#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
ALK	238	genome.wustl.edu	37	2	29455275	29455275	+	Missense_Mutation	SNP	C	C	T			TCGA-E2-A1BD-01A-11D-A12Q-09	TCGA-E2-A1BD-10A-01D-A12Q-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f5ac1986-272b-48d2-9a73-4a550e38a997	dcd144ae-c12f-492f-b5b4-3dd4626e27a4	g.chr2:29455275C>T	ENST00000389048.3	-	15	3433	c.2527G>A	c.(2527-2529)Gga>Aga	p.G843R	ALK_ENST00000431873.1_Intron	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	843	Gly-rich.				activation of MAPK activity (GO:0000187)|cell proliferation (GO:0008283)|neuron development (GO:0048666)|NIK/NF-kappaB signaling (GO:0038061)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|protein complex (GO:0043234)	ATP binding (GO:0005524)|NF-kappaB-inducing kinase activity (GO:0004704)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		ATIC/ALK(24)|FN1/ALK(2)|C2orf44/ALK(2)|TPM3/ALK(33)|KLC1/ALK(2)|VCL/ALK(4)|TPM4/ALK(12)|KIF5B/ALK(8)|RANBP2/ALK(34)|SQSTM1/ALK(2)|EML4/ALK(543)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|NPM1/ALK(632)|CLTC/ALK(44)|CARS/ALK(5)|MSN/ALK(6)|TFG/ALK(9)	NS(2)|autonomic_ganglia(198)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(4)|large_intestine(25)|lung(61)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|soft_tissue(3)|stomach(2)|thyroid(2)	340	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)|Crizotinib(DB08865)	CCACCACCTCCGGCTGCAATG	0.587			"""T, Mis, A"""	"""NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALO17, CARS, EML4, KIF5B, C2orf22"""	"""ALCL, NSCLC, Neuroblastoma"""	neuroblastoma			Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																													dbGAP	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"""L, E, M"""	0													71.0	65.0	67.0					2																	29455275		2203	4300	6503	-	-	-	SO:0001583	missense	0	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	D45915	CCDS33172.1	2p23	2014-09-17	2008-01-23		ENSG00000171094	ENSG00000171094		"""CD molecules"""	427	protein-coding gene	gene with protein product		105590	"""anaplastic lymphoma kinase (Ki-1)"""			8122112	Standard	NM_004304		Approved	CD246	uc002rmy.3	Q9UM73	OTTHUMG00000152034	ENST00000389048.3:c.2527G>A	2.37:g.29455275C>T	ENSP00000373700:p.Gly843Arg	Somatic		WXS	Illumina GAIIx	Phase_IV	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Missense_Mutation	SNP	pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Prot_kinase_cat_dom,pfam_MAM_dom,superfamily_Kinase-like_dom,superfamily_ConA-like_lec_gl,superfamily_LDrepeatLR_classA_rpt,smart_LDrepeatLR_classA_rpt,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_MAM_dom,pfscan_Prot_kinase_cat_dom,prints_Ser-Thr/Tyr_kinase_cat_dom	p.G843R	ENST00000389048.3	37	c.2527	CCDS33172.1	2	.	.	.	.	.	.	.	.	.	.	C	26.9	4.778317	0.90195	.	.	ENSG00000171094	ENST00000389048	T	0.63580	-0.05	5.41	5.41	0.78517	.	0.000000	0.47852	D	0.000213	D	0.84710	0.5532	M	0.92923	3.36	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.88171	0.2864	9	.	.	.	.	19.2048	0.93726	0.0:1.0:0.0:0.0	.	843	Q9UM73	ALK_HUMAN	R	843	ENSP00000373700:G843R	.	G	-	1	0	ALK	29308779	1.000000	0.71417	0.162000	0.22713	0.815000	0.46073	7.168000	0.77570	2.534000	0.85438	0.555000	0.69702	GGA	ALK	-	NULL	ENSG00000171094		0.587	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ALK	HGNC	protein_coding	OTTHUMT00000324994.1	136	0.00	0	C	NM_004304		29455275	29455275	-1	no_errors	ENST00000389048	ensembl	human	known	69_37n	missense	17	68.52	37	SNP	0.998	T
CACNA1A	773	genome.wustl.edu	37	19	13414649	13414649	+	Missense_Mutation	SNP	G	G	T			TCGA-E2-A1BD-01A-11D-A12Q-09	TCGA-E2-A1BD-10A-01D-A12Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f5ac1986-272b-48d2-9a73-4a550e38a997	dcd144ae-c12f-492f-b5b4-3dd4626e27a4	g.chr19:13414649G>T	ENST00000360228.5	-	16	2035	c.2036C>A	c.(2035-2037)tCt>tAt	p.S679Y	CACNA1A_ENST00000573710.2_Missense_Mutation_p.S680Y	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	680					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	GCCCCCCTGAGACTTGATCCC	0.567																																						dbGAP											0													169.0	173.0	172.0					19																	13414649		2026	4177	6203	-	-	-	SO:0001583	missense	0			U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.2036C>A	19.37:g.13414649G>T	ENSP00000353362:p.Ser679Tyr	Somatic		WXS	Illumina GAIIx	Phase_IV	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Missense_Mutation	SNP	pfam_Ion_trans_dom,pfam_VDCC_a1su_IQ,pfam_PKD1_2_channel,prints_VDCCAlpha1,prints_VDCC_P/Q_a1su	p.S679Y	ENST00000360228.5	37	c.2036	CCDS45998.1	19	.	.	.	.	.	.	.	.	.	.	G	18.22	3.576749	0.65878	.	.	ENSG00000141837	ENST00000360228;ENST00000418012;ENST00000357018;ENST00000325084	D	0.97404	-4.37	4.58	4.58	0.56647	Ion transport (1);	0.000000	0.64402	D	0.000001	D	0.98251	0.9421	M	0.78344	2.41	0.58432	D	0.999995	D;D;D	0.89917	1.0;1.0;0.998	D;D;D	0.91635	0.999;0.998;0.996	D	0.99308	1.0903	10	0.87932	D	0	.	16.302	0.82825	0.0:0.0:1.0:0.0	.	680;680;679	O00555;E9PD31;Q9NS88	CAC1A_HUMAN;.;.	Y	679;680;680;680	ENSP00000353362:S679Y	ENSP00000317661:S680Y	S	-	2	0	CACNA1A	13275649	1.000000	0.71417	0.994000	0.49952	0.978000	0.69477	9.507000	0.97996	2.371000	0.80710	0.591000	0.81541	TCT	CACNA1A	-	pfam_Ion_trans_dom,pfam_PKD1_2_channel	ENSG00000141837		0.567	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	CACNA1A	HGNC	protein_coding	OTTHUMT00000104062.2	188	0.00	0	G	NM_000068		13414649	13414649	-1	no_errors	ENST00000360228	ensembl	human	known	69_37n	missense	56	44.55	45	SNP	1.000	T
CCT8L2	150160	genome.wustl.edu	37	22	17071880	17071880	+	Missense_Mutation	SNP	C	C	T			TCGA-E2-A1BD-01A-11D-A12Q-09	TCGA-E2-A1BD-10A-01D-A12Q-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f5ac1986-272b-48d2-9a73-4a550e38a997	dcd144ae-c12f-492f-b5b4-3dd4626e27a4	g.chr22:17071880C>T	ENST00000359963.3	-	1	1820	c.1561G>A	c.(1561-1563)Gta>Ata	p.V521I		NM_014406.4	NP_055221.1	Q96SF2	TCPQM_HUMAN	chaperonin containing TCP1, subunit 8 (theta)-like 2	521					anion transport (GO:0006820)|cellular protein metabolic process (GO:0044267)|potassium ion transmembrane transport (GO:0071805)|transport (GO:0006810)	cytoplasm (GO:0005737)	anion channel activity (GO:0005253)|ATP binding (GO:0005524)|calcium-activated potassium channel activity (GO:0015269)			breast(3)|endometrium(7)|kidney(1)|large_intestine(8)|liver(2)|lung(37)|ovary(3)|prostate(3)|skin(2)|stomach(1)	67	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.0157)|Lung NSC(13;0.147)|all_lung(157;0.175)				TTGGCCACTACGATTTCATCT	0.493																																						dbGAP											0													122.0	110.0	114.0					22																	17071880		2203	4300	6503	-	-	-	SO:0001583	missense	0			AP003553	CCDS13738.1	22q11.1	2011-09-01			ENSG00000198445	ENSG00000198445			15553	protein-coding gene	gene with protein product							Standard	NM_014406		Approved	CESK1	uc002zlp.1	Q96SF2	OTTHUMG00000141302	ENST00000359963.3:c.1561G>A	22.37:g.17071880C>T	ENSP00000353048:p.Val521Ile	Somatic		WXS	Illumina GAIIx	Phase_IV	A4QPH3|Q9UJS3	Missense_Mutation	SNP	pfam_Cpn60/TCP-1,superfamily_Cpn60/TCP-1,prints_Chaperone_TCP-1	p.V521I	ENST00000359963.3	37	c.1561	CCDS13738.1	22	.	.	.	.	.	.	.	.	.	.	c	0.003	-2.541020	0.00142	.	.	ENSG00000198445	ENST00000359963	T	0.73681	-0.77	1.98	-1.99	0.07457	.	0.720448	0.11307	N	0.577504	T	0.36880	0.0983	N	0.02403	-0.565	0.09310	N	1	B	0.21905	0.062	B	0.21917	0.037	T	0.40459	-0.9562	10	0.02654	T	1	-9.5824	2.7722	0.05337	0.0:0.4531:0.2685:0.2785	.	521	Q96SF2	TCPQM_HUMAN	I	521	ENSP00000353048:V521I	ENSP00000353048:V521I	V	-	1	0	CCT8L2	15451880	0.000000	0.05858	0.109000	0.21407	0.266000	0.26442	-1.288000	0.02783	-0.055000	0.13244	0.379000	0.24179	GTA	CCT8L2	-	pfam_Cpn60/TCP-1,superfamily_Cpn60/TCP-1	ENSG00000198445		0.493	CCT8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CCT8L2	HGNC	protein_coding	OTTHUMT00000280580.1	181	0.00	0	C			17071880	17071880	-1	no_errors	ENST00000359963	ensembl	human	known	69_37n	missense	49	31.94	23	SNP	0.030	T
