#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_Chromosome_hg18	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_End_position_hg18	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_Start_position_hg18	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_classification	i_context	i_dataset	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	i_type
ABCF1	23	hgsc.bcm.edu	37	6	30553726	30553726	+	Missense_Mutation	SNP	G	G	C			TCGA-13-0717-01	TCGA-13-0717-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chr6:30553726G>C	ENST00000326195.8	+	17	1783	c.1671G>C	c.(1669-1671)aaG>aaC	p.K557N	ABCF1_ENST00000376545.3_Missense_Mutation_p.K519N|ABCF1_ENST00000396515.4_Intron|MIR877_ENST00000401282.1_RNA	NM_001025091.1	NP_001020262.1	Q8NE71	ABCF1_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 1	557					inflammatory response (GO:0006954)|positive regulation of translation (GO:0045727)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|polysomal ribosome (GO:0042788)|ribosome (GO:0005840)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)|translation activator activity (GO:0008494)|translation factor activity, nucleic acid binding (GO:0008135)	p.K557N(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(3)|skin(2)	21						AAGAGAAAAAGCTGAAGGAGC	0.552																																																1	Substitution - Missense(1)	ovary(1)	6											26.0	22.0	23.0					6																	30553726		1511	2709	4220	30661705	SO:0001583	missense	23			AF027302	CCDS34380.1, CCDS34381.1	6p21.33	2012-03-14			ENSG00000204574	ENSG00000204574		"""ATP binding cassette transporters / subfamily F"""	70	protein-coding gene	gene with protein product		603429		ABC50		9790762	Standard	NM_001025091		Approved	EST123147	uc003nql.3	Q8NE71	OTTHUMG00000031094	ENST00000326195.8:c.1671G>C	6.37:g.30553726G>C	ENSP00000313603:p.Lys557Asn	Somatic		Capture	SOLID	Phase_IV	30661705	A2BF75|O14897|Q69YP6	Missense_Mutation	SNP	ENST00000326195.8	37	CCDS34380.1	SNP	34	Baylor	.	.	.	.	.	.	.	.	.	.	G	15.69	2.906686	0.52333	.	.	ENSG00000204574	ENST00000326195;ENST00000376545	T;T	0.56444	0.46;0.92	4.79	3.9	0.45041	.	0.269175	0.40469	N	0.001094	T	0.34308	0.0893	L	0.56769	1.78	0.80722	D	1	B;B;B	0.30236	0.274;0.274;0.274	B;B;B	0.34301	0.179;0.115;0.115	T	0.38866	-0.9641	10	0.59425	D	0.04	-22.084	8.9325	0.35680	0.1764:0.0:0.8236:0.0	.	519;557;557	Q2L6I2;Q8NE71;A2BF75	.;ABCF1_HUMAN;.	N	557;519	ENSP00000313603:K557N;ENSP00000365728:K519N	ENSP00000313603:K557N	K	+	3	2	ABCF1	30661705	1.000000	0.71417	0.997000	0.53966	0.989000	0.77384	1.705000	0.37867	1.207000	0.43291	0.484000	0.47621	AAG		0.552	ABCF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076137.3			Missense_Mutation
ADAM12	8038	hgsc.bcm.edu	37	10	127753556	127753556	+	Silent	SNP	T	T	A			TCGA-13-0717-01	TCGA-13-0717-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chr10:127753556T>A	ENST00000368679.4	-	14	1746	c.1437A>T	c.(1435-1437)ggA>ggT	p.G479G	ADAM12_ENST00000467145.1_5'UTR|ADAM12_ENST00000368676.4_Silent_p.G479G	NM_003474.4	NP_003465.3	O43184	ADA12_HUMAN	ADAM metallopeptidase domain 12	479	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.		G -> E (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cell adhesion (GO:0007155)|epidermal growth factor receptor signaling pathway (GO:0007173)|myoblast fusion (GO:0007520)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			biliary_tract(1)|breast(7)|central_nervous_system(4)|endometrium(5)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69		all_epithelial(44;7.06e-05)|all_lung(145;0.00563)|Lung NSC(174;0.00834)|Colorectal(57;0.102)|all_neural(114;0.107)|Breast(234;0.22)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.216)		TGCACGCTGTTCCTGCAGGCT	0.602																																																0			10											61.0	60.0	60.0					10																	127753556		2203	4300	6503	127743546	SO:0001819	synonymous_variant	8038			AF023476	CCDS7653.1, CCDS7654.1	10q26	2008-07-29	2008-07-29		ENSG00000148848	ENSG00000148848		"""ADAM metallopeptidase domain containing"""	190	protein-coding gene	gene with protein product	"""meltrin alpha"""	602714	"""a disintegrin and metalloproteinase domain 12 (meltrin alpha)"""			9417060, 18342566	Standard	NM_003474		Approved	MCMPMltna, MLTN	uc001ljk.2	O43184	OTTHUMG00000019243	ENST00000368679.4:c.1437A>T	10.37:g.127753556T>A		Somatic		Capture	SOLID	Phase_IV	127743546	O60470|Q5JRP0|Q5JRP1|Q6P9E3|Q6UWB0	Silent	SNP	ENST00000368679.4	37	CCDS7653.1	SNP	62	Baylor																																																																																				0.602	ADAM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050961.1			Silent
ADAM8	101	hgsc.bcm.edu	37	10	135076677	135076678	+	Frame_Shift_Ins	INS	-	-	T	rs58683011|rs146838825|rs397733581|rs561363568		TCGA-13-0717-01	TCGA-13-0717-10	-	-	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chr10:135076677_135076678insT	ENST00000445355.3	-	23	2507_2508	c.2457_2458insA	c.(2455-2460)ggagctfs	p.A820fs	ADAM8_ENST00000415217.3_3'UTR|ADAM8_ENST00000485491.2_Frame_Shift_Ins_p.A729fs	NM_001109.4	NP_001100.3	P78325	ADAM8_HUMAN	ADAM metallopeptidase domain 8	820					activation of MAPK activity involved in innate immune response (GO:0035419)|angiogenesis (GO:0001525)|cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inflammatory response (GO:0006954)|leukocyte migration involved in inflammatory response (GO:0002523)|lymphocyte chemotaxis (GO:0048247)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of bone resorption (GO:0045780)|positive regulation of cell adhesion (GO:0045785)|positive regulation of eosinophil migration (GO:2000418)|positive regulation of fibronectin-dependent thymocyte migration (GO:2000415)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of neutrophil extravasation (GO:2000391)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein processing (GO:0010954)|positive regulation of protein secretion (GO:0050714)|positive regulation of T cell differentiation in thymus (GO:0033089)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of tumor necrosis factor (ligand) superfamily member 11 production (GO:2000309)|regulation of cell-cell adhesion (GO:0022407)|single organismal cell-cell adhesion (GO:0016337)	alpha9-beta1 integrin-ADAM8 complex (GO:0071133)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dense core granule membrane (GO:0032127)|integral component of plasma membrane (GO:0005887)|phagolysosome (GO:0032010)|plasma membrane (GO:0005886)|podosome (GO:0002102)|specific granule (GO:0042581)|tertiary granule (GO:0070820)	calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|protein self-association (GO:0043621)|zinc ion binding (GO:0008270)	p.L820fs*6(1)		central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(6)|ovary(1)|prostate(2)	17		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		all cancers(32;7.72e-06)|OV - Ovarian serous cystadenocarcinoma(35;8.23e-06)|Epithelial(32;1.02e-05)		GCTGTGGGAGCTCCGGCTCCTT	0.569																																																1	Insertion - Frameshift(1)	ovary(1)	10																																								134926669	SO:0001589	frameshift_variant	101			D26579	CCDS31319.2, CCDS58102.1, CCDS58103.1	10q26.3	2014-03-20	2005-08-18		ENSG00000151651	ENSG00000151651		"""ADAM metallopeptidase domain containing"", ""CD molecules"""	215	protein-coding gene	gene with protein product		602267	"""a disintegrin and metalloproteinase domain 8"""			9126482	Standard	NM_001109		Approved	CD156, MS2, CD156a	uc021qbe.1	P78325	OTTHUMG00000019309	ENST00000445355.3:c.2458dupA	10.37:g.135076678_135076678dupT	ENSP00000453302:p.Ala820fs	Somatic		Capture	SOLID	Phase_IV	134926668	B4DVM6|H0YL36|H0YLR0|H0YN39	Frame_Shift_Ins	INS	ENST00000445355.3	37	CCDS31319.2	INS	28	Baylor																																																																																				0.569	ADAM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051118.4	NM_001109		Frame_Shift_Ins
AP3B2	8120	hgsc.bcm.edu	37	15	83348495	83348495	+	Missense_Mutation	SNP	T	T	C	rs375502817|rs28581493		TCGA-13-0717-01	TCGA-13-0717-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chr15:83348495T>C	ENST00000261722.3	-	10	1375	c.1168A>G	c.(1168-1170)Att>Gtt	p.I390V	RP11-752G15.3_ENST00000560650.1_RNA|AP3B2_ENST00000535359.1_Missense_Mutation_p.I390V|AP3B2_ENST00000535348.1_Missense_Mutation_p.I358V	NM_004644.3	NP_004635.2	Q13367	AP3B2_HUMAN	adaptor-related protein complex 3, beta 2 subunit	390					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|intracellular protein transport (GO:0006886)|post-Golgi vesicle-mediated transport (GO:0006892)	AP-3 adaptor complex (GO:0030123)|COPI-coated vesicle (GO:0030137)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	transporter activity (GO:0005215)			breast(4)|endometrium(1)|kidney(1)|large_intestine(4)|lung(21)|ovary(4)|pancreas(1)|prostate(3)|urinary_tract(2)	41			BRCA - Breast invasive adenocarcinoma(143;0.229)			AGGATCTTAATCTGGGTGGGG	0.577																																																0			15											88.0	99.0	96.0					15																	83348495		1970	4139	6109	81145550	SO:0001583	missense	8120			U37673	CCDS45331.1, CCDS61736.1, CCDS61737.1	15q	2008-07-07			ENSG00000103723	ENSG00000103723			567	protein-coding gene	gene with protein product		602166				7671305, 1851215	Standard	NM_004644		Approved	NAPTB	uc010uoh.2	Q13367	OTTHUMG00000168009	ENST00000261722.3:c.1168A>G	15.37:g.83348495T>C	ENSP00000261722:p.Ile390Val	Somatic		Capture	SOLID	Phase_IV	81145550	A4Z4T7|B7ZKR7|B7ZKS0|O14808|Q52LY8	Missense_Mutation	SNP	ENST00000261722.3	37	CCDS45331.1	SNP	52	Baylor	.	.	.	.	.	.	.	.	.	.	T	16.22	3.062745	0.55432	.	.	ENSG00000103723	ENST00000261722;ENST00000535348;ENST00000535359	T;T;T	0.34472	1.36;1.36;1.36	4.94	4.94	0.65067	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	.	.	.	.	T	0.39226	0.1070	N	0.11284	0.12	0.80722	D	1	D;P;B	0.53151	0.958;0.592;0.041	D;B;B	0.70716	0.97;0.241;0.124	T	0.33085	-0.9882	9	0.27785	T	0.31	-13.5958	15.0635	0.71973	0.0:0.0:0.0:1.0	rs28581493	358;390;390	B7ZKR7;B7ZKS0;Q13367	.;.;AP3B2_HUMAN	V	390;358;390	ENSP00000261722:I390V;ENSP00000438721:I358V;ENSP00000440984:I390V	ENSP00000261722:I390V	I	-	1	0	AP3B2	81145550	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.801000	0.85960	2.199000	0.70637	0.533000	0.62120	ATT		0.577	AP3B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397463.1			Missense_Mutation
ARID1B	57492	hgsc.bcm.edu	37	6	157527996	157527997	+	Frame_Shift_Ins	INS	-	-	T			TCGA-13-0717-01	TCGA-13-0717-10	-	-	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chr6:157527996_157527997insT	ENST00000350026.5	+	19	5683_5684	c.5682_5683insT	c.(5683-5685)cagfs	p.Q1895fs	ARID1B_ENST00000275248.4_Frame_Shift_Ins_p.Q1890fs|ARID1B_ENST00000367148.1_Frame_Shift_Ins_p.Q1948fs|ARID1B_ENST00000346085.5_Frame_Shift_Ins_p.Q1908fs	NM_017519.2	NP_059989.2	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	1895					chromatin-mediated maintenance of transcription (GO:0048096)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)	p.Q1890fs*36(1)		NS(2)|breast(5)|central_nervous_system(4)|endometrium(12)|kidney(4)|large_intestine(11)|lung(30)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(3)	81		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		CCTTTGGTATCCAGCAAGCCAA	0.584																																																1	Insertion - Frameshift(1)	ovary(1)	6																																								157569689	SO:0001589	frameshift_variant	57492			AF521671	CCDS5251.1, CCDS5251.2, CCDS55072.1	6q25.3	2014-09-17			ENSG00000049618	ENSG00000049618		"""-"""	18040	protein-coding gene	gene with protein product		614556					Standard	NM_017519		Approved	KIAA1235, ELD/OSA1, p250R, BAF250b, DAN15, 6A3-5	uc003qqo.3	Q8NFD5	OTTHUMG00000015890	Exception_encountered	6.37:g.157527996_157527997insT	ENSP00000055163:p.Gln1895fs	Somatic		Capture	SOLID	Phase_IV	157569688	Q5JRD1|Q5VYC4|Q8IZY8|Q8TEV0|Q8TF02|Q99491|Q9ULI5	Frame_Shift_Ins	INS	ENST00000350026.5	37	CCDS5251.2	INS	30	Baylor																																																																																				0.584	ARID1B-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372723.1	NM_020732		Frame_Shift_Ins
ASCC3	10973	hgsc.bcm.edu	37	6	100965891	100965891	+	Missense_Mutation	SNP	T	T	C			TCGA-13-0717-01	TCGA-13-0717-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Sanger_PCR_WGA	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chr6:100965891T>C	ENST00000369162.2	-	38	6247	c.5903A>G	c.(5902-5904)gAa>gGa	p.E1968G		NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	1968	SEC63 2.				cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA duplex unwinding (GO:0032508)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|poly(A) RNA binding (GO:0044822)	p.E1968G(1)		breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(20)|liver(1)|lung(36)|ovary(6)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	92		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)		ATGATGGTTTTCTATGTTTGG	0.348																																																1	Substitution - Missense(1)	ovary(1)	6											83.0	84.0	84.0					6																	100965891		2203	4300	6503	101072612	SO:0001583	missense	10973			AJ223948	CCDS5046.1, CCDS5047.1, CCDS75497.1	6q16	2008-02-05		2004-07-28	ENSG00000112249	ENSG00000112249			18697	protein-coding gene	gene with protein product	"""RNA helicase family"""	614217	"""helicase, ATP binding 1"""	HELIC1		10218103	Standard	NM_006828		Approved	RNAH, ASC1p200, dJ121G13.4, dJ467N11.1	uc003pqk.3	Q8N3C0	OTTHUMG00000015279	ENST00000369162.2:c.5903A>G	6.37:g.100965891T>C	ENSP00000358159:p.Glu1968Gly	Somatic		Capture	SOLID	Phase_IV	101072612	E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Missense_Mutation	SNP	ENST00000369162.2	37	CCDS5046.1	SNP	62	Baylor	.	.	.	.	.	.	.	.	.	.	T	22.7	4.320908	0.81469	.	.	ENSG00000112249	ENST00000369162	T	0.58358	0.34	4.83	4.83	0.62350	Sec63 domain (3);	0.000000	0.85682	D	0.000000	T	0.47451	0.1446	L	0.53249	1.67	0.80722	D	1	P	0.42296	0.775	P	0.51297	0.665	T	0.40961	-0.9535	10	0.23891	T	0.37	.	14.6995	0.69147	0.0:0.0:0.0:1.0	.	1968	Q8N3C0	HELC1_HUMAN	G	1968	ENSP00000358159:E1968G	ENSP00000358159:E1968G	E	-	2	0	ASCC3	101072612	1.000000	0.71417	0.938000	0.37757	0.940000	0.58332	7.905000	0.87416	1.947000	0.56498	0.377000	0.23210	GAA		0.348	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828		Missense_Mutation
