#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_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_EVS_AA	i_EVS_All	i_EVS_EA	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_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains_WU	i_amino_acid_change_WU	i_annotation_transcript	i_build	i_c_position_WU	i_ccds_id	i_chromosome_name_WU	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_default_gene_name_WU	i_deletion_substructures_WU	i_domain_WU	i_ensembl_gene_id	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_WU	i_gene_name_source_WU	i_gene_type	i_havana_transcript	i_normal_ref_reads	i_normal_vaf	i_normal_var_reads	i_reference_WU	i_refseq_mrna_id	i_secondary_variant_classification	i_start_WU	i_stop_WU	i_strand_WU	i_transcript_error_WU	i_transcript_name_WU	i_transcript_source_WU	i_transcript_species_WU	i_transcript_status_WU	i_transcript_version_WU	i_trv_type_WU	i_tumor_ref_reads	i_tumor_vaf	i_tumors_var_reads	i_type_WU	i_ucsc_cons_WU	i_variant_WU
ANKRD30BL	554226	genome.wustl.edu	37	2	132905500	132905500	+	3'UTR	SNP	C	C	T	rs3114236	byFrequency	TCGA-AR-A2LJ-01A-12D-A19Y-09	TCGA-AR-A2LJ-10A-01D-A19Y-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	5ce74a42-4e07-4bb4-8c86-f24518d7152d	e1344996-bfac-4686-811b-4be7bbd84c50	g.chr2:132905500C>T	ENST00000409867.1	-	0	1230				ANKRD30BL_ENST00000470729.1_5'UTR			A7E2S9	A30BL_HUMAN	ankyrin repeat domain 30B-like											endometrium(1)|kidney(3)	4						tagaagggggctgtttaatga	0.423													T|||	3415	0.681909	0.944	0.634	5008	,	,		15261	0.5169		0.5507	False		,,,				2504	0.6667					dbGAP											0																																										-	-	-	SO:0001624	3_prime_UTR_variant	0					2q21.2	2013-01-22	2010-06-14	2010-06-14	ENSG00000163046	ENSG00000163046		"""Ankyrin repeat domain containing"""	35167	protein-coding gene	gene with protein product			"""non-protein coding RNA 164"", ""ankyrin repeat domain 30B pseudogene 3"""	NCRNA00164, ANKRD30BP3		17114284	Standard	NR_027019		Approved		uc002tti.3	A7E2S9	OTTHUMG00000153491	ENST00000409867.1:c.*204G>A	2.37:g.132905500C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	B8ZZL7	RNA	SNP	-	NULL	ENST00000409867.1	37	NULL		2																																																																																			ANKRD30BL	-	-	ENSG00000163046		0.423	ANKRD30BL-001	NOVEL	basic|appris_principal	protein_coding	ANKRD30BL	HGNC	protein_coding	OTTHUMT00000331353.2	8	0.00	0	C	NR_027019		132905500	132905500	-1	no_errors	ENST00000465868	ensembl	human	known	69_37n	rna	2	75.00	6	SNP	0.349	T
CD47	961	genome.wustl.edu	37	3	107770938	107770938	+	Intron	SNP	T	T	A	rs9855486	byFrequency	TCGA-AR-A2LJ-01A-12D-A19Y-09	TCGA-AR-A2LJ-10A-01D-A19Y-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	5ce74a42-4e07-4bb4-8c86-f24518d7152d	e1344996-bfac-4686-811b-4be7bbd84c50	g.chr3:107770938T>A	ENST00000361309.5	-	8	983				CD47_ENST00000355354.7_Intron|CD47_ENST00000471694.1_5'UTR	NM_001777.3	NP_001768.1	Q08722	CD47_HUMAN	CD47 molecule						blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|opsonization (GO:0008228)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of inflammatory response (GO:0050729)|positive regulation of phagocytosis (GO:0050766)|positive regulation of T cell activation (GO:0050870)|response to bacterium (GO:0009617)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	thrombospondin receptor activity (GO:0070053)			endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|urinary_tract(1)	9			OV - Ovarian serous cystadenocarcinoma(3;0.0191)|Epithelial(53;0.118)			GAGATGTTAATGAAAGAGTTC	0.284													T|||	424	0.0846645	0.0431	0.1037	5008	,	,		18516	0.0288		0.1759	False		,,,				2504	0.091					dbGAP											0																																										-	-	-	SO:0001627	intron_variant	0				CCDS43125.1, CCDS43126.1	3q13.1-q13.2	2013-01-11	2006-03-28		ENSG00000196776	ENSG00000196776		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1682	protein-coding gene	gene with protein product	"""antigen identified by monoclonal antibody 1D8"", ""antigenic surface determinant protein OA3"", ""integrin associated protein"", ""Rh-related antigen"", ""leukocyte surface antigen CD47"", ""CD47 glycoprotein"""	601028	"""CD47 antigen (Rh-related antigen, integrin-associated signal transducer)"""	MER6		8294396, 2277087	Standard	XM_005247908		Approved	IAP, OA3	uc003dwt.1	Q08722	OTTHUMG00000044216	ENST00000361309.5:c.878-121A>T	3.37:g.107770938T>A		Somatic		WXS	Illumina GAIIx	Phase_IV	A8K198|D3DN59|Q53Y71|Q96A60	RNA	SNP	-	NULL	ENST00000361309.5	37	NULL	CCDS43126.1	3																																																																																			CD47	-	-	ENSG00000196776		0.284	CD47-004	KNOWN	basic|CCDS	protein_coding	CD47	HGNC	protein_coding	OTTHUMT00000102793.1	9	0.00	0	T	NM_001777		107770938	107770938	-1	no_errors	ENST00000471694	ensembl	human	known	69_37n	rna	10	37.50	6	SNP	0.083	A
