#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_ ensembl_gene_id	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_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_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_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	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_dbSNP	i_default_gene_name	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_name_source	i_gene_type	i_havana_transcript	i_n_alt_count	i_n_alt_count_full	i_n_alt_count_val	i_n_ref_count	i_n_ref_count_full	i_n_ref_count_val	i_normal_vaf	i_normal_vaf_val	i_reference	i_refseq_mrna_id	i_secondary_variant_classification	i_stop	i_strand	i_t_alt_count_full	i_t_alt_count_val	i_t_ref_count_full	i_t_ref_count_val	i_tier	i_transcript_error	i_transcript_name	i_transcript_source	i_transcript_species	i_transcript_status	i_transcript_version	i_trv_type	i_tumor_vaf	i_tumor_vaf_val	i_type	i_ucsc_cons	i_variant	t_alt_count	t_ref_count
RAD17	5884	genome.wustl.edu	37	5	68692375	68692376	+	Splice_Site	INS	-	-	A	rs377737971|rs34097088|rs75928221		TCGA-3B-A9HJ-01A-11D-A387-09	TCGA-3B-A9HJ-10A-01D-A38A-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	18382739-a33f-49e6-856f-fcf720c49363	dd637e7a-2892-4bd4-b8ad-ef88f676791d	g.chr5:68692375_68692376insA	ENST00000509734.1	+	15	2283		c.e15+2		RAD17_ENST00000521422.1_Splice_Site|RAD17_ENST00000305138.4_Splice_Site|RAD17_ENST00000504177.1_Intron|RAD17_ENST00000361732.2_Splice_Site|RAD17_ENST00000358030.2_Splice_Site|RAD17_ENST00000345306.6_Splice_Site|RAD17_ENST00000380774.3_Splice_Site|RAD17_ENST00000282891.6_Splice_Site|RAD17_ENST00000354312.3_Splice_Site|RAD17_ENST00000354868.5_Splice_Site			O75943	RAD17_HUMAN	RAD17 homolog (S. pombe)						cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of DNA replication (GO:0008156)|regulation of phosphorylation (GO:0042325)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)						Lung NSC(167;5.19e-05)|Prostate(74;0.0143)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;9.36e-57)|Epithelial(20;1.21e-52)|all cancers(19;3.34e-48)|Lung(70;0.0183)		AATAAAAAGGTAAAAAAAAAAA	0.322								Other conserved DNA damage response genes					ENSG00000152942																																					0																																										SO:0001630	splice_region_variant	0				AF085736	CCDS4003.1, CCDS4004.1, CCDS4005.1, CCDS47226.1	5q13	2010-09-24	2001-11-28		ENSG00000152942	ENSG00000152942			9807	protein-coding gene	gene with protein product		603139	"""RAD1 (S. pombe) homolog"""			9869296, 9660800	Standard	NM_133343		Approved	Rad24, RAD17Sp, CCYC	uc003jwo.3	O75943	OTTHUMG00000099357	ENST00000509734.1:c.1605+2->A	5.37:g.68692386_68692386dupA			A8K8X2|D3DWA5|O75714|Q7Z3S4|Q9UNK7|Q9UNR7|Q9UNR8|Q9UPF5	Splice_Site	INS	-	e13+2	ENST00000509734.1	37	c.1605+2_1605+1	CCDS4003.1	5																																																																																				RAD17	-	-		0.322	RAD17-008	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	RAD17	HGNC	protein_coding	OTTHUMT00000369171.1	0	0		13	13		0.00		-	NM_133344	Intron	68692376	+1	11		15		tier1	no_errors	ENST00000380774	ensembl	human	known	74_37	splice_site_ins	42.31		INS	1.000:0.992	A	11	15
NRG2	9542	genome.wustl.edu	37	5	139228073	139228078	+	In_Frame_Del	DEL	CCGGGT	CCGGGT	-	rs185375193|rs200668592		TCGA-3B-A9HJ-01A-11D-A387-09	TCGA-3B-A9HJ-10A-01D-A38A-09	CCGGGT	CCGGGT					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	18382739-a33f-49e6-856f-fcf720c49363	dd637e7a-2892-4bd4-b8ad-ef88f676791d	g.chr5:139228073_139228078delCCGGGT	ENST00000361474.1	-	10	2201_2206	c.1977_1982delACCCGG	c.(1975-1983)ggacccggg>ggg	p.659_661GPG>G	NRG2_ENST00000289422.7_In_Frame_Del_p.667_669GPG>G|NRG2_ENST00000358522.3_In_Frame_Del_p.661_663GPG>G|NRG2_ENST00000289409.4_In_Frame_Del_p.653_655GPG>G|NRG2_ENST00000340391.3_In_Frame_Del_p.456_458GPG>G|NRG2_ENST00000545385.1_In_Frame_Del_p.661_663GPG>G|NRG2_ENST00000394770.1_3'UTR|NRG2_ENST00000541337.1_In_Frame_Del_p.593_595GPG>G|CTB-35F21.4_ENST00000504413.1_RNA	NM_004883.2	NP_004874.1	O14511	NRG2_HUMAN	neuregulin 2	659					embryo development (GO:0009790)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	25			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			gggcccgggcccgggtccgggtcccg	0.791													ENSG00000158458																																					0									,,,,	145,405		65,15,195					,,,,		0.3			1	321,1153		148,25,564	no	coding,coding,coding,coding,coding	NRG2	NM_013983.2,NM_013982.2,NM_013981.3,NM_004883.2,NM_001184935.1	,,,,	213,40,759	A1A1,A1R,RR		21.7775,26.3636,23.0237	,,,,	,,,,		466,1558				SO:0001651	inframe_deletion	0					CCDS4217.1, CCDS54910.1	5q23-q33	2013-01-11			ENSG00000158458	ENSG00000158458		"""Immunoglobulin superfamily / I-set domain containing"""	7998	protein-coding gene	gene with protein product	"""neural- and thymus-derived activator for ErbB kinases"", ""divergent of neuregulin-1"""	603818				9168114, 9168115	Standard	NM_004883		Approved	Don-1, NTAK, HRG2	uc003lev.2	O14511	OTTHUMG00000129241	ENST00000361474.1:c.1977_1982delACCCGG	5.37:g.139228079_139228084delCCGGGT	ENSP00000354910:p.Gly665_Pro666del			In_Frame_Del	DEL	pfam_Neuregulin_1_C,pfam_Ig_I-set,pfam_Immunoglobulin,smart_Ig_sub,smart_Ig_sub2,pfscan_EG-like_dom,pfscan_Ig-like_dom	p.GP665in_frame_del	ENST00000361474.1	37	c.1988_1983	CCDS4217.1	5																																																																																				NRG2	-	pfam_Neuregulin_1_C		0.791	NRG2-001	KNOWN	basic|CCDS	protein_coding	NRG2	HGNC	protein_coding	OTTHUMT00000251340.1									CCGGGT	NM_013982		139228078	-1					tier1	no_errors	ENST00000545385	ensembl	human	known	74_37	in_frame_del			DEL	0.243:0.240:0.236:0.085:0.074:0.062	-		