ARID1B	57492	hgsc.bcm.edu	37	6	157528001	157528001	+	Missense_Mutation	SNP	A	A	C			TCGA-13-0717-01	TCGA-13-0717-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chr6:157528001A>C	ENST00000350026.5	+	19	5688	c.5687A>C	c.(5686-5688)cAa>cCa	p.Q1896P	ARID1B_ENST00000275248.4_Missense_Mutation_p.Q1891P|ARID1B_ENST00000367148.1_Missense_Mutation_p.Q1949P|ARID1B_ENST00000346085.5_Missense_Mutation_p.Q1909P	NM_017519.2	NP_059989.2	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	1896					chromatin-mediated maintenance of transcription (GO:0048096)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)	p.Q1891P(1)		NS(2)|breast(5)|central_nervous_system(4)|endometrium(12)|kidney(4)|large_intestine(11)|lung(30)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(3)	81		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		GGTATCCAGCAAGCCAAAAGT	0.592																																																1	Substitution - Missense(1)	ovary(1)	6											96.0	93.0	94.0					6																	157528001		2203	4296	6499	157569693	SO:0001583	missense	57492			AF521671	CCDS5251.1, CCDS5251.2, CCDS55072.1	6q25.3	2014-09-17			ENSG00000049618	ENSG00000049618		"""-"""	18040	protein-coding gene	gene with protein product		614556					Standard	NM_017519		Approved	KIAA1235, ELD/OSA1, p250R, BAF250b, DAN15, 6A3-5	uc003qqo.3	Q8NFD5	OTTHUMG00000015890	ENST00000350026.5:c.5687A>C	6.37:g.157528001A>C	ENSP00000055163:p.Gln1896Pro	Somatic		Capture	SOLID	Phase_IV	157569693	Q5JRD1|Q5VYC4|Q8IZY8|Q8TEV0|Q8TF02|Q99491|Q9ULI5	Missense_Mutation	SNP	ENST00000350026.5	37	CCDS5251.2	SNP	5	Baylor	.	.	.	.	.	.	.	.	.	.	A	7.886	0.731295	0.15507	.	.	ENSG00000049618	ENST00000346085;ENST00000350026;ENST00000367148;ENST00000275248;ENST00000414678	T;T;T;T;T	0.02032	4.8;4.8;4.8;4.8;4.49	5.08	5.08	0.68730	.	0.305820	0.35677	N	0.003047	T	0.00580	0.0019	N	0.16098	0.37	0.42671	D	0.993519	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.04013	0.0;0.001;0.001	T	0.37731	-0.9693	10	0.05436	T	0.98	.	14.858	0.70355	1.0:0.0:0.0:0.0	.	1896;1909;1891	Q8NFD5;Q8NFD5-2;G3XAA0	ARI1B_HUMAN;.;.	P	1909;1896;1949;1891;1418	ENSP00000344546:Q1909P;ENSP00000055163:Q1896P;ENSP00000356116:Q1949P;ENSP00000275248:Q1891P;ENSP00000412835:Q1418P	ENSP00000275248:Q1891P	Q	+	2	0	ARID1B	157569693	1.000000	0.71417	0.485000	0.27403	0.810000	0.45777	5.916000	0.69981	1.903000	0.55091	0.460000	0.39030	CAA		0.592	ARID1B-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372723.1	NM_020732		Missense_Mutation
ASTE1	28990	hgsc.bcm.edu	37	3	130733047	130733047	+	Frame_Shift_Del	DEL	T	T	-			TCGA-13-0717-01	TCGA-13-0717-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chr3:130733047delT	ENST00000264992.3	-	6	2335	c.1894delA	c.(1894-1896)aggfs	p.R632fs	ATP2C1_ENST00000422190.2_Intron|ATP2C1_ENST00000513801.1_Intron|ATP2C1_ENST00000393221.4_Intron|ATP2C1_ENST00000533801.2_Intron|ATP2C1_ENST00000504381.1_Intron|ATP2C1_ENST00000359644.3_Intron|ATP2C1_ENST00000328560.8_Intron|ASTE1_ENST00000514044.1_Frame_Shift_Del_p.R657fs|ATP2C1_ENST00000507488.2_Intron	NM_014065.2	NP_054784.2	Q2TB18	ASTE1_HUMAN	asteroid homolog 1 (Drosophila)	632					DNA repair (GO:0006281)		nuclease activity (GO:0004518)	p.R632fs*33(2)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(6)|ovary(2)|prostate(1)	22						TTCTTCTGCCTTTTTTTTTTT	0.403																																																2	Deletion - Frameshift(2)	ovary(2)	3											57.0	55.0	56.0					3																	130733047		2203	4300	6503	132215737	SO:0001589	frameshift_variant	28990			AF113539	CCDS3068.1, CCDS75007.1	3q21.3	2005-11-17			ENSG00000034533	ENSG00000034533			25021	protein-coding gene	gene with protein product							Standard	NM_014065		Approved	HT001	uc003env.1	Q2TB18	OTTHUMG00000159644	ENST00000264992.3:c.1894delA	3.37:g.130733047delT	ENSP00000264992:p.Arg632fs	Somatic		Capture	SOLID	Phase_IV	132215737	B4DFL9|Q3MIB6|Q8N6G4|Q96JY1|Q9UHX6	Frame_Shift_Del	DEL	ENST00000264992.3	37	CCDS3068.1	DEL	56	Baylor																																																																																				0.403	ASTE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356659.1	NM_014065		Frame_Shift_Del
PRRC2B	84726	hgsc.bcm.edu	37	9	134358766	134358766	+	Silent	SNP	A	A	T			TCGA-13-0717-01	TCGA-13-0717-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chr9:134358766A>T	ENST00000357304.4	+	22	5449	c.5394A>T	c.(5392-5394)ccA>ccT	p.P1798P	SNORD62A_ENST00000428514.1_RNA|PRRC2B_ENST00000405995.1_Silent_p.P1104P|PRRC2B_ENST00000458550.1_Silent_p.P1104P|PRRC2B_ENST00000372249.1_5'UTR	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	1798							poly(A) RNA binding (GO:0044822)	p.P1798P(1)		cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(20)|ovary(2)	44						TCAGCTTGCCACCTGGTTCTG	0.498																																																1	Substitution - coding silent(1)	ovary(1)	9											136.0	128.0	131.0					9																	134358766		1943	4171	6114	133348587	SO:0001819	synonymous_variant	84726			AB011087	CCDS48044.1	9q34.13	2010-12-09	2010-12-09	2010-12-09	ENSG00000130723	ENSG00000130723			28121	protein-coding gene	gene with protein product			"""KIAA0515"", ""HLA-B associated transcript 2-like"", ""HLA-B associated transcript 2-like 1"""	KIAA0515, BAT2L, BAT2L1		9628581	Standard	NM_013318		Approved	MGC10526, LQFBS-1	uc004can.4	Q5JSZ5	OTTHUMG00000020827	ENST00000357304.4:c.5394A>T	9.37:g.134358766A>T		Somatic		Capture	SOLID	Phase_IV	133348587	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Silent	SNP	ENST00000357304.4	37	CCDS48044.1	SNP	6	Baylor	.	.	.	.	.	.	.	.	.	.	A	1.777	-0.482985	0.04383	.	.	ENSG00000130723	ENST00000451855	.	.	.	5.51	-11.0	0.00169	.	.	.	.	.	T	0.46560	0.1399	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59558	-0.7432	4	.	.	.	-16.9936	9.5875	0.39526	0.6874:0.059:0.1608:0.0929	.	.	.	.	S	531	.	.	T	+	1	0	PRRC2B	133348587	0.000000	0.05858	0.215000	0.23724	0.198000	0.23893	-2.435000	0.01020	-2.526000	0.00494	-1.044000	0.02363	ACC		0.498	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				Silent
LAMTOR1	55004	hgsc.bcm.edu	37	11	71809888	71809888	+	Missense_Mutation	SNP	A	A	T			TCGA-13-0717-01	TCGA-13-0717-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chr11:71809888A>T	ENST00000278671.5	-	3	367	c.205T>A	c.(205-207)Tct>Act	p.S69T	LRTOMT_ENST00000435085.1_Intron|LAMTOR1_ENST00000535107.1_Missense_Mutation_p.S69T|LRTOMT_ENST00000419228.1_Intron|LAMTOR1_ENST00000539797.1_5'UTR|LAMTOR1_ENST00000538404.1_Missense_Mutation_p.S69T|LRTOMT_ENST00000307198.7_Intron|LAMTOR1_ENST00000545249.1_Missense_Mutation_p.S69T|LRTOMT_ENST00000439209.1_Intron	NM_017907.2	NP_060377.1	Q6IAA8	LTOR1_HUMAN	late endosomal/lysosomal adaptor, MAPK and MTOR activator 1	69				S -> P (in Ref. 2; CAG33528). {ECO:0000305}.	cell growth (GO:0016049)|cellular protein localization (GO:0034613)|cellular response to amino acid stimulus (GO:0071230)|cholesterol homeostasis (GO:0042632)|endosome localization (GO:0032439)|endosome organization (GO:0007032)|lysosome localization (GO:0032418)|lysosome organization (GO:0007040)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of TOR signaling (GO:0032008)|regulation of cholesterol efflux (GO:0010874)|regulation of cholesterol esterification (GO:0010872)|regulation of cholesterol import (GO:0060620)|regulation of receptor recycling (GO:0001919)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|late endosome membrane (GO:0031902)|lysosome (GO:0005764)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|Ragulator complex (GO:0071986)				cervix(1)	1						TCTGCAGCAGACACATCAATG	0.567																																																0			11											85.0	56.0	66.0					11																	71809888		2010	3829	5839	71487536	SO:0001583	missense	55004			AK000632	CCDS8209.1	11q13.4	2011-05-18	2011-02-15	2011-02-15	ENSG00000149357	ENSG00000149357			26068	protein-coding gene	gene with protein product	"""p27kip1 releasing factor from RhoA"", ""protein associated with DRMs and endosomes"""	613510	"""chromosome 11 open reading frame 59"""	C11orf59		12358155	Standard	NM_017907		Approved	FLJ20625, p18, p27RF-Rho, Pdro, Ragulator1	uc001ort.3	Q6IAA8	OTTHUMG00000167869	ENST00000278671.5:c.205T>A	11.37:g.71809888A>T	ENSP00000278671:p.Ser69Thr	Somatic		Capture	SOLID	Phase_IV	71487536	Q8WZ09|Q9NWT0	Missense_Mutation	SNP	ENST00000278671.5	37	CCDS8209.1	SNP	10	Baylor	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	31|31	5.102961|5.102961	0.94245|0.94245	.|.	.|.	ENSG00000149357|ENSG00000149357	ENST00000544594|ENST00000545249;ENST00000535107;ENST00000278671;ENST00000538404	.|T;T;T;T	.|0.45668	.|0.89;0.89;0.89;0.89	5.8|5.8	5.8|5.8	0.92144|0.92144	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	.|T	.|0.47248	.|0.1435	M|M	0.70275|0.70275	2.135|2.135	0.80722|0.80722	D|D	1|1	.|P	.|0.42518	.|0.782	.|B	.|0.40375	.|0.327	.|T	.|0.53408	.|-0.8443	.|10	0.56958|0.62326	D|D	0.05|0.03	.|.	15.8237|15.8237	0.78678|0.78678	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|69	.|Q6IAA8	.|LTOR1_HUMAN	X|T	55|69	.|ENSP00000440738:S69T;ENSP00000445170:S69T;ENSP00000278671:S69T;ENSP00000439011:S69T	ENSP00000439482:C50X|ENSP00000278671:S69T	C|S	-|-	3|1	2|0	LAMTOR1|LAMTOR1	71487536|71487536	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.823000|0.823000	0.46562|0.46562	6.875000|6.875000	0.75551|0.75551	2.224000|2.224000	0.72417|0.72417	0.533000|0.533000	0.62120|0.62120	TGT|TCT		0.567	LAMTOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396733.1	NM_017907		Missense_Mutation
CACNA1G	8913	hgsc.bcm.edu	37	17	48678091	48678091	+	Missense_Mutation	SNP	A	A	G			TCGA-13-0717-01	TCGA-13-0717-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chr17:48678091A>G	ENST00000359106.5	+	18	3695	c.3695A>G	c.(3694-3696)aAa>aGa	p.K1232R	CACNA1G_ENST00000507896.1_Missense_Mutation_p.K1232R|CACNA1G_ENST00000416767.4_Missense_Mutation_p.K1232R|CACNA1G_ENST00000515165.1_Missense_Mutation_p.K1232R|CACNA1G_ENST00000510366.1_Missense_Mutation_p.K1232R|CACNA1G_ENST00000515411.1_Missense_Mutation_p.K1232R|CACNA1G_ENST00000358244.5_Missense_Mutation_p.K1209R|CACNA1G_ENST00000514717.1_Missense_Mutation_p.K1209R|CACNA1G_ENST00000429973.2_Missense_Mutation_p.K1232R|CACNA1G_ENST00000352832.5_Missense_Mutation_p.K1209R|CACNA1G_ENST00000514181.1_Missense_Mutation_p.K1232R|CACNA1G_ENST00000512389.1_Missense_Mutation_p.K1232R|CACNA1G_ENST00000505165.1_Missense_Mutation_p.K1232R|CACNA1G_ENST00000442258.2_Missense_Mutation_p.K1209R|CACNA1G_ENST00000513964.1_Missense_Mutation_p.K1232R|CACNA1G_ENST00000503485.1_Missense_Mutation_p.K1232R|CACNA1G_ENST00000354983.4_Missense_Mutation_p.K1209R|CACNA1G_ENST00000507510.2_Missense_Mutation_p.K1232R|CACNA1G_ENST00000502264.1_Missense_Mutation_p.K1209R|CACNA1G_ENST00000360761.4_Missense_Mutation_p.K1209R|CACNA1G_ENST00000515765.1_Missense_Mutation_p.K1232R|CACNA1G_ENST00000514079.1_Missense_Mutation_p.K1232R|CACNA1G_ENST00000507609.1_Missense_Mutation_p.K1232R|CACNA1G_ENST00000510115.1_Missense_Mutation_p.K1209R|CACNA1G_ENST00000513689.2_Missense_Mutation_p.K1232R|CACNA1G_ENST00000507336.1_Missense_Mutation_p.K1232R	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	1232					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|response to nickel cation (GO:0010045)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|scaffold protein binding (GO:0097110)			breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Cinnarizine(DB00568)|Ethosuximide(DB00593)|Flunarizine(DB04841)|Methsuximide(DB05246)|Spironolactone(DB00421)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	CTGCAGAGCAAAGGGGAACGG	0.617																																																0			17											49.0	59.0	56.0					17																	48678091		2046	4181	6227	46033090	SO:0001583	missense	8913			AC004590	CCDS45730.1, CCDS45731.1, CCDS45732.1, CCDS45733.1, CCDS45734.1, CCDS45735.1, CCDS45736.1, CCDS45737.1, CCDS54142.1, CCDS54143.1, CCDS54144.1, CCDS54145.1, CCDS54146.1, CCDS58565.1, CCDS58566.1, CCDS58567.1, CCDS58568.1, CCDS58569.1, CCDS58570.1, CCDS58571.1, CCDS58572.1, CCDS58573.1, CCDS58574.1, CCDS58575.1, CCDS58576.1	17q22	2012-03-07	2007-02-16		ENSG00000006283	ENSG00000006283		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1394	protein-coding gene	gene with protein product		604065				9495342, 16382099	Standard	NM_001256334		Approved	Cav3.1, NBR13	uc002irk.2	O43497	OTTHUMG00000162180	ENST00000359106.5:c.3695A>G	17.37:g.48678091A>G	ENSP00000352011:p.Lys1232Arg	Somatic		Capture	SOLID	Phase_IV	46033090	D6RA64|E7EPR0|O43498|O94770|Q19QY8|Q19QY9|Q19QZ0|Q19QZ1|Q19QZ2|Q19QZ3|Q19QZ4|Q19QZ5|Q19QZ6|Q19QZ7|Q19QZ8|Q19QZ9|Q19R00|Q19R01|Q19R02|Q19R03|Q19R04|Q19R05|Q19R06|Q19R07|Q19R08|Q19R09|Q19R10|Q19R11|Q19R12|Q19R13|Q19R15|Q19R16|Q19R17|Q19R18|Q2TAC4|Q9NYU4|Q9NYU5|Q9NYU6|Q9NYU7|Q9NYU8|Q9NYU9|Q9NYV0|Q9NYV1|Q9UHN9|Q9UHP0|Q9ULU6|Q9UNG7|Q9Y5T2|Q9Y5T3	Missense_Mutation	SNP	ENST00000359106.5	37	CCDS45730.1	SNP	1	Baylor	.	.	.	.	.	.	.	.	.	.	a	6.882	0.532133	0.13127	.	.	ENSG00000006283	ENST00000360761;ENST00000352832;ENST00000416767;ENST00000354983;ENST00000442258;ENST00000502264;ENST00000512389;ENST00000513964;ENST00000514717;ENST00000510366;ENST00000503485;ENST00000507510;ENST00000507336;ENST00000513689;ENST00000507609;ENST00000510115;ENST00000515165;ENST00000514181;ENST00000515765;ENST00000514079;ENST00000358244;ENST00000359106;ENST00000429973;ENST00000515411;ENST00000505165;ENST00000507896;ENST00000506520	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97352	-3.94;-3.94;-4.11;-3.89;-3.95;-3.94;-3.97;-4.05;-4.01;-4.04;-4.04;-3.9;-3.91;-3.99;-3.93;-3.88;-3.97;-3.93;-3.91;-3.96;-3.94;-3.91;-3.97;-3.9;-3.97;-3.97;-4.35	5.46	3.06	0.35304	.	0.583320	0.18005	N	0.154776	D	0.86053	0.5841	N	0.01705	-0.755	0.28783	N	0.899713	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.09022	0.001;0.0;0.0;0.0;0.0;0.001;0.001;0.0;0.001;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.001;0.0;0.0;0.0;0.002;0.0	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.09377	0.002;0.0;0.001;0.004;0.002;0.001;0.003;0.002;0.003;0.001;0.002;0.001;0.0;0.001;0.001;0.0;0.001;0.001;0.002;0.001;0.001;0.0;0.001;0.0;0.002;0.002	T	0.77672	-0.2500	10	0.11485	T	0.65	.	2.9205	0.05767	0.6329:0.1464:0.0801:0.1406	.	1209;1232;1232;1232;1232;1232;1232;1232;1232;1232;1232;1209;1232;1232;1232;1232;1232;1209;1232;1209;1209;1209;1209;1232;1209;1232	Q19QZ5;Q19QZ1;Q19QZ4;Q19R07;Q19QY8;Q19R10;Q19QZ6;Q19QZ3;Q19R06;Q19R00;Q19R04;O43497-10;Q19QZ9;Q19QZ7;Q19R08;Q19QZ8;Q19R03;O43497-4;Q19R02;Q19R12;Q19R17;Q19R11;Q2TAC4;O43497;Q19R13;O43497-11	.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;CAC1G_HUMAN;.;.	R	1209;1209;1232;1209;1209;1209;1232;1232;1209;1232;1232;1232;1232;1232;1232;1209;1232;1232;1232;1232;1209;1232;1232;1232;1232;1232;47	ENSP00000353990:K1209R;ENSP00000339302:K1209R;ENSP00000392390:K1232R;ENSP00000347078:K1209R;ENSP00000409759:K1209R;ENSP00000425522:K1209R;ENSP00000426261:K1232R;ENSP00000425451:K1232R;ENSP00000422407:K1209R;ENSP00000426814:K1232R;ENSP00000427238:K1232R;ENSP00000423112:K1232R;ENSP00000420918:K1232R;ENSP00000426172:K1232R;ENSP00000423045:K1232R;ENSP00000427173:K1209R;ENSP00000426098:K1232R;ENSP00000425698:K1232R;ENSP00000426232:K1232R;ENSP00000423317:K1232R;ENSP00000350979:K1209R;ENSP00000352011:K1232R;ENSP00000414388:K1232R;ENSP00000423155:K1232R;ENSP00000422268:K1232R;ENSP00000421518:K1232R;ENSP00000427697:K47R	ENSP00000339302:K1209R	K	+	2	0	CACNA1G	46033090	1.000000	0.71417	1.000000	0.80357	0.100000	0.18952	2.220000	0.42908	0.893000	0.36288	0.533000	0.62120	AAA		0.617	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1	NM_018896		Missense_Mutation