CDH1	999	genome.wustl.edu	37	16	68842432	68842432	+	Missense_Mutation	SNP	G	G	C			TCGA-AR-A2LJ-01A-12D-A19Y-09	TCGA-AR-A2LJ-10A-01D-A19Y-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	5ce74a42-4e07-4bb4-8c86-f24518d7152d	e1344996-bfac-4686-811b-4be7bbd84c50	g.chr16:68842432G>C	ENST00000261769.5	+	4	684	c.493G>C	c.(493-495)Gaa>Caa	p.E165Q	CDH1_ENST00000422392.2_Missense_Mutation_p.E165Q|CDH1_ENST00000562836.1_3'UTR	NM_004360.3	NP_004351.1	P12830	CADH1_HUMAN	cadherin 1, type 1, E-cadherin (epithelial)	165	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to amino acid stimulus (GO:0071230)|cellular response to indole-3-methanol (GO:0071681)|cellular response to lithium ion (GO:0071285)|cochlea development (GO:0090102)|epithelial cell morphogenesis (GO:0003382)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|homophilic cell adhesion (GO:0007156)|intestinal epithelial cell development (GO:0060576)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of epithelial cell proliferation (GO:0050680)|neuron projection development (GO:0031175)|pituitary gland development (GO:0021983)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|protein metabolic process (GO:0019538)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of immune response (GO:0050776)|regulation of neuron migration (GO:2001222)|regulation of protein localization to cell surface (GO:2000008)|regulation of water loss via skin (GO:0033561)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)|salivary gland cavitation (GO:0060662)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|tight junction assembly (GO:0070830)|trophectodermal cell differentiation (GO:0001829)	actin cytoskeleton (GO:0015629)|aggresome (GO:0016235)|apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|axon terminus (GO:0043679)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell junction (GO:0030054)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|node of Ranvier (GO:0033268)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|trans-Golgi network (GO:0005802)	ankyrin binding (GO:0030506)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|gamma-catenin binding (GO:0045295)|glycoprotein binding (GO:0001948)|GTPase activating protein binding (GO:0032794)	p.?(2)|p.V157_Q177del(1)|p.E165_P170del(1)		NS(6)|biliary_tract(8)|breast(161)|central_nervous_system(4)|endometrium(9)|kidney(4)|large_intestine(13)|lung(13)|oesophagus(3)|ovary(2)|prostate(3)|soft_tissue(2)|stomach(76)|thyroid(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	311		all_neural(199;0.0189)|Ovarian(137;0.0563)		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)		CAGCTGCCCAGAAAATGAAAA	0.468			"""Mis, N, F, S"""		"""lobular breast, gastric"""	gastric			Hereditary Diffuse Gastric Cancer																													dbGAP	yes	Rec	yes	Familial gastric carcinoma	16	16q22.1	999	"""cadherin 1, type 1, E-cadherin (epithelial) (ECAD)"""		E	4	Unknown(2)|Deletion - In frame(2)	breast(2)|lung(1)|stomach(1)											62.0	63.0	63.0					16																	68842432		2198	4300	6498	-	-	-	SO:0001583	missense	0	Familial Cancer Database	HDGC	L08599	CCDS10869.1	16q22.1	2014-09-17			ENSG00000039068	ENSG00000039068		"""CD molecules"", ""Cadherins / Major cadherins"""	1748	protein-coding gene	gene with protein product	"""E-Cadherin"""	192090		UVO		9925936	Standard	NM_004360		Approved	uvomorulin, CD324	uc002ewg.1	P12830	OTTHUMG00000137561	ENST00000261769.5:c.493G>C	16.37:g.68842432G>C	ENSP00000261769:p.Glu165Gln	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K1U7|Q13799|Q14216|Q15855|Q16194|Q4PJ14|Q9UII8	Missense_Mutation	SNP	pfam_Cadherin,pfam_Cadherin_cytoplasmic-dom,pfam_Cadherin_pro_dom,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin,prints_Cadherin	p.E165Q	ENST00000261769.5	37	c.493	CCDS10869.1	16	.	.	.	.	.	.	.	.	.	.	G	16.22	3.061824	0.55432	.	.	ENSG00000039068	ENST00000261769;ENST00000379120;ENST00000268794;ENST00000422392	T;T	0.75938	-0.98;-0.98	5.87	5.87	0.94306	Cadherin (1);Cadherin-like (2);	0.000000	0.52532	D	0.000078	D	0.91650	0.7361	H	0.97131	3.945	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.93402	0.6761	10	0.87932	D	0	.	20.1777	0.98189	0.0:0.0:1.0:0.0	.	165;165	Q9UII8;P12830	.;CADH1_HUMAN	Q	165	ENSP00000261769:E165Q;ENSP00000414946:E165Q	ENSP00000261769:E165Q	E	+	1	0	CDH1	67399933	1.000000	0.71417	0.998000	0.56505	0.967000	0.64934	7.570000	0.82390	2.941000	0.99782	0.655000	0.94253	GAA	CDH1	-	pfam_Cadherin,superfamily_Cadherin-like	ENSG00000039068		0.468	CDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CDH1	HGNC	protein_coding	OTTHUMT00000268897.2	56	0.00	0	G	NM_004360		68842432	68842432	+1	no_errors	ENST00000261769	ensembl	human	known	69_37n	missense	25	19.35	6	SNP	1.000	C
CDH4	1002	genome.wustl.edu	37	20	60485520	60485520	+	Missense_Mutation	SNP	G	G	A			TCGA-AR-A2LJ-01A-12D-A19Y-09	TCGA-AR-A2LJ-10A-01D-A19Y-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	5ce74a42-4e07-4bb4-8c86-f24518d7152d	e1344996-bfac-4686-811b-4be7bbd84c50	g.chr20:60485520G>A	ENST00000360469.5	+	9	1319	c.1231G>A	c.