#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_CAF	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains	i_amino_acid_change	i_annotation_transcript	i_build	i_c_position	i_ccds_id	i_chromosome_name	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_deletion_substructures	i_domain	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	i_gene_type	i_havana_transcript	i_normal_ref_reads	i_normal_ref_reads_val	i_normal_vaf	i_normal_vaf_val	i_normal_var_reads	i_normal_var_reads_val	i_reference	i_refseq_mrna_id	i_rsID	i_rsID_ref_var_alleles	i_secondary_variant_classification	i_stop	i_strand	i_transcript_error	i_transcript_name	i_transcript_source	i_transcript_species	i_transcript_status	i_transcript_version	i_trv_type	i_tumor_ref_reads	i_tumor_ref_reads_val	i_tumor_vaf	i_tumor_vaf_val	i_tumor_var_reads	i_tumor_var_reads_val	i_type	i_ucsc_cons	i_variant
HTATSF1	27336	genome.wustl.edu	37	X	135582344	135582344	+	Missense_Mutation	SNP	A	A	G			TCGA-XU-AAY0-01A-11D-A428-09	TCGA-XU-AAY0-10A-01D-A42B-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	1bd31f65-a32e-4d78-ba3f-4b9788ceb252	4f346292-ef69-4ac9-b212-0c01f61f4039	g.chrX:135582344A>G	ENST00000218364.4	+	3	569	c.395A>G	c.(394-396)aAt>aGt	p.N132S	HTATSF1_ENST00000535601.1_Missense_Mutation_p.N132S	NM_014500.4	NP_055315.2	O43719	HTSF1_HUMAN	HIV-1 Tat specific factor 1	132					regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(14)|ovary(3)|prostate(1)	30	Acute lymphoblastic leukemia(192;0.000127)					GAAGACAGAAATACAAATGTA	0.269																																							0											0													80.0	90.0	87.0					X																	135582344		2201	4292	6493	SO:0001583	missense	0			U76992	CCDS14657.1	Xq26.3	2013-02-12	2006-01-09		ENSG00000102241	ENSG00000102241		"""RNA binding motif (RRM) containing"""	5276	protein-coding gene	gene with protein product		300346	"""HIV TAT specific factor 1"""			8849451	Standard	NM_014500		Approved	TAT-SF1	uc004ezx.3	O43719	OTTHUMG00000022510	ENST00000218364.4:c.395A>G	X.37:g.135582344A>G	ENSP00000218364:p.Asn132Ser		D3DWG9|Q59G06|Q99730	Missense_Mutation	SNP	pfam_RRM_dom,smart_RRM_dom,pfscan_RRM_dom	p.N132S	ENST00000218364.4	37	c.395	CCDS14657.1	X	.	.	.	.	.	.	.	.	.	.	A	21.5	4.155525	0.78114	.	.	ENSG00000102241	ENST00000535601;ENST00000448450;ENST00000425695;ENST00000218364;ENST00000415377	T;T;T;T	0.33438	3.49;1.41;1.41;3.49	5.73	5.73	0.89815	Nucleotide-binding, alpha-beta plait (1);	0.044247	0.85682	D	0.000000	T	0.58779	0.2146	M	0.80982	2.52	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.64694	-0.6347	10	0.87932	D	0	-22.8836	15.0205	0.71627	1.0:0.0:0.0:0.0	.	132	O43719	HTSF1_HUMAN	S	132	ENSP00000442699:N132S;ENSP00000411381:N132S;ENSP00000412420:N132S;ENSP00000218364:N132S	ENSP00000218364:N132S	N	+	2	0	HTATSF1	135410010	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	5.628000	0.67791	1.930000	0.55929	0.412000	0.27726	AAT	0	NULL		0.269	HTATSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HTATSF1	protein_coding	OTTHUMT00000058497.1	340	205	0	0.00	0	0	A	NM_014500	0	0		135582344	1	no_errors	ENST00000218364	ensembl	human	known	74_37	missense	199	258	7.87	13.09	17	39	SNP	1	G
