#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_ENSG_ID	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_Ens_Gene	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GMAF	i_HGNC	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_Normal_Alt_Count	i_Normal_Ref_Count	i_Normal_VAF	i_ORegAnno_bin	i_PurityEst	i_RNA_Tum_Ref_count	i_RNA_Tum_VAF	i_RNA_Tum_Var_count	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_Tier	i_Tumor_Alt_Count	i_Tumor_Ref_Count	i_Tumor_VAF	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_WGS_Norm_Ref_count	i_WGS_Norm_VAF	i_WGS_Norm_Var_count	i_WGS_Tum_Ref_count	i_WGS_Tum_VAF	i_WGS_Tum_Var_count	i_all_domains	i_amino_acid_change	i_annotation_transcript	i_build	i_c_position	i_ccds_id	i_chromosome_name	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_deletion_substructures	i_domain	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	i_gene_type	i_havana_transcript	i_reference	i_refseq_mrna_id	i_rs_id	i_secondary_variant_classification	i_stop	i_strand	i_transcript_error	i_transcript_name	i_transcript_source	i_transcript_species	i_transcript_status	i_transcript_version	i_trv_type	i_type	i_ucsc_cons	i_variant
WASH3P	374666	genome.wustl.edu	37	15	102516816	102516816	+	RNA	SNP	G	G	T			TCGA-DX-A23T-01A-11D-A26G-09	TCGA-DX-A23T-10A-01D-A26G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc6f717-fbc5-40d2-b105-da9a150b454f	b5482bab-e0c8-4a78-b485-a9d4bcfe9203	g.chr15:102516816G>T	ENST00000557932.1	+	0	1679				DDX11L9_ENST00000562189.1_RNA			C4AMC7	WASH3_HUMAN	WAS protein family homolog 3 pseudogene						Arp2/3 complex-mediated actin nucleation (GO:0034314)|endosomal transport (GO:0016197)|retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|membrane (GO:0016020)|recycling endosome (GO:0055037)|WASH complex (GO:0071203)	alpha-tubulin binding (GO:0043014)			central_nervous_system(1)|endometrium(6)|kidney(11)|prostate(5)|stomach(1)|urinary_tract(1)	25						GGATGCAAACGTCTCGGGGTC	0.527																																																	0								ENSG00000248472																																			DDX11L9			0			-	HGNC			15q26.3	2014-03-20	2008-01-16	2008-01-16	ENSG00000185596	ENSG00000185596		"""WAS protein homologs"""	24362	pseudogene	pseudogene			"""family with sequence similarity 39, member D pseudogene"""	FAM39DP		11701968, 18159949	Standard	NR_003659		Approved	FLJ25222	uc002cdi.3	C4AMC7	OTTHUMG00000172275		15.37:g.102516816G>T		Somatic	0	9	0.00		0.6002030607454749	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	5	44.44		RNA	SNP	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000557932.1	37	NULL		15																																																																																			-	-		0.527	WASH3P-001	KNOWN	basic	processed_transcript	DDX11L9	pseudogene	OTTHUMT00000417608.1	G	NM_199163	-		102516816	-1	no_errors	ENST00000559159	ensembl	human	known	74_37	rna	SNP	0.000	T
CTTNBP2NL	55917	genome.wustl.edu	37	1	112958898	112958899	+	Intron	INS	-	-	A	rs370406156		TCGA-DX-A23T-01A-11D-A26G-09	TCGA-DX-A23T-10A-01D-A26G-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc6f717-fbc5-40d2-b105-da9a150b454f	b5482bab-e0c8-4a78-b485-a9d4bcfe9203	g.chr1:112958898_112958899insA	ENST00000271277.6	+	3	324					NM_018704.2	NP_061174.1	Q9P2B4	CT2NL_HUMAN	CTTNBP2 N-terminal like						negative regulation of transmembrane transport (GO:0034763)|negative regulation of transporter activity (GO:0032410)|protein dephosphorylation (GO:0006470)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	protein phosphatase 2A binding (GO:0051721)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	29		all_cancers(81;0.00064)|all_epithelial(167;0.000415)|all_lung(203;0.00045)|Lung NSC(69;0.000705)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TATGTTAAAAGAAAAAAAAAAA	0.322																																																	0								ENSG00000143079																																			CTTNBP2NL	SO:0001627	intron_variant	0				HGNC	AB037854	CCDS845.1	1p13.2	2008-02-05			ENSG00000143079	ENSG00000143079			25330	protein-coding gene	gene with protein product		615100				10718198	Standard	NM_018704		Approved	DKFZp547A023	uc001ebx.3	Q9P2B4	OTTHUMG00000011154	ENST00000271277.6:c.99+12->A	1.37:g.112958909_112958909dupA		Somatic	0	30	0.00		0.6002030607454749	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	31	8.82	B3KMS5|Q96B40	RNA	INS	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000271277.6	37	NULL	CCDS845.1	1																																																																																			-	-		0.322	CTTNBP2NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CTTNBP2NL	protein_coding	OTTHUMT00000030686.1	-	NM_018704			112958899	+1	no_errors	ENST00000502356	ensembl	human	known	74_37	rna	INS	0.000:0.000	A
SDK1	221935	genome.wustl.edu	37	7	4091396	4091396	+	Silent	SNP	C	C	T			TCGA-DX-A23T-01A-11D-A26G-09	TCGA-DX-A23T-10A-01D-A26G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc6f717-fbc5-40d2-b105-da9a150b454f	b5482bab-e0c8-4a78-b485-a9d4bcfe9203	g.chr7:4091396C>T	ENST00000404826.2	+	19	2984	c.2845C>T	c.(2845-2847)Ctg>Ttg	p.L949L	SDK1_ENST00000389531.3_Silent_p.L949L	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	949	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		CACTTCCGTTCTGTGCTTCAC	0.542																																																	0								ENSG00000146555						159.0	143.0	148.0					7																	4091396		2203	4300	6503	SDK1	SO:0001819	synonymous_variant	0			-	HGNC	AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	19307	protein-coding gene	gene with protein product		607216	"""sidekick homolog 1 (chicken)"", ""sidekick homolog 1, cell adhesion molecule (chicken)"""			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.2845C>T	7.37:g.4091396C>T		Somatic	0	32	0.00		0.6002030607454749	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	34	190	15.18	Q8TEN9|Q8TEP5|Q96N44	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_Fibronectin_type3,pfam_Ig_I-set,pfam_Immunoglobulin,pfam_Ig_V-set,superfamily_Fibronectin_type3,smart_Ig_sub,smart_Ig_sub2,smart_Fibronectin_type3,pfscan_Fibronectin_type3,pfscan_Ig-like_dom	p.L949	ENST00000404826.2	37	c.2845	CCDS34590.1	7																																																																																			-	pfam_Fibronectin_type3,superfamily_Fibronectin_type3,smart_Fibronectin_type3,pfscan_Fibronectin_type3		0.542	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SDK1	protein_coding	OTTHUMT00000323702.1	C	NM_152744	-		4091396	+1	no_errors	ENST00000404826	ensembl	human	known	74_37	silent	SNP	0.979	T
PLCZ1	89869	genome.wustl.edu	37	12	18854541	18854549	+	In_Frame_Del	DEL	TCCTCCTCC	TCCTCCTCC	-	rs71064021|rs11279217|rs531863439|rs76947474		TCGA-DX-A23T-01A-11D-A26G-09	TCGA-DX-A23T-10A-01D-A26G-09	TCCTCCTCC	TCCTCCTCC					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc6f717-fbc5-40d2-b105-da9a150b454f	b5482bab-e0c8-4a78-b485-a9d4bcfe9203	g.chr12:18854541_18854549delTCCTCCTCC	ENST00000538330.1	-	5	630_638	c.249_257delGGAGGAGGA	c.(247-258)gaggaggaggat>gat	p.EEE83del	PLCZ1_ENST00000266505.7_Intron|PLCZ1_ENST00000542762.1_Intron|PLCZ1_ENST00000435379.1_Intron|PLCZ1_ENST00000541695.1_Intron|PLCZ1_ENST00000447925.2_Intron|PLCZ1_ENST00000539875.1_Intron					phospholipase C, zeta 1											NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	31	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.0241)					TTTGAATTTAtcctcctcctcctcctcct	0.44																																																	0								ENSG00000139151																																			PLCZ1	SO:0001651	inframe_deletion	0				HGNC	AY035866	CCDS8680.1	12p13.31	2013-01-10			ENSG00000139151	ENSG00000139151	3.1.4.11	"""EF-hand domain containing"""	19218	protein-coding gene	gene with protein product		608075				12117804	Standard	NM_033123		Approved	NYD-SP27, PLCzeta	uc021qvx.2	Q86YW0	OTTHUMG00000168937	ENST00000538330.1:c.249_257delGGAGGAGGA	12.37:g.18854550_18854558delTCCTCCTCC	ENSP00000445880:p.Glu83_Glu85del	Somatic	NA	NA	NA		0.6002030607454749	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA		In_Frame_Del	DEL	NA	NA	NA	NA	NA	NA	pfam_PLipase_C_Pinositol-sp_Y,pfam_C2_dom,superfamily_PLC-like_Pdiesterase_TIM-brl,superfamily_C2_dom,smart_PLipase_C_Pinositol-sp_Y,smart_C2_dom,pfscan_C2_dom,pfscan_PLipase_C_PInositol-sp_X_dom,pfscan_PLipase_C_Pinositol-sp_Y,prints_Pinositol_PLipase_C	p.EEE83in_frame_del	ENST00000538330.1	37	c.257_249		12																																																																																			-	superfamily_PLC-like_Pdiesterase_TIM-brl		0.440	PLCZ1-002	PUTATIVE	basic|exp_conf	protein_coding	PLCZ1	protein_coding	OTTHUMT00000401666.3	TCCTCCTCC	NM_033123			18854549	-1	no_errors	ENST00000538330	ensembl	human	putative	74_37	in_frame_del	DEL	0.019:0.025:0.029:0.032:0.034:0.034:0.032:0.029:0.024	-
