#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
BICD2	23299	genome.wustl.edu	37	9	95526977	95526977	+	Missense_Mutation	SNP	G	G	T			TCGA-LL-A440-01A-11D-A243-09	TCGA-LL-A440-10A-01D-A243-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	c033740f-b98c-453b-b290-6a1d7d81b72a	3ad6a505-3409-4b03-80fc-f69d88303bb9	g.chr9:95526977G>T	ENST00000375512.3	-	1	117	c.50C>A	c.(49-51)gCg>gAg	p.A17E	BICD2_ENST00000356884.6_Missense_Mutation_p.A17E	NM_015250.3	NP_056065.1	Q8TD16	BICD2_HUMAN	bicaudal D homolog 2 (Drosophila)	17					cell death (GO:0008219)|microtubule anchoring at microtubule organizing center (GO:0072393)|minus-end-directed organelle transport along microtubule (GO:0072385)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	Rab GTPase binding (GO:0017137)			cervix(3)|endometrium(4)|kidney(1)|large_intestine(6)|lung(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	23						CTCCGGCTGCGCCTCCATCAC	0.731																																						dbGAP											0													9.0	10.0	9.0					9																	95526977		2068	4116	6184	-	-	-	SO:0001583	missense	0			AB014599	CCDS6700.1, CCDS35064.1	9q22.32	2008-02-05			ENSG00000185963	ENSG00000185963			17208	protein-coding gene	gene with protein product		609797				9734811	Standard	NM_001003800		Approved	KIAA0699	uc004asp.1	Q8TD16	OTTHUMG00000021036	ENST00000375512.3:c.50C>A	9.37:g.95526977G>T	ENSP00000364662:p.Ala17Glu	Somatic		WXS	Illumina GAIIx	Phase_IV	O75181|Q5TBQ2|Q5TBQ3|Q96LH2|Q9BT84|Q9H561	Missense_Mutation	SNP	pfam_Bicaudal-D_microtubule-assoc	p.A17E	ENST00000375512.3	37	c.50	CCDS6700.1	9	.	.	.	.	.	.	.	.	.	.	.	16.77	3.215213	0.58452	.	.	ENSG00000185963	ENST00000356884;ENST00000375512	T;T	0.44881	0.91;0.92	4.35	4.35	0.52113	.	0.211686	0.38548	N	0.001654	T	0.42539	0.1207	L	0.34521	1.04	0.43512	D	0.995772	D;P	0.55800	0.973;0.954	P;P	0.53360	0.724;0.534	T	0.10660	-1.0620	10	0.17832	T	0.49	-38.5328	15.1518	0.72706	0.0:0.0:1.0:0.0	.	17;17	Q8TD16-2;Q8TD16	.;BICD2_HUMAN	E	17	ENSP00000349351:A17E;ENSP00000364662:A17E	ENSP00000349351:A17E	A	-	2	0	BICD2	94566798	1.000000	0.71417	1.000000	0.80357	0.857000	0.48899	8.700000	0.91322	2.349000	0.79799	0.195000	0.17529	GCG	BICD2	-	NULL	ENSG00000185963		0.731	BICD2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	BICD2	HGNC	protein_coding	OTTHUMT00000055508.1	25	0.00	0	G	NM_015250		95526977	95526977	-1	no_errors	ENST00000356884	ensembl	human	known	69_37n	missense	12	41.67	10	SNP	1.000	T
CHEK2	11200	genome.wustl.edu	37	22	29120886	29120886	+	Intron	SNP	C	C	T			TCGA-LL-A440-01A-11D-A243-09	TCGA-LL-A440-10A-01D-A243-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	c033740f-b98c-453b-b290-6a1d7d81b72a	3ad6a505-3409-4b03-80fc-f69d88303bb9	g.chr22:29120886C>T	ENST00000405598.1	-	5	784				CHEK2_ENST00000382566.1_Intron|CHEK2_ENST00000402731.1_Intron|CHEK2_ENST00000403642.1_Intron|CHEK2_ENST00000544772.1_Intron|CHEK2_ENST00000404276.1_Intron|CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000348295.3_Intron|CHEK2_ENST00000382578.1_Intron|CHEK2_ENST00000328354.6_Intron|CHEK2_ENST00000382580.2_Intron			O96017	CHK2_HUMAN	checkpoint kinase 2						cellular protein catabolic process (GO:0044257)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|double-strand break repair (GO:0006302)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|replicative senescence (GO:0090399)|response to gamma radiation (GO:0010332)|signal transduction in response to DNA damage (GO:0042770)|signal transduction involved in intra-S DNA damage checkpoint (GO:0072428)|spindle assembly involved in mitosis (GO:0090307)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						AAACCATATTCTGTAAGGACA	0.413			F			breast		Direct reversal of damage;Other conserved DNA damage response genes																														