#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
BAGE2	85319	genome.wustl.edu	37	21	11060198	11060198	+	RNA	SNP	G	G	A	rs209031	byFrequency	TCGA-E9-A2JT-01A-22D-A18P-09	TCGA-E9-A2JT-10A-01D-A18P-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	4a0f9f07-6b43-4b77-864a-e3c744d4d835	ef077907-6ca1-4a35-a819-15aeb2ddf7da	g.chr21:11060198G>A	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2							extracellular region (GO:0005576)								Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		GAAAGTTCACGTAAATGTCGA	0.303																																						dbGAP											0																																										-	-	-			0			AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172			15723	protein-coding gene	gene with protein product	"""cancer/testis antigen family 2, member 2"""					12461691	Standard	NM_182482		Approved	CT2.2		Q86Y30	OTTHUMG00000074128		21.37:g.11060198G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	A8K925|Q08ER0	RNA	SNP	-	NULL	ENST00000470054.1	37	NULL		21																																																																																			BAGE2	-	-	ENSG00000187172		0.303	BAGE2-001	KNOWN	basic	processed_transcript	BAGE2	HGNC	pseudogene	OTTHUMT00000157417.3	10	0.00	0	G	NM_182482		11060198	11060198	-1	no_errors	ENST00000474011	ensembl	human	known	69_37n	rna	9	40.00	6	SNP	0.000	A
CDH1	999	genome.wustl.edu	37	16	68847282	68847282	+	Missense_Mutation	SNP	G	G	C			TCGA-E9-A2JT-01A-22D-A18P-09	TCGA-E9-A2JT-10A-01D-A18P-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	4a0f9f07-6b43-4b77-864a-e3c744d4d835	ef077907-6ca1-4a35-a819-15aeb2ddf7da	g.chr16:68847282G>C	ENST00000261769.5	+	9	1395	c.1204G>C	c.(1204-1206)Gat>Cat	p.D402H	CDH1_ENST00000562836.1_3'UTR|RP11-354M1.2_ENST00000563916.1_RNA|CDH1_ENST00000422392.2_Intron	NM_004360.3	NP_004351.1	P12830	CADH1_HUMAN	cadherin 1, type 1, E-cadherin (epithelial)	402	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to amino acid stimulus (GO:0071230)|cellular response to indole-3-methanol (GO:0071681)|cellular response to lithium ion (GO:0071285)|cochlea development (GO:0090102)|epithelial cell morphogenesis (GO:0003382)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|homophilic cell adhesion (GO:0007156)|intestinal epithelial cell development (GO:0060576)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of epithelial cell proliferation (GO:0050680)|neuron projection development (GO:0031175)|pituitary gland development (GO:0021983)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|protein metabolic process (GO:0019538)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of immune response (GO:0050776)|regulation of neuron migration (GO:2001222)|regulation of protein localization to cell surface (GO:2000008)|regulation of water loss via skin (GO:0033561)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)|salivary gland cavitation (GO:0060662)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|tight junction assembly (GO:0070830)|trophectodermal cell differentiation (GO:0001829)	actin cytoskeleton (GO:0015629)|aggresome (GO:0016235)|apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|axon terminus (GO:0043679)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell junction (GO:0030054)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|node of Ranvier (GO:0033268)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|trans-Golgi network (GO:0005802)	ankyrin binding (GO:0030506)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|gamma-catenin binding (GO:0045295)|glycoprotein binding (GO:0001948)|GTPase activating protein binding (GO:0032794)	p.Y380_K440del(2)|p.D402N(2)|p.D402H(1)|p.?