SWI2, SNF2-BETA, SNF2LB, FLJ39786	uc010dxo.3	P51532	OTTHUMG00000169272	ENST00000429416.3:c.2651A>G	19.37:g.11132435A>G	ENSP00000395654:p.His884Arg		B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	37	CCDS12253.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.397831	0.83120	.	.	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	D;D;D;D;D;D;D	0.98313	-4.86;-4.86;-4.86;-4.86;-4.86;-4.86;-4.86	4.66	4.66	0.58398	DEAD-like helicase (2);SNF2-related (1);	0.000000	0.85682	D	0.000000	D	0.99378	0.9781	H	0.98901	4.365	0.80722	D	1	D;D;D;P;P;D;D;D	0.89917	0.975;0.975;0.975;0.933;0.592;1.0;0.975;0.975	P;P;P;P;P;D;P;P	0.76575	0.838;0.838;0.838;0.759;0.449;0.988;0.838;0.838	D	0.98260	1.0498	10	0.87932	D	0	-53.571	13.2208	0.59885	1.0:0.0:0.0:0.0	.	884;884;884;884;884;104;884;884	B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;B4E0F1;A7E2E1;P51532	.;.;.;.;.;.;.;SMCA4_HUMAN	R	884;884;948;884;884;884;884;884	ENSP00000395654:H884R;ENSP00000350720:H884R;ENSP00000343896:H884R;ENSP00000445036:H884R;ENSP00000392837:H884R;ENSP00000397783:H884R;ENSP00000414727:H884R	ENSP00000343896:H884R	H	+	2	0	SMARCA4	10993435	1.000000	0.71417	1.000000	0.80357	0.891000	0.51852	9.139000	0.94554	1.964000	0.57103	0.533000	0.62120	CAC		0.622	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072		10	21	10	21
URI1	8725	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	30503230	30503230	+	Missense_Mutation	SNP	G	G	A	rs140683632		TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr19:30503230G>A	ENST00000542441.2	+	10	1514	c.1217G>A	c.(1216-1218)cGc>cAc	p.R406H	URI1_ENST00000360605.4_Missense_Mutation_p.R388H|URI1_ENST00000312051.6_Missense_Mutation_p.R366H|URI1_ENST00000392271.1_Missense_Mutation_p.R330H			O94763	RMP_HUMAN	URI1, prefoldin-like chaperone	406					cellular response to growth factor stimulus (GO:0071363)|cellular response to steroid hormone stimulus (GO:0071383)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of phosphatase activity (GO:0010923)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein folding (GO:0006457)|regulation of cell growth (GO:0001558)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to virus (GO:0009615)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, core complex (GO:0005665)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|prefoldin complex (GO:0016272)	chromatin binding (GO:0003682)|protein phosphatase inhibitor activity (GO:0004864)|RNA polymerase II transcription corepressor activity (GO:0001106)										TATGTCCCTCGCAAATCCATC	0.408																																																0								G	HIS/ARG,HIS/ARG	0,4406		0,0,2203	170.0	157.0	161.0		1217,1097	5.5	1.0	19	dbSNP_134	161	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	C19orf2	NM_003796.2,NM_134447.1	29,29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	406/536,366/496	30503230	1,13005	2203	4300	6503	SO:0001583	missense	8725			AF091095	CCDS12420.1, CCDS58658.1	19q12	2012-04-17	2011-11-21	2011-11-21	ENSG00000105176	ENSG00000105176		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	13236	protein-coding gene	gene with protein product	"""unconventional prefoldin RPB5 interactor"", ""RPB5-mediating protein"", ""protein phosphatase 1, regulatory subunit 19"""	603494	"""chromosome 19 open reading frame 2"""	C19orf2		9878255, 9819440	Standard	NM_003796		Approved	RMP, NNX3, FLJ10575, URI, PPP1R19	uc002nsr.3	O94763		ENST00000542441.2:c.1217G>A	19.37:g.30503230G>A	ENSP00000442436:p.Arg406His		A8K805|H7BY42|Q8TC23|Q9UNU3	Missense_Mutation	SNP	ENST00000542441.2	37	CCDS12420.1	.	.	.	.	.	.	.	.	.	.	G	17.82	3.482760	0.63962	0.0	1.16E-4	ENSG00000105176	ENST00000360605;ENST00000392271;ENST00000542441;ENST00000312051	T	0.60040	0.22	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.59418	0.2192	L	0.51422	1.61	0.80722	D	1	P;P;P	0.52577	0.894;0.954;0.901	P;B;B	0.44673	0.457;0.269;0.184	T	0.63695	-0.6579	10	0.59425	D	0.04	-12.3638	19.4888	0.95042	0.0:0.0:1.0:0.0	.	366;406;403	F8W9T0;O94763;Q8TC23	.;RMP_HUMAN;.	H	404;330;406;366	ENSP00000442436:R406H	ENSP00000312530:R366H	R	+	2	0	C19orf2	35195070	1.000000	0.71417	0.992000	0.48379	0.021000	0.10359	9.148000	0.94652	2.607000	0.88179	0.585000	0.79938	CGC		0.408	URI1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439756.1	NM_134447		51	167	51	167
GDAP2	54834	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	118441728	118441728	+	Silent	SNP	C	C	A			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr1:118441728C>A	ENST00000369443.5	-	7	996	c.747G>T	c.(745-747)gtG>gtT	p.V249V	GDAP2_ENST00000464026.1_5'UTR|GDAP2_ENST00000369442.3_Silent_p.V249V	NM_017686.3	NP_060156.1	Q9NXN4	GDAP2_HUMAN	ganglioside induced differentiation associated protein 2	249					response to retinoic acid (GO:0032526)	lysosomal membrane (GO:0005765)				kidney(2)|large_intestine(3)|lung(9)|ovary(2)	16		all_cancers(81;0.0156)|all_lung(203;5.81e-05)|Lung NSC(69;0.000446)|all_epithelial(167;0.00295)		Lung(183;0.0583)|LUSC - Lung squamous cell carcinoma(189;0.194)		GTTCAGGTACCACAGGCTCCC	0.438																																																0													166.0	157.0	160.0					1																	118441728		2203	4300	6503	SO:0001819	synonymous_variant	54834			AK000149	CCDS897.1, CCDS44201.1	1q11	2011-10-20			ENSG00000196505	ENSG00000196505			18010	protein-coding gene	gene with protein product						1021725	Standard	NM_017686		Approved	FLJ20142, dJ776P7.1, MACROD3	uc001ehf.3	Q9NXN4	OTTHUMG00000012199	ENST00000369443.5:c.747G>T	1.37:g.118441728C>A			Q96DZ0	Silent	SNP	ENST00000369443.5	37	CCDS897.1																																																																																				0.438	GDAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033732.2	NM_017686		64	128	64	128