COMMD5	28991	genome.wustl.edu	37	8	146076483	146076483	+	Nonsense_Mutation	SNP	G	G	A			TCGA-E2-A1BD-01A-11D-A12Q-09	TCGA-E2-A1BD-10A-01D-A12Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f5ac1986-272b-48d2-9a73-4a550e38a997	dcd144ae-c12f-492f-b5b4-3dd4626e27a4	g.chr8:146076483G>A	ENST00000305103.3	-	2	493	c.241C>T	c.(241-243)Cag>Tag	p.Q81*	COMMD5_ENST00000450361.2_Nonsense_Mutation_p.Q81*|COMMD5_ENST00000402718.3_Nonsense_Mutation_p.Q81*|AF235103.1_ENST00000578937.1_RNA	NM_014066.3	NP_054785.2	Q9GZQ3	COMD5_HUMAN	COMM domain containing 5	81						nucleus (GO:0005634)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|ovary(1)|pancreas(1)	11	all_cancers(97;1.14e-11)|all_epithelial(106;7.74e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Epithelial(56;8.75e-39)|OV - Ovarian serous cystadenocarcinoma(54;1.13e-38)|all cancers(56;8.48e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)			GCACCCAGCTGCTCCTCCGGC	0.647																																						dbGAP											0													20.0	19.0	19.0					8																	146076483		2198	4292	6490	-	-	-	SO:0001587	stop_gained	0			AK023070	CCDS6436.1	8q24.3	2006-11-06				ENSG00000170619			17902	protein-coding gene	gene with protein product		608216				15799966, 10918053	Standard	NM_014066		Approved	HT002, FLJ13008, HCaRG	uc003zem.3	Q9GZQ3		ENST00000305103.3:c.241C>T	8.37:g.146076483G>A	ENSP00000304544:p.Gln81*	Somatic		WXS	Illumina GAIIx	Phase_IV	D3DWN7|Q9NVN6|Q9UHX5	Nonsense_Mutation	SNP	pfam_HCaRG	p.Q81*	ENST00000305103.3	37	c.241	CCDS6436.1	8	.	.	.	.	.	.	.	.	.	.	G	11.98	1.799150	0.31777	.	.	ENSG00000170619	ENST00000402718;ENST00000450361;ENST00000305103;ENST00000529143;ENST00000533270	.	.	.	4.1	4.1	0.47936	.	0.690030	0.13758	N	0.364817	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.05620	T	0.96	.	12.0319	0.53401	0.0:0.0:1.0:0.0	.	.	.	.	X	81	.	ENSP00000304544:Q81X	Q	-	1	0	COMMD5	146047287	0.008000	0.16893	0.530000	0.27963	0.209000	0.24338	0.290000	0.18975	2.296000	0.77279	0.460000	0.39030	CAG	COMMD5	-	pfam_HCaRG	ENSG00000170619		0.647	COMMD5-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	COMMD5	HGNC	protein_coding	OTTHUMT00000382962.1	11	0.00	0	G	NM_014066		146076483	146076483	-1	no_errors	ENST00000450361	ensembl	human	known	69_37n	nonsense	6	40.00	4	SNP	0.786	A
DNAH6	1768	genome.wustl.edu	37	2	84846872	84846872	+	Silent	SNP	C	C	T			TCGA-E2-A1BD-01A-11D-A12Q-09	TCGA-E2-A1BD-10A-01D-A12Q-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f5ac1986-272b-48d2-9a73-4a550e38a997	dcd144ae-c12f-492f-b5b4-3dd4626e27a4	g.chr2:84846872C>T	ENST00000237449.6	+	23	3644	c.3636C>T	c.(3634-3636)gcC>gcT	p.A1212A	DNAH6_ENST00000389394.3_Silent_p.A1212A|DNAH6_ENST00000398278.2_Silent_p.A1212A			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	1212	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						ATCCACAGGCCGTGCAGCCAC	0.418																																						dbGAP											0													114.0	95.0	101.0					2																	84846872		692	1591	2283	-	-	-	SO:0001819	synonymous_variant	0			U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"""Axonemal dyneins"""	2951	protein-coding gene	gene with protein product		603336	"""dynein, axonemal, heavy polypeptide 6"", ""dynein heavy chain-like 1"""	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.3636C>T	2.37:g.84846872C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Silent	SNP	pfam_Dynein_heavy,pfam_Dynein_heavy_dom-2,pfam_ATPase_dyneun-rel_AAA,smart_AAA+_ATPase	p.A1212	ENST00000237449.6	37	c.3636	CCDS46348.1	2																																																																																			DNAH6	-	pfam_Dynein_heavy_dom-2	ENSG00000115423		0.418	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DNAH6	HGNC	protein_coding	OTTHUMT00000328537.2	221	0.00	0	C	NM_001370		84846872	84846872	+1	no_errors	ENST00000237449	ensembl	human	known	69_37n	silent	61	54.07	73	SNP	0.970	T
ELMO2	63916	genome.wustl.edu	37	20	45021747	45021747	+	Frame_Shift_Del	DEL	T	T	-			TCGA-E2-A1BD-01A-11D-A12Q-09	TCGA-E2-A1BD-10A-01D-A12Q-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f5ac1986-272b-48d2-9a73-4a550e38a997	dcd144ae-c12f-492f-b5b4-3dd4626e27a4	g.chr20:45021747delT	ENST00000290246.6	-	6	422	c.228delA	c.(226-228)caafs	p.Q76fs	ELMO2_ENST00000396391.1_Frame_Shift_Del_p.Q76fs|ELMO2_ENST00000445496.2_5'UTR|ELMO2_ENST00000372176.1_5'UTR|ELMO2_ENST00000352077.2_Frame_Shift_Del_p.Q76fs|ELMO2_ENST00000488853.1_5'UTR|ELMO2_ENST00000439931.2_Frame_Shift_Del_p.Q76fs	NM_133171.3	NP_573403.1	Q96JJ3	ELMO2_HUMAN	engulfment and cell motility 2	76					apoptotic process (GO:0006915)|cell chemotaxis (GO:0060326)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)	receptor tyrosine kinase binding (GO:0030971)			breast(1)|endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|urinary_tract(1)	16		Myeloproliferative disorder(115;0.0122)				AGATAGCCAGTTGTAAGATTG	0.373																																						dbGAP											0													91.0	94.0	93.0					20																	45021747		2203	4300	6503	-	-	-	SO:0001589	frameshift_variant	0			AF398886	CCDS13398.1	20q13	2010-03-18	2006-01-20		ENSG00000062598	ENSG00000062598		"""Engulfment and cell motility proteins"""	17233	protein-coding gene	gene with protein product		606421	"""engulfment and cell motility 2 (ced-12 homolog, C. elegans)"""			11595183	Standard	NM_133171		Approved	CED12, ELMO-2, CED-12, KIAA1834, FLJ11656	uc002xru.1	Q96JJ3	OTTHUMG00000033070	ENST00000290246.6:c.228delA	20.37:g.45021747delT	ENSP00000290246:p.Gln76fs	Somatic		WXS	Illumina GAIIx	Phase_IV	E1P5T3|Q5JVZ6|Q7Z5G9|Q96CJ2|Q96ME5|Q96PA9|Q9H938|Q9H9L5|Q9HAH0|Q9NQQ6	Frame_Shift_Del	DEL	pfam_DUF3361,pfam_Engulfment_cell_motility_ELMO,superfamily_ARM-type_fold	p.Q76fs	ENST00000290246.6	37	c.228	CCDS13398.1	20																																																																																			ELMO2	-	NULL	ENSG00000062598		0.373	ELMO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	ELMO2	HGNC	protein_coding	OTTHUMT00000080466.1	270	0.00	0	T	NM_022086		45021747	45021747	-1	no_errors	ENST00000439931	ensembl	human	known	69_37n	frame_shift_del	132	33.17	66	DEL	0.999	-
FGF16	8823	genome.wustl.edu	37	X	76709703	76709703	+	Missense_Mutation	SNP	C	C	A			TCGA-E2-A1BD-01A-11D-A12Q-09	TCGA-E2-A1BD-10A-01D-A12Q-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f5ac1986-272b-48d2-9a73-4a550e38a997	dcd144ae-c12f-492f-b5b4-3dd4626e27a4	g.chrX:76709703C>A	ENST00000439435.1	+	1	56	c.56C>A	c.(55-57)aCt>aAt	p.T19N				O43320	FGF16_HUMAN	fibroblast growth factor 16	0					cell-cell signaling (GO:0007267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|metabolic process (GO:0008152)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of brown fat cell proliferation (GO:0070349)|response to temperature stimulus (GO:0009266)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	growth factor activity (GO:0008083)			NS(1)|breast(1)|lung(2)	4						GGGGAGTGGACTCTGGCCTGT	0.428																																						dbGAP											0													87.0	81.0	83.0					X																	76709703		1918	4116	6034	-	-	-	SO:0001583	missense	0			AB009391	CCDS75996.1	Xq21.1	2014-01-31			ENSG00000196468	ENSG00000196468			3672	protein-coding gene	gene with protein product		300827	"""metacarpal 4-5 fusion"""	MF4		9473496, 11474196, 23709756	Standard	NM_003868		Approved		uc011mqp.2	O43320	OTTHUMG00000013133	ENST00000439435.1:c.56C>A	X.37:g.76709703C>A	ENSP00000399324:p.Thr19Asn	Somatic		WXS	Illumina GAIIx	Phase_IV		Missense_Mutation	SNP	pfam_IL1_HBGF,superfamily_Cytokine_IL1-like,smart_IL1_HBGF,prints_IL1_HBGF,prints_GF_heparin-bd	p.T19N	ENST00000439435.1	37	c.56		X	.	.	.	.	.	.	.	.	.	.	C	2.120	-0.401551	0.04865	.	.	ENSG00000196468	ENST00000439435	.	.	.	4.3	3.43	0.39272	.	.	.	.	.	T	0.53190	0.1781	.	.	.	.	.	.	.	.	.	.	.	.	T	0.61969	-0.6953	3	.	.	.	.	10.2249	0.43220	0.0:0.8263:0.0:0.1737	.	.	.	.	N	19	.	.	T	+	2	0	FGF16	76596359	0.994000	0.37717	1.000000	0.80357	0.961000	0.63080	0.356000	0.20181	0.932000	0.37266	0.600000	0.82982	ACT	FGF16	-	pfam_IL1_HBGF,superfamily_Cytokine_IL1-like,smart_IL1_HBGF,prints_IL1_HBGF	ENSG00000196468		0.428	FGF16-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal	protein_coding	FGF16	HGNC	protein_coding	OTTHUMT00000036814.1	352	0.28	1	C	NM_003868		76709703	76709703	+1	no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region	ENST00000439435	ensembl	human	known	69_37n	missense	170	42.57	126	SNP	1.000	A
GAK	2580	genome.wustl.edu	37	4	906526	906526	+	Missense_Mutation	SNP	G	G	T	rs567572883		TCGA-E2-A1BD-01A-11D-A12Q-09	TCGA-E2-A1BD-10A-01D-A12Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f5ac1986-272b-48d2-9a73-4a550e38a997	dcd144ae-c12f-492f-b5b4-3dd4626e27a4	g.chr4:906526G>T	ENST00000314167.4	-	3	374	c.264C>A	c.(262-264)ttC>ttA	p.F88L	GAK_ENST00000511163.1_Intron	NM_005255.2	NP_005246.2	O14976	GAK_HUMAN	cyclin G associated kinase	88	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|cell development (GO:0048468)|clathrin coat disassembly (GO:0072318)|clathrin-mediated endocytosis (GO:0072583)|endoplasmic reticulum organization (GO:0007029)|epidermal cell differentiation (GO:0009913)|establishment of skin barrier (GO:0061436)|forebrain morphogenesis (GO:0048853)|Golgi organization (GO:0007030)|intrahepatic bile duct development (GO:0035622)|positive regulation of neural precursor cell proliferation (GO:2000179)	cell junction (GO:0030054)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(16)|skin(7)|urinary_tract(2)	39				Colorectal(103;0.219)		AGGATACCATGAAGCAAACTT	0.502																																						dbGAP											0													162.0	147.0	152.0					4																	906526		2203	4300	6503	-	-	-	SO:0001583	missense	0			D88435	CCDS3340.1	4p16	2011-09-07			ENSG00000178950	ENSG00000178950		"""Heat shock proteins / DNAJ (HSP40)"""	4113	protein-coding gene	gene with protein product	"""auxilin-2"""	602052				9299234	Standard	NM_005255		Approved	DNAJC26	uc003gbm.4	O14976	OTTHUMG00000088301	ENST00000314167.4:c.264C>A	4.37:g.906526G>T	ENSP00000314499:p.Phe88Leu	Somatic		WXS	Illumina GAIIx	Phase_IV	Q5U4P5|Q9BVY6	Missense_Mutation	SNP	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Tensin_phosphatase_C2-dom,pfam_DnaJ_N,superfamily_Kinase-like_dom,superfamily_DnaJ_N,superfamily_C2_Ca/lipid-bd_dom_CaLB,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,smart_DnaJ_N,pfscan_Prot_kinase_cat_dom,pfscan_Phosphatase_tensin-typ,pfscan_Tensin_phosphatase_C2-dom,pfscan_DnaJ_N	p.F88L	ENST00000314167.4	37	c.264	CCDS3340.1	4	.	