#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_EVS_AA	i_EVS_All	i_EVS_EA	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains_WU	i_amino_acid_change_WU	i_annotation_transcript	i_build	i_c_position_WU	i_ccds_id	i_chromosome_name_WU	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_default_gene_name_WU	i_deletion_substructures_WU	i_domain_WU	i_ensembl_gene_id	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_name_WU	i_gene_name_source_WU	i_gene_type	i_havana_transcript	i_normal_ref_reads	i_normal_vaf	i_normal_var_reads	i_reference_WU	i_refseq_mrna_id	i_secondary_variant_classification	i_start_WU	i_stop_WU	i_strand_WU	i_transcript_error_WU	i_transcript_name_WU	i_transcript_source_WU	i_transcript_species_WU	i_transcript_status_WU	i_transcript_version_WU	i_trv_type_WU	i_tumor_ref_reads	i_tumor_vaf	i_tumors_var_reads	i_type_WU	i_ucsc_cons_WU	i_variant_WU
C17orf102	400591	genome.wustl.edu	37	17	32906191	32906192	+	Missense_Mutation	DNP	CT	CT	TA			TCGA-BH-A0RX-01A-21D-A099-09	TCGA-BH-A0RX-10A-01D-A099-09	C|T	C|T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	48115e9a-5027-455a-a88e-c3d991dbf966	c99e4cec-5fc3-4dc9-9c38-b72dbea39d3f	g.chr17:32906191_32906192CT>TA	ENST00000357754.1	-	1	196_197	c.108_109AG>TA	c.(106-111)gtAGac>gtTAac	p.D37N	TMEM132E_ENST00000321639.5_5'Flank	NM_207454.2	NP_997337.2	A2RUQ5	CQ102_HUMAN	chromosome 17 open reading frame 102	37										central_nervous_system(1)|cervix(1)|large_intestine(3)|lung(3)|ovary(1)	9						GCGGTGGCGTCTACCCTGGAGA	0.658																																						dbGAP											0																																										-	-	-	SO:0001583	missense	0				CCDS42297.1	17q12	2009-02-11			ENSG00000197322	ENSG00000197322			34412	protein-coding gene	gene with protein product							Standard	NM_207454		Approved	FLJ44815	uc002hie.1	A2RUQ5	OTTHUMG00000156883	ENST00000357754.1:c.108_109delinsTA	17.37:g.32906191_32906192delinsTA	ENSP00000350392:p.Asp37Asn	Somatic		WXS	Illumina GAIIx	Phase_IV	A5PKX0|Q6ZTB3	Missense_Mutation|Silent	SNP	NULL	p.D37N|p.V36	ENST00000357754.1	37	c.109|c.108	CCDS42297.1	17																																																																																			C17orf102	-	NULL	ENSG00000197322		0.658	C17orf102-001	KNOWN	basic|appris_principal|CCDS	protein_coding	C17orf102	HGNC	protein_coding	OTTHUMT00000346435.1	29|28	0.00	0	C|T	NM_207454		32906191|32906192	32906191|32906192	-1	no_errors	ENST00000357754	ensembl	human	known	69_37n	missense|silent	19	24.00|23.08	6	SNP	0.231|0.001	T|A
CARD11	84433	genome.wustl.edu	37	7	2987388	2987388	+	Missense_Mutation	SNP	G	G	A			TCGA-BH-A0RX-01A-21D-A099-09	TCGA-BH-A0RX-10A-01D-A099-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	48115e9a-5027-455a-a88e-c3d991dbf966	c99e4cec-5fc3-4dc9-9c38-b72dbea39d3f	g.chr7:2987388G>A	ENST00000396946.4	-	3	444	c.41C>T	c.(40-42)aCg>aTg	p.T14M	AC004906.3_ENST00000423194.1_RNA	NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	14					Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|nucleotide phosphorylation (GO:0046939)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell proliferation (GO:0042102)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of T cell differentiation (GO:0045580)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|thymic T cell selection (GO:0045061)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)|guanylate kinase activity (GO:0004385)	p.T7M(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(62)|kidney(11)|large_intestine(13)|lung(31)|ovary(4)|prostate(5)|skin(7)|upper_aerodigestive_tract(2)	150		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		ATCCTTCAGCGTCTCCATGTA	0.512			Mis		DLBCL																																	dbGAP		Dom	yes		7	7p22	84433	"""caspase recruitment domain family, member 11"""		L	1	Substitution - Missense(1)	breast(1)											232.0	201.0	212.0					7																	2987388		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF322641	CCDS5336.2	7p22	2014-09-17			ENSG00000198286	ENSG00000198286			16393	protein-coding gene	gene with protein product	"""card-maguk protein 1"", ""bcl10-interacting maguk protein 3"""	607210				11278692, 11356195	Standard	NM_032415		Approved	CARMA1, BIMP3	uc003smv.3	Q9BXL7	OTTHUMG00000023023	ENST00000396946.4:c.41C>T	7.37:g.2987388G>A	ENSP00000380150:p.Thr14Met	Somatic		WXS	Illumina GAIIx	Phase_IV	A4D1Z7|Q2NKN7|Q548H3	Missense_Mutation	SNP	pfam_CARD,superfamily_DEATH-like,superfamily_PDZ,pfscan_CARD	p.T14M	ENST00000396946.4	37	c.41	CCDS5336.2	7	.	.	.	.	.	.	.	.	.	.	G	10.99	1.506643	0.26949	.	.	ENSG00000198286	ENST00000396946;ENST00000356408	T;T	0.58797	1.33;0.31	5.21	4.29	0.51040	.	0.099815	0.64402	D	0.000002	T	0.40595	0.1123	L	0.41824	1.3	0.45607	D	0.998544	P	0.43607	0.812	B	0.31191	0.125	T	0.40534	-0.9558	10	0.66056	D	0.02	-25.8846	8.3273	0.32165	0.0777:0.0:0.766:0.1564	.	14	Q9BXL7	CAR11_HUMAN	M	14	ENSP00000380150:T14M;ENSP00000348779:T14M	ENSP00000348779:T14M	T	-	2	0	CARD11	2953914	1.000000	0.71417	0.988000	0.46212	0.956000	0.61745	3.435000	0.52849	1.128000	0.42052	0.561000	0.74099	ACG	CARD11	-	NULL	ENSG00000198286		0.512	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	CARD11	HGNC	protein_coding	OTTHUMT00000059344.4	125	0.00	0	G	NM_032415		2987388	2987388	-1	no_errors	ENST00000396946	ensembl	human	known	69_37n	missense	136	13.92	22	SNP	0.982	A
