#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_EVS_AA	i_EVS_All	i_EVS_EA	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains_WU	i_amino_acid_change_WU	i_annotation_transcript	i_build	i_c_position_WU	i_ccds_id	i_chromosome_name_WU	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_default_gene_name_WU	i_deletion_substructures_WU	i_domain_WU	i_ensembl_gene_id	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_name_WU	i_gene_name_source_WU	i_gene_type	i_havana_transcript	i_normal_ref_reads	i_normal_vaf	i_normal_var_reads	i_reference_WU	i_refseq_mrna_id	i_secondary_variant_classification	i_start_WU	i_stop_WU	i_strand_WU	i_transcript_error_WU	i_transcript_name_WU	i_transcript_source_WU	i_transcript_species_WU	i_transcript_status_WU	i_transcript_version_WU	i_trv_type_WU	i_tumor_ref_reads	i_tumor_vaf	i_tumors_var_reads	i_type_WU	i_ucsc_cons_WU	i_variant_WU
ARHGAP12	94134	genome.wustl.edu	37	10	32106730	32106730	+	Missense_Mutation	SNP	T	T	C			TCGA-AN-A041-01A-11W-A050-09	TCGA-AN-A041-10A-01W-A055-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f18c7389-6c8d-485f-a7f7-a450a42e3719	69c06be5-4545-42b9-85ea-dbb7e260ae00	g.chr10:32106730T>C	ENST00000344936.2	-	13	1951	c.1717A>G	c.(1717-1719)Aca>Gca	p.T573A	ARHGAP12_ENST00000375250.5_Missense_Mutation_p.T543A|ARHGAP12_ENST00000375245.4_Missense_Mutation_p.T521A|ARHGAP12_ENST00000492028.1_5'UTR|ARHGAP12_ENST00000396144.4_Missense_Mutation_p.T568A|ARHGAP12_ENST00000311380.4_Missense_Mutation_p.T521A	NM_001270697.1|NM_018287.6	NP_001257626.1|NP_060757.4	Q8IWW6	RHG12_HUMAN	Rho GTPase activating protein 12	573	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				morphogenesis of an epithelial sheet (GO:0002011)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.T573A(1)		NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(11)|lung(10)|skin(1)|urinary_tract(2)	31		Prostate(175;0.0199)				TTATTGATTGTACTACTAAGA	0.318																																						dbGAP											1	Substitution - Missense(1)	breast(1)											101.0	104.0	103.0					10																	32106730		2203	4300	6503	-	-	-	SO:0001583	missense	0			AY033594	CCDS7170.1, CCDS59214.1, CCDS59215.1, CCDS59216.1, CCDS73082.1	10p11.22	2013-01-10			ENSG00000165322	ENSG00000165322		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	16348	protein-coding gene	gene with protein product		610577				11854031	Standard	NM_001270695		Approved	FLJ20737, FLJ10971, FLJ21785	uc001ivz.2	Q8IWW6	OTTHUMG00000017911	ENST00000344936.2:c.1717A>G	10.37:g.32106730T>C	ENSP00000345808:p.Thr573Ala	Somatic		WXS	Illumina GAIIx	Phase_IV	B1ANY0|B1ANY1|B1ANY2|Q504X1|Q86UB3|Q8IWW7|Q8N3L1|Q9NT76	Missense_Mutation	SNP	pfam_RhoGAP_dom,pfam_Pleckstrin_homology,pfam_SH3_domain,superfamily_Rho_GTPase_activation_prot,superfamily_SH3_domain,superfamily_WW_Rsp5_WWP,smart_SH3_domain,smart_WW_Rsp5_WWP,smart_Pleckstrin_homology,smart_RhoGAP_dom,pfscan_Pleckstrin_homology,pfscan_SH3_domain,pfscan_WW_Rsp5_WWP,pfscan_RhoGAP_dom	p.T573A	ENST00000344936.2	37	c.1717	CCDS7170.1	10	.	.	.	.	.	.	.	.	.	.	T	14.18	2.459579	0.43736	.	.	ENSG00000165322	ENST00000311380;ENST00000375250;ENST00000344936;ENST00000396144;ENST00000375245	T;T;T;T;T	0.74842	-0.88;-0.88;-0.88;-0.88;-0.88	5.03	5.03	0.67393	Pleckstrin homology domain (3);	0.093243	0.64402	D	0.000001	T	0.55321	0.1913	N	0.16656	0.425	0.54753	D	0.999988	B;B;B;B;B;B	0.16396	0.008;0.017;0.014;0.017;0.017;0.014	B;B;B;B;B;B	0.22386	0.019;0.039;0.023;0.039;0.039;0.008	T	0.50224	-0.8853	10	0.09843	T	0.71	.	10.3231	0.43777	0.0:0.078:0.0:0.922	.	526;543;543;568;573;521	Q1RLN5;B3KR88;Q8IWW6-2;Q504X1;Q8IWW6;Q8IWW6-3	.;.;.;.;RHG12_HUMAN;.	A	521;543;573;568;521	ENSP00000310984:T521A;ENSP00000364399:T543A;ENSP00000345808:T573A;ENSP00000379448:T568A;ENSP00000364394:T521A	ENSP00000310984:T521A	T	-	1	0	ARHGAP12	32146736	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.426000	0.52778	1.996000	0.58369	0.533000	0.62120	ACA	ARHGAP12	-	pfam_Pleckstrin_homology,smart_Pleckstrin_homology,pfscan_Pleckstrin_homology	ENSG00000165322		0.318	ARHGAP12-009	KNOWN	basic|CCDS	protein_coding	ARHGAP12	HGNC	protein_coding	OTTHUMT00000047465.1	137	0.72	1	T			32106730	32106730	-1	no_errors	ENST00000344936	ensembl	human	known	69_37n	missense	283	18.21	63	SNP	1.000	C
CD1B	910	genome.wustl.edu	37	1	158299375	158299375	+	Missense_Mutation	SNP	C	C	T			TCGA-AN-A041-01A-11W-A050-09	TCGA-AN-A041-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f18c7389-6c8d-485f-a7f7-a450a42e3719	69c06be5-4545-42b9-85ea-dbb7e260ae00	g.chr1:158299375C>T	ENST00000368168.3	-	4	778	c.671G>A	c.(670-672)tGc>tAc	p.C224Y		NM_001764.2	NP_001755.1	P29016	CD1B_HUMAN	CD1b molecule	224	Ig-like.				antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	cell surface (GO:0009986)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)		p.C224Y(1)		breast(2)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	30	all_hematologic(112;0.0378)					TGAGACATGGCACACAAGCTG	0.572																																						dbGAP											1	Substitution - Missense(1)	breast(1)											78.0	76.0	76.0					1																	158299375		2203	4300	6503	-	-	-	SO:0001583	missense	0			M28826	CCDS1176.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158485	ENSG00000158485		"""CD molecules"", ""Immunoglobulin superfamily / C1-set domain containing"""	1635	protein-coding gene	gene with protein product		188360	"""CD1B antigen, b polypeptide"", ""CD1b antigen"""	CD1		2447586	Standard	NM_001764		Approved		uc001frx.3	P29016	OTTHUMG00000017513	ENST00000368168.3:c.671G>A	1.37:g.158299375C>T	ENSP00000357150:p.Cys224Tyr	Somatic		WXS	Illumina GAIIx	Phase_IV	Q5TDK9|Q5TDL0|Q9UMM2	Missense_Mutation	SNP	pfam_Ig_C1-set,superfamily_MHC_I/II-like_Ag-recog,smart_Ig_C1-set,pfscan_Ig-like	p.C224Y	ENST00000368168.3	37	c.671	CCDS1176.1	1	.	.	.	.	.	.	.	.	.	.	C	17.92	3.507081	0.64410	.	.	ENSG00000158485	ENST00000368168	D	0.93488	-3.23	4.26	4.26	0.50523	Immunoglobulin-like (1);MHC class I-like antigen recognition (1);Immunoglobulin C1-set (2);	0.000000	0.46442	D	0.000285	D	0.98178	0.9398	H	0.99626	4.665	0.45342	D	0.998332	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98294	1.0515	10	0.87932	D	0	-35.8329	12.3598	0.55197	0.0:1.0:0.0:0.0	.	224;224	P29016;P29016-2	CD1B_HUMAN;.	Y	224	ENSP00000357150:C224Y	ENSP00000357150:C224Y	C	-	2	0	CD1B	156565999	0.992000	0.36948	0.991000	0.47740	0.972000	0.66771	3.174000	0.50847	2.365000	0.80145	0.655000	0.94253	TGC	CD1B	-	pfam_Ig_C1-set,smart_Ig_C1-set,pfscan_Ig-like	ENSG00000158485		0.572	CD1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CD1B	HGNC	protein_coding	OTTHUMT00000046350.2	268	0.00	0	C	NM_001764		158299375	158299375	-1	no_errors	ENST00000368168	ensembl	human	known	69_37n	missense	326	13.91	53	SNP	0.992	T
