#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
AKR1CL1	340811	genome.wustl.edu	37	10	5200861	5200861	+	IGR	SNP	C	C	A	rs2020172	byFrequency	TCGA-B6-A0RQ-01A-11D-A10Y-09	TCGA-B6-A0RQ-10A-01D-A110-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f425edf3-0d08-49bf-94f6-f03343873a6c	fe1d77e9-f21d-4914-ae1a-2cc6dd6f8cba	g.chr10:5200861C>A	ENST00000334314.3	-	0	492				AKR1CL1_ENST00000465430.1_Intron			Q5T2L2	AKCL1_HUMAN	aldo-keto reductase family 1, member C-like 1							cytoplasm (GO:0005737)	oxidoreductase activity (GO:0016491)			cervix(1)|endometrium(1)|large_intestine(2)|lung(2)	6						CTTGGACTTGCAGAACTCCAG	0.448													C|||	864	0.172524	0.1732	0.183	5008	,	,		17338	0.0		0.3579	False		,,,				2504	0.1513				Ovarian(129;1623 1737 25446 28757 47467)	dbGAP											0																																										-	-	-	SO:0001628	intergenic_variant	0					10p15.2	2014-05-06			ENSG00000196326	ENSG00000264006			23469	protein-coding gene	gene with protein product						15164054	Standard	NR_027916		Approved		uc009xhz.2	Q5T2L2	OTTHUMG00000184213		10.37:g.5200861C>A		Somatic		WXS	Illumina GAIIx	Phase_IV	A6NF66|Q6ZN81	Missense_Mutation	SNP	pfam_NADP_OxRdtase_dom,superfamily_NADP_OxRdtase_dom,prints_Aldo/keto_reductase_subgr	p.C34F	ENST00000334314.3	37	c.101		10	440	0.20146520146520147	99	0.20121951219512196	81	0.22375690607734808	0	0.0	260	0.34300791556728233	C	19.60	3.858582	0.71834	.	.	ENSG00000196326	ENST00000473890	T	0.28454	1.61	3.73	3.73	0.42828	.	0.000000	0.64402	U	0.000012	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.31752	-0.9932	6	0.87932	D	0	.	13.7685	0.63010	0.0:1.0:0.0:0.0	rs2020172;rs2020172	.	.	.	F	34	ENSP00000417959:C34F	ENSP00000417959:C34F	C	-	2	0	AKR1CL1	5190861	1.000000	0.71417	0.989000	0.46669	0.951000	0.60555	3.694000	0.54742	2.014000	0.59158	0.484000	0.47621	TGC	AKR1CL1	-	pfam_NADP_OxRdtase_dom,superfamily_NADP_OxRdtase_dom,prints_Aldo/keto_reductase_subgr	ENSG00000196326		0.448	AKR1CL1-201	KNOWN	basic|appris_candidate_longest	protein_coding	AKR1CL1	HGNC	protein_coding		9	0.00	0	C	NR_027916		5200861	5200861	-1	no_errors	ENST00000473890	ensembl	human	novel	69_37n	missense	19	32.14	9	SNP	1.000	A
CCNI2	645121	genome.wustl.edu	37	5	132084048	132084048	+	Missense_Mutation	SNP	T	T	C			TCGA-B6-A0RQ-01A-11D-A10Y-09	TCGA-B6-A0RQ-10A-01D-A110-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f425edf3-0d08-49bf-94f6-f03343873a6c	fe1d77e9-f21d-4914-ae1a-2cc6dd6f8cba	g.chr5:132084048T>C	ENST00000378731.1	+	2	490	c.439T>C	c.(439-441)Tgc>Cgc	p.C147R		NM_001039780.2	NP_001034869.1	Q6ZMN8	CCNI2_HUMAN	cyclin I family, member 2	147					regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)					haematopoietic_and_lymphoid_tissue(1)|prostate(1)|urinary_tract(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GGATGAAATCTGCGACGCCTT	0.597																																						dbGAP											0													76.0	71.0	73.0					5																	132084048		2203	4300	6503	-	-	-	SO:0001583	missense	0			BC132837	CCDS34236.1, CCDS75297.1	5q31.1	2014-07-03			ENSG00000205089	ENSG00000205089			33869	protein-coding gene	gene with protein product						23707792	Standard	NM_001287252		Approved	FLJ16793	uc003kxq.1	Q6ZMN8	OTTHUMG00000059737	ENST00000378731.1:c.439T>C	5.37:g.132084048T>C	ENSP00000368005:p.Cys147Arg	Somatic		WXS	Illumina GAIIx	Phase_IV	B2RNE2|B7ZMB7|B7ZMB8	Missense_Mutation	SNP	pfam_Cyclin_N,superfamily_Cyclin-like,smart_Cyclin-like,pirsf_Cyclin_A/B/D/E	p.C147R	ENST00000378731.1	37	c.439	CCDS34236.1	5	.	.	.	.	.	.	.	.	.	.	t	4.313	0.057480	0.08339	.	.	ENSG00000205089	ENST00000378731	T	0.16457	2.34	4.65	-4.37	0.03633	Cyclin-like (1);	0.854030	0.10609	N	0.654659	T	0.09024	0.0223	L	0.29908	0.895	0.09310	N	0.999999	B;B;B	0.10296	0.003;0.002;0.0	B;B;B	0.09377	0.003;0.001;0.004	T	0.37820	-0.9689	10	0.21540	T	0.41	.	5.6102	0.17400	0.0:0.3562:0.2741:0.3697	.	148;147;147	B7ZMB7;B7ZMB8;Q6ZMN8	.;.;CCNI2_HUMAN	R	147	ENSP00000368005:C147R	ENSP00000368005:C147R	C	+	1	0	CCNI2	132111947	0.000000	0.05858	0.002000	0.10522	0.022000	0.10575	-2.851000	0.00732	-0.511000	0.06514	0.529000	0.55759	TGC	CCNI2	-	superfamily_Cyclin-like,pirsf_Cyclin_A/B/D/E	ENSG00000205089		0.597	CCNI2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	CCNI2	HGNC	protein_coding	OTTHUMT00000132833.1	113	0.00	0	T	NM_001039780		132084048	132084048	+1	no_errors	ENST00000378731	ensembl	human	novel	69_37n	missense	126	11.81	17	SNP	0.036	C
CDH1	999	genome.wustl.edu	37	16	68772218	68772218	+	Nonsense_Mutation	SNP	C	C	T			TCGA-B6-A0RQ-01A-11D-A10Y-09	TCGA-B6-A0RQ-10A-01D-A110-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f425edf3-0d08-49bf-94f6-f03343873a6c	fe1d77e9-f21d-4914-ae1a-2cc6dd6f8cba	g.chr16:68772218C>T	ENST00000261769.5	+	2	258	c.67C>T	c.(67-69)Cag>Tag	p.Q23*	CDH1_ENST00000422392.2_Nonsense_Mutation_p.Q23*	NM_004360.3	NP_004351.1	P12830	CADH1_HUMAN	cadherin 1, type 1, E-cadherin (epithelial)	23					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.V17fs*1(3)|p.?