#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
ADD3	120	genome.wustl.edu	37	10	111860581	111860581	+	Missense_Mutation	SNP	G	G	A			TCGA-AN-A0AS-01A-11W-A019-09	TCGA-AN-A0AS-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	2257c942-1274-47e7-86ad-b92ecfafc205	0ec33f45-45dc-4fd6-b1c9-0312bff04da4	g.chr10:111860581G>A	ENST00000356080.4	+	2	537	c.170G>A	c.(169-171)cGa>cAa	p.R57Q	ADD3_ENST00000360162.3_Missense_Mutation_p.R57Q|ADD3_ENST00000497125.1_3'UTR|ADD3_ENST00000277900.8_Missense_Mutation_p.R57Q	NM_016824.3	NP_058432.1	Q9UEY8	ADDG_HUMAN	adducin 3 (gamma)	57						cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|condensed nuclear chromosome (GO:0000794)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	29		Breast(234;0.052)|Lung NSC(174;0.223)		Epithelial(162;4.15e-05)|all cancers(201;0.000587)|BRCA - Breast invasive adenocarcinoma(275;0.0742)		CAGAGGAAACGAGTTACTCAG	0.388																																						dbGAP											0													72.0	67.0	69.0					10																	111860581		2203	4300	6503	-	-	-	SO:0001583	missense	0			U37122	CCDS7561.1, CCDS7562.1	10q25.2	2005-11-08			ENSG00000148700	ENSG00000148700			245	protein-coding gene	gene with protein product		601568		ADDL		8893809	Standard	XM_005269529		Approved		uc001kyv.3	Q9UEY8	OTTHUMG00000019032	ENST00000356080.4:c.170G>A	10.37:g.111860581G>A	ENSP00000348381:p.Arg57Gln	Somatic		WXS	Illumina GAIIx	Phase_IV	D3DRA8|O43243|Q5VU09|Q92773|Q9UEY7	Missense_Mutation	SNP	pfam_Aldolase_II/adducin_N,superfamily_Aldolase_II/adducin_N	p.R57Q	ENST00000356080.4	37	c.170	CCDS7561.1	10	.	.	.	.	.	.	.	.	.	.	G	37	6.302305	0.97458	.	.	ENSG00000148700	ENST00000360162;ENST00000356080;ENST00000277900	T;T;T	0.31510	1.49;1.49;1.49	6.06	6.06	0.98353	.	0.054026	0.64402	D	0.000001	T	0.65698	0.2716	M	0.89095	3.005	0.80722	D	1	D;D	0.89917	1.0;0.997	D;P	0.91635	0.999;0.875	T	0.69745	-0.5062	10	0.87932	D	0	-4.0528	20.6397	0.99537	0.0:0.0:1.0:0.0	.	57;57	Q9UEY8;Q9UEY8-2	ADDG_HUMAN;.	Q	57	ENSP00000353286:R57Q;ENSP00000348381:R57Q;ENSP00000277900:R57Q	ENSP00000277900:R57Q	R	+	2	0	ADD3	111850571	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	9.869000	0.99810	2.880000	0.98712	0.650000	0.86243	CGA	ADD3	-	NULL	ENSG00000148700		0.388	ADD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	ADD3	HGNC	protein_coding	OTTHUMT00000050289.1	102	0.00	0	G	NM_019903		111860581	111860581	+1	no_errors	ENST00000356080	ensembl	human	known	69_37n	missense	48	26.15	17	SNP	1.000	A
AKAP4	8852	genome.wustl.edu	37	X	49957446	49957446	+	Missense_Mutation	SNP	C	C	G			TCGA-AN-A0AS-01A-11W-A019-09	TCGA-AN-A0AS-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	2257c942-1274-47e7-86ad-b92ecfafc205	0ec33f45-45dc-4fd6-b1c9-0312bff04da4	g.chrX:49957446C>G	ENST00000376056.2	-	5	2041	c.1891G>C	c.(1891-1893)Gag>Cag	p.E631Q	AKAP4_ENST00000376064.3_Missense_Mutation_p.E631Q|AKAP4_ENST00000481402.1_5'UTR|AKAP4_ENST00000376058.2_Missense_Mutation_p.E257Q|AKAP4_ENST00000358526.2_Missense_Mutation_p.E640Q					A kinase (PRKA) anchor protein 4											NS(2)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(6)|lung(14)|ovary(1)|skin(4)	41	Ovarian(276;0.236)					AAGGGGTTCTCATTAAGCAGT	0.473																																						dbGAP											0													163.0	131.0	142.0					X																	49957446		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF072756	CCDS14329.1, CCDS14330.1	Xp11.2	2009-03-12			ENSG00000147081	ENSG00000147081		"""A-kinase anchor proteins"""	374	protein-coding gene	gene with protein product	"""A-kinase anchor protein 82 kDa"", ""testis-specific gene HI"", ""protein kinase A anchoring protein 4"", ""cancer/testis antigen 99"""	300185				9822690, 9514854	Standard	NM_003886		Approved	p82, hAKAP82, AKAP82, Fsc1, HI, CT99	uc004dow.1	Q5JQC9	OTTHUMG00000021517	ENST00000376056.2:c.1891G>C	X.37:g.49957446C>G	ENSP00000365224:p.Glu631Gln	Somatic		WXS	Illumina GAIIx	Phase_IV		Missense_Mutation	SNP	pfam_AKAP_110_C,pfam_RII_binding_1,smart_AKAP_110	p.E640Q	ENST00000376056.2	37	c.1918	CCDS14330.1	X	.	.	.	.	.	.	.	.	.	.	C	10.73	1.431192	0.25726	.	.	ENSG00000147081	ENST00000376056;ENST00000376058;ENST00000358526;ENST00000376064	T;T;T;T	0.13657	2.57;2.57;2.57;2.57	5.14	5.14	0.70334	A-kinase anchor 110kDa, C-terminal (1);	0.222920	0.31279	N	0.007931	T	0.36303	0.0962	M	0.76328	2.33	0.09310	N	1	P;D	0.89917	0.924;1.0	P;D	0.75484	0.784;0.986	T	0.15867	-1.0422	9	.	.	.	-21.2424	13.0662	0.59034	0.0:1.0:0.0:0.0	.	640;257	Q5JQC9;A6ND82	AKAP4_HUMAN;.	Q	631;257;640;631	ENSP00000365224:E631Q;ENSP00000365226:E257Q;ENSP00000351327:E640Q;ENSP00000365232:E631Q	.	E	-	1	0	AKAP4	49844186	0.965000	0.33210	0.046000	0.18839	0.143000	0.21401	2.855000	0.48333	2.144000	0.66660	0.529000	0.55759	GAG	AKAP4	-	pfam_AKAP_110_C,smart_AKAP_110	ENSG00000147081		0.473	AKAP4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	AKAP4	HGNC	protein_coding	OTTHUMT00000056552.1	510	0.00	0	C	NM_003886		49957446	49957446	-1	no_errors	ENST00000358526	ensembl	human	known	69_37n	missense	448	12.16	62	SNP	0.170	G
AMOTL2	51421	genome.wustl.edu	37	3	134089691	134089692	+	Frame_Shift_Ins	INS	-	-	G			TCGA-AN-A0AS-01A-11W-A019-09	TCGA-AN-A0AS-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	2257c942-1274-47e7-86ad-b92ecfafc205	0ec33f45-45dc-4fd6-b1c9-0312bff04da4	g.chr3:134089691_134089692insG	ENST00000422605.2	-	2	750_751	c.584_585insC	c.(583-585)ccafs	p.P195fs	AMOTL2_ENST00000514516.1_Frame_Shift_Ins_p.P253fs|AMOTL2_ENST00000513145.1_Frame_Shift_Ins_p.P195fs|AMOTL2_ENST00000249883.5_Frame_Shift_Ins_p.P195fs|AMOTL2_ENST00000511759.1_Intron			Q9Y2J4	AMOL2_HUMAN	angiomotin like 2	195					hippo signaling (GO:0035329)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|tight junction (GO:0005923)				endometrium(8)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	19						GGCCCCTCAGTGGGGGGCCCTG	0.663																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AF175966	CCDS33860.1, CCDS63783.1, CCDS63784.1	3q21-q22	2008-07-18			ENSG00000114019	ENSG00000114019			17812	protein-coding gene	gene with protein product	"""Leman coiled-coil protein"", ""angiomotin-like protein 2"""	614658					Standard	NM_016201		Approved	LCCP	uc003eqg.1	Q9Y2J4	OTTHUMG00000159777	ENST00000422605.2:c.585dupC	3.37:g.134089697_134089697dupG	ENSP00000409999:p.Pro195fs	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K6F1|B7Z5Q1|E9PHW3|Q53EP1|Q96F99|Q9UKB4	Frame_Shift_Ins	INS	pfam_Angiomotin_C,prints_Angiomotin	p.L196fs	ENST00000422605.2	37	c.585_584		3																																																																																			AMOTL2	-	NULL	ENSG00000114019		0.663	AMOTL2-014	KNOWN	basic|appris_candidate_longest	protein_coding	AMOTL2	HGNC	protein_coding	OTTHUMT00000358149.1	22	0.00	0	-	NM_016201		134089691	134089692	-1	no_errors	ENST00000249883	ensembl	human	known	69_37n	frame_shift_ins	16	11.11	2	INS	0.000:0.000	G
AOX1	316	genome.wustl.edu	37	2	201478612	201478612	+	Missense_Mutation	SNP	G	G	C			TCGA-AN-A0AS-01A-11W-A019-09	TCGA-AN-A0AS-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	2257c942-1274-47e7-86ad-b92ecfafc205	0ec33f45-45dc-4fd6-b1c9-0312bff04da4	g.chr2:201478612G>C	ENST00000374700.2	+	15	1775	c.1534G>C	c.(1534-1536)Gtg>Ctg	p.V512L	AOX1_ENST00000485106.1_3'UTR	NM_001159.3	NP_001150.3	Q06278	AOXA_HUMAN	aldehyde oxidase 1	512					inflammatory response (GO:0006954)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|vitamin B6 metabolic process (GO:0042816)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	2 iron, 2 sulfur cluster binding (GO:0051537)|aldehyde oxidase activity (GO:0004031)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|NAD binding (GO:0051287)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)			breast(5)|endometrium(3)|kidney(4)|large_intestine(13)|lung(38)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	81					Allopurinol(DB00437)|Aminocaproic Acid(DB00513)|Brimonidine(DB00484)|Famciclovir(DB00426)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Pyrazinamide(DB00339)|Raloxifene(DB00481)|Zaleplon(DB00962)|Zonisamide(DB00909)	AGGTGGGAAAGTGGAGTTCAA	0.453																																						dbGAP											0													101.0	99.0	100.0					2																	201478612		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF017060	CCDS33360.1	2q33	2008-05-20			ENSG00000138356	ENSG00000138356			553	protein-coding gene	gene with protein product		602841				7570184	Standard	NM_001159		Approved	AO, AOH1	uc002uvx.3	Q06278	OTTHUMG00000154536	ENST00000374700.2:c.1534G>C	2.37:g.201478612G>C	ENSP00000363832:p.Val512Leu	Somatic		WXS	Illumina GAIIx	Phase_IV	O14765|Q53RR8|Q53TV3|Q9BYF0|Q9UPG6	Missense_Mutation	SNP	pfam_AldOxase/xan_DH_Mopterin-bd,pfam_Mopterin_DH_FAD-bd,pfam_Ald_Oxase/Xan_DH_a/b,pfam_2Fe-2S-bd,pfam_CO_DH_flav_C,pfam_2Fe-2S_ferredoxin-type,superfamily_AldOxase/xan_DH_Mopterin-bd,superfamily_FAD-bd_2,superfamily_Ald_Oxase/Xan_DH_a/b,superfamily_2Fe-2S-bd,superfamily_CO_DH_flav_C,superfamily_2Fe-2S_ferredoxin-type,pirsf_Ald_Oxase/xanthine_DH,pfscan_2Fe-2S_ferredoxin-type,tigrfam_Aldehyde_oxidase	p.V512L	ENST00000374700.2	37	c.1534	CCDS33360.1	2	.	.	.	.	.	.	.	.	.	.	G	16.64	3.178948	0.57692	.	.	ENSG00000138356	ENST00000374700	T	0.25085	1.82	5.33	5.33	0.75918	CO dehydrogenase flavoprotein, C-terminal (3);	0.060024	0.64402	D	0.000003	T	0.43787	0.1263	M	0.92880	3.355	0.58432	D	0.999999	P	0.36874	0.572	B	0.39935	0.314	T	0.54384	-0.8302	10	0.72032	D	0.01	-43.066	13.4791	0.61326	0.0744:0.0:0.9256:0.0	.	512	Q06278	ADO_HUMAN	L	512	ENSP00000363832:V512L	ENSP00000363832:V512L	V	+	1	0	AOX1	201186857	1.000000	0.71417	0.993000	0.49108	0.026000	0.11368	7.107000	0.77047	2.768000	0.95171	0.655000	0.94253	GTG	AOX1	-	pfam_CO_DH_flav_C,superfamily_CO_DH_flav_C,pirsf_Ald_Oxase/xanthine_DH,tigrfam_Aldehyde_oxidase	ENSG00000138356		0.453	AOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	AOX1	HGNC	protein_coding	OTTHUMT00000335844.1	147	0.00	0	G	NM_001159		201478612	201478612	+1	no_errors	ENST00000374700	ensembl	human	known	69_37n	missense	115	19.01	27	SNP	0.999	C
AQP12B	653437	genome.wustl.edu	37	2	241621869	241621869	+	Missense_Mutation	SNP	G	G	A	rs74882485	byFrequency	TCGA-AN-A0AS-01A-11W-A019-09	TCGA-AN-A0AS-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	2257c942-1274-47e7-86ad-b92ecfafc205	0ec33f45-45dc-4fd6-b1c9-0312bff04da4	g.chr2:241621869G>A	ENST00000407834.3	-	1	448	c.386C>T	c.(385-387)aCg>aTg	p.T129M		NM_001102467.1	NP_001095937.1	A6NM10	AQ12B_HUMAN	aquaporin 12B	117						integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|lung(8)|ovary(1)	13		all_epithelial(40;1.71e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|all_neural(83;0.0459)|Lung NSC(271;0.094)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;2.2e-31)|all cancers(36;1.08e-28)|OV - Ovarian serous cystadenocarcinoma(60;2.13e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.52e-06)|Lung(119;0.00163)|LUSC - Lung squamous cell carcinoma(224;0.008)|Colorectal(34;0.0124)|COAD - Colon adenocarcinoma(134;0.0757)		GCAGAGGCGCGTCAGGGTGCA	0.697																																						dbGAP											0													24.0	24.0	24.0					2																	241621869		2196	4279	6475	-	-	-	SO:0001583	missense	0			BC041460	CCDS46560.1	2q37.3	2007-12-14	2005-05-26	2005-05-26	ENSG00000185176	ENSG00000185176		"""Ion channels / Aquaporins"""	6096	protein-coding gene	gene with protein product			"""insulin synthesis associated 3"""	INSSA3			Standard	NM_001102467		Approved		uc010fzj.3	A6NM10	OTTHUMG00000152263	ENST00000407834.3:c.386C>T	2.37:g.241621869G>A	ENSP00000384894:p.Thr129Met	Somatic		WXS	Illumina GAIIx	Phase_IV	A4QPB9	Missense_Mutation	SNP	pfam_MIP,superfamily_Aquaporin-like,pirsf_Aquaporin_11/12,prints_Aquaporin_12,prints_MIP	p.T129M	ENST00000407834.3	37	c.386	CCDS46560.1	2	.	.	.	.	.	.	.	.	.	.	.	7.337	0.620131	0.14193	.	.	ENSG00000185176	ENST00000407834	T	0.15017	2.46	2.84	1.94	0.25998	.	0.293024	0.38492	N	0.001671	T	0.26810	0.0656	.	.	.	0.80722	P	0.0	D	0.71674	0.998	P	0.61592	0.891	T	0.30995	-0.9959	8	0.28530	T	0.3	-0.0254	8.3053	0.32038	0.1286:0.0:0.8714:0.0	.	129	A6NM10-2	.	M	129	ENSP00000384894:T129M	ENSP00000384894:T129M	T	-	2	0	AQP12B	241270542	0.997000	0.39634	0.002000	0.10522	0.132000	0.20833	5.268000	0.65536	0.748000	0.32831	0.473000	0.43528	ACG	AQP12B	-	pfam_MIP,superfamily_Aquaporin-like,pirsf_Aquaporin_11/12,prints_Aquaporin_12	ENSG00000185176		0.697	AQP12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	AQP12B	HGNC	protein_coding	OTTHUMT00000325625.1	13	0.00	0	G			241621869	241621869	-1	no_errors	ENST00000407834	ensembl	human	known	69_37n	missense	10	44.44	8	SNP	0.017	A
