#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_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_Start_position_hg18	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_classification	i_context	i_dataset	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	i_type
ANGEL1	23357	hgsc.bcm.edu	37	14	77273001	77273001	+	Nonsense_Mutation	SNP	G	G	A			TCGA-24-1105-01	TCGA-24-1105-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Sanger_PCR_WGA	.	.	Illumina GAIIx	TCGA-24-1105-01	TCGA-24-1105-10	g.chr14:77273001G>A	ENST00000251089.2	-	5	1250	c.1138C>T	c.(1138-1140)Caa>Taa	p.Q380*	ANGEL1_ENST00000557179.1_5'Flank|ANGEL1_ENST00000554941.1_5'Flank	NM_015305.3	NP_056120.2	Q9UNK9	ANGE1_HUMAN	angel homolog 1 (Drosophila)	380								p.Q380*(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(2)|lung(9)|ovary(2)|skin(1)|stomach(1)|urinary_tract(1)	22			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0285)		ACCGAGACTTGTCCCAGGCCT	0.577																																																1	Substitution - Nonsense(1)	ovary(1)	14											76.0	77.0	77.0					14																	77273001		2203	4300	6503	76342754	SO:0001587	stop_gained	23357			AF111169	CCDS9852.1	14q24.3	2014-06-17		2005-08-04	ENSG00000013523	ENSG00000013523			19961	protein-coding gene	gene with protein product				KIAA0759		11943475	Standard	NM_015305		Approved	Ccr4e	uc001xsv.3	Q9UNK9	OTTHUMG00000171494	ENST00000251089.2:c.1138C>T	14.37:g.77273001G>A	ENSP00000251089:p.Gln380*	Somatic		Capture	SOLID	Phase_IV	76342754	B4DWL7|O94859|Q8NCS9	Nonsense_Mutation	SNP	ENST00000251089.2	37	CCDS9852.1	SNP	48	Baylor	.	.	.	.	.	.	.	.	.	.	G	38	6.989864	0.97987	.	.	ENSG00000013523	ENST00000251089	.	.	.	5.97	5.97	0.96955	.	0.674762	0.15332	N	0.267936	.	.	.	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	.	.	.	.	0.05833	T	0.94	-3.128	15.0204	0.71627	0.0:0.1413:0.8587:0.0	.	.	.	.	X	380	.	ENSP00000251089:Q380X	Q	-	1	0	ANGEL1	76342754	0.026000	0.19158	0.988000	0.46212	0.979000	0.70002	1.565000	0.36386	2.836000	0.97738	0.655000	0.94253	CAA		0.577	ANGEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413712.2	NM_015305		Nonsense_Mutation
CACNA1E	777	hgsc.bcm.edu	37	1	181740453	181740453	+	Missense_Mutation	SNP	G	G	A			TCGA-24-1105-01	TCGA-24-1105-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-24-1105-01	TCGA-24-1105-10	g.chr1:181740453G>A	ENST00000367573.2	+	36	4906	c.4906G>A	c.(4906-4908)Gag>Aag	p.E1636K	CACNA1E_ENST00000358338.5_Missense_Mutation_p.E1568K|CACNA1E_ENST00000367570.1_Missense_Mutation_p.E1636K|CACNA1E_ENST00000367567.4_Missense_Mutation_p.E1243K|CACNA1E_ENST00000357570.5_Missense_Mutation_p.E1587K|CACNA1E_ENST00000526775.1_Missense_Mutation_p.E1617K|RNA5SP70_ENST00000517168.1_RNA|CACNA1E_ENST00000360108.3_Missense_Mutation_p.E1617K	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	1636					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)	p.E1636K(1)		NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						AAAATTAGACGAGGAGAGTCA	0.458																																																1	Substitution - Missense(1)	ovary(1)	1											96.0	88.0	91.0					1																	181740453		1931	4124	6055	180007076	SO:0001583	missense	777			AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.4906G>A	1.37:g.181740453G>A	ENSP00000356545:p.Glu1636Lys	Somatic		Capture	SOLID	Phase_IV	180007076	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	37	CCDS55664.1	SNP	37	Baylor	.	.	.	.	.	.	.	.	.	.	G	36	5.847394	0.97023	.	.	ENSG00000198216	ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D	0.98280	-4.84;-4.84;-4.84;-4.84;-4.84;-4.84;-4.84	5.61	5.61	0.85477	Ion transport (1);	0.089852	0.85682	D	0.000000	D	0.98046	0.9356	L	0.45744	1.44	0.80722	D	1	P;D;D	0.65815	0.949;0.989;0.995	P;P;P	0.59825	0.582;0.864;0.749	D	0.97171	0.9844	10	0.24483	T	0.36	.	19.5968	0.95544	0.0:0.0:1.0:0.0	.	1617;1636;1636	Q15878-2;Q15878;Q15878-3	.;CAC1E_HUMAN;.	K	1636;1617;1587;1568;1243;1617;1636	ENSP00000356542:E1636K;ENSP00000434814:E1617K;ENSP00000350183:E1587K;ENSP00000351101:E1568K;ENSP00000356539:E1243K;ENSP00000353222:E1617K;ENSP00000356545:E1636K	ENSP00000350183:E1587K	E	+	1	0	CACNA1E	180007076	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.675000	0.98638	2.793000	0.96121	0.655000	0.94253	GAG		0.458	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		Missense_Mutation
CHD6	84181	hgsc.bcm.edu	37	20	40050566	40050566	+	Missense_Mutation	SNP	T	T	C	rs142605942		TCGA-24-1105-01	TCGA-24-1105-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-24-1105-01	TCGA-24-1105-10	g.chr20:40050566T>C	ENST00000373233.3	-	31	4886	c.4709A>G	c.(4708-4710)tAc>tGc	p.Y1570C		NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	1570					ATP catabolic process (GO:0006200)|chromatin modification (GO:0016568)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|transcription cofactor binding (GO:0001221)	p.Y1570C(1)		breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129		Myeloproliferative disorder(115;0.00425)				GACTGGGAGGTAGAGGCTGGG	0.557																																																1	Substitution - Missense(1)	ovary(1)	20											83.0	58.0	66.0					20																	40050566		2203	4300	6503	39483980	SO:0001583	missense	84181			AF525085	CCDS13317.1	20q12	2003-03-07			ENSG00000124177	ENSG00000124177			19057	protein-coding gene	gene with protein product						11889561	Standard	NM_032221		Approved	KIAA1335, FLJ22369, dJ620E11.1, CHD5, RIGB	uc002xka.1	Q8TD26	OTTHUMG00000032487	ENST00000373233.3:c.4709A>G	20.37:g.40050566T>C	ENSP00000362330:p.Tyr1570Cys	Somatic		Capture	SOLID	Phase_IV	39483980	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Missense_Mutation	SNP	ENST00000373233.3	37	CCDS13317.1	SNP	57	Baylor	.	.	.	.	.	.	.	.	.	.	T	18.10	3.547899	0.65311	.	.	ENSG00000124177	ENST00000373233	D	0.87029	-2.2	5.89	4.78	0.61160	.	0.000000	0.56097	D	0.000034	D	0.92208	0.7529	M	0.71581	2.175	0.80722	D	1	D	0.69078	0.997	D	0.71184	0.972	D	0.92525	0.6028	10	0.87932	D	0	-9.5991	13.4331	0.61068	0.0:0.0:0.1309:0.8691	.	1570	Q8TD26	CHD6_HUMAN	C	1570	ENSP00000362330:Y1570C	ENSP00000362330:Y1570C	Y	-	2	0	CHD6	39483980	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.296000	0.72751	1.057000	0.40506	0.529000	0.55759	TAC		0.557	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1			Missense_Mutation
