#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_AAChange	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_Codon	i_COSMIC_Gene	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Drug_Target	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_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	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_NTotCov	i_NVarCov	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_TTotCov	i_TVarCov	i_Transcript_Id	i_Trna_alt1	i_Trna_alt2	i_Trna_ref	i_Trna_tot	i_Trna_var	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_dbSNPPopFreq	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
PRDM2	7799	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	14068533	14068533	+	Missense_Mutation	SNP	G	G	T			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr1:14068533G>T	ENST00000235372.7	+	5	1121	c.265G>T	c.(265-267)Gat>Tat	p.D89Y	PRDM2_ENST00000502727.1_3'UTR|PRDM2_ENST00000311066.5_Missense_Mutation_p.D89Y|PRDM2_ENST00000376048.5_Missense_Mutation_p.D89Y	NM_012231.4	NP_036363.2	Q13029	PRDM2_HUMAN	PR domain containing 2, with ZNF domain	89	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				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)		GATGTGCATTGATGCCACTGA	0.383																																					p.D89Y		.											.	PRDM2-116	0			c.G265T						.						78.0	72.0	74.0					1																	14068533		2203	4300	6503	SO:0001583	missense	7799	exon5			TGCATTGATGCCA	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.265G>T	1.37:g.14068533G>T	ENSP00000235372:p.Asp89Tyr	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	65	35	NM_015866	0	0	1	4	3	B1AJZ4|B5MC68|Q13149|Q14550|Q5THJ1|Q5VUL9	Missense_Mutation	SNP	ENST00000235372.7	37	CCDS150.1	.	.	.	.	.	.	.	.	.	.	G	16.57	3.160930	0.57368	.	.	ENSG00000116731	ENST00000484063;ENST00000376048;ENST00000235372;ENST00000311066;ENST00000400800	D;D;D;D	0.94330	-3.4;-3.4;-3.4;-3.4	5.95	5.95	0.96441	SET domain (2);	0.000000	0.85682	D	0.000000	D	0.97826	0.9286	H	0.94620	3.56	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.98389	1.0562	10	0.87932	D	0	.	18.957	0.92662	0.0:0.0:1.0:0.0	.	89;89;89	Q13029;Q13029-2;B1AJZ4	PRDM2_HUMAN;.;.	Y	80;89;89;89;89	ENSP00000423010:D80Y;ENSP00000365216:D89Y;ENSP00000235372:D89Y;ENSP00000312352:D89Y	ENSP00000235372:D89Y	D	+	1	0	PRDM2	13941120	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.957000	0.93082	2.824000	0.97209	0.655000	0.94253	GAT	.		0.383	PRDM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021792.2	NM_012231	
INSRR	3645	broad.mit.edu	37	1	156818724	156818724	+	Silent	SNP	G	G	A	rs544109301		TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr1:156818724G>A	ENST00000368195.3	-	7	1956	c.1560C>T	c.(1558-1560)taC>taT	p.Y520Y	NTRK1_ENST00000392302.2_Intron	NM_014215.2	NP_055030.1	P14616	INSRR_HUMAN	insulin receptor-related receptor	520	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton reorganization (GO:0031532)|cellular response to alkaline pH (GO:0071469)|male sex determination (GO:0030238)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(7)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	42	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					ACTCCTTGTAGTACACGATGA	0.672																																					p.Y520Y													.	INSRR-1403	0			c.C1560T						.						13.0	14.0	13.0					1																	156818724		2194	4295	6489	SO:0001819	synonymous_variant	3645	exon7			CTTGTAGTACACG	J05046	CCDS1160.1	1q21-q23	2013-02-11			ENSG00000027644	ENSG00000027644		"""Fibronectin type III domain containing"""	6093	protein-coding gene	gene with protein product		147671				2768234, 2249481	Standard	NM_014215		Approved	IRR	uc010pht.2	P14616	OTTHUMG00000041291	ENST00000368195.3:c.1560C>T	1.37:g.156818724G>A		Somatic	14	0		WXS	Illumina HiSeq	Phase_I	8	3	NM_014215	0	0	0	0	0	O60724|Q5VZS3	Silent	SNP	ENST00000368195.3	37	CCDS1160.1																																																																																			.		0.672	INSRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098929.1	NM_014215	
NEK2	4751	broad.mit.edu	37	1	211843673	211843673	+	Missense_Mutation	SNP	G	G	C			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr1:211843673G>C	ENST00000366999.4	-	5	853	c.715C>G	c.(715-717)Cgt>Ggt	p.R239G	NEK2_ENST00000540251.1_Missense_Mutation_p.R196G|NEK2_ENST00000462283.1_5'UTR|NEK2_ENST00000366998.3_Missense_Mutation_p.R239G	NM_002497.3	NP_002488.1	P51955	NEK2_HUMAN	NIMA-related kinase 2	239	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				blastocyst development (GO:0001824)|centrosome separation (GO:0051299)|chromosome segregation (GO:0007059)|G2/M transition of mitotic cell cycle (GO:0000086)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of centriole-centriole cohesion (GO:1903126)|negative regulation of DNA binding (GO:0043392)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of mitosis (GO:0007088)|regulation of mitotic centrosome separation (GO:0046602)|spindle assembly (GO:0051225)|spindle assembly involved in mitosis (GO:0090307)	centrosome (GO:0005813)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|microtubule (GO:0005874)|midbody (GO:0030496)|nucleus (GO:0005634)|protein complex (GO:0043234)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activity (GO:0004674)	p.R239S(2)		breast(2)|stomach(1)	3				OV - Ovarian serous cystadenocarcinoma(81;0.00203)|all cancers(67;0.0339)|Epithelial(68;0.0546)		TCAGAGTAACGGTATGGAATT	0.363																																					p.R239G													.	NEK2-765	2	Substitution - Missense(2)	lung(2)	c.C715G						.						156.0	163.0	160.0					1																	211843673		2203	4300	6503	SO:0001583	missense	4751	exon5			AGTAACGGTATGG	U11050	CCDS1500.1, CCDS55682.1, CCDS73024.1	1q32.3	2014-06-12	2012-11-15		ENSG00000117650	ENSG00000117650			7745	protein-coding gene	gene with protein product	"""HsPK 21"", ""protein phosphatase 1, regulatory subunit 111"""	604043	"""NIMA (never in mitosis gene a)-related kinase 2"""			8274451, 24043777	Standard	NM_002497		Approved	NLK1, NEK2A, RP67, PPP1R111	uc001hir.2	P51955	OTTHUMG00000037121	ENST00000366999.4:c.715C>G	1.37:g.211843673G>C	ENSP00000355966:p.Arg239Gly	Somatic	200	0		WXS	Illumina HiSeq	Phase_I	218	5	NM_002497	0	0	2	2	0	Q53FD6|Q5I1Z9|Q5VXZ1|Q6NZX8|Q7Z634|Q86XH2|Q96QN9	Missense_Mutation	SNP	ENST00000366999.4	37	CCDS1500.1	.	.	.	.	.	.	.	.	.	.	G	15.71	2.914393	0.52546	.	.	ENSG00000117650	ENST00000366999;ENST00000540251;ENST00000366998	T;T;T	0.65364	-0.15;-0.15;-0.15	5.45	5.45	0.79879	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.47875	0.1469	N	0.13168	0.305	0.80722	D	1	B;B;B	0.13145	0.007;0.006;0.003	B;B;B	0.13407	0.005;0.009;0.005	T	0.36648	-0.9739	10	0.36615	T	0.2	.	17.4884	0.87694	0.0:0.0:1.0:0.0	.	239;239;239	P51955-2;P51955;P51955-4	.;NEK2_HUMAN;.	G	239;196;239	ENSP00000355966:R239G;ENSP00000440237:R196G;ENSP00000355965:R239G	ENSP00000355965:R239G	R	-	1	0	NEK2	209910296	1.000000	0.71417	0.997000	0.53966	0.995000	0.86356	9.507000	0.97996	2.550000	0.86006	0.655000	0.94253	CGT	.		0.363	NEK2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090154.1	NM_002497	
PCDH15	65217	broad.mit.edu;ucsc.edu	37	10	55568839	55568839	+	Missense_Mutation	SNP	T	T	A			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr10:55568839T>A	ENST00000395445.1	-	36	5365	c.4971A>T	c.(4969-4971)aaA>aaT	p.K1657N	PCDH15_ENST00000395446.1_Missense_Mutation_p.K853N|PCDH15_ENST00000373965.2_Intron|PCDH15_ENST00000414778.1_Intron|PCDH15_ENST00000395442.1_Missense_Mutation_p.K522N|PCDH15_ENST00000395438.1_3'UTR|PCDH15_ENST00000409834.1_3'UTR|PCDH15_ENST00000395440.1_Missense_Mutation_p.K591N	NM_001142769.1	NP_001136241.1	Q96QU1	PCD15_HUMAN	protocadherin-related 15	0					equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				GCACAATGTTTTTCCTTGCTT	0.473										HNSCC(58;0.16)																											.													.	PCDH15-193	0			.						.						123.0	94.0	103.0					10																	55568839		1568	3582	5150	SO:0001583	missense	65217	.			AATGTTTTTCCTT	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"""Cadherins / Cadherin-related"""	14674	protein-coding gene	gene with protein product	"""cadherin-related family member 15"""	605514	"""deafness, autosomal recessive 23"", ""protocadherin 15"""	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000395445.1:c.4971A>T	10.37:g.55568839T>A	ENSP00000378832:p.Lys1657Asn	Somatic	29	0		WXS	Illumina HiSeq	Phase_I	27	13	.	0	0	0	0	0	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000395445.1	37		.	.	.	.	.	.	.	.	.	.	T	12.19	1.863009	0.32884	.	.	ENSG00000150275	ENST00000395445;ENST00000395446;ENST00000395442;ENST00000395440	T;D;D;D	0.97089	-0.31;-4.24;-4.24;-4.24	5.55	-4.49	0.03504	.	.	.	.	.	D	0.89656	0.6778	N	0.14661	0.345	0.21841	N	0.99951	P;P	0.38922	0.651;0.501	B;B	0.29785	0.107;0.107	T	0.82623	-0.0366	9	0.62326	D	0.03	.	9.0437	0.36333	0.1044:0.4727:0.0:0.4229	.	1655;1657	C6ZEF5;A2A3E2	.;.	N	1657;853;522;591	ENSP00000378832:K1657N;ENSP00000378833:K853N;ENSP00000378829:K522N;ENSP00000378827:K591N	ENSP00000378827:K591N	K	-	3	2	PCDH15	55238845	0.945000	0.32115	0.056000	0.19401	0.489000	0.33432	0.441000	0.21611	-0.418000	0.07450	-0.290000	0.09829	AAA	.		0.473	PCDH15-007	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000291335.1	NM_033056	
AP3M1	26985	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	10	75898090	75898090	+	Silent	SNP	T	T	C	rs147488745		TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr10:75898090T>C	ENST00000355264.4	-	2	359	c.48A>G	c.(46-48)ctA>ctG	p.L16L	AP3M1_ENST00000372745.1_Silent_p.L16L|AP3M1_ENST00000487653.1_5'UTR	NM_012095.4	NP_036227.1	Q9Y2T2	AP3M1_HUMAN	adaptor-related protein complex 3, mu 1 subunit	16					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|protein targeting to lysosome (GO:0006622)	clathrin adaptor complex (GO:0030131)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	Rab GTPase binding (GO:0017137)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(1)|lung(1)|prostate(1)|skin(1)	13	Prostate(51;0.0112)					AGTGCTTCTCTAGAAATATGT	0.358																																					p.L16L		.											.	AP3M1-90	0			c.A48G						.						76.0	76.0	76.0					10																	75898090		2203	4300	6503	SO:0001819	synonymous_variant	26985	exon3			CTTCTCTAGAAAT	AF092092	CCDS7342.1	10q22.1-q22.3	2008-07-07			ENSG00000185009	ENSG00000185009			569	protein-coding gene	gene with protein product		610366				10024875	Standard	NM_207012		Approved		uc001jwh.3	Q9Y2T2	OTTHUMG00000018497	ENST00000355264.4:c.48A>G	10.37:g.75898090T>C		Somatic	71	0		WXS	Illumina HiSeq	Phase_I	93	50	NM_207012	0	0	4	14	10	Q5JQ12|Q9H5L2	Silent	SNP	ENST00000355264.4	37	CCDS7342.1																																																																																			T|1.000;G|0.000		0.358	AP3M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048747.1		
MUC2	4583	broad.mit.edu	37	11	1098668	1098668	+	Silent	SNP	G	G	A			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr11:1098668G>A	ENST00000441003.2	+	37	7065	c.7038G>A	c.(7036-7038)gtG>gtA	p.V2346V	MUC2_ENST00000361558.6_3'UTR	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	4708					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	ACGCACTGGTGCCCCCGCAGC	0.652																																					p.V2342V													.	MUC2-90	0			c.G7026A						.						21.0	26.0	24.0					11																	1098668		2108	4219	6327	SO:0001819	synonymous_variant	4583	exon38			ACTGGTGCCCCCG	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.7038G>A	11.37:g.1098668G>A		Somatic	45	0		WXS	Illumina HiSeq	Phase_I	25	8	NM_002457	0	0	0	0	0	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				.		0.652	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
