#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_ORegAnno_bin	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
ARHGEF4	50649	genome.wustl.edu	37	2	131796570	131796570	+	Missense_Mutation	SNP	G	G	A			TCGA-BH-A18I-01A-11D-A12B-09	TCGA-BH-A18I-10A-01D-A12B-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	f0ca4831-d56d-4bae-b304-bb43c5d2f09b	1928c46f-5e68-4b04-b9e8-b3f0363684a0	g.chr2:131796570G>A	ENST00000326016.5	+	6	1231	c.712G>A	c.(712-714)Gat>Aat	p.D238N	ARHGEF4_ENST00000392953.3_Missense_Mutation_p.D238N|ARHGEF4_ENST00000428230.2_Intron|ARHGEF4_ENST00000525839.1_Missense_Mutation_p.D238N|ARHGEF4_ENST00000439368.2_3'UTR|ARHGEF4_ENST00000409303.1_Missense_Mutation_p.D238N|ARHGEF4_ENST00000355771.3_Missense_Mutation_p.D167N	NM_015320.2	NP_056135.2	Q9NR80	ARHG4_HUMAN	Rho guanine nucleotide exchange factor (GEF) 4	238	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				apoptotic signaling pathway (GO:0097190)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|protein domain specific binding (GO:0019904)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)	p.D238Y(1)		NS(1)|breast(4)|cervix(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(4)	29		Prostate(154;0.055)		BRCA - Breast invasive adenocarcinoma(221;0.097)		CCGGGTCGCCGATGGCGAGGG	0.592																																						dbGAP											1	Substitution - Missense(1)	lung(1)											57.0	51.0	53.0					2																	131796570		2203	4300	6503	-	-	-	SO:0001583	missense	0			AL137289	CCDS2165.1, CCDS42754.1	2q22	2013-01-10			ENSG00000136002	ENSG00000136002		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	684	protein-coding gene	gene with protein product	"""APC-stimulated guanine nucleotide exchange factor"""	605216				10873612	Standard	NM_015320		Approved	STM6, KIAA1112, ASEF	uc002tsa.1	Q9NR80	OTTHUMG00000131657	ENST00000326016.5:c.712G>A	2.37:g.131796570G>A	ENSP00000316845:p.Asp238Asn		Q9HDC6|Q9UPP0	Missense_Mutation	SNP	pfam_DH-domain,pfam_SH3_domain,pfam_SH3_2,pfam_Pleckstrin_homology,superfamily_DH-domain,superfamily_SH3_domain,smart_SH3_domain,smart_DH-domain,smart_Pleckstrin_homology,pfscan_Pleckstrin_homology,pfscan_SH3_domain,pfscan_DH-domain	p.D238N	ENST00000326016.5	37	c.712	CCDS2165.1	2	.	.	.	.	.	.	.	.	.	.	G	21.1	4.098794	0.76870	.	.	ENSG00000136002	ENST00000326016;ENST00000392953;ENST00000525839;ENST00000409303;ENST00000355771	T;T;T;T;T	0.47177	0.85;0.85;0.85;0.85;0.85	4.57	4.57	0.56435	Src homology-3 domain (4);	0.000000	0.85682	D	0.000000	T	0.56396	0.1982	L	0.28776	0.89	0.58432	D	0.999999	D;D;D	0.76494	0.999;0.994;0.999	D;D;D	0.72982	0.979;0.922;0.979	T	0.60100	-0.7329	10	0.59425	D	0.04	.	15.1989	0.73120	0.0:0.0:1.0:0.0	.	238;238;238	E9PEM0;Q9NR80-4;Q9NR80	.;.;ARHG4_HUMAN	N	238;238;238;238;167	ENSP00000316845:D238N;ENSP00000376680:D238N;ENSP00000432267:D238N;ENSP00000387285:D238N;ENSP00000348017:D167N	ENSP00000316845:D238N	D	+	1	0	ARHGEF4	131513040	1.000000	0.71417	0.011000	0.14972	0.336000	0.28762	9.053000	0.93860	2.248000	0.74166	0.563000	0.77884	GAT	ARHGEF4	-	pfam_SH3_domain,pfam_SH3_2,superfamily_SH3_domain,smart_SH3_domain,pfscan_SH3_domain	ENSG00000136002		0.592	ARHGEF4-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	ARHGEF4	HGNC	protein_coding	OTTHUMT00000254554.4	59	0.00	0	G			131796570	131796570	+1	no_errors	ENST00000326016	ensembl	human	known	69_37n	missense	31	45.76	27	SNP	0.886	A
ATP10A	57194	genome.wustl.edu	37	15	25947227	25947227	+	Missense_Mutation	SNP	G	G	A			TCGA-BH-A18I-01A-11D-A12B-09	TCGA-BH-A18I-10A-01D-A12B-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	f0ca4831-d56d-4bae-b304-bb43c5d2f09b	1928c46f-5e68-4b04-b9e8-b3f0363684a0	g.chr15:25947227G>A	ENST00000356865.6	-	13	2707	c.2596C>T	c.(2596-2598)Cgc>Tgc	p.R866C		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	866					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		TCCTGCAGGCGGTCTTCAATC	0.532																																						dbGAP											0													82.0	81.0	81.0					15																	25947227		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"""ATPases / P-type"""	13542	protein-coding gene	gene with protein product		605855	"""ATPase, Class V, type 10C"", ""ATPase, Class V, type 10A"""	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.2596C>T	15.37:g.25947227G>A	ENSP00000349325:p.Arg866Cys		Q4G0S9|Q969I4	Missense_Mutation	SNP	pfam_ATPase_P-typ_ATPase-assoc-dom,pfam_Dehalogen-like_hydro,superfamily_HAD-like_dom,superfamily_ATPase_cation_domN,prints_ATPase_P-typ_ion-transptr,tigrfam_ATPase_P-typ_Plipid-transl,tigrfam_ATPase_P-typ_ion-transptr	p.R866C	ENST00000356865.6	37	c.2596	CCDS32178.1	15	.	.	.	.	.	.	.	.	.	.	G	25.6	4.655721	0.88056	.	.	ENSG00000206190	ENST00000356865	T	0.66995	-0.24	5.31	5.31	0.75309	ATPase, cation-transporting, domain N (1);HAD-like domain (2);	0.000000	0.85682	D	0.000000	D	0.86623	0.5977	M	0.92923	3.36	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.89816	0.3985	10	0.87932	D	0	-33.4503	18.9798	0.92751	0.0:0.0:1.0:0.0	.	866	O60312	AT10A_HUMAN	C	866	ENSP00000349325:R866C	ENSP00000349325:R866C	R	-	1	0	ATP10A	23498320	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	7.553000	0.82203	2.485000	0.83878	0.561000	0.74099	CGC	ATP10A	-	pfam_Dehalogen-like_hydro,superfamily_HAD-like_dom,superfamily_ATPase_cation_domN,tigrfam_ATPase_P-typ_Plipid-transl	ENSG00000206190		0.532	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ATP10A	HGNC	protein_coding	OTTHUMT00000414830.1	91	0.00	0	G	NM_024490		25947227	25947227	-1	no_errors	ENST00000356865	ensembl	human	known	69_37n	missense	75	37.50	45	SNP	1.000	A
BCHE	590	genome.wustl.edu	37	3	165504044	165504044	+	Nonsense_Mutation	SNP	C	C	A			TCGA-BH-A18I-01A-11D-A12B-09	TCGA-BH-A18I-10A-01D-A12B-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	f0ca4831-d56d-4bae-b304-bb43c5d2f09b	1928c46f-5e68-4b04-b9e8-b3f0363684a0	g.chr3:165504044C>A	ENST00000264381.3	-	3	1739	c.1573G>T	c.(1573-1575)Gaa>Taa	p.E525*	BCHE_ENST00000540653.1_5'UTR	NM_000055.2	NP_000046.1	P06276	CHLE_HUMAN	butyrylcholinesterase	525			E -> V (in BChE deficiency; allele J variant). {ECO:0000269|PubMed:1349196}.		cellular protein metabolic process (GO:0044267)|choline metabolic process (GO:0019695)|cocaine metabolic process (GO:0050783)|learning (GO:0007612)|negative regulation of cell proliferation (GO:0008285)|negative regulation of synaptic transmission (GO:0050805)|neuroblast differentiation (GO:0014016)|response to alkaloid (GO:0043279)|response to drug (GO:0042493)|response to folic acid (GO:0051593)|response to glucocorticoid (GO:0051384)|synaptic transmission, cholinergic (GO:0007271)	blood microparticle (GO:0072562)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)	acetylcholinesterase activity (GO:0003990)|beta-amyloid binding (GO:0001540)|catalytic activity (GO:0003824)|choline binding (GO:0033265)|cholinesterase activity (GO:0004104)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)			breast(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(34)|ovary(4)|pancreas(2)|stomach(1)	55					Aclidinium(DB08897)|Ambenonium(DB01122)|Bambuterol(DB01408)|Chloroprocaine(DB01161)|Chlorphenesin(DB00856)|Chlorpromazine(DB00477)|Choline(DB00122)|Cinchocaine(DB00527)|Cisplatin(DB00515)|Clevidipine(DB04920)|Cyclopentolate(DB00979)|Decamethonium(DB01245)|Demecarium(DB00944)|Diethylcarbamazine(DB00711)|Dipivefrin(DB00449)|Doxacurium