#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_EVS_AA	i_EVS_All	i_EVS_EA	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains_WU	i_amino_acid_change_WU	i_annotation_transcript	i_build	i_c_position_WU	i_ccds_id	i_chromosome_name_WU	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_default_gene_name_WU	i_deletion_substructures_WU	i_domain_WU	i_ensembl_gene_id	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_name_WU	i_gene_name_source_WU	i_gene_type	i_havana_transcript	i_normal_ref_reads	i_normal_vaf	i_normal_var_reads	i_reference_WU	i_refseq_mrna_id	i_secondary_variant_classification	i_start_WU	i_stop_WU	i_strand_WU	i_transcript_error_WU	i_transcript_name_WU	i_transcript_source_WU	i_transcript_species_WU	i_transcript_status_WU	i_transcript_version_WU	i_trv_type_WU	i_tumor_ref_reads	i_tumor_vaf	i_tumors_var_reads	i_type_WU	i_ucsc_cons_WU	i_variant_WU
ADA	100	genome.wustl.edu	37	20	43255195	43255195	+	Silent	SNP	C	C	T			TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	e5fd7cbd-8fce-49e9-8d2c-d2a2e61367a5	a496949e-c185-40d9-82d2-c09d64d8b77f	g.chr20:43255195C>T	ENST00000372874.4	-	4	398	c.264G>A	c.(262-264)gaG>gaA	p.E88E	ADA_ENST00000537820.1_Silent_p.E88E|ADA_ENST00000464097.1_5'Flank	NM_000022.2	NP_000013.2	P00813	ADA_HUMAN	adenosine deaminase	88					adenosine catabolic process (GO:0006154)|aging (GO:0007568)|cell adhesion (GO:0007155)|dATP catabolic process (GO:0046061)|deoxyadenosine catabolic process (GO:0006157)|embryonic digestive tract development (GO:0048566)|germinal center B cell differentiation (GO:0002314)|histamine secretion (GO:0001821)|hypoxanthine salvage (GO:0043103)|inosine biosynthetic process (GO:0046103)|liver development (GO:0001889)|lung alveolus development (GO:0048286)|negative regulation of adenosine receptor signaling pathway (GO:0060169)|negative regulation of circadian sleep/wake cycle, non-REM sleep (GO:0042323)|negative regulation of inflammatory response (GO:0050728)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of mature B cell apoptotic process (GO:0002906)|negative regulation of mucus secretion (GO:0070256)|negative regulation of penile erection (GO:0060407)|negative regulation of thymocyte apoptotic process (GO:0070244)|nucleobase-containing small molecule metabolic process (GO:0055086)|Peyer's patch development (GO:0048541)|placenta development (GO:0001890)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of germinal center formation (GO:0002636)|positive regulation of heart rate (GO:0010460)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of T cell differentiation in thymus (GO:0033089)|positive regulation of T cell receptor signaling pathway (GO:0050862)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide salvage (GO:0032261)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|purine-containing compound salvage (GO:0043101)|regulation of cell-cell adhesion mediated by integrin (GO:0033632)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to hypoxia (GO:0001666)|response to morphine (GO:0043278)|response to vitamin E (GO:0033197)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|trophectodermal cell differentiation (GO:0001829)|xanthine biosynthetic process (GO:0046111)	cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|lysosome (GO:0005764)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	adenosine deaminase activity (GO:0004000)|purine nucleoside binding (GO:0001883)|zinc ion binding (GO:0008270)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|pancreas(2)|prostate(3)|skin(2)|urinary_tract(1)	18		all_lung(126;1.24e-07)|Lung NSC(126;1.94e-07)|Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)		Adenosine(DB00640)|Dipyridamole(DB00975)|Edetic Acid(DB00974)|Nelarabine(DB01280)|Pentostatin(DB00552)|Theophylline(DB00277)|Vidarabine(DB00194)	TGGCCTTCATCTCTACAAACT	0.577									Adenosine Deaminase Deficiency																													dbGAP											0													173.0	127.0	143.0					20																	43255195		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0	Familial Cancer Database	Severe Combined Immunodeficiency (SCID) due to ADA-deficiency	X02994	CCDS13335.1	20q13.12	2014-09-17			ENSG00000196839	ENSG00000196839	3.5.4.4		186	protein-coding gene	gene with protein product		608958				6198240, 6090454	Standard	NM_000022		Approved		uc002xmj.3	P00813	OTTHUMG00000033081	ENST00000372874.4:c.264G>A	20.37:g.43255195C>T			Q53F92|Q6LA59	Silent	SNP	pfam_A/AMP_deaminase_dom,tigrfam_Ado/ade_deaminase	p.E88	ENST00000372874.4	37	c.264	CCDS13335.1	20																																																																																			ADA	-	pfam_A/AMP_deaminase_dom,tigrfam_Ado/ade_deaminase	ENSG00000196839		0.577	ADA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ADA	HGNC	protein_coding	OTTHUMT00000080509.2	186	0.00	0	C	NM_000022		43255195	43255195	-1	no_errors	ENST00000372874	ensembl	human	known	69_37n	silent	99	34.44	52	SNP	1.000	T
AKAP1	8165	genome.wustl.edu	37	17	55183677	55183677	+	Silent	SNP	G	G	A			TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	e5fd7cbd-8fce-49e9-8d2c-d2a2e61367a5	a496949e-c185-40d9-82d2-c09d64d8b77f	g.chr17:55183677G>A	ENST00000337714.3	+	2	1085	c.852G>A	c.(850-852)gcG>gcA	p.A284A	AKAP1_ENST00000571629.1_Silent_p.A284A|AKAP1_ENST00000539273.1_Silent_p.A284A|AKAP1_ENST00000314126.3_Silent_p.A284A|AKAP1_ENST00000572557.1_Silent_p.A284A	NM_003488.3	NP_003479.1	Q92667	AKAP1_HUMAN	A kinase (PRKA) anchor protein 1	284					blood coagulation (GO:0007596)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(2)|liver(1)|lung(7)|ovary(2)|pancreas(1)|skin(1)	14	Breast(9;5.46e-08)					AGGACGATGCGGCGCCAGCAC	0.587																																						dbGAP											0													89.0	90.0	89.0					17																	55183677		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			X97335	CCDS11594.1	17q22	2013-01-23			ENSG00000121057	ENSG00000121057		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Tudor domain containing"""	367	protein-coding gene	gene with protein product	"""protein kinase anchoring protein 1"", ""dual specificity A-kinase-anchoring protein 1"", ""protein phosphatase 1, regulatory subunit 43"", ""tudor domain containing 17"""	602449		PRKA1		8769136, 7499250	Standard	NM_003488		Approved	AKAP121, AKAP149, SAKAP84, S-AKAP84, AKAP84, D-AKAP1, PPP1R43, TDRD17	uc002iux.3	Q92667	OTTHUMG00000140369	ENST00000337714.3:c.852G>A	17.37:g.55183677G>A			A8K8Q1|D3DTZ0|Q13320|Q9BW14	Silent	SNP	pfam_Tudor,pfam_KH_dom_type_1,smart_KH_dom,smart_Tudor,pfscan_Tudor,pfscan_KH_dom_type_1	p.A284	ENST00000337714.3	37	c.852	CCDS11594.1	17																																																																																			AKAP1	-	NULL	ENSG00000121057		0.587	AKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	AKAP1	HGNC	protein_coding	OTTHUMT00000277069.1	205	0.00	0	G			55183677	55183677	+1	no_errors	ENST00000337714	ensembl	human	known	69_37n	silent	138	43.09	106	SNP	0.001	A
ASB2	51676	genome.wustl.edu	37	14	94417514	94417514	+	Silent	SNP	G	G	A			TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	e5fd7cbd-8fce-49e9-8d2c-d2a2e61367a5	a496949e-c185-40d9-82d2-c09d64d8b77f	g.chr14:94417514G>A	ENST00000315988.4	-	4	1055	c.567C>T	c.(565-567)cgC>cgT	p.R189R	ASB2_ENST00000555019.1_Silent_p.R237R|MIR4506_ENST00000584693.1_RNA|ASB2_ENST00000556337.1_Intron	NM_016150.4	NP_057234.2	Q96Q27	ASB2_HUMAN	ankyrin repeat and SOCS box containing 2	189					intracellular signal transduction (GO:0035556)|myoblast differentiation (GO:0045445)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|signal transduction (GO:0007165)|skeletal muscle cell differentiation (GO:0035914)	Cul5-RING ubiquitin ligase complex (GO:0031466)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|soft_tissue(1)|urinary_tract(1)	27		all_cancers(154;0.13)		COAD - Colon adenocarcinoma(157;0.217)|Epithelial(152;0.232)		CGGTCCAGCCGCGGTTGCAGC	0.612																																						dbGAP											0													70.0	59.0	63.0					14																	94417514		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AF159164	CCDS9915.1, CCDS55940.1	14q31-q32	2013-01-10	2011-01-25					"""Ankyrin repeat domain containing"""	16012	protein-coding gene	gene with protein product		605759	"""ankyrin repeat and SOCS box-containing 2"""				Standard	NM_016150		Approved	ASB-2	uc001ycd.3	Q96Q27		ENST00000315988.4:c.567C>T	14.37:g.94417514G>A			B2RDP9|B4E166|Q9NSU5|Q9Y567	Silent	SNP	pfam_Ankyrin_rpt,pfam_SOCS_C,superfamily_Ankyrin_rpt-contain_dom,smart_Ankyrin_rpt,smart_SOCS_C,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom,pfscan_SOCS_C,prints_Ankyrin_rpt	p.R189	ENST00000315988.4	37	c.567	CCDS9915.1	14																																																																																			ASB2	-	superfamily_Ankyrin_rpt-contain_dom,smart_Ankyrin_rpt,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom	ENSG00000100628		0.612	ASB2-001	KNOWN	basic|CCDS	protein_coding	ASB2	HGNC	protein_coding	OTTHUMT00000412845.1	78	0.00	0	G			94417514	94417514	-1	no_errors	ENST00000315988	ensembl	human	known	69_37n	silent	32	54.93	39	SNP	0.001	A
