#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
ANKRD36BP2	645784	genome.wustl.edu	37	2	89104384	89104384	+	RNA	SNP	G	G	A			TCGA-A8-A08Z-01A-21W-A019-09	TCGA-A8-A08Z-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	96afb6d0-29ea-4bd5-8a9d-130e42954707	35c8c6d8-68b5-4175-9d5b-2859dc94a67a	g.chr2:89104384G>A	ENST00000393525.3	+	0	4858									ankyrin repeat domain 36B pseudogene 2																		ATCCTGCAGCGTTCAAGTTTG	0.348																																						dbGAP											0																																										-	-	-			0					2q11.2	2010-09-30			ENSG00000230006	ENSG00000230006			33607	pseudogene	pseudogene							Standard	NR_015424		Approved		uc010fhg.4		OTTHUMG00000151690		2.37:g.89104384G>A		Somatic		WXS	Illumina GAIIx	Phase_IV		RNA	SNP	-	NULL	ENST00000393525.3	37	NULL		2																																																																																			ANKRD36BP2	-	-	ENSG00000230006		0.348	ANKRD36BP2-003	KNOWN	basic	processed_transcript	ANKRD36BP2	HGNC	pseudogene	OTTHUMT00000323523.1	33	0.00	0	G			89104384	89104384	+1	no_errors	ENST00000393515	ensembl	human	known	69_37n	rna	25	19.35	6	SNP	0.004	A
C16orf62	57020	genome.wustl.edu	37	16	19702725	19702727	+	In_Frame_Del	DEL	AAC	AAC	-			TCGA-A8-A08Z-01A-21W-A019-09	TCGA-A8-A08Z-10A-01W-A021-09	AAC	AAC					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	96afb6d0-29ea-4bd5-8a9d-130e42954707	35c8c6d8-68b5-4175-9d5b-2859dc94a67a	g.chr16:19702725_19702727delAAC	ENST00000251143.5	+	29	2590_2592	c.2578_2580delAAC	c.(2578-2580)aacdel	p.N861del	C16orf62_ENST00000542263.1_In_Frame_Del_p.N857del|C16orf62_ENST00000438132.3_In_Frame_Del_p.N950del|C16orf62_ENST00000417362.2_In_Frame_Del_p.N768del|C16orf62_ENST00000448695.1_In_Frame_Del_p.N711del|C16orf62_ENST00000543152.1_In_Frame_Del_p.N610del			Q7Z3J2	CP062_HUMAN	chromosome 16 open reading frame 62	861						integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	36						CCTGGCAGAAAACAACAAGCTGT	0.576																																						dbGAP											0																																										-	-	-	SO:0001651	inframe_deletion	0				CCDS32397.1, CCDS32397.2, CCDS73840.1	16p12.3	2012-05-30			ENSG00000103544	ENSG00000103544			24641	protein-coding gene	gene with protein product						10493829	Standard	NM_020314		Approved	MGC16824	uc002dgn.3	Q7Z3J2	OTTHUMG00000167925	ENST00000251143.5:c.2578_2580delAAC	16.37:g.19702728_19702730delAAC	ENSP00000251143:p.Asn861del	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K2M1|O43329|Q69YI1|Q6PDA0|Q7L371|Q86W66|Q8WXA5|Q9H0L7|Q9H7C8	In_Frame_Del	DEL	NULL	p.N950in_frame_del	ENST00000251143.5	37	c.2845_2847		16																																																																																			C16orf62	-	NULL	ENSG00000103544		0.576	C16orf62-201	KNOWN	basic|appris_principal	protein_coding	C16orf62	HGNC	protein_coding		35	0.00	0	AAC	NM_020314		19702725	19702727	+1	no_errors	ENST00000438132	ensembl	human	known	69_37n	in_frame_del	25	42.22	19	DEL	1.000:1.000:1.000	-
CELA2B	51032	genome.wustl.edu	37	1	15802970	15802970	+	Missense_Mutation	SNP	C	C	T			TCGA-A8-A08Z-01A-21W-A019-09	TCGA-A8-A08Z-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	96afb6d0-29ea-4bd5-8a9d-130e42954707	35c8c6d8-68b5-4175-9d5b-2859dc94a67a	g.chr1:15802970C>T	ENST00000375910.3	+	2	84	c.59C>T	c.(58-60)tCc>tTc	p.S20F	CELA2B_ENST00000494280.1_3'UTR	NM_015849.2	NP_056933	P08218	CEL2B_HUMAN	chymotrypsin-like elastase family, member 2B	20						extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(1)|large_intestine(1)|lung(4)|ovary(1)	8						TGTGGGGTCTCCACTTACGCG	0.537																																						dbGAP											0													124.0	118.0	120.0					1																	15802970		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS30605.1	1p36.21	2009-07-09			ENSG00000215704	ENSG00000215704			29995	protein-coding gene	gene with protein product	"""pancreatic elastase IIB"""	609444				3646943, 16327289	Standard	NM_015849		Approved	RP11-265F14.2, ELA2B	uc001awl.3	P08218	OTTHUMG00000002259	ENST00000375910.3:c.59C>T	1.37:g.15802970C>T	ENSP00000365075:p.Ser20Phe	Somatic		WXS	Illumina GAIIx	Phase_IV	Q14D16|Q6ISM5|Q96QV5	Missense_Mutation	SNP	pfam_Peptidase_S1_S6,superfamily_Pept_cys/ser_Trypsin-like,smart_Peptidase_S1_S6,pfscan_Peptidase_S1_S6,prints_Peptidase_S1A	p.S20F	ENST00000375910.3	37	c.59	CCDS30605.1	1	.	.	.	.	.	.	.	.	.	.	C	12.53	1.964680	0.34659	.	.	ENSG00000215704	ENST00000375910;ENST00000422901	D;D	0.92965	-3.14;-2.9	4.39	4.39	0.52855	Peptidase cysteine/serine, trypsin-like (1);	0.126578	0.34435	U	0.003977	D	0.88187	0.6369	L	0.39020	1.185	0.24732	N	0.993086	B	0.33073	0.396	B	0.35859	0.212	D	0.83809	0.0240	10	0.87932	D	0	.	12.4786	0.55829	0.0:1.0:0.0:0.0	.	20	P08218	CEL2B_HUMAN	F	20;4	ENSP00000365075:S20F;ENSP00000399811:S4F	ENSP00000365075:S20F	S	+	2	0	CELA2B	15675557	0.078000	0.21339	0.542000	0.28115	0.024000	0.10985	3.519000	0.53458	2.005000	0.58758	0.205000	0.17691	TCC	CELA2B	-	superfamily_Pept_cys/ser_Trypsin-like	ENSG00000215704		0.537	CELA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CELA2B	HGNC	protein_coding	OTTHUMT00000006448.1	76	0.00	0	C	NM_015849		15802970	15802970	+1	no_errors	ENST00000375910	ensembl	human	known	69_37n	missense	53	30.26	23	SNP	0.970	T
CLCA2	9635	genome.wustl.edu	37	1	86894174	86894174	+	Missense_Mutation	SNP	G	G	A	rs577301689		TCGA-A8-A08Z-01A-21W-A019-09	TCGA-A8-A08Z-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	96afb6d0-29ea-4bd5-8a9d-130e42954707	35c8c6d8-68b5-4175-9d5b-2859dc94a67a	g.chr1:86894174G>A	ENST00000370565.4	+	3	560	c.398G>A	c.(397-399)gGa>gAa	p.G133E		NM_006536.5	NP_006527.1	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2	133	Metalloprotease domain. {ECO:0000250|UniProtKB:A8K7I4}.				cell adhesion (GO:0007155)|transport (GO:0006810)	cell junction (GO:0030054)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)|ligand-gated ion channel activity (GO:0015276)			NS(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	42		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)		AGAGGGTGTGGAAAAGAGGGA	0.393													G|||	1	0.000199681	0.0	0.0	5008	,	,		21447	0.0		0.0	False		,,,				2504	0.001				Melanoma(157;1000 1898 5363 5664 48018)|Ovarian(88;135 1366 2838 28875 34642)	dbGAP											0													134.0	118.0	124.0					1																	86894174		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS708.1	1p22.3	2012-02-26	2009-01-29		ENSG00000137975	ENSG00000137975			2016	protein-coding gene	gene with protein product		604003	"""chloride channel, calcium activated, family member 2"", ""chloride channel regulator 2"""				Standard	NM_006536		Approved	CLCRG2	uc001dlr.4	Q9UQC9	OTTHUMG00000010256	ENST00000370565.4:c.398G>A	1.37:g.86894174G>A	ENSP00000359596:p.Gly133Glu	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K2T3|Q9Y6N2	Missense_Mutation	SNP	pfam_Cl_channel_Ca,pfam_DUF1973,pfam_VWF_A,smart_VWF_A,pfscan_VWF_A,tigrfam_CaCC_prot	p.G133E	ENST00000370565.4	37	c.398	CCDS708.1	1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	24.3|24.3	4.515133|4.515133	0.85389|0.85389	.|.	.|.	ENSG00000137975|ENSG00000137975	ENST00000439777|ENST00000370565	.|T	.|0.14391	.|2.51	5.59|5.59	5.59|5.59	0.84812|0.84812	.|Chloride channel calcium-activated (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.34106|0.34106	0.0886|0.0886	M|M	0.78285|0.78285	2.405|2.405	0.58432|0.58432	D|D	0.999992|0.999992	.|D	.|0.89917	.|1.0	.|D	.|0.97110	.|1.0	T|T	0.03993|0.03993	-1.0986|-1.0986	6|10	0.06236|0.54805	T|T	0.91|0.06	-19.5853|-19.5853	19.5457|19.5457	0.95295|0.95295	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|133	.|Q9UQC9	.|CLCA2_HUMAN	K|E	127|133	.|ENSP00000359596:G133E	ENSP00000403373:E127K|ENSP00000359596:G133E	E|G	+|+	1|2	0|0	CLCA2|CLCA2	86666762|86666762	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.974000|0.974000	0.67602|0.67602	7.261000|7.261000	0.78400|0.78400	2.763000|2.763000	0.94921|0.94921	0.655000|0.655000	0.94253|0.94253	GAA|GGA	CLCA2	-	pfam_Cl_channel_Ca,tigrfam_CaCC_prot	ENSG00000137975		0.393	CLCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CLCA2	HGNC	protein_coding	OTTHUMT00000028284.1	197	0.00	0	G	NM_006536		86894174	86894174	+1	no_errors	ENST00000370565	ensembl	human	known	69_37n	missense	141	18.97	33	SNP	1.000	A
CD1E	913	genome.wustl.edu	37	1	158326619	158326619	+	Missense_Mutation	SNP	C	C	T			TCGA-A8-A08Z-01A-21W-A019-09	TCGA-A8-A08Z-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	96afb6d0-29ea-4bd5-8a9d-130e42954707	35c8c6d8-68b5-4175-9d5b-2859dc94a67a	g.chr1:158326619C>T	ENST00000368167.3	+	6	1339	c.1100C>T	c.(1099-1101)gCa>gTa	p.A367V	CD1E_ENST00000452291.2_Missense_Mutation_p.A178V|CD1E_ENST00000368157.1_Missense_Mutation_p.A111V|CD1E_ENST00000444681.2_Missense_Mutation_p.A268V|CD1E_ENST00000368164.3_3'UTR|CD1E_ENST00000368163.3_Missense_Mutation_p.A300V|CD1E_ENST00000368165.3_Missense_Mutation_p.A277V|CD1E_ENST00000368161.3_3'UTR|CD1E_ENST00000368160.3_Missense_Mutation_p.A355V|CD1E_ENST00000368166.3_Missense_Mutation_p.A166V|CD1E_ENST00000368155.3_Missense_Mutation_p.A210V|CD1E_ENST00000368156.1_Missense_Mutation_p.A265V|CD1E_ENST00000368154.1_Missense_Mutation_p.A123V	NM_030893.3	NP_112155.2	P15812	CD1E_HUMAN	CD1e molecule	367					antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	lipid binding (GO:0008289)			breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(27)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|urinary_tract(1)	49	all_hematologic(112;0.0378)					TTCTGCTTGGCACAAGTATCG	0.428																																						dbGAP											0													118.0	113.0	115.0					1																	158326619		1914	4135	6049	-	-	-	SO:0001583	missense	0			AJ289111	CCDS41417.1, CCDS41418.1, CCDS41419.1, CCDS41420.1, CCDS41421.1, CCDS41422.1, CCDS53387.1, CCDS53388.1, CCDS53389.1, CCDS53390.1, CCDS53384.1, CCDS53385.1, CCDS53386.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158488	ENSG00000158488		"""CD molecules"", ""Immunoglobulin superfamily / C1-set domain containing"""	1638	protein-coding gene	gene with protein product		188411	"""CD1E antigen, e polypeptide"", ""CD1e antigen"""			10948205	Standard	NM_001042585		Approved		uc001fse.3	P15812	OTTHUMG00000017515	ENST00000368167.3:c.1100C>T	1.37:g.158326619C>T	ENSP00000357149:p.Ala367Val	Somatic		WXS	Illumina GAIIx	Phase_IV	B4DZV3|E7EP01|Q5TDJ9|Q5TDK3|Q5TDK4|Q5TDK5|Q5TDK6|Q5TDK8|Q5TDL1|Q712E4|Q712E5|Q712E6|Q712E7|Q712E8|Q712E9|Q712F0|Q712F1|Q712F2|Q712F3|Q712F4|Q712F5|Q96TD0|Q96TD1|Q9UMM1|Q9Y5M3	Missense_Mutation	SNP	pfam_Ig_C1-set,superfamily_MHC_I/II-like_Ag-recog,smart_Ig_C1-set,pfscan_Ig-like	p.A367V	ENST00000368167.3	37	c.1100	CCDS41417.1	1	.	.	.	.	.	.	.	.	.	.	C	18.00	3.524492	0.64747	.	.	ENSG00000158488	ENST00000444681;ENST00000368167;ENST00000452291;ENST00000368165;ENST00000368166;ENST00000368163;ENST00000368157;ENST00000368160;ENST00000368156;ENST00000368155;ENST00000368154	T;T;T;T;T;T;T;T;T;T;T	0.57907	4.92;4.38;3.05;3.05;3.21;2.63;0.37;4.44;3.17;2.82;0.39	4.76	3.85	0.44370	.	0.770342	0.11074	N	0.602538	T	0.54398	0.1856	L	0.60455	1.87	0.09310	N	1	D;D;B;D;D;D;D;D;D;B	0.71674	0.993;0.995;0.192;0.995;0.995;0.991;0.996;0.998;0.997;0.077	P;D;B;P;P;P;P;D;D;B	0.76071	0.767;0.917;0.037;0.844;0.844;0.703;0.883;0.987;0.91;0.037	T	0.45131	-0.9282	10	0.87932	D	0	-1.7945	8.8597	0.35249	0.0:0.8979:0.0:0.1021	.	268;277;210;166;355;367;178;123;265;300	E7EP01;P15812-5;P15812-7;P15812-9;P15812-2;P15812;P15812-8;P15812-11;P15812-6;P15812-4	.;.;.;.;.;CD1E_HUMAN;.;.;.;.	V	268;367;178;277;166;300;111;355;265;210;123	ENSP00000402906:A268V;ENSP00000357149:A367V;ENSP00000416228:A178V;ENSP00000357147:A277V;ENSP00000357148:A166V;ENSP00000357145:A300V;ENSP00000357139:A111V;ENSP00000357142:A355V;ENSP00000357138:A265V;ENSP00000357137:A210V;ENSP00000357136:A123V	ENSP00000357136:A123V	A	+	2	0	CD1E	156593243	0.000000	0.05858	0.002000	0.10522	0.106000	0.19336	0.137000	0.15995	1.226000	0.43582	0.655000	0.94253	GCA	CD1E	-	NULL	ENSG00000158488		0.428	CD1E-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	CD1E	HGNC	protein_coding	OTTHUMT00000046353.3	272	0.00	0	C	NM_030893		158326619	158326619	+1	no_errors	ENST00000368167	ensembl	human	known	69_37n	missense	256	15.79	48	SNP	0.002	T
