#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
ARG1	383	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	131904255	131904256	+	Frame_Shift_Ins	INS	-	-	T			TCGA-CZ-5454-01A-01D-1501-10	TCGA-CZ-5454-11A-01D-1501-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d9fd1928-7b7d-4147-aeff-1618393ba26c	46d95289-69d8-4437-b2f3-5a3e5ccf7ef6	g.chr6:131904255_131904256insT	ENST00000368087.3	+	6	755_756	c.616_617insT	c.(616-618)ctafs	p.L206fs	MED23_ENST00000354577.4_Intron|ARG1_ENST00000356962.2_Frame_Shift_Ins_p.L214fs			P05089	ARGI1_HUMAN	arginase 1	206					arginine catabolic process (GO:0006527)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to glucagon stimulus (GO:0071377)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to interleukin-4 (GO:0071353)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen biosynthetic process (GO:0032964)|liver development (GO:0001889)|lung development (GO:0030324)|mammary gland involution (GO:0060056)|maternal process involved in female pregnancy (GO:0060135)|positive regulation of endothelial cell proliferation (GO:0001938)|protein homotrimerization (GO:0070207)|regulation of L-arginine import (GO:0010963)|response to amine (GO:0014075)|response to amino acid (GO:0043200)|response to axon injury (GO:0048678)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to herbicide (GO:0009635)|response to manganese ion (GO:0010042)|response to methylmercury (GO:0051597)|response to selenium ion (GO:0010269)|response to vitamin A (GO:0033189)|response to vitamin E (GO:0033197)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|urea cycle (GO:0000050)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	arginase activity (GO:0004053)|manganese ion binding (GO:0030145)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|ovary(1)|skin(3)	14	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0106)|OV - Ovarian serous cystadenocarcinoma(155;0.0713)	L-Ornithine(DB00129)	AGTGGACAGACTAGGAATTGGC	0.356																																																	0																																										SO:0001589	frameshift_variant	383				CCDS5145.1, CCDS59038.1	6q23	2013-05-01	2013-05-01		ENSG00000118520	ENSG00000118520	3.5.3.1		663	protein-coding gene	gene with protein product		608313	"""arginase, liver"""			22959135	Standard	NM_000045		Approved		uc003qcp.2	P05089	OTTHUMG00000015566	ENST00000368087.3:c.617dupT	6.37:g.131904256_131904256dupT	ENSP00000357066:p.Leu206fs	Somatic		WXS	Illumina HiSeq	Phase_I	A6NEA0|Q5JWT5|Q5JWT6|Q8TE72|Q9BS50	Frame_Shift_Ins	INS	ENST00000368087.3	37	CCDS5145.1																																																																																				0.356	ARG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042223.1			
ATAD5	79915	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	29182285	29182285	+	Missense_Mutation	SNP	G	G	T			TCGA-CZ-5454-01A-01D-1501-10	TCGA-CZ-5454-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d9fd1928-7b7d-4147-aeff-1618393ba26c	46d95289-69d8-4437-b2f3-5a3e5ccf7ef6	g.chr17:29182285G>T	ENST00000321990.4	+	7	2953	c.2575G>T	c.(2575-2577)Gtg>Ttg	p.V859L	CTD-2349P21.11_ENST00000580873.1_RNA	NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	859					cellular response to DNA damage stimulus (GO:0006974)	nucleus (GO:0005634)	ATP binding (GO:0005524)	p.V859L(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(18)|lung(13)|ovary(3)|pancreas(1)	51		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				TGCGCTGGATGTGTACAATGC	0.393																																																	1	Substitution - Missense(1)	kidney(1)											89.0	77.0	81.0					17																	29182285		2203	4300	6503	SO:0001583	missense	79915				CCDS11260.1	17q11.2	2010-04-21	2007-02-08	2007-02-08	ENSG00000176208	ENSG00000176208		"""ATPases / AAA-type"""	25752	protein-coding gene	gene with protein product	"""enhanced level of genomic instability 1 homolog (S. cerevisiae)"""	609534	"""chromosome 17 open reading frame 41"""	C17orf41		15983387, 11468690, 19755857	Standard	NM_024857		Approved	FLJ12735, FRAG1, ELG1	uc002hfs.1	Q96QE3	OTTHUMG00000132794	ENST00000321990.4:c.2575G>T	17.37:g.29182285G>T	ENSP00000313171:p.Val859Leu	Somatic		WXS	Illumina HiSeq	Phase_I	Q05DH0|Q69YR6|Q9H9I1	Missense_Mutation	SNP	ENST00000321990.4	37	CCDS11260.1	.	.	.	.	.	.	.	.	.	.	G	8.462	0.855452	0.17106	.	.	ENSG00000176208	ENST00000321990	D	0.85484	-1.99	5.6	2.48	0.30137	.	0.497469	0.21785	N	0.069157	T	0.79587	0.4471	M	0.63428	1.95	0.23953	N	0.996368	B;B	0.22276	0.008;0.067	B;B	0.12837	0.007;0.008	T	0.65944	-0.6045	10	0.31617	T	0.26	.	7.7549	0.28919	0.1401:0.0:0.7264:0.1335	.	859;859	Q96QE3-2;Q96QE3	.;ATAD5_HUMAN	L	859	ENSP00000313171:V859L	ENSP00000313171:V859L	V	+	1	0	ATAD5	26206411	0.991000	0.36638	0.698000	0.30274	0.127000	0.20565	0.847000	0.27696	0.686000	0.31488	0.514000	0.50259	GTG		0.393	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2		NM_024857	
MEIOB	254528	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	1884331	1884331	+	Missense_Mutation	SNP	T	T	A			TCGA-CZ-5454-01A-01D-1501-10	TCGA-CZ-5454-11A-01D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d9fd1928-7b7d-4147-aeff-1618393ba26c	46d95289-69d8-4437-b2f3-5a3e5ccf7ef6	g.chr16:1884331T>A	ENST00000397344.3	-	13	1449	c.1255A>T	c.(1255-1257)Att>Ttt	p.I419F	FAHD1_ENST00000382668.4_Intron|MEIOB_ENST00000412554.2_Missense_Mutation_p.I448F|MEIOB_ENST00000452149.2_Missense_Mutation_p.I419F|MEIOB_ENST00000325962.3_Missense_Mutation_p.I448F|FAHD1_ENST00000382666.4_Intron|MEIOB_ENST00000470044.1_Missense_Mutation_p.I241F	NM_152764.2	NP_689977.2	Q8N635	MEIOB_HUMAN	meiosis specific with OB domains	419					double-strand break repair via homologous recombination (GO:0000724)|female meiosis I (GO:0007144)|fertilization (GO:0009566)|male meiosis (GO:0007140)|male meiosis I (GO:0007141)|resolution of meiotic recombination intermediates (GO:0000712)|synapsis (GO:0007129)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|single-stranded DNA 3'-5' exodeoxyribonuclease activity (GO:0008310)|single-stranded DNA binding (GO:0003697)	p.I175F(1)|p.I448F(1)									AGTACACTAATTTTCAATCCA	0.383																																																	2	Substitution - Missense(2)	kidney(2)											97.0	92.0	94.0					16																	1884331		2199	4300	6499	SO:0001583	missense	0			BC029829	CCDS10449.2, CCDS53983.1	16p13.3	2012-08-13	2012-08-13	2012-08-13	ENSG00000162039	ENSG00000162039			28569	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 73"""	C16orf73		12477932	Standard	NM_152764		Approved	MGC35212	uc010uvq.1	Q8N635	OTTHUMG00000128683	ENST00000397344.3:c.1255A>T	16.37:g.1884331T>A	ENSP00000380504:p.Ile419Phe	Somatic		WXS	Illumina HiSeq	Phase_I	B1AK39|C9J0S1|Q96RY0	Missense_Mutation	SNP	ENST00000397344.3	37	CCDS10449.2	.	.	.	.	.	.	.	.	.	.	T	10.61	1.398215	0.25205	.	.	ENSG00000162039	ENST00000412554;ENST00000452149;ENST00000325962;ENST00000397344	T;T;T;T	0.09723	2.95;2.95;2.95;2.95	5.81	0.11	0.14611	.	0.748493	0.13056	N	0.417292	T	0.13030	0.0316	L	0.50333	1.59	0.09310	N	0.999999	B;P	0.37636	0.036;0.603	B;B	0.42422	0.019;0.387	T	0.19289	-1.0310	10	0.34782	T	0.22	.	10.3861	0.44140	0.0:0.5241:0.0:0.4759	.	448;419	C9J0S1;Q8N635	.;CP073_HUMAN	F	448;419;448;419	ENSP00000390778:I448F;ENSP00000391033:I419F;ENSP00000314484:I448F;ENSP00000380504:I419F	ENSP00000314484:I448F	I	-	1	0	C16orf73	1824332	0.002000	0.14202	0.037000	0.18230	0.414000	0.31173	-0.296000	0.08287	-0.237000	0.09739	0.528000	0.53228	ATT		0.383	MEIOB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250580.1		NM_152764	