(2)|p.W20fs*7(1)|p.Q23*(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)		TTGGCTCTGCCAGGAGCCGGA	0.677			"""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	7	Deletion - Frameshift(4)|Unknown(2)|Substitution - Nonsense(1)	breast(7)											14.0	17.0	16.0					16																	68772218		1763	3312	5075	-	-	-	SO:0001587	stop_gained	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.67C>T	16.37:g.68772218C>T	ENSP00000261769:p.Gln23*	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K1U7|Q13799|Q14216|Q15855|Q16194|Q4PJ14|Q9UII8	Nonsense_Mutation	SNP	pfam_Cadherin,pfam_Cadherin_cytoplasmic-dom,pfam_Cadherin_pro_dom,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin,prints_Cadherin	p.Q23*	ENST00000261769.5	37	c.67	CCDS10869.1	16	.	.	.	.	.	.	.	.	.	.	C	21.6	4.175447	0.78564	.	.	ENSG00000039068	ENST00000261769;ENST00000379120;ENST00000268794;ENST00000422392	.	.	.	4.76	1.47	0.22746	.	0.000000	0.34652	N	0.003783	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06236	T	0.91	.	13.0323	0.58848	0.0:0.551:0.449:0.0	.	.	.	.	X	23	.	ENSP00000261769:Q23X	Q	+	1	0	CDH1	67329719	0.998000	0.40836	0.961000	0.40146	0.242000	0.25591	0.719000	0.25881	0.574000	0.29417	0.563000	0.77884	CAG	CDH1	-	superfamily_Cadherin-like	ENSG00000039068		0.677	CDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CDH1	HGNC	protein_coding	OTTHUMT00000268897.2	42	0.00	0	C	NM_004360		68772218	68772218	+1	no_errors	ENST00000261769	ensembl	human	known	69_37n	nonsense	34	10.53	4	SNP	0.982	T
DEPDC1	55635	genome.wustl.edu	37	1	68954121	68954121	+	Frame_Shift_Del	DEL	T	T	-			TCGA-B6-A0RQ-01A-11D-A10Y-09	TCGA-B6-A0RQ-10A-01D-A110-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f425edf3-0d08-49bf-94f6-f03343873a6c	fe1d77e9-f21d-4914-ae1a-2cc6dd6f8cba	g.chr1:68954121delT	ENST00000456315.2	-	5	771	c.657delA	c.(655-657)caafs	p.Q219fs	DEPDC1_ENST00000370966.5_Frame_Shift_Del_p.Q219fs	NM_001114120.1	NP_001107592.1	Q5TB30	DEP1A_HUMAN	DEP domain containing 1	219					intracellular signal transduction (GO:0035556)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	GTPase activator activity (GO:0005096)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	13				OV - Ovarian serous cystadenocarcinoma(397;7.21e-36)		ACATTATATATTGGGGAATTA	0.299																																						dbGAP											0													138.0	131.0	133.0					1																	68954121		2202	4299	6501	-	-	-	SO:0001589	frameshift_variant	0			AK000361	CCDS644.1, CCDS44159.1	1p31.2	2008-08-19			ENSG00000024526	ENSG00000024526			22949	protein-coding gene	gene with protein product		612002					Standard	NM_001114120		Approved	DEP.8, FLJ20354, SDP35, DEPDC1A	uc001dem.4	Q5TB30	OTTHUMG00000009212	ENST00000456315.2:c.657delA	1.37:g.68954121delT	ENSP00000412292:p.Gln219fs	Somatic		WXS	Illumina GAIIx	Phase_IV	A8QXE0|A8QXE1|Q05DU3|Q5TB28|Q9H9I3|Q9NX21|Q9NXZ0	Frame_Shift_Del	DEL	pfam_DEP_dom,superfamily_Rho_GTPase_activation_prot,smart_DEP_dom,pfscan_DEP_dom	p.Q219fs	ENST00000456315.2	37	c.657	CCDS44159.1	1																																																																																			DEPDC1	-	NULL	ENSG00000024526		0.299	DEPDC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	DEPDC1	HGNC	protein_coding	OTTHUMT00000025514.2	377	0.00	0	T	NM_017779		68954121	68954121	-1	no_errors	ENST00000456315	ensembl	human	known	69_37n	frame_shift_del	558	10.24	64	DEL	0.702	-
GRID2IP	392862	genome.wustl.edu	37	7	6545509	6545509	+	Silent	SNP	C	C	A			TCGA-B6-A0RQ-01A-11D-A10Y-09	TCGA-B6-A0RQ-10A-01D-A110-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f425edf3-0d08-49bf-94f6-f03343873a6c	fe1d77e9-f21d-4914-ae1a-2cc6dd6f8cba	g.chr7:6545509C>A	ENST00000457091.2	-	14	2573	c.2574G>T	c.(2572-2574)ctG>ctT	p.L858L	GRID2IP_ENST00000435185.1_Silent_p.L674L|GRID2IP_ENST00000452113.1_Silent_p.L667L	NM_001145118.1	NP_001138590.1	A4D2P6	GRD2I_HUMAN	glutamate receptor, ionotropic, delta 2 (Grid2) interacting protein	858	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				long term synaptic depression (GO:0060292)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)				endometrium(4)	4						CCATGTCACTCAGCTTATCGT	0.592																																						dbGAP											0													78.0	66.0	70.0					7																	6545509		692	1591	2283	-	-	-	SO:0001819	synonymous_variant	0				CCDS47537.1	7p22	2007-10-05	2006-03-01		ENSG00000215045	ENSG00000215045			18464	protein-coding gene	gene with protein product		610639	"""glutamate receptor, ionotropic, delta 2 (Grid2) interacting protein 1"""			14612983	Standard	NM_001145118		Approved		uc011jwx.2	A4D2P6	OTTHUMG00000155531	ENST00000457091.2:c.2574G>T	7.37:g.6545509C>A		Somatic		WXS	Illumina GAIIx	Phase_IV		Silent	SNP	pfam_FH2_actin-bd,pfam_PDZ,superfamily_FH2_actin-bd,superfamily_PDZ,smart_PDZ,smart_Actin-bd_FH2/DRF_autoreg,pfscan_PDZ	p.L858	ENST00000457091.2	37	c.2574	CCDS47537.1	7																																																																																			GRID2IP	-	pfam_FH2_actin-bd,superfamily_FH2_actin-bd,smart_Actin-bd_FH2/DRF_autoreg	ENSG00000215045		0.592	GRID2IP-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	GRID2IP	HGNC	protein_coding	OTTHUMT00000340534.1	86	0.00	0	C	XM_294249		6545509	6545509	-1	no_errors	ENST00000457091	ensembl	human	putative	69_37n	silent	96	10.19	11	SNP	1.000	A