COL27A1	85301	genome.wustl.edu	37	9	116930357	116930357	+	Silent	SNP	C	C	T			TCGA-A8-A08Z-01A-21W-A019-09	TCGA-A8-A08Z-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	96afb6d0-29ea-4bd5-8a9d-130e42954707	35c8c6d8-68b5-4175-9d5b-2859dc94a67a	g.chr9:116930357C>T	ENST00000356083.3	+	3	913	c.522C>T	c.(520-522)tgC>tgT	p.C174C		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	174	Laminin G-like.				extracellular matrix organization (GO:0030198)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|fibrillar collagen trimer (GO:0005583)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(30)|ovary(4)|prostate(6)|skin(3)|soft_tissue(1)|stomach(1)|urinary_tract(3)	80						TGACTGCCTGCGGGCAGCGCC	0.682																																						dbGAP											0													18.0	20.0	19.0					9																	116930357		2186	4277	6463	-	-	-	SO:0001819	synonymous_variant	0			AB058773	CCDS6802.1	9q33.1	2013-01-16			ENSG00000196739	ENSG00000196739		"""Collagens"""	22986	protein-coding gene	gene with protein product		608461				12766169	Standard	NM_032888		Approved	KIAA1870, MGC11337, FLJ11895	uc011lxl.2	Q8IZC6	OTTHUMG00000020537	ENST00000356083.3:c.522C>T	9.37:g.116930357C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	Q66K43|Q96JF7	Silent	SNP	pfam_Collagen,pfam_Fib_collagen_C,superfamily_ConA-like_lec_gl,smart_Laminin_G,smart_Fib_collagen_C	p.C174	ENST00000356083.3	37	c.522	CCDS6802.1	9																																																																																			COL27A1	-	superfamily_ConA-like_lec_gl,smart_Laminin_G	ENSG00000196739		0.682	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	COL27A1	HGNC	protein_coding	OTTHUMT00000053763.1	23	0.00	0	C	NM_032888		116930357	116930357	+1	no_errors	ENST00000356083	ensembl	human	known	69_37n	silent	14	39.13	9	SNP	0.992	T
DAB2IP	153090	genome.wustl.edu	37	9	124519319	124519319	+	Silent	SNP	G	G	A			TCGA-A8-A08Z-01A-21W-A019-09	TCGA-A8-A08Z-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	96afb6d0-29ea-4bd5-8a9d-130e42954707	35c8c6d8-68b5-4175-9d5b-2859dc94a67a	g.chr9:124519319G>A	ENST00000408936.3	+	4	572	c.390G>A	c.(388-390)gaG>gaA	p.E130E	DAB2IP_ENST00000309989.1_Silent_p.E6E|DAB2IP_ENST00000487716.1_3'UTR|DAB2IP_ENST00000259371.2_Silent_p.E102E			Q5VWQ8	DAB2P_HUMAN	DAB2 interacting protein	130	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				activation of JUN kinase activity (GO:0007257)|activation of MAPKKK activity (GO:0000185)|angiogenesis (GO:0001525)|cell cycle (GO:0007049)|cell motility involved in cerebral cortex radial glia guided migration (GO:0021814)|cellular protein catabolic process (GO:0044257)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial cell apoptotic process (GO:0072577)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|layer formation in cerebral cortex (GO:0021819)|negative regulation of angiogenesis (GO:0016525)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of G0 to G1 transition (GO:0070317)|negative regulation of GTPase activity (GO:0034260)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphatidylinositol 3-kinase activity (GO:0043553)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of Ras GTPase activity (GO:0034261)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|neuron projection morphogenesis (GO:0048812)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of dendrite development (GO:1900006)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron migration (GO:2001224)|positive regulation of neuron projection development (GO:0010976)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of synapse maturation (GO:0090129)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of ARF GTPase activity (GO:0032312)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein complex assembly (GO:0043254)|response to unfolded protein (GO:0006986)|transformed cell apoptotic process (GO:0006927)|tube formation (GO:0035148)|vascular endothelial growth factor receptor-2 signaling pathway (GO:0036324)	axon (GO:0030424)|cerebellar mossy fiber (GO:0044300)|climbing fiber (GO:0044301)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|neuronal cell body (GO:0043025)|neuronal cell body membrane (GO:0032809)|parallel fiber (GO:1990032)|plasma membrane (GO:0005886)	14-3-3 protein binding (GO:0071889)|death receptor binding (GO:0005123)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|mitogen-activated protein kinase kinase binding (GO:0031434)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulatory subunit binding (GO:0036312)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein phosphatase 2A binding (GO:0051721)|Ras GTPase activator activity (GO:0005099)|SH3 domain binding (GO:0017124)|signaling adaptor activity (GO:0035591)|vascular endothelial growth factor receptor 2 binding (GO:0043184)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(8)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	27						GGCTGAAGGAGTCTCGCTCCC	0.647																																						dbGAP											0													114.0	97.0	102.0					9																	124519319		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AF367051	CCDS6832.1, CCDS6833.2	9q33.1-q33.3	2008-07-21			ENSG00000136848	ENSG00000136848			17294	protein-coding gene	gene with protein product	"""nGAP-like protein"", ""DOC-2/DAB2 interactive protein"", ""ASK-interacting protein"", ""ASK1-interacting protein 1"""	609205				11944990, 11812785	Standard	XM_005251721		Approved	AF9Q34, DIP1/2, KIAA1743, AIP1	uc004bln.3	Q5VWQ8	OTTHUMG00000020595	ENST00000408936.3:c.390G>A	9.37:g.124519319G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	A6H8V2|A6NHI9|B0QZB1|G3XA90|Q8TDL2|Q96SE1|Q9C0C0	Silent	SNP	pfam_DUF3498,pfam_RasGAP,pfam_C2_Ca-dep,superfamily_Rho_GTPase_activation_prot,superfamily_C2_Ca/lipid-bd_dom_CaLB,smart_Pleckstrin_homology,smart_C2_Ca-dep,smart_RasGAP,pfscan_Pleckstrin_homology,pfscan_RasGAP	p.E130	ENST00000408936.3	37	c.390		9																																																																																			DAB2IP	-	smart_Pleckstrin_homology	ENSG00000136848		0.647	DAB2IP-009	KNOWN	basic|appris_candidate_longest	protein_coding	DAB2IP	HGNC	protein_coding	OTTHUMT00000317857.1	32	0.00	0	G	NM_032552		124519319	124519319	+1	no_errors	ENST00000408936	ensembl	human	known	69_37n	silent	12	25.00	4	SNP	1.000	A
EIF4A2	1974	genome.wustl.edu	37	3	186503952	186503952	+	Splice_Site	SNP	G	G	A			TCGA-A8-A08Z-01A-21W-A019-09	TCGA-A8-A08Z-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	96afb6d0-29ea-4bd5-8a9d-130e42954707	35c8c6d8-68b5-4175-9d5b-2859dc94a67a	g.chr3:186503952G>A	ENST00000323963.5	+	6	581		c.e6-1		SNORA63_ENST00000363548.1_RNA|SNORA63_ENST00000363450.1_RNA|SNORA81_ENST00000408493.2_RNA|RP11-573D15.9_ENST00000577781.1_RNA|EIF4A2_ENST00000356531.5_Splice_Site|SNORD2_ENST00000459163.1_RNA|SNORA4_ENST00000584302.1_RNA|EIF4A2_ENST00000440191.2_Splice_Site			Q14240	IF4A2_HUMAN	eukaryotic translation initiation factor 4A2						cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|translation initiation factor activity (GO:0003743)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(2)|urinary_tract(1)	28	all_cancers(143;2.68e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.07e-20)	GBM - Glioblastoma multiforme(93;0.0704)		GTTTCTAACAGCTCCAAAATG	0.308			T	BCL6	NHL																																	dbGAP		Dom	yes		3	3q27.3	1974	"""eukaryotic translation initiation factor 4A, isoform 2"""		L	0													73.0	71.0	72.0					3																	186503952		2203	4300	6503	-	-	-	SO:0001630	splice_region_variant	0			D30655	CCDS3282.1	3q28	2012-02-23	2010-02-10		ENSG00000156976	ENSG00000156976	3.6.1.1	"""DEAD-boxes"""	3284	protein-coding gene	gene with protein product		601102	"""eukaryotic translation initiation factor 4A, isoform 2"""	EIF4F		8521730	Standard	NM_001967		Approved	DDX2B, EIF4A, BM-010	uc003fqs.3	Q14240	OTTHUMG00000156564	ENST00000323963.5:c.518-1G>A	3.37:g.186503952G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	D3DNU9|Q53XJ6|Q96B90|Q96EA8	Splice_Site	SNP	-	e6-1	ENST00000323963.5	37	c.521-1	CCDS3282.1	3	.	.	.	.	.	.	.	.	.	.	G	16.41	3.116301	0.56505	.	.	ENSG00000156976	ENST00000323963;ENST00000440191;ENST00000356531	.	.	.	5.13	5.13	0.70059	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.4642	0.84073	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	EIF4A2	187986646	1.000000	0.71417	1.000000	0.80357	0.900000	0.52787	8.941000	0.92964	2.827000	0.97445	0.650000	0.86243	.	EIF4A2	-	-	ENSG00000156976		0.308	EIF4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	EIF4A2	HGNC	protein_coding	OTTHUMT00000344609.1	99	0.00	0	G	NM_001967	Intron	186503952	186503952	+1	no_errors	ENST00000440191	ensembl	human	known	69_37n	splice_site	53	29.33	22	SNP	1.000	A
