#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_Chromosome_hg18	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_End_position_hg18	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_NormalRefReads_WU	i_NormalVAF_WU	i_NormalVarReads_WU	i_ORegAnno_bin	i_RNARefReads_WU	i_RNAVAF_WU	i_RNAVarReads_WU	i_Start_position_hg18	i_TumorRefReads_WU	i_TumorVAF_WU	i_TumorVarReads_WU	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains	i_amino_acid_change	i_annotation_transcript	i_build	i_c_position	i_ccds_id	i_chromosome_name	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_deletion_substructures	i_domain	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_name	i_gene_type	i_havana_transcript	i_reference	i_refseq_mrna_id	i_secondary_variant_classification	i_stop	i_strand	i_transcript_error	i_transcript_name	i_transcript_source	i_transcript_species	i_transcript_status	i_transcript_version	i_trv_type	i_type	i_ucsc_cons	i_variant
Unknown	0	genome.wustl.edu	37	Unknown	0	0	+	IGR	SNP	T	T	C			TCGA-AB-2943-03A-01W-0745-08	TCGA-AB-2943-11A-01W-0745-08	T	T	T	C	T	T	Verified	Invalid:failed_liftOver	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	9ffddf15-3f38-4dac-a9f6-2636130c050b	32623a30-c839-4621-a7df-af0b615c01c1	g.chrUnknown:0T>C								None (None upstream) : None (None downstream)																								0.0																																						dbGAP											0			MT																																								4598	SO:0001628	intergenic_variant	0																															Unknown.37:g.0T>C		1171	0.75	9		NA	NA	NA	4598	633	32.06	302		Missense_Mutation	SNP	HMMPfam_Oxidored_q1,HMMPfam_NADH_dehy_S2_C	p.V43A		37	c.128		MT																																																																																			-	HMMPfam_Oxidored_q1	0	0					MT-ND2			T			4598	+1	no_stop_codon:bad_bp_length_for_coding_region	ENST00000361453	ensembl	human	known	54_36p	missense	SNP	NULL	C
PRAMEF11	440560	genome.wustl.edu	37	1	12884983	12884983	+	Silent	SNP	C	C	T	rs565253612	byFrequency	TCGA-AB-2943-03A-01W-0745-08	TCGA-AB-2943-11A-01W-0745-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	9ffddf15-3f38-4dac-a9f6-2636130c050b	32623a30-c839-4621-a7df-af0b615c01c1	g.chr1:12884983C>T	ENST00000535591.1	-	4	1323	c.1128G>A	c.(1126-1128)ccG>ccA	p.P376P	RP5-845O24.8_ENST00000438401.1_lincRNA	NM_001146344.1	NP_001139816.1	O60813	PRA11_HUMAN	PRAME family member 11	376					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|lung(7)|pancreas(2)|skin(4)|urinary_tract(1)	27						AACTTTCCTGCGGGGCAGGAT	0.502													.|||	5	0.000998403	0.0	0.0	5008	,	,		22726	0.003		0.0	False		,,,				2504	0.002					dbGAP											0			1											96.0	71.0	79.0					1																	12884983		692	1590	2282	12807570	SO:0001819	synonymous_variant	0			AL049680	CCDS53268.1	1p36.21	2013-01-17			ENSG00000204513	ENSG00000239810		"""-"""	14086	protein-coding gene	gene with protein product							Standard	XM_006710645		Approved		uc001auk.2	O60813	OTTHUMG00000001929	ENST00000535591.1:c.1128G>A	1.37:g.12884983C>T		44	0.00	0		NA	NA	NA	12807570	61	21.79	17		Missense_Mutation	SNP	NULL	p.R453H	ENST00000535591.1	37	c.1358	CCDS53268.1	1																																																																																			-	NULL		0.502	PRAMEF11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	PRAMEF11	protein_coding		C	XM_496341		12807570	-1	pseudogene:no_stop_codon:bad_bp_length_for_coding_region	XM_001714837.1	genbank	human	model	54_36p	missense	SNP	0.033	T
USP48	84196	genome.wustl.edu	37	1	22033076	22033076	+	Nonsense_Mutation	SNP	C	C	A			TCGA-AB-2943-03A-01W-0745-08	TCGA-AB-2943-11A-01W-0745-08	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	9ffddf15-3f38-4dac-a9f6-2636130c050b	32623a30-c839-4621-a7df-af0b615c01c1	g.chr1:22033076C>A	ENST00000308271.9	-	17	2743	c.2095G>T	c.(2095-2097)Gaa>Taa	p.E699*	USP48_ENST00000400301.1_Nonsense_Mutation_p.E699*|USP48_ENST00000529637.1_Nonsense_Mutation_p.E711*|USP48_ENST00000374732.3_Nonsense_Mutation_p.E237*	NM_032236.5	NP_115612.4	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 48	699					ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			NS(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(14)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		Colorectal(325;3.46e-05)|all_lung(284;4.29e-05)|Lung NSC(340;4.66e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|OV - Ovarian serous cystadenocarcinoma(117;4.74e-26)|COAD - Colon adenocarcinoma(152;1.3e-05)|GBM - Glioblastoma multiforme(114;1.86e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000614)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00711)|Lung(427;0.0327)|READ - Rectum adenocarcinoma(331;0.0657)|LUSC - Lung squamous cell carcinoma(448;0.0753)		CCTTCTCTTTCTAAAATCTGA	0.438																																						dbGAP											0			1											97.0	98.0	97.0					1																	22033076		2203	4300	6503	21905663	SO:0001587	stop_gained	0			AF502942	CCDS30623.1, CCDS44084.1	1p36.12	2008-02-05	2005-08-08	2004-04-07	ENSG00000090686	ENSG00000090686		"""Ubiquitin-specific peptidases"""	18533	protein-coding gene	gene with protein product			"""ubiquitin specific protease 31"", ""ubiquitin specific protease 48"""	USP31		12838346	Standard	XM_005246009		Approved	FLJ23277, FLJ11328, FLJ20103, FLJ23054, MGC14879	uc001bfb.3	Q86UV5	OTTHUMG00000007798	ENST00000308271.9:c.2095G>T	1.37:g.22033076C>A	ENSP00000309262:p.Glu699*	120	0.00	0		56	48.62	53	21905663	146	52.72	165	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Nonsense_Mutation	SNP	HMMPfam_UCH,PatternScan_UCH_2_2,superfamily_Cysteine proteinases,superfamily_Ubiquitin-like	p.E699*	ENST00000308271.9	37	c.2095	CCDS30623.1	1	.	