(1)		NS(6)|biliary_tract(8)|breast(161)|central_nervous_system(4)|endometrium(9)|kidney(4)|large_intestine(13)|lung(13)|oesophagus(3)|ovary(2)|prostate(3)|soft_tissue(2)|stomach(76)|thyroid(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	311		all_neural(199;0.0189)|Ovarian(137;0.0563)		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)		GACTGATGCTGATGCCCCCAA	0.473			"""Mis, N, F, S"""		"""lobular breast, gastric"""	gastric			Hereditary Diffuse Gastric Cancer																													dbGAP	yes	Rec	yes	Familial gastric carcinoma	16	16q22.1	999	"""cadherin 1, type 1, E-cadherin (epithelial) (ECAD)"""		E	6	Substitution - Missense(3)|Deletion - In frame(2)|Unknown(1)	stomach(4)|breast(2)											204.0	172.0	183.0					16																	68847282		2198	4300	6498	-	-	-	SO:0001583	missense	0	Familial Cancer Database	HDGC	L08599	CCDS10869.1	16q22.1	2014-09-17			ENSG00000039068	ENSG00000039068		"""CD molecules"", ""Cadherins / Major cadherins"""	1748	protein-coding gene	gene with protein product	"""E-Cadherin"""	192090		UVO		9925936	Standard	NM_004360		Approved	uvomorulin, CD324	uc002ewg.1	P12830	OTTHUMG00000137561	ENST00000261769.5:c.1204G>C	16.37:g.68847282G>C	ENSP00000261769:p.Asp402His	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K1U7|Q13799|Q14216|Q15855|Q16194|Q4PJ14|Q9UII8	Missense_Mutation	SNP	pfam_Cadherin,pfam_Cadherin_cytoplasmic-dom,pfam_Cadherin_pro_dom,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin,prints_Cadherin	p.D402H	ENST00000261769.5	37	c.1204	CCDS10869.1	16	.	.	.	.	.	.	.	.	.	.	G	23.1	4.370961	0.82573	.	.	ENSG00000039068	ENST00000261769;ENST00000379120;ENST00000268794	T	0.74632	-0.86	6.04	5.08	0.68730	Cadherin (4);Cadherin-like (1);	0.000000	0.52532	D	0.000073	D	0.91915	0.7440	H	0.98487	4.245	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95266	0.8373	10	0.87932	D	0	.	17.0639	0.86554	0.0:0.1271:0.8729:0.0	.	402	P12830	CADH1_HUMAN	H	402	ENSP00000261769:D402H	ENSP00000261769:D402H	D	+	1	0	CDH1	67404783	1.000000	0.71417	0.034000	0.17996	0.066000	0.16364	8.638000	0.91019	1.552000	0.49463	0.561000	0.74099	GAT	CDH1	-	pfam_Cadherin,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin	ENSG00000039068		0.473	CDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CDH1	HGNC	protein_coding	OTTHUMT00000268897.2	65	0.00	0	G	NM_004360		68847282	68847282	+1	no_errors	ENST00000261769	ensembl	human	known	69_37n	missense	40	13.04	6	SNP	0.974	C
HTATSF1	27336	genome.wustl.edu	37	X	135593757	135593757	+	Missense_Mutation	SNP	G	G	C	rs146112744	byFrequency	TCGA-E9-A2JT-01A-22D-A18P-09	TCGA-E9-A2JT-10A-01D-A18P-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	4a0f9f07-6b43-4b77-864a-e3c744d4d835	ef077907-6ca1-4a35-a819-15aeb2ddf7da	g.chrX:135593757G>C	ENST00000218364.4	+	9	2027	c.1853G>C	c.(1852-1854)aGa>aCa	p.R618T	HTATSF1_ENST00000535601.1_Missense_Mutation_p.R618T	NM_014500.4	NP_055315.2	O43719	HTSF1_HUMAN	HIV-1 Tat specific factor 1	618	Asp/Glu-rich (acidic).|Mediates interaction with the P-TEFb complex.				regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.R618I(1)		NS(1)|biliary_tract(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(14)|ovary(3)|prostate(1)	30	Acute lymphoblastic leukemia(192;0.000127)					GGCTCTGAGAGAGAGTTTGAC	0.368																																						dbGAP											1	Substitution - Missense(1)	lung(1)											83.0	87.0	86.0					X																	135593757		2202	4298	6500	-	-	-	SO:0001583	missense	0			U76992	CCDS14657.1	Xq26.3	2013-02-12	2006-01-09		ENSG00000102241	ENSG00000102241		"""RNA binding motif (RRM) containing"""	5276	protein-coding gene	gene with protein product		300346	"""HIV TAT specific factor 1"""			8849451	Standard	NM_014500		Approved	TAT-SF1	uc004ezx.3	O43719	OTTHUMG00000022510	ENST00000218364.4:c.1853G>C	X.37:g.135593757G>C	ENSP00000218364:p.Arg618Thr	Somatic		WXS	Illumina GAIIx	Phase_IV	D3DWG9|Q59G06|Q99730	Missense_Mutation	SNP	pfam_RRM_dom,smart_RRM_dom,pfscan_RRM_dom	p.R618T	ENST00000218364.4	37	c.1853	CCDS14657.1	X	.	.	.	.	.	.	.	.	.	.	G	3.174	-0.169379	0.06461	.	.	ENSG00000102241	ENST00000535601;ENST00000218364;ENST00000415377	T;T	0.04156	3.69;3.69	4.22	-0.744	0.11101	.	0.226096	0.31784	N	0.007070	T	0.03095	0.0091	N	0.19112	0.55	0.09310	N	1	B	0.23735	0.09	B	0.15870	0.014	T	0.37430	-0.9706	10	0.72032	D	0.01	-4.8256	8.5825	0.33637	0.5008:0.0:0.4992:0.0	.	618	O43719	HTSF1_HUMAN	T	618	ENSP00000442699:R618T;ENSP00000218364:R618T	ENSP00000218364:R618T	R	+	2	0	HTATSF1	135421423	0.000000	0.05858	0.000000	0.03702	0.164000	0.22412	-0.074000	0.11450	-0.306000	0.08818	0.523000	0.50628	AGA	HTATSF1	-	NULL	ENSG00000102241		0.368	HTATSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HTATSF1	HGNC	protein_coding	OTTHUMT00000058497.1	33	0.00	0	G	NM_014500		135593757	135593757	+1	no_errors	ENST00000218364	ensembl	human	known	69_37n	missense	40	11.11	5	SNP	0.000	C
KIAA1429	25962	genome.wustl.edu	37	8	95538749	95538749	+	Missense_Mutation	SNP	C	C	G			TCGA-E9-A2JT-01A-22D-A18P-09	TCGA-E9-A2JT-10A-01D-A18P-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	4a0f9f07-6b43-4b77-864a-e3c744d4d835	ef077907-6ca1-4a35-a819-15aeb2ddf7da	g.chr8:95538749C>G	ENST00000297591.5	-	8	1798	c.1723G>C	c.(1723-1725)Gag>Cag	p.E575Q	KIAA1429_ENST00000437199.1_Missense_Mutation_p.E575Q|KIAA1429_ENST00000421249.2_Missense_Mutation_p.E575Q	NM_015496.4	NP_056311.2	Q69YN4	VIR_HUMAN	KIAA1429	575					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(16)|lung(28)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	66	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)			GAAGTCTTCTCTGCTAAATGG	0.423																																						dbGAP											0													141.0	138.0	139.0					8																	95538749		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB037850	CCDS34923.1, CCDS47894.1	8q22.1	2008-11-25			ENSG00000164944	ENSG00000164944			24500	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 121"""					10718198	Standard	NM_015496		Approved	DKFZP434I116, fSAP121	uc003ygo.2	Q69YN4	OTTHUMG00000164426	ENST00000297591.5:c.1723G>C	8.37:g.95538749C>G	ENSP00000297591:p.Glu575Gln	Somatic		WXS	Illumina GAIIx	Phase_IV	Q2M1N0|Q6AHX9|Q6NT78|Q7Z6C7|Q8IXH4|Q9BTH4|Q9H9C9|Q9NWR3|Q9P2B8|Q9UFW1	Missense_Mutation	SNP	superfamily_ARM-type_fold	p.E575Q	ENST00000297591.5	37	c.1723	CCDS34923.1	8	.	.	.	.	.	.	.	.	.	.	C	14.35	2.510287	0.44660	.	.	ENSG00000164944	ENST00000297591;ENST00000437199;ENST00000421249	T;T;T	0.46451	0.87;0.87;0.87	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.35248	0.0925	L	0.29908	0.895	0.49213	D	0.999765	P;B	0.37015	0.578;0.435	B;B	0.33042	0.157;0.157	T	0.09037	-1.0693	10	0.42905	T	0.14	-14.7679	20.3748	0.98911	0.0:1.0:0.0:0.0	.	