RIC8A	60626	genome.wustl.edu	37	11	205996	205996	+	5'Flank	SNP	G	G	A			TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	e5fd7cbd-8fce-49e9-8d2c-d2a2e61367a5	a496949e-c185-40d9-82d2-c09d64d8b77f	g.chr11:205996G>A	ENST00000526104.1	+	0	0				BET1L_ENST00000410108.1_Nonsense_Mutation_p.R23*|RP11-304M2.5_ENST00000526963.1_RNA|BET1L_ENST00000486280.1_5'UTR|RIC8A_ENST00000325207.5_5'Flank|BET1L_ENST00000382762.3_Nonsense_Mutation_p.R23*|BET1L_ENST00000332865.6_Nonsense_Mutation_p.R23*|BET1L_ENST00000325147.9_Nonsense_Mutation_p.R23*|BET1L_ENST00000529614.2_Nonsense_Mutation_p.R23*			Q9NPQ8	RIC8A_HUMAN	RIC8 guanine nucleotide exchange factor A						adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|basement membrane organization (GO:0071711)|cell migration involved in gastrulation (GO:0042074)|cell-cell adhesion involved in gastrulation (GO:0070586)|in utero embryonic development (GO:0001701)|vasculature development (GO:0001944)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)			endometrium(3)|kidney(1)|large_intestine(3)|lung(3)|pancreas(1)|prostate(1)|skin(1)	13		all_cancers(49;9.23e-07)|all_epithelial(84;0.000315)|Breast(177;0.00122)|Ovarian(85;0.0202)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;4.45e-27)|Epithelial(43;2.94e-26)|OV - Ovarian serous cystadenocarcinoma(40;5.86e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.105)|LUSC - Lung squamous cell carcinoma(625;0.122)		TCAGCCATTCGCTTGTTCTCC	0.587																																						dbGAP											0													109.0	97.0	101.0					11																	205996		2203	4300	6503	-	-	-	SO:0001631	upstream_gene_variant	0			AK022870	CCDS7690.1, CCDS65982.1	11p15.5	2013-08-05	2013-08-05		ENSG00000177963	ENSG00000177963			29550	protein-coding gene	gene with protein product		609146	"""resistance to inhibitors of cholinesterase 8 homolog A (C. elegans)"""			10985349, 11230166	Standard	XM_005253052		Approved	synembryn, synembryn-A	uc001lof.3	Q9NPQ8	OTTHUMG00000119069		11.37:g.205996G>A	Exception_encountered		Q0P508|Q2T9J1|Q7Z352|Q96EZ1|Q96SZ2|Q9H064|Q9H5H3|Q9H9E7	Nonsense_Mutation	SNP	pfam_T_SNARE_dom,pfscan_T_SNARE_dom	p.R23*	ENST00000526104.1	37	c.67		11	.	.	.	.	.	.	.	.	.	.	G	18.40	3.615261	0.66672	.	.	ENSG00000177951	ENST00000410108;ENST00000325147;ENST00000382762;ENST00000332865;ENST00000529614	.	.	.	4.17	3.25	0.37280	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.3225	0.60440	0.0:0.0:0.8403:0.1597	.	.	.	.	X	23	.	ENSP00000339093:R23X	R	-	1	2	BET1L	195996	1.000000	0.71417	1.000000	0.80357	0.369000	0.29798	7.119000	0.77145	1.331000	0.45412	-0.324000	0.08512	CGA	BET1L	-	pfam_T_SNARE_dom,pfscan_T_SNARE_dom	ENSG00000177951		0.587	RIC8A-002	KNOWN	basic|appris_candidate	protein_coding	BET1L	HGNC	protein_coding	OTTHUMT00000384761.1	137	0.00	0	G	NM_021932		205996	205996	-1	no_errors	ENST00000382762	ensembl	human	known	69_37n	nonsense	57	40.40	40	SNP	1.000	A
CHD5	26038	genome.wustl.edu	37	1	6202309	6202309	+	Missense_Mutation	SNP	G	G	A			TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	e5fd7cbd-8fce-49e9-8d2c-d2a2e61367a5	a496949e-c185-40d9-82d2-c09d64d8b77f	g.chr1:6202309G>A	ENST00000262450.3	-	15	2414	c.2315C>T	c.(2314-2316)gCg>gTg	p.A772V	CHD5_ENST00000378021.1_5'UTR	NM_015557.2	NP_056372.1	O00258	WRB_HUMAN	chromodomain helicase DNA binding protein 5	0					tail-anchored membrane protein insertion into ER membrane (GO:0071816)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)		p.A772V(1)		breast(3)|central_nervous_system(3)|liver(1)|lung(1)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	16	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)		GAAGTCGGGCGCCCACATCTC	0.607																																						dbGAP											1	Substitution - Missense(1)	large_intestine(1)											98.0	95.0	96.0					1																	6202309		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF425231	CCDS57.1	1p36.3	2013-01-28			ENSG00000116254	ENSG00000116254		"""Zinc fingers, PHD-type"""	16816	protein-coding gene	gene with protein product		610771				11889561, 12592387	Standard	NM_015557		Approved		uc001amb.2	Q8TDI0	OTTHUMG00000000952	ENST00000262450.3:c.2315C>T	1.37:g.6202309G>A	ENSP00000262450:p.Ala772Val		A8KAP8|A8MQ44|D3DSH9|O60740	Missense_Mutation	SNP	pfam_CHD_C2,pfam_SNF2_N,pfam_DUF1086,pfam_CHD_N,pfam_DUF1087,pfam_Znf_PHD-finger,pfam_Chromo_domain,pfam_Helicase_C,pfam_Helicase/UvrB_dom,superfamily_Chromodomain-like,superfamily_Znf_FYVE_PHD,superfamily_HMG_superfamily,smart_Znf_PHD,smart_Chromo_domain/shadow,smart_Helicase_ATP-bd,smart_Helicase_C,pfscan_Znf_PHD-finger,pfscan_Helicase_ATP-bd,pfscan_Helicase_C,pfscan_Chromo_domain/shadow	p.A772V	ENST00000262450.3	37	c.2315	CCDS57.1	1	.	.	.	.	.	.	.	.	.	.	G	31	5.086309	0.94100	.	.	ENSG00000116254	ENST00000262450;ENST00000378006;ENST00000536802;ENST00000538279	D	0.93604	-3.25	4.07	4.07	0.47477	DEAD-like helicase (2);SNF2-related (1);	0.000000	0.64402	D	0.000001	D	0.95623	0.8577	L	0.58302	1.8	0.80722	D	1	D	0.76494	0.999	D	0.79108	0.992	D	0.95855	0.8878	10	0.54805	T	0.06	-21.7301	16.6218	0.84932	0.0:0.0:1.0:0.0	.	772	Q8TDI0	CHD5_HUMAN	V	772;288;180;180	ENSP00000262450:A772V	ENSP00000262450:A772V	A	-	2	0	CHD5	6124896	1.000000	0.71417	0.912000	0.35992	0.986000	0.74619	9.702000	0.98712	1.977000	0.57605	0.561000	0.74099	GCG	CHD5	-	pfam_SNF2_N,pfam_Helicase/UvrB_dom,smart_Helicase_ATP-bd,pfscan_Helicase_ATP-bd	ENSG00000116254		0.607	CHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CHD5	HGNC	protein_coding	OTTHUMT00000002823.2	124	0.00	0	G	NM_015557		6202309	6202309	-1	no_errors	ENST00000262450	ensembl	human	known	69_37n	missense	51	45.16	42	SNP	1.000	A
CNTN6	27255	genome.wustl.edu	37	3	1414040	1414040	+	Missense_Mutation	SNP	T	T	C			TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	e5fd7cbd-8fce-49e9-8d2c-d2a2e61367a5	a496949e-c185-40d9-82d2-c09d64d8b77f	g.chr3:1414040T>C	ENST00000446702.2	+	13	2177	c.1550T>C	c.(1549-1551)aTa>aCa	p.I517T	CNTN6_ENST00000539053.1_Missense_Mutation_p.I445T|CNTN6_ENST00000350110.2_Missense_Mutation_p.I517T			Q9UQ52	CNTN6_HUMAN	contactin 6	517	Ig-like C2-type 6.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|Notch signaling pathway (GO:0007219)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(34)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		GGCGAGAGTATAGTGCTACCA	0.388																																						dbGAP											0													135.0	125.0	128.0					3																	1414040		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB003592	CCDS2557.1	3p26-p25	2013-02-11			ENSG00000134115	ENSG00000134115		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	2176	protein-coding gene	gene with protein product	"""neural adhesion molecule"""	607220				9486763	Standard	NM_014461		Approved	NB-3	uc003bpa.3	Q9UQ52	OTTHUMG00000119030	ENST00000446702.2:c.1550T>C	3.37:g.1414040T>C	ENSP00000407822:p.Ile517Thr		Q2KHM2	Missense_Mutation	SNP	pfam_Ig_I-set,pfam_Fibronectin_type3,pfam_Ig_V-set,pfam_Immunoglobulin,superfamily_Fibronectin_type3,smart_Ig_sub,smart_Ig_sub2,smart_Fibronectin_type3,pfscan_Fibronectin_type3,pfscan_Ig-like	p.I517T	ENST00000446702.2	37	c.1550	CCDS2557.1	3	.	.	.	.	.	.	.	.	.	.	T	17.06	3.292569	0.59976	.	.	ENSG00000134115	ENST00000446702;ENST00000539053;ENST00000350110	T;T;T	0.44881	0.91;0.91;0.91	5.8	5.8	0.92144	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000005	T	0.65811	0.2727	M	0.74258	2.255	0.46458	D	0.999056	D	0.76494	0.999	D	0.85130	0.997	T	0.69423	-0.5149	10	0.72032	D	0.01	.	16.1506	0.81618	0.0:0.0:0.0:1.0	.	517	Q9UQ52	CNTN6_HUMAN	T	517;445;517	ENSP00000407822:I517T;ENSP00000442791:I445T;ENSP00000341882:I517T	ENSP00000341882:I517T	I	+	2	0	CNTN6	1389040	1.000000	0.71417	0.237000	0.24090	0.548000	0.35241	5.850000	0.69473	2.206000	0.71126	0.528000	0.53228	ATA	CNTN6	-	pfam_Ig_I-set,smart_Ig_sub,smart_Ig_sub2,pfscan_Ig-like	ENSG00000134115		0.388	CNTN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CNTN6	HGNC	protein_coding	OTTHUMT00000239235.2	229	0.00	0	T	NM_014461		1414040	1414040	+1	no_errors	ENST00000350110	ensembl	human	known	69_37n	missense	166	40.14	112	SNP	0.943	C
