#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_ORegAnno_bin	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
ADH1B	125	genome.wustl.edu	37	4	100232778	100232778	+	Silent	SNP	G	G	T			TCGA-AN-A0XL-01A-11D-A10M-09	TCGA-AN-A0XL-10A-01D-A10M-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	1b08a181-a73b-4506-aaa3-3521f2c57207	1acce21e-7513-402f-b586-423415f7cc2c	g.chr4:100232778G>T	ENST00000305046.8	-	7	931	c.864C>A	c.(862-864)ggC>ggA	p.G288G	ADH1B_ENST00000394887.3_Silent_p.G248G			P00325	ADH1B_HUMAN	alcohol dehydrogenase 1B (class I), beta polypeptide	288					ethanol oxidation (GO:0006069)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(12)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	33				OV - Ovarian serous cystadenocarcinoma(123;1.02e-07)	Ethanol(DB00898)|Fomepizole(DB01213)	TGACGCTTGTGCCACATGCCT	0.483																																						dbGAP											0													212.0	196.0	201.0					4																	100232778		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AF153821	CCDS34033.1, CCDS68761.1	4q23	2008-02-05	2007-11-06		ENSG00000196616	ENSG00000196616	1.1.1.1	"""Alcohol dehydrogenases"""	250	protein-coding gene	gene with protein product		103720		ADH2		3006456	Standard	NM_000668		Approved		uc003hus.4	P00325	OTTHUMG00000161413	ENST00000305046.8:c.864C>A	4.37:g.100232778G>T			A8MYN5|B4DRS9|B4DVC3|Q13711|Q4ZGI9|Q96KI7	Silent	SNP	pfam_ADH_GroES-like,pfam_ADH_C,superfamily_GroES-like,smart_PKS_ER	p.G288	ENST00000305046.8	37	c.864	CCDS34033.1	4																																																																																			ADH1B	-	pfam_ADH_C,smart_PKS_ER	ENSG00000196616		0.483	ADH1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ADH1B	HGNC	protein_coding	OTTHUMT00000364853.1	156	0.00	0	G	NM_000668		100232778	100232778	-1	no_errors	ENST00000305046	ensembl	human	known	69_37n	silent	163	31.51	75	SNP	0.000	T
AKAP13	11214	genome.wustl.edu	37	15	86124520	86124520	+	Missense_Mutation	SNP	C	C	T			TCGA-AN-A0XL-01A-11D-A10M-09	TCGA-AN-A0XL-10A-01D-A10M-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	1b08a181-a73b-4506-aaa3-3521f2c57207	1acce21e-7513-402f-b586-423415f7cc2c	g.chr15:86124520C>T	ENST00000394518.2	+	7	3316	c.3221C>T	c.(3220-3222)tCc>tTc	p.S1074F	RP11-815J21.2_ENST00000561409.1_RNA|AKAP13_ENST00000361243.2_Missense_Mutation_p.S1074F	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	1074					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nuclear export (GO:0051168)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle hypertrophy (GO:0010611)|regulation of glucocorticoid mediated signaling pathway (GO:1900169)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cAMP-dependent protein kinase activity (GO:0004691)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|central_nervous_system(4)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(13)|liver(1)|lung(43)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	98						AACACTCAATCCCAGGGAAAA	0.507																																					Melanoma(94;603 1453 3280 32295 32951)	dbGAP											0													77.0	77.0	77.0					15																	86124520		2202	4299	6501	-	-	-	SO:0001583	missense	0			M90360	CCDS32319.1, CCDS32320.1, CCDS73778.1	15q24-q25	2013-01-10	2002-06-13			ENSG00000170776		"""A-kinase anchor proteins"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	371	protein-coding gene	gene with protein product		604686	"""lymphoid blast crisis oncogene"""	LBC		9627117, 1860836	Standard	NM_007200		Approved	Ht31, BRX, AKAP-Lbc, c-lbc, PROTO-LB, HA-3, ARHGEF13	uc002blu.2	Q12802		ENST00000394518.2:c.3221C>T	15.37:g.86124520C>T	ENSP00000378026:p.Ser1074Phe		Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Missense_Mutation	SNP	pfam_DH-domain,pfam_Pleckstrin_homology,superfamily_DH-domain,superfamily_Ankyrin_rpt-contain_dom,smart_Prot_Kinase_C-like_PE/DAG-bd,smart_DH-domain,smart_Pleckstrin_homology,pfscan_Pleckstrin_homology,pfscan_Prot_Kinase_C-like_PE/DAG-bd,pfscan_DH-domain	p.S1074F	ENST00000394518.2	37	c.3221	CCDS32319.1	15	.	.	.	.	.	.	.	.	.	.	C	8.604	0.887539	0.17540	.	.	ENSG00000170776	ENST00000361243;ENST00000394518;ENST00000394516;ENST00000458540	T;T	0.13538	2.58;2.58	5.2	-1.81	0.07882	.	.	.	.	.	T	0.06508	0.0167	N	0.17082	0.46	0.09310	N	0.999999	B;B	0.06786	0.0;0.001	B;B	0.09377	0.002;0.004	T	0.36768	-0.9734	9	0.33940	T	0.23	.	2.7977	0.05406	0.1855:0.2928:0.3947:0.1269	.	1074;1074	Q12802;Q12802-2	AKP13_HUMAN;.	F	1074;1074;1073;1073	ENSP00000354718:S1074F;ENSP00000378026:S1074F	ENSP00000354718:S1074F	S	+	2	0	AKAP13	83925524	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.758000	0.04766	-0.733000	0.04850	-0.929000	0.02709	TCC	AKAP13	-	NULL	ENSG00000170776		0.507	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	AKAP13	HGNC	protein_coding	OTTHUMT00000417318.1	22	0.00	0	C	NM_007200		86124520	86124520	+1	no_errors	ENST00000361243	ensembl	human	known	69_37n	missense	22	23.33	7	SNP	0.000	T
ANPEP	290	genome.wustl.edu	37	15	90347735	90347736	+	Frame_Shift_Ins	INS	-	-	G			TCGA-AN-A0XL-01A-11D-A10M-09	TCGA-AN-A0XL-10A-01D-A10M-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	1b08a181-a73b-4506-aaa3-3521f2c57207	1acce21e-7513-402f-b586-423415f7cc2c	g.chr15:90347735_90347736insG	ENST00000300060.6	-	5	1323_1324	c.1010_1011insC	c.(1009-1011)ccafs	p.P337fs	ANPEP_ENST00000558177.1_5'Flank	NM_001150.2	NP_001141.2	P15144	AMPN_HUMAN	alanyl (membrane) aminopeptidase	337	Interaction with HCoV-229E.|Metalloprotease.				angiogenesis (GO:0001525)|angiotensin maturation (GO:0002003)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|viral process (GO:0016032)	endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|receptor activity (GO:0004872)|virus receptor activity (GO:0001618)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	57	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.169)		Ezetimibe(DB00973)|Icatibant(DB06196)	ATTTTGGGAGTGGGTAGGGTGT	0.609																																					NSCLC(30;827 977 2459 19669 26125)	dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			M22324	CCDS10356.1	15q25-q26	2008-07-31	2008-07-31		ENSG00000166825	ENSG00000166825	3.4.11.2	"""CD molecules"""	500	protein-coding gene	gene with protein product	"""aminopeptidase N"", ""aminopeptidase M"", ""microsomal aminopeptidase"""	151530		CD13, PEPN		2428842, 1977688	Standard	NM_001150		Approved	LAP1, gp150, p150	uc002bop.4	P15144	OTTHUMG00000149814	ENST00000300060.6:c.1011dupC	15.37:g.90347738_90347738dupG	ENSP00000300060:p.Pro337fs		Q16728|Q6GT90|Q8IUK3|Q8IVH3|Q9UCE0	Frame_Shift_Ins	INS	pfam_Peptidase_M1_N,prints_Peptidase_M1_N	p.L338fs	ENST00000300060.6	37	c.1011_1010	CCDS10356.1	15																																																																																			ANPEP	-	pfam_Peptidase_M1_N	ENSG00000166825		0.609	ANPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ANPEP	HGNC	protein_coding	OTTHUMT00000313425.1	37	0.00	0	-			90347735	90347736	-1	no_errors	ENST00000300060	ensembl	human	known	69_37n	frame_shift_ins	67	15.19	12	INS	0.115:1.000	G
BBOX1	8424	genome.wustl.edu	37	11	27148982	27148982	+	Silent	SNP	G	G	A	rs375535107		TCGA-AN-A0XL-01A-11D-A10M-09	TCGA-AN-A0XL-10A-01D-A10M-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	1b08a181-a73b-4506-aaa3-3521f2c57207	1acce21e-7513-402f-b586-423415f7cc2c	g.chr11:27148982G>A	ENST00000529202.1	+	8	1485	c.1146G>A	c.(1144-1146)agG>agA	p.R382R	BBOX1_ENST00000528583.1_Silent_p.R382R|RP11-1L12.3_ENST00000530430.1_RNA|RP11-1L12.3_ENST00000526061.1_RNA|RP11-1L12.3_ENST00000525302.1_RNA|BBOX1_ENST00000263182.3_Silent_p.R382R|BBOX1_ENST00000525090.1_Silent_p.R382R			O75936	BODG_HUMAN	butyrobetaine (gamma), 2-oxoglutarate dioxygenase (gamma-butyrobetaine hydroxylase) 1	382					carnitine biosynthetic process (GO:0045329)|cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	gamma-butyrobetaine dioxygenase activity (GO:0008336)|iron ion binding (GO:0005506)|zinc ion binding (GO:0008270)	p.R382S(1)		breast(1)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	23					Succinic acid(DB00139)|Vitamin C(DB00126)	TAAGGCAGAGGGTGGAGAATG	0.418																																						dbGAP											1	Substitution - Missense(1)	upper_aerodigestive_tract(1)											111.0	99.0	103.0					11																	27148982		2202	4299	6501	-	-	-	SO:0001819	synonymous_variant	0			AF082868	CCDS7862.1	11p	2008-02-01			ENSG00000129151	ENSG00000129151	1.14.11.1		964	protein-coding gene	gene with protein product		603312		BBOX		9753662	Standard	XM_005253159		Approved	gamma-BBH, G-BBH, BBH	uc001mre.1	O75936	OTTHUMG00000166121	ENST00000529202.1:c.1146G>A	11.37:g.27148982G>A			B2R8L7|D3DQZ1|Q6IBJ2	Silent	SNP	pfam_Taurine_dOase,pfam_DUF971,tigrfam_2-oxoglut_dOase	p.R382	ENST00000529202.1	37	c.1146	CCDS7862.1	11																																																																																			BBOX1	-	NULL	ENSG00000129151		0.418	BBOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	BBOX1	HGNC	protein_coding	OTTHUMT00000387946.1	74	0.00	0	G	NM_003986		27148982	27148982	+1	no_errors	ENST00000263182	ensembl	human	known	69_37n	silent	50	60.32	76	SNP	0.000	A