CDK12	51755	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	37682372	37682372	+	Frame_Shift_Del	DEL	T	T	-			TCGA-CZ-5454-01A-01D-1501-10	TCGA-CZ-5454-11A-01D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d9fd1928-7b7d-4147-aeff-1618393ba26c	46d95289-69d8-4437-b2f3-5a3e5ccf7ef6	g.chr17:37682372delT	ENST00000447079.4	+	13	3596	c.3563delT	c.(3562-3564)atcfs	p.I1188fs	CDK12_ENST00000430627.2_Frame_Shift_Del_p.I1188fs	NM_015083.1|NM_016507.2	NP_055898.1|NP_057591.2	Q9NYV4	CDK12_HUMAN	cyclin-dependent kinase 12	1188					mRNA processing (GO:0006397)|phosphorylation of RNA polymerase II C-terminal domain (GO:0070816)|protein autophosphorylation (GO:0046777)|regulation of MAP kinase activity (GO:0043405)|RNA splicing (GO:0008380)	cyclin K-CDK12 complex (GO:0002944)|nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			NS(4)|breast(3)|endometrium(5)|kidney(4)|large_intestine(11)|lung(23)|ovary(11)|prostate(4)|skin(2)|urinary_tract(3)	70						GCCCCAGTGATCCTGCCTTCA	0.527			"""Mis, N, F"""		serous ovarian					TCGA Ovarian(9;0.13)																														Rec	yes		17	17q12	51755	cyclin-dependent kinase 12		E	0													67.0	64.0	65.0					17																	37682372		2203	4300	6503	SO:0001589	frameshift_variant	51755			AF227198	CCDS11337.1, CCDS45666.1	17q12	2011-10-25	2009-12-16	2009-12-16	ENSG00000167258	ENSG00000167258		"""Cyclin-dependent kinases"""	24224	protein-coding gene	gene with protein product	"""CDC2 related protein kinase 7"""	615514	"""Cdc2-related kinase, arginine/serine-rich"""	CRKRS		10048485, 11683387, 19884882	Standard	XM_005257456		Approved	CRK7, CRKR, KIAA0904	uc010cvv.3	Q9NYV4	OTTHUMG00000133214	ENST00000447079.4:c.3563delT	17.37:g.37682372delT	ENSP00000398880:p.Ile1188fs	Somatic		WXS	Illumina HiSeq	Phase_I	A7E2B2|B4DYX4|B9EIQ6|O94978	Frame_Shift_Del	DEL	ENST00000447079.4	37	CCDS11337.1																																																																																				0.527	CDK12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256941.4		NM_016507	
DDX42	11325	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	61890626	61890626	+	Missense_Mutation	SNP	A	A	T			TCGA-CZ-5454-01A-01D-1501-10	TCGA-CZ-5454-11A-01D-1501-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d9fd1928-7b7d-4147-aeff-1618393ba26c	46d95289-69d8-4437-b2f3-5a3e5ccf7ef6	g.chr17:61890626A>T	ENST00000578681.1	+	16	2315	c.1714A>T	c.(1714-1716)Aac>Tac	p.N572Y	DDX42_ENST00000583590.1_Missense_Mutation_p.N572Y|DDX42_ENST00000389924.2_Missense_Mutation_p.N572Y|DDX42_ENST00000359353.5_Missense_Mutation_p.N453Y|DDX42_ENST00000457800.2_Missense_Mutation_p.N572Y	NM_007372.2	NP_031398.2	Q86XP3	DDX42_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 42	572	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				protein localization (GO:0008104)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)	p.N572Y(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(3)	46						GACTGTCATTAACTATGATGT	0.443																																																	1	Substitution - Missense(1)	kidney(1)											90.0	80.0	83.0					17																	61890626		2203	4300	6503	SO:0001583	missense	11325			BC015505	CCDS32704.1	17q23	2014-02-14	2013-05-13			ENSG00000198231		"""DEAD-boxes"""	18676	protein-coding gene	gene with protein product	"""splicing factor 3b, subunit 8"""	613369	"""DEAD (Asp-Glu-Ala-Asp) box polypeptide 42"""			10727850, 16397294	Standard	NM_007372		Approved	RNAHP, RHELP, SF3b125, SF3B8	uc002jbv.3	Q86XP3		ENST00000578681.1:c.1714A>T	17.37:g.61890626A>T	ENSP00000464050:p.Asn572Tyr	Somatic		WXS	Illumina HiSeq	Phase_I	A6NML1|A8KA43|O75619|Q68G51|Q96BK1|Q96HR7|Q9Y3V8	Missense_Mutation	SNP	ENST00000578681.1	37	CCDS32704.1	.	.	.	.	.	.	.	.	.	.	A	27.5	4.832914	0.91036	.	.	ENSG00000198231	ENST00000389924;ENST00000457800;ENST00000359353	T;T	0.05649	3.41;3.41	5.52	5.52	0.82312	Helicase, C-terminal (3);	0.039730	0.85682	D	0.000000	T	0.41396	0.1157	H	0.97829	4.085	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.62923	-0.6751	10	0.87932	D	0	-21.2105	15.1322	0.72533	1.0:0.0:0.0:0.0	.	118;572	B3KV84;Q86XP3	.;DDX42_HUMAN	Y	572;572;308	ENSP00000374574:N572Y;ENSP00000390121:N572Y	ENSP00000352308:N308Y	N	+	1	0	DDX42	59244358	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.253000	0.95501	2.230000	0.72887	0.528000	0.53228	AAC		0.443	DDX42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444368.1		NM_007372	
GALNT7	51809	broad.mit.edu;ucsc.edu	37	4	174216550	174216550	+	Missense_Mutation	SNP	A	A	G			TCGA-CZ-5454-01A-01D-1501-10	TCGA-CZ-5454-11A-01D-1501-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d9fd1928-7b7d-4147-aeff-1618393ba26c	46d95289-69d8-4437-b2f3-5a3e5ccf7ef6	g.chr4:174216550A>G	ENST00000265000.4	+	4	841	c.758A>G	c.(757-759)cAc>cGc	p.H253R	GALNT7_ENST00000502407.1_3'UTR|GALNT7_ENST00000512285.1_Missense_Mutation_p.H253R	NM_017423.2	NP_059119.2	Q86SF2	GALT7_HUMAN	polypeptide N-acetylgalactosaminyltransferase 7	253	Catalytic subdomain A.				carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.H253R(1)		central_nervous_system(1)|kidney(3)|large_intestine(5)|liver(1)|lung(9)	19		Prostate(90;0.0132)|Renal(120;0.0183)|Melanoma(52;0.0749)|all_hematologic(60;0.107)|all_neural(102;0.122)		all cancers(43;1.87e-18)|Epithelial(43;3.44e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-09)|STAD - Stomach adenocarcinoma(60;0.0019)|GBM - Glioblastoma multiforme(59;0.0119)|LUSC - Lung squamous cell carcinoma(193;0.0199)		TTAACAGAACACTTAAAAGAA	0.313																																																	1	Substitution - Missense(1)	kidney(1)											65.0	73.0	70.0					4																	174216550		2200	4298	6498	SO:0001583	missense	51809			AJ002744	CCDS3815.1	4q31.1	2014-03-13	2014-03-13		ENSG00000109586	ENSG00000109586		"""Glycosyltransferase family 2 domain containing"""	4129	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 7"""	605005	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 7 (GalNAc-T7)"""			10544240	Standard	NM_017423		Approved	GALNAC-T7	uc003isz.4	Q86SF2	OTTHUMG00000160817	ENST00000265000.4:c.758A>G	4.37:g.174216550A>G	ENSP00000265000:p.His253Arg	Somatic		WXS	Illumina GAIIx	Phase_I	B3KQU3|Q7Z5W7|Q9UJ28	Missense_Mutation	SNP	ENST00000265000.4	37	CCDS3815.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	19.75|19.75	3.885746|3.885746	0.72410|0.72410	.|.	.|.	ENSG00000109586|ENSG00000109586	ENST00000265000;ENST00000512285;ENST00000458613|ENST00000505308	T;T|.	0.58940|.	0.3;0.3|.	5.76|5.76	5.76|5.76	0.90799|0.90799	Glycosyl transferase, family 2 (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.78534|0.78534	0.4298|0.4298	M|M	0.83118|0.83118	2.625|2.625	0.80722|0.80722	D|D	1|1	D;D|.	0.76494|.	0.998;0.999|.	D;D|.	0.72625|.	0.978;0.959|.	T|T	0.80390|0.80390	-0.1402|-0.1402	10|5	0.87932|.	D|.	0|.	.|.	16.0676|16.0676	0.80897|0.80897	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	30;253|.	B4DIB4;Q86SF2|.	.;GALT7_HUMAN|.	R|A	253;253;30|50	ENSP00000265000:H253R;ENSP00000427050:H253R|.	ENSP00000265000:H253R|.	H|T	+|+	2|1	0|0	GALNT7|GALNT7	174453125|174453125	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.708000|0.708000	0.40852|0.40852	8.395000|8.395000	0.90188|0.90188	2.201000|2.201000	0.70794|0.70794	0.533000|0.533000	0.62120|0.62120	CAC|ACT		0.313	GALNT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362456.2		NM_017423	
GGT7	2686	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	33437795	33437795	+	Silent	SNP	C	C	T	rs375464567		TCGA-CZ-5454-01A-01D-1501-10	TCGA-CZ-5454-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d9fd1928-7b7d-4147-aeff-1618393ba26c	46d95289-69d8-4437-b2f3-5a3e5ccf7ef6	g.chr20:33437795C>T	ENST00000336431.5	-	14	1838	c.1794G>A	c.(1792-1794)ccG>ccA	p.P598P	GGT7_ENST00000469018.1_5'UTR	NM_178026.2	NP_821158.2	Q9UJ14	GGT7_HUMAN	gamma-glutamyltransferase 7	598					glutathione biosynthetic process (GO:0006750)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)	anchored component of external side of plasma membrane (GO:0031362)|integral component of membrane (GO:0016021)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)	p.P598P(2)		NS(2)|breast(1)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|skin(2)	20						ACTGCAGGTCCGGGTGTAGGC	0.607																																																	2	Substitution - coding silent(2)	large_intestine(1)|kidney(1)						C		0,3860		0,0,1930	31.0	35.0	33.0		1794	-9.4	0.9	20		33	1,8261		0,1,4130	no	coding-synonymous	GGT7	NM_178026.2		0,1,6060	TT,TC,CC		0.0121,0.0,0.0082		598/663	33437795	1,12121	1930	4131	6061	SO:0001819	synonymous_variant	2686			AL049709	CCDS13242.2	20q11.22	2008-11-24	2008-03-10	2008-03-10	ENSG00000131067	ENSG00000131067		"""Gamma-glutamyltransferases"""	4259	protein-coding gene	gene with protein product		612342	"""gamma-glutamyltransferase-like 3"""	GGTL5, GGTL3		8104871, 18357469	Standard	NM_178026		Approved	D20S101, dJ18C9.2	uc002xay.3	Q9UJ14	OTTHUMG00000032314	ENST00000336431.5:c.1794G>A	20.37:g.33437795C>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q8N899|Q8NF66|Q9BYP5|Q9BYP6	Silent	SNP	ENST00000336431.5	37	CCDS13242.2																																																																																				0.607	GGT7-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078816.2		NM_178026	