COL12A1	1303	hgsc.bcm.edu	37	6	75855866	75855866	+	Silent	SNP	G	G	A			TCGA-24-1105-01	TCGA-24-1105-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-24-1105-01	TCGA-24-1105-10	g.chr6:75855866G>A	ENST00000322507.8	-	24	4821	c.4512C>T	c.(4510-4512)atC>atT	p.I1504I	COL12A1_ENST00000483888.2_Silent_p.I1504I|COL12A1_ENST00000416123.2_Silent_p.I1504I|COL12A1_ENST00000345356.6_Silent_p.I340I	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	1504	Fibronectin type-III 10. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)	p.I1504I(1)		breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						TGTATGACAAGATGTAGCCAG	0.463																																																1	Substitution - coding silent(1)	ovary(1)	6											98.0	98.0	98.0					6																	75855866		1965	4170	6135	75912586	SO:0001819	synonymous_variant	1303			U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"", ""Fibronectin type III domain containing"""	2188	protein-coding gene	gene with protein product	"""collagen type XII proteoglycan"""	120320	"""collagen, type XII, alpha 1-like"""	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.4512C>T	6.37:g.75855866G>A		Somatic		Capture	SOLID	Phase_IV	75912586	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Silent	SNP	ENST00000322507.8	37	CCDS43482.1	SNP	33	Baylor	.	.	.	.	.	.	.	.	.	.	G	11.20	1.569611	0.28003	.	.	ENSG00000111799	ENST00000419671	.	.	.	5.19	-2.47	0.06442	.	.	.	.	.	T	0.07548	0.0190	.	.	.	0.09310	N	0.999998	.	.	.	.	.	.	T	0.35425	-0.9789	4	.	.	.	.	3.2115	0.06684	0.5115:0.1817:0.2108:0.096	.	.	.	.	F	246	.	.	L	-	1	0	COL12A1	75912586	0.449000	0.25689	0.003000	0.11579	0.717000	0.41224	0.061000	0.14366	-0.436000	0.07254	0.655000	0.94253	CTT		0.463	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		Silent
COL12A1	1303	hgsc.bcm.edu	37	6	75855879	75855879	+	Missense_Mutation	SNP	G	G	C			TCGA-24-1105-01	TCGA-24-1105-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-24-1105-01	TCGA-24-1105-10	g.chr6:75855879G>C	ENST00000322507.8	-	24	4808	c.4499C>G	c.(4498-4500)gCt>gGt	p.A1500G	COL12A1_ENST00000483888.2_Missense_Mutation_p.A1500G|COL12A1_ENST00000416123.2_Missense_Mutation_p.A1500G|COL12A1_ENST00000345356.6_Missense_Mutation_p.A336G	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	1500	Fibronectin type-III 10. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)	p.A1500G(1)|p.A1500V(1)		breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						GTAGCCAGTAGCTCCTCCCAC	0.463																																																2	Substitution - Missense(2)	ovary(1)|large_intestine(1)	6											92.0	91.0	92.0					6																	75855879		1980	4184	6164	75912599	SO:0001583	missense	1303			U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"", ""Fibronectin type III domain containing"""	2188	protein-coding gene	gene with protein product	"""collagen type XII proteoglycan"""	120320	"""collagen, type XII, alpha 1-like"""	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.4499C>G	6.37:g.75855879G>C	ENSP00000325146:p.Ala1500Gly	Somatic		Capture	SOLID	Phase_IV	75912599	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	ENST00000322507.8	37	CCDS43482.1	SNP	34	Baylor	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	23.1|23.1	4.376213|4.376213	0.82682|0.82682	.|.	.|.	ENSG00000111799|ENSG00000111799	ENST00000322507;ENST00000432784;ENST00000345356;ENST00000416123;ENST00000483888|ENST00000419671	T;T;T;T|.	0.57595|.	0.39;0.39;0.39;0.39|.	5.08|5.08	4.2|4.2	0.49525|0.49525	Fibronectin, type III (4);Immunoglobulin-like fold (1);|.	0.082161|.	0.50627|.	D|.	0.000107|.	T|T	0.70141|0.70141	0.3190|0.3190	M|M	0.82323|0.82323	2.585|2.585	0.49798|0.49798	D|D	0.999825|0.999825	D;D|.	0.89917|.	0.999;1.0|.	D;D|.	0.75020|.	0.95;0.985|.	T|T	0.73069|0.73069	-0.4099|-0.4099	10|5	0.49607|.	T|.	0.09|.	.|.	12.9249|12.9249	0.58254|0.58254	0.0785:0.0:0.9215:0.0|0.0785:0.0:0.9215:0.0	.|.	336;1500|.	Q99715-2;Q99715|.	.;COCA1_HUMAN|.	G|R	1500;1500;336;1500;1500|241	ENSP00000325146:A1500G;ENSP00000305147:A336G;ENSP00000412864:A1500G;ENSP00000421216:A1500G|.	ENSP00000325146:A1500G|.	A|S	-|-	2|3	0|2	COL12A1|COL12A1	75912599|75912599	1.000000|1.000000	0.71417|0.71417	0.945000|0.945000	0.38365|0.38365	0.923000|0.923000	0.55619|0.55619	6.898000|6.898000	0.75676|0.75676	2.358000|2.358000	0.79984|0.79984	0.655000|0.655000	0.94253|0.94253	GCT|AGC		0.463	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		Missense_Mutation
LCLAT1	253558	hgsc.bcm.edu	37	2	30863099	30863099	+	Missense_Mutation	SNP	C	C	T			TCGA-24-1105-01	TCGA-24-1105-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA	.	.	Illumina GAIIx	TCGA-24-1105-01	TCGA-24-1105-10	g.chr2:30863099C>T	ENST00000309052.4	+	7	1068	c.859C>T	c.