#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
ALOX5	240	genome.wustl.edu	37	10	45878089	45878089	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AO-A0J7-01A-11W-A050-09	TCGA-AO-A0J7-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	a53056d9-e8bd-4cb1-ad67-85879ccc925d	30586533-e188-4eb3-8ffd-0ce7c98a1b6b	g.chr10:45878089G>A	ENST00000374391.2	+	2	362	c.309G>A	c.(307-309)tgG>tgA	p.W103*	ALOX5_ENST00000542434.1_Nonsense_Mutation_p.W103*	NM_000698.3|NM_001256153.1	NP_000689.1|NP_001243082.1	P09917	LOX5_HUMAN	arachidonate 5-lipoxygenase	103	PLAT. {ECO:0000255|PROSITE- ProRule:PRU00152}.	Essential for stabilizing binding to COTL1.			arachidonic acid metabolic process (GO:0019369)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|leukotriene production involved in inflammatory response (GO:0002540)|lipoxin metabolic process (GO:2001300)|lipoxygenase pathway (GO:0019372)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular space (GO:0005615)|nuclear envelope (GO:0005635)|nuclear envelope lumen (GO:0005641)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)	arachidonate 5-lipoxygenase activity (GO:0004051)|iron ion binding (GO:0005506)	p.W103*(1)		breast(1)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(14)|ovary(2)|pancreas(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		Lung SC(717;0.0257)			Aminosalicylic Acid(DB00233)|Balsalazide(DB01014)|Diclofenac(DB00586)|Diethylcarbamazine(DB00711)|Masoprocol(DB00179)|Meclofenamic acid(DB00939)|Mesalazine(DB00244)|Minocycline(DB01017)|Montelukast(DB00471)|Sulfasalazine(DB00795)|Vitamin E(DB00163)|Zileuton(DB00744)	GCTACCGCTGGATCACCGGCG	0.597																																						dbGAP											1	Substitution - Nonsense(1)	breast(1)											67.0	55.0	59.0					10																	45878089		2203	4300	6503	-	-	-	SO:0001587	stop_gained	0			J03571	CCDS7212.1, CCDS58078.1	10q11.2	2008-03-18			ENSG00000012779	ENSG00000012779	1.13.11.34	"""Arachidonate lipoxygenases"""	435	protein-coding gene	gene with protein product		152390				2565035	Standard	NM_001256153		Approved	5-LOX	uc001jce.4	P09917	OTTHUMG00000018081	ENST00000374391.2:c.309G>A	10.37:g.45878089G>A	ENSP00000363512:p.Trp103*	Somatic		WXS	Illumina GAIIx	Phase_IV	B7ZLS0|E5FPY5|E5FPY7|E5FPY8|Q5JQ14	Nonsense_Mutation	SNP	pfam_LipOase_C,pfam_LipOase_LH2,superfamily_LipOase_C,superfamily_Lipase_LipOase,smart_LipOase_LH2,prints_LipOase_mml,prints_LipOase_C,pfscan_LipOase_LH2	p.W103*	ENST00000374391.2	37	c.309	CCDS7212.1	10	.	.	.	.	.	.	.	.	.	.	G	37	6.405710	0.97542	.	.	ENSG00000012779	ENST00000542434;ENST00000374391	.	.	.	5.07	5.07	0.68467	.	0.116888	0.64402	D	0.000006	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.4637	15.9724	0.80031	0.0:0.0:1.0:0.0	.	.	.	.	X	103	.	ENSP00000363512:W103X	W	+	3	0	ALOX5	45198095	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	9.657000	0.98554	2.639000	0.89480	0.655000	0.94253	TGG	ALOX5	-	pfam_LipOase_LH2,superfamily_Lipase_LipOase,smart_LipOase_LH2,pfscan_LipOase_LH2	ENSG00000012779		0.597	ALOX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ALOX5	HGNC	protein_coding	OTTHUMT00000047780.1	94	0.00	0	G			45878089	45878089	+1	no_errors	ENST00000374391	ensembl	human	known	69_37n	nonsense	37	35.09	20	SNP	1.000	A
BRSK2	9024	genome.wustl.edu	37	11	1466879	1466880	+	Frame_Shift_Ins	INS	-	-	C			TCGA-AO-A0J7-01A-11W-A050-09	TCGA-AO-A0J7-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	a53056d9-e8bd-4cb1-ad67-85879ccc925d	30586533-e188-4eb3-8ffd-0ce7c98a1b6b	g.chr11:1466879_1466880insC	ENST00000528841.1	+	11	1440_1441	c.1056_1057insC	c.(1057-1059)cccfs	p.P353fs	BRSK2_ENST00000544817.1_Frame_Shift_Ins_p.P48fs|BRSK2_ENST00000526678.1_Frame_Shift_Ins_p.P353fs|BRSK2_ENST00000308230.5_Frame_Shift_Ins_p.P353fs|BRSK2_ENST00000308219.9_Frame_Shift_Ins_p.P353fs|BRSK2_ENST00000382179.1_Frame_Shift_Ins_p.P399fs|BRSK2_ENST00000531197.1_Frame_Shift_Ins_p.P353fs|BRSK2_ENST00000528710.1_Frame_Shift_Ins_p.P293fs			Q8IWQ3	BRSK2_HUMAN	BR serine/threonine kinase 2	353					actin cytoskeleton reorganization (GO:0031532)|axonogenesis (GO:0007409)|establishment of cell polarity (GO:0030010)|exocytosis (GO:0006887)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|mitotic nuclear division (GO:0007067)|neuron differentiation (GO:0030182)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)			endometrium(4)|large_intestine(1)|lung(5)	10		all_epithelial(84;4.17e-05)|Breast(177;0.000307)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00144)|Lung(200;0.0713)|LUSC - Lung squamous cell carcinoma(625;0.0842)		ATGAGGACCTGCCCCCCCGGAA	0.649																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AF020089	CCDS41590.1, CCDS58106.1, CCDS58107.1, CCDS58108.1, CCDS60696.1	11p15.5	2008-02-05	2003-09-11	2005-01-27	ENSG00000174672	ENSG00000174672			11405	protein-coding gene	gene with protein product	"""serine/threonine kinase 29"""	609236	"""chromsosome 11 open reading frame 7"""	C11orf7, STK29		9852686, 9929968	Standard	NM_001256629		Approved	PEN11B	uc001ltm.4	Q8IWQ3	OTTHUMG00000167089	ENST00000528841.1:c.1063dupC	11.37:g.1466886_1466886dupC	ENSP00000432000:p.Pro353fs	Somatic		WXS	Illumina GAIIx	Phase_IV	B3KVE9|E9PLM7|O60843|O95099|Q5J5B4|Q6ZMQ4|Q8TB60	Frame_Shift_Ins	INS	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_cat_dom	p.R400fs	ENST00000528841.1	37	c.1194_1195	CCDS58107.1	11																																																																																			BRSK2	-	superfamily_Kinase-like_dom	ENSG00000174672		0.649	BRSK2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	BRSK2	HGNC	protein_coding	OTTHUMT00000393033.1	24	0.00	0	-	NM_003957		1466879	1466880	+1	no_errors	ENST00000382179	ensembl	human	known	69_37n	frame_shift_ins	16	15.79	3	INS	0.972:1.000	C
CPAMD8	27151	genome.wustl.edu	37	19	17032750	17032750	+	Silent	SNP	G	G	A			TCGA-AO-A0J7-01A-11W-A050-09	TCGA-AO-A0J7-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	a53056d9-e8bd-4cb1-ad67-85879ccc925d	30586533-e188-4eb3-8ffd-0ce7c98a1b6b	g.chr19:17032750G>A	ENST00000443236.1	-	27	3766	c.3735C>T	c.(3733-3735)agC>agT	p.S1245S		NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	1198	Poly-Gln.					extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.S1245S(1)		breast(11)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(14)|ovary(7)|pancreas(2)|prostate(4)|skin(5)	82						CCCCAAACGCGCTGTAGGAGC	0.682																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											28.0	37.0	34.0					19																	17032750		1808	3601	5409	-	-	-	SO:0001819	synonymous_variant	0			AY101765	CCDS42519.1	19p13.12	2008-02-05			ENSG00000160111	ENSG00000160111			23228	protein-coding gene	gene with protein product		608841				10574462	Standard	NM_015692		Approved	KIAA1283, VIP, K-CAP	uc002nfb.3	Q8IZJ3	OTTHUMG00000133549	ENST00000443236.1:c.3735C>T	19.37:g.17032750G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	Q8NC09|Q9ULD7	Missense_Mutation	SNP	pfam_A2M_comp,pfam_A2M_N_2,pfam_Methyltransf_FA,pfam_Macroglobln_a2,pfam_A-macroglobulin_rcpt-bd,pfam_A2M_N,pfam_MacrogloblnA2_thiol-ester-bond,pfam_Kazal-type_dom,pfam_Prot_inh_Kazal,superfamily_Terpenoid_cyclase/PrenylTrfase,superfamily_A-macroglobulin_rcpt-bd,smart_Prot_inh_Kazal	p.A1256V	ENST00000443236.1	37	c.3767	CCDS42519.1	19	.	.	.	.	.	.	.	.	.	.	G	9.369	1.070034	0.20147	.	.	ENSG00000160111	ENST00000443236	.	.	.	2.84	-2.66	0.06077	.	.	.	.	.	T	0.54695	0.1874	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50659	-0.8802	4	.	.	.	.	10.0344	0.42120	0.6131:0.0:0.3869:0.0	.	.	.	.	V	1256	.	.	A	-	2	0	CPAMD8	16893750	0.979000	0.34478	0.224000	0.23877	0.931000	0.56810	0.056000	0.14256	-0.683000	0.05190	0.561000	0.74099	GCG	CPAMD8	-	pfam_A2M_comp,superfamily_Terpenoid_cyclase/PrenylTrfase	ENSG00000160111		0.682	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CPAMD8	HGNC	protein_coding	OTTHUMT00000257531.2	45	0.00	0	G	NM_015692		17032750	17032750	-1	no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region	ENST00000443236	ensembl	human	known	69_37n	missense	46	45.88	39	SNP	0.986	A