dbGAP	yes	Rec		familial breast cancer	22	22q12.1	11200	CHK2 checkpoint homolog (S. pombe)		E	0													22.0	23.0	23.0					22																	29120886		876	1990	2866	-	-	-	SO:0001627	intron_variant	0			AF086904	CCDS13843.1, CCDS13844.1, CCDS33629.1	22q12.1	2014-09-17	2011-11-11	2001-09-27	ENSG00000183765	ENSG00000183765			16627	protein-coding gene	gene with protein product		604373	"""CHK2 (checkpoint, S.pombe) homolog"", ""CHK2 checkpoint homolog (S. pombe)"""	RAD53		9836640, 10097108	Standard	NM_001257387		Approved	CDS1, CHK2, HuCds1, PP1425, bA444G7	uc003adt.1	O96017	OTTHUMG00000151023	ENST00000405598.1:c.592+78G>A	22.37:g.29120886C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Missense_Mutation	SNP	superfamily_SMAD_FHA_domain	p.R157K	ENST00000405598.1	37	c.470	CCDS13843.1	22	.	.	.	.	.	.	.	.	.	.	C	4.024	0.001925	0.07819	.	.	ENSG00000183765	ENST00000447421	T	0.57752	0.38	4.06	0.771	0.18504	.	.	.	.	.	T	0.40619	0.1124	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.30446	-0.9978	6	0.31617	T	0.26	.	6.3385	0.21309	0.0:0.6833:0.0:0.3167	.	.	.	.	K	157	ENSP00000397478:R157K	ENSP00000403659:R157K	R	-	2	0	CHEK2	27450886	0.000000	0.05858	0.000000	0.03702	0.124000	0.20399	0.002000	0.13061	0.266000	0.21894	0.460000	0.39030	AGA	CHEK2	-	NULL	ENSG00000183765		0.413	CHEK2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	CHEK2	HGNC	protein_coding	OTTHUMT00000321150.1	27	0.00	0	C	NM_001005735		29120886	29120886	-1	no_errors	ENST00000448511	ensembl	human	known	69_37n	missense	27	12.90	4	SNP	0.000	T
GALNT3	2591	genome.wustl.edu	37	2	166621457	166621457	+	Missense_Mutation	SNP	G	G	T			TCGA-LL-A440-01A-11D-A243-09	TCGA-LL-A440-10A-01D-A243-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	c033740f-b98c-453b-b290-6a1d7d81b72a	3ad6a505-3409-4b03-80fc-f69d88303bb9	g.chr2:166621457G>T	ENST00000392701.3	-	3	1400	c.625C>A	c.(625-627)Ctc>Atc	p.L209I		NM_004482.3	NP_004473.2	Q14435	GALT3_HUMAN	polypeptide N-acetylgalactosaminyltransferase 3	209	Catalytic subdomain A.				carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation via serine (GO:0018242)|protein O-linked glycosylation via threonine (GO:0018243)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|manganese ion binding (GO:0030145)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.L209F(3)		NS(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|skin(1)	20						GAAGAATAGAGCACACTGTGG	0.423																																						dbGAP											3	Substitution - Missense(3)	prostate(3)											169.0	155.0	160.0					2																	166621457		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS2226.1	2q24-q31	2014-03-13	2014-03-13		ENSG00000115339	ENSG00000115339	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4125	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 3"""	601756	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 3 (GalNAc-T3)"""			9592121, 15133511	Standard	NM_004482		Approved	GalNAc-T3, HHS, HFTC	uc010fph.1	Q14435	OTTHUMG00000132157	ENST00000392701.3:c.625C>A	2.37:g.166621457G>T	ENSP00000376465:p.Leu209Ile	Somatic		WXS	Illumina GAIIx	Phase_IV	Q53TG9|Q7Z476	Missense_Mutation	SNP	pfam_Glyco_trans_2,pfam_Ricin_B_lectin,superfamily_Ricin_B_lectin,smart_Ricin_B_lectin,pfscan_Ricin_B_lectin	p.L209I	ENST00000392701.3	37	c.625	CCDS2226.1	2	.	.	.	.	.	.	.	.	.	.	G	5.876	0.345858	0.11126	.	.	ENSG00000115339	ENST00000392701;ENST00000412248	T;T	0.64991	-0.13;-0.13	5.8	4.92	0.64577	Glycosyl transferase, family 2 (1);	0.130705	0.51477	D	0.000093	T	0.63153	0.2487	L	0.41961	1.31	0.80722	D	1	B	0.31519	0.327	P	0.45195	0.473	T	0.58346	-0.7652	10	0.22706	T	0.39	.	13.2478	0.60033	0.0:0.0:0.5676:0.4324	.	209	Q14435	GALT3_HUMAN	I	209	ENSP00000376465:L209I;ENSP00000412643:L209I	ENSP00000376465:L209I	L	-	1	0	GALNT3	166329703	1.000000	0.71417	1.000000	0.80357	0.006000	0.05464	4.024000	0.57218	1.434000	0.47414	-0.310000	0.09108	CTC	GALNT3	-	pfam_Glyco_trans_2	ENSG00000115339		0.423	GALNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GALNT3	HGNC	protein_coding	OTTHUMT00000255205.2	24	0.00	0	G	NM_004482		166621457	166621457	-1	no_errors	ENST00000392701	ensembl	human	known	69_37n	missense	14	17.65	3	SNP	1.000	T
