#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_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_annotation_transcript	i_build	i_ccds_id	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_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_type	i_havana_transcript	i_match_norm_validation_allele1	i_refseq_mrna_id	i_secondary_variant_classification
ABI2	10152	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	204281636	204281636	+	Missense_Mutation	SNP	G	G	T			TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr2:204281636G>T	ENST00000422511.2	+	10	1130	c.1099G>T	c.(1099-1101)Gat>Tat	p.D367Y	ABI2_ENST00000261018.7_Missense_Mutation_p.D186Y|ABI2_ENST00000430574.1_3'UTR|RAPH1_ENST00000457812.1_Intron|ABI2_ENST00000424558.1_Missense_Mutation_p.D394Y|ABI2_ENST00000261016.6_Missense_Mutation_p.D288Y|ABI2_ENST00000295851.5_Missense_Mutation_p.D400Y|ABI2_ENST00000261017.5_Missense_Mutation_p.D362Y|ABI2_ENST00000430418.1_Missense_Mutation_p.D345Y			Q9NYB9	ABI2_HUMAN	abl-interactor 2	400	Pro-rich.				actin polymerization or depolymerization (GO:0008154)|cell migration (GO:0016477)|cellular component movement (GO:0006928)|cytoskeleton organization (GO:0007010)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of Arp2/3 complex-mediated actin nucleation (GO:2000601)|Rac protein signal transduction (GO:0016601)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|SCAR complex (GO:0031209)	cytoskeletal adaptor activity (GO:0008093)|DNA binding (GO:0003677)|kinase binding (GO:0019900)|proline-rich region binding (GO:0070064)|protein complex binding (GO:0032403)|SH3 domain binding (GO:0017124)|ubiquitin protein ligase binding (GO:0031625)	p.D362Y(1)		breast(1)|kidney(3)|large_intestine(1)|liver(2)|lung(4)|prostate(2)|skin(1)|urinary_tract(1)	15						CTTAGTTTCAGATACACCACC	0.458																																																	1	Substitution - Missense(1)	kidney(1)											107.0	103.0	104.0					2																	204281636		2203	4300	6503	SO:0001583	missense	10152			AF260261	CCDS2358.1, CCDS63093.1, CCDS63094.1, CCDS74634.1	2q33	2010-09-20	2009-07-23		ENSG00000138443	ENSG00000138443			24011	protein-coding gene	gene with protein product		606442				7590236, 10964520	Standard	XM_005246217		Approved	ABI-2, AIP-1, ABI2B, AblBP3, argBPIA, SSH3BP2	uc002uzz.3	Q9NYB9	OTTHUMG00000132879	ENST00000422511.2:c.1099G>T	2.37:g.204281636G>T	ENSP00000396249:p.Asp367Tyr	Somatic		WXS	Illumina HiSeq	Phase_I	B4DSN1|Q13147|Q13249|Q13801|Q9BV70	Missense_Mutation	SNP	ENST00000422511.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	22.1|22.1	4.238968|4.238968	0.79800|0.79800	.|.	.|.	ENSG00000138443|ENSG00000138443	ENST00000295851;ENST00000261017;ENST00000430418;ENST00000424558;ENST00000261016;ENST00000417864;ENST00000422511;ENST00000261018|ENST00000454023	T;T;T;T;T;T;T;T|.	0.41400|.	1.12;1.04;1.32;1.13;1.01;1.27;1.12;1.0|.	6.03|6.03	6.03|6.03	0.97812|0.97812	.|.	0.333480|.	0.37761|.	N|.	0.001945|.	T|T	0.76212|0.76212	0.3956|0.3956	M|M	0.68317|0.68317	2.08|2.08	0.80722|0.80722	D|D	1|1	P;D;P;P;P;P;P;B|.	0.55385|.	0.897;0.971;0.823;0.925;0.799;0.946;0.877;0.313|.	P;P;P;P;B;P;P;B|.	0.56960|.	0.492;0.707;0.492;0.81;0.226;0.714;0.65;0.272|.	T|T	0.72394|0.72394	-0.4307|-0.4307	10|5	0.62326|.	D|.	0.03|.	-21.2947|-21.2947	20.5666|20.5666	0.99351|0.99351	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	264;125;277;394;345;288;400;362|.	B7Z612;B4DMM5;B7Z836;Q9NYB9-4;E9PEZ7;Q9NYB9-3;Q9NYB9;Q9NYB9-2|.	.;.;.;.;.;.;ABI2_HUMAN;.|.	Y|H	400;362;345;394;288;400;367;186|179	ENSP00000295851:D400Y;ENSP00000261017:D362Y;ENSP00000408898:D345Y;ENSP00000391433:D394Y;ENSP00000261016:D288Y;ENSP00000414703:D400Y;ENSP00000396249:D367Y;ENSP00000261018:D186Y|.	ENSP00000261016:D288Y|.	D|Q	+|+	1|3	0|2	ABI2|ABI2	203989881|203989881	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.964000|0.964000	0.63967|0.63967	7.366000|7.366000	0.79548|0.79548	2.854000|2.854000	0.98071|0.98071	0.655000|0.655000	0.94253|0.94253	GAT|CAG		0.458	ABI2-007	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000336179.2		NM_005759	
ARF1	375	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	228285075	228285075	+	Missense_Mutation	SNP	A	A	C			TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr1:228285075A>C	ENST00000541182.1	+	3	443	c.181A>C	c.(181-183)Atc>Ctc	p.I61L	ARF1_ENST00000540651.1_Missense_Mutation_p.I61L|ARF1_ENST00000272102.5_Missense_Mutation_p.I61L|MIR3620_ENST00000584469.1_RNA|ARF1_ENST00000478424.1_3'UTR	NM_001024227.1|NM_001024228.1	NP_001019398.1|NP_001019399.1	P84077	ARF1_HUMAN	ADP-ribosylation factor 1	61					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular copper ion homeostasis (GO:0006878)|COPI coating of Golgi vesicle (GO:0048205)|dendritic spine organization (GO:0097061)|GTP catabolic process (GO:0006184)|long term synaptic depression (GO:0060292)|membrane organization (GO:0061024)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)|regulation of Arp2/3 complex-mediated actin nucleation (GO:0034315)|regulation of defense response to virus by virus (GO:0050690)|regulation of receptor internalization (GO:0002090)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|receptor signaling protein activity (GO:0005057)	p.I61L(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(4)	10		Prostate(94;0.0405)				GTACAAGAACATCAGCTTCAC	0.627																																																	1	Substitution - Missense(1)	kidney(1)											94.0	91.0	92.0					1																	228285075		2203	4300	6503	SO:0001583	missense	375			M84326	CCDS1565.1	1q42.13	2014-01-30			ENSG00000143761	ENSG00000143761		"""ADP-ribosylation factors"", ""Endogenous ligands"""	652	protein-coding gene	gene with protein product		103180				1577740	Standard	NM_001658		Approved		uc001hrr.3	P84077	OTTHUMG00000037595	ENST00000541182.1:c.181A>C	1.37:g.228285075A>C	ENSP00000440005:p.Ile61Leu	Somatic		WXS	Illumina HiSeq	Phase_I	P10947|P32889	Missense_Mutation	SNP	ENST00000541182.1	37	CCDS1565.1	.	.	.	.	.	.	.	.	.	.	A	16.54	3.151767	0.57151	.	.	ENSG00000143761	ENST00000272102;ENST00000540651;ENST00000542941;ENST00000541182	T;T;T	0.61859	0.07;0.07;0.07	5.25	4.11	0.48088	Small GTP-binding protein domain (1);	0.000000	0.64402	D	0.000012	T	0.47673	0.1458	L	0.31845	0.965	0.80722	D	1	B	0.06786	0.001	B	0.20577	0.03	T	0.44772	-0.9306	10	0.62326	D	0.03	-23.2715	12.645	0.56729	0.8617:0.1383:0.0:0.0	.	61	P84077	ARF1_HUMAN	L	61	ENSP00000272102:I61L;ENSP00000442980:I61L;ENSP00000440005:I61L	ENSP00000272102:I61L	I	+	1	0	ARF1	226351698	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.228000	0.78079	1.093000	0.41377	0.482000	0.46254	ATC		0.627	ARF1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091650.1		NM_001024227	
CAB39	51719	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	231682474	231682474	+	Silent	SNP	C	C	T			TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr2:231682474C>T	ENST00000258418.5	+	8	1128	c.699C>T	c.(697-699)ctC>ctT	p.L233L	CAB39_ENST00000409788.3_Silent_p.L233L|CAB39_ENST00000410084.3_Silent_p.L233L	NM_016289.3	NP_057373.1	Q9Y376	CAB39_HUMAN	calcium binding protein 39	233					activation of protein kinase activity (GO:0032147)|cell cycle arrest (GO:0007050)|cellular hypotonic response (GO:0071476)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of rubidium ion transmembrane transporter activity (GO:2000687)|negative regulation of rubidium ion transport (GO:2000681)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|protein heterooligomerization (GO:0051291)|signal transduction by phosphorylation (GO:0023014)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	kinase binding (GO:0019900)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activator activity (GO:0043539)	p.L233L(1)		central_nervous_system(1)|large_intestine(1)|skin(1)	3		all_lung(227;4.63e-07)|all_hematologic(139;1.83e-06)|Lung NSC(271;2.11e-05)|Acute lymphoblastic leukemia(138;5.51e-05)|Hepatocellular(293;0.0207)|Lung SC(224;0.187)		all cancers(144;1.64e-12)|Epithelial(121;5.29e-11)|LUSC - Lung squamous cell carcinoma(224;0.0154)|Lung(119;0.0177)|COAD - Colon adenocarcinoma(134;0.226)		CTCAGCTTCTCGGTGAACTAC	0.289																																																	1	Substitution - coding silent(1)	kidney(1)											74.0	78.0	77.0					2																	231682474		2203	4300	6503	SO:0001819	synonymous_variant	51719			AF113536	CCDS2478.1	2q37.1	2008-02-05			ENSG00000135932	ENSG00000135932			20292	protein-coding gene	gene with protein product		612174					Standard	NM_016289		Approved	CGI-66, MO25	uc002vqx.3	Q9Y376	OTTHUMG00000133220	ENST00000258418.5:c.699C>T	2.37:g.231682474C>T		Somatic		WXS	Illumina HiSeq	Phase_I	A8K8L7	Silent	SNP	ENST00000258418.5	37	CCDS2478.1																																																																																				0.289	CAB39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256955.2		NM_016289	
CECR1	51816	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	22	17690279	17690279	+	Nonsense_Mutation	SNP	G	G	A	rs370709874		TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr22:17690279G>A	ENST00000399839.1	-	2	559	c.289C>T	c.(289-291)Caa>Taa	p.Q97*	CECR1_ENST00000449907.2_Nonsense_Mutation_p.Q55*|CECR1_ENST00000399837.2_Nonsense_Mutation_p.Q97*|CECR1_ENST00000262607.3_Nonsense_Mutation_p.Q97*	NM_001282227.1|NM_001282228.1	NP_001269156.1|NP_001269157.1	Q9NZK5	CECR1_HUMAN	cat eye syndrome chromosome region, candidate 1	97	Dimerization.				adenosine catabolic process (GO:0006154)|hypoxanthine salvage (GO:0043103)|inosine biosynthetic process (GO:0046103)|multicellular organismal development (GO:0007275)	extracellular space (GO:0005615)	adenosine deaminase activity (GO:0004000)|adenosine receptor binding (GO:0031685)|growth factor activity (GO:0008083)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|zinc ion binding (GO:0008270)	p.Q97*(1)		endometrium(1)|kidney(2)|large_intestine(6)|liver(1)|lung(10)|ovary(2)|prostate(2)|stomach(1)	25		all_epithelial(15;0.0152)|Lung NSC(13;0.0875)|all_lung(157;0.106)				TTAAACACTTGACTTCTCTCA	0.483																																																	1	Substitution - Nonsense(1)	kidney(1)											69.0	65.0	67.0					22																	17690279		2203	4300	6503	SO:0001587	stop_gained	51816			AF190746	CCDS13742.1, CCDS13743.1, CCDS63395.1, CCDS74809.1	22q11.2	2008-02-22			ENSG00000093072	ENSG00000093072			1839	protein-coding gene	gene with protein product		607575		IDGFL		10756095	Standard	NM_001282225		Approved	ADGF	uc002zmk.1	Q9NZK5	OTTHUMG00000030726	ENST00000399839.1:c.289C>T	22.37:g.17690279G>A	ENSP00000382733:p.Gln97*	Somatic		WXS	Illumina HiSeq	Phase_I	A8K9H4|Q6ICF1|Q86UB6|Q8NCJ2|Q96K41	Nonsense_Mutation	SNP	ENST00000399839.1	37	CCDS13742.1	.	.	.	.	.	.	.	.	.	.	G	27.2	4.805377	0.90623	.	.	ENSG00000093072	ENST00000399839;ENST00000262607;ENST00000449907;ENST00000399837;ENST00000543038;ENST00000441548	.	.	.	3.97	-2.36	0.06663	.	0.837550	0.10603	N	0.655387	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.9986	0.41916	0.0:0.5231:0.3131:0.1637	.	.	.	.	X	97;97;55;97;97;97	.	ENSP00000262607:Q97X	Q	-	1	0	CECR1	16070279	0.000000	0.05858	0.002000	0.10522	0.463000	0.32649	-0.227000	0.09126	-0.108000	0.12066	0.561000	0.74099	CAA		0.483	CECR1-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316079.1			
CHAT	1103	broad.mit.edu;hgsc.bcm.edu	37	10	50833615	50833615	+	Silent	SNP	C	C	T			TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr10:50833615C>T	ENST00000337653.2	+	6	1002	c.849C>T	c.(847-849)ccC>ccT	p.P283P	CHAT_ENST00000455728.2_Silent_p.P165P|CHAT_ENST00000395562.2_Silent_p.P201P|CHAT_ENST00000339797.1_Silent_p.P165P|CHAT_ENST00000351556.3_Silent_p.P165P|CHAT_ENST00000395559.2_Silent_p.P165P	NM_001142929.1|NM_020549.4	NP_001136401.1|NP_065574	P28329	CLAT_HUMAN	choline O-acetyltransferase	283					adult walking behavior (GO:0007628)|dendrite development (GO:0016358)|establishment of synaptic specificity at neuromuscular junction (GO:0007529)|glycerophospholipid biosynthetic process (GO:0046474)|muscle organ development (GO:0007517)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|rhythmic behavior (GO:0007622)|rhythmic excitation (GO:0043179)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	choline O-acetyltransferase activity (GO:0004102)	p.P283P(1)		central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(11)|lung(34)|prostate(3)|urinary_tract(1)	56		all_neural(218;0.107)		GBM - Glioblastoma multiforme(2;0.000585)	Choline(DB00122)|Nicotine(DB00184)	ACCGGCTCCCCGGCCATACCC	0.587																																																	1	Substitution - coding silent(1)	kidney(1)											47.0	36.0	40.0					10																	50833615		2203	4300	6503	SO:0001819	synonymous_variant	1103			AF305907	CCDS7232.1, CCDS7233.1, CCDS44389.1	10q11.2	2010-05-11	2010-05-11		ENSG00000070748	ENSG00000070748	2.3.1.6		1912	protein-coding gene	gene with protein product		118490	"""choline acetyltransferase"""			1840566	Standard	NM_020984		Approved		uc001jhz.2	P28329	OTTHUMG00000018198	ENST00000337653.2:c.849C>T	10.37:g.50833615C>T		Somatic		WXS	Illumina HiSeq	Phase_I	A2BDF4|A2BDF5|Q16488|Q9BQ23|Q9BQ35|Q9BQE1	Silent	SNP	ENST00000337653.2	37	CCDS7232.1																																																																																				0.587	CHAT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047997.1		NM_020549	
CLDN10	9071	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	13	96086287	96086287	+	Frame_Shift_Del	DEL	T	T	-	rs557844998	byFrequency	TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr13:96086287delT	ENST00000376873.3	+	1	430	c.200delT	c.(199-201)atcfs	p.I67fs		NM_001160100.1|NM_182848.3	NP_001153572.1|NP_878268.1	P78369	CLD10_HUMAN	claudin 10	69					calcium-independent cell-cell adhesion (GO:0016338)|cell adhesion (GO:0007155)|ion transport (GO:0006811)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			endometrium(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|skin(1)	15	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.18)			CATTTTACTATCTTCAAAGTA	0.488																																																	0													87.0	86.0	87.0					13																	96086287		2203	4300	6503	SO:0001589	frameshift_variant	9071			U89916	CCDS9475.1, CCDS9476.1	13q31-q34	2008-07-18			ENSG00000134873	ENSG00000134873		"""Claudins"""	2033	protein-coding gene	gene with protein product						18025272	Standard	NM_182848		Approved	OSP-L, CPETRL3	uc001vmh.2	P78369	OTTHUMG00000017217	ENST00000376873.3:c.200delT	13.37:g.96086287delT	ENSP00000366069:p.Ile67fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q6IBF9|Q96N78	Frame_Shift_Del	DEL	ENST00000376873.3	37	CCDS9475.1																																																																																				0.488	CLDN10-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045483.3		NM_006984	