CHRM4	1132	genome.wustl.edu	37	11	46406905	46406905	+	Silent	SNP	C	C	T	rs200209431		TCGA-BH-A0RX-01A-21D-A099-09	TCGA-BH-A0RX-10A-01D-A099-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	48115e9a-5027-455a-a88e-c3d991dbf966	c99e4cec-5fc3-4dc9-9c38-b72dbea39d3f	g.chr11:46406905C>T	ENST00000433765.2	-	1	1202	c.1203G>A	c.(1201-1203)acG>acA	p.T401T		NM_000741.2	NP_000732.2	P08173	ACM4_HUMAN	cholinergic receptor, muscarinic 4	401					adenylate cyclase-inhibiting G-protein coupled acetylcholine receptor signaling pathway (GO:0007197)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|regulation of locomotion (GO:0040012)|signal transduction (GO:0007165)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled acetylcholine receptor activity (GO:0016907)	p.T401T(1)		breast(1)|endometrium(7)|kidney(1)|large_intestine(1)|lung(6)|prostate(3)|skin(1)	20				GBM - Glioblastoma multiforme(35;0.0254)|Lung(87;0.14)	Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Aripiprazole(DB01238)|Atropine(DB00572)|Brompheniramine(DB00835)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cryptenamine(DB00785)|Darifenacin(DB00496)|Desipramine(DB01151)|Doxepin(DB01142)|Fesoterodine(DB06702)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Isopropamide(DB01625)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paroxetine(DB00715)|Pethidine(DB00454)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Tolterodine(DB01036)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Ziprasidone(DB00246)	TGGCAAAGATCGTTCGTGTCA	0.617																																					Esophageal Squamous(171;1020 1936 4566 30205 42542)	dbGAP											1	Substitution - coding silent(1)	breast(1)											107.0	110.0	109.0					11																	46406905		2199	4298	6497	-	-	-	SO:0001819	synonymous_variant	0			M16405	CCDS44581.1	11p12-p11.2	2012-08-08			ENSG00000180720	ENSG00000180720		"""Cholinergic receptors"", ""GPCR / Class A : Cholinergic receptors, muscarinic"""	1953	protein-coding gene	gene with protein product	"""acetylcholine receptor, muscarinic 4"""	118495				1577490	Standard	NM_000741		Approved		uc001nct.1	P08173	OTTHUMG00000154371	ENST00000433765.2:c.1203G>A	11.37:g.46406905C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	B2RPP4|Q0VD60|Q4VBK7	Silent	SNP	pfam_7TM_GPCR_Rhodpsn,pfam_7TM_GPCR_olfarory/Srsx,pfscan_GPCR_Rhodpsn_supfam,prints_Musac_rcpt,prints_7TM_GPCR_Rhodpsn,prints_Musac_M4_rcpt	p.T401	ENST00000433765.2	37	c.1203	CCDS44581.1	11																																																																																			CHRM4	-	pfam_7TM_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_supfam,prints_7TM_GPCR_Rhodpsn	ENSG00000180720		0.617	CHRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CHRM4	HGNC	protein_coding	OTTHUMT00000334985.1	93	0.00	0	C	NM_000741		46406905	46406905	-1	no_errors	ENST00000433765	ensembl	human	known	69_37n	silent	92	17.12	19	SNP	1.000	T
CYGB	114757	genome.wustl.edu	37	17	74527737	74527737	+	Silent	SNP	G	G	A			TCGA-BH-A0RX-01A-21D-A099-09	TCGA-BH-A0RX-10A-01D-A099-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	48115e9a-5027-455a-a88e-c3d991dbf966	c99e4cec-5fc3-4dc9-9c38-b72dbea39d3f	g.chr17:74527737G>A	ENST00000293230.5	-	2	542	c.180C>T	c.(178-180)ttC>ttT	p.F60F	CYGB_ENST00000589342.1_Silent_p.F60F|PRCD_ENST00000592432.1_Intron|CYGB_ENST00000589145.1_5'UTR|CYGB_ENST00000590175.1_5'UTR|CYGB_ENST00000586160.1_5'Flank	NM_134268.4	NP_599030.1	Q8WWM9	CYGB_HUMAN	cytoglobin	60	Globin.				oxidation-reduction process (GO:0055114)|oxygen transport (GO:0015671)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|oxygen transporter activity (GO:0005344)|peroxidase activity (GO:0004601)	p.F60F(1)		breast(1)|endometrium(2)|large_intestine(1)|lung(2)|ovary(1)	7						TGAACTGGCTGAAGTACTGCT	0.627																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											55.0	58.0	57.0					17																	74527737		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AJ315162	CCDS11746.1	17q25	2008-07-18				ENSG00000161544			16505	protein-coding gene	gene with protein product	"""stellate cell activation-associated protein"", ""histoglobin"""	608759				11919282	Standard	NM_134268		Approved	HGB, STAP	uc002jru.2	Q8WWM9		ENST00000293230.5:c.180C>T	17.37:g.74527737G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	Q541Y7|Q8N2X5	Silent	SNP	pfam_Globin,superfamily_Globin-like,pfscan_Globin,prints_Globin_lamprey/hagfish,prints_Myoglobin	p.F60	ENST00000293230.5	37	c.180	CCDS11746.1	17																																																																																			CYGB	-	pfam_Globin,superfamily_Globin-like,pfscan_Globin,prints_Globin_lamprey/hagfish,prints_Myoglobin	ENSG00000161544		0.627	CYGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CYGB	HGNC	protein_coding	OTTHUMT00000450590.1	68	0.00	0	G	NM_134268		74527737	74527737	-1	no_errors	ENST00000293230	ensembl	human	known	69_37n	silent	115	16.67	23	SNP	1.000	A
SDCBPP2	100129960	genome.wustl.edu	37	8	70856514	70856514	+	IGR	DEL	T	T	-	rs369639024		TCGA-BH-A0RX-01A-21D-A099-09	TCGA-BH-A0RX-10A-01D-A099-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	48115e9a-5027-455a-a88e-c3d991dbf966	c99e4cec-5fc3-4dc9-9c38-b72dbea39d3f	g.chr8:70856514delT								AC090574.1 (5879 upstream) : PRDM14 (107371 downstream)																							ATCTTTGAACttttttttttt	0.433																																						dbGAP											0																																										-	-	-	SO:0001628	intergenic_variant	0																															8.37:g.70856514delT		Somatic		WXS	Illumina GAIIx	Phase_IV		Splice_Site	DEL	-	NULL		37	c.NULL		8																																																																																			RP11-449M6.1	-	-	ENSG00000247570	0	0.433					ENSG00000247570	Clone_based_vega_gene			12	0.00	0	T			70856514	70856514	+1	no_coding_region:pseudogene	ENST00000424643	ensembl	human	known	69_37n	splice_site_del	34	12.20	5	DEL	0.228	-