CRIPAK	285464	genome.wustl.edu	37	4	1388790	1388790	+	Missense_Mutation	SNP	T	T	C	rs79415192		TCGA-AO-A0J7-01A-11W-A050-09	TCGA-AO-A0J7-10A-01W-A055-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	a53056d9-e8bd-4cb1-ad67-85879ccc925d	30586533-e188-4eb3-8ffd-0ce7c98a1b6b	g.chr4:1388790T>C	ENST00000324803.4	+	1	3451	c.491T>C	c.(490-492)gTg>gCg	p.V164A		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	164					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.V164A(1)		NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CGTGCCGACGTGGAGTGCCCG	0.692																																						dbGAP											1	Substitution - Missense(1)	lung(1)											180.0	124.0	143.0					4																	1388790		2201	4281	6482	-	-	-	SO:0001583	missense	0			AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.491T>C	4.37:g.1388790T>C	ENSP00000323978:p.Val164Ala	Somatic		WXS	Illumina GAIIx	Phase_IV	Q8NB03	Missense_Mutation	SNP	smart_Post-SET_dom	p.V164A	ENST00000324803.4	37	c.491	CCDS3349.1	4	.	.	.	.	.	.	.	.	.	.	t	1.148	-0.647432	0.03506	.	.	ENSG00000179979	ENST00000324803	T	0.24350	1.86	1.25	-2.49	0.06403	.	.	.	.	.	T	0.08714	0.0216	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.20174	-1.0283	9	0.14252	T	0.57	.	0.8761	0.01224	0.1598:0.3215:0.2492:0.2695	.	164	Q8N1N5	CRPAK_HUMAN	A	164	ENSP00000323978:V164A	ENSP00000323978:V164A	V	+	2	0	CRIPAK	1378790	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.847000	0.04331	-2.974000	0.00285	-1.550000	0.00899	GTG	CRIPAK	-	NULL	ENSG00000179979		0.692	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CRIPAK	HGNC	protein_coding	OTTHUMT00000241607.2	14	0.00	0	T	NM_175918		1388790	1388790	+1	no_errors	ENST00000324803	ensembl	human	known	69_37n	missense	5	64.29	9	SNP	0.000	C
FAM205A	259308	genome.wustl.edu	37	9	34723329	34723329	+	Missense_Mutation	SNP	G	G	A			TCGA-AO-A0J7-01A-11W-A050-09	TCGA-AO-A0J7-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	a53056d9-e8bd-4cb1-ad67-85879ccc925d	30586533-e188-4eb3-8ffd-0ce7c98a1b6b	g.chr9:34723329G>A	ENST00000378788.3	-	4	3947	c.3908C>T	c.(3907-3909)tCc>tTc	p.S1303F		NM_001141917.1	NP_001135389.1	Q6ZU69	F205A_HUMAN	family with sequence similarity 205, member A	1303						integral component of membrane (GO:0016021)|nucleus (GO:0005634)		p.S1303F(2)		breast(1)|endometrium(2)|kidney(1)	4						AGGTTGTCTGGAGTGTAGCCG	0.617																																						dbGAP											2	Substitution - Missense(2)	breast(2)											66.0	67.0	67.0					9																	34723329		692	1591	2283	-	-	-	SO:0001583	missense	0				CCDS55305.1	9p13.3	2014-05-16			ENSG00000205108	ENSG00000205108			41911	protein-coding gene	gene with protein product							Standard	NM_001141917		Approved	C9orf144B	uc011lor.2	Q6ZU69	OTTHUMG00000000448	ENST00000378788.3:c.3908C>T	9.37:g.34723329G>A	ENSP00000417711:p.Ser1303Phe	Somatic		WXS	Illumina GAIIx	Phase_IV	A8MVW7	Missense_Mutation	SNP	NULL	p.S1303F	ENST00000378788.3	37	c.3908	CCDS55305.1	9	.	.	.	.	.	.	.	.	.	.	G	13.51	2.259364	0.39995	.	.	ENSG00000205108	ENST00000378788	T	0.31247	1.5	3.01	2.11	0.27256	.	.	.	.	.	T	0.40498	0.1119	L	0.43152	1.355	0.09310	N	1	D	0.69078	0.997	D	0.65684	0.937	T	0.11991	-1.0565	9	0.87932	D	0	.	5.7588	0.18188	0.15:0.0:0.85:0.0	.	1303	Q6ZU69	F205A_HUMAN	F	1303	ENSP00000417711:S1303F	ENSP00000417711:S1303F	S	-	2	0	RP11-195F19.10	34713329	0.000000	0.05858	0.026000	0.17262	0.048000	0.14542	0.314000	0.19432	0.822000	0.34565	0.555000	0.69702	TCC	FAM205A	-	NULL	ENSG00000205108		0.617	FAM205A-001	NOVEL	basic|appris_principal|CCDS	protein_coding	FAM205A	HGNC	protein_coding	OTTHUMT00000001150.2	76	0.00	0	G	NM_001141917		34723329	34723329	-1	no_errors	ENST00000378788	ensembl	human	novel	69_37n	missense	42	48.78	40	SNP	0.029	A
FCGBP	8857	genome.wustl.edu	37	19	40383820	40383820	+	Missense_Mutation	SNP	C	C	T			TCGA-AO-A0J7-01A-11W-A050-09	TCGA-AO-A0J7-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	a53056d9-e8bd-4cb1-ad67-85879ccc925d	30586533-e188-4eb3-8ffd-0ce7c98a1b6b	g.chr19:40383820C>T	ENST00000221347.6	-	21	9797	c.9790G>A	c.(9790-9792)Ggc>Agc	p.G3264S		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	3264			G -> S (in dbSNP:rs6508919).			extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			GGCTGGCAGCCGTGCTGGCCG	0.662																																						dbGAP											0																																										-	-	-	SO:0001583	missense	0			D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.9790G>A	19.37:g.40383820C>T	ENSP00000221347:p.Gly3264Ser	Somatic		WXS	Illumina GAIIx	Phase_IV	O95784	Missense_Mutation	SNP	pfam_VWF_type-D,pfam_Unchr_dom_Cys-rich,pfam_TIL_dom,superfamily_TIL_dom,smart_Fol_N,smart_VWF_type-D,smart_Unchr_dom_Cys-rich,smart_EGF-like,smart_VWF_C,smart_VWC_out	p.G3264S	ENST00000221347.6	37	c.9790	CCDS12546.1	19	.	.	.	.	.	.	.	.	.	.	C	17.89	3.500296	0.64298	.	.	ENSG00000090920	ENST00000221347	T	0.05025	3.51	3.01	3.01	0.34805	von Willebrand factor, type D domain (1);	.	.	.	.	T	0.17066	0.0410	M	0.77103	2.36	0.21445	N	0.99968	D	0.71674	0.998	D	0.68192	0.956	T	0.15636	-1.0430	9	0.11182	T	0.66	.	5.4472	0.16541	0.0:0.7348:0.0:0.2652	.	3264	Q9Y6R7	FCGBP_HUMAN	S	3264	ENSP00000221347:G3264S	ENSP00000221347:G3264S	G	-	1	0	FCGBP	45075660	0.004000	0.15560	0.859000	0.33776	0.956000	0.61745	0.708000	0.25719	1.388000	0.46506	0.400000	0.26472	GGC	FCGBP	-	smart_VWC_out,smart_VWF_type-D	ENSG00000090920		0.662	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FCGBP	HGNC	protein_coding	OTTHUMT00000462507.1	21	0.00	0	C	NM_003890		40383820	40383820	-1	no_errors	ENST00000221347	ensembl	human	known	69_37n	missense	42	23.64	13	SNP	0.796	T
G6PC2	57818	genome.wustl.edu	37	2	169757925	169757925	+	Missense_Mutation	SNP	T	T	A			TCGA-AO-A0J7-01A-11W-A050-09	TCGA-AO-A0J7-10A-01W-A055-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	a53056d9-e8bd-4cb1-ad67-85879ccc925d	30586533-e188-4eb3-8ffd-0ce7c98a1b6b	g.chr2:169757925T>A	ENST00000375363.3	+	1	176	c.84T>A	c.(82-84)ttT>ttA	p.F28L	SPC25_ENST00000472216.2_Intron|G6PC2_ENST00000421979.1_Missense_Mutation_p.F28L|G6PC2_ENST00000429379.2_Missense_Mutation_p.F28L	NM_021176.2	NP_066999.1	Q9NQR9	G6PC2_HUMAN	glucose-6-phosphatase, catalytic, 2	28					carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	glucose-6-phosphatase activity (GO:0004346)	p.F28L(1)		breast(1)|endometrium(1)|large_intestine(1)|lung(5)|pancreas(1)|prostate(1)|skin(1)|stomach(2)	13						TTCTAAATTTTATGTCCAATG	0.368																																						dbGAP											1	Substitution - Missense(1)	breast(1)											127.0	129.0	128.0					2																	169757925		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF283575	CCDS2230.1, CCDS46443.1	2q24-q31	2008-02-05			ENSG00000152254	ENSG00000152254			28906	protein-coding gene	gene with protein product	"""islet specific glucose 6 phosphatase catalytic subunit related protein"""	608058				10078553, 10078554	Standard	NM_021176		Approved	IGRP	uc002uem.3	Q9NQR9	OTTHUMG00000132182	ENST00000375363.3:c.84T>A	2.37:g.169757925T>A	ENSP00000364512:p.Phe28Leu	Somatic		WXS	Illumina GAIIx	Phase_IV	E9PAX2|Q6AHZ0	Missense_Mutation	SNP	pfam_P_Acid_Pase_2/haloperoxidase,superfamily_P_Acid_Pase_2/haloperoxidase,smart_P_Acid_Pase_2/haloperoxidase,pirsf_Glucose-6-phosphatase	p.F28L	ENST00000375363.3	37	c.84	CCDS2230.1	2	.	