#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
ADAD2	161931	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	84229248	84229248	+	Missense_Mutation	SNP	G	G	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr16:84229248G>T	ENST00000315906.5	+	6	1049	c.997G>T	c.(997-999)Gtc>Ttc	p.V333F	RP11-486L19.2_ENST00000536986.1_RNA|ADAD2_ENST00000268624.3_Missense_Mutation_p.V415F|RP11-486L19.2_ENST00000569834.1_RNA|RP11-486L19.2_ENST00000561900.1_RNA|RP11-486L19.2_ENST00000565643.1_RNA	NM_001145400.1	NP_001138872.1	Q8NCV1	ADAD2_HUMAN	adenosine deaminase domain containing 2	333	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.				RNA processing (GO:0006396)		adenosine deaminase activity (GO:0004000)|RNA binding (GO:0003723)	p.V415F(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|skin(1)	13						CAAGCCCCGCGTCTTCCTGCA	0.711																																																	1	Substitution - Missense(1)	kidney(1)											23.0	30.0	27.0					16																	84229248		2199	4299	6498	SO:0001583	missense	161931			AF447586	CCDS10944.1, CCDS45536.1	16q24.1	2007-05-31			ENSG00000140955	ENSG00000140955			30714	protein-coding gene	gene with protein product							Standard	NM_139174		Approved	TENRL, FLJ00337	uc002fhr.2	Q8NCV1	OTTHUMG00000137637	ENST00000315906.5:c.997G>T	16.37:g.84229248G>T	ENSP00000325153:p.Val333Phe	Somatic		WXS	Illumina HiSeq	Phase_I	B2RCL6|Q8NA94	Missense_Mutation	SNP	ENST00000315906.5	37	CCDS45536.1	.	.	.	.	.	.	.	.	.	.	G	6.505	0.461447	0.12342	.	.	ENSG00000140955	ENST00000315906;ENST00000268624	D;D	0.94793	-3.52;-3.52	5.22	1.68	0.24146	Adenosine deaminase/editase (2);	0.269123	0.34110	N	0.004256	D	0.91040	0.7181	M	0.62723	1.935	0.28715	N	0.903335	B;B	0.27656	0.184;0.006	B;B	0.31442	0.13;0.023	D	0.84946	0.0868	10	0.87932	D	0	-29.2739	3.0906	0.06293	0.6164:0.0:0.2064:0.1772	.	333;415	Q8NCV1;Q8NCV1-2	ADAD2_HUMAN;.	F	333;415	ENSP00000325153:V333F;ENSP00000268624:V415F	ENSP00000268624:V415F	V	+	1	0	ADAD2	82786749	0.403000	0.25319	0.279000	0.24732	0.048000	0.14542	0.717000	0.25851	0.069000	0.16605	-0.312000	0.09012	GTC		0.711	ADAD2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433385.1		NM_139174	
ADAMTS12	81792	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	33588814	33588814	+	Missense_Mutation	SNP	G	G	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr5:33588814G>T	ENST00000504830.1	-	18	3090	c.2755C>A	c.(2755-2757)Cag>Aag	p.Q919K	ADAMTS12_ENST00000504582.1_5'UTR|ADAMTS12_ENST00000352040.3_Missense_Mutation_p.Q834K	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	919	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727)	extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.Q919K(1)		NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						GGGAGAGCCTGCTCGTCAGAG	0.637										HNSCC(64;0.19)																																							1	Substitution - Missense(1)	kidney(1)											128.0	124.0	125.0					5																	33588814		2203	4300	6503	SO:0001583	missense	81792			AJ250725	CCDS34140.1	5q35	2008-07-18	2005-08-19		ENSG00000151388	ENSG00000151388		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	14605	protein-coding gene	gene with protein product		606184	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 12"""			11279086	Standard	NM_030955		Approved		uc003jia.1	P58397	OTTHUMG00000162088	ENST00000504830.1:c.2755C>A	5.37:g.33588814G>T	ENSP00000422554:p.Gln919Lys	Somatic		WXS	Illumina HiSeq	Phase_I	A2RRN9|A5D6V6|Q6UWL3	Missense_Mutation	SNP	ENST00000504830.1	37	CCDS34140.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.184939	0.78677	.	.	ENSG00000151388	ENST00000504830;ENST00000352040	T;T	0.59638	0.29;0.25	5.98	5.98	0.97165	.	0.110120	0.64402	D	0.000005	T	0.68476	0.3005	M	0.75264	2.295	0.80722	D	1	B;P	0.38048	0.42;0.616	B;P	0.51550	0.187;0.673	T	0.61451	-0.7060	10	0.09590	T	0.72	.	15.8809	0.79205	0.0:0.1347:0.8653:0.0	.	834;919	P58397-3;P58397	.;ATS12_HUMAN	K	919;834	ENSP00000422554:Q919K;ENSP00000344847:Q834K	ENSP00000344847:Q834K	Q	-	1	0	ADAMTS12	33624571	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	4.141000	0.58038	2.838000	0.97847	0.591000	0.81541	CAG		0.637	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2		NM_030955	
AHNAK	79026	broad.mit.edu;hgsc.bcm.edu	37	11	62290074	62290074	+	Nonsense_Mutation	SNP	T	T	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr11:62290074T>A	ENST00000378024.4	-	5	12089	c.11815A>T	c.(11815-11817)Aag>Tag	p.K3939*	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	3939					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)	p.K3939*(1)		NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				ATGCTGATCTTGGGCATTTTT	0.502																																																	1	Substitution - Nonsense(1)	kidney(1)											229.0	243.0	238.0					11																	62290074		2202	4299	6501	SO:0001587	stop_gained	79026			M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"""desmoyokin"""	103390	"""AHNAK nucleoprotein (desmoyokin)"""			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.11815A>T	11.37:g.62290074T>A	ENSP00000367263:p.Lys3939*	Somatic		WXS	Illumina HiSeq	Phase_I	A1A586	Nonsense_Mutation	SNP	ENST00000378024.4	37	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	-	53	20.094304	0.99927	.	.	ENSG00000124942	ENST00000378024	.	.	.	4.71	4.71	0.59529	.	0.199810	0.24587	U	0.037244	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.7759	9.3135	0.37919	0.1604:0.0:0.0:0.8396	.	.	.	.	X	3939	.	ENSP00000367263:K3939X	K	-	1	0	AHNAK	62046650	1.000000	0.71417	1.000000	0.80357	0.213000	0.24496	1.625000	0.37029	1.745000	0.51790	0.408000	0.27601	AAG		0.502	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1		NM_024060	
AMY2B	280	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	104116348	104116348	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr1:104116348G>A	ENST00000361355.4	+	6	1148	c.532G>A	c.(532-534)Gtt>Att	p.V178I	AMY2B_ENST00000491397.1_3'UTR	NM_020978.3	NP_066188.1	P19961	AMY2B_HUMAN	amylase, alpha 2B (pancreatic)	178					carbohydrate metabolic process (GO:0005975)|digestion (GO:0007586)	extracellular vesicular exosome (GO:0070062)	alpha-amylase activity (GO:0004556)|metal ion binding (GO:0046872)	p.V178I(1)		breast(1)|endometrium(7)|kidney(4)|large_intestine(1)|lung(30)|prostate(1)|skin(1)|urinary_tract(1)	46		all_epithelial(167;3.05e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000451)		Colorectal(144;0.0669)|all cancers(265;0.083)|Epithelial(280;0.094)|Lung(183;0.112)		TTGTCGTCTGGTTGGTCTTCT	0.363																																																	1	Substitution - Missense(1)	kidney(1)											379.0	365.0	370.0					1																	104116348		2203	4300	6503	SO:0001583	missense	280			M24895	CCDS782.1	1p21	2010-08-02	2006-04-27		ENSG00000240038	ENSG00000240038	3.2.1.1		478	protein-coding gene	gene with protein product		104660	"""amylase, alpha 2B; pancreatic"""	AMY2		8268204	Standard	NM_020978		Approved		uc001duq.3	P19961	OTTHUMG00000011024	ENST00000361355.4:c.532G>A	1.37:g.104116348G>A	ENSP00000354610:p.Val178Ile	Somatic		WXS	Illumina HiSeq	Phase_I	B3KTI1|B3KXB7|D3DT76|Q9UBH3	Missense_Mutation	SNP	ENST00000361355.4	37	CCDS782.1	.	.	.	.	.	.	.	.	.	.	G	14.05	2.420169	0.42918	.	.	ENSG00000240038	ENST00000361355	D	0.98345	-4.88	4.74	-1.31	0.09230	Glycoside hydrolase, subgroup, catalytic domain (1);Glycosyl hydrolase, family 13, catalytic domain (1);Glycoside hydrolase, superfamily (1);Glycosyl hydrolase, family 13, subfamily, catalytic domain (1);	0.892392	0.09555	N	0.786356	D	0.96228	0.8770	M	0.90870	3.155	0.27177	N	0.960776	B	0.30973	0.302	B	0.39339	0.297	D	0.92533	0.6035	10	0.87932	D	0	.	1.4058	0.02280	0.1999:0.1088:0.2798:0.4115	.	178	P19961	AMY2B_HUMAN	I	178	ENSP00000354610:V178I	ENSP00000354610:V178I	V	+	1	0	AMY2B	103917871	0.022000	0.18835	0.147000	0.22382	0.987000	0.75469	0.309000	0.19332	-0.233000	0.09797	-0.208000	0.12717	GTT		0.363	AMY2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030318.1		NM_020978	
APOOL	139322	hgsc.bcm.edu;ucsc.edu	37	X	84342599	84342602	+	Frame_Shift_Del	DEL	CAAC	CAAC	-	rs183377356		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	CAAC	CAAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chrX:84342599_84342602delCAAC	ENST00000373173.2	+	9	809_812	c.722_725delCAAC	c.(721-726)gcaaccfs	p.AT241fs		NM_198450.5	NP_940852.3	Q6UXV4	MIC27_HUMAN	apolipoprotein O-like	241						integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(1)	8						TTATCAGGTGCAACCCAGTTTATG	0.397																																																	0																																										SO:0001589	frameshift_variant	139322			AK130506	CCDS48138.1	Xq21.1	2007-01-17	2007-01-17	2007-01-17	ENSG00000155008	ENSG00000155008			24009	protein-coding gene	gene with protein product			"""chromosome X open reading frame 33"", ""family with sequence similarity 121A"""	CXorf33, FAM121A		12975309	Standard	NM_198450		Approved	UNQ8193, AAIR8193	uc004eem.3	Q6UXV4	OTTHUMG00000021930	ENST00000373173.2:c.722_725delCAAC	X.37:g.84342599_84342602delCAAC	ENSP00000362268:p.Ala241fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q3KNU7|Q5H9D1	Frame_Shift_Del	DEL	ENST00000373173.2	37	CCDS48138.1																																																																																				0.397	APOOL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057385.2		NM_198450	
CCER1	196477	hgsc.bcm.edu	37	12	91347561	91347581	+	In_Frame_Del	DEL	TCTTCCTCCTCATCTTCGACC	TCTTCCTCCTCATCTTCGACC	-	rs374196591|rs370409256|rs558083520|rs376547014	byFrequency	TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	TCTTCCTCCTCATCTTCGACC	TCTTCCTCCTCATCTTCGACC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr12:91347561_91347581delTCTTCCTCCTCATCTTCGACC	ENST00000358859.2	-	1	1372_1392	c.939_959delGGTCGAAGATGAGGAGGAAGA	c.(937-960)gaggtcgaagatgaggaggaagaa>gaa	p.313_320EVEDEEEE>E	CCER1_ENST00000548187.1_Intron	NM_152638.2	NP_689851.1	Q8TC90	CCER1_HUMAN	coiled-coil glutamate-rich protein 1	313	Glu-rich.																ttcgacctcttcttcctcctcatcttcgacctcttcctcct	0.534														78	0.0155751	0.0	0.0159	5008	,	,		21928	0.0516		0.008	False		,,,				2504	0.0072																0										20,4244		0,20,2112						-8.4	0.0		dbSNP_107	182	102,8152		2,98,4027	no	coding	C12orf12	NM_152638.2		2,118,6139	A1A1,A1R,RR		1.2358,0.469,0.9746				122,12396				SO:0001651	inframe_deletion	0			BC024183	CCDS9036.1	12q21.33	2012-05-30	2012-05-30	2012-05-30	ENSG00000197651	ENSG00000197651			28373	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 12"""	C12orf12		17967063	Standard	NM_152638		Approved	MGC26598	uc001tbj.3	Q8TC90	OTTHUMG00000170070	ENST00000358859.2:c.939_959delGGTCGAAGATGAGGAGGAAGA	12.37:g.91347561_91347581delTCTTCCTCCTCATCTTCGACC	ENSP00000351727:p.Glu313_Glu319del	Somatic		WXS	Illumina HiSeq	Phase_I	Q8TC47	In_Frame_Del	DEL	ENST00000358859.2	37	CCDS9036.1																																																																																				0.534	CCER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407142.2		NM_152638	
C1orf94	84970	broad.mit.edu;ucsc.edu	37	1	34677961	34677961	+	Missense_Mutation	SNP	C	C	G			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr1:34677961C>G	ENST00000488417.1	+	6	1795	c.1675C>G	c.(1675-1677)Cta>Gta	p.L559V	C1orf94_ENST00000373374.3_Missense_Mutation_p.L369V	NM_001134734.1	NP_001128206.1	Q6P1W5	CA094_HUMAN	chromosome 1 open reading frame 94	559								p.L559V(1)|p.L369V(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(15)|skin(4)|upper_aerodigestive_tract(2)	32		Myeloproliferative disorder(586;0.0393)				AGACCCTCCCCTAATGGCAGG	0.567																																																	2	Substitution - Missense(2)	kidney(2)											90.0	80.0	83.0					1																	34677961		2203	4300	6503	SO:0001583	missense	84970			AK123355	CCDS381.1, CCDS44108.1	1p34.3	2012-06-26			ENSG00000142698	ENSG00000142698			28250	protein-coding gene	gene with protein product						12477932	Standard	NM_001134734		Approved	MGC15882	uc001bxt.3	Q6P1W5	OTTHUMG00000004012	ENST00000488417.1:c.1675C>G	1.37:g.34677961C>G	ENSP00000435634:p.Leu559Val	Somatic		WXS	Illumina GAIIx	Phase_I	B3KVT1|D3DPR3|E9PJ76|Q96IC8	Missense_Mutation	SNP	ENST00000488417.1	37	CCDS44108.1	.	.	.	.	.	.	.	.	.	.	c	10.53	1.375485	0.24857	.	.	ENSG00000142698	ENST00000373374;ENST00000488417	T;T	0.22336	1.97;1.96	5.18	4.25	0.50352	.	0.000000	0.64402	D	0.000011	T	0.11537	0.0281	N	0.08118	0	0.18873	N	0.999989	B	0.02656	0.0	B	0.01281	0.0	T	0.20840	-1.0263	10	0.66056	D	0.02	-35.54	11.0251	0.47741	0.1865:0.8135:0.0:0.0	.	559	Q6P1W5	CA094_HUMAN	V	369;559	ENSP00000362472:L369V;ENSP00000435634:L559V	ENSP00000362472:L369V	L	+	1	2	C1orf94	34450548	1.000000	0.71417	0.989000	0.46669	0.460000	0.32559	2.872000	0.48467	1.161000	0.42604	-0.187000	0.12897	CTA		0.567	C1orf94-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036845.2		NM_032884	
FAM221B	392307	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	35826098	35826098	+	Missense_Mutation	SNP	G	G	C			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr9:35826098G>C	ENST00000423537.2	-	2	330	c.61C>G	c.(61-63)Cct>Gct	p.P21A	TMEM8B_ENST00000377996.1_Intron	NM_001012446.3	NP_001012448.2	A6H8Z2	F221B_HUMAN	family with sequence similarity 221, member B	21								p.P21A(3)		endometrium(2)|kidney(1)|lung(4)	7						TCCTTTGAAGGGGGGTGCTTC	0.498											OREG0019180	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					3	Substitution - Missense(3)	kidney(3)											67.0	67.0	67.0					9																	35826098		1924	4121	6045	SO:0001583	missense	0			BX648702	CCDS43799.1, CCDS43799.2	9p13.3	2012-04-02	2012-04-02	2012-04-02	ENSG00000204930	ENSG00000204930			30762	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 128"""	C9orf128			Standard	NM_001012446		Approved		uc010mlc.2	A6H8Z2	OTTHUMG00000019880	ENST00000423537.2:c.61C>G	9.37:g.35826098G>C	ENSP00000415299:p.Pro21Ala	Somatic	858	WXS	Illumina HiSeq	Phase_I	Q5TCW2	Missense_Mutation	SNP	ENST00000423537.2	37	CCDS43799.2	.	.	.	.	.	.	.	.	.	.	g	0.027	-1.364478	0.01235	.	.	ENSG00000204930	ENST00000423537;ENST00000377984;ENST00000472182	T;T;T	0.29397	2.64;2.37;1.57	4.23	1.65	0.23941	.	0.518270	0.16457	N	0.213595	T	0.11922	0.0290	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.33471	-0.9867	10	0.10377	T	0.69	.	5.6695	0.17715	0.7728:0.0:0.2272:0.0	.	21	A6H8Z2	CI128_HUMAN	A	21	ENSP00000415299:P21A;ENSP00000367222:P21A;ENSP00000420279:P21A	ENSP00000367222:P21A	P	-	1	0	C9orf128	35816098	0.957000	0.32711	0.071000	0.20095	0.067000	0.16453	1.020000	0.30027	0.282000	0.22254	-0.487000	0.04747	CCT		0.498	FAM221B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355861.1		NM_001012446	
C9orf114	51490	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	131587284	131587284	+	Silent	SNP	A	A	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr9:131587284A>T	ENST00000361256.5	-	8	724	c.684T>A	c.(682-684)acT>acA	p.T228T		NM_016390.3	NP_057474.2	Q5T280	CI114_HUMAN	chromosome 9 open reading frame 114	228							poly(A) RNA binding (GO:0044822)	p.T228T(1)		kidney(2)|large_intestine(4)|ovary(1)	7						TCAGTCGCACAGTCACCCGAA	0.592																																																	1	Substitution - coding silent(1)	kidney(1)											30.0	29.0	30.0					9																	131587284		2201	4298	6499	SO:0001819	synonymous_variant	51490				CCDS6913.1	9q34.11	2014-05-29			ENSG00000198917	ENSG00000198917			26933	protein-coding gene	gene with protein product	"""centromere protein 32"""					20813266	Standard	NM_016390		Approved	HSPC109, CENP-32	uc004bwd.3	Q5T280	OTTHUMG00000020762	ENST00000361256.5:c.684T>A	9.37:g.131587284A>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q0D2P6|Q6P469|Q6PGP9|Q6PIJ1|Q6PJV9	Silent	SNP	ENST00000361256.5	37	CCDS6913.1																																																																																				0.592	C9orf114-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054500.1		NM_016390	
TMA7	51372	hgsc.bcm.edu	37	3	48485282	48485282	+	Frame_Shift_Del	DEL	A	A	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr3:48485282delA	ENST00000438607.2	+	4	227	c.187delA	c.(187-189)aaafs	p.K64fs	ATRIP_ENST00000320211.3_5'Flank|RP11-24C3.2_ENST00000438872.1_RNA|RP11-24C3.2_ENST00000435578.1_RNA|ATRIP_ENST00000346691.4_5'Flank|ATRIP_ENST00000357105.6_5'Flank	NM_015933.3	NP_057017.1	Q9Y2S6	TMA7_HUMAN	translation machinery associated 7 homolog (S. cerevisiae)	64										lung(1)	1						GAAATCTGGCAAAAAGTAAGC	0.418																																																	0													79.0	76.0	77.0					3																	48485282		1828	4078	5906	SO:0001589	frameshift_variant	0			AF077202	CCDS46823.1	3p21.31	2013-02-22	2013-02-22	2012-06-07	ENSG00000232112	ENSG00000232112			26932	protein-coding gene	gene with protein product		615808	"""coiled-coil domain containing 72"""	CCDC72		11042152, 15740594	Standard	NM_015933		Approved	HSPC016	uc003cte.1	Q9Y2S6	OTTHUMG00000156588	ENST00000438607.2:c.187delA	3.37:g.48485282delA	ENSP00000397843:p.Lys64fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q9P052	Frame_Shift_Del	DEL	ENST00000438607.2	37	CCDS46823.1																																																																																				0.418	TMA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344688.1		NM_015933	
CDK14	5218	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	90356089	90356089	+	Missense_Mutation	SNP	A	A	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr7:90356089A>T	ENST00000380050.3	+	3	463	c.332A>T	c.(331-333)gAg>gTg	p.E111V	CDK14_ENST00000406263.1_Missense_Mutation_p.E65V|CDK14_ENST00000265741.3_Missense_Mutation_p.E93V|CDK14_ENST00000436577.2_Missense_Mutation_p.S14C			O94921	CDK14_HUMAN	cyclin-dependent kinase 14	111					cell division (GO:0051301)|G2/M transition of mitotic cell cycle (GO:0000086)|regulation of canonical Wnt signaling pathway (GO:0060828)|regulation of cell cycle (GO:0051726)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytoplasmic cyclin-dependent protein kinase holoenzyme complex (GO:0000308)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)	p.E111V(1)|p.E93V(1)		breast(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|liver(1)|lung(12)|ovary(1)|skin(4)	32						ACTGGCAAAGAGTCACCTAAA	0.438																																					GBM(83;1228 1256 8311 16577 31299)												2	Substitution - Missense(2)	kidney(2)											92.0	84.0	87.0					7																	90356089		2203	4299	6502	SO:0001583	missense	5218				CCDS5619.1, CCDS75626.1, CCDS75627.1, CCDS75628.1	7q21-q22	2011-11-08	2009-12-16	2009-12-16	ENSG00000058091	ENSG00000058091		"""Cyclin-dependent kinases"""	8883	protein-coding gene	gene with protein product		610679	"""PFTAIRE protein kinase 1"""	PFTK1		9202329, 11313143, 19884882	Standard	XM_005250436		Approved	PFTAIRE1	uc003ukz.1	O94921	OTTHUMG00000023649	ENST00000380050.3:c.332A>T	7.37:g.90356089A>T	ENSP00000369390:p.Glu111Val	Somatic		WXS	Illumina HiSeq	Phase_I	A4D1E6|A6NK51|A8WFP6|B4DHG5|B4DNM2|Q75N06|Q75N22|Q8N764|Q9H3D7|Q9UDR0	Missense_Mutation	SNP	ENST00000380050.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.76|12.76	2.035429|2.035429	0.35893|0.35893	.|.	.|.	ENSG00000058091|ENSG00000058091	ENST00000449528;ENST00000446224;ENST00000430760;ENST00000456689;ENST00000380050;ENST00000446790;ENST00000265741;ENST00000406263|ENST00000436577	T;T;T;T;T;T;T|T	0.71579|0.72282	2.16;2.16;2.16;2.16;-0.58;-0.58;-0.57|-0.64	5.51|5.51	4.32|4.32	0.51571|0.51571	.|.	0.140352|.	0.45126|.	N|.	0.000392|.	T|T	0.51635|0.51635	0.1686|0.1686	N|N	0.19112|0.19112	0.55|0.55	0.29341|0.29341	N|N	0.866039|0.866039	B;B|P	0.09022|0.46327	0.002;0.001|0.876	B;B|B	0.08055|0.33042	0.003;0.002|0.157	T|T	0.51068|0.51068	-0.8752|-0.8752	10|9	0.25106|0.87932	T|D	0.35|0	-9.3333|-9.3333	11.6772|11.6772	0.51436|0.51436	0.8671:0.0:0.0:0.1329|0.8671:0.0:0.0:0.1329	.|.	93;111|14	O94921-2;O94921|E7EUK8	.;CDK14_HUMAN|.	V|C	65;65;65;65;111;65;93;65|14	ENSP00000393616:E65V;ENSP00000410770:E65V;ENSP00000394570:E65V;ENSP00000406848:E65V;ENSP00000369390:E111V;ENSP00000265741:E93V;ENSP00000385034:E65V|ENSP00000398936:S14C	ENSP00000265741:E93V|ENSP00000398936:S14C	E|S	+|+	2|1	0|0	CDK14|CDK14	90194025|90194025	1.000000|1.000000	0.71417|0.71417	0.985000|0.985000	0.45067|0.45067	0.984000|0.984000	0.73092|0.73092	8.513000|8.513000	0.90542|0.90542	0.883000|0.883000	0.36040|0.36040	0.460000|0.460000	0.39030|0.39030	GAG|AGT		0.438	CDK14-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000059970.5		NM_012395	
