#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_ ensembl_gene_id	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_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GMAF	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_dbSNP	i_default_gene_name	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_name_source	i_gene_type	i_havana_transcript	i_n_alt_count	i_n_alt_count_full	i_n_alt_count_val	i_n_ref_count	i_n_ref_count_full	i_n_ref_count_val	i_normal_vaf	i_normal_vaf_val	i_reference	i_refseq_mrna_id	i_secondary_variant_classification	i_stop	i_strand	i_t_alt_count_full	i_t_alt_count_val	i_t_ref_count_full	i_t_ref_count_val	i_tier	i_transcript_error	i_transcript_name	i_transcript_source	i_transcript_species	i_transcript_status	i_transcript_version	i_trv_type	i_tumor_vaf	i_tumor_vaf_val	i_type	i_ucsc_cons	i_variant	t_alt_count	t_ref_count
CNTLN	54875	genome.wustl.edu	37	9	17394809	17394809	+	Missense_Mutation	SNP	A	A	T			TCGA-DX-AB3C-01A-11D-A417-09	TCGA-DX-AB3C-10A-01D-A41A-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	7764d76b-a6eb-45bc-b804-abb1baebbbf4	4f3fe851-ad44-4399-88d5-eb4247f4e04b	g.chr9:17394809A>T	ENST00000380647.3	+	15	2441	c.2357A>T	c.(2356-2358)aAt>aTt	p.N786I	CNTLN_ENST00000262360.5_Missense_Mutation_p.N786I|CNTLN_ENST00000425824.1_Missense_Mutation_p.N786I			Q9NXG0	CNTLN_HUMAN	centlein, centrosomal protein	786					centriole-centriole cohesion (GO:0010457)|protein localization to organelle (GO:0033365)	centriole (GO:0005814)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)|protein binding, bridging (GO:0030674)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(6)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53				GBM - Glioblastoma multiforme(50;6.14e-10)		GCATTGAGAAATGAAAATGAA	0.423													ENSG00000044459																																					0													87.0	88.0	88.0					9																	17394809		1963	4172	6135	SO:0001583	missense	0			-	AK000283	CCDS43789.1, CCDS47953.1	9p22.2-p22.1	2008-11-11	2008-02-08	2008-02-08	ENSG00000044459	ENSG00000044459			23432	protein-coding gene	gene with protein product		611870	"""chromosome 9 open reading frame 101"", ""chromosome 9 open reading frame 39"""	C9orf101, C9orf39		18086554	Standard	XM_005251492		Approved	FLJ20276, bA340N12.1, OTTHUMG00000019597	uc003zmy.3	Q9NXG0	OTTHUMG00000019599	ENST00000380647.3:c.2357A>T	9.37:g.17394809A>T	ENSP00000370021:p.Asn786Ile		A5Z2X6|Q5VYJ0|Q8N1G9|Q9HAJ5	Missense_Mutation	SNP	superfamily_Prefoldin	p.N786I	ENST00000380647.3	37	c.2357	CCDS43789.1	9	.	.	.	.	.	.	.	.	.	.	A	14.64	2.596227	0.46318	.	.	ENSG00000044459	ENST00000380647;ENST00000425824;ENST00000262360	T;T;T	0.18657	2.2;2.2;2.47	5.26	4.08	0.47627	.	.	.	.	.	T	0.28234	0.0697	L	0.51422	1.61	0.25367	N	0.988735	D;P;P	0.54964	0.969;0.899;0.899	P;P;P	0.51016	0.656;0.568;0.568	T	0.08534	-1.0717	9	0.66056	D	0.02	.	8.6695	0.34140	0.8467:0.0:0.1533:0.0	.	786;786;786	Q9NXG0;C9J1F9;Q9NXG0-2	CNTLN_HUMAN;.;.	I	786	ENSP00000370021:N786I;ENSP00000392798:N786I;ENSP00000262360:N786I	ENSP00000262360:N786I	N	+	2	0	CNTLN	17384809	0.999000	0.42202	1.000000	0.80357	0.993000	0.82548	2.145000	0.42207	0.891000	0.36235	0.528000	0.53228	AAT	-	CNTLN	-	NULL		0.423	CNTLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	CNTLN	HGNC	protein_coding	OTTHUMT00000051793.3	0	0	1	40	40	82	0.00	1.20	A	NM_017738		17394809	+1	11	25	18	48	tier1	no_errors	ENST00000380647	ensembl	human	known	74_37	missense	37.93	34.25	SNP	0.998	T	11	18