ARHGEF17	9828	genome.wustl.edu	37	11	73076908	73076908	+	Missense_Mutation	SNP	G	G	A			TCGA-AN-A0XL-01A-11D-A10M-09	TCGA-AN-A0XL-10A-01D-A10M-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	1b08a181-a73b-4506-aaa3-3521f2c57207	1acce21e-7513-402f-b586-423415f7cc2c	g.chr11:73076908G>A	ENST00000263674.3	+	20	6261	c.5911G>A	c.(5911-5913)Ggc>Agc	p.G1971S		NM_014786.3	NP_055601.2	Q96PE2	ARHGH_HUMAN	Rho guanine nucleotide exchange factor (GEF) 17	1971					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|skin(2)	32						GGGACACACCGGCCACGTCCG	0.652																																						dbGAP											0													54.0	54.0	54.0					11																	73076908		2200	4293	6493	-	-	-	SO:0001583	missense	0			AF378754	CCDS8221.1	11q13.3	2011-11-16			ENSG00000110237	ENSG00000110237		"""Rho guanine nucleotide exchange factors"""	21726	protein-coding gene	gene with protein product	"""Rho-specific guanine-nucleotide exchange factor 164 kDa"", ""tumor endothelial marker 4"""					11559528, 12071859	Standard	NM_014786		Approved	TEM4, KIAA0337, p164-RhoGEF	uc001otu.3	Q96PE2	OTTHUMG00000167971	ENST00000263674.3:c.5911G>A	11.37:g.73076908G>A	ENSP00000263674:p.Gly1971Ser		B2RP20|Q86XU2|Q8N2S0|Q9Y4G3	Missense_Mutation	SNP	pfam_DH-domain,superfamily_DH-domain,superfamily_WD40_repeat_dom,superfamily_Vinculin/catenin,smart_DH-domain,pfscan_DH-domain	p.G1971S	ENST00000263674.3	37	c.5911	CCDS8221.1	11	.	.	.	.	.	.	.	.	.	.	G	34	5.388045	0.95988	.	.	ENSG00000110237	ENST00000263674	T	0.36699	1.24	5.28	5.28	0.74379	WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.63165	0.2488	M	0.78049	2.395	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.65800	-0.6080	10	0.66056	D	0.02	-30.9689	18.0725	0.89415	0.0:0.0:1.0:0.0	.	1971	Q96PE2	ARHGH_HUMAN	S	1971	ENSP00000263674:G1971S	ENSP00000263674:G1971S	G	+	1	0	ARHGEF17	72754556	1.000000	0.71417	0.967000	0.41034	0.920000	0.55202	8.737000	0.91562	2.755000	0.94549	0.655000	0.94253	GGC	ARHGEF17	-	superfamily_WD40_repeat_dom	ENSG00000110237		0.652	ARHGEF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ARHGEF17	HGNC	protein_coding	OTTHUMT00000397365.1	11	0.00	0	G	NM_014786		73076908	73076908	+1	no_errors	ENST00000263674	ensembl	human	known	69_37n	missense	29	17.14	6	SNP	1.000	A
CD1C	911	genome.wustl.edu	37	1	158261934	158261934	+	Missense_Mutation	SNP	G	G	A			TCGA-AN-A0XL-01A-11D-A10M-09	TCGA-AN-A0XL-10A-01D-A10M-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	1b08a181-a73b-4506-aaa3-3521f2c57207	1acce21e-7513-402f-b586-423415f7cc2c	g.chr1:158261934G>A	ENST00000368170.3	+	3	668	c.389G>A	c.(388-390)gGc>gAc	p.G130D		NM_001765.2	NP_001756.2	P29017	CD1C_HUMAN	CD1c molecule	130					antigen processing and presentation (GO:0019882)|T cell activation involved in immune response (GO:0002286)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	endogenous lipid antigen binding (GO:0030883)|exogenous lipid antigen binding (GO:0030884)|glycolipid binding (GO:0051861)|lipopeptide binding (GO:0071723)			NS(1)|endometrium(3)|large_intestine(4)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	39	all_hematologic(112;0.0378)					AGCCCAGAAGGCTTCTTTCAG	0.463																																						dbGAP											0													104.0	110.0	108.0					1																	158261934		2203	4300	6503	-	-	-	SO:0001583	missense	0			M28827	CCDS1175.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158481	ENSG00000158481		"""CD molecules"", ""Immunoglobulin superfamily / C1-set domain containing"""	1636	protein-coding gene	gene with protein product		188340	"""CD1C antigen, c polypeptide"", ""CD1c antigen"""	CD1		2447586	Standard	NM_001765		Approved		uc001fru.3	P29017	OTTHUMG00000017514	ENST00000368170.3:c.389G>A	1.37:g.158261934G>A	ENSP00000357152:p.Gly130Asp		Q5TDJ7|Q6IAS4|Q9UMM0|Q9UN96	Missense_Mutation	SNP	pfam_Ig_C1-set,superfamily_MHC_I/II-like_Ag-recog,smart_Ig_C1-set,pfscan_Ig-like	p.G130D	ENST00000368170.3	37	c.389	CCDS1175.1	1	.	.	.	.	.	.	.	.	.	.	-	10.33	1.320760	0.23994	.	.	ENSG00000158481	ENST00000368169;ENST00000368170	T	0.10192	2.9	3.36	-0.745	0.11098	MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	1.281130	0.05629	N	0.581433	T	0.07638	0.0192	M	0.66297	2.02	0.09310	N	1	B	0.26120	0.142	B	0.44163	0.443	T	0.53099	-0.8486	10	0.41790	T	0.15	.	2.9004	0.05703	0.3433:0.0:0.4593:0.1974	.	130	P29017	CD1C_HUMAN	D	130	ENSP00000357152:G130D	ENSP00000357151:G130D	G	+	2	0	CD1C	156528558	0.001000	0.12720	0.000000	0.03702	0.009000	0.06853	-0.025000	0.12413	-0.131000	0.11578	0.644000	0.83932	GGC	CD1C	-	superfamily_MHC_I/II-like_Ag-recog	ENSG00000158481		0.463	CD1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CD1C	HGNC	protein_coding	OTTHUMT00000046351.2	70	0.00	0	G	NM_001765		158261934	158261934	+1	no_errors	ENST00000368170	ensembl	human	known	69_37n	missense	148	14.94	26	SNP	0.001	A
CHL1	10752	genome.wustl.edu	37	3	436516	436516	+	Nonsense_Mutation	SNP	A	A	T			TCGA-AN-A0XL-01A-11D-A10M-09	TCGA-AN-A0XL-10A-01D-A10M-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	1b08a181-a73b-4506-aaa3-3521f2c57207	1acce21e-7513-402f-b586-423415f7cc2c	g.chr3:436516A>T	ENST00000256509.2	+	24	3697	c.3055A>T	c.(3055-3057)Aaa>Taa	p.K1019*	CHL1_ENST00000397491.2_Nonsense_Mutation_p.K1003*	NM_001253387.1|NM_001253388.1|NM_006614.3	NP_001240316.1|NP_001240317.1|NP_006605.2	Q96FC9	DDX11_HUMAN	cell adhesion molecule L1-like	0					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			NS(1)|central_nervous_system(5)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|lung(31)|ovary(1)|prostate(4)|skin(10)|stomach(1)	93		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)		GGGCTGTGGAAAACCGATCAC	0.438																																						dbGAP											0													72.0	68.0	70.0					3																	436516		2203	4300	6503	-	-	-	SO:0001587	stop_gained	0			AF002246	CCDS2556.1, CCDS58812.1, CCDS74887.1	3p26	2013-05-01	2013-05-01		ENSG00000134121	ENSG00000134121		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	1939	protein-coding gene	gene with protein product	"""neural cell adhesion molecule"", ""close homolog of L1"""	607416	"""cell adhesion molecule with homology to L1CAM (close homologue of L1)"", ""cell adhesion molecule with homology to L1CAM (close homolog of L1)"""			9799093	Standard	NM_006614		Approved	CALL, L1CAM2, FLJ44930, MGC132578	uc003bot.3	O00533	OTTHUMG00000090601	ENST00000256509.2:c.3055A>T	3.37:g.436516A>T	ENSP00000256509:p.Lys1019*		Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Nonsense_Mutation	SNP	pfam_Ig_I-set,pfam_Fibronectin_type3,pfam_Immunoglobulin,superfamily_Fibronectin_type3,smart_Ig_sub,smart_Ig_sub2,smart_Fibronectin_type3,pfscan_Fibronectin_type3,pfscan_Ig-like	p.K1019*	ENST00000256509.2	37	c.3055	CCDS2556.1	3	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	45|45	11.387998|11.387998	0.99554|0.99554	.|.	.|.	ENSG00000134121|ENSG00000134121	ENST00000445697|ENST00000256509;ENST00000397491	.|.	.|.	.|.	5.58|5.58	4.42|4.42	0.53409|0.53409	.|.	.|0.261330	.|0.39475	.|N	.|0.001341	T|.	0.27933|.	0.0688|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.29610|.	-1.0006|.	3|.	.|0.05721	.|T	.|0.95	.|.	11.1724|11.1724	0.48579|0.48579	0.9276:0.0:0.0724:0.0|0.9276:0.0:0.0724:0.0	.|.	.|.	.|.	.|.	D|X	205|1019;1003	.|.	.|ENSP00000256509:K1019X	E|K	+|+	3|1	2|0	CHL1|CHL1	411516|411516	0.983000|0.983000	0.35010|0.35010	0.510000|0.510000	0.27712|0.27712	0.840000|0.840000	0.47671|0.47671	3.697000|3.697000	0.54764|0.54764	0.942000|0.942000	0.37525|0.37525	0.482000|0.482000	0.46254|0.46254	GAA|AAA	CHL1	-	pfam_Fibronectin_type3,superfamily_Fibronectin_type3,pfscan_Fibronectin_type3	ENSG00000134121		0.438	CHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CHL1	HGNC	protein_coding	OTTHUMT00000207155.2	86	0.00	0	A	NM_006614		436516	436516	+1	no_errors	ENST00000256509	ensembl	human	known	69_37n	nonsense	87	15.53	16	SNP	0.053	T