FAM117B	150864	genome.wustl.edu	37	2	203591033	203591036	+	Frame_Shift_Del	DEL	AAAG	AAAG	-			TCGA-BH-A0RX-01A-21D-A099-09	TCGA-BH-A0RX-10A-01D-A099-09	AAAG	AAAG					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	48115e9a-5027-455a-a88e-c3d991dbf966	c99e4cec-5fc3-4dc9-9c38-b72dbea39d3f	g.chr2:203591033_203591036delAAAG	ENST00000392238.2	+	4	907_910	c.907_910delAAAG	c.(907-912)aaagaafs	p.KE303fs	FAM117B_ENST00000303116.6_Frame_Shift_Del_p.KE59fs			Q6P1L5	F117B_HUMAN	family with sequence similarity 117, member B	303								p.E60fs*27(1)|p.E304fs*27(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(4)|lung(5)|ovary(1)	17						TCATCGAGATAAAGAAAGACAGTC	0.397																																						dbGAP											2	Deletion - Frameshift(2)	breast(2)																																								-	-	-	SO:0001589	frameshift_variant	0			AB053315	CCDS33362.1, CCDS33362.2	2q33	2008-08-18	2008-08-18	2008-08-18	ENSG00000138439	ENSG00000138439			14440	protein-coding gene	gene with protein product			"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 13"""	ALS2CR13		11586298	Standard	NM_173511		Approved	FLJ38771	uc010zhx.2	Q6P1L5	OTTHUMG00000154550	ENST00000392238.2:c.907_910delAAAG	2.37:g.203591037_203591040delAAAG	ENSP00000376071:p.Lys303fs	Somatic		WXS	Illumina GAIIx	Phase_IV	Q53QZ5|Q585T9|Q8N8W1|Q96Q34	Frame_Shift_Del	DEL	NULL	p.E304fs	ENST00000392238.2	37	c.907_910	CCDS33362.2	2																																																																																			FAM117B	-	NULL	ENSG00000138439		0.397	FAM117B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	FAM117B	HGNC	protein_coding	OTTHUMT00000335888.3	85	0.00	0	AAAG	NM_173511		203591033	203591036	+1	no_errors	ENST00000392238	ensembl	human	known	69_37n	frame_shift_del	117	10.00	13	DEL	1.000:1.000:1.000:1.000	-
FAM53C	51307	genome.wustl.edu	37	5	137681156	137681162	+	Frame_Shift_Del	DEL	GGCGACC	GGCGACC	-	rs535078590	byFrequency	TCGA-BH-A0RX-01A-21D-A099-09	TCGA-BH-A0RX-10A-01D-A099-09	GGCGACC	GGCGACC					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	48115e9a-5027-455a-a88e-c3d991dbf966	c99e4cec-5fc3-4dc9-9c38-b72dbea39d3f	g.chr5:137681156_137681162delGGCGACC	ENST00000239906.5	+	4	1207_1213	c.779_785delGGCGACC	c.(778-786)tggcgacctfs	p.WRP260fs	RP11-256P1.1_ENST00000504539.1_RNA|FAM53C_ENST00000434981.2_Frame_Shift_Del_p.WRP260fs|FAM53C_ENST00000513056.1_Frame_Shift_Del_p.GDL70fs	NM_016605.2	NP_057689.1	Q9NYF3	FA53C_HUMAN	family with sequence similarity 53, member C	260								p.W260fs*44(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			GAGCTGCCCTGGCGACCTCGAGGTCTC	0.681																																						dbGAP											1	Deletion - Frameshift(1)	breast(1)																																								-	-	-	SO:0001589	frameshift_variant	0			AF251040	CCDS4204.1	5q31	2008-02-05	2004-11-24	2004-11-26	ENSG00000120709	ENSG00000120709			1336	protein-coding gene	gene with protein product		609372	"""chromosome 5 open reading frame 6"""	C5orf6		11087669, 11161817	Standard	NM_001135647		Approved		uc003lcv.3	Q9NYF3	OTTHUMG00000129201	ENST00000239906.5:c.779_785delGGCGACC	5.37:g.137681156_137681162delGGCGACC	ENSP00000239906:p.Trp260fs	Somatic		WXS	Illumina GAIIx	Phase_IV	B2RDJ5|D3DQB9	Frame_Shift_Del	DEL	NULL	p.W260fs	ENST00000239906.5	37	c.779_785	CCDS4204.1	5																																																																																			FAM53C	-	NULL	ENSG00000120709		0.681	FAM53C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FAM53C	HGNC	protein_coding	OTTHUMT00000251278.2	39	0.00	0	GGCGACC	NM_016605		137681156	137681162	+1	no_errors	ENST00000239906	ensembl	human	known	69_37n	frame_shift_del	48	18.64	11	DEL	1.000:1.000:1.000:1.000:1.000:1.000:0.793	-
HELB	92797	genome.wustl.edu	37	12	66717817	66717817	+	Missense_Mutation	SNP	G	G	T			TCGA-BH-A0RX-01A-21D-A099-09	TCGA-BH-A0RX-10A-01D-A099-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	48115e9a-5027-455a-a88e-c3d991dbf966	c99e4cec-5fc3-4dc9-9c38-b72dbea39d3f	g.chr12:66717817G>T	ENST00000247815.4	+	10	2411	c.2352G>T	c.(2350-2352)agG>agT	p.R784S		NM_033647.3	NP_387467.2	Q8NG08	HELB_HUMAN	helicase (DNA) B	784					DNA duplex unwinding (GO:0032508)|DNA replication (GO:0006260)|DNA replication, synthesis of RNA primer (GO:0006269)		ATP binding (GO:0005524)|ATP-dependent 5'-3' DNA helicase activity (GO:0043141)|single-stranded DNA-dependent ATP-dependent DNA helicase activity (GO:0017116)	p.R784S(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(15)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	40			GBM - Glioblastoma multiforme(2;0.000142)	GBM - Glioblastoma multiforme(28;0.0265)		GTTGTACCAGGAATGCATACC	0.368																																						dbGAP											1	Substitution - Missense(1)	breast(1)											140.0	155.0	150.0					12																	66717817		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF319995	CCDS8976.1	12q14.2	2009-01-15			ENSG00000127311	ENSG00000127311			17196	protein-coding gene	gene with protein product		614539				12181327	Standard	NM_033647		Approved		uc001sti.3	Q8NG08	OTTHUMG00000169006	ENST00000247815.4:c.2352G>T	12.37:g.66717817G>T	ENSP00000247815:p.Arg784Ser	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K4C9|Q4G0T2|Q9H7L5	Missense_Mutation	SNP	NULL	p.R784S	ENST00000247815.4	37	c.2352	CCDS8976.1	12	.	.	.	.	.	.	.	.	.	.	G	12.62	1.991408	0.35131	.	.	ENSG00000127311	ENST00000247815	T	0.17528	2.27	5.2	2.21	0.28008	.	0.467999	0.22121	N	0.064326	T	0.34454	0.0898	M	0.91920	3.255	0.34076	D	0.659066	P	0.50819	0.939	P	0.51324	0.666	T	0.52749	-0.8534	9	.	.	.	-8.3686	6.3976	0.21620	0.2452:0.1317:0.6231:0.0	.	784	Q8NG08	HELB_HUMAN	S	784	ENSP00000247815:R784S	.	R	+	3	2	HELB	65004084	0.998000	0.40836	0.987000	0.45799	0.129000	0.20672	0.893000	0.28336	0.612000	0.30071	-0.345000	0.07892	AGG	HELB	-	NULL	ENSG00000127311		0.368	HELB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HELB	HGNC	protein_coding	OTTHUMT00000401919.1	90	0.00	0	G			66717817	66717817	+1	no_errors	ENST00000247815	ensembl	human	known	69_37n	missense	154	14.36	26	SNP	0.991	T