OR2W3	343171	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	248059264	248059264	+	Missense_Mutation	SNP	A	A	G			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr1:248059264A>G	ENST00000360358.3	+	1	376	c.376A>G	c.(376-378)Atc>Gtc	p.I126V	OR2W3_ENST00000537741.1_Missense_Mutation_p.I126V	NM_001001957.2	NP_001001957.2	Q7Z3T1	OR2W3_HUMAN	olfactory receptor, family 2, subfamily W, member 3	126						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(2)|large_intestine(2)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)	49	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0319)			GTGTGTGGCTATCTGCAAGCC	0.607																																																0													110.0	85.0	93.0					1																	248059264		2203	4300	6503	SO:0001583	missense	343171			N75737	CCDS31099.1	1q44	2012-08-09		2004-03-10	ENSG00000238243	ENSG00000238243		"""GPCR / Class A : Olfactory receptors"""	15021	protein-coding gene	gene with protein product				OR2W8P, OR2W3P		14983052	Standard	NM_001001957		Approved	OST718	uc010pzb.2	Q7Z3T1	OTTHUMG00000040204	ENST00000360358.3:c.376A>G	1.37:g.248059264A>G	ENSP00000353516:p.Ile126Val		Q6IF06|Q8NG86	Missense_Mutation	SNP	ENST00000360358.3	37	CCDS31099.1	.	.	.	.	.	.	.	.	.	.	A	0	-2.587295	0.00128	.	.	ENSG00000238243	ENST00000537741;ENST00000360358	T;T	0.50813	0.73;0.73	5.28	-2.65	0.06095	GPCR, rhodopsin-like superfamily (1);	0.479877	0.19405	N	0.115074	T	0.24509	0.0594	L	0.31664	0.95	0.09310	N	1	B	0.02656	0.0	B	0.09377	0.004	T	0.35919	-0.9769	10	0.02654	T	1	.	8.4344	0.32778	0.623:0.1194:0.2576:0.0	.	126	Q7Z3T1	OR2W3_HUMAN	V	126	ENSP00000445853:I126V;ENSP00000353516:I126V	ENSP00000353516:I126V	I	+	1	0	OR2W3	246125887	0.017000	0.18338	0.013000	0.15412	0.006000	0.05464	0.318000	0.19504	-0.377000	0.07930	-1.010000	0.02471	ATC		0.607	OR2W3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096861.1	NM_001001957		20	61	20	61
SPTBN1	6711	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	54880943	54880943	+	Silent	SNP	C	C	G			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr2:54880943C>G	ENST00000356805.4	+	27	6056	c.5775C>G	c.(5773-5775)ctC>ctG	p.L1925L	SPTBN1_ENST00000333896.5_Silent_p.L1912L	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	1925	Interaction with ANK2.				actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			ACCTCATGCTCTGGATGGAGG	0.577																																																0													53.0	50.0	51.0					2																	54880943		2203	4300	6503	SO:0001819	synonymous_variant	6711				CCDS33198.1, CCDS33199.1	2p21	2013-01-10			ENSG00000115306	ENSG00000115306		"""Pleckstrin homology (PH) domain containing"""	11275	protein-coding gene	gene with protein product		182790					Standard	NM_003128		Approved		uc002rxu.3	Q01082	OTTHUMG00000133746	ENST00000356805.4:c.5775C>G	2.37:g.54880943C>G			B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Silent	SNP	ENST00000356805.4	37	CCDS33198.1																																																																																				0.577	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3			14	22	14	22
NEB	4703	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	152474871	152474871	+	Missense_Mutation	SNP	C	C	T			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr2:152474871C>T	ENST00000172853.10	-	70	10412	c.10265G>A	c.(10264-10266)cGt>cAt	p.R3422H	NEB_ENST00000427231.2_Missense_Mutation_p.R3665H|NEB_ENST00000603639.1_Missense_Mutation_p.R3665H|NEB_ENST00000409198.1_Missense_Mutation_p.R3422H|NEB_ENST00000604864.1_Missense_Mutation_p.R3665H|NEB_ENST00000397345.3_Missense_Mutation_p.R3665H			P20929	NEBU_HUMAN	nebulin	3422					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		CGTTTCTGGACGCTGACGGTA	0.443																																																0													178.0	173.0	174.0					2																	152474871		1942	4148	6090	SO:0001583	missense	4703			X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"""nemaline myopathy type 2"""	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.10265G>A	2.37:g.152474871C>T	ENSP00000172853:p.Arg3422His		F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		.	.	.	.	.	.	.	.	.	.	C	7.236	0.600232	0.13939	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853	T;T;T;T	0.05855	3.39;3.39;3.38;3.4	5.68	1.51	0.23008	.	0.426129	0.24056	N	0.041947	T	0.03136	0.0092	N	0.10972	0.075	0.54753	D	0.999988	B	0.10296	0.003	B	0.04013	0.001	T	0.46938	-0.9155	10	0.39692	T	0.17	.	6.1616	0.20368	0.0:0.3659:0.2483:0.3858	.	3422	P20929	NEBU_HUMAN	H	3422;3665;3665;3422	ENSP00000386259:R3422H;ENSP00000380505:R3665H;ENSP00000416578:R3665H;ENSP00000172853:R3422H	ENSP00000172853:R3422H	R	-	2	0	NEB	152183117	0.009000	0.17119	0.995000	0.50966	0.096000	0.18686	0.077000	0.14738	0.441000	0.26529	-0.143000	0.13931	CGT		0.443	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		54	210	54	210
