#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
BRCA1	672	genome.wustl.edu	37	17	41258536	41258536	+	Missense_Mutation	SNP	T	T	G			TCGA-A2-A4S0-01A-21D-A25Q-09	TCGA-A2-A4S0-10A-01D-A25Q-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9929b767-3bd5-4081-824c-f127623f2730	2a035c54-5e78-4f3a-8bb3-ad04e96d899e	g.chr17:41258536T>G	ENST00000357654.3	-	4	267	c.149A>C	c.(148-150)aAa>aCa	p.K50T	BRCA1_ENST00000351666.3_Missense_Mutation_p.K50T|BRCA1_ENST00000352993.3_Missense_Mutation_p.K50T|BRCA1_ENST00000471181.2_Missense_Mutation_p.K50T|BRCA1_ENST00000468300.1_Missense_Mutation_p.K50T|BRCA1_ENST00000591849.1_Intron|BRCA1_ENST00000586385.1_Intron|BRCA1_ENST00000309486.4_5'UTR|BRCA1_ENST00000346315.3_Missense_Mutation_p.K50T|BRCA1_ENST00000354071.3_Missense_Mutation_p.K50T|BRCA1_ENST00000491747.2_Missense_Mutation_p.K50T|BRCA1_ENST00000493795.1_Missense_Mutation_p.K3T|BRCA1_ENST00000591534.1_Intron	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	50					androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to indole-3-methanol (GO:0071681)|cellular response to tumor necrosis factor (GO:0071356)|chromosome segregation (GO:0007059)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|fatty acid biosynthetic process (GO:0006633)|G2 DNA damage checkpoint (GO:0031572)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of centriole replication (GO:0046600)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of DNA repair (GO:0045739)|positive regulation of gene expression (GO:0010628)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 acetylation (GO:2000617)|positive regulation of histone H4-K16 acetylation (GO:2000620)|positive regulation of histone H4-K20 methylation (GO:0070512)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to estrogen (GO:0043627)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|gamma-tubulin ring complex (GO:0008274)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|RNA binding (GO:0003723)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(30)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(28)|ovary(36)|skin(2)|stomach(4)|urinary_tract(2)	120		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)		GTTGAGAAGTTTCAGCATGCA	0.313			"""D, Mis, N, F, S"""		ovarian	"""breast, ovarian"""		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)																												dbGAP	yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	familial breast/ovarian cancer gene 1		E	0													42.0	41.0	41.0					17																	41258536		2202	4295	6497	-	-	-	SO:0001583	missense	0	Familial Cancer Database		U14680	CCDS11453.1, CCDS11454.1, CCDS11455.1, CCDS11456.1, CCDS11459.1, CCDS11455.2, CCDS11456.2, CCDS11459.2, CCDS11454.2	17q21.31	2014-09-17			ENSG00000012048	ENSG00000012048		"""RING-type (C3HC4) zinc fingers"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1100	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-containing complex, subunit 1"", ""protein phosphatase 1, regulatory subunit 53"""	113705				1676470	Standard	NM_007300		Approved	RNF53, BRCC1, PPP1R53	uc002ict.3	P38398	OTTHUMG00000157426	ENST00000357654.3:c.149A>C	17.37:g.41258536T>G	ENSP00000350283:p.Lys50Thr	Somatic		WXS	Illumina GAIIx	Phase_IV	O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	Missense_Mutation	SNP	pirsf_BRCA1,pfam_BRCT_dom,pfam_Znf_C3HC4_RING-type,superfamily_BRCT_dom,smart_Znf_RING,smart_BRCT_dom,pfscan_BRCT_dom,pfscan_Znf_RING	p.K50T	ENST00000357654.3	37	c.149	CCDS11453.1	17	.	.	.	.	.	.	.	.	.	.	T	20.6	4.022590	0.75275	.	.	ENSG00000012048	ENST00000357654;ENST00000412061;ENST00000354071;ENST00000352993;ENST00000346315;ENST00000351666;ENST00000468300;ENST00000393691;ENST00000471181;ENST00000493795;ENST00000491747;ENST00000478531;ENST00000493919;ENST00000470026;ENST00000494123;ENST00000476777	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.86769	-2.17;-2.17;-2.17;-2.17;-2.17;-2.17;-1.93;-2.17;-1.93;-2.17;-2.17;-1.93;-2.17;-2.17;-2.17	5.17	5.17	0.71159	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.000000	0.52532	D	0.000064	D	0.86781	0.6015	N	0.12471	0.22	0.80722	D	1	D;D;D;P;D;D;D	0.89917	1.0;0.997;0.999;0.79;1.0;1.0;0.979	D;D;D;P;D;D;P	0.91635	0.996;0.992;0.999;0.561;0.999;0.999;0.871	D	0.89028	0.3440	10	0.87932	D	0	-24.6445	12.6756	0.56893	0.0:0.0:0.0:1.0	.	