BAZ1B	9031	genome.wustl.edu	37	7	72892315	72892315	+	Missense_Mutation	SNP	C	C	A			TCGA-AN-A0AS-01A-11W-A019-09	TCGA-AN-A0AS-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	2257c942-1274-47e7-86ad-b92ecfafc205	0ec33f45-45dc-4fd6-b1c9-0312bff04da4	g.chr7:72892315C>A	ENST00000339594.4	-	7	1814	c.1476G>T	c.(1474-1476)agG>agT	p.R492S	BAZ1B_ENST00000404251.1_Missense_Mutation_p.R492S	NM_032408.3	NP_115784.1	Q9UIG0	BAZ1B_HUMAN	bromodomain adjacent to zinc finger domain, 1B	492	Lys-rich.				cellular response to DNA damage stimulus (GO:0006974)|chromatin assembly or disassembly (GO:0006333)|chromatin-mediated maintenance of transcription (GO:0048096)|double-strand break repair (GO:0006302)|heart morphogenesis (GO:0003007)|histone phosphorylation (GO:0016572)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed chromosome (GO:0000793)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|histone kinase activity (GO:0035173)|lysine-acetylated histone binding (GO:0070577)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|vitamin D receptor activator activity (GO:0071884)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(5)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		Lung NSC(55;0.0659)|all_lung(88;0.152)				ACAGGGCGCTCCTCTTGTCCT	0.468																																					Esophageal Squamous(112;1167 1561 21085 43672 48228)	dbGAP											0													109.0	109.0	109.0					7																	72892315		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF084479	CCDS5549.1	7q11.23	2013-01-28			ENSG00000009954	ENSG00000009954		"""Zinc fingers, PHD-type"""	961	protein-coding gene	gene with protein product	"""Williams-Beuren syndrome chromosome region 9"", ""Williams-Beuren syndrome chromosome region 10"", ""transcription factor WSTF"""	605681		WBSCR9, WBSCR10		9858827, 9828126	Standard	NM_032408		Approved	WSTF	uc003tyc.3	Q9UIG0	OTTHUMG00000023847	ENST00000339594.4:c.1476G>T	7.37:g.72892315C>A	ENSP00000342434:p.Arg492Ser	Somatic		WXS	Illumina GAIIx	Phase_IV	B9EGK3|D3DXE9|O95039|O95247|O95277|Q6P1K4|Q86UJ6	Missense_Mutation	SNP	pfam_WSTF_Acf1_Cbp146,pfam_Bromodomain,pfam_Znf_PHD-finger,superfamily_Bromodomain,superfamily_Znf_FYVE_PHD,superfamily_ARM-type_fold,smart_DDT_dom_subgr,smart_Znf_PHD,smart_Bromodomain,pfscan_WSTF_Acf1_Cbp146,pfscan_Znf_PHD-finger,pfscan_Znf_RING,pfscan_DDT_dom_superfamily,pfscan_Bromodomain,prints_Bromodomain	p.R492S	ENST00000339594.4	37	c.1476	CCDS5549.1	7	.	.	.	.	.	.	.	.	.	.	C	12.27	1.887876	0.33348	.	.	ENSG00000009954	ENST00000339594;ENST00000404251	T;T	0.55930	0.49;0.49	5.71	5.71	0.89125	.	0.043180	0.85682	D	0.000000	T	0.30262	0.0759	N	0.08118	0	0.25928	N	0.98303	B	0.17038	0.02	B	0.14023	0.01	T	0.09574	-1.0668	10	0.38643	T	0.18	-16.4057	8.3837	0.32488	0.0:0.8345:0.0:0.1655	.	492	Q9UIG0	BAZ1B_HUMAN	S	492	ENSP00000342434:R492S;ENSP00000385442:R492S	ENSP00000342434:R492S	R	-	3	2	BAZ1B	72530251	1.000000	0.71417	1.000000	0.80357	0.864000	0.49448	1.407000	0.34657	2.699000	0.92147	0.655000	0.94253	AGG	BAZ1B	-	superfamily_ARM-type_fold	ENSG00000009954		0.468	BAZ1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	BAZ1B	HGNC	protein_coding	OTTHUMT00000252123.4	204	0.00	0	C	NM_032408		72892315	72892315	-1	no_errors	ENST00000339594	ensembl	human	known	69_37n	missense	156	27.98	61	SNP	1.000	A
BRPF1	7862	genome.wustl.edu	37	3	9786077	9786078	+	Frame_Shift_Ins	INS	-	-	C			TCGA-AN-A0AS-01A-11W-A019-09	TCGA-AN-A0AS-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	2257c942-1274-47e7-86ad-b92ecfafc205	0ec33f45-45dc-4fd6-b1c9-0312bff04da4	g.chr3:9786077_9786078insC	ENST00000457855.1	+	8	2798_2799	c.2787_2788insC	c.(2788-2790)cccfs	p.P930fs	BRPF1_ENST00000302054.3_Frame_Shift_Ins_p.P930fs|BRPF1_ENST00000433861.2_Intron|BRPF1_ENST00000424362.1_Frame_Shift_Ins_p.P929fs|BRPF1_ENST00000383829.2_Frame_Shift_Ins_p.P936fs			P55201	BRPF1_HUMAN	bromodomain and PHD finger containing, 1	930	Required for RUNX1 and RUNX2 transcriptional activation.				chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(15)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	49	Medulloblastoma(99;0.227)					GTCCTGTGGGGCCCCCCCAGCT	0.658																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			M91585	CCDS2575.1, CCDS33692.1	3p26-p25	2008-07-18			ENSG00000156983	ENSG00000156983			14255	protein-coding gene	gene with protein product	"""peregrin"", ""bromodomain-containing protein, 140kD"""	602410				8946209, 7906940	Standard	NM_001003694		Approved	BR140	uc003bsf.3	P55201	OTTHUMG00000097033	ENST00000457855.1:c.2794dupC	3.37:g.9786084_9786084dupC	ENSP00000410210:p.Pro930fs	Somatic		WXS	Illumina GAIIx	Phase_IV	B4DEZ6|Q7Z6E0|Q8TCM6|Q9UHI0	Frame_Shift_Ins	INS	pfam_Enhancer_polycomb-like_N,pfam_Bromodomain,pfam_PWWP,superfamily_Bromodomain,superfamily_Znf_FYVE_PHD,smart_Znf_PHD,smart_Bromodomain,smart_PWWP,prints_Bromodomain,pfscan_PWWP,pfscan_Znf_PHD-finger,pfscan_Znf_C2H2,pfscan_Bromodomain	p.Q937fs	ENST00000457855.1	37	c.2805_2806	CCDS2575.1	3																																																																																			BRPF1	-	NULL	ENSG00000156983		0.658	BRPF1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	BRPF1	HGNC	protein_coding	OTTHUMT00000338485.1	34	0.00	0	-	NM_001003694		9786077	9786078	+1	no_errors	ENST00000383829	ensembl	human	known	69_37n	frame_shift_ins	30	11.76	4	INS	1.000:1.000	C
CEP290	80184	genome.wustl.edu	37	12	88514773	88514773	+	Splice_Site	SNP	C	C	A			TCGA-AN-A0AS-01A-11W-A019-09	TCGA-AN-A0AS-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	2257c942-1274-47e7-86ad-b92ecfafc205	0ec33f45-45dc-4fd6-b1c9-0312bff04da4	g.chr12:88514773C>A	ENST00000552810.1	-	14	1703		c.e14+1		CEP290_ENST00000397838.3_Splice_Site|CEP290_ENST00000309041.7_Splice_Site	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa						cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038)				breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73						AAAATACATACCGATTCATAA	0.363																																						dbGAP											0													80.0	78.0	78.0					12																	88514773		1837	4078	5915	-	-	-	SO:0001630	splice_region_variant	0			AB002371	CCDS55858.1	12q21.33	2014-09-17				ENSG00000198707			29021	protein-coding gene	gene with protein product	"""Joubert syndrome 5"", ""nephrocystin-6"", ""cancer/testis antigen 87"", ""POC3 centriolar protein homolog (Chlamydomonas)"", ""Meckel syndrome, type 4"""	610142				15474516, 16682973, 16632484	Standard	NM_025114		Approved	KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3	uc001tar.3	O15078		ENST00000552810.1:c.1359+1G>T	12.37:g.88514773C>A		Somatic		WXS	Illumina GAIIx	Phase_IV	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Splice_Site	SNP	-	e13+1	ENST00000552810.1	37	c.1359+1	CCDS55858.1	12	.	.	.	.	.	.	.	.	.	.	C	25.1	4.607035	0.87157	.	.	ENSG00000198707	ENST00000552810;ENST00000309041;ENST00000536998;ENST00000545139	.	.	.	5.61	5.61	0.85477	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.646	0.95777	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CEP290	87038904	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.623000	0.74238	2.645000	0.89757	0.591000	0.81541	.	CEP290	-	-	ENSG00000198707		0.363	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	CEP290	HGNC	protein_coding	OTTHUMT00000406344.1	120	0.00	0	C	NM_025114	Intron	88514773	88514773	-1	no_errors	ENST00000309041	ensembl	human	known	69_37n	splice_site	59	16.90	12	SNP	1.000	A
CITED1	4435	genome.wustl.edu	37	X	71521748	71521748	+	Missense_Mutation	SNP	A	A	G			TCGA-AN-A0AS-01A-11W-A019-09	TCGA-AN-A0AS-10A-01W-A021-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	2257c942-1274-47e7-86ad-b92ecfafc205	0ec33f45-45dc-4fd6-b1c9-0312bff04da4	g.chrX:71521748A>G	ENST00000246139.5	-	3	982	c.407T>C	c.(406-408)cTc>cCc	p.L136P	CITED1_ENST00000445983.1_Missense_Mutation_p.L136P|CITED1_ENST00000373619.3_Missense_Mutation_p.L136P|CITED1_ENST00000431381.1_Missense_Mutation_p.L162P	NM_004143.3	NP_004134.2	Q99966	CITE1_HUMAN	Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 1	136					apoptotic process (GO:0006915)|brain development (GO:0007420)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell proliferation (GO:0008283)|embryonic axis specification (GO:0000578)|labyrinthine layer development (GO:0060711)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|mesenchymal to epithelial transition (GO:0060231)|metanephros development (GO:0001656)|negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003340)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|nucleocytoplasmic transport (GO:0006913)|pigmentation (GO:0043473)|placenta development (GO:0001890)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cAMP (GO:0051591)|response to cytokine (GO:0034097)|response to estrogen (GO:0043627)|response to insulin (GO:0032868)|response to interferon-gamma (GO:0034341)|response to interleukin-1 (GO:0070555)|response to interleukin-11 (GO:0071105)|response to interleukin-2 (GO:0070669)|response to interleukin-4 (GO:0070670)|response to interleukin-6 (GO:0070741)|response to interleukin-9 (GO:0071104)|response to lipopolysaccharide (GO:0032496)|response to parathyroid hormone (GO:0071107)|response to transforming growth factor beta (GO:0071559)|SMAD protein signal transduction (GO:0060395)|spongiotrophoblast layer development (GO:0060712)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|co-SMAD binding (GO:0070410)|LBD domain binding (GO:0050693)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			skin(1)	1	Renal(35;0.156)					AGAAGGAGAGAGTGATTCTGC	0.622																																						dbGAP											0													62.0	55.0	57.0					X																	71521748		2203	4300	6503	-	-	-	SO:0001583	missense	0			U65092	CCDS14419.1, CCDS48136.1	Xq13.1	2008-02-05			ENSG00000125931	ENSG00000125931			1986	protein-coding gene	gene with protein product		300149		MSG1		8901575, 9721210	Standard	NM_004143		Approved		uc011mqc.2	Q99966	OTTHUMG00000021812	ENST00000246139.5:c.407T>C	X.37:g.71521748A>G	ENSP00000246139:p.Leu136Pro	Somatic		WXS	Illumina GAIIx	Phase_IV	B5BU50|B5BUI2	Missense_Mutation	SNP	pfam_CITED	p.L162P	ENST00000246139.5	37	c.485	CCDS14419.1	X	.	.	.	.	.	.	.	.	.	.	A	11.80	1.746125	0.30955	.	.	ENSG00000125931	ENST00000453707;ENST00000431381;ENST00000445983;ENST00000373619;ENST00000246139;ENST00000417400	T;T;T;T;T;T	0.62364	0.03;0.03;0.03;0.03;0.03;0.03	5.38	1.49	0.22878	.	1.208860	0.06173	N	0.677998	T	0.49304	0.1549	L	0.27053	0.805	0.09310	N	0.999995	P;P	0.46220	0.874;0.773	B;P	0.45377	0.347;0.478	T	0.35724	-0.9777	10	0.35671	T	0.21	0.876	1.9878	0.03440	0.5836:0.1635:0.0922:0.1607	.	162;136	Q99966-2;Q99966	.;CITE1_HUMAN	P	162;162;136;136;136;136	ENSP00000401764:L162P;ENSP00000388548:L162P;ENSP00000403274:L136P;ENSP00000362721:L136P;ENSP00000246139:L136P;ENSP00000414781:L136P	ENSP00000246139:L136P	L	-	2	0	CITED1	71438473	0.000000	0.05858	0.004000	0.12327	0.725000	0.41563	0.027000	0.13621	0.193000	0.20303	0.486000	0.48141	CTC	CITED1	-	pfam_CITED	ENSG00000125931		0.622	CITED1-002	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	CITED1	HGNC	protein_coding	OTTHUMT00000057181.1	50	0.00	0	A	NM_004143		71521748	71521748	-1	no_errors	ENST00000431381	ensembl	human	known	69_37n	missense	18	35.71	10	SNP	0.000	G