CCNA1	8900	hgsc.bcm.edu	37	13	37015329	37015329	+	Silent	SNP	T	T	A			TCGA-13-0717-01	TCGA-13-0717-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chr13:37015329T>A	ENST00000255465.4	+	7	1437	c.1173T>A	c.(1171-1173)gcT>gcA	p.A391A	CCNA1_ENST00000440264.1_Silent_p.A347A|CCNA1_ENST00000449823.1_Silent_p.A347A|CCNA1_ENST00000418263.1_Silent_p.A390A			P78396	CCNA1_HUMAN	cyclin A1	391	Poly-Ala.				G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|male meiosis I (GO:0007141)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)		p.A391A(2)		breast(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(10)|ovary(3)|prostate(1)|skin(2)|stomach(2)|urinary_tract(1)	35		Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.91e-07)|Epithelial(112;1.22e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0119)|GBM - Glioblastoma multiforme(144;0.0242)		CTGCAGCAGCTTTTTGCCTGG	0.398																																																2	Substitution - coding silent(2)	ovary(2)	13											151.0	132.0	139.0					13																	37015329		2203	4300	6503	35913329	SO:0001819	synonymous_variant	8900			U66838	CCDS9357.1, CCDS45031.1	13q12.3-q13	2014-01-21			ENSG00000133101	ENSG00000133101			1577	protein-coding gene	gene with protein product		604036				9041194	Standard	NM_003914		Approved	CT146	uc001uvr.4	P78396	OTTHUMG00000016733	ENST00000255465.4:c.1173T>A	13.37:g.37015329T>A		Somatic		Capture	SOLID	Phase_IV	35913329	B7Z7E3|Q5T3V0|Q5U0G2|Q8IY91	Silent	SNP	ENST00000255465.4	37	CCDS9357.1	SNP	56	Baylor																																																																																				0.398	CCNA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044514.2	NM_003914		Silent
CHD4	1108	hgsc.bcm.edu	37	12	6710554	6710554	+	Missense_Mutation	SNP	C	C	A			TCGA-13-0717-01	TCGA-13-0717-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chr12:6710554C>A	ENST00000357008.2	-	6	863	c.700G>T	c.(700-702)Gta>Tta	p.V234L	CHD4_ENST00000544040.1_Missense_Mutation_p.V227L|CHD4_ENST00000544484.1_Missense_Mutation_p.V231L|CHD4_ENST00000309577.6_Missense_Mutation_p.V234L	NM_001273.2	NP_001264.2	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4	234	Poly-Ala.				ATP-dependent chromatin remodeling (GO:0043044)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spindle assembly (GO:0051225)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|RNA polymerase II repressing transcription factor binding (GO:0001103)|zinc ion binding (GO:0008270)	p.V234L(1)		central_nervous_system(2)	2						ACCACAGCTACCGCTGCTGCT	0.582																																					Colon(32;586 792 4568 16848 45314)											1	Substitution - Missense(1)	ovary(1)	12											85.0	92.0	90.0					12																	6710554		2203	4300	6503	6580815	SO:0001583	missense	1108			X86691	CCDS8552.1	12p13	2013-01-28				ENSG00000111642		"""Zinc fingers, PHD-type"""	1919	protein-coding gene	gene with protein product		603277				7575689, 8843877	Standard	XM_006718958		Approved	Mi-2b, Mi2-BETA	uc001qpo.3	Q14839		ENST00000357008.2:c.700G>T	12.37:g.6710554C>A	ENSP00000349508:p.Val234Leu	Somatic		Capture	SOLID	Phase_IV	6580815	Q8IXZ5	Missense_Mutation	SNP	ENST00000357008.2	37	CCDS8552.1	SNP	18	Baylor	.	.	.	.	.	.	.	.	.	.	C	16.05	3.013513	0.54468	.	.	ENSG00000111642	ENST00000544484;ENST00000544040;ENST00000309577;ENST00000357008;ENST00000537464;ENST00000545942	D;D;D;D;T	0.90004	-2.59;-2.6;-2.6;-2.6;0.85	5.87	5.87	0.94306	.	0.225066	0.37809	N	0.001925	D	0.87609	0.6220	L	0.53249	1.67	0.50813	D	0.999898	B;B;B	0.32101	0.341;0.349;0.356	B;B;B	0.33454	0.085;0.079;0.164	D	0.83927	0.0304	10	0.23302	T	0.38	-0.6394	20.2084	0.98285	0.0:1.0:0.0:0.0	.	234;234;227	Q14839-2;Q14839;F5GWX5	.;CHD4_HUMAN;.	L	231;227;234;234;208;234	ENSP00000440392:V231L;ENSP00000440542:V227L;ENSP00000312419:V234L;ENSP00000349508:V234L;ENSP00000437506:V234L	ENSP00000312419:V234L	V	-	1	0	CHD4	6580815	.	.	0.981000	0.43875	0.826000	0.46750	.	.	2.774000	0.95407	0.650000	0.86243	GTA		0.582	CHD4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001273		Missense_Mutation
CNTN6	27255	hgsc.bcm.edu	37	3	1424790	1424790	+	Missense_Mutation	SNP	A	A	T			TCGA-13-0717-01	TCGA-13-0717-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chr3:1424790A>T	ENST00000446702.2	+	18	2958	c.2331A>T	c.(2329-2331)aaA>aaT	p.K777N	CNTN6_ENST00000539053.1_Missense_Mutation_p.K705N|CNTN6_ENST00000350110.2_Missense_Mutation_p.K777N			Q9UQ52	CNTN6_HUMAN	contactin 6	777	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|Notch signaling pathway (GO:0007219)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.K777N(1)		breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(34)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		TTGAAGTCAAAGTGGGTGTGT	0.443																																																1	Substitution - Missense(1)	ovary(1)	3											142.0	130.0	134.0					3																	1424790		2203	4300	6503	1399790	SO:0001583	missense	27255			AB003592	CCDS2557.1	3p26-p25	2013-02-11			ENSG00000134115	ENSG00000134115		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	2176	protein-coding gene	gene with protein product	"""neural adhesion molecule"""	607220				9486763	Standard	NM_014461		Approved	NB-3	uc003bpa.3	Q9UQ52	OTTHUMG00000119030	ENST00000446702.2:c.2331A>T	3.37:g.1424790A>T	ENSP00000407822:p.Lys777Asn	Somatic		Capture	SOLID	Phase_IV	1399790	Q2KHM2	Missense_Mutation	SNP	ENST00000446702.2	37	CCDS2557.1	SNP	3	Baylor	.	.	.	.	.	.	.	.	.	.	A	20.4	3.982972	0.74474	.	.	ENSG00000134115	ENST00000446702;ENST00000539053;ENST00000350110	T;T;T	0.55052	0.54;0.54;0.54	6.08	2.14	0.27477	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000007	T	0.76772	0.4034	H	0.95187	3.635	0.53005	D	0.999963	D	0.76494	0.999	D	0.78314	0.991	T	0.76854	-0.2805	10	0.87932	D	0	.	8.6282	0.33904	0.6816:0.0:0.3184:0.0	.	777	Q9UQ52	CNTN6_HUMAN	N	777;705;777	ENSP00000407822:K777N;ENSP00000442791:K705N;ENSP00000341882:K777N	ENSP00000341882:K777N	K	+	3	2	CNTN6	1399790	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.080000	0.41586	0.113000	0.18004	0.533000	0.62120	AAA		0.443	CNTN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239235.2	NM_014461		Missense_Mutation
DCHS2	54798	hgsc.bcm.edu	37	4	155155778	155155778	+	Missense_Mutation	SNP	C	C	G			TCGA-13-0717-01	TCGA-13-0717-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chr4:155155778C>G	ENST00000357232.4	-	25	8660	c.8661G>C	c.(8659-8661)ttG>ttC	p.L2887F		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	2887					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.L2887F(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		ACAGTGGAGACAAGGCAGGAG	0.463																																																1	Substitution - Missense(1)	ovary(1)	4											139.0	126.0	130.0					4																	155155778		2203	4300	6503	155375228	SO:0001583	missense	54798			BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"""Cadherins / Cadherin-related"""	23111	protein-coding gene	gene with protein product	"""cadherin-related family member 7"""	612486	"""cadherin-like 27"", ""dachsous 2 (Drosophila)"""	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.8661G>C	4.37:g.155155778C>G	ENSP00000349768:p.Leu2887Phe	Somatic		Capture	SOLID	Phase_IV	155375228	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	SNP	17	Baylor	.	.	.	.	.	.	.	.	.	.	C	8.179	0.793336	0.16327	.	.	ENSG00000197410	ENST00000357232	T	0.55234	0.53	5.93	2.34	0.29019	.	0.913541	0.09478	N	0.796781	T	0.34483	0.0899	L	0.36672	1.1	0.45452	D	0.998429	B	0.31519	0.327	B	0.21360	0.034	T	0.20638	-1.0269	10	0.33141	T	0.24	.	2.335	0.04245	0.127:0.487:0.1115:0.2745	.	2887	Q6V1P9	PCD23_HUMAN	F	2887	ENSP00000349768:L2887F	ENSP00000349768:L2887F	L	-	3	2	DCHS2	155375228	0.128000	0.22383	0.006000	0.13384	0.203000	0.24098	0.678000	0.25277	0.415000	0.25817	0.655000	0.94253	TTG		0.463	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		Missense_Mutation
DIP2B	57609	hgsc.bcm.edu	37	12	51097921	51097921	+	Splice_Site	SNP	A	A	T			TCGA-13-0717-01	TCGA-13-0717-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chr12:51097921A>T	ENST00000301180.5	+	20	2359		c.e20-1			NM_173602.2	NP_775873.2	Q9P265	DIP2B_HUMAN	DIP2 disco-interacting protein 2 homolog B (Drosophila)							cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	catalytic activity (GO:0003824)	p.?(1)		breast(1)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(15)|lung(18)|ovary(4)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	60						TTTGTCTCTTAGGTAATTCCA	0.363																																																1	Unknown(1)	ovary(1)	12											125.0	119.0	121.0					12																	51097921		2203	4300	6503	49384188	SO:0001630	splice_region_variant	57609			AB040896	CCDS31799.1	12q13.12	2012-10-02	2006-01-13		ENSG00000066084	ENSG00000066084			29284	protein-coding gene	gene with protein product		611379					Standard	XM_005269044		Approved	KIAA1463, FLJ34278	uc001rwv.3	Q9P265	OTTHUMG00000169475	ENST00000301180.5:c.2326-1A>T	12.37:g.51097921A>T		Somatic		Capture	SOLID	Phase_IV	49384188	Q6B011|Q8N1L5|Q8NB38	Splice_Site_SNP	SNP	ENST00000301180.5	37	CCDS31799.1	SNP	15	Baylor	.	.	.	.	.	.	.	.	.	.	A	16.02	3.004284	0.54254	.	.	ENSG00000066084	ENST00000301180	.	.	.	4.95	4.95	0.65309	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0991	0.72258	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	DIP2B	49384188	1.000000	0.71417	0.886000	0.34754	0.489000	0.33432	8.991000	0.93514	2.216000	0.71823	0.533000	0.62120	.		0.363	DIP2B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404243.1	NM_173602	Intron	Splice_Site_SNP
EGFR	1956	hgsc.bcm.edu	37	7	55259458	55259458	+	Missense_Mutation	SNP	C	C	T			TCGA-13-0717-01	TCGA-13-0717-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chr7:55259458C>T	ENST00000275493.2	+	21	2693	c.2516C>T	c.(2515-2517)gCa>gTa	p.A839V	EGFR-AS1_ENST00000442411.1_RNA|EGFR_ENST00000455089.1_Missense_Mutation_p.A794V|EGFR_ENST00000454757.2_Missense_Mutation_p.A786V|EGFR_ENST00000442591.1_Intron	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	839	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)	p.A839V(1)		NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	CGCGACCTGGCAGCCAGGAAC	0.532		8	"""A, O, Mis"""		"""glioma, NSCLC"""	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																												yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"""epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"""		"""E, O"""	1	Substitution - Missense(1)	ovary(1)	7											117.0	102.0	107.0					7																	55259458		2203	4300	6503	55226952	SO:0001583	missense	1956	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"""erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"""	131550	"""epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"""	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.2516C>T	7.37:g.55259458C>T	ENSP00000275493:p.Ala839Val	Somatic		Capture	SOLID	Phase_IV	55226952	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Missense_Mutation	SNP	ENST00000275493.2	37	CCDS5514.1	SNP	25	Baylor	.	.	.	.	.	.	.	.	.	.	C	36	5.708595	0.96821	.	.	ENSG00000146648	ENST00000455089;ENST00000395504;ENST00000275493;ENST00000454757	T;T;T	0.63580	-0.05;-0.05;-0.05	5.82	5.82	0.92795	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.87692	0.6241	H	0.98256	4.185	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.972;0.999	D	0.91724	0.5391	10	0.87932	D	0	.	18.6604	0.91470	0.0:1.0:0.0:0.0	.	794;839	Q504U8;P00533	.;EGFR_HUMAN	V	794;709;839;786	ENSP00000415559:A794V;ENSP00000275493:A839V;ENSP00000395243:A786V	ENSP00000275493:A839V	A	+	2	0	EGFR	55226952	1.000000	0.71417	0.972000	0.41901	0.998000	0.95712	7.692000	0.84203	2.751000	0.94390	0.650000	0.86243	GCA		0.532	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228		Missense_Mutation
EP400	57634	hgsc.bcm.edu	37	12	132502845	132502845	+	Missense_Mutation	SNP	C	C	T	rs201961439		TCGA-13-0717-01	TCGA-13-0717-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chr12:132502845C>T	ENST00000333577.4	+	22	4418	c.4309C>T	c.(4309-4311)Cgg>Tgg	p.R1437W	EP400_ENST00000389562.2_Missense_Mutation_p.R1400W|EP400_ENST00000389561.2_Missense_Mutation_p.R1401W|EP400_ENST00000332482.4_Missense_Mutation_p.R1364W|EP400_ENST00000330386.6_Missense_Mutation_p.R1401W			Q96L91	EP400_HUMAN	E1A binding protein p400	1437					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.R1400W(1)		NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		AAAGATACCGCGGAAACTCAT	0.517																																																1	Substitution - Missense(1)	ovary(1)	12						C	TRP/ARG	0,4406		0,0,2203	56.0	57.0	57.0		4201	5.4	0.5	12		57	3,8597	3.0+/-9.4	0,3,4297	yes	missense	EP400	NM_015409.4	101	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	probably-damaging	1401/3124	132502845	3,13003	2203	4300	6503	131068798	SO:0001583	missense	57634			U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"""trinucleotide repeat containing 12"""	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.4309C>T	12.37:g.132502845C>T	ENSP00000333602:p.Arg1437Trp	Somatic		Capture	SOLID	Phase_IV	131068798	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Missense_Mutation	SNP	ENST00000333577.4	37		SNP	27	Baylor	.	.	.	.	.	.	.	.	.	.	C	8.092	0.774832	0.16051	0.0	3.49E-4	ENSG00000183495	ENST00000333577;ENST00000389561;ENST00000389562;ENST00000332482;ENST00000330386;ENST00000541296;ENST00000542457	D;D;D;D;D	0.91740	-2.9;-2.89;-2.89;-2.88;-2.78	5.43	5.43	0.79202	.	0.119075	0.56097	D	0.000024	D	0.92941	0.7754	M	0.68952	2.095	0.34631	D	0.719658	D;D;D	0.61697	0.99;0.99;0.99	P;P;P	0.51833	0.681;0.681;0.681	D	0.95971	0.8970	10	0.87932	D	0	.	12.3901	0.55355	0.2838:0.7162:0.0:0.0	.	1401;1401;1400	Q96L91-2;Q96L91-4;Q96L91-5	.;.;.	W	1437;1401;1400;1364;1401;1401;1401	ENSP00000333602:R1437W;ENSP00000374212:R1401W;ENSP00000374213:R1400W;ENSP00000331737:R1364W;ENSP00000330620:R1401W	ENSP00000330620:R1401W	R	+	1	2	EP400	131068798	1.000000	0.71417	0.541000	0.28102	0.007000	0.05969	4.908000	0.63307	2.545000	0.85829	0.655000	0.94253	CGG		0.517	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409		Missense_Mutation