DALRD3	55152	genome.wustl.edu	37	3	49055227	49055227	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AN-A041-01A-11W-A050-09	TCGA-AN-A041-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f18c7389-6c8d-485f-a7f7-a450a42e3719	69c06be5-4545-42b9-85ea-dbb7e260ae00	g.chr3:49055227delC	ENST00000341949.4	-	3	543	c.537delG	c.(535-537)tggfs	p.W179fs	NDUFAF3_ENST00000326912.4_5'Flank|MIR191_ENST00000384873.1_RNA|DALRD3_ENST00000313778.5_Frame_Shift_Del_p.W12fs|DALRD3_ENST00000440857.1_Frame_Shift_Del_p.W12fs|DALRD3_ENST00000395462.4_Frame_Shift_Del_p.W12fs|MIR425_ENST00000362162.1_RNA|DALRD3_ENST00000441576.2_Frame_Shift_Del_p.W179fs|DALRD3_ENST00000496568.1_5'UTR	NM_001009996.1	NP_001009996.1	Q5D0E6	DALD3_HUMAN	DALR anticodon binding domain containing 3	179					arginyl-tRNA aminoacylation (GO:0006420)		arginine-tRNA ligase activity (GO:0004814)|ATP binding (GO:0005524)			breast(2)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)	12				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		AGGCAGCGGGCCAGTCCACCC	0.652																																						dbGAP											0													40.0	32.0	35.0					3																	49055227		2203	4300	6503	-	-	-	SO:0001589	frameshift_variant	0			BC014099	CCDS2783.1, CCDS33754.1, CCDS63632.1	3p21.31	2005-01-10			ENSG00000178149	ENSG00000178149			25536	protein-coding gene	gene with protein product						12477932	Standard	NM_001009996		Approved	FLJ10496	uc003cvk.2	Q5D0E6	OTTHUMG00000156748	ENST00000341949.4:c.537delG	3.37:g.49055227delC	ENSP00000344989:p.Trp179fs	Somatic		WXS	Illumina GAIIx	Phase_IV	Q7Z5S7|Q86WY1|Q8N105|Q8NA89|Q9NVU8	Frame_Shift_Del	DEL	pfam_DALR_anticod-bd,superfamily_tRNAsynth_1a_anticodon-bd,smart_DALR_anticod-bd	p.W179fs	ENST00000341949.4	37	c.537	CCDS33754.1	3																																																																																			DALRD3	-	NULL	ENSG00000178149		0.652	DALRD3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	DALRD3	HGNC	protein_coding	OTTHUMT00000345581.1	19	0.00	0	C	NM_018114		49055227	49055227	-1	no_errors	ENST00000341949	ensembl	human	known	69_37n	frame_shift_del	4	33.33	2	DEL	1.000	-
DHX8	1659	genome.wustl.edu	37	17	41590796	41590796	+	Missense_Mutation	SNP	C	C	T			TCGA-AN-A041-01A-11W-A050-09	TCGA-AN-A041-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f18c7389-6c8d-485f-a7f7-a450a42e3719	69c06be5-4545-42b9-85ea-dbb7e260ae00	g.chr17:41590796C>T	ENST00000262415.3	+	17	2641	c.2569C>T	c.(2569-2571)Cca>Tca	p.P857S	DHX8_ENST00000540306.1_Missense_Mutation_p.P857S	NM_004941.1	NP_004932.1	Q14562	DHX8_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 8	857	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)	p.P857S(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	42		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.08)		TGTGGTGGACCCAGGATTCGT	0.478																																					NSCLC(56;1548 1661 49258 49987)	dbGAP											1	Substitution - Missense(1)	breast(1)											183.0	146.0	158.0					17																	41590796		2203	4300	6503	-	-	-	SO:0001583	missense	0			D50487	CCDS11464.1	17q21.31	2005-08-19	2003-06-13	2003-06-20		ENSG00000067596		"""DEAH-boxes"""	2749	protein-coding gene	gene with protein product		600396	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 8 (RNA helicase)"""	DDX8		7935475	Standard	NM_004941		Approved	HRH1, PRP22, PRPF22	uc002idu.1	Q14562		ENST00000262415.3:c.2569C>T	17.37:g.41590796C>T	ENSP00000262415:p.Pro857Ser	Somatic		WXS	Illumina GAIIx	Phase_IV		Missense_Mutation	SNP	pfam_Helicase-assoc_dom,pfam_DUF1605,pfam_Rbsml_prot_S1_RNA-bd_dom,pfam_Helicase_C,pfam_DNA/RNA_helicase_DEAD/DEAH_N,superfamily_NA-bd_OB-fold-like,smart_RNA-binding_domain_S1,smart_Helicase_ATP-bd,smart_Helicase_C,smart_Helicase-assoc_dom,pfscan_Rbsml_prot_S1_RNA-bd_dom,pfscan_Helicase_ATP-bd,pfscan_Helicase_C	p.P857S	ENST00000262415.3	37	c.2569	CCDS11464.1	17	.	.	.	.	.	.	.	.	.	.	C	32	5.163897	0.94727	.	.	ENSG00000067596	ENST00000540306;ENST00000262415	T;T	0.74315	-0.83;-0.83	5.87	5.87	0.94306	Helicase, C-terminal (3);	0.000000	0.85682	D	0.000000	T	0.77538	0.4145	N	0.12611	0.24	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.97110	1.0;0.992	T	0.81614	-0.0853	10	0.87932	D	0	.	19.262	0.93971	0.0:1.0:0.0:0.0	.	857;857	F5H658;Q14562	.;DHX8_HUMAN	S	857	ENSP00000437886:P857S;ENSP00000262415:P857S	ENSP00000262415:P857S	P	+	1	0	DHX8	38946322	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.635000	0.83286	2.797000	0.96272	0.650000	0.86243	CCA	DHX8	-	pfam_Helicase_C,smart_Helicase_C,pfscan_Helicase_C	ENSG00000067596		0.478	DHX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DHX8	HGNC	protein_coding	OTTHUMT00000453485.1	146	0.00	0	C			41590796	41590796	+1	no_errors	ENST00000262415	ensembl	human	known	69_37n	missense	400	11.09	50	SNP	1.000	T
DYNC1H1	1778	genome.wustl.edu	37	14	102494097	102494097	+	Missense_Mutation	SNP	G	G	A			TCGA-AN-A041-01A-11W-A050-09	TCGA-AN-A041-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f18c7389-6c8d-485f-a7f7-a450a42e3719	69c06be5-4545-42b9-85ea-dbb7e260ae00	g.chr14:102494097G>A	ENST00000360184.4	+	47	9354	c.9190G>A	c.(9190-9192)Gtc>Atc	p.V3064I		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	3064	AAA 4. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)	p.V3064I(1)		NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						CAACCTCCACGTCGTGTTCAC	0.577																																						dbGAP											1	Substitution - Missense(1)	breast(1)											135.0	120.0	125.0					14																	102494097		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"""Cytoplasmic dyneins"""	2961	protein-coding gene	gene with protein product		600112	"""dynein, cytoplasmic, heavy polypeptide 1"""	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.9190G>A	14.37:g.102494097G>A	ENSP00000348965:p.Val3064Ile	Somatic		WXS	Illumina GAIIx	Phase_IV	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Missense_Mutation	SNP	pfam_Dynein_heavy,pfam_Dynein_heavy_dom-1,pfam_Dynein_heavy_dom-2,pfam_ATPase_dyneun-rel_AAA,superfamily_Thioredoxin-like_fold,superfamily_Glutathione-S-Trfase_C-like,smart_AAA+_ATPase	p.V3064I	ENST00000360184.4	37	c.9190	CCDS9966.1	14	.	.	.	.	.	.	.	.	.	.	G	35	5.481712	0.96307	.	.	ENSG00000197102	ENST00000360184	T	0.39787	1.06	5.87	5.87	0.94306	Dynein heavy chain, P-loop containing D4 domain (1);ATPase, AAA+ type, core (1);	0.125811	0.53938	D	0.000042	T	0.36908	0.0984	L	0.35593	1.075	0.80722	D	1	P	0.51791	0.948	B	0.41666	0.363	T	0.05616	-1.0874	10	0.27785	T	0.31	.	20.2191	0.98319	0.0:0.0:1.0:0.0	.	3064	Q14204	DYHC1_HUMAN	I	3064	ENSP00000348965:V3064I	ENSP00000348965:V3064I	V	+	1	0	DYNC1H1	101563850	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.531000	0.98054	2.780000	0.95670	0.655000	0.94253	GTC	DYNC1H1	-	pfam_ATPase_dyneun-rel_AAA,smart_AAA+_ATPase	ENSG00000197102		0.577	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DYNC1H1	HGNC	protein_coding	OTTHUMT00000414574.1	134	0.00	0	G	NM_001376		102494097	102494097	+1	no_errors	ENST00000360184	ensembl	human	known	69_37n	missense	131	23.70	41	SNP	1.000	A
FLG	2312	genome.wustl.edu	37	1	152279873	152279873	+	Missense_Mutation	SNP	A	A	G	rs541771362	byFrequency	TCGA-AN-A041-01A-11W-A050-09	TCGA-AN-A041-10A-01W-A055-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f18c7389-6c8d-485f-a7f7-a450a42e3719	69c06be5-4545-42b9-85ea-dbb7e260ae00	g.chr1:152279873A>G	ENST00000368799.1	-	3	7524	c.7489T>C	c.(7489-7491)Tcc>Ccc	p.S2497P	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2497	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.S2497P(1)		autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTTCCCTGGGATGTGGTGTGG	0.557									Ichthyosis				A|||	3	0.000599042	0.0	0.0	5008	,	,		20768	0.003		0.0	False		,,,				2504	0.0					dbGAP											1	Substitution - Missense(1)	breast(1)											336.0	321.0	326.0					1																	152279873		2203	4300	6503	-	-	-	SO:0001583	missense	0	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.7489T>C	1.37:g.152279873A>G	ENSP00000357789:p.Ser2497Pro	Somatic		WXS	Illumina GAIIx	Phase_IV	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	pfam_Filaggrin,pfam_S100_Ca-bd_sub,pfscan_EF_HAND_2,prints_Filaggrin	p.S2497P	ENST00000368799.1	37	c.7489	CCDS30860.1	1	.	.	.	.	.	.	.	.	.	.	A	5.448	0.267823	0.10349	.	.	ENSG00000143631	ENST00000368799	T	0.01725	4.67	2.27	-4.11	0.03928	.	.	.	.	.	T	0.00552	0.0018	L	0.59967	1.855	0.09310	N	1	B	0.11235	0.004	B	0.04013	0.001	T	0.45116	-0.9283	9	0.27082	T	0.32	.	2.2743	0.04098	0.3222:0.0:0.2656:0.4122	.	2497	P20930	FILA_HUMAN	P	2497	ENSP00000357789:S2497P	ENSP00000357789:S2497P	S	-	1	0	FLG	150546497	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.408000	0.07169	-0.685000	0.05177	0.254000	0.18369	TCC	FLG	-	NULL	ENSG00000143631		0.557	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FLG	HGNC	protein_coding	OTTHUMT00000033742.1	299	0.66	2	A	NM_002016		152279873	152279873	-1	no_errors	ENST00000368799	ensembl	human	known	69_37n	missense	255	13.22	39	SNP	0.000	G
