#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
AMPH	273	genome.wustl.edu	37	7	38431426	38431426	+	Missense_Mutation	SNP	G	G	T			TCGA-E2-A15C-01A-31D-A12B-09	TCGA-E2-A15C-10A-01D-A12B-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	10c594a1-0843-4740-9d96-00211a9509fb	3ec15582-48e3-4bb5-bdfe-7c909a259130	g.chr7:38431426G>T	ENST00000356264.2	-	19	2016	c.1801C>A	c.(1801-1803)Cca>Aca	p.P601T	AMPH_ENST00000428293.2_Missense_Mutation_p.P559T|AMPH_ENST00000471913.1_5'Flank|AMPH_ENST00000325590.5_Missense_Mutation_p.P559T	NM_001635.3	NP_001626.1	P49418	AMPH_HUMAN	amphiphysin	601					endocytosis (GO:0006897)|learning (GO:0007612)|synaptic transmission (GO:0007268)|synaptic vesicle endocytosis (GO:0048488)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|leading edge membrane (GO:0031256)|synaptic vesicle (GO:0008021)	phospholipid binding (GO:0005543)	p.P601T(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(12)|liver(3)|lung(27)|ovary(3)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)	62						CCCATGGCTGGTGCAGAAGGC	0.597																																						dbGAP											1	Substitution - Missense(1)	lung(1)											52.0	50.0	50.0					7																	38431426		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS5456.1, CCDS47574.1	7p14-p13	2007-06-19	2007-06-19		ENSG00000078053	ENSG00000078053			471	protein-coding gene	gene with protein product		600418	"""amphiphysin (Stiff-Mann syndrome with breast cancer 128kD autoantigen)"", ""amphiphysin (Stiff-Man syndrome with breast cancer 128kDa autoantigen)"""			8245793	Standard	NM_139316		Approved		uc003tgu.3	P49418	OTTHUMG00000023725	ENST00000356264.2:c.1801C>A	7.37:g.38431426G>T	ENSP00000348602:p.Pro601Thr	Somatic		WXS	Illumina GAIIx	Phase_IV	A4D1X8|A4D1X9|O43538|Q75MJ8|Q75MK5|Q75MM3|Q8N4G0	Missense_Mutation	SNP	pfam_BAR_dom,pfam_SH3_2,superfamily_SH3_domain,smart_BAR_dom,smart_SH3_domain,pfscan_BAR_dom,pfscan_SH3_domain,prints_Amphiphysin,prints_Amphiphysin_1,prints_SH3_domain	p.P601T	ENST00000356264.2	37	c.1801	CCDS5456.1	7	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.088|0.088	-1.172673|-1.172673	0.01646|0.01646	.|.	.|.	ENSG00000078053|ENSG00000078053	ENST00000325590;ENST00000356264;ENST00000428293;ENST00000353242|ENST00000441628	T;T;T|.	0.60040|.	0.22;0.24;0.23|.	4.81|4.81	0.184|0.184	0.15086|0.15086	.|.	0.528419|.	0.15191|.	U|.	0.275570|.	T|T	0.21103|0.21103	0.0508|0.0508	N|N	0.19112|0.19112	0.55|0.55	0.09310|0.09310	N|N	1|1	B;B;B|.	0.33379|.	0.152;0.049;0.41|.	B;B;B|.	0.23275|.	0.036;0.026;0.045|.	T|T	0.27434|0.27434	-1.0074|-1.0074	10|5	0.10902|.	T|.	0.67|.	0.1252|0.1252	5.6965|5.6965	0.17859|0.17859	0.1779:0.3818:0.4403:0.0|0.1779:0.3818:0.4403:0.0	.|.	559;601;489|.	P49418-2;P49418;Q8NFL4|.	.;AMPH_HUMAN;.|.	T|N	559;601;559;503|483	ENSP00000317441:P559T;ENSP00000348602:P601T;ENSP00000390734:P559T|.	ENSP00000317441:P559T|.	P|T	-|-	1|2	0|0	AMPH|AMPH	38397951|38397951	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.016000|0.016000	0.09150|0.09150	0.385000|0.385000	0.20685|0.20685	0.183000|0.183000	0.20059|0.20059	0.591000|0.591000	0.81541|0.81541	CCA|ACC	AMPH	-	NULL	ENSG00000078053		0.597	AMPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	AMPH	HGNC	protein_coding	OTTHUMT00000226953.2	76	0.00	0	G	NM_001635		38431426	38431426	-1	no_errors	ENST00000356264	ensembl	human	known	69_37n	missense	42	30.00	18	SNP	0.000	T
CRAT	1384	genome.wustl.edu	37	9	131860626	131860626	+	Silent	SNP	G	G	A	rs374143667		TCGA-E2-A15C-01A-31D-A12B-09	TCGA-E2-A15C-10A-01D-A12B-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	10c594a1-0843-4740-9d96-00211a9509fb	3ec15582-48e3-4bb5-bdfe-7c909a259130	g.chr9:131860626G>A	ENST00000318080.2	-	10	1524	c.1230C>T	c.(1228-1230)acC>acT	p.T410T	RP11-247A12.1_ENST00000434250.1_RNA	NM_000755.3|NM_001257363.1	NP_000746|NP_001244292.1	P43155	CACP_HUMAN	carnitine O-acetyltransferase	410					carnitine metabolic process, CoA-linked (GO:0019254)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	carnitine O-acetyltransferase activity (GO:0004092)|receptor binding (GO:0005102)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(4)|skin(1)|urinary_tract(2)	13				UCEC - Uterine corpus endometrioid carcinoma (4;0.0178)	L-Carnitine(DB00583)	ACACCATCACGGTGATATCCA	0.582																																						dbGAP											0													77.0	78.0	78.0					9																	131860626		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			X78706	CCDS6919.1	9q34.1	2010-04-27	2010-04-27		ENSG00000095321	ENSG00000095321	2.3.1.7		2342	protein-coding gene	gene with protein product		600184	"""carnitine acetyltransferase"""			7829107	Standard	NM_000755		Approved	CAT1	uc004bxh.3	P43155	OTTHUMG00000147343	ENST00000318080.2:c.1230C>T	9.37:g.131860626G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	Q5T952|Q9BW16	Missense_Mutation	SNP	pfam_Carn_acyl_trans	p.R9C	ENST00000318080.2	37	c.25	CCDS6919.1	9	.	.	.	.	.	.	.	.	.	.	G	6.684	0.494765	0.12702	.	.	ENSG00000095321	ENST00000455396	.	.	.	5.13	-10.3	0.00346	.	.	.	.	.	T	0.16300	0.0392	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.08554	-1.0716	4	.	.	.	-0.1922	3.9443	0.09341	0.1628:0.0855:0.423:0.3287	.	.	.	.	C	9	.	.	R	-	1	0	CRAT	130900447	0.000000	0.05858	0.000000	0.03702	0.728000	0.41692	-1.559000	0.02162	-2.956000	0.00291	-0.397000	0.06425	CGT	CRAT	-	pfam_Carn_acyl_trans	ENSG00000095321		0.582	CRAT-006	KNOWN	basic|appris_principal|CCDS	protein_coding	CRAT	HGNC	protein_coding	OTTHUMT00000253700.1	139	0.00	0	G			131860626	131860626	-1	no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region	ENST00000455396	ensembl	human	novel	69_37n	missense	117	10.00	13	SNP	0.000	A
CREB1	1385	genome.wustl.edu	37	2	208442363	208442363	+	Missense_Mutation	SNP	C	C	T			TCGA-E2-A15C-01A-31D-A12B-09	TCGA-E2-A15C-10A-01D-A12B-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	10c594a1-0843-4740-9d96-00211a9509fb	3ec15582-48e3-4bb5-bdfe-7c909a259130	g.chr2:208442363C>T	ENST00000432329.2	+	8	1116	c.865C>T	c.(865-867)Cgt>Tgt	p.R289C	CREB1_ENST00000430624.1_Missense_Mutation_p.R275C|CREB1_ENST00000374397.4_Missense_Mutation_p.R178C|CREB1_ENST00000353267.3_Missense_Mutation_p.R275C	NM_134442.3	NP_604391.1	P16220	CREB1_HUMAN	cAMP responsive element binding protein 1	289	Basic motif. {ECO:0000255|PROSITE- ProRule:PRU00978}.|bZIP. {ECO:0000255|PROSITE- ProRule:PRU00978}.				activation of phospholipase C activity (GO:0007202)|axon guidance (GO:0007411)|cellular response to zinc ion (GO:0071294)|circadian rhythm (GO:0007623)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|lactation (GO:0007595)|lung saccule development (GO:0060430)|memory (GO:0007613)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of transcription by competitive promoter binding (GO:0010944)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|pituitary gland development (GO:0021983)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of hormone secretion (GO:0046887)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of cell size (GO:0008361)|response to drug (GO:0042493)|response to glucagon (GO:0033762)|response to organic substance (GO:0010033)|secretory granule organization (GO:0033363)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|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)|transcription from RNA polymerase II promoter (GO:0006366)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|Type I pneumocyte differentiation (GO:0060509)|viral process (GO:0016032)	nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	cAMP response element binding (GO:0035497)|enzyme binding (GO:0019899)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)		EWSR1/CREB1(44)	NS(1)|breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|upper_aerodigestive_tract(1)	5				LUSC - Lung squamous cell carcinoma(261;0.0768)|Epithelial(149;0.127)|Lung(261;0.145)	Adenosine monophosphate(DB00131)|Naloxone(DB01183)	GAGAGAGGTCCGTCTAATGAA	0.453			T	EWSR1	"""clear cell sarcoma, angiomatoid fibrous histiocytoma"""																																	dbGAP		Dom	yes		2	2q34	1385	cAMP responsive element binding protein 1		M	0													122.0	108.0	112.0					2																	208442363		2203	4300	6503	-	-	-	SO:0001583	missense	0			M27691	CCDS2374.1, CCDS2375.1	2q34	2013-01-10			ENSG00000118260	ENSG00000118260		"""basic leucine zipper proteins"""	2345	protein-coding gene	gene with protein product		123810					Standard	NM_134442		Approved		uc002vcc.3	P16220	OTTHUMG00000132936	ENST00000432329.2:c.865C>T	2.37:g.208442363C>T	ENSP00000387699:p.Arg289Cys	Somatic		WXS	Illumina GAIIx	Phase_IV	P21934|Q6V963|Q9UMA7	Missense_Mutation	SNP	pfam_Coactivator_CBP_pKID,pfam_bZIP_1,pfam_bZIP_2,superfamily_Euk_TF_DNA-bd,smart_bZIP,pfscan_Coactivator_CBP_pKID,pfscan_bZIP,prints_Leuzip_CREB	p.R289C	ENST00000432329.2	37	c.865	CCDS2375.1	2	.	.	.	.	.	.	.	.	.	.	C	21.4	4.137018	0.77775	.	.	ENSG00000118260	ENST00000430624;ENST00000432329;ENST00000353267;ENST00000374397;ENST00000448277;ENST00000455757	T;T;T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29;-0.29;-0.14	5.86	5.86	0.93980	Basic-leucine zipper (bZIP) transcription factor (3);bZIP transcription factor, bZIP-1 (1);	0.000000	0.85682	D	0.000000	D	0.89515	0.6737	H	0.99156	4.45	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.93148	0.6547	10	0.87932	D	0	-9.4566	14.9532	0.71091	0.1429:0.8571:0.0:0.0	.	275;289	Q53X93;P16220	.;CREB1_HUMAN	C	275;289;275;178;235;102	ENSP00000405539:R275C;ENSP00000387699:R289C;ENSP00000236995:R275C;ENSP00000363518:R178C;ENSP00000405711:R235C;ENSP00000401803:R102C	ENSP00000236995:R275C	R	+	1	0	CREB1	208150608	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	5.930000	0.70104	2.774000	0.95407	0.585000	0.79938	CGT	CREB1	-	pfam_bZIP_1,pfam_bZIP_2,superfamily_Euk_TF_DNA-bd,smart_bZIP,pfscan_bZIP,prints_Leuzip_CREB	ENSG00000118260		0.453	CREB1-001	KNOWN	basic|CCDS	protein_coding	CREB1	HGNC	protein_coding	OTTHUMT00000256467.3	307	0.00	0	C	NM_134442		208442363	208442363	+1	no_errors	ENST00000432329	ensembl	human	known	69_37n	missense	182	35.00	98	SNP	1.000	T