MROH5	389690	hgsc.bcm.edu	37	8	142476593	142476593	+	RNA	SNP	G	G	T			TCGA-13-0717-01	TCGA-13-0717-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chr8:142476593G>T	ENST00000430863.1	-	0	2473					NM_207414.2	NP_997297.2	Q6ZUA9	MROH5_HUMAN	maestro heat-like repeat family member 5									p.T798N(1)									GGCGTGCAGGGTCTTTTCCTT	0.637																																																1	Substitution - Missense(1)	ovary(1)	8											76.0	88.0	84.0					8																	142476593		2144	4234	6378	142545775			389690					8q24.3	2012-12-20			ENSG00000226807	ENSG00000226807		"""maestro heat-like repeat containing"""	42976	protein-coding gene	gene with protein product							Standard	NM_207414		Approved	FLJ43860	uc003ywi.2	Q6ZUA9	OTTHUMG00000155944		8.37:g.142476593G>T		Somatic		Capture	SOLID	Phase_IV	142545775		Missense_Mutation	SNP	ENST00000430863.1	37		SNP	44	Baylor																																																																																				0.637	MROH5-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000342412.4	NM_207414		Missense_Mutation
FLNC	2318	hgsc.bcm.edu	37	7	128493544	128493544	+	Missense_Mutation	SNP	G	G	T			TCGA-13-0717-01	TCGA-13-0717-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chr7:128493544G>T	ENST00000325888.8	+	38	6491	c.6230G>T	c.(6229-6231)aGt>aTt	p.S2077I	RP11-309L24.2_ENST00000469965.1_RNA|FLNC_ENST00000346177.6_Missense_Mutation_p.S2044I	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	2077					cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)			biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						TTGGGGCTGAGTATTGAAGGC	0.577																																																0			7											89.0	97.0	94.0					7																	128493544		2053	4191	6244	128280780	SO:0001583	missense	2318			AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"""actin binding protein 280"""	102565	"""filamin C, gamma (actin binding protein 280)"""	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.6230G>T	7.37:g.128493544G>T	ENSP00000327145:p.Ser2077Ile	Somatic		Capture	SOLID	Phase_IV	128280780	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Missense_Mutation	SNP	ENST00000325888.8	37	CCDS43644.1	SNP	36	Baylor	.	.	.	.	.	.	.	.	.	.	G	20.7	4.034507	0.75617	.	.	ENSG00000128591	ENST00000325888;ENST00000346177	D;D	0.84730	-1.89;-1.89	5.42	5.42	0.78866	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.110985	0.64402	D	0.000012	D	0.93093	0.7801	M	0.88704	2.975	0.46096	D	0.998868	D;D	0.89917	1.0;0.998	D;D	0.91635	0.999;0.983	D	0.94003	0.7277	10	0.87932	D	0	.	13.8235	0.63338	0.0:0.2783:0.7217:0.0	.	2044;2077	Q14315-2;Q14315	.;FLNC_HUMAN	I	2077;2044	ENSP00000327145:S2077I;ENSP00000344002:S2044I	ENSP00000327145:S2077I	S	+	2	0	FLNC	128280780	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	6.849000	0.75414	2.539000	0.85634	0.561000	0.74099	AGT		0.577	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3			Missense_Mutation
GREB1	9687	hgsc.bcm.edu	37	2	11725903	11725903	+	Missense_Mutation	SNP	C	C	A	rs201149740		TCGA-13-0717-01	TCGA-13-0717-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chr2:11725903C>A	ENST00000381486.2	+	9	1331	c.1031C>A	c.(1030-1032)tCc>tAc	p.S344Y	RN7SL674P_ENST00000463397.2_RNA|GREB1_ENST00000234142.5_Missense_Mutation_p.S344Y|GREB1_ENST00000381483.2_Missense_Mutation_p.S344Y|GREB1_ENST00000263834.5_Missense_Mutation_p.S344Y	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	344						integral component of membrane (GO:0016021)				breast(3)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)	30	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		GCAGGCATGTCCTGCGTGCCG	0.517																																					Ovarian(39;850 945 2785 23371 33093)											0			2											90.0	81.0	84.0					2																	11725903		2203	4300	6503	11643354	SO:0001583	missense	9687				CCDS33146.1, CCDS33147.1, CCDS42655.1	2p25.1	2010-02-17	2009-09-10		ENSG00000196208	ENSG00000196208			24885	protein-coding gene	gene with protein product	"""gene regulated by estrogen in breast cancer"""	611736				11103799	Standard	NM_014668		Approved	KIAA0575	uc002rbk.1	Q4ZG55	OTTHUMG00000141276	ENST00000381486.2:c.1031C>A	2.37:g.11725903C>A	ENSP00000370896:p.Ser344Tyr	Somatic		Capture	SOLID	Phase_IV	11643354	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Missense_Mutation	SNP	ENST00000381486.2	37	CCDS42655.1	SNP	30	Baylor	.	.	.	.	.	.	.	.	.	.	C	13.53	2.263431	0.39995	.	.	ENSG00000196208	ENST00000381486;ENST00000263834;ENST00000381483;ENST00000234142	T;T;T;T	0.18960	3.19;2.18;2.19;3.19	5.23	5.23	0.72850	.	0.799097	0.11593	N	0.548486	T	0.28566	0.0707	L	0.40543	1.245	0.41250	D	0.986707	D;P;P	0.54047	0.964;0.904;0.547	P;P;B	0.47981	0.526;0.563;0.346	T	0.05869	-1.0859	10	0.59425	D	0.04	-13.0457	16.9865	0.86341	0.0:1.0:0.0:0.0	.	344;344;344	Q4ZG55-2;Q4ZG55-3;Q4ZG55	.;.;GREB1_HUMAN	Y	344	ENSP00000370896:S344Y;ENSP00000263834:S344Y;ENSP00000370892:S344Y;ENSP00000234142:S344Y	ENSP00000234142:S344Y	S	+	2	0	GREB1	11643354	0.297000	0.24408	0.827000	0.32855	0.035000	0.12851	2.242000	0.43106	2.454000	0.82982	0.650000	0.86243	TCC		0.517	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668		Missense_Mutation
HPS3	84343	hgsc.bcm.edu	37	3	148868392	148868392	+	Silent	SNP	C	C	T			TCGA-13-0717-01	TCGA-13-0717-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chr3:148868392C>T	ENST00000296051.2	+	6	1310	c.1170C>T	c.(1168-1170)aaC>aaT	p.N390N	HPS3_ENST00000460120.1_Silent_p.N225N	NM_032383.3	NP_115759.2	Q969F9	HPS3_HUMAN	Hermansky-Pudlak syndrome 3	390					organelle organization (GO:0006996)|pigmentation (GO:0043473)	BLOC-2 complex (GO:0031084)		p.N390N(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	34			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			TCAGTAACAACCTGCAGTGTT	0.552									Hermansky-Pudlak syndrome																																							1	Substitution - coding silent(1)	ovary(1)	3											111.0	98.0	103.0					3																	148868392		2203	4300	6503	150351082	SO:0001819	synonymous_variant	84343	Familial Cancer Database	HPS, HPS1-8	AY033141	CCDS3140.1	3q24	2014-06-18			ENSG00000163755	ENSG00000163755			15597	protein-coding gene	gene with protein product		606118				11455388	Standard	NM_032383		Approved	SUTAL	uc003ewu.1	Q969F9	OTTHUMG00000159548	ENST00000296051.2:c.1170C>T	3.37:g.148868392C>T		Somatic		Capture	SOLID	Phase_IV	150351082	A8K6G6|Q8WTV6|Q96AP1|Q96MR3|Q9H608	Silent	SNP	ENST00000296051.2	37	CCDS3140.1	SNP	18	Baylor																																																																																				0.552	HPS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356151.1	NM_032383		Silent
IL20RA	53832	hgsc.bcm.edu	37	6	137323042	137323042	+	Missense_Mutation	SNP	C	C	T			TCGA-13-0717-01	TCGA-13-0717-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chr6:137323042C>T	ENST00000316649.5	-	7	1550	c.1315G>A	c.(1315-1317)Gca>Aca	p.A439T	IL20RA_ENST00000541547.1_Missense_Mutation_p.A390T|IL20RA_ENST00000468393.1_5'Flank|RP11-204P2.3_ENST00000458017.1_RNA|IL20RA_ENST00000367748.1_Missense_Mutation_p.A328T	NM_001278722.1|NM_014432.2	NP_001265651.1|NP_055247	Q9UHF4	I20RA_HUMAN	interleukin 20 receptor, alpha	439					cytokine-mediated signaling pathway (GO:0019221)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|regulation of bone resorption (GO:0045124)	integral component of membrane (GO:0016021)		p.A439T(1)		NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	27	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000351)|OV - Ovarian serous cystadenocarcinoma(155;0.00459)		CCCAAGACTGCCAACGCTGCC	0.582																																																1	Substitution - Missense(1)	ovary(1)	6											75.0	64.0	68.0					6																	137323042		2203	4300	6503	137364735	SO:0001583	missense	53832			AF184971	CCDS5181.1, CCDS64535.1, CCDS64536.1	6q23.3	2008-02-05			ENSG00000016402	ENSG00000016402		"""Interleukins and interleukin receptors"""	6003	protein-coding gene	gene with protein product		605620				10875937, 11163236	Standard	NM_001278724		Approved	ZCYTOR7, IL-20R1	uc003qhj.3	Q9UHF4	OTTHUMG00000015654	ENST00000316649.5:c.1315G>A	6.37:g.137323042C>T	ENSP00000314976:p.Ala439Thr	Somatic		Capture	SOLID	Phase_IV	137364735	B4DLR5|F5H675|Q14CW2|Q6UWA9|Q96SH8	Missense_Mutation	SNP	ENST00000316649.5	37	CCDS5181.1	SNP	26	Baylor	.	.	.	.	.	.	.	.	.	.	C	13.48	2.251222	0.39797	.	.	ENSG00000016402	ENST00000316649;ENST00000367748;ENST00000541547	T;T;T	0.62788	0.27;1.73;0.0	5.76	3.05	0.35203	.	2.391960	0.01134	N	0.006042	T	0.30854	0.0778	L	0.31926	0.97	0.09310	N	1	B;B	0.25563	0.129;0.051	B;B	0.23419	0.046;0.02	T	0.10382	-1.0632	10	0.33940	T	0.23	-3.5837	7.5199	0.27622	0.0:0.6655:0.0:0.3345	.	328;439	Q9UHF4-2;Q9UHF4	.;I20RA_HUMAN	T	439;328;390	ENSP00000314976:A439T;ENSP00000356722:A328T;ENSP00000437843:A390T	ENSP00000314976:A439T	A	-	1	0	IL20RA	137364735	0.001000	0.12720	0.001000	0.08648	0.006000	0.05464	0.248000	0.18198	0.371000	0.24564	0.655000	0.94253	GCA		0.582	IL20RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042393.1	NM_014432		Missense_Mutation
ITGB7	3695	hgsc.bcm.edu	37	12	53591327	53591327	+	Missense_Mutation	SNP	C	C	G			TCGA-13-0717-01	TCGA-13-0717-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chr12:53591327C>G	ENST00000267082.5	-	5	755	c.524G>C	c.(523-525)gGg>gCg	p.G175A	ITGB7_ENST00000550743.2_Missense_Mutation_p.G175A|ITGB7_ENST00000422257.3_Missense_Mutation_p.G175A|ITGB7_ENST00000338737.4_Missense_Mutation_p.G175A	NM_000889.1	NP_000880.1	P26010	ITB7_HUMAN	integrin, beta 7	175	VWFA.				cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cell-matrix adhesion involved in ameboidal cell migration (GO:0003366)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte tethering or rolling (GO:0050901)|multicellular organismal development (GO:0007275)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|substrate adhesion-dependent cell spreading (GO:0034446)|T cell migration (GO:0072678)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alpha4-beta7 complex (GO:0034669)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)|virus receptor activity (GO:0001618)	p.G175A(1)		NS(2)|breast(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(3)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						CAGAGCGTGCCCGAGCTGGCG	0.617																																																1	Substitution - Missense(1)	large_intestine(1)	12											79.0	70.0	73.0					12																	53591327		2203	4300	6503	51877594	SO:0001583	missense	3695				CCDS8849.1	12q13.1	2010-03-23				ENSG00000139626		"""Integrins"""	6162	protein-coding gene	gene with protein product		147559				2040616	Standard	XM_005268851		Approved		uc001scc.3	P26010		ENST00000267082.5:c.524G>C	12.37:g.53591327C>G	ENSP00000267082:p.Gly175Ala	Somatic		Capture	SOLID	Phase_IV	51877594	Q9UCP7|Q9UCS7	Missense_Mutation	SNP	ENST00000267082.5	37	CCDS8849.1	SNP	22	Baylor	.	.	.	.	.	.	.	.	.	.	C	34	5.310534	0.95629	.	.	ENSG00000139626	ENST00000422257;ENST00000267082;ENST00000338737;ENST00000542497	D;D;D;D	0.95724	-3.79;-3.79;-3.79;-3.79	4.91	4.91	0.64330	Integrin beta subunit, N-terminal (2);von Willebrand factor, type A (1);	0.000000	0.35436	N	0.003220	D	0.97256	0.9103	M	0.67517	2.055	0.80722	D	1	D;D	0.89917	0.995;1.0	D;D	0.91635	0.967;0.999	D	0.97787	1.0236	10	0.66056	D	0.02	.	17.3056	0.87194	0.0:1.0:0.0:0.0	.	175;175	B7Z769;P26010	.;ITB7_HUMAN	A	175	ENSP00000408741:G175A;ENSP00000267082:G175A;ENSP00000345501:G175A;ENSP00000437375:G175A	ENSP00000267082:G175A	G	-	2	0	ITGB7	51877594	1.000000	0.71417	0.816000	0.32577	0.995000	0.86356	7.598000	0.82745	2.459000	0.83118	0.555000	0.69702	GGG		0.617	ITGB7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405821.2			Missense_Mutation
KLF15	28999	hgsc.bcm.edu	37	3	126071521	126071521	+	Missense_Mutation	SNP	G	G	C			TCGA-13-0717-01	TCGA-13-0717-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chr3:126071521G>C	ENST00000296233.3	-	2	475	c.245C>G	c.(244-246)tCc>tGc	p.S82C	KLF15_ENST00000509675.1_5'UTR	NM_014079.3	NP_054798.1	Q9UIH9	KLF15_HUMAN	Kruppel-like factor 15	82					cardiac muscle hypertrophy in response to stress (GO:0014898)|cellular response to peptide (GO:1901653)|glial cell differentiation (GO:0010001)|glomerular visceral epithelial cell differentiation (GO:0072112)|glucose transport (GO:0015758)|negative regulation of peptidyl-lysine acetylation (GO:2000757)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|transcription regulatory region DNA binding (GO:0044212)	p.S82C(1)		endometrium(1)|lung(7)|ovary(2)|skin(2)	12				GBM - Glioblastoma multiforme(114;0.147)		CGTGGCCTGGGACAATAGGAA	0.687																																																1	Substitution - Missense(1)	ovary(1)	3											10.0	10.0	10.0					3																	126071521		2192	4286	6478	127554211	SO:0001583	missense	28999			AB029254	CCDS3036.1	3q21.3	2013-01-08			ENSG00000163884	ENSG00000163884		"""Kruppel-like transcription factors"", ""Zinc fingers, C2H2-type"""	14536	protein-coding gene	gene with protein product	"""kidney-enriched Kruppel-like factor"""	606465				10982849	Standard	NM_014079		Approved	KKLF	uc011bkk.1	Q9UIH9	OTTHUMG00000162689	ENST00000296233.3:c.245C>G	3.37:g.126071521G>C	ENSP00000296233:p.Ser82Cys	Somatic		Capture	SOLID	Phase_IV	127554211		Missense_Mutation	SNP	ENST00000296233.3	37	CCDS3036.1	SNP	41	Baylor	.	.	.	.	.	.	.	.	.	.	G	15.65	2.895995	0.52121	.	.	ENSG00000163884	ENST00000296233	T	0.25749	1.78	4.3	3.42	0.39159	.	0.050406	0.85682	D	0.000000	T	0.44767	0.1309	M	0.61703	1.905	0.58432	D	0.999997	D	0.76494	0.999	D	0.80764	0.994	T	0.40683	-0.9550	10	0.87932	D	0	.	10.3835	0.44125	0.1011:0.0:0.8989:0.0	.	82	Q9UIH9	KLF15_HUMAN	C	82	ENSP00000296233:S82C	ENSP00000296233:S82C	S	-	2	0	KLF15	127554211	1.000000	0.71417	1.000000	0.80357	0.537000	0.34900	9.807000	0.99171	1.099000	0.41499	0.591000	0.81541	TCC		0.687	KLF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370096.1	NM_014079		Missense_Mutation
MUC4	4585	hgsc.bcm.edu	37	3	195480011	195480011	+	Missense_Mutation	SNP	C	C	T			TCGA-13-0717-01	TCGA-13-0717-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chr3:195480011C>T	ENST00000346145.4	-	19	2750	c.2711G>A	c.(2710-2712)gGc>gAc	p.G904D	MUC4_ENST00000349607.4_Missense_Mutation_p.G853D|MUC4_ENST00000463781.3_Missense_Mutation_p.G5140D|MUC4_ENST00000475231.1_Missense_Mutation_p.G5088D	NM_004532.5	NP_004523.3	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	1897	Ser-rich.				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)			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)		GGGCTGACAGCCCAGAGTCTG	0.572																																																0			3											143.0	134.0	137.0					3																	195480011		2203	4300	6503	196965682	SO:0001583	missense	4585			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	ENST00000346145.4:c.2711G>A	3.37:g.195480011C>T	ENSP00000304207:p.Gly904Asp	Somatic		Capture	SOLID	Phase_IV	196965682	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000346145.4	37	CCDS3310.1	SNP	26	Baylor	.	.	.	.	.	.	.	.	.	.	.	9.153	1.016713	0.19355	.	.	ENSG00000145113	ENST00000349607;ENST00000346145;ENST00000463781;ENST00000475231;ENST00000392409	T;T;T;T	0.37584	1.19;1.54;1.49;1.49	5.25	-7.08	0.01558	.	1.023590	0.07803	N	0.956884	T	0.16811	0.0404	N	0.22421	0.69	0.09310	N	0.999998	B;B;B;B;B;B	0.26081	0.141;0.004;0.004;0.001;0.001;0.045	B;B;B;B;B;B	0.20184	0.028;0.006;0.006;0.003;0.003;0.028	T	0.31420	-0.9944	10	0.10377	T	0.69	-3.0561	7.9797	0.30177	0.0:0.1887:0.3855:0.4258	.	5012;853;904;5140;5088;1845	E7ESK3;Q99102-12;Q99102-13;E9PDY6;E7ENC5;Q99102-10	.;.;.;.;.;.	D	853;904;5140;5088;1640	ENSP00000338109:G853D;ENSP00000304207:G904D;ENSP00000417498:G5140D;ENSP00000420243:G5088D	ENSP00000304207:G904D	G	-	2	0	MUC4	196965682	0.000000	0.05858	0.004000	0.12327	0.037000	0.13140	-2.867000	0.00722	-1.242000	0.02523	0.549000	0.68633	GGC		0.572	MUC4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341862.1	NM_018406		Missense_Mutation