CHM	1121	genome.wustl.edu	37	X	85282501	85282501	+	Missense_Mutation	SNP	A	A	G			TCGA-AN-A0XL-01A-11D-A10M-09	TCGA-AN-A0XL-10A-01D-A10M-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	1b08a181-a73b-4506-aaa3-3521f2c57207	1acce21e-7513-402f-b586-423415f7cc2c	g.chrX:85282501A>G	ENST00000357749.2	-	2	139	c.110T>C	c.(109-111)gTt>gCt	p.V37A	CHM_ENST00000467744.2_5'UTR|CHM_ENST00000358786.4_Missense_Mutation_p.V37A|CHM_ENST00000537751.1_Intron	NM_000390.2	NP_000381.1	P24386	RAE1_HUMAN	choroideremia (Rab escort protein 1)	37					blood vessel development (GO:0001568)|protein geranylgeranylation (GO:0018344)|protein targeting to membrane (GO:0006612)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytosol (GO:0005829)|Rab-protein geranylgeranyltransferase complex (GO:0005968)	GTPase activator activity (GO:0005096)|Rab geranylgeranyltransferase activity (GO:0004663)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|prostate(1)	20		all_lung(315;5.41e-06)				TTACGAATCAACATGCAGAAC	0.343																																						dbGAP											0													64.0	56.0	59.0					X																	85282501		2203	4300	6503	-	-	-	SO:0001583	missense	0			X78121	CCDS14454.1, CCDS48139.1	Xq21.1-q21.3	2014-09-17			ENSG00000188419	ENSG00000188419			1940	protein-coding gene	gene with protein product		300390		TCD, DXS540		1373238	Standard	XM_006724615		Approved	REP-1	uc004eet.3	P24386	OTTHUMG00000021937	ENST00000357749.2:c.110T>C	X.37:g.85282501A>G	ENSP00000350386:p.Val37Ala		A1L4D2|O43732	Missense_Mutation	SNP	pfam_GDP_dissociation_inhibitor,pirsf_Rab_geranylTrfase_A_euk,prints_Rab_escort,prints_GDP_dissociation_inhibitor	p.V37A	ENST00000357749.2	37	c.110	CCDS14454.1	X	.	.	.	.	.	.	.	.	.	.	A	22.1	4.240141	0.79912	.	.	ENSG00000188419	ENST00000357749;ENST00000358786	T;T	0.63580	-0.05;-0.05	5.28	5.28	0.74379	.	0.297764	0.33650	N	0.004698	T	0.74535	0.3729	M	0.78049	2.395	0.80722	D	1	P;P	0.40931	0.733;0.659	P;P	0.51615	0.668;0.675	T	0.78145	-0.2318	10	0.87932	D	0	-5.5486	14.2794	0.66200	1.0:0.0:0.0:0.0	.	37;37	A1L4D2;P24386	.;RAE1_HUMAN	A	37	ENSP00000350386:V37A;ENSP00000362228:V37A	ENSP00000350386:V37A	V	-	2	0	CHM	85169157	1.000000	0.71417	1.000000	0.80357	0.852000	0.48524	6.769000	0.74985	1.750000	0.51863	0.356000	0.21956	GTT	CHM	-	pfam_GDP_dissociation_inhibitor,pirsf_Rab_geranylTrfase_A_euk,prints_GDP_dissociation_inhibitor	ENSG00000188419		0.343	CHM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CHM	HGNC	protein_coding	OTTHUMT00000057396.3	68	0.00	0	A	NM_000390		85282501	85282501	-1	no_errors	ENST00000357749	ensembl	human	known	69_37n	missense	66	29.47	28	SNP	1.000	G
CLEC17A	388512	genome.wustl.edu	37	19	14710534	14710534	+	Missense_Mutation	SNP	G	G	A			TCGA-AN-A0XL-01A-11D-A10M-09	TCGA-AN-A0XL-10A-01D-A10M-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	1b08a181-a73b-4506-aaa3-3521f2c57207	1acce21e-7513-402f-b586-423415f7cc2c	g.chr19:14710534G>A	ENST00000417570.1	+	11	690	c.652G>A	c.(652-654)Ggc>Agc	p.G218S	CLEC17A_ENST00000397439.2_Missense_Mutation_p.G201S|CLEC17A_ENST00000547437.1_Missense_Mutation_p.G218S	NM_001204118.1	NP_001191047.1	Q6ZS10	CL17A_HUMAN	C-type lectin domain family 17, member A	218						cell surface (GO:0009986)|integral component of membrane (GO:0016021)	fucose binding (GO:0042806)|mannose binding (GO:0005537)|metal ion binding (GO:0046872)										GACAGTGACTGGCATGGCAGG	0.542																																						dbGAP											0													38.0	42.0	41.0					19																	14710534		2057	4205	6262	-	-	-	SO:0001583	missense	0			AK127809	CCDS46002.1, CCDS46002.2, CCDS56087.1	19p13.12	2009-06-26			ENSG00000187912	ENSG00000187912		"""C-type lectin domain containing"""	34520	protein-coding gene	gene with protein product	"""prolectin"""					19419970	Standard	NM_207390		Approved	FLJ45910	uc010dzn.2	Q6ZS10		ENST00000417570.1:c.652G>A	19.37:g.14710534G>A	ENSP00000393719:p.Gly218Ser		A8MX68|B2RTX0|B7ZMM4	Missense_Mutation	SNP	pfam_C-type_lectin,superfamily_C-type_lectin_fold,smart_C-type_lectin,pfscan_C-type_lectin,prints_AntifreezeII	p.G218S	ENST00000417570.1	37	c.652	CCDS56087.1	19	.	.	.	.	.	.	.	.	.	.	G	12.31	1.898496	0.33535	.	.	ENSG00000187912	ENST00000547437;ENST00000397439;ENST00000417570	T;T;T	0.62105	0.05;0.05;0.05	3.97	2.94	0.34122	.	0.224693	0.23748	N	0.044943	T	0.61123	0.2322	N	0.19112	0.55	0.24790	N	0.992762	D;D;D	0.76494	0.999;0.999;0.997	D;D;D	0.74023	0.982;0.974;0.922	T	0.49908	-0.8889	10	0.62326	D	0.03	-0.4145	7.2305	0.26040	0.1224:0.0:0.8776:0.0	.	218;218;218	Q6ZS10-2;Q6ZS10-3;Q6ZS10	.;.;CL17A_HUMAN	S	218;201;218	ENSP00000450065:G218S;ENSP00000380581:G201S;ENSP00000393719:G218S	ENSP00000341620:G218S	G	+	1	0	CLEC17A	14571534	0.995000	0.38212	0.905000	0.35620	0.184000	0.23303	3.259000	0.51515	1.009000	0.39289	0.655000	0.94253	GGC	CLEC17A	-	NULL	ENSG00000187912		0.542	CLEC17A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	CLEC17A	HGNC	protein_coding	OTTHUMT00000403400.1	23	0.00	0	G	NM_207390		14710534	14710534	+1	no_errors	ENST00000417570	ensembl	human	known	69_37n	missense	40	18.37	9	SNP	0.885	A
COMP	1311	genome.wustl.edu	37	19	18895094	18895094	+	Missense_Mutation	SNP	C	C	T			TCGA-AN-A0XL-01A-11D-A10M-09	TCGA-AN-A0XL-10A-01D-A10M-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	1b08a181-a73b-4506-aaa3-3521f2c57207	1acce21e-7513-402f-b586-423415f7cc2c	g.chr19:18895094C>T	ENST00000222271.2	-	17	2038	c.1994G>A	c.(1993-1995)cGg>cAg	p.R665Q	COMP_ENST00000425807.1_Missense_Mutation_p.R612Q|COMP_ENST00000542601.2_Missense_Mutation_p.R632Q	NM_000095.2	NP_000086.2	P49747	COMP_HUMAN	cartilage oligomeric matrix protein	665	Mediates cell survival and induction of the IAP family of survival proteins.|TSP C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00635}.				apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|limb development (GO:0060173)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)|protease binding (GO:0002020)			breast(6)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32						CCACAGCAGCCGCACCTGGGA	0.602																																						dbGAP											0													81.0	75.0	77.0					19																	18895094		2203	4300	6503	-	-	-	SO:0001583	missense	0			L32137	CCDS12385.1	19p13.1	2008-02-05				ENSG00000105664			2227	protein-coding gene	gene with protein product	"""thrombospondin-5"""	600310	"""cartilage oligomeric matrix protein (pseudoachondroplasia, epiphyseal dysplasia 1, multiple)"""	PSACH, EDM1, EPD1		7713493, 8307576	Standard	NM_000095		Approved	MED, THBS5	uc002nke.3	P49747	OTTHUMG00000169318	ENST00000222271.2:c.1994G>A	19.37:g.18895094C>T	ENSP00000222271:p.Arg665Gln		B4DKJ3|O14592|Q16388|Q16389|Q2NL86|Q8N4T2	Missense_Mutation	SNP	pfam_Thrombospondin_C,pfam_EGF-like_Ca-bd,pfam_Thbs/COMP_coiled-coil,pfam_Thrombospondin_3-like_rpt,superfamily_ConA-like_lec_gl,smart_EGF-like,smart_EGF-like_Ca-bd,pfscan_EG-like_dom	p.R665Q	ENST00000222271.2	37	c.1994	CCDS12385.1	19	.	.	.	.	.	.	.	.	.	.	C	17.97	3.517877	0.64634	.	.	ENSG00000105664	ENST00000542601;ENST00000222271;ENST00000425807;ENST00000454701	D;D;D	0.91295	-2.82;-2.82;-2.82	4.71	2.39	0.29439	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Thrombospondin, C-terminal (2);	0.332080	0.23828	U	0.044163	D	0.90638	0.7064	M	0.77486	2.375	0.40955	D	0.984577	P;D	0.67145	0.718;0.996	B;P	0.51385	0.253;0.668	D	0.89040	0.3448	10	0.72032	D	0.01	-21.9159	4.2797	0.10827	0.0:0.5071:0.0:0.4929	.	612;665	B4DKJ3;P49747	.;COMP_HUMAN	Q	632;665;612;652	ENSP00000439156:R632Q;ENSP00000222271:R665Q;ENSP00000403792:R612Q	ENSP00000222271:R665Q	R	-	2	0	COMP	18756094	0.574000	0.26684	1.000000	0.80357	0.906000	0.53458	1.041000	0.30291	0.988000	0.38734	0.460000	0.39030	CGG	COMP	-	pfam_Thrombospondin_C,superfamily_ConA-like_lec_gl	ENSG00000105664		0.602	COMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	COMP	HGNC	protein_coding	OTTHUMT00000403457.1	10	0.00	0	C	NM_000095		18895094	18895094	-1	no_errors	ENST00000222271	ensembl	human	known	69_37n	missense	32	30.43	14	SNP	1.000	T
CROT	54677	genome.wustl.edu	37	7	87005203	87005203	+	Silent	SNP	G	G	A			TCGA-AN-A0XL-01A-11D-A10M-09	TCGA-AN-A0XL-10A-01D-A10M-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	1b08a181-a73b-4506-aaa3-3521f2c57207	1acce21e-7513-402f-b586-423415f7cc2c	g.chr7:87005203G>A	ENST00000331536.3	+	9	995	c.810G>A	c.(808-810)caG>caA	p.Q270Q	CROT_ENST00000419147.2_Silent_p.Q298Q|CROT_ENST00000442291.1_Silent_p.Q270Q	NM_021151.3	NP_066974.2	Q9UKG9	OCTC_HUMAN	carnitine O-octanoyltransferase	270					carnitine metabolic process (GO:0009437)|cellular lipid metabolic process (GO:0044255)|coenzyme A metabolic process (GO:0015936)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|fatty acid metabolic process (GO:0006631)|fatty acid transport (GO:0015908)|generation of precursor metabolites and energy (GO:0006091)|medium-chain fatty acid metabolic process (GO:0051791)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	carnitine O-octanoyltransferase activity (GO:0008458)|receptor binding (GO:0005102)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				L-Carnitine(DB00583)	AAAAAATTCAGAGTAGTTTAC	0.363																																						dbGAP											0													83.0	83.0	83.0					7																	87005203		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0				CCDS5604.1, CCDS47634.1, CCDS59062.1	7q21.1	2010-02-26			ENSG00000005469	ENSG00000005469			2366	protein-coding gene	gene with protein product		606090				10486279	Standard	NM_021151		Approved	COT	uc003uit.3	Q9UKG9	OTTHUMG00000023653	ENST00000331536.3:c.810G>A	7.37:g.87005203G>A			A4D1D6|E7EQF2|Q86V17|Q8IUW9|Q9Y6I2	Silent	SNP	pfam_Carn_acyl_trans	p.Q270	ENST00000331536.3	37	c.810	CCDS5604.1	7																																																																																			CROT	-	pfam_Carn_acyl_trans	ENSG00000005469		0.363	CROT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CROT	HGNC	protein_coding	OTTHUMT00000253485.1	144	0.00	0	G	NM_021151		87005203	87005203	+1	no_errors	ENST00000331536	ensembl	human	known	69_37n	silent	155	18.85	36	SNP	1.000	A
