#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_refseq_mrna_id	i_secondary_variant_classification
PALD1	27143	broad.mit.edu;hgsc.bcm.edu;ucsc.edu;mdanderson.org	37	10	72293731	72293731	+	Silent	SNP	C	C	G			TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr10:72293731C>G	ENST00000263563.6	+	8	1192	c.924C>G	c.(922-924)ctC>ctG	p.L308L		NM_014431.2	NP_055246.2	Q9ULE6	PALD_HUMAN	phosphatase domain containing, paladin 1	308						cytosol (GO:0005829)											CCCCAGCCCTCGTCTTCAGCT	0.657																																						.											0													36.0	33.0	34.0					10																	72293731		2203	4300	6503	SO:0001819	synonymous_variant	27143			AB033100	CCDS31215.1	10q22.2	2012-07-17	2012-07-17	2012-07-17	ENSG00000107719	ENSG00000107719			23530	protein-coding gene	gene with protein product		614656	"""paladin"", ""KIAA1274"""	PALD, KIAA1274			Standard	NM_014431		Approved		uc001jrd.4	Q9ULE6	OTTHUMG00000018411	ENST00000263563.6:c.924C>G	10.37:g.72293731C>G		Somatic		WXS	Illumina HiSeq	Phase_I	B2RMS1|B9EGC6|Q5JTK7|Q5JTK8	Silent	SNP	ENST00000263563.6	37	CCDS31215.1																																																																																				0.657	PALD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048515.2	NM_014431	
DDIT4	54541	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	10	74034518	74034518	+	Missense_Mutation	SNP	C	C	A			TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr10:74034518C>A	ENST00000307365.3	+	3	472	c.271C>A	c.(271-273)Cac>Aac	p.H91N	RP11-442H21.2_ENST00000491934.2_RNA	NM_019058.2	NP_061931.1	Q9NX09	DDIT4_HUMAN	DNA-damage-inducible transcript 4	91					brain development (GO:0007420)|cell proliferation (GO:0008283)|defense response to virus (GO:0051607)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|negative regulation of glycolytic process (GO:0045820)|negative regulation of intracellular signal transduction (GO:1902532)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of TOR signaling (GO:0032007)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of neuron death (GO:1901216)|protein complex disassembly (GO:0043241)|reactive oxygen species metabolic process (GO:0072593)|response to hypoxia (GO:0001666)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|mitochondrion (GO:0005739)				cervix(1)|endometrium(2)|lung(5)|pancreas(1)|prostate(2)|urinary_tract(1)	12						TGAGGATGAACACTTGTGTGC	0.617											OREG0020262	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										.											0													124.0	124.0	124.0					10																	74034518		2203	4300	6503	SO:0001583	missense	54541			AK000507	CCDS7315.1	10q22.1	2008-05-14			ENSG00000168209	ENSG00000168209			24944	protein-coding gene	gene with protein product	"""HIF-1 responsive RTP801"""	607729				11884613	Standard	NM_019058		Approved	RTP801, FLJ20500, REDD-1, REDD1, Dig2	uc001jsx.1	Q9NX09	OTTHUMG00000018435	ENST00000307365.3:c.271C>A	10.37:g.74034518C>A	ENSP00000307305:p.His91Asn	Somatic	1149	WXS	Illumina HiSeq	Phase_I	Q9H0S3	Missense_Mutation	SNP	ENST00000307365.3	37	CCDS7315.1	.	.	.	.	.	.	.	.	.	.	C	12.28	1.890774	0.33348	.	.	ENSG00000168209	ENST00000307365	T	0.41400	1.0	5.08	5.08	0.68730	.	0.414258	0.28790	N	0.014133	T	0.27731	0.0682	N	0.14661	0.345	0.33043	D	0.531739	B	0.26744	0.158	B	0.24394	0.053	T	0.20174	-1.0283	10	0.15066	T	0.55	-20.3523	18.1098	0.89532	0.0:1.0:0.0:0.0	.	91	Q9NX09	DDIT4_HUMAN	N	91	ENSP00000307305:H91N	ENSP00000307305:H91N	H	+	1	0	DDIT4	73704524	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	3.432000	0.52824	2.359000	0.80004	0.561000	0.74099	CAC		0.617	DDIT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048577.1	NM_019058	
MTOR	2475	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	1	11174395	11174395	+	Missense_Mutation	SNP	A	A	C			TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr1:11174395A>C	ENST00000361445.4	-	53	7356	c.7280T>G	c.(7279-7281)cTg>cGg	p.L2427R	MTOR_ENST00000376838.1_Missense_Mutation_p.L632R	NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	2427	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				cell growth (GO:0016049)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell development (GO:0007281)|growth (GO:0040007)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of macroautophagy (GO:0016242)|negative regulation of NFAT protein import into nucleus (GO:0051534)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of gene expression (GO:0010628)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of carbohydrate utilization (GO:0043610)|regulation of fatty acid beta-oxidation (GO:0031998)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of protein kinase activity (GO:0045859)|regulation of Rac GTPase activity (GO:0032314)|regulation of response to food (GO:0032095)|response to amino acid (GO:0043200)|response to nutrient (GO:0007584)|response to stress (GO:0006950)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|phosphatidylinositol 3-kinase complex (GO:0005942)|PML body (GO:0016605)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	ATP binding (GO:0005524)|drug binding (GO:0008144)|kinase activity (GO:0016301)|phosphoprotein binding (GO:0051219)|protein serine/threonine kinase activity (GO:0004674)|ribosome binding (GO:0043022)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149					Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	CCTCCAGTTCAGCAAGGGGTC	0.537																																						.											0													135.0	115.0	122.0					1																	11174395		2203	4300	6503	SO:0001583	missense	2475			L34075	CCDS127.1	1p36	2014-09-17	2009-05-29	2009-05-29	ENSG00000198793	ENSG00000198793			3942	protein-coding gene	gene with protein product	"""FK506 binding protein 12-rapamycin associated protein 2"", ""rapamycin target protein"", ""FKBP12-rapamycin complex-associated protein 1"", ""FKBP-rapamycin associated protein"", ""rapamycin associated protein FRAP2"", ""dJ576K7.1 (FK506 binding protein 12-rapamycin associated protein 1)"", ""rapamycin and FKBP12 target 1"", ""mammalian target of rapamycin"""	601231	"""FK506 binding protein 12-rapamycin associated protein 1"""	FRAP, FRAP2, FRAP1		8008069, 8660990	Standard	NM_004958		Approved	RAFT1, RAPT1, FLJ44809	uc001asd.3	P42345	OTTHUMG00000002001	ENST00000361445.4:c.7280T>G	1.37:g.11174395A>C	ENSP00000354558:p.Leu2427Arg	Somatic		WXS	Illumina HiSeq	Phase_I	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Missense_Mutation	SNP	ENST00000361445.4	37	CCDS127.1	.	.	.	.	.	.	.	.	.	.	A	26.6	4.750738	0.89753	.	.	ENSG00000198793	ENST00000361445;ENST00000376838;ENST00000455339	T;T;T	0.80033	-1.33;-1.33;-1.33	5.89	5.89	0.94794	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (4);	0.000000	0.85682	D	0.000000	D	0.91730	0.7385	M	0.92026	3.265	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.93392	0.6752	10	0.87932	D	0	-16.8498	15.497	0.75662	1.0:0.0:0.0:0.0	.	2427	P42345	MTOR_HUMAN	R	2427;632;83	ENSP00000354558:L2427R;ENSP00000366034:L632R;ENSP00000398745:L83R	ENSP00000354558:L2427R	L	-	2	0	MTOR	11096982	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.923000	0.92808	2.254000	0.74563	0.533000	0.62120	CTG		0.537	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958	
ZNF668	79759	broad.mit.edu;hgsc.bcm.edu;ucsc.edu;mdanderson.org	37	16	31073370	31073370	+	Silent	SNP	C	C	G			TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr16:31073370C>G	ENST00000538906.1	-	3	1663	c.879G>C	c.(877-879)tcG>tcC	p.S293S	ZNF668_ENST00000535577.1_Silent_p.S293S|ZNF668_ENST00000417110.2_Silent_p.L186L|ZNF668_ENST00000539836.3_Silent_p.S316S|ZNF668_ENST00000394983.2_Silent_p.S293S|ZNF668_ENST00000426488.2_Silent_p.S316S|ZNF668_ENST00000564456.1_5'Flank|ZNF668_ENST00000300849.4_Silent_p.S293S	NM_001172668.1	NP_001166139	Q96K58	ZN668_HUMAN	zinc finger protein 668	293					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)			breast(6)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	27						GACGGAAGCTCGAGGGGTCGG	0.677																																					Colon(181;1111 1980 5060 10512 25785)	.											0													37.0	36.0	36.0					16																	31073370		2197	4298	6495	SO:0001819	synonymous_variant	79759				CCDS10701.1, CCDS54003.1	16p11.2	2013-01-08			ENSG00000167394	ENSG00000167394		"""Zinc fingers, C2H2-type"""	25821	protein-coding gene	gene with protein product						12477932	Standard	NM_024706		Approved	FLJ13479	uc021tgt.1	Q96K58	OTTHUMG00000047357	ENST00000538906.1:c.879G>C	16.37:g.31073370C>G		Somatic		WXS	Illumina HiSeq	Phase_I	C9JHH8|F5H7E7|Q59EV1|Q8N669|Q9H8L4	Silent	SNP	ENST00000538906.1	37	CCDS10701.1																																																																																				0.677	ZNF668-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108516.2	NM_024706	
ZNF521	25925	broad.mit.edu;hgsc.bcm.edu	37	18	22930911	22930911	+	5'UTR	SNP	C	C	A			TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr18:22930911C>A	ENST00000361524.3	-	0	148				ZNF521_ENST00000579111.1_5'UTR|ZNF521_ENST00000584787.1_Intron|ZNF521_ENST00000538137.2_5'UTR	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521						cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)			NS(1)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(21)|lung(97)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	149	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					GGCGAGACATCCTAAAAGCAA	0.607			T	PAX5	ALL																																	.		Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	0													53.0	53.0	53.0					18																	22930911		2149	4207	6356	SO:0001623	5_prime_UTR_variant	25925			AK027354	CCDS32806.1	18q11.2	2013-01-08				ENSG00000198795		"""Zinc fingers, C2H2-type"""	24605	protein-coding gene	gene with protein product	"""early hematopoietic zinc finger"""	610974				11984006, 14630787	Standard	NM_015461		Approved	EHZF, Evi3	uc002kvk.2	Q96K83		ENST00000361524.3:c.-1G>T	18.37:g.22930911C>A		Somatic		WXS	Illumina HiSeq	Phase_I	A3QVP7|B0YJB7|Q8IXI0|Q8TES6|Q9C065|Q9HAL5|Q9UFK4	Splice_Site	SNP	ENST00000361524.3	37	CCDS32806.1																																																																																				0.607	ZNF521-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446781.2	NM_015461	
ZNF271	10778	hgsc.bcm.edu	37	18	32888397	32888398	+	RNA	INS	-	-	AA	rs63352060		TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr18:32888397_32888398insAA	ENST00000399070.3	+	0	2791_2792					NR_024565.1|NR_024566.1		Q14591	ZN271_HUMAN	zinc finger protein 271						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(3)|lung(9)	12						aaaaaaaaaagaaaaaaaaaCT	0.421																																						.											0																																												10778			X78930		18q12.2	2013-04-03			ENSG00000257267	ENSG00000257267		"""Zinc fingers, C2H2-type"""	13065	other	unknown		604754				7865130, 11777961	Standard	NR_024565		Approved	HZF7, ZNFEB	uc002kyp.4	Q14591	OTTHUMG00000132563		18.37:g.32888404_32888405dupAA		Somatic		WXS	Illumina HiSeq	Phase_I	B3KN34|Q96T29|Q9BSX2|Q9UN33|Q9Y5B7	RNA	INS	ENST00000399070.3	37																																																																																					0.421	ZNF271-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000255767.2	NR_024565	
DGCR6	8214	broad.mit.edu;hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	22	18900771	18900771	+	IGR	SNP	C	C	T			TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr22:18900771C>T	ENST00000331444.6	+	0	1214				PRODH_ENST00000420436.1_Missense_Mutation_p.G466S|PRODH_ENST00000357068.6_Missense_Mutation_p.G574S|PRODH_ENST00000334029.2_Missense_Mutation_p.G466S	NM_005675.4	NP_005666.2	Q14129	DGCR6_HUMAN	DiGeorge syndrome critical region gene 6						cell adhesion (GO:0007155)|organ morphogenesis (GO:0009887)	nucleus (GO:0005634)|proteinaceous extracellular matrix (GO:0005578)				central_nervous_system(1)|cervix(1)|upper_aerodigestive_tract(1)	3						CGATGGGTGCCCTTCATGAGG	0.662																																						.											0													23.0	21.0	22.0					22																	18900771		2183	4257	6440	SO:0001628	intergenic_variant	5625			X96484	CCDS13753.1	22q11.21	2008-06-12			ENSG00000183628	ENSG00000183628			2846	protein-coding gene	gene with protein product		601279				8733130	Standard	NM_005675		Approved		uc002zoh.4	Q14129	OTTHUMG00000150162		22.37:g.18900771C>T		Somatic		WXS	Illumina HiSeq	Phase_I	B2RCH5|D3DX15|G5E9J8|Q9BY28	Missense_Mutation	SNP	ENST00000331444.6	37	CCDS13753.1	.	.	.	.	.	.	.	.	.	.	N	25.4	4.638432	0.87760	.	.	ENSG00000100033	ENST00000357068;ENST00000313755	T	0.30981	1.51	4.43	4.43	0.53597	Proline dehydrogenase (1);	0.000000	0.85682	D	0.000000	T	0.54334	0.1852	M	0.73372	2.23	0.54753	D	0.999981	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.58797	-0.7573	10	0.62326	D	0.03	-26.3236	14.911	0.70758	0.0:1.0:0.0:0.0	.	490;574;466	O43272-1;O43272;E7EQL6	.;PROD_HUMAN;.	S	574;219	ENSP00000349577:G574S	ENSP00000318329:G219S	G	-	1	0	PRODH	17280771	1.000000	0.71417	0.996000	0.52242	0.484000	0.33280	1.102000	0.31050	2.196000	0.70406	0.505000	0.49811	GGC		0.662	DGCR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316631.2	NM_005675	
