#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_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_Chromosome_hg18	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_End_position_hg18	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_Start_position_hg18	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	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_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_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
ELAVL4	1996	hgsc.bcm.edu	37	1	50666792	50666792	+	Missense_Mutation	SNP	G	G	A	rs377132231		TCGA-23-1109-01A-01W-0484-10	TCGA-23-1109-10A-01W-0484-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_III	WXS	454_PCR_WGA			SOLID	5afcf837-a7d9-4b97-b4c7-a0f2652f5200	4bbc6ec2-2d1c-4fef-a40a-e90d608c4673	g.chr1:50666792G>A	ENST00000371823.4	+	7	1309	c.1085G>A	c.(1084-1086)cGc>cAc	p.R362H	ELAVL4_ENST00000371827.1_Missense_Mutation_p.R348H|ELAVL4_ENST00000448907.2_Missense_Mutation_p.R351H|ELAVL4_ENST00000371819.1_Missense_Mutation_p.R353H|ELAVL4_ENST00000371821.1_Missense_Mutation_p.R367H|ELAVL4_ENST00000357083.4_Missense_Mutation_p.R365H|ELAVL4_ENST00000371824.1_Missense_Mutation_p.R348H	NM_001144774.1|NM_021952.3	NP_001138246.1|NP_068771.2	P26378	ELAV4_HUMAN	ELAV like neuron-specific RNA binding protein 4	362	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|RNA processing (GO:0006396)		AU-rich element binding (GO:0017091)|mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.R362H(1)		NS(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(2)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	32						AACGGGTACCGCCTGGGAGAC	0.443																																																1	Substitution - Missense(1)	ovary(1)	1						G	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	0,4406		0,0,2203	51.0	48.0	49.0		1043,1094,1043,1052,1085	6.1	1.0	1		49	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense	ELAVL4	NM_001144774.1,NM_001144775.1,NM_001144776.1,NM_001144777.1,NM_021952.3	29,29,29,29,29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	348/367,365/384,348/367,351/370,362/381	50666792	1,13005	2203	4300	6503	50439379	SO:0001583	missense	1996			AY033998	CCDS553.1, CCDS44138.1, CCDS44139.1, CCDS44140.1, CCDS53315.1, CCDS72788.1	1p34	2013-10-03	2013-10-03		ENSG00000162374	ENSG00000162374		"""RNA binding motif (RRM) containing"""	3315	protein-coding gene	gene with protein product	"""Hu antigen D"""	168360	"""ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4 (Hu antigen D)"", ""ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4"""	HUD		8222755	Standard	XM_005270581		Approved	PNEM	uc001csb.2	P26378	OTTHUMG00000007877	ENST00000371823.4:c.1085G>A	1.37:g.50666792G>A	ENSP00000360888:p.Arg362His		50439379	B1APY6|B1APY7|B7Z4G7|Q8IYD4|Q96J74|Q96J75|Q9UD24	Missense_Mutation	SNP	ENST00000371823.4	37	CCDS553.1	.	.	.	.	.	.	.	.	.	.	G	19.95	3.922027	0.73213	0.0	1.16E-4	ENSG00000162374	ENST00000448907;ENST00000371827;ENST00000357083;ENST00000371824;ENST00000371823;ENST00000371821;ENST00000371819	T;T;T;T;T;T;T	0.16597	2.33;2.33;2.33;2.33;2.33;2.33;2.33	6.07	6.07	0.98685	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.29620	0.0739	N	0.21142	0.635	0.80722	D	1	D;D;D;D;D;D	0.69078	0.997;0.993;0.997;0.996;0.992;0.997	P;P;P;P;P;D	0.63957	0.841;0.753;0.895;0.753;0.753;0.92	T	0.00920	-1.1514	10	0.44086	T	0.13	.	20.6593	0.99626	0.0:0.0:1.0:0.0	.	353;348;362;365;348;351	B1APY9;P26378-2;P26378;P26378-3;P26378-4;B7Z4G7	.;.;ELAV4_HUMAN;.;.;.	H	351;348;365;348;362;367;353	ENSP00000399939:R351H;ENSP00000360892:R348H;ENSP00000349594:R365H;ENSP00000360889:R348H;ENSP00000360888:R362H;ENSP00000360886:R367H;ENSP00000360884:R353H	ENSP00000349594:R365H	R	+	2	0	ELAVL4	50439379	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.414000	0.97362	2.885000	0.99019	0.655000	0.94253	CGC		0.443	ELAVL4-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000021712.1	NM_021952	