FEM1C	56929	genome.wustl.edu	37	5	114860080	114860080	+	Silent	SNP	G	G	A			TCGA-DX-A23T-01A-11D-A26G-09	TCGA-DX-A23T-10A-01D-A26G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc6f717-fbc5-40d2-b105-da9a150b454f	b5482bab-e0c8-4a78-b485-a9d4bcfe9203	g.chr5:114860080G>A	ENST00000274457.3	-	3	2340	c.1779C>T	c.(1777-1779)gtC>gtT	p.V593V		NM_020177.2	NP_064562.1	Q96JP0	FEM1C_HUMAN	fem-1 homolog c (C. elegans)	593					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				breast(5)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|liver(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	18		all_cancers(142;0.000575)|all_epithelial(76;9.98e-06)|Prostate(80;0.00955)|Ovarian(225;0.0443)|all_lung(232;0.132)|Breast(839;0.195)		OV - Ovarian serous cystadenocarcinoma(64;2.5e-07)|Epithelial(69;2.66e-07)|all cancers(49;1.39e-05)		GATTCACTATGACACGAGCAG	0.358																																																	0								ENSG00000145780						83.0	87.0	85.0					5																	114860080		2202	4300	6502	FEM1C	SO:0001819	synonymous_variant	0			-	HGNC		CCDS4118.1	5q22	2013-01-10	2006-11-08		ENSG00000145780	ENSG00000145780		"""Ankyrin repeat domain containing"""	16933	protein-coding gene	gene with protein product		608767				14527725, 11733146	Standard	NM_020177		Approved	KIAA1785, EUROIMAGE686608, EUROIMAGE783647, FEM1A	uc003krb.1	Q96JP0	OTTHUMG00000128895	ENST00000274457.3:c.1779C>T	5.37:g.114860080G>A		Somatic	0	45	0.00		0.6002030607454749	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	15	79	15.79	B2RE47|Q8N3V8|Q9H704|Q9NPL6|Q9NPL9	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_Ankyrin_rpt,superfamily_Ankyrin_rpt-contain_dom,smart_Ankyrin_rpt,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom,prints_Ankyrin_rpt	p.V593	ENST00000274457.3	37	c.1779	CCDS4118.1	5																																																																																			-	NULL		0.358	FEM1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FEM1C	protein_coding	OTTHUMT00000250857.3	G	NM_020177	-		114860080	-1	no_errors	ENST00000274457	ensembl	human	known	74_37	silent	SNP	1.000	A
CPQ	10404	genome.wustl.edu	37	8	97797117	97797118	+	5'UTR	INS	-	-	A	rs201719687	byFrequency	TCGA-DX-A23T-01A-11D-A26G-09	TCGA-DX-A23T-10A-01D-A26G-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc6f717-fbc5-40d2-b105-da9a150b454f	b5482bab-e0c8-4a78-b485-a9d4bcfe9203	g.chr8:97797117_97797118insA	ENST00000220763.5	+	0	202_203					NM_016134.2	NP_057218.1	Q9Y646	CBPQ_HUMAN	carboxypeptidase Q						peptide catabolic process (GO:0043171)|proteolysis (GO:0006508)|thyroid hormone generation (GO:0006590)|tissue regeneration (GO:0042246)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)	carboxypeptidase activity (GO:0004180)|metal ion binding (GO:0046872)|metallodipeptidase activity (GO:0070573)|protein homodimerization activity (GO:0042803)										AAACCAACTGGAAAAAAAAATG	0.371													AAAAAAAA|AAAAAAAAA|AAAAAAAAAA|cryptic_indel	12	0.00239617	0.0083	0.0	5008	,	,		19115	0.0		0.001	False		,,,				2504	0.0																0								ENSG00000104324																																			CPQ	SO:0001623	5_prime_UTR_variant	0				HGNC	AF107834	CCDS6273.1	8q22.2	2012-02-17			ENSG00000104324	ENSG00000104324			16910	protein-coding gene	gene with protein product	"""lysosomal dipeptidase"", ""Ser-Met dipeptidase"", ""plasma glutamate carboxypeptidase"""					10206990	Standard	NM_016134		Approved	LDP, PGCP	uc003yhw.3	Q9Y646	OTTHUMG00000164690	ENST00000220763.5:c.-8->A	8.37:g.97797126_97797126dupA		Somatic	0	27	0.00		0.6002030607454749	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	2	13	13.33	B2RD88|Q8NBZ1|Q9UNM8|Q9Y5X6	RNA	INS	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000220763.5	37	NULL	CCDS6273.1	8																																																																																			-	-		0.371	CPQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CPQ	protein_coding	OTTHUMT00000379757.2	-	NM_016134			97797118	+1	no_errors	ENST00000525310	ensembl	human	known	74_37	rna	INS	0.002:0.002	A
ADAM32	203102	genome.wustl.edu	37	8	39080584	39080584	+	Missense_Mutation	SNP	G	G	C			TCGA-DX-A23T-01A-11D-A26G-09	TCGA-DX-A23T-10A-01D-A26G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc6f717-fbc5-40d2-b105-da9a150b454f	b5482bab-e0c8-4a78-b485-a9d4bcfe9203	g.chr8:39080584G>C	ENST00000379907.4	+	14	1479	c.1352G>C	c.(1351-1353)aGg>aCg	p.R451T	ADAM32_ENST00000437682.2_Missense_Mutation_p.R352T|ADAM32_ENST00000519315.1_Missense_Mutation_p.R345T	NM_145004.5	NP_659441	Q8TC27	ADA32_HUMAN	ADAM metallopeptidase domain 32	451	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.					integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)	31		all_cancers(7;3e-05)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00771)|Breast(189;0.0503)	LUSC - Lung squamous cell carcinoma(45;6.2e-07)|Colorectal(1;0.00699)|READ - Rectum adenocarcinoma(1;0.146)			GTTGAATGTAGGCCGAAAGCA	0.333																																																	0								ENSG00000197140						56.0	52.0	53.0					8																	39080584		1873	4100	5973	ADAM32	SO:0001583	missense	0			-	HGNC	BC026085	CCDS47846.1	8p11.22	2005-08-18	2005-08-18		ENSG00000197140	ENSG00000197140		"""ADAM metallopeptidase domain containing"""	15479	protein-coding gene	gene with protein product			"""a disintegrin and metalloproteinase domain 32"""			12568724	Standard	NM_145004		Approved		uc003xmt.4	Q8TC27	OTTHUMG00000164071	ENST00000379907.4:c.1352G>C	8.37:g.39080584G>C	ENSP00000369238:p.Arg451Thr	Somatic	0	28	0.00		0.6002030607454749	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	23	11.54	Q8TC42	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Peptidase_M12B,pfam_Peptidase_M12B_N,pfam_ADAM_Cys-rich,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_EG-like_dom,pfscan_Peptidase_M12B	p.R451T	ENST00000379907.4	37	c.1352	CCDS47846.1	8	.	.	.	.	.	.	.	.	.	.	G	15.86	2.959251	0.53400	.	.	ENSG00000197140	ENST00000437682;ENST00000519315;ENST00000379907	T;T;T	0.18960	2.18;2.18;2.18	5.55	5.55	0.83447	Disintegrin, conserved site (1);Blood coagulation inhibitor, Disintegrin (5);	0.000000	0.37053	N	0.002264	T	0.58566	0.2131	H	0.94423	3.535	0.36007	D	0.837763	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.999;1.0	T	0.75218	-0.3395	10	0.87932	D	0	.	15.3512	0.74389	0.0:0.0:1.0:0.0	.	352;345;451	E7EPX8;E7ER82;Q8TC27	.;.;ADA32_HUMAN	T	352;345;451	ENSP00000405978:R352T;ENSP00000429422:R345T;ENSP00000369238:R451T	ENSP00000369238:R451T	R	+	2	0	ADAM32	39199741	0.998000	0.40836	0.853000	0.33588	0.179000	0.23085	4.644000	0.61397	2.763000	0.94921	0.655000	0.94253	AGG	-	pfam_Blood-coag_inhib_Disintegrin,superfamily_Blood-coag_inhib_Disintegrin,smart_Blood-coag_inhib_Disintegrin,pfscan_Blood-coag_inhib_Disintegrin		0.333	ADAM32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ADAM32	protein_coding	OTTHUMT00000377089.1	G	NM_145004	-		39080584	+1	no_errors	ENST00000379907	ensembl	human	known	74_37	missense	SNP	0.978	C