(1231-1233)Gca>Aca	p.A411T	CDH4_ENST00000543233.1_Missense_Mutation_p.A337T	NM_001794.3	NP_001785.2	P55283	CADH4_HUMAN	cadherin 4, type 1, R-cadherin (retinal)	411	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(2)|lung(25)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			GACCGTGGTCGCAAACCTCAC	0.542																																						dbGAP											0													108.0	85.0	93.0					20																	60485520		2203	4300	6503	-	-	-	SO:0001583	missense	0			L34059	CCDS13488.1, CCDS58784.1	20q13.3	2010-01-26			ENSG00000179242	ENSG00000179242		"""Cadherins / Major cadherins"""	1763	protein-coding gene	gene with protein product	"""R-Cadherin"""	603006				10191097, 10516427	Standard	NM_001794		Approved		uc002ybn.2	P55283	OTTHUMG00000032890	ENST00000360469.5:c.1231G>A	20.37:g.60485520G>A	ENSP00000353656:p.Ala411Thr	Somatic		WXS	Illumina GAIIx	Phase_IV	B3KWB8|G3V1P8|Q2M208|Q5VZ44|Q9BZ05	Missense_Mutation	SNP	pfam_Cadherin,pfam_Cadherin_cytoplasmic-dom,pfam_Cadherin_pro_dom,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin,prints_Cadherin,prints_Desmocollin	p.A411T	ENST00000360469.5	37	c.1231	CCDS13488.1	20	.	.	.	.	.	.	.	.	.	.	g	13.30	2.196550	0.38806	.	.	ENSG00000179242	ENST00000360469;ENST00000536643;ENST00000543233	T;T	0.52754	0.65;0.65	4.66	4.66	0.58398	Cadherin (3);Cadherin-like (1);	0.109676	0.64402	D	0.000009	T	0.36635	0.0974	L	0.33093	0.98	0.58432	D	0.999996	P	0.45569	0.861	B	0.37550	0.253	T	0.20706	-1.0267	9	.	.	.	.	17.1368	0.86742	0.0:0.0:1.0:0.0	.	411	P55283	CADH4_HUMAN	T	411;319;337	ENSP00000353656:A411T;ENSP00000443301:A337T	.	A	+	1	0	CDH4	59918915	1.000000	0.71417	0.308000	0.25141	0.192000	0.23643	6.022000	0.70839	2.145000	0.66743	0.556000	0.70494	GCA	CDH4	-	pfam_Cadherin,superfamily_Cadherin-like,pfscan_Cadherin	ENSG00000179242		0.542	CDH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CDH4	HGNC	protein_coding	OTTHUMT00000079965.2	20	0.00	0	G	NM_001794		60485520	60485520	+1	no_errors	ENST00000360469	ensembl	human	known	69_37n	missense	16	23.81	5	SNP	0.978	A
DIP2C	22982	genome.wustl.edu	37	10	373069	373069	+	Silent	SNP	C	C	T			TCGA-AR-A2LJ-01A-12D-A19Y-09	TCGA-AR-A2LJ-10A-01D-A19Y-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	5ce74a42-4e07-4bb4-8c86-f24518d7152d	e1344996-bfac-4686-811b-4be7bbd84c50	g.chr10:373069C>T	ENST00000280886.6	-	31	3888	c.3801G>A	c.(3799-3801)gcG>gcA	p.A1267A		NM_014974.2	NP_055789.1	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C (Drosophila)	1267						nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(8)|endometrium(6)|kidney(10)|large_intestine(13)|lung(26)|ovary(3)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	81		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		GCCTCTCTTCCGCCACAACCA	0.617																																						dbGAP											0													69.0	59.0	62.0					10																	373069		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			BC035216	CCDS7054.1	10p15.3	2006-01-13	2006-01-13	2006-01-13	ENSG00000151240	ENSG00000151240			29150	protein-coding gene	gene with protein product		611380	"""KIAA0934"""	KIAA0934			Standard	NM_014974		Approved		uc001ifp.3	Q9Y2E4	OTTHUMG00000017532	ENST00000280886.6:c.3801G>A	10.37:g.373069C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	B4DPI5|Q5SS78	Missense_Mutation	SNP	pfam_AMP-dep_Synth/Lig	p.G73R	ENST00000280886.6	37	c.217	CCDS7054.1	10	.	.	.	.	.	.	.	.	.	.	C	0.492	-0.874996	0.02550	.	.	ENSG00000151240	ENST00000434695	.	.	.	5.8	-8.57	0.00900	.	.	.	.	.	T	0.35335	0.0928	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.39840	-0.9594	4	.	.	.	-27.5392	3.2312	0.06749	0.2489:0.3803:0.0823:0.2885	.	.	.	.	R	73	.	.	G	-	1	0	DIP2C	363069	0.021000	0.18746	0.176000	0.23000	0.024000	0.10985	-0.770000	0.04705	-2.127000	0.00819	-2.630000	0.00154	GGA	DIP2C	-	pfam_AMP-dep_Synth/Lig	ENSG00000151240		0.617	DIP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DIP2C	HGNC	protein_coding	OTTHUMT00000046389.1	13	0.00	0	C	NM_014974		373069	373069	-1	no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region	ENST00000434695	ensembl	human	known	69_37n	missense	11	31.25	5	SNP	0.088	T
KLHL6	89857	genome.wustl.edu	37	3	183225934	183225934	+	Silent	SNP	C	C	T			TCGA-AR-A2LJ-01A-12D-A19Y-09	TCGA-AR-A2LJ-10A-01D-A19Y-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	5ce74a42-4e07-4bb4-8c86-f24518d7152d	e1344996-bfac-4686-811b-4be7bbd84c50	g.chr3:183225934C>T	ENST00000341319.3	-	3	857	c.822G>A	c.(820-822)acG>acA	p.T274T		NM_130446.2	NP_569713.2	Q8WZ60	KLHL6_HUMAN	kelch-like family member 6	274	BACK.				B cell receptor signaling pathway (GO:0050853)|germinal center formation (GO:0002467)					breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(7)|kidney(1)|large_intestine(6)|liver(1)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	44	all_cancers(143;9.2e-12)|Ovarian(172;0.0172)		all cancers(12;1.29e-44)|Epithelial(37;1.24e-38)|LUSC - Lung squamous cell carcinoma(7;2.58e-24)|Lung(8;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.32e-22)			CTGCTTCCACCGTCTCCACAA	0.567																																						dbGAP											0													127.0	118.0	121.0					3																	183225934		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AF441792	CCDS3245.2	3q27.3	2013-01-30	2013-01-30		ENSG00000172578	ENSG00000172578		"""Kelch-like"", ""BTB/POZ domain containing"""	18653	protein-coding gene	gene with protein product	"""kelch-like protein KLHL6"""	614214	"""kelch-like 6 (Drosophila)"""			11214971, 12617994	Standard	NM_130446		Approved	FLJ00029	uc003flr.3	Q8WZ60	OTTHUMG00000148673	ENST00000341319.3:c.822G>A	3.37:g.183225934C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	B2RB31|D3DNS8|Q8N5I1|Q8N892	Silent	SNP	pfam_Kelch_1,pfam_BACK,pfam_BTB_POZ,pfam_Kelch_2,superfamily_BTB/POZ_fold,smart_BTB/POZ-like,smart_BACK,smart_Kelch_1,pirsf_Kelch-like_gigaxonin,pfscan_BTB/POZ-like	p.T274	ENST00000341319.3	37	c.822	CCDS3245.2	3																																																																																			KLHL6	-	pfam_BACK,smart_BACK,pirsf_Kelch-like_gigaxonin	ENSG00000172578		0.567	KLHL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KLHL6	HGNC	protein_coding	OTTHUMT00000309024.1	51	0.00	0	C	NM_130446		183225934	183225934	-1	no_errors	ENST00000341319	ensembl	human	known	69_37n	silent	36	10.00	4	SNP	0.850	T