CNKSR1	10256	broad.mit.edu;hgsc.bcm.edu	37	1	26514973	26514973	+	Silent	SNP	G	G	A			TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr1:26514973G>A	ENST00000374253.5	+	18	1629	c.1590G>A	c.(1588-1590)gaG>gaA	p.E530E	CNKSR1_ENST00000531191.1_Silent_p.E265E|CNKSR1_ENST00000361530.6_Silent_p.E523E|CATSPER4_ENST00000456354.2_5'Flank	NM_006314.2	NP_006305.2	Q969H4	CNKR1_HUMAN	connector enhancer of kinase suppressor of Ras 1	530					Ras protein signal transduction (GO:0007265)|Rho protein signal transduction (GO:0007266)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|plasma membrane (GO:0005886)	protein binding, bridging (GO:0030674)	p.E523E(1)		breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(8)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	28		Colorectal(325;3.46e-05)|all_lung(284;0.000116)|Lung NSC(340;0.000154)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0133)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;2.72e-26)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00072)|BRCA - Breast invasive adenocarcinoma(304;0.000959)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00823)|READ - Rectum adenocarcinoma(331;0.0649)		CGGACGATGAGGCTGGGTCCC	0.617																																					NSCLC(180;1396 2109 28270 30756 34275)												1	Substitution - coding silent(1)	kidney(1)											17.0	18.0	18.0					1																	26514973		2200	4297	6497	SO:0001819	synonymous_variant	10256			AF100153	CCDS276.1, CCDS72732.1	1p35.3	2013-01-10			ENSG00000142675	ENSG00000142675		"""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"""	19700	protein-coding gene	gene with protein product		603272				9814705	Standard	NM_006314		Approved	CNK1, KSR, CNK	uc001blm.4	Q969H4	OTTHUMG00000007541	ENST00000374253.5:c.1590G>A	1.37:g.26514973G>A		Somatic		WXS	Illumina HiSeq	Phase_I	B1AMW9|O95381	Silent	SNP	ENST00000374253.5	37																																																																																					0.617	CNKSR1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000089943.2		NM_006314	
CTSB	1508	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	11710155	11710155	+	Missense_Mutation	SNP	C	C	A			TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr8:11710155C>A	ENST00000353047.6	-	3	429	c.176G>T	c.(175-177)tGt>tTt	p.C59F	CTSB_ENST00000533455.1_Missense_Mutation_p.C59F|CTSB_ENST00000531089.1_Missense_Mutation_p.C59F|CTSB_ENST00000453527.2_Missense_Mutation_p.C59F|CTSB_ENST00000525076.1_5'UTR|CTSB_ENST00000534510.1_Missense_Mutation_p.C59F|CTSB_ENST00000530640.2_Missense_Mutation_p.C59F|CTSB_ENST00000345125.3_Missense_Mutation_p.C59F|CTSB_ENST00000434271.1_Missense_Mutation_p.C59F|CTSB_ENST00000415599.2_Missense_Mutation_p.C59F	NM_001908.3	NP_001899.1	P07858	CATB_HUMAN	cathepsin B	59					cellular response to thyroid hormone stimulus (GO:0097067)|collagen catabolic process (GO:0030574)|decidualization (GO:0046697)|epithelial cell differentiation (GO:0030855)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of apoptotic process (GO:0042981)|regulation of catalytic activity (GO:0050790)|toll-like receptor signaling pathway (GO:0002224)	endolysosome lumen (GO:0036021)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|perinuclear region of cytoplasm (GO:0048471)	collagen binding (GO:0005518)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|peptidase activity (GO:0008233)|proteoglycan binding (GO:0043394)	p.C59F(1)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(1)	16	all_epithelial(15;0.205)		STAD - Stomach adenocarcinoma(15;0.00546)	COAD - Colon adenocarcinoma(149;0.184)		GAAGGTACCACATAGCCTCTT	0.597																																																	1	Substitution - Missense(1)	kidney(1)											134.0	102.0	113.0					8																	11710155		2203	4300	6503	SO:0001583	missense	1508			M14221	CCDS5986.1	8p23.1	2012-10-02			ENSG00000164733	ENSG00000164733	3.4.22.1	"""Cathepsins"""	2527	protein-coding gene	gene with protein product		116810				8112600, 3463996	Standard	XM_006716244		Approved		uc003wuq.3	P07858	OTTHUMG00000090799	ENST00000353047.6:c.176G>T	8.37:g.11710155C>A	ENSP00000345672:p.Cys59Phe	Somatic		WXS	Illumina HiSeq	Phase_I	B3KQR5|B3KRR5|Q503A6|Q96D87	Missense_Mutation	SNP	ENST00000353047.6	37	CCDS5986.1	.	.	.	.	.	.	.	.	.	.	C	19.40	3.820223	0.71028	.	.	ENSG00000164733	ENST00000434271;ENST00000353047;ENST00000530640;ENST00000531089;ENST00000453527;ENST00000415599;ENST00000345125;ENST00000533455;ENST00000534510;ENST00000534636;ENST00000533572;ENST00000530296;ENST00000526195;ENST00000527243;ENST00000534149;ENST00000526645;ENST00000530573;ENST00000505496;ENST00000524500;ENST00000531502;ENST00000527215;ENST00000532656;ENST00000534382	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.31769	1.48;1.48;1.48;1.48;1.48;1.48;1.48;1.48;1.48;1.48;1.48;1.48;1.48;1.48;1.48;1.48;1.48;1.48;1.48;1.48;1.48	5.85	5.85	0.93711	Peptidase C1A, propeptide (1);	0.000000	0.85682	D	0.000000	T	0.65954	0.2741	M	0.92026	3.265	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.69859	-0.5031	10	0.46703	T	0.11	.	19.1459	0.93467	0.0:1.0:0.0:0.0	.	59	P07858	CATB_HUMAN	F	59	ENSP00000415889:C59F;ENSP00000345672:C59F;ENSP00000435105:C59F;ENSP00000433215:C59F;ENSP00000409917:C59F;ENSP00000411254:C59F;ENSP00000342070:C59F;ENSP00000432244:C59F;ENSP00000434217:C59F;ENSP00000436159:C59F;ENSP00000433995:C59F;ENSP00000435074:C59F;ENSP00000436627:C59F;ENSP00000434725:C59F;ENSP00000436122:C59F;ENSP00000431518:C59F;ENSP00000435650:C59F;ENSP00000436074:C59F;ENSP00000435886:C59F;ENSP00000431143:C59F;ENSP00000435260:C59F	ENSP00000342070:C59F	C	-	2	0	CTSB	11747564	1.000000	0.71417	0.999000	0.59377	0.448000	0.32197	6.916000	0.75776	2.767000	0.95098	0.655000	0.94253	TGT		0.597	CTSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207586.3		NM_147780	
CSMD3	114788	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	113650949	113650949	+	Nonsense_Mutation	SNP	C	C	A			TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr8:113650949C>A	ENST00000297405.5	-	21	3746	c.3502G>T	c.(3502-3504)Gaa>Taa	p.E1168*	CSMD3_ENST00000352409.3_Nonsense_Mutation_p.E1168*|CSMD3_ENST00000343508.3_Nonsense_Mutation_p.E1128*|CSMD3_ENST00000455883.2_Nonsense_Mutation_p.E1064*	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	1168	CUB 6. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.E1168*(1)|p.E1128*(1)		breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						TTAAATCCTTCATATGATATT	0.338										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																																							2	Substitution - Nonsense(2)	kidney(2)											51.0	53.0	53.0					8																	113650949		2202	4300	6502	SO:0001587	stop_gained	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.3502G>T	8.37:g.113650949C>A	ENSP00000297405:p.Glu1168*	Somatic		WXS	Illumina HiSeq	Phase_I	Q96PZ3	Nonsense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	C	45	11.547935	0.99574	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	.	.	.	4.91	4.91	0.64330	.	0.149187	0.44902	D	0.000417	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.20046	T	0.44	.	18.4581	0.90728	0.0:1.0:0.0:0.0	.	.	.	.	X	1128;1168;508;1064;1168	.	ENSP00000297405:E1168X	E	-	1	0	CSMD3	113720125	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.772000	0.62324	2.448000	0.82819	0.491000	0.48974	GAA		0.338	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1		NM_052900	
ACKR3	57007	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	237489349	237489349	+	Missense_Mutation	SNP	T	T	A			TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr2:237489349T>A	ENST00000272928.3	+	2	551	c.241T>A	c.(241-243)Tgc>Agc	p.C81S		NM_020311.2	NP_064707.1	P25106	ACKR3_HUMAN	atypical chemokine receptor 3	81					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|receptor internalization (GO:0031623)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell surface (GO:0009986)|coated pit (GO:0005905)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	C-X-C chemokine binding (GO:0019958)|C-X-C chemokine receptor activity (GO:0016494)|coreceptor activity (GO:0015026)|scavenger receptor activity (GO:0005044)	p.C81S(1)									TGACACGCACTGCTACATCTT	0.547																																																	1	Substitution - Missense(1)	kidney(1)											176.0	145.0	155.0					2																	237489349		2203	4300	6503	SO:0001583	missense	57007			BC008459	CCDS2516.1	2q37.3	2013-07-17	2013-07-16	2013-07-16	ENSG00000144476	ENSG00000144476		"""CD molecules"", ""GPCR / Class A : Chemokine receptors : Atypical"""	23692	protein-coding gene	gene with protein product		610376	"""chemokine orphan receptor 1"", ""chemokine (C-X-C motif) receptor 7"""	CMKOR1, CXCR7		16107333, 16148	Standard	NM_020311		Approved	RDC1, GPR159	uc002vwd.3	P25106	OTTHUMG00000133295	ENST00000272928.3:c.241T>A	2.37:g.237489349T>A	ENSP00000272928:p.Cys81Ser	Somatic		WXS	Illumina HiSeq	Phase_I	A8K6J4|Q53RV4|Q8NE10|Q92938|Q92986	Missense_Mutation	SNP	ENST00000272928.3	37	CCDS2516.1	.	.	.	.	.	.	.	.	.	.	T	14.80	2.642936	0.47153	.	.	ENSG00000144476	ENST00000447924;ENST00000272928	T;T	0.71934	-0.61;-0.61	5.57	4.44	0.53790	GPCR, rhodopsin-like superfamily (1);	0.331373	0.31760	N	0.007107	T	0.46464	0.1394	N	0.08118	0	0.38843	D	0.956105	B	0.25007	0.116	B	0.28011	0.085	T	0.50432	-0.8829	10	0.59425	D	0.04	.	3.2466	0.06799	0.0:0.3479:0.0:0.6521	.	81	P25106	CXCR7_HUMAN	S	81	ENSP00000405945:C81S;ENSP00000272928:C81S	ENSP00000272928:C81S	C	+	1	0	CXCR7	237154088	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	3.052000	0.49893	2.117000	0.64856	0.460000	0.39030	TGC		0.547	ACKR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257079.2		NM_020311	
DOCK5	80005	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	25167945	25167945	+	Silent	SNP	C	C	G			TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr8:25167945C>G	ENST00000276440.7	+	13	1259	c.1215C>G	c.(1213-1215)ctC>ctG	p.L405L		NM_024940.6	NP_079216.4	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	405					positive regulation of GTPase activity (GO:0043547)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.L405L(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(9)|large_intestine(13)|lung(20)|ovary(3)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)		CCTTGAAGCTCTTGCCCGGTG	0.403																																					Pancreas(145;34 1887 3271 10937 30165)												1	Substitution - coding silent(1)	kidney(1)											89.0	90.0	89.0					8																	25167945		2203	4300	6503	SO:0001819	synonymous_variant	80005				CCDS6047.1	8p21.2	2009-04-17			ENSG00000147459	ENSG00000147459			23476	protein-coding gene	gene with protein product						12432077	Standard	NM_024940		Approved	FLJ21034	uc003xeg.3	Q9H7D0	OTTHUMG00000131991	ENST00000276440.7:c.1215C>G	8.37:g.25167945C>G		Somatic		WXS	Illumina HiSeq	Phase_I	B2RNY0|Q5XKD5|Q6AI11|Q6PJS6|Q6ZTS6	Silent	SNP	ENST00000276440.7	37	CCDS6047.1	.	.	.	.	.	.	.	.	.	.	C	4.442	0.081738	0.08533	.	.	ENSG00000147459	ENST00000444569	T	0.17370	2.28	6.08	-12.2	0.00006	.	0.000000	0.64402	D	0.000002	T	0.12050	0.0293	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.65990	-0.6034	7	0.27082	T	0.32	.	6.7632	0.23552	0.0716:0.3212:0.3671:0.2401	.	.	.	.	V	177	ENSP00000414125:L177V	ENSP00000414125:L177V	L	+	1	0	DOCK5	25223862	0.000000	0.05858	0.001000	0.08648	0.751000	0.42716	-2.813000	0.00753	-4.535000	0.00043	-2.033000	0.00422	CTT		0.403	DOCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254955.2		NM_024940	
RIPPLY3	53820	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	21	38385914	38385914	+	Missense_Mutation	SNP	G	G	C			TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr21:38385914G>C	ENST00000329553.2	+	3	445	c.235G>C	c.(235-237)Gta>Cta	p.V79L	RIPPLY3_ENST00000485272.1_3'UTR	NM_018962.2	NP_061835.1	P57055	DSCR6_HUMAN	ripply transcriptional repressor 3	79	Ripply homology domain.				heart development (GO:0007507)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|pharyngeal system development (GO:0060037)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.V79L(1)									TCAGCATCCTGTAAGGTAATA	0.388																																																	1	Substitution - Missense(1)	kidney(1)											108.0	89.0	95.0					21																	38385914		2203	4300	6503	SO:0001583	missense	53820			AB037158	CCDS13648.1	21q22.2	2013-07-23	2013-07-23	2013-06-04	ENSG00000183145	ENSG00000183145			3047	protein-coding gene	gene with protein product		609892	"""Down syndrome critical region gene 6"", ""ripply3 homolog (zebrafish)"""	DSCR6		10814524, 22354841	Standard	NM_018962		Approved			P57055	OTTHUMG00000086639	ENST00000329553.2:c.235G>C	21.37:g.38385914G>C	ENSP00000331734:p.Val79Leu	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000329553.2	37	CCDS13648.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.960838	0.74016	.	.	ENSG00000183145	ENST00000329553	.	.	.	4.49	4.49	0.54785	.	0.184400	0.33005	N	0.005385	T	0.78666	0.4319	M	0.80332	2.49	0.45295	D	0.998292	D	0.76494	0.999	D	0.80764	0.994	T	0.81583	-0.0866	9	0.72032	D	0.01	-6.5541	13.4335	0.61071	0.0:0.0:1.0:0.0	.	79	P57055	DSCR6_HUMAN	L	79	.	ENSP00000331734:V79L	V	+	1	0	DSCR6	37307784	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	3.150000	0.50662	2.433000	0.82419	0.462000	0.41574	GTA		0.388	RIPPLY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194703.1			
FAM83A	84985	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	124204063	124204063	+	Silent	SNP	T	T	C			TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr8:124204063T>C	ENST00000518448.1	+	3	2515	c.501T>C	c.(499-501)gaT>gaC	p.D167D	FAM83A_ENST00000318462.6_Silent_p.D167D|FAM83A_ENST00000536633.1_Silent_p.D167D|FAM83A_ENST00000522648.1_Intron|FAM83A_ENST00000546351.1_Intron|FAM83A_ENST00000276699.6_Silent_p.D167D			Q86UY5	FA83A_HUMAN	family with sequence similarity 83, member A	167								p.D167D(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(3)|prostate(2)|skin(1)	17	Lung NSC(37;1.55e-09)|Ovarian(258;0.0205)		STAD - Stomach adenocarcinoma(47;0.00527)			TCCTGATGGATGTGTTCACGG	0.557																																																	1	Substitution - coding silent(1)	kidney(1)											218.0	197.0	204.0					8																	124204063		2203	4300	6503	SO:0001819	synonymous_variant	84985			BC052300	CCDS6339.1, CCDS6340.1, CCDS75784.1	8q24.13	2014-03-13			ENSG00000147689	ENSG00000147689			28210	protein-coding gene	gene with protein product						22886303	Standard	XM_005251087		Approved	MGC14128, BJ-TSA-9	uc003ypx.3	Q86UY5	OTTHUMG00000165083	ENST00000518448.1:c.501T>C	8.37:g.124204063T>C		Somatic		WXS	Illumina HiSeq	Phase_I	Q71HL2|Q8N7I1|Q96I47	Silent	SNP	ENST00000518448.1	37	CCDS6340.1																																																																																				0.557	FAM83A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381737.1		NM_032899	