TNFAIP6	7130	genome.wustl.edu	37	2	152236046	152236046	+	Stop_Codon_Del	DEL	A	A	-	rs71403164|rs35060021	byFrequency	TCGA-3B-A9HJ-01A-11D-A387-09	TCGA-3B-A9HJ-10A-01D-A38A-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	18382739-a33f-49e6-856f-fcf720c49363	dd637e7a-2892-4bd4-b8ad-ef88f676791d	g.chr2:152236046delA	ENST00000243347.3	+	0	908					NM_007115.3	NP_009046.2	P98066	TSG6_HUMAN	tumor necrosis factor, alpha-induced protein 6						cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|inflammatory response (GO:0006954)|signal transduction (GO:0007165)		hyaluronic acid binding (GO:0005540)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.131)	Hyaluronan(DB08818)	AGCCACTTATAAAAAAAAAAA	0.289													ENSG00000123610	|||unknown(HR)	2457	0.490615	0.4425	0.4207	5008	,	,		15615	0.5208		0.5189	False		,,,				2504	0.545																0													20.0	21.0	21.0					2																	152236046		2160	4277	6437	SO:0001567	stop_retained_variant	0					CCDS2193.1	2q23.3	2008-11-18			ENSG00000123610	ENSG00000123610			11898	protein-coding gene	gene with protein product		600410				1730767, 8568267, 15060082	Standard	NM_007115		Approved	TSG6, TSG-6	uc002txk.3	P98066	OTTHUMG00000131884	Exception_encountered	2.37:g.152236046delA			Q53TI7|Q8WWI9	Frame_Shift_Del	DEL	pfam_CUB_dom,pfam_Link,superfamily_CUB_dom,superfamily_C-type_lectin_fold,smart_Link,smart_CUB_dom,pfscan_CUB_dom,pfscan_Link,prints_Link	p.*278fs	ENST00000243347.3	37	c.833	CCDS2193.1	2																																																																																				TNFAIP6	-	NULL		0.289	TNFAIP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TNFAIP6	HGNC	protein_coding	OTTHUMT00000254834.2	0	0		9	9		0.00		A	NM_007115		152236046	+1	5		24		tier1	no_errors	ENST00000243347	ensembl	human	known	74_37	frame_shift_del	17.24		DEL	0.961	-	5	24
TRIM47	91107	genome.wustl.edu	37	17	73872969	73872970	+	Intron	INS	-	-	G	rs3833085	byFrequency	TCGA-3B-A9HJ-01A-11D-A387-09	TCGA-3B-A9HJ-10A-01D-A38A-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	18382739-a33f-49e6-856f-fcf720c49363	dd637e7a-2892-4bd4-b8ad-ef88f676791d	g.chr17:73872969_73872970insG	ENST00000254816.2	-	2	702				TRIM47_ENST00000587339.1_Intron|RP11-552F3.9_ENST00000586076.1_RNA	NM_033452.2	NP_258411.2	Q96LD4	TRI47_HUMAN	tripartite motif containing 47							cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(3)|endometrium(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	22			Epithelial(20;4.23e-06)|all cancers(21;5.24e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00092)|LUSC - Lung squamous cell carcinoma(166;0.154)			AGGCCTTGCCAGGGGAGAGAAG	0.619													ENSG00000267801	GGGG|GGGG|GGGGG|insertion	953	0.190296	0.3646	0.1369	5008	,	,		19439	0.1042		0.169	False		,,,				2504	0.1033																0																																										SO:0001627	intron_variant	0				AY026763	CCDS32737.1	17q25	2013-01-09	2011-01-25			ENSG00000132481		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19020	protein-coding gene	gene with protein product		611041	"""tripartite motif-containing 47"""				Standard	NM_033452		Approved	GOA, RNF100	uc002jpw.3	Q96LD4		ENST00000254816.2:c.676-75->C	17.37:g.73872973_73872973dupG			Q96AD0|Q96GU5|Q9BRN7	R	INS	-	NULL	ENST00000254816.2	37	NULL	CCDS32737.1	17																																																																																				RP11-552F3.9	-	-		0.619	TRIM47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ENSG00000267801	Clone_based_vega_gene	protein_coding	OTTHUMT00000448934.1	0	0		13	13		0.00		-			73872970	+1	9		11		tier1	no_errors	ENST00000586076	ensembl	human	known	74_37	rna	45.00		INS	0.001:0.000	G	9	11
RXRA	6256	genome.wustl.edu	37	9	137331938	137331938	+	3'UTR	DEL	A	A	-	rs369993354		TCGA-3B-A9HJ-01A-11D-A387-09	TCGA-3B-A9HJ-10A-01D-A38A-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	18382739-a33f-49e6-856f-fcf720c49363	dd637e7a-2892-4bd4-b8ad-ef88f676791d	g.chr9:137331938delA	ENST00000356384.4	+	0	5277							P19793	RXRA_HUMAN	retinoid X receptor, alpha						camera-type eye development (GO:0043010)|cardiac muscle cell proliferation (GO:0060038)|cellular lipid metabolic process (GO:0044255)|cholesterol metabolic process (GO:0008203)|embryo implantation (GO:0007566)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|maternal placenta development (GO:0001893)|modulation by virus of host morphology or physiology (GO:0019048)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peroxisome proliferator activated receptor signaling pathway (GO:0035357)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homotetramerization (GO:0051289)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|response to retinoic acid (GO:0032526)|retinoic acid receptor signaling pathway (GO:0048384)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular cardiac muscle cell differentiation (GO:0055012)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|vitamin metabolic process (GO:0006766)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	9-cis retinoic acid receptor activity (GO:0004886)|chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein heterodimerization activity (GO:0046982)|retinoic acid receptor activity (GO:0003708)|retinoic acid-responsive element binding (GO:0044323)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|vitamin D receptor binding (GO:0042809)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19				OV - Ovarian serous cystadenocarcinoma(145;4.66e-08)|Epithelial(140;6.72e-08)|all cancers(34;2.22e-07)	Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Bexarotene(DB00307)|Etodolac(DB00749)	CTGGAAAGGTAAAAAAAAAAA	0.378													ENSG00000186350																																					0																																										SO:0001624	3_prime_UTR_variant	0				X52773	CCDS35172.1	9q34	2013-01-16			ENSG00000186350	ENSG00000186350		"""Nuclear hormone receptors"""	10477	protein-coding gene	gene with protein product	"""nuclear receptor subfamily 2 group B member 1"""	180245				2159111	Standard	XM_005263409		Approved	NR2B1	uc004cfa.1	P19793	OTTHUMG00000020887	ENST00000356384.4:c.*5274A>-	9.37:g.137331938delA			B3KY83|Q2NL52|Q2V504	R	DEL	-	NULL	ENST00000356384.4	37	NULL		9																																																																																				RXRA	-	-		0.378	RXRA-001	KNOWN	basic	processed_transcript	RXRA	HGNC	protein_coding	OTTHUMT00000054948.1	0	0		33	33		0.00		A	NM_002957		137331938	+1	5		26		tier1	no_errors	ENST00000356384	ensembl	human	known	74_37	rna	16.13		DEL	0.998	-	5	26