3;50;50;50;50;50;50	B4DES0;E7ETR2;Q5YLB2;P38398-3;Q6IN79;E9PFC7;P38398	.;.;.;.;.;.;BRCA1_HUMAN	T	50;50;50;50;50;50;50;3;50;3;50;50;3;50;50;50	ENSP00000350283:K50T;ENSP00000326002:K50T;ENSP00000312236:K50T;ENSP00000246907:K50T;ENSP00000338007:K50T;ENSP00000417148:K50T;ENSP00000377294:K3T;ENSP00000418960:K50T;ENSP00000418775:K3T;ENSP00000420705:K50T;ENSP00000420412:K50T;ENSP00000418819:K3T;ENSP00000419274:K50T;ENSP00000419103:K50T;ENSP00000417554:K50T	ENSP00000246907:K50T	K	-	2	0	BRCA1	38512062	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	4.152000	0.58111	2.075000	0.62263	0.482000	0.46254	AAA	BRCA1	-	pirsf_BRCA1,pfam_Znf_C3HC4_RING-type,smart_Znf_RING,pfscan_Znf_RING	ENSG00000012048		0.313	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	BRCA1	HGNC	protein_coding	OTTHUMT00000348798.2	47	0.00	0	T	NM_007294		41258536	41258536	-1	no_errors	ENST00000471181	ensembl	human	known	69_37n	missense	35	28.57	14	SNP	1.000	G
B4GALNT2	124872	genome.wustl.edu	37	17	47247044	47247044	+	Missense_Mutation	SNP	A	A	G			TCGA-A2-A4S0-01A-21D-A25Q-09	TCGA-A2-A4S0-10A-01D-A25Q-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9929b767-3bd5-4081-824c-f127623f2730	2a035c54-5e78-4f3a-8bb3-ad04e96d899e	g.chr17:47247044A>G	ENST00000300404.2	+	11	1714	c.1655A>G	c.(1654-1656)aAg>aGg	p.K552R	RP11-708H21.4_ENST00000575159.1_lincRNA|B4GALNT2_ENST00000504681.1_Missense_Mutation_p.K466R|B4GALNT2_ENST00000393354.2_Missense_Mutation_p.K492R	NM_153446.2	NP_703147.2	Q8NHY0	B4GN2_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 2	552					lipid glycosylation (GO:0030259)|negative regulation of cell-cell adhesion (GO:0022408)|protein glycosylation (GO:0006486)|UDP-N-acetylgalactosamine metabolic process (GO:0019276)|UDP-N-acetylglucosamine metabolic process (GO:0006047)	integral component of Golgi membrane (GO:0030173)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)			endometrium(3)|large_intestine(6)|liver(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	24			all cancers(6;0.000316)			GTCCAGTTCAAGCTGGCCCTC	0.532																																					GBM(124;244 1635 8663 18097 33175)	dbGAP											0													80.0	68.0	72.0					17																	47247044		2203	4300	6503	-	-	-	SO:0001583	missense	0			AJ517770	CCDS11544.1, CCDS54139.1, CCDS54140.1	17q21.33	2013-02-22	2006-01-08	2006-01-08	ENSG00000167080	ENSG00000167080	2.4.1.-	"""Beta 4-glycosyltransferases"", ""Glycosyltransferase family 2 domain containing"""	24136	protein-coding gene	gene with protein product		111730	"""UDP-GalNAc:Neu5Acalpha2-3Galbeta-R beta1,4-N-acetylgalactosaminyltransferase"""	GALGT2		8782649, 12678917	Standard	NM_153446		Approved	Sda, Cad	uc002ion.2	Q8NHY0	OTTHUMG00000161307	ENST00000300404.2:c.1655A>G	17.37:g.47247044A>G	ENSP00000300404:p.Lys552Arg	Somatic		WXS	Illumina GAIIx	Phase_IV	B4DZE4|Q14CP1|Q86Y40	Missense_Mutation	SNP	pfam_Glyco_trans_2,pirsf_GM2_synthase	p.K552R	ENST00000300404.2	37	c.1655	CCDS11544.1	17	.	.	.	.	.	.	.	.	.	.	A	22.3	4.272707	0.80580	.	.	ENSG00000167080	ENST00000504681;ENST00000393354;ENST00000300404	T;T;T	0.26810	1.72;1.71;1.98	5.79	4.72	0.59763	.	0.069782	0.53938	D	0.000054	T	0.41971	0.1182	L	0.50919	1.6	0.43930	D	0.996586	D;D	0.89917	1.0;0.998	D;P	0.91635	0.999;0.82	T	0.12268	-1.0554	10	0.35671	T	0.21	-26.132	10.655	0.45669	0.9238:0.0:0.0762:0.0	.	492;552	Q8NHY0-2;Q8NHY0	.;B4GN2_HUMAN	R	466;492;552	ENSP00000425510:K466R;ENSP00000377022:K492R;ENSP00000300404:K552R	ENSP00000300404:K552R	K	+	2	0	B4GALNT2	44602043	1.000000	0.71417	0.981000	0.43875	0.821000	0.46438	5.783000	0.68982	1.031000	0.39867	0.459000	0.35465	AAG	B4GALNT2	-	pirsf_GM2_synthase	ENSG00000167080		0.532	B4GALNT2-001	KNOWN	basic|CCDS	protein_coding	B4GALNT2	HGNC	protein_coding	OTTHUMT00000364477.1	79	0.00	0	A	NM_153446		47247044	47247044	+1	no_errors	ENST00000300404	ensembl	human	known	69_37n	missense	39	44.29	31	SNP	1.000	G
CATSPER2P1	440278	genome.wustl.edu	37	15	44028223	44028223	+	RNA	SNP	C	C	T			TCGA-A2-A4S0-01A-21D-A25Q-09	TCGA-A2-A4S0-10A-01D-A25Q-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9929b767-3bd5-4081-824c-f127623f2730	2a035c54-5e78-4f3a-8bb3-ad04e96d899e	g.chr15:44028223C>T	ENST00000381680.2	-	0	1561				RNU6-354P_ENST00000383862.1_RNA	NR_002318.2				cation channel, sperm associated 2 pseudogene 1																		gacccatccccctcggcctcc	0.468																																						dbGAP											0																																										-	-	-			0			BC066967		15q15.3	2010-07-12			ENSG00000205771	ENSG00000205771			31054	pseudogene	pseudogene							Standard	NR_002318		Approved		uc001zss.3		OTTHUMG00000059938		15.37:g.44028223C>T		Somatic		WXS	Illumina GAIIx	Phase_IV		RNA	SNP	-	NULL	ENST00000381680.2	37	NULL		15																																																																																			CATSPER2P1	-	-	ENSG00000205771		0.468	CATSPER2P1-002	KNOWN	basic	processed_transcript	CATSPER2P1	HGNC	pseudogene	OTTHUMT00000133242.1	14	0.00	0	C	NR_002318		44028223	44028223	-1	no_errors	ENST00000381680	ensembl	human	known	69_37n	rna	13	27.78	5	SNP	0.000	T
