#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_BAM_File	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_EVS_AA	i_EVS_All	i_EVS_EA	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_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains_WU	i_amino_acid_change_WU	i_annotation_transcript	i_build	i_c_position_WU	i_ccds_id	i_chromosome_name_WU	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_default_gene_name_WU	i_deletion_substructures_WU	i_domain_WU	i_ensembl_gene_id	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_name_WU	i_gene_name_source_WU	i_gene_type	i_havana_transcript	i_normal_ref_reads	i_normal_vaf	i_normal_var_reads	i_reference_WU	i_refseq_mrna_id	i_secondary_variant_classification	i_start_WU	i_stop_WU	i_strand_WU	i_transcript_error_WU	i_transcript_name_WU	i_transcript_source_WU	i_transcript_species_WU	i_transcript_status_WU	i_transcript_version_WU	i_trv_type_WU	i_tumor_ref_reads	i_tumor_vaf	i_tumors_var_reads	i_type_WU	i_ucsc_cons_WU	i_variant_WU
ACTG1	71	genome.wustl.edu	37	17	79478213	79478215	+	Splice_Site	DEL	CCC	CCC	-	rs200506997		TCGA-A8-A09T-01A-11W-A019-09	TCGA-A8-A09T-10A-01W-A021-09	CCC	CCC					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	e565da2b-4a3f-4be1-9cf7-2845145d1dbc	8c267083-4672-4f9e-b5ec-19a13e897f78	g.chr17:79478213_79478215delCCC	ENST00000575842.1	-	3	1227_1229	c.801_803delGGG	c.(799-804)ctgggt>ctt	p.G268del	AC139149.1_ENST00000584254.1_RNA|ACTG1_ENST00000331925.2_Splice_Site_p.G268del|ACTG1_ENST00000575087.1_Splice_Site_p.G268del|ACTG1_ENST00000573283.1_Splice_Site_p.G268del|RP13-766D20.2_ENST00000430912.1_RNA			P63261	ACTG_HUMAN	actin, gamma 1	268					adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|platelet aggregation (GO:0070527)|retina homeostasis (GO:0001895)|sarcomere organization (GO:0045214)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|membrane (GO:0016020)|myofibril (GO:0030016)|nucleus (GO:0005634)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|lung(8)|ovary(2)|prostate(5)|urinary_tract(1)	29	all_neural(118;0.0878)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0547)			ACAACACCTACCCAGGAAGGAAG	0.557																																						dbGAP											0																																										-	-	-	SO:0001630	splice_region_variant	0				CCDS11782.1	17q25	2010-04-23	2004-05-19		ENSG00000184009	ENSG00000184009			144	protein-coding gene	gene with protein product		102560	"""deafness, autosomal dominant 20; deafness, autosomal dominant 26"""	ACTG, DFNA20, DFNA26		14684684	Standard	NM_001614		Approved		uc002kal.2	P63261		ENST00000575842.1:c.802+1GGG>-	17.37:g.79478213_79478215delCCC		Somatic		WXS	Illumina GAIIx	Phase_IV	A8K7C2|P02571|P14104|P99022|Q5U032|Q96E67	Splice_Site	DEL	-	e4-1	ENST00000575842.1	37	c.802+3_802+1	CCDS11782.1	17																																																																																			ACTG1	-	-	ENSG00000184009		0.557	ACTG1-012	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	ACTG1	HGNC	protein_coding	OTTHUMT00000439935.2	26	0.00	0	CCC	NM_001614	In_Frame_Del	79478213	79478215	-1	no_errors	ENST00000331925	ensembl	human	known	69_37n	splice_site_del	12	33.33	6	DEL	1.000:1.000:0.986	-
ANKRD34B	340120	genome.wustl.edu	37	5	79855031	79855031	+	Missense_Mutation	SNP	C	C	A			TCGA-A8-A09T-01A-11W-A019-09	TCGA-A8-A09T-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	e565da2b-4a3f-4be1-9cf7-2845145d1dbc	8c267083-4672-4f9e-b5ec-19a13e897f78	g.chr5:79855031C>A	ENST00000338682.3	-	5	1480	c.808G>T	c.(808-810)Gat>Tat	p.D270Y		NM_001004441.2	NP_001004441.2	A5PLL1	AN34B_HUMAN	ankyrin repeat domain 34B	270						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(13)|pancreas(1)|prostate(1)|urinary_tract(1)	28		Lung NSC(167;0.0427)|all_lung(232;0.0464)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;2.17e-46)|Epithelial(54;5.64e-41)|all cancers(79;3.24e-36)		GGTGTAATATCCTGGAGCTCC	0.507																																						dbGAP											0													56.0	60.0	59.0					5																	79855031		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS34194.1	5q14.1	2014-08-12			ENSG00000189127	ENSG00000189127		"""Ankyrin repeat domain containing"""	33736	protein-coding gene	gene with protein product							Standard	NM_001004441		Approved	DP58	uc003kgw.3	A5PLL1	OTTHUMG00000162541	ENST00000338682.3:c.808G>T	5.37:g.79855031C>A	ENSP00000339802:p.Asp270Tyr	Somatic		WXS	Illumina GAIIx	Phase_IV	B2RPH1|Q68D79	Missense_Mutation	SNP	pfam_Ankyrin_rpt,superfamily_Ankyrin_rpt-contain_dom,smart_Ankyrin_rpt,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom	p.D270Y	ENST00000338682.3	37	c.808	CCDS34194.1	5	.	.	.	.	.	.	.	.	.	.	C	16.68	3.191569	0.58017	.	.	ENSG00000189127	ENST00000338682	T	0.21932	1.98	5.96	5.96	0.96718	.	0.070917	0.52532	D	0.000069	T	0.37073	0.0990	M	0.67953	2.075	0.53005	D	0.999964	D	0.60575	0.988	P	0.54664	0.758	T	0.01795	-1.1272	10	0.37606	T	0.19	-16.1169	14.7035	0.69171	0.1455:0.8545:0.0:0.0	.	270	A5PLL1	AN34B_HUMAN	Y	270	ENSP00000339802:D270Y	ENSP00000339802:D270Y	D	-	1	0	ANKRD34B	79890787	0.985000	0.35326	0.948000	0.38648	0.980000	0.70556	0.912000	0.28597	2.832000	0.97577	0.655000	0.94253	GAT	ANKRD34B	-	NULL	ENSG00000189127		0.507	ANKRD34B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ANKRD34B	HGNC	protein_coding	OTTHUMT00000369475.1	114	0.00	0	C	NM_001004441		79855031	79855031	-1	no_errors	ENST00000338682	ensembl	human	known	69_37n	missense	85	34.11	44	SNP	0.998	A
APOBR	55911	genome.wustl.edu	37	16	28507424	28507424	+	Intron	SNP	C	C	T	rs148114931|rs441214	byFrequency	TCGA-A8-A09T-01A-11W-A019-09	TCGA-A8-A09T-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	e565da2b-4a3f-4be1-9cf7-2845145d1dbc	8c267083-4672-4f9e-b5ec-19a13e897f78	g.chr16:28507424C>T	ENST00000431282.1	+	3	1058				APOBR_ENST00000328423.5_Intron|APOBR_ENST00000564831.1_Silent_p.A354A|CLN3_ENST00000567160.1_5'Flank|CLN3_ENST00000569430.1_5'Flank			Q0VD83	APOBR_HUMAN	apolipoprotein B receptor						cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|triglyceride metabolic process (GO:0006641)	chylomicron (GO:0042627)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	very-low-density lipoprotein particle receptor activity (GO:0030229)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(11)|prostate(1)|skin(2)|stomach(1)	29						GGGAGGAGGCCGGGACAGCCT	0.711																																						dbGAP											0													8.0	11.0	10.0					16																	28507424		1858	4004	5862	-	-	-	SO:0001627	intron_variant	0			AK025123	CCDS58442.1	16p11.2	2011-02-14			ENSG00000184730	ENSG00000184730			24087	protein-coding gene	gene with protein product	"""apolipoprotein B48 receptor"", ""apolipoprotein B100 receptor"""	605220				10852956	Standard	NM_018690		Approved	APOB48R, APOB100R	uc002dqb.2	Q0VD83		ENST00000431282.1:c.1049-14C>T	16.37:g.28507424C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	H3BU97|Q0VD81|Q8NC15|Q9NPJ9	Silent	SNP	NULL	p.A354	ENST00000431282.1	37	c.1062		16																																																																																			APOBR	-	NULL	ENSG00000184730		0.711	APOBR-202	KNOWN	basic|appris_candidate	protein_coding	APOBR	HGNC	protein_coding		9	0.00	0	C	NM_182804		28507424	28507424	+1	no_errors	ENST00000564831	ensembl	human	known	69_37n	silent	25	28.57	10	SNP	0.000	T
ARHGAP33	115703	genome.wustl.edu	37	19	36279197	36279198	+	Frame_Shift_Ins	INS	-	-	G			TCGA-A8-A09T-01A-11W-A019-09	TCGA-A8-A09T-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	e565da2b-4a3f-4be1-9cf7-2845145d1dbc	8c267083-4672-4f9e-b5ec-19a13e897f78	g.chr19:36279197_36279198insG	ENST00000007510.4	+	21	3874_3875	c.3730_3731insG	c.(3730-3732)aggfs	p.R1244fs	AC002398.5_ENST00000433059.1_lincRNA|ARHGAP33_ENST00000378944.5_Frame_Shift_Ins_p.R1080fs|ARHGAP33_ENST00000314737.5_Frame_Shift_Ins_p.R1083fs			O14559	RHG33_HUMAN	Rho GTPase activating protein 33	1244					protein transport (GO:0015031)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|Rac GTPase activator activity (GO:0030675)			endometrium(7)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	37						AGCCTACGGAAGGGGGGGCGAG	0.698																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AY044864	CCDS12477.1, CCDS54254.1	19q13.13	2011-06-29	2010-02-19	2010-02-19		ENSG00000004777		"""Rho GTPase activating proteins"""	23085	protein-coding gene	gene with protein product		614902	"""sorting nexin 26"""	SNX26		12297274, 12461558	Standard	NM_052948		Approved	FLJ39019, TCGAP	uc002obs.2	O14559		ENST00000007510.4:c.3737dupG	19.37:g.36279204_36279204dupG	ENSP00000007510:p.Arg1244fs	Somatic		WXS	Illumina GAIIx	Phase_IV	O14552|O14560|Q6ZSP6|Q96CP3|Q9NT23	Frame_Shift_Ins	INS	pfam_RhoGAP_dom,pfam_SH3_2,pfam_SH3_domain,superfamily_Rho_GTPase_activation_prot,superfamily_SH3_domain,superfamily_Phox,smart_SH3_domain,smart_RhoGAP_dom,pfscan_SH3_domain,pfscan_RhoGAP_dom	p.E1247fs	ENST00000007510.4	37	c.3730_3731		19																																																																																			ARHGAP33	-	NULL	ENSG00000004777		0.698	ARHGAP33-201	KNOWN	basic	protein_coding	ARHGAP33	HGNC	protein_coding		10	0.00	0	-	NM_052948		36279197	36279198	+1	no_errors	ENST00000007510	ensembl	human	known	69_37n	frame_shift_ins	3	40.00	2	INS	0.606:0.488	G