UBR3	130507	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	170917865	170917865	+	Missense_Mutation	SNP	A	A	G			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr2:170917865A>G	ENST00000272793.5	+	35	4981	c.4931A>G	c.(4930-4932)aAa>aGa	p.K1644R	UBR3_ENST00000418381.1_Missense_Mutation_p.K1644R|UBR3_ENST00000392631.1_Missense_Mutation_p.K465R			Q6ZT12	UBR3_HUMAN	ubiquitin protein ligase E3 component n-recognin 3 (putative)	1644					embryo development (GO:0009790)|in utero embryonic development (GO:0001701)|olfactory behavior (GO:0042048)|sensory perception of smell (GO:0007608)|suckling behavior (GO:0001967)|ubiquitin-dependent protein catabolic process (GO:0006511)	integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(9)|liver(1)|lung(8)|ovary(1)|prostate(3)|stomach(1)	33						TCCATGGAAAAATGCTTACAG	0.363																																																0													166.0	165.0	165.0					2																	170917865		2203	4300	6503	SO:0001583	missense	130507			AL834144	CCDS2238.2	2q31.1	2008-06-23	2008-06-23	2007-11-29	ENSG00000144357	ENSG00000144357		"""Ubiquitin protein ligase E3 component n-recognins"""	30467	protein-coding gene	gene with protein product		613831	"""zinc finger protein 650"""	ZNF650		17462990	Standard	NM_172070		Approved	KIAA2024, DKFZp434P117, FLJ37422	uc010zdi.2	Q6ZT12	OTTHUMG00000132229	ENST00000272793.5:c.4931A>G	2.37:g.170917865A>G	ENSP00000272793:p.Lys1644Arg		B4DZR7|Q2KHN5|Q6ZR55|Q6ZSC2|Q8IVE7|Q8ND96	Missense_Mutation	SNP	ENST00000272793.5	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	5.288|5.288	0.238584|0.238584	0.10023|0.10023	.|.	.|.	ENSG00000144357|ENSG00000144357	ENST00000272793;ENST00000442603;ENST00000418381;ENST00000392631;ENST00000439681|ENST00000392632	T;T;T;T|.	0.37915|.	1.17;1.17;1.17;1.17|.	5.92|5.92	2.3|2.3	0.28687|0.28687	.|.	0.483458|.	0.25810|.	N|.	0.028147|.	T|T	0.14614|0.14614	0.0353|0.0353	N|N	0.04724|0.04724	-0.175|-0.175	0.09310|0.09310	N|N	0.999995|0.999995	B;B;B|.	0.02656|.	0.0;0.0;0.0|.	B;B;B|.	0.01281|.	0.0;0.0;0.0|.	T|T	0.23547|0.23547	-1.0185|-1.0185	10|5	0.09590|.	T|.	0.72|.	.|.	3.9548|3.9548	0.09385|0.09385	0.4942:0.0:0.3457:0.1601|0.4942:0.0:0.3457:0.1601	.|.	1644;465;1673|.	Q6ZT12;Q6ZT12-2;E7EVK3|.	UBR3_HUMAN;.;.|.	R|D	1644;1673;1644;465;344|706	ENSP00000272793:K1644R;ENSP00000396068:K1644R;ENSP00000376408:K465R;ENSP00000389097:K344R|.	ENSP00000272793:K1644R|.	K|N	+|+	2|1	0|0	UBR3|UBR3	170626111|170626111	1.000000|1.000000	0.71417|0.71417	0.991000|0.991000	0.47740|0.47740	0.944000|0.944000	0.59088|0.59088	1.194000|1.194000	0.32174|0.32174	0.500000|0.500000	0.27991|0.27991	0.528000|0.528000	0.53228|0.53228	AAA|AAT		0.363	UBR3-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255290.2	NM_172070		109	188	109	188
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr2:209113112C>T	ENST00000415913.1	-	4	776	c.395G>A	c.(394-396)cGt>cAt	p.R132H	IDH1_ENST00000345146.2_Missense_Mutation_p.R132H|IDH1_ENST00000446179.1_Missense_Mutation_p.R132H	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132			R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:19117336}.|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation). {ECO:0000269|PubMed:19117336}.|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:19117336}.|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.		2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.R132H(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		ATAAGCATGACGACCTATGAT	0.393			Mis		gliobastoma																																Pancreas(158;264 1958 3300 35450 36047)		Dom	yes		2	2q33.3	3417	"""isocitrate dehydrogenase 1 (NADP+), soluble"""		O	2835	Substitution - Missense(2834)|Complex - compound substitution(1)	central_nervous_system(2579)|haematopoietic_and_lymphoid_tissue(205)|bone(43)|prostate(4)|biliary_tract(2)|urinary_tract(1)|skin(1)											79.0	73.0	75.0					2																	209113112		2203	4300	6503	SO:0001583	missense	3417				CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.395G>A	2.37:g.209113112C>T	ENSP00000390265:p.Arg132His		Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	37	CCDS2381.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.657324	0.88154	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913;ENST00000415282	D;D;D;D	0.86956	-2.19;-2.19;-2.19;-2.19	5.57	4.69	0.59074	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.93145	0.7817	H	0.99379	4.54	0.80722	D	1	B	0.25486	0.127	B	0.25405	0.06	D	0.92324	0.5868	10	0.87932	D	0	-20.0399	14.3783	0.66895	0.0:0.9288:0.0:0.0712	.	132	O75874	IDHC_HUMAN	H	132	ENSP00000260985:R132H;ENSP00000410513:R132H;ENSP00000390265:R132H;ENSP00000391075:R132H	ENSP00000260985:R132H	R	-	2	0	IDH1	208821357	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	6.088000	0.71371	1.356000	0.45884	0.555000	0.69702	CGT		0.393	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1			31	68	31	68