DDX23	9416	genome.wustl.edu	37	12	49228171	49228171	+	Missense_Mutation	SNP	G	G	A			TCGA-E2-A15C-01A-31D-A12B-09	TCGA-E2-A15C-10A-01D-A12B-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	10c594a1-0843-4740-9d96-00211a9509fb	3ec15582-48e3-4bb5-bdfe-7c909a259130	g.chr12:49228171G>A	ENST00000308025.3	-	12	1571	c.1492C>T	c.(1492-1494)Cgc>Tgc	p.R498C	DDX23_ENST00000553182.1_5'Flank	NM_004818.2	NP_004809.2	Q9BUQ8	DDX23_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 23	498	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|cis assembly of pre-catalytic spliceosome (GO:0000354)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|U5 snRNP (GO:0005682)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|kidney(4)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(2)|urinary_tract(3)	36						GCCACAGTGCGGATACCTAGC	0.542																																						dbGAP											0													114.0	100.0	105.0					12																	49228171		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF026402	CCDS8770.1	12q13.11	2013-07-16				ENSG00000174243		"""DEAD-boxes"""	17347	protein-coding gene	gene with protein product		612172	"""PRP28 homolog, yeast"""			9409622, 9539711	Standard	NM_004818		Approved	prp28, U5-100K, PRPF28, SNRNP100	uc001rsm.3	Q9BUQ8		ENST00000308025.3:c.1492C>T	12.37:g.49228171G>A	ENSP00000310723:p.Arg498Cys	Somatic		WXS	Illumina GAIIx	Phase_IV	B2R600|B4DH15|O43188	Missense_Mutation	SNP	pfam_DNA/RNA_helicase_DEAD/DEAH_N,pfam_Helicase_C,smart_Helicase_ATP-bd,smart_Helicase_C,pfscan_Helicase_ATP-bd,pfscan_Helicase_C,pfscan_RNA_helicase_DEAD_Q_motif	p.R498C	ENST00000308025.3	37	c.1492	CCDS8770.1	12	.	.	.	.	.	.	.	.	.	.	G	24.9	4.583649	0.86748	.	.	ENSG00000174243	ENST00000308025	T	0.19105	2.17	5.13	5.13	0.70059	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.054980	0.85682	D	0.000000	T	0.53174	0.1780	M	0.91663	3.23	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	T	0.62029	-0.6940	10	0.87932	D	0	-9.0229	12.5717	0.56341	0.0:0.0:0.8336:0.1664	.	498	Q9BUQ8	DDX23_HUMAN	C	498	ENSP00000310723:R498C	ENSP00000310723:R498C	R	-	1	0	DDX23	47514438	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.493000	0.81493	2.667000	0.90743	0.460000	0.39030	CGC	DDX23	-	pfam_DNA/RNA_helicase_DEAD/DEAH_N,smart_Helicase_ATP-bd,pfscan_Helicase_ATP-bd	ENSG00000174243		0.542	DDX23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DDX23	HGNC	protein_coding	OTTHUMT00000408897.2	371	0.00	0	G	NM_004818		49228171	49228171	-1	no_errors	ENST00000308025	ensembl	human	known	69_37n	missense	275	32.10	130	SNP	1.000	A
DYSF	8291	genome.wustl.edu	37	2	71894557	71894557	+	Missense_Mutation	SNP	C	C	T			TCGA-E2-A15C-01A-31D-A12B-09	TCGA-E2-A15C-10A-01D-A12B-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	10c594a1-0843-4740-9d96-00211a9509fb	3ec15582-48e3-4bb5-bdfe-7c909a259130	g.chr2:71894557C>T	ENST00000258104.3	+	47	5529	c.5252C>T	c.(5251-5253)gCt>gTt	p.A1751V	DYSF_ENST00000409582.3_Missense_Mutation_p.A1789V|DYSF_ENST00000409651.1_Missense_Mutation_p.A1783V|DYSF_ENST00000410041.1_Missense_Mutation_p.A1769V|DYSF_ENST00000429174.2_Missense_Mutation_p.A1772V|DYSF_ENST00000413539.2_Missense_Mutation_p.A1782V|DYSF_ENST00000409366.1_Missense_Mutation_p.A1773V|DYSF_ENST00000409744.1_Missense_Mutation_p.A1759V|DYSF_ENST00000394120.2_Missense_Mutation_p.A1752V|DYSF_ENST00000410020.3_Missense_Mutation_p.A1790V|DYSF_ENST00000409762.1_Missense_Mutation_p.A1768V|DYSF_ENST00000479049.2_3'UTR	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	1751					plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)			autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						GAGCGTCTGGCTCTGCATGTG	0.627																																						dbGAP											0													72.0	75.0	74.0					2																	71894557		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"""fer-1-like family member 1"""	603009	"""limb girdle muscular dystrophy 2B (autosomal recessive)"""	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.5252C>T	2.37:g.71894557C>T	ENSP00000258104:p.Ala1751Val	Somatic		WXS	Illumina GAIIx	Phase_IV	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Missense_Mutation	SNP	pfam_C2_Ca-dep,pfam_Ferlin_B-domain,pfam_FerIin-domain,pfam_Ferlin_A-domain,superfamily_C2_Ca/lipid-bd_dom_CaLB,superfamily_MFS_dom_general_subst_transpt,smart_C2_Ca-dep,smart_Peroxin/Ferlin,pfscan_C2_membr_targeting	p.A1782V	ENST00000258104.3	37	c.5345	CCDS1918.1	2	.	.	.	.	.	.	.	.	.	.	C	25.4	4.634006	0.87660	.	.	ENSG00000135636	ENST00000413539;ENST00000409762;ENST00000409582;ENST00000429174;ENST00000258104;ENST00000409651;ENST00000394120;ENST00000409744;ENST00000409366;ENST00000410020;ENST00000410041	D;D;D;D;D;D;D;D;D;D;D	0.85773	-2.03;-2.03;-2.0;-2.0;-2.03;-2.03;-2.03;-1.99;-2.0;-2.0;-2.03	5.05	5.05	0.67936	.	0.151462	0.64402	D	0.000019	D	0.94079	0.8102	M	0.93197	3.39	0.58432	D	0.999998	D;D;D;P;P;P;D;D;D;D;D;D;P;P;P	0.76494	0.965;0.982;0.982;0.951;0.951;0.943;0.989;0.97;0.999;0.982;0.996;0.996;0.913;0.951;0.919	P;P;P;P;P;P;D;D;D;P;D;D;P;P;P	0.74674	0.806;0.864;0.864;0.864;0.864;0.844;0.944;0.913;0.984;0.864;0.973;0.944;0.864;0.864;0.735	D	0.95274	0.8380	10	0.87932	D	0	-16.2896	15.9365	0.79712	0.0:1.0:0.0:0.0	.	515;1783;1790;1773;1738;1769;1759;1768;1758;1782;1789;1772;1737;1752;1751	B7Z8G4;O75923-8;O75923-13;O75923-10;O75923-9;O75923-11;O75923-12;O75923-5;O75923-6;O75923-2;O75923-7;O75923-4;O75923-3;O75923-14;O75923	.;.;.;.;.;.;.;.;.;.;.;.;.;.;DYSF_HUMAN	V	1782;1768;1789;1772;1751;1783;1752;1759;1773;1790;1769	ENSP00000407046:A1782V;ENSP00000387137:A1768V;ENSP00000386547:A1789V;ENSP00000398305:A1772V;ENSP00000258104:A1751V;ENSP00000386683:A1783V;ENSP00000377678:A1752V;ENSP00000386285:A1759V;ENSP00000386512:A1773V;ENSP00000386881:A1790V;ENSP00000386617:A1769V	ENSP00000258104:A1751V	A	+	2	0	DYSF	71748065	1.000000	0.71417	0.970000	0.41538	0.425000	0.31504	4.738000	0.62073	2.639000	0.89480	0.491000	0.48974	GCT	DYSF	-	NULL	ENSG00000135636		0.627	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	DYSF	HGNC	protein_coding	OTTHUMT00000251970.3	34	0.00	0	C	NM_003494		71894557	71894557	+1	no_errors	ENST00000413539	ensembl	human	known	69_37n	missense	44	10.20	5	SNP	1.000	T
FBXO31	79791	genome.wustl.edu	37	16	87367507	87367507	+	Frame_Shift_Del	DEL	C	C	-			TCGA-E2-A15C-01A-31D-A12B-09	TCGA-E2-A15C-10A-01D-A12B-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	10c594a1-0843-4740-9d96-00211a9509fb	3ec15582-48e3-4bb5-bdfe-7c909a259130	g.chr16:87367507delC	ENST00000311635.7	-	8	1394	c.1382delG	c.(1381-1383)cgafs	p.R461fs	RP11-178L8.4_ENST00000568879.1_Frame_Shift_Del_p.E125fs	NM_001282683.1|NM_024735.3	NP_001269612.1|NP_079011.3	Q5XUX0	FBX31_HUMAN	F-box protein 31	461					cellular response to DNA damage stimulus (GO:0006974)|cyclin catabolic process (GO:0008054)|mitotic G1 DNA damage checkpoint (GO:0031571)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)	17				BRCA - Breast invasive adenocarcinoma(80;0.0272)		CCTGCAGGTTCGGGGGTAGTC	0.687																																						dbGAP											0													55.0	64.0	61.0					16																	87367507		2189	4285	6474	-	-	-	SO:0001589	frameshift_variant	0			BC002985	CCDS32501.1, CCDS73922.1	16q24	2008-12-18	2004-05-27			ENSG00000103264		"""F-boxes /  ""other"""""	16510	protein-coding gene	gene with protein product		609102	"""F-box only protein 31"""				Standard	NM_024735		Approved	FBX14, FBXO14, Fbx31, MGC15419	uc002fjw.3	Q5XUX0		ENST00000311635.7:c.1382delG	16.37:g.87367507delC	ENSP00000310841:p.Arg461fs	Somatic		WXS	Illumina GAIIx	Phase_IV	Q5K680|Q8WYV1|Q96D73|Q9UFV4	Frame_Shift_Del	DEL	pfam_F-box_dom_cyclin-like,superfamily_F-box_dom_cyclin-like,smart_F-box_dom_cyclin-like,pfscan_F-box_dom_cyclin-like	p.R461fs	ENST00000311635.7	37	c.1382	CCDS32501.1	16																																																																																			FBXO31	-	NULL	ENSG00000103264		0.687	FBXO31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FBXO31	HGNC	protein_coding	OTTHUMT00000430799.2	30	0.00	0	C	NM_024735		87367507	87367507	-1	no_errors	ENST00000311635	ensembl	human	known	69_37n	frame_shift_del	15	22.73	5	DEL	1.000	-