ESR2	2100	hgsc.bcm.edu	37	14	64727260	64727260	+	Missense_Mutation	SNP	C	C	T			TCGA-23-1109-01A-01W-0484-10	TCGA-23-1109-10A-01W-0484-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_III	WXS	454_PCR_WGA			SOLID	5afcf837-a7d9-4b97-b4c7-a0f2652f5200	4bbc6ec2-2d1c-4fef-a40a-e90d608c4673	g.chr14:64727260C>T	ENST00000341099.4	-	5	1276	c.859G>A	c.(859-861)Gcg>Acg	p.A287T	ESR2_ENST00000542956.1_Missense_Mutation_p.A287T|ESR2_ENST00000358599.5_Missense_Mutation_p.A287T|ESR2_ENST00000357782.2_Missense_Mutation_p.A287T|ESR2_ENST00000554572.1_Missense_Mutation_p.A287T|ESR2_ENST00000555278.1_Missense_Mutation_p.A287T|ESR2_ENST00000553796.1_Missense_Mutation_p.A287T|ESR2_ENST00000353772.3_Missense_Mutation_p.A287T|ESR2_ENST00000557772.1_Missense_Mutation_p.A287T|ESR2_ENST00000267525.6_Missense_Mutation_p.A287T|ESR2_ENST00000555483.1_5'UTR	NM_001437.2	NP_001428.1	Q92731	ESR2_HUMAN	estrogen receptor 2 (ER beta)	287	Steroid-binding.				brain development (GO:0007420)|cell-cell signaling (GO:0007267)|epithelial cell maturation involved in prostate gland development (GO:0060743)|extracellular negative regulation of signal transduction (GO:1900116)|gene expression (GO:0010467)|hormone-mediated apoptotic signaling pathway (GO:0008628)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|ovarian follicle development (GO:0001541)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|prostate gland epithelium morphogenesis (GO:0060740)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|uterus development (GO:0060065)|vagina development (GO:0060068)	extracellular region (GO:0005576)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|estrogen receptor activity (GO:0030284)|estrogen response element binding (GO:0034056)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|receptor antagonist activity (GO:0048019)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.A287T(1)		central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	23				all cancers(60;0.00916)|OV - Ovarian serous cystadenocarcinoma(108;0.0111)|BRCA - Breast invasive adenocarcinoma(234;0.0437)	Diethylstilbestrol(DB00255)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estropipate(DB04574)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Trilostane(DB01108)	GTGAAGGGCGCACTGGGGCGG	0.642																																																1	Substitution - Missense(1)	ovary(1)	14											68.0	70.0	69.0					14																	64727260		2203	4300	6503	63797013	SO:0001583	missense	2100			X99101	CCDS9762.1, CCDS32096.1, CCDS55920.1, CCDS61469.1, CCDS61470.1	14q21-q22	2013-01-16			ENSG00000140009	ENSG00000140009		"""Nuclear hormone receptors"""	3468	protein-coding gene	gene with protein product		601663				8769313	Standard	NM_001214902		Approved	NR3A2, Erb	uc001xha.1	Q92731	OTTHUMG00000141306	ENST00000341099.4:c.859G>A	14.37:g.64727260C>T	ENSP00000343925:p.Ala287Thr		63797013	A8K8K5|G3V5M5|O60608|O60685|O60702|O60703|O75583|O75584|Q0MWT5|Q0MWT6|Q86Z31|Q9UEV6|Q9UHD3|Q9UQK9	Missense_Mutation	SNP	ENST00000341099.4	37	CCDS9762.1	.	.	.	.	.	.	.	.	.	.	C	13.01	2.109085	0.37242	.	.	