CLCN6	1185	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	11894362	11894362	+	Silent	SNP	G	G	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr1:11894362G>T	ENST00000346436.6	+	16	1648	c.1596G>T	c.(1594-1596)ggG>ggT	p.G532G	CLCN6_ENST00000312413.6_3'UTR|CLCN6_ENST00000376487.3_Silent_p.G510G|CLCN6_ENST00000376496.3_Silent_p.G532G	NM_001286.3	NP_001277	P51797	CLCN6_HUMAN	chloride channel, voltage-sensitive 6	532					cell volume homeostasis (GO:0006884)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|response to mechanical stimulus (GO:0009612)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|voltage-gated chloride channel activity (GO:0005247)	p.G532G(1)		cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|prostate(2)|skin(4)	36	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.000816)|KIRC - Kidney renal clear cell carcinoma(229;0.00268)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)		TCTTGGGCGGGGTGGTCCGCA	0.552																																																	1	Substitution - coding silent(1)	kidney(1)											106.0	96.0	99.0					1																	11894362		2203	4300	6503	SO:0001819	synonymous_variant	1185			X83378	CCDS138.1, CCDS57972.1	1p36	2012-09-26	2012-02-23		ENSG00000011021	ENSG00000011021		"""Ion channels / Chloride channels : Voltage-sensitive"""	2024	protein-coding gene	gene with protein product		602726	"""chloride channel 6"""			8543009	Standard	NM_001286		Approved	CLC-6, KIAA0046, ClC-6	uc001ate.5	P51797	OTTHUMG00000002299	ENST00000346436.6:c.1596G>T	1.37:g.11894362G>T		Somatic		WXS	Illumina HiSeq	Phase_I	A8K1T4|B4DGT7|F8W9R3|O60818|O60819|O60820|O60821|P78520|P78521|Q17R81|Q5SNW2|Q5SNW3|Q5SNX1|Q5SNX2|Q5SNX3|Q99427|Q99428|Q99429	Silent	SNP	ENST00000346436.6	37	CCDS138.1																																																																																				0.552	CLCN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006639.2		NM_001286	
CLGN	1047	broad.mit.edu;hgsc.bcm.edu	37	4	141321553	141321553	+	Missense_Mutation	SNP	T	T	C			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr4:141321553T>C	ENST00000325617.5	-	7	1092	c.652A>G	c.(652-654)Aaa>Gaa	p.K218E	CLGN_ENST00000537281.1_Missense_Mutation_p.K218E|CLGN_ENST00000414773.1_Missense_Mutation_p.K218E	NM_004362.2	NP_004353.1	O14967	CLGN_HUMAN	calmegin	218					binding of sperm to zona pellucida (GO:0007339)|protein complex assembly (GO:0006461)|protein folding (GO:0006457)|single fertilization (GO:0007338)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)	calcium ion binding (GO:0005509)|unfolded protein binding (GO:0051082)	p.K218E(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(5)|ovary(2)|prostate(3)|skin(4)|urinary_tract(1)	25	all_hematologic(180;0.162)					AAGAACTTTTTAAGGTCTACA	0.328																																																	1	Substitution - Missense(1)	kidney(1)											129.0	134.0	132.0					4																	141321553		2203	4300	6503	SO:0001583	missense	1047			D86322	CCDS3751.1	4q28.3-q31.1	2008-02-05			ENSG00000153132	ENSG00000153132			2060	protein-coding gene	gene with protein product		601858					Standard	NM_004362		Approved		uc003iii.3	O14967	OTTHUMG00000133414	ENST00000325617.5:c.652A>G	4.37:g.141321553T>C	ENSP00000326699:p.Lys218Glu	Somatic		WXS	Illumina HiSeq	Phase_I	B3KS90|B4DXV8|D3DNY8	Missense_Mutation	SNP	ENST00000325617.5	37	CCDS3751.1	.	.	.	.	.	.	.	.	.	.	T	15.91	2.973171	0.53614	.	.	ENSG00000153132	ENST00000325617;ENST00000414773;ENST00000537281;ENST00000545667	T;T;T	0.52526	0.66;0.66;0.66	5.63	5.63	0.86233	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.082252	0.85682	D	0.000000	T	0.54208	0.1844	L	0.39245	1.2	0.50039	D	0.99984	D	0.64830	0.994	D	0.63703	0.917	T	0.46148	-0.9212	10	0.07175	T	0.84	-31.1458	16.1277	0.81406	0.0:0.0:0.0:1.0	.	218	O14967	CLGN_HUMAN	E	218;218;218;135	ENSP00000326699:K218E;ENSP00000392782:K218E;ENSP00000439381:K218E	ENSP00000326699:K218E	K	-	1	0	CLGN	141541003	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	6.252000	0.72447	2.273000	0.75805	0.482000	0.46254	AAA		0.328	CLGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257272.2		NM_004362	
DAPK2	23604	broad.mit.edu;hgsc.bcm.edu	37	15	64200798	64200798	+	Splice_Site	SNP	C	C	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr15:64200798C>A	ENST00000457488.1	-	12	1064	c.1034G>T	c.(1033-1035)aGg>aTg	p.R345M	DAPK2_ENST00000261891.3_Splice_Site_p.R345M	NM_014326.3	NP_055141.2	Q9UIK4	DAPK2_HUMAN	death-associated protein kinase 2	345					anoikis (GO:0043276)|apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of intrinsic apoptotic signaling pathway (GO:2001242)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|protein serine/threonine kinase activity (GO:0004674)	p.R345M(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|skin(1)|stomach(1)	11				LUAD - Lung adenocarcinoma(2;0.215)		CTCACAGTTCCTCTGGAGAAA	0.587																																																	1	Substitution - Missense(1)	kidney(1)											35.0	27.0	29.0					15																	64200798		2202	4299	6501	SO:0001630	splice_region_variant	23604			AB018001	CCDS10188.1	15q22.1	2008-07-18			ENSG00000035664	ENSG00000035664			2675	protein-coding gene	gene with protein product						10376525	Standard	XM_005254265		Approved	DRP-1, MGC119312	uc002amr.3	Q9UIK4	OTTHUMG00000132947	ENST00000457488.1:c.1033-1G>T	15.37:g.64200798C>A		Somatic		WXS	Illumina HiSeq	Phase_I	E9JGM7|O75892|Q24JS1	Missense_Mutation	SNP	ENST00000457488.1	37	CCDS10188.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.019223	0.75275	.	.	ENSG00000035664	ENST00000261891;ENST00000457488	T;T	0.69685	-0.42;-0.42	5.26	5.26	0.73747	Protein kinase-like domain (1);	0.000000	0.64402	D	0.000005	T	0.75466	0.3853	L	0.59436	1.845	0.58432	D	0.999991	D	0.63880	0.993	P	0.58391	0.838	T	0.76110	-0.3079	10	0.48119	T	0.1	.	15.5961	0.76583	0.0:1.0:0.0:0.0	.	345	Q9UIK4	DAPK2_HUMAN	M	345	ENSP00000261891:R345M;ENSP00000408277:R345M	ENSP00000261891:R345M	R	-	2	0	DAPK2	61987851	1.000000	0.71417	1.000000	0.80357	0.800000	0.45204	3.557000	0.53741	2.458000	0.83093	0.655000	0.94253	AGG		0.587	DAPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256479.1		NM_014326	Missense_Mutation
DEFB129	140881	broad.mit.edu;ucsc.edu	37	20	207960	207960	+	Missense_Mutation	SNP	C	C	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr20:207960C>T	ENST00000246105.4	+	1	62	c.31C>T	c.(31-33)Ctc>Ttc	p.L11F		NM_080831.3	NP_543021.1	Q9H1M3	DB129_HUMAN	defensin, beta 129	11					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)		p.L11F(1)		endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(1)|ovary(1)|stomach(1)	9		all_cancers(10;7.65e-05)|Lung NSC(37;0.0417)|all_epithelial(17;0.0676)|all_lung(30;0.0713)|Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.122)			CTTTGCCAGCCTCATGCTACA	0.483																																																	1	Substitution - Missense(1)	kidney(1)											190.0	159.0	170.0					20																	207960		2203	4300	6503	SO:0001583	missense	140881			AY358186	CCDS12992.1	20p13	2010-03-30	2002-05-09	2002-05-10	ENSG00000125903	ENSG00000125903		"""Defensins, beta"""	16218	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 87"""	C20orf87		11854508	Standard	NM_080831		Approved	bA530N10.3, DEFB-29	uc002wda.3	Q9H1M3	OTTHUMG00000031618	ENST00000246105.4:c.31C>T	20.37:g.207960C>T	ENSP00000246105:p.Leu11Phe	Somatic		WXS	Illumina GAIIx	Phase_I	Q8NES7	Missense_Mutation	SNP	ENST00000246105.4	37	CCDS12992.1	.	.	.	.	.	.	.	.	.	.	C	17.63	3.437687	0.62955	.	.	ENSG00000125903	ENST00000246105	T	0.53206	0.63	4.38	3.44	0.39384	.	0.000000	0.45606	D	0.000352	T	0.28300	0.0699	L	0.27053	0.805	0.29083	N	0.882576	P	0.43633	0.813	B	0.33454	0.164	T	0.31503	-0.9941	10	0.87932	D	0	-4.5265	8.5104	0.33213	0.0:0.8959:0.0:0.1041	.	11	Q9H1M3	DB129_HUMAN	F	11	ENSP00000246105:L11F	ENSP00000246105:L11F	L	+	1	0	DEFB129	155960	0.970000	0.33590	1.000000	0.80357	0.949000	0.60115	1.537000	0.36083	1.439000	0.47511	0.650000	0.86243	CTC		0.483	DEFB129-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077430.2		NM_080831	
DMXL1	1657	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	118502399	118502399	+	Missense_Mutation	SNP	T	T	G			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr5:118502399T>G	ENST00000311085.8	+	22	5139	c.5059T>G	c.(5059-5061)Tct>Gct	p.S1687A	DMXL1_ENST00000539542.1_Missense_Mutation_p.S1687A	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	1687								p.S1687A(1)		breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		GAATGCTTTTTCTTTGCTAGG	0.358																																																	1	Substitution - Missense(1)	kidney(1)											98.0	100.0	99.0					5																	118502399		2202	4300	6502	SO:0001583	missense	1657			AJ005821	CCDS4125.1, CCDS75289.1	5q22	2013-01-10			ENSG00000172869	ENSG00000172869		"""WD repeat domain containing"""	2937	protein-coding gene	gene with protein product		605671				10708522	Standard	NM_005509		Approved		uc003ksd.2	Q9Y485	OTTHUMG00000128898	ENST00000311085.8:c.5059T>G	5.37:g.118502399T>G	ENSP00000309690:p.Ser1687Ala	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000311085.8	37	CCDS4125.1	.	.	.	.	.	.	.	.	.	.	T	13.84	2.358645	0.41801	.	.	ENSG00000172869	ENST00000311085;ENST00000539542	T;T	0.28895	1.59;1.59	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	T	0.19886	0.0478	N	0.13098	0.295	0.58432	D	0.999999	P;P	0.38729	0.644;0.56	B;B	0.40659	0.269;0.336	T	0.03910	-1.0993	10	0.02654	T	1	-18.2577	16.2159	0.82217	0.0:0.0:0.0:1.0	.	1687;1687	F5H269;Q9Y485	.;DMXL1_HUMAN	A	1687	ENSP00000309690:S1687A;ENSP00000439479:S1687A	ENSP00000309690:S1687A	S	+	1	0	DMXL1	118530298	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.976000	0.70484	2.243000	0.73865	0.533000	0.62120	TCT		0.358	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1		NM_005509	
EXPH5	23086	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	108382795	108382795	+	Missense_Mutation	SNP	T	T	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr11:108382795T>A	ENST00000265843.4	-	6	3549	c.3439A>T	c.(3439-3441)Atg>Ttg	p.M1147L	EXPH5_ENST00000428840.1_Missense_Mutation_p.M1071L|EXPH5_ENST00000524840.1_5'Flank|EXPH5_ENST00000525344.1_Missense_Mutation_p.M1140L|EXPH5_ENST00000443411.1_Missense_Mutation_p.M959L	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	1147			M -> I (in dbSNP:rs34012545).		intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)	p.M1147L(1)		breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		GAAGCATCCATGCCTGAGGTC	0.468																																																	1	Substitution - Missense(1)	kidney(1)											97.0	99.0	98.0					11																	108382795		2201	4298	6499	SO:0001583	missense	23086				CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"""synaptotagmin-like homologue lacking C2 domains b"""	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.3439A>T	11.37:g.108382795T>A	ENSP00000265843:p.Met1147Leu	Somatic		WXS	Illumina HiSeq	Phase_I	Q2KHM1|Q9Y4D6	Missense_Mutation	SNP	ENST00000265843.4	37	CCDS8341.1	.	.	.	.	.	.	.	.	.	.	T	1.334	-0.595905	0.03771	.	.	ENSG00000110723	ENST00000265843;ENST00000428840;ENST00000443411;ENST00000525344;ENST00000526312;ENST00000533052	T;T;T;T;T;T	0.03524	4.53;4.45;4.3;4.53;4.37;3.9	5.77	0.655	0.17839	.	0.702507	0.13726	N	0.367039	T	0.01730	0.0055	N	0.19112	0.55	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.47446	-0.9117	10	0.02654	T	1	1.0693	1.4835	0.02442	0.3017:0.0825:0.157:0.4589	.	1147	Q8NEV8	EXPH5_HUMAN	L	1147;1071;959;1140;1071;959	ENSP00000265843:M1147L;ENSP00000391966:M1071L;ENSP00000411390:M959L;ENSP00000432546:M1140L;ENSP00000432683:M1071L;ENSP00000446434:M959L	ENSP00000265843:M1147L	M	-	1	0	EXPH5	107888005	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.050000	0.11904	0.072000	0.16694	-0.313000	0.08912	ATG		0.468	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1		NM_015065	
F2RL2	2151	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	75914170	75914170	+	Missense_Mutation	SNP	A	A	C			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr5:75914170A>C	ENST00000296641.4	-	2	565	c.362T>G	c.(361-363)tTc>tGc	p.F121C	IQGAP2_ENST00000502745.1_Intron|IQGAP2_ENST00000379730.3_Intron|IQGAP2_ENST00000274364.6_Intron|F2RL2_ENST00000504899.1_Missense_Mutation_p.F99C|IQGAP2_ENST00000396234.3_Intron	NM_004101.3	NP_004092.1	O00254	PAR3_HUMAN	coagulation factor II (thrombin) receptor-like 2	121					blood coagulation (GO:0007596)|metabolic process (GO:0008152)|platelet activation (GO:0030168)|response to wounding (GO:0009611)	apical plasma membrane (GO:0016324)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphatidylinositol phospholipase C activity (GO:0004435)|thrombin receptor activity (GO:0015057)	p.F121C(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(3)	32		all_lung(232;0.000462)|Lung NSC(167;0.00124)|Prostate(461;0.00955)|Ovarian(174;0.0129)		all cancers(79;4.43e-43)		TCTGGTCCTGAAGAAAAGCAT	0.453																																																	1	Substitution - Missense(1)	kidney(1)											94.0	94.0	94.0					5																	75914170		2203	4300	6503	SO:0001583	missense	2151			U92971	CCDS4031.1, CCDS58959.1	5q13	2012-08-08			ENSG00000164220	ENSG00000164220		"""GPCR / Class A : Protease activated receptors"""	3539	protein-coding gene	gene with protein product	"""proteinase-activated receptor-3"""	601919				9087410, 9722561	Standard	NM_004101		Approved	PAR3	uc003kem.4	O00254	OTTHUMG00000102119	ENST00000296641.4:c.362T>G	5.37:g.75914170A>C	ENSP00000296641:p.Phe121Cys	Somatic		WXS	Illumina HiSeq	Phase_I	B2R754|B4DQ13|Q52M68|Q7Z3W3	Missense_Mutation	SNP	ENST00000296641.4	37	CCDS4031.1	.	.	.	.	.	.	.	.	.	.	A	14.48	2.547925	0.45383	.	.	ENSG00000164220	ENST00000296641;ENST00000504899	T;T	0.37915	1.17;1.17	5.15	3.95	0.45737	GPCR, rhodopsin-like superfamily (1);	0.530154	0.21970	N	0.066480	T	0.35451	0.0932	L	0.38733	1.17	0.22888	N	0.99861	D	0.56287	0.975	P	0.53689	0.732	T	0.09907	-1.0653	10	0.30854	T	0.27	-8.772	6.3626	0.21437	0.7844:0.0:0.0761:0.1395	.	121	O00254	PAR3_HUMAN	C	121;99	ENSP00000296641:F121C;ENSP00000426703:F99C	ENSP00000296641:F121C	F	-	2	0	F2RL2	75949926	0.990000	0.36364	0.936000	0.37596	0.784000	0.44337	1.585000	0.36600	0.754000	0.32968	0.455000	0.32223	TTC		0.453	F2RL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219958.3			
FAF1	11124	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	50956260	50956260	+	Splice_Site	SNP	C	C	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr1:50956260C>T	ENST00000396153.2	-	17	2104	c.1653G>A	c.(1651-1653)gaG>gaA	p.E551E	FAF1_ENST00000371778.4_Splice_Site_p.E551E|FAF1_ENST00000545823.1_Splice_Site_p.E309E	NM_007051.2	NP_008982.1	Q9UNN5	FAF1_HUMAN	Fas (TNFRSF6) associated factor 1	551					apoptotic process (GO:0006915)|cell death (GO:0008219)|cytoplasmic sequestering of NF-kappaB (GO:0007253)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of protein complex assembly (GO:0031334)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of cell adhesion (GO:0030155)|regulation of protein catabolic process (GO:0042176)|regulation of protein kinase activity (GO:0045859)	CD95 death-inducing signaling complex (GO:0031265)|Cdc48p-Npl4p-Ufd1p AAA ATPase complex (GO:0034098)|cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	heat shock protein binding (GO:0031072)|NF-kappaB binding (GO:0051059)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)	p.E551E(1)		breast(2)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|pancreas(2)|upper_aerodigestive_tract(1)	24				GBM - Glioblastoma multiforme(3;3.18e-11)|all cancers(3;0.00526)		TATGCCCCACCTCACGTTCCT	0.418																																																	1	Substitution - coding silent(1)	kidney(1)											226.0	195.0	206.0					1																	50956260		2203	4300	6503	SO:0001630	splice_region_variant	11124			AF132938	CCDS554.1	1p32.3	2012-09-20			ENSG00000185104	ENSG00000185104		"""UBX domain containing"""	3578	protein-coding gene	gene with protein product	"""TNFRSF6-associated factor 1"", ""UBX domain protein 3A"""	604460				10462485	Standard	NM_007051		Approved	CGI-03, hFAF1, HFAF1s, UBXD12, UBXN3A	uc001cse.1	Q9UNN5	OTTHUMG00000007930	ENST00000396153.2:c.1653+1G>A	1.37:g.50956260C>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q549F0|Q9UF34|Q9UNT3|Q9Y2Z3	Silent	SNP	ENST00000396153.2	37	CCDS554.1																																																																																				0.418	FAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021807.1		NM_007051	Silent
FCGR3A	2214	broad.mit.edu;hgsc.bcm.edu	37	1	161599827	161599827	+	Intron	SNP	T	T	G			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr1:161599827T>G	ENST00000540048.1	-	2	94				FCGR2B_ENST00000367962.4_Intron|FCGR3B_ENST00000294800.3_Splice_Site|FCGR2B_ENST00000428605.2_Intron|FCGR2B_ENST00000367960.5_Intron|FCGR2B_ENST00000403078.3_Intron|FCGR3B_ENST00000531221.1_Splice_Site|FCGR3B_ENST00000367964.2_Splice_Site			P08637	FCG3A_HUMAN	Fc fragment of IgG, low affinity IIIa, receptor (CD16a)						Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of immune response (GO:0050776)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.?(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	24	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Intravenous Immunoglobulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	GGAGATCTTCTGAGGAGCCAA	0.557																																																	1	Unknown(1)	kidney(1)											22.0	26.0	25.0					1																	161599827		2092	4254	6346	SO:0001627	intron_variant	2215			BC036723	CCDS1232.1, CCDS44266.1	1q23	2014-09-17	2005-02-02		ENSG00000203747	ENSG00000203747		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3619	protein-coding gene	gene with protein product		146740	"""Fc fragment of IgG, low affinity IIIa, receptor for (CD16)"""	FCGR3, FCG3		2139735	Standard	NM_001127592		Approved	CD16, CD16a	uc001gar.3	P08637	OTTHUMG00000034466	ENST00000540048.1:c.61+330A>C	1.37:g.161599827T>G		Somatic		WXS	Illumina HiSeq	Phase_I	A2N6W9|Q53FJ0|Q53FL6|Q5EBR4|Q65ZM6|Q6PIJ0	Splice_Site	SNP	ENST00000540048.1	37		.	.	.	.	.	.	.	.	.	.	T	9.433	1.086123	0.20390	.	.	ENSG00000162747	ENST00000367964;ENST00000294800;ENST00000531221;ENST00000534776	.	.	.	2.79	0.322	0.15888	.	.	.	.	.	.	.	.	.	.	.	0.21020	N	0.99981	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.6939	0.12793	0.0:0.31:0.0:0.69	.	.	.	.	.	-1	.	.	.	-	.	.	FCGR3B	159866451	0.227000	0.23707	0.019000	0.16419	0.484000	0.33280	2.079000	0.41577	-0.049000	0.13379	0.319000	0.21371	.		0.557	FCGR3A-203	KNOWN	basic|appris_principal	protein_coding	protein_coding			NM_000569	