COL22A1	169044	genome.wustl.edu	37	8	139675984	139675984	+	Splice_Site	SNP	C	C	A			TCGA-AN-A0AS-01A-11W-A019-09	TCGA-AN-A0AS-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	2257c942-1274-47e7-86ad-b92ecfafc205	0ec33f45-45dc-4fd6-b1c9-0312bff04da4	g.chr8:139675984C>A	ENST00000303045.6	-	42	3597		c.e42-1		COL22A1_ENST00000435777.1_Splice_Site|COL22A1_ENST00000341807.4_Splice_Site	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1						extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			CGGAAGGGCCCTAGAAACAAA	0.443										HNSCC(7;0.00092)																												dbGAP											0													97.0	97.0	97.0					8																	139675984		2203	4300	6503	-	-	-	SO:0001630	splice_region_variant	0			AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"""Collagens"""	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.3151-1G>T	8.37:g.139675984C>A		Somatic		WXS	Illumina GAIIx	Phase_IV	B7ZMH0|C9K0G4|Q8IVT9	Splice_Site	SNP	-	e41-1	ENST00000303045.6	37	c.3151-1	CCDS6376.1	8	.	.	.	.	.	.	.	.	.	.	C	16.64	3.179005	0.57692	.	.	ENSG00000169436	ENST00000303045;ENST00000435777;ENST00000545577	.	.	.	4.5	3.62	0.41486	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.5543	0.33471	0.0:0.8939:0.0:0.1061	.	.	.	.	.	-1	.	.	.	-	.	.	COL22A1	139745166	1.000000	0.71417	0.902000	0.35471	0.983000	0.72400	3.847000	0.55895	1.240000	0.43803	0.591000	0.81541	.	COL22A1	-	-	ENSG00000169436		0.443	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	COL22A1	HGNC	protein_coding	OTTHUMT00000315905.2	85	0.00	0	C	XM_291257	Intron	139675984	139675984	-1	no_errors	ENST00000303045	ensembl	human	known	69_37n	splice_site	138	25.00	46	SNP	0.973	A
COL4A5	1287	genome.wustl.edu	37	X	107829952	107829952	+	Silent	SNP	T	T	C			TCGA-AN-A0AS-01A-11W-A019-09	TCGA-AN-A0AS-10A-01W-A021-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	2257c942-1274-47e7-86ad-b92ecfafc205	0ec33f45-45dc-4fd6-b1c9-0312bff04da4	g.chrX:107829952T>C	ENST00000361603.2	+	19	1384	c.1140T>C	c.(1138-1140)ggT>ggC	p.G380G	COL4A5_ENST00000328300.6_Silent_p.G380G	NM_000495.4	NP_000486.1	P29400	CO4A5_HUMAN	collagen, type IV, alpha 5	380	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|neuromuscular junction (GO:0031594)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(32)|ovary(4)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	99						GAATACAGGGTCCACCTGGCC	0.438									Alport syndrome with Diffuse Leiomyomatosis																													dbGAP											0													108.0	102.0	104.0					X																	107829952		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0	Familial Cancer Database		M90464	CCDS14543.1, CCDS35366.1	Xq22	2014-09-17	2008-07-28		ENSG00000188153	ENSG00000188153		"""Collagens"""	2207	protein-coding gene	gene with protein product		303630	"""Alport syndrome"""	ASLN, ATS			Standard	NM_000495		Approved		uc004enz.2	P29400	OTTHUMG00000022182	ENST00000361603.2:c.1140T>C	X.37:g.107829952T>C		Somatic		WXS	Illumina GAIIx	Phase_IV	Q16006|Q16126|Q6LD84|Q7Z700|Q9NUB7	Silent	SNP	pfam_Collagen,pfam_Collagen_VI_NC,superfamily_C-type_lectin_fold,smart_Collagen_VI_NC	p.G380	ENST00000361603.2	37	c.1140	CCDS14543.1	X																																																																																			COL4A5	-	NULL	ENSG00000188153		0.438	COL4A5-001	KNOWN	basic|CCDS	protein_coding	COL4A5	HGNC	protein_coding	OTTHUMT00000057880.2	506	0.00	0	T			107829952	107829952	+1	no_errors	ENST00000328300	ensembl	human	known	69_37n	silent	466	17.20	97	SNP	1.000	C
EPAS1	2034	genome.wustl.edu	37	2	46588075	46588075	+	Missense_Mutation	SNP	A	A	G			TCGA-AN-A0AS-01A-11W-A019-09	TCGA-AN-A0AS-10A-01W-A021-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	2257c942-1274-47e7-86ad-b92ecfafc205	0ec33f45-45dc-4fd6-b1c9-0312bff04da4	g.chr2:46588075A>G	ENST00000263734.3	+	6	1135	c.625A>G	c.(625-627)Aat>Gat	p.N209D		NM_001430.4	NP_001421.2	Q99814	EPAS1_HUMAN	endothelial PAS domain protein 1	209					angiogenesis (GO:0001525)|blood vessel remodeling (GO:0001974)|cell maturation (GO:0048469)|cellular response to hypoxia (GO:0071456)|embryonic placenta development (GO:0001892)|erythrocyte differentiation (GO:0030218)|lung development (GO:0030324)|mitochondrion organization (GO:0007005)|myoblast fate commitment (GO:0048625)|norepinephrine metabolic process (GO:0042415)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of heart rate (GO:0002027)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|surfactant homeostasis (GO:0043129)|transcription from RNA polymerase II promoter (GO:0006366)|visual perception (GO:0007601)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|histone acetyltransferase binding (GO:0035035)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	LUSC - Lung squamous cell carcinoma(58;0.151)			CCCTCCTCACAATAGTCTGTG	0.567																																						dbGAP											0													108.0	101.0	103.0					2																	46588075		2203	4300	6503	-	-	-	SO:0001583	missense	0			U81984	CCDS1825.1	2p21-p16	2013-05-21			ENSG00000116016	ENSG00000116016		"""Basic helix-loop-helix proteins"""	3374	protein-coding gene	gene with protein product	"""HIF-1 alpha-like factor"""	603349				9000051, 9079689, 18378852	Standard	NM_001430		Approved	MOP2, PASD2, HIF2A, HLF, bHLHe73	uc002ruv.3	Q99814	OTTHUMG00000128818	ENST00000263734.3:c.625A>G	2.37:g.46588075A>G	ENSP00000263734:p.Asn209Asp	Somatic		WXS	Illumina GAIIx	Phase_IV	Q86VA2|Q99630	Missense_Mutation	SNP	pfam_PAS_fold_3,pfam_HIF-1_TAD_C,pfam_HIF_alpha_subunit,pfam_PAS_fold,superfamily_HLH_DNA-bd,smart_HLH_DNA-bd,smart_PAS,smart_PAC,prints_Nuc_translocat,pfscan_PAS,pfscan_HLH_DNA-bd,tigrfam_PAS	p.N209D	ENST00000263734.3	37	c.625	CCDS1825.1	2	.	.	.	.	.	.	.	.	.	.	A	10.85	1.467938	0.26335	.	.	ENSG00000116016	ENST00000449347;ENST00000263734	T;T	0.47177	2.28;0.85	4.77	2.39	0.29439	.	0.702644	0.15308	N	0.269244	T	0.25158	0.0611	N	0.14661	0.345	0.19775	N	0.999956	B	0.16166	0.016	B	0.14578	0.011	T	0.14309	-1.0477	10	0.29301	T	0.29	.	3.9773	0.09479	0.6182:0.0:0.2371:0.1448	.	209	Q99814	EPAS1_HUMAN	D	209	ENSP00000406137:N209D;ENSP00000263734:N209D	ENSP00000263734:N209D	N	+	1	0	EPAS1	46441579	0.000000	0.05858	0.808000	0.32385	0.707000	0.40811	1.118000	0.31246	0.340000	0.23745	0.459000	0.35465	AAT	EPAS1	-	NULL	ENSG00000116016		0.567	EPAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	EPAS1	HGNC	protein_coding	OTTHUMT00000250752.2	92	0.00	0	A	NM_001430		46588075	46588075	+1	no_errors	ENST00000263734	ensembl	human	known	69_37n	missense	53	29.33	22	SNP	0.678	G
FAM47B	170062	genome.wustl.edu	37	X	34961802	34961802	+	Missense_Mutation	SNP	C	C	T			TCGA-AN-A0AS-01A-11W-A019-09	TCGA-AN-A0AS-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	2257c942-1274-47e7-86ad-b92ecfafc205	0ec33f45-45dc-4fd6-b1c9-0312bff04da4	g.chrX:34961802C>T	ENST00000329357.5	+	1	890	c.854C>T	c.(853-855)cCg>cTg	p.P285L		NM_152631.2	NP_689844.2	Q8NA70	FA47B_HUMAN	family with sequence similarity 47, member B	285	Pro-rich.									breast(3)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)	71						CATCTCTGCCCGGAGCCTCCC	0.622																																						dbGAP											0													55.0	53.0	54.0					X																	34961802		2202	4300	6502	-	-	-	SO:0001583	missense	0			BC035026	CCDS14236.1	Xp21.1	2004-08-09			ENSG00000189132	ENSG00000189132			26659	protein-coding gene	gene with protein product						14702039	Standard	NM_152631		Approved	FLJ35782	uc004ddi.2	Q8NA70	OTTHUMG00000021345	ENST00000329357.5:c.854C>T	X.37:g.34961802C>T	ENSP00000328307:p.Pro285Leu	Somatic		WXS	Illumina GAIIx	Phase_IV	Q5JQN5|Q6PIG3	Missense_Mutation	SNP	NULL	p.P285L	ENST00000329357.5	37	c.854	CCDS14236.1	X	.	.	.	.	.	.	.	.	.	.	C	0.032	-1.327165	0.01309	.	.	ENSG00000189132	ENST00000329357	T	0.22743	1.94	1.03	1.03	0.20045	.	.	.	.	.	T	0.12646	0.0307	N	0.20986	0.625	0.36614	D	0.875393	B	0.14438	0.01	B	0.13407	0.009	T	0.11616	-1.0580	9	0.38643	T	0.18	.	7.8105	0.29228	0.0:0.9999:0.0:1.0E-4	.	285	Q8NA70	FA47B_HUMAN	L	285	ENSP00000328307:P285L	ENSP00000328307:P285L	P	+	2	0	FAM47B	34871723	0.067000	0.21026	0.005000	0.12908	0.005000	0.04900	1.164000	0.31810	0.288000	0.22398	0.292000	0.19580	CCG	FAM47B	-	NULL	ENSG00000189132		0.622	FAM47B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FAM47B	HGNC	protein_coding	OTTHUMT00000056211.1	218	0.00	0	C	NM_152631		34961802	34961802	+1	no_errors	ENST00000329357	ensembl	human	known	69_37n	missense	217	38.42	136	SNP	0.874	T
FREM2	341640	genome.wustl.edu	37	13	39450219	39450219	+	Missense_Mutation	SNP	G	G	A			TCGA-AN-A0AS-01A-11W-A019-09	TCGA-AN-A0AS-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	2257c942-1274-47e7-86ad-b92ecfafc205	0ec33f45-45dc-4fd6-b1c9-0312bff04da4	g.chr13:39450219G>A	ENST00000280481.7	+	19	8558	c.8342G>A	c.(8341-8343)cGc>cAc	p.R2781H		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	2781					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		TTTTCCCTCCGCCTCATAAGG	0.418																																						dbGAP											0													161.0	151.0	154.0					13																	39450219		2203	4300	6503	-	-	-	SO:0001583	missense	0			BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.8342G>A	13.37:g.39450219G>A	ENSP00000280481:p.Arg2781His	Somatic		WXS	Illumina GAIIx	Phase_IV	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	pfam_Calx_beta,superfamily_Cadherin-like,smart_Calx_beta	p.R2781H	ENST00000280481.7	37	c.8342	CCDS31960.1	13	.	.	.	.	.	.	.	.	.	.	G	11.91	1.780004	0.31502	.	.	ENSG00000150893	ENST00000280481	T	0.18960	2.18	5.8	1.93	0.25924	.	0.295656	0.37178	N	0.002201	T	0.14830	0.0358	L	0.27053	0.805	0.22918	N	0.998565	B	0.06786	0.001	B	0.04013	0.001	T	0.18053	-1.0349	10	0.49607	T	0.09	.	12.1726	0.54167	0.2729:0.0:0.7271:0.0	.	2781	Q5SZK8	FREM2_HUMAN	H	2781	ENSP00000280481:R2781H	ENSP00000280481:R2781H	R	+	2	0	FREM2	38348219	0.142000	0.22610	0.968000	0.41197	0.752000	0.42762	0.915000	0.28638	0.056000	0.16144	-1.119000	0.02030	CGC	FREM2	-	NULL	ENSG00000150893		0.418	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FREM2	HGNC	protein_coding	OTTHUMT00000044599.2	280	0.00	0	G	NM_207361		39450219	39450219	+1	no_errors	ENST00000280481	ensembl	human	known	69_37n	missense	459	17.41	97	SNP	0.995	A
LHX9	56956	genome.wustl.edu	37	1	197890729	197890729	+	Missense_Mutation	SNP	G	G	A			TCGA-AN-A0AS-01A-11W-A019-09	TCGA-AN-A0AS-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	2257c942-1274-47e7-86ad-b92ecfafc205	0ec33f45-45dc-4fd6-b1c9-0312bff04da4	g.chr1:197890729G>A	ENST00000367387.4	+	3	1098	c.673G>A	c.(673-675)Ggg>Agg	p.G225R	LHX9_ENST00000337020.2_Missense_Mutation_p.G225R|LHX9_ENST00000367390.3_Missense_Mutation_p.G216R|LHX9_ENST00000561173.1_Missense_Mutation_p.G231R|LHX9_ENST00000367391.1_Missense_Mutation_p.G216R	NM_020204.2	NP_064589.2	Q9NQ69	LHX9_HUMAN	LIM homeobox 9	225					cell proliferation (GO:0008283)|female gonad development (GO:0008585)|gonad morphogenesis (GO:0035262)|male gonad development (GO:0008584)|motor neuron axon guidance (GO:0008045)|negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			endometrium(8)|kidney(1)|large_intestine(6)|liver(2)|lung(14)|ovary(2)|skin(1)|stomach(1)	35						CGTGCAGAAAGGGCGGCCCCG	0.662																																						dbGAP											0													27.0	25.0	25.0					1																	197890729		2203	4300	6503	-	-	-	SO:0001583	missense	0			AJ277915	CCDS1393.1, CCDS30962.1	1q31.1	2011-06-20			ENSG00000143355	ENSG00000143355		"""Homeoboxes / LIM class"""	14222	protein-coding gene	gene with protein product		606066					Standard	NM_020204		Approved		uc001guk.1	Q9NQ69	OTTHUMG00000035656	ENST00000367387.4:c.673G>A	1.37:g.197890729G>A	ENSP00000356357:p.Gly225Arg	Somatic		WXS	Illumina GAIIx	Phase_IV	Q5VUE2|Q5VUE3|Q5VUE6|Q86UH2|Q9BYU6|Q9NQ70	Missense_Mutation	SNP	pfam_Znf_LIM,pfam_Homeodomain,superfamily_Homeodomain-like,smart_Znf_LIM,smart_Homeodomain,pfscan_Znf_LIM,pfscan_Homeodomain	p.G225R	ENST00000367387.4	37	c.673	CCDS1393.1	1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.756693	0.89843	.	.	ENSG00000143355	ENST00000367391;ENST00000367390;ENST00000337020;ENST00000367387	T;D;T;D	0.89485	0.45;-2.5;0.34;-2.52	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	D	0.91425	0.7294	M	0.69823	2.125	0.80722	D	1	B;P;B	0.39748	0.096;0.686;0.245	B;P;B	0.45856	0.062;0.495;0.222	D	0.90944	0.4800	10	0.54805	T	0.06	.	19.9142	0.97043	0.0:0.0:1.0:0.0	.	225;216;216	Q9NQ69;Q9NQ69-3;Q9NQ69-2	LHX9_HUMAN;.;.	R	216;216;225;225	ENSP00000356361:G216R;ENSP00000356360:G216R;ENSP00000337969:G225R;ENSP00000356357:G225R	ENSP00000337969:G225R	G	+	1	0	LHX9	196157352	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.263000	0.95617	2.941000	0.99782	0.655000	0.94253	GGG	LHX9	-	NULL	ENSG00000143355		0.662	LHX9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	LHX9	HGNC	protein_coding	OTTHUMT00000086547.2	22	0.00	0	G	NM_020204		197890729	197890729	+1	no_errors	ENST00000367387	ensembl	human	known	69_37n	missense	26	23.53	8	SNP	1.000	A