GATA3	2625	genome.wustl.edu	37	10	8111498	8111499	+	Frame_Shift_Del	DEL	GA	GA	-			TCGA-AN-A041-01A-11W-A050-09	TCGA-AN-A041-10A-01W-A055-09	GA	GA					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f18c7389-6c8d-485f-a7f7-a450a42e3719	69c06be5-4545-42b9-85ea-dbb7e260ae00	g.chr10:8111498_8111499delGA	ENST00000346208.3	+	5	1439_1440	c.984_985delGA	c.(982-987)tggaggfs	p.R330fs	GATA3_ENST00000379328.3_Frame_Shift_Del_p.R331fs|GATA3_ENST00000461472.1_3'UTR			P23771	GATA3_HUMAN	GATA binding protein 3	330					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.R330fs*22(1)		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						CCACACTCTGGAGGAGGAATGC	0.55			"""F, N, S"""		breast		"""HDR syndrome (HYPOPARATHYROIDISM, SENSORINEURAL DEAFNESS, AND RENAL DISEASE)"""																															dbGAP		Rec	yes		10	10p15	2625	GATA binding protein 3	yes	E	1	Deletion - Frameshift(1)	breast(1)																																								-	-	-	SO:0001589	frameshift_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.984_985delGA	10.37:g.8111498_8111499delGA	ENSP00000341619:p.Arg330fs	Somatic		WXS	Illumina GAIIx	Phase_IV	Q5VWG7|Q5VWG8|Q96J16	Frame_Shift_Del	DEL	pfam_Znf_GATA,smart_Znf_GATA,pirsf_TF_GATA-1/2/3,pfscan_Znf_GATA,prints_Znf_GATA	p.R330fs	ENST00000346208.3	37	c.987_988	CCDS7083.1	10																																																																																			GATA3	-	pfam_Znf_GATA,smart_Znf_GATA,pirsf_TF_GATA-1/2/3,pfscan_Znf_GATA	ENSG00000107485		0.550	GATA3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	GATA3	HGNC	protein_coding	OTTHUMT00000046719.1	158	0.00	0	GA	NM_001002295		8111498	8111499	+1	no_errors	ENST00000379328	ensembl	human	known	69_37n	frame_shift_del	197	30.48	89	DEL	1.000:1.000	-
ISG20L2	81875	genome.wustl.edu	37	1	156697031	156697031	+	Missense_Mutation	SNP	C	C	A			TCGA-AN-A041-01A-11W-A050-09	TCGA-AN-A041-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f18c7389-6c8d-485f-a7f7-a450a42e3719	69c06be5-4545-42b9-85ea-dbb7e260ae00	g.chr1:156697031C>A	ENST00000313146.6	-	1	1196	c.414G>T	c.(412-414)aaG>aaT	p.K138N	RRNAD1_ENST00000368218.4_5'Flank|RRNAD1_ENST00000368216.4_5'Flank|ISG20L2_ENST00000472824.2_5'Flank|ISG20L2_ENST00000368219.1_Missense_Mutation_p.K138N|RRNAD1_ENST00000524343.1_5'Flank	NM_030980.1	NP_112242.1	Q9H9L3	I20L2_HUMAN	interferon stimulated exonuclease gene 20kDa-like 2	138					ribosome biogenesis (GO:0042254)	nucleus (GO:0005634)	exonuclease activity (GO:0004527)|poly(A) RNA binding (GO:0044822)	p.K138N(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	16	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					GGGAGCTCTTCTTCTGAGAGC	0.473											OREG0013885	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										dbGAP											1	Substitution - Missense(1)	breast(1)											93.0	100.0	97.0					1																	156697031		2203	4300	6503	-	-	-	SO:0001583	missense	0			AK095697	CCDS1153.1	1q23.1	2013-10-11			ENSG00000143319	ENSG00000143319			25745	protein-coding gene	gene with protein product		611930				18065403	Standard	NM_030980		Approved	FLJ12671	uc001fps.1	Q9H9L3	OTTHUMG00000041301	ENST00000313146.6:c.414G>T	1.37:g.156697031C>A	ENSP00000323424:p.Lys138Asn	Somatic	1780	WXS	Illumina GAIIx	Phase_IV	D3DVC6|Q64KA2	Missense_Mutation	SNP	pfam_Exonuclease_RNaseT/DNA_pol3,superfamily_RNaseH-like_dom,smart_Exonuclease	p.K138N	ENST00000313146.6	37	c.414	CCDS1153.1	1	.	.	.	.	.	.	.	.	.	.	c	3.117	-0.181313	0.06380	.	.	ENSG00000143319	ENST00000313146;ENST00000368219	T;T	0.24908	1.83;1.83	4.16	1.16	0.20824	.	4.145870	0.00465	N	0.000115	T	0.14917	0.0360	L	0.27053	0.805	0.31531	N	0.661203	D	0.76494	0.999	P	0.61275	0.886	T	0.18618	-1.0331	10	0.17832	T	0.49	.	5.86	0.18740	0.0:0.6425:0.0:0.3575	.	138	Q9H9L3	I20L2_HUMAN	N	138	ENSP00000323424:K138N;ENSP00000357202:K138N	ENSP00000323424:K138N	K	-	3	2	ISG20L2	154963655	0.998000	0.40836	0.969000	0.41365	0.234000	0.25298	1.943000	0.40253	0.265000	0.21872	-0.136000	0.14681	AAG	ISG20L2	-	NULL	ENSG00000143319		0.473	ISG20L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ISG20L2	HGNC	protein_coding	OTTHUMT00000098969.1	94	0.00	0	C	NM_030980		156697031	156697031	-1	no_errors	ENST00000313146	ensembl	human	known	69_37n	missense	110	36.78	64	SNP	0.992	A
MIR17HG	407975	genome.wustl.edu	37	13	92003631	92003633	+	RNA	DEL	GCC	GCC	-			TCGA-AN-A041-01A-11W-A050-09	TCGA-AN-A041-10A-01W-A055-09	GCC	GCC					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f18c7389-6c8d-485f-a7f7-a450a42e3719	69c06be5-4545-42b9-85ea-dbb7e260ae00	g.chr13:92003631_92003633delGCC	ENST00000362310.2	+	0	184				MIR17HG_ENST00000385233.2_RNA|MIR17HG_ENST00000384829.1_RNA|MIR17HG_ENST00000362279.1_RNA|MIR17HG_ENST00000384878.1_RNA|MIR17HG_ENST00000385012.1_RNA	NR_029488.1		Q75NE6	MIRH1_HUMAN	miR-17-92 cluster host gene (non-protein coding)							integral component of membrane (GO:0016021)											ACTTGTCCCGGCCTGTTGAGTTT	0.384																																						dbGAP											0																																										-	-	-			0			AB176707		13q31.3	2014-07-18	2011-02-14	2009-07-24	ENSG00000215417	ENSG00000215417		"""-"""	23564	non-coding RNA	RNA, long non-coding	"""non-protein coding RNA 48"", ""long intergenic non-protein coding RNA 48"""	609415	"""chromosome 13 open reading frame 25"", ""microRNA host gene 1 (non-protein coding)"", ""MIR17 host gene (non-protein coding)"""	C13orf25, MIRHG1		15126345, 15944707, 16266980, 17210683, 23551855	Standard	NR_027349		Approved	FLJ14178, MIRH1, MIHG1, NCRNA00048, miR-17-92, LINC00048	uc010tie.1	Q75NE6	OTTHUMG00000017195		13.37:g.92003631_92003633delGCC		Somatic		WXS	Illumina GAIIx	Phase_IV	A4QMU7|Q75NE7	RNA	DEL	-	NULL	ENST00000362310.2	37	NULL		13																																																																																			MIR92A1	-	-	ENSG00000207968		0.384	MIR17HG-202	KNOWN	basic	miRNA	MIR92A1	HGNC	processed_transcript		165	0.00	0	GCC	NR_027349		92003631	92003633	+1	no_errors	ENST00000385233	ensembl	human	known	69_37n	rna	414	45.45	360	DEL	1.000:1.000:1.000	-
NCOA6	23054	genome.wustl.edu	37	20	33345587	33345587	+	Missense_Mutation	SNP	G	G	C			TCGA-AN-A041-01A-11W-A050-09	TCGA-AN-A041-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f18c7389-6c8d-485f-a7f7-a450a42e3719	69c06be5-4545-42b9-85ea-dbb7e260ae00	g.chr20:33345587G>C	ENST00000374796.2	-	8	3534	c.964C>G	c.(964-966)Cct>Gct	p.P322A	NCOA6_ENST00000359003.2_Missense_Mutation_p.P322A			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	322	CREBBP-binding region.|Gln-rich.|NCOA1-binding region.|TBP/GTF2A-binding region.				brain development (GO:0007420)|cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-templated transcription, initiation (GO:0006352)|glucocorticoid receptor signaling pathway (GO:0042921)|heart development (GO:0007507)|intracellular estrogen receptor signaling pathway (GO:0030520)|labyrinthine layer blood vessel development (GO:0060716)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)	histone methyltransferase complex (GO:0035097)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)	p.P322A(1)		NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	107						GCTCCAGAAGGCAGCTGGTTC	0.587																																						dbGAP											1	Substitution - Missense(1)	breast(1)											121.0	113.0	116.0					20																	33345587		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF128458	CCDS13241.1, CCDS74720.1	20q11	2008-08-01			ENSG00000198646	ENSG00000198646			15936	protein-coding gene	gene with protein product	"""nuclear receptor coactivator RAP250"", ""activating signal cointegrator-2"", ""peroxisome proliferator-activated receptor interacting protein"""	605299				8724849, 8263591	Standard	NM_014071		Approved	KIAA0181, RAP250, ASC2, AIB3, PRIP, TRBP, NRC	uc002xaw.3	Q14686	OTTHUMG00000032311	ENST00000374796.2:c.964C>G	20.37:g.33345587G>C	ENSP00000363929:p.Pro322Ala	Somatic		WXS	Illumina GAIIx	Phase_IV	A6NLF1|B2RMN5|E1P5P7|Q9NTZ9|Q9UH74|Q9UK86	Missense_Mutation	SNP	NULL	p.P322A	ENST00000374796.2	37	c.964	CCDS13241.1	20	.	