LPCAT3	10162	genome.wustl.edu	37	12	7087848	7087848	+	Missense_Mutation	SNP	G	G	T			TCGA-AR-A2LJ-01A-12D-A19Y-09	TCGA-AR-A2LJ-10A-01D-A19Y-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	5ce74a42-4e07-4bb4-8c86-f24518d7152d	e1344996-bfac-4686-811b-4be7bbd84c50	g.chr12:7087848G>T	ENST00000261407.4	-	8	875	c.790C>A	c.(790-792)Cac>Aac	p.H264N	LPCAT3_ENST00000535021.1_5'UTR|U47924.30_ENST00000606112.1_lincRNA	NM_005768.5	NP_005759.4	Q6P1A2	MBOA5_HUMAN	lysophosphatidylcholine acyltransferase 3	264					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|regulation of plasma lipoprotein particle levels (GO:0097006)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	1-acylglycerophosphocholine O-acyltransferase activity (GO:0047184)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(4)|ovary(1)|skin(2)	17						CAGAAGGGGTGGTTCTTGAGG	0.463																																						dbGAP											0													88.0	77.0	80.0					12																	7087848		2203	4300	6503	-	-	-	SO:0001583	missense	0			U72515	CCDS8572.1	12p13.31	2010-05-12	2008-06-24	2008-06-24	ENSG00000111684	ENSG00000111684			30244	protein-coding gene	gene with protein product		611950	"""O-acyltransferase (membrane bound) domain containing 5"", ""membrane bound O-acyltransferase domain containing 5"""	OACT5, MBOAT5		8723724, 9074930, 18195019	Standard	NM_005768		Approved	C3F, nessy	uc001qsi.3	Q6P1A2	OTTHUMG00000168970	ENST00000261407.4:c.790C>A	12.37:g.7087848G>T	ENSP00000261407:p.His264Asn	Somatic		WXS	Illumina GAIIx	Phase_IV	B2RDH0|B7Z3N3|Q7KZS1|Q92980|Q9BW40	Missense_Mutation	SNP	pfam_MBOAT_fam	p.H264N	ENST00000261407.4	37	c.790	CCDS8572.1	12	.	.	.	.	.	.	.	.	.	.	G	9.151	1.016271	0.19355	.	.	ENSG00000111684	ENST00000261407	T	0.72615	-0.67	5.54	3.64	0.41730	.	0.734274	0.13721	N	0.367364	T	0.63920	0.2552	L	0.54323	1.7	0.09310	N	1	B	0.14438	0.01	B	0.15870	0.014	T	0.52208	-0.8606	10	0.27785	T	0.31	-13.1503	10.5688	0.45188	0.0:0.1083:0.559:0.3326	.	264	Q6P1A2	MBOA5_HUMAN	N	264	ENSP00000261407:H264N	ENSP00000261407:H264N	H	-	1	0	LPCAT3	6958109	0.976000	0.34144	0.128000	0.21923	0.381000	0.30169	4.071000	0.57556	1.327000	0.45338	0.655000	0.94253	CAC	LPCAT3	-	pfam_MBOAT_fam	ENSG00000111684		0.463	LPCAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LPCAT3	HGNC	protein_coding	OTTHUMT00000401812.1	23	0.00	0	G	NM_005768		7087848	7087848	-1	no_errors	ENST00000261407	ensembl	human	known	69_37n	missense	18	14.29	3	SNP	0.026	T
MUC4	4585	genome.wustl.edu	37	3	195506303	195506303	+	Missense_Mutation	SNP	G	G	T	rs192584273	byFrequency	TCGA-AR-A2LJ-01A-12D-A19Y-09	TCGA-AR-A2LJ-10A-01D-A19Y-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	5ce74a42-4e07-4bb4-8c86-f24518d7152d	e1344996-bfac-4686-811b-4be7bbd84c50	g.chr3:195506303G>T	ENST00000463781.3	-	2	12607	c.12148C>A	c.(12148-12150)Cct>Act	p.P4050T	MUC4_ENST00000475231.1_Missense_Mutation_p.P4050T|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.P4050T(3)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TTGGTGACAGGAAGAGGGGTG	0.572													.|||	585	0.116813	0.3132	0.0922	5008	,	,		10067	0.0169		0.0845	False		,,,				2504	0.0051					dbGAP											3	Substitution - Missense(3)	haematopoietic_and_lymphoid_tissue(2)|kidney(1)											36.0	20.0	25.0					3																	195506303		593	1229	1822	-	-	-	SO:0001583	missense	0			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.12148C>A	3.37:g.195506303G>T	ENSP00000417498:p.Pro4050Thr	Somatic		WXS	Illumina GAIIx	Phase_IV	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	pfam_Nidogen_extracell_dom,pfam_AMOP,pfam_VWF_type-D,smart_Nidogen_extracell_dom,smart_AMOP,smart_VWF_type-D,smart_EGF-like,pfscan_AMOP,pfscan_EG-like_dom	p.P4050T	ENST00000463781.3	37	c.12148	CCDS54700.1	3	167	0.07646520146520147	97	0.19715447154471544	31	0.0856353591160221	3	0.005244755244755245	36	0.047493403693931395	g	1.949	-0.441794	0.04604	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32023	1.47;1.53	.	.	.	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.15141	0.012	B	0.01281	0.0	T	0.37865	-0.9687	6	.	.	.	.	4.7077	0.12858	1.0E-4:0.0:0.6463:0.3536	.	3922	E7ESK3	.	T	4050	ENSP00000417498:P4050T;ENSP00000420243:P4050T	.	P	-	1	0	MUC4	196991082	0.000000	0.05858	0.001000	0.08648	0.060000	0.15804	-0.709000	0.05030	-0.833000	0.04245	0.064000	0.15345	CCT	MUC4	-	NULL	ENSG00000145113		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	MUC4	HGNC	protein_coding	OTTHUMT00000324081.6	25	0.00	0	G	NM_018406		195506303	195506303	-1	no_errors	ENST00000463781	ensembl	human	known	69_37n	missense	16	23.81	5	SNP	0.009	T