FAM208B	54906	genome.wustl.edu	37	10	5756146	5756146	+	Intron	SNP	A	A	G			TCGA-A2-A4S0-01A-21D-A25Q-09	TCGA-A2-A4S0-10A-01D-A25Q-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9929b767-3bd5-4081-824c-f127623f2730	2a035c54-5e78-4f3a-8bb3-ad04e96d899e	g.chr10:5756146A>G	ENST00000328090.5	+	2	434				RP11-336A10.2_ENST00000411512.2_RNA|RP11-336A10.2_ENST00000596567.1_RNA|FAM208B_ENST00000463468.1_3'UTR	NM_017782.4	NP_060252	Q5VWN6	F208B_HUMAN	family with sequence similarity 208, member B																		CAGTGCTGTTACCACTCTGGG	0.363																																						dbGAP											0																																										-	-	-	SO:0001627	intron_variant	0			BX649177	CCDS41485.1	10p15.1	2011-09-14	2011-09-14	2011-09-14	ENSG00000108021	ENSG00000108021			23484	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 18"""	C10orf18		12477932	Standard	NM_017782		Approved	FLJ20360, bA318E3.2, KIAA2006	uc001iij.3	Q5VWN6	OTTHUMG00000017605	ENST00000328090.5:c.-192+1265A>G	10.37:g.5756146A>G		Somatic		WXS	Illumina GAIIx	Phase_IV	Q2YD91|Q5VWN5|Q6ZRQ8|Q8IVG4|Q9BUZ7|Q9H5J9|Q9H7A4|Q9H996|Q9NXA1	RNA	SNP	-	NULL	ENST00000328090.5	37	NULL	CCDS41485.1	10																																																																																			FAM208B	-	-	ENSG00000108021		0.363	FAM208B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	FAM208B	HGNC	protein_coding	OTTHUMT00000046571.2	51	0.00	0	A	NM_017782		5756146	5756146	+1	no_errors	ENST00000463468	ensembl	human	known	69_37n	rna	25	35.90	14	SNP	0.254	G
FAM83B	222584	genome.wustl.edu	37	6	54805818	54805818	+	Silent	SNP	T	T	C			TCGA-A2-A4S0-01A-21D-A25Q-09	TCGA-A2-A4S0-10A-01D-A25Q-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9929b767-3bd5-4081-824c-f127623f2730	2a035c54-5e78-4f3a-8bb3-ad04e96d899e	g.chr6:54805818T>C	ENST00000306858.7	+	5	2165	c.2049T>C	c.(2047-2049)taT>taC	p.Y683Y	RP3-523K23.2_ENST00000562834.1_RNA	NM_001010872.1	NP_001010872.1	Q5T0W9	FA83B_HUMAN	family with sequence similarity 83, member B	683										autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(28)|ovary(6)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	71	Lung NSC(77;0.0178)|Renal(3;0.122)					GTAAGCATTATGTATATAGTA	0.358																																						dbGAP											0													67.0	71.0	70.0					6																	54805818		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AK055204	CCDS34479.1	6p12.1	2014-03-13	2006-03-23	2006-03-23	ENSG00000168143	ENSG00000168143			21357	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 143"""	C6orf143		22886302	Standard	NM_001010872		Approved	FLJ30642	uc003pck.4	Q5T0W9	OTTHUMG00000014899	ENST00000306858.7:c.2049T>C	6.37:g.54805818T>C		Somatic		WXS	Illumina GAIIx	Phase_IV	Q2M1P3|Q96DQ2	Silent	SNP	pfam_DUF1669	p.Y683	ENST00000306858.7	37	c.2049	CCDS34479.1	6																																																																																			FAM83B	-	NULL	ENSG00000168143		0.358	FAM83B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FAM83B	HGNC	protein_coding	OTTHUMT00000040994.1	53	0.00	0	T	XM_294139		54805818	54805818	+1	no_errors	ENST00000306858	ensembl	human	known	69_37n	silent	30	38.78	19	SNP	1.000	C
LECT2	3950	genome.wustl.edu	37	5	135276438	135276438	+	Intron	SNP	T	T	C	rs75937403	byFrequency	TCGA-A2-A4S0-01A-21D-A25Q-09	TCGA-A2-A4S0-10A-01D-A25Q-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9929b767-3bd5-4081-824c-f127623f2730	2a035c54-5e78-4f3a-8bb3-ad04e96d899e	g.chr5:135276438T>C	ENST00000522943.1	-	3	418				FBXL21_ENST00000467490.1_RNA|LECT2_ENST00000471827.1_Intron|FBXL21_ENST00000297158.9_RNA			O14960	LECT2_HUMAN	leukocyte cell-derived chemotaxin 2						chemotaxis (GO:0006935)|negative regulation of Wnt signaling pathway (GO:0030178)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	identical protein binding (GO:0042802)			large_intestine(1)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			ATTATATACCTATGAAGCATA	0.229													T|||	163	0.0325479	0.121	0.0043	5008	,	,		14010	0.0		0.0	False		,,,				2504	0.0					dbGAP											0																																										-	-	-	SO:0001627	