CSTF2	1478	genome.wustl.edu	37	X	100083082	100083082	+	Missense_Mutation	SNP	C	C	T			TCGA-AN-A0XL-01A-11D-A10M-09	TCGA-AN-A0XL-10A-01D-A10M-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	1b08a181-a73b-4506-aaa3-3521f2c57207	1acce21e-7513-402f-b586-423415f7cc2c	g.chrX:100083082C>T	ENST00000372972.2	+	8	896	c.880C>T	c.(880-882)Cgg>Tgg	p.R294W	CSTF2_ENST00000415585.2_Missense_Mutation_p.R294W	NM_001325.2	NP_001316.1	P33240	CSTF2_HUMAN	cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa	294	Gly/Pro-rich.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cleavage body (GO:0071920)|mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(6)|skin(2)|stomach(1)	13						GTCCATGGAACGGGGGCAAGG	0.443																																						dbGAP											0													94.0	86.0	89.0					X																	100083082		2203	4300	6503	-	-	-	SO:0001583	missense	0			BC017712	CCDS14473.1	Xq22.1	2013-02-12	2002-08-29		ENSG00000101811	ENSG00000101811		"""RNA binding motif (RRM) containing"""	2484	protein-coding gene	gene with protein product		300907	"""cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kD"""			1741396	Standard	XM_006724622		Approved		uc004egh.3	P33240	OTTHUMG00000022709	ENST00000372972.2:c.880C>T	X.37:g.100083082C>T	ENSP00000362063:p.Arg294Trp		Q5H951|Q6LA74|Q8N502	Missense_Mutation	SNP	pfam_RRM_dom,smart_RRM_dom,pfscan_RRM_dom	p.R294W	ENST00000372972.2	37	c.880	CCDS14473.1	X	.	.	.	.	.	.	.	.	.	.	C	17.25	3.340908	0.60963	.	.	ENSG00000101811	ENST00000415585;ENST00000372972;ENST00000458320	T;T	0.15017	2.49;2.46	5.13	2.08	0.27032	.	0.230912	0.39274	N	0.001409	T	0.29684	0.0741	L	0.52573	1.65	0.47214	D	0.999351	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.77557	0.987;0.99;0.983	T	0.01232	-1.1411	10	0.52906	T	0.07	-13.0416	7.3958	0.26936	0.4315:0.489:0.0:0.0795	.	294;277;294	E7EWR4;P33240-2;P33240	.;.;CSTF2_HUMAN	W	294;294;270	ENSP00000387996:R294W;ENSP00000362063:R294W	ENSP00000362063:R294W	R	+	1	2	CSTF2	99969738	0.955000	0.32602	0.937000	0.37676	0.973000	0.67179	0.401000	0.20948	0.450000	0.26774	0.594000	0.82650	CGG	CSTF2	-	NULL	ENSG00000101811		0.443	CSTF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CSTF2	HGNC	protein_coding	OTTHUMT00000058926.1	211	0.00	0	C	NM_001325		100083082	100083082	+1	no_errors	ENST00000415585	ensembl	human	known	69_37n	missense	220	25.34	75	SNP	0.762	T
DNAJB8	165721	genome.wustl.edu	37	3	128181429	128181429	+	Silent	SNP	C	C	T			TCGA-AN-A0XL-01A-11D-A10M-09	TCGA-AN-A0XL-10A-01D-A10M-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	1b08a181-a73b-4506-aaa3-3521f2c57207	1acce21e-7513-402f-b586-423415f7cc2c	g.chr3:128181429C>T	ENST00000469083.1	-	2	3217	c.660G>A	c.(658-660)gtG>gtA	p.V220V	DNAJB8-AS1_ENST00000471626.1_RNA|DNAJB8_ENST00000319153.3_Silent_p.V220V			Q8NHS0	DNJB8_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 8	220					chaperone-mediated protein folding (GO:0061077)|negative regulation of inclusion body assembly (GO:0090084)	cytosol (GO:0005829)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|protein binding involved in protein folding (GO:0044183)|unfolded protein binding (GO:0051082)			kidney(1)|large_intestine(4)|lung(4)|prostate(1)|skin(1)	11				GBM - Glioblastoma multiforme(114;0.177)		CCTTGCCGTTCACAGTCACCG	0.617																																						dbGAP											0													170.0	135.0	147.0					3																	128181429		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0				CCDS3048.1	3q21.3	2014-01-21			ENSG00000179407	ENSG00000179407		"""Heat shock proteins / DNAJ (HSP40)"""	23699	protein-coding gene	gene with protein product		611337					Standard	NM_153330		Approved	MGC33884, CT156	uc003ekk.2	Q8NHS0	OTTHUMG00000159690	ENST00000469083.1:c.660G>A	3.37:g.128181429C>T			B3KWV7	Silent	SNP	pfam_DnaJ_N,superfamily_DnaJ_N,smart_DnaJ_N,pfscan_DnaJ_N,prints_Hsp_DnaJ	p.V220	ENST00000469083.1	37	c.660	CCDS3048.1	3																																																																																			DNAJB8	-	NULL	ENSG00000179407		0.617	DNAJB8-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	DNAJB8	HGNC	protein_coding	OTTHUMT00000356933.1	8	0.00	0	C	NM_153330		128181429	128181429	-1	no_errors	ENST00000319153	ensembl	human	known	69_37n	silent	41	24.07	13	SNP	0.724	T
GABPA	2551	genome.wustl.edu	37	21	27141488	27141488	+	Missense_Mutation	SNP	C	C	G			TCGA-AN-A0XL-01A-11D-A10M-09	TCGA-AN-A0XL-10A-01D-A10M-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	1b08a181-a73b-4506-aaa3-3521f2c57207	1acce21e-7513-402f-b586-423415f7cc2c	g.chr21:27141488C>G	ENST00000354828.3	+	10	1837	c.1310C>G	c.(1309-1311)cCa>cGa	p.P437R	GABPA_ENST00000400075.3_Missense_Mutation_p.P437R	NM_001197297.1	NP_001184226.1	Q06546	GABPA_HUMAN	GA binding protein transcription factor, alpha subunit 60kDa	437					cell differentiation (GO:0030154)|in utero embryonic development (GO:0001701)|negative regulation of megakaryocyte differentiation (GO:0045653)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|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)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(5)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	24						ATTGCCCAGCCAGTCACAGCA	0.448																																						dbGAP											0													32.0	36.0	35.0					21																	27141488		2202	4291	6493	-	-	-	SO:0001583	missense	0				CCDS13575.1	21q21-q22.1	2008-07-31	2002-08-29		ENSG00000154727	ENSG00000154727			4071	protein-coding gene	gene with protein product	"""human nuclear respiratory factor-2 subunit alpha"", ""nuclear respiratory factor 2 alpha subunit"""	600609	"""GA-binding protein transcription factor, alpha subunit (60kD)"""			8441384	Standard	NM_002040		Approved	E4TF1A, NFT2, NRF2, E4TF1-60, NRF2A	uc002yly.4	Q06546	OTTHUMG00000078443	ENST00000354828.3:c.1310C>G	21.37:g.27141488C>G	ENSP00000346886:p.Pro437Arg		Q12939	Missense_Mutation	SNP	pfam_GABP_asu_N,pfam_Ets,pfam_Pointed_dom,superfamily_SAM/pointed,smart_Pointed_dom,smart_Ets,pirsf_TF_GA-bd_asu,prints_Ets,pfscan_Ets	p.P437R	ENST00000354828.3	37	c.1310	CCDS13575.1	21	.	.	.	.	.	.	.	.	.	.	C	16.15	3.043114	0.55003	.	.	ENSG00000154727	ENST00000354828;ENST00000400075	T;T	0.16196	2.36;2.36	5.72	5.72	0.89469	.	0.213072	0.50627	D	0.000116	T	0.32436	0.0829	L	0.27053	0.805	0.80722	D	1	D	0.71674	0.998	D	0.76071	0.987	T	0.04811	-1.0925	10	0.87932	D	0	.	19.4683	0.94952	0.0:1.0:0.0:0.0	.	437	Q06546	GABPA_HUMAN	R	437	ENSP00000346886:P437R;ENSP00000382948:P437R	ENSP00000346886:P437R	P	+	2	0	GABPA	26063359	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	7.393000	0.79851	2.708000	0.92522	0.585000	0.79938	CCA	GABPA	-	pirsf_TF_GA-bd_asu	ENSG00000154727		0.448	GABPA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	GABPA	HGNC	protein_coding	OTTHUMT00000171365.1	46	0.00	0	C	NM_002040		27141488	27141488	+1	no_errors	ENST00000354828	ensembl	human	known	69_37n	missense	41	29.31	17	SNP	1.000	G
HIST2H2BF	440689	genome.wustl.edu	37	1	149783828	149783828	+	Missense_Mutation	SNP	C	C	A			TCGA-AN-A0XL-01A-11D-A10M-09	TCGA-AN-A0XL-10A-01D-A10M-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	1b08a181-a73b-4506-aaa3-3521f2c57207	1acce21e-7513-402f-b586-423415f7cc2c	g.chr1:149783828C>A	ENST00000369167.1	-	1	86	c.51G>T	c.(49-51)aaG>aaT	p.K17N	RP11-196G18.21_ENST00000420462.1_RNA|HIST2H2BF_ENST00000427880.2_Missense_Mutation_p.K17N|HIST2H2BF_ENST00000545683.1_Missense_Mutation_p.K17N|HIST2H2BF_ENST00000469483.1_5'UTR	NM_001024599.4	NP_001019770.1	Q5QNW6	H2B2F_HUMAN	histone cluster 2, H2bf	17					chromatin organization (GO:0006325)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	Breast(34;0.0124)|all_hematologic(923;0.127)					TCGTAACAGCCTTTTTGGAGC	0.512																																						dbGAP											0													104.0	103.0	103.0					1																	149783828		2203	4300	6503	-	-	-	SO:0001583	missense	0			BC110793	CCDS30846.1, CCDS53359.1	1q21.2	2013-06-03	2006-10-11		ENSG00000203814	ENSG00000203814		"""Histones / Replication-dependent"""	24700	protein-coding gene	gene with protein product			"""histone 2, H2bf"""				Standard	NM_001161334		Approved		uc010pbj.2	Q5QNW6	OTTHUMG00000183159	ENST00000369167.1:c.51G>T	1.37:g.149783828C>A	ENSP00000358164:p.Lys17Asn		A8K0U9|B4DLA9	Missense_Mutation	SNP	pfam_Histone_core_D,pfam_CBFA_NFYB_domain,superfamily_Histone-fold,smart_Histone_H2B,prints_Histone_H2B	p.K17N	ENST00000369167.1	37	c.51	CCDS30846.1	1	.	.	.	.	.	.	.	.	.	.	C	14.17	2.454902	0.43634	.	.	ENSG00000203814	ENST00000545683;ENST00000427880;ENST00000369167	T;T;T	0.23950	1.88;1.88;1.88	3.56	-4.74	0.03249	Histone-fold (2);	0.000000	0.50627	D	0.000115	T	0.40272	0.1110	M	0.90309	3.105	0.35530	D	0.802155	D;P;P	0.67145	0.996;0.9;0.9	D;P;P	0.68943	0.961;0.859;0.544	T	0.58509	-0.7624	10	0.72032	D	0.01	.	14.9547	0.71104	0.0:0.1566:0.0:0.8434	.	17;17;17	B4DR52;B4DLA9;Q5QNW6	.;.;H2B2F_HUMAN	N	17	ENSP00000445831:K17N;ENSP00000407461:K17N;ENSP00000358164:K17N	ENSP00000358164:K17N	K	-	3	2	HIST2H2BF	148050452	0.000000	0.05858	0.133000	0.22050	0.838000	0.47535	-3.492000	0.00453	-1.205000	0.02645	0.195000	0.17529	AAG	HIST2H2BF	-	superfamily_Histone-fold	ENSG00000203814		0.512	HIST2H2BF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HIST2H2BF	HGNC	protein_coding	OTTHUMT00000033453.2	105	0.94	1	C	NM_001024599		149783828	149783828	-1	no_errors	ENST00000427880	ensembl	human	known	69_37n	missense	207	31.68	96	SNP	0.854	A