NMUR2	56923	hgsc.bcm.edu	37	5	151784061	151784061	+	Missense_Mutation	SNP	G	G	A			TCGA-13-0717-01	TCGA-13-0717-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chr5:151784061G>A	ENST00000255262.3	-	1	779	c.614C>T	c.(613-615)aCg>aTg	p.T205M	NMUR2_ENST00000518933.1_Intron	NM_020167.4	NP_064552.3	Q9GZQ4	NMUR2_HUMAN	neuromedin U receptor 2	205					activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|arachidonic acid secretion (GO:0050482)|calcium ion transport (GO:0006816)|calcium-mediated signaling (GO:0019722)|cell-cell signaling (GO:0007267)|central nervous system development (GO:0007417)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|feeding behavior (GO:0007631)|grooming behavior (GO:0007625)|inositol phosphate-mediated signaling (GO:0048016)|neuropeptide signaling pathway (GO:0007218)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|reduction of food intake in response to dietary excess (GO:0002023)|regulation of smooth muscle contraction (GO:0006940)|response to pain (GO:0048265)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|GTP binding (GO:0005525)|intracellular calcium activated chloride channel activity (GO:0005229)|neuromedin U binding (GO:0042924)|neuromedin U receptor activity (GO:0001607)	p.T205M(2)		breast(1)|endometrium(1)|kidney(2)|large_intestine(12)|liver(1)|lung(15)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	44		Medulloblastoma(196;0.091)|all_hematologic(541;0.103)	Kidney(363;0.000106)|KIRC - Kidney renal clear cell carcinoma(527;0.000672)			CTTGATGACCGTACAGGTGGC	0.542																																																2	Substitution - Missense(2)	ovary(1)|kidney(1)	5											173.0	166.0	169.0					5																	151784061		2203	4300	6503	151764254	SO:0001583	missense	56923			AF242874	CCDS4321.1	5q33.1	2012-08-08		2004-05-28	ENSG00000132911	ENSG00000132911		"""GPCR / Class A : Neuromedin U receptors"""	16454	protein-coding gene	gene with protein product		605108		NMU2R		8940772, 10894543	Standard	NM_020167		Approved		uc003luv.2	Q9GZQ4	OTTHUMG00000130131	ENST00000255262.3:c.614C>T	5.37:g.151784061G>A	ENSP00000255262:p.Thr205Met	Somatic		Capture	SOLID	Phase_IV	151764254	Q7LC54|Q96AM5|Q9NRA6	Missense_Mutation	SNP	ENST00000255262.3	37	CCDS4321.1	SNP	40	Baylor	.	.	.	.	.	.	.	.	.	.	G	4.452	0.083741	0.08533	.	.	ENSG00000132911	ENST00000255262	T	0.38077	1.16	5.44	3.61	0.41365	GPCR, rhodopsin-like superfamily (1);	0.370788	0.28198	N	0.016226	T	0.28134	0.0694	L	0.45698	1.435	0.09310	N	1	P	0.40398	0.716	B	0.35655	0.207	T	0.10337	-1.0634	10	0.45353	T	0.12	0.2937	9.1507	0.36962	0.0759:0.0:0.767:0.1571	.	205	Q9GZQ4	NMUR2_HUMAN	M	205	ENSP00000255262:T205M	ENSP00000255262:T205M	T	-	2	0	NMUR2	151764254	0.998000	0.40836	0.001000	0.08648	0.057000	0.15508	4.073000	0.57570	0.622000	0.30249	-0.237000	0.12165	ACG		0.542	NMUR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252439.1	NM_020167		Missense_Mutation
NOS3	4846	hgsc.bcm.edu	37	7	150699340	150699340	+	Missense_Mutation	SNP	T	T	C			TCGA-13-0717-01	TCGA-13-0717-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chr7:150699340T>C	ENST00000484524.1	+	13	1700	c.1700T>C	c.(1699-1701)gTg>gCg	p.V567A	NOS3_ENST00000297494.3_Missense_Mutation_p.V567A|NOS3_ENST00000461406.1_Missense_Mutation_p.V361A|NOS3_ENST00000467517.1_Missense_Mutation_p.V567A	NM_001160111.1	NP_001153583.1	P60323	NANO3_HUMAN	nitric oxide synthase 3 (endothelial cell)	0					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic signaling pathway (GO:2001234)|oogenesis (GO:0048477)|regulation of cell cycle (GO:0051726)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.V567A(1)		NS(3)|breast(3)|central_nervous_system(5)|endometrium(1)|kidney(4)|large_intestine(6)|liver(2)|lung(11)|ovary(3)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	50	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GAGACGCTGGTGCTGGTGGTA	0.587																																																1	Substitution - Missense(1)	ovary(1)	7											56.0	46.0	50.0					7																	150699340		2202	4295	6497	150330273	SO:0001583	missense	4846				CCDS5912.1, CCDS55182.1, CCDS55183.1	7q36	2007-02-15			ENSG00000164867	ENSG00000164867	1.14.13.39		7876	protein-coding gene	gene with protein product	"""endothelial nitric oxide synthase"""	163729				1379542	Standard	NM_000603		Approved	ECNOS, eNOS	uc003wif.3	P29474	OTTHUMG00000158343	ENST00000484524.1:c.1700T>C	7.37:g.150699340T>C	ENSP00000420215:p.Val567Ala	Somatic		Capture	SOLID	Phase_IV	150330273	Q495E5	Missense_Mutation	SNP	ENST00000484524.1	37	CCDS55182.1	SNP	59	Baylor	.	.	.	.	.	.	.	.	.	.	T	24.0	4.481722	0.84747	.	.	ENSG00000164867	ENST00000297494;ENST00000461406;ENST00000484524;ENST00000467517	T;T;T;T	0.74526	-0.85;-0.85;-0.85;-0.85	4.5	4.5	0.54988	Flavodoxin/nitric oxide synthase (2);	0.000000	0.53938	D	0.000049	T	0.80670	0.4667	L	0.51914	1.62	0.50039	D	0.999842	D;D;D;D;D	0.69078	0.977;0.987;0.993;0.993;0.997	D;D;D;D;D	0.76575	0.929;0.963;0.973;0.963;0.988	T	0.78645	-0.2123	10	0.33141	T	0.24	-16.7725	12.0839	0.53686	0.0:0.0:0.0:1.0	.	567;567;567;361;567	A0S0A6;E9PFR2;A0S0A8;E7ESA7;P29474	.;.;.;.;NOS3_HUMAN	A	567;361;567;567	ENSP00000297494:V567A;ENSP00000417143:V361A;ENSP00000420215:V567A;ENSP00000420551:V567A	ENSP00000297494:V567A	V	+	2	0	NOS3	150330273	1.000000	0.71417	0.991000	0.47740	0.968000	0.65278	7.825000	0.86693	2.014000	0.59158	0.459000	0.35465	GTG		0.587	NOS3-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000351550.1	NM_000603		Missense_Mutation
OR52N5	390075	hgsc.bcm.edu	37	11	5799652	5799652	+	Frame_Shift_Del	DEL	A	A	-			TCGA-13-0717-01	TCGA-13-0717-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chr11:5799652delA	ENST00000317093.2	-	1	245	c.213delT	c.(211-213)tttfs	p.F71fs	TRIM5_ENST00000380027.1_Intron	NM_001001922.2	NP_001001922.2	Q8NH56	O52N5_HUMAN	olfactory receptor, family 52, subfamily N, member 5	71						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F71fs*59(1)		endometrium(2)|large_intestine(3)|liver(1)|lung(17)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;3.05e-11)|LUSC - Lung squamous cell carcinoma(625;0.112)|BRCA - Breast invasive adenocarcinoma(625;0.135)|Lung(200;0.195)		GAGCATGGCCAAAAAAAAAAT	0.428																																																1	Deletion - Frameshift(1)	ovary(1)	11								21,37,4048		0,0,21,1,35,1996	123.0	117.0	119.0			2.7	0.6	11		123	37,129,7678		1,0,35,6,117,3763	no	codingComplex	OR52N5	NM_001001922.2		1,0,56,7,152,5759	A1A1,A1A2,A1R,A2A2,A2R,RR		2.1163,1.4126,1.8745			5799652	58,166,11726	2125	4088	6213	5756228	SO:0001589	frameshift_variant	390075			AB065535	CCDS31397.1	11p15.4	2012-08-09			ENSG00000181009	ENSG00000181009		"""GPCR / Class A : Olfactory receptors"""	15231	protein-coding gene	gene with protein product							Standard	NM_001001922		Approved	OR52N5Q	uc010qzn.2	Q8NH56	OTTHUMG00000168799	ENST00000317093.2:c.213delT	11.37:g.5799652delA	ENSP00000322866:p.Phe71fs	Somatic		Capture	SOLID	Phase_IV	5756228	B9EH12|Q6IFG2	Frame_Shift_Del	DEL	ENST00000317093.2	37	CCDS31397.1	DEL	5	Baylor																																																																																				0.428	OR52N5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401141.1	NM_001001922		Frame_Shift_Del
OR9G4	283189	hgsc.bcm.edu	37	11	56510545	56510545	+	Missense_Mutation	SNP	C	C	T			TCGA-13-0717-01	TCGA-13-0717-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chr11:56510545C>T	ENST00000302957.3	-	1	742	c.743G>A	c.(742-744)gGa>gAa	p.G248E		NM_001005284.1	NP_001005284.1	Q8NGQ1	OR9G4_HUMAN	olfactory receptor, family 9, subfamily G, member 4	248						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.G248E(1)		NS(1)|autonomic_ganglia(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	34						CTTGTGTCTTCCTGAAGCTGA	0.473																																																1	Substitution - Missense(1)	ovary(1)	11											152.0	126.0	135.0					11																	56510545		2201	4296	6497	56267121	SO:0001583	missense	283189			BK004400	CCDS31537.1	11q11	2012-08-09			ENSG00000172457	ENSG00000172457		"""GPCR / Class A : Olfactory receptors"""	15322	protein-coding gene	gene with protein product							Standard	NM_001005284		Approved		uc010rjo.2	Q8NGQ1	OTTHUMG00000166932	ENST00000302957.3:c.743G>A	11.37:g.56510545C>T	ENSP00000307515:p.Gly248Glu	Somatic		Capture	SOLID	Phase_IV	56267121	Q6IF62|Q96RA9	Missense_Mutation	SNP	ENST00000302957.3	37	CCDS31537.1	SNP	30	Baylor	.	.	.	.	.	.	.	.	.	.	C	16.85	3.236955	0.58886	.	.	ENSG00000172457	ENST00000302957	T	0.00287	8.29	5.07	5.07	0.68467	GPCR, rhodopsin-like superfamily (1);	0.000000	0.38720	N	0.001588	T	0.00998	0.0033	M	0.91510	3.215	0.43841	D	0.996421	D	0.89917	1.0	D	0.97110	1.0	T	0.61831	-0.6982	10	0.87932	D	0	-14.5238	17.2062	0.86918	0.0:1.0:0.0:0.0	.	248	Q8NGQ1	OR9G4_HUMAN	E	248	ENSP00000307515:G248E	ENSP00000307515:G248E	G	-	2	0	OR9G4	56267121	0.185000	0.23213	1.000000	0.80357	0.717000	0.41224	2.268000	0.43338	2.636000	0.89361	0.643000	0.83706	GGA		0.473	OR9G4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391945.1	NM_001005284		Missense_Mutation
PI4K2A	55361	hgsc.bcm.edu	37	10	99416699	99416699	+	Missense_Mutation	SNP	T	T	C			TCGA-13-0717-01	TCGA-13-0717-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chr10:99416699T>C	ENST00000370631.3	+	4	947	c.890T>C	c.(889-891)tTg>tCg	p.L297S	PI4K2A_ENST00000555577.1_Missense_Mutation_p.L267S|PI4K2A_ENST00000370649.3_Missense_Mutation_p.L267S	NM_018425.2	NP_060895.1	Q9BTU6	P4K2A_HUMAN	phosphatidylinositol 4-kinase type 2 alpha	297	PI3K/PI4K.				basophil degranulation (GO:0002561)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|early endosome membrane (GO:0031901)|endosome (GO:0005768)|exocytic vesicle (GO:0070382)|Golgi apparatus (GO:0005794)|growing cell tip (GO:0035838)|host cell presynaptic membrane (GO:0044231)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|presynaptic membrane (GO:0042734)|protein complex (GO:0043234)|synaptic vesicle membrane (GO:0030672)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|AP-3 adaptor complex binding (GO:0035651)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)	p.L297S(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|skin(1)	12		Colorectal(252;0.162)		Epithelial(162;1.24e-10)|all cancers(201;1.2e-08)		TTTGAGCGGTTGGTGGTGCTG	0.552																																																1	Substitution - Missense(1)	ovary(1)	10											87.0	81.0	83.0					10																	99416699		2203	4300	6503	99406689	SO:0001583	missense	55361			AF070611	CCDS7469.1	10q24	2011-02-09			ENSG00000155252	ENSG00000155252			30031	protein-coding gene	gene with protein product		609763				11244087, 11279162	Standard	NM_018425		Approved	PI4KII, DKFZP761G1923, PIK42A	uc001kog.1	Q9BTU6	OTTHUMG00000018863	ENST00000370631.3:c.890T>C	10.37:g.99416699T>C	ENSP00000359665:p.Leu297Ser	Somatic		Capture	SOLID	Phase_IV	99406689	D3DR59|Q9NSG8	Missense_Mutation	SNP	ENST00000370631.3	37	CCDS7469.1	SNP	63	Baylor	.	.	.	.	.	.	.	.	.	.	T	18.20	3.572110	0.65765	.	.	ENSG00000155252;ENSG00000155252;ENSG00000249967	ENST00000555577;ENST00000370631;ENST00000370649	T;T;T	0.78816	-1.21;-1.21;-1.21	5.35	5.35	0.76521	Phosphatidylinositol 3-/4-kinase, catalytic (1);	0.000000	0.85682	D	0.000000	D	0.91761	0.7394	H	0.96489	3.83	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.97110	1.0;0.987	D	0.94304	0.7539	10	0.87932	D	0	-10.2998	15.372	0.74573	0.0:0.0:0.0:1.0	.	267;297	E9PAM4;Q9BTU6	.;P4K2A_HUMAN	S	267;297;267	ENSP00000452243:L267S;ENSP00000359665:L297S;ENSP00000359683:L267S	ENSP00000359665:L297S	L	+	2	0	PI4K2A;RP11-548K23.11	99406689	1.000000	0.71417	0.998000	0.56505	0.969000	0.65631	8.040000	0.89188	2.044000	0.60594	0.477000	0.44152	TTG		0.552	PI4K2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049735.1	NM_018425		Missense_Mutation
PILRB	29990	hgsc.bcm.edu	37	7	99957129	99957131	+	In_Frame_Del	DEL	CCT	CCT	-	rs397890520|rs5886120|rs62640024	byFrequency	TCGA-13-0717-01	TCGA-13-0717-10	CCT	CCT	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chr7:99957129_99957131delCCT	ENST00000452089.1	+	8	1683_1685	c.624_626delCCT	c.(622-627)tgcctc>tgc	p.L212del	STAG3L5P-PVRIG2P-PILRB_ENST00000310771.4_RNA|PILRB_ENST00000609309.1_In_Frame_Del_p.L212del|PILRB_ENST00000610247.1_In_Frame_Del_p.L212del|PILRB_ENST00000444073.1_In_Frame_Del_p.L212del|PILRB_ENST00000448382.1_In_Frame_Del_p.P264del			Q9UKJ0	PILRB_HUMAN	paired immunoglobin-like type 2 receptor beta	212				Missing (in Ref. 2; CAC19193). {ECO:0000305}.	activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)		p.L212delL(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	13	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GACTGCTGTGCCTCCTCCTCCTG	0.552														525	0.104832	0.1074	0.1023	5008	,	,		20509	0.0278		0.1759	False		,,,				2504	0.1094															1	Deletion - In frame(1)	ovary(1)	7								558,3692		34,490,1601						1.1	0.0		dbSNP_126	89	1608,6644		150,1308,2668	no	coding	PILRB	NM_178238.2		184,1798,4269	A1A1,A1R,RR		19.4862,13.1294,17.3252				2166,10336				99795067	SO:0001651	inframe_deletion	29990			AF161081, AJ400845	CCDS43622.1	7q22.1	2014-05-16			ENSG00000121716	ENSG00000121716		"""Immunoglobulin superfamily / V-set domain containing"""	18297	protein-coding gene	gene with protein product		605342				10660620	Standard	NM_178238		Approved	FDFACT1, FDFACT2	uc022ail.1	Q9UKJ0	OTTHUMG00000155363	ENST00000452089.1:c.624_626delCCT	7.37:g.99957138_99957140delCCT	ENSP00000391748:p.Leu212del	Somatic		Capture	SOLID	Phase_IV	99795065	Q69YF9|Q9HBS0	In_Frame_Del	DEL	ENST00000452089.1	37	CCDS43622.1	DEL	26	Baylor																																																																																				0.552	PILRB-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339923.2	NM_178238		In_Frame_Del
