#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
ABCA3	21	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	2328063	2328063	+	Missense_Mutation	SNP	C	C	T			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	dbc5420c-5c60-4d1e-8554-9d2f6e55c502	19effa42-4c58-4a24-9cd0-264cf686c9dc	g.chr16:2328063C>T	ENST00000301732.5	-	31	5426	c.4726G>A	c.(4726-4728)Gag>Aag	p.E1576K	ABCA3_ENST00000382381.3_Missense_Mutation_p.E1518K	NM_001089.2	NP_001080.2	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 3	1576	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)	alveolar lamellar body (GO:0097208)|alveolar lamellar body membrane (GO:0097233)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)	p.E1576K(1)		breast(7)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(20)|ovary(7)|prostate(5)|skin(6)|upper_aerodigestive_tract(1)	70		Ovarian(90;0.17)			Imatinib(DB00619)	GCCTCACACTCCTCCATGCTG	0.622																																																	1	Substitution - Missense(1)	kidney(1)											27.0	29.0	28.0					16																	2328063		2198	4300	6498	SO:0001583	missense	21			U78735	CCDS10466.1	16p13.3	2012-03-14			ENSG00000167972	ENSG00000167972		"""ATP binding cassette transporters / subfamily A"""	33	protein-coding gene	gene with protein product		601615		ABC3		8706931	Standard	NM_001089		Approved	ABC-C, EST111653, LBM180	uc002cpy.1	Q99758	OTTHUMG00000128845	ENST00000301732.5:c.4726G>A	16.37:g.2328063C>T	ENSP00000301732:p.Glu1576Lys	Somatic		WXS	Illumina HiSeq	Phase_I	B2RU09|Q54A95|Q6P5P9|Q92473	Missense_Mutation	SNP	ENST00000301732.5	37	CCDS10466.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.231589	0.79688	.	.	ENSG00000167972	ENST00000301732;ENST00000382381	D	0.99515	-6.06	5.29	5.29	0.74685	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.000000	0.85682	D	0.000000	D	0.99658	0.9873	M	0.93150	3.385	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.992	D	0.97697	1.0182	10	0.87932	D	0	.	17.5036	0.87738	0.0:1.0:0.0:0.0	.	1580;1576	Q4LE27;Q99758	.;ABCA3_HUMAN	K	1576;1580	ENSP00000301732:E1576K	ENSP00000301732:E1576K	E	-	1	0	ABCA3	2268064	1.000000	0.71417	1.000000	0.80357	0.683000	0.39861	7.740000	0.84986	2.480000	0.83734	0.407000	0.27541	GAG		0.622	ABCA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250784.2		NM_001089	
ACACA	31	broad.mit.edu;hgsc.bcm.edu	37	17	35581913	35581913	+	Splice_Site	SNP	C	C	T			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc5420c-5c60-4d1e-8554-9d2f6e55c502	19effa42-4c58-4a24-9cd0-264cf686c9dc	g.chr17:35581913C>T	ENST00000394406.2	-	27	3553	c.3363G>A	c.(3361-3363)caG>caA	p.Q1121Q	ACACA_ENST00000353139.5_Splice_Site_p.Q1158Q|ACACA_ENST00000335166.5_Splice_Site_p.Q1043Q|ACACA_ENST00000360679.3_Splice_Site_p.Q1063Q	NM_198836.1	NP_942133.1	Q13085	ACACA_HUMAN	acetyl-CoA carboxylase alpha	1121					acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|lipid homeostasis (GO:0055088)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|malonyl-CoA biosynthetic process (GO:2001295)|multicellular organismal protein metabolic process (GO:0044268)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|small molecule metabolic process (GO:0044281)|tissue homeostasis (GO:0001894)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)	p.Q1063Q(1)|p.Q1158Q(1)		NS(2)|breast(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(24)|lung(23)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	83		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	atatatataCCTGCAGGTTCT	0.343																																					Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)												2	Substitution - coding silent(2)	kidney(2)											41.0	41.0	41.0					17																	35581913		2203	4300	6503	SO:0001630	splice_region_variant	31			U19822	CCDS11317.1, CCDS11318.1, CCDS42302.1, CCDS42303.1	17q21	2014-05-06	2010-04-30		ENSG00000132142	ENSG00000278540	6.4.1.2		84	protein-coding gene	gene with protein product	"""acetyl-CoA carboxylase 1"""	200350	"""acetyl-Coenzyme A carboxylase alpha"""	ACAC, ACC			Standard	NM_198837		Approved	ACC1	uc002hno.3	Q13085	OTTHUMG00000188463	ENST00000394406.2:c.3363+1G>A	17.37:g.35581913C>T		Somatic		WXS	Illumina HiSeq	Phase_I	B2RP68|Q6KEV6|Q6XDA8|Q7Z2G8|Q7Z561|Q7Z563|Q7Z564|Q86WB2|Q86WB3	Silent	SNP	ENST00000394406.2	37	CCDS11317.1																																																																																				0.343	ACACA-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256696.1		NM_198836	Silent
ACSS2	55902	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	33500951	33500951	+	Missense_Mutation	SNP	G	G	T			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc5420c-5c60-4d1e-8554-9d2f6e55c502	19effa42-4c58-4a24-9cd0-264cf686c9dc	g.chr20:33500951G>T	ENST00000360596.2	+	3	638	c.427G>T	c.(427-429)Gtc>Ttc	p.V143F	ACSS2_ENST00000336325.4_Missense_Mutation_p.V93F|ACSS2_ENST00000253382.5_Missense_Mutation_p.V143F|ACSS2_ENST00000476922.1_Intron	NM_018677.3	NP_061147.1	Q9NR19	ACSA_HUMAN	acyl-CoA synthetase short-chain family member 2	143					acetate biosynthetic process (GO:0019413)|acetyl-CoA biosynthetic process from acetate (GO:0019427)|ethanol oxidation (GO:0006069)|lipid biosynthetic process (GO:0008610)|propionate biosynthetic process (GO:0019542)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	acetate-CoA ligase activity (GO:0003987)|AMP binding (GO:0016208)|ATP binding (GO:0005524)	p.V143F(2)		cervix(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(6)|lung(9)	21					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	TCAGCTTCTGGTCCAAGTGTG	0.522																																																	2	Substitution - Missense(2)	kidney(2)											165.0	150.0	155.0					20																	33500951		2203	4300	6503	SO:0001583	missense	55902			AF263614	CCDS13243.1, CCDS42868.1, CCDS42868.2	20q11.22	2012-07-13	2005-09-08	2005-09-08	ENSG00000131069	ENSG00000131069	6.2.1.1	"""Acyl-CoA synthetase family"""	15814	protein-coding gene	gene with protein product		605832	"""acetyl-Coenzyme A synthetase 2 (ADP forming)"""	ACAS2		10843999	Standard	NM_018677		Approved	ACS, ACSA, AceCS, dJ1161H23.1	uc010gey.2	Q9NR19	OTTHUMG00000032317	ENST00000360596.2:c.427G>T	20.37:g.33500951G>T	ENSP00000353804:p.Val143Phe	Somatic		WXS	Illumina HiSeq	Phase_I	A6NE90|Q5QPH2|Q5QPH3|Q8N238|Q96EL0|Q9NQP7|Q9UJ15	Missense_Mutation	SNP	ENST00000360596.2	37	CCDS13243.1	.	.	.	.	.	.	.	.	.	.	G	12.01	1.808492	0.31961	.	.	ENSG00000131069	ENST00000488172;ENST00000336325;ENST00000360596;ENST00000374693;ENST00000484354;ENST00000493805;ENST00000473172;ENST00000253382	T;T;T;T;T;T;T	0.53640	0.61;0.61;0.61;0.61;1.03;1.03;0.61	5.34	0.879	0.19155	AMP-dependent synthetase/ligase (1);	0.968380	0.08582	N	0.924352	T	0.42787	0.1218	L	0.42744	1.35	0.24462	N	0.994436	B;B	0.20988	0.05;0.05	B;B	0.38683	0.217;0.279	T	0.54241	-0.8323	10	0.72032	D	0.01	-22.6483	0.8236	0.01116	0.3718:0.1718:0.3039:0.1526	.	143;143	Q5QPH3;Q9NR19	.;ACSA_HUMAN	F	93;93;143;143;135;161;156;143	ENSP00000417783:V93F;ENSP00000337190:V93F;ENSP00000353804:V143F;ENSP00000419167:V135F;ENSP00000418812:V161F;ENSP00000419925:V156F;ENSP00000253382:V143F	ENSP00000253382:V143F	V	+	1	0	ACSS2	32964612	0.003000	0.15002	0.996000	0.52242	0.991000	0.79684	0.039000	0.13884	0.359000	0.24239	-0.140000	0.14226	GTC		0.522	ACSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078823.3		NM_018677	
ACTBL2	345651	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	56778275	56778275	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc5420c-5c60-4d1e-8554-9d2f6e55c502	19effa42-4c58-4a24-9cd0-264cf686c9dc	g.chr5:56778275C>A	ENST00000423391.1	-	1	361	c.260G>T	c.(259-261)tGg>tTg	p.W87L	CTD-2023N9.1_ENST00000506106.1_RNA|AC025470.1_ENST00000584598.1_RNA	NM_001017992.3	NP_001017992.1	Q562R1	ACTBL_HUMAN	actin, beta-like 2	87						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)	p.W87L(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(3)|pancreas(1)|prostate(2)	28		Lung NSC(810;0.000135)|Prostate(74;0.055)|Breast(144;0.0707)|Ovarian(174;0.182)		OV - Ovarian serous cystadenocarcinoma(10;4.24e-37)		TGTGTGGTACCAGATCTTTTC	0.537																																																	1	Substitution - Missense(1)	kidney(1)											97.0	81.0	87.0					5																	56778275		2203	4300	6503	SO:0001583	missense	345651				CCDS34163.1	5q11.2	2014-08-08			ENSG00000169067	ENSG00000169067			17780	protein-coding gene	gene with protein product		614835					Standard	NM_001017992		Approved	DKFZp686D0972	uc003jrm.3	Q562R1	OTTHUMG00000162330	ENST00000423391.1:c.260G>T	5.37:g.56778275C>A	ENSP00000416706:p.Trp87Leu	Somatic		WXS	Illumina HiSeq	Phase_I	B2RPJ1|Q562R2|Q562S9|Q562X8	Missense_Mutation	SNP	ENST00000423391.1	37	CCDS34163.1	.	.	.	.	.	.	.	.	.	.	C	15.30	2.792302	0.50102	.	.	ENSG00000169067	ENST00000423391	D	0.95482	-3.72	4.91	4.91	0.64330	.	0.000000	0.64402	D	0.000005	D	0.97349	0.9133	M	0.81614	2.55	0.58432	D	0.999998	P	0.39094	0.659	P	0.56612	0.802	D	0.97969	1.0342	10	0.87932	D	0	.	15.6308	0.76906	0.0:1.0:0.0:0.0	.	87	Q562R1	ACTBL_HUMAN	L	87	ENSP00000416706:W87L	ENSP00000416706:W87L	W	-	2	0	ACTBL2	56814032	1.000000	0.71417	1.000000	0.80357	0.707000	0.40811	7.645000	0.83430	2.544000	0.85801	0.655000	0.94253	TGG		0.537	ACTBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368579.1		NM_001017992	