ITPR3	3710	genome.wustl.edu	37	6	33655053	33655053	+	Silent	SNP	G	G	A			TCGA-BH-A0RX-01A-21D-A099-09	TCGA-BH-A0RX-10A-01D-A099-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	48115e9a-5027-455a-a88e-c3d991dbf966	c99e4cec-5fc3-4dc9-9c38-b72dbea39d3f	g.chr6:33655053G>A	ENST00000374316.5	+	46	7186	c.6126G>A	c.(6124-6126)tcG>tcA	p.S2042S	ITPR3_ENST00000605930.1_Silent_p.S2042S			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	2042					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)	inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)	p.S2042S(2)		NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85					Caffeine(DB00201)	GTGAGAACTCGGAGGTGAGCC	0.607																																						dbGAP											2	Substitution - coding silent(2)	breast(2)											72.0	61.0	65.0					6																	33655053		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			D26351	CCDS4783.1	6p21.31	2011-11-24	2011-04-28		ENSG00000096433	ENSG00000096433		"""Ion channels / Inositol triphosphate receptors"""	6182	protein-coding gene	gene with protein product		147267	"""inositol 1,4,5-triphosphate receptor, type 3"""			8081734, 8288584	Standard	NM_002224		Approved	IP3R3	uc021ywr.1	Q14573	OTTHUMG00000014532	ENST00000374316.5:c.6126G>A	6.37:g.33655053G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	Q14649|Q5TAQ2	Silent	SNP	pfam_Ca-rel_channel,pfam_Ins145_P3_rcpt,pfam_MIR,pfam_RIH_assoc-dom,pfam_Ion_trans_dom,superfamily_MIR,superfamily_ARM-type_fold,smart_MIR_motif,pfscan_MIR_motif,prints_InsP3_rcpt-bd	p.S2042	ENST00000374316.5	37	c.6126	CCDS4783.1	6																																																																																			ITPR3	-	NULL	ENSG00000096433		0.607	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ITPR3	HGNC	protein_coding	OTTHUMT00000040204.2	62	0.00	0	G	NM_002224		33655053	33655053	+1	no_errors	ENST00000374316	ensembl	human	known	69_37n	silent	59	16.90	12	SNP	0.003	A
MUC6	4588	genome.wustl.edu	37	11	1019367	1019368	+	Frame_Shift_Del	DEL	GC	GC	-	rs373080345		TCGA-BH-A0RX-01A-21D-A099-09	TCGA-BH-A0RX-10A-01D-A099-09	GC	GC					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	48115e9a-5027-455a-a88e-c3d991dbf966	c99e4cec-5fc3-4dc9-9c38-b72dbea39d3f	g.chr11:1019367_1019368delGC	ENST00000421673.2	-	30	3987_3988	c.3937_3938delGC	c.(3937-3939)gccfs	p.A1313fs		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1313	Pro-rich.|Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)	p.A1313fs*83(2)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GGCTGGGCTGGCGGTCGACGCC	0.624																																						dbGAP											2	Deletion - Frameshift(2)	breast(2)																																								-	-	-	SO:0001589	frameshift_variant	0			U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.3937_3938delGC	11.37:g.1019367_1019368delGC	ENSP00000406861:p.Ala1313fs	Somatic		WXS	Illumina GAIIx	Phase_IV	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Frame_Shift_Del	DEL	pfam_VWF_type-D,pfam_Unchr_dom_Cys-rich,pfam_TIL_dom,superfamily_TIL_dom,smart_VWF_type-D,smart_Unchr_dom_Cys-rich,smart_VWC_out,smart_Cys_knot_C,pfscan_Cys_knot_C	p.A1313fs	ENST00000421673.2	37	c.3938_3937	CCDS44513.1	11																																																																																			MUC6	-	NULL	ENSG00000184956		0.624	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MUC6	HGNC	protein_coding	OTTHUMT00000382120.2	293	0.00	0	GC	XM_290540		1019367	1019368	-1	no_errors	ENST00000421673	ensembl	human	known	69_37n	frame_shift_del	277	11.11	35	DEL	0.002:0.000	-
PCNX	22990	genome.wustl.edu	37	14	71543011	71543011	+	Missense_Mutation	SNP	G	G	A			TCGA-BH-A0RX-01A-21D-A099-09	TCGA-BH-A0RX-10A-01D-A099-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	48115e9a-5027-455a-a88e-c3d991dbf966	c99e4cec-5fc3-4dc9-9c38-b72dbea39d3f	g.chr14:71543011G>A	ENST00000304743.2	+	28	5658	c.5212G>A	c.(5212-5214)Gtg>Atg	p.V1738M	PCNX_ENST00000238570.5_Missense_Mutation_p.V1666M|PCNX_ENST00000439984.3_Missense_Mutation_p.V1627M	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	1738						integral component of membrane (GO:0016021)		p.V1738M(1)		NS(2)|biliary_tract(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(14)|liver(2)|lung(40)|ovary(1)|prostate(7)|skin(2)|urinary_tract(1)	87			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)		TTATGTCGATGTGGACCCGAC	0.448																																						dbGAP											1	Substitution - Missense(1)	breast(1)											179.0	156.0	164.0					14																	71543011		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF233450, AB018348	CCDS9806.1	14q24.2	2014-07-03							19740	protein-coding gene	gene with protein product			"""pecanex-like 1 (Drosophila)"""	PCNXL1		9244429, 15777640	Standard	NM_014982		Approved	KIAA0995, KIAA0805, pecanex	uc001xmo.2	Q96RV3		ENST00000304743.2:c.5212G>A	14.37:g.71543011G>A	ENSP00000304192:p.Val1738Met	Somatic		WXS	Illumina GAIIx	Phase_IV	B2RTR6|O94897|Q96AI7|Q9Y2J9	Missense_Mutation	SNP	pfam_Pecanex	p.V1738M	ENST00000304743.2	37	c.5212	CCDS9806.1	14	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.31|16.31	3.086655|3.086655	0.55861|0.55861	.