.	.	.	.	.	.	.	.	.	C	40	8.112111	0.98659	.	.	ENSG00000090686	ENST00000400301;ENST00000308271;ENST00000374732;ENST00000529637	.	.	.	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	.	19.0088	0.92863	0.0:1.0:0.0:0.0	.	.	.	.	X	699;699;237;711	.	ENSP00000309262:E699X	E	-	1	0	USP48	21905663	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	6.759000	0.74934	2.745000	0.94114	0.557000	0.71058	GAA	-	NULL		0.438	USP48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	USP48	protein_coding	OTTHUMT00000021372.1	C	NM_032236		21905663	-1	no_errors	NM_032236.1	genbank	human	reviewed	54_36p	nonsense	SNP	1.000	A
PPIEL	728448	genome.wustl.edu	37	1	40007490	40007490	+	RNA	SNP	G	G	C			TCGA-AB-2943-03A-01W-0745-08	TCGA-AB-2943-11A-01W-0745-08	G	G	G	C	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	9ffddf15-3f38-4dac-a9f6-2636130c050b	32623a30-c839-4621-a7df-af0b615c01c1	g.chr1:40007490G>C	ENST00000440190.1	-	0	455				RP11-69E11.4_ENST00000450157.1_RNA|RP11-69E11.4_ENST00000431553.1_RNA|RP11-69E11.4_ENST00000417869.1_RNA																							TCCTTTAAATGGGTGCACATG	0.453																																						dbGAP											0			1																																								39780077			0																															1.37:g.40007490G>C		129	0.00	0		9	83.05	49	39780077	132	47.89	125		RNA	SNP	-	NULL	ENST00000440190.1	37	NULL		1																																																																																			-	-		0.453	RP11-69E11.4-003	KNOWN	basic	antisense	LOC728448	antisense	OTTHUMT00000025214.1	G			39780077	-1	pseudogene	NR_003929.2	genbank	human	validated	54_36p	rna	SNP	1.000	C
CACNA2D3	55799	genome.wustl.edu	37	3	54930839	54930839	+	Nonsense_Mutation	SNP	C	C	A	rs548413237		TCGA-AB-2943-03A-01W-0745-08	TCGA-AB-2943-11A-01W-0745-08	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	9ffddf15-3f38-4dac-a9f6-2636130c050b	32623a30-c839-4621-a7df-af0b615c01c1	g.chr3:54930839C>A	ENST00000474759.1	+	26	2358	c.2310C>A	c.(2308-2310)taC>taA	p.Y770*	CACNA2D3_ENST00000490478.1_Nonsense_Mutation_p.Y676*|CACNA2D3-AS1_ENST00000471265.1_RNA|CACNA2D3_ENST00000288197.5_Nonsense_Mutation_p.Y770*|CACNA2D3_ENST00000415676.2_Nonsense_Mutation_p.Y770*	NM_018398.2	NP_060868.2	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 3	770						integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(3)	59				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)	Amlodipine(DB00381)|Nilvadipine(DB06712)|Spironolactone(DB00421)	CTCTCTGGTACCGAAGAGCCG	0.522																																						dbGAP											0			3											120.0	121.0	121.0					3																	54930839		1972	4153	6125	54905879	SO:0001587	stop_gained	0			AJ272268	CCDS54598.1	3p21.1	2010-10-05	2008-02-26		ENSG00000157445	ENSG00000157445		"""Calcium channel subunits"""	15460	protein-coding gene	gene with protein product		606399				11245980	Standard	XM_005265318		Approved	HSA272268	uc003dhf.3	Q8IZS8	OTTHUMG00000158580	ENST00000474759.1:c.2310C>A	3.37:g.54930839C>A	ENSP00000419101:p.Tyr770*	77	2.53	2		NA	NA	NA	54905879	169	31.87	80	B2RPL6|Q9NY16|Q9NY18	Nonsense_Mutation	SNP	HMMPfam_VWA,HMMSmart_SM00327,HMMPfam_Cache_1,HMMPfam_VWA_N,superfamily_vWA-like	p.Y770*	ENST00000474759.1	37	c.2310	CCDS54598.1	3	.	.	.	.	.	.	.	.	.	.	C	40	8.203584	0.98704	.	.	ENSG00000157445	ENST00000415676;ENST00000474759;ENST00000288197;ENST00000490478;ENST00000398624	.	.	.	5.54	3.73	0.42828	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.3092	0.43699	0.0:0.8448:0.0:0.1552	.	.	.	.	X	770;770;770;676;676	.	ENSP00000288197:Y770X	Y	+	3	2	CACNA2D3	54905879	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.159000	0.42339	1.471000	0.48121	0.655000	0.94253	TAC	-	NULL		0.522	CACNA2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CACNA2D3	protein_coding	OTTHUMT00000351402.1	C			54905879	+1	no_errors	NM_018398.2	genbank	human	reviewed	54_36p	nonsense	SNP	1.000	A
CADPS	8618	genome.wustl.edu	37	3	62578313	62578313	+	Splice_Site	SNP	C	C	T	rs147388715		TCGA-AB-2943-03A-01W-0745-08	TCGA-AB-2943-11A-01W-0745-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	9ffddf15-3f38-4dac-a9f6-2636130c050b	32623a30-c839-4621-a7df-af0b615c01c1	g.chr3:62578313C>T	ENST00000383710.4	-	7	1785	c.1436G>A	c.(1435-1437)cGg>cAg	p.R479Q	CADPS_ENST00000357948.3_Splice_Site_p.R479Q|CADPS_ENST00000283269.9_Splice_Site_p.R479Q	NM_003716.3	NP_003707.2	Q9ULU8	CAPS1_HUMAN	Ca++-dependent secretion activator	479	C2.				