GPER1	2852	genome.wustl.edu	37	7	1132016	1132016	+	Missense_Mutation	SNP	G	G	C	rs199736734		TCGA-LL-A440-01A-11D-A243-09	TCGA-LL-A440-10A-01D-A243-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	c033740f-b98c-453b-b290-6a1d7d81b72a	3ad6a505-3409-4b03-80fc-f69d88303bb9	g.chr7:1132016G>C	ENST00000297469.3	+	2	1343	c.652G>C	c.(652-654)Gag>Cag	p.E218Q	GPER1_ENST00000401670.1_Missense_Mutation_p.E218Q|GPER1_ENST00000397088.3_Missense_Mutation_p.E218Q|GPER1_ENST00000397092.1_Missense_Mutation_p.E218Q|C7orf50_ENST00000397100.2_Intron|C7orf50_ENST00000357429.6_Intron|C7orf50_ENST00000488073.1_Intron|C7orf50_ENST00000397098.3_Intron	NM_001505.2	NP_001496.1	Q99527	GPER1_HUMAN	G protein-coupled estrogen receptor 1	218					apoptotic chromosome condensation (GO:0030263)|cell cycle (GO:0007049)|cellular response to estradiol stimulus (GO:0071392)|cellular response to glucose stimulus (GO:0071333)|cellular response to mineralocorticoid stimulus (GO:0071389)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to tumor necrosis factor (GO:0071356)|cytosolic calcium ion homeostasis (GO:0051480)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|mineralocorticoid receptor signaling pathway (GO:0031959)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA metabolic process (GO:0051053)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of gene expression (GO:0010629)|negative regulation of inflammatory response (GO:0050728)|negative regulation of leukocyte activation (GO:0002695)|negative regulation of lipid biosynthetic process (GO:0051055)|neuronal action potential (GO:0019228)|nuclear fragmentation involved in apoptotic nuclear change (GO:0030264)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of gene expression (GO:0010628)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|positive regulation of insulin secretion (GO:0032024)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neurogenesis (GO:0050769)|positive regulation of neurotransmitter secretion (GO:0001956)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of uterine smooth muscle contraction (GO:0070474)|positive regulation of vasodilation (GO:0045909)|steroid hormone mediated signaling pathway (GO:0043401)	axon (GO:0030424)|axon terminus (GO:0043679)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|dendrite (GO:0030425)|dendritic shaft (GO:0043198)|dendritic spine head (GO:0044327)|dendritic spine membrane (GO:0032591)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|keratin filament (GO:0045095)|mitochondrial membrane (GO:0031966)|neuronal postsynaptic density (GO:0097481)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	chromatin binding (GO:0003682)|estrogen receptor activity (GO:0030284)|G-protein coupled receptor activity (GO:0004930)|mineralocorticoid receptor activity (GO:0017082)|steroid binding (GO:0005496)										GCAGTGGCTCGAGGTCACGCT	0.667																																						dbGAP											0													68.0	48.0	55.0					7																	1132016		2199	4298	6497	-	-	-	SO:0001583	missense	0			U63917	CCDS5322.1	7p22	2013-08-14	2007-07-03	2013-08-14	ENSG00000164850	ENSG00000164850			4485	protein-coding gene	gene with protein product		601805	"""G protein-coupled receptor 30"""	CMKRL2, GPR30, GPER		9479505, 17655271	Standard	NM_001098201		Approved	FEG-1, GPCR-Br, LERGU, LERGU2, DRY12, LyGPR, CEPR	uc003skb.2	Q99527	OTTHUMG00000023680	ENST00000297469.3:c.652G>C	7.37:g.1132016G>C	ENSP00000297469:p.Glu218Gln	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K6C5|B5BUJ1|O00143|O43494|Q13631|Q6FHL1|Q96F42|Q99981	Missense_Mutation	SNP	pfam_7TM_GPCR_Rhodpsn,pfam_7TM_GPCR_olfarory/Srsx,prints_7TM_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_supfam	p.E218Q	ENST00000297469.3	37	c.652	CCDS5322.1	7	.	