CROCCP3	114819	genome.wustl.edu	37	1	16812131	16812131	+	RNA	SNP	C	C	T	rs551275495	byFrequency	TCGA-XU-AAY0-01A-11D-A428-09	TCGA-XU-AAY0-10A-01D-A42B-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	1bd31f65-a32e-4d78-ba3f-4b9788ceb252	4f346292-ef69-4ac9-b212-0c01f61f4039	g.chr1:16812131C>T	ENST00000263511.4	-	0	1420					NR_023386.1		Q8IVE0	CROL2_HUMAN	ciliary rootlet coiled-coil, rootletin pseudogene 3						centrosome organization (GO:0051297)	ciliary rootlet (GO:0035253)											CTTCTGAAGACGCTTCACTGC	0.592													.|||	2	0.000399361	0.0	0.0	5008	,	,		22977	0.0		0.0	False		,,,				2504	0.002						0.9996,0.0003994											0																																												0			AB067509		1p36.13	2010-07-08	2010-07-08	2010-07-08	ENSG00000080947	ENSG00000080947			29405	pseudogene	pseudogene			"""ciliary rootlet coiled-coil, rootletin-like 2"""	CROCCL2		11572484	Standard	NR_023386		Approved	KIAA1922	uc001ayt.2	Q8IVE0	OTTHUMG00000037885		1.37:g.16812131C>T			Q96PW6	RNA	SNP	0	NULL	ENST00000263511.4	37	NULL		1																																																																																			0	0		0.592	CROCCP3-002	KNOWN	basic	processed_transcript	CROCCP3	pseudogene	OTTHUMT00000458172.1	81	22	0	0.00	0	0	C	XM_057040	rs551275495	C->T		16812131	-1	no_errors	ENST00000263511	ensembl	human	known	74_37	rna	31	36	16.22	12.20	6	5	SNP	0.993	T
NRXN1	9378	genome.wustl.edu	37	2	50850457	50850457	+	Missense_Mutation	SNP	G	G	A			TCGA-XU-AAY0-01A-11D-A428-09	TCGA-XU-AAY0-10A-01D-A42B-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	1bd31f65-a32e-4d78-ba3f-4b9788ceb252	4f346292-ef69-4ac9-b212-0c01f61f4039	g.chr2:50850457G>A	ENST00000406316.2	-	6	2605	c.1129C>T	c.(1129-1131)Cgt>Tgt	p.R377C	NRXN1_ENST00000402717.3_Missense_Mutation_p.R377C|NRXN1_ENST00000331040.5_5'UTR|NRXN1_ENST00000406859.3_Missense_Mutation_p.R377C|NRXN1_ENST00000401669.2_Missense_Mutation_p.R377C|NRXN1_ENST00000405472.3_Missense_Mutation_p.R377C|NRXN1_ENST00000404971.1_Missense_Mutation_p.R410C	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	377	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			GTTACCTGACGCAGATTCCTG	0.443																																							0											0													57.0	57.0	57.0					2																	50850457		1998	4184	6182	SO:0001583	missense	0			AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.1129C>T	2.37:g.50850457G>A	ENSP00000384311:p.Arg377Cys		A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Missense_Mutation	SNP	pfam_Laminin_G,superfamily_ConA-like_lec_gl_sf,smart_Laminin_G,smart_EG-like_dom,smart_Neurexin-like,pfscan_EG-like_dom,pfscan_Laminin_G	p.R377C	ENST00000406316.2	37	c.1129	CCDS54360.1	2	.	.	.	.	.	.	.	.	.	.	G	20.4	3.978588	0.74360	.	.	ENSG00000179915	ENST00000404971;ENST00000406316;ENST00000405472;ENST00000401669;ENST00000536085;ENST00000402717;ENST00000406859	T;T;T;T;T;T	0.79352	-1.26;-1.26;-1.26;-1.26;-1.26;-1.26	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	D	0.89643	0.6774	M	0.82433	2.59	0.58432	D	0.999997	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.989;0.998;0.999	D	0.90323	0.4346	10	0.87932	D	0	.	19.9037	0.96999	0.0:0.0:1.0:0.0	.	410;377;377	Q9ULB1-3;F8WB18;A7E294	.;.;.	C	410;377;377;377;411;377;377	ENSP00000385142:R410C;ENSP00000384311:R377C;ENSP00000434015:R377C;ENSP00000385017:R377C;ENSP00000385434:R377C;ENSP00000385681:R377C	ENSP00000385017:R377C	R	-	1	0	NRXN1	50703961	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.928000	0.87587	2.708000	0.92522	0.557000	0.71058	CGT	0	pfam_Laminin_G,superfamily_ConA-like_lec_gl_sf,smart_Laminin_G,pfscan_Laminin_G		0.443	NRXN1-001	KNOWN	basic|CCDS	protein_coding	NRXN1	protein_coding	OTTHUMT00000325291.2	57	221	0	0.00	0	0	G		0	0		50850457	-1	no_errors	ENST00000402717	ensembl	human	known	74_37	missense	37	196	19.57	13.27	9	30	SNP	1	A