ADRBK1	156	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	67050628	67050628	+	Silent	SNP	T	T	C			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc5420c-5c60-4d1e-8554-9d2f6e55c502	19effa42-4c58-4a24-9cd0-264cf686c9dc	g.chr11:67050628T>C	ENST00000308595.5	+	15	1547	c.1257T>C	c.(1255-1257)ccT>ccC	p.P419P	ADRBK1_ENST00000526285.1_Intron|ADRBK1_ENST00000527176.1_3'UTR	NM_001619.3	NP_001610.2	P25098	ARBK1_HUMAN	adrenergic, beta, receptor kinase 1	419	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase C activity (GO:0007202)|cardiac muscle contraction (GO:0060048)|desensitization of G-protein coupled receptor protein signaling pathway (GO:0002029)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|heart development (GO:0007507)|innate immune response (GO:0045087)|negative regulation of striated muscle contraction (GO:0045988)|negative regulation of the force of heart contraction by chemical signal (GO:0003108)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of catecholamine secretion (GO:0033605)|receptor internalization (GO:0031623)|signal transduction (GO:0007165)|tachykinin receptor signaling pathway (GO:0007217)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	alpha-2A adrenergic receptor binding (GO:0031694)|ATP binding (GO:0005524)|beta-adrenergic receptor kinase activity (GO:0047696)|Edg-2 lysophosphatidic acid receptor binding (GO:0031755)|G-protein coupled receptor kinase activity (GO:0004703)|protein kinase activity (GO:0004672)	p.P419P(1)		cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(2)|liver(2)|lung(8)|prostate(2)	22			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)		Adenosine triphosphate(DB00171)	CCTTCTCCCCTGAACTACGCT	0.632																																																	1	Substitution - coding silent(1)	kidney(1)											118.0	120.0	119.0					11																	67050628		2200	4295	6495	SO:0001819	synonymous_variant	156			X61157	CCDS8156.1	11q13	2013-01-10			ENSG00000173020	ENSG00000173020		"""Pleckstrin homology (PH) domain containing"""	289	protein-coding gene	gene with protein product		109635				2037065	Standard	NM_001619		Approved	GRK2, BARK1	uc009yrn.1	P25098	OTTHUMG00000167104	ENST00000308595.5:c.1257T>C	11.37:g.67050628T>C		Somatic		WXS	Illumina HiSeq	Phase_I	B0ZBE1|Q13837|Q6GTT3	Silent	SNP	ENST00000308595.5	37	CCDS8156.1																																																																																				0.632	ADRBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393153.1		NM_001619	
ARHGEF3	50650	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	56779390	56779390	+	Missense_Mutation	SNP	A	A	G			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc5420c-5c60-4d1e-8554-9d2f6e55c502	19effa42-4c58-4a24-9cd0-264cf686c9dc	g.chr3:56779390A>G	ENST00000296315.3	-	7	881	c.713T>C	c.(712-714)cTa>cCa	p.L238P	ARHGEF3_ENST00000495373.1_Missense_Mutation_p.L238P|ARHGEF3_ENST00000338458.4_Missense_Mutation_p.L270P|ARHGEF3_ENST00000413728.2_Missense_Mutation_p.L244P|ARHGEF3_ENST00000497267.1_Missense_Mutation_p.L209P|ARHGEF3_ENST00000496106.1_Missense_Mutation_p.L244P	NM_019555.2	NP_062455.1	Q9NR81	ARHG3_HUMAN	Rho guanine nucleotide exchange factor (GEF) 3	238	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|intracellular (GO:0005622)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.L238P(2)|p.L270P(1)		cervix(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|urinary_tract(1)	25				KIRC - Kidney renal clear cell carcinoma(284;0.0161)|Kidney(284;0.019)|OV - Ovarian serous cystadenocarcinoma(275;0.193)		ACATCGCTGTAGGAAATCCTG	0.493																																																	3	Substitution - Missense(3)	kidney(3)											187.0	199.0	195.0					3																	56779390		2203	4300	6503	SO:0001583	missense	50650			AB209661	CCDS2878.1, CCDS46854.1, CCDS46855.1, CCDS74948.1	3p14.3	2012-09-20			ENSG00000163947	ENSG00000163947		"""Rho guanine nucleotide exchange factors"""	683	protein-coding gene	gene with protein product	"""exchange factor found in platelets and leukemic and neuronal tissues, XPLN"", ""RhoGEF protein"""	612115				10873612	Standard	NM_019555		Approved	STA3, XPLN, GEF3, DKFZP434F2429	uc003dih.2	Q9NR81	OTTHUMG00000158857	ENST00000296315.3:c.713T>C	3.37:g.56779390A>G	ENSP00000296315:p.Leu238Pro	Somatic		WXS	Illumina HiSeq	Phase_I	A8K5U7|Q4FZB6|Q4QQI5|Q4QQQ0|Q59F00|Q6NUN3|Q7Z4U2|Q7Z5T2|Q9H7T4	Missense_Mutation	SNP	ENST00000296315.3	37	CCDS2878.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.542534	0.85917	.	.	ENSG00000163947	ENST00000296315;ENST00000338458;ENST00000413728;ENST00000496106;ENST00000497267;ENST00000495373	T;T;T;T;T;T	0.70631	-0.5;-0.5;-0.5;-0.5;-0.5;-0.5	5.45	5.45	0.79879	Dbl homology (DH) domain (5);	0.000000	0.85682	D	0.000000	D	0.88537	0.6463	H	0.94385	3.53	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;1.0;0.999;1.0;1.0;1.0;1.0	D	0.91666	0.5346	10	0.87932	D	0	-16.6955	16.226	0.82293	1.0:0.0:0.0:0.0	.	244;209;36;238;270;238;244	E9PG37;E7EU49;Q9NR81-4;C9J586;Q9NR81-2;Q9NR81;Q9NR81-3	.;.;.;.;.;ARHG3_HUMAN;.	P	238;270;244;244;209;238	ENSP00000296315:L238P;ENSP00000341071:L270P;ENSP00000410922:L244P;ENSP00000420420:L244P;ENSP00000418826:L209P;ENSP00000417986:L238P	ENSP00000296315:L238P	L	-	2	0	ARHGEF3	56754430	1.000000	0.71417	0.943000	0.38184	0.994000	0.84299	9.287000	0.95975	2.371000	0.80710	0.533000	0.62120	CTA		0.493	ARHGEF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352431.2		NM_019555	
CFAP43	80217	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	105942200	105942200	+	Missense_Mutation	SNP	G	G	T			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc5420c-5c60-4d1e-8554-9d2f6e55c502	19effa42-4c58-4a24-9cd0-264cf686c9dc	g.chr10:105942200G>T	ENST00000278064.2	-	17	2331	c.2006C>A	c.(2005-2007)gCc>gAc	p.A669D	WDR96_ENST00000357060.3_Missense_Mutation_p.A738D|WDR96_ENST00000428666.1_Missense_Mutation_p.A739D														p.A738D(1)		NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(14)|lung(21)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						CTTGTCCATGGCGCTGCTCAG	0.393																																																	1	Substitution - Missense(1)	kidney(1)											179.0	160.0	166.0					10																	105942200		2203	4300	6503	SO:0001583	missense	0																														ENST00000278064.2:c.2006C>A	10.37:g.105942200G>T	ENSP00000278064:p.Ala669Asp	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000278064.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.03|11.03	1.518206|1.518206	0.27211|0.27211	.|.	.|.	ENSG00000197748|ENSG00000197748	ENST00000357060;ENST00000428666;ENST00000278064|ENST00000434629	T;T;T|.	0.14766|.	2.51;2.5;2.48|.	4.95|4.95	0.194|0.194	0.15143|0.15143	.|.	0.761995|.	0.11912|.	N|.	0.517504|.	T|T	0.18593|0.18593	0.0446|0.0446	N|N	0.14661|0.14661	0.345|0.345	0.09310|0.09310	N|N	1|1	B;B;B|.	0.16396|.	0.016;0.011;0.017|.	B;B;B|.	0.16289|.	0.015;0.014;0.011|.	T|T	0.27434|0.27434	-1.0074|-1.0074	10|5	0.38643|.	T|.	0.18|.	.|.	5.2071|5.2071	0.15297|0.15297	0.2052:0.4124:0.3824:0.0|0.2052:0.4124:0.3824:0.0	.|.	739;739;738|.	G5E9L1;B4DHB6;Q8NDM7|.	.;.;WDR96_HUMAN|.	D|T	738;739;669|99	ENSP00000349568:A738D;ENSP00000400289:A739D;ENSP00000278064:A669D|.	ENSP00000278064:A669D|.	A|P	-|-	2|1	0|0	WDR96|WDR96	105932190|105932190	0.002000|0.002000	0.14202|0.14202	0.046000|0.046000	0.18839|0.18839	0.003000|0.003000	0.03518|0.03518	-0.355000|-0.355000	0.07671|0.07671	0.204000|0.204000	0.20548|0.20548	0.557000|0.557000	0.71058|0.71058	GCC|CCA		0.393	WDR96-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050200.1			
KANSL2	54934	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	49047945	49047945	+	Missense_Mutation	SNP	A	A	C			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc5420c-5c60-4d1e-8554-9d2f6e55c502	19effa42-4c58-4a24-9cd0-264cf686c9dc	g.chr12:49047945A>C	ENST00000420613.2	-	10	1408	c.1361T>G	c.(1360-1362)aTg>aGg	p.M454R	SNORA34_ENST00000408564.2_RNA|KANSL2_ENST00000553086.1_Missense_Mutation_p.M416R|KANSL2_ENST00000550347.1_Missense_Mutation_p.M637R|SNORA2A_ENST00000383885.1_RNA|KANSL2_ENST00000548701.1_5'UTR	NM_017822.3	NP_060292.3	Q9H9L4	KANL2_HUMAN	KAT8 regulatory NSL complex subunit 2	454					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)		p.M454R(2)									ATCTCCAGCCATCTGCATCTG	0.453																																																	2	Substitution - Missense(2)	kidney(2)											50.0	46.0	47.0					12																	49047945		1876	4116	5992	SO:0001583	missense	0			AK094528	CCDS44869.1	12q13.11	2011-10-31	2011-10-31	2011-10-31	ENSG00000139620	ENSG00000139620			26024	protein-coding gene	gene with protein product		615488	"""chromosome 12 open reading frame 41"""	C12orf41		12477932	Standard	NM_017822		Approved	FLJ20436, NSL2	uc001rrz.2	Q9H9L4	OTTHUMG00000170392	ENST00000420613.2:c.1361T>G	12.37:g.49047945A>C	ENSP00000415436:p.Met454Arg	Somatic		WXS	Illumina HiSeq	Phase_I	Q8N3B5|Q96CV0|Q9NX51	Missense_Mutation	SNP	ENST00000420613.2	37	CCDS44869.1	.	.	.	.	.	.	.	.	.	.	A	10.72	1.428325	0.25726	.	.	ENSG00000139620	ENST00000550347;ENST00000420613;ENST00000547087;ENST00000553086	T;T;T;T	0.39997	1.51;1.05;1.05;1.51	5.37	2.94	0.34122	.	0.758825	0.13325	N	0.396381	T	0.21387	0.0515	N	0.08118	0	0.46356	D	0.999009	B;B;B	0.30068	0.267;0.004;0.007	B;B;B	0.32762	0.152;0.013;0.018	T	0.04165	-1.0972	10	0.18276	T	0.48	-0.0262	7.0846	0.25249	0.8209:0.0:0.1791:0.0	.	637;454;225	F8VX10;Q9H9L4;Q9H9L4-2	.;CL041_HUMAN;.	R	637;454;168;416	ENSP00000449747:M637R;ENSP00000415436:M454R;ENSP00000447608:M168R;ENSP00000448833:M416R	ENSP00000415436:M454R	M	-	2	0	C12orf41	47334212	0.141000	0.22595	0.509000	0.27700	0.993000	0.82548	1.523000	0.35932	0.457000	0.26962	0.528000	0.53228	ATG		0.453	KANSL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408841.1		NM_017822	