FREM1	158326	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	14748627	14748627	+	Frame_Shift_Del	DEL	A	A	-			TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr9:14748627delA	ENST00000380880.3	-	31	6351	c.5568delT	c.(5566-5568)catfs	p.H1856fs	FREM1_ENST00000380881.4_Frame_Shift_Del_p.H1857fs|FREM1_ENST00000422223.2_Frame_Shift_Del_p.H1856fs|FREM1_ENST00000380894.1_Frame_Shift_Del_p.H392fs			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	1856					cell communication (GO:0007154)|cell-matrix adhesion (GO:0007160)|craniofacial suture morphogenesis (GO:0097094)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(40)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	100				GBM - Glioblastoma multiforme(50;3.53e-06)		AATATGAAGGATGGCATTGTC	0.507																																																	0													205.0	211.0	209.0					9																	14748627		2070	4215	6285	SO:0001589	frameshift_variant	158326			AK058190	CCDS47952.1, CCDS55293.1	9p22.3	2010-06-04	2004-12-15	2004-12-15	ENSG00000164946	ENSG00000164946			23399	protein-coding gene	gene with protein product		608944	"""chromosome 9 open reading frame 154"""	C9orf154		12838346, 15345741	Standard	NM_144966		Approved	FLJ25461, C9orf145, C9orf143, DKFZp686M16108, TILRR	uc003zlm.3	Q5H8C1	OTTHUMG00000019575	ENST00000380880.3:c.5568delT	9.37:g.14748627delA	ENSP00000370262:p.His1856fs	Somatic		WXS	Illumina HiSeq	Phase_I	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Frame_Shift_Del	DEL	ENST00000380880.3	37	CCDS47952.1																																																																																				0.507	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2		NM_144966	
GP2	2813	broad.mit.edu;hgsc.bcm.edu	37	16	20331781	20331781	+	Nonsense_Mutation	SNP	G	G	A	rs538424340		TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr16:20331781G>A	ENST00000381362.4	-	6	746	c.670C>T	c.(670-672)Cag>Tag	p.Q224*	GP2_ENST00000341642.5_Nonsense_Mutation_p.Q74*|GP2_ENST00000302555.5_Nonsense_Mutation_p.Q221*|GP2_ENST00000573897.1_5'UTR|GP2_ENST00000381360.5_Nonsense_Mutation_p.Q77*	NM_001007240.1|NM_001502.2	NP_001007241.2|NP_001493.2	P55259	GP2_HUMAN	glycoprotein 2 (zymogen granule membrane)	224	EGF-like.				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)	p.Q221*(1)		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						AGCTGAGGCTGCAAACTGTGG	0.532													G|||	1	0.000199681	0.0008	0.0	5008	,	,		21990	0.0		0.0	False		,,,				2504	0.0																1	Substitution - Nonsense(1)	kidney(1)											46.0	42.0	43.0					16																	20331781		2203	4300	6503	SO:0001587	stop_gained	2813			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.670C>T	16.37:g.20331781G>A	ENSP00000370767:p.Gln224*	Somatic		WXS	Illumina HiSeq	Phase_I	A6NFM9|A6NJA8|Q13338|Q9UIF1	Nonsense_Mutation	SNP	ENST00000381362.4	37	CCDS42128.1	.	.	.	.	.	.	.	.	.	.	G	12.16	1.855883	0.32791	.	.	ENSG00000169347	ENST00000302555;ENST00000381362;ENST00000381360;ENST00000341642;ENST00000537520	.	.	.	5.43	0.977	0.19733	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.08381	T	0.77	-6.2708	8.5997	0.33736	0.0:0.1419:0.4192:0.4389	.	.	.	.	X	221;224;77;74;202	.	ENSP00000304044:Q221X	Q	-	1	0	GP2	20239282	1.000000	0.71417	0.788000	0.31933	0.155000	0.21991	0.862000	0.27899	-0.032000	0.13758	-0.182000	0.12963	CAG		0.532	GP2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000436920.1		NM_016295	
ITGA9	3680	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	37821430	37821442	+	Frame_Shift_Del	DEL	ACTGTAACTTTAG	ACTGTAACTTTAG	-			TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	ACTGTAACTTTAG	ACTGTAACTTTAG	ACTGTAACTTTAG	-	ACTGTAACTTTAG	ACTGTAACTTTAG	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr3:37821430_37821442delACTGTAACTTTAG	ENST00000264741.5	+	25	2961_2973	c.2705_2717delACTGTAACTTTAG	c.(2704-2718)cactgtaactttagtfs	p.HCNFS902fs	AC093415.2_ENST00000438136.1_RNA	NM_002207.2	NP_002198.2	Q13797	ITA9_HUMAN	integrin, alpha 9	902					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|neutrophil chemotaxis (GO:0030593)|wound healing (GO:0042060)	basal plasma membrane (GO:0009925)|integrin alpha9-beta1 complex (GO:0034679)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(17)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|urinary_tract(1)	44				KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)		CTAACAGCACACTGTAACTTTAGTGCTCTTGCT	0.371																																																	0																																										SO:0001589	frameshift_variant	3680			L24158	CCDS2669.1	3p21.3	2010-03-23			ENSG00000144668	ENSG00000144668		"""Integrins"""	6145	protein-coding gene	gene with protein product	"""integrin, alpha 4-like"""	603963				8245132, 8290272	Standard	NM_002207		Approved	RLC, ITGA4L, ALPHA-RLC	uc003chd.3	Q13797	OTTHUMG00000130815	ENST00000264741.5:c.2705_2717delACTGTAACTTTAG	3.37:g.37821430_37821442delACTGTAACTTTAG	ENSP00000264741:p.His902fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q14638	Frame_Shift_Del	DEL	ENST00000264741.5	37	CCDS2669.1																																																																																				0.371	ITGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253361.1		NM_002207	
ITSN1	6453	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	21	35254745	35254745	+	Frame_Shift_Del	DEL	A	A	-			TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr21:35254745delA	ENST00000381318.3	+	35	4828	c.4540delA	c.(4540-4542)aaafs	p.K1514fs	ITSN1_ENST00000399326.3_3'UTR|ITSN1_ENST00000381285.4_Frame_Shift_Del_p.K1514fs|ITSN1_ENST00000399367.3_Frame_Shift_Del_p.K1509fs|AP000304.12_ENST00000429238.1_Intron|ITSN1_ENST00000437442.2_Frame_Shift_Del_p.K1453fs	NM_003024.2	NP_003015.2	Q15811	ITSN1_HUMAN	intersectin 1 (SH3 domain protein)	1514	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|guanyl-nucleotide exchange factor activity (GO:0005085)|kinase activator activity (GO:0019209)|proline-rich region binding (GO:0070064)|protein complex scaffold (GO:0032947)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(16)|lung(26)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	67						CCTGCAGTATAAAATGTATAA	0.433																																																	0													47.0	49.0	48.0					21																	35254745		2203	4300	6503	SO:0001589	frameshift_variant	6453			AF064244	CCDS33545.1, CCDS33546.1	21q22.1-q22.2	2013-01-10			ENSG00000205726	ENSG00000205726		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"", ""EF-hand domain containing"""	6183	protein-coding gene	gene with protein product	"""SH3 domain protein-1A"", ""human intersectin-SH3 domain-containing protein SH3P17"", ""Src homology 3 domain-containing protein"", ""intersectin 1 short form variant, 11"", ""intersectin 1 short form variant 3"", ""intersectin short variant 12"""	602442		SH3D1A, ITSN		9799604, 9813051	Standard	NM_003024		Approved	SH3P17, MGC134948, MGC134949	uc002yta.1	Q15811	OTTHUMG00000065284	ENST00000381318.3:c.4540delA	21.37:g.35254745delA	ENSP00000370719:p.Lys1514fs	Somatic		WXS	Illumina HiSeq	Phase_I	A7Y322|A8CTX8|A8CTY3|A8CTY7|A8D7D0|A8DCP3|B4DTM2|E7ERJ1|E9PE44|E9PG01|E9PHV2|O95216|Q0PW94|Q0PW95|Q0PW97|Q14BD3|Q1ED40|Q20BK3|Q9UET5|Q9UK60|Q9UNK1|Q9UNK2|Q9UQ92	Frame_Shift_Del	DEL	ENST00000381318.3	37	CCDS33545.1																																																																																				0.433	ITSN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000140070.4		NM_003024	
KEAP1	9817	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	10602352	10602352	+	Missense_Mutation	SNP	A	A	G			TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr19:10602352A>G	ENST00000171111.5	-	3	1773	c.1226T>C	c.(1225-1227)aTg>aCg	p.M409T	KEAP1_ENST00000588024.1_5'Flank|CTC-429L19.3_ENST00000592671.1_RNA|KEAP1_ENST00000393623.2_Missense_Mutation_p.M409T	NM_203500.1	NP_987096.1	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	409					cellular response to interleukin-4 (GO:0071353)|in utero embryonic development (GO:0001701)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein ubiquitination (GO:0016567)|regulation of epidermal cell differentiation (GO:0045604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)		p.M409T(1)		breast(3)|endometrium(2)|kidney(4)|large_intestine(4)|liver(2)|lung(69)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	92			OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05)		Dimethyl fumarate(DB08908)	GGGCACGCTCATGGGGGCGCA	0.662																																																	1	Substitution - Missense(1)	kidney(1)											34.0	29.0	30.0					19																	10602352		2202	4300	6502	SO:0001583	missense	9817			AF361886	CCDS12239.1	19p13.2	2013-01-30				ENSG00000079999		"""Kelch-like"", ""BTB/POZ domain containing"""	23177	protein-coding gene	gene with protein product	"""kelch-like family member 19"""	606016					Standard	NM_012289		Approved	KIAA0132, MGC10630, MGC1114, MGC20887, MGC4407, MGC9454, INrf2, KLHL19	uc002mor.1	Q14145		ENST00000171111.5:c.1226T>C	19.37:g.10602352A>G	ENSP00000171111:p.Met409Thr	Somatic		WXS	Illumina HiSeq	Phase_I	B3KPD5|Q6LEP0|Q8WTX1|Q9BPY9	Missense_Mutation	SNP	ENST00000171111.5	37	CCDS12239.1	.	.	.	.	.	.	.	.	.	.	A	14.25	2.478332	0.44044	.	.	ENSG00000079999	ENST00000171111;ENST00000393623	D;D	0.83992	-1.79;-1.79	5.77	4.76	0.60689	Kelch-type beta propeller (1);	0.038111	0.85682	D	0.000000	D	0.91280	0.7251	M	0.92122	3.275	0.58432	D	0.999998	P	0.44627	0.839	P	0.60789	0.879	D	0.89986	0.4104	10	0.33940	T	0.23	.	9.8842	0.41251	0.9196:0.0:0.0804:0.0	.	409	Q14145	KEAP1_HUMAN	T	409	ENSP00000171111:M409T;ENSP00000377245:M409T	ENSP00000171111:M409T	M	-	2	0	KEAP1	10463352	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	7.312000	0.78968	1.032000	0.39892	0.533000	0.62120	ATG		0.662	KEAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452000.1		NM_012289	
KRBA2	124751	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	8273274	8273274	+	Missense_Mutation	SNP	T	T	A			TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr17:8273274T>A	ENST00000331336.2	-	2	662	c.657A>T	c.(655-657)aaA>aaT	p.K219N	RP11-849F2.7_ENST00000582471.1_3'UTR|KRBA2_ENST00000396267.1_Missense_Mutation_p.K137N|RP11-849F2.5_ENST00000580537.1_RNA|RP11-849F2.5_ENST00000583963.1_RNA	NM_213597.2	NP_998762.1	Q6ZNG9	KRBA2_HUMAN	KRAB-A domain containing 2	219					DNA integration (GO:0015074)|regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	nucleic acid binding (GO:0003676)	p.K219N(1)		endometrium(2)|kidney(2)|large_intestine(7)|lung(5)|stomach(1)|urinary_tract(1)	18						CATTCCCATATTTTCCTTGCA	0.433																																																	1	Substitution - Missense(1)	kidney(1)											129.0	120.0	123.0					17																	8273274		2203	4300	6503	SO:0001583	missense	124751			BC024723	CCDS11141.1	17p13.1	2013-01-08	2006-08-15		ENSG00000184619	ENSG00000184619		"""-"""	26989	protein-coding gene	gene with protein product			"""KRAB A domain containing 2"""			12477932	Standard	NM_213597		Approved		uc002glf.1	Q6ZNG9	OTTHUMG00000132864	ENST00000331336.2:c.657A>T	17.37:g.8273274T>A	ENSP00000328017:p.Lys219Asn	Somatic		WXS	Illumina HiSeq	Phase_I	Q8IYY0	Missense_Mutation	SNP	ENST00000331336.2	37	CCDS11141.1	.	.	.	.	.	.	.	.	.	.	T	15.57	2.871552	0.51695	.	.	ENSG00000184619	ENST00000396267;ENST00000331336	T;T	0.25414	1.81;1.8	2.64	2.64	0.31445	.	.	.	.	.	T	0.24392	0.0591	L	0.55481	1.735	0.25912	N	0.983221	B	0.22683	0.073	B	0.24269	0.052	T	0.21793	-1.0235	9	0.87932	D	0	.	7.1797	0.25765	0.0:0.0:0.0:1.0	.	219	Q6ZNG9	KRBA2_HUMAN	N	137;219	ENSP00000379565:K137N;ENSP00000328017:K219N	ENSP00000328017:K219N	K	-	3	2	KRBA2	8213999	0.997000	0.39634	0.973000	0.42090	0.987000	0.75469	0.781000	0.26774	1.474000	0.48178	0.528000	0.53228	AAA		0.433	KRBA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256338.1		NM_213597	
LRP5	4041	broad.mit.edu;ucsc.edu	37	11	68181463	68181474	+	In_Frame_Del	DEL	GCAGCCGCAACT	GCAGCCGCAACT	-	rs369139308|rs376937882		TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	GCAGCCGCAACT	GCAGCCGCAACT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr11:68181463_68181474delGCAGCCGCAACT	ENST00000294304.7	+	12	2916_2927	c.2810_2821delGCAGCCGCAACT	c.(2809-2823)agcagccgcaactgc>agc	p.SRNC938del		NM_002335.2	NP_002326.2	O75197	LRP5_HUMAN	low density lipoprotein receptor-related protein 5	938	EGF-like 3.				adipose tissue development (GO:0060612)|anatomical structure regression (GO:0060033)|anterior/posterior pattern specification (GO:0009952)|apoptotic process involved in patterning of blood vessels (GO:1902262)|bone marrow development (GO:0048539)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|cell migration involved in gastrulation (GO:0042074)|cell-cell signaling involved in mammary gland development (GO:0060764)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic limb morphogenesis (GO:0030326)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endocytosis (GO:0006897)|extracellular matrix-cell signaling (GO:0035426)|gastrulation with mouth forming second (GO:0001702)|glucose catabolic process (GO:0006007)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|osteoblast development (GO:0002076)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of mitosis (GO:0045840)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of bone remodeling (GO:0046850)|regulation of canonical Wnt signaling pathway (GO:0060828)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|response to peptide hormone (GO:0043434)|retina morphogenesis in camera-type eye (GO:0060042)|retinal blood vessel morphogenesis (GO:0061304)|somatic stem cell maintenance (GO:0035019)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	coreceptor activity (GO:0015026)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			autonomic_ganglia(1)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(24)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						CTGGACCCCAGCAGCCGCAACTGCAGCCGTAA	0.627																																																	0																																										SO:0001651	inframe_deletion	4041			AF064548	CCDS8181.1	11q13.4	2014-01-28	2003-03-12		ENSG00000162337	ENSG00000162337		"""Low density lipoprotein receptors"""	6697	protein-coding gene	gene with protein product		603506	"""osteoporosis pseudoglioma syndrome"", ""exudative vitreoretinopathy 1"""	LRP7, OPPG, EVR1		9714764, 10049586	Standard	XM_005273994		Approved	LR3, BMND1, HBM, OPS, OPTA1, VBCH2, EVR4	uc001ont.3	O75197	OTTHUMG00000167570	ENST00000294304.7:c.2810_2821delGCAGCCGCAACT	11.37:g.68181463_68181474delGCAGCCGCAACT	ENSP00000294304:p.Ser938_Cys941del	Somatic		WXS	Illumina GAIIx	Phase_I	Q96TD6|Q9UES7|Q9UP66	In_Frame_Del	DEL	ENST00000294304.7	37	CCDS8181.1																																																																																				0.627	LRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395088.1		NM_002335	