.	.	.	.	.	.	.	.	.	T	4.181	0.032167	0.08101	.	.	ENSG00000152254	ENST00000375363;ENST00000429379;ENST00000421979	T;T;D	0.82081	-0.91;-0.91;-1.57	5.62	3.27	0.37495	Phosphatidic acid phosphatase/chloroperoxidase, N-terminal (1);	0.072056	0.52532	N	0.000079	T	0.69833	0.3155	L	0.38175	1.15	0.38422	D	0.946204	B;B	0.32071	0.355;0.355	B;B	0.28638	0.092;0.092	T	0.63051	-0.6723	10	0.14656	T	0.56	-12.2784	8.3404	0.32241	0.0:0.2543:0.0:0.7457	.	28;28	E9PAX2;Q9NQR9	.;G6PC2_HUMAN	L	28	ENSP00000364512:F28L;ENSP00000396939:F28L;ENSP00000392183:F28L	ENSP00000282075:F28L	F	+	3	2	G6PC2	169466171	0.997000	0.39634	1.000000	0.80357	0.228000	0.25075	0.439000	0.21575	0.959000	0.37980	0.533000	0.62120	TTT	G6PC2	-	superfamily_P_Acid_Pase_2/haloperoxidase,pirsf_Glucose-6-phosphatase	ENSG00000152254		0.368	G6PC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	G6PC2	HGNC	protein_coding	OTTHUMT00000255234.2	421	0.00	0	T	NM_021176		169757925	169757925	+1	no_errors	ENST00000375363	ensembl	human	known	69_37n	missense	116	52.85	130	SNP	1.000	A
HECTD4	283450	genome.wustl.edu	37	12	112623045	112623046	+	Frame_Shift_Ins	INS	-	-	C	rs368404348		TCGA-AO-A0J7-01A-11W-A050-09	TCGA-AO-A0J7-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	a53056d9-e8bd-4cb1-ad67-85879ccc925d	30586533-e188-4eb3-8ffd-0ce7c98a1b6b	g.chr12:112623045_112623046insC	ENST00000430131.2	-	60	9603_9604	c.8458_8459insG	c.(8458-8460)gcgfs	p.A2820fs	HECTD4_ENST00000550722.1_Frame_Shift_Ins_p.A3096fs|HECTD4_ENST00000377560.5_Frame_Shift_Ins_p.A3070fs			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	2820					glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)										Accggccgccgcccccccggag	0.639																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AK091473		12q24.13	2013-07-17	2012-08-14	2012-08-14	ENSG00000173064	ENSG00000173064			26611	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 51"""	C12orf51		21270382	Standard	NM_001109662		Approved	FLJ34154, KIAA0614	uc021reb.1	Q9Y4D8	OTTHUMG00000150719	ENST00000430131.2:c.8459dupG	12.37:g.112623052_112623052dupC	ENSP00000404379:p.Ala2820fs	Somatic		WXS	Illumina GAIIx	Phase_IV	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Frame_Shift_Ins	INS	pfam_HECT,superfamily_HECT,superfamily_ConA-like_lec_gl,smart_HECT,pfscan_HECT	p.A3070fs	ENST00000430131.2	37	c.9209_9208		12																																																																																			HECTD4	-	NULL	ENSG00000173064		0.639	HECTD4-202	KNOWN	basic	protein_coding	HECTD4	HGNC	protein_coding		14	0.00	0	-	NM_173813		112623045	112623046	-1	no_errors	ENST00000377560	ensembl	human	known	69_37n	frame_shift_ins	15	16.67	3	INS	0.000:0.001	C
HRNR	388697	genome.wustl.edu	37	1	152186708	152186708	+	Missense_Mutation	SNP	C	C	T			TCGA-AO-A0J7-01A-11W-A050-09	TCGA-AO-A0J7-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	a53056d9-e8bd-4cb1-ad67-85879ccc925d	30586533-e188-4eb3-8ffd-0ce7c98a1b6b	g.chr1:152186708C>T	ENST00000368801.2	-	3	7472	c.7397G>A	c.(7396-7398)cGc>cAc	p.R2466H	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	2466					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTGTCCTGAGCGAGACTCTCG	0.557																																						dbGAP											0																																										-	-	-	SO:0001583	missense	0			AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"""EF-hand domain containing"""	20846	protein-coding gene	gene with protein product	"""filaggrin family member 3"""						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.7397G>A	1.37:g.152186708C>T	ENSP00000357791:p.Arg2466His	Somatic		WXS	Illumina GAIIx	Phase_IV	Q5DT20|Q5U1F4	Missense_Mutation	SNP	pfam_S100_Ca-bd_sub,pfscan_EF_HAND_2	p.R2466H	ENST00000368801.2	37	c.7397	CCDS30859.1	1	.	.	.	.	.	.	.	.	.	.	-	5.335	0.247135	0.10130	.	.	ENSG00000197915	ENST00000368801	T	0.01745	4.66	3.45	-2.29	0.06805	.	.	.	.	.	T	0.00356	0.0011	L	0.29908	0.895	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.46978	-0.9152	9	0.12766	T	0.61	.	0.1441	0.00086	0.3045:0.2442:0.1494:0.3019	.	2466	Q86YZ3	HORN_HUMAN	H	2466	ENSP00000357791:R2466H	ENSP00000357791:R2466H	R	-	2	0	HRNR	150453332	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.037000	0.13840	-0.321000	0.08627	-1.999000	0.00445	CGC	HRNR	-	NULL	ENSG00000197915		0.557	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HRNR	HGNC	protein_coding	OTTHUMT00000034016.1	37	0.00	0	C	XM_373868		152186708	152186708	-1	no_errors	ENST00000368801	ensembl	human	known	69_37n	missense	22	12.00	3	SNP	0.000	T
INTS10	55174	genome.wustl.edu	37	8	19679949	19679949	+	Splice_Site	SNP	G	G	A			TCGA-AO-A0J7-01A-11W-A050-09	TCGA-AO-A0J7-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	a53056d9-e8bd-4cb1-ad67-85879ccc925d	30586533-e188-4eb3-8ffd-0ce7c98a1b6b	g.chr8:19679949G>A	ENST00000397977.3	+	5	839		c.e5-1		INTS10_ENST00000521758.1_Splice_Site	NM_018142.2	NP_060612.2	Q9NVR2	INT10_HUMAN	integrator complex subunit 10						snRNA processing (GO:0016180)	integrator complex (GO:0032039)		p.?(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	20				Colorectal(111;0.057)|COAD - Colon adenocarcinoma(73;0.215)		TTTTGAAATAGGTTGGCCTTG	0.323																																						dbGAP											1	Unknown(1)	breast(1)											62.0	60.0	60.0					8																	19679949		1807	4067	5874	-	-	-	SO:0001630	splice_region_variant	0			AK001431	CCDS6011.2	8p21.3	2006-04-26	2006-03-15	2006-03-15	ENSG00000104613	ENSG00000104613			25548	protein-coding gene	gene with protein product		611353	"""chromosome 8 open reading frame 35"""	C8orf35		16239144	Standard	XM_005273558		Approved	FLJ10569, INT10	uc003wzj.3	Q9NVR2	OTTHUMG00000131065	ENST00000397977.3:c.442-1G>A	8.37:g.19679949G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	Q6IA93|Q7L538|Q7L8C8|Q9H3W8	Splice_Site	SNP	-	e5-1	ENST00000397977.3	37	c.442-1	CCDS6011.2	8	.	.	.	.	.	.	.	.	.	.	G	19.01	3.744065	0.69418	.	.	ENSG00000104613	ENST00000397977	.	.	.	5.46	5.46	0.80206	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.8632	0.88787	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	INTS10	19724229	1.000000	0.71417	1.000000	0.80357	0.816000	0.46133	9.162000	0.94745	2.570000	0.86706	0.655000	0.94253	.	INTS10	-	-	ENSG00000104613		0.323	INTS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	INTS10	HGNC	protein_coding	OTTHUMT00000253724.2	182	0.00	0	G	NM_018142	Intron	19679949	19679949	+1	no_errors	ENST00000397977	ensembl	human	known	69_37n	splice_site	76	35.04	41	SNP	1.000	A