AC008836.1	0	genome.wustl.edu	37	5	60853118	60853118	+	RNA	SNP	G	G	C			TCGA-XU-AAY0-01A-11D-A428-09	TCGA-XU-AAY0-10A-01D-A42B-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	1bd31f65-a32e-4d78-ba3f-4b9788ceb252	4f346292-ef69-4ac9-b212-0c01f61f4039	g.chr5:60853118G>C	ENST00000411268.1	+	0	9																											TTATGGTTCAGAGTGTGTTTA	0.308																																							0											0																																												0																															5.37:g.60853118G>C				RNA	SNP	0	NULL	ENST00000411268.1	37	NULL		5																																																																																			0	0		0.308	AC008836.1-201	NOVEL	basic	miRNA	ENSG00000223200	miRNA		41	86	0	0.00	0	0	G		0	0		60853118	1	no_errors	ENST00000411268	ensembl	human	novel	74_37	rna	25	104	24.24	19.38	8	25	SNP	0	C
GTF2I	2969	genome.wustl.edu	37	7	74146970	74146970	+	Missense_Mutation	SNP	T	T	A			TCGA-XU-AAY0-01A-11D-A428-09	TCGA-XU-AAY0-10A-01D-A42B-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	1bd31f65-a32e-4d78-ba3f-4b9788ceb252	4f346292-ef69-4ac9-b212-0c01f61f4039	g.chr7:74146970T>A	ENST00000324896.4	+	15	1660	c.1271T>A	c.(1270-1272)cTt>cAt	p.L424H	GTF2I_ENST00000346152.4_Missense_Mutation_p.L403H|GTF2I_ENST00000416070.1_Missense_Mutation_p.L383H|GTF2I_ENST00000353920.4_Missense_Mutation_p.L404H	NM_032999.2	NP_127492.1	P78347	GTF2I_HUMAN	general transcription factor IIi	424					negative regulation of angiogenesis (GO:0016525)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(7)|kidney(1)|large_intestine(1)|lung(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	19						AGGATATTACTTGCAAAGGAA	0.378																																							0											0													13.0	13.0	13.0					7																	74146970		1741	3768	5509	SO:0001583	missense	0			U77948	CCDS5573.1, CCDS5574.1, CCDS5575.1, CCDS47614.1, CCDS64680.1	7q11.23	2011-05-25	2009-07-23			ENSG00000263001		"""General transcription factors"""	4659	protein-coding gene	gene with protein product		601679	"""general transcription factor II, i"""	WBSCR6		9334314, 9012831	Standard	NM_032999		Approved	TFII-I, BAP-135, SPIN, BTKAP1, DIWS, IB291	uc003uau.3	P78347		ENST00000324896.4:c.1271T>A	7.37:g.74146970T>A	ENSP00000322542:p.Leu424His		O14743|O15359|O43546|O43588|O43589|Q75M85|Q75M86|Q75M87|Q75M88|Q86U51|Q9BSZ4	Missense_Mutation	SNP	pfam_GTF2I,superfamily_GTF2I,pirsf_TF_II-I,pfscan_GTF2I	p.L424H	ENST00000324896.4	37	c.1271	CCDS5573.1	7	.	.	.	.	.	.	.	.	.	.	T	18.18	3.565904	0.65651	.	.	ENSG00000077809	ENST00000324896;ENST00000539339;ENST00000353920;ENST00000346152;ENST00000416070	T;T;T;T	0.29142	1.58;1.58;1.58;1.58	4.72	4.72	0.59763	.	0.110120	0.39544	N	0.001322	T	0.37019	0.0988	N	0.14661	0.345	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;0.998;1.0;0.999	D;D;P;D;D	0.74348	0.983;0.979;0.874;0.971;0.963	T	0.36089	-0.9762	10	0.56958	D	0.05	-16.5588	13.3771	0.60745	0.0:0.0:0.0:1.0	.	402;383;404;403;424	Q499G6;P78347-2;P78347-3;P78347-4;P78347	.;.;.;.;GTF2I_HUMAN	H	424;419;404;403;383	ENSP00000322542:L424H;ENSP00000322671:L404H;ENSP00000322599:L403H;ENSP00000387651:L383H	ENSP00000322542:L424H	L	+	2	0	GTF2I	73784906	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	5.342000	0.65970	1.753000	0.51906	0.477000	0.44152	CTT	0	pfam_GTF2I,superfamily_GTF2I,pirsf_TF_II-I,pfscan_GTF2I		0.378	GTF2I-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	GTF2I	protein_coding	OTTHUMT00000252708.1	383	113	0	0.00	0	0	T	NM_032999	0	0		74146970	1	no_errors	ENST00000324896	ensembl	human	known	74_37	missense	213	107	10.46	14.40	25	18	SNP	1	A