(859-861)Cgg>Tgg	p.R287W	LCLAT1_ENST00000379509.3_Missense_Mutation_p.R249W|LCLAT1_ENST00000540623.1_Missense_Mutation_p.R249W|LCLAT1_ENST00000491680.2_3'UTR	NM_182551.3	NP_872357.2	Q6UWP7	LCLT1_HUMAN	lysocardiolipin acyltransferase 1	287					cardiolipin acyl-chain remodeling (GO:0035965)|CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|multicellular organismal development (GO:0007275)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)	p.R287W(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)	19						TCACGTCCACCGGTATCCAAT	0.507																																																1	Substitution - Missense(1)	ovary(1)	2											96.0	92.0	93.0					2																	30863099		2203	4300	6503	30716603	SO:0001583	missense	253558			AK095284	CCDS1772.1, CCDS42670.1	2p23.1	2008-12-15	2008-12-15	2008-12-15	ENSG00000172954	ENSG00000172954			26756	protein-coding gene	gene with protein product		614241	"""lysocardiolipin acyltransferase"""	LYCAT		18931347, 15152008, 16620771, 17675553	Standard	NM_001002257		Approved	FLJ37965, ALCAT1, AGPAT8	uc002rnl.3	Q6UWP7	OTTHUMG00000099349	ENST00000309052.4:c.859C>T	2.37:g.30863099C>T	ENSP00000310551:p.Arg287Trp	Somatic		Capture	SOLID	Phase_IV	30716603	A6H8Z7|Q8N1Q7	Missense_Mutation	SNP	ENST00000309052.4	37	CCDS1772.1	SNP	23	Baylor	.	.	.	.	.	.	.	.	.	.	C	13.29	2.192263	0.38707	.	.	ENSG00000172954	ENST00000379509;ENST00000444270;ENST00000309052;ENST00000540623	T;T;T	0.41758	0.99;0.99;0.99	5.77	2.63	0.31362	.	0.098864	0.64402	D	0.000002	T	0.68430	0.3000	M	0.88241	2.94	0.53688	D	0.999974	D	0.89917	1.0	D	0.85130	0.997	T	0.76187	-0.3051	10	0.72032	D	0.01	-18.7519	14.6333	0.68671	0.5279:0.4721:0.0:0.0	.	287	Q6UWP7	LCLT1_HUMAN	W	249;249;287;249	ENSP00000368823:R249W;ENSP00000310551:R287W;ENSP00000442857:R249W	ENSP00000310551:R287W	R	+	1	2	LCLAT1	30716603	0.803000	0.28956	0.233000	0.24025	0.059000	0.15707	1.579000	0.36536	0.750000	0.32877	0.557000	0.71058	CGG		0.507	LCLAT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000216780.1	NM_182551		Missense_Mutation
MCM2	4171	hgsc.bcm.edu	37	3	127339643	127339643	+	Missense_Mutation	SNP	G	G	A	rs369079696		TCGA-24-1105-01	TCGA-24-1105-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA	.	.	Illumina GAIIx	TCGA-24-1105-01	TCGA-24-1105-10	g.chr3:127339643G>A	ENST00000265056.7	+	14	2612	c.2368G>A	c.(2368-2370)Gac>Aac	p.D790N	MCM2_ENST00000468414.1_3'UTR	NM_004526.2	NP_004517.2	P49736	MCM2_HUMAN	minichromosome maintenance complex component 2	790					cell cycle (GO:0007049)|cellular response to interleukin-4 (GO:0071353)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|nucleosome assembly (GO:0006334)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|MCM complex (GO:0042555)|microtubule cytoskeleton (GO:0015630)|nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA replication origin binding (GO:0003688)|metal ion binding (GO:0046872)	p.D790N(1)		ovary(3)|skin(2)|stomach(1)	6						GATCGAAGACGACGTCAACAT	0.597																																																1	Substitution - Missense(1)	ovary(1)	3						G	ASN/ASP	1,4405	2.1+/-5.4	0,1,2202	121.0	105.0	111.0		2368	5.7	0.8	3		111	0,8600		0,0,4300	no	missense	MCM2	NM_004526.2	23	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	790/905	127339643	1,13005	2203	4300	6503	128822333	SO:0001583	missense	4171			X67334	CCDS3043.1	3q21	2007-04-04	2007-04-04		ENSG00000073111	ENSG00000073111			6944	protein-coding gene	gene with protein product	"""mitotin"""	116945	"""minichromosome maintenance deficient (S. cerevisiae) 2 (mitotin)"", ""MCM2 minichromosome maintenance deficient 2, mitotin (S. cerevisiae)"""	CCNL1, CDCL1		1710453, 8258304	Standard	NM_004526		Approved	D3S3194, KIAA0030, BM28, cdc19	uc003ejp.4	P49736	OTTHUMG00000159637	ENST00000265056.7:c.2368G>A	3.37:g.127339643G>A	ENSP00000265056:p.Asp790Asn	Somatic		Capture	SOLID	Phase_IV	128822333	Q14577|Q15023|Q8N2V1|Q969W7|Q96AE1|Q9BRM7	Missense_Mutation	SNP	ENST00000265056.7	37	CCDS3043.1	SNP	37	Baylor	.	.	.	.	.	.	.	.	.	.	G	25.4	4.633759	0.87660	2.27E-4	0.0	ENSG00000073111	ENST00000265056;ENST00000539922;ENST00000543142	T	0.16897	2.31	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.61702	0.2368	H	0.98089	4.145	0.80722	D	1	D;D;D	0.89917	0.997;1.0;1.0	P;D;D	0.81914	0.799;0.991;0.995	T	0.76924	-0.2779	10	0.87932	D	0	-46.746	19.9	0.96981	0.0:0.0:1.0:0.0	.	840;660;790	F5H1E9;B4DSV5;P49736	.;.;MCM2_HUMAN	N	790;694;840	ENSP00000265056:D790N	ENSP00000265056:D790N	D	+	1	0	MCM2	128822333	1.000000	0.71417	0.844000	0.33320	0.172000	0.22775	9.223000	0.95203	2.698000	0.92095	0.650000	0.86243	GAC		0.597	MCM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356612.1			Missense_Mutation
MYO3A	53904	hgsc.bcm.edu	37	10	26385321	26385321	+	Missense_Mutation	SNP	A	A	G			TCGA-24-1105-01	TCGA-24-1105-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-24-1105-01	TCGA-24-1105-10	g.chr10:26385321A>G	ENST00000265944.5	+	16	1740	c.1574A>G	c.(1573-1575)aAt>aGt	p.N525S	MYO3A_ENST00000543632.1_Missense_Mutation_p.N525S	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	525	Myosin motor.		N -> K (in an ovarian mucinous carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.N525S(2)		NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						GGAGAAAAAAATTTTCATATT	0.323																																																2	Substitution - Missense(2)	ovary(2)	10											30.0	34.0	33.0					10																	26385321		2194	4287	6481	26425327	SO:0001583	missense	53904			AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"""Myosins / Myosin superfamily : Class III"""	7601	protein-coding gene	gene with protein product		606808	"""deafness, autosomal recessive 30"""	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.1574A>G	10.37:g.26385321A>G	ENSP00000265944:p.Asn525Ser	Somatic		Capture	SOLID	Phase_IV	26425327	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	37	CCDS7148.1	SNP	4	Baylor	.	.	.	.	.	.	.	.	.	.	A	19.86	3.904706	0.72868	.	.	ENSG00000095777	ENST00000265944;ENST00000543632	T;D	0.88431	-0.92;-2.38	5.48	4.33	0.51752	Myosin head, motor domain (2);	0.042713	0.85682	D	0.000000	D	0.93006	0.7774	M	0.66439	2.03	0.80722	D	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.97110	0.99;0.994;1.0	D	0.93010	0.6431	10	0.87932	D	0	.	12.136	0.53972	0.8716:0.0:0.0:0.1284	.	525;525;525	F5H0U9;Q0VD65;Q8NEV4	.;.;MYO3A_HUMAN	S	525	ENSP00000265944:N525S;ENSP00000445909:N525S	ENSP00000265944:N525S	N	+	2	0	MYO3A	26425327	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.910000	0.92685	0.993000	0.38866	0.533000	0.62120	AAT		0.323	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433		Missense_Mutation