catecholamine secretion (GO:0050432)|exocytosis (GO:0006887)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)|vesicle organization (GO:0016050)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)|synapse (GO:0045202)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(24)|lung(38)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(2)	92		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)		AGTGCTTACCCGCCCAAGCTC	0.562																																						dbGAP											0			3						C	GLN/ARG,GLN/ARG,GLN/ARG	0,4406		0,0,2203	140.0	124.0	130.0		1436,1436,1436	5.4	1.0	3	dbSNP_134	130	1,8599	1.2+/-3.3	0,1,4299	no	missense-near-splice,missense-near-splice,missense-near-splice	CADPS	NM_003716.3,NM_183393.2,NM_183394.2	43,43,43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging	479/1354,479/1275,479/1315	62578313	1,13005	2203	4300	6503	62553353	SO:0001630	splice_region_variant	0			U36448	CCDS2898.1, CCDS2899.1, CCDS46858.1	3p21.1	2013-01-10	2008-08-28		ENSG00000163618	ENSG00000163618		"""Pleckstrin homology (PH) domain containing"""	1426	protein-coding gene	gene with protein product		604667				1516133	Standard	NM_183393		Approved	CAPS, KIAA1121, CAPS1	uc003dll.2	Q9ULU8	OTTHUMG00000158651	ENST00000383710.4:c.1437+1G>A	3.37:g.62578313C>T		107	0.00	0		NA	NA	NA	62553353	161	19.00	38	A6NF60|Q13339|Q6GQQ6|Q8N2Z5|Q8N3M7|Q8NFR0|Q96BC2	Missense_Mutation	SNP	HMMPfam_C2,HMMPfam_PH,HMMSmart_SM00233,HMMPfam_DUF1041,superfamily_PH domain-like	p.R479Q	ENST00000383710.4	37	c.1436	CCDS46858.1	3	.	.	.	.	.	.	.	.	.	.	C	24.9	4.577818	0.86645	0.0	1.16E-4	ENSG00000163618	ENST00000383709;ENST00000383710;ENST00000357948;ENST00000283269	T;T;T	0.70986	-0.53;-0.53;-0.53	5.41	5.41	0.78517	C2 calcium-dependent membrane targeting (1);	0.000000	0.85682	D	0.000000	T	0.75503	0.3858	M	0.63843	1.955	0.80722	D	1	D;P;P	0.55385	0.971;0.681;0.913	P;B;B	0.47864	0.559;0.093;0.062	T	0.78193	-0.2299	10	0.59425	D	0.04	.	19.5461	0.95297	0.0:1.0:0.0:0.0	.	479;479;479	Q9ULU8-2;Q9ULU8-3;Q9ULU8	.;.;CAPS1_HUMAN	Q	479	ENSP00000373215:R479Q;ENSP00000350632:R479Q;ENSP00000283269:R479Q	ENSP00000283269:R479Q	R	-	2	0	CADPS	62553353	1.000000	0.71417	1.000000	0.80357	0.851000	0.48451	3.902000	0.56310	2.688000	0.91661	0.655000	0.94253	CGG	-	HMMPfam_C2		0.562	CADPS-013	KNOWN	basic|appris_principal|CCDS	protein_coding	CADPS	protein_coding	OTTHUMT00000351951.5	C	NM_003716, NM_183393, NM_183394	Missense_Mutation	62553353	-1	no_errors	NM_003716.3	genbank	human	reviewed	54_36p	missense	SNP	0.998	T
PRICKLE2	166336	genome.wustl.edu	37	3	64085285	64085285	+	Silent	SNP	G	G	A	rs376252127		TCGA-AB-2943-03A-01W-0745-08	TCGA-AB-2943-11A-01W-0745-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	9ffddf15-3f38-4dac-a9f6-2636130c050b	32623a30-c839-4621-a7df-af0b615c01c1	g.chr3:64085285G>A	ENST00000295902.6	-	8	2562	c.1977C>T	c.(1975-1977)ggC>ggT	p.G659G	PRICKLE2-AS1_ENST00000476308.1_RNA|RP11-129B22.1_ENST00000482609.1_RNA|PRICKLE2-AS1_ENST00000460946.1_RNA|PRICKLE2_ENST00000564377.1_Silent_p.G715G	NM_198859.3	NP_942559.1	Q7Z3G6	PRIC2_HUMAN	prickle homolog 2 (Drosophila)	659					establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|neuron projection development (GO:0031175)	apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|large_intestine(9)|liver(1)|lung(10)|ovary(4)|prostate(2)|skin(2)|stomach(1)	32		Lung NSC(201;0.136)		BRCA - Breast invasive adenocarcinoma(55;0.000971)|KIRC - Kidney renal clear cell carcinoma(15;0.00443)|Kidney(15;0.00497)		GGATCCTCACGCCCTCCTGCC	0.607													G|||	1	0.000199681	0.0008	0.0	5008	,	,		18413	0.0		0.0	False		,,,				2504	0.0					dbGAP											0			3						G		1,4405	2.1+/-5.4	0,1,2202	73.0	68.0	70.0		1977	-4.4	0.2	3		70	0,8600		0,0,4300	no	coding-synonymous	PRICKLE2	NM_198859.3		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		659/845	64085285	1,13005	2203	4300	6503	64060325	SO:0001819	synonymous_variant	0			AK127839	CCDS2902.1	3p14.3	2006-09-12	2006-09-12		ENSG00000163637	ENSG00000163637			20340	protein-coding gene	gene with protein product		608501	"""prickle-like 2 (Drosophila)"""			12525887	Standard	NM_198859		Approved	DKFZp686D143	uc003dmf.3	Q7Z3G6	OTTHUMG00000158789	ENST00000295902.6:c.1977C>T	3.37:g.64085285G>A		35	0.00	0		NA	NA	NA	64060325	86	25.83	31	Q0VF44	Silent	SNP	HMMPfam_LIM,HMMSmart_LIM,PatternScan_LIM_DOMAIN_1,HMMPfam_PET,superfamily_SSF57716	p.G659	ENST00000295902.6	37	c.1977	CCDS2902.1	3																																																																																			-	NULL		0.607	PRICKLE2-001	KNOWN	basic|CCDS	protein_coding	PRICKLE2	protein_coding	OTTHUMT00000352219.1	G	NM_198859		64060325	-1	no_errors	NM_198859.3	genbank	human	validated	54_36p	silent	SNP	0.036	A
EPHA3	2042	genome.wustl.edu	37	3	89528572	89528572	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2943-03A-01W-0745-08	TCGA-AB-2943-11A-01W-0745-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	9ffddf15-3f38-4dac-a9f6-2636130c050b	32623a30-c839-4621-a7df-af0b615c01c1	g.chr3:89528572G>A	ENST00000336596.2	+	17	3097	c.2872G>A	c.(2872-2874)Gtg>Atg	p.V958M	EPHA3_ENST00000494014.1_3'UTR	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	958	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		TGGTGTCACCGTGGTTGGGCC	0.413										TSP Lung(6;0.00050)																												dbGAP											0			3											91.0	81.0	85.0					3																	89528572		2203	4300	6503	89611262	SO:0001583	missense	0			M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3387	protein-coding gene	gene with protein product		179611	"""EphA3"""	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.2872G>A	3.37:g.89528572G>A	ENSP00000337451:p.Val958Met	65	0.00	0		NA	NA	NA	89611262	104	26.90	39	Q9H2V3|Q9H2V4	Missense_Mutation	SNP	HMMPfam_Ephrin_lbd,HMMSmart_SM00615,HMMPfam_Pkinase_Tyr,HMMSmart_SM00219,PatternScan_RECEPTOR_TYR_KIN_V_1,PatternScan_RECEPTOR_TYR_KIN_V_2,HMMSmart_SM00454,HMMSmart_SM00220,HMMPfam_fn3,HMMSmart_SM00060,PatternScan_PROTEIN_KINASE_TYR,superfamily_Fibronectin type III,superfamily_Galactose-binding domain-like,superfamily_SAM/Pointed domain,superfamily_Protein kinase-like (PK-like),HMMPfam_SAM_2,PatternScan_EGF_2,PatternScan_PROTEIN_KINASE_ATP	p.V958M	ENST00000336596.2	37	c.2872	CCDS2922.1	3	.	