NDRG1	10397	genome.wustl.edu	37	8	134271450	134271450	+	Missense_Mutation	SNP	T	T	A			TCGA-XU-AAY0-01A-11D-A428-09	TCGA-XU-AAY0-10A-01D-A42B-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	1bd31f65-a32e-4d78-ba3f-4b9788ceb252	4f346292-ef69-4ac9-b212-0c01f61f4039	g.chr8:134271450T>A	ENST00000414097.2	-	6	1217	c.350A>T	c.(349-351)cAg>cTg	p.Q117L	NDRG1_ENST00000522476.1_Missense_Mutation_p.Q51L|NDRG1_ENST00000323851.7_Missense_Mutation_p.Q117L|NDRG1_ENST00000518066.1_Intron|NDRG1_ENST00000537882.1_Missense_Mutation_p.Q36L|NDRG1_ENST00000354944.5_Intron|NDRG1_ENST00000518176.1_Intron	NM_001135242.1	NP_001128714.1	Q92597	NDRG1_HUMAN	N-myc downstream regulated 1	117					cell death (GO:0008219)|cellular response to hypoxia (GO:0071456)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|mast cell activation (GO:0045576)|peripheral nervous system myelin maintenance (GO:0032287)|positive regulation of spindle checkpoint (GO:0090232)|response to metal ion (GO:0010038)	cell-cell adherens junction (GO:0005913)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)	cadherin binding (GO:0045296)|gamma-tubulin binding (GO:0043015)|microtubule binding (GO:0008017)|Rab GTPase binding (GO:0017137)		NDRG1/ERG(5)	endometrium(2)|kidney(2)|large_intestine(2)|lung(5)|ovary(4)|prostate(1)|skin(1)	17	all_epithelial(106;4.26e-24)|Lung NSC(106;7.26e-07)|all_lung(105;2.77e-06)|Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0107)			TTCAGCCAGCTGATCCATGGA	0.527			T	ERG	prostate																																		0		Dom	yes		8	8q24.3	10397	N-myc downstream regulated 1		E	0													128.0	118.0	121.0					8																	134271450		2203	4300	6503	SO:0001583	missense	0			X92845	CCDS34945.1, CCDS59112.1, CCDS59113.1	8q24	2014-09-17	2008-09-12		ENSG00000104419	ENSG00000104419			7679	protein-coding gene	gene with protein product		605262		CAP43		9251681, 8939898, 18455888	Standard	NM_006096		Approved	DRG1, RTP, TDD5, NDR1	uc003yue.2	Q92597	OTTHUMG00000164441	ENST00000414097.2:c.350A>T	8.37:g.134271450T>A	ENSP00000404854:p.Gln117Leu		B3KR80|B7Z446|O15207|Q6IBG2|Q9NYR6|Q9UK29	Missense_Mutation	SNP	pfam_Ndr	p.Q117L	ENST00000414097.2	37	c.350	CCDS34945.1	8	.	.	.	.	.	.	.	.	.	.	T	21.6	4.166391	0.78339	.	.	ENSG00000104419	ENST00000323851;ENST00000414097;ENST00000537882;ENST00000522476;ENST00000520230;ENST00000518480;ENST00000519228;ENST00000519580;ENST00000522890;ENST00000520943;ENST00000521544	T;T;T;T;T;T;T;T;T;T;T	0.28454	1.61;1.61;2.19;2.19;2.19;2.19;2.19;2.19;2.19;2.19;2.19	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	T	0.27241	0.0668	L	0.51914	1.62	0.80722	D	1	P	0.36162	0.54	B	0.28139	0.086	T	0.06991	-1.0796	10	0.49607	T	0.09	-27.7466	14.131	0.65253	0.0:0.0:0.0:1.0	.	117	Q92597	NDRG1_HUMAN	L	117;117;36;51;134;51;117;117;117;128;117	ENSP00000319977:Q117L;ENSP00000404854:Q117L;ENSP00000437443:Q36L;ENSP00000427894:Q51L;ENSP00000428345:Q134L;ENSP00000428802:Q51L;ENSP00000429994:Q117L;ENSP00000429272:Q117L;ENSP00000428384:Q117L;ENSP00000429840:Q128L;ENSP00000429524:Q117L	ENSP00000319977:Q117L	Q	-	2	0	NDRG1	134340632	1.000000	0.71417	0.999000	0.59377	0.977000	0.68977	7.732000	0.84908	2.009000	0.58944	0.459000	0.35465	CAG	0	pfam_Ndr		0.527	NDRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NDRG1	protein_coding	OTTHUMT00000378805.1	33	139	0	0.00	0	0	T		0	0		134271450	-1	no_errors	ENST00000323851	ensembl	human	known	74_37	missense	32	169	11.11	6.11	4	11	SNP	1	A