MYOM3	127294	hgsc.bcm.edu	37	1	24433676	24433676	+	Nonsense_Mutation	SNP	G	G	A			TCGA-24-1105-01	TCGA-24-1105-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-24-1105-01	TCGA-24-1105-10	g.chr1:24433676G>A	ENST00000374434.3	-	4	451	c.289C>T	c.(289-291)Cga>Tga	p.R97*	MYOM3_ENST00000475306.1_5'UTR|MYOM3_ENST00000330966.7_Nonsense_Mutation_p.R98*|MYOM3_ENST00000329601.7_Nonsense_Mutation_p.R97*	NM_152372.3	NP_689585.3	Q5VTT5	MYOM3_HUMAN	myomesin 3	97						M band (GO:0031430)	protein homodimerization activity (GO:0042803)	p.R97*(1)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(3)|lung(40)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	68		Colorectal(325;3.55e-05)|Renal(390;0.000703)|Lung NSC(340;0.001)|all_lung(284;0.0014)|Ovarian(437;0.00351)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;5.31e-24)|Colorectal(126;7.52e-08)|COAD - Colon adenocarcinoma(152;4.01e-06)|GBM - Glioblastoma multiforme(114;4.36e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00108)|KIRC - Kidney renal clear cell carcinoma(1967;0.00404)|STAD - Stomach adenocarcinoma(196;0.00966)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.153)		TTCTGCCCTCGCTCCTCCAGC	0.677																																																1	Substitution - Nonsense(1)	ovary(1)	1											29.0	32.0	31.0					1																	24433676		1997	4179	6176	24306263	SO:0001587	stop_gained	127294			AK093280	CCDS41281.1	1p36	2013-02-11	2012-10-17		ENSG00000142661	ENSG00000142661		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	26679	protein-coding gene	gene with protein product			"""myomesin family, member 3"""			18177667	Standard	NM_152372		Approved	FLJ35961	uc001bin.4	Q5VTT5	OTTHUMG00000002969	ENST00000374434.3:c.289C>T	1.37:g.24433676G>A	ENSP00000363557:p.Arg97*	Somatic		Capture	SOLID	Phase_IV	24306263	A6NF75|Q5VTT6|Q6AWC0|Q6AWC1|Q6NXF9|Q6ZRG7|Q7Z3G9|Q8NA11|Q96C54	Nonsense_Mutation	SNP	ENST00000374434.3	37	CCDS41281.1	SNP	38	Baylor	.	.	.	.	.	.	.	.	.	.	G	38	7.119918	0.98077	.	.	ENSG00000142661	ENST00000374434;ENST00000330966;ENST00000329601	.	.	.	4.98	2.94	0.34122	.	0.173630	0.37715	N	0.001980	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.6407	0.45592	0.0:0.0:0.5494:0.4506	.	.	.	.	X	97;98;97	.	ENSP00000328415:R97X	R	-	1	2	MYOM3	24306263	0.999000	0.42202	0.996000	0.52242	0.993000	0.82548	0.948000	0.29096	1.209000	0.43321	0.561000	0.74099	CGA		0.677	MYOM3-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008272.2	NM_152372		Nonsense_Mutation
OR2T3	343173	hgsc.bcm.edu	37	1	248637193	248637194	+	Frame_Shift_Ins	INS	-	-	T			TCGA-24-1105-01	TCGA-24-1105-10	-	-	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-24-1105-01	TCGA-24-1105-10	g.chr1:248637193_248637194insT	ENST00000359594.2	+	1	567_568	c.542_543insT	c.(541-546)agttttfs	p.SF181fs		NM_001005495.1	NP_001005495.1	Q8NH03	OR2T3_HUMAN	olfactory receptor, family 2, subfamily T, member 3	181						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S181T(1)|p.C184fs*2(1)		breast(2)|endometrium(5)|lung(19)|ovary(1)|prostate(1)|skin(3)	31	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			AAAATCCTGAGTTTTTTCTGTG	0.525																																																2	Substitution - Missense(1)|Insertion - Frameshift(1)	ovary(1)|lung(1)	1																																								246703817	SO:0001589	frameshift_variant	343173				CCDS31117.1	1q44	2012-08-09			ENSG00000196539	ENSG00000196539		"""GPCR / Class A : Olfactory receptors"""	14727	protein-coding gene	gene with protein product							Standard	NM_001005495		Approved		uc001iel.1	Q8NH03	OTTHUMG00000040452	ENST00000359594.2:c.548dupT	1.37:g.248637199_248637199dupT	ENSP00000352604:p.Ser181fs	Somatic		Capture	SOLID	Phase_IV	246703816	B2RNJ1	Frame_Shift_Ins	INS	ENST00000359594.2	37	CCDS31117.1	INS	36	Baylor																																																																																				0.525	OR2T3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097348.1	NM_001005495		Frame_Shift_Ins
PDAP1	11333	hgsc.bcm.edu	37	7	99001069	99001069	+	Frame_Shift_Del	DEL	C	C	-			TCGA-24-1105-01	TCGA-24-1105-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-24-1105-01	TCGA-24-1105-10	g.chr7:99001069delC	ENST00000350498.3	-	3	445	c.165delG	c.(163-165)aagfs	p.K56fs		NM_014891.6	NP_055706.1	Q13442	HAP28_HUMAN	PDGFA associated protein 1	56					cell proliferation (GO:0008283)|signal transduction (GO:0007165)		poly(A) RNA binding (GO:0044822)	p.K56fs*3(2)		breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|ovary(2)|prostate(1)|skin(1)	9	all_cancers(62;3.49e-09)|all_epithelial(64;2.57e-10)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		STAD - Stomach adenocarcinoma(171;0.215)			CTAGAGATTTCTTCTCCTTTT	0.443																																																2	Deletion - Frameshift(2)	ovary(2)	7											187.0	160.0	169.0					7																	99001069		2203	4297	6500	98839005	SO:0001589	frameshift_variant	11333			U41745	CCDS5662.1	7q	2008-07-18			ENSG00000106244	ENSG00000106244			14634	protein-coding gene	gene with protein product	"""PDGF associated protein"""	607075				8780057	Standard	NM_014891		Approved	PAP1, PAP, HASPP28	uc003uqe.3	Q13442	OTTHUMG00000154629	ENST00000350498.3:c.165delG	7.37:g.99001069delC	ENSP00000222968:p.Lys56fs	Somatic		Capture	SOLID	Phase_IV	98839005	D6W5S5|Q92906	Frame_Shift_Del	DEL	ENST00000350498.3	37	CCDS5662.1	DEL	32	Baylor																																																																																				0.443	PDAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336388.2	NM_014891		Frame_Shift_Del