.	.	.	.	.	.	.	.	.	G	14.36	2.510815	0.44660	.	.	ENSG00000178950	ENST00000398567;ENST00000314167	T	0.61742	0.08	4.56	2.33	0.28932	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.32376	0.0827	N	0.05608	-0.01	0.80722	D	1	B	0.19935	0.04	B	0.23419	0.046	T	0.10753	-1.0616	10	0.51188	T	0.08	-28.0313	5.2279	0.15406	0.1442:0.0:0.6567:0.1991	.	88	O14976	GAK_HUMAN	L	88	ENSP00000314499:F88L	ENSP00000314499:F88L	F	-	3	2	GAK	896526	1.000000	0.71417	0.989000	0.46669	0.731000	0.41821	1.277000	0.33167	1.007000	0.39238	0.557000	0.71058	TTC	GAK	-	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	ENSG00000178950		0.502	GAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GAK	HGNC	protein_coding	OTTHUMT00000239188.1	240	0.00	0	G	NM_005255		906526	906526	-1	no_errors	ENST00000314167	ensembl	human	known	69_37n	missense	84	28.81	34	SNP	1.000	T
GNAI1	2770	genome.wustl.edu	37	7	79818279	79818279	+	Missense_Mutation	SNP	C	C	T			TCGA-E2-A1BD-01A-11D-A12Q-09	TCGA-E2-A1BD-10A-01D-A12Q-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f5ac1986-272b-48d2-9a73-4a550e38a997	dcd144ae-c12f-492f-b5b4-3dd4626e27a4	g.chr7:79818279C>T	ENST00000351004.3	+	2	504	c.131C>T	c.(130-132)tCt>tTt	p.S44F	GNAI1_ENST00000490206.1_3'UTR|GNAI1_ENST00000457358.2_5'UTR	NM_002069.5	NP_002060.4	P63096	GNAI1_HUMAN	guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 1	44					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|cell cycle (GO:0007049)|cell division (GO:0051301)|G-protein coupled receptor signaling pathway (GO:0007186)|platelet activation (GO:0030168)|response to peptide hormone (GO:0043434)|synaptic transmission (GO:0007268)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled serotonin receptor binding (GO:0031821)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	19						GCTGGTGAATCTGGTAAAAGT	0.313																																						dbGAP											0													139.0	145.0	143.0					7																	79818279		2203	4300	6503	-	-	-	SO:0001583	missense	0			AL049933	CCDS5595.1, CCDS59061.1	7q21-q22	2008-07-18			ENSG00000127955	ENSG00000127955			4384	protein-coding gene	gene with protein product	"""Gi1 protein alpha subunit"""	139310				3110783	Standard	NM_002069		Approved		uc003uhb.1	P63096	OTTHUMG00000023523	ENST00000351004.3:c.131C>T	7.37:g.79818279C>T	ENSP00000343027:p.Ser44Phe	Somatic		WXS	Illumina GAIIx	Phase_IV	A8KA88|B4E2V1|C9J3A4|P04898|P11015|P31871|Q5U074|Q8TAN5|Q9UGA4	Missense_Mutation	SNP	pfam_Gprotein_alpha_su,pfam_Small_GTPase_ARF/SAR,superfamily_GproteinA_insert,smart_Gprotein_alpha_su,prints_Gprotein_alpha_su,prints_Gprotein_alpha_I,prints_Fungi_GproteinA	p.S44F	ENST00000351004.3	37	c.131	CCDS5595.1	7	.	.	.	.	.	.	.	.	.	.	C	29.7	5.032447	0.93575	.	.	ENSG00000127955	ENST00000351004	D	0.95853	-3.83	5.89	5.89	0.94794	G protein alpha subunit, helical insertion (1);	0.000000	0.85682	D	0.000000	D	0.98972	0.9650	H	0.99357	4.53	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98900	1.0776	9	.	.	.	.	20.4167	0.99026	0.0:1.0:0.0:0.0	.	44	P63096	GNAI1_HUMAN	F	44	ENSP00000343027:S44F	.	S	+	2	0	GNAI1	79656215	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.782000	0.85680	2.834000	0.97654	0.579000	0.79373	TCT	GNAI1	-	pfam_Gprotein_alpha_su,smart_Gprotein_alpha_su,prints_Gprotein_alpha_su	ENSG00000127955		0.313	GNAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GNAI1	HGNC	protein_coding	OTTHUMT00000253254.1	567	0.00	0	C	NM_002069		79818279	79818279	+1	no_errors	ENST00000351004	ensembl	human	known	69_37n	missense	225	50.44	229	SNP	1.000	T
GP2	2813	genome.wustl.edu	37	16	20327362	20327362	+	Splice_Site	SNP	A	A	T			TCGA-E2-A1BD-01A-11D-A12Q-09	TCGA-E2-A1BD-10A-01D-A12Q-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f5ac1986-272b-48d2-9a73-4a550e38a997	dcd144ae-c12f-492f-b5b4-3dd4626e27a4	g.chr16:20327362A>T	ENST00000381362.4	-	10	1502	c.1426T>A	c.(1426-1428)Tct>Act	p.S476T	GP2_ENST00000381360.5_Splice_Site_p.S329T|GP2_ENST00000573897.1_5'Flank|GP2_ENST00000302555.5_Splice_Site_p.S473T|GP2_ENST00000341642.5_Splice_Site_p.S326T	NM_001007240.1|NM_001502.2	NP_001007241.2|NP_001493.2	P55259	GP2_HUMAN	glycoprotein 2 (zymogen granule membrane)	476	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				antigen transcytosis by M cells in mucosal-associated lymphoid tissue (GO:0002412)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)	antigen binding (GO:0003823)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(25)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	48						CTTGAGCAAGACTGTAGGGAT	0.478																																						dbGAP											0													97.0	91.0	93.0					16																	20327362		2203	4300	6503	-	-	-	SO:0001630	splice_region_variant	0			U36221	CCDS10582.2, CCDS42128.1, CCDS45432.1, CCDS45433.1	16p12.3	2008-02-05			ENSG00000169347	ENSG00000169347			4441	protein-coding gene	gene with protein product		602977				9605860	Standard	XM_005255259		Approved		uc002dgw.3	P55259	OTTHUMG00000131489	ENST00000381362.4:c.1426-1T>A	16.37:g.20327362A>T		Somatic		WXS	Illumina GAIIx	Phase_IV	A6NFM9|A6NJA8|Q13338|Q9UIF1	Missense_Mutation	SNP	pfam_Zona_pellucida_Endoglin/CD105,smart_Zona_pellucida_Endoglin/CD105,pfscan_Zona_pellucida_Endoglin/CD105,prints_Endoglin/CD105_subgr	p.S476T	ENST00000381362.4	37	c.1426	CCDS42128.1	16	.	.	.	.	.	.	.	.	.	.	A	4.313	0.057463	0.08339	.	.	ENSG00000169347	ENST00000302555;ENST00000381362;ENST00000381360;ENST00000341642;ENST00000537520	D;D;D;D	0.82344	-1.6;-1.6;-1.6;-1.6	5.37	1.8	0.24995	Zona pellucida sperm-binding protein (3);	.	.	.	.	T	0.62720	0.2451	N	0.17312	0.475	0.32057	N	0.596257	B;B;B;B	0.28419	0.002;0.046;0.211;0.008	B;B;B;B	0.28139	0.009;0.086;0.066;0.041	T	0.57171	-0.7857	9	0.05525	T	0.97	-0.0818	5.2198	0.15362	0.5111:0.1564:0.0:0.3325	.	326;454;473;476	P55259-4;B7Z1G2;P55259-3;P55259	.;.;.;GP2_HUMAN	T	473;476;329;326;454	ENSP00000304044:S473T;ENSP00000370767:S476T;ENSP00000370765:S329T;ENSP00000343861:S326T	ENSP00000304044:S473T	S	-	1	0	GP2	20234863	0.999000	0.42202	0.782000	0.31804	0.869000	0.49853	0.410000	0.21098	0.016000	0.14998	0.533000	0.62120	TCT	GP2	-	pfam_Zona_pellucida_Endoglin/CD105,smart_Zona_pellucida_Endoglin/CD105,pfscan_Zona_pellucida_Endoglin/CD105	ENSG00000169347		0.478	GP2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	GP2	HGNC	protein_coding	OTTHUMT00000436920.1	167	0.00	0	A	NM_016295	Missense_Mutation	20327362	20327362	-1	no_errors	ENST00000381362	ensembl	human	known	69_37n	missense	78	51.25	82	SNP	0.997	T
GRIA3	2892	genome.wustl.edu	37	X	122599568	122599568	+	Missense_Mutation	SNP	C	C	T	rs1052542		TCGA-E2-A1BD-01A-11D-A12Q-09	TCGA-E2-A1BD-10A-01D-A12Q-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f5ac1986-272b-48d2-9a73-4a550e38a997	dcd144ae-c12f-492f-b5b4-3dd4626e27a4	g.chrX:122599568C>T	ENST00000371251.1	+	14	2420	c.2368C>T	c.(2368-2370)Ctc>Ttc	p.L790F	GRIA3_ENST00000264357.5_Missense_Mutation_p.L790F|AL356213.1_ENST00000577653.1_RNA|GRIA3_ENST00000542149.1_Missense_Mutation_p.L790F|GRIA3_ENST00000371256.5_Intron			P42263	GRIA3_HUMAN	glutamate receptor, ionotropic, AMPA 3	790					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)			breast(2)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(8)|lung(25)|ovary(3)|pancreas(2)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	57					Lithium(DB01356)	TGAGCAAGGCCTCTTGGACAA	0.438																																						dbGAP											0													96.0	84.0	88.0					X																	122599568		2203	4300	6503	-	-	-	SO:0001583	missense	0			U10301	CCDS14604.1, CCDS14605.1, CCDS76017.1	Xq25	2012-08-29	2012-02-03		ENSG00000125675	ENSG00000125675		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4573	protein-coding gene	gene with protein product		305915	"""glutamate receptor, ionotrophic, AMPA 3"""	GLUR3		1319477, 10644433	Standard	NM_007325		Approved	GluA3, GLURC, MRX94	uc004etr.4	P42263	OTTHUMG00000022685	ENST00000371251.1:c.2368C>T	X.37:g.122599568C>T	ENSP00000360297:p.Leu790Phe	Somatic		WXS	Illumina GAIIx	Phase_IV	D3DTF1|Q4VXD5|Q4VXD6|Q9HDA0|Q9HDA1|Q9HDA2|Q9P0H1	Missense_Mutation	SNP	pfam_Iontro_glu_rcpt,pfam_ANF_lig-bd_rcpt,pfam_Glu_rcpt_Glu/Gly-bd,pfam_SBP_bac_3,smart_Iontro_glu_rcpt,smart_Glu_rcpt_Glu/Gly-bd,prints_NMDA_rcpt	p.L790F	ENST00000371251.1	37	c.2368	CCDS14604.1	X	.	.	.	.	.	.	.	.	.	.	c	13.45	2.240669	0.39598	.	.	ENSG00000125675	ENST00000264357;ENST00000542149;ENST00000371251	T;T;T	0.39229	1.09;1.09;1.09	5.78	5.78	0.91487	Ionotropic glutamate receptor (2);	0.441442	0.26535	N	0.023821	T	0.28034	0.0691	N	0.02286	-0.61	0.80722	D	1	P	0.37101	0.582	B	0.42214	0.38	T	0.40136	-0.9579	10	0.49607	T	0.09	.	17.8317	0.88684	0.0:1.0:0.0:0.0	.	790	P42263	GRIA3_HUMAN	F	790	ENSP00000264357:L790F;ENSP00000446146:L790F;ENSP00000360297:L790F	ENSP00000264357:L790F	L	+	1	0	GRIA3	122427249	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.430000	0.82344	0.591000	0.81541	CTC	GRIA3	-	pfam_Iontro_glu_rcpt,pfam_SBP_bac_3,smart_Iontro_glu_rcpt	ENSG00000125675		0.438	GRIA3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	GRIA3	HGNC	protein_coding	OTTHUMT00000058854.1	453	0.00	0	C	NM_000828		122599568	122599568	+1	no_errors	ENST00000264357	ensembl	human	known	69_37n	missense	156	40.23	105	SNP	1.000	T