GPATCH2	55105	genome.wustl.edu	37	1	217688214	217688214	+	Silent	SNP	T	T	G			TCGA-AN-A0XL-01A-11D-A10M-09	TCGA-AN-A0XL-10A-01D-A10M-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	1b08a181-a73b-4506-aaa3-3521f2c57207	1acce21e-7513-402f-b586-423415f7cc2c	g.chr1:217688214T>G	ENST00000366935.3	-	6	1226	c.1116A>C	c.(1114-1116)ccA>ccC	p.P372P		NM_018040.2	NP_060510.1	Q9NW75	GPTC2_HUMAN	G patch domain containing 2	372					negative regulation of phosphatase activity (GO:0010923)		nucleic acid binding (GO:0003676)			NS(1)|breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(3)|stomach(1)	35				OV - Ovarian serous cystadenocarcinoma(81;0.0397)|all cancers(67;0.0744)|GBM - Glioblastoma multiforme(131;0.0872)		TGTTACCCACTGGGCCAGGAA	0.348																																						dbGAP											0													44.0	44.0	44.0					1																	217688214		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AK001114	CCDS1518.1, CCDS73031.1	1q41	2013-01-28		2006-12-13	ENSG00000092978	ENSG00000092978		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""G patch domain containing"""	25499	protein-coding gene	gene with protein product	"""cancer/testis antigen 110"", ""protein phosphatase 1, regulatory subunit 30"""			GPATC2		19432882, 15375528	Standard	XM_005273174		Approved	FLJ10252, CT110, PPP1R30	uc001hlf.1	Q9NW75	OTTHUMG00000000527	ENST00000366935.3:c.1116A>C	1.37:g.217688214T>G			Q5VYK7|Q5VYK8|Q86YE7	Silent	SNP	pfam_G_patch_dom,smart_G_patch_dom,pfscan_G_patch_dom	p.P372	ENST00000366935.3	37	c.1116	CCDS1518.1	1																																																																																			GPATCH2	-	NULL	ENSG00000092978		0.348	GPATCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GPATCH2	HGNC	protein_coding	OTTHUMT00000001272.1	103	0.00	0	T	NM_018040		217688214	217688214	-1	no_errors	ENST00000366935	ensembl	human	known	69_37n	silent	63	23.17	19	SNP	0.191	G
IFNE	338376	genome.wustl.edu	37	9	21481249	21481249	+	Nonsense_Mutation	SNP	G	G	A	rs147478752		TCGA-AN-A0XL-01A-11D-A10M-09	TCGA-AN-A0XL-10A-01D-A10M-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	1b08a181-a73b-4506-aaa3-3521f2c57207	1acce21e-7513-402f-b586-423415f7cc2c	g.chr9:21481249G>A	ENST00000448696.3	-	1	1063	c.445C>T	c.(445-447)Cga>Tga	p.R149*	MIR31HG_ENST00000304425.3_RNA	NM_176891.4	NP_795372.1	Q86WN2	IFNE_HUMAN	interferon, epsilon	149					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)	extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)			large_intestine(2)|lung(1)|skin(1)	4						TGGATCCTTCGGAAGTACATT	0.443																																						dbGAP											0													179.0	172.0	175.0					9																	21481249		2203	4300	6503	-	-	-	SO:0001587	stop_gained	0			AY190045	CCDS34997.1	9p21.1	2008-12-12			ENSG00000184995	ENSG00000184995			18163	protein-coding gene	gene with protein product		615223				15546383, 17287131	Standard	NM_176891		Approved	IFNE1	uc003zpg.3	Q86WN2	OTTHUMG00000019672	ENST00000448696.3:c.445C>T	9.37:g.21481249G>A	ENSP00000418018:p.Arg149*			Nonsense_Mutation	SNP	pfam_Interferon_alpha/beta/delta,superfamily_4_helix_cytokine-like_core,smart_Interferon_alpha/beta/delta,prints_Interferon_alpha/beta/delta	p.R149*	ENST00000448696.3	37	c.445	CCDS34997.1	9	.	.	.	.	.	.	.	.	.	.	G	37	6.483393	0.97603	.	.	ENSG00000184995	ENST00000448696	.	.	.	4.72	0.407	0.16371	.	0.622492	0.14749	U	0.300682	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.25106	T	0.35	.	6.5388	0.22369	0.0867:0.0:0.4393:0.4741	.	.	.	.	X	149	.	ENSP00000418018:R149X	R	-	1	2	IFNE	21471249	0.011000	0.17503	0.034000	0.17996	0.389000	0.30415	0.048000	0.14078	-0.021000	0.14009	0.655000	0.94253	CGA	IFNE	-	pfam_Interferon_alpha/beta/delta,superfamily_4_helix_cytokine-like_core,smart_Interferon_alpha/beta/delta	ENSG00000184995		0.443	IFNE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	IFNE	HGNC	protein_coding	OTTHUMT00000051901.2	110	0.00	0	G	NM_176891		21481249	21481249	-1	no_errors	ENST00000448696	ensembl	human	known	69_37n	nonsense	124	26.63	45	SNP	0.142	A
INHBA	3624	genome.wustl.edu	37	7	41729515	41729515	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AN-A0XL-01A-11D-A10M-09	TCGA-AN-A0XL-10A-01D-A10M-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	1b08a181-a73b-4506-aaa3-3521f2c57207	1acce21e-7513-402f-b586-423415f7cc2c	g.chr7:41729515C>T	ENST00000242208.4	-	3	1260	c.1014G>A	c.(1012-1014)tgG>tgA	p.W338*	AC005027.3_ENST00000416150.1_RNA|INHBA_ENST00000464515.1_5'UTR|INHBA_ENST00000442711.1_Nonsense_Mutation_p.W338*	NM_002192.2	NP_002183.1	P08476	INHBA_HUMAN	inhibin, beta A	338					activin receptor signaling pathway (GO:0032924)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular response to cholesterol (GO:0071397)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|defense response (GO:0006952)|endodermal cell differentiation (GO:0035987)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|eyelid development in camera-type eye (GO:0061029)|G1/S transition of mitotic cell cycle (GO:0000082)|growth (GO:0040007)|hair follicle development (GO:0001942)|hematopoietic progenitor cell differentiation (GO:0002244)|hemoglobin biosynthetic process (GO:0042541)|male gonad development (GO:0008584)|mesodermal cell differentiation (GO:0048333)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of follicle-stimulating hormone secretion (GO:0046882)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of phosphorylation (GO:0042326)|nervous system development (GO:0007399)|odontogenesis (GO:0042476)|ovarian follicle development (GO:0001541)|palate development (GO:0060021)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of follicle-stimulating hormone secretion (GO:0046881)|positive regulation of ovulation (GO:0060279)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|progesterone secretion (GO:0042701)|regulation of follicle-stimulating hormone secretion (GO:0046880)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to drug (GO:0042493)	activin A complex (GO:0043509)|extracellular region (GO:0005576)|inhibin A complex (GO:0043512)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|hormone activity (GO:0005179)|identical protein binding (GO:0042802)|peptide hormone binding (GO:0017046)|type II activin receptor binding (GO:0070699)			biliary_tract(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(15)|lung(26)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						GAGCAATGATCCAGTCATTCC	0.552										TSP Lung(11;0.080)																												dbGAP											0													114.0	113.0	114.0					7																	41729515		2203	4300	6503	-	-	-	SO:0001587	stop_gained	0				CCDS5464.1	7p15-p13	2014-01-30	2007-07-30		ENSG00000122641	ENSG00000122641		"""Endogenous ligands"""	6066	protein-coding gene	gene with protein product		147290	"""inhibin, beta A (activin A, activin AB alpha polypeptide)"""			3345731	Standard	NM_002192		Approved		uc003thr.3	P08476	OTTHUMG00000023574	ENST00000242208.4:c.1014G>A	7.37:g.41729515C>T	ENSP00000242208:p.Trp338*		Q14599	Nonsense_Mutation	SNP	pfam_TGF-b_C,pfam_TGF-b_N,smart_TGF-b_C,prints_Inhibin_betaA,prints_Inhibin_asu	p.W338*	ENST00000242208.4	37	c.1014	CCDS5464.1	7	.	.	.	.	.	.	.	.	.	.	.	37	6.386186	0.97524	.	.	ENSG00000122641	ENST00000242208;ENST00000442711	.	.	.	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.621	20.4135	0.99023	0.0:1.0:0.0:0.0	.	.	.	.	X	338	.	ENSP00000242208:W338X	W	-	3	0	INHBA	41696040	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.757000	0.85209	2.835000	0.97688	0.591000	0.81541	TGG	INHBA	-	pfam_TGF-b_C,smart_TGF-b_C,prints_Inhibin_asu	ENSG00000122641		0.552	INHBA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	INHBA	HGNC	protein_coding	OTTHUMT00000250793.1	25	0.00	0	C			41729515	41729515	-1	no_errors	ENST00000242208	ensembl	human	known	69_37n	nonsense	56	30.00	24	SNP	1.000	T
RPL38	6169	genome.wustl.edu	37	17	72206133	72206134	+	3'UTR	INS	-	-	C	rs369752137|rs567147030	byFrequency	TCGA-AN-A0XL-01A-11D-A10M-09	TCGA-AN-A0XL-10A-01D-A10M-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	1b08a181-a73b-4506-aaa3-3521f2c57207	1acce21e-7513-402f-b586-423415f7cc2c	g.chr17:72206133_72206134insC	ENST00000311111.6	+	0	509_510				CTD-2514K5.2_ENST00000499670.2_RNA|CTD-2514K5.2_ENST00000532794.1_RNA|CTD-2514K5.2_ENST00000531617.1_RNA			P63173	RL38_HUMAN	ribosomal protein L38						90S preribosome assembly (GO:0034463)|axial mesoderm development (GO:0048318)|cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|middle ear morphogenesis (GO:0042474)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ossification (GO:0001503)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|eukaryotic 80S initiation complex (GO:0033291)|focal adhesion (GO:0005925)	RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			large_intestine(1)|pancreas(1)	2						TTttttttttttttctttcttt	0.5																																						dbGAP											0																																										-	-	-	SO:0001624	3_prime_UTR_variant	0			AB007185	CCDS11696.1	17q25.1	2013-06-19			ENSG00000172809	ENSG00000172809		"""L ribosomal proteins"""	10349	protein-coding gene	gene with protein product		604182				9582194	Standard	NM_000999		Approved	L38	uc002jka.3	P63173	OTTHUMG00000166016	ENST00000311111.6:c.*166->C	17.37:g.72206133_72206134insC			B2R5A8|P23411	RNA	INS	-	NULL	ENST00000311111.6	37	NULL	CCDS11696.1	17																																																																																			CTD-2514K5.2	-	-	ENSG00000246731		0.500	RPL38-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	MGC16275	Clone_based_vega_gene	protein_coding	OTTHUMT00000387450.2	24	0.00	0	-	NM_000999		72206133	72206134	-1	no_errors	ENST00000499670	ensembl	human	known	69_37n	rna	4	33.33	2	INS	0.082:0.088	C