GPNMB	10457	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	23309735	23309735	+	Missense_Mutation	SNP	C	C	T			TCGA-CZ-5454-01A-01D-1501-10	TCGA-CZ-5454-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d9fd1928-7b7d-4147-aeff-1618393ba26c	46d95289-69d8-4437-b2f3-5a3e5ccf7ef6	g.chr7:23309735C>T	ENST00000381990.2	+	9	1567	c.1406C>T	c.(1405-1407)aCc>aTc	p.T469I	GPNMB_ENST00000539136.1_Missense_Mutation_p.T358I|GPNMB_ENST00000258733.4_Missense_Mutation_p.T457I|GPNMB_ENST00000453162.2_Missense_Mutation_p.T411I	NM_001005340.1|NM_002510.2	NP_001005340.1|NP_002501.1	Q14956	GPNMB_HUMAN	glycoprotein (transmembrane) nmb	469					bone mineralization (GO:0030282)|cell adhesion (GO:0007155)|negative regulation of cell proliferation (GO:0008285)|osteoblast differentiation (GO:0001649)	cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)	p.T469I(1)		breast(5)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(2)|lung(17)|ovary(3)|stomach(2)	41			GBM - Glioblastoma multiforme(13;0.154)			GTGAACCTCACCCTGGGGGAT	0.512																																																	1	Substitution - Missense(1)	kidney(1)											168.0	129.0	143.0					7																	23309735		2203	4300	6503	SO:0001583	missense	10457			X76534	CCDS5380.1, CCDS34610.1	7p	2008-07-18			ENSG00000136235	ENSG00000136235			4462	protein-coding gene	gene with protein product	"""transmembrane glycoprotein"", ""glycoprotein NMB"", ""glycoprotein nmb-like protein"", ""osteoactivin"""	604368				7814155	Standard	NM_002510		Approved	NMB, HGFIN	uc003swc.3	Q14956	OTTHUMG00000022811	ENST00000381990.2:c.1406C>T	7.37:g.23309735C>T	ENSP00000371420:p.Thr469Ile	Somatic		WXS	Illumina HiSeq	Phase_I	A4D155|Q6UVX1|Q8N1A1	Missense_Mutation	SNP	ENST00000381990.2	37	CCDS34610.1	.	.	.	.	.	.	.	.	.	.	C	16.96	3.265156	0.59431	.	.	ENSG00000136235	ENST00000258733;ENST00000435486;ENST00000381990;ENST00000425903;ENST00000539136;ENST00000453162	T;T;T;T	0.18338	2.24;2.23;2.24;2.22	6.03	5.15	0.70609	.	0.000000	0.85682	D	0.000000	T	0.47600	0.1454	M	0.82923	2.615	0.58432	D	0.999998	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.996	T	0.55976	-0.8055	10	0.72032	D	0.01	-21.0222	17.4798	0.87670	0.0:0.876:0.124:0.0	.	358;411;469;457	F6SKP1;F5GY20;Q14956;Q14956-2	.;.;GPNMB_HUMAN;.	I	457;504;469;352;358;411	ENSP00000258733:T457I;ENSP00000371420:T469I;ENSP00000445266:T358I;ENSP00000405586:T411I	ENSP00000258733:T457I	T	+	2	0	GPNMB	23276260	1.000000	0.71417	0.988000	0.46212	0.119000	0.20118	6.260000	0.72502	1.553000	0.49476	0.557000	0.71058	ACC		0.512	GPNMB-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327152.1		NM_001005340	
GTDC1	79712	hgsc.bcm.edu;ucsc.edu	37	2	144899563	144899564	+	Frame_Shift_Del	DEL	GA	GA	-	rs114650281	byFrequency	TCGA-CZ-5454-01A-01D-1501-10	TCGA-CZ-5454-11A-01D-1501-10	GA	GA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d9fd1928-7b7d-4147-aeff-1618393ba26c	46d95289-69d8-4437-b2f3-5a3e5ccf7ef6	g.chr2:144899563_144899564delGA	ENST00000392869.2	-	5	558_559	c.406_407delTC	c.(406-408)tccfs	p.S136fs	GTDC1_ENST00000463875.2_Frame_Shift_Del_p.S7fs|GTDC1_ENST00000542155.1_Frame_Shift_Del_p.S136fs|GTDC1_ENST00000392867.3_Frame_Shift_Del_p.S136fs|GTDC1_ENST00000344850.4_Frame_Shift_Del_p.S136fs|GTDC1_ENST00000409298.1_Frame_Shift_Del_p.S136fs|GTDC1_ENST00000241391.5_Frame_Shift_Del_p.S136fs|GTDC1_ENST00000409214.1_Frame_Shift_Del_p.S136fs	NM_001284234.1	NP_001271163.1	Q4AE62	GTDC1_HUMAN	glycosyltransferase-like domain containing 1	136					biosynthetic process (GO:0009058)		transferase activity, transferring glycosyl groups (GO:0016757)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|liver(1)|lung(17)|ovary(1)	25				BRCA - Breast invasive adenocarcinoma(221;0.0914)		TTTTCCCATGGAAGTGAGAAAT	0.406																																																	0																																										SO:0001589	frameshift_variant	79712			AY281366	CCDS2185.1, CCDS33300.1, CCDS63029.1, CCDS74582.1, CCDS74583.1	2q22.3	2013-02-22			ENSG00000121964	ENSG00000121964		"""Glycosyltransferase group 1 domain containing"""	20887	protein-coding gene	gene with protein product	"""mannosyltransferase-like"""	610165				15068588, 21821951	Standard	NM_024659		Approved	FLJ11753, Hmat-Xa	uc010fnn.3	Q4AE62	OTTHUMG00000131835	ENST00000392869.2:c.406_407delTC	2.37:g.144899563_144899564delGA	ENSP00000376608:p.Ser136fs	Somatic		WXS	Illumina HiSeq	Phase_I	A8K5P2|D3DP81|Q53SM7|Q53TC5|Q6P7E7|Q6PJB6|Q6WKW6|Q9HAE5	Frame_Shift_Del	DEL	ENST00000392869.2	37	CCDS33300.1																																																																																				0.406	GTDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254779.2		NM_024659	
HOXA1	3198	hgsc.bcm.edu	37	7	27135314	27135316	+	In_Frame_Del	DEL	CGA	CGA	-	rs368428758|rs10951154|rs544314279	byFrequency	TCGA-CZ-5454-01A-01D-1501-10	TCGA-CZ-5454-11A-01D-1501-10	CGA	CGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d9fd1928-7b7d-4147-aeff-1618393ba26c	46d95289-69d8-4437-b2f3-5a3e5ccf7ef6	g.chr7:27135314_27135316delCGA	ENST00000343060.4	-	1	277_279	c.216_218delTCG	c.(214-219)catcgc>cac	p.R73del	HOTAIRM1_ENST00000434063.3_RNA|HOTAIRM1_ENST00000429611.3_RNA|HOXA1_ENST00000355633.5_In_Frame_Del_p.R73del|HOTAIRM1_ENST00000425358.2_RNA|HOTAIRM1_ENST00000495032.1_RNA	NM_005522.4	NP_005513	P49639	HXA1_HUMAN	homeobox A1	73	Poly-His.		H -> R (frequent polymorphism in individuals of European or African origin; dbSNP:rs10951154). {ECO:0000269|PubMed:11091361, ECO:0000269|PubMed:14702039}.		abducens nerve formation (GO:0021599)|anatomical structure morphogenesis (GO:0009653)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|artery morphogenesis (GO:0048844)|central nervous system neuron differentiation (GO:0021953)|cochlea development (GO:0090102)|cochlea morphogenesis (GO:0090103)|cognition (GO:0050890)|embryonic neurocranium morphogenesis (GO:0048702)|facial nerve structural organization (GO:0021612)|facial nucleus development (GO:0021754)|inner ear development (GO:0048839)|motor neuron axon guidance (GO:0008045)|multicellular organismal development (GO:0007275)|neuromuscular process (GO:0050905)|optokinetic behavior (GO:0007634)|outer ear morphogenesis (GO:0042473)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of behavior (GO:0050795)|rhombomere 3 development (GO:0021569)|rhombomere 4 development (GO:0021570)|rhombomere 5 development (GO:0021571)|semicircular canal formation (GO:0060876)|sensory perception of sound (GO:0007605)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(2)|kidney(2)|large_intestine(4)|liver(1)|lung(14)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						Ctgggggtggcgatggtggtggt	0.65											OREG0003750	type=REGULATORY REGION|Gene=BC031342|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay		37	0.00738818	0.0	0.0144	5008	,	,		11776	0.001		0.0209	False		,,,				2504	0.0051																0																																										SO:0001651	inframe_deletion	3198				CCDS5401.1, CCDS5402.2	7p15.2	2011-06-20	2005-12-22		ENSG00000105991	ENSG00000105991		"""Homeoboxes / ANTP class : HOXL subclass"""	5099	protein-coding gene	gene with protein product		142955	"""homeo box A1"""	HOX1F, HOX1		1973146	Standard	NM_153620		Approved		uc003sye.3	P49639	OTTHUMG00000023207	ENST00000343060.4:c.216_218delTCG	7.37:g.27135314_27135316delCGA	ENSP00000343246:p.Arg73del	Somatic	792	WXS	Illumina HiSeq	Phase_I	A4D184|B2R8U7|O43363	In_Frame_Del	DEL	ENST00000343060.4	37	CCDS5401.1																																																																																				0.650	HOXA1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000358454.1			
LMLN	89782	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	197748373	197748373	+	Silent	SNP	C	C	A			TCGA-CZ-5454-01A-01D-1501-10	TCGA-CZ-5454-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d9fd1928-7b7d-4147-aeff-1618393ba26c	46d95289-69d8-4437-b2f3-5a3e5ccf7ef6	g.chr3:197748373C>A	ENST00000330198.4	+	13	1444	c.1422C>A	c.(1420-1422)tcC>tcA	p.S474S	LMLN_ENST00000420910.2_Silent_p.S511S|LMLN_ENST00000332636.5_Silent_p.S422S|LMLN_ENST00000482695.1_Silent_p.S459S	NM_033029.3	NP_149018.2	Q96KR4	LMLN_HUMAN	leishmanolysin-like (metallopeptidase M8 family)	474					cell adhesion (GO:0007155)|mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|lipid particle (GO:0005811)|membrane (GO:0016020)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)	p.S474S(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)	Lung NSC(153;0.132)	Epithelial(36;9.84e-24)|all cancers(36;3.18e-22)|OV - Ovarian serous cystadenocarcinoma(49;5.35e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.111)		ATGGTGGCTCCGTGGAAATTG	0.393																																																	1	Substitution - coding silent(1)	kidney(1)											169.0	168.0	168.0					3																	197748373		2203	4300	6503	SO:0001819	synonymous_variant	89782			AJ312398	CCDS3332.1, CCDS46988.1	3q29	2008-02-04			ENSG00000185621	ENSG00000185621	3.4.24.36		15991	protein-coding gene	gene with protein product		609380					Standard	NM_033029		Approved	Gp63, Msp	uc010iar.3	Q96KR4	OTTHUMG00000155375	ENST00000330198.4:c.1422C>A	3.37:g.197748373C>A		Somatic		WXS	Illumina HiSeq	Phase_I	B3LDG9|B3LDH0|C9J796|F8WB28|Q96KR5	Silent	SNP	ENST00000330198.4	37	CCDS3332.1																																																																																				0.393	LMLN-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339701.1		NM_033029	