ATAD5	79915	genome.wustl.edu	37	17	29221047	29221047	+	Missense_Mutation	SNP	A	A	G			TCGA-A8-A09T-01A-11W-A019-09	TCGA-A8-A09T-10A-01W-A021-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	e565da2b-4a3f-4be1-9cf7-2845145d1dbc	8c267083-4672-4f9e-b5ec-19a13e897f78	g.chr17:29221047A>G	ENST00000321990.4	+	21	5554	c.5176A>G	c.(5176-5178)Aaa>Gaa	p.K1726E		NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	1726					cellular response to DNA damage stimulus (GO:0006974)	nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(18)|lung(13)|ovary(3)|pancreas(1)	51		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				TGCTATTTCAAAAGCATTGGA	0.363																																						dbGAP											0													60.0	62.0	62.0					17																	29221047		2203	4299	6502	-	-	-	SO:0001583	missense	0				CCDS11260.1	17q11.2	2010-04-21	2007-02-08	2007-02-08	ENSG00000176208	ENSG00000176208		"""ATPases / AAA-type"""	25752	protein-coding gene	gene with protein product	"""enhanced level of genomic instability 1 homolog (S. cerevisiae)"""	609534	"""chromosome 17 open reading frame 41"""	C17orf41		15983387, 11468690, 19755857	Standard	NM_024857		Approved	FLJ12735, FRAG1, ELG1	uc002hfs.1	Q96QE3	OTTHUMG00000132794	ENST00000321990.4:c.5176A>G	17.37:g.29221047A>G	ENSP00000313171:p.Lys1726Glu	Somatic		WXS	Illumina GAIIx	Phase_IV	Q05DH0|Q69YR6|Q9H9I1	Missense_Mutation	SNP	pfam_ATPase_AAA_core,smart_AAA+_ATPase	p.K1726E	ENST00000321990.4	37	c.5176	CCDS11260.1	17	.	.	.	.	.	.	.	.	.	.	A	11.92	1.781263	0.31502	.	.	ENSG00000176208	ENST00000321990	T	0.07800	3.16	6.08	4.95	0.65309	.	0.399966	0.31577	N	0.007409	T	0.10637	0.0260	M	0.62723	1.935	0.27016	N	0.964587	B	0.32071	0.355	B	0.24974	0.057	T	0.10706	-1.0618	10	0.66056	D	0.02	.	12.7809	0.57476	0.7522:0.2478:0.0:0.0	.	1726	Q96QE3	ATAD5_HUMAN	E	1726	ENSP00000313171:K1726E	ENSP00000313171:K1726E	K	+	1	0	ATAD5	26245173	0.995000	0.38212	1.000000	0.80357	0.919000	0.55068	1.565000	0.36386	2.333000	0.79357	0.482000	0.46254	AAA	ATAD5	-	NULL	ENSG00000176208		0.363	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ATAD5	HGNC	protein_coding	OTTHUMT00000256206.2	95	0.00	0	A	NM_024857		29221047	29221047	+1	no_errors	ENST00000321990	ensembl	human	known	69_37n	missense	82	36.92	48	SNP	0.997	G
CDH1	999	genome.wustl.edu	37	16	68835780	68835781	+	Frame_Shift_Ins	INS	-	-	C	rs115418995		TCGA-A8-A09T-01A-11W-A019-09	TCGA-A8-A09T-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	e565da2b-4a3f-4be1-9cf7-2845145d1dbc	8c267083-4672-4f9e-b5ec-19a13e897f78	g.chr16:68835780_68835781insC	ENST00000261769.5	+	3	562_563	c.371_372insC	c.(370-375)cgccccfs	p.RP124fs	CDH1_ENST00000422392.2_Frame_Shift_Ins_p.RP124fs|CDH1_ENST00000562836.1_3'UTR	NM_004360.3	NP_004351.1	P12830	CADH1_HUMAN	cadherin 1, type 1, E-cadherin (epithelial)	124					adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to amino acid stimulus (GO:0071230)|cellular response to indole-3-methanol (GO:0071681)|cellular response to lithium ion (GO:0071285)|cochlea development (GO:0090102)|epithelial cell morphogenesis (GO:0003382)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|homophilic cell adhesion (GO:0007156)|intestinal epithelial cell development (GO:0060576)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of epithelial cell proliferation (GO:0050680)|neuron projection development (GO:0031175)|pituitary gland development (GO:0021983)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|protein metabolic process (GO:0019538)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of immune response (GO:0050776)|regulation of neuron migration (GO:2001222)|regulation of protein localization to cell surface (GO:2000008)|regulation of water loss via skin (GO:0033561)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)|salivary gland cavitation (GO:0060662)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|tight junction assembly (GO:0070830)|trophectodermal cell differentiation (GO:0001829)	actin cytoskeleton (GO:0015629)|aggresome (GO:0016235)|apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|axon terminus (GO:0043679)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell junction (GO:0030054)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|node of Ranvier (GO:0033268)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|trans-Golgi network (GO:0005802)	ankyrin binding (GO:0030506)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|gamma-catenin binding (GO:0045295)|glycoprotein binding (GO:0001948)|GTPase activating protein binding (GO:0032794)	p.?(2)|p.P126fs*89(1)|p.P127fs*41(1)		NS(6)|biliary_tract(8)|breast(161)|central_nervous_system(4)|endometrium(9)|kidney(4)|large_intestine(13)|lung(13)|oesophagus(3)|ovary(2)|prostate(3)|soft_tissue(2)|stomach(76)|thyroid(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	311		all_neural(199;0.0189)|Ovarian(137;0.0563)		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)		CACCACCACCGCCCCCCGCCCC	0.5			"""Mis, N, F, S"""		"""lobular breast, gastric"""	gastric			Hereditary Diffuse Gastric Cancer																													dbGAP	yes	Rec	yes	Familial gastric carcinoma	16	16q22.1	999	"""cadherin 1, type 1, E-cadherin (epithelial) (ECAD)"""		E	4	Unknown(2)|Insertion - Frameshift(1)|Deletion - Frameshift(1)	breast(4)																																								-	-	-	SO:0001589	frameshift_variant	0	Familial Cancer Database	HDGC	L08599	CCDS10869.1	16q22.1	2014-09-17			ENSG00000039068	ENSG00000039068		"""CD molecules"", ""Cadherins / Major cadherins"""	1748	protein-coding gene	gene with protein product	"""E-Cadherin"""	192090		UVO		9925936	Standard	NM_004360		Approved	uvomorulin, CD324	uc002ewg.1	P12830	OTTHUMG00000137561	ENST00000261769.5:c.377dupC	16.37:g.68835786_68835786dupC	ENSP00000261769:p.Arg124fs	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K1U7|Q13799|Q14216|Q15855|Q16194|Q4PJ14|Q9UII8	Frame_Shift_Ins	INS	pfam_Cadherin,pfam_Cadherin_cytoplasmic-dom,pfam_Cadherin_pro_dom,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin,prints_Cadherin	p.P127fs	ENST00000261769.5	37	c.371_372	CCDS10869.1	16																																																																																			CDH1	-	superfamily_Cadherin-like	ENSG00000039068		0.500	CDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CDH1	HGNC	protein_coding	OTTHUMT00000268897.2	75	0.00	0	-	NM_004360		68835780	68835781	+1	no_errors	ENST00000261769	ensembl	human	known	69_37n	frame_shift_ins	66	32.65	32	INS	0.005:0.015	C
COL4A2	1284	genome.wustl.edu	37	13	111156284	111156284	+	Missense_Mutation	SNP	G	G	A			TCGA-A8-A09T-01A-11W-A019-09	TCGA-A8-A09T-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	e565da2b-4a3f-4be1-9cf7-2845145d1dbc	8c267083-4672-4f9e-b5ec-19a13e897f78	g.chr13:111156284G>A	ENST00000360467.5	+	44	4535	c.4229G>A	c.(4228-4230)cGa>cAa	p.R1410Q	COL4A2-AS1_ENST00000417970.2_RNA	NM_001846.2	NP_001837.2	P08572	CO4A2_HUMAN	collagen, type IV, alpha 2	1410	Triple-helical region.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of angiogenesis (GO:0016525)|transcription, DNA-templated (GO:0006351)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	extracellular matrix structural constituent (GO:0005201)			NS(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|liver(2)|lung(48)|ovary(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	80	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)			CAGGGGAGGCGAGGCCCCCCT	0.731																																						dbGAP											0													26.0	29.0	28.0					13																	111156284		1790	4054	5844	-	-	-	SO:0001583	missense	0			AK025912	CCDS41907.1	13q34	2013-09-05			ENSG00000134871	ENSG00000134871		"""Collagens"""	2203	protein-coding gene	gene with protein product	"""canstatin"", ""collagen type IV alpha 2"""	120090				2439508, 3025878	Standard	NM_001846		Approved	FLJ22259, DKFZp686I14213	uc001vqx.3	P08572	OTTHUMG00000017344	ENST00000360467.5:c.4229G>A	13.37:g.111156284G>A	ENSP00000353654:p.Arg1410Gln	Somatic		WXS	Illumina GAIIx	Phase_IV	Q14052|Q548C3|Q5VZA9|Q66K23	Missense_Mutation	SNP	pfam_Collagen,pfam_Collagen_VI_NC,superfamily_C-type_lectin_fold,smart_Collagen_VI_NC	p.R1410Q	ENST00000360467.5	37	c.4229	CCDS41907.1	13	.	.	.	.	.	.	.	.	.	.	G	3.583	-0.085247	0.07097	.	.	ENSG00000134871	ENST00000360467;ENST00000257309	D	0.90788	-2.73	5.2	3.46	0.39613	.	0.516058	0.18184	N	0.149049	T	0.74703	0.3751	N	0.05467	-0.045	0.18873	N	0.999989	P	0.34837	0.472	B	0.34824	0.19	T	0.64351	-0.6428	10	0.11794	T	0.64	.	3.0877	0.06283	0.1583:0.1393:0.5588:0.1436	.	1410	P08572	CO4A2_HUMAN	Q	1410	ENSP00000353654:R1410Q	ENSP00000257309:R1410Q	R	+	2	0	COL4A2	109954285	0.079000	0.21365	0.992000	0.48379	0.418000	0.31294	0.248000	0.18198	1.192000	0.43071	0.561000	0.74099	CGA	COL4A2	-	pfam_Collagen	ENSG00000134871		0.731	COL4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	COL4A2	HGNC	protein_coding	OTTHUMT00000045761.2	12	0.00	0	G	NM_001846		111156284	111156284	+1	no_errors	ENST00000360467	ensembl	human	known	69_37n	missense	12	25.00	4	SNP	0.352	A
