#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_EVS_AA	i_EVS_All	i_EVS_EA	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains_WU	i_amino_acid_change_WU	i_annotation_transcript	i_build	i_c_position_WU	i_ccds_id	i_chromosome_name_WU	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_default_gene_name_WU	i_deletion_substructures_WU	i_domain_WU	i_ensembl_gene_id	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_name_WU	i_gene_name_source_WU	i_gene_type	i_havana_transcript	i_normal_ref_reads	i_normal_vaf	i_normal_var_reads	i_reference_WU	i_refseq_mrna_id	i_secondary_variant_classification	i_start_WU	i_stop_WU	i_strand_WU	i_transcript_error_WU	i_transcript_name_WU	i_transcript_source_WU	i_transcript_species_WU	i_transcript_status_WU	i_transcript_version_WU	i_trv_type_WU	i_tumor_ref_reads	i_tumor_vaf	i_tumors_var_reads	i_type_WU	i_ucsc_cons_WU	i_variant_WU
ANKRD36B	57730	genome.wustl.edu	37	2	98165911	98165911	+	RNA	SNP	T	T	C	rs1839230|rs112877086	byFrequency	TCGA-A2-A0EP-01A-52D-A22X-09	TCGA-A2-A0EP-10A-01D-A22X-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	524b38df-3bfc-43b7-92fd-163f89a0c81f	a2779eee-d38c-4f4b-9b82-6d0141fe1bb1	g.chr2:98165911T>C	ENST00000443455.1	-	0	1558							Q8N2N9	AN36B_HUMAN	ankyrin repeat domain 36B																		ATCCTTTTTTTCTCTGGCTAT	0.308													.|||	980	0.195687	0.5703	0.1239	5008	,	,		38822	0.0069		0.1004	False		,,,				2504	0.0327					dbGAP											0													45.0	18.0	26.0					2																	98165911		1759	3782	5541	-	-	-			0			AK024934	CCDS74543.1	2q11.2	2013-01-11	2008-03-25	2008-03-25	ENSG00000196912	ENSG00000196912		"""Ankyrin repeat domain containing"""	29333	protein-coding gene	gene with protein product	"""melanoma-associated antigen"", ""CLL-associated antigen KW-1"""		"""KIAA1641"""	KIAA1641		10997877	Standard	NM_025190		Approved	FLJ21281	uc010yvc.1	Q8N2N9	OTTHUMG00000130547		2.37:g.98165911T>C		Somatic		WXS	Illumina GAIIx	Phase_IV	Q08AK5|Q6IPR0|Q6PI49|Q8IZM7|Q8TDH6|Q96N30|Q9H759	RNA	SNP	-	NULL	ENST00000443455.1	37	NULL		2																																																																																			ANKRD36B	-	-	ENSG00000196912		0.308	ANKRD36B-003	KNOWN	basic	processed_transcript	ANKRD36B	HGNC	pseudogene	OTTHUMT00000328967.2	110	0.90	1	T	NM_025190		98165911	98165911	-1	no_errors	ENST00000443455	ensembl	human	known	69_37n	rna	244	12.81	36	SNP	0.003	C
CACNA1A	773	genome.wustl.edu	37	19	13322934	13322934	+	Missense_Mutation	SNP	G	G	T	rs377711021		TCGA-A2-A0EP-01A-52D-A22X-09	TCGA-A2-A0EP-10A-01D-A22X-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	524b38df-3bfc-43b7-92fd-163f89a0c81f	a2779eee-d38c-4f4b-9b82-6d0141fe1bb1	g.chr19:13322934G>T	ENST00000360228.5	-	43	6285	c.6286C>A	c.