KCNF1	3754	genome.wustl.edu	37	2	11053551	11053551	+	Silent	SNP	G	G	A			TCGA-B6-A0RQ-01A-11D-A10Y-09	TCGA-B6-A0RQ-10A-01D-A110-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f425edf3-0d08-49bf-94f6-f03343873a6c	fe1d77e9-f21d-4914-ae1a-2cc6dd6f8cba	g.chr2:11053551G>A	ENST00000295082.1	+	1	1489	c.999G>A	c.(997-999)gtG>gtA	p.V333V		NM_002236.4	NP_002227.2	Q9H3M0	KCNF1_HUMAN	potassium voltage-gated channel, subfamily F, member 1	333					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)			NS(1)|endometrium(2)|large_intestine(2)|lung(10)|ovary(2)|skin(1)|urinary_tract(1)	19	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.128)		ACCTGGCAGTGGGTATCTTCG	0.592																																						dbGAP											0													94.0	84.0	87.0					2																	11053551		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AF033382	CCDS1676.1	2p25	2011-07-05			ENSG00000162975	ENSG00000162975		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6246	protein-coding gene	gene with protein product		603787		KCNF		9434767, 16382104	Standard	NM_002236		Approved	Kv5.1, kH1, IK8	uc002rax.3	Q9H3M0	OTTHUMG00000119054	ENST00000295082.1:c.999G>A	2.37:g.11053551G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	O43527|Q585L3	Silent	SNP	pfam_Ion_trans_dom,pfam_T1-type_BTB,pfam_Ion_trans_2,pfam_PKD1_2_channel,superfamily_BTB/POZ_fold,prints_K_chnl,prints_K_chnl_volt-dep_Kv,prints_K_chnl_volt-dep_Kv9,prints_K_chnl_volt-dep_Kv1,prints_K_chnl_volt-dep_Kv6	p.V333	ENST00000295082.1	37	c.999	CCDS1676.1	2																																																																																			KCNF1	-	pfam_Ion_trans_dom,pfam_Ion_trans_2,pfam_PKD1_2_channel,prints_K_chnl,prints_K_chnl_volt-dep_Kv	ENSG00000162975		0.592	KCNF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KCNF1	HGNC	protein_coding	OTTHUMT00000239265.1	137	0.00	0	G	NM_002236		11053551	11053551	+1	no_errors	ENST00000295082	ensembl	human	known	69_37n	silent	89	10.10	10	SNP	1.000	A
KIR3DL2	3812	genome.wustl.edu	37	19	55363677	55363677	+	Missense_Mutation	SNP	C	C	T	rs376049512		TCGA-B6-A0RQ-01A-11D-A10Y-09	TCGA-B6-A0RQ-10A-01D-A110-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f425edf3-0d08-49bf-94f6-f03343873a6c	fe1d77e9-f21d-4914-ae1a-2cc6dd6f8cba	g.chr19:55363677C>T	ENST00000326321.3	+	3	328	c.295C>T	c.(295-297)Cgc>Tgc	p.R99C	KIR3DL2_ENST00000270442.5_Missense_Mutation_p.R99C|KIR3DL1_ENST00000402254.2_Intron	NM_006737.3	NP_006728.2	P43630	KI3L2_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 2	99	Ig-like C2-type 1.				cellular defense response (GO:0006968)|regulation of immune response (GO:0050776)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	23				GBM - Glioblastoma multiforme(193;0.0192)		TCGGGGTTCACGCCCACACTC	0.592																																						dbGAP											0													65.0	59.0	61.0					19																	55363677		2162	4125	6287	-	-	-	SO:0001583	missense	0			L41270	CCDS12906.1, CCDS58677.1	19q13.4	2014-05-22			ENSG00000240403	ENSG00000240403		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6339	protein-coding gene	gene with protein product		604947				7716543, 8662091	Standard	NM_006737		Approved	cl-5, nkat4, nkat4a, nkat4b, CD158K	uc002qho.4	P43630	OTTHUMG00000065935	ENST00000326321.3:c.295C>T	19.37:g.55363677C>T	ENSP00000325525:p.Arg99Cys	Somatic		WXS	Illumina GAIIx	Phase_IV	Q13238|Q14947|Q14948|Q92684|Q95366|Q95367|Q95368	Missense_Mutation	SNP	pfam_Immunoglobulin,smart_Ig_sub	p.R99C	ENST00000326321.3	37	c.295	CCDS12906.1	19	.	.	.	.	.	.	.	.	.	.	c	7.544	0.661200	0.14645	.	.	ENSG00000240403	ENST00000326321;ENST00000270442	T;T	0.00753	5.74;5.74	1.62	-3.23	0.05109	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	3.044860	0.02291	U	0.070352	T	0.00724	0.0024	L	0.35854	1.095	0.09310	N	1	P;B	0.49090	0.919;0.006	B;B	0.35899	0.213;0.009	T	0.45175	-0.9279	10	0.72032	D	0.01	.	3.3555	0.07168	0.0:0.428:0.2244:0.3475	.	99;99	Q95366;P43630	.;KI3L2_HUMAN	C	99	ENSP00000325525:R99C;ENSP00000270442:R99C	ENSP00000270442:R99C	R	+	1	0	KIR3DL2	60055489	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-2.084000	0.01363	-1.094000	0.03054	0.184000	0.17185	CGC	KIR3DL2	-	smart_Ig_sub	ENSG00000240403		0.592	KIR3DL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	KIR3DL2	HGNC	protein_coding	OTTHUMT00000141241.1	58	0.00	0	C			55363677	55363677	+1	no_errors	ENST00000326321	ensembl	human	known	69_37n	missense	74	23.71	23	SNP	0.000	T
MGMT	4255	genome.wustl.edu	37	10	131565093	131565093	+	Silent	SNP	C	C	T			TCGA-B6-A0RQ-01A-11D-A10Y-09	TCGA-B6-A0RQ-10A-01D-A110-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f425edf3-0d08-49bf-94f6-f03343873a6c	fe1d77e9-f21d-4914-ae1a-2cc6dd6f8cba	g.chr10:131565093C>T	ENST00000306010.7	+	5	581	c.549C>T	c.(547-549)agC>agT	p.S183S	RP11-109A6.3_ENST00000428273.1_lincRNA	NM_002412.3	NP_002403.2	P16455	MGMT_HUMAN	O-6-methylguanine-DNA methyltransferase	152					cellular response to ionizing radiation (GO:0071479)|cellular response to organic cyclic compound (GO:0071407)|cellular response to oxidative stress (GO:0034599)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA ligation (GO:0006266)|DNA methylation (GO:0006306)|DNA repair (GO:0006281)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell death (GO:0060548)|positive regulation of DNA repair (GO:0045739)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to folic acid (GO:0051593)|response to toxic substance (GO:0009636)	membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|DNA-methyltransferase activity (GO:0009008)|methylated-DNA-[protein]-cysteine S-methyltransferase activity (GO:0003908)|methyltransferase activity (GO:0008168)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	10		all_cancers(35;9.44e-09)|all_epithelial(44;6.98e-08)|Lung NSC(174;0.0157)|all_lung(145;0.0201)|all_neural(114;0.0732)|Colorectal(57;0.0792)|Breast(234;0.167)		OV - Ovarian serous cystadenocarcinoma(35;0.00291)	L-Cysteine(DB00151)	TCTGCAGCAGCGGAGCCGTGG	0.637								Direct reversal of damage																														dbGAP											0													38.0	37.0	37.0					10																	131565093		2202	4300	6502	-	-	-	SO:0001819	synonymous_variant	0			M29971	CCDS7660.2	10q26	2005-10-06			ENSG00000170430	ENSG00000170430			7059	protein-coding gene	gene with protein product		156569					Standard	NM_002412		Approved		uc001lkh.2	P16455	OTTHUMG00000019261	ENST00000306010.7:c.549C>T	10.37:g.131565093C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	Q5VY78	Silent	SNP	pfam_MethylDNA_cys_MeTrfase_DNA-bd,pfam_MethylG_MeTrfase,superfamily_MethylDNA_cys_MeTrfase_DNA-bd,tigrfam_MethylDNA_cys_MeTrfase_DNA-bd	p.S183	ENST00000306010.7	37	c.549	CCDS7660.2	10																																																																																			MGMT	-	pfam_MethylDNA_cys_MeTrfase_DNA-bd,superfamily_MethylDNA_cys_MeTrfase_DNA-bd,tigrfam_MethylDNA_cys_MeTrfase_DNA-bd	ENSG00000170430		0.637	MGMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MGMT	HGNC	protein_coding	OTTHUMT00000051009.3	58	0.00	0	C	NM_002412		131565093	131565093	+1	no_errors	ENST00000306010	ensembl	human	known	69_37n	silent	55	16.42	11	SNP	0.984	T
MYH7	4625	genome.wustl.edu	37	14	23899017	23899017	+	Missense_Mutation	SNP	G	G	A			TCGA-B6-A0RQ-01A-11D-A10Y-09	TCGA-B6-A0RQ-10A-01D-A110-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f425edf3-0d08-49bf-94f6-f03343873a6c	fe1d77e9-f21d-4914-ae1a-2cc6dd6f8cba	g.chr14:23899017G>A	ENST00000355349.3	-	12	1267	c.1105C>T	c.(1105-1107)Cgg>Tgg	p.R369W		NM_000257.2	NP_000248.2	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	369	Myosin motor.				adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)			NS(3)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(19)|lung(57)|ovary(5)|prostate(9)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	137	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		TGCTCCTCCCGCTGCTTCAGC	0.542																																						dbGAP											0													92.0	85.0	87.0					14																	23899017		2203	4300	6503	-	-	-	SO:0001583	missense	0			M58018	CCDS9601.1	14q11.2-q13	2014-09-17	2006-09-29		ENSG00000092054	ENSG00000092054		"""Myosins / Myosin superfamily : Class II"""	7577	protein-coding gene	gene with protein product		160760	"""myopathy, distal 1"", ""myosin, heavy polypeptide 7, cardiac muscle, beta"""	CMH1, MPD1		2494889, 8483915, 15322983	Standard	XM_005267696		Approved	CMD1S	uc001wjx.3	P12883	OTTHUMG00000028755	ENST00000355349.3:c.1105C>T	14.37:g.23899017G>A	ENSP00000347507:p.Arg369Trp	Somatic		WXS	Illumina GAIIx	Phase_IV	A2TDB6|B6D424|Q14836|Q14837|Q14904|Q16579|Q2M1Y6|Q92679|Q9H1D5|Q9UDA2|Q9UMM8	Missense_Mutation	SNP	pfam_Myosin_tail,pfam_Myosin_head_motor_dom,pfam_Myosin_N,superfamily_Prefoldin,smart_Myosin_head_motor_dom,smart_IQ_motif_EF-hand-BS,pfscan_IQ_motif_EF-hand-BS,prints_Myosin_head_motor_dom	p.R369W	ENST00000355349.3	37	c.1105	CCDS9601.1	14	.	.	.	.	.	.	.	.	.	.	G	18.10	3.548778	0.65311	.	.	ENSG00000092054	ENST00000355349;ENST00000544444	D	0.87966	-2.32	3.94	-1.0	0.10196	Myosin head, motor domain (2);	.	.	.	.	D	0.95720	0.8608	H	0.99074	4.42	0.53688	D	0.999979	D	0.67145	0.996	D	0.66497	0.944	D	0.96677	0.9501	9	0.87932	D	0	.	15.2664	0.73666	0.0:0.0:0.4699:0.5301	.	369	P12883	MYH7_HUMAN	W	369	ENSP00000347507:R369W	ENSP00000347507:R369W	R	-	1	2	MYH7	22968857	1.000000	0.71417	0.997000	0.53966	0.993000	0.82548	2.805000	0.47939	-0.022000	0.13986	0.457000	0.33378	CGG	MYH7	-	pfam_Myosin_head_motor_dom,smart_Myosin_head_motor_dom	ENSG00000092054		0.542	MYH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MYH7	HGNC	protein_coding	OTTHUMT00000071798.3	241	0.00	0	G	NM_000257		23899017	23899017	-1	no_errors	ENST00000355349	ensembl	human	known	69_37n	missense	209	11.34	27	SNP	0.995	A
OBSCN	84033	genome.wustl.edu	37	1	228559663	228559663	+	Missense_Mutation	SNP	C	C	T			TCGA-B6-A0RQ-01A-11D-A10Y-09	TCGA-B6-A0RQ-10A-01D-A110-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f425edf3-0d08-49bf-94f6-f03343873a6c	fe1d77e9-f21d-4914-ae1a-2cc6dd6f8cba	g.chr1:228559663C>T	ENST00000422127.1	+	94	21228	c.21184C>T	c.(21184-21186)Cct>Tct	p.P7062S	OBSCN_ENST00000570156.2_Missense_Mutation_p.P8019S|OBSCN_ENST00000366707.4_Missense_Mutation_p.P4696S	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	7062	Pro-rich.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				TGGCTCCTTCCCTCCAGGATC	0.672																																						dbGAP											0													36.0	39.0	38.0					1																	228559663		1887	4106	5993	-	-	-	SO:0001583	missense	0			AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.21184C>T	1.37:g.228559663C>T	ENSP00000409493:p.Pro7062Ser	Somatic		WXS	Illumina GAIIx	Phase_IV	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	pfam_Ig_I-set,pfam_Immunoglobulin,pfam_Ig_V-set,pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Fibronectin_type3,pfam_DH-domain,pfam_IQ_motif_EF-hand-BS,superfamily_Kinase-like_dom,superfamily_DH-domain,superfamily_Fibronectin_type3,superfamily_SH3_domain,smart_Ig_sub,smart_Ig_sub2,smart_Ig_V-set_subgr,smart_Fibronectin_type3,smart_IQ_motif_EF-hand-BS,smart_DH-domain,smart_Pleckstrin_homology,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Fibronectin_type3,pfscan_IQ_motif_EF-hand-BS,pfscan_Pleckstrin_homology,pfscan_Prot_kinase_cat_dom,pfscan_Ig-like,pfscan_DH-domain	p.P7062S	ENST00000422127.1	37	c.21184	CCDS58065.1	1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.31|17.31	3.356459|3.356459	0.61293|0.61293	.