GAL3ST3	89792	genome.wustl.edu	37	11	65810935	65810935	+	Silent	SNP	C	C	T			TCGA-E2-A15C-01A-31D-A12B-09	TCGA-E2-A15C-10A-01D-A12B-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	10c594a1-0843-4740-9d96-00211a9509fb	3ec15582-48e3-4bb5-bdfe-7c909a259130	g.chr11:65810935C>T	ENST00000312006.4	-	3	620	c.339G>A	c.(337-339)gcG>gcA	p.A113A	GAL3ST3_ENST00000527878.1_Silent_p.A113A	NM_033036.2	NP_149025.1	Q96A11	G3ST3_HUMAN	galactose-3-O-sulfotransferase 3	113					monosaccharide metabolic process (GO:0005996)|oligosaccharide metabolic process (GO:0009311)|poly-N-acetyllactosamine metabolic process (GO:0030309)|proteoglycan biosynthetic process (GO:0030166)|sulfur compound metabolic process (GO:0006790)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|carbohydrate binding (GO:0030246)|galactose 3-O-sulfotransferase activity (GO:0050694)|galactosylceramide sulfotransferase activity (GO:0001733)|proteoglycan sulfotransferase activity (GO:0050698)			kidney(1)|lung(9)|ovary(2)|skin(2)	14						GCACGAAGTGCGCCGAGAAGT	0.692																																						dbGAP											0													19.0	19.0	19.0					11																	65810935		2199	4290	6489	-	-	-	SO:0001819	synonymous_variant	0			AY026481	CCDS8128.1	11q13.1	2014-08-12			ENSG00000175229	ENSG00000175229		"""Sulfotransferases, membrane-bound"""	24144	protein-coding gene	gene with protein product		608234				11323440, 11356829	Standard	NM_033036		Approved	GAL3ST2	uc001ogw.3	Q96A11	OTTHUMG00000166667	ENST00000312006.4:c.339G>A	11.37:g.65810935C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	Q14D05	Silent	SNP	pfam_Gal-3-0_sulfotransfrase	p.A113	ENST00000312006.4	37	c.339	CCDS8128.1	11																																																																																			GAL3ST3	-	pfam_Gal-3-0_sulfotransfrase	ENSG00000175229		0.692	GAL3ST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GAL3ST3	HGNC	protein_coding	OTTHUMT00000391052.1	23	0.00	0	C	NM_033036		65810935	65810935	-1	no_errors	ENST00000312006	ensembl	human	known	69_37n	silent	15	31.82	7	SNP	0.993	T
GPR174	84636	genome.wustl.edu	37	X	78426998	78426998	+	Missense_Mutation	SNP	G	G	T			TCGA-E2-A15C-01A-31D-A12B-09	TCGA-E2-A15C-10A-01D-A12B-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	10c594a1-0843-4740-9d96-00211a9509fb	3ec15582-48e3-4bb5-bdfe-7c909a259130	g.chrX:78426998G>T	ENST00000276077.1	+	1	530	c.494G>T	c.(493-495)aGg>aTg	p.R165M		NM_032553.1	NP_115942.1	Q9BXC1	GP174_HUMAN	G protein-coupled receptor 174	165						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(19)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	38						TCTGGCAATAGGACCAAATGC	0.478										HNSCC(63;0.18)																												dbGAP											0													141.0	118.0	126.0					X																	78426998		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF345567	CCDS14443.1	Xq13.3	2012-08-21			ENSG00000147138	ENSG00000147138		"""GPCR / Class A : Orphans"""	30245	protein-coding gene	gene with protein product		300903					Standard	NM_032553		Approved	FKSG79	uc004edg.1	Q9BXC1	OTTHUMG00000021898	ENST00000276077.1:c.494G>T	X.37:g.78426998G>T	ENSP00000276077:p.Arg165Met	Somatic		WXS	Illumina GAIIx	Phase_IV	Q2M3F7	Missense_Mutation	SNP	pfam_7TM_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_supfam,prints_7TM_GPCR_Rhodpsn,prints_P2_purnocptor	p.R165M	ENST00000276077.1	37	c.494	CCDS14443.1	X	.	.	.	.	.	.	.	.	.	.	g	5.124	0.208415	0.09757	.	.	ENSG00000147138	ENST00000276077	T	0.37584	1.19	4.9	0.766	0.18476	GPCR, rhodopsin-like superfamily (1);	0.691905	0.13961	N	0.350852	T	0.20251	0.0487	N	0.24115	0.695	0.09310	N	1	B	0.06786	0.001	B	0.14023	0.01	T	0.16482	-1.0401	10	0.46703	T	0.11	.	3.607	0.08046	0.3971:0.0:0.4286:0.1743	.	165	Q9BXC1	GP174_HUMAN	M	165	ENSP00000276077:R165M	ENSP00000276077:R165M	R	+	2	0	GPR174	78313654	.	.	0.983000	0.44433	0.589000	0.36550	.	.	0.328000	0.23435	0.488000	0.48403	AGG	GPR174	-	pfam_7TM_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_supfam	ENSG00000147138		0.478	GPR174-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GPR174	HGNC	protein_coding	OTTHUMT00000057327.1	439	0.23	1	G	NM_032553		78426998	78426998	+1	no_errors	ENST00000276077	ensembl	human	known	69_37n	missense	290	34.31	152	SNP	0.010	T
HCFC1	3054	genome.wustl.edu	37	X	153222202	153222202	+	Missense_Mutation	SNP	C	C	A			TCGA-E2-A15C-01A-31D-A12B-09	TCGA-E2-A15C-10A-01D-A12B-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	10c594a1-0843-4740-9d96-00211a9509fb	3ec15582-48e3-4bb5-bdfe-7c909a259130	g.chrX:153222202C>A	ENST00000310441.7	-	15	3475	c.2509G>T	c.(2509-2511)Ggg>Tgg	p.G837W	HCFC1_ENST00000354233.3_Missense_Mutation_p.G768W|HCFC1_ENST00000369984.4_Missense_Mutation_p.G837W	NM_005334.2	NP_005325.2	P51610	HCFC1_HUMAN	host cell factor C1	837	Interaction with GABP2.|Interaction with ZBTB17.				cell cycle (GO:0007049)|chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell cycle (GO:0045787)|positive regulation of gene expression (GO:0010628)|protein stabilization (GO:0050821)|regulation of protein complex assembly (GO:0043254)|regulation of transcription, DNA-templated (GO:0006355)|release from viral latency (GO:0019046)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|membrane (GO:0016020)|mitochondrion (GO:0005739)|MLL1 complex (GO:0071339)|MLL5-L complex (GO:0070688)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	chromatin binding (GO:0003682)|identical protein binding (GO:0042802)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(3)|large_intestine(3)|lung(18)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	all_cancers(53;6.23e-16)|all_epithelial(53;5.61e-10)|all_lung(58;3.99e-07)|Lung NSC(58;5.02e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CCCGGGGCCCCCTTAAGCACC	0.667																																						dbGAP											0													57.0	64.0	62.0					X																	153222202		2114	4203	6317	-	-	-	SO:0001583	missense	0				CCDS44020.1	Xq28	2014-06-12	2014-06-09		ENSG00000172534	ENSG00000172534			4839	protein-coding gene	gene with protein product	"""VP16-accessory protein"", ""protein phosphatase 1, regulatory subunit 89"""	300019	"""mental retardation, X-linked 3"", ""host cell factor C1 (VP16-accessory protein)"""	HFC1, MRX3		8392914, 23000143	Standard	XM_005274664		Approved	HCF-1, HCF1, CFF, VCAF, MGC70925, PPP1R89	uc004fjp.3	P51610	OTTHUMG00000024222	ENST00000310441.7:c.2509G>T	X.37:g.153222202C>A	ENSP00000309555:p.Gly837Trp	Somatic		WXS	Illumina GAIIx	Phase_IV	Q6P4G5	Missense_Mutation	SNP	pfam_Kelch_2,pfam_Kelch_1,superfamily_Fibronectin_type3,smart_Fibronectin_type3	p.G837W	ENST00000310441.7	37	c.2509	CCDS44020.1	X	.	.	.	.	.	.	.	.	.	.	C	28.3	4.910416	0.92107	.	.	ENSG00000172534	ENST00000310441;ENST00000369984;ENST00000354233	T;T;T	0.03468	3.92;3.95;3.92	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.11367	0.0277	L	0.29908	0.895	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.09250	-1.0683	10	0.52906	T	0.07	.	17.1119	0.86678	0.0:1.0:0.0:0.0	.	837	P51610	HCFC1_HUMAN	W	837;837;768	ENSP00000309555:G837W;ENSP00000359001:G837W;ENSP00000346174:G768W	ENSP00000309555:G837W	G	-	1	0	HCFC1	152875396	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	7.337000	0.79256	2.305000	0.77605	0.429000	0.28392	GGG	HCFC1	-	NULL	ENSG00000172534		0.667	HCFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HCFC1	HGNC	protein_coding	OTTHUMT00000061099.4	88	0.00	0	C	NM_005334		153222202	153222202	-1	no_errors	ENST00000310441	ensembl	human	known	69_37n	missense	49	25.37	17	SNP	1.000	A
KLF15	28999	genome.wustl.edu	37	3	126062602	126062602	+	Missense_Mutation	SNP	G	G	A			TCGA-E2-A15C-01A-31D-A12B-09	TCGA-E2-A15C-10A-01D-A12B-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	10c594a1-0843-4740-9d96-00211a9509fb	3ec15582-48e3-4bb5-bdfe-7c909a259130	g.chr3:126062602G>A	ENST00000296233.3	-	3	1449	c.1219C>T	c.(1219-1221)Cgg>Tgg	p.R407W		NM_014079.3	NP_054798.1	Q9UIH9	KLF15_HUMAN	Kruppel-like factor 15	407					cardiac muscle hypertrophy in response to stress (GO:0014898)|cellular response to peptide (GO:1901653)|glial cell differentiation (GO:0010001)|glomerular visceral epithelial cell differentiation (GO:0072112)|glucose transport (GO:0015758)|negative regulation of peptidyl-lysine acetylation (GO:2000757)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|transcription regulatory region DNA binding (GO:0044212)			endometrium(1)|lung(7)|ovary(2)|skin(2)	12				GBM - Glioblastoma multiforme(114;0.147)		CGGCTGCTCCGCGGGAAGCGG	0.612																																						dbGAP											0													45.0	46.0	46.0					3																	126062602		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB029254	CCDS3036.1	3q21.3	2013-01-08			ENSG00000163884	ENSG00000163884		"""Kruppel-like transcription factors"", ""Zinc fingers, C2H2-type"""	14536	protein-coding gene	gene with protein product	"""kidney-enriched Kruppel-like factor"""	606465				10982849	Standard	NM_014079		Approved	KKLF	uc011bkk.1	Q9UIH9	OTTHUMG00000162689	ENST00000296233.3:c.1219C>T	3.37:g.126062602G>A	ENSP00000296233:p.Arg407Trp	Somatic		WXS	Illumina GAIIx	Phase_IV		Missense_Mutation	SNP	pfam_Znf_C2H2,smart_Znf_C2H2-like,pfscan_Znf_C2H2	p.R407W	ENST00000296233.3	37	c.1219	CCDS3036.1	3	.	.	.	.	.	.	.	.	.	.	G	21.9	4.215347	0.79352	.	.	ENSG00000163884	ENST00000296233	T	0.10860	2.83	5.19	3.25	0.37280	Zinc finger, C2H2 (1);	0.000000	0.85682	D	0.000000	T	0.22781	0.0550	L	0.42245	1.32	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	T	0.00800	-1.1561	10	0.87932	D	0	.	10.642	0.45598	0.0:0.0:0.5208:0.4792	.	407	Q9UIH9	KLF15_HUMAN	W	407	ENSP00000296233:R407W	ENSP00000296233:R407W	R	-	1	2	KLF15	127545292	1.000000	0.71417	0.985000	0.45067	0.995000	0.86356	2.861000	0.48380	1.154000	0.42482	0.491000	0.48974	CGG	KLF15	-	pfscan_Znf_C2H2	ENSG00000163884		0.612	KLF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KLF15	HGNC	protein_coding	OTTHUMT00000370096.1	47	0.00	0	G	NM_014079		126062602	126062602	-1	no_errors	ENST00000296233	ensembl	human	known	69_37n	missense	27	35.71	15	SNP	0.964	A
