#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
AHCTF1	25909	genome.wustl.edu	37	1	247016578	247016578	+	Missense_Mutation	SNP	C	C	T			TCGA-E2-A1IF-01A-11D-A142-09	TCGA-E2-A1IF-10A-01D-A142-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	7751c2d5-e548-4439-aac1-e7b9dce97583	34cbed4d-6aff-4293-8f12-931ad2f174ca	g.chr1:247016578C>T	ENST00000391829.2	-	32	4501	c.4378G>A	c.(4378-4380)Ggt>Agt	p.G1460S	AHCTF1_ENST00000366508.1_Missense_Mutation_p.G1495S|AHCTF1_ENST00000326225.3_Missense_Mutation_p.G1469S|AHCTF1_ENST00000470300.1_5'UTR			Q8WYP5	ELYS_HUMAN	AT hook containing transcription factor 1	1460	Disordered. {ECO:0000250}.|Mediates transcriptional activity. {ECO:0000250}.|Necessary for nuclear localization. {ECO:0000250}.				cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(6)|cervix(3)|endometrium(8)|kidney(6)|large_intestine(12)|liver(2)|lung(21)|ovary(5)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	74	all_cancers(71;3.05e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			GAGTTTCCACCATCACCAAGG	0.398																																					Colon(145;197 1800 4745 15099 26333)	dbGAP											0													48.0	44.0	45.0					1																	247016578		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS1629.1, CCDS1629.2	1q44	2008-09-09			ENSG00000153207	ENSG00000153207			24618	protein-coding gene	gene with protein product	"""ELYS transcription factor like protein TMBS62"""	610853				11952839	Standard	NM_015446		Approved	ELYS	uc001ibv.2	Q8WYP5	OTTHUMG00000040706	ENST00000391829.2:c.4378G>A	1.37:g.247016578C>T	ENSP00000375705:p.Gly1460Ser	Somatic		WXS	Illumina GAIIx	Phase_IV	A6NGM0|A8MSG9|A8MZ86|Q7Z4E3|Q8IZA4|Q96EH9|Q9Y4Q6	Missense_Mutation	SNP	superfamily_Quinonprotein_ADH-like	p.G1469S	ENST00000391829.2	37	c.4405		1	.	.	.	.	.	.	.	.	.	.	C	0.011	-1.696069	0.00731	.	.	ENSG00000153207	ENST00000366508;ENST00000326225;ENST00000391829	T;T;T	0.26957	1.7;1.7;1.71	5.76	2.18	0.27775	.	0.848915	0.10590	N	0.656909	T	0.05227	0.0139	N	0.00237	-1.79	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.36962	-0.9726	10	0.02654	T	1	-1.7429	7.8282	0.29328	0.0:0.2444:0.0:0.7556	.	321;1495;1460	B3KTD2;Q8WYP5-2;Q8WYP5	.;.;ELYS_HUMAN	S	1495;1469;1460	ENSP00000355464:G1495S;ENSP00000355465:G1469S;ENSP00000375705:G1460S	ENSP00000355465:G1469S	G	-	1	0	AHCTF1	245083201	0.000000	0.05858	0.014000	0.15608	0.019000	0.09904	0.140000	0.16056	0.114000	0.18032	-0.295000	0.09555	GGT	AHCTF1	-	NULL	ENSG00000153207		0.398	AHCTF1-201	KNOWN	basic|appris_candidate	protein_coding	AHCTF1	HGNC	protein_coding		34	0.00	0	C	NM_015446		247016578	247016578	-1	no_errors	ENST00000326225	ensembl	human	known	69_37n	missense	43	31.75	20	SNP	0.102	T
APBA1	320	genome.wustl.edu	37	9	72073092	72073092	+	Missense_Mutation	SNP	A	A	C			TCGA-E2-A1IF-01A-11D-A142-09	TCGA-E2-A1IF-10A-01D-A142-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	7751c2d5-e548-4439-aac1-e7b9dce97583	34cbed4d-6aff-4293-8f12-931ad2f174ca	g.chr9:72073092A>C	ENST00000265381.4	-	6	1717	c.1495T>G	c.(1495-1497)Tta>Gta	p.L499V	APBA1_ENST00000470082.1_Intron	NM_001163.3	NP_001154.2	Q02410	APBA1_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 1	499	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				axon cargo transport (GO:0008088)|cell adhesion (GO:0007155)|gamma-aminobutyric acid secretion (GO:0014051)|glutamate secretion (GO:0014047)|in utero embryonic development (GO:0001701)|intracellular protein transport (GO:0006886)|locomotory behavior (GO:0007626)|multicellular organism growth (GO:0035264)|nervous system development (GO:0007399)|protein complex assembly (GO:0006461)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synaptic vesicle (GO:0008021)	beta-amyloid binding (GO:0001540)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			endometrium(4)|kidney(2)|large_intestine(12)|lung(13)|prostate(3)|skin(3)	37						CTTTTGGCTAATTTCTGGGCC	0.373																																						dbGAP											0													246.0	209.0	221.0					9																	72073092		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF029106	CCDS6630.1	9q13-q21	2008-07-18	2008-07-18		ENSG00000107282	ENSG00000107282			578	protein-coding gene	gene with protein product		602414		MINT1		7678331, 7719031	Standard	NM_001163		Approved	D9S411E, X11	uc004ahh.2	Q02410	OTTHUMG00000019984	ENST00000265381.4:c.1495T>G	9.37:g.72073092A>C	ENSP00000265381:p.Leu499Val	Somatic		WXS	Illumina GAIIx	Phase_IV	O14914|O60570|Q5VYR8	Missense_Mutation	SNP	pfam_PTyr_interaction_dom,pfam_PDZ,superfamily_PDZ,smart_PTyr_interaction_dom,smart_PDZ,pfscan_PDZ,pfscan_PTyr_interaction_dom	p.L499V	ENST00000265381.4	37	c.1495	CCDS6630.1	9	.	.	.	.	.	.	.	.	.	.	A	12.26	1.883496	0.33255	.	.	ENSG00000107282	ENST00000265381	T	0.21191	2.02	5.75	5.75	0.90469	Phosphotyrosine interaction domain (3);Pleckstrin homology-type (1);	0.169740	0.39985	N	0.001218	T	0.19886	0.0478	L	0.38175	1.15	0.48830	D	0.999718	B	0.17268	0.021	B	0.17722	0.019	T	0.02333	-1.1175	10	0.33940	T	0.23	-3.5541	16.0449	0.80714	1.0:0.0:0.0:0.0	.	499	Q02410	APBA1_HUMAN	V	499	ENSP00000265381:L499V	ENSP00000265381:L499V	L	-	1	2	APBA1	71262912	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.033000	0.49743	2.188000	0.69820	0.533000	0.62120	TTA	APBA1	-	pfam_PTyr_interaction_dom,smart_PTyr_interaction_dom,pfscan_PTyr_interaction_dom	ENSG00000107282		0.373	APBA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	APBA1	HGNC	protein_coding	OTTHUMT00000052589.2	86	0.00	0	A	NM_001163		72073092	72073092	-1	no_errors	ENST00000265381	ensembl	human	known	69_37n	missense	62	19.48	15	SNP	1.000	C