.	.	.	.	.	.	.	.	.	G	9.518	1.107554	0.20714	.	.	ENSG00000198646	ENST00000374796;ENST00000359003;ENST00000397675	T;T	0.38077	1.16;1.16	4.86	4.86	0.63082	.	0.101534	0.43416	D	0.000571	T	0.24236	0.0587	N	0.19112	0.55	0.58432	D	0.999998	B;B	0.17667	0.001;0.023	B;B	0.14578	0.004;0.011	T	0.04930	-1.0917	10	0.27785	T	0.31	-5.6264	13.2556	0.60076	0.0:0.2942:0.7058:0.0	.	322;322	F6M2K2;Q14686	.;NCOA6_HUMAN	A	322;322;279	ENSP00000363929:P322A;ENSP00000351894:P322A	ENSP00000351894:P322A	P	-	1	0	NCOA6	32809248	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.998000	0.70653	2.253000	0.74438	0.467000	0.42956	CCT	NCOA6	-	NULL	ENSG00000198646		0.587	NCOA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NCOA6	HGNC	protein_coding	OTTHUMT00000078811.2	461	0.00	0	G	NM_014071		33345587	33345587	-1	no_errors	ENST00000359003	ensembl	human	known	69_37n	missense	359	35.20	195	SNP	1.000	C
PLXDC2	84898	genome.wustl.edu	37	10	20290912	20290912	+	Silent	SNP	C	C	A			TCGA-AN-A041-01A-11W-A050-09	TCGA-AN-A041-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f18c7389-6c8d-485f-a7f7-a450a42e3719	69c06be5-4545-42b9-85ea-dbb7e260ae00	g.chr10:20290912C>A	ENST00000377252.4	+	2	1162	c.321C>A	c.(319-321)atC>atA	p.I107I	PLXDC2_ENST00000377242.3_Silent_p.I107I	NM_001282736.1|NM_032812.7	NP_001269665.1|NP_116201.7	Q6UX71	PXDC2_HUMAN	plexin domain containing 2	107					multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.I107I(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|liver(1)|lung(9)|ovary(2)|skin(3)|stomach(1)	34						ACACTCAGATCGAGGTAGATA	0.438																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											58.0	54.0	55.0					10																	20290912		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AF378757	CCDS7132.1, CCDS60497.1	10p12.33	2006-04-12			ENSG00000120594	ENSG00000120594			21013	protein-coding gene	gene with protein product	"""tumor endothelial marker 7-related precursor"""	606827				11559528	Standard	NM_001282736		Approved	TEM7R, FLJ14623	uc001iqg.1	Q6UX71	OTTHUMG00000017781	ENST00000377252.4:c.321C>A	10.37:g.20290912C>A		Somatic		WXS	Illumina GAIIx	Phase_IV	Q96E59|Q96PD9|Q96SU9	Silent	SNP	pfam_Plexin_repeat,superfamily_Plexin-like_fold,smart_Plexin-like	p.I107	ENST00000377252.4	37	c.321	CCDS7132.1	10																																																																																			PLXDC2	-	NULL	ENSG00000120594		0.438	PLXDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PLXDC2	HGNC	protein_coding	OTTHUMT00000047101.2	139	0.00	0	C	NM_032812		20290912	20290912	+1	no_errors	ENST00000377252	ensembl	human	known	69_37n	silent	180	15.89	34	SNP	0.946	A
RARB	5915	genome.wustl.edu	37	3	25502731	25502731	+	Missense_Mutation	SNP	C	C	T			TCGA-AN-A041-01A-11W-A050-09	TCGA-AN-A041-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f18c7389-6c8d-485f-a7f7-a450a42e3719	69c06be5-4545-42b9-85ea-dbb7e260ae00	g.chr3:25502731C>T	ENST00000404969.1	+	2	226	c.226C>T	c.(226-228)Cca>Tca	p.P76S	RARB_ENST00000462272.1_3'UTR|RARB_ENST00000437042.2_5'UTR|RARB_ENST00000330688.4_Missense_Mutation_p.P69S|RARB_ENST00000458646.1_5'UTR			P10826	RARB_HUMAN	retinoic acid receptor, beta	76	Modulating.				embryonic digestive tract development (GO:0048566)|embryonic eye morphogenesis (GO:0048048)|embryonic hindlimb morphogenesis (GO:0035116)|gene expression (GO:0010467)|glandular epithelial cell development (GO:0002068)|growth plate cartilage development (GO:0003417)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of myelination (GO:0031641)|retinal pigment epithelium development (GO:0003406)|signal transduction (GO:0007165)|striatum development (GO:0021756)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ureteric bud development (GO:0001657)|ventricular cardiac muscle cell differentiation (GO:0055012)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|drug binding (GO:0008144)|retinoic acid receptor activity (GO:0003708)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.P76S(1)|p.P69S(1)		breast(3)|kidney(1)|large_intestine(10)|lung(11)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	28					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Tamibarotene(DB04942)|Tazarotene(DB00799)	CCCAAGCCCCCCATCTCCACT	0.493																																						dbGAP											2	Substitution - Missense(2)	breast(2)											103.0	108.0	107.0					3																	25502731		2203	4300	6503	-	-	-	SO:0001583	missense	0			Y00291	CCDS2642.1, CCDS46775.1	3p24	2013-01-16			ENSG00000077092	ENSG00000077092		"""Nuclear hormone receptors"""	9865	protein-coding gene	gene with protein product		180220					Standard	NM_016152		Approved	HAP, NR1B2, RRB2	uc003cdh.3	P10826	OTTHUMG00000130480	ENST00000404969.1:c.226C>T	3.37:g.25502731C>T	ENSP00000385865:p.Pro76Ser	Somatic		WXS	Illumina GAIIx	Phase_IV	P12891|Q00989|Q15298|Q9UN48	Missense_Mutation	SNP	pfam_Znf_hrmn_rcpt,pfam_Nucl_hrmn_rcpt_lig-bd_core,superfamily_Nucl_hormone_rcpt_ligand-bd,smart_Znf_hrmn_rcpt,smart_Nucl_hrmn_rcpt_lig-bd_core,pfscan_Znf_hrmn_rcpt,prints_Retinoic_acid_rcpt,prints_Str_hrmn_rcpt,prints_Znf_hrmn_rcpt,prints_Nuc_orph_rcpt,prints_Retinoid-X_rcpt/HNF4	p.P76S	ENST00000404969.1	37	c.226		3	.	.	.	.	.	.	.	.	.	.	C	34	5.374309	0.95923	.	.	ENSG00000077092	ENST00000383772;ENST00000404969;ENST00000538226;ENST00000330688	D;D;D	0.92858	-2.89;-3.12;-3.07	5.71	5.71	0.89125	.	0.120835	0.56097	N	0.000030	D	0.94899	0.8351	L	0.56280	1.765	0.80722	D	1	D;D	0.69078	0.997;0.967	D;P	0.65987	0.94;0.839	D	0.94246	0.7489	10	0.49607	T	0.09	.	19.9109	0.97025	0.0:1.0:0.0:0.0	.	76;69	P10826;F1D8S6	RARB_HUMAN;.	S	76;76;76;69	ENSP00000373282:P76S;ENSP00000385865:P76S;ENSP00000332296:P69S	ENSP00000332296:P69S	P	+	1	0	RARB	25477735	1.000000	0.71417	0.994000	0.49952	0.989000	0.77384	7.818000	0.86416	2.723000	0.93209	0.644000	0.83932	CCA	RARB	-	prints_Retinoic_acid_rcpt	ENSG00000077092		0.493	RARB-201	KNOWN	basic	protein_coding	RARB	HGNC	protein_coding		323	0.00	0	C	NM_000965, NM_016152		25502731	25502731	+1	no_errors	ENST00000404969	ensembl	human	known	69_37n	missense	399	24.57	130	SNP	1.000	T