intron_variant	0			AB007546	CCDS4190.1	5q31.1	2008-05-15			ENSG00000145826	ENSG00000145826			6550	protein-coding gene	gene with protein product		602882				9545637	Standard	NM_002302		Approved	chm-II, chm2	uc003lbe.1	O14960	OTTHUMG00000129146	ENST00000522943.1:c.289+10473A>G	5.37:g.135276438T>C		Somatic		WXS	Illumina GAIIx	Phase_IV	B2RA90|O14565|Q52M49	RNA	SNP	-	NULL	ENST00000522943.1	37	NULL		5																																																																																			FBXL21	-	-	ENSG00000164616		0.229	LECT2-005	PUTATIVE	basic	protein_coding	FBXL21	HGNC	protein_coding	OTTHUMT00000381629.1	30	0.00	0	T	NM_002302		135276438	135276438	+1	no_errors	ENST00000467490	ensembl	human	known	69_37n	rna	20	13.04	3	SNP	0.001	C
HMCN2	256158	genome.wustl.edu	37	9	133266442	133266442	+	3'UTR	SNP	C	C	T	rs45488294	byFrequency	TCGA-A2-A4S0-01A-21D-A25Q-09	TCGA-A2-A4S0-10A-01D-A25Q-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9929b767-3bd5-4081-824c-f127623f2730	2a035c54-5e78-4f3a-8bb3-ad04e96d899e	g.chr9:133266442C>T	ENST00000487727.2	+	0	696							Q8NDA2	HMCN2_HUMAN	hemicentin 2						response to stimulus (GO:0050896)	proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)										CAGGCGGGCACCTACACGTGC	0.701													C|||	136	0.0271565	0.0045	0.0418	5008	,	,		13915	0.0		0.0656	False		,,,				2504	0.0358					dbGAP											0																																										-	-	-	SO:0001624	3_prime_UTR_variant	0			AK074396		9q34.11	2013-01-29			ENSG00000148357	ENSG00000148357		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	21293	protein-coding gene	gene with protein product							Standard	XM_006710218		Approved	DKFZp434P0216, FLJ23816		Q8NDA2	OTTHUMG00000140096	ENST00000487727.2:c.*693C>T	9.37:g.133266442C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	Q8N225|Q8TCI8	RNA	SNP	-	NULL	ENST00000487727.2	37	NULL		9																																																																																			HMCN2	-	-	ENSG00000148357		0.701	HMCN2-006	KNOWN	mRNA_start_NF|basic	processed_transcript	HMCN2	HGNC	protein_coding	OTTHUMT00000054659.3	8	0.00	0	C	XM_175125		133266442	133266442	+1	no_errors	ENST00000487727	ensembl	human	known	69_37n	rna	4	50.00	4	SNP	1.000	T
KRT16P1	729252	genome.wustl.edu	37	17	18345128	18345128	+	RNA	SNP	C	C	T			TCGA-A2-A4S0-01A-21D-A25Q-09	TCGA-A2-A4S0-10A-01D-A25Q-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9929b767-3bd5-4081-824c-f127623f2730	2a035c54-5e78-4f3a-8bb3-ad04e96d899e	g.chr17:18345128C>T	ENST00000581027.1	+	0	957									keratin 16 pseudogene 1																		AGTCCCAGCTCAGCATAGTAT	0.577																																						dbGAP											0																																										-	-	-			0					17p11.2	2012-08-13	2010-02-25	2010-02-25	ENSG00000214856	ENSG00000214856			6420	pseudogene	pseudogene			"""keratin 14 pseudogene"""	KRT14P			Standard	NR_073414		Approved		uc010vya.2		OTTHUMG00000059249		17.37:g.18345128C>T		Somatic		WXS	Illumina GAIIx	Phase_IV		RNA	SNP	-	NULL	ENST00000581027.1	37	NULL		17																																																																																			KRT16P1	-	-	ENSG00000214856		0.577	KRT16P1-003	KNOWN	basic	processed_transcript	KRT16P1	HGNC	pseudogene	OTTHUMT00000446576.1	14	0.00	0	C	NG_007001		18345128	18345128	+1	no_errors	ENST00000581027	ensembl	human	known	69_37n	rna	2	50.00	2	SNP	1.000	T
NOD1	10392	genome.wustl.edu	37	7	30492497	30492498	+	Frame_Shift_Del	DEL	CT	CT	-			TCGA-A2-A4S0-01A-21D-A25Q-09	TCGA-A2-A4S0-10A-01D-A25Q-09	CT	CT					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9929b767-3bd5-4081-824c-f127623f2730	2a035c54-5e78-4f3a-8bb3-ad04e96d899e	g.chr7:30492497_30492498delCT	ENST00000222823.4	-	6	1060_1061	c.535_536delAG	c.(535-537)agcfs	p.S179fs	NOD1_ENST00000423334.2_Frame_Shift_Del_p.S179fs	NM_006092.2	NP_006083.1	Q9Y239	NOD1_HUMAN	nucleotide-binding oligomerization domain containing 1	179					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of MAPK activity (GO:0000187)|apoptotic process (GO:0006915)|defense response (GO:0006952)|defense response to bacterium (GO:0042742)|defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|detection of biotic stimulus (GO:0009595)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-8 biosynthetic process (GO:0042228)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of tumor necrosis factor production (GO:0032760)|protein oligomerization (GO:0051259)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|identical protein binding (GO:0042802)|peptidoglycan