chloride(DB01135)|Drospirenone(DB01395)|Echothiophate(DB01057)|Edrophonium(DB01010)|Ephedrine(DB01364)|Ethopropazine(DB00392)|Galantamine(DB00674)|Hexafluronium(DB00941)|Irinotecan(DB00762)|Isoflurophate(DB00677)|Malathion(DB00772)|Mefloquine(DB00358)|Mirabegron(DB08893)|Mivacurium(DB01226)|Neostigmine(DB01400)|Nizatidine(DB00585)|Oxybuprocaine(DB00892)|Pancuronium(DB01337)|Pegvisomant(DB00082)|Pentagastrin(DB00183)|Perindopril(DB00790)|Pipecuronium(DB01338)|Pralidoxime(DB00733)|Procainamide(DB01035)|Procaine(DB00721)|Pyridostigmine(DB00545)|Ramipril(DB00178)|Rivastigmine(DB00989)|Succinylcholine(DB00202)|Sulpiride(DB00391)|Terbutaline(DB00871)|Triamcinolone(DB00620)|Triflupromazine(DB00508)|Trimethaphan(DB01116)	TATTTTTGTTCAGTGCTTTTG	0.328																																						dbGAP											0													139.0	129.0	132.0					3																	165504044		2203	4300	6503	-	-	-	SO:0001587	stop_gained	0			M16541	CCDS3198.1	3q26.1-q26.2	2013-07-10			ENSG00000114200	ENSG00000114200	3.1.1.8		983	protein-coding gene	gene with protein product		177400	"""cholinesterase 1"", ""cholinesterase (serum) 2"""	CHE1, CHE2		1769657, 2318303	Standard	NM_000055		Approved	E1	uc003fem.4	P06276	OTTHUMG00000158131	ENST00000264381.3:c.1573G>T	3.37:g.165504044C>A	ENSP00000264381:p.Glu525*		A8K7P8	Nonsense_Mutation	SNP	pfam_CarbesteraseB,pfam_AChE_tetra,pfam_AB_hydrolase_3,prints_Cholinesterase	p.E525*	ENST00000264381.3	37	c.1573	CCDS3198.1	3	.	.	.	.	.	.	.	.	.	.	C	36	5.691286	0.96793	.	.	ENSG00000114200	ENST00000264381;ENST00000479451;ENST00000488954	.	.	.	5.48	5.48	0.80851	.	0.310592	0.35320	N	0.003283	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.21014	T	0.42	.	18.3458	0.90321	0.0:1.0:0.0:0.0	.	.	.	.	X	525;55;55	.	ENSP00000264381:E525X	E	-	1	0	BCHE	166986738	0.997000	0.39634	0.993000	0.49108	0.321000	0.28281	3.878000	0.56130	2.589000	0.87451	0.655000	0.94253	GAA	BCHE	-	pfam_CarbesteraseB	ENSG00000114200		0.328	BCHE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	BCHE	HGNC	protein_coding	OTTHUMT00000350254.1	471	0.00	0	C			165504044	165504044	-1	no_errors	ENST00000264381	ensembl	human	known	69_37n	nonsense	376	35.95	211	SNP	0.985	A
CAMKK2	10645	genome.wustl.edu	37	12	121712041	121712041	+	Missense_Mutation	SNP	G	G	A	rs200801054		TCGA-BH-A18I-01A-11D-A12B-09	TCGA-BH-A18I-10A-01D-A12B-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	f0ca4831-d56d-4bae-b304-bb43c5d2f09b	1928c46f-5e68-4b04-b9e8-b3f0363684a0	g.chr12:121712041G>A	ENST00000324774.5	-	2	1117	c.289C>T	c.(289-291)Cgc>Tgc	p.R97C	CAMKK2_ENST00000446440.2_Missense_Mutation_p.R97C|CAMKK2_ENST00000535524.1_5'UTR|CAMKK2_ENST00000392473.2_Missense_Mutation_p.R97C|CAMKK2_ENST00000347034.2_Missense_Mutation_p.R97C|CAMKK2_ENST00000392474.2_Missense_Mutation_p.R97C|CAMKK2_ENST00000538733.1_Missense_Mutation_p.R97C|CAMKK2_ENST00000412367.2_Missense_Mutation_p.R97C|CAMKK2_ENST00000404169.3_Missense_Mutation_p.R97C|CAMKK2_ENST00000402834.4_Missense_Mutation_p.R97C|CAMKK2_ENST00000337174.3_Missense_Mutation_p.R97C	NM_006549.3	NP_006540.3	Q96RR4	KKCC2_HUMAN	calcium/calmodulin-dependent protein kinase kinase 2, beta	97					calcium-mediated signaling (GO:0019722)|MAPK cascade (GO:0000165)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of protein kinase activity (GO:0045859)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|protein tyrosine kinase activity (GO:0004713)			endometrium(2)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	17	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					GACAGCTTGCGACCGGAGAGG	0.706																																						dbGAP											0													19.0	24.0	22.0					12																	121712041		2200	4297	6497	-	-	-	SO:0001583	missense	0			AF101264	CCDS9216.1, CCDS9217.1, CCDS9218.1, CCDS9219.1, CCDS44999.1, CCDS53837.1, CCDS58283.1	12q24.2	2002-08-13				ENSG00000110931			1470	protein-coding gene	gene with protein product		615002				9662074	Standard	NM_172226		Approved	CAMKK, KIAA0787, CAMKKB, MGC15254	uc001tzu.3	Q96RR4		ENST00000324774.5:c.289C>T	12.37:g.121712041G>A	ENSP00000312741:p.Arg97Cys		A8K7Q7|O94883|Q8IUG2|Q8IUG3|Q8N3I4|Q8WY03|Q8WY04|Q8WY05|Q8WY06|Q96RP1|Q96RP2|Q96RR3|Q9BWE9|Q9UER3|Q9UES2|Q9Y5N2	Missense_Mutation	SNP	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_cat_dom	p.R97C	ENST00000324774.5	37	c.289	CCDS9216.1	12	.	.	.	.	.	.	.	.	.	.	G	16.50	3.141675	0.57044	.	.	ENSG00000110931	ENST00000392474;ENST00000347034;ENST00000538733;ENST00000337174;ENST00000324774;ENST00000412367;ENST00000404169;ENST00000360452;ENST00000446440;ENST00000392473;ENST00000543477	T;T;T;T;T;T;T;T;T;T	0.77229	-1.06;-1.05;-1.01;-1.05;-1.08;-1.05;-1.08;-1.03;-1.04;1.17	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	T	0.80864	0.4705	L	0.27053	0.805	0.58432	D	0.999994	D;D;D;D;D;D;D	0.89917	1.0;1.0;0.999;0.997;0.999;0.998;1.0	D;D;D;D;D;P;D	0.97110	1.0;1.0;0.968;0.927;0.948;0.889;1.0	T	0.82629	-0.0363	10	0.87932	D	0	0.204	13.307	0.60357	0.0:0.0:0.8419:0.1581	.	97;97;97;97;97;97;97	Q96RR4-6;Q96RR4-2;Q96RR4-7;Q96RR4-5;Q96RR4-4;Q96RR4;Q96RR4-3	.;.;.;.;.;KKCC2_HUMAN;.	C	97;97;97;97;97;97;97;80;97;97;97	ENSP00000376266:R97C;ENSP00000321230:R97C;ENSP00000445944:R97C;ENSP00000336634:R97C;ENSP00000312741:R97C;ENSP00000388368:R97C;ENSP00000384600:R97C;ENSP00000388273:R97C;ENSP00000376265:R97C;ENSP00000444894:R97C	ENSP00000312741:R97C	R	-	1	0	CAMKK2	120196424	1.000000	0.71417	0.977000	0.42913	0.352000	0.29268	2.413000	0.44618	2.643000	0.89663	0.462000	0.41574	CGC	CAMKK2	-	NULL	ENSG00000110931		0.706	CAMKK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	CAMKK2	HGNC	protein_coding	OTTHUMT00000402563.1	18	0.00	0	G	NM_172226		121712041	121712041	-1	no_errors	ENST00000324774	ensembl	human	known	69_37n	missense	12	47.83	11	SNP	0.981	A
CEP192	55125	genome.wustl.edu	37	18	13059100	13059100	+	Missense_Mutation	SNP	G	G	A	rs200272635		TCGA-BH-A18I-01A-11D-A12B-09	TCGA-BH-A18I-10A-01D-A12B-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	f0ca4831-d56d-4bae-b304-bb43c5d2f09b	1928c46f-5e68-4b04-b9e8-b3f0363684a0	g.chr18:13059100G>A	ENST00000325971.8	+	19	4082	c.2489G>A	c.(2488-2490)cGt>cAt	p.R830H	CEP192_ENST00000506447.1_Missense_Mutation_p.R1426H|CEP192_ENST00000430049.2_Missense_Mutation_p.R951H			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa	830					centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(36)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						TCAACATATCGTTGTTTAGTT	0.358													G|||	1	0.000199681	0.0	0.0	5008	,	,		19939	0.0		0.001	False		,,,				2504	0.0					dbGAP											0													95.0	91.0	92.0					18																	13059100		2203	4300	6503	-	-	-	SO:0001583	missense	0			AK074074	CCDS32792.1, CCDS32792.2	18p11.21	2014-02-20				ENSG00000101639		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	25515	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 62"""					11230166, 14654843	Standard	NM_032142		Approved	KIAA1569, FLJ10352, PPP1R62	uc010xac.2	Q8TEP8		ENST00000325971.8:c.2489G>A	18.37:g.13059100G>A	ENSP00000317156:p.Arg830His		A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Missense_Mutation	SNP	NULL	p.R1426H	ENST00000325971.8	37	c.4277		18	.	.	.	.	.	.	.	.	.	.	G	13.18	2.160966	0.38119	.	.	ENSG00000101639	ENST00000506447;ENST00000325971;ENST00000399863;ENST00000430049	T;T;T	0.23147	1.92;1.92;1.92	5.08	1.76	0.24704	.	0.370250	0.28549	N	0.014955	T	0.09905	0.0243	N	0.04508	-0.205	0.28126	N	0.930385	B;B;B	0.22800	0.006;0.075;0.026	B;B;B	0.15052	0.003;0.012;0.005	T	0.16129	-1.0413	10	0.38643	T	0.18	-3.9736	6.3601	0.21422	0.365:0.3778:0.2572:0.0	.	951;1426;830	C9JT09;E9PF99;Q8TEP8	.;.;CE192_HUMAN	H	1426;830;830;951	ENSP00000427550:R1426H;ENSP00000317156:R830H;ENSP00000389190:R951H	ENSP00000317156:R830H	R	+	2	0	CEP192	13049100	0.998000	0.40836	0.994000	0.49952	0.997000	0.91878	1.345000	0.33953	0.643000	0.30638	0.591000	0.81541	CGT	CEP192	-	NULL	ENSG00000101639		0.358	CEP192-201	KNOWN	basic	protein_coding	CEP192	HGNC	protein_coding		132	0.00	0	G	NM_032142		13059100	13059100	+1	no_errors	ENST00000506447	ensembl	human	known	69_37n	missense	97	43.27	74	SNP	1.000	A