RASGRP2	10235	genome.wustl.edu	37	11	64497599	64497600	+	Frame_Shift_Ins	INS	-	-	C			TCGA-AN-A041-01A-11W-A050-09	TCGA-AN-A041-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f18c7389-6c8d-485f-a7f7-a450a42e3719	69c06be5-4545-42b9-85ea-dbb7e260ae00	g.chr11:64497599_64497600insC	ENST00000354024.3	-	13	1731_1732	c.1479_1480insG	c.(1477-1482)gggcgcfs	p.R494fs	RASGRP2_ENST00000377497.3_Frame_Shift_Ins_p.R494fs|RASGRP2_ENST00000394432.3_Frame_Shift_Ins_p.R494fs|RASGRP2_ENST00000377494.1_Frame_Shift_Ins_p.R494fs	NM_153819.1	NP_722541.1	Q7LDG7	GRP2_HUMAN	RAS guanyl releasing protein 2 (calcium and DAG-regulated)	494					blood coagulation (GO:0007596)|cellular response to calcium ion (GO:0071277)|platelet activation (GO:0030168)|positive regulation of Rap GTPase activity (GO:0032854)|Ras protein signal transduction (GO:0007265)|regulation of cell growth (GO:0001558)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytosol (GO:0005829)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|diacylglycerol binding (GO:0019992)|guanyl-nucleotide exchange factor activity (GO:0005085)|lipid binding (GO:0008289)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						AAGCCCATGCGCCCCCCCAACA	0.644																																						dbGAP											0									,,	14,3776		3,8,1884					,,	4.5	1.0			26	8,7356		1,6,3675	no	frameshift,frameshift,frameshift	RASGRP2	NM_153819.1,NM_001098671.1,NM_001098670.1	,,	4,14,5559	A1A1,A1R,RR		0.1086,0.3694,0.1972	,,	,,		22,11132				-	-	-	SO:0001589	frameshift_variant	0			U78170	CCDS31598.1	11q13	2014-09-17			ENSG00000068831	ENSG00000068831		"""EF-hand domain containing"""	9879	protein-coding gene	gene with protein product		605577				9789079	Standard	NM_001098670		Approved	CALDAG-GEFI	uc009ypv.3	Q7LDG7	OTTHUMG00000045420	ENST00000354024.3:c.1480dupG	11.37:g.64497606_64497606dupC	ENSP00000338864:p.Arg494fs	Somatic		WXS	Illumina GAIIx	Phase_IV	A6NDC7|O00538|Q9UL65	Frame_Shift_Ins	INS	pfam_RasGRF_CDC25,pfam_Ras-like_Gua-exchang_fac_N,pfam_Prot_Kinase_C-like_PE/DAG-bd,superfamily_Ras_GEF_dom,smart_Ras-like_Gua-exchang_fac_N,smart_RasGRF_CDC25,smart_EF_hand_Ca-bd,smart_Prot_Kinase_C-like_PE/DAG-bd,pfscan_EF_HAND_2,pfscan_Prot_Kinase_C-like_PE/DAG-bd,pfscan_RasGRF_CDC25,pfscan_Ras-like_Gua-exchang_fac_N	p.R493fs	ENST00000354024.3	37	c.1480_1479	CCDS31598.1	11																																																																																			RASGRP2	-	NULL	ENSG00000068831		0.644	RASGRP2-002	NOVEL	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	RASGRP2	HGNC	protein_coding	OTTHUMT00000142062.1	18	0.00	0	-	NM_153819		64497599	64497600	-1	no_errors	ENST00000377494	ensembl	human	known	69_37n	frame_shift_ins	31	11.43	4	INS	1.000:1.000	C
RTN4	57142	genome.wustl.edu	37	2	55253661	55253661	+	Missense_Mutation	SNP	G	G	A			TCGA-AN-A041-01A-11W-A050-09	TCGA-AN-A041-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f18c7389-6c8d-485f-a7f7-a450a42e3719	69c06be5-4545-42b9-85ea-dbb7e260ae00	g.chr2:55253661G>A	ENST00000337526.6	-	3	1817	c.1574C>T	c.(1573-1575)tCt>tTt	p.S525F	RTN4_ENST00000354474.6_Missense_Mutation_p.S293F|RTN4_ENST00000317610.7_Intron|RTN4_ENST00000357732.4_Intron|RTN4_ENST00000357376.3_Missense_Mutation_p.S319F|RTN4_ENST00000402434.2_Intron|RTN4_ENST00000404909.1_Missense_Mutation_p.S319F|RTN4_ENST00000394611.2_Missense_Mutation_p.S319F|RTN4_ENST00000405240.1_Missense_Mutation_p.S319F	NM_020532.4	NP_065393.1	Q9NQC3	RTN4_HUMAN	reticulon 4	525					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonal fasciculation (GO:0007413)|cardiac epithelial to mesenchymal transition (GO:0060317)|cerebral cortex radial glia guided migration (GO:0021801)|endoplasmic reticulum tubular network organization (GO:0071786)|negative regulation of axon extension (GO:0030517)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell growth (GO:0030308)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of apoptotic process (GO:0042981)|regulation of axonogenesis (GO:0050770)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of cell migration (GO:0030334)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of endoplasmic reticulum membrane (GO:0030176)|intracellular (GO:0005622)|neuronal cell body (GO:0043025)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)	p.S525F(1)|p.S319F(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|prostate(1)|skin(1)|stomach(1)	36						ATCTGTCTCAGAATCCTGTGC	0.398																																						dbGAP											2	Substitution - Missense(2)	breast(2)											137.0	133.0	134.0					2																	55253661		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF087901	CCDS1851.1, CCDS1852.1, CCDS42683.1, CCDS42684.1, CCDS42685.1	2p14-p13	2008-05-23			ENSG00000115310	ENSG00000115310			14085	protein-coding gene	gene with protein product		604475				10667797, 10773680	Standard	NM_020532		Approved	NSP-CL, KIAA0886, NOGO, ASY	uc002rye.3	Q9NQC3	OTTHUMG00000129337	ENST00000337526.6:c.1574C>T	2.37:g.55253661G>A	ENSP00000337838:p.Ser525Phe	Somatic		WXS	Illumina GAIIx	Phase_IV	O94962|Q7L7Q5|Q7L7Q6|Q7L7Q8|Q8IUA4|Q96B16|Q9BXG5|Q9H212|Q9H3I3|Q9UQ42|Q9Y293|Q9Y2Y7|Q9Y5U6	Missense_Mutation	SNP	pfam_Reticulon,pfscan_Reticulon	p.S525F	ENST00000337526.6	37	c.1574	CCDS42684.1	2	.	.	.	.	.	.	.	.	.	.	G	15.38	2.817140	0.50633	.	.	ENSG00000115310	ENST00000405240;ENST00000357376;ENST00000337526;ENST00000394611;ENST00000404909;ENST00000354474	T;T;T;T;T;T	0.20332	2.08;2.08;2.21;2.08;2.08;2.09	5.94	2.99	0.34606	.	0.411799	0.25535	N	0.030006	T	0.17195	0.0413	L	0.51422	1.61	0.09310	N	0.999998	P	0.51933	0.949	B	0.40901	0.343	T	0.18335	-1.0340	10	0.72032	D	0.01	-6.9915	6.1575	0.20346	0.0778:0.28:0.5354:0.1068	.	525	Q9NQC3	RTN4_HUMAN	F	319;319;525;319;319;293	ENSP00000384471:S319F;ENSP00000349944:S319F;ENSP00000337838:S525F;ENSP00000378109:S319F;ENSP00000385650:S319F;ENSP00000346465:S293F	ENSP00000337838:S525F	S	-	2	0	RTN4	55107165	0.162000	0.22906	0.999000	0.59377	0.983000	0.72400	0.225000	0.17757	1.480000	0.48289	0.650000	0.86243	TCT	RTN4	-	NULL	ENSG00000115310		0.398	RTN4-001	KNOWN	basic|CCDS	protein_coding	RTN4	HGNC	protein_coding	OTTHUMT00000251484.1	381	0.00	0	G			55253661	55253661	-1	no_errors	ENST00000337526	ensembl	human	known	69_37n	missense	674	20.33	172	SNP	0.230	A
SAFB	6294	genome.wustl.edu	37	19	5664427	5664427	+	Missense_Mutation	SNP	A	A	T			TCGA-AN-A041-01A-11W-A050-09	TCGA-AN-A041-10A-01W-A055-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f18c7389-6c8d-485f-a7f7-a450a42e3719	69c06be5-4545-42b9-85ea-dbb7e260ae00	g.chr19:5664427A>T	ENST00000292123.5	+	17	2418	c.2311A>T	c.(2311-2313)Atg>Ttg	p.M771L	SAFB_ENST00000433404.1_Missense_Mutation_p.M601L|SAFB_ENST00000592224.1_Missense_Mutation_p.M770L|SAFB_ENST00000588852.1_Missense_Mutation_p.M771L|SAFB_ENST00000538656.1_Missense_Mutation_p.M613L|SAFB_ENST00000454510.1_Missense_Mutation_p.M702L	NM_001201338.1|NM_001201339.1|NM_002967.3	NP_001188267.1|NP_001188268.1|NP_002958.2	Q15424	SAFB1_HUMAN	scaffold attachment factor B	771	Arg-rich.|Interaction with POLR2A.|Interaction with SAFB2.				chromatin organization (GO:0006325)|growth (GO:0040007)|hormone metabolic process (GO:0042445)|intracellular estrogen receptor signaling pathway (GO:0030520)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.M771L(1)		breast(3)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|liver(1)|lung(6)|ovary(2)|skin(1)	23				UCEC - Uterine corpus endometrioid carcinoma (162;0.000222)		TTCAAGGTCAATGATGGGAGA	0.463																																					Colon(88;338 1345 6184 8214 20897)	dbGAP											1	Substitution - Missense(1)	breast(1)											97.0	93.0	94.0					19																	5664427		2203	4300	6503	-	-	-	SO:0001583	missense	0			L43631	CCDS12142.1, CCDS56077.1, CCDS59339.1, CCDS59340.1	19p13.3-p13.2	2013-02-12				ENSG00000160633		"""RNA binding motif (RRM) containing"""	10520	protein-coding gene	gene with protein product	"""Hsp27 ERE-TATA binding protein"""	602895				9605873, 8600450	Standard	NM_002967		Approved	HET, SAFB1	uc002mcg.3	Q15424		ENST00000292123.5:c.2311A>T	19.37:g.5664427A>T	ENSP00000292123:p.Met771Leu	Somatic		WXS	Illumina GAIIx	Phase_IV	A0AV56|B7Z5B6|B7ZLP6|F5H0H3|O60406|Q59HH8	Missense_Mutation	SNP	pfam_RRM_dom,pfam_SAP_DNA-bd,smart_SAP_DNA-bd,smart_RRM_dom,pfscan_SAP_DNA-bd,pfscan_RRM_dom	p.M771L	ENST00000292123.5	37	c.2311	CCDS12142.1	19	.	.	.	.	.	.	.	.	.	.	A	13.74	2.327087	0.41197	.	.	ENSG00000160633	ENST00000454510;ENST00000540206;ENST00000433404;ENST00000292123;ENST00000538656	T;T;T;T	0.10573	2.88;3.06;2.86;2.86	5.04	5.04	0.67666	.	0.100350	0.44097	D	0.000495	T	0.09598	0.0236	L	0.44542	1.39	0.49798	D	0.999825	B;B;B;B;B;B;B	0.25486	0.127;0.003;0.005;0.003;0.003;0.003;0.003	B;B;B;B;B;B;B	0.20767	0.031;0.002;0.005;0.004;0.004;0.004;0.004	T	0.10776	-1.0615	10	0.10111	T	0.7	-14.0594	13.3436	0.60559	1.0:0.0:0.0:0.0	.	570;613;702;770;771;771;770	B7Z1C7;B7Z2F6;F5H0H3;B7ZLP5;A0AV56;Q15424;B7ZLP6	.;.;.;.;.;SAFB1_HUMAN;.	L	702;666;601;771;613	ENSP00000415895:M702L;ENSP00000404545:M601L;ENSP00000292123:M771L;ENSP00000438880:M613L	ENSP00000292123:M771L	M	+	1	0	SAFB	5615427	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	4.510000	0.60455	2.018000	0.59344	0.533000	0.62120	ATG	SAFB	-	NULL	ENSG00000160633		0.463	SAFB-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	SAFB	HGNC	protein_coding	OTTHUMT00000451641.2	86	0.00	0	A			5664427	5664427	+1	no_errors	ENST00000588852	ensembl	human	known	69_37n	missense	66	25.00	22	SNP	1.000	T