SYNJ1	8867	genome.wustl.edu	37	21	34029016	34029016	+	Missense_Mutation	SNP	C	C	T			TCGA-DX-A23T-01A-11D-A26G-09	TCGA-DX-A23T-10A-01D-A26G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc6f717-fbc5-40d2-b105-da9a150b454f	b5482bab-e0c8-4a78-b485-a9d4bcfe9203	g.chr21:34029016C>T	ENST00000322229.7	-	20	2775	c.2776G>A	c.(2776-2778)Ggt>Agt	p.G926S	SYNJ1_ENST00000357345.3_Missense_Mutation_p.G926S|SYNJ1_ENST00000382491.3_Missense_Mutation_p.G921S|SYNJ1_ENST00000464778.1_5'UTR|SYNJ1_ENST00000382499.2_Missense_Mutation_p.G965S|SYNJ1_ENST00000433931.2_Missense_Mutation_p.G965S			O43426	SYNJ1_HUMAN	synaptojanin 1	926	Pro-rich.|RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cell death (GO:0008219)|inositol phosphate metabolic process (GO:0043647)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of synaptic vesicle uncoating (GO:1903390)|regulation of synaptic vesicle membrane organization (GO:1901632)|small molecule metabolic process (GO:0044281)|synaptic vesicle endocytosis (GO:0048488)	cytosol (GO:0005829)	inositol-polyphosphate 5-phosphatase activity (GO:0004445)|nucleotide binding (GO:0000166)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|lung(11)|ovary(4)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	57						ATAACTTCACCAAAACTTGCA	0.318																																																	0								ENSG00000159082						32.0	33.0	32.0					21																	34029016		2202	4300	6502	SYNJ1	SO:0001583	missense	0			-	HGNC	AF009040	CCDS33539.1, CCDS33540.1, CCDS33539.2, CCDS33540.2, CCDS54483.1	21q22.2	2008-06-23			ENSG00000159082	ENSG00000159082			11503	protein-coding gene	gene with protein product		604297				9428629, 10773674	Standard	NM_203446		Approved	INPP5G	uc002yqh.2	O43426	OTTHUMG00000064926	ENST00000322229.7:c.2776G>A	21.37:g.34029016C>T	ENSP00000322234:p.Gly926Ser	Somatic	0	23	0.00		0.6002030607454749	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	13	18.75	O43425|O94984|Q4KMR1	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Syja_N,pfam_Endo/exonuclease/phosphatase,pfam_DUF1866,superfamily_Endo/exonuclease/phosphatase,smart_IPPc,pfscan_RRM_dom,pfscan_Syja_N	p.G965S	ENST00000322229.7	37	c.2893	CCDS54484.1	21	.	.	.	.	.	.	.	.	.	.	C	32	5.186751	0.94923	.	.	ENSG00000159082	ENST00000382491;ENST00000357345;ENST00000382499;ENST00000433931;ENST00000322229	D;D;D;D;D	0.97752	-3.46;-4.09;-4.52;-3.66;-3.57	5.35	5.35	0.76521	Domain of unknown function DUF1866 (1);Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (1);	0.000000	0.85682	D	0.000000	D	0.98735	0.9575	M	0.80422	2.495	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;0.999	D	0.99849	1.1069	10	0.87932	D	0	.	19.0499	0.93039	0.0:1.0:0.0:0.0	.	921;965;926;926;926	B9EGN3;C9JFZ1;O43426-2;O43426;O43426-4	.;.;.;SYNJ1_HUMAN;.	S	921;926;965;965;926	ENSP00000371931:G921S;ENSP00000349903:G926S;ENSP00000371939:G965S;ENSP00000409667:G965S;ENSP00000322234:G926S	ENSP00000322234:G926S	G	-	1	0	SYNJ1	32950887	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.625000	0.83145	2.506000	0.84524	0.491000	0.48974	GGT	-	pfam_DUF1866,pfscan_RRM_dom		0.318	SYNJ1-201	KNOWN	basic|CCDS	protein_coding	SYNJ1	protein_coding		C		-		34029016	-1	no_errors	ENST00000433931	ensembl	human	known	74_37	missense	SNP	1.000	T
GRN	2896	genome.wustl.edu	37	17	42427059	42427059	+	Missense_Mutation	SNP	C	C	T			TCGA-DX-A23T-01A-11D-A26G-09	TCGA-DX-A23T-10A-01D-A26G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc6f717-fbc5-40d2-b105-da9a150b454f	b5482bab-e0c8-4a78-b485-a9d4bcfe9203	g.chr17:42427059C>T	ENST00000053867.3	+	4	351	c.289C>T	c.(289-291)Cac>Tac	p.H97Y	GRN_ENST00000589265.1_Missense_Mutation_p.H97Y	NM_002087.2	NP_002078.1	P28799	GRN_HUMAN	granulin	97					blastocyst hatching (GO:0001835)|cell death (GO:0008219)|embryo implantation (GO:0007566)|positive regulation of epithelial cell proliferation (GO:0050679)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)	growth factor activity (GO:0008083)|poly(A) RNA binding (GO:0044822)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.189)		GGATGGCCATCACTGCTGCCC	0.602																																																	0								ENSG00000030582						45.0	46.0	46.0					17																	42427059		2203	4300	6503	GRN	SO:0001583	missense	0			-	HGNC	M75161	CCDS11483.1	17q21.32	2014-09-17				ENSG00000030582			4601	protein-coding gene	gene with protein product	"""progranulin"""	138945				1417868, 9826678	Standard	XM_005257253		Approved	PCDGF, PGRN, CLN11	uc002igp.1	P28799		ENST00000053867.3:c.289C>T	17.37:g.42427059C>T	ENSP00000053867:p.His97Tyr	Somatic	0	30	0.00		0.6002030607454749	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	33	10.81	D3DX55|P23781|P23782|P23783|P23784|Q53HQ8|Q53Y88|Q540U8|Q9BWE7|Q9H8S1|Q9UCH0	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Granulin,smart_Granulin	p.H97Y	ENST00000053867.3	37	c.289	CCDS11483.1	17	.	.	.	.	.	.	.	.	.	.	c	15.24	2.776109	0.49786	.	.	ENSG00000030582	ENST00000053867;ENST00000357351	T	0.76316	-1.01	4.04	4.04	0.47022	Granulin (3);	0.000000	0.56097	D	0.000034	T	0.76919	0.4055	M	0.74389	2.26	0.47374	D	0.9994	B	0.14805	0.011	B	0.23716	0.048	T	0.74627	-0.3602	10	0.33940	T	0.23	-24.2919	13.7647	0.62988	0.0:1.0:0.0:0.0	.	97	P28799	GRN_HUMAN	Y	97	ENSP00000053867:H97Y	ENSP00000053867:H97Y	H	+	1	0	GRN	39782585	0.998000	0.40836	0.926000	0.36857	0.652000	0.38707	4.134000	0.57990	2.087000	0.62958	0.394000	0.25966	CAC	-	pfam_Granulin,smart_Granulin		0.602	GRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GRN	protein_coding	OTTHUMT00000457766.1	C	NM_002087	-		42427059	+1	no_errors	ENST00000053867	ensembl	human	known	74_37	missense	SNP	0.996	T
MSH3	4437	genome.wustl.edu	37	5	79950709	79950717	+	In_Frame_Del	DEL	GCAGCGGCC	GCAGCGGCC	-	rs144776112|rs201874762|rs2431220|rs201906899	byFrequency	TCGA-DX-A23T-01A-11D-A26G-09	TCGA-DX-A23T-10A-01D-A26G-09	GCAGCGGCC	GCAGCGGCC					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc6f717-fbc5-40d2-b105-da9a150b454f	b5482bab-e0c8-4a78-b485-a9d4bcfe9203	g.chr5:79950709_79950717delGCAGCGGCC	ENST00000265081.6	+	1	243_251	c.163_171delGCAGCGGCC	c.(163-171)gcagcggccdel	p.AAA58del	DHFR_ENST00000513048.1_5'Flank|DHFR_ENST00000511032.1_5'Flank|DHFR_ENST00000439211.2_5'UTR|DHFR_ENST00000505337.1_5'Flank|DHFR_ENST00000504396.1_5'Flank	NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	58	Poly-Ala.		Missing. {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8942985}.		ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|maintenance of DNA repeat elements (GO:0043570)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|heteroduplex DNA loop binding (GO:0000404)|Y-form DNA binding (GO:0000403)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		Tgcagcggctgcagcggccgcagcggccg	0.694								Mismatch excision repair (MMR)																													Melanoma(88;1010 1399 13793 26548 36275)												0								ENSG00000113318		,	841,2699		233,375,1162					,		0.1		dbSNP_100	9	1241,5749		368,505,2622	no	coding,utr-5	DHFR,MSH3	NM_002439.3,NM_000791.3	,	601,880,3784	A1A1,A1R,RR		17.7539,23.7571,19.7721	,	,		2082,8448				MSH3	SO:0001651	inframe_deletion	0				HGNC	U61981	CCDS34195.1	5q11-q12	2013-09-12	2013-09-12		ENSG00000113318	ENSG00000113318			7326	protein-coding gene	gene with protein product	"""Divergent upstream protein"", ""Mismatch repair protein 1"""	600887	"""mutS (E. coli) homolog 3"", ""mutS homolog 3 (E. coli)"""				Standard	NM_002439		Approved	DUP, MRP1	uc003kgz.4	P20585	OTTHUMG00000162540	ENST00000265081.6:c.163_171delGCAGCGGCC	5.37:g.79950718_79950726delGCAGCGGCC	ENSP00000265081:p.Ala58_Ala60del	Somatic	NA	NA	NA		0.6002030607454749	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	In_Frame_Del	DEL	NA	NA	NA	NA	NA	NA	pfam_DNA_mismatch_repair_MutS_C,pfam_DNA_mismatch_repair_MutS_core,pfam_DNA_mmatch_repair_MutS_con_dom,pfam_DNA_mismatch_repair_MutS-lik_N,pfam_DNA_mismatch_repair_MutS_clamp,superfamily_DNA_mismatch_repair_MutS_core,superfamily_P-loop_NTPase,superfamily_DNA_mismatch_repair_MutS_N,superfamily_DNA_mmatch_repair_MutS_con_dom,smart_DNA_mismatch_repair_MutS_core,smart_DNA_mismatch_repair_MutS_C	p.AAA58in_frame_del	ENST00000265081.6	37	c.163_171	CCDS34195.1	5																																																																																			-	NULL		0.694	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	MSH3	protein_coding	OTTHUMT00000369471.1	GCAGCGGCC	NM_002439			79950717	+1	no_errors	ENST00000265081	ensembl	human	known	74_37	in_frame_del	DEL	0.338:0.304:0.271:0.238:0.205:0.172:0.140:0.107:0.075	-