OR8I2	120586	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	55861472	55861472	+	Missense_Mutation	SNP	C	C	G			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr11:55861472C>G	ENST00000302124.2	+	1	720	c.689C>G	c.(688-690)gCa>gGa	p.A230G		NM_001003750.1	NP_001003750.1	Q8N0Y5	OR8I2_HUMAN	olfactory receptor, family 8, subfamily I, member 2	230						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A230E(1)		NS(1)|breast(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(24)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	53	Esophageal squamous(21;0.00693)					ATCCAGTCAGCAGCAGGCAGG	0.468																																					p.A230G		.											.	OR8I2-113	1	Substitution - Missense(1)	lung(1)	c.C689G						.						148.0	133.0	138.0					11																	55861472		2201	4296	6497	SO:0001583	missense	120586	exon1			AGTCAGCAGCAGG	AB065656	CCDS31517.1	11q11	2012-08-09			ENSG00000172154	ENSG00000172154		"""GPCR / Class A : Olfactory receptors"""	15310	protein-coding gene	gene with protein product							Standard	NM_001003750		Approved		uc010rix.2	Q8N0Y5	OTTHUMG00000166831	ENST00000302124.2:c.689C>G	11.37:g.55861472C>G	ENSP00000303864:p.Ala230Gly	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	91	26	NM_001003750	0	0	0	0	0	B2RNN4|Q6IFC0|Q96RC5	Missense_Mutation	SNP	ENST00000302124.2	37	CCDS31517.1	.	.	.	.	.	.	.	.	.	.	C	7.367	0.625989	0.14257	.	.	ENSG00000172154	ENST00000302124	T	0.00207	8.55	4.33	3.41	0.39046	GPCR, rhodopsin-like superfamily (1);	0.410674	0.17770	U	0.162617	T	0.00241	0.0007	L	0.60904	1.88	0.09310	N	1	B	0.19935	0.04	B	0.25614	0.062	T	0.31613	-0.9937	10	0.62326	D	0.03	-0.4958	11.6945	0.51536	0.0:0.9111:0.0:0.0889	.	230	Q8N0Y5	OR8I2_HUMAN	G	230	ENSP00000303864:A230G	ENSP00000303864:A230G	A	+	2	0	OR8I2	55618048	0.000000	0.05858	0.014000	0.15608	0.555000	0.35460	0.408000	0.21065	0.934000	0.37316	0.440000	0.28878	GCA	.		0.468	OR8I2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001003750	
TNKS1BP1	85456	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	57076186	57076186	+	Silent	SNP	C	C	T			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr11:57076186C>T	ENST00000532437.1	-	5	4310	c.3999G>A	c.(3997-3999)ggG>ggA	p.G1333G	TNKS1BP1_ENST00000358252.3_Silent_p.G1333G|TNKS1BP1_ENST00000530920.1_5'Flank			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	1333	Acidic.|Gly-rich.				gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|RNA metabolic process (GO:0016070)|telomere maintenance via telomerase (GO:0007004)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nuclear telomeric heterochromatin (GO:0005724)|nucleus (GO:0005634)	ankyrin binding (GO:0030506)|enzyme binding (GO:0019899)			breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	64		all_epithelial(135;0.21)				ATCCCCGTAGCCCCTGAGAAC	0.607																																					p.G1333G		.											.	TNKS1BP1-91	0			c.G3999A						.						134.0	146.0	142.0					11																	57076186		2201	4296	6497	SO:0001819	synonymous_variant	85456	exon6			CCGTAGCCCCTGA	AB051528	CCDS7951.1	11q12.2	2008-07-21			ENSG00000149115	ENSG00000149115			19081	protein-coding gene	gene with protein product		607104				11854288	Standard	NM_033396		Approved	TAB182, KIAA1741, FLJ45975	uc001njs.3	Q9C0C2	OTTHUMG00000167022	ENST00000532437.1:c.3999G>A	11.37:g.57076186C>T		Somatic	404	2		WXS	Illumina HiSeq	Phase_I	244	100	NM_033396	0	0	17	39	22	A7E2F8|Q6PJ35|Q6ZV74	Silent	SNP	ENST00000532437.1	37	CCDS7951.1																																																																																			.		0.607	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1	NM_033396	
SLC3A2	6520	ucsc.edu	37	11	62648666	62648666	+	Silent	SNP	G	G	A			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr11:62648666G>A	ENST00000377890.2	+	4	642	c.474G>A	c.(472-474)gcG>gcA	p.A158A	SLC3A2_ENST00000338663.7_Silent_p.A57A|SLC3A2_ENST00000535296.1_Silent_p.A127A|SLC3A2_ENST00000377891.2_Silent_p.A159A|SLC3A2_ENST00000377892.1_Silent_p.A189A|SLC3A2_ENST00000536981.1_5'Flank|SLC3A2_ENST00000377889.2_Silent_p.A96A	NM_002394.5	NP_002385.3	P08195	4F2_HUMAN	solute carrier family 3 (amino acid transporter heavy chain), member 2	158				A -> P (in Ref. 3; AAA51540). {ECO:0000305}.	amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|carbohydrate metabolic process (GO:0005975)|cell growth (GO:0016049)|ion transport (GO:0006811)|leucine import (GO:0060356)|leukocyte migration (GO:0050900)|response to exogenous dsRNA (GO:0043330)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|tryptophan transport (GO:0015827)	cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium:sodium antiporter activity (GO:0005432)|catalytic activity (GO:0003824)|cation binding (GO:0043169)|double-stranded RNA binding (GO:0003725)|neutral amino acid transmembrane transporter activity (GO:0015175)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(2)	22						CGGCAGCCGCGGCTAAGTTCA	0.677											OREG0021031	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A159A													.	SLC3A2-90	0			c.G477A						.						15.0	19.0	18.0					11																	62648666		2193	4292	6485	SO:0001819	synonymous_variant	6520	exon4			AGCCGCGGCTAAG		CCDS8039.2, CCDS31588.1, CCDS31589.1, CCDS31590.1	11q12-q22	2013-07-19	2013-07-19		ENSG00000168003	ENSG00000168003		"""Solute carriers"""	11026	protein-coding gene	gene with protein product	"""antigen identified by monoclonal antibodies 4F2, TRA1.10, TROP4, and T43"", ""antigen defined by monoclonal antibody 4F2"", ""heavy chain"", ""4F2 heavy chain"", ""CD98 heavy chain"", ""monoclonal antibody 44D7"", ""4F2 cell-surface antigen heavy chain"", ""lymphocyte activation antigen 4F2 large subunit"""	158070	"""solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2"""	MDU1		3036867	Standard	NM_001012662		Approved	4T2HC, 4F2, NACAE, CD98, CD98HC, 4F2HC	uc001nwd.3	P08195	OTTHUMG00000074091	ENST00000377890.2:c.474G>A	11.37:g.62648666G>A		Somatic	25	0	1062	WXS	Illumina HiSeq		18	4	NM_001012662	1	0	248	249	0	Q13543	Silent	SNP	ENST00000377890.2	37	CCDS8039.2	.	.	.	.	.	.	.	.	.	.	G	0.757	-0.770850	0.02974	.	.	ENSG00000168003	ENST00000538084	.	.	.	4.22	-1.89	0.07689	.	.	.	.	.	T	0.43166	0.1235	.	.	.	0.41309	D	0.987096	.	.	.	.	.	.	T	0.29274	-1.0017	4	.	.	.	-2.3345	4.2588	0.10730	0.0792:0.3374:0.3594:0.224	.	.	.	.	Q	129	.	.	R	+	2	0	SLC3A2	62405242	0.017000	0.18338	0.015000	0.15790	0.058000	0.15608	-0.108000	0.10857	-0.509000	0.06532	-1.268000	0.01426	CGG	.		0.677	SLC3A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000157306.1	NM_001012661	
DSCAML1	57453	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	117375681	117375681	+	Missense_Mutation	SNP	C	C	T			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr11:117375681C>T	ENST00000321322.6	-	10	2321	c.2320G>A	c.(2320-2322)Gac>Aac	p.D774N	DSCAML1_ENST00000527706.1_Missense_Mutation_p.D504N	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	714	Ig-like C2-type 8.				axonogenesis (GO:0007409)|brain development (GO:0007420)|cell fate determination (GO:0001709)|central nervous system development (GO:0007417)|dendrite self-avoidance (GO:0070593)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|homophilic cell adhesion (GO:0007156)|negative regulation of cell adhesion (GO:0007162)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(24)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	110	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		GGGTAGCCGTCCACCGAGCAG	0.602																																					p.D774N		.											.	DSCAML1-159	0			c.G2320A						.						88.0	77.0	81.0					11																	117375681		2201	4296	6497	SO:0001583	missense	57453	exon10			AGCCGTCCACCGA		CCDS8384.1	11q22.2-q22.3	2013-02-11			ENSG00000177103	ENSG00000177103		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	14656	protein-coding gene	gene with protein product		611782				11453658	Standard	NM_020693		Approved	KIAA1132	uc001prh.1	Q8TD84	OTTHUMG00000167071	ENST00000321322.6:c.2320G>A	11.37:g.117375681C>T	ENSP00000315465:p.Asp774Asn	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	67	27	NM_020693	0	0	13	23	10	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Missense_Mutation	SNP	ENST00000321322.6	37	CCDS8384.1	.	.	.	.	.	.	.	.	.	.	C	19.37	3.813851	0.70912	.	.	ENSG00000177103	ENST00000527706;ENST00000321322;ENST00000446508	T;T	0.66995	-0.24;-0.24	4.32	4.32	0.51571	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.54727	0.1876	N	0.21097	0.63	0.58432	D	0.999999	B	0.18013	0.025	B	0.21360	0.034	T	0.52358	-0.8586	9	0.38643	T	0.18	.	16.5931	0.84781	0.0:1.0:0.0:0.0	.	714	Q8TD84	DSCL1_HUMAN	N	504;774;481	ENSP00000434335:D504N;ENSP00000315465:D774N	ENSP00000315465:D774N	D	-	1	0	DSCAML1	116880891	1.000000	0.71417	0.939000	0.37840	0.852000	0.48524	7.559000	0.82265	2.222000	0.72286	0.313000	0.20887	GAC	.		0.602	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693	
LIMA1	51474	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	50571511	50571511	+	Missense_Mutation	SNP	C	C	G			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr12:50571511C>G	ENST00000341247.4	-	11	1765	c.1616G>C	c.(1615-1617)gGa>gCa	p.G539A	LIMA1_ENST00000547825.1_Missense_Mutation_p.G237A|LIMA1_ENST00000552909.1_Missense_Mutation_p.G378A|LIMA1_ENST00000552783.1_Missense_Mutation_p.G380A|LIMA1_ENST00000394943.3_Missense_Mutation_p.G540A|LIMA1_ENST00000552823.1_Missense_Mutation_p.G379A|LIMA1_ENST00000552491.1_Missense_Mutation_p.G236A	NM_001113546.1|NM_016357.4	NP_001107018.1|NP_057441.1	Q9UHB6	LIMA1_HUMAN	LIM domain and actin binding 1	539					actin filament bundle assembly (GO:0051017)|negative regulation of actin filament depolymerization (GO:0030835)|ruffle organization (GO:0031529)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)|actin monomer binding (GO:0003785)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(2)	44						TCCTGAACTTCCAAGTTCAGT	0.532																																					p.G540A		.											.	LIMA1-91	0			c.G1619C						.						113.0	118.0	116.0					12																	50571511		2203	4300	6503	SO:0001583	missense	51474	exon11			GAACTTCCAAGTT	AF198454	CCDS8802.1, CCDS44877.1, CCDS55826.1, CCDS58230.1	12q13.12	2006-04-12				ENSG00000050405			24636	protein-coding gene	gene with protein product	"""epithelial protein lost in neoplasm beta"""	608364				10806352, 10618726, 12566430	Standard	NM_016357		Approved	EPLIN	uc001rwk.4	Q9UHB6		ENST00000341247.4:c.1616G>C	12.37:g.50571511C>G	ENSP00000340184:p.Gly539Ala	Somatic	213	0		WXS	Illumina HiSeq	Phase_I	193	89	NM_001113546	0	0	35	66	31	B2RB09|Q2TAN7|Q59FE8|Q9BVF2|Q9H8J1|Q9HBN5|Q9NX96|Q9NXC3|Q9NXU6|Q9P0H8|Q9UHB5	Missense_Mutation	SNP	ENST00000341247.4	37	CCDS8802.1	.	.	.	.	.	.	.	.	.	.	C	17.76	3.467708	0.63625	.	.	ENSG00000050405	ENST00000552491;ENST00000547825;ENST00000552823;ENST00000394943;ENST00000341247;ENST00000552783;ENST00000552909;ENST00000420992	T;T;T;D;T;T;T	0.84800	-1.15;-1.15;-1.49;-1.9;-1.16;-1.49;-1.49	5.73	4.83	0.62350	.	0.635701	0.18245	N	0.147130	D	0.82779	0.5111	L	0.44542	1.39	0.30474	N	0.773064	B;B;P	0.38129	0.072;0.293;0.619	B;B;B	0.39339	0.067;0.078;0.297	T	0.81895	-0.0723	10	0.49607	T	0.09	.	17.0525	0.86523	0.0:0.8729:0.1271:0.0	.	549;539;378	Q59FE8;Q9UHB6;F8VQE1	.;LIMA1_HUMAN;.	A	236;237;379;540;539;380;378;458	ENSP00000448463:G236A;ENSP00000448706:G237A;ENSP00000450266:G379A;ENSP00000378400:G540A;ENSP00000340184:G539A;ENSP00000448779:G380A;ENSP00000450087:G378A	ENSP00000340184:G539A	G	-	2	0	LIMA1	48857778	0.928000	0.31464	0.969000	0.41365	0.973000	0.67179	4.892000	0.63193	1.530000	0.49136	0.655000	0.94253	GGA	.		0.532	LIMA1-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406235.2	NM_016357	