ITGA11	22801	genome.wustl.edu	37	15	68613777	68613777	+	Missense_Mutation	SNP	C	C	T			TCGA-E2-A1BD-01A-11D-A12Q-09	TCGA-E2-A1BD-10A-01D-A12Q-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f5ac1986-272b-48d2-9a73-4a550e38a997	dcd144ae-c12f-492f-b5b4-3dd4626e27a4	g.chr15:68613777C>T	ENST00000315757.7	-	19	2473	c.2387G>A	c.(2386-2388)cGg>cAg	p.R796Q	ITGA11_ENST00000423218.2_Missense_Mutation_p.R796Q	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	796					cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-matrix adhesion (GO:0007160)|collagen-activated signaling pathway (GO:0038065)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|osteoblast differentiation (GO:0001649)|substrate-dependent cell migration (GO:0006929)	focal adhesion (GO:0005925)|integrin alpha11-beta1 complex (GO:0034681)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(6)|lung(22)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	52						CAGGTCACTCCGGGCATCCAA	0.652																																						dbGAP											0													48.0	60.0	56.0					15																	68613777		2118	4223	6341	-	-	-	SO:0001583	missense	0			AF109681	CCDS45291.1	15q22.3-q23	2010-03-23				ENSG00000137809		"""Integrins"""	6136	protein-coding gene	gene with protein product		604789				10486209	Standard	NM_001004439		Approved	HsT18964	uc002ari.3	Q9UKX5		ENST00000315757.7:c.2387G>A	15.37:g.68613777C>T	ENSP00000327290:p.Arg796Gln	Somatic		WXS	Illumina GAIIx	Phase_IV	J3KQM2|Q8WYI8|Q9UKQ1	Missense_Mutation	SNP	pfam_Integrin_alpha-2,pfam_VWF_A,pfam_FG-GAP,smart_Int_alpha_beta-p,smart_VWF_A,pfscan_VWF_A,prints_Integrin_alpha	p.R796Q	ENST00000315757.7	37	c.2387	CCDS45291.1	15	.	.	.	.	.	.	.	.	.	.	C	11.05	1.523567	0.27299	.	.	ENSG00000137809	ENST00000315757;ENST00000423218;ENST00000535491	T;T	0.44083	0.93;0.93	5.21	1.78	0.24846	Integrin alpha-2 (1);	0.457372	0.25509	N	0.030196	T	0.23249	0.0562	N	0.17082	0.46	0.09310	N	1	B;B	0.15930	0.015;0.006	B;B	0.13407	0.009;0.004	T	0.17561	-1.0365	10	0.21014	T	0.42	.	9.5079	0.39058	0.0:0.6703:0.0:0.3297	.	796;796	A8K8T0;Q9UKX5	.;ITA11_HUMAN	Q	796;796;431	ENSP00000327290:R796Q;ENSP00000403392:R796Q	ENSP00000327290:R796Q	R	-	2	0	ITGA11	66400831	0.000000	0.05858	0.990000	0.47175	0.993000	0.82548	-0.266000	0.08631	0.578000	0.29487	0.561000	0.74099	CGG	ITGA11	-	pfam_Integrin_alpha-2	ENSG00000137809		0.652	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	ITGA11	HGNC	protein_coding		92	0.00	0	C	NM_012211		68613777	68613777	-1	no_errors	ENST00000315757	ensembl	human	known	69_37n	missense	22	24.14	7	SNP	0.002	T
KCNA1	3736	genome.wustl.edu	37	12	5021915	5021915	+	Silent	SNP	C	C	T			TCGA-E2-A1BD-01A-11D-A12Q-09	TCGA-E2-A1BD-10A-01D-A12Q-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f5ac1986-272b-48d2-9a73-4a550e38a997	dcd144ae-c12f-492f-b5b4-3dd4626e27a4	g.chr12:5021915C>T	ENST00000382545.3	+	2	2478	c.1371C>T	c.(1369-1371)atC>atT	p.I457I	KCNA1_ENST00000543874.2_Intron	NM_000217.2	NP_000208.2	Q09470	KCNA1_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 1 (episodic ataxia with myokymia)	457					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	apical plasma membrane (GO:0016324)|dendrite (GO:0030425)|juxtaparanode region of axon (GO:0044224)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|potassium ion transmembrane transporter activity (GO:0015079)			NS(1)|breast(3)|cervix(2)|endometrium(5)|kidney(1)|large_intestine(14)|lung(23)|ovary(3)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	63					Amitriptyline(DB00321)|Dalfampridine(DB06637)|Desflurane(DB01189)|Enflurane(DB00228)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Nifedipine(DB01115)|Sevoflurane(DB01236)	ACATGGAGATCGAAGAGGATA	0.463																																						dbGAP											0													191.0	186.0	188.0					12																	5021915		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			L02750	CCDS8535.1	12p13	2012-07-05			ENSG00000111262	ENSG00000111262		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6218	protein-coding gene	gene with protein product		176260		AEMK		1349297, 8821794, 16382104	Standard	NM_000217		Approved	Kv1.1, RBK1, HUK1, MBK1	uc001qnh.3	Q09470	OTTHUMG00000044398	ENST00000382545.3:c.1371C>T	12.37:g.5021915C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	A6NM83|Q3MIQ9	Silent	SNP	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,prints_K_chnl_volt-dep_Kv1.1,prints_K_chnl_volt-dep_Kv,prints_K_chnl_volt-dep_Kv1.3	p.I457	ENST00000382545.3	37	c.1371	CCDS8535.1	12																																																																																			KCNA1	-	NULL	ENSG00000111262		0.463	KCNA1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	KCNA1	HGNC	protein_coding	OTTHUMT00000103343.2	123	0.00	0	C	NM_000217		5021915	5021915	+1	no_errors	ENST00000382545	ensembl	human	known	69_37n	silent	64	15.79	12	SNP	0.984	T
MAP3K1	4214	genome.wustl.edu	37	5	56177011	56177014	+	Frame_Shift_Del	DEL	ATAG	ATAG	-	rs570313957	byFrequency	TCGA-E2-A1BD-01A-11D-A12Q-09	TCGA-E2-A1BD-10A-01D-A12Q-09	ATAG	ATAG					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f5ac1986-272b-48d2-9a73-4a550e38a997	dcd144ae-c12f-492f-b5b4-3dd4626e27a4	g.chr5:56177011_56177014delATAG	ENST00000399503.3	+	13	2281_2284	c.2281_2284delATAG	c.(2281-2286)atagatfs	p.ID761fs		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	761					activation of MAPKK activity (GO:0000186)|apoptotic mitochondrial changes (GO:0008637)|cellular response to mechanical stimulus (GO:0071260)|epithelial cell morphogenesis (GO:0003382)|eyelid development in camera-type eye (GO:0061029)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of actin filament polymerization (GO:0030838)|protein phosphorylation (GO:0006468)|regulation of cell migration (GO:0030334)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	cytosol (GO:0005829)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)			NS(1)|breast(19)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(11)|ovary(1)|skin(3)|urinary_tract(1)	57		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)		CCTTTGTCTTATAGATAGACTGTT	0.363																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			U29671, AF042838	CCDS43318.1	5q11.2	2012-02-23	2012-02-23		ENSG00000095015	ENSG00000095015		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6848	protein-coding gene	gene with protein product		600982	"""mitogen-activated protein kinase kinase kinase 1"""	MEKK1		8597633	Standard	NM_005921		Approved	MEKK, MAPKKK1	uc003jqw.4	Q13233	OTTHUMG00000059486	ENST00000399503.3:c.2281_2284delATAG	5.37:g.56177015_56177018delATAG	ENSP00000382423:p.Ile761fs	Somatic		WXS	Illumina GAIIx	Phase_IV		Frame_Shift_Del	DEL	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,superfamily_ARM-type_fold,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Znf_RING,pfscan_Znf_SWIM,pfscan_Prot_kinase_cat_dom	p.R763fs	ENST00000399503.3	37	c.2281_2284	CCDS43318.1	5																																																																																			MAP3K1	-	superfamily_ARM-type_fold	ENSG00000095015		0.363	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	MAP3K1	HGNC	protein_coding	OTTHUMT00000132309.2	535	0.00	0	ATAG	XM_042066		56177011	56177014	+1	no_errors	ENST00000399503	ensembl	human	novel	69_37n	frame_shift_del	239	37.85	148	DEL	0.994:0.998:0.969:1.000	-