CFAP69	79846	genome.wustl.edu	37	7	89938682	89938683	+	Splice_Site	INS	-	-	T			TCGA-E2-A1IF-01A-11D-A142-09	TCGA-E2-A1IF-10A-01D-A142-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	7751c2d5-e548-4439-aac1-e7b9dce97583	34cbed4d-6aff-4293-8f12-931ad2f174ca	g.chr7:89938682_89938683insT	ENST00000389297.4	+	22	2906		c.e22+1		C7orf63_ENST00000497910.1_Splice_Site|C7orf63_ENST00000316089.8_Splice_Site	NM_001039706.2|NM_001160138.1	NP_001034795.2|NP_001153610.1	A5D8W1	CG063_HUMAN												breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(14)|ovary(1)|prostate(3)	37						TAACACAACGGTAAGATTCTTT	0.312																																						dbGAP											0																																										-	-	-	SO:0001630	splice_region_variant	0																														ENST00000389297.4:c.2655+1->T	7.37:g.89938683_89938683dupT		Somatic		WXS	Illumina GAIIx	Phase_IV	A3KMP9|B4DYW6|B4DZP7|B9EIM7|Q6V705|Q8IY89|Q9H7C2	Splice_Site	INS	-	e22+1	ENST00000389297.4	37	c.2655+1_2655+1	CCDS43613.2	7																																																																																			C7orf63	-	-	ENSG00000105792		0.312	C7orf63-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	C7orf63	HGNC	protein_coding	OTTHUMT00000139891.4	37	0.00	0	-		Intron	89938682	89938683	+1	no_errors	ENST00000389297	ensembl	human	known	69_37n	splice_site_ins	24	20.00	6	INS	1.000:1.000	T
COQ5	84274	genome.wustl.edu	37	12	120966842	120966842	+	Missense_Mutation	SNP	C	C	A	rs376339245		TCGA-E2-A1IF-01A-11D-A142-09	TCGA-E2-A1IF-10A-01D-A142-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	7751c2d5-e548-4439-aac1-e7b9dce97583	34cbed4d-6aff-4293-8f12-931ad2f174ca	g.chr12:120966842C>A	ENST00000288532.6	-	1	143	c.103G>T	c.(103-105)Ggg>Tgg	p.G35W	COQ5_ENST00000445328.2_Missense_Mutation_p.G35W	NM_032314.3	NP_115690.3	Q5HYK3	COQ5_HUMAN	coenzyme Q5 homolog, methyltransferase (S. cerevisiae)	35					small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	mitochondrion (GO:0005739)	methyltransferase activity (GO:0008168)	p.G35W(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(8)|ovary(1)|prostate(1)|urinary_tract(3)	20	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					AGTAGGTCCCCGGGCCAAGAG	0.652																																						dbGAP											1	Substitution - Missense(1)	prostate(1)											68.0	70.0	69.0					12																	120966842		2203	4300	6503	-	-	-	SO:0001583	missense	0			AK057777	CCDS31912.1	12q24.31	2011-09-16	2006-04-04		ENSG00000110871	ENSG00000110871	2.1.1.201		28722	protein-coding gene	gene with protein product	"""2-methoxy-6-polyprenyl-1,4-benzoquinol methylase"""		"""coenzyme Q5 homolog, methyltransferase (yeast)"""				Standard	NM_032314		Approved	MGC4767	uc001tyn.3	Q5HYK3	OTTHUMG00000169375	ENST00000288532.6:c.103G>T	12.37:g.120966842C>A	ENSP00000288532:p.Gly35Trp	Somatic		WXS	Illumina GAIIx	Phase_IV	B4DEJ4|Q32Q28|Q53HH0|Q96LV1|Q9BSP8	Missense_Mutation	SNP	pfam_UbiE/COQ5_MeTrFase,pfam_Methyltransf_11,pfam_Methyltransf_12,tigrfam_UbiE/COQ5_MeTrFase	p.G35W	ENST00000288532.6	37	c.103	CCDS31912.1	12	.	.	.	.	.	.	.	.	.	.	C	14.18	2.459877	0.43736	.	.	ENSG00000110871	ENST00000288532;ENST00000302223;ENST00000445328;ENST00000547943	T;T;T	0.77489	-0.08;-1.1;-0.16	5.58	-4.53	0.03462	.	1.144910	0.06125	N	0.669531	T	0.49012	0.1532	N	0.08118	0	0.09310	N	1	P;B	0.35872	0.525;0.002	B;B	0.32724	0.151;0.002	T	0.43327	-0.9398	10	0.36615	T	0.2	.	0.7438	0.00979	0.2126:0.1748:0.3139:0.2986	.	35;35	B4DP72;Q5HYK3	.;COQ5_HUMAN	W	35	ENSP00000288532:G35W;ENSP00000401798:G35W;ENSP00000449874:G35W	ENSP00000288532:G35W	G	-	1	0	COQ5	119451225	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-0.053000	0.11846	-0.399000	0.07668	-0.165000	0.13383	GGG	COQ5	-	NULL	ENSG00000110871		0.652	COQ5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	COQ5	HGNC	protein_coding	OTTHUMT00000403767.2	42	0.00	0	C	NM_032314		120966842	120966842	-1	no_errors	ENST00000288532	ensembl	human	known	69_37n	missense	44	13.73	7	SNP	0.000	A
EHBP1	23301	genome.wustl.edu	37	2	63206352	63206353	+	Frame_Shift_Del	DEL	GA	GA	-			TCGA-E2-A1IF-01A-11D-A142-09	TCGA-E2-A1IF-10A-01D-A142-09	GA	GA					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	7751c2d5-e548-4439-aac1-e7b9dce97583	34cbed4d-6aff-4293-8f12-931ad2f174ca	g.chr2:63206352_63206353delGA	ENST00000263991.5	+	16	3077_3078	c.2595_2596delGA	c.