#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_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_NormalRefReads_WU	i_NormalVAF_WU	i_NormalVarReads_WU	i_ORegAnno_bin	i_RNARefReads_WU	i_RNAVAF_WU	i_RNAVarReads_WU	i_Start_position_hg18	i_TumorRefReads_WU	i_TumorVAF_WU	i_TumorVarReads_WU	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_reference	i_refseq_mrna_id	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_type	i_ucsc_cons	i_variant
DAG1	1605	genome.wustl.edu	37	3	49568345	49568345	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2841-03B-01W-0728-08	TCGA-AB-2841-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	a101f87f-d1fb-492c-88bb-715de3a865ad	404c79b4-f058-43dd-b1ff-581907da8da9	g.chr3:49568345G>A	ENST00000539901.1	+	3	959	c.401G>A	c.(400-402)aGc>aAc	p.S134N	DAG1_ENST00000308775.2_Missense_Mutation_p.S134N|DAG1_ENST00000545947.1_Missense_Mutation_p.S134N|DAG1_ENST00000515359.2_Missense_Mutation_p.S134N|DAG1_ENST00000538711.1_Missense_Mutation_p.S134N|DAG1_ENST00000541308.1_Missense_Mutation_p.S134N	NM_001177644.2	NP_001171115	Q14118	DAG1_HUMAN	dystroglycan 1 (dystrophin-associated glycoprotein 1)	134	Required for laminin recognition.				basement membrane organization (GO:0071711)|branching involved in salivary gland morphogenesis (GO:0060445)|calcium-dependent cell-matrix adhesion (GO:0016340)|commissural neuron axon guidance (GO:0071679)|cytoskeletal anchoring at plasma membrane (GO:0007016)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|extracellular matrix organization (GO:0030198)|membrane protein ectodomain proteolysis (GO:0006509)|microtubule anchoring (GO:0034453)|modulation by virus of host morphology or physiology (GO:0019048)|morphogenesis of an epithelial sheet (GO:0002011)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cell migration (GO:0030336)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase B signaling (GO:0051898)|nerve maturation (GO:0021682)|NLS-bearing protein import into nucleus (GO:0006607)|response to peptide hormone (GO:0043434)	basement membrane (GO:0005604)|basolateral plasma membrane (GO:0016323)|cell outer membrane (GO:0009279)|cell-cell adherens junction (GO:0005913)|contractile ring (GO:0070938)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystroglycan complex (GO:0016011)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|membrane raft (GO:0045121)|node of Ranvier (GO:0033268)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|alpha-actinin binding (GO:0051393)|calcium ion binding (GO:0005509)|laminin-1 binding (GO:0043237)|SH2 domain binding (GO:0042169)|structural constituent of muscle (GO:0008307)|tubulin binding (GO:0015631)|vinculin binding (GO:0017166)|virus receptor activity (GO:0001618)			NS(1)|autonomic_ganglia(2)|breast(2)|endometrium(1)|large_intestine(8)|lung(5)|ovary(2)|prostate(1)|skin(1)	23				BRCA - Breast invasive adenocarcinoma(193;5.13e-05)|Kidney(197;0.00241)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)		ATTTCAGTGAGCGCTACACGG	0.592																																						dbGAP											0			3											51.0	45.0	47.0					3																	49568345		2203	4300	6503	49543349	SO:0001583	missense	0			L19711	