|.	.|.	ENSG00000154358|ENSG00000154358	ENST00000441106|ENST00000422127;ENST00000366707	.|T;T	.|0.62105	.|0.08;0.05	4.4|4.4	-3.88|-3.88	0.04205|0.04205	.|.	367.945000|367.945000	0.00166|0.00166	N|U	0.000000|0.000000	T|T	0.44993|0.44993	0.1320|0.1320	L|L	0.32530|0.32530	0.975|0.975	0.09310|0.09310	N|N	0.999999|0.999999	.|B	.|0.14438	.|0.01	.|B	.|0.09377	.|0.004	T|T	0.22800|0.22800	-1.0206|-1.0206	6|10	.|0.09084	.|T	.|0.74	.|.	6.3505|6.3505	0.21373|0.21373	0.1279:0.3223:0.0:0.5498|0.1279:0.3223:0.0:0.5498	.|.	.|7062	.|Q5VST9	.|OBSCN_HUMAN	L|S	1678|7062;4696	.|ENSP00000409493:P7062S;ENSP00000355668:P4696S	.|ENSP00000355668:P4696S	P|P	+|+	2|1	0|0	OBSCN|OBSCN	226626286|226626286	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.059000|0.059000	0.15707|0.15707	-0.619000|-0.619000	0.05572|0.05572	-0.378000|-0.378000	0.07918|0.07918	-0.266000|-0.266000	0.10368|0.10368	CCC|CCT	OBSCN	-	NULL	ENSG00000154358		0.672	OBSCN-204	KNOWN	basic|CCDS	protein_coding	OBSCN	HGNC	protein_coding		66	0.00	0	C	NM_052843		228559663	228559663	+1	no_errors	ENST00000422127	ensembl	human	known	69_37n	missense	51	15.00	9	SNP	0.000	T
PIK3CA	5290	genome.wustl.edu	37	3	178936083	178936083	+	Missense_Mutation	SNP	A	A	G			TCGA-B6-A0RQ-01A-11D-A10Y-09	TCGA-B6-A0RQ-10A-01D-A110-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f425edf3-0d08-49bf-94f6-f03343873a6c	fe1d77e9-f21d-4914-ae1a-2cc6dd6f8cba	g.chr3:178936083A>G	ENST00000263967.3	+	10	1782	c.1625A>G	c.(1624-1626)gAa>gGa	p.E542G		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	542	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.		E -> K (in CLOVE, KERSEB, CRC and BC; also found in glioblastoma multiforme and endometrial carcinoma; shows an increase in lipid kinase activity; oncogenic in vivo; occurs in the interface between the PI3K helical domain and the nSH2 (N- terminal SH2) region of the p85 regulatory subunit and may reduce the inhibitory effect of p85; requires interaction with RAS to induce cellular transformation). {ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15924253, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:22658544}.|E -> Q (found in an endometrial carcinoma sample; unknown pathological significance). {ECO:0000269|PubMed:16322209}.|E -> V (in BC; unknown pathological significance). {ECO:0000269|PubMed:16353168}.		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.E542V(8)|p.E542A(4)|p.E542G(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)	CCTCTCTCTGAAATCACTGAG	0.333		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"""	13	Substitution - Missense(13)	large_intestine(5)|endometrium(5)|breast(2)|ovary(1)											57.0	57.0	57.0					3																	178936083		1809	4069	5878	-	-	-	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.1625A>G	3.37:g.178936083A>G	ENSP00000263967:p.Glu542Gly	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.E542G	ENST00000263967.3	37	c.1625	CCDS43171.1	3	.	.	.	.	.	.	.	.	.	.	A	18.14	3.558430	0.65538	.	.	ENSG00000121879	ENST00000263967	T	0.65178	-0.14	5.78	5.78	0.91487	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.56761	0.2007	L	0.37850	1.14	0.80722	D	1	B	0.30634	0.288	B	0.36289	0.221	T	0.53380	-0.8447	10	0.27082	T	0.32	-23.9623	16.1026	0.81194	1.0:0.0:0.0:0.0	.	542	P42336	PK3CA_HUMAN	G	542	ENSP00000263967:E542G	ENSP00000263967:E542G	E	+	2	0	PIK3CA	180418777	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	8.962000	0.93254	2.198000	0.70561	0.383000	0.25322	GAA	PIK3CA	-	pfam_PInositide-3_kin_accessory_dom,superfamily_ARM-type_fold,smart_PInositide-3_kin_accessory_dom	ENSG00000121879		0.333	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	PIK3CA	HGNC	protein_coding	OTTHUMT00000348409.2	125	0.00	0	A			178936083	178936083	+1	no_errors	ENST00000263967	ensembl	human	known	69_37n	missense	136	12.26	19	SNP	1.000	G
PITPNM3	83394	genome.wustl.edu	37	17	6380354	6380354	+	Silent	SNP	G	G	A			TCGA-B6-A0RQ-01A-11D-A10Y-09	TCGA-B6-A0RQ-10A-01D-A110-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f425edf3-0d08-49bf-94f6-f03343873a6c	fe1d77e9-f21d-4914-ae1a-2cc6dd6f8cba	g.chr17:6380354G>A	ENST00000262483.8	-	9	1167	c.1080C>T	c.