ERBB2	2064	genome.wustl.edu	37	17	37881332	37881332	+	Missense_Mutation	SNP	G	G	A			TCGA-A8-A08Z-01A-21W-A019-09	TCGA-A8-A08Z-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	96afb6d0-29ea-4bd5-8a9d-130e42954707	35c8c6d8-68b5-4175-9d5b-2859dc94a67a	g.chr17:37881332G>A	ENST00000269571.5	+	21	2683	c.2524G>A	c.(2524-2526)Gta>Ata	p.V842I	ERBB2_ENST00000584601.1_Missense_Mutation_p.V812I|ERBB2_ENST00000584450.1_Missense_Mutation_p.V842I|ERBB2_ENST00000406381.2_Missense_Mutation_p.V812I|ERBB2_ENST00000540147.1_Missense_Mutation_p.V812I|ERBB2_ENST00000541774.1_Missense_Mutation_p.V827I|MIR4728_ENST00000580969.1_RNA|ERBB2_ENST00000445658.2_Missense_Mutation_p.V566I			P04626	ERBB2_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2	842	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|enzyme linked receptor protein signaling pathway (GO:0007167)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|motor neuron axon guidance (GO:0008045)|myelination (GO:0042552)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine phosphorylation (GO:0018108)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of angiogenesis (GO:0045765)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of microtubule-based process (GO:0032886)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|ErbB-3 class receptor binding (GO:0043125)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|RNA polymerase I core binding (GO:0001042)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)	p.V842I(6)		NS(1)|breast(16)|central_nervous_system(17)|endometrium(6)|haematopoietic_and_lymphoid_tissue(8)|kidney(4)|large_intestine(16)|liver(3)|lung(125)|ovary(18)|pancreas(1)|prostate(4)|skin(1)|stomach(14)|upper_aerodigestive_tract(9)|urinary_tract(4)	247	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)	Ovarian(249;0.0547)|Colorectal(1115;0.234)	UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0767)	ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Lapatinib(DB01259)|Pertuzumab(DB06366)|Trastuzumab(DB00072)	TGTGCGGCTCGTACACAGGGA	0.597		1	"""A, Mis, O"""		"""breast, ovarian, other tumour types, NSCLC, gastric"""					TCGA GBM(5;<1E-08)																												dbGAP		Dom	yes		17	17q21.1	2064	"""v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)"""		E	6	Substitution - Missense(6)	large_intestine(5)|stomach(1)											70.0	61.0	64.0					17																	37881332		2203	4300	6503	-	-	-	SO:0001583	missense	0			X03363	CCDS32642.1, CCDS45667.1, CCDS74052.1	17q11.2-q12	2014-09-17	2013-07-09			ENSG00000141736		"""CD molecules"""	3430	protein-coding gene	gene with protein product	"""neuro/glioblastoma derived oncogene homolog"""	164870	"""v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2 (neuro/glioblastoma derived oncogene homolog)"""	NGL			Standard	XM_005257140		Approved	NEU, HER-2, CD340, HER2	uc002hso.3	P04626		ENST00000269571.5:c.2524G>A	17.37:g.37881332G>A	ENSP00000269571:p.Val842Ile	Somatic		WXS	Illumina GAIIx	Phase_IV	B2RZG3|B4DHN3|Q14256|Q6LDV1|Q9UMK4|X5D2V5	Missense_Mutation	SNP	pirsf_Tyr_kinase_EGF/ERB/XmrK_rcpt,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_EGF_rcpt_L,pfam_Prot_kinase_cat_dom,pfam_Furin-like_Cys-rich_dom,superfamily_Kinase-like_dom,superfamily_Growth_fac_rcpt,smart_Furin_repeat,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,prints_Ser-Thr/Tyr_kinase_cat_dom,pfscan_Prot_kinase_cat_dom	p.V842I	ENST00000269571.5	37	c.2524	CCDS32642.1	17	.	.	.	.	.	.	.	.	.	.	G	16.87	3.241303	0.58995	.	.	ENSG00000141736	ENST00000406381;ENST00000541774;ENST00000445658;ENST00000269571;ENST00000540147	D;D;D;D;D	0.83163	-1.69;-1.69;-1.69;-1.69;-1.69	5.09	5.09	0.68999	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	D	0.85106	0.5621	N	0.21142	0.635	0.80722	D	1	D;D;D	0.76494	0.997;0.979;0.999	D;P;D	0.64506	0.92;0.559;0.926	D	0.87344	0.2333	9	0.87932	D	0	.	18.2846	0.90110	0.0:0.0:1.0:0.0	.	566;827;842	B4DTR1;P04626-4;P04626	.;.;ERBB2_HUMAN	I	812;827;566;842;812	ENSP00000385185:V812I;ENSP00000446466:V827I;ENSP00000404047:V566I;ENSP00000269571:V842I;ENSP00000443562:V812I	ENSP00000269571:V842I	V	+	1	0	ERBB2	35134858	1.000000	0.71417	0.919000	0.36401	0.900000	0.52787	9.657000	0.98554	2.651000	0.90000	0.563000	0.77884	GTA	ERBB2	-	pirsf_Tyr_kinase_EGF/ERB/XmrK_rcpt,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Prot_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,prints_Ser-Thr/Tyr_kinase_cat_dom,pfscan_Prot_kinase_cat_dom	ENSG00000141736		0.597	ERBB2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	ERBB2	HGNC	protein_coding	OTTHUMT00000445621.2	79	0.00	0	G			37881332	37881332	+1	no_errors	ENST00000269571	ensembl	human	known	69_37n	missense	19	41.18	14	SNP	1.000	A
SUPT20H	55578	genome.wustl.edu	37	13	37584782	37584782	+	Silent	SNP	C	C	T			TCGA-A8-A08Z-01A-21W-A019-09	TCGA-A8-A08Z-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	96afb6d0-29ea-4bd5-8a9d-130e42954707	35c8c6d8-68b5-4175-9d5b-2859dc94a67a	g.chr13:37584782C>T	ENST00000350612.6	-	25	2329	c.2109G>A	c.(2107-2109)caG>caA	p.Q703Q	SUPT20H_ENST00000464744.1_Intron|SUPT20H_ENST00000356185.3_Intron|SUPT20H_ENST00000475892.1_Intron|SUPT20H_ENST00000360252.4_Intron	NM_001014286.2	NP_001014308.2	Q8NEM7	SP20H_HUMAN	suppressor of Ty 20 homolog (S. cerevisiae)	703	Gln-rich.				autophagy (GO:0006914)|chromatin organization (GO:0006325)|gastrulation (GO:0007369)	SAGA complex (GO:0000124)|SAGA-type complex (GO:0070461)	transcription cofactor activity (GO:0003712)										CAGAGCCAAGCTGAGACAACA	0.468																																						dbGAP											0													69.0	67.0	68.0					13																	37584782		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AF093250	CCDS9362.1, CCDS31959.1, CCDS61311.1	13q13	2012-11-29	2012-11-29	2012-11-29	ENSG00000102710	ENSG00000102710			20596	protein-coding gene	gene with protein product	"""p38 interacting protein"", ""transcription factor (p38 interacting protein)"""	613417	"""chromosome 13 open reading frame 19"", ""family with sequence similarity 48, member A"""	C13orf19, FAM48A		12070015 , 16685401	Standard	NM_001278480		Approved	SPT20, bA421P11.4, P38IP	uc001uwg.3	Q8NEM7	OTTHUMG00000016747	ENST00000350612.6:c.2109G>A	13.37:g.37584782C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	E7ER46|Q71RF3|Q9Y6A6	Missense_Mutation	SNP	NULL	p.S246N	ENST00000350612.6	37	c.737	CCDS31959.1	13	.	.	.	.	.	.	.	.	.	.	C	4.411	0.076036	0.08485	.	.	ENSG00000102710	ENST00000469488	.	.	.	5.55	5.55	0.83447	.	.	.	.	.	T	0.74876	0.3774	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.72050	-0.4407	4	.	.	.	.	18.671	0.91512	0.0:1.0:0.0:0.0	.	.	.	.	N	246	.	.	S	-	2	0	FAM48A	36482782	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.120000	0.71596	2.885000	0.99019	0.655000	0.94253	AGC	FAM48A	-	NULL	ENSG00000102710		0.468	SUPT20H-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	FAM48A	HGNC	protein_coding	OTTHUMT00000354766.1	94	0.00	0	C	NM_017569		37584782	37584782	-1	no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region	ENST00000469488	ensembl	human	putative	69_37n	missense	45	25.00	15	SNP	1.000	T
FAT3	120114	genome.wustl.edu	37	11	92087511	92087511	+	Missense_Mutation	SNP	A	A	T			TCGA-A8-A08Z-01A-21W-A019-09	TCGA-A8-A08Z-10A-01W-A021-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	96afb6d0-29ea-4bd5-8a9d-130e42954707	35c8c6d8-68b5-4175-9d5b-2859dc94a67a	g.chr11:92087511A>T	ENST00000298047.6	+	1	2250	c.2233A>T	c.(2233-2235)Att>Ttt	p.I745F	FAT3_ENST00000409404.2_Missense_Mutation_p.I745F|FAT3_ENST00000541502.1_Missense_Mutation_p.I745F|FAT3_ENST00000525166.1_Missense_Mutation_p.I595F			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	745	Cadherin 7. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				TGGTGCTAACATTCTGAAGAT	0.358										TCGA Ovarian(4;0.039)																												dbGAP											0													147.0	150.0	149.0					11																	92087511		1905	4129	6034	-	-	-	SO:0001583	missense	0			AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"""Cadherins / Cadherin-related"""	23112	protein-coding gene	gene with protein product	"""cadherin-related family member 10"""	612483	"""FAT tumor suppressor homolog 3 (Drosophila)"""			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.2233A>T	11.37:g.92087511A>T	ENSP00000298047:p.Ile745Phe	Somatic		WXS	Illumina GAIIx	Phase_IV	B5MDB0|Q96AU6	Missense_Mutation	SNP	pfam_Cadherin,pfam_Laminin_G,pfam_EGF-like_Ca-bd,superfamily_ConA-like_lec_gl,superfamily_Cadherin-like,smart_Cadherin,smart_EGF-like,smart_Laminin_G,smart_EGF-like_Ca-bd,prints_Cadherin,pfscan_EG-like_dom,pfscan_Laminin_G,pfscan_Cadherin	p.I745F	ENST00000298047.6	37	c.2233		11	.	.	.	.	.	.	.	.	.	.	A	16.92	3.256545	0.59321	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000541502;ENST00000525166	T;T;T;T	0.55052	0.54;0.54;0.54;0.54	5.47	5.47	0.80525	.	.	.	.	.	T	0.67618	0.2912	M	0.73372	2.23	0.52501	D	0.999952	D	0.60575	0.988	P	0.58520	0.84	T	0.72239	-0.4351	9	0.87932	D	0	.	14.7334	0.69399	1.0:0.0:0.0:0.0	.	745	Q8TDW7-3	.	F	745;745;745;595	ENSP00000298047:I745F;ENSP00000387040:I745F;ENSP00000443786:I745F;ENSP00000432586:I595F	ENSP00000298047:I745F	I	+	1	0	FAT3	91727159	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.399000	0.79935	2.075000	0.62263	0.383000	0.25322	ATT	FAT3	-	pfam_Cadherin,superfamily_Cadherin-like,pfscan_Cadherin	ENSG00000165323		0.358	FAT3-201	KNOWN	basic	protein_coding	FAT3	HGNC	protein_coding		428	0.00	0	A	NM_001008781		92087511	92087511	+1	no_errors	ENST00000298047	ensembl	human	known	69_37n	missense	204	35.65	113	SNP	1.000	T
FLI1	2313	genome.wustl.edu	37	11	128680832	128680832	+	Silent	SNP	C	C	T			TCGA-A8-A08Z-01A-21W-A019-09	TCGA-A8-A08Z-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	96afb6d0-29ea-4bd5-8a9d-130e42954707	35c8c6d8-68b5-4175-9d5b-2859dc94a67a	g.chr11:128680832C>T	ENST00000527786.2	+	9	1797	c.1308C>T	c.(1306-1308)gtC>gtT	p.V436V	FLI1_ENST00000525560.1_Silent_p.V243V|FLI1_ENST00000534087.2_Silent_p.V403V|FLI1_ENST00000344954.6_Silent_p.V403V|FLI1_ENST00000281428.8_Silent_p.V370V	NM_001271010.1|NM_002017.4	NP_001257939.1|NP_002008.2	Q01543	FLI1_HUMAN	Fli-1 proto-oncogene, ETS transcription factor	436					blood circulation (GO:0008015)|cell differentiation (GO:0030154)|hemostasis (GO:0007599)|megakaryocyte development (GO:0035855)|organ morphogenesis (GO:0009887)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|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 distal enhancer sequence-specific DNA binding (GO:0000980)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)		EWSR1/FLI1(2569)	NS(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(3)|prostate(2)	31	all_hematologic(175;0.0641)	Lung NSC(97;0.00588)|all_lung(97;0.00764)|Breast(109;0.0115)|Medulloblastoma(222;0.0523)|all_neural(223;0.0862)|all_hematologic(192;0.182)		OV - Ovarian serous cystadenocarcinoma(99;0.01)|LUSC - Lung squamous cell carcinoma(976;0.0324)|Lung(977;0.0327)		ACCCCAACGTCCCCCGCCATC	0.562			T	EWSR1	Ewing sarcoma																																	dbGAP		Dom	yes		11	11q24	2313	Friend leukemia virus integration 1		M	0													105.0	105.0	105.0					11																	128680832		1983	4146	6129	-	-	-	SO:0001819	synonymous_variant	0			M98833	CCDS44768.1, CCDS53725.1, CCDS59230.1, CCDS59231.1	11q24.1-q24.3	2014-09-17	2013-08-07		ENSG00000151702	ENSG00000151702			3749	protein-coding gene	gene with protein product		193067	"""Friend leukemia virus integration 1"""			1765382	Standard	NM_001167681		Approved	SIC-1, EWSR2	uc010sbu.2	Q01543	OTTHUMG00000165792	ENST00000527786.2:c.1308C>T	11.37:g.128680832C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	B2R8H2|B4DFV4|B4DTC6|G3V183|Q14319|Q92480|Q9UE07	Silent	SNP	pfam_Ets,pfam_Pointed_dom,superfamily_SAM/pointed,smart_Pointed_dom,smart_Ets,pfscan_Ets,prints_Ets	p.V436	ENST00000527786.2	37	c.1308	CCDS44768.1	11																																																																																			FLI1	-	NULL	ENSG00000151702		0.562	FLI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FLI1	HGNC	protein_coding	OTTHUMT00000386226.2	296	0.00	0	C	NM_002017		128680832	128680832	+1	no_errors	ENST00000429175	ensembl	human	known	69_37n	silent	115	27.67	44	SNP	0.765	T