LAMP1	3916	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	13	113964011	113964011	+	Silent	SNP	C	C	T			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr13:113964011C>T	ENST00000332556.4	+	3	431	c.237C>T	c.(235-237)tcC>tcT	p.S79S	LAMP1_ENST00000397181.3_Silent_p.S79S	NM_005561.3	NP_005552.3	P11279	LAMP1_HUMAN	lysosomal-associated membrane protein 1	79	First lumenal domain.				autophagic cell death (GO:0048102)|autophagy (GO:0006914)|establishment of protein localization to organelle (GO:0072594)|Golgi to lysosome transport (GO:0090160)|granzyme-mediated apoptotic signaling pathway (GO:0008626)|positive regulation of natural killer cell degranulation (GO:0043323)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|protein stabilization (GO:0050821)|regulation of organelle transport along microtubule (GO:1902513)	alveolar lamellar body (GO:0097208)|cytolytic granule (GO:0044194)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|melanosome (GO:0042470)|membrane (GO:0016020)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|phagolysosome membrane (GO:0061474)|sarcolemma (GO:0042383)	enzyme binding (GO:0019899)			NS(1)|central_nervous_system(2)|endometrium(3)|large_intestine(4)|lung(2)|prostate(1)|skin(1)|stomach(2)	16	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0482)|all_epithelial(44;0.0148)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.025)|GBM - Glioblastoma multiforme(44;0.206)|Epithelial(84;0.246)			ACCGCAGCTCCTGTGGAAAAG	0.448																																					p.S79S		.											.	LAMP1-514	0			c.C237T						.						110.0	114.0	113.0					13																	113964011		1968	4157	6125	SO:0001819	synonymous_variant	3916	exon3			CAGCTCCTGTGGA	J03263	CCDS41909.1	13q34	2011-11-24			ENSG00000185896	ENSG00000185896		"""CD molecules"""	6499	protein-coding gene	gene with protein product		153330					Standard	NM_005561		Approved	CD107a	uc001vtm.1	P11279	OTTHUMG00000017380	ENST00000332556.4:c.237C>T	13.37:g.113964011C>T		Somatic	116	0		WXS	Illumina HiSeq	Phase_I	117	64	NM_005561	0	0	275	546	271	B4DWL3|Q8WU33|Q96I40|Q9BRD2|Q9NP13	Silent	SNP	ENST00000332556.4	37	CCDS41909.1																																																																																			.		0.448	LAMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045876.2		
BAZ1A	11177	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	14	35242930	35242930	+	Silent	SNP	A	A	G			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr14:35242930A>G	ENST00000382422.2	-	19	3327	c.3000T>C	c.(2998-3000)gtT>gtC	p.V1000V	BAZ1A_ENST00000358716.4_Silent_p.V968V|BAZ1A_ENST00000360310.1_Silent_p.V1000V			Q9NRL2	BAZ1A_HUMAN	bromodomain adjacent to zinc finger domain, 1A	1000					chromatin remodeling (GO:0006338)|DNA-dependent DNA replication (GO:0006261)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	ACF complex (GO:0016590)|CHRAC (GO:0008623)|nuclear chromosome (GO:0000228)	zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(2)|large_intestine(7)|lung(19)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48	Breast(36;0.0388)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;7.23e-05)|Lung(238;0.00019)|Epithelial(34;0.0793)|all cancers(34;0.175)	GBM - Glioblastoma multiforme(112;0.0659)		GTCGATCTGTAACCTGTAACA	0.323																																					p.V1000V		.											.	BAZ1A-291	0			c.T3000C						.						87.0	78.0	81.0					14																	35242930		2203	4300	6503	SO:0001819	synonymous_variant	11177	exon20			ATCTGTAACCTGT	AB032252	CCDS9651.1, CCDS41943.1	14q13.2	2013-01-28			ENSG00000198604	ENSG00000198604		"""Zinc fingers, PHD-type"""	960	protein-coding gene	gene with protein product		605680				10662543	Standard	NM_013448		Approved	hACF1, ACF1, WALp1, WCRF180	uc001wsk.3	Q9NRL2	OTTHUMG00000140216	ENST00000382422.2:c.3000T>C	14.37:g.35242930A>G		Somatic	43	0		WXS	Illumina HiSeq	Phase_I	46	26	NM_013448	0	0	0	0	0	Q9NZ15|Q9P065|Q9UIG1|Q9Y3V3	Silent	SNP	ENST00000382422.2	37	CCDS9651.1																																																																																			.		0.323	BAZ1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276646.1		
ESR2	2100	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	14	64746749	64746749	+	Missense_Mutation	SNP	C	C	G			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr14:64746749C>G	ENST00000341099.4	-	3	902	c.485G>C	c.(484-486)gGa>gCa	p.G162A	ESR2_ENST00000358599.5_Missense_Mutation_p.G162A|ESR2_ENST00000553796.1_Missense_Mutation_p.G162A|ESR2_ENST00000557772.1_Missense_Mutation_p.G162A|ESR2_ENST00000357782.2_Missense_Mutation_p.G162A|ESR2_ENST00000555483.1_Intron|ESR2_ENST00000353772.3_Missense_Mutation_p.G162A|ESR2_ENST00000554572.1_Missense_Mutation_p.G162A|ESR2_ENST00000555278.1_Missense_Mutation_p.G162A|ESR2_ENST00000542956.1_Missense_Mutation_p.G162A|ESR2_ENST00000267525.6_Missense_Mutation_p.G162A	NM_001437.2	NP_001428.1	Q92731	ESR2_HUMAN	estrogen receptor 2 (ER beta)	162					brain development (GO:0007420)|cell-cell signaling (GO:0007267)|epithelial cell maturation involved in prostate gland development (GO:0060743)|extracellular negative regulation of signal transduction (GO:1900116)|gene expression (GO:0010467)|hormone-mediated apoptotic signaling pathway (GO:0008628)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|ovarian follicle development (GO:0001541)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|prostate gland epithelium morphogenesis (GO:0060740)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|uterus development (GO:0060065)|vagina development (GO:0060068)	extracellular region (GO:0005576)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|estrogen receptor activity (GO:0030284)|estrogen response element binding (GO:0034056)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|receptor antagonist activity (GO:0048019)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	23				all cancers(60;0.00916)|OV - Ovarian serous cystadenocarcinoma(108;0.0111)|BRCA - Breast invasive adenocarcinoma(234;0.0437)	Diethylstilbestrol(DB00255)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estropipate(DB04574)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Trilostane(DB01108)	CGACCAGACTCCATAGTGATA	0.453																																					p.G162A		.											.	ESR2-611	0			c.G485C						.						236.0	229.0	232.0					14																	64746749		2203	4300	6503	SO:0001583	missense	2100	exon2			CAGACTCCATAGT	X99101	CCDS9762.1, CCDS32096.1, CCDS55920.1, CCDS61469.1, CCDS61470.1	14q21-q22	2013-01-16			ENSG00000140009	ENSG00000140009		"""Nuclear hormone receptors"""	3468	protein-coding gene	gene with protein product		601663				8769313	Standard	NM_001214902		Approved	NR3A2, Erb	uc001xha.1	Q92731	OTTHUMG00000141306	ENST00000341099.4:c.485G>C	14.37:g.64746749C>G	ENSP00000343925:p.Gly162Ala	Somatic	426	1		WXS	Illumina HiSeq	Phase_I	345	152	NM_001214902	0	0	0	0	0	A8K8K5|G3V5M5|O60608|O60685|O60702|O60703|O75583|O75584|Q0MWT5|Q0MWT6|Q86Z31|Q9UEV6|Q9UHD3|Q9UQK9	Missense_Mutation	SNP	ENST00000341099.4	37	CCDS9762.1	.	.	.	.	.	.	.	.	.	.	C	32	5.148027	0.94603	.	.	ENSG00000140009	ENST00000556275;ENST00000542956;ENST00000554572;ENST00000353772;ENST00000358599;ENST00000555278;ENST00000553796;ENST00000357782;ENST00000557772;ENST00000341099;ENST00000267525	D;D;D;D;D;D;D;D;D;D;D	0.97575	-4.44;-4.44;-4.44;-4.44;-4.44;-4.44;-4.44;-4.44;-4.44;-4.44;-4.44	5.56	5.56	0.83823	Zinc finger, NHR/GATA-type (1);Zinc finger, nuclear hormone receptor-type (5);	0.000000	0.85682	D	0.000000	D	0.99312	0.9759	H	0.99425	4.56	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	D	0.98376	1.0556	10	0.87932	D	0	.	19.5206	0.95183	0.0:1.0:0.0:0.0	.	162;162;162;162;162	Q92731-7;Q92731;Q92731-6;Q92731-5;F1D8N3	.;ESR2_HUMAN;.;.;.	A	162	ENSP00000452485:G162A;ENSP00000441792:G162A;ENSP00000450699:G162A;ENSP00000335551:G162A;ENSP00000351412:G162A;ENSP00000450488:G162A;ENSP00000452426:G162A;ENSP00000350427:G162A;ENSP00000451582:G162A;ENSP00000343925:G162A;ENSP00000267525:G162A	ENSP00000267525:G162A	G	-	2	0	ESR2	63816502	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	7.647000	0.83462	2.623000	0.88846	0.557000	0.71058	GGA	.		0.453	ESR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280621.1		
HERC1	8925	ucsc.edu	37	15	63901303	63901303	+	Missense_Mutation	SNP	C	C	T			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr15:63901303C>T	ENST00000443617.2	-	78	14650	c.14563G>A	c.(14563-14565)Gag>Aag	p.E4855K		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	4855					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						TCGGAGCCCTCGGCGTTGTCC	0.537																																					p.E4855K													.	HERC1-666	0			c.G14563A						.						71.0	79.0	76.0					15																	63901303		2131	4230	6361	SO:0001583	missense	8925	exon78			AGCCCTCGGCGTT	U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"""WD repeat domain containing"""	4867	protein-coding gene	gene with protein product		605109	"""hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"""			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.14563G>A	15.37:g.63901303C>T	ENSP00000390158:p.Glu4855Lys	Somatic	34	0		WXS	Illumina HiSeq		36	4	NM_003922	0	0	17	17	0	Q8IW65	Missense_Mutation	SNP	ENST00000443617.2	37	CCDS45277.1	.	.	.	.	.	.	.	.	.	.	C	36	5.744559	0.96882	.	.	ENSG00000103657	ENST00000443617	T	0.25250	1.81	5.42	5.42	0.78866	.	0.073125	0.51477	U	0.000085	T	0.12817	0.0311	N	0.08118	0	0.80722	D	1	P	0.44006	0.824	B	0.27500	0.08	T	0.09422	-1.0675	10	0.46703	T	0.11	.	19.2521	0.93929	0.0:1.0:0.0:0.0	.	4855	Q15751	HERC1_HUMAN	K	4855	ENSP00000390158:E4855K	ENSP00000390158:E4855K	E	-	1	0	HERC1	61688356	1.000000	0.71417	0.989000	0.46669	0.993000	0.82548	7.703000	0.84585	2.542000	0.85734	0.655000	0.94253	GAG	.		0.537	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922	
CCP110	9738	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	16	19548870	19548870	+	Missense_Mutation	SNP	T	T	A			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr16:19548870T>A	ENST00000381396.5	+	4	2126	c.1879T>A	c.(1879-1881)Ttc>Atc	p.F627I	CCP110_ENST00000396212.2_Missense_Mutation_p.F627I|CCP110_ENST00000396208.2_Missense_Mutation_p.F627I	NM_001199022.1	NP_001185951	O43303	CP110_HUMAN	centriolar coiled coil protein 110kDa	627					cell projection organization (GO:0030030)|centriole replication (GO:0007099)|centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of cytokinesis (GO:0032465)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|protein complex (GO:0043234)				breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(8)|stomach(3)|urinary_tract(1)	21						GGGATCTGGCTTCGTTAACAA	0.348																																					p.F627I		.											.	CCP110-90	0			c.T1879A						.						40.0	42.0	42.0					16																	19548870		2197	4300	6497	SO:0001583	missense	9738	exon4			TCTGGCTTCGTTA	AB007879	CCDS10579.1, CCDS55992.1	16p12.3	2014-02-20	2011-05-27		ENSG00000103540	ENSG00000103540			24342	protein-coding gene	gene with protein product		609544				9455477, 12361598, 16760425	Standard	NM_014711		Approved	KIAA0419, CP110	uc002dgl.4	O43303	OTTHUMG00000131459	ENST00000381396.5:c.1879T>A	16.37:g.19548870T>A	ENSP00000370803:p.Phe627Ile	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	62	25	NM_001199022	0	0	4	11	7	B7WP23|O43335|Q68DV9|Q8NE13	Missense_Mutation	SNP	ENST00000381396.5	37	CCDS55992.1	.	.	.	.	.	.	.	.	.	.	T	12.32	1.901950	0.33535	.	.	ENSG00000103540	ENST00000396212;ENST00000381396;ENST00000396208	T;T;T	0.13307	2.6;2.6;2.6	5.39	1.56	0.23342	.	0.876000	0.09983	N	0.730791	T	0.05318	0.0141	N	0.03608	-0.345	0.22213	N	0.999282	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.39251	-0.9623	10	0.37606	T	0.19	-0.0461	3.164	0.06529	0.1377:0.0766:0.1437:0.642	.	627;627	O43303;O43303-2	CP110_HUMAN;.	I	627	ENSP00000379515:F627I;ENSP00000370803:F627I;ENSP00000379511:F627I	ENSP00000370803:F627I	F	+	1	0	CCP110	19456371	0.389000	0.25205	0.861000	0.33841	0.927000	0.56198	0.910000	0.28571	0.291000	0.22468	0.460000	0.39030	TTC	.		0.348	CCP110-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254284.2	NM_014711	