MADCAM1	8174	genome.wustl.edu	37	19	501725	501725	+	Missense_Mutation	SNP	G	G	A	rs62130833		TCGA-AN-A0AS-01A-11W-A019-09	TCGA-AN-A0AS-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	2257c942-1274-47e7-86ad-b92ecfafc205	0ec33f45-45dc-4fd6-b1c9-0312bff04da4	g.chr19:501725G>A	ENST00000215637.3	+	4	770	c.724G>A	c.(724-726)Gac>Aac	p.D242N	MADCAM1_ENST00000346144.4_Intron|MADCAM1_ENST00000587541.1_Missense_Mutation_p.D23N|AC005775.2_ENST00000592413.1_RNA|MADCAM1_ENST00000382683.4_Intron	NM_130760.2	NP_570116.2	Q13477	MADCA_HUMAN	mucosal vascular addressin cell adhesion molecule 1	242	5.5 X 8 AA tandem repeats of [PS]-P-D-T- T-S-[QP]-E.|Mucin-like.			D -> N (in Ref. 2; AAB02194 and 3; AAC51354). {ECO:0000305}.	aging (GO:0007568)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|embryo development (GO:0009790)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)|keratinocyte differentiation (GO:0030216)|leukocyte tethering or rolling (GO:0050901)|positive regulation of leukocyte migration (GO:0002687)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	integrin binding involved in cell-matrix adhesion (GO:0098640)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(4)|prostate(1)|skin(2)	10		all_cancers(10;4.25e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGAGTCTCCCGACACCACCTC	0.682																																						dbGAP											0													26.0	42.0	36.0					19																	501725		2201	4299	6500	-	-	-	SO:0001583	missense	0			U43628	CCDS12028.1, CCDS12029.1	19p13.3	2013-01-11			ENSG00000099866	ENSG00000099866		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6765	protein-coding gene	gene with protein product	"""mucosal addressin cell adhesion molecule-1"""	102670				9162097, 8609404	Standard	NM_130762		Approved	MACAM1	uc002los.3	Q13477	OTTHUMG00000180548	ENST00000215637.3:c.724G>A	19.37:g.501725G>A	ENSP00000215637:p.Asp242Asn	Somatic		WXS	Illumina GAIIx	Phase_IV	A5PKV4|B2RPL9|O60222|O75867|Q5UGI7	Missense_Mutation	SNP	pfam_Adhes-Ig-like,smart_Ig_sub,pfscan_Ig-like	p.D242N	ENST00000215637.3	37	c.724	CCDS12028.1	19	618	0.28296703296703296	75	0.1524390243902439	133	0.3674033149171271	184	0.32167832167832167	226	0.29815303430079154	g	7.171	0.587634	0.13812	.	.	ENSG00000099866	ENST00000537731;ENST00000542525;ENST00000543297;ENST00000215637	T	0.10288	2.89	3.55	-1.32	0.09201	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.48670	-0.9015	8	0.22109	T	0.4	.	3.1363	0.06439	0.2817:0.0:0.3626:0.3557	rs62130833	242	Q13477	MADCA_HUMAN	N	266;258;250;242	ENSP00000215637:D242N	ENSP00000215637:D242N	D	+	1	0	MADCAM1	452725	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.632000	0.05489	-0.229000	0.09854	-0.378000	0.06908	GAC	MADCAM1	-	NULL	ENSG00000099866		0.682	MADCAM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	MADCAM1	HGNC	protein_coding	OTTHUMT00000451884.1	10	0.00	0	G	NM_130760		501725	501725	+1	no_errors	ENST00000215637	ensembl	human	known	69_37n	missense	1	80.00	4	SNP	0.000	A
MADD	8567	genome.wustl.edu	37	11	47304168	47304168	+	Splice_Site	SNP	G	G	T			TCGA-AN-A0AS-01A-11W-A019-09	TCGA-AN-A0AS-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	2257c942-1274-47e7-86ad-b92ecfafc205	0ec33f45-45dc-4fd6-b1c9-0312bff04da4	g.chr11:47304168G>T	ENST00000311027.5	+	9	1870		c.e9+1		MADD_ENST00000402799.1_Splice_Site|MADD_ENST00000406482.1_Splice_Site|MADD_ENST00000342922.4_Splice_Site|MADD_ENST00000407859.3_Splice_Site|MADD_ENST00000349238.3_Splice_Site|MADD_ENST00000395336.3_Splice_Site|MADD_ENST00000402192.2_Splice_Site|MADD_ENST00000395344.3_Splice_Site	NM_003682.3	NP_003673.3			MAP-kinase activating death domain											breast(7)|central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(19)|lung(26)|ovary(6)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	84				Lung(87;0.182)		ATTCACAACAGTGAGTCTACC	0.498																																						dbGAP											0													58.0	39.0	45.0					11																	47304168		2201	4298	6499	-	-	-	SO:0001630	splice_region_variant	0			AB002356	CCDS7930.1, CCDS7931.1, CCDS7932.1, CCDS41642.1, CCDS44586.1, CCDS44587.1, CCDS44588.1, CCDS44589.1, CCDS44590.1	11p11.2	2012-10-04			ENSG00000110514	ENSG00000110514		"""DENN/MADD domain containing"""	6766	protein-coding gene	gene with protein product		603584				9115275, 9796103	Standard	NM_130476		Approved	DENN, KIAA0358, RAB3GEP	uc001ner.1	Q8WXG6	OTTHUMG00000150350	ENST00000311027.5:c.1705+1G>T	11.37:g.47304168G>T		Somatic		WXS	Illumina GAIIx	Phase_IV		Splice_Site	SNP	-	e8+1	ENST00000311027.5	37	c.1705+1	CCDS7930.1	11	.	.	.	.	.	.	.	.	.	.	G	26.7	4.764370	0.89932	.	.	ENSG00000110514	ENST00000342922;ENST00000395342;ENST00000402799;ENST00000406482;ENST00000349238;ENST00000311027;ENST00000407859;ENST00000395344;ENST00000395336;ENST00000402192	.	.	.	5.77	5.77	0.91146	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.3473	0.98799	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MADD	47260744	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.386000	0.97228	2.884000	0.98904	0.655000	0.94253	.	MADD	-	-	ENSG00000110514		0.498	MADD-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	MADD	HGNC	protein_coding	OTTHUMT00000317746.1	99	0.00	0	G		Intron	47304168	47304168	+1	no_errors	ENST00000311027	ensembl	human	known	69_37n	splice_site	74	29.52	31	SNP	1.000	T
MAP3K1	4214	genome.wustl.edu	37	5	56170931	56170932	+	Frame_Shift_Ins	INS	-	-	T			TCGA-AN-A0AS-01A-11W-A019-09	TCGA-AN-A0AS-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	2257c942-1274-47e7-86ad-b92ecfafc205	0ec33f45-45dc-4fd6-b1c9-0312bff04da4	g.chr5:56170931_56170932insT	ENST00000399503.3	+	10	1759_1760	c.1759_1760insT	c.(1759-1761)cttfs	p.L587fs		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	587					activation of MAPKK activity (GO:0000186)|apoptotic mitochondrial changes (GO:0008637)|cellular response to mechanical stimulus (GO:0071260)|epithelial cell morphogenesis (GO:0003382)|eyelid development in camera-type eye (GO:0061029)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of actin filament polymerization (GO:0030838)|protein phosphorylation (GO:0006468)|regulation of cell migration (GO:0030334)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	cytosol (GO:0005829)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)			NS(1)|breast(19)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(11)|ovary(1)|skin(3)|urinary_tract(1)	57		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)		CCTCAGGCGTCTTTCCCATGAT	0.525																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			U29671, AF042838	CCDS43318.1	5q11.2	2012-02-23	2012-02-23		ENSG00000095015	ENSG00000095015		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6848	protein-coding gene	gene with protein product		600982	"""mitogen-activated protein kinase kinase kinase 1"""	MEKK1		8597633	Standard	NM_005921		Approved	MEKK, MAPKKK1	uc003jqw.4	Q13233	OTTHUMG00000059486	ENST00000399503.3:c.1762dupT	5.37:g.56170934_56170934dupT	ENSP00000382423:p.Leu587fs	Somatic		WXS	Illumina GAIIx	Phase_IV		Frame_Shift_Ins	INS	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,superfamily_ARM-type_fold,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Znf_RING,pfscan_Znf_SWIM,pfscan_Prot_kinase_cat_dom	p.S588fs	ENST00000399503.3	37	c.1759_1760	CCDS43318.1	5																																																																																			MAP3K1	-	superfamily_ARM-type_fold	ENSG00000095015		0.525	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	MAP3K1	HGNC	protein_coding	OTTHUMT00000132309.2	271	0.00	0	-	XM_042066		56170931	56170932	+1	no_errors	ENST00000399503	ensembl	human	novel	69_37n	frame_shift_ins	95	46.33	82	INS	1.000:1.000	T
NEFH	4744	genome.wustl.edu	37	22	29879515	29879515	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AN-A0AS-01A-11W-A019-09	TCGA-AN-A0AS-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	2257c942-1274-47e7-86ad-b92ecfafc205	0ec33f45-45dc-4fd6-b1c9-0312bff04da4	g.chr22:29879515delG	ENST00000310624.6	+	2	1068	c.1035delG	c.(1033-1035)cagfs	p.Q345fs		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	345	Coil 2B.|Rod.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						TGGAGAGGCAGCGCTCTGAGC	0.617																																						dbGAP											0													93.0	70.0	78.0					22																	29879515		2203	4300	6503	-	-	-	SO:0001589	frameshift_variant	0				CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"""Intermediate filaments type IV"""	7737	protein-coding gene	gene with protein product		162230	"""neurofilament, heavy polypeptide 200kDa"""				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1035delG	22.37:g.29879515delG	ENSP00000311997:p.Gln345fs	Somatic		WXS	Illumina GAIIx	Phase_IV	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Frame_Shift_Del	DEL	pfam_F,pfam_DUF1388	p.Q345fs	ENST00000310624.6	37	c.1035	CCDS13858.1	22																																																																																			NEFH	-	pfam_F	ENSG00000100285		0.617	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NEFH	HGNC	protein_coding	OTTHUMT00000321553.2	66	0.00	0	G	NM_021076		29879515	29879515	+1	no_errors	ENST00000310624	ensembl	human	known	69_37n	frame_shift_del	26	31.58	12	DEL	1.000	-
NEFH	4744	genome.wustl.edu	37	22	29879522	29879522	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AN-A0AS-01A-11W-A019-09	TCGA-AN-A0AS-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	2257c942-1274-47e7-86ad-b92ecfafc205	0ec33f45-45dc-4fd6-b1c9-0312bff04da4	g.chr22:29879522delG	ENST00000310624.6	+	2	1075	c.1042delG	c.(1042-1044)gagfs	p.E348fs		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	348	Coil 2B.|Rod.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						GCAGCGCTCTGAGCTGGAGGA	0.607																																						dbGAP											0													84.0	63.0	70.0					22																	29879522		2203	4300	6503	-	-	-	SO:0001589	frameshift_variant	0				CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"""Intermediate filaments type IV"""	7737	protein-coding gene	gene with protein product		162230	"""neurofilament, heavy polypeptide 200kDa"""				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1042delG	22.37:g.29879522delG	ENSP00000311997:p.Glu348fs	Somatic		WXS	Illumina GAIIx	Phase_IV	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Frame_Shift_Del	DEL	pfam_F,pfam_DUF1388	p.E348fs	ENST00000310624.6	37	c.1042	CCDS13858.1	22																																																																																			NEFH	-	pfam_F	ENSG00000100285		0.607	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NEFH	HGNC	protein_coding	OTTHUMT00000321553.2	65	0.00	0	G	NM_021076		29879522	29879522	+1	no_errors	ENST00000310624	ensembl	human	known	69_37n	frame_shift_del	26	31.58	12	DEL	1.000	-
OR14C36	127066	genome.wustl.edu	37	1	248512969	248512969	+	Missense_Mutation	SNP	C	C	T			TCGA-AN-A0AS-01A-11W-A019-09	TCGA-AN-A0AS-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	2257c942-1274-47e7-86ad-b92ecfafc205	0ec33f45-45dc-4fd6-b1c9-0312bff04da4	g.chr1:248512969C>T	ENST00000317861.1	+	1	893	c.893C>T	c.(892-894)gCc>gTc	p.A298V		NM_001001918.1	NP_001001918.1	Q8NHC7	O14CZ_HUMAN	olfactory receptor, family 14, subfamily C, member 36	298						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|liver(2)|lung(20)|ovary(2)|prostate(3)|skin(7)|upper_aerodigestive_tract(2)	43						ATAAAGGTGGCCATCAAGAAA	0.378																																						dbGAP											0													63.0	78.0	73.0					1																	248512969		2145	4163	6308	-	-	-	SO:0001583	missense	0			BK004466	CCDS31112.1	1q44	2012-08-09	2008-04-02	2008-04-02	ENSG00000177174	ENSG00000177174		"""GPCR / Class A : Olfactory receptors"""	15026	protein-coding gene	gene with protein product			"""olfactory receptor, family 5, subfamily BF, member 1"""	OR5BF1			Standard	NM_001001918		Approved		uc010pzl.2	Q8NHC7	OTTHUMG00000040463	ENST00000317861.1:c.893C>T	1.37:g.248512969C>T	ENSP00000324534:p.Ala298Val	Somatic		WXS	Illumina GAIIx	Phase_IV	Q6IEZ6	Missense_Mutation	SNP	pfam_7TM_GPCR_Rhodpsn,pfam_7TM_GPCR_olfarory/Srsx,prints_Olfact_rcpt,prints_7TM_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_supfam	p.A298V	ENST00000317861.1	37	c.893	CCDS31112.1	1	.	.	.	.	.	.	.	.	.	.	C	15.64	2.894541	0.52121	.	.	ENSG00000177174	ENST00000317861	T	0.44881	0.91	3.81	2.88	0.33553	.	0.720360	0.11126	N	0.596906	T	0.50377	0.1612	L	0.45581	1.43	0.09310	N	1	D	0.58268	0.982	P	0.56127	0.792	T	0.37454	-0.9705	10	0.72032	D	0.01	.	10.9569	0.47362	0.0:0.9044:0.0:0.0956	.	298	Q8NHC7	O14CZ_HUMAN	V	298	ENSP00000324534:A298V	ENSP00000324534:A298V	A	+	2	0	OR14C36	246579592	0.054000	0.20591	0.006000	0.13384	0.045000	0.14185	0.982000	0.29539	0.809000	0.34255	0.395000	0.25975	GCC	OR14C36	-	NULL	ENSG00000177174		0.378	OR14C36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	OR14C36	HGNC	protein_coding	OTTHUMT00000097359.1	238	0.42	1	C	NM_001001918		248512969	248512969	+1	no_errors	ENST00000317861	ensembl	human	known	69_37n	missense	90	46.11	77	SNP	0.089	T