CCDS2799.1	3p21	2014-09-17			ENSG00000173402	ENSG00000173402			2666	protein-coding gene	gene with protein product	"""alpha-dystroglycan"", ""dystrophin-associated glycoprotein-1"", ""beta-dystroglycan"""	128239				7774920, 1741056	Standard	NM_001177643		Approved	A3a, 156DAG, AGRNR, DAG	uc021wyd.1	Q14118	OTTHUMG00000156869	ENST00000539901.1:c.401G>A	3.37:g.49568345G>A	ENSP00000439334:p.Ser134Asn	82	1.19	1		6	57.14	8	49543349	99	41.86	72	A8K6M7|Q969J9	Missense_Mutation	SNP	HMMSmart_CADG,HMMPfam_DAG1,superfamily_Cadherin,superfamily_SSF111006	p.S134N	ENST00000539901.1	37	c.401	CCDS2799.1	3	.	.	.	.	.	.	.	.	.	.	G	3.957	-0.011003	0.07727	.	.	ENSG00000173402	ENST00000515359;ENST00000308775;ENST00000545947;ENST00000541308;ENST00000539901;ENST00000538711	D;D;D;D;D;D	0.98512	-4.97;-4.97;-4.97;-4.97;-4.97;-4.97	5.92	3.9	0.45041	Dystroglycan-type cadherin-like (1);Cadherin-like (1);Immunoglobulin-like fold (1);	0.293572	0.43747	N	0.000527	D	0.92090	0.7493	N	0.12182	0.205	0.31963	N	0.608211	B	0.18166	0.026	B	0.04013	0.001	D	0.86960	0.2091	9	.	.	.	-10.7005	3.3039	0.06993	0.2771:0.2177:0.5051:0.0	.	134	Q14118	DAG1_HUMAN	N	134	ENSP00000440705:S134N;ENSP00000312435:S134N;ENSP00000442600:S134N;ENSP00000440590:S134N;ENSP00000439334:S134N;ENSP00000438421:S134N	.	S	+	2	0	DAG1	49543349	0.815000	0.29118	0.945000	0.38365	0.252000	0.25951	1.397000	0.34543	1.502000	0.48669	0.655000	0.94253	AGC	-	HMMSmart_CADG,HMMPfam_DAG1,superfamily_Cadherin		0.592	DAG1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	DAG1	protein_coding	OTTHUMT00000346326.1	G			49543349	+1	no_errors	NM_004393.2	genbank	human	reviewed	54_36p	missense	SNP	0.264	A
C3orf56	285311	genome.wustl.edu	37	3	126915795	126915795	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2841-03B-01W-0728-08	TCGA-AB-2841-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	a101f87f-d1fb-492c-88bb-715de3a865ad	404c79b4-f058-43dd-b1ff-581907da8da9	g.chr3:126915795G>A	ENST00000398112.1	+	2	507	c.267G>A	c.(265-267)atG>atA	p.M89I		NM_001007534.2	NP_001007535.1	Q8N813	CC056_HUMAN	chromosome 3 open reading frame 56	89										breast(1)|endometrium(2)|kidney(1)|lung(5)	9				GBM - Glioblastoma multiforme(114;0.142)		ATCTCTGGATGGGTTATCCCC	0.582																																						dbGAP											0			3											61.0	67.0	65.0					3																	126915795		1923	4135	6058	128398485	SO:0001583	missense	0			AK097460	CCDS63757.1	3q21.3	2012-08-08			ENSG00000214324	ENSG00000214324			32481	protein-coding gene	gene with protein product						14702039	Standard	NM_001007534		Approved	FLJ40141	uc003eji.1	Q8N813	OTTHUMG00000159593	ENST00000398112.1:c.267G>A	3.37:g.126915795G>A	ENSP00000381182:p.Met89Ile	33	0.00	0		NA	NA	NA	128398485	77	39.85	53	B2RNW5	Missense_Mutation	SNP	NULL	p.M89I	ENST00000398112.1	37	c.267		3	.	.	.	.	.	.	.	.	.	.	G	3.675	-0.066658	0.07273	.	.	ENSG00000214324	ENST00000398112	.	.	.	2.27	-4.54	0.03452	.	.	.	.	.	T	0.24005	0.0581	.	.	.	0.09310	N	1	B	0.10296	0.003	B	0.10450	0.005	T	0.24584	-1.0156	7	0.87932	D	0	.	0.19	0.00133	0.3475:0.1492:0.2024:0.3009	.	89	Q8N813	CC056_HUMAN	I	89	.	ENSP00000381182:M89I	M	+	3	0	C3orf56	128398485	0.000000	0.05858	0.000000	0.03702	0.096000	0.18686	-0.617000	0.05584	-1.854000	0.01163	-0.302000	0.09304	ATG	-	NULL		0.582	C3orf56-001	KNOWN	basic|appris_principal	protein_coding	C3orf56	protein_coding	OTTHUMT00000356354.1	G			128398485	+1	no_errors	ENST00000398112	ensembl	human	known	54_36p	missense	SNP	0.000	A