TNRC6A	27327	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	16	24826534	24826534	+	Missense_Mutation	SNP	G	G	A			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr16:24826534G>A	ENST00000395799.3	+	19	4868	c.4739G>A	c.(4738-4740)aGt>aAt	p.S1580N	TNRC6A_ENST00000432286.2_Missense_Mutation_p.S58N|CTD-2515A14.1_ENST00000568895.1_RNA|TNRC6A_ENST00000315183.7_Missense_Mutation_p.S1531N	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	1580					cellular response to starvation (GO:0009267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64				GBM - Glioblastoma multiforme(48;0.0394)		ATGAACAGCAGTACTTCACCA	0.458																																					p.S1580N		.											.	TNRC6A-92	0			c.G4739A						.						89.0	87.0	88.0					16																	24826534		2197	4300	6497	SO:0001583	missense	27327	exon19			ACAGCAGTACTTC	U80739	CCDS10624.2	16p11.2	2009-09-22	2004-12-17	2004-12-17	ENSG00000090905	ENSG00000090905		"""Trinucleotide (CAG) repeat containing"""	11969	protein-coding gene	gene with protein product		610739	"""trinucleotide repeat containing 6"""	TNRC6		9225980	Standard	NM_014494		Approved	CAGH26, KIAA1460, GW182	uc002dmm.3	Q8NDV7	OTTHUMG00000096999	ENST00000395799.3:c.4739G>A	16.37:g.24826534G>A	ENSP00000379144:p.Ser1580Asn	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	136	36	NM_014494	0	0	14	17	3	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Missense_Mutation	SNP	ENST00000395799.3	37	CCDS10624.2	.	.	.	.	.	.	.	.	.	.	G	24.7	4.561278	0.86335	.	.	ENSG00000090905	ENST00000315183;ENST00000395799;ENST00000432286	T;T	0.14022	2.58;2.54	5.92	5.92	0.95590	.	0.042755	0.85682	D	0.000000	T	0.29458	0.0734	L	0.59436	1.845	0.58432	D	0.999998	P;B;B;D	0.63880	0.718;0.427;0.392;0.993	B;B;B;P	0.54629	0.366;0.254;0.315;0.757	T	0.00097	-1.2072	10	0.33141	T	0.24	-13.8994	20.3206	0.98668	0.0:0.0:1.0:0.0	.	247;719;1531;1580	B3KSX2;C9JA83;Q8NDV7-6;Q8NDV7	.;.;.;TNR6A_HUMAN	N	1531;1580;58	ENSP00000326900:S1531N;ENSP00000379144:S1580N	ENSP00000326900:S1531N	S	+	2	0	TNRC6A	24734035	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.423000	0.90264	2.809000	0.96659	0.655000	0.94253	AGT	.		0.458	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847	
CNOT1	23019	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	16	58585134	58585134	+	Missense_Mutation	SNP	T	T	C			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr16:58585134T>C	ENST00000317147.5	-	24	3576	c.3244A>G	c.(3244-3246)Aca>Gca	p.T1082A	CNOT1_ENST00000569240.1_Missense_Mutation_p.T1077A|CNOT1_ENST00000569732.1_5'Flank|SNORA46_ENST00000384762.1_RNA|CNOT1_ENST00000441024.2_Missense_Mutation_p.T1082A|CNOT1_ENST00000245138.4_5'UTR	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	1082					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of stem cell maintenance (GO:2000036)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)	estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)			breast(1)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(24)|lung(25)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	87				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		GTTTGATCTGTGGCCACAAGC	0.323																																					p.T1082A		.											.	CNOT1-95	0			c.A3244G						.						106.0	124.0	118.0					16																	58585134		2197	4300	6497	SO:0001583	missense	23019	exon24			GATCTGTGGCCAC	AL833549	CCDS10799.1, CCDS45501.1, CCDS58468.1	16q21	2008-02-05			ENSG00000125107	ENSG00000125107			7877	protein-coding gene	gene with protein product		604917		NOT1		14702039	Standard	NM_016284		Approved	CDC39, NOT1H, KIAA1007, AD-005	uc002env.4	A5YKK6	OTTHUMG00000133487	ENST00000317147.5:c.3244A>G	16.37:g.58585134T>C	ENSP00000320949:p.Thr1082Ala	Somatic	226	0		WXS	Illumina HiSeq	Phase_I	464	292	NM_206999	1	1	14	57	41	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Missense_Mutation	SNP	ENST00000317147.5	37	CCDS10799.1	.	.	.	.	.	.	.	.	.	.	T	25.7	4.669566	0.88348	.	.	ENSG00000125107	ENST00000317147;ENST00000422872;ENST00000394200;ENST00000441024	T;T	0.45668	0.93;0.89	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	T	0.51449	0.1675	L	0.37561	1.115	0.80722	D	1	D;P;P	0.56035	0.974;0.851;0.939	D;B;P	0.70487	0.969;0.253;0.625	T	0.39522	-0.9610	10	0.13470	T	0.59	.	15.4218	0.75018	0.0:0.0:0.0:1.0	.	1082;1082;1077	A5YKK6-4;A5YKK6;A5YKK6-2	.;CNOT1_HUMAN;.	A	1082;511;1077;1082	ENSP00000320949:T1082A;ENSP00000413113:T1082A	ENSP00000320949:T1082A	T	-	1	0	CNOT1	57142635	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.040000	0.89188	2.051000	0.60960	0.383000	0.25322	ACA	.		0.323	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284	
GP1BA	2811	hgsc.bcm.edu;broad.mit.edu	37	17	4837101	4837101	+	Missense_Mutation	SNP	C	C	T			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr17:4837101C>T	ENST00000329125.5	+	2	1277	c.1202C>T	c.(1201-1203)aCc>aTc	p.T401I		NM_000173.5	NP_000164.5	P07359	GP1BA_HUMAN	glycoprotein Ib (platelet), alpha polypeptide	401	Pro/Thr-rich.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell morphogenesis (GO:0000902)|cell surface receptor signaling pathway (GO:0007166)|fibrinolysis (GO:0042730)|platelet activation (GO:0030168)|regulation of blood coagulation (GO:0030193)|thrombin receptor signaling pathway (GO:0070493)	anchored component of external side of plasma membrane (GO:0031362)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	thrombin receptor activity (GO:0015057)			central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(5)|stomach(1)|urinary_tract(1)	20						AACATGACCACCCTGGAGCCC	0.667																																					p.T401I		.											.	.	0			c.C1202T						.						55.0	65.0	62.0					17																	4837101		1878	4093	5971	SO:0001583	missense	2811	exon2			TGACCACCCTGGA		CCDS54068.1	17p13.2	2014-09-17			ENSG00000185245	ENSG00000185245		"""CD molecules"""	4439	protein-coding gene	gene with protein product		606672		GP1B		3353370	Standard	NM_000173		Approved	CD42b	uc021tnz.1	P07359	OTTHUMG00000177946	ENST00000329125.5:c.1202C>T	17.37:g.4837101C>T	ENSP00000329380:p.Thr401Ile	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	56	14	NM_000173	0	0	2	3	1	E7ES66|Q14441|Q16469|Q8N1F3|Q8NG39|Q9HDC7|Q9UEK1|Q9UQS4	Missense_Mutation	SNP	ENST00000329125.5	37	CCDS54068.1	.	.	.	.	.	.	.	.	.	.	C	11.61	1.690103	0.29962	.	.	ENSG00000185245	ENST00000329125;ENST00000438881	T	0.51574	0.7	4.67	2.67	0.31697	.	1.707120	0.04180	N	0.326245	T	0.46580	0.1400	L	0.59436	1.845	0.09310	N	1	B	0.17667	0.023	B	0.12837	0.008	T	0.38520	-0.9657	10	0.66056	D	0.02	-8.9214	6.613	0.22761	0.0:0.7822:0.0:0.2178	.	401	A5CKE2	.	I	401	ENSP00000329380:T401I	ENSP00000329380:T401I	T	+	2	0	GP1BA	4777881	0.007000	0.16637	0.005000	0.12908	0.001000	0.01503	0.611000	0.24268	0.962000	0.38057	-0.671000	0.03813	ACC	.		0.667	GP1BA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439889.1		
TVP23C	201158	ucsc.edu	37	17	15457087	15457087	+	Missense_Mutation	SNP	C	C	T			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr17:15457087C>T	ENST00000225576.3	-	3	247	c.152G>A	c.(151-153)tGt>tAt	p.C51Y	TVP23C_ENST00000428082.2_Missense_Mutation_p.C51Y|TVP23C-CDRT4_ENST00000522212.2_Missense_Mutation_p.C51Y|TVP23C_ENST00000518321.1_Missense_Mutation_p.C51Y|TVP23C_ENST00000519970.1_Intron|TVP23C_ENST00000584811.1_5'UTR|TVP23C_ENST00000438826.3_Missense_Mutation_p.C51Y	NM_145301.2	NP_660344.2	Q96ET8	TV23C_HUMAN	trans-golgi network vesicle protein 23 homolog C (S. cerevisiae)	51						integral component of membrane (GO:0016021)											ACAGAGAAGACAGACGATGAT	0.373																																					p.C51Y													.	.	0			c.G152A						.						274.0	265.0	268.0					17																	15457087		2203	4300	6503	SO:0001583	missense	201158	exon3			AGAAGACAGACGA	BC011952	CCDS11170.1, CCDS45617.1	17p12	2012-11-29	2012-11-29	2012-11-29	ENSG00000175106	ENSG00000175106			30453	protein-coding gene	gene with protein product			"""family with sequence similarity 18, member B2"""	FAM18B2			Standard	NM_001135036		Approved	MGC8763	uc002goq.2	Q96ET8	OTTHUMG00000171461	ENST00000225576.3:c.152G>A	17.37:g.15457087C>T	ENSP00000225576:p.Cys51Tyr	Somatic	334	49		WXS	Illumina HiSeq		632	81	NM_145301	0	0	12	89	77	Q3LIC7	Missense_Mutation	SNP	ENST00000225576.3	37	CCDS11170.1	.	.	.	.	.	.	.	.	.	.	.	2.368	-0.344949	0.05208	.	.	ENSG00000259024;ENSG00000175106;ENSG00000175106;ENSG00000175106	ENST00000522212;ENST00000225576;ENST00000428082;ENST00000438826	T;T;T;T	0.25749	1.78;1.78;1.78;1.78	4.47	4.47	0.54385	.	0.000000	0.85682	N	0.000000	T	0.02571	0.0078	N	0.00004	-3.335	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.0;0.0;0.002	T	0.38457	-0.9660	10	0.02654	T	1	-3.8701	9.492	0.38965	0.0:0.0877:0.0:0.9123	.	51;51;51	Q96ET8-2;Q96ET8-3;Q96ET8	.;.;F18B2_HUMAN	Y	51	ENSP00000429865:C51Y;ENSP00000225576:C51Y;ENSP00000406387:C51Y;ENSP00000413355:C51Y	ENSP00000225576:C51Y	C	-	2	0	RP11-726O12.1;FAM18B2	15397812	1.000000	0.71417	1.000000	0.80357	0.703000	0.40648	6.178000	0.71968	0.670000	0.31165	-0.442000	0.05670	TGT	.		0.373	TVP23C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000130705.2	NM_145301	
UBB	7314	broad.mit.edu	37	17	16285476	16285476	+	Silent	SNP	C	C	G	rs370706400		TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr17:16285476C>G	ENST00000395837.1	+	2	436	c.255C>G	c.(253-255)acC>acG	p.T85T	UBB_ENST00000395839.1_Silent_p.T85T|RP11-138I1.4_ENST00000583934.1_RNA|UBB_ENST00000302182.3_Silent_p.T85T|UBB_ENST00000535788.1_Intron|UBB_ENST00000578649.1_Intron	NM_001281718.1|NM_001281720.1	NP_001268647.1|NP_001268649.1	P0CG47	UBB_HUMAN	ubiquitin B	85	Ubiquitin-like 2. {ECO:0000255|PROSITE- ProRule:PRU00214}.		GMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFV KTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFA GKQLEDGRTLSDYNIQKESTLHLVLRLRGGC -> YADLRE DPDRQDHHPGSGAQ (in UBB(+1); loss of polyubiquitination; impairs the ubiquitin-proteasome pathway; refractory to disassembly by DUBs; slow degradation by UCHL3).		activation of MAPK activity (GO:0000187)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|carbohydrate metabolic process (GO:0005975)|cellular response to hypoxia (GO:0071456)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular transport of virus (GO:0075733)|ion transmembrane transport (GO:0034220)|JNK cascade (GO:0007254)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of type I interferon production (GO:0032480)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of type I interferon production (GO:0032479)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)		AGACCCTGACCGGCAAGACCA	0.552																																					p.T85T	Melanoma(163;1126 3406 34901)												.	UBB-47	0			c.C255G						.						69.0	69.0	69.0					17																	16285476		2203	4297	6500	SO:0001819	synonymous_variant	7314	exon2			CCTGACCGGCAAG		CCDS11177.1	17p12-p11.2	2010-11-25			ENSG00000170315	ENSG00000170315			12463	protein-coding gene	gene with protein product	"""polyubiquitin B"""	191339				2154095	Standard	NM_018955		Approved	MGC8385, FLJ25987	uc002gpx.3	P0CG47	OTTHUMG00000058987	ENST00000395837.1:c.255C>G	17.37:g.16285476C>G		Somatic	159	0		WXS	Illumina HiSeq	Phase_I	189	4	NM_018955	2	8	6944	6957	3	P02248|P02249|P02250|P62988|Q29120|Q6LBL4|Q6LDU5|Q8WYN8|Q91887|Q91888|Q9BWD6|Q9BX98|Q9UEF2|Q9UEG1|Q9UEK8|Q9UPK7	Silent	SNP	ENST00000395837.1	37	CCDS11177.1																																																																																			.		0.552	UBB-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000130459.1	NM_018955	