NEURL4	84461	genome.wustl.edu	37	17	7228218	7228218	+	Missense_Mutation	SNP	G	G	T	rs377496192		TCGA-3B-A9HJ-01A-11D-A387-09	TCGA-3B-A9HJ-10A-01D-A38A-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	18382739-a33f-49e6-856f-fcf720c49363	dd637e7a-2892-4bd4-b8ad-ef88f676791d	g.chr17:7228218G>T	ENST00000399464.2	-	9	1728	c.1713C>A	c.(1711-1713)gaC>gaA	p.D571E	NEURL4_ENST00000315614.7_Missense_Mutation_p.D571E|NEURL4_ENST00000570460.1_Missense_Mutation_p.D549E	NM_032442.2	NP_115818.2	Q96JN8	NEUL4_HUMAN	neuralized E3 ubiquitin protein ligase 4	571	NHR 3. {ECO:0000255|PROSITE- ProRule:PRU00400}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						CCACCATCTTGTCGATGCGCA	0.587											OREG0024134	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	ENSG00000215041																																					0								G	GLU/ASP,GLU/ASP	0,4342		0,0,2171	206.0	217.0	213.0		1713,1713	4.7	1.0	17		213	1,8545		0,1,4272	no	missense,missense	NEURL4	NM_001005408.1,NM_032442.2	45,45	0,1,6443	TT,TG,GG		0.0117,0.0,0.0078	benign,benign	571/1561,571/1563	7228218	1,12887	2171	4273	6444	SO:0001583	missense	0			-		CCDS42251.1, CCDS42252.1	17p13	2013-10-24	2013-10-24		ENSG00000215041	ENSG00000215041			34410	protein-coding gene	gene with protein product		615865	"""neuralized homolog 4 (Drosophila)"""			22261722, 22441691	Standard	NM_001005408		Approved	KIAA1787	uc002gga.1	Q96JN8	OTTHUMG00000132319	ENST00000399464.2:c.1713C>A	17.37:g.7228218G>T	ENSP00000382390:p.Asp571Glu	640	Q6GPI8|Q96IU9|Q9H0B0	Missense_Mutation	SNP	pfam_Neu_Z,superfamily_ConA-like_lec_gl_sf,smart_Neu_Z,pfscan_Neu_Z	p.D571E	ENST00000399464.2	37	c.1713	CCDS42251.1	17	.	.	.	.	.	.	.	.	.	.	G	16.24	3.067866	0.55539	0.0	1.17E-4	ENSG00000215041	ENST00000315614;ENST00000399464	T;T	0.73575	-0.76;-0.76	4.73	4.73	0.59995	Concanavalin A-like lectin/glucanase (1);NEUZ (3);	0.000000	0.85682	D	0.000000	T	0.64249	0.2581	N	0.13140	0.3	0.42452	D	0.992754	P;P	0.46784	0.884;0.788	P;P	0.47470	0.509;0.548	T	0.61168	-0.7117	10	0.14656	T	0.56	-34.022	16.9946	0.86363	0.0:0.0:1.0:0.0	.	571;571	Q96JN8-2;Q96JN8	.;NEUL4_HUMAN	E	571	ENSP00000319826:D571E;ENSP00000382390:D571E	ENSP00000319826:D571E	D	-	3	2	NEURL4	7168942	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.296000	0.65698	2.608000	0.88229	0.655000	0.94253	GAC	-	NEURL4	-	pfam_Neu_Z,superfamily_ConA-like_lec_gl_sf,smart_Neu_Z,pfscan_Neu_Z		0.587	NEURL4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NEURL4	HGNC	protein_coding	OTTHUMT00000255434.2	0	0		41	41		0.00		G	NM_032442		7228218	-1	5		54		tier1	no_errors	ENST00000399464	ensembl	human	known	74_37	missense	8.47		SNP	1.000	T	5	54
EMR1	2015	genome.wustl.edu	37	19	6916370	6916370	+	Missense_Mutation	SNP	G	G	C			TCGA-3B-A9HJ-01A-11D-A387-09	TCGA-3B-A9HJ-10A-01D-A38A-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	18382739-a33f-49e6-856f-fcf720c49363	dd637e7a-2892-4bd4-b8ad-ef88f676791d	g.chr19:6916370G>C	ENST00000312053.4	+	12	1448	c.1411G>C	c.(1411-1413)Gaa>Caa	p.E471Q	EMR1_ENST00000381404.4_Missense_Mutation_p.E419Q|EMR1_ENST00000381407.5_Missense_Mutation_p.E330Q|EMR1_ENST00000450315.3_Missense_Mutation_p.E294Q|EMR1_ENST00000250572.8_Missense_Mutation_p.E471Q	NM_001974.4	NP_001965.3	Q14246	EMR1_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 1	471	Ser/Thr-rich.				cell adhesion (GO:0007155)|G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(31)|ovary(3)|prostate(1)|skin(8)	62	all_hematologic(4;0.166)					TGAGGAATCTGAATCCACAGG	0.443													ENSG00000174837																																					0													153.0	134.0	140.0					19																	6916370		2203	4300	6503	SO:0001583	missense	0			-	X81479	CCDS12175.1, CCDS58643.1, CCDS58644.1, CCDS58645.1, CCDS58646.1	19p13.3	2014-08-08	2003-11-26					"""-"", ""GPCR / Class B : Orphans"""	3336	protein-coding gene	gene with protein product		600493	"""egf-like module containing, mucin-like, hormone receptor-like sequence 1"""	TM7LN3		7601460, 9500513	Standard	NM_001974		Approved		uc002mfw.4	Q14246		ENST00000312053.4:c.1411G>C	19.37:g.6916370G>C	ENSP00000311545:p.Glu471Gln		A6NHV2|B7Z486|B7Z489|E7EPX9|E9PD45|H9KV79|Q2I7G5|Q6ZMN0|Q8NGA7	Missense_Mutation	SNP	pfam_GPCR_2_secretin-like,pfam_EGF-like_Ca-bd_dom,pfam_GPS_dom,smart_EGF-like_Ca-bd_dom,smart_EG-like_dom,smart_GPS_dom,pfscan_EG-like_dom,pfscan_GPS_dom,pfscan_GPCR_2-like,prints_GPCR_2_EMR1_rcpt,prints_GPCR_2_secretin-like	p.E471Q	ENST00000312053.4	37	c.1411	CCDS12175.1	19	.	.	.	.	.	.	.	.	.	.	G	7.596	0.671802	0.14776	.	.	ENSG00000174837	ENST00000543519;ENST00000312053;ENST00000381404;ENST00000250572;ENST00000381407;ENST00000450315	T;T;T;T;T	0.78364	-1.15;-1.17;-1.17;0.01;0.34	4.15	-0.476	0.12100	.	.	.	.	.	T	0.74718	0.3753	M	0.62723	1.935	0.09310	N	1	P;P;P;P;P	0.51653	0.947;0.893;0.763;0.868;0.868	P;B;B;B;B	0.49752	0.621;0.293;0.387;0.23;0.312	T	0.63116	-0.6709	9	0.20046	T	0.44	.	6.5735	0.22551	0.4263:0.0:0.5737:0.0	.	294;330;471;419;471	E7EPX9;B7Z486;Q14246-2;E9PD45;Q14246	.;.;.;.;EMR1_HUMAN	Q	471;471;419;471;330;294	ENSP00000311545:E471Q;ENSP00000370811:E419Q;ENSP00000250572:E471Q;ENSP00000370814:E330Q;ENSP00000405974:E294Q	ENSP00000250572:E471Q	E	+	1	0	EMR1	6867370	0.000000	0.05858	0.003000	0.11579	0.104000	0.19210	0.285000	0.18883	-0.144000	0.11314	0.591000	0.81541	GAA	-	EMR1	-	NULL		0.443	EMR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	EMR1	HGNC	protein_coding	OTTHUMT00000458485.1	0	0		32	32		0.00		G			6916370	+1	10		89		tier1	no_errors	ENST00000312053	ensembl	human	known	74_37	missense	10.10		SNP	0.005	C	10	89
MIR510	574515	genome.wustl.edu	37	X	146353918	146353918	+	RNA	SNP	G	G	T			TCGA-3B-A9HJ-01A-11D-A387-09	TCGA-3B-A9HJ-10A-01D-A38A-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	18382739-a33f-49e6-856f-fcf720c49363	dd637e7a-2892-4bd4-b8ad-ef88f676791d	g.chrX:146353918G>T	ENST00000384909.1	-	0	8					NR_030237.1				microRNA 510																		CTCCTGAGTAGGACACCACAC	0.388													ENSG00000207641																																					0													124.0	94.0	103.0					X																	146353918		1568	3582	5150			0			-			Xq27.3	2011-09-12		2008-12-18	ENSG00000207641	ENSG00000207641		"""ncRNAs / Micro RNAs"""	32147	non-coding RNA	RNA, micro		300866		MIRN510			Standard	NR_030237		Approved	hsa-mir-510	uc022cga.1				X.37:g.146353918G>T				R	SNP	-	NULL	ENST00000384909.1	37	NULL		X																																																																																			-	MIR510	-	-		0.388	MIR510-201	KNOWN	basic	miRNA	MIR510	HGNC	miRNA		0	0		17	17		0.00		G	NR_030237		146353918	-1	5		30		tier1	no_errors	ENST00000384909	ensembl	human	known	74_37	rna	14.29		SNP	0.001	T	5	30