binding (GO:0042834)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(2)|prostate(1)|skin(2)	39						GCAGGCCAGGCTGTTCAGGCTG	0.589																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AF126484	CCDS5427.1	7p15-p14	2006-12-08	2006-12-08	2006-12-08	ENSG00000106100	ENSG00000106100		"""Nucleotide-binding domain and leucine rich repeat containing"""	16390	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 1"", ""NLR family, CARD domain containing 1"""	605980	"""caspase recruitment domain family, member 4"""	CARD4		10224040, 10329646	Standard	NM_006092		Approved	NLRC1, CLR7.1	uc003tav.3	Q9Y239	OTTHUMG00000023923	ENST00000222823.4:c.535_536delAG	7.37:g.30492497_30492498delCT	ENSP00000222823:p.Ser179fs	Somatic		WXS	Illumina GAIIx	Phase_IV	B4DTU3|Q549U4|Q8IWF5	Frame_Shift_Del	DEL	pfam_CARD,superfamily_DEATH-like,smart_Leu-rich_rpt_RNase_inh_sub-typ,pfscan_NACHT_NTPase,pfscan_CARD	p.S179fs	ENST00000222823.4	37	c.536_535	CCDS5427.1	7																																																																																			NOD1	-	NULL	ENSG00000106100		0.589	NOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NOD1	HGNC	protein_coding	OTTHUMT00000250443.2	50	0.00	0	CT			30492497	30492498	-1	no_errors	ENST00000222823	ensembl	human	known	69_37n	frame_shift_del	26	46.94	23	DEL	0.732:0.095	-
LIMK1	3984	genome.wustl.edu	37	7	73535625	73535625	+	Silent	SNP	C	C	T	rs536008549		TCGA-A2-A4S0-01A-21D-A25Q-09	TCGA-A2-A4S0-10A-01D-A25Q-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9929b767-3bd5-4081-824c-f127623f2730	2a035c54-5e78-4f3a-8bb3-ad04e96d899e	g.chr7:73535625C>T	ENST00000336180.2	+	16	1989	c.1938C>T	c.(1936-1938)ccC>ccT	p.P646P	LIMK1_ENST00000538333.3_Silent_p.P612P|LIMK1_ENST00000418310.1_Silent_p.P676P	NM_002314.3	NP_002305.1	P53667	LIMK1_HUMAN	LIM domain kinase 1	646					actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|nervous system development (GO:0007399)|positive regulation of actin filament bundle assembly (GO:0032233)|positive regulation of axon extension (GO:0045773)|positive regulation of stress fiber assembly (GO:0051496)|protein phosphorylation (GO:0006468)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|nucleus (GO:0005634)	ATP binding (GO:0005524)|heat shock protein binding (GO:0031072)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	21		Lung NSC(55;0.137)			Dabrafenib(DB08912)	CTGAGGTCCCCGACTGAGCCA	0.692																																						dbGAP											0													16.0	18.0	17.0					7																	73535625		2190	4289	6479	-	-	-	SO:0001819	synonymous_variant	0			D26309	CCDS5563.1, CCDS56491.1	7q11.23	2005-01-21			ENSG00000106683	ENSG00000106683			6613	protein-coding gene	gene with protein product		601329				8673124, 8812460	Standard	NM_002314		Approved	LIMK	uc003uaa.2	P53667	OTTHUMG00000023448	ENST00000336180.2:c.1938C>T	7.37:g.73535625C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	B7Z6I8|D3DXF4|D3DXF5|O15283|Q15820|Q15821|Q75MU3|Q9Y5Q1	Silent	SNP	pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Prot_kinase_cat_dom,pfam_Znf_LIM,pfam_PDZ,pfam_LipoPS_kinase,superfamily_Kinase-like_dom,superfamily_PDZ,smart_Znf_LIM,smart_PDZ,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Znf_LIM,pfscan_PDZ,pfscan_Prot_kinase_cat_dom,prints_Ser-Thr/Tyr_kinase_cat_dom	p.P646	ENST00000336180.2	37	c.1938	CCDS5563.1	7																																																																																			LIMK1	-	NULL	ENSG00000106683		0.692	LIMK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LIMK1	HGNC	protein_coding	OTTHUMT00000252335.2	24	0.00	0	C	NM_002314		73535625	73535625	+1	no_errors	ENST00000336180	ensembl	human	known	69_37n	silent	12	40.00	8	SNP	0.275	T
SAMD11	148398	genome.wustl.edu	37	1	879085	879085	+	Missense_Mutation	SNP	G	G	T			TCGA-A2-A4S0-01A-21D-A25Q-09	TCGA-A2-A4S0-10A-01D-A25Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9929b767-3bd5-4081-824c-f127623f2730	2a035c54-5e78-4f3a-8bb3-ad04e96d899e	g.chr1:879085G>T	ENST00000342066.3	+	13	1780	c.1697G>T	c.