GEMIN5	25929	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	154270986	154270986	+	Silent	SNP	G	G	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr5:154270986G>A	ENST00000285873.7	-	26	4152	c.4077C>T	c.(4075-4077)ctC>ctT	p.L1359L		NM_001252156.1|NM_015465.4	NP_001239085.1|NP_056280.2	Q8TEQ6	GEMI5_HUMAN	gem (nuclear organelle) associated protein 5	1359					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|protein complex assembly (GO:0006461)|RNA metabolic process (GO:0016070)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)	poly(A) RNA binding (GO:0044822)|snRNA binding (GO:0017069)	p.L1359L(1)		breast(1)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			TTTCTGAAAAGAGCTCCTTAA	0.468																																																	1	Substitution - coding silent(1)	kidney(1)											156.0	153.0	154.0					5																	154270986		2203	4300	6503	SO:0001819	synonymous_variant	25929			AK022748	CCDS4330.1	5q34	2013-01-10			ENSG00000082516	ENSG00000082516		"""WD repeat domain containing"""	20043	protein-coding gene	gene with protein product		607005				11714716	Standard	NM_015465		Approved		uc003lvx.3	Q8TEQ6	OTTHUMG00000130189	ENST00000285873.7:c.4077C>T	5.37:g.154270986G>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q14CV0|Q8WWV4|Q969W4|Q9H9K3|Q9UFI5	Silent	SNP	ENST00000285873.7	37	CCDS4330.1																																																																																				0.468	GEMIN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252507.1			
GLI1	2735	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	57861144	57861144	+	Missense_Mutation	SNP	G	G	T	rs373249560		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr12:57861144G>T	ENST00000228682.2	+	9	1032	c.941G>T	c.(940-942)cGc>cTc	p.R314L	GLI1_ENST00000546141.1_Missense_Mutation_p.R273L|GLI1_ENST00000543426.1_Missense_Mutation_p.R186L	NM_005269.2	NP_005260.1	P08151	GLI1_HUMAN	GLI family zinc finger 1	314					cerebellar cortex morphogenesis (GO:0021696)|digestive tract morphogenesis (GO:0048546)|dorsal/ventral pattern formation (GO:0009953)|epidermal cell differentiation (GO:0009913)|lung development (GO:0030324)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|notochord regression (GO:0060032)|osteoblast differentiation (GO:0001649)|pituitary gland development (GO:0021983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proximal/distal pattern formation (GO:0009954)|regulation of smoothened signaling pathway (GO:0008589)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938)|spermatogenesis (GO:0007283)|ventral midline development (GO:0007418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|primary cilium (GO:0072372)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|transcription regulatory region DNA binding (GO:0044212)	p.R314L(1)		NS(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(8)|lung(22)|ovary(6)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69			GBM - Glioblastoma multiforme(3;3.99e-32)			TCATACTCACGCCTCGAAAAC	0.542																																					Pancreas(157;841 1936 10503 41495 50368)												1	Substitution - Missense(1)	kidney(1)											110.0	97.0	101.0					12																	57861144		2203	4300	6503	SO:0001583	missense	2735				CCDS8940.1, CCDS53806.1, CCDS53807.1	12q13.2-q13.3	2013-01-25	2009-03-05	2005-01-14		ENSG00000111087		"""Zinc fingers, C2H2-type"""	4317	protein-coding gene	gene with protein product		165220	"""glioma-associated oncogene homolog 1 (zinc finger protein)"", ""glioma-associated oncogene family zinc finger 1"""	GLI		2850480	Standard	NM_005269		Approved		uc001snx.3	P08151		ENST00000228682.2:c.941G>T	12.37:g.57861144G>T	ENSP00000228682:p.Arg314Leu	Somatic		WXS	Illumina HiSeq	Phase_I	D0EUY3|E9PQQ9|F5H6H8|Q8TDN9	Missense_Mutation	SNP	ENST00000228682.2	37	CCDS8940.1	.	.	.	.	.	.	.	.	.	.	G	34	5.334825	0.95758	.	.	ENSG00000111087	ENST00000543426;ENST00000228682;ENST00000546141;ENST00000528467;ENST00000443131	T;T;T;T	0.42131	0.98;0.98;0.98;0.98	4.64	4.64	0.57946	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.53938	D	0.000056	T	0.53642	0.1809	L	0.31157	0.91	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.58188	-0.7680	10	0.87932	D	0	.	16.8311	0.85944	0.0:0.0:1.0:0.0	.	314	P08151	GLI1_HUMAN	L	186;314;273;273;186	ENSP00000437607:R186L;ENSP00000228682:R314L;ENSP00000441006:R273L;ENSP00000434408:R273L	ENSP00000228682:R314L	R	+	2	0	GLI1	56147411	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.561000	0.98142	2.575000	0.86900	0.563000	0.77884	CGC		0.542	GLI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394197.1		NM_005269	
GPR116	221395	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	46826546	46826546	+	Missense_Mutation	SNP	C	C	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr6:46826546C>T	ENST00000283296.7	-	17	3382	c.3094G>A	c.(3094-3096)Gtt>Att	p.V1032I	GPR116_ENST00000362015.4_Missense_Mutation_p.V1032I|GPR116_ENST00000545669.1_Missense_Mutation_p.V461I|GPR116_ENST00000456426.2_Missense_Mutation_p.V890I|GPR116_ENST00000265417.7_Missense_Mutation_p.V1032I	NM_001098518.1	NP_001091988.1	Q8IZF2	GP116_HUMAN	G protein-coupled receptor 116	1032					energy reserve metabolic process (GO:0006112)|fat cell differentiation (GO:0045444)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|neuropeptide signaling pathway (GO:0007218)|regulation of lipid metabolic process (GO:0019216)|surfactant homeostasis (GO:0043129)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.V1032I(1)		breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(21)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59			Lung(136;0.192)			GCTTCCACAACTAGACAGGCT	0.507																																					NSCLC(59;410 1274 8751 36715 50546)												1	Substitution - Missense(1)	kidney(1)											48.0	49.0	49.0					6																	46826546		2203	4300	6503	SO:0001583	missense	221395			AB018301	CCDS4919.1	6p12.3	2014-08-08			ENSG00000069122	ENSG00000069122		"""-"", ""GPCR / Class B : Orphans"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	19030	protein-coding gene	gene with protein product						12435584	Standard	NM_001098518		Approved	DKFZp564O1923, KIAA0758	uc003oyo.3	Q8IZF2	OTTHUMG00000014793	ENST00000283296.7:c.3094G>A	6.37:g.46826546C>T	ENSP00000283296:p.Val1032Ile	Somatic		WXS	Illumina HiSeq	Phase_I	O94858|Q5TF06|Q6RGN2|Q86SP0|Q9Y3Z2	Missense_Mutation	SNP	ENST00000283296.7	37	CCDS4919.1	.	.	.	.	.	.	.	.	.	.	C	2.499	-0.315709	0.05422	.	.	ENSG00000069122	ENST00000452370;ENST00000283296;ENST00000362015;ENST00000456426;ENST00000545557;ENST00000265417;ENST00000545669	T;T;T;T;T	0.36878	1.23;1.23;1.23;1.23;1.23	5.61	3.8	0.43715	GPCR, family 2-like (1);	0.340286	0.24899	N	0.034717	T	0.03695	0.0105	N	0.01257	-0.925	0.09310	N	1	B;B;B;B;B	0.25521	0.009;0.003;0.128;0.006;0.128	B;B;B;B;B	0.26517	0.01;0.015;0.07;0.028;0.07	T	0.35599	-0.9782	10	0.02654	T	1	-10.0018	12.0363	0.53427	0.0:0.8328:0.0:0.1672	.	461;587;1032;890;1032	F5GWK9;B4DTV3;E9PBS6;Q8IZF2-3;Q8IZF2	.;.;.;.;GP116_HUMAN	I	1032;1032;1032;890;403;1032;461	ENSP00000283296:V1032I;ENSP00000354563:V1032I;ENSP00000412866:V890I;ENSP00000265417:V1032I;ENSP00000441581:V461I	ENSP00000265417:V1032I	V	-	1	0	GPR116	46934505	0.010000	0.17322	0.166000	0.22797	0.733000	0.41908	0.177000	0.16801	2.642000	0.89623	0.650000	0.86243	GTT		0.507	GPR116-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040806.2		NM_015234	
GPR98	84059	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	90074272	90074272	+	Missense_Mutation	SNP	A	A	C			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr5:90074272A>C	ENST00000405460.2	+	63	12791	c.12695A>C	c.(12694-12696)aAa>aCa	p.K4232T	GPR98_ENST00000425867.2_5'Flank	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	4232	Calx-beta 28. {ECO:0000305|PubMed:11606593}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.K4232T(1)		NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		CCCGAGGAAAAAAGCTTCTAT	0.453																																																	1	Substitution - Missense(1)	kidney(1)											38.0	37.0	37.0					5																	90074272		1946	4148	6094	SO:0001583	missense	84059			AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"""-"", ""GPCR / Class B : Orphans"""	17416	protein-coding gene	gene with protein product		602851	"""monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"""	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.12695A>C	5.37:g.90074272A>C	ENSP00000384582:p.Lys4232Thr	Somatic		WXS	Illumina HiSeq	Phase_I	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	A	12.16	1.853344	0.32791	.	.	ENSG00000164199	ENST00000405460;ENST00000296619	T	0.26373	1.74	5.62	4.48	0.54585	.	0.092352	0.64402	D	0.000001	T	0.24586	0.0596	L	0.56769	1.78	0.80722	D	1	P	0.42827	0.791	B	0.38378	0.272	T	0.03503	-1.1030	10	0.41790	T	0.15	.	10.9944	0.47567	0.9273:0.0:0.0727:0.0	.	4232	Q8WXG9	GPR98_HUMAN	T	4232	ENSP00000384582:K4232T	ENSP00000296619:K4232T	K	+	2	0	GPR98	90110028	1.000000	0.71417	0.845000	0.33349	0.012000	0.07955	5.401000	0.66326	2.119000	0.64992	0.533000	0.62120	AAA		0.453	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2		NM_032119	
GREB1	9687	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	11706655	11706655	+	Silent	SNP	G	G	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr2:11706655G>A	ENST00000381486.2	+	4	627	c.327G>A	c.(325-327)gaG>gaA	p.E109E	GREB1_ENST00000263834.5_Silent_p.E109E|GREB1_ENST00000389825.3_5'UTR|GREB1_ENST00000234142.5_Silent_p.E109E|GREB1_ENST00000381483.2_Silent_p.E109E	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	109						integral component of membrane (GO:0016021)		p.E109E(3)		breast(3)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)	30	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		TTTCCAACGAGCCCATGGATG	0.637																																					Ovarian(39;850 945 2785 23371 33093)												3	Substitution - coding silent(3)	kidney(3)											80.0	76.0	77.0					2																	11706655		2203	4300	6503	SO:0001819	synonymous_variant	9687				CCDS33146.1, CCDS33147.1, CCDS42655.1	2p25.1	2010-02-17	2009-09-10		ENSG00000196208	ENSG00000196208			24885	protein-coding gene	gene with protein product	"""gene regulated by estrogen in breast cancer"""	611736				11103799	Standard	NM_014668		Approved	KIAA0575	uc002rbk.1	Q4ZG55	OTTHUMG00000141276	ENST00000381486.2:c.327G>A	2.37:g.11706655G>A		Somatic		WXS	Illumina HiSeq	Phase_I	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Silent	SNP	ENST00000381486.2	37	CCDS42655.1																																																																																				0.637	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1		NM_014668	
RP3-470B24.5	0	hgsc.bcm.edu	37	6	168376967	168376968	+	lincRNA	INS	-	-	G	rs74216590|rs200262961		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr6:168376967_168376968insG	ENST00000538528.1	-	0	651_652																											CTGCAGTGTGTTGGGAGGAGGA	0.634																																																	0																																												100128124																															6.37:g.168376967_168376968insG		Somatic		WXS	Illumina HiSeq	Phase_I		Frame_Shift_Ins	INS	ENST00000538528.1	37																																																																																					0.634	RP3-470B24.5-201	KNOWN	basic	lincRNA	lincRNA				
RP3-470B24.5	0	hgsc.bcm.edu	37	6	168376968	168376969	+	lincRNA	INS	-	-	G	rs74216590|rs200262961		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr6:168376968_168376969insG	ENST00000538528.1	-	0	650_651																											TGCAGTGTGTTGGGAGGAGGAG	0.639																																																	0																																												100128124																															6.37:g.168376971_168376971dupG		Somatic		WXS	Illumina HiSeq	Phase_I		Frame_Shift_Ins	INS	ENST00000538528.1	37																																																																																					0.639	RP3-470B24.5-201	KNOWN	basic	lincRNA	lincRNA				
HMGCS2	3158	broad.mit.edu;ucsc.edu	37	1	120307055	120307055	+	Missense_Mutation	SNP	T	T	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr1:120307055T>A	ENST00000369406.3	-	2	348	c.299A>T	c.(298-300)gAg>gTg	p.E100V	HMGCS2_ENST00000544913.2_Missense_Mutation_p.E100V|HMGCS2_ENST00000476640.1_5'UTR	NM_005518.3	NP_005509.1	P54868	HMCS2_HUMAN	3-hydroxy-3-methylglutaryl-CoA synthase 2 (mitochondrial)	100					cellular ketone body metabolic process (GO:0046950)|cellular lipid metabolic process (GO:0044255)|cholesterol biosynthetic process (GO:0006695)|isoprenoid biosynthetic process (GO:0008299)|ketone body biosynthetic process (GO:0046951)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	hydroxymethylglutaryl-CoA synthase activity (GO:0004421)	p.E100V(1)		NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(1)|lung(13)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	28	all_cancers(5;6.38e-10)|all_epithelial(5;1.1e-10)|Melanoma(3;1.93e-05)|Breast(55;0.218)|all_neural(166;0.219)	all_lung(203;1.29e-06)|Lung NSC(69;9.35e-06)|all_epithelial(167;0.00124)		Lung(183;0.0112)|LUSC - Lung squamous cell carcinoma(189;0.0595)		GTTGATGTCCTCTTGGACTGA	0.552																																																	1	Substitution - Missense(1)	kidney(1)											157.0	141.0	147.0					1																	120307055		2203	4300	6503	SO:0001583	missense	3158			BC044217	CCDS905.1, CCDS53353.1	1p13-p12	2014-09-17	2010-04-30		ENSG00000134240	ENSG00000134240			5008	protein-coding gene	gene with protein product		600234	"""3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2 (mitochondrial)"""			7851882, 7893153	Standard	NM_005518		Approved		uc001eid.3	P54868	OTTHUMG00000012101	ENST00000369406.3:c.299A>T	1.37:g.120307055T>A	ENSP00000358414:p.Glu100Val	Somatic		WXS	Illumina GAIIx	Phase_I	B7Z8R3|D3Y5K6|Q5SZU2|Q6IBF4	Missense_Mutation	SNP	ENST00000369406.3	37	CCDS905.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.485875	0.84854	.	.	ENSG00000134240	ENST00000369406;ENST00000544913	D;D	0.91843	-2.92;-2.62	5.22	5.22	0.72569	Hydroxymethylglutaryl-coenzyme A synthase, N-terminal (1);Thiolase-like, subgroup (1);Thiolase-like (1);	0.000000	0.64402	D	0.000007	D	0.97732	0.9256	H	0.99211	4.47	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99174	1.0865	10	0.87932	D	0	-0.2132	14.232	0.65898	0.0:0.0:0.0:1.0	.	100;100	B7Z8R3;P54868	.;HMCS2_HUMAN	V	100	ENSP00000358414:E100V;ENSP00000439495:E100V	ENSP00000358414:E100V	E	-	2	0	HMGCS2	120108578	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.541000	0.82084	2.097000	0.63578	0.477000	0.44152	GAG		0.552	HMGCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033469.2		NM_005518	
INO80	54617	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	41279359	41279359	+	Silent	SNP	G	G	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr15:41279359G>A	ENST00000361937.3	-	31	4186	c.3762C>T	c.(3760-3762)ttC>ttT	p.F1254F	INO80_ENST00000561244.1_5'UTR|INO80_ENST00000401393.3_Silent_p.F1254F			Q9ULG1	INO80_HUMAN	INO80 complex subunit	1254	Assembles INO80 complex module consisting of conserved components INO80B, INO80C, ACTR5, RVBL1, RVBL2.|Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|mitotic sister chromatid segregation (GO:0000070)|positive regulation of cell growth (GO:0030307)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|spindle assembly (GO:0051225)|UV-damage excision repair (GO:0070914)	Ino80 complex (GO:0031011)|microtubule (GO:0005874)|nucleus (GO:0005634)	alpha-tubulin binding (GO:0043014)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)	p.F1254F(2)		NS(1)|breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						TATCTGGTTTGAAGTTCCCAC	0.438																																																	2	Substitution - coding silent(2)	kidney(2)											109.0	91.0	97.0					15																	41279359		2203	4300	6503	SO:0001819	synonymous_variant	54617			AB033085	CCDS10071.1	15q15.1	2013-08-21	2013-08-21	2008-08-07	ENSG00000128908	ENSG00000128908	3.6.1.3	"""INO80 complex subunits"""	26956	protein-coding gene	gene with protein product	"""INO80 complex subunit A"""	610169	"""INO80 complex homolog 1 (S. cerevisiae)"", ""INO80 homolog (S. cerevisiae)"""	INOC1		16298340, 16230350, 20237820	Standard	NM_017553		Approved	KIAA1259, Ino80, hINO80, INO80A	uc001zni.3	Q9ULG1	OTTHUMG00000130209	ENST00000361937.3:c.3762C>T	15.37:g.41279359G>A		Somatic		WXS	Illumina HiSeq	Phase_I	A6H8X4|Q9NTG6	Silent	SNP	ENST00000361937.3	37	CCDS10071.1																																																																																				0.438	INO80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252527.2		NM_017553	
JAK2	3717	broad.mit.edu;hgsc.bcm.edu	37	9	5126444	5126444	+	Nonsense_Mutation	SNP	G	G	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr9:5126444G>T	ENST00000381652.3	+	24	3783	c.3289G>T	c.(3289-3291)Gag>Tag	p.E1097*	JAK2_ENST00000539801.1_Nonsense_Mutation_p.E1097*|JAK2_ENST00000544510.1_Nonsense_Mutation_p.E948*|JAK2_ENST00000487310.1_3'UTR	NM_004972.3	NP_004963.1	O60674	JAK2_HUMAN	Janus kinase 2	1097	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin filament polymerization (GO:0030041)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activation of JAK2 kinase activity (GO:0042977)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon regeneration (GO:0031103)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular component movement (GO:0006928)|cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|G-protein coupled receptor signaling pathway (GO:0007186)|growth hormone receptor signaling pathway (GO:0060396)|histone H3-Y41 phosphorylation (GO:0035409)|hormone-mediated signaling pathway (GO:0009755)|host programmed cell death induced by symbiont (GO:0034050)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-12-mediated signaling pathway (GO:0035722)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|mammary gland epithelium development (GO:0061180)|mesoderm development (GO:0007498)|mineralocorticoid receptor signaling pathway (GO:0031959)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of DNA binding (GO:0043392)|negative regulation of heart contraction (GO:0045822)|negative regulation of neuron apoptotic process (GO:0043524)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell activation (GO:0050867)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA binding (GO:0043388)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|positive regulation of inflammatory response (GO:0050729)|positive regulation of insulin secretion (GO:0032024)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to antibiotic (GO:0046677)|response to hydroperoxide (GO:0033194)|response to interleukin-12 (GO:0070671)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|tyrosine phosphorylation of STAT protein (GO:0007260)|tyrosine phosphorylation of Stat1 protein (GO:0042508)|tyrosine phosphorylation of Stat3 protein (GO:0042503)|tyrosine phosphorylation of Stat5 protein (GO:0042506)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endosome lumen (GO:0031904)|membrane raft (GO:0045121)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|heme binding (GO:0020037)|histone binding (GO:0042393)|histone kinase activity (H3-Y41 specific) (GO:0035401)|interleukin-12 receptor binding (GO:0005143)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|SH2 domain binding (GO:0042169)	p.E1097*(1)	BCR/JAK2(6)|SSBP2/JAK2(4)|SEC31A/JAK2(4)|ETV6/JAK2(11)|PCM1/JAK2(30)|PAX5/JAK2(18)	breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(32944)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(4)|skin(2)|urinary_tract(1)	32998	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0198)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0237)|Lung(218;0.133)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	ATGCCCAGATGAGGTAACAAT	0.363		1	"""T, Mis, O"""	"""ETV6, PCM1, BCR"""	"""ALL, AML, MPD,  CML"""				Polycythemia Vera, Familial																															Dom	yes		9	9p24	3717	Janus kinase 2		L	1	Substitution - Nonsense(1)	kidney(1)											92.0	85.0	87.0					9																	5126444		2203	4300	6503	SO:0001587	stop_gained	3717	Familial Cancer Database			CCDS6457.1	9p24	2014-09-17	2009-04-23		ENSG00000096968	ENSG00000096968	2.7.10.1	"""SH2 domain containing"""	6192	protein-coding gene	gene with protein product		147796				1848670	Standard	NM_004972		Approved	JTK10	uc003ziw.3	O60674	OTTHUMG00000019490	ENST00000381652.3:c.3289G>T	9.37:g.5126444G>T	ENSP00000371067:p.Glu1097*	Somatic		WXS	Illumina HiSeq	Phase_I	O14636|O75297	Nonsense_Mutation	SNP	ENST00000381652.3	37	CCDS6457.1	.	.	.	.	.	.	.	.	.	.	G	43	10.006360	0.99315	.	.	ENSG00000096968	ENST00000539801;ENST00000381652;ENST00000544510	.	.	.	5.41	4.48	0.54585	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.44086	T	0.13	-15.7092	15.5385	0.76021	0.0:0.0:0.8615:0.1385	.	.	.	.	X	1097;1097;948	.	ENSP00000371067:E1097X	E	+	1	0	JAK2	5116444	1.000000	0.71417	1.000000	0.80357	0.871000	0.50021	6.325000	0.72901	2.539000	0.85634	0.655000	0.94253	GAG		0.363	JAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051609.1			