FEM1C	56929	genome.wustl.edu	37	5	114860112	114860112	+	Missense_Mutation	SNP	G	G	A			TCGA-DX-A23T-01A-11D-A26G-09	TCGA-DX-A23T-10A-01D-A26G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc6f717-fbc5-40d2-b105-da9a150b454f	b5482bab-e0c8-4a78-b485-a9d4bcfe9203	g.chr5:114860112G>A	ENST00000274457.3	-	3	2308	c.1747C>T	c.(1747-1749)Cat>Tat	p.H583Y		NM_020177.2	NP_064562.1	Q96JP0	FEM1C_HUMAN	fem-1 homolog c (C. elegans)	583					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				breast(5)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|liver(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	18		all_cancers(142;0.000575)|all_epithelial(76;9.98e-06)|Prostate(80;0.00955)|Ovarian(225;0.0443)|all_lung(232;0.132)|Breast(839;0.195)		OV - Ovarian serous cystadenocarcinoma(64;2.5e-07)|Epithelial(69;2.66e-07)|all cancers(49;1.39e-05)		AATGTGGTATGATTTATAGGC	0.378																																																	0								ENSG00000145780						104.0	105.0	104.0					5																	114860112		2202	4300	6502	FEM1C	SO:0001583	missense	0			-	HGNC		CCDS4118.1	5q22	2013-01-10	2006-11-08		ENSG00000145780	ENSG00000145780		"""Ankyrin repeat domain containing"""	16933	protein-coding gene	gene with protein product		608767				14527725, 11733146	Standard	NM_020177		Approved	KIAA1785, EUROIMAGE686608, EUROIMAGE783647, FEM1A	uc003krb.1	Q96JP0	OTTHUMG00000128895	ENST00000274457.3:c.1747C>T	5.37:g.114860112G>A	ENSP00000274457:p.His583Tyr	Somatic	0	39	0.00		0.6002030607454749	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	18	75	19.35	B2RE47|Q8N3V8|Q9H704|Q9NPL6|Q9NPL9	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Ankyrin_rpt,superfamily_Ankyrin_rpt-contain_dom,smart_Ankyrin_rpt,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom,prints_Ankyrin_rpt	p.H583Y	ENST00000274457.3	37	c.1747	CCDS4118.1	5	.	.	.	.	.	.	.	.	.	.	G	0	-2.612869	0.00120	.	.	ENSG00000145780	ENST00000274457	T	0.65178	-0.14	4.84	3.98	0.46160	.	0.000000	0.85682	D	0.000000	T	0.35364	0.0929	N	0.05280	-0.08	0.50467	D	0.999875	B	0.06786	0.001	B	0.08055	0.003	T	0.29243	-1.0018	10	0.02654	T	1	-12.9878	13.0454	0.58922	0.0784:0.0:0.9216:0.0	.	583	Q96JP0	FEM1C_HUMAN	Y	583	ENSP00000274457:H583Y	ENSP00000274457:H583Y	H	-	1	0	FEM1C	114888011	1.000000	0.71417	0.885000	0.34714	0.007000	0.05969	7.931000	0.87625	1.035000	0.39972	-0.379000	0.06801	CAT	-	NULL		0.378	FEM1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FEM1C	protein_coding	OTTHUMT00000250857.3	G	NM_020177	-		114860112	-1	no_errors	ENST00000274457	ensembl	human	known	74_37	missense	SNP	1.000	A
FAM153C	653316	genome.wustl.edu	37	5	177457620	177457620	+	Intron	SNP	C	C	T	rs200476067		TCGA-DX-A23T-01A-11D-A26G-09	TCGA-DX-A23T-10A-01D-A26G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc6f717-fbc5-40d2-b105-da9a150b454f	b5482bab-e0c8-4a78-b485-a9d4bcfe9203	g.chr5:177457620C>T	ENST00000507848.1	+	3	145				FAM153C_ENST00000398106.2_Intron|FAM153C_ENST00000511189.1_Silent_p.L9L			Q494X1	F153C_HUMAN	family with sequence similarity 153, member C											kidney(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	4	all_cancers(89;0.00176)|Renal(175;0.000269)|Lung NSC(126;0.00858)|all_lung(126;0.0139)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GTTGTTGCCTCGAAGGTATGT	0.393																																																	0								ENSG00000204677																																			FAM153C	SO:0001627	intron_variant	0			-	HGNC	BC101338		5q35.3	2008-01-09				ENSG00000204677			33936	protein-coding gene	gene with protein product							Standard	NR_038353		Approved	NY-REN-7-like	uc011dge.2	Q494X1		ENST00000507848.1:c.-56-4477C>T	5.37:g.177457620C>T		Somatic	0	40	0.00		0.6002030607454749	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	6	41	12.77	A4IF33|B2RUV5|B7ZW12	Silent	SNP	NA	NA	NA	NA	NA	NA	prints_FAM153	p.L9	ENST00000507848.1	37	c.27		5																																																																																			-	NULL		0.393	FAM153C-002	KNOWN	basic|appris_candidate	protein_coding	FAM153C	protein_coding	OTTHUMT00000373556.1	C	NM_001079527	rs200476067		177457620	+1	no_errors	ENST00000511189	ensembl	human	novel	74_37	silent	SNP	0.000	T
FKBP7	51661	genome.wustl.edu	37	2	179330469	179330469	+	3'UTR	DEL	A	A	-	rs75348694|rs11336824	byFrequency	TCGA-DX-A23T-01A-11D-A26G-09	TCGA-DX-A23T-10A-01D-A26G-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc6f717-fbc5-40d2-b105-da9a150b454f	b5482bab-e0c8-4a78-b485-a9d4bcfe9203	g.chr2:179330469delA	ENST00000424785.2	-	0	755				FKBP7_ENST00000464248.1_5'UTR	NM_001135212.1|NM_181342.2	NP_001128684.1|NP_851939.1	Q9Y680	FKBP7_HUMAN	FK506 binding protein 7						chaperone-mediated protein folding (GO:0061077)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum membrane (GO:0005789)	calcium ion binding (GO:0005509)|FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	8			OV - Ovarian serous cystadenocarcinoma(117;0.00406)|Epithelial(96;0.0159)|all cancers(119;0.0564)			GTAAATAGCTAAAAAAAAAAA	0.318														2149	0.429113	0.5144	0.2622	5008	,	,		19034	0.6637		0.2435	False		,,,				2504	0.3814				Melanoma(26;682 927 5286 17599 46613)												0								ENSG00000079150		,	22,0,2021,2223		0,0,5,17,0,0,0,442,1132,537	23.0	31.0	29.0		,	-0.9	0.0	2	dbSNP_130	38	39,11,1862,6340		0,0,4,35,0,1,10,124,1609,2343	no	utr-3,utr-3	FKBP7	NM_181342.2,NM_001135212.1	,	0,0,9,52,0,1,10,566,2741,2880	A1A1,A1A2,A1A3,A1R,A2A2,A2A3,A2R,A3A3,A3R,RR		23.1701,47.8903,31.5945	,	,	179330469	61,11,3883,8563	2187	4293	6480	FKBP7	SO:0001624	3_prime_UTR_variant	0				HGNC	AF092137	CCDS2280.1, CCDS46462.1	2q31.2	2013-01-10	2001-11-28		ENSG00000079150	ENSG00000079150		"""EF-hand domain containing"""	3723	protein-coding gene	gene with protein product		607062	"""FK506-binding protein 7"""			9806833	Standard	NM_181342		Approved	FKBP23	uc002umk.3	Q9Y680	OTTHUMG00000132577	ENST00000424785.2:c.*28T>-	2.37:g.179330469delA		Somatic	0	22	0.00		0.6002030607454749	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	5	25	16.67	Q4ZG70|Q6V3B2|Q86U65|Q96DA4|Q9Y6B0	RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000424785.2	37	NULL	CCDS2280.1	2																																																																																			-	-		0.318	FKBP7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	FKBP7	protein_coding	OTTHUMT00000255783.1	A	NM_181342			179330469	-1	no_errors	ENST00000464248	ensembl	human	known	74_37	rna	DEL	0.000	-
CP	1356	genome.wustl.edu	37	3	148919931	148919931	+	Missense_Mutation	SNP	G	G	C			TCGA-DX-A23T-01A-11D-A26G-09	TCGA-DX-A23T-10A-01D-A26G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc6f717-fbc5-40d2-b105-da9a150b454f	b5482bab-e0c8-4a78-b485-a9d4bcfe9203	g.chr3:148919931G>C	ENST00000264613.6	-	7	1568	c.1306C>G	c.(1306-1308)Cga>Gga	p.R436G		NM_000096.3	NP_000087	P00450	CERU_HUMAN	ceruloplasmin (ferroxidase)	436	F5/8 type A 2.|Plastocyanin-like 3.				cellular iron ion homeostasis (GO:0006879)|copper ion transport (GO:0006825)|transmembrane transport (GO:0055085)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)	chaperone binding (GO:0051087)|copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)			breast(6)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152)	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		Drotrecogin alfa(DB00055)	CTCTCCTTTCGATTTGTGAAG	0.453																																																	0								ENSG00000047457						129.0	128.0	128.0					3																	148919931		2203	4300	6503	CP	SO:0001583	missense	0			-	HGNC	M13536	CCDS3141.1	3q23-q25	2010-07-01			ENSG00000047457	ENSG00000047457	1.16.3.1		2295	protein-coding gene	gene with protein product		117700					Standard	NM_000096		Approved		uc003ewy.4	P00450	OTTHUMG00000159563	ENST00000264613.6:c.1306C>G	3.37:g.148919931G>C	ENSP00000264613:p.Arg436Gly	Somatic	0	43	0.00		0.6002030607454749	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	8	45	15.09	Q14063|Q2PP18|Q9UKS4	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Cu-oxidase_2,pfam_Cu-oxidase_3,pfam_Cu-oxidase,superfamily_Cupredoxin	p.R436G	ENST00000264613.6	37	c.1306	CCDS3141.1	3	.	.	.	.	.	.	.	.	.	.	G	10.21	1.288601	0.23478	.	.	ENSG00000047457	ENST00000264613;ENST00000494544	D;D	0.98862	-5.19;-5.19	5.67	2.75	0.32379	Cupredoxin (2);	0.679047	0.15015	N	0.285360	D	0.97225	0.9093	M	0.67569	2.06	0.09310	N	1	P;P;P;P	0.39391	0.671;0.671;0.671;0.671	B;B;B;B	0.35770	0.139;0.21;0.139;0.139	D	0.91453	0.5183	10	0.49607	T	0.09	-0.0566	13.8297	0.63373	0.0:0.0:0.4672:0.5328	.	436;436;436;436	A5PL27;A8K5A4;P00450;Q1L857	.;.;CERU_HUMAN;.	G	436;219	ENSP00000264613:R436G;ENSP00000420545:R219G	ENSP00000264613:R436G	R	-	1	2	CP	150402621	0.000000	0.05858	0.000000	0.03702	0.334000	0.28698	0.546000	0.23284	0.344000	0.23847	0.650000	0.86243	CGA	-	superfamily_Cupredoxin		0.453	CP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CP	protein_coding	OTTHUMT00000317498.1	G	NM_000096	-		148919931	-1	no_errors	ENST00000264613	ensembl	human	known	74_37	missense	SNP	0.000	C