.	.	.	.	.	.	.	.	.	G	14.33	2.502560	0.44455	.	.	ENSG00000044524	ENST00000336596	D	0.84660	-1.88	5.72	4.83	0.62350	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 2 (1);	0.108661	0.64402	D	0.000007	T	0.67107	0.2858	N	0.02539	-0.55	0.80722	D	1	P	0.52463	0.953	P	0.45856	0.495	T	0.66740	-0.5847	9	.	.	.	.	9.0086	0.36127	0.206:0.0:0.794:0.0	.	958	P29320	EPHA3_HUMAN	M	958	ENSP00000337451:V958M	.	V	+	1	0	EPHA3	89611262	1.000000	0.71417	0.999000	0.59377	0.958000	0.62258	3.091000	0.50199	2.857000	0.98124	0.650000	0.86243	GTG	-	HMMSmart_SM00454,superfamily_SAM/Pointed domain,HMMPfam_SAM_2		0.413	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	EPHA3	protein_coding	OTTHUMT00000352995.1	G	NM_005233		89611262	+1	no_errors	NM_005233.5	genbank	human	reviewed	54_36p	missense	SNP	0.994	A
YEATS2	55689	genome.wustl.edu	37	3	183521065	183521065	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2943-03A-01W-0745-08	TCGA-AB-2943-11A-01W-0745-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	9ffddf15-3f38-4dac-a9f6-2636130c050b	32623a30-c839-4621-a7df-af0b615c01c1	g.chr3:183521065C>T	ENST00000305135.5	+	26	3719	c.3524C>T	c.(3523-3525)tCt>tTt	p.S1175F	AC131160.1_ENST00000401347.1_RNA	NM_018023.4	NP_060493.3	Q9ULM3	YETS2_HUMAN	YEATS domain containing 2	1175					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|mitotic spindle (GO:0072686)	TBP-class protein binding (GO:0017025)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(24)|ovary(3)|prostate(2)|skin(3)	49	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.38e-42)|Epithelial(37;1.9e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			AGCTGCTTTTCTGCAAAGTCT	0.512																																						dbGAP											0			3											81.0	84.0	83.0					3																	183521065		1954	4151	6105	185003759	SO:0001583	missense	0			AB033023	CCDS43175.1	3q27.3	2004-08-18			ENSG00000163872	ENSG00000163872			25489	protein-coding gene	gene with protein product		613373				10574462	Standard	NM_018023		Approved	FLJ10201, FLJ12841, FLJ13308, KIAA1197	uc003fly.2	Q9ULM3	OTTHUMG00000156898	ENST00000305135.5:c.3524C>T	3.37:g.183521065C>T	ENSP00000306983:p.Ser1175Phe	92	0.00	0		27	12.90	4	185003759	103	28.86	43	A7E2B9|D3DNS9|Q641P6|Q9NW96	Missense_Mutation	SNP	HMMPfam_YEATS	p.S1175F	ENST00000305135.5	37	c.3524	CCDS43175.1	3	.	.	.	.	.	.	.	.	.	.	C	19.17	3.776324	0.70107	.	.	ENSG00000163872	ENST00000421660;ENST00000305135	D	0.86366	-2.11	5.65	4.76	0.60689	.	0.059228	0.64402	D	0.000002	T	0.80722	0.4677	L	0.38175	1.15	0.41019	D	0.985069	P	0.46395	0.877	B	0.38562	0.276	D	0.84062	0.0375	10	0.87932	D	0	-18.9128	12.925	0.58254	0.0:0.603:0.397:0.0	.	1175	Q9ULM3	YETS2_HUMAN	F	1175	ENSP00000306983:S1175F	ENSP00000306983:S1175F	S	+	2	0	YEATS2	185003759	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.795000	0.69074	2.662000	0.90505	0.655000	0.94253	TCT	-	NULL		0.512	YEATS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	YEATS2	protein_coding	OTTHUMT00000346507.2	C	NM_018023		185003759	+1	no_errors	NM_018023.3	genbank	human	provisional	54_36p	missense	SNP	1.000	T
C6orf106	64771	genome.wustl.edu	37	6	34622530	34622530	+	Missense_Mutation	SNP	T	T	C			TCGA-AB-2943-03A-01W-0745-08	TCGA-AB-2943-11A-01W-0745-08	T	T	T	C	T	T	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	9ffddf15-3f38-4dac-a9f6-2636130c050b	32623a30-c839-4621-a7df-af0b615c01c1	g.chr6:34622530T>C	ENST00000374023.3	-	2	428	c.185A>G	c.(184-186)tAt>tGt	p.Y62C	C6orf106_ENST00000374021.1_5'UTR|C6orf106_ENST00000374026.3_Missense_Mutation_p.Y62C	NM_024294.2	NP_077270.1	Q9H6K1	CF106_HUMAN	chromosome 6 open reading frame 106	62										endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(2)	10						AAAGTCATAATAGGCGCCAAT	0.408																																						dbGAP											0			6											118.0	114.0	115.0					6																	34622530		2203	4300	6503	34730508	SO:0001583	missense	0			AF052106	CCDS4795.1, CCDS4796.1	6p21.31	2012-01-27			ENSG00000196821	ENSG00000196821			21215	protein-coding gene	gene with protein product		612217					Standard	XM_005249298		Approved	FLJ22195, dJ391O22.4	uc003ojr.2	Q9H6K1	OTTHUMG00000014553	ENST00000374023.3:c.185A>G	6.37:g.34622530T>C	ENSP00000363135:p.Tyr62Cys	56	1.75	1		65	26.97	24	34730508	145	31.78	68	B2R8K7|Q5VV77|Q96MG5|Q9BUR9	Missense_Mutation	SNP	superfamily_UBA-like	p.Y62C	ENST00000374023.3	37	c.185	CCDS4796.1	6	.	.	.	.	.	.	.	.	.	.	T	18.02	3.530962	0.64972	.	.	ENSG00000196821	ENST00000374023;ENST00000374026	.	.	.	5.44	5.44	0.79542	UBA-like (1);	0.000000	0.85682	D	0.000000	T	0.64382	0.2593	M	0.82193	2.58	0.80722	D	1	P;B	0.40211	0.707;0.246	P;B	0.44921	0.464;0.086	T	0.72760	-0.4196	9	0.87932	D	0	-7.2938	15.8043	0.78481	0.0:0.0:0.0:1.0	.	62;62	Q9H6K1-2;Q9H6K1	.;CF106_HUMAN	C	62	.	ENSP00000363135:Y62C	Y	-	2	0	C6orf106	34730508	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.997000	0.88414	2.197000	0.70478	0.528000	0.53228	TAT	-	superfamily_UBA-like		0.408	C6orf106-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	C6orf106	protein_coding	OTTHUMT00000040251.1	T	NM_022758		34730508	-1	no_errors	NM_024294.4	genbank	human	validated	54_36p	missense	SNP	1.000	C