BCL6	604	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	187449545	187449545	+	Missense_Mutation	SNP	A	A	G			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr3:187449545A>G	ENST00000406870.2	-	4	701	c.335T>C	c.(334-336)cTg>cCg	p.L112P	RP11-211G3.3_ENST00000437407.1_Intron|BCL6_ENST00000232014.4_Missense_Mutation_p.L112P|BCL6_ENST00000450123.2_Missense_Mutation_p.L112P|RP11-211G3.3_ENST00000449623.1_Intron	NM_001706.4	NP_001697.2	P41182	BCL6_HUMAN	B-cell CLL/lymphoma 6	112					actin cytoskeleton organization (GO:0030036)|B cell differentiation (GO:0030183)|cell morphogenesis (GO:0000902)|cellular response to DNA damage stimulus (GO:0006974)|erythrocyte development (GO:0048821)|germinal center formation (GO:0002467)|inflammatory response (GO:0006954)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of isotype switching to IgE isotypes (GO:0048294)|negative regulation of mast cell cytokine production (GO:0032764)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of T-helper 2 cell differentiation (GO:0045629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cellular component movement (GO:0051272)|protein import into nucleus, translocation (GO:0000060)|regulation of germinal center formation (GO:0002634)|regulation of immune response (GO:0050776)|regulation of inflammatory response (GO:0050727)|regulation of memory T cell differentiation (GO:0043380)|regulation of Rho GTPase activity (GO:0032319)|Rho protein signal transduction (GO:0007266)|spermatogenesis (GO:0007283)|type 2 immune response (GO:0042092)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|metal ion binding (GO:0046872)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(9)|lung(10)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	40	all_cancers(143;9.45e-12)|Ovarian(172;0.0418)		OV - Ovarian serous cystadenocarcinoma(80;1.76e-18)	GBM - Glioblastoma multiforme(93;0.0141)		CTCCATCTGCAGGTACATAGC	0.537			"""T, Mis"""	"""IG loci, ZNFN1A1, LCP1, PIM1, TFRC, CIITA, NACA, HSPCB, HSPCA, HIST1H4I, IL21R,  POU2AF1, ARHH, EIF4A2, SFRS3"""	"""NHL, CLL"""																																		Dom	yes		3	3q27	604	B-cell CLL/lymphoma 6		L	0													85.0	77.0	80.0					3																	187449545		2203	4300	6503	SO:0001583	missense	604				CCDS3289.1, CCDS46975.1	3q27	2013-01-09	2008-08-01		ENSG00000113916	ENSG00000113916		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	1001	protein-coding gene	gene with protein product		109565	"""zinc finger protein 51"""	ZNF51			Standard	NM_001130845		Approved	ZBTB27, LAZ3, BCL5, BCL6A	uc003frq.2	P41182	OTTHUMG00000156441	ENST00000406870.2:c.335T>C	3.37:g.187449545A>G	ENSP00000384371:p.Leu112Pro		A7E241|B8PSA7|D3DNV5	Missense_Mutation	SNP	ENST00000406870.2	37	CCDS3289.1	.	.	.	.	.	.	.	.	.	.	A	25.9	4.682379	0.88542	.	.	ENSG00000113916	ENST00000406870;ENST00000232014;ENST00000450123;ENST00000430339	T;T;T;T	0.74947	-0.89;-0.89;-0.89;-0.89	5.76	5.76	0.90799	BTB/POZ-like (1);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	D	0.91164	0.7217	H	0.97540	4.025	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.94056	0.7322	10	0.87932	D	0	.	15.5574	0.76208	1.0:0.0:0.0:0.0	.	112;112	B8PSA7;P41182	.;BCL6_HUMAN	P	112	ENSP00000384371:L112P;ENSP00000232014:L112P;ENSP00000413122:L112P;ENSP00000415574:L112P	ENSP00000232014:L112P	L	-	2	0	BCL6	188932239	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	8.962000	0.93254	2.333000	0.79357	0.482000	0.46254	CTG		0.537	BCL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344202.1	NM_138931		20	51	20	51
WDFY3	23001	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	85600267	85600267	+	Missense_Mutation	SNP	C	C	T			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr4:85600267C>T	ENST00000295888.4	-	65	10359	c.9952G>A	c.(9952-9954)Gca>Aca	p.A3318T	WDFY3_ENST00000322366.6_Missense_Mutation_p.A3301T	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	3318	Interaction with ATG5.|Interaction with SQSTM1.				aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		GCGGCTGTTGCGCGGCAGGAG	0.582																																																0													51.0	51.0	51.0					4																	85600267		2203	4300	6503	SO:0001583	missense	23001			AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"""Zinc fingers, FYVE domain containing"", ""WD repeat domain containing"""	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.9952G>A	4.37:g.85600267C>T	ENSP00000295888:p.Ala3318Thr		Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Missense_Mutation	SNP	ENST00000295888.4	37	CCDS3609.1	.	.	.	.	.	.	.	.	.	.	C	10.28	1.307491	0.23821	.	.	ENSG00000163625	ENST00000322366;ENST00000295888	T;T	0.64438	-0.1;-0.1	4.82	4.82	0.62117	WD40 repeat-like-containing domain (1);	0.158992	0.53938	D	0.000041	T	0.44685	0.1305	N	0.12182	0.205	0.44175	D	0.996981	B	0.09022	0.002	B	0.04013	0.001	T	0.33007	-0.9885	10	0.15952	T	0.53	.	18.0974	0.89494	0.0:1.0:0.0:0.0	.	3318	Q8IZQ1	WDFY3_HUMAN	T	3301;3318	ENSP00000318466:A3301T;ENSP00000295888:A3318T	ENSP00000295888:A3318T	A	-	1	0	WDFY3	85819291	0.992000	0.36948	0.191000	0.23289	0.003000	0.03518	2.890000	0.48609	2.488000	0.83962	0.655000	0.94253	GCA		0.582	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991		26	35	26	35