(1078-1080)ctC>ctT	p.L360L	PITPNM3_ENST00000421306.3_Silent_p.L324L	NM_031220.3	NP_112497.2	Q9BZ71	PITM3_HUMAN	PITPNM family member 3	360					phosphatidylinositol metabolic process (GO:0046488)|phospholipid transport (GO:0015914)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)	calcium ion binding (GO:0005509)|lipid binding (GO:0008289)|phosphatidylinositol transporter activity (GO:0008526)|receptor tyrosine kinase binding (GO:0030971)			autonomic_ganglia(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|prostate(3)|skin(2)	36				Colorectal(2;0.000372)|READ - Rectum adenocarcinoma(2;0.0276)|LUAD - Lung adenocarcinoma(2;0.0836)|COAD - Colon adenocarcinoma(228;0.185)		GCTACCTTGAGAGGAAGGCAT	0.617																																						dbGAP											0													71.0	60.0	64.0					17																	6380354		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AF334586	CCDS11076.1, CCDS54080.1	17p13	2013-07-18	2013-07-18	2013-07-18	ENSG00000091622	ENSG00000091622		"""GPCR / Class A : Chemokine receptors : Atypical"""	21043	protein-coding gene	gene with protein product	"""atypical chemokine receptor 6"""	608921	"""cone rod dystrophy 5"""	CORD5		10022914	Standard	NM_031220		Approved	NIR1, RDGBA3, ACKR6	uc002gdd.4	Q9BZ71	OTTHUMG00000102039	ENST00000262483.8:c.1080C>T	17.37:g.6380354G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	A1A5D0|F8WEW5|Q59GH9|Q9NPQ4	Silent	SNP	pfam_DDHD,pfam_LNS2,superfamily_HAD-like_dom,smart_LNS2,pfscan_DDHD	p.L360	ENST00000262483.8	37	c.1080	CCDS11076.1	17																																																																																			PITPNM3	-	NULL	ENSG00000091622		0.617	PITPNM3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	PITPNM3	HGNC	protein_coding	OTTHUMT00000219824.2	115	0.00	0	G	NM_031220		6380354	6380354	-1	no_errors	ENST00000262483	ensembl	human	known	69_37n	silent	122	11.59	16	SNP	0.992	A
PNMA2	10687	genome.wustl.edu	37	8	26365666	26365666	+	Missense_Mutation	SNP	C	C	G			TCGA-B6-A0RQ-01A-11D-A10Y-09	TCGA-B6-A0RQ-10A-01D-A110-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f425edf3-0d08-49bf-94f6-f03343873a6c	fe1d77e9-f21d-4914-ae1a-2cc6dd6f8cba	g.chr8:26365666C>G	ENST00000522362.2	-	3	1500	c.606G>C	c.(604-606)aaG>aaC	p.K202N	PNMA2_ENST00000522764.1_5'Flank	NM_007257.5	NP_009188.1	Q9UL42	PNMA2_HUMAN	paraneoplastic Ma antigen 2	202					positive regulation of apoptotic process (GO:0043065)	nucleus (GO:0005634)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)	11		all_cancers(63;0.109)|Ovarian(32;2.61e-05)|all_epithelial(46;0.105)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0196)|Epithelial(17;3.13e-11)|Colorectal(74;0.123)		gccaccttttcttttctgcct	0.572																																						dbGAP											0													81.0	84.0	83.0					8																	26365666		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS34868.1	8p21.1	2012-02-09	2012-02-09		ENSG00000240694	ENSG00000240694		"""Paraneoplastic Ma antigens"""	9159	protein-coding gene	gene with protein product		603970	"""paraneoplastic antigen MA2"""			10362822	Standard	NM_007257		Approved	MA2, RGAG2	uc003xez.2	Q9UL42	OTTHUMG00000163816	ENST00000522362.2:c.606G>C	8.37:g.26365666C>G	ENSP00000429344:p.Lys202Asn	Somatic		WXS	Illumina GAIIx	Phase_IV	B3KNY9|O94959|O95145|Q49A18|Q9UL43	Missense_Mutation	SNP	pfam_Retrotrans_gag	p.K202N	ENST00000522362.2	37	c.606	CCDS34868.1	8	.	.	.	.	.	.	.	.	.	.	C	17.08	3.297297	0.60086	.	.	ENSG00000240694	ENST00000522362	T	0.11930	2.73	4.22	4.22	0.49857	.	.	.	.	.	T	0.31827	0.0809	L	0.58510	1.815	0.35607	D	0.80833	D	0.71674	0.998	D	0.75484	0.986	T	0.28427	-1.0044	9	0.87932	D	0	-4.5784	12.388	0.55343	0.0:1.0:0.0:0.0	.	202	Q9UL42	PNMA2_HUMAN	N	202	ENSP00000429344:K202N	ENSP00000429344:K202N	K	-	3	2	PNMA2	26421583	1.000000	0.71417	1.000000	0.80357	0.677000	0.39632	2.922000	0.48860	2.640000	0.89533	0.655000	0.94253	AAG	PNMA2	-	NULL	ENSG00000240694		0.572	PNMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PNMA2	HGNC	protein_coding	OTTHUMT00000375709.2	54	0.00	0	C	NM_007257		26365666	26365666	-1	no_errors	ENST00000522362	ensembl	human	known	69_37n	missense	59	11.94	8	SNP	1.000	G
PPP1R16B	26051	genome.wustl.edu	37	20	37546989	37546989	+	Missense_Mutation	SNP	G	G	A			TCGA-B6-A0RQ-01A-11D-A10Y-09	TCGA-B6-A0RQ-10A-01D-A110-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f425edf3-0d08-49bf-94f6-f03343873a6c	fe1d77e9-f21d-4914-ae1a-2cc6dd6f8cba	g.chr20:37546989G>A	ENST00000299824.1	+	11	1573	c.1384G>A	c.(1384-1386)Gtg>Atg	p.V462M	PPP1R16B_ENST00000373331.2_Missense_Mutation_p.V420M	NM_015568.2	NP_056383.1	Q96T49	PP16B_HUMAN	protein phosphatase 1, regulatory subunit 16B	462					regulation of filopodium assembly (GO:0051489)|signal transduction (GO:0007165)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein phosphatase binding (GO:0019903)			biliary_tract(1)|endometrium(4)|kidney(3)|large_intestine(10)|lung(23)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	49		Myeloproliferative disorder(115;0.00878)				CAACCCTGGCGTGGCCGACGC	0.652																																						dbGAP											0													96.0	91.0	93.0					20																	37546989		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB020630	CCDS13309.1, CCDS54462.1	20q11.23	2013-01-10	2011-10-04		ENSG00000101445	ENSG00000101445		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ankyrin repeat domain containing"""	15850	protein-coding gene	gene with protein product	"""TGF-beta-inhibited membrane-associated protein"", ""ankyrin repeat domain protein 4"""	613275	"""protein phosphatase 1, regulatory (inhibitor) subunit 16B"""			10048485, 12055102	Standard	NM_001172735		Approved	KIAA0823, TIMAP, ANKRD4	uc002xje.3	Q96T49	OTTHUMG00000032465	ENST00000299824.1:c.1384G>A	20.37:g.37546989G>A	ENSP00000299824:p.Val462Met	Somatic		WXS	Illumina GAIIx	Phase_IV	A2RRR6|E9PFS8|O94912|Q5W9G4|Q9NQG4	Missense_Mutation	SNP	pfam_Ankyrin_rpt,superfamily_Ankyrin_rpt-contain_dom,smart_Ankyrin_rpt,pirsf_Pase-1_reg_su_16AB_euk,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom	p.V462M	ENST00000299824.1	37	c.1384	CCDS13309.1	20	.	