ATP6V1C1	528	genome.wustl.edu	37	8	104068114	104068114	+	Missense_Mutation	SNP	G	G	T			TCGA-AB-2943-03A-01W-0745-08	TCGA-AB-2943-11A-01W-0745-08	G	G	G	T	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	9ffddf15-3f38-4dac-a9f6-2636130c050b	32623a30-c839-4621-a7df-af0b615c01c1	g.chr8:104068114G>T	ENST00000395862.3	+	8	750	c.591G>T	c.(589-591)tgG>tgT	p.W197C	ATP6V1C1_ENST00000518857.1_Missense_Mutation_p.W122C|ATP6V1C1_ENST00000518738.1_Missense_Mutation_p.W197C|ATP6V1C1_ENST00000521514.1_Missense_Mutation_p.W122C	NM_001695.4	NP_001686.1	P21283	VATC1_HUMAN	ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C1	197					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical part of cell (GO:0045177)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|proton-transporting two-sector ATPase complex (GO:0016469)|proton-transporting V-type ATPase, V1 domain (GO:0033180)	hydrogen-exporting ATPase activity, phosphorylative mechanism (GO:0008553)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|transporter activity (GO:0005215)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(6)|urinary_tract(1)	13	Lung NSC(17;0.000427)|all_lung(17;0.000533)		OV - Ovarian serous cystadenocarcinoma(57;3.57e-05)|STAD - Stomach adenocarcinoma(118;0.133)			ACAACGACTGGATTAAGCAGT	0.363																																						dbGAP											0			8											121.0	105.0	110.0					8																	104068114		2203	4300	6503	104137290	SO:0001583	missense	0			X69151	CCDS6296.1	8p22.3	2011-05-24	2006-01-13	2002-05-10	ENSG00000155097	ENSG00000155097	3.6.3.14	"""ATPases / V-type"""	856	protein-coding gene	gene with protein product		603097	"""ATPase, H+ transporting, lysosomal (vacuolar proton pump) 42kD"", ""ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C, isoform 1"""	ATP6D, ATP6C		8250920, 14580332	Standard	NM_001695		Approved	VATC, Vma5	uc003ykz.4	P21283	OTTHUMG00000164761	ENST00000395862.3:c.591G>T	8.37:g.104068114G>T	ENSP00000379203:p.Trp197Cys	54	0.00	0		43	48.81	41	104137290	149	31.82	70		Missense_Mutation	SNP	HMMPfam_V-ATPase_C	p.W197C	ENST00000395862.3	37	c.591	CCDS6296.1	8	.	.	.	.	.	.	.	.	.	.	G	24.6	4.554560	0.86231	.	.	ENSG00000155097	ENST00000518857;ENST00000395862;ENST00000521514;ENST00000518738	T;T;T;T	0.61158	0.13;0.13;0.13;0.13	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	D	0.84763	0.5544	H	0.96175	3.78	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.88933	0.3374	10	0.87932	D	0	.	19.9651	0.97262	0.0:0.0:1.0:0.0	.	197	P21283	VATC1_HUMAN	C	122;197;122;197	ENSP00000428204:W122C;ENSP00000379203:W197C;ENSP00000430129:W122C;ENSP00000430282:W197C	ENSP00000379203:W197C	W	+	3	0	ATP6V1C1	104137290	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.869000	0.99810	2.793000	0.96121	0.655000	0.94253	TGG	-	HMMPfam_V-ATPase_C		0.363	ATP6V1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ATP6V1C1	protein_coding	OTTHUMT00000380101.1	G	NM_001695		104137290	+1	no_errors	NM_001695.4	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
DHTKD1	55526	genome.wustl.edu	37	10	12154955	12154955	+	Silent	SNP	T	T	G			TCGA-AB-2943-03A-01W-0745-08	TCGA-AB-2943-11A-01W-0745-08	T	T	T	G	T	T	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	9ffddf15-3f38-4dac-a9f6-2636130c050b	32623a30-c839-4621-a7df-af0b615c01c1	g.chr10:12154955T>G	ENST00000263035.4	+	13	2273	c.2211T>G	c.(2209-2211)gtT>gtG	p.V737V		NM_018706.5	NP_061176	Q96HY7	DHTK1_HUMAN	dehydrogenase E1 and transketolase domain containing 1	737					cell death (GO:0008219)|generation of precursor metabolites and energy (GO:0006091)|glycolytic process (GO:0006096)|hematopoietic progenitor cell differentiation (GO:0002244)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)	oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(1)	44		Renal(717;0.228)	BRCA - Breast invasive adenocarcinoma(52;0.188)			TGTTTGTGGTTCACCCAACAA	0.478																																						dbGAP											0			10											190.0	163.0	172.0					10																	12154955		2203	4300	6503	12194961	SO:0001819	synonymous_variant	0			BC002477	CCDS7087.1	10p14	2003-11-24			ENSG00000181192	ENSG00000181192			23537	protein-coding gene	gene with protein product		614984				10997877	Standard	NM_018706		Approved	KIAA1630, MGC3090, DKFZP762M115	uc001ild.5	Q96HY7	OTTHUMG00000017677	ENST00000263035.4:c.2211T>G	10.37:g.12154955T>G		183	0.00	0		19	26.92	7	12194961	161	24.19	52	Q68CU5|Q9BUM8|Q9HCE2	Silent	SNP	HMMPfam_E1_dh,HMMPfam_Transket_pyr,superfamily_Thiamin diphosphate-binding fold (THDP-binding)	p.V737	ENST00000263035.4	37	c.2211	CCDS7087.1	10																																																																																			-	HMMPfam_Transket_pyr,superfamily_Thiamin diphosphate-binding fold (THDP-binding)		0.478	DHTKD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DHTKD1	protein_coding	OTTHUMT00000046777.1	T	NM_018706		12194961	+1	no_errors	NM_018706.5	genbank	human	validated	54_36p	silent	SNP	0.112	G