OR7D4	125958	genome.wustl.edu	37	19	9325248	9325248	+	Missense_Mutation	SNP	C	C	T			TCGA-3B-A9HJ-01A-11D-A387-09	TCGA-3B-A9HJ-10A-01D-A38A-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	18382739-a33f-49e6-856f-fcf720c49363	dd637e7a-2892-4bd4-b8ad-ef88f676791d	g.chr19:9325248C>T	ENST00000308682.2	-	1	294	c.266G>A	c.(265-267)aGc>aAc	p.S89N		NM_001005191.2	NP_001005191.1	Q8NG98	OR7D4_HUMAN	olfactory receptor, family 7, subfamily D, member 4	89						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(2)|skin(3)|stomach(1)	26						GATGTCTTTGCTCCGTGCCTG	0.498													ENSG00000174667																																					0													81.0	72.0	75.0					19																	9325248		2203	4300	6503	SO:0001583	missense	0			-		CCDS32901.1	19p13.2	2013-12-17		2004-03-10	ENSG00000174667	ENSG00000174667		"""GPCR / Class A : Olfactory receptors"""	8380	protein-coding gene	gene with protein product		611538		OR7D4P			Standard	NM_001005191		Approved	hg105, OR19-B	uc002mla.2	Q8NG98	OTTHUMG00000179936	ENST00000308682.2:c.266G>A	19.37:g.9325248C>T	ENSP00000310488:p.Ser89Asn		A8CAH8|A8CAH9|A8CAI0|A8CAI1|B9EH79	Missense_Mutation	SNP	pfam_GPCR_Rhodpsn,pfam_7TM_GPCR_olfarory/Srsx,pfscan_GPCR_Rhodpsn_7TM,prints_Olfact_rcpt,prints_GPCR_Rhodpsn	p.S89N	ENST00000308682.2	37	c.266	CCDS32901.1	19	.	.	.	.	.	.	.	.	.	.	C	0.020	-1.446329	0.01089	.	.	ENSG00000174667	ENST00000308682	T	0.03004	4.08	4.0	-3.63	0.04529	GPCR, rhodopsin-like superfamily (1);	0.364425	0.27027	N	0.021288	T	0.01765	0.0056	N	0.25144	0.715	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.42361	-0.9456	10	0.23302	T	0.38	.	1.5991	0.02670	0.1177:0.3361:0.2313:0.3149	.	89	Q8NG98	OR7D4_HUMAN	N	89	ENSP00000310488:S89N	ENSP00000310488:S89N	S	-	2	0	OR7D4	9186248	0.000000	0.05858	0.001000	0.08648	0.011000	0.07611	-3.284000	0.00527	-0.364000	0.08088	-1.379000	0.01178	AGC	-	OR7D4	-	pfam_GPCR_Rhodpsn,pfam_7TM_GPCR_olfarory/Srsx,pfscan_GPCR_Rhodpsn_7TM		0.498	OR7D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	OR7D4	HGNC	protein_coding	OTTHUMT00000449004.1	0	0		51	51		0.00		C			9325248	-1	15		113		tier1	no_errors	ENST00000308682	ensembl	human	known	74_37	missense	11.72		SNP	0.000	T	15	113
FAM153C	653316	genome.wustl.edu	37	5	177457621	177457621	+	Intron	SNP	G	G	A			TCGA-3B-A9HJ-01A-11D-A387-09	TCGA-3B-A9HJ-10A-01D-A38A-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	18382739-a33f-49e6-856f-fcf720c49363	dd637e7a-2892-4bd4-b8ad-ef88f676791d	g.chr5:177457621G>A	ENST00000507848.1	+	3	145				FAM153C_ENST00000398106.2_Intron|FAM153C_ENST00000511189.1_Missense_Mutation_p.E10K			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)			TTGTTGCCTCGAAGGTATGTA	0.393													ENSG00000204677																																					0																																										SO:0001627	intron_variant	0			-	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.-56-4476G>A	5.37:g.177457621G>A			A4IF33|B2RUV5|B7ZW12	Missense_Mutation	SNP	prints_FAM153	p.E10K	ENST00000507848.1	37	c.28		5	.	.	.	.	.	.	.	.	.	.	G	7.770	0.707352	0.15239	.	.	ENSG00000204677	ENST00000511856;ENST00000511189	.	.	.	0.472	-0.944	0.10392	.	.	.	.	.	T	0.28830	0.0715	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.32322	-0.9911	4	0.87932	D	0	.	.	.	.	.	.	.	.	K	10	.	ENSP00000426621:E10K	E	+	1	0	FAM153C	177390227	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	-0.882000	0.04174	-1.431000	0.01982	-1.310000	0.01310	GAA	-	FAM153C	-	NULL		0.393	FAM153C-002	KNOWN	basic|appris_candidate	protein_coding	FAM153C	HGNC	protein_coding	OTTHUMT00000373556.1	0	0		51	51		0.00		G	NM_001079527		177457621	+1	11		118		tier1	no_errors	ENST00000511189	ensembl	human	novel	74_37	missense	8.53		SNP	0.000	A	11	118
VAPB	9217	genome.wustl.edu	37	20	57020740	57020741	+	3'UTR	INS	-	-	TGTG	rs138225455|rs146547877|rs200528716		TCGA-3B-A9HJ-01A-11D-A387-09	TCGA-3B-A9HJ-10A-01D-A38A-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	18382739-a33f-49e6-856f-fcf720c49363	dd637e7a-2892-4bd4-b8ad-ef88f676791d	g.chr20:57020740_57020741insTGTG	ENST00000475243.1	+	0	2519_2520				VAPB_ENST00000265619.2_3'UTR	NM_004738.4	NP_004729.1	O95292	VAPB_HUMAN	VAMP (vesicle-associated membrane protein)-associated protein B and C						activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cell death (GO:0008219)|cellular calcium ion homeostasis (GO:0006874)|endoplasmic reticulum unfolded protein response (GO:0030968)|modulation by virus of host morphology or physiology (GO:0019048)|positive regulation of viral genome replication (GO:0045070)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	beta-tubulin binding (GO:0048487)|enzyme binding (GO:0019899)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|structural molecule activity (GO:0005198)			kidney(2)|lung(3)|prostate(1)	6	Lung NSC(12;0.000615)|all_lung(29;0.00186)		BRCA - Breast invasive adenocarcinoma(13;6.2e-12)|Epithelial(14;3.7e-08)|all cancers(14;3.88e-07)			TGATTTAACTCtgtgtgtgtgt	0.351													ENSG00000124164																																					0																																										SO:0001624	3_prime_UTR_variant	0				AF086628	CCDS33498.1, CCDS56198.1	20q13	2014-09-17			ENSG00000124164	ENSG00000124164			12649	protein-coding gene	gene with protein product		605704				9920726	Standard	NM_004738		Approved	VAP-B, VAP-C, ALS8	uc002xza.3	O95292	OTTHUMG00000032840	ENST00000475243.1:c.*1450->TGTG	20.37:g.57020745_57020748dupTGTG			A2A2F2|O95293|Q9P0H0	R	INS	-	NULL	ENST00000475243.1	37	NULL	CCDS33498.1	20																																																																																				VAPB	-	-		0.351	VAPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	VAPB	HGNC	protein_coding	OTTHUMT00000079875.2	0	0		9	9		0.00		-			57020741	+1	5		29		tier1	no_errors	ENST00000265619	ensembl	human	known	74_37	rna	14.71		INS	0.000:0.001	TGTG	5	29