LRIF1	55791	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	111494480	111494480	+	Silent	SNP	A	A	T			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc5420c-5c60-4d1e-8554-9d2f6e55c502	19effa42-4c58-4a24-9cd0-264cf686c9dc	g.chr1:111494480A>T	ENST00000369763.4	-	2	1416	c.1026T>A	c.(1024-1026)ccT>ccA	p.P342P	LRIF1_ENST00000494675.1_Intron|LRIF1_ENST00000485275.2_Intron|RP11-96K19.2_ENST00000440689.1_RNA	NM_018372.3	NP_060842.3	Q5T3J3	LRIF1_HUMAN	ligand dependent nuclear receptor interacting factor 1	342					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)		p.P342P(1)		endometrium(2)|kidney(2)|large_intestine(7)|lung(12)|ovary(2)|skin(1)|urinary_tract(2)	28						GCGTCCCACTAGGATCGATGG	0.348																																																	1	Substitution - coding silent(1)	kidney(1)											76.0	79.0	78.0					1																	111494480		2203	4300	6503	SO:0001819	synonymous_variant	0			AY190122	CCDS30800.1, CCDS41366.1	1p13.3	2011-04-15	2011-04-15	2011-04-15	ENSG00000121931	ENSG00000121931			30299	protein-coding gene	gene with protein product	"""receptor interacting factor 1"""	615354	"""chromosome 1 open reading frame 103"""	C1orf103		17455211	Standard	NM_018372		Approved	RIF1, FLJ11269	uc001eaa.3	Q5T3J3	OTTHUMG00000011913	ENST00000369763.4:c.1026T>A	1.37:g.111494480A>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q86XS4|Q8N3B6|Q96HT4|Q9NUM5|Q9NV32	Silent	SNP	ENST00000369763.4	37	CCDS30800.1																																																																																				0.348	LRIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000032932.2		NM_018372	
CNGA4	1262	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	6262833	6262833	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc5420c-5c60-4d1e-8554-9d2f6e55c502	19effa42-4c58-4a24-9cd0-264cf686c9dc	g.chr11:6262833C>A	ENST00000379936.2	+	5	1205	c.1090C>A	c.(1090-1092)Ctg>Atg	p.L364M	CNGA4_ENST00000533426.1_Missense_Mutation_p.L133M	NM_001037329.3	NP_001032406.1	Q8IV77	CNGA4_HUMAN	cyclic nucleotide gated channel alpha 4	364					phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|sensory perception of smell (GO:0007608)	integral component of plasma membrane (GO:0005887)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)	p.L364M(1)		endometrium(2)|kidney(1)|large_intestine(9)|lung(24)|prostate(3)|skin(1)	40		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;2.04e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GGTGCTGAAGCTGCAGCCCCA	0.582																																																	1	Substitution - Missense(1)	kidney(1)											144.0	131.0	136.0					11																	6262833		2201	4296	6497	SO:0001583	missense	1262			AK122736	CCDS31408.1	11p15.4	2011-07-05		2002-01-18		ENSG00000132259		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2152	protein-coding gene	gene with protein product		609472	"""cyclic nucleotide gated channel beta 2"""	CNCA2, CNGB2		11764791, 16382102	Standard	NM_001037329		Approved	OCNC2, OCNCb, CNG5	uc001mco.3	Q8IV77		ENST00000379936.2:c.1090C>A	11.37:g.6262833C>A	ENSP00000369268:p.Leu364Met	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000379936.2	37	CCDS31408.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.058355	0.76074	.	.	ENSG00000132259	ENST00000533426;ENST00000379936	D;D	0.96830	-4.14;-4.14	5.19	4.25	0.50352	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (2);	0.000000	0.64402	D	0.000001	D	0.97028	0.9029	L	0.55017	1.72	0.58432	D	0.999996	D;D;D	0.89917	0.997;0.978;1.0	D;P;D	0.85130	0.96;0.764;0.997	D	0.96323	0.9238	10	0.52906	T	0.07	.	13.0781	0.59099	0.0:0.9196:0.0:0.0803	.	133;364;324	B4DYQ8;Q8IV77;Q8IV77-2	.;CNGA4_HUMAN;.	M	133;364	ENSP00000433399:L133M;ENSP00000369268:L364M	ENSP00000369268:L364M	L	+	1	2	CNGA4	6219409	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.001000	0.49488	2.691000	0.91804	0.655000	0.94253	CTG		0.582	CNGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383765.2		NM_001037329	
COL18A1	80781	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	21	46912469	46912469	+	Silent	SNP	G	G	A	rs556113991		TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc5420c-5c60-4d1e-8554-9d2f6e55c502	19effa42-4c58-4a24-9cd0-264cf686c9dc	g.chr21:46912469G>A	ENST00000359759.4	+	22	3444	c.3423G>A	c.(3421-3423)ccG>ccA	p.P1141P	COL18A1_ENST00000400337.2_Silent_p.P726P|COL18A1_ENST00000355480.5_Silent_p.P906P			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	1141	Nonhelical region 5 (NC5).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)	p.P906P(1)		breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		TGAGCGTGCCGGGACCTGAGG	0.587													G|||	1	0.000199681	0.0008	0.0	5008	,	,		14841	0.0		0.0	False		,,,				2504	0.0																1	Substitution - coding silent(1)	kidney(1)											132.0	144.0	140.0					21																	46912469		1928	4127	6055	SO:0001819	synonymous_variant	80781				CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"""Collagens"""	2195	protein-coding gene	gene with protein product	"""endostatin"""	120328	"""Knobloch syndrome, type 1"""	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.3423G>A	21.37:g.46912469G>A		Somatic		WXS	Illumina HiSeq	Phase_I	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Silent	SNP	ENST00000359759.4	37																																																																																					0.587	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1			
CUBN	8029	broad.mit.edu;hgsc.bcm.edu	37	10	16882524	16882524	+	Silent	SNP	A	A	G			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08	A	A	A	G	A	A	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc5420c-5c60-4d1e-8554-9d2f6e55c502	19effa42-4c58-4a24-9cd0-264cf686c9dc	g.chr10:16882524A>G	ENST00000377833.4	-	62	9902	c.9837T>C	c.(9835-9837)ggT>ggC	p.G3279G		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	3279	CUB 25. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)	p.G3279G(1)		breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	TGTATGTTCCACCACAAGGCA	0.453																																																	1	Substitution - coding silent(1)	kidney(1)											85.0	85.0	85.0					10																	16882524		2203	4300	6503	SO:0001819	synonymous_variant	8029			AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.9837T>C	10.37:g.16882524A>G		Somatic		WXS	Illumina HiSeq	Phase_I	B0YIZ4|Q5VTA6|Q96RU9	Silent	SNP	ENST00000377833.4	37	CCDS7113.1																																																																																				0.453	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1		NM_001081	
DDX10	1662	broad.mit.edu;hgsc.bcm.edu	37	11	108810996	108810996	+	Missense_Mutation	SNP	T	T	C			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc5420c-5c60-4d1e-8554-9d2f6e55c502	19effa42-4c58-4a24-9cd0-264cf686c9dc	g.chr11:108810996T>C	ENST00000322536.3	+	18	2603	c.2474T>C	c.(2473-2475)aTg>aCg	p.M825T	DDX10_ENST00000534221.1_3'UTR	NM_004398.2	NP_004389.2	Q13206	DDX10_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 10	825					metabolic process (GO:0008152)		ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)	p.M825T(1)		breast(2)|endometrium(5)|kidney(2)|large_intestine(4)|lung(11)|pancreas(1)|prostate(2)	27		all_cancers(61;1.29e-11)|all_epithelial(67;2.96e-07)|Melanoma(852;1.54e-05)|Acute lymphoblastic leukemia(157;4.24e-05)|all_hematologic(158;0.000141)|Breast(348;0.026)|all_neural(223;0.0729)		BRCA - Breast invasive adenocarcinoma(274;2.48e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.000609)|OV - Ovarian serous cystadenocarcinoma(223;0.133)		AAGCAGGGGATGAAGAAGAGG	0.418			T	NUP98	AML*																																			Dom	yes		11	11q22-q23	1662	DEAD (Asp-Glu-Ala-Asp) box polypeptide 10		L	1	Substitution - Missense(1)	kidney(1)											87.0	78.0	81.0					11																	108810996		2201	4298	6499	SO:0001583	missense	1662			U28042	CCDS8342.1	11q22-q23	2005-10-11	2003-06-13		ENSG00000178105	ENSG00000178105		"""DEAD-boxes"""	2735	protein-coding gene	gene with protein product		601235	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 10 (RNA helicase)"""			8660968	Standard	NM_004398		Approved	HRH-J8	uc001pkm.3	Q13206	OTTHUMG00000166540	ENST00000322536.3:c.2474T>C	11.37:g.108810996T>C	ENSP00000314348:p.Met825Thr	Somatic		WXS	Illumina HiSeq	Phase_I	B2RCQ3|Q5BJD8	Missense_Mutation	SNP	ENST00000322536.3	37	CCDS8342.1	.	.	.	.	.	.	.	.	.	.	T	0.060	-1.226129	0.01518	.	.	ENSG00000178105	ENST00000322536;ENST00000456020	T	0.38401	1.14	6.07	2.42	0.29668	.	0.563759	0.17797	N	0.161688	T	0.17492	0.0420	N	0.16478	0.41	0.39119	D	0.96163	B	0.02656	0.0	B	0.04013	0.001	T	0.10359	-1.0633	10	0.15499	T	0.54	-8.6865	4.5096	0.11905	0.1428:0.1554:0.0:0.7018	.	825	Q13206	DDX10_HUMAN	T	825;731	ENSP00000314348:M825T	ENSP00000314348:M825T	M	+	2	0	DDX10	108316206	0.984000	0.35163	0.927000	0.36925	0.006000	0.05464	-0.022000	0.12480	0.162000	0.19483	-0.259000	0.10710	ATG		0.418	DDX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390343.1		NM_004398	