LRP4	4038	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	46895081	46895081	+	Silent	SNP	G	G	A	rs17848229		TCGA-CZ-5454-01A-01D-1501-10	TCGA-CZ-5454-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d9fd1928-7b7d-4147-aeff-1618393ba26c	46d95289-69d8-4437-b2f3-5a3e5ccf7ef6	g.chr11:46895081G>A	ENST00000378623.1	-	29	4535	c.4293C>T	c.(4291-4293)gaC>gaT	p.D1431D	LRP4-AS1_ENST00000531719.1_RNA|LRP4-AS1_ENST00000502049.2_RNA	NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	1431					dendrite morphogenesis (GO:0048813)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|limb development (GO:0060173)|negative regulation of axonogenesis (GO:0050771)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ossification (GO:0030279)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of presynaptic membrane organization (GO:1901631)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|proximal/distal pattern formation (GO:0009954)|regulation of protein phosphorylation (GO:0001932)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|synapse organization (GO:0050808)|synaptic growth at neuromuscular junction (GO:0051124)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|synaptic membrane (GO:0097060)	calcium ion binding (GO:0005509)|receptor tyrosine kinase binding (GO:0030971)|scaffold protein binding (GO:0097110)	p.D1431D(1)		breast(7)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(24)|ovary(3)|pancreas(2)|prostate(5)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	70				Lung(87;0.159)		CTGCCAGCCCGTCAGTGGTCT	0.592																																																	1	Substitution - coding silent(1)	kidney(1)						G		0,4402		0,0,2201	86.0	76.0	79.0		4293	-5.5	0.7	11	dbSNP_123	79	2,8596	2.2+/-6.3	0,2,4297	no	coding-synonymous	LRP4	NM_002334.3		0,2,6498	AA,AG,GG		0.0233,0.0,0.0154		1431/1906	46895081	2,12998	2201	4299	6500	SO:0001819	synonymous_variant	4038			AB011540	CCDS31478.1	11p11.2	2013-05-29			ENSG00000134569	ENSG00000134569		"""Low density lipoprotein receptors"""	6696	protein-coding gene	gene with protein product		604270				9693030	Standard	NM_002334		Approved	MEGF7, CLSS, LRP-4, SOST2	uc001ndn.4	O75096	OTTHUMG00000166700	ENST00000378623.1:c.4293C>T	11.37:g.46895081G>A		Somatic		WXS	Illumina HiSeq	Phase_I	B2RN39|Q4AC85|Q5KTZ5	Silent	SNP	ENST00000378623.1	37	CCDS31478.1																																																																																				0.592	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391133.1		NM_002334	
LAMTOR1	55004	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	71816983	71816983	+	5'Flank	SNP	G	G	A			TCGA-CZ-5454-01A-01D-1501-10	TCGA-CZ-5454-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d9fd1928-7b7d-4147-aeff-1618393ba26c	46d95289-69d8-4437-b2f3-5a3e5ccf7ef6	g.chr11:71816983G>A	ENST00000278671.5	-	0	0				LRTOMT_ENST00000439209.1_Intron|LRTOMT_ENST00000307198.7_Splice_Site_p.A29T|LAMTOR1_ENST00000545249.1_5'Flank|LAMTOR1_ENST00000535107.1_5'Flank|LRTOMT_ENST00000419228.1_Intron|snoU13_ENST00000459046.1_RNA|LRTOMT_ENST00000435085.1_Splice_Site_p.A29T|LAMTOR1_ENST00000538404.1_5'Flank	NM_017907.2	NP_060377.1	Q6IAA8	LTOR1_HUMAN	late endosomal/lysosomal adaptor, MAPK and MTOR activator 1						cell growth (GO:0016049)|cellular protein localization (GO:0034613)|cellular response to amino acid stimulus (GO:0071230)|cholesterol homeostasis (GO:0042632)|endosome localization (GO:0032439)|endosome organization (GO:0007032)|lysosome localization (GO:0032418)|lysosome organization (GO:0007040)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of TOR signaling (GO:0032008)|regulation of cholesterol efflux (GO:0010874)|regulation of cholesterol esterification (GO:0010872)|regulation of cholesterol import (GO:0060620)|regulation of receptor recycling (GO:0001919)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|late endosome membrane (GO:0031902)|lysosome (GO:0005764)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|Ragulator complex (GO:0071986)		p.A29T(1)		cervix(1)	1						CCACCCCAGGGCCCAGGTAGG	0.527																																																	1	Substitution - Missense(1)	kidney(1)											54.0	54.0	54.0					11																	71816983		692	1591	2283	SO:0001631	upstream_gene_variant	220074			AK000632	CCDS8209.1	11q13.4	2011-05-18	2011-02-15	2011-02-15	ENSG00000149357	ENSG00000149357			26068	protein-coding gene	gene with protein product	"""p27kip1 releasing factor from RhoA"", ""protein associated with DRMs and endosomes"""	613510	"""chromosome 11 open reading frame 59"""	C11orf59		12358155	Standard	NM_017907		Approved	FLJ20625, p18, p27RF-Rho, Pdro, Ragulator1	uc001ort.3	Q6IAA8	OTTHUMG00000167869		11.37:g.71816983G>A	Exception_encountered	Somatic		WXS	Illumina HiSeq	Phase_I	Q8WZ09|Q9NWT0	Missense_Mutation	SNP	ENST00000278671.5	37	CCDS8209.1	.	.	.	.	.	.	.	.	.	.	G	0.619	-0.821783	0.02755	.	.	ENSG00000184154	ENST00000435085;ENST00000307198	D;D	0.88818	-2.43;-2.43	4.01	0.911	0.19343	.	.	.	.	.	T	0.70351	0.3214	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.56673	-0.7940	9	0.02654	T	1	.	5.2488	0.15512	0.3604:0.0:0.5035:0.1361	.	29	Q8WZ04	TOMT_HUMAN	T	29	ENSP00000409789:A29T;ENSP00000305742:A29T	ENSP00000409789:A29T	A	+	1	0	LRTOMT	71494631	0.014000	0.17966	0.035000	0.18076	0.233000	0.25261	-0.137000	0.10389	-0.137000	0.11455	-1.598000	0.00824	GCC		0.527	LAMTOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396733.1		NM_017907	
NLRP9	338321	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	56243947	56243947	+	Missense_Mutation	SNP	C	C	A	rs563256174		TCGA-CZ-5454-01A-01D-1501-10	TCGA-CZ-5454-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d9fd1928-7b7d-4147-aeff-1618393ba26c	46d95289-69d8-4437-b2f3-5a3e5ccf7ef6	g.chr19:56243947C>A	ENST00000332836.2	-	2	1277	c.1250G>T	c.(1249-1251)aGg>aTg	p.R417M		NM_176820.2	NP_789790.2	Q7RTR0	NALP9_HUMAN	NLR family, pyrin domain containing 9	417	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.					cytoplasm (GO:0005737)	ATP binding (GO:0005524)	p.R417M(1)		NS(2)|breast(5)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(15)|lung(21)|ovary(2)|prostate(3)|skin(7)|urinary_tract(3)	74		Colorectal(82;0.000133)|Ovarian(87;0.133)		GBM - Glioblastoma multiforme(193;0.123)		TAACCCATTCCTCCGGAGATC	0.498													C|||	1	0.000199681	0.0	0.0	5008	,	,		18586	0.0		0.0	False		,,,				2504	0.001																1	Substitution - Missense(1)	kidney(1)											85.0	87.0	86.0					19																	56243947		2203	4300	6503	SO:0001583	missense	338321			AY154464	CCDS12934.1	19q13.43	2006-12-08	2006-12-08	2006-12-08				"""Nucleotide-binding domain and leucine rich repeat containing"""	22941	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 9"""	609663	"""NACHT, leucine rich repeat and PYD containing 9"""	NALP9		12563287	Standard	NM_176820		Approved	NOD6, PAN12, CLR19.1	uc002qly.3	Q7RTR0		ENST00000332836.2:c.1250G>T	19.37:g.56243947C>A	ENSP00000331857:p.Arg417Met	Somatic		WXS	Illumina HiSeq	Phase_I	B2RN12|Q86W27	Missense_Mutation	SNP	ENST00000332836.2	37	CCDS12934.1	.	.	.	.	.	.	.	.	.	.	C	12.06	1.824699	0.32237	.	.	ENSG00000185792	ENST00000332836;ENST00000333452	D	0.84146	-1.81	2.56	1.52	0.23074	.	.	.	.	.	D	0.90000	0.6878	M	0.80982	2.52	0.09310	N	1	D	0.89917	1.0	D	0.70935	0.971	T	0.78460	-0.2195	9	0.87932	D	0	.	4.6757	0.12710	0.0:0.7013:0.0:0.2987	.	417	Q7RTR0	NALP9_HUMAN	M	417	ENSP00000331857:R417M	ENSP00000331857:R417M	R	-	2	0	NLRP9	60935759	0.001000	0.12720	0.002000	0.10522	0.027000	0.11550	0.624000	0.24462	0.678000	0.31325	0.644000	0.83932	AGG		0.498	NLRP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453653.1		NM_176820	