.	.	.	.	.	.	.	.	.	G	17.27	3.347008	0.61183	.	.	ENSG00000164850	ENST00000401670;ENST00000397092;ENST00000297469;ENST00000397088;ENST00000508834	T;T;T;T	0.71934	-0.61;-0.61;-0.61;-0.61	5.41	5.41	0.78517	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.80793	0.4691	L	0.58101	1.795	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	T	0.75144	-0.3421	10	0.14656	T	0.56	-23.3501	18.2014	0.89839	0.0:0.0:1.0:0.0	.	218	Q99527	GPER_HUMAN	Q	218	ENSP00000385151:E218Q;ENSP00000380281:E218Q;ENSP00000297469:E218Q;ENSP00000380277:E218Q	ENSP00000297469:E218Q	E	+	1	0	GPER	1098542	1.000000	0.71417	0.986000	0.45419	0.053000	0.15095	7.384000	0.79751	2.543000	0.85770	0.643000	0.83706	GAG	GPER	-	pfam_7TM_GPCR_Rhodpsn,pfam_7TM_GPCR_olfarory/Srsx,prints_7TM_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_supfam	ENSG00000164850		0.667	GPER1-030	KNOWN	basic|appris_principal|CCDS	protein_coding	GPER	HGNC	protein_coding	OTTHUMT00000060001.1	41	0.00	0	G	NM_001039966		1132016	1132016	+1	no_errors	ENST00000297469	ensembl	human	known	69_37n	missense	21	54.35	25	SNP	1.000	C
IFI16	3428	genome.wustl.edu	37	1	158984516	158984516	+	Missense_Mutation	SNP	G	G	T			TCGA-LL-A440-01A-11D-A243-09	TCGA-LL-A440-10A-01D-A243-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	c033740f-b98c-453b-b290-6a1d7d81b72a	3ad6a505-3409-4b03-80fc-f69d88303bb9	g.chr1:158984516G>T	ENST00000295809.7	+	2	301	c.46G>T	c.(46-48)Gtc>Ttc	p.V16F	IFI16_ENST00000368132.3_Missense_Mutation_p.V16F|IFI16_ENST00000340979.6_Missense_Mutation_p.V16F|IFI16_ENST00000368131.4_Missense_Mutation_p.V16F|IFI16_ENST00000430894.2_Missense_Mutation_p.V20F|IFI16_ENST00000448393.2_Missense_Mutation_p.V16F|IFI16_ENST00000359709.3_Missense_Mutation_p.V16F			Q16666	IF16_HUMAN	interferon, gamma-inducible protein 16	16	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.|Lys-rich.				activation of cysteine-type endopeptidase activity (GO:0097202)|activation of innate immune response (GO:0002218)|autophagy (GO:0006914)|cell proliferation (GO:0008283)|cellular response to glucose starvation (GO:0042149)|cellular response to ionizing radiation (GO:0071479)|defense response to virus (GO:0051607)|hemopoiesis (GO:0030097)|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)|monocyte differentiation (GO:0030224)|myeloid cell differentiation (GO:0030099)|negative regulation of cysteine-type endopeptidase activity (GO:2000117)|negative regulation of DNA binding (GO:0043392)|negative regulation of innate immune response (GO:0045824)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral genome replication (GO:0045071)|positive regulation of cytokine production (GO:0001819)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of autophagy (GO:0010506)|regulation of gene expression, epigenetic (GO:0040029)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter binding (GO:0001047)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_hematologic(112;0.0429)					AGGATTAGAGGTCATCAATGA	0.303																																						dbGAP											0													69.0	72.0	71.0					1																	158984516		2203	4300	6503	-	-	-	SO:0001583	missense	0			M63838	CCDS1180.3, CCDS58039.1	1q22	2008-02-05			ENSG00000163565	ENSG00000163565			5395	protein-coding gene	gene with protein product		147586				1526658, 7959953	Standard	NM_005531		Approved	IFNGIP1, PYHIN2	uc010pis.2	Q16666	OTTHUMG00000037108	ENST00000295809.7:c.46G>T	1.37:g.158984516G>T	ENSP00000295809:p.Val16Phe	Somatic		WXS	Illumina GAIIx	Phase_IV	B4DJT8|H3BLV7|Q59GX0|Q5T3W7|Q5T3W8|Q5T3X0|Q5T3X1|Q5T3X2|Q8N9E5|Q8NEQ7|Q96AJ5|Q9UH78	Missense_Mutation	SNP	pfam_HIN200/IF120x,pfam_DAPIN,superfamily_DEATH-like,pfscan_DAPIN,pfscan_HIN200/IF120x	p.V16F	ENST00000295809.7	37	c.46		1	.	