RALY	22913	hgsc.bcm.edu	37	20	32661419	32661419	+	Nonsense_Mutation	SNP	A	A	T			TCGA-24-1105-01	TCGA-24-1105-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-24-1105-01	TCGA-24-1105-10	g.chr20:32661419A>T	ENST00000246194.3	+	4	809	c.307A>T	c.(307-309)Aga>Tga	p.R103*	RALY_ENST00000493399.1_3'UTR|RALY_ENST00000375114.3_Nonsense_Mutation_p.R103*	NM_016732.2	NP_057951.1	Q9UKM9	RALY_HUMAN	RALY heterogeneous nuclear ribonucleoprotein	103					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.R103*(1)		kidney(2)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	12						GGGGCTAAAGAGAGCAGCATC	0.532																																																1	Substitution - Nonsense(1)	ovary(1)	20											185.0	154.0	164.0					20																	32661419		2203	4300	6503	32125080	SO:0001587	stop_gained	22913			AF148457	CCDS13229.1, CCDS13230.1	20q11.21-q11.23	2013-08-06	2013-08-06		ENSG00000125970	ENSG00000125970		"""RNA binding motif (RRM) containing"""	15921	protein-coding gene	gene with protein product		614663	"""RNA-binding protein (autoantigenic, hnRNP-associated with lethal yellow)"", ""RNA binding protein, autoantigenic (hnRNP-associated with lethal yellow homolog (mouse))"""			10500250, 23614458	Standard	NM_016732		Approved	P542, HNRPCL2	uc002xab.3	Q9UKM9	OTTHUMG00000032283	ENST00000246194.3:c.307A>T	20.37:g.32661419A>T	ENSP00000246194:p.Arg103*	Somatic		Capture	SOLID	Phase_IV	32125080	Q14621|Q2M365|Q5QPL8|Q9BQX6|Q9UJE3	Nonsense_Mutation	SNP	ENST00000246194.3	37	CCDS13230.1	SNP	11	Baylor	.	.	.	.	.	.	.	.	.	.	A	42	9.170112	0.99089	.	.	ENSG00000125970	ENST00000375114;ENST00000448364;ENST00000246194;ENST00000442805	.	.	.	5.4	4.28	0.50868	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-15.9456	7.4369	0.27160	0.7831:0.1422:0.0746:0.0	.	.	.	.	X	103	.	ENSP00000246194:R103X	R	+	1	2	RALY	32125080	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.182000	0.50910	2.273000	0.75805	0.482000	0.46254	AGA		0.532	RALY-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078753.1			Nonsense_Mutation
SLC39A12	221074	hgsc.bcm.edu	37	10	18289716	18289716	+	Missense_Mutation	SNP	C	C	T			TCGA-24-1105-01	TCGA-24-1105-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-24-1105-01	TCGA-24-1105-10	g.chr10:18289716C>T	ENST00000377369.2	+	11	1994	c.1721C>T	c.(1720-1722)aCg>aTg	p.T574M	SLC39A12_ENST00000377374.4_Missense_Mutation_p.T537M|SLC39A12-AS1_ENST00000445287.1_RNA|SLC39A12-AS1_ENST00000439319.1_RNA|SLC39A12_ENST00000539911.1_Missense_Mutation_p.T440M|SLC39A12_ENST00000377371.3_Missense_Mutation_p.T573M	NM_001145195.1|NM_001282733.1|NM_001282734.1	NP_001138667.1|NP_001269662.1|NP_001269663.1	Q504Y0	S39AC_HUMAN	solute carrier family 39 (zinc transporter), member 12	574					regulation of microtubule polymerization (GO:0031113)|regulation of neuron projection development (GO:0010975)|signal transduction (GO:0007165)|zinc ion transmembrane import (GO:0071578)	integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	zinc ion transmembrane transporter activity (GO:0005385)	p.T537M(1)		NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|kidney(3)|large_intestine(5)|lung(38)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	60						GTGACCACTACGATTGCTATC	0.443																																																1	Substitution - Missense(1)	ovary(1)	10											140.0	117.0	125.0					10																	18289716		2203	4300	6503	18329722	SO:0001583	missense	221074				CCDS7124.1, CCDS44362.1, CCDS60493.1, CCDS60494.1	10p12.33	2013-05-22			ENSG00000148482	ENSG00000148482		"""Solute carriers"""	20860	protein-coding gene	gene with protein product		608734	"""solute carrier family 39 (metal ion transporter), member 12"""			12659941	Standard	NM_152725		Approved	FLJ30499	uc001ipo.2	Q504Y0	OTTHUMG00000017759	ENST00000377369.2:c.1721C>T	10.37:g.18289716C>T	ENSP00000366586:p.Thr574Met	Somatic		Capture	SOLID	Phase_IV	18329722	B7ZL35|C9JJL4|Q49AN8|Q4G0L3|Q5VWV8|Q5VWV9|Q6NZY5|Q96NN4	Missense_Mutation	SNP	ENST00000377369.2	37	CCDS44362.1	SNP	19	Baylor	.	.	.	.	.	.	.	.	.	.	C	23.4	4.408167	0.83340	.	.	ENSG00000148482	ENST00000377369;ENST00000377374;ENST00000377371;ENST00000539911;ENST00000425219	T;T;T;T	0.50277	0.75;0.75;0.75;0.75	5.62	5.62	0.85841	.	0.044917	0.85682	D	0.000000	T	0.72653	0.3487	M	0.80183	2.485	0.80722	D	1	D;D;D	0.89917	1.0;0.994;1.0	D;P;D	0.83275	0.995;0.874;0.996	T	0.74478	-0.3652	10	0.66056	D	0.02	-17.5442	20.0281	0.97530	0.0:1.0:0.0:0.0	.	573;574;537	Q504Y0-4;Q504Y0;Q504Y0-3	.;S39AC_HUMAN;.	M	574;537;573;440;494	ENSP00000366586:T574M;ENSP00000366591:T537M;ENSP00000366588:T573M;ENSP00000440445:T440M	ENSP00000366586:T574M	T	+	2	0	SLC39A12	18329722	1.000000	0.71417	0.320000	0.25306	0.726000	0.41606	7.776000	0.85560	2.818000	0.97014	0.655000	0.94253	ACG		0.443	SLC39A12-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_152725		Missense_Mutation
SLC4A8	9498	hgsc.bcm.edu	37	12	51888785	51888785	+	Silent	SNP	C	C	T			TCGA-24-1105-01	TCGA-24-1105-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-24-1105-01	TCGA-24-1105-10	g.chr12:51888785C>T	ENST00000453097.2	+	21	3043	c.2826C>T	c.(2824-2826)atC>atT	p.I942I	SLC4A8_ENST00000358657.3_Silent_p.I969I	NM_001039960.2|NM_001258401.2	NP_001035049.1|NP_001245330.1			solute carrier family 4, sodium bicarbonate cotransporter, member 8									p.I942I(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(18)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|stomach(2)|urinary_tract(5)	55				BRCA - Breast invasive adenocarcinoma(357;0.15)		CAGATTTCATCTACCTGCGGC	0.527																																																1	Substitution - coding silent(1)	ovary(1)	12											147.0	125.0	133.0					12																	51888785		2203	4300	6503	50175052	SO:0001819	synonymous_variant	9498			AB018282	CCDS44890.1, CCDS58232.1, CCDS58233.1, CCDS73470.1	12q13.13	2013-05-22			ENSG00000050438	ENSG00000050438		"""Solute carriers"""	11034	protein-coding gene	gene with protein product		605024				11133997	Standard	NM_001039960		Approved	NBC3	uc001rys.2	Q2Y0W8	OTTHUMG00000169489	ENST00000453097.2:c.2826C>T	12.37:g.51888785C>T		Somatic		Capture	SOLID	Phase_IV	50175052		Silent	SNP	ENST00000453097.2	37	CCDS44890.1	SNP	32	Baylor																																																																																				0.527	SLC4A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404356.1	NM_004858		Silent