MICAL3	57553	genome.wustl.edu	37	22	18463645	18463645	+	Intron	SNP	C	C	A	rs572987231		TCGA-AN-A0XL-01A-11D-A10M-09	TCGA-AN-A0XL-10A-01D-A10M-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	1b08a181-a73b-4506-aaa3-3521f2c57207	1acce21e-7513-402f-b586-423415f7cc2c	g.chr22:18463645C>A	ENST00000441493.2	-	1	279				MICAL3_ENST00000429452.1_Intron|MIR648_ENST00000385046.1_RNA|XXbac-B476C20.14_ENST00000429618.1_RNA|MICAL3_ENST00000444520.1_Intron|MICAL3_ENST00000207726.7_Intron	NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3						actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|exocytosis (GO:0006887)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	4		all_epithelial(15;0.198)		Lung(27;0.0427)		ACCCTCACTTCCGACTAAGTG	0.632																																						dbGAP											0													76.0	73.0	74.0					22																	18463645		1568	3582	5150	-	-	-	SO:0001627	intron_variant	0			AB037785	CCDS46659.1, CCDS46660.1, CCDS46661.1	22q11.21	2013-03-26	2013-03-26		ENSG00000243156	ENSG00000243156			24694	protein-coding gene	gene with protein product		608882				12110185	Standard	NM_015241		Approved	KIAA0819	uc002zng.4	Q7RTP6	OTTHUMG00000150067	ENST00000441493.2:c.73+43401G>T	22.37:g.18463645C>A			B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	RNA	SNP	-	NULL	ENST00000441493.2	37	NULL	CCDS46659.1	22																																																																																			MIR648	-	-	ENSG00000207780		0.632	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	MIR648	HGNC	protein_coding	OTTHUMT00000447351.1	23	0.00	0	C			18463645	18463645	-1	no_errors	ENST00000385046	ensembl	human	known	69_37n	rna	52	22.39	15	SNP	0.002	A
MKI67	4288	genome.wustl.edu	37	10	129905447	129905447	+	Missense_Mutation	SNP	C	C	A	rs371337191		TCGA-AN-A0XL-01A-11D-A10M-09	TCGA-AN-A0XL-10A-01D-A10M-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	1b08a181-a73b-4506-aaa3-3521f2c57207	1acce21e-7513-402f-b586-423415f7cc2c	g.chr10:129905447C>A	ENST00000368654.3	-	13	5032	c.4657G>T	c.(4657-4659)Gca>Tca	p.A1553S	MKI67_ENST00000368653.3_Missense_Mutation_p.A1193S	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	1553	16 X 122 AA approximate repeats.				cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				CCCATAAATGCGTAGATGTTT	0.483																																						dbGAP											0													296.0	262.0	274.0					10																	129905447		2203	4300	6503	-	-	-	SO:0001583	missense	0			X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 105"""	176741	"""antigen identified by monoclonal antibody Ki-67"""			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.4657G>T	10.37:g.129905447C>A	ENSP00000357643:p.Ala1553Ser		Q5VWH2	Missense_Mutation	SNP	pfam_K167R,pfam_FHA_dom,superfamily_SMAD_FHA_domain,smart_FHA_dom,pfscan_FHA_dom	p.A1553S	ENST00000368654.3	37	c.4657	CCDS7659.1	10	.	.	.	.	.	.	.	.	.	.	C	3.570	-0.087812	0.07097	.	.	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.02552	4.25;4.25	2.71	-4.63	0.03359	.	1.808920	0.02749	N	0.117206	T	0.04770	0.0129	L	0.43152	1.355	0.09310	N	1	P;D;P	0.63046	0.935;0.992;0.898	P;P;P	0.53102	0.597;0.718;0.7	T	0.45702	-0.9243	10	0.09338	T	0.73	.	6.9891	0.24745	0.4654:0.4009:0.1337:0.0	.	1552;1193;1553	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	S	1553;1193;1552	ENSP00000357643:A1553S;ENSP00000357642:A1193S	ENSP00000357642:A1193S	A	-	1	0	MKI67	129795437	0.009000	0.17119	0.000000	0.03702	0.002000	0.02628	0.240000	0.18042	-0.998000	0.03446	0.462000	0.41574	GCA	MKI67	-	pfam_K167R	ENSG00000148773		0.483	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	MKI67	HGNC	protein_coding	OTTHUMT00000050999.1	347	0.00	0	C	NM_002417		129905447	129905447	-1	no_errors	ENST00000368654	ensembl	human	known	69_37n	missense	339	26.30	121	SNP	0.000	A
MTERF3	51001	genome.wustl.edu	37	8	97263275	97263277	+	In_Frame_Del	DEL	AGG	AGG	-			TCGA-AN-A0XL-01A-11D-A10M-09	TCGA-AN-A0XL-10A-01D-A10M-09	AGG	AGG					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	1b08a181-a73b-4506-aaa3-3521f2c57207	1acce21e-7513-402f-b586-423415f7cc2c	g.chr8:97263275_97263277delAGG	ENST00000287025.3	-	4	632_634	c.534_536delCCT	c.(532-537)ctcctt>ctt	p.178_179LL>L	MTERFD1_ENST00000522822.1_In_Frame_Del_p.57_58LL>L|MTERFD1_ENST00000523821.1_In_Frame_Del_p.178_179LL>L|MTERFD1_ENST00000524341.1_5'UTR	NM_015942.3	NP_057026.3	Q96E29	MTEF3_HUMAN		178					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)	transcription regulatory region DNA binding (GO:0044212)			endometrium(1)|kidney(1)|large_intestine(7)|lung(7)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	24	Breast(36;5.16e-05)					CAGTCTCAGAAGGAGGTTTGCTG	0.35																																						dbGAP											0																																										-	-	-	SO:0001651	inframe_deletion	0																														ENST00000287025.3:c.534_536delCCT	8.37:g.97263278_97263280delAGG	ENSP00000287025:p.Leu180del		B3KMG6|G3V130|Q9Y301	In_Frame_Del	DEL	pfam_Mit_transcrip_term-rel,smart_Mit_transcrip_term-rel	p.L180in_frame_del	ENST00000287025.3	37	c.536_534	CCDS6270.1	8																																																																																			MTERFD1	-	pfam_Mit_transcrip_term-rel,smart_Mit_transcrip_term-rel	ENSG00000156469		0.350	MTERFD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	MTERFD1	HGNC	protein_coding	OTTHUMT00000379876.1	249	0.00	0	AGG			97263275	97263277	-1	no_errors	ENST00000287025	ensembl	human	known	69_37n	in_frame_del	234	13.97	38	DEL	1.000:1.000:0.998	-
PIK3CA	5290	genome.wustl.edu	37	3	178952085	178952085	+	Missense_Mutation	SNP	A	A	G	rs121913279		TCGA-AN-A0XL-01A-11D-A10M-09	TCGA-AN-A0XL-10A-01D-A10M-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	1b08a181-a73b-4506-aaa3-3521f2c57207	1acce21e-7513-402f-b586-423415f7cc2c	g.chr3:178952085A>G	ENST00000263967.3	+	21	3297	c.3140A>G	c.(3139-3141)cAt>cGt	p.H1047R	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1047	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.		H -> L (in BC; unknown pathological significance). {ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16353168}.|H -> R (in CLOVE, KERSEB, CRC, BC and OC; also found in an endometrial carcinoma sample; shows an increase in lipid kinase activity; oncogenic in vivo; requires binding to p85 regulatory subunit to induce cellular transformation but not interaction with RAS; may mimic the conformatitonal change triggered by the interaction with RAS; enhances invadopodia-mediated extracellular matrix degradation and invasion in breast cancer cells; increases lipid kinase activity; may alter the interaction of the PI3K/ PI4K kinase domain with the cell membrane). {ECO:0000269|PubMed:15016963, ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15712344, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16114017, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:22658544}.|H -> Y (in MCAP; also found in an endometrial carcinoma sample). {ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:22729224}.		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.H1047R(1387)|p.H1047L(194)|p.H1047P(1)		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)	AATGATGCACATCATGGTGGC	0.378	H1047L(EFM19_BREAST)|H1047R(BT20_BREAST)|H1047R(CAL29_URINARY_TRACT)|H1047R(CAL33_UPPER_AERODIGESTIVE_TRACT)|H1047R(DETROIT562_UPPER_AERODIGESTIVE_TRACT)|H1047R(HCC1954_BREAST)|H1047R(HCT116_LARGE_INTESTINE)|H1047R(HSC2_UPPER_AERODIGESTIVE_TRACT)|H1047R(LS180_LARGE_INTESTINE)|H1047R(MCAS_OVARY)|H1047R(MDAMB453_BREAST)|H1047R(NCIH1048_LUNG)|H1047R(RKO_LARGE_INTESTINE)|H1047R(SKOV3_OVARY)|H1047R(T47D_BREAST)	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"""	1582	Substitution - Missense(1582)	breast(961)|large_intestine(245)|endometrium(114)|ovary(77)|urinary_tract(36)|upper_aerodigestive_tract(26)|lung(19)|central_nervous_system(19)|stomach(19)|haematopoietic_and_lymphoid_tissue(11)|thyroid(10)|NS(9)|liver(7)|kidney(6)|soft_tissue(6)|skin(4)|prostate(4)|pituitary(3)|pancreas(3)|meninges(1)|cervix(1)|bone(1)											99.0	89.0	92.0					3																	178952085		1912	4130	6042	-	-	-	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.3140A>G	3.37:g.178952085A>G	ENSP00000263967:p.His1047Arg		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.H1047R	ENST00000263967.3	37	c.3140	CCDS43171.1	3	.	.	.	.	.	.	.	.	.	.	A	14.34	2.506328	0.44558	.	.	ENSG00000121879	ENST00000263967	T	0.80214	-1.35	6.08	6.08	0.98989	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.000000	0.85682	D	0.000000	T	0.62466	0.2430	N	0.08118	0	0.80722	D	1	P	0.38597	0.639	B	0.28011	0.085	T	0.67526	-0.5648	10	0.40728	T	0.16	-21.2893	16.6512	0.85203	1.0:0.0:0.0:0.0	.	1047	P42336	PK3CA_HUMAN	R	1047	ENSP00000263967:H1047R	ENSP00000263967:H1047R	H	+	2	0	PIK3CA	180434779	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	8.859000	0.92264	2.333000	0.79357	0.482000	0.46254	CAT	PIK3CA	-	superfamily_Kinase-like_dom,smart_PI3/4_kinase_cat_dom,pfscan_PI3/4_kinase_cat_dom	ENSG00000121879		0.378	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	PIK3CA	HGNC	protein_coding	OTTHUMT00000348409.2	79	0.00	0	A			178952085	178952085	+1	no_errors	ENST00000263967	ensembl	human	known	69_37n	missense	79	48.03	73	SNP	1.000	G