.	.	.	.	.	.	.	.	.	.	4.919	0.170817	0.09391	.	.	ENSG00000163565	ENST00000359709;ENST00000426592;ENST00000447473;ENST00000295809;ENST00000340979;ENST00000368131;ENST00000368132;ENST00000430894	T;T;T;T;T;T;T;T	0.41065	1.01;1.01;1.01;1.01;1.01;1.01;1.01;1.01	3.14	-3.16	0.05217	Pyrin (2);DEATH-like (1);	.	.	.	.	T	0.07818	0.0196	N	0.22421	0.69	0.09310	N	1	P;B;P	0.40107	0.703;0.03;0.453	B;B;B	0.36885	0.235;0.012;0.151	T	0.25012	-1.0144	9	0.10377	T	0.69	.	8.8766	0.35350	0.0:0.5886:0.2841:0.1273	.	20;16;16	E7EPR3;Q16666-2;Q16666	.;.;IF16_HUMAN	F	16;16;16;16;16;16;16;20	ENSP00000352740:V16F;ENSP00000406406:V16F;ENSP00000407052:V16F;ENSP00000295809:V16F;ENSP00000342741:V16F;ENSP00000357113:V16F;ENSP00000357114:V16F;ENSP00000394935:V20F	ENSP00000295809:V16F	V	+	1	0	IFI16	157251140	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-2.277000	0.01160	-0.673000	0.05259	0.455000	0.32223	GTC	IFI16	-	pfam_DAPIN,superfamily_DEATH-like,pfscan_DAPIN	ENSG00000163565		0.303	IFI16-013	KNOWN	basic	protein_coding	IFI16	HGNC	protein_coding	OTTHUMT00000421720.1	39	0.00	0	G	NM_005531		158984516	158984516	+1	no_errors	ENST00000295809	ensembl	human	known	69_37n	missense	39	11.36	5	SNP	0.000	T
MTSS1L	92154	genome.wustl.edu	37	16	70698201	70698201	+	Silent	SNP	C	C	A			TCGA-LL-A440-01A-11D-A243-09	TCGA-LL-A440-10A-01D-A243-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	c033740f-b98c-453b-b290-6a1d7d81b72a	3ad6a505-3409-4b03-80fc-f69d88303bb9	g.chr16:70698201C>A	ENST00000338779.6	-	15	1897	c.1623G>T	c.(1621-1623)ggG>ggT	p.G541G	FLJ00418_ENST00000597002.1_5'UTR	NM_138383.2	NP_612392.1	Q765P7	MTSSL_HUMAN	metastasis suppressor 1-like	541					filopodium assembly (GO:0046847)|signal transduction (GO:0007165)					breast(1)|central_nervous_system(2)|endometrium(1)|liver(1)|lung(1)|skin(1)	7						CGGTGGGCAGCCCAGCAGTGG	0.711																																						dbGAP											0													22.0	24.0	24.0					16																	70698201		2188	4278	6466	-	-	-	SO:0001819	synonymous_variant	0				CCDS32476.1	16q22.1	2008-12-16				ENSG00000132613			25094	protein-coding gene	gene with protein product	"""actin-bundling protein with BAIAP2 homology"""					12477932	Standard	XM_006721335		Approved	ABBA-1, LOC92154	uc002ezj.3	Q765P7		ENST00000338779.6:c.1623G>T	16.37:g.70698201C>A		Somatic		WXS	Illumina GAIIx	Phase_IV	A6NJI7|Q9BUA8	Silent	SNP	pfam_IRSp53/MIM_homology_IMD	p.G541	ENST00000338779.6	37	c.1623	CCDS32476.1	16																																																																																			MTSS1L	-	NULL	ENSG00000132613		0.711	MTSS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MTSS1L	HGNC	protein_coding	OTTHUMT00000434927.3	45	0.00	0	C	NM_138383		70698201	70698201	-1	no_errors	ENST00000338779	ensembl	human	known	69_37n	silent	32	38.89	21	SNP	0.988	A
SF3A2	8175	genome.wustl.edu	37	19	2245452	2245452	+	Silent	SNP	C	C	A			TCGA-LL-A440-01A-11D-A243-09	TCGA-LL-A440-10A-01D-A243-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	c033740f-b98c-453b-b290-6a1d7d81b72a	3ad6a505-3409-4b03-80fc-f69d88303bb9	g.chr19:2245452C>A	ENST00000221494.5	+	5	671	c.253C>A	c.