575;575	Q69YN4-4;Q69YN4	.;VIR_HUMAN	Q	575	ENSP00000297591:E575Q;ENSP00000395600:E575Q;ENSP00000398390:E575Q	ENSP00000297591:E575Q	E	-	1	0	KIAA1429	95607925	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.054000	0.57434	2.817000	0.96982	0.563000	0.77884	GAG	KIAA1429	-	NULL	ENSG00000164944		0.423	KIAA1429-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KIAA1429	HGNC	protein_coding	OTTHUMT00000378720.2	63	0.00	0	C	NM_015496		95538749	95538749	-1	no_errors	ENST00000297591	ensembl	human	known	69_37n	missense	52	10.34	6	SNP	1.000	G
LRRN3	54674	genome.wustl.edu	37	7	110763866	110763866	+	Silent	SNP	C	C	T			TCGA-E9-A2JT-01A-22D-A18P-09	TCGA-E9-A2JT-10A-01D-A18P-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	4a0f9f07-6b43-4b77-864a-e3c744d4d835	ef077907-6ca1-4a35-a819-15aeb2ddf7da	g.chr7:110763866C>T	ENST00000422987.3	+	2	1869	c.1038C>T	c.(1036-1038)ctC>ctT	p.L346L	IMMP2L_ENST00000447215.1_Intron|IMMP2L_ENST00000415362.1_Intron|IMMP2L_ENST00000450877.1_Intron|IMMP2L_ENST00000331762.3_Intron|LRRN3_ENST00000308478.5_Silent_p.L346L|IMMP2L_ENST00000489381.1_Intron|IMMP2L_ENST00000405709.2_Intron|IMMP2L_ENST00000437687.1_Intron|LRRN3_ENST00000451085.1_Silent_p.L346L|IMMP2L_ENST00000452895.1_Intron	NM_018334.4	NP_060804.3	Q9H3W5	LRRN3_HUMAN	leucine rich repeat neuronal 3	346					positive regulation of protein phosphorylation (GO:0001934)	clathrin adaptor complex (GO:0030131)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(15)|lung(20)|ovary(2)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	55				UCEC - Uterine corpus endometrioid carcinoma (4;0.245)|LUSC - Lung squamous cell carcinoma(290;0.0715)|Lung(3;0.0864)|STAD - Stomach adenocarcinoma(3;0.125)		GCAATGCTCTCAGTGCCCTGT	0.458																																						dbGAP											0													104.0	95.0	98.0					7																	110763866		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AB060967	CCDS5754.1	7q31.1	2013-02-11			ENSG00000173114	ENSG00000173114		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	17200	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 5"""					11549284	Standard	NM_001099660		Approved	NLRR3, FLJ11129, FIGLER5	uc003vfs.4	Q9H3W5	OTTHUMG00000155039	ENST00000422987.3:c.1038C>T	7.37:g.110763866C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	O43377|Q6I9V8|Q8IYQ6	Silent	SNP	pfam_Ig_I-set,pfam_Leu-rich_rpt,pfam_Fibronectin_type3,pfam_Immunoglobulin,pfam_LRR-contain_N,superfamily_Fibronectin_type3,smart_LRR-contain_N,smart_Leu-rich_rpt_typical-subtyp,smart_Cys-rich_flank_reg_C,smart_Ig_sub,smart_Ig_sub2,pfscan_Fibronectin_type3,pfscan_Ig-like	p.L346	ENST00000422987.3	37	c.1038	CCDS5754.1	7																																																																																			LRRN3	-	smart_Leu-rich_rpt_typical-subtyp	ENSG00000173114		0.458	LRRN3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	LRRN3	HGNC	protein_coding	OTTHUMT00000338171.2	50	0.00	0	C	NM_018334		110763866	110763866	+1	no_errors	ENST00000308478	ensembl	human	known	69_37n	silent	35	10.26	4	SNP	0.066	T