PRSS35	167681	hgsc.bcm.edu	37	6	84234349	84234349	+	Missense_Mutation	SNP	G	G	A			TCGA-13-0717-01	TCGA-13-0717-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chr6:84234349G>A	ENST00000369700.3	+	2	1366	c.1189G>A	c.(1189-1191)Gcc>Acc	p.A397T	PRSS35_ENST00000536636.1_Missense_Mutation_p.A397T	NM_153362.2	NP_699193.2	Q8N3Z0	PRS35_HUMAN	protease, serine, 35	397	Peptidase S1.					extracellular region (GO:0005576)|mitochondrion (GO:0005739)	serine-type endopeptidase activity (GO:0004252)	p.A397T(1)		breast(2)|endometrium(2)|large_intestine(12)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	32		all_cancers(76;0.000113)|Acute lymphoblastic leukemia(125;1.09e-08)|all_hematologic(105;3.12e-05)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0768)		CCTAAAATACGCCCAGATTTG	0.507																																																1	Substitution - Missense(1)	ovary(1)	6											63.0	46.0	52.0					6																	84234349		2203	4300	6503	84291068	SO:0001583	missense	167681			BC037170	CCDS4999.1	6q14.2	2010-05-12	2004-07-09	2004-07-09	ENSG00000146250	ENSG00000146250		"""Serine peptidases / Serine peptidases"""	21387	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 158"""	C6orf158			Standard	NM_153362		Approved	MGC46520, dJ223E3.1	uc003pjz.3	Q8N3Z0	OTTHUMG00000015113	ENST00000369700.3:c.1189G>A	6.37:g.84234349G>A	ENSP00000358714:p.Ala397Thr	Somatic		Capture	SOLID	Phase_IV	84291068	A8K7B3|Q9BQP6	Missense_Mutation	SNP	ENST00000369700.3	37	CCDS4999.1	SNP	38	Baylor	.	.	.	.	.	.	.	.	.	.	G	27.7	4.852822	0.91355	.	.	ENSG00000146250	ENST00000536636;ENST00000369700	T;T	0.50548	0.74;0.74	5.91	5.91	0.95273	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (1);	0.000000	0.85682	D	0.000000	T	0.67896	0.2942	M	0.79258	2.445	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.69840	-0.5036	10	0.87932	D	0	-26.7098	20.2946	0.98546	0.0:0.0:1.0:0.0	.	397	Q8N3Z0	PRS35_HUMAN	T	397	ENSP00000440870:A397T;ENSP00000358714:A397T	ENSP00000358714:A397T	A	+	1	0	PRSS35	84291068	1.000000	0.71417	0.986000	0.45419	0.953000	0.61014	7.636000	0.83301	2.804000	0.96469	0.462000	0.41574	GCC		0.507	PRSS35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041352.1	NM_153362		Missense_Mutation
PTCH1	5727	hgsc.bcm.edu	37	9	98239936	98239936	+	Missense_Mutation	SNP	G	G	C			TCGA-13-0717-01	TCGA-13-0717-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chr9:98239936G>C	ENST00000331920.6	-	10	1695	c.1396C>G	c.(1396-1398)Cag>Gag	p.Q466E	PTCH1_ENST00000429896.2_Missense_Mutation_p.Q315E|PTCH1_ENST00000430669.2_Missense_Mutation_p.Q400E|PTCH1_ENST00000375274.2_Missense_Mutation_p.Q465E|PTCH1_ENST00000437951.1_Missense_Mutation_p.Q400E|PTCH1_ENST00000418258.1_Missense_Mutation_p.Q315E|PTCH1_ENST00000421141.1_Missense_Mutation_p.Q315E|PTCH1_ENST00000548379.1_5'Flank	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	466	SSD. {ECO:0000255|PROSITE- ProRule:PRU00199}.				brain development (GO:0007420)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation involved in kidney development (GO:0061005)|cell proliferation involved in metanephros development (GO:0072203)|cellular response to cholesterol (GO:0071397)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|embryonic organ development (GO:0048568)|epidermis development (GO:0008544)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|hindlimb morphogenesis (GO:0035137)|in utero embryonic development (GO:0001701)|keratinocyte proliferation (GO:0043616)|limb morphogenesis (GO:0035108)|mammary gland duct morphogenesis (GO:0060603)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell division (GO:0051782)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate axis specification (GO:0021997)|neural tube closure (GO:0001843)|neural tube patterning (GO:0021532)|organ morphogenesis (GO:0009887)|pharyngeal system development (GO:0060037)|positive regulation of cholesterol efflux (GO:0010875)|protein processing (GO:0016485)|protein targeting to plasma membrane (GO:0072661)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein localization (GO:0032880)|regulation of smoothened signaling pathway (GO:0008589)|renal system development (GO:0072001)|response to chlorate (GO:0010157)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to mechanical stimulus (GO:0009612)|response to retinoic acid (GO:0032526)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|somite development (GO:0061053)|spinal cord motor neuron differentiation (GO:0021522)	axonal growth cone (GO:0044295)|caveola (GO:0005901)|dendritic growth cone (GO:0044294)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)	cholesterol binding (GO:0015485)|cyclin binding (GO:0030332)|hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|heparin binding (GO:0008201)|smoothened binding (GO:0005119)	p.Q466E(2)|p.Q465E(1)|p.Q466*(1)		NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1)	490		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				ACGGCACCCTGGGACTTGGAG	0.567																																																4	Substitution - Missense(3)|Substitution - Nonsense(1)	ovary(3)|skin(1)	9											42.0	42.0	42.0					9																	98239936		2203	4300	6503	97279757	SO:0001583	missense	5727			AI494442	CCDS6714.1, CCDS43851.1, CCDS47995.1, CCDS47996.1	9q22.1-q31	2014-09-17	2010-06-24	2006-09-26	ENSG00000185920	ENSG00000185920			9585	protein-coding gene	gene with protein product		601309	"""patched (Drosophila) homolog"", ""patched homolog (Drosophila)"", ""patched homolog 1 (Drosophila)"""	NBCCS, PTCH		8658145	Standard	NM_001083603		Approved	BCNS	uc004avk.4	Q13635	OTTHUMG00000020280	ENST00000331920.6:c.1396C>G	9.37:g.98239936G>C	ENSP00000332353:p.Gln466Glu	Somatic		Capture	SOLID	Phase_IV	97279757	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Missense_Mutation	SNP	ENST00000331920.6	37	CCDS6714.1	SNP	47	Baylor	.	.	.	.	.	.	.	.	.	.	G	29.8	5.036451	0.93630	.	.	ENSG00000185920	ENST00000331920;ENST00000437951;ENST00000421141;ENST00000418258;ENST00000430669;ENST00000429896;ENST00000375274	D;D;D;D;D;D;D	0.95656	-3.77;-3.77;-3.77;-3.77;-3.77;-3.77;-3.77	5.06	5.06	0.68205	Sterol-sensing domain (1);	0.000000	0.85682	D	0.000000	D	0.97751	0.9262	M	0.82323	2.585	0.80722	D	1	D;D;D	0.71674	0.998;0.986;0.997	D;P;D	0.71414	0.954;0.878;0.973	D	0.98333	1.0534	10	0.72032	D	0.01	-21.6948	18.6256	0.91336	0.0:0.0:1.0:0.0	.	400;465;466	Q13635-3;Q13635-2;Q13635	.;.;PTC1_HUMAN	E	466;400;315;315;400;315;465	ENSP00000332353:Q466E;ENSP00000389744:Q400E;ENSP00000399981:Q315E;ENSP00000396135:Q315E;ENSP00000410287:Q400E;ENSP00000414823:Q315E;ENSP00000364423:Q465E	ENSP00000332353:Q466E	Q	-	1	0	PTCH1	97279757	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.263000	0.95617	2.619000	0.88677	0.655000	0.94253	CAG		0.567	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264		Missense_Mutation
RRAD	6236	hgsc.bcm.edu	37	16	66956141	66956141	+	Missense_Mutation	SNP	C	C	G			TCGA-13-0717-01	TCGA-13-0717-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chr16:66956141C>G	ENST00000299759.6	-	5	1015	c.765G>C	c.(763-765)agG>agC	p.R255S	RRAD_ENST00000420652.1_Missense_Mutation_p.R255S			P55042	RAD_HUMAN	Ras-related associated with diabetes	255					small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(2)|kidney(4)|large_intestine(3)|lung(4)|prostate(2)|skin(1)|urinary_tract(1)	17		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0862)|Epithelial(162;0.198)		CTTTGCTGTCCCTGCGCAGGC	0.587																																																0			16											93.0	71.0	78.0					16																	66956141		2200	4300	6500	65513642	SO:0001583	missense	6236			L24564	CCDS10824.1	16q22	2014-05-09			ENSG00000166592	ENSG00000166592			10446	protein-coding gene	gene with protein product		179503				7859947	Standard	NM_004165		Approved	REM3, RAD	uc002eqo.2	P55042	OTTHUMG00000137511	ENST00000299759.6:c.765G>C	16.37:g.66956141C>G	ENSP00000299759:p.Arg255Ser	Somatic		Capture	SOLID	Phase_IV	65513642	Q96F39	Missense_Mutation	SNP	ENST00000299759.6	37	CCDS10824.1	SNP	22	Baylor	.	.	.	.	.	.	.	.	.	.	C	15.50	2.851221	0.51270	.	.	ENSG00000166592	ENST00000420652;ENST00000299759	T;T	0.79940	-1.32;-1.32	5.93	0.643	0.17770	.	0.041315	0.85682	D	0.000000	T	0.69233	0.3088	L	0.59436	1.845	0.38912	D	0.957567	P	0.39044	0.656	B	0.24701	0.055	T	0.68674	-0.5346	10	0.52906	T	0.07	.	10.094	0.42464	0.0:0.5055:0.0:0.4945	.	255	P55042	RAD_HUMAN	S	255	ENSP00000388744:R255S;ENSP00000299759:R255S	ENSP00000299759:R255S	R	-	3	2	RRAD	65513642	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	0.788000	0.26872	0.401000	0.25424	0.561000	0.74099	AGG		0.587	RRAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268830.1	NM_004165		Missense_Mutation
SHISA3	152573	hgsc.bcm.edu	37	4	42403147	42403147	+	Missense_Mutation	SNP	G	G	C			TCGA-13-0717-01	TCGA-13-0717-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chr4:42403147G>C	ENST00000319234.4	+	2	614	c.396G>C	c.(394-396)caG>caC	p.Q132H		NM_001080505.1	NP_001073974.1	A0PJX4	SHSA3_HUMAN	shisa family member 3	132					multicellular organismal development (GO:0007275)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)		p.Q132H(1)		endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	12						CCTCGCAGCAGCCAATCCGCT	0.577																																																1	Substitution - Missense(1)	ovary(1)	4											189.0	202.0	197.0					4																	42403147		2203	4300	6503	42097904	SO:0001583	missense	152573			BC012029	CCDS33979.1	4p13	2013-07-31	2013-07-31		ENSG00000178343	ENSG00000178343		"""Shisa homologs"""	25159	protein-coding gene	gene with protein product			"""shisa homolog 3 (Xenopus laevis)"""				Standard	NM_001080505		Approved	hShisa3	uc003gwp.3	A0PJX4	OTTHUMG00000161043	ENST00000319234.4:c.396G>C	4.37:g.42403147G>C	ENSP00000326445:p.Gln132His	Somatic		Capture	SOLID	Phase_IV	42097904	A0PJX3|Q96EQ5	Missense_Mutation	SNP	ENST00000319234.4	37	CCDS33979.1	SNP	34	Baylor	.	.	.	.	.	.	.	.	.	.	G	17.34	3.364826	0.61513	.	.	ENSG00000178343	ENST00000319234	T	0.45668	0.89	4.94	2.24	0.28232	.	0.000000	0.85682	D	0.000000	T	0.55289	0.1911	M	0.61703	1.905	0.54753	D	0.99998	D	0.65815	0.995	D	0.68353	0.957	T	0.52457	-0.8573	10	0.62326	D	0.03	-11.5341	8.5436	0.33408	0.309:0.0:0.691:0.0	.	132	A0PJX4	SHSA3_HUMAN	H	132	ENSP00000326445:Q132H	ENSP00000326445:Q132H	Q	+	3	2	SHISA3	42097904	1.000000	0.71417	0.996000	0.52242	0.857000	0.48899	1.805000	0.38883	0.267000	0.21916	0.655000	0.94253	CAG		0.577	SHISA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363539.1	NM_001080505		Missense_Mutation
SIPA1L2	57568	hgsc.bcm.edu	37	1	232581296	232581296	+	Missense_Mutation	SNP	C	C	T	rs557448632		TCGA-13-0717-01	TCGA-13-0717-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chr1:232581296C>T	ENST00000366630.1	-	10	3690	c.3332G>A	c.(3331-3333)cGg>cAg	p.R1111Q	SIPA1L2_ENST00000262861.4_Missense_Mutation_p.R1111Q|SIPA1L2_ENST00000308942.4_Missense_Mutation_p.R185Q			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	1111					regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)	p.R1111Q(1)		NS(1)|breast(5)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(49)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	103		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)				GGGCAGCTTCCGGTCGAAGGA	0.612																																																1	Substitution - Missense(1)	ovary(1)	1											35.0	40.0	38.0					1																	232581296		2014	4173	6187	230647919	SO:0001583	missense	57568			AB037810	CCDS41474.1	1q42.2	2008-02-05			ENSG00000116991	ENSG00000116991			23800	protein-coding gene	gene with protein product		611609					Standard	NM_020808		Approved	KIAA1389	uc001hvg.3	Q9P2F8	OTTHUMG00000037820	ENST00000366630.1:c.3332G>A	1.37:g.232581296C>T	ENSP00000355589:p.Arg1111Gln	Somatic		Capture	SOLID	Phase_IV	230647919	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Missense_Mutation	SNP	ENST00000366630.1	37	CCDS41474.1	SNP	23	Baylor	.	.	.	.	.	.	.	.	.	.	C	15.53	2.861376	0.51482	.	.	ENSG00000116991	ENST00000366630;ENST00000262861;ENST00000308942	T;T;T	0.60548	0.18;0.18;0.18	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	T	0.55289	0.1911	L	0.54323	1.7	0.43936	D	0.996594	P;D	0.54601	0.944;0.967	B;P	0.47044	0.182;0.535	T	0.50617	-0.8807	10	0.15499	T	0.54	-23.0501	12.6564	0.56790	0.0:0.9244:0.0:0.0756	.	1111;185	Q9P2F8;Q9P2F8-2	SI1L2_HUMAN;.	Q	1111;1111;185	ENSP00000355589:R1111Q;ENSP00000262861:R1111Q;ENSP00000309102:R185Q	ENSP00000262861:R1111Q	R	-	2	0	SIPA1L2	230647919	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	4.593000	0.61034	2.560000	0.86352	0.655000	0.94253	CGG		0.612	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839		Missense_Mutation
SLC12A6	9990	hgsc.bcm.edu	37	15	34532906	34532906	+	Missense_Mutation	SNP	C	C	A			TCGA-13-0717-01	TCGA-13-0717-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Sanger_PCR_WGA	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chr15:34532906C>A	ENST00000354181.3	-	19	2884	c.2392G>T	c.(2392-2394)Ggg>Tgg	p.G798W	SLC12A6_ENST00000397707.2_Missense_Mutation_p.G783W|SLC12A6_ENST00000397702.2_Missense_Mutation_p.G739W|SLC12A6_ENST00000558589.1_Missense_Mutation_p.G789W|SLC12A6_ENST00000458406.2_Missense_Mutation_p.G739W|SLC12A6_ENST00000558667.1_Missense_Mutation_p.G798W|SLC12A6_ENST00000560611.1_Missense_Mutation_p.G798W|SLC12A6_ENST00000451844.2_Missense_Mutation_p.G610W|SLC12A6_ENST00000290209.5_Missense_Mutation_p.G747W|SLC12A6_ENST00000560164.1_Missense_Mutation_p.G610W			Q9UHW9	S12A6_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 6	798					angiogenesis (GO:0001525)|cellular hypotonic response (GO:0071476)|cellular hypotonic salinity response (GO:0071477)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|rubidium ion transport (GO:0035826)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium ion transmembrane transporter activity (GO:0015079)|potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)|rubidium ion transmembrane transporter activity (GO:0035827)	p.G747W(1)		central_nervous_system(5)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|skin(3)	45		all_lung(180;2.78e-08)		all cancers(64;3.43e-17)|GBM - Glioblastoma multiforme(113;2.6e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0301)	Potassium Chloride(DB00761)	AGGAAGTTCCCCACGATGACA	0.468																																																1	Substitution - Missense(1)	ovary(1)	15											125.0	110.0	115.0					15																	34532906		2201	4298	6499	32320198	SO:0001583	missense	9990			AF108831	CCDS10036.1, CCDS42010.1, CCDS42011.1, CCDS42012.1, CCDS58352.1	15q13	2014-09-17	2013-07-18		ENSG00000140199	ENSG00000140199		"""Solute carriers"""	10914	protein-coding gene	gene with protein product		604878	"""agenesis of corpus callosum and peripheral neuropathy (Andermann syndrome)"""	KCC3, ACCPN		10187864, 10347194	Standard	NM_133647		Approved		uc001zhw.3	Q9UHW9	OTTHUMG00000129441	ENST00000354181.3:c.2392G>T	15.37:g.34532906C>A	ENSP00000346112:p.Gly798Trp	Somatic		Capture	SOLID	Phase_IV	32320198	A0AV76|Q2VI00|Q7Z2E7|Q7Z4G5|Q8TDD4|Q9UFR2|Q9Y642|Q9Y665	Missense_Mutation	SNP	ENST00000354181.3	37	CCDS58352.1	SNP	22	Baylor	.	.	.	.	.	.	.	.	.	.	C	26.2	4.714426	0.89112	.	.	ENSG00000140199	ENST00000290209;ENST00000397707;ENST00000354181;ENST00000397702;ENST00000458406;ENST00000451844	D;D;D;D;D	0.96104	-3.91;-3.91;-3.91;-3.91;-3.91	4.98	4.98	0.66077	.	0.000000	0.85682	D	0.000000	D	0.98448	0.9483	H	0.95574	3.69	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.998;0.999;0.997	D	0.99560	1.0968	10	0.87932	D	0	.	17.1908	0.86879	0.0:1.0:0.0:0.0	.	783;798;747;610	Q9UHW9-3;Q9UHW9;A0AV76;B3KXX3	.;S12A6_HUMAN;.;.	W	747;783;789;739;739;610	ENSP00000290209:G747W;ENSP00000380819:G783W;ENSP00000380814:G739W;ENSP00000387725:G739W;ENSP00000390199:G610W	ENSP00000290209:G747W	G	-	1	0	SLC12A6	32320198	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.651000	0.83577	2.580000	0.87095	0.591000	0.81541	GGG		0.468	SLC12A6-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000417991.1	NM_005135		Missense_Mutation