NR1I2	8856	broad.mit.edu;hgsc.bcm.edu	37	3	119528965	119528965	+	Silent	SNP	G	G	A			TCGA-CZ-5454-01A-01D-1501-10	TCGA-CZ-5454-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d9fd1928-7b7d-4147-aeff-1618393ba26c	46d95289-69d8-4437-b2f3-5a3e5ccf7ef6	g.chr3:119528965G>A	ENST00000337940.4	+	3	420	c.372G>A	c.(370-372)gaG>gaA	p.E124E	NR1I2_ENST00000393716.2_Silent_p.E85E|NR1I2_ENST00000466380.1_Silent_p.E85E	NM_022002.2	NP_071285.1	O75469	NR1I2_HUMAN	nuclear receptor subfamily 1, group I, member 2	85	Hinge.				drug export (GO:0046618)|exogenous drug catabolic process (GO:0042738)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|steroid metabolic process (GO:0008202)|transcription initiation from RNA polymerase II promoter (GO:0006367)|xenobiotic metabolic process (GO:0006805)|xenobiotic transport (GO:0042908)	nucleoplasm (GO:0005654)	drug binding (GO:0008144)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.E124E(1)		breast(2)|endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(2)|prostate(2)|skin(3)	23				GBM - Glioblastoma multiforme(114;0.175)	Docetaxel(DB01248)|Erlotinib(DB00530)|Estradiol(DB00783)|Ethinyl Estradiol(DB00977)|Paclitaxel(DB01229)|Rifampicin(DB01045)|Rifaximin(DB01220)|Rilpivirine(DB08864)|Vitamin E(DB00163)	GCGCCTGCGAGATCACCCGGA	0.692																																																	1	Substitution - coding silent(1)	kidney(1)											18.0	23.0	22.0					3																	119528965		2203	4300	6503	SO:0001819	synonymous_variant	8856			AF061056	CCDS2995.1, CCDS43136.1, CCDS54627.1	3q12-q13.3	2013-03-25			ENSG00000144852	ENSG00000144852		"""Nuclear hormone receptors"""	7968	protein-coding gene	gene with protein product	"""pregnane X receptor"", ""orphan nuclear receptor PXR"""	603065				9727070, 9770465	Standard	NM_003889		Approved	ONR1, PXR, BXR, SXR, PAR2	uc003edk.3	O75469	OTTHUMG00000159400	ENST00000337940.4:c.372G>A	3.37:g.119528965G>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q006P5|Q008C8|Q96AC7|Q9UJ22|Q9UJ23|Q9UJ24|Q9UJ25|Q9UJ26|Q9UJ27|Q9UNW4	Silent	SNP	ENST00000337940.4	37	CCDS2995.1																																																																																				0.692	NR1I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355126.1			
PAPOLA	10914	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	97009231	97009231	+	Splice_Site	SNP	G	G	A			TCGA-CZ-5454-01A-01D-1501-10	TCGA-CZ-5454-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d9fd1928-7b7d-4147-aeff-1618393ba26c	46d95289-69d8-4437-b2f3-5a3e5ccf7ef6	g.chr14:97009231G>A	ENST00000216277.8	+	14	1509		c.e14+1		PAPOLA_ENST00000392990.2_Splice_Site	NM_032632.4	NP_116021.2	P51003	PAPOA_HUMAN	poly(A) polymerase alpha						gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA splicing, via spliceosome (GO:0000398)|RNA polyadenylation (GO:0043631)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|polynucleotide adenylyltransferase activity (GO:0004652)|RNA binding (GO:0003723)	p.?(1)		breast(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(6)|skin(1)|urinary_tract(1)	21		all_cancers(154;0.0555)|all_epithelial(191;0.149)|Melanoma(154;0.155)		COAD - Colon adenocarcinoma(157;0.213)		ATCCCGACAAGTAAGCCCTTT	0.353																																					NSCLC(19;254 734 11908 35501 39234)												1	Unknown(1)	kidney(1)											91.0	98.0	95.0					14																	97009231		2203	4300	6503	SO:0001630	splice_region_variant	10914			X76770	CCDS9946.1, CCDS58334.1, CCDS58335.1	14q32.1-q32.2	2008-02-08				ENSG00000090060	2.7.7.19		14981	protein-coding gene	gene with protein product		605553				8302877, 10429366	Standard	NM_032632		Approved	PAP	uc001yfq.3	P51003		ENST00000216277.8:c.1289+1G>A	14.37:g.97009231G>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q86SX4|Q86TV0|Q8IYF5|Q9BVU2	Splice_Site	SNP	ENST00000216277.8	37	CCDS9946.1	.	.	.	.	.	.	.	.	.	.	G	19.27	3.795706	0.70452	.	.	ENSG00000090060	ENST00000216277;ENST00000546064;ENST00000392990;ENST00000555626	.	.	.	5.21	5.21	0.72293	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.7668	0.91876	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PAPOLA	96078984	1.000000	0.71417	1.000000	0.80357	0.803000	0.45373	9.869000	0.99810	2.442000	0.82660	0.591000	0.81541	.		0.353	PAPOLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413411.2			Intron
PBRM1	55193	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	52696199	52696199	+	Nonsense_Mutation	SNP	C	C	A			TCGA-CZ-5454-01A-01D-1501-10	TCGA-CZ-5454-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d9fd1928-7b7d-4147-aeff-1618393ba26c	46d95289-69d8-4437-b2f3-5a3e5ccf7ef6	g.chr3:52696199C>A	ENST00000296302.7	-	4	479	c.478G>T	c.(478-480)Gaa>Taa	p.E160*	PBRM1_ENST00000356770.4_Nonsense_Mutation_p.E160*|PBRM1_ENST00000337303.4_Nonsense_Mutation_p.E160*|PBRM1_ENST00000409057.1_Nonsense_Mutation_p.E160*|PBRM1_ENST00000409767.1_Nonsense_Mutation_p.E160*|PBRM1_ENST00000394830.3_Nonsense_Mutation_p.E160*|PBRM1_ENST00000410007.1_Nonsense_Mutation_p.E160*|PBRM1_ENST00000409114.3_Nonsense_Mutation_p.E160*			Q86U86	PB1_HUMAN	polybromo 1	160			E -> A (found in a malignant melanoma cell line). {ECO:0000269|PubMed:21248752}.		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.E160*(3)		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)		TCATCATCTTCGTCATCTGCT	0.453			"""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)											333.0	291.0	306.0					3																	52696199		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.478G>T	3.37:g.52696199C>A	ENSP00000296302:p.Glu160*	Somatic		WXS	Illumina HiSeq	Phase_I	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Nonsense_Mutation	SNP	ENST00000296302.7	37		.	.	.	.	.	.	.	.	.	.	C	25.5	4.643951	0.87859	.	.	ENSG00000163939	ENST00000356770;ENST00000394830;ENST00000296302;ENST00000337303;ENST00000409057;ENST00000410007;ENST00000409114;ENST00000409767;ENST00000423351;ENST00000446103;ENST00000431678	.	.	.	5.5	5.5	0.81552	.	0.298816	0.36066	N	0.002804	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06365	T	0.9	-2.7705	19.4035	0.94640	0.0:1.0:0.0:0.0	.	.	.	.	X	160;160;160;160;160;160;160;160;160;104;160	.	ENSP00000296302:E160X	E	-	1	0	PBRM1	52671239	1.000000	0.71417	0.993000	0.49108	0.967000	0.64934	7.277000	0.78572	2.590000	0.87494	0.650000	0.86243	GAA		0.453	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1		NM_018165	
PSMD3	5709	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	38153787	38153787	+	Missense_Mutation	SNP	G	G	C			TCGA-CZ-5454-01A-01D-1501-10	TCGA-CZ-5454-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d9fd1928-7b7d-4147-aeff-1618393ba26c	46d95289-69d8-4437-b2f3-5a3e5ccf7ef6	g.chr17:38153787G>C	ENST00000264639.4	+	12	1732	c.1558G>C	c.(1558-1560)Gag>Cag	p.E520Q	PSMD3_ENST00000541736.1_3'UTR	NM_002809.3	NP_002800.2	O43242	PSMD3_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 3	520					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of protein catabolic process (GO:0042176)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	enzyme regulator activity (GO:0030234)	p.E520Q(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	Colorectal(19;0.000442)					GCAGGACTTGGAGTTTGCCAA	0.607																																					Ovarian(186;531 2051 6385 19668 48409)												1	Substitution - Missense(1)	kidney(1)											88.0	85.0	86.0					17																	38153787		2203	4300	6503	SO:0001583	missense	5709			D67025	CCDS11356.1	17q21.2	2010-07-23			ENSG00000108344	ENSG00000108344		"""Proteasome (prosome, macropain) subunits"""	9560	protein-coding gene	gene with protein product			"""tissue specific transplantation antigen 2"""	TSTA2		9017604	Standard	NM_002809		Approved	S3, P58, Rpn3	uc002htn.2	O43242	OTTHUMG00000133251	ENST00000264639.4:c.1558G>C	17.37:g.38153787G>C	ENSP00000264639:p.Glu520Gln	Somatic		WXS	Illumina HiSeq	Phase_I	B3KMW9|B4DT72|Q96EI2|Q9BQA4	Missense_Mutation	SNP	ENST00000264639.4	37	CCDS11356.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.490339	0.84962	.	.	ENSG00000108344	ENST00000264639;ENST00000415039;ENST00000540504	.	.	.	5.14	4.17	0.49024	26S proteasome regulatory subunit, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.80319	0.4601	M	0.87180	2.865	0.80722	D	1	D	0.71674	0.998	D	0.70935	0.971	D	0.84247	0.0475	9	0.87932	D	0	-29.8112	13.6043	0.62037	0.0754:0.0:0.9246:0.0	.	520	O43242	PSMD3_HUMAN	Q	520;507;101	.	ENSP00000264639:E520Q	E	+	1	0	PSMD3	35407313	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.548000	0.98103	1.392000	0.46585	0.561000	0.74099	GAG		0.607	PSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257018.1		NM_002809	