|.	.|.	ENSG00000100731|ENSG00000100731	ENST00000554691|ENST00000304743;ENST00000238570;ENST00000439984	.|T;T;T	.|0.10763	.|3.28;3.3;2.84	5.11|5.11	5.11|5.11	0.69529|0.69529	.|.	.|0.124720	.|0.56097	.|D	.|0.000039	T|T	0.18045|0.18045	0.0433|0.0433	L|L	0.48642|0.48642	1.525|1.525	0.28141|0.28141	N|N	0.929784|0.929784	.|P;D;P	.|0.55172	.|0.919;0.97;0.949	.|P;P;B	.|0.49361	.|0.51;0.608;0.443	T|T	0.01930|0.01930	-1.1245|-1.1245	5|10	.|0.33141	.|T	.|0.24	.|.	19.0887|19.0887	0.93217|0.93217	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1666;1627;1738	.|Q96RV3-3;B2RTR6;Q96RV3	.|.;.;PCX1_HUMAN	I|M	724|1738;1666;1627	.|ENSP00000304192:V1738M;ENSP00000238570:V1666M;ENSP00000396617:V1627M	.|ENSP00000238570:V1666M	M|V	+|+	3|1	0|0	PCNX|PCNX	70612764|70612764	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.338000|0.338000	0.28826|0.28826	3.058000|3.058000	0.49939|0.49939	2.826000|2.826000	0.97356|0.97356	0.655000|0.655000	0.94253|0.94253	ATG|GTG	PCNX	-	NULL	ENSG00000100731		0.448	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PCNX	HGNC	protein_coding	OTTHUMT00000412479.1	88	0.00	0	G	NM_014982		71543011	71543011	+1	no_errors	ENST00000304743	ensembl	human	known	69_37n	missense	88	16.19	17	SNP	1.000	A
POLR3C	10623	genome.wustl.edu	37	1	145608467	145608467	+	Missense_Mutation	SNP	C	C	T			TCGA-BH-A0RX-01A-21D-A099-09	TCGA-BH-A0RX-10A-01D-A099-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	48115e9a-5027-455a-a88e-c3d991dbf966	c99e4cec-5fc3-4dc9-9c38-b72dbea39d3f	g.chr1:145608467C>T	ENST00000334163.3	-	3	500	c.340G>A	c.(340-342)Ggc>Agc	p.G114S	POLR3C_ENST00000369294.1_Missense_Mutation_p.G114S|RNF115_ENST00000369291.5_5'Flank|POLR3C_ENST00000471254.1_5'UTR	NM_006468.6	NP_006459.3	Q9BUI4	RPC3_HUMAN	polymerase (RNA) III (DNA directed) polypeptide C (62kD)	114					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)	p.G114S(1)		breast(2)|endometrium(4)|kidney(1)|large_intestine(3)|liver(1)|lung(8)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)		Epithelial(2;7.55e-13)			GTCAGTTTGCCGTTCAACAGA	0.468																																						dbGAP											1	Substitution - Missense(1)	breast(1)											127.0	111.0	116.0					1																	145608467		2203	4300	6503	-	-	-	SO:0001583	missense	0			AJ238234	CCDS72864.1	1q21	2013-01-21			ENSG00000186141	ENSG00000186141		"""RNA polymerase subunits"""	30076	protein-coding gene	gene with protein product						9171375, 12391170	Standard	NM_006468		Approved	RPC62, RPC3	uc001eoh.3	Q9BUI4	OTTHUMG00000013753	ENST00000334163.3:c.340G>A	1.37:g.145608467C>T	ENSP00000334564:p.Gly114Ser	Somatic		WXS	Illumina GAIIx	Phase_IV	O15317|Q9Y3R6	Missense_Mutation	SNP	pfam_RNA_pol_III_Rpc82_C,pfam_RNA_pol_III_RPC82-rel_HTH	p.G114S	ENST00000334163.3	37	c.340	CCDS921.1	1	.	.	.	.	.	.	.	.	.	.	C	28.0	4.885405	0.91814	.	.	ENSG00000186141	ENST00000334163;ENST00000369294	T;T	0.77098	-1.07;-0.99	4.89	4.89	0.63831	.	0.000000	0.85682	D	0.000000	D	0.85444	0.5698	M	0.75264	2.295	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.975;0.993;0.999	D	0.87083	0.2167	10	0.87932	D	0	-14.2101	15.5812	0.76445	0.0:1.0:0.0:0.0	.	114;114;114	E9PHH9;Q9BUI4;Q53F76	.;RPC3_HUMAN;.	S	114	ENSP00000334564:G114S;ENSP00000358300:G114S	ENSP00000334564:G114S	G	-	1	0	POLR3C	144319824	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	7.059000	0.76684	2.530000	0.85305	0.655000	0.94253	GGC	POLR3C	-	NULL	ENSG00000186141		0.468	POLR3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	POLR3C	HGNC	protein_coding	OTTHUMT00000038542.1	89	0.00	0	C	NM_006468		145608467	145608467	-1	no_errors	ENST00000334163	ensembl	human	known	69_37n	missense	133	14.19	22	SNP	1.000	T
SEMA3E	9723	genome.wustl.edu	37	7	82997122	82997122	+	Missense_Mutation	SNP	G	G	A	rs121918341		TCGA-BH-A0RX-01A-21D-A099-09	TCGA-BH-A0RX-10A-01D-A099-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	48115e9a-5027-455a-a88e-c3d991dbf966	c99e4cec-5fc3-4dc9-9c38-b72dbea39d3f	g.chr7:82997122G>A	ENST00000307792.3	-	17	2575	c.2108C>T	c.(2107-2109)tCg>tTg	p.S703L	SEMA3E_ENST00000427262.1_Missense_Mutation_p.S643L	NM_012431.2	NP_036563.1	O15041	SEM3E_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	703					axon guidance (GO:0007411)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell-matrix adhesion (GO:0001953)|patterning of blood vessels (GO:0001569)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell shape (GO:0008360)|semaphorin-plexin signaling pathway (GO:0071526)|sprouting angiogenesis (GO:0002040)|synapse organization (GO:0050808)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	receptor activity (GO:0004872)	p.S703L(1)		breast(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(19)|ovary(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	51		Medulloblastoma(109;0.109)				TGCTCCCTGCGAGATGCTACT	0.478																																						dbGAP											1	Substitution - Missense(1)	breast(1)	GRCh37	CM041830	SEMA3E	M	rs121918341						140.0	123.0	129.0					7																	82997122		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB002329	CCDS34674.1, CCDS55121.1	7q21.11	2013-01-11			ENSG00000170381	ENSG00000170381		"""Semaphorins"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10727	protein-coding gene	gene with protein product	"""M-sema H"""	608166		SEMAH		9205841, 9515811	Standard	NM_012431		Approved	M-SemaK, KIAA0331, coll-5	uc003uhy.2	O15041	OTTHUMG00000154693	ENST00000307792.3:c.2108C>T	7.37:g.82997122G>A	ENSP00000303212:p.Ser703Leu	Somatic		WXS	Illumina GAIIx	Phase_IV	B4E1P1|Q75M94|Q75M97	Missense_Mutation	SNP	pfam_Semaphorin/CD100_Ag,pfam_Immunoglobulin,pfam_Ig_V-set,superfamily_Semaphorin/CD100_Ag,superfamily_Plexin-like_fold,smart_Semaphorin/CD100_Ag,smart_Plexin-like,pfscan_Semaphorin/CD100_Ag,pfscan_Ig-like	p.S703L	ENST00000307792.3	37	c.2108	CCDS34674.1	7	.	