KIF4A	24137	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	69622483	69622483	+	Missense_Mutation	SNP	C	C	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chrX:69622483C>T	ENST00000374403.3	+	23	2639	c.2557C>T	c.(2557-2559)Cgc>Tgc	p.R853C	KIF4A_ENST00000374388.3_Missense_Mutation_p.R853C	NM_012310.4	NP_036442.3	O95239	KIF4A_HUMAN	kinesin family member 4A	853	Interaction with PRC1.				anterograde axon cargo transport (GO:0008089)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|organelle organization (GO:0006996)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)	p.R853C(1)		breast(6)|endometrium(9)|kidney(3)|large_intestine(8)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	51						ACCAAAACAACGCTGGGAGAA	0.468																																																	1	Substitution - Missense(1)	kidney(1)											89.0	72.0	77.0					X																	69622483		2203	4300	6503	SO:0001583	missense	24137			AF179308	CCDS14401.1	Xq13.1	2008-08-11			ENSG00000090889	ENSG00000090889		"""Kinesins"""	13339	protein-coding gene	gene with protein product	"""chromokinesin"""	300521				10773663	Standard	NM_012310		Approved	KIF4-G1, KIF4, HSA271784, FLJ12530, FLJ12655, FLJ14204, FLJ20631	uc004dyg.3	O95239	OTTHUMG00000021775	ENST00000374403.3:c.2557C>T	X.37:g.69622483C>T	ENSP00000363524:p.Arg853Cys	Somatic		WXS	Illumina HiSeq	Phase_I	B2R7V5|D3DVU4|Q86TN3|Q86XX7|Q9NNY6|Q9NY24|Q9UMW3	Missense_Mutation	SNP	ENST00000374403.3	37	CCDS14401.1	.	.	.	.	.	.	.	.	.	.	C	14.30	2.495056	0.44352	.	.	ENSG00000090889	ENST00000374388;ENST00000374403;ENST00000544650	T;T	0.71222	-0.55;-0.53	5.3	4.42	0.53409	.	0.098532	0.45606	N	0.000349	T	0.67468	0.2896	M	0.81341	2.54	0.80722	D	1	B	0.15930	0.015	B	0.04013	0.001	T	0.64795	-0.6323	9	.	.	.	.	7.6465	0.28323	0.1614:0.7523:0.0:0.0862	.	853	O95239	KIF4A_HUMAN	C	853;853;155	ENSP00000363509:R853C;ENSP00000363524:R853C	.	R	+	1	0	KIF4A	69539208	0.999000	0.42202	0.999000	0.59377	0.937000	0.57800	2.689000	0.46993	2.443000	0.82685	0.594000	0.82650	CGC		0.468	KIF4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057068.1		NM_012310	
UBAP1L	390595	broad.mit.edu;ucsc.edu	37	15	65386873	65386873	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr15:65386873C>A	ENST00000559089.1	-	5	1171	c.951G>T	c.(949-951)caG>caT	p.Q317H	UBAP1L_ENST00000502113.2_Missense_Mutation_p.Q317H			F5GYI3	UBA1L_HUMAN	ubiquitin associated protein 1-like	317								p.Q317H(2)		breast(1)|endometrium(1)|kidney(1)	3						CCTCATATCCCTGACGTAACA	0.632																																																	2	Substitution - Missense(2)	kidney(2)											81.0	74.0	76.0					15																	65386873		691	1590	2281	SO:0001583	missense	0				CCDS53948.1	15q22.31	2011-08-15			ENSG00000246922	ENSG00000246922			40028	protein-coding gene	gene with protein product							Standard	NM_001163692		Approved		uc010uit.2	F5GYI3		ENST00000559089.1:c.951G>T	15.37:g.65386873C>A	ENSP00000454012:p.Gln317His	Somatic		WXS	Illumina GAIIx	Phase_I		Missense_Mutation	SNP	ENST00000559089.1	37	CCDS53948.1	.	.	.	.	.	.	.	.	.	.	C	12.92	2.082706	0.36758	.	.	ENSG00000246922	ENST00000502113	.	.	.	4.49	2.51	0.30379	.	.	.	.	.	T	0.44052	0.1275	N	0.14661	0.345	0.37713	D	0.924658	D	0.89917	1.0	D	0.70935	0.971	T	0.48115	-0.9063	8	0.56958	D	0.05	.	4.4425	0.11580	0.1531:0.5842:0.0:0.2628	.	317	F5GYI3	UBA1L_HUMAN	H	317	.	ENSP00000440243:Q317H	Q	-	3	2	AC013553.1	63173926	1.000000	0.71417	0.992000	0.48379	0.263000	0.26337	1.148000	0.31614	0.392000	0.25172	-0.300000	0.09419	CAG		0.632	UBAP1L-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418469.1		NM_001163692	
LPHN3	23284	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	62800598	62800598	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr4:62800598C>A	ENST00000514591.1	+	13	2278	c.1949C>A	c.(1948-1950)gCt>gAt	p.A650D	LPHN3_ENST00000511324.1_Missense_Mutation_p.A718D|LPHN3_ENST00000545650.1_Missense_Mutation_p.A650D|LPHN3_ENST00000508946.1_Missense_Mutation_p.A650D|LPHN3_ENST00000514157.1_Missense_Mutation_p.A650D|LPHN3_ENST00000508693.1_Missense_Mutation_p.A718D|LPHN3_ENST00000506700.1_Missense_Mutation_p.A650D|LPHN3_ENST00000514996.1_Missense_Mutation_p.A650D|LPHN3_ENST00000512091.2_Missense_Mutation_p.A650D|LPHN3_ENST00000509896.1_Missense_Mutation_p.A718D|LPHN3_ENST00000504896.1_Missense_Mutation_p.A650D|LPHN3_ENST00000506720.1_Missense_Mutation_p.A718D|LPHN3_ENST00000508078.1_3'UTR|LPHN3_ENST00000507164.1_Missense_Mutation_p.A718D|LPHN3_ENST00000507625.1_Missense_Mutation_p.A718D|LPHN3_ENST00000506746.1_Missense_Mutation_p.A718D			Q9HAR2	LPHN3_HUMAN	latrophilin 3	637					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)	p.A650D(3)		breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(21)|lung(73)|ovary(1)|pancreas(1)|prostate(6)|upper_aerodigestive_tract(1)	125						CAGCCACAAGCTTTGAATGCA	0.478																																																	3	Substitution - Missense(3)	kidney(3)											84.0	86.0	86.0					4																	62800598		2046	4215	6261	SO:0001583	missense	23284			AB018311	CCDS54768.1	4q13.1	2014-08-08				ENSG00000150471		"""-"", ""GPCR / Class B : Orphans"""	20974	protein-coding gene	gene with protein product						10994649	Standard	NM_015236		Approved	KIAA0768, LEC3	uc010ihh.3	Q9HAR2		ENST00000514591.1:c.1949C>A	4.37:g.62800598C>A	ENSP00000422533:p.Ala650Asp	Somatic		WXS	Illumina HiSeq	Phase_I	E9PE04|O94867|Q9NWK5	Missense_Mutation	SNP	ENST00000514591.1	37	CCDS54768.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.66|17.66	3.445199|3.445199	0.63178|0.63178	.|.	.|.	ENSG00000150471|ENSG00000150471	ENST00000512091;ENST00000514591;ENST00000509896;ENST00000511324;ENST00000506700;ENST00000534975;ENST00000545650;ENST00000295349;ENST00000280009;ENST00000507164;ENST00000508693;ENST00000507625;ENST00000514157;ENST00000504896;ENST00000508946;ENST00000506720;ENST00000506746;ENST00000514996|ENST00000502815	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T|.	0.11169|.	2.8;2.8;2.8;2.8;2.8;2.8;2.8;2.8;2.8;2.8;2.8;2.8;2.8;2.8;2.8|.	5.43|5.43	5.43|5.43	0.79202|0.79202	Domain of unknown function DUF3497 (1);|.	0.109679|.	0.64402|.	D|.	0.000008|.	T|T	0.73024|0.73024	0.3534|0.3534	L|L	0.60455|0.60455	1.87|1.87	0.80722|0.80722	D|D	1|1	B;B;B|.	0.18166|.	0.026;0.026;0.021|.	B;B;B|.	0.19946|.	0.027;0.027;0.016|.	T|T	0.69198|0.69198	-0.5208|-0.5208	10|5	0.62326|.	D|.	0.03|.	.|.	19.4372|19.4372	0.94801|0.94801	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	650;637;650|.	E9PE04;Q9HAR2;Q9HAR2-2|.	.;LPHN3_HUMAN;.|.	D|R	650;650;718;718;650;637;650;637;650;718;718;718;650;650;650;718;718;650|107	ENSP00000423388:A650D;ENSP00000422533:A650D;ENSP00000423787:A718D;ENSP00000425033:A718D;ENSP00000424120:A650D;ENSP00000439831:A650D;ENSP00000421476:A718D;ENSP00000424030:A718D;ENSP00000421372:A718D;ENSP00000425201:A650D;ENSP00000423434:A650D;ENSP00000421627:A650D;ENSP00000420931:A718D;ENSP00000425884:A718D;ENSP00000424258:A650D|.	ENSP00000280009:A650D|.	A|S	+|+	2|3	0|2	LPHN3|LPHN3	62483193|62483193	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.987000|0.987000	0.75469|0.75469	7.651000|7.651000	0.83577|0.83577	2.827000|2.827000	0.97445|0.97445	0.650000|0.650000	0.86243|0.86243	GCT|AGC		0.478	LPHN3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000361765.1			
MYO10	4651	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	16818168	16818168	+	Missense_Mutation	SNP	C	C	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr5:16818168C>T	ENST00000513610.1	-	3	683	c.229G>A	c.(229-231)Ggc>Agc	p.G77S	MYO10_ENST00000507288.1_Missense_Mutation_p.G77S	NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	77	Myosin motor.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)	p.G77S(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						ATGATGGAGCCGCCATGGAGC	0.448																																																	1	Substitution - Missense(1)	kidney(1)											56.0	57.0	57.0					5																	16818168		1948	4135	6083	SO:0001583	missense	4651			AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"""Myosins / Myosin superfamily : Class X"", ""Pleckstrin homology (PH) domain containing"""	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.229G>A	5.37:g.16818168C>T	ENSP00000421280:p.Gly77Ser	Somatic		WXS	Illumina HiSeq	Phase_I	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Missense_Mutation	SNP	ENST00000513610.1	37	CCDS54834.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.814492	0.90790	.	.	ENSG00000145555	ENST00000513610;ENST00000513882;ENST00000502436;ENST00000507288	T;T;T;D	0.95035	-0.52;-0.52;-0.52;-3.59	6.08	6.08	0.98989	Myosin head, motor domain (2);	.	.	.	.	D	0.94909	0.8354	L	0.44542	1.39	0.80722	D	1	D;P;D	0.58970	0.971;0.918;0.984	P;P;P	0.52424	0.453;0.653;0.698	D	0.94757	0.7932	9	0.72032	D	0.01	.	20.6634	0.99662	0.0:1.0:0.0:0.0	.	77;44;77	Q8IVX5;E9PCN3;Q9HD67	.;.;MYO10_HUMAN	S	77;88;44;77	ENSP00000421280:G77S;ENSP00000421309:G88S;ENSP00000426783:G44S;ENSP00000426664:G77S	ENSP00000426783:G44S	G	-	1	0	MYO10	16871168	1.000000	0.71417	0.926000	0.36857	0.568000	0.35870	7.102000	0.77005	2.894000	0.99253	0.655000	0.94253	GGC		0.448	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1		NM_012334	
NASP	4678	hgsc.bcm.edu	37	1	46073362	46073362	+	Missense_Mutation	SNP	A	A	G	rs75187774	byFrequency	TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr1:46073362A>G	ENST00000350030.3	+	6	866	c.779A>G	c.(778-780)cAg>cGg	p.Q260R	NASP_ENST00000402363.3_Missense_Mutation_p.Q262R|NASP_ENST00000537798.1_Missense_Mutation_p.Q196R|NASP_ENST00000351223.3_Intron|NASP_ENST00000372052.4_Intron	NM_002482.3	NP_002473.2	P49321	NASP_HUMAN	nuclear autoantigenic sperm protein (histone-binding)	260	Glu-rich (acidic).				blastocyst development (GO:0001824)|cell cycle (GO:0007049)|cell proliferation (GO:0008283)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone exchange (GO:0043486)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)	Hsp90 protein binding (GO:0051879)			breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	17	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.211)					AAAGGAGGTCAGGAGAAGCAG	0.478																																																	0													45.0	47.0	46.0					1																	46073362		2203	4300	6503	SO:0001583	missense	4678			M97856	CCDS524.1, CCDS525.1, CCDS55597.1	1p34.1	2013-01-10			ENSG00000132780	ENSG00000132780		"""Tetratricopeptide (TTC) repeat domain containing"""	7644	protein-coding gene	gene with protein product		603185				1426632	Standard	NM_002482		Approved	FLB7527, FLJ31599, FLJ35510, MGC19722, MGC20372, MGC2297, DKFZp547F162, PRO1999	uc001coi.2	P49321	OTTHUMG00000007826	ENST00000350030.3:c.779A>G	1.37:g.46073362A>G	ENSP00000255120:p.Gln260Arg	Somatic		WXS	Illumina HiSeq	Phase_I	A8K6H2|B4DQP3|D3DQ07|F5H3J2|Q53GW5|Q5T622|Q5T625|Q96A69|Q9BTW2	Missense_Mutation	SNP	ENST00000350030.3	37	CCDS524.1	.	.	.	.	.	.	.	.	.	.	A	14.28	2.487349	0.44249	.	.	ENSG00000132780	ENST00000537798;ENST00000402363;ENST00000341288;ENST00000350030;ENST00000470768	D;D;D;D	0.94758	-3.51;-3.51;-3.51;-3.51	5.0	5.0	0.66597	.	0.414434	0.26446	N	0.024338	D	0.90417	0.7000	N	0.14661	0.345	0.27816	N	0.941959	B;P;D;B;P	0.54047	0.447;0.734;0.964;0.319;0.59	B;B;P;B;B	0.47981	0.202;0.188;0.563;0.1;0.202	D	0.85121	0.0969	9	.	.	.	-0.1249	15.3918	0.74751	1.0:0.0:0.0:0.0	.	196;260;160;260;262	F5H3J2;Q53H03;B4DS57;P49321;P49321-3	.;.;.;NASP_HUMAN;.	R	196;262;160;260;223	ENSP00000438871:Q196R;ENSP00000384529:Q262R;ENSP00000255120:Q260R;ENSP00000436924:Q223R	.	Q	+	2	0	NASP	45845949	0.321000	0.24625	1.000000	0.80357	0.958000	0.62258	1.592000	0.36676	2.182000	0.69389	0.528000	0.53228	CAG		0.478	NASP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021533.2		NM_002482	
NAV3	89795	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	78401106	78401106	+	Silent	SNP	C	C	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr12:78401106C>T	ENST00000397909.2	+	8	1961	c.1788C>T	c.(1786-1788)tcC>tcT	p.S596S	NAV3_ENST00000266692.7_Silent_p.S596S|NAV3_ENST00000228327.6_Silent_p.S596S|NAV3_ENST00000536525.2_Silent_p.S596S			Q8IVL0	NAV3_HUMAN	neuron navigator 3	596						membrane (GO:0016020)|nuclear envelope (GO:0005635)		p.S596S(1)		NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						CTTCTGGTTCCTGTACCATGA	0.522										HNSCC(70;0.22)																																							1	Substitution - coding silent(1)	kidney(1)											123.0	119.0	120.0					12																	78401106		2035	4194	6229	SO:0001819	synonymous_variant	89795			AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"""pore membrane and/or filament interacting like protein 1"", ""steerin 3"""	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.1788C>T	12.37:g.78401106C>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q8NFW7|Q9Y2E7	Silent	SNP	ENST00000397909.2	37																																																																																					0.522	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1		NM_001024383	
OGDHL	55753	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	50960187	50960187	+	Missense_Mutation	SNP	G	G	A	rs571841376		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr10:50960187G>A	ENST00000374103.4	-	5	671	c.586C>T	c.(586-588)Cgc>Tgc	p.R196C	OGDHL_ENST00000419399.1_Missense_Mutation_p.R139C|OGDHL_ENST00000432695.1_5'UTR	NM_018245.2	NP_060715.2	Q9ULD0	OGDHL_HUMAN	oxoglutarate dehydrogenase-like	196					glycolytic process (GO:0006096)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)	p.R196C(1)		central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)	61						ACCTCCAGGCGCCGAATGATC	0.567													G|||	1	0.000199681	0.0008	0.0	5008	,	,		18491	0.0		0.0	False		,,,				2504	0.0																1	Substitution - Missense(1)	kidney(1)											47.0	48.0	48.0					10																	50960187		2203	4300	6503	SO:0001583	missense	55753			AK001713	CCDS7234.1, CCDS44390.1, CCDS44391.1	10q11.23	2013-09-20			ENSG00000197444	ENSG00000197444			25590	protein-coding gene	gene with protein product						10574462	Standard	NM_018245		Approved	FLJ10851	uc001jie.3	Q9ULD0	OTTHUMG00000018200	ENST00000374103.4:c.586C>T	10.37:g.50960187G>A	ENSP00000363216:p.Arg196Cys	Somatic		WXS	Illumina HiSeq	Phase_I	A8K2G1|B4DKG2|B4E193|Q8TAN9|Q9NVA0	Missense_Mutation	SNP	ENST00000374103.4	37	CCDS7234.1	.	.	.	.	.	.	.	.	.	.	G	19.69	3.875196	0.72180	.	.	ENSG00000197444	ENST00000374103;ENST00000419399	T;T	0.14516	2.5;2.5	5.55	4.62	0.57501	.	0.000000	0.85682	D	0.000000	T	0.35566	0.0936	M	0.72894	2.215	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.07654	-1.0761	10	0.49607	T	0.09	.	13.3059	0.60352	0.0:0.0:0.7119:0.2881	.	139;196	Q9ULD0-2;Q9ULD0	.;OGDHL_HUMAN	C	196;139	ENSP00000363216:R196C;ENSP00000401356:R139C	ENSP00000363216:R196C	R	-	1	0	OGDHL	50630193	1.000000	0.71417	0.999000	0.59377	0.949000	0.60115	3.693000	0.54735	1.306000	0.44926	0.591000	0.81541	CGC		0.567	OGDHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048007.1		NM_018245	
PAIP2	51247	broad.mit.edu;ucsc.edu	37	5	138699475	138699475	+	Start_Codon_SNP	SNP	T	T	C			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr5:138699475T>C	ENST00000394795.2	+	2	993	c.2T>C	c.(1-3)aTg>aCg	p.M1T	PAIP2_ENST00000511381.1_Intron|PAIP2_ENST00000265192.4_Start_Codon_SNP_p.M1T|CTB-43P18.1_ENST00000503553.3_RNA|PAIP2_ENST00000510080.1_Start_Codon_SNP_p.M1T|PAIP2_ENST00000511706.1_Start_Codon_SNP_p.M1T			Q9BPZ3	PAIP2_HUMAN	poly(A) binding protein interacting protein 2	1					memory (GO:0007613)|negative regulation of translational initiation (GO:0045947)|regulation of long-term synaptic potentiation (GO:1900271)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	mRNA binding (GO:0003729)|translation repressor activity (GO:0030371)	p.M1T(1)		kidney(1)|large_intestine(2)|lung(2)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			ACATCAGCCATGAAAGATCCA	0.383																																																	1	Substitution - Missense(1)	kidney(1)											89.0	79.0	82.0					5																	138699475		2203	4300	6503	SO:0001582	initiator_codon_variant	51247			AF151052	CCDS4211.1	5q32	2008-02-05			ENSG00000120727	ENSG00000120727			17970	protein-coding gene	gene with protein product		605604				11172725, 16804161	Standard	NM_016480		Approved	PAIP2A	uc003led.3	Q9BPZ3	OTTHUMG00000129227	ENST00000394795.2:c.2T>C	5.37:g.138699475T>C	ENSP00000378275:p.Met1Thr	Somatic		WXS	Illumina GAIIx	Phase_I	B2RBI1|D3DQC6|Q49A06|Q9H0Y5|Q9P0Q8	Missense_Mutation	SNP	ENST00000394795.2	37	CCDS4211.1	.	.	.	.	.	.	.	.	.	.	T	14.30	2.495421	0.44352	.	.	ENSG00000120727	ENST00000507755;ENST00000265192;ENST00000511706;ENST00000394795;ENST00000510080	.	.	.	5.87	4.71	0.59529	.	0.000000	0.85682	D	0.000000	T	0.53318	0.1789	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.52320	-0.8591	8	0.87932	D	0	-22.1789	10.4267	0.44383	0.0:0.0745:0.0:0.9255	.	1	Q9BPZ3	PAIP2_HUMAN	T	1	.	ENSP00000265192:M1T	M	+	2	0	PAIP2	138727374	1.000000	0.71417	1.000000	0.80357	0.836000	0.47400	6.396000	0.73234	1.149000	0.42402	0.533000	0.62120	ATG		0.383	PAIP2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373002.1		NM_016480	Missense_Mutation