KIAA1462	57608	genome.wustl.edu	37	10	30317392	30317392	+	Missense_Mutation	SNP	T	T	C			TCGA-XU-AAY0-01A-11D-A428-09	TCGA-XU-AAY0-10A-01D-A42B-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	1bd31f65-a32e-4d78-ba3f-4b9788ceb252	4f346292-ef69-4ac9-b212-0c01f61f4039	g.chr10:30317392T>C	ENST00000375377.1	-	3	1786	c.1685A>G	c.(1684-1686)cAa>cGa	p.Q562R		NM_020848.2	NP_065899.1	Q9P266	JCAD_HUMAN	KIAA1462	562					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)				breast(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|lung(23)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	75						AGTCCCAGTTTGGAACTTTTT	0.463																																							0											0													99.0	100.0	100.0					10																	30317392		1873	4111	5984	SO:0001583	missense	0			AB040895	CCDS41500.1	10p12.1	2013-04-23			ENSG00000165757	ENSG00000165757			29283	protein-coding gene	gene with protein product	"""junctional protein associated with coronary artery disease"""	614398				10819331, 21884682	Standard	NM_020848		Approved	JCAD	uc001iux.3	Q9P266	OTTHUMG00000017885	ENST00000375377.1:c.1685A>G	10.37:g.30317392T>C	ENSP00000364526:p.Gln562Arg		Q5HYA7|Q5T992|Q86WZ9|Q9BYJ2	Missense_Mutation	SNP	NULL	p.Q562R	ENST00000375377.1	37	c.1685	CCDS41500.1	10	.	.	.	.	.	.	.	.	.	.	T	13.65	2.301727	0.40694	.	.	ENSG00000165757	ENST00000375377	T	0.11821	2.74	5.62	5.62	0.85841	.	0.161766	0.51477	D	0.000081	T	0.12008	0.0292	N	0.22421	0.69	0.30408	N	0.779399	B	0.19817	0.039	B	0.18871	0.023	T	0.05500	-1.0881	10	0.72032	D	0.01	-21.2059	15.806	0.78513	0.0:0.0:0.0:1.0	.	562	Q9P266	K1462_HUMAN	R	562	ENSP00000364526:Q562R	ENSP00000364526:Q562R	Q	-	2	0	KIAA1462	30357398	1.000000	0.71417	0.956000	0.39512	0.166000	0.22503	4.534000	0.60622	2.142000	0.66516	0.459000	0.35465	CAA	0	NULL		0.463	KIAA1462-002	KNOWN	basic|appris_principal|CCDS	protein_coding	KIAA1462	protein_coding	OTTHUMT00000047409.1	41	245	0	0.00	0	0	T	NM_020848	0	0		30317392	-1	no_errors	ENST00000375377	ensembl	human	known	74_37	missense	27	258	15.62	9.79	5	28	SNP	1	C
ZNF487	642819	genome.wustl.edu	37	10	43977042	43977042	+	Missense_Mutation	SNP	G	G	T			TCGA-XU-AAY0-01A-11D-A428-09	TCGA-XU-AAY0-10A-01D-A42B-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	1bd31f65-a32e-4d78-ba3f-4b9788ceb252	4f346292-ef69-4ac9-b212-0c01f61f4039	g.chr10:43977042G>T	ENST00000431662.1	+	4	491	c.491G>T	c.(490-492)cGt>cTt	p.R164L	ZNF487_ENST00000437590.2_Missense_Mutation_p.R100L			B1APH4	ZN487_HUMAN	zinc finger protein 487	164					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)										AGAAAAATACGTGGCAACTGT	0.328																																							0											0																																										SO:0001583	missense	0					10q11.21	2013-06-03	2013-03-06	2013-03-06	ENSG00000243660	ENSG00000243660			23488	other	unknown			"""KRAB domain only 1"", ""zinc finger protein 487, pseudogene"""	KRBO1, ZNF487P			Standard	NR_026693		Approved			B1APH4	OTTHUMG00000185507	ENST00000431662.1:c.491G>T	10.37:g.43977042G>T	ENSP00000388421:p.Arg164Leu		B1APH5|B7Z7S5	Missense_Mutation	SNP	pfam_Krueppel-associated_box,pfam_Znf_C2H2,superfamily_Krueppel-associated_box,smart_Krueppel-associated_box,smart_Znf_C2H2-like,pfscan_Znf_C2H2,pfscan_Krueppel-associated_box	p.R164L	ENST00000431662.1	37	c.491		10	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.016|0.016	-1.535798|-1.535798	0.00942|0.00942	.