(2593-2598)ctgagafs	p.R866fs	EHBP1_ENST00000405289.1_Frame_Shift_Del_p.R831fs|EHBP1_ENST00000431489.1_Frame_Shift_Del_p.R831fs|EHBP1_ENST00000354487.3_Frame_Shift_Del_p.R831fs|EHBP1_ENST00000496857.1_3'UTR|EHBP1_ENST00000405015.3_Frame_Shift_Del_p.R831fs	NM_015252.3	NP_056067.2	Q8NDI1	EHBP1_HUMAN	EH domain binding protein 1	866						cytoplasm (GO:0005737)|membrane (GO:0016020)		p.R868fs*22(1)		biliary_tract(1)|breast(3)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(8)|lung(22)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	47	Lung NSC(7;0.0951)|all_lung(7;0.169)		LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189)			GTCGGCAGCTGAGAGAGAGAGC	0.426																																						dbGAP											1	Deletion - Frameshift(1)	large_intestine(1)																																								-	-	-	SO:0001589	frameshift_variant	0			AL833968	CCDS1872.1, CCDS46299.1, CCDS46300.1	2p15	2008-02-05			ENSG00000115504	ENSG00000115504			29144	protein-coding gene	gene with protein product		609922				10048485	Standard	NM_015252		Approved	KIAA0903, NACSIN	uc002sby.3	Q8NDI1	OTTHUMG00000129453	ENST00000263991.5:c.2595_2596delGA	2.37:g.63206360_63206361delGA	ENSP00000263991:p.Arg866fs	Somatic		WXS	Illumina GAIIx	Phase_IV	O94977|Q53TG7|Q53TV6|Q580X2|Q6NX72|Q6PIT3|Q6QNV2|Q9NWI9	Frame_Shift_Del	DEL	pfam_DUF3585,pfam_CH-domain,pfam_CAMSAP_CH,superfamily_CH-domain,smart_CH-domain,pfscan_CH-domain	p.R868fs	ENST00000263991.5	37	c.2595_2596	CCDS1872.1	2																																																																																			EHBP1	-	NULL	ENSG00000115504		0.426	EHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	EHBP1	HGNC	protein_coding	OTTHUMT00000251616.1	29	0.00	0	GA	NM_015252		63206352	63206353	+1	no_errors	ENST00000263991	ensembl	human	known	69_37n	frame_shift_del	25	10.71	3	DEL	1.000:1.000	-
HS6ST1	9394	genome.wustl.edu	37	2	129075877	129075877	+	Missense_Mutation	SNP	G	G	T	rs200979099		TCGA-E2-A1IF-01A-11D-A142-09	TCGA-E2-A1IF-10A-01D-A142-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	7751c2d5-e548-4439-aac1-e7b9dce97583	34cbed4d-6aff-4293-8f12-931ad2f174ca	g.chr2:129075877G>T	ENST00000259241.6	-	1	274	c.261C>A	c.(259-261)gaC>gaA	p.D87E	HS6ST1_ENST00000494089.1_5'UTR	NM_004807.2	NP_004798.3	O60243	H6ST1_HUMAN	heparan sulfate 6-O-sulfotransferase 1	87					angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process, enzymatic modification (GO:0015015)|labyrinthine layer blood vessel development (GO:0060716)|lung alveolus development (GO:0048286)|neuron development (GO:0048666)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)	heparan sulfate 6-O-sulfotransferase activity (GO:0017095)|sulfotransferase activity (GO:0008146)			endometrium(3)|liver(1)|lung(7)|pancreas(1)|prostate(2)|skin(1)	15	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.117)		AGACGATCACGTCGTCGCCCT	0.657																																						dbGAP											0													10.0	16.0	14.0					2																	129075877		1658	4004	5662	-	-	-	SO:0001583	missense	0			AB006179	CCDS42748.1	2q21	2010-03-19		2002-08-23	ENSG00000136720	ENSG00000136720		"""Sulfotransferases, membrane-bound"""	5201	protein-coding gene	gene with protein product		604846		HS6ST		9535912	Standard	NM_004807		Approved		uc002tpt.4	O60243	OTTHUMG00000153542	ENST00000259241.6:c.261C>A	2.37:g.129075877G>T	ENSP00000259241:p.Asp87Glu	Somatic		WXS	Illumina GAIIx	Phase_IV	B4DEP2|B4DJ29|Q53SL2|Q9BVI1	Missense_Mutation	SNP	pfam_Sulfotransferase	p.D87E	ENST00000259241.6	37	c.261	CCDS42748.1	2	.	.	.	.	.	.	.	.	.	.	g	21.7	4.181914	0.78677	.	.	ENSG00000136720	ENST00000259241	T	0.74947	-0.89	3.69	2.78	0.32641	.	0.000000	0.85682	U	0.000000	D	0.84924	0.5580	M	0.88031	2.925	0.80722	D	1	D	0.69078	0.997	D	0.78314	0.991	D	0.84908	0.0846	9	.	.	.	.	6.5213	0.22277	0.2434:0.0:0.7566:0.0	.	87	O60243	H6ST1_HUMAN	E	87	ENSP00000259241:D87E	.	D	-	3	2	HS6ST1	128792347	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	1.938000	0.40203	1.600000	0.50102	0.313000	0.20887	GAC	HS6ST1	-	pfam_Sulfotransferase	ENSG00000136720		0.657	HS6ST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HS6ST1	HGNC	protein_coding	OTTHUMT00000331572.1	13	0.00	0	G	NM_004807		129075877	129075877	-1	no_errors	ENST00000259241	ensembl	human	known	69_37n	missense	8	46.67	7	SNP	1.000	T
KCNA4	3739	genome.wustl.edu	37	11	30033418	30033418	+	Missense_Mutation	SNP	G	G	A			TCGA-E2-A1IF-01A-11D-A142-09	TCGA-E2-A1IF-10A-01D-A142-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	7751c2d5-e548-4439-aac1-e7b9dce97583	34cbed4d-6aff-4293-8f12-931ad2f174ca	g.chr11:30033418G>A	ENST00000328224.6	-	2	2041	c.808C>T	c.(808-810)Cgg>Tgg	p.R270W	KCNA4_ENST00000526518.1_5'Flank	NM_002233.3	NP_002224.1	P22459	KCNA4_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 4	270					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	potassium ion binding (GO:0030955)|voltage-gated potassium channel activity (GO:0005249)			central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(39)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	78					Dalfampridine(DB06637)	TCGTCCTCCCGAAACTTCAAC	0.512																																						dbGAP											0													68.0	62.0	64.0					11																	30033418		1877	4131	6008	-	-	-	SO:0001583	missense	0			M55514	CCDS41629.1	11p14	2012-07-05	2002-07-10			ENSG00000182255		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6222	protein-coding gene	gene with protein product		176266	"""potassium voltage-gated channel, shaker-related subfamily, member 4-like"""	KCNA4L		2263489, 16382104	Standard	NM_002233		Approved	Kv1.4, HK1, HPCN2	uc001msk.3	P22459		ENST00000328224.6:c.808C>T	11.37:g.30033418G>A	ENSP00000328511:p.Arg270Trp	Somatic		WXS	Illumina GAIIx	Phase_IV		Missense_Mutation	SNP	pfam_K_chnl_volt-dep_Kv1.4_TID,pfam_Ion_trans_dom,pfam_T1-type_BTB,pfam_Ion_trans_2,superfamily_BTB/POZ_fold,smart_BTB/POZ-like,prints_K_chnl,prints_K_chnl_volt-dep_Kv1.4,prints_K_chnl_volt-dep_Kv1,prints_K_chnl_volt-dep_Kv	p.R270W	ENST00000328224.6	37	c.808	CCDS41629.1	11	.	