TBC1D3	729873	genome.wustl.edu	37	17	36339584	36339584	+	Missense_Mutation	SNP	G	G	T	rs370901010		TCGA-DX-A23T-01A-11D-A26G-09	TCGA-DX-A23T-10A-01D-A26G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc6f717-fbc5-40d2-b105-da9a150b454f	b5482bab-e0c8-4a78-b485-a9d4bcfe9203	g.chr17:36339584G>T	ENST00000354664.4	-	13	1229	c.1073C>A	c.(1072-1074)cCa>cAa	p.P358Q	TBC1D3_ENST00000339023.4_3'UTR|TBC1D3_ENST00000519532.1_Missense_Mutation_p.P336Q|TBC1D3_ENST00000537432.1_Missense_Mutation_p.P358Q	NM_001123391.2	NP_001116863.2	Q8IZP1	TBC3A_HUMAN	TBC1 domain family, member 3	358				P -> Q (in Ref. 3; BAF82061). {ECO:0000305}.		plasma membrane (GO:0005886)	Rab GTPase activator activity (GO:0005097)			breast(1)|large_intestine(1)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	5	Breast(7;2.97e-12)	Breast(25;0.102)|Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		ACCTGGGGGTGGCAGGTCCCC	0.597																																																	0								ENSG00000197681						5.0	6.0	6.0					17																	36339584		790	1683	2473	TBC1D3	SO:0001583	missense	0			-	HGNC		CCDS45658.1	17q12	2014-09-16			ENSG00000274611	ENSG00000274419			19031	protein-coding gene	gene with protein product	"""prostate cancer gene 17"""	607741				12604796, 12359748, 16863688	Standard	NM_001123391		Approved	TBC1D3A, DKFZp434P2235, PRC17	uc002hoo.2	Q8IZP1	OTTHUMG00000188487	ENST00000354664.4:c.1073C>A	17.37:g.36339584G>T	ENSP00000346691:p.Pro358Gln	Somatic	0	25	0.00		0.6002030607454749	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	7	15	31.82	A6NGX2|A8K007|Q6DCB4|Q9H0B9|Q9UDD4	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Rab-GTPase-TBC_dom,superfamily_Rab-GTPase-TBC_dom,smart_Rab-GTPase-TBC_dom,pfscan_Rab-GTPase-TBC_dom	p.P358Q	ENST00000354664.4	37	c.1073	CCDS45658.1	17	.	.	.	.	.	.	.	.	.	.	-	11.91	1.779522	0.31502	.	.	ENSG00000197681	ENST00000518551;ENST00000354664;ENST00000431880;ENST00000519532;ENST00000537432	T;T;T;T	0.33438	2.47;2.39;1.41;2.39	0.109	0.109	0.14578	.	0.000000	0.85682	U	0.000000	T	0.40272	0.1110	L	0.59436	1.845	0.80722	D	1	D;D	0.58620	0.983;0.973	P;P	0.56823	0.747;0.807	T	0.27606	-1.0069	9	0.59425	D	0.04	.	.	.	.	.	358;336	Q8IZP1;F6U074	TBC3A_HUMAN;.	Q	402;358;108;336;358	ENSP00000428847:P402Q;ENSP00000346691:P358Q;ENSP00000429926:P336Q;ENSP00000439621:P358Q	ENSP00000346691:P358Q	P	-	2	0	TBC1D3	33593390	0.982000	0.34865	0.156000	0.22583	0.161000	0.22273	0.823000	0.27366	0.181000	0.19994	0.184000	0.17185	CCA	-	NULL		0.597	TBC1D3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	TBC1D3	protein_coding	OTTHUMT00000378681.1	G	NM_001123391	-		36339584	-1	no_errors	ENST00000354664	ensembl	human	known	74_37	missense	SNP	1.000	T
FEM1C	56929	genome.wustl.edu	37	5	114860070	114860070	+	Missense_Mutation	SNP	G	G	A			TCGA-DX-A23T-01A-11D-A26G-09	TCGA-DX-A23T-10A-01D-A26G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc6f717-fbc5-40d2-b105-da9a150b454f	b5482bab-e0c8-4a78-b485-a9d4bcfe9203	g.chr5:114860070G>A	ENST00000274457.3	-	3	2350	c.1789C>T	c.(1789-1791)Cat>Tat	p.H597Y		NM_020177.2	NP_064562.1	Q96JP0	FEM1C_HUMAN	fem-1 homolog c (C. elegans)	597					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				breast(5)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|liver(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	18		all_cancers(142;0.000575)|all_epithelial(76;9.98e-06)|Prostate(80;0.00955)|Ovarian(225;0.0443)|all_lung(232;0.132)|Breast(839;0.195)		OV - Ovarian serous cystadenocarcinoma(64;2.5e-07)|Epithelial(69;2.66e-07)|all cancers(49;1.39e-05)		TATATTCTATGATTCACTATG	0.363																																																	0								ENSG00000145780						70.0	75.0	74.0					5																	114860070		2202	4300	6502	FEM1C	SO:0001583	missense	0			-	HGNC		CCDS4118.1	5q22	2013-01-10	2006-11-08		ENSG00000145780	ENSG00000145780		"""Ankyrin repeat domain containing"""	16933	protein-coding gene	gene with protein product		608767				14527725, 11733146	Standard	NM_020177		Approved	KIAA1785, EUROIMAGE686608, EUROIMAGE783647, FEM1A	uc003krb.1	Q96JP0	OTTHUMG00000128895	ENST00000274457.3:c.1789C>T	5.37:g.114860070G>A	ENSP00000274457:p.His597Tyr	Somatic	0	42	0.00		0.6002030607454749	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	16	80	16.49	B2RE47|Q8N3V8|Q9H704|Q9NPL6|Q9NPL9	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Ankyrin_rpt,superfamily_Ankyrin_rpt-contain_dom,smart_Ankyrin_rpt,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom,prints_Ankyrin_rpt	p.H597Y	ENST00000274457.3	37	c.1789	CCDS4118.1	5	.	.	.	.	.	.	.	.	.	.	G	0.606	-0.827180	0.02734	.	.	ENSG00000145780	ENST00000274457	T	0.66815	-0.23	4.84	3.96	0.45880	.	0.052438	0.85682	D	0.000000	T	0.57725	0.2073	L	0.46670	1.46	0.50039	D	0.999844	B	0.11235	0.004	B	0.06405	0.002	T	0.51741	-0.8667	10	0.16896	T	0.51	-19.6047	14.3748	0.66867	0.0:0.0:0.8507:0.1493	.	597	Q96JP0	FEM1C_HUMAN	Y	597	ENSP00000274457:H597Y	ENSP00000274457:H597Y	H	-	1	0	FEM1C	114887969	1.000000	0.71417	1.000000	0.80357	0.001000	0.01503	6.645000	0.74343	1.009000	0.39289	-0.521000	0.04368	CAT	-	NULL		0.363	FEM1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FEM1C	protein_coding	OTTHUMT00000250857.3	G	NM_020177	-		114860070	-1	no_errors	ENST00000274457	ensembl	human	known	74_37	missense	SNP	1.000	A
CSPG4P5	114817	genome.wustl.edu	37	15	84959328	84959328	+	RNA	SNP	G	G	A			TCGA-DX-A23T-01A-11D-A26G-09	TCGA-DX-A23T-10A-01D-A26G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc6f717-fbc5-40d2-b105-da9a150b454f	b5482bab-e0c8-4a78-b485-a9d4bcfe9203	g.chr15:84959328G>A	ENST00000558801.1	-	0	5401									DNM1 pseudogene 51																		GGTGATCCACGGGGAGGCCAG	0.647																																																	0								ENSG00000235370																																			DNM1P51			0			-	HGNC			15q25.2	2013-05-16			ENSG00000259297	ENSG00000235370			48500	pseudogene	pseudogene							Standard			Approved				OTTHUMG00000172438		15.37:g.84959328G>A		Somatic	0	54	0.00		0.6002030607454749	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	15	71	17.44		RNA	SNP	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000558801.1	37	NULL		15																																																																																			-	-		0.647	DNM1P51-001	KNOWN	basic	processed_transcript	DNM1P51	pseudogene	OTTHUMT00000471721.1	G		-		84959328	-1	no_errors	ENST00000558801	ensembl	human	known	74_37	rna	SNP	0.754	A
GAPVD1	26130	genome.wustl.edu	37	9	128025963	128025989	+	Intron	DEL	CAGCACTCCATCTGTAGGTATGTCTGT	CAGCACTCCATCTGTAGGTATGTCTGT	-	rs551743640|rs71374244|rs143312600	byFrequency	TCGA-DX-A23T-01A-11D-A26G-09	TCGA-DX-A23T-10A-01D-A26G-09	CAGCACTCCATCTGTAGGTATGTCTGT	CAGCACTCCATCTGTAGGTATGTCTGT					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc6f717-fbc5-40d2-b105-da9a150b454f	b5482bab-e0c8-4a78-b485-a9d4bcfe9203	g.chr9:128025963_128025989delCAGCACTCCATCTGTAGGTATGTCTGT	ENST00000495955.1	+	1	92				GAPVD1_ENST00000265956.4_Intron|GAPVD1_ENST00000394104.2_Intron|GAPVD1_ENST00000470056.1_Intron|GAPVD1_ENST00000469528.1_3'UTR|GAPVD1_ENST00000394084.1_Intron|GAPVD1_ENST00000297933.6_Intron|GAPVD1_ENST00000394105.2_Intron|GAPVD1_ENST00000394083.2_Intron			Q14C86	GAPD1_HUMAN	GTPase activating protein and VPS9 domains 1						endocytosis (GO:0006897)|positive regulation of GTPase activity (GO:0043547)|regulation of protein transport (GO:0051223)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)	GTPase activating protein binding (GO:0032794)|GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(10)|lung(11)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44						CTAAGTGGCACAGCACTCCATCTGTAGGTATGTCTGTCAGCACTCCA	0.564														2105	0.420327	0.4516	0.3818	5008	,	,		19587	0.4454		0.3777	False		,,,				2504	0.4233																0								ENSG00000165219																																			GAPVD1	SO:0001627	intron_variant	0				HGNC		CCDS65130.1, CCDS65131.1, CCDS65132.1	9q34.11	2008-02-05			ENSG00000165219	ENSG00000165219			23375	protein-coding gene	gene with protein product		611714					Standard	XM_005251901		Approved	DKFZP434C212, KIAA1521	uc004bpr.3	Q14C86	OTTHUMG00000020678	ENST00000495955.1:c.-199+1725CAGCACTCCATCTGTAGGTATGTCTGT>-	9.37:g.128025963_128025989delCAGCACTCCATCTGTAGGTATGTCTGT		Somatic	NA	NA	NA		0.6002030607454749	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	A8MYK3|B0QZ62|B0QZ63|B0QZ64|Q14C76|Q2Q1W1|Q8ND92|Q8WU86|Q96CZ4|Q9NXQ1|Q9P207|Q9Y4N0	Splice_Site	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000495955.1	37	c.NULL		9																																																																																			-	-		0.564	GAPVD1-014	KNOWN	alternative_5_UTR|basic	protein_coding	GAPVD1	protein_coding	OTTHUMT00000355644.1	CAGCACTCCATCTGTAGGTATGTCTGT				128025989	+1	no_errors	ENST00000469528	ensembl	human	known	74_37	splice_site_del	DEL	1.000:1.000:1.000:1.000:1.000:0.999:0.996:0.980:0.970:0.963:0.961:0.959:0.952:0.948:0.947:0.950:0.961:0.966:0.966:0.969:0.974:0.982:0.984:0.985:0.984:0.985:0.993	-