KIF27	55582	genome.wustl.edu	37	9	86518547	86518547	+	Missense_Mutation	SNP	C	C	T			TCGA-DX-AB3C-01A-11D-A417-09	TCGA-DX-AB3C-10A-01D-A41A-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	7764d76b-a6eb-45bc-b804-abb1baebbbf4	4f3fe851-ad44-4399-88d5-eb4247f4e04b	g.chr9:86518547C>T	ENST00000297814.2	-	4	1029	c.886G>A	c.(886-888)Gct>Act	p.A296T	KIF27_ENST00000413982.1_Missense_Mutation_p.A296T|KIF27_ENST00000334204.2_Missense_Mutation_p.A296T	NM_017576.1	NP_060046.1	Q86VH2	KIF27_HUMAN	kinesin family member 27	296	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|cilium assembly (GO:0042384)|epithelial cilium movement (GO:0003351)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(7)|lung(17)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	43						GTAATTTTAGCATCCCTATAT	0.448													ENSG00000165115																																					0													69.0	74.0	72.0					9																	86518547		2203	4300	6503	SO:0001583	missense	0			-	AY237536	CCDS6665.1, CCDS65071.1, CCDS65072.1	9q21.32	2008-03-03			ENSG00000165115	ENSG00000165115		"""Kinesins"""	18632	protein-coding gene	gene with protein product		611253					Standard	NM_017576		Approved	DKFZp434D0917	uc004ana.4	Q86VH2	OTTHUMG00000020109	ENST00000297814.2:c.886G>A	9.37:g.86518547C>T	ENSP00000297814:p.Ala296Thr		B2RTR8|Q5T6W0|Q86VH0|Q86VH1|Q9UF54	Missense_Mutation	SNP	pfam_Kinesin_motor_dom,superfamily_P-loop_NTPase,smart_Kinesin_motor_dom,pfscan_Kinesin_motor_dom,prints_Kinesin_motor_dom	p.A296T	ENST00000297814.2	37	c.886	CCDS6665.1	9	.	.	.	.	.	.	.	.	.	.	C	21.2	4.118946	0.77323	.	.	ENSG00000165115	ENST00000297814;ENST00000413982;ENST00000334204	T;T;T	0.74947	-0.89;-0.89;-0.89	5.66	3.72	0.42706	Kinesin, motor domain (4);	0.101606	0.41712	N	0.000838	T	0.62221	0.2410	N	0.03608	-0.345	0.44668	D	0.997654	P;P;P	0.46859	0.513;0.885;0.815	B;P;P	0.53266	0.147;0.61;0.722	T	0.69465	-0.5138	10	0.87932	D	0	.	10.1375	0.42715	0.1368:0.7926:0.0:0.0707	.	296;296;296	Q86VH2-3;Q86VH2-2;Q86VH2	.;.;KIF27_HUMAN	T	296	ENSP00000297814:A296T;ENSP00000401688:A296T;ENSP00000333928:A296T	ENSP00000297814:A296T	A	-	1	0	KIF27	85708367	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.914000	0.39966	1.387000	0.46486	0.655000	0.94253	GCT	-	KIF27	-	pfam_Kinesin_motor_dom,superfamily_P-loop_NTPase,smart_Kinesin_motor_dom,prints_Kinesin_motor_dom		0.448	KIF27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KIF27	HGNC	protein_coding	OTTHUMT00000052861.1	0	0	0	35	35	79	0.00	0.00	C	NM_017576		86518547	-1	14	32	15	40	tier1	no_errors	ENST00000297814	ensembl	human	known	74_37	missense	48.28	44.44	SNP	1.000	T	14	15