FGFR3	2261	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	1807850	1807850	+	Missense_Mutation	SNP	G	G	T			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	dbc5420c-5c60-4d1e-8554-9d2f6e55c502	19effa42-4c58-4a24-9cd0-264cf686c9dc	g.chr4:1807850G>T	ENST00000260795.2	+	13	2011	c.1909G>T	c.(1909-1911)Ggg>Tgg	p.G637W	FGFR3_ENST00000481110.2_Missense_Mutation_p.G638W|FGFR3_ENST00000352904.1_Missense_Mutation_p.G525W|FGFR3_ENST00000440486.2_Missense_Mutation_p.G637W|FGFR3_ENST00000340107.4_Missense_Mutation_p.G639W|FGFR3_ENST00000412135.2_Missense_Mutation_p.G525W			P22607	FGFR3_HUMAN	fibroblast growth factor receptor 3	637	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				alveolar secondary septum development (GO:0061144)|axonogenesis involved in innervation (GO:0060385)|bone maturation (GO:0070977)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cell-cell signaling (GO:0007267)|central nervous system myelination (GO:0022010)|chondrocyte differentiation (GO:0002062)|chondrocyte proliferation (GO:0035988)|cochlea development (GO:0090102)|digestive tract morphogenesis (GO:0048546)|endochondral bone growth (GO:0003416)|endochondral ossification (GO:0001958)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell fate commitment (GO:0072148)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor apoptotic signaling pathway (GO:1902178)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inner ear receptor cell differentiation (GO:0060113)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade (GO:0007259)|lens fiber cell development (GO:0070307)|lens morphogenesis in camera-type eye (GO:0002089)|MAPK cascade (GO:0000165)|morphogenesis of an epithelium (GO:0002009)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of developmental growth (GO:0048640)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|substantia nigra development (GO:0021762)	cell surface (GO:0009986)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|protein tyrosine kinase activity (GO:0004713)	p.G639W(1)|p.G637W(1)		NS(1)|central_nervous_system(5)|cervix(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(40)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(9)|skin(339)|soft_tissue(4)|testis(2)|upper_aerodigestive_tract(58)|urinary_tract(2607)	3091		Breast(71;0.212)|all_epithelial(65;0.241)	all cancers(2;0.000145)|OV - Ovarian serous cystadenocarcinoma(23;0.0019)|Epithelial(3;0.00221)|GBM - Glioblastoma multiforme(2;0.234)		Palifermin(DB00039)|Pazopanib(DB06589)|Ponatinib(DB08901)	CGCAGACTTCGGGCTGGCCCG	0.652		1	"""Mis, T"""	"""IGH@, ETV6"""	"""bladder, MM, T-cell lymphoma"""		"""Hypochondroplasia, Thanatophoric dysplasia"""		Saethre-Chotzen syndrome;Muenke syndrome																															Dom	yes		4	4p16.3	2261	fibroblast growth factor receptor 3	yes	"""L, E"""	2	Substitution - Missense(2)	kidney(2)											42.0	42.0	42.0					4																	1807850		2202	4300	6502	SO:0001583	missense	2261	Familial Cancer Database	Acrocephalosyndactyly type III;Muenke Nonsyndromic Coronal Craniosynostosis, FGFR3-related Craniosynostosis	M64347	CCDS3353.1, CCDS3354.1, CCDS54706.1	4p16.3	2013-01-11	2008-08-01		ENSG00000068078	ENSG00000068078		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3690	protein-coding gene	gene with protein product		134934	"""achondroplasia, thanatophoric dwarfism"""	ACH		1847508	Standard	NM_000142		Approved	CEK2, JTK4, CD333	uc003gdu.2	P22607	OTTHUMG00000121148	ENST00000260795.2:c.1909G>T	4.37:g.1807850G>T	ENSP00000260795:p.Gly637Trp	Somatic		WXS	Illumina HiSeq	Phase_I	D3DVP9|D3DVQ0|Q14308|Q16294|Q16608|Q59FL9	Missense_Mutation	SNP	ENST00000260795.2	37	CCDS3353.1	.	.	.	.	.	.	.	.	.	.	g	15.65	2.897125	0.52121	.	.	ENSG00000068078	ENST00000481110;ENST00000340107;ENST00000440486;ENST00000412135;ENST00000260795;ENST00000352904	D;D;D;D;D;D	0.99298	-5.71;-5.71;-5.71;-5.71;-5.71;-5.71	4.35	4.35	0.52113	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.99750	0.9900	H	0.99609	4.655	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.96582	0.9431	10	0.87932	D	0	.	17.2158	0.86943	0.0:0.0:1.0:0.0	.	639;525;637;638	P22607-2;P22607-3;P22607;F8W9L4	.;.;FGFR3_HUMAN;.	W	638;639;637;525;637;525	ENSP00000420533:G638W;ENSP00000339824:G639W;ENSP00000414914:G637W;ENSP00000412903:G525W;ENSP00000260795:G637W;ENSP00000231803:G525W	ENSP00000260795:G637W	G	+	1	0	FGFR3	1777648	1.000000	0.71417	0.990000	0.47175	0.281000	0.26958	9.427000	0.97472	2.127000	0.65507	0.448000	0.29417	GGG		0.652	FGFR3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000241632.2		NM_000142	
IGFN1	91156	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	201190737	201190737	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc5420c-5c60-4d1e-8554-9d2f6e55c502	19effa42-4c58-4a24-9cd0-264cf686c9dc	g.chr1:201190737C>A	ENST00000335211.4	+	19	10194	c.10064C>A	c.(10063-10065)aCc>aAc	p.T3355N	RP11-567E21.3_ENST00000453155.1_RNA|IGFN1_ENST00000295591.8_Missense_Mutation_p.T515N	NM_001164586.1	NP_001158058.1	Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1	898						nucleus (GO:0005634)|Z disc (GO:0030018)		p.T3355N(1)|p.T515N(1)		autonomic_ganglia(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						CATGTGGGCACCGTGCCAGTC	0.637																																																	2	Substitution - Missense(2)	kidney(2)											52.0	44.0	46.0					1																	201190737		2203	4300	6503	SO:0001583	missense	91156			AY245430	CCDS53455.1	1q32.1	2013-02-11			ENSG00000163395	ENSG00000163395		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	24607	protein-coding gene	gene with protein product							Standard	NM_001164586		Approved	DKFZp434B1231, EEF1A2BP1	uc001gwc.3	Q86VF2	OTTHUMG00000035728	ENST00000335211.4:c.10064C>A	1.37:g.201190737C>A	ENSP00000334714:p.Thr3355Asn	Somatic		WXS	Illumina HiSeq	Phase_I	F8WAI1|Q9NT72	Missense_Mutation	SNP	ENST00000335211.4	37	CCDS53455.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.33|17.33	3.361872|3.361872	0.61403|0.61403	.|.	.|.	ENSG00000163395|ENSG00000163395	ENST00000412892|ENST00000335211;ENST00000295591	.|T;T	.|0.57273	.|0.41;0.41	4.64|4.64	2.74|2.74	0.32292|0.32292	.|.	.|0.407546	.|0.21425	.|N	.|0.074755	T|T	0.57036|0.57036	0.2026|0.2026	L|L	0.49513|0.49513	1.565|1.565	0.09310|0.09310	N|N	1|1	.|D	.|0.60575	.|0.988	.|P	.|0.57620	.|0.824	T|T	0.46162|0.46162	-0.9211|-0.9211	5|10	.|0.56958	.|D	.|0.05	.|.	8.2497|8.2497	0.31710|0.31710	0.0:0.8114:0.0:0.1886|0.0:0.8114:0.0:0.1886	.|.	.|3355	.|F8WAI1	.|.	Q|N	772|3355;515	.|ENSP00000334714:T3355N;ENSP00000295591:T515N	.|ENSP00000295591:T515N	H|T	+|+	3|2	2|0	IGFN1|IGFN1	199457360|199457360	0.090000|0.090000	0.21635|0.21635	0.248000|0.248000	0.24265|0.24265	0.075000|0.075000	0.17131|0.17131	2.263000|2.263000	0.43293|0.43293	0.936000|0.936000	0.37367|0.37367	0.305000|0.305000	0.20034|0.20034	CAC|ACC		0.637	IGFN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			NM_178275	
KANSL1	284058	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	44248412	44248412	+	Silent	SNP	T	T	C			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc5420c-5c60-4d1e-8554-9d2f6e55c502	19effa42-4c58-4a24-9cd0-264cf686c9dc	g.chr17:44248412T>C	ENST00000262419.6	-	2	1568	c.1098A>G	c.(1096-1098)ggA>ggG	p.G366G	KANSL1_ENST00000572904.1_Silent_p.G366G|KANSL1_ENST00000432791.1_Silent_p.G366G|KANSL1_ENST00000393476.3_5'UTR|KANSL1_ENST00000574590.1_Silent_p.G366G|KANSL1_ENST00000576248.1_5'UTR|KANSL1_ENST00000575318.1_Silent_p.G366G	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	366					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.G366G(1)									AGTTGCTAAGTCCCTCTGAAG	0.458																																																	1	Substitution - coding silent(1)	kidney(1)											79.0	102.0	94.0					17																	44248412		2203	4300	6503	SO:0001819	synonymous_variant	0			BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"""centromere protein 36"""	612452	"""KIAA1267"""	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.1098A>G	17.37:g.44248412T>C		Somatic		WXS	Illumina HiSeq	Phase_I	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Silent	SNP	ENST00000262419.6	37	CCDS11503.1																																																																																				0.458	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1		NM_015443	
LRRC37A16P	651250	broad.mit.edu	37	17	66123962	66123962	+	RNA	SNP	C	C	T			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc5420c-5c60-4d1e-8554-9d2f6e55c502	19effa42-4c58-4a24-9cd0-264cf686c9dc	g.chr17:66123962C>T	ENST00000590019.1	-	0	371									leucine rich repeat containing 37, member A16, pseudogene																		GGCTGGACTGCATAAGCATGG	0.343																																																	0																																												0					17q24.2	2012-10-18				ENSG00000267023			43820	pseudogene	pseudogene							Standard	NG_023507		Approved				OTTHUMG00000180160		17.37:g.66123962C>T		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP	ENST00000590019.1	37																																																																																					0.343	LRRC37A16P-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000450078.1			