.	.	.	.	.	.	.	.	.	G	8.301	0.820032	0.16678	.	.	ENSG00000101445	ENST00000299824;ENST00000373331	T;T	0.70749	-0.32;-0.51	5.2	-9.12	0.00707	.	1.089880	0.06987	N	0.821015	T	0.34164	0.0888	N	0.08118	0	0.09310	N	1	P;B	0.44309	0.832;0.013	B;B	0.21708	0.036;0.004	T	0.46205	-0.9208	10	0.38643	T	0.18	.	8.4672	0.32964	0.4192:0.2569:0.3239:0.0	.	420;462	E9PFS8;Q96T49	.;PP16B_HUMAN	M	462;420	ENSP00000299824:V462M;ENSP00000362428:V420M	ENSP00000299824:V462M	V	+	1	0	PPP1R16B	36980403	0.000000	0.05858	0.004000	0.12327	0.312000	0.27988	-0.713000	0.05007	-1.123000	0.02940	-0.768000	0.03414	GTG	PPP1R16B	-	pirsf_Pase-1_reg_su_16AB_euk	ENSG00000101445		0.652	PPP1R16B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PPP1R16B	HGNC	protein_coding	OTTHUMT00000079220.2	73	0.00	0	G	NM_015568		37546989	37546989	+1	no_errors	ENST00000299824	ensembl	human	known	69_37n	missense	64	14.67	11	SNP	0.000	A
RIPK1	8737	genome.wustl.edu	37	6	3077012	3077012	+	5'UTR	DEL	G	G	-	rs202096237	byFrequency	TCGA-B6-A0RQ-01A-11D-A10Y-09	TCGA-B6-A0RQ-10A-01D-A110-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f425edf3-0d08-49bf-94f6-f03343873a6c	fe1d77e9-f21d-4914-ae1a-2cc6dd6f8cba	g.chr6:3077012delG	ENST00000259808.4	+	0	253				RIPK1_ENST00000380409.2_5'Flank|RIPK1_ENST00000541791.1_5'Flank|RIPK1_ENST00000479389.1_Intron			Q13546	RIPK1_HUMAN	receptor (TNFRSF)-interacting serine-threonine kinase 1						activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of JUN kinase activity (GO:0007257)|amyloid fibril formation (GO:1990000)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular protein catabolic process (GO:0044257)|cellular response to growth factor stimulus (GO:0071363)|cellular response to tumor necrosis factor (GO:0071356)|extrinsic apoptotic signaling pathway (GO:0097191)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|necroptotic signaling pathway (GO:0097527)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|peptidyl-serine autophosphorylation (GO:0036289)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of necroptotic process (GO:0060545)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of programmed cell death (GO:0043068)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type I interferon production (GO:0032481)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of ATP:ADP antiporter activity (GO:0070926)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|response to tumor necrosis factor (GO:0034612)|ripoptosome assembly (GO:0097343)|ripoptosome assembly involved in necroptotic process (GO:1901026)|T cell apoptotic process (GO:0070231)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytosol (GO:0005829)|death-inducing signaling complex (GO:0031264)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|receptor complex (GO:0043235)|ripoptosome (GO:0097342)	ATP binding (GO:0005524)|death domain binding (GO:0070513)|death receptor binding (GO:0005123)|identical protein binding (GO:0042802)|protein complex binding (GO:0032403)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	23	Ovarian(93;0.0386)	all_hematologic(90;0.0895)				CAGCTCTGCCGGGGGGGGAAA	0.388																																						dbGAP											0													28.0	28.0	28.0					6																	3077012		2203	4300	6503	-	-	-	SO:0001623	5_prime_UTR_variant	0			U25994	CCDS4482.1	6p25.2	2008-02-05			ENSG00000137275	ENSG00000137275			10019	protein-coding gene	gene with protein product		603453				7538908, 8612133	Standard	XM_005249458		Approved	RIP	uc003mux.3	Q13546	OTTHUMG00000014134	ENST00000259808.4:c.-46G>-	6.37:g.3077012delG		Somatic		WXS	Illumina GAIIx	Phase_IV	A0AV89|B2RAG1|B4E3F9|Q13180|Q59H33	RNA	DEL	-	NULL	ENST00000259808.4	37	NULL	CCDS4482.1	6																																																																																			RIPK1	-	-	ENSG00000137275		0.388	RIPK1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	RIPK1	HGNC	protein_coding	OTTHUMT00000039659.2	36	0.00	0	G	NM_003804		3077012	3077012	+1	no_errors	ENST00000490396	ensembl	human	known	69_37n	rna	46	11.54	6	DEL	0.000	-
TAGLN	6876	genome.wustl.edu	37	11	117075033	117075033	+	Silent	SNP	C	C	A	rs139773620		TCGA-B6-A0RQ-01A-11D-A10Y-09	TCGA-B6-A0RQ-10A-01D-A110-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f425edf3-0d08-49bf-94f6-f03343873a6c	fe1d77e9-f21d-4914-ae1a-2cc6dd6f8cba	g.chr11:117075033C>A	ENST00000532870.1	+	4	1705	c.564C>A	c.(562-564)gcC>gcA	p.A188A	TAGLN_ENST00000392951.4_Silent_p.A188A|PCSK7_ENST00000529458.1_5'Flank|TAGLN_ENST00000530649.1_Silent_p.A188A			Q01995	TAGL_HUMAN	transgelin	188					epithelial cell differentiation (GO:0030855)|muscle organ development (GO:0007517)	cytoplasm (GO:0005737)				central_nervous_system(1)|large_intestine(4)|lung(1)|urinary_tract(1)	7	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.63e-06)|Epithelial(105;5.49e-05)|all cancers(92;0.000435)		CCTCCCAGGCCGGCATGACAG	0.622																																						dbGAP											0													72.0	75.0	74.0					11																	117075033		2201	4296	6497	-	-	-	SO:0001819	synonymous_variant	0			M95787	CCDS8381.1	11q23.2	2008-07-21				ENSG00000149591			11553	protein-coding gene	gene with protein product	"""SM22-alpha"", ""transgelin variant 2"""	600818				8117285, 1520290	Standard	NM_003186		Approved	SM22, WS3-10, TAGLN1, SMCC, DKFZp686P11128	uc001pqm.3	Q01995		ENST00000532870.1:c.564C>A	11.37:g.117075033C>A		Somatic		WXS	Illumina GAIIx	Phase_IV	O15542	Missense_Mutation	SNP	pfam_Calponin_repeat,pfam_CH-domain,superfamily_CH-domain,smart_CH-domain,pfscan_CH-domain,pfscan_Calponin_repeat,prints_Transgelin,prints_SM22_calponin	p.P138Q	ENST00000532870.1	37	c.413	CCDS8381.1	11	.	