DYNC1I2P1	728532	genome.wustl.edu	37	10	52024774	52024774	+	IGR	SNP	C	C	T			TCGA-AB-2943-03A-01W-0745-08	TCGA-AB-2943-11A-01W-0745-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	9ffddf15-3f38-4dac-a9f6-2636130c050b	32623a30-c839-4621-a7df-af0b615c01c1	g.chr10:52024774C>T								ASAH2 (16404 upstream) : SGMS1 (40585 downstream)																							TGAGTTGGAACGTAAGAAGCA	0.448																																						dbGAP											0			10																																								51694780	SO:0001628	intergenic_variant	0																															10.37:g.52024774C>T		53	0.00	0		47	0.00	0	51694780	134	34.63	71		RNA	SNP	-	NULL		37	NULL		10																																																																																			-	-	0	0.448					LOC728532			C			51694780	+1	pseudogene	XR_015428.2	genbank	human	model	54_36p	rna	SNP	1.000	T
ST13P13	401648	genome.wustl.edu	37	10	104975971	104975971	+	IGR	SNP	A	A	G	rs201185102		TCGA-AB-2943-03A-01W-0745-08	TCGA-AB-2943-11A-01W-0745-08	A	A	A	G	A	A	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	9ffddf15-3f38-4dac-a9f6-2636130c050b	32623a30-c839-4621-a7df-af0b615c01c1	g.chr10:104975971A>G								NT5C2 (22915 upstream) : RP11-332O19.5 (29672 downstream)																							TGACAGAGCCATTGAAATAAA	0.468																																						dbGAP											0			10																																								104965961	SO:0001628	intergenic_variant	0																															10.37:g.104975971A>G		25	7.41	2		33	2.94	1	104965961	25	37.50	15		RNA	SNP	-	NULL		37	NULL		10																																																																																			-	-	0	0.468					LOC401648			A			104965961	+1	pseudogene	XR_017482.1	genbank	human	model	54_36p	rna	SNP	0.999	G
FLT1	2321	genome.wustl.edu	37	13	29001448	29001448	+	Silent	SNP	G	G	C			TCGA-AB-2943-03A-01W-0745-08	TCGA-AB-2943-11A-01W-0745-08	G	G	G	C	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	9ffddf15-3f38-4dac-a9f6-2636130c050b	32623a30-c839-4621-a7df-af0b615c01c1	g.chr13:29001448G>C	ENST00000282397.4	-	10	1535	c.1284C>G	c.(1282-1284)ccC>ccG	p.P428P	FLT1_ENST00000541932.1_Silent_p.P428P|FLT1_ENST00000539099.1_Silent_p.P428P	NM_002019.4	NP_002010.2	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1	428	Ig-like C2-type 5.				blood vessel morphogenesis (GO:0048514)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic morphogenesis (GO:0048598)|monocyte chemotaxis (GO:0002548)|patterning of blood vessels (GO:0001569)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor receptor-1 signaling pathway (GO:0036323)|vascular endothelial growth factor signaling pathway (GO:0038084)	endosome (GO:0005768)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|placental growth factor-activated receptor activity (GO:0036332)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)|VEGF-A-activated receptor activity (GO:0036326)|VEGF-B-activated receptor activity (GO:0036327)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(8)|kidney(3)|large_intestine(20)|lung(55)|ovary(3)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	115	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CGTAAATCTGGGGTTTCACTG	0.502																																						dbGAP											0			13											70.0	63.0	65.0					13																	29001448		2203	4300	6503	27899448	SO:0001819	synonymous_variant	0			AF063657	CCDS9330.1, CCDS53860.1, CCDS53861.1, CCDS73556.1	13q12	2014-09-17	2012-11-19		ENSG00000102755	ENSG00000102755	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3763	protein-coding gene	gene with protein product	"""vascular endothelial growth factor receptor 1"", ""vascular permeability factor receptor"""	165070	"""fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor)"""	FLT		2158038	Standard	NM_001159920		Approved	VEGFR1	uc001usb.3	P17948	OTTHUMG00000016648	ENST00000282397.4:c.1284C>G	13.37:g.29001448G>C		70	0.00	0		2	0.00	0	27899448	109	23.61	34	A3E342|A3E344|A8KA71|B0LPF1|B2BF46|B2BF47|B2BF48|B3FR89|B5A923|F5H5L6|O60722|P16057|Q12954	Silent	SNP	HMMPfam_Pkinase_Tyr,HMMSmart_SM00219,PatternScan_RECEPTOR_TYR_KIN_III,HMMSmart_SM00220,HMMSmart_SM00406,HMMSmart_SM00408,HMMSmart_SM00409,PatternScan_PROTEIN_KINASE_TYR,superfamily_Protein kinase-like (PK-like),HMMPfam_I-set,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_Immunoglobulin	p.P428	ENST00000282397.4	37	c.1284	CCDS9330.1	13																																																																																			-	superfamily_Immunoglobulin		0.502	FLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FLT1	protein_coding	OTTHUMT00000044322.1	G			27899448	-1	no_errors	NM_002019.3	genbank	human	validated	54_36p	silent	SNP	0.997	C
SERPINA12	145264	genome.wustl.edu	37	14	94964457	94964457	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2943-03A-01W-0745-08	TCGA-AB-2943-11A-01W-0745-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	9ffddf15-3f38-4dac-a9f6-2636130c050b	32623a30-c839-4621-a7df-af0b615c01c1	g.chr14:94964457C>T	ENST00000341228.2	-	3	1073	c.278G>A	c.(277-279)aGc>aAc	p.S93N	SERPINA12_ENST00000556881.1_Missense_Mutation_p.S93N	NM_173850.2	NP_776249.1	Q8IW75	SPA12_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 12	93					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	33				COAD - Colon adenocarcinoma(157;0.235)		GTCCAGGGTGCTGTCCTGGGC	0.517																																						dbGAP											0			14											89.0	89.0	89.0					14																	94964457		2203	4300	6503	94034210	SO:0001583	missense	0			AY177692	CCDS9926.1	14q32.13	2014-02-21	2005-08-18		ENSG00000165953	ENSG00000165953		"""Serine (or cysteine) peptidase inhibitors"""	18359	protein-coding gene	gene with protein product			"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 12"""			24172014	Standard	NM_173850		Approved	OL-64, Vaspin	uc001ydj.3	Q8IW75	OTTHUMG00000171349	ENST00000341228.2:c.278G>A	14.37:g.94964457C>T	ENSP00000342109:p.Ser93Asn	112	0.00	0		NA	NA	NA	94034210	162	30.64	72		Missense_Mutation	SNP	HMMPfam_Serpin,HMMSmart_SERPIN,PatternScan_SERPIN,superfamily_Prot_inh_serpin	p.S93N	ENST00000341228.2	37	c.278	CCDS9926.1	14	.	