MAP3K1	4214	genome.wustl.edu	37	5	56179424	56179425	+	Frame_Shift_Ins	INS	-	-	T			TCGA-E2-A1BD-01A-11D-A12Q-09	TCGA-E2-A1BD-10A-01D-A12Q-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f5ac1986-272b-48d2-9a73-4a550e38a997	dcd144ae-c12f-492f-b5b4-3dd4626e27a4	g.chr5:56179424_56179425insT	ENST00000399503.3	+	15	3737_3738	c.3737_3738insT	c.(3736-3741)ggtcaafs	p.Q1247fs		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	1247	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPKK activity (GO:0000186)|apoptotic mitochondrial changes (GO:0008637)|cellular response to mechanical stimulus (GO:0071260)|epithelial cell morphogenesis (GO:0003382)|eyelid development in camera-type eye (GO:0061029)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of actin filament polymerization (GO:0030838)|protein phosphorylation (GO:0006468)|regulation of cell migration (GO:0030334)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	cytosol (GO:0005829)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)			NS(1)|breast(19)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(11)|ovary(1)|skin(3)|urinary_tract(1)	57		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)		TGGCTGAAAGGTCAACAGATAG	0.396																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			U29671, AF042838	CCDS43318.1	5q11.2	2012-02-23	2012-02-23		ENSG00000095015	ENSG00000095015		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6848	protein-coding gene	gene with protein product		600982	"""mitogen-activated protein kinase kinase kinase 1"""	MEKK1		8597633	Standard	NM_005921		Approved	MEKK, MAPKKK1	uc003jqw.4	Q13233	OTTHUMG00000059486	ENST00000399503.3:c.3738dupT	5.37:g.56179425_56179425dupT	ENSP00000382423:p.Gln1247fs	Somatic		WXS	Illumina GAIIx	Phase_IV		Frame_Shift_Ins	INS	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,superfamily_ARM-type_fold,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Znf_RING,pfscan_Znf_SWIM,pfscan_Prot_kinase_cat_dom	p.Q1247fs	ENST00000399503.3	37	c.3737_3738	CCDS43318.1	5																																																																																			MAP3K1	-	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	ENSG00000095015		0.396	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	MAP3K1	HGNC	protein_coding	OTTHUMT00000132309.2	425	0.00	0	-	XM_042066		56179424	56179425	+1	no_errors	ENST00000399503	ensembl	human	novel	69_37n	frame_shift_ins	173	37.09	102	INS	1.000:0.940	T
MAP1B	4131	genome.wustl.edu	37	5	71479590	71479590	+	Nonsense_Mutation	SNP	C	C	T			TCGA-E2-A1BD-01A-11D-A12Q-09	TCGA-E2-A1BD-10A-01D-A12Q-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f5ac1986-272b-48d2-9a73-4a550e38a997	dcd144ae-c12f-492f-b5b4-3dd4626e27a4	g.chr5:71479590C>T	ENST00000296755.7	+	3	605	c.307C>T	c.(307-309)Cga>Tga	p.R103*		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	103					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		CCTTCATCACCGAAGTGACGT	0.498																																					Melanoma(17;367 822 11631 31730 47712)	dbGAP											0													143.0	135.0	138.0					5																	71479590		2203	4300	6503	-	-	-	SO:0001587	stop_gained	0			L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 102"""	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.307C>T	5.37:g.71479590C>T	ENSP00000296755:p.Arg103*	Somatic		WXS	Illumina GAIIx	Phase_IV	A2BDK5	Nonsense_Mutation	SNP	pfam_MAP1B_neuraxin	p.R103*	ENST00000296755.7	37	c.307	CCDS4012.1	5	.	.	.	.	.	.	.	.	.	.	C	24.7	4.562115	0.86335	.	.	ENSG00000131711	ENST00000512974;ENST00000296755;ENST00000511641	.	.	.	5.02	4.15	0.48705	.	0.127290	0.35291	N	0.003317	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.6222	12.471	0.55787	0.457:0.543:0.0:0.0	.	.	.	.	X	103	.	ENSP00000296755:R103X	R	+	1	2	MAP1B	71515346	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	4.182000	0.58310	1.228000	0.43614	0.637000	0.83480	CGA	MAP1B	-	NULL	ENSG00000131711		0.498	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MAP1B	HGNC	protein_coding	OTTHUMT00000218561.6	267	0.00	0	C	NM_005909		71479590	71479590	+1	no_errors	ENST00000296755	ensembl	human	known	69_37n	nonsense	147	18.78	34	SNP	1.000	T
MATN4	8785	genome.wustl.edu	37	20	43927055	43927055	+	Missense_Mutation	SNP	C	C	T			TCGA-E2-A1BD-01A-11D-A12Q-09	TCGA-E2-A1BD-10A-01D-A12Q-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f5ac1986-272b-48d2-9a73-4a550e38a997	dcd144ae-c12f-492f-b5b4-3dd4626e27a4	g.chr20:43927055C>T	ENST00000372754.1	-	7	1312	c.1304G>A	c.(1303-1305)cGc>cAc	p.R435H	MATN4_ENST00000537548.1_Missense_Mutation_p.R394H|MATN4_ENST00000360607.6_Missense_Mutation_p.R353H|MATN4_ENST00000372756.1_Missense_Mutation_p.R394H|MATN4_ENST00000372751.4_Missense_Mutation_p.R245H|MATN4_ENST00000342716.4_Missense_Mutation_p.R394H|MATN4_ENST00000353917.5_Missense_Mutation_p.R312H			O95460	MATN4_HUMAN	matrilin 4	435	VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				extracellular matrix organization (GO:0030198)|response to axon injury (GO:0048678)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	27		Myeloproliferative disorder(115;0.0122)				GAACTCGGTGCGCACGCGGCT	0.652																																						dbGAP											0													52.0	46.0	48.0					20																	43927055		2203	4299	6502	-	-	-	SO:0001583	missense	0			AJ007581	CCDS13348.1, CCDS46607.1	20q13.1-q13.2	2008-07-07			ENSG00000124159	ENSG00000124159			6910	protein-coding gene	gene with protein product		603897				9827539, 9027493	Standard	NM_003833		Approved		uc002xnn.2	O95460	OTTHUMG00000033043	ENST00000372754.1:c.1304G>A	20.37:g.43927055C>T	ENSP00000361840:p.Arg435His	Somatic		WXS	Illumina GAIIx	Phase_IV	A6NH94|A6NKN5|Q5QPU2|Q5QPU3|Q5QPU4|Q8N2M5|Q8N2M7|Q9H1F8|Q9H1F9	Missense_Mutation	SNP	pfam_VWF_A,pfam_EGF-like_Ca-bd,pfam_Matrilin_coiled-coil_trimer,smart_VWF_A,smart_EGF-like_Ca-bd,smart_EGF-like,pfscan_VWF_A	p.R435H	ENST00000372754.1	37	c.1304		20	.	.	.	.	.	.	.	.	.	.	C	27.7	4.853327	0.91355	.	.	ENSG00000124159	ENST00000372753;ENST00000372754;ENST00000372756;ENST00000353917;ENST00000360607;ENST00000342716;ENST00000537548;ENST00000255132;ENST00000372751	D;D;D;D;D;D;D;D	0.83591	-1.74;-1.74;-1.74;-1.74;-1.74;-1.74;-1.74;-1.74	5.45	5.45	0.79879	.	0.000000	0.44902	D	0.000411	D	0.90892	0.7138	M	0.74467	2.265	0.58432	D	0.999995	D;D;D	0.89917	0.998;1.0;1.0	D;D;D	0.91635	0.929;0.999;0.999	D	0.90377	0.4385	10	0.45353	T	0.12	.	18.3404	0.90303	0.0:1.0:0.0:0.0	.	312;353;394	A6NNA4;O95460-4;O95460-2	.;.;.	H	245;435;394;312;353;394;394;435;245	ENSP00000361839:R245H;ENSP00000361840:R435H;ENSP00000361842:R394H;ENSP00000243983:R312H;ENSP00000353819:R353H;ENSP00000343164:R394H;ENSP00000440328:R394H;ENSP00000361837:R245H	ENSP00000255132:R435H	R	-	2	0	MATN4	43360469	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.912000	0.63335	2.562000	0.86427	0.650000	0.86243	CGC	MATN4	-	pfam_VWF_A,smart_VWF_A,pfscan_VWF_A	ENSG00000124159		0.652	MATN4-002	KNOWN	non_canonical_conserved|non_canonical_U12|not_organism_supported|basic|appris_candidate_longest	protein_coding	MATN4	HGNC	protein_coding	OTTHUMT00000080335.1	15	0.00	0	C			43927055	43927055	-1	no_errors	ENST00000372754	ensembl	human	known	69_37n	missense	10	33.33	5	SNP	1.000	T
MUC5B	727897	genome.wustl.edu	37	11	1251822	1251822	+	Frame_Shift_Del	DEL	G	G	-			TCGA-E2-A1BD-01A-11D-A12Q-09	TCGA-E2-A1BD-10A-01D-A12Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f5ac1986-272b-48d2-9a73-4a550e38a997	dcd144ae-c12f-492f-b5b4-3dd4626e27a4	g.chr11:1251822delG	ENST00000529681.1	+	12	1520	c.1462delG	c.(1462-1464)gggfs	p.G488fs	MUC5B_ENST00000447027.1_Frame_Shift_Del_p.G491fs	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	488	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		CCTGGACGGCGGGGACACGGT	0.672																																						dbGAP											0													31.0	39.0	36.0					11																	1251822		2124	4223	6347	-	-	-	SO:0001589	frameshift_variant	0			U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"""Mucins"""	7516	protein-coding gene	gene with protein product		600770	"""mucin 5, subtype B, tracheobronchial"""	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.1462delG	11.37:g.1251822delG	ENSP00000436812:p.Gly488fs	Somatic		WXS	Illumina GAIIx	Phase_IV	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Frame_Shift_Del	DEL	pfam_VWF_type-D,pfam_Unchr_dom_Cys-rich,pfam_TIL_dom,pfam_VWF_C,superfamily_TIL_dom,smart_VWF_type-D,smart_Unchr_dom_Cys-rich,smart_VWC_out,smart_VWF_C,smart_Cys_knot_C,pfscan_Cys_knot_C,pfscan_VWF_C	p.D492fs	ENST00000529681.1	37	c.1471	CCDS44515.2	11																																																																																			MUC5B	-	pfam_VWF_type-D,smart_VWF_type-D	ENSG00000117983		0.672	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	MUC5B	HGNC	protein_coding	OTTHUMT00000390041.2	49	0.00	0	G	XM_001126093		1251822	1251822	+1	no_errors	ENST00000447027	ensembl	human	known	69_37n	frame_shift_del	9	18.18	2	DEL	0.618	-