MAP3K1	4214	genome.wustl.edu	37	5	56161239	56161240	+	Frame_Shift_Ins	INS	-	-	CT	rs140697922|rs373748407	byFrequency	TCGA-E2-A15C-01A-31D-A12B-09	TCGA-E2-A15C-10A-01D-A12B-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	10c594a1-0843-4740-9d96-00211a9509fb	3ec15582-48e3-4bb5-bdfe-7c909a259130	g.chr5:56161239_56161240insCT	ENST00000399503.3	+	5	1108_1109	c.1108_1109insCT	c.(1108-1110)cctfs	p.P370fs		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	370					activation of MAPKK activity (GO:0000186)|apoptotic mitochondrial changes (GO:0008637)|cellular response to mechanical stimulus (GO:0071260)|epithelial cell morphogenesis (GO:0003382)|eyelid development in camera-type eye (GO:0061029)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of actin filament polymerization (GO:0030838)|protein phosphorylation (GO:0006468)|regulation of cell migration (GO:0030334)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|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)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	cytosol (GO:0005829)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)			NS(1)|breast(19)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(11)|ovary(1)|skin(3)|urinary_tract(1)	57		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)		TCAACTAGAACCTTCAGACCCA	0.337																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			U29671, AF042838	CCDS43318.1	5q11.2	2012-02-23	2012-02-23		ENSG00000095015	ENSG00000095015		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6848	protein-coding gene	gene with protein product		600982	"""mitogen-activated protein kinase kinase kinase 1"""	MEKK1		8597633	Standard	NM_005921		Approved	MEKK, MAPKKK1	uc003jqw.4	Q13233	OTTHUMG00000059486	ENST00000399503.3:c.1109_1110dupCT	5.37:g.56161240_56161241dupCT	ENSP00000382423:p.Pro370fs	Somatic		WXS	Illumina GAIIx	Phase_IV		Frame_Shift_Ins	INS	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,superfamily_ARM-type_fold,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Znf_RING,pfscan_Znf_SWIM,pfscan_Prot_kinase_cat_dom	p.S371fs	ENST00000399503.3	37	c.1108_1109	CCDS43318.1	5																																																																																			MAP3K1	-	NULL	ENSG00000095015		0.337	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	MAP3K1	HGNC	protein_coding	OTTHUMT00000132309.2	178	0.00	0	-	XM_042066		56161239	56161240	+1	no_errors	ENST00000399503	ensembl	human	novel	69_37n	frame_shift_ins	146	32.41	70	INS	1.000:1.000	CT
MBD3	53615	genome.wustl.edu	37	19	1585064	1585064	+	Missense_Mutation	SNP	T	T	C			TCGA-E2-A15C-01A-31D-A12B-09	TCGA-E2-A15C-10A-01D-A12B-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	10c594a1-0843-4740-9d96-00211a9509fb	3ec15582-48e3-4bb5-bdfe-7c909a259130	g.chr19:1585064T>C	ENST00000434436.3	-	2	389	c.260A>G	c.(259-261)aAc>aGc	p.N87S	MBD3_ENST00000585967.1_5'UTR|MBD3_ENST00000592012.1_Missense_Mutation_p.N55S|UQCR11_ENST00000585937.1_3'UTR|MBD3_ENST00000156825.1_Missense_Mutation_p.N87S|AC005943.4_ENST00000592406.1_RNA|MBD3_ENST00000590550.2_Missense_Mutation_p.N31S	NM_001281453.1	NP_001268382.1	O95983	MBD3_HUMAN	methyl-CpG binding domain protein 3	87					ATP-dependent chromatin remodeling (GO:0043044)|histone acetylation (GO:0016573)|in utero embryonic development (GO:0001701)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|tissue development (GO:0009888)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nuclear chromatin (GO:0000790)|NuRD complex (GO:0016581)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|methyl-CpG binding (GO:0008327)			central_nervous_system(1)|large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	8		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|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)|Lung(535;0.179)|STAD - Stomach adenocarcinoma(1328;0.18)		CTTGACCTGGTTGGAGGAGTC	0.662																																						dbGAP											0													84.0	56.0	65.0					19																	1585064		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF072247	CCDS12072.1, CCDS62481.1	19p13	2008-07-17				ENSG00000071655			6918	protein-coding gene	gene with protein product		603573				9774669, 10441743	Standard	NM_001281454		Approved		uc002ltl.1	O95983		ENST00000434436.3:c.260A>G	19.37:g.1585064T>C	ENSP00000412302:p.Asn87Ser	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K4B7|D6W5Z2|Q6PIL9|Q6PJZ9|Q86XF4	Missense_Mutation	SNP	pfam_Methyl_CpG_DNA-bd,superfamily_DNA-bd_integrase-typ,superfamily_ARM-type_fold,smart_Methyl_CpG_DNA-bd,pfscan_Methyl_CpG_DNA-bd	p.N87S	ENST00000434436.3	37	c.260	CCDS12072.1	19	.	.	.	.	.	.	.	.	.	.	T	8.711	0.911941	0.17907	.	.	ENSG00000071655	ENST00000434436;ENST00000156825	D	0.95853	-3.83	5.09	-7.35	0.01422	Methyl-CpG DNA binding (1);DNA-binding, integrase-type (1);	0.452187	0.27696	N	0.018231	D	0.84229	0.5426	N	0.16368	0.405	0.09310	N	0.999999	B;B	0.11235	0.0;0.004	B;B	0.13407	0.0;0.009	T	0.76822	-0.2817	10	0.10902	T	0.67	-26.0491	7.0499	0.25067	0.0:0.3003:0.3008:0.3989	.	55;87	O95983-2;O95983	.;MBD3_HUMAN	S	55;87	ENSP00000156825:N87S	ENSP00000156825:N87S	N	-	2	0	MBD3	1536064	0.841000	0.29509	0.028000	0.17463	0.303000	0.27691	-0.101000	0.10973	-1.143000	0.02866	0.379000	0.24179	AAC	MBD3	-	superfamily_DNA-bd_integrase-typ	ENSG00000071655		0.662	MBD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MBD3	HGNC	protein_coding	OTTHUMT00000449658.2	136	0.00	0	T	NM_003926		1585064	1585064	-1	no_errors	ENST00000156825	ensembl	human	known	69_37n	missense	88	29.60	37	SNP	0.023	C
MEGF11	84465	genome.wustl.edu	37	15	66257398	66257398	+	Silent	SNP	G	G	A			TCGA-E2-A15C-01A-31D-A12B-09	TCGA-E2-A15C-10A-01D-A12B-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	10c594a1-0843-4740-9d96-00211a9509fb	3ec15582-48e3-4bb5-bdfe-7c909a259130	g.chr15:66257398G>A	ENST00000409699.2	-	9	1132	c.960C>T	c.(958-960)tgC>tgT	p.C320C	MEGF11_ENST00000395625.2_Silent_p.C245C|MEGF11_ENST00000288745.3_Silent_p.C245C|MEGF11_ENST00000395614.1_5'UTR|MEGF11_ENST00000422354.1_Silent_p.C320C|MEGF11_ENST00000360698.4_Silent_p.C320C			A6BM72	MEG11_HUMAN	multiple EGF-like-domains 11	320	EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00076}.				homotypic cell-cell adhesion (GO:0034109)|retina layer formation (GO:0010842)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	19						CCCCATTGTGGCAGTCACAGT	0.667																																						dbGAP											0													26.0	24.0	25.0					15																	66257398		2198	4291	6489	-	-	-	SO:0001819	synonymous_variant	0			AB058677	CCDS10213.2	15q22.31	2006-03-31			ENSG00000157890	ENSG00000157890			29635	protein-coding gene	gene with protein product		612454				11347906	Standard	NM_032445		Approved	KIAA1781, DKFZp434L121	uc002apm.2	A6BM72	OTTHUMG00000133175	ENST00000409699.2:c.960C>T	15.37:g.66257398G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	Q17R86|Q6UXS5|Q8ND91|Q96KG6	Silent	SNP	pfam_EGF_laminin,pfam_EGF_extracell,smart_EGF-like,smart_EGF_laminin,pfscan_EG-like_dom,pfscan_EGF_laminin,pfscan_EMI_domain	p.C320	ENST00000409699.2	37	c.960	CCDS10213.2	15																																																																																			MEGF11	-	pfam_EGF_laminin,pfam_EGF_extracell,smart_EGF-like,smart_EGF_laminin,pfscan_EG-like_dom	ENSG00000157890		0.667	MEGF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MEGF11	HGNC	protein_coding	OTTHUMT00000329307.2	56	0.00	0	G	NM_032445		66257398	66257398	-1	no_errors	ENST00000409699	ensembl	human	known	69_37n	silent	35	36.36	20	SNP	1.000	A
MMRN1	22915	genome.wustl.edu	37	4	90833166	90833166	+	Missense_Mutation	SNP	G	G	T			TCGA-E2-A15C-01A-31D-A12B-09	TCGA-E2-A15C-10A-01D-A12B-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	10c594a1-0843-4740-9d96-00211a9509fb	3ec15582-48e3-4bb5-bdfe-7c909a259130	g.chr4:90833166G>T	ENST00000394980.1	+	4	1134	c.815G>T	c.(814-816)tGt>tTt	p.C272F	MMRN1_ENST00000264790.2_Missense_Mutation_p.C272F|MMRN1_ENST00000508372.1_Missense_Mutation_p.C14F|MMRN1_ENST00000394981.1_Missense_Mutation_p.C238F			Q13201	MMRN1_HUMAN	multimerin 1	272	EMI. {ECO:0000255|PROSITE- ProRule:PRU00384}.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)				breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|liver(2)|lung(34)|ovary(5)|prostate(1)|skin(6)|stomach(1)|urinary_tract(2)	72		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.96e-05)		TGGAGGTGCTGTCCTGGATAC	0.373																																						dbGAP											0													93.0	86.0	88.0					4																	90833166		2203	4299	6502	-	-	-	SO:0001583	missense	0			U27109	CCDS3635.1	4q22	2008-02-05	2004-03-02	2004-03-02	ENSG00000138722	ENSG00000138722		"""EMI domain containing"""	7178	protein-coding gene	gene with protein product	"""glycoprotein Ia*"""	601456	"""multimerin"""	MMRN		7629143, 10828608	Standard	NM_007351		Approved	ECM, EMILIN4, GPIa*	uc003hst.3	Q13201	OTTHUMG00000130947	ENST00000394980.1:c.815G>T	4.37:g.90833166G>T	ENSP00000378431:p.Cys272Phe	Somatic		WXS	Illumina GAIIx	Phase_IV	Q4W5L1|Q6P3T8|Q6ZUL9	Missense_Mutation	SNP	pfam_C1q,pfam_EMI_domain,pfam_EGF-like_dom,superfamily_Tumour_necrosis_fac-like,smart_EGF-like,smart_EGF-like_Ca-bd,smart_C1q,pfscan_C1q,pfscan_EG-like_dom,pfscan_EMI_domain,prints_C1q	p.C272F	ENST00000394980.1	37	c.815	CCDS3635.1	4	.	.	.	.	.	.	.	.	.	.	G	20.3	3.963774	0.74131	.	.	ENSG00000138722	ENST00000394980;ENST00000264790;ENST00000394981;ENST00000508372	D;D;D;D	0.93604	-2.54;-2.54;-2.54;-3.25	5.16	5.16	0.70880	EMI domain (2);	0.000000	0.85682	D	0.000000	D	0.97093	0.9050	M	0.87269	2.87	0.46078	D	0.998852	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.97483	1.0048	10	0.87932	D	0	.	17.71	0.88319	0.0:0.0:1.0:0.0	.	238;272	Q13201-2;Q13201	.;MMRN1_HUMAN	F	272;272;238;14	ENSP00000378431:C272F;ENSP00000264790:C272F;ENSP00000378432:C238F;ENSP00000426461:C14F	ENSP00000264790:C272F	C	+	2	0	MMRN1	91052189	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	5.479000	0.66813	2.797000	0.96272	0.561000	0.74099	TGT	MMRN1	-	pfam_EMI_domain,pfscan_EMI_domain	ENSG00000138722		0.373	MMRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MMRN1	HGNC	protein_coding	OTTHUMT00000253546.2	289	0.00	0	G	NM_007351		90833166	90833166	+1	no_errors	ENST00000264790	ensembl	human	known	69_37n	missense	163	33.06	81	SNP	1.000	T