KCNH7	90134	genome.wustl.edu	37	2	163302895	163302895	+	Missense_Mutation	SNP	T	T	C			TCGA-AO-A0J7-01A-11W-A050-09	TCGA-AO-A0J7-10A-01W-A055-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	a53056d9-e8bd-4cb1-ad67-85879ccc925d	30586533-e188-4eb3-8ffd-0ce7c98a1b6b	g.chr2:163302895T>C	ENST00000332142.5	-	7	1286	c.1187A>G	c.(1186-1188)aAc>aGc	p.N396S	KCNH7_ENST00000328032.4_Missense_Mutation_p.N389S	NM_033272.3	NP_150375.2	Q9NS40	KCNH7_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 7	396					circadian rhythm (GO:0007623)|potassium ion transmembrane transport (GO:0071805)|protein heterooligomerization (GO:0051291)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)|signal transducer activity (GO:0004871)|voltage-gated potassium channel activity (GO:0005249)	p.N396S(1)|p.N389S(1)		NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(22)|lung(53)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	108					Doxazosin(DB00590)|Ibutilide(DB00308)|Miconazole(DB01110)|Prazosin(DB00457)|Terazosin(DB01162)	CGTAAACTTGTTGATGCGTGG	0.423																																					GBM(196;1492 2208 17507 24132 45496)	dbGAP											2	Substitution - Missense(2)	breast(2)											90.0	86.0	87.0					2																	163302895		2203	4299	6502	-	-	-	SO:0001583	missense	0			AF032897	CCDS2219.1, CCDS2220.1	2q24.3	2012-07-05			ENSG00000184611	ENSG00000184611		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	18863	protein-coding gene	gene with protein product		608169				16382104	Standard	NM_173162		Approved	Kv11.3, HERG3, erg3	uc002uch.2	Q9NS40	OTTHUMG00000132069	ENST00000332142.5:c.1187A>G	2.37:g.163302895T>C	ENSP00000331727:p.Asn396Ser	Somatic		WXS	Illumina GAIIx	Phase_IV	Q53QU4|Q53TB7|Q53TP9|Q8IV15	Missense_Mutation	SNP	pfam_Ion_trans_dom,pfam_cNMP-bd_dom,pfam_Ion_trans_2,pfam_PAS_fold_3,superfamily_cNMP-bd-like,smart_cNMP-bd_dom,prints_K_chnl_volt-dep_EAG/ELK/ERG,prints_K_chnl_volt-dep_ERG,pfscan_cNMP-bd_dom,tigrfam_PAS	p.N396S	ENST00000332142.5	37	c.1187	CCDS2219.1	2	.	.	.	.	.	.	.	.	.	.	T	16.83	3.230607	0.58777	.	.	ENSG00000184611	ENST00000332142;ENST00000328032	D;D	0.92805	-3.11;-3.11	5.55	5.55	0.83447	.	0.134936	0.64402	D	0.000002	T	0.78735	0.4330	N	0.01874	-0.695	0.80722	D	1	B;B	0.17038	0.02;0.008	B;B	0.19666	0.026;0.008	T	0.75814	-0.3185	10	0.05959	T	0.93	.	15.6901	0.77442	0.0:0.0:0.0:1.0	.	389;396	Q9NS40-2;Q9NS40	.;KCNH7_HUMAN	S	396;389	ENSP00000331727:N396S;ENSP00000333781:N389S	ENSP00000333781:N389S	N	-	2	0	KCNH7	163011141	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.991000	0.88244	2.114000	0.64651	0.528000	0.53228	AAC	KCNH7	-	NULL	ENSG00000184611		0.423	KCNH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KCNH7	HGNC	protein_coding	OTTHUMT00000255093.1	135	0.00	0	T	NM_033272		163302895	163302895	-1	no_errors	ENST00000332142	ensembl	human	known	69_37n	missense	88	29.03	36	SNP	1.000	C
KRT79	338785	genome.wustl.edu	37	12	53215777	53215778	+	Frame_Shift_Ins	INS	-	-	C			TCGA-AO-A0J7-01A-11W-A050-09	TCGA-AO-A0J7-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	a53056d9-e8bd-4cb1-ad67-85879ccc925d	30586533-e188-4eb3-8ffd-0ce7c98a1b6b	g.chr12:53215777_53215778insC	ENST00000330553.5	-	9	1520_1521	c.1486_1487insG	c.(1486-1488)gccfs	p.A496fs		NM_175834.2	NP_787028.1	Q5XKE5	K2C79_HUMAN	keratin 79	496	Tail.					extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	enzyme binding (GO:0019899)|structural molecule activity (GO:0005198)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						ACCCTTGGTGGCCCCCCCACTC	0.619																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AJ564105	CCDS8839.1	12q13.13	2014-02-12	2007-07-03		ENSG00000185640	ENSG00000185640		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28930	protein-coding gene	gene with protein product	"""keratin 6-like"""	611160				11683385	Standard	NM_175834		Approved	K6L, KRT6L	uc001sbb.3	Q5XKE5	OTTHUMG00000169878	ENST00000330553.5:c.1487dupG	12.37:g.53215784_53215784dupC	ENSP00000328358:p.Ala496fs	Somatic		WXS	Illumina GAIIx	Phase_IV	Q6P465|Q7Z793	Frame_Shift_Ins	INS	pfam_F,superfamily_STAT_TF_coiled-coil,prints_Keratin_II	p.A496fs	ENST00000330553.5	37	c.1487_1486	CCDS8839.1	12																																																																																			KRT79	-	NULL	ENSG00000185640		0.619	KRT79-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KRT79	HGNC	protein_coding	OTTHUMT00000406376.1	64	0.00	0	-	NM_175834		53215777	53215778	-1	no_errors	ENST00000330553	ensembl	human	known	69_37n	frame_shift_ins	70	11.39	9	INS	0.000:0.000	C
KSR1	8844	genome.wustl.edu	37	17	25910015	25910016	+	Frame_Shift_Ins	INS	-	-	C			TCGA-AO-A0J7-01A-11W-A050-09	TCGA-AO-A0J7-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	a53056d9-e8bd-4cb1-ad67-85879ccc925d	30586533-e188-4eb3-8ffd-0ce7c98a1b6b	g.chr17:25910015_25910016insC	ENST00000319524.6	+	4	864_865	c.864_865insC	c.(865-867)cccfs	p.P289fs	KSR1_ENST00000268763.6_Frame_Shift_Ins_p.P152fs|KSR1_ENST00000398988.3_Frame_Shift_Ins_p.P152fs|KSR1_ENST00000509603.2_Frame_Shift_Ins_p.P289fs			Q8IVT5	KSR1_HUMAN	kinase suppressor of ras 1	289	Poly-Pro.				Ras protein signal transduction (GO:0007265)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.P292fs*22(2)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(12)|prostate(2)|urinary_tract(1)	28	Lung NSC(42;0.00836)		BRCA - Breast invasive adenocarcinoma(3;0.00122)	UCEC - Uterine corpus endometrioid carcinoma (53;0.168)		CACCACGGACGCCCCCCCCACC	0.678																																					Esophageal Squamous(88;1120 1336 6324 10502 16832)	dbGAP											2	Insertion - Frameshift(2)	large_intestine(2)																																								-	-	-	SO:0001589	frameshift_variant	0			U43586	CCDS58532.1	17q11.2	2012-05-23	2005-12-14	2005-12-14	ENSG00000141068	ENSG00000141068			6465	protein-coding gene	gene with protein product		601132	"""kinase suppressor of ras"""	KSR		8521512	Standard	XM_006722151		Approved	RSU2	uc031qzj.1	Q8IVT5	OTTHUMG00000132051	ENST00000319524.6:c.872dupC	17.37:g.25910023_25910023dupC	ENSP00000323178:p.Pro289fs	Somatic		WXS	Illumina GAIIx	Phase_IV	F8WEA9|H7BYU0|Q13476	Frame_Shift_Ins	INS	pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Prot_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Prot_Kinase_C-like_PE/DAG-bd,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_Kinase_C-like_PE/DAG-bd,pfscan_Prot_kinase_cat_dom,prints_Ser-Thr/Tyr_kinase_cat_dom	p.P291fs	ENST00000319524.6	37	c.864_865		17																																																																																			KSR1	-	NULL	ENSG00000141068		0.678	KSR1-202	KNOWN	basic|appris_candidate_longest	protein_coding	KSR1	HGNC	protein_coding		21	0.00	0	-	NM_014238		25910015	25910016	+1	no_errors	ENST00000319524	ensembl	human	known	69_37n	frame_shift_ins	26	10.34	3	INS	0.261:0.999	C
LRP1	4035	genome.wustl.edu	37	12	57597181	57597182	+	Frame_Shift_Ins	INS	-	-	C			TCGA-AO-A0J7-01A-11W-A050-09	TCGA-AO-A0J7-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	a53056d9-e8bd-4cb1-ad67-85879ccc925d	30586533-e188-4eb3-8ffd-0ce7c98a1b6b	g.chr12:57597181_57597182insC	ENST00000243077.3	+	70	11294_11295	c.10828_10829insC	c.(10828-10830)accfs	p.T3610fs		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	3610	LDL-receptor class A 27. {ECO:0000255|PROSITE-ProRule:PRU00124}.				aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	GAAAGACTGCACCCCCCGCTGT	0.644																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"""CD molecules"", ""Low density lipoprotein receptors"""	6692	protein-coding gene	gene with protein product		107770	"""alpha-2-macroglobulin receptor"""	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.10834dupC	12.37:g.57597187_57597187dupC	ENSP00000243077:p.Thr3610fs	Somatic		WXS	Illumina GAIIx	Phase_IV	Q2PP12|Q86SW0|Q8IVG8	Frame_Shift_Ins	INS	pfam_LDrepeatLR_classA_rpt,pfam_LDLR_classB_rpt,superfamily_Growth_fac_rcpt,superfamily_LDrepeatLR_classA_rpt,smart_LDrepeatLR_classA_rpt,smart_EGF-like_Ca-bd,smart_EGF-like,smart_LDLR_classB_rpt,pfscan_EG-like_dom,pfscan_LDrepeatLR_classA_rpt,pfscan_LDLR_classB_rpt	p.R3612fs	ENST00000243077.3	37	c.10828_10829	CCDS8932.1	12																																																																																			LRP1	-	pfam_LDrepeatLR_classA_rpt,superfamily_LDrepeatLR_classA_rpt,smart_LDrepeatLR_classA_rpt,pfscan_LDrepeatLR_classA_rpt	ENSG00000123384		0.644	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LRP1	HGNC	protein_coding	OTTHUMT00000412772.2	28	0.00	0	-	NM_002332		57597181	57597182	+1	no_errors	ENST00000243077	ensembl	human	known	69_37n	frame_shift_ins	17	10.53	2	INS	0.495:0.403	C