PODXL2	50512	genome.wustl.edu	37	3	127358204	127358205	+	Frame_Shift_Ins	INS	-	-	C			TCGA-AN-A0AS-01A-11W-A019-09	TCGA-AN-A0AS-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	2257c942-1274-47e7-86ad-b92ecfafc205	0ec33f45-45dc-4fd6-b1c9-0312bff04da4	g.chr3:127358204_127358205insC	ENST00000342480.6	+	2	226_227	c.187_188insC	c.(187-189)gagfs	p.E63fs		NM_015720.2	NP_056535.1	Q9NZ53	PDXL2_HUMAN	podocalyxin-like 2	63					leukocyte tethering or rolling (GO:0050901)	integral component of plasma membrane (GO:0005887)	glycosaminoglycan binding (GO:0005539)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	26						GGACTCAGAGGAGCCTAGTGAG	0.639																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AF219137	CCDS3044.1	3q21.3	2005-02-18			ENSG00000114631	ENSG00000114631			17936	protein-coding gene	gene with protein product	"""endoglycan"""					10722749	Standard	NM_015720		Approved	PODLX2, endoglycan	uc003ejq.3	Q9NZ53	OTTHUMG00000159642	Exception_encountered	3.37:g.127358204_127358205insC	ENSP00000345359:p.Glu63fs	Somatic		WXS	Illumina GAIIx	Phase_IV	Q6UVY4|Q8WUV6	Frame_Shift_Ins	INS	pfam_CD34/Podocalyxin	p.E63fs	ENST00000342480.6	37	c.187_188	CCDS3044.1	3																																																																																			PODXL2	-	NULL	ENSG00000114631		0.639	PODXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PODXL2	HGNC	protein_coding	OTTHUMT00000356638.1	80	0.00	0	-	NM_015720		127358204	127358205	+1	no_errors	ENST00000342480	ensembl	human	known	69_37n	frame_shift_ins	111	31.06	50	INS	1.000:1.000	C
RAD17	5884	genome.wustl.edu	37	5	68692264	68692264	+	Missense_Mutation	SNP	C	C	T			TCGA-AN-A0AS-01A-11W-A019-09	TCGA-AN-A0AS-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	2257c942-1274-47e7-86ad-b92ecfafc205	0ec33f45-45dc-4fd6-b1c9-0312bff04da4	g.chr5:68692264C>T	ENST00000509734.1	+	15	2174	c.1496C>T	c.(1495-1497)aCg>aTg	p.T499M	RAD17_ENST00000361732.2_Missense_Mutation_p.T488M|RAD17_ENST00000521422.1_Missense_Mutation_p.T323M|RAD17_ENST00000504177.1_Intron|RAD17_ENST00000345306.6_Missense_Mutation_p.T488M|RAD17_ENST00000282891.6_Missense_Mutation_p.T402M|RAD17_ENST00000358030.2_Missense_Mutation_p.T323M|RAD17_ENST00000354868.5_Missense_Mutation_p.T488M|RAD17_ENST00000380774.3_Missense_Mutation_p.T499M|RAD17_ENST00000354312.3_Missense_Mutation_p.T488M|RAD17_ENST00000305138.4_Missense_Mutation_p.T488M			O75943	RAD17_HUMAN	RAD17 homolog (S. pombe)	499	Interaction with MCM7.				cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of DNA replication (GO:0008156)|regulation of phosphorylation (GO:0042325)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)						Lung NSC(167;5.19e-05)|Prostate(74;0.0143)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;9.36e-57)|Epithelial(20;1.21e-52)|all cancers(19;3.34e-48)|Lung(70;0.0183)		TCTATAGCTACGAGAGGTGTG	0.403								Other conserved DNA damage response genes																														dbGAP											0													73.0	65.0	67.0					5																	68692264		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF085736	CCDS4003.1, CCDS4004.1, CCDS4005.1, CCDS47226.1	5q13	2010-09-24	2001-11-28		ENSG00000152942	ENSG00000152942			9807	protein-coding gene	gene with protein product		603139	"""RAD1 (S. pombe) homolog"""			9869296, 9660800	Standard	NM_133343		Approved	Rad24, RAD17Sp, CCYC	uc003jwo.3	O75943	OTTHUMG00000099357	ENST00000509734.1:c.1496C>T	5.37:g.68692264C>T	ENSP00000426191:p.Thr499Met	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K8X2|D3DWA5|O75714|Q7Z3S4|Q9UNK7|Q9UNR7|Q9UNR8|Q9UPF5	Missense_Mutation	SNP	tigrfam_Checkpoint_prot_Rad24_fun/met	p.T499M	ENST00000509734.1	37	c.1496	CCDS4003.1	5	.	.	.	.	.	.	.	.	.	.	C	20.3	3.964999	0.74131	.	.	ENSG00000152942	ENST00000361732;ENST00000509734;ENST00000354868;ENST00000521422;ENST00000354312;ENST00000345306;ENST00000305138;ENST00000282891;ENST00000358030;ENST00000380774;ENST00000513214	T;T;T;T;T;T;T;T;T;T;T	0.24538	1.85;1.85;1.85;1.85;1.85;1.85;1.85;1.85;1.85;1.85;1.85	5.24	5.24	0.73138	.	0.203368	0.50627	D	0.000105	T	0.47619	0.1455	M	0.65975	2.015	0.58432	D	0.999993	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.68192	0.956;0.927;0.927	T	0.45293	-0.9271	10	0.72032	D	0.01	-26.0808	13.6742	0.62443	0.0:0.8446:0.1554:0.0	.	499;402;488	O75943;O75943-4;O75943-2	RAD17_HUMAN;.;.	M	488;499;488;323;488;488;488;402;323;499;107	ENSP00000355226:T488M;ENSP00000426191:T499M;ENSP00000346938:T488M;ENSP00000427743:T323M;ENSP00000346271:T488M;ENSP00000311227:T488M;ENSP00000303134:T488M;ENSP00000282891:T402M;ENSP00000350725:T323M;ENSP00000370151:T499M;ENSP00000425005:T107M	ENSP00000282891:T402M	T	+	2	0	RAD17	68728020	1.000000	0.71417	0.282000	0.24776	0.986000	0.74619	5.013000	0.64023	2.597000	0.87782	0.557000	0.71058	ACG	RAD17	-	tigrfam_Checkpoint_prot_Rad24_fun/met	ENSG00000152942		0.403	RAD17-008	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	RAD17	HGNC	protein_coding	OTTHUMT00000369171.1	86	0.00	0	C	NM_133344		68692264	68692264	+1	no_errors	ENST00000380774	ensembl	human	known	69_37n	missense	51	23.88	16	SNP	0.996	T
RYR3	6263	genome.wustl.edu	37	15	33927942	33927942	+	Silent	SNP	C	C	T			TCGA-AN-A0AS-01A-11W-A019-09	TCGA-AN-A0AS-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	2257c942-1274-47e7-86ad-b92ecfafc205	0ec33f45-45dc-4fd6-b1c9-0312bff04da4	g.chr15:33927942C>T	ENST00000389232.4	+	26	3373	c.3303C>T	c.(3301-3303)gtC>gtT	p.V1101V	RYR3_ENST00000415757.3_Silent_p.V1101V	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	1101	4 X approximate repeats.|B30.2/SPRY 2. {ECO:0000255|PROSITE- ProRule:PRU00548}.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)	p.V1101V(1)		NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		ACATGCGAGTCGGCTGGGCGA	0.502																																						dbGAP											1	Substitution - coding silent(1)	large_intestine(1)											62.0	65.0	64.0					15																	33927942		2027	4198	6225	-	-	-	SO:0001819	synonymous_variant	0				CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.3303C>T	15.37:g.33927942C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	O15175|Q15412	Silent	SNP	pfam_Ryanodine_rcpt,pfam_Ca-rel_channel,pfam_Ryanrecept_TM4-6,pfam_SPRY_rcpt,pfam_Ins145_P3_rcpt,pfam_MIR,pfam_RIH_assoc-dom,pfam_Ion_trans_dom,superfamily_MIR,superfamily_ConA-like_lec_gl,superfamily_4_helix_cytokine-like_core,superfamily_ARM-type_fold,smart_MIR_motif,smart_SPla/RYanodine_receptor_subgr,prints_Ryan_recept,pfscan_B30.2/SPRY,pfscan_EF_HAND_2,pfscan_MIR_motif	p.V1101	ENST00000389232.4	37	c.3303	CCDS45210.1	15																																																																																			RYR3	-	pfam_SPRY_rcpt,superfamily_ConA-like_lec_gl,smart_SPla/RYanodine_receptor_subgr,pfscan_B30.2/SPRY	ENSG00000198838		0.502	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	RYR3	HGNC	protein_coding	OTTHUMT00000417514.1	44	0.00	0	C			33927942	33927942	+1	no_errors	ENST00000389232	ensembl	human	known	69_37n	silent	36	16.28	7	SNP	0.003	T
SCAPER	49855	genome.wustl.edu	37	15	77025641	77025641	+	Missense_Mutation	SNP	T	T	C			TCGA-AN-A0AS-01A-11W-A019-09	TCGA-AN-A0AS-10A-01W-A021-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	2257c942-1274-47e7-86ad-b92ecfafc205	0ec33f45-45dc-4fd6-b1c9-0312bff04da4	g.chr15:77025641T>C	ENST00000563290.1	-	16	2046	c.1951A>G	c.(1951-1953)Agg>Ggg	p.R651G	SCAPER_ENST00000538941.2_Missense_Mutation_p.R405G|SCAPER_ENST00000324767.7_Missense_Mutation_p.R651G			Q9BY12	SCAPE_HUMAN	S-phase cyclin A-associated protein in the ER	651	Glu-rich.					endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(16)|ovary(2)|prostate(2)|skin(1)|urinary_tract(2)	39						TCATTAAGCCTCTGTTCATAT	0.363																																						dbGAP											0													129.0	116.0	120.0					15																	77025641		1870	4117	5987	-	-	-	SO:0001583	missense	0			AB040887, AF242528	CCDS53961.1, CCDS53962.1	15q24.3	2012-10-05	2009-03-11	2007-08-20	ENSG00000140386	ENSG00000140386		"""Zinc fingers, C2H2-type"""	13081	protein-coding gene	gene with protein product		611611	"""zinc finger protein 291"""	ZNF291		17698606	Standard	NM_020843		Approved	Zfp291	uc002bby.3	Q9BY12	OTTHUMG00000172655	ENST00000563290.1:c.1951A>G	15.37:g.77025641T>C	ENSP00000454973:p.Arg651Gly	Somatic		WXS	Illumina GAIIx	Phase_IV	F5H7X8|H3BNR7|Q3B7X7|Q96BS9|Q9H3D8|Q9NT03|Q9P274	Missense_Mutation	SNP	smart_Znf_U1	p.R651G	ENST00000563290.1	37	c.1951	CCDS53962.1	15	.	.	.	.	.	.	.	.	.	.	T	20.6	4.010001	0.75046	.	.	ENSG00000140386	ENST00000324767;ENST00000538941;ENST00000303521	T;T	0.55930	0.57;0.49	5.65	4.46	0.54185	.	0.000000	0.85682	D	0.000000	T	0.70962	0.3284	M	0.73598	2.24	0.52501	D	0.999951	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.75297	-0.3367	10	0.87932	D	0	.	13.4387	0.61099	0.0:0.0:0.2063:0.7937	.	672;405	Q9BY12-2;F5H7X8	.;.	G	651;405;673	ENSP00000326924:R651G;ENSP00000442190:R405G	ENSP00000303560:R673G	R	-	1	2	SCAPER	74812696	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.247000	0.43151	2.143000	0.66587	0.528000	0.53228	AGG	SCAPER	-	NULL	ENSG00000140386		0.363	SCAPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SCAPER	HGNC	protein_coding	OTTHUMT00000419698.1	40	0.00	0	T	NM_020843		77025641	77025641	-1	no_errors	ENST00000324767	ensembl	human	known	69_37n	missense	32	15.79	6	SNP	1.000	C
SLC6A7	6534	genome.wustl.edu	37	5	149574323	149574323	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AN-A0AS-01A-11W-A019-09	TCGA-AN-A0AS-10A-01W-A021-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	2257c942-1274-47e7-86ad-b92ecfafc205	0ec33f45-45dc-4fd6-b1c9-0312bff04da4	g.chr5:149574323delT	ENST00000230671.2	+	2	437	c.66delT	c.(64-66)agtfs	p.S22fs	SLC6A7_ENST00000524041.1_Frame_Shift_Del_p.S22fs	NM_014228.3	NP_055043.2	Q99884	SC6A7_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 7	22					proline transport (GO:0015824)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|liver(1)|lung(4)|skin(1)|stomach(1)	16		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		L-Proline(DB00172)	TGACCCCCAGTGACCAGGGCG	0.577																																						dbGAP											0													61.0	53.0	56.0					5																	149574323		2203	4300	6503	-	-	-	SO:0001589	frameshift_variant	0			S80071	CCDS4305.1	5q32	2013-07-19	2013-07-19		ENSG00000011083	ENSG00000011083		"""Solute carriers"""	11054	protein-coding gene	gene with protein product	"""brain-specific L-proline transporter"", ""sodium-dependent proline transporter"""	606205	"""solute carrier family 6 (neurotransmitter transporter, L-proline), member 7"""			7651355	Standard	NM_014228		Approved	PROT	uc003lrr.3	Q99884	OTTHUMG00000130046	ENST00000230671.2:c.66delT	5.37:g.149574323delT	ENSP00000230671:p.Ser22fs	Somatic		WXS	Illumina GAIIx	Phase_IV	Q0VG81|Q52LU6	Frame_Shift_Del	DEL	pfam_Na/ntran_symport,pfscan_Na/ntran_symport,prints_Na/ntran_symport	p.S22fs	ENST00000230671.2	37	c.66	CCDS4305.1	5																																																																																			SLC6A7	-	NULL	ENSG00000011083		0.577	SLC6A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SLC6A7	HGNC	protein_coding	OTTHUMT00000252325.1	26	0.00	0	T	NM_014228		149574323	149574323	+1	no_errors	ENST00000230671	ensembl	human	known	69_37n	frame_shift_del	10	33.33	5	DEL	1.000	-