COL7A1	1294	genome.wustl.edu	37	3	48612280	48612280	+	Missense_Mutation	SNP	C	C	A			TCGA-A8-A09T-01A-11W-A019-09	TCGA-A8-A09T-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	e565da2b-4a3f-4be1-9cf7-2845145d1dbc	8c267083-4672-4f9e-b5ec-19a13e897f78	g.chr3:48612280C>A	ENST00000328333.8	-	76	6405	c.6298G>T	c.(6298-6300)Ggt>Tgt	p.G2100C	COL7A1_ENST00000454817.1_Missense_Mutation_p.G2068C	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	2100	Triple-helical region.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen type VII trimer (GO:0005590)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(3)|breast(8)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(57)|ovary(7)|prostate(5)|skin(9)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	137				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		AGTCCAGGACCTGGCTCATCC	0.567																																						dbGAP											0													45.0	43.0	44.0					3																	48612280		2203	4300	6503	-	-	-	SO:0001583	missense	0			L02870	CCDS2773.1	3p21.1	2014-09-17	2008-08-01		ENSG00000114270	ENSG00000114270		"""Collagens"", ""Fibronectin type III domain containing"""	2214	protein-coding gene	gene with protein product	"""collagen VII, alpha-1 polypeptide"", ""LC collagen"""	120120	"""epidermolysis bullosa, dystrophic, dominant and recessive"""	EBDCT, EBD1, EBR1		1871109	Standard	NM_000094		Approved		uc003ctz.2	Q02388	OTTHUMG00000133541	ENST00000328333.8:c.6298G>T	3.37:g.48612280C>A	ENSP00000332371:p.Gly2100Cys	Somatic		WXS	Illumina GAIIx	Phase_IV	Q14054|Q16507	Missense_Mutation	SNP	pfam_Collagen,pfam_Fibronectin_type3,pfam_VWF_A,pfam_Prot_inh_Kunz-m,superfamily_Fibronectin_type3,superfamily_Prot_inh_Kunz-m,smart_VWF_A,smart_Fibronectin_type3,pfscan_Fibronectin_type3,pfscan_VWF_A,pfscan_Prot_inh_Kunz-m,prints_Prot_inh_Kunz-m	p.G2100C	ENST00000328333.8	37	c.6298	CCDS2773.1	3	.	.	.	.	.	.	.	.	.	.	C	10.56	1.384057	0.25031	.	.	ENSG00000114270	ENST00000328333;ENST00000454817	D;D	0.97976	-4.64;-4.64	4.95	4.0	0.46444	.	0.000000	0.41097	D	0.000951	D	0.96420	0.8832	N	0.14661	0.345	0.32034	N	0.5992	D	0.76494	0.999	D	0.70487	0.969	D	0.95084	0.8216	10	0.52906	T	0.07	.	11.8329	0.52305	0.1745:0.8255:0.0:0.0	.	2100	Q02388	CO7A1_HUMAN	C	2100;2068	ENSP00000332371:G2100C;ENSP00000412569:G2068C	ENSP00000332371:G2100C	G	-	1	0	COL7A1	48587284	0.001000	0.12720	0.130000	0.21974	0.050000	0.14768	0.727000	0.25999	2.451000	0.82905	0.462000	0.41574	GGT	COL7A1	-	NULL	ENSG00000114270		0.567	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	COL7A1	HGNC	protein_coding	OTTHUMT00000257519.1	22	0.00	0	C	NM_000094		48612280	48612280	-1	no_errors	ENST00000328333	ensembl	human	known	69_37n	missense	17	43.33	13	SNP	0.720	A
CSNK2A2	1459	genome.wustl.edu	37	16	58200581	58200581	+	Missense_Mutation	SNP	C	C	G			TCGA-A8-A09T-01A-11W-A019-09	TCGA-A8-A09T-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	e565da2b-4a3f-4be1-9cf7-2845145d1dbc	8c267083-4672-4f9e-b5ec-19a13e897f78	g.chr16:58200581C>G	ENST00000262506.3	-	9	917	c.734G>C	c.(733-735)cGc>cCc	p.R245P	CSNK2A2_ENST00000566813.1_5'UTR	NM_001896.2	NP_001887.1	P19784	CSK22_HUMAN	casein kinase 2, alpha prime polypeptide	245	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|mitotic cell cycle (GO:0000278)|mitotic spindle checkpoint (GO:0071174)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)	1						CTTGGCAATGCGAACAAGCTG	0.453																																					Melanoma(54;119 1219 18349 35700 39738)	dbGAP											0													184.0	155.0	165.0					16																	58200581		2198	4300	6498	-	-	-	SO:0001583	missense	0			M55268	CCDS10794.1	16q21	2013-01-17			ENSG00000070770	ENSG00000070770			2459	protein-coding gene	gene with protein product		115442				2174700, 1766873	Standard	NM_001896		Approved	CSNK2A1	uc002enc.3	P19784	OTTHUMG00000133488	ENST00000262506.3:c.734G>C	16.37:g.58200581C>G	ENSP00000262506:p.Arg245Pro	Somatic		WXS	Illumina GAIIx	Phase_IV		Missense_Mutation	SNP	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Aminoglycoside_PTrfase,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_cat_dom	p.R245P	ENST00000262506.3	37	c.734	CCDS10794.1	16	.	.	.	.	.	.	.	.	.	.	C	16.46	3.130771	0.56828	.	.	ENSG00000070770	ENST00000262506	T	0.66460	-0.21	6.16	6.16	0.99307	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.85053	0.5609	M	0.87900	2.915	0.80722	D	1	D	0.71674	0.998	D	0.73380	0.98	D	0.86086	0.1547	10	0.87932	D	0	-19.2124	19.848	0.96722	0.0:1.0:0.0:0.0	.	245	P19784	CSK22_HUMAN	P	245	ENSP00000262506:R245P	ENSP00000262506:R245P	R	-	2	0	CSNK2A2	56758082	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.937000	0.99478	0.650000	0.86243	CGC	CSNK2A2	-	pfam_Prot_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_cat_dom	ENSG00000070770		0.453	CSNK2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CSNK2A2	HGNC	protein_coding	OTTHUMT00000257386.2	134	0.00	0	C	NM_001896		58200581	58200581	-1	no_errors	ENST00000262506	ensembl	human	known	69_37n	missense	48	51.52	51	SNP	1.000	G
CYFIP1	23191	genome.wustl.edu	37	15	23000246	23000246	+	Intron	SNP	A	A	G			TCGA-A8-A09T-01A-11W-A019-09	TCGA-A8-A09T-10A-01W-A021-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	e565da2b-4a3f-4be1-9cf7-2845145d1dbc	8c267083-4672-4f9e-b5ec-19a13e897f78	g.chr15:23000246A>G	ENST00000313077.7	+	30	3722				CYFIP1_ENST00000560848.1_Intron|CYFIP1_ENST00000435939.2_Intron	NM_014608.2	NP_055423.1			cytoplasmic FMR1 interacting protein 1											endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|liver(1)|lung(14)|ovary(4)|pancreas(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	40		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.22e-06)|Epithelial(43;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00101)		AAAATGTGGTATGTGGATGAA	0.393																																						dbGAP											0													104.0	92.0	96.0					15																	23000246		2203	4300	6503	-	-	-	SO:0001627	intron_variant	0			D38549	CCDS73695.1, CCDS73696.1	15q11	2008-07-18			ENSG00000068793	ENSG00000273749			13759	protein-coding gene	gene with protein product	"""selective hybridizing clone"", ""cytoplasmic FMRP interacting protein 1"""	606322				11438699	Standard	XM_005272543		Approved	KIAA0068, P140SRA-1, SHYC	uc001yus.3	Q7L576	OTTHUMG00000129100	ENST00000313077.7:c.3597+3A>G	15.37:g.23000246A>G		Somatic		WXS	Illumina GAIIx	Phase_IV		Silent	SNP	pfam_Cytoplasmic_FMR1-int,prints_Cytoplasmic_FMR1-int	p.V174	ENST00000313077.7	37	c.522	CCDS10009.1	15																																																																																			CYFIP1	-	NULL	ENSG00000068793		0.393	CYFIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CYFIP1	HGNC	protein_coding	OTTHUMT00000251136.2	119	0.00	0	A	NM_014608		23000246	23000246	+1	no_start_codon	ENST00000561263	ensembl	human	putative	69_37n	silent	75	30.56	33	SNP	1.000	G