MAP3K1	4214	genome.wustl.edu	37	5	56178637	56178638	+	Frame_Shift_Del	DEL	AT	AT	-	rs368673262		TCGA-AO-A0J7-01A-11W-A050-09	TCGA-AO-A0J7-10A-01W-A055-09	AT	AT					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	a53056d9-e8bd-4cb1-ad67-85879ccc925d	30586533-e188-4eb3-8ffd-0ce7c98a1b6b	g.chr5:56178637_56178638delAT	ENST00000399503.3	+	14	3610_3611	c.3610_3611delAT	c.(3610-3612)atafs	p.I1204fs		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	1204					activation of MAPKK activity (GO:0000186)|apoptotic mitochondrial changes (GO:0008637)|cellular response to mechanical stimulus (GO:0071260)|epithelial cell morphogenesis (GO:0003382)|eyelid development in camera-type eye (GO:0061029)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of actin filament polymerization (GO:0030838)|protein phosphorylation (GO:0006468)|regulation of cell migration (GO:0030334)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	cytosol (GO:0005829)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)			NS(1)|breast(19)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(11)|ovary(1)|skin(3)|urinary_tract(1)	57		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)		TGCCCTCCCCATAGTTCCTCAG	0.411																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			U29671, AF042838	CCDS43318.1	5q11.2	2012-02-23	2012-02-23		ENSG00000095015	ENSG00000095015		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6848	protein-coding gene	gene with protein product		600982	"""mitogen-activated protein kinase kinase kinase 1"""	MEKK1		8597633	Standard	NM_005921		Approved	MEKK, MAPKKK1	uc003jqw.4	Q13233	OTTHUMG00000059486	ENST00000399503.3:c.3610_3611delAT	5.37:g.56178637_56178638delAT	ENSP00000382423:p.Ile1204fs	Somatic		WXS	Illumina GAIIx	Phase_IV		Frame_Shift_Del	DEL	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,superfamily_ARM-type_fold,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Znf_RING,pfscan_Znf_SWIM,pfscan_Prot_kinase_cat_dom	p.I1204fs	ENST00000399503.3	37	c.3610_3611	CCDS43318.1	5																																																																																			MAP3K1	-	NULL	ENSG00000095015		0.411	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	MAP3K1	HGNC	protein_coding	OTTHUMT00000132309.2	164	0.00	0	AT	XM_042066		56178637	56178638	+1	no_errors	ENST00000399503	ensembl	human	novel	69_37n	frame_shift_del	77	40.60	54	DEL	0.050:0.201	-
NCSTN	23385	genome.wustl.edu	37	1	160323977	160323977	+	Missense_Mutation	SNP	A	A	G	rs143039637	byFrequency	TCGA-AO-A0J7-01A-11W-A050-09	TCGA-AO-A0J7-10A-01W-A055-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	a53056d9-e8bd-4cb1-ad67-85879ccc925d	30586533-e188-4eb3-8ffd-0ce7c98a1b6b	g.chr1:160323977A>G	ENST00000294785.5	+	11	1374	c.1249A>G	c.(1249-1251)Aat>Gat	p.N417D	NCSTN_ENST00000368063.1_Missense_Mutation_p.N397D|NCSTN_ENST00000368065.4_Missense_Mutation_p.N159D|NCSTN_ENST00000459963.1_3'UTR|NCSTN_ENST00000535857.1_Missense_Mutation_p.N279D|NCSTN_ENST00000392212.4_Missense_Mutation_p.N397D	NM_015331.2	NP_056146.1	Q92542	NICA_HUMAN	nicastrin	417					amyloid precursor protein catabolic process (GO:0042987)|apoptotic signaling pathway (GO:0097190)|beta-amyloid metabolic process (GO:0050435)|epithelial cell proliferation (GO:0050673)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|myeloid cell homeostasis (GO:0002262)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of apoptotic process (GO:0043065)|positive regulation of catalytic activity (GO:0043085)|protein processing (GO:0016485)|proteolysis (GO:0006508)|T cell proliferation (GO:0042098)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	endopeptidase activity (GO:0004175)	p.N417D(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(16)|ovary(1)|prostate(1)|skin(2)	34	all_cancers(52;8.15e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			CAGGAGGCCAAATCAGTCCCA	0.562																																						dbGAP											1	Substitution - Missense(1)	breast(1)											164.0	129.0	141.0					1																	160323977		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF240468	CCDS1203.1	1q22-q23	2014-09-17			ENSG00000162736	ENSG00000162736			17091	protein-coding gene	gene with protein product		605254				9039502, 10993067	Standard	XM_005245053		Approved	KIAA0253, APH2	uc001fvx.3	Q92542	OTTHUMG00000033110	ENST00000294785.5:c.1249A>G	1.37:g.160323977A>G	ENSP00000294785:p.Asn417Asp	Somatic		WXS	Illumina GAIIx	Phase_IV	Q5T207|Q5T208|Q86VV5	Missense_Mutation	SNP	pfam_Nicastrin	p.N417D	ENST00000294785.5	37	c.1249	CCDS1203.1	1	.	.	.	.	.	.	.	.	.	.	A	7.828	0.719286	0.15372	.	.	ENSG00000162736	ENST00000294785;ENST00000368063;ENST00000535857;ENST00000368067;ENST00000392212;ENST00000368065;ENST00000424754	T;T;T;T;T;T	0.71698	-0.59;-0.59;-0.59;-0.59;-0.59;-0.59	5.3	-0.795	0.10915	.	1.399860	0.03975	N	0.292320	T	0.21387	0.0515	N	0.02158	-0.66	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.09377	0.004;0.001;0.002	T	0.07158	-1.0787	10	0.24483	T	0.36	-0.0353	9.9032	0.41359	0.4243:0.0:0.5757:0.0	.	279;397;417	F6Y097;Q92542-2;Q92542	.;.;NICA_HUMAN	D	417;397;279;124;397;159;161	ENSP00000294785:N417D;ENSP00000357042:N397D;ENSP00000442605:N279D;ENSP00000376047:N397D;ENSP00000357044:N159D;ENSP00000410124:N161D	ENSP00000294785:N417D	N	+	1	0	NCSTN	158590601	0.000000	0.05858	0.000000	0.03702	0.964000	0.63967	0.308000	0.19314	0.055000	0.16094	0.533000	0.62120	AAT	NCSTN	-	pfam_Nicastrin	ENSG00000162736		0.562	NCSTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NCSTN	HGNC	protein_coding	OTTHUMT00000080622.1	274	0.00	0	A	NM_015331		160323977	160323977	+1	no_errors	ENST00000294785	ensembl	human	known	69_37n	missense	191	40.91	135	SNP	0.000	G