VAV2	7410	genome.wustl.edu	37	9	136726433	136726433	+	Intron	SNP	G	G	T			TCGA-DX-AB3C-01A-11D-A417-09	TCGA-DX-AB3C-10A-01D-A41A-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	7764d76b-a6eb-45bc-b804-abb1baebbbf4	4f3fe851-ad44-4399-88d5-eb4247f4e04b	g.chr9:136726433G>T	ENST00000371850.3	-	3	412				VAV2_ENST00000486113.1_5'UTR|VAV2_ENST00000371851.1_Intron|VAV2_ENST00000406606.3_Intron	NM_001134398.1	NP_001127870.1	P52735	VAV2_HUMAN	vav 2 guanine nucleotide exchange factor						angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(3)|endometrium(1)|kidney(3)|large_intestine(5)|lung(13)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(1)	35				OV - Ovarian serous cystadenocarcinoma(145;3.9e-07)|Epithelial(140;2.07e-06)|all cancers(34;9.39e-06)		TCTGTGACAAGGCACGCTGGT	0.582													ENSG00000160293																																					0													84.0	86.0	85.0					9																	136726433		692	1591	2283	SO:0001627	intron_variant	0			-		CCDS6979.1, CCDS48053.1	9q34.1	2013-02-14	2007-07-25		ENSG00000160293	ENSG00000160293		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	12658	protein-coding gene	gene with protein product		600428	"""vav 2 oncogene"""			7762982	Standard	NM_003371		Approved		uc004ces.3	P52735	OTTHUMG00000020882	ENST00000371850.3:c.380+62C>A	9.37:g.136726433G>T			A2RUM4|A8MQ12|B6ZDF5|Q5SYV3|Q5SYV4|Q5SYV5|Q6N012|Q6PIJ9|Q6Q317	R	SNP	-	NULL	ENST00000371850.3	37	NULL	CCDS48053.1	9																																																																																			-	VAV2	-	-		0.582	VAV2-001	KNOWN	basic|CCDS	protein_coding	VAV2	HGNC	protein_coding	OTTHUMT00000054939.1	0	0	0	44	44	67	0.00	0.00	G			136726433	-1	5	6	33	77	tier1	no_errors	ENST00000486113	ensembl	human	known	74_37	rna	13.16	7.23	SNP	0.021	T	5	33
MEG3	55384	genome.wustl.edu	37	14	101301191	101301191	+	RNA	SNP	G	G	C	rs544144032	byFrequency	TCGA-DX-AB3C-01A-11D-A417-09	TCGA-DX-AB3C-10A-01D-A41A-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	7764d76b-a6eb-45bc-b804-abb1baebbbf4	4f3fe851-ad44-4399-88d5-eb4247f4e04b	g.chr14:101301191G>C	ENST00000554041.1	-	0	143																											TTTTTGAGAGGTGTGTGAGCA	0.577													ENSG00000214548																																					0																																												0			-																													14.37:g.101301191G>C				R	SNP	-	NULL	ENST00000554041.1	37	NULL		14																																																																																			-	MEG3	-	-		0.577	RP11-123M6.2-001	KNOWN	basic	antisense	MEG3	HGNC	antisense	OTTHUMT00000414687.1	0	0	0	15	15	110	0.00	0.00	G			101301191	+1	8	6	5	65	tier1	no_errors	ENST00000398461	ensembl	human	known	74_37	rna	61.54	8.45	SNP	0.002	C	8	5
TBC1D3P3	653017	genome.wustl.edu	37	17	20451533	20451533	+	lincRNA	SNP	G	G	T			TCGA-DX-AB3C-01A-11D-A417-09	TCGA-DX-AB3C-10A-01D-A41A-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	7764d76b-a6eb-45bc-b804-abb1baebbbf4	4f3fe851-ad44-4399-88d5-eb4247f4e04b	g.chr17:20451533G>T	ENST00000591705.1	+	0	2850																											AGTATTTTTTGGGGTGTTTTG	0.532													ENSG00000267075																																					0																																												0			-																													17.37:g.20451533G>T				R	SNP	-	NULL	ENST00000591705.1	37	NULL		17																																																																																			-	RP11-434D2.3	-	-		0.532	RP11-434D2.3-001	KNOWN	basic	lincRNA	ENSG00000267075	Clone_based_vega_gene	lincRNA	OTTHUMT00000441761.2	0	0	1	32	32	37	0.00	2.63	G			20451533	+1	18	17	18	26	tier1	no_errors	ENST00000591705	ensembl	human	known	74_37	rna	50.00	39.53	SNP	0.947	T	18	18