(6286-6288)Ctc>Atc	p.L2096I	CACNA1A_ENST00000573710.2_Missense_Mutation_p.L2097I	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	2097					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	TCTGCAGGGAGGCGGGGCATG	0.672																																						dbGAP											0													28.0	30.0	29.0					19																	13322934		2010	4162	6172	-	-	-	SO:0001583	missense	0			U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.6286C>A	19.37:g.13322934G>T	ENSP00000353362:p.Leu2096Ile	Somatic		WXS	Illumina GAIIx	Phase_IV	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Missense_Mutation	SNP	pfam_Ion_trans_dom,pfam_VDCC_a1su_IQ,pfam_PKD1_2_channel,prints_VDCCAlpha1,prints_VDCC_P/Q_a1su	p.L2096I	ENST00000360228.5	37	c.6286	CCDS45998.1	19	.	.	.	.	.	.	.	.	.	.	G	17.39	3.376632	0.61735	.	.	ENSG00000141837	ENST00000360228;ENST00000418012;ENST00000357018;ENST00000325084	T	0.79749	-1.3	4.45	4.45	0.53987	.	0.336194	0.19164	U	0.121105	D	0.89171	0.6639	M	0.78456	2.415	0.53688	D	0.999976	P;P;D;D	0.63880	0.956;0.833;0.993;0.991	P;P;D;D	0.70016	0.772;0.772;0.967;0.911	D	0.89958	0.4084	10	0.54805	T	0.06	.	15.8854	0.79244	0.0:0.0:1.0:0.0	.	2097;2102;2096;2097	O00555;E9PD31;Q9NS88;E7EVF2	CAC1A_HUMAN;.;.;.	I	2096;2102;2097;2097	ENSP00000353362:L2096I	ENSP00000317661:L2097I	L	-	1	0	CACNA1A	13183934	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.039000	0.93777	2.039000	0.60335	0.484000	0.47621	CTC	CACNA1A	-	NULL	ENSG00000141837		0.672	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	CACNA1A	HGNC	protein_coding	OTTHUMT00000104062.2	26	0.00	0	G	NM_000068		13322934	13322934	-1	no_errors	ENST00000360228	ensembl	human	known	69_37n	missense	23	14.81	4	SNP	1.000	T
CROCCP2	84809	genome.wustl.edu	37	1	16957123	16957123	+	lincRNA	SNP	C	C	T	rs2786805	byFrequency	TCGA-A2-A0EP-01A-52D-A22X-09	TCGA-A2-A0EP-10A-01D-A22X-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	524b38df-3bfc-43b7-92fd-163f89a0c81f	a2779eee-d38c-4f4b-9b82-6d0141fe1bb1	g.chr1:16957123C>T	ENST00000412962.1	-	0	294							Q86T23	CROL1_HUMAN	ciliary rootlet coiled-coil, rootletin pseudogene 2						centrosome organization (GO:0051297)	ciliary rootlet (GO:0035253)											CTAACACTGTCGCAGCCTCCT	0.627													.|||	1993	0.397963	0.472	0.4193	5008	,	,		42300	0.3611		0.3738	False		,,,				2504	0.3456					dbGAP											0																																										-	-	-			0			AK090414		1p36.13	2010-07-08	2010-07-08	2010-07-08	ENSG00000215908	ENSG00000215908			28170	pseudogene	pseudogene			"""ciliary rootlet coiled-coil, rootletin-like 1"""	CROCCL1		12477932	Standard	NR_026752		Approved	MGC12760	uc001azf.3	Q86T23	OTTHUMG00000037884		1.37:g.16957123C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	Q8NF65|Q96FR5|Q9BRE8	RNA	SNP	-	NULL	ENST00000412962.1	37	NULL		1																																																																																			CROCCP2	-	-	ENSG00000215908		0.627	CROCCP2-003	KNOWN	basic	lincRNA	CROCCP2	HGNC	lincRNA	OTTHUMT00000092784.1	8	0.00	0	C	NR_026752.1		16957123	16957123	-1	no_errors	ENST00000362058	ensembl	human	known	69_37n	rna	9	35.71	5	SNP	0.007	T