|.	.|.	ENSG00000243660|ENSG00000243660	ENST00000431662;ENST00000455398;ENST00000456416;ENST00000442349;ENST00000437590|ENST00000315429	T;T;T|.	0.15139|.	3.73;2.45;6.67|.	1.54|1.54	-0.658|-0.658	0.11428|0.11428	.|.	.|.	.|.	.|.	.|.	T|T	0.21145|0.21145	0.0509|0.0509	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	B|.	0.16396|.	0.017|.	B|.	0.15484|.	0.013|.	T|T	0.24799|0.24799	-1.0150|-1.0150	7|4	.|.	.|.	.|.	.|.	2.8116|2.8116	0.05443|0.05443	0.0:0.3059:0.2806:0.4135|0.0:0.3059:0.2806:0.4135	.|.	100|.	B7Z7S5|.	.|.	L|L	164;100;68;100;100|162	ENSP00000388421:R164L;ENSP00000395343:R68L;ENSP00000392335:R100L|.	.|.	R|V	+|+	2|1	0|0	ZNF487P|ZNF487P	43297048|43297048	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.265000|0.265000	0.26407|0.26407	-0.492000|-0.492000	0.06467|0.06467	-0.202000|-0.202000	0.10268|0.10268	-0.499000|-0.499000	0.04595|0.04595	CGT|GTG	0	NULL		0.328	ZNF487-201	KNOWN	basic|appris_principal	protein_coding	ZNF487	protein_coding		145	198	0	0.00	0	0	G	XM_926224	0	0		43977042	1	no_errors	ENST00000431662	ensembl	human	known	74_37	missense	102	308	9.73	4.94	11	16	SNP	0.001	T
TCAM1P	146771	genome.wustl.edu	37	17	61939720	61939720	+	RNA	SNP	G	G	A			TCGA-XU-AAY0-01A-11D-A428-09	TCGA-XU-AAY0-10A-01D-A42B-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	1bd31f65-a32e-4d78-ba3f-4b9788ceb252	4f346292-ef69-4ac9-b212-0c01f61f4039	g.chr17:61939720G>A	ENST00000478379.1	+	0	1491					NR_002947.2				testicular cell adhesion molecule 1, pseudogene																		ACACACGCTCGCCTGCGTCCC	0.547																																							0											0																																												0			AB026156		17q23.3	2013-09-26	2012-12-07	2010-03-12	ENSG00000240280	ENSG00000240280			30707	pseudogene	pseudogene		612756	"""testicular cell adhesion molecule 1 homolog (mouse)"", ""testicular cell adhesion molecule 1 homolog (mouse), pseudogene"""	TCAM1		11195349, 2744760, 19766163	Standard	NR_002947		Approved		uc031rdl.1		OTTHUMG00000154404		17.37:g.61939720G>A				RNA	SNP	0	NULL	ENST00000478379.1	37	NULL		17																																																																																			0	0		0.547	TCAM1P-002	KNOWN	basic	processed_transcript	TCAM1P	pseudogene	OTTHUMT00000335083.1	45	107	0	0.93	0	1	G		0	0		61939720	1	no_errors	ENST00000478379	ensembl	human	known	74_37	rna	23	133	11.54	5.00	3	7	SNP	0.146	A
SCN8A	6334	genome.wustl.edu	37	12	52204038	52204039	+	3'UTR	INS	-	-	A	rs74092804|rs11833203|rs201910276	byFrequency	TCGA-XU-AAY0-01A-11D-A428-09	TCGA-XU-AAY0-10A-01D-A42B-09	-	-	-	A	-	-	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	1bd31f65-a32e-4d78-ba3f-4b9788ceb252	4f346292-ef69-4ac9-b212-0c01f61f4039	g.chr12:52204038_52204039insA	ENST00000354534.6	+	0	8946_8947				AC068987.1_ENST00000599343.1_Frame_Shift_Ins_p.LK27fs|RP11-923I11.3_ENST00000565518.1_lincRNA	NM_001177984.2|NM_014191.3	NP_001171455.1|NP_055006.1	Q9UQD0	SCN8A_HUMAN	sodium channel, voltage gated, type VIII, alpha subunit						adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|membrane depolarization during action potential (GO:0086010)|muscle organ development (GO:0007517)|myelination (GO:0042552)|nervous system development (GO:0007399)|neuromuscular process (GO:0050905)|neuronal action potential (GO:0019228)|peripheral nervous system development (GO:0007422)|response to toxic substance (GO:0009636)|sensory perception of sound (GO:0007605)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	