NKPD1	284353	genome.wustl.edu	37	19	45662050	45662050	+	5'Flank	SNP	G	G	T			TCGA-AR-A2LJ-01A-12D-A19Y-09	TCGA-AR-A2LJ-10A-01D-A19Y-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	5ce74a42-4e07-4bb4-8c86-f24518d7152d	e1344996-bfac-4686-811b-4be7bbd84c50	g.chr19:45662050G>T	ENST00000438936.2	-	0	0				NKPD1_ENST00000317951.4_Missense_Mutation_p.P134T			Q17RQ9	NKPD1_HUMAN	NTPase, KAP family P-loop domain containing 1							integral component of membrane (GO:0016021)				endometrium(1)|lung(4)|prostate(2)|urinary_tract(1)	8		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00863)|GBM - Glioblastoma multiforme(486;0.231)		GCCATGGCTGGTGCCGTGGTG	0.711																																						dbGAP											0													10.0	18.0	15.0					19																	45662050		689	1585	2274	-	-	-	SO:0001631	upstream_gene_variant	0			AK090919		19q13.32	2012-07-02		2012-07-02	ENSG00000179846	ENSG00000179846			24739	protein-coding gene	gene with protein product						14702039	Standard	NM_198478		Approved	FLJ33600	uc010xxi.2	Q17RQ9	OTTHUMG00000160521		19.37:g.45662050G>T	Exception_encountered	Somatic		WXS	Illumina GAIIx	Phase_IV	B7ZLG6|D6RH15|Q8N2A2	Missense_Mutation	SNP	pfam_KAP_NTPase	p.P134T	ENST00000438936.2	37	c.400		19	.	.	.	.	.	.	.	.	.	.	G	0.006	-2.022182	0.00414	.	.	ENSG00000179846	ENST00000317951	T	0.63096	-0.02	3.62	1.3	0.21679	.	.	.	.	.	T	0.49474	0.1559	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.37979	-0.9682	5	.	.	.	.	6.3414	0.21324	0.1046:0.0:0.7148:0.1806	.	.	.	.	T	134	ENSP00000321976:P134T	.	P	-	1	0	NKPD1	50353890	0.000000	0.05858	0.000000	0.03702	0.045000	0.14185	0.547000	0.23299	0.291000	0.22468	0.561000	0.74099	CCA	NKPD1	-	NULL	ENSG00000179846		0.711	NKPD1-001	KNOWN	basic	protein_coding	NKPD1	HGNC	protein_coding	OTTHUMT00000360950.2	35	0.00	0	G	NM_198478		45662050	45662050	-1	no_errors	ENST00000317951	ensembl	human	known	69_37n	missense	21	16.00	4	SNP	0.001	T
NOP2	4839	genome.wustl.edu	37	12	6677049	6677049	+	Silent	SNP	C	C	T			TCGA-AR-A2LJ-01A-12D-A19Y-09	TCGA-AR-A2LJ-10A-01D-A19Y-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	5ce74a42-4e07-4bb4-8c86-f24518d7152d	e1344996-bfac-4686-811b-4be7bbd84c50	g.chr12:6677049C>T	ENST00000322166.5	-	2	157	c.36G>A	c.(34-36)cgG>cgA	p.R12R	NOP2_ENST00000541778.1_Silent_p.R12R|NOP2_ENST00000382421.3_Silent_p.R12R|NOP2_ENST00000537442.1_Silent_p.R12R|NOP2_ENST00000540228.1_Silent_p.R12R|NOP2_ENST00000545915.1_Silent_p.R12R|NOP2_ENST00000542015.1_5'UTR|NOP2_ENST00000545200.1_Silent_p.R12R|NOP2_ENST00000399466.2_Silent_p.R12R	NM_001258308.1|NM_006170.3	NP_001245237.1|NP_006161.2	P46087	NOP2_HUMAN	NOP2 nucleolar protein	12					positive regulation of cell proliferation (GO:0008284)|rRNA processing (GO:0006364)	nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)			breast(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	19						GGCCTGGCCCCCGCTTCTCCT	0.612																																						dbGAP											0													67.0	72.0	71.0					12																	6677049		1933	4129	6062	-	-	-	SO:0001819	synonymous_variant	0				CCDS44811.1, CCDS58202.1, CCDS58203.1, CCDS58204.1	12p13	2012-12-10	2012-12-10	2008-10-13	ENSG00000111641	ENSG00000111641		"""NOP2/Sun domain containing"""	7867	protein-coding gene	gene with protein product	"""NOP2/Sun domain family, member 1"""	164031	"""nucleolar protein 1 (120kD)"", ""nucleolar protein 1, 120kDa"", ""nucleolar protein 2 homolog (yeast)"", ""NOP2 nucleolar protein homolog (yeast)"""	NOL1		8088812	Standard	NM_006170		Approved	NOP120, NSUN1, p120	uc021qtz.2	P46087	OTTHUMG00000169163	ENST00000322166.5:c.36G>A	12.37:g.6677049C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	A1A4Z3|B3KPD6|Q05BA7|Q0P5S5|Q3KQS4|Q58F30	Silent	SNP	pfam_Fmu/NOL1/Nop2p,pfam_P120R,pfam_rRNA_MeTrfase_FtsJ_dom,prints_RCMT,prints_RCMT_NOP2,tigrfam_Nop2p	p.R12	ENST00000322166.5	37	c.36	CCDS58203.1	12																																																																																			NOP2	-	NULL	ENSG00000111641		0.612	NOP2-007	KNOWN	basic|appris_principal|CCDS	protein_coding	NOP2	HGNC	protein_coding	OTTHUMT00000402614.1	34	0.00	0	C	NM_006170		6677049	6677049	-1	no_errors	ENST00000322166	ensembl	human	known	69_37n	silent	26	13.33	4	SNP	0.960	T
OR4F17	81099	genome.wustl.edu	37	19	111016	111016	+	Missense_Mutation	SNP	T	T	G	rs200336441		TCGA-AR-A2LJ-01A-12D-A19Y-09	TCGA-AR-A2LJ-10A-01D-A19Y-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	5ce74a42-4e07-4bb4-8c86-f24518d7152d	e1344996-bfac-4686-811b-4be7bbd84c50	g.chr19:111016T>G	ENST00000585993.1	+	2	477	c.338T>G	c.(337-339)tTt>tGt	p.F113C	OR4F17_ENST00000318050.3_Missense_Mutation_p.F113C			Q8NGA8	O4F17_HUMAN	olfactory receptor, family 4, subfamily F, member 17	113						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			lung(2)	2		all_cancers(10;1.05e-30)|all_epithelial(18;3.04e-19)|Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;2.49e-05)|all_lung(49;4.36e-05)|Breast(49;0.000304)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCCATGGGCTTTGACAGATAT	0.463																																						dbGAP											0													1.0	1.0	1.0					19																	111016		76	150	226	-	-	-	SO:0001583	missense	0			AC005605	CCDS32854.1	19p13.3	2012-08-09						"""GPCR / Class A : Olfactory receptors"""	15381	protein-coding gene	gene with protein product				OR4F19, OR4F11P, OR4F18			Standard	NM_001005240		Approved		uc002loc.1	Q8NGA8		ENST00000585993.1:c.338T>G	19.37:g.111016T>G	ENSP00000467301:p.Phe113Cys	Somatic		WXS	Illumina GAIIx	Phase_IV	B2RNE8	Missense_Mutation	SNP	pfam_7TM_GPCR_Rhodpsn,pfam_7TM_GPCR_olfarory/Srsx,pfscan_GPCR_Rhodpsn_supfam,prints_Olfact_rcpt,prints_7TM_GPCR_Rhodpsn	p.F113C	ENST00000585993.1	37	c.338	CCDS32854.1	19	.	