SLC6A7	6534	genome.wustl.edu	37	5	149574326	149574327	+	Frame_Shift_Del	DEL	CC	CC	-			TCGA-AN-A0AS-01A-11W-A019-09	TCGA-AN-A0AS-10A-01W-A021-09	CC	CC					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	2257c942-1274-47e7-86ad-b92ecfafc205	0ec33f45-45dc-4fd6-b1c9-0312bff04da4	g.chr5:149574326_149574327delCC	ENST00000230671.2	+	2	440_441	c.69_70delCC	c.(67-72)gaccagfs	p.DQ23fs	SLC6A7_ENST00000524041.1_Frame_Shift_Del_p.DQ23fs	NM_014228.3	NP_055043.2	Q99884	SC6A7_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 7	23					proline transport (GO:0015824)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|liver(1)|lung(4)|skin(1)|stomach(1)	16		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		L-Proline(DB00172)	CCCCCAGTGACCAGGGCGATGT	0.584																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			S80071	CCDS4305.1	5q32	2013-07-19	2013-07-19		ENSG00000011083	ENSG00000011083		"""Solute carriers"""	11054	protein-coding gene	gene with protein product	"""brain-specific L-proline transporter"", ""sodium-dependent proline transporter"""	606205	"""solute carrier family 6 (neurotransmitter transporter, L-proline), member 7"""			7651355	Standard	NM_014228		Approved	PROT	uc003lrr.3	Q99884	OTTHUMG00000130046	ENST00000230671.2:c.69_70delCC	5.37:g.149574326_149574327delCC	ENSP00000230671:p.Asp23fs	Somatic		WXS	Illumina GAIIx	Phase_IV	Q0VG81|Q52LU6	Frame_Shift_Del	DEL	pfam_Na/ntran_symport,pfscan_Na/ntran_symport,prints_Na/ntran_symport	p.D23fs	ENST00000230671.2	37	c.69_70	CCDS4305.1	5																																																																																			SLC6A7	-	NULL	ENSG00000011083		0.584	SLC6A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SLC6A7	HGNC	protein_coding	OTTHUMT00000252325.1	25	0.00	0	CC	NM_014228		149574326	149574327	+1	no_errors	ENST00000230671	ensembl	human	known	69_37n	frame_shift_del	10	33.33	5	DEL	1.000:1.000	-
SMARCD3	6604	genome.wustl.edu	37	7	150936239	150936239	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AN-A0AS-01A-11W-A019-09	TCGA-AN-A0AS-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	2257c942-1274-47e7-86ad-b92ecfafc205	0ec33f45-45dc-4fd6-b1c9-0312bff04da4	g.chr7:150936239delG	ENST00000262188.8	-	13	1812	c.1402delC	c.(1402-1404)cagfs	p.Q469fs	SMARCD3_ENST00000392811.2_Frame_Shift_Del_p.Q456fs|RP4-548D19.3_ENST00000607902.1_RNA|SMARCD3_ENST00000477169.1_5'Flank|MIR671_ENST00000390183.1_RNA|SMARCD3_ENST00000356800.2_Frame_Shift_Del_p.Q456fs	NM_001003801.1	NP_001003801.1	Q6STE5	SMRD3_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3	469					cardiac right ventricle formation (GO:0003219)|cellular lipid metabolic process (GO:0044255)|chromatin remodeling (GO:0006338)|muscle cell differentiation (GO:0042692)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of protein binding (GO:0043393)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|secondary heart field specification (GO:0003139)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|receptor binding (GO:0005102)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(6)|ovary(2)	15			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CTGCGCTGCTGGATCTTTAGA	0.572																																						dbGAP											0													107.0	105.0	106.0					7																	150936239		2203	4300	6503	-	-	-	SO:0001589	frameshift_variant	0			U66619	CCDS5924.1, CCDS34780.1	7q35-q36	2008-07-18			ENSG00000082014	ENSG00000082014			11108	protein-coding gene	gene with protein product	"""mammalian chromatin remodeling complex BRG1-associated factor 60C"", ""Swp73-like protein"", ""SWI/SNF complex 60 kDa subunit C"", ""60kDa BRG-1/Brm associated factor subunit c"""	601737				8804307, 9693044	Standard	NM_001003801		Approved	BAF60C, Rsc6p, CRACD3	uc003wjs.3	Q6STE5	OTTHUMG00000157431	ENST00000262188.8:c.1402delC	7.37:g.150936239delG	ENSP00000262188:p.Gln469fs	Somatic		WXS	Illumina GAIIx	Phase_IV	D3DX10|Q2YD86|Q75MJ2|Q75MR8|Q92926|Q9BUH1	Frame_Shift_Del	DEL	pfam_SWIB_MDM2_domain,superfamily_SWIB_MDM2_domain,smart_SWIB_domain	p.Q468fs	ENST00000262188.8	37	c.1402	CCDS34780.1	7																																																																																			SMARCD3	-	NULL	ENSG00000082014		0.572	SMARCD3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	SMARCD3	HGNC	protein_coding	OTTHUMT00000348825.1	61	0.00	0	G	NM_001003801		150936239	150936239	-1	no_errors	ENST00000262188	ensembl	human	known	69_37n	frame_shift_del	15	11.76	2	DEL	1.000	-
TAF1	6872	genome.wustl.edu	37	X	70627430	70627430	+	Missense_Mutation	SNP	C	C	T			TCGA-AN-A0AS-01A-11W-A019-09	TCGA-AN-A0AS-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	2257c942-1274-47e7-86ad-b92ecfafc205	0ec33f45-45dc-4fd6-b1c9-0312bff04da4	g.chrX:70627430C>T	ENST00000373790.4	+	27	4162	c.4111C>T	c.(4111-4113)Cat>Tat	p.H1371Y	TAF1_ENST00000449580.1_Missense_Mutation_p.H1371Y|TAF1_ENST00000423759.1_Missense_Mutation_p.H1392Y|TAF1_ENST00000276072.3_Missense_Mutation_p.H1392Y	NM_004606.3|NM_138923.2	NP_004597.2|NP_620278.1	P21675	TAF1_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa	1371	Interaction with ASF1A and ASF1B.				cellular response to DNA damage stimulus (GO:0006974)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|protein autophosphorylation (GO:0046777)|regulation of transcription involved in G2/M transition of mitotic cell cycle (GO:0000117)|RNA polymerase II transcriptional preinitiation complex assembly (GO:0051123)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	ATP binding (GO:0005524)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)|sequence-specific DNA binding (GO:0043565)|TBP-class protein binding (GO:0017025)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(13)|central_nervous_system(6)|cervix(1)|endometrium(25)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(16)|lung(34)|ovary(9)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	124	Renal(35;0.156)	all_lung(315;0.000321)				TTAGAGACCTCATAAGTCCAT	0.473																																						dbGAP											0													87.0	79.0	82.0					X																	70627430		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS14412.1, CCDS35325.1, CCDS69783.1	Xq13.1	2011-07-01	2002-08-29	2001-12-07	ENSG00000147133	ENSG00000147133		"""Chromatin-modifying enzymes / K-acetyltransferases"""	11535	protein-coding gene	gene with protein product		313650	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, A, 250kD"", ""dystonia 3 (with Parkinsonism)"""	TAF2A, BA2R, CCG1, CCGS, DYT3		3556424, 12928496, 17952504	Standard	XM_005262295		Approved	NSCL2, TAFII250, KAT4, DYT3/TAF1	uc004dzt.4	P21675	OTTHUMG00000022723	ENST00000373790.4:c.4111C>T	X.37:g.70627430C>T	ENSP00000362895:p.His1371Tyr	Somatic		WXS	Illumina GAIIx	Phase_IV	A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	Missense_Mutation	SNP	pirsf_TAF1_animal,pfam_TFIID_sub1_DUF3591,pfam_Bromodomain,pfam_TAF_II_230-bd,superfamily_Bromodomain,superfamily_TAF_II_230-bd,smart_Bromodomain,prints_Bromodomain,pfscan_Bromodomain	p.H1371Y	ENST00000373790.4	37	c.4111	CCDS35325.1	X	.	.	.	.	.	.	.	.	.	.	.	13.93	2.384765	0.42308	.	.	ENSG00000147133	ENST00000373790;ENST00000449580;ENST00000423759;ENST00000395779;ENST00000538124;ENST00000276072	T;T;T;T	0.18174	2.23;2.23;2.23;2.23	4.95	4.95	0.65309	Bromodomain (1);	0.000000	0.85682	D	0.000000	T	0.09158	0.0226	N	0.08118	0	0.80722	D	1	B;P;B	0.42518	0.024;0.782;0.02	B;B;B	0.31495	0.026;0.131;0.017	T	0.19353	-1.0308	10	0.72032	D	0.01	.	17.4533	0.87599	0.0:1.0:0.0:0.0	.	1371;1371;1392	P21675-4;P21675;P21675-2	.;TAF1_HUMAN;.	Y	1371;1371;1392;77;77;1392	ENSP00000362895:H1371Y;ENSP00000389000:H1371Y;ENSP00000406549:H1392Y;ENSP00000276072:H1392Y	ENSP00000276072:H1392Y	H	+	1	0	TAF1	70544155	1.000000	0.71417	1.000000	0.80357	0.787000	0.44495	5.484000	0.66844	2.305000	0.77605	0.462000	0.41574	CAT	TAF1	-	pirsf_TAF1_animal,superfamily_Bromodomain	ENSG00000147133		0.473	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	TAF1	HGNC	protein_coding	OTTHUMT00000058995.2	220	0.00	0	C	NM_004606		70627430	70627430	+1	no_errors	ENST00000449580	ensembl	human	known	69_37n	missense	139	15.76	26	SNP	1.000	T
SRPK3	26576	genome.wustl.edu	37	X	153050911	153050912	+	Missense_Mutation	DNP	AG	AG	GC			TCGA-AN-A0AS-01A-11W-A019-09	TCGA-AN-A0AS-10A-01W-A021-09	A|G	A|G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	2257c942-1274-47e7-86ad-b92ecfafc205	0ec33f45-45dc-4fd6-b1c9-0312bff04da4	g.chrX:153050911_153050912AG>GC	ENST00000370101.3	+	15	1686_1687	c.1640_1641AG>GC	c.(1639-1641)gAG>gGC	p.E547G	SRPK3_ENST00000370108.3_Missense_Mutation_p.E514G|SRPK3_ENST00000370104.1_Missense_Mutation_p.E546G|SRPK3_ENST00000370100.1_Missense_Mutation_p.E472G|SRPK3_ENST00000393786.3_Missense_Mutation_p.E513G|IDH3G_ENST00000497043.1_5'Flank|SRPK3_ENST00000489426.1_Missense_Mutation_p.E614G	NM_001170760.1|NM_014370.3	NP_001164231.1|NP_055185.2	Q9UPE1	SRPK3_HUMAN	SRSF protein kinase 3	547	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell differentiation (GO:0030154)|muscle tissue development (GO:0060537)|skeletal muscle tissue development (GO:0007519)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(2)|lung(4)|ovary(2)|pancreas(2)|urinary_tract(1)	13	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)					CCCATGATGGAGTACATCCCCG	0.614																																					Esophageal Squamous(167;766 3400 32156)	dbGAP											0																																										-	-	-	SO:0001583	missense	0			AF027406	CCDS35441.1, CCDS55537.1, CCDS55538.1	Xq28	2010-06-23	2010-06-23	2006-08-17	ENSG00000184343	ENSG00000184343			11402	protein-coding gene	gene with protein product			"""serine/threonine kinase 23"", ""SFRS protein kinase 3"""	STK23		16140986	Standard	NM_014370		Approved	MSSK1	uc004fil.3	Q9UPE1	OTTHUMG00000024207	Exception_encountered	X.37:g.153050911_153050912delinsGC	ENSP00000359119:p.Glu547Gly	Somatic		WXS	Illumina GAIIx	Phase_IV	Q13583|Q4F970|Q562F5|Q9UM62	Missense_Mutation	SNP	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,pfscan_Prot_kinase_cat_dom	p.E547G|p.E547D	ENST00000370101.3	37	c.1640|c.1641	CCDS35441.1	X																																																																																			SRPK3	-	pfam_Prot_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,pfscan_Prot_kinase_cat_dom	ENSG00000184343		0.614	SRPK3-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	SRPK3	HGNC	protein_coding	OTTHUMT00000354501.1	13|14	0.00	0	A|G	NM_014370		153050911|153050912	153050911|153050912	+1	no_errors	ENST00000370101	ensembl	human	known	69_37n	missense	5|4	77.27|68.42	17|13	SNP	1.000	G|C
TBC1D10A	83874	genome.wustl.edu	37	22	30691731	30691732	+	Frame_Shift_Ins	INS	-	-	C			TCGA-AN-A0AS-01A-11W-A019-09	TCGA-AN-A0AS-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	2257c942-1274-47e7-86ad-b92ecfafc205	0ec33f45-45dc-4fd6-b1c9-0312bff04da4	g.chr22:30691731_30691732insC	ENST00000215790.7	-	4	682_683	c.518_519insG	c.(517-519)ggcfs	p.G173fs	TBC1D10A_ENST00000403362.1_Frame_Shift_Ins_p.G85fs|TBC1D10A_ENST00000403477.3_Frame_Shift_Ins_p.G180fs|RP1-130H16.18_ENST00000447976.1_Frame_Shift_Ins_p.G47fs	NM_031937.2	NP_114143.1	Q9BXI6	TB10A_HUMAN	TBC1 domain family, member 10A	173	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				activation of cysteine-type endopeptidase activity (GO:0097202)|positive regulation of proteolysis (GO:0045862)|retrograde transport, endosome to Golgi (GO:0042147)	extracellular vesicular exosome (GO:0070062)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|PDZ domain binding (GO:0030165)|Rab GTPase activator activity (GO:0005097)			cervix(2)|endometrium(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	23						CTCACCCGTGGCCCCCCCGGGA	0.609																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AF331038	CCDS13874.1, CCDS56227.1	22q12.2	2013-07-09	2005-03-10	2005-03-10	ENSG00000099992	ENSG00000099992			23609	protein-coding gene	gene with protein product	"""EBP50-PDZ interactor of 64 kD"""	610020	"""TBC1 domain family, member 10"""	TBC1D10		11285285, 20404108	Standard	NM_001204240		Approved	EPI64, AC004997.C22.2	uc010gvu.3	Q9BXI6	OTTHUMG00000150924	ENST00000215790.7:c.519dupG	22.37:g.30691738_30691738dupC	ENSP00000215790:p.Gly173fs	Somatic		WXS	Illumina GAIIx	Phase_IV	B3KXT8|O76053|Q20WK7|Q543A2	Frame_Shift_Ins	INS	pfam_Rab-GTPase-TBC_dom,superfamily_Rab-GTPase-TBC_dom,smart_Rab-GTPase-TBC_dom,pfscan_Rab-GTPase-TBC_dom	p.H174fs	ENST00000215790.7	37	c.519_518	CCDS13874.1	22																																																																																			TBC1D10A	-	pfam_Rab-GTPase-TBC_dom,superfamily_Rab-GTPase-TBC_dom,smart_Rab-GTPase-TBC_dom,pfscan_Rab-GTPase-TBC_dom	ENSG00000099992		0.609	TBC1D10A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	TBC1D10A	HGNC	protein_coding	OTTHUMT00000320550.1	26	0.00	0	-	NM_031937		30691731	30691732	-1	no_errors	ENST00000215790	ensembl	human	known	69_37n	frame_shift_ins	9	18.18	2	INS	0.998:1.000	C
