#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
ADAM21	8747	genome.wustl.edu	37	14	70924602	70924602	+	Missense_Mutation	SNP	T	T	G	rs72735759	byFrequency	TCGA-GM-A3XN-01A-12D-A22X-09	TCGA-GM-A3XN-10A-01D-A22X-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	dbdb932c-cf13-4b20-be5b-b33061e50a01	63229112-0438-4c3d-99f0-1120430c5c66	g.chr14:70924602T>G	ENST00000603540.1	+	2	644	c.386T>G	c.(385-387)tTt>tGt	p.F129C	RP11-486O13.4_ENST00000556646.1_lincRNA|ADAM21_ENST00000267499.3_Missense_Mutation_p.F129C	NM_003813.3	NP_003804.2	Q9UKJ8	ADA21_HUMAN	ADAM metallopeptidase domain 21	129					binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	axon (GO:0030424)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(10)|lung(10)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	31				all cancers(60;0.00326)|BRCA - Breast invasive adenocarcinoma(234;0.00646)|OV - Ovarian serous cystadenocarcinoma(108;0.0401)		AGTGCTTGTTTTGGGGGCTTT	0.463																																						dbGAP											0													84.0	100.0	94.0					14																	70924602		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF029900	CCDS9804.1	14q24.1	2008-09-05	2005-08-18		ENSG00000139985	ENSG00000139985		"""ADAM metallopeptidase domain containing"""	200	protein-coding gene	gene with protein product		603713	"""a disintegrin and metalloproteinase domain 21"""			9469942	Standard	NM_003813		Approved	ADAM31	uc001xmd.3	Q9UKJ8		ENST00000603540.1:c.386T>G	14.37:g.70924602T>G	ENSP00000474385:p.Phe129Cys	Somatic		WXS	Illumina GAIIx	Phase_IV	O43507|Q2VPC6|Q32MR0	Missense_Mutation	SNP	pfam_Peptidase_M12B,pfam_ADAM_Cys-rich,pfam_Peptidase_M12B_N,pfam_Blood-coag_inhib_Disintegrin,superfamily_Blood-coag_inhib_Disintegrin,smart_Blood-coag_inhib_Disintegrin,smart_ADAM_Cys-rich,pfscan_Blood-coag_inhib_Disintegrin,pfscan_Peptidase_M12B,prints_Blood-coag_inhib_Disintegrin	p.F129C	ENST00000603540.1	37	c.386	CCDS9804.1	14	.	.	.	.	.	.	.	.	.	.	T	0.044	-1.273422	0.01421	.	.	ENSG00000139985	ENST00000267499	T	0.01133	5.29	3.76	-7.52	0.01341	Peptidase M12B, propeptide (1);	1.704650	0.03782	U	0.261498	T	0.01523	0.0049	L	0.60067	1.865	0.09310	N	1	B	0.33299	0.407	B	0.37780	0.258	T	0.14924	-1.0455	10	0.46703	T	0.11	.	1.36	0.02189	0.2433:0.3101:0.2623:0.1842	.	129	Q9UKJ8	ADA21_HUMAN	C	129	ENSP00000267499:F129C	ENSP00000267499:F129C	F	+	2	0	ADAM21	69994355	0.000000	0.05858	0.007000	0.13788	0.108000	0.19459	-1.073000	0.03430	-2.633000	0.00433	-0.379000	0.06801	TTT	ADAM21	-	pfam_Peptidase_M12B_N	ENSG00000139985		0.463	ADAM21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ADAM21	HGNC	protein_coding	OTTHUMT00000413008.3	27	0.00	0	T			70924602	70924602	+1	no_errors	ENST00000267499	ensembl	human	known	69_37n	missense	39	11.36	5	SNP	0.000	G
ANKFY1	51479	genome.wustl.edu	37	17	4080476	4080476	+	Nonsense_Mutation	SNP	A	A	T			TCGA-GM-A3XN-01A-12D-A22X-09	TCGA-GM-A3XN-10A-01D-A22X-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	dbdb932c-cf13-4b20-be5b-b33061e50a01	63229112-0438-4c3d-99f0-1120430c5c66	g.chr17:4080476A>T	ENST00000341657.4	-	19	2755	c.2720T>A	c.(2719-2721)tTg>tAg	p.L907*	CYB5D2_ENST00000573984.1_Intron|ANKFY1_ENST00000574367.1_Nonsense_Mutation_p.L908*|ANKFY1_ENST00000570535.1_Nonsense_Mutation_p.L949*	NM_016376.3	NP_057460.3	Q9P2R3	ANFY1_HUMAN	ankyrin repeat and FYVE domain containing 1	907					endosomal vesicle fusion (GO:0034058)|endosome localization (GO:0032439)|Golgi to lysosome transport (GO:0090160)|positive regulation of pinocytosis (GO:0048549)|retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|macropinosome (GO:0044354)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phosphatidylinositol phosphate binding (GO:1901981)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(11)|liver(1)|lung(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32						CAGGGGGGTCAACTTGGAGGC	0.448																																						dbGAP											0													112.0	107.0	109.0					17																	4080476		1985	4174	6159	-	-	-	SO:0001587	stop_gained	0			AB033081	CCDS42236.1, CCDS58502.1	17p13.3	2013-01-10			ENSG00000185722	ENSG00000185722		"""Zinc fingers, FYVE domain containing"", ""BTB/POZ domain containing"", ""Ankyrin repeat domain containing"""	20763	protein-coding gene	gene with protein product		607927				10940552, 17273843	Standard	NM_016376		Approved	ANKHZN, KIAA1255, ZFYVE14, BTBD23	uc002fxn.3	Q9P2R3	OTTHUMG00000177727	ENST00000341657.4:c.2720T>A	17.37:g.4080476A>T	ENSP00000343362:p.Leu907*	Somatic		WXS	Illumina GAIIx	Phase_IV	A8KA65|Q5RKV4|Q9ULG5	Nonsense_Mutation	SNP	pfam_Ankyrin_rpt,pfam_Znf_FYVE,pfam_BTB_POZ,superfamily_Ankyrin_rpt-contain_dom,superfamily_BTB/POZ_fold,superfamily_Znf_FYVE_PHD,smart_BTB/POZ-like,smart_Ankyrin_rpt,smart_Znf_FYVE,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom,pfscan_BTB/POZ-like,pfscan_Znf_FYVE-rel,prints_Ankyrin_rpt	p.L949*	ENST00000341657.4	37	c.2846		17	.	.	.	.	.	.	.	.	.	.	A	40	7.963966	0.98585	.	.	ENSG00000185722	ENST00000341657;ENST00000535427	.	.	.	5.95	5.95	0.96441	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07482	T	0.82	-10.1345	15.5912	0.76530	1.0:0.0:0.0:0.0	.	.	.	.	X	908;849	.	ENSP00000343362:L908X	L	-	2	0	ANKFY1	4027225	1.000000	0.71417	1.000000	0.80357	0.900000	0.52787	7.148000	0.77389	2.280000	0.76307	0.460000	0.39030	TTG	ANKFY1	-	superfamily_Ankyrin_rpt-contain_dom,smart_Ankyrin_rpt,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom	ENSG00000185722		0.448	ANKFY1-008	KNOWN	basic|appris_candidate	protein_coding	ANKFY1	HGNC	protein_coding	OTTHUMT00000438702.1	70	0.00	0	A	NM_016376		4080476	4080476	-1	no_errors	ENST00000570535	ensembl	human	known	69_37n	nonsense	93	23.14	28	SNP	1.000	T
APBB3	10307	genome.wustl.edu	37	5	139943219	139943219	+	Missense_Mutation	SNP	C	C	T			TCGA-GM-A3XN-01A-12D-A22X-09	TCGA-GM-A3XN-10A-01D-A22X-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	dbdb932c-cf13-4b20-be5b-b33061e50a01	63229112-0438-4c3d-99f0-1120430c5c66	g.chr5:139943219C>T	ENST00000357560.4	-	3	693	c.250G>A	c.(250-252)Ggg>Agg	p.G84R	APBB3_ENST00000507279.1_5'UTR|APBB3_ENST00000354402.5_Missense_Mutation_p.G84R|APBB3_ENST00000412920.3_Missense_Mutation_p.G84R|SLC35A4_ENST00000323146.3_5'Flank|APBB3_ENST00000508496.2_Intron|APBB3_ENST00000356738.2_Missense_Mutation_p.G84R|APBB3_ENST00000511201.2_Missense_Mutation_p.G84R|APBB3_ENST00000358580.5_Missense_Mutation_p.G84R|SLC35A4_ENST00000514199.1_5'Flank	NM_006051.3|NM_133173.2	NP_006042.3|NP_573419.2	O95704	APBB3_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 3	84						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AAGGATCTCCCTTTGGGGGGC	0.567																																						dbGAP											0													71.0	67.0	68.0					5																	139943219		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB018247	CCDS4227.1, CCDS4228.1, CCDS4229.1, CCDS47279.1	5q31	2008-02-05			ENSG00000113108	ENSG00000113108			20708	protein-coding gene	gene with protein product		602711				9407065	Standard	NM_133172		Approved	FE65L2	uc003lgd.1	O95704	OTTHUMG00000129504	ENST00000357560.4:c.250G>A	5.37:g.139943219C>T	ENSP00000350171:p.Gly84Arg	Somatic		WXS	Illumina GAIIx	Phase_IV	B3KQN9|Q08AG4|Q96Q18|Q9BYD4|Q9NYX6|Q9NYX7|Q9NYX8	Missense_Mutation	SNP	pfam_PTyr_interaction_dom,pfam_WW_Rsp5_WWP,superfamily_WW_Rsp5_WWP,smart_WW_Rsp5_WWP,smart_PTyr_interaction_dom,pfscan_PTyr_interaction_dom,pfscan_WW_Rsp5_WWP	p.G84R	ENST00000357560.4	37	c.250	CCDS4229.1	5	.	.	.	.	.	.	.	.	.	.	C	12.17	1.857593	0.32791	.	.	ENSG00000113108	ENST00000358580;ENST00000356738;ENST00000354402;ENST00000357560;ENST00000412920;ENST00000511201	T;T;T;T;T;T	0.22539	1.95;1.96;1.96;1.96;1.96;1.95	4.69	3.82	0.43975	.	0.799307	0.11756	N	0.532631	T	0.19287	0.0463	N	0.19112	0.55	0.45852	D	0.998712	D;D;D	0.61080	0.96;0.976;0.989	B;P;P	0.49953	0.339;0.563;0.627	T	0.02132	-1.1208	9	.	.	.	-6.5022	9.8527	0.41066	0.0:0.9039:0.0:0.0961	.	84;84;84	O95704;O95704-2;O95704-3	APBB3_HUMAN;.;.	R	84	ENSP00000351389:G84R;ENSP00000349177:G84R;ENSP00000346378:G84R;ENSP00000350171:G84R;ENSP00000402591:G84R;ENSP00000424317:G84R	.	G	-	1	0	APBB3	139923403	0.051000	0.20477	0.993000	0.49108	0.855000	0.48748	0.938000	0.28965	1.192000	0.43071	0.561000	0.74099	GGG	APBB3	-	NULL	ENSG00000113108		0.567	APBB3-003	KNOWN	basic|CCDS	protein_coding	APBB3	HGNC	protein_coding	OTTHUMT00000251677.2	50	0.00	0	C	NM_006051		139943219	139943219	-1	no_errors	ENST00000356738	ensembl	human	known	69_37n	missense	127	11.11	16	SNP	0.983	T