(253-255)Cga>Aga	p.R85R		NM_007165.4	NP_009096.2	Q15428	SF3A2_HUMAN	splicing factor 3a, subunit 2, 66kDa	85					gene expression (GO:0010467)|mRNA 3'-splice site recognition (GO:0000389)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(1)|lung(2)	4		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CAGGGCCCGGCGAGCAGCCAA	0.667																																						dbGAP											0													20.0	26.0	24.0					19																	2245452		1695	3131	4826	-	-	-	SO:0001819	synonymous_variant	0			L21990	CCDS12084.1	19p13.3	2012-10-02	2002-08-29		ENSG00000104897	ENSG00000104897			10766	protein-coding gene	gene with protein product		600796	"""splicing factor 3a, subunit 2, 66kD"""			8211113, 8541848	Standard	NM_007165		Approved	SF3a66, SAP62, PRPF11, Prp11	uc002lvg.3	Q15428	OTTHUMG00000180414	ENST00000221494.5:c.253C>A	19.37:g.2245452C>A		Somatic		WXS	Illumina GAIIx	Phase_IV	B2RBU1|D6W605|O75245	Silent	SNP	smart_Znf_U1,pfscan_Znf_C2H2_matrin	p.R85	ENST00000221494.5	37	c.253	CCDS12084.1	19																																																																																			SF3A2	-	smart_Znf_U1	ENSG00000104897		0.667	SF3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SF3A2	HGNC	protein_coding	OTTHUMT00000451268.3	47	0.00	0	C			2245452	2245452	+1	no_errors	ENST00000221494	ensembl	human	known	69_37n	silent	34	33.33	17	SNP	0.986	A
SRCIN1	80725	genome.wustl.edu	37	17	36701522	36701522	+	Intron	SNP	G	G	T			TCGA-LL-A440-01A-11D-A243-09	TCGA-LL-A440-10A-01D-A243-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	c033740f-b98c-453b-b290-6a1d7d81b72a	3ad6a505-3409-4b03-80fc-f69d88303bb9	g.chr17:36701522G>T	ENST00000264659.7	-	18	3495				SRCIN1_ENST00000398579.4_Intron|SRCIN1_ENST00000578925.1_Intron	NM_025248.2	NP_079524.2	Q9C0H9	SRCN1_HUMAN	SRC kinase signaling inhibitor 1						exocytosis (GO:0006887)|negative regulation of protein tyrosine kinase activity (GO:0061099)|positive regulation of protein tyrosine kinase activity (GO:0061098)|regulation of cell migration (GO:0030334)|regulation of dendritic spine morphogenesis (GO:0061001)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	protein kinase binding (GO:0019901)			endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)	19						CCCTGGTGGGGACTGTGGGCC	0.667																																						dbGAP											0																																										-	-	-	SO:0001627	intron_variant	0				CCDS45660.1	17q12	2009-12-14			ENSG00000017373	ENSG00000277363			29506	protein-coding gene	gene with protein product	"""p130Cas-associated protein"", ""SNAP-25-interacting protein"""	610786				11214970	Standard	NM_025248		Approved	SNIP, p140Cap, KIAA1684	uc002hqd.3	Q9C0H9		ENST00000264659.7:c.3271-1318C>A	17.37:g.36701522G>T		Somatic		WXS	Illumina GAIIx	Phase_IV	Q75T46|Q8N4W8	RNA	SNP	-	NULL	ENST00000264659.7	37	NULL	CCDS45660.1	17																																																																																			SRCIN1	-	-	ENSG00000017373		0.667	SRCIN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	SRCIN1	HGNC	protein_coding	OTTHUMT00000441878.4	35	0.00	0	G	NM_025248		36701522	36701522	-1	no_errors	ENST00000584491	ensembl	human	known	69_37n	rna	38	15.56	7	SNP	0.000	T
STAT4	6775	genome.wustl.edu	37	2	192011485	192011485	+	Splice_Site	SNP	T	T	A			TCGA-LL-A440-01A-11D-A243-09	TCGA-LL-A440-10A-01D-A243-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	c033740f-b98c-453b-b290-6a1d7d81b72a	3ad6a505-3409-4b03-80fc-f69d88303bb9	g.chr2:192011485T>A	ENST00000392320.2	-	3	443		c.e3-2		STAT4_ENST00000409995.1_Splice_Site|STAT4_ENST00000358470.4_Splice_Site	NM_003151.3	NP_003142.1	Q14765	STAT4_HUMAN	signal transducer and activator of transcription 4						cell proliferation (GO:0008283)|cytokine-mediated signaling pathway (GO:0019221)|JAK-STAT cascade (GO:0007259)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(4)|endometrium(1)|kidney(2)|large_intestine(6)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(117;0.00854)|Epithelial(96;0.0864)|all cancers(119;0.204)			GCTGCCTCCCTAAAAAAAAAA	0.308																																						dbGAP											0													48.0	47.0	47.0					2																	192011485		2202	4300	6502	-	-	-	SO:0001630	splice_region_variant	0				CCDS2310.1	2q32.2-q32.3	2013-02-14			ENSG00000138378	ENSG00000138378		"""SH2 domain containing"""	11365	protein-coding gene	gene with protein product		600558				8007943, 8700208	Standard	NM_003151		Approved		uc002usn.2	Q14765	OTTHUMG00000132700	ENST00000392320.2:c.129-2A>T	2.37:g.192011485T>A		Somatic		WXS	Illumina GAIIx	Phase_IV	Q96NZ6	Splice_Site	SNP	-	e2-2	ENST00000392320.2	37	c.129-2	CCDS2310.1	2	.	