CLUAP1	23059	hgsc.bcm.edu	37	16	3586166	3586166	+	Silent	SNP	C	C	T	rs377189683		TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr16:3586166C>T	ENST00000576634.1	+	12	1281	c.1137C>T	c.(1135-1137)gaC>gaT	p.D379D	CLUAP1_ENST00000571025.1_3'UTR|NLRC3_ENST00000448023.2_RNA|NLRC3_ENST00000419350.2_RNA|CLUAP1_ENST00000572600.1_Silent_p.D213D|CLUAP1_ENST00000445795.2_Silent_p.D157D|NLRC3_ENST00000359128.5_RNA|NLRC3_ENST00000301749.7_RNA|CLUAP1_ENST00000417763.2_Silent_p.D213D|CLUAP1_ENST00000341633.5_Silent_p.D398D	NM_015041.2	NP_055856.1	Q96AJ1	CLUA1_HUMAN	clusterin associated protein 1	379	Asp-rich.				cilium assembly (GO:0042384)	centrosome (GO:0005813)|cilium (GO:0005929)|intracellular membrane-bounded organelle (GO:0043231)|intraciliary transport particle B (GO:0030992)|nucleus (GO:0005634)		p.D379D(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(1)|ovary(1)|pancreas(1)|urinary_tract(2)	16						ATGATGATGACGAGGATGACG	0.483																																						.											1	Substitution - coding silent(1)	large_intestine(1)											125.0	111.0	116.0					16																	3586166		2197	4300	6497	SO:0001819	synonymous_variant	23059			BC017070	CCDS32381.1, CCDS45398.1	16p13.3	2014-07-18				ENSG00000103351		"""Intraflagellar transport homologs"""	19009	protein-coding gene	gene with protein product	"""flagellar associated protein 22, qilin-like protein, homolog (Chlamydomonas)"", ""cilia and flagella associated protein 22"""					15480429, 9734811, 19253336	Standard	NM_015041		Approved	FLJ13297, KIAA0643, FAP22, CFAP22	uc002cvk.2	Q96AJ1		ENST00000576634.1:c.1137C>T	16.37:g.3586166C>T		Somatic		WXS	Illumina HiSeq	Phase_I	O75138|Q65ZA3|Q9H8R4|Q9H8T1	Silent	SNP	ENST00000576634.1	37	CCDS32381.1																																																																																				0.483	CLUAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437883.2	NM_024793	
MFSD11	79157	hgsc.bcm.edu	37	17	74765928	74765928	+	Silent	SNP	T	T	C			TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr17:74765928T>C	ENST00000588460.1	+	10	2891	c.849T>C	c.(847-849)atT>atC	p.I283I	MFSD11_ENST00000593181.1_Silent_p.I231I|MFSD11_ENST00000355954.3_Silent_p.I231I|MFSD11_ENST00000586622.1_Silent_p.I283I|MFSD11_ENST00000590514.1_Silent_p.I283I|MFSD11_ENST00000336509.4_Silent_p.I283I	NM_001242534.1	NP_001229463.1	O43934	MFS11_HUMAN	major facilitator superfamily domain containing 11	283						integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|skin(1)	17						TTTCTGGCATTTTCATCGGCA	0.318																																						.											0													142.0	151.0	148.0					17																	74765928		2203	4300	6503	SO:0001819	synonymous_variant	79157			BC002753	CCDS11750.1, CCDS56045.1	17q25.1	2012-03-09			ENSG00000092931	ENSG00000092931			25458	protein-coding gene	gene with protein product						9358160	Standard	NM_001242532		Approved	FLJ22196, FLJ20226	uc002jte.3	O43934		ENST00000588460.1:c.849T>C	17.37:g.74765928T>C		Somatic		WXS	Illumina HiSeq	Phase_I	O43442|Q9NXI5	Silent	SNP	ENST00000588460.1	37	CCDS11750.1																																																																																				0.318	MFSD11-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451516.1	NM_024311	
ZNF345	25850	hgsc.bcm.edu	37	19	37368304	37368304	+	Missense_Mutation	SNP	G	G	T	rs199871319		TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr19:37368304G>T	ENST00000529555.1	+	2	1360	c.572G>T	c.(571-573)cGg>cTg	p.R191L	ZNF345_ENST00000432005.2_Intron|ZNF345_ENST00000589046.1_Missense_Mutation_p.R191L|ZNF345_ENST00000420450.1_Missense_Mutation_p.R191L|ZNF345_ENST00000526123.1_Intron			Q14585	ZN345_HUMAN	zinc finger protein 345	191					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(5)|ovary(2)|prostate(1)	24	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			GCCCTTATTCGGCATCACAGA	0.428																																						.											0													66.0	63.0	64.0					19																	37368304		2203	4300	6503	SO:0001583	missense	25850			X78933	CCDS12497.1	19q13.12	2013-01-08			ENSG00000251247	ENSG00000251247		"""Zinc fingers, C2H2-type"""	16367	protein-coding gene	gene with protein product						7865130	Standard	NM_003419		Approved	HZF10	uc002oey.4	Q14585	OTTHUMG00000048162	ENST00000529555.1:c.572G>T	19.37:g.37368304G>T	ENSP00000431202:p.Arg191Leu	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000529555.1	37	CCDS12497.1	.	.	.	.	.	.	.	.	.	.	G	7.717	0.696334	0.15106	.	.	ENSG00000251247	ENST00000420450;ENST00000529555	T;T	0.34667	1.35;1.35	3.86	0.409	0.16382	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.21921	0.0528	L	0.33624	1.015	0.09310	N	1	B	0.27679	0.185	B	0.22880	0.042	T	0.19224	-1.0312	8	.	.	.	.	5.1742	0.15126	0.2137:0.1775:0.6088:0.0	.	191	Q14585	ZN345_HUMAN	L	191	ENSP00000431216:R191L;ENSP00000431202:R191L	.	R	+	2	0	ZNF345	42060144	0.000000	0.05858	0.997000	0.53966	0.969000	0.65631	-2.856000	0.00729	0.361000	0.24292	0.561000	0.74099	CGG		0.428	ZNF345-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388258.1		
SRRM5	100170229	broad.mit.edu;hgsc.bcm.edu	37	19	44117020	44117020	+	Silent	SNP	C	C	T			TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr19:44117020C>T	ENST00000607544.1	+	3	1069	c.747C>T	c.(745-747)atC>atT	p.I249I	SRRM5_ENST00000417606.1_Silent_p.I249I|ZNF428_ENST00000300811.3_Intron|SRRM5_ENST00000526798.1_Silent_p.I264I			B3KS81	SRRM5_HUMAN	serine/arginine repetitive matrix 5	249	Ser-rich.									endometrium(11)|kidney(2)|skin(1)|stomach(1)	15						GTCAGATGATCATCCCCAGTA	0.537																																						.											0													108.0	107.0	107.0					19																	44117020		692	1591	2283	SO:0001819	synonymous_variant	100170229			AK297891	CCDS46095.1	19q13.31	2013-09-20			ENSG00000226763	ENSG00000226763			37248	protein-coding gene	gene with protein product							Standard	NM_001145641		Approved		uc010xwr.2	B3KS81	OTTHUMG00000165480	ENST00000607544.1:c.747C>T	19.37:g.44117020C>T		Somatic		WXS	Illumina HiSeq	Phase_I	B4DNF0	Silent	SNP	ENST00000607544.1	37	CCDS46095.1																																																																																				0.537	SRRM5-001	KNOWN	alternative_5_UTR|upstream_ATG|basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000384398.2	NM_001145641	
CCNE2	9134	hgsc.bcm.edu	37	8	95897417	95897417	+	Missense_Mutation	SNP	C	C	T	rs549362026		TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr8:95897417C>T	ENST00000520509.1	-	9	961	c.709G>A	c.(709-711)Gaa>Aaa	p.E237K	CCNE2_ENST00000308108.4_Missense_Mutation_p.E237K|CCNE2_ENST00000396133.3_Missense_Mutation_p.E237K|RP11-347C18.5_ENST00000605911.1_RNA|CCNE2_ENST00000523476.1_5'Flank			O96020	CCNE2_HUMAN	cyclin E2	237					cell cycle checkpoint (GO:0000075)|cell division (GO:0051301)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)			cervix(1)|endometrium(2)|large_intestine(3)|lung(4)|prostate(1)	11	Breast(36;8.75e-07)					GGACAAAGTTCCCATTTTAAA	0.358													C|||	1	0.000199681	0.0	0.0014	5008	,	,		18526	0.0		0.0	False		,,,				2504	0.0					.											0													70.0	74.0	73.0					8																	95897417		2203	4297	6500	SO:0001583	missense	9134			AF091433	CCDS6264.1	8q22.1	2005-10-18			ENSG00000175305	ENSG00000175305			1590	protein-coding gene	gene with protein product		603775				9840927, 9840943	Standard	NM_057749		Approved	CYCE2	uc003yhc.3	O96020	OTTHUMG00000164696	ENST00000520509.1:c.709G>A	8.37:g.95897417C>T	ENSP00000429089:p.Glu237Lys	Somatic		WXS	Illumina HiSeq	Phase_I	O95439	Missense_Mutation	SNP	ENST00000520509.1	37	CCDS6264.1	.	.	.	.	.	.	.	.	.	.	C	16.63	3.175750	0.57692	.	.	ENSG00000175305	ENST00000520509;ENST00000308108;ENST00000542725;ENST00000396133	T;T;T	0.11063	2.81;2.81;2.81	5.58	4.68	0.58851	Cyclin, N-terminal (1);Cyclin-like (2);	0.134136	0.64402	D	0.000002	T	0.15609	0.0376	L	0.39397	1.21	0.58432	D	0.999991	B;P	0.50528	0.425;0.936	B;P	0.50082	0.159;0.63	T	0.04413	-1.0953	10	0.22109	T	0.4	.	16.0982	0.81144	0.0:0.8658:0.1342:0.0	.	237;237	Q8WUE3;O96020	.;CCNE2_HUMAN	K	237;237;129;237	ENSP00000429089:E237K;ENSP00000309181:E237K;ENSP00000379437:E237K	ENSP00000309181:E237K	E	-	1	0	CCNE2	95966593	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.803000	0.47924	1.289000	0.44618	0.650000	0.86243	GAA		0.358	CCNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379808.1	NM_057749, NM_004702	
PRDM2	7799	broad.mit.edu	37	1	14107869	14107869	+	Silent	SNP	T	T	C			TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr1:14107869T>C	ENST00000235372.7	+	8	4435	c.3579T>C	c.(3577-3579)tgT>tgC	p.C1193C	PRDM2_ENST00000343137.4_Silent_p.C992C|PRDM2_ENST00000503842.1_Intron|PRDM2_ENST00000413440.1_Silent_p.C992C|PRDM2_ENST00000505823.1_Intron|PRDM2_ENST00000376048.5_Intron|PRDM2_ENST00000311066.5_Silent_p.C1193C	NM_012231.4	NP_036363.2	Q13029	PRDM2_HUMAN	PR domain containing 2, with ZNF domain	1193					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(16)|lung(20)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	55	Ovarian(185;0.249)	all_lung(284;2.56e-05)|Lung NSC(185;4.94e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)	GBM - Glioblastoma multiforme(2;0.00182)	UCEC - Uterine corpus endometrioid carcinoma (279;0.00224)|Colorectal(212;3.23e-08)|BRCA - Breast invasive adenocarcinoma(304;2.16e-05)|COAD - Colon adenocarcinoma(227;2.53e-05)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00446)|READ - Rectum adenocarcinoma(331;0.0276)|Lung(427;0.145)		TCTTTGTGTGTTCTGTTTGTA	0.413																																						.											0													97.0	95.0	95.0					1																	14107869		2203	4300	6503	SO:0001819	synonymous_variant	7799			U17838	CCDS150.1, CCDS151.1, CCDS30603.1, CCDS44061.1	1p36	2011-07-01			ENSG00000116731	ENSG00000116731		"""Chromatin-modifying enzymes / K-methyltransferases"""	9347	protein-coding gene	gene with protein product	"""retinoblastoma protein-binding zinc finger protein"", ""retinoblastoma protein-interacting zinc finger protein"", ""MTE-binding protein"", ""zinc-finger DNA-binding protein"", ""GATA-3 binding protein G3B"""	601196				7538672	Standard	NM_012231		Approved	RIZ, RIZ1, RIZ2, KMT8, MTB-ZF, HUMHOXY1	uc001avi.3	Q13029	OTTHUMG00000007917	ENST00000235372.7:c.3579T>C	1.37:g.14107869T>C		Somatic		WXS	Illumina HiSeq	Phase_I	B1AJZ4|B5MC68|Q13149|Q14550|Q5THJ1|Q5VUL9	Silent	SNP	ENST00000235372.7	37	CCDS150.1																																																																																				0.413	PRDM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021792.2	NM_012231	
TAS1R2	80834	broad.mit.edu	37	1	19166380	19166380	+	Missense_Mutation	SNP	A	A	G			TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr1:19166380A>G	ENST00000375371.3	-	6	2254	c.2233T>C	c.(2233-2235)Ttc>Ctc	p.F745L		NM_152232.2	NP_689418.2	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2	745					detection of chemical stimulus involved in sensory perception of sweet taste (GO:0001582)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytokinesis (GO:0032467)|sensory perception of sweet taste (GO:0050916)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(10)|lung(14)|ovary(1)|pancreas(3)|prostate(1)|skin(3)|stomach(1)	45		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00466)|BRCA - Breast invasive adenocarcinoma(304;3.56e-05)|Kidney(64;0.000177)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)	Aspartame(DB00168)	ATGTAGGCGAAGCTGAAACCC	0.542																																						.											0													133.0	118.0	123.0					1																	19166380		2203	4300	6503	SO:0001583	missense	80834				CCDS187.1	1p36.13	2012-08-22	2003-03-07		ENSG00000179002	ENSG00000179002		"""Taste receptors / Type 1"", ""GPCR / Unclassified : Taste receptors"""	14905	protein-coding gene	gene with protein product		606226	"""G protein-coupled receptor 71"""	GPR71			Standard	NM_152232		Approved	T1R2, TR2	uc001bba.1	Q8TE23	OTTHUMG00000002442	ENST00000375371.3:c.2233T>C	1.37:g.19166380A>G	ENSP00000364520:p.Phe745Leu	Somatic		WXS	Illumina HiSeq	Phase_I	Q5TZ19	Missense_Mutation	SNP	ENST00000375371.3	37	CCDS187.1	.	.	.	.	.	.	.	.	.	.	A	14.97	2.693428	0.48202	.	.	ENSG00000179002	ENST00000375371	D	0.85484	-1.99	5.07	5.07	0.68467	GPCR, family 3, C-terminal (2);	0.000000	0.50627	D	0.000110	D	0.89203	0.6648	M	0.77313	2.365	0.43857	D	0.996458	D	0.89917	1.0	D	0.91635	0.999	D	0.87051	0.2147	10	0.05525	T	0.97	.	9.1243	0.36805	0.8157:0.1843:0.0:0.0	.	745	Q8TE23	TS1R2_HUMAN	L	745	ENSP00000364520:F745L	ENSP00000364520:F745L	F	-	1	0	TAS1R2	19038967	0.990000	0.36364	0.981000	0.43875	0.166000	0.22503	3.097000	0.50251	1.916000	0.55485	0.533000	0.62120	TTC		0.542	TAS1R2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000006953.1		