ABL1	25	genome.wustl.edu	37	9	133738153	133738156	+	Frame_Shift_Del	DEL	TACG	TACG	-			TCGA-DX-AB3C-01A-11D-A417-09	TCGA-DX-AB3C-10A-01D-A41A-09	TACG	TACG	TACG	-	TACG	TACG	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	7764d76b-a6eb-45bc-b804-abb1baebbbf4	4f3fe851-ad44-4399-88d5-eb4247f4e04b	g.chr9:133738153_133738156delTACG	ENST00000318560.5	+	4	934_937	c.553_556delTACG	c.(553-558)tacgtcfs	p.YV185fs		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	185	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				actin cytoskeleton organization (GO:0030036)|autophagy (GO:0006914)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to dopamine (GO:1903351)|cellular response to oxidative stress (GO:0034599)|DNA damage induced protein phosphorylation (GO:0006975)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mismatch repair (GO:0006298)|mitochondrial depolarization (GO:0051882)|mitotic nuclear division (GO:0007067)|muscle cell differentiation (GO:0042692)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|regulation of response to DNA damage stimulus (GO:2001020)|regulation of transcription, DNA-templated (GO:0006355)|response to oxidative stress (GO:0006979)|signal transduction in response to DNA damage (GO:0042770)	actin cytoskeleton (GO:0015629)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|mitogen-activated protein kinase binding (GO:0051019)|nicotinate-nucleotide adenylyltransferase activity (GO:0004515)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|proline-rich region binding (GO:0070064)|protein C-terminus binding (GO:0008022)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|SH3 domain binding (GO:0017124)|syntaxin binding (GO:0019905)	p.V186I(2)		breast(3)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1149)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	1195		all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.4e-05)	Adenosine triphosphate(DB00171)|Bosutinib(DB06616)|Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Ponatinib(DB08901)|Regorafenib(DB08896)	CCTTCAGCTCTACGTCTCCTCCGA	0.554			"""T, Mis"""	"""BCR, ETV6, NUP214"""	"""CML, ALL, T-ALL"""								ENSG00000097007																												Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	2	Substitution - Missense(2)	endometrium(2)																																								SO:0001589	frameshift_variant	0				M14752	CCDS35165.1, CCDS35166.1	9q34.1	2014-09-17	2014-06-26		ENSG00000097007	ENSG00000097007		"""SH2 domain containing"""	76	protein-coding gene	gene with protein product		189980	"""v-abl Abelson murine leukemia viral oncogene homolog 1"", ""c-abl oncogene 1, receptor tyrosine kinase"", ""c-abl oncogene 1, non-receptor tyrosine kinase"""	ABL		1857987, 12626632	Standard	NM_007313		Approved	JTK7, c-ABL, p150	uc004bzv.3	P00519	OTTHUMG00000020813	ENST00000318560.5:c.553_556delTACG	9.37:g.133738153_133738156delTACG	ENSP00000323315:p.Tyr185fs		A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Frame_Shift_Del	DEL	pfam_F-actin_binding,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Prot_kinase_dom,pfam_SH2,pfam_SH3_domain,pfam_SH3_2,superfamily_Kinase-like_dom,superfamily_SH3_domain,smart_SH3_domain,smart_SH2,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,smart_F-actin_binding,pfscan_SH2,pfscan_SH3_domain,pfscan_Prot_kinase_dom,prints_Ser-Thr/Tyr_kinase_cat_dom,prints_SH2	