TBC1D2	55357	genome.wustl.edu	37	9	100971322	100971322	+	Missense_Mutation	SNP	A	A	C			TCGA-AB-2841-03B-01W-0728-08	TCGA-AB-2841-11B-01W-0729-08	A	A	A	C	A	A	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	a101f87f-d1fb-492c-88bb-715de3a865ad	404c79b4-f058-43dd-b1ff-581907da8da9	g.chr9:100971322A>C	ENST00000375064.1	-	9	1816	c.1778T>G	c.(1777-1779)cTg>cGg	p.L593R	TBC1D2_ENST00000375066.5_Missense_Mutation_p.L593R|TBC1D2_ENST00000375063.1_Missense_Mutation_p.L133R|TBC1D2_ENST00000342112.5_Missense_Mutation_p.L375R|TBC1D2_ENST00000493589.2_5'UTR	NM_001267571.1	NP_001254500.1	Q9BYX2	TBD2A_HUMAN	TBC1 domain family, member 2	593					positive regulation of Rab GTPase activity (GO:0032851)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)	cadherin binding (GO:0045296)|Rab GTPase activator activity (GO:0005097)			breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	24		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.55e-37)		CTCGAGGCCCAGCAGGTGGTG	0.627																																						dbGAP											0			9											137.0	145.0	143.0					9																	100971322		2203	4299	6502	100011143	SO:0001583	missense	0			AY026527	CCDS35080.1, CCDS59137.1, CCDS75865.1	9q22.32	2011-11-30			ENSG00000095383	ENSG00000095383			18026	protein-coding gene	gene with protein product	"""prostate antigen recognized and identified by SEREX"""	609871					Standard	NM_018421		Approved	PARIS1, TBC1D2A, Armus	uc011lvb.2	Q9BYX2	OTTHUMG00000020343	ENST00000375064.1:c.1778T>G	9.37:g.100971322A>C	ENSP00000364205:p.Leu593Arg	49	0.00	0		6	76.67	23	100011143	65	45.83	55	B3KWD1|B4DQ05|B9A6J7|Q59EU0|Q5TBQ5|Q6IPC7|Q7L1K8|Q8WYT1|Q9H6A2|Q9NSH4	Missense_Mutation	SNP	HMMPfam_TBC,HMMSmart_TBC,superfamily_RabGAP_TBC,HMMPfam_PH,HMMSmart_PH,superfamily_SSF50729	p.L593R	ENST00000375064.1	37	c.1778		9	.	.	.	.	.	.	.	.	.	.	A	15.21	2.766174	0.49574	.	.	ENSG00000095383	ENST00000375064;ENST00000375066;ENST00000342112;ENST00000375063	T;T;T;T	0.09538	3.27;2.97;3.39;3.03	5.71	5.71	0.89125	.	0.155218	0.44688	D	0.000436	T	0.13114	0.0318	L	0.42245	1.32	0.80722	D	1	P;P	0.41313	0.745;0.54	B;B	0.41666	0.199;0.363	T	0.04413	-1.0953	10	0.33940	T	0.23	.	14.9602	0.71151	1.0:0.0:0.0:0.0	.	593;593	Q9BYX2;Q9BYX2-2	TBD2A_HUMAN;.	R	593;593;375;133	ENSP00000364205:L593R;ENSP00000364207:L593R;ENSP00000341567:L375R;ENSP00000364203:L133R	ENSP00000341567:L375R	L	-	2	0	TBC1D2	100011143	1.000000	0.71417	1.000000	0.80357	0.857000	0.48899	2.646000	0.46630	2.187000	0.69744	0.459000	0.35465	CTG	-	NULL		0.627	TBC1D2-001	KNOWN	basic|appris_principal	protein_coding	TBC1D2	protein_coding	OTTHUMT00000053366.1	A	NM_018421		100011143	-1	no_errors	NM_018421.3	genbank	human	validated	54_36p	missense	SNP	1.000	C