GNAS	2778	genome.wustl.edu	37	20	57484420	57484420	+	Missense_Mutation	SNP	C	C	T	rs11554273		TCGA-A8-A09T-01A-11W-A019-09	TCGA-A8-A09T-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	e565da2b-4a3f-4be1-9cf7-2845145d1dbc	8c267083-4672-4f9e-b5ec-19a13e897f78	g.chr20:57484420C>T	ENST00000371085.3	+	8	1025	c.601C>T	c.(601-603)Cgt>Tgt	p.R201C	GNAS_ENST00000371100.4_Missense_Mutation_p.R844C|GNAS_ENST00000313949.7_3'UTR|GNAS_ENST00000306090.10_Missense_Mutation_p.R187C|GNAS_ENST00000265620.7_Missense_Mutation_p.R186C|GNAS_ENST00000354359.7_Missense_Mutation_p.R202C|GNAS_ENST00000371075.3_3'UTR|GNAS_ENST00000371102.4_Missense_Mutation_p.R830C|GNAS_ENST00000464624.2_3'UTR|GNAS_ENST00000371095.3_Missense_Mutation_p.R187C	NM_000516.4	NP_000507.1	P63092	GNAS2_HUMAN	GNAS complex locus	201			R -> C (in MAS and somatotrophinoma; dbSNP:rs11554273). {ECO:0000269|PubMed:1944469, ECO:0000269|PubMed:2549426}.|R -> G (in MAS). {ECO:0000269|PubMed:10571700}.|R -> H (in MAS, somatotrophinoma and AIMAH1). {ECO:0000269|PubMed:12727968, ECO:0000269|PubMed:1594625, ECO:0000269|PubMed:1944469, ECO:0000269|PubMed:2549426}.|R -> L (in non-MAS endocrine tumors). {ECO:0000269|PubMed:7751320}.|R -> S (in AIMAH1, pituitary tumor and polyostotic fibrous dysplasia). {ECO:0000269|PubMed:12727968, ECO:0000269|PubMed:8766942, ECO:0000269|PubMed:9267696}.		activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|bone development (GO:0060348)|cAMP biosynthetic process (GO:0006171)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|cognition (GO:0050890)|developmental growth (GO:0048589)|energy reserve metabolic process (GO:0006112)|hair follicle placode formation (GO:0060789)|intracellular transport (GO:0046907)|platelet aggregation (GO:0070527)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of insulin secretion (GO:0050796)|sensory perception of smell (GO:0007608)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|intrinsic component of membrane (GO:0031224)|membrane (GO:0016020)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	adenylate cyclase activity (GO:0004016)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)	p.R201C(228)|p.R844C(9)|p.R201S(5)		adrenal_gland(12)|autonomic_ganglia(1)|biliary_tract(5)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(37)|liver(9)|lung(9)|ovary(16)|pancreas(56)|parathyroid(5)|pituitary(228)|prostate(2)|small_intestine(1)|stomach(1)|testis(2)|thyroid(35)|upper_aerodigestive_tract(3)|urinary_tract(1)	441	all_lung(29;0.0104)		BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109)			GCTTCGCTGCCGTGTCCTGAC	0.428			Mis		pituitary adenoma		"""McCune-Albright syndrome; pseudohypoparathyroidism, type IA"""			TSP Lung(22;0.16)																											Colon(117;935 1597 6045 8307 46442)	dbGAP		Dom	yes		20	20q13.2	2778	"""guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"""	yes	E	242	Substitution - Missense(242)	pituitary(141)|pancreas(35)|large_intestine(14)|ovary(12)|thyroid(10)|adrenal_gland(7)|biliary_tract(6)|parathyroid(5)|liver(3)|kidney(3)|testis(2)|upper_aerodigestive_tract(2)|autonomic_ganglia(1)|haematopoietic_and_lymphoid_tissue(1)											80.0	78.0	79.0					20																	57484420		2203	4300	6503	-	-	-	SO:0001583	missense	0			M21142	CCDS13471.1, CCDS13472.1, CCDS42892.1, CCDS46622.1, CCDS46623.1, CCDS46624.1	20q13.2-q13.3	2010-03-01	2001-12-19	2001-12-20	ENSG00000087460	ENSG00000087460			4392	protein-coding gene	gene with protein product	"""secretogranin VI"""	139320	"""guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"""	GNAS1			Standard	NM_000516		Approved	NESP55, NESP, GNASXL, GPSA, SCG6	uc002xzw.3	O95467	OTTHUMG00000033069	ENST00000371085.3:c.601C>T	20.37:g.57484420C>T	ENSP00000360126:p.Arg201Cys	Somatic		WXS	Illumina GAIIx	Phase_IV	A6NI00|E1P5G5|P04895|Q12927|Q14433|Q32P26|Q5JWD2|Q5JWD4|Q5JWD5|Q6NR75|Q6NXS0|Q8TBC0|Q96H70	Missense_Mutation	SNP	pfam_Gprotein_alpha_su,pfam_Small_GTPase_ARF/SAR,superfamily_GproteinA_insert,smart_Gprotein_alpha_su,prints_Gprotein_alpha_S,prints_Gprotein_alpha_su	p.R202C	ENST00000371085.3	37	c.604	CCDS13472.1	20	.	.	.	.	.	.	.	.	.	.	C	21.9	4.215896	0.79352	.	.	ENSG00000087460	ENST00000371100;ENST00000371102;ENST00000371095;ENST00000371085;ENST00000354359;ENST00000265620;ENST00000306090	D;D;D;D;D;D;D	0.99466	-5.95;-5.95;-5.95;-5.95;-5.95;-2.99;-5.95	5.53	4.53	0.55603	G protein alpha subunit, helical insertion (2);	0.000000	0.85682	D	0.000000	D	0.99775	0.9907	H	0.99732	4.735	0.80722	D	1	D;D;D;D	0.89917	0.999;0.983;0.979;1.0	D;P;P;D	0.97110	0.939;0.845;0.643;1.0	D	0.96814	0.9599	10	0.87932	D	0	.	13.0593	0.58997	0.2437:0.7563:0.0:0.0	rs11554273	201;202;186;844	P63092;A6NI00;P63092-3;Q5JWF2	GNAS2_HUMAN;.;.;GNAS1_HUMAN	C	844;830;187;201;202;186;187	ENSP00000360141:R844C;ENSP00000360143:R830C;ENSP00000360136:R187C;ENSP00000360126:R201C;ENSP00000346328:R202C;ENSP00000265620:R186C;ENSP00000304472:R187C	ENSP00000265620:R186C	R	+	1	0	GNAS	56917815	1.000000	0.71417	0.998000	0.56505	0.941000	0.58515	4.055000	0.57441	2.596000	0.87737	0.563000	0.77884	CGT	GNAS	-	pfam_Gprotein_alpha_su,superfamily_GproteinA_insert,smart_Gprotein_alpha_su,prints_Gprotein_alpha_su	ENSG00000087460		0.428	GNAS-015	KNOWN	basic|CCDS	protein_coding	GNAS	HGNC	protein_coding	OTTHUMT00000080431.2	151	0.00	0	C	NM_000516		57484420	57484420	+1	no_errors	ENST00000354359	ensembl	human	known	69_37n	missense	150	43.61	116	SNP	1.000	T
KIAA1429	25962	genome.wustl.edu	37	8	95508070	95508070	+	Missense_Mutation	SNP	A	A	G			TCGA-A8-A09T-01A-11W-A019-09	TCGA-A8-A09T-10A-01W-A021-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	e565da2b-4a3f-4be1-9cf7-2845145d1dbc	8c267083-4672-4f9e-b5ec-19a13e897f78	g.chr8:95508070A>G	ENST00000297591.5	-	19	4508	c.4433T>C	c.(4432-4434)gTt>gCt	p.V1478A	KIAA1429_ENST00000437199.1_3'UTR	NM_015496.4	NP_056311.2	Q69YN4	VIR_HUMAN	KIAA1429	1478					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(16)|lung(28)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	66	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)			CTTAAGTCCAACTACACTGTC	0.413																																						dbGAP											0													113.0	98.0	103.0					8																	95508070		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB037850	CCDS34923.1, CCDS47894.1	8q22.1	2008-11-25			ENSG00000164944	ENSG00000164944			24500	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 121"""					10718198	Standard	NM_015496		Approved	DKFZP434I116, fSAP121	uc003ygo.2	Q69YN4	OTTHUMG00000164426	ENST00000297591.5:c.4433T>C	8.37:g.95508070A>G	ENSP00000297591:p.Val1478Ala	Somatic		WXS	Illumina GAIIx	Phase_IV	Q2M1N0|Q6AHX9|Q6NT78|Q7Z6C7|Q8IXH4|Q9BTH4|Q9H9C9|Q9NWR3|Q9P2B8|Q9UFW1	Missense_Mutation	SNP	superfamily_ARM-type_fold	p.V1478A	ENST00000297591.5	37	c.4433	CCDS34923.1	8	.	.	.	.	.	.	.	.	.	.	A	15.83	2.949977	0.53186	.	.	ENSG00000164944	ENST00000297591	T	0.67523	-0.27	5.34	5.34	0.76211	.	0.416710	0.26380	N	0.024704	T	0.53012	0.1770	L	0.40543	1.245	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.48658	-0.9016	10	0.21540	T	0.41	-5.7213	7.9505	0.30012	0.8458:0.0:0.1542:0.0	.	1478	Q69YN4	VIR_HUMAN	A	1478	ENSP00000297591:V1478A	ENSP00000297591:V1478A	V	-	2	0	KIAA1429	95577246	1.000000	0.71417	0.975000	0.42487	0.971000	0.66376	5.529000	0.67135	2.020000	0.59435	0.528000	0.53228	GTT	KIAA1429	-	NULL	ENSG00000164944		0.413	KIAA1429-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KIAA1429	HGNC	protein_coding	OTTHUMT00000378720.2	128	0.00	0	A	NM_015496		95508070	95508070	-1	no_errors	ENST00000297591	ensembl	human	known	69_37n	missense	166	38.52	104	SNP	0.999	G
MAGEC1	9947	genome.wustl.edu	37	X	140994265	140994265	+	Missense_Mutation	SNP	G	G	A			TCGA-A8-A09T-01A-11W-A019-09	TCGA-A8-A09T-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	e565da2b-4a3f-4be1-9cf7-2845145d1dbc	8c267083-4672-4f9e-b5ec-19a13e897f78	g.chrX:140994265G>A	ENST00000285879.4	+	4	1361	c.1075G>A	c.(1075-1077)Gag>Aag	p.E359K	MAGEC1_ENST00000406005.2_Intron	NM_005462.4	NP_005453.2	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	359										breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(22)|lung(60)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(1)	127	Acute lymphoblastic leukemia(192;6.56e-05)					GAGTTCTCCTGAGAGTGCTCA	0.468										HNSCC(15;0.026)																												dbGAP											0													106.0	106.0	106.0					X																	140994265		2200	4293	6493	-	-	-	SO:0001583	missense	0			AF064589	CCDS35417.1	Xq26	2009-03-18			ENSG00000155495	ENSG00000155495			6812	protein-coding gene	gene with protein product	"""cancer/testis antigen family 7, member 1"""	300223				9485030, 9618514	Standard	NM_005462		Approved	MAGE-C1, CT7, MGC39366, CT7.1	uc004fbt.3	O60732	OTTHUMG00000022569	ENST00000285879.4:c.1075G>A	X.37:g.140994265G>A	ENSP00000285879:p.Glu359Lys	Somatic		WXS	Illumina GAIIx	Phase_IV	A0PK03|O75451|Q8TCV4	Missense_Mutation	SNP	pfam_MAGE,pfscan_MAGE	p.E359K	ENST00000285879.4	37	c.1075	CCDS35417.1	X	.	.	.	.	.	.	.	.	.	.	g	4.214	0.038598	0.08148	.	.	ENSG00000155495	ENST00000285879	T	0.02421	4.3	0.896	0.896	0.19253	.	.	.	.	.	T	0.01695	0.0054	N	0.08118	0	0.09310	N	1	B	0.14805	0.011	B	0.01281	0.0	T	0.46359	-0.9197	9	0.87932	D	0	.	4.3811	0.11295	1.0E-4:0.0:0.6215:0.3784	.	359	O60732	MAGC1_HUMAN	K	359	ENSP00000285879:E359K	ENSP00000285879:E359K	E	+	1	0	MAGEC1	140821931	0.131000	0.22433	0.004000	0.12327	0.004000	0.04260	0.527000	0.22987	0.148000	0.19059	0.150000	0.16122	GAG	MAGEC1	-	NULL	ENSG00000155495		0.468	MAGEC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	MAGEC1	HGNC	protein_coding	OTTHUMT00000058604.1	858	0.00	0	G	NM_005462		140994265	140994265	+1	no_errors	ENST00000285879	ensembl	human	known	69_37n	missense	350	62.15	578	SNP	0.021	A