CDC16	8881	genome.wustl.edu	37	13	115011252	115011252	+	Intron	SNP	C	C	T	rs17291201	byFrequency	TCGA-GM-A3XN-01A-12D-A22X-09	TCGA-GM-A3XN-10A-01D-A22X-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	dbdb932c-cf13-4b20-be5b-b33061e50a01	63229112-0438-4c3d-99f0-1120430c5c66	g.chr13:115011252C>T	ENST00000356221.3	+	10	955				CDC16_ENST00000375308.1_Intron|MIR548AR_ENST00000582191.1_RNA|CDC16_ENST00000375312.3_Intron|CDC16_ENST00000375310.1_Intron|CDC16_ENST00000252457.5_Intron|CDC16_ENST00000252458.6_Intron|CDC16_ENST00000360383.3_Intron			Q13042	CDC16_HUMAN	cell division cycle 16						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of mitosis (GO:0007088)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|spindle (GO:0005819)				endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22	Lung NSC(43;0.00299)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0191)|all_epithelial(44;0.00716)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.238)	BRCA - Breast invasive adenocarcinoma(86;0.0886)			CTGCAGTATTCGGGAAGTGCT	0.468													C|||	142	0.0283546	0.0061	0.0389	5008	,	,		19014	0.0437		0.0547	False		,,,				2504	0.0082					dbGAP											0																																										-	-	-	SO:0001627	intron_variant	0			U18291	CCDS9542.2	13q34	2013-01-17	2013-01-17		ENSG00000130177	ENSG00000130177		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1720	protein-coding gene	gene with protein product	"""anaphase-promoting complex, subunit 6"""	603461	"""CDC16 (cell division cycle 16, S. cerevisiae, homolog)"", ""CDC16 cell division cycle 16 homolog (S. cerevisiae)"", ""cell division cycle 16 homolog (S. cerevisiae)"""			7736578	Standard	NM_001078645		Approved	APC6, ANAPC6, CUT9	uc001vul.1	Q13042	OTTHUMG00000017402	ENST00000356221.3:c.848-223C>T	13.37:g.115011252C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	A2A365|Q5T8C8|Q96AE6|Q9Y564	RNA	SNP	-	NULL	ENST00000356221.3	37	NULL	CCDS9542.2	13																																																																																			CDC16	-	-	ENSG00000130177		0.468	CDC16-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	CDC16	HGNC	protein_coding	OTTHUMT00000276737.1	10	0.00	0	C	NM_003903		115011252	115011252	+1	no_errors	ENST00000494581	ensembl	human	known	69_37n	rna	11	47.62	10	SNP	0.000	T
CDH1	999	genome.wustl.edu	37	16	68835599	68835600	+	Frame_Shift_Ins	INS	-	-	A			TCGA-GM-A3XN-01A-12D-A22X-09	TCGA-GM-A3XN-10A-01D-A22X-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	dbdb932c-cf13-4b20-be5b-b33061e50a01	63229112-0438-4c3d-99f0-1120430c5c66	g.chr16:68835599_68835600insA	ENST00000261769.5	+	3	381_382	c.190_191insA	c.(190-192)caafs	p.Q64fs	CDH1_ENST00000422392.2_Frame_Shift_Ins_p.Q64fs|CDH1_ENST00000562836.1_3'UTR	NM_004360.3	NP_004351.1	P12830	CADH1_HUMAN	cadherin 1, type 1, E-cadherin (epithelial)	64					adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to amino acid stimulus (GO:0071230)|cellular response to indole-3-methanol (GO:0071681)|cellular response to lithium ion (GO:0071285)|cochlea development (GO:0090102)|epithelial cell morphogenesis (GO:0003382)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|homophilic cell adhesion (GO:0007156)|intestinal epithelial cell development (GO:0060576)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of epithelial cell proliferation (GO:0050680)|neuron projection development (GO:0031175)|pituitary gland development (GO:0021983)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|protein metabolic process (GO:0019538)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of immune response (GO:0050776)|regulation of neuron migration (GO:2001222)|regulation of protein localization to cell surface (GO:2000008)|regulation of water loss via skin (GO:0033561)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)|salivary gland cavitation (GO:0060662)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|tight junction assembly (GO:0070830)|trophectodermal cell differentiation (GO:0001829)	actin cytoskeleton (GO:0015629)|aggresome (GO:0016235)|apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|axon terminus (GO:0043679)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell junction (GO:0030054)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|node of Ranvier (GO:0033268)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|trans-Golgi network (GO:0005802)	ankyrin binding (GO:0030506)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|gamma-catenin binding (GO:0045295)|glycoprotein binding (GO:0001948)|GTPase activating protein binding (GO:0032794)	p.?(2)		NS(6)|biliary_tract(8)|breast(161)|central_nervous_system(4)|endometrium(9)|kidney(4)|large_intestine(13)|lung(13)|oesophagus(3)|ovary(2)|prostate(3)|soft_tissue(2)|stomach(76)|thyroid(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	311		all_neural(199;0.0189)|Ovarian(137;0.0563)		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)		CACCGGTCGACAAAGGACAGCC	0.45			"""Mis, N, F, S"""		"""lobular breast, gastric"""	gastric			Hereditary Diffuse Gastric Cancer																													dbGAP	yes	Rec	yes	Familial gastric carcinoma	16	16q22.1	999	"""cadherin 1, type 1, E-cadherin (epithelial) (ECAD)"""		E	2	Unknown(2)	breast(2)	GRCh37	CM990356	CDH1	M																																				-	-	-	SO:0001589	frameshift_variant	0	Familial Cancer Database	HDGC	L08599	CCDS10869.1	16q22.1	2014-09-17			ENSG00000039068	ENSG00000039068		"""CD molecules"", ""Cadherins / Major cadherins"""	1748	protein-coding gene	gene with protein product	"""E-Cadherin"""	192090		UVO		9925936	Standard	NM_004360		Approved	uvomorulin, CD324	uc002ewg.1	P12830	OTTHUMG00000137561	ENST00000261769.5:c.193dupA	16.37:g.68835602_68835602dupA	ENSP00000261769:p.Gln64fs	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K1U7|Q13799|Q14216|Q15855|Q16194|Q4PJ14|Q9UII8	Frame_Shift_Ins	INS	pfam_Cadherin,pfam_Cadherin_cytoplasmic-dom,pfam_Cadherin_pro_dom,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin,prints_Cadherin	p.R65fs	ENST00000261769.5	37	c.190_191	CCDS10869.1	16																																																																																			CDH1	-	pfam_Cadherin_pro_dom,superfamily_Cadherin-like	ENSG00000039068		0.450	CDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CDH1	HGNC	protein_coding	OTTHUMT00000268897.2	54	0.00	0	-	NM_004360		68835599	68835600	+1	no_errors	ENST00000261769	ensembl	human	known	69_37n	frame_shift_ins	72	12.20	10	INS	0.036:0.025	A