TEAD2	8463	genome.wustl.edu	37	19	49850509	49850509	+	Missense_Mutation	SNP	C	C	T			TCGA-AN-A0AS-01A-11W-A019-09	TCGA-AN-A0AS-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	2257c942-1274-47e7-86ad-b92ecfafc205	0ec33f45-45dc-4fd6-b1c9-0312bff04da4	g.chr19:49850509C>T	ENST00000311227.2	-	9	937	c.847G>A	c.(847-849)Ggt>Agt	p.G283S	TEAD2_ENST00000593945.1_Missense_Mutation_p.G287S|TEAD2_ENST00000598810.1_Missense_Mutation_p.G287S|TEAD2_ENST00000377214.4_Missense_Mutation_p.G286S|TEAD2_ENST00000601519.1_Missense_Mutation_p.G286S|TEAD2_ENST00000598397.1_5'UTR|TEAD2_ENST00000539846.1_Missense_Mutation_p.G155S	NM_001256659.1|NM_003598.1	NP_001243588.1|NP_003589.1	Q15562	TEAD2_HUMAN	TEA domain family member 2	283	Transcriptional activation. {ECO:0000255}.				gene expression (GO:0010467)|hippo signaling (GO:0035329)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)	29		all_lung(116;7.65e-05)|Lung NSC(112;0.000132)|all_neural(266;0.0506)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00093)|GBM - Glioblastoma multiforme(486;0.0467)		CGGAGGCCACCCTTTTTCTCA	0.572																																						dbGAP											0													146.0	158.0	154.0					19																	49850509		2203	4300	6503	-	-	-	SO:0001583	missense	0			X94440	CCDS12761.1, CCDS58670.1, CCDS58671.1, CCDS59406.1	19q13.3	2008-07-22							11715	protein-coding gene	gene with protein product		601729				9889009, 8702974	Standard	NM_003598		Approved	TEF-4, ETF, TEF4	uc031rls.1	Q15562		ENST00000311227.2:c.847G>A	19.37:g.49850509C>T	ENSP00000310701:p.Gly283Ser	Somatic		WXS	Illumina GAIIx	Phase_IV	B4DTJ6|M0R1T9|Q8NA25|Q96IG3	Missense_Mutation	SNP	pfam_TEA/ATTS,smart_TEA/ATTS,pirsf_TEF,pfscan_TEA/ATTS,prints_TEA/ATTS	p.G286S	ENST00000311227.2	37	c.856	CCDS12761.1	19	.	.	.	.	.	.	.	.	.	.	C	21.1	4.095762	0.76870	.	.	ENSG00000074219	ENST00000311227;ENST00000377214;ENST00000539846	T;T;T	0.30182	1.54;1.54;1.54	5.03	5.03	0.67393	.	0.000000	0.64402	D	0.000004	T	0.57740	0.2074	M	0.78049	2.395	0.80722	D	1	D;D;D	0.76494	0.999;0.993;0.999	D;D;D	0.91635	0.999;0.974;0.999	T	0.62642	-0.6811	10	0.87932	D	0	-20.2964	16.2347	0.82365	0.0:1.0:0.0:0.0	.	155;283;286	B4DTJ6;Q15562;Q8NA25	.;TEAD2_HUMAN;.	S	283;286;155	ENSP00000310701:G283S;ENSP00000366419:G286S;ENSP00000437928:G155S	ENSP00000310701:G283S	G	-	1	0	TEAD2	54542321	1.000000	0.71417	0.998000	0.56505	0.066000	0.16364	6.033000	0.70925	2.529000	0.85273	0.655000	0.94253	GGT	TEAD2	-	pfam_TEA/ATTS,pirsf_TEF	ENSG00000074219		0.572	TEAD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	TEAD2	HGNC	protein_coding	OTTHUMT00000465465.1	128	0.00	0	C	NM_003598		49850509	49850509	-1	no_errors	ENST00000377214	ensembl	human	known	69_37n	missense	58	26.58	21	SNP	1.000	T
TGFA	7039	genome.wustl.edu	37	2	70742012	70742012	+	Missense_Mutation	SNP	T	T	C			TCGA-AN-A0AS-01A-11W-A019-09	TCGA-AN-A0AS-10A-01W-A021-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	2257c942-1274-47e7-86ad-b92ecfafc205	0ec33f45-45dc-4fd6-b1c9-0312bff04da4	g.chr2:70742012T>C	ENST00000295400.6	-	2	320	c.73A>G	c.(73-75)Aac>Gac	p.N25D	TGFA_ENST00000444975.1_Missense_Mutation_p.N31D|TGFA_ENST00000450929.1_Missense_Mutation_p.N31D|TGFA_ENST00000460808.1_5'UTR|TGFA_ENST00000418333.2_Missense_Mutation_p.N25D|TGFA_ENST00000445399.1_Missense_Mutation_p.N25D	NM_001099691.2|NM_003236.3	NP_001093161.1|NP_003227.1	P01135	TGFA_HUMAN	transforming growth factor, alpha	25					activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|cell proliferation (GO:0008283)|epidermal growth factor receptor signaling pathway (GO:0007173)|mammary gland alveolus development (GO:0060749)|MAPK cascade (GO:0000165)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell division (GO:0051781)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mitosis (GO:0045840)|response to drug (GO:0042493)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	epidermal growth factor receptor binding (GO:0005154)|growth factor activity (GO:0008083)|MAP kinase kinase activity (GO:0004708)			haematopoietic_and_lymphoid_tissue(1)|lung(2)|prostate(1)	4						GACGTGCTGTTCTCCAAGGCC	0.592																																						dbGAP											0													79.0	67.0	71.0					2																	70742012		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS1905.1, CCDS46316.1	2p13	2012-10-02			ENSG00000163235	ENSG00000163235			11765	protein-coding gene	gene with protein product		190170				3459638, 10552925	Standard	NM_003236		Approved		uc002sgs.4	P01135	OTTHUMG00000129669	ENST00000295400.6:c.73A>G	2.37:g.70742012T>C	ENSP00000295400:p.Asn25Asp	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K286|Q15577|Q53SK7|Q9BS56|Q9UEI3|Q9UKM1|Q9UKM2|Q9UKM3	Missense_Mutation	SNP	pfscan_EG-like_dom	p.N25D	ENST00000295400.6	37	c.73	CCDS1905.1	2	.	.	.	.	.	.	.	.	.	.	T	17.36	3.371068	0.61624	.	.	ENSG00000163235	ENST00000295400;ENST00000445399;ENST00000418333;ENST00000450929;ENST00000444975;ENST00000394241	T;T;T;T;T;T	0.20738	2.17;2.16;2.16;2.17;2.05;2.19	5.14	5.14	0.70334	.	0.000000	0.85682	D	0.000000	T	0.37972	0.1023	L	0.50333	1.59	0.35889	D	0.829548	D;D;D;D;B;D;D	0.67145	0.996;0.996;0.996;0.996;0.275;0.974;0.974	D;D;D;D;B;D;D	0.76071	0.987;0.987;0.987;0.987;0.056;0.953;0.953	T	0.42649	-0.9439	10	0.45353	T	0.12	.	11.5282	0.50593	0.0:0.0:0.0:1.0	.	31;31;25;25;25;25;25	E7EPT6;F8VNR3;P01135-5;Q9UKM3;P01135-3;P01135-2;P01135	.;.;.;.;.;.;TGFA_HUMAN	D	25;25;25;31;31;25	ENSP00000295400:N25D;ENSP00000387493:N25D;ENSP00000404099:N25D;ENSP00000414127:N31D;ENSP00000404131:N31D;ENSP00000377787:N25D	ENSP00000295400:N25D	N	-	1	0	TGFA	70595520	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	3.692000	0.54727	2.288000	0.76882	0.533000	0.62120	AAC	TGFA	-	NULL	ENSG00000163235		0.592	TGFA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	TGFA	HGNC	protein_coding	OTTHUMT00000251870.2	26	0.00	0	T			70742012	70742012	-1	no_errors	ENST00000295400	ensembl	human	known	69_37n	missense	14	26.32	5	SNP	1.000	C
TIMELESS	8914	genome.wustl.edu	37	12	56815795	56815795	+	Missense_Mutation	SNP	C	C	A			TCGA-AN-A0AS-01A-11W-A019-09	TCGA-AN-A0AS-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	2257c942-1274-47e7-86ad-b92ecfafc205	0ec33f45-45dc-4fd6-b1c9-0312bff04da4	g.chr12:56815795C>A	ENST00000553532.1	-	21	2680	c.2530G>T	c.(2530-2532)Gat>Tat	p.D844Y	TIMELESS_ENST00000229201.4_Missense_Mutation_p.D843Y|TIMELESS_ENST00000554616.1_Intron					timeless circadian clock											NS(1)|breast(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(8)|lung(14)|ovary(7)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	49						TCCACCACATCCTGCCCTGGC	0.547																																						dbGAP											0													115.0	103.0	107.0					12																	56815795		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF098162	CCDS8918.1	12q13.3	2012-12-14	2012-12-14		ENSG00000111602	ENSG00000111602			11813	protein-coding gene	gene with protein product	"""Tof1 homolog (S. cerevisiae)"", ""timeless circadian clock 1"""	603887	"""timeless (Drosophila) homolog"", ""timeless homolog (Drosophila)"""			9856465	Standard	NM_003920		Approved	hTIM, TIM, TIM1	uc001slf.2	Q9UNS1	OTTHUMG00000170600	ENST00000553532.1:c.2530G>T	12.37:g.56815795C>A	ENSP00000450607:p.Asp844Tyr	Somatic		WXS	Illumina GAIIx	Phase_IV		Missense_Mutation	SNP	pfam_TIMELESS_C,pfam_Timeless	p.D844Y	ENST00000553532.1	37	c.2530	CCDS8918.1	12	.	.	.	.	.	.	.	.	.	.	C	26.4	4.730314	0.89390	.	.	ENSG00000111602	ENST00000229201;ENST00000553532	T;T	0.17370	2.28;2.28	5.19	5.19	0.71726	Timeless C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.44582	0.1300	M	0.75085	2.285	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.41556	-0.9502	10	0.87932	D	0	-12.1077	17.8454	0.88729	0.0:1.0:0.0:0.0	.	844	Q9UNS1	TIM_HUMAN	Y	843;844	ENSP00000229201:D843Y;ENSP00000450607:D844Y	ENSP00000229201:D844Y	D	-	1	0	TIMELESS	55102062	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	6.357000	0.73051	2.595000	0.87683	0.555000	0.69702	GAT	TIMELESS	-	pfam_TIMELESS_C	ENSG00000111602		0.547	TIMELESS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	TIMELESS	HGNC	protein_coding	OTTHUMT00000409771.1	248	0.00	0	C	NM_003920		56815795	56815795	-1	no_errors	ENST00000553532	ensembl	human	known	69_37n	missense	299	13.08	45	SNP	1.000	A
TMEM44	93109	genome.wustl.edu	37	3	194331653	194331653	+	Missense_Mutation	SNP	C	C	G	rs566340131		TCGA-AN-A0AS-01A-11W-A019-09	TCGA-AN-A0AS-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	2257c942-1274-47e7-86ad-b92ecfafc205	0ec33f45-45dc-4fd6-b1c9-0312bff04da4	g.chr3:194331653C>G	ENST00000392432.2	-	9	1355	c.1150G>C	c.(1150-1152)Gtg>Ctg	p.V384L	TMEM44_ENST00000381975.3_Missense_Mutation_p.V337L|TMEM44_ENST00000473092.1_Missense_Mutation_p.V337L|TMEM44_ENST00000347147.4_Missense_Mutation_p.V337L|TMEM44_ENST00000273580.7_Missense_Mutation_p.V337L	NM_001166305.1	NP_001159777.1	Q2T9K0	TMM44_HUMAN	transmembrane protein 44	384						integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(1)|liver(1)|lung(3)|urinary_tract(1)	8	all_cancers(143;1.41e-08)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;4.34e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;9.06e-06)		ACCTGCTGCACAGGCTCGATG	0.542																																						dbGAP											0													108.0	76.0	87.0					3																	194331653		2203	4300	6503	-	-	-	SO:0001583	missense	0			AL833026	CCDS3308.1, CCDS33921.1, CCDS3308.2, CCDS54698.1, CCDS54699.1	3q29	2005-08-16			ENSG00000145014	ENSG00000145014			25120	protein-coding gene	gene with protein product							Standard	NM_138399		Approved	DKFZp686O18124	uc010hzn.3	Q2T9K0	OTTHUMG00000156023	ENST00000392432.2:c.1150G>C	3.37:g.194331653C>G	ENSP00000376227:p.Val384Leu	Somatic		WXS	Illumina GAIIx	Phase_IV	A1L3V7|B7ZLZ5|B7ZLZ6|C9JJ62|E9PGA9|Q0P6F7|Q6ZT47|Q8IXR1|Q8N4G3	Missense_Mutation	SNP	NULL	p.V384L	ENST00000392432.2	37	c.1150	CCDS54699.1	3	.	.	.	.	.	.	.	.	.	.	C	14.78	2.637429	0.47049	.	.	ENSG00000145014	ENST00000392432;ENST00000273580;ENST00000432352;ENST00000347147;ENST00000381975;ENST00000473092;ENST00000452358;ENST00000429560	T;T;T;T;T;T;T;T	0.37584	1.19;1.19;1.19;1.19;1.19;1.19;1.19;1.19	5.13	3.34	0.38264	.	0.427345	0.19991	N	0.101541	T	0.32852	0.0843	L	0.56769	1.78	0.26956	N	0.965928	P;P;P;B;B;P	0.38335	0.465;0.465;0.627;0.154;0.16;0.465	B;B;B;B;B;B	0.37198	0.243;0.177;0.198;0.074;0.041;0.243	T	0.19943	-1.0290	10	0.56958	D	0.05	-8.5928	8.3895	0.32520	0.0:0.8152:0.0:0.1848	.	337;384;69;337;337;337	E9PGA9;Q2T9K0;Q6PL43;Q2T9K0-4;Q2T9K0-2;Q2T9K0-6	.;TMM44_HUMAN;.;.;.;.	L	384;337;95;337;337;337;170;69	ENSP00000376227:V384L;ENSP00000273580:V337L;ENSP00000409963:V95L;ENSP00000333355:V337L;ENSP00000371402:V337L;ENSP00000418674:V337L;ENSP00000414333:V170L;ENSP00000403053:V69L	ENSP00000273580:V337L	V	-	1	0	TMEM44	195812942	0.855000	0.29742	0.453000	0.27007	0.768000	0.43524	1.863000	0.39459	0.663000	0.31027	0.591000	0.81541	GTG	TMEM44	-	NULL	ENSG00000145014		0.542	TMEM44-002	KNOWN	basic|CCDS	protein_coding	TMEM44	HGNC	protein_coding	OTTHUMT00000342750.1	53	0.00	0	C	NM_138399		194331653	194331653	-1	no_errors	ENST00000392432	ensembl	human	known	69_37n	missense	56	18.84	13	SNP	0.721	G