BLMH	642	hgsc.bcm.edu;broad.mit.edu	37	17	28601215	28601215	+	Splice_Site	SNP	T	T	C			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr17:28601215T>C	ENST00000261714.6	-	7	820	c.646A>G	c.(646-648)Ata>Gta	p.I216V	BLMH_ENST00000582669.1_5'UTR|BLMH_ENST00000394819.3_Splice_Site_p.I129V	NM_000386.3	NP_000377.1	Q13867	BLMH_HUMAN	bleomycin hydrolase	216					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|carboxypeptidase activity (GO:0004180)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(2)|ovary(1)|prostate(1)|stomach(1)	13					Bleomycin(DB00290)	ACTCGGAATATCTGGAAGAGA	0.408																																					p.I216V	Pancreas(127;628 1772 12912 33293 36203)	.											.	BLMH-91	0			c.A646G						.						52.0	52.0	52.0					17																	28601215		2203	4300	6503	SO:0001630	splice_region_variant	642	exon7			GGAATATCTGGAA	X92106	CCDS32604.1	17q11.2	2004-02-16				ENSG00000108578			1059	protein-coding gene	gene with protein product		602403				9407121, 9331073	Standard	NM_000386		Approved	BH	uc002hez.2	Q13867		ENST00000261714.6:c.646-1A>G	17.37:g.28601215T>C		Somatic	58	1		WXS	Illumina HiSeq	Phase_I	85	14	NM_000386	0	0	0	0	0	B2R796|Q53F86|Q9UER9	Missense_Mutation	SNP	ENST00000261714.6	37	CCDS32604.1	.	.	.	.	.	.	.	.	.	.	T	11.42	1.634591	0.29068	.	.	ENSG00000108578	ENST00000261714;ENST00000394819	T;T	0.47869	0.83;0.83	5.91	3.38	0.38709	.	0.142143	0.64402	N	0.000007	T	0.21631	0.0521	N	0.04820	-0.15	0.39774	D	0.972206	B;B	0.02656	0.0;0.0	B;B	0.11329	0.006;0.005	T	0.05818	-1.0862	10	0.16896	T	0.51	-15.4969	6.3794	0.21525	0.0:0.3117:0.0:0.6883	.	129;216	E7EMN3;Q13867	.;BLMH_HUMAN	V	216;129	ENSP00000261714:I216V;ENSP00000378296:I129V	ENSP00000261714:I216V	I	-	1	0	BLMH	25625341	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	3.118000	0.50414	1.064000	0.40671	0.533000	0.62120	ATA	.		0.408	BLMH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447940.1	NM_000386	Missense_Mutation
MED24	9862	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	38182477	38182477	+	Silent	SNP	C	C	T	rs572516214		TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr17:38182477C>T	ENST00000394128.2	-	19	1998	c.1917G>A	c.(1915-1917)tcG>tcA	p.S639S	MED24_ENST00000356271.3_Silent_p.S626S|MED24_ENST00000501516.3_Silent_p.S658S|MED24_ENST00000394126.1_Silent_p.S664S|SNORD124_ENST00000459577.1_RNA|MED24_ENST00000394127.2_Silent_p.S626S	NM_014815.3	NP_055630.2	O75448	MED24_HUMAN	mediator complex subunit 24	639					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			autonomic_ganglia(1)|breast(2)|endometrium(9)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	41	Colorectal(19;0.000442)					TCATCTGCAGCGACTTCTCAC	0.567																																					p.S639S		.											.	MED24-187	0			c.G1917A						.						143.0	129.0	134.0					17																	38182477		2203	4300	6503	SO:0001819	synonymous_variant	9862	exon19			CTGCAGCGACTTC	AF055995	CCDS11359.1, CCDS42315.1	17q21.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000008838	ENSG00000008838			22963	protein-coding gene	gene with protein product		607000	"""thyroid hormone receptor associated protein 4"", ""cofactor required for Sp1 transcriptional activation, subunit 4, 100kDa"""	THRAP4, CRSP4			Standard	NM_001079518		Approved	TRAP100, KIAA0130, DRIP100, CRSP100	uc002htt.3	O75448	OTTHUMG00000133329	ENST00000394128.2:c.1917G>A	17.37:g.38182477C>T		Somatic	203	0		WXS	Illumina HiSeq	Phase_I	200	45	NM_014815	0	0	62	95	33	A8K4S5|B3KMR9|Q14143|Q9NNY5	Silent	SNP	ENST00000394128.2	37	CCDS11359.1																																																																																			.		0.567	MED24-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257147.2	NM_014815	
ITGB3	3690	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	45369560	45369560	+	Missense_Mutation	SNP	C	C	T			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr17:45369560C>T	ENST00000559488.1	+	10	1332	c.1316C>T	c.(1315-1317)tCc>tTc	p.S439F	ITGB3_ENST00000435993.2_Missense_Mutation_p.S392F|ITGB3_ENST00000560629.1_Silent_p.V427V	NM_000212.2	NP_000203.2	P05106	ITB3_HUMAN	integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61)	439					activation of protein kinase activity (GO:0032147)|angiogenesis involved in wound healing (GO:0060055)|apolipoprotein A-I-mediated signaling pathway (GO:0038027)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|mesodermal cell differentiation (GO:0048333)|negative chemotaxis (GO:0050919)|negative regulation of lipid storage (GO:0010888)|negative regulation of lipid transport (GO:0032369)|negative regulation of lipoprotein metabolic process (GO:0050748)|negative regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045715)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein folding (GO:0006457)|regulation of bone resorption (GO:0045124)|smooth muscle cell migration (GO:0014909)|substrate adhesion-dependent cell spreading (GO:0034446)|tube development (GO:0035295)|viral entry into host cell (GO:0046718)|wound healing (GO:0042060)	alphav-beta3 integrin-vitronectin complex (GO:0071062)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin alphav-beta3 complex (GO:0034683)|integrin complex (GO:0008305)|lamellipodium membrane (GO:0031258)|melanosome (GO:0042470)|microvillus membrane (GO:0031528)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)|receptor complex (GO:0043235)|ruffle membrane (GO:0032587)	cell adhesion molecule binding (GO:0050839)|extracellular matrix binding (GO:0050840)|fibronectin binding (GO:0001968)|identical protein binding (GO:0042802)|platelet-derived growth factor receptor binding (GO:0005161)|protease binding (GO:0002020)|protein disulfide isomerase activity (GO:0003756)|receptor activity (GO:0004872)|vascular endothelial growth factor receptor 2 binding (GO:0043184)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	39					Abciximab(DB00054)|Antithymocyte globulin(DB00098)|Eptifibatide(DB00063)|Tirofiban(DB00775)	AAGGAGAAGTCCTTTACCATA	0.522																																					p.S439F		.											.	ITGB3-714	0			c.C1316T						.						94.0	78.0	84.0					17																	45369560		2203	4300	6503	SO:0001583	missense	3690	exon10			AGAAGTCCTTTAC		CCDS11511.1	17q21.32	2014-09-17			ENSG00000259207	ENSG00000259207		"""CD molecules"", ""Integrins"""	6156	protein-coding gene	gene with protein product	"""platelet glycoprotein IIIa"""	173470		GP3A		2454952	Standard	NM_000212		Approved	CD61, GPIIIa	uc002ilj.3	P05106	OTTHUMG00000171956	ENST00000559488.1:c.1316C>T	17.37:g.45369560C>T	ENSP00000452786:p.Ser439Phe	Somatic	108	0		WXS	Illumina HiSeq	Phase_I	104	67	NM_000212	0	0	52	145	93	A0PJW2|D3DXJ8|O15495|Q12806|Q13413|Q14648|Q16499	Missense_Mutation	SNP	ENST00000559488.1	37	CCDS11511.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.558922	0.86231	.	.	ENSG00000178852	ENST00000262017;ENST00000435993	T	0.67171	-0.25	5.4	5.4	0.78164	Integrin beta subunit, N-terminal (2);	0.153255	0.56097	D	0.000025	T	0.78960	0.4366	L	0.60455	1.87	0.51233	D	0.99991	D	0.64830	0.994	D	0.65573	0.936	T	0.80324	-0.1430	10	0.66056	D	0.02	.	17.9137	0.88942	0.0:1.0:0.0:0.0	.	439	P05106	ITB3_HUMAN	F	439;392	ENSP00000407801:S392F	ENSP00000262017:S439F	S	+	2	0	C17orf57	42724559	0.998000	0.40836	1.000000	0.80357	0.953000	0.61014	3.315000	0.51951	2.531000	0.85337	0.462000	0.41574	TCC	.		0.522	ITGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416111.3	NM_000212	
HOXB2	3212	broad.mit.edu	37	17	46620496	46620496	+	Silent	SNP	A	A	G			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr17:46620496A>G	ENST00000330070.4	-	2	2172	c.1005T>C	c.(1003-1005)ccT>ccC	p.P335P	HOXB2_ENST00000504772.3_5'UTR|HOXB-AS1_ENST00000508688.1_RNA|HOXB-AS1_ENST00000435312.1_RNA|HOXB-AS1_ENST00000504972.3_RNA	NM_002145.3	NP_002136.1	P14652	HXB2_HUMAN	homeobox B2	335					anterior/posterior pattern specification (GO:0009952)|blood circulation (GO:0008015)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|facial nerve structural organization (GO:0021612)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|neural nucleus development (GO:0048857)|rhombomere 3 development (GO:0021569)|rhombomere 4 development (GO:0021570)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P335P(2)		NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|prostate(1)|skin(1)	11						CCTCGGAAAAAGGGACCGGGC	0.587																																					p.P335P													.	HOXB2-90	2	Substitution - coding silent(2)	lung(2)	c.T1005C						.						80.0	83.0	82.0					17																	46620496		2203	4300	6503	SO:0001819	synonymous_variant	3212	exon2			GGAAAAAGGGACC		CCDS11527.1	17q21.32	2012-02-22	2005-12-22		ENSG00000173917	ENSG00000173917		"""Homeoboxes / ANTP class : HOXL subclass"""	5113	protein-coding gene	gene with protein product		142967	"""homeo box B2"""	HOX2, HOX2H		1973146, 1358459	Standard	XM_005257276		Approved		uc002inm.3	P14652	OTTHUMG00000159930	ENST00000330070.4:c.1005T>C	17.37:g.46620496A>G		Somatic	138	0		WXS	Illumina HiSeq	Phase_I	160	3	NM_002145	0	0	89	89	0	P10913|P17485	Silent	SNP	ENST00000330070.4	37	CCDS11527.1																																																																																			.		0.587	HOXB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358384.2		
HSF5	124535	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	56540550	56540550	+	Missense_Mutation	SNP	C	C	G			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr17:56540550C>G	ENST00000323777.3	-	4	1244	c.1135G>C	c.(1135-1137)Gtt>Ctt	p.V379L		NM_001080439.1	NP_001073908.1	Q4G112	HSF5_HUMAN	heat shock transcription factor family member 5	379					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|ovary(3)|skin(1)	16	Medulloblastoma(34;0.127)|all_neural(34;0.237)					AACTCATCAACTATCTGAAAG	0.438																																					p.V379L		.											.	HSF5-71	0			c.G1135C						.						101.0	97.0	98.0					17																	56540550		2203	4300	6503	SO:0001583	missense	124535	exon4			CATCAACTATCTG	BC033020	CCDS32690.1	17q23.2	2006-04-25				ENSG00000176160			26862	protein-coding gene	gene with protein product							Standard	NM_001080439		Approved	FLJ40311	uc002iwi.1	Q4G112		ENST00000323777.3:c.1135G>C	17.37:g.56540550C>G	ENSP00000313243:p.Val379Leu	Somatic	144	0		WXS	Illumina HiSeq	Phase_I	227	69	NM_001080439	0	0	0	0	0	Q08EH7|Q8N7V2	Missense_Mutation	SNP	ENST00000323777.3	37	CCDS32690.1	.	.	.	.	.	.	.	.	.	.	C	13.97	2.396051	0.42512	.	.	ENSG00000176160	ENST00000412540;ENST00000323777	T	0.43294	0.95	5.47	4.49	0.54785	.	0.247257	0.28754	N	0.014249	T	0.30448	0.0765	L	0.27053	0.805	0.38062	D	0.936116	B	0.06786	0.001	B	0.08055	0.003	T	0.11372	-1.0590	10	0.34782	T	0.22	.	12.6737	0.56882	0.1654:0.8346:0.0:0.0	.	379	Q4G112	HSF5_HUMAN	L	279;379	ENSP00000313243:V379L	ENSP00000313243:V379L	V	-	1	0	HSF5	53895549	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.377000	0.44300	1.273000	0.44346	0.650000	0.86243	GTT	.		0.438	HSF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444719.1	XM_064190	