HERC2P9	440248	genome.wustl.edu	37	15	28916947	28916947	+	RNA	SNP	C	C	T			TCGA-A2-A0EP-01A-52D-A22X-09	TCGA-A2-A0EP-10A-01D-A22X-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	524b38df-3bfc-43b7-92fd-163f89a0c81f	a2779eee-d38c-4f4b-9b82-6d0141fe1bb1	g.chr15:28916947C>T	ENST00000528584.1	+	0	1568					NR_036443.1				hect domain and RLD 2 pseudogene 9																		CCTCTGTCACCACACCAAAAT	0.383																																						dbGAP											0																																										-	-	-			0			BC047911		15q13.1	2011-05-24			ENSG00000206149	ENSG00000206149			30495	pseudogene	pseudogene							Standard	NR_036443		Approved	FLJ59185	uc010azc.3		OTTHUMG00000167114		15.37:g.28916947C>T		Somatic		WXS	Illumina GAIIx	Phase_IV		RNA	SNP	-	NULL	ENST00000528584.1	37	NULL		15																																																																																			HERC2P9	-	-	ENSG00000206149		0.383	HERC2P9-002	KNOWN	basic	processed_transcript	HERC2P9	HGNC	pseudogene	OTTHUMT00000393268.1	14	0.00	0	C	NR_036443		28916947	28916947	+1	no_errors	ENST00000528584	ensembl	human	known	69_37n	rna	13	45.83	11	SNP	0.975	T
RXRA	6256	genome.wustl.edu	37	9	137293881	137293881	+	Intron	SNP	A	A	C	rs34683648	byFrequency	TCGA-A2-A0EP-01A-52D-A22X-09	TCGA-A2-A0EP-10A-01D-A22X-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	524b38df-3bfc-43b7-92fd-163f89a0c81f	a2779eee-d38c-4f4b-9b82-6d0141fe1bb1	g.chr9:137293881A>C	ENST00000481739.1	+	2	331				RXRA_ENST00000356384.4_Intron	NM_002957.4	NP_002948.1	P19793	RXRA_HUMAN	retinoid X receptor, alpha						camera-type eye development (GO:0043010)|cardiac muscle cell proliferation (GO:0060038)|cellular lipid metabolic process (GO:0044255)|cholesterol metabolic process (GO:0008203)|embryo implantation (GO:0007566)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|maternal placenta development (GO:0001893)|modulation by virus of host morphology or physiology (GO:0019048)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peroxisome proliferator activated receptor signaling pathway (GO:0035357)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homotetramerization (GO:0051289)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|response to retinoic acid (GO:0032526)|retinoic acid receptor signaling pathway (GO:0048384)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular cardiac muscle cell differentiation (GO:0055012)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|vitamin metabolic process (GO:0006766)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	9-cis retinoic acid receptor activity (GO:0004886)|chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein heterodimerization activity (GO:0046982)|retinoic acid receptor activity (GO:0003708)|retinoic acid-responsive element binding (GO:0044323)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|vitamin D receptor binding (GO:0042809)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19				OV - Ovarian serous cystadenocarcinoma(145;4.66e-08)|Epithelial(140;6.72e-08)|all cancers(34;2.22e-07)	Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Bexarotene(DB00307)|Etodolac(DB00749)	CGGGGAGCAGAGTGCCGTGGG	0.627													C|||	609	0.121605	0.4297	0.0461	5008	,	,		13490	