COL8A1	1295	genome.wustl.edu	37	3	99513227	99513227	+	Missense_Mutation	SNP	G	G	T			TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	e5fd7cbd-8fce-49e9-8d2c-d2a2e61367a5	a496949e-c185-40d9-82d2-c09d64d8b77f	g.chr3:99513227G>T	ENST00000261037.3	+	5	862	c.482G>T	c.(481-483)gGt>gTt	p.G161V	COL8A1_ENST00000273342.4_Missense_Mutation_p.G161V	NM_001850.4	NP_001841.2	P27658	CO8A1_HUMAN	collagen, type VIII, alpha 1	161	Triple-helical region (COL1).				angiogenesis (GO:0001525)|camera-type eye morphogenesis (GO:0048593)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epithelial cell proliferation (GO:0050673)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	collagen type VIII trimer (GO:0005591)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)				breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(15)|skin(5)|upper_aerodigestive_tract(1)	27						GGAAAGCCAGGTATGCCTGGA	0.562																																						dbGAP											0													44.0	47.0	46.0					3																	99513227		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF170702	CCDS2934.1	3q11.1-q13.2	2013-01-16			ENSG00000144810	ENSG00000144810		"""Collagens"""	2215	protein-coding gene	gene with protein product		120251	"""chromosome 3 open reading frame 7"""	C3orf7		2029894	Standard	NM_001850		Approved	MGC9568	uc003dth.2	P27658	OTTHUMG00000148669	ENST00000261037.3:c.482G>T	3.37:g.99513227G>T	ENSP00000261037:p.Gly161Val		D3DN42|Q53XI6|Q96D07	Missense_Mutation	SNP	pfam_Collagen,pfam_C1q,superfamily_Tumour_necrosis_fac-like,smart_C1q,pfscan_C1q,prints_C1q	p.G161V	ENST00000261037.3	37	c.482	CCDS2934.1	3	.	.	.	.	.	.	.	.	.	.	G	15.61	2.885804	0.51908	.	.	ENSG00000144810	ENST00000261037;ENST00000273342	D;D	0.99637	-6.29;-6.29	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	D	0.99708	0.9888	M	0.92970	3.365	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97541	1.0086	10	0.87932	D	0	.	16.849	0.85988	0.0:0.0:1.0:0.0	.	162;161	E7EPK9;P27658	.;CO8A1_HUMAN	V	161	ENSP00000261037:G161V;ENSP00000273342:G161V	ENSP00000261037:G161V	G	+	2	0	COL8A1	100995917	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.804000	0.99143	2.583000	0.87209	0.655000	0.94253	GGT	COL8A1	-	pfam_Collagen	ENSG00000144810		0.562	COL8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	COL8A1	HGNC	protein_coding	OTTHUMT00000309001.1	131	0.76	1	G	NM_001850		99513227	99513227	+1	no_errors	ENST00000261037	ensembl	human	known	69_37n	missense	97	39.38	63	SNP	1.000	T
DCHS1	8642	genome.wustl.edu	37	11	6645350	6645350	+	Missense_Mutation	SNP	G	G	C			TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	e5fd7cbd-8fce-49e9-8d2c-d2a2e61367a5	a496949e-c185-40d9-82d2-c09d64d8b77f	g.chr11:6645350G>C	ENST00000299441.3	-	21	7968	c.7557C>G	c.(7555-7557)gaC>gaG	p.D2519E	RP11-732A19.5_ENST00000526456.1_RNA	NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	2519	Cadherin 24. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGATGCTGTAGTCCACAGCGG	0.642																																						dbGAP											0													27.0	27.0	27.0					11																	6645350		2200	4296	6496	-	-	-	SO:0001583	missense	0			AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"""Cadherins / Cadherin-related"""	13681	protein-coding gene	gene with protein product	"""cadherin-related family member 6"""	603057	"""protocadherin 16"", ""dachsous 1 (Drosophila)"""	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.7557C>G	11.37:g.6645350G>C	ENSP00000299441:p.Asp2519Glu		O15098	Missense_Mutation	SNP	pfam_Cadherin,superfamily_Cadherin-like,smart_Cadherin,prints_Cadherin,pfscan_Cadherin	p.D2519E	ENST00000299441.3	37	c.7557	CCDS7771.1	11	.	.	.	.	.	.	.	.	.	.	G	9.564	1.119356	0.20877	.	.	ENSG00000166341	ENST00000299441	T	0.50001	0.76	4.78	3.87	0.44632	Cadherin (4);Cadherin-like (1);	0.157330	0.29660	N	0.011531	T	0.39200	0.1069	N	0.05124	-0.11	0.38849	D	0.956234	D	0.76494	0.999	D	0.72075	0.976	T	0.34725	-0.9817	10	0.02654	T	1	.	11.0601	0.47942	0.0785:0.1352:0.7863:0.0	.	2519	Q96JQ0	PCD16_HUMAN	E	2519	ENSP00000299441:D2519E	ENSP00000299441:D2519E	D	-	3	2	DCHS1	6601926	1.000000	0.71417	1.000000	0.80357	0.422000	0.31414	2.396000	0.44468	0.637000	0.30526	-1.943000	0.00494	GAC	DCHS1	-	pfam_Cadherin,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin	ENSG00000166341		0.642	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DCHS1	HGNC	protein_coding	OTTHUMT00000257258.1	43	0.00	0	G	NM_003737		6645350	6645350	-1	no_errors	ENST00000299441	ensembl	human	known	69_37n	missense	18	47.06	16	SNP	1.000	C
FEM1B	10116	genome.wustl.edu	37	15	68582869	68582869	+	Silent	SNP	T	T	A			TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	e5fd7cbd-8fce-49e9-8d2c-d2a2e61367a5	a496949e-c185-40d9-82d2-c09d64d8b77f	g.chr15:68582869T>A	ENST00000306917.4	+	2	1788	c.1173T>A	c.(1171-1173)gtT>gtA	p.V391V		NM_015322.4	NP_056137.1	Q9UK73	FEM1B_HUMAN	fem-1 homolog b (C. elegans)	391					apoptotic process (GO:0006915)|branching involved in prostate gland morphogenesis (GO:0060442)|epithelial cell maturation involved in prostate gland development (GO:0060743)|regulation of DNA damage checkpoint (GO:2000001)|regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902041)|regulation of ubiquitin-protein transferase activity (GO:0051438)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	death receptor binding (GO:0005123)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|urinary_tract(1)	9						TTGCTCAAGTTTTCTCACAAA	0.403																																						dbGAP											0													80.0	78.0	79.0					15																	68582869		2200	4298	6498	-	-	-	SO:0001819	synonymous_variant	0				CCDS10228.1	15q22	2013-02-19	2001-11-28		ENSG00000169018	ENSG00000169018		"""Ankyrin repeat domain containing"""	3649	protein-coding gene	gene with protein product		613539	"""FEM-1 (C. elegans) homolog b"""			10623617	Standard	NM_015322		Approved		uc002arg.3	Q9UK73	OTTHUMG00000133285	ENST00000306917.4:c.1173T>A	15.37:g.68582869T>A			O43146	Silent	SNP	pfam_Ankyrin_rpt,superfamily_Ankyrin_rpt-contain_dom,smart_Ankyrin_rpt,prints_Ankyrin_rpt,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom	p.V391	ENST00000306917.4	37	c.1173	CCDS10228.1	15																																																																																			FEM1B	-	NULL	ENSG00000169018		0.403	FEM1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FEM1B	HGNC	protein_coding	OTTHUMT00000257065.1	142	0.00	0	T			68582869	68582869	+1	no_errors	ENST00000306917	ensembl	human	known	69_37n	silent	103	43.72	80	SNP	0.986	A
FOXJ2	55810	genome.wustl.edu	37	12	8203193	8203193	+	Missense_Mutation	SNP	A	A	G			TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	e5fd7cbd-8fce-49e9-8d2c-d2a2e61367a5	a496949e-c185-40d9-82d2-c09d64d8b77f	g.chr12:8203193A>G	ENST00000162391.3	+	10	2758	c.1613A>G	c.(1612-1614)gAc>gGc	p.D538G	FOXJ2_ENST00000539192.1_3'UTR	NM_018416.2	NP_060886.1	Q9P0K8	FOXJ2_HUMAN	forkhead box J2	538					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)	nucleolus (GO:0005730)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)			autonomic_ganglia(1)|large_intestine(2)|lung(6)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	16				Kidney(36;0.0944)		CCCACCCAGGACTCAGCAGGA	0.502																																						dbGAP											0													125.0	115.0	118.0					12																	8203193		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF155132	CCDS8587.1	12p13.31	2006-12-15				ENSG00000065970		"""Forkhead boxes"""	24818	protein-coding gene	gene with protein product						10777590, 10966786	Standard	NM_018416		Approved	FHX	uc001qtu.3	Q9P0K8		ENST00000162391.3:c.1613A>G	12.37:g.8203193A>G	ENSP00000162391:p.Asp538Gly		A0AVK4|B2RMP3|Q96PS9|Q9NSN5	Missense_Mutation	SNP	pfam_TF_fork_head,smart_TF_fork_head,pfscan_TF_fork_head,prints_TF_fork_head	p.D538G	ENST00000162391.3	37	c.1613	CCDS8587.1	12	.	.	.	.	.	.	.	.	.	.	A	19.91	3.914002	0.72983	.	.	ENSG00000065970	ENST00000162391	D	0.94232	-3.38	5.13	5.13	0.70059	.	0.719043	0.12980	N	0.423351	D	0.89171	0.6639	L	0.34521	1.04	0.80722	D	1	B	0.23316	0.083	B	0.27262	0.078	D	0.83820	0.0246	10	0.27785	T	0.31	.	11.2579	0.49065	1.0:0.0:0.0:0.0	.	538	Q9P0K8	FOXJ2_HUMAN	G	538	ENSP00000162391:D538G	ENSP00000162391:D538G	D	+	2	0	FOXJ2	8094460	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	5.440000	0.66563	2.146000	0.66826	0.533000	0.62120	GAC	FOXJ2	-	NULL	ENSG00000065970		0.502	FOXJ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FOXJ2	HGNC	protein_coding	OTTHUMT00000400088.1	226	0.00	0	A	NM_018416		8203193	8203193	+1	no_errors	ENST00000162391	ensembl	human	known	69_37n	missense	126	44.05	100	SNP	1.000	G