PCM1	5108	genome.wustl.edu	37	8	17838141	17838141	+	Missense_Mutation	SNP	A	A	C			TCGA-E2-A1BD-01A-11D-A12Q-09	TCGA-E2-A1BD-10A-01D-A12Q-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f5ac1986-272b-48d2-9a73-4a550e38a997	dcd144ae-c12f-492f-b5b4-3dd4626e27a4	g.chr8:17838141A>C	ENST00000519253.1	+	24	4236	c.3985A>C	c.(3985-3987)Aaa>Caa	p.K1329Q	PCM1_ENST00000327578.8_Missense_Mutation_p.K9Q|PCM1_ENST00000325083.8_Missense_Mutation_p.K1329Q|PCM1_ENST00000524226.1_Intron			Q15154	PCM1_HUMAN	pericentriolar material 1	1329	Interaction with HAP1.				centrosome organization (GO:0051297)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|interkinetic nuclear migration (GO:0022027)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|microtubule anchoring (GO:0034453)|microtubule anchoring at centrosome (GO:0034454)|mitotic cell cycle (GO:0000278)|negative regulation of neurogenesis (GO:0050768)|neuronal stem cell maintenance (GO:0097150)|positive regulation of intracellular protein transport (GO:0090316)|protein localization to centrosome (GO:0071539)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|pericentriolar material (GO:0000242)|protein complex (GO:0043234)	identical protein binding (GO:0042802)		PCM1/JAK2(30)	breast(4)|endometrium(8)|kidney(5)|large_intestine(16)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	48				Colorectal(111;0.0789)		TGAACCTTGCAAAAGTAGGAA	0.368			T	"""RET, JAK2"""	"""papillary thyroid, CML, MPD"""																																	dbGAP		Dom	yes		8	8p22-p21.3	5108	pericentriolar material 1  (PTC4)		"""E, L"""	0													111.0	105.0	107.0					8																	17838141		1850	4102	5952	-	-	-	SO:0001583	missense	0				CCDS47812.1	8p22-p21.3	2008-08-08			ENSG00000078674	ENSG00000078674			8727	protein-coding gene	gene with protein product		600299				8120099, 15659651	Standard	NM_006197		Approved	PTC4	uc003wyi.4	Q15154	OTTHUMG00000163699	ENST00000519253.1:c.3985A>C	8.37:g.17838141A>C	ENSP00000431099:p.Lys1329Gln	Somatic		WXS	Illumina GAIIx	Phase_IV	Q58F13|Q6P1K7|Q8NB85|Q9BWC1|Q9H4A2	Missense_Mutation	SNP	NULL	p.K1329Q	ENST00000519253.1	37	c.3985		8	.	.	.	.	.	.	.	.	.	.	A	12.19	1.862930	0.32884	.	.	ENSG00000078674	ENST00000325083;ENST00000519253;ENST00000327578	T;T;T	0.21361	3.56;3.56;2.01	5.42	5.42	0.78866	.	0.270936	0.45126	D	0.000388	T	0.12263	0.0298	N	0.12182	0.205	0.33246	D	0.557939	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.12156	0.007;0.007;0.007	T	0.14448	-1.0472	10	0.26408	T	0.33	-29.5198	11.7357	0.51763	0.8528:0.1472:0.0:0.0	.	1329;1329;1329	D3DSQ0;E7ETA6;Q15154	.;.;PCM1_HUMAN	Q	1329;1329;9	ENSP00000327077:K1329Q;ENSP00000431099:K1329Q;ENSP00000328332:K9Q	ENSP00000327077:K1329Q	K	+	1	0	PCM1	17882421	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.413000	0.52686	2.197000	0.70478	0.528000	0.53228	AAA	PCM1	-	NULL	ENSG00000078674		0.368	PCM1-003	NOVEL	basic|exp_conf	protein_coding	PCM1	HGNC	protein_coding	OTTHUMT00000374800.1	232	0.00	0	A	NM_006197		17838141	17838141	+1	no_errors	ENST00000325083	ensembl	human	known	69_37n	missense	114	13.64	18	SNP	1.000	C
PIK3CA	5290	genome.wustl.edu	37	3	178952085	178952085	+	Missense_Mutation	SNP	A	A	G	rs121913279		TCGA-E2-A1BD-01A-11D-A12Q-09	TCGA-E2-A1BD-10A-01D-A12Q-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f5ac1986-272b-48d2-9a73-4a550e38a997	dcd144ae-c12f-492f-b5b4-3dd4626e27a4	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	197	0.00	0	A			178952085	178952085	+1	no_errors	ENST00000263967	ensembl	human	known	69_37n	missense	42	58.82	60	SNP	1.000	G
PLCB1	23236	genome.wustl.edu	37	20	8721040	8721040	+	Silent	SNP	G	G	T			TCGA-E2-A1BD-01A-11D-A12Q-09	TCGA-E2-A1BD-10A-01D-A12Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f5ac1986-272b-48d2-9a73-4a550e38a997	dcd144ae-c12f-492f-b5b4-3dd4626e27a4	g.chr20:8721040G>T	ENST00000338037.6	+	22	2385	c.2358G>T	c.(2356-2358)ctG>ctT	p.L786L	PLCB1_ENST00000378641.3_Silent_p.L786L|PLCB1_ENST00000494924.1_3'UTR|PLCB1_ENST00000378637.2_Silent_p.L786L	NM_015192.2	NP_056007.1	Q9NQ66	PLCB1_HUMAN	phospholipase C, beta 1 (phosphoinositide-specific)	786					activation of meiosis involved in egg activation (GO:0060466)|cerebral cortex development (GO:0021987)|fat cell differentiation (GO:0045444)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G2/M transition of mitotic cell cycle (GO:0000086)|glutamate receptor signaling pathway (GO:0007215)|inositol phosphate metabolic process (GO:0043647)|insulin-like growth factor receptor signaling pathway (GO:0048009)|interleukin-1-mediated signaling pathway (GO:0070498)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-15-mediated signaling pathway (GO:0035723)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|memory (GO:0007613)|negative regulation of monocyte extravasation (GO:2000438)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphatidylinositol metabolic process (GO:0046488)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of CD24 biosynthetic process (GO:2000560)|positive regulation of developmental growth (GO:0048639)|positive regulation of embryonic development (GO:0040019)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of GTPase activity (GO:0043547)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of JNK cascade (GO:0046330)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fertilization (GO:0080154)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|phosphatidylinositol phospholipase C activity (GO:0004435)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein homodimerization activity (GO:0042803)|signal transducer activity (GO:0004871)			NS(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(11)|liver(2)|lung(41)|ovary(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	95						CTCTGACGCTGCCTGCTGTCT	0.408																																						dbGAP											0													117.0	110.0	112.0					20																	8721040		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AB011153	CCDS13102.1, CCDS13103.1	20p12	2008-03-18			ENSG00000182621	ENSG00000182621	3.1.4.11		15917	protein-coding gene	gene with protein product		607120				10760467, 11118617	Standard	NM_015192		Approved	KIAA0581, PLC-I, PLC154	uc002wnb.4	Q9NQ66	OTTHUMG00000031849	ENST00000338037.6:c.2358G>T	20.37:g.8721040G>T		Somatic		WXS	Illumina GAIIx	Phase_IV	D3DW12|D3DW13|O60325|Q17RQ6|Q5TFF7|Q5TGC9|Q8IV93|Q9BQW2|Q9H4H2|Q9H8H5|Q9NQ65|Q9NQH9|Q9NTH4|Q9UJP6|Q9UM26	Missense_Mutation	SNP	pfam_PLipase_C_PInositol-sp_X_dom,pfam_PLC-beta_C,pfam_PLipase_C_Pinositol-sp_Y,pfam_PLipase_C_EF-hand-like,pfam_PLC-beta_CS,superfamily_PLC-like_Pdiesterase_TIM-brl,superfamily_C2_Ca/lipid-bd_dom_CaLB,smart_PLipase_C_PInositol-sp_X_dom,smart_PLipase_C_Pinositol-sp_Y,smart_C2_Ca-dep,pfscan_C2_membr_targeting,pfscan_PLipase_C_PInositol-sp_X_dom,pfscan_PLipase_C_Pinositol-sp_Y,prints_Pinositol_PLipase_C	p.C527F	ENST00000338037.6	37	c.1580	CCDS13102.1	20																																																																																			PLCB1	-	superfamily_C2_Ca/lipid-bd_dom_CaLB	ENSG00000182621		0.408	PLCB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	PLCB1	HGNC	protein_coding	OTTHUMT00000077938.3	228	0.44	1	G			8721040	8721040	+1	no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region	ENST00000487210	ensembl	human	known	69_37n	missense	61	47.86	56	SNP	0.144	T
RERGL	79785	genome.wustl.edu	37	12	18234200	18234200	+	Missense_Mutation	SNP	C	C	G			TCGA-E2-A1BD-01A-11D-A12Q-09	TCGA-E2-A1BD-10A-01D-A12Q-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f5ac1986-272b-48d2-9a73-4a550e38a997	dcd144ae-c12f-492f-b5b4-3dd4626e27a4	g.chr12:18234200C>G	ENST00000229002.2	-	6	749	c.543G>C	c.(541-543)aaG>aaC	p.K181N	RERGL_ENST00000541632.1_5'Flank|RERGL_ENST00000538724.1_Missense_Mutation_p.K180N	NM_024730.2	NP_079006.1	Q9H628	RERGL_HUMAN	RERG/RAS-like	181	Small GTPase-like.				GTP catabolic process (GO:0006184)|small GTPase mediated signal transduction (GO:0007264)	membrane (GO:0016020)	GTP binding (GO:0005525)			endometrium(1)|large_intestine(5)|lung(8)|prostate(1)|skin(1)|urinary_tract(1)	17						TGGGACGTCTCTTTTCTTTGA	0.383																																						dbGAP											0													125.0	119.0	121.0					12																	18234200		2203	4300	6503	-	-	-	SO:0001583	missense	0			AK026308	CCDS8679.1, CCDS66332.1	12p12.3	2014-08-12			ENSG00000111404	ENSG00000111404			26213	protein-coding gene	gene with protein product						24127187	Standard	NM_001286201		Approved	FLJ22655	uc001rdq.3	Q9H628	OTTHUMG00000168820	ENST00000229002.2:c.543G>C	12.37:g.18234200C>G	ENSP00000229002:p.Lys181Asn	Somatic		WXS	Illumina GAIIx	Phase_IV		Missense_Mutation	SNP	pfam_Small_GTPase,pfam_MIRO-like,smart_Small_GTPase_Ras,smart_Small_GTPase_Rab_type	p.K181N	ENST00000229002.2	37	c.543	CCDS8679.1	12	.	.	.	.	.	.	.	.	.	.	C	13.00	2.106820	0.37145	.	.	ENSG00000111404	ENST00000229002;ENST00000538724	T;T	0.80123	-1.34;-1.34	5.0	3.16	0.36331	.	0.386692	0.25205	N	0.032359	T	0.65544	0.2701	N	0.14661	0.345	0.80722	D	1	B;P	0.43094	0.027;0.799	B;B	0.40901	0.037;0.343	T	0.64470	-0.6400	10	0.52906	T	0.07	.	9.4782	0.38884	0.0:0.8353:0.0:0.1647	.	180;181	F5H686;Q9H628	.;RERGL_HUMAN	N	181;180	ENSP00000229002:K181N;ENSP00000437814:K180N	ENSP00000229002:K181N	K	-	3	2	RERGL	18125467	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	0.838000	0.27572	0.604000	0.29930	0.557000	0.71058	AAG	RERGL	-	NULL	ENSG00000111404		0.383	RERGL-001	KNOWN	basic|CCDS	protein_coding	RERGL	HGNC	protein_coding	OTTHUMT00000401198.1	302	0.00	0	C	NM_024730		18234200	18234200	-1	no_errors	ENST00000229002	ensembl	human	known	69_37n	missense	124	18.42	28	SNP	1.000	G