PCNXL2	80003	genome.wustl.edu	37	1	233134902	233134902	+	Missense_Mutation	SNP	C	C	T			TCGA-AO-A0J7-01A-11W-A050-09	TCGA-AO-A0J7-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	a53056d9-e8bd-4cb1-ad67-85879ccc925d	30586533-e188-4eb3-8ffd-0ce7c98a1b6b	g.chr1:233134902C>T	ENST00000258229.9	-	31	5786	c.5552G>A	c.(5551-5553)gGa>gAa	p.G1851E	PCNXL2_ENST00000344698.2_Missense_Mutation_p.G503E	NM_014801.3	NP_055616.3	A6NKB5	PCX2_HUMAN	pecanex-like 2 (Drosophila)	1851						integral component of membrane (GO:0016021)		p.G1851E(1)		NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(7)|large_intestine(19)|lung(30)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86		all_cancers(173;0.0347)|Prostate(94;0.137)				AGTGATGGGTCCACCCCAGAT	0.527																																						dbGAP											1	Substitution - Missense(1)	breast(1)											76.0	76.0	76.0					1																	233134902		1938	4129	6067	-	-	-	SO:0001583	missense	0			AK055374	CCDS44335.1	1q42.2	2008-02-05	2001-11-28		ENSG00000135749	ENSG00000135749			8736	protein-coding gene	gene with protein product			"""pecanex (Drosophila)-like 2"""			12477932	Standard	NM_014801		Approved	KIAA0435, FLJ11383	uc001hvl.2	A6NKB5	OTTHUMG00000037824	ENST00000258229.9:c.5552G>A	1.37:g.233134902C>T	ENSP00000258229:p.Gly1851Glu	Somatic		WXS	Illumina GAIIx	Phase_IV	O43162|Q5T9Z8|Q5TDF1|Q8TEP4|Q96HP9|Q9HAL8	Missense_Mutation	SNP	pfam_Pecanex,superfamily_Pept_cys/ser_Trypsin-like	p.G1851E	ENST00000258229.9	37	c.5552	CCDS44335.1	1	.	.	.	.	.	.	.	.	.	.	C	17.67	3.445793	0.63178	.	.	ENSG00000135749	ENST00000344698;ENST00000258229	T;T	0.26660	1.72;2.82	5.88	5.88	0.94601	.	0.099075	0.64402	D	0.000001	T	0.32793	0.0841	L	0.60455	1.87	0.80722	D	1	P;P	0.47302	0.82;0.893	P;B	0.45881	0.496;0.394	T	0.03077	-1.1075	10	0.56958	D	0.05	.	13.4402	0.61108	0.0:0.9287:0.0:0.0713	.	1851;503	A6NKB5;A6NKB5-3	PCX2_HUMAN;.	E	503;1851	ENSP00000340759:G503E;ENSP00000258229:G1851E	ENSP00000258229:G1851E	G	-	2	0	PCNXL2	231201525	0.977000	0.34250	0.373000	0.26003	0.379000	0.30106	4.550000	0.60733	2.788000	0.95919	0.650000	0.86243	GGA	PCNXL2	-	NULL	ENSG00000135749		0.527	PCNXL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	PCNXL2	HGNC	protein_coding	OTTHUMT00000092480.3	261	0.00	0	C	NM_014801		233134902	233134902	-1	no_errors	ENST00000258229	ensembl	human	known	69_37n	missense	141	41.25	99	SNP	1.000	T
PGBD2	267002	genome.wustl.edu	37	1	249210906	249210906	+	Silent	SNP	G	G	A			TCGA-AO-A0J7-01A-11W-A050-09	TCGA-AO-A0J7-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	a53056d9-e8bd-4cb1-ad67-85879ccc925d	30586533-e188-4eb3-8ffd-0ce7c98a1b6b	g.chr1:249210906G>A	ENST00000329291.5	+	3	270	c.123G>A	c.(121-123)gaG>gaA	p.E41E	PGBD2_ENST00000355360.4_Intron|PGBD2_ENST00000539153.1_Silent_p.E38E|PGBD2_ENST00000462488.1_Intron	NM_170725.2	NP_733843.1	Q6P3X8	PGBD2_HUMAN	piggyBac transposable element derived 2	41								p.E41E(1)		NS(1)|endometrium(3)|lung(6)|ovary(1)|skin(3)	14	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.012)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)			ACAGGGAAGAGATTTTCATTG	0.522																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											81.0	77.0	79.0					1																	249210906		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AF229602	CCDS31128.1, CCDS31129.1	1q	2008-02-05			ENSG00000185220	ENSG00000185220			19399	protein-coding gene	gene with protein product							Standard	XM_005270333		Approved		uc001ifh.3	Q6P3X8	OTTHUMG00000040424	ENST00000329291.5:c.123G>A	1.37:g.249210906G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	B3KVR8|Q6MZF8	Silent	SNP	NULL	p.E41	ENST00000329291.5	37	c.123	CCDS31128.1	1																																																																																			PGBD2	-	NULL	ENSG00000185220		0.522	PGBD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	PGBD2	HGNC	protein_coding	OTTHUMT00000097318.1	148	0.00	0	G			249210906	249210906	+1	no_errors	ENST00000329291	ensembl	human	known	69_37n	silent	116	32.56	56	SNP	0.748	A
PGR	5241	genome.wustl.edu	37	11	100996740	100996741	+	Frame_Shift_Ins	INS	-	-	C			TCGA-AO-A0J7-01A-11W-A050-09	TCGA-AO-A0J7-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	a53056d9-e8bd-4cb1-ad67-85879ccc925d	30586533-e188-4eb3-8ffd-0ce7c98a1b6b	g.chr11:100996740_100996741insC	ENST00000325455.5	-	2	3239_3240	c.1786_1787insG	c.(1786-1788)gaafs	p.E596fs	PGR_ENST00000534013.1_Frame_Shift_Ins_p.E2fs|PGR_ENST00000263463.5_Frame_Shift_Ins_p.E596fs	NM_000926.4|NM_001202474.1|NM_001271162.1	NP_000917.3|NP_001189403.1|NP_001258091.1	P06401	PRGR_HUMAN	progesterone receptor	596					cell-cell signaling (GO:0007267)|epithelial cell maturation (GO:0002070)|gene expression (GO:0010467)|negative regulation of gene expression (GO:0010629)|ovulation from ovarian follicle (GO:0001542)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|progesterone receptor signaling pathway (GO:0050847)|regulation of epithelial cell proliferation (GO:0050678)|signal transduction (GO:0007165)|tertiary branching involved in mammary gland duct morphogenesis (GO:0060748)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mitochondrial outer membrane (GO:0005741)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.E596fs*13(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|liver(1)|lung(18)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	36		Acute lymphoblastic leukemia(157;0.000885)|all_hematologic(158;0.014)		LUSC - Lung squamous cell carcinoma(1;0.0387)|BRCA - Breast invasive adenocarcinoma(274;0.124)|OV - Ovarian serous cystadenocarcinoma(223;0.148)|Lung(307;0.164)	Allylestrenol(DB01431)|Danazol(DB01406)|Desogestrel(DB00304)|Drospirenone(DB01395)|Dydrogesterone(DB00378)|Ethynodiol(DB00823)|Etonogestrel(DB00294)|Fluticasone Propionate(DB00588)|Levonorgestrel(DB00367)|Medroxyprogesterone Acetate(DB00603)|Megestrol acetate(DB00351)|Mifepristone(DB00834)|Norelgestromin(DB06713)|Norethindrone(DB00717)|Norgestimate(DB00957)|Progesterone(DB00396)|Spironolactone(DB00421)	GAGCCTACCTTCCATTGCCCTC	0.381																																					Pancreas(124;2271 2354 21954 22882)	dbGAP											1	Insertion - Frameshift(1)	breast(1)																																								-	-	-	SO:0001589	frameshift_variant	0			M15716	CCDS8310.1, CCDS59229.1	11q22-q23	2013-01-16			ENSG00000082175	ENSG00000082175		"""Nuclear hormone receptors"""	8910	protein-coding gene	gene with protein product		607311					Standard	NM_000926		Approved	PR, NR3C3	uc001pgh.2	P06401	OTTHUMG00000167531	ENST00000325455.5:c.1787dupG	11.37:g.100996742_100996742dupC	ENSP00000325120:p.Glu596fs	Somatic		WXS	Illumina GAIIx	Phase_IV	A7LQ08|A7X8B0|B4E3T0|Q8TDS3|Q9UPF7	Frame_Shift_Ins	INS	pfam_Progest_rcpt,pfam_Znf_hrmn_rcpt,pfam_Nucl_hrmn_rcpt_lig-bd_core,superfamily_Nucl_hormone_rcpt_ligand-bd,smart_Znf_hrmn_rcpt,smart_Nucl_hrmn_rcpt_lig-bd_core,pfscan_Znf_hrmn_rcpt,prints_Progest_rcpt,prints_Znf_hrmn_rcpt,prints_Str_hrmn_rcpt	p.E596fs	ENST00000325455.5	37	c.1787_1786	CCDS8310.1	11																																																																																			PGR	-	pfam_Znf_hrmn_rcpt,smart_Znf_hrmn_rcpt,pfscan_Znf_hrmn_rcpt,prints_Znf_hrmn_rcpt	ENSG00000082175		0.381	PGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PGR	HGNC	protein_coding	OTTHUMT00000394934.1	159	0.00	0	-			100996740	100996741	-1	no_errors	ENST00000325455	ensembl	human	known	69_37n	frame_shift_ins	12	63.64	21	INS	1.000:1.000	C