MTO1	25821	genome.wustl.edu	37	6	74190485	74190485	+	Missense_Mutation	SNP	G	G	A			TCGA-E2-A15C-01A-31D-A12B-09	TCGA-E2-A15C-10A-01D-A12B-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	10c594a1-0843-4740-9d96-00211a9509fb	3ec15582-48e3-4bb5-bdfe-7c909a259130	g.chr6:74190485G>A	ENST00000370300.4	+	8	1382	c.1292G>A	c.(1291-1293)gGa>gAa	p.G431E	MTO1_ENST00000498286.1_Missense_Mutation_p.G406E|MTO1_ENST00000370305.1_Missense_Mutation_p.G357E|MTO1_ENST00000415954.2_Missense_Mutation_p.G406E	NM_012123.3|NM_133645.2	NP_036255.2|NP_598400.1	Q9Y2Z2	MTO1_HUMAN	mitochondrial tRNA translation optimization 1	431					mitochondrial tRNA wobble uridine modification (GO:0070899)|oxidation-reduction process (GO:0055114)	mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|stomach(1)	27						TTCTTTGCTGGACAGATCAAT	0.428																																						dbGAP											0													138.0	121.0	126.0					6																	74190485		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF132937	CCDS4979.1, CCDS34485.1, CCDS47452.1	6q14.1	2013-05-07	2013-05-07		ENSG00000135297	ENSG00000135297			19261	protein-coding gene	gene with protein product		614667	"""mitochondrial translation optimization 1 homolog (S. cerevisiae)"""			12011058, 22608499	Standard	NM_012123		Approved		uc003pgy.4	Q9Y2Z2	OTTHUMG00000015032	ENST00000370300.4:c.1292G>A	6.37:g.74190485G>A	ENSP00000359323:p.Gly431Glu	Somatic		WXS	Illumina GAIIx	Phase_IV	B3KQB5|Q5SWL2|Q5SWL3|Q5SWL4|Q8NDN7|Q8WZ57|Q96FE6|Q9BS06	Missense_Mutation	SNP	pfam_GIDA-rel,pfam_FAD_bind_dom,prints_FAD_pyr_nucl-diS_OxRdtase,tigrfam_GidA	p.G406E	ENST00000370300.4	37	c.1217	CCDS4979.1	6	.	.	.	.	.	.	.	.	.	.	G	32	5.174503	0.94807	.	.	ENSG00000135297	ENST00000415954;ENST00000498286;ENST00000357845;ENST00000370305;ENST00000370300	D;D;D;D	0.97480	-4.4;-4.4;-4.4;-4.4	5.15	5.15	0.70609	Glucose-inhibited division protein A-related, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.99140	0.9703	H	0.97340	3.985	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.99226	1.0880	10	0.87932	D	0	-19.131	18.617	0.91306	0.0:0.0:1.0:0.0	.	406;309;406;431	Q9Y2Z2-6;Q9Y2Z2-2;Q9Y2Z2-4;Q9Y2Z2	.;.;.;MTO1_HUMAN	E	406;406;309;357;431	ENSP00000402038:G406E;ENSP00000419561:G406E;ENSP00000359328:G357E;ENSP00000359323:G431E	ENSP00000350506:G309E	G	+	2	0	MTO1	74247206	1.000000	0.71417	1.000000	0.80357	0.912000	0.54170	9.158000	0.94723	2.392000	0.81423	0.591000	0.81541	GGA	MTO1	-	pfam_GIDA-rel,tigrfam_GidA	ENSG00000135297		0.428	MTO1-003	KNOWN	basic|CCDS	protein_coding	MTO1	HGNC	protein_coding	OTTHUMT00000041215.2	389	0.00	0	G	NM_012123		74190485	74190485	+1	no_errors	ENST00000415954	ensembl	human	known	69_37n	missense	349	15.29	63	SNP	1.000	A
OR5P2	120065	genome.wustl.edu	37	11	7817592	7817592	+	Missense_Mutation	SNP	C	C	T			TCGA-E2-A15C-01A-31D-A12B-09	TCGA-E2-A15C-10A-01D-A12B-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	10c594a1-0843-4740-9d96-00211a9509fb	3ec15582-48e3-4bb5-bdfe-7c909a259130	g.chr11:7817592C>T	ENST00000329434.2	-	1	928	c.898G>A	c.(898-900)Gag>Aag	p.E300K	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153444.1	NP_703145.1	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P, member 2	300						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	22				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		CTAACAAGCTCTCTCTTCAGA	0.398																																						dbGAP											0													87.0	114.0	105.0					11																	7817592		2104	4292	6396	-	-	-	SO:0001583	missense	0			AF173006	CCDS7782.1	11p15.4	2012-08-09			ENSG00000183303	ENSG00000183303		"""GPCR / Class A : Olfactory receptors"""	14783	protein-coding gene	gene with protein product							Standard	NM_153444		Approved	JCG3	uc001mfp.1	Q8WZ92	OTTHUMG00000165668	ENST00000329434.2:c.898G>A	11.37:g.7817592C>T	ENSP00000331823:p.Glu300Lys	Somatic		WXS	Illumina GAIIx	Phase_IV	Q3MIS8	Missense_Mutation	SNP	pfam_7TM_GPCR_Rhodpsn,pfam_7TM_GPCR_olfarory/Srsx,pfscan_GPCR_Rhodpsn_supfam,prints_Olfact_rcpt,prints_7TM_GPCR_Rhodpsn	p.E300K	ENST00000329434.2	37	c.898	CCDS7782.1	11	.	.	.	.	.	.	.	.	.	.	C	10.27	1.304770	0.23736	.	.	ENSG00000183303	ENST00000329434	T	0.36157	1.27	5.46	-5.9	0.02275	.	1.943540	0.02119	N	0.055470	T	0.18718	0.0449	N	0.02247	-0.625	0.09310	N	0.999999	B	0.06786	0.001	B	0.06405	0.002	T	0.19031	-1.0318	10	0.28530	T	0.3	1.1401	18.1517	0.89676	0.0:0.1513:0.7767:0.0721	.	300	Q8WZ92	OR5P2_HUMAN	K	300	ENSP00000331823:E300K	ENSP00000331823:E300K	E	-	1	0	OR5P2	7774168	0.004000	0.15560	0.134000	0.22075	0.209000	0.24338	0.000000	0.12993	-0.760000	0.04677	0.549000	0.68633	GAG	OR5P2	-	NULL	ENSG00000183303		0.398	OR5P2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	OR5P2	HGNC	protein_coding	OTTHUMT00000385696.1	262	0.00	0	C	NM_153444		7817592	7817592	-1	no_errors	ENST00000329434	ensembl	human	known	69_37n	missense	189	27.59	72	SNP	0.001	T
PCDHB10	56126	genome.wustl.edu	37	5	140573470	140573470	+	Missense_Mutation	SNP	C	C	T			TCGA-E2-A15C-01A-31D-A12B-09	TCGA-E2-A15C-10A-01D-A12B-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	10c594a1-0843-4740-9d96-00211a9509fb	3ec15582-48e3-4bb5-bdfe-7c909a259130	g.chr5:140573470C>T	ENST00000239446.4	+	1	1529	c.1345C>T	c.(1345-1347)Ccc>Tcc	p.P449S		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	449	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(30)|ovary(4)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	76			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TGACAACGCCCCCGCCTTCAC	0.597																																						dbGAP											0													60.0	60.0	60.0					5																	140573470		2203	4292	6495	-	-	-	SO:0001583	missense	0			AF152489	CCDS4252.1	5q31.3	2010-06-15			ENSG00000120324	ENSG00000120324		"""Cadherins / Protocadherins : Clustered"""	8681	other	protocadherin		606336				10380929	Standard	NM_018930		Approved		uc003lix.3	Q9UN67	OTTHUMG00000129626	ENST00000239446.4:c.1345C>T	5.37:g.140573470C>T	ENSP00000239446:p.Pro449Ser	Somatic		WXS	Illumina GAIIx	Phase_IV	Q96T99	Missense_Mutation	SNP	pfam_Cadherin,pfam_Cadherin_N,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin,prints_Cadherin	p.P449S	ENST00000239446.4	37	c.1345	CCDS4252.1	5	.	.	.	.	.	.	.	.	.	.	c	18.69	3.677959	0.68042	.	.	ENSG00000120324	ENST00000239446	D	0.84800	-1.9	3.22	3.22	0.36961	Cadherin (4);Cadherin conserved site (1);Cadherin-like (1);	.	.	.	.	D	0.96012	0.8701	H	0.99794	4.785	0.50632	D	0.999885	D	0.89917	1.0	D	0.97110	1.0	D	0.97710	1.0190	9	0.87932	D	0	.	14.6182	0.68565	0.0:1.0:0.0:0.0	.	449	Q9UN67	PCDBA_HUMAN	S	449	ENSP00000239446:P449S	ENSP00000239446:P449S	P	+	1	0	PCDHB10	140553654	1.000000	0.71417	0.986000	0.45419	0.709000	0.40893	7.557000	0.82243	1.819000	0.53055	0.549000	0.68633	CCC	PCDHB10	-	superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin,prints_Cadherin	ENSG00000120324		0.597	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PCDHB10	HGNC	protein_coding	OTTHUMT00000251821.1	142	0.00	0	C	NM_018930		140573470	140573470	+1	no_errors	ENST00000239446	ensembl	human	known	69_37n	missense	118	23.87	37	SNP	1.000	T
PGBD2	267002	genome.wustl.edu	37	1	249210807	249210807	+	Silent	SNP	C	C	G			TCGA-E2-A15C-01A-31D-A12B-09	TCGA-E2-A15C-10A-01D-A12B-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	10c594a1-0843-4740-9d96-00211a9509fb	3ec15582-48e3-4bb5-bdfe-7c909a259130	g.chr1:249210807C>G	ENST00000329291.5	+	3	171	c.24C>G	c.(22-24)gtC>gtG	p.V8V	PGBD2_ENST00000355360.4_Intron|PGBD2_ENST00000539153.1_Silent_p.V5V|PGBD2_ENST00000462488.1_Intron	NM_170725.2	NP_733843.1	Q6P3X8	PGBD2_HUMAN	piggyBac transposable element derived 2	8										NS(1)|endometrium(3)|lung(6)|ovary(1)|skin(3)	14	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.012)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)			ACAGAGATGTCATTGCTGGGA	0.473																																						dbGAP											0													67.0	65.0	66.0					1																	249210807		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AF229602	CCDS31128.1, CCDS31129.1	1q	2008-02-05			ENSG00000185220	ENSG00000185220			19399	protein-coding gene	gene with protein product							Standard	XM_005270333		Approved		uc001ifh.3	Q6P3X8	OTTHUMG00000040424	ENST00000329291.5:c.24C>G	1.37:g.249210807C>G		Somatic		WXS	Illumina GAIIx	Phase_IV	B3KVR8|Q6MZF8	Silent	SNP	NULL	p.V8	ENST00000329291.5	37	c.24	CCDS31128.1	1																																																																																			PGBD2	-	NULL	ENSG00000185220		0.473	PGBD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	PGBD2	HGNC	protein_coding	OTTHUMT00000097318.1	189	0.00	0	C			249210807	249210807	+1	no_errors	ENST00000329291	ensembl	human	known	69_37n	silent	123	38.19	76	SNP	0.000	G