.	.	.	.	.	.	.	.	.	G	18.60	3.657912	0.67586	.	.	ENSG00000182255	ENST00000328224	T	0.77098	-1.07	5.05	5.05	0.67936	BTB/POZ-like (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	T	0.80226	0.4584	M	0.81112	2.525	0.80722	D	1	P	0.46457	0.878	B	0.43867	0.434	D	0.83584	0.0119	10	0.62326	D	0.03	.	13.3409	0.60545	0.0:0.0:0.8015:0.1985	.	270	P22459	KCNA4_HUMAN	W	270	ENSP00000328511:R270W	ENSP00000328511:R270W	R	-	1	2	KCNA4	29989994	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	4.106000	0.57804	2.355000	0.79922	0.655000	0.94253	CGG	KCNA4	-	superfamily_BTB/POZ_fold,smart_BTB/POZ-like,prints_K_chnl_volt-dep_Kv1	ENSG00000182255		0.512	KCNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KCNA4	HGNC	protein_coding	OTTHUMT00000388074.2	24	0.00	0	G	NM_002233		30033418	30033418	-1	no_errors	ENST00000328224	ensembl	human	known	69_37n	missense	14	26.32	5	SNP	1.000	A
KLHL31	401265	genome.wustl.edu	37	6	53519409	53519409	+	Missense_Mutation	SNP	A	A	C			TCGA-E2-A1IF-01A-11D-A142-09	TCGA-E2-A1IF-10A-01D-A142-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	7751c2d5-e548-4439-aac1-e7b9dce97583	34cbed4d-6aff-4293-8f12-931ad2f174ca	g.chr6:53519409A>C	ENST00000407079.1	-	1	661	c.662T>G	c.(661-663)aTa>aGa	p.I221R	KLHL31_ENST00000370905.3_Missense_Mutation_p.I221R			Q9H511	KLH31_HUMAN	kelch-like family member 31	221	BACK.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)					autonomic_ganglia(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|prostate(3)	20	Lung NSC(77;0.0158)					GTCATCATCTATAAGAAGTTC	0.348																																						dbGAP											0													77.0	78.0	77.0					6																	53519409		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS34478.1	6p12.1	2013-09-27	2013-02-22	2007-01-09	ENSG00000124743	ENSG00000124743		"""Kelch-like"", ""BTB/POZ domain containing"""	21353	protein-coding gene	gene with protein product		610749	"""kelch repeat and BTB (POZ) domain containing 1"", ""kelch-like 31 (Drosophila)"""	KBTBD1			Standard	NM_001003760		Approved	bA345L23.2, BKLHD6	uc003pcb.4	Q9H511	OTTHUMG00000014882	ENST00000407079.1:c.662T>G	6.37:g.53519409A>C	ENSP00000384644:p.Ile221Arg	Somatic		WXS	Illumina GAIIx	Phase_IV	A6N9J2|B2RP49	Missense_Mutation	SNP	pfam_Kelch_1,pfam_BACK,pfam_BTB_POZ,pfam_DUF1668_ORYSA,superfamily_BTB/POZ_fold,smart_BTB/POZ-like,smart_BACK,smart_Kelch_1,pirsf_Kelch-like_gigaxonin,pfscan_BTB/POZ-like	p.I221R	ENST00000407079.1	37	c.662	CCDS34478.1	6	.	.	.	.	.	.	.	.	.	.	A	7.570	0.666589	0.14710	.	.	ENSG00000124743	ENST00000370905;ENST00000407079	T;T	0.66460	-0.21;-0.21	6.04	6.04	0.98038	BTB/Kelch-associated (2);	0.452771	0.28521	N	0.015050	T	0.17152	0.0412	N	0.00413	-1.525	0.42723	D	0.993681	B	0.06786	0.001	B	0.08055	0.003	T	0.20505	-1.0273	10	0.56958	D	0.05	.	9.0101	0.36135	0.8933:0.0:0.1067:0.0	.	221	Q9H511	KLH31_HUMAN	R	221	ENSP00000359942:I221R;ENSP00000384644:I221R	ENSP00000359942:I221R	I	-	2	0	KLHL31	53627368	1.000000	0.71417	0.989000	0.46669	0.996000	0.88848	4.809000	0.62591	2.317000	0.78254	0.459000	0.35465	ATA	KLHL31	-	pfam_BACK,smart_BACK,pirsf_Kelch-like_gigaxonin	ENSG00000124743		0.348	KLHL31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KLHL31	HGNC	protein_coding	OTTHUMT00000040965.1	52	0.00	0	A	NM_001003760		53519409	53519409	-1	no_errors	ENST00000370905	ensembl	human	known	69_37n	missense	30	16.67	6	SNP	0.954	C
KRAS	3845	genome.wustl.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	C	T	rs121913529		TCGA-E2-A1IF-01A-11D-A142-09	TCGA-E2-A1IF-10A-01D-A142-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	7751c2d5-e548-4439-aac1-e7b9dce97583	34cbed4d-6aff-4293-8f12-931ad2f174ca	g.chr12:25398284C>T	ENST00000256078.4	-	2	98	c.35G>A	c.(34-36)gGt>gAt	p.G12D	KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"""pancreatic, colorectal, lung, thyroid, AML, others"""				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)	dbGAP		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"""L, E, M, O"""	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)											91.0	81.0	85.0					12																	25398284		2203	4300	6503	-	-	-	SO:0001583	missense	0	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"""v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog"", ""v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"""	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>A	12.37:g.25398284C>T	ENSP00000256078:p.Gly12Asp	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	pfam_Small_GTPase,pfam_MIRO-like,pfam_Small_GTPase_ARF/SAR,pfam_ProtSyn_GTP-bd,smart_Small_GTPase_Ras,smart_Small_GTPase_Rab_type,smart_Small_GTPase_Rho,smart_Ran_GTPase,prints_Small_GTPase,tigrfam_Small_GTP-bd_dom	p.G12D	ENST00000256078.4	37	c.35	CCDS8703.1	12	.	.	.	.	.	.	.	.	.	.	C	23.4	4.409094	0.83340	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.85919	0.5809	M	0.91818	3.245	0.80722	D	1	B;P	0.35714	0.385;0.517	B;B	0.41619	0.257;0.361	D	0.87870	0.2670	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	D	12	ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D	ENSP00000256078:G12D	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT	KRAS	-	pfam_Small_GTPase,pfam_MIRO-like,pfam_Small_GTPase_ARF/SAR,smart_Small_GTPase_Ras,smart_Small_GTPase_Rab_type,smart_Small_GTPase_Rho,smart_Ran_GTPase,prints_Small_GTPase,tigrfam_Small_GTP-bd_dom	ENSG00000133703		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	KRAS	HGNC	protein_coding	OTTHUMT00000412232.1	69	0.00	0	C	NM_033360		25398284	25398284	-1	no_errors	ENST00000256078	ensembl	human	known	69_37n	missense	35	18.60	8	SNP	1.000	T