CNTNAP5	129684	genome.wustl.edu	37	2	125547610	125547610	+	Missense_Mutation	SNP	A	A	T			TCGA-BH-A18I-01A-11D-A12B-09	TCGA-BH-A18I-10A-01D-A12B-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	f0ca4831-d56d-4bae-b304-bb43c5d2f09b	1928c46f-5e68-4b04-b9e8-b3f0363684a0	g.chr2:125547610A>T	ENST00000431078.1	+	18	3245	c.2881A>T	c.(2881-2883)Agc>Tgc	p.S961C		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	961	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.			PGHCSS -> SIKKLK (in Ref. 4; BAB71205). {ECO:0000305}.	cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(24)|lung(100)|ovary(10)|prostate(12)|skin(4)|upper_aerodigestive_tract(3)	176				BRCA - Breast invasive adenocarcinoma(221;0.248)		CGGCCACTGCAGCAGCTACGG	0.547																																						dbGAP											0													46.0	54.0	51.0					2																	125547610		2119	4239	6358	-	-	-	SO:0001583	missense	0			AB077881	CCDS46401.1	2q14.1	2008-02-05			ENSG00000155052	ENSG00000155052			18748	protein-coding gene	gene with protein product		610519					Standard	NM_130773		Approved	caspr5, FLJ31966	uc002tno.3	Q8WYK1	OTTHUMG00000153356	ENST00000431078.1:c.2881A>T	2.37:g.125547610A>T	ENSP00000399013:p.Ser961Cys		Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Missense_Mutation	SNP	pfam_Laminin_G,pfam_Coagulation_fac_5/8-C_type_dom,superfamily_Galactose-bd-like,superfamily_ConA-like_lec_gl,superfamily_Fibrinogen_a/b/g_C,smart_Coagulation_fac_5/8-C_type_dom,smart_Laminin_G,smart_EGF-like,pfscan_EG-like_dom,pfscan_Coagulation_fac_5/8-C_type_dom,pfscan_Laminin_G	p.S961C	ENST00000431078.1	37	c.2881	CCDS46401.1	2	.	.	.	.	.	.	.	.	.	.	A	14.52	2.560674	0.45590	.	.	ENSG00000155052	ENST00000431078	T	0.79845	-1.31	5.24	5.24	0.73138	Concanavalin A-like lectin/glucanase, subgroup (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.64402	D	0.000010	D	0.90143	0.6920	H	0.96996	3.92	0.49389	D	0.999786	D	0.67145	0.996	P	0.55161	0.77	D	0.92019	0.5624	10	0.72032	D	0.01	.	9.1781	0.37125	0.9184:0.0:0.0816:0.0	.	961	Q8WYK1	CNTP5_HUMAN	C	961	ENSP00000399013:S961C	ENSP00000399013:S961C	S	+	1	0	CNTNAP5	125264080	1.000000	0.71417	1.000000	0.80357	0.256000	0.26092	6.189000	0.72051	2.116000	0.64780	0.533000	0.62120	AGC	CNTNAP5	-	smart_EGF-like,pfscan_EG-like_dom	ENSG00000155052		0.547	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CNTNAP5	HGNC	protein_coding	OTTHUMT00000330864.3	58	0.00	0	A			125547610	125547610	+1	no_errors	ENST00000431078	ensembl	human	known	69_37n	missense	38	20.83	10	SNP	1.000	T
GAB1	2549	genome.wustl.edu	37	4	144360988	144360988	+	Missense_Mutation	SNP	G	G	A			TCGA-BH-A18I-01A-11D-A12B-09	TCGA-BH-A18I-10A-01D-A12B-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	f0ca4831-d56d-4bae-b304-bb43c5d2f09b	1928c46f-5e68-4b04-b9e8-b3f0363684a0	g.chr4:144360988G>A	ENST00000262994.4	+	5	1531	c.1229G>A	c.(1228-1230)cGa>cAa	p.R410Q	GAB1_ENST00000262995.4_Missense_Mutation_p.R410Q|GAB1_ENST00000505913.1_Missense_Mutation_p.R307Q	NM_002039.3	NP_002030.2	Q13480	GAB1_HUMAN	GRB2-associated binding protein 1	410					activation of JUN kinase activity (GO:0007257)|cell proliferation (GO:0008283)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis development (GO:0008544)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|interleukin-6-mediated signaling pathway (GO:0070102)|labyrinthine layer development (GO:0060711)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|regulation of cell migration (GO:0030334)|response to oxidative stress (GO:0006979)	cytosol (GO:0005829)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			breast(3)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	30	all_hematologic(180;0.158)					GATATTCCACGAGCATTTCCA	0.368																																						dbGAP											0													143.0	139.0	140.0					4																	144360988		2203	4300	6503	-	-	-	SO:0001583	missense	0			U43885	CCDS3759.1, CCDS3760.1	4q31.1	2013-01-10			ENSG00000109458	ENSG00000109458		"""Pleckstrin homology (PH) domain containing"""	4066	protein-coding gene	gene with protein product		604439				8596638	Standard	NM_207123		Approved		uc003ijd.3	Q13480	OTTHUMG00000161432	ENST00000262994.4:c.1229G>A	4.37:g.144360988G>A	ENSP00000262994:p.Arg410Gln		A8K152|Q4W5G2|Q6P1W2	Missense_Mutation	SNP	pfam_Pleckstrin_homology,smart_Pleckstrin_homology,pfscan_Pleckstrin_homology	p.R410Q	ENST00000262994.4	37	c.1229	CCDS3759.1	4	.	.	.	.	.	.	.	.	.	.	G	21.2	4.107010	0.77096	.	.	ENSG00000109458	ENST00000262995;ENST00000262994;ENST00000505913	T;T;T	0.32988	1.43;1.43;1.43	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	T	0.48059	0.1479	L	0.41492	1.28	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.992;0.997	T	0.18713	-1.0328	10	0.26408	T	0.33	-14.6036	19.3349	0.94312	0.0:0.0:1.0:0.0	.	410;410	Q13480;Q13480-2	GAB1_HUMAN;.	Q	410;410;307	ENSP00000262995:R410Q;ENSP00000262994:R410Q;ENSP00000424554:R307Q	ENSP00000262994:R410Q	R	+	2	0	GAB1	144580438	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	8.993000	0.93524	2.583000	0.87209	0.655000	0.94253	CGA	GAB1	-	NULL	ENSG00000109458		0.368	GAB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	GAB1	HGNC	protein_coding	OTTHUMT00000364998.1	326	0.31	1	G	NM_002039		144360988	144360988	+1	no_errors	ENST00000262995	ensembl	human	known	69_37n	missense	284	32.86	139	SNP	1.000	A
GLCCI1	113263	genome.wustl.edu	37	7	8099816	8099816	+	Missense_Mutation	SNP	A	A	G			TCGA-BH-A18I-01A-11D-A12B-09	TCGA-BH-A18I-10A-01D-A12B-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	f0ca4831-d56d-4bae-b304-bb43c5d2f09b	1928c46f-5e68-4b04-b9e8-b3f0363684a0	g.chr7:8099816A>G	ENST00000223145.5	+	5	1461	c.904A>G	c.(904-906)Ata>Gta	p.I302V	GLCCI1_ENST00000474269.1_3'UTR	NM_138426.3	NP_612435.1	Q86VQ1	GLCI1_HUMAN	glucocorticoid induced transcript 1	302						cytoplasm (GO:0005737)				endometrium(4)|large_intestine(4)|lung(13)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	25		Ovarian(82;0.0608)		UCEC - Uterine corpus endometrioid carcinoma (126;0.206)		TGTAGAAGGAATAAGTCCTGA	0.373																																						dbGAP											0													122.0	113.0	116.0					7																	8099816		2203	4300	6503	-	-	-	SO:0001583	missense	0			BC050291	CCDS34601.1	7p22.2	2008-08-18			ENSG00000106415	ENSG00000106415			18713	protein-coding gene	gene with protein product		614283					Standard	NM_138426		Approved	GIG18, FAM117C, TSSN1	uc003srk.4	Q86VQ1	OTTHUMG00000151984	ENST00000223145.5:c.904A>G	7.37:g.8099816A>G	ENSP00000223145:p.Ile302Val		A4D103|Q96FD0	Missense_Mutation	SNP	NULL	p.I302V	ENST00000223145.5	37	c.904	CCDS34601.1	7	.	.	.	.	.	.	.	.	.	.	A	16.42	3.117970	0.56505	.	.	ENSG00000106415	ENST00000223145;ENST00000414914	.	.	.	4.98	3.73	0.42828	.	0.090661	0.85682	D	0.000000	T	0.61788	0.2375	L	0.44542	1.39	0.50632	D	0.999889	D	0.53885	0.963	P	0.57057	0.812	T	0.63616	-0.6597	9	0.52906	T	0.07	-8.2052	12.0728	0.53626	0.8564:0.1436:0.0:0.0	.	302	Q86VQ1	GLCI1_HUMAN	V	302;160	.	ENSP00000223145:I302V	I	+	1	0	GLCCI1	8066341	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.420000	0.73349	2.190000	0.69967	0.477000	0.44152	ATA	GLCCI1	-	NULL	ENSG00000106415		0.373	GLCCI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GLCCI1	HGNC	protein_coding	OTTHUMT00000324672.1	250	0.00	0	A	NM_138426		8099816	8099816	+1	no_errors	ENST00000223145	ensembl	human	known	69_37n	missense	216	33.13	107	SNP	1.000	G