LCK	3932	broad.mit.edu	37	1	32741193	32741193	+	Missense_Mutation	SNP	G	G	A			TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr1:32741193G>A	ENST00000336890.5	+	6	539	c.401G>A	c.(400-402)cGc>cAc	p.R134H	LCK_ENST00000333070.4_Missense_Mutation_p.R134H|LCK_ENST00000373564.3_Missense_Mutation_p.R192H	NM_005356.3	NP_005347.3	P06239	LCK_HUMAN	LCK proto-oncogene, Src family tyrosine kinase	134	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|aging (GO:0007568)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cellular zinc ion homeostasis (GO:0006882)|dephosphorylation (GO:0016311)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hemopoiesis (GO:0030097)|innate immune response (GO:0045087)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of gene expression (GO:0010628)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell receptor signaling pathway (GO:0050862)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|positive regulation of uterine smooth muscle contraction (GO:0070474)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of defense response to virus by virus (GO:0050690)|regulation of lymphocyte activation (GO:0051249)|release of sequestered calcium ion into cytosol (GO:0051209)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to mechanical stimulus (GO:0009612)|response to zinc ion (GO:0010043)|T cell costimulation (GO:0031295)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|pericentriolar material (GO:0000242)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|ATP binding (GO:0005524)|ATPase binding (GO:0051117)|CD4 receptor binding (GO:0042609)|CD8 receptor binding (GO:0042610)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine kinase activity (GO:0004713)|SH2 domain binding (GO:0042169)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(5)|lung(15)|ovary(2)|skin(2)|urinary_tract(1)	37		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.212)			Dasatinib(DB01254)|Ponatinib(DB08901)	AACCTGAGCCGCAAGGACGCG	0.682			T	TRB@	T-ALL																																	.		Dom	yes		1	1p35-p34.3	3932	lymphocyte-specific protein tyrosine kinase		L	0													7.0	9.0	8.0					1																	32741193		2164	4254	6418	SO:0001583	missense	3932			M36881	CCDS359.1	1p34.3	2014-09-17	2014-06-25		ENSG00000182866	ENSG00000182866	2.7.10.1	"""SH2 domain containing"""	6524	protein-coding gene	gene with protein product		153390	"""lymphocyte-specific protein tyrosine kinase"""			2787474	Standard	XM_005270862		Approved		uc001buy.3	P06239	OTTHUMG00000007463	ENST00000336890.5:c.401G>A	1.37:g.32741193G>A	ENSP00000337825:p.Arg134His	Somatic		WXS	Illumina HiSeq	Phase_I	D3DPP8|P07100|Q12850|Q13152|Q5TDH8|Q5TDH9|Q7RTZ3|Q96DW4|Q9NYT8	Missense_Mutation	SNP	ENST00000336890.5	37	CCDS359.1	.	.	.	.	.	.	.	.	.	.	g	35	5.545253	0.96488	.	.	ENSG00000182866	ENST00000336890;ENST00000482949;ENST00000495610;ENST00000373562;ENST00000373557;ENST00000333070;ENST00000436824;ENST00000373564	D;T;D;T;D;D;D	0.93019	-3.15;-0.17;-3.15;-0.18;-3.15;-3.15;-3.15	5.12	5.12	0.69794	SH2 motif (5);	0.195954	0.33161	N	0.005219	D	0.98419	0.9474	H	0.99464	4.58	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.97110	1.0;0.988;0.98;1.0	D	0.99737	1.1014	10	0.87932	D	0	.	17.7565	0.88450	0.0:0.0:1.0:0.0	.	178;192;134;134	E7EN21;Q573B4;P06239-3;P06239	.;.;.;LCK_HUMAN	H	134;192;134;134;178;134;178;192	ENSP00000337825:R134H;ENSP00000431517:R192H;ENSP00000435605:R134H;ENSP00000362663:R134H;ENSP00000362658:R178H;ENSP00000328213:R134H;ENSP00000362665:R192H	ENSP00000328213:R134H	R	+	2	0	LCK	32513780	1.000000	0.71417	1.000000	0.80357	0.860000	0.49131	9.765000	0.98953	2.571000	0.86741	0.505000	0.49811	CGC		0.682	LCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019616.4	NM_005356	
RPAP3	79657	broad.mit.edu	37	12	48095315	48095315	+	Frame_Shift_Del	DEL	T	T	-			TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr12:48095315delT	ENST00000005386.3	-	3	341	c.226delA	c.(226-228)accfs	p.T76fs	RPAP3_ENST00000432584.3_5'UTR|RPAP3_ENST00000380650.4_Frame_Shift_Del_p.T76fs	NM_024604.2	NP_078880.2	Q9H6T3	RPAP3_HUMAN	RNA polymerase II associated protein 3	76										endometrium(2)|large_intestine(4)|liver(1)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	16	Lung SC(27;0.192)					TCCTCTCTGGTTTTTTTGGAA	0.323																																						.											0													181.0	172.0	175.0					12																	48095315		2202	4299	6501	SO:0001589	frameshift_variant	79657			AK025561	CCDS8753.1, CCDS53782.1, CCDS53783.1	12q13.11	2013-01-10				ENSG00000005175		"""Tetratricopeptide (TTC) repeat domain containing"""	26151	protein-coding gene	gene with protein product		611477				17643375	Standard	NM_024604		Approved	FLJ21908, spag	uc001rpr.3	Q9H6T3	OTTHUMG00000169668	ENST00000005386.3:c.226delA	12.37:g.48095315delT	ENSP00000005386:p.Thr76fs	Somatic		WXS	Illumina HiSeq	Phase_I	B4DRW9|Q6PHR5	Frame_Shift_Del	DEL	ENST00000005386.3	37	CCDS8753.1																																																																																				0.323	RPAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405340.1	NM_024604	
OTOA	146183	broad.mit.edu	37	16	21698797	21698797	+	Missense_Mutation	SNP	G	G	A			TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr16:21698797G>A	ENST00000286149.4	+	7	464	c.463G>A	c.(463-465)Gtg>Atg	p.V155M	OTOA_ENST00000388956.4_Missense_Mutation_p.V76M|OTOA_ENST00000388958.3_Missense_Mutation_p.V155M			Q7RTW8	OTOAN_HUMAN	otoancorin	155					cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|liver(2)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)	46				GBM - Glioblastoma multiforme(48;0.0414)		GAGCCCTGGCGTGAACCGCAG	0.542																																						.											0													125.0	116.0	119.0					16																	21698797		2199	4300	6499	SO:0001583	missense	146183			AK057335	CCDS10600.2, CCDS32403.1, CCDS53994.1	16p12.2	2009-08-18	2002-07-05		ENSG00000155719	ENSG00000155719			16378	protein-coding gene	gene with protein product	"""cancer/testis antigen 108"""	607038	"""deafness, autosomal recessive 22"""	DFNB22		11972037, 19088187	Standard	NM_170664		Approved	CT108	uc002djh.3	Q7RTW8	OTTHUMG00000090721	ENST00000286149.4:c.463G>A	16.37:g.21698797G>A	ENSP00000286149:p.Val155Met	Somatic		WXS	Illumina HiSeq	Phase_I	A1L3A8|A2VDI0|B3KWU3|E9PF51|Q8NA86|Q96M76	Missense_Mutation	SNP	ENST00000286149.4	37		.	.	.	.	.	.	.	.	.	.	G	17.69	3.452811	0.63290	.	.	ENSG00000155719	ENST00000388958;ENST00000286149;ENST00000388956	T;T;T	0.15487	2.42;2.42;2.42	4.91	3.95	0.45737	.	0.258322	0.30492	N	0.009503	T	0.32734	0.0839	L	0.56769	1.78	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.64237	0.923;0.923	T	0.02668	-1.1126	10	0.54805	T	0.06	-15.1079	10.6677	0.45741	0.0939:0.0:0.9061:0.0	.	76;155	B3KWU3;E9PF51	.;.	M	155;155;76	ENSP00000373610:V155M;ENSP00000286149:V155M;ENSP00000373608:V76M	ENSP00000286149:V155M	V	+	1	0	OTOA	21606298	0.987000	0.35691	0.836000	0.33094	0.996000	0.88848	1.928000	0.40104	1.054000	0.40438	0.650000	0.86243	GTG		0.542	OTOA-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000430021.1		
SLC2A4	6517	broad.mit.edu	37	17	7186903	7186903	+	Missense_Mutation	SNP	T	T	C			TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr17:7186903T>C	ENST00000317370.8	+	3	530	c.262T>C	c.(262-264)Ttt>Ctt	p.F88L	RP1-4G17.2_ENST00000576271.1_RNA|SLC2A4_ENST00000571308.1_Missense_Mutation_p.F88L|SLC2A4_ENST00000424875.2_Missense_Mutation_p.F78L	NM_001042.2	NP_001033.1	P14672	GTR4_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 4	88					amylopectin biosynthetic process (GO:0010021)|brown fat cell differentiation (GO:0050873)|carbohydrate metabolic process (GO:0005975)|cellular response to insulin stimulus (GO:0032869)|cellular response to osmotic stress (GO:0071470)|glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|membrane organization (GO:0061024)|response to ethanol (GO:0045471)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|endomembrane system (GO:0012505)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|insulin-responsive compartment (GO:0032593)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|multivesicular body (GO:0005771)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|trans-Golgi network transport vesicle (GO:0030140)|vesicle membrane (GO:0012506)	D-glucose transmembrane transporter activity (GO:0055056)|glucose transmembrane transporter activity (GO:0005355)			breast(1)|endometrium(3)|large_intestine(7)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	17						CGTGGCCATCTTTTCCGTGGG	0.622																																						.											0													106.0	105.0	105.0					17																	7186903		2203	4300	6503	SO:0001583	missense	6517			M20747	CCDS11097.1	17p13	2013-05-22			ENSG00000181856	ENSG00000181856		"""Solute carriers"""	11009	protein-coding gene	gene with protein product		138190		GLUT4			Standard	NM_001042		Approved		uc002gfp.3	P14672	OTTHUMG00000102181	ENST00000317370.8:c.262T>C	17.37:g.7186903T>C	ENSP00000320935:p.Phe88Leu	Somatic		WXS	Illumina HiSeq	Phase_I	Q05BQ3|Q14CX2	Missense_Mutation	SNP	ENST00000317370.8	37	CCDS11097.1	.	.	.	.	.	.	.	.	.	.	T	24.3	4.519126	0.85495	.	.	ENSG00000181856	ENST00000317370;ENST00000424875	T;T	0.74526	0.12;-0.85	5.31	5.31	0.75309	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	D	0.82305	0.5008	L	0.53729	1.69	0.58432	D	0.999999	D;D	0.76494	0.999;0.998	D;P	0.75020	0.985;0.88	D	0.83584	0.0119	10	0.62326	D	0.03	.	13.256	0.60079	0.0:0.0:0.0:1.0	.	88;78	P14672;F5H081	GTR4_HUMAN;.	L	88;78	ENSP00000320935:F88L;ENSP00000396887:F78L	ENSP00000320935:F88L	F	+	1	0	SLC2A4	7127627	1.000000	0.71417	1.000000	0.80357	0.860000	0.49131	7.525000	0.81892	2.234000	0.73211	0.459000	0.35465	TTT		0.622	SLC2A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220031.3		
STXBP4	252983	broad.mit.edu	37	17	53077156	53077156	+	Missense_Mutation	SNP	A	A	G			TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr17:53077156A>G	ENST00000376352.2	+	6	658	c.451A>G	c.(451-453)Acc>Gcc	p.T151A	STXBP4_ENST00000405898.1_Missense_Mutation_p.T151A|STXBP4_ENST00000299341.4_Missense_Mutation_p.T76A|STXBP4_ENST00000398391.2_Missense_Mutation_p.T76A|STXBP4_ENST00000434978.2_Missense_Mutation_p.T151A	NM_178509.5	NP_848604.3	Q6ZWJ1	STXB4_HUMAN	syntaxin binding protein 4	151					cellular response to DNA damage stimulus (GO:0006974)|glucose transport (GO:0015758)|insulin receptor signaling pathway (GO:0008286)|positive regulation of cell cycle G1/S phase transition (GO:1902808)|positive regulation of keratinocyte proliferation (GO:0010838)|protein stabilization (GO:0050821)|protein targeting (GO:0006605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(4)|ovary(1)|upper_aerodigestive_tract(2)	19						AATCCCAAAGACCTCATCCAC	0.353																																						.											0													84.0	81.0	82.0					17																	53077156		2203	4300	6503	SO:0001583	missense	252983			BC041485	CCDS11584.2	17q22	2008-02-05			ENSG00000166263	ENSG00000166263			19694	protein-coding gene	gene with protein product		610415				12855681	Standard	XM_005257187		Approved	Synip, MGC50337	uc002iuf.1	Q6ZWJ1	OTTHUMG00000074043	ENST00000376352.2:c.451A>G	17.37:g.53077156A>G	ENSP00000365530:p.Thr151Ala	Somatic		WXS	Illumina HiSeq	Phase_I	Q8IVZ5	Missense_Mutation	SNP	ENST00000376352.2	37	CCDS11584.2	.	.	.	.	.	.	.	.	.	.	A	13.50	2.256374	0.39896	.	.	ENSG00000166263	ENST00000376352;ENST00000299341;ENST00000405898;ENST00000434978;ENST00000398391	T;T;T;T;T	0.29655	1.56;1.56;1.56;1.56;1.56	5.35	3.15	0.36227	.	0.702796	0.14653	N	0.306480	T	0.33498	0.0865	M	0.70595	2.14	0.27885	N	0.939557	B;P;B	0.40230	0.329;0.708;0.323	B;B;B	0.43274	0.113;0.414;0.114	T	0.14504	-1.0470	10	0.27082	T	0.32	-0.0072	6.5428	0.22390	0.8135:0.0:0.1865:0.0	.	151;76;151	E7EPP7;Q6ZWJ1-2;Q6ZWJ1	.;.;STXB4_HUMAN	A	151;76;151;151;76	ENSP00000365530:T151A;ENSP00000299341:T76A;ENSP00000385944:T151A;ENSP00000391087:T151A;ENSP00000381427:T76A	ENSP00000299341:T76A	T	+	1	0	STXBP4	50432155	1.000000	0.71417	0.942000	0.38095	0.995000	0.86356	2.090000	0.41682	0.489000	0.27749	0.533000	0.62120	ACC		0.353	STXBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157184.1	NM_178509	