DPYSL4	10570	genome.wustl.edu	37	10	134006321	134006321	+	Silent	SNP	G	G	A	rs142741301		TCGA-GM-A3XN-01A-12D-A22X-09	TCGA-GM-A3XN-10A-01D-A22X-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	dbdb932c-cf13-4b20-be5b-b33061e50a01	63229112-0438-4c3d-99f0-1120430c5c66	g.chr10:134006321G>A	ENST00000338492.4	+	3	452	c.288G>A	c.(286-288)gcG>gcA	p.A96A	DPYSL4_ENST00000368627.1_Silent_p.A19A|DPYSL4_ENST00000493882.1_3'UTR|DPYSL4_ENST00000368629.1_Silent_p.A19A	NM_006426.2	NP_006417.2	O14531	DPYL4_HUMAN	dihydropyrimidinase-like 4	96					axon guidance (GO:0007411)|nervous system development (GO:0007399)|pyrimidine nucleobase catabolic process (GO:0006208)	cytosol (GO:0005829)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)			NS(1)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		all_cancers(35;4.33e-08)|all_epithelial(44;6.75e-06)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)|Colorectal(31;0.19)		OV - Ovarian serous cystadenocarcinoma(35;7.21e-05)|Epithelial(32;8.01e-05)|all cancers(32;9.29e-05)|BRCA - Breast invasive adenocarcinoma(275;0.206)		CCAAGGCAGCGCTAGCAGGAG	0.617													G|||	1	0.000199681	0.0	0.0	5008	,	,		17164	0.0		0.001	False		,,,				2504	0.0					dbGAP											0													103.0	74.0	84.0					10																	134006321		2202	4300	6502	-	-	-	SO:0001819	synonymous_variant	0			AB006713	CCDS7665.1	10q25.2-q26	2008-05-14			ENSG00000151640	ENSG00000151640			3016	protein-coding gene	gene with protein product		608407				8973361, 9652388	Standard	NM_006426		Approved	ULIP4, DRP-4	uc009ybb.3	O14531	OTTHUMG00000019283	ENST00000338492.4:c.288G>A	10.37:g.134006321G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	B2RMQ1|D3DRG5|O00240|Q5T0Q7	Silent	SNP	pfam_Amidohydro_1,superfamily_Metal-dep_hydrolase_composite,tigrfam_Hydantoinase/dihydroPyrase	p.A96	ENST00000338492.4	37	c.288	CCDS7665.1	10																																																																																			DPYSL4	-	pfam_Amidohydro_1,tigrfam_Hydantoinase/dihydroPyrase	ENSG00000151640		0.617	DPYSL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DPYSL4	HGNC	protein_coding	OTTHUMT00000051050.2	44	0.00	0	G			134006321	134006321	+1	no_errors	ENST00000338492	ensembl	human	known	69_37n	silent	59	25.32	20	SNP	0.068	A
EFCAB6	64800	genome.wustl.edu	37	22	44127685	44127685	+	Silent	SNP	C	C	T			TCGA-GM-A3XN-01A-12D-A22X-09	TCGA-GM-A3XN-10A-01D-A22X-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	dbdb932c-cf13-4b20-be5b-b33061e50a01	63229112-0438-4c3d-99f0-1120430c5c66	g.chr22:44127685C>T	ENST00000262726.7	-	8	904	c.651G>A	c.(649-651)tcG>tcA	p.S217S	EFCAB6_ENST00000358439.4_Silent_p.S111S|EFCAB6_ENST00000356087.4_Silent_p.S111S|EFCAB6_ENST00000396231.2_Silent_p.S65S	NM_022785.3	NP_073622.2	Q5THR3	EFCB6_HUMAN	EF-hand calcium binding domain 6	217					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(16)|lung(25)|ovary(4)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	68		Ovarian(80;0.0247)|all_neural(38;0.025)				TGTAGTGTTTCGAAAACCTAA	0.333																																						dbGAP											0													110.0	101.0	104.0					22																	44127685		2202	4299	6501	-	-	-	SO:0001819	synonymous_variant	0			Z82201	CCDS14049.1, CCDS14050.1	22q13.2	2013-01-10			ENSG00000186976	ENSG00000186976		"""EF-hand domain containing"""	24204	protein-coding gene	gene with protein product						11258795, 12612053	Standard	NM_022785		Approved	FLJ23588, DJBP, HSCBCIP1, KIAA1672, dJ185D5.1	uc003bdy.2	Q5THR3	OTTHUMG00000150522	ENST00000262726.7:c.651G>A	22.37:g.44127685C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	A8K8P6|A8K8Y3|B0QYI4|B0QYI6|Q5U5T6|Q9BY88|Q9H5C4|Q9NSF5	Silent	SNP	pfam_EF_hand_Ca-bd_contain_6,smart_EF_hand_Ca-bd,pfscan_EF_HAND_2	p.S217	ENST00000262726.7	37	c.651	CCDS14049.1	22																																																																																			EFCAB6	-	NULL	ENSG00000186976		0.333	EFCAB6-010	KNOWN	basic|appris_principal|CCDS	protein_coding	EFCAB6	HGNC	protein_coding	OTTHUMT00000353176.1	35	0.00	0	C	NM_022785		44127685	44127685	-1	no_errors	ENST00000262726	ensembl	human	known	69_37n	silent	51	29.17	21	SNP	0.001	T
FAT1	2195	genome.wustl.edu	37	4	187540196	187540196	+	Missense_Mutation	SNP	T	T	C			TCGA-GM-A3XN-01A-12D-A22X-09	TCGA-GM-A3XN-10A-01D-A22X-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	dbdb932c-cf13-4b20-be5b-b33061e50a01	63229112-0438-4c3d-99f0-1120430c5c66	g.chr4:187540196T>C	ENST00000441802.2	-	10	7753	c.7544A>G	c.(7543-7545)aAa>aGa	p.K2515R		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2515	Cadherin 23. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						ATCCGTAGTTTTCACCTCCAT	0.413										HNSCC(5;0.00058)																											Colon(197;1040 2055 4143 4984 49344)	dbGAP											0													200.0	187.0	191.0					4																	187540196		1865	4107	5972	-	-	-	SO:0001583	missense	0			X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.7544A>G	4.37:g.187540196T>C	ENSP00000406229:p.Lys2515Arg	Somatic		WXS	Illumina GAIIx	Phase_IV		Missense_Mutation	SNP	pfam_Cadherin,pfam_Laminin_G,pfam_EGF-like_dom,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.K2515R	ENST00000441802.2	37	c.7544	CCDS47177.1	4	.	.	.	.	.	.	.	.	.	.	T	0.012	-1.670188	0.00758	.	.	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.01745	4.66	5.09	3.92	0.45320	Cadherin (4);Cadherin-like (1);	0.248475	0.45606	N	0.000345	T	0.01661	0.0053	L	0.37630	1.12	0.34207	D	0.67381	B	0.14805	0.011	B	0.18871	0.023	T	0.31888	-0.9927	10	0.09590	T	0.72	.	8.818	0.35007	0.0:0.2049:0.0:0.7951	.	2515	Q14517	FAT1_HUMAN	R	2515;2517	ENSP00000406229:K2515R	ENSP00000260147:K2517R	K	-	2	0	FAT1	187777190	1.000000	0.71417	0.022000	0.16811	0.003000	0.03518	3.293000	0.51779	1.079000	0.41038	0.528000	0.53228	AAA	FAT1	-	pfam_Cadherin,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin	ENSG00000083857		0.413	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FAT1	HGNC	protein_coding	OTTHUMT00000360209.3	39	0.00	0	T	NM_005245		187540196	187540196	-1	no_errors	ENST00000441802	ensembl	human	known	69_37n	missense	72	21.74	20	SNP	0.601	C
LINC01597	400841	genome.wustl.edu	37	20	29515126	29515126	+	lincRNA	SNP	C	C	T	rs6118966	byFrequency	TCGA-GM-A3XN-01A-12D-A22X-09	TCGA-GM-A3XN-10A-01D-A22X-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	dbdb932c-cf13-4b20-be5b-b33061e50a01	63229112-0438-4c3d-99f0-1120430c5c66	g.chr20:29515126C>T	ENST00000380888.3	-	0	1783																											TTCTGAGGGGCCTAGATGCCT	0.552													.|||	585	0.116813	0.2284	0.1196	5008	,	,		18297	0.0		0.1511	False		,,,				2504	0.0491					dbGAP											0																																										-	-	-			0																															20.37:g.29515126C>T		Somatic		WXS	Illumina GAIIx	Phase_IV		RNA	SNP	-	NULL	ENST00000380888.3	37	NULL		20																																																																																			RP4-610C12.4	-	-	ENSG00000205611		0.552	RP4-610C12.4-001	KNOWN	basic	lincRNA	FLJ45832	Clone_based_vega_gene	lincRNA	OTTHUMT00000256907.1	8	0.00	0	C			29515126	29515126	-1	no_errors	ENST00000380888	ensembl	human	known	69_37n	rna	17	29.17	7	SNP	0.008	T