HCFC1	3054	genome.wustl.edu	37	X	153224817	153224817	+	Missense_Mutation	SNP	G	G	A			TCGA-A8-A08Z-01A-21W-A019-09	TCGA-A8-A08Z-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	96afb6d0-29ea-4bd5-8a9d-130e42954707	35c8c6d8-68b5-4175-9d5b-2859dc94a67a	g.chrX:153224817G>A	ENST00000310441.7	-	9	2536	c.1570C>T	c.(1570-1572)Cgg>Tgg	p.R524W	HCFC1_ENST00000354233.3_Missense_Mutation_p.R455W|HCFC1_ENST00000369984.4_Missense_Mutation_p.R524W|HCFC1_ENST00000461098.1_5'Flank	NM_005334.2	NP_005325.2	P51610	HCFC1_HUMAN	host cell factor C1	524	Required for interaction with OGT.				cell cycle (GO:0007049)|chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell cycle (GO:0045787)|positive regulation of gene expression (GO:0010628)|protein stabilization (GO:0050821)|regulation of protein complex assembly (GO:0043254)|regulation of transcription, DNA-templated (GO:0006355)|release from viral latency (GO:0019046)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|membrane (GO:0016020)|mitochondrion (GO:0005739)|MLL1 complex (GO:0071339)|MLL5-L complex (GO:0070688)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	chromatin binding (GO:0003682)|identical protein binding (GO:0042802)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(3)|large_intestine(3)|lung(18)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	all_cancers(53;6.23e-16)|all_epithelial(53;5.61e-10)|all_lung(58;3.99e-07)|Lung NSC(58;5.02e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					ACAACCATCCGCACTCCGGCG	0.597																																						dbGAP											0													120.0	127.0	125.0					X																	153224817		2131	4215	6346	-	-	-	SO:0001583	missense	0				CCDS44020.1	Xq28	2014-06-12	2014-06-09		ENSG00000172534	ENSG00000172534			4839	protein-coding gene	gene with protein product	"""VP16-accessory protein"", ""protein phosphatase 1, regulatory subunit 89"""	300019	"""mental retardation, X-linked 3"", ""host cell factor C1 (VP16-accessory protein)"""	HFC1, MRX3		8392914, 23000143	Standard	XM_005274664		Approved	HCF-1, HCF1, CFF, VCAF, MGC70925, PPP1R89	uc004fjp.3	P51610	OTTHUMG00000024222	ENST00000310441.7:c.1570C>T	X.37:g.153224817G>A	ENSP00000309555:p.Arg524Trp	Somatic		WXS	Illumina GAIIx	Phase_IV	Q6P4G5	Missense_Mutation	SNP	pfam_Kelch_2,pfam_Kelch_1,superfamily_Fibronectin_type3,smart_Fibronectin_type3	p.R524W	ENST00000310441.7	37	c.1570	CCDS44020.1	X	.	.	.	.	.	.	.	.	.	.	G	15.02	2.708643	0.48517	.	.	ENSG00000172534	ENST00000310441;ENST00000369984;ENST00000354233	T;T;T	0.03553	3.93;3.92;3.89	5.0	2.15	0.27550	Fibronectin, type III (1);	0.000000	0.85682	D	0.000000	T	0.11324	0.0276	L	0.48642	1.525	0.46011	D	0.998819	D	0.76494	0.999	D	0.71870	0.975	T	0.00171	-1.1960	10	0.72032	D	0.01	.	12.6112	0.56552	0.0:0.0:0.5707:0.4293	.	524	P51610	HCFC1_HUMAN	W	524;524;455	ENSP00000309555:R524W;ENSP00000359001:R524W;ENSP00000346174:R455W	ENSP00000309555:R524W	R	-	1	2	HCFC1	152878011	1.000000	0.71417	0.922000	0.36590	0.175000	0.22909	4.620000	0.61226	0.016000	0.14998	-0.351000	0.07748	CGG	HCFC1	-	smart_Fibronectin_type3	ENSG00000172534		0.597	HCFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HCFC1	HGNC	protein_coding	OTTHUMT00000061099.4	76	0.00	0	G	NM_005334		153224817	153224817	-1	no_errors	ENST00000310441	ensembl	human	known	69_37n	missense	21	43.24	16	SNP	0.999	A
LHX9	56956	genome.wustl.edu	37	1	197889140	197889140	+	Silent	SNP	C	C	T			TCGA-A8-A08Z-01A-21W-A019-09	TCGA-A8-A08Z-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	96afb6d0-29ea-4bd5-8a9d-130e42954707	35c8c6d8-68b5-4175-9d5b-2859dc94a67a	g.chr1:197889140C>T	ENST00000367387.4	+	2	638	c.213C>T	c.(211-213)tgC>tgT	p.C71C	LHX9_ENST00000367390.3_Silent_p.C62C|LHX9_ENST00000337020.2_Silent_p.C71C|LHX9_ENST00000561173.1_Silent_p.C77C|LHX9_ENST00000367391.1_Silent_p.C62C	NM_020204.2	NP_064589.2	Q9NQ69	LHX9_HUMAN	LIM homeobox 9	71	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.				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						CCGCCCTGTGCGCCGGCTGCG	0.647																																						dbGAP											0													84.0	96.0	92.0					1																	197889140		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	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.213C>T	1.37:g.197889140C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	Q5VUE2|Q5VUE3|Q5VUE6|Q86UH2|Q9BYU6|Q9NQ70	Silent	SNP	pfam_Znf_LIM,pfam_Homeodomain,superfamily_Homeodomain-like,smart_Znf_LIM,smart_Homeodomain,pfscan_Znf_LIM,pfscan_Homeodomain	p.C71	ENST00000367387.4	37	c.213	CCDS1393.1	1																																																																																			LHX9	-	pfam_Znf_LIM,smart_Znf_LIM,pfscan_Znf_LIM	ENSG00000143355		0.647	LHX9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	LHX9	HGNC	protein_coding	OTTHUMT00000086547.2	85	0.00	0	C	NM_020204		197889140	197889140	+1	no_errors	ENST00000367387	ensembl	human	known	69_37n	silent	51	21.54	14	SNP	1.000	T
KIAA1804	84451	genome.wustl.edu	37	1	233518401	233518401	+	Missense_Mutation	SNP	A	A	G			TCGA-A8-A08Z-01A-21W-A019-09	TCGA-A8-A08Z-10A-01W-A021-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	96afb6d0-29ea-4bd5-8a9d-130e42954707	35c8c6d8-68b5-4175-9d5b-2859dc94a67a	g.chr1:233518401A>G	ENST00000366624.3	+	10	3316	c.3055A>G	c.(3055-3057)Agg>Ggg	p.R1019G	MLK4_ENST00000366622.1_Missense_Mutation_p.R465G	NM_032435.2	NP_115811.2																					GTGCAGAATGAGGAGCAAAAC	0.453																																						dbGAP											0													84.0	71.0	76.0					1																	233518401		2203	4300	6503	-	-	-	SO:0001583	missense	0																														ENST00000366624.3:c.3055A>G	1.37:g.233518401A>G	ENSP00000355583:p.Arg1019Gly	Somatic		WXS	Illumina GAIIx	Phase_IV		Missense_Mutation	SNP	pirsf_MAPKKK9/10/11,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Prot_kinase_cat_dom,pfam_SH3_domain,pfam_SH3_2,superfamily_Kinase-like_dom,superfamily_SH3_domain,smart_SH3_domain,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,prints_Ser-Thr/Tyr_kinase_cat_dom,prints_SH3_domain,pfscan_SH3_domain,pfscan_Prot_kinase_cat_dom	p.R1019G	ENST00000366624.3	37	c.3055	CCDS1598.1	1	.	.	.	.	.	.	.	.	.	.	A	12.85	2.061638	0.36373	.	.	ENSG00000143674	ENST00000366624;ENST00000366622	T;T	0.73789	-0.78;3.31	4.92	4.92	0.64577	.	0.496657	0.18839	N	0.129727	T	0.55924	0.1951	N	0.11560	0.145	0.27935	N	0.937717	B;B	0.32467	0.372;0.156	B;B	0.30316	0.114;0.037	T	0.55003	-0.8208	10	0.41790	T	0.15	.	13.2935	0.60284	1.0:0.0:0.0:0.0	.	466;1019	Q5TCX8-3;Q5TCX8	.;M3KL4_HUMAN	G	1019;465	ENSP00000355583:R1019G;ENSP00000355581:R465G	ENSP00000355581:R465G	R	+	1	2	RP5-862P8.2	231585024	1.000000	0.71417	0.026000	0.17262	0.974000	0.67602	3.219000	0.51200	2.061000	0.61500	0.460000	0.39030	AGG	RP5-862P8.2	-	pirsf_MAPKKK9/10/11	ENSG00000143674		0.453	MLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KIAA1804	Clone_based_vega_gene	protein_coding	OTTHUMT00000092495.1	159	0.00	0	A			233518401	233518401	+1	no_errors	ENST00000366624	ensembl	human	known	69_37n	missense	169	20.28	43	SNP	1.000	G
MAP3K1	4214	genome.wustl.edu	37	5	56177537	56177538	+	Frame_Shift_Del	DEL	TG	TG	-			TCGA-A8-A08Z-01A-21W-A019-09	TCGA-A8-A08Z-10A-01W-A021-09	TG	TG					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	96afb6d0-29ea-4bd5-8a9d-130e42954707	35c8c6d8-68b5-4175-9d5b-2859dc94a67a	g.chr5:56177537_56177538delTG	ENST00000399503.3	+	14	2510_2511	c.2510_2511delTG	c.(2509-2511)ctgfs	p.L838fs		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	838					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)		TTTTCAAAACTGTTAGAAATGC	0.446																																						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.2510_2511delTG	5.37:g.56177537_56177538delTG	ENSP00000382423:p.Leu838fs	Somatic		WXS	Illumina GAIIx	Phase_IV		Frame_Shift_Del	DEL	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.L838fs	ENST00000399503.3	37	c.2510_2511	CCDS43318.1	5																																																																																			MAP3K1	-	NULL	ENSG00000095015		0.446	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	MAP3K1	HGNC	protein_coding	OTTHUMT00000132309.2	279	0.00	0	TG	XM_042066		56177537	56177538	+1	no_errors	ENST00000399503	ensembl	human	novel	69_37n	frame_shift_del	144	30.14	63	DEL	1.000:0.998	-
MAP3K1	4214	genome.wustl.edu	37	5	56178169	56178169	+	Nonsense_Mutation	SNP	C	C	T			TCGA-A8-A08Z-01A-21W-A019-09	TCGA-A8-A08Z-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	96afb6d0-29ea-4bd5-8a9d-130e42954707	35c8c6d8-68b5-4175-9d5b-2859dc94a67a	g.chr5:56178169C>T	ENST00000399503.3	+	14	3142	c.3142C>T	c.(3142-3144)Cag>Tag	p.Q1048*		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	1048					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)		AGTCTTTACTCAGTCAAGACC	0.438																																						dbGAP											0													74.0	72.0	72.0					5																	56178169		1873	4094	5967	-	-	-	SO:0001587	stop_gained	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.3142C>T	5.37:g.56178169C>T	ENSP00000382423:p.Gln1048*	Somatic		WXS	Illumina GAIIx	Phase_IV		Nonsense_Mutation	SNP	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.Q1048*	ENST00000399503.3	37	c.3142	CCDS43318.1	5	.	.	.	.	.	.	.	.	.	.	C	39	7.642573	0.98406	.	.	ENSG00000095015	ENST00000399503	.	.	.	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.42905	T	0.14	.	20.1772	0.98182	0.0:1.0:0.0:0.0	.	.	.	.	X	1048	.	ENSP00000382423:Q1048X	Q	+	1	0	MAP3K1	56213926	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.473000	0.73572	2.778000	0.95560	0.655000	0.94253	CAG	MAP3K1	-	NULL	ENSG00000095015		0.438	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	MAP3K1	HGNC	protein_coding	OTTHUMT00000132309.2	304	0.00	0	C	XM_042066		56178169	56178169	+1	no_errors	ENST00000399503	ensembl	human	novel	69_37n	nonsense	134	31.63	62	SNP	1.000	T
MST1L	11223	genome.wustl.edu	37	1	17085006	17085006	+	RNA	SNP	C	C	T	rs201784242	byFrequency	TCGA-A8-A08Z-01A-21W-A019-09	TCGA-A8-A08Z-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	96afb6d0-29ea-4bd5-8a9d-130e42954707	35c8c6d8-68b5-4175-9d5b-2859dc94a67a	g.chr1:17085006C>T	ENST00000455405.2	-	0	182							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)										CGGATGGCCCCCAGCCACGCG	0.607																																						dbGAP											0																																										-	-	-			0			U28055, AF083416		1p36.33	2013-03-27	2012-11-09	2012-11-09	ENSG00000186715	ENSG00000186715			7390	other	unknown			"""macrophage stimulating, pseudogene 7"", ""macrophage stimulating, pseudogene 9"", ""macrophage stimulating 1 (hepatocyte growth factor-like) pseudogene 9"""	MSTP7, MSTP9, MST1P9		10728827	Standard	NM_001271733		Approved	D1F15S1A, MSPL7, MSPL-7	uc010ock.3	Q2TV78	OTTHUMG00000002578		1.37:g.17085006C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	B7WPB1|Q13209	Missense_Mutation	SNP	pfam_Kringle,pfam_Peptidase_S1_S6,pfam_PAN-1_domain,superfamily_Pept_cys/ser_Trypsin-like,superfamily_Kringle-like,smart_Pan_app,smart_Kringle,smart_Peptidase_S1_S6,pfscan_Pan_app,pfscan_Kringle,pfscan_Peptidase_S1_S6	p.G490E	ENST00000455405.2	37	c.1469		1	.	.	.	.	.	.	.	.	.	.	.	11.84	1.758278	0.31137	.	.	ENSG00000186715	ENST00000389184;ENST00000334998;ENST00000442552	.	.	.	.	.	.	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (2);	0.000000	0.42964	D	0.000638	T	0.62636	0.2444	.	.	.	.	.	.	D;D	0.89917	1.0;1.0	D;D	0.85130	0.995;0.997	T	0.65524	-0.6147	6	0.35671	T	0.21	.	6.8326	0.23919	0.0:0.9999:0.0:1.0E-4	.	490;490	Q2TV78-2;Q2TV78	.;MSTP9_HUMAN	E	459;490;490	.	ENSP00000439273:G490E	G	-	2	0	MST1P9	16957593	0.982000	0.34865	0.000000	0.03702	0.000000	0.00434	2.313000	0.43735	-0.000000	0.14550	0.000000	0.15137	GGG	MST1P9	-	superfamily_Pept_cys/ser_Trypsin-like,smart_Peptidase_S1_S6,pfscan_Peptidase_S1_S6	ENSG00000186715		0.607	MST1L-002	KNOWN	basic	processed_transcript	MST1P9	HGNC	pseudogene	OTTHUMT00000400328.1	103	0.96	1	C	NM_001271733		17085006	17085006	-1	no_errors	ENST00000334998	ensembl	human	known	69_37n	missense	47	14.55	8	SNP	0.998	T