.	.	.	.	.	.	.	.	.	.	9.777	1.174271	0.21704	.	.	ENSG00000176695	ENST00000442916;ENST00000318050	T	0.00520	6.85	2.55	2.55	0.30701	GPCR, rhodopsin-like superfamily (1);	0.156294	0.30193	N	0.010181	T	0.01189	0.0039	M	0.75884	2.315	0.31291	N	0.689393	D	0.76494	0.999	D	0.74674	0.984	T	0.24154	-1.0168	10	0.72032	D	0.01	.	4.9478	0.13999	0.2703:0.0:0.0:0.7297	.	113	Q8NGA8	O4F17_HUMAN	C	161;113	ENSP00000315047:F113C	ENSP00000315047:F113C	F	+	2	0	OR4F17	62016	0.698000	0.27777	1.000000	0.80357	0.325000	0.28411	0.344000	0.19962	1.410000	0.46936	0.346000	0.21813	TTT	OR4F17	-	pfam_7TM_GPCR_Rhodpsn,pfam_7TM_GPCR_olfarory/Srsx,pfscan_GPCR_Rhodpsn_supfam,prints_7TM_GPCR_Rhodpsn	ENSG00000176695		0.463	OR4F17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	OR4F17	HGNC	protein_coding	OTTHUMT00000451410.1	9	0.00	0	T			111016	111016	+1	no_errors	ENST00000318050	ensembl	human	known	69_37n	missense	11	35.29	6	SNP	0.999	G
PCDHGA2	56113	genome.wustl.edu	37	5	140720013	140720013	+	Missense_Mutation	SNP	C	C	T			TCGA-AR-A2LJ-01A-12D-A19Y-09	TCGA-AR-A2LJ-10A-01D-A19Y-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	5ce74a42-4e07-4bb4-8c86-f24518d7152d	e1344996-bfac-4686-811b-4be7bbd84c50	g.chr5:140720013C>T	ENST00000394576.2	+	1	1475	c.1475C>T	c.(1474-1476)gCg>gTg	p.A492V	PCDHGA1_ENST00000517417.1_Intron	NM_018915.2	NP_061738.1	Q9Y5H1	PCDG2_HUMAN	protocadherin gamma subfamily A, 2	492	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(32)|ovary(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TACTCTTTCGCGGAGGACACT	0.512																																						dbGAP											0													86.0	89.0	88.0					5																	140720013		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF152508	CCDS47289.1	5q31	2011-03-28			ENSG00000081853	ENSG00000081853		"""Cadherins / Protocadherins : Clustered"""	8700	other	protocadherin		606289				10380929	Standard	NM_018915		Approved	PCDH-GAMMA-A2		Q9Y5H1	OTTHUMG00000163679	ENST00000394576.2:c.1475C>T	5.37:g.140720013C>T	ENSP00000378077:p.Ala492Val	Somatic		WXS	Illumina GAIIx	Phase_IV	Q52LL6|Q9Y5D5	Missense_Mutation	SNP	pfam_Cadherin,pfam_Cadherin_N,superfamily_Cadherin-like,smart_Cadherin,prints_Cadherin,pfscan_Cadherin	p.A492V	ENST00000394576.2	37	c.1475	CCDS47289.1	5	.	.	.	.	.	.	.	.	.	.	.	0.016	-1.511641	0.00984	.	.	ENSG00000081853	ENST00000394576	T	0.01804	4.63	5.24	-3.92	0.04155	Cadherin (4);Cadherin-like (1);	1.490410	0.04716	N	0.418484	T	0.00998	0.0033	N	0.11023	0.085	0.09310	N	1	B;B	0.27316	0.008;0.175	B;B	0.19391	0.009;0.025	T	0.47275	-0.9130	10	0.02654	T	1	.	9.5596	0.39360	0.0:0.2861:0.1045:0.6093	.	492;492	Q9Y5H1-2;Q9Y5H1	.;PCDG2_HUMAN	V	492	ENSP00000378077:A492V	ENSP00000378077:A492V	A	+	2	0	PCDHGA2	140700197	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.870000	0.04228	-0.452000	0.07087	-1.616000	0.00795	GCG	PCDHGA2	-	pfam_Cadherin,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin	ENSG00000081853		0.512	PCDHGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PCDHGA2	HGNC	protein_coding	OTTHUMT00000374738.1	47	0.00	0	C	NM_018915		140720013	140720013	+1	no_errors	ENST00000394576	ensembl	human	known	69_37n	missense	29	14.71	5	SNP	0.000	T
PIK3CA	5290	genome.wustl.edu	37	3	178952085	178952085	+	Missense_Mutation	SNP	A	A	G	rs121913279		TCGA-AR-A2LJ-01A-12D-A19Y-09	TCGA-AR-A2LJ-10A-01D-A19Y-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	5ce74a42-4e07-4bb4-8c86-f24518d7152d	e1344996-bfac-4686-811b-4be7bbd84c50	g.chr3:178952085A>G	ENST00000263967.3	+	21	3297	c.3140A>G	c.(3139-3141)cAt>cGt	p.H1047R	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1047	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.		H -> L (in BC; unknown pathological significance). {ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16353168}.|H -> R (in CLOVE, KERSEB, CRC, BC and OC; also found in an endometrial carcinoma sample; shows an increase in lipid kinase activity; oncogenic in vivo; requires binding to p85 regulatory subunit to induce cellular transformation but not interaction with RAS; may mimic the conformatitonal change triggered by the interaction with RAS; enhances invadopodia-mediated extracellular matrix degradation and invasion in breast cancer cells; increases lipid kinase activity; may alter the interaction of the PI3K/ PI4K kinase domain with the cell membrane). {ECO:0000269|PubMed:15016963, ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15712344, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16114017, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:22658544}.