DUSP10	11221	genome.wustl.edu	37	1	221875156	221875157	+	3'UTR	INS	-	-	A	rs571834010		TCGA-3B-A9HJ-01A-11D-A387-09	TCGA-3B-A9HJ-10A-01D-A38A-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	18382739-a33f-49e6-856f-fcf720c49363	dd637e7a-2892-4bd4-b8ad-ef88f676791d	g.chr1:221875156_221875157insA	ENST00000366899.3	-	0	2284_2285				DUSP10_ENST00000468085.1_5'UTR|DUSP10_ENST00000323825.3_3'UTR|DUSP10_ENST00000544095.1_3'UTR	NM_007207.4	NP_009138.1	Q9Y6W6	DUS10_HUMAN	dual specificity phosphatase 10						inactivation of MAPK activity (GO:0000188)|JNK cascade (GO:0007254)|negative regulation of JNK cascade (GO:0046329)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of respiratory burst involved in inflammatory response (GO:0060266)|oligodendrocyte differentiation (GO:0048709)|protein dephosphorylation (GO:0006470)|regulation of adaptive immune response (GO:0002819)|response to lipopolysaccharide (GO:0032496)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	MAP kinase phosphatase activity (GO:0033549)|MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|phosphatase activity (GO:0016791)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(16)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				GBM - Glioblastoma multiforme(131;0.0103)		CCCAGAGAAGGAAAAAAAAAAA	0.351													ENSG00000143507																																					0																																										SO:0001624	3_prime_UTR_variant	0				AB026436	CCDS1528.1	1q41	2011-06-09			ENSG00000143507	ENSG00000143507		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"""	3065	protein-coding gene	gene with protein product		608867				10391943, 10597297	Standard	NM_007207		Approved	MKP-5, MKP5	uc001hmy.2	Q9Y6W6	OTTHUMG00000037269	ENST00000366899.3:c.*598->T	1.37:g.221875167_221875167dupA			D3DTB4|Q6GSI4|Q9H9Z5	R	INS	-	NULL	ENST00000366899.3	37	NULL	CCDS1528.1	1																																																																																				DUSP10	-	-		0.351	DUSP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DUSP10	HGNC	protein_coding	OTTHUMT00000090716.1	0	0		17	17		0.00		-	NM_007207		221875157	-1	4		21		tier1	no_errors	ENST00000468085	ensembl	human	known	74_37	rna	16.00		INS	0.002:0.000	A	4	21
SMG6	23293	genome.wustl.edu	37	17	1964759	1964760	+	3'UTR	INS	-	-	G	rs36097261|rs397730291|rs145926620	byFrequency	TCGA-3B-A9HJ-01A-11D-A387-09	TCGA-3B-A9HJ-10A-01D-A38A-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	18382739-a33f-49e6-856f-fcf720c49363	dd637e7a-2892-4bd4-b8ad-ef88f676791d	g.chr17:1964759_1964760insG	ENST00000263073.6	-	0	4336_4337				SMG6_ENST00000354901.4_3'UTR|SMG6_ENST00000573166.1_5'UTR|SMG6_ENST00000544865.1_3'UTR|SMG6_ENST00000536871.2_3'UTR	NM_017575.4	NP_060045.4	Q86US8	EST1A_HUMAN	SMG6 nonsense mediated mRNA decay factor						gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|telomere maintenance (GO:0000723)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|telomerase holoenzyme complex (GO:0005697)	endoribonuclease activity (GO:0004521)|metal ion binding (GO:0046872)|telomeric DNA binding (GO:0042162)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(10)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						AACGGTTCCACGGGGGGGGGGC	0.629													ENSG00000070366	|||unknown(HR)	2696	0.538339	0.5234	0.5821	5008	,	,		16576	0.5923		0.5258	False		,,,				2504	0.4847				Melanoma(59;28 1088 11621 25887 46638 50814)												0																																										SO:0001624	3_prime_UTR_variant	0				AB018275	CCDS11016.1, CCDS58498.1	17p13.3	2013-07-02	2013-07-02	2006-02-16	ENSG00000070366	ENSG00000070366			17809	protein-coding gene	gene with protein product	"""EST1 telomerase component homolog A (S. cerevisiae)"""	610963	"""chromosome 17 open reading frame 31"", ""smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	C17orf31		12676087, 12699629	Standard	NM_017575		Approved	KIAA0732, SMG-6, EST1A	uc002fub.1	Q86US8	OTTHUMG00000177578	ENST00000263073.6:c.*27->C	17.37:g.1964769_1964769dupG			B7Z874|O94837|Q86VH6|Q9UF60	R	INS	-	NULL	ENST00000263073.6	37	NULL	CCDS11016.1	17																																																																																				SMG6	-	-		0.629	SMG6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SMG6	HGNC	protein_coding	OTTHUMT00000437826.3	0	0		44	44		0.00		-			1964760	-1	14		61		tier1	no_errors	ENST00000570756	ensembl	human	known	74_37	rna	18.67		INS	0.024:0.027	G	14	61
TROVE2	6738	genome.wustl.edu	37	1	193053996	193053997	+	3'UTR	INS	-	-	A	rs201693727|rs78476132|rs549404223		TCGA-3B-A9HJ-01A-11D-A387-09	TCGA-3B-A9HJ-10A-01D-A38A-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	18382739-a33f-49e6-856f-fcf720c49363	dd637e7a-2892-4bd4-b8ad-ef88f676791d	g.chr1:193053996_193053997insA	ENST00000367446.3	+	0	1962_1963				TROVE2_ENST00000367445.3_Intron|TROVE2_ENST00000367443.1_Intron|TROVE2_ENST00000432079.1_3'UTR|TROVE2_ENST00000460715.2_3'UTR|TROVE2_ENST00000367441.1_3'UTR|TROVE2_ENST00000367444.3_Intron|TROVE2_ENST00000400968.2_3'UTR	NM_004600.5	NP_004591.2	P10155	RO60_HUMAN	TROVE domain family, member 2						cilium morphogenesis (GO:0060271)|immune system development (GO:0002520)|response to UV (GO:0009411)|smoothened signaling pathway (GO:0007224)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	metal ion binding (GO:0046872)|RNA binding (GO:0003723)|U2 snRNA binding (GO:0030620)			biliary_tract(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(7)|prostate(2)|urinary_tract(1)	21						TTACCTTACTGAAAAAAAAAAA	0.361													ENSG00000116747																																					0																																										SO:0001624	3_prime_UTR_variant	0				BC036658	CCDS41449.1, CCDS1379.1, CCDS41450.1, CCDS41450.2, CCDS53451.1	1q31	2014-08-06	2005-06-14	2005-06-14	ENSG00000116747	ENSG00000116747			11313	protein-coding gene	gene with protein product		600063	"""Sjogren syndrome antigen A2 (60kDa, ribonucleoprotein autoantigen SS-A/Ro)"""	SSA2		8188321	Standard	NM_001042369		Approved	Ro60	uc001gss.3	P10155	OTTHUMG00000035675	ENST00000367446.3:c.*136->A	1.37:g.193054007_193054007dupA			B2RBB9|Q5LJ98|Q5LJ99|Q5LJA0|Q86WL3|Q86WL4|Q92787|Q9H1W6	R	INS	-	NULL	ENST00000367446.3	37	NULL	CCDS1379.1	1																																																																																				TROVE2	-	-		0.361	TROVE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	TROVE2	HGNC	protein_coding	OTTHUMT00000086688.1	0	0		23	23		0.00		-	NM_004600		193053997	+1	6		37		tier1	no_errors	ENST00000460715	ensembl	human	known	74_37	rna	13.95		INS	0.000:0.000	A	6	37