NR4A2	4929	genome.wustl.edu	37	2	157186269	157186269	+	Frame_Shift_Del	DEL	C	C	-			TCGA-E2-A1IF-01A-11D-A142-09	TCGA-E2-A1IF-10A-01D-A142-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	7751c2d5-e548-4439-aac1-e7b9dce97583	34cbed4d-6aff-4293-8f12-931ad2f174ca	g.chr2:157186269delC	ENST00000339562.4	-	3	792	c.430delG	c.(430-432)gacfs	p.D145fs	NR4A2_ENST00000426264.1_Frame_Shift_Del_p.D82fs|NR4A2_ENST00000409572.1_Frame_Shift_Del_p.D145fs|NR4A2_ENST00000429376.1_Frame_Shift_Del_p.D82fs|NR4A2_ENST00000409108.2_Frame_Shift_Del_p.D145fs|NR4A2_ENST00000539077.1_Frame_Shift_Del_p.D156fs	NM_006186.3	NP_006177.1	P43354	NR4A2_HUMAN	nuclear receptor subfamily 4, group A, member 2	145	Pro-rich.				adult locomotory behavior (GO:0008344)|cellular response to extracellular stimulus (GO:0031668)|cellular response to oxidative stress (GO:0034599)|central nervous system projection neuron axonogenesis (GO:0021952)|death (GO:0016265)|dopamine biosynthetic process (GO:0042416)|dopaminergic neuron differentiation (GO:0071542)|gene expression (GO:0010467)|general adaptation syndrome (GO:0051866)|habenula development (GO:0021986)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of neuron apoptotic process (GO:0043524)|neuron maturation (GO:0042551)|neuron migration (GO:0001764)|positive regulation of catalytic activity (GO:0043085)|post-embryonic development (GO:0009791)|regulation of dopamine metabolic process (GO:0042053)|regulation of respiratory gaseous exchange (GO:0043576)|response to amphetamine (GO:0001975)|response to hypoxia (GO:0001666)|response to inorganic substance (GO:0010035)|response to insecticide (GO:0017085)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(15)|ovary(5)|prostate(1)|skin(3)|urinary_tract(1)	40						CCCGGGTCGTCCCACATGGGG	0.627																																						dbGAP											0													74.0	87.0	82.0					2																	157186269		2203	4300	6503	-	-	-	SO:0001589	frameshift_variant	0			X75918	CCDS2201.1	2q22-q23	2013-01-16			ENSG00000153234	ENSG00000153234		"""Nuclear hormone receptors"""	7981	protein-coding gene	gene with protein product		601828		NURR1		7706727	Standard	NM_006186		Approved	TINUR, NOT, RNR1, HZF-3	uc002tyz.4	P43354	OTTHUMG00000131950	ENST00000339562.4:c.430delG	2.37:g.157186269delC	ENSP00000344479:p.Asp145fs	Somatic		WXS	Illumina GAIIx	Phase_IV	Q16311|Q53RZ2|Q6NXU0	Frame_Shift_Del	DEL	pfam_Znf_hrmn_rcpt,pfam_Nucl_hrmn_rcpt_lig-bd_core,superfamily_Nucl_hormone_rcpt_ligand-bd,smart_Znf_hrmn_rcpt,smart_Nucl_hrmn_rcpt_lig-bd_core,pfscan_Znf_hrmn_rcpt,prints_NURR_rcpt,prints_Nuc_orph_rcpt,prints_Str_hrmn_rcpt,prints_Znf_hrmn_rcpt,prints_Retinoic_acid_rcpt	p.D155fs	ENST00000339562.4	37	c.463	CCDS2201.1	2																																																																																			NR4A2	-	prints_NURR_rcpt,prints_Nuc_orph_rcpt	ENSG00000153234		0.627	NR4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NR4A2	HGNC	protein_coding	OTTHUMT00000254909.2	39	0.00	0	C			157186269	157186269	-1	no_errors	ENST00000539077	ensembl	human	known	69_37n	frame_shift_del	29	14.29	5	DEL	1.000	-
PARP4	143	genome.wustl.edu	37	13	25021263	25021263	+	Missense_Mutation	SNP	T	T	C	rs77269056		TCGA-E2-A1IF-01A-11D-A142-09	TCGA-E2-A1IF-10A-01D-A142-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	7751c2d5-e548-4439-aac1-e7b9dce97583	34cbed4d-6aff-4293-8f12-931ad2f174ca	g.chr13:25021263T>C	ENST00000381989.3	-	26	3281	c.3176A>G	c.(3175-3177)cAg>cGg	p.Q1059R		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	1059					cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		ATTGAGTTGCTGCCATTTGAC	0.483																																						dbGAP											0													68.0	64.0	66.0					13																	25021263		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"""Poly (ADP-ribose) polymerases"""	271	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 5C"""	607519	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"""	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.3176A>G	13.37:g.25021263T>C	ENSP00000371419:p.Gln1059Arg	Somatic		WXS	Illumina GAIIx	Phase_IV	O75903|Q14682|Q5QNZ9|Q9H1M6	Missense_Mutation	SNP	pfam_Poly(ADP-ribose)pol_cat_dom,pfam_VIT,pfam_VWF_A,pfam_BRCT_dom,superfamily_Poly(ADP-ribose)pol_reg_dom,superfamily_BRCT_dom,smart_BRCT_dom,smart_VIT,smart_VWF_A,pfscan_BRCT_dom,pfscan_VWF_A,pfscan_Poly(ADP-ribose)pol_cat_dom,pfscan_Poly(ADP-ribose)pol_reg_dom	p.Q1059R	ENST00000381989.3	37	c.3176	CCDS9307.1	13	.	.	.	.	.	.	.	.	.	.	T	15.12	2.738796	0.49045	.	.	ENSG00000102699	ENST00000381989	T	0.01918	4.56	4.71	4.71	0.59529	.	0.121088	0.56097	D	0.000023	T	0.08582	0.0213	M	0.76328	2.33	0.38495	D	0.948071	D	0.69078	0.997	P	0.60789	0.879	T	0.01053	-1.1467	10	0.87932	D	0	-17.7634	7.9397	0.29950	0.1828:0.0:0.0:0.8172	.	1059	Q9UKK3	PARP4_HUMAN	R	1059	ENSP00000371419:Q1059R	ENSP00000371419:Q1059R	Q	-	2	0	PARP4	23919263	1.000000	0.71417	0.999000	0.59377	0.339000	0.28857	4.391000	0.59652	2.113000	0.64589	0.524000	0.50904	CAG	PARP4	-	NULL	ENSG00000102699		0.483	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PARP4	HGNC	protein_coding	OTTHUMT00000044189.1	35	0.00	0	T	NM_006437		25021263	25021263	-1	no_errors	ENST00000381989	ensembl	human	known	69_37n	missense	22	18.52	5	SNP	1.000	C