GPN2	54707	genome.wustl.edu	37	1	27210723	27210723	+	Missense_Mutation	SNP	A	A	T			TCGA-BH-A18I-01A-11D-A12B-09	TCGA-BH-A18I-10A-01D-A12B-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	f0ca4831-d56d-4bae-b304-bb43c5d2f09b	1928c46f-5e68-4b04-b9e8-b3f0363684a0	g.chr1:27210723A>T	ENST00000374135.4	-	4	988	c.788T>A	c.(787-789)tTc>tAc	p.F263Y	GPN2_ENST00000461282.1_5'Flank|GPN2_ENST00000374133.3_Missense_Mutation_p.F84Y	NM_018066.3	NP_060536.3			GPN-loop GTPase 2											endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|urinary_tract(1)	9						TTGGGCTCTGAAACAGTATCC	0.527																																						dbGAP											0													87.0	76.0	80.0					1																	27210723		2203	4300	6503	-	-	-	SO:0001583	missense	0			AK001211	CCDS289.1	1p36.11	2008-04-30	2008-04-30	2008-04-30	ENSG00000142751	ENSG00000142751		"""GPN-loop GTPases"""	25513	protein-coding gene	gene with protein product			"""ATP binding domain 1 family, member B"""	ATPBD1B		12975309	Standard	NM_018066		Approved	FLJ10349	uc001bnd.1	Q9H9Y4	OTTHUMG00000004227	ENST00000374135.4:c.788T>A	1.37:g.27210723A>T	ENSP00000363250:p.Phe263Tyr			Missense_Mutation	SNP	pfam_Uncharacterised_ATP-bd	p.F263Y	ENST00000374135.4	37	c.788	CCDS289.1	1	.	.	.	.	.	.	.	.	.	.	A	18.20	3.571685	0.65765	.	.	ENSG00000142751	ENST00000374135;ENST00000374133	T;T	0.28895	2.13;1.59	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	T	0.17492	0.0420	N	0.08118	0	0.58432	D	0.999999	B	0.31599	0.33	B	0.27887	0.084	T	0.08452	-1.0721	10	0.38643	T	0.18	-32.0992	15.2329	0.73404	1.0:0.0:0.0:0.0	.	263	Q9H9Y4	GPN2_HUMAN	Y	263;84	ENSP00000363250:F263Y;ENSP00000363248:F84Y	ENSP00000363248:F84Y	F	-	2	0	GPN2	27083310	1.000000	0.71417	0.924000	0.36721	0.861000	0.49209	8.962000	0.93254	2.079000	0.62486	0.402000	0.26972	TTC	GPN2	-	NULL	ENSG00000142751		0.527	GPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GPN2	HGNC	protein_coding	OTTHUMT00000012175.2	71	0.00	0	A	NM_018066		27210723	27210723	-1	no_errors	ENST00000374135	ensembl	human	known	69_37n	missense	53	31.17	24	SNP	1.000	T
GRK6	2870	genome.wustl.edu	37	5	176860631	176860631	+	Missense_Mutation	SNP	C	C	T			TCGA-BH-A18I-01A-11D-A12B-09	TCGA-BH-A18I-10A-01D-A12B-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	f0ca4831-d56d-4bae-b304-bb43c5d2f09b	1928c46f-5e68-4b04-b9e8-b3f0363684a0	g.chr5:176860631C>T	ENST00000355472.5	+	8	860	c.692C>T	c.(691-693)gCg>gTg	p.A231V	GRK6_ENST00000355958.5_Missense_Mutation_p.A231V|GRK6_ENST00000393576.3_Missense_Mutation_p.A231V|GRK6_ENST00000528793.1_Missense_Mutation_p.A231V|GRK6_ENST00000507633.1_Missense_Mutation_p.A231V	NM_001004106.2|NM_002082.3	NP_001004106.1|NP_002073.2	P43250	GRK6_HUMAN	G protein-coupled receptor kinase 6	231	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway (GO:0016055)	membrane (GO:0016020)	ATP binding (GO:0005524)|G-protein coupled receptor kinase activity (GO:0004703)			breast(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(6)|ovary(1)|prostate(5)|stomach(1)	25	all_cancers(89;1.15e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GAGGCCATGGCGCTGAACGAG	0.562																																						dbGAP											0													127.0	116.0	120.0					5																	176860631		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS34303.1, CCDS43406.1, CCDS47348.1	5q35	2011-01-14	2004-02-04	2004-02-06	ENSG00000198055	ENSG00000198055			4545	protein-coding gene	gene with protein product		600869		GPRK6		8415712	Standard	NM_002082		Approved		uc021yiu.1	P43250	OTTHUMG00000163401	ENST00000355472.5:c.692C>T	5.37:g.176860631C>T	ENSP00000347655:p.Ala231Val		O60541|Q13652	Missense_Mutation	SNP	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Regulat_G_prot_signal,superfamily_Kinase-like_dom,superfamily_Regulat_G_prot_signal_superfam,smart_Regulat_G_prot_signal,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,smart_AGC-kinase_C,prints_GPCR_kinase,pfscan_Regulat_G_prot_signal,pfscan_Prot_kinase_cat_dom	p.A231V	ENST00000355472.5	37	c.692	CCDS34303.1	5	.	.	.	.	.	.	.	.	.	.	C	27.2	4.813728	0.90790	.	.	ENSG00000198055	ENST00000506296;ENST00000355472;ENST00000507633;ENST00000393576;ENST00000355958;ENST00000528793	T;T;T;T;T;T	0.23754	3.19;1.89;1.89;1.89;1.89;1.89	5.77	5.77	0.91146	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.30978	0.0782	N	0.03903	-0.33	0.80722	D	1	D;D;D;D	0.89917	0.988;0.969;0.997;1.0	P;P;P;D	0.85130	0.499;0.447;0.53;0.997	T	0.48305	-0.9047	10	0.38643	T	0.18	-14.1086	19.9983	0.97395	0.0:1.0:0.0:0.0	.	231;201;231;231	P43250;B3KPS5;P43250-2;D6RHX8	GRK6_HUMAN;.;.;.	V	199;231;231;231;231;231	ENSP00000421055:A199V;ENSP00000347655:A231V;ENSP00000427581:A231V;ENSP00000377204:A231V;ENSP00000348230:A231V;ENSP00000433511:A231V	ENSP00000347655:A231V	A	+	2	0	GRK6	176793237	1.000000	0.71417	0.966000	0.40874	0.970000	0.65996	7.770000	0.85390	2.724000	0.93272	0.561000	0.74099	GCG	GRK6	-	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,prints_GPCR_kinase,pfscan_Prot_kinase_cat_dom	ENSG00000198055		0.562	GRK6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	GRK6	HGNC	protein_coding	OTTHUMT00000373204.1	163	0.00	0	C	NM_002082		176860631	176860631	+1	no_errors	ENST00000528793	ensembl	human	known	69_37n	missense	100	33.33	50	SNP	1.000	T
HACE1	57531	genome.wustl.edu	37	6	105198288	105198288	+	Silent	SNP	G	G	A			TCGA-BH-A18I-01A-11D-A12B-09	TCGA-BH-A18I-10A-01D-A12B-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	f0ca4831-d56d-4bae-b304-bb43c5d2f09b	1928c46f-5e68-4b04-b9e8-b3f0363684a0	g.chr6:105198288G>A	ENST00000262903.4	-	20	2547	c.2271C>T	c.(2269-2271)atC>atT	p.I757I	HACE1_ENST00000369125.2_Silent_p.I542I|HACE1_ENST00000517995.1_5'UTR	NM_020771.3	NP_065822.2	Q8IYU2	HACE1_HUMAN	HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1	757	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				cell cycle (GO:0007049)|Golgi organization (GO:0007030)|membrane fusion (GO:0061025)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|Rac protein signal transduction (GO:0016601)|regulation of cell migration (GO:0030334)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	ligase activity (GO:0016874)|Rab GTPase binding (GO:0017137)|Rac GTPase binding (GO:0048365)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|lung(17)|ovary(5)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	44		all_cancers(87;6.89e-05)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0216)|Colorectal(196;0.202)		BRCA - Breast invasive adenocarcinoma(108;0.122)|Epithelial(106;0.204)		AAAAAGCATTGATCTGAGGCT	0.383																																						dbGAP											0													111.0	105.0	107.0					6																	105198288		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			BC034982	CCDS5050.1	6q21	2013-01-10	2012-02-23		ENSG00000085382	ENSG00000085382		"""Ankyrin repeat domain containing"""	21033	protein-coding gene	gene with protein product		610876				10718198	Standard	NM_020771		Approved	KIAA1320	uc003pqu.1	Q8IYU2	OTTHUMG00000015287	ENST00000262903.4:c.2271C>T	6.37:g.105198288G>A			A8K6U5|B3KY89|B4DFM6|B4DTQ4|B7Z9X6|E9PGP0|Q5VU99|Q5VUA0|Q8ND12|Q9P2M6	Silent	SNP	pfam_HECT,pfam_Ankyrin_rpt,superfamily_HECT,superfamily_Ankyrin_rpt-contain_dom,smart_Ankyrin_rpt,smart_HECT,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom,pfscan_HECT,prints_Ankyrin_rpt	p.I757	ENST00000262903.4	37	c.2271	CCDS5050.1	6																																																																																			HACE1	-	pfam_HECT,superfamily_HECT,smart_HECT,pfscan_HECT	ENSG00000085382		0.383	HACE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	HACE1	HGNC	protein_coding	OTTHUMT00000041643.2	325	0.61	2	G	XM_045095		105198288	105198288	-1	no_errors	ENST00000262903	ensembl	human	known	69_37n	silent	112	51.93	121	SNP	1.000	A