ATP binding (GO:0005524)|voltage-gated sodium channel activity (GO:0005248)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(19)|ovary(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55				BRCA - Breast invasive adenocarcinoma(357;0.181)	Valproic Acid(DB00313)	TTTCACTTTTTAAAAAAAAAAT	0.475																																							0											0																																										SO:0001624	3_prime_UTR_variant	0			AB027567	CCDS44891.1, CCDS53794.1	12q13.1	2012-02-26	2007-01-23			ENSG00000196876		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10596	protein-coding gene	gene with protein product		600702	"""sodium channel, voltage gated, type VIII, alpha polypeptide"""	MED		7670495, 9828131, 16382098	Standard	NM_014191		Approved	Nav1.6, NaCh6, PN4, CerIII	uc001ryw.4	Q9UQD0		ENST00000354534.6:c.*2826->A	12.37:g.52204048_52204048dupA			B9VWG8|O95788|Q9NYX2|Q9UPB2	Frame_Shift_Ins	INS	NULL	p.K31fs	ENST00000354534.6	37	c.80_81	CCDS44891.1	12																																																																																			0	NULL		0.475	SCN8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ENSG00000260415	protein_coding	OTTHUMT00000404372.3	28	75	0	1.32	0	1	0	NM_014191	0	0		52204039	1	no_errors	ENST00000599343	ensembl	human	known	74_37	frame_shift_ins	7	78	22.22	7.14	2	6	INS	0.000:0.001	A
ARL6IP5	10550	genome.wustl.edu	37	3	69149138	69149138	+	Intron	SNP	C	C	T			TCGA-XU-AAY0-01A-11D-A428-09	TCGA-XU-AAY0-10A-01D-A42B-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	1bd31f65-a32e-4d78-ba3f-4b9788ceb252	4f346292-ef69-4ac9-b212-0c01f61f4039	g.chr3:69149138C>T	ENST00000273258.3	+	2	280				ARL6IP5_ENST00000478935.1_Intron	NM_006407.3	NP_006398.1	O75915	PRAF3_HUMAN	ADP-ribosylation factor-like 6 interacting protein 5						intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|L-glutamate transport (GO:0015813)|negative regulation of mitochondrial membrane potential (GO:0010917)|negative regulation of transport (GO:0051051)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of stress-activated MAPK cascade (GO:0032874)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				biliary_tract(1)|endometrium(1)|large_intestine(2)|ovary(1)|prostate(1)|urinary_tract(1)	7		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;7.78e-05)|Epithelial(33;0.000818)|LUSC - Lung squamous cell carcinoma(21;0.0118)|Lung(16;0.0189)|KIRC - Kidney renal clear cell carcinoma(39;0.203)|Kidney(39;0.238)		agtgcaatggcgtgatctcag	0.478																																							0											0																																										SO:0001627	intron_variant	0			AF070523	CCDS2912.1	3p14	2014-05-12	2014-05-12		ENSG00000144746	ENSG00000144746			16937	protein-coding gene	gene with protein product	"""PRA1 domain family 3"""	605709				11242046, 11042152	Standard	NM_006407		Approved	PRAF3, JWA, GTRAP3-18, DERP11, HSPC127	uc003dnr.3	O75915	OTTHUMG00000158773	ENST00000273258.3:c.177-1852C>T	3.37:g.69149138C>T			B2R6V5|Q53ES3|Q5KU08	Silent	SNP	pfam_Prenylated_rab_accept_PRA1	p.G64	ENST00000273258.3	37	c.192	CCDS2912.1	3																																																																																			0	NULL		0.478	ARL6IP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ARL6IP5	protein_coding	OTTHUMT00000352132.1	32	0	0	0.00	0	0	C	NM_006407	0	0		69149138	1	no_errors	ENST00000484921	ensembl	human	known	74_37	silent	14	2	17.65	0.00	3	0	SNP	0.002	T