FRG1B	284802	genome.wustl.edu	37	20	29632612	29632614	+	Splice_Site	DEL	AAG	AAG	-			TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	AAG	AAG					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	e5fd7cbd-8fce-49e9-8d2c-d2a2e61367a5	a496949e-c185-40d9-82d2-c09d64d8b77f	g.chr20:29632612_29632614delAAG	ENST00000278882.3	+	8	807_809	c.427_429delAAG	c.(427-429)aagdel	p.K144del	FRG1B_ENST00000358464.4_Splice_Site_p.K144del			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	144										endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						TCTTTGCAGAAAGAAATTTCAGA	0.276																																						dbGAP											0																																										-	-	-	SO:0001630	splice_region_variant	0					20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531			15792	other	unknown			"""chromosome 20 open reading frame 80"""	C20orf80			Standard	NR_003579		Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.426-1AAG>-	20.37:g.29632612_29632614delAAG			C4AME5	In_Frame_Del	DEL	pfam_FRG1,superfamily_Actin_cross-linking	p.K144in_frame_del	ENST00000278882.3	37	c.427_429		20																																																																																			FRG1B	-	pfam_FRG1	ENSG00000149531		0.276	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	FRG1B	HGNC	protein_coding	OTTHUMT00000078494.2	25	0.00	0	AAG	NR_003579	In_Frame_Del	29632612	29632614	+1	no_errors	ENST00000278882	ensembl	human	known	69_37n	in_frame_del	67	10.67	8	DEL	1.000:1.000:1.000	-
GATA3	2625	genome.wustl.edu	37	10	8111433	8111434	+	Splice_Site	DEL	CA	CA	-	rs111853237		TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	CA	CA					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	e5fd7cbd-8fce-49e9-8d2c-d2a2e61367a5	a496949e-c185-40d9-82d2-c09d64d8b77f	g.chr10:8111433_8111434delCA	ENST00000346208.3	+	5	1376		c.e5-1		GATA3_ENST00000379328.3_Splice_Site|GATA3_ENST00000461472.1_Splice_Site			P23771	GATA3_HUMAN	GATA binding protein 3						anatomical structure formation involved in morphogenesis (GO:0048646)|anatomical structure morphogenesis (GO:0009653)|aortic valve morphogenesis (GO:0003180)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|canonical Wnt signaling pathway involved in metanephric kidney development (GO:0061290)|cardiac right ventricle morphogenesis (GO:0003215)|cell fate determination (GO:0001709)|cell maturation (GO:0048469)|cellular response to BMP stimulus (GO:0071773)|cellular response to interferon-alpha (GO:0035457)|cellular response to interleukin-4 (GO:0071353)|cellular response to tumor necrosis factor (GO:0071356)|defense response (GO:0006952)|developmental growth (GO:0048589)|ear development (GO:0043583)|embryonic hemopoiesis (GO:0035162)|erythrocyte differentiation (GO:0030218)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|interferon-gamma secretion (GO:0072643)|interleukin-4 secretion (GO:0072602)|kidney development (GO:0001822)|lens development in camera-type eye (GO:0002088)|lymphocyte migration (GO:0072676)|male gonad development (GO:0008584)|mast cell differentiation (GO:0060374)|mesenchymal to epithelial transition (GO:0060231)|mesonephros development (GO:0001823)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell motility (GO:2000146)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell proliferation involved in mesonephros development (GO:2000607)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway involved in ureteric bud formation (GO:2000703)|negative regulation of glial cell-derived neurotrophic factor receptor signaling pathway involved in ureteric bud formation (GO:2000734)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of transcription, DNA-templated (GO:0045892)|nephric duct formation (GO:0072179)|nephric duct morphogenesis (GO:0072178)|neuron migration (GO:0001764)|norepinephrine biosynthetic process (GO:0042421)|otic vesicle development (GO:0071599)|parathyroid gland development (GO:0060017)|parathyroid hormone secretion (GO:0035898)|pharyngeal system development (GO:0060037)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of interleukin-13 production (GO:0032736)|positive regulation of interleukin-13 secretion (GO:2000667)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-5 production (GO:0032754)|positive regulation of interleukin-5 secretion (GO:2000664)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of signal transduction (GO:0009967)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of thyroid hormone generation (GO:2000611)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ureteric bud formation (GO:0072107)|post-embryonic development (GO:0009791)|pro-T cell differentiation (GO:0002572)|regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043370)|regulation of cellular response to X-ray (GO:2000683)|regulation of cytokine biosynthetic process (GO:0042035)|regulation of establishment of cell polarity (GO:2000114)|regulation of histone H3-K27 methylation (GO:0061085)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of neuron apoptotic process (GO:0043523)|regulation of neuron projection development (GO:0010975)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to gamma radiation (GO:0010332)|response to virus (GO:0009615)|signal transduction (GO:0007165)|sympathetic nervous system development (GO:0048485)|T cell receptor signaling pathway (GO:0050852)|T-helper 2 cell differentiation (GO:0045064)|thymic T cell selection (GO:0045061)|thymus development (GO:0048538)|TOR signaling (GO:0031929)|transcription from RNA polymerase II promoter (GO:0006366)|type IV hypersensitivity (GO:0001806)|ureter maturation (GO:0035799)|ureteric bud formation (GO:0060676)|uterus development (GO:0060065)|ventricular septum development (GO:0003281)	nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter proximal region sequence-specific DNA binding (GO:0000987)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|E-box binding (GO:0070888)|enhancer sequence-specific DNA binding (GO:0001158)|HMG box domain binding (GO:0071837)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|zinc ion binding (GO:0008270)	p.?(7)		NS(1)|breast(44)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(24)|ovary(3)|skin(2)	87						TCCCCACTCTCAGTCTGCAGCC	0.48			"""F, N, S"""		breast		"""HDR syndrome (HYPOPARATHYROIDISM, SENSORINEURAL DEAFNESS, AND RENAL DISEASE)"""																															dbGAP		Rec	yes		10	10p15	2625	GATA binding protein 3	yes	E	7	Unknown(7)	breast(7)																																								-	-	-	SO:0001630	splice_region_variant	0			X55122	CCDS7083.1, CCDS31143.1	10p15	2013-01-25	2001-11-28		ENSG00000107485	ENSG00000107485		"""GATA zinc finger domain containing"""	4172	protein-coding gene	gene with protein product		131320	"""GATA-binding protein 3"""			2050118, 15087456	Standard	NM_002051		Approved	HDR	uc001ijz.3	P23771	OTTHUMG00000017640	ENST00000346208.3:c.922-1CA>-	10.37:g.8111433_8111434delCA			Q5VWG7|Q5VWG8|Q96J16	Splice_Site	DEL	-	e4-2	ENST00000346208.3	37	c.925-3_925-2	CCDS7083.1	10																																																																																			GATA3	-	-	ENSG00000107485		0.480	GATA3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	GATA3	HGNC	protein_coding	OTTHUMT00000046719.1	149	0	0	CA	NM_001002295	Intron	8111433	8111434	+1	no_errors	ENST00000379328	ensembl	human	known	69_37n	splice_site_del	80	33.61	41	DEL	1.000:1.000	-