OR2T35	403244	genome.wustl.edu	37	1	248801953	248801954	+	Frame_Shift_Ins	INS	-	-	T	rs140070233	byFrequency	TCGA-A8-A09T-01A-11W-A019-09	TCGA-A8-A09T-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	e565da2b-4a3f-4be1-9cf7-2845145d1dbc	8c267083-4672-4f9e-b5ec-19a13e897f78	g.chr1:248801953_248801954insT	ENST00000317450.3	-	1	605_606	c.606_607insA	c.(604-609)tgctgcfs	p.C203fs		NM_001001827.1	NP_001001827.1	Q8NGX2	O2T35_HUMAN	olfactory receptor, family 2, subfamily T, member 35	203						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(1)|lung(1)|ovary(1)|prostate(1)|skin(1)	6	all_cancers(71;2.04e-05)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.237)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			ATCAGCACGCAGCAGGCATACA	0.525																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			BK004475	CCDS31123.1	1q44	2012-08-09			ENSG00000177151	ENSG00000177151		"""GPCR / Class A : Olfactory receptors"""	31257	protein-coding gene	gene with protein product							Standard	NM_001001827		Approved		uc001ies.1	Q8NGX2	OTTHUMG00000040380	ENST00000317450.3:c.606_607insA	1.37:g.248801953_248801954insT	ENSP00000324369:p.Cys203fs	Somatic		WXS	Illumina GAIIx	Phase_IV	Q6IEY7	Frame_Shift_Ins	INS	pfam_7TM_GPCR_Rhodpsn,pfam_7TM_GPCR_olfarory/Srsx,pfscan_GPCR_Rhodpsn_supfam,prints_Olfact_rcpt,prints_7TM_GPCR_Rhodpsn	p.C202fs	ENST00000317450.3	37	c.607_606	CCDS31123.1	1																																																																																			OR2T35	-	pfam_7TM_GPCR_Rhodpsn,pfam_7TM_GPCR_olfarory/Srsx,pfscan_GPCR_Rhodpsn_supfam,prints_7TM_GPCR_Rhodpsn	ENSG00000177151		0.525	OR2T35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	OR2T35	HGNC	protein_coding	OTTHUMT00000097130.1	8	0.00	0	-	NM_001001827		248801953	248801954	-1	no_errors	ENST00000317450	ensembl	human	known	69_37n	frame_shift_ins	5	28.57	2	INS	0.101:0.095	T
PCDHB11	56125	genome.wustl.edu	37	5	140581014	140581015	+	In_Frame_Ins	INS	-	-	CCC			TCGA-A8-A09T-01A-11W-A019-09	TCGA-A8-A09T-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	e565da2b-4a3f-4be1-9cf7-2845145d1dbc	8c267083-4672-4f9e-b5ec-19a13e897f78	g.chr5:140581014_140581015insCCC	ENST00000354757.3	+	1	1667_1668	c.1667_1668insCCC	c.(1666-1671)gacaac>gaCCCcaac	p.556_557DN>DPN	PCDHB11_ENST00000536699.1_In_Frame_Ins_p.191_192DN>DPN	NM_018931.2	NP_061754.1	Q9Y5F2	PCDBB_HUMAN	protocadherin beta 11	556	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(23)|ovary(4)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	63			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GACGCCAACGACAACTCGCCCT	0.718																																						dbGAP											0																																										-	-	-	SO:0001652	inframe_insertion	0			AF152490	CCDS4253.1	5q31	2010-01-26			ENSG00000197479	ENSG00000197479		"""Cadherins / Protocadherins : Clustered"""	8682	other	protocadherin	"""cadherin ME2"""	606337				10380929	Standard	NM_018931		Approved	PCDH-BETA11, ME2	uc003liy.3	Q9Y5F2	OTTHUMG00000129618	Exception_encountered	5.37:g.140581014_140581015insCCC	ENSP00000346802:p.Asp556_Asn557insPro	Somatic		WXS	Illumina GAIIx	Phase_IV	B4DSF7|Q2M223	In_Frame_Ins	INS	pfam_Cadherin,pfam_Cadherin_N,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin,prints_Cadherin	p.557in_frame_insP	ENST00000354757.3	37	c.1667_1668	CCDS4253.1	5																																																																																			PCDHB11	-	superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin,prints_Cadherin	ENSG00000197479		0.718	PCDHB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PCDHB11	HGNC	protein_coding	OTTHUMT00000251813.1	34	0.00	0	-	NM_018931		140581014	140581015	+1	no_errors	ENST00000354757	ensembl	human	known	69_37n	in_frame_ins	29	14.71	5	INS	1.000:1.000	CCC
PLCXD2	257068	genome.wustl.edu	37	3	111432878	111432878	+	Missense_Mutation	SNP	C	C	T	rs527314934		TCGA-A8-A09T-01A-11W-A019-09	TCGA-A8-A09T-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	e565da2b-4a3f-4be1-9cf7-2845145d1dbc	8c267083-4672-4f9e-b5ec-19a13e897f78	g.chr3:111432878C>T	ENST00000477665.1	+	3	1093	c.769C>T	c.(769-771)Cgg>Tgg	p.R257W	PLCXD2_ENST00000472215.1_3'UTR|PLCXD2_ENST00000393934.3_Missense_Mutation_p.R257W	NM_001185106.1	NP_001172035.1	Q0VAA5	PLCX2_HUMAN	phosphatidylinositol-specific phospholipase C, X domain containing 2	257					lipid catabolic process (GO:0016042)		phosphoric diester hydrolase activity (GO:0008081)|signal transducer activity (GO:0004871)			endometrium(1)|large_intestine(5)|lung(9)|prostate(1)|skin(1)	17						GCGGGCCTCACGGGGCTCCTT	0.582													C|||	1	0.000199681	0.0	0.0014	5008	,	,		13367	0.0		0.0	False		,,,				2504	0.0					dbGAP											0													58.0	59.0	59.0					3																	111432878		2203	4300	6503	-	-	-	SO:0001583	missense	0			AK056141	CCDS2961.1, CCDS54619.1	3q13.2	2004-09-09			ENSG00000240891	ENSG00000240891			26462	protein-coding gene	gene with protein product							Standard	NM_001185106		Approved	FLJ31579	uc003dxz.3	Q0VAA5	OTTHUMG00000159279	ENST00000477665.1:c.769C>T	3.37:g.111432878C>T	ENSP00000420686:p.Arg257Trp	Somatic		WXS	Illumina GAIIx	Phase_IV	Q96N12	Missense_Mutation	SNP	pfam_PLipase_C_PInositol-sp_X_dom,superfamily_PLC-like_Pdiesterase_TIM-brl,smart_PLipase_C_PInositol-sp_X_dom,pfscan_PLipase_C_PInositol-sp_X_dom	p.R257W	ENST00000477665.1	37	c.769	CCDS54619.1	3	.	.	.	.	.	.	.	.	.	.	C	10.56	1.385612	0.25031	.	.	ENSG00000240891	ENST00000393934;ENST00000477665	.	.	.	5.39	3.51	0.40186	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);	.	.	.	.	T	0.26159	0.0638	L	0.36672	1.1	0.09310	N	1	P;P	0.46327	0.876;0.566	B;B	0.36186	0.153;0.219	T	0.06250	-1.0837	8	0.66056	D	0.02	-0.1057	10.0479	0.42197	0.1559:0.6939:0.1502:0.0	.	257;257	Q0VAA5;Q0VAA5-2	PLCX2_HUMAN;.	W	257	.	ENSP00000377511:R257W	R	+	1	2	PLCXD2	112915568	0.000000	0.05858	0.000000	0.03702	0.487000	0.33371	0.414000	0.21164	0.580000	0.29522	0.563000	0.77884	CGG	PLCXD2	-	superfamily_PLC-like_Pdiesterase_TIM-brl	ENSG00000240891		0.582	PLCXD2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	PLCXD2	HGNC	protein_coding	OTTHUMT00000354322.1	241	0.00	0	C	NM_153268		111432878	111432878	+1	no_errors	ENST00000477665	ensembl	human	known	69_37n	missense	96	34.01	50	SNP	0.000	T
PREPL	9581	genome.wustl.edu	37	2	44556197	44556197	+	Nonsense_Mutation	SNP	G	G	A			TCGA-A8-A09T-01A-11W-A019-09	TCGA-A8-A09T-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	e565da2b-4a3f-4be1-9cf7-2845145d1dbc	8c267083-4672-4f9e-b5ec-19a13e897f78	g.chr2:44556197G>A	ENST00000409936.1	-	10	1845	c.1408C>T	c.(1408-1410)Cag>Tag	p.Q470*	PREPL_ENST00000410081.1_Nonsense_Mutation_p.Q470*|PREPL_ENST00000541738.1_Nonsense_Mutation_p.Q381*|PREPL_ENST00000378520.3_Nonsense_Mutation_p.Q404*|PREPL_ENST00000378511.3_Nonsense_Mutation_p.Q408*|PREPL_ENST00000409411.1_Nonsense_Mutation_p.Q381*|PREPL_ENST00000409957.1_Nonsense_Mutation_p.Q381*|PREPL_ENST00000409272.1_Nonsense_Mutation_p.Q470*|PREPL_ENST00000260648.6_Nonsense_Mutation_p.Q470*	NM_001171606.1	NP_001165077.1	Q4J6C6	PPCEL_HUMAN	prolyl endopeptidase-like	470						cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)	serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)			breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(19)|ovary(1)|prostate(1)|skin(2)	33		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				GGTTTCTTCTGCAAGTCCTCA	0.388																																						dbGAP											0													97.0	95.0	95.0					2																	44556197		2203	4300	6503	-	-	-	SO:0001587	stop_gained	0			AB007896	CCDS33190.1, CCDS42675.1, CCDS42676.1, CCDS54353.1	2p22.1	2008-02-05			ENSG00000138078	ENSG00000138078			30228	protein-coding gene	gene with protein product		609557				11524703	Standard	NM_006036		Approved	KIAA0436	uc002ruk.2	Q4J6C6	OTTHUMG00000152791	ENST00000409936.1:c.1408C>T	2.37:g.44556197G>A	ENSP00000386543:p.Gln470*	Somatic		WXS	Illumina GAIIx	Phase_IV	A7E2X6|D6W5A3|O43163|Q4J6C3|Q4J6C4|Q4ZG39|Q6ZMW7|Q96DW7	Nonsense_Mutation	SNP	pfam_Peptidase_S9,pfam_Peptidase_S9A_B_C_N,superfamily_Peptidase_S9A_B_C_N,prints_Peptidase_S9A	p.Q470*	ENST00000409936.1	37	c.1408	CCDS33190.1	2	.	.	.	.	.	.	.	.	.	.	G	36	5.685054	0.96784	.	.	ENSG00000138078	ENST00000541738;ENST00000409411;ENST00000409957;ENST00000409936;ENST00000260648;ENST00000409272;ENST00000410081;ENST00000378520;ENST00000378511	.	.	.	6.16	5.27	0.74061	.	0.511109	0.22531	N	0.058860	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-5.8706	8.7512	0.34616	0.0677:0.0:0.661:0.2713	.	.	.	.	X	381;381;381;470;470;470;470;404;408	.	ENSP00000260648:Q470X	Q	-	1	0	PREPL	44409701	1.000000	0.71417	0.996000	0.52242	0.994000	0.84299	1.138000	0.31491	1.571000	0.49722	0.650000	0.86243	CAG	PREPL	-	NULL	ENSG00000138078		0.388	PREPL-008	KNOWN	basic|appris_principal|CCDS	protein_coding	PREPL	HGNC	protein_coding	OTTHUMT00000327900.1	397	0.00	0	G	NM_006036		44556197	44556197	-1	no_errors	ENST00000260648	ensembl	human	known	69_37n	nonsense	268	23.86	84	SNP	0.619	A