DNM1P47	100216544	genome.wustl.edu	37	15	102295710	102295710	+	RNA	SNP	C	C	A	rs200118705	byFrequency	TCGA-XU-AAY0-01A-11D-A428-09	TCGA-XU-AAY0-10A-01D-A42B-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	1bd31f65-a32e-4d78-ba3f-4b9788ceb252	4f346292-ef69-4ac9-b212-0c01f61f4039	g.chr15:102295710C>A	ENST00000561463.1	+	0	3756									DNM1 pseudogene 47																		TGCTGTCCAACCTGTACTCGC	0.592																																							0											0																																												0			AJ576276		15q26.3	2013-04-25			ENSG00000259660	ENSG00000259660			35200	pseudogene	pseudogene				DNM1DN14@			Standard	NG_009149		Approved	DNM1DN14-3			OTTHUMG00000172265		15.37:g.102295710C>A				RNA	SNP	0	NULL	ENST00000561463.1	37	NULL		15																																																																																			0	0		0.592	DNM1P47-001	KNOWN	basic	processed_transcript	DNM1P47	pseudogene	OTTHUMT00000417589.1	34	4	0	0.00	0	0	C	NG_009149	rs200118705	C->A		102295710	1	no_errors	ENST00000561463	ensembl	human	known	74_37	rna	17	5	22.73	0.00	5	0	SNP	1	A
DNM1P47	100216544	genome.wustl.edu	37	15	102295714	102295714	+	RNA	SNP	T	T	C	rs201074749	byFrequency	TCGA-XU-AAY0-01A-11D-A428-09	TCGA-XU-AAY0-10A-01D-A42B-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	1bd31f65-a32e-4d78-ba3f-4b9788ceb252	4f346292-ef69-4ac9-b212-0c01f61f4039	g.chr15:102295714T>C	ENST00000561463.1	+	0	3760									DNM1 pseudogene 47																		GTCCAACCTGTACTCGCGTGG	0.592																																							0											0																																												0			AJ576276		15q26.3	2013-04-25			ENSG00000259660	ENSG00000259660			35200	pseudogene	pseudogene				DNM1DN14@			Standard	NG_009149		Approved	DNM1DN14-3			OTTHUMG00000172265		15.37:g.102295714T>C				RNA	SNP	0	NULL	ENST00000561463.1	37	NULL		15																																																																																			0	0		0.592	DNM1P47-001	KNOWN	basic	processed_transcript	DNM1P47	pseudogene	OTTHUMT00000417589.1	33	4	0	0.00	0	0	T	NG_009149	rs201074749	T->C		102295714	1	no_errors	ENST00000561463	ensembl	human	known	74_37	rna	16	5	27.27	0.00	6	0	SNP	0.998	C
C6orf132	647024	genome.wustl.edu	37	6	42074969	42074970	+	Frame_Shift_Ins	INS	-	-	G			TCGA-XU-AAY0-01A-11D-A428-09	TCGA-XU-AAY0-10A-01D-A42B-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	1bd31f65-a32e-4d78-ba3f-4b9788ceb252	4f346292-ef69-4ac9-b212-0c01f61f4039	g.chr6:42074969_42074970insG	ENST00000341865.4	-	4	679_680	c.680_681insC	c.(679-681)ccafs	p.P227fs		NM_001164446.1	NP_001157918.1	Q5T0Z8	CF132_HUMAN	chromosome 6 open reading frame 132	227										breast(1)	1						CAGGAGGCGGTGGGGGGGCTAG	0.629																																							0											0																																										SO:0001589	frameshift_variant	0				CCDS47428.1	6p21.1	2012-02-06			ENSG00000188112	ENSG00000188112			21288	protein-coding gene	gene with protein product							Standard	NM_001164446		Approved	bA7K24.2	uc003orw.2	Q5T0Z8	OTTHUMG00000014695	ENST00000341865.4:c.681dupC	6.37:g.42074976_42074976dupG	ENSP00000341368:p.Pro227fs		A6NI05	Frame_Shift_Ins	INS	NULL	p.P228fs	ENST00000341865.4	37	c.681_680	CCDS47428.1	6																																																																																			0	NULL		0.629	C6orf132-001	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	C6orf132	protein_coding	OTTHUMT00000040548.2	9	6	0	0.00	0	0	0	NM_001164446	0	0		42074970	-1	no_errors	ENST00000341865	ensembl	human	putative	74_37	frame_shift_ins	4	5	33.33	0.00	2	0	INS	0.001:0.050	G