(1696-1698)aGg>aTg	p.R566M		NM_152486.2	NP_689699	Q96NU1	SAM11_HUMAN	sterile alpha motif domain containing 11	566	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;1.74e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.93e-23)|Colorectal(212;0.000159)|COAD - Colon adenocarcinoma(227;0.000193)|BRCA - Breast invasive adenocarcinoma(365;0.000472)|Kidney(185;0.0023)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0342)|Lung(427;0.199)		CAGGTCTTCAGGGAGCAGGGG	0.667																																						dbGAP											0													13.0	15.0	14.0					1																	879085		2186	4282	6468	-	-	-	SO:0001583	missense	0			BC024295	CCDS2.2	1p36.33	2013-01-10			ENSG00000187634	ENSG00000187634		"""Sterile alpha motif (SAM) domain containing"""	28706	protein-coding gene	gene with protein product						12477932	Standard	NM_152486		Approved	MGC45873	uc001abw.1	Q96NU1	OTTHUMG00000040719	ENST00000342066.3:c.1697G>T	1.37:g.879085G>T	ENSP00000342313:p.Arg566Met	Somatic		WXS	Illumina GAIIx	Phase_IV	A2AA76|I7FV78|I7FV81|I7G0Z6|Q5SV96|Q5SV99|Q5SVA0|Q8N195|Q8TB59	Missense_Mutation	SNP	pfam_SAM_2,pfam_SAM_type1,superfamily_SAM/pointed,smart_SAM,pfscan_SAM	p.R566M	ENST00000342066.3	37	c.1697	CCDS2.2	1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.82|18.82	3.706044|3.706044	0.68615|0.68615	.|.	.|.	ENSG00000187634|ENSG00000187634	ENST00000341065;ENST00000455979|ENST00000342066	.|D	.|0.85861	.|-2.04	5.43|5.43	5.43|5.43	0.79202|0.79202	.|Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 2 (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.92734|0.92734	0.7690|0.7690	M|M	0.82056|0.82056	2.57|2.57	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|0.999;1.0	.|D;D	.|0.97110	.|0.935;1.0	D|D	0.93455|0.93455	0.6805|0.6805	5|10	.|0.87932	.|D	.|0	-16.0094|-16.0094	17.8379|17.8379	0.88706|0.88706	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|550;566	.|Q96NU1-1;Q96NU1	.|.;SAM11_HUMAN	W|M	474;393|566	.|ENSP00000342313:R566M	.|ENSP00000342313:R566M	G|R	+|+	1|2	0|0	SAMD11|SAMD11	868948|868948	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.888000|0.888000	0.51559|0.51559	7.577000|7.577000	0.82486|0.82486	2.567000|2.567000	0.86603|0.86603	0.555000|0.555000	0.69702|0.69702	GGG|AGG	SAMD11	-	pfam_SAM_2,pfam_SAM_type1,superfamily_SAM/pointed,smart_SAM,pfscan_SAM	ENSG00000187634		0.667	SAMD11-010	KNOWN	basic|appris_principal|CCDS	protein_coding	SAMD11	HGNC	protein_coding	OTTHUMT00000276866.2	34	0.00	0	G	NM_152486		879085	879085	+1	no_errors	ENST00000342066	ensembl	human	known	69_37n	missense	23	14.81	4	SNP	1.000	T
PCNXL2	80003	genome.wustl.edu	37	1	233119951	233119951	+	3'UTR	SNP	C	C	T	rs2885	byFrequency	TCGA-A2-A4S0-01A-21D-A25Q-09	TCGA-A2-A4S0-10A-01D-A25Q-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9929b767-3bd5-4081-824c-f127623f2730	2a035c54-5e78-4f3a-8bb3-ad04e96d899e	g.chr1:233119951C>T	ENST00000258229.9	-	0	6747				PCNXL2_ENST00000344698.2_3'UTR	NM_014801.3	NP_055616.3	A6NKB5	PCX2_HUMAN	pecanex-like 2 (Drosophila)							integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(7)|large_intestine(19)|lung(30)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86		all_cancers(173;0.0347)|Prostate(94;0.137)				CCTCATGGATCGCGGTATTGG	0.512													C|||	871	0.173922	0.2307	0.1254	5008	,	,		15617	0.1647		0.1958	False		,,,				2504	0.1186					dbGAP											0																																										-	-	-	SO:0001624	3_prime_UTR_variant	0			AK055374	CCDS44335.1	1q42.2	2008-02-05	2001-11-28		ENSG00000135749	ENSG00000135749			8736	protein-coding gene	gene with protein product			"""pecanex (Drosophila)-like 2"""			12477932	Standard	NM_014801		Approved	KIAA0435, FLJ11383	uc001hvl.2	A6NKB5	OTTHUMG00000037824	ENST00000258229.9:c.*99G>A	1.37:g.233119951C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	O43162|Q5T9Z8|Q5TDF1|Q8TEP4|Q96HP9|Q9HAL8	RNA	SNP	-	NULL	ENST00000258229.9	37	NULL	CCDS44335.1	1																																																																																			PCNXL2	-	-	ENSG00000135749		0.512	PCNXL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	PCNXL2	HGNC	protein_coding	OTTHUMT00000092480.3	27	0.00	0	C	NM_014801		233119951	233119951	-1	no_errors	ENST00000462762	ensembl	human	known	69_37n	rna	31	13.51	5	SNP	0.000	T
SLC12A7	10723	genome.wustl.edu	37	5	1075565	1075565	+	Missense_Mutation	SNP	T	T	C			TCGA-A2-A4S0-01A-21D-A25Q-09	TCGA-A2-A4S0-10A-01D-A25Q-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9929b767-3bd5-4081-824c-f127623f2730	2a035c54-5e78-4f3a-8bb3-ad04e96d899e	g.chr5:1075565T>C	ENST00000264930.5	-	15	1931	c.1888A>G	c.