NDUFAF7	55471	broad.mit.edu	37	2	37473258	37473258	+	Missense_Mutation	SNP	T	T	C			TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr2:37473258T>C	ENST00000002125.4	+	8	896	c.856T>C	c.(856-858)Tct>Cct	p.S286P	NDUFAF7_ENST00000336237.6_Missense_Mutation_p.S188P|NDUFAF7_ENST00000483999.1_3'UTR	NM_144736.4	NP_653337.1	Q7L592	NDUF7_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 7	286					methylation (GO:0032259)|mitochondrial respiratory chain complex I assembly (GO:0032981)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	enzyme binding (GO:0019899)|methyltransferase activity (GO:0008168)										CGAGGAACTTTCTCAACGCAT	0.413																																						.											0													210.0	167.0	181.0					2																	37473258		2203	4300	6503	SO:0001583	missense	55471				CCDS1788.1, CCDS42673.1	2p22.2	2012-10-12	2012-10-12	2012-10-12	ENSG00000003509	ENSG00000003509		"""Mitochondrial respiratory chain complex assembly factors"""	28816	protein-coding gene	gene with protein product	"""mitochondrial dysfunction protein A homolog"""	615898	"""chromosome 2 open reading frame 56"""	C2orf56			Standard	NM_144736		Approved	PRO1853, MidA	uc002rqa.4	Q7L592	OTTHUMG00000128468	ENST00000002125.4:c.856T>C	2.37:g.37473258T>C	ENSP00000002125:p.Ser286Pro	Somatic		WXS	Illumina HiSeq	Phase_I	Q7Z399|Q9P1G3	Missense_Mutation	SNP	ENST00000002125.4	37	CCDS1788.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.082869	0.76642	.	.	ENSG00000003509	ENST00000002125;ENST00000336237;ENST00000431821;ENST00000439218	T;T;T;T	0.77877	-1.13;-1.13;-1.13;-1.13	5.67	4.5	0.54988	.	0.102077	0.64402	D	0.000004	D	0.87704	0.6244	M	0.83774	2.66	0.43263	D	0.995204	P;D;D;P	0.69078	0.933;0.997;0.997;0.933	P;D;D;P	0.70227	0.756;0.968;0.947;0.824	D	0.88629	0.3168	10	0.87932	D	0	-13.3875	12.8745	0.57982	0.0:0.0:0.5259:0.474	.	259;215;188;286	E7EUC2;B4DQY3;Q7L592-2;Q7L592	.;.;.;MIDA_HUMAN	P	286;188;207;244	ENSP00000002125:S286P;ENSP00000337431:S188P;ENSP00000399207:S207P;ENSP00000394436:S244P	ENSP00000002125:S286P	S	+	1	0	C2orf56	37326762	1.000000	0.71417	0.975000	0.42487	0.654000	0.38779	1.544000	0.36158	0.911000	0.36747	0.533000	0.62120	TCT		0.413	NDUFAF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250267.1	NM_144736	
CBR1	873	broad.mit.edu	37	21	37443310	37443310	+	Missense_Mutation	SNP	A	A	G			TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr21:37443310A>G	ENST00000290349.6	+	2	527	c.352A>G	c.(352-354)Acc>Gcc	p.T118A	AP000688.14_ENST00000535199.1_RNA|SETD4_ENST00000399201.1_Intron|CBR1_ENST00000399191.3_Missense_Mutation_p.T118A|CBR1_ENST00000439427.2_Missense_Mutation_p.T118A|CBR1_ENST00000466328.2_3'UTR|CBR1_ENST00000530908.1_Missense_Mutation_p.T118A	NM_001757.2	NP_001748.1	P16152	CBR1_HUMAN	carbonyl reductase 1	118					arachidonic acid metabolic process (GO:0019369)|cyclooxygenase pathway (GO:0019371)|drug metabolic process (GO:0017144)|epithelial cell differentiation (GO:0030855)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|vitamin K metabolic process (GO:0042373)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	15-hydroxyprostaglandin dehydrogenase (NADP+) activity (GO:0047021)|carbonyl reductase (NADPH) activity (GO:0004090)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|prostaglandin-E2 9-reductase activity (GO:0050221)			endometrium(2)|kidney(3)	5					Doxorubicin(DB00997)|Haloperidol(DB00502)|Lubiprostone(DB01046)|Tetrabenazine(DB04844)	TTTCTTTGGTACCCGAGATGT	0.433																																						.											0													114.0	102.0	106.0					21																	37443310		2203	4300	6503	SO:0001583	missense	873				CCDS13641.1, CCDS68202.1	21q22.1	2011-09-14			ENSG00000159228	ENSG00000159228	1.1.1.184	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	1548	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 21C, member 1"""	114830		CBR		8432528, 19027726	Standard	NM_001757		Approved	SDR21C1	uc002yvb.1	P16152	OTTHUMG00000086618	ENST00000290349.6:c.352A>G	21.37:g.37443310A>G	ENSP00000290349:p.Thr118Ala	Somatic		WXS	Illumina HiSeq	Phase_I	B2RBZ7|B4DFK7|Q3LHW8	Missense_Mutation	SNP	ENST00000290349.6	37	CCDS13641.1	.	.	.	.	.	.	.	.	.	.	A	15.14	2.745192	0.49151	.	.	ENSG00000159228	ENST00000530908;ENST00000290349;ENST00000439427;ENST00000399191	D;D;D;D	0.85258	-1.96;-1.96;-1.96;-1.96	5.76	5.76	0.90799	NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.80407	0.4617	L	0.33668	1.02	0.80722	D	1	P;B;B	0.38300	0.626;0.408;0.285	B;B;B	0.38156	0.266;0.256;0.198	T	0.81189	-0.1046	10	0.48119	T	0.1	-18.8594	16.0766	0.80971	1.0:0.0:0.0:0.0	.	118;118;118	B4DFK7;E9PQ63;P16152	.;.;CBR1_HUMAN	A	118	ENSP00000434613:T118A;ENSP00000290349:T118A;ENSP00000395132:T118A;ENSP00000382143:T118A	ENSP00000290349:T118A	T	+	1	0	CBR1	36365180	1.000000	0.71417	0.764000	0.31436	0.176000	0.22953	5.420000	0.66441	2.202000	0.70862	0.533000	0.62120	ACC		0.433	CBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194633.2		
CLRN1	7401	broad.mit.edu	37	3	150659389	150659389	+	Missense_Mutation	SNP	T	T	A			TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr3:150659389T>A	ENST00000327047.1	-	2	703	c.413A>T	c.(412-414)tAc>tTc	p.Y138F	RP11-166N6.2_ENST00000469268.1_RNA|CLRN1_ENST00000328863.4_Missense_Mutation_p.Y138F|CLRN1_ENST00000295911.2_Missense_Mutation_p.Y62F|CLRN1-AS1_ENST00000476886.1_RNA|RP11-166N6.3_ENST00000569170.1_Missense_Mutation_p.T48S	NM_174878.2	NP_777367.1	P58418	CLRN1_HUMAN	clarin 1	138					actin filament organization (GO:0007015)|auditory receptor cell stereocilium organization (GO:0060088)|cell motility (GO:0048870)|equilibrioception (GO:0050957)|photoreceptor cell maintenance (GO:0045494)|positive regulation of lamellipodium assembly (GO:0010592)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|microvillus (GO:0005902)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|skin(2)	14			LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			GCTCAAAAGGTACAGCCCTAG	0.388																																						.											0													79.0	80.0	79.0					3																	150659389		2203	4300	6503	SO:0001583	missense	7401			AF388366	CCDS3153.1, CCDS35492.1, CCDS56285.1	3q25.1	2014-09-17	2006-11-23	2006-11-23	ENSG00000163646	ENSG00000163646			12605	protein-coding gene	gene with protein product		606397	"""Usher syndrome 3A"""	USH3, USH3A, RP61		7711740, 8975700	Standard	NM_052995		Approved		uc021xfr.1	P58418	OTTHUMG00000140368	ENST00000327047.1:c.413A>T	3.37:g.150659389T>A	ENSP00000322280:p.Tyr138Phe	Somatic		WXS	Illumina HiSeq	Phase_I	D3DNJ3|E1ACU9|Q8N6A9	Missense_Mutation	SNP	ENST00000327047.1	37	CCDS3153.1	.	.	.	.	.	.	.	.	.	.	T	17.40	3.381113	0.61845	.	.	ENSG00000163646	ENST00000295911;ENST00000327047;ENST00000328863;ENST00000468836;ENST00000485607	D;D;D;D;D	0.81996	-1.56;-1.56;-1.56;-1.56;-1.56	5.1	5.1	0.69264	.	0.000000	0.85682	D	0.000000	D	0.89767	0.6810	M	0.65975	2.015	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.87578	0.998;0.994	D	0.90338	0.4357	10	0.54805	T	0.06	-18.5149	15.1742	0.72899	0.0:0.0:0.0:1.0	.	138;62	P58418;P58418-1	CLRN1_HUMAN;.	F	62;138;138;62;26	ENSP00000295911:Y62F;ENSP00000322280:Y138F;ENSP00000329158:Y138F;ENSP00000419892:Y62F;ENSP00000419244:Y26F	ENSP00000295911:Y62F	Y	-	2	0	CLRN1	152142079	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	6.852000	0.75430	2.041000	0.60428	0.533000	0.62120	TAC		0.388	CLRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277060.1		
MUC4	4585	broad.mit.edu	37	3	195505843	195505843	+	Missense_Mutation	SNP	G	G	C			TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr3:195505843G>C	ENST00000463781.3	-	2	13067	c.12608C>G	c.(12607-12609)aCa>aGa	p.T4203R	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T4203R|MUC4_ENST00000349607.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GGCGTGACCTGTGGATGCTGA	0.592																																						.											0													17.0	14.0	15.0					3																	195505843		691	1576	2267	SO:0001583	missense	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.12608C>G	3.37:g.195505843G>C	ENSP00000417498:p.Thr4203Arg	Somatic		WXS	Illumina HiSeq	Phase_I	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	1.391	-0.580696	0.03854	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.37752	1.18;1.25	.	.	.	.	.	.	.	.	T	0.37652	0.1011	N	0.19112	0.55	0.23784	N	0.996856	D	0.65815	0.995	D	0.69142	0.962	T	0.21449	-1.0245	6	.	.	.	.	.	.	.	.	4075	E7ESK3	.	R	4203	ENSP00000417498:T4203R;ENSP00000420243:T4203R	.	T	-	2	0	MUC4	196990622	0.978000	0.34361	0.016000	0.15963	0.045000	0.14185	2.166000	0.42406	0.452000	0.26830	0.074000	0.15403	ACA		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PRSS35	167681	broad.mit.edu	37	6	84233685	84233685	+	Silent	SNP	G	G	A			TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr6:84233685G>A	ENST00000369700.3	+	2	702	c.525G>A	c.(523-525)aaG>aaA	p.K175K	PRSS35_ENST00000536636.1_Silent_p.K175K	NM_153362.2	NP_699193.2	Q8N3Z0	PRS35_HUMAN	protease, serine, 35	175	Peptidase S1.					extracellular region (GO:0005576)|mitochondrion (GO:0005739)	serine-type endopeptidase activity (GO:0004252)	p.K175N(1)		breast(2)|endometrium(2)|large_intestine(12)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	32		all_cancers(76;0.000113)|Acute lymphoblastic leukemia(125;1.09e-08)|all_hematologic(105;3.12e-05)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0768)		ATGATGGAAAGGACTATGTCA	0.478																																						.											1	Substitution - Missense(1)	large_intestine(1)											100.0	104.0	103.0					6																	84233685		2203	4300	6503	SO:0001819	synonymous_variant	167681			BC037170	CCDS4999.1	6q14.2	2010-05-12	2004-07-09	2004-07-09	ENSG00000146250	ENSG00000146250		"""Serine peptidases / Serine peptidases"""	21387	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 158"""	C6orf158			Standard	NM_153362		Approved	MGC46520, dJ223E3.1	uc003pjz.3	Q8N3Z0	OTTHUMG00000015113	ENST00000369700.3:c.525G>A	6.37:g.84233685G>A		Somatic		WXS	Illumina HiSeq	Phase_I	A8K7B3|Q9BQP6	Silent	SNP	ENST00000369700.3	37	CCDS4999.1																																																																																				0.478	PRSS35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041352.1	NM_153362	
IGF2R	3482	broad.mit.edu	37	6	160485473	160485473	+	Missense_Mutation	SNP	A	A	T			TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr6:160485473A>T	ENST00000356956.1	+	28	4075	c.3927A>T	c.(3925-3927)ttA>ttT	p.L1309F		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	1309					insulin-like growth factor receptor signaling pathway (GO:0048009)|liver development (GO:0001889)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|clathrin coat (GO:0030118)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network transport vesicle (GO:0030140)	G-protein coupled receptor activity (GO:0004930)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|insulin-like growth factor-activated receptor activity (GO:0005010)|mannose binding (GO:0005537)|phosphoprotein binding (GO:0051219)|receptor activity (GO:0004872)|retinoic acid binding (GO:0001972)|transporter activity (GO:0005215)			breast(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(27)|lung(31)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)	Mecasermin(DB01277)	ATGGCTTGTTAAAAATGAACT	0.483																																						.											0													111.0	122.0	118.0					6																	160485473		2203	4300	6503	SO:0001583	missense	3482			J03528	CCDS5273.1	6q25.3	2014-09-16			ENSG00000197081	ENSG00000197081		"""CD molecules"""	5467	protein-coding gene	gene with protein product	"""cation-independent mannose-6 phosphate receptor"""	147280					Standard	NM_000876		Approved	CD222, MPRI, MPR1, CIMPR, M6P-R	uc003qta.3	P11717	OTTHUMG00000015945	ENST00000356956.1:c.3927A>T	6.37:g.160485473A>T	ENSP00000349437:p.Leu1309Phe	Somatic		WXS	Illumina HiSeq	Phase_I	Q7Z7G9|Q96PT5	Missense_Mutation	SNP	ENST00000356956.1	37	CCDS5273.1	.	.	.	.	.	.	.	.	.	.	A	15.47	2.841715	0.51057	.	.	ENSG00000197081	ENST00000356956	T	0.05199	3.48	5.48	2.02	0.26589	Mannose-6-phosphate receptor, binding (1);	0.132235	0.47455	D	0.000222	T	0.08582	0.0213	M	0.86028	2.79	0.44234	D	0.997074	D	0.58268	0.982	P	0.60473	0.875	T	0.11372	-1.0590	10	0.41790	T	0.15	-19.3313	0.1485	0.00090	0.2717:0.1596:0.2555:0.3131	.	1309	P11717	MPRI_HUMAN	F	1309	ENSP00000349437:L1309F	ENSP00000349437:L1309F	L	+	3	2	IGF2R	160405463	0.998000	0.40836	0.943000	0.38184	0.408000	0.30992	0.535000	0.23114	0.516000	0.28340	0.533000	0.62120	TTA		0.483	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876	
Unknown	0	broad.mit.edu	37	7	101988975	101988976	+	IGR	DEL	TG	TG	-			TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr7:101988975_101988976delTG								Y_RNA (11593 upstream) : PRKRIP1 (15367 downstream)																							CGGTTCTTCCTGGCCCTCGGGT	0.545																																						.											0																																										SO:0001628	intergenic_variant	729597																															7.37:g.101988975_101988976delTG		Somatic		WXS	Illumina HiSeq	Phase_I		Frame_Shift_Del	DEL		37																																																																																				0	0.545								