NR1H2	7376	genome.wustl.edu	37	19	50882307	50882307	+	Missense_Mutation	SNP	C	C	T			TCGA-A8-A08Z-01A-21W-A019-09	TCGA-A8-A08Z-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	96afb6d0-29ea-4bd5-8a9d-130e42954707	35c8c6d8-68b5-4175-9d5b-2859dc94a67a	g.chr19:50882307C>T	ENST00000253727.5	+	7	1031	c.796C>T	c.(796-798)Cgc>Tgc	p.R266C	NR1H2_ENST00000542413.1_Intron|NR1H2_ENST00000593926.1_Missense_Mutation_p.R266C|NR1H2_ENST00000599105.1_Intron|NR1H2_ENST00000598168.1_Intron|NR1H2_ENST00000411902.2_Missense_Mutation_p.R169C	NM_007121.5	NP_009052	P55055	NR1H2_HUMAN	nuclear receptor subfamily 1, group H, member 2	266	Ligand-binding. {ECO:0000255}.				cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of interferon-gamma-mediated signaling pathway (GO:0060336)|negative regulation of lipid transport (GO:0032369)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of pinocytosis (GO:0048550)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of cholesterol transport (GO:0032376)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of cholesterol homeostasis (GO:2000188)|retinoic acid receptor signaling pathway (GO:0048384)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	apolipoprotein A-I receptor binding (GO:0034191)|ATPase binding (GO:0051117)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific transcription regulatory region DNA binding RNA polymerase II transcription factor recruiting transcription factor activity (GO:0001133)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(1)|lung(3)|upper_aerodigestive_tract(2)	8		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00757)|GBM - Glioblastoma multiforme(134;0.0186)		CCGCCAGCAACGCTTTGCCCA	0.632																																						dbGAP											0													68.0	79.0	75.0					19																	50882307		2153	4281	6434	-	-	-	SO:0001583	missense	0			U14534	CCDS42593.1, CCDS58673.1	19q13.3	2013-01-16				ENSG00000131408		"""Nuclear hormone receptors"""	7965	protein-coding gene	gene with protein product	"""liver X receptor-beta"""	600380	"""ubiquitously-expressed nuclear receptor"""	UNR		7782080, 7971966	Standard	NM_007121		Approved	NER, NER-I, RIP15, LXR-b	uc010enw.4	P55055		ENST00000253727.5:c.796C>T	19.37:g.50882307C>T	ENSP00000253727:p.Arg266Cys	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K490|B4DNM6|E7EWA6|Q12970|Q5I0Y1	Missense_Mutation	SNP	pfam_Nucl_hrmn_rcpt_lig-bd_core,pfam_Znf_hrmn_rcpt,superfamily_Nucl_hormone_rcpt_ligand-bd,smart_Znf_hrmn_rcpt,smart_Nucl_hrmn_rcpt_lig-bd_core,pfscan_Znf_hrmn_rcpt,prints_Liver_X_rcpt,prints_Str_hrmn_rcpt,prints_Znf_hrmn_rcpt,prints_Ecdystd_rcpt,prints_ThyrH_rcpt	p.R266C	ENST00000253727.5	37	c.796	CCDS42593.1	19	.	.	.	.	.	.	.	.	.	.	C	19.00	3.742482	0.69418	.	.	ENSG00000131408	ENST00000253727;ENST00000411902;ENST00000376942	D;D	0.96745	-4.11;-4.11	4.28	3.24	0.37175	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (1);	0.094208	0.41396	N	0.000881	D	0.97365	0.9138	M	0.80183	2.485	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.96683	0.9505	10	0.87932	D	0	.	6.4568	0.21934	0.1807:0.7231:0.0:0.0962	.	266;169	P55055;E7EWA6	NR1H2_HUMAN;.	C	266;169;266	ENSP00000253727:R266C;ENSP00000396151:R169C	ENSP00000253727:R266C	R	+	1	0	NR1H2	55574119	1.000000	0.71417	0.993000	0.49108	0.893000	0.52053	3.273000	0.51623	1.156000	0.42514	0.561000	0.74099	CGC	NR1H2	-	superfamily_Nucl_hormone_rcpt_ligand-bd,prints_Ecdystd_rcpt	ENSG00000131408		0.632	NR1H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NR1H2	HGNC	protein_coding	OTTHUMT00000464724.2	50	0.00	0	C			50882307	50882307	+1	no_errors	ENST00000253727	ensembl	human	known	69_37n	missense	24	40.00	16	SNP	1.000	T
PCDHGA5	56110	genome.wustl.edu	37	5	140744719	140744719	+	Silent	SNP	C	C	T			TCGA-A8-A08Z-01A-21W-A019-09	TCGA-A8-A08Z-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	96afb6d0-29ea-4bd5-8a9d-130e42954707	35c8c6d8-68b5-4175-9d5b-2859dc94a67a	g.chr5:140744719C>T	ENST00000518069.1	+	1	822	c.822C>T	c.(820-822)aaC>aaT	p.N274N	PCDHGA1_ENST00000517417.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB2_ENST00000522605.1_Intron	NM_018918.2|NM_032054.1	NP_061741.1|NP_114443.1	Q9Y5G8	PCDG5_HUMAN	protocadherin gamma subfamily A, 5	274	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(5)|upper_aerodigestive_tract(3)	18			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGGGAATAAACGGGAAATTGA	0.478																																						dbGAP											0													47.0	47.0	47.0					5																	140744719		1949	4148	6097	-	-	-	SO:0001819	synonymous_variant	0			AF152512	CCDS54925.1, CCDS75333.1	5q31	2010-01-26				ENSG00000253485		"""Cadherins / Protocadherins : Clustered"""	8703	other	protocadherin	"""cadherin ME3"""	606292				10380929	Standard	NM_018918		Approved	CDH-GAMMA-A5, ME3, PCDH-GAMMA-A5		Q9Y5G8		ENST00000518069.1:c.822C>T	5.37:g.140744719C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	Q2M3F5|Q9Y5D2	Silent	SNP	pfam_Cadherin,pfam_Cadherin_N,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin,prints_Cadherin	p.N274	ENST00000518069.1	37	c.822	CCDS54925.1	5																																																																																			PCDHGA5	-	pfam_Cadherin,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin	ENSG00000253485		0.478	PCDHGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PCDHGA5	HGNC	protein_coding	OTTHUMT00000374742.1	119	0.83	1	C	NM_018918		140744719	140744719	+1	no_errors	ENST00000518069	ensembl	human	known	69_37n	silent	51	23.88	16	SNP	0.266	T
PDE6C	5146	genome.wustl.edu	37	10	95380689	95380689	+	Missense_Mutation	SNP	G	G	T			TCGA-A8-A08Z-01A-21W-A019-09	TCGA-A8-A08Z-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	96afb6d0-29ea-4bd5-8a9d-130e42954707	35c8c6d8-68b5-4175-9d5b-2859dc94a67a	g.chr10:95380689G>T	ENST00000371447.3	+	3	813	c.675G>T	c.(673-675)agG>agT	p.R225S		NM_006204.3	NP_006195.3	P51160	PDE6C_HUMAN	phosphodiesterase 6C, cGMP-specific, cone, alpha prime	225					phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|visual perception (GO:0007601)	plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(12)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	42		Colorectal(252;0.123)			Caffeine(DB00201)	TCATCCTAAGGCTTCATCACA	0.408																																						dbGAP											0													369.0	364.0	365.0					10																	95380689		2203	4300	6503	-	-	-	SO:0001583	missense	0			U31973	CCDS7429.1	10q24	2013-01-23			ENSG00000095464	ENSG00000095464	3.1.4.17	"""Phosphodiesterases"""	8787	protein-coding gene	gene with protein product		600827					Standard	NM_006204		Approved	PDEA2, ACHM5, COD4	uc001kiu.4	P51160	OTTHUMG00000018775	ENST00000371447.3:c.675G>T	10.37:g.95380689G>T	ENSP00000360502:p.Arg225Ser	Somatic		WXS	Illumina GAIIx	Phase_IV	A6NCR6|Q5VY29	Missense_Mutation	SNP	pfam_PDEase_catalytic_dom,pfam_GAF,smart_GAF,smart_HD/PDEase_dom,prints_PDEase	p.R225S	ENST00000371447.3	37	c.675	CCDS7429.1	10	.	.	.	.	.	.	.	.	.	.	G	12.84	2.059896	0.36373	.	.	ENSG00000095464	ENST00000371447	T	0.69040	-0.37	5.13	3.28	0.37604	GAF (1);	0.493750	0.24688	N	0.036417	T	0.49355	0.1552	L	0.29908	0.895	0.26761	N	0.97	B	0.20780	0.048	B	0.15052	0.012	T	0.40757	-0.9546	10	0.45353	T	0.12	.	6.2896	0.21053	0.396:0.0:0.604:0.0	.	225	P51160	PDE6C_HUMAN	S	225	ENSP00000360502:R225S	ENSP00000360502:R225S	R	+	3	2	PDE6C	95370679	1.000000	0.71417	0.996000	0.52242	0.550000	0.35303	1.019000	0.30014	0.866000	0.35629	0.655000	0.94253	AGG	PDE6C	-	smart_GAF	ENSG00000095464		0.408	PDE6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PDE6C	HGNC	protein_coding	OTTHUMT00000049437.1	1250	0.00	0	G	NM_006204		95380689	95380689	+1	no_errors	ENST00000371447	ensembl	human	known	69_37n	missense	889	30.92	398	SNP	0.976	T
PIK3CA	5290	genome.wustl.edu	37	3	178952085	178952085	+	Missense_Mutation	SNP	A	A	G	rs121913279		TCGA-A8-A08Z-01A-21W-A019-09	TCGA-A8-A08Z-10A-01W-A021-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	96afb6d0-29ea-4bd5-8a9d-130e42954707	35c8c6d8-68b5-4175-9d5b-2859dc94a67a	g.chr3:178952085A>G	ENST00000263967.3	+	21	3297	c.3140A>G	c.(3139-3141)cAt>cGt	p.H1047R	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1047	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.		H -> L (in BC; unknown pathological significance). {ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16353168}.|H -> R (in CLOVE, KERSEB, CRC, BC and OC; also found in an endometrial carcinoma sample; shows an increase in lipid kinase activity; oncogenic in vivo; requires binding to p85 regulatory subunit to induce cellular transformation but not interaction with RAS; may mimic the conformatitonal change triggered by the interaction with RAS; enhances invadopodia-mediated extracellular matrix degradation and invasion in breast cancer cells; increases lipid kinase activity; may alter the interaction of the PI3K/ PI4K kinase domain with the cell membrane). {ECO:0000269|PubMed:15016963, ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15712344, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16114017, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:22658544}.