.	.	.	.	.	.	.	.	.	C	10.50	1.367209	0.24771	.	.	ENSG00000149591	ENST00000529622	.	.	.	4.63	-6.55	0.01854	.	.	.	.	.	T	0.48187	0.1486	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51395	-0.8711	4	.	.	.	.	8.0016	0.30299	0.0:0.4921:0.2148:0.2931	.	.	.	.	Q	138	.	.	P	+	2	0	TAGLN	116580243	0.093000	0.21703	0.955000	0.39395	0.996000	0.88848	-0.904000	0.04080	-1.204000	0.02648	0.491000	0.48974	CCG	TAGLN	-	pfam_Calponin_repeat,pfscan_Calponin_repeat,prints_SM22_calponin	ENSG00000149591		0.622	TAGLN-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	TAGLN	HGNC	protein_coding	OTTHUMT00000392864.1	84	0.00	0	C	NM_001001522		117075033	117075033	+1	no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region	ENST00000529622	ensembl	human	putative	69_37n	missense	116	11.94	16	SNP	0.934	A
TSC2	7249	genome.wustl.edu	37	16	2134569	2134569	+	Missense_Mutation	SNP	C	C	G	rs397514939		TCGA-B6-A0RQ-01A-11D-A10Y-09	TCGA-B6-A0RQ-10A-01D-A110-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f425edf3-0d08-49bf-94f6-f03343873a6c	fe1d77e9-f21d-4914-ae1a-2cc6dd6f8cba	g.chr16:2134569C>G	ENST00000219476.3	+	34	4976	c.4346C>G	c.(4345-4347)tCc>tGc	p.S1449C	TSC2_ENST00000382538.6_Missense_Mutation_p.S1334C|TSC2_ENST00000353929.4_Missense_Mutation_p.S1406C|TSC2_ENST00000401874.2_Missense_Mutation_p.S1382C|TSC2_ENST00000350773.4_Missense_Mutation_p.S1426C|TSC2_ENST00000439673.2_Missense_Mutation_p.S1346C|TSC2_ENST00000568454.1_Missense_Mutation_p.S1393C	NM_000548.3	NP_000539.2	P49815	TSC2_HUMAN	tuberous sclerosis 2	1449					acute-phase response (GO:0006953)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of TOR signaling (GO:0032007)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive chemotaxis (GO:0050918)|positive regulation of Ras GTPase activity (GO:0032320)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein import into nucleus (GO:0006606)|protein kinase B signaling (GO:0043491)|protein localization (GO:0008104)|regulation of cell cycle (GO:0051726)|regulation of endocytosis (GO:0030100)|regulation of insulin receptor signaling pathway (GO:0046626)|response to hypoxia (GO:0001666)|vesicle-mediated transport (GO:0016192)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|TSC1-TSC2 complex (GO:0033596)	GTPase activator activity (GO:0005096)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(3)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|soft_tissue(1)	56		Hepatocellular(780;0.0202)				CCTTCCAGCTCCCCCCGCTCG	0.687			"""D, Mis, N, F, S"""			"""hamartoma, renal cell"""			Tuberous Sclerosis																													dbGAP	yes	Rec		Tuberous sclerosis 2	16	16p13.3	7249	tuberous sclerosis 2 gene		"""E, O"""	0													14.0	18.0	17.0					16																	2134569		2184	4289	6473	-	-	-	SO:0001583	missense	0	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	AB014460	CCDS10458.1, CCDS45384.1, CCDS58408.1	16p13.3	2014-09-17			ENSG00000103197	ENSG00000103197			12363	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 160"""	191092		TSC4		1303246, 7558029	Standard	NM_001077183		Approved	tuberin, LAM, PPP1R160	uc002con.3	P49815	OTTHUMG00000128745	ENST00000219476.3:c.4346C>G	16.37:g.2134569C>G	ENSP00000219476:p.Ser1449Cys	Somatic		WXS	Illumina GAIIx	Phase_IV	A7E2E2|B4DIL8|B4DIQ7|B4DRN2|B7Z2B8|C9J378|O75275|Q4LE71|Q8TAZ1	Missense_Mutation	SNP	pfam_Tuberin-type_domain,pfam_Tuberin_N,pfam_Rap_GAP,superfamily_ARM-type_fold,prints_Tuberin,pfscan_Rap_GAP	p.S1449C	ENST00000219476.3	37	c.4346	CCDS10458.1	16	.	.	.	.	.	.	.	.	.	.	C	4.919	0.170819	0.09391	.	.	ENSG00000103197	ENST00000219476;ENST00000401874;ENST00000353929;ENST00000439673;ENST00000382538;ENST00000350773	D;D;D;D;D	0.90069	-2.5;-2.5;-2.61;-2.57;-2.52	5.16	2.11	0.27256	.	0.863156	0.10173	N	0.706880	D	0.86239	0.5885	N	0.08118	0	0.19575	N	0.999964	B;B;B;B;B;B;D	0.76494	0.0;0.001;0.001;0.009;0.001;0.001;0.999	B;B;B;B;B;B;D	0.76071	0.002;0.005;0.001;0.006;0.005;0.005;0.987	T	0.75196	-0.3403	10	0.36615	T	0.2	-8.156	7.5189	0.27616	0.0:0.488:0.3474:0.1646	.	1334;1346;1426;224;1405;1382;1449	B4DIL8;P49815-6;P49815-4;B3KSR9;P49815-3;P49815-5;P49815	.;.;.;.;.;.;TSC2_HUMAN	C	1449;1383;1406;1346;1334;1426	ENSP00000219476:S1449C;ENSP00000248099:S1406C;ENSP00000399232:S1346C;ENSP00000371978:S1334C;ENSP00000344383:S1426C	ENSP00000219476:S1449C	S	+	2	0	TSC2	2074570	0.900000	0.30661	0.156000	0.22583	0.715000	0.41141	1.815000	0.38981	0.200000	0.20447	-0.225000	0.12378	TCC	TSC2	-	NULL	ENSG00000103197		0.687	TSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	TSC2	HGNC	protein_coding	OTTHUMT00000250657.2	19	0.00	0	C	NM_000548		2134569	2134569	+1	no_errors	ENST00000219476	ensembl	human	known	69_37n	missense	27	20.59	7	SNP	0.007	G