KDR	3791	genome.wustl.edu	37	4	55980332	55980332	+	Missense_Mutation	SNP	A	A	T			TCGA-DX-A23T-01A-11D-A26G-09	TCGA-DX-A23T-10A-01D-A26G-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc6f717-fbc5-40d2-b105-da9a150b454f	b5482bab-e0c8-4a78-b485-a9d4bcfe9203	g.chr4:55980332A>T	ENST00000263923.4	-	6	1054	c.759T>A	c.(757-759)aaT>aaA	p.N253K		NM_002253.2	NP_002244.1	P35968	VGFR2_HUMAN	kinase insert domain receptor (a type III receptor tyrosine kinase)	253	Ig-like C2-type 3.				angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion homeostasis (GO:0055074)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic hemopoiesis (GO:0035162)|endothelial cell differentiation (GO:0045446)|endothelium development (GO:0003158)|extracellular matrix organization (GO:0030198)|lung alveolus development (GO:0048286)|lymph vessel development (GO:0001945)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vasculogenesis (GO:2001214)|protein autophosphorylation (GO:0046777)|regulation of cell shape (GO:0008360)|signal transduction by phosphorylation (GO:0023014)|surfactant homeostasis (GO:0043129)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sorting endosome (GO:0097443)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|Hsp90 protein binding (GO:0051879)|integrin binding (GO:0005178)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(16)|lung(71)|ovary(2)|prostate(2)|skin(10)|soft_tissue(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	135	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Axitinib(DB06626)|Cabozantinib(DB08875)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CAATCCCCACATTTAGTTCAG	0.398			Mis		"""NSCLC, angiosarcoma"""					TSP Lung(20;0.16)																														Dom	yes		4	4q11-q12	3791	vascular endothelial growth factor receptor 2		E	0								ENSG00000128052						186.0	178.0	181.0					4																	55980332		2203	4300	6503	KDR	SO:0001583	missense	0			-	HGNC	AF035121	CCDS3497.1	4q11-q12	2013-01-29			ENSG00000128052	ENSG00000128052	2.7.10.1	"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6307	protein-coding gene	gene with protein product		191306				1417831	Standard	NM_002253		Approved	FLK1, VEGFR, VEGFR2, CD309	uc003has.3	P35968	OTTHUMG00000128734	ENST00000263923.4:c.759T>A	4.37:g.55980332A>T	ENSP00000263923:p.Asn253Lys	Somatic	0	50	0.00		0.6002030607454749	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	6	50	10.71	A2RRS0|B5A925|C5IFA0|O60723|Q14178	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Ig_I-set,pfam_Prot_kinase_dom,pfam_Ig_V-set,pfam_Immunoglobulin,pfam_CD80_C2-set,superfamily_Kinase-like_dom,smart_Ig_sub,smart_Ig_sub2,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_dom,pfscan_Ig-like_dom,prints_VEGFR2_rcpt	p.N253K	ENST00000263923.4	37	c.759	CCDS3497.1	4	.	.	.	.	.	.	.	.	.	.	A	14.50	2.554609	0.45487	.	.	ENSG00000128052	ENST00000263923	T	0.65549	-0.16	5.45	-7.43	0.01383	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.048538	0.85682	D	0.000000	T	0.75148	0.3810	M	0.83774	2.66	0.47341	D	0.999398	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.993	T	0.81006	-0.1128	10	0.45353	T	0.12	.	16.7983	0.85608	0.4354:0.0:0.5646:0.0	.	253;253	P35968-2;P35968	.;VGFR2_HUMAN	K	253	ENSP00000263923:N253K	ENSP00000263923:N253K	N	-	3	2	KDR	55675089	0.529000	0.26322	0.166000	0.22797	0.047000	0.14425	-0.149000	0.10204	-1.423000	0.02002	-0.313000	0.08912	AAT	-	pfam_Ig_I-set,pfam_Ig_V-set,pfam_Immunoglobulin,smart_Ig_sub,smart_Ig_sub2,pfscan_Ig-like_dom		0.398	KDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KDR	protein_coding	OTTHUMT00000250645.1	A		-		55980332	-1	no_errors	ENST00000263923	ensembl	human	known	74_37	missense	SNP	0.692	T
MT-CO1	4512	genome.wustl.edu	37	M	7176	7176	+	Missense_Mutation	SNP	T	T	C			TCGA-DX-A23T-01A-11D-A26G-09	TCGA-DX-A23T-10A-01D-A26G-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc6f717-fbc5-40d2-b105-da9a150b454f	b5482bab-e0c8-4a78-b485-a9d4bcfe9203	g.chrM:7176T>C	ENST00000361624.2	+	1	1273	c.1273T>C	c.(1273-1275)Ttc>Ctc	p.F425L	MT-TC_ENST00000387405.1_RNA|MT-ATP8_ENST00000361851.1_5'Flank|MT-ND3_ENST00000361227.2_5'Flank|MT-CO3_ENST00000362079.2_5'Flank|MT-CO2_ENST00000361739.1_5'Flank|MT-TM_ENST00000387377.1_RNA|MT-TQ_ENST00000387372.1_RNA|MT-TD_ENST00000387419.1_RNA|MT-TK_ENST00000387421.1_RNA|MT-TI_ENST00000387365.1_RNA|MT-TS1_ENST00000387416.2_RNA|MT-ATP6_ENST00000361899.2_5'Flank|MT-TG_ENST00000387429.1_RNA|MT-TW_ENST00000387382.1_RNA|MT-TN_ENST00000387400.1_RNA|MT-TY_ENST00000387409.1_RNA|MT-TA_ENST00000387392.1_RNA			P00395	COX1_HUMAN	mitochondrially encoded cytochrome c oxidase I	425					aerobic respiration (GO:0009060)|cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|oxidative phosphorylation (GO:0006119)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex IV (GO:0005751)|respiratory chain complex IV (GO:0045277)	cytochrome-c oxidase activity (GO:0004129)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(4)|endometrium(25)|kidney(19)|lung(3)|prostate(3)	54						TAAATCTAACTTTCTTCCCAC	0.468																																																	0								ENSG00000198804																																			MT-CO1	SO:0001583	missense	0			-	HGNC			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198804	ENSG00000198804		"""Mitochondrial respiratory chain complex / Complex IV"""	7419	protein-coding gene	gene with protein product		516030	"""cytochrome c oxidase I"""	MTCO1		7219534	Standard			Approved	COX1, COI		P00395		ENST00000361624.2:c.1273T>C	M.37:g.7176T>C	ENSP00000354499:p.Phe425Leu	Somatic	0	17	0.00		0.6002030607454749	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	22	73	23.16	Q34770	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Cyt_c_Oxase_su1,superfamily_Cyt_c_Oxase_su1_dom,pfscan_Cyt_c_Oxase_su1_dom,prints_Cyt_c_Oxase_su1	p.F425L	ENST00000361624.2	37	c.1273		MT																																																																																			-	pfam_Cyt_c_Oxase_su1,superfamily_Cyt_c_Oxase_su1_dom,pfscan_Cyt_c_Oxase_su1_dom,prints_Cyt_c_Oxase_su1		0.468	MT-CO1-201	KNOWN	basic|appris_principal	protein_coding	MT-CO1	protein_coding		T	YP_003024028	-		7176	+1	no_errors	ENST00000361624	ensembl	human	known	74_37	missense	SNP	NULL	C
MOSPD1	56180	genome.wustl.edu	37	X	134033227	134033227	+	Intron	DEL	T	T	-			TCGA-DX-A23T-01A-11D-A26G-09	TCGA-DX-A23T-10A-01D-A26G-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc6f717-fbc5-40d2-b105-da9a150b454f	b5482bab-e0c8-4a78-b485-a9d4bcfe9203	g.chrX:134033227delT	ENST00000370783.3	-	3	341				MOSPD1_ENST00000370777.1_Intron|MOSPD1_ENST00000491609.1_Intron|MOSPD1_ENST00000370779.4_Intron	NM_019556.1	NP_062456.1	Q9UJG1	MSPD1_HUMAN	motile sperm domain containing 1						negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(1)|ovary(1)	9	Acute lymphoblastic leukemia(192;0.000127)					GCCATTAGTGTTTTTTTTTTT	0.353																																																	0								ENSG00000101928			79,762,2880		0,0,64,15,2,555,203,971,319	70.0	70.0	70.0			2.5	0.8	X		76	131,1554,4799		0,0,77,54,0,865,689,1415,1027	no	intron	MOSPD1	NM_019556.1		0,0,141,69,2,1420,892,2386,1346	A1A1,A1A2,A1R,A1,A2A2,A2R,A2,RR,R		25.987,22.6015,24.7526			134033227	210,2316,7679	2203	4300	6503	MOSPD1	SO:0001627	intron_variant	0				HGNC	Z83826	CCDS14645.1	Xq26.3	2008-02-05			ENSG00000101928	ENSG00000101928			25235	protein-coding gene	gene with protein product		300674				15533722	Standard	XM_005262446		Approved	dJ473B4	uc004eyb.3	Q9UJG1	OTTHUMG00000035315	ENST00000370783.3:c.155-32A>-	X.37:g.134033227delT		Somatic	0	48	0.00		0.6002030607454749	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	38	9.52	B2RE62|D3DTG5|Q5H9C5|Q5H9C7	RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000370783.3	37	NULL	CCDS14645.1	X																																																																																			-	-		0.353	MOSPD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	MOSPD1	protein_coding	OTTHUMT00000085439.1	T	NM_019556			134033227	-1	no_errors	ENST00000462060	ensembl	human	known	74_37	rna	DEL	0.001	-