HNRNPR	10236	genome.wustl.edu	37	1	23637492	23637492	+	Missense_Mutation	SNP	C	C	A			TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	e5fd7cbd-8fce-49e9-8d2c-d2a2e61367a5	a496949e-c185-40d9-82d2-c09d64d8b77f	g.chr1:23637492C>A	ENST00000374612.1	-	11	1480	c.1357G>T	c.(1357-1359)Ggg>Tgg	p.G453W	HNRNPR_ENST00000478691.1_Missense_Mutation_p.G355W|HNRNPR_ENST00000606561.1_Missense_Mutation_p.G314W|HNRNPR_ENST00000427764.2_Missense_Mutation_p.G415W|HNRNPR_ENST00000374616.3_Missense_Mutation_p.G456W|HNRNPR_ENST00000476660.1_5'UTR|HNRNPR_ENST00000426846.2_Missense_Mutation_p.G293W|HNRNPR_ENST00000302271.6_Missense_Mutation_p.G453W	NM_001102398.1|NM_005826.3	NP_001095868.1|NP_005817.1	O43390	HNRPR_HUMAN	heterogeneous nuclear ribonucleoprotein R	453	RNA-binding RGG-box.				gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Breast(348;0.00394)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;6.83e-27)|Colorectal(126;6.01e-08)|COAD - Colon adenocarcinoma(152;3.32e-06)|GBM - Glioblastoma multiforme(114;6.69e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00101)|KIRC - Kidney renal clear cell carcinoma(1967;0.00357)|STAD - Stomach adenocarcinoma(196;0.0131)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0875)|LUSC - Lung squamous cell carcinoma(448;0.19)		CCTCTCCCCCCACCACGACCC	0.458																																						dbGAP											0													95.0	102.0	99.0					1																	23637492		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF000364	CCDS232.1, CCDS44085.1, CCDS60020.1, CCDS72726.1, CCDS72727.1	1p36.12	2013-02-12		2007-08-16	ENSG00000125944	ENSG00000125944		"""RNA binding motif (RRM) containing"""	5047	protein-coding gene	gene with protein product		607201		HNRPR		9421497	Standard	XM_005245711		Approved	hnRNP-R	uc001bgp.4	O43390	OTTHUMG00000003224	ENST00000374612.1:c.1357G>T	1.37:g.23637492C>A	ENSP00000363741:p.Gly453Trp		Q2L7G6|Q5TEH1|Q9BV64|S4R3J4	Missense_Mutation	SNP	pfam_RRM_dom,smart_RRM_dom,pfscan_RRM_dom,tigrfam_HnRNP_R/Q_splicing_fac	p.G456W	ENST00000374612.1	37	c.1366	CCDS232.1	1	.	.	.	.	.	.	.	.	.	.	C	10.59	1.392082	0.25118	.	.	ENSG00000125944	ENST00000374616;ENST00000374612;ENST00000302271;ENST00000427764;ENST00000426846	T;T;T;T;T	0.24538	1.85;1.88;1.88;2.13;2.68	4.82	4.82	0.62117	.	0.000000	0.85682	D	0.000000	T	0.49236	0.1545	M	0.77820	2.39	0.80722	D	1	D;D;D;D;D;D	0.69078	0.991;0.995;0.976;0.991;0.995;0.997	P;P;P;P;P;D	0.66351	0.878;0.878;0.466;0.878;0.878;0.943	T	0.51450	-0.8704	10	0.59425	D	0.04	.	13.2772	0.60194	0.0:1.0:0.0:0.0	.	293;415;314;433;453;456	E7ETM7;Q2L7G6;B4DT28;Q6MZS5;O43390;O43390-2	.;.;.;.;HNRPR_HUMAN;.	W	456;453;453;415;293	ENSP00000363745:G456W;ENSP00000363741:G453W;ENSP00000304405:G453W;ENSP00000392799:G415W;ENSP00000415042:G293W	ENSP00000304405:G453W	G	-	1	0	HNRNPR	23510079	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.737000	0.55060	2.511000	0.84671	0.650000	0.86243	GGG	HNRNPR	-	tigrfam_HnRNP_R/Q_splicing_fac	ENSG00000125944		0.458	HNRNPR-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	HNRNPR	HGNC	protein_coding	OTTHUMT00000008889.1	230	0.00	0	C	NM_005826		23637492	23637492	-1	no_errors	ENST00000374616	ensembl	human	known	69_37n	missense	128	50.00	128	SNP	1.000	A
GPATCH2	55105	genome.wustl.edu	37	1	217783712	217783712	+	Missense_Mutation	SNP	C	C	A			TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	e5fd7cbd-8fce-49e9-8d2c-d2a2e61367a5	a496949e-c185-40d9-82d2-c09d64d8b77f	g.chr1:217783712C>A	ENST00000366935.3	-	5	1159	c.1049G>T	c.(1048-1050)gGa>gTa	p.G350V	GPATCH2_ENST00000366934.3_Missense_Mutation_p.G350V	NM_018040.2	NP_060510.1	Q9NW75	GPTC2_HUMAN	G patch domain containing 2	350					negative regulation of phosphatase activity (GO:0010923)		nucleic acid binding (GO:0003676)			NS(1)|breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(3)|stomach(1)	35				OV - Ovarian serous cystadenocarcinoma(81;0.0397)|all cancers(67;0.0744)|GBM - Glioblastoma multiforme(131;0.0872)		TGAAGACATTCCATGAAGGCG	0.358																																						dbGAP											0													103.0	108.0	107.0					1																	217783712		2203	4300	6503	-	-	-	SO:0001583	missense	0			AK001114	CCDS1518.1, CCDS73031.1	1q41	2013-01-28		2006-12-13	ENSG00000092978	ENSG00000092978		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""G patch domain containing"""	25499	protein-coding gene	gene with protein product	"""cancer/testis antigen 110"", ""protein phosphatase 1, regulatory subunit 30"""			GPATC2		19432882, 15375528	Standard	XM_005273174		Approved	FLJ10252, CT110, PPP1R30	uc001hlf.1	Q9NW75	OTTHUMG00000000527	ENST00000366935.3:c.1049G>T	1.37:g.217783712C>A	ENSP00000355902:p.Gly350Val		Q5VYK7|Q5VYK8|Q86YE7	Missense_Mutation	SNP	pfam_G_patch_dom,smart_G_patch_dom,pfscan_G_patch_dom	p.G350V	ENST00000366935.3	37	c.1049	CCDS1518.1	1	.	.	.	.	.	.	.	.	.	.	C	16.76	3.212450	0.58452	.	.	ENSG00000092978	ENST00000366935;ENST00000366934	T;T	0.59638	1.21;0.25	6.08	6.08	0.98989	.	0.054132	0.64402	D	0.000001	T	0.71854	0.3389	M	0.75264	2.295	0.80722	D	1	D;D	0.61697	0.984;0.99	P;P	0.56700	0.804;0.743	T	0.74417	-0.3672	10	0.87932	D	0	-20.1001	16.0764	0.80971	0.0:0.8669:0.1331:0.0	.	350;350	Q9NW75-2;Q9NW75	.;GPTC2_HUMAN	V	350	ENSP00000355902:G350V;ENSP00000355901:G350V	ENSP00000355901:G350V	G	-	2	0	GPATCH2	215850335	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.237000	0.58681	2.894000	0.99253	0.591000	0.81541	GGA	GPATCH2	-	NULL	ENSG00000092978		0.358	GPATCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GPATCH2	HGNC	protein_coding	OTTHUMT00000001272.1	167	0.00	0	C	NM_018040		217783712	217783712	-1	no_errors	ENST00000366935	ensembl	human	known	69_37n	missense	117	65.89	226	SNP	1.000	A
INSIG2	51141	genome.wustl.edu	37	2	118860893	118860893	+	Missense_Mutation	SNP	G	G	A			TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	e5fd7cbd-8fce-49e9-8d2c-d2a2e61367a5	a496949e-c185-40d9-82d2-c09d64d8b77f	g.chr2:118860893G>A	ENST00000245787.4	+	3	571	c.365G>A	c.(364-366)aGt>aAt	p.S122N	INSIG2_ENST00000485520.1_3'UTR	NM_016133.2	NP_057217.2	Q9Y5U4	INSI2_HUMAN	insulin induced gene 2	122					cholesterol biosynthetic process (GO:0006695)|cranial suture morphogenesis (GO:0060363)|inner ear morphogenesis (GO:0042472)|middle ear morphogenesis (GO:0042474)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of steroid biosynthetic process (GO:0010894)|palate development (GO:0060021)|response to fatty acid (GO:0070542)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)|SREBP signaling pathway (GO:0032933)|triglyceride metabolic process (GO:0006641)	endoplasmic reticulum membrane (GO:0005789)|SREBP-SCAP-Insig complex (GO:0032937)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(5)|ovary(1)	13						AATCATGCCAGTGCTGTATCC	0.393																																						dbGAP											0													218.0	211.0	213.0					2																	118860893		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF527632	CCDS2122.1	2q14.1	2008-02-05			ENSG00000125629	ENSG00000125629			20452	protein-coding gene	gene with protein product		608660				12242332	Standard	NM_016133		Approved		uc002tlk.3	Q9Y5U4	OTTHUMG00000058518	ENST00000245787.4:c.365G>A	2.37:g.118860893G>A	ENSP00000245787:p.Ser122Asn		A8K5W8|Q8TBI8	Missense_Mutation	SNP	pfam_INSIG_fam	p.S122N	ENST00000245787.4	37	c.365	CCDS2122.1	2	.	.	.	.	.	.	.	.	.	.	G	33	5.255621	0.95336	.	.	ENSG00000125629	ENST00000245787	.	.	.	5.4	5.4	0.78164	.	0.080320	0.85682	D	0.000000	D	0.83252	0.5214	M	0.80616	2.505	0.80722	D	1	D;B	0.69078	0.997;0.099	D;B	0.79108	0.992;0.095	D	0.84130	0.0411	9	0.59425	D	0.04	.	19.3716	0.94490	0.0:0.0:1.0:0.0	.	14;122	B4DQ23;Q9Y5U4	.;INSI2_HUMAN	N	122	.	ENSP00000245787:S122N	S	+	2	0	INSIG2	118577363	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.595000	0.98260	2.805000	0.96524	0.655000	0.94253	AGT	INSIG2	-	pfam_INSIG_fam	ENSG00000125629		0.393	INSIG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	INSIG2	HGNC	protein_coding	OTTHUMT00000129624.1	320	0.00	0	G	NM_016133		118860893	118860893	+1	no_errors	ENST00000245787	ensembl	human	known	69_37n	missense	199	38.53	126	SNP	1.000	A