PIK3CA	5290	genome.wustl.edu	37	3	178952085	178952085	+	Missense_Mutation	SNP	A	A	G	rs121913279		TCGA-E2-A1IF-01A-11D-A142-09	TCGA-E2-A1IF-10A-01D-A142-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	7751c2d5-e548-4439-aac1-e7b9dce97583	34cbed4d-6aff-4293-8f12-931ad2f174ca	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	44	0.00	0	A			178952085	178952085	+1	no_errors	ENST00000263967	ensembl	human	known	69_37n	missense	25	16.67	5	SNP	1.000	G
PLA2G1B	5319	genome.wustl.edu	37	12	120763747	120763747	+	Silent	SNP	C	C	A			TCGA-E2-A1IF-01A-11D-A142-09	TCGA-E2-A1IF-10A-01D-A142-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	7751c2d5-e548-4439-aac1-e7b9dce97583	34cbed4d-6aff-4293-8f12-931ad2f174ca	g.chr12:120763747C>A	ENST00000308366.4	-	2	146	c.111G>T	c.(109-111)ggG>ggT	p.G37G	PLA2G1B_ENST00000549767.1_Silent_p.G8G|PLA2G1B_ENST00000423423.3_Silent_p.G37G	NM_000928.2	NP_000919.1	P04054	PA21B_HUMAN	phospholipase A2, group IB (pancreas)	37					actin filament organization (GO:0007015)|activation of MAPK activity (GO:0000187)|activation of phospholipase A2 activity (GO:0032431)|antibacterial humoral response (GO:0019731)|arachidonic acid secretion (GO:0050482)|cellular response to insulin stimulus (GO:0032869)|defense response to Gram-positive bacterium (GO:0050830)|fatty acid biosynthetic process (GO:0006633)|glucose transport (GO:0015758)|glycerophospholipid biosynthetic process (GO:0046474)|innate immune response in mucosa (GO:0002227)|interleukin-8 production (GO:0032637)|intracellular signal transduction (GO:0035556)|leukotriene biosynthetic process (GO:0019370)|multicellular organismal lipid catabolic process (GO:0044240)|neutrophil chemotaxis (GO:0030593)|neutrophil mediated immunity (GO:0002446)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylcholine metabolic process (GO:0046470)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of DNA replication (GO:0045740)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of immune response (GO:0050778)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein secretion (GO:0050714)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|secretory granule (GO:0030141)	bile acid binding (GO:0032052)|calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)|phospholipase A2 activity (GO:0004623)|receptor binding (GO:0005102)			endometrium(1)|large_intestine(1)|lung(3)|skin(2)	7	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)				Niflumic Acid(DB04552)|Sulfasalazine(DB00795)	AGGGGTCACTCCCCGGGATCA	0.597											OREG0022189	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									NSCLC(64;1781 1795 22266 42732)|Esophageal Squamous(30;459 829 25326 35148)	dbGAP											0													121.0	122.0	122.0					12																	120763747		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0				CCDS9195.1	12q24.31	2013-09-19			ENSG00000170890	ENSG00000170890	3.1.1.4		9030	protein-coding gene	gene with protein product		172410		PLA2, PPLA2, PLA2A		8175726	Standard	NM_000928		Approved		uc001tyd.3	P04054	OTTHUMG00000169343	ENST00000308366.4:c.111G>T	12.37:g.120763747C>A		Somatic	1506	WXS	Illumina GAIIx	Phase_IV	B2R4H5|Q3KPI1	Silent	SNP	pfam_PLipase_A2_euk,superfamily_PLipase_A2,smart_PLipase_A2,prints_PLipase_A2_euk	p.G37	ENST00000308366.4	37	c.111	CCDS9195.1	12																																																																																			PLA2G1B	-	pfam_PLipase_A2_euk,superfamily_PLipase_A2,smart_PLipase_A2	ENSG00000170890		0.597	PLA2G1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PLA2G1B	HGNC	protein_coding	OTTHUMT00000403626.1	40	0.00	0	C			120763747	120763747	-1	no_errors	ENST00000308366	ensembl	human	known	69_37n	silent	29	21.62	8	SNP	0.028	A
PPP1R12B	4660	genome.wustl.edu	37	1	202411672	202411672	+	Missense_Mutation	SNP	T	T	C			TCGA-E2-A1IF-01A-11D-A142-09	TCGA-E2-A1IF-10A-01D-A142-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	7751c2d5-e548-4439-aac1-e7b9dce97583	34cbed4d-6aff-4293-8f12-931ad2f174ca	g.chr1:202411672T>C	ENST00000608999.1	+	12	1792	c.1639T>C	c.