0.0		0.004	False		,,,				2504	0.0051					dbGAP											0																																										-	-	-	SO:0001627	intron_variant	0			X52773	CCDS35172.1	9q34	2013-01-16			ENSG00000186350	ENSG00000186350		"""Nuclear hormone receptors"""	10477	protein-coding gene	gene with protein product	"""nuclear receptor subfamily 2 group B member 1"""	180245				2159111	Standard	XM_005263409		Approved	NR2B1	uc004cfa.1	P19793	OTTHUMG00000020887	ENST00000481739.1:c.279+153A>C	9.37:g.137293881A>C		Somatic		WXS	Illumina GAIIx	Phase_IV	B3KY83|Q2NL52|Q2V504	RNA	SNP	-	NULL	ENST00000481739.1	37	NULL	CCDS35172.1	9																																																																																			RXRA	-	-	ENSG00000186350		0.627	RXRA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	RXRA	HGNC	protein_coding	OTTHUMT00000054949.1	27	0.00	0	A	NM_002957		137293881	137293881	+1	no_errors	ENST00000484822	ensembl	human	known	69_37n	rna	33	10.81	4	SNP	0.000	C
TCEB3C	162699	genome.wustl.edu	37	18	44554806	44554806	+	Missense_Mutation	SNP	C	C	G	rs200799485		TCGA-A2-A0EP-01A-52D-A22X-09	TCGA-A2-A0EP-10A-01D-A22X-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	524b38df-3bfc-43b7-92fd-163f89a0c81f	a2779eee-d38c-4f4b-9b82-6d0141fe1bb1	g.chr18:44554806C>G	ENST00000330682.2	-	1	1643	c.1408G>C	c.(1408-1410)Gca>Cca	p.A470P	KATNAL2_ENST00000245121.5_Intron|KATNAL2_ENST00000592005.1_Intron|KATNAL2_ENST00000356157.7_Intron	NM_145653.3	NP_663628.2	Q8NG57	ELOA3_HUMAN	transcription elongation factor B polypeptide 3C (elongin A3)	470					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(1)|lung(16)|skin(2)	30						GCGGCTCCTGCAGACTTCTCT	0.622																																						dbGAP											0													2.0	2.0	2.0					18																	44554806		429	1013	1442	-	-	-	SO:0001583	missense	0			AB076840	CCDS11931.1	18q21.1	2008-08-13			ENSG00000183791	ENSG00000183791			24617	protein-coding gene	gene with protein product	"""elongin A3"""					11932239, 11994304	Standard	NM_145653		Approved	HsT829, TCEB3L2	uc010xdb.2	Q8NG57	OTTHUMG00000132651	ENST00000330682.2:c.1408G>C	18.37:g.44554806C>G	ENSP00000328232:p.Ala470Pro	Somatic		WXS	Illumina GAIIx	Phase_IV		Missense_Mutation	SNP	pfam_RNA_pol_II_trans_fac_SIII_A,pfam_TFIIS_N,superfamily_TFIIS_N,smart_TFIIS/CRSP70_N_sub	p.A470P	ENST00000330682.2	37	c.1408	CCDS11931.1	18	.	.	.	.	.	.	.	.	.	.	c	13.45	2.239417	0.39598	.	.	ENSG00000183791	ENST00000330682	T	0.12255	2.7	1.37	1.37	0.22104	.	0.328640	0.21328	U	0.076354	T	0.07683	0.0193	N	0.22421	0.69	0.09310	N	1	D	0.59357	0.985	B	0.40659	0.336	T	0.27640	-1.0068	10	0.52906	T	0.07	-0.157	6.2213	0.20683	0.0:1.0:0.0:0.0	.	470	Q8NG57	ELOA3_HUMAN	P	470	ENSP00000328232:A470P	ENSP00000328232:A470P	A	-	1	0	TCEB3C	42808804	0.016000	0.18221	0.002000	0.10522	0.009000	0.06853	1.060000	0.30530	1.095000	0.41419	0.485000	0.47835	GCA	TCEB3C	-	NULL	ENSG00000183791		0.622	TCEB3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TCEB3C	HGNC	protein_coding	OTTHUMT00000255902.1	12	0.00	0	C	NM_145653		44554806	44554806	-1	no_errors	ENST00000330682	ensembl	human	known	69_37n	missense	13	27.78	5	SNP	0.004	G