RAPGEF2	9693	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	160277114	160277114	+	Silent	SNP	G	G	A	rs374199273		TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr4:160277114G>A	ENST00000264431.4	+	23	4697	c.4278G>A	c.(4276-4278)ccG>ccA	p.P1426P		NM_014247.2	NP_055062.1	Q9Y4G8	RPGF2_HUMAN	Rap guanine nucleotide exchange factor (GEF) 2	1426					adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|blood vessel development (GO:0001568)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|cellular response to nerve growth factor stimulus (GO:1990090)|establishment of endothelial barrier (GO:0061028)|forebrain neuron development (GO:0021884)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|negative regulation of cell proliferation (GO:0008285)|negative regulation of dendrite morphogenesis (GO:0050774)|negative regulation of melanin biosynthetic process (GO:0048022)|nerve growth factor signaling pathway (GO:0038180)|neuron migration (GO:0001764)|neuron projection development (GO:0031175)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron migration (GO:2001224)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein binding (GO:0032092)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of vasculogenesis (GO:2001214)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|regulation of synaptic plasticity (GO:0048167)|small GTPase mediated signal transduction (GO:0007264)|ventricular system development (GO:0021591)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synapse (GO:0045202)	beta-1 adrenergic receptor binding (GO:0031697)|calcium ion binding (GO:0005509)|cAMP binding (GO:0030552)|diacylglycerol binding (GO:0019992)|PDZ domain binding (GO:0030165)|Rap GTPase activator activity (GO:0046582)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|signal transducer activity (GO:0004871)|WW domain binding (GO:0050699)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	70	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0817)		GGAAACCGCCGGACTACAACG	0.612																																																0								G		0,4022		0,0,2011	23.0	25.0	24.0		4278	-11.1	0.0	4		24	1,8333		0,1,4166	no	coding-synonymous	RAPGEF2	NM_014247.2		0,1,6177	AA,AG,GG		0.012,0.0,0.0081		1426/1500	160277114	1,12355	2011	4167	6178	SO:0001819	synonymous_variant	9693			AB002311	CCDS43277.1	4q32.1	2004-03-01	2004-03-01	2004-03-01					16854	protein-coding gene	gene with protein product	"""Rap GEP"""	609530	"""PDZ domain containing guanine nucleotide exchange factor (GEF) 1"""	PDZGEF1		9205841, 10934204	Standard	NM_014247		Approved	PDZ-GEF1, RA-GEF, DKFZP586O1422, KIAA0313	uc003iqg.4	Q9Y4G8		ENST00000264431.4:c.4278G>A	4.37:g.160277114G>A			D3DP27	Silent	SNP	ENST00000264431.4	37	CCDS43277.1																																																																																				0.612	RAPGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364980.2	NM_014247		10	26	10	26
PRDM9	56979	hgsc.bcm.edu;broad.mit.edu	37	5	23526956	23526956	+	Missense_Mutation	SNP	C	C	T			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr5:23526956C>T	ENST00000296682.3	+	11	1941	c.1759C>T	c.(1759-1761)Cgg>Tgg	p.R587W		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	587					meiotic gene conversion (GO:0006311)|positive regulation of meiosis I (GO:0060903)|positive regulation of reciprocal meiotic recombination (GO:0010845)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|metal ion binding (GO:0046872)|recombination hotspot binding (GO:0010844)|sequence-specific DNA binding (GO:0043565)	p.R587R(1)|p.R587W(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						GGAGTGTGGGCGGGGCTTTAG	0.607										HNSCC(3;0.000094)																																						2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|lung(1)											45.0	51.0	49.0					5																	23526956		2174	4277	6451	SO:0001583	missense	56979			AF275816	CCDS43307.1	5p14.2	2014-06-03			ENSG00000164256	ENSG00000164256		"""-"", ""Zinc fingers, C2H2-type"""	13994	protein-coding gene	gene with protein product	"""PR-domain containing protein 9"""	609760	"""minisatellite binding protein 3, 115kDa"", ""minisatellite binding protein 3 (115kD)"""	MSBP3		10668202, 2062643, 24634223	Standard	NM_020227		Approved	PFM6, ZNF899	uc003jgo.3	Q9NQV7	OTTHUMG00000161918	ENST00000296682.3:c.1759C>T	5.37:g.23526956C>T	ENSP00000296682:p.Arg587Trp		B4DX22|Q27Q50	Missense_Mutation	SNP	ENST00000296682.3	37	CCDS43307.1	.	.	.	.	.	.	.	.	.	.	C	11.85	1.761742	0.31228	.	.	ENSG00000164256	ENST00000296682;ENST00000253473	T	0.19806	2.12	2.31	2.31	0.28768	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.19087	0.0458	L	0.51914	1.62	0.27726	N	0.944952	B	0.34399	0.452	B	0.34779	0.189	T	0.17868	-1.0355	9	0.87932	D	0	-0.8007	6.3198	0.21211	0.295:0.7049:0.0:0.0	.	587	Q9NQV7	PRDM9_HUMAN	W	587;353	ENSP00000296682:R587W	ENSP00000253473:R353W	R	+	1	2	PRDM9	23562713	0.003000	0.15002	0.991000	0.47740	0.651000	0.38670	1.685000	0.37659	1.575000	0.49775	0.400000	0.26472	CGG		0.607	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227		45	78	45	78