JAK3	3718	genome.wustl.edu	37	19	17945965	17945965	+	Silent	SNP	C	C	T			TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	e5fd7cbd-8fce-49e9-8d2c-d2a2e61367a5	a496949e-c185-40d9-82d2-c09d64d8b77f	g.chr19:17945965C>T	ENST00000527670.1	-	14	2003	c.1974G>A	c.(1972-1974)gaG>gaA	p.E658E	JAK3_ENST00000534444.1_Silent_p.E658E|JAK3_ENST00000458235.1_Silent_p.E658E			P52333	JAK3_HUMAN	Janus kinase 3	658	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				B cell differentiation (GO:0030183)|enzyme linked receptor protein signaling pathway (GO:0007167)|innate immune response (GO:0045087)|interleukin-4-mediated signaling pathway (GO:0035771)|intracellular signal transduction (GO:0035556)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of dendritic cell cytokine production (GO:0002731)|negative regulation of FasL biosynthetic process (GO:0045221)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of T cell activation (GO:0050868)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|negative regulation of thymocyte apoptotic process (GO:0070244)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of T cell apoptotic process (GO:0070232)|response to interleukin-15 (GO:0070672)|response to interleukin-2 (GO:0070669)|response to interleukin-4 (GO:0070670)|response to interleukin-9 (GO:0071104)|STAT protein import into nucleus (GO:0007262)|T cell homeostasis (GO:0043029)|tyrosine phosphorylation of STAT protein (GO:0007260)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)			breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(85)|kidney(4)|large_intestine(11)|lung(22)|ovary(3)|prostate(5)|skin(1)|stomach(2)|upper_aerodigestive_tract(5)	147					Tofacitinib(DB08895)	CATCAGCCCCCTCCCGAGCCA	0.627		2	Mis		"""acute megakaryocytic leukemia, ETP ALL"""																																	dbGAP		Dom	yes		19	19p13.1	3718	Janus kinase 3		L	0													39.0	40.0	40.0					19																	17945965		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			U31601	CCDS12366.1	19p13-p12	2014-09-17	2009-04-23		ENSG00000105639	ENSG00000105639	2.7.10.1		6193	protein-coding gene	gene with protein product	"""tyrosine-protein kinase JAK3"", ""leukocyte Janus kinase"""	600173				8921370, 9226382	Standard	NM_000215		Approved	L-JAK, JAKL, LJAK, JAK3_HUMAN, JAK-3	uc002nhn.4	P52333	OTTHUMG00000165648	ENST00000527670.1:c.1974G>A	19.37:g.17945965C>T			Q13259|Q13260|Q13611|Q8N1E8|Q99699|Q9Y6S2	Silent	SNP	pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Prot_kinase_cat_dom,superfamily_Kinase-like_dom,superfamily_FERM_central,smart_Band_41_domain,smart_SH2,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pirsf_Tyr_kinase_non-rcpt_Jak/Tyk2,prints_Tyr_kinase_non-rcpt_Jak/Tyk2,prints_Tyr_kinase_non-rcpt_Jak3,prints_Ser-Thr/Tyr_kinase_cat_dom,pfscan_FERM_domain,pfscan_Prot_kinase_cat_dom	p.E658	ENST00000527670.1	37	c.1974	CCDS12366.1	19																																																																																			JAK3	-	pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Prot_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pirsf_Tyr_kinase_non-rcpt_Jak/Tyk2,pfscan_Prot_kinase_cat_dom	ENSG00000105639		0.627	JAK3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	JAK3	HGNC	protein_coding	OTTHUMT00000385549.1	49	0.00	0	C	NM_000215		17945965	17945965	-1	no_errors	ENST00000458235	ensembl	human	known	69_37n	silent	21	38.24	13	SNP	0.999	T
LRP1	4035	genome.wustl.edu	37	12	57548459	57548459	+	Missense_Mutation	SNP	G	G	A			TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	e5fd7cbd-8fce-49e9-8d2c-d2a2e61367a5	a496949e-c185-40d9-82d2-c09d64d8b77f	g.chr12:57548459G>A	ENST00000243077.3	+	8	1668	c.1202G>A	c.(1201-1203)cGc>cAc	p.R401H	LRP1_ENST00000554174.1_Missense_Mutation_p.R401H	NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	401					aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	GGCAAGGGCCGCCAGACCATC	0.572																																						dbGAP											0													40.0	35.0	37.0					12																	57548459		2198	4295	6493	-	-	-	SO:0001583	missense	0			X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"""CD molecules"", ""Low density lipoprotein receptors"""	6692	protein-coding gene	gene with protein product		107770	"""alpha-2-macroglobulin receptor"""	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.1202G>A	12.37:g.57548459G>A	ENSP00000243077:p.Arg401His		Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	pfam_LDrepeatLR_classA_rpt,pfam_LDLR_classB_rpt,superfamily_Growth_fac_rcpt,superfamily_LDrepeatLR_classA_rpt,smart_LDrepeatLR_classA_rpt,smart_EGF-like_Ca-bd,smart_EGF-like,smart_LDLR_classB_rpt,pfscan_EG-like_dom,pfscan_LDrepeatLR_classA_rpt,pfscan_LDLR_classB_rpt	p.R401H	ENST00000243077.3	37	c.1202	CCDS8932.1	12	.	.	.	.	.	.	.	.	.	.	G	19.22	3.784926	0.70222	.	.	ENSG00000123384	ENST00000243077;ENST00000554174	D;D	0.91894	-2.93;-2.93	4.53	4.53	0.55603	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.64402	D	0.000008	D	0.96420	0.8832	M	0.89095	3.005	0.58432	D	0.99999	D;D	0.89917	0.999;1.0	D;D	0.91635	0.98;0.999	D	0.96898	0.9658	10	0.72032	D	0.01	.	15.1647	0.72814	0.0:0.0:1.0:0.0	.	401;401	Q07954;Q6PJ72	LRP1_HUMAN;.	H	401	ENSP00000243077:R401H;ENSP00000451737:R401H	ENSP00000243077:R401H	R	+	2	0	LRP1	55834726	1.000000	0.71417	1.000000	0.80357	0.872000	0.50106	9.657000	0.98554	2.521000	0.84997	0.650000	0.86243	CGC	LRP1	-	smart_LDLR_classB_rpt,pfscan_LDLR_classB_rpt	ENSG00000123384		0.572	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LRP1	HGNC	protein_coding	OTTHUMT00000412772.2	61	0.00	0	G	NM_002332		57548459	57548459	+1	no_errors	ENST00000243077	ensembl	human	known	69_37n	missense	48	37.50	30	SNP	1.000	A
LTBP4	8425	genome.wustl.edu	37	19	41113324	41113324	+	Missense_Mutation	SNP	G	G	A	rs577339340	byFrequency	TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	e5fd7cbd-8fce-49e9-8d2c-d2a2e61367a5	a496949e-c185-40d9-82d2-c09d64d8b77f	g.chr19:41113324G>A	ENST00000308370.7	+	10	1246	c.1246G>A	c.(1246-1248)Ggc>Agc	p.G416S	LTBP4_ENST00000602240.1_3'UTR|LTBP4_ENST00000204005.9_Missense_Mutation_p.G379S|RN7SL758P_ENST00000580450.1_RNA|LTBP4_ENST00000545697.1_5'UTR|LTBP4_ENST00000396819.3_Missense_Mutation_p.G349S	NM_001042544.1	NP_001036009.1	Q8N2S1	LTBP4_HUMAN	latent transforming growth factor beta binding protein 4	416	TB 2.				extracellular matrix organization (GO:0030198)|growth hormone secretion (GO:0030252)|multicellular organismal development (GO:0007275)|protein folding (GO:0006457)|regulation of cell differentiation (GO:0045595)|regulation of cell growth (GO:0001558)|regulation of proteolysis (GO:0030162)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|glycosaminoglycan binding (GO:0005539)|integrin binding (GO:0005178)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta-activated receptor activity (GO:0005024)			central_nervous_system(1)	1			Lung(22;0.000158)|LUSC - Lung squamous cell carcinoma(20;0.000384)			GCTCCGCGACGGCGGCTGTTC	0.657																																						dbGAP											0													26.0	29.0	28.0					19																	41113324		1986	4170	6156	-	-	-	SO:0001583	missense	0			Y13622	CCDS74368.1, CCDS74369.1, CCDS74370.1	19q13.1-q13.2	2011-10-20				ENSG00000090006		"""Latent transforming growth factor, beta binding proteins"""	6717	protein-coding gene	gene with protein product		604710				9660815, 9271198	Standard	NM_003573		Approved	LTBP-4, LTBP-4L, FLJ46318, FLJ90018	uc002ooh.1	Q8N2S1		ENST00000308370.7:c.1246G>A	19.37:g.41113324G>A	ENSP00000311905:p.Gly416Ser		O00508|O75412|O75413	Missense_Mutation	SNP	pfam_EGF-like_Ca-bd,pfam_TB_dom,superfamily_TB_dom,smart_EGF-like,smart_EGF-like_Ca-bd,pfscan_EG-like_dom	p.G416S	ENST00000308370.7	37	c.1246		19	.	.	.	.	.	.	.	.	.	.	G	25.3	4.619737	0.87460	.	.	ENSG00000090006	ENST00000204005;ENST00000308370;ENST00000396819	D;D;D	0.91295	-2.82;-2.82;-2.82	4.35	4.35	0.52113	Matrix fibril-associated (2);TGF-beta binding (1);	0.000000	0.38897	N	0.001525	D	0.94069	0.8099	M	0.62154	1.92	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.80764	0.994;0.994;0.994	D	0.94460	0.7675	10	0.56958	D	0.05	.	15.707	0.77592	0.0:0.0:1.0:0.0	.	349;416;379	E7EUU1;Q8N2S1;E7ENG9	.;LTBP4_HUMAN;.	S	379;416;349	ENSP00000204005:G379S;ENSP00000311905:G416S;ENSP00000380031:G349S	ENSP00000204005:G379S	G	+	1	0	LTBP4	45805164	1.000000	0.71417	0.618000	0.29105	0.976000	0.68499	3.689000	0.54706	1.985000	0.57927	0.306000	0.20318	GGC	LTBP4	-	superfamily_TB_dom	ENSG00000090006		0.657	LTBP4-203	KNOWN	basic|appris_candidate_longest	protein_coding	LTBP4	HGNC	protein_coding		52	0.00	0	G	NM_003573		41113324	41113324	+1	no_errors	ENST00000308370	ensembl	human	known	69_37n	missense	26	35.71	15	SNP	0.988	A