PRSS42	339906	genome.wustl.edu	37	3	46873464	46873464	+	Missense_Mutation	SNP	A	A	G			TCGA-AO-A0J7-01A-11W-A050-09	TCGA-AO-A0J7-10A-01W-A055-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	a53056d9-e8bd-4cb1-ad67-85879ccc925d	30586533-e188-4eb3-8ffd-0ce7c98a1b6b	g.chr3:46873464A>G	ENST00000429665.1	-	4	693	c.694T>C	c.(694-696)Tgt>Cgt	p.C232R	PRSS42_ENST00000447340.1_Intron	NM_182702.1	NP_874361.1	Q7Z5A4	PRS42_HUMAN	protease, serine, 42	232	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				germ cell development (GO:0007281)|spermatogenesis (GO:0007283)	anchored component of plasma membrane (GO:0046658)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)	p.C232R(1)		breast(1)|kidney(1)|large_intestine(1)|lung(4)|pancreas(1)	8						ATCTTATTACATTCCTCATAG	0.373																																						dbGAP											1	Substitution - Missense(1)	breast(1)											154.0	145.0	148.0					3																	46873464		1869	4113	5982	-	-	-	SO:0001583	missense	0				CCDS46816.1	3p21.31	2010-05-07			ENSG00000178055	ENSG00000178055		"""Serine peptidases / Serine peptidases"""	30716	protein-coding gene	gene with protein product	"""testis serine protease 2"""					12838346	Standard	NM_182702		Approved	TESSP2	uc011bap.2	Q7Z5A4	OTTHUMG00000156496	ENST00000429665.1:c.694T>C	3.37:g.46873464A>G	ENSP00000401701:p.Cys232Arg	Somatic		WXS	Illumina GAIIx	Phase_IV		Missense_Mutation	SNP	pfam_Peptidase_S1_S6,pfam_Peptidase_S1A_nudel,superfamily_Pept_cys/ser_Trypsin-like,smart_Peptidase_S1_S6,prints_Peptidase_S1A,pfscan_Peptidase_S1_S6	p.C232R	ENST00000429665.1	37	c.694	CCDS46816.1	3	.	.	.	.	.	.	.	.	.	.	A	14.51	2.556719	0.45487	.	.	ENSG00000178055	ENST00000429665	T	0.55234	0.53	4.72	3.56	0.40772	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.41294	D	0.000902	T	0.81226	0.4778	H	0.99182	4.46	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.82468	-0.0442	10	0.87932	D	0	.	7.1655	0.25687	0.8993:0.0:0.1007:0.0	.	232	Q7Z5A4	PRS42_HUMAN	R	232	ENSP00000401701:C232R	ENSP00000401701:C232R	C	-	1	0	PRSS42	46848468	0.530000	0.26330	0.423000	0.26634	0.035000	0.12851	2.843000	0.48238	0.936000	0.37367	0.496000	0.49642	TGT	PRSS42	-	pfam_Peptidase_S1_S6,pfam_Peptidase_S1A_nudel,superfamily_Pept_cys/ser_Trypsin-like,smart_Peptidase_S1_S6,pfscan_Peptidase_S1_S6	ENSG00000178055		0.373	PRSS42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PRSS42	HGNC	protein_coding	OTTHUMT00000344347.1	102	0.00	0	A	NM_182702		46873464	46873464	-1	no_errors	ENST00000429665	ensembl	human	known	69_37n	missense	40	48.75	39	SNP	0.599	G
PLXNA1	5361	genome.wustl.edu	37	3	126752825	126752825	+	Missense_Mutation	SNP	G	G	A			TCGA-AO-A0J7-01A-11W-A050-09	TCGA-AO-A0J7-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	a53056d9-e8bd-4cb1-ad67-85879ccc925d	30586533-e188-4eb3-8ffd-0ce7c98a1b6b	g.chr3:126752825G>A	ENST00000393409.2	+	31	5656	c.5656G>A	c.(5656-5658)Gag>Aag	p.E1886K	PLXNA1_ENST00000505278.1_3'UTR|PLXNA1_ENST00000251772.4_Missense_Mutation_p.E1863K	NM_032242.3	NP_115618.3	Q9UIW2	PLXA1_HUMAN	plexin A1	1886					axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|multicellular organismal development (GO:0007275)|regulation of smooth muscle cell migration (GO:0014910)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)	p.E1863K(1)		breast(3)|central_nervous_system(5)|endometrium(10)|kidney(5)|large_intestine(4)|lung(32)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	67				GBM - Glioblastoma multiforme(114;0.155)		GAGCAAGCTGGAGCAGGTGGT	0.667																																						dbGAP											1	Substitution - Missense(1)	breast(1)											29.0	29.0	29.0					3																	126752825		2199	4297	6496	-	-	-	SO:0001583	missense	0			X87832	CCDS33847.1, CCDS33847.2	3q21.2	2006-12-19				ENSG00000114554		"""Plexins"""	9099	protein-coding gene	gene with protein product		601055		PLXN1		8570614	Standard	NM_032242		Approved	NOV	uc003ejg.3	Q9UIW2		ENST00000393409.2:c.5656G>A	3.37:g.126752825G>A	ENSP00000377061:p.Glu1886Lys	Somatic		WXS	Illumina GAIIx	Phase_IV		Missense_Mutation	SNP	pfam_Plexin_cytoplasmic_RasGAP_dom,pfam_Semaphorin/CD100_Ag,pfam_IPT_TIG_rcpt,pfam_Plexin_repeat,superfamily_Semaphorin/CD100_Ag,superfamily_Rho_GTPase_activation_prot,superfamily_Ig_E-set,superfamily_Plexin-like_fold,smart_Semaphorin/CD100_Ag,smart_Plexin-like,smart_IPT_TIG_rcpt,pfscan_Semaphorin/CD100_Ag	p.E1886K	ENST00000393409.2	37	c.5656	CCDS33847.2	3	.	.	.	.	.	.	.	.	.	.	G	20.9	4.059669	0.76074	.	.	ENSG00000114554	ENST00000393409;ENST00000251772	T;T	0.11712	2.75;2.76	4.02	3.11	0.35812	.	0.000000	0.53938	D	0.000058	T	0.20292	0.0488	M	0.85630	2.765	0.58432	D	0.999999	B;B	0.23442	0.038;0.085	B;B	0.30105	0.082;0.111	T	0.07009	-1.0795	10	0.87932	D	0	.	13.0165	0.58759	0.0:0.1638:0.8362:0.0	.	500;1886	Q6ZTY7;Q9UIW2	.;PLXA1_HUMAN	K	1886;1863	ENSP00000377061:E1886K;ENSP00000251772:E1863K	ENSP00000251772:E1863K	E	+	1	0	PLXNA1	128235515	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	9.482000	0.97935	0.848000	0.35191	0.313000	0.20887	GAG	PLXNA1	-	NULL	ENSG00000114554		0.667	PLXNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PLXNA1	HGNC	protein_coding	OTTHUMT00000356451.1	12	0.00	0	G	NM_032242		126752825	126752825	+1	no_errors	ENST00000393409	ensembl	human	known	69_37n	missense	7	36.36	4	SNP	1.000	A
PIK3CA	5290	genome.wustl.edu	37	3	178936094	178936094	+	Missense_Mutation	SNP	C	C	A	rs121913286		TCGA-AO-A0J7-01A-11W-A050-09	TCGA-AO-A0J7-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	a53056d9-e8bd-4cb1-ad67-85879ccc925d	30586533-e188-4eb3-8ffd-0ce7c98a1b6b	g.chr3:178936094C>A	ENST00000263967.3	+	10	1793	c.1636C>A	c.(1636-1638)Cag>Aag	p.Q546K		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	546	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.		Q -> E (in BC; unknown pathological significance). {ECO:0000269|PubMed:15520168}.|Q -> K (in OC; unknown pathological significance). {ECO:0000269|PubMed:15520168}.|Q -> P (found in an anaplastic astrocytoma sample; unknown pathological significance). {ECO:0000269|PubMed:15289301}.|Q -> R (in BC; unknown pathological significance). {ECO:0000269|PubMed:16353168}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.Q546K(89)|p.Q546E(12)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	AATCACTGAGCAGGAGAAAGA	0.358		57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)	dbGAP		Dom	yes		3	3q26.3	5290	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""		"""E, O"""	101	Substitution - Missense(101)	large_intestine(55)|breast(17)|endometrium(15)|central_nervous_system(3)|lung(3)|ovary(3)|skin(2)|cervix(1)|stomach(1)|haematopoietic_and_lymphoid_tissue(1)											61.0	61.0	61.0					3																	178936094		1814	4072	5886	-	-	-	SO:0001583	missense	0				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1636C>A	3.37:g.178936094C>A	ENSP00000263967:p.Gln546Lys	Somatic		WXS	Illumina GAIIx	Phase_IV	Q14CW1|Q99762	Missense_Mutation	SNP	pfam_PInositide-3_kin_accessory_dom,pfam_PI3/4_kinase_cat_dom,pfam_PI3K_Ras-bd_dom,pfam_PI3K_C2_dom,pfam_PI3K_adapt-bd_dom,superfamily_Kinase-like_dom,superfamily_ARM-type_fold,superfamily_C2_Ca/lipid-bd_dom_CaLB,smart_PI3K_adapt-bd_dom,smart_PI3K_Ras-bd_dom,smart_PI3K_C2_dom,smart_PInositide-3_kin_accessory_dom,smart_PI3/4_kinase_cat_dom,pfscan_PI3/4_kinase_cat_dom	p.Q546K	ENST00000263967.3	37	c.1636	CCDS43171.1	3	.	.	.	.	.	.	.	.	.	.	C	27.5	4.838482	0.91117	.	.	ENSG00000121879	ENST00000263967	T	0.62232	0.04	5.78	5.78	0.91487	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.75191	0.3816	M	0.64404	1.975	0.80722	D	1	D	0.58970	0.984	P	0.58660	0.843	T	0.73833	-0.3858	10	0.46703	T	0.11	-14.2064	20.0024	0.97423	0.0:1.0:0.0:0.0	.	546	P42336	PK3CA_HUMAN	K	546	ENSP00000263967:Q546K	ENSP00000263967:Q546K	Q	+	1	0	PIK3CA	180418788	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	7.487000	0.81328	2.722000	0.93159	0.467000	0.42956	CAG	PIK3CA	-	pfam_PInositide-3_kin_accessory_dom,superfamily_ARM-type_fold,smart_PInositide-3_kin_accessory_dom	ENSG00000121879		0.358	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	PIK3CA	HGNC	protein_coding	OTTHUMT00000348409.2	138	0.00	0	C			178936094	178936094	+1	no_errors	ENST00000263967	ensembl	human	known	69_37n	missense	65	41.44	46	SNP	1.000	A