THSD7B	80731	genome.wustl.edu	37	2	137639789	137639789	+	Nonsense_Mutation	SNP	G	G	A			TCGA-A2-A0EP-01A-52D-A22X-09	TCGA-A2-A0EP-10A-01D-A22X-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	524b38df-3bfc-43b7-92fd-163f89a0c81f	a2779eee-d38c-4f4b-9b82-6d0141fe1bb1	g.chr2:137639789G>A	ENST00000409968.1	+	2	219	c.41G>A	c.(40-42)tGg>tAg	p.W14*	THSD7B_ENST00000272643.3_Nonsense_Mutation_p.W14*			Q9C0I4	THS7B_HUMAN	thrombospondin, type I, domain containing 7B	14						integral component of membrane (GO:0016021)				NS(3)|breast(3)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(14)|lung(57)|ovary(4)|pancreas(3)|prostate(11)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	134				BRCA - Breast invasive adenocarcinoma(221;0.19)		TGCTGGGTATGGAGGAGCATG	0.423																																						dbGAP											0																																										-	-	-	SO:0001587	stop_gained	0					2q22.1	2006-11-24			ENSG00000144229	ENSG00000144229			29348	protein-coding gene	gene with protein product						11214970	Standard	NM_001080427		Approved	KIAA1679	uc002tva.1	Q9C0I4	OTTHUMG00000153590	ENST00000409968.1:c.41G>A	2.37:g.137639789G>A	ENSP00000387145:p.Trp14*	Somatic		WXS	Illumina GAIIx	Phase_IV		Nonsense_Mutation	SNP	pfam_Thrombospondin_1_rpt,superfamily_Thrombospondin_1_rpt,smart_Thrombospondin_1_rpt,pfscan_Thrombospondin_1_rpt	p.W14*	ENST00000409968.1	37	c.41		2	.	.	.	.	.	.	.	.	.	.	G	28.9	4.960696	0.92791	.	.	ENSG00000144229	ENST00000409968;ENST00000272643	.	.	.	5.34	4.44	0.53790	.	1.039370	0.07870	U	0.967668	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.12766	T	0.61	.	12.8572	0.57892	0.0:0.1712:0.8287:0.0	.	.	.	.	X	14	.	ENSP00000272643:W14X	W	+	2	0	THSD7B	137356259	1.000000	0.71417	0.630000	0.29268	0.109000	0.19521	3.224000	0.51238	1.201000	0.43203	0.563000	0.77884	TGG	THSD7B	-	NULL	ENSG00000144229		0.423	THSD7B-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	THSD7B	HGNC	protein_coding	OTTHUMT00000331769.2	69	0.00	0	G	XM_046570.9		137639789	137639789	+1	no_errors	ENST00000272643	ensembl	human	known	69_37n	nonsense	94	11.32	12	SNP	0.802	A
UQCC1	55245	genome.wustl.edu	37	20	33891661	33891661	+	3'UTR	SNP	G	G	T			TCGA-A2-A0EP-01A-52D-A22X-09	TCGA-A2-A0EP-10A-01D-A22X-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	524b38df-3bfc-43b7-92fd-163f89a0c81f	a2779eee-d38c-4f4b-9b82-6d0141fe1bb1	g.chr20:33891661G>T	ENST00000374385.5	-	0	1154				UQCC1_ENST00000374384.2_3'UTR|UQCC1_ENST00000540457.1_3'UTR|UQCC1_ENST00000407996.2_3'UTR|UQCC1_ENST00000374377.5_3'UTR|UQCC1_ENST00000397556.3_3'UTR|UQCC1_ENST00000359226.2_3'UTR|UQCC1_ENST00000374380.2_3'UTR|UQCC1_ENST00000349714.5_3'UTR	NM_018244.4	NP_060714.3	Q9NVA1	UQCC1_HUMAN	ubiquinol-cytochrome c reductase complex assembly factor 1							cytoplasmic membrane-bounded vesicle (GO:0016023)|mitochondrion (GO:0005739)											CTTTCTGCAGGGTCCTGGACC	0.567											OREG0025888	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										