GEMIN7	79760	genome.wustl.edu	37	19	45593382	45593382	+	Missense_Mutation	SNP	C	C	A			TCGA-GM-A3XN-01A-12D-A22X-09	TCGA-GM-A3XN-10A-01D-A22X-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	dbdb932c-cf13-4b20-be5b-b33061e50a01	63229112-0438-4c3d-99f0-1120430c5c66	g.chr19:45593382C>A	ENST00000270257.4	+	3	257	c.10C>A	c.(10-12)Cca>Aca	p.P4T	CTB-179K24.3_ENST00000586744.1_RNA|GEMIN7_ENST00000591747.1_Missense_Mutation_p.P4T|CTB-179K24.3_ENST00000586556.1_RNA|PPP1R37_ENST00000421905.1_5'Flank|PPP1R37_ENST00000221462.4_5'Flank|GEMIN7_ENST00000391951.2_Missense_Mutation_p.P4T|GEMIN7_ENST00000591607.1_Missense_Mutation_p.P4T	NM_001007269.1|NM_001007270.1|NM_024707.2	NP_001007270.1|NP_001007271.1|NP_078983.1	Q9H840	GEMI7_HUMAN	gem (nuclear organelle) associated protein 7	4					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)				endometrium(1)|kidney(1)|lung(4)|ovary(1)	7		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0131)		AATGCAAACTCCAGTGAACAT	0.577																																						dbGAP											0													94.0	104.0	101.0					19																	45593382		2202	4299	6501	-	-	-	SO:0001583	missense	0			AK024018	CCDS12654.1	19q13.32	2008-02-05				ENSG00000142252			20045	protein-coding gene	gene with protein product		607419				12065586	Standard	NM_024707		Approved	FLJ13956	uc002pap.1	Q9H840		ENST00000270257.4:c.10C>A	19.37:g.45593382C>A	ENSP00000270257:p.Pro4Thr	Somatic		WXS	Illumina GAIIx	Phase_IV	Q6IA34	Missense_Mutation	SNP	pfam_SMN_gemin7	p.P4T	ENST00000270257.4	37	c.10	CCDS12654.1	19	.	.	.	.	.	.	.	.	.	.	C	14.73	2.622476	0.46840	.	.	ENSG00000142252	ENST00000270257;ENST00000391951	.	.	.	5.02	1.43	0.22495	.	1.077420	0.07139	N	0.846935	T	0.35278	0.0926	L	0.44542	1.39	0.21897	N	0.999484	B	0.24186	0.099	B	0.21917	0.037	T	0.37957	-0.9683	9	0.87932	D	0	-12.6983	6.7523	0.23493	0.0:0.6904:0.1451:0.1646	.	4	Q9H840	GEMI7_HUMAN	T	4	.	ENSP00000270257:P4T	P	+	1	0	GEMIN7	50285222	0.000000	0.05858	0.286000	0.24833	0.605000	0.37080	0.125000	0.15749	0.524000	0.28502	0.549000	0.68633	CCA	GEMIN7	-	NULL	ENSG00000142252		0.577	GEMIN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GEMIN7	HGNC	protein_coding	OTTHUMT00000457533.1	117	0.00	0	C			45593382	45593382	+1	no_errors	ENST00000270257	ensembl	human	known	69_37n	missense	191	17.52	41	SNP	0.096	A
GPR50	9248	genome.wustl.edu	37	X	150348960	150348960	+	Missense_Mutation	SNP	G	G	A			TCGA-GM-A3XN-01A-12D-A22X-09	TCGA-GM-A3XN-10A-01D-A22X-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	dbdb932c-cf13-4b20-be5b-b33061e50a01	63229112-0438-4c3d-99f0-1120430c5c66	g.chrX:150348960G>A	ENST00000218316.3	+	2	974	c.905G>A	c.(904-906)cGa>cAa	p.R302Q	GPR50-AS1_ENST00000454196.1_RNA|AF003625.3_ENST00000602313.1_lincRNA	NM_004224.3	NP_004215.2	Q13585	MTR1L_HUMAN	G protein-coupled receptor 50	302					cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|identical protein binding (GO:0042802)|melatonin receptor activity (GO:0008502)			breast(4)|central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(6)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	38	Acute lymphoblastic leukemia(192;6.56e-05)					GAGAATTTCCGAAGAGAATAC	0.502																																						dbGAP											0													114.0	110.0	111.0					X																	150348960		2002	4158	6160	-	-	-	SO:0001583	missense	0			U52219	CCDS44012.1	Xq28	2012-08-21			ENSG00000102195	ENSG00000102195		"""GPCR / Class A : Orphans"""	4506	protein-coding gene	gene with protein product		300207				9933574, 18400093	Standard	NM_004224		Approved	H9, Mel1c	uc010ntg.2	Q13585	OTTHUMG00000024166	ENST00000218316.3:c.905G>A	X.37:g.150348960G>A	ENSP00000218316:p.Arg302Gln	Somatic		WXS	Illumina GAIIx	Phase_IV	Q0VGG3|Q3ZAR0	Missense_Mutation	SNP	pfam_7TM_GPCR_Rhodpsn,pfam_7TM_GPCR_olfarory/Srsx,pfam_7TM_GPCR_serpentine_rcpt_Srx,pfscan_GPCR_Rhodpsn_supfam,prints_Mel_rcpt_1X,prints_7TM_GPCR_Rhodpsn,prints_Melatonin_rcpt,prints_NPY_rcpt	p.R302Q	ENST00000218316.3	37	c.905	CCDS44012.1	X	.	.	.	.	.	.	.	.	.	.	G	23.9	4.476328	0.84640	.	.	ENSG00000102195	ENST00000218316	T	0.57273	0.41	4.24	4.24	0.50183	.	0.000000	0.85682	D	0.000000	T	0.56963	0.2021	N	0.24115	0.695	0.50813	D	0.99989	D	0.76494	0.999	D	0.68483	0.958	T	0.60757	-0.7200	10	0.52906	T	0.07	-3.4923	13.5977	0.62000	0.0:0.0:1.0:0.0	.	302	Q13585	MTR1L_HUMAN	Q	302	ENSP00000218316:R302Q	ENSP00000218316:R302Q	R	+	2	0	GPR50	150099618	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	9.650000	0.98490	1.860000	0.53959	0.468000	0.43344	CGA	GPR50	-	pfam_7TM_GPCR_olfarory/Srsx,prints_7TM_GPCR_Rhodpsn,prints_NPY_rcpt	ENSG00000102195		0.502	GPR50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GPR50	HGNC	protein_coding	OTTHUMT00000060874.1	63	0.00	0	G	NM_004224		150348960	150348960	+1	no_errors	ENST00000218316	ensembl	human	known	69_37n	missense	72	28.71	29	SNP	1.000	A
GUSBP11	91316	genome.wustl.edu	37	22	24001837	24001837	+	RNA	SNP	T	T	G	rs7289879	byFrequency	TCGA-GM-A3XN-01A-12D-A22X-09	TCGA-GM-A3XN-10A-01D-A22X-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	dbdb932c-cf13-4b20-be5b-b33061e50a01	63229112-0438-4c3d-99f0-1120430c5c66	g.chr22:24001837T>G	ENST00000455485.1	-	0	3360				KB-1572G7.2_ENST00000421064.1_RNA|AP000347.2_ENST00000417194.1_RNA			Q6P575	BGP11_HUMAN	glucuronidase, beta pseudogene 11						carbohydrate metabolic process (GO:0005975)		hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)										TCCTGTTTGCTTTTTGACTGT	0.433													T|||	855	0.170727	0.4009	0.1369	5008	,	,		19699	0.0179		0.167	False		,,,				2504	0.045					dbGAP											0																																										-	-	-			0					22q11.23	2011-06-09			ENSG00000228315	ENSG00000228315			42325	pseudogene	pseudogene							Standard	NR_024448		Approved		uc011aiz.2	Q6P575	OTTHUMG00000150709		22.37:g.24001837T>G		Somatic		WXS	Illumina GAIIx	Phase_IV		RNA	SNP	-	NULL	ENST00000455485.1	37	NULL		22																																																																																			GUSBP11	-	-	ENSG00000228315		0.433	GUSBP11-005	KNOWN	basic|readthrough_transcript	processed_transcript	GUSBP11	HGNC	processed_transcript	OTTHUMT00000319697.1	45	0.00	0	T			24001837	24001837	-1	no_errors	ENST00000417194	ensembl	human	known	69_37n	rna	61	11.59	8	SNP	0.117	G
IGHV3-66	28412	genome.wustl.edu	37	14	107131147	107131147	+	RNA	SNP	G	G	A			TCGA-GM-A3XN-01A-12D-A22X-09	TCGA-GM-A3XN-10A-01D-A22X-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	dbdb932c-cf13-4b20-be5b-b33061e50a01	63229112-0438-4c3d-99f0-1120430c5c66	g.chr14:107131147G>A	ENST00000390632.2	-	0	312									immunoglobulin heavy variable 3-66																		CGGAGTCTGCGTAGTATGTGC	0.532																																						dbGAP											0													112.0	126.0	121.0					14																	107131147		2133	4260	6393	-	-	-			0			X92218		14q32.33	2012-02-08			ENSG00000211972	ENSG00000211972		"""Immunoglobulins / IGH locus"""	5619	other	immunoglobulin gene							Standard	NG_001019		Approved				OTTHUMG00000151880		14.37:g.107131147G>A		Somatic		WXS	Illumina GAIIx	Phase_IV		Silent	SNP	pfam_Ig_V-set,smart_Ig_V-set_subgr,pfscan_Ig-like	p.Y78	ENST00000390632.2	37	c.234		14																																																																																			IGHV3-66	-	pfam_Ig_V-set,smart_Ig_V-set_subgr,pfscan_Ig-like	ENSG00000211972		0.532	IGHV3-66-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IGHV3-66	HGNC	IG_V_gene	OTTHUMT00000324225.1	141	0.00	0	G	NG_001019		107131147	107131147	-1	no_stop_codon	ENST00000390632	ensembl	human	known	69_37n	silent	228	17.33	48	SNP	0.009	A