HMBOX1	79618	genome.wustl.edu	37	8	28827654	28827654	+	Frame_Shift_Del	DEL	A	A	-			TCGA-BH-A18I-01A-11D-A12B-09	TCGA-BH-A18I-10A-01D-A12B-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	f0ca4831-d56d-4bae-b304-bb43c5d2f09b	1928c46f-5e68-4b04-b9e8-b3f0363684a0	g.chr8:28827654delA	ENST00000397358.3	+	4	822	c.118delA	c.(118-120)aaafs	p.K40fs	HMBOX1_ENST00000355231.5_Frame_Shift_Del_p.K40fs|HMBOX1_ENST00000519047.1_Frame_Shift_Del_p.K40fs|HMBOX1_ENST00000444075.1_Frame_Shift_Del_p.K40fs|HMBOX1_ENST00000524238.1_Frame_Shift_Del_p.K40fs|HMBOX1_ENST00000523613.1_Frame_Shift_Del_p.K40fs|HMBOX1_ENST00000558662.1_Frame_Shift_Del_p.K40fs|HMBOX1_ENST00000403668.2_Frame_Shift_Del_p.K40fs|HMBOX1_ENST00000287701.10_Frame_Shift_Del_p.K40fs	NM_024567.3	NP_078843.2	Q6NT76	HMBX1_HUMAN	homeobox containing 1	40					negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)	11		Ovarian(32;0.0192)		KIRC - Kidney renal clear cell carcinoma(542;0.135)|Kidney(114;0.161)		TGGAATGACTAAACATGAAAT	0.423																																						dbGAP											0													102.0	97.0	98.0					8																	28827654		2203	4300	6503	-	-	-	SO:0001589	frameshift_variant	0			AY522342	CCDS6071.1	8p12	2013-05-23			ENSG00000147421	ENSG00000147421		"""Homeoboxes / HNF class"""	26137	protein-coding gene	gene with protein product	"""homeobox telomere-binding protein 1"""					16825764	Standard	NM_024567		Approved	HNF1LA, PBHNF, FLJ21616, HOT1	uc003xhd.4	Q6NT76	OTTHUMG00000172138	ENST00000397358.3:c.118delA	8.37:g.28827654delA	ENSP00000380516:p.Lys40fs		A4K385|A8K3R8|B4DHY5|D3DSU0|Q3Y6P1|Q96GS5|Q9H701	Frame_Shift_Del	DEL	pfam_HNF-1_N,pfam_Homeodomain,superfamily_Lambda_DNA-bd_dom,superfamily_Homeodomain-like,smart_Homeodomain,pfscan_Homeodomain	p.K40fs	ENST00000397358.3	37	c.118	CCDS6071.1	8																																																																																			HMBOX1	-	pfam_HNF-1_N	ENSG00000147421		0.423	HMBOX1-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	HMBOX1	HGNC	protein_coding	OTTHUMT00000255267.4	91	0.00	0	A	NM_024567		28827654	28827654	+1	no_errors	ENST00000444075	ensembl	human	known	69_37n	frame_shift_del	28	41.67	20	DEL	1.000	-
IQGAP3	128239	genome.wustl.edu	37	1	156499903	156499903	+	Silent	SNP	C	C	T			TCGA-BH-A18I-01A-11D-A12B-09	TCGA-BH-A18I-10A-01D-A12B-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	f0ca4831-d56d-4bae-b304-bb43c5d2f09b	1928c46f-5e68-4b04-b9e8-b3f0363684a0	g.chr1:156499903C>T	ENST00000361170.2	-	34	4408	c.4398G>A	c.(4396-4398)ctG>ctA	p.L1466L	snoU13_ENST00000458777.1_RNA	NM_178229.4	NP_839943.2	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3	1466					activation of MAPK activity (GO:0000187)|cellular response to organic substance (GO:0071310)|ERK1 and ERK2 cascade (GO:0070371)|G1/S transition of mitotic cell cycle (GO:0000082)|negative regulation of gene expression (GO:0010629)|positive regulation of gene expression (GO:0010628)|positive regulation of mammary gland epithelial cell proliferation (GO:0033601)|Ras protein signal transduction (GO:0007265)|regulation of cell size (GO:0008361)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)	Ras GTPase activator activity (GO:0005099)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(14)|lung(29)|ovary(5)|prostate(5)|skin(5)|urinary_tract(3)	75	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					TTACCTTGGCCAGCTCGTCCA	0.602																																						dbGAP											0													42.0	27.0	32.0					1																	156499903		2203	4299	6502	-	-	-	SO:0001819	synonymous_variant	0			AY253300	CCDS1144.1	1q21.3	2008-02-05			ENSG00000183856	ENSG00000183856			20669	protein-coding gene	gene with protein product							Standard	NM_178229		Approved		uc001fpf.3	Q86VI3	OTTHUMG00000033114	ENST00000361170.2:c.4398G>A	1.37:g.156499903C>T			Q5T3H8	Silent	SNP	pfam_RasGAP,pfam_RasGAP_C,pfam_IQ_motif_EF-hand-BS,pfam_CH-domain,superfamily_Rho_GTPase_activation_prot,superfamily_CH-domain,superfamily_WW_Rsp5_WWP,smart_CH-domain,smart_IQ_motif_EF-hand-BS,smart_RasGAP,pfscan_CH-domain,pfscan_IQ_motif_EF-hand-BS,pfscan_RasGAP	p.L1466	ENST00000361170.2	37	c.4398	CCDS1144.1	1																																																																																			IQGAP3	-	pfam_RasGAP_C	ENSG00000183856		0.602	IQGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	IQGAP3	HGNC	protein_coding	OTTHUMT00000080657.1	22	0.00	0	C	NM_178229		156499903	156499903	-1	no_errors	ENST00000361170	ensembl	human	known	69_37n	silent	18	41.94	13	SNP	1.000	T
LCT	3938	genome.wustl.edu	37	2	136570313	136570313	+	Frame_Shift_Del	DEL	A	A	-			TCGA-BH-A18I-01A-11D-A12B-09	TCGA-BH-A18I-10A-01D-A12B-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	f0ca4831-d56d-4bae-b304-bb43c5d2f09b	1928c46f-5e68-4b04-b9e8-b3f0363684a0	g.chr2:136570313delA	ENST00000264162.2	-	7	1931	c.1921delT	c.(1921-1923)tacfs	p.Y641fs	Y_RNA_ENST00000363794.1_RNA	NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	641	4 X approximate repeats.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)			breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	GTGGCTGGGTAGTCTCCATCC	0.582																																						dbGAP											0													105.0	91.0	96.0					2																	136570313		2203	4300	6503	-	-	-	SO:0001589	frameshift_variant	0			X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202					Standard	NM_002299		Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.1921delT	2.37:g.136570313delA	ENSP00000264162:p.Tyr641fs		Q4ZG58	Frame_Shift_Del	DEL	pfam_Glyco_hydro_1,superfamily_Glycoside_hydrolase_SF,prints_Glyco_hydro_1	p.Y641fs	ENST00000264162.2	37	c.1921	CCDS2178.1	2																																																																																			LCT	-	pfam_Glyco_hydro_1,superfamily_Glycoside_hydrolase_SF	ENSG00000115850		0.582	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LCT	HGNC	protein_coding	OTTHUMT00000254657.1	115	0.00	0	A	NM_002299		136570313	136570313	-1	no_errors	ENST00000264162	ensembl	human	known	69_37n	frame_shift_del	87	22.81	26	DEL	1.000	-