QSOX1	5768	genome.wustl.edu	37	1	180159688	180159689	+	Frame_Shift_Ins	INS	-	-	A			TCGA-AN-A0XL-01A-11D-A10M-09	TCGA-AN-A0XL-10A-01D-A10M-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	1b08a181-a73b-4506-aaa3-3521f2c57207	1acce21e-7513-402f-b586-423415f7cc2c	g.chr1:180159688_180159689insA	ENST00000367602.3	+	10	1335_1336	c.1261_1262insA	c.(1261-1263)caafs	p.Q421fs	QSOX1_ENST00000367600.5_Frame_Shift_Ins_p.Q421fs			O00391	QSOX1_HUMAN	quiescin Q6 sulfhydryl oxidase 1	421	ERV/ALR sulfhydryl oxidase. {ECO:0000255|PROSITE-ProRule:PRU00654}.				cell redox homeostasis (GO:0045454)|protein folding (GO:0006457)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of Golgi membrane (GO:0030173)	flavin-linked sulfhydryl oxidase activity (GO:0016971)|protein disulfide isomerase activity (GO:0003756)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	31						GGCAGCTCGGCAAAATGTAGAC	0.614																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			U97276	CCDS1337.1, CCDS30950.1	1q24	2008-02-05	2007-04-23	2007-04-23	ENSG00000116260	ENSG00000116260			9756	protein-coding gene	gene with protein product		603120	"""quiescin Q6"""	QSCN6		9878249, 8396966	Standard	NM_002826		Approved		uc001gnz.3	O00391	OTTHUMG00000035256	ENST00000367602.3:c.1265dupA	1.37:g.180159692_180159692dupA	ENSP00000356574:p.Gln421fs		Q59G29|Q5T2X0|Q8TDL6|Q8WVP4	Frame_Shift_Ins	INS	pfam_Evr1_Alr,pfam_Thioredoxin_domain,superfamily_Evr1_Alr,superfamily_Thioredoxin-like_fold	p.N422fs	ENST00000367602.3	37	c.1261_1262	CCDS1337.1	1																																																																																			QSOX1	-	pfam_Evr1_Alr,superfamily_Evr1_Alr	ENSG00000116260		0.614	QSOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	QSOX1	HGNC	protein_coding	OTTHUMT00000085289.1	23	0.00	0	-	NM_002826		180159688	180159689	+1	no_errors	ENST00000367602	ensembl	human	known	69_37n	frame_shift_ins	105	21.05	28	INS	0.003:0.001	A
RERE	473	genome.wustl.edu	37	1	8421506	8421506	+	Missense_Mutation	SNP	A	A	C			TCGA-AN-A0XL-01A-11D-A10M-09	TCGA-AN-A0XL-10A-01D-A10M-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	1b08a181-a73b-4506-aaa3-3521f2c57207	1acce21e-7513-402f-b586-423415f7cc2c	g.chr1:8421506A>C	ENST00000337907.3	-	19	2695	c.2061T>G	c.(2059-2061)agT>agG	p.S687R	RERE_ENST00000400907.2_Intron|RERE_ENST00000377464.1_Missense_Mutation_p.S419R|RERE_ENST00000400908.2_Missense_Mutation_p.S687R|RERE_ENST00000476556.1_Missense_Mutation_p.S133R	NM_012102.3	NP_036234.3	Q9P2R6	RERE_HUMAN	arginine-glutamic acid dipeptide (RE) repeats	687					chromatin remodeling (GO:0006338)|multicellular organismal development (GO:0007275)|NLS-bearing protein import into nucleus (GO:0006607)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|poly-glutamine tract binding (GO:0008267)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(1)|lung(16)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	49	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)		GACTGTCTGAACTCTCTCCCT	0.602																																						dbGAP											0													115.0	105.0	108.0					1																	8421506		2197	4295	6492	-	-	-	SO:0001583	missense	0			AF016005	CCDS95.1, CCDS41243.1	1p36.23	2013-01-25			ENSG00000142599	ENSG00000142599		"""GATA zinc finger domain containing"""	9965	protein-coding gene	gene with protein product		605226		ATN1L		10814707, 10729226	Standard	NM_012102		Approved	KIAA0458, ARP, ARG, DNB1	uc001apf.3	Q9P2R6	OTTHUMG00000001765	ENST00000337907.3:c.2061T>G	1.37:g.8421506A>C	ENSP00000338629:p.Ser687Arg		O43393|O75046|O75359|Q5VXL9|Q6P6B9|Q9Y2W4	Missense_Mutation	SNP	pfam_Atrophin-like,pfam_BAH_dom,pfam_ELM2_dom,pfam_Znf_GATA,superfamily_Homeodomain-like,smart_BAH_dom,smart_SANT/Myb,smart_Znf_GATA,pfscan_BAH_dom,pfscan_ELM2_dom	p.S687R	ENST00000337907.3	37	c.2061	CCDS95.1	1	.	.	.	.	.	.	.	.	.	.	A	24.6	4.544768	0.86022	.	.	ENSG00000142599	ENST00000337907;ENST00000377464;ENST00000476556;ENST00000400908	T;T;T;T	0.04119	3.7;3.7;3.7;3.7	5.6	-3.71	0.04424	.	.	.	.	.	T	0.16514	0.0397	M	0.67953	2.075	0.52501	D	0.999951	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.996	T	0.00295	-1.1839	9	0.51188	T	0.08	-16.305	15.8713	0.79122	0.2711:0.0:0.7289:0.0	.	419;687	B1AKN3;Q9P2R6	.;RERE_HUMAN	R	687;419;133;687	ENSP00000338629:S687R;ENSP00000366684:S419R;ENSP00000422246:S133R;ENSP00000383700:S687R	ENSP00000338629:S687R	S	-	3	2	RERE	8344093	1.000000	0.71417	0.711000	0.30485	0.972000	0.66771	1.673000	0.37534	-0.734000	0.04843	0.459000	0.35465	AGT	RERE	-	pfam_Atrophin-like	ENSG00000142599		0.602	RERE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RERE	HGNC	protein_coding	OTTHUMT00000004916.1	38	0.00	0	A			8421506	8421506	-1	no_errors	ENST00000337907	ensembl	human	known	69_37n	missense	82	33.33	41	SNP	1.000	C
RNF157	114804	genome.wustl.edu	37	17	74154520	74154520	+	Missense_Mutation	SNP	G	G	A			TCGA-AN-A0XL-01A-11D-A10M-09	TCGA-AN-A0XL-10A-01D-A10M-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	1b08a181-a73b-4506-aaa3-3521f2c57207	1acce21e-7513-402f-b586-423415f7cc2c	g.chr17:74154520G>A	ENST00000269391.6	-	13	1499	c.1367C>T	c.(1366-1368)tCg>tTg	p.S456L	RNF157_ENST00000319945.6_Missense_Mutation_p.S456L	NM_052916.2	NP_443148.1	Q96PX1	RN157_HUMAN	ring finger protein 157	456	Ser-rich.						zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(3)|lung(12)|ovary(2)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	25			LUSC - Lung squamous cell carcinoma(166;0.187)			CTGTGTCTCCGACTCGCTGCA	0.517																																					GBM(186;507 2120 27388 27773 52994)	dbGAP											0													145.0	127.0	133.0					17																	74154520		2203	4300	6503	-	-	-	SO:0001583	missense	0			AK091467	CCDS32740.1	17q25.3	2004-02-27			ENSG00000141576	ENSG00000141576		"""RING-type (C3HC4) zinc fingers"""	29402	protein-coding gene	gene with protein product						11572484	Standard	NM_052916		Approved	KIAA1917	uc002jqz.3	Q96PX1	OTTHUMG00000132627	ENST00000269391.6:c.1367C>T	17.37:g.74154520G>A	ENSP00000269391:p.Ser456Leu		Q8NB72|Q96N56	Missense_Mutation	SNP	smart_Znf_RING,pfscan_Znf_RING	p.S456L	ENST00000269391.6	37	c.1367	CCDS32740.1	17	.	.	.	.	.	.	.	.	.	.	G	22.1	4.246554	0.80024	.	.	ENSG00000141576	ENST00000269391;ENST00000319945	T;T	0.28454	1.61;1.71	5.7	5.7	0.88788	.	0.062554	0.64402	D	0.000003	T	0.34164	0.0888	L	0.58101	1.795	0.80722	D	1	D;D	0.56287	0.975;0.966	B;B	0.40134	0.32;0.238	T	0.25813	-1.0121	10	0.59425	D	0.04	-20.4135	18.8209	0.92097	0.0:0.0:1.0:0.0	.	456;456	Q96PX1-2;Q96PX1	.;RN157_HUMAN	L	456	ENSP00000269391:S456L;ENSP00000321837:S456L	ENSP00000269391:S456L	S	-	2	0	RNF157	71666115	1.000000	0.71417	0.540000	0.28089	0.902000	0.53008	5.752000	0.68728	2.670000	0.90874	0.655000	0.94253	TCG	RNF157	-	NULL	ENSG00000141576		0.517	RNF157-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RNF157	HGNC	protein_coding	OTTHUMT00000255874.2	35	0.00	0	G	XM_290732		74154520	74154520	-1	no_errors	ENST00000269391	ensembl	human	known	69_37n	missense	74	25.25	25	SNP	0.998	A
CTBS	1486	genome.wustl.edu	37	1	85018771	85018772	+	3'UTR	INS	-	-	A			TCGA-AN-A0XL-01A-11D-A10M-09	TCGA-AN-A0XL-10A-01D-A10M-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	1b08a181-a73b-4506-aaa3-3521f2c57207	1acce21e-7513-402f-b586-423415f7cc2c	g.chr1:85018771_85018772insA	ENST00000370630.5	-	0	3116_3117				CTBS_ENST00000477677.1_5'Flank	NM_004388.2	NP_004379.1	Q01459	DIAC_HUMAN	chitobiase, di-N-acetyl-						chitin catabolic process (GO:0006032)|oligosaccharide catabolic process (GO:0009313)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	chitinase activity (GO:0004568)	p.I452fs*1(2)		breast(1)|endometrium(1)|large_intestine(4)|lung(2)|ovary(1)	9				all cancers(265;0.00727)|Epithelial(280;0.0192)|OV - Ovarian serous cystadenocarcinoma(397;0.166)		AACTGGCACAGAAAAAAAAAAT	0.238																																						dbGAP											2	Deletion - Frameshift(2)	large_intestine(1)|central_nervous_system(1)																																								-	-	-	SO:0001624	3_prime_UTR_variant	0			M95767	CCDS698.1	1p22	2010-05-04			ENSG00000117151	ENSG00000117151	3.2.1.-		2496	protein-coding gene	gene with protein product		600873		CTB		1549114, 7606925	Standard	NM_004388		Approved		uc001dka.2	Q01459	OTTHUMG00000009922	ENST00000370630.5:c.*1911->T	1.37:g.85018781_85018781dupA			Q5VX50	RNA	INS	-	NULL	ENST00000370630.5	37	NULL	CCDS698.1	1																																																																																			SPATA1	-	-	ENSG00000122432		0.238	CTBS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SPATA1	HGNC	protein_coding	OTTHUMT00000027457.2	49	0.00	0	-	NM_004388		85018771	85018772	+1	no_errors	ENST00000460286	ensembl	human	known	69_37n	rna	27	10.00	3	INS	1.000:1.000	A