RCVRN	5957	genome.wustl.edu	37	17	9801316	9801317	+	3'UTR	INS	-	-	GTGTGTGTGC	rs531533066|rs376748693	byFrequency	TCGA-3B-A9HJ-01A-11D-A387-09	TCGA-3B-A9HJ-10A-01D-A38A-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	18382739-a33f-49e6-856f-fcf720c49363	dd637e7a-2892-4bd4-b8ad-ef88f676791d	g.chr17:9801316_9801317insGTGTGTGTGC	ENST00000226193.5	-	0	1138_1139				RCVRN_ENST00000570909.3_5'UTR	NM_002903.2	NP_002894.1	P35243	RECO_HUMAN	recoverin						phototransduction, visible light (GO:0007603)|positive regulation of guanylate cyclase activity (GO:0031284)|regulation of calcium ion transport (GO:0051924)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)|visual perception (GO:0007601)	dendrite (GO:0030425)	calcium ion binding (GO:0005509)|calcium sensitive guanylate cyclase activator activity (GO:0008048)			endometrium(1)|kidney(1)|large_intestine(6)|lung(3)|upper_aerodigestive_tract(1)	12						tgtgtgtgtgtgcgcgcgcgtg	0.589													ENSG00000109047																																					0																																										SO:0001624	3_prime_UTR_variant	0				BC001720	CCDS11151.1	17p13.1	2013-01-10		2006-09-26	ENSG00000109047	ENSG00000109047		"""EF-hand domain containing"""	9937	protein-coding gene	gene with protein product		179618		RCV1		1387789, 12507501, 1467959, 12789533	Standard	NM_002903		Approved		uc002gme.1	P35243	OTTHUMG00000130268	ENST00000226193.5:c.*96->GCACACACAC	17.37:g.9801316_9801317insGTGTGTGTGC			Q53XL0	R	INS	-	NULL	ENST00000226193.5	37	NULL	CCDS11151.1	17																																																																																				RCVRN	-	-		0.589	RCVRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RCVRN	HGNC	protein_coding	OTTHUMT00000252600.2									-	NM_002903		9801317	-1					tier1	no_errors	ENST00000570909	ensembl	human	putative	74_37	rna			INS	0.000:0.000	GTGTGTGTGC		
SH3PXD2B	285590	genome.wustl.edu	37	5	171866699	171866704	+	Intron	DEL	CACACA	CACACA	-			TCGA-3B-A9HJ-01A-11D-A387-09	TCGA-3B-A9HJ-10A-01D-A38A-09	CACACA	CACACA					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	18382739-a33f-49e6-856f-fcf720c49363	dd637e7a-2892-4bd4-b8ad-ef88f676791d	g.chr5:171866699_171866704delCACACA	ENST00000311601.5	-	1	246				AC011407.1_ENST00000401308.1_RNA|SH3PXD2B_ENST00000519643.1_Intron	NM_001017995.2	NP_001017995.1	A1X283	SPD2B_HUMAN	SH3 and PX domains 2B						adipose tissue development (GO:0060612)|bone development (GO:0060348)|cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|eye development (GO:0001654)|heart development (GO:0007507)|podosome assembly (GO:0071800)|positive regulation of fat cell differentiation (GO:0045600)|protein localization to membrane (GO:0072657)|skeletal system development (GO:0001501)|superoxide metabolic process (GO:0006801)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|podosome (GO:0002102)	phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)|SH2 domain binding (GO:0042169)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(12)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	36	Renal(175;0.000159)|Lung NSC(126;0.011)|all_lung(126;0.0175)	Medulloblastoma(196;0.0207)|all_neural(177;0.0625)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			cgcgcgcgcacacacacacacacaca	0.524													ENSG00000216127																																					0																																										SO:0001627	intron_variant	0				AK095834	CCDS34291.1	5q35.2	2008-02-05	2006-02-13	2006-02-13	ENSG00000174705	ENSG00000174705			29242	protein-coding gene	gene with protein product		613293	"""KIAA1295"""	KIAA1295		10718198	Standard	NM_001017995		Approved	FLJ20831	uc003mbr.3	A1X283	OTTHUMG00000163280	ENST00000311601.5:c.75+14577TGTGTG>-	5.37:g.171866705_171866710delCACACA			B6F0V2|Q9P2Q1	R	DEL	-	NULL	ENST00000311601.5	37	NULL	CCDS34291.1	5																																																																																				AC011407.1	-	-		0.524	SH3PXD2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ENSG00000216127	Clone_based_ensembl_gene	protein_coding	OTTHUMT00000372449.1									CACACA	NM_017963		171866704	-1					tier1	no_errors	ENST00000401308	ensembl	human	novel	74_37	rna			DEL	0.000:0.000:0.000:0.000:0.001:0.000	-		
ZSWIM4	65249	genome.wustl.edu	37	19	13919958	13919958	+	Silent	SNP	G	G	A			TCGA-3B-A9HJ-01A-11D-A387-09	TCGA-3B-A9HJ-10A-01D-A38A-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	18382739-a33f-49e6-856f-fcf720c49363	dd637e7a-2892-4bd4-b8ad-ef88f676791d	g.chr19:13919958G>A	ENST00000254323.2	+	5	1125	c.936G>A	c.(934-936)caG>caA	p.Q312Q	ZSWIM4_ENST00000440752.2_Silent_p.Q29Q	NM_023072.2	NP_075560.2	Q9H7M6	ZSWM4_HUMAN	zinc finger, SWIM-type containing 4	312							zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27			OV - Ovarian serous cystadenocarcinoma(19;2.94e-23)|Epithelial(5;4.58e-19)			AGTTCCTGCAGGACACGCGCC	0.682													ENSG00000132003																																					0													45.0	50.0	48.0					19																	13919958		2202	4300	6502	SO:0001819	synonymous_variant	0			-	AK022283	CCDS32924.1	19p13.13	2012-02-23			ENSG00000132003	ENSG00000132003		"""Zinc fingers, SWIM-type"""	25704	protein-coding gene	gene with protein product							Standard	NM_023072		Approved	FLJ12221	uc002mxh.1	Q9H7M6		ENST00000254323.2:c.936G>A	19.37:g.13919958G>A				Silent	SNP	pfscan_Znf_SWIM	p.Q312	ENST00000254323.2	37	c.936	CCDS32924.1	19																																																																																			-	ZSWIM4	-	NULL		0.682	ZSWIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ZSWIM4	HGNC	protein_coding	OTTHUMT00000457457.1	0	0		47	47		0.00		G	XM_031342		13919958	+1	18		91		tier1	no_errors	ENST00000254323	ensembl	human	known	74_37	silent	16.51		SNP	1.000	A	18	91