dbGAP											0																																										-	-	-	SO:0001624	3_prime_UTR_variant	0			AK001712	CCDS13252.1, CCDS13253.1, CCDS13253.2, CCDS54458.1	20q11.22	2013-09-20	2013-09-20	2013-09-20	ENSG00000101019	ENSG00000101019		"""Mitochondrial respiratory chain complex assembly factors"""	15891	protein-coding gene	gene with protein product	"""Basic FGF-repressed Zic-binding protein"", ""cytochrome B protein synthesis 3 homolog (S. cerevisiae)"""	611797	"""chromosome 20 open reading frame 44"", ""ubiquinol-cytochrome c reductase complex chaperone"""	C20orf44, UQCC			Standard	NM_018244		Approved	FLJ10850, CBP3, BFZB	uc002xcd.3	Q9NVA1	OTTHUMG00000032335	ENST00000374385.5:c.*77C>A	20.37:g.33891661G>T		Somatic	843	WXS	Illumina GAIIx	Phase_IV	B1AKV5|Q0VF37|Q5T348|Q5T351|Q5T353|Q86YU3|Q86YU4|Q96H66|Q9H438|Q9H452|Q9H9K8|Q9H9R5	RNA	SNP	-	NULL	ENST00000374385.5	37	NULL	CCDS13252.1	20																																																																																			UQCC	-	-	ENSG00000101019		0.567	UQCC1-010	KNOWN	basic|appris_principal|CCDS	protein_coding	UQCC	HGNC	protein_coding	OTTHUMT00000078866.1	32	0.00	0	G	NM_018244		33891661	33891661	-1	no_errors	ENST00000496812	ensembl	human	known	69_37n	rna	40	11.11	5	SNP	0.639	T
ZBTB21	49854	genome.wustl.edu	37	21	43429588	43429588	+	Intron	SNP	G	G	A	rs399856	byFrequency	TCGA-A2-A0EP-01A-52D-A22X-09	TCGA-A2-A0EP-10A-01D-A22X-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	524b38df-3bfc-43b7-92fd-163f89a0c81f	a2779eee-d38c-4f4b-9b82-6d0141fe1bb1	g.chr21:43429588G>A	ENST00000310826.5	-	1	106				ZBTB21_ENST00000398505.3_Intron|ZBTB21_ENST00000398511.3_Intron|ZBTB21_ENST00000465968.1_Intron|ZBTB21_ENST00000398499.1_Intron	NM_001098402.1	NP_001091872.1	Q9ULJ3	ZBT21_HUMAN	zinc finger and BTB domain containing 21						negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyl-CpG binding (GO:0008327)										CGGACGGGGGGAAGGGGGCTC	0.746													G|||	2690	0.537141	0.7239	0.4251	5008	,	,		10353	0.1409		0.6332	False		,,,				2504	0.6738					dbGAP											0																																										-	-	-	SO:0001627	intron_variant	0			AB033053	CCDS13678.1, CCDS42934.1	21q22.3	2013-01-09	2013-01-09	2013-01-09	ENSG00000173276	ENSG00000173276		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	13083	protein-coding gene	gene with protein product			"""zinc finger protein 295"""	ZNF295			Standard	NM_020727		Approved	KIAA1227	uc002yzy.4	Q9ULJ3	OTTHUMG00000086789	ENST00000310826.5:c.77+772C>T	21.37:g.43429588G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	Q5R2W1|Q5R2W2|Q6P4R0	RNA	SNP	-	NULL	ENST00000310826.5	37	NULL	CCDS13678.1	21																																																																																			ZNF295-AS1	-	-	ENSG00000237232		0.746	ZBTB21-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	ZNF295-AS1	HGNC	protein_coding	OTTHUMT00000195308.1	8	0.00	0	G	NM_020727		43429588	43429588	+1	no_errors	ENST00000412906	ensembl	human	known	69_37n	rna	0	100.00	8	SNP	0.000	A