RIMBP2	23504	genome.wustl.edu	37	12	130935809	130935809	+	Silent	SNP	C	C	T			TCGA-E2-A1BD-01A-11D-A12Q-09	TCGA-E2-A1BD-10A-01D-A12Q-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f5ac1986-272b-48d2-9a73-4a550e38a997	dcd144ae-c12f-492f-b5b4-3dd4626e27a4	g.chr12:130935809C>T	ENST00000261655.4	-	5	547	c.384G>A	c.(382-384)ccG>ccA	p.P128P	RIMBP2_ENST00000535703.1_Silent_p.P36P|RIMBP2_ENST00000536002.1_Silent_p.P36P	NM_015347.4	NP_056162.4	O15034	RIMB2_HUMAN	RIMS binding protein 2	128					negative regulation of phosphatase activity (GO:0010923)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|synapse (GO:0045202)				NS(2)|breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(33)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	96	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)		ACAGAGGCTCCGGCCTGTCAC	0.617																																						dbGAP											0													55.0	54.0	54.0					12																	130935809		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AB002316	CCDS31925.1	12q24.33	2014-06-13				ENSG00000060709			30339	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 133"""	611602				10748113	Standard	NM_015347		Approved	KIAA0318, RBP2, MGC15831, RIM-BP2, PPP1R133	uc001uil.2	O15034		ENST00000261655.4:c.384G>A	12.37:g.130935809C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	Q96ID2	Silent	SNP	pfam_SH3_2,pfam_SH3_domain,superfamily_SH3_domain,superfamily_Fibronectin_type3,smart_SH3_domain,smart_Fibronectin_type3,pfscan_Fibronectin_type3,pfscan_SH3_domain,prints_SH3_domain	p.P128	ENST00000261655.4	37	c.384	CCDS31925.1	12																																																																																			RIMBP2	-	NULL	ENSG00000060709		0.617	RIMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RIMBP2	HGNC	protein_coding	OTTHUMT00000399520.1	62	0.00	0	C	NM_015347		130935809	130935809	-1	no_errors	ENST00000261655	ensembl	human	known	69_37n	silent	21	32.26	10	SNP	0.437	T
RNASEL	6041	genome.wustl.edu	37	1	182554944	182554944	+	Missense_Mutation	SNP	G	G	T			TCGA-E2-A1BD-01A-11D-A12Q-09	TCGA-E2-A1BD-10A-01D-A12Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f5ac1986-272b-48d2-9a73-4a550e38a997	dcd144ae-c12f-492f-b5b4-3dd4626e27a4	g.chr1:182554944G>T	ENST00000367559.3	-	2	1251	c.998C>A	c.(997-999)gCt>gAt	p.A333D	RNASEL_ENST00000539397.1_Missense_Mutation_p.A333D|RNASEL_ENST00000444138.1_Missense_Mutation_p.A333D	NM_021133.3	NP_066956.1	Q05823	RN5A_HUMAN	ribonuclease L (2',5'-oligoisoadenylate synthetase-dependent)	333					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|mRNA processing (GO:0006397)|negative regulation of viral genome replication (GO:0045071)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|rRNA processing (GO:0006364)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nuclear matrix (GO:0016363)	ATP binding (GO:0005524)|endoribonuclease activity (GO:0004521)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|RNA binding (GO:0003723)|rRNA binding (GO:0019843)			NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(9)|ovary(4)|prostate(1)|stomach(1)|urinary_tract(1)	27						CCAGTCTTCAGCAGGAGGGTG	0.483																																						dbGAP											0													47.0	50.0	49.0					1																	182554944		2203	4300	6503	-	-	-	SO:0001583	missense	0			L10381	CCDS1347.1	1q25	2013-01-10			ENSG00000135828	ENSG00000135828	3.1.26.-	"""Ankyrin repeat domain containing"""	10050	protein-coding gene	gene with protein product		180435	"""prostate cancer 1"""	RNS4, PRCA1		7514564	Standard	NM_021133		Approved		uc009wxz.2	Q05823	OTTHUMG00000035213	ENST00000367559.3:c.998C>A	1.37:g.182554944G>T	ENSP00000356530:p.Ala333Asp	Somatic		WXS	Illumina GAIIx	Phase_IV	Q5W0L2|Q6AI46	Missense_Mutation	SNP	pfam_Ankyrin_rpt,pfam_KEN_RNase_activator,pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_LipoPS_kinase,superfamily_Ankyrin_rpt-contain_dom,superfamily_Kinase-like_dom,smart_Ankyrin_rpt,smart_Ser/Thr_dual-sp_kinase_dom,smart_PUG-dom,prints_Ankyrin_rpt,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom,pfscan_Prot_kinase_cat_dom	p.A333D	ENST00000367559.3	37	c.998	CCDS1347.1	1	.	.	.	.	.	.	.	.	.	.	G	5.391	0.257385	0.10239	.	.	ENSG00000135828	ENST00000367559;ENST00000444138;ENST00000539397	T;T;T	0.32753	1.44;1.44;1.46	5.8	2.61	0.31194	.	0.711434	0.13524	N	0.381443	T	0.24392	0.0591	L	0.56769	1.78	0.09310	N	1	B;B;B	0.12630	0.006;0.001;0.006	B;B;B	0.11329	0.006;0.001;0.006	T	0.26018	-1.0115	10	0.11794	T	0.64	-3.0218	6.0858	0.19966	0.1463:0.0:0.5371:0.3166	.	333;333;333	Q5W0L2;Q6AI46;Q05823	.;.;RN5A_HUMAN	D	333	ENSP00000356530:A333D;ENSP00000411147:A333D;ENSP00000440844:A333D	ENSP00000356530:A333D	A	-	2	0	RNASEL	180821567	0.000000	0.05858	0.002000	0.10522	0.106000	0.19336	-0.237000	0.08990	1.450000	0.47717	0.650000	0.86243	GCT	RNASEL	-	NULL	ENSG00000135828		0.483	RNASEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RNASEL	HGNC	protein_coding	OTTHUMT00000085189.1	50	0.00	0	G	NM_021133		182554944	182554944	-1	no_errors	ENST00000367559	ensembl	human	known	69_37n	missense	63	14.86	11	SNP	0.000	T
RNF41	10193	genome.wustl.edu	37	12	56601499	56601499	+	Missense_Mutation	SNP	C	C	T			TCGA-E2-A1BD-01A-11D-A12Q-09	TCGA-E2-A1BD-10A-01D-A12Q-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f5ac1986-272b-48d2-9a73-4a550e38a997	dcd144ae-c12f-492f-b5b4-3dd4626e27a4	g.chr12:56601499C>T	ENST00000345093.4	-	6	902	c.533G>A	c.(532-534)cGt>cAt	p.R178H	RNF41_ENST00000394013.2_Missense_Mutation_p.R107H|RNF41_ENST00000552244.1_Missense_Mutation_p.R178H|RNF41_ENST00000552656.1_Missense_Mutation_p.R178H	NM_005785.3|NM_194359.2	NP_005776.1|NP_919340.1	Q9H4P4	RNF41_HUMAN	ring finger protein 41, E3 ubiquitin protein ligase	178					extrinsic apoptotic signaling pathway (GO:0097191)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|proteasomal protein catabolic process (GO:0010498)|protein autoubiquitination (GO:0051865)|protein polyubiquitination (GO:0000209)|regulation of establishment of cell polarity (GO:2000114)|regulation of lymphocyte differentiation (GO:0045619)|regulation of MAPK cascade (GO:0043408)|regulation of myeloid cell differentiation (GO:0045637)|regulation of protein kinase B signaling (GO:0051896)|regulation of reactive oxygen species metabolic process (GO:2000377)	cytosol (GO:0005829)	acid-amino acid ligase activity (GO:0016881)|protein tag (GO:0031386)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|large_intestine(2)|lung(1)|skin(2)|urinary_tract(1)	11						GCGGATTGCACGCATGTATGC	0.458																																						dbGAP											0													307.0	257.0	274.0					12																	56601499		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF077599	CCDS8909.1, CCDS8910.1	12q13.13	2014-03-24	2014-03-24		ENSG00000181852	ENSG00000181852		"""RING-type (C3HC4) zinc fingers"""	18401	protein-coding gene	gene with protein product			"""ring finger protein 41"""				Standard	NM_005785		Approved	SBBI03, NRDP1	uc001skg.2	Q9H4P4	OTTHUMG00000170328	ENST00000345093.4:c.533G>A	12.37:g.56601499C>T	ENSP00000342755:p.Arg178His	Somatic		WXS	Illumina GAIIx	Phase_IV	A6NFW0|B2RBT8|O75598	Missense_Mutation	SNP	pfam_USP8_interacting,pfam_Znf_C3HC4_RING-type,pfam_Ubox_domain,superfamily_TRAF-like,smart_Znf_RING,pfscan_Znf_RING,pfscan_Znf_SIAH	p.R178H	ENST00000345093.4	37	c.533	CCDS8909.1	12	.	.	.	.	.	.	.	.	.	.	C	24.1	4.492177	0.84962	.	.	ENSG00000181852	ENST00000345093;ENST00000394013;ENST00000448057;ENST00000552656;ENST00000551711;ENST00000552244;ENST00000549038	T;T;T;T	0.09817	3.0;3.0;2.96;2.94	5.85	5.85	0.93711	USP8 interacting (1);	0.000000	0.85682	D	0.000000	T	0.16769	0.0403	M	0.62723	1.935	0.80722	D	1	P;B	0.40083	0.702;0.432	B;B	0.37422	0.249;0.2	T	0.00510	-1.1697	10	0.62326	D	0.03	.	19.3176	0.94223	0.0:1.0:0.0:0.0	.	165;178	B4E353;Q9H4P4	.;RNF41_HUMAN	H	178;107;165;178;107;178;178	ENSP00000342755:R178H;ENSP00000447303:R178H;ENSP00000448187:R178H;ENSP00000446595:R178H	ENSP00000342755:R178H	R	-	2	0	RNF41	54887766	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.037000	0.70956	2.941000	0.99782	0.655000	0.94253	CGT	RNF41	-	pfam_USP8_interacting	ENSG00000181852		0.458	RNF41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RNF41	HGNC	protein_coding	OTTHUMT00000408525.1	403	0.00	0	C	NM_005785		56601499	56601499	-1	no_errors	ENST00000345093	ensembl	human	known	69_37n	missense	133	41.67	95	SNP	1.000	T