PHKA2	5256	genome.wustl.edu	37	X	18944633	18944633	+	Missense_Mutation	SNP	G	G	A	rs191267737		TCGA-E2-A15C-01A-31D-A12B-09	TCGA-E2-A15C-10A-01D-A12B-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	10c594a1-0843-4740-9d96-00211a9509fb	3ec15582-48e3-4bb5-bdfe-7c909a259130	g.chrX:18944633G>A	ENST00000379942.4	-	14	2062	c.1397C>T	c.(1396-1398)gCg>gTg	p.A466V		NM_000292.2	NP_000283.1	P46019	KPB2_HUMAN	phosphorylase kinase, alpha 2 (liver)	466					carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			NS(1)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(23)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	61	Hepatocellular(33;0.183)					ATGAATGTCCGCGATACTCTG	0.458													G|||	1	0.000264901	0.0	0.0	3775	,	,		15190	0.001		0.0	False		,,,				2504	0.0					dbGAP											0													175.0	138.0	150.0					X																	18944633		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS14190.1	Xp22.2-p22.1	2009-07-10			ENSG00000044446	ENSG00000044446	2.7.11.19		8926	protein-coding gene	gene with protein product		300798		PHK, PYK		2387090	Standard	NM_000292		Approved		uc004cyv.4	P46019	OTTHUMG00000021222	ENST00000379942.4:c.1397C>T	X.37:g.18944633G>A	ENSP00000369274:p.Ala466Val	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K1T1|Q6LAJ5|Q7Z6W0|Q96CR3|Q9UDA1	Missense_Mutation	SNP	pfam_Glyco_hydro_15,superfamily_6-hairpin_glycosidase-like	p.A466V	ENST00000379942.4	37	c.1397	CCDS14190.1	X	1	6.027727546714888E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	16.32	3.091165	0.55968	.	.	ENSG00000044446	ENST00000379942	D	0.91180	-2.8	5.38	5.38	0.77491	Glycoside hydrolase 15-related (1);	0.207947	0.51477	D	0.000087	D	0.89298	0.6675	M	0.80982	2.52	0.54753	D	0.999983	P	0.37233	0.588	B	0.30572	0.117	D	0.89015	0.3431	10	0.41790	T	0.15	-14.0755	13.7211	0.62728	0.0:0.1504:0.8496:0.0	.	466	P46019	KPB2_HUMAN	V	466	ENSP00000369274:A466V	ENSP00000369274:A466V	A	-	2	0	PHKA2	18854554	1.000000	0.71417	0.887000	0.34795	0.469000	0.32828	7.271000	0.78506	2.383000	0.81215	0.600000	0.82982	GCG	PHKA2	-	pfam_Glyco_hydro_15	ENSG00000044446		0.458	PHKA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PHKA2	HGNC	protein_coding	OTTHUMT00000055960.1	365	0.00	0	G	NM_000292		18944633	18944633	-1	no_errors	ENST00000379942	ensembl	human	known	69_37n	missense	183	40.84	127	SNP	0.997	A
PIK3CA	5290	genome.wustl.edu	37	3	178952085	178952085	+	Missense_Mutation	SNP	A	A	G	rs121913279		TCGA-E2-A15C-01A-31D-A12B-09	TCGA-E2-A15C-10A-01D-A12B-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	10c594a1-0843-4740-9d96-00211a9509fb	3ec15582-48e3-4bb5-bdfe-7c909a259130	g.chr3:178952085A>G	ENST00000263967.3	+	21	3297	c.3140A>G	c.(3139-3141)cAt>cGt	p.H1047R	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1047	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.		H -> L (in BC; unknown pathological significance). {ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16353168}.|H -> R (in CLOVE, KERSEB, CRC, BC and OC; also found in an endometrial carcinoma sample; shows an increase in lipid kinase activity; oncogenic in vivo; requires binding to p85 regulatory subunit to induce cellular transformation but not interaction with RAS; may mimic the conformatitonal change triggered by the interaction with RAS; enhances invadopodia-mediated extracellular matrix degradation and invasion in breast cancer cells; increases lipid kinase activity; may alter the interaction of the PI3K/ PI4K kinase domain with the cell membrane). {ECO:0000269|PubMed:15016963, ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15712344, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16114017, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:22658544}.|H -> Y (in MCAP; also found in an endometrial carcinoma sample). {ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:22729224}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.H1047R(1387)|p.H1047L(194)|p.H1047P(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	AATGATGCACATCATGGTGGC	0.378	H1047L(EFM19_BREAST)|H1047R(BT20_BREAST)|H1047R(CAL29_URINARY_TRACT)|H1047R(CAL33_UPPER_AERODIGESTIVE_TRACT)|H1047R(DETROIT562_UPPER_AERODIGESTIVE_TRACT)|H1047R(HCC1954_BREAST)|H1047R(HCT116_LARGE_INTESTINE)|H1047R(HSC2_UPPER_AERODIGESTIVE_TRACT)|H1047R(LS180_LARGE_INTESTINE)|H1047R(MCAS_OVARY)|H1047R(MDAMB453_BREAST)|H1047R(NCIH1048_LUNG)|H1047R(RKO_LARGE_INTESTINE)|H1047R(SKOV3_OVARY)|H1047R(T47D_BREAST)	57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)	dbGAP		Dom	yes		3	3q26.3	5290	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""		"""E, O"""	1582	Substitution - Missense(1582)	breast(961)|large_intestine(245)|endometrium(114)|ovary(77)|urinary_tract(36)|upper_aerodigestive_tract(26)|lung(19)|central_nervous_system(19)|stomach(19)|haematopoietic_and_lymphoid_tissue(11)|thyroid(10)|NS(9)|liver(7)|kidney(6)|soft_tissue(6)|skin(4)|prostate(4)|pituitary(3)|pancreas(3)|meninges(1)|cervix(1)|bone(1)											99.0	89.0	92.0					3																	178952085		1912	4130	6042	-	-	-	SO:0001583	missense	0				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.3140A>G	3.37:g.178952085A>G	ENSP00000263967:p.His1047Arg	Somatic		WXS	Illumina GAIIx	Phase_IV	Q14CW1|Q99762	Missense_Mutation	SNP	pfam_PInositide-3_kin_accessory_dom,pfam_PI3/4_kinase_cat_dom,pfam_PI3K_Ras-bd_dom,pfam_PI3K_C2_dom,pfam_PI3K_adapt-bd_dom,superfamily_Kinase-like_dom,superfamily_ARM-type_fold,superfamily_C2_Ca/lipid-bd_dom_CaLB,smart_PI3K_adapt-bd_dom,smart_PI3K_Ras-bd_dom,smart_PI3K_C2_dom,smart_PInositide-3_kin_accessory_dom,smart_PI3/4_kinase_cat_dom,pfscan_PI3/4_kinase_cat_dom	p.H1047R	ENST00000263967.3	37	c.3140	CCDS43171.1	3	.	.	.	.	.	.	.	.	.	.	A	14.34	2.506328	0.44558	.	.	ENSG00000121879	ENST00000263967	T	0.80214	-1.35	6.08	6.08	0.98989	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.000000	0.85682	D	0.000000	T	0.62466	0.2430	N	0.08118	0	0.80722	D	1	P	0.38597	0.639	B	0.28011	0.085	T	0.67526	-0.5648	10	0.40728	T	0.16	-21.2893	16.6512	0.85203	1.0:0.0:0.0:0.0	.	1047	P42336	PK3CA_HUMAN	R	1047	ENSP00000263967:H1047R	ENSP00000263967:H1047R	H	+	2	0	PIK3CA	180434779	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	8.859000	0.92264	2.333000	0.79357	0.482000	0.46254	CAT	PIK3CA	-	superfamily_Kinase-like_dom,smart_PI3/4_kinase_cat_dom,pfscan_PI3/4_kinase_cat_dom	ENSG00000121879		0.378	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	PIK3CA	HGNC	protein_coding	OTTHUMT00000348409.2	233	0.00	0	A			178952085	178952085	+1	no_errors	ENST00000263967	ensembl	human	known	69_37n	missense	164	42.25	120	SNP	1.000	G
PLIN1	5346	genome.wustl.edu	37	15	90213364	90213364	+	Missense_Mutation	SNP	C	C	T	rs200235164	byFrequency	TCGA-E2-A15C-01A-31D-A12B-09	TCGA-E2-A15C-10A-01D-A12B-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	10c594a1-0843-4740-9d96-00211a9509fb	3ec15582-48e3-4bb5-bdfe-7c909a259130	g.chr15:90213364C>T	ENST00000300055.5	-	5	610	c.445G>A	c.(445-447)Ggg>Agg	p.G149R	PLIN1_ENST00000430628.2_Missense_Mutation_p.G149R	NM_002666.4	NP_002657.3	O60240	PLIN1_HUMAN	perilipin 1	149					lipid metabolic process (GO:0006629)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|lipid particle (GO:0005811)	lipid binding (GO:0008289)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|skin(2)	13						AGCTCGCACCCGGCCAAAGCG	0.647													C|||	3	0.000599042	0.0	0.0014	5008	,	,		16539	0.0		0.002	False		,,,				2504	0.0					dbGAP											0													31.0	33.0	33.0					15																	90213364		2200	4299	6499	-	-	-	SO:0001583	missense	0			AB005293	CCDS10353.1	15q26	2009-08-12	2009-08-12	2009-08-12	ENSG00000166819	ENSG00000166819		"""Perilipins"""	9076	protein-coding gene	gene with protein product		170290	"""perilipin"""	PLIN		9521880, 19638644	Standard	NM_002666		Approved		uc010upx.1	O60240	OTTHUMG00000149813	ENST00000300055.5:c.445G>A	15.37:g.90213364C>T	ENSP00000300055:p.Gly149Arg	Somatic		WXS	Illumina GAIIx	Phase_IV	Q8N5Y6	Missense_Mutation	SNP	pfam_Perilipin,pirsf_Perilipin	p.G149R	ENST00000300055.5	37	c.445	CCDS10353.1	15	.	.	.	.	.	.	.	.	.	.	C	14.40	2.522837	0.44866	.	.	ENSG00000166819	ENST00000300055;ENST00000430628	T;T	0.09445	2.98;2.98	5.21	-0.118	0.13547	.	0.887861	0.09806	N	0.753424	T	0.19565	0.0470	L	0.58428	1.81	0.37256	D	0.906781	D	0.60160	0.987	P	0.54889	0.763	T	0.24154	-1.0168	10	0.49607	T	0.09	-18.9503	8.8852	0.35398	0.0:0.5914:0.0:0.4086	.	149	O60240	PLIN1_HUMAN	R	149	ENSP00000300055:G149R;ENSP00000402167:G149R	ENSP00000300055:G149R	G	-	1	0	PLIN1	88014368	0.155000	0.22806	0.790000	0.31976	0.253000	0.25986	0.282000	0.18829	-0.294000	0.08973	0.305000	0.20034	GGG	PLIN1	-	pfam_Perilipin,pirsf_Perilipin	ENSG00000166819		0.647	PLIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PLIN1	HGNC	protein_coding	OTTHUMT00000313424.2	85	0.00	0	C	NM_002666		90213364	90213364	-1	no_errors	ENST00000300055	ensembl	human	known	69_37n	missense	59	29.76	25	SNP	0.789	T