ENSG00000140009	ENST00000556275;ENST00000542956;ENST00000554572;ENST00000353772;ENST00000358599;ENST00000555278;ENST00000553796;ENST00000357782;ENST00000557772;ENST00000341099;ENST00000267525	D;D;D;D;D;D;D;D;D;D;T	0.96619	-4.07;-4.07;-4.07;-4.07;-4.07;-4.07;-4.07;-4.07;-4.07;-4.07;0.66	5.83	-11.7	0.00046	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (1);	0.654924	0.16758	N	0.200721	D	0.84383	0.5460	N	0.04880	-0.145	0.09310	N	1	B;B;B;B;B	0.10296	0.003;0.0;0.0;0.0;0.0	B;B;B;B;B	0.11329	0.006;0.001;0.0;0.0;0.0	T	0.69796	-0.5048	10	0.30854	T	0.27	.	7.3614	0.26748	0.3309:0.4253:0.0:0.2438	.	287;287;287;287;287	Q92731-7;Q92731;Q92731-6;Q92731-5;F1D8N3	.;ESR2_HUMAN;.;.;.	T	287	ENSP00000452485:A287T;ENSP00000441792:A287T;ENSP00000450699:A287T;ENSP00000335551:A287T;ENSP00000351412:A287T;ENSP00000450488:A287T;ENSP00000452426:A287T;ENSP00000350427:A287T;ENSP00000451582:A287T;ENSP00000343925:A287T;ENSP00000267525:A287T	ENSP00000267525:A287T	A	-	1	0	ESR2	63797013	0.000000	0.05858	0.000000	0.03702	0.710000	0.40934	-0.476000	0.06591	-3.548000	0.00143	-0.309000	0.09137	GCG		0.642	ESR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280621.1		
MGA	23269	hgsc.bcm.edu	37	15	41961093	41961093	+	Start_Codon_SNP	SNP	A	A	G			TCGA-23-1109-01A-01W-0484-10	TCGA-23-1109-10A-01W-0484-10	A	A	G	G	A	A	Unknown	Valid	Somatic	Phase_III	WXS	454_PCR_WGA			SOLID	5afcf837-a7d9-4b97-b4c7-a0f2652f5200	4bbc6ec2-2d1c-4fef-a40a-e90d608c4673	g.chr15:41961093A>G	ENST00000570161.1	+	1	1	c.1A>G	c.(1-3)Atg>Gtg	p.M1V	MGA_ENST00000566586.1_Start_Codon_SNP_p.M1V|MGA_ENST00000219905.7_Start_Codon_SNP_p.M1V|MGA_ENST00000545763.1_Start_Codon_SNP_p.M1V|MGA_ENST00000389936.4_Start_Codon_SNP_p.M1V|MGA_ENST00000568630.1_Intron			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0					carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)	p.M1V(1)		NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TACTGAAATCATGGAGGAGAA	0.408																																																1	Substitution - Missense(1)	ovary(1)	15											116.0	112.0	114.0					15																	41961093		1944	4159	6103	39748385	SO:0001582	initiator_codon_variant	23269			AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"""MAX dimerization proteins"", ""T-boxes"""	14010	protein-coding gene	gene with protein product			"""MAX gene associated"""				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.1A>G	15.37:g.41961093A>G	ENSP00000457035:p.Met1Val		39748385	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000570161.1	37	CCDS55959.1	.	.	.	.	.	.	.	.	.	.	A	15.03	2.712015	0.48517	.	.	ENSG00000174197	ENST00000219905;ENST00000389936;ENST00000545763	D;D;D	0.83755	-1.75;-1.76;-1.73	5.37	5.37	0.77165	.	0.232985	0.30185	N	0.010214	D	0.88055	0.6334	.	.	.	0.80722	D	1	P;P	0.39576	0.679;0.551	P;P	0.50791	0.65;0.448	D	0.89256	0.3594	9	0.87932	D	0	.	15.6626	0.77199	1.0:0.0:0.0:0.0	.	1;1	F5H7K2;E7ENI0	.;.	V	1	ENSP00000219905:M1V;ENSP00000374586:M1V;ENSP00000442467:M1V	ENSP00000219905:M1V	M	+	1	0	MGA	39748385	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.461000	0.53035	2.161000	0.67846	0.528000	0.53228	ATG		0.408	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1	Missense_Mutation
MYO5C	55930	hgsc.bcm.edu	37	15	52564779	52564779	+	Missense_Mutation	SNP	G	G	T			TCGA-23-1109-01A-01W-0484-10	TCGA-23-1109-10A-01W-0484-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_III	WXS	454_PCR_WGA			SOLID	5afcf837-a7d9-4b97-b4c7-a0f2652f5200	4bbc6ec2-2d1c-4fef-a40a-e90d608c4673	g.chr15:52564779G>T	ENST00000261839.7	-	6	909	c.748C>A	c.(748-750)Caa>Aaa	p.Q250K	MYO5C_ENST00000541028.1_5'UTR|MYO5C_ENST00000443683.2_Missense_Mutation_p.Q193K	NM_018728.3	NP_061198.2	Q9NQX4	MYO5C_HUMAN	myosin VC	250	Myosin motor.