NOTCH2	4853	broad.mit.edu	37	1	120539779	120539780	+	Frame_Shift_Ins	INS	-	-	G			TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr1:120539779_120539780insG	ENST00000256646.2	-	4	810_811	c.591_592insC	c.(589-594)acctgcfs	p.C198fs	NOTCH2_ENST00000602566.1_Frame_Shift_Ins_p.C159fs	NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	198	EGF-like 5; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|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)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872)			breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		AGGTTGAGGCAGGTGCCACCAT	0.559			"""N, F, Mis"""		"""marginal zone lymphoma, DLBCL"""				Alagille Syndrome																													.		Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	0																																										SO:0001589	frameshift_variant	4853	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	AF315356	CCDS908.1	1p13-p11	2013-01-10	2010-06-24		ENSG00000134250	ENSG00000134250		"""Ankyrin repeat domain containing"""	7882	protein-coding gene	gene with protein product		600275	"""Notch (Drosophila) homolog 2"", ""Notch homolog 2 (Drosophila)"""			7698746	Standard	NM_001200001		Approved		uc001eik.3	Q04721	OTTHUMG00000012177	ENST00000256646.2:c.592dupC	1.37:g.120539781_120539781dupG	ENSP00000256646:p.Cys198fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q5T3X7|Q99734|Q9H240	Frame_Shift_Ins	INS	ENST00000256646.2	37	CCDS908.1																																																																																				0.559	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408	
SHANK2	22941	broad.mit.edu	37	11	70824380	70824381	+	In_Frame_Ins	INS	-	-	TTT			TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr11:70824380_70824381insTTT	ENST00000338508.4	-	3	440_441	c.441_442insAAA	c.(439-444)caagcc>caaAAAgcc	p.147_148QA>QKA				Q9UPX8	SHAN2_HUMAN	SH3 and multiple ankyrin repeat domains 2	0	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				adult behavior (GO:0030534)|learning (GO:0007612)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell junction (GO:0030054)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|growth cone (GO:0030426)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GKAP/Homer scaffold activity (GO:0030160)|ionotropic glutamate receptor binding (GO:0035255)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(30)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	62			LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071)			TCGAGACTGGCTTGTTTATACA	0.465																																						.											0																																										SO:0001652	inframe_insertion	22941			AF141901		11q13.2	2013-01-10			ENSG00000162105	ENSG00000162105		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	14295	protein-coding gene	gene with protein product		603290	"""cortactin binding protein 1"""	CORTBP1		10506216	Standard	XM_005277930		Approved	CTTNBP1, ProSAP1, SHANK, SPANK-3	uc001oqc.3	Q9UPX8	OTTHUMG00000154615	ENST00000338508.4:c.441_442insAAA	11.37:g.70824380_70824381insTTT	ENSP00000345193:p.Gln147_Ala148insLys	Somatic		WXS	Illumina HiSeq	Phase_I	C0SPG8|C0SPG9|Q3Y8G9|Q52LK2|Q9UKP1	In_Frame_Ins	INS	ENST00000338508.4	37																																																																																					0.465	SHANK2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_012309	
ROBO3	64221	broad.mit.edu	37	11	124739923	124739924	+	Frame_Shift_Ins	INS	-	-	G	rs115272137	byFrequency	TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr11:124739923_124739924insG	ENST00000397801.1	+	4	917_918	c.725_726insG	c.(724-729)gcgggafs	p.AG242fs	ROBO3_ENST00000538940.1_Frame_Shift_Ins_p.AG220fs	NM_022370.3	NP_071765.2	Q96MS0	ROBO3_HUMAN	roundabout, axon guidance receptor, homolog 3 (Drosophila)	242	Ig-like C2-type 2.				axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|neuron migration (GO:0001764)	axon (GO:0030424)|integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	35	all_hematologic(175;0.215)	Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|Breast(109;0.0481)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0296)		TCCAACATGGCGGGAGAACGGG	0.525																																						.											0																																										SO:0001589	frameshift_variant	64221			AK024697	CCDS44755.1	11q24	2013-02-11	2001-11-28		ENSG00000154134	ENSG00000154134		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	13433	protein-coding gene	gene with protein product		608630	"""roundabout (axon guidance receptor, Drosophila) homolog 3"", ""horizontal gaze palsy with progressive scoliosis"""	HGPPS		15105459	Standard	NM_022370		Approved	RBIG1, FLJ21044, HGPS	uc001qbc.3	Q96MS0	OTTHUMG00000165934	ENST00000397801.1:c.728dupG	11.37:g.124739926_124739926dupG	ENSP00000380903:p.Ala242fs	Somatic		WXS	Illumina HiSeq	Phase_I		Frame_Shift_Ins	INS	ENST00000397801.1	37	CCDS44755.1																																																																																				0.525	ROBO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387091.1	XM_370663	
DPPA3	359787	broad.mit.edu	37	12	7869647	7869648	+	Frame_Shift_Ins	INS	-	-	A			TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr12:7869647_7869648insA	ENST00000345088.2	+	4	571_572	c.454_455insA	c.(454-456)caafs	p.Q152fs		NM_199286.2	NP_954980.1	Q6W0C5	DPPA3_HUMAN	developmental pluripotency associated 3	152					chromatin modification (GO:0016568)|embryonic cleavage (GO:0040016)|negative regulation of DNA demethylation (GO:1901536)|protection of DNA demethylation of female pronucleus (GO:0044726)|regulation of genetic imprinting (GO:2000653)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|nucleus (GO:0005634)	methylated histone binding (GO:0035064)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|skin(2)	8				Kidney(36;0.0887)		AATAGGGAATCAAGACACCAAG	0.376																																						.											0																																										SO:0001589	frameshift_variant	359787			AY317075	CCDS8582.1	12p13.31	2012-10-02			ENSG00000187569	ENSG00000187569			19199	protein-coding gene	gene with protein product		608408					Standard	NM_199286		Approved	Stella	uc001qtf.3	Q6W0C5	OTTHUMG00000168434	ENST00000345088.2:c.456dupA	12.37:g.7869649_7869649dupA	ENSP00000339250:p.Gln152fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q0P5U3|Q6JZS6	Frame_Shift_Ins	INS	ENST00000345088.2	37	CCDS8582.1																																																																																				0.376	DPPA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399718.1	NM_199286	
TLE3	7090	broad.mit.edu	37	15	70386891	70386892	+	Frame_Shift_Ins	INS	-	-	A			TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr15:70386891_70386892insA	ENST00000558939.1	-	4	1590_1591	c.213_214insT	c.(211-216)ttgaacfs	p.N72fs	TLE3_ENST00000539550.1_Frame_Shift_Ins_p.N6fs|TLE3_ENST00000451782.2_Frame_Shift_Ins_p.N72fs|TLE3_ENST00000559048.1_Frame_Shift_Ins_p.N78fs|TLE3_ENST00000317509.8_Frame_Shift_Ins_p.N72fs|TLE3_ENST00000558379.1_Frame_Shift_Ins_p.N72fs|TLE3_ENST00000560589.1_Frame_Shift_Ins_p.N16fs|TLE3_ENST00000440567.3_Frame_Shift_Ins_p.N65fs|TLE3_ENST00000558201.1_Frame_Shift_Ins_p.N78fs|TLE3_ENST00000559929.1_Frame_Shift_Ins_p.N72fs|TLE3_ENST00000442299.2_Frame_Shift_Ins_p.N72fs|TLE3_ENST00000559191.1_Intron|TLE3_ENST00000559574.1_5'Flank|TLE3_ENST00000557997.1_Frame_Shift_Ins_p.N72fs|TLE3_ENST00000560939.1_Frame_Shift_Ins_p.N78fs|TLE3_ENST00000557907.1_Frame_Shift_Ins_p.N72fs	NM_001282979.1|NM_001282980.1|NM_001282981.1	NP_001269908.1|NP_001269909.1|NP_001269910.1	Q04726	TLE3_HUMAN	transducin-like enhancer of split 3	72	Gln-rich.				Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						ATTTCAATGTTCAAGCCATAGG	0.287																																						.											0																																										SO:0001589	frameshift_variant	7090			M99438	CCDS45293.1, CCDS45294.1, CCDS58375.1, CCDS61689.1, CCDS61691.1, CCDS61692.1, CCDS73747.1	15q22	2014-03-07	2014-03-07			ENSG00000140332		"""WD repeat domain containing"""	11839	protein-coding gene	gene with protein product		600190	"""transducin-like enhancer of split 3, homolog of Drosophila E(sp1)"", ""transducin-like enhancer of split 3 (E(sp1) homolog, Drosophila)"""			8365415	Standard	XM_005254623		Approved	ESG, ESG3, KIAA1547, HsT18976, GRG3	uc002asm.2	Q04726		ENST00000558939.1:c.213_214insT	15.37:g.70386891_70386892insA	ENSP00000452871:p.Asn72fs	Somatic		WXS	Illumina HiSeq	Phase_I	B4DPT0|E9PD64|F8W964|Q6PI57|Q8IVV6|Q8WVR2|Q9HCM5	Nonsense_Mutation	INS	ENST00000558939.1	37	CCDS45293.1																																																																																				0.287	TLE3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416913.1	NM_005078	
CCDC74A	90557	broad.mit.edu	37	2	132290264	132290265	+	Frame_Shift_Ins	INS	-	-	C			TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr2:132290264_132290265insC	ENST00000295171.6	+	5	924_925	c.786_787insC	c.(787-789)cccfs	p.P263fs	CCDC74A_ENST00000467992.2_3'UTR|CCDC74A_ENST00000409856.3_Frame_Shift_Ins_p.P197fs	NM_001258304.1|NM_001258305.1|NM_138770.2	NP_001245233.1|NP_001245234.1|NP_620125.1	Q96AQ1	CC74A_HUMAN	coiled-coil domain containing 74A	263										endometrium(4)|large_intestine(3)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19						CAATGATCCTGCCCCTTCCCCT	0.624																																						.											0																																										SO:0001589	frameshift_variant	90557				CCDS2167.1, CCDS58732.1, CCDS74578.1	2q21.1	2008-02-05		2006-02-16	ENSG00000163040	ENSG00000163040			25197	protein-coding gene	gene with protein product						12477932	Standard	NM_138770		Approved	FLJ40345	uc002ttb.4	Q96AQ1	OTTHUMG00000131667	ENST00000295171.6:c.790dupC	2.37:g.132290268_132290268dupC	ENSP00000295171:p.Pro263fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q6P4I5	Frame_Shift_Ins	INS	ENST00000295171.6	37	CCDS2167.1																																																																																				0.624	CCDC74A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254570.2	NM_138770	
CBWD6	644019	broad.mit.edu	37	9	69256826	69256827	+	Frame_Shift_Ins	INS	-	-	C			TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr9:69256826_69256827insC	ENST00000377457.5	-	3	409_410	c.304_305insG	c.(304-306)gaafs	p.E102fs	CBWD6_ENST00000377441.1_Frame_Shift_Ins_p.E102fs|CBWD6_ENST00000377449.1_Frame_Shift_Ins_p.E66fs|CBWD6_ENST00000382399.4_Frame_Shift_Ins_p.E102fs	NM_001085457.1	NP_001078926.1	Q4V339	CBWD6_HUMAN	COBW domain containing 6	102							ATP binding (GO:0005524)			lung(4)	4						GTTTCTAAGTTCCAGCCACTCT	0.376																																						.											0																																										SO:0001589	frameshift_variant	644019				CCDS43827.1	9q13	2006-06-30			ENSG00000204790	ENSG00000204790			31978	protein-coding gene	gene with protein product							Standard	NM_001085457		Approved	OTTHUMG00000066820	uc004afj.4	Q4V339	OTTHUMG00000066820	ENST00000377457.5:c.305dupG	9.37:g.69256828_69256828dupC	ENSP00000366677:p.Glu102fs	Somatic		WXS	Illumina HiSeq	Phase_I		Frame_Shift_Ins	INS	ENST00000377457.5	37	CCDS43827.1																																																																																				0.376	CBWD6-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143172.2	XM_928822	
ATRX	546	broad.mit.edu	37	X	76763910	76763911	+	Frame_Shift_Ins	INS	-	-	C			TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chrX:76763910_76763911insC	ENST00000373344.5	-	35	7611_7612	c.7397_7398insG	c.(7396-7398)ggtfs	p.G2466fs	ATRX_ENST00000480283.1_5'UTR|ATRX_ENST00000395603.3_Frame_Shift_Ins_p.G2428fs	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	2466					ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						GTGGCTGCATACCACCAGCCAC	0.465			"""Mis, F, N"""		"""Pancreatic neuroendocrine tumors, paediatric GBM"""		ATR-X (alpha thalassemia/mental retardation) syndrome																															.		Rec	yes		X	Xq21.1	546	alpha thalassemia/mental retardation syndrome X-linked	yes	E	0																																										SO:0001589	frameshift_variant	546			U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"""RAD54 homolog (S. cerevisiae)"""	300032	"""alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)"", ""Juberg-Marsidi syndrome"""	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.7398dupG	X.37:g.76763912_76763912dupC	ENSP00000362441:p.Gly2466fs	Somatic		WXS	Illumina HiSeq	Phase_I	D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Frame_Shift_Ins	INS	ENST00000373344.5	37	CCDS14434.1																																																																																				0.465	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489	