MCPH1	79648	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	6302771	6302771	+	Missense_Mutation	SNP	T	T	G			TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr8:6302771T>G	ENST00000344683.5	+	8	1604	c.1528T>G	c.(1528-1530)Tgt>Ggt	p.C510G	MCPH1_ENST00000522905.1_Missense_Mutation_p.C462G|MCPH1_ENST00000519480.1_Missense_Mutation_p.C510G	NM_024596.3	NP_078872	Q8NEM0	MCPH1_HUMAN	microcephalin 1	510					cerebral cortex development (GO:0021987)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleoplasm (GO:0005654)	identical protein binding (GO:0042802)	p.C510G(1)	AGPAT5/MCPH1(2)	central_nervous_system(1)|large_intestine(4)|skin(1)	6		Hepatocellular(245;0.0663)		Colorectal(4;0.0505)		CCTAAGGTGTTGTAGACAGGC	0.493																																					Colon(95;1448 1467 8277 34473 35819)												1	Substitution - Missense(1)	kidney(1)											83.0	85.0	84.0					8																	6302771		1914	4122	6036	SO:0001583	missense	79648			AK022909	CCDS43689.1, CCDS55190.1, CCDS55191.1	8p23.1	2012-11-26	2007-11-26		ENSG00000147316	ENSG00000147316			6954	protein-coding gene	gene with protein product	"""BRCT-repeat inhibitor of TERT expression 1"""	607117	"""microcephaly, primary autosomal recessive 1"""			9683597, 17925396	Standard	NM_024596		Approved	FLJ12847, BRIT1	uc003wqi.3	Q8NEM0	OTTHUMG00000163618	ENST00000344683.5:c.1528T>G	8.37:g.6302771T>G	ENSP00000342924:p.Cys510Gly	Somatic		WXS	Illumina HiSeq	Phase_I	B4DWW2|E9PGU5|E9PH63|Q66GU1|Q9H9C7	Missense_Mutation	SNP	ENST00000344683.5	37	CCDS43689.1	.	.	.	.	.	.	.	.	.	.	T	4.410	0.075685	0.08485	.	.	ENSG00000147316	ENST00000344683;ENST00000519480;ENST00000522905	T;T;T	0.14640	2.49;2.49;2.49	5.2	-10.4	0.00318	.	1.546610	0.03657	N	0.242057	T	0.06508	0.0167	N	0.16166	0.38	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.0	B;B;B	0.20577	0.003;0.03;0.002	T	0.19353	-1.0308	10	0.15952	T	0.53	5.2015	8.6649	0.34114	0.0:0.4232:0.33:0.2468	.	462;510;510	E9PH63;Q8NEM0;E9PGU5	.;MCPH1_HUMAN;.	G	510;510;462	ENSP00000342924:C510G;ENSP00000430962:C510G;ENSP00000430768:C462G	ENSP00000342924:C510G	C	+	1	0	MCPH1	6290179	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.111000	0.01333	-2.533000	0.00490	-0.291000	0.09656	TGT		0.493	MCPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374532.2		NM_024596	
NCOA3	8202	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	46268421	46268421	+	Missense_Mutation	SNP	C	C	G			TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr20:46268421C>G	ENST00000371998.3	+	15	2999	c.2808C>G	c.(2806-2808)aaC>aaG	p.N936K	NCOA3_ENST00000371997.3_Missense_Mutation_p.N931K|NCOA3_ENST00000372004.3_Missense_Mutation_p.N936K|NCOA3_ENST00000341724.6_Missense_Mutation_p.N866K			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	936					androgen receptor signaling pathway (GO:0030521)|developmental growth (GO:0048589)|histone acetylation (GO:0016573)|labyrinthine layer morphogenesis (GO:0060713)|mammary gland branching involved in thelarche (GO:0060744)|multicellular organism growth (GO:0035264)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor transactivation (GO:0035624)|regulation of RNA biosynthetic process (GO:2001141)|transcription, DNA-templated (GO:0006351)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)	p.N936K(1)		breast(3)|endometrium(3)|kidney(4)|large_intestine(12)|lung(19)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						TGAATTCAAACTCCATGGGAA	0.493																																																	1	Substitution - Missense(1)	kidney(1)											124.0	132.0	129.0					20																	46268421		2203	4300	6503	SO:0001583	missense	8202			AF012108	CCDS13406.1, CCDS13407.1, CCDS54472.1	20q12	2011-07-01			ENSG00000124151	ENSG00000124151		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Basic helix-loop-helix proteins"""	7670	protein-coding gene	gene with protein product	"""receptor-associated coactivator 3"", ""thyroid hormone receptor activator molecule 1"""	601937				9252329, 9346901	Standard	NM_181659		Approved	RAC3, AIB1, ACTR, p/CIP, TRAM-1, CAGH16, TNRC16, KAT13B, bHLHe42, SRC-3, SRC3	uc002xtk.3	Q9Y6Q9	OTTHUMG00000033061	ENST00000371998.3:c.2808C>G	20.37:g.46268421C>G	ENSP00000361066:p.Asn936Lys	Somatic		WXS	Illumina HiSeq	Phase_I	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Missense_Mutation	SNP	ENST00000371998.3	37	CCDS13407.1	.	.	.	.	.	.	.	.	.	.	C	8.587	0.883618	0.17467	.	.	ENSG00000124151	ENST00000340189;ENST00000341724;ENST00000372004;ENST00000371998;ENST00000371997	T;T;T;T	0.01933	4.56;4.73;4.73;4.55	5.89	-1.33	0.09172	.	1.049970	0.07366	N	0.884904	T	0.02455	0.0075	L	0.36672	1.1	0.09310	N	1	B;B;B;B;B;B	0.25486	0.022;0.127;0.004;0.046;0.003;0.002	B;B;B;B;B;B	0.27076	0.045;0.076;0.011;0.045;0.026;0.011	T	0.47058	-0.9146	10	0.52906	T	0.07	-3.8871	6.5507	0.22431	0.1483:0.1912:0.0:0.6605	.	936;931;940;936;936;936	A8K0W8;Q9Y6Q9-3;Q59EE8;Q0IIN7;Q9Y6Q9-5;Q9Y6Q9	.;.;.;.;.;NCOA3_HUMAN	K	936;866;936;936;931	ENSP00000342123:N866K;ENSP00000361073:N936K;ENSP00000361066:N936K;ENSP00000361065:N931K	ENSP00000345671:N936K	N	+	3	2	NCOA3	45701828	0.000000	0.05858	0.001000	0.08648	0.894000	0.52154	-0.159000	0.10056	-0.089000	0.12484	0.557000	0.71058	AAC		0.493	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1		NM_006534	
NEK3	4752	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	13	52709999	52709999	+	Splice_Site	SNP	C	C	T			TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr13:52709999C>T	ENST00000400357.2	-	12	2417	c.1124G>A	c.(1123-1125)gGt>gAt	p.G375D	NEK3_ENST00000339406.3_Splice_Site_p.G392D|NEK3_ENST00000452082.2_Splice_Site_p.G396D|NEK3_ENST00000378101.2_Splice_Site_p.G392D			P51956	NEK3_HUMAN	NIMA-related kinase 3	392					mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.G392D(1)		central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|stomach(2)	18		Breast(56;0.000207)|Lung NSC(96;0.00145)|Prostate(109;0.034)|Hepatocellular(98;0.065)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.81e-08)		TACAGAACCACCTAGTTGCAA	0.353																																																	1	Substitution - Missense(1)	kidney(1)											107.0	99.0	101.0					13																	52709999		1823	4068	5891	SO:0001630	splice_region_variant	4752			AK290259, BC019916	CCDS73576.1	13q14.2-q21.1	2014-07-17	2012-11-15		ENSG00000136098	ENSG00000136098	2.7.11.1		7746	protein-coding gene	gene with protein product	"""serine/threonine-protein kinase NEK3"", ""phosphorylase B kinase kinase"", ""glycogen synthase A kinase"", ""hydroxyalkyl-protein kinase"""	604044	"""NIMA (never in mitosis gene a)-related kinase 3"""			8274451, 7522034	Standard	NM_002498		Approved	HSPK36, MGC29949	uc010tgy.2	P51956	OTTHUMG00000016958	ENST00000400357.2:c.1124-1G>A	13.37:g.52709999C>T		Somatic		WXS	Illumina HiSeq	Phase_I	A8K2J4|Q5TAP2|Q8J023|Q8WUN5	Missense_Mutation	SNP	ENST00000400357.2	37	CCDS53871.1	.	.	.	.	.	.	.	.	.	.	C	12.79	2.042210	0.35989	.	.	ENSG00000136098	ENST00000339406;ENST00000378101;ENST00000400357;ENST00000452082;ENST00000547422	T;T;T;T;T	0.72167	-0.52;-0.52;-0.63;-0.51;-0.47	5.21	4.37	0.52481	.	0.359222	0.29616	N	0.011644	T	0.72803	0.3506	M	0.67953	2.075	0.38986	D	0.959054	D;P;P	0.58268	0.982;0.879;0.926	P;B;P	0.51701	0.677;0.418;0.622	T	0.71530	-0.4565	10	0.20519	T	0.43	.	10.5981	0.45349	0.0:0.845:0.0:0.155	.	392;396;369	P51956;Q6ZN64;F8VS47	NEK3_HUMAN;.;.	D	392;392;375;396;369	ENSP00000339429:G392D;ENSP00000367341:G392D;ENSP00000383210:G375D;ENSP00000404197:G396D;ENSP00000448716:G369D	ENSP00000339429:G392D	G	-	2	0	NEK3	51608000	1.000000	0.71417	0.993000	0.49108	0.154000	0.21943	3.557000	0.53741	1.319000	0.45190	-0.136000	0.14681	GGT		0.353	NEK3-002	KNOWN	upstream_ATG|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045047.3			Missense_Mutation
NOS1AP	9722	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	162324977	162324977	+	Splice_Site	SNP	G	G	T			TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr1:162324977G>T	ENST00000361897.5	+	7	998	c.596G>T	c.(595-597)gGc>gTc	p.G199V	NOS1AP_ENST00000530878.1_Splice_Site_p.G194V	NM_001164757.1|NM_014697.2	NP_001158229.1|NP_055512.1	O75052	CAPON_HUMAN	nitric oxide synthase 1 (neuronal) adaptor protein	199					regulation of apoptotic process (GO:0042981)|regulation of nitric oxide biosynthetic process (GO:0045428)|regulation of nitric-oxide synthase activity (GO:0050999)		nitric-oxide synthase binding (GO:0050998)	p.G199V(2)		NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(12)|skin(1)|upper_aerodigestive_tract(2)	32	all_hematologic(112;0.203)		BRCA - Breast invasive adenocarcinoma(70;0.0537)			GTTCCTGCAGGCCGCCAGCTC	0.557																																																	2	Substitution - Missense(2)	kidney(2)											56.0	57.0	57.0					1																	162324977		2203	4300	6503	SO:0001630	splice_region_variant	9722			AB007933	CCDS1237.1, CCDS44267.1, CCDS53421.1	1q23.3	2010-08-20			ENSG00000198929	ENSG00000198929			16859	protein-coding gene	gene with protein product	"""C-terminal PDZ domain ligand of neuronal nitric oxide synthase"""	605551				9455484, 9459447	Standard	NM_001126060		Approved	KIAA0464, CAPON	uc001gbv.2	O75052	OTTHUMG00000024049	ENST00000361897.5:c.596-1G>T	1.37:g.162324977G>T		Somatic		WXS	Illumina HiSeq	Phase_I	B7ZLF5|O43564|Q3T551|Q5VU95	Missense_Mutation	SNP	ENST00000361897.5	37	CCDS1237.1	.	.	.	.	.	.	.	.	.	.	G	14.42	2.530852	0.45073	.	.	ENSG00000198929	ENST00000530878;ENST00000361897	T;T	0.77098	-1.07;-1.07	5.41	4.47	0.54385	.	0.327097	0.31370	N	0.007767	T	0.53384	0.1793	L	0.46157	1.445	.	.	.	P;B;B	0.35077	0.483;0.02;0.02	B;B;B	0.27887	0.084;0.01;0.01	T	0.57100	-0.7869	8	.	.	.	.	11.1261	0.48320	0.0:0.2849:0.7151:0.0	.	194;194;199	E9PSG0;B7ZLF5;O75052	.;.;CAPON_HUMAN	V	194;199	ENSP00000431586:G194V;ENSP00000355133:G199V	.	G	+	2	0	NOS1AP	160591601	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	1.528000	0.35985	2.523000	0.85059	0.655000	0.94253	GGC		0.557	NOS1AP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060555.2		NM_014697	Missense_Mutation
PBRM1	55193	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	52651382	52651383	+	Frame_Shift_Ins	INS	-	-	A			TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr3:52651382_52651383insA	ENST00000296302.7	-	14	1714_1715	c.1713_1714insT	c.(1711-1716)attgagfs	p.E572fs	PBRM1_ENST00000394830.3_Frame_Shift_Ins_p.E572fs|PBRM1_ENST00000409057.1_Frame_Shift_Ins_p.E572fs|PBRM1_ENST00000356770.4_Frame_Shift_Ins_p.E540fs|PBRM1_ENST00000337303.4_Frame_Shift_Ins_p.E572fs|PBRM1_ENST00000409767.1_Frame_Shift_Ins_p.E587fs|PBRM1_ENST00000410007.1_Frame_Shift_Ins_p.E572fs|PBRM1_ENST00000409114.3_Frame_Shift_Ins_p.E587fs			Q86U86	PB1_HUMAN	polybromo 1	572	Bromo 4. {ECO:0000255|PROSITE- ProRule:PRU00035}.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.E572fs*16(2)|p.E540fs*16(1)		breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		ATGTTATGCTCAATTATTTTCA	0.401			"""Mis, N, F, S, D, O"""		"""clear cell renal carcinoma, breast"""																																			Rec	yes		3	3p21	55193	polybromo 1		E	3	Insertion - Frameshift(3)	kidney(3)																																								SO:0001589	frameshift_variant	55193			BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.1714dupT	3.37:g.52651384_52651384dupA	ENSP00000296302:p.Glu572fs	Somatic		WXS	Illumina HiSeq	Phase_I	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Frame_Shift_Del	INS	ENST00000296302.7	37																																																																																					0.401	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1		NM_018165	
PGAM2	5224	hgsc.bcm.edu;ucsc.edu	37	7	44104731	44104735	+	Frame_Shift_Del	DEL	TAGTA	TAGTA	-			TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	TAGTA	TAGTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr7:44104731_44104735delTAGTA	ENST00000297283.3	-	1	451_455	c.394_398delTACTA	c.(394-399)tactacfs	p.YY132fs	AC017116.11_ENST00000445938.1_RNA	NM_000290.3	NP_000281.2	P15259	PGAM2_HUMAN	phosphoglycerate mutase 2 (muscle)	132					carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|response to mercury ion (GO:0046689)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|striated muscle contraction (GO:0006941)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity (GO:0046538)|bisphosphoglycerate 2-phosphatase activity (GO:0004083)|bisphosphoglycerate mutase activity (GO:0004082)|cofactor binding (GO:0048037)|phosphoglycerate mutase activity (GO:0004619)			large_intestine(2)|lung(4)|ovary(1)|stomach(1)	8						AATGGAGTTGTAGTAGGGGTGCTTC	0.634																																																	0																																										SO:0001589	frameshift_variant	5224				CCDS34624.1	7p13-p12	2008-11-17			ENSG00000164708	ENSG00000164708	5.4.2.1, 3.1.3.13, 5.4.2.4		8889	protein-coding gene	gene with protein product		612931					Standard	NM_000290		Approved	PGAM-M	uc003tjs.3	P15259	OTTHUMG00000155355	ENST00000297283.3:c.394_398delTACTA	7.37:g.44104731_44104735delTAGTA	ENSP00000297283:p.Tyr132fs	Somatic		WXS	Illumina HiSeq	Phase_I		Frame_Shift_Del	DEL	ENST00000297283.3	37	CCDS34624.1																																																																																				0.634	PGAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339614.1			
POLR2A	5430	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	7416113	7416113	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr17:7416113G>A	ENST00000322644.6	+	28	5026	c.4627G>A	c.(4627-4629)Gca>Aca	p.A1543T		NM_000937.4	NP_000928	P24928	RPB1_HUMAN	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	1543					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA-directed RNA polymerase activity (GO:0003968)|ubiquitin protein ligase binding (GO:0031625)	p.A1543T(1)		breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(17)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	50		Prostate(122;0.173)				GACCCCAGGGGCAGCCGGCTT	0.637																																																	1	Substitution - Missense(1)	kidney(1)											61.0	71.0	68.0					17																	7416113		2203	4300	6503	SO:0001583	missense	5430					17p13.1	2013-01-21	2002-08-29		ENSG00000181222	ENSG00000181222	2.7.7.6	"""RNA polymerase subunits"""	9187	protein-coding gene	gene with protein product	"""DNA-directed RNA polymerase II largest subunit, RNA polymerase II 220 kd subunit"", ""RNA polymerase II subunit B1"""	180660	"""polymerase (RNA) II (DNA directed) polypeptide A (220kD)"""	POLR2			Standard	NM_000937		Approved	POLRA, RPB1	uc002ghf.4	P24928	OTTHUMG00000177594	ENST00000322644.6:c.4627G>A	17.37:g.7416113G>A	ENSP00000314949:p.Ala1543Thr	Somatic		WXS	Illumina HiSeq	Phase_I	A6NN93|B9EH88|Q6NX41	Missense_Mutation	SNP	ENST00000322644.6	37	CCDS32548.1	.	.	.	.	.	.	.	.	.	.	G	11.67	1.706483	0.30232	.	.	ENSG00000181222	ENST00000535204;ENST00000545644;ENST00000322644	T	0.70749	-0.51	4.04	4.04	0.47022	.	0.000000	0.64402	D	0.000002	T	0.55321	0.1913	N	0.24115	0.695	0.80722	D	1	P	0.35328	0.495	B	0.28465	0.09	T	0.63193	-0.6692	10	0.56958	D	0.05	-8.6992	15.5284	0.75932	0.0:0.0:1.0:0.0	.	1543	P24928	RPB1_HUMAN	T	1499;442;1543	ENSP00000314949:A1543T	ENSP00000314949:A1543T	A	+	1	0	SLC35G6	7356837	1.000000	0.71417	0.945000	0.38365	0.345000	0.29048	8.299000	0.89946	2.242000	0.73789	0.456000	0.33151	GCA		0.637	POLR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437967.1		NM_000937	