RFC1	5981	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	39297338	39297338	+	Silent	SNP	C	C	T			TCGA-CZ-5454-01A-01D-1501-10	TCGA-CZ-5454-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d9fd1928-7b7d-4147-aeff-1618393ba26c	46d95289-69d8-4437-b2f3-5a3e5ccf7ef6	g.chr4:39297338C>T	ENST00000381897.1	-	22	2986	c.2853G>A	c.(2851-2853)ggG>ggA	p.G951G	RFC1_ENST00000349703.2_Silent_p.G950G|RNU6-32P_ENST00000383948.1_RNA	NM_001204747.1|NM_002913.4	NP_001191676.1|NP_002904.3	P35251	RFC1_HUMAN	replication factor C (activator 1) 1, 145kDa	951					DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA-dependent DNA replication (GO:0006261)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of catalytic activity (GO:0043085)|positive regulation of transcription, DNA-templated (GO:0045893)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|telomere maintenance via telomerase (GO:0007004)|transcription, DNA-templated (GO:0006351)|transcription-coupled nucleotide-excision repair (GO:0006283)	cell junction (GO:0030054)|DNA replication factor C complex (GO:0005663)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA clamp loader activity (GO:0003689)|double-stranded DNA binding (GO:0003690)|enzyme activator activity (GO:0008047)|sequence-specific DNA binding (GO:0043565)	p.G951G(1)		haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	16						GGGTCATGTACCCCCTCATCA	0.458																																					Colon(109;59 1555 12203 17579 39824)|Esophageal Squamous(18;360 542 16186 28570 51157)												1	Substitution - coding silent(1)	kidney(1)											100.0	88.0	92.0					4																	39297338		2203	4300	6503	SO:0001819	synonymous_variant	5981			L23320	CCDS3450.1, CCDS56329.1	4p14-p13	2010-04-21	2002-08-29		ENSG00000035928	ENSG00000035928		"""ATPases / AAA-type"""	9969	protein-coding gene	gene with protein product		102579	"""replication factor C (activator 1) 1 (145kD)"""			8114700	Standard	NM_002913		Approved	A1, PO-GA, RFC140, MHCBFB	uc003gty.2	P35251	OTTHUMG00000099363	ENST00000381897.1:c.2853G>A	4.37:g.39297338C>T		Somatic		WXS	Illumina HiSeq	Phase_I	A8K6E7|Q5XKF5|Q6PKU0|Q86V41|Q86V46	Silent	SNP	ENST00000381897.1	37	CCDS56329.1																																																																																				0.458	RFC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216808.1		NM_002913	
RIPK2	8767	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	90796294	90796294	+	Missense_Mutation	SNP	G	G	T			TCGA-CZ-5454-01A-01D-1501-10	TCGA-CZ-5454-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d9fd1928-7b7d-4147-aeff-1618393ba26c	46d95289-69d8-4437-b2f3-5a3e5ccf7ef6	g.chr8:90796294G>T	ENST00000220751.4	+	8	1270	c.956G>T	c.(955-957)aGt>aTt	p.S319I	RIPK2_ENST00000540020.1_Missense_Mutation_p.S182I	NM_003821.5	NP_003812.1	O43353	RIPK2_HUMAN	receptor-interacting serine-threonine kinase 2	319					activation of MAPK activity (GO:0000187)|adaptive immune response (GO:0002250)|apoptotic process (GO:0006915)|cellular response to lipoteichoic acid (GO:0071223)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to peptidoglycan (GO:0071224)|defense response to Gram-positive bacterium (GO:0050830)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing 1 signaling pathway (GO:0070427)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of apoptotic process (GO:0043065)|positive regulation of chemokine production (GO:0032722)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of immature T cell proliferation (GO:0033091)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of T-helper 1 cell differentiation (GO:0045627)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|response to exogenous dsRNA (GO:0043330)|response to interleukin-1 (GO:0070555)|response to interleukin-12 (GO:0070671)|response to interleukin-18 (GO:0070673)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|T cell proliferation (GO:0042098)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|protein complex (GO:0043234)|vesicle (GO:0031982)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|LIM domain binding (GO:0030274)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)	p.S319I(1)		kidney(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(2)	10			BRCA - Breast invasive adenocarcinoma(11;0.0474)			AGTGTTTCAAGTGCCATTCAC	0.279																																																	1	Substitution - Missense(1)	kidney(1)											60.0	64.0	63.0					8																	90796294		2203	4297	6500	SO:0001583	missense	8767			AC004003	CCDS6247.1	8q21	2008-05-02			ENSG00000104312	ENSG00000104312			10020	protein-coding gene	gene with protein product		603455				9575181, 9705938	Standard	XM_005251092		Approved	RICK, RIP2, CARDIAK, CARD3	uc003yee.3	O43353	OTTHUMG00000163809	ENST00000220751.4:c.956G>T	8.37:g.90796294G>T	ENSP00000220751:p.Ser319Ile	Somatic		WXS	Illumina HiSeq	Phase_I	B7Z748|Q6UWF0	Missense_Mutation	SNP	ENST00000220751.4	37	CCDS6247.1	.	.	.	.	.	.	.	.	.	.	G	7.128	0.579340	0.13686	.	.	ENSG00000104312	ENST00000220751;ENST00000540020	T;D	0.82255	-1.35;-1.59	5.59	4.49	0.54785	.	0.407803	0.21001	N	0.081878	T	0.70351	0.3214	N	0.24115	0.695	0.09310	N	0.999996	B	0.21147	0.052	B	0.20184	0.028	T	0.60576	-0.7236	10	0.66056	D	0.02	-3.8126	7.2095	0.25925	0.1437:0.0:0.8563:0.0	.	319	O43353	RIPK2_HUMAN	I	319;182	ENSP00000220751:S319I;ENSP00000441623:S182I	ENSP00000220751:S319I	S	+	2	0	RIPK2	90865435	0.137000	0.22531	0.131000	0.22000	0.043000	0.13939	1.583000	0.36579	2.763000	0.94921	0.655000	0.94253	AGT		0.279	RIPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375686.1			
RNF43	54894	broad.mit.edu;ucsc.edu	37	17	56440700	56440700	+	Missense_Mutation	SNP	A	A	G	rs145164323		TCGA-CZ-5454-01A-01D-1501-10	TCGA-CZ-5454-11A-01D-1501-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d9fd1928-7b7d-4147-aeff-1618393ba26c	46d95289-69d8-4437-b2f3-5a3e5ccf7ef6	g.chr17:56440700A>G	ENST00000584437.1	-	4	2473	c.518T>C	c.(517-519)aTg>aCg	p.M173T	RNF43_ENST00000407977.2_Missense_Mutation_p.M173T|BZRAP1-AS1_ENST00000583841.1_RNA|RNF43_ENST00000577716.1_Missense_Mutation_p.M173T|RNF43_ENST00000581868.1_Missense_Mutation_p.M46T|RNF43_ENST00000577625.1_Missense_Mutation_p.M46T|RNF43_ENST00000500597.2_Missense_Mutation_p.M132T|RNF43_ENST00000583753.1_Missense_Mutation_p.M132T			Q68DV7	RNF43_HUMAN	ring finger protein 43	173					negative regulation of Wnt signaling pathway (GO:0030178)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|stem cell proliferation (GO:0072089)|Wnt receptor catabolic process (GO:0038018)|Wnt signaling pathway (GO:0016055)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	frizzled binding (GO:0005109)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.M173T(1)		NS(1)|biliary_tract(5)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(14)|lung(9)|ovary(2)|pancreas(10)|prostate(1)|skin(4)	60	Medulloblastoma(34;0.127)|all_neural(34;0.237)					CACAAACTCCATCAGCTTCTC	0.587																																																	1	Substitution - Missense(1)	kidney(1)											135.0	132.0	133.0					17																	56440700		2203	4300	6503	SO:0001583	missense	54894				CCDS11607.1	17q23.2	2013-01-09						"""RING-type (C3HC4) zinc fingers"""	18505	protein-coding gene	gene with protein product		612482					Standard	NM_017763		Approved	FLJ20315, DKFZp781H0392, URCC	uc002iwh.4	Q68DV7		ENST00000584437.1:c.518T>C	17.37:g.56440700A>G	ENSP00000463069:p.Met173Thr	Somatic		WXS	Illumina GAIIx	Phase_I	A8K4R2|B7Z443|B7Z5D5|B7Z5J5|Q65ZA4|Q6AI04|Q9NXD0	Missense_Mutation	SNP	ENST00000584437.1	37	CCDS11607.1	.	.	.	.	.	.	.	.	.	.	A	24.3	4.511593	0.85389	.	.	ENSG00000108375	ENST00000407977;ENST00000500597	T;T	0.09630	3.07;2.96	5.68	5.68	0.88126	.	0.096495	0.85682	D	0.000000	T	0.22166	0.0534	L	0.34521	1.04	0.52501	D	0.999955	D;D;D	0.63880	0.991;0.993;0.985	D;D;P	0.66497	0.924;0.944;0.777	T	0.00679	-1.1613	10	0.56958	D	0.05	-2.9233	15.0991	0.72258	1.0:0.0:0.0:0.0	.	132;173;173	Q68DV7-2;Q68DV7-4;Q68DV7	.;.;RNF43_HUMAN	T	173;132	ENSP00000385328:M173T;ENSP00000441969:M132T	ENSP00000385328:M173T	M	-	2	0	RNF43	53795699	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	8.454000	0.90352	2.167000	0.68274	0.482000	0.46254	ATG		0.587	RNF43-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444713.1		NM_017763	