PBRM1	55193	broad.mit.edu;ucsc.edu	37	3	52597493	52597493	+	Nonsense_Mutation	SNP	G	G	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr3:52597493G>A	ENST00000296302.7	-	24	3893	c.3892C>T	c.(3892-3894)Cag>Tag	p.Q1298*	PBRM1_ENST00000337303.4_Nonsense_Mutation_p.Q1298*|RNU6ATAC16P_ENST00000408591.1_RNA|SMIM4_ENST00000476842.1_Intron|PBRM1_ENST00000409767.1_Nonsense_Mutation_p.Q1313*|PBRM1_ENST00000356770.4_Nonsense_Mutation_p.Q1266*|PBRM1_ENST00000394830.3_Nonsense_Mutation_p.Q1273*|PBRM1_ENST00000409057.1_Nonsense_Mutation_p.Q1298*|PBRM1_ENST00000409114.3_Nonsense_Mutation_p.Q1313*|PBRM1_ENST00000410007.1_Nonsense_Mutation_p.Q1273*			Q86U86	PB1_HUMAN	polybromo 1	1298					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.Q1298*(5)|p.Q1266*(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)		GGCTCCTTCTGAGGAACAATT	0.408			"""Mis, N, F, S, D, O"""		"""clear cell renal carcinoma, breast"""																																			Rec	yes		3	3p21	55193	polybromo 1		E	6	Substitution - Nonsense(6)	kidney(6)											101.0	94.0	96.0					3																	52597493		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.3892C>T	3.37:g.52597493G>A	ENSP00000296302:p.Gln1298*	Somatic		WXS	Illumina GAIIx	Phase_I	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Nonsense_Mutation	SNP	ENST00000296302.7	37		.	.	.	.	.	.	.	.	.	.	G	42	9.755557	0.99256	.	.	ENSG00000163939	ENST00000356770;ENST00000394830;ENST00000296302;ENST00000337303;ENST00000409057;ENST00000410007;ENST00000409114;ENST00000409767;ENST00000423351	.	.	.	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.28530	T	0.3	-10.7303	17.9915	0.89170	0.0:0.0:1.0:0.0	.	.	.	.	X	1266;1273;1298;1298;1298;1273;1313;1313;1297	.	ENSP00000296302:Q1298X	Q	-	1	0	PBRM1	52572533	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	7.818000	0.86416	2.746000	0.94184	0.561000	0.74099	CAG		0.408	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1		NM_018165	
PIWIL1	9271	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	130839159	130839159	+	Silent	SNP	G	G	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr12:130839159G>T	ENST00000245255.3	+	10	1394	c.1122G>T	c.(1120-1122)ggG>ggT	p.G374G		NM_001190971.1|NM_004764.4	NP_001177900.1|NP_004755.2	Q96J94	PIWL1_HUMAN	piwi-like RNA-mediated gene silencing 1	374	PAZ. {ECO:0000255|PROSITE- ProRule:PRU00142}.				gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|mRNA cap binding complex (GO:0005845)|P granule (GO:0043186)|polysome (GO:0005844)	mRNA binding (GO:0003729)|piRNA binding (GO:0034584)|single-stranded RNA binding (GO:0003727)	p.G374G(1)		breast(6)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(26)|ovary(2)|prostate(4)|skin(3)|urinary_tract(1)	57	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.02e-06)|Epithelial(86;3.85e-05)|all cancers(50;4.65e-05)		GCCCTGGGGGGACACTGCCAG	0.542																																																	1	Substitution - coding silent(1)	kidney(1)											62.0	70.0	67.0					12																	130839159		2203	4300	6503	SO:0001819	synonymous_variant	9271			AF104260	CCDS9268.1	12q24.33	2014-01-21	2013-02-15		ENSG00000125207	ENSG00000125207		"""Argonaute/PIWI family"""	9007	protein-coding gene	gene with protein product		605571	"""piwi (Drosophila)-like 1"", ""piwi-like 1 (Drosophila)"""			9851978, 12906857	Standard	NM_004764		Approved	PIWI, HIWI, CT80.1	uc001uik.3	Q96J94	OTTHUMG00000168382	ENST00000245255.3:c.1122G>T	12.37:g.130839159G>T		Somatic		WXS	Illumina HiSeq	Phase_I	A4F266|O95404|Q8NA60|Q8TBY5|Q96JD5	Silent	SNP	ENST00000245255.3	37	CCDS9268.1																																																																																				0.542	PIWIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399510.1			
PKHD1	5314	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	51612746	51612746	+	Nonsense_Mutation	SNP	G	G	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr6:51612746G>T	ENST00000371117.3	-	58	9943	c.9668C>A	c.(9667-9669)tCa>tAa	p.S3223*	PKHD1_ENST00000340994.4_Nonsense_Mutation_p.S3223*	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	3223					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)	p.S3223*(2)		NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					CAAGTTGGCTGAGTGCGGCTT	0.463																																																	2	Substitution - Nonsense(2)	kidney(2)											114.0	111.0	112.0					6																	51612746		2203	4300	6503	SO:0001587	stop_gained	5314			AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"""tigmin"", ""polyductin"", ""fibrocystin"""	606702	"""TIG multiple domains 1"""	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.9668C>A	6.37:g.51612746G>T	ENSP00000360158:p.Ser3223*	Somatic		WXS	Illumina HiSeq	Phase_I	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Nonsense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	G	51	18.494556	0.99906	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	.	.	.	5.75	5.75	0.90469	.	0.176101	0.40064	N	0.001186	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.9315	0.92568	0.0:0.0:1.0:0.0	.	.	.	.	X	3223	.	ENSP00000341097:S3223X	S	-	2	0	PKHD1	51720705	1.000000	0.71417	0.968000	0.41197	0.562000	0.35680	6.432000	0.73400	2.716000	0.92895	0.655000	0.94253	TCA		0.463	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1		NM_138694	
POFUT2	23275	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	21	46689908	46689908	+	Silent	SNP	G	G	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr21:46689908G>A	ENST00000349485.5	-	7	884	c.858C>T	c.(856-858)ggC>ggT	p.G286G	POFUT2_ENST00000471540.1_5'UTR|POFUT2_ENST00000331343.7_Silent_p.G286G	NM_133635.4	NP_598368.2	Q9Y2G5	OFUT2_HUMAN	protein O-fucosyltransferase 2	286					fucose metabolic process (GO:0006004)|mesoderm formation (GO:0001707)|protein O-linked fucosylation (GO:0036066)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of gene expression (GO:0010468)|regulation of secretion (GO:0051046)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)	peptide-O-fucosyltransferase activity (GO:0046922)	p.G286G(2)		breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|liver(1)|lung(9)|skin(2)|upper_aerodigestive_tract(2)	20				Colorectal(79;0.243)		CCAGGTAGGGGCCCCCTAGCG	0.602																																																	2	Substitution - coding silent(2)	kidney(2)											43.0	49.0	47.0					21																	46689908		2203	4300	6503	SO:0001819	synonymous_variant	23275			AJ203079	CCDS13719.1, CCDS13721.1	21q22.3	2013-03-06	2004-06-07	2004-06-09	ENSG00000186866	ENSG00000186866	2.4.1.221	"""Fucosyltransferases"""	14683	protein-coding gene	gene with protein product	"""peptide-O-fucosyltransferase"", ""GDP-fucose protein O-fucosyltransferase 2"""	610249	"""chromosome 21 open reading frame 80"""	C21orf80			Standard	NM_133635		Approved	KIAA0958, FUT13	uc002zhc.3	Q9Y2G5	OTTHUMG00000084874	ENST00000349485.5:c.858C>T	21.37:g.46689908G>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q6PJV1|Q7Z4N0|Q8WWU6|Q9BQS4|Q9BQS5|Q9UFY3	Silent	SNP	ENST00000349485.5	37	CCDS13719.1	.	.	.	.	.	.	.	.	.	.	G	0.488	-0.876883	0.02550	.	.	ENSG00000186866	ENST00000451615	.	.	.	4.67	-4.54	0.03452	.	.	.	.	.	T	0.36110	0.0955	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40251	-0.9573	4	.	.	.	-9.6324	0.9019	0.01276	0.2611:0.3432:0.164:0.2317	.	.	.	.	S	209	.	.	P	-	1	0	POFUT2	45514336	0.002000	0.14202	0.587000	0.28692	0.006000	0.05464	-1.981000	0.01490	-0.472000	0.06881	-0.932000	0.02703	CCC		0.602	POFUT2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192573.2		NM_015227	
PTPN6	5777	hgsc.bcm.edu;ucsc.edu	37	12	7064112	7064112	+	Frame_Shift_Del	DEL	C	C	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr12:7064112delC	ENST00000318974.9	+	4	715	c.471delC	c.(469-471)ggcfs	p.G157fs	PTPN6_ENST00000399448.1_Frame_Shift_Del_p.G159fs|PTPN6_ENST00000456013.1_Frame_Shift_Del_p.G157fs|PTPN6_ENST00000447931.2_Frame_Shift_Del_p.G118fs	NM_002831.5	NP_002822.2	P29350	PTN6_HUMAN	protein tyrosine phosphatase, non-receptor type 6	157	SH2 2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				abortive mitotic cell cycle (GO:0033277)|apoptotic process (GO:0006915)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cytokine-mediated signaling pathway (GO:0019221)|G-protein coupled receptor signaling pathway (GO:0007186)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|leukocyte migration (GO:0050900)|megakaryocyte development (GO:0035855)|natural killer cell mediated cytotoxicity (GO:0042267)|negative regulation of B cell receptor signaling pathway (GO:0050859)|negative regulation of cell proliferation (GO:0008285)|negative regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002924)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of T cell receptor signaling pathway (GO:0050860)|peptidyl-tyrosine dephosphorylation (GO:0035335)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell proliferation (GO:0008284)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|protein dephosphorylation (GO:0006470)|regulation of B cell differentiation (GO:0045577)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|T cell costimulation (GO:0031295)|type I interferon signaling pathway (GO:0060337)	alpha-beta T cell receptor complex (GO:0042105)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|prostate(3)	18						CCAAGGCTGGCCCAGGCTCCC	0.642																																																	0													51.0	57.0	55.0					12																	7064112		1998	4162	6160	SO:0001589	frameshift_variant	5777				CCDS41744.1, CCDS44820.1, CCDS44821.1	12p13.31	2013-02-14			ENSG00000111679	ENSG00000111679		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"", ""SH2 domain containing"""	9658	protein-coding gene	gene with protein product		176883				1639416	Standard	NM_080548		Approved	HCP, HCPH, PTP-1C, SHP-1, SHP1	uc001qsa.1	P29350	OTTHUMG00000168518	ENST00000318974.9:c.471delC	12.37:g.7064112delC	ENSP00000326010:p.Gly157fs	Somatic		WXS	Illumina HiSeq	Phase_I	A8K306|G3V0F8|Q969V8|Q9UK67	Frame_Shift_Del	DEL	ENST00000318974.9	37	CCDS44820.1																																																																																				0.642	PTPN6-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400023.1		NM_002831	
RARA	5914	hgsc.bcm.edu	37	17	38510748	38510748	+	Silent	SNP	C	C	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr17:38510748C>T	ENST00000254066.5	+	7	1457	c.1002C>T	c.(1000-1002)ctC>ctT	p.L334L	RARA_ENST00000420042.1_3'UTR|RARA_ENST00000394089.2_Silent_p.L334L|RARA_ENST00000425707.3_Silent_p.L237L|RARA_ENST00000394086.3_Silent_p.L350L|RARA_ENST00000394081.3_Silent_p.L329L	NM_000964.3	NP_000955.1	P10276	RARA_HUMAN	retinoic acid receptor, alpha	334	Ligand-binding.				apoptotic cell clearance (GO:0043277)|cellular response to estrogen stimulus (GO:0071391)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to retinoic acid (GO:0071300)|chondroblast differentiation (GO:0060591)|embryonic camera-type eye development (GO:0031076)|face development (GO:0060324)|female pregnancy (GO:0007565)|gene expression (GO:0010467)|germ cell development (GO:0007281)|glandular epithelial cell development (GO:0002068)|growth plate cartilage development (GO:0003417)|intracellular estrogen receptor signaling pathway (GO:0030520)|limb development (GO:0060173)|liver development (GO:0001889)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell proliferation (GO:0008285)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translational initiation (GO:0045947)|negative regulation of tumor necrosis factor production (GO:0032720)|neural tube closure (GO:0001843)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of binding (GO:0051099)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of interleukin-13 production (GO:0032736)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-5 production (GO:0032754)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein phosphorylation (GO:0006468)|regulation of myelination (GO:0031641)|regulation of synaptic plasticity (GO:0048167)|response to cytokine (GO:0034097)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to retinoic acid (GO:0032526)|response to vitamin A (GO:0033189)|retinoic acid receptor signaling pathway (GO:0048384)|Sertoli cell fate commitment (GO:0060010)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|trachea cartilage development (GO:0060534)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ureteric bud development (GO:0001657)|ventricular cardiac muscle cell differentiation (GO:0055012)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	chromatin DNA binding (GO:0031490)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|mRNA 5'-UTR binding (GO:0048027)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein domain specific binding (GO:0019904)|protein heterodimerization activity (GO:0046982)|protein kinase A binding (GO:0051018)|protein kinase B binding (GO:0043422)|receptor binding (GO:0005102)|retinoic acid binding (GO:0001972)|retinoic acid receptor activity (GO:0003708)|retinoic acid-responsive element binding (GO:0044323)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|translation repressor activity, nucleic acid binding (GO:0000900)|zinc ion binding (GO:0008270)			breast(1)|kidney(4)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)|urinary_tract(2)	16		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00143)		Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Isotretinoin(DB00982)|Tamibarotene(DB04942)|Tazarotene(DB00799)	CCATCTGCCTCATCTGCGGAG	0.677			T	"""PML, ZNF145, TIF1, NUMA1, NPM1"""	APL																																			Dom	yes		17	17q12	5914	"""retinoic acid receptor, alpha"""		L	0													30.0	32.0	32.0					17																	38510748		2203	4299	6502	SO:0001819	synonymous_variant	5914			X06538	CCDS11366.1, CCDS42317.1, CCDS45671.1	17q21.1	2014-01-20			ENSG00000131759	ENSG00000131759		"""Nuclear hormone receptors"""	9864	protein-coding gene	gene with protein product		180240				2825036, 8244378	Standard	NM_001145301		Approved	RAR, NR1B1	uc002huk.2	P10276	OTTHUMG00000133328	ENST00000254066.5:c.1002C>T	17.37:g.38510748C>T		Somatic		WXS	Illumina HiSeq	Phase_I	B8Y636|P78456|Q13440|Q13441|Q96S41|Q9NQS0	Silent	SNP	ENST00000254066.5	37	CCDS11366.1																																																																																				0.677	RARA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257136.2			
RCSD1	92241	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	167663406	167663406	+	Missense_Mutation	SNP	T	T	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr1:167663406T>A	ENST00000367854.3	+	5	672	c.341T>A	c.(340-342)aTg>aAg	p.M114K	RCSD1_ENST00000537350.1_Missense_Mutation_p.M84K	NM_052862.3	NP_443094.3	Q6JBY9	CPZIP_HUMAN	RCSD domain containing 1	114					cellular hyperosmotic response (GO:0071474)|skeletal muscle contraction (GO:0003009)	actin filament (GO:0005884)	actin filament binding (GO:0051015)	p.M114K(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(2)|ovary(2)|prostate(2)|skin(2)|urinary_tract(1)	24	all_hematologic(923;0.215)					CTCAAGGCTATGGTGTCGCCA	0.557																																																	1	Substitution - Missense(1)	kidney(1)											87.0	81.0	83.0					1																	167663406		2203	4300	6503	SO:0001583	missense	92241			BC072399	CCDS1263.1	1q24.2	2008-02-05			ENSG00000198771	ENSG00000198771			28310	protein-coding gene	gene with protein product		610579				12477932	Standard	NM_052862		Approved	MK2S4, MGC21854	uc001gem.3	Q6JBY9	OTTHUMG00000035318	ENST00000367854.3:c.341T>A	1.37:g.167663406T>A	ENSP00000356828:p.Met114Lys	Somatic		WXS	Illumina HiSeq	Phase_I	B1AK48|Q4G0E7|Q6IN93|Q8IZM2|Q96DX0|Q9NST4	Missense_Mutation	SNP	ENST00000367854.3	37	CCDS1263.1	.	.	.	.	.	.	.	.	.	.	T	14.33	2.502927	0.44558	.	.	ENSG00000198771	ENST00000367854;ENST00000361496;ENST00000537350	T;T	0.46063	0.88;0.89	5.18	-0.797	0.10909	.	0.942290	0.08958	N	0.869078	T	0.14830	0.0358	L	0.34521	1.04	0.34273	D	0.681205	P;P	0.34462	0.454;0.454	B;B	0.29663	0.105;0.045	T	0.08764	-1.0706	9	0.59425	D	0.04	-0.3862	12.5252	0.56083	0.0:0.0987:0.0:0.9013	.	84;114	B7ZKW8;Q6JBY9	.;CPZIP_HUMAN	K	114;90;84	ENSP00000356828:M114K;ENSP00000439409:M84K	ENSP00000355291:M90K	M	+	2	0	RCSD1	165930030	0.317000	0.24589	0.095000	0.20976	0.959000	0.62525	0.477000	0.22196	-0.232000	0.09811	0.533000	0.62120	ATG		0.557	RCSD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085451.1		NM_052862	
SDC1	6382	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	20403727	20403727	+	Silent	SNP	C	C	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr2:20403727C>T	ENST00000254351.4	-	3	718	c.474G>A	c.(472-474)caG>caA	p.Q158Q	SDC1_ENST00000381150.1_Silent_p.Q158Q|SDC1_ENST00000403076.1_Silent_p.Q158Q|SDC1_ENST00000482879.1_Intron	NM_002997.4	NP_002988	P18827	SDC1_HUMAN	syndecan 1	158					canonical Wnt signaling pathway (GO:0060070)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|inflammatory response (GO:0006954)|lipoprotein metabolic process (GO:0042157)|myoblast development (GO:0048627)|odontogenesis (GO:0042476)|phototransduction, visible light (GO:0007603)|response to calcium ion (GO:0051592)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|response to hydrogen peroxide (GO:0042542)|response to toxic substance (GO:0009636)|retinoid metabolic process (GO:0001523)|Sertoli cell development (GO:0060009)|small molecule metabolic process (GO:0044281)|striated muscle cell development (GO:0055002)|ureteric bud development (GO:0001657)|wound healing (GO:0042060)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	protein C-terminus binding (GO:0008022)	p.Q158Q(1)		NS(1)|breast(1)|kidney(2)|large_intestine(2)|lung(9)|ovary(4)|skin(2)	21	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)			OV - Ovarian serous cystadenocarcinoma(76;0.221)		GGTGGCCAGGCTGCATGTCCC	0.657																																																	1	Substitution - coding silent(1)	kidney(1)											100.0	96.0	97.0					2																	20403727		2203	4300	6503	SO:0001819	synonymous_variant	6382			AJ551176	CCDS1697.1	2p24.1	2008-02-05			ENSG00000115884	ENSG00000115884		"""CD molecules"", ""Proteoglycans / Cell Surface : Syndecans"""	10658	protein-coding gene	gene with protein product	"""syndecan proteoglycan 1"""	186355		SDC			Standard	XM_005262621		Approved	CD138, syndecan, SYND1	uc002rdo.1	P18827	OTTHUMG00000090751	ENST00000254351.4:c.474G>A	2.37:g.20403727C>T		Somatic		WXS	Illumina HiSeq	Phase_I	D6W523|Q53QV0|Q546D3|Q96HB7	Silent	SNP	ENST00000254351.4	37	CCDS1697.1																																																																																				0.657	SDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207495.1		NM_001006946	
SETD2	29072	broad.mit.edu;ucsc.edu	37	3	47127736	47127736	+	Nonsense_Mutation	SNP	C	C	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr3:47127736C>T	ENST00000409792.3	-	11	5388	c.5346G>A	c.(5344-5346)tgG>tgA	p.W1782*	snoU13_ENST00000516129.1_RNA|SETD2_ENST00000492397.1_5'Flank	NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1782					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)	p.W1279*(1)|p.W1782*(1)		breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		GCTCTGCCATCCAGATCCACA	0.478			"""N, F, S, Mis"""		clear cell renal carcinoma																																			Rec	yes		3	3p21.31	29072	SET domain containing 2		E	2	Substitution - Nonsense(2)	kidney(2)											139.0	121.0	127.0					3																	47127736		2203	4300	6503	SO:0001587	stop_gained	29072			AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"""Chromatin-modifying enzymes / K-methyltransferases"""	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.5346G>A	3.37:g.47127736C>T	ENSP00000386759:p.Trp1782*	Somatic		WXS	Illumina GAIIx	Phase_I	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Nonsense_Mutation	SNP	ENST00000409792.3	37	CCDS2749.2	.	.	.	.	.	.	.	.	.	.	C	45	11.399636	0.99556	.	.	ENSG00000181555	ENST00000451092;ENST00000409792	.	.	.	5.47	5.47	0.80525	.	0.000000	0.52532	D	0.000065	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.3513	0.94387	0.0:1.0:0.0:0.0	.	.	.	.	X	1782	.	ENSP00000386759:W1782X	W	-	3	0	SETD2	47102740	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.523000	0.53488	2.571000	0.86741	0.650000	0.86243	TGG		0.478	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2		NM_014159	