SMYD2	56950	hgsc.bcm.edu	37	1	214491481	214491481	+	Splice_Site	SNP	A	A	G			TCGA-24-1105-01	TCGA-24-1105-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Sanger_PCR_WGA	.	.	Illumina GAIIx	TCGA-24-1105-01	TCGA-24-1105-10	g.chr1:214491481A>G	ENST00000366957.5	+	4	430	c.408A>G	c.(406-408)tcA>tcG	p.S136S	SMYD2_ENST00000415093.2_Splice_Site_p.S136S|SMYD2_ENST00000491455.1_3'UTR	NM_020197.2	NP_064582.2	Q9NRG4	SMYD2_HUMAN	SET and MYND domain containing 2	136	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)|regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043516)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	histone methyltransferase activity (H3-K36 specific) (GO:0046975)|metal ion binding (GO:0046872)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|RNA polymerase II core binding (GO:0000993)	p.S136S(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(81;0.0122)|all cancers(67;0.0209)|GBM - Glioblastoma multiforme(131;0.106)|Epithelial(68;0.144)		AGTTTGAATCACGTAAGTCTT	0.463																																																1	Substitution - coding silent(1)	ovary(1)	1											98.0	101.0	100.0					1																	214491481		2203	4300	6503	212558104	SO:0001630	splice_region_variant	56950			AF226053	CCDS31022.1	1q32.3	2011-07-01			ENSG00000143499	ENSG00000143499		"""Zinc fingers, MYND-type"", ""Chromatin-modifying enzymes / K-methyltransferases"""	20982	protein-coding gene	gene with protein product		610663					Standard	NM_020197		Approved	HSKM-B, ZMYND14, KMT3C	uc021pix.1	Q9NRG4	OTTHUMG00000037066	ENST00000366957.5:c.409+1A>G	1.37:g.214491481A>G		Somatic		Capture	SOLID	Phase_IV	212558104	B2R9P9|I6L9H7|Q4V765|Q5VSH9|Q96AI4	Silent	SNP	ENST00000366957.5	37	CCDS31022.1	SNP	6	Baylor																																																																																				0.463	SMYD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089998.1	NM_020197	Silent	Silent
STMN4	81551	hgsc.bcm.edu	37	8	27097669	27097669	+	Missense_Mutation	SNP	G	G	A			TCGA-24-1105-01	TCGA-24-1105-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-24-1105-01	TCGA-24-1105-10	g.chr8:27097669G>A	ENST00000265770.7	-	5	465	c.329C>T	c.(328-330)gCg>gTg	p.A110V	STMN4_ENST00000350889.4_Missense_Mutation_p.A137V|STMN4_ENST00000523048.1_Missense_Mutation_p.A137V|STMN4_ENST00000522908.1_Missense_Mutation_p.A137V|STMN4_ENST00000519997.1_Missense_Mutation_p.A101V|STMN4_ENST00000519614.1_Missense_Mutation_p.A110V			Q9H169	STMN4_HUMAN	stathmin-like 4	110	SLD. {ECO:0000255|PROSITE- ProRule:PRU00998}.				regulation of microtubule polymerization or depolymerization (GO:0031110)	cell projection (GO:0042995)|Golgi apparatus (GO:0005794)		p.A137V(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|pancreas(1)	11		Ovarian(32;0.00167)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0214)|Epithelial(17;9.82e-10)|Colorectal(74;0.142)	Lomustine(DB01206)	CAGGAGCTCCGCTTCCTGGTA	0.493																																																1	Substitution - Missense(1)	ovary(1)	8											121.0	116.0	118.0					8																	27097669		2203	4300	6503	27153586	SO:0001583	missense	81551				CCDS6055.1, CCDS64851.1, CCDS64852.1, CCDS64854.1	8p21.2	2006-12-09			ENSG00000015592	ENSG00000015592			16078	protein-coding gene	gene with protein product						11230166	Standard	NM_001283054		Approved	RB3	uc003xfj.3	Q9H169	OTTHUMG00000099461	ENST00000265770.7:c.329C>T	8.37:g.27097669G>A	ENSP00000265770:p.Ala110Val	Somatic		Capture	SOLID	Phase_IV	27153586	B7Z2Z7|B7Z4I9|D3DSS8|D3DSS9|G5EA16|Q2TAB9	Missense_Mutation	SNP	ENST00000265770.7	37		SNP	38	Baylor	.	.	.	.	.	.	.	.	.	.	G	26.5	4.743418	0.89663	.	.	ENSG00000015592	ENST00000350889;ENST00000519997;ENST00000265770;ENST00000523048;ENST00000519614;ENST00000522908	.	.	.	5.86	4.99	0.66335	.	0.049987	0.85682	D	0.000000	T	0.77731	0.4174	M	0.78285	2.405	0.58432	D	0.999999	D;D;D;D;D;D	0.89917	1.0;1.0;0.996;1.0;0.975;0.996	P;D;P;D;B;P	0.72075	0.905;0.92;0.55;0.976;0.222;0.55	T	0.79332	-0.1847	9	0.51188	T	0.08	-24.0282	12.7295	0.57191	0.0792:0.0:0.9208:0.0	.	137;101;137;110;110;137	E7EVN3;B7Z2Z7;G5EA16;E5RIR6;Q9H169;Q9H169-2	.;.;.;.;STMN4_HUMAN;.	V	137;101;110;137;110;137	.	ENSP00000265770:A110V	A	-	2	0	STMN4	27153586	1.000000	0.71417	0.996000	0.52242	0.940000	0.58332	9.869000	0.99810	1.494000	0.48533	0.655000	0.94253	GCG		0.493	STMN4-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000375941.1	NM_030795		Missense_Mutation
TBC1D17	79735	hgsc.bcm.edu	37	19	50381769	50381770	+	In_Frame_Ins	INS	-	-	CTG			TCGA-24-1105-01	TCGA-24-1105-10	-	-	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-24-1105-01	TCGA-24-1105-10	g.chr19:50381769_50381770insCTG	ENST00000221543.5	+	3	434_435	c.135_136insCTG	c.