POM121L12	285877	genome.wustl.edu	37	7	53103484	53103484	+	Silent	SNP	C	C	G			TCGA-E2-A15C-01A-31D-A12B-09	TCGA-E2-A15C-10A-01D-A12B-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	10c594a1-0843-4740-9d96-00211a9509fb	3ec15582-48e3-4bb5-bdfe-7c909a259130	g.chr7:53103484C>G	ENST00000408890.4	+	1	136	c.120C>G	c.(118-120)ccC>ccG	p.P40P		NM_182595.3	NP_872401.3	Q8N7R1	P1L12_HUMAN	POM121 transmembrane nucleoporin-like 12	40										endometrium(5)|kidney(1)|large_intestine(5)|lung(44)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	61						CCAGCACGCCCCAGACCACGC	0.682																																						dbGAP											0													24.0	30.0	28.0					7																	53103484		2039	4186	6225	-	-	-	SO:0001819	synonymous_variant	0				CCDS43584.1	7p12.1	2012-03-13	2012-03-13		ENSG00000221900	ENSG00000221900			25369	protein-coding gene	gene with protein product			"""POM121 membrane glycoprotein-like 12"""				Standard	NM_182595		Approved	DKFZp564N2472	uc003tpz.3	Q8N7R1	OTTHUMG00000155995	ENST00000408890.4:c.120C>G	7.37:g.53103484C>G		Somatic		WXS	Illumina GAIIx	Phase_IV	Q8NDI9	Silent	SNP	NULL	p.P40	ENST00000408890.4	37	c.120	CCDS43584.1	7																																																																																			POM121L12	-	NULL	ENSG00000221900		0.682	POM121L12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	POM121L12	HGNC	protein_coding	OTTHUMT00000342656.1	19	0.00	0	C	NM_182595		53103484	53103484	+1	no_errors	ENST00000408890	ensembl	human	known	69_37n	silent	10	44.44	8	SNP	0.000	G
PTPRD	5789	genome.wustl.edu	37	9	8341168	8341168	+	Missense_Mutation	SNP	G	G	A			TCGA-E2-A15C-01A-31D-A12B-09	TCGA-E2-A15C-10A-01D-A12B-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	10c594a1-0843-4740-9d96-00211a9509fb	3ec15582-48e3-4bb5-bdfe-7c909a259130	g.chr9:8341168G>A	ENST00000381196.4	-	38	5591	c.5048C>T	c.(5047-5049)tCc>tTc	p.S1683F	PTPRD_ENST00000356435.5_Missense_Mutation_p.S1683F|PTPRD_ENST00000397606.3_Missense_Mutation_p.S1276F|PTPRD_ENST00000397611.3_Missense_Mutation_p.S1273F|PTPRD_ENST00000537002.1_Missense_Mutation_p.S1273F|PTPRD_ENST00000360074.4_Missense_Mutation_p.S1670F|PTPRD_ENST00000355233.5_Missense_Mutation_p.S1277F|PTPRD_ENST00000486161.1_Missense_Mutation_p.S1276F|PTPRD_ENST00000397617.3_Missense_Mutation_p.S1276F|PTPRD_ENST00000358503.5_Missense_Mutation_p.S1661F|PTPRD_ENST00000540109.1_Missense_Mutation_p.S1683F	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	1683	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				heterophilic cell-cell adhesion (GO:0007157)|neuron differentiation (GO:0030182)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|protein dephosphorylation (GO:0006470)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cell adhesion molecule binding (GO:0050839)|receptor binding (GO:0005102)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(83)|ovary(4)|pancreas(1)|prostate(7)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	168		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		TACCCTTGTGGATTCATATGG	0.413										TSP Lung(15;0.13)																												dbGAP											0													199.0	206.0	204.0					9																	8341168		2203	4300	6503	-	-	-	SO:0001583	missense	0			X54133	CCDS6472.1, CCDS43786.1, CCDS6472.2, CCDS55288.1, CCDS55289.1, CCDS55290.1, CCDS75813.1	9p24.1-p23	2013-02-11			ENSG00000153707	ENSG00000153707		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9668	protein-coding gene	gene with protein product		601598				7896816, 8355697	Standard	NM_002839		Approved	PTPD, HPTP	uc003zkk.3	P23468	OTTHUMG00000021005	ENST00000381196.4:c.5048C>T	9.37:g.8341168G>A	ENSP00000370593:p.Ser1683Phe	Somatic		WXS	Illumina GAIIx	Phase_IV	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Missense_Mutation	SNP	pfam_Tyr_Pase_rcpt/non-rcpt,pfam_Fibronectin_type3,pfam_Ig_I-set,superfamily_Fibronectin_type3,smart_Ig_sub,smart_Ig_sub2,smart_Fibronectin_type3,smart_Tyr_Pase_rcpt/non-rcpt,smart_Tyr_Pase_cat,pfscan_Fibronectin_type3,pfscan_Tyr/Dual-specificity_Pase,pfscan_Tyr_Pase_rcpt/non-rcpt,pfscan_Ig-like,prints_Tyr_Pase_rcpt/non-rcpt	p.S1683F	ENST00000381196.4	37	c.5048	CCDS43786.1	9	.	.	.	.	.	.	.	.	.	.	G	17.41	3.383655	0.61845	.	.	ENSG00000153707	ENST00000381196;ENST00000356435;ENST00000360074;ENST00000358503;ENST00000355233;ENST00000397617;ENST00000397611;ENST00000537002;ENST00000346816;ENST00000540109;ENST00000486161;ENST00000397606	T;T;T;T;T;T;T;T;T;T;T	0.11821	2.74;2.74;2.74;2.74;2.74;2.74;2.74;2.74;2.74;2.74;2.74	6.07	6.07	0.98685	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.103535	0.64402	D	0.000002	T	0.20536	0.0494	N	0.17345	0.48	0.58432	D	0.999996	P;P;P;P;D;P;P;D;P	0.54772	0.888;0.888;0.888;0.888;0.968;0.864;0.805;0.963;0.929	P;P;P;P;P;B;B;P;P	0.57548	0.581;0.581;0.581;0.581;0.686;0.445;0.249;0.823;0.683	T	0.02320	-1.1177	9	.	.	.	.	20.6593	0.99626	0.0:0.0:1.0:0.0	.	1276;1267;1276;1277;1273;1273;1670;1683;1683	Q3KPJ2;Q3KPI9;Q3KPJ0;Q3KPJ1;F5GWT7;F5GWY7;G3XAE2;Q2HXI4;P23468	.;.;.;.;.;.;.;.;PTPRD_HUMAN	F	1683;1683;1670;1661;1277;1276;1273;1273;1154;1683;1276;1276	ENSP00000370593:S1683F;ENSP00000348812:S1683F;ENSP00000353187:S1670F;ENSP00000351293:S1661F;ENSP00000347373:S1277F;ENSP00000380741:S1276F;ENSP00000380735:S1273F;ENSP00000440515:S1273F;ENSP00000438164:S1683F;ENSP00000417093:S1276F;ENSP00000380731:S1276F	.	S	-	2	0	PTPRD	8331168	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.823000	0.86660	2.885000	0.99019	0.655000	0.94253	TCC	PTPRD	-	pfam_Tyr_Pase_rcpt/non-rcpt,smart_Tyr_Pase_rcpt/non-rcpt,pfscan_Tyr_Pase_rcpt/non-rcpt	ENSG00000153707		0.413	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	PTPRD	HGNC	protein_coding	OTTHUMT00000055395.3	451	0.00	0	G			8341168	8341168	-1	no_errors	ENST00000356435	ensembl	human	known	69_37n	missense	294	26.13	104	SNP	1.000	A
CAPN1	823	genome.wustl.edu	37	11	64981401	64981401	+	IGR	SNP	C	C	T			TCGA-E2-A15C-01A-31D-A12B-09	TCGA-E2-A15C-10A-01D-A12B-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	10c594a1-0843-4740-9d96-00211a9509fb	3ec15582-48e3-4bb5-bdfe-7c909a259130	g.chr11:64981401C>T	ENST00000527323.1	+	0	3086				SLC22A20_ENST00000525437.1_RNA			P07384	CAN1_HUMAN	calpain 1, (mu/I) large subunit						extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of cell proliferation (GO:0008284)|proteolysis (GO:0006508)|receptor catabolic process (GO:0032801)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			breast(2)|endometrium(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)	13		Lung NSC(402;0.094)|Melanoma(852;0.16)		Lung(977;0.00168)|LUSC - Lung squamous cell carcinoma(976;0.00813)		CCGCTTCCAGCTCAACCACAC	0.657																																						dbGAP											0													17.0	22.0	21.0					11																	64981401		2002	4169	6171	-	-	-	SO:0001628	intergenic_variant	0			X04366	CCDS44644.1	11q13	2013-01-10			ENSG00000014216	ENSG00000014216	3.4.22.52	"""EF-hand domain containing"""	1476	protein-coding gene	gene with protein product		114220				3017764, 2209092	Standard	NM_005186		Approved	muCANP, muCL, CANP, CANPL1	uc009yqd.2	P07384	OTTHUMG00000165614		11.37:g.64981401C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	Q2TTR0|Q6DHV4	RNA	SNP	-	NULL	ENST00000527323.1	37	NULL	CCDS44644.1	11																																																																																			SLC22A20	-	-	ENSG00000197847		0.657	CAPN1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	SLC22A20	HGNC	protein_coding	OTTHUMT00000385325.1	28	0.00	0	C			64981401	64981401	+1	no_errors	ENST00000525264	ensembl	human	known	69_37n	rna	24	40.00	16	SNP	0.946	T
RPS6KB2	6199	genome.wustl.edu	37	11	67200919	67200919	+	Splice_Site	SNP	G	G	T			TCGA-E2-A15C-01A-31D-A12B-09	TCGA-E2-A15C-10A-01D-A12B-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	10c594a1-0843-4740-9d96-00211a9509fb	3ec15582-48e3-4bb5-bdfe-7c909a259130	g.chr11:67200919G>T	ENST00000312629.5	+	10	951		c.e10+1		AP003419.16_ENST00000535922.1_RNA	NM_003952.2	NP_003943.2	Q9UBS0	KS6B2_HUMAN	ribosomal protein S6 kinase, 70kDa, polypeptide 2						epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of translational initiation (GO:0045948)|protein kinase B signaling (GO:0043491)|signal transduction (GO:0007165)|translation (GO:0006412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|peptide binding (GO:0042277)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|ribosomal protein S6 kinase activity (GO:0004711)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)|prostate(3)|salivary_gland(1)|stomach(2)	25			BRCA - Breast invasive adenocarcinoma(15;3.26e-06)			TGTCAAAAAGGTGCAGCTCCC	0.617																																						dbGAP											0													60.0	69.0	66.0					11																	67200919		1952	4133	6085	-	-	-	SO:0001630	splice_region_variant	0			AB019245	CCDS41677.1	11q13.1	2011-04-05	2002-08-29		ENSG00000175634	ENSG00000175634			10437	protein-coding gene	gene with protein product		608939	"""ribosomal protein S6 kinase, 70kD, polypeptide 2"""			9878560, 9804755	Standard	XM_005274164		Approved	p70S6Kb, P70-BETA, STK14B, KLS	uc001old.3	Q9UBS0	OTTHUMG00000167673	ENST00000312629.5:c.906+1G>T	11.37:g.67200919G>T		Somatic		WXS	Illumina GAIIx	Phase_IV	B2RMZ9|B4DML8|O94809|Q9UEC1	Splice_Site	SNP	-	e10+1	ENST00000312629.5	37	c.906+1	CCDS41677.1	11	.	.	.	.	.	.	.	.	.	.	G	12.38	1.920104	0.33908	.	.	ENSG00000175634	ENST00000312629	.	.	.	4.51	2.57	0.30868	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.0892	0.64977	0.0:0.2877:0.7123:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	RPS6KB2	66957495	1.000000	0.71417	0.964000	0.40570	0.526000	0.34562	8.948000	0.93006	0.491000	0.27793	0.462000	0.41574	.	RPS6KB2	-	-	ENSG00000175634		0.617	RPS6KB2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	RPS6KB2	HGNC	protein_coding	OTTHUMT00000395508.1	83	0.00	0	G	NM_003952	Intron	67200919	67200919	+1	no_errors	ENST00000312629	ensembl	human	known	69_37n	splice_site	58	35.56	32	SNP	1.000	T