.	.	.	.	.	.	.	.	.	G	3.481	-0.105945	0.06924	.	.	ENSG00000170381	ENST00000307792;ENST00000427262;ENST00000541514	T;T	0.75050	-0.9;-0.9	5.74	4.86	0.63082	.	2.507260	0.01570	N	0.020549	T	0.67795	0.2931	N	0.19112	0.55	0.09310	A	1.26061e-07	B	0.06786	0.001	B	0.06405	0.002	T	0.50882	-0.8775	9	0.32370	T	0.25	.	14.8685	0.70437	0.0689:0.0:0.9311:0.0	.	703	O15041	SEM3E_HUMAN	L	703;643;703	ENSP00000303212:S703L;ENSP00000405052:S643L	ENSP00000303212:S703L	S	-	2	0	SEMA3E	82835058	0.906000	0.30813	0.002000	0.10522	0.027000	0.11550	4.721000	0.61951	1.440000	0.47531	0.585000	0.79938	TCG	SEMA3E	-	NULL	ENSG00000170381		0.478	SEMA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SEMA3E	HGNC	protein_coding	OTTHUMT00000336606.1	73	0.00	0	G	NM_012431		82997122	82997122	-1	no_errors	ENST00000307792	ensembl	human	known	69_37n	missense	75	12.79	11	SNP	0.044	A
SPATA18	132671	genome.wustl.edu	37	4	52946023	52946023	+	Missense_Mutation	SNP	G	G	C	rs79854970	byFrequency	TCGA-BH-A0RX-01A-21D-A099-09	TCGA-BH-A0RX-10A-01D-A099-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	48115e9a-5027-455a-a88e-c3d991dbf966	c99e4cec-5fc3-4dc9-9c38-b72dbea39d3f	g.chr4:52946023G>C	ENST00000295213.4	+	9	1667	c.1293G>C	c.(1291-1293)caG>caC	p.Q431H	SPATA18_ENST00000419395.2_Missense_Mutation_p.Q399H	NM_145263.2	NP_660306.1	Q8TC71	MIEAP_HUMAN	spermatogenesis associated 18	431					cellular response to DNA damage stimulus (GO:0006974)|mitochondrial protein catabolic process (GO:0035694)|mitochondrion degradation by induced vacuole formation (GO:0035695)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial outer membrane (GO:0005741)				breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41			GBM - Glioblastoma multiforme(4;1.77e-13)|LUSC - Lung squamous cell carcinoma(32;0.00204)			TTGCAATGCAGGCCTTAGAAC	0.428																																						dbGAP											0													245.0	230.0	235.0					4																	52946023		2203	4300	6503	-	-	-	SO:0001583	missense	0			BC025396	CCDS3489.1, CCDS75124.1	4q11	2012-01-23	2012-01-23		ENSG00000163071	ENSG00000163071			29579	protein-coding gene	gene with protein product		612814	"""spermatogenesis associated 18 homolog (rat)"""			21300779	Standard	XR_245253		Approved	FLJ32906	uc003gzl.3	Q8TC71	OTTHUMG00000128698	ENST00000295213.4:c.1293G>C	4.37:g.52946023G>C	ENSP00000295213:p.Gln431His	Somatic		WXS	Illumina GAIIx	Phase_IV	B4E2R0|E5RLK1|Q8IY48|Q8N7D7	Missense_Mutation	SNP	NULL	p.Q431H	ENST00000295213.4	37	c.1293	CCDS3489.1	4	.	.	.	.	.	.	.	.	.	.	G	13.79	2.341173	0.41498	.	.	ENSG00000163071	ENST00000295213;ENST00000419395	T;T	0.35789	1.3;1.29	5.35	4.42	0.53409	.	0.000000	0.85682	D	0.000000	T	0.55210	0.1906	M	0.63843	1.955	0.52099	D	0.999941	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.87578	0.998;0.998;0.997	T	0.58255	-0.7668	10	0.87932	D	0	-23.743	11.4801	0.50320	0.0941:0.0:0.9059:0.0	.	399;431;431	Q8TC71-2;Q8TC71;Q96M13	.;MIEAP_HUMAN;.	H	431;399	ENSP00000295213:Q431H;ENSP00000415309:Q399H	ENSP00000295213:Q431H	Q	+	3	2	SPATA18	52640780	1.000000	0.71417	0.973000	0.42090	0.534000	0.34807	2.019000	0.41001	1.332000	0.45431	0.655000	0.94253	CAG	SPATA18	-	NULL	ENSG00000163071		0.428	SPATA18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SPATA18	HGNC	protein_coding	OTTHUMT00000250597.2	69	0.00	0	G	NM_145263		52946023	52946023	+1	no_errors	ENST00000295213	ensembl	human	known	69_37n	missense	114	11.54	15	SNP	1.000	C
ST18	9705	genome.wustl.edu	37	8	53038615	53038615	+	Missense_Mutation	SNP	C	C	T			TCGA-BH-A0RX-01A-21D-A099-09	TCGA-BH-A0RX-10A-01D-A099-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	48115e9a-5027-455a-a88e-c3d991dbf966	c99e4cec-5fc3-4dc9-9c38-b72dbea39d3f	g.chr8:53038615C>T	ENST00000276480.7	-	23	3435	c.2752G>A	c.(2752-2754)Ggg>Agg	p.G918R		NM_014682.2	NP_055497.1	O60284	ST18_HUMAN	suppression of tumorigenicity 18, zinc finger	918					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.G918W(1)|p.G918R(1)		NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(14)|lung(38)|ovary(4)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	85		Lung NSC(129;0.131)|all_epithelial(80;0.217)|all_lung(136;0.229)				CTCTTACCCCCAGTTGCTTTG	0.493																																						dbGAP											2	Substitution - Missense(2)	lung(1)|breast(1)											188.0	145.0	160.0					8																	53038615		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB011107	CCDS6149.1	8q11.23	2014-03-24	2014-03-24	2002-12-13	ENSG00000147488	ENSG00000147488		"""Zinc fingers, C2HC-type containing"""	18695	protein-coding gene	gene with protein product	"""neural zinc finger transcription factor 3"""		"""zinc finger protein 387"", ""suppression of tumorigenicity 18 (breast carcinoma) (zinc finger protein)"""	ZNF387		15489893	Standard	NM_014682		Approved	KIAA0535, ZC2HC10, NZF3	uc003xra.2	O60284	OTTHUMG00000164233	ENST00000276480.7:c.2752G>A	8.37:g.53038615C>T	ENSP00000276480:p.Gly918Arg	Somatic		WXS	Illumina GAIIx	Phase_IV	Q17RY1	Missense_Mutation	SNP	pfam_Myelin_TF,pfam_Znf_C2HC	p.G918R	ENST00000276480.7	37	c.2752	CCDS6149.1	8	.	