POLR2A	5430	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	7416181	7416181	+	Nonsense_Mutation	SNP	G	G	A			TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr17:7416181G>A	ENST00000322644.6	+	28	5094	c.4695G>A	c.(4693-4695)tgG>tgA	p.W1565*		NM_000937.4	NP_000928	P24928	RPB1_HUMAN	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	1565					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA-directed RNA polymerase activity (GO:0003968)|ubiquitin protein ligase binding (GO:0031625)	p.W1565*(1)		breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(17)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	50		Prostate(122;0.173)				CCCCTGCCTGGTCTCCCACAC	0.632																																																	1	Substitution - Nonsense(1)	kidney(1)											56.0	67.0	63.0					17																	7416181		2203	4300	6503	SO:0001587	stop_gained	5430					17p13.1	2013-01-21	2002-08-29		ENSG00000181222	ENSG00000181222	2.7.7.6	"""RNA polymerase subunits"""	9187	protein-coding gene	gene with protein product	"""DNA-directed RNA polymerase II largest subunit, RNA polymerase II 220 kd subunit"", ""RNA polymerase II subunit B1"""	180660	"""polymerase (RNA) II (DNA directed) polypeptide A (220kD)"""	POLR2			Standard	NM_000937		Approved	POLRA, RPB1	uc002ghf.4	P24928	OTTHUMG00000177594	ENST00000322644.6:c.4695G>A	17.37:g.7416181G>A	ENSP00000314949:p.Trp1565*	Somatic		WXS	Illumina HiSeq	Phase_I	A6NN93|B9EH88|Q6NX41	Nonsense_Mutation	SNP	ENST00000322644.6	37	CCDS32548.1	.	.	.	.	.	.	.	.	.	.	G	46	12.554086	0.99677	.	.	ENSG00000181222	ENST00000535204;ENST00000545644;ENST00000322644	.	.	.	4.04	4.04	0.47022	.	0.000000	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.8045	15.5284	0.75932	0.0:0.0:1.0:0.0	.	.	.	.	X	1521;464;1565	.	ENSP00000314949:W1565X	W	+	3	0	SLC35G6	7356905	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	6.116000	0.71571	2.242000	0.73789	0.456000	0.33151	TGG		0.632	POLR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437967.1		NM_000937	
PSG1	5669	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	43376181	43376181	+	Silent	SNP	G	G	A			TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr19:43376181G>A	ENST00000436291.2	-	3	563	c.447C>T	c.(445-447)ccC>ccT	p.P149P	PSG1_ENST00000244296.2_Silent_p.P149P|PSG1_ENST00000403380.3_Intron|PSG1_ENST00000312439.6_Silent_p.P149P|PSG1_ENST00000595124.1_Intron|PSG1_ENST00000595356.1_Silent_p.P149P	NM_001184825.1|NM_001184826.1	NP_001171754.1|NP_001171755.1	P11464	PSG1_HUMAN	pregnancy specific beta-1-glycoprotein 1	149	Ig-like C2-type 1.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)		p.P149P(2)		breast(2)|endometrium(4)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	30		Prostate(69;0.00682)				TGGAGATGGAGGGCTTAGGAG	0.512																																																	2	Substitution - coding silent(2)	kidney(2)											152.0	144.0	147.0					19																	43376181		2201	4299	6500	SO:0001819	synonymous_variant	5669				CCDS12612.1, CCDS54275.1, CCDS59392.1, CCDS74380.1	19q13.2	2013-01-29			ENSG00000231924	ENSG00000231924		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9514	protein-coding gene	gene with protein product		176390		PSBG1			Standard	NM_006905		Approved	PSGGA, CD66f, PBG1		P11464	OTTHUMG00000151123	ENST00000436291.2:c.447C>T	19.37:g.43376181G>A		Somatic		WXS	Illumina HiSeq	Phase_I	O75236|P11462|P11463|Q15231|Q15241|Q15243|Q16660|Q6ICR4|Q9P1W5|Q9UQ79	Silent	SNP	ENST00000436291.2	37	CCDS54275.1																																																																																				0.512	PSG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321426.1			
RABGGTB	5876	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	76254935	76254935	+	Missense_Mutation	SNP	G	G	C			TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr1:76254935G>C	ENST00000319942.3	+	3	274	c.203G>C	c.(202-204)aGa>aCa	p.R68T	SNORD45A_ENST00000384512.1_RNA|RABGGTB_ENST00000496055.1_3'UTR|SNORD45C_ENST00000383893.1_RNA|RABGGTB_ENST00000370826.3_Missense_Mutation_p.R68T|SNORD45B_ENST00000364617.1_RNA|RABGGTB_ENST00000535300.1_5'UTR	NM_004582.3	NP_004573.2	P53611	PGTB2_HUMAN	Rab geranylgeranyltransferase, beta subunit	68					cellular protein modification process (GO:0006464)|protein geranylgeranylation (GO:0018344)|visual perception (GO:0007601)	Rab-protein geranylgeranyltransferase complex (GO:0005968)	Rab geranylgeranyltransferase activity (GO:0004663)|Rab GTPase binding (GO:0017137)|zinc ion binding (GO:0008270)	p.R68T(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(7)|ovary(1)	19						CGCATGAATAGAGAAGAGATT	0.383																																																	1	Substitution - Missense(1)	kidney(1)											158.0	148.0	151.0					1																	76254935		2203	4300	6503	SO:0001583	missense	5876			U49245	CCDS669.1	1p31	2008-02-05			ENSG00000137955	ENSG00000137955			9796	protein-coding gene	gene with protein product		179080				8706741, 8954794	Standard	NM_004582		Approved		uc001dgy.2	P53611	OTTHUMG00000009786	ENST00000319942.3:c.203G>C	1.37:g.76254935G>C	ENSP00000317473:p.Arg68Thr	Somatic		WXS	Illumina HiSeq	Phase_I	Q92697	Missense_Mutation	SNP	ENST00000319942.3	37	CCDS669.1	.	.	.	.	.	.	.	.	.	.	G	13.81	2.346727	0.41599	.	.	ENSG00000137955	ENST00000319942;ENST00000370824;ENST00000370826	T;T	0.47528	0.84;0.84	4.79	2.86	0.33363	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);	0.327957	0.34223	N	0.004149	T	0.23014	0.0556	L	0.58969	1.84	0.80722	D	1	B;B	0.12630	0.006;0.001	B;B	0.16722	0.011;0.016	T	0.12268	-1.0554	10	0.45353	T	0.12	-16.2955	5.2469	0.15502	0.4304:0.0:0.5696:0.0	.	68;68	Q59GT6;P53611	.;PGTB2_HUMAN	T	68	ENSP00000317473:R68T;ENSP00000359862:R68T	ENSP00000317473:R68T	R	+	2	0	RABGGTB	76027523	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	1.573000	0.36472	0.967000	0.38186	0.563000	0.77884	AGA		0.383	RABGGTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026972.1		NM_004582	
RAPGEF6	51735	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	130841087	130841087	+	Silent	SNP	T	T	G			TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr5:130841087T>G	ENST00000509018.1	-	10	1276	c.1071A>C	c.(1069-1071)ggA>ggC	p.G357G	CTC-432M15.3_ENST00000514667.1_Silent_p.G407G|RAPGEF6_ENST00000308008.6_Silent_p.G357G|RAPGEF6_ENST00000296859.6_Silent_p.G357G|RAPGEF6_ENST00000510071.1_Silent_p.G357G|RAPGEF6_ENST00000512052.1_Silent_p.G72G|RAPGEF6_ENST00000507093.1_Silent_p.G357G|RAPGEF6_ENST00000307984.5_Silent_p.G357G	NM_001164386.1|NM_016340.5	NP_001157858.1|NP_057424.3	Q8TEU7	RPGF6_HUMAN	Rap guanine nucleotide exchange factor (GEF) 6	357					positive regulation of GTPase activity (GO:0043547)|Ras protein signal transduction (GO:0007265)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTP-dependent protein binding (GO:0030742)|guanyl-nucleotide exchange factor activity (GO:0005085)|Ras GTPase binding (GO:0017016)	p.G357G(3)|p.G407G(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|skin(1)|stomach(1)	31			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)		TCCTGACAATTCCATGCATGT	0.383																																					Melanoma(168;435 1955 13113 13877 23213)												4	Substitution - coding silent(4)	kidney(4)											120.0	115.0	117.0					5																	130841087		2203	4300	6503	SO:0001819	synonymous_variant	51735			AF117947	CCDS34225.1, CCDS54897.1, CCDS54898.1, CCDS54899.1, CCDS54900.1	5q31.1	2008-02-05	2004-03-01	2004-03-02	ENSG00000158987	ENSG00000158987			20655	protein-coding gene	gene with protein product		610499	"""PDZ domain containing guanine nucleotide exchange factor (GEF) 2"""	PDZGEF2		11524421, 12095257	Standard	NM_016340		Approved	RA-GEF-2, PDZ-GEF2	uc010jdi.2	Q8TEU7	OTTHUMG00000162683	ENST00000509018.1:c.1071A>C	5.37:g.130841087T>G		Somatic		WXS	Illumina HiSeq	Phase_I	A3KN82|A5PLL6|B7ZML2|E9PDV7|Q8NI21|Q8TEU6|Q96PC1	Silent	SNP	ENST00000509018.1	37	CCDS34225.1																																																																																				0.383	RAPGEF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370059.1		NM_016340	
RLTPR	146206	hgsc.bcm.edu	37	16	67688684	67688685	+	Frame_Shift_Ins	INS	-	-	G	rs199924683|rs200968420		TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr16:67688684_67688685insG	ENST00000334583.6	+	32	3914_3915	c.3586_3587insG	c.(3586-3588)cggfs	p.R1196fs	RLTPR_ENST00000545661.1_Frame_Shift_Ins_p.R1160fs	NM_001013838.1	NP_001013860.1	Q6F5E8	LR16C_HUMAN	RGD motif, leucine rich repeats, tropomodulin domain and proline-rich containing	1196					cell migration (GO:0016477)|establishment of protein localization (GO:0045184)|homeostasis of number of cells (GO:0048872)|maintenance of cell polarity (GO:0030011)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interferon-gamma secretion (GO:1902715)|positive regulation of interleukin-2 secretion (GO:1900042)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell proliferation (GO:0042102)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|F-actin capping protein complex (GO:0008290)|immunological synapse (GO:0001772)|membrane (GO:0016020)				breast(1)|cervix(1)|endometrium(4)|kidney(1)|lung(9)|urinary_tract(2)	18		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0146)|Epithelial(162;0.0481)|all cancers(182;0.232)		TCCCTAGCGGCGGCCCCTGGAG	0.634																																																	0										24,3654		2,20,1817						4.9	1.0		dbSNP_120	75	45,7823		0,45,3889	no	frameshift	RLTPR	NM_001013838.1		2,65,5706	A1A1,A1R,RR		0.5719,0.6525,0.5976				69,11477				SO:0001589	frameshift_variant	146206			AB113647	CCDS45513.1	16q22.1	2010-09-10				ENSG00000159753			27089	protein-coding gene	gene with protein product	"""RGD, leucine-rich repeat, tropomodulin and proline-rich containing protein"", ""leucine rich repeat containing 16C"""	610859				15588584, 19846667	Standard	XM_005255807		Approved	LRRC16C, CARMIL2	uc002etn.3	Q6F5E8		ENST00000334583.6:c.3588dupG	16.37:g.67688686_67688686dupG	ENSP00000334958:p.Arg1196fs	Somatic		WXS	Illumina HiSeq	Phase_I	B8X2Z3	Frame_Shift_Ins	INS	ENST00000334583.6	37	CCDS45513.1																																																																																				0.634	RLTPR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467858.1		NM_001013838	
RPS6KC1	26750	broad.mit.edu;hgsc.bcm.edu	37	1	213349818	213349818	+	Missense_Mutation	SNP	C	C	G			TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr1:213349818C>G	ENST00000366960.3	+	8	1177	c.1027C>G	c.(1027-1029)Ctt>Gtt	p.L343V	RPS6KC1_ENST00000543470.1_Intron|RPS6KC1_ENST00000490299.1_3'UTR|RPS6KC1_ENST00000366959.3_Missense_Mutation_p.L331V|RPS6KC1_ENST00000543354.1_Missense_Mutation_p.L46V	NM_012424.3	NP_036556.2	Q96S38	KS6C1_HUMAN	ribosomal protein S6 kinase, 52kDa, polypeptide 1	343					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)	p.L343V(1)		breast(1)|endometrium(6)|kidney(4)|large_intestine(8)|liver(2)|lung(15)|ovary(3)|prostate(1)|urinary_tract(3)	43				OV - Ovarian serous cystadenocarcinoma(81;0.00705)|all cancers(67;0.016)|GBM - Glioblastoma multiforme(131;0.0663)|Epithelial(68;0.145)		CTTCAGAGTCCTTGGGGTGAT	0.448																																																	1	Substitution - Missense(1)	kidney(1)											129.0	125.0	126.0					1																	213349818		2203	4300	6503	SO:0001583	missense	26750			AF037447	CCDS1513.1, CCDS44317.1, CCDS73028.1, CCDS73029.1, CCDS73030.1	1q41	2011-04-05	2002-08-29		ENSG00000136643	ENSG00000136643			10439	protein-coding gene	gene with protein product			"""ribosomal protein S6 kinase, 52kD, polypeptide 1"""			10552933	Standard	XM_005273095		Approved	humS6PKh1	uc010ptr.2	Q96S38	OTTHUMG00000036926	ENST00000366960.3:c.1027C>G	1.37:g.213349818C>G	ENSP00000355927:p.Leu343Val	Somatic		WXS	Illumina HiSeq	Phase_I	B1APS8|B3KVM4|D3DTA4|Q8TDD3|Q9NSF4|Q9UL66	Missense_Mutation	SNP	ENST00000366960.3	37	CCDS1513.1	.	.	.	.	.	.	.	.	.	.	C	18.98	3.738593	0.69304	.	.	ENSG00000136643	ENST00000366960;ENST00000366959;ENST00000543354	T;T;T	0.52526	1.26;1.27;0.66	5.86	5.86	0.93980	.	0.068202	0.64402	D	0.000014	T	0.60625	0.2283	L	0.41632	1.29	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.48352	-0.9043	10	0.13853	T	0.58	-36.3423	20.1859	0.98214	0.0:1.0:0.0:0.0	.	343;331	Q96S38;B1APS8	KS6C1_HUMAN;.	V	343;331;46	ENSP00000355927:L343V;ENSP00000355926:L331V;ENSP00000439282:L46V	ENSP00000355926:L331V	L	+	1	0	RPS6KC1	211416441	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.649000	0.61433	2.777000	0.95525	0.591000	0.81541	CTT		0.448	RPS6KC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089690.3		NM_012424	
SEPT3	55964	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	22	42383654	42383654	+	Nonsense_Mutation	SNP	G	G	T			TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr22:42383654G>T	ENST00000396426.3	+	5	697	c.442G>T	c.(442-444)Gag>Tag	p.E148*	SEPT3_ENST00000406029.1_Nonsense_Mutation_p.E84*|SEPT3_ENST00000396425.3_Nonsense_Mutation_p.E148*|SEPT3_ENST00000328414.8_Missense_Mutation_p.M77I|SEPT3_ENST00000291236.11_Nonsense_Mutation_p.E84*	NM_145733.2	NP_663786.2	Q9UH03	SEPT3_HUMAN	septin 3	148	Septin-type G.				cell cycle (GO:0007049)|cell division (GO:0051301)	cell junction (GO:0030054)|septin complex (GO:0031105)|synapse (GO:0045202)	GTP binding (GO:0005525)	p.E148*(2)		breast(1)|kidney(3)|large_intestine(5)|lung(6)|prostate(1)|skin(1)	17						GTACATCAATGAGCAGTACGA	0.507																																																	2	Substitution - Nonsense(2)	kidney(2)											185.0	136.0	152.0					22																	42383654		2203	4300	6503	SO:0001587	stop_gained	55964			AF285107	CCDS14026.2, CCDS14027.2	22q13.2	2013-01-21			ENSG00000100167	ENSG00000100167		"""Septins"""	10750	protein-coding gene	gene with protein product		608314		SEP3			Standard	NM_019106		Approved		uc003bbr.4	Q9UH03	OTTHUMG00000030494	ENST00000396426.3:c.442G>T	22.37:g.42383654G>T	ENSP00000379704:p.Glu148*	Somatic		WXS	Illumina HiSeq	Phase_I	B1AHR0|Q2NKJ7|Q59GF7|Q6IBZ6|Q8N3P3|Q9HD35	Nonsense_Mutation	SNP	ENST00000396426.3	37	CCDS14026.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	34|34	5.404019|5.404019	0.96051|0.96051	.|.	.|.	ENSG00000100167|ENSG00000100167	ENST00000449288;ENST00000396426;ENST00000406029;ENST00000396425;ENST00000291236|ENST00000328414	.|.	.|.	.|.	5.19|5.19	5.19|5.19	0.71726|0.71726	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.62780	.|0.2456	.|.	.|.	.|.	0.27727|0.27727	N|N	0.944936|0.944936	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.59936	.|-0.7360	.|5	0.46703|0.87932	T|D	0.11|0	.|.	19.1075|19.1075	0.93301|0.93301	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|I	135;148;84;148;84|77	.|.	ENSP00000291236:E84X|ENSP00000332866:M77I	E|M	+|+	1|3	0|0	SEPT3|SEPT3	40713600|40713600	1.000000|1.000000	0.71417|0.71417	0.825000|0.825000	0.32803|0.32803	0.989000|0.989000	0.77384|0.77384	9.787000|9.787000	0.99055|0.99055	2.590000|2.590000	0.87494|0.87494	0.563000|0.563000	0.77884|0.77884	GAG|ATG		0.507	SEPT3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322051.1		NM_145734	