TP53	7157	genome.wustl.edu	37	17	7579356	7579358	+	In_Frame_Del	DEL	GAC	GAC	-	rs11540654|rs587780066	byFrequency	TCGA-AN-A0AS-01A-11W-A019-09	TCGA-AN-A0AS-10A-01W-A021-09	GAC	GAC					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	2257c942-1274-47e7-86ad-b92ecfafc205	0ec33f45-45dc-4fd6-b1c9-0312bff04da4	g.chr17:7579356_7579358delGAC	ENST00000269305.4	-	4	518_520	c.329_331delGTC	c.(328-333)cgtctg>ctg	p.R110del	TP53_ENST00000413465.2_In_Frame_Del_p.R110del|TP53_ENST00000359597.4_In_Frame_Del_p.R110del|TP53_ENST00000445888.2_In_Frame_Del_p.R110del|TP53_ENST00000420246.2_In_Frame_Del_p.R110del|TP53_ENST00000455263.2_In_Frame_Del_p.R110del|TP53_ENST00000574684.1_5'Flank	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	110	Interaction with HIPK1. {ECO:0000250}.|Interaction with WWOX.|Required for interaction with ZNF385A.		R -> C (in sporadic cancers; somatic mutation).|R -> G (in a sporadic cancer; somatic mutation).|R -> H (in sporadic cancers; somatic mutation).|R -> L (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation; does not induce SNAI1 degradation).|R -> P (in sporadic cancers; somatic mutation; dbSNP:rs11540654). {ECO:0000269|PubMed:17224074}.|R -> S (in a sporadic cancer; 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.R110L(36)|p.R110P(9)|p.0?(8)|p.G59fs*23(3)|p.R110fs*13(2)|p.F109_R110delFR(2)|p.R110H(2)|p.V73fs*9(1)|p.G105_T125del21(1)|p.R110fs*39(1)|p.Y107fs*44(1)|p.L111M(1)|p.L111fs*10(1)|p.Y103_G112>C(1)|p.P13fs*18(1)|p.S33fs*23(1)|p.Y107fs*38(1)|p.Y103_L111>L(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)	AAGAAGCCCAGACGGAAACCGTA	0.616		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"""	73	Substitution - Missense(48)|Deletion - Frameshift(10)|Whole gene deletion(8)|Deletion - In frame(3)|Complex - deletion inframe(2)|Insertion - Frameshift(1)|Complex - frameshift(1)	upper_aerodigestive_tract(15)|lung(14)|breast(8)|large_intestine(5)|urinary_tract(5)|liver(5)|bone(4)|soft_tissue(3)|oesophagus(3)|ovary(3)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|stomach(1)|skin(1)|pancreas(1)|autonomic_ganglia(1)	GRCh37	CM984590	TP53	M	rs11540654																																			-	-	-	SO:0001651	inframe_deletion	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.329_331delGTC	17.37:g.7579356_7579358delGAC	ENSP00000269305:p.Arg110del	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	In_Frame_Del	DEL	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.R110in_frame_del	ENST00000269305.4	37	c.331_329	CCDS11118.1	17																																																																																			TP53	-	pfam_p53_DNA-bd,superfamily_p53-like_TF_DNA-bd	ENSG00000141510		0.616	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TP53	HGNC	protein_coding	OTTHUMT00000367397.1	236	0.00	0	GAC	NM_000546		7579356	7579358	-1	no_errors	ENST00000269305	ensembl	human	known	69_37n	in_frame_del	126	45.53	107	DEL	0.011:0.000:0.004	-
TRIOBP	11078	genome.wustl.edu	37	22	38121788	38121789	+	Frame_Shift_Ins	INS	-	-	C			TCGA-AN-A0AS-01A-11W-A019-09	TCGA-AN-A0AS-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	2257c942-1274-47e7-86ad-b92ecfafc205	0ec33f45-45dc-4fd6-b1c9-0312bff04da4	g.chr22:38121788_38121789insC	ENST00000406386.3	+	7	3480_3481	c.3225_3226insC	c.(3226-3228)cccfs	p.P1076fs		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	1076					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					GGGCGTCCTCGCCCCCCCGCCA	0.653																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"""Pleckstrin homology (PH) domain containing"""	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.3232dupC	22.37:g.38121795_38121795dupC	ENSP00000384312:p.Pro1076fs	Somatic		WXS	Illumina GAIIx	Phase_IV	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Frame_Shift_Ins	INS	pfam_Pleckstrin_homology,smart_Pleckstrin_homology,pfscan_Pleckstrin_homology	p.R1077fs	ENST00000406386.3	37	c.3225_3226	CCDS43015.1	22																																																																																			TRIOBP	-	NULL	ENSG00000100106		0.653	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	TRIOBP	HGNC	protein_coding	OTTHUMT00000319439.2	18	0.00	0	-			38121788	38121789	+1	no_errors	ENST00000406386	ensembl	human	known	69_37n	frame_shift_ins	21	16.00	4	INS	0.986:0.998	C
TTN	7273	genome.wustl.edu	37	2	179455719	179455719	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AN-A0AS-01A-11W-A019-09	TCGA-AN-A0AS-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	2257c942-1274-47e7-86ad-b92ecfafc205	0ec33f45-45dc-4fd6-b1c9-0312bff04da4	g.chr2:179455719G>A	ENST00000591111.1	-	254	56034	c.55810C>T	c.(55810-55812)Cga>Tga	p.R18604*	TTN_ENST00000460472.2_Nonsense_Mutation_p.R11180*|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000589042.1_Nonsense_Mutation_p.R20245*|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000342992.6_Nonsense_Mutation_p.R17677*|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000590743.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Nonsense_Mutation_p.R11372*|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Nonsense_Mutation_p.R11305*|TTN-AS1_ENST00000590932.1_RNA			Q8WZ42	TITIN_HUMAN	titin	18604	Fibronectin type-III 34. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GCTCTAACTCGGAAAACATAT	0.463																																						dbGAP											0													207.0	205.0	206.0					2																	179455719		1910	4127	6037	-	-	-	SO:0001587	stop_gained	0			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.55810C>T	2.37:g.179455719G>A	ENSP00000465570:p.Arg18604*	Somatic		WXS	Illumina GAIIx	Phase_IV	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Nonsense_Mutation	SNP	pfam_Ig_I-set,pfam_Fibronectin_type3,pfam_Immunoglobulin,pfam_Ig_V-set,pfam_Titin_Z,pfam_PPAK_motif,pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,superfamily_Fibronectin_type3,superfamily_Calpain_domain_III,superfamily_RNaseH-like_dom,smart_Ig_sub,smart_Ig_sub2,smart_Ig_V-set_subgr,smart_Fibronectin_type3,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Fibronectin_type3,pfscan_Prot_kinase_cat_dom,pfscan_Ig-like	p.R17677*	ENST00000591111.1	37	c.53029		2	.	.	.	.	.	.	.	.	.	.	G	61	52.539969	0.99988	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	.	.	.	6.11	4.26	0.50523	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	15.3883	0.74723	0.0:0.0:0.7382:0.2617	.	.	.	.	X	17677;11180;11372;11305;11178	.	ENSP00000340554:R11372X	R	-	1	2	TTN	179163965	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	3.699000	0.54778	0.848000	0.35191	-0.182000	0.12963	CGA	TTN	-	pfam_Fibronectin_type3,superfamily_Calpain_domain_III,superfamily_Fibronectin_type3,superfamily_RNaseH-like_dom,smart_Fibronectin_type3,pfscan_Fibronectin_type3	ENSG00000155657		0.463	TTN-019	PUTATIVE	basic	protein_coding	TTN	HGNC	protein_coding	OTTHUMT00000460310.1	233	0.00	0	G	NM_133378		179455719	179455719	-1	no_errors	ENST00000342992	ensembl	human	known	69_37n	nonsense	192	17.24	40	SNP	1.000	A
WRNIP1	56897	genome.wustl.edu	37	6	2785330	2785330	+	Silent	SNP	G	G	A			TCGA-AN-A0AS-01A-11W-A019-09	TCGA-AN-A0AS-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	2257c942-1274-47e7-86ad-b92ecfafc205	0ec33f45-45dc-4fd6-b1c9-0312bff04da4	g.chr6:2785330G>A	ENST00000380773.4	+	7	2021	c.1812G>A	c.(1810-1812)ctG>ctA	p.L604L	WRNIP1_ENST00000380764.1_Silent_p.L220L|WRNIP1_ENST00000380771.4_Silent_p.L579L|WRNIP1_ENST00000380769.4_Silent_p.L384L	NM_020135.2	NP_064520.2			Werner helicase interacting protein 1											breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(2)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	14	Ovarian(93;0.0412)	all_hematologic(90;0.0895)				AAGCCTGCCTGAGGAACCACC	0.577																																						dbGAP											0													77.0	77.0	77.0					6																	2785330		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AB056152	CCDS4475.1, CCDS4476.1	6p25.2	2010-04-21			ENSG00000124535	ENSG00000124535		"""ATPases / AAA-type"""	20876	protein-coding gene	gene with protein product		608196				11301316	Standard	NM_020135		Approved	WHIP, FLJ22526, bA420G6.2	uc003mtz.3	Q96S55	OTTHUMG00000014126	ENST00000380773.4:c.1812G>A	6.37:g.2785330G>A		Somatic		WXS	Illumina GAIIx	Phase_IV		Silent	SNP	pfam_MgsA_C,pfam_ATPase_AAA_core,pfam_DNA_helicase_Holl-junc_RuvB_N,pfam_ATPase_dyneun-rel_AAA,pfam_DUF815,pfam_IstB_ATP-bd,pfam_ATPase_AAA-2,smart_Znf_Rad18_put,smart_AAA+_ATPase	p.L604	ENST00000380773.4	37	c.1812	CCDS4475.1	6																																																																																			WRNIP1	-	pfam_MgsA_C	ENSG00000124535		0.577	WRNIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	WRNIP1	HGNC	protein_coding	OTTHUMT00000039641.1	86	0.00	0	G	NM_130395		2785330	2785330	+1	no_errors	ENST00000380773	ensembl	human	known	69_37n	silent	66	34.65	35	SNP	1.000	A
XYLT2	64132	genome.wustl.edu	37	17	48431826	48431827	+	Frame_Shift_Ins	INS	-	-	C			TCGA-AN-A0AS-01A-11W-A019-09	TCGA-AN-A0AS-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	2257c942-1274-47e7-86ad-b92ecfafc205	0ec33f45-45dc-4fd6-b1c9-0312bff04da4	g.chr17:48431826_48431827insC	ENST00000017003.2	+	3	735_736	c.686_687insC	c.(685-690)ggccccfs	p.GP229fs	XYLT2_ENST00000507602.1_Frame_Shift_Ins_p.GP229fs	NM_022167.2	NP_071450.2	Q9H1B5	XYLT2_HUMAN	xylosyltransferase II	229					chondroitin sulfate biosynthetic process (GO:0030206)|glycosaminoglycan biosynthetic process (GO:0006024)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein xylosyltransferase activity (GO:0030158)			endometrium(2)|kidney(2)|large_intestine(4)|pancreas(1)|prostate(2)|urinary_tract(1)	12	Breast(11;7.18e-19)					CCCATGGATGGCCCCCCGGTGC	0.629																																						dbGAP											0										6,4258		0,6,2126						4.5	1.0			35	4,8250		0,4,4123	no	frameshift	XYLT2	NM_022167.2		0,10,6249	A1A1,A1R,RR		0.0485,0.1407,0.0799				10,12508				-	-	-	SO:0001589	frameshift_variant	0			AJ277442	CCDS11563.1	17q21.33	2013-02-25			ENSG00000015532	ENSG00000015532	2.4.2.26		15517	protein-coding gene	gene with protein product	"""protein xylosyltransferase 2"""	608125				11099377	Standard	NM_022167		Approved	XT-II, PXYLT2	uc002iqo.3	Q9H1B5	OTTHUMG00000162057	ENST00000017003.2:c.692dupC	17.37:g.48431832_48431832dupC	ENSP00000017003:p.Gly229fs	Somatic		WXS	Illumina GAIIx	Phase_IV	Q6UY41|Q86V00	Frame_Shift_Ins	INS	pfam_XylT_met,pfam_Glyco_trans_14	p.V232fs	ENST00000017003.2	37	c.686_687	CCDS11563.1	17																																																																																			XYLT2	-	NULL	ENSG00000015532		0.629	XYLT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	XYLT2	HGNC	protein_coding	OTTHUMT00000367046.1	39	0.00	0	-	NM_022167		48431826	48431827	+1	no_errors	ENST00000017003	ensembl	human	known	69_37n	frame_shift_ins	8	20.00	2	INS	0.998:0.995	C
ZNF711	7552	genome.wustl.edu	37	X	84525072	84525072	+	Missense_Mutation	SNP	G	G	A			TCGA-AN-A0AS-01A-11W-A019-09	TCGA-AN-A0AS-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	2257c942-1274-47e7-86ad-b92ecfafc205	0ec33f45-45dc-4fd6-b1c9-0312bff04da4	g.chrX:84525072G>A	ENST00000373165.3	+	8	1334	c.1028G>A	c.(1027-1029)tGt>tAt	p.C343Y	ZNF711_ENST00000542798.1_Missense_Mutation_p.C185Y|ZNF711_ENST00000276123.3_Missense_Mutation_p.C343Y|ZNF711_ENST00000395402.1_Missense_Mutation_p.C351Y|ZNF711_ENST00000360700.4_Missense_Mutation_p.C389Y	NM_021998.4	NP_068838.3	Q9Y462	ZN711_HUMAN	zinc finger protein 711	343					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|liver(1)|lung(14)|ovary(3)|skin(4)	28						CTTCAAATTTGTGACGGCATT	0.353																																						dbGAP											0													88.0	82.0	84.0					X																	84525072		2203	4300	6503	-	-	-	SO:0001583	missense	0			BC006349	CCDS35344.1	Xq21.1	2014-02-19	2006-06-29	2006-06-29	ENSG00000147180	ENSG00000147180		"""Zinc fingers, C2H2-type"""	13128	protein-coding gene	gene with protein product		314990	"""zinc finger protein 6 (CMPX1)"", ""zinc finger protein 6"""	ZNF6		19377476	Standard	XM_005262186		Approved	CMPX1, ZNF4, ZNF5, dJ75N13.1, Zfp711, MRX97	uc004eeo.3	Q9Y462	OTTHUMG00000021933	ENST00000373165.3:c.1028G>A	X.37:g.84525072G>A	ENSP00000362260:p.Cys343Tyr	Somatic		WXS	Illumina GAIIx	Phase_IV	B4DSV4|Q6NX42|Q9Y4J6	Missense_Mutation	SNP	pfam_Transcrp_activ_Zfx/Zfy-dom,pfam_Znf_C2H2,pfam_Znf_C2H2_jaz,smart_Znf_C2H2-like,pfscan_Znf_C2H2	p.C351Y	ENST00000373165.3	37	c.1052	CCDS35344.1	X	.	.	.	.	.	.	.	.	.	.	G	15.97	2.990491	0.54041	.	.	ENSG00000147180	ENST00000395402;ENST00000373165;ENST00000276123;ENST00000360700;ENST00000542798	T;T;T;T;T	0.43294	0.95;0.95;0.95;0.95;0.95	4.91	4.01	0.46588	Transcriptional activator, Zfx / Zfy domain (1);	0.000000	0.46758	U	0.000279	T	0.44705	0.1306	L	0.56769	1.78	0.35824	D	0.824801	P;P	0.50710	0.731;0.938	B;P	0.45856	0.444;0.495	T	0.60939	-0.7163	10	0.48119	T	0.1	-6.2947	14.4496	0.67376	0.0:0.1437:0.8563:0.0	.	389;343	Q9Y462-3;Q9Y462	.;ZN711_HUMAN	Y	351;343;343;389;185	ENSP00000378798:C351Y;ENSP00000362260:C343Y;ENSP00000276123:C343Y;ENSP00000353922:C389Y;ENSP00000442071:C185Y	ENSP00000276123:C343Y	C	+	2	0	ZNF711	84411728	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	5.059000	0.64306	2.008000	0.58898	0.556000	0.70494	TGT	ZNF711	-	pfam_Transcrp_activ_Zfx/Zfy-dom	ENSG00000147180		0.353	ZNF711-001	KNOWN	basic|CCDS	protein_coding	ZNF711	HGNC	protein_coding	OTTHUMT00000057388.2	179	0.00	0	G	NM_021998		84525072	84525072	+1	no_errors	ENST00000395402	ensembl	human	known	69_37n	missense	155	15.30	28	SNP	1.000	A