MED23	9439	genome.wustl.edu	37	6	131946081	131946081	+	Nonsense_Mutation	SNP	G	G	A			TCGA-GM-A3XN-01A-12D-A22X-09	TCGA-GM-A3XN-10A-01D-A22X-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	dbdb932c-cf13-4b20-be5b-b33061e50a01	63229112-0438-4c3d-99f0-1120430c5c66	g.chr6:131946081G>A	ENST00000368068.3	-	4	387	c.208C>T	c.(208-210)Cag>Tag	p.Q70*	MED23_ENST00000403834.3_Nonsense_Mutation_p.Q70*|MED23_ENST00000368053.4_Nonsense_Mutation_p.Q70*|MED23_ENST00000368060.3_Nonsense_Mutation_p.Q70*|MED23_ENST00000540546.1_Nonsense_Mutation_p.Q70*|MED23_ENST00000368058.1_Nonsense_Mutation_p.Q70*|MED23_ENST00000354577.4_Nonsense_Mutation_p.Q70*|MED23_ENST00000539158.1_Nonsense_Mutation_p.Q70*	NM_004830.3	NP_004821.2	Q9ULK4	MED23_HUMAN	mediator complex subunit 23	70					gene expression (GO:0010467)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(12)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	44	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0115)|OV - Ovarian serous cystadenocarcinoma(155;0.0608)		GGACTATGCTGACCATGAATA	0.373																																						dbGAP											0													101.0	101.0	101.0					6																	131946081		2203	4300	6503	-	-	-	SO:0001587	stop_gained	0			AF104255	CCDS5146.1, CCDS5147.1, CCDS59039.1	6q22.33-q24.1	2008-02-05	2007-08-08	2007-07-30	ENSG00000112282	ENSG00000112282			2372	protein-coding gene	gene with protein product		605042	"""cofactor required for Sp1 transcriptional activation, subunit 3, 130kDa"""	CRSP3		9989412	Standard	NM_004830		Approved	CRSP130, DRIP130, Sur2	uc003qcs.2	Q9ULK4	OTTHUMG00000015565	ENST00000368068.3:c.208C>T	6.37:g.131946081G>A	ENSP00000357047:p.Gln70*	Somatic		WXS	Illumina GAIIx	Phase_IV	B9TX55|O95403|Q5JWT3|Q5JWT4|Q6P9H6|Q9H0J2|Q9NTT9|Q9NTU0|Q9Y5P7|Q9Y667	Nonsense_Mutation	SNP	pfam_Mediator_Med23	p.Q70*	ENST00000368068.3	37	c.208	CCDS5147.1	6	.	.	.	.	.	.	.	.	.	.	G	38	7.110958	0.98070	.	.	ENSG00000112282	ENST00000354577;ENST00000368068;ENST00000403834;ENST00000368060;ENST00000368058;ENST00000368053;ENST00000540546;ENST00000539158	.	.	.	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.2442	20.1882	0.98224	0.0:0.0:1.0:0.0	.	.	.	.	X	70	.	ENSP00000346588:Q70X	Q	-	1	0	MED23	131987774	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	9.869000	0.99810	2.783000	0.95769	0.591000	0.81541	CAG	MED23	-	pfam_Mediator_Med23	ENSG00000112282		0.373	MED23-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	MED23	HGNC	protein_coding	OTTHUMT00000042215.1	46	0.00	0	G			131946081	131946081	-1	no_errors	ENST00000368058	ensembl	human	known	69_37n	nonsense	50	25.00	17	SNP	1.000	A
MIR4477B	100616194	genome.wustl.edu	37	9	68415386	68415386	+	RNA	SNP	G	G	A	rs1844035	byFrequency	TCGA-GM-A3XN-01A-12D-A22X-09	TCGA-GM-A3XN-10A-01D-A22X-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	dbdb932c-cf13-4b20-be5b-b33061e50a01	63229112-0438-4c3d-99f0-1120430c5c66	g.chr9:68415386G>A	ENST00000581659.1	+	0	79					NR_039688.1|NR_039689.1				microRNA 4477b																		gatgggaggaggatgaaatat	0.413																																						dbGAP											0																																										-	-	-			0					9	2011-09-12						"""ncRNAs / Micro RNAs"""	41898	non-coding RNA	RNA, micro							Standard	NR_039689		Approved	hsa-mir-4477b					9.37:g.68415386G>A		Somatic		WXS	Illumina GAIIx	Phase_IV		RNA	SNP	-	NULL	ENST00000581659.1	37	NULL		9																																																																																			MIR4477A	-	-	ENSG00000266017		0.413	MIR4477B-201	KNOWN	basic	miRNA	MIR4477A	HGNC	miRNA		12	0.00	0	G	NR_039689		68415386	68415386	+1	no_errors	ENST00000581659	ensembl	human	known	69_37n	rna	18	28.00	7	SNP	0.066	A
NDUFB1	4707	genome.wustl.edu	37	14	92587733	92587733	+	5'UTR	SNP	G	G	C	rs7143608	byFrequency	TCGA-GM-A3XN-01A-12D-A22X-09	TCGA-GM-A3XN-10A-01D-A22X-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	dbdb932c-cf13-4b20-be5b-b33061e50a01	63229112-0438-4c3d-99f0-1120430c5c66	g.chr14:92587733G>C	ENST00000555441.1	-	0	15				NDUFB1_ENST00000556555.1_5'UTR|NDUFB1_ENST00000605997.1_Intron|NDUFB1_ENST00000553514.1_Intron|CPSF2_ENST00000298875.4_5'Flank|NDUFB1_ENST00000329559.3_Intron			O75438	NDUB1_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 1, 7kDa						cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			large_intestine(1)|lung(1)	2		all_cancers(154;0.0766)		COAD - Colon adenocarcinoma(157;0.205)		GGCGGTCACTGGGTCACATCT	0.602													G|||	1220	0.24361	0.2995	0.1009	5008	,	,		14564	0.3204		0.161	False		,,,				2504	0.2751					dbGAP											0																																										-	-	-	SO:0001623	5_prime_UTR_variant	0			BC104672	CCDS9901.1	14q31.3	2011-07-04	2002-08-29		ENSG00000183648	ENSG00000183648		"""Mitochondrial respiratory chain complex / Complex I"""	7695	protein-coding gene	gene with protein product	"""complex I MNLL subunit"""	603837	"""NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 1 (7kD, MNLL)"""			9763677	Standard	NM_004545		Approved	MNLL, CI-MNLL	uc001yaf.3	O75438		ENST00000555441.1:c.-199C>G	14.37:g.92587733G>C		Somatic		WXS	Illumina GAIIx	Phase_IV	A0AV68	RNA	SNP	-	NULL	ENST00000555441.1	37	NULL		14																																																																																			NDUFB1	-	-	ENSG00000183648		0.602	NDUFB1-006	KNOWN	basic|appris_principal	protein_coding	NDUFB1	HGNC	protein_coding	OTTHUMT00000412121.1	10	0.00	0	G	NM_004545		92587733	92587733	-1	no_errors	ENST00000556555	ensembl	human	putative	69_37n	rna	5	44.44	4	SNP	0.013	C
NRXN2	9379	genome.wustl.edu	37	11	64453251	64453251	+	Missense_Mutation	SNP	G	G	A			TCGA-GM-A3XN-01A-12D-A22X-09	TCGA-GM-A3XN-10A-01D-A22X-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	dbdb932c-cf13-4b20-be5b-b33061e50a01	63229112-0438-4c3d-99f0-1120430c5c66	g.chr11:64453251G>A	ENST00000377551.1	-	5	1230	c.1019C>T	c.(1018-1020)tCc>tTc	p.S340F	NRXN2_ENST00000377559.3_Missense_Mutation_p.S316F|NRXN2_ENST00000409571.1_Missense_Mutation_p.S340F|NRXN2_ENST00000265459.6_Missense_Mutation_p.S340F			Q9P2S2	NRX2A_HUMAN	neurexin 2	340	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|gephyrin clustering (GO:0097116)|neuroligin clustering (GO:0097118)|neuron cell-cell adhesion (GO:0007158)|neurotransmitter secretion (GO:0007269)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	integral component of membrane (GO:0016021)	calcium channel regulator activity (GO:0005246)|cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)|neuroligin family protein binding (GO:0097109)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(6)|urinary_tract(1)	71						AGACTTGAGGGACAGGTTGAC	0.587																																						dbGAP											0													244.0	211.0	222.0					11																	64453251		2201	4297	6498	-	-	-	SO:0001583	missense	0				CCDS8077.1, CCDS31597.1, CCDS8078.1	11q13	2008-07-18			ENSG00000110076	ENSG00000110076			8009	protein-coding gene	gene with protein product	"""neurexin II"""	600566				1621094	Standard	NM_015080		Approved		uc021qkw.1	P58401	OTTHUMG00000045214	ENST00000377551.1:c.1019C>T	11.37:g.64453251G>A	ENSP00000366774:p.Ser340Phe	Somatic		WXS	Illumina GAIIx	Phase_IV	A7E2C1|Q9Y2D6	Missense_Mutation	SNP	pfam_Laminin_G,superfamily_ConA-like_lec_gl,smart_Laminin_G,smart_EGF-like,smart_Neurexin-like,pfscan_EG-like_dom,pfscan_Laminin_G	p.S340F	ENST00000377551.1	37	c.1019	CCDS8077.1	11	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	24.0|24.0	4.476553|4.476553	0.84640|0.84640	.