(136-138)ctg>CTGctg	p.46_46L>LL	TBC1D17_ENST00000598789.1_3'UTR|AKT1S1_ENST00000391835.1_5'Flank|AKT1S1_ENST00000344175.5_5'Flank|AKT1S1_ENST00000482622.1_5'Flank|TBC1D17_ENST00000535102.2_In_Frame_Ins_p.13_13L>LL|AKT1S1_ENST00000391831.1_5'Flank|AKT1S1_ENST00000391832.3_5'Flank|AKT1S1_ENST00000391834.2_5'Flank	NM_024682.2	NP_078958	Q9HA65	TBC17_HUMAN	TBC1 domain family, member 17	46					autophagy (GO:0006914)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)	Rab GTPase activator activity (GO:0005097)	p.L45_L46insL(1)		NS(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	15		all_lung(116;0.000338)|Lung NSC(112;0.000446)|all_neural(266;0.107)|Ovarian(192;0.231)		GBM - Glioblastoma multiforme(134;0.0116)|OV - Ovarian serous cystadenocarcinoma(262;0.017)		ATGACGTCCTCCTGCACTGGGC	0.535																																																1	Insertion - In frame(1)	ovary(1)	19																																								55073582	SO:0001652	inframe_insertion	79735			AK090606	CCDS12785.1, CCDS54294.1	19q13.33	2013-07-09				ENSG00000104946			25699	protein-coding gene	gene with protein product						22854040	Standard	NM_024682		Approved	FLJ12168	uc002pqo.3	Q9HA65		ENST00000221543.5:c.136_138dupCTG	19.37:g.50381770_50381772dupCTG	ENSP00000221543:p.Leu46dup	Somatic		Capture	SOLID	Phase_IV	55073581	B4DT12|B9A6L8|F5H1W7	In_Frame_Ins	INS	ENST00000221543.5	37	CCDS12785.1	INS	30	Baylor																																																																																				0.535	TBC1D17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466404.1	NM_024682		In_Frame_Ins
TOP2A	7153	hgsc.bcm.edu	37	17	38569199	38569200	+	Frame_Shift_Del	DEL	CT	CT	-			TCGA-24-1105-01	TCGA-24-1105-10	CT	CT	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-24-1105-01	TCGA-24-1105-10	g.chr17:38569199_38569200delCT	ENST00000423485.1	-	7	758_759	c.600_601delAG	c.(598-603)agagctfs	p.RA200fs		NM_001067.3	NP_001058.2	P11388	TOP2A_HUMAN	topoisomerase (DNA) II alpha 170kDa	200					apoptotic chromosome condensation (GO:0030263)|ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromosome segregation (GO:0007059)|DNA ligation (GO:0006266)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|embryonic cleavage (GO:0040016)|hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cell cycle (GO:0000278)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|positive regulation of apoptotic process (GO:0043065)|positive regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral genome replication (GO:0045070)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|DNA-dependent ATPase activity (GO:0008094)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|magnesium ion binding (GO:0000287)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|ubiquitin binding (GO:0043130)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(9)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	39		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00183)		Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385)	ATCTCACCAGCTCTTCCCATAT	0.351																																																0			17																																								35822726	SO:0001589	frameshift_variant	7153				CCDS45672.1	17q21-q22	2008-08-06	2002-08-29		ENSG00000131747	ENSG00000131747	5.99.1.2		11989	protein-coding gene	gene with protein product		126430	"""topoisomerase (DNA) II alpha (170kD)"""	TOP2			Standard	NM_001067		Approved		uc002huq.3	P11388	OTTHUMG00000155008	ENST00000423485.1:c.600_601delAG	17.37:g.38569201_38569202delCT	ENSP00000411532:p.Arg200fs	Somatic		Capture	SOLID	Phase_IV	35822725	B2RTS1|Q71UN1|Q71UQ5|Q9HB24|Q9HB25|Q9HB26|Q9UP44|Q9UQP9	Frame_Shift_Del	DEL	ENST00000423485.1	37	CCDS45672.1	DEL	28	Baylor																																																																																				0.351	TOP2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338035.1			Frame_Shift_Del
TP53	7157	hgsc.bcm.edu	37	17	7578461	7578461	+	Missense_Mutation	SNP	C	C	A	rs121912654		TCGA-24-1105-01	TCGA-24-1105-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Sanger_PCR_WGA	.	.	Illumina GAIIx	TCGA-24-1105-01	TCGA-24-1105-10	g.chr17:7578461C>A	ENST00000269305.4	-	5	658	c.469G>T	c.(469-471)Gtc>Ttc	p.V157F	TP53_ENST00000455263.2_Missense_Mutation_p.V157F|TP53_ENST00000420246.2_Missense_Mutation_p.V157F|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Missense_Mutation_p.V157F|TP53_ENST00000413465.2_Missense_Mutation_p.V157F|TP53_ENST00000445888.2_Missense_Mutation_p.V157F	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	157	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		V -> A (in sporadic cancers; somatic mutation).|V -> D (in sporadic cancers; somatic mutation).|V -> F (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974}.|V -> G (in sporadic cancers; somatic mutation).|V -> I (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:9419979}.|V -> L (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.V157F(161)|p.V157I(10)|p.0?(8)|p.V157L(6)|p.V64F(6)|p.V25F(6)|p.R156_I162delRVRAMAI(2)|p.T155fs*23(2)|p.V157del(2)|p.V157fs*9(2)|p.P153fs*22(2)|p.V157fs*22(2)|p.V157fs*24(2)|p.V157_C176del20(1)|p.R156_A161delRVRAMA(1)|p.P151_V173del23(1)|p.R156_V157del(1)|p.R156_V157insV(1)|p.R156_R158delRVR(1)|p.R156fs*12(1)|p.R156fs*18(1)|p.R156_A161del(1)|p.V157_M160delVRAM(1)|p.D148fs*23(1)|p.V157_R158delVR(1)|p.S149fs*72(1)|p.T155_A161delTRVRAMA(1)|p.G154fs*22(1)|p.R156fs*20(1)|p.V157_I162delVRAMAI(1)|p.V157fs*23(1)|p.V157fs*21(1)|p.V157fs*25(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	ATGGCGCGGACGCGGGTGCCG	0.617		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	231	Substitution - Missense(189)|Deletion - Frameshift(15)|Deletion - In frame(14)|Whole gene deletion(8)|Insertion - Frameshift(3)|Insertion - In frame(1)|Complex - frameshift(1)	lung(69)|liver(30)|upper_aerodigestive_tract(26)|breast(19)|oesophagus(14)|ovary(13)|stomach(9)|large_intestine(7)|haematopoietic_and_lymphoid_tissue(7)|central_nervous_system(6)|bone(5)|vulva(4)|urinary_tract(4)|skin(3)|pancreas(3)|endometrium(2)|kidney(2)|biliary_tract(2)|soft_tissue(2)|prostate(1)|adrenal_gland(1)|salivary_gland(1)|thymus(1)	17											50.0	52.0	51.0					17																	7578461		2202	4300	6502	7519186	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.469G>T	17.37:g.7578461C>A	ENSP00000269305:p.Val157Phe	Somatic		Capture	SOLID	Phase_IV	7519186	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	SNP	19	Baylor	.	