.	.	.	.	.	.	.	.	.	C	2.466	-0.323045	0.05350	.	.	ENSG00000165953	ENST00000556881;ENST00000341228	D;D	0.87412	-2.25;-2.25	5.59	2.28	0.28536	Serpin domain (3);	1.049790	0.07450	N	0.898841	T	0.78285	0.4259	N	0.20328	0.56	0.09310	N	1	B	0.25441	0.126	B	0.24701	0.055	T	0.63292	-0.6670	10	0.28530	T	0.3	.	9.3954	0.38399	0.0:0.1078:0.5136:0.3785	.	93	Q8IW75	SPA12_HUMAN	N	93	ENSP00000451738:S93N;ENSP00000342109:S93N	ENSP00000342109:S93N	S	-	2	0	SERPINA12	94034210	0.007000	0.16637	0.216000	0.23742	0.002000	0.02628	0.665000	0.25083	0.648000	0.30732	-0.878000	0.02970	AGC	-	HMMPfam_Serpin,HMMSmart_SERPIN,superfamily_Prot_inh_serpin		0.517	SERPINA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SERPINA12	protein_coding	OTTHUMT00000413097.1	C	NM_173850		94034210	-1	no_errors	NM_173850.2	genbank	human	provisional	54_36p	missense	SNP	0.049	T
TP53	7157	genome.wustl.edu	37	17	7577121	7577121	+	Missense_Mutation	SNP	G	G	A	rs121913343		TCGA-AB-2943-03A-01W-0745-08	TCGA-AB-2943-11A-01W-0745-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	9ffddf15-3f38-4dac-a9f6-2636130c050b	32623a30-c839-4621-a7df-af0b615c01c1	g.chr17:7577121G>A	ENST00000269305.4	-	8	1006	c.817C>T	c.(817-819)Cgt>Tgt	p.R273C	TP53_ENST00000420246.2_Missense_Mutation_p.R273C|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Missense_Mutation_p.R273C|TP53_ENST00000413465.2_Intron|TP53_ENST00000445888.2_Missense_Mutation_p.R273C|TP53_ENST00000455263.2_Missense_Mutation_p.R273C	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	273	Interaction with AXIN1. {ECO:0000250}.|Interaction with DNA.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		R -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17224074, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:9450901}.|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in LFS; germline mutation and in sporadic cancers; somatic mutation; abolishes sequence-specific DNA binding; does not induce SNAI1 degradation; dbSNP:rs28934576). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:1565144, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1699228, ECO:0000269|PubMed:1868473, ECO:0000269|PubMed:7682763, ECO:0000269|Ref.14}.|R -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974}.|R -> N (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in sporadic cancers; somatic mutation).|R -> S (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> Y (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).		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.R273C(481)|p.R273S(16)|p.R273G(9)|p.0?(8)|p.?(2)|p.R273fs*72(2)|p.R273fs*33(2)|p.R273fs*32(2)|p.V272>?(2)|p.F270fs*72(1)|p.R273_C275delRVC(1)|p.L265_K305del41(1)|p.S269fs*21(1)|p.E258fs*71(1)|p.R273fs*71(1)|p.F270_D281del12(1)|p.E271_R273delEVR(1)|p.V272_K292del21(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)	GCACAAACACGCACCTCAAAG	0.542	R273C(8MGBA_CENTRAL_NERVOUS_SYSTEM)|R273C(BL70_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(EFO27_OVARY)|R273C(KARPAS299_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(MFE319_ENDOMETRIUM)|R273C(NCIH1048_LUNG)|R273C(PANC0213_PANCREAS)|R273C(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(RDES_BONE)|R273C(RH30_SOFT_TISSUE)|R273C(RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(SH10TC_STOMACH)|R273C(SJRH30_SOFT_TISSUE)|R273C(SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(SW1710_URINARY_TRACT)|R273C(SW1783_CENTRAL_NERVOUS_SYSTEM)|R273C(TT2609C02_THYROID)	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)	dbGAP	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	533	Substitution - Missense(506)|Whole gene deletion(8)|Deletion - Frameshift(8)|Deletion - In frame(5)|Insertion - Frameshift(2)|Unknown(2)|Complex(2)	central_nervous_system(117)|large_intestine(108)|ovary(32)|haematopoietic_and_lymphoid_tissue(31)|upper_aerodigestive_tract(30)|stomach(25)|urinary_tract(23)|lung(21)|breast(21)|liver(20)|endometrium(17)|oesophagus(17)|bone(16)|pancreas(15)|prostate(8)|skin(7)|cervix(6)|biliary_tract(6)|kidney(3)|thyroid(3)|vulva(2)|genital_tract(1)|penis(1)|adrenal_gland(1)|salivary_gland(1)|small_intestine(1)	17	GRCh37	CM010471|CM010473|CM951233	TP53	M	rs121913343						65.0	56.0	59.0					17																	7577121		2203	4300	6503	7517846	SO:0001583	missense	0	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.817C>T	17.37:g.7577121G>A	ENSP00000269305:p.Arg273Cys	98	6.54	7		17	88.96	137	7517846	46	74.61	144	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	PatternScan_P53,superfamily_p53-like transcription factors,HMMPfam_P53_tetramer,superfamily_p53 tetramerization domain,HMMPfam_P53,HMMPfam_P53_TAD	p.R273C	ENST00000269305.4	37	c.817	CCDS11118.1	17	.	.	.	.	.	.	.	.	.	.	