SALL3	27164	genome.wustl.edu	37	18	76753938	76753939	+	Frame_Shift_Ins	INS	-	-	G			TCGA-AN-A041-01A-11W-A050-09	TCGA-AN-A041-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f18c7389-6c8d-485f-a7f7-a450a42e3719	69c06be5-4545-42b9-85ea-dbb7e260ae00	g.chr18:76753938_76753939insG	ENST00000537592.2	+	2	1947_1948	c.1947_1948insG	c.(1948-1950)gggfs	p.G650fs	SALL3_ENST00000536229.3_Frame_Shift_Ins_p.G517fs|SALL3_ENST00000575389.2_Frame_Shift_Ins_p.G650fs	NM_171999.3	NP_741996.2	Q9BXA9	SALL3_HUMAN	spalt-like transcription factor 3	650					forelimb morphogenesis (GO:0035136)|hindlimb morphogenesis (GO:0035137)|negative regulation of smoothened signaling pathway (GO:0045879)|olfactory bulb interneuron development (GO:0021891)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(40)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)|Melanoma(33;0.16)|Prostate(75;0.167)		OV - Ovarian serous cystadenocarcinoma(15;4.69e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0256)		AGTTTCCGTTCGGGGGGCTGCT	0.639																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AJ007421	CCDS12013.1	18q23	2013-10-17	2013-10-17		ENSG00000256463	ENSG00000256463		"""Zinc fingers, C2H2-type"""	10527	protein-coding gene	gene with protein product		605079	"""sal (Drosophila)-like 3"", ""sal-like 3 (Drosophila)"""			10610715	Standard	NM_171999		Approved	ZNF796	uc002lmt.3	Q9BXA9	OTTHUMG00000132896	ENST00000537592.2:c.1953dupG	18.37:g.76753944_76753944dupG	ENSP00000441823:p.Gly650fs	Somatic		WXS	Illumina GAIIx	Phase_IV	Q9UGH1	Frame_Shift_Ins	INS	pfam_Znf_C2H2,smart_Znf_C2H2-like,pfscan_Znf_C2H2	p.L651fs	ENST00000537592.2	37	c.1947_1948	CCDS12013.1	18																																																																																			SALL3	-	NULL	ENSG00000256463		0.639	SALL3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	SALL3	HGNC	protein_coding	OTTHUMT00000256397.1	15	0.00	0	-	NM_171999		76753938	76753939	+1	no_errors	ENST00000537592	ensembl	human	known	69_37n	frame_shift_ins	3	40.00	2	INS	0.981:1.000	G
SHC3	53358	genome.wustl.edu	37	9	91727508	91727508	+	Silent	SNP	T	T	G			TCGA-AN-A041-01A-11W-A050-09	TCGA-AN-A041-10A-01W-A055-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f18c7389-6c8d-485f-a7f7-a450a42e3719	69c06be5-4545-42b9-85ea-dbb7e260ae00	g.chr9:91727508T>G	ENST00000375835.4	-	2	814	c.508A>C	c.(508-510)Agg>Cgg	p.R170R	SHC3_ENST00000375830.1_5'UTR|RP11-82L18.2_ENST00000429700.1_RNA	NM_016848.5	NP_058544.3	Q92529	SHC3_HUMAN	SHC (Src homology 2 domain containing) transforming protein 3	170	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				central nervous system development (GO:0007417)|epidermal growth factor receptor signaling pathway (GO:0007173)|insulin receptor signaling pathway (GO:0008286)|learning or memory (GO:0007611)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Ras protein signal transduction (GO:0007265)|synaptic transmission, glutamatergic (GO:0035249)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)	signal transducer activity (GO:0004871)	p.R170R(1)		breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|skin(3)	28						TCAAGAGACCTCATTGAGCGC	0.408																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											109.0	103.0	105.0					9																	91727508		2203	4299	6502	-	-	-	SO:0001819	synonymous_variant	0			D84361	CCDS6681.1	9q22.1	2013-02-14	2005-05-24		ENSG00000148082	ENSG00000148082		"""SH2 domain containing"""	18181	protein-coding gene	gene with protein product		605263	"""src homology 2 domain containing transforming protein C3"""			8808684	Standard	NM_016848		Approved	N-Shc, NSHC, SHCC	uc004aqf.2	Q92529	OTTHUMG00000020179	ENST00000375835.4:c.508A>C	9.37:g.91727508T>G		Somatic		WXS	Illumina GAIIx	Phase_IV	Q5T7I7|Q8TAP2|Q9UCX5	Silent	SNP	pfam_PTyr_interaction_dom,pfam_SH2,smart_PTyr_interaction_dom,smart_SH2,pfscan_PTyr_interaction_dom,pfscan_SH2,prints_PID_domain,prints_SH2	p.R170	ENST00000375835.4	37	c.508	CCDS6681.1	9																																																																																			SHC3	-	pfam_PTyr_interaction_dom,smart_PTyr_interaction_dom,pfscan_PTyr_interaction_dom,prints_PID_domain	ENSG00000148082		0.408	SHC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SHC3	HGNC	protein_coding	OTTHUMT00000052986.1	222	0.00	0	T	NM_016848		91727508	91727508	-1	no_errors	ENST00000375835	ensembl	human	known	69_37n	silent	281	21.29	76	SNP	1.000	G
SNRNP200	23020	genome.wustl.edu	37	2	96944396	96944396	+	Missense_Mutation	SNP	G	G	C			TCGA-AN-A041-01A-11W-A050-09	TCGA-AN-A041-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f18c7389-6c8d-485f-a7f7-a450a42e3719	69c06be5-4545-42b9-85ea-dbb7e260ae00	g.chr2:96944396G>C	ENST00000323853.5	-	38	5454	c.5377C>G	c.(5377-5379)Ctg>Gtg	p.L1793V	SNRNP200_ENST00000349783.5_Intron	NM_014014.4	NP_054733.2	O75643	U520_HUMAN	small nuclear ribonucleoprotein 200kDa (U5)	1793					ATP catabolic process (GO:0006200)|cis assembly of pre-catalytic spliceosome (GO:0000354)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U5 snRNP (GO:0005682)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)	p.L1793V(1)		breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|lung(37)|ovary(7)|prostate(4)|skin(5)|stomach(1)|urinary_tract(1)	90						AGGTCACTCAGGGTCTGCTCC	0.567																																						dbGAP											1	Substitution - Missense(1)	breast(1)											93.0	89.0	90.0					2																	96944396		2203	4300	6503	-	-	-	SO:0001583	missense	0			AL831994	CCDS2020.1	2q11.2	2013-05-13	2008-10-29	2008-10-29	ENSG00000144028	ENSG00000144028			30859	protein-coding gene	gene with protein product	"""U5 snRNP specific protein, 200 KD"""	601664	"""activating signal cointegrator 1 complex subunit 3-like 1"", ""retinitis pigmentosa 33 (autosomal dominant)"""	ASCC3L1, RP33		9872452, 8670905, 9774689, 9539711, 16612614, 19878916	Standard	NM_014014		Approved	U5-200KD, HELIC2, KIAA0788, BRR2	uc002svu.3	O75643	OTTHUMG00000130455	ENST00000323853.5:c.5377C>G	2.37:g.96944396G>C	ENSP00000317123:p.Leu1793Val	Somatic		WXS	Illumina GAIIx	Phase_IV	O94884|Q6NZY0|Q6PX59|Q8NBE6|Q96IF2|Q9H7S0	Missense_Mutation	SNP	pfam_Sec63-dom,pfam_DNA/RNA_helicase_DEAD/DEAH_N,pfam_Helicase/UvrB_dom,pfam_Helicase_C,smart_Helicase_ATP-bd,smart_Helicase_C,smart_Sec63-dom,pfscan_Helicase_ATP-bd,pfscan_Helicase_C	p.L1793V	ENST00000323853.5	37	c.5377	CCDS2020.1	2	.	.	.	.	.	.	.	.	.	.	G	14.02	2.410450	0.42715	.	.	ENSG00000144028	ENST00000323853;ENST00000536601;ENST00000543553	T	0.48522	0.81	5.77	4.67	0.58626	.	0.000000	0.64402	D	0.000002	T	0.47911	0.1471	L	0.58101	1.795	0.80722	D	1	B	0.23735	0.09	B	0.34093	0.175	T	0.45804	-0.9236	10	0.46703	T	0.11	-12.1086	12.2049	0.54346	0.1145:0.0:0.8855:0.0	.	1793	O75643	U520_HUMAN	V	1793;252;376	ENSP00000317123:L1793V	ENSP00000317123:L1793V	L	-	1	2	SNRNP200	96308123	0.967000	0.33354	1.000000	0.80357	0.999000	0.98932	1.568000	0.36418	2.884000	0.98904	0.655000	0.94253	CTG	SNRNP200	-	NULL	ENSG00000144028		0.567	SNRNP200-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SNRNP200	HGNC	protein_coding	OTTHUMT00000252846.2	172	0.00	0	G	NM_014014		96944396	96944396	-1	no_errors	ENST00000323853	ensembl	human	known	69_37n	missense	158	14.59	27	SNP	1.000	C