MLLT1	4298	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	6270745	6270745	+	Missense_Mutation	SNP	A	A	T			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc5420c-5c60-4d1e-8554-9d2f6e55c502	19effa42-4c58-4a24-9cd0-264cf686c9dc	g.chr19:6270745A>T	ENST00000252674.7	-	2	201	c.38T>A	c.(37-39)cTg>cAg	p.L13Q		NM_005934.3	NP_005925.2	Q03111	ENL_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 1	13	YEATS. {ECO:0000255|PROSITE- ProRule:PRU00376}.				negative regulation of protein kinase activity (GO:0006469)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	DNA binding (GO:0003677)	p.L13Q(1)		endometrium(3)|kidney(3)|large_intestine(2)|lung(5)|prostate(2)|skin(2)	17						GCGATGCCCCAGCTCTAACCT	0.617			T	MLL	AL						OREG0025198	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																												Dom	yes		19	19p13.3	4298	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 1 (ENL)"""		L	1	Substitution - Missense(1)	kidney(1)											91.0	70.0	77.0					19																	6270745		2203	4300	6503	SO:0001583	missense	4298				CCDS12160.1	19p13.3	2012-10-04	2001-11-28		ENSG00000130382	ENSG00000130382			7134	protein-coding gene	gene with protein product		159556	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 1"""				Standard	XM_005259561		Approved	ENL, LTG19, YEATS1	uc002mek.3	Q03111	OTTHUMG00000180757	ENST00000252674.7:c.38T>A	19.37:g.6270745A>T	ENSP00000252674:p.Leu13Gln	Somatic	632	WXS	Illumina HiSeq	Phase_I	Q14768	Missense_Mutation	SNP	ENST00000252674.7	37	CCDS12160.1	.	.	.	.	.	.	.	.	.	.	A	27.0	4.788138	0.90367	.	.	ENSG00000130382	ENST00000252674	.	.	.	5.41	5.41	0.78517	.	0.164448	0.39909	N	0.001240	T	0.75162	0.3812	L	0.59436	1.845	0.80722	D	1	D	0.60575	0.988	D	0.76071	0.987	T	0.77795	-0.2454	9	0.87932	D	0	-18.3703	13.3955	0.60849	1.0:0.0:0.0:0.0	.	13	Q03111	ENL_HUMAN	Q	13	.	ENSP00000252674:L13Q	L	-	2	0	MLLT1	6221745	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.228000	0.95250	2.051000	0.60960	0.459000	0.35465	CTG		0.617	MLLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452909.1		NM_005934	
MRVI1	10335	broad.mit.edu	37	11	10647673	10647673	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc5420c-5c60-4d1e-8554-9d2f6e55c502	19effa42-4c58-4a24-9cd0-264cf686c9dc	g.chr11:10647673C>A	ENST00000436272.1	-	8	1205	c.1127G>T	c.(1126-1128)gGc>gTc	p.G376V	MRVI1_ENST00000545852.1_Missense_Mutation_p.G88V|MRVI1_ENST00000558540.1_Missense_Mutation_p.G88V|MRVI1_ENST00000424001.1_Missense_Mutation_p.G88V|MRVI1_ENST00000423302.2_Missense_Mutation_p.G403V|MRVI1_ENST00000421747.1_Missense_Mutation_p.G394V|MRVI1_ENST00000527509.2_Missense_Mutation_p.G312V|MRVI1_ENST00000541483.1_Intron|MRVI1_ENST00000531107.1_Missense_Mutation_p.G395V|MRVI1_ENST00000534266.2_Missense_Mutation_p.G88V|MRVI1_ENST00000552103.1_Missense_Mutation_p.G312V|MRVI1_ENST00000547195.1_Missense_Mutation_p.G312V			Q9Y6F6	MRVI1_HUMAN	murine retrovirus integration site 1 homolog	376					blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|relaxation of vascular smooth muscle (GO:0060087)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)		p.G376V(1)		central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|prostate(2)	22				all cancers(16;2.68e-07)|Epithelial(150;3.04e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0723)		CAGCCGGGGGCCAGGTTCTTC	0.662																																																	1	Substitution - Missense(1)	kidney(1)											16.0	18.0	18.0					11																	10647673		1868	4084	5952	SO:0001583	missense	10335			AF081249	CCDS44538.1, CCDS44539.1, CCDS44540.1, CCDS44538.2, CCDS55745.1, CCDS55746.1	11p15.4	2014-09-11			ENSG00000072952	ENSG00000072952			7237	protein-coding gene	gene with protein product	"""inositol 1,4,5-triphosphate-associated cGMP kinase substrate"", ""IP3R-associated cGMP kinase substrate"""	604673				10321731	Standard	NM_001098579		Approved	JAW1L, IRAG	uc010rcb.1	Q9Y6F6	OTTHUMG00000165773	ENST00000436272.1:c.1127G>T	11.37:g.10647673C>A	ENSP00000412229:p.Gly376Val	Somatic		WXS	Illumina GAIIx	Phase_I	B7Z3T4|B7Z6I2|B7Z9A3|E9PQY6|F5H6A1|J3KQZ7|Q17S00|Q9UNY1	Missense_Mutation	SNP	ENST00000436272.1	37		.	.	.	.	.	.	.	.	.	.	C	12.77	2.039047	0.35989	.	.	ENSG00000072952	ENST00000421747;ENST00000308763;ENST00000436272;ENST00000547195;ENST00000552103;ENST00000545852;ENST00000424001;ENST00000423302;ENST00000531107;ENST00000527509	T;T;T;T;T;T;T;T;T	0.16597	2.33;2.33;2.33;2.33;2.33;2.33;2.33;2.33;2.33	5.71	2.82	0.32997	.	0.058264	0.64402	D	0.000002	T	0.30417	0.0764	L	0.51422	1.61	0.21256	N	0.999746	D;D;D	0.67145	0.996;0.996;0.973	D;D;P	0.63597	0.916;0.916;0.73	T	0.02560	-1.1141	10	0.72032	D	0.01	-7.7837	11.3507	0.49585	0.0:0.8088:0.0:0.1912	.	376;395;394	Q9Y6F6;E9PQY6;Q9Y6F6-4	MRVI1_HUMAN;.;.	V	394;377;376;312;312;88;88;403;395;312	ENSP00000414598:G394V;ENSP00000412229:G376V;ENSP00000448278:G312V;ENSP00000446764:G312V;ENSP00000441971:G88V;ENSP00000401205:G88V;ENSP00000412130:G403V;ENSP00000432436:G395V;ENSP00000432067:G312V	ENSP00000307885:G377V	G	-	2	0	MRVI1	10604249	0.518000	0.26234	0.409000	0.26459	0.337000	0.28794	1.637000	0.37155	1.438000	0.47492	-0.251000	0.11542	GGC		0.662	MRVI1-203	KNOWN	basic	protein_coding	protein_coding			NM_001098579	
MXRA7	439921	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	74673741	74673741	+	Missense_Mutation	SNP	C	C	G			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc5420c-5c60-4d1e-8554-9d2f6e55c502	19effa42-4c58-4a24-9cd0-264cf686c9dc	g.chr17:74673741C>G	ENST00000355797.3	-	4	552	c.544G>C	c.(544-546)Gac>Cac	p.D182H		NM_001008528.1	NP_001008528.1	P84157	MXRA7_HUMAN	matrix-remodelling associated 7	182						integral component of membrane (GO:0016021)		p.D182H(1)		kidney(1)|large_intestine(2)|lung(2)|skin(1)	6						TCCTTGTTGTCTTTCATGAGC	0.567																																																	1	Substitution - Missense(1)	kidney(1)											146.0	126.0	133.0					17																	74673741		2203	4300	6503	SO:0001583	missense	439921			BC053983	CCDS32745.1, CCDS32746.1, CCDS45786.1	17q25.1	2007-08-01				ENSG00000182534			7541	protein-coding gene	gene with protein product							Standard	XM_005257382		Approved	FLJ46603, TMAP1, PS1TP1	uc002jsk.1	P84157		ENST00000355797.3:c.544G>C	17.37:g.74673741C>G	ENSP00000348050:p.Asp182His	Somatic		WXS	Illumina HiSeq	Phase_I	Q0P5W3	Missense_Mutation	SNP	ENST00000355797.3	37	CCDS32745.1	.	.	.	.	.	.	.	.	.	.	C	14.52	2.560079	0.45590	.	.	ENSG00000182534	ENST00000355797	T	0.33865	1.39	5.54	5.54	0.83059	.	.	.	.	.	T	0.50343	0.1610	L	0.43152	1.355	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	T	0.49707	-0.8911	9	0.72032	D	0.01	.	11.7089	0.51614	0.0:0.9184:0.0:0.0816	.	182	P84157	MXRA7_HUMAN	H	182	ENSP00000348050:D182H	ENSP00000348050:D182H	D	-	1	0	MXRA7	72185336	1.000000	0.71417	0.998000	0.56505	0.318000	0.28184	4.987000	0.63857	2.611000	0.88343	0.643000	0.83706	GAC		0.567	MXRA7-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450983.1		NM_001008529	
NUP205	23165	hgsc.bcm.edu;ucsc.edu	37	7	135292022	135292022	+	Frame_Shift_Del	DEL	T	T	-			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc5420c-5c60-4d1e-8554-9d2f6e55c502	19effa42-4c58-4a24-9cd0-264cf686c9dc	g.chr7:135292022delT	ENST00000285968.6	+	22	3124	c.3098delT	c.(3097-3099)cttfs	p.L1033fs		NM_015135.2	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa	1033					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)			breast(4)|central_nervous_system(2)|endometrium(9)|kidney(7)|large_intestine(17)|liver(4)|lung(36)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	93						CGGACATGCCTTCACGCCATT	0.453																																																	0													114.0	107.0	109.0					7																	135292022		2203	4300	6503	SO:0001589	frameshift_variant	23165			D86978	CCDS34759.1	7q31.32	2007-03-26	2004-01-06	2004-01-07	ENSG00000155561	ENSG00000155561			18658	protein-coding gene	gene with protein product		614352	"""chromosome 7 open reading frame 14"""	C7orf14		9039502, 9348540	Standard	NM_015135		Approved	KIAA0225	uc003vsw.3	Q92621	OTTHUMG00000155497	ENST00000285968.6:c.3098delT	7.37:g.135292022delT	ENSP00000285968:p.Leu1033fs	Somatic		WXS	Illumina HiSeq	Phase_I	A6H8X3|Q86YC1	Frame_Shift_Del	DEL	ENST00000285968.6	37	CCDS34759.1																																																																																				0.453	NUP205-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340358.1			
NUPL2	11097	hgsc.bcm.edu	37	7	23221797	23221798	+	In_Frame_Ins	INS	-	-	CGGCAGCAACCG	rs200880793|rs371896223	byFrequency	TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc5420c-5c60-4d1e-8554-9d2f6e55c502	19effa42-4c58-4a24-9cd0-264cf686c9dc	g.chr7:23221797_23221798insCGGCAGCAACCG	ENST00000258742.5	+	1	352_353	c.93_94insCGGCAGCAACCG	c.(94-96)cgg>CGGCAGCAACCGcgg	p.32_32R>RQQPR	NUPL2_ENST00000487595.1_3'UTR|AC005082.1_ENST00000366347.4_Intron|NUPL2_ENST00000410002.3_In_Frame_Ins_p.32_32R>RQQPR	NM_007342.2	NP_031368.1	O15504	NUPL2_HUMAN	nucleoporin like 2	32					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein export from nucleus (GO:0006611)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nuclear export signal receptor activity (GO:0005049)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(4)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						CAGGAGGAGGACGGCAGCAACC	0.649														62	0.0123802	0.0015	0.0303	5008	,	,		15515	0.0		0.0368	False		,,,				2504	0.002																0										35,4229		1,33,2098						-0.0	1.0			54	407,7847		9,389,3729	no	coding	NUPL2	NM_007342.2		10,422,5827	A1A1,A1R,RR		4.9309,0.8208,3.5309				442,12076				SO:0001652	inframe_insertion	11097			U97198	CCDS5379.1	7p15	2003-08-07			ENSG00000136243	ENSG00000136243			17010	protein-coding gene	gene with protein product	"""nucleoporin-like protein 1"""					10358091, 9450185	Standard	NM_007342		Approved	NLP_1, CG1, hCG1, H_RG271G13.9	uc003svu.3	O15504	OTTHUMG00000096955	ENST00000258742.5:c.94_105dupCGGCAGCAACCG	7.37:g.23221797_23221798insCGGCAGCAACCG	Exception_encountered	Somatic		WXS	Illumina HiSeq	Phase_I	A4D143|B4DP42|Q49AE7|Q9BS49	In_Frame_Ins	INS	ENST00000258742.5	37	CCDS5379.1																																																																																				0.649	NUPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214017.2		NM_007342	