.	.	.	.	.	.	.	.	.	C	16.69	3.193738	0.58017	.	.	ENSG00000147488	ENST00000276480	T	0.41065	1.01	5.78	5.78	0.91487	.	0.100668	0.64402	D	0.000001	T	0.44307	0.1287	N	0.08118	0	0.43835	D	0.996419	D	0.67145	0.996	D	0.63283	0.913	T	0.46247	-0.9205	10	0.30854	T	0.27	.	20.0067	0.97435	0.0:1.0:0.0:0.0	.	918	O60284	ST18_HUMAN	R	918	ENSP00000276480:G918R	ENSP00000276480:G918R	G	-	1	0	ST18	53201168	1.000000	0.71417	0.858000	0.33744	0.186000	0.23388	5.365000	0.66116	2.731000	0.93534	0.650000	0.86243	GGG	ST18	-	NULL	ENSG00000147488		0.493	ST18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ST18	HGNC	protein_coding	OTTHUMT00000377867.1	92	0.00	0	C			53038615	53038615	-1	no_errors	ENST00000276480	ensembl	human	known	69_37n	missense	172	17.31	36	SNP	0.993	T
TFDP1	7027	genome.wustl.edu	37	13	114292199	114292199	+	Missense_Mutation	SNP	G	G	T			TCGA-BH-A0RX-01A-21D-A099-09	TCGA-BH-A0RX-10A-01D-A099-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	48115e9a-5027-455a-a88e-c3d991dbf966	c99e4cec-5fc3-4dc9-9c38-b72dbea39d3f	g.chr13:114292199G>T	ENST00000375370.5	+	11	1285	c.1073G>T	c.(1072-1074)aGg>aTg	p.R358M	TFDP1_ENST00000544902.1_Missense_Mutation_p.R329M|TFDP1_ENST00000538138.1_Splice_Site_p.S263I	NM_007111.4	NP_009042.1	Q14186	TFDP1_HUMAN	transcription factor Dp-1	358					anoikis (GO:0043276)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|epidermis development (GO:0008544)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|intrinsic apoptotic signaling pathway (GO:0097193)|mitotic cell cycle (GO:0000278)|Notch signaling pathway (GO:0007219)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA biosynthetic process (GO:2000278)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)	p.R358M(1)		breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(10)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	26	Lung NSC(43;0.0113)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.132)|all_epithelial(44;0.0731)|all_lung(25;0.149)|Breast(118;0.153)	all cancers(43;0.0576)			AACGGCACAAGGTTCTCTGCC	0.587										TSP Lung(29;0.18)																												dbGAP											1	Substitution - Missense(1)	breast(1)											113.0	99.0	104.0					13																	114292199		2203	4300	6503	-	-	-	SO:0001583	missense	0			BC011685	CCDS9538.1	13q34	2008-07-18			ENSG00000198176	ENSG00000198176			11749	protein-coding gene	gene with protein product		189902				8413592, 9027491	Standard	NM_007111		Approved	Dp-1, DRTF1, DP1	uc001vtw.3	Q14186	OTTHUMG00000017388	ENST00000375370.5:c.1073G>T	13.37:g.114292199G>T	ENSP00000364519:p.Arg358Met	Somatic		WXS	Illumina GAIIx	Phase_IV	B4DLQ9|Q5JSB4|Q8IZL5	Missense_Mutation	SNP	pfam_Transc_factor_DP_C,pfam_E2F_TDP,pirsf_Transcription_factor_DP_subgr	p.R358M	ENST00000375370.5	37	c.1073	CCDS9538.1	13	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.89|12.89	2.074092|2.074092	0.36566|0.36566	.|.	.|.	ENSG00000198176|ENSG00000198176	ENST00000375370;ENST00000544902|ENST00000538138	T;T|T	0.54479|0.45276	1.9;0.57|0.9	4.64|4.64	3.79|3.79	0.43588|0.43588	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.42337|0.42337	0.1198|0.1198	M|M	0.70275|0.70275	2.135|2.135	0.33650|0.33650	D|D	0.608404|0.608404	D;D|P	0.71674|0.39282	0.998;0.981|0.666	P;P|B	0.61658|0.36885	0.892;0.635|0.235	T|T	0.59888|0.59888	-0.7369|-0.7369	10|9	0.46703|0.54805	T|T	0.11|0.06	.|.	11.8725|11.8725	0.52529|0.52529	0.0857:0.0:0.9143:0.0|0.0857:0.0:0.9143:0.0	.|.	329;358|263	F5H452;Q14186|B4DLQ9	.;TFDP1_HUMAN|.	M|I	358;329|263	ENSP00000364519:R358M;ENSP00000438450:R329M|ENSP00000443878:S263I	ENSP00000364519:R358M|ENSP00000443878:S263I	R|S	+|+	2|2	0|0	TFDP1|TFDP1	113340200|113340200	1.000000|1.000000	0.71417|0.71417	0.962000|0.962000	0.40283|0.40283	0.080000|0.080000	0.17528|0.17528	5.465000|5.465000	0.66725|0.66725	1.061000|1.061000	0.40601|0.40601	0.561000|0.561000	0.74099|0.74099	AGG|AGT	TFDP1	-	pirsf_Transcription_factor_DP_subgr	ENSG00000198176		0.587	TFDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TFDP1	HGNC	protein_coding	OTTHUMT00000045918.3	102	0.00	0	G	NM_007111		114292199	114292199	+1	no_errors	ENST00000375370	ensembl	human	known	69_37n	missense	89	11.00	11	SNP	1.000	T
TP53	7157	genome.wustl.edu	37	17	7574003	7574003	+	Nonsense_Mutation	SNP	G	G	A			TCGA-BH-A0RX-01A-21D-A099-09	TCGA-BH-A0RX-10A-01D-A099-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	48115e9a-5027-455a-a88e-c3d991dbf966	c99e4cec-5fc3-4dc9-9c38-b72dbea39d3f	g.chr17:7574003G>A	ENST00000269305.4	-	10	1213	c.1024C>T	c.(1024-1026)Cga>Tga	p.R342*	TP53_ENST00000420246.2_3'UTR|TP53_ENST00000455263.2_3'UTR|TP53_ENST00000413465.2_Intron|TP53_ENST00000359597.4_Intron|TP53_ENST00000445888.2_Nonsense_Mutation_p.R342*	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	342	Interaction with CARM1.|Interaction with HIPK1. {ECO:0000250}.|Interaction with HIPK2.|Oligomerization.		R -> L (in a sporadic cancer; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R342*(70)|p.0?(8)|p.R342fs*3(8)|p.?