SLC26A5	375611	hgsc.bcm.edu	37	7	103018944	103018944	+	Silent	SNP	G	G	A	rs577037869		TCGA-13-0717-01	TCGA-13-0717-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chr7:103018944G>A	ENST00000306312.3	-	17	1995	c.1734C>T	c.(1732-1734)taC>taT	p.Y578Y	SLC26A5_ENST00000393723.1_Silent_p.Y546Y|SLC26A5_ENST00000354356.4_Silent_p.Y11Y|SLC26A5_ENST00000393729.1_Silent_p.Y541Y|SLC26A5_ENST00000432958.2_Silent_p.Y546Y|SLC26A5_ENST00000339444.6_Silent_p.Y578Y|SLC26A5_ENST00000393727.1_Silent_p.Y578Y|SLC26A5_ENST00000356767.4_Intron|SLC26A5_ENST00000393730.1_Silent_p.Y546Y|SLC26A5_ENST00000393735.2_Intron	NM_198999.2	NP_945350.1	P58743	S26A5_HUMAN	solute carrier family 26 (anion exchanger), member 5	578	STAS. {ECO:0000255|PROSITE- ProRule:PRU00198}.				regulation of cell shape (GO:0008360)|regulation of membrane potential (GO:0042391)|sensory perception of sound (GO:0007605)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)	secondary active sulfate transmembrane transporter activity (GO:0008271)	p.Y578Y(1)		endometrium(5)|kidney(2)|large_intestine(9)|lung(15)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)	43						CTTCCTTAGCGTACTTCCGCA	0.453													G|||	1	0.000199681	0.0	0.0	5008	,	,		19434	0.001		0.0	False		,,,				2504	0.0															1	Substitution - coding silent(1)	ovary(1)	7											275.0	217.0	236.0					7																	103018944		2203	4300	6503	102806180	SO:0001819	synonymous_variant	375611			AC005064	CCDS5733.1, CCDS43630.1, CCDS55150.1, CCDS5732.1, CCDS43629.1	7q22	2013-07-18	2013-07-18	2005-09-13	ENSG00000170615	ENSG00000170615		"""Solute carriers"""	9359	protein-coding gene	gene with protein product	"""deafness, neurosensory, autosomal recessive, 61"""	604943	"""prestin (motor protein)"""	PRES		10821263	Standard	NM_206883		Approved	DFNB61	uc003vbz.3	P58743	OTTHUMG00000149911	ENST00000306312.3:c.1734C>T	7.37:g.103018944G>A		Somatic		Capture	SOLID	Phase_IV	102806180	Q496J2|Q7Z7F3|Q86UF8|Q86UF9|Q86UG0	Silent	SNP	ENST00000306312.3	37	CCDS5733.1	SNP	40	Baylor																																																																																				0.453	SLC26A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313860.1	NM_198999		Silent
SLC27A4	10999	hgsc.bcm.edu	37	9	131117732	131117732	+	Silent	SNP	G	G	T			TCGA-13-0717-01	TCGA-13-0717-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chr9:131117732G>T	ENST00000300456.4	+	11	1635	c.1518G>T	c.(1516-1518)ggG>ggT	p.G506G	SLC27A4_ENST00000372870.1_Silent_p.G100G	NM_005094.3	NP_005085.2	Q6P1M0	S27A4_HUMAN	solute carrier family 27 (fatty acid transporter), member 4	506					fatty acid transport (GO:0015908)|lipid metabolic process (GO:0006629)|long-chain fatty acid import (GO:0044539)|long-chain fatty acid metabolic process (GO:0001676)|long-chain fatty acid transport (GO:0015909)|medium-chain fatty acid transport (GO:0001579)|response to nutrient (GO:0007584)|skin development (GO:0043588)|transmembrane transport (GO:0055085)|transport (GO:0006810)|very long-chain fatty acid catabolic process (GO:0042760)	brush border membrane (GO:0031526)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	fatty acid transporter activity (GO:0015245)|long-chain fatty acid-CoA ligase activity (GO:0004467)|nucleotide binding (GO:0000166)|very long-chain fatty acid-CoA ligase activity (GO:0031957)			autonomic_ganglia(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(2)	13						ACCGCACTGGGGACACGTTCC	0.642																																					Pancreas(107;1554 2241 10946 12953)											0			9											55.0	43.0	47.0					9																	131117732		2203	4300	6503	130157553	SO:0001819	synonymous_variant	10999			AF055899	CCDS6899.1	9q34.13	2013-05-22			ENSG00000167114	ENSG00000167114		"""Acyl-CoA synthetase family"", ""Solute carriers"""	10998	protein-coding gene	gene with protein product		604194				9878842	Standard	NM_005094		Approved	FATP4, ACSVL4	uc004but.3	Q6P1M0	OTTHUMG00000020746	ENST00000300456.4:c.1518G>T	9.37:g.131117732G>T		Somatic		Capture	SOLID	Phase_IV	130157553	A8K2F7|O95186|Q96G53	Silent	SNP	ENST00000300456.4	37	CCDS6899.1	SNP	43	Baylor																																																																																				0.642	SLC27A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054432.2			Silent
SLC8A1	6546	hgsc.bcm.edu	37	2	40392065	40392065	+	Frame_Shift_Del	DEL	C	C	-			TCGA-13-0717-01	TCGA-13-0717-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chr2:40392065delC	ENST00000403092.1	-	8	2131	c.2098delG	c.(2098-2100)gaafs	p.E700fs	SLC8A1-AS1_ENST00000593878.1_RNA|SLC8A1_ENST00000408028.2_Frame_Shift_Del_p.E692fs|SLC8A1_ENST00000406391.2_Frame_Shift_Del_p.E664fs|SLC8A1-AS1_ENST00000601679.1_RNA|SLC8A1-AS1_ENST00000593848.1_RNA|SLC8A1-AS1_ENST00000435515.1_RNA|SLC8A1-AS1_ENST00000598247.1_RNA|SLC8A1-AS1_ENST00000599956.1_RNA|SLC8A1_ENST00000542024.1_Frame_Shift_Del_p.E664fs|SLC8A1_ENST00000332839.4_Frame_Shift_Del_p.E700fs|SLC8A1-AS1_ENST00000444629.1_RNA|SLC8A1_ENST00000402441.1_Frame_Shift_Del_p.E664fs|SLC8A1-AS1_ENST00000596532.1_RNA|SLC8A1-AS1_ENST00000599740.1_RNA|SLC8A1_ENST00000405269.1_Frame_Shift_Del_p.E664fs|SLC8A1_ENST00000406785.2_Frame_Shift_Del_p.E664fs|SLC8A1_ENST00000542756.1_Frame_Shift_Del_p.E695fs|SLC8A1-AS1_ENST00000597385.1_RNA|SLC8A1_ENST00000405901.3_Frame_Shift_Del_p.E695fs|SLC8A1-AS1_ENST00000599268.1_RNA|SLC8A1-AS1_ENST00000597170.1_RNA			P32418	NAC1_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 1	700					blood coagulation (GO:0007596)|calcium ion export (GO:1901660)|calcium ion homeostasis (GO:0055074)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|cardiac muscle cell development (GO:0055013)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular response to caffeine (GO:0071313)|cellular response to reactive oxygen species (GO:0034614)|cellular sodium ion homeostasis (GO:0006883)|cytosolic calcium ion transport (GO:0060401)|embryonic heart tube development (GO:0035050)|embryonic placenta development (GO:0001892)|heart morphogenesis (GO:0003007)|ion transport (GO:0006811)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|muscle contraction (GO:0006936)|muscle fiber development (GO:0048747)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|post-embryonic development (GO:0009791)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|relaxation of smooth muscle (GO:0044557)|sodium ion export (GO:0071436)|sodium ion import (GO:0097369)|transmembrane transport (GO:0055085)|vascular smooth muscle contraction (GO:0014829)	basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|calcium:sodium antiporter activity (GO:0005432)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)	p.E700fs*15(1)		NS(1)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|liver(1)|lung(57)|ovary(2)|pancreas(1)|skin(7)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(2)	100					Alpha-Linolenic Acid(DB00132)|Icosapent(DB00159)	CGCCCCATTTCTGCAATGCGC	0.502																																																1	Deletion - Frameshift(1)	ovary(1)	2											187.0	179.0	181.0					2																	40392065		2203	4300	6503	40245569	SO:0001589	frameshift_variant	6546				CCDS1806.1, CCDS46264.1, CCDS46265.1, CCDS59430.1	2p22.1	2013-07-15			ENSG00000183023	ENSG00000183023		"""Solute carriers"""	11068	protein-coding gene	gene with protein product	"""Na+/Ca++ exchanger"""	182305		NCX1		1559714	Standard	NM_021097		Approved		uc002rrx.3	P32418	OTTHUMG00000102183	ENST00000403092.1:c.2098delG	2.37:g.40392065delC	ENSP00000384763:p.Glu700fs	Somatic		Capture	SOLID	Phase_IV	40245569	A8K6N1|D6W595|O95849|Q4QQG6|Q587I6|Q59GN4|Q9UBL8|Q9UD55|Q9UDN1|Q9UDN2|Q9UKX6	Frame_Shift_Del	DEL	ENST00000403092.1	37	CCDS1806.1	DEL	32	Baylor																																																																																				0.502	SLC8A1-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326065.1	NM_021097		Frame_Shift_Del
SPEG	10290	hgsc.bcm.edu	37	2	220315873	220315873	+	Missense_Mutation	SNP	C	C	A			TCGA-13-0717-01	TCGA-13-0717-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chr2:220315873C>A	ENST00000312358.7	+	5	2261	c.2129C>A	c.(2128-2130)tCc>tAc	p.S710Y	SPEG_ENST00000485813.1_3'UTR|SPEG_ENST00000396695.2_5'UTR|SPEG_ENST00000396698.1_Missense_Mutation_p.S606Y	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	710					cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.S710Y(1)		breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		TCGGATGACTCCTACGTGTCC	0.602																																																1	Substitution - Missense(1)	ovary(1)	2											112.0	113.0	113.0					2																	220315873		1970	4146	6116	220024117	SO:0001583	missense	10290			BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"""Immunoglobulin superfamily / I-set domain containing"""	16901	protein-coding gene	gene with protein product		615950	"""aortic preferentially expressed gene 1"""	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.2129C>A	2.37:g.220315873C>A	ENSP00000311684:p.Ser710Tyr	Somatic		Capture	SOLID	Phase_IV	220024117	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Missense_Mutation	SNP	ENST00000312358.7	37	CCDS42824.1	SNP	30	Baylor	.	.	.	.	.	.	.	.	.	.	C	24.9	4.580912	0.86748	.	.	ENSG00000072195	ENST00000312358;ENST00000265327;ENST00000396698	T;T	0.67865	-0.29;-0.01	5.43	5.43	0.79202	.	0.000000	0.41194	D	0.000935	T	0.73418	0.3584	N	0.24115	0.695	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.76594	-0.2902	10	0.62326	D	0.03	.	18.835	0.92159	0.0:1.0:0.0:0.0	.	710	Q15772	SPEG_HUMAN	Y	710;710;606	ENSP00000311684:S710Y;ENSP00000379926:S606Y	ENSP00000265327:S710Y	S	+	2	0	SPEG	220024117	1.000000	0.71417	1.000000	0.80357	0.897000	0.52465	7.453000	0.80700	2.556000	0.86216	0.655000	0.94253	TCC		0.602	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876		Missense_Mutation
TBX1	6899	hgsc.bcm.edu	37	22	19752518	19752518	+	Missense_Mutation	SNP	T	T	C			TCGA-13-0717-01	TCGA-13-0717-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chr22:19752518T>C	ENST00000329705.7	+	6	851	c.722T>C	c.(721-723)tTc>tCc	p.F241S	TBX1_ENST00000332710.4_Missense_Mutation_p.F241S|TBX1_ENST00000359500.3_Missense_Mutation_p.F241S	NM_080646.1	NP_542377.1	O43435	TBX1_HUMAN	T-box 1	241					angiogenesis (GO:0001525)|anterior/posterior pattern specification (GO:0009952)|aorta morphogenesis (GO:0035909)|artery morphogenesis (GO:0048844)|blood vessel development (GO:0001568)|blood vessel morphogenesis (GO:0048514)|blood vessel remodeling (GO:0001974)|cell fate specification (GO:0001708)|cell proliferation (GO:0008283)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to retinoic acid (GO:0071300)|cochlea morphogenesis (GO:0090103)|coronary artery morphogenesis (GO:0060982)|determination of left/right symmetry (GO:0007368)|ear morphogenesis (GO:0042471)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic viscerocranium morphogenesis (GO:0048703)|enamel mineralization (GO:0070166)|epithelial cell differentiation (GO:0030855)|face morphogenesis (GO:0060325)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|inner ear morphogenesis (GO:0042472)|lymph vessel development (GO:0001945)|mesenchymal cell apoptotic process (GO:0097152)|mesoderm development (GO:0007498)|middle ear morphogenesis (GO:0042474)|muscle cell fate commitment (GO:0042693)|muscle organ development (GO:0007517)|muscle organ morphogenesis (GO:0048644)|muscle tissue morphogenesis (GO:0060415)|negative regulation of cell differentiation (GO:0045596)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|otic vesicle morphogenesis (GO:0071600)|outer ear morphogenesis (GO:0042473)|outflow tract morphogenesis (GO:0003151)|outflow tract septum morphogenesis (GO:0003148)|parathyroid gland development (GO:0060017)|pattern specification process (GO:0007389)|pharyngeal system development (GO:0060037)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of secondary heart field cardioblast proliferation (GO:0072513)|positive regulation of tongue muscle cell differentiation (GO:2001037)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of organ morphogenesis (GO:2000027)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|retinoic acid receptor signaling pathway (GO:0048384)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|social behavior (GO:0035176)|soft palate development (GO:0060023)|thymus development (GO:0048538)|thyroid gland development (GO:0030878)|tongue morphogenesis (GO:0043587)|transcription, DNA-templated (GO:0006351)|vagus nerve morphogenesis (GO:0021644)	nucleus (GO:0005634)	DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)	p.F241S(1)		breast(2)|central_nervous_system(1)|lung(3)|ovary(2)	8	Colorectal(54;0.0993)	all_lung(157;3.05e-06)				CAGCCCCGCTTCCACGTGGTC	0.542																																																1	Substitution - Missense(1)	ovary(1)	22											97.0	94.0	95.0					22																	19752518		2203	4300	6503	18132518	SO:0001583	missense	6899			AF012131	CCDS13765.1, CCDS13766.1, CCDS13767.1	22q11.21	2014-09-17			ENSG00000184058	ENSG00000184058		"""T-boxes"""	11592	protein-coding gene	gene with protein product		602054	"""velocardiofacial syndrome"""	VCF		9268629, 23000736	Standard	NM_080646		Approved	CATCH22	uc002zqa.1	O43435	OTTHUMG00000150421	ENST00000329705.7:c.722T>C	22.37:g.19752518T>C	ENSP00000331176:p.Phe241Ser	Somatic		Capture	SOLID	Phase_IV	18132518	C6G493|C6G494|O43436|Q96RJ2	Missense_Mutation	SNP	ENST00000329705.7	37	CCDS13766.1	SNP	62	Baylor	.	.	.	.	.	.	.	.	.	.	T	25.2	4.615311	0.87359	.	.	ENSG00000184058	ENST00000332710;ENST00000329705;ENST00000359500	D;D;D	0.90069	-2.61;-2.61;-2.61	4.18	4.18	0.49190	p53-like transcription factor, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.95271	0.8466	M	0.92219	3.285	0.80722	D	1	D;D;P	0.89917	1.0;0.992;0.922	D;D;P	0.76071	0.987;0.939;0.761	D	0.96116	0.9081	10	0.87932	D	0	.	13.0464	0.58928	0.0:0.0:0.0:1.0	.	241;241;241	Q152R5;O43435;D9ZGG0	.;TBX1_HUMAN;.	S	241	ENSP00000331791:F241S;ENSP00000331176:F241S;ENSP00000352483:F241S	ENSP00000331176:F241S	F	+	2	0	TBX1	18132518	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	7.754000	0.85163	1.765000	0.52091	0.402000	0.26972	TTC		0.542	TBX1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318033.1	NM_080647		Missense_Mutation