PYCARD	29108	genome.wustl.edu	37	16	31213061	31213061	+	Nonsense_Mutation	SNP	G	G	A			TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	e5fd7cbd-8fce-49e9-8d2c-d2a2e61367a5	a496949e-c185-40d9-82d2-c09d64d8b77f	g.chr16:31213061G>A	ENST00000247470.9	-	3	734	c.433C>T	c.(433-435)Cag>Tag	p.Q145*	PYCARD_ENST00000350605.4_Nonsense_Mutation_p.Q126*|C16orf98_ENST00000561916.2_5'Flank	NM_013258.4	NP_037390.2	Q9ULZ3	ASC_HUMAN	PYD and CARD domain containing	145	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of innate immune response (GO:0002218)|apoptotic process (GO:0006915)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to tumor necrosis factor (GO:0071356)|defense response to Gram-negative bacterium (GO:0050829)|defense response to virus (GO:0051607)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|macropinocytosis (GO:0044351)|myeloid dendritic cell activation (GO:0001773)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of interferon-beta production (GO:0032688)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of adaptive immune response (GO:0002821)|positive regulation of antigen processing and presentation of peptide antigen via MHC class II (GO:0002588)|positive regulation of apoptotic process (GO:0043065)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of cysteine-type endopeptidase activity (GO:2001056)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of interleukin-10 secretion (GO:2001181)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-6 secretion (GO:2000778)|positive regulation of interleukin-8 secretion (GO:2000484)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phagocytosis (GO:0050766)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell migration (GO:2000406)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of intrinsic apoptotic signaling pathway (GO:2001242)|regulation of protein stability (GO:0031647)|regulation of tumor necrosis factor-mediated signaling pathway (GO:0010803)|signal transduction (GO:0007165)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	AIM2 inflammasome complex (GO:0097169)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|IkappaB kinase complex (GO:0008385)|mitochondrion (GO:0005739)|NLRP1 inflammasome complex (GO:0072558)|NLRP3 inflammasome complex (GO:0072559)|nucleolus (GO:0005730)|nucleus (GO:0005634)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|protein homodimerization activity (GO:0042803)|Pyrin domain binding (GO:0032090)			NS(1)|kidney(1)	2						GCCTGGTACTGCTCATCCGTC	0.587																																						dbGAP											0													114.0	96.0	102.0					16																	31213061		2197	4300	6497	-	-	-	SO:0001587	stop_gained	0			AB023416	CCDS10708.1, CCDS10709.1	16p11.2	2013-01-22			ENSG00000103490	ENSG00000103490			16608	protein-coding gene	gene with protein product		606838					Standard	NM_013258		Approved	TMS-1, CARD5, ASC	uc010cak.3	Q9ULZ3	OTTHUMG00000176753	ENST00000247470.9:c.433C>T	16.37:g.31213061G>A	ENSP00000247470:p.Gln145*		Q96D12|Q9BSZ5|Q9HBD0|Q9NXJ8	Nonsense_Mutation	SNP	pfam_CARD,pfam_DAPIN,superfamily_DEATH-like,pfscan_CARD,pfscan_DAPIN	p.Q145*	ENST00000247470.9	37	c.433	CCDS10708.1	16	.	.	.	.	.	.	.	.	.	.	G	28.1	4.890341	0.91889	.	.	ENSG00000103490	ENST00000350605;ENST00000247470;ENST00000355986	.	.	.	5.5	5.5	0.81552	.	0.128968	0.35407	N	0.003225	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	17.2624	0.87073	0.0:0.0:1.0:0.0	.	.	.	.	X	126;145;85	.	ENSP00000247470:Q145X	Q	-	1	0	PYCARD	31120562	0.998000	0.40836	0.960000	0.40013	0.212000	0.24457	3.211000	0.51137	2.757000	0.94681	0.655000	0.94253	CAG	PYCARD	-	pfam_CARD,superfamily_DEATH-like,pfscan_CARD	ENSG00000103490		0.587	PYCARD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	PYCARD	HGNC	protein_coding	OTTHUMT00000255539.13	132	0.00	0	G	NM_013258		31213061	31213061	-1	no_errors	ENST00000247470	ensembl	human	known	69_37n	nonsense	47	61.90	78	SNP	0.973	A
RAB9B	51209	genome.wustl.edu	37	X	103080672	103080672	+	Missense_Mutation	SNP	C	C	A			TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	e5fd7cbd-8fce-49e9-8d2c-d2a2e61367a5	a496949e-c185-40d9-82d2-c09d64d8b77f	g.chrX:103080672C>A	ENST00000243298.2	-	3	327	c.43G>T	c.(43-45)Gat>Tat	p.D15Y		NM_016370.2	NP_057454.1	Q9NP90	RAB9B_HUMAN	RAB9B, member RAS oncogene family	15					protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)			endometrium(1)|kidney(1)|large_intestine(1)|lung(11)	14						ACTCCACCATCACCCAAGAGA	0.428																																						dbGAP											0													133.0	125.0	128.0					X																	103080672		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB036693	CCDS14515.1	Xq22.1-q22.3	2010-04-19			ENSG00000123570	ENSG00000123570		"""RAB, member RAS oncogene"""	14090	protein-coding gene	gene with protein product		300285				11043518	Standard	NM_016370		Approved	RAB9L	uc004ell.2	Q9NP90	OTTHUMG00000022112	ENST00000243298.2:c.43G>T	X.37:g.103080672C>A	ENSP00000243298:p.Asp15Tyr		B2R8M0|Q52LX2	Missense_Mutation	SNP	pfam_Small_GTPase,pfam_MIRO-like,pfam_Small_GTPase_ARF/SAR,pfam_Gtr1_RagA,pfam_ProtSyn_GTP-bd,smart_Small_GTPase_Ras,smart_Small_GTPase_Rab_type,smart_Small_GTPase_Rho,smart_Ran_GTPase,prints_Small_GTPase,tigrfam_Small_GTP-bd_dom	p.D15Y	ENST00000243298.2	37	c.43	CCDS14515.1	X	.	.	.	.	.	.	.	.	.	.	C	17.90	3.502312	0.64298	.	.	ENSG00000123570	ENST00000243298	T	0.80653	-1.4	5.95	5.95	0.96441	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.92156	0.7513	M	0.93106	3.38	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93681	0.6998	10	0.87932	D	0	-6.7301	16.5572	0.84488	0.0:1.0:0.0:0.0	.	15	Q9NP90	RAB9B_HUMAN	Y	15	ENSP00000243298:D15Y	ENSP00000243298:D15Y	D	-	1	0	RAB9B	102967328	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.518000	0.84900	0.600000	0.82982	GAT	RAB9B	-	pfam_Small_GTPase,pfam_MIRO-like,pfam_Small_GTPase_ARF/SAR,pfam_Gtr1_RagA,pfam_ProtSyn_GTP-bd,smart_Small_GTPase_Ras,smart_Small_GTPase_Rab_type,smart_Small_GTPase_Rho,smart_Ran_GTPase,prints_Small_GTPase,tigrfam_Small_GTP-bd_dom	ENSG00000123570		0.428	RAB9B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RAB9B	HGNC	protein_coding	OTTHUMT00000057746.1	152	0.00	0	C			103080672	103080672	-1	no_errors	ENST00000243298	ensembl	human	known	69_37n	missense	116	38.30	72	SNP	1.000	A
RIMS2	9699	genome.wustl.edu	37	8	104948831	104948831	+	Missense_Mutation	SNP	T	T	G			TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	e5fd7cbd-8fce-49e9-8d2c-d2a2e61367a5	a496949e-c185-40d9-82d2-c09d64d8b77f	g.chr8:104948831T>G	ENST00000436393.2	+	11	2003	c.1762T>G	c.(1762-1764)Tgg>Ggg	p.W588G	RIMS2_ENST00000406091.3_Missense_Mutation_p.W810G|RIMS2_ENST00000507740.1_Missense_Mutation_p.W602G|RIMS2_ENST00000262231.10_Missense_Mutation_p.W649G			Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	872					calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cAMP-mediated signaling (GO:0019933)|insulin secretion (GO:0030073)|intracellular protein transport (GO:0006886)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(22)|liver(1)|lung(68)|ovary(6)|pancreas(2)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(10)|urinary_tract(1)	144			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			GGAACCCAAATGGAACCAAAC	0.353										HNSCC(12;0.0054)																												dbGAP											0													103.0	97.0	99.0					8																	104948831		1832	4076	5908	-	-	-	SO:0001583	missense	0			AB018294	CCDS43761.1, CCDS64948.1, CCDS64949.1	8q22.3	2008-08-08	2002-06-12	2002-06-14					17283	protein-coding gene	gene with protein product		606630	"""RAB3 interacting protein 3"""	RAB3IP3		9872452, 12578829	Standard	NM_014677		Approved	KIAA0751, RIM2, OBOE	uc003ylp.3	Q9UQ26		ENST00000436393.2:c.1762T>G	8.37:g.104948831T>G	ENSP00000390665:p.Trp588Gly		B3KX91|F8WD47|O43413|Q86XL9|Q8IWV9|Q8IWW1	Missense_Mutation	SNP	pfam_C2_Ca-dep,pfam_PDZ,superfamily_C2_Ca/lipid-bd_dom_CaLB,superfamily_Znf_FYVE_PHD,superfamily_PDZ,smart_PDZ,smart_C2_Ca-dep,pfscan_C2_membr_targeting,pfscan_PDZ,pfscan_Rab-bd_domain,pfscan_Znf_FYVE-rel	p.W810G	ENST00000436393.2	37	c.2428		8	.	.	.	.	.	.	.	.	.	.	T	20.1	3.935817	0.73442	.	.	ENSG00000176406	ENST00000504942;ENST00000329869;ENST00000406091;ENST00000402998;ENST00000515551;ENST00000262231;ENST00000507740;ENST00000408894;ENST00000436393	D;D;D;D;D;D;D	0.84298	-1.83;-1.83;-1.83;-1.83;-1.83;-1.83;-1.83	4.69	4.69	0.59074	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	.	.	.	.	D	0.95705	0.8603	H	0.99117	4.435	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;0.997;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0	D	0.97498	1.0058	9	0.87932	D	0	.	14.4452	0.67345	0.0:0.0:0.0:1.0	.	872;872;588;649;602;810	Q9UQ26;Q9UQ26-2;D6RA03;Q9UQ26-1;Q9UQ26-3;F8WD47	RIMS2_HUMAN;.;.;.;.;.	G	810;825;810;872;602;649;602;602;588	ENSP00000427018:W810G;ENSP00000384892:W810G;ENSP00000425205:W602G;ENSP00000262231:W649G;ENSP00000423559:W602G;ENSP00000386228:W602G;ENSP00000390665:W588G	ENSP00000262231:W649G	W	+	1	0	RIMS2	105018007	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.948000	0.87774	1.872000	0.54250	0.383000	0.25322	TGG	RIMS2	-	pfam_C2_Ca-dep,superfamily_C2_Ca/lipid-bd_dom_CaLB,smart_C2_Ca-dep,pfscan_C2_membr_targeting	ENSG00000176406		0.353	RIMS2-007	NOVEL	basic|exp_conf	protein_coding	RIMS2	HGNC	protein_coding	OTTHUMT00000367217.1	129	0.00	0	T	NM_001100117		104948831	104948831	+1	no_errors	ENST00000406091	ensembl	human	known	69_37n	missense	189	28.20	75	SNP	1.000	G