|.	.|.	ENSG00000110076|ENSG00000110076	ENST00000417749|ENST00000377551;ENST00000377559;ENST00000265459;ENST00000345863;ENST00000409571;ENST00000442300	.|T;T;T;T;T	.|0.78707	.|-1.2;-1.2;-1.2;-1.2;-1.2	4.0|4.0	4.0|4.0	0.46444|0.46444	.|Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	.|0.000000	.|0.43416	.|U	.|0.000573	D|D	0.82688|0.82688	0.5091|0.5091	L|L	0.41906|0.41906	1.305|1.305	0.58432|0.58432	D|D	0.999998|0.999998	.|D;P;D	.|0.76494	.|0.999;0.789;0.999	.|D;B;D	.|0.87578	.|0.983;0.411;0.998	D|D	0.84887|0.84887	0.0834|0.0834	5|10	.|0.87932	.|D	.|0	.|.	13.9838|13.9838	0.64321|0.64321	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|316;340;93	.|Q9P2S2-2;Q9P2S2;E7EV67	.|.;NRX2A_HUMAN;.	S|F	101|340;316;340;316;340;111	.|ENSP00000366774:S340F;ENSP00000366782:S316F;ENSP00000265459:S340F;ENSP00000386416:S340F;ENSP00000388971:S111F	.|ENSP00000265459:S340F	P|S	-|-	1|2	0|0	NRXN2|NRXN2	64209827|64209827	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	9.864000|9.864000	0.99589|0.99589	1.951000|1.951000	0.56629|0.56629	0.467000|0.467000	0.42956|0.42956	CCC|TCC	NRXN2	-	pfam_Laminin_G,superfamily_ConA-like_lec_gl,smart_Laminin_G,pfscan_Laminin_G	ENSG00000110076		0.587	NRXN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NRXN2	HGNC	protein_coding	OTTHUMT00000104967.3	113	0.00	0	G	NM_015080		64453251	64453251	-1	no_errors	ENST00000265459	ensembl	human	known	69_37n	missense	165	17.41	35	SNP	1.000	A
PIK3CA	5290	genome.wustl.edu	37	3	178952085	178952085	+	Missense_Mutation	SNP	A	A	T	rs121913279		TCGA-GM-A3XN-01A-12D-A22X-09	TCGA-GM-A3XN-10A-01D-A22X-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	dbdb932c-cf13-4b20-be5b-b33061e50a01	63229112-0438-4c3d-99f0-1120430c5c66	g.chr3:178952085A>T	ENST00000263967.3	+	21	3297	c.3140A>T	c.(3139-3141)cAt>cTt	p.H1047L	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>T	3.37:g.178952085A>T	ENSP00000263967:p.His1047Leu	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.H1047L	ENST00000263967.3	37	c.3140	CCDS43171.1	3	.	.	.	.	.	.	.	.	.	.	A	4.518	0.096038	0.08681	.	.	ENSG00000121879	ENST00000263967	T	0.78126	-1.15	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	0.47002	0.1422	N	0.00611	-1.325	0.80722	D	1	B	0.14438	0.01	B	0.12156	0.007	T	0.58053	-0.7704	10	0.02654	T	1	-21.2893	16.6512	0.85203	1.0:0.0:0.0:0.0	.	1047	P42336	PK3CA_HUMAN	L	1047	ENSP00000263967:H1047L	ENSP00000263967:H1047L	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	33	0.00	0	A			178952085	178952085	+1	no_errors	ENST00000263967	ensembl	human	known	69_37n	missense	36	15.56	7	SNP	1.000	T
POTEI	653269	genome.wustl.edu	37	2	131220828	131220828	+	Missense_Mutation	SNP	G	G	A	rs190931019	byFrequency	TCGA-GM-A3XN-01A-12D-A22X-09	TCGA-GM-A3XN-10A-01D-A22X-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	dbdb932c-cf13-4b20-be5b-b33061e50a01	63229112-0438-4c3d-99f0-1120430c5c66	g.chr2:131220828G>A	ENST00000451531.2	-	15	3219	c.2789C>T	c.(2788-2790)gCg>gTg	p.A930V		NM_001277406.1	NP_001264335.1	P0CG38	POTEI_HUMAN	POTE ankyrin domain family, member I	930	Actin-like.				retina homeostasis (GO:0001895)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				lung(11)	11						GCTGGAGGCCGCCATGGCCAT	0.607													a|||	74	0.0147764	0.0129	0.0101	5008	,	,		3588	0.0288		0.0119	False		,,,				2504	0.0092					dbGAP											0																																										-	-	-	SO:0001583	missense	0				CCDS59431.1	2q21.1	2013-01-10			ENSG00000196834	ENSG00000196834		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	37093	protein-coding gene	gene with protein product						16364570	Standard	NM_001277406		Approved	POTE2beta	uc031rpa.1	P0CG38	OTTHUMG00000153925	ENST00000451531.2:c.2789C>T	2.37:g.131220828G>A	ENSP00000392718:p.Ala930Val	Somatic		WXS	Illumina GAIIx	Phase_IV		Missense_Mutation	SNP	pfam_Actin-like,pfam_Ankyrin_rpt,superfamily_Ankyrin_rpt-contain_dom,smart_Ankyrin_rpt,smart_Actin-like,prints_Actin-like,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom	p.A930V	ENST00000451531.2	37	c.2789	CCDS59431.1	2	269	0.12316849816849818	38	0.07723577235772358	49	0.13535911602209943	97	0.16958041958041958	85	0.11213720316622691	.	15.69	2.908541	0.52439	.	.	ENSG00000196834	ENST00000451531	D	0.94650	-3.48	.	.	.	.	.	.	.	.	T	0.06234	0.0161	M	0.86343	2.81	0.39417	P	0.03315999999999997	.	.	.	.	.	.	T	0.58075	-0.7700	5	0.48119	T	0.1	.	5.9051	0.18992	8.0E-4:0.0:0.9992:0.0	.	.	.	.	V	930	ENSP00000392718:A930V	ENSP00000392718:A930V	A	-	2	0	POTEI	130937298	1.000000	0.71417	0.281000	0.24762	0.285000	0.27093	6.500000	0.73687	0.119000	0.18210	0.121000	0.15741	GCG	POTEI	-	pfam_Actin-like,smart_Actin-like	ENSG00000196834		0.607	POTEI-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	POTEI	HGNC	protein_coding	OTTHUMT00000333222.2	12	0.00	0	G	XM_928585		131220828	131220828	-1	no_errors	ENST00000451531	ensembl	human	novel	69_37n	missense	8	27.27	3	SNP	1.000	A
PPP4R1	9989	genome.wustl.edu	37	18	9550110	9550110	+	Silent	SNP	C	C	T			TCGA-GM-A3XN-01A-12D-A22X-09	TCGA-GM-A3XN-10A-01D-A22X-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	dbdb932c-cf13-4b20-be5b-b33061e50a01	63229112-0438-4c3d-99f0-1120430c5c66	g.chr18:9550110C>T	ENST00000400556.3	-	18	2560	c.2487G>A	c.(2485-2487)gtG>gtA	p.V829V	PPP4R1_ENST00000400555.3_Silent_p.V812V	NM_001042388.2	NP_001035847.1	Q8TF05	PP4R1_HUMAN	protein phosphatase 4, regulatory subunit 1	829					dephosphorylation (GO:0016311)|protein phosphorylation (GO:0006468)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	protein phosphatase 4 complex (GO:0030289)	protein phosphatase type 4 regulator activity (GO:0030362)			large_intestine(1)|skin(2)	3						CAAAGTTCTCCACAAGCTCAT	0.537																																					Melanoma(188;1232 2082 5061 11948 35994)	dbGAP											0													83.0	95.0	91.0					18																	9550110		2033	4193	6226	-	-	-	SO:0001819	synonymous_variant	0			AF111106	CCDS42412.1, CCDS42413.1	18p11.22	2010-06-18			ENSG00000154845	ENSG00000154845		"""Serine/threonine phosphatases / Protein phosphatase 4, regulatory subunits"""	9320	protein-coding gene	gene with protein product		604908				10026142	Standard	NM_001042388		Approved	PP4R1	uc002koe.2	Q8TF05	OTTHUMG00000137466	ENST00000400556.3:c.2487G>A	18.37:g.9550110C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	Q99774|Q9UNQ7	Silent	SNP	pfam_HEAT,superfamily_ARM-type_fold,pfscan_HEAT_type_2	p.V829	ENST00000400556.3	37	c.2487	CCDS42412.1	18																																																																																			PPP4R1	-	superfamily_ARM-type_fold	ENSG00000154845		0.537	PPP4R1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	PPP4R1	HGNC	protein_coding	OTTHUMT00000268571.1	78	0.00	0	C	NM_005134		9550110	9550110	-1	no_errors	ENST00000400556	ensembl	human	known	69_37n	silent	151	14.20	25	SNP	0.575	T