|H -> Y (in MCAP; also found in an endometrial carcinoma sample). {ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:22729224}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.H1047R(1387)|p.H1047L(194)|p.H1047P(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	AATGATGCACATCATGGTGGC	0.378	H1047L(EFM19_BREAST)|H1047R(BT20_BREAST)|H1047R(CAL29_URINARY_TRACT)|H1047R(CAL33_UPPER_AERODIGESTIVE_TRACT)|H1047R(DETROIT562_UPPER_AERODIGESTIVE_TRACT)|H1047R(HCC1954_BREAST)|H1047R(HCT116_LARGE_INTESTINE)|H1047R(HSC2_UPPER_AERODIGESTIVE_TRACT)|H1047R(LS180_LARGE_INTESTINE)|H1047R(MCAS_OVARY)|H1047R(MDAMB453_BREAST)|H1047R(NCIH1048_LUNG)|H1047R(RKO_LARGE_INTESTINE)|H1047R(SKOV3_OVARY)|H1047R(T47D_BREAST)	57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)	dbGAP		Dom	yes		3	3q26.3	5290	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""		"""E, O"""	1582	Substitution - Missense(1582)	breast(961)|large_intestine(245)|endometrium(114)|ovary(77)|urinary_tract(36)|upper_aerodigestive_tract(26)|lung(19)|central_nervous_system(19)|stomach(19)|haematopoietic_and_lymphoid_tissue(11)|thyroid(10)|NS(9)|liver(7)|kidney(6)|soft_tissue(6)|skin(4)|prostate(4)|pituitary(3)|pancreas(3)|meninges(1)|cervix(1)|bone(1)											99.0	89.0	92.0					3																	178952085		1912	4130	6042	-	-	-	SO:0001583	missense	0				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.3140A>G	3.37:g.178952085A>G	ENSP00000263967:p.His1047Arg	Somatic		WXS	Illumina GAIIx	Phase_IV	Q14CW1|Q99762	Missense_Mutation	SNP	pfam_PInositide-3_kin_accessory_dom,pfam_PI3/4_kinase_cat_dom,pfam_PI3K_Ras-bd_dom,pfam_PI3K_C2_dom,pfam_PI3K_adapt-bd_dom,superfamily_Kinase-like_dom,superfamily_ARM-type_fold,superfamily_C2_Ca/lipid-bd_dom_CaLB,smart_PI3K_adapt-bd_dom,smart_PI3K_Ras-bd_dom,smart_PI3K_C2_dom,smart_PInositide-3_kin_accessory_dom,smart_PI3/4_kinase_cat_dom,pfscan_PI3/4_kinase_cat_dom	p.H1047R	ENST00000263967.3	37	c.3140	CCDS43171.1	3	.	.	.	.	.	.	.	.	.	.	A	14.34	2.506328	0.44558	.	.	ENSG00000121879	ENST00000263967	T	0.80214	-1.35	6.08	6.08	0.98989	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.000000	0.85682	D	0.000000	T	0.62466	0.2430	N	0.08118	0	0.80722	D	1	P	0.38597	0.639	B	0.28011	0.085	T	0.67526	-0.5648	10	0.40728	T	0.16	-21.2893	16.6512	0.85203	1.0:0.0:0.0:0.0	.	1047	P42336	PK3CA_HUMAN	R	1047	ENSP00000263967:H1047R	ENSP00000263967:H1047R	H	+	2	0	PIK3CA	180434779	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	8.859000	0.92264	2.333000	0.79357	0.482000	0.46254	CAT	PIK3CA	-	superfamily_Kinase-like_dom,smart_PI3/4_kinase_cat_dom,pfscan_PI3/4_kinase_cat_dom	ENSG00000121879		0.378	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	PIK3CA	HGNC	protein_coding	OTTHUMT00000348409.2	21	0.00	0	A			178952085	178952085	+1	no_errors	ENST00000263967	ensembl	human	known	69_37n	missense	19	29.63	8	SNP	1.000	G
ZNF512B	57473	genome.wustl.edu	37	20	62626323	62626323	+	Intron	SNP	G	G	A			TCGA-AR-A2LJ-01A-12D-A19Y-09	TCGA-AR-A2LJ-10A-01D-A19Y-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	5ce74a42-4e07-4bb4-8c86-f24518d7152d	e1344996-bfac-4686-811b-4be7bbd84c50	g.chr20:62626323G>A	ENST00000450537.1	-	2	56				ZNF512B_ENST00000217130.3_Intron|PRPF6_ENST00000535781.1_Missense_Mutation_p.D165N			Q96KM6	Z512B_HUMAN	zinc finger protein 512B						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(16)|ovary(1)|prostate(4)|skin(1)	33	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					CGAGGTTGGCGATGCCAGAAA	0.478																																						dbGAP											0													83.0	83.0	83.0					20																	62626323		2203	4300	6503	-	-	-	SO:0001627	intron_variant	0			AB033022	CCDS13548.1	20q13.33	2011-02-09			ENSG00000196700	ENSG00000196700			29212	protein-coding gene	gene with protein product						10574462	Standard	NM_020713		Approved	GM632, MGC149845, MGC149846	uc002yhl.2	Q96KM6	OTTHUMG00000033008	ENST00000450537.1:c.5-27015C>T	20.37:g.62626323G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	Q08AK9|Q9ULM4	Missense_Mutation	SNP	pfam_PRP1_N,smart_HAT,smart_TPR_repeat,pfscan_TPR-contain_dom	p.D165N	ENST00000450537.1	37	c.493	CCDS13548.1	20	.	.	.	.	.	.	.	.	.	.	G	33	5.214286	0.95104	.	.	ENSG00000101161	ENST00000266079;ENST00000535781	D;D	0.84944	-1.83;-1.92	5.71	5.71	0.89125	PRP1 splicing factor, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.92525	0.7626	M	0.78801	2.425	0.80722	D	1	D;D	0.89917	0.992;1.0	P;D	0.80764	0.792;0.994	D	0.91238	0.5019	10	0.40728	T	0.16	.	19.8599	0.96779	0.0:0.0:1.0:0.0	.	165;165	O94906-2;O94906	.;PRP6_HUMAN	N	165	ENSP00000266079:D165N;ENSP00000446216:D165N	ENSP00000266079:D165N	D	+	1	0	PRPF6	62096767	1.000000	0.71417	0.998000	0.56505	0.764000	0.43329	9.778000	0.99011	2.710000	0.92621	0.655000	0.94253	GAT	PRPF6	-	pfam_PRP1_N	ENSG00000101161		0.478	ZNF512B-202	KNOWN	basic|appris_principal|CCDS	protein_coding	PRPF6	HGNC	protein_coding	OTTHUMT00000080246.1	34	0.00	0	G	NM_020713		62626323	62626323	+1	no_errors	ENST00000266079	ensembl	human	known	69_37n	missense	24	20.00	6	SNP	1.000	A