SH3BP4	23677	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	235949909	235949910	+	Frame_Shift_Del	DEL	CA	CA	-			TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	CA	CA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr2:235949909_235949910delCA	ENST00000409212.1	+	4	1003_1004	c.496_497delCA	c.(496-498)cagfs	p.Q166fs	SH3BP4_ENST00000392011.2_Frame_Shift_Del_p.Q166fs|SH3BP4_ENST00000344528.4_Frame_Shift_Del_p.Q166fs			Q9P0V3	SH3B4_HUMAN	SH3-domain binding protein 4	166					cellular response to amino acid stimulus (GO:0071230)|endocytosis (GO:0006897)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of GTPase activity (GO:0034260)|negative regulation of TOR signaling (GO:0032007)|positive regulation of autophagy (GO:0010508)|protein localization to lysosome (GO:0061462)|regulation of catalytic activity (GO:0050790)	coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	GDP-dissociation inhibitor activity (GO:0005092)|identical protein binding (GO:0042802)|Ras GTPase binding (GO:0017016)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(6)|stomach(3)|urinary_tract(2)	44		Breast(86;0.000332)|Renal(207;0.00339)|all_lung(227;0.00458)|all_hematologic(139;0.0296)|Lung NSC(271;0.0419)		Epithelial(121;7.66e-20)|BRCA - Breast invasive adenocarcinoma(100;0.000402)|Lung(119;0.00299)|LUSC - Lung squamous cell carcinoma(224;0.00645)|GBM - Glioblastoma multiforme(43;0.237)		GAATGGGGTCCAGACCAATCCA	0.505																																																	0																																										SO:0001589	frameshift_variant	23677			AF147747	CCDS2513.1	2q37.1-q37.2	2008-05-15			ENSG00000130147	ENSG00000130147			10826	protein-coding gene	gene with protein product		605611				10644451	Standard	NM_014521		Approved		uc002vvp.3	Q9P0V3	OTTHUMG00000133292	ENST00000409212.1:c.496_497delCA	2.37:g.235949909_235949910delCA	ENSP00000386862:p.Gln166fs	Somatic		WXS	Illumina HiSeq	Phase_I	O95082|Q309A3|Q53QD0|Q53TD1	Frame_Shift_Del	DEL	ENST00000409212.1	37	CCDS2513.1																																																																																				0.505	SH3BP4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329763.1			
SLC6A16	28968	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	49797187	49797187	+	Silent	SNP	C	C	T	rs368968956		TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr19:49797187C>T	ENST00000335875.4	-	9	1756	c.1515G>A	c.(1513-1515)ttG>ttA	p.L505L	SLC6A16_ENST00000454748.3_Silent_p.L505L	NM_014037.2	NP_054756.2	Q9GZN6	S6A16_HUMAN	solute carrier family 6, member 16	505					neurotransmitter transport (GO:0006836)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)	neurotransmitter transporter activity (GO:0005326)|neurotransmitter:sodium symporter activity (GO:0005328)	p.L505L(1)		NS(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00099)|GBM - Glioblastoma multiforme(486;0.0336)		CCATGGCCAGCAACATCAGGA	0.498																																																	1	Substitution - coding silent(1)	kidney(1)											161.0	165.0	163.0					19																	49797187		2027	4188	6215	SO:0001819	synonymous_variant	28968			AF265578	CCDS42590.1	19q13.33	2013-05-22			ENSG00000063127	ENSG00000063127		"""Solute carriers"""	13622	protein-coding gene	gene with protein product	"""NTT5 protein"""	607972	"""solute carrier family 6 (neurotransmitter transporter), member 16"""			10471414, 11112352	Standard	XM_005258820		Approved	NTT5	uc002pmz.3	Q9GZN6		ENST00000335875.4:c.1515G>A	19.37:g.49797187C>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q8IYV4|Q9Y5I9	Silent	SNP	ENST00000335875.4	37	CCDS42590.1																																																																																				0.498	SLC6A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465503.2		NM_014037	
STX8	9482	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	9153958	9153958	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr17:9153958C>T	ENST00000306357.4	-	8	1075	c.648G>A	c.(646-648)atG>atA	p.M216I	STX8_ENST00000574431.1_Missense_Mutation_p.M105I	NM_004853.2	NP_004844.1	Q9UNK0	STX8_HUMAN	syntaxin 8	216					endosome to lysosome transport (GO:0008333)|intracellular protein transport (GO:0006886)|transport (GO:0006810)|vesicle fusion (GO:0006906)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)	p.M216I(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|skin(1)|urinary_tract(1)	12						TCACCATGATCATCCCTGGAA	0.458																																																	1	Substitution - Missense(1)	kidney(1)											129.0	115.0	120.0					17																	9153958		2202	4299	6501	SO:0001583	missense	9482			AF115323	CCDS32565.1	17p13.1	2012-05-25			ENSG00000170310	ENSG00000170310			11443	protein-coding gene	gene with protein product		604203				9852078, 10198254	Standard	NM_004853		Approved	CARB	uc002glx.3	Q9UNK0	OTTHUMG00000177844	ENST00000306357.4:c.648G>A	17.37:g.9153958C>T	ENSP00000305255:p.Met216Ile	Somatic		WXS	Illumina HiSeq	Phase_I	O60712|Q53XT8	Missense_Mutation	SNP	ENST00000306357.4	37	CCDS32565.1	.	.	.	.	.	.	.	.	.	.	C	17.79	3.476014	0.63737	.	.	ENSG00000170310	ENST00000306357	.	.	.	4.94	4.94	0.65067	.	0.000000	0.85682	D	0.000000	T	0.56062	0.1960	M	0.74881	2.28	0.80722	D	1	P	0.39116	0.66	B	0.35550	0.205	T	0.57562	-0.7790	9	0.25106	T	0.35	-23.8486	15.476	0.75481	0.0:1.0:0.0:0.0	.	216	Q9UNK0	STX8_HUMAN	I	216	.	ENSP00000305255:M216I	M	-	3	0	STX8	9094683	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	5.332000	0.65911	2.565000	0.86533	0.655000	0.94253	ATG		0.458	STX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439206.3		NM_004853	
SYF2	25949	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	25549846	25549846	+	Missense_Mutation	SNP	T	T	A			TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr1:25549846T>A	ENST00000236273.4	-	7	668	c.643A>T	c.(643-645)Aat>Tat	p.N215Y	SYF2_ENST00000354361.3_Missense_Mutation_p.N173Y	NM_015484.4	NP_056299.1	O95926	SYF2_HUMAN	SYF2 pre-mRNA-splicing factor	215					embryonic organ development (GO:0048568)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|mitotic G2 DNA damage checkpoint (GO:0007095)|mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.N215Y(1)		kidney(1)|large_intestine(1)|lung(4)	6		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0101)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.5e-26)|Colorectal(126;2.54e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000455)|STAD - Stomach adenocarcinoma(196;0.000766)|KIRC - Kidney renal clear cell carcinoma(1967;0.00145)|GBM - Glioblastoma multiforme(114;0.00443)|READ - Rectum adenocarcinoma(331;0.0936)|Lung(427;0.201)		AATTTGGCATTCCTTTCATTA	0.358																																																	1	Substitution - Missense(1)	kidney(1)											187.0	192.0	190.0					1																	25549846		2203	4300	6503	SO:0001583	missense	25949			AF273089	CCDS258.1, CCDS259.1	1p36.11	2013-08-21	2013-08-21	2005-09-14	ENSG00000117614	ENSG00000117614			19824	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 29"""	607090	"""CCNDBP1 interactor"", ""SYF2 homolog, RNA splicing factor (S. cerevisiae)"""	CBPIN		11118353	Standard	NM_207170		Approved	p29, DKFZp564O2082, NTC31, fSAP29	uc001bjt.1	O95926	OTTHUMG00000043610	ENST00000236273.4:c.643A>T	1.37:g.25549846T>A	ENSP00000236273:p.Asn215Tyr	Somatic		WXS	Illumina HiSeq	Phase_I	Q5TH73	Missense_Mutation	SNP	ENST00000236273.4	37	CCDS259.1	.	.	.	.	.	.	.	.	.	.	T	14.85	2.658003	0.47467	.	.	ENSG00000117614	ENST00000236273;ENST00000354361	D;D	0.86097	-2.07;-1.74	5.56	4.43	0.53597	.	0.000000	0.85682	D	0.000000	D	0.93893	0.8046	H	0.95611	3.695	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.79784	0.993;0.991	D	0.94191	0.7441	10	0.87932	D	0	-1.7055	10.6532	0.45659	0.0:0.0762:0.0:0.9238	.	215;215	B2RBX8;O95926	.;SYF2_HUMAN	Y	215;173	ENSP00000236273:N215Y;ENSP00000346330:N173Y	ENSP00000236273:N215Y	N	-	1	0	SYF2	25422433	1.000000	0.71417	1.000000	0.80357	0.130000	0.20726	7.617000	0.83032	1.049000	0.40321	-0.256000	0.11100	AAT		0.358	SYF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000101962.1		NM_015484	
TMX3	54495	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	18	66348333	66348333	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr18:66348333G>A	ENST00000299608.2	-	14	1236	c.920C>T	c.(919-921)cCa>cTa	p.P307L		NM_019022.3	NP_061895.3	Q96JJ7	TMX3_HUMAN	thioredoxin-related transmembrane protein 3	307					cell redox homeostasis (GO:0045454)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein disulfide isomerase activity (GO:0003756)	p.P307L(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	17						AACTACAGTTGGGACTGTCAA	0.294																																																	1	Substitution - Missense(1)	kidney(1)											95.0	96.0	96.0					18																	66348333		2203	4300	6503	SO:0001583	missense	54495			BX647846	CCDS32840.1	18q22	2011-10-19	2009-02-23	2009-02-23		ENSG00000166479		"""Protein disulfide isomerases"""	24718	protein-coding gene	gene with protein product	"""protein disulfide isomerase family A, member 13"""		"""thioredoxin domain containing 10"""	TXNDC10		15623505	Standard	NM_019022		Approved	FLJ20793, KIAA1830, PDIA13	uc002lkf.3	Q96JJ7		ENST00000299608.2:c.920C>T	18.37:g.66348333G>A	ENSP00000299608:p.Pro307Leu	Somatic		WXS	Illumina HiSeq	Phase_I	B3KV75|Q52LT7|Q8N5J0|Q9NWJ9	Missense_Mutation	SNP	ENST00000299608.2	37	CCDS32840.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.220212	0.79464	.	.	ENSG00000166479	ENST00000299608;ENST00000544714	T	0.77750	-1.12	5.81	5.81	0.92471	.	0.049959	0.85682	N	0.000000	D	0.86083	0.5848	L	0.52126	1.63	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.86510	0.1809	10	0.87932	D	0	.	19.0557	0.93064	0.0:0.0:1.0:0.0	.	307	Q96JJ7	TMX3_HUMAN	L	307	ENSP00000299608:P307L	ENSP00000299608:P307L	P	-	2	0	TMX3	64499313	1.000000	0.71417	0.945000	0.38365	0.922000	0.55478	8.831000	0.92068	2.755000	0.94549	0.655000	0.94253	CCA		0.294	TMX3-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420155.1		NM_019022	
TPR	7175	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	186302399	186302399	+	Silent	SNP	T	T	C			TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr1:186302399T>C	ENST00000367478.4	-	37	5606	c.5310A>G	c.(5308-5310)acA>acG	p.T1770T		NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	1770					carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)	p.T1770T(1)|p.T1771T(1)		autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		CTGTAGCCTGTGTTTGTTGCT	0.423			T	NTRK1	papillary thyroid																																			Dom	yes		1	1q25	7175	translocated promoter region		E	2	Substitution - coding silent(2)	kidney(2)											159.0	153.0	155.0					1																	186302399		1922	4125	6047	SO:0001819	synonymous_variant	7175			U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410			12017	protein-coding gene	gene with protein product		189940	"""translocated promoter region (to activated MET oncogene)"""			1611909, 15229283	Standard	NM_003292		Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.5310A>G	1.37:g.186302399T>C		Somatic		WXS	Illumina HiSeq	Phase_I	Q15655|Q5SWY0|Q99968	Silent	SNP	ENST00000367478.4	37	CCDS41446.1																																																																																				0.423	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2		NM_003292	
TRERF1	55809	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	42232448	42232448	+	Silent	SNP	G	G	A			TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr6:42232448G>A	ENST00000372922.4	-	7	2191	c.1629C>T	c.(1627-1629)ctC>ctT	p.L543L	TRERF1_ENST00000340840.2_Silent_p.L543L|TRERF1_ENST00000541110.1_Silent_p.L543L|TRERF1_ENST00000372917.4_Silent_p.L543L|TRERF1_ENST00000354325.2_Silent_p.L543L	NM_033502.2	NP_277037.1	Q96PN7	TREF1_HUMAN	transcriptional regulating factor 1	543	Interacts with CREBBP.				cholesterol catabolic process (GO:0006707)|homeostatic process (GO:0042592)|multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hormone biosynthetic process (GO:0046885)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|steroid biosynthetic process (GO:0006694)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.L543L(1)		breast(1)|central_nervous_system(2)|endometrium(7)|kidney(1)|large_intestine(12)|lung(13)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(2)	45	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			TAACCTGTTTGAGGTTGGGGG	0.582																																																	1	Substitution - coding silent(1)	kidney(1)											82.0	76.0	78.0					6																	42232448		2203	4300	6503	SO:0001819	synonymous_variant	55809			AF297872	CCDS4867.1, CCDS75455.1	6p21.1-p12.1	2012-09-25			ENSG00000124496	ENSG00000124496			18273	protein-coding gene	gene with protein product		610322	"""breast cancer anti-estrogen resistance 2"""	BCAR2		11349124	Standard	XM_005249223		Approved	TReP-132, HSA277276, RAPA, dJ139D8.5	uc003osd.2	Q96PN7	OTTHUMG00000014698	ENST00000372922.4:c.1629C>T	6.37:g.42232448G>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q05GC6|Q7Z6T2|Q7Z6T3|Q9NQ72|Q9NQ73|Q9NUN9	Silent	SNP	ENST00000372922.4	37	CCDS4867.1																																																																																				0.582	TRERF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040551.2		NM_033502	
UACA	55075	hgsc.bcm.edu;ucsc.edu	37	15	70961379	70961380	+	Frame_Shift_Ins	INS	-	-	TA			TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr15:70961379_70961380insTA	ENST00000322954.6	-	16	1828_1829	c.1643_1644insTA	c.(1642-1644)gacfs	p.D548fs	UACA_ENST00000560441.1_Frame_Shift_Ins_p.D533fs|UACA_ENST00000379983.2_Frame_Shift_Ins_p.D535fs|UACA_ENST00000539319.1_Frame_Shift_Ins_p.D439fs	NM_018003.2	NP_060473.2	Q9BZF9	UACA_HUMAN	uveal autoantigen with coiled-coil domains and ankyrin repeats	548					intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of protein import into nucleus (GO:0042307)|response to UV (GO:0009411)	apoptosome (GO:0043293)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				breast(2)|endometrium(7)|kidney(4)|large_intestine(13)|lung(17)|ovary(2)|pancreas(1)|prostate(2)|skin(2)	50						TTACTTTCAAGTCTTTCAACTG	0.391																																																	0																																										SO:0001589	frameshift_variant	55075			AF322916	CCDS10235.1, CCDS32280.1	15q22-q24	2013-01-10			ENSG00000137831	ENSG00000137831		"""Ankyrin repeat domain containing"""	15947	protein-coding gene	gene with protein product		612516				11162650, 10997877	Standard	NM_001008224		Approved	FLJ10128, KIAA1561	uc002asr.3	Q9BZF9	OTTHUMG00000133363	ENST00000322954.6:c.1643_1644insTA	15.37:g.70961379_70961380insTA	ENSP00000314556:p.Asp548fs	Somatic		WXS	Illumina HiSeq	Phase_I	G3XAG2|Q14DD3|Q8N3B8|Q96NH6|Q9HCL1|Q9NWC6	Frame_Shift_Ins	INS	ENST00000322954.6	37	CCDS10235.1																																																																																				0.391	UACA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257199.2			