RAB40A	142684	broad.mit.edu	37	X	102755467	102755468	+	Frame_Shift_Ins	INS	-	-	C			TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chrX:102755467_102755468insC	ENST00000372633.1	-	1	2335_2336	c.217_218insG	c.(217-219)cagfs	p.Q73fs	RAB40A_ENST00000304236.1_Frame_Shift_Ins_p.Q73fs|LL0XNC01-250H12.3_ENST00000445990.1_RNA			Q8WXH6	RB40A_HUMAN	RAB40A, member RAS oncogene family	73					protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	GTP binding (GO:0005525)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|skin(1)	12						AAATCTTCCCTGCCCCGACGTA	0.564																																						.											0																																										SO:0001589	frameshift_variant	142684			AF132748	CCDS35357.1	Xq22.1	2009-08-25			ENSG00000172476	ENSG00000172476		"""RAB, member RAS oncogene"""	18283	protein-coding gene	gene with protein product						11697911	Standard	NM_080879		Approved	RAR2A, Rar-2	uc004ekk.3	Q8WXH6	OTTHUMG00000022100	ENST00000372633.1:c.217_218insG	X.37:g.102755467_102755468insC	ENSP00000361716:p.Gln73fs	Somatic		WXS	Illumina HiSeq	Phase_I	O00407|Q17RQ5|Q6DK06|Q8TF06	Frame_Shift_Ins	INS	ENST00000372633.1	37	CCDS35357.1																																																																																				0.564	RAB40A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057714.1		
C5orf42	65250	ucsc.edu;mdanderson.org	37	5	37221454	37221454	+	Silent	SNP	T	T	A			TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr5:37221454T>A	ENST00000508244.1	-	14	2811	c.2718A>T	c.(2716-2718)ctA>ctT	p.L906L	C5orf42_ENST00000274258.7_5'UTR|C5orf42_ENST00000425232.2_Silent_p.L906L			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	906						integral component of membrane (GO:0016021)				breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			CTTTTACAGGTAGTTGGGACC	0.363																																						.											0													119.0	93.0	101.0					5																	37221454		692	1591	2283	SO:0001819	synonymous_variant	65250				CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.2718A>T	5.37:g.37221454T>A		Somatic		WXS	Illumina HiSeq	Phase_I	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Silent	SNP	ENST00000508244.1	37	CCDS34146.2																																																																																				0.363	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073	
DNAJC13	23317	ucsc.edu	37	3	132193881	132193881	+	Silent	SNP	A	A	G			TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr3:132193881A>G	ENST00000260818.6	+	22	2645	c.2397A>G	c.(2395-2397)agA>agG	p.R799R		NM_015268.3	NP_056083.3	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	799					osteoblast differentiation (GO:0001649)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)				breast(4)|endometrium(2)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|urinary_tract(1)	34						ATATTGACAGAGAACTTGGAA	0.343																																						.											0													114.0	123.0	120.0					3																	132193881		2203	4300	6503	SO:0001819	synonymous_variant	23317			AB014578	CCDS33857.1	3q22.1	2011-09-02			ENSG00000138246	ENSG00000138246		"""Heat shock proteins / DNAJ (HSP40)"""	30343	protein-coding gene	gene with protein product		614334				12438707	Standard	NM_015268		Approved	RME8, KIAA0678	uc003eor.3	O75165	OTTHUMG00000159674	ENST00000260818.6:c.2397A>G	3.37:g.132193881A>G		Somatic		WXS	Illumina HiSeq	Phase_I	Q3L0T1|Q6PI82|Q6UJ77|Q6ZSW1|Q6ZUT5|Q86XG3|Q96DC1|Q9BWK9	Silent	SNP	ENST00000260818.6	37	CCDS33857.1																																																																																				0.343	DNAJC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356807.2	NM_015268	
G3BP2	9908	ucsc.edu	37	4	76573848	76573848	+	Silent	SNP	A	A	G			TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr4:76573848A>G	ENST00000359707.4	-	9	1688	c.903T>C	c.(901-903)ggT>ggC	p.G301G	G3BP2_ENST00000395719.3_Silent_p.G301G|G3BP2_ENST00000357854.3_Silent_p.G268G	NM_203505.2	NP_987101.1	Q9UN86	G3BP2_HUMAN	GTPase activating protein (SH3 domain) binding protein 2	301					cytoplasmic sequestering of NF-kappaB (GO:0007253)|mRNA transport (GO:0051028)|Ras protein signal transduction (GO:0007265)	cytoplasm (GO:0005737)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|receptor signaling complex scaffold activity (GO:0030159)			breast(3)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	27			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			TAGGAGGAAAACCAGGTCGTT	0.403																																						.											0													93.0	84.0	87.0					4																	76573848		2203	4300	6503	SO:0001819	synonymous_variant	9908			AB014560	CCDS3571.1, CCDS3572.1	4q21.1	2013-02-12	2006-11-01		ENSG00000138757	ENSG00000138757		"""RNA binding motif (RRM) containing"""	30291	protein-coding gene	gene with protein product	"""Ras-GTPase activating protein SH3 domain-binding protein 2"""					9734811, 9575347	Standard	NM_203504		Approved	KIAA0660	uc003his.3	Q9UN86	OTTHUMG00000130097	ENST00000359707.4:c.903T>C	4.37:g.76573848A>G		Somatic		WXS	Illumina HiSeq	Phase_I	A8K6X1|O60606|O75149|Q9UPA1	Silent	SNP	ENST00000359707.4	37	CCDS3571.1																																																																																				0.403	G3BP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252399.2	NM_012297	
INTS3	65123	ucsc.edu	37	1	153735835	153735835	+	Missense_Mutation	SNP	G	G	T			TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr1:153735835G>T	ENST00000318967.2	+	16	2331	c.1763G>T	c.(1762-1764)gGg>gTg	p.G588V	INTS3_ENST00000512605.1_Missense_Mutation_p.G382V|INTS3_ENST00000456435.1_Missense_Mutation_p.G382V|INTS3_ENST00000476843.1_3'UTR|INTS3_ENST00000435409.2_Missense_Mutation_p.G588V	NM_023015.3	NP_075391.3	Q68E01	INT3_HUMAN	integrator complex subunit 3	589					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|mitotic cell cycle checkpoint (GO:0007093)|response to ionizing radiation (GO:0010212)|snRNA processing (GO:0016180)	integrator complex (GO:0032039)|nucleus (GO:0005634)|SOSS complex (GO:0070876)				breast(1)|cervix(4)|endometrium(10)|kidney(1)|large_intestine(6)|lung(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	38	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			CTACAGAAGGGGAGGTGGGTA	0.527																																						.											0													110.0	106.0	107.0					1																	153735835		2203	4300	6503	SO:0001583	missense	65123			BX640950	CCDS1052.1	1q21.3	2012-03-16	2006-03-15	2006-03-15	ENSG00000143624	ENSG00000143624			26153	protein-coding gene	gene with protein product	"""sensor of single-strand DNA complex subunit A"""	611347	"""chromosome 1 open reading frame 60"""	C1orf60		16239144	Standard	NM_023015		Approved	FLJ21919, INT3, SOSS-A	uc001fct.3	Q68E01	OTTHUMG00000037089	ENST00000318967.2:c.1763G>T	1.37:g.153735835G>T	ENSP00000318641:p.Gly588Val	Somatic		WXS	Illumina HiSeq	Phase_I	A8K1W0|B4DQC8|B4E3U9|D3DV57|Q4G0E5|Q5VUQ5|Q5VUQ6|Q5VUR0|Q5VUR1|Q68DJ1|Q69YR5|Q6AI57|Q6DKG7|Q6MZQ4|Q6MZZ9|Q8NC46|Q8TB23|Q9H6S9	Missense_Mutation	SNP	ENST00000318967.2	37	CCDS1052.1	.	.	.	.	.	.	.	.	.	.	G	11.44	1.638801	0.29157	.	.	ENSG00000143624	ENST00000318967;ENST00000456435;ENST00000435409;ENST00000512605	.	.	.	5.06	4.15	0.48705	.	0.135836	0.48767	D	0.000171	T	0.19087	0.0458	N	0.14661	0.345	0.58432	D	0.999999	B;B;B	0.26809	0.16;0.047;0.032	B;B;B	0.33799	0.17;0.017;0.037	T	0.06881	-1.0802	9	0.31617	T	0.26	.	7.6135	0.28144	0.1861:0.0:0.8139:0.0	.	382;589;588	Q68E01-3;Q68E01;Q68E01-2	.;INT3_HUMAN;.	V	588;382;588;382	.	ENSP00000318641:G588V	G	+	2	0	INTS3	152002459	1.000000	0.71417	0.958000	0.39756	0.847000	0.48162	4.681000	0.61663	1.361000	0.45981	0.561000	0.74099	GGG		0.527	INTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090045.2	NM_023015	
LCTL	197021	ucsc.edu	37	15	66840924	66840924	+	Missense_Mutation	SNP	C	C	T			TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr15:66840924C>T	ENST00000341509.5	-	13	1739	c.1608G>A	c.(1606-1608)atG>atA	p.M536I	ZWILCH_ENST00000307897.5_3'UTR|LCTL_ENST00000537670.1_Missense_Mutation_p.M363I|ZWILCH_ENST00000446801.2_3'UTR	NM_207338.2	NP_997221.2	Q6UWM7	LCTL_HUMAN	lactase-like	536					carbohydrate metabolic process (GO:0005975)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)			NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						TAACCATTTGCATGTGACTTA	0.458																																						.											0													124.0	114.0	117.0					15																	66840924		2201	4299	6500	SO:0001583	missense	197021			AY358729	CCDS10220.1, CCDS61678.1	15q21.3	2008-02-05			ENSG00000188501	ENSG00000188501			15583	protein-coding gene	gene with protein product	"""klotho gamma"", ""KL lactase phlorizin hydrolase"""					12084582	Standard	NM_207338		Approved	KLPH, FLJ33279, KLG	uc002aqc.3	Q6UWM7	OTTHUMG00000133207	ENST00000341509.5:c.1608G>A	15.37:g.66840924C>T	ENSP00000343490:p.Met536Ile	Somatic		WXS	Illumina HiSeq	Phase_I	B3KQY0	Missense_Mutation	SNP	ENST00000341509.5	37	CCDS10220.1	.	.	.	.	.	.	.	.	.	.	C	11.65	1.701984	0.30232	.	.	ENSG00000188501	ENST00000537670;ENST00000341509	T;T	0.30182	1.74;1.54	5.6	4.67	0.58626	.	0.082404	0.85682	N	0.000000	T	0.24851	0.0603	L	0.29908	0.895	0.58432	D	0.999997	B;B	0.12630	0.002;0.006	B;B	0.08055	0.003;0.003	T	0.02269	-1.1185	10	0.37606	T;T	0.19;0.19	-24.6251	15.4825	0.75539	0.0:0.8609:0.1391:0.0	.	363;536	B3KQY0;Q6UWM7	.;LCTL_HUMAN	I	363;536	ENSP00000445419:M363I;ENSP00000343490:M536I	ENSP00000343490:M536I;ENSP00000343490:M536I	M	-	3	0	LCTL	64627978	1.000000	0.71417	0.995000	0.50966	0.095000	0.18619	7.016000	0.76393	1.337000	0.45525	0.655000	0.94253	ATG		0.458	LCTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256921.2	NM_207338	
PAIP2	51247	ucsc.edu	37	5	138700258	138700258	+	Silent	SNP	A	A	G			TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr5:138700258A>G	ENST00000394795.2	+	3	1135	c.144A>G	c.(142-144)gaA>gaG	p.E48E	PAIP2_ENST00000511706.1_Intron|PAIP2_ENST00000265192.4_Silent_p.E48E|PAIP2_ENST00000511381.1_3'UTR|PAIP2_ENST00000510080.1_Silent_p.E48E|CTB-43P18.1_ENST00000503553.3_RNA			Q9BPZ3	PAIP2_HUMAN	poly(A) binding protein interacting protein 2	48	Glu-rich.|PABPC1-interacting motif-1 (PAM1).				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)			kidney(1)|large_intestine(2)|lung(2)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			TCTAGATAGAAGAGGAGTTAT	0.353																																						.											0													57.0	58.0	57.0					5																	138700258		2203	4300	6503	SO:0001819	synonymous_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.144A>G	5.37:g.138700258A>G		Somatic		WXS	Illumina HiSeq	Phase_I	B2RBI1|D3DQC6|Q49A06|Q9H0Y5|Q9P0Q8	Silent	SNP	ENST00000394795.2	37	CCDS4211.1																																																																																				0.353	PAIP2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373002.1	NM_016480	
ZNF521	25925	ucsc.edu;mdanderson.org	37	18	22930910	22930911	+	Start_Codon_SNP	DNP	TC	TC	AA			TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	TC	TC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr18:22930910_22930911TC>AA	ENST00000538137.2	-	2	197_198	c.0_1GA>TT	c.(-2-3)agGAtg>agTTtg	p.0_1insSL	ZNF521_ENST00000579111.1_5'UTR|ZNF521_ENST00000361524.3_Splice_Site|ZNF521_ENST00000584787.1_Intron			Q96K83	ZN521_HUMAN	zinc finger protein 521	0					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)			NS(1)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(21)|lung(97)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	149	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					CGGCGAGACATCCTAAAAGCAA	0.609			T	PAX5	ALL																																	.		Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	0																																										SO:0001582	initiator_codon_variant	25925			AK027354	CCDS32806.1	18q11.2	2013-01-08				ENSG00000198795		"""Zinc fingers, C2H2-type"""	24605	protein-coding gene	gene with protein product	"""early hematopoietic zinc finger"""	610974				11984006, 14630787	Standard	NM_015461		Approved	EHZF, Evi3	uc002kvk.2	Q96K83		ENST00000538137.2:c.1_1delinsAA	18.37:g.22930910_22930911delinsAA	Exception_encountered	Somatic		WXS	Illumina HiSeq	Phase_I	A3QVP7|B0YJB7|Q8IXI0|Q8TES6|Q9C065|Q9HAL5|Q9UFK4	Splice_Site	DNP	ENST00000538137.2	37	CCDS32806.1																																																																																				0.609	ZNF521-002	KNOWN	alternative_5_UTR|upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446782.1	NM_015461	Missense_Mutation