TAF1B	9014	genome.wustl.edu	37	2	9989571	9989571	+	Frame_Shift_Del	DEL	A	A	-	rs528368939		TCGA-DX-A23T-01A-11D-A26G-09	TCGA-DX-A23T-10A-01D-A26G-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc6f717-fbc5-40d2-b105-da9a150b454f	b5482bab-e0c8-4a78-b485-a9d4bcfe9203	g.chr2:9989571delA	ENST00000263663.5	+	3	375	c.187delA	c.(187-189)aaafs	p.K65fs	TAF1B_ENST00000402170.1_3'UTR|TAF1B_ENST00000396242.3_5'UTR	NM_005680.2	NP_005671	Q53T94	TAF1B_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kDa	65	B-reader.				gene expression (GO:0010467)|RNA polymerase I transcriptional preinitiation complex assembly at the promoter for the nuclear large rRNA transcript (GO:0001189)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|RNA polymerase I core factor complex (GO:0070860)	metal ion binding (GO:0046872)|RNA polymerase I CORE element sequence-specific DNA binding (GO:0001164)|RNA polymerase I CORE element sequence-specific DNA binding transcription factor recruiting transcription factor activity (GO:0001187)|sequence-specific DNA binding transcription factor activity (GO:0003700)|TBP-class protein binding (GO:0017025)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|lung(4)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	14	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					CCGGGGGCTTAAAAAAAAAAA	0.333																																																	0								ENSG00000115750			139,495,3606		1,2,135,2,489,1491	20.0	22.0	21.0			1.7	0.9	2		23	207,946,7081		0,0,207,0,946,2964	no	codingComplex	TAF1B	NM_005680.2		1,2,342,2,1435,4455	A1A1,A1A2,A1R,A2A2,A2R,RR		14.0029,14.9528,14.3258			9989571	346,1441,10687	2194	4292	6486	TAF1B	SO:0001589	frameshift_variant	0				HGNC	L39061	CCDS33143.1	2p25	2008-06-02	2002-08-29		ENSG00000115750	ENSG00000115750			11533	protein-coding gene	gene with protein product		604904	"""TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kD"""			7801123	Standard	NM_005680		Approved	TAFI63, SL1, RAF1B, RAFI63	uc002qzz.3	Q53T94	OTTHUMG00000151673	ENST00000263663.5:c.187delA	2.37:g.9989571delA	ENSP00000263663:p.Lys65fs	Somatic	0	11	0.00		0.6002030607454749	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	21	16.00	B4DI42|F8WD72|Q15574|Q8WVC3	Frame_Shift_Del	DEL	NA	NA	NA	NA	NA	NA	pfam_TF_Rrn7	p.N66fs	ENST00000263663.5	37	c.187	CCDS33143.1	2																																																																																			-	NULL		0.333	TAF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TAF1B	protein_coding	OTTHUMT00000323426.2	A	NM_005680			9989571	+1	no_errors	ENST00000263663	ensembl	human	known	74_37	frame_shift_del	DEL	0.991	-
NAT10	55226	genome.wustl.edu	37	11	34130376	34130376	+	Missense_Mutation	SNP	A	A	G			TCGA-DX-A23T-01A-11D-A26G-09	TCGA-DX-A23T-10A-01D-A26G-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc6f717-fbc5-40d2-b105-da9a150b454f	b5482bab-e0c8-4a78-b485-a9d4bcfe9203	g.chr11:34130376A>G	ENST00000257829.3	+	3	402	c.196A>G	c.(196-198)Agc>Ggc	p.S66G	NAT10_ENST00000531159.2_Intron|NAT10_ENST00000527971.1_Missense_Mutation_p.S66G	NM_024662.2	NP_078938	Q9H0A0	NAT10_HUMAN	N-acetyltransferase 10 (GCN5-related)	66						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|N-acetyltransferase activity (GO:0008080)|poly(A) RNA binding (GO:0044822)			endometrium(4)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	23		Acute lymphoblastic leukemia(5;0.0119)|all_hematologic(20;0.0231)				GCTGGGGTTTAGCAGGTAAGC	0.408																																																	0								ENSG00000135372						138.0	124.0	129.0					11																	34130376		2202	4298	6500	NAT10	SO:0001583	missense	0			-	HGNC	AF489535	CCDS7889.1, CCDS44568.1	11p13	2011-11-16	2008-09-24		ENSG00000135372	ENSG00000135372	2.3.1.-		29830	protein-coding gene	gene with protein product		609221	"""N-acetyltransferase 10"""			14592445, 21177859	Standard	NM_024662		Approved	hALP, FLJ10774, FLJ12179, NET43, KIAA1709	uc001mvk.3	Q9H0A0	OTTHUMG00000166249	ENST00000257829.3:c.196A>G	11.37:g.34130376A>G	ENSP00000257829:p.Ser66Gly	Somatic	0	57	0.00		0.6002030607454749	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	5	55	8.33	B4DFD5|E7ESU4|E9PMN9|Q86WK5|Q9C0F4|Q9HA61|Q9NVF2	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Helicase_dom,pfam_DUF1726,superfamily_Acyl_CoA_acyltransferase,superfamily_P-loop_NTPase,pfscan_GNAT_dom	p.S66G	ENST00000257829.3	37	c.196	CCDS7889.1	11	.	.	.	.	.	.	.	.	.	.	A	20.4	3.981966	0.74474	.	.	ENSG00000135372	ENST00000257829;ENST00000529523;ENST00000527971	T;T;T	0.32023	1.47;1.47;1.47	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	T	0.54919	0.1888	M	0.87180	2.865	0.80722	D	1	D	0.61080	0.989	P	0.55923	0.787	T	0.63292	-0.6670	10	0.52906	T	0.07	-19.5323	15.3465	0.74343	1.0:0.0:0.0:0.0	.	66	Q9H0A0	NAT10_HUMAN	G	66	ENSP00000257829:S66G;ENSP00000435569:S66G;ENSP00000437324:S66G	ENSP00000257829:S66G	S	+	1	0	NAT10	34086952	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	9.109000	0.94291	2.029000	0.59856	0.459000	0.35465	AGC	-	NULL		0.408	NAT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NAT10	protein_coding	OTTHUMT00000388693.1	A	NM_024662	-		34130376	+1	no_errors	ENST00000257829	ensembl	human	known	74_37	missense	SNP	1.000	G
BX119917.1	0	genome.wustl.edu	37	X	71372202	71372209	+	RNA	DEL	CGCGCGCA	CGCGCGCA	-	rs6625958|rs72357649|rs72197346|rs59980083|rs6625957|rs200056633|rs10856127		TCGA-DX-A23T-01A-11D-A26G-09	TCGA-DX-A23T-10A-01D-A26G-09	CGCGCGCA	CGCGCGCA					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc6f717-fbc5-40d2-b105-da9a150b454f	b5482bab-e0c8-4a78-b485-a9d4bcfe9203	g.chrX:71372202_71372209delCGCGCGCA	ENST00000401114.1	-	0	55_62																											TGTGCATGCGCGCGCGcacacacacaca	0.495																																																	0								ENSG00000215933																																			BX119917.1			0				Clone_based_ensembl_gene																													X.37:g.71372202_71372209delCGCGCGCA		Somatic	NA	NA	NA		0.6002030607454749	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA		RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000401114.1	37	NULL		X																																																																																			-	-		0.495	BX119917.1-201	NOVEL	basic	miRNA	ENSG00000215933	miRNA		CGCGCGCA				71372209	-1	no_errors	ENST00000401114	ensembl	human	novel	74_37	rna	DEL	0.000:0.000:0.000:0.000:0.000:0.001:0.015:0.009	-
FLG	2312	genome.wustl.edu	37	1	152278006	152278006	+	Missense_Mutation	SNP	C	C	T			TCGA-DX-A23T-01A-11D-A26G-09	TCGA-DX-A23T-10A-01D-A26G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc6f717-fbc5-40d2-b105-da9a150b454f	b5482bab-e0c8-4a78-b485-a9d4bcfe9203	g.chr1:152278006C>T	ENST00000368799.1	-	3	9391	c.9356G>A	c.(9355-9357)gGa>gAa	p.G3119E	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3119	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTGCCTTCCTCCTCTGCTTGA	0.592									Ichthyosis																																								0								ENSG00000143631						103.0	148.0	133.0					1																	152278006		2180	4281	6461	FLG	SO:0001583	missense	0	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	-	HGNC	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.9356G>A	1.37:g.152278006C>T	ENSP00000357789:p.Gly3119Glu	Somatic	0	60	0.00		0.6002030607454749	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	14	62	18.42	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Filaggrin,pfam_S100_Ca-bd_sub,pfscan_EF_hand_dom,prints_Filaggrin	p.G3119E	ENST00000368799.1	37	c.9356	CCDS30860.1	1	.	.	.	.	.	.	.	.	.	.	C	10.98	1.505775	0.26949	.	.	ENSG00000143631	ENST00000368799	T	0.01629	4.72	3.66	2.71	0.32032	.	.	.	.	.	T	0.01287	0.0042	M	0.76574	2.34	0.09310	N	1	D	0.59357	0.985	P	0.51974	0.686	T	0.18178	-1.0345	9	0.02654	T	1	.	9.2296	0.37428	0.0:0.7768:0.2232:0.0	.	3119	P20930	FILA_HUMAN	E	3119	ENSP00000357789:G3119E	ENSP00000357789:G3119E	G	-	2	0	FLG	150544630	0.000000	0.05858	0.001000	0.08648	0.059000	0.15707	-1.049000	0.03514	0.610000	0.30035	0.449000	0.29647	GGA	-	NULL		0.592	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FLG	protein_coding	OTTHUMT00000033742.1	C	NM_002016	-		152278006	-1	no_errors	ENST00000368799	ensembl	human	known	74_37	missense	SNP	0.003	T