PUM1	9698	genome.wustl.edu	37	1	31478843	31478843	+	Missense_Mutation	SNP	T	T	C			TCGA-AR-A2LJ-01A-12D-A19Y-09	TCGA-AR-A2LJ-10A-01D-A19Y-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	5ce74a42-4e07-4bb4-8c86-f24518d7152d	e1344996-bfac-4686-811b-4be7bbd84c50	g.chr1:31478843T>C	ENST00000257075.5	-	5	670	c.577A>G	c.(577-579)Aga>Gga	p.R193G	PUM1_ENST00000423018.2_Intron|PUM1_ENST00000373747.3_Missense_Mutation_p.R193G|PUM1_ENST00000440538.2_Missense_Mutation_p.R193G|PUM1_ENST00000424085.2_Intron|PUM1_ENST00000373741.4_Missense_Mutation_p.R229G|PUM1_ENST00000373742.2_Intron|PUM1_ENST00000426105.2_Missense_Mutation_p.R193G	NM_014676.2	NP_055491.1	Q14671	PUM1_HUMAN	pumilio RNA-binding family member 1	193					membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of translation (GO:0006417)	cytosol (GO:0005829)	poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(17)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48		Colorectal(325;0.0211)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|all_neural(195;0.0381)|Breast(348;0.0848)|Medulloblastoma(700;0.123)		STAD - Stomach adenocarcinoma(196;0.0232)|READ - Rectum adenocarcinoma(331;0.0681)		TGACCAGGTCTTCTCTGCACC	0.463																																						dbGAP											0													110.0	105.0	106.0					1																	31478843		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF315592	CCDS338.1, CCDS44099.1	1p35.2	2013-09-02	2013-09-02		ENSG00000134644	ENSG00000134644			14957	protein-coding gene	gene with protein product		607204	"""pumilio (Drosophila) homolog 1"", ""pumilio homolog 1 (Drosophila)"""				Standard	NM_001020658		Approved	PUMH1, KIAA0099	uc001bsh.1	Q14671	OTTHUMG00000003795	ENST00000257075.5:c.577A>G	1.37:g.31478843T>C	ENSP00000257075:p.Arg193Gly	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K6W4|B4DG92|D3DPN3|E9PCJ0|Q53HH5|Q5VXY7|Q9HAN1	Missense_Mutation	SNP	pfam_Pumilio_RNA-bd_rpt,superfamily_ARM-type_fold,smart_Pumilio_RNA-bd_rpt,pfscan_Pumilio_RNA-bd_rpt	p.R193G	ENST00000257075.5	37	c.577	CCDS338.1	1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.85|17.85	3.490865|3.490865	0.64074|0.64074	.|.	.|.	ENSG00000134644|ENSG00000134644	ENST00000525843|ENST00000257075;ENST00000373747;ENST00000426105;ENST00000440538;ENST00000373741;ENST00000543952	.|T;T;T;T;T	.|0.21932	.|1.98;2.26;2.25;2.19;2.24	5.8|5.8	4.61|4.61	0.57282|0.57282	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.43523|0.43523	0.1251|0.1251	M|M	0.72118|0.72118	2.19|2.19	0.80722|0.80722	D|D	1|1	.|P;D;P;P;P	.|0.57899	.|0.947;0.981;0.917;0.862;0.917	.|P;D;B;B;B	.|0.69142	.|0.585;0.962;0.445;0.445;0.445	T|T	0.40739|0.40739	-0.9547|-0.9547	5|10	.|0.87932	.|D	.|0	-10.7289|-10.7289	12.68|12.68	0.56916|0.56916	0.0:0.0:0.1375:0.8625|0.0:0.0:0.1375:0.8625	.|.	.|229;193;193;193;193	.|Q5T1Z8;Q14671-2;Q14671;E9PCJ0;Q5T1Z4	.|.;.;PUM1_HUMAN;.;.	R|G	209|193;193;193;193;229;193	.|ENSP00000257075:R193G;ENSP00000362852:R193G;ENSP00000391723:R193G;ENSP00000401777:R193G;ENSP00000362846:R229G	.|ENSP00000257075:R193G	K|R	-|-	2|1	0|2	PUM1|PUM1	31251430|31251430	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	4.173000|4.173000	0.58249|0.58249	2.221000|2.221000	0.72209|0.72209	0.528000|0.528000	0.53228|0.53228	AAG|AGA	PUM1	-	NULL	ENSG00000134644		0.463	PUM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	PUM1	HGNC	protein_coding	OTTHUMT00000010671.1	19	0.00	0	T			31478843	31478843	-1	no_errors	ENST00000426105	ensembl	human	known	69_37n	missense	16	20.00	4	SNP	1.000	C
SYCP2	10388	genome.wustl.edu	37	20	58491609	58491609	+	Nonsense_Mutation	SNP	C	C	A			TCGA-AR-A2LJ-01A-12D-A19Y-09	TCGA-AR-A2LJ-10A-01D-A19Y-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	5ce74a42-4e07-4bb4-8c86-f24518d7152d	e1344996-bfac-4686-811b-4be7bbd84c50	g.chr20:58491609C>A	ENST00000357552.3	-	8	670	c.445G>T	c.(445-447)Gaa>Taa	p.E149*	SYCP2_ENST00000476314.1_5'Flank|SYCP2_ENST00000371001.2_Nonsense_Mutation_p.E149*			Q9BX26	SYCP2_HUMAN	synaptonemal complex protein 2	149					female meiotic division (GO:0007143)|fertilization (GO:0009566)|male genitalia morphogenesis (GO:0048808)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|synaptonemal complex assembly (GO:0007130)	lateral element (GO:0000800)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	DNA binding (GO:0003677)			NS(4)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;1.19e-09)			ACGAAACTTTCCACTACTTGT	0.299																																						dbGAP											0													78.0	78.0	78.0					20																	58491609		2203	4300	6503	-	-	-	SO:0001587	stop_gained	0			Y08982	CCDS13482.1	20q13.33	2007-07-02			ENSG00000196074	ENSG00000196074			11490	protein-coding gene	gene with protein product		604105				10341103, 9592139	Standard	NM_014258		Approved	SCP2	uc002yaz.3	Q9BX26	OTTHUMG00000032872	ENST00000357552.3:c.445G>T	20.37:g.58491609C>A	ENSP00000350162:p.Glu149*	Somatic		WXS	Illumina GAIIx	Phase_IV	A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27	Nonsense_Mutation	SNP	NULL	p.E149*	ENST00000357552.3	37	c.445	CCDS13482.1	20	.	.	.	.	.	.	.	.	.	.	C	39	7.743717	0.98465	.	.	ENSG00000196074	ENST00000371001;ENST00000357552;ENST00000446834	.	.	.	5.67	4.73	0.59995	.	0.177793	0.39687	N	0.001296	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-24.0376	13.7348	0.62811	0.0:0.9254:0.0:0.0746	.	.	.	.	X	149	.	ENSP00000350162:E149X	E	-	1	0	SYCP2	57925004	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	3.680000	0.54641	2.673000	0.90976	0.467000	0.42956	GAA	SYCP2	-	NULL	ENSG00000196074		0.299	SYCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SYCP2	HGNC	protein_coding	OTTHUMT00000079930.3	35	0.00	0	C	NM_014258		58491609	58491609	-1	no_errors	ENST00000357552	ensembl	human	known	69_37n	nonsense	20	23.08	6	SNP	1.000	A