CDH13	1012	genome.wustl.edu	37	16	82875704	82875747	+	Intron	DEL	TATATATATATATGTATATATATATATATATATATATATACACA	TATATATATATATGTATATATATATATATATATATATATACACA	-	rs373030820|rs376507307|rs62035171|rs370767262|rs373196037|rs369963241|rs62035173|rs189985116|rs62035174|rs555668577|rs62035172|rs12933953|rs12446276|rs146750065|rs370949442|rs12446273|rs543969962|rs377363592	byFrequency	TCGA-3B-A9HJ-01A-11D-A387-09	TCGA-3B-A9HJ-10A-01D-A38A-09	TATATATATATATGTATATATATATATATATATATATATACACA	TATATATATATATGTATATATATATATATATATATATATACACA					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	18382739-a33f-49e6-856f-fcf720c49363	dd637e7a-2892-4bd4-b8ad-ef88f676791d	g.chr16:82875704_82875747delTATATATATATATGTATATATATATATATATATATATATACACA	ENST00000566620.1	+	2	335				RN7SL134P_ENST00000579756.1_RNA|CDH13_ENST00000268613.10_Intron|AC099506.1_ENST00000408468.1_RNA|CDH13_ENST00000428848.3_Intron|CDH13_ENST00000565636.1_Intron|CDH13_ENST00000431540.3_Intron|CDH13_ENST00000567445.1_Intron|CDH13_ENST00000446376.2_Intron	NM_001220488.1|NM_001220489.1|NM_001220490.1|NM_001257.4	NP_001207417.1|NP_001207418.1|NP_001207419.1|NP_001248.1	P55290	CAD13_HUMAN	cadherin 13						adherens junction organization (GO:0034332)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|endothelial cell migration (GO:0043542)|homophilic cell adhesion (GO:0007156)|keratinocyte proliferation (GO:0043616)|lamellipodium assembly (GO:0030032)|localization within membrane (GO:0051668)|low-density lipoprotein particle mediated signaling (GO:0055096)|mitotic cell cycle (GO:0000278)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell proliferation (GO:0008285)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|Rac protein signal transduction (GO:0016601)|regulation of cell growth (GO:0001558)|regulation of endocytosis (GO:0030100)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|Rho protein signal transduction (GO:0007266)|sprouting angiogenesis (GO:0002040)	anchored component of membrane (GO:0031225)|caveola (GO:0005901)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	adiponectin binding (GO:0055100)|cadherin binding (GO:0045296)|calcium ion binding (GO:0005509)|lipoprotein particle binding (GO:0071813)|low-density lipoprotein particle binding (GO:0030169)			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)		tacatatatatatatatatatatgtatatatatatatatatatatatatacacatatatatata	0.299													ENSG00000221395																																					0																																										SO:0001627	intron_variant	0				U59288	CCDS56009.1, CCDS56010.1, CCDS58485.1, CCDS58486.1, CCDS58487.1	16q23.3	2013-08-27	2013-08-27			ENSG00000140945		"""Cadherins / Major cadherins"""	1753	protein-coding gene	gene with protein product	"""T-cadherin"", ""H-cadherin (heart)"""	601364				8673923, 9468307	Standard	NM_001257		Approved	CDHH	uc010vns.2	P55290		ENST00000566620.1:c.46-16220TATATATATATATGTATATATATATATATATATATATATACACA>-	16.37:g.82875704_82875747delTATATATATATATGTATATATATATATATATATATATATACACA			A8W476|A8W477|B7Z590|C9JRI6|J3KN62|Q6GTW4|Q8TBX3	R	DEL	-	NULL	ENST00000566620.1	37	NULL	CCDS58486.1	16																																																																																				AC099506.1	-	-		0.299	CDH13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ENSG00000221395	Clone_based_ensembl_gene	protein_coding	OTTHUMT00000432917.1									TATATATATATATGTATATATATATATATATATATATATACACA	NM_001257		82875747	+1					tier1	no_errors	ENST00000408468	ensembl	human	novel	74_37	rna			DEL	0.008:0.000:0.000:0.000:0.000:0.000:0.000:0.001:0.001:0.001:0.000:0.001:0.000:0.000:0.000:0.000:0.001:0.001:0.001:0.000:0.000:0.000:0.001:0.000:0.000:0.000:0.000:0.000:0.000:0.000:0.000:0.003:0.004:0.008:0.010:0.010:0.011:0.010:0.008:0.008:0.004:0.003:0.002:0.004	-		
AC010543.1	0	genome.wustl.edu	37	16	57908380	57908381	+	RNA	INS	-	-	A	rs57339735	byFrequency	TCGA-3B-A9HJ-01A-11D-A387-09	TCGA-3B-A9HJ-10A-01D-A38A-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	18382739-a33f-49e6-856f-fcf720c49363	dd637e7a-2892-4bd4-b8ad-ef88f676791d	g.chr16:57908380_57908381insA	ENST00000580935.1	-	0	53_54																											tacttaagcttaaaaaaaaaaa	0.307													ENSG00000265209																																					0																																												0																																16.37:g.57908391_57908391dupA				R	INS	-	NULL	ENST00000580935.1	37	NULL		16																																																																																				AC010543.1	-	-		0.307	AC010543.1-201	NOVEL	basic	miRNA	ENSG00000265209	Clone_based_ensembl_gene	miRNA		0	0		12	12		0.00		-			57908381	-1	5		32		tier1	no_errors	ENST00000580935	ensembl	human	novel	74_37	rna	13.51		INS	0.000:0.000	A	5	32
OR7D4	125958	genome.wustl.edu	37	19	9324756	9324756	+	Missense_Mutation	SNP	C	C	T			TCGA-3B-A9HJ-01A-11D-A387-09	TCGA-3B-A9HJ-10A-01D-A38A-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	18382739-a33f-49e6-856f-fcf720c49363	dd637e7a-2892-4bd4-b8ad-ef88f676791d	g.chr19:9324756C>T	ENST00000308682.2	-	1	786	c.758G>A	c.(757-759)gGa>gAa	p.G253E		NM_001005191.2	NP_001005191.1	Q8NG98	OR7D4_HUMAN	olfactory receptor, family 7, subfamily D, member 4	253						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(2)|skin(3)|stomach(1)	26						AAGTCCTGTTCCATAGAACAA	0.527													ENSG00000174667																																					0													63.0	58.0	60.0					19																	9324756		2203	4300	6503	SO:0001583	missense	0			-		CCDS32901.1	19p13.2	2013-12-17		2004-03-10	ENSG00000174667	ENSG00000174667		"""GPCR / Class A : Olfactory receptors"""	8380	protein-coding gene	gene with protein product		611538		OR7D4P			Standard	NM_001005191		Approved	hg105, OR19-B	uc002mla.2	Q8NG98	OTTHUMG00000179936	ENST00000308682.2:c.758G>A	19.37:g.9324756C>T	ENSP00000310488:p.Gly253Glu		A8CAH8|A8CAH9|A8CAI0|A8CAI1|B9EH79	Missense_Mutation	SNP	pfam_GPCR_Rhodpsn,pfam_7TM_GPCR_olfarory/Srsx,pfscan_GPCR_Rhodpsn_7TM,prints_Olfact_rcpt,prints_GPCR_Rhodpsn	p.G253E	ENST00000308682.2	37	c.758	CCDS32901.1	19	.	.	.	.	.	.	.	.	.	.	C	12.48	1.951132	0.34471	.	.	ENSG00000174667	ENST00000308682	T	0.39056	1.1	3.84	3.84	0.44239	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000025	T	0.75532	0.3862	H	0.98849	4.35	0.20764	N	0.999855	D	0.76494	0.999	D	0.79784	0.993	T	0.71255	-0.4647	10	0.59425	D	0.04	.	10.2925	0.43605	0.1976:0.8024:0.0:0.0	.	253	Q8NG98	OR7D4_HUMAN	E	253	ENSP00000310488:G253E	ENSP00000310488:G253E	G	-	2	0	OR7D4	9185756	0.013000	0.17824	0.906000	0.35671	0.297000	0.27493	0.536000	0.23129	2.172000	0.68678	0.205000	0.17691	GGA	-	OR7D4	-	pfam_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_7TM		0.527	OR7D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	OR7D4	HGNC	protein_coding	OTTHUMT00000449004.1	0	0		38	38		0.00		C			9324756	-1	18		129		tier1	no_errors	ENST00000308682	ensembl	human	known	74_37	missense	12.24		SNP	0.295	T	18	129