.	.	.	.	.	.	.	.	.	T	18.55	3.649129	0.67358	.	.	ENSG00000138378	ENST00000358470;ENST00000392320;ENST00000413064;ENST00000409995;ENST00000450994	.	.	.	5.45	5.45	0.79879	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.6799	0.77360	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	STAT4	191719730	1.000000	0.71417	0.993000	0.49108	0.848000	0.48234	6.251000	0.72441	2.289000	0.77006	0.533000	0.62120	.	STAT4	-	-	ENSG00000138378		0.308	STAT4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	STAT4	HGNC	protein_coding	OTTHUMT00000335586.1	41	0.00	0	T	NM_003151	Intron	192011485	192011485	-1	no_errors	ENST00000358470	ensembl	human	known	69_37n	splice_site	45	10.00	5	SNP	1.000	A
TRIM2	23321	genome.wustl.edu	37	4	154191552	154191552	+	Silent	SNP	C	C	A			TCGA-LL-A440-01A-11D-A243-09	TCGA-LL-A440-10A-01D-A243-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	c033740f-b98c-453b-b290-6a1d7d81b72a	3ad6a505-3409-4b03-80fc-f69d88303bb9	g.chr4:154191552C>A	ENST00000437508.2	+	2	216	c.15C>A	c.(13-15)ggC>ggA	p.G5G	TRIM2_ENST00000494872.1_3'UTR|TRIM2_ENST00000338700.5_Silent_p.G32G	NM_001130067.1	NP_001123539.1	Q9C040	TRIM2_HUMAN	tripartite motif containing 2	5					cell death (GO:0008219)|regulation of neuron apoptotic process (GO:0043523)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|prostate(1)	19	all_hematologic(180;0.093)	Medulloblastoma(177;0.00225)		GBM - Glioblastoma multiforme(119;0.0102)|LUSC - Lung squamous cell carcinoma(193;0.0703)		CCAGTGAAGGCACCAACATCC	0.507																																						dbGAP											0																																										-	-	-	SO:0001819	synonymous_variant	0			AF220018	CCDS3781.2, CCDS47147.1	4q31.3	2013-01-09	2011-01-25		ENSG00000109654	ENSG00000109654		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	15974	protein-coding gene	gene with protein product		614141	"""tripartite motif-containing 2"""			9628581, 11331580	Standard	NM_015271		Approved	KIAA0517, RNF86	uc003inh.2	Q9C040	OTTHUMG00000155991	ENST00000437508.2:c.15C>A	4.37:g.154191552C>A		Somatic		WXS	Illumina GAIIx	Phase_IV	D3DP09|O60272|Q9BSI9|Q9UFZ1	Silent	SNP	pfam_NHL_repeat,pfam_Filamin/ABP280_repeat-like,pfam_Znf_B-box,pfam_Znf_C3HC4_RING-type,superfamily_Ig_E-set,smart_Znf_RING,smart_Znf_B-box,smart_Bbox_C,smart_Filamin,pfscan_Filamin/ABP280_repeat-like,pfscan_NHL_repeat_subgr,pfscan_Znf_B-box,pfscan_Znf_RING	p.G32	ENST00000437508.2	37	c.96	CCDS47147.1	4																																																																																			TRIM2	-	NULL	ENSG00000109654		0.507	TRIM2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	TRIM2	HGNC	protein_coding	OTTHUMT00000342652.1	49	0.00	0	C			154191552	154191552	+1	no_errors	ENST00000338700	ensembl	human	known	69_37n	silent	38	25.49	13	SNP	1.000	A