PTPN14	5784	genome.wustl.edu	37	1	214557496	214557496	+	Missense_Mutation	SNP	G	G	A			TCGA-A8-A09T-01A-11W-A019-09	TCGA-A8-A09T-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	e565da2b-4a3f-4be1-9cf7-2845145d1dbc	8c267083-4672-4f9e-b5ec-19a13e897f78	g.chr1:214557496G>A	ENST00000366956.5	-	13	1896	c.1702C>T	c.(1702-1704)Ccc>Tcc	p.P568S	PTPN14_ENST00000543945.1_3'UTR	NM_005401.4	NP_005392.2	Q15678	PTN14_HUMAN	protein tyrosine phosphatase, non-receptor type 14	568	Poly-Pro.				lymphangiogenesis (GO:0001946)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of protein export from nucleus (GO:0046825)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)			NS(2)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(9)|liver(3)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	58				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)		GGGTAGGGGGGCGGTGGCCTG	0.652																																					Colon(92;557 1424 24372 34121 40073)	dbGAP											0													50.0	53.0	52.0					1																	214557496		2203	4300	6503	-	-	-	SO:0001583	missense	0			X82676	CCDS1514.1	1q32.2	2011-06-09			ENSG00000152104	ENSG00000152104		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9647	protein-coding gene	gene with protein product		603155				7733990	Standard	NM_005401		Approved	PEZ	uc001hkk.2	Q15678	OTTHUMG00000037039	ENST00000366956.5:c.1702C>T	1.37:g.214557496G>A	ENSP00000355923:p.Pro568Ser	Somatic		WXS	Illumina GAIIx	Phase_IV	Q5VSI0	Missense_Mutation	SNP	pfam_Tyr_Pase_rcpt/non-rcpt,pfam_FERM_central,pfam_FERM_N,pfam_FERM_PH-like_C,pfam_Dual-sp_phosphatase_cat-dom,superfamily_FERM_central,smart_Band_41_domain,smart_Tyr_Pase_rcpt/non-rcpt,smart_Tyr_Pase_cat,pirsf_Tyr_Pase_non-rcpt_typ-14/21,pfscan_FERM_domain,pfscan_Tyr/Dual-specificity_Pase,pfscan_Tyr_Pase_rcpt/non-rcpt,prints_Tyr_Pase_rcpt/non-rcpt,prints_Band_41_fam	p.P568S	ENST00000366956.5	37	c.1702	CCDS1514.1	1	.	.	.	.	.	.	.	.	.	.	G	25.5	4.643620	0.87859	.	.	ENSG00000152104	ENST00000366956	D	0.91740	-2.9	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	D	0.96125	0.8737	M	0.78049	2.395	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.94980	0.8125	10	0.41790	T	0.15	.	19.989	0.97359	0.0:0.0:1.0:0.0	.	568	Q15678	PTN14_HUMAN	S	568	ENSP00000355923:P568S	ENSP00000355923:P568S	P	-	1	0	PTPN14	212624119	1.000000	0.71417	0.994000	0.49952	0.995000	0.86356	7.744000	0.85034	2.803000	0.96430	0.650000	0.86243	CCC	PTPN14	-	pirsf_Tyr_Pase_non-rcpt_typ-14/21	ENSG00000152104		0.652	PTPN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PTPN14	HGNC	protein_coding	OTTHUMT00000089918.2	58	0.00	0	G	NM_005401		214557496	214557496	-1	no_errors	ENST00000366956	ensembl	human	known	69_37n	missense	27	47.06	24	SNP	1.000	A
RAB30	27314	genome.wustl.edu	37	11	82698729	82698729	+	Silent	SNP	G	G	A			TCGA-A8-A09T-01A-11W-A019-09	TCGA-A8-A09T-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	e565da2b-4a3f-4be1-9cf7-2845145d1dbc	8c267083-4672-4f9e-b5ec-19a13e897f78	g.chr11:82698729G>A	ENST00000533486.1	-	5	545	c.261C>T	c.(259-261)ctC>ctT	p.L87L	RAB30_ENST00000534141.1_Silent_p.L87L|RAB30_ENST00000527633.1_Silent_p.L87L|RAB30_ENST00000260056.2_Silent_p.L87L|RAB30_ENST00000525117.1_Silent_p.L59L|RAB30_ENST00000532548.1_Silent_p.L87L|RP11-659G9.3_ENST00000527550.1_RNA	NM_014488.3	NP_055303.2	Q15771	RAB30_HUMAN	RAB30, member RAS oncogene family	87					Golgi organization (GO:0007030)|GTP catabolic process (GO:0006184)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	cis-Golgi network (GO:0005801)|Golgi cisterna (GO:0031985)|Golgi stack (GO:0005795)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(3)|kidney(1)|large_intestine(2)|liver(1)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	13						TGTCATAGGTGAGGATCAAGG	0.488																																						dbGAP											0													198.0	177.0	184.0					11																	82698729		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			U57092	CCDS8264.1	11q12-q14	2008-07-21				ENSG00000137502		"""RAB, member RAS oncogene"""	9770	protein-coding gene	gene with protein product		605693				8863739, 9792283	Standard	NM_014488		Approved		uc001ozu.3	Q15771		ENST00000533486.1:c.261C>T	11.37:g.82698729G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	Q6FGK1|Q6MZH2|Q96CI8	Silent	SNP	pfam_Small_GTPase,pfam_MIRO-like,pfam_Small_GTPase_ARF/SAR,pfam_Gtr1_RagA,pfam_ProtSyn_GTP-bd,smart_Small_GTPase_Ras,smart_Small_GTPase_Rab_type,smart_Small_GTPase_Rho,smart_Ran_GTPase,prints_Small_GTPase,tigrfam_Small_GTP-bd_dom	p.L87	ENST00000533486.1	37	c.261	CCDS8264.1	11																																																																																			RAB30	-	pfam_Small_GTPase,pfam_MIRO-like,pfam_Small_GTPase_ARF/SAR,pfam_Gtr1_RagA,pfam_ProtSyn_GTP-bd,smart_Small_GTPase_Ras,smart_Small_GTPase_Rab_type,smart_Small_GTPase_Rho,smart_Ran_GTPase,tigrfam_Small_GTP-bd_dom	ENSG00000137502		0.488	RAB30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RAB30	HGNC	protein_coding	OTTHUMT00000392141.1	263	0.00	0	G	NM_014488		82698729	82698729	-1	no_errors	ENST00000260056	ensembl	human	known	69_37n	silent	111	44.22	88	SNP	0.997	A
RETSAT	54884	genome.wustl.edu	37	2	85571455	85571455	+	Missense_Mutation	SNP	A	A	T			TCGA-A8-A09T-01A-11W-A019-09	TCGA-A8-A09T-10A-01W-A021-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	e565da2b-4a3f-4be1-9cf7-2845145d1dbc	8c267083-4672-4f9e-b5ec-19a13e897f78	g.chr2:85571455A>T	ENST00000295802.4	-	8	1385	c.1273T>A	c.(1273-1275)Tcc>Acc	p.S425T	RETSAT_ENST00000263854.6_Missense_Mutation_p.S425T|RETSAT_ENST00000457495.2_Missense_Mutation_p.S364T|RETSAT_ENST00000475624.2_Intron	NM_017750.3	NP_060220.3	Q6NUM9	RETST_HUMAN	retinol saturase (all-trans-retinol 13,14-reductase)	425					oxidation-reduction process (GO:0055114)|retinol metabolic process (GO:0042572)	endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|nuclear outer membrane (GO:0005640)	all-trans-retinol 13,14-reductase activity (GO:0051786)|oxidoreductase activity (GO:0016491)			NS(2)|breast(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|prostate(2)|skin(2)|urinary_tract(1)	30					Vitamin A(DB00162)	CTGGGCATGGAGACGTAGCGC	0.562																																						dbGAP											0													80.0	75.0	77.0					2																	85571455		2203	4300	6503	-	-	-	SO:0001583	missense	0			AK075261	CCDS1972.1	2p11.2	2008-02-05			ENSG00000042445	ENSG00000042445	1.3.99.23		25991	protein-coding gene	gene with protein product						12975309, 15358783	Standard	NM_017750		Approved	FLJ20296	uc002spd.3	Q6NUM9	OTTHUMG00000154611	ENST00000295802.4:c.1273T>A	2.37:g.85571455A>T	ENSP00000295802:p.Ser425Thr	Somatic		WXS	Illumina GAIIx	Phase_IV	A6NIK3|Q53R95|Q53SA9|Q6UX05|Q8N2H5|Q96FA4|Q9NXE5	Missense_Mutation	SNP	pfam_Amino_oxidase,pfam_FAD_bind_dom,pfam_FAD-dep_OxRdtase,pfam_Pyr_nucl-diS_OxRdtase_FAD/NAD,pfam_mOase_FAD-bd	p.S425T	ENST00000295802.4	37	c.1273	CCDS1972.1	2	.	.	.	.	.	.	.	.	.	.	A	10.87	1.472721	0.26423	.	.	ENSG00000042445	ENST00000295802;ENST00000263854;ENST00000457495	T;T	0.22945	1.94;1.93	4.58	3.42	0.39159	.	0.365694	0.30989	N	0.008480	T	0.22859	0.0552	M	0.67953	2.075	0.09310	N	1	B;B;B	0.33413	0.232;0.411;0.409	B;B;B	0.34489	0.113;0.176;0.184	T	0.15009	-1.0452	10	0.38643	T	0.18	-19.1725	3.5785	0.07943	0.6996:0.0:0.1047:0.1957	.	364;364;425	G5E9N3;B4DKE1;Q6NUM9	.;.;RETST_HUMAN	T	425;425;364	ENSP00000295802:S425T;ENSP00000405040:S364T	ENSP00000263854:S425T	S	-	1	0	RETSAT	85424966	0.000000	0.05858	0.056000	0.19401	0.146000	0.21551	0.243000	0.18106	1.827000	0.53221	0.459000	0.35465	TCC	RETSAT	-	NULL	ENSG00000042445		0.562	RETSAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RETSAT	HGNC	protein_coding	OTTHUMT00000252489.1	42	0.00	0	A	NM_017750		85571455	85571455	-1	no_errors	ENST00000295802	ensembl	human	known	69_37n	missense	28	28.21	11	SNP	0.004	T