SYT15	83849	genome.wustl.edu	37	10	46968665	46968665	+	Silent	SNP	G	G	A	rs200814731	byFrequency	TCGA-AB-2841-03B-01W-0728-08	TCGA-AB-2841-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	a101f87f-d1fb-492c-88bb-715de3a865ad	404c79b4-f058-43dd-b1ff-581907da8da9	g.chr10:46968665G>A	ENST00000374321.4	-	3	337	c.271C>T	c.(271-273)Ctg>Ttg	p.L91L	RP11-38L15.3_ENST00000506914.1_RNA|SYT15_ENST00000374323.4_Silent_p.L144L|SYT15_ENST00000374325.3_Silent_p.L91L|SYT15_ENST00000503753.1_Silent_p.L91L	NM_031912.4	NP_114118.2	Q9BQS2	SYT15_HUMAN	synaptotagmin XV	91						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				cervix(1)|endometrium(5)|kidney(2)|lung(5)	13						CCACTGTGCAGGGGCACCCAA	0.632													G|||	469	0.0936502	0.1051	0.0764	5008	,	,		35813	0.0496		0.1282	False		,,,				2504	0.1002				Ovarian(57;1152 1428 19651 37745)	dbGAP											0			10						G	,	277,3977		0,277,1850	55.0	65.0	62.0		271,271	2.7	0.2	10	dbSNP_132	62	613,7885		0,613,3636	no	coding-synonymous,coding-synonymous	SYT15	NM_031912.4,NM_181519.2	,	0,890,5486	AA,AG,GG		7.2135,6.5115,6.9793	,	91/422,91/391	46968665	890,11862	2127	4249	6376	46388671	SO:0001819	synonymous_variant	0			AJ303363	CCDS73103.1, CCDS73104.1	10q11.1	2013-01-21			ENSG00000204176	ENSG00000204176		"""Synaptotagmins"""	17167	protein-coding gene	gene with protein product		608081				11543631	Standard	NM_031912		Approved	CHR10SYT	uc001jea.3	Q9BQS2	OTTHUMG00000018103	ENST00000374321.4:c.271C>T	10.37:g.46968665G>A		209	4.55	10		0	0.00	0	46388671	130	24.00	42	A5D6W8|Q5VY53|Q5VY55|Q7Z439|Q7Z440	Silent	SNP	HMMPfam_C2,HMMSmart_SM00239,superfamily_C2 domain (Calcium/lipid-binding domain CaLB),PatternScan_CNMP_BINDING_1	p.L91	ENST00000374321.4	37	c.271	CCDS44376.1	10																																																																																			-	NULL		0.632	SYT15-004	KNOWN	basic|appris_principal|CCDS	protein_coding	SYT15	protein_coding	OTTHUMT00000367008.1	G	NM_031912		46388671	-1	no_errors	NM_031912.3	genbank	human	reviewed	54_36p	silent	SNP	0.005	A
KRT79	338785	genome.wustl.edu	37	12	53217985	53217985	+	Silent	SNP	G	G	A			TCGA-AB-2841-03B-01W-0728-08	TCGA-AB-2841-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	a101f87f-d1fb-492c-88bb-715de3a865ad	404c79b4-f058-43dd-b1ff-581907da8da9	g.chr12:53217985G>A	ENST00000330553.5	-	5	1051	c.1017C>T	c.(1015-1017)acC>acT	p.T339T		NM_175834.2	NP_787028.1	Q5XKE5	K2C79_HUMAN	keratin 79	339	Coil 2.|Rod.					extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	enzyme binding (GO:0019899)|structural molecule activity (GO:0005198)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						CTCTCACCTTGGTCTGGTACC	0.642																																						dbGAP											0			12											82.0	82.0	82.0					12																	53217985		2203	4300	6503	51504252	SO:0001819	synonymous_variant	0			AJ564105	CCDS8839.1	12q13.13	2014-02-12	2007-07-03		ENSG00000185640	ENSG00000185640		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28930	protein-coding gene	gene with protein product	"""keratin 6-like"""	611160				11683385	Standard	NM_175834		Approved	K6L, KRT6L	uc001sbb.3	Q5XKE5	OTTHUMG00000169878	ENST00000330553.5:c.1017C>T	12.37:g.53217985G>A		88	0.00	0		NA	NA	NA	51504252	72	47.83	66	Q6P465|Q7Z793	Silent	SNP	superfamily_Prefoldin,HMMPfam_Filament,PatternScan_IF	p.T339	ENST00000330553.5	37	c.1017	CCDS8839.1	12																																																																																			-	superfamily_Prefoldin,HMMPfam_Filament		0.642	KRT79-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KRT79	protein_coding	OTTHUMT00000406376.1	G	NM_175834		51504252	-1	no_errors	NM_175834.2	genbank	human	validated	54_36p	silent	SNP	0.988	A