(1888-1890)Atg>Gtg	p.M630V		NM_006598.2	NP_006589.2	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 7	630					cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	32	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)		Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)		Potassium Chloride(DB00761)	CAGATGAACATCAGCGCCAGG	0.647																																						dbGAP											0													75.0	65.0	68.0					5																	1075565		2201	4300	6501	-	-	-	SO:0001583	missense	0			AF105365	CCDS34129.1	5p15	2013-07-18	2013-07-18		ENSG00000113504	ENSG00000113504		"""Solute carriers"""	10915	protein-coding gene	gene with protein product		604879				10347194	Standard	NM_006598		Approved	KCC4, DKFZP434F076	uc003jbu.3	Q9Y666	OTTHUMG00000161931	ENST00000264930.5:c.1888A>G	5.37:g.1075565T>C	ENSP00000264930:p.Met630Val	Somatic		WXS	Illumina GAIIx	Phase_IV	A6NDS8|Q4G0F3|Q96I81|Q9H7I3|Q9H7I7|Q9UFW2	Missense_Mutation	SNP	pfam_AA-permease_dom,prints_KCL_cotranspt,tigrfam_Na/K/Cl_cotransptS	p.M630V	ENST00000264930.5	37	c.1888	CCDS34129.1	5	.	.	.	.	.	.	.	.	.	.	t	16.51	3.142882	0.57044	.	.	ENSG00000113504	ENST00000264930	D	0.98862	-5.19	4.27	4.27	0.50696	Amino acid permease domain (1);	0.000000	0.85682	D	0.000000	D	0.99263	0.9743	H	0.96048	3.76	0.80722	D	1	D	0.69078	0.997	D	0.64321	0.924	D	0.98974	1.0802	10	0.87932	D	0	.	11.6184	0.51102	0.0:0.0:0.0:1.0	.	630	Q9Y666	S12A7_HUMAN	V	630	ENSP00000264930:M630V	ENSP00000264930:M630V	M	-	1	0	SLC12A7	1128565	1.000000	0.71417	0.937000	0.37676	0.845000	0.48019	7.142000	0.77339	1.693000	0.51124	0.402000	0.26972	ATG	SLC12A7	-	pfam_AA-permease_dom,tigrfam_Na/K/Cl_cotransptS	ENSG00000113504		0.647	SLC12A7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	SLC12A7	HGNC	protein_coding	OTTHUMT00000366446.2	44	0.00	0	T	NM_006598		1075565	1075565	-1	no_errors	ENST00000264930	ensembl	human	known	69_37n	missense	14	39.13	9	SNP	1.000	C
SMG1	23049	genome.wustl.edu	37	16	18877754	18877754	+	Intron	SNP	A	A	G	rs60842123	byFrequency	TCGA-A2-A4S0-01A-21D-A25Q-09	TCGA-A2-A4S0-10A-01D-A25Q-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9929b767-3bd5-4081-824c-f127623f2730	2a035c54-5e78-4f3a-8bb3-ad04e96d899e	g.chr16:18877754A>G	ENST00000446231.2	-	23	3763				SMG1_ENST00000389467.3_Intron			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase						DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						CTTCAGTAAGAAAGGCACTCA	0.393													A|||	92	0.0183706	0.0681	0.0029	5008	,	,		21013	0.0		0.0	False		,,,				2504	0.0					dbGAP											0																																										-	-	-	SO:0001627	intron_variant	0			AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"""phosphatidylinositol 3-kinase-related kinase"""	607032	"""smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"""			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.3350+188T>C	16.37:g.18877754A>G		Somatic		WXS	Illumina GAIIx	Phase_IV	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	RNA	SNP	-	NULL	ENST00000446231.2	37	NULL	CCDS45430.1	16																																																																																			SMG1	-	-	ENSG00000157106		0.393	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	SMG1	HGNC	protein_coding	OTTHUMT00000391817.1	55	0.00	0	A	NM_015092		18877754	18877754	-1	no_errors	ENST00000566328	ensembl	human	known	69_37n	rna	35	10.26	4	SNP	0.649	G
USP5	8078	genome.wustl.edu	37	12	6964624	6964624	+	Silent	SNP	T	T	C			TCGA-A2-A4S0-01A-21D-A25Q-09	TCGA-A2-A4S0-10A-01D-A25Q-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9929b767-3bd5-4081-824c-f127623f2730	2a035c54-5e78-4f3a-8bb3-ad04e96d899e	g.chr12:6964624T>C	ENST00000229268.8	+	2	223	c.171T>C	c.(169-171)taT>taC	p.Y57Y	USP5_ENST00000389231.5_Silent_p.Y57Y	NM_001098536.1	NP_001092006.1	P45974	UBP5_HUMAN	ubiquitin specific peptidase 5 (isopeptidase T)	57					positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)	lysosome (GO:0005764)	cysteine-type endopeptidase activity (GO:0004197)|omega peptidase activity (GO:0008242)|ubiquitin thiolesterase activity (GO:0004221)|zinc ion binding (GO:0008270)			breast(6)|endometrium(4)|kidney(2)|large_intestine(6)|lung(14)|skin(2)|urinary_tract(2)	36						GGAAACAGTATGTGGAGAGAC	0.562																																						dbGAP											0													127.0	136.0	133.0					12																	6964624		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			U35116	CCDS31733.1, CCDS41743.1	12p13	2007-03-02	2005-08-08		ENSG00000111667	ENSG00000111667		"""Ubiquitin-specific peptidases"""	12628	protein-coding gene	gene with protein product		601447	"""ubiquitin specific protease 5 (isopeptidase T)"""			12838346, 8723724	Standard	NM_003481		Approved	IsoT	uc001qri.4	P45974	OTTHUMG00000169233	ENST00000229268.8:c.171T>C	12.37:g.6964624T>C		Somatic		WXS	Illumina GAIIx	Phase_IV	D3DUS7|D3DUS8|Q96J22	Silent	SNP	pfam_Peptidase_C19,pfam_UBA/transl_elong_EF1B_N,pfam_Znf_UBP,superfamily_UBA-like,smart_Znf_UBP,smart_UBA/transl_elong_EF1B_N_euk,pirsf_Ubiquitinyl_hydrolase,pfscan_UBA/transl_elong_EF1B_N_euk,pfscan_Znf_UBP,pfscan_Peptidase_C19	p.Y57	ENST00000229268.8	37	c.171	CCDS41743.1	12																																																																																			USP5	-	pirsf_Ubiquitinyl_hydrolase	ENSG00000111667		0.562	USP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	USP5	HGNC	protein_coding	OTTHUMT00000402982.1	59	0.00	0	T			6964624	6964624	+1	no_errors	ENST00000229268	ensembl	human	known	69_37n	silent	37	28.85	15	SNP	1.000	C