SGSM2	9905	genome.wustl.edu	37	17	2279517	2279518	+	Frame_Shift_Ins	INS	-	-	C	rs146837751|rs559496493	byFrequency	TCGA-A8-A09T-01A-11W-A019-09	TCGA-A8-A09T-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	e565da2b-4a3f-4be1-9cf7-2845145d1dbc	8c267083-4672-4f9e-b5ec-19a13e897f78	g.chr17:2279517_2279518insC	ENST00000426855.2	+	18	2611_2612	c.2436_2437insC	c.(2437-2439)cccfs	p.P813fs	SGSM2_ENST00000268989.3_Frame_Shift_Ins_p.P858fs|SGSM2_ENST00000574563.1_Frame_Shift_Ins_p.P813fs|RP1-59D14.5_ENST00000573007.1_RNA|RP1-59D14.5_ENST00000574290.1_RNA	NM_001098509.1	NP_001091979.1	O43147	SGSM2_HUMAN	small G protein signaling modulator 2	813	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				late endosome to Golgi transport (GO:0034499)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)		Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				Colorectal(2;5.15e-05)|READ - Rectum adenocarcinoma(2;0.000115)		GGTACTTCACGCCCCCCAACCT	0.584																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			BC039204	CCDS32526.1, CCDS45570.1	17p13.3	2013-07-10	2007-08-14	2007-08-14		ENSG00000141258		"""Small G protein signaling modulators"""	29026	protein-coding gene	gene with protein product		611418	"""RUN and TBC1 domain containing 1"""	RUTBC1		9455477, 17509819, 21808068	Standard	NM_014853		Approved	KIAA0397	uc002fum.4	O43147		ENST00000426855.2:c.2442dupC	17.37:g.2279523_2279523dupC	ENSP00000415107:p.Pro813fs	Somatic		WXS	Illumina GAIIx	Phase_IV	A5LGW2|B4DH69|Q49AC2|Q6ZUY2|Q8IXU4	Frame_Shift_Ins	INS	pfam_Run,pfam_Rab-GTPase-TBC_dom,superfamily_Rab-GTPase-TBC_dom,smart_Run,smart_Rab-GTPase-TBC_dom,pfscan_Run,pfscan_Rab-GTPase-TBC_dom	p.N859fs	ENST00000426855.2	37	c.2571_2572	CCDS45570.1	17																																																																																			SGSM2	-	pfam_Rab-GTPase-TBC_dom,superfamily_Rab-GTPase-TBC_dom,smart_Rab-GTPase-TBC_dom,pfscan_Rab-GTPase-TBC_dom	ENSG00000141258		0.584	SGSM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SGSM2	HGNC	protein_coding	OTTHUMT00000438186.1	13	0.00	0	-	NM_014853		2279517	2279518	+1	no_errors	ENST00000268989	ensembl	human	known	69_37n	frame_shift_ins	6	25.00	2	INS	0.000:0.001	C
TAF1B	9014	genome.wustl.edu	37	2	9989571	9989571	+	Frame_Shift_Del	DEL	A	A	-	rs528368939		TCGA-A8-A09T-01A-11W-A019-09	TCGA-A8-A09T-10A-01W-A021-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	e565da2b-4a3f-4be1-9cf7-2845145d1dbc	8c267083-4672-4f9e-b5ec-19a13e897f78	g.chr2:9989571delA	ENST00000263663.5	+	3	375	c.187delA	c.(187-189)aaafs	p.K65fs	TAF1B_ENST00000396242.3_5'UTR|TAF1B_ENST00000402170.1_3'UTR	NM_005680.2	NP_005671	Q53T94	TAF1B_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kDa	65	B-reader.				gene expression (GO:0010467)|RNA polymerase I transcriptional preinitiation complex assembly at the promoter for the nuclear large rRNA transcript (GO:0001189)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|RNA polymerase I core factor complex (GO:0070860)	metal ion binding (GO:0046872)|RNA polymerase I CORE element sequence-specific DNA binding (GO:0001164)|RNA polymerase I CORE element sequence-specific DNA binding transcription factor recruiting transcription factor activity (GO:0001187)|sequence-specific DNA binding transcription factor activity (GO:0003700)|TBP-class protein binding (GO:0017025)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|lung(4)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	14	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					CCGGGGGCTTAAAAAAAAAAA	0.333																																						dbGAP											0										139,495,3606		1,2,135,2,489,1491	20.0	22.0	21.0			1.7	0.9	2		23	207,946,7081		0,0,207,0,946,2964	no	codingComplex	TAF1B	NM_005680.2		1,2,342,2,1435,4455	A1A1,A1A2,A1R,A2A2,A2R,RR		14.0029,14.9528,14.3258			9989571	346,1441,10687	2194	4292	6486	-	-	-	SO:0001589	frameshift_variant	0			L39061	CCDS33143.1	2p25	2008-06-02	2002-08-29		ENSG00000115750	ENSG00000115750			11533	protein-coding gene	gene with protein product		604904	"""TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kD"""			7801123	Standard	NM_005680		Approved	TAFI63, SL1, RAF1B, RAFI63	uc002qzz.3	Q53T94	OTTHUMG00000151673	ENST00000263663.5:c.187delA	2.37:g.9989571delA	ENSP00000263663:p.Lys65fs	Somatic		WXS	Illumina GAIIx	Phase_IV	B4DI42|F8WD72|Q15574|Q8WVC3	Frame_Shift_Del	DEL	pfam_TF_Rrn7	p.N66fs	ENST00000263663.5	37	c.187	CCDS33143.1	2																																																																																			TAF1B	-	NULL	ENSG00000115750		0.333	TAF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TAF1B	HGNC	protein_coding	OTTHUMT00000323426.2	30	0.00	0	A	NM_005680		9989571	9989571	+1	no_errors	ENST00000263663	ensembl	human	known	69_37n	frame_shift_del	21	15.38	4	DEL	0.991	-
TMPRSS11B	132724	genome.wustl.edu	37	4	69101719	69101719	+	Splice_Site	DEL	C	C	-	rs200870287		TCGA-A8-A09T-01A-11W-A019-09	TCGA-A8-A09T-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	e565da2b-4a3f-4be1-9cf7-2845145d1dbc	8c267083-4672-4f9e-b5ec-19a13e897f78	g.chr4:69101719delC	ENST00000332644.5	-	4	470		c.e4+1			NM_182502.3	NP_872308.2	Q86T26	TM11B_HUMAN	transmembrane protease, serine 11B							extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|skin(1)	27						CTTGTACTTACAGAAGTTTGA	0.269																																						dbGAP											0													43.0	44.0	44.0					4																	69101719		2189	4264	6453	-	-	-	SO:0001630	splice_region_variant	0			BX537945	CCDS3521.1	4q13.2	2010-04-13			ENSG00000185873	ENSG00000185873		"""Serine peptidases / Transmembrane"""	25398	protein-coding gene	gene with protein product							Standard	NM_182502		Approved		uc003hdw.4	Q86T26	OTTHUMG00000129301	ENST00000332644.5:c.308+1G>-	4.37:g.69101719delC		Somatic		WXS	Illumina GAIIx	Phase_IV	A8K4D9	Splice_Site	DEL	-	e4+1	ENST00000332644.5	37	c.308+1	CCDS3521.1	4																																																																																			TMPRSS11B	-	-	ENSG00000185873		0.269	TMPRSS11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TMPRSS11B	HGNC	protein_coding	OTTHUMT00000251431.2	137	0.00	0	C	NM_182502	Intron	69101719	69101719	-1	no_errors	ENST00000332644	ensembl	human	known	69_37n	splice_site_del	92	27.94	38	DEL	0.861	-
TRPM3	80036	genome.wustl.edu	37	9	73442886	73442886	+	Missense_Mutation	SNP	C	C	A			TCGA-A8-A09T-01A-11W-A019-09	TCGA-A8-A09T-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	e565da2b-4a3f-4be1-9cf7-2845145d1dbc	8c267083-4672-4f9e-b5ec-19a13e897f78	g.chr9:73442886C>A	ENST00000377111.2	-	6	1093	c.850G>T	c.(850-852)Gtt>Ttt	p.V284F	TRPM3_ENST00000396292.4_Missense_Mutation_p.V131F|TRPM3_ENST00000377105.1_Missense_Mutation_p.V131F|TRPM3_ENST00000377101.1_Missense_Mutation_p.V131F|TRPM3_ENST00000358082.3_Missense_Mutation_p.V131F|TRPM3_ENST00000361823.5_Missense_Mutation_p.V131F|TRPM3_ENST00000408909.2_Missense_Mutation_p.V131F|TRPM3_ENST00000377110.3_Missense_Mutation_p.V284F|TRPM3_ENST00000396280.5_Missense_Mutation_p.V131F|TRPM3_ENST00000357533.2_Missense_Mutation_p.V286F|TRPM3_ENST00000396283.1_Missense_Mutation_p.V131F|TRPM3_ENST00000396285.1_Missense_Mutation_p.V131F|TRPM3_ENST00000423814.3_Missense_Mutation_p.V286F|TRPM3_ENST00000360823.2_Missense_Mutation_p.V131F|TRPM3_ENST00000377106.1_Missense_Mutation_p.V131F	NM_001007471.2	NP_001007472.2	Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	284					calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|sensory perception of temperature stimulus (GO:0050951)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)			NS(2)|breast(4)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(18)|liver(1)|lung(46)|ovary(3)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(1)	95						CTGTTGAGAACAGTGAGCTTG	0.463																																						dbGAP											0													209.0	189.0	196.0					9																	73442886		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB046836	CCDS6634.1, CCDS6635.1, CCDS6636.1, CCDS6637.1, CCDS43835.1, CCDS65064.1	9q21.11	2011-12-14			ENSG00000083067	ENSG00000083067		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17992	protein-coding gene	gene with protein product	"""melastatin 2"""	608961				16382100	Standard	NM_206946		Approved	KIAA1616, LTRPC3, GON-2	uc004aid.3	Q9HCF6	OTTHUMG00000019997	ENST00000377111.2:c.850G>T	9.37:g.73442886C>A	ENSP00000366315:p.Val284Phe	Somatic		WXS	Illumina GAIIx	Phase_IV	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Missense_Mutation	SNP	pfam_Ion_trans_dom	p.V286F	ENST00000377111.2	37	c.856		9	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.73|17.73	3.460796|3.460796	0.63513|0.63513	.