SLC16A1	6566	hgsc.bcm.edu;ucsc.edu	37	1	113460278	113460279	+	Frame_Shift_Ins	INS	-	-	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr1:113460278_113460279insT	ENST00000538576.1	-	4	1580_1581	c.749_750insA	c.(748-750)aatfs	p.N250fs	SLC16A1_ENST00000433570.4_Frame_Shift_Ins_p.N250fs|SLC16A1_ENST00000369626.3_Frame_Shift_Ins_p.N250fs	NM_001166496.1	NP_001159968.1	P53985	MOT1_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 1	250					behavioral response to nutrient (GO:0051780)|blood coagulation (GO:0007596)|cellular metabolic process (GO:0044237)|cellular response to organic cyclic compound (GO:0071407)|centrosome organization (GO:0051297)|glucose homeostasis (GO:0042593)|leukocyte migration (GO:0050900)|lipid metabolic process (GO:0006629)|mevalonate transport (GO:0015728)|monocarboxylic acid transport (GO:0015718)|plasma membrane lactate transport (GO:0035879)|pyruvate metabolic process (GO:0006090)|regulation of insulin secretion (GO:0050796)|response to food (GO:0032094)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	centrosome (GO:0005813)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	mevalonate transmembrane transporter activity (GO:0015130)|monocarboxylic acid transmembrane transporter activity (GO:0008028)|organic cyclic compound binding (GO:0097159)|secondary active monocarboxylate transmembrane transporter activity (GO:0015355)|symporter activity (GO:0015293)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(8)|skin(1)|urinary_tract(1)	20	Lung SC(450;0.246)	all_cancers(81;7.6e-08)|all_epithelial(167;3.82e-07)|all_lung(203;3.07e-05)|Lung NSC(69;5.51e-05)|Prostate(1639;0.00232)		Epithelial(280;7.31e-13)|all cancers(265;5.1e-10)|Kidney(133;5.29e-07)|KIRC - Kidney renal clear cell carcinoma(1967;8.63e-06)|OV - Ovarian serous cystadenocarcinoma(397;1.48e-05)|BRCA - Breast invasive adenocarcinoma(282;0.003)|LUSC - Lung squamous cell carcinoma(189;0.008)|Lung(183;0.00948)|Colorectal(144;0.0325)|COAD - Colon adenocarcinoma(174;0.0643)	Acetic acid(DB03166)|Aminohippurate(DB00345)|Ampicillin(DB00415)|Foscarnet(DB00529)|Gamma Hydroxybutyric Acid(DB01440)|Methotrexate(DB00563)|Nateglinide(DB00731)|Niacin(DB00627)|Niflumic Acid(DB04552)|Pravastatin(DB00175)|Probenecid(DB01032)|Pyruvic acid(DB00119)|Salicylic acid(DB00936)|Valproic Acid(DB00313)	CCAGGAACTGATTAATTGTTTG	0.396																																																	0																																										SO:0001589	frameshift_variant	6566			BC026317	CCDS858.1	1p12	2013-07-18	2013-07-18		ENSG00000155380	ENSG00000155380		"""Solute carriers"""	10922	protein-coding gene	gene with protein product		600682	"""solute carrier family 16 (monocarboxylic acid transporters), member 1"", ""solute carrier family 16, member 1 (monocarboxylic acid transporter 1)"""			8124722, 7835905	Standard	NM_003051		Approved	MCT, MCT1	uc001ecy.3	P53985	OTTHUMG00000012129	ENST00000538576.1:c.750dupA	1.37:g.113460280_113460280dupT	ENSP00000441065:p.Asn250fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q49A45|Q5T8R6|Q9NSJ9	Frame_Shift_Ins	INS	ENST00000538576.1	37	CCDS858.1																																																																																				0.396	SLC16A1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033539.1		NM_003051	
SLC44A3	126969	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	95360437	95360437	+	Missense_Mutation	SNP	A	A	G			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr1:95360437A>G	ENST00000271227.6	+	15	2023	c.1921A>G	c.(1921-1923)Agg>Ggg	p.R641G	SLC44A3_ENST00000532427.1_Missense_Mutation_p.R561G|SLC44A3_ENST00000527077.1_Missense_Mutation_p.R573G|SLC44A3_ENST00000529450.1_Missense_Mutation_p.R608G|SLC44A3_ENST00000467909.1_Missense_Mutation_p.R593G|SLC44A3_ENST00000446120.2_Missense_Mutation_p.R605G	NM_001114106.2|NM_001258340.1|NM_001258341.1	NP_001107578.1|NP_001245269.1|NP_001245270.1	Q8N4M1	CTL3_HUMAN	solute carrier family 44, member 3	641					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R641G(1)|p.R593G(1)		breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(6)|prostate(2)|stomach(1)|urinary_tract(1)	23		all_lung(203;0.000712)|Lung NSC(277;0.00316)		all cancers(265;0.039)|Epithelial(280;0.124)	Choline(DB00122)	GCACTCATTAAGGAATGAGGA	0.378																																																	2	Substitution - Missense(2)	kidney(2)											97.0	87.0	91.0					1																	95360437		2203	4300	6503	SO:0001583	missense	126969			BC033858	CCDS751.1, CCDS44176.1, CCDS58011.1, CCDS58012.1, CCDS58013.1, CCDS72827.1	1p22.1	2013-05-22	2005-09-06		ENSG00000143036	ENSG00000143036		"""Solute carriers"""	28689	protein-coding gene	gene with protein product			"""solute carrier family, member 3"""			15715662, 12975309	Standard	NM_001114106		Approved	MGC45474, CTL3	uc001dqv.5	Q8N4M1	OTTHUMG00000010700	ENST00000271227.6:c.1921A>G	1.37:g.95360437A>G	ENSP00000271227:p.Arg641Gly	Somatic		WXS	Illumina HiSeq	Phase_I	B4DVY4|B4E1M4|B7ZA08|E9PJH2|E9PJY8|Q6UWT1|Q7Z6C5|Q9BWY7	Missense_Mutation	SNP	ENST00000271227.6	37	CCDS44176.1	.	.	.	.	.	.	.	.	.	.	A	10.61	1.398131	0.25205	.	.	ENSG00000143036	ENST00000446120;ENST00000271227;ENST00000527077;ENST00000529450;ENST00000467909;ENST00000532427;ENST00000532670	T;T;T;T;T;T	0.18338	2.7;2.9;2.22;2.22;2.7;2.22	5.91	0.871	0.19107	.	1.722310	0.02788	N	0.121755	T	0.02267	0.0070	N	0.14661	0.345	0.09310	N	1	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.06405	0.0;0.002;0.0;0.0;0.0	T	0.35425	-0.9789	10	0.18276	T	0.48	-0.1043	1.3307	0.02134	0.4989:0.1459:0.2226:0.1326	.	561;605;573;608;641	E9PIC5;Q8N4M1-3;E9PJY8;E9PJH2;Q8N4M1	.;.;.;.;CTL3_HUMAN	G	605;641;573;608;593;561;97	ENSP00000389143:R605G;ENSP00000271227:R641G;ENSP00000433641:R573G;ENSP00000431836:R608G;ENSP00000432789:R593G;ENSP00000436661:R561G	ENSP00000271227:R641G	R	+	1	2	SLC44A3	95133025	0.000000	0.05858	0.001000	0.08648	0.034000	0.12701	0.171000	0.16685	0.137000	0.18759	0.454000	0.30748	AGG		0.378	SLC44A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029544.3		NM_152369	
SLX4	84464	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	3641170	3641170	+	Nonsense_Mutation	SNP	C	C	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr16:3641170C>T	ENST00000294008.3	-	12	3109	c.2469G>A	c.(2467-2469)tgG>tgA	p.W823*		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	823	Glu-rich.|Interaction with PLK1 and TERF2-TERF2IP.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)	p.W823*(1)		breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						CTTCATCTGCCCACATTGACC	0.458								Direct reversal of damage																																									1	Substitution - Nonsense(1)	kidney(1)											168.0	178.0	175.0					16																	3641170		2197	4300	6497	SO:0001587	stop_gained	84464			AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827		"""Fanconi anemia, complementation groups"", ""BTB/POZ domain containing"""	23845	protein-coding gene	gene with protein product	"""Fanconi anemia, complementation group P"""	613278	"""BTB (POZ) domain containing 12"", ""SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)"""	BTBD12		11347906, 19595721	Standard	NM_032444		Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.2469G>A	16.37:g.3641170C>T	ENSP00000294008:p.Trp823*	Somatic		WXS	Illumina HiSeq	Phase_I	Q69YT8|Q8TF15|Q96JP1	Nonsense_Mutation	SNP	ENST00000294008.3	37	CCDS10506.2	.	.	.	.	.	.	.	.	.	.	C	46	12.924030	0.99706	.	.	ENSG00000188827	ENST00000294008	.	.	.	5.57	5.57	0.84162	.	0.000000	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.5351	0.91008	0.0:1.0:0.0:0.0	.	.	.	.	X	823	.	ENSP00000294008:W823X	W	-	3	0	SLX4	3581171	1.000000	0.71417	0.968000	0.41197	0.994000	0.84299	5.766000	0.68843	2.619000	0.88677	0.561000	0.74099	TGG		0.458	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3		NM_032444	
TBX4	9496	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	59557596	59557596	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr17:59557596C>A	ENST00000240335.1	+	7	982	c.937C>A	c.(937-939)Ctc>Atc	p.L313I	TBX4_ENST00000393853.4_Missense_Mutation_p.L313I|TBX4_ENST00000589449.1_3'UTR	NM_018488.2	NP_060958.2	P57082	TBX4_HUMAN	T-box 4	313					angiogenesis (GO:0001525)|embryonic limb morphogenesis (GO:0030326)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|morphogenesis of an epithelium (GO:0002009)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.L313I(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|liver(2)|lung(15)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	40						ACACTCACAGCTCGCGGAGCC	0.647																																																	1	Substitution - Missense(1)	kidney(1)											63.0	58.0	60.0					17																	59557596		2203	4300	6503	SO:0001583	missense	9496			AF188703	CCDS11629.1	17q21-q22	2005-10-11				ENSG00000121075		"""T-boxes"""	11603	protein-coding gene	gene with protein product		601719				10945475	Standard	NM_018488		Approved		uc002izi.3	P57082		ENST00000240335.1:c.937C>A	17.37:g.59557596C>A	ENSP00000240335:p.Leu313Ile	Somatic		WXS	Illumina HiSeq	Phase_I	A5PKU7|B2RMT1|B7ZLV3	Missense_Mutation	SNP	ENST00000240335.1	37	CCDS11629.1	.	.	.	.	.	.	.	.	.	.	C	6.625	0.483733	0.12581	.	.	ENSG00000121075	ENST00000393853;ENST00000240335	T;T	0.77229	-1.08;-1.08	5.84	4.77	0.60923	.	0.488460	0.24247	N	0.040202	T	0.55970	0.1954	N	0.08118	0	0.22001	N	0.999428	B;B	0.12630	0.0;0.006	B;B	0.10450	0.001;0.005	T	0.40079	-0.9582	9	.	.	.	.	9.0673	0.36471	0.0:0.0897:0.0:0.9103	.	313;313	A5PKU7;P57082	.;TBX4_HUMAN	I	313	ENSP00000377435:L313I;ENSP00000240335:L313I	.	L	+	1	0	TBX4	56912378	1.000000	0.71417	0.996000	0.52242	0.032000	0.12392	3.745000	0.55119	1.088000	0.41272	0.655000	0.94253	CTC		0.647	TBX4-002	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000449649.1		NM_018488	
TEX2	55852	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	62228234	62228234	+	Silent	SNP	G	G	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr17:62228234G>A	ENST00000583097.1	-	11	3400	c.3228C>T	c.(3226-3228)gaC>gaT	p.D1076D	TEX2_ENST00000258991.3_Silent_p.D1083D|TEX2_ENST00000581812.1_5'UTR|TEX2_ENST00000584379.1_Silent_p.D1076D			Q8IWB9	TEX2_HUMAN	testis expressed 2	1076					signal transduction (GO:0007165)|sphingolipid metabolic process (GO:0006665)	integral component of membrane (GO:0016021)		p.D1083D(1)		breast(3)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41			BRCA - Breast invasive adenocarcinoma(8;1.33e-10)	READ - Rectum adenocarcinoma(1115;0.0689)		TCTCTATCCAGTCTGTCACAT	0.438																																																	1	Substitution - coding silent(1)	kidney(1)											174.0	165.0	168.0					17																	62228234		2203	4300	6503	SO:0001819	synonymous_variant	55852			AB051525	CCDS11658.1, CCDS74131.1	17q23.3	2007-03-13	2007-03-13			ENSG00000136478			30884	protein-coding gene	gene with protein product	"""transmembrane protein 96"""		"""testis expressed sequence 2"""			11214970	Standard	XM_005257507		Approved	HT008, TMEM96, KIAA1738	uc002jee.3	Q8IWB9		ENST00000583097.1:c.3228C>T	17.37:g.62228234G>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q6AHZ5|Q8N3L0|Q9C0C5	Silent	SNP	ENST00000583097.1	37																																																																																					0.438	TEX2-003	KNOWN	alternative_5_UTR|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000443745.1		NM_018469	
ST6GALNAC2	10610	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	74563616	74563616	+	Missense_Mutation	SNP	C	C	G			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr17:74563616C>G	ENST00000225276.5	-	8	1195	c.876G>C	c.(874-876)ttG>ttC	p.L292F	RP11-666A8.9_ENST00000588104.1_RNA	NM_006456.2	NP_006447.2	Q9UJ37	SIA7B_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2	292					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	sialyltransferase activity (GO:0008373)	p.L292F(1)		NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	11						GTGTGTTAATCAACTTTGATT	0.438																																																	1	Substitution - Missense(1)	kidney(1)											110.0	104.0	106.0					17																	74563616		2200	4300	6500	SO:0001583	missense	10610			U14550	CCDS11747.1	17q25.1	2013-03-01	2003-12-05	2005-02-07	ENSG00000070731	ENSG00000070731	2.4.99.7	"""Sialyltransferases"""	10867	protein-coding gene	gene with protein product		610137	"""sialyltransferase 7 ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase)"", ""sialyltransferase-like 1"""	SIAT7, SIAT7B, SIATL1		11984005	Standard	NM_006456		Approved	ST6GalNAII, STHM	uc002jsg.4	Q9UJ37	OTTHUMG00000180301	ENST00000225276.5:c.876G>C	17.37:g.74563616C>G	ENSP00000225276:p.Leu292Phe	Somatic		WXS	Illumina HiSeq	Phase_I	Q12971	Missense_Mutation	SNP	ENST00000225276.5	37	CCDS11747.1	.	.	.	.	.	.	.	.	.	.	C	12.97	2.096447	0.36952	.	.	ENSG00000070731	ENST00000225276	T	0.31510	1.49	5.42	0.64	0.17752	.	1.039850	0.07616	N	0.926263	T	0.42877	0.1222	M	0.69185	2.1	0.09310	N	1	D	0.58970	0.984	P	0.62435	0.902	T	0.26395	-1.0104	10	0.30854	T	0.27	-7.5924	1.5782	0.02629	0.1303:0.2698:0.3483:0.2515	.	292	Q9UJ37	SIA7B_HUMAN	F	292	ENSP00000225276:L292F	ENSP00000225276:L292F	L	-	3	2	ST6GALNAC2	72075211	0.057000	0.20700	0.021000	0.16686	0.662000	0.39071	-0.330000	0.07925	0.208000	0.20626	-0.157000	0.13467	TTG		0.438	ST6GALNAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450650.1		NM_006456	
NELFCD	51497	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	57561823	57561823	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr20:57561823G>A	ENST00000344018.3	+	3	245	c.218G>A	c.(217-219)gGa>gAa	p.G73E	NELFCD_ENST00000602795.1_Missense_Mutation_p.G82E			Q8IXH7	NELFD_HUMAN	negative elongation factor complex member C/D	73					gene expression (GO:0010467)|negative regulation of transcription, DNA-templated (GO:0045892)|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)	membrane (GO:0016020)|NELF complex (GO:0032021)|nucleoplasm (GO:0005654)		p.G73E(1)									TTTCAGGCAGGAGGGTCTCCA	0.483																																																	1	Substitution - Missense(1)	kidney(1)											198.0	195.0	196.0					20																	57561823		2203	4300	6503	SO:0001583	missense	51497			AF161479	CCDS13473.1, CCDS13473.2	20q13	2013-01-31	2013-01-31	2013-01-31	ENSG00000101158	ENSG00000101158			15934	protein-coding gene	gene with protein product	"""trihydrophobin 1"""	605297	"""TH1-like (Drosophila homolog)"", ""TH1-like (Drosophila)"""	TH1L		11030415, 11042152	Standard	NM_198976		Approved	HSPC130, TH1, NELF-C, NELF-D	uc002yag.4	Q8IXH7	OTTHUMG00000032861	ENST00000344018.3:c.218G>A	20.37:g.57561823G>A	ENSP00000342300:p.Gly73Glu	Somatic		WXS	Illumina HiSeq	Phase_I	B4DE06|Q9BYL2|Q9H405|Q9H888|Q9H8T3|Q9NVX5|Q9P029|Q9UGN1|Q9UGN2|Q9UGN3	Missense_Mutation	SNP	ENST00000344018.3	37		.	.	.	.	.	.	.	.	.	.	G	32	5.154590	0.94686	.	.	ENSG00000101158	ENST00000344018	.	.	.	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	D	0.84097	0.5397	M	0.86573	2.825	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;0.999	D	0.85109	0.0962	9	0.45353	T	0.12	-21.7003	17.4261	0.87526	0.0:0.0:1.0:0.0	.	73;82;73	B4E2K1;E1P5H4;Q8IXH7	.;.;NELFD_HUMAN	E	73	.	ENSP00000342300:G73E	G	+	2	0	TH1L	56995218	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.084000	0.94076	2.538000	0.85594	0.655000	0.94253	GGA		0.483	NELFCD-201	KNOWN	basic|appris_principal	protein_coding	protein_coding			NM_198976	
TNIK	23043	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	170802027	170802027	+	Missense_Mutation	SNP	T	T	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr3:170802027T>A	ENST00000436636.2	-	26	3430	c.3086A>T	c.(3085-3087)aAc>aTc	p.N1029I	TNIK_ENST00000369326.5_Missense_Mutation_p.N1007I|TNIK_ENST00000475336.1_Missense_Mutation_p.N937I|TNIK_ENST00000341852.6_Missense_Mutation_p.N945I|TNIK_ENST00000460047.1_Missense_Mutation_p.N966I|TNIK_ENST00000488470.1_Missense_Mutation_p.N974I|TNIK_ENST00000284483.8_Missense_Mutation_p.N1021I|TNIK_ENST00000538048.1_Missense_Mutation_p.N981I|TNIK_ENST00000470834.1_Missense_Mutation_p.N992I|TNIK_ENST00000357327.5_Missense_Mutation_p.N1000I	NM_015028.2	NP_055843.1	Q9UKE5	TNIK_HUMAN	TRAF2 and NCK interacting kinase	1029	Mediates interaction with NEDD4.				actin cytoskeleton reorganization (GO:0031532)|activation of JNKK activity (GO:0007256)|cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of dendrite morphogenesis (GO:0048814)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)	p.N1029I(2)		cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(22)|ovary(5)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)	62	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)			AGGCCGAATGTTGGTTGGGTT	0.408																																																	2	Substitution - Missense(2)	kidney(2)											133.0	128.0	129.0					3																	170802027		1860	4104	5964	SO:0001583	missense	23043			AF172264	CCDS46956.1, CCDS54673.1, CCDS54674.1, CCDS54675.1, CCDS54676.1, CCDS54677.1, CCDS54678.1, CCDS54679.1	3q26.31	2008-01-23			ENSG00000154310	ENSG00000154310			30765	protein-coding gene	gene with protein product		610005				9628581, 10521462	Standard	NR_027767		Approved	KIAA0551	uc003fhh.2	Q9UKE5	OTTHUMG00000159036	ENST00000436636.2:c.3086A>T	3.37:g.170802027T>A	ENSP00000399511:p.Asn1029Ile	Somatic		WXS	Illumina HiSeq	Phase_I	A7E2A3|A8K4U1|D3DNQ6|O60298|Q8WUY7|Q9UKD8|Q9UKD9|Q9UKE0|Q9UKE1|Q9UKE2|Q9UKE3|Q9UKE4	Missense_Mutation	SNP	ENST00000436636.2	37	CCDS46956.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.358171	0.82243	.	.	ENSG00000154310	ENST00000436636;ENST00000369326;ENST00000538048;ENST00000341852;ENST00000284483;ENST00000475336;ENST00000357327;ENST00000460047;ENST00000488470;ENST00000470834	T;T;T;T;T;T;T;T;T;T	0.75589	-0.94;-0.92;-0.94;-0.94;-0.94;-0.94;-0.94;-0.95;-0.95;-0.94	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	D	0.86715	0.5999	M	0.81802	2.56	0.80722	D	1	D;P;D;D;D;P;D;D	0.76494	0.997;0.851;0.997;0.997;0.998;0.851;0.997;0.999	D;B;D;D;D;B;D;D	0.80764	0.994;0.355;0.994;0.994;0.974;0.355;0.994;0.943	D	0.88518	0.3094	10	0.87932	D	0	.	16.16	0.81698	0.0:0.0:0.0:1.0	.	937;992;966;945;1021;1000;974;1029	Q9UKE5-8;Q9UKE5-6;Q9UKE5-7;Q9UKE5-5;Q9UKE5-4;Q9UKE5-2;Q9UKE5-3;Q9UKE5	.;.;.;.;.;.;.;TNIK_HUMAN	I	1029;1007;981;945;1021;937;1000;966;974;992	ENSP00000399511:N1029I;ENSP00000358332:N1007I;ENSP00000443278:N981I;ENSP00000345352:N945I;ENSP00000284483:N1021I;ENSP00000418156:N937I;ENSP00000349880:N1000I;ENSP00000418916:N966I;ENSP00000418378:N974I;ENSP00000419990:N992I	ENSP00000284483:N1021I	N	-	2	0	TNIK	172284721	1.000000	0.71417	1.000000	0.80357	0.795000	0.44927	7.651000	0.83577	2.266000	0.75297	0.528000	0.53228	AAC		0.408	TNIK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352973.2		XM_039796	