PBRM1	55193	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	52661377	52661377	+	Nonsense_Mutation	SNP	T	T	A			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	dbc5420c-5c60-4d1e-8554-9d2f6e55c502	19effa42-4c58-4a24-9cd0-264cf686c9dc	g.chr3:52661377T>A	ENST00000296302.7	-	13	1454	c.1453A>T	c.(1453-1455)Aaa>Taa	p.K485*	PBRM1_ENST00000337303.4_Nonsense_Mutation_p.K485*|PBRM1_ENST00000356770.4_Nonsense_Mutation_p.K453*|PBRM1_ENST00000409057.1_Nonsense_Mutation_p.K485*|PBRM1_ENST00000409767.1_Nonsense_Mutation_p.K485*|PBRM1_ENST00000410007.1_Nonsense_Mutation_p.K485*|PBRM1_ENST00000409114.3_Nonsense_Mutation_p.K485*|PBRM1_ENST00000394830.3_Nonsense_Mutation_p.K485*			Q86U86	PB1_HUMAN	polybromo 1	485					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.K485*(2)|p.K453*(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)		GCAAGCTCTTTCTTCTTTGCC	0.428			"""Mis, N, F, S, D, O"""		"""clear cell renal carcinoma, breast"""																																			Rec	yes		3	3p21	55193	polybromo 1		E	3	Substitution - Nonsense(3)	kidney(3)											110.0	98.0	102.0					3																	52661377		2203	4300	6503	SO:0001587	stop_gained	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.1453A>T	3.37:g.52661377T>A	ENSP00000296302:p.Lys485*	Somatic		WXS	Illumina HiSeq	Phase_I	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Nonsense_Mutation	SNP	ENST00000296302.7	37		.	.	.	.	.	.	.	.	.	.	T	39	7.632946	0.98403	.	.	ENSG00000163939	ENST00000356770;ENST00000394830;ENST00000296302;ENST00000337303;ENST00000409057;ENST00000410007;ENST00000409114;ENST00000409767;ENST00000423351;ENST00000446103	.	.	.	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	1.818	16.3943	0.83563	0.0:0.0:0.0:1.0	.	.	.	.	X	453;485;485;485;485;485;485;485;485;429	.	ENSP00000296302:K485X	K	-	1	0	PBRM1	52636417	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.412000	0.80091	2.281000	0.76405	0.533000	0.62120	AAA		0.428	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1		NM_018165	
NELFE	7936	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	31922556	31922556	+	Missense_Mutation	SNP	C	C	G			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc5420c-5c60-4d1e-8554-9d2f6e55c502	19effa42-4c58-4a24-9cd0-264cf686c9dc	g.chr6:31922556C>G	ENST00000375429.3	-	7	744	c.518G>C	c.(517-519)cGc>cCc	p.R173P	NELFE_ENST00000444811.2_Missense_Mutation_p.R143P|NELFE_ENST00000375425.5_Missense_Mutation_p.R180P|MIR1236_ENST00000408340.1_RNA	NM_002904.5	NP_002895.3	P18615	NELFE_HUMAN	negative elongation factor complex member E	173					gene expression (GO:0010467)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	NELF complex (GO:0032021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.R173P(1)									GGCACCACTGCGTTCTTCATA	0.632																																																	1	Substitution - Missense(1)	kidney(1)											63.0	68.0	66.0					6																	31922556		2203	4300	6503	SO:0001583	missense	7936			M33230	CCDS4730.1	6p21.3	2013-02-12	2013-01-31	2013-01-31	ENSG00000204356	ENSG00000204356		"""RNA binding motif (RRM) containing"""	13974	protein-coding gene	gene with protein product		154040	"""RD RNA-binding protein"", ""RD RNA binding protein"""	RDBP			Standard	XM_006715205		Approved	RD, D6S45, NELF-E, RDP	uc003nyk.3	P18615	OTTHUMG00000031046	ENST00000375429.3:c.518G>C	6.37:g.31922556C>G	ENSP00000364578:p.Arg173Pro	Somatic		WXS	Illumina HiSeq	Phase_I	A2BE08|B4DUN1|B4DYX9|Q5JP74|Q5JP75|Q96F56|Q9NPK2	Missense_Mutation	SNP	ENST00000375429.3	37	CCDS4730.1	.	.	.	.	.	.	.	.	.	.	C	9.682	1.149569	0.21288	.	.	ENSG00000204356	ENST00000375429;ENST00000375425;ENST00000444811;ENST00000441998;ENST00000454913;ENST00000436289	T;T;T;T;T	0.49720	0.77;0.77;0.95;0.95;0.95	5.15	1.36	0.22044	.	0.260360	0.31554	N	0.007448	T	0.08626	0.0214	N	0.08118	0	0.23962	N	0.996338	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.001;0.001;0.001	T	0.25745	-1.0123	10	0.54805	T	0.06	-1.7649	4.2187	0.10547	0.0:0.5456:0.1696:0.2848	.	143;168;168;173	B4DUN1;A2ABK1;E9PCL7;P18615	.;.;.;NELFE_HUMAN	P	173;180;143;168;173;168	ENSP00000364578:R173P;ENSP00000364574:R180P;ENSP00000388400:R143P;ENSP00000397914:R168P;ENSP00000414029:R168P	ENSP00000364574:R180P	R	-	2	0	RDBP	32030535	0.976000	0.34144	0.097000	0.21041	0.184000	0.23303	2.549000	0.45803	0.064000	0.16427	-0.136000	0.14681	CGC		0.632	NELFE-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076047.4			
SCRN2	90507	broad.mit.edu;ucsc.edu	37	17	45918176	45918176	+	Missense_Mutation	SNP	A	A	T			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc5420c-5c60-4d1e-8554-9d2f6e55c502	19effa42-4c58-4a24-9cd0-264cf686c9dc	g.chr17:45918176A>T	ENST00000290216.9	-	2	159	c.34T>A	c.(34-36)Tgc>Agc	p.C12S	SCRN2_ENST00000407215.3_Missense_Mutation_p.C12S|SCRN2_ENST00000584123.1_Missense_Mutation_p.C20S	NM_001145023.1|NM_138355.3	NP_001138495.1|NP_612364.2	Q96FV2	SCRN2_HUMAN	secernin 2	12						extracellular vesicular exosome (GO:0070062)	dipeptidase activity (GO:0016805)	p.C12S(1)		cervix(1)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|skin(1)	14						AAGCAGTCGCAGGAACATGGG	0.667																																																	1	Substitution - Missense(1)	kidney(1)											28.0	34.0	32.0					17																	45918176		2203	4300	6503	SO:0001583	missense	90507			BC002980	CCDS11519.1, CCDS45723.1	17q21	2008-02-05							30381	protein-coding gene	gene with protein product		614966				12221138	Standard	NM_001145023		Approved		uc002imd.3	Q96FV2		ENST00000290216.9:c.34T>A	17.37:g.45918176A>T	ENSP00000290216:p.Cys12Ser	Somatic		WXS	Illumina GAIIx	Phase_I	A8K3N1|B7Z8S7|E9PBV5|Q96AC3|Q9BU04	Missense_Mutation	SNP	ENST00000290216.9	37	CCDS11519.1	.	.	.	.	.	.	.	.	.	.	a	28.0	4.879682	0.91740	.	.	ENSG00000141295	ENST00000290216;ENST00000407215	T;T	0.19532	2.15;2.14	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.50069	0.1594	M	0.82823	2.61	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.80764	0.994;0.994;0.994	T	0.56619	-0.7949	10	0.87932	D	0	-20.9632	14.6923	0.69096	1.0:0.0:0.0:0.0	.	12;12;12	E9PBV5;Q96FV2;B7Z8S7	.;SCRN2_HUMAN;.	S	12	ENSP00000290216:C12S;ENSP00000383935:C12S	ENSP00000290216:C12S	C	-	1	0	SCRN2	43273175	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	7.274000	0.78538	2.130000	0.65690	0.529000	0.55759	TGC		0.667	SCRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441383.1		NM_138355	
SEMA4D	10507	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	92008488	92008488	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc5420c-5c60-4d1e-8554-9d2f6e55c502	19effa42-4c58-4a24-9cd0-264cf686c9dc	g.chr9:92008488G>A	ENST00000450295.1	-	7	1273	c.497C>T	c.(496-498)tCc>tTc	p.S166F	SEMA4D_ENST00000356444.2_Missense_Mutation_p.S166F|SEMA4D_ENST00000420987.1_Missense_Mutation_p.S166F|SEMA4D_ENST00000339861.4_Missense_Mutation_p.S166F|SEMA4D_ENST00000343780.4_Missense_Mutation_p.S166F|SEMA4D_ENST00000422704.2_Missense_Mutation_p.S166F|SEMA4D_ENST00000455551.2_Missense_Mutation_p.S166F|SEMA4D_ENST00000438547.2_Missense_Mutation_p.S166F			Q92854	SEM4D_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	166	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|immune response (GO:0006955)|leukocyte aggregation (GO:0070486)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|ossification involved in bone maturation (GO:0043931)|positive regulation of cell migration (GO:0030335)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell projection organization (GO:0031344)|regulation of cell shape (GO:0008360)|regulation of dendrite morphogenesis (GO:0048814)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)	p.S166F(1)		NS(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(8)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	34						AACCATGACGGATGTGTAGCT	0.428																																																	1	Substitution - Missense(1)	kidney(1)											271.0	201.0	225.0					9																	92008488		2203	4300	6503	SO:0001583	missense	10507			U60800	CCDS6685.1, CCDS47991.1	9q22-q31	2013-01-11			ENSG00000187764	ENSG00000187764		"""Semaphorins"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10732	protein-coding gene	gene with protein product	"""M-sema G"""	601866	"""chromosome 9 open reading frame 164"""	SEMAJ, C9orf164		8876214, 8969198	Standard	NM_006378		Approved	CD100, coll-4, FLJ39737	uc004aqo.1	Q92854	OTTHUMG00000020185	ENST00000450295.1:c.497C>T	9.37:g.92008488G>A	ENSP00000416523:p.Ser166Phe	Somatic		WXS	Illumina HiSeq	Phase_I	B2RPM6|Q7Z5S4|Q8N8B0	Missense_Mutation	SNP	ENST00000450295.1	37	CCDS6685.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.618695	0.87460	.	.	ENSG00000187764	ENST00000339861;ENST00000420987;ENST00000455551;ENST00000343780;ENST00000450295;ENST00000438547;ENST00000356444;ENST00000422704	T;T;T;T;T;T;T;T	0.12984	2.63;2.63;2.63;2.63;2.63;2.63;2.63;2.63	4.59	4.59	0.56863	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.105137	0.64402	D	0.000003	T	0.42720	0.1215	M	0.84156	2.68	0.58432	D	0.999993	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.48681	-0.9014	10	0.87932	D	0	.	17.9498	0.89048	0.0:0.0:1.0:0.0	.	166;166	Q92854-2;Q92854	.;SEM4D_HUMAN	F	166	ENSP00000344923:S166F;ENSP00000391733:S166F;ENSP00000411981:S166F;ENSP00000343418:S166F;ENSP00000416523:S166F;ENSP00000405102:S166F;ENSP00000348822:S166F;ENSP00000388768:S166F	ENSP00000344923:S166F	S	-	2	0	SEMA4D	91198308	1.000000	0.71417	0.676000	0.29932	0.973000	0.67179	9.086000	0.94088	2.539000	0.85634	0.655000	0.94253	TCC		0.428	SEMA4D-018	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342411.1		NM_006378	