KLF7	8609	genome.wustl.edu	37	2	207998800	207998800	+	Intron	SNP	C	C	T	rs2284934	byFrequency	TCGA-BH-A18I-01A-11D-A12B-09	TCGA-BH-A18I-10A-01D-A12B-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	f0ca4831-d56d-4bae-b304-bb43c5d2f09b	1928c46f-5e68-4b04-b9e8-b3f0363684a0	g.chr2:207998800C>T	ENST00000309446.6	-	2	479				KLF7_ENST00000421199.1_Intron|KLF7_ENST00000423015.1_Intron|KLF7_ENST00000412414.2_Silent_p.P3P|KLF7_ENST00000458272.1_Intron	NM_003709.3	NP_003700.1	O75840	KLF7_HUMAN	Kruppel-like factor 7 (ubiquitous)						axon guidance (GO:0007411)|dendrite morphogenesis (GO:0048813)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|large_intestine(3)|liver(1)|lung(4)|skin(1)	11				LUSC - Lung squamous cell carcinoma(261;0.0856)|Lung(261;0.166)|Epithelial(149;0.173)		CTGGCCAAGACGGGAACATGC	0.507													T|||	3250	0.648962	0.5348	0.7594	5008	,	,		15303	0.6587		0.672	False		,,,				2504	0.6912					dbGAP											0																																										-	-	-	SO:0001627	intron_variant	0			AB015132	CCDS2373.1, CCDS59438.1, CCDS59439.1, CCDS59440.1	2q32	2013-01-08			ENSG00000118263	ENSG00000118263		"""Kruppel-like transcription factors"", ""Zinc fingers, C2H2-type"""	6350	protein-coding gene	gene with protein product		604865				9774444	Standard	NM_003709		Approved	UKLF	uc010zix.2	O75840	OTTHUMG00000132935	ENST00000309446.6:c.103-9672G>A	2.37:g.207998800C>T			B2RB03|B7Z4F7|C9JF04|E7EWH1|L0R4P2|Q7Z3H8|Q96E51	Silent	SNP	pfam_Znf_C2H2,smart_Znf_C2H2-like,pfscan_Znf_C2H2	p.P3	ENST00000309446.6	37	c.9	CCDS2373.1	2																																																																																			KLF7	-	NULL	ENSG00000118263		0.507	KLF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KLF7	HGNC	protein_coding	OTTHUMT00000256466.2	8	0.00	0	C	NM_003709		207998800	207998800	-1	no_errors	ENST00000412414	ensembl	human	known	69_37n	silent	3	66.67	6	SNP	0.901	T
MAP1A	4130	genome.wustl.edu	37	15	43814174	43814174	+	Missense_Mutation	SNP	G	G	A			TCGA-BH-A18I-01A-11D-A12B-09	TCGA-BH-A18I-10A-01D-A12B-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	f0ca4831-d56d-4bae-b304-bb43c5d2f09b	1928c46f-5e68-4b04-b9e8-b3f0363684a0	g.chr15:43814174G>A	ENST00000300231.5	+	4	953	c.503G>A	c.(502-504)cGc>cAc	p.R168H	MAP1A_ENST00000399453.1_Missense_Mutation_p.R168H|MAP1A_ENST00000382031.1_Missense_Mutation_p.R406H			P78559	MAP1A_HUMAN	microtubule-associated protein 1A	168					microtubule cytoskeleton organization (GO:0000226)|sensory perception of sound (GO:0007605)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(5)|pancreas(3)|prostate(2)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	66		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.05e-06)	Estramustine(DB01196)	CACTTAAACCGCCTGGGCATC	0.557																																						dbGAP											0													61.0	61.0	61.0					15																	43814174		1991	4173	6164	-	-	-	SO:0001583	missense	0			U38292	CCDS42031.1	15q15.3	2006-06-15			ENSG00000166963	ENSG00000166963			6835	protein-coding gene	gene with protein product		600178		MAP1L		7806212, 7629894	Standard	XM_005254385		Approved		uc001zrt.3	P78559	OTTHUMG00000059756	ENST00000300231.5:c.503G>A	15.37:g.43814174G>A	ENSP00000300231:p.Arg168His		O95643|Q12973|Q15882|Q9UJT4	Missense_Mutation	SNP	NULL	p.R168H	ENST00000300231.5	37	c.503	CCDS42031.1	15	.	.	.	.	.	.	.	.	.	.	G	13.54	2.267942	0.40095	.	.	ENSG00000166963	ENST00000382031;ENST00000399453;ENST00000300231;ENST00000442025	T;T;T	0.03607	3.87;3.87;3.87	5.1	5.1	0.69264	.	.	.	.	.	T	0.08223	0.0205	N	0.21373	0.66	0.46954	D	0.999266	D	0.76494	0.999	D	0.72338	0.977	T	0.11372	-1.0590	9	0.87932	D	0	-9.2532	9.3829	0.38325	0.1564:0.0:0.8436:0.0	.	168	P78559	MAP1A_HUMAN	H	406;168;168;168	ENSP00000371462:R406H;ENSP00000382380:R168H;ENSP00000300231:R168H	ENSP00000300231:R168H	R	+	2	0	MAP1A	41601466	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	6.276000	0.72601	2.659000	0.90383	0.561000	0.74099	CGC	MAP1A	-	NULL	ENSG00000166963		0.557	MAP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	MAP1A	HGNC	protein_coding	OTTHUMT00000132894.5	94	0.00	0	G	NM_002373		43814174	43814174	+1	no_errors	ENST00000399453	ensembl	human	known	69_37n	missense	62	31.63	31	SNP	1.000	A
MYO9A	4649	genome.wustl.edu	37	15	72192139	72192139	+	Missense_Mutation	SNP	A	A	G			TCGA-BH-A18I-01A-11D-A12B-09	TCGA-BH-A18I-10A-01D-A12B-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	f0ca4831-d56d-4bae-b304-bb43c5d2f09b	1928c46f-5e68-4b04-b9e8-b3f0363684a0	g.chr15:72192139A>G	ENST00000356056.5	-	24	3831	c.3359T>C	c.(3358-3360)aTt>aCt	p.I1120T	MYO9A_ENST00000563542.1_5'UTR|MYO9A_ENST00000566885.1_Missense_Mutation_p.I740T|MYO9A_ENST00000444904.1_Missense_Mutation_p.I1101T|MYO9A_ENST00000564571.1_Missense_Mutation_p.I1120T|MYO9A_ENST00000424560.1_Missense_Mutation_p.I1120T	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	1120	IQ 4. {ECO:0000255|PROSITE- ProRule:PRU00116}.|Neck or regulatory domain.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|visual perception (GO:0007601)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|motor activity (GO:0003774)			NS(4)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(29)|lung(27)|ovary(1)|pancreas(1)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						TTGTATGCAAATAGCAGCCAT	0.443																																						dbGAP											0													83.0	78.0	80.0					15																	72192139		2199	4297	6496	-	-	-	SO:0001583	missense	0			AF117888	CCDS10239.1	15q22-q23	2011-09-27			ENSG00000066933	ENSG00000066933		"""Myosins / Myosin superfamily : Class IX"""	7608	protein-coding gene	gene with protein product		604875				10409426	Standard	NM_006901		Approved	FLJ11061, FLJ13244, MGC71859	uc002atl.5	B2RTY4	OTTHUMG00000133440	ENST00000356056.5:c.3359T>C	15.37:g.72192139A>G	ENSP00000348349:p.Ile1120Thr		B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Missense_Mutation	SNP	pfam_Myosin_head_motor_dom,pfam_RhoGAP_dom,pfam_Ras-assoc,pfam_IQ_motif_EF-hand-BS,superfamily_Rho_GTPase_activation_prot,smart_Ras-assoc,smart_Myosin_head_motor_dom,smart_IQ_motif_EF-hand-BS,smart_Prot_Kinase_C-like_PE/DAG-bd,smart_RhoGAP_dom,pfscan_IQ_motif_EF-hand-BS,pfscan_Ras-assoc,pfscan_Prot_Kinase_C-like_PE/DAG-bd,pfscan_RhoGAP_dom,prints_Myosin_head_motor_dom	p.I1120T	ENST00000356056.5	37	c.3359	CCDS10239.1	15	.	.	.	.	.	.	.	.	.	.	A	0.017	-1.510318	0.00984	.	.	ENSG00000066933	ENST00000356056;ENST00000424560;ENST00000444904;ENST00000261864	T;T;T	0.73469	-0.75;-0.65;-0.65	5.51	0.0879	0.14452	.	.	.	.	.	T	0.51227	0.1662	N	0.05230	-0.09	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.001	T	0.38178	-0.9673	9	0.37606	T	0.19	.	9.7856	0.40675	0.3765:0.0:0.6235:0.0	.	1101;1101;1120	B2RTY4-2;B7WP69;B2RTY4	.;.;MYO9A_HUMAN	T	1120;1120;1101;1101	ENSP00000348349:I1120T;ENSP00000399162:I1120T;ENSP00000398250:I1101T	ENSP00000261864:I1101T	I	-	2	0	MYO9A	69979193	0.000000	0.05858	0.003000	0.11579	0.120000	0.20174	0.853000	0.27777	0.142000	0.18901	0.533000	0.62120	ATT	MYO9A	-	pfam_IQ_motif_EF-hand-BS,smart_IQ_motif_EF-hand-BS,pfscan_IQ_motif_EF-hand-BS	ENSG00000066933		0.443	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MYO9A	HGNC	protein_coding	OTTHUMT00000257308.1	160	0.00	0	A	NM_006901		72192139	72192139	-1	no_errors	ENST00000424560	ensembl	human	known	69_37n	missense	108	33.74	55	SNP	0.000	G
NLRC3	197358	genome.wustl.edu	37	16	3611738	3611738	+	RNA	SNP	C	C	T			TCGA-BH-A18I-01A-11D-A12B-09	TCGA-BH-A18I-10A-01D-A12B-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	f0ca4831-d56d-4bae-b304-bb43c5d2f09b	1928c46f-5e68-4b04-b9e8-b3f0363684a0	g.chr16:3611738C>T	ENST00000301749.7	-	0	2385				NLRC3_ENST00000359128.5_RNA|NLRC3_ENST00000603507.1_RNA|NLRC3_ENST00000324659.8_RNA|NLRC3_ENST00000448023.2_RNA|NLRC3_ENST00000419350.2_RNA	NM_178844.2	NP_849172.2	Q7RTR2	NLRC3_HUMAN	NLR family, CARD domain containing 3						I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|regulation of protein ubiquitination (GO:0031396)|response to lipopolysaccharide (GO:0032496)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(16)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						TCCCACTCAGCACGCTGCCCA	0.617																																						dbGAP											0													88.0	98.0	95.0					16																	3611738		2087	4213	6300	-	-	-			0			BK001112	CCDS73817.1	16p13.3	2014-03-25			ENSG00000167984	ENSG00000167984		"""Nucleotide-binding domain and leucine rich repeat containing"""	29889	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 3"", ""NOD-like receptor C3"""	615648				15705585, 12766759	Standard	NM_178844		Approved	CLR16.2, FLJ00348, NOD3	uc010btn.3	Q7RTR2	OTTHUMG00000177561		16.37:g.3611738C>T			Q5EY36|Q8NF48|Q8NI01|Q8NI02|Q8TEL3	Silent	SNP	smart_Leu-rich_rpt_RNase_inh_sub-typ,pfscan_NACHT_NTPase	p.V707	ENST00000301749.7	37	c.2121		16																																																																																			NLRC3	-	NULL	ENSG00000167984		0.617	NLRC3-201	KNOWN	basic|appris_principal	protein_coding	NLRC3	HGNC	polymorphic_pseudogene		66	0.00	0	C	NM_178844		3611738	3611738	-1	no_errors	ENST00000448023	ensembl	human	known	69_37n	silent	47	56.48	61	SNP	0.999	T