(1639-1641)Tcc>Ccc	p.S547P	RP11-175B9.2_ENST00000602961.1_RNA|PPP1R12B_ENST00000336894.4_Missense_Mutation_p.S547P	NM_001197131.1|NM_002481.3	NP_001184060.1|NP_002472.2	O60237	MYPT2_HUMAN	protein phosphatase 1, regulatory subunit 12B	547					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of catalytic activity (GO:0043085)|regulation of muscle contraction (GO:0006937)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	enzyme activator activity (GO:0008047)			central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(7)|lung(17)|ovary(4)|skin(3)|urinary_tract(1)	41			BRCA - Breast invasive adenocarcinoma(75;0.166)			AATTGCTCCCTCCACCTATGT	0.463																																						dbGAP											0													95.0	91.0	92.0					1																	202411672		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB003062	CCDS1426.1, CCDS44294.1, CCDS44295.1, CCDS53458.1, CCDS53459.1, CCDS73005.1	1q32.1	2013-01-10	2011-10-04	2001-08-10	ENSG00000077157	ENSG00000077157		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ankyrin repeat domain containing"""	7619	protein-coding gene	gene with protein product	"""myosin phosphatase regulatory subunit"", ""myosin phosphatase, target subunit 2"""	603768	"""protein phosphatase 1, regulatory (inhibitor) subunit 12B"""	MYPT2		9570949	Standard	NM_002481		Approved	MGC87886, MGC131980, PP1bp55	uc001gya.2	O60237	OTTHUMG00000041393	ENST00000608999.1:c.1639T>C	1.37:g.202411672T>C	ENSP00000476755:p.Ser547Pro	Somatic		WXS	Illumina GAIIx	Phase_IV	A8MYF5|B7ZMN6|Q2TAI8|Q5T506|Q5VUK2|Q8N179|Q9HCB7|Q9HCB8	Missense_Mutation	SNP	pfam_Ankyrin_rpt,superfamily_Ankyrin_rpt-contain_dom,smart_Ankyrin_rpt,pirsf_Pase-1_reg_su_12A/B/C_euk,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom	p.S547P	ENST00000608999.1	37	c.1639	CCDS1426.1	1	.	.	.	.	.	.	.	.	.	.	T	13.39	2.222559	0.39300	.	.	ENSG00000077157	ENST00000406302;ENST00000336894	T;T	0.40225	1.04;1.06	5.66	5.66	0.87406	.	0.100076	0.45361	D	0.000380	T	0.32912	0.0845	L	0.45581	1.43	0.80722	D	1	B;B	0.12630	0.006;0.002	B;B	0.11329	0.003;0.006	T	0.21211	-1.0252	10	0.32370	T	0.25	.	6.3106	0.21163	0.1418:0.0761:0.0:0.7821	.	547;547	O60237;F8W8M3	MYPT2_HUMAN;.	P	547	ENSP00000384496:S547P;ENSP00000337897:S547P	ENSP00000337897:S547P	S	+	1	0	PPP1R12B	200678295	0.992000	0.36948	0.691000	0.30163	0.902000	0.53008	1.640000	0.37186	2.154000	0.67381	0.460000	0.39030	TCC	PPP1R12B	-	pirsf_Pase-1_reg_su_12A/B/C_euk	ENSG00000077157		0.463	PPP1R12B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	PPP1R12B	HGNC	protein_coding	OTTHUMT00000099166.3	41	0.00	0	T	NM_032105		202411672	202411672	+1	no_errors	ENST00000336894	ensembl	human	known	69_37n	missense	39	13.33	6	SNP	0.996	C
TBX3	6926	genome.wustl.edu	37	12	115120669	115120669	+	Missense_Mutation	SNP	A	A	G			TCGA-E2-A1IF-01A-11D-A142-09	TCGA-E2-A1IF-10A-01D-A142-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	7751c2d5-e548-4439-aac1-e7b9dce97583	34cbed4d-6aff-4293-8f12-931ad2f174ca	g.chr12:115120669A>G	ENST00000257566.3	-	1	726	c.337T>C	c.(337-339)Tgg>Cgg	p.W113R	TBX3_ENST00000349155.2_Missense_Mutation_p.W113R	NM_016569.3	NP_057653.3	O15119	TBX3_HUMAN	T-box 3	113					anterior/posterior axis specification, embryo (GO:0008595)|atrioventricular bundle cell differentiation (GO:0003167)|blood vessel development (GO:0001568)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cardiac muscle cell fate commitment (GO:0060923)|cell aging (GO:0007569)|cellular senescence (GO:0090398)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|female genitalia development (GO:0030540)|follicle-stimulating hormone secretion (GO:0046884)|forelimb morphogenesis (GO:0035136)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|limbic system development (GO:0021761)|luteinizing hormone secretion (GO:0032275)|male genitalia development (GO:0030539)|mammary gland development (GO:0030879)|mammary placode formation (GO:0060596)|mesoderm morphogenesis (GO:0048332)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|organ morphogenesis (GO:0009887)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sinoatrial node cell development (GO:0060931)|skeletal system development (GO:0001501)|specification of organ position (GO:0010159)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum morphogenesis (GO:0060412)	nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|endometrium(1)|kidney(1)|large_intestine(6)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0574)		AACTGATCCCAAAGTTCTTTA	0.577																																						dbGAP											0													52.0	54.0	53.0					12																	115120669		2203	4299	6502	-	-	-	SO:0001583	missense	0			BC025258	CCDS9175.1, CCDS9176.1	12q24.21	2013-09-05	2008-07-31		ENSG00000135111	ENSG00000135111		"""T-boxes"""	11602	protein-coding gene	gene with protein product		601621	"""ulnar mammary syndrome"""	UMS		8988164	Standard	NM_005996		Approved	TBX3-ISO, XHL	uc001tvt.1	O15119	OTTHUMG00000169586	ENST00000257566.3:c.337T>C	12.37:g.115120669A>G	ENSP00000257566:p.Trp113Arg	Somatic		WXS	Illumina GAIIx	Phase_IV	Q8TB20|Q9UKF8	Missense_Mutation	SNP	pfam_TF_T-box,pfam_TBX,superfamily_p53-like_TF_DNA-bd,smart_TF_T-box,pfscan_TF_T-box,prints_TF_T-box	p.W113R	ENST00000257566.3	37	c.337	CCDS9176.1	12	.	.	.	.	.	.	.	.	.	.	A	22.7	4.330149	0.81690	.	.	ENSG00000135111	ENST00000349155;ENST00000257566;ENST00000361100	D;D	0.97553	-4.43;-4.43	5.48	5.48	0.80851	Transcription factor, T-box, conserved site (1);p53-like transcription factor, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.99205	0.9724	H	0.99104	4.43	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.97110	0.998;1.0;1.0	D	0.98678	1.0691	10	0.87932	D	0	.	15.5682	0.76309	1.0:0.0:0.0:0.0	.	113;113;113	B4E3A6;O15119-2;O15119	.;.;TBX3_HUMAN	R	113	ENSP00000257567:W113R;ENSP00000257566:W113R	ENSP00000257566:W113R	W	-	1	0	TBX3	113605052	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.962000	0.93254	2.075000	0.62263	0.533000	0.62120	TGG	TBX3	-	pfam_TF_T-box,superfamily_p53-like_TF_DNA-bd,smart_TF_T-box,pfscan_TF_T-box	ENSG00000135111		0.577	TBX3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	TBX3	HGNC	protein_coding	OTTHUMT00000404947.2	11	0.00	0	A	NM_016569, NM_005996		115120669	115120669	-1	no_errors	ENST00000257566	ensembl	human	known	69_37n	missense	8	33.33	4	SNP	1.000	G