RBMXL3	139804	genome.wustl.edu	37	X	114425181	114425181	+	Missense_Mutation	SNP	A	A	G	rs55659078|rs66891148		TCGA-GM-A3XN-01A-12D-A22X-09	TCGA-GM-A3XN-10A-01D-A22X-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	dbdb932c-cf13-4b20-be5b-b33061e50a01	63229112-0438-4c3d-99f0-1120430c5c66	g.chrX:114425181A>G	ENST00000424776.3	+	1	1219	c.1177A>G	c.(1177-1179)Aga>Gga	p.R393G	LRCH2_ENST00000538422.1_Intron|LRCH2_ENST00000317135.8_Intron	NM_001145346.1	NP_001138818.1	Q8N7X1	RMXL3_HUMAN	RNA binding motif protein, X-linked-like 3	393	Gly-rich.						nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			endometrium(13)|kidney(2)|skin(1)	16						CGAGGAGTACAGAGGCCGCTC	0.622																																						dbGAP											0													14.0	15.0	15.0					X																	114425181		689	1585	2274	-	-	-	SO:0001583	missense	0			AK097568	CCDS55478.1	Xq23	2013-02-12	2009-03-24	2009-03-24	ENSG00000175718	ENSG00000175718		"""RNA binding motif (RRM) containing"""	26859	protein-coding gene	gene with protein product			"""chromosome X open reading frame 55"""	CXorf55			Standard	NM_001145346		Approved	FLJ40249	uc011mte.1	Q8N7X1	OTTHUMG00000022230	ENST00000424776.3:c.1177A>G	X.37:g.114425181A>G	ENSP00000417451:p.Arg393Gly	Somatic		WXS	Illumina GAIIx	Phase_IV	B4DXC0	Missense_Mutation	SNP	pfam_RRM_dom,smart_RRM_dom,pfscan_RRM_dom	p.R393G	ENST00000424776.3	37	c.1177	CCDS55478.1	X	.	.	.	.	.	.	.	.	.	.	A	8.693	0.907954	0.17833	.	.	ENSG00000175718	ENST00000424776	T	0.05855	3.38	0.341	0.341	0.15991	.	.	.	.	.	T	0.03263	0.0095	N	0.08118	0	0.19775	N	0.999956	B	0.10296	0.003	B	0.01281	0.0	T	0.41448	-0.9508	9	0.87932	D	0	.	5.0049	0.14282	0.9998:0.0:2.0E-4:0.0	.	393	Q8N7X1	RMXL3_HUMAN	G	393	ENSP00000417451:R393G	ENSP00000417451:R393G	R	+	1	2	RBMXL3	114331437	0.014000	0.17966	0.074000	0.20217	0.114000	0.19823	-0.464000	0.06688	0.353000	0.24079	0.104000	0.15600	AGA	RBMXL3	-	NULL	ENSG00000175718		0.622	RBMXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RBMXL3	HGNC	protein_coding	OTTHUMT00000057968.3	50	0.00	0	A	NM_001145346		114425181	114425181	+1	no_errors	ENST00000424776	ensembl	human	known	69_37n	missense	60	10.45	7	SNP	0.738	G
SFXN4	119559	genome.wustl.edu	37	10	120921865	120921865	+	Missense_Mutation	SNP	G	G	A			TCGA-GM-A3XN-01A-12D-A22X-09	TCGA-GM-A3XN-10A-01D-A22X-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	dbdb932c-cf13-4b20-be5b-b33061e50a01	63229112-0438-4c3d-99f0-1120430c5c66	g.chr10:120921865G>A	ENST00000355697.2	-	3	258	c.239C>T	c.(238-240)tCg>tTg	p.S80L	SFXN4_ENST00000330036.6_Missense_Mutation_p.S80L|SFXN4_ENST00000461438.1_5'UTR	NM_213649.1	NP_998814.1	Q6P4A7	SFXN4_HUMAN	sideroflexin 4	80					iron ion homeostasis (GO:0055072)	integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial inner membrane (GO:0005743)	cation transmembrane transporter activity (GO:0008324)			central_nervous_system(1)|cervix(1)|kidney(3)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	11		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0261)		TTGGTCCGCCGAGGCAGGGCT	0.453																																						dbGAP											0													141.0	123.0	129.0					10																	120921865		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS7610.1	10q26.11	2006-03-13			ENSG00000183605	ENSG00000183605		"""Sideroflexins"""	16088	protein-coding gene	gene with protein product		615564				14756423	Standard	NM_213649		Approved		uc001leb.3	Q6P4A7	OTTHUMG00000019147	ENST00000355697.2:c.239C>T	10.37:g.120921865G>A	ENSP00000347924:p.Ser80Leu	Somatic		WXS	Illumina GAIIx	Phase_IV	Q6WSU4|Q86TD9	Missense_Mutation	SNP	pfam_Mtc	p.S80L	ENST00000355697.2	37	c.239	CCDS7610.1	10	.	.	.	.	.	.	.	.	.	.	g	4.111	0.018709	0.07959	.	.	ENSG00000183605	ENST00000355697;ENST00000330036	T;T	0.29655	1.95;1.56	3.41	-2.41	0.06562	.	1.547880	0.04340	N	0.353976	T	0.18045	0.0433	N	0.22421	0.69	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.17992	-1.0351	10	0.27785	T	0.31	-0.5526	4.1159	0.10081	0.3893:0.206:0.4047:0.0	.	80	Q6P4A7	SFXN4_HUMAN	L	80	ENSP00000347924:S80L;ENSP00000333200:S80L	ENSP00000333200:S80L	S	-	2	0	SFXN4	120911855	0.000000	0.05858	0.000000	0.03702	0.040000	0.13550	0.106000	0.15354	-0.379000	0.07906	-1.587000	0.00848	TCG	SFXN4	-	pfam_Mtc	ENSG00000183605		0.453	SFXN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SFXN4	HGNC	protein_coding	OTTHUMT00000050642.3	79	0.00	0	G	XM_058406		120921865	120921865	-1	no_errors	ENST00000355697	ensembl	human	known	69_37n	missense	97	19.01	23	SNP	0.000	A
SLITRK3	22865	genome.wustl.edu	37	3	164907426	164907426	+	Missense_Mutation	SNP	T	T	C			TCGA-GM-A3XN-01A-12D-A22X-09	TCGA-GM-A3XN-10A-01D-A22X-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	dbdb932c-cf13-4b20-be5b-b33061e50a01	63229112-0438-4c3d-99f0-1120430c5c66	g.chr3:164907426T>C	ENST00000475390.1	-	2	1636	c.1193A>G	c.(1192-1194)aAt>aGt	p.N398S	SLITRK3_ENST00000241274.3_Missense_Mutation_p.N398S			O94933	SLIK3_HUMAN	SLIT and NTRK-like family, member 3	398	LRRNT.				axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(66)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(5)	119						AGAAATGTTATTAAATCCTCG	0.408										HNSCC(40;0.11)																												dbGAP											0													111.0	111.0	111.0					3																	164907426		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB020655	CCDS3197.1	3q26.1	2004-07-28			ENSG00000121871	ENSG00000121871			23501	protein-coding gene	gene with protein product		609679				10048485, 14557068	Standard	NM_014926		Approved	KIAA0848	uc003fek.3	O94933	OTTHUMG00000158072	ENST00000475390.1:c.1193A>G	3.37:g.164907426T>C	ENSP00000420091:p.Asn398Ser	Somatic		WXS	Illumina GAIIx	Phase_IV	Q1RMY6	Missense_Mutation	SNP	pfam_Leu-rich_rpt,smart_Leu-rich_rpt_typical-subtyp,smart_Cys-rich_flank_reg_C	p.N398S	ENST00000475390.1	37	c.1193	CCDS3197.1	3	.	.	.	.	.	.	.	.	.	.	T	6.360	0.434546	0.12045	.	.	ENSG00000121871	ENST00000475390;ENST00000241274	T;T	0.60548	0.18;0.18	5.58	4.42	0.53409	Leucine-rich repeat-containing N-terminal (1);	0.000000	0.40385	N	0.001101	T	0.28101	0.0693	N	0.01576	-0.805	0.39395	D	0.966489	B	0.16603	0.018	B	0.14023	0.01	T	0.09037	-1.0693	10	0.21540	T	0.41	-13.507	11.4179	0.49962	0.0:0.0701:0.0:0.9299	.	398	O94933	SLIK3_HUMAN	S	398	ENSP00000420091:N398S;ENSP00000241274:N398S	ENSP00000241274:N398S	N	-	2	0	SLITRK3	166390120	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.874000	0.63064	1.125000	0.41998	0.533000	0.62120	AAT	SLITRK3	-	NULL	ENSG00000121871		0.408	SLITRK3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	SLITRK3	HGNC	protein_coding	OTTHUMT00000350126.1	59	0.00	0	T	NM_014926		164907426	164907426	-1	no_errors	ENST00000241274	ensembl	human	known	69_37n	missense	108	11.48	14	SNP	1.000	C
TRAF4	9618	genome.wustl.edu	37	17	27075546	27075546	+	Silent	SNP	C	C	T			TCGA-GM-A3XN-01A-12D-A22X-09	TCGA-GM-A3XN-10A-01D-A22X-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	dbdb932c-cf13-4b20-be5b-b33061e50a01	63229112-0438-4c3d-99f0-1120430c5c66	g.chr17:27075546C>T	ENST00000262395.5	+	6	771	c.642C>T	c.