PCDHGA1	56114	genome.wustl.edu	37	5	140710391	140710391	+	Missense_Mutation	SNP	A	A	G			TCGA-BH-A18I-01A-11D-A12B-09	TCGA-BH-A18I-10A-01D-A12B-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	f0ca4831-d56d-4bae-b304-bb43c5d2f09b	1928c46f-5e68-4b04-b9e8-b3f0363684a0	g.chr5:140710391A>G	ENST00000517417.1	+	1	140	c.140A>G	c.(139-141)aAc>aGc	p.N47S	PCDHGA1_ENST00000378105.3_Missense_Mutation_p.N47S|AC005618.6_ENST00000606901.1_lincRNA	NM_018912.2	NP_061735.1	Q9Y5H4	PCDG1_HUMAN	protocadherin gamma subfamily A, 1	47	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|lung(32)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTCGTAGGCAACATCGCCAAG	0.552																																						dbGAP											0													102.0	108.0	106.0					5																	140710391		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF152318	CCDS54922.1	5q31	2010-01-26				ENSG00000204956		"""Cadherins / Protocadherins : Clustered"""	8696	other	protocadherin		606288				10380929	Standard	NM_018912		Approved	PCDH-GAMMA-A1		Q9Y5H4		ENST00000517417.1:c.140A>G	5.37:g.140710391A>G	ENSP00000431083:p.Asn47Ser		Q2M273|Q9Y5D6	Missense_Mutation	SNP	pfam_Cadherin,pfam_Cadherin_N,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin,prints_Cadherin	p.N47S	ENST00000517417.1	37	c.140	CCDS54922.1	5	.	.	.	.	.	.	.	.	.	.	A	13.59	2.283339	0.40394	.	.	ENSG00000204956	ENST00000517417;ENST00000378105	T;T	0.38077	1.16;1.16	4.37	3.21	0.36854	Cadherin, N-terminal (1);Cadherin (2);Cadherin-like (1);	0.586022	0.15191	N	0.275543	T	0.41003	0.1140	M	0.79258	2.445	0.21719	N	0.999575	B;B	0.27656	0.092;0.184	B;B	0.31869	0.121;0.137	T	0.38394	-0.9663	10	0.52906	T	0.07	.	9.0133	0.36155	0.9094:0.0:0.0906:0.0	.	47;47	Q9Y5H4-2;Q9Y5H4	.;PCDG1_HUMAN	S	47	ENSP00000431083:N47S;ENSP00000367345:N47S	ENSP00000367345:N47S	N	+	2	0	PCDHGA1	140690575	0.007000	0.16637	0.992000	0.48379	0.846000	0.48090	2.527000	0.45615	0.842000	0.35045	0.533000	0.62120	AAC	PCDHGA1	-	pfam_Cadherin_N,superfamily_Cadherin-like,smart_Cadherin	ENSG00000204956		0.552	PCDHGA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	PCDHGA1	HGNC	protein_coding	OTTHUMT00000374737.1	132	0.00	0	A	NM_018912		140710391	140710391	+1	no_errors	ENST00000517417	ensembl	human	known	69_37n	missense	106	32.91	52	SNP	0.990	G
PCDHGB6	56100	genome.wustl.edu	37	5	140788500	140788500	+	Missense_Mutation	SNP	G	G	A			TCGA-BH-A18I-01A-11D-A12B-09	TCGA-BH-A18I-10A-01D-A12B-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	f0ca4831-d56d-4bae-b304-bb43c5d2f09b	1928c46f-5e68-4b04-b9e8-b3f0363684a0	g.chr5:140788500G>A	ENST00000520790.1	+	1	731	c.731G>A	c.(730-732)aGa>aAa	p.R244K	PCDHGA6_ENST00000517434.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron	NM_018926.2|NM_032100.1	NP_061749.1|NP_115271.1	Q9Y5F9	PCDGI_HUMAN	protocadherin gamma subfamily B, 6	244	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(2)|endometrium(9)|kidney(1)|large_intestine(10)|lung(16)|ovary(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)	48			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTTTTCAGCAGAGACGAATAT	0.498																																						dbGAP											0													33.0	34.0	34.0					5																	140788500		1847	4096	5943	-	-	-	SO:0001583	missense	0			AF152522	CCDS54929.1, CCDS75342.1	5q31	2010-01-26				ENSG00000253305		"""Cadherins / Protocadherins : Clustered"""	8713	other	protocadherin		606303				10380929	Standard	NM_018926		Approved	PCDH-GAMMA-B6		Q9Y5F9		ENST00000520790.1:c.731G>A	5.37:g.140788500G>A	ENSP00000428603:p.Arg244Lys		Q9Y5C5	Missense_Mutation	SNP	pfam_Cadherin,pfam_Cadherin_N,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin,prints_Cadherin	p.R244K	ENST00000520790.1	37	c.731	CCDS54929.1	5	.	.	.	.	.	.	.	.	.	.	g	11.00	1.509989	0.27036	.	.	ENSG00000253305	ENST00000520790	T	0.60424	0.19	5.34	4.11	0.48088	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.35595	0.0937	N	0.04508	-0.205	0.22531	N	0.999016	B;B	0.02656	0.0;0.0	B;B	0.06405	0.001;0.002	T	0.27054	-1.0085	9	0.52906	T	0.07	.	10.721	0.46040	0.9232:0.0:0.0768:0.0	.	244;244	Q9Y5F9;Q9Y5F9-2	PCDGI_HUMAN;.	K	244	ENSP00000428603:R244K	ENSP00000428603:R244K	R	+	2	0	PCDHGB6	140768684	0.001000	0.12720	0.412000	0.26496	0.528000	0.34623	1.717000	0.37991	0.860000	0.35481	-0.670000	0.03821	AGA	PCDHGB6	-	superfamily_Cadherin-like,pfscan_Cadherin,prints_Cadherin	ENSG00000253305		0.498	PCDHGB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PCDHGB6	HGNC	protein_coding	OTTHUMT00000374746.1	106	0.00	0	G	NM_018926		140788500	140788500	+1	no_errors	ENST00000520790	ensembl	human	known	69_37n	missense	85	30.89	38	SNP	0.842	A
PIK3CA	5290	genome.wustl.edu	37	3	178936082	178936082	+	Missense_Mutation	SNP	G	G	A	rs121913273		TCGA-BH-A18I-01A-11D-A12B-09	TCGA-BH-A18I-10A-01D-A12B-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	f0ca4831-d56d-4bae-b304-bb43c5d2f09b	1928c46f-5e68-4b04-b9e8-b3f0363684a0	g.chr3:178936082G>A	ENST00000263967.3	+	10	1781	c.1624G>A	c.(1624-1626)Gaa>Aaa	p.E542K		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	542	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.		E -> K (in CLOVE, KERSEB, CRC and BC; also found in glioblastoma multiforme and endometrial carcinoma; shows an increase in lipid kinase activity; oncogenic in vivo; occurs in the interface between the PI3K helical domain and the nSH2 (N- terminal SH2) region of the p85 regulatory subunit and may reduce the inhibitory effect of p85; requires interaction with RAS to induce cellular transformation). {ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15924253, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:22658544}.|E -> Q (found in an endometrial carcinoma sample; unknown pathological significance). {ECO:0000269|PubMed:16322209}.|E -> V (in BC; unknown pathological significance). {ECO:0000269|PubMed:16353168}.		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.E542K(545)|p.E542Q(10)		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)	TCCTCTCTCTGAAATCACTGA	0.333	E542K(BT483_BREAST)|E542K(CAL51_BREAST)|E542K(HGC27_STOMACH)|E542K(IM95_STOMACH)|E542K(JHUEM1_ENDOMETRIUM)|E542K(NCIH1341_LUNG)|E542K(SW948_LARGE_INTESTINE)|E542K(T84_LARGE_INTESTINE)|E542K(VMCUB1_URINARY_TRACT)	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"""	555	Substitution - Missense(555)	breast(176)|large_intestine(166)|urinary_tract(45)|endometrium(37)|skin(19)|lung(18)|stomach(16)|ovary(16)|thyroid(14)|upper_aerodigestive_tract(9)|central_nervous_system(7)|cervix(6)|liver(6)|oesophagus(5)|penis(4)|kidney(3)|soft_tissue(2)|haematopoietic_and_lymphoid_tissue(2)|prostate(2)|biliary_tract(1)|pituitary(1)											56.0	56.0	56.0					3																	178936082		1809	4069	5878	-	-	-	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.1624G>A	3.37:g.178936082G>A	ENSP00000263967:p.Glu542Lys		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.E542K	ENST00000263967.3	37	c.1624	CCDS43171.1	3	.	.	.	.	.	.	.	.	.	.	G	34	5.360420	0.95877	.	.	ENSG00000121879	ENST00000263967	T	0.62105	0.05	5.78	5.78	0.91487	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.69287	0.3094	L	0.41356	1.27	0.80722	D	1	D	0.65815	0.995	D	0.63192	0.912	T	0.60296	-0.7291	10	0.09843	T	0.71	-23.9623	20.0024	0.97423	0.0:0.0:1.0:0.0	.	542	P42336	PK3CA_HUMAN	K	542	ENSP00000263967:E542K	ENSP00000263967:E542K	E	+	1	0	PIK3CA	180418776	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.476000	0.97823	2.722000	0.93159	0.467000	0.42956	GAA	PIK3CA	-	pfam_PInositide-3_kin_accessory_dom,superfamily_ARM-type_fold,smart_PInositide-3_kin_accessory_dom	ENSG00000121879		0.333	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	PIK3CA	HGNC	protein_coding	OTTHUMT00000348409.2	277	0.00	0	G			178936082	178936082	+1	no_errors	ENST00000263967	ensembl	human	known	69_37n	missense	162	30.77	72	SNP	1.000	A