.	.	.	.	.	.	.	.	.	C	12.19	1.865109	0.32977	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315;ENST00000508793	D;D;D;D;D;D;D;D;D	0.99822	-6.94;-6.94;-6.94;-6.94;-6.94;-6.94;-6.94;-6.94;-6.94	5.47	2.42	0.29668	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.216722	0.39210	N	0.001429	D	0.99718	0.9891	M	0.86420	2.815	0.33606	D	0.603	D;D;D;D;D;D;D	0.89917	1.0;0.998;0.999;0.999;0.999;1.0;1.0	D;D;D;D;D;D;D	0.87578	0.997;0.994;0.984;0.981;0.996;0.998;0.996	D	0.97998	1.0358	10	0.72032	D	0.01	-16.7152	5.3541	0.16051	0.0:0.6119:0.146:0.2421	.	118;157;157;64;157;157;157	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	F	157;157;157;157;157;157;146;64;25;64;25;157	ENSP00000410739:V157F;ENSP00000352610:V157F;ENSP00000269305:V157F;ENSP00000398846:V157F;ENSP00000391127:V157F;ENSP00000391478:V157F;ENSP00000425104:V25F;ENSP00000423862:V64F;ENSP00000424104:V157F	ENSP00000269305:V157F	V	-	1	0	TP53	7519186	0.137000	0.22531	0.013000	0.15412	0.150000	0.21749	0.548000	0.23314	0.386000	0.24997	-0.253000	0.11424	GTC		0.617	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		Missense_Mutation
TUSC3	7991	hgsc.bcm.edu	37	8	15517134	15517134	+	Missense_Mutation	SNP	T	T	C			TCGA-24-1105-01	TCGA-24-1105-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Sanger_PCR_WGA	.	.	Illumina GAIIx	TCGA-24-1105-01	TCGA-24-1105-10	g.chr8:15517134T>C	ENST00000503731.1	+	4	693	c.545T>C	c.(544-546)aTt>aCt	p.I182T	TUSC3_ENST00000503191.1_3'UTR|TUSC3_ENST00000382020.4_Missense_Mutation_p.I182T|TUSC3_ENST00000506802.1_Missense_Mutation_p.I182T|TUSC3_ENST00000509380.1_Missense_Mutation_p.I182T	NM_006765.3	NP_006756.2	Q13454	TUSC3_HUMAN	tumor suppressor candidate 3	182	Thioredoxin.				cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|cognition (GO:0050890)|magnesium ion transport (GO:0015693)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|oligosaccharyltransferase complex (GO:0008250)	magnesium ion transmembrane transporter activity (GO:0015095)	p.I182T(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(10)|ovary(2)	28				Colorectal(111;0.113)		GCAAAGTGGATTGCTGACAGA	0.383																																																1	Substitution - Missense(1)	ovary(1)	8											122.0	119.0	120.0					8																	15517134		2203	4300	6503	15561505	SO:0001583	missense	7991			AK026149	CCDS5993.1, CCDS5994.1	8p22	2010-10-22			ENSG00000104723	ENSG00000104723			30242	protein-coding gene	gene with protein product	"""oligosaccharyltransferase 3 homolog A (S. cerevisiae)"""	601385				8661104, 10097140	Standard	NM_178234		Approved	MGC13453, N33, OST3A, MRT7	uc003wwt.3	Q13454	OTTHUMG00000094803	ENST00000503731.1:c.545T>C	8.37:g.15517134T>C	ENSP00000424544:p.Ile182Thr	Somatic		Capture	SOLID	Phase_IV	15561505	A8MSM0|D3DSP2|Q14911|Q14912|Q96FW0	Missense_Mutation	SNP	ENST00000503731.1	37	CCDS5994.1	SNP	52	Baylor	.	.	.	.	.	.	.	.	.	.	T	20.4	3.991065	0.74703	.	.	ENSG00000104723	ENST00000382020;ENST00000506802;ENST00000509380;ENST00000503731	T;T;T;T	0.47177	0.85;0.85;0.85;0.85	5.52	4.36	0.52297	Thioredoxin-like fold (2);	0.044020	0.85682	N	0.000000	T	0.64571	0.2610	M	0.72353	2.195	0.45883	D	0.998731	P;P;D;P;P;B	0.53462	0.86;0.949;0.96;0.949;0.949;0.061	P;P;D;P;P;B	0.66979	0.89;0.719;0.948;0.756;0.719;0.018	T	0.66842	-0.5821	10	0.87932	D	0	-15.9751	10.9576	0.47366	0.0:0.0736:0.0:0.9264	.	182;182;182;182;182;182	D6RDV0;D6RIY7;Q13454-2;Q13454;D6RA37;A8MSM0	.;.;.;TUSC3_HUMAN;.;.	T	182	ENSP00000371450:I182T;ENSP00000425777:I182T;ENSP00000423426:I182T;ENSP00000424544:I182T	ENSP00000221167:I182T	I	+	2	0	TUSC3	15561505	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.698000	0.84413	1.035000	0.39972	0.528000	0.53228	ATT		0.383	TUSC3-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000365367.1	NM_006765		Missense_Mutation
VPS13D	55187	hgsc.bcm.edu	37	1	12313802	12313802	+	Missense_Mutation	SNP	G	G	T			TCGA-24-1105-01	TCGA-24-1105-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-24-1105-01	TCGA-24-1105-10	g.chr1:12313802G>T	ENST00000358136.3	+	7	718	c.588G>T	c.(586-588)aaG>aaT	p.K196N	VPS13D_ENST00000356315.4_Missense_Mutation_p.K196N	NM_015378.2	NP_056193.2			vacuolar protein sorting 13 homolog D (S. cerevisiae)									p.K196N(1)		NS(1)|breast(6)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(28)|lung(44)|ovary(5)|pancreas(1)|prostate(8)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(4)	130	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		TGCGGAAAAAGCAATTAGACG	0.398																																																1	Substitution - Missense(1)	ovary(1)	1											157.0	147.0	150.0					1																	12313802		2203	4300	6503	12236389	SO:0001583	missense	55187			AJ608774	CCDS30588.1, CCDS30589.1	1p36.21	2008-02-05	2006-04-04		ENSG00000048707	ENSG00000048707			23595	protein-coding gene	gene with protein product		608877	"""vacuolar protein sorting 13D (yeast)"""				Standard	NM_015378		Approved	FLJ10619, KIAA0453	uc001atv.3	Q5THJ4	OTTHUMG00000013155	ENST00000358136.3:c.588G>T	1.37:g.12313802G>T	ENSP00000350854:p.Lys196Asn	Somatic		Capture	SOLID	Phase_IV	12236389		Missense_Mutation	SNP	ENST00000358136.3	37	CCDS30588.1	SNP	34	Baylor	.	.	.	.	.	.	.	.	.	.	G	19.86	3.904967	0.72868	.	.	ENSG00000048707	ENST00000356315;ENST00000358136	T;T	0.63913	-0.07;-0.07	5.48	-0.302	0.12796	.	0.000000	0.85682	D	0.000000	T	0.74913	0.3779	M	0.78049	2.395	0.80722	D	1	D;D	0.76494	0.999;0.999	P;D	0.75484	0.889;0.986	T	0.75062	-0.3450	10	0.62326	D	0.03	.	11.1559	0.48486	0.4983:0.0:0.5017:0.0	.	196;196	Q5THJ4-2;Q5THJ4	.;VP13D_HUMAN	N	196	ENSP00000348666:K196N;ENSP00000350854:K196N	ENSP00000348666:K196N	K	+	3	2	VPS13D	12236389	1.000000	0.71417	0.997000	0.53966	0.975000	0.68041	0.867000	0.27968	0.025000	0.15241	0.650000	0.86243	AAG		0.398	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378		Missense_Mutation