RPL3	6122	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	22	39713525	39713525	+	Silent	SNP	G	G	A			TCGA-CZ-5454-01A-01D-1501-10	TCGA-CZ-5454-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d9fd1928-7b7d-4147-aeff-1618393ba26c	46d95289-69d8-4437-b2f3-5a3e5ccf7ef6	g.chr22:39713525G>A	ENST00000216146.4	-	3	479	c.306C>T	c.(304-306)ttC>ttT	p.F102F	SNORD83A_ENST00000386747.1_RNA|RPL3_ENST00000401609.1_Silent_p.F50F|RPL3_ENST00000465618.1_5'UTR|SNORD43_ENST00000583861.1_RNA	NM_000967.3|NM_001033853.1	NP_000958.1|NP_001029025.1	P39023	RL3_HUMAN	ribosomal protein L3	102					cellular protein metabolic process (GO:0044267)|cellular response to interleukin-4 (GO:0071353)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)	p.F102F(1)		breast(1)|kidney(4)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	12	Melanoma(58;0.04)				Homoharringtonine(DB04865)	AGACAGTCTTGAAGGTCCGGA	0.542																																																	1	Substitution - coding silent(1)	kidney(1)											118.0	117.0	117.0					22																	39713525		2203	4300	6503	SO:0001819	synonymous_variant	6122			AB007166	CCDS13988.1	22q13	2011-04-06			ENSG00000100316	ENSG00000100316		"""L ribosomal proteins"""	10332	protein-coding gene	gene with protein product		604163				2891103, 9582194	Standard	NM_000967		Approved	L3	uc003axi.3	P39023	OTTHUMG00000151079	ENST00000216146.4:c.306C>T	22.37:g.39713525G>A		Somatic		WXS	Illumina HiSeq	Phase_I	B2RDV9|Q15548|Q5I0G0	Silent	SNP	ENST00000216146.4	37	CCDS13988.1	.	.	.	.	.	.	.	.	.	.	G	9.986	1.229614	0.22542	.	.	ENSG00000100316	ENST00000427905	.	.	.	5.2	0.233	0.15386	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.8943	0.18931	0.312:0.1225:0.5655:0.0	.	.	.	.	X	134	.	.	Q	-	1	0	RPL3	38043471	1.000000	0.71417	0.998000	0.56505	0.821000	0.46438	1.996000	0.40776	0.120000	0.18254	-0.291000	0.09656	CAA		0.542	RPL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321196.1		NM_000967	
SEC61B	10952	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	101984847	101984847	+	Missense_Mutation	SNP	G	G	C			TCGA-CZ-5454-01A-01D-1501-10	TCGA-CZ-5454-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d9fd1928-7b7d-4147-aeff-1618393ba26c	46d95289-69d8-4437-b2f3-5a3e5ccf7ef6	g.chr9:101984847G>C	ENST00000223641.4	+	2	86	c.23G>C	c.(22-24)gGc>gCc	p.G8A	ALG2_ENST00000319033.6_5'Flank|SEC61B_ENST00000498603.1_5'UTR|ALG2_ENST00000476832.1_5'Flank|SEC61B_ENST00000481573.1_3'UTR	NM_006808.2	NP_006799.1	P60468	SC61B_HUMAN	Sec61 beta subunit	8					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|gene expression (GO:0010467)|protein import into nucleus, translocation (GO:0000060)|retrograde protein transport, ER to cytosol (GO:0030970)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum Sec complex (GO:0031205)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	epidermal growth factor binding (GO:0048408)|poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)	p.G8A(1)		kidney(1)|large_intestine(1)	2		Acute lymphoblastic leukemia(62;0.0559)				ACCCCCAGTGGCACTAACGTG	0.672																																																	1	Substitution - Missense(1)	kidney(1)											21.0	21.0	21.0					9																	101984847		2181	4264	6445	SO:0001583	missense	10952			L25085	CCDS6741.1	9q22.32-q31.3	2009-03-19			ENSG00000106803	ENSG00000106803			16993	protein-coding gene	gene with protein product		609214				8107851, 10212142	Standard	NM_006808		Approved		uc004azh.3	P60468	OTTHUMG00000020354	ENST00000223641.4:c.23G>C	9.37:g.101984847G>C	ENSP00000223641:p.Gly8Ala	Somatic		WXS	Illumina HiSeq	Phase_I	P38390|P38391|Q6IBC1	Missense_Mutation	SNP	ENST00000223641.4	37	CCDS6741.1	.	.	.	.	.	.	.	.	.	.	G	9.808	1.182332	0.21870	.	.	ENSG00000106803	ENST00000223641	.	.	.	4.3	3.39	0.38822	.	0.122706	0.53938	N	0.000060	T	0.34890	0.0913	.	.	.	0.40603	D	0.981607	B	0.02656	0.0	B	0.01281	0.0	T	0.20140	-1.0284	8	0.05959	T	0.93	.	13.0847	0.59133	0.0:0.5149:0.4851:0.0	.	8	P60468	SC61B_HUMAN	A	8	.	ENSP00000223641:G8A	G	+	2	0	SEC61B	101024668	1.000000	0.71417	0.998000	0.56505	0.930000	0.56654	2.953000	0.49105	0.973000	0.38340	0.561000	0.74099	GGC		0.672	SEC61B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053391.1		NM_006808	
SLC2A4RG	56731	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	62373331	62373331	+	Silent	SNP	T	T	A			TCGA-CZ-5454-01A-01D-1501-10	TCGA-CZ-5454-11A-01D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d9fd1928-7b7d-4147-aeff-1618393ba26c	46d95289-69d8-4437-b2f3-5a3e5ccf7ef6	g.chr20:62373331T>A	ENST00000266077.2	+	4	553	c.501T>A	c.(499-501)tcT>tcA	p.S167S	SLC2A4RG_ENST00000493772.1_Intron|RP4-583P15.10_ENST00000447343.2_RNA	NM_020062.3	NP_064446.2	Q9NR83	S2A4R_HUMAN	SLC2A4 regulator	167					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S167S(1)		NS(1)|kidney(1)|lung(2)|prostate(2)|skin(1)	7	all_cancers(38;1.13e-12)|all_epithelial(29;2.64e-14)|Lung NSC(23;4.79e-10)|all_lung(23;1.7e-09)					ACCAGTCCTCTCCGTCCACCC	0.672																																																	1	Substitution - coding silent(1)	kidney(1)											29.0	34.0	33.0					20																	62373331		2197	4299	6496	SO:0001819	synonymous_variant	56731			AF249267	CCDS13537.1	20q13.33	2010-03-11			ENSG00000125520	ENSG00000125520			15930	protein-coding gene	gene with protein product	"""GLUT4 enhancer factor"", ""Huntington's disease gene regulatory region-binding protein 1"""	609493				10825161	Standard	NM_020062		Approved	GEF, HDBP1, Si-1-2, Si-1-2-19	uc002ygq.3	Q9NR83	OTTHUMG00000032997	ENST00000266077.2:c.501T>A	20.37:g.62373331T>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q2PHL5|Q6F6I6|Q6F6I7|Q6GTK5|Q8TAH5|Q8WVW7|Q96QD3|Q9BV85	Silent	SNP	ENST00000266077.2	37	CCDS13537.1																																																																																				0.672	SLC2A4RG-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080202.1		NM_020062	
STMN2	11075	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	80549106	80549106	+	Missense_Mutation	SNP	G	G	A	rs200432248		TCGA-CZ-5454-01A-01D-1501-10	TCGA-CZ-5454-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d9fd1928-7b7d-4147-aeff-1618393ba26c	46d95289-69d8-4437-b2f3-5a3e5ccf7ef6	g.chr8:80549106G>A	ENST00000220876.7	+	2	471	c.89G>A	c.(88-90)cGc>cAc	p.R30H	STMN2_ENST00000518491.1_Missense_Mutation_p.R19H|STMN2_ENST00000518111.1_Missense_Mutation_p.R30H	NM_001199214.1|NM_007029.3	NP_001186143.1|NP_008960.2	Q93045	STMN2_HUMAN	stathmin 2	30					cellular response to nerve growth factor stimulus (GO:1990090)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of microtubule polymerization (GO:0031115)|negative regulation of neuron projection development (GO:0010977)|positive regulation of microtubule depolymerization (GO:0031117)|positive regulation of neuron projection development (GO:0010976)	cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|vesicle (GO:0031982)	calcium-dependent protein binding (GO:0048306)	p.R30H(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	11	all_lung(9;8.34e-05)		Epithelial(68;0.0229)|all cancers(69;0.0874)			CCGGAACCTCGCAACATCAAC	0.393																																																	1	Substitution - Missense(1)	kidney(1)						G	HIS/ARG,HIS/ARG	2,3842		0,2,1920	115.0	104.0	108.0		89,89	5.5	1.0	8		108	0,8298		0,0,4149	yes	missense,missense	STMN2	NM_001199214.1,NM_007029.3	29,29	0,2,6069	AA,AG,GG		0.0,0.052,0.0165	benign,benign	30/188,30/180	80549106	2,12140	1922	4149	6071	SO:0001583	missense	11075				CCDS43748.1, CCDS56542.1	8q21.13	2014-04-01	2014-04-01	2001-07-13	ENSG00000104435	ENSG00000104435			10577	protein-coding gene	gene with protein product		600621	"""stathmin-like 2"""	SCGN10		8622778, 12140291	Standard	NM_007029		Approved	SCG10	uc022awk.1	Q93045	OTTHUMG00000164610	ENST00000220876.7:c.89G>A	8.37:g.80549106G>A	ENSP00000220876:p.Arg30His	Somatic		WXS	Illumina HiSeq	Phase_I	A8K9M2|G3V110|O14952|Q6PK68	Missense_Mutation	SNP	ENST00000220876.7	37	CCDS43748.1	.	.	.	.	.	.	.	.	.	.	G	12.35	1.912331	0.33721	5.2E-4	0.0	ENSG00000104435	ENST00000220876;ENST00000414622;ENST00000518111;ENST00000518491	.	.	.	5.52	5.52	0.82312	.	0.044063	0.85682	D	0.000000	T	0.51584	0.1683	L	0.34521	1.04	0.80722	D	1	B;B	0.19331	0.035;0.005	B;B	0.10450	0.005;0.002	T	0.48980	-0.8986	9	0.09843	T	0.71	-1.8166	19.4437	0.94838	0.0:0.0:1.0:0.0	.	30;30	B7Z4K3;Q93045	.;STMN2_HUMAN	H	30;30;30;19	.	ENSP00000220876:R30H	R	+	2	0	STMN2	80711661	1.000000	0.71417	1.000000	0.80357	0.750000	0.42670	5.666000	0.68059	2.600000	0.87896	0.561000	0.74099	CGC		0.393	STMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379261.2		NM_007029	