BAGE2	85319	genome.wustl.edu	37	21	11098733	11098733	+	RNA	SNP	G	G	A			TCGA-AB-2841-03B-01W-0728-08	TCGA-AB-2841-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	a101f87f-d1fb-492c-88bb-715de3a865ad	404c79b4-f058-43dd-b1ff-581907da8da9	g.chr21:11098733G>A	ENST00000470054.1	-	0	192							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2							extracellular region (GO:0005576)								Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		tgctccggccgccatcttact	0.632																																						dbGAP											0			21											104.0	151.0	135.0					21																	11098733		2124	4261	6385	10120604			0			AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172			15723	protein-coding gene	gene with protein product	"""cancer/testis antigen family 2, member 2"""					12461691	Standard	NM_182482		Approved	CT2.2		Q86Y30	OTTHUMG00000074128		21.37:g.11098733G>A		76	0.00	0		NA	NA	NA	10120604	56	19.44	14	A8K925|Q08ER0	Missense_Mutation	SNP	HMMPfam_BAGE	p.A2V	ENST00000470054.1	37	c.5		21																																																																																			-	HMMPfam_BAGE		0.632	BAGE2-001	KNOWN	basic	processed_transcript	BAGE4	pseudogene	OTTHUMT00000157417.3	G	NM_182482		10120604	-1	no_errors	NM_181704.1	genbank	human	provisional	54_36p	missense	SNP	0.000	A
ICA1L	130026	genome.wustl.edu	37	2	203705825	203705827	+	Intron	DEL	GCT	GCT	-			TCGA-AB-2841-03B-01W-0728-08	TCGA-AB-2841-11B-01W-0729-08	GCT	GCT	GCT	-	GCT	GCT	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	a101f87f-d1fb-492c-88bb-715de3a865ad	404c79b4-f058-43dd-b1ff-581907da8da9	g.chr2:203705825_203705827delGCT	ENST00000392237.2	-	3	151				ICA1L_ENST00000358299.2_Intron|ICA1L_ENST00000418208.1_Intron	NM_138468.4	NP_612477.3	Q8NDH6	ICA1L_HUMAN	islet cell autoantigen 1,69kDa-like											breast(1)|endometrium(1)|large_intestine(7)|lung(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						TCTTCATACAGCTGCCCGAGGAG	0.502																																						dbGAP											0			2																																								203414072	SO:0001627	intron_variant	0			AB053317	CCDS2354.1, CCDS74632.1	2q33	2008-02-05	2006-05-26	2006-05-26	ENSG00000163596	ENSG00000163596			14442	protein-coding gene	gene with protein product			"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 15"", ""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 14"""	ALS2CR15, ALS2CR14		11586298	Standard	NM_138468		Approved		uc002uzh.1	Q8NDH6	OTTHUMG00000132856	ENST00000392237.2:c.7-12086AGC>-	2.37:g.203705825_203705827delGCT		0	0.00	0		0	0.00	0	203414070	0	34.07	62	B3KRW6|Q53P45|Q53QZ4|Q53T97|Q96N47|Q96Q32|Q9BVQ2	RNA	DEL	-	NULL	ENST00000392237.2	37	NULL	CCDS2354.1	2																																																																																			-	-		0.502	ICA1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KRT8P15	protein_coding	OTTHUMT00000256330.1	GCT	NM_138468		203414072	-1	pseudogene	XR_016994.2	genbank	human	model	54_36p	rna	DEL	1.000:0.999:0.999	-