TNXB	7148	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	32039776	32039776	+	Missense_Mutation	SNP	C	C	T			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr6:32039776C>T	ENST00000375244.3	-	13	5182	c.4981G>A	c.(4981-4983)Gca>Aca	p.A1661T	TNXB_ENST00000375247.2_Missense_Mutation_p.A1661T			P22105	TENX_HUMAN	tenascin XB	1743	Fibronectin type-III 9. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						CCCGTCTTTGCCTCCACAGAG	0.592																																																0													32.0	33.0	33.0					6																	32039776		1999	4170	6169	SO:0001583	missense	7148			X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.4981G>A	6.37:g.32039776C>T	ENSP00000364393:p.Ala1661Thr		P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	37		.	.	.	.	.	.	.	.	.	.	C	20.5	3.999096	0.74818	.	.	ENSG00000168477	ENST00000375244;ENST00000375247	T;T	0.55760	0.66;0.5	5.55	4.69	0.59074	.	0.494990	0.16931	N	0.193670	T	0.38665	0.1049	M	0.73962	2.25	0.25228	N	0.989853	P	0.43607	0.812	P	0.45474	0.482	T	0.33650	-0.9860	10	0.15952	T	0.53	.	11.6133	0.51074	0.0:0.9163:0.0:0.0837	.	1661	P22105-3	.	T	1661	ENSP00000364393:A1661T;ENSP00000364396:A1661T	ENSP00000364393:A1661T	A	-	1	0	TNXB	32147754	0.973000	0.33851	0.921000	0.36526	0.923000	0.55619	1.585000	0.36600	1.358000	0.45922	-0.229000	0.12294	GCA		0.592	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105		10	12	10	12
PLEKHA8	84725	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	30092391	30092391	+	Silent	SNP	C	C	T			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr7:30092391C>T	ENST00000449726.1	+	7	1055	c.705C>T	c.(703-705)atC>atT	p.I235I	PLEKHA8_ENST00000258679.7_Silent_p.I235I|PLEKHA8_ENST00000396257.2_Silent_p.I235I|PLEKHA8_ENST00000396259.1_Silent_p.I235I	NM_001197027.1	NP_001183956.1	Q96JA3	PKHA8_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 8	235					ER to Golgi ceramide transport (GO:0035621)|lipid transport (GO:0006869)|protein transport (GO:0015031)	membrane (GO:0016020)|trans-Golgi network (GO:0005802)	ceramide binding (GO:0097001)|glycolipid binding (GO:0051861)|glycolipid transporter activity (GO:0017089)|phosphatidylinositol-4-phosphate binding (GO:0070273)			breast(4)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)	17						AGGAAGAAATCCTAATGAAAA	0.308																																																0													29.0	30.0	29.0					7																	30092391		2194	4285	6479	SO:0001819	synonymous_variant	84725			BC053990	CCDS5424.1, CCDS56473.1, CCDS75574.1	7p21-p11.2	2013-01-10			ENSG00000106086	ENSG00000106086		"""Pleckstrin homology (PH) domain containing"""	30037	protein-coding gene	gene with protein product		608639				11001876	Standard	NM_001197027		Approved	FAPP2, MGC3358	uc003taq.3	Q96JA3	OTTHUMG00000097751	ENST00000449726.1:c.705C>T	7.37:g.30092391C>T			B4DH00|Q7Z5V8|Q9BU78|Q9H274|Q9H8Z7	Silent	SNP	ENST00000449726.1	37	CCDS56473.1																																																																																				0.308	PLEKHA8-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032639		21	106	21	106
ZMIZ2	83637	hgsc.bcm.edu;broad.mit.edu	37	7	44805131	44805131	+	Missense_Mutation	SNP	C	C	A			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr7:44805131C>A	ENST00000309315.4	+	16	2318	c.2195C>A	c.(2194-2196)cCc>cAc	p.P732H	ZMIZ2_ENST00000441627.1_Missense_Mutation_p.P732H|ZMIZ2_ENST00000413916.1_Missense_Mutation_p.P674H|ZMIZ2_ENST00000433667.1_Missense_Mutation_p.P700H|ZMIZ2_ENST00000265346.7_Missense_Mutation_p.P706H	NM_031449.3	NP_113637.3	Q8NF64	ZMIZ2_HUMAN	zinc finger, MIZ-type containing 2	732	Pro-rich.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|zinc ion binding (GO:0008270)			breast(3)|endometrium(2)|kidney(3)|large_intestine(6)|lung(10)|ovary(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35						CCCTTTGCCCCCCTGCAGCCC	0.687																																					NSCLC(20;604 852 1948 16908 50522)											0													9.0	11.0	10.0					7																	44805131		1883	4079	5962	SO:0001583	missense	83637			AK090415	CCDS43576.1, CCDS43577.1, CCDS75591.1	7p13	2009-11-06			ENSG00000122515	ENSG00000122515		"""Zinc fingers, MIZ-type"""	22229	protein-coding gene	gene with protein product		611196					Standard	XM_005249866		Approved	KIAA1886, hZIMP7, ZIMP7, DKFZp761I2123, NET27	uc003tlr.3	Q8NF64	OTTHUMG00000155817	ENST00000309315.4:c.2195C>A	7.37:g.44805131C>A	ENSP00000311778:p.Pro732His		A4D2K7|D3DVL1|O94790|Q0VGB4|Q659A8|Q6JKL5|Q8WTX8|Q96Q01|Q9BQH7	Missense_Mutation	SNP	ENST00000309315.4	37	CCDS43576.1	.	