TEX14	56155	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	56663339	56663339	+	Missense_Mutation	SNP	G	G	C			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr17:56663339G>C	ENST00000240361.8	-	18	2996	c.2911C>G	c.(2911-2913)Ccc>Gcc	p.P971A	TEX14_ENST00000349033.5_Missense_Mutation_p.P965A|TEX14_ENST00000389934.3_Missense_Mutation_p.P965A			Q8IWB6	TEX14_HUMAN	testis expressed 14	971					attachment of spindle microtubules to kinetochore (GO:0008608)|intercellular bridge organization (GO:0043063)|male meiosis (GO:0007140)|mitotic sister chromatid separation (GO:0051306)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of cytokinesis (GO:0032466)|negative regulation of protein binding (GO:0032091)	cell (GO:0005623)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|midbody (GO:0030496)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)			breast(6)|endometrium(5)|kidney(3)|large_intestine(22)|liver(1)|lung(24)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	81	Medulloblastoma(34;0.127)|all_neural(34;0.237)					AGGGCGTCGGGCTCATTTTCA	0.512																																					p.P971A		.											.	TEX14-810	0			c.C2911G						.						145.0	146.0	146.0					17																	56663339		2203	4300	6503	SO:0001583	missense	56155	exon18			CGTCGGGCTCATT	AF285601	CCDS32692.1, CCDS32693.1, CCDS56042.1	17q22	2013-09-20	2007-03-13		ENSG00000121101	ENSG00000121101			11737	protein-coding gene	gene with protein product	"""cancer/testis antigen 113"""	605792	"""testis expressed sequence 14"""			11279525, 12711554	Standard	NM_031272		Approved	CT113	uc010dcz.2	Q8IWB6	OTTHUMG00000179245	ENST00000240361.8:c.2911C>G	17.37:g.56663339G>C	ENSP00000240361:p.Pro971Ala	Somatic	209	1		WXS	Illumina HiSeq	Phase_I	257	74	NM_001201457	0	0	0	0	0	A6NH19|Q7RTP3|Q8ND97|Q9BXT9	Missense_Mutation	SNP	ENST00000240361.8	37	CCDS56042.1	.	.	.	.	.	.	.	.	.	.	G	13.81	2.349191	0.41599	.	.	ENSG00000121101	ENST00000240361;ENST00000389934;ENST00000349033	T;T;T	0.78126	-1.15;-1.15;-1.1	5.38	-0.87	0.10646	.	1.113020	0.06645	N	0.761719	T	0.69450	0.3112	L	0.57536	1.79	0.09310	N	1	B;B;B	0.12630	0.006;0.002;0.002	B;B;B	0.14023	0.003;0.01;0.01	T	0.55648	-0.8108	10	0.45353	T	0.12	-3.8719	2.7702	0.05332	0.3122:0.0:0.3257:0.3621	.	971;965;965	Q8IWB6;Q8IWB6-3;Q8IWB6-2	TEX14_HUMAN;.;.	A	971;965;965	ENSP00000240361:P971A;ENSP00000374584:P965A;ENSP00000268910:P965A	ENSP00000240361:P971A	P	-	1	0	TEX14	54018338	0.000000	0.05858	0.003000	0.11579	0.431000	0.31685	-0.152000	0.10159	0.220000	0.20860	0.561000	0.74099	CCC	.		0.512	TEX14-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445446.1		
METTL2A	339175	broad.mit.edu	37	17	60501296	60501296	+	Silent	SNP	A	A	G			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr17:60501296A>G	ENST00000311506.5	+	1	69	c.33A>G	c.(31-33)gcA>gcG	p.A11A		NM_181725.3	NP_859076.3	Q96IZ6	MET2A_HUMAN	methyltransferase like 2A	11					tRNA methylation (GO:0030488)		tRNA (cytosine) methyltransferase activity (GO:0016427)			breast(2)|central_nervous_system(1)|endometrium(1)|upper_aerodigestive_tract(2)	6			BRCA - Breast invasive adenocarcinoma(2;1.08e-10)			GTGCACCTGCAGTCCTCGCCG	0.597											OREG0024635	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A11A													.	METTL2A-248	0			c.A33G						.						57.0	67.0	64.0					17																	60501296		692	1591	2283	SO:0001819	synonymous_variant	339175	exon1			ACCTGCAGTCCTC	AK000991	CCDS45752.1	17q23.3	2012-12-20		2006-02-10	ENSG00000087995	ENSG00000087995			25755	protein-coding gene	gene with protein product						12477932	Standard	NM_181725		Approved	FLJ12760, METTL2	uc002izv.2	Q96IZ6	OTTHUMG00000164527	ENST00000311506.5:c.33A>G	17.37:g.60501296A>G		Somatic	47	0	1046	WXS	Illumina HiSeq	Phase_I	63	21	NM_181725	0	0	42	67	25	A6NNC4|Q9H9G9|Q9NUI8|Q9P0B5	Silent	SNP	ENST00000311506.5	37	CCDS45752.1																																																																																			.		0.597	METTL2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445130.1	NM_181725	
CYB561	1534	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	61511913	61511913	+	Silent	SNP	G	G	A			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr17:61511913G>A	ENST00000392976.1	-	6	905	c.606C>T	c.(604-606)aaC>aaT	p.N202N	CYB561_ENST00000582997.1_Silent_p.N209N|CYB561_ENST00000581573.1_Silent_p.N202N|CYB561_ENST00000584031.1_3'UTR|RP11-269G24.4_ENST00000584608.1_lincRNA|CYB561_ENST00000392975.2_Silent_p.N202N|CYB561_ENST00000582297.1_Intron|CYB561_ENST00000581163.1_5'UTR|CYB561_ENST00000448884.2_3'UTR|CYB561_ENST00000582034.1_Silent_p.N173N|CYB561_ENST00000360793.3_Silent_p.N202N|CYB561_ENST00000542042.1_Silent_p.N269N	NM_001017916.1	NP_001017916.1	P49447	CY561_HUMAN	cytochrome b561	202	Cytochrome b561. {ECO:0000255|PROSITE- ProRule:PRU00242}.				electron transport chain (GO:0022900)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	ferric-chelate reductase activity (GO:0000293)|metal ion binding (GO:0046872)|transmembrane electron transfer carrier (GO:0022865)			lung(2)|ovary(1)|prostate(1)	4				READ - Rectum adenocarcinoma(1115;0.0689)		GGCCCAGCACGTTGGCCAGGA	0.642																																					p.N202N		.											.	CYB561-91	0			c.C606T						.						48.0	48.0	48.0					17																	61511913		2203	4300	6503	SO:0001819	synonymous_variant	1534	exon6			CAGCACGTTGGCC		CCDS11636.1	17q23.3	2013-03-14	2013-03-14		ENSG00000008283	ENSG00000008283		"""Cytochrome b genes"""	2571	protein-coding gene	gene with protein product	"""ferric-chelate reductase 2"", ""cytochrome b561 family, member A1"""	600019				7959749, 23249217	Standard	XM_005257091		Approved	FRRS2, CYB561A1	uc002jas.3	P49447		ENST00000392976.1:c.606C>T	17.37:g.61511913G>A		Somatic	44	0		WXS	Illumina HiSeq	Phase_I	50	33	NM_001915	0	0	57	142	85	B2RE96|B7Z775|D3DU11|Q5BJG9|Q9BU05|Q9BWR9	Silent	SNP	ENST00000392976.1	37	CCDS11636.1																																																																																			.		0.642	CYB561-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444843.1	NM_001915	
ABCA5	23461	hgsc.bcm.edu;broad.mit.edu	37	17	67303077	67303077	+	Missense_Mutation	SNP	G	G	A			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr17:67303077G>A	ENST00000392676.3	-	6	641	c.577C>T	c.(577-579)Ctt>Ttt	p.L193F	ABCA5_ENST00000392677.2_Missense_Mutation_p.L193F|ABCA5_ENST00000588877.1_Missense_Mutation_p.L193F			Q8WWZ7	ABCA5_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 5	193					cholesterol efflux (GO:0033344)|high-density lipoprotein particle remodeling (GO:0034375)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|reverse cholesterol transport (GO:0043691)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(18)|lung(19)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	54	Breast(10;3.72e-11)				Tacrolimus(DB00864)	TCCTTCCAAAGAGAAACATTG	0.348																																					p.L193F		.											.	ABCA5-93	0			c.C577T						.						56.0	60.0	59.0					17																	67303077		2198	4294	6492	SO:0001583	missense	23461	exon5			TCCAAAGAGAAAC	U66672	CCDS11685.1	17q24.3	2012-03-14			ENSG00000154265	ENSG00000154265		"""ATP binding cassette transporters / subfamily A"""	35	protein-coding gene	gene with protein product		612503				8894702	Standard	NM_172232		Approved	EST90625	uc002jig.2	Q8WWZ7		ENST00000392676.3:c.577C>T	17.37:g.67303077G>A	ENSP00000376443:p.Leu193Phe	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	113	39	NM_018672	0	0	2	4	2	Q8IVJ2|Q96LJ1|Q96MS4|Q96PZ9|Q9NY14	Missense_Mutation	SNP	ENST00000392676.3	37	CCDS11685.1	.	.	.	.	.	.	.	.	.	.	G	15.45	2.836993	0.50951	.	.	ENSG00000154265	ENST00000392677;ENST00000392676	D;D	0.87966	-2.32;-2.32	5.22	-9.14	0.00701	.	1.842040	0.03300	N	0.188828	T	0.60625	0.2283	N	0.01352	-0.895	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.08055	0.001;0.003	T	0.57452	-0.7809	9	.	.	.	.	6.752	0.23491	0.1697:0.5331:0.2205:0.0768	.	193;193	Q8WWZ7-2;Q8WWZ7	.;ABCA5_HUMAN	F	193	ENSP00000376444:L193F;ENSP00000376443:L193F	.	L	-	1	0	ABCA5	64814672	0.090000	0.21635	0.839000	0.33178	0.999000	0.98932	0.440000	0.21592	-1.239000	0.02532	0.650000	0.86243	CTT	.		0.348	ABCA5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450654.1	NM_018672	
NOTUM	147111	broad.mit.edu	37	17	79913365	79913365	+	Silent	SNP	G	G	A			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr17:79913365G>A	ENST00000409678.3	-	9	1427	c.1044C>T	c.(1042-1044)aaC>aaT	p.N348N		NM_178493.5	NP_848588.3	Q6P988	NOTUM_HUMAN	notum pectinacetylesterase homolog (Drosophila)	348						extracellular region (GO:0005576)	hydrolase activity (GO:0016787)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)|ovary(1)|skin(1)|urinary_tract(1)	15	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)			TCAGGTGCACGTTGTCCACCG	0.687																																					p.N348N													.	NOTUM-22	0			c.C1044T						.						23.0	20.0	21.0					17																	79913365		2202	4285	6487	SO:0001819	synonymous_variant	147111	exon9			GTGCACGTTGTCC	BC060882	CCDS32771.2	17q25.3	2008-02-05			ENSG00000185269	ENSG00000185269			27106	protein-coding gene	gene with protein product		609847					Standard	NM_178493		Approved		uc010wvg.2	Q6P988	OTTHUMG00000154416	ENST00000409678.3:c.1044C>T	17.37:g.79913365G>A		Somatic	43	0		WXS	Illumina HiSeq	Phase_I	54	20	NM_178493	0	0	0	0	0	Q8N410|Q8NI82	Silent	SNP	ENST00000409678.3	37	CCDS32771.2																																																																																			.		0.687	NOTUM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335123.2	NM_178493	
HCN2	610	broad.mit.edu	37	19	615935	615935	+	Missense_Mutation	SNP	G	G	C			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr19:615935G>C	ENST00000251287.2	+	8	2184	c.2131G>C	c.(2131-2133)Gtg>Ctg	p.V711L	AC005559.2_ENST00000591847.1_RNA	NM_001194.3	NP_001185.3	Q9UL51	HCN2_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 2	711					cell-cell signaling (GO:0007267)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	cAMP binding (GO:0030552)|identical protein binding (GO:0042802)|intracellular cAMP activated cation channel activity (GO:0005222)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)			endometrium(5)|lung(4)	9		all_epithelial(18;2.78e-22)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGGTCAGCGCGTGGGCCTCTT	0.692																																					p.V711L	Melanoma(145;1175 2427 8056 36306)												.	HCN2-90	0			c.G2131C						.						26.0	22.0	23.0					19																	615935		2198	4296	6494	SO:0001583	missense	610	exon8			CAGCGCGTGGGCC	AF064877	CCDS12035.1	19p13	2011-07-05				ENSG00000099822		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	4846	protein-coding gene	gene with protein product		602781		BCNG2		9405696, 9630217, 16382102	Standard	NM_001194		Approved	BCNG-2, HAC-1	uc002lpe.3	Q9UL51		ENST00000251287.2:c.2131G>C	19.37:g.615935G>C	ENSP00000251287:p.Val711Leu	Somatic	36	0		WXS	Illumina HiSeq	Phase_I	22	3	NM_001194	0	0	0	0	0	O60742|O60743|O75267|Q9UBS2	Missense_Mutation	SNP	ENST00000251287.2	37	CCDS12035.1	.	.	.	.	.	.	.	.	.	.	.	9.846	1.192309	0.21954	.	.	ENSG00000099822	ENST00000251287	T	0.42900	0.96	3.52	3.52	0.40303	.	.	.	.	.	T	0.19485	0.0468	N	0.08118	0	0.09310	N	1	B	0.15141	0.012	B	0.12837	0.008	T	0.19679	-1.0298	9	0.07325	T	0.83	.	8.5564	0.33483	0.1283:0.0:0.8717:0.0	.	711	Q9UL51	HCN2_HUMAN	L	711	ENSP00000251287:V711L	ENSP00000251287:V711L	V	+	1	0	HCN2	566935	0.009000	0.17119	0.104000	0.21259	0.845000	0.48019	0.661000	0.25023	1.697000	0.51169	0.478000	0.44815	GTG	.		0.692	HCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452100.1	NM_001194	