ULBP2	80328	genome.wustl.edu	37	6	150263287	150263287	+	Missense_Mutation	SNP	C	C	G	rs200438471	byFrequency	TCGA-LL-A440-01A-11D-A243-09	TCGA-LL-A440-10A-01D-A243-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	c033740f-b98c-453b-b290-6a1d7d81b72a	3ad6a505-3409-4b03-80fc-f69d88303bb9	g.chr6:150263287C>G	ENST00000367351.3	+	1	152	c.79C>G	c.(79-81)Cga>Gga	p.R27G		NM_025217.2	NP_079493.1	Q9BZM5	N2DL2_HUMAN	UL16 binding protein 2	27					antigen processing and presentation (GO:0019882)|natural killer cell activation (GO:0030101)|natural killer cell mediated cytotoxicity (GO:0042267)	anchored component of plasma membrane (GO:0046658)|cell surface (GO:0009986)|extracellular space (GO:0005615)	natural killer cell lectin-like receptor binding (GO:0046703)			breast(3)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|skin(1)	10		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.58e-12)		CCGGGCTGGGCGAGCCGGTGA	0.657																																						dbGAP											0													19.0	22.0	21.0					6																	150263287		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF304378	CCDS5222.1	6q25	2008-04-11			ENSG00000131015	ENSG00000131015			14894	protein-coding gene	gene with protein product		605698				11239445	Standard	NM_025217		Approved	RAET1H	uc003qno.3	Q9BZM5	OTTHUMG00000015803	ENST00000367351.3:c.79C>G	6.37:g.150263287C>G	ENSP00000356320:p.Arg27Gly	Somatic		WXS	Illumina GAIIx	Phase_IV	Q5VUN4	Missense_Mutation	SNP	pfam_MHC_I_a_a1/a2,superfamily_MHC_I/II-like_Ag-recog	p.R27G	ENST00000367351.3	37	c.79	CCDS5222.1	6	.	.	.	.	.	.	.	.	.	.	-	1.548	-0.539926	0.04053	.	.	ENSG00000131015	ENST00000367351	T	0.00675	5.88	1.14	-2.28	0.06826	.	.	.	.	.	T	0.00328	0.0010	M	0.65320	2	0.09310	N	1	B;B	0.09022	0.001;0.002	B;B	0.10450	0.003;0.005	T	0.34004	-0.9846	9	0.29301	T	0.29	.	4.4372	0.11555	0.2353:0.2985:0.4663:0.0	.	27;27	B4DSS7;Q9BZM5	.;N2DL2_HUMAN	G	27	ENSP00000356320:R27G	ENSP00000356320:R27G	R	+	1	2	ULBP2	150304980	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.912000	0.04046	-1.052000	0.03222	-1.873000	0.00551	CGA	ULBP2	-	NULL	ENSG00000131015		0.657	ULBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ULBP2	HGNC	protein_coding	OTTHUMT00000042669.1	150	0.65	1	C			150263287	150263287	+1	no_errors	ENST00000367351	ensembl	human	known	69_37n	missense	131	21.56	36	SNP	0.000	G
ZNF668	79759	genome.wustl.edu	37	16	31075646	31075646	+	Silent	SNP	C	C	A			TCGA-LL-A440-01A-11D-A243-09	TCGA-LL-A440-10A-01D-A243-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	c033740f-b98c-453b-b290-6a1d7d81b72a	3ad6a505-3409-4b03-80fc-f69d88303bb9	g.chr16:31075646C>A	ENST00000538906.1	-	2	919	c.135G>T	c.(133-135)ggG>ggT	p.G45G	ZNF668_ENST00000539836.3_Silent_p.G68G|ZNF668_ENST00000426488.2_Silent_p.G68G|ZNF668_ENST00000394983.2_Silent_p.G45G|ZNF668_ENST00000535577.1_Silent_p.G45G|ZNF668_ENST00000300849.4_Silent_p.G45G|ZNF668_ENST00000564456.1_5'Flank|AC135050.5_ENST00000568708.1_RNA	NM_001172668.1	NP_001166139	Q96K58	ZN668_HUMAN	zinc finger protein 668	45					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(6)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	27						AGTCTGCCGGCCCATGTGTGG	0.647																																					Colon(181;1111 1980 5060 10512 25785)	dbGAP											0													69.0	70.0	70.0					16																	31075646		2197	4300	6497	-	-	-	SO:0001819	synonymous_variant	0				CCDS10701.1, CCDS54003.1	16p11.2	2013-01-08			ENSG00000167394	ENSG00000167394		"""Zinc fingers, C2H2-type"""	25821	protein-coding gene	gene with protein product						12477932	Standard	NM_024706		Approved	FLJ13479	uc021tgt.1	Q96K58	OTTHUMG00000047357	ENST00000538906.1:c.135G>T	16.37:g.31075646C>A		Somatic		WXS	Illumina GAIIx	Phase_IV	C9JHH8|F5H7E7|Q59EV1|Q8N669|Q9H8L4	Silent	SNP	pfam_Znf_C2H2,smart_Znf_C2H2-like,pfscan_Znf_C2H2	p.G68	ENST00000538906.1	37	c.204	CCDS10701.1	16																																																																																			ZNF668	-	NULL	ENSG00000167394		0.647	ZNF668-202	KNOWN	basic|appris_principal|CCDS	protein_coding	ZNF668	HGNC	protein_coding	OTTHUMT00000108516.2	25	0.00	0	C	NM_024706		31075646	31075646	-1	no_errors	ENST00000426488	ensembl	human	known	69_37n	silent	16	38.46	10	SNP	0.047	A