|H -> Y (in MCAP; also found in an endometrial carcinoma sample). {ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:22729224}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.H1047R(1387)|p.H1047L(194)|p.H1047P(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	AATGATGCACATCATGGTGGC	0.378	H1047L(EFM19_BREAST)|H1047R(BT20_BREAST)|H1047R(CAL29_URINARY_TRACT)|H1047R(CAL33_UPPER_AERODIGESTIVE_TRACT)|H1047R(DETROIT562_UPPER_AERODIGESTIVE_TRACT)|H1047R(HCC1954_BREAST)|H1047R(HCT116_LARGE_INTESTINE)|H1047R(HSC2_UPPER_AERODIGESTIVE_TRACT)|H1047R(LS180_LARGE_INTESTINE)|H1047R(MCAS_OVARY)|H1047R(MDAMB453_BREAST)|H1047R(NCIH1048_LUNG)|H1047R(RKO_LARGE_INTESTINE)|H1047R(SKOV3_OVARY)|H1047R(T47D_BREAST)	57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)	dbGAP		Dom	yes		3	3q26.3	5290	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""		"""E, O"""	1582	Substitution - Missense(1582)	breast(961)|large_intestine(245)|endometrium(114)|ovary(77)|urinary_tract(36)|upper_aerodigestive_tract(26)|lung(19)|central_nervous_system(19)|stomach(19)|haematopoietic_and_lymphoid_tissue(11)|thyroid(10)|NS(9)|liver(7)|kidney(6)|soft_tissue(6)|skin(4)|prostate(4)|pituitary(3)|pancreas(3)|meninges(1)|cervix(1)|bone(1)											99.0	89.0	92.0					3																	178952085		1912	4130	6042	-	-	-	SO:0001583	missense	0				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.3140A>G	3.37:g.178952085A>G	ENSP00000263967:p.His1047Arg	Somatic		WXS	Illumina GAIIx	Phase_IV	Q14CW1|Q99762	Missense_Mutation	SNP	pfam_PInositide-3_kin_accessory_dom,pfam_PI3/4_kinase_cat_dom,pfam_PI3K_Ras-bd_dom,pfam_PI3K_C2_dom,pfam_PI3K_adapt-bd_dom,superfamily_Kinase-like_dom,superfamily_ARM-type_fold,superfamily_C2_Ca/lipid-bd_dom_CaLB,smart_PI3K_adapt-bd_dom,smart_PI3K_Ras-bd_dom,smart_PI3K_C2_dom,smart_PInositide-3_kin_accessory_dom,smart_PI3/4_kinase_cat_dom,pfscan_PI3/4_kinase_cat_dom	p.H1047R	ENST00000263967.3	37	c.3140	CCDS43171.1	3	.	.	.	.	.	.	.	.	.	.	A	14.34	2.506328	0.44558	.	.	ENSG00000121879	ENST00000263967	T	0.80214	-1.35	6.08	6.08	0.98989	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.000000	0.85682	D	0.000000	T	0.62466	0.2430	N	0.08118	0	0.80722	D	1	P	0.38597	0.639	B	0.28011	0.085	T	0.67526	-0.5648	10	0.40728	T	0.16	-21.2893	16.6512	0.85203	1.0:0.0:0.0:0.0	.	1047	P42336	PK3CA_HUMAN	R	1047	ENSP00000263967:H1047R	ENSP00000263967:H1047R	H	+	2	0	PIK3CA	180434779	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	8.859000	0.92264	2.333000	0.79357	0.482000	0.46254	CAT	PIK3CA	-	superfamily_Kinase-like_dom,smart_PI3/4_kinase_cat_dom,pfscan_PI3/4_kinase_cat_dom	ENSG00000121879		0.378	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	PIK3CA	HGNC	protein_coding	OTTHUMT00000348409.2	252	0.00	0	A			178952085	178952085	+1	no_errors	ENST00000263967	ensembl	human	known	69_37n	missense	131	28.42	52	SNP	1.000	G
RAD17	5884	genome.wustl.edu	37	5	68684870	68684870	+	Missense_Mutation	SNP	A	A	G			TCGA-A8-A08Z-01A-21W-A019-09	TCGA-A8-A08Z-10A-01W-A021-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	96afb6d0-29ea-4bd5-8a9d-130e42954707	35c8c6d8-68b5-4175-9d5b-2859dc94a67a	g.chr5:68684870A>G	ENST00000509734.1	+	11	1615	c.937A>G	c.(937-939)Aaa>Gaa	p.K313E	RAD17_ENST00000305138.4_Missense_Mutation_p.K302E|RAD17_ENST00000521422.1_Missense_Mutation_p.K137E|RAD17_ENST00000380774.3_Missense_Mutation_p.K313E|RAD17_ENST00000354868.5_Missense_Mutation_p.K302E|RAD17_ENST00000345306.6_Missense_Mutation_p.K302E|RAD17_ENST00000354312.3_Missense_Mutation_p.K302E|RAD17_ENST00000358030.2_Missense_Mutation_p.K137E|RAD17_ENST00000504177.1_Intron|RAD17_ENST00000361732.2_Missense_Mutation_p.K302E|RAD17_ENST00000282891.6_Missense_Mutation_p.K216E			O75943	RAD17_HUMAN	RAD17 homolog (S. pombe)	313					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)		GAATGGAGGAAAAATTACTGT	0.303								Other conserved DNA damage response genes																														dbGAP											0													53.0	53.0	53.0					5																	68684870		2200	4300	6500	-	-	-	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.937A>G	5.37:g.68684870A>G	ENSP00000426191:p.Lys313Glu	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K8X2|D3DWA5|O75714|Q7Z3S4|Q9UNK7|Q9UNR7|Q9UNR8|Q9UPF5	Missense_Mutation	SNP	tigrfam_Checkpoint_prot_Rad24_fun/met	p.K313E	ENST00000509734.1	37	c.937	CCDS4003.1	5	.	.	.	.	.	.	.	.	.	.	A	13.94	2.387993	0.42308	.	.	ENSG00000152942	ENST00000361732;ENST00000509734;ENST00000354868;ENST00000521422;ENST00000354312;ENST00000345306;ENST00000305138;ENST00000282891;ENST00000358030;ENST00000380774	T;T;T;T;T;T;T;T;T;T	0.42131	2.3;2.3;2.3;0.98;2.3;2.3;2.3;2.3;0.98;2.3	5.2	5.2	0.72013	.	0.242638	0.47093	D	0.000260	T	0.39091	0.1065	L	0.50333	1.59	0.51233	D	0.999915	B;B;B	0.11235	0.004;0.001;0.003	B;B;B	0.16722	0.016;0.005;0.009	T	0.16988	-1.0384	10	0.32370	T	0.25	-21.7605	14.3365	0.66595	1.0:0.0:0.0:0.0	.	313;216;302	O75943;O75943-4;O75943-2	RAD17_HUMAN;.;.	E	302;313;302;137;302;302;302;216;137;313	ENSP00000355226:K302E;ENSP00000426191:K313E;ENSP00000346938:K302E;ENSP00000427743:K137E;ENSP00000346271:K302E;ENSP00000311227:K302E;ENSP00000303134:K302E;ENSP00000282891:K216E;ENSP00000350725:K137E;ENSP00000370151:K313E	ENSP00000282891:K216E	K	+	1	0	RAD17	68720626	1.000000	0.71417	0.983000	0.44433	0.969000	0.65631	5.961000	0.70356	2.094000	0.63399	0.455000	0.32223	AAA	RAD17	-	tigrfam_Checkpoint_prot_Rad24_fun/met	ENSG00000152942		0.303	RAD17-008	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	RAD17	HGNC	protein_coding	OTTHUMT00000369171.1	63	0.00	0	A	NM_133344		68684870	68684870	+1	no_errors	ENST00000380774	ensembl	human	known	69_37n	missense	36	33.33	18	SNP	1.000	G
RFC1	5981	genome.wustl.edu	37	4	39308302	39308302	+	Silent	SNP	G	G	A			TCGA-A8-A08Z-01A-21W-A019-09	TCGA-A8-A08Z-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	96afb6d0-29ea-4bd5-8a9d-130e42954707	35c8c6d8-68b5-4175-9d5b-2859dc94a67a	g.chr4:39308302G>A	ENST00000381897.1	-	14	2041	c.1908C>T	c.(1906-1908)tcC>tcT	p.S636S	RFC1_ENST00000349703.2_Silent_p.S635S	NM_001204747.1|NM_002913.4	NP_001191676.1|NP_002904.3	P35251	RFC1_HUMAN	replication factor C (activator 1) 1, 145kDa	636					DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA-dependent DNA replication (GO:0006261)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of catalytic activity (GO:0043085)|positive regulation of transcription, DNA-templated (GO:0045893)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|telomere maintenance via telomerase (GO:0007004)|transcription, DNA-templated (GO:0006351)|transcription-coupled nucleotide-excision repair (GO:0006283)	cell junction (GO:0030054)|DNA replication factor C complex (GO:0005663)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA clamp loader activity (GO:0003689)|double-stranded DNA binding (GO:0003690)|enzyme activator activity (GO:0008047)|sequence-specific DNA binding (GO:0043565)			haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	16						CATCTTTGCCGGAAAATTTAC	0.458																																					Colon(109;59 1555 12203 17579 39824)|Esophageal Squamous(18;360 542 16186 28570 51157)	dbGAP											0													80.0	80.0	80.0					4																	39308302		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			L23320	CCDS3450.1, CCDS56329.1	4p14-p13	2010-04-21	2002-08-29		ENSG00000035928	ENSG00000035928		"""ATPases / AAA-type"""	9969	protein-coding gene	gene with protein product		102579	"""replication factor C (activator 1) 1 (145kD)"""			8114700	Standard	NM_002913		Approved	A1, PO-GA, RFC140, MHCBFB	uc003gty.2	P35251	OTTHUMG00000099363	ENST00000381897.1:c.1908C>T	4.37:g.39308302G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	A8K6E7|Q5XKF5|Q6PKU0|Q86V41|Q86V46	Silent	SNP	pfam_DNA_replication_fac_RFC1_C,pfam_BRCT_dom,pfam_ATPase_AAA_core,superfamily_DNA_pol3_clamp-load_cplx_C,superfamily_BRCT_dom,smart_BRCT_dom,smart_AAA+_ATPase,pirsf_DNA_replication_fac_C_lsu,pfscan_BRCT_dom	p.S636	ENST00000381897.1	37	c.1908	CCDS56329.1	4																																																																																			RFC1	-	pirsf_DNA_replication_fac_C_lsu	ENSG00000035928		0.458	RFC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	RFC1	HGNC	protein_coding	OTTHUMT00000216808.1	81	0.00	0	G	NM_002913		39308302	39308302	-1	no_errors	ENST00000381897	ensembl	human	known	69_37n	silent	55	15.15	10	SNP	0.022	A
RS1	6247	genome.wustl.edu	37	X	18662718	18662718	+	Missense_Mutation	SNP	G	G	C			TCGA-A8-A08Z-01A-21W-A019-09	TCGA-A8-A08Z-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	96afb6d0-29ea-4bd5-8a9d-130e42954707	35c8c6d8-68b5-4175-9d5b-2859dc94a67a	g.chrX:18662718G>C	ENST00000379984.3	-	5	394	c.354C>G	c.(352-354)gaC>gaG	p.D118E	CDKL5_ENST00000379996.3_Intron|RS1_ENST00000476595.1_5'UTR|CDKL5_ENST00000379989.3_Intron	NM_000330.3	NP_000321.1	O15537	XLRS1_HUMAN	retinoschisin 1	118	F5/8 type C. {ECO:0000255|PROSITE- ProRule:PRU00081}.				adaptation of rhodopsin mediated signaling (GO:0016062)|cell adhesion (GO:0007155)|multicellular organismal development (GO:0007275)|retina layer formation (GO:0010842)|visual perception (GO:0007601)	extracellular space (GO:0005615)|extrinsic component of plasma membrane (GO:0019897)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)|phosphatidylserine binding (GO:0001786)			cervix(1)|endometrium(4)|large_intestine(5)|lung(2)|ovary(2)|skin(1)	15	Hepatocellular(33;0.183)					ACTGGCTACTGTCCTGGAACT	0.547																																						dbGAP											0													120.0	92.0	101.0					X																	18662718		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF014459	CCDS14187.1	Xp22.2-p22.1	2014-09-17	2008-07-29		ENSG00000102104	ENSG00000102104			10457	protein-coding gene	gene with protein product		300839	"""retinoschisis (X-linked, juvenile) 1"""	RS		9326935, 17804407	Standard	NM_000330		Approved	XLRS1	uc004cyo.3	O15537	OTTHUMG00000021216	ENST00000379984.3:c.354C>G	X.37:g.18662718G>C	ENSP00000369320:p.Asp118Glu	Somatic		WXS	Illumina GAIIx	Phase_IV	Q0QD39	Missense_Mutation	SNP	pfam_Coagulation_fac_5/8-C_type_dom,superfamily_Galactose-bd-like,smart_Coagulation_fac_5/8-C_type_dom,pfscan_Coagulation_fac_5/8-C_type_dom	p.D118E	ENST00000379984.3	37	c.354	CCDS14187.1	X	.	.	.	.	.	.	.	.	.	.	g	17.11	3.305831	0.60305	.	.	ENSG00000102104	ENST00000379984	D	0.99051	-5.37	5.21	3.45	0.39498	Coagulation factor 5/8 C-terminal type domain (4);Galactose-binding domain-like (1);	0.041485	0.85682	D	0.000000	D	0.98526	0.9508	M	0.68952	2.095	0.49483	D	0.999792	D	0.56968	0.978	P	0.57911	0.829	D	0.97729	1.0201	10	0.59425	D	0.04	.	7.6104	0.28126	0.3331:0.0:0.6669:0.0	.	118	O15537	XLRS1_HUMAN	E	118	ENSP00000369320:D118E	ENSP00000369320:D118E	D	-	3	2	RS1	18572639	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	3.828000	0.55753	0.589000	0.29677	-0.203000	0.12734	GAC	RS1	-	pfam_Coagulation_fac_5/8-C_type_dom,superfamily_Galactose-bd-like,smart_Coagulation_fac_5/8-C_type_dom,pfscan_Coagulation_fac_5/8-C_type_dom	ENSG00000102104		0.547	RS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RS1	HGNC	protein_coding	OTTHUMT00000055949.1	191	0.00	0	G			18662718	18662718	-1	no_errors	ENST00000379984	ensembl	human	known	69_37n	missense	225	10.00	25	SNP	1.000	C