ZNF284	342909	broad.mit.edu	37	19	44590761	44590761	+	Missense_Mutation	SNP	G	G	C			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr19:44590761G>C	ENST00000421176.3	+	5	1346	c.1130G>C	c.(1129-1131)gGg>gCg	p.G377A	ZNF223_ENST00000591793.1_3'UTR|RNU6-902P_ENST00000517212.1_RNA	NM_001037813.2	NP_001032902.1	Q2VY69	ZN284_HUMAN	zinc finger protein 284	377					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|kidney(2)|large_intestine(6)|lung(4)|upper_aerodigestive_tract(1)	15		Prostate(69;0.0435)				AATGTATGTGGGAAGGGCTTC	0.428																																					p.G377A													.	.	0			c.G1130C						.						100.0	106.0	104.0					19																	44590761		2104	4238	6342	SO:0001583	missense	342909	exon5			TATGTGGGAAGGG	AY166789	CCDS46099.1	19q13.32	2013-01-08				ENSG00000186026		"""Zinc fingers, C2H2-type"", ""-"""	13078	protein-coding gene	gene with protein product						12743021	Standard	NM_001037813		Approved	DKFZp781F1775	uc002oyg.1	Q2VY69		ENST00000421176.3:c.1130G>C	19.37:g.44590761G>C	ENSP00000411032:p.Gly377Ala	Somatic	112	0		WXS	Illumina HiSeq	Phase_I	110	4	NM_001037813	0	0	2	2	0	Q86WM1	Missense_Mutation	SNP	ENST00000421176.3	37	CCDS46099.1	.	.	.	.	.	.	.	.	.	.	G	15.01	2.707297	0.48412	.	.	ENSG00000186026	ENST00000421176	T	0.07114	3.22	2.15	1.06	0.20224	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.28962	0.0719	M	0.87827	2.91	0.29133	N	0.879512	D	0.89917	1.0	D	0.97110	1.0	T	0.06607	-1.0817	9	0.87932	D	0	.	7.7642	0.28970	0.1413:0.0:0.8587:0.0	.	377	Q2VY69	ZN284_HUMAN	A	377	ENSP00000411032:G377A	ENSP00000411032:G377A	G	+	2	0	ZNF284	49282601	1.000000	0.71417	0.015000	0.15790	0.070000	0.16714	3.579000	0.53900	0.228000	0.21019	0.462000	0.41574	GGG	.		0.428	ZNF284-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460473.1	NM_001037813	
EEF1B2	1933	broad.mit.edu	37	2	207025358	207025358	+	Missense_Mutation	SNP	A	A	G			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr2:207025358A>G	ENST00000392222.2	+	2	502	c.127A>G	c.(127-129)Agc>Ggc	p.S43G	NDUFS1_ENST00000423725.1_5'Flank|SNORA41_ENST00000384675.1_RNA|SNORD51_ENST00000384320.2_RNA|NDUFS1_ENST00000449699.1_5'Flank|NDUFS1_ENST00000233190.6_5'Flank|EEF1B2_ENST00000236957.5_Missense_Mutation_p.S43G|NDUFS1_ENST00000432169.1_5'Flank|NDUFS1_ENST00000455934.2_5'Flank|EEF1B2_ENST00000392221.1_Missense_Mutation_p.S43G|NDUFS1_ENST00000457011.1_5'Flank|NDUFS1_ENST00000440274.1_5'Flank	NM_001959.3	NP_001950.1	P24534	EF1B_HUMAN	eukaryotic translation elongation factor 1 beta 2	43	GST C-terminal.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|translation (GO:0006412)|translational elongation (GO:0006414)	cytosol (GO:0005829)|eukaryotic translation elongation factor 1 complex (GO:0005853)	translation elongation factor activity (GO:0003746)	p.S43G(4)		breast(1)|endometrium(5)|kidney(3)|large_intestine(1)|lung(6)	16						AGCCGTGTCCAGCCCACCGCC	0.468																																					p.S43G													.	EEF1B2-227	4	Substitution - Missense(4)	endometrium(2)|lung(1)|kidney(1)	c.A127G						.						109.0	99.0	102.0					2																	207025358		2203	4300	6503	SO:0001583	missense	1933	exon3			GTGTCCAGCCCAC	X60489	CCDS2367.1	2q33.3	2011-04-28			ENSG00000114942	ENSG00000114942			3208	protein-coding gene	gene with protein product		600655				8250921	Standard	NM_001959		Approved		uc002vbf.1	P24534	OTTHUMG00000132891	ENST00000392222.2:c.127A>G	2.37:g.207025358A>G	ENSP00000376056:p.Ser43Gly	Somatic	133	3		WXS	Illumina HiSeq	Phase_I	111	5	NM_021121	1	1	812	814	0	A8K795|Q6IBH9	Missense_Mutation	SNP	ENST00000392222.2	37	CCDS2367.1	.	.	.	.	.	.	.	.	.	.	A	0.014	-1.585588	0.00872	.	.	ENSG00000114942	ENST00000236957;ENST00000392221;ENST00000392222;ENST00000445505	T;T;T;T	0.44482	0.92;0.92;0.92;0.92	5.47	0.911	0.19343	Glutathione S-transferase, C-terminal-like (2);	0.442134	0.26800	N	0.022437	T	0.19846	0.0477	N	0.16098	0.37	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.18745	-1.0327	10	0.17832	T	0.49	-2.1703	6.3337	0.21285	0.2348:0.0:0.6384:0.1268	.	43	P24534	EF1B_HUMAN	G	43	ENSP00000236957:S43G;ENSP00000376055:S43G;ENSP00000376056:S43G;ENSP00000407730:S43G	ENSP00000236957:S43G	S	+	1	0	EEF1B2	206733603	0.049000	0.20398	0.145000	0.22337	0.051000	0.14879	0.879000	0.28146	-0.027000	0.13873	-0.252000	0.11476	AGC	.		0.468	EEF1B2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336436.1	NM_001037663	
ANKZF1	55139	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	220099828	220099828	+	Missense_Mutation	SNP	G	G	T			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr2:220099828G>T	ENST00000323348.5	+	10	1659	c.1485G>T	c.(1483-1485)tgG>tgT	p.W495C	GLB1L_ENST00000497855.1_5'Flank|ANKZF1_ENST00000409849.1_Missense_Mutation_p.W285C|ANKZF1_ENST00000410034.3_Missense_Mutation_p.W495C	NM_018089.2	NP_060559.2	Q9H8Y5	ANKZ1_HUMAN	ankyrin repeat and zinc finger domain containing 1	495						membrane (GO:0016020)	metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	23		Renal(207;0.0474)		Epithelial(149;1.2e-06)|all cancers(144;0.000197)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CAGAGCTCTGGAATGCACTGC	0.587																																					p.W495C		.											.	ANKZF1-92	0			c.G1485T						.						51.0	55.0	53.0					2																	220099828		2017	4171	6188	SO:0001583	missense	55139	exon10			GCTCTGGAATGCA	AF364318	CCDS42821.1, CCDS63129.1	2q35	2013-01-10			ENSG00000163516	ENSG00000163516		"""Zinc fingers, C2H2-type"", ""Ankyrin repeat domain containing"""	25527	protein-coding gene	gene with protein product						12477932	Standard	NM_018089		Approved	FLJ10415, ZNF744	uc002vkg.3	Q9H8Y5	OTTHUMG00000154533	ENST00000323348.5:c.1485G>T	2.37:g.220099828G>T	ENSP00000321617:p.Trp495Cys	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	57	22	NM_001042410	0	0	18	28	10	Q9NVZ4	Missense_Mutation	SNP	ENST00000323348.5	37	CCDS42821.1	.	.	.	.	.	.	.	.	.	.	G	11.67	1.709332	0.30322	.	.	ENSG00000163516	ENST00000323348;ENST00000409849;ENST00000410034	T;T;T	0.52983	0.64;0.64;0.64	5.41	4.51	0.55191	Ankyrin repeat-containing domain (2);	0.253027	0.37955	N	0.001878	T	0.43942	0.1270	M	0.65975	2.015	0.53005	D	0.999964	B	0.15141	0.012	B	0.17722	0.019	T	0.38265	-0.9669	10	0.37606	T	0.19	-6.7572	8.4061	0.32616	0.0:0.1513:0.5358:0.313	.	495	Q9H8Y5	ANKZ1_HUMAN	C	495;285;495	ENSP00000321617:W495C;ENSP00000386815:W285C;ENSP00000386337:W495C	ENSP00000321617:W495C	W	+	3	0	ANKZF1	219808072	1.000000	0.71417	0.983000	0.44433	0.353000	0.29299	1.765000	0.38481	1.473000	0.48159	0.591000	0.81541	TGG	.		0.587	ANKZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335790.1	NM_018089	
RIN2	54453	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	20	19955386	19955386	+	Silent	SNP	C	C	T			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr20:19955386C>T	ENST00000255006.6	+	8	1013	c.864C>T	c.(862-864)tcC>tcT	p.S288S	RIN2_ENST00000484638.1_3'UTR|RIN2_ENST00000440354.2_Intron	NM_001242581.1|NM_018993.3	NP_001229510.1|NP_061866.1	Q8WYP3	RIN2_HUMAN	Ras and Rab interactor 2	239					endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of catalytic activity (GO:0050790)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	GTPase activator activity (GO:0005096)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|small GTPase regulator activity (GO:0005083)			autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|urinary_tract(2)	27						GTCCTGCCTCCCTGCGTCAGC	0.547																																					p.S288S		.											.	RIN2-660	0			c.C864T						.						73.0	77.0	75.0					20																	19955386		1935	4144	6079	SO:0001819	synonymous_variant	54453	exon8			TGCCTCCCTGCGT	AB060339	CCDS56182.1	20p11.22	2008-07-30			ENSG00000132669	ENSG00000132669			18750	protein-coding gene	gene with protein product		610222				11733506, 1849280, 16423831	Standard	NM_018993		Approved	RASSF4	uc002wro.2	Q8WYP3	OTTHUMG00000031996	ENST00000255006.6:c.864C>T	20.37:g.19955386C>T		Somatic	105	0		WXS	Illumina HiSeq	Phase_I	68	33	NM_001242581	0	0	11	18	7	Q00425|Q5TFT8|Q9BQL3|Q9H071	Silent	SNP	ENST00000255006.6	37	CCDS56182.1																																																																																			.		0.547	RIN2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078212.1		
RBFOX2	23543	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	22	36206007	36206007	+	Silent	SNP	A	A	G			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr22:36206007A>G	ENST00000438146.2	-	3	281	c.282T>C	c.(280-282)ccT>ccC	p.P94P	RBFOX2_ENST00000262829.7_Silent_p.P24P|RBFOX2_ENST00000414461.2_Silent_p.P24P|RBFOX2_ENST00000359369.4_Silent_p.P4P|RBFOX2_ENST00000397303.2_Silent_p.P4P|RBFOX2_ENST00000449924.2_Silent_p.P24P|RBFOX2_ENST00000416721.2_Silent_p.P24P|RBFOX2_ENST00000405409.2_Silent_p.P24P	NM_001082578.1|NM_001082579.1	NP_001076047|NP_001076048.1	O43251	RFOX2_HUMAN	RNA binding protein, fox-1 homolog (C. elegans) 2	34					dendrite morphogenesis (GO:0048813)|intracellular estrogen receptor signaling pathway (GO:0030520)|mRNA processing (GO:0006397)|negative regulation of transcription, DNA-templated (GO:0045892)|neuromuscular process controlling balance (GO:0050885)|radial glia guided migration of Purkinje cell (GO:0021942)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of cell proliferation (GO:0042127)|regulation of definitive erythrocyte differentiation (GO:0010724)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			endometrium(4)|large_intestine(7)|lung(7)	18						TGGTAGTAAAAGGCTGAACCA	0.473																																					p.P94P		.											.	RBFOX2-90	0			c.T282C						.						148.0	133.0	138.0					22																	36206007		2203	4300	6503	SO:0001819	synonymous_variant	23543	exon3			AGTAAAAGGCTGA	AL009266	CCDS13921.1, CCDS43013.1, CCDS46699.1, CCDS46700.1, CCDS46701.1	22q12-q13	2013-02-12	2010-09-10	2010-09-10	ENSG00000100320	ENSG00000100320		"""RNA binding motif (RRM) containing"""	9906	protein-coding gene	gene with protein product	"""hexaribonucleotide binding protein 2"""	612149	"""RNA binding motif protein 9"""	RBM9			Standard	NM_014309		Approved	HNRBP2, FOX-2, HRNBP2	uc003aon.4	O43251	OTTHUMG00000150585	ENST00000438146.2:c.282T>C	22.37:g.36206007A>G		Somatic	172	1		WXS	Illumina HiSeq	Phase_I	131	58	NM_001082579	0	0	25	49	24	A4F5G8|A8K5Z5|B0QYY8|B0QYY9|Q0PRL5|Q0VH35|Q5TF71|Q6IC09|Q8TD00|Q8WYB1|Q96DZ6|Q96NL7|Q9UGW4|Q9UH33	Silent	SNP	ENST00000438146.2	37	CCDS43013.1																																																																																			.		0.473	RBFOX2-005	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319299.3		
PLCL2	23228	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	17051783	17051783	+	Missense_Mutation	SNP	G	G	T			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr3:17051783G>T	ENST00000418129.2	+	2	1032	c.567G>T	c.(565-567)ttG>ttT	p.L189F	PLCL2_ENST00000432376.1_Missense_Mutation_p.L189F|PLCL2_ENST00000460467.1_Intron|PLCL2_ENST00000396755.2_Missense_Mutation_p.L189F	NM_001144382.1	NP_001137854.1	Q9UPR0	PLCL2_HUMAN	phospholipase C-like 2	315	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				B cell proliferation involved in immune response (GO:0002322)|B-1a B cell differentiation (GO:0002337)|gamma-aminobutyric acid signaling pathway (GO:0007214)|intracellular signal transduction (GO:0035556)|lipid metabolic process (GO:0006629)|negative regulation of B cell receptor signaling pathway (GO:0050859)|positive regulation of receptor binding (GO:1900122)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of synaptic transmission, GABAergic (GO:0032228)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|GABA receptor binding (GO:0050811)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			breast(4)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(2)|skin(7)|urinary_tract(1)	43						TCAAAGAATTGCATAAATCAA	0.348																																					p.L189F		.											.	PLCL2-229	0			c.G567T						.						61.0	64.0	63.0					3																	17051783		2203	4300	6503	SO:0001583	missense	23228	exon2			AGAATTGCATAAA	AB029015	CCDS33713.1, CCDS74911.1	3p25.3-p25.1	2008-03-18	2002-02-18	2002-02-22	ENSG00000154822	ENSG00000154822			9064	protein-coding gene	gene with protein product		614276	"""phospholipase C, epsilon 2"""	PLCE2		10470851	Standard	NM_015184		Approved	KIAA1092	uc011awd.2	Q9UPR0	OTTHUMG00000155467	ENST00000418129.2:c.567G>T	3.37:g.17051783G>T	ENSP00000409637:p.Leu189Phe	Somatic	102	1		WXS	Illumina HiSeq	Phase_I	161	53	NM_015184	0	0	10	14	4	A8K5V4|Q8N498|Q9H8L0|Q9UFP9	Missense_Mutation	SNP	ENST00000418129.2	37	CCDS33713.1	.	.	.	.	.	.	.	.	.	.	G	6.609	0.480810	0.12581	.	.	ENSG00000154822	ENST00000418129;ENST00000285094;ENST00000396755;ENST00000432376	T;T;T	0.45276	0.9;0.9;0.9	5.54	5.54	0.83059	EF-hand-like domain (1);	0.063928	0.64402	D	0.000008	T	0.53142	0.1778	.	.	.	0.54753	D	0.999982	D	0.52996	0.957	P	0.57502	0.822	T	0.51980	-0.8636	8	.	.	.	.	9.7379	0.40399	0.1594:0.0:0.8406:0.0	.	315	Q9UPR0	PLCL2_HUMAN	F	189;316;189;189	ENSP00000409637:L189F;ENSP00000379979:L189F;ENSP00000412836:L189F	.	L	+	3	2	PLCL2	17026787	0.998000	0.40836	0.999000	0.59377	0.977000	0.68977	0.452000	0.21795	2.600000	0.87896	0.563000	0.77884	TTG	.		0.348	PLCL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340250.3		