UFL1	23376	genome.wustl.edu	37	6	96969559	96969578	+	5'Flank	DEL	AACCCCCAGCGCCGCGGTAC	AACCCCCAGCGCCGCGGTAC	-	rs3841018|rs112373805|rs67707404	byFrequency	TCGA-3B-A9HJ-01A-11D-A387-09	TCGA-3B-A9HJ-10A-01D-A38A-09	AACCCCCAGCGCCGCGGTAC	AACCCCCAGCGCCGCGGTAC					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	18382739-a33f-49e6-856f-fcf720c49363	dd637e7a-2892-4bd4-b8ad-ef88f676791d	g.chr6:96969559_96969578delAACCCCCAGCGCCGCGGTAC	ENST00000369278.4	+	0	0				UFL1_ENST00000461673.1_3'UTR|UFL1-AS1_ENST00000430796.1_RNA	NM_015323.4	NP_056138.1	O94874	UFL1_HUMAN	UFM1-specific ligase 1						negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein ubiquitination (GO:0031397)|osteoblast differentiation (GO:0001649)|protein ufmylation (GO:0071569)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)	UFM1 conjugating enzyme activity (GO:0071568)										CGCCGGGAGGAACCCCCAGCGCCGCGGTACAACCACGGCA	0.7													ENSG00000014123		677	0.135184	0.1036	0.1772	5008	,	,		14561	0.0387		0.2157	False		,,,				2504	0.1646																0																																										SO:0001631	upstream_gene_variant	0				BC036379	CCDS5034.1	6q16.3	2011-08-18	2011-08-18	2011-08-18	ENSG00000014123	ENSG00000014123			23039	protein-coding gene	gene with protein product	"""novel LZAP-binding protein"", ""Regulator of CDK5RAP3 and DDRGK1"""	613372	"""KIAA0776"""	KIAA0776		20018847, 20164180, 20228063, 20531390	Standard	NM_015323		Approved	NLBP, Maxer, RCAD	uc003por.3	O94874	OTTHUMG00000015238		6.37:g.96969559_96969578delAACCCCCAGCGCCGCGGTAC	Exception_encountered		A0PJ53|B4DJ57|C0H5X5|Q8N765|Q9NTQ0	R	DEL	-	NULL	ENST00000369278.4	37	NULL	CCDS5034.1	6																																																																																				UFL1	-	-		0.700	UFL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	UFL1	HGNC	protein_coding	OTTHUMT00000041557.1									AACCCCCAGCGCCGCGGTAC	NM_015323		96969578	+1					tier1	no_errors	ENST00000461673	ensembl	human	known	74_37	rna			DEL	0.000:0.000:0.000:0.000:0.000:0.001:0.001:0.000:0.001:0.001:0.003:0.006:0.006:0.002:0.000:0.000:0.000:0.000:0.000:0.000	-		
IRF2BPL	64207	genome.wustl.edu	37	14	77493780	77493794	+	In_Frame_Del	DEL	TGCTGCTGCTGCTGT	TGCTGCTGCTGCTGT	-	rs377151545|rs28718623|rs71125518|rs28692724	byFrequency	TCGA-3B-A9HJ-01A-11D-A387-09	TCGA-3B-A9HJ-10A-01D-A38A-09	TGCTGCTGCTGCTGT	TGCTGCTGCTGCTGT					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	18382739-a33f-49e6-856f-fcf720c49363	dd637e7a-2892-4bd4-b8ad-ef88f676791d	g.chr14:77493780_77493794delTGCTGCTGCTGCTGT	ENST00000238647.3	-	1	1240_1254	c.342_356delACAGCAGCAGCAGCA	c.(340-357)caacagcagcagcagcag>cag	p.114_119QQQQQQ>Q		NM_024496.3	NP_078772.1	Q9H1B7	I2BPL_HUMAN	interferon regulatory factor 2 binding protein-like	114	Poly-Gln.				development of secondary female sexual characteristics (GO:0046543)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	extracellular space (GO:0005615)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	11						ctgctgctgctgctgctgctgctgttgctgctgct	0.693													ENSG00000119669																																					0																																										SO:0001651	inframe_deletion	0				AJ277365	CCDS9854.1	14q24.3	2011-02-23	2011-02-23	2011-02-23	ENSG00000119669	ENSG00000119669			14282	protein-coding gene	gene with protein product	"""enhanced at puberty 1"""	611720	"""chromosome 14 open reading frame 4"""	C14orf4		11095982, 17627301	Standard	NM_024496		Approved	EAP1, KIAA1865	uc001xsy.4	Q9H1B7		ENST00000238647.3:c.342_356delACAGCAGCAGCAGCA	14.37:g.77493780_77493794delTGCTGCTGCTGCTGT	ENSP00000238647:p.Gln119_Gln123del		Q8NDQ2|Q96JG2|Q9H3I7	In_Frame_Del	DEL	pfam_Interferon_reg_fac2-bd1_2_Znf	p.QQQQQ118in_frame_del	ENST00000238647.3	37	c.356_342	CCDS9854.1	14																																																																																				IRF2BPL	-	pfam_Interferon_reg_fac2-bd1_2_Znf		0.693	IRF2BPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	IRF2BPL	HGNC	protein_coding	OTTHUMT00000414298.1									TGCTGCTGCTGCTGT	NM_024496		77493794	-1					tier1	no_errors	ENST00000238647	ensembl	human	known	74_37	in_frame_del			DEL	0.967:0.974:0.967:0.993:0.991:0.990:1.000:1.000:1.000:0.997:0.987:0.121:0.050:0.052:0.060	-		
FAT3	120114	genome.wustl.edu	37	11	92616273	92616273	+	Silent	SNP	C	C	T			TCGA-3B-A9HJ-01A-11D-A387-09	TCGA-3B-A9HJ-10A-01D-A38A-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	18382739-a33f-49e6-856f-fcf720c49363	dd637e7a-2892-4bd4-b8ad-ef88f676791d	g.chr11:92616273C>T	ENST00000298047.6	+	23	12668	c.12651C>T	c.(12649-12651)gaC>gaT	p.D4217D	FAT3_ENST00000533797.1_Silent_p.D552D|FAT3_ENST00000525166.1_Silent_p.D4067D|FAT3_ENST00000409404.2_Silent_p.D4217D			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	4217					homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				GCAGTGGGGACGGCCGCAACG	0.657										TCGA Ovarian(4;0.039)			ENSG00000165323																																					0													53.0	66.0	62.0					11																	92616273		1976	4146	6122	SO:0001819	synonymous_variant	0			-	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"""Cadherins / Cadherin-related"""	23112	protein-coding gene	gene with protein product	"""cadherin-related family member 10"""	612483	"""FAT tumor suppressor homolog 3 (Drosophila)"""			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.12651C>T	11.37:g.92616273C>T			B5MDB0|Q96AU6	Silent	SNP	pfam_Cadherin,pfam_Laminin_G,pfam_EGF-like_Ca-bd_dom,superfamily_ConA-like_lec_gl_sf,superfamily_Cadherin-like,smart_Cadherin,smart_EG-like_dom,smart_Laminin_G,smart_EGF-like_Ca-bd_dom,pfscan_EG-like_dom,pfscan_Laminin_G,pfscan_Cadherin,prints_Cadherin	p.D4217	ENST00000298047.6	37	c.12651		11																																																																																			-	FAT3	-	NULL		0.657	FAT3-201	KNOWN	basic	protein_coding	FAT3	HGNC	protein_coding		0	0		40	40		0.00		C	NM_001008781		92616273	+1	8		90		tier1	no_errors	ENST00000298047	ensembl	human	known	74_37	silent	8.16		SNP	0.001	T	8	90