RTN4RL2	349667	genome.wustl.edu	37	11	57235333	57235333	+	Missense_Mutation	SNP	T	T	A			TCGA-A8-A08Z-01A-21W-A019-09	TCGA-A8-A08Z-10A-01W-A021-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	96afb6d0-29ea-4bd5-8a9d-130e42954707	35c8c6d8-68b5-4175-9d5b-2859dc94a67a	g.chr11:57235333T>A	ENST00000533205.1	+	2	292	c.283T>A	c.(283-285)Tcc>Acc	p.S95T	RTN4RL2_ENST00000395120.2_Missense_Mutation_p.S95T|RTN4RL2_ENST00000335099.3_Missense_Mutation_p.S95T					reticulon 4 receptor-like 2											NS(1)|endometrium(1)|large_intestine(2)|lung(2)	6						CAACAACCTCTCCACCATCTA	0.627																																						dbGAP											0													168.0	145.0	153.0					11																	57235333		2201	4296	6497	-	-	-	SO:0001583	missense	0			BK001302	CCDS7957.1	11q12.1	2008-02-05			ENSG00000186907	ENSG00000186907			23053	protein-coding gene	gene with protein product		610462					Standard	NM_178570		Approved	NgR2, NGRH1	uc010rjt.2	Q86UN3	OTTHUMG00000167028	ENST00000533205.1:c.283T>A	11.37:g.57235333T>A	ENSP00000435606:p.Ser95Thr	Somatic		WXS	Illumina GAIIx	Phase_IV		Missense_Mutation	SNP	pfam_Leu-rich_rpt,smart_Leu-rich_rpt_typical-subtyp,smart_Cys-rich_flank_reg_C	p.S95T	ENST00000533205.1	37	c.283		11	.	.	.	.	.	.	.	.	.	.	T	5.443	0.266821	0.10294	.	.	ENSG00000186907	ENST00000335099;ENST00000533205;ENST00000395120	T;D;D	0.83250	4.31;-1.7;-1.7	4.96	3.83	0.44106	.	0.000000	0.41001	D	0.000976	T	0.68943	0.3056	L	0.28014	0.82	0.30678	N	0.752667	B	0.25563	0.129	B	0.29524	0.103	T	0.58526	-0.7621	10	0.02654	T	1	.	10.4341	0.44424	0.0:0.0785:0.0:0.9215	.	95	Q86UN3	R4RL2_HUMAN	T	95	ENSP00000335397:S95T;ENSP00000435606:S95T;ENSP00000378552:S95T	ENSP00000335397:S95T	S	+	1	0	RTN4RL2	56991909	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.992000	0.40737	0.858000	0.35431	0.459000	0.35465	TCC	RTN4RL2	-	smart_Leu-rich_rpt_typical-subtyp	ENSG00000186907		0.627	RTN4RL2-003	PUTATIVE	basic|exp_conf	protein_coding	RTN4RL2	HGNC	protein_coding	OTTHUMT00000392538.1	213	0.00	0	T	NM_178570		57235333	57235333	+1	no_errors	ENST00000335099	ensembl	human	known	69_37n	missense	88	30.71	39	SNP	1.000	A
RUNX1	861	genome.wustl.edu	37	21	36252856	36252857	+	Frame_Shift_Ins	INS	-	-	T			TCGA-A8-A08Z-01A-21W-A019-09	TCGA-A8-A08Z-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	96afb6d0-29ea-4bd5-8a9d-130e42954707	35c8c6d8-68b5-4175-9d5b-2859dc94a67a	g.chr21:36252856_36252857insT	ENST00000344691.4	-	2	2001_2002	c.424_425insA	c.(424-426)agafs	p.R142fs	RUNX1_ENST00000358356.5_Frame_Shift_Ins_p.R142fs|RUNX1_ENST00000399240.1_Frame_Shift_Ins_p.R142fs|RUNX1_ENST00000437180.1_Frame_Shift_Ins_p.R169fs|RUNX1_ENST00000325074.5_Frame_Shift_Ins_p.R157fs|RUNX1_ENST00000300305.3_Frame_Shift_Ins_p.R169fs|RUNX1_ENST00000486278.2_Frame_Shift_Ins_p.R145fs	NM_001001890.2	NP_001001890.1	Q01196	RUNX1_HUMAN	runt-related transcription factor 1	142	Interaction with DNA.|Runt. {ECO:0000255|PROSITE- ProRule:PRU00399}.				behavioral response to pain (GO:0048266)|cellular response to transforming growth factor beta stimulus (GO:0071560)|central nervous system development (GO:0007417)|definitive hemopoiesis (GO:0060216)|embryonic hemopoiesis (GO:0035162)|hair follicle morphogenesis (GO:0031069)|hematopoietic stem cell proliferation (GO:0071425)|hemopoiesis (GO:0030097)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|myeloid cell differentiation (GO:0030099)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of granulocyte differentiation (GO:0030853)|peripheral nervous system neuron development (GO:0048935)|positive regulation of angiogenesis (GO:0045766)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of progesterone secretion (GO:2000872)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hair follicle cell proliferation (GO:0071336)|regulation of signal transduction (GO:0009966)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	basement membrane (GO:0005604)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.R169fs*44(1)|p.R169fs*11(1)|p.R169fs*10(1)		breast(5)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(428)|large_intestine(3)|lung(6)|oesophagus(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	452						TAACGTACCTCTTCCACTTCGA	0.421			T	"""RPL22, MDS1, EVI1, CBFA2T3, CBFA2T1, ETV6, LAF4"""	"""AML, preB- ALL, T-ALL"""																																	dbGAP		Dom	yes		21	21q22.3	861	runt-related transcription factor 1  (AML1)		L	3	Insertion - Frameshift(3)	haematopoietic_and_lymphoid_tissue(2)|breast(1)																																								-	-	-	SO:0001589	frameshift_variant	0			X79549	CCDS13639.1, CCDS42922.1, CCDS46646.1	21q22.3	2014-09-17	2008-07-29		ENSG00000159216	ENSG00000159216			10471	protein-coding gene	gene with protein product	"""aml1 oncogene"""	151385	"""acute myeloid leukemia 1"""	AML1, CBFA2		1427868, 7835892	Standard	NM_001001890		Approved	PEBP2A2, AMLCR1	uc010gmv.3	Q01196	OTTHUMG00000086299	ENST00000344691.4:c.425dupA	21.37:g.36252858_36252858dupT	ENSP00000340690:p.Arg142fs	Somatic		WXS	Illumina GAIIx	Phase_IV	A8MV94|B2RMS4|D3DSG1|O60472|O60473|O76047|O76089|Q13081|Q13755|Q13756|Q13757|Q13758|Q13759|Q15341|Q15343|Q16122|Q16284|Q16285|Q16286|Q16346|Q16347|Q92479	Frame_Shift_Ins	INS	pfam_AML1/Runt_N,pfam_RunxI,superfamily_p53-like_TF_DNA-bd,pirsf_TF_Runt-rel_RUNX,pfscan_AML1/Runt_N,prints_AML1_Runt	p.R169fs	ENST00000344691.4	37	c.506_505	CCDS42922.1	21																																																																																			RUNX1	-	pfam_AML1/Runt_N,superfamily_p53-like_TF_DNA-bd,pirsf_TF_Runt-rel_RUNX,pfscan_AML1/Runt_N,prints_AML1_Runt	ENSG00000159216		0.421	RUNX1-001	KNOWN	basic|CCDS	protein_coding	RUNX1	HGNC	protein_coding	OTTHUMT00000194230.1	108	0.00	0	-			36252856	36252857	-1	no_errors	ENST00000300305	ensembl	human	known	69_37n	frame_shift_ins	43	25.86	15	INS	1.000:0.998	T
SLC4A3	6508	genome.wustl.edu	37	2	220504281	220504282	+	Frame_Shift_Ins	INS	-	-	G			TCGA-A8-A08Z-01A-21W-A019-09	TCGA-A8-A08Z-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	96afb6d0-29ea-4bd5-8a9d-130e42954707	35c8c6d8-68b5-4175-9d5b-2859dc94a67a	g.chr2:220504281_220504282insG	ENST00000358055.3	+	20	3613_3614	c.3101_3102insG	c.(3100-3105)ctggggfs	p.LG1034fs	SLC4A3_ENST00000373762.3_Frame_Shift_Ins_p.LG1061fs|SLC4A3_ENST00000317151.3_Frame_Shift_Ins_p.LG1034fs|SLC4A3_ENST00000273063.6_Frame_Shift_Ins_p.LG1061fs|SLC4A3_ENST00000373760.2_Frame_Shift_Ins_p.LG1034fs			P48751	B3A3_HUMAN	solute carrier family 4 (anion exchanger), member 3	1034	Membrane (anion exchange).				bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|regulation of intracellular pH (GO:0051453)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	51		Renal(207;0.0183)		Epithelial(149;2.53e-07)|all cancers(144;5.57e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		ATTGGCTCCCTGGGGGGGCTCT	0.644																																						dbGAP											0									,	9,4257		0,9,2124					,	4.4	1.0			56	7,8247		0,7,4120	no	frameshift,frameshift	SLC4A3	NM_201574.2,NM_005070.3	,	0,16,6244	A1A1,A1R,RR		0.0848,0.211,0.1278	,	,		16,12504				-	-	-	SO:0001589	frameshift_variant	0				CCDS2445.1, CCDS2446.1	2q35	2013-07-19	2013-07-19		ENSG00000114923	ENSG00000114923		"""Solute carriers"""	11029	protein-coding gene	gene with protein product	"""Anion exchanger 3, neuronal"""	106195	"""solute carrier family 4, anion exchanger, member 3"""			8001971	Standard	NM_005070		Approved	AE3, SLC2C	uc002vmo.4	P48751	OTTHUMG00000059238	ENST00000358055.3:c.3108dupG	2.37:g.220504288_220504288dupG	ENSP00000350756:p.Leu1034fs	Somatic		WXS	Illumina GAIIx	Phase_IV	A6H8L2|A8K1Q9|B7ZVX6|B9EGD1|Q6YIQ9	Frame_Shift_Ins	INS	pfam_HCO3_transpt_C,pfam_HCO3_transpt_cyt,superfamily_PTrfase/Anion_transptr,prints_HCO3_transpt_euk,prints_Anion_exchange_3,prints_Anion_exchange,tigrfam_HCO3_transpt_euk	p.L1064fs	ENST00000358055.3	37	c.3182_3183	CCDS2445.1	2																																																																																			SLC4A3	-	pfam_HCO3_transpt_C,tigrfam_HCO3_transpt_euk	ENSG00000114923		0.644	SLC4A3-009	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	SLC4A3	HGNC	protein_coding	OTTHUMT00000316472.1	53	0.00	0	-	NM_005070		220504281	220504282	+1	no_errors	ENST00000273063	ensembl	human	known	69_37n	frame_shift_ins	39	13.33	6	INS	1.000:1.000	G
TBL1XR1	79718	genome.wustl.edu	37	3	176771560	176771560	+	Splice_Site	SNP	C	C	G			TCGA-A8-A08Z-01A-21W-A019-09	TCGA-A8-A08Z-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	96afb6d0-29ea-4bd5-8a9d-130e42954707	35c8c6d8-68b5-4175-9d5b-2859dc94a67a	g.chr3:176771560C>G	ENST00000430069.1	-	4	464		c.e4+1		TBL1XR1_ENST00000457928.2_Splice_Site			Q9BZK7	TBL1R_HUMAN	transducin (beta)-like 1 X-linked receptor 1						canonical Wnt signaling pathway (GO:0060070)|cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|histone binding (GO:0042393)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(7)|liver(1)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	31	all_cancers(143;1.44e-17)|Ovarian(172;0.00163)|Breast(254;0.214)	Acute lymphoblastic leukemia(1;0.00599)|all_hematologic(1;0.0632)|Prostate(884;0.215)	OV - Ovarian serous cystadenocarcinoma(80;9.83e-31)			GTCTTCCTTACCTCATTAATA	0.373																																						dbGAP											0													78.0	75.0	76.0					3																	176771560		1947	4153	6100	-	-	-	SO:0001630	splice_region_variant	0			AK022956	CCDS46961.1	3q26.33	2013-01-10	2008-01-17		ENSG00000177565	ENSG00000177565		"""WD repeat domain containing"""	29529	protein-coding gene	gene with protein product		608628	"""transducin (beta)-like 1X-linked receptor 1"""			11063877, 11931768	Standard	NM_024665		Approved	IRA1, FLJ12894, TBLR1, C21, DC42	uc003fix.4	Q9BZK7	OTTHUMG00000157140	ENST00000430069.1:c.204+1G>C	3.37:g.176771560C>G		Somatic		WXS	Illumina GAIIx	Phase_IV	D3DNQ9|Q14DC3|Q9H2I1|Q9H9A1	Splice_Site	SNP	-	e2+1	ENST00000430069.1	37	c.204+1	CCDS46961.1	3	.	.	.	.	.	.	.	.	.	.	C	23.7	4.450455	0.84101	.	.	ENSG00000177565	ENST00000430069;ENST00000457928;ENST00000352800;ENST00000437738;ENST00000450267;ENST00000431674;ENST00000422066;ENST00000443315	.	.	.	5.21	5.21	0.72293	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.1089	0.89528	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TBL1XR1	178254254	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	7.818000	0.86416	2.601000	0.87937	0.655000	0.94253	.	TBL1XR1	-	-	ENSG00000177565		0.373	TBL1XR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TBL1XR1	HGNC	protein_coding	OTTHUMT00000347587.3	122	0.00	0	C	NM_024665	Intron	176771560	176771560	-1	no_errors	ENST00000430069	ensembl	human	known	69_37n	splice_site	87	31.50	40	SNP	1.000	G