STK3	6788	genome.wustl.edu	37	8	99719442	99719442	+	Missense_Mutation	SNP	C	C	A			TCGA-AN-A041-01A-11W-A050-09	TCGA-AN-A041-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f18c7389-6c8d-485f-a7f7-a450a42e3719	69c06be5-4545-42b9-85ea-dbb7e260ae00	g.chr8:99719442C>A	ENST00000419617.2	-	5	589	c.449G>T	c.(448-450)gGa>gTa	p.G150V	STK3_ENST00000523601.1_Missense_Mutation_p.G178V	NM_006281.3	NP_006272.2	Q13188	STK3_HUMAN	serine/threonine kinase 3	150	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cell differentiation involved in embryonic placenta development (GO:0060706)|central nervous system development (GO:0007417)|endocardium development (GO:0003157)|hepatocyte apoptotic process (GO:0097284)|hippo signaling (GO:0035329)|intracellular signal transduction (GO:0035556)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of organ growth (GO:0046621)|neural tube formation (GO:0001841)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|primitive hemopoiesis (GO:0060215)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein dimerization activity (GO:0046983)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activator activity (GO:0043539)|protein serine/threonine kinase activity (GO:0004674)	p.G150V(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	17	Breast(36;2.4e-06)	Breast(495;0.106)	OV - Ovarian serous cystadenocarcinoma(57;0.0382)	KIRC - Kidney renal clear cell carcinoma(542;9.44e-06)		GAGAATATTTCCAGCTTTTAT	0.323																																						dbGAP											1	Substitution - Missense(1)	breast(1)											62.0	59.0	60.0					8																	99719442		1822	4115	5937	-	-	-	SO:0001583	missense	0			BC010640	CCDS47900.1, CCDS59108.1, CCDS75774.1	8q22.2	2011-05-24	2010-06-25		ENSG00000104375	ENSG00000104375			11406	protein-coding gene	gene with protein product		605030	"""serine/threonine kinase 3 (Ste20, yeast homolog)"""			8816758	Standard	NM_006281		Approved	MST2, KRS1	uc003yip.4	Q13188	OTTHUMG00000164651	ENST00000419617.2:c.449G>T	8.37:g.99719442C>A	ENSP00000390500:p.Gly150Val	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K722|B3KYA7|Q15445|Q15801|Q96FM6	Missense_Mutation	SNP	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_SARAH_domain,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_SARAH,pfscan_Prot_kinase_cat_dom	p.G150V	ENST00000419617.2	37	c.449	CCDS47900.1	8	.	.	.	.	.	.	.	.	.	.	C	25.2	4.612735	0.87258	.	.	ENSG00000104375	ENST00000419617;ENST00000523601	T;T	0.14766	2.48;2.48	5.32	5.32	0.75619	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.36744	0.0978	L	0.60012	1.86	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.07177	-1.0786	10	0.87932	D	0	.	18.9913	0.92793	0.0:1.0:0.0:0.0	.	150;178	Q13188;B3KYA7	STK3_HUMAN;.	V	150;178	ENSP00000390500:G150V;ENSP00000429744:G178V	ENSP00000390500:G150V	G	-	2	0	STK3	99788618	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.493000	0.84123	0.561000	0.74099	GGA	STK3	-	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_cat_dom	ENSG00000104375		0.323	STK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	STK3	HGNC	protein_coding	OTTHUMT00000379635.1	138	0.00	0	C	NM_006281		99719442	99719442	-1	no_errors	ENST00000419617	ensembl	human	known	69_37n	missense	348	11.22	44	SNP	1.000	A
TNFAIP8	25816	genome.wustl.edu	37	5	118728611	118728611	+	Silent	SNP	C	C	T			TCGA-AN-A041-01A-11W-A050-09	TCGA-AN-A041-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f18c7389-6c8d-485f-a7f7-a450a42e3719	69c06be5-4545-42b9-85ea-dbb7e260ae00	g.chr5:118728611C>T	ENST00000503646.1	+	3	820	c.132C>T	c.(130-132)gaC>gaT	p.D44D	TNFAIP8_ENST00000274456.6_Silent_p.D34D|TNFAIP8_ENST00000415806.2_3'UTR|TNFAIP8_ENST00000504771.2_Silent_p.D44D|TNFAIP8_ENST00000504642.1_Silent_p.D46D|TNFAIP8_ENST00000513374.1_Silent_p.D56D			O95379	TFIP8_HUMAN	tumor necrosis factor, alpha-induced protein 8	44					defense response to Gram-positive bacterium (GO:0050830)|interleukin-1 beta production (GO:0032611)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)	cytoplasm (GO:0005737)	cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)	p.D44D(1)		ovary(1)	1		all_cancers(142;0.0317)|Prostate(80;0.111)|Breast(839;0.231)		Epithelial(69;4.63e-83)|OV - Ovarian serous cystadenocarcinoma(64;1.39e-82)|all cancers(49;4.88e-75)|GBM - Glioblastoma multiforme(465;0.00338)|BRCA - Breast invasive adenocarcinoma(61;0.0148)|COAD - Colon adenocarcinoma(49;0.0829)		CCTTAATAGACGACACAAGTA	0.463																																						dbGAP											1	Substitution - coding silent(1)	breast(1)																																								-	-	-	SO:0001819	synonymous_variant	0			AF070671	CCDS47257.1, CCDS47258.1, CCDS68933.1	5q23.1	2008-02-05			ENSG00000145779	ENSG00000145779			17260	protein-coding gene	gene with protein product		612111				10233894, 10644768	Standard	NM_001286813		Approved	GG2-1, MDC-3.13, SCC-S2	uc003ksi.3	O95379	OTTHUMG00000162949	ENST00000503646.1:c.132C>T	5.37:g.118728611C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	B3KMH1|B3KMI2|B7Z713|Q9P1Q1|Q9UER5|Q9UP47	Silent	SNP	pfam_DUF758	p.D44	ENST00000503646.1	37	c.132	CCDS47258.1	5																																																																																			TNFAIP8	-	pfam_DUF758	ENSG00000145779		0.463	TNFAIP8-002	PUTATIVE	alternative_5_UTR|basic|exp_conf|CCDS	protein_coding	TNFAIP8	HGNC	protein_coding	OTTHUMT00000371134.2	128	0.00	0	C	NM_014350		118728611	118728611	+1	no_errors	ENST00000504771	ensembl	human	known	69_37n	silent	108	19.40	26	SNP	0.445	T
TGFBI	7045	genome.wustl.edu	37	5	135385250	135385250	+	Silent	SNP	C	C	T	rs556797846		TCGA-AN-A041-01A-11W-A050-09	TCGA-AN-A041-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f18c7389-6c8d-485f-a7f7-a450a42e3719	69c06be5-4545-42b9-85ea-dbb7e260ae00	g.chr5:135385250C>T	ENST00000442011.2	+	7	1055	c.894C>T	c.(892-894)ggC>ggT	p.G298G	TGFBI_ENST00000305126.8_Silent_p.G298G	NM_000358.2	NP_000349.1	Q15582	BGH3_HUMAN	transforming growth factor, beta-induced, 68kDa	298	FAS1 2. {ECO:0000255|PROSITE- ProRule:PRU00082}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|chondrocyte differentiation (GO:0002062)|extracellular matrix organization (GO:0030198)|negative regulation of cell adhesion (GO:0007162)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	collagen binding (GO:0005518)|extracellular matrix binding (GO:0050840)|integrin binding (GO:0005178)	p.G298G(1)		breast(6)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	32			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			GTATCCTGGGCGACCCAGAAG	0.542													C|||	1	0.000199681	0.0	0.0	5008	,	,		21842	0.0		0.0	False		,,,				2504	0.001					dbGAP											1	Substitution - coding silent(1)	breast(1)											48.0	51.0	50.0					5																	135385250		1986	4153	6139	-	-	-	SO:0001819	synonymous_variant	0			M77349	CCDS47266.1	5q31	2008-02-05	2002-08-29		ENSG00000120708	ENSG00000120708			11771	protein-coding gene	gene with protein product		601692	"""transforming growth factor, beta-induced, 68kD"""	CSD3, LCD1, CSD1, CSD2		9463327	Standard	NM_000358		Approved	BIGH3, CDB1, CDGG1	uc003lbf.4	Q15582	OTTHUMG00000163213	ENST00000442011.2:c.894C>T	5.37:g.135385250C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	D3DQB1|O14471|O14472|O14476|O43216|O43217|O43218|O43219|Q53XM1	Nonsense_Mutation	SNP	pfam_FAS1_domain,superfamily_FAS1_domain,smart_FAS1_domain,pfscan_FAS1_domain	p.R16*	ENST00000442011.2	37	c.46	CCDS47266.1	5	.	.	.	.	.	.	.	.	.	.	C	1.652	-0.513697	0.04200	.	.	ENSG00000120708	ENST00000508767;ENST00000514554	.	.	.	5.94	-9.61	0.00550	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	0.1155	2.142	0.03777	0.2352:0.3172:0.2968:0.1508	.	.	.	.	X	74;16	.	.	R	+	1	2	TGFBI	135413149	0.337000	0.24766	0.328000	0.25416	0.256000	0.26092	-0.362000	0.07602	-2.550000	0.00480	-2.630000	0.00154	CGA	TGFBI	-	pfam_FAS1_domain,superfamily_FAS1_domain,smart_FAS1_domain,pfscan_FAS1_domain	ENSG00000120708		0.542	TGFBI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TGFBI	HGNC	protein_coding	OTTHUMT00000372108.1	96	0.00	0	C			135385250	135385250	+1	no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region	ENST00000514554	ensembl	human	novel	69_37n	nonsense	107	11.57	14	SNP	0.530	T