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.Q250K(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(7)|large_intestine(15)|lung(12)|ovary(7)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66				all cancers(107;0.0137)		ATACTTACTTGAAAGACAACT	0.348																																																1	Substitution - Missense(1)	ovary(1)	15											108.0	100.0	103.0					15																	52564779		1817	4075	5892	50352071	SO:0001583	missense	55930			AF272390	CCDS42036.1	15q21	2011-09-27				ENSG00000128833		"""Myosins / Myosin superfamily : Class V"""	7604	protein-coding gene	gene with protein product	"""myosin 5C"""	610022				11870218	Standard	NM_018728		Approved	MGC74969	uc010bff.3	Q9NQX4		ENST00000261839.7:c.748C>A	15.37:g.52564779G>T	ENSP00000261839:p.Gln250Lys		50352071	Q6P1W8	Missense_Mutation	SNP	ENST00000261839.7	37	CCDS42036.1	.	.	.	.	.	.	.	.	.	.	G	34	5.348055	0.95807	.	.	ENSG00000128833	ENST00000261839;ENST00000443683;ENST00000541028	D;D	0.88975	-2.45;-2.45	5.98	5.98	0.97165	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	D	0.97595	0.9212	H	0.99634	4.67	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.91635	0.999;0.999	D	0.98521	1.0623	10	0.72032	D	0.01	.	20.4434	0.99119	0.0:0.0:1.0:0.0	.	213;250	F5H231;Q9NQX4	.;MYO5C_HUMAN	K	250;193;213	ENSP00000261839:Q250K;ENSP00000410582:Q193K	ENSP00000261839:Q250K	Q	-	1	0	MYO5C	50352071	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.869000	0.99810	2.838000	0.97847	0.655000	0.94253	CAA		0.348	MYO5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419562.1	NM_018728	
SRPX2	27286	hgsc.bcm.edu	37	X	99921808	99921808	+	Missense_Mutation	SNP	C	C	T			TCGA-23-1109-01A-01W-0484-10	TCGA-23-1109-10A-01W-0484-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_III	WXS	454_PCR_WGA			SOLID	5afcf837-a7d9-4b97-b4c7-a0f2652f5200	4bbc6ec2-2d1c-4fef-a40a-e90d608c4673	g.chrX:99921808C>T	ENST00000373004.3	+	8	1267	c.839C>T	c.(838-840)gCg>gTg	p.A280V		NM_014467.2	NP_055282.1	O60687	SRPX2_HUMAN	sushi-repeat containing protein, X-linked 2	280	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.				angiogenesis (GO:0001525)|cell motility (GO:0048870)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|positive regulation of synapse assembly (GO:0051965)|regulation of phosphorylation (GO:0042325)|single organismal cell-cell adhesion (GO:0016337)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|excitatory synapse (GO:0060076)|extracellular space (GO:0005615)|synaptic membrane (GO:0097060)	hepatocyte growth factor binding (GO:0036458)|identical protein binding (GO:0042802)|receptor binding (GO:0005102)	p.A280V(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(10)|ovary(2)|upper_aerodigestive_tract(1)	19						TGCACCTCAGCGGGGGACAAC	0.572																																																1	Substitution - Missense(1)	ovary(1)	X											61.0	52.0	55.0					X																	99921808		2203	4300	6503	99808464	SO:0001583	missense	27286			AF393649	CCDS14471.1	Xq21.33-q23	2011-01-25	2011-01-25		ENSG00000102359	ENSG00000102359			30668	protein-coding gene	gene with protein product		300642	"""sushi-repeat-containing protein, X-linked 2"""			9864177	Standard	NM_014467		Approved	SRPUL	uc004egb.3	O60687	OTTHUMG00000022003	ENST00000373004.3:c.839C>T	X.37:g.99921808C>T	ENSP00000362095:p.Ala280Val		99808464	B3KQT3|Q8WW85	Missense_Mutation	SNP	ENST00000373004.3	37	CCDS14471.1	.	.	.	.	.	.	.	.	.	.	C	11.65	1.701842	0.30232	.	.	ENSG00000102359	ENST00000373004	T	0.64618	-0.11	5.7	1.73	0.24493	Complement control module (2);Sushi/SCR/CCP (3);	0.356956	0.32244	N	0.006364	T	0.50051	0.1593	L	0.55017	1.72	0.22511	N	0.999033	B	0.06786	0.001	B	0.06405	0.002	T	0.34675	-0.9819	9	.	.	.	-1.9363	6.5492	0.22423	0.3457:0.5087:0.0:0.1456	.	280	O60687	SRPX2_HUMAN	V	280	ENSP00000362095:A280V	.	A	+	2	0	SRPX2	99808464	0.186000	0.23225	0.175000	0.22980	0.519000	0.34347	0.760000	0.26475	0.195000	0.20347	-0.191000	0.12829	GCG		0.572	SRPX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057486.1	NM_014467	