AHNAK2	113146	mdanderson.org	37	14	105410382	105410382	+	Silent	SNP	T	T	C	rs201817721	byFrequency	TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr14:105410382T>C	ENST00000333244.5	-	7	11525	c.11406A>G	c.(11404-11406)aaA>aaG	p.K3802K	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3802						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			GCATTTTGAATTTGCTGTCTT	0.587													.|||	118	0.0235623	0.0401	0.0058	5008	,	,		20893	0.0268		0.0	False		,,,				2504	0.0348					.											0													252.0	250.0	250.0					14																	105410382		1990	4160	6150	SO:0001819	synonymous_variant	113146			AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.11406A>G	14.37:g.105410382T>C		Somatic		WXS	Illumina HiSeq	Phase_I	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																				0.587	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
AP5Z1	9907	mdanderson.org	37	7	4825307	4825307	+	Missense_Mutation	SNP	T	T	A	rs11772411	byFrequency	TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr7:4825307T>A	ENST00000348624.4	+	9	1218	c.1124T>A	c.(1123-1125)cTg>cAg	p.L375Q	MIR4656_ENST00000579503.1_RNA|AP5Z1_ENST00000401897.1_Missense_Mutation_p.L375Q	NM_014855.2	NP_055670.1	O43299	AP5Z1_HUMAN	adaptor-related protein complex 5, zeta 1 subunit	375					cell death (GO:0008219)|double-strand break repair via homologous recombination (GO:0000724)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	AP-5 adaptor complex (GO:0044599)|AP-type membrane coat adaptor complex (GO:0030119)|cytoplasm (GO:0005737)|nucleus (GO:0005634)											CACTTCTTCCTGAGCCACGGT	0.592													T|||	359	0.0716853	0.0091	0.0317	5008	,	,		13424	0.0506		0.0676	False		,,,				2504	0.2106					.											0								T	GLN/LEU	72,4098		0,72,2013	6.0	7.0	6.0		1124	5.6	0.9	7	dbSNP_120	6	528,7844		17,494,3675	no	missense	KIAA0415	NM_014855.2	113	17,566,5688	AA,AT,TT		6.3067,1.7266,4.7839	probably-damaging	375/808	4825307	600,11942	2085	4186	6271	SO:0001583	missense	9907			AB007875	CCDS47528.1	7p22.1	2012-03-20	2012-03-20	2012-03-20	ENSG00000242802	ENSG00000242802			22197	protein-coding gene	gene with protein product		613653	"""KIAA0415"""	KIAA0415		20613862, 22022230	Standard	NM_014855		Approved	SPG48, zeta	uc003sne.3	O43299	OTTHUMG00000151754	ENST00000348624.4:c.1124T>A	7.37:g.4825307T>A	ENSP00000297562:p.Leu375Gln	Somatic		WXS	Illumina HiSeq	Phase_I	Q8N3X2|Q96H80	Missense_Mutation	SNP	ENST00000348624.4	37	CCDS47528.1	98	0.04487179487179487	7	0.014227642276422764	15	0.04143646408839779	30	0.05244755244755245	46	0.06068601583113457	t	16.98	3.271083	0.59540	0.017266	0.063067	ENSG00000242802	ENST00000348624;ENST00000401897	T;T	0.63417	-0.01;-0.04	5.62	5.62	0.85841	.	0.000000	0.64402	D	0.000002	T	0.36496	0.0969	M	0.83483	2.645	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	T	0.69457	-0.5140	10	0.87932	D	0	.	13.5539	0.61749	0.0:0.0:0.0:1.0	rs11772411	375	O43299	K0415_HUMAN	Q	375	ENSP00000297562:L375Q;ENSP00000384980:L375Q	ENSP00000297562:L375Q	L	+	2	0	KIAA0415	4791833	1.000000	0.71417	0.879000	0.34478	0.057000	0.15508	7.654000	0.83653	2.141000	0.66446	0.454000	0.30748	CTG		0.592	AP5Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323771.1		
AP5Z1	9907	mdanderson.org	37	7	4825314	4825314	+	Splice_Site	SNP	C	C	T	rs11768079	byFrequency	TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr7:4825314C>T	ENST00000348624.4	+	9	1225	c.1131C>T	c.(1129-1131)caC>caT	p.H377H	MIR4656_ENST00000579503.1_RNA|AP5Z1_ENST00000401897.1_Splice_Site_p.H377H	NM_014855.2	NP_055670.1	O43299	AP5Z1_HUMAN	adaptor-related protein complex 5, zeta 1 subunit	377					cell death (GO:0008219)|double-strand break repair via homologous recombination (GO:0000724)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	AP-5 adaptor complex (GO:0044599)|AP-type membrane coat adaptor complex (GO:0030119)|cytoplasm (GO:0005737)|nucleus (GO:0005634)											TCCTGAGCCACGGTGAGCCCA	0.582													C|||	359	0.0716853	0.0091	0.0317	5008	,	,		13363	0.0506		0.0676	False		,,,				2504	0.2106					.											0								C		75,4103		0,75,2014	6.0	6.0	6.0		1131	-0.4	0.9	7	dbSNP_120	6	532,7858		19,494,3682	yes	coding-synonymous-near-splice	KIAA0415	NM_014855.2		19,569,5696	TT,TC,CC		6.3409,1.7951,4.8297		377/808	4825314	607,11961	2089	4195	6284	SO:0001630	splice_region_variant	9907			AB007875	CCDS47528.1	7p22.1	2012-03-20	2012-03-20	2012-03-20	ENSG00000242802	ENSG00000242802			22197	protein-coding gene	gene with protein product		613653	"""KIAA0415"""	KIAA0415		20613862, 22022230	Standard	NM_014855		Approved	SPG48, zeta	uc003sne.3	O43299	OTTHUMG00000151754	ENST00000348624.4:c.1132+1C>T	7.37:g.4825314C>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q8N3X2|Q96H80	Silent	SNP	ENST00000348624.4	37	CCDS47528.1																																																																																				0.582	AP5Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323771.1		Silent
BRD4	23476	mdanderson.org	37	19	15350594	15350594	+	Silent	SNP	G	G	A	rs11669901	byFrequency	TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr19:15350594G>A	ENST00000263377.2	-	16	3542	c.3321C>T	c.(3319-3321)ctC>ctT	p.L1107L		NM_058243.2	NP_490597.1	O60885	BRD4_HUMAN	bromodomain containing 4	1107	C-terminal (CTD) region.				cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|chromosome segregation (GO:0007059)|histone H3-K14 acetylation (GO:0044154)|histone H4-K12 acetylation (GO:0043983)|inner cell mass cell proliferation (GO:0001833)|negative regulation of DNA damage checkpoint (GO:2000002)|positive regulation of DNA binding (GO:0043388)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of phosphorylation of RNA polymerase II C-terminal domain (GO:1901407)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|positive transcription elongation factor complex b (GO:0008024)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|urinary_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(3;3.02e-24)|Epithelial(3;4.71e-20)|all cancers(3;2.26e-18)			TCACCACCACGAGGGGCTGGG	0.701			T	C15orf55	lethal midline carcinoma of young people								G|||	661	0.131989	0.1362	0.1009	5008	,	,		14853	0.0615		0.1879	False		,,,				2504	0.1636					.		Dom	yes		19	19p13.1	23476	bromodomain containing 4		E	0								G		600,3806	255.8+/-260.9	51,498,1654	40.0	45.0	43.0		3321	2.0	1.0	19	dbSNP_120	43	1498,7102	279.3+/-293.9	133,1232,2935	no	coding-synonymous	BRD4	NM_058243.2		184,1730,4589	AA,AG,GG		17.4186,13.6178,16.131		1107/1363	15350594	2098,10908	2203	4300	6503	SO:0001819	synonymous_variant	23476			Y12059	CCDS12328.1, CCDS46004.1	19p13.12	2013-09-20	2002-01-14		ENSG00000141867	ENSG00000141867			13575	protein-coding gene	gene with protein product	"""chromosome-associated protein"""	608749	"""bromodomain-containing 4"""			10938129	Standard	NM_058243		Approved	HUNKI, MCAP, CAP, HUNK1	uc002nar.3	O60885	OTTHUMG00000183252	ENST00000263377.2:c.3321C>T	19.37:g.15350594G>A		Somatic		WXS	Illumina HiSeq	Phase_I	O60433|Q4G0X8|Q86YS8|Q96PD3	Silent	SNP	ENST00000263377.2	37	CCDS12328.1																																																																																				0.701	BRD4-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465800.3	NM_058243	
FRG1B	284802	mdanderson.org	37	20	29625955	29625955	+	Nonsense_Mutation	SNP	A	A	T			TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr20:29625955A>T	ENST00000278882.3	+	5	579	c.199A>T	c.(199-201)Aga>Tga	p.R67*	FRG1B_ENST00000439954.2_Nonsense_Mutation_p.R72*|FRG1B_ENST00000358464.4_Nonsense_Mutation_p.R67*			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	67										endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						AATTGGACCAAGAGAACAATG	0.338																																						.											0																																										SO:0001587	stop_gained	284802					20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531			15792	other	unknown			"""chromosome 20 open reading frame 80"""	C20orf80			Standard	NR_003579		Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.199A>T	20.37:g.29625955A>T	ENSP00000278882:p.Arg67*	Somatic		WXS	Illumina HiSeq	Phase_I	C4AME5	RNA	SNP	ENST00000278882.3	37		.	.	.	.	.	.	.	.	.	.	a	29.6	5.022161	0.93462	.	.	ENSG00000149531	ENST00000278882;ENST00000439954;ENST00000358464	.	.	.	1.68	1.68	0.24146	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.20519	T	0.43	.	7.3757	0.26827	1.0:0.0:0.0:0.0	.	.	.	.	X	67;72;67	.	ENSP00000278882:R67X	R	+	1	2	FRG1B	28239616	1.000000	0.71417	1.000000	0.80357	0.120000	0.20174	3.670000	0.54569	1.028000	0.39785	0.155000	0.16302	AGA		0.338	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078494.2	NR_003579	
MKL1	57591	mdanderson.org	37	22	40814636	40814636	+	Silent	SNP	C	C	T	rs4821944	byFrequency	TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr22:40814636C>T	ENST00000355630.3	-	12	2396	c.1806G>A	c.(1804-1806)gcG>gcA	p.A602A	MKL1_ENST00000396617.3_Silent_p.A602A|MKL1_ENST00000402042.1_Silent_p.A552A|MKL1_ENST00000407029.1_Silent_p.A602A	NM_020831.3	NP_065882.1	Q969V6	MKL1_HUMAN	megakaryoblastic leukemia (translocation) 1	602	Pro-rich.				negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription via serum response element binding (GO:0010735)|smooth muscle cell differentiation (GO:0051145)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	actin binding (GO:0003779)|actin monomer binding (GO:0003785)|leucine zipper domain binding (GO:0043522)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(13)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	30						TGGCTGGGGCCGCCAGGCTGG	0.701			T	RBM15	acute megakaryocytic leukemia								C|||	983	0.196286	0.1324	0.1988	5008	,	,		10064	0.0099		0.3052	False		,,,				2504	0.3609					.		Dom	yes		22	22q13	57591	megakaryoblastic leukemia (translocation) 1		L	0								C		645,3593		64,517,1538	7.0	10.0	9.0		1806	-9.1	0.0	22	dbSNP_111	9	2472,5952		376,1720,2116	no	coding-synonymous	MKL1	NM_020831.3		440,2237,3654	TT,TC,CC		29.3447,15.2194,24.617		602/932	40814636	3117,9545	2119	4212	6331	SO:0001819	synonymous_variant	57591			AB037859	CCDS14003.1, CCDS74865.1, CCDS74866.1	22q13	2008-06-12			ENSG00000196588	ENSG00000196588			14334	protein-coding gene	gene with protein product	"""megakaryocytic acute leukemia"", ""myocardin-related transcription factor A"", ""basic, SAP and coiled-coil domain"""	606078				11431691, 12019265, 14970199	Standard	XM_005261692		Approved	KIAA1438, MAL, MRTF-A, BSAC	uc003ayw.1	Q969V6	OTTHUMG00000151146	ENST00000355630.3:c.1806G>A	22.37:g.40814636C>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q8TCL1|Q96SC5|Q96SC6|Q9P2B0	Silent	SNP	ENST00000355630.3	37	CCDS14003.1																																																																																				0.701	MKL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321522.1	NM_020831	
MUC4	4585	mdanderson.org	37	3	195509029	195509029	+	Missense_Mutation	SNP	C	C	T			TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr3:195509029C>T	ENST00000463781.3	-	2	9881	c.9422G>A	c.(9421-9423)aGc>aAc	p.S3141N	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.S3141N|MUC4_ENST00000349607.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGAGGAAGTGCTGGTGACAGG	0.592																																						.											0																																										SO:0001583	missense	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.9422G>A	3.37:g.195509029C>T	ENSP00000417498:p.Ser3141Asn	Somatic		WXS	Illumina HiSeq	Phase_I	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	c	4.536	0.099491	0.08681	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.31510	1.49;1.49	.	.	.	.	.	.	.	.	T	0.14356	0.0347	N	0.19112	0.55	0.09310	N	1	B	0.26512	0.151	B	0.14023	0.01	T	0.24657	-1.0154	7	.	.	.	.	3.585	0.07967	0.0:0.5:0.5:0.0	.	3013	E7ESK3	.	N	3141	ENSP00000417498:S3141N;ENSP00000420243:S3141N	.	S	-	2	0	MUC4	196993808	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	-1.190000	0.03058	-0.000000	0.14550	0.000000	0.15137	AGC		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PSG6	5675	mdanderson.org	37	19	43411778	43411778	+	Missense_Mutation	SNP	C	C	T	rs151146504	byFrequency	TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr19:43411778C>T	ENST00000292125.2	-	4	979	c.935G>A	c.(934-936)cGg>cAg	p.R312Q	PSG6_ENST00000402603.4_Intron|PSG6_ENST00000187910.2_Missense_Mutation_p.R312Q	NM_002782.4	NP_002773.1	Q00889	PSG6_HUMAN	pregnancy specific beta-1-glycoprotein 6	312	Ig-like C2-type 2.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(19)|ovary(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	44		Prostate(69;0.00899)				ATATCGGTCCCGTATTTCACA	0.502													.|||	6	0.00119808	0.0	0.0029	5008	,	,		21760	0.0		0.004	False		,,,				2504	0.0					.											0													158.0	144.0	149.0					19																	43411778		2202	4295	6497	SO:0001583	missense	5675				CCDS12613.1, CCDS33038.1	19q13.2	2013-01-29			ENSG00000170848	ENSG00000170848		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9523	protein-coding gene	gene with protein product		176395				1690992	Standard	NM_002782		Approved			Q00889	OTTHUMG00000151127	ENST00000292125.2:c.935G>A	19.37:g.43411778C>T	ENSP00000292125:p.Arg312Gln	Somatic		WXS	Illumina HiSeq	Phase_I	O75244|Q15224|Q15235|Q549K1	Missense_Mutation	SNP	ENST00000292125.2	37	CCDS12613.1	.	.	.	.	.	.	.	.	.	.	N	4.566	0.105064	0.08731	.	.	ENSG00000170848	ENST00000187910;ENST00000292125	T;T	0.12672	2.66;2.66	1.42	0.312	0.15837	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.03871	0.0109	N	0.01618	-0.8	0.09310	N	1	D;B	0.54772	0.968;0.09	B;B	0.41236	0.351;0.045	T	0.22730	-1.0208	9	0.37606	T	0.19	.	3.255	0.06828	0.0:0.7031:0.0:0.2969	.	312;312	Q00889;Q00889-2	PSG6_HUMAN;.	Q	312	ENSP00000187910:R312Q;ENSP00000292125:R312Q	ENSP00000187910:R312Q	R	-	2	0	PSG6	48103618	0.000000	0.05858	0.007000	0.13788	0.019000	0.09904	-0.820000	0.04457	0.792000	0.33850	0.134000	0.15878	CGG		0.502	PSG6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321436.1	NM_002782	