CD247	919	genome.wustl.edu	37	1	167400667	167400675	+	3'UTR	DEL	ACCTGCACC	ACCTGCACC	-	rs34484379	byFrequency	TCGA-DX-A23T-01A-11D-A26G-09	TCGA-DX-A23T-10A-01D-A26G-09	ACCTGCACC	ACCTGCACC					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc6f717-fbc5-40d2-b105-da9a150b454f	b5482bab-e0c8-4a78-b485-a9d4bcfe9203	g.chr1:167400667_167400675delACCTGCACC	ENST00000362089.5	-	0	810_818				CD247_ENST00000483825.1_5'UTR|CD247_ENST00000392122.3_3'UTR			P20963	CD3Z_HUMAN	CD247 molecule						Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|regulation of defense response to virus by virus (GO:0050690)|regulation of immune response (GO:0050776)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	alpha-beta T cell receptor complex (GO:0042105)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(1)|skin(1)	6			LUSC - Lung squamous cell carcinoma(543;0.236)		Muromonab(DB00075)	AGACAGGTCTACCTGCACCACCGGCAAAC	0.579														126	0.0251597	0.0159	0.0216	5008	,	,		19923	0.0		0.0507	False		,,,				2504	0.0399				Ovarian(192;1815 2869 36877 43334)												0								ENSG00000198821																																			CD247	SO:0001624	3_prime_UTR_variant	0				HGNC	BC025703	CCDS1260.1, CCDS1261.1	1q24.2	2014-09-17	2006-03-28	2006-03-09	ENSG00000198821	ENSG00000198821		"""CD molecules"""	1677	protein-coding gene	gene with protein product		186780	"""CD3z antigen, zeta polypeptide (TiT3 complex)"", ""CD247 antigen"""	CD3Z		2974162	Standard	NM_198053		Approved	CD3H, CD3Q	uc001gei.4	P20963	OTTHUMG00000034593	ENST00000362089.5:c.*251GGTGCAGGT>-	1.37:g.167400667_167400675delACCTGCACC		Somatic	NA	NA	NA		0.6002030607454749	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	B1AK49|Q5VX13|Q8TAX4	RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000362089.5	37	NULL	CCDS1261.1	1																																																																																			-	-		0.579	CD247-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	CD247	protein_coding	OTTHUMT00000083707.1	ACCTGCACC	NM_198053			167400675	-1	no_errors	ENST00000470379	ensembl	human	known	74_37	rna	DEL	0.002:0.001:0.002:0.000:0.000:0.000:0.000:0.000:0.000	-
PDE3B	5140	genome.wustl.edu	37	11	14889058	14889058	+	Missense_Mutation	SNP	G	G	A			TCGA-DX-A23T-01A-11D-A26G-09	TCGA-DX-A23T-10A-01D-A26G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc6f717-fbc5-40d2-b105-da9a150b454f	b5482bab-e0c8-4a78-b485-a9d4bcfe9203	g.chr11:14889058G>A	ENST00000282096.4	+	15	3246	c.2893G>A	c.(2893-2895)Gaa>Aaa	p.E965K	PDE3B_ENST00000455098.2_Missense_Mutation_p.E914K	NM_000922.3	NP_000913.2	Q13370	PDE3B_HUMAN	phosphodiesterase 3B, cGMP-inhibited	965	Catalytic. {ECO:0000250}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cellular response to insulin stimulus (GO:0032869)|endocrine pancreas development (GO:0031018)|glucose homeostasis (GO:0042593)|insulin receptor signaling pathway (GO:0008286)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cAMP-mediated signaling (GO:0043951)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of lipid catabolic process (GO:0050995)|regulation of insulin secretion (GO:0050796)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|guanyl-nucleotide exchange factor complex (GO:0032045)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity (GO:0004119)|metal ion binding (GO:0046872)|protein kinase B binding (GO:0043422)			NS(1)|breast(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(15)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39					Caffeine(DB00201)	GCAGGGAGATGAAGAAGCAAA	0.363																																																	0								ENSG00000152270						79.0	73.0	75.0					11																	14889058		2200	4294	6494	PDE3B	SO:0001583	missense	0			-	HGNC	U38178	CCDS7817.1	11p15.2	2008-03-18			ENSG00000152270	ENSG00000152270	3.1.4.17	"""Phosphodiesterases"""	8779	protein-coding gene	gene with protein product		602047				8884271, 16395595	Standard	NM_000922		Approved	HcGIP1	uc001mln.3	Q13370	OTTHUMG00000165898	ENST00000282096.4:c.2893G>A	11.37:g.14889058G>A	ENSP00000282096:p.Glu965Lys	Somatic	0	30	0.00		0.6002030607454749	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	29	12.12	B7ZM37|O00639|Q14408|Q6SEI4	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_PDEase_catalytic_dom,smart_HD/PDEase_dom	p.E965K	ENST00000282096.4	37	c.2893	CCDS7817.1	11	.	.	.	.	.	.	.	.	.	.	G	26.8	4.770036	0.90020	.	.	ENSG00000152270	ENST00000282096;ENST00000455098	T;T	0.79141	-1.24;-1.24	5.74	5.74	0.90152	5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);	0.000000	0.85682	D	0.000000	D	0.84261	0.5433	L	0.39467	1.215	0.58432	D	0.999999	D;D	0.89917	0.976;1.0	D;D	0.91635	0.938;0.999	D	0.84395	0.0557	10	0.54805	T	0.06	.	18.099	0.89499	0.0:0.0:1.0:0.0	.	914;965	B7ZM37;Q13370	.;PDE3B_HUMAN	K	965;914	ENSP00000282096:E965K;ENSP00000388644:E914K	ENSP00000282096:E965K	E	+	1	0	PDE3B	14845634	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	9.476000	0.97823	2.711000	0.92665	0.561000	0.74099	GAA	-	pfam_PDEase_catalytic_dom		0.363	PDE3B-001	KNOWN	basic|CCDS	protein_coding	PDE3B	protein_coding	OTTHUMT00000386974.1	G	NM_000922	-		14889058	+1	no_errors	ENST00000282096	ensembl	human	known	74_37	missense	SNP	1.000	A
RAPGEF2	9693	genome.wustl.edu	37	4	160216906	160216906	+	Intron	SNP	T	T	C	rs66478721|rs373967945|rs10024829|rs113715111|rs60091174		TCGA-DX-A23T-01A-11D-A26G-09	TCGA-DX-A23T-10A-01D-A26G-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc6f717-fbc5-40d2-b105-da9a150b454f	b5482bab-e0c8-4a78-b485-a9d4bcfe9203	g.chr4:160216906T>C	ENST00000264431.4	+	2	479				RAPGEF2_ENST00000504604.1_Intron|AC105316.1_ENST00000401270.1_RNA	NM_014247.2	NP_055062.1	Q9Y4G8	RPGF2_HUMAN	Rap guanine nucleotide exchange factor (GEF) 2						adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|blood vessel development (GO:0001568)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|cellular response to nerve growth factor stimulus (GO:1990090)|establishment of endothelial barrier (GO:0061028)|forebrain neuron development (GO:0021884)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|negative regulation of cell proliferation (GO:0008285)|negative regulation of dendrite morphogenesis (GO:0050774)|negative regulation of melanin biosynthetic process (GO:0048022)|nerve growth factor signaling pathway (GO:0038180)|neuron migration (GO:0001764)|neuron projection development (GO:0031175)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron migration (GO:2001224)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein binding (GO:0032092)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of vasculogenesis (GO:2001214)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|regulation of synaptic plasticity (GO:0048167)|small GTPase mediated signal transduction (GO:0007264)|ventricular system development (GO:0021591)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synapse (GO:0045202)	beta-1 adrenergic receptor binding (GO:0031697)|calcium ion binding (GO:0005509)|cAMP binding (GO:0030552)|diacylglycerol binding (GO:0019992)|PDZ domain binding (GO:0030165)|Rap GTPase activator activity (GO:0046582)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|signal transducer activity (GO:0004871)|WW domain binding (GO:0050699)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	70	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0817)		tgtgtgtgtgtgcgcgcgcgc	0.423																																																	0								ENSG00000216089																																			AC105316.1	SO:0001627	intron_variant	0			-	Clone_based_ensembl_gene	AB002311	CCDS43277.1	4q32.1	2004-03-01	2004-03-01	2004-03-01					16854	protein-coding gene	gene with protein product	"""Rap GEP"""	609530	"""PDZ domain containing guanine nucleotide exchange factor (GEF) 1"""	PDZGEF1		9205841, 10934204	Standard	NM_014247		Approved	PDZ-GEF1, RA-GEF, DKFZP586O1422, KIAA0313	uc003iqg.4	Q9Y4G8		ENST00000264431.4:c.61-8588T>C	4.37:g.160216906T>C		Somatic	0	13	0.00		0.6002030607454749	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	10	28.57	D3DP27	RNA	SNP	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000264431.4	37	NULL	CCDS43277.1	4																																																																																			-	-		0.423	RAPGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ENSG00000216089	protein_coding	OTTHUMT00000364980.2	T	NM_014247	rs10024829		160216906	+1	no_errors	ENST00000401270	ensembl	human	novel	74_37	rna	SNP	0.000	C