USP44	84101	genome.wustl.edu	37	12	95926683	95926683	+	Silent	SNP	G	G	T			TCGA-A2-A4S0-01A-21D-A25Q-09	TCGA-A2-A4S0-10A-01D-A25Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9929b767-3bd5-4081-824c-f127623f2730	2a035c54-5e78-4f3a-8bb3-ad04e96d899e	g.chr12:95926683G>T	ENST00000258499.3	-	2	1638	c.1350C>A	c.(1348-1350)atC>atA	p.I450I	USP44_ENST00000393091.2_Silent_p.I450I|USP44_ENST00000552440.1_Silent_p.I450I|USP44_ENST00000537435.2_Silent_p.I450I	NM_001278393.1|NM_032147.2	NP_001265322.1|NP_115523.2	Q9H0E7	UBP44_HUMAN	ubiquitin specific peptidase 44	450	USP.				mitotic nuclear division (GO:0007067)|negative regulation of mitotic anaphase-promoting complex activity (GO:0060564)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein deubiquitination (GO:0016579)|regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090266)|regulation of spindle checkpoint (GO:0090231)	nucleus (GO:0005634)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(5)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	36						GAGAAGTGGGGATAAGAGCTG	0.358																																						dbGAP											0													105.0	106.0	106.0					12																	95926683		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AK027434	CCDS9053.1	12q21.33	2005-08-08	2005-08-08			ENSG00000136014		"""Ubiquitin-specific peptidases"""	20064	protein-coding gene	gene with protein product		610993	"""ubiquitin specific protease 44"""			12838346	Standard	NM_001278393		Approved	FLJ14528	uc001teg.3	Q9H0E7		ENST00000258499.3:c.1350C>A	12.37:g.95926683G>T		Somatic		WXS	Illumina GAIIx	Phase_IV	B2RDW3	Silent	SNP	pfam_Peptidase_C19,pfam_Znf_UBP,smart_Znf_UBP,pfscan_Znf_UBP,pfscan_Peptidase_C19	p.I450	ENST00000258499.3	37	c.1350	CCDS9053.1	12																																																																																			USP44	-	pfam_Peptidase_C19,pfscan_Peptidase_C19	ENSG00000136014		0.358	USP44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	USP44	HGNC	protein_coding	OTTHUMT00000408312.1	38	0.00	0	G	NM_032147		95926683	95926683	-1	no_errors	ENST00000258499	ensembl	human	known	69_37n	silent	22	12.00	3	SNP	1.000	T
VCX3B	425054	genome.wustl.edu	37	X	8434192	8434193	+	Frame_Shift_Ins	INS	-	-	C			TCGA-A2-A4S0-01A-21D-A25Q-09	TCGA-A2-A4S0-10A-01D-A25Q-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9929b767-3bd5-4081-824c-f127623f2730	2a035c54-5e78-4f3a-8bb3-ad04e96d899e	g.chrX:8434192_8434193insC	ENST00000381032.1	+	3	816_817	c.509_510insC	c.(508-513)gtggaafs	p.E171fs	VCX3B_ENST00000381029.4_Frame_Shift_Ins_p.E139fs|VCX3B_ENST00000453306.1_Frame_Shift_Ins_p.E171fs|VCX3B_ENST00000444481.1_Frame_Shift_Ins_p.E141fs|VCX3B_ENST00000440654.2_Frame_Shift_Ins_p.E121fs	NM_001001888.3	NP_001001888.3	Q9H321	VCX3B_HUMAN	variable charge, X-linked 3B	171	14 X 10 AA tandem repeats of L-S-Q-E-S- [EQ]-V-E-E-P.					nucleolus (GO:0005730)|nucleus (GO:0005634)				NS(1)|large_intestine(1)|lung(2)|prostate(1)|skin(3)|urinary_tract(3)	11						GAGAGCGAGGTGGAAGAACCAC	0.589																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0				CCDS48077.1, CCDS48077.2	Xp22.31	2009-01-14			ENSG00000205642	ENSG00000205642			31838	protein-coding gene	gene with protein product							Standard	NM_001001888		Approved	VCX-C	uc011mht.2	Q9H321	OTTHUMG00000021106	Exception_encountered	X.37:g.8434192_8434193insC	ENSP00000370420:p.Glu171fs	Somatic		WXS	Illumina GAIIx	Phase_IV	C9JS46|Q4KN12	Frame_Shift_Ins	INS	NULL	p.E141fs	ENST00000381032.1	37	c.419_420	CCDS48077.2	X																																																																																			VCX3B	-	NULL	ENSG00000205642		0.589	VCX3B-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	VCX3B	HGNC	protein_coding	OTTHUMT00000055691.1	36	0.00	0	-			8434192	8434193	+1	no_errors	ENST00000444481	ensembl	human	known	69_37n	frame_shift_ins	9	18.18	2	INS	0.000:0.001	C