.	.	.	.	.	.	.	.	.	C	19.64	3.864699	0.71949	.	.	ENSG00000122515	ENST00000413916;ENST00000309315;ENST00000441627;ENST00000433667;ENST00000265346;ENST00000414051	T;T;T;T;T	0.34859	1.34;1.34;1.34;1.34;1.35	5.14	5.14	0.70334	.	0.215333	0.32593	N	0.005897	T	0.52517	0.1739	M	0.65498	2.005	0.30650	N	0.755525	P;P;D	0.59357	0.941;0.919;0.985	P;P;P	0.58970	0.849;0.764;0.849	T	0.56655	-0.7943	10	0.51188	T	0.08	-6.7181	13.3874	0.60803	0.1574:0.8426:0.0:0.0	.	706;732;674	Q8NF64-2;Q8NF64;Q8NF64-3	.;ZMIZ2_HUMAN;.	H	674;732;732;700;706;735	ENSP00000409648:P674H;ENSP00000311778:P732H;ENSP00000414723:P732H;ENSP00000396601:P700H;ENSP00000265346:P706H	ENSP00000265346:P706H	P	+	2	0	ZMIZ2	44771656	0.004000	0.15560	0.940000	0.37924	0.818000	0.46254	1.932000	0.40143	2.686000	0.91538	0.561000	0.74099	CCC		0.687	ZMIZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341790.1	NM_031449		30	13	30	13
ABCB4	5244	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	87046828	87046828	+	Missense_Mutation	SNP	T	T	C			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr7:87046828T>C	ENST00000265723.4	-	21	2593	c.2482A>G	c.(2482-2484)Aca>Gca	p.T828A	ABCB4_ENST00000358400.3_Missense_Mutation_p.T828A|ABCB4_ENST00000359206.3_Missense_Mutation_p.T828A|ABCB4_ENST00000545634.1_Missense_Mutation_p.T828A|ABCB4_ENST00000453593.1_Missense_Mutation_p.T828A	NM_000443.3|NM_018849.2	NP_000434.1|NP_061337.1	P21439	MDR3_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 4	828	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				cellular lipid metabolic process (GO:0044255)|lipid metabolic process (GO:0006629)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|xenobiotic-transporting ATPase activity (GO:0008559)			breast(5)|endometrium(7)|kidney(2)|large_intestine(15)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				Colchicine(DB01394)|Etravirine(DB06414)|Silodosin(DB06207)	CTGGTTCCTGTGGCCTGGGAG	0.428																																																0													51.0	48.0	49.0					7																	87046828		2203	4300	6503	SO:0001583	missense	5244			M23234	CCDS5605.1, CCDS5606.1, CCDS5607.1	7q21	2012-03-14			ENSG00000005471	ENSG00000005471		"""ATP binding cassette transporters / subfamily B"""	45	protein-coding gene	gene with protein product		171060		PGY3, MDR3		2892668, 11313316	Standard	NM_018850		Approved	MDR2, PFIC-3, GBD1	uc003uiv.1	P21439	OTTHUMG00000023396	ENST00000265723.4:c.2482A>G	7.37:g.87046828T>C	ENSP00000265723:p.Thr828Ala		A0A2V7|A4D1D3|A4D1D4|A4D1D5|D6W5P3|D6W5P4|Q14813	Missense_Mutation	SNP	ENST00000265723.4	37	CCDS5606.1	.	.	.	.	.	.	.	.	.	.	T	14.01	2.408435	0.42715	.	.	ENSG00000005471	ENST00000359206;ENST00000358400;ENST00000265723;ENST00000453593;ENST00000545634	D;D;D;D;D	0.89552	-2.53;-2.53;-2.53;-2.53;-2.53	5.82	5.82	0.92795	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.048377	0.85682	D	0.000000	D	0.87811	0.6271	L	0.52364	1.645	0.58432	D	0.999998	B;B;B	0.28470	0.213;0.01;0.012	B;B;B	0.35413	0.202;0.031;0.052	D	0.84909	0.0847	10	0.33940	T	0.23	-18.8014	16.1998	0.82063	0.0:0.0:0.0:1.0	.	828;828;828	A4D1D5;P21439-2;P21439	.;.;MDR3_HUMAN	A	828	ENSP00000352135:T828A;ENSP00000351172:T828A;ENSP00000265723:T828A;ENSP00000392983:T828A;ENSP00000437465:T828A	ENSP00000265723:T828A	T	-	1	0	ABCB4	86884764	1.000000	0.71417	1.000000	0.80357	0.846000	0.48090	2.848000	0.48278	2.232000	0.73038	0.528000	0.53228	ACA		0.428	ABCB4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000336083.1	NM_000443		21	43	21	43
RGAG1	57529	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	109694416	109694416	+	Missense_Mutation	SNP	T	T	C			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chrX:109694416T>C	ENST00000465301.2	+	3	817	c.571T>C	c.(571-573)Tcc>Ccc	p.S191P	RGAG1_ENST00000540313.1_Missense_Mutation_p.S191P	NM_020769.2	NP_065820.1	Q8NET4	RGAG1_HUMAN	retrotransposon gag domain containing 1	191										NS(1)|autonomic_ganglia(1)|breast(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	73						TGAGGCAATGTCCACACCATT	0.483																																																0													147.0	126.0	133.0					X																	109694416		2203	4300	6503	SO:0001583	missense	57529			AY121804	CCDS14552.1	Xq23	2008-02-05			ENSG00000243978	ENSG00000243978			29245	protein-coding gene	gene with protein product						10718198, 15716091, 16093683	Standard	NM_020769		Approved	KIAA1318, Mart9, Mar9	uc004eor.2	Q8NET4	OTTHUMG00000022196	ENST00000465301.2:c.571T>C	X.37:g.109694416T>C	ENSP00000419786:p.Ser191Pro		Q9P2M8	Missense_Mutation	SNP	ENST00000465301.2	37	CCDS14552.1	.	.	.	.	.	.	.	.	.	.	T	15.30	2.792442	0.50102	.	.	ENSG00000243978	ENST00000465301;ENST00000540313;ENST00000540483	T;T	0.52983	0.64;0.64	3.65	2.45	0.29901	.	0.000000	0.35805	N	0.002962	T	0.42154	0.1190	L	0.27053	0.805	0.24301	N	0.995129	D	0.55385	0.971	P	0.55455	0.776	T	0.15407	-1.0438	9	.	.	.	-3.4815	6.2296	0.20728	0.0:0.0:0.2565:0.7435	.	191	Q8NET4	RGAG1_HUMAN	P	191	ENSP00000419786:S191P;ENSP00000441452:S191P	.	S	+	1	0	RGAG1	109581072	0.426000	0.25506	0.955000	0.39395	0.863000	0.49368	0.424000	0.21330	0.572000	0.29383	0.486000	0.48141	TCC		0.483	RGAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057906.2	NM_020769		67	48	67	48