G	17.48	3.400216	0.62177	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99869	-7.34;-7.34;-7.34;-7.34;-7.34;-7.34	4.92	3.95	0.45737	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99851	0.9931	M	0.90759	3.145	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.998;0.998;0.999;0.996	D	0.96877	0.9643	10	0.87932	D	0	-11.9995	11.2235	0.48869	0.0895:0.0:0.9105:0.0	.	273;273;273;273	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	C	273;273;273;273;273;262;141	ENSP00000352610:R273C;ENSP00000269305:R273C;ENSP00000398846:R273C;ENSP00000391127:R273C;ENSP00000391478:R273C;ENSP00000425104:R141C	ENSP00000269305:R273C	R	-	1	0	TP53	7517846	1.000000	0.71417	0.066000	0.19879	0.723000	0.41478	4.540000	0.60664	1.299000	0.44798	0.462000	0.41574	CGT	-	superfamily_p53-like transcription factors,HMMPfam_P53		0.542	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TP53	protein_coding	OTTHUMT00000367397.1	G	NM_000546		7517846	-1	no_errors	NM_000546.4	genbank	human	reviewed	54_36p	missense	SNP	0.797	A
ZNF460	10794	genome.wustl.edu	37	19	57803013	57803013	+	Missense_Mutation	SNP	A	A	T			TCGA-AB-2943-03A-01W-0745-08	TCGA-AB-2943-11A-01W-0745-08	A	A	A	T	A	A	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	9ffddf15-3f38-4dac-a9f6-2636130c050b	32623a30-c839-4621-a7df-af0b615c01c1	g.chr19:57803013A>T	ENST00000360338.3	+	3	1426	c.1104A>T	c.(1102-1104)caA>caT	p.Q368H	ZNF460_ENST00000537645.1_Missense_Mutation_p.Q327H	NM_006635.3	NP_006626.3	Q14592	ZN460_HUMAN	zinc finger protein 460	368					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(3)|large_intestine(2)|lung(9)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		TGTGCAGTCAATGTGGAAAGG	0.493																																						dbGAP											0			19											85.0	83.0	83.0					19																	57803013		2203	4300	6503	62494825	SO:0001583	missense	0			X78931	CCDS12949.1	19q13.4	2013-01-08				ENSG00000197714		"""Zinc fingers, C2H2-type"", ""-"""	21628	protein-coding gene	gene with protein product		604755	"""zinc finger protein 272"""	ZNF272		15004467	Standard	NM_006635		Approved	HZF8	uc002qog.2	Q14592		ENST00000360338.3:c.1104A>T	19.37:g.57803013A>T	ENSP00000353491:p.Gln368His	40	0.00	0		30	40.00	20	62494825	90	27.20	34	A4FU64|B4DNX9|Q2VPC7|Q6VSF8	Missense_Mutation	SNP	HMMPfam_KRAB,HMMSmart_KRAB,superfamily_Krueppel-associated_box,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,superfamily_SSF57667	p.Q368H	ENST00000360338.3	37	c.1104	CCDS12949.1	19	.	.	.	.	.	.	.	.	.	.	A	9.865	1.197259	0.22037	.	.	ENSG00000197714	ENST00000537645;ENST00000360338	T;T	0.36520	3.18;1.25	1.68	-3.35	0.04928	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.16938	0.0407	N	0.04820	-0.15	0.09310	N	0.999998	P	0.41265	0.744	B	0.39119	0.291	T	0.20974	-1.0259	9	0.87932	D	0	.	8.7057	0.34354	0.6253:0.0:0.3747:0.0	.	368	Q14592	ZN460_HUMAN	H	327;368	ENSP00000446167:Q327H;ENSP00000353491:Q368H	ENSP00000353491:Q368H	Q	+	3	2	ZNF460	62494825	0.000000	0.05858	0.016000	0.15963	0.701000	0.40568	-6.570000	0.00061	-1.339000	0.02230	-1.181000	0.01715	CAA	-	HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,superfamily_SSF57667		0.493	ZNF460-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ZNF460	protein_coding	OTTHUMT00000465727.1	A	NM_006635		62494825	+1	no_errors	NM_006635.3	genbank	human	validated	54_36p	missense	SNP	0.012	T
DESI1	27351	genome.wustl.edu	37	22	42000072	42000072	+	Missense_Mutation	SNP	G	G	T	rs145019403		TCGA-AB-2943-03A-01W-0745-08	TCGA-AB-2943-11A-01W-0745-08	G	G	G	T	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	9ffddf15-3f38-4dac-a9f6-2636130c050b	32623a30-c839-4621-a7df-af0b615c01c1	g.chr22:42000072G>T	ENST00000263256.6	-	4	522	c.266C>A	c.(265-267)tCc>tAc	p.S89Y	DESI1_ENST00000463886.1_5'UTR	NM_015704.2	NP_056519.1	Q6ICB0	DESI1_HUMAN	desumoylating isopeptidase 1	89	PPPDE peptidase.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	peptidase activity (GO:0008233)										CCCCAGGGAGGAGAGGTACTC	0.547																																						dbGAP											0			22											92.0	95.0	94.0					22																	42000072		2203	4300	6503	40330018	SO:0001583	missense	0			AF038183	CCDS33652.1	22q13.2	2012-05-16	2012-05-16	2012-05-16	ENSG00000100418	ENSG00000100418			24577	protein-coding gene	gene with protein product		614637	"""family with sequence similarity 152, member B"", ""PPPDE peptidase domain containing 2"""	FAM152B, PPPDE2		8619474, 9110174, 22370726	Standard	NM_015704		Approved	D15Wsu75e	uc003bam.2	Q6ICB0	OTTHUMG00000044632	ENST00000263256.6:c.266C>A	22.37:g.42000072G>T	ENSP00000263256:p.Ser89Tyr	57	1.72	1		179	13.53	28	40330018	97	20.16	25		Missense_Mutation	SNP	HMMPfam_DUF862	p.S89Y	ENST00000263256.6	37	c.266	CCDS33652.1	22	.	.	.	.	.	.	.	.	.	.	G	25.8	4.674274	0.88445	.	.	ENSG00000100418	ENST00000263256	.	.	.	5.74	5.74	0.90152	Domain of unknown function DUF862, eukaryotic (1);	0.000000	0.85682	D	0.000000	T	0.70263	0.3204	L	0.61387	1.9	0.80722	D	1	P	0.45634	0.863	P	0.47915	0.561	T	0.72283	-0.4339	9	0.72032	D	0.01	-29.5061	20.3473	0.98799	0.0:0.0:1.0:0.0	.	89	Q6ICB0	PPDE2_HUMAN	Y	89	.	ENSP00000263256:S89Y	S	-	2	0	PPPDE2	40330018	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.952000	0.87827	2.890000	0.99128	0.650000	0.86243	TCC	-	HMMPfam_DUF862		0.547	DESI1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	PPPDE2	protein_coding	OTTHUMT00000104124.3	G	NM_015704		40330018	-1	no_errors	NM_015704.1	genbank	human	provisional	54_36p	missense	SNP	1.000	T