(640-642)tgC>tgT	p.C214C	AC010761.9_ENST00000577325.1_RNA|TRAF4_ENST00000444415.3_Silent_p.C214C|AC010761.10_ENST00000579468.1_RNA|TRAF4_ENST00000262396.6_Intron	NM_004295.3	NP_004286.2	Q9BUZ4	TRAF4_HUMAN	TNF receptor-associated factor 4	214					activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein homodimerization activity (GO:0090073)|positive regulation of protein kinase activity (GO:0045860)|regulation of apoptotic process (GO:0042981)|respiratory gaseous exchange (GO:0007585)|respiratory tube development (GO:0030323)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	DNA binding (GO:0003677)|thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|WW domain binding (GO:0050699)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	10	Lung NSC(42;0.01)		Epithelial(11;3.26e-05)|all cancers(11;0.000272)|OV - Ovarian serous cystadenocarcinoma(11;0.235)			AGTACCAGTGCCCAAGGCTGC	0.607																																						dbGAP											0													48.0	39.0	42.0					17																	27075546		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			X80200	CCDS11243.1	17q11-q21.3	2013-01-09			ENSG00000076604	ENSG00000076604		"""RING-type (C3HC4) zinc fingers"""	12034	protein-coding gene	gene with protein product		602464				7592751, 7490069	Standard	NM_004295		Approved	CART1, MLN62, RNF83	uc002hcs.3	Q9BUZ4	OTTHUMG00000132677	ENST00000262395.5:c.642C>T	17.37:g.27075546C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	O75615|Q14848|Q2KJU4|Q2PJN8	Silent	SNP	pfam_MATH,pfam_Znf_C3HC4_RING-type,superfamily_TRAF-like,smart_Znf_RING,smart_MATH,pirsf_TNF_rcpt--assoc_TRAF,pfscan_MATH,pfscan_Znf_RING,pfscan_Znf_TRAF	p.C214	ENST00000262395.5	37	c.642	CCDS11243.1	17																																																																																			TRAF4	-	superfamily_TRAF-like,pirsf_TNF_rcpt--assoc_TRAF,pfscan_Znf_TRAF	ENSG00000076604		0.607	TRAF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TRAF4	HGNC	protein_coding	OTTHUMT00000255944.2	83	0.00	0	C	NM_145751		27075546	27075546	+1	no_errors	ENST00000262395	ensembl	human	known	69_37n	silent	130	16.67	26	SNP	1.000	T
TRIM43	129868	genome.wustl.edu	37	2	96265165	96265165	+	Silent	SNP	C	C	T	rs200456827		TCGA-GM-A3XN-01A-12D-A22X-09	TCGA-GM-A3XN-10A-01D-A22X-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	dbdb932c-cf13-4b20-be5b-b33061e50a01	63229112-0438-4c3d-99f0-1120430c5c66	g.chr2:96265165C>T	ENST00000272395.2	+	7	1321	c.1185C>T	c.(1183-1185)taC>taT	p.Y395Y		NM_001164464.1|NM_138800.1	NP_001157936.1|NP_620155.1	Q96BQ3	TRI43_HUMAN	tripartite motif containing 43	395	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					intracellular (GO:0005622)	zinc ion binding (GO:0008270)			breast(1)|large_intestine(3)|lung(7)|ovary(1)	12						TTCCTCACTACATAGAGAAAC	0.418																																						dbGAP											0													1.0	1.0	1.0					2																	96265165		500	1208	1708	-	-	-	SO:0001819	synonymous_variant	0			BK000505	CCDS2015.1	2q11	2014-02-17	2011-01-25		ENSG00000144015	ENSG00000144015		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19015	protein-coding gene	gene with protein product			"""tripartite motif-containing 43"""				Standard	NM_138800		Approved	TRIM43A	uc002suv.3	Q96BQ3	OTTHUMG00000130401	ENST00000272395.2:c.1185C>T	2.37:g.96265165C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	Q53TJ7	Silent	SNP	pfam_SPRY_rcpt,superfamily_ConA-like_lec_gl,smart_Znf_RING,smart_Znf_B-box,smart_SPla/RYanodine_receptor_subgr,prints_Butyrophylin,pfscan_B30.2/SPRY,pfscan_Znf_B-box,pfscan_Znf_RING	p.Y395	ENST00000272395.2	37	c.1185	CCDS2015.1	2																																																																																			TRIM43	-	pfam_SPRY_rcpt,superfamily_ConA-like_lec_gl,smart_SPla/RYanodine_receptor_subgr,prints_Butyrophylin,pfscan_B30.2/SPRY	ENSG00000144015		0.418	TRIM43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TRIM43	HGNC	protein_coding	OTTHUMT00000252784.1	8	0.00	0	C	NM_138800		96265165	96265165	+1	no_errors	ENST00000272395	ensembl	human	known	69_37n	silent	8	57.89	11	SNP	0.000	T
TTL	150465	genome.wustl.edu	37	2	113288949	113288949	+	3'UTR	SNP	C	C	A			TCGA-GM-A3XN-01A-12D-A22X-09	TCGA-GM-A3XN-10A-01D-A22X-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	dbdb932c-cf13-4b20-be5b-b33061e50a01	63229112-0438-4c3d-99f0-1120430c5c66	g.chr2:113288949C>A	ENST00000233336.6	+	0	3902				TTL_ENST00000460450.1_3'UTR	NM_153712.4	NP_714923.1	Q8NG68	TTL_HUMAN	tubulin tyrosine ligase						cellular protein modification process (GO:0006464)|microtubule cytoskeleton organization (GO:0000226)|regulation of axon extension (GO:0030516)		ATP binding (GO:0005524)|tubulin-tyrosine ligase activity (GO:0004835)			breast(1)|large_intestine(2)|ovary(1)	4		Ovarian(717;0.024)		BRCA - Breast invasive adenocarcinoma(221;6.17e-07)|STAD - Stomach adenocarcinoma(1183;0.00644)		agcctgttaacctctctgtgc	0.473			T	ETV6	ALL																																	dbGAP		Dom	yes		2	2q13	150465	tubulin tyrosine ligase		L	0																																										-	-	-	SO:0001624	3_prime_UTR_variant	0				CCDS2096.1	2q13	2010-04-21			ENSG00000114999	ENSG00000114999	6.3.2.25		21586	protein-coding gene	gene with protein product		608291				11431336	Standard	NM_153712		Approved	MGC46235	uc002thu.3	Q8NG68	OTTHUMG00000131316	ENST00000233336.6:c.*2577C>A	2.37:g.113288949C>A		Somatic		WXS	Illumina GAIIx	Phase_IV	Q585T3|Q7Z302|Q8N426	RNA	SNP	-	NULL	ENST00000233336.6	37	NULL	CCDS2096.1	2																																																																																			TTL	-	-	ENSG00000114999		0.473	TTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TTL	HGNC	protein_coding	OTTHUMT00000254085.2	53	0.00	0	C	NM_153712		113288949	113288949	+1	no_errors	ENST00000460450	ensembl	human	known	69_37n	rna	87	17.92	19	SNP	0.992	A
ZBTB7C	201501	genome.wustl.edu	37	18	45567396	45567396	+	Missense_Mutation	SNP	C	C	T			TCGA-GM-A3XN-01A-12D-A22X-09	TCGA-GM-A3XN-10A-01D-A22X-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	dbdb932c-cf13-4b20-be5b-b33061e50a01	63229112-0438-4c3d-99f0-1120430c5c66	g.chr18:45567396C>T	ENST00000588982.1	-	3	584	c.83G>A	c.(82-84)cGg>cAg	p.R28Q	ZBTB7C_ENST00000586438.1_Missense_Mutation_p.R28Q|ZBTB7C_ENST00000590800.1_Missense_Mutation_p.R28Q|ZBTB7C_ENST00000535628.2_Missense_Mutation_p.R28Q|ZBTB7C_ENST00000332053.2_Missense_Mutation_p.R28Q			A1YPR0	ZBT7C_HUMAN	zinc finger and BTB domain containing 7C	28							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)	p.R28Q(1)		endometrium(8)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23						GCCATCGTGCCGTTGCTCATT	0.582																																						dbGAP											1	Substitution - Missense(1)	ovary(1)											84.0	77.0	79.0					18																	45567396		2203	4300	6503	-	-	-	SO:0001583	missense	0			Y14591	CCDS32830.1	18q21.1	2013-01-08		2005-04-07	ENSG00000184828	ENSG00000184828		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	31700	protein-coding gene	gene with protein product			"""zinc finger and BTB domain containing 36"""	ZBTB36			Standard	NM_001039360		Approved	ZNF857C	uc002ldb.3	A1YPR0		ENST00000588982.1:c.83G>A	18.37:g.45567396C>T	ENSP00000468782:p.Arg28Gln	Somatic		WXS	Illumina GAIIx	Phase_IV	O73453	Missense_Mutation	SNP	pfam_BTB_POZ,pfam_Znf_C2H2,superfamily_BTB/POZ_fold,smart_BTB/POZ-like,smart_Znf_C2H2-like,pfscan_BTB/POZ-like,pfscan_Znf_C2H2	p.R28Q	ENST00000588982.1	37	c.83	CCDS32830.1	18	.	.	.	.	.	.	.	.	.	.	C	28.3	4.908657	0.92107	.	.	ENSG00000184828	ENST00000535628;ENST00000332053	T;T	0.73152	-0.72;-0.72	5.04	5.04	0.67666	BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	D	0.87414	0.6171	M	0.90019	3.08	0.58432	D	0.999998	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.996;0.996	D	0.90252	0.4294	10	0.87932	D	0	.	18.3518	0.90340	0.0:1.0:0.0:0.0	.	28;28;28	B4DKU0;B2RG49;A1YPR0	.;.;ZBT7C_HUMAN	Q	28	ENSP00000439781:R28Q;ENSP00000328732:R28Q	ENSP00000328732:R28Q	R	-	2	0	ZBTB7C	43821394	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.818000	0.86416	2.332000	0.79248	0.561000	0.74099	CGG	ZBTB7C	-	pfam_BTB_POZ,superfamily_BTB/POZ_fold	ENSG00000184828		0.582	ZBTB7C-025	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	ZBTB7C	HGNC	protein_coding	OTTHUMT00000450731.1	37	0.00	0	C	NM_001039360		45567396	45567396	-1	no_errors	ENST00000332053	ensembl	human	known	69_37n	missense	63	11.27	8	SNP	1.000	T