TPP2	7174	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	13	103275383	103275383	+	Silent	SNP	C	C	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr13:103275383C>T	ENST00000376065.4	+	6	813	c.777C>T	c.(775-777)acC>acT	p.T259T	TPP2_ENST00000376052.3_Silent_p.T259T	NM_003291.2	NP_003282.2	P29144	TPP2_HUMAN	tripeptidyl peptidase II	259	Peptidase S8.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)|tripeptidyl-peptidase activity (GO:0008240)	p.T259T(1)		breast(2)|endometrium(5)|kidney(2)|large_intestine(12)|lung(21)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	52	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					CCATTGTGACCAGTGGAGGTA	0.403																																																	1	Substitution - coding silent(1)	kidney(1)											143.0	149.0	147.0					13																	103275383		2203	4300	6503	SO:0001819	synonymous_variant	7174			M55169	CCDS9502.1	13q32-q33	2008-02-05			ENSG00000134900	ENSG00000134900	3.4.14.10		12016	protein-coding gene	gene with protein product		190470				1670990	Standard	NM_003291		Approved		uc001vpi.4	P29144	OTTHUMG00000017305	ENST00000376065.4:c.777C>T	13.37:g.103275383C>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q5VZU8	Silent	SNP	ENST00000376065.4	37	CCDS9502.1																																																																																				0.403	TPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045683.2			
TPR	7175	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	186310211	186310211	+	Silent	SNP	T	T	G	rs376859703		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr1:186310211T>G	ENST00000367478.4	-	29	4265	c.3969A>C	c.(3967-3969)gcA>gcC	p.A1323A		NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	1323					carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)	p.A1324A(1)|p.A1323A(1)		autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		GCTTCTTCTCTGCCTGCAACA	0.393			T	NTRK1	papillary thyroid																																			Dom	yes		1	1q25	7175	translocated promoter region		E	2	Substitution - coding silent(2)	kidney(2)											180.0	164.0	169.0					1																	186310211		1931	4151	6082	SO:0001819	synonymous_variant	7175			U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410			12017	protein-coding gene	gene with protein product		189940	"""translocated promoter region (to activated MET oncogene)"""			1611909, 15229283	Standard	NM_003292		Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.3969A>C	1.37:g.186310211T>G		Somatic		WXS	Illumina HiSeq	Phase_I	Q15655|Q5SWY0|Q99968	Silent	SNP	ENST00000367478.4	37	CCDS41446.1																																																																																				0.393	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2		NM_003292	
TRIM34	53840	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	5655129	5655129	+	Splice_Site	SNP	G	G	C			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr11:5655129G>C	ENST00000514226.1	+	3	856	c.519G>C	c.(517-519)aaG>aaC	p.K173N	TRIM6-TRIM34_ENST00000457787.2_Splice_Site_p.K173N|HBG2_ENST00000380259.2_Intron|TRIM6-TRIM34_ENST00000354852.5_Splice_Site_p.K527N|TRIM34_ENST00000429814.2_Splice_Site_p.K173N	NM_001003827.1	NP_001003827.1	Q9BYJ4	TRI34_HUMAN	tripartite motif containing 34	173					positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein trimerization (GO:0070206)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)	p.K173N(1)|p.K527N(1)		NS(1)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	17		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;5.72e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CTTCCTGGAAGGCAAGAGGAG	0.473																																																	2	Substitution - Missense(2)	kidney(2)											63.0	65.0	64.0					11																	5655129		2201	4297	6498	SO:0001630	splice_region_variant	53840			AB039902	CCDS31391.1	11p15	2013-01-09	2011-01-25	2001-11-23		ENSG00000258659		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	10063	protein-coding gene	gene with protein product		605684	"""tripartite motif-containing 34"""	RNF21			Standard	NM_130390		Approved			Q9BYJ4	OTTHUMG00000066892	ENST00000514226.1:c.519+1G>C	11.37:g.5655129G>C		Somatic		WXS	Illumina HiSeq	Phase_I	D3DQS7|Q9C016|Q9HCR0|Q9HCR1|Q9HCR2	Missense_Mutation	SNP	ENST00000514226.1	37	CCDS31391.1	.	.	.	.	.	.	.	.	.	.	G	19.32	3.804992	0.70682	.	.	ENSG00000258659;ENSG00000258659;ENSG00000258659;ENSG00000258659;ENSG00000258588	ENST00000337072;ENST00000514226;ENST00000429814;ENST00000457787;ENST00000354852	T;T;T;T	0.29142	3.47;3.47;3.47;1.58	3.64	3.64	0.41730	.	0.000000	0.33610	N	0.004729	T	0.48409	0.1498	M	0.81112	2.525	0.24658	N	0.993486	P;P;P	0.50443	0.935;0.816;0.693	P;P;B	0.55713	0.782;0.69;0.367	T	0.41610	-0.9499	10	0.66056	D	0.02	.	11.1174	0.48268	0.0:0.0:1.0:0.0	.	173;173;527	Q9BYJ4-2;Q9BYJ4;B2RNG4	.;TRI34_HUMAN;.	N	527;173;173;173;527	ENSP00000422947:K173N;ENSP00000402595:K173N;ENSP00000395982:K173N;ENSP00000346916:K527N	ENSP00000402595:K173N	K	+	3	2	TRIM34;TRIM6-TRIM34	5611705	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	3.061000	0.49963	2.331000	0.79229	0.655000	0.94253	AAG		0.473	TRIM34-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143357.2		NM_001003827	Missense_Mutation
UGGT1	56886	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	128928844	128928844	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr2:128928844C>A	ENST00000259253.6	+	28	3137	c.3090C>A	c.(3088-3090)gaC>gaA	p.D1030E	UGGT1_ENST00000375990.3_Missense_Mutation_p.D1006E	NM_020120.3	NP_064505.1	Q9NYU2	UGGG1_HUMAN	UDP-glucose glycoprotein glucosyltransferase 1	1030					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)|unfolded protein binding (GO:0051082)	p.D1030E(1)		NS(1)|breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(14)|lung(20)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						AACTTTCTGACATGCCTTTAA	0.338																																																	1	Substitution - Missense(1)	kidney(1)											86.0	84.0	85.0					2																	128928844		2203	4300	6503	SO:0001583	missense	56886			AF227905	CCDS2154.1	2q14.3	2009-07-23	2009-07-23	2009-07-23	ENSG00000136731	ENSG00000136731			15663	protein-coding gene	gene with protein product		605897	"""UDP-glucose ceramide glucosyltransferase-like 1"""	UGCGL1		10694380	Standard	NM_020120		Approved	HUGT1	uc002tps.3	Q9NYU2	OTTHUMG00000131570	ENST00000259253.6:c.3090C>A	2.37:g.128928844C>A	ENSP00000259253:p.Asp1030Glu	Somatic		WXS	Illumina HiSeq	Phase_I	Q53QP2|Q53SL3|Q8IW30|Q9H8I4	Missense_Mutation	SNP	ENST00000259253.6	37	CCDS2154.1	.	.	.	.	.	.	.	.	.	.	C	3.421	-0.118081	0.06838	.	.	ENSG00000136731	ENST00000375990;ENST00000259253	T;T	0.25579	1.79;1.79	5.53	3.71	0.42584	.	0.096661	0.64402	D	0.000001	T	0.05593	0.0147	N	0.00313	-1.665	0.39371	D	0.966088	B;B	0.02656	0.0;0.0	B;B	0.11329	0.002;0.006	T	0.17379	-1.0371	9	.	.	.	.	7.4148	0.27038	0.0:0.6143:0.2392:0.1465	.	1006;1030	Q9NYU2-2;Q9NYU2	.;UGGG1_HUMAN	E	1006;1030	ENSP00000365158:D1006E;ENSP00000259253:D1030E	.	D	+	3	2	UGGT1	128645314	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	0.734000	0.26101	1.347000	0.45714	-0.145000	0.13849	GAC		0.338	UGGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254435.2		NM_020120	
ULK4	54986	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	41504634	41504634	+	Missense_Mutation	SNP	C	C	G			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr3:41504634C>G	ENST00000301831.4	-	33	3799	c.3337G>C	c.(3337-3339)Gat>Cat	p.D1113H		NM_017886.2	NP_060356.2	Q96C45	ULK4_HUMAN	unc-51 like kinase 4	1113					cilium morphogenesis (GO:0060271)|epithelial cilium movement (GO:0003351)|microtubule cytoskeleton organization (GO:0000226)|regulation of JNK cascade (GO:0046328)|regulation of MAPK cascade (GO:0043408)|regulation of neuron migration (GO:2001222)|regulation of neuron projection development (GO:0010975)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein kinase C signaling (GO:0090036)|ventricular system development (GO:0021591)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.D1113H(1)|p.D265H(1)		breast(2)|cervix(1)|large_intestine(6)|lung(7)|prostate(5)|skin(1)	22				KIRC - Kidney renal clear cell carcinoma(284;0.214)		TGCAAAATATCAAGCAGGGAA	0.473																																																	2	Substitution - Missense(2)	kidney(2)											171.0	163.0	166.0					3																	41504634		2000	4183	6183	SO:0001583	missense	54986			AK000581	CCDS43071.1	3p22.1	2013-07-02	2013-07-02		ENSG00000168038	ENSG00000168038			15784	protein-coding gene	gene with protein product			"""unc-51-like kinase 4 (C. elegans)"""			12477932	Standard	NM_017886		Approved	FLJ20574, REC01035, FAM7C1	uc003ckv.4	Q96C45	OTTHUMG00000156210	ENST00000301831.4:c.3337G>C	3.37:g.41504634C>G	ENSP00000301831:p.Asp1113His	Somatic		WXS	Illumina HiSeq	Phase_I	A6NF15|Q8IW79|Q9NWV6|Q9UF96	Missense_Mutation	SNP	ENST00000301831.4	37	CCDS43071.1	.	.	.	.	.	.	.	.	.	.	C	14.86	2.660618	0.47572	.	.	ENSG00000168038	ENST00000301831	T	0.66638	-0.22	4.75	4.75	0.60458	Armadillo-like helical (1);Armadillo-type fold (1);	0.120003	0.30879	U	0.008690	T	0.74298	0.3698	L	0.50333	1.59	0.80722	D	1	D	0.64830	0.994	P	0.56700	0.804	T	0.78321	-0.2249	10	0.87932	D	0	.	17.7419	0.88409	0.0:1.0:0.0:0.0	.	1113	Q96C45	ULK4_HUMAN	H	1113	ENSP00000301831:D1113H	ENSP00000301831:D1113H	D	-	1	0	ULK4	41479638	0.999000	0.42202	0.037000	0.18230	0.221000	0.24807	5.658000	0.68003	2.187000	0.69744	0.491000	0.48974	GAT		0.473	ULK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343490.1		XM_929989	
UPB1	51733	broad.mit.edu;hgsc.bcm.edu	37	22	24906778	24906778	+	Silent	SNP	A	A	G			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr22:24906778A>G	ENST00000326010.5	+	4	770	c.426A>G	c.(424-426)gcA>gcG	p.A142A	UPB1_ENST00000413389.2_Silent_p.A74A	NM_016327.2	NP_057411.1	Q9UBR1	BUP1_HUMAN	ureidopropionase, beta	142	CN hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00054}.				beta-alanine biosynthetic process (GO:0019483)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	beta-ureidopropionase activity (GO:0003837)|metal ion binding (GO:0046872)	p.A142A(2)		endometrium(4)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	22	Colorectal(2;0.0339)					CTGAGTCAGCAGAGGATGGGC	0.488																																																	2	Substitution - coding silent(2)	urinary_tract(1)|kidney(1)											85.0	80.0	82.0					22																	24906778		2203	4300	6503	SO:0001819	synonymous_variant	51733			AB013885	CCDS13827.1	22q11.2	2008-04-11			ENSG00000100024	ENSG00000100024			16297	protein-coding gene	gene with protein product		606673				10542323	Standard	XR_244378		Approved	BUP1	uc003aaf.3	Q9UBR1	OTTHUMG00000150749	ENST00000326010.5:c.426A>G	22.37:g.24906778A>G		Somatic		WXS	Illumina HiSeq	Phase_I	A3KMF8|Q9UIR3	Silent	SNP	ENST00000326010.5	37	CCDS13827.1																																																																																				0.488	UPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319869.1			
UTRN	7402	broad.mit.edu;ucsc.edu	37	6	144811221	144811221	+	Silent	SNP	G	G	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr6:144811221G>A	ENST00000367545.3	+	30	4149	c.4149G>A	c.(4147-4149)gaG>gaA	p.E1383E		NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	1383	Interaction with SYNM.				aging (GO:0007568)|muscle cell differentiation (GO:0042692)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|neuron projection morphogenesis (GO:0048812)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane (GO:0016020)|membrane raft (GO:0045121)|myofibril (GO:0030016)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)	p.E1383E(1)		NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		TCCAAGCAGAGATCTCAGCCC	0.423																																																	1	Substitution - coding silent(1)	kidney(1)											91.0	102.0	98.0					6																	144811221		2203	4300	6503	SO:0001819	synonymous_variant	7402			AK023675	CCDS34547.1	6q24	2008-02-05	2006-12-13		ENSG00000152818	ENSG00000152818			12635	protein-coding gene	gene with protein product		128240	"""utrophin (homologous to dystrophin)"""	DMDL		1426262	Standard	NM_007124		Approved	DRP, DRP1	uc003qkt.3	P46939	OTTHUMG00000015746	ENST00000367545.3:c.4149G>A	6.37:g.144811221G>A		Somatic		WXS	Illumina GAIIx	Phase_I	Q5SYY1|Q5SZ57|Q9UJ40	Silent	SNP	ENST00000367545.3	37	CCDS34547.1																																																																																				0.423	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1			
VHL	7428	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	10191488	10191488	+	Nonsense_Mutation	SNP	C	C	T	rs5030818		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr3:10191488C>T	ENST00000256474.2	+	3	1321	c.481C>T	c.(481-483)Cga>Tga	p.R161*	VHL_ENST00000345392.2_Nonsense_Mutation_p.R120*|VHL_ENST00000477538.1_3'UTR	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	161	Interaction with Elongin BC complex.		R -> G (in VHLD; type II; dbSNP:rs5030818).|R -> P (in pheochromocytoma and VHLD; type I). {ECO:0000269|PubMed:12000816, ECO:0000269|PubMed:8956040}.|R -> Q (in pheochromocytoma and VHLD; type II). {ECO:0000269|PubMed:12000816, ECO:0000269|PubMed:9829912}.		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.R161*(13)|p.E160fs*9(2)|p.R161del(1)|p.R161fs*13(1)|p.?fs(1)|p.L158fs*6(1)|p.E160fs*13(1)|p.R161fs*9(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)		TCTGAAAGAGCGATGCCTCCA	0.502		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"""	21	Substitution - Nonsense(13)|Deletion - Frameshift(4)|Insertion - Frameshift(3)|Deletion - In frame(1)	kidney(17)|soft_tissue(2)|paratesticular_tissues(1)|pancreas(1)	GRCh37	CM941381|CM961432	VHL	M	rs5030818						91.0	83.0	86.0					3																	10191488		2203	4300	6503	SO:0001587	stop_gained	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.481C>T	3.37:g.10191488C>T	ENSP00000256474:p.Arg161*	Somatic		WXS	Illumina HiSeq	Phase_I	B2RE45|Q13599|Q6PDA9	Nonsense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	C	19.45	3.829386	0.71258	.	.	ENSG00000134086	ENST00000256474;ENST00000345392;ENST00000450183	.	.	.	4.86	2.94	0.34122	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.8766	11.9485	0.52942	0.3106:0.6894:0.0:0.0	rs5030818	.	.	.	X	161;120;79	.	ENSP00000256474:R161X	R	+	1	2	VHL	10166488	0.997000	0.39634	0.933000	0.37362	0.704000	0.40688	1.161000	0.31773	1.416000	0.47057	-0.122000	0.15005	CGA		0.502	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1		NM_000551	
WDFY3	23001	hgsc.bcm.edu;ucsc.edu	37	4	85611661	85611662	+	Frame_Shift_Ins	INS	-	-	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr4:85611661_85611662insT	ENST00000295888.4	-	61	9767_9768	c.9360_9361insA	c.(9358-9363)aaacagfs	p.Q3121fs	RN7SL552P_ENST00000462094.2_RNA|WDFY3_ENST00000322366.6_Frame_Shift_Ins_p.Q3104fs	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	3121	Interaction with ATG5.|Interaction with SQSTM1.				aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		TCTCTTACCTGTTTGAGGGTGA	0.5																																																	0																																										SO:0001589	frameshift_variant	23001			AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"""Zinc fingers, FYVE domain containing"", ""WD repeat domain containing"""	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.9361dupA	4.37:g.85611664_85611664dupT	ENSP00000295888:p.Gln3121fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Frame_Shift_Ins	INS	ENST00000295888.4	37	CCDS3609.1																																																																																				0.500	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2		NM_014991	
ZNF165	7718	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	28054028	28054028	+	Missense_Mutation	SNP	C	C	G			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr6:28054028C>G	ENST00000377325.1	+	3	1046	c.490C>G	c.(490-492)Cag>Gag	p.Q164E		NM_003447.3	NP_003438.1	P49910	ZN165_HUMAN	zinc finger protein 165	164					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Q164E(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(14)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						TGTCAAGTTACAGCCAGTGGA	0.438																																																	1	Substitution - Missense(1)	kidney(1)											121.0	108.0	112.0					6																	28054028		2203	4300	6503	SO:0001583	missense	7718			U78722	CCDS4643.1	6p21	2013-01-09			ENSG00000197279	ENSG00000197279		"""-"", ""Zinc fingers, C2H2-type"""	12953	protein-coding gene	gene with protein product	"""cancer/testis antigen 53"""	600834				7490084	Standard	NM_003447		Approved	ZSCAN7, CT53	uc021yro.1	P49910	OTTHUMG00000014505	ENST00000377325.1:c.490C>G	6.37:g.28054028C>G	ENSP00000366542:p.Gln164Glu	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000377325.1	37	CCDS4643.1	.	.	.	.	.	.	.	.	.	.	C	1.568	-0.534903	0.04082	.	.	ENSG00000197279	ENST00000377325	T	0.05996	3.36	2.47	1.58	0.23477	.	.	.	.	.	T	0.02156	0.0067	L	0.50333	1.59	0.21782	N	0.999549	P	0.42692	0.787	B	0.37387	0.248	T	0.43637	-0.9379	9	0.44086	T	0.13	.	7.1847	0.25793	0.0:0.7213:0.2787:0.0	.	164	P49910	ZN165_HUMAN	E	164	ENSP00000366542:Q164E	ENSP00000366542:Q164E	Q	+	1	0	ZNF165	28162007	0.306000	0.24490	0.525000	0.27900	0.008000	0.06430	1.326000	0.33735	0.619000	0.30197	-0.165000	0.13383	CAG		0.438	ZNF165-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040173.1		NM_003447	
XPO5	57510	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	43528033	43528033	+	Missense_Mutation	SNP	C	C	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr6:43528033C>T	ENST00000265351.7	-	11	1313	c.1103G>A	c.(1102-1104)cGc>cAc	p.R368H	RP3-337H4.10_ENST00000607635.1_RNA|XPO5_ENST00000424378.2_5'Flank	NM_020750.2	NP_065801.1	Q9HAV4	XPO5_HUMAN	exportin 5	368					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|RNA binding (GO:0003723)|tRNA binding (GO:0000049)	p.R368H(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(8)|large_intestine(4)|lung(10)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	34	all_cancers(18;2.08e-05)|Lung NSC(15;0.000907)|all_lung(25;0.00243)		all cancers(41;0.000321)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0524)			AGTTGAAGAGCGTAGAAACTA	0.363																																																	1	Substitution - Missense(1)	kidney(1)											42.0	38.0	39.0					6																	43528033		1816	4069	5885	SO:0001583	missense	57510			AB033117	CCDS47430.1	6p21.1	2011-04-13			ENSG00000124571	ENSG00000124571		"""Exportins"""	17675	protein-coding gene	gene with protein product		607845				11777942, 12426392	Standard	NM_020750		Approved	KIAA1291	uc003ovp.3	Q9HAV4	OTTHUMG00000014742	ENST00000265351.7:c.1103G>A	6.37:g.43528033C>T	ENSP00000265351:p.Arg368His	Somatic		WXS	Illumina HiSeq	Phase_I	Q5JTE6|Q96G48|Q96HN3|Q9BWM6|Q9BZV5|Q9H9M4|Q9NT89|Q9NW39|Q9ULC9	Missense_Mutation	SNP	ENST00000265351.7	37	CCDS47430.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.322182	0.81580	.	.	ENSG00000124571	ENST00000265351;ENST00000436943	T	0.71461	-0.57	5.58	5.58	0.84498	Armadillo-like helical (1);Armadillo-type fold (1);	0.110225	0.64402	D	0.000015	T	0.64316	0.2587	L	0.50333	1.59	0.51482	D	0.999921	D	0.69078	0.997	P	0.52481	0.7	T	0.60762	-0.7199	10	0.20519	T	0.43	-13.643	15.0975	0.72247	0.0:0.8588:0.1412:0.0	.	368	Q9HAV4	XPO5_HUMAN	H	368;73	ENSP00000265351:R368H	ENSP00000265351:R368H	R	-	2	0	XPO5	43636011	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.057000	0.57455	2.623000	0.88846	0.460000	0.39030	CGC		0.363	XPO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040657.2		NM_020750	