SLC45A1	50651	genome.wustl.edu	37	1	8385359	8385359	+	Splice_Site	SNP	A	A	G			TCGA-E2-A1BD-01A-11D-A12Q-09	TCGA-E2-A1BD-10A-01D-A12Q-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f5ac1986-272b-48d2-9a73-4a550e38a997	dcd144ae-c12f-492f-b5b4-3dd4626e27a4	g.chr1:8385359A>G	ENST00000471889.1	+	3	784	c.399A>G	c.(397-399)ggA>ggG	p.G133G	SLC45A1_ENST00000377479.2_Splice_Site_p.G167G|Y_RNA_ENST00000516445.1_RNA|SLC45A1_ENST00000289877.8_Splice_Site_p.G133G			Q9Y2W3	S45A1_HUMAN	solute carrier family 45, member 1	133					carbohydrate transport (GO:0008643)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|liver(1)|lung(12)|ovary(2)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(2)	33	Ovarian(185;0.0661)|all_lung(157;0.127)	all_epithelial(116;1.22e-15)|all_lung(118;0.000147)|Lung NSC(185;0.000251)|Renal(390;0.000469)|Colorectal(325;0.00578)|Breast(348;0.00686)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.11)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;3.95e-66)|GBM - Glioblastoma multiforme(8;5.93e-33)|Colorectal(212;2.86e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|Kidney(185;5.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000513)|KIRC - Kidney renal clear cell carcinoma(229;0.000979)|STAD - Stomach adenocarcinoma(132;0.00199)|READ - Rectum adenocarcinoma(331;0.0649)		CTGTTTCAGGATTCCTACTGC	0.547																																						dbGAP											0													141.0	123.0	129.0					1																	8385359		2203	4300	6503	-	-	-	SO:0001630	splice_region_variant	0			AF118274	CCDS30577.1	1p36.23	2014-01-28	2005-10-04	2005-10-04	ENSG00000162426	ENSG00000162426		"""Solute carriers"""	17939	protein-coding gene	gene with protein product	"""H+/sugar symporter"""	605763	"""deleted in neuroblastoma 5"""	DNB5		10729226	Standard	XM_005263467		Approved		uc001apb.3	Q9Y2W3	OTTHUMG00000000503	ENST00000471889.1:c.398-1A>G	1.37:g.8385359A>G		Somatic		WXS	Illumina GAIIx	Phase_IV	Q5VY46|Q5VY49	Silent	SNP	pfam_MFS,superfamily_MFS_dom_general_subst_transpt	p.G167	ENST00000471889.1	37	c.501	CCDS30577.1	1																																																																																			SLC45A1	-	pfam_MFS,superfamily_MFS_dom_general_subst_transpt	ENSG00000162426		0.547	SLC45A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SLC45A1	HGNC	protein_coding	OTTHUMT00000001245.5	292	0.34	1	A		Silent	8385359	8385359	+1	no_errors	ENST00000377479	ensembl	human	known	69_37n	silent	179	21.83	50	SNP	0.994	G
SYTL5	94122	genome.wustl.edu	37	X	37893157	37893157	+	Silent	SNP	A	A	T			TCGA-E2-A1BD-01A-11D-A12Q-09	TCGA-E2-A1BD-10A-01D-A12Q-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f5ac1986-272b-48d2-9a73-4a550e38a997	dcd144ae-c12f-492f-b5b4-3dd4626e27a4	g.chrX:37893157A>T	ENST00000357972.5	+	2	561	c.15A>T	c.(13-15)tcA>tcT	p.S5S	SYTL5_ENST00000456733.2_Silent_p.S5S|SYTL5_ENST00000297875.2_Silent_p.S5S|TM4SF2_ENST00000465127.1_Intron			Q8TDW5	SYTL5_HUMAN	synaptotagmin-like 5	5					exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)	membrane (GO:0016020)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(23)|prostate(1)|skin(2)|urinary_tract(1)	44						CTAAGAACTCAGAGTTCATCA	0.383																																						dbGAP											0													80.0	70.0	74.0					X																	37893157		2202	4300	6502	-	-	-	SO:0001819	synonymous_variant	0				CCDS14244.1, CCDS55399.1	Xp21.1	2008-02-05			ENSG00000147041	ENSG00000147041			15589	protein-coding gene	gene with protein product	"""exophilin 9"""						Standard	NM_138780		Approved		uc004ddx.3	Q8TDW5	OTTHUMG00000033176	ENST00000357972.5:c.15A>T	X.37:g.37893157A>T		Somatic		WXS	Illumina GAIIx	Phase_IV	A2RRF2	Silent	SNP	pfam_C2_Ca-dep,superfamily_C2_Ca/lipid-bd_dom_CaLB,superfamily_Znf_FYVE_PHD,smart_C2_Ca-dep,pfscan_C2_membr_targeting,pfscan_Rab-bd_domain	p.S5	ENST00000357972.5	37	c.15	CCDS14244.1	X																																																																																			SYTL5	-	NULL	ENSG00000147041		0.383	SYTL5-201	KNOWN	basic|CCDS	protein_coding	SYTL5	HGNC	protein_coding	OTTHUMT00000080883.1	259	0.00	0	A	NM_138780		37893157	37893157	+1	no_errors	ENST00000456733	ensembl	human	known	69_37n	silent	75	40.94	52	SNP	0.004	T
UBE3B	89910	genome.wustl.edu	37	12	109948241	109948241	+	Missense_Mutation	SNP	C	C	G			TCGA-E2-A1BD-01A-11D-A12Q-09	TCGA-E2-A1BD-10A-01D-A12Q-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f5ac1986-272b-48d2-9a73-4a550e38a997	dcd144ae-c12f-492f-b5b4-3dd4626e27a4	g.chr12:109948241C>G	ENST00000342494.3	+	17	2429	c.1834C>G	c.(1834-1836)Ccc>Gcc	p.P612A	UBE3B_ENST00000434735.2_Missense_Mutation_p.P612A|UBE3B_ENST00000280774.5_Missense_Mutation_p.P612A|UBE3B_ENST00000535900.1_3'UTR	NM_130466.3	NP_569733.2	Q7Z3V4	UBE3B_HUMAN	ubiquitin protein ligase E3B	612					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(3)|endometrium(6)|kidney(4)|large_intestine(7)|lung(20)|ovary(2)|urinary_tract(2)	45						GCGCTTCACCCCCGAGGACCA	0.642																																						dbGAP											0													32.0	29.0	30.0					12																	109948241		2203	4300	6503	-	-	-	SO:0001583	missense	0			BC032301	CCDS9129.1, CCDS58277.1	12q24.12	2004-03-02			ENSG00000151148	ENSG00000151148			13478	protein-coding gene	gene with protein product		608047					Standard	NM_130466		Approved		uc001toq.4	Q7Z3V4	OTTHUMG00000169254	ENST00000342494.3:c.1834C>G	12.37:g.109948241C>G	ENSP00000340596:p.Pro612Ala	Somatic		WXS	Illumina GAIIx	Phase_IV	A5D8Z3|Q05BX9|Q659F7|Q7Z7Q1|Q9BXZ4	Missense_Mutation	SNP	pfam_HECT,pfam_IQ_motif_EF-hand-BS,superfamily_HECT,smart_IQ_motif_EF-hand-BS,smart_HECT,pfscan_HECT,pfscan_IQ_motif_EF-hand-BS	p.P612A	ENST00000342494.3	37	c.1834	CCDS9129.1	12	.	.	.	.	.	.	.	.	.	.	C	29.1	4.973118	0.92919	.	.	ENSG00000151148	ENST00000434735;ENST00000280774;ENST00000539599;ENST00000342494;ENST00000539584	T;T;T;T	0.59364	0.99;0.27;1.07;0.99	5.09	5.09	0.68999	.	0.000000	0.85682	D	0.000000	T	0.71082	0.3298	M	0.66378	2.025	0.80722	D	1	D	0.69078	0.997	P	0.58210	0.835	T	0.75158	-0.3416	10	0.72032	D	0.01	-11.3364	17.4677	0.87638	0.0:1.0:0.0:0.0	.	612	Q7Z3V4	UBE3B_HUMAN	A	612;612;612;612;39	ENSP00000391529:P612A;ENSP00000280774:P612A;ENSP00000443131:P612A;ENSP00000340596:P612A	ENSP00000280774:P612A	P	+	1	0	UBE3B	108432624	1.000000	0.71417	0.995000	0.50966	0.983000	0.72400	7.440000	0.80464	2.370000	0.80446	0.462000	0.41574	CCC	UBE3B	-	NULL	ENSG00000151148		0.642	UBE3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	UBE3B	HGNC	protein_coding	OTTHUMT00000403119.1	60	0.00	0	C	NM_183415		109948241	109948241	+1	no_errors	ENST00000342494	ensembl	human	known	69_37n	missense	15	50.00	15	SNP	1.000	G
ZNF250	58500	genome.wustl.edu	37	8	146107918	146107918	+	Missense_Mutation	SNP	G	G	T			TCGA-E2-A1BD-01A-11D-A12Q-09	TCGA-E2-A1BD-10A-01D-A12Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	f5ac1986-272b-48d2-9a73-4a550e38a997	dcd144ae-c12f-492f-b5b4-3dd4626e27a4	g.chr8:146107918G>T	ENST00000292579.7	-	6	781	c.665C>A	c.(664-666)aCt>aAt	p.T222N	ZNF250_ENST00000342660.6_Intron|ZNF250_ENST00000543949.1_Intron|ZNF250_ENST00000417550.2_Missense_Mutation_p.T217N	NM_001109689.3|NM_021061.4	NP_001103159.1|NP_066405.1	P15622	ZN250_HUMAN	zinc finger protein 250	222					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(2)|lung(8)|skin(1)	15	all_cancers(97;8.72e-12)|all_epithelial(106;1.07e-10)|Lung NSC(106;7.18e-05)|all_lung(105;0.00021)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Epithelial(56;2.53e-38)|OV - Ovarian serous cystadenocarcinoma(54;4.07e-38)|all cancers(56;2.27e-33)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;0.0654)		CTTCTCTCCAGTGTGGATACG	0.537																																					NSCLC(16;520 556 24096 40084 43446)	dbGAP											0													89.0	77.0	81.0					8																	146107918		2203	4300	6503	-	-	-	SO:0001583	missense	0			AK095705	CCDS34972.1, CCDS55282.1	8q24.3	2013-01-08	2004-11-08			ENSG00000196150		"""Zinc fingers, C2H2-type"", ""-"""	13044	protein-coding gene	gene with protein product			"""zinc finger protein 647"""	ZNF647		12477932	Standard	NM_021061		Approved	MGC9718, ZFP647	uc003zer.4	P15622		ENST00000292579.7:c.665C>A	8.37:g.146107918G>T	ENSP00000292579:p.Thr222Asn	Somatic		WXS	Illumina GAIIx	Phase_IV	D3DWP1|Q59HE9|Q8N942|Q96AH9	Missense_Mutation	SNP	pfam_Znf_C2H2,pfam_Krueppel-associated_box,superfamily_Krueppel-associated_box,smart_Krueppel-associated_box,smart_Znf_C2H2-like,pfscan_Znf_C2H2,pfscan_Krueppel-associated_box	p.T222N	ENST00000292579.7	37	c.665	CCDS34972.1	8	.	.	.	.	.	.	.	.	.	.	G	16.61	3.170535	0.57584	.	.	ENSG00000196150	ENST00000292579;ENST00000417550;ENST00000394912	T;T	0.26067	1.76;1.76	3.94	3.94	0.45596	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.50627	D	0.000111	T	0.46171	0.1379	L	0.56340	1.77	0.80722	D	1	D;D	0.76494	0.991;0.999	D;D	0.87578	0.987;0.998	T	0.45644	-0.9247	10	0.62326	D	0.03	-22.5582	15.944	0.79779	0.0:0.0:1.0:0.0	.	217;222	D3DWP1;P15622	.;ZN250_HUMAN	N	222;217;217	ENSP00000292579:T222N;ENSP00000393442:T217N	ENSP00000292579:T222N	T	-	2	0	ZNF250	146078722	0.997000	0.39634	0.986000	0.45419	0.690000	0.40134	2.450000	0.44943	2.511000	0.84671	0.313000	0.20887	ACT	ZNF250	-	pfscan_Znf_C2H2	ENSG00000196150		0.537	ZNF250-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	ZNF250	HGNC	protein_coding	OTTHUMT00000382968.1	235	0.00	0	G	NM_021061		146107918	146107918	-1	no_errors	ENST00000292579	ensembl	human	known	69_37n	missense	125	22.84	37	SNP	0.999	T