SLC35A1	10559	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	88210968	88210968	+	Silent	SNP	T	T	C			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc5420c-5c60-4d1e-8554-9d2f6e55c502	19effa42-4c58-4a24-9cd0-264cf686c9dc	g.chr6:88210968T>C	ENST00000369552.4	+	4	474	c.447T>C	c.(445-447)ttT>ttC	p.F149F	SLC35A1_ENST00000369556.3_Silent_p.F149F|SLC35A1_ENST00000464978.1_3'UTR|SLC35A1_ENST00000369557.5_Silent_p.F149F|C6orf165_ENST00000506888.1_3'UTR|SLC35A1_ENST00000544441.1_Silent_p.F15F	NM_006416.4	NP_006407.1	P78382	S35A1_HUMAN	solute carrier family 35 (CMP-sialic acid transporter), member A1	149					carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|CMP-N-acetylneuraminate transport (GO:0015782)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)	CMP-N-acetylneuraminate transmembrane transporter activity (GO:0005456)|sugar:proton symporter activity (GO:0005351)	p.F149F(1)		breast(1)|kidney(3)|large_intestine(2)|lung(3)	9		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0429)		TTTCAGTTTTTATGCTGTGTG	0.403																																					NSCLC(183;214 2117 17033 22638 44782)|Ovarian(87;1008 1343 9644 42916 50932)												1	Substitution - coding silent(1)	kidney(1)											111.0	109.0	109.0					6																	88210968		2203	4300	6503	SO:0001819	synonymous_variant	10559			D87969	CCDS5010.1, CCDS55043.1	6q15	2013-05-22			ENSG00000164414	ENSG00000164414		"""Solute carriers"""	11021	protein-coding gene	gene with protein product		605634	"""solute carrier family 35 (UDP-galactose transporter), member 1"""			9010752, 9644260	Standard	NM_006416		Approved	CMPST, hCST	uc011dzj.2	P78382	OTTHUMG00000015177	ENST00000369552.4:c.447T>C	6.37:g.88210968T>C		Somatic		WXS	Illumina HiSeq	Phase_I	Q5W1L8	Silent	SNP	ENST00000369552.4	37	CCDS5010.1																																																																																				0.403	SLC35A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041446.1			
SUPT6H	6830	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	27023953	27023953	+	Silent	SNP	T	T	C			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc5420c-5c60-4d1e-8554-9d2f6e55c502	19effa42-4c58-4a24-9cd0-264cf686c9dc	g.chr17:27023953T>C	ENST00000314616.6	+	30	4345	c.4062T>C	c.(4060-4062)gaT>gaC	p.D1354D	SUPT6H_ENST00000347486.4_Silent_p.D1354D	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)	1354	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				chromatin remodeling (GO:0006338)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|negative regulation of histone H3-K27 methylation (GO:0061086)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|regulation of isotype switching (GO:0045191)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of muscle cell differentiation (GO:0051147)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|hydrolase activity, acting on ester bonds (GO:0016788)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D1354D(1)		NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	Lung NSC(42;0.00431)					ACCAGGGTGATGTGATTATCC	0.498																																																	1	Substitution - coding silent(1)	kidney(1)											173.0	142.0	152.0					17																	27023953		2203	4300	6503	SO:0001819	synonymous_variant	6830			U38658	CCDS32596.1	17q11.2	2013-02-14	2001-11-28			ENSG00000109111		"""SH2 domain containing"""	11470	protein-coding gene	gene with protein product		601333	"""suppressor of Ty (S.cerevisiae) 6 homolog"""			8786132	Standard	XM_005258026		Approved	KIAA0162, SPT6H	uc002hby.3	Q7KZ85		ENST00000314616.6:c.4062T>C	17.37:g.27023953T>C		Somatic		WXS	Illumina HiSeq	Phase_I	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Silent	SNP	ENST00000314616.6	37	CCDS32596.1																																																																																				0.498	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2		NM_003170	
VHL	7428	hgsc.bcm.edu;ucsc.edu	37	3	10188297	10188297	+	Frame_Shift_Del	DEL	T	T	-			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc5420c-5c60-4d1e-8554-9d2f6e55c502	19effa42-4c58-4a24-9cd0-264cf686c9dc	g.chr3:10188297delT	ENST00000256474.2	+	2	1280	c.440delT	c.(439-441)attfs	p.I147fs	VHL_ENST00000477538.1_3'UTR|VHL_ENST00000345392.2_Intron	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	147	Involved in binding to CCT complex.		I -> T (in pheochromocytoma). {ECO:0000269|PubMed:9663592}.		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.A149fs*25(4)|p.F148fs*11(4)|p.I147fs*25(1)|p.I147fs*11(1)|p.I147fs*27(1)|p.I147fs*13(1)|p.I147_F148del(1)|p.I147fs*10(1)|p.F148fs*25(1)|p.P146fs*23(1)|p.G144fs*19(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)		GGACAGCCTATTTTTGCCAAT	0.418		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"""	17	Deletion - Frameshift(10)|Insertion - Frameshift(6)|Deletion - In frame(1)	kidney(17)	GRCh37	CM982009	VHL	M							204.0	190.0	195.0					3																	10188297		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.440delT	3.37:g.10188297delT	ENSP00000256474:p.Ile147fs	Somatic		WXS	Illumina HiSeq	Phase_I	B2RE45|Q13599|Q6PDA9	Frame_Shift_Del	DEL	ENST00000256474.2	37	CCDS2597.1																																																																																				0.418	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1		NM_000551	
TSEN2	80746	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	12544895	12544895	+	Missense_Mutation	SNP	A	A	C			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc5420c-5c60-4d1e-8554-9d2f6e55c502	19effa42-4c58-4a24-9cd0-264cf686c9dc	g.chr3:12544895A>C	ENST00000284995.6	+	5	830	c.443A>C	c.(442-444)cAa>cCa	p.Q148P	TSEN2_ENST00000402228.3_Missense_Mutation_p.Q148P|TSEN2_ENST00000314571.7_Missense_Mutation_p.Q148P|TSEN2_ENST00000454502.2_Missense_Mutation_p.Q148P|RNU6-404P_ENST00000515968.1_RNA|TSEN2_ENST00000444864.1_Missense_Mutation_p.Q148P|TSEN2_ENST00000383797.5_Missense_Mutation_p.Q148P|TSEN2_ENST00000415684.1_Missense_Mutation_p.Q148P	NM_025265.3	NP_079541.1	Q8NCE0	SEN2_HUMAN	TSEN2 tRNA splicing endonuclease subunit	148					mRNA processing (GO:0006397)|tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|tRNA-intron endonuclease complex (GO:0000214)	lyase activity (GO:0016829)|nucleic acid binding (GO:0003676)|tRNA-intron endonuclease activity (GO:0000213)	p.Q148P(1)		central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(7)	19						GAAGAGGCTCAAGTGCATGAC	0.507																																																	1	Substitution - Missense(1)	kidney(1)											107.0	103.0	104.0					3																	12544895		2203	4300	6503	SO:0001583	missense	80746			BC019582	CCDS2611.1, CCDS46757.1, CCDS46758.1, CCDS46759.1	3p25.2	2013-08-06	2013-08-06		ENSG00000154743	ENSG00000154743		"""tRNA splicing endonuclease subunits"""	28422	protein-coding gene	gene with protein product		608753	"""tRNA splicing endonuclease 2 homolog (SEN2, S. cerevisiae)"", ""tRNA splicing endonuclease 2 homolog (S. cerevisiae)"""			15109492	Standard	NM_025265		Approved	SEN2, SEN2L, MGC2776	uc003bxb.3	Q8NCE0	OTTHUMG00000129765	ENST00000284995.6:c.443A>C	3.37:g.12544895A>C	ENSP00000284995:p.Gln148Pro	Somatic		WXS	Illumina HiSeq	Phase_I	B7Z6K1|C9IZI7|G5E9Q3|Q8WTW7|Q9BPU7	Missense_Mutation	SNP	ENST00000284995.6	37	CCDS2611.1	.	.	.	.	.	.	.	.	.	.	A	6.353	0.433238	0.12045	.	.	ENSG00000154743	ENST00000446004;ENST00000314571;ENST00000454502;ENST00000383797;ENST00000402228;ENST00000284995;ENST00000444864;ENST00000537959;ENST00000415684	T;T;T;T;T;T;T;T	0.55930	0.5;0.5;0.49;0.51;0.51;0.51;0.49;0.5	4.5	-9.01	0.00744	.	1.198800	0.05937	N	0.636264	T	0.29389	0.0732	N	0.11927	0.2	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.0;0.001;0.0	T	0.24870	-1.0148	10	0.22706	T	0.39	0.0802	13.1562	0.59518	0.1865:0.7311:0.0823:0.0	.	148;148;148;148	G5E9Q3;Q8NCE0;Q8NCE0-3;C9IZI7	.;SEN2_HUMAN;.;.	P	148;148;148;148;148;148;148;121;148	ENSP00000406238:Q148P;ENSP00000323188:Q148P;ENSP00000392029:Q148P;ENSP00000373307:Q148P;ENSP00000385976:Q148P;ENSP00000284995:Q148P;ENSP00000407974:Q148P;ENSP00000416510:Q148P	ENSP00000284995:Q148P	Q	+	2	0	TSEN2	12519895	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.693000	0.01917	-1.355000	0.02186	0.496000	0.49642	CAA		0.507	TSEN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251981.1		NM_025265	