ZNF300	91975	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	150276423	150276423	+	Silent	SNP	T	T	C			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr5:150276423T>C	ENST00000274599.5	-	6	798	c.378A>G	c.(376-378)aaA>aaG	p.K126K	ZNF300_ENST00000446148.2_Silent_p.K142K|ZNF300_ENST00000418587.2_Silent_p.K90K|ZNF300_ENST00000427179.1_3'UTR|ZNF300_ENST00000394226.2_Silent_p.K126K	NM_052860.2	NP_443092.1	Q96RE9	ZN300_HUMAN	zinc finger protein 300	126					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K126K(1)		endometrium(4)|kidney(3)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(2)	27		Medulloblastoma(196;0.109)|all_hematologic(541;0.131)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CTTGACAGACTTTTAAAATGG	0.423																																																	1	Substitution - coding silent(1)	kidney(1)											102.0	97.0	99.0					5																	150276423		2203	4299	6502	SO:0001819	synonymous_variant	91975			AF395541	CCDS4311.2, CCDS54939.1, CCDS54940.1	5q33.1	2013-01-08			ENSG00000145908	ENSG00000145908		"""Zinc fingers, C2H2-type"", ""-"""	13091	protein-coding gene	gene with protein product		612429				14746915	Standard	NM_052860		Approved		uc021yfx.1	Q96RE9	OTTHUMG00000130076	ENST00000274599.5:c.378A>G	5.37:g.150276423T>C		Somatic		WXS	Illumina HiSeq	Phase_I	A8MY91|B3KU35|B4DU78|F5GWS1|Q06DQ3|Q17RP3|Q5H9N5	Silent	SNP	ENST00000274599.5	37	CCDS4311.2																																																																																				0.423	ZNF300-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding			NM_052860	
ZNF300	91975	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	150276453	150276453	+	Silent	SNP	T	T	C			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr5:150276453T>C	ENST00000274599.5	-	6	768	c.348A>G	c.(346-348)acA>acG	p.T116T	ZNF300_ENST00000446148.2_Silent_p.T132T|ZNF300_ENST00000418587.2_Silent_p.T80T|ZNF300_ENST00000427179.1_3'UTR|ZNF300_ENST00000394226.2_Silent_p.T116T	NM_052860.2	NP_443092.1	Q96RE9	ZN300_HUMAN	zinc finger protein 300	116					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T116T(1)		endometrium(4)|kidney(3)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(2)	27		Medulloblastoma(196;0.109)|all_hematologic(541;0.131)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AACCATCCCTTGTGACTCCTT	0.408																																																	1	Substitution - coding silent(1)	kidney(1)											81.0	77.0	78.0					5																	150276453		2203	4299	6502	SO:0001819	synonymous_variant	91975			AF395541	CCDS4311.2, CCDS54939.1, CCDS54940.1	5q33.1	2013-01-08			ENSG00000145908	ENSG00000145908		"""Zinc fingers, C2H2-type"", ""-"""	13091	protein-coding gene	gene with protein product		612429				14746915	Standard	NM_052860		Approved		uc021yfx.1	Q96RE9	OTTHUMG00000130076	ENST00000274599.5:c.348A>G	5.37:g.150276453T>C		Somatic		WXS	Illumina HiSeq	Phase_I	A8MY91|B3KU35|B4DU78|F5GWS1|Q06DQ3|Q17RP3|Q5H9N5	Silent	SNP	ENST00000274599.5	37	CCDS4311.2																																																																																				0.408	ZNF300-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding			NM_052860	
ZNF717	100131827	hgsc.bcm.edu	37	3	75790810	75790811	+	Frame_Shift_Ins	INS	-	-	T	rs199577560	byFrequency	TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr3:75790810_75790811insT	ENST00000477374.1	-	3	305_306	c.134_135insA	c.(133-135)accfs	p.T45fs	ZNF717_ENST00000422325.1_Frame_Shift_Ins_p.T45fs|ZNF717_ENST00000478296.1_5'UTR|ZNF717_ENST00000491507.1_5'UTR|ZNF717_ENST00000400845.3_Frame_Shift_Ins_p.T38fs			Q9BY31	ZN717_HUMAN	zinc finger protein 717	38	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						CCCTGTACAGGGTCCTCTGAGC	0.51																																																	0																																										SO:0001589	frameshift_variant	100131827			AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124		"""Zinc fingers, C2H2-type"", ""-"""	29448	protein-coding gene	gene with protein product			"""zinc finger protein 838"""	ZNF838			Standard	NM_001128223		Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000477374.1:c.134_135insA	3.37:g.75790810_75790811insT	ENSP00000417902:p.Thr45fs	Somatic		WXS	Illumina HiSeq	Phase_I		Frame_Shift_Ins	INS	ENST00000477374.1	37																																																																																					0.510	ZNF717-005	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000352767.1		NM_001128223	
ABCF1	23	broad.mit.edu	37	6	30551602	30551602	+	Missense_Mutation	SNP	T	T	C			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr6:30551602T>C	ENST00000326195.8	+	12	1149	c.1037T>C	c.(1036-1038)cTc>cCc	p.L346P	ABCF1_ENST00000376545.3_Missense_Mutation_p.L308P|ABCF1_ENST00000396515.4_Intron|MIR877_ENST00000401282.1_RNA	NM_001025091.1	NP_001020262.1	Q8NE71	ABCF1_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 1	346	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				inflammatory response (GO:0006954)|positive regulation of translation (GO:0045727)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|polysomal ribosome (GO:0042788)|ribosome (GO:0005840)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)|translation activator activity (GO:0008494)|translation factor activity, nucleic acid binding (GO:0008135)	p.L346P(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(3)|skin(2)	21						ACCACACTCCTCAAGCACATT	0.547																																																	1	Substitution - Missense(1)	kidney(1)											101.0	83.0	89.0					6																	30551602		1511	2709	4220	SO:0001583	missense	23			AF027302	CCDS34380.1, CCDS34381.1	6p21.33	2012-03-14			ENSG00000204574	ENSG00000204574		"""ATP binding cassette transporters / subfamily F"""	70	protein-coding gene	gene with protein product		603429		ABC50		9790762	Standard	NM_001025091		Approved	EST123147	uc003nql.3	Q8NE71	OTTHUMG00000031094	ENST00000326195.8:c.1037T>C	6.37:g.30551602T>C	ENSP00000313603:p.Leu346Pro	Somatic		WXS	Illumina GAIIx	Phase_I	A2BF75|O14897|Q69YP6	Missense_Mutation	SNP	ENST00000326195.8	37	CCDS34380.1	.	.	.	.	.	.	.	.	.	.	T	18.45	3.627003	0.66901	.	.	ENSG00000204574	ENST00000326195;ENST00000376545;ENST00000455943	D;D	0.95788	-3.81;-3.81	5.19	3.95	0.45737	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.000000	0.85682	D	0.000000	D	0.98157	0.9391	H	0.96996	3.92	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	D	0.98600	1.0658	10	0.87932	D	0	-15.8715	10.8619	0.46831	0.0:0.0:0.1578:0.8421	.	308;346;346	Q2L6I2;Q8NE71;A2BF75	.;ABCF1_HUMAN;.	P	346;308;347	ENSP00000313603:L346P;ENSP00000365728:L308P	ENSP00000313603:L346P	L	+	2	0	ABCF1	30659581	1.000000	0.71417	0.999000	0.59377	0.809000	0.45718	5.607000	0.67648	1.960000	0.56953	0.260000	0.18958	CTC		0.547	ABCF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076137.3			
PIANP	196500	broad.mit.edu	37	12	6806817	6806817	+	Silent	SNP	C	C	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr12:6806817C>T	ENST00000540656.1	-	3	497	c.159G>A	c.(157-159)tcG>tcA	p.S53S	PIANP_ENST00000320591.5_Silent_p.S53S|PIANP_ENST00000534837.1_Silent_p.S53S	NM_001244015.1	NP_001230944.1	Q8IYJ0	PIANP_HUMAN	PILR alpha associated neural protein	53						integral component of membrane (GO:0016021)		p.S53S(1)									GACGTGGGGCCGAGGGGCCTC	0.697																																																	1	Substitution - coding silent(1)	kidney(1)											7.0	8.0	8.0					12																	6806817		1833	3990	5823	SO:0001819	synonymous_variant	0			BC035736	CCDS44818.1, CCDS58205.1	12p13.31	2012-08-17	2012-08-17	2012-08-17	ENSG00000139200	ENSG00000139200			25338	protein-coding gene	gene with protein product	"""PILR-associating neural protein"""		"""chromosome 12 open reading frame 53"""	C12orf53		12975309	Standard	NM_153685		Approved	DKFZp547D2210, PANP	uc001qqf.2	Q8IYJ0	OTTHUMG00000168664	ENST00000540656.1:c.159G>A	12.37:g.6806817C>T		Somatic		WXS	Illumina GAIIx	Phase_I	A8K0T3|B3KPF7|B3KRI6|Q6UX35	Silent	SNP	ENST00000540656.1	37	CCDS44818.1	.	.	.	.	.	.	.	.	.	.	C	7.344	0.621548	0.14193	.	.	ENSG00000139200	ENST00000439553	.	.	.	4.06	-8.12	0.01078	.	.	.	.	.	.	.	.	.	.	.	0.40242	D	0.977979	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.8664	0.24096	0.3799:0.4043:0.0:0.2158	.	.	.	.	.	-1	.	.	.	-	.	.	C12orf53	6677078	0.000000	0.05858	0.550000	0.28217	0.859000	0.49053	-3.543000	0.00436	-3.009000	0.00273	-0.657000	0.03884	.		0.697	PIANP-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400524.1		NM_153685	
GOLGA6L3	100133220	broad.mit.edu	37	15	83014132	83014132	+	Missense_Mutation	SNP	C	C	G			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr15:83014132C>G	ENST00000557886.1	-	6	550	c.451G>C	c.(451-453)Gag>Cag	p.E151Q															p.E151Q(4)		endometrium(6)|kidney(5)|prostate(1)	12						GCTGGGGGCTCTGGGGCCAGG	0.522																																																	4	Substitution - Missense(4)	kidney(4)																																								SO:0001583	missense	647042																														ENST00000557886.1:c.451G>C	15.37:g.83014132C>G	ENSP00000452844:p.Glu151Gln	Somatic		WXS	Illumina GAIIx	Phase_I		Missense_Mutation	SNP	ENST00000557886.1	37																																																																																					0.522	RP13-996F3.4-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000419277.1			
POLR2F	5435	broad.mit.edu	37	22	38349736	38349736	+	5'UTR	SNP	C	C	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr22:38349736C>A	ENST00000442738.2	+	0	67				POLR2F_ENST00000460648.1_5'UTR|POLR2F_ENST00000470701.1_5'UTR|RP5-1039K5.17_ENST00000609976.1_RNA|C22orf23_ENST00000403305.1_5'Flank|POLR2F_ENST00000606538.1_5'UTR|C22orf23_ENST00000403026.1_5'Flank|C22orf23_ENST00000249079.2_5'Flank|POLR2F_ENST00000488684.1_5'UTR|POLR2F_ENST00000407936.1_5'UTR|POLR2F_ENST00000405557.1_5'UTR	NM_021974.3	NP_068809.1	P61218	RPAB2_HUMAN	polymerase (RNA) II (DNA directed) polypeptide F						7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of type I interferon production (GO:0032481)|positive regulation of viral transcription (GO:0050434)|RNA splicing (GO:0008380)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	cytosol (GO:0005829)|DNA-directed RNA polymerase I complex (GO:0005736)|DNA-directed RNA polymerase II, core complex (GO:0005665)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			breast(1)|urinary_tract(2)	3	Melanoma(58;0.045)					CGTAGTGTCGCTGTTTGCGGG	0.657																																																	0													25.0	30.0	29.0					22																	38349736		692	1591	2283	SO:0001623	5_prime_UTR_variant	5435				CCDS13963.1	22q13.1	2013-01-21			ENSG00000100142	ENSG00000100142		"""RNA polymerase subunits"""	9193	protein-coding gene	gene with protein product	"""DNA directed RNA polymerase II 14.4 kda polypeptide"""	604414				8786150	Standard	XR_112241		Approved	RPB6, HRBP14.4	uc010gxi.3	P61218	OTTHUMG00000151160	ENST00000442738.2:c.-59C>A	22.37:g.38349736C>A		Somatic		WXS	Illumina GAIIx	Phase_I	P41584|Q6IAY3	Translation_Start_Site	SNP	ENST00000442738.2	37	CCDS13963.1																																																																																				0.657	POLR2F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321570.1		NM_021974	
RTN1	6252	broad.mit.edu	37	14	60194207	60194207	+	Frame_Shift_Del	DEL	G	G	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr14:60194207delG	ENST00000267484.5	-	3	1530	c.1195delC	c.(1195-1197)ctgfs	p.L399fs		NM_021136.2	NP_066959.1	Q16799	RTN1_HUMAN	reticulon 1	399					neuron differentiation (GO:0030182)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)				central_nervous_system(2)|kidney(2)|large_intestine(9)|lung(30)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	49				OV - Ovarian serous cystadenocarcinoma(108;0.0968)		TCGTGGTCCAGGGGGCTGGGG	0.687																																																	0													13.0	13.0	13.0					14																	60194207		2196	4285	6481	SO:0001589	frameshift_variant	6252			L10333	CCDS9740.1, CCDS9741.1	14q21-q22	2008-08-29			ENSG00000139970	ENSG00000139970			10467	protein-coding gene	gene with protein product		600865	"""neuroendocrine-specific protein"""	NSP		8275708	Standard	NM_206852		Approved		uc001xen.1	Q16799	OTTHUMG00000028947	ENST00000267484.5:c.1195delC	14.37:g.60194207delG	ENSP00000267484:p.Leu399fs	Somatic		WXS	Illumina GAIIx	Phase_I	Q16800|Q16801|Q5BKZ4|Q9BQ59	Frame_Shift_Del	DEL	ENST00000267484.5	37	CCDS9740.1																																																																																				0.687	RTN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000072278.2			
ZRSR1	7310	broad.mit.edu	37	5	112228273	112228273	+	Missense_Mutation	SNP	A	A	G			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr5:112228273A>G	ENST00000391338.1	+	1	961	c.937A>G	c.(937-939)Aaa>Gaa	p.K313E	CTC-487M23.5_ENST00000602872.1_RNA|REEP5_ENST00000504247.1_Intron|REEP5_ENST00000474542.2_Intron|CTC-487M23.8_ENST00000506997.1_3'UTR|REEP5_ENST00000545426.1_3'UTR|CTC-487M23.8_ENST00000512790.1_3'UTR|REEP5_ENST00000379638.4_Intron|REEP5_ENST00000513339.1_Intron	NM_001204199.1	NP_001191128.1	Q15695	U2AFL_HUMAN	zinc finger (CCCH type), RNA-binding motif and serine/arginine rich 1	313						nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(1)|skin(1)|stomach(2)	4						GACCCGGTGGAAAATGGCGAT	0.448																																																	0																																										SO:0001583	missense	6728			D49676		5q22.2	2013-02-12	2006-09-26	2006-09-26	ENSG00000212643	ENSG00000212643		"""Zinc fingers, CCCH-type domain containing"", ""RNA binding motif (RRM) containing"""	12456	protein-coding gene	gene with protein product	"""U2(RNU2) small nuclear RNA auxiliary factor pseudogene 1"""	601079	"""U2(RNU2) small nuclear RNA auxiliary factor binding protein-like"", ""U2(RNU2) small nuclear RNA auxillary factor 1-like 1"", ""U2 small nuclear RNA auxillary factor 1-like 1"""	U2AFBPL, U2AF1P, U2AF1L1		7956352	Standard	NG_005419		Approved	U2AF1-RS1, U2AF1RS1	uc021ycm.1	Q15695	OTTHUMG00000163143	ENST00000391338.1:c.937A>G	5.37:g.112228273A>G	ENSP00000375133:p.Lys313Glu	Somatic		WXS	Illumina GAIIx	Phase_I	B2R901|Q13570|Q2M3R8	Missense_Mutation	SNP	ENST00000391338.1	37		.	.	.	.	.	.	.	.	.	.	A	17.02	3.282693	0.59867	.	.	ENSG00000212643	ENST00000391338	.	.	.	1.58	0.192	0.15134	Zinc finger, CCCH-type (2);	0.044980	0.85682	D	0.000000	T	0.61123	0.2322	.	.	.	0.48571	D	0.99967	D	0.61080	0.989	P	0.56700	0.804	T	0.57888	-0.7733	8	0.51188	T	0.08	.	5.5098	0.16874	0.7148:0.2852:0.0:0.0	.	313	Q15695	U2AFL_HUMAN	E	313	.	ENSP00000375133:K313E	K	+	1	0	ZRSR1	112256172	1.000000	0.71417	0.293000	0.24932	0.953000	0.61014	5.973000	0.70456	0.042000	0.15717	0.383000	0.25322	AAA		0.448	ZRSR1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000371801.1		NM_005083	
SMG1P7	100506060	broad.mit.edu	37	16	70268080	70268081	+	RNA	DNP	TG	TG	CA			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	T|G	T|G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr16:70268080_70268081TG>CA	ENST00000459379.1	-	0	0																											GTCTTACTGTTGGCTAAAAGGC	0.376																																																	0																																												0																														Exception_encountered	16.37:g.70268080_70268081delinsCA		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP	ENST00000459379.1	37																																																																																					0.376	snoU13.216-201	NOVEL	basic	snoRNA	snoRNA				
VAC14	55697	broad.mit.edu	37	16	70834811	70834811	+	De_novo_Start_OutOfFrame	SNP	G	G	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr16:70834811G>T	ENST00000261776.5	-	0	253				RP11-424M24.5_ENST00000574178.1_lincRNA	NM_018052.3	NP_060522.3	Q08AM6	VAC14_HUMAN	Vac14 homolog (S. cerevisiae)						phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|regulation of lipid kinase activity (GO:0043550)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)|PAS complex (GO:0070772)	receptor activity (GO:0004872)			breast(2)|endometrium(2)|kidney(10)|large_intestine(1)|lung(10)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	33		Ovarian(137;0.0699)				CATGGTGGCAGCTGGGGGAAC	0.701																																																	0																																												55697			AK056433	CCDS10896.1	16q22.1	2010-03-23	2005-02-09		ENSG00000103043	ENSG00000103043			25507	protein-coding gene	gene with protein product		604632	"""Tax1 (human T-cell leukemia virus type I) binding protein 2"""	TAX1BP2		15542851, 12719380	Standard	NM_018052		Approved	FLJ10305, ArPIKfyve	uc002ezm.3	Q08AM6	OTTHUMG00000137583	ENST00000261776.5:c.-8C>A	16.37:g.70834811G>T		Somatic		WXS	Illumina GAIIx	Phase_I	B3KPJ5|B3KSM8|Q13174|Q6IA12|Q7L4Y1|Q9BW96|Q9H6V6	Translation_Start_Site	SNP	ENST00000261776.5	37	CCDS10896.1																																																																																				0.701	VAC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268973.3		NM_018052	
YAP1	10413	broad.mit.edu	37	11	101984953	101984953	+	Silent	SNP	T	T	C			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8aa293-650b-4661-b130-8b70f0949b86	ae90c0a2-1155-4615-a6f4-effe4dd84861	g.chr11:101984953T>C	ENST00000282441.5	+	2	788	c.400T>C	c.(400-402)Ttg>Ctg	p.L134L	YAP1_ENST00000345877.2_Silent_p.L134L|YAP1_ENST00000531439.1_Silent_p.L134L|YAP1_ENST00000524575.1_5'UTR|YAP1_ENST00000537274.1_Silent_p.L134L|YAP1_ENST00000526343.1_Silent_p.L134L	NM_001130145.2|NM_001282101.1	NP_001123617.1|NP_001269030.1	P46937	YAP1_HUMAN	Yes-associated protein 1	134					cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|contact inhibition (GO:0060242)|embryonic heart tube morphogenesis (GO:0003143)|gene expression (GO:0010467)|hippo signaling (GO:0035329)|keratinocyte differentiation (GO:0030216)|lateral mesoderm development (GO:0048368)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|notochord development (GO:0030903)|paraxial mesoderm development (GO:0048339)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell proliferation (GO:0008284)|positive regulation of organ growth (GO:0046622)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of keratinocyte proliferation (GO:0010837)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|regulation of stem cell proliferation (GO:0072091)|somatic stem cell maintenance (GO:0035019)|transcription initiation from RNA polymerase II promoter (GO:0006367)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)	p.L134L(1)		central_nervous_system(1)|large_intestine(1)|lung(1)|ovary(1)	4	all_cancers(8;0.000575)|all_epithelial(12;0.00564)	Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.00936)	Lung(13;0.245)	BRCA - Breast invasive adenocarcinoma(274;0.0189)		TTCTCTGCAGTTGGGAGCTGT	0.527																																					Colon(50;247 1103 7861 28956)												1	Substitution - coding silent(1)	kidney(1)											67.0	66.0	66.0					11																	101984953		2203	4299	6502	SO:0001819	synonymous_variant	10413				CCDS8314.1, CCDS44716.1, CCDS8314.2, CCDS53699.1, CCDS53700.1, CCDS60944.1, CCDS73373.1, CCDS73374.1	11q13	2010-03-19	2010-03-19		ENSG00000137693	ENSG00000137693			16262	protein-coding gene	gene with protein product		606608	"""Yes-associated protein 1, 65kDa"""			7782338	Standard	NM_001130145		Approved	YAP65	uc001pgt.3	P46937	OTTHUMG00000167322	ENST00000282441.5:c.400T>C	11.37:g.101984953T>C		Somatic		WXS	Illumina GAIIx	Phase_I	B4DTY1|B7ZA01|E3WEB5|E3WEB6|E9PRV2|F5H202|K0KQ18|K0KYZ8|K0L195|K0L1G3|Q7Z574|Q8IUY9	Silent	SNP	ENST00000282441.5	37	CCDS44716.1																																																																																				0.527	YAP1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394151.1		NM_006106	