(1)|p.R342_N345delRELN(1)|p.I332fs*5(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TTCAGCTCTCGGAACATCTCG	0.557		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	dbGAP	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	89	Substitution - Nonsense(70)|Whole gene deletion(8)|Deletion - Frameshift(7)|Insertion - Frameshift(2)|Deletion - In frame(1)|Unknown(1)	breast(16)|upper_aerodigestive_tract(11)|large_intestine(9)|central_nervous_system(9)|ovary(7)|lung(6)|skin(5)|liver(5)|haematopoietic_and_lymphoid_tissue(4)|pancreas(4)|bone(4)|stomach(2)|urinary_tract(2)|oesophagus(2)|kidney(1)|peritoneum(1)|endometrium(1)	GRCh37	CM004908	TP53	M							62.0	48.0	53.0					17																	7574003		2203	4300	6503	-	-	-	SO:0001587	stop_gained	0	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.1024C>T	17.37:g.7574003G>A	ENSP00000269305:p.Arg342*	Somatic		WXS	Illumina GAIIx	Phase_IV	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Nonsense_Mutation	SNP	pfam_p53_DNA-bd,pfam_p53_tetrameristn,pfam_p53_transactivation_domain,superfamily_p53-like_TF_DNA-bd,superfamily_p53_tetrameristn,prints_p53_tumour_suppressor	p.R342*	ENST00000269305.4	37	c.1024	CCDS11118.1	17	.	.	.	.	.	.	.	.	.	.	G	37	6.061927	0.97246	.	.	ENSG00000141510	ENST00000269305;ENST00000445888;ENST00000396473	.	.	.	5.43	3.43	0.39272	.	0.217683	0.37906	N	0.001893	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09338	T	0.73	-0.3792	6.4477	0.21885	0.0845:0.0:0.5925:0.323	.	.	.	.	X	342;342;331	.	ENSP00000269305:R342X	R	-	1	2	TP53	7514728	0.820000	0.29190	0.702000	0.30337	0.859000	0.49053	2.169000	0.42434	0.657000	0.30906	0.561000	0.74099	CGA	TP53	-	pfam_p53_tetrameristn,superfamily_p53_tetrameristn,prints_p53_tumour_suppressor	ENSG00000141510		0.557	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TP53	HGNC	protein_coding	OTTHUMT00000367397.1	35	0.00	0	G	NM_000546		7574003	7574003	-1	no_errors	ENST00000269305	ensembl	human	known	69_37n	nonsense	45	15.09	8	SNP	0.307	A
VANGL2	57216	genome.wustl.edu	37	1	160389104	160389104	+	Missense_Mutation	SNP	C	C	T			TCGA-BH-A0RX-01A-21D-A099-09	TCGA-BH-A0RX-10A-01D-A099-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	48115e9a-5027-455a-a88e-c3d991dbf966	c99e4cec-5fc3-4dc9-9c38-b72dbea39d3f	g.chr1:160389104C>T	ENST00000368061.2	+	4	979	c.505C>T	c.(505-507)Cgc>Tgc	p.R169C		NM_020335.2	NP_065068.1	Q9ULK5	VANG2_HUMAN	VANGL planar cell polarity protein 2	169					anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|cell migration involved in kidney development (GO:0035787)|cochlea morphogenesis (GO:0090103)|convergent extension involved in axis elongation (GO:0060028)|convergent extension involved in neural plate elongation (GO:0022007)|digestive tract morphogenesis (GO:0048546)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity involved in neural tube closure (GO:0090177)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|glomerulus development (GO:0032835)|hair follicle development (GO:0001942)|heart looping (GO:0001947)|inner ear receptor stereocilium organization (GO:0060122)|kidney morphogenesis (GO:0060993)|lateral sprouting involved in lung morphogenesis (GO:0060490)|membranous septum morphogenesis (GO:0003149)|muscular septum morphogenesis (GO:0003150)|neural tube closure (GO:0001843)|nonmotile primary cilium assembly (GO:0035058)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in axis elongation (GO:0003402)|planar cell polarity pathway involved in heart morphogenesis (GO:0061346)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|positive regulation of JUN kinase activity (GO:0043507)|post-anal tail morphogenesis (GO:0036342)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of Wnt signaling pathway (GO:0030111)|Rho protein signal transduction (GO:0007266)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell pole (GO:0060187)|cell-cell junction (GO:0005911)|ER to Golgi transport vesicle (GO:0030134)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)		p.R169C(1)		biliary_tract(1)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(1)	37	all_cancers(52;1.08e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			TCTGTTCTTCCGCCGGCCCAA	0.627																																						dbGAP											1	Substitution - Missense(1)	breast(1)											77.0	73.0	74.0					1																	160389104		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB033041	CCDS30915.1	1q22-q23	2013-03-05	2013-03-05		ENSG00000162738	ENSG00000162738			15511	protein-coding gene	gene with protein product	"""vang, van gogh-like 2"", ""loop-tail-associated protein"", ""strabismus"""	600533	"""vang (van gogh, Drosophila)-like 2, vang, van gogh-like 2 (Drosophila)"", ""vang-like 2 (van gogh, Drosophila)"""			11431695	Standard	NM_020335		Approved	KIAA1215, LTAP, LPP1, STBM, STB1, STBM1, MGC119403, MGC119404	uc001fwc.2	Q9ULK5	OTTHUMG00000033122	ENST00000368061.2:c.505C>T	1.37:g.160389104C>T	ENSP00000357040:p.Arg169Cys	Somatic		WXS	Illumina GAIIx	Phase_IV	D3DVE9|Q5T212	Missense_Mutation	SNP	pfam_Strabismus,pirsf_Strabismus	p.R169C	ENST00000368061.2	37	c.505	CCDS30915.1	1	.	.	.	.	.	.	.	.	.	.	C	28.2	4.897616	0.91962	.	.	ENSG00000162738	ENST00000368061	D	0.87334	-2.24	5.08	5.08	0.68730	.	0.000000	0.85682	D	0.000000	D	0.94192	0.8136	M	0.90252	3.1	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.95094	0.8224	10	0.87932	D	0	-26.3961	17.3919	0.87434	0.0:1.0:0.0:0.0	.	169	Q9ULK5	VANG2_HUMAN	C	169	ENSP00000357040:R169C	ENSP00000357040:R169C	R	+	1	0	VANGL2	158655728	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.385000	0.79763	2.503000	0.84419	0.563000	0.77884	CGC	VANGL2	-	pfam_Strabismus,pirsf_Strabismus	ENSG00000162738		0.627	VANGL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	VANGL2	HGNC	protein_coding	OTTHUMT00000080677.1	78	0.00	0	C	NM_020335		160389104	160389104	+1	no_errors	ENST00000368061	ensembl	human	known	69_37n	missense	93	16.96	19	SNP	1.000	T