UBE2O	63893	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	74392558	74392558	+	Silent	SNP	G	G	T			TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr17:74392558G>T	ENST00000319380.7	-	14	2524	c.2460C>A	c.(2458-2460)atC>atA	p.I820I	UBE2O_ENST00000587581.1_5'Flank	NM_022066.3	NP_071349.3	Q9C0C9	UBE2O_HUMAN	ubiquitin-conjugating enzyme E2O	820					positive regulation of BMP signaling pathway (GO:0030513)|protein K63-linked ubiquitination (GO:0070534)|protein monoubiquitination (GO:0006513)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)	p.I820I(2)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(2)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	36						GGCTCTCCAGGATCTTGATGG	0.617																																																	2	Substitution - coding silent(2)	kidney(2)											119.0	126.0	124.0					17																	74392558		2203	4300	6503	SO:0001819	synonymous_variant	63893			AB051521	CCDS32742.1	17q25.1	2013-10-09			ENSG00000175931	ENSG00000175931			29554	protein-coding gene	gene with protein product						11311559, 11214970	Standard	NM_022066		Approved	E2-230K	uc002jrm.4	Q9C0C9	OTTHUMG00000180178	ENST00000319380.7:c.2460C>A	17.37:g.74392558G>T		Somatic		WXS	Illumina HiSeq	Phase_I	A6NDU5|Q69YP4|Q6PIZ2|Q86UA4|Q8N425|Q8TBN1|Q9BSW1|Q9H6E6|Q9H7E4|Q9H9B2	Silent	SNP	ENST00000319380.7	37	CCDS32742.1																																																																																				0.617	UBE2O-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450123.1		NM_022066	
VHL	7428	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	10188248	10188248	+	Frame_Shift_Del	DEL	A	A	-			TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr3:10188248delA	ENST00000256474.2	+	2	1231	c.391delA	c.(391-393)aacfs	p.N131fs	VHL_ENST00000345392.2_Intron|VHL_ENST00000477538.1_3'UTR	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	131	Involved in binding to CCT complex.		N -> K (in VHLD; type I). {ECO:0000269|PubMed:9829912}.|N -> T (in VHLD; type I). {ECO:0000269|PubMed:9829911}.		cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.N131fs*28(2)|p.N131fs*2(2)|p.N131Y(2)|p.N131*(1)|p.H125fs*27(1)|p.?fs(1)|p.V130fs*28(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		GCTTCTGGTTAACCAAACTGA	0.458		1	"""D, Mis, N, F, S"""		"""renal, hemangioma, pheochromocytoma"""	"""renal, hemangioma, pheochromocytoma"""			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																														yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"""E, M, O"""	10	Deletion - Frameshift(5)|Insertion - Frameshift(3)|Substitution - Missense(2)	kidney(10)											206.0	190.0	195.0					3																	10188248		2203	4300	6503	SO:0001589	frameshift_variant	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"""von Hippel-Lindau syndrome"", ""von Hippel-Lindau tumor suppressor"""			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.391delA	3.37:g.10188248delA	ENSP00000256474:p.Asn131fs	Somatic		WXS	Illumina HiSeq	Phase_I	B2RE45|Q13599|Q6PDA9	Frame_Shift_Del	DEL	ENST00000256474.2	37	CCDS2597.1																																																																																				0.458	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1		NM_000551	
VWA2	340706	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	116038497	116038497	+	Frame_Shift_Del	DEL	C	C	-			TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr10:116038497delC	ENST00000392982.3	+	8	970	c.720delC	c.(718-720)cacfs	p.H240fs	VWA2_ENST00000603594.1_Frame_Shift_Del_p.H240fs			Q5GFL6	VWA2_HUMAN	von Willebrand factor A domain containing 2	240					calcium-independent cell-matrix adhesion (GO:0007161)|protein homooligomerization (GO:0051260)|regulation of insulin receptor signaling pathway (GO:0046626)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)			central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)	26				Epithelial(162;0.036)|all cancers(201;0.0793)		TCGAGGCTCACCCCTGTGAGC	0.647																																																	0													118.0	92.0	100.0					10																	116038497		2203	4300	6503	SO:0001589	frameshift_variant	340706			AK127756	CCDS7589.1, CCDS7589.2	10q25.3	2009-11-06			ENSG00000165816	ENSG00000165816			24709	protein-coding gene	gene with protein product						15580307, 14506275	Standard	NM_001272046		Approved	FLJ45857, FLJ16213, CCSP-2, AMACO, NET42	uc001lbl.2	Q5GFL6	OTTHUMG00000019082	ENST00000392982.3:c.720delC	10.37:g.116038497delC	ENSP00000376708:p.His240fs	Somatic		WXS	Illumina HiSeq	Phase_I	A1A5D4|B5MDJ8|Q6ZS39|Q6ZWJ7|Q708C5|Q70UZ8	Frame_Shift_Del	DEL	ENST00000392982.3	37																																																																																					0.647	VWA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050456.3		NM_198496	
ZFP36L2	678	hgsc.bcm.edu	37	2	43452740	43452740	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr2:43452740G>A	ENST00000282388.3	-	2	496	c.203C>T	c.(202-204)gCg>gTg	p.A68V	THADA_ENST00000330266.7_Intron	NM_006887.4	NP_008818.3	P47974	TISD_HUMAN	ZFP36 ring finger protein-like 2	68					cell proliferation (GO:0008283)|definitive hemopoiesis (GO:0060216)|hemopoiesis (GO:0030097)|mRNA catabolic process (GO:0006402)|negative regulation of stem cell differentiation (GO:2000737)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	15		Acute lymphoblastic leukemia(82;0.00323)|all_hematologic(82;0.00824)				GGGGCTGGGCGCGGGGTGGGC	0.766																																																	0													4.0	6.0	5.0					2																	43452740		1893	3795	5688	SO:0001583	missense	678			X78992	CCDS1811.1	2p22.3-p21	2012-11-27	2012-11-27	2001-11-23	ENSG00000152518	ENSG00000152518		"""RING-type (C3HC4) zinc fingers"""	1108	protein-coding gene	gene with protein product		612053	"""zinc finger protein 36, C3H type-like 1"", ""zinc finger protein 36, C3H type-like 2"""	BRF2		7835719, 8545129, 14981510, 17172869	Standard	NM_006887		Approved	ERF2, RNF162C, TIS11D	uc002rsv.4	P47974	OTTHUMG00000128642	ENST00000282388.3:c.203C>T	2.37:g.43452740G>A	ENSP00000282388:p.Ala68Val	Somatic		WXS	Illumina HiSeq	Phase_I	Q53TB4|Q9BSJ3	Missense_Mutation	SNP	ENST00000282388.3	37	CCDS1811.1	.	.	.	.	.	.	.	.	.	.	G	15.40	2.821679	0.50633	.	.	ENSG00000152518	ENST00000282388	T	0.47177	0.85	5.13	3.1	0.35709	Tis11B-like protein, N-terminal (1);	0.694656	0.12501	N	0.463370	T	0.25419	0.0618	N	0.12182	0.205	0.80722	D	1	B	0.06786	0.001	B	0.08055	0.003	T	0.06534	-1.0821	10	0.14252	T	0.57	-9.0207	7.0806	0.25229	0.0979:0.0:0.6793:0.2228	.	68	P47974	TISD_HUMAN	V	68	ENSP00000282388:A68V	ENSP00000282388:A68V	A	-	2	0	ZFP36L2	43306244	0.809000	0.29036	1.000000	0.80357	0.934000	0.57294	1.496000	0.35638	1.151000	0.42436	0.462000	0.41574	GCG		0.766	ZFP36L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250513.2		NM_006887	
XPO1	7514	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	61709537	61709537	+	Missense_Mutation	SNP	A	A	G			TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr2:61709537A>G	ENST00000401558.2	-	23	3677	c.2950T>C	c.(2950-2952)Tcg>Ccg	p.S984P	RP11-355B11.2_ENST00000603652.1_RNA|XPO1_ENST00000406957.1_Missense_Mutation_p.S984P|RP11-355B11.2_ENST00000605437.1_RNA|XPO1_ENST00000404992.2_Missense_Mutation_p.S984P|RP11-355B11.2_ENST00000603028.1_RNA|RP11-355B11.2_ENST00000578974.2_RNA|RP11-355B11.2_ENST00000603199.1_RNA	NM_003400.3	NP_003391.1	O14980	XPO1_HUMAN	exportin 1	984					gene expression (GO:0010467)|intracellular transport of virus (GO:0075733)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|mRNA transport (GO:0051028)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|protein export from nucleus (GO:0006611)|protein localization to nucleus (GO:0034504)|regulation of centrosome duplication (GO:0010824)|regulation of protein catabolic process (GO:0042176)|regulation of protein export from nucleus (GO:0046825)|response to drug (GO:0042493)|ribosomal large subunit export from nucleus (GO:0000055)|ribosomal small subunit export from nucleus (GO:0000056)|RNA metabolic process (GO:0016070)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral life cycle (GO:0019058)|viral process (GO:0016032)	annulate lamellae (GO:0005642)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleocytoplasmic transporter activity (GO:0005487)|protein transporter activity (GO:0008565)|RNA binding (GO:0003723)|transporter activity (GO:0005215)	p.S984P(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(5)|lung(5)|ovary(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	39			LUSC - Lung squamous cell carcinoma(7;5.71e-05)|Epithelial(17;0.0662)|all cancers(80;0.226)			GGGAAGGCCGACTTAAGGAGA	0.398			Mis		CLL																																		-'	Dom	yes		2	2p15	7514	"""exportin 1 (CRM1 homolog, yeast)"""		L	1	Substitution - Missense(1)	kidney(1)											131.0	132.0	132.0					2																	61709537		2203	4300	6503	SO:0001583	missense	7514			Y08614	CCDS33205.1	2p15	2014-02-19	2014-02-19		ENSG00000082898	ENSG00000082898		"""Exportins"""	12825	protein-coding gene	gene with protein product	"""chromosome region maintenance 1 homolog (yeast)"""	602559	"""exportin 1 (CRM1, yeast, homolog)"", ""exportin 1 (CRM1 homolog, yeast)"""			9205132, 9368044	Standard	XM_005264544		Approved	CRM1, emb	uc002sbj.3	O14980	OTTHUMG00000152316	ENST00000401558.2:c.2950T>C	2.37:g.61709537A>G	ENSP00000384863:p.Ser984Pro	Somatic		WXS	Illumina HiSeq	Phase_I	A6NL14|A8K1K5|D6W5E2|Q63HP8|Q68CP3|Q99433	Missense_Mutation	SNP	ENST00000401558.2	37	CCDS33205.1	.	.	.	.	.	.	.	.	.	.	A	17.52	3.409070	0.62399	.	.	ENSG00000082898	ENST00000401558;ENST00000404992;ENST00000406957	T;T;T	0.66638	-0.22;-0.22;-0.22	5.46	5.46	0.80206	Armadillo-like helical (1);Armadillo-type fold (2);Exportin 1, C-terminal (1);	0.055426	0.85682	D	0.000000	T	0.67998	0.2953	M	0.75615	2.305	0.54753	D	0.999989	B;B	0.27882	0.192;0.124	B;B	0.25506	0.025;0.061	T	0.69544	-0.5117	10	0.66056	D	0.02	-16.6961	15.8252	0.78698	1.0:0.0:0.0:0.0	.	631;984	B3KWD0;O14980	.;XPO1_HUMAN	P	984	ENSP00000384863:S984P;ENSP00000385942:S984P;ENSP00000385559:S984P	ENSP00000384863:S984P	S	-	1	0	XPO1	61563041	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	5.312000	0.65792	2.197000	0.70478	0.482000	0.46254	TCG		0.398	XPO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325872.3		NM_003400	
ZFR2	23217	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	3813939	3813939	+	Missense_Mutation	SNP	C	C	G			TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr19:3813939C>G	ENST00000262961.4	-	14	2131	c.2121G>C	c.(2119-2121)gaG>gaC	p.E707D		NM_015174.1	NP_055989.1	Q9UPR6	ZFR2_HUMAN	zinc finger RNA binding protein 2	707	DZF. {ECO:0000255|PROSITE- ProRule:PRU01040}.						nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.E707D(1)		central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(5)|pancreas(1)|prostate(1)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00514)|STAD - Stomach adenocarcinoma(1328;0.19)		AGACCTCATACTCATCCTCGG	0.537																																																	1	Substitution - Missense(1)	kidney(1)											67.0	72.0	70.0					19																	3813939		2079	4205	6284	SO:0001583	missense	23217			AB029009	CCDS45921.1, CCDS45922.1	19p13.3	2012-10-05	2008-03-25	2008-03-25	ENSG00000105278	ENSG00000105278			29189	protein-coding gene	gene with protein product			"""KIAA1086"""	KIAA1086		10470851	Standard	NM_015174		Approved		uc002lyw.2	Q9UPR6	OTTHUMG00000180918	ENST00000262961.4:c.2121G>C	19.37:g.3813939C>G	ENSP00000262961:p.Glu707Asp	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000262961.4	37	CCDS45921.1	.	.	.	.	.	.	.	.	.	.	C	15.85	2.955059	0.53293	.	.	ENSG00000105278	ENST00000262961	T	0.06849	3.25	4.72	3.68	0.42216	DZF (2);	0.276201	0.29722	U	0.011362	T	0.07143	0.0181	N	0.14661	0.345	0.80722	D	1	B	0.34349	0.45	B	0.41723	0.365	T	0.37865	-0.9687	10	0.59425	D	0.04	-18.6146	8.9623	0.35854	0.0:0.8952:0.0:0.1048	.	707	Q9UPR6	ZFR2_HUMAN	D	707	ENSP00000262961:E707D	ENSP00000262961:E707D	E	-	3	2	ZFR2	3764939	1.000000	0.71417	0.715000	0.30552	0.799000	0.45148	2.779000	0.47734	0.967000	0.38186	0.591000	0.81541	GAG		0.537	ZFR2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453648.2		NM_015174	
ZFR2	23217	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	3813948	3813948	+	Silent	SNP	G	G	T	rs375016343		TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr19:3813948G>T	ENST00000262961.4	-	14	2122	c.2112C>A	c.(2110-2112)acC>acA	p.T704T		NM_015174.1	NP_055989.1	Q9UPR6	ZFR2_HUMAN	zinc finger RNA binding protein 2	704	DZF. {ECO:0000255|PROSITE- ProRule:PRU01040}.						nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.T704T(1)		central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(5)|pancreas(1)|prostate(1)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00514)|STAD - Stomach adenocarcinoma(1328;0.19)		ACTCATCCTCGGTCACCATCT	0.507																																																	1	Substitution - coding silent(1)	kidney(1)											58.0	62.0	61.0					19																	3813948		2073	4205	6278	SO:0001819	synonymous_variant	23217			AB029009	CCDS45921.1, CCDS45922.1	19p13.3	2012-10-05	2008-03-25	2008-03-25	ENSG00000105278	ENSG00000105278			29189	protein-coding gene	gene with protein product			"""KIAA1086"""	KIAA1086		10470851	Standard	NM_015174		Approved		uc002lyw.2	Q9UPR6	OTTHUMG00000180918	ENST00000262961.4:c.2112C>A	19.37:g.3813948G>T		Somatic		WXS	Illumina HiSeq	Phase_I		Silent	SNP	ENST00000262961.4	37	CCDS45921.1																																																																																				0.507	ZFR2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453648.2		NM_015174	
ZNF266	10781	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	9525150	9525150	+	Frame_Shift_Del	DEL	T	T	-			TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr19:9525150delT	ENST00000592904.1	-	5	2527	c.451delA	c.(451-453)acafs	p.T151fs	ZNF266_ENST00000588221.1_Frame_Shift_Del_p.T151fs|ZNF266_ENST00000588933.1_Frame_Shift_Del_p.T151fs|ZNF266_ENST00000590306.1_Frame_Shift_Del_p.T151fs|ZNF266_ENST00000361151.1_Frame_Shift_Del_p.T151fs|ZNF266_ENST00000592292.1_Frame_Shift_Del_p.T151fs|ZNF266_ENST00000361451.2_Frame_Shift_Del_p.T151fs			Q14584	ZN266_HUMAN	zinc finger protein 266	151					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(2)|large_intestine(11)|lung(8)|ovary(1)|skin(2)|stomach(1)	28						TTCTCTCCTGTGCACGTTCTC	0.438																																																	0													149.0	133.0	139.0					19																	9525150		2203	4300	6503	SO:0001589	frameshift_variant	10781			X78924	CCDS12213.1	19p13.2	2013-01-08				ENSG00000174652		"""Zinc fingers, C2H2-type"""	13059	protein-coding gene	gene with protein product		604751				7865130	Standard	NM_006631		Approved	HZF1	uc002mlo.4	Q14584		ENST00000592904.1:c.451delA	19.37:g.9525150delT	ENSP00000466714:p.Thr151fs	Somatic		WXS	Illumina HiSeq	Phase_I	A0AV90|A4FU85|Q6IQ07|Q6U8A5|Q8IVG3|Q8WVX1|Q96SX9	Frame_Shift_Del	DEL	ENST00000592904.1	37	CCDS12213.1																																																																																				0.438	ZNF266-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449033.1			