COL17A1	1308	hgsc.bcm.edu	37	10	105800875	105800875	+	Splice_Site	SNP	C	C	T			TCGA-23-1109-01A-01W-0484-10	TCGA-23-1109-10A-01W-0484-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_III	WXS	Sanger_PCR_WGA			SOLID	5afcf837-a7d9-4b97-b4c7-a0f2652f5200	4bbc6ec2-2d1c-4fef-a40a-e90d608c4673	g.chr10:105800875C>T	ENST00000353479.5	-	39	2939	c.2649G>A	c.(2647-2649)ggG>ggA	p.G883G	COL17A1_ENST00000369733.3_Splice_Site_p.G883G	NM_000494.3	NP_000485.3	Q9UMD9	COHA1_HUMAN	collagen, type XVII, alpha 1	883	Triple-helical region.				cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|hemidesmosome (GO:0030056)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)		p.G883G(1)		NS(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|liver(1)|lung(22)|ovary(5)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	62		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;2.5e-09)|all cancers(201;7.94e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		GCAAACCCTCCCCTAGGAAAG	0.572																																																1	Substitution - coding silent(1)	ovary(1)	10											97.0	99.0	99.0					10																	105800875		2203	4300	6503	105790865	SO:0001630	splice_region_variant	1308			M91669	CCDS7554.1	10q24.3	2013-01-16			ENSG00000065618	ENSG00000065618		"""Collagens"""	2194	protein-coding gene	gene with protein product		113811		BPAG2		7916703	Standard	NM_000494		Approved	BP180	uc001kxr.3	Q9UMD9	OTTHUMG00000018998	ENST00000353479.5:c.2648-1G>A	10.37:g.105800875C>T			105790865	Q02802|Q5JV36|Q99018|Q9NQK9|Q9UC14	Splice_Site	SNP	ENST00000353479.5	37	CCDS7554.1																																																																																				0.572	COL17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050181.1	NM_130778, NM_000494	Silent
EPHA3	2042	hgsc.bcm.edu	37	3	89448466	89448466	+	Splice_Site	SNP	A	A	G			TCGA-23-1109-01A-01W-0484-10	TCGA-23-1109-10A-01W-0484-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_III	WXS	Sanger_PCR_WGA			SOLID	5afcf837-a7d9-4b97-b4c7-a0f2652f5200	4bbc6ec2-2d1c-4fef-a40a-e90d608c4673	g.chr3:89448466A>G	ENST00000336596.2	+	7	1656		c.e7-1		EPHA3_ENST00000494014.1_Splice_Site|EPHA3_ENST00000452448.2_Splice_Site	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3						cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)	p.?(1)		NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		CTGACCTCAAAGCAGGAACAA	0.338										TSP Lung(6;0.00050)																																						1	Unknown(1)	ovary(1)	3											64.0	66.0	65.0					3																	89448466		2203	4300	6503	89531156	SO:0001630	splice_region_variant	2042			M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3387	protein-coding gene	gene with protein product		179611	"""EphA3"""	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.1432-1A>G	3.37:g.89448466A>G			89531156	Q9H2V3|Q9H2V4	Splice_Site	SNP	ENST00000336596.2	37	CCDS2922.1	.	.	.	.	.	.	.	.	.	.	A	24.2	4.510330	0.85389	.	.	ENSG00000044524	ENST00000336596;ENST00000452448;ENST00000494014	.	.	.	5.5	5.5	0.81552	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.602	0.76631	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	EPHA3	89531156	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.339000	0.96797	2.082000	0.62665	0.460000	0.39030	.		0.338	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233	Intron