SMARCA4	6597	genome.wustl.edu	37	19	11129678	11129678	+	Silent	SNP	C	C	G			TCGA-E2-A15C-01A-31D-A12B-09	TCGA-E2-A15C-10A-01D-A12B-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	10c594a1-0843-4740-9d96-00211a9509fb	3ec15582-48e3-4bb5-bdfe-7c909a259130	g.chr19:11129678C>G	ENST00000429416.3	+	18	2765	c.2484C>G	c.(2482-2484)tcC>tcG	p.S828S	SMARCA4_ENST00000541122.2_Silent_p.S828S|SMARCA4_ENST00000590574.1_Silent_p.S828S|SMARCA4_ENST00000450717.3_Silent_p.S828S|CTC-215O4.4_ENST00000587831.1_RNA|SMARCA4_ENST00000413806.3_Silent_p.S828S|SMARCA4_ENST00000589677.1_Silent_p.S828S|SMARCA4_ENST00000344626.4_Silent_p.S828S|SMARCA4_ENST00000444061.3_Silent_p.S828S|SMARCA4_ENST00000358026.2_Silent_p.S828S	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	828	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				GGGCCCCCTCCGTGGTGAAGG	0.557			"""F, N, Mis"""		NSCLC																																	dbGAP		Rec	yes		19	19p13.2	6597	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"""		E	1	Unknown(1)	lung(1)											155.0	132.0	140.0					19																	11129678		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			D26156	CCDS12253.1, CCDS45972.1, CCDS45973.1, CCDS54217.1, CCDS54218.1	19p13.3	2014-09-17	2006-11-09		ENSG00000127616	ENSG00000127616			11100	protein-coding gene	gene with protein product	"""SNF2-like 4"", ""global transcription activator homologous sequence"", ""sucrose nonfermenting-like 4"", ""mitotic growth and transcription activator"", ""BRM/SWI2-related gene 1"", ""homeotic gene regulator"", ""nuclear protein GRB1"", ""brahma protein-like 1"", ""ATP-dependent helicase SMARCA4"""	603254		SNF2L4		8208605	Standard	NM_003072		Approved	hSNF2b, BRG1, BAF190, SNF2, SWI2, SNF2-BETA, SNF2LB, FLJ39786	uc010dxo.3	P51532	OTTHUMG00000169272	ENST00000429416.3:c.2484C>G	19.37:g.11129678C>G		Somatic		WXS	Illumina GAIIx	Phase_IV	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Silent	SNP	pfam_SNF2_N,pfam_Bromodomain,pfam_BRK_domain,pfam_HSA,pfam_Helicase_C,pfam_Gln-Leu-Gln_QLQ,superfamily_Bromodomain,smart_Gln-Leu-Gln_QLQ,smart_HAS_subgr,smart_BRK_domain,smart_Helicase_ATP-bd,smart_Helicase_C,smart_Bromodomain,pfscan_Helicase/SANT-assoc_DNA-bd,pfscan_Helicase_ATP-bd,pfscan_Helicase_C,pfscan_Bromodomain,prints_Bromodomain	p.S828	ENST00000429416.3	37	c.2484	CCDS12253.1	19																																																																																			SMARCA4	-	pfam_SNF2_N,smart_Helicase_ATP-bd,pfscan_Helicase_ATP-bd	ENSG00000127616		0.557	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	SMARCA4	HGNC	protein_coding	OTTHUMT00000452638.2	315	0.00	0	C	NM_003072		11129678	11129678	+1	no_errors	ENST00000358026	ensembl	human	known	69_37n	silent	229	33.43	115	SNP	0.243	G
TTC21B	79809	genome.wustl.edu	37	2	166788288	166788289	+	Frame_Shift_Ins	INS	-	-	A	rs554531474		TCGA-E2-A15C-01A-31D-A12B-09	TCGA-E2-A15C-10A-01D-A12B-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	10c594a1-0843-4740-9d96-00211a9509fb	3ec15582-48e3-4bb5-bdfe-7c909a259130	g.chr2:166788288_166788289insA	ENST00000243344.7	-	8	1010_1011	c.873_874insT	c.(871-876)attacafs	p.T292fs	AC010127.5_ENST00000443032.1_RNA|AC010127.5_ENST00000440322.1_RNA	NM_024753.4	NP_079029.3	Q7Z4L5	TT21B_HUMAN	tetratricopeptide repeat domain 21B	292					forebrain dorsal/ventral pattern formation (GO:0021798)|intraciliary retrograde transport (GO:0035721)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|protein localization to cilium (GO:0061512)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intraciliary transport particle A (GO:0030991)|nuclear chromatin (GO:0000790)				breast(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(9)|lung(28)|ovary(2)|pancreas(2)|skin(2)|urinary_tract(1)	58						AAGGCGAGTGTAATGTTATAGA	0.421																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AB082523	CCDS33315.1	2q24.3	2014-09-04			ENSG00000123607	ENSG00000123607		"""Tetratricopeptide (TTC) repeat domain containing"", ""Intraflagellar transport homologs"""	25660	protein-coding gene	gene with protein product		612014				12056414, 21258341	Standard	NM_024753		Approved	FLJ11457, JBTS11, NPHP12, IFT139, THM1	uc002udk.3	Q7Z4L5	OTTHUMG00000154083	ENST00000243344.7:c.874dupT	2.37:g.166788290_166788290dupA	ENSP00000243344:p.Thr292fs	Somatic		WXS	Illumina GAIIx	Phase_IV	A8MUZ3|Q3LIE4|Q53T84|Q6P4A1|Q6PIF5|Q8NCN3|Q96MA4|Q9HAK8	Frame_Shift_Ins	INS	smart_TPR_repeat,pfscan_TPR_repeat,pfscan_TPR-contain_dom	p.T291fs	ENST00000243344.7	37	c.874_873	CCDS33315.1	2																																																																																			TTC21B	-	NULL	ENSG00000123607		0.421	TTC21B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TTC21B	HGNC	protein_coding	OTTHUMT00000333770.1	620	0.00	0	-	NM_024753		166788288	166788289	-1	no_errors	ENST00000243344	ensembl	human	known	69_37n	frame_shift_ins	374	34.39	196	INS	1.000:0.998	A
ZC3H4	23211	genome.wustl.edu	37	19	47570929	47570929	+	Missense_Mutation	SNP	G	G	A			TCGA-E2-A15C-01A-31D-A12B-09	TCGA-E2-A15C-10A-01D-A12B-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	10c594a1-0843-4740-9d96-00211a9509fb	3ec15582-48e3-4bb5-bdfe-7c909a259130	g.chr19:47570929G>A	ENST00000253048.5	-	15	2633	c.2596C>T	c.(2596-2598)Cgg>Tgg	p.R866W	ZC3H4_ENST00000594019.1_Intron	NM_015168.1	NP_055983.1	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4	866							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)	41		all_cancers(25;3.3e-08)|all_epithelial(76;2.28e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.0889)		OV - Ovarian serous cystadenocarcinoma(262;5.76e-05)|all cancers(93;7.69e-05)|Epithelial(262;0.00354)|GBM - Glioblastoma multiforme(486;0.0372)		CTGGGGTCCCGGCTGAGGCGA	0.711																																						dbGAP											0													8.0	11.0	10.0					19																	47570929		1858	4061	5919	-	-	-	SO:0001583	missense	0			AB028987	CCDS42582.1	19q13.33	2012-07-05	2007-10-18	2007-10-18		ENSG00000130749		"""Zinc fingers, CCCH-type domain containing"""	17808	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 7"""	C19orf7			Standard	NM_015168		Approved	KIAA1064	uc002pga.4	Q9UPT8		ENST00000253048.5:c.2596C>T	19.37:g.47570929G>A	ENSP00000253048:p.Arg866Trp	Somatic		WXS	Illumina GAIIx	Phase_IV	Q9Y420	Missense_Mutation	SNP	pfam_Znf_CCCH,smart_Znf_CCCH	p.R866W	ENST00000253048.5	37	c.2596	CCDS42582.1	19	.	.	.	.	.	.	.	.	.	.	G	19.14	3.769631	0.69992	.	.	ENSG00000130749	ENST00000253048	T	0.20881	2.04	5.52	3.1	0.35709	.	0.000000	0.64402	D	0.000002	T	0.40423	0.1116	L	0.53249	1.67	0.51767	D	0.999938	D	0.89917	1.0	D	0.91635	0.999	T	0.38735	-0.9647	10	0.72032	D	0.01	.	14.0797	0.64912	0.0:0.0:0.6817:0.3183	.	866	Q9UPT8	ZC3H4_HUMAN	W	866	ENSP00000253048:R866W	ENSP00000253048:R866W	R	-	1	2	ZC3H4	52262769	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	2.025000	0.41059	1.425000	0.47237	0.655000	0.94253	CGG	ZC3H4	-	NULL	ENSG00000130749		0.711	ZC3H4-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	ZC3H4	HGNC	protein_coding	OTTHUMT00000466667.1	8	0.00	0	G			47570929	47570929	-1	no_errors	ENST00000253048	ensembl	human	known	69_37n	missense	14	26.32	5	SNP	0.999	A
ZNRF3	84133	genome.wustl.edu	37	22	29445672	29445672	+	Silent	SNP	G	G	A			TCGA-E2-A15C-01A-31D-A12B-09	TCGA-E2-A15C-10A-01D-A12B-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	10c594a1-0843-4740-9d96-00211a9509fb	3ec15582-48e3-4bb5-bdfe-7c909a259130	g.chr22:29445672G>A	ENST00000544604.2	+	8	1678	c.1503G>A	c.(1501-1503)ccG>ccA	p.P501P	ZNRF3_ENST00000402174.1_Silent_p.P401P|ZNRF3_ENST00000332811.4_Silent_p.P401P|ZNRF3_ENST00000406323.3_Silent_p.P401P	NM_001206998.1	NP_001193927.1	Q9ULT6	ZNRF3_HUMAN	zinc and ring finger 3	501					canonical Wnt signaling pathway (GO:0060070)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of non-canonical Wnt signaling pathway (GO:2000051)|protein ubiquitination (GO:0016567)|stem cell proliferation (GO:0072089)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt receptor catabolic process (GO:0038018)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	integral component of plasma membrane (GO:0005887)	frizzled binding (GO:0005109)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|liver(4)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	28						CCTTTCCTCCGAGCGGCAGTG	0.697																																						dbGAP											0													17.0	19.0	19.0					22																	29445672		2052	4172	6224	-	-	-	SO:0001819	synonymous_variant	0			AB051436	CCDS42999.1, CCDS56225.1	22q12.1	2013-01-09			ENSG00000183579	ENSG00000183579		"""RING-type (C3HC4) zinc fingers"""	18126	protein-coding gene	gene with protein product		612062				10574461	Standard	NM_032173		Approved	KIAA1133, BK747E2.3, FLJ22057, RNF203	uc003aeg.3	Q9ULT6	OTTHUMG00000151009	ENST00000544604.2:c.1503G>A	22.37:g.29445672G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	B3KU18|Q6ICH1|Q6NTF8|Q8WU18	Silent	SNP	pfam_Znf_C3HC4_RING-type,smart_Znf_RING,pfscan_Znf_RING	p.P501	ENST00000544604.2	37	c.1503	CCDS56225.1	22																																																																																			ZNRF3	-	NULL	ENSG00000183579		0.697	ZNRF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	ZNRF3	HGNC	protein_coding	OTTHUMT00000320943.2	35	0.00	0	G	XM_290972		29445672	29445672	+1	no_errors	ENST00000544604	ensembl	human	known	69_37n	silent	4	69.23	9	SNP	0.000	A