POU2F2	5452	genome.wustl.edu	37	19	42599576	42599576	+	Silent	SNP	G	G	A	rs535353969	byFrequency	TCGA-BH-A18I-01A-11D-A12B-09	TCGA-BH-A18I-10A-01D-A12B-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	f0ca4831-d56d-4bae-b304-bb43c5d2f09b	1928c46f-5e68-4b04-b9e8-b3f0363684a0	g.chr19:42599576G>A	ENST00000526816.2	-	11	1008	c.993C>T	c.(991-993)gcC>gcT	p.A331A	POU2F2_ENST00000389341.5_Silent_p.A315A|POU2F2_ENST00000560398.1_Silent_p.A337A|POU2F2_ENST00000560558.1_Silent_p.A276A|POU2F2_ENST00000533720.1_Silent_p.A315A|POU2F2_ENST00000529952.1_Silent_p.A331A|POU2F2_ENST00000342301.4_Silent_p.A331A|POU2F2_ENST00000529067.1_Silent_p.A315A			P09086	PO2F2_HUMAN	POU class 2 homeobox 2	331					cell maturation (GO:0048469)|humoral immune response (GO:0006959)|immunoglobulin secretion involved in immune response (GO:0002380)|mature B cell differentiation (GO:0002335)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(5)|lung(4)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Prostate(69;0.059)			Dolutegravir(DB08930)	GCAGCTGCTCGGCGATCAGCA	0.647																																						dbGAP											0													55.0	51.0	53.0					19																	42599576		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0				CCDS33035.1, CCDS56094.1, CCDS56095.1, CCDS58665.1	19q13.2	2011-06-20	2007-07-13					"""Homeoboxes / POU class"""	9213	protein-coding gene	gene with protein product		164176	"""POU domain class 2, transcription factor 2"""	OTF2			Standard	NM_001207026		Approved	OCT2	uc002osp.3	P09086		ENST00000526816.2:c.993C>T	19.37:g.42599576G>A			Q16648|Q7M4M8|Q9BRS4	Silent	SNP	pfam_POU_specific,pfam_Homeodomain,superfamily_Lambda_DNA-bd_dom,superfamily_Homeodomain-like,smart_POU_specific,smart_Homeodomain,pfscan_Homeodomain,pfscan_POU_specific,prints_POU,prints_TF_octamer	p.A331	ENST00000526816.2	37	c.993	CCDS56095.1	19																																																																																			POU2F2	-	pfam_Homeodomain,superfamily_Homeodomain-like,smart_Homeodomain,pfscan_Homeodomain,prints_POU	ENSG00000028277		0.647	POU2F2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	POU2F2	HGNC	protein_coding	OTTHUMT00000387329.3	81	0.00	0	G			42599576	42599576	-1	no_errors	ENST00000342301	ensembl	human	known	69_37n	silent	46	17.86	10	SNP	0.228	A
UGGT2	55757	genome.wustl.edu	37	13	96529583	96529583	+	Missense_Mutation	SNP	C	C	G	rs200544724	byFrequency	TCGA-BH-A18I-01A-11D-A12B-09	TCGA-BH-A18I-10A-01D-A12B-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	f0ca4831-d56d-4bae-b304-bb43c5d2f09b	1928c46f-5e68-4b04-b9e8-b3f0363684a0	g.chr13:96529583C>G	ENST00000376747.3	-	29	3493	c.3423G>C	c.(3421-3423)tgG>tgC	p.W1141C		NM_020121.3	NP_064506.3	Q9NYU1	UGGG2_HUMAN	UDP-glucose glycoprotein glucosyltransferase 2	1141					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-glucosylation (GO:0097359)	endoplasmic reticulum lumen (GO:0005788)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(17)|lung(20)|ovary(3)|pancreas(1)|prostate(4)|urinary_tract(2)	60						ACCTCAGTATCCAAGCACCTG	0.313																																						dbGAP											0													91.0	99.0	96.0					13																	96529583		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF227906	CCDS9480.1	13q32.1	2009-07-23	2009-07-23	2009-07-23	ENSG00000102595	ENSG00000102595			15664	protein-coding gene	gene with protein product	"""UDP-glucose:glycoprotein glucosyltransferase 2"""	605898	"""UDP-glucose ceramide glucosyltransferase-like 2"""	UGCGL2		10694380	Standard	NM_020121		Approved	FLJ11485, HUGT2, FLJ10873, MGC150689, MGC87276, MGC117360	uc001vmt.3	Q9NYU1	OTTHUMG00000017230	ENST00000376747.3:c.3423G>C	13.37:g.96529583C>G	ENSP00000365938:p.Trp1141Cys		A6NKL4|Q08AD0|Q5JQR8|Q8N5K0|Q9UFC4	Missense_Mutation	SNP	pfam_UDP-g_GGtrans,pfam_Glyco_trans_8	p.W1141C	ENST00000376747.3	37	c.3423	CCDS9480.1	13	.	.	.	.	.	.	.	.	.	.	C	14.92	2.678853	0.47886	.	.	ENSG00000102595	ENST00000376747	T	0.19532	2.14	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.56863	0.2014	M	0.90082	3.085	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.66504	-0.5907	10	0.87932	D	0	-5.3049	19.0955	0.93249	0.0:1.0:0.0:0.0	.	1141	Q9NYU1	UGGG2_HUMAN	C	1141	ENSP00000365938:W1141C	ENSP00000365938:W1141C	W	-	3	0	UGGT2	95327584	1.000000	0.71417	1.000000	0.80357	0.133000	0.20885	7.142000	0.77339	2.511000	0.84671	0.655000	0.94253	TGG	UGGT2	-	NULL	ENSG00000102595		0.313	UGGT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	UGGT2	HGNC	protein_coding	OTTHUMT00000045507.1	275	0.00	0	C	NM_020121		96529583	96529583	-1	no_errors	ENST00000376747	ensembl	human	known	69_37n	missense	227	30.79	101	SNP	1.000	G
ZFHX4	79776	genome.wustl.edu	37	8	77775608	77775609	+	Frame_Shift_Ins	INS	-	-	A			TCGA-BH-A18I-01A-11D-A12B-09	TCGA-BH-A18I-10A-01D-A12B-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	f0ca4831-d56d-4bae-b304-bb43c5d2f09b	1928c46f-5e68-4b04-b9e8-b3f0363684a0	g.chr8:77775608_77775609insA	ENST00000521891.2	+	11	10106_10107	c.9658_9659insA	c.(9658-9660)gaafs	p.E3220fs	ZFHX4_ENST00000518282.1_Frame_Shift_Ins_p.E3194fs|ZFHX4_ENST00000050961.6_Frame_Shift_Ins_p.E3171fs|ZFHX4_ENST00000455469.2_Frame_Shift_Ins_p.E3175fs	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	3171					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			CAAAAAAGAGGAAAAAATCTCA	0.406										HNSCC(33;0.089)																												dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0				CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"""Homeoboxes / ZF class"""	30939	protein-coding gene	gene with protein product		606940	"""zinc finger homeodomain 4"""			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.9664dupA	8.37:g.77775614_77775614dupA	ENSP00000430497:p.Glu3220fs		G3V138|Q18PS0|Q6ZN20	Frame_Shift_Ins	INS	pfam_Homeodomain,superfamily_Homeodomain-like,superfamily_Adenylate_cyclase-assoc_CAP_N,smart_Znf_C2H2-like,smart_Znf_U1,smart_Homeodomain,pfscan_Homeodomain,pfscan_Znf_C2H2	p.I3222fs	ENST00000521891.2	37	c.9658_9659	CCDS47878.2	8																																																																																			ZFHX4	-	NULL	ENSG00000091656		0.406	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	ZFHX4	HGNC	protein_coding	OTTHUMT00000379197.2	369	0.00	0	-	NM_024721		77775608	77775609	+1	no_errors	ENST00000521891	ensembl	human	known	69_37n	frame_shift_ins	296	56.79	389	INS	1.000:1.000	A