FAM118B	79607	broad.mit.edu;ucsc.edu	37	11	126126563	126126563	+	Silent	SNP	C	C	G			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr11:126126563C>G	ENST00000533050.1	+	7	1291	c.798C>G	c.(796-798)gtC>gtG	p.V266V	FAM118B_ENST00000529731.1_Silent_p.V190V|FAM118B_ENST00000360194.4_Silent_p.V266V	NM_024556.3	NP_078832.1	Q9BPY3	F118B_HUMAN	family with sequence similarity 118, member B	266										breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|skin(1)	13	all_hematologic(175;0.145)	Breast(109;0.00156)|Lung NSC(97;0.00948)|all_lung(97;0.0101)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0784)		TGGAGGCTGTCAAGCATAAAT	0.448																																																0													93.0	93.0	93.0					11																	126126563		2201	4299	6500	SO:0001819	synonymous_variant	79607			BC001340	CCDS8470.1	11q24.2	2014-03-13				ENSG00000197798			26110	protein-coding gene	gene with protein product						24569877	Standard	NM_024556		Approved	FLJ21103	uc001qdf.3	Q9BPY3		ENST00000533050.1:c.798C>G	11.37:g.126126563C>G			Q9H7B0	Silent	SNP	ENST00000533050.1	37	CCDS8470.1																																																																																				0.448	FAM118B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386346.1	NM_024556		39	52	39	52
CSMD3	114788	broad.mit.edu;ucsc.edu	37	8	113304784	113304784	+	Missense_Mutation	SNP	G	G	A			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr8:113304784G>A	ENST00000297405.5	-	55	9014	c.8770C>T	c.(8770-8772)Cct>Tct	p.P2924S	CSMD3_ENST00000455883.2_Missense_Mutation_p.P2755S|CSMD3_ENST00000343508.3_Missense_Mutation_p.P2884S|CSMD3_ENST00000352409.3_Missense_Mutation_p.P2854S	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2924	Sushi 19. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.P2924T(1)		breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						ATAGGTGGAGGATGGCTCCAC	0.403										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																																						1	Substitution - Missense(1)	lung(1)											194.0	173.0	180.0					8																	113304784		2203	4300	6503	SO:0001583	missense	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.8770C>T	8.37:g.113304784G>A	ENSP00000297405:p.Pro2924Ser		Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	G	18.18	3.567044	0.65651	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.64260	-0.09;-0.09;-0.09;-0.09;-0.09	5.76	5.76	0.90799	Complement control module (2);Sushi/SCR/CCP (3);	0.162866	0.41938	D	0.000793	T	0.65281	0.2676	L	0.33792	1.035	0.58432	D	0.999992	P;P;D	0.61697	0.837;0.775;0.99	P;P;P	0.60682	0.476;0.61;0.878	T	0.57814	-0.7746	10	0.16420	T	0.52	.	15.0958	0.72232	0.0696:0.0:0.9304:0.0	.	2755;2924;2884	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	S	2884;2924;2194;2755;2854	ENSP00000345799:P2884S;ENSP00000297405:P2924S;ENSP00000341558:P2194S;ENSP00000412263:P2755S;ENSP00000343124:P2854S	ENSP00000297405:P2924S	P	-	1	0	CSMD3	113373960	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.797000	0.75150	2.724000	0.93272	0.650000	0.86243	CCT		0.403	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		59	243	59	243
KRT20	54474	broad.mit.edu;hgsc.bcm.edu	37	17	39034595	39034596	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr17:39034595_39034596delAG	ENST00000167588.3	-	6	981_982	c.940_941delCT	c.(940-942)ctafs	p.L314fs		NM_019010.2	NP_061883.1	P35900	K1C20_HUMAN	keratin 20	314	Coil 2.|Rod.				apoptotic process (GO:0006915)|cellular response to stress (GO:0033554)|intermediate filament organization (GO:0045109)|regulation of protein secretion (GO:0050708)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)	structural constituent of cytoskeleton (GO:0005200)			NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|skin(1)	14		Breast(137;0.000301)|Ovarian(249;0.15)				GGTCTCCTCTAGAGTGTGCTCC	0.46																																																0																																										SO:0001589	frameshift_variant	54474			BC031559	CCDS11379.1	17q21.2	2013-01-16			ENSG00000171431	ENSG00000171431		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	20412	protein-coding gene	gene with protein product		608218				8359595, 12515621, 16831889	Standard	NM_019010		Approved	CK20, K20, MGC35423	uc002hvl.3	P35900	OTTHUMG00000133366	ENST00000167588.3:c.940_941delCT	17.37:g.39034597_39034598delAG	ENSP00000167588:p.Leu314fs		B2R6W7	Frame_Shift_Del	DEL	ENST00000167588.3	37	CCDS11379.1																																																																																				0.460	KRT20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257202.2			30	86	30	86