CFAP43	80217	genome.wustl.edu	37	10	105990439	105990439	+	Frame_Shift_Del	DEL	G	G	-			TCGA-E2-A1IF-01A-11D-A142-09	TCGA-E2-A1IF-10A-01D-A142-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	7751c2d5-e548-4439-aac1-e7b9dce97583	34cbed4d-6aff-4293-8f12-931ad2f174ca	g.chr10:105990439delG	ENST00000278064.2	-	2	343	c.18delC	c.(16-18)cccfs	p.P6fs	WDR96_ENST00000357060.3_Frame_Shift_Del_p.P76fs|WDR96_ENST00000369720.1_Frame_Shift_Del_p.P6fs|WDR96_ENST00000369719.1_Frame_Shift_Del_p.P6fs|WDR96_ENST00000428666.1_Frame_Shift_Del_p.P76fs																NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(14)|lung(21)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						CAACTTCACAGGGGATGTTAG	0.393																																						dbGAP											0													134.0	123.0	127.0					10																	105990439		2203	4300	6503	-	-	-	SO:0001589	frameshift_variant	0																														ENST00000278064.2:c.18delC	10.37:g.105990439delG	ENSP00000278064:p.Pro6fs	Somatic		WXS	Illumina GAIIx	Phase_IV		Frame_Shift_Del	DEL	superfamily_WD40_repeat_dom,superfamily_Quino_amine_DH_bsu	p.C77fs	ENST00000278064.2	37	c.228		10																																																																																			WDR96	-	superfamily_Quino_amine_DH_bsu	ENSG00000197748		0.393	WDR96-003	KNOWN	basic	protein_coding	WDR96	HGNC	protein_coding	OTTHUMT00000050200.1	66	0.00	0	G			105990439	105990439	-1	no_errors	ENST00000357060	ensembl	human	known	69_37n	frame_shift_del	40	16.67	8	DEL	0.000	-
ZNF747	65988	genome.wustl.edu	37	16	30545573	30545573	+	Missense_Mutation	SNP	C	C	T			TCGA-E2-A1IF-01A-11D-A142-09	TCGA-E2-A1IF-10A-01D-A142-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	7751c2d5-e548-4439-aac1-e7b9dce97583	34cbed4d-6aff-4293-8f12-931ad2f174ca	g.chr16:30545573C>T	ENST00000252799.3	-	1	1095	c.428G>A	c.(427-429)gGg>gAg	p.G143E	ZNF747_ENST00000569360.1_Nonsense_Mutation_p.W96*|AC002310.12_ENST00000457283.3_RNA|ZNF747_ENST00000535210.1_Nonsense_Mutation_p.W96*|AC002310.13_ENST00000568114.1_Nonsense_Mutation_p.W85*|ZNF747_ENST00000568028.1_Nonsense_Mutation_p.W96*|ZNF747_ENST00000395094.3_Missense_Mutation_p.G143E|AC002310.12_ENST00000569752.1_RNA	NM_023931.2	NP_076420.1	Q9BV97	ZN747_HUMAN	zinc finger protein 747	143					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	nucleic acid binding (GO:0003676)			kidney(1)|lung(3)|prostate(1)	5						CAGCCGGATCCCACAGTTCGG	0.652																																						dbGAP											0													23.0	20.0	21.0					16																	30545573		2196	4298	6494	-	-	-	SO:0001583	missense	0			BC001361	CCDS10682.1	16p11.2	2013-01-08			ENSG00000169955	ENSG00000169955		"""Zinc fingers, C2H2-type"", ""-"""	28350	protein-coding gene	gene with protein product						10493829	Standard	NM_023931		Approved	MGC2474	uc002dyn.3	Q9BV97	OTTHUMG00000132401	ENST00000252799.3:c.428G>A	16.37:g.30545573C>T	ENSP00000252799:p.Gly143Glu	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K827|B7WNU3|Q59FB4|Q96NW0	Nonsense_Mutation	SNP	pfam_Krueppel-associated_box,pfam_Znf_C2H2,superfamily_Krueppel-associated_box,smart_Krueppel-associated_box,smart_Znf_C2H2-like,pfscan_Znf_C2H2,pfscan_Krueppel-associated_box	p.W96*	ENST00000252799.3	37	c.288	CCDS10682.1	16	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.82|16.82	3.229262|3.229262	0.58777|0.58777	.|.	.|.	ENSG00000169955|ENSG00000169955	ENST00000252799;ENST00000395094|ENST00000535210	T;T|.	0.02236|.	4.38;4.48|.	2.43|2.43	2.43|2.43	0.29744|0.29744	.|.	.|.	.|.	.|.	.|.	T|.	0.35970|.	0.0950|.	N|N	0.19112|0.19112	0.55|0.55	0.80722|0.80722	A|A	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.83275|.	0.996;0.99|.	T|.	0.47368|.	-0.9123|.	8|.	0.35671|0.26408	T|T	0.21|0.33	.|.	10.9758|10.9758	0.47465|0.47465	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	143;143|.	Q9BV97-2;Q9BV97|.	.;ZN747_HUMAN|.	E|X	143|96	ENSP00000252799:G143E;ENSP00000378528:G143E|.	ENSP00000252799:G143E|ENSP00000441702:W96X	G|W	-|-	2|3	0|0	ZNF747|ZNF747	30453074|30453074	0.000000|0.000000	0.05858|0.05858	0.534000|0.534000	0.28014|0.28014	0.063000|0.063000	0.16089|0.16089	-0.248000|-0.248000	0.08854|0.08854	1.675000|1.675000	0.50919|0.50919	0.305000|0.305000	0.20034|0.20034	GGG|TGG	ZNF747	-	smart_Krueppel-associated_box,pfscan_Krueppel-associated_box	ENSG00000169955		0.652	ZNF747-001	KNOWN	NAGNAG_splice_site|basic|CCDS	protein_coding	ZNF747	HGNC	protein_coding	OTTHUMT00000255532.2	13	0.00	0	C	NM_023931		30545573	30545573	-1	no_errors	ENST00000535210	ensembl	human	known	69_37n	nonsense	10	50.00	10	SNP	0.967	T