TNFSF9	8744	genome.wustl.edu	37	19	6534674	6534675	+	Frame_Shift_Ins	INS	-	-	G			TCGA-AN-A041-01A-11W-A050-09	TCGA-AN-A041-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f18c7389-6c8d-485f-a7f7-a450a42e3719	69c06be5-4545-42b9-85ea-dbb7e260ae00	g.chr19:6534674_6534675insG	ENST00000245817.3	+	3	400_401	c.362_363insG	c.(361-366)acggggfs	p.TG121fs		NM_003811.3	NP_003802.1	P41273	TNFL9_HUMAN	tumor necrosis factor (ligand) superfamily, member 9	121					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|immune response (GO:0006955)|myeloid dendritic cell differentiation (GO:0043011)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of cytotoxic T cell differentiation (GO:0045585)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			central_nervous_system(1)|lung(1)|ovary(1)|prostate(1)|skin(1)	5						GTGTCCCTGACGGGGGGCCTGA	0.599																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			U03398	CCDS12169.1	19p13.3	2008-07-22				ENSG00000125657		"""Tumor necrosis factor (ligand) superfamily"""	11939	protein-coding gene	gene with protein product	"""receptor 4-1BB ligand"", ""homolog of mouse 4-1BB-L"""	606182				8405064, 8088337	Standard	NM_003811		Approved	4-1BB-L	uc002mfh.2	P41273		ENST00000245817.3:c.368dupG	19.37:g.6534680_6534680dupG	ENSP00000245817:p.Thr121fs	Somatic		WXS	Illumina GAIIx	Phase_IV	Q2M3S2	Frame_Shift_Ins	INS	pfam_TNF,superfamily_Tumour_necrosis_fac-like,smart_TNF,pfscan_TNF	p.L124fs	ENST00000245817.3	37	c.362_363	CCDS12169.1	19																																																																																			TNFSF9	-	pfam_TNF,superfamily_Tumour_necrosis_fac-like,smart_TNF,pfscan_TNF	ENSG00000125657		0.599	TNFSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TNFSF9	HGNC	protein_coding	OTTHUMT00000457856.1	18	0.00	0	-	NM_003811		6534674	6534675	+1	no_errors	ENST00000245817	ensembl	human	known	69_37n	frame_shift_ins	13	27.78	5	INS	0.004:0.000	G
ZAP70	7535	genome.wustl.edu	37	2	98354541	98354541	+	Silent	SNP	C	C	T			TCGA-AN-A041-01A-11W-A050-09	TCGA-AN-A041-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f18c7389-6c8d-485f-a7f7-a450a42e3719	69c06be5-4545-42b9-85ea-dbb7e260ae00	g.chr2:98354541C>T	ENST00000264972.5	+	13	1922	c.1707C>T	c.(1705-1707)taC>taT	p.Y569Y	ZAP70_ENST00000451498.2_Silent_p.Y262Y|ZAP70_ENST00000463643.1_3'UTR|ZAP70_ENST00000442208.1_Silent_p.Y443Y	NM_001079.3	NP_001070.2	P43403	ZAP70_HUMAN	zeta-chain (TCR) associated protein kinase 70kDa	569	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adaptive immune response (GO:0002250)|B cell activation (GO:0042113)|beta selection (GO:0043366)|immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|negative thymic T cell selection (GO:0045060)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of T cell differentiation (GO:0045582)|positive thymic T cell selection (GO:0045059)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|T cell activation (GO:0042110)|T cell aggregation (GO:0070489)|T cell differentiation (GO:0030217)|T cell migration (GO:0072678)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)	p.Y569Y(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	29						CCGAACTGTACGCACTCATGA	0.607																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											83.0	80.0	81.0					2																	98354541		2203	4299	6502	-	-	-	SO:0001819	synonymous_variant	0			L05148	CCDS33254.1, CCDS33255.1	2q11-q13	2014-09-17	2002-08-29		ENSG00000115085	ENSG00000115085		"""SH2 domain containing"""	12858	protein-coding gene	gene with protein product		176947	"""zeta-chain (TCR) associated protein kinase (70 kD)"""	SRK		1423621	Standard	NM_001079		Approved	ZAP-70, STD	uc002syd.1	P43403	OTTHUMG00000153060	ENST00000264972.5:c.1707C>T	2.37:g.98354541C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	A6NFP4|Q6PIA4|Q8IXD6|Q9UBS6	Silent	SNP	pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Prot_kinase_cat_dom,pfam_SH2,superfamily_Kinase-like_dom,smart_SH2,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pirsf_Tyr_kinase_non-rcpt_SYK/ZAP70,prints_Ser-Thr/Tyr_kinase_cat_dom,prints_SH2,pfscan_SH2,pfscan_Prot_kinase_cat_dom	p.Y569	ENST00000264972.5	37	c.1707	CCDS33254.1	2																																																																																			ZAP70	-	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_SYK/ZAP70,prints_Ser-Thr/Tyr_kinase_cat_dom,pfscan_Prot_kinase_cat_dom	ENSG00000115085		0.607	ZAP70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ZAP70	HGNC	protein_coding	OTTHUMT00000329278.1	238	0.00	0	C			98354541	98354541	+1	no_errors	ENST00000264972	ensembl	human	known	69_37n	silent	256	18.21	57	SNP	0.165	T
ZCCHC2	54877	genome.wustl.edu	37	18	60230264	60230264	+	Missense_Mutation	SNP	C	C	A			TCGA-AN-A041-01A-11W-A050-09	TCGA-AN-A041-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f18c7389-6c8d-485f-a7f7-a450a42e3719	69c06be5-4545-42b9-85ea-dbb7e260ae00	g.chr18:60230264C>A	ENST00000269499.5	+	9	1991	c.1573C>A	c.(1573-1575)Cca>Aca	p.P525T	ZCCHC2_ENST00000586834.1_Missense_Mutation_p.P204T	NM_017742.4	NP_060212.4	Q9C0B9	ZCHC2_HUMAN	zinc finger, CCHC domain containing 2	525						cytoplasm (GO:0005737)	nucleic acid binding (GO:0003676)|phosphatidylinositol binding (GO:0035091)|zinc ion binding (GO:0008270)	p.P525T(1)		breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(10)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	25						AAGTTGTTCTCCATTGGATGG	0.388																																						dbGAP											1	Substitution - Missense(1)	breast(1)											114.0	109.0	111.0					18																	60230264		1894	4124	6018	-	-	-	SO:0001583	missense	0			AB051531	CCDS45880.1	18q21.33	2012-04-19			ENSG00000141664	ENSG00000141664		"""Zinc fingers, CCHC domain containing"""	22916	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 49"""	C18orf49		11214970	Standard	NM_017742		Approved	FLJ20281, KIAA1744, FLJ20222	uc002lip.4	Q9C0B9		ENST00000269499.5:c.1573C>A	18.37:g.60230264C>A	ENSP00000269499:p.Pro525Thr	Somatic		WXS	Illumina GAIIx	Phase_IV	B2RPG6|Q8N3S1|Q9NXF6	Missense_Mutation	SNP	pfam_Znf_CCHC,superfamily_Phox,superfamily_Znf_CCHC,smart_Znf_CCHC,pfscan_Znf_CCHC	p.P525T	ENST00000269499.5	37	c.1573	CCDS45880.1	18	.	.	.	.	.	.	.	.	.	.	C	11.82	1.751807	0.31046	.	.	ENSG00000141664	ENST00000269499	T	0.26518	1.73	6.03	5.06	0.68205	.	0.412814	0.23452	N	0.048026	T	0.17789	0.0427	L	0.27053	0.805	0.39986	D	0.974988	B	0.28713	0.22	B	0.30401	0.115	T	0.05750	-1.0866	10	0.56958	D	0.05	-6.6656	7.3353	0.26607	0.0:0.8202:0.0:0.1798	.	525	Q9C0B9	ZCHC2_HUMAN	T	525	ENSP00000269499:P525T	ENSP00000269499:P525T	P	+	1	0	ZCCHC2	58381244	1.000000	0.71417	0.995000	0.50966	0.431000	0.31685	2.465000	0.45075	2.854000	0.98071	0.655000	0.94253	CCA	ZCCHC2	-	NULL	ENSG00000141664		0.388	ZCCHC2-005	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	ZCCHC2	HGNC	protein_coding	OTTHUMT00000450083.1	227	0.00	0	C	NM_017742		60230264	60230264	+1	no_errors	ENST00000269499	ensembl	human	known	69_37n	missense	241	20.59	63	SNP	1.000	A