TPM1	7168	genome.wustl.edu	37	15	63353074	63353074	+	Missense_Mutation	SNP	C	C	G			TCGA-A8-A08Z-01A-21W-A019-09	TCGA-A8-A08Z-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	96afb6d0-29ea-4bd5-8a9d-130e42954707	35c8c6d8-68b5-4175-9d5b-2859dc94a67a	g.chr15:63353074C>G	ENST00000403994.3	+	5	579	c.499C>G	c.(499-501)Cgt>Ggt	p.R167G	TPM1_ENST00000288398.6_Missense_Mutation_p.R167G|TPM1_ENST00000334895.5_Missense_Mutation_p.R131G|TPM1_ENST00000560445.1_Intron|TPM1_ENST00000559556.1_Missense_Mutation_p.R167G|TPM1_ENST00000357980.4_Missense_Mutation_p.R209G|TPM1_ENST00000559281.1_Missense_Mutation_p.R131G|TPM1_ENST00000358278.3_Missense_Mutation_p.R167G|TPM1_ENST00000267996.7_Missense_Mutation_p.R167G|TPM1_ENST00000317516.7_Missense_Mutation_p.R131G|TPM1_ENST00000559397.1_Missense_Mutation_p.R167G|TPM1_ENST00000560959.1_Missense_Mutation_p.R131G|TPM1_ENST00000404484.4_Missense_Mutation_p.R131G	NM_001018005.1	NP_001018005.1	P09493	TPM1_HUMAN	tropomyosin 1 (alpha)	167					cardiac muscle contraction (GO:0060048)|cellular component movement (GO:0006928)|cellular response to reactive oxygen species (GO:0034614)|cytoskeleton organization (GO:0007010)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|negative regulation of cell migration (GO:0030336)|positive regulation of ATPase activity (GO:0032781)|positive regulation of cell adhesion (GO:0045785)|positive regulation of heart rate by epinephrine (GO:0003065)|positive regulation of stress fiber assembly (GO:0051496)|regulation of heart contraction (GO:0008016)|regulation of muscle contraction (GO:0006937)|ruffle organization (GO:0031529)|sarcomere organization (GO:0045214)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|wound healing (GO:0042060)	bleb (GO:0032059)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|muscle thin filament tropomyosin (GO:0005862)|ruffle membrane (GO:0032587)|sarcomere (GO:0030017)|stress fiber (GO:0001725)	actin binding (GO:0003779)|cytoskeletal protein binding (GO:0008092)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)			endometrium(1)|large_intestine(1)|lung(2)	4						GCAGGTGGCCCGTAAGCTGGT	0.597																																						dbGAP											0													88.0	83.0	84.0					15																	63353074		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB209041	CCDS10181.1, CCDS32262.1, CCDS32263.1, CCDS32264.1, CCDS45273.1, CCDS58368.1, CCDS58369.1	15q22.1	2014-09-17			ENSG00000140416	ENSG00000140416		"""Tropomyosins"""	12010	protein-coding gene	gene with protein product		191010	"""chromosome 15 open reading frame 13"", ""cardiomyopathy, hypertrophic 3"""	C15orf13, CMH3		10343096, 8205619	Standard	XM_005254637		Approved		uc002all.3	P09493	OTTHUMG00000132803	ENST00000403994.3:c.499C>G	15.37:g.63353074C>G	ENSP00000385107:p.Arg167Gly	Somatic		WXS	Illumina GAIIx	Phase_IV	B7Z5T7|D9YZV2|D9YZV3|D9YZV8|P09494|P10469|Q6DV89|Q6DV90|Q7Z6L8|Q86W64|Q96IK2|Q9UCI1|Q9UCI2|Q9UCY9|Q9Y427	Missense_Mutation	SNP	pfam_Tropomyosin,prints_Tropomyosin	p.R167G	ENST00000403994.3	37	c.499	CCDS45273.1	15	.	.	.	.	.	.	.	.	.	.	C	17.00	3.275513	0.59649	.	.	ENSG00000140416	ENST00000288398;ENST00000267996;ENST00000358278;ENST00000403994;ENST00000357980;ENST00000404484;ENST00000334895;ENST00000317516	D;D;D;D;D;D	0.98362	-4.89;-4.89;-4.89;-4.89;-4.89;-4.89	5.8	5.8	0.92144	.	0.000000	0.51477	D	0.000098	D	0.99199	0.9722	M	0.92026	3.265	0.80722	D	1	B;B;B;B;P;B;P;D;B;P;P;P;B;P	0.71674	0.094;0.053;0.332;0.015;0.953;0.024;0.513;0.998;0.383;0.553;0.557;0.873;0.022;0.513	B;B;P;B;P;B;P;D;P;B;P;P;B;P	0.80764	0.364;0.197;0.62;0.055;0.864;0.042;0.676;0.994;0.58;0.443;0.794;0.658;0.287;0.676	D	0.99425	1.0934	10	0.87932	D	0	-3.1773	19.0375	0.92985	0.0:1.0:0.0:0.0	.	131;131;167;133;131;131;167;209;167;167;167;167;167;167	B7Z722;B7Z596;P09493-6;F5H7S3;D9YZV7;Q1ZYL5;D9YZV4;Q6ZN40;D9YZV8;D9YZV5;Q9Y427;D9YZV3;D9YZV2;P09493	.;.;.;.;.;.;.;.;.;.;.;.;.;TPM1_HUMAN	G	167;167;167;167;209;189;131;133	ENSP00000288398:R167G;ENSP00000267996:R167G;ENSP00000351022:R167G;ENSP00000385107:R167G;ENSP00000350667:R209G;ENSP00000334624:R131G	ENSP00000267996:R167G	R	+	1	0	TPM1	61140127	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.818000	0.86416	2.745000	0.94114	0.491000	0.48974	CGT	TPM1	-	pfam_Tropomyosin,prints_Tropomyosin	ENSG00000140416		0.597	TPM1-002	KNOWN	basic|CCDS	protein_coding	TPM1	HGNC	protein_coding	OTTHUMT00000417083.2	59	0.00	0	C	NM_001018004		63353074	63353074	+1	no_errors	ENST00000267996	ensembl	human	known	69_37n	missense	27	25.00	9	SNP	1.000	G
USP13	8975	genome.wustl.edu	37	3	179478911	179478911	+	Missense_Mutation	SNP	G	G	C			TCGA-A8-A08Z-01A-21W-A019-09	TCGA-A8-A08Z-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	96afb6d0-29ea-4bd5-8a9d-130e42954707	35c8c6d8-68b5-4175-9d5b-2859dc94a67a	g.chr3:179478911G>C	ENST00000263966.3	+	17	2431	c.1960G>C	c.(1960-1962)Gat>Cat	p.D654H	USP13_ENST00000496897.1_Missense_Mutation_p.D589H	NM_003940.2	NP_003931.2	Q92995	UBP13_HUMAN	ubiquitin specific peptidase 13 (isopeptidase T-3)	654	UBA 1. {ECO:0000255|PROSITE- ProRule:PRU00212}.|USP.				autophagy (GO:0006914)|cell proliferation (GO:0008283)|melanocyte differentiation (GO:0030318)|protein K63-linked deubiquitination (GO:0070536)|protein stabilization (GO:0050821)|regulation of autophagy (GO:0010506)|regulation of transcription, DNA-templated (GO:0006355)|ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type endopeptidase activity (GO:0004197)|omega peptidase activity (GO:0008242)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(20)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	46	all_cancers(143;7.79e-15)|Ovarian(172;0.0338)|Breast(254;0.148)		OV - Ovarian serous cystadenocarcinoma(80;1e-25)|GBM - Glioblastoma multiforme(14;0.0169)			ATCAGACATCGATGAGTCATC	0.507																																						dbGAP											0													134.0	125.0	128.0					3																	179478911		2203	4300	6503	-	-	-	SO:0001583	missense	0			U75362	CCDS3235.1	3q26.2-q26.3	2008-04-11	2005-08-08		ENSG00000058056	ENSG00000058056		"""Ubiquitin-specific peptidases"""	12611	protein-coding gene	gene with protein product		603591	"""ubiquitin specific protease 13 (isopeptidase T-3)"""			12838346	Standard	NM_003940		Approved	IsoT-3	uc003fkh.3	Q92995	OTTHUMG00000157783	ENST00000263966.3:c.1960G>C	3.37:g.179478911G>C	ENSP00000263966:p.Asp654His	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K2S3|B4DYF3|D3DNS2|Q96B25	Missense_Mutation	SNP	pfam_Peptidase_C19,pfam_UBA/transl_elong_EF1B_N,pfam_Znf_UBP,superfamily_UBA-like,smart_Znf_UBP,smart_UBA/transl_elong_EF1B_N_euk,pirsf_Ubiquitinyl_hydrolase,pfscan_UBA/transl_elong_EF1B_N_euk,pfscan_Znf_UBP,pfscan_Peptidase_C19	p.D654H	ENST00000263966.3	37	c.1960	CCDS3235.1	3	.	.	.	.	.	.	.	.	.	.	G	24.2	4.500177	0.85176	.	.	ENSG00000058056	ENST00000263966;ENST00000496897;ENST00000497155	T;T	0.25414	1.8;1.8	4.81	4.81	0.61882	Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote (2);Ubiquitin-associated/translation elongation factor EF1B, N-terminal (1);Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.59348	0.2187	M	0.88979	2.995	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.68849	-0.5300	10	0.72032	D	0.01	-20.265	18.2312	0.89936	0.0:0.0:1.0:0.0	.	654	Q92995	UBP13_HUMAN	H	654;589;291	ENSP00000263966:D654H;ENSP00000417146:D589H	ENSP00000263966:D654H	D	+	1	0	USP13	180961605	1.000000	0.71417	0.986000	0.45419	0.787000	0.44495	9.420000	0.97426	2.377000	0.81083	0.585000	0.79938	GAT	USP13	-	pfam_Peptidase_C19,pfam_UBA/transl_elong_EF1B_N,smart_UBA/transl_elong_EF1B_N_euk,pirsf_Ubiquitinyl_hydrolase,pfscan_UBA/transl_elong_EF1B_N_euk,pfscan_Peptidase_C19	ENSG00000058056		0.507	USP13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	USP13	HGNC	protein_coding	OTTHUMT00000349617.1	151	0.00	0	G			179478911	179478911	+1	no_errors	ENST00000263966	ensembl	human	known	69_37n	missense	68	31.31	31	SNP	1.000	C
USP29	57663	genome.wustl.edu	37	19	57640254	57640254	+	Missense_Mutation	SNP	C	C	T			TCGA-A8-A08Z-01A-21W-A019-09	TCGA-A8-A08Z-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	96afb6d0-29ea-4bd5-8a9d-130e42954707	35c8c6d8-68b5-4175-9d5b-2859dc94a67a	g.chr19:57640254C>T	ENST00000254181.4	+	4	665	c.211C>T	c.(211-213)Cac>Tac	p.H71Y	USP29_ENST00000598197.1_Missense_Mutation_p.H71Y	NM_020903.2	NP_065954.1	Q9HBJ7	UBP29_HUMAN	ubiquitin specific peptidase 29	71					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)			breast(3)|endometrium(4)|kidney(3)|large_intestine(15)|lung(47)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	85		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		AAGACAAAGTCACCTGCGTTT	0.343																																						dbGAP											0													54.0	54.0	54.0					19																	57640254		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS33124.1	19q13.4	2008-06-23	2005-08-08			ENSG00000131864		"""Ubiquitin-specific peptidases"""	18563	protein-coding gene	gene with protein product		609546	"""ubiquitin specific protease 29"""			12838346	Standard	NM_020903		Approved		uc002qny.3	Q9HBJ7		ENST00000254181.4:c.211C>T	19.37:g.57640254C>T	ENSP00000254181:p.His71Tyr	Somatic		WXS	Illumina GAIIx	Phase_IV		Missense_Mutation	SNP	pfam_Peptidase_C19,pfscan_Peptidase_C19	p.H71Y	ENST00000254181.4	37	c.211	CCDS33124.1	19	.	.	.	.	.	.	.	.	.	.	C	0.774	-0.764900	0.02996	.	.	ENSG00000131864	ENST00000254181	T	0.46819	0.86	2.79	-5.07	0.02938	.	2.018590	0.03006	U	0.148810	T	0.28366	0.0701	N	0.25890	0.77	0.09310	N	1	B	0.22276	0.067	B	0.12837	0.008	T	0.07462	-1.0771	10	0.48119	T	0.1	1.463	0.6853	0.00882	0.1932:0.2189:0.1536:0.4343	.	71	Q9HBJ7	UBP29_HUMAN	Y	71	ENSP00000254181:H71Y	ENSP00000254181:H71Y	H	+	1	0	USP29	62332066	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.059000	0.11731	-1.099000	0.03034	-0.229000	0.12294	CAC	USP29	-	NULL	ENSG00000131864		0.343	USP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	USP29	HGNC	protein_coding	OTTHUMT00000465075.1	93	0.00	0	C			57640254	57640254	+1	no_errors	ENST00000254181	ensembl	human	known	69_37n	missense	140	10.83	17	SNP	0.000	T
TBC1D31	93594	genome.wustl.edu	37	8	124132397	124132397	+	Silent	SNP	C	C	T			TCGA-A8-A08Z-01A-21W-A019-09	TCGA-A8-A08Z-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	96afb6d0-29ea-4bd5-8a9d-130e42954707	35c8c6d8-68b5-4175-9d5b-2859dc94a67a	g.chr8:124132397C>T	ENST00000287380.1	+	11	1629	c.1539C>T	c.(1537-1539)ctC>ctT	p.L513L	TBC1D31_ENST00000522420.1_Silent_p.L408L|TBC1D31_ENST00000378080.2_Silent_p.L408L|TBC1D31_ENST00000327098.5_Silent_p.L513L|TBC1D31_ENST00000518805.1_Silent_p.L146L|TBC1D31_ENST00000521676.1_Silent_p.L390L|TBC1D31_ENST00000309336.3_Silent_p.L513L	NM_145647.3	NP_663622.2	Q96DN5	TBC31_HUMAN	TBC1 domain family, member 31	513	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.					centrosome (GO:0005813)	Rab GTPase activator activity (GO:0005097)										ACAACCAACTCATCTGTTTTG	0.338																																						dbGAP											0													99.0	85.0	90.0					8																	124132397		2202	4298	6500	-	-	-	SO:0001819	synonymous_variant	0			AK094612	CCDS6338.1, CCDS47916.1	8q24.13	2013-07-10	2013-07-10	2013-07-10	ENSG00000156787	ENSG00000156787		"""WD repeat domain containing"""	30888	protein-coding gene	gene with protein product			"""WD repeat domain 67"""	WDR67		12477932	Standard	NM_001145088		Approved	MGC21654, Gm85	uc003ypp.2	Q96DN5	OTTHUMG00000165081	ENST00000287380.1:c.1539C>T	8.37:g.124132397C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	B7ZL19|Q2M2J9|Q3MIR6|Q8TBP9	Silent	SNP	pfam_Rab-GTPase-TBC_dom,pfam_WD40_repeat,superfamily_WD40_repeat_dom,superfamily_Rab-GTPase-TBC_dom,smart_WD40_repeat,pfscan_Rab-GTPase-TBC_dom,pfscan_WD40_repeat_dom	p.L513	ENST00000287380.1	37	c.1539	CCDS6338.1	8																																																																																			WDR67	-	pfam_Rab-GTPase-TBC_dom,pfscan_Rab-GTPase-TBC_dom	ENSG00000156787		0.338	TBC1D31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	WDR67	HGNC	protein_coding	OTTHUMT00000381721.1	43	0.00	0	C	NM_145647		124132397	124132397	+1	no_errors	ENST00000287380	ensembl	human	known	69_37n	silent	33	29.79	14	SNP	1.000	T