TRPM1	4308	hgsc.bcm.edu	37	15	31295171	31295171	+	Silent	SNP	T	T	C			TCGA-13-0717-01	TCGA-13-0717-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chr15:31295171T>C	ENST00000256552.6	-	28	3879	c.3732A>G	c.(3730-3732)gaA>gaG	p.E1244E	RP11-348B17.1_ENST00000561299.1_RNA|TRPM1_ENST00000542188.1_Silent_p.E1261E|TRPM1_ENST00000397795.2_Silent_p.E1222E	NM_001252024.1	NP_001238953.1			transient receptor potential cation channel, subfamily M, member 1											NS(2)|breast(3)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(15)|lung(48)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(3)	99		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)		TGTTAGATAATTCTTCTAGCT	0.428																																																0			15											93.0	89.0	90.0					15																	31295171		1902	4125	6027	29082463	SO:0001819	synonymous_variant	4308			AF071787	CCDS10024.2, CCDS58345.1, CCDS58346.1, CCDS58347.1	15q13.3	2014-01-28		2002-01-18	ENSG00000134160	ENSG00000134160		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	7146	protein-coding gene	gene with protein product		603576	"""melastatin 1"""	MLSN1		9806836, 9537257, 16382100	Standard	NM_001252020		Approved	LTRPC1, CSNB1C	uc021sia.1	Q7Z4N2	OTTHUMG00000129267	ENST00000256552.6:c.3732A>G	15.37:g.31295171T>C		Somatic		Capture	SOLID	Phase_IV	29082463		Silent	SNP	ENST00000256552.6	37	CCDS58346.1	SNP	52	Baylor																																																																																				0.428	TRPM1-004	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417166.2	NM_002420		Silent
NME8	51314	hgsc.bcm.edu	37	7	37907457	37907457	+	Missense_Mutation	SNP	G	G	A			TCGA-13-0717-01	TCGA-13-0717-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chr7:37907457G>A	ENST00000199447.4	+	11	1147	c.775G>A	c.(775-777)Gaa>Aaa	p.E259K	NME8_ENST00000440017.1_Missense_Mutation_p.E259K|EPDR1_ENST00000476620.1_Intron	NM_016616.4	NP_057700.3	Q8N427	TXND3_HUMAN	NME/NM23 family member 8	259					cell differentiation (GO:0030154)|cell redox homeostasis (GO:0045454)|CTP biosynthetic process (GO:0006241)|GTP biosynthetic process (GO:0006183)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)|UTP biosynthetic process (GO:0006228)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)	p.E259K(1)									ACCTGAGGTCGAAGCCCAGGT	0.448																																																1	Substitution - Missense(1)	ovary(1)	7											98.0	81.0	87.0					7																	37907457		2203	4300	6503	37873982	SO:0001583	missense	51314			AF202051	CCDS5452.1	7p15.2	2012-05-18	2012-05-18	2012-05-18	ENSG00000086288	ENSG00000086288			16473	protein-coding gene	gene with protein product	"""sperm-specific thioredoxin 2"""	607421	"""thioredoxin domain containing 3 (spermatozoa)"""	TXNDC3		11737268, 11768308, 19852809	Standard	NM_016616		Approved	CILD6, SPTRX2, NM23-H8	uc003tfn.3	Q8N427	OTTHUMG00000023716	ENST00000199447.4:c.775G>A	7.37:g.37907457G>A	ENSP00000199447:p.Glu259Lys	Somatic		Capture	SOLID	Phase_IV	37873982	Q9NZH1	Missense_Mutation	SNP	ENST00000199447.4	37	CCDS5452.1	SNP	37	Baylor	.	.	.	.	.	.	.	.	.	.	G	8.443	0.851308	0.17034	.	.	ENSG00000086288	ENST00000199447;ENST00000440017	T;T	0.36157	1.27;1.27	3.73	-1.99	0.07457	.	1.254880	0.05903	N	0.630249	T	0.14442	0.0349	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.22103	-1.0226	10	0.06365	T	0.9	0.2498	4.7353	0.12984	0.289:0.3117:0.3994:0.0	.	259	Q8N427	TXND3_HUMAN	K	259	ENSP00000199447:E259K;ENSP00000397063:E259K	ENSP00000199447:E259K	E	+	1	0	TXNDC3	37873982	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.237000	0.08990	-0.633000	0.05545	-1.565000	0.00878	GAA		0.448	NME8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219946.1	NM_016616		Missense_Mutation
UBR4	23352	hgsc.bcm.edu	37	1	19518749	19518749	+	Nonsense_Mutation	SNP	G	G	A			TCGA-13-0717-01	TCGA-13-0717-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chr1:19518749G>A	ENST00000375254.3	-	11	1354	c.1327C>T	c.(1327-1329)Cga>Tga	p.R443*	UBR4_ENST00000375267.2_Nonsense_Mutation_p.R443*|UBR4_ENST00000375217.2_Nonsense_Mutation_p.R443*|UBR4_ENST00000375226.2_Nonsense_Mutation_p.R443*	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	443					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R443*(1)		breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		TCTCTGACTCGGAGGGCAGCC	0.488																																																1	Substitution - Nonsense(1)	ovary(1)	1											68.0	70.0	69.0					1																	19518749		2203	4300	6503	19391336	SO:0001587	stop_gained	23352			AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"""Ubiquitin protein ligase E3 component n-recognins"""	30313	protein-coding gene	gene with protein product		609890	"""zinc finger, UBR1 type 1"""	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.1327C>T	1.37:g.19518749G>A	ENSP00000364403:p.Arg443*	Somatic		Capture	SOLID	Phase_IV	19391336	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Nonsense_Mutation	SNP	ENST00000375254.3	37	CCDS189.1	SNP	39	Baylor	.	.	.	.	.	.	.	.	.	.	G	38	6.837197	0.97873	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226	.	.	.	5.6	4.61	0.57282	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.05351	T	0.99	.	14.3038	0.66373	0.0:0.0:0.7732:0.2268	.	.	.	.	X	443	.	ENSP00000364365:R443X	R	-	1	2	UBR4	19391336	1.000000	0.71417	0.992000	0.48379	0.998000	0.95712	6.148000	0.71788	2.630000	0.89119	0.591000	0.81541	CGA		0.488	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		Nonsense_Mutation
ULK4	54986	hgsc.bcm.edu	37	3	41860985	41860985	+	Frame_Shift_Del	DEL	T	T	-	rs76318575		TCGA-13-0717-01	TCGA-13-0717-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chr3:41860985delT	ENST00000301831.4	-	19	2240	c.1778delA	c.(1777-1779)aagfs	p.K593fs		NM_017886.2	NP_060356.2	Q96C45	ULK4_HUMAN	unc-51 like kinase 4	593					cilium morphogenesis (GO:0060271)|epithelial cilium movement (GO:0003351)|microtubule cytoskeleton organization (GO:0000226)|regulation of JNK cascade (GO:0046328)|regulation of MAPK cascade (GO:0043408)|regulation of neuron migration (GO:2001222)|regulation of neuron projection development (GO:0010975)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein kinase C signaling (GO:0090036)|ventricular system development (GO:0021591)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.K593fs*17(1)		breast(2)|cervix(1)|large_intestine(6)|lung(7)|prostate(5)|skin(1)	22				KIRC - Kidney renal clear cell carcinoma(284;0.214)		TCTAGGGTTCTTTTTTTTTTC	0.448																																																1	Deletion - Frameshift(1)	ovary(1)	3											62.0	63.0	63.0					3																	41860985		1844	4089	5933	41835989	SO:0001589	frameshift_variant	54986			AK000581	CCDS43071.1	3p22.1	2013-07-02	2013-07-02		ENSG00000168038	ENSG00000168038			15784	protein-coding gene	gene with protein product			"""unc-51-like kinase 4 (C. elegans)"""			12477932	Standard	NM_017886		Approved	FLJ20574, REC01035, FAM7C1	uc003ckv.4	Q96C45	OTTHUMG00000156210	ENST00000301831.4:c.1778delA	3.37:g.41860985delT	ENSP00000301831:p.Lys593fs	Somatic		Capture	SOLID	Phase_IV	41835989	A6NF15|Q8IW79|Q9NWV6|Q9UF96	Frame_Shift_Del	DEL	ENST00000301831.4	37	CCDS43071.1	DEL	56	Baylor																																																																																				0.448	ULK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343490.1	XM_929989		Frame_Shift_Del
SUN1	23353	hgsc.bcm.edu	37	7	897508	897508	+	Missense_Mutation	SNP	C	C	A	rs565714490		TCGA-13-0717-01	TCGA-13-0717-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chr7:897508C>A	ENST00000405266.1	+	14	1573	c.1549C>A	c.(1549-1551)Ctg>Atg	p.L517M	SUN1_ENST00000389574.3_Missense_Mutation_p.L397M|SUN1_ENST00000401592.1_Missense_Mutation_p.L480M|SUN1_ENST00000413514.2_Missense_Mutation_p.L278M|SUN1_ENST00000452783.2_Missense_Mutation_p.L377M|SUN1_ENST00000456758.2_Missense_Mutation_p.L669M|SUN1_ENST00000425407.2_Missense_Mutation_p.L397M			O94901	SUN1_HUMAN	Sad1 and UNC84 domain containing 1	507					cytoskeletal anchoring at nuclear membrane (GO:0090286)|nuclear envelope organization (GO:0006998)|nuclear matrix anchoring at nuclear membrane (GO:0090292)	acrosomal membrane (GO:0002080)|integral component of nuclear inner membrane (GO:0005639)|nuclear envelope (GO:0005635)|SUN-KASH complex (GO:0034993)				NS(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(17)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						GCACCTCCAGCTGGAGCTGGA	0.567																																																0			7											152.0	165.0	161.0					7																	897508		2069	4202	6271	864034	SO:0001583	missense	23353			AF202724	CCDS43533.1, CCDS47525.1, CCDS55078.1, CCDS55079.1, CCDS55080.1	7p22.3	2010-01-27	2010-01-27	2010-01-27	ENSG00000164828	ENSG00000164828			18587	protein-coding gene	gene with protein product	"""Sad1 unc-84 domain protein 1"""	607723	"""unc-84 homolog A (C. elegans)"""	UNC84A		11593002	Standard	NM_001130965		Approved	KIAA0810, FLJ12407	uc021zym.1	O94901	OTTHUMG00000151426	ENST00000405266.1:c.1549C>A	7.37:g.897508C>A	ENSP00000384116:p.Leu517Met	Somatic		Capture	SOLID	Phase_IV	864034	A5PL20|B3KMV7|B4DZF7|B7WNY4|B7WP53|E9PDU4|E9PF23|F8WD13|Q96CZ7|Q9HA14|Q9UH98	Missense_Mutation	SNP	ENST00000405266.1	37		SNP	28	Baylor	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	4.985|4.985	0.183024|0.183024	0.09495|0.09495	.|.	.|.	ENSG00000164828|ENSG00000164828	ENST00000433212|ENST00000456758;ENST00000389574;ENST00000452783;ENST00000405266;ENST00000401592;ENST00000297445;ENST00000425407;ENST00000429178;ENST00000413514	.|T;T;T;T;T;T;T;T	.|0.23754	.|2.19;2.21;2.22;2.21;2.21;2.21;1.89;1.91	5.15|5.15	0.891|0.891	0.19224|0.19224	.|.	.|1.183060	.|0.05864	.|N	.|0.623484	T|T	0.20820|0.20820	0.0501|0.0501	L|L	0.36672|0.36672	1.1|1.1	0.09310|0.09310	N|N	1|1	.|B;B;B;B;B;P	.|0.35575	.|0.06;0.06;0.209;0.295;0.209;0.51	.|B;B;B;B;B;B	.|0.35770	.|0.027;0.044;0.066;0.091;0.045;0.21	T|T	0.29274|0.29274	-1.0017|-1.0017	5|10	.|0.48119	.|T	.|0.1	-0.8244|-0.8244	5.722|5.722	0.17992|0.17992	0.1309:0.5428:0.2539:0.0724|0.1309:0.5428:0.2539:0.0724	.|.	.|278;377;480;669;507;397	.|E7EP45;E9PDU4;E9PF23;A4D2Q0;O94901;O94901-5	.|.;.;.;.;SUN1_HUMAN;.	D|M	328|669;397;377;517;480;507;397;405;278	.|ENSP00000388743:L669M;ENSP00000374225:L397M;ENSP00000413439:L377M;ENSP00000384116:L517M;ENSP00000384015:L480M;ENSP00000392309:L397M;ENSP00000409909:L405M;ENSP00000389313:L278M	.|ENSP00000297445:L507M	A|L	+|+	2|1	0|2	SUN1|SUN1	864034|864034	0.000000|0.000000	0.05858|0.05858	0.004000|0.004000	0.12327|0.12327	0.003000|0.003000	0.03518|0.03518	-0.081000|-0.081000	0.11321|0.11321	0.246000|0.246000	0.21394|0.21394	-0.140000|-0.140000	0.14226|0.14226	GCT|CTG		0.567	SUN1-001	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000322566.1	NM_025154		Missense_Mutation
XPNPEP2	7512	hgsc.bcm.edu	37	X	128886141	128886141	+	Missense_Mutation	SNP	G	G	T			TCGA-13-0717-01	TCGA-13-0717-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chrX:128886141G>T	ENST00000371106.3	+	10	1029	c.837G>T	c.(835-837)aaG>aaT	p.K279N		NM_003399.5	NP_003390.4	O43895	XPP2_HUMAN	X-prolyl aminopeptidase (aminopeptidase P) 2, membrane-bound	279						anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)			endometrium(3)|kidney(3)|large_intestine(5)|liver(1)|lung(20)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	37						TTGCAAACAAGAGTCGCTTTA	0.527																																																0			X											101.0	92.0	95.0					X																	128886141		2203	4299	6502	128713822	SO:0001583	missense	7512			U90724	CCDS14613.1	Xq25	2008-02-05			ENSG00000122121	ENSG00000122121	3.4.11.9		12823	protein-coding gene	gene with protein product		300145				9375790, 9628831	Standard	NM_003399		Approved		uc004eut.1	O43895	OTTHUMG00000022373	ENST00000371106.3:c.837G>T	X.37:g.128886141G>T	ENSP00000360147:p.Lys279Asn	Somatic		Capture	SOLID	Phase_IV	128713822	A0AV16|O75994	Missense_Mutation	SNP	ENST00000371106.3	37	CCDS14613.1	SNP	33	Baylor	.	.	.	.	.	.	.	.	.	.	G	6.291	0.421798	0.11928	.	.	ENSG00000122121	ENST00000371106	T	0.74421	-0.84	5.78	3.01	0.34805	.	0.594266	0.19847	N	0.104728	T	0.57621	0.2066	L	0.38175	1.15	0.29158	N	0.877942	B	0.27166	0.17	B	0.21546	0.035	T	0.45323	-0.9269	10	0.18276	T	0.48	-13.8505	6.0396	0.19726	0.234:0.1348:0.6312:0.0	.	279	O43895	XPP2_HUMAN	N	279	ENSP00000360147:K279N	ENSP00000360147:K279N	K	+	3	2	XPNPEP2	128713822	0.725000	0.28048	0.984000	0.44739	0.501000	0.33797	0.991000	0.29654	0.591000	0.29711	0.529000	0.55759	AAG		0.527	XPNPEP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058210.1	NM_003399		Missense_Mutation
ZRANB1	54764	hgsc.bcm.edu	37	10	126673561	126673561	+	Stop_Codon_Del	DEL	A	A	-	rs74898717		TCGA-13-0717-01	TCGA-13-0717-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-13-0717-01	TCGA-13-0717-10	g.chr10:126673561delA	ENST00000359653.4	+	0	2498					NM_017580.2	NP_060050.2	Q9UGI0	ZRAN1_HUMAN	zinc finger, RAN-binding domain containing 1						cell migration (GO:0016477)|cytoskeleton organization (GO:0007010)|positive regulation of Wnt signaling pathway (GO:0030177)|protein deubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0071947)|protein K29-linked deubiquitination (GO:0035523)|protein K33-linked deubiquitination (GO:1990168)|protein K63-linked deubiquitination (GO:0070536)|regulation of cell morphogenesis (GO:0022604)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	K63-linked polyubiquitin binding (GO:0070530)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.*709fs?(1)		NS(1)|breast(1)|endometrium(5)|kidney(5)|large_intestine(2)|lung(3)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	23		all_lung(145;0.0132)|Lung NSC(174;0.0193)|all_neural(114;0.116)|Colorectal(57;0.172)		Colorectal(40;0.113)|COAD - Colon adenocarcinoma(40;0.119)		AAGATGAATGAAAAAAAAAAT	0.448																																																1	Deletion - Frameshift(1)	ovary(1)	10								287,34,3943		12,0,263,0,34,1823	26.0	25.0	26.0			4.2	1.0	10	dbSNP_132	26	912,64,7278		43,0,826,0,64,3194	no	codingComplex	ZRANB1	NM_017580.2		55,0,1089,0,98,5017	A1A1,A1A2,A1R,A2A2,A2R,RR		11.8246,7.5281,10.3611			126673561	1199,98,11221	2203	4300	6503	126663551	SO:0001567	stop_retained_variant	54764			AJ252060	CCDS7642.1	10q26.12	2014-02-24			ENSG00000019995	ENSG00000019995		"""Zinc fingers, RAN-binding domain containing"", ""OTU domain containing"""	18224	protein-coding gene	gene with protein product		611749				11463333	Standard	NM_017580		Approved	TRABID	uc001lic.3	Q9UGI0	OTTHUMG00000019223	Exception_encountered	10.37:g.126673561delA		Somatic		Capture	SOLID	Phase_IV	126663551	B4DZ98|D3DRF4|Q5SQP6|Q69YK3	Frame_Shift_Del	DEL	ENST00000359653.4	37	CCDS7642.1	DEL	9	Baylor																																																																																				0.448	ZRANB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050898.1	NM_017580		Frame_Shift_Del