TRAF3IP2	10758	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	111913024	111913024	+	Missense_Mutation	SNP	T	T	A			TCGA-CZ-5454-01A-01D-1501-10	TCGA-CZ-5454-11A-01D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d9fd1928-7b7d-4147-aeff-1618393ba26c	46d95289-69d8-4437-b2f3-5a3e5ccf7ef6	g.chr6:111913024T>A	ENST00000340026.6	-	3	887	c.293A>T	c.(292-294)gAg>gTg	p.E98V	TRAF3IP2_ENST00000392556.4_5'UTR|TRAF3IP2_ENST00000359831.4_Missense_Mutation_p.E89V|TRAF3IP2_ENST00000368761.5_Missense_Mutation_p.E89V|TRAF3IP2-AS1_ENST00000532353.1_RNA			O43734	CIKS_HUMAN	TRAF3 interacting protein 2	98	Mediates interaction with TRAF6.				B cell apoptotic process (GO:0001783)|humoral immune response (GO:0006959)|immunoglobulin secretion (GO:0048305)|intracellular signal transduction (GO:0035556)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)			p.E98V(1)		central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)|urinary_tract(1)	18		all_cancers(87;7.87e-06)|Acute lymphoblastic leukemia(125;3.61e-09)|all_hematologic(75;2.63e-07)|all_epithelial(87;0.0024)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.033)|all cancers(137;0.0412)|Epithelial(106;0.0732)		TTCACTGTCCTCCAGAACTTG	0.567																																																	1	Substitution - Missense(1)	kidney(1)											64.0	66.0	65.0					6																	111913024		2203	4300	6503	SO:0001583	missense	10758			AF136405	CCDS5093.1, CCDS55049.1, CCDS55050.1	6q21	2008-09-05	2002-06-20	2005-04-13	ENSG00000056972	ENSG00000056972			1343	protein-coding gene	gene with protein product		607043	"""chromosome 6 open reading frame 5"", ""chromosome 6 open reading frame 2"""	C6orf4, C6orf5, C6orf6, C6orf2		10962033, 10962024	Standard	NR_028338		Approved	DKFZP586G0522, ACT1, CIKS	uc003pvf.4	O43734	OTTHUMG00000015379	ENST00000340026.6:c.293A>T	6.37:g.111913024T>A	ENSP00000345984:p.Glu98Val	Somatic		WXS	Illumina HiSeq	Phase_I	B2RAY9|E1P555|Q5R3A3|Q7Z6Q1|Q7Z6Q2|Q7Z6Q3|Q9H5W2|Q9H6Y3|Q9NS14|Q9UG72	Missense_Mutation	SNP	ENST00000340026.6	37		.	.	.	.	.	.	.	.	.	.	T	15.14	2.745022	0.49151	.	.	ENSG00000056972	ENST00000392555;ENST00000368761;ENST00000340026;ENST00000359831	T;T;T	0.51071	0.76;0.74;0.72	5.91	4.75	0.60458	.	0.077674	0.56097	D	0.000039	T	0.27798	0.0684	M	0.61703	1.905	0.80722	D	1	B;P;B	0.40431	0.441;0.717;0.162	B;B;B	0.37198	0.087;0.243;0.037	T	0.20140	-1.0284	10	0.66056	D	0.02	-2.0436	7.9929	0.30250	0.1225:0.0:0.2776:0.5999	.	98;89;89	O43734;O43734-2;Q7Z6Q1	CIKS_HUMAN;.;.	V	98;89;98;89	ENSP00000357750:E89V;ENSP00000345984:E98V;ENSP00000352889:E89V	ENSP00000345984:E98V	E	-	2	0	TRAF3IP2	112019717	0.998000	0.40836	1.000000	0.80357	0.948000	0.59901	0.734000	0.26101	1.044000	0.40200	0.454000	0.30748	GAG		0.567	TRAF3IP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000041841.2			
TTC37	9652	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	94876456	94876456	+	Silent	SNP	T	T	G			TCGA-CZ-5454-01A-01D-1501-10	TCGA-CZ-5454-11A-01D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d9fd1928-7b7d-4147-aeff-1618393ba26c	46d95289-69d8-4437-b2f3-5a3e5ccf7ef6	g.chr5:94876456T>G	ENST00000358746.2	-	8	779	c.481A>C	c.(481-483)Aga>Cga	p.R161R		NM_014639.3	NP_055454.1	Q6PGP7	TTC37_HUMAN	tetratricopeptide repeat domain 37	161						cytoplasm (GO:0005737)|nucleus (GO:0005634)|Ski complex (GO:0055087)|transcriptionally active chromatin (GO:0035327)		p.R161R(1)		breast(2)|endometrium(6)|kidney(3)|large_intestine(13)|liver(1)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	47						GTCAATTTTCTCCATAGTTGA	0.378																																																	1	Substitution - coding silent(1)	kidney(1)											171.0	165.0	167.0					5																	94876456		2203	4300	6503	SO:0001819	synonymous_variant	9652			AB002370	CCDS4072.1	5q15	2014-09-17	2008-06-11	2008-06-11	ENSG00000198677	ENSG00000198677		"""Tetratricopeptide (TTC) repeat domain containing"""	23639	protein-coding gene	gene with protein product		614589	"""KIAA0372"""	KIAA0372		9205841	Standard	NM_014639		Approved		uc003klb.3	Q6PGP7	OTTHUMG00000121165	ENST00000358746.2:c.481A>C	5.37:g.94876456T>G		Somatic		WXS	Illumina HiSeq	Phase_I	O15077|Q6PJI3	Silent	SNP	ENST00000358746.2	37	CCDS4072.1																																																																																				0.378	TTC37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241651.1		NM_014639	
YTHDF3	253943	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	64099319	64099319	+	Silent	SNP	G	G	A	rs61745071		TCGA-CZ-5454-01A-01D-1501-10	TCGA-CZ-5454-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d9fd1928-7b7d-4147-aeff-1618393ba26c	46d95289-69d8-4437-b2f3-5a3e5ccf7ef6	g.chr8:64099319G>A	ENST00000539294.1	+	4	1063	c.747G>A	c.(745-747)ccG>ccA	p.P249P	YTHDF3_ENST00000521674.1_3'UTR|YTHDF3_ENST00000517371.1_Intron|YTHDF3_ENST00000542911.2_Silent_p.P60P	NM_001277817.1|NM_001277818.1|NM_152758.4	NP_001264746.1|NP_001264747.1|NP_689971.4	Q7Z739	YTHD3_HUMAN	YTH domain family, member 3	250							N6-methyladenosine-containing RNA binding (GO:1990247)|poly(A) RNA binding (GO:0044822)					Breast(64;0.0716)	all_cancers(86;0.169)|Lung NSC(129;0.0324)|all_lung(136;0.0593)|all_epithelial(80;0.146)	BRCA - Breast invasive adenocarcinoma(89;0.161)			AACCTCAACCGAAACTTAAAC	0.488																																																	0								G		4,3906		0,4,1951	105.0	106.0	106.0		749	4.8	1.0	8	dbSNP_129	106	0,8300		0,0,4150	no	coding-synonymous	YTHDF3	NM_152758.4		0,4,6101	AA,AG,GG		0.0,0.1023,0.0328		250/586	64099319	4,12206	1955	4150	6105	SO:0001819	synonymous_variant	253943			BC052970	CCDS75747.1, CCDS75748.1, CCDS75749.1	8q12.3	2013-06-07	2004-11-16		ENSG00000185728	ENSG00000185728			26465	protein-coding gene	gene with protein product			"""YTH domain family 3"""			12477932	Standard	NM_152758		Approved	FLJ31657	uc003xuz.4	Q7Z739	OTTHUMG00000164369	ENST00000539294.1:c.747G>A	8.37:g.64099319G>A		Somatic		WXS	Illumina HiSeq	Phase_I	B3KXL4|Q63Z37|Q659A3	Missense_Mutation	SNP	ENST00000539294.1	37																																																																																					0.488	YTHDF3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding			NM_152758	
FAM92A1P2	403315	broad.mit.edu	37	4	183959522	183959522	+	RNA	DEL	A	A	-	rs3039659|rs574821751	byFrequency	TCGA-CZ-5454-01A-01D-1501-10	TCGA-CZ-5454-11A-01D-1501-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d9fd1928-7b7d-4147-aeff-1618393ba26c	46d95289-69d8-4437-b2f3-5a3e5ccf7ef6	g.chr4:183959522delA	ENST00000502308.1	+	0	705					NR_003612.1				family with sequence similarity 92, member A1 pseudogene 2																		ctaaaaatacaaaaaaaaaaa	0.478																																																	0																																												0			BC022019		4q35.1	2012-04-19	2012-04-19	2012-04-19	ENSG00000230219	ENSG00000230219			32287	pseudogene	pseudogene			"""family with sequence similarity 92, member A3"""	FAM92A3		12477932	Standard	NR_003612		Approved	MGC71735, MGC102964	uc003ivi.4		OTTHUMG00000160675		4.37:g.183959522delA		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	DEL	ENST00000502308.1	37																																																																																					0.478	FAM92A1P2-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000361814.1			
CHEK2P2	646096	broad.mit.edu	37	15	20488228	20488229	+	RNA	INS	-	-	TGAA	rs374719316		TCGA-CZ-5454-01A-01D-1501-10	TCGA-CZ-5454-11A-01D-1501-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d9fd1928-7b7d-4147-aeff-1618393ba26c	46d95289-69d8-4437-b2f3-5a3e5ccf7ef6	g.chr15:20488228_20488229insTGAA	ENST00000555186.1	+	0	231					NR_038836.1				checkpoint kinase 2 pseudogene 2																		ggCAGAATAGGtgaatgaatga	0.49																																																	0																																												0					15q11.1	2011-11-11			ENSG00000259156	ENSG00000259156			43578	pseudogene	pseudogene							Standard	NR_038836		Approved		uc001ytf.1		OTTHUMG00000171660		15.37:g.20488233_20488236dupTGAA		Somatic		WXS	Illumina GAIIx	Phase_I		Splice_Site	INS	ENST00000555186.1	37																																																																																					0.490	CHEK2P2-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000414654.1		NR_038836	
MIR4477B	100616194	broad.mit.edu	37	9	68414581	68414581	+	RNA	SNP	T	T	A	rs375185736		TCGA-CZ-5454-01A-01D-1501-10	TCGA-CZ-5454-11A-01D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d9fd1928-7b7d-4147-aeff-1618393ba26c	46d95289-69d8-4437-b2f3-5a3e5ccf7ef6	g.chr9:68414581T>A	ENST00000581659.1	+	0	0					NR_039688.1|NR_039689.1				microRNA 4477b																		tactgaatattttaatcccac	0.353																																																	0																																												0					9	2011-09-12						"""ncRNAs / Micro RNAs"""	41898	non-coding RNA	RNA, micro							Standard	NR_039689		Approved	hsa-mir-4477b					9.37:g.68414581T>A		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP	ENST00000581659.1	37																																																																																					0.353	MIR4477B-201	KNOWN	basic	miRNA	miRNA			NR_039689	