ZNF257	113835	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	22270900	22270900	+	Silent	SNP	C	C	A			TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr19:22270900C>A	ENST00000594947.1	+	4	492	c.348C>A	c.(346-348)ggC>ggA	p.G116G	ZNF257_ENST00000600162.1_3'UTR	NM_033468.2	NP_258429.2	Q9Y2Q1	ZN257_HUMAN	zinc finger protein 257	116					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.G116G(1)		haematopoietic_and_lymphoid_tissue(2)|lung(4)	6		all_lung(12;0.0961)|Lung NSC(12;0.103)				TAAGAAAGGGCTGTAAAAGTG	0.348																																																	1	Substitution - coding silent(1)	kidney(1)											75.0	82.0	79.0					19																	22270900		2172	4279	6451	SO:0001819	synonymous_variant	113835			AF070651	CCDS46030.1	19p12	2014-02-14			ENSG00000197134	ENSG00000197134		"""Zinc fingers, C2H2-type"", ""-"""	13498	protein-coding gene	gene with protein product		606957				10585455	Standard	NM_033468		Approved	BMZF-4	uc010ecx.3	Q9Y2Q1	OTTHUMG00000182927	ENST00000594947.1:c.348C>A	19.37:g.22270900C>A		Somatic		WXS	Illumina HiSeq	Phase_I	B3KPS4|E9PG34|Q8NE34	Silent	SNP	ENST00000594947.1	37	CCDS46030.1																																																																																				0.348	ZNF257-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464382.1			
ZNF568	374900	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	37428114	37428114	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr19:37428114G>A	ENST00000333987.7	+	6	834	c.328G>A	c.(328-330)Gag>Aag	p.E110K	ZNF568_ENST00000455427.2_Missense_Mutation_p.E46K|ZNF568_ENST00000427117.1_Missense_Mutation_p.E110K|ZNF568_ENST00000415168.1_Missense_Mutation_p.E46K	NM_001204835.1|NM_198539.3	NP_001191764.1|NP_940941.2	Q3ZCX4	ZN568_HUMAN	zinc finger protein 568	110	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				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)	p.E110K(1)|p.E46K(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(9)|ovary(1)	29	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CTGGGTGATGGAGGAAGAAAT	0.443																																																	2	Substitution - Missense(2)	kidney(2)											101.0	105.0	104.0					19																	37428114		2106	4258	6364	SO:0001583	missense	374900			BX640681	CCDS42558.1, CCDS56092.1, CCDS56093.1, CCDS74351.1	19q13.12	2013-09-20			ENSG00000198453	ENSG00000198453		"""Zinc fingers, C2H2-type"", ""-"""	25392	protein-coding gene	gene with protein product							Standard	NM_198539		Approved	DKFZp686B0797	uc002ofc.3	Q3ZCX4	OTTHUMG00000048160	ENST00000333987.7:c.328G>A	19.37:g.37428114G>A	ENSP00000334685:p.Glu110Lys	Somatic		WXS	Illumina HiSeq	Phase_I	B4DS92|E7ER33|Q6N060|Q8NA64	Missense_Mutation	SNP	ENST00000333987.7	37	CCDS42558.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.155996	0.78114	.	.	ENSG00000198453	ENST00000427117;ENST00000333987;ENST00000415168;ENST00000444991;ENST00000455427	T;T;T;T;T	0.54866	0.55;0.55;0.55;0.55;0.55	5.2	4.11	0.48088	Krueppel-associated box (1);	0.000000	0.37219	N	0.002183	T	0.59459	0.2195	L	0.41632	1.29	0.80722	D	1	D;D;D;P	0.71674	0.978;0.978;0.998;0.603	P;P;D;B	0.75484	0.714;0.714;0.986;0.232	T	0.50466	-0.8825	10	0.23302	T	0.38	.	11.7649	0.51924	0.0:0.1763:0.8237:0.0	.	46;46;110;110	E7ER33;B4DS92;C9JZ58;Q3ZCX4	.;.;.;ZN568_HUMAN	K	110;110;46;110;46	ENSP00000407012:E110K;ENSP00000334685:E110K;ENSP00000394514:E46K;ENSP00000389794:E110K;ENSP00000413396:E46K	ENSP00000334685:E110K	E	+	1	0	ZNF568	42119954	0.736000	0.28164	0.957000	0.39632	0.998000	0.95712	0.762000	0.26503	2.689000	0.91719	0.655000	0.94253	GAG		0.443	ZNF568-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109572.2		NM_198539	
C9orf114	51490	broad.mit.edu	37	9	131587330	131587330	+	Splice_Site	DEL	T	T	-			TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr9:131587330delT	ENST00000361256.5	-	8	680		c.e8-2			NM_016390.3	NP_057474.2	Q5T280	CI114_HUMAN	chromosome 9 open reading frame 114								poly(A) RNA binding (GO:0044822)			kidney(2)|large_intestine(4)|ovary(1)	7						CTTCACCTCCTGGGGAGAAGC	0.617																																																	0													19.0	19.0	19.0					9																	131587330		2195	4289	6484	SO:0001630	splice_region_variant	51490				CCDS6913.1	9q34.11	2014-05-29			ENSG00000198917	ENSG00000198917			26933	protein-coding gene	gene with protein product	"""centromere protein 32"""					20813266	Standard	NM_016390		Approved	HSPC109, CENP-32	uc004bwd.3	Q5T280	OTTHUMG00000020762	ENST00000361256.5:c.640-2A>-	9.37:g.131587330delT		Somatic		WXS	Illumina GAIIx	Phase_I	Q0D2P6|Q6P469|Q6PGP9|Q6PIJ1|Q6PJV9	Splice_Site	DEL	ENST00000361256.5	37	CCDS6913.1																																																																																				0.617	C9orf114-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054500.1		NM_016390	Intron
ALG1L13P	106479038	broad.mit.edu	37	8	8093750	8093750	+	RNA	SNP	C	C	T			TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr8:8093750C>T	ENST00000523017.1	-	0	765									asparagine-linked glycosylation 1-like 13, pseudogene																		GACAATGGCCCAGCGCTGGAC	0.567																																																	0																																												0					8p23.1	2012-11-07			ENSG00000253981	ENSG00000253981			44382	pseudogene	pseudogene							Standard			Approved				OTTHUMG00000163708		8.37:g.8093750C>T		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP	ENST00000523017.1	37																																																																																					0.567	ALG1L13P-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000374862.1			
HOXD11	3237	broad.mit.edu	37	2	176972132	176972132	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr2:176972132C>T	ENST00000249504.5	+	1	119	c.49C>T	c.(49-51)Ccg>Tcg	p.P17S	AC009336.1_ENST00000401374.2_RNA|HOXD11_ENST00000498438.1_Intron	NM_021192.2	NP_067015.2	P31277	HXD11_HUMAN	homeobox D11	17					anterior/posterior pattern specification (GO:0009952)|branching involved in ureteric bud morphogenesis (GO:0001658)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|developmental growth (GO:0048589)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic skeletal joint morphogenesis (GO:0060272)|metanephros development (GO:0001656)|organ induction (GO:0001759)|positive regulation of cell development (GO:0010720)|positive regulation of chondrocyte differentiation (GO:0032332)|proximal/distal pattern formation (GO:0009954)|regulation of transcription, DNA-templated (GO:0006355)|single fertilization (GO:0007338)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)	p.P17S(1)						OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18)	Colorectal(32;0.0521)|READ - Rectum adenocarcinoma(9;0.0678)		CATGTACCTGCCGGGCTGCGC	0.637			T	NUP98	AML																																			Dom	yes		2	2q31-q32	3237	homeo box D11		L	1	Substitution - Missense(1)	kidney(1)											30.0	26.0	28.0					2																	176972132		2198	4292	6490	SO:0001583	missense	3237				CCDS2265.1	2q31.1	2011-06-20	2005-12-22		ENSG00000128713	ENSG00000128713		"""Homeoboxes / ANTP class : HOXL subclass"""	5134	protein-coding gene	gene with protein product		142986	"""homeo box D11"""	HOX4, HOX4F		1973146, 1358459	Standard	NM_021192		Approved		uc002uki.3	P31277	OTTHUMG00000132510	ENST00000249504.5:c.49C>T	2.37:g.176972132C>T	ENSP00000249504:p.Pro17Ser	Somatic		WXS	Illumina GAIIx	Phase_I	A6NIS4|Q9NS02	Missense_Mutation	SNP	ENST00000249504.5	37	CCDS2265.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.290824	0.80914	.	.	ENSG00000128713	ENST00000249504;ENST00000392538	D	0.98474	-4.95	3.63	3.63	0.41609	.	0.000000	0.32328	U	0.006255	D	0.98937	0.9639	M	0.88450	2.955	0.54753	D	0.999987	D	0.89917	1.0	D	0.70227	0.968	D	0.99486	1.0949	10	0.87932	D	0	.	15.0743	0.72066	0.0:1.0:0.0:0.0	.	17	P31277	HXD11_HUMAN	S	17;4	ENSP00000249504:P17S	ENSP00000249504:P17S	P	+	1	0	HOXD11	176680378	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	6.921000	0.75805	1.860000	0.53959	0.400000	0.26472	CCG		0.637	HOXD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359250.2			
ZNF138	7697	broad.mit.edu	37	7	64313515	64313515	+	IGR	SNP	A	A	G			TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr7:64313515A>G								ZNF138 (19461 upstream) : ZNF273 (29355 downstream)																							CCGTGTCTCAAAGGAATGACA	0.443																																																	0																																										SO:0001628	intergenic_variant	0																															7.37:g.64313515A>G		Somatic		WXS	Illumina GAIIx	Phase_I		Silent	SNP		37																																																																																				0	0.443									
MUC4	4585	broad.mit.edu	37	3	195505763	195505763	+	Missense_Mutation	SNP	G	G	A	rs534260673	byFrequency	TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr3:195505763G>A	ENST00000463781.3	-	2	13147	c.12688C>T	c.(12688-12690)Ctt>Ttt	p.L4230F	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.L4230F	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	987					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.L4230F(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACTGAGGAAAGGCTGGTGACA	0.582																																																	2	Substitution - Missense(2)	kidney(2)											42.0	42.0	42.0					3																	195505763		2092	4200	6292	SO:0001583	missense	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.12688C>T	3.37:g.195505763G>A	ENSP00000417498:p.Leu4230Phe	Somatic		WXS	Illumina GAIIx	Phase_I	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	N	10.21	1.286628	0.23478	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.31769	1.48;1.49	1.78	0.849	0.18972	.	.	.	.	.	T	0.13756	0.0333	N	0.19112	0.55	0.09310	N	1	P	0.35139	0.486	B	0.19946	0.027	T	0.16276	-1.0408	8	.	.	.	.	6.3726	0.21489	0.0:0.3086:0.6914:0.0	.	4102	E7ESK3	.	F	4230	ENSP00000417498:L4230F;ENSP00000420243:L4230F	.	L	-	1	0	MUC4	196990542	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	-0.092000	0.11129	0.347000	0.23924	-0.229000	0.12294	CTT		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6		NM_018406	
SUMO1P1	391257	broad.mit.edu	37	20	52491953	52491953	+	IGR	SNP	C	C	A	rs572035070	byFrequency	TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr20:52491953C>A								AC006076.1 (74096 upstream) : AC005220.3 (64745 downstream)														p.K48N(2)									AGTACGATTTCTTGAGTTTCT	0.388													C|||	2	0.000399361	0.0015	0.0	5008	,	,		19789	0.0		0.0	False		,,,				2504	0.0																2	Substitution - Missense(2)	kidney(2)																																								SO:0001628	intergenic_variant	391257																															20.37:g.52491953C>A		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP		37																																																																																				0	0.388									
TCF7	6932	broad.mit.edu	37	5	133451702	133451702	+	Missense_Mutation	SNP	A	A	C	rs552034914		TCGA-BP-5183-01A-01D-1429-08	TCGA-BP-5183-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cd4c37c3-95f2-4612-b6a8-9d6d1dfb5fd4	3ac4a265-3777-4983-a7ce-c4a1674df004	g.chr5:133451702A>C	ENST00000321584.4	+	3	615	c.419A>C	c.(418-420)cAc>cCc	p.H140P	TCF7_ENST00000432532.2_Missense_Mutation_p.H25P|TCF7_ENST00000395023.1_Missense_Mutation_p.H25P|TCF7_ENST00000342854.5_Missense_Mutation_p.H140P|TCF7_ENST00000520958.1_Missense_Mutation_p.H25P|TCF7_ENST00000518915.1_Missense_Mutation_p.H25P|TCF7_ENST00000378560.4_Missense_Mutation_p.H25P|TCF7_ENST00000378564.1_Missense_Mutation_p.H140P|TCF7_ENST00000395029.1_Missense_Mutation_p.H140P|TCF7_ENST00000321603.6_Missense_Mutation_p.H140P			P36402	TCF7_HUMAN	transcription factor 7 (T-cell specific, HMG-box)	140					alpha-beta T cell differentiation (GO:0046632)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|cellular response to interleukin-4 (GO:0071353)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic genitalia morphogenesis (GO:0030538)|embryonic hindgut morphogenesis (GO:0048619)|generation of neurons (GO:0048699)|immune response (GO:0006955)|neural tube development (GO:0021915)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|T cell receptor V(D)J recombination (GO:0033153)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.H140P(4)|p.H25P(2)		kidney(2)|large_intestine(7)|lung(2)|skin(1)	12		Breast(839;0.058)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GCAGGGCAGCACCCCCAGCCG	0.652																																																	6	Substitution - Missense(6)	kidney(6)											34.0	34.0	34.0					5																	133451702		2202	4300	6502	SO:0001583	missense	6932			Z47362	CCDS4169.1, CCDS4170.1, CCDS43362.1, CCDS47263.1, CCDS47263.2	5q31	2008-02-05			ENSG00000081059	ENSG00000081059			11639	protein-coding gene	gene with protein product		189908					Standard	NM_003202		Approved	TCF-1	uc003kyt.3	P36402	OTTHUMG00000129124	ENST00000321584.4:c.419A>C	5.37:g.133451702A>C	ENSP00000326540:p.His140Pro	Somatic		WXS	Illumina GAIIx	Phase_I	B3KSH3|Q86WR9|Q9UKI4	Missense_Mutation	SNP	ENST00000321584.4	37		.	.	.	.	.	.	.	.	.	.	A	16.20	3.055423	0.55325	.	.	ENSG00000081059	ENST00000342854;ENST00000361590;ENST00000321603;ENST00000321584;ENST00000378564;ENST00000395029;ENST00000518887;ENST00000517851;ENST00000521639;ENST00000522375;ENST00000378560;ENST00000432532;ENST00000520958;ENST00000518915;ENST00000395023	D;D;D;D;D;D;D;D;D;D	0.99121	-5.38;-5.39;-5.39;-5.41;-5.4;-5.45;-5.44;-5.42;-5.39;-5.42	5.2	1.09	0.20402	CTNNB1 binding, N-teminal (1);	0.548777	0.18063	N	0.152870	D	0.91646	0.7360	N	0.00771	-1.2	0.25619	N	0.986426	B;B;B;B	0.23442	0.085;0.0;0.0;0.0	B;B;B;B	0.25759	0.063;0.0;0.0;0.0	D	0.89337	0.3651	10	0.23302	T	0.38	.	5.3059	0.15803	0.5584:0.3475:0.0941:0.0	.	140;140;140;140	P36402-9;B7WNT5;P36402;P36402-5	.;.;TCF7_HUMAN;.	P	140;140;140;140;140;140;25;25;25;25;25;25;25;25;25	ENSP00000340347:H140P;ENSP00000326654:H140P;ENSP00000326540:H140P;ENSP00000367827:H140P;ENSP00000378472:H140P;ENSP00000367822:H25P;ENSP00000397946:H25P;ENSP00000429547:H25P;ENSP00000430179:H25P;ENSP00000378469:H25P	ENSP00000326540:H140P	H	+	2	0	TCF7	133479601	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	1.767000	0.38501	0.791000	0.33826	0.456000	0.33151	CAC		0.652	TCF7-201	KNOWN	basic	protein_coding	protein_coding			NM_201634	