p.Y204fs	ENST00000318560.5	37	c.610_613	CCDS35166.1	9																																																																																				ABL1	-	pfam_SH2,smart_SH2,pfscan_SH2		0.554	ABL1-001	KNOWN	basic|CCDS	protein_coding	ABL1	HGNC	protein_coding	OTTHUMT00000054684.1	0	0	1	22	22	29	0.00	3.33	TACG	NM_007313		133738156	+1	10	29	11	29	tier1	no_errors	ENST00000372348	ensembl	human	known	74_37	frame_shift_del	47.62	50.00	DEL	1.000:1.000:1.000:1.000	-	10	11
MT-ND5	4540	genome.wustl.edu	37	M	13589	13589	+	Missense_Mutation	SNP	T	T	C			TCGA-DX-AB3C-01A-11D-A417-09	TCGA-DX-AB3C-10A-01D-A41A-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	7764d76b-a6eb-45bc-b804-abb1baebbbf4	4f3fe851-ad44-4399-88d5-eb4247f4e04b	g.chrM:13589T>C	ENST00000361567.2	+	1	1253	c.1253T>C	c.(1252-1254)cTg>cCg	p.L418P	MT-CYB_ENST00000361789.2_5'Flank|MT-TL2_ENST00000387456.1_RNA|MT-TP_ENST00000387461.2_RNA|MT-TH_ENST00000387441.1_RNA|MT-TT_ENST00000387460.2_RNA|MT-TE_ENST00000387459.1_RNA|MT-TS2_ENST00000387449.1_RNA			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	418					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						CGCTACCTCCCTGACAAGCGC	0.458													ENSG00000198786																																					0																																										SO:0001583	missense	0			-			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.1253T>C	M.37:g.13589T>C	ENSP00000354813:p.Leu418Pro		Q34773|Q8WCY3	Missense_Mutation	SNP	pfam_DH_UbQ/plastoQ_OxRdtase,pfam_DH_DH_su5_C,pfam_DH_UbQ_OxRdtase_chain5/L_N,tigrfam_DHpl_OxRdtase_5	p.L418P	ENST00000361567.2	37	c.1253		MT																																																																																			-	MT-ND5	-	tigrfam_DHpl_OxRdtase_5		0.458	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	MT-ND5	HGNC	protein_coding		0	0	0	32	32	5	0.00	0.00	T	YP_003024036		13589	+1	2	0	7	0	tier1	no_errors	ENST00000361567	ensembl	human	known	74_37	missense	22.22	0.00	SNP	NULL	C	2	7
ATXN2	6311	genome.wustl.edu	37	12	112036781	112036785	+	Frame_Shift_Del	DEL	GTTGC	GTTGC	-	rs76696028		TCGA-DX-AB3C-01A-11D-A417-09	TCGA-DX-AB3C-10A-01D-A41A-09	GTTGC	GTTGC					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	7764d76b-a6eb-45bc-b804-abb1baebbbf4	4f3fe851-ad44-4399-88d5-eb4247f4e04b	g.chr12:112036781_112036785delGTTGC	ENST00000377617.3	-	1	695_699	c.534_538delGCAAC	c.(532-540)cagcaacagfs	p.QQQ178fs	ATXN2_ENST00000608853.1_Frame_Shift_Del_p.QQQ18fs|RP11-686G8.2_ENST00000547021.1_RNA|ATXN2_ENST00000389153.4_5'Flank|ATXN2_ENST00000535949.1_Intron|ATXN2_ENST00000550104.1_Frame_Shift_Del_p.QQQ178fs|ATXN2_ENST00000549455.1_5'UTR|ATXN2_ENST00000542287.2_Intron	NM_002973.3	NP_002964.3	Q99700	ATX2_HUMAN	ataxin 2	178	Poly-Gln.				cell death (GO:0008219)|cerebellar Purkinje cell differentiation (GO:0021702)|cytoplasmic mRNA processing body assembly (GO:0033962)|homeostasis of number of cells (GO:0048872)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of receptor internalization (GO:0002091)|neuromuscular process (GO:0050905)|neuron projection morphogenesis (GO:0048812)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA transport (GO:0050658)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|trans-Golgi network (GO:0005802)	epidermal growth factor receptor binding (GO:0005154)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	37						tgctgctgctgttgctgctgctgct	0.732													ENSG00000204842																																					0																																										SO:0001589	frameshift_variant	0				U80749	CCDS31902.1	12q23-q24.1	2014-09-17	2004-08-12	2004-08-13	ENSG00000204842	ENSG00000204842		"""Ataxins"""	10555	protein-coding gene	gene with protein product	"""trinucleotide repeat containing 13"""	601517	"""spinocerebellar ataxia 2 (olivopontocerebellar ataxia 2, autosomal dominant, ataxin 2)"""	SCA2, TNRC13		8358438, 9225980	Standard	NM_002973		Approved	ATX2	uc001tsj.3	Q99700	OTTHUMG00000133475	ENST00000377617.3:c.534_538delGCAAC	12.37:g.112036781_112036785delGTTGC	ENSP00000366843:p.Gln178fs		A6NLD4|Q6ZQZ7|Q99493	Frame_Shift_Del	DEL	pfam_LsmAD_domain,pfam_Ataxin-2_C,superfamily_LSM_dom	p.Q179fs	ENST00000377617.3	37	c.538_534	CCDS31902.1	12																																																																																				ATXN2	-	NULL		0.732	ATXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ATXN2	HGNC	protein_coding	OTTHUMT00000257351.3	0	0	0	0	0	0	0.00	0.00	GTTGC	NM_002973		112036785	-1	0	0	0	0	tier1	no_errors	ENST00000377617	ensembl	human	known	74_37	frame_shift_del	0.00	0.00	DEL	0.009:0.008:0.017:0.025:0.032	-	0	0
GNPTAB	79158	genome.wustl.edu	37	12	102190269	102190270	+	Intron	INS	-	-	T			TCGA-DX-AB3C-01A-11D-A417-09	TCGA-DX-AB3C-10A-01D-A41A-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	7764d76b-a6eb-45bc-b804-abb1baebbbf4	4f3fe851-ad44-4399-88d5-eb4247f4e04b	g.chr12:102190269_102190270insT	ENST00000299314.7	-	2	466				GNPTAB_ENST00000392919.4_Intron|GNPTAB_ENST00000549940.1_Intron|RNU6-172P_ENST00000411000.1_RNA	NM_024312.4	NP_077288.2	Q3T906	GNPTA_HUMAN	N-acetylglucosamine-1-phosphate transferase, alpha and beta subunits						carbohydrate phosphorylation (GO:0046835)|cell differentiation (GO:0030154)|lysosome organization (GO:0007040)|protein secretion (GO:0009306)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity (GO:0003976)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(8)|lung(8)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	37						tatcgttccagtttttttttcc	0.351													ENSG00000222932																																					0																																										SO:0001627	intron_variant	0				AY687932	CCDS9088.1	12q23.3	2013-01-10				ENSG00000111670		"""EF-hand domain containing"""	29670	protein-coding gene	gene with protein product		607840		GNPTA		10574462, 16116615	Standard	NM_024312		Approved	KIAA1208, MGC4170	uc001tit.3	Q3T906	OTTHUMG00000170444	ENST00000299314.7:c.203+184->A	12.37:g.102190278_102190278dupT			A2RRQ9|Q3ZQK2|Q6IPW5|Q86TQ2|Q96N13|Q9ULL2	R	INS	-	NULL	ENST00000299314.7	37	NULL	CCDS9088.1	12																																																																																				RNU6-172P	-	-		0.351	GNPTAB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RNU6-172P	HGNC	protein_coding	OTTHUMT00000409182.1	0	0	0	13	13	37	0.00	0.00	-			102190270	-1	3	3	7	51	tier1	no_errors	ENST00000411000	ensembl	human	known	74_37	rna	30.00	5.56	INS	0.000:0.004	T	3	7