|.	.|.	ENSG00000083067|ENSG00000083067	ENST00000396280|ENST00000377111;ENST00000377110;ENST00000377106;ENST00000360823;ENST00000377105;ENST00000357533;ENST00000408909;ENST00000396285;ENST00000396292;ENST00000358082;ENST00000423814;ENST00000377101;ENST00000396283;ENST00000361823;ENST00000455451	.|T;T;T;T;T;T;T;T;T;T;T;T;T;T	.|0.03124	.|4.04;4.04;4.04;4.04;4.04;4.04;4.04;4.04;4.04;4.04;4.04;4.04;4.04;4.04	5.83|5.83	4.93|4.93	0.64822|0.64822	.|.	.|0.065702	.|0.64402	.|D	.|0.000011	T|T	0.14657|0.14657	0.0354|0.0354	M|M	0.64997|0.64997	1.995|1.995	0.53688|0.53688	D|D	0.999977|0.999977	.|P;D;P;D;P;D;B;D;D;P;D	.|0.71674	.|0.76;0.995;0.887;0.978;0.563;0.998;0.442;0.982;0.998;0.843;0.988	.|B;D;P;D;B;D;B;P;D;P;P	.|0.66351	.|0.416;0.931;0.673;0.923;0.138;0.943;0.213;0.839;0.943;0.62;0.837	T|T	0.00327|0.00327	-1.1814|-1.1814	5|10	.|0.72032	.|D	.|0.01	-9.8811|-9.8811	14.841|14.841	0.70223|0.70223	0.0:0.9314:0.0:0.0686|0.0:0.9314:0.0:0.0686	.|.	.|284;286;131;284;284;284;286;131;131;284;131	.|Q9HCF6;Q4VXD2;Q504Y1;Q9HCF6-2;Q9HCF6-10;Q9HCF6-4;A2A3F7;A2A3F4;G5E9G1;Q9HCF6-8;A2A3F3	.|TRPM3_HUMAN;.;.;.;.;.;.;.;.;.;.	F|F	130|284;284;131;131;131;286;131;131;131;131;286;131;131;131;131	.|ENSP00000366315:V284F;ENSP00000366314:V284F;ENSP00000366310:V131F;ENSP00000354066:V131F;ENSP00000366309:V131F;ENSP00000350140:V286F;ENSP00000386127:V131F;ENSP00000379581:V131F;ENSP00000379587:V131F;ENSP00000350791:V131F;ENSP00000389542:V286F;ENSP00000366305:V131F;ENSP00000379579:V131F;ENSP00000355395:V131F	.|ENSP00000350140:V286F	C|V	-|-	2|1	0|0	TRPM3|TRPM3	72632706|72632706	1.000000|1.000000	0.71417|0.71417	0.989000|0.989000	0.46669|0.46669	0.990000|0.990000	0.78478|0.78478	4.857000|4.857000	0.62939|0.62939	1.490000|1.490000	0.48466|0.48466	0.650000|0.650000	0.86243|0.86243	TGT|GTT	TRPM3	-	NULL	ENSG00000083067		0.463	TRPM3-007	NOVEL	basic|exp_conf	protein_coding	TRPM3	HGNC	protein_coding	OTTHUMT00000214157.5	246	0.00	0	C	NM_206945		73442886	73442886	-1	no_errors	ENST00000423814	ensembl	human	known	69_37n	missense	81	39.10	52	SNP	0.997	A
TTC4	7268	genome.wustl.edu	37	1	55194092	55194092	+	Missense_Mutation	SNP	T	T	C			TCGA-A8-A09T-01A-11W-A019-09	TCGA-A8-A09T-10A-01W-A021-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	e565da2b-4a3f-4be1-9cf7-2845145d1dbc	8c267083-4672-4f9e-b5ec-19a13e897f78	g.chr1:55194092T>C	ENST00000371281.3	+	6	755	c.668T>C	c.(667-669)cTc>cCc	p.L223P	MROH7-TTC4_ENST00000414150.2_3'UTR|TTC4_ENST00000371284.5_3'UTR	NM_004623.4	NP_004614.3	O95801	TTC4_HUMAN	tetratricopeptide repeat domain 4	223										breast(2)|endometrium(3)|kidney(1)|lung(2)|stomach(1)	9						GAGGCTTTACTCCAGGCCATC	0.408																																						dbGAP											0													115.0	118.0	117.0					1																	55194092		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS596.1	1p32	2013-01-11			ENSG00000243725	ENSG00000243725		"""Tetratricopeptide (TTC) repeat domain containing"""	12394	protein-coding gene	gene with protein product		606753				9933562	Standard	NM_004623		Approved	MGC5097, FLJ41930	uc001cxx.4	O95801	OTTHUMG00000009914	ENST00000371281.3:c.668T>C	1.37:g.55194092T>C	ENSP00000360329:p.Leu223Pro	Somatic		WXS	Illumina GAIIx	Phase_IV	Q53Y95|Q5TA96|Q9H3I2	Missense_Mutation	SNP	smart_TPR_repeat,pfscan_TPR-contain_dom	p.L223P	ENST00000371281.3	37	c.668	CCDS596.1	1	.	.	.	.	.	.	.	.	.	.	T	13.96	2.392893	0.42410	.	.	ENSG00000243725	ENST00000371281;ENST00000371284	T	0.16324	2.35	4.99	4.99	0.66335	.	.	.	.	.	T	0.21227	0.0511	M	0.72894	2.215	0.80722	D	1	B;B	0.23058	0.025;0.079	B;B	0.25291	0.024;0.059	T	0.02546	-1.1143	9	0.30854	T	0.27	-4.1246	11.6589	0.51334	0.0:0.0:0.0:1.0	.	223;234	O95801;Q5TA95	TTC4_HUMAN;.	P	223;234	ENSP00000360329:L223P	ENSP00000360329:L223P	L	+	2	0	TTC4	54966680	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.306000	0.65756	2.184000	0.69523	0.533000	0.62120	CTC	TTC4	-	NULL	ENSG00000243725		0.408	TTC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TTC4	HGNC	protein_coding	OTTHUMT00000027432.1	101	0.00	0	T	NM_004623		55194092	55194092	+1	no_errors	ENST00000371281	ensembl	human	known	69_37n	missense	89	34.56	47	SNP	1.000	C
VGLL3	389136	genome.wustl.edu	37	3	87018135	87018135	+	Missense_Mutation	SNP	G	G	A			TCGA-A8-A09T-01A-11W-A019-09	TCGA-A8-A09T-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	e565da2b-4a3f-4be1-9cf7-2845145d1dbc	8c267083-4672-4f9e-b5ec-19a13e897f78	g.chr3:87018135G>A	ENST00000398399.2	-	3	905	c.542C>T	c.(541-543)gCa>gTa	p.A181V	VGLL3_ENST00000383698.3_Missense_Mutation_p.A181V	NM_016206.2	NP_057290.2			vestigial-like family member 3											NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(11)	19	all_cancers(8;0.109)|Lung SC(3;0.184)	Lung NSC(201;0.0777)		LUSC - Lung squamous cell carcinoma(29;0.00241)|Lung(72;0.00712)		GGGATCAGCTGCAGAAAAGGT	0.587																																						dbGAP											0													62.0	65.0	64.0					3																	87018135		1993	4174	6167	-	-	-	SO:0001583	missense	0			AF099505	CCDS43110.1	3p12.1	2014-03-03	2014-03-03		ENSG00000206538	ENSG00000206538			24327	protein-coding gene	gene with protein product		609980	"""vestigial like 3 (Drosophila)"""			12376544	Standard	NM_016206		Approved	VGL-3	uc003dqn.3	A8MV65	OTTHUMG00000158984	ENST00000398399.2:c.542C>T	3.37:g.87018135G>A	ENSP00000381436:p.Ala181Val	Somatic		WXS	Illumina GAIIx	Phase_IV		Missense_Mutation	SNP	pfam_Vg_Tdu,smart_TDU_repeat	p.A181V	ENST00000398399.2	37	c.542	CCDS43110.1	3	.	.	.	.	.	.	.	.	.	.	G	14.68	2.607402	0.46527	.	.	ENSG00000206538	ENST00000398399;ENST00000383698	T;T	0.46063	0.89;0.88	5.81	5.81	0.92471	.	0.686444	0.13941	N	0.352211	T	0.42200	0.1192	L	0.50333	1.59	0.20489	N	0.999893	B	0.17038	0.02	B	0.16722	0.016	T	0.31308	-0.9948	10	0.56958	D	0.05	-0.1522	15.1874	0.73016	0.0:0.1406:0.8593:0.0	.	181	A8MV65	VGLL3_HUMAN	V	181	ENSP00000381436:A181V;ENSP00000373199:A181V	ENSP00000373199:A181V	A	-	2	0	VGLL3	87100825	0.243000	0.23878	0.342000	0.25602	0.984000	0.73092	2.721000	0.47260	2.756000	0.94617	0.511000	0.50034	GCA	VGLL3	-	NULL	ENSG00000206538		0.587	VGLL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	VGLL3	HGNC	protein_coding	OTTHUMT00000352805.1	200	0.00	0	G	NM_016206		87018135	87018135	-1	no_errors	ENST00000398399	ensembl	human	known	69_37n	missense	96	27.27	36	SNP	0.714	A
ZNF729	100287226	genome.wustl.edu	37	19	22496594	22496594	+	Silent	SNP	T	T	C			TCGA-A8-A09T-01A-11W-A019-09	TCGA-A8-A09T-10A-01W-A021-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	e565da2b-4a3f-4be1-9cf7-2845145d1dbc	8c267083-4672-4f9e-b5ec-19a13e897f78	g.chr19:22496594T>C	ENST00000601693.1	+	4	493	c.375T>C	c.(373-375)gaT>gaC	p.D125D	ZNF729_ENST00000357491.6_Silent_p.D125D			A6NN14	ZN729_HUMAN	zinc finger protein 729	125					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(1)|lung(32)|ovary(3)	41						TAAGAAAAGATTGTAAAAGTG	0.353																																						dbGAP											0																																										-	-	-	SO:0001819	synonymous_variant	0				CCDS59368.1	19p12	2014-02-14			ENSG00000196350	ENSG00000196350		"""Zinc fingers, C2H2-type"", ""-"""	32464	protein-coding gene	gene with protein product							Standard	NM_001242680		Approved		uc021urs.1	A6NN14	OTTHUMG00000182938	ENST00000601693.1:c.375T>C	19.37:g.22496594T>C		Somatic		WXS	Illumina GAIIx	Phase_IV	M0QY45	Silent	SNP	pfam_Znf_C2H2,pfam_Krueppel-associated_box,superfamily_Krueppel-associated_box,smart_Krueppel-associated_box,smart_Znf_C2H2-like,pfscan_Znf_C2H2,pfscan_Krueppel-associated_box	p.D125	ENST00000601693.1	37	c.375	CCDS59368.1	19																																																																																			ZNF729	-	NULL	ENSG00000196350		0.353	ZNF729-001	NOVEL	basic|appris_principal|CCDS	protein_coding	ZNF729	HGNC	protein_coding	OTTHUMT00000464396.1	50	0.00	0	T	XM_496301		22496594	22496594	+1	no_stop_codon	ENST00000357491	ensembl	human	known	69_37n	silent	81	33.61	41	SNP	0.021	C