TARBP1	6894	genome.wustl.edu	37	1	234566040	234566040	+	Missense_Mutation	SNP	G	G	T			TCGA-AN-A0XL-01A-11D-A10M-09	TCGA-AN-A0XL-10A-01D-A10M-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	1b08a181-a73b-4506-aaa3-3521f2c57207	1acce21e-7513-402f-b586-423415f7cc2c	g.chr1:234566040G>T	ENST00000040877.1	-	15	2401	c.2402C>A	c.(2401-2403)aCa>aAa	p.T801K		NM_005646.3	NP_005637.3	Q13395	TARB1_HUMAN	TAR (HIV-1) RNA binding protein 1	801					regulation of transcription from RNA polymerase II promoter (GO:0006357)|RNA processing (GO:0006396)	nucleus (GO:0005634)	RNA binding (GO:0003723)|RNA methyltransferase activity (GO:0008173)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(7)|large_intestine(6)|lung(22)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	55	Ovarian(103;0.0339)	all_cancers(173;0.00995)|Prostate(94;0.0115)|all_epithelial(177;0.172)	OV - Ovarian serous cystadenocarcinoma(106;0.000263)			ACTTCCAACTGTTGGCTCCTG	0.463																																						dbGAP											0													60.0	56.0	58.0					1																	234566040		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS1601.1	1q42.2	2012-06-12	2007-06-26		ENSG00000059588	ENSG00000059588			11568	protein-coding gene	gene with protein product	"""tRNA methyltransferase 3 homolog (S. cerevisiae)"""	605052	"""Tar (HIV-1) RNA binding protein 1"""			1936997	Standard	NM_005646		Approved	TRP-185, TRM3	uc001hwd.3	Q13395	OTTHUMG00000037947	ENST00000040877.1:c.2402C>A	1.37:g.234566040G>T	ENSP00000040877:p.Thr801Lys		Q9H581	Missense_Mutation	SNP	pfam_SpoU_MeTrfase,superfamily_ARM-type_fold	p.T801K	ENST00000040877.1	37	c.2402	CCDS1601.1	1	.	.	.	.	.	.	.	.	.	.	G	2.516	-0.311819	0.05422	.	.	ENSG00000059588	ENST00000040877	T	0.05199	3.48	4.84	1.86	0.25419	.	0.651463	0.16219	N	0.224107	T	0.04227	0.0117	L	0.41236	1.265	0.09310	N	1	B	0.12013	0.005	B	0.08055	0.003	T	0.45716	-0.9242	10	0.07175	T	0.84	-5.6134	4.6102	0.12399	0.176:0.0:0.358:0.466	.	801	Q13395	TARB1_HUMAN	K	801	ENSP00000040877:T801K	ENSP00000040877:T801K	T	-	2	0	TARBP1	232632663	0.001000	0.12720	0.002000	0.10522	0.170000	0.22686	0.609000	0.24238	0.711000	0.32018	0.655000	0.94253	ACA	TARBP1	-	NULL	ENSG00000059588		0.463	TARBP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	TARBP1	HGNC	protein_coding	OTTHUMT00000092616.1	8	0.00	0	G	NM_005646		234566040	234566040	-1	no_errors	ENST00000040877	ensembl	human	known	69_37n	missense	21	25.00	7	SNP	0.001	T
TCF7L2	6934	genome.wustl.edu	37	10	114849224	114849224	+	Intron	SNP	T	T	C			TCGA-AN-A0XL-01A-11D-A10M-09	TCGA-AN-A0XL-10A-01D-A10M-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	1b08a181-a73b-4506-aaa3-3521f2c57207	1acce21e-7513-402f-b586-423415f7cc2c	g.chr10:114849224T>C	ENST00000355995.4	+	5	1059				TCF7L2_ENST00000545257.1_Intron|TCF7L2_ENST00000355717.4_Silent_p.T183T|TCF7L2_ENST00000369395.1_Silent_p.T184T|TCF7L2_ENST00000536810.1_Intron|TCF7L2_ENST00000369397.4_Intron|TCF7L2_ENST00000543371.1_Intron|TCF7L2_ENST00000538897.1_Intron|TCF7L2_ENST00000349937.2_Intron|TCF7L2_ENST00000534894.1_Intron|TCF7L2_ENST00000542695.1_Intron|TCF7L2_ENST00000352065.5_Intron			Q9NQB0	TF7L2_HUMAN	transcription factor 7-like 2 (T-cell specific, HMG-box)						blood vessel development (GO:0001568)|bone mineralization (GO:0030282)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|catenin import into nucleus (GO:0035411)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cellular response to starvation (GO:0009267)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic genitalia morphogenesis (GO:0030538)|embryonic hindgut morphogenesis (GO:0048619)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|generation of neurons (GO:0048699)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycogen metabolic process (GO:0005977)|insulin metabolic process (GO:1901142)|maintenance of DNA repeat elements (GO:0043570)|multicellular organism growth (GO:0035264)|myoblast fate commitment (GO:0048625)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of organ growth (GO:0046621)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neural tube development (GO:0021915)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte development (GO:0014003)|pancreas development (GO:0031016)|pituitary gland development (GO:0021983)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of insulin secretion (GO:0032024)|positive regulation of protein binding (GO:0032092)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|post-embryonic development (GO:0009791)|regulation of hormone metabolic process (GO:0032350)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of myelination (GO:0031641)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of skeletal muscle tissue development (GO:0048641)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to glucose (GO:0009749)|secretory granule localization (GO:0032252)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	beta-catenin-TCF7L2 complex (GO:0070369)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|gamma-catenin binding (GO:0045295)|nuclear hormone receptor binding (GO:0035257)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)		VTI1A/TCF7L2(8)	central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(24)|liver(2)|lung(8)|ovary(1)|skin(1)	41		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)		CAGACTTCACTGTCAGCACTC	0.542			T	VTI1A	colorectal																																	dbGAP		Dom	yes		10	10q25.3	6934	transcription factor 7-like 2		E	0													57.0	52.0	53.0					10																	114849224		1568	3582	5150	-	-	-	SO:0001627	intron_variant	0			X62871	CCDS7576.1, CCDS53578.1, CCDS55729.1, CCDS73196.1, CCDS73197.1, CCDS73198.1	10q25.3	2006-11-24			ENSG00000148737	ENSG00000148737			11641	protein-coding gene	gene with protein product		602228		TCF4		1741298	Standard	NM_001146283		Approved	TCF-4	uc001lae.4	Q9NQB0	OTTHUMG00000019070	ENST00000355995.4:c.552+49339T>C	10.37:g.114849224T>C			B4DRJ8|B9X074|C6ZRJ8|C6ZRK0|E2GH14|E2GH19|E2GH20|E2GH24|E2GH25|E9PFH9|F8W742|F8W7T5|O00185|Q9NQB1|Q9NQB2|Q9NQB3|Q9NQB4|Q9NQB5|Q9NQB6|Q9NQB7|Q9ULC2	Silent	SNP	pfam_CTNNB1-bd_N,pfam_HMG_superfamily,superfamily_HMG_superfamily,smart_HMG_superfamily,pfscan_HMG_superfamily	p.T183	ENST00000355995.4	37	c.549		10																																																																																			TCF7L2	-	pfam_CTNNB1-bd_N	ENSG00000148737		0.542	TCF7L2-203	KNOWN	basic	protein_coding	TCF7L2	HGNC	protein_coding		65	0.00	0	T	NM_030756		114849224	114849224	+1	no_errors	ENST00000355717	ensembl	human	known	69_37n	silent	53	29.33	22	SNP	1.000	C
TRAPPC8	22878	genome.wustl.edu	37	18	29497565	29497565	+	Nonsense_Mutation	SNP	C	C	A			TCGA-AN-A0XL-01A-11D-A10M-09	TCGA-AN-A0XL-10A-01D-A10M-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	1b08a181-a73b-4506-aaa3-3521f2c57207	1acce21e-7513-402f-b586-423415f7cc2c	g.chr18:29497565C>A	ENST00000283351.4	-	3	753	c.418G>T	c.(418-420)Gaa>Taa	p.E140*	TRAPPC8_ENST00000582539.1_Nonsense_Mutation_p.E86*|TRAPPC8_ENST00000582513.1_Nonsense_Mutation_p.E140*	NM_014939.3	NP_055754	Q9Y2L5	TPPC8_HUMAN	trafficking protein particle complex 8	140					vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(7)|liver(2)|lung(13)|ovary(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						TTCAGAAATTCATGATCCAAT	0.323																																						dbGAP											0													149.0	161.0	157.0					18																	29497565		2203	4300	6503	-	-	-	SO:0001587	stop_gained	0			AB023229	CCDS11901.1	18q12.1	2011-10-10	2010-06-29	2010-06-29	ENSG00000153339	ENSG00000153339		"""Trafficking protein particle complex"""	29169	protein-coding gene	gene with protein product	"""general sporulation gene 1 homolog (S. cerevisiae)"""	614136	"""KIAA1012"""	KIAA1012		10231032, 11230166	Standard	NM_014939		Approved	HsT2706, TRS85, GSG1	uc002kxc.4	Q9Y2L5	OTTHUMG00000132267	ENST00000283351.4:c.418G>T	18.37:g.29497565C>A	ENSP00000283351:p.Glu140*		A0JP15|B3KME5|Q9H0L2	Nonsense_Mutation	SNP	NULL	p.E140*	ENST00000283351.4	37	c.418	CCDS11901.1	18	.	.	.	.	.	.	.	.	.	.	C	37	6.049139	0.97236	.	.	ENSG00000153339	ENST00000283351	.	.	.	6.05	6.05	0.98169	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	20.6013	0.99457	0.0:1.0:0.0:0.0	.	.	.	.	X	140	.	ENSP00000283351:E140X	E	-	1	0	TRAPPC8	27751563	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.487000	0.81328	2.878000	0.98634	0.650000	0.86243	GAA	TRAPPC8	-	NULL	ENSG00000153339		0.323	TRAPPC8-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	TRAPPC8	HGNC	protein_coding	OTTHUMT00000255355.1	119	0.00	0	C	NM_014939		29497565	29497565	-1	no_errors	ENST00000283351	ensembl	human	known	69_37n	nonsense	107	15.75	20	SNP	1.000	A