SH3BP4	23677	genome.wustl.edu	37	2	235950945	235950945	+	Missense_Mutation	SNP	G	G	A	rs35521640	byFrequency	TCGA-AO-A0J7-01A-11W-A050-09	TCGA-AO-A0J7-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	a53056d9-e8bd-4cb1-ad67-85879ccc925d	30586533-e188-4eb3-8ffd-0ce7c98a1b6b	g.chr2:235950945G>A	ENST00000409212.1	+	4	2039	c.1532G>A	c.(1531-1533)cGc>cAc	p.R511H	SH3BP4_ENST00000344528.4_Missense_Mutation_p.R511H|SH3BP4_ENST00000392011.2_Missense_Mutation_p.R511H			Q9P0V3	SH3B4_HUMAN	SH3-domain binding protein 4	511					cellular response to amino acid stimulus (GO:0071230)|endocytosis (GO:0006897)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of GTPase activity (GO:0034260)|negative regulation of TOR signaling (GO:0032007)|positive regulation of autophagy (GO:0010508)|protein localization to lysosome (GO:0061462)|regulation of catalytic activity (GO:0050790)	coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	GDP-dissociation inhibitor activity (GO:0005092)|identical protein binding (GO:0042802)|Ras GTPase binding (GO:0017016)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(6)|stomach(3)|urinary_tract(2)	44		Breast(86;0.000332)|Renal(207;0.00339)|all_lung(227;0.00458)|all_hematologic(139;0.0296)|Lung NSC(271;0.0419)		Epithelial(121;7.66e-20)|BRCA - Breast invasive adenocarcinoma(100;0.000402)|Lung(119;0.00299)|LUSC - Lung squamous cell carcinoma(224;0.00645)|GBM - Glioblastoma multiforme(43;0.237)		GAGGTCACACGCCAGGCACCC	0.577																																						dbGAP											0													66.0	68.0	68.0					2																	235950945		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF147747	CCDS2513.1	2q37.1-q37.2	2008-05-15			ENSG00000130147	ENSG00000130147			10826	protein-coding gene	gene with protein product		605611				10644451	Standard	NM_014521		Approved		uc002vvp.3	Q9P0V3	OTTHUMG00000133292	ENST00000409212.1:c.1532G>A	2.37:g.235950945G>A	ENSP00000386862:p.Arg511His	Somatic		WXS	Illumina GAIIx	Phase_IV	O95082|Q309A3|Q53QD0|Q53TD1	Missense_Mutation	SNP	pfam_SH3_2,pfam_SH3_domain,pfam_ZU5,superfamily_SH3_domain,smart_SH3_domain,pfscan_SH3_domain	p.R511H	ENST00000409212.1	37	c.1532	CCDS2513.1	2	.	.	.	.	.	.	.	.	.	.	G	10.16	1.274560	0.23307	.	.	ENSG00000130147	ENST00000392011;ENST00000420127;ENST00000409212;ENST00000344528	T;T;T	0.14022	2.54;2.54;2.54	5.06	4.16	0.48862	.	0.178768	0.48767	D	0.000172	T	0.13841	0.0335	L	0.55481	1.735	0.43863	D	0.99646	B;B	0.14805	0.011;0.011	B;B	0.08055	0.003;0.003	T	0.03761	-1.1006	10	0.87932	D	0	-20.6891	8.083	0.30756	0.1933:0.0:0.8067:0.0	.	511;511	A8K594;Q9P0V3	.;SH3B4_HUMAN	H	511	ENSP00000375867:R511H;ENSP00000386862:R511H;ENSP00000340237:R511H	ENSP00000340237:R511H	R	+	2	0	SH3BP4	235615684	1.000000	0.71417	1.000000	0.80357	0.474000	0.32979	3.711000	0.54868	1.068000	0.40764	0.655000	0.94253	CGC	SH3BP4	-	NULL	ENSG00000130147		0.577	SH3BP4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	SH3BP4	HGNC	protein_coding	OTTHUMT00000329763.1	89	0.00	0	G			235950945	235950945	+1	no_errors	ENST00000344528	ensembl	human	known	69_37n	missense	46	31.34	21	SNP	0.998	A
STOX1	219736	genome.wustl.edu	37	10	70644128	70644128	+	Silent	SNP	C	C	T			TCGA-AO-A0J7-01A-11W-A050-09	TCGA-AO-A0J7-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	a53056d9-e8bd-4cb1-ad67-85879ccc925d	30586533-e188-4eb3-8ffd-0ce7c98a1b6b	g.chr10:70644128C>T	ENST00000298596.6	+	3	659	c.576C>T	c.(574-576)taC>taT	p.Y192Y	STOX1_ENST00000421961.2_Silent_p.Y82Y|STOX1_ENST00000399165.4_Silent_p.Y192Y|STOX1_ENST00000399169.4_Silent_p.Y192Y|STOX1_ENST00000399162.2_Intron	NM_152709.4	NP_689922.3	Q6ZVD7	STOX1_HUMAN	storkhead box 1	192						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.Y192Y(1)		breast(5)|endometrium(2)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|prostate(1)|skin(3)	28						CTCAGACTTACTTCATTACAA	0.413																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											96.0	92.0	93.0					10																	70644128		1903	4118	6021	-	-	-	SO:0001819	synonymous_variant	0			AK057891	CCDS41535.1, CCDS44416.1, CCDS44417.1	10q22.1	2005-11-29	2005-04-04	2005-04-04	ENSG00000165730	ENSG00000165730			23508	protein-coding gene	gene with protein product		609397	"""chromosome 10 open reading frame 24"""	C10orf24			Standard	NM_152709		Approved	FLJ25162	uc001joq.3	Q6ZVD7	OTTHUMG00000018367	ENST00000298596.6:c.576C>T	10.37:g.70644128C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	A2A3Q9|A5D6Y7|B0QZA4|B0QZA5|B0QZA6|Q4F8Q6|Q5I946|Q5I947|Q5I948|Q5VX38|Q5VX39|Q6ZRY3|Q96LR3|Q96LS0	Silent	SNP	pfam_Storkhead-box_winged-helix	p.Y192	ENST00000298596.6	37	c.576	CCDS41535.1	10																																																																																			STOX1	-	NULL	ENSG00000165730		0.413	STOX1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	STOX1	HGNC	protein_coding	OTTHUMT00000276849.3	44	0.00	0	C	NM_152709		70644128	70644128	+1	no_errors	ENST00000298596	ensembl	human	known	69_37n	silent	26	35.00	14	SNP	1.000	T
TRMT2B	79979	genome.wustl.edu	37	X	100275554	100275554	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AO-A0J7-01A-11W-A050-09	TCGA-AO-A0J7-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	a53056d9-e8bd-4cb1-ad67-85879ccc925d	30586533-e188-4eb3-8ffd-0ce7c98a1b6b	g.chrX:100275554G>A	ENST00000372936.3	-	11	1862	c.1090C>T	c.(1090-1092)Cag>Tag	p.Q364*	TRMT2B_ENST00000372935.1_Nonsense_Mutation_p.Q364*|TRMT2B_ENST00000372939.1_Nonsense_Mutation_p.Q319*|TRMT2B_ENST00000338687.7_Nonsense_Mutation_p.Q319*|TRMT2B_ENST00000372931.5_Nonsense_Mutation_p.Q364*|TRMT2B_ENST00000545398.1_Nonsense_Mutation_p.Q364*	NM_024917.5	NP_079193.2	Q96GJ1	TRM2_HUMAN	tRNA methyltransferase 2 homolog B (S. cerevisiae)	364						mitochondrion (GO:0005739)	S-adenosylmethionine-dependent tRNA (m5U54) methyltransferase activity (GO:0030697)	p.Q364*(1)		breast(3)|endometrium(2)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	24						GATGTATGCTGAGCCAGAGAG	0.448																																						dbGAP											1	Substitution - Nonsense(1)	breast(1)											157.0	130.0	139.0					X																	100275554		2203	4300	6503	-	-	-	SO:0001587	stop_gained	0			BC020116	CCDS14477.1, CCDS55464.1	Xq22.1	2012-06-12	2012-06-12	2008-09-17	ENSG00000188917	ENSG00000188917			25748	protein-coding gene	gene with protein product			"""chromosome X open reading frame 34"""	CXorf34		14702039	Standard	NM_024917		Approved	FLJ12687	uc004egq.3	Q96GJ1	OTTHUMG00000022017	ENST00000372936.3:c.1090C>T	X.37:g.100275554G>A	ENSP00000362027:p.Gln364*	Somatic		WXS	Illumina GAIIx	Phase_IV	A6NDG5|A6NEI9|A6NMG6|Q5JPF0|Q5JVY6|Q96HU7|Q96IH9|Q9H9K2	Nonsense_Mutation	SNP	pfam_U5_MeTrfase,pfam_Small_mtfrase_dom	p.Q364*	ENST00000372936.3	37	c.1090	CCDS14477.1	X	.	.	.	.	.	.	.	.	.	.	G	42	9.384775	0.99155	.	.	ENSG00000188917	ENST00000338687;ENST00000545398;ENST00000372939;ENST00000372935;ENST00000372936;ENST00000372931	.	.	.	4.57	1.71	0.24356	.	0.765204	0.12262	N	0.484674	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05959	T	0.93	-19.0577	3.1699	0.06549	0.0976:0.3197:0.4163:0.1664	.	.	.	.	X	319;364;319;364;364;364	.	ENSP00000340970:Q319X	Q	-	1	0	TRMT2B	100162210	0.979000	0.34478	0.158000	0.22627	0.691000	0.40173	2.091000	0.41691	0.005000	0.14708	0.600000	0.82982	CAG	TRMT2B	-	pfam_U5_MeTrfase,pfam_Small_mtfrase_dom	ENSG00000188917		0.448	TRMT2B-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	TRMT2B	HGNC	protein_coding	OTTHUMT00000057512.1	200	0.50	1	G	NM_024917		100275554	100275554	-1	no_errors	ENST00000372935	ensembl	human	known	69_37n	nonsense	130	43.23	99	SNP	0.184	A