TBC1D3F	84218	mdanderson.org	37	17	36288278	36288278	+	Missense_Mutation	SNP	T	T	A	rs11550750		TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr17:36288278T>A	ENST00000327454.6	+	6	510	c.364T>A	c.(364-366)Ttg>Atg	p.L122M	TBC1D3F_ENST00000539424.1_Missense_Mutation_p.L42M|TBC1D3F_ENST00000378174.5_Missense_Mutation_p.L122M|TBC1D3F_ENST00000505415.1_Missense_Mutation_p.L122M	NM_032258.2	NP_115634.2	A6NER0	TBC3F_HUMAN	TBC1 domain family, member 3F	122	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.					plasma membrane (GO:0005886)	Rab GTPase activator activity (GO:0005097)			liver(1)|pancreas(1)	2						GGAAATGAAGTTGAAAAACCC	0.562																																						.											0								T	MET/LEU	15,1737		0,15,861	239.0	158.0	183.0		364		0.0	17	dbSNP_120	183	101,3869		0,101,1884	no	missense	TBC1D3F	NM_032258.2	15	0,116,2745	AA,AT,TT		2.5441,0.8562,2.0273	possibly-damaging	122/550	36288278	116,5606	876	1985	2861	SO:0001583	missense	729873					17q12	2014-09-16				ENSG00000275954			18257	protein-coding gene	gene with protein product		610809				16863688	Standard	NM_032258		Approved			A6NER0	OTTHUMG00000188428	ENST00000327454.6:c.364T>A	17.37:g.36288278T>A	ENSP00000329256:p.Leu122Met	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000327454.6	37	CCDS45657.1	.	.	.	.	.	.	.	.	.	.	t	5.859	0.342710	0.11069	0.008562	0.025441	ENSG00000185128	ENST00000327454;ENST00000378174;ENST00000505415;ENST00000539424	T;T;T;T	0.11495	2.77;2.77;2.77;2.77	.	.	.	Rab-GAP/TBC domain (8);	1.135460	0.06527	U	0.740661	T	0.02807	0.0084	L	0.43923	1.385	0.09310	N	0.999995	B;B;B;B	0.31153	0.042;0.31;0.024;0.12	B;B;B;B	0.29524	0.103;0.048;0.103;0.055	T	0.37126	-0.9719	9	0.46703	T	0.11	.	4.5487	0.12098	0.0:6.0E-4:0.0:0.9994	.	122;122;122;122	B9A6J9;A6NFD7;P0C7X1;A6NER0	.;.;TBC3H_HUMAN;TBC3F_HUMAN	M	122;122;122;42	ENSP00000329256:L122M;ENSP00000367416:L122M;ENSP00000421962:L122M;ENSP00000443859:L42M	ENSP00000329256:L122M	L	+	1	2	TBC1D3F	33362660	0.686000	0.27661	0.026000	0.17262	0.026000	0.11368	-0.164000	0.09983	0.103000	0.17682	0.102000	0.15555	TTG		0.562	TBC1D3F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256100.3	NM_032258.2	
TCEAL5	340543	mdanderson.org	37	X	102529084	102529084	+	Silent	SNP	T	T	C			TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chrX:102529084T>C	ENST00000372680.1	-	3	702	c.408A>G	c.(406-408)caA>caG	p.Q136Q		NM_001012979.2	NP_001012997.1	Q5H9L2	TCAL5_HUMAN	transcription elongation factor A (SII)-like 5	136					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.Q136Q(2)		breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|skin(1)	11						GATGCCTTTCTTGTAAGTCCT	0.498																																						.											2	Substitution - coding silent(2)	kidney(1)|endometrium(1)											203.0	174.0	184.0					X																	102529084		2203	4300	6503	SO:0001819	synonymous_variant	340543				CCDS35356.1	Xq22.2	2014-03-21			ENSG00000204065	ENSG00000204065			22282	protein-coding gene	gene with protein product						16221301	Standard	NM_001012979		Approved	WEX4	uc004ejz.2	Q5H9L2	OTTHUMG00000022092	ENST00000372680.1:c.408A>G	X.37:g.102529084T>C		Somatic		WXS	Illumina HiSeq	Phase_I	A2RUJ4	Silent	SNP	ENST00000372680.1	37	CCDS35356.1																																																																																				0.498	TCEAL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057696.1	XM_291334	
OTUB1	55611	bcgsc.ca	37	11	63756163	63756163	+	Missense_Mutation	SNP	A	A	G			TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr11:63756163A>G	ENST00000538426.1	+	3	202	c.158A>G	c.(157-159)gAg>gGg	p.E53G	OTUB1_ENST00000541478.1_Intron|OTUB1_ENST00000543004.1_Missense_Mutation_p.E62G|OTUB1_ENST00000422031.2_Missense_Mutation_p.E90G|OTUB1_ENST00000543988.1_Missense_Mutation_p.E23G|OTUB1_ENST00000428192.2_Missense_Mutation_p.E53G|OTUB1_ENST00000535715.1_Missense_Mutation_p.E53G|OTUB1_ENST00000536443.1_3'UTR	NM_017670.2	NP_060140.2	Q96FW1	OTUB1_HUMAN	OTU deubiquitinase, ubiquitin aldehyde binding 1	53					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|immune system process (GO:0002376)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein K48-linked deubiquitination (GO:0071108)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	NEDD8-specific protease activity (GO:0019784)|omega peptidase activity (GO:0008242)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)	6						GAGCGGCTGGAGCTCTCGGTC	0.562																																						.											0													110.0	111.0	111.0					11																	63756163		2201	4297	6498	SO:0001583	missense	55611			AY177200	CCDS8055.1	11q13.1	2014-02-24	2014-02-24			ENSG00000167770		"""OTU domain containing"""	23077	protein-coding gene	gene with protein product		608337	"""OTU domain, ubiquitin aldehyde binding 1"""			12704427, 19383985	Standard	NM_017670		Approved	FLJ20113, FLJ40710	uc001nyf.1	Q96FW1		ENST00000538426.1:c.158A>G	11.37:g.63756163A>G	ENSP00000444357:p.Glu53Gly	Somatic		WXS	Illumina HiSeq	Phase_I	Q32Q78|Q96II3|Q9NXQ4|Q9P0B8	Missense_Mutation	SNP	ENST00000538426.1	37	CCDS8055.1	.	.	.	.	.	.	.	.	.	.	A	18.28	3.589609	0.66105	.	.	ENSG00000167770	ENST00000535715;ENST00000428192;ENST00000422031;ENST00000538426;ENST00000543004;ENST00000543988	T;T;T;T;T;T	0.45668	0.89;0.89;0.89;0.89;0.89;0.89	5.49	4.35	0.52113	.	.	.	.	.	T	0.37433	0.1003	L	0.58669	1.825	0.40960	D	0.984618	P;P	0.38473	0.633;0.633	B;B	0.35971	0.215;0.162	T	0.29212	-1.0019	9	0.54805	T	0.06	.	9.2666	0.37645	0.916:0.0:0.084:0.0	.	90;53	B4DPD5;Q96FW1	.;OTUB1_HUMAN	G	53;53;90;53;62;23	ENSP00000440211:E53G;ENSP00000402551:E53G;ENSP00000416973:E90G;ENSP00000444357:E53G;ENSP00000437453:E62G;ENSP00000441328:E23G	ENSP00000416973:E90G	E	+	2	0	OTUB1	63512739	1.000000	0.71417	0.993000	0.49108	0.983000	0.72400	6.254000	0.72460	1.024000	0.39682	0.482000	0.46254	GAG		0.562	OTUB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396277.1	NM_017670	
TPTE2	93492	bcgsc.ca	37	13	20066994	20066994	+	Missense_Mutation	SNP	T	T	C	rs78472618	byFrequency	TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr13:20066994T>C	ENST00000400230.2	-	3	159	c.115A>G	c.(115-117)Aaa>Gaa	p.K39E	TPTE2_ENST00000382975.4_Missense_Mutation_p.K39E|TPTE2_ENST00000390680.2_Missense_Mutation_p.K39E|TPTE2_ENST00000382978.1_Missense_Mutation_p.K39E|TPTE2_ENST00000255310.6_Missense_Mutation_p.K39E|TPTE2_ENST00000382977.4_Missense_Mutation_p.K39E|TPTE2_ENST00000400103.2_Missense_Mutation_p.K39E|TPTE2_ENST00000457266.2_Missense_Mutation_p.K39E			Q6XPS3	TPTE2_HUMAN	transmembrane phosphoinositide 3-phosphatase and tensin homolog 2	39					phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.K39E(3)		NS(2)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(8)|lung(21)|pancreas(1)|prostate(8)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)		ACTCACCTTTTACTGATAGGT	0.388																																						.											3	Substitution - Missense(3)	prostate(2)|NS(1)											103.0	91.0	95.0					13																	20066994		2203	4300	6503	SO:0001583	missense	93492			AJ421032	CCDS9285.1, CCDS45013.1, CCDS45014.1	13q12.11	2012-12-10			ENSG00000132958	ENSG00000132958		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	17299	protein-coding gene	gene with protein product		606791				11716755, 12717346, 15057823	Standard	NM_130785		Approved	TPIP	uc001umd.3	Q6XPS3	OTTHUMG00000016493	ENST00000400230.2:c.115A>G	13.37:g.20066994T>C	ENSP00000383089:p.Lys39Glu	Somatic		WXS	Illumina HiSeq	Phase_I	A1A4X0|A1A4X1|A8MX64|B1AQ16|B4DWZ2|Q5VUH2|Q8WWL4|Q8WWL5	Missense_Mutation	SNP	ENST00000400230.2	37	CCDS45014.1	.	.	.	.	.	.	.	.	.	.	T	0.931	-0.712684	0.03206	.	.	ENSG00000132958	ENST00000382978;ENST00000400103;ENST00000400230;ENST00000255310;ENST00000390680;ENST00000382977;ENST00000382975;ENST00000457266;ENST00000343548;ENST00000419256	D;D;D;D;D;D;D;D	0.95205	-3.64;-3.51;-3.47;-3.49;-3.49;-3.47;-3.64;-3.51	1.03	-1.53	0.08611	.	0.321368	0.27539	N	0.018903	D	0.84915	0.5578	N	0.21448	0.665	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.71059	-0.4702	9	.	.	.	.	4.2942	0.10894	0.0:0.5094:0.0:0.4906	.	39;39;39	A8MX64;Q6XPS3-3;Q6XPS3	.;.;TPTE2_HUMAN	E	39	ENSP00000372438:K39E;ENSP00000382974:K39E;ENSP00000383089:K39E;ENSP00000255310:K39E;ENSP00000375098:K39E;ENSP00000372437:K39E;ENSP00000372435:K39E;ENSP00000442218:K39E	.	K	-	1	0	TPTE2	18964994	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.444000	0.02403	-0.630000	0.05567	-0.464000	0.05259	AAA		0.388	TPTE2-205	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_199254	
EIF4A3	9775	bcgsc.ca	37	17	78109803	78109803	+	Splice_Site	SNP	C	C	T			TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chr17:78109803C>T	ENST00000269349.3	-	11	1440	c.1219G>A	c.(1219-1221)Gtt>Att	p.V407I		NM_014740.3	NP_055555.1	P38919	IF4A3_HUMAN	eukaryotic translation initiation factor 4A3	407	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|cytokine-mediated signaling pathway (GO:0019221)|embryonic cranial skeleton morphogenesis (GO:0048701)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|mRNA transport (GO:0051028)|negative regulation of translation (GO:0017148)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|mRNA binding (GO:0003729)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	10	all_neural(118;0.117)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.139)			GATTTCCTACCGTTCATCGGC	0.428																																						.											0													114.0	107.0	110.0					17																	78109803		2203	4300	6503	SO:0001630	splice_region_variant	9775			BC004386	CCDS11767.1	17q25.3	2010-02-10	2010-02-10	2006-11-27		ENSG00000141543		"""DEAD-boxes"""	18683	protein-coding gene	gene with protein product		608546	"""DEAD (Asp-Glu-Ala-Asp) box polypeptide 48"", ""eukaryotic translation initiation factor 4A, isoform 3"""	DDX48		10623621, 14730019	Standard	NM_014740		Approved	KIAA0111, EIF4AIII	uc002jxs.3	P38919		ENST00000269349.3:c.1219+1G>A	17.37:g.78109803C>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q15033|Q6IBQ2|Q96A18	Missense_Mutation	SNP	ENST00000269349.3	37	CCDS11767.1	.	.	.	.	.	.	.	.	.	.	C	12.76	2.034577	0.35893	.	.	ENSG00000141543	ENST00000269349	T	0.27104	1.69	3.64	3.64	0.41730	Helicase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.09069	0.0224	N	0.01482	-0.84	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.16660	-1.0395	9	.	.	.	.	12.8311	0.57746	0.0:1.0:0.0:0.0	.	407	P38919	IF4A3_HUMAN	I	407	ENSP00000269349:V407I	.	V	-	1	0	EIF4A3	75724398	1.000000	0.71417	0.972000	0.41901	0.469000	0.32828	7.212000	0.77941	1.878000	0.54408	0.484000	0.47621	GTT		0.428	EIF4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437446.1	NM_014740	Missense_Mutation
MT-ND5	4540	bcgsc.ca	37	M	13232	13232	+	Frame_Shift_Del	DEL	A	A	-			TCGA-KN-8437-01A-11D-2310-10	TCGA-KN-8437-11A-01D-2311-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	345a06d6-fa5c-4674-a847-88a6b537cf3c	a1283c7d-6305-46d3-b518-47cb8b37ba18	g.chrM:13232delA	ENST00000361567.2	+	1	896	c.896delA	c.(895-897)aaafs	p.K300fs	MT-TE_ENST00000387459.1_RNA|MT-TH_ENST00000387441.1_RNA|MT-TT_ENST00000387460.2_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TR_ENST00000387439.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TP_ENST00000387461.2_RNA			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	300					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						AAATGACATCAAAAAAATCGT	0.448																																						.											0																																										SO:0001589	frameshift_variant	0					mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.896delA	M.37:g.13232delA	ENSP00000354813:p.Lys300fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q34773|Q8WCY3	Frame_Shift_Del	DEL	ENST00000361567.2	37																																																																																					0.448	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036	