VPS28	51160	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	145649316	145649316	+	Intron	SNP	A	A	C			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc5420c-5c60-4d1e-8554-9d2f6e55c502	19effa42-4c58-4a24-9cd0-264cf686c9dc	g.chr8:145649316A>C	ENST00000526054.1	-	9	586				VPS28_ENST00000529182.1_Missense_Mutation_p.L219R|VPS28_ENST00000292510.4_Intron|VPS28_ENST00000526734.1_5'Flank|VPS28_ENST00000377348.2_Missense_Mutation_p.L219R			Q9UK41	VPS28_HUMAN	vacuolar protein sorting 28 homolog (S. cerevisiae)						endosomal transport (GO:0016197)|intracellular transport of virus (GO:0075733)|membrane organization (GO:0061024)|negative regulation of protein ubiquitination (GO:0031397)|protein transport (GO:0015031)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|endosome membrane (GO:0010008)|ESCRT I complex (GO:0000813)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)		p.L219R(1)		kidney(1)|large_intestine(1)|lung(4)|prostate(1)	7	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;8.67e-41)|all cancers(56;1.1e-35)|BRCA - Breast invasive adenocarcinoma(115;0.035)|Colorectal(110;0.055)			CTGGGAGTGCAGCACAGGGCA	0.677																																																	1	Substitution - Missense(1)	kidney(1)											42.0	46.0	45.0					8																	145649316		2203	4299	6502	SO:0001627	intron_variant	51160			AF316887	CCDS6425.1, CCDS34967.1	8q24.3	2014-08-12	2006-04-04		ENSG00000160948	ENSG00000160948			18178	protein-coding gene	gene with protein product		611952	"""vacuolar protein sorting 28 (yeast)"""				Standard	NM_183057		Approved		uc003zct.1	Q9UK41	OTTHUMG00000165209	ENST00000526054.1:c.549-11T>G	8.37:g.145649316A>C		Somatic		WXS	Illumina HiSeq	Phase_I	Q86VK0	Missense_Mutation	SNP	ENST00000526054.1	37	CCDS6425.1	.	.	.	.	.	.	.	.	.	.	a	15.84	2.952119	0.53293	.	.	ENSG00000160948	ENST00000529182;ENST00000377348	.	.	.	3.7	2.56	0.30785	.	13.725800	0.00868	N	0.001985	T	0.45677	0.1354	.	.	.	0.09310	N	1	P	0.40794	0.729	P	0.45232	0.474	T	0.35375	-0.9791	8	0.87932	D	0	.	7.3067	0.26451	0.8908:0.0:0.1091:0.0	.	219	Q9UK41-2	.	R	219	.	ENSP00000366565:L219R	L	-	2	0	VPS28	145620124	0.000000	0.05858	0.017000	0.16124	0.015000	0.08874	-0.036000	0.12185	0.796000	0.33947	0.492000	0.49549	CTG		0.677	VPS28-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382694.1			
VSIG1	340547	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	107319363	107319363	+	Missense_Mutation	SNP	A	A	T			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc5420c-5c60-4d1e-8554-9d2f6e55c502	19effa42-4c58-4a24-9cd0-264cf686c9dc	g.chrX:107319363A>T	ENST00000217957.5	+	6	862	c.745A>T	c.(745-747)Atc>Ttc	p.I249F	VSIG1_ENST00000415430.3_Missense_Mutation_p.I285F	NM_182607.4	NP_872413.1	Q86XK7	VSIG1_HUMAN	V-set and immunoglobulin domain containing 1	249						integral component of membrane (GO:0016021)		p.I285F(2)|p.I249F(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	17						AGGTGCCGCCATCATCATCTC	0.428																																																	3	Substitution - Missense(3)	kidney(3)											192.0	165.0	175.0					X																	107319363		2203	4300	6503	SO:0001583	missense	340547			BX648658	CCDS14535.1, CCDS55474.1	Xq22.3	2013-01-29			ENSG00000101842	ENSG00000101842		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	28675	protein-coding gene	gene with protein product		300620				12477932	Standard	NM_182607		Approved	MGC44287	uc011msk.2	Q86XK7	OTTHUMG00000022175	ENST00000217957.5:c.745A>T	X.37:g.107319363A>T	ENSP00000217957:p.Ile249Phe	Somatic		WXS	Illumina HiSeq	Phase_I	C9J4P2|Q6MZS4	Missense_Mutation	SNP	ENST00000217957.5	37	CCDS14535.1	.	.	.	.	.	.	.	.	.	.	A	12.49	1.952850	0.34471	.	.	ENSG00000101842	ENST00000415430;ENST00000217957	T;T	0.77358	-1.09;-0.86	4.91	3.69	0.42338	.	0.279045	0.28853	N	0.013924	T	0.81763	0.4891	M	0.66939	2.045	0.21967	N	0.999446	D;D	0.63880	0.99;0.993	P;P	0.59288	0.784;0.855	T	0.71318	-0.4629	10	0.39692	T	0.17	.	8.0488	0.30566	0.9059:0.0:0.0941:0.0	.	285;249	C9J4P2;Q86XK7	.;VSIG1_HUMAN	F	285;249	ENSP00000402219:I285F;ENSP00000217957:I249F	ENSP00000217957:I249F	I	+	1	0	VSIG1	107206019	0.995000	0.38212	0.078000	0.20375	0.092000	0.18411	1.691000	0.37721	0.673000	0.31224	0.486000	0.48141	ATC		0.428	VSIG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057858.1		NM_182607	
ZMYM6	9204	broad.mit.edu;hgsc.bcm.edu	37	1	35457966	35457966	+	Missense_Mutation	SNP	A	A	T			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc5420c-5c60-4d1e-8554-9d2f6e55c502	19effa42-4c58-4a24-9cd0-264cf686c9dc	g.chr1:35457966A>T	ENST00000357182.4	-	15	2242	c.2015T>A	c.(2014-2016)aTg>aAg	p.M672K	ZMYM6_ENST00000487874.1_Missense_Mutation_p.M672K|ZMYM6_ENST00000493328.1_5'UTR|ZMYM6_ENST00000373340.2_Missense_Mutation_p.M672K	NM_007167.3	NP_009098.3	O95789	ZMYM6_HUMAN	zinc finger, MYM-type 6	672					cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.M672K(1)		breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(10)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	44		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.13)				TGGAAATTTCATAGCATCTTC	0.373																																																	1	Substitution - Missense(1)	kidney(1)											145.0	137.0	140.0					1																	35457966		2203	4300	6503	SO:0001583	missense	9204			AF055470	CCDS387.2	1p34.2	2014-05-12	2005-09-12	2005-09-12	ENSG00000163867	ENSG00000163867		"""Zinc fingers, MYM type"", ""Zinc fingers, BED-type"""	13050	protein-coding gene	gene with protein product	"""zinc finger, BED-type containing 7"""	613567	"""zinc finger protein 258"", ""zinc finger, MYM-type containing 6"""	ZNF258		10486218, 23533661	Standard	NM_007167		Approved	ZNF198L4, MYM, Buster2, ZBED7	uc001byh.3	O95789	OTTHUMG00000004163	ENST00000357182.4:c.2015T>A	1.37:g.35457966A>T	ENSP00000349708:p.Met672Lys	Somatic		WXS	Illumina HiSeq	Phase_I	B4DRJ6|Q32Q23|Q4G108|Q5SVZ9|Q5SW00|Q69YL4|Q96IY0|Q9NWF1|Q9P2J4	Missense_Mutation	SNP	ENST00000357182.4	37	CCDS387.2	.	.	.	.	.	.	.	.	.	.	A	7.258	0.604565	0.14002	.	.	ENSG00000163867	ENST00000373340;ENST00000357182	T;T	0.22134	1.97;3.12	4.47	-2.47	0.06442	.	1.497270	0.03469	N	0.213422	T	0.13927	0.0337	L	0.40543	1.245	0.09310	N	0.999998	B;B;B	0.15141	0.012;0.001;0.002	B;B;B	0.14578	0.011;0.003;0.005	T	0.22312	-1.0220	10	0.06236	T	0.91	3.7425	5.0045	0.14280	0.5526:0.0:0.3153:0.1321	.	575;672;672	B4DWC0;O95789;O95789-1	.;ZMYM6_HUMAN;.	K	672	ENSP00000362437:M672K;ENSP00000349708:M672K	ENSP00000349708:M672K	M	-	2	0	ZMYM6	35230553	0.366000	0.25014	0.005000	0.12908	0.190000	0.23558	0.156000	0.16382	-0.550000	0.06183	0.477000	0.44152	ATG		0.373	ZMYM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011999.1		NM_007167	
ZNF354A	6940	hgsc.bcm.edu	37	5	178140409	178140424	+	Frame_Shift_Del	DEL	CTTTCTATAGTGGGGA	CTTTCTATAGTGGGGA	-	rs147082488|rs77426342|rs77501345|rs201214103	byFrequency	TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08	CTTTCTATAGTGGGGA	CTTTCTATAGTGGGGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc5420c-5c60-4d1e-8554-9d2f6e55c502	19effa42-4c58-4a24-9cd0-264cf686c9dc	g.chr5:178140409_178140424delCTTTCTATAGTGGGGA	ENST00000335815.2	-	5	652_667	c.455_470delTCCCCACTATAGAAAG	c.(454-471)atccccactatagaaagafs	p.IPTIER152fs		NM_005649.2	NP_005640.2	O60765	Z354A_HUMAN	zinc finger protein 354A	152					regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|sensory perception of sound (GO:0007605)|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)			breast(1)|endometrium(2)|large_intestine(7)|lung(3)|ovary(2)|skin(2)|stomach(2)	19	all_cancers(89;0.000536)|Renal(175;0.000159)|all_epithelial(37;0.000221)|Lung NSC(126;0.00308)|all_lung(126;0.00536)	all_cancers(40;0.0452)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.185)		TTTATGGCTTCTTTCTATAGTGGGGATTTTTTTGTG	0.361																																																	0																																										SO:0001589	frameshift_variant	6940			AF116030	CCDS4438.1	5q35.3	2013-01-08		2001-11-23	ENSG00000169131	ENSG00000169131		"""Zinc fingers, C2H2-type"", ""-"""	11628	protein-coding gene	gene with protein product		602444		TCF17		9465904	Standard	NM_005649		Approved	KID-1, EZNF, HKL1, KID1	uc003mjj.3	O60765	OTTHUMG00000130895	ENST00000335815.2:c.455_470delTCCCCACTATAGAAAG	5.37:g.178140409_178140424delCTTTCTATAGTGGGGA	ENSP00000337122:p.Ile152fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q9UNJ8	Frame_Shift_Del	DEL	ENST00000335815.2	37	CCDS4438.1																																																																																				0.361	ZNF354A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253481.1		NM_005649	
ZSCAN16	80345	hgsc.bcm.edu;ucsc.edu	37	6	28097728	28097729	+	Stop_Codon_Del	DEL	AT	AT	-			TCGA-CJ-4908-01A-01D-1429-08	TCGA-CJ-4908-11A-01D-1429-08	AT	AT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dbc5420c-5c60-4d1e-8554-9d2f6e55c502	19effa42-4c58-4a24-9cd0-264cf686c9dc	g.chr6:28097728_28097729delAT	ENST00000340487.4	+	0	1196_1197				ZSCAN16-AS1_ENST00000600652.1_RNA|ZSCAN16-AS1_ENST00000602810.1_RNA	NM_025231.1	NP_079507.1	Q9H4T2	ZSC16_HUMAN	zinc finger and SCAN domain containing 16						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)			large_intestine(5)|liver(1)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	10						AACTCTACTAATATAGCAGTAA	0.361																																																	0																																										SO:0001567	stop_retained_variant	80345			AK025844	CCDS4644.1	6p21.33	2013-01-08	2007-02-20	2007-02-20	ENSG00000196812	ENSG00000196812		"""-"", ""Zinc fingers, C2H2-type"""	20813	protein-coding gene	gene with protein product			"""zinc finger protein 392"", ""zinc finger protein 435"""	ZNF392, ZNF435			Standard	NM_025231		Approved	FLJ22191, dJ265C24.3	uc003nkm.3	Q9H4T2	OTTHUMG00000014509	Exception_encountered	6.37:g.28097730_28097731delAT		Somatic		WXS	Illumina HiSeq	Phase_I	Q9H6K2	Frame_Shift_Del	DEL	ENST00000340487.4	37	CCDS4644.1																																																																																				0.361	ZSCAN16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040177.1		NM_025231	