USP36	57602	genome.wustl.edu	37	17	76803588	76803588	+	Missense_Mutation	SNP	G	G	A			TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	e5fd7cbd-8fce-49e9-8d2c-d2a2e61367a5	a496949e-c185-40d9-82d2-c09d64d8b77f	g.chr17:76803588G>A	ENST00000542802.3	-	14	1981	c.1538C>T	c.(1537-1539)tCc>tTc	p.S513F	USP36_ENST00000449938.2_Missense_Mutation_p.S213F|USP36_ENST00000312010.6_Missense_Mutation_p.S513F|USP36_ENST00000588467.1_5'Flank			Q9P275	UBP36_HUMAN	ubiquitin specific peptidase 36	513					protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	34			BRCA - Breast invasive adenocarcinoma(99;0.000842)|OV - Ovarian serous cystadenocarcinoma(97;0.151)			GGGGGAAGGGGACCCCGAGGG	0.577																																						dbGAP											0													56.0	51.0	53.0					17																	76803588		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB040886	CCDS32755.1	17q25.3	2008-02-05	2005-08-08			ENSG00000055483		"""Ubiquitin-specific peptidases"""	20062	protein-coding gene	gene with protein product		612543	"""ubiquitin specific protease 36"""			12838346	Standard	NM_025090		Approved	KIAA1453, FLJ12851	uc002jvz.1	Q9P275		ENST00000542802.3:c.1538C>T	17.37:g.76803588G>A	ENSP00000441214:p.Ser513Phe		Q05C98|Q05DD0|Q6IQ38|Q8NDM8|Q9NVC8	Missense_Mutation	SNP	pfam_Peptidase_C19,pfscan_Peptidase_C19	p.S513F	ENST00000542802.3	37	c.1538	CCDS32755.1	17	.	.	.	.	.	.	.	.	.	.	G	13.72	2.322600	0.41096	.	.	ENSG00000055483	ENST00000312010;ENST00000449938;ENST00000542802;ENST00000432878	T;T;T	0.21191	3.06;2.02;3.06	5.76	2.45	0.29901	.	0.981686	0.08387	N	0.953509	T	0.39911	0.1096	M	0.69823	2.125	0.35656	D	0.812145	D;D	0.65815	0.991;0.995	P;P	0.61800	0.786;0.894	T	0.43130	-0.9410	10	0.72032	D	0.01	-16.5156	6.4848	0.22083	0.1548:0.2839:0.5613:0.0	.	513;513	Q9P275;Q9P275-2	UBP36_HUMAN;.	F	513;213;513;513	ENSP00000310590:S513F;ENSP00000401119:S213F;ENSP00000441214:S513F	ENSP00000310590:S513F	S	-	2	0	USP36	74315183	0.997000	0.39634	0.601000	0.28877	0.027000	0.11550	2.869000	0.48444	0.746000	0.32786	0.655000	0.94253	TCC	USP36	-	NULL	ENSG00000055483		0.577	USP36-003	KNOWN	basic|appris_principal|CCDS	protein_coding	USP36	HGNC	protein_coding	OTTHUMT00000437472.3	173	0.57	1	G	NM_025090		76803588	76803588	-1	no_errors	ENST00000312010	ensembl	human	known	69_37n	missense	112	37.91	69	SNP	0.871	A
VAV2	7410	genome.wustl.edu	37	9	136634607	136634607	+	Missense_Mutation	SNP	T	T	C			TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	e5fd7cbd-8fce-49e9-8d2c-d2a2e61367a5	a496949e-c185-40d9-82d2-c09d64d8b77f	g.chr9:136634607T>C	ENST00000371850.3	-	28	2397	c.2366A>G	c.(2365-2367)aAc>aGc	p.N789S	VAV2_ENST00000371851.1_Missense_Mutation_p.N779S|VAV2_ENST00000406606.3_Intron	NM_001134398.1	NP_001127870.1	P52735	VAV2_HUMAN	vav 2 guanine nucleotide exchange factor	789					angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(3)|endometrium(1)|kidney(3)|large_intestine(5)|lung(13)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(1)	35				OV - Ovarian serous cystadenocarcinoma(145;3.9e-07)|Epithelial(140;2.07e-06)|all cancers(34;9.39e-06)		AAAAGAAAAGTTGTAGGAAGC	0.637																																						dbGAP											0													63.0	62.0	62.0					9																	136634607		1568	3581	5149	-	-	-	SO:0001583	missense	0				CCDS6979.1, CCDS48053.1	9q34.1	2013-02-14	2007-07-25		ENSG00000160293	ENSG00000160293		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	12658	protein-coding gene	gene with protein product		600428	"""vav 2 oncogene"""			7762982	Standard	NM_003371		Approved		uc004ces.3	P52735	OTTHUMG00000020882	ENST00000371850.3:c.2366A>G	9.37:g.136634607T>C	ENSP00000360916:p.Asn789Ser		A2RUM4|A8MQ12|B6ZDF5|Q5SYV3|Q5SYV4|Q5SYV5|Q6N012|Q6PIJ9|Q6Q317	Missense_Mutation	SNP	pfam_DH-domain,pfam_SH3_2,pfam_CAMSAP_CH,pfam_SH3_domain,pfam_SH2,pfam_CH-domain,pfam_Prot_Kinase_C-like_PE/DAG-bd,pfam_Pleckstrin_homology,superfamily_DH-domain,superfamily_CH-domain,superfamily_SH3_domain,smart_CH-domain,smart_DH-domain,smart_Pleckstrin_homology,smart_Prot_Kinase_C-like_PE/DAG-bd,smart_SH3_domain,smart_SH2,pfscan_CH-domain,pfscan_Pleckstrin_homology,pfscan_SH2,pfscan_SH3_domain,pfscan_Prot_Kinase_C-like_PE/DAG-bd,pfscan_DH-domain,prints_SH2,prints_SH3_domain	p.N789S	ENST00000371850.3	37	c.2366	CCDS48053.1	9	.	.	.	.	.	.	.	.	.	.	T	17.29	3.351961	0.61183	.	.	ENSG00000160293	ENST00000371850;ENST00000371851;ENST00000325440	T;T	0.61742	0.08;0.25	4.12	0.123	0.14709	Src homology-3 domain (1);	0.066276	0.56097	N	0.000023	T	0.54663	0.1872	N	0.22421	0.69	0.33887	D	0.63681	D	0.63880	0.993	D	0.68192	0.956	T	0.59663	-0.7412	10	0.33940	T	0.23	.	8.0086	0.30340	0.0:0.254:0.0:0.746	.	789	P52735	VAV2_HUMAN	S	789;779;779	ENSP00000360916:N789S;ENSP00000360917:N779S	ENSP00000317258:N779S	N	-	2	0	VAV2	135624428	1.000000	0.71417	0.997000	0.53966	0.964000	0.63967	0.867000	0.27968	-0.268000	0.09312	0.260000	0.18958	AAC	VAV2	-	superfamily_SH3_domain	ENSG00000160293		0.637	VAV2-001	KNOWN	basic|CCDS	protein_coding	VAV2	HGNC	protein_coding	OTTHUMT00000054939.1	133	0.00	0	T			136634607	136634607	-1	no_errors	ENST00000371850	ensembl	human	known	69_37n	missense	64	45.30	53	SNP	1.000	C
VGLL4	9686	genome.wustl.edu	37	3	11684952	11684952	+	Nonsense_Mutation	SNP	A	A	T			TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	e5fd7cbd-8fce-49e9-8d2c-d2a2e61367a5	a496949e-c185-40d9-82d2-c09d64d8b77f	g.chr3:11684952A>T	ENST00000430365.2	-	1	446	c.41T>A	c.(40-42)tTg>tAg	p.L14*	VGLL4_ENST00000404339.1_Intron|VGLL4_ENST00000273038.3_Intron	NM_001128219.1	NP_001121691.1	Q14135	VGLL4_HUMAN	vestigial-like family member 4	0					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				NS(1)|endometrium(1)|large_intestine(1)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	10				LUSC - Lung squamous cell carcinoma(1;0.089)|Lung(1;0.111)		CATCTTGTCCAAGTACTGATA	0.443																																						dbGAP											0													200.0	192.0	195.0					3																	11684952		1568	3582	5150	-	-	-	SO:0001587	stop_gained	0			D50911	CCDS2606.1, CCDS46754.1, CCDS46755.1, CCDS46756.1, CCDS68342.1, CCDS68343.1	3p25.2	2014-03-03	2014-03-03		ENSG00000144560	ENSG00000144560			28966	protein-coding gene	gene with protein product			"""vestigial like 4 (Drosophila)"""			8590280, 15140898	Standard	NM_001284390		Approved	KIAA0121	uc010hdx.1	Q14135	OTTHUMG00000129739	ENST00000430365.2:c.41T>A	3.37:g.11684952A>T	ENSP00000404251:p.Leu14*		B4DTS7|J3KN68|Q7L5V0|Q9BQ78	Nonsense_Mutation	SNP	smart_TDU_repeat	p.L14*	ENST00000430365.2	37	c.41	CCDS46754.1	3	.	.	.	.	.	.	.	.	.	.	A	43	9.983880	0.99310	.	.	ENSG00000144560	ENST00000430365	.	.	.	5.63	5.63	0.86233	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.1671	14.441	0.67318	1.0:0.0:0.0:0.0	.	.	.	.	X	14	.	ENSP00000404251:L14X	L	-	2	0	VGLL4	11659952	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.313000	0.89978	2.145000	0.66743	0.533000	0.62120	TTG	VGLL4	-	NULL	ENSG00000144560		0.443	VGLL4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	VGLL4	HGNC	protein_coding	OTTHUMT00000339133.1	181	0.55	1	A	NM_014667		11684952	11684952	-1	no_errors	ENST00000430365	ensembl	human	known	69_37n	nonsense	92	49.45	90	SNP	1.000	T