SLFN14	342618	genome.wustl.edu	37	17	33879870	33879870	+	Missense_Mutation	SNP	G	G	C	rs568286589		TCGA-E9-A2JT-01A-22D-A18P-09	TCGA-E9-A2JT-10A-01D-A18P-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	4a0f9f07-6b43-4b77-864a-e3c744d4d835	ef077907-6ca1-4a35-a819-15aeb2ddf7da	g.chr17:33879870G>C	ENST00000415846.3	-	3	1818	c.1783C>G	c.(1783-1785)Cca>Gca	p.P595A	RP11-1094M14.12_ENST00000588445.1_RNA	NM_001129820.1	NP_001123292.1	P0C7P3	SLN14_HUMAN	schlafen family member 14	595							ATP binding (GO:0005524)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(3)	9						CTGACTCCTGGAAAGCAGTAG	0.423																																						dbGAP											0													90.0	78.0	82.0					17																	33879870		692	1591	2283	-	-	-	SO:0001583	missense	0				CCDS45650.1	17q12	2009-09-22				ENSG00000236320			32689	protein-coding gene	gene with protein product		614958				9846487	Standard	NM_001129820		Approved		uc010ctu.1	P0C7P3		ENST00000415846.3:c.1783C>G	17.37:g.33879870G>C	ENSP00000391101:p.Pro595Ala	Somatic		WXS	Illumina GAIIx	Phase_IV	B2RTW9	Missense_Mutation	SNP	pfam_ATPase_AAA-4	p.P595A	ENST00000415846.3	37	c.1783	CCDS45650.1	17	.	.	.	.	.	.	.	.	.	.	G	18.56	3.651166	0.67472	.	.	ENSG00000236320	ENST00000415846	D	0.94793	-3.52	5.28	5.28	0.74379	.	.	.	.	.	D	0.96525	0.8866	M	0.69463	2.115	0.31316	N	0.686548	D	0.76494	0.999	D	0.80764	0.994	D	0.94909	0.8063	9	0.51188	T	0.08	-8.7662	14.2969	0.66318	0.0:0.0:1.0:0.0	.	595	P0C7P3	SLN14_HUMAN	A	595	ENSP00000391101:P595A	ENSP00000391101:P595A	P	-	1	0	SLFN14	30903983	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	5.919000	0.70005	2.756000	0.94617	0.655000	0.94253	CCA	SLFN14	-	NULL	ENSG00000236320		0.423	SLFN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SLFN14	HGNC	protein_coding	OTTHUMT00000448928.1	56	0.00	0	G	NM_001129820		33879870	33879870	-1	no_errors	ENST00000415846	ensembl	human	known	69_37n	missense	52	10.34	6	SNP	1.000	C
TRIM49C	642612	genome.wustl.edu	37	11	89774397	89774397	+	Silent	SNP	T	T	C	rs150273819	byFrequency	TCGA-E9-A2JT-01A-22D-A18P-09	TCGA-E9-A2JT-10A-01D-A18P-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	4a0f9f07-6b43-4b77-864a-e3c744d4d835	ef077907-6ca1-4a35-a819-15aeb2ddf7da	g.chr11:89774397T>C	ENST00000448984.1	+	8	1367	c.1038T>C	c.(1036-1038)caT>caC	p.H346H	TRIM49C_ENST00000432771.1_Intron	NM_001195234.1	NP_001182163.1	P0CI26	TR49C_HUMAN	tripartite motif containing 49C	346	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(3)|kidney(1)|lung(4)	8						GGGAGGTCCATGTAGGGGACT	0.448																																						dbGAP											0																																										-	-	-	SO:0001819	synonymous_variant	0			BC126470	CCDS53694.1	11q14.3	2014-02-17	2012-05-18	2012-05-18	ENSG00000204449	ENSG00000204449		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	38877	protein-coding gene	gene with protein product			"""tripartite motif containing 49-like 2"""	TRIM49L2			Standard	NM_001195234		Approved		uc010rua.2	P0CI26		ENST00000448984.1:c.1038T>C	11.37:g.89774397T>C		Somatic		WXS	Illumina GAIIx	Phase_IV	A0AVR7|A0AVR9|Q6DJV1|Q9NS80	Silent	SNP	pfam_SPRY_rcpt,pfam_Znf_B-box,superfamily_ConA-like_lec_gl,superfamily_Lambda_DNA-bd_dom,smart_Znf_RING,smart_Znf_B-box,smart_SPla/RYanodine_receptor_subgr,pfscan_B30.2/SPRY,pfscan_Znf_B-box,pfscan_Znf_RING,prints_Butyrophylin	p.H346	ENST00000448984.1	37	c.1038	CCDS53694.1	11																																																																																			TRIM49C	-	pfam_SPRY_rcpt,superfamily_ConA-like_lec_gl,smart_SPla/RYanodine_receptor_subgr,pfscan_B30.2/SPRY,prints_Butyrophylin	ENSG00000204449		0.448	TRIM49C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	TRIM49C	HGNC	protein_coding	OTTHUMT00000395455.1	14	0.00	0	T	NM_001195234		89774397	89774397	+1	no_errors	ENST00000448984	ensembl	human	known	69_37n	silent	18	35.71	10	SNP	0.074	C