TRAK1	22906	ucsc.edu	37	3	42251523	42251523	+	Intron	SNP	A	A	C			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr3:42251523A>C	ENST00000327628.5	+	14	2363				TRAK1_ENST00000396175.1_Intron|TRAK1_ENST00000487159.1_Intron|TRAK1_ENST00000341421.3_Missense_Mutation_p.Y612S	NM_001042646.2	NP_001036111.1	Q9UPV9	TRAK1_HUMAN	trafficking protein, kinesin binding 1						endosome to lysosome transport (GO:0008333)|protein O-linked glycosylation (GO:0006493)|protein targeting (GO:0006605)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	22						AGCAGAAGTTACCCGAGCCGG	0.637																																					p.Y670S	GBM(44;195 884 22595 31865 41850)												.	TRAK1-91	0			c.A2009C						.						53.0	51.0	52.0					3																	42251523		2203	4300	6503	SO:0001627	intron_variant	22906	exon14			GAAGTTACCCGAG		CCDS2695.1, CCDS43072.1, CCDS58826.1, CCDS74922.1	3p22.1	2012-03-05			ENSG00000182606	ENSG00000182606			29947	protein-coding gene	gene with protein product	"""OGT(O Glc NAc transferase) interacting protein 106 KDa"", ""O-linked N-acetylglucosamine transferase interacting protein 106"", ""milton homolog 1 (Drosophila)"""	608112				10470851, 12435728, 16380713, 20230862	Standard	NM_014965		Approved	OIP106, KIAA1042, MILT1	uc003cky.4	Q9UPV9	OTTHUMG00000131795	ENST00000327628.5:c.1963+46A>C	3.37:g.42251523A>C		Somatic	75	3		WXS	Illumina HiSeq		65	3	NM_001265608	0	0	9	11	2	E9PDS2|J3KNT7|Q63HR0|Q659B5|Q96B69	Missense_Mutation	SNP	ENST00000327628.5	37	CCDS43072.1	.	.	.	.	.	.	.	.	.	.	A	9.834	1.189127	0.21954	.	.	ENSG00000182606	ENST00000341421	T	0.07688	3.17	4.97	-3.01	0.05463	.	.	.	.	.	T	0.03305	0.0096	N	0.14661	0.345	0.21256	N	0.999741	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.0;0.001	T	0.45920	-0.9228	8	.	.	.	.	0.4311	0.00471	0.3368:0.2619:0.1475:0.2538	.	596;670;612	B7Z218;B7Z347;Q9UPV9-2	.;.;.	S	612	ENSP00000340702:Y612S	.	Y	+	2	0	TRAK1	42226527	0.992000	0.36948	0.952000	0.39060	0.981000	0.71138	0.277000	0.18734	-0.288000	0.09051	-0.290000	0.09829	TAC	.		0.637	TRAK1-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343413.1	NM_014965	
C3orf27	23434	broad.mit.edu	37	3	128292497	128292497	+	Missense_Mutation	SNP	C	C	T	rs141693917		TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr3:128292497C>T	ENST00000356020.2	-	3	1042	c.76G>A	c.(76-78)Gtc>Atc	p.V26I		NM_007354.2	NP_031380.1	O15544	GR6_HUMAN	chromosome 3 open reading frame 27	26								p.V26I(2)		large_intestine(2)|lung(5)|prostate(1)	8				GBM - Glioblastoma multiforme(114;0.176)		AGGCGGGAGACGCTGAGTCTA	0.592																																					p.V26I													.	C3orf27-90	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G76A						.	C	ILE/VAL	0,4402		0,0,2201	28.0	29.0	29.0		76	-1.2	0.0	3	dbSNP_134	29	1,8597		0,1,4298	no	missense	C3orf27	NM_007354.2	29	0,1,6499	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	26/150	128292497	1,12999	2201	4299	6500	SO:0001583	missense	23434	exon3			GGGAGACGCTGAG	AF008192	CCDS3050.1	3q21	2005-12-19			ENSG00000198685	ENSG00000198685			17099	protein-coding gene	gene with protein product						9307271	Standard	NR_125802		Approved	GR6	uc003ekq.3	O15544	OTTHUMG00000159688	ENST00000356020.2:c.76G>A	3.37:g.128292497C>T	ENSP00000348302:p.Val26Ile	Somatic	50	0		WXS	Illumina HiSeq	Phase_I	58	10	NM_007354	0	0	0	0	0		Missense_Mutation	SNP	ENST00000356020.2	37	CCDS3050.1	.	.	.	.	.	.	.	.	.	.	C	9.932	1.215195	0.22373	0.0	1.16E-4	ENSG00000198685	ENST00000356020	.	.	.	2.35	-1.23	0.09465	.	.	.	.	.	T	0.11750	0.0286	N	0.08118	0	0.09310	N	1	P	0.39404	0.672	B	0.29942	0.109	T	0.16158	-1.0412	8	0.87932	D	0	.	6.0846	0.19960	0.157:0.6855:0.0:0.1575	.	26	O15544	GR6_HUMAN	I	26	.	ENSP00000348302:V26I	V	-	1	0	C3orf27	129775187	0.000000	0.05858	0.001000	0.08648	0.388000	0.30384	-0.996000	0.03709	-0.054000	0.13266	0.313000	0.20887	GTC	C|1.000;T|0.000		0.592	C3orf27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356924.1	NM_007354	
KY	339855	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	134323200	134323200	+	Nonsense_Mutation	SNP	C	C	A			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr3:134323200C>A	ENST00000423778.2	-	11	1268	c.1207G>T	c.(1207-1209)Gag>Tag	p.E403*	KY_ENST00000508956.1_Nonsense_Mutation_p.E382*|KY_ENST00000503669.1_3'UTR	NM_178554.4	NP_848649.3	Q8NBH2	KY_HUMAN	kyphoscoliosis peptidase	403					muscle organ development (GO:0007517)|neuromuscular junction development (GO:0007528)	cytoskeleton (GO:0005856)|Z disc (GO:0030018)	peptidase activity (GO:0008233)			central_nervous_system(1)|endometrium(3)|kidney(1)|lung(12)|ovary(2)|upper_aerodigestive_tract(2)	21						GGGTACACCTCCAACTTCATC	0.542																																					p.E403X		.											.	KY-24	0			c.G1207T						.						87.0	86.0	86.0					3																	134323200		2128	4244	6372	SO:0001587	stop_gained	339855	exon11			ACACCTCCAACTT	AK090526	CCDS46920.1	3q22.1	2010-11-23			ENSG00000174611	ENSG00000174611			26576	protein-coding gene	gene with protein product		605739					Standard	NM_178554		Approved	FLJ33207	uc010hty.3	Q8NBH2	OTTHUMG00000159788	ENST00000423778.2:c.1207G>T	3.37:g.134323200C>A	ENSP00000397598:p.Glu403*	Somatic	111	0		WXS	Illumina HiSeq	Phase_I	143	104	NM_178554	0	0	4	6	2	B7Z1S4|Q6ZT15	Nonsense_Mutation	SNP	ENST00000423778.2	37	CCDS46920.1	.	.	.	.	.	.	.	.	.	.	C	36	5.846292	0.97016	.	.	ENSG00000174611	ENST00000508956;ENST00000423778;ENST00000310263	.	.	.	5.48	5.48	0.80851	.	0.368781	0.27393	N	0.019579	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	-14.9747	19.3474	0.94370	0.0:1.0:0.0:0.0	.	.	.	.	X	382;403;403	.	ENSP00000309520:E403X	E	-	1	0	KY	135805890	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.042000	0.57347	2.578000	0.87016	0.561000	0.74099	GAG	.		0.542	KY-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357320.1	NM_178554	
HPS3	84343	hgsc.bcm.edu;broad.mit.edu	37	3	148885021	148885021	+	Missense_Mutation	SNP	G	G	T	rs551986971		TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr3:148885021G>T	ENST00000296051.2	+	15	2930	c.2790G>T	c.(2788-2790)gaG>gaT	p.E930D	HPS3_ENST00000460120.1_Missense_Mutation_p.E765D	NM_032383.3	NP_115759.2	Q969F9	HPS3_HUMAN	Hermansky-Pudlak syndrome 3	930					organelle organization (GO:0006996)|pigmentation (GO:0043473)	BLOC-2 complex (GO:0031084)				breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	34			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			TGAAAGAAGAGAACCGGGTAT	0.403									Hermansky-Pudlak syndrome																												p.E930D		.											.	HPS3-158	0			c.G2790T						.						74.0	75.0	75.0					3																	148885021		2203	4300	6503	SO:0001583	missense	84343	exon15	Familial Cancer Database	HPS, HPS1-8	AGAAGAGAACCGG	AY033141	CCDS3140.1	3q24	2014-06-18			ENSG00000163755	ENSG00000163755			15597	protein-coding gene	gene with protein product		606118				11455388	Standard	NM_032383		Approved	SUTAL	uc003ewu.1	Q969F9	OTTHUMG00000159548	ENST00000296051.2:c.2790G>T	3.37:g.148885021G>T	ENSP00000296051:p.Glu930Asp	Somatic	29	1		WXS	Illumina HiSeq	Phase_I	45	26	NM_032383	0	0	1	1	0	A8K6G6|Q8WTV6|Q96AP1|Q96MR3|Q9H608	Missense_Mutation	SNP	ENST00000296051.2	37	CCDS3140.1	.	.	.	.	.	.	.	.	.	.	G	9.373	1.071040	0.20147	.	.	ENSG00000163755	ENST00000296051;ENST00000460120	T;T	0.63417	-0.03;-0.04	6.01	0.327	0.15913	.	0.542522	0.23534	N	0.047155	T	0.32466	0.0830	N	0.15975	0.35	0.49582	D	0.999804	B;B	0.10296	0.003;0.001	B;B	0.11329	0.006;0.002	T	0.14448	-1.0472	10	0.06494	T	0.89	-9.9199	4.0764	0.09906	0.1806:0.318:0.4022:0.0992	.	765;930	G5E9V4;Q969F9	.;HPS3_HUMAN	D	930;765	ENSP00000296051:E930D;ENSP00000418230:E765D	ENSP00000296051:E930D	E	+	3	2	HPS3	150367711	0.080000	0.21391	0.995000	0.50966	0.991000	0.79684	-0.222000	0.09190	0.105000	0.17753	0.650000	0.86243	GAG	.		0.403	HPS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356151.1	NM_032383	
VPS8	23355	ucsc.edu	37	3	184603940	184603940	+	Nonsense_Mutation	SNP	C	C	T			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr3:184603940C>T	ENST00000437079.3	+	22	1948	c.1777C>T	c.(1777-1779)Cga>Tga	p.R593*	VPS8_ENST00000446204.2_Intron|VPS8_ENST00000436792.2_Nonsense_Mutation_p.R591*|VPS8_ENST00000287546.4_Nonsense_Mutation_p.R593*	NM_001009921.2	NP_001009921.1	Q8N3P4	VPS8_HUMAN	vacuolar protein sorting 8 homolog (S. cerevisiae)	593							zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	54	all_cancers(143;2.51e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.02e-33)|OV - Ovarian serous cystadenocarcinoma(80;4.81e-22)			TCTGCTGCAGCGAAAGTGAGT	0.433																																					p.R593X													.	VPS8-91	0			c.C1777T						.						194.0	190.0	191.0					3																	184603940		1977	4153	6130	SO:0001587	stop_gained	23355	exon21			CTGCAGCGAAAGT	AK056661	CCDS46972.1	3q27.2	2006-07-07	2006-07-07	2006-07-07	ENSG00000156931	ENSG00000156931			29122	protein-coding gene	gene with protein product			"""KIAA0804"""	KIAA0804		9872452	Standard	NM_001009921		Approved	FLJ32099	uc003fpb.1	Q8N3P4	OTTHUMG00000156707	ENST00000437079.3:c.1777C>T	3.37:g.184603940C>T	ENSP00000397879:p.Arg593*	Somatic	21	0		WXS	Illumina HiSeq		40	4	NM_001009921	0	0	0	0	0	A8K8Q8|B9EIQ1|C9JB61|O94896|Q63HP2|Q9BVP9|Q9H9B0	Nonsense_Mutation	SNP	ENST00000437079.3	37	CCDS46971.1	.	.	.	.	.	.	.	.	.	.	C	41	8.738117	0.98935	.	.	ENSG00000156931	ENST00000287546;ENST00000437079;ENST00000436792	.	.	.	5.83	3.99	0.46301	.	0.053175	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07644	T	0.81	-8.1278	15.0324	0.71717	0.2602:0.7397:0.0:0.0	.	.	.	.	X	593;593;591	.	ENSP00000287546:R593X	R	+	1	2	VPS8	186086634	1.000000	0.71417	1.000000	0.80357	0.817000	0.46193	2.885000	0.48570	0.761000	0.33130	-0.181000	0.13052	CGA	.		0.433	VPS8-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015303	
CRIPAK	285464	broad.mit.edu	37	4	1388729	1388729	+	Missense_Mutation	SNP	G	G	C			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr4:1388729G>C	ENST00000324803.4	+	1	3390	c.430G>C	c.(430-432)Gga>Cga	p.G144R		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	144					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			GTGCCCATGCGGAGTGCCCGC	0.701																																					p.G144R													.	CRIPAK-90	0			c.G430C						.						37.0	37.0	37.0					4																	1388729		2033	3881	5914	SO:0001583	missense	285464	exon1			CCATGCGGAGTGC	AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.430G>C	4.37:g.1388729G>C	ENSP00000323978:p.Gly144Arg	Somatic	394	1		WXS	Illumina HiSeq	Phase_I	254	4	NM_175918	0	0	19	19	0	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	-|-	10.33|10.33	1.320122|1.320122	0.23994|0.23994	.|.	.|.	ENSG00000179979|ENSG00000179979	ENST00000324803|ENST00000382944	T|.	0.17370|.	2.28|.	0.948|0.948	0.948|0.948	0.19561|0.19561	Post-SET domain (1);|.	.|.	.|.	.|.	.|.	T|T	0.18841|0.18841	0.0452|0.0452	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	D|.	0.76494|.	0.999|.	D|.	0.70487|.	0.969|.	T|T	0.25082|0.25082	-1.0142|-1.0142	9|6	0.19147|0.32370	T|T	0.46|0.25	.|.	7.86|7.86	0.29504|0.29504	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	144|.	Q8N1N5|.	CRPAK_HUMAN|.	R|P	144|127	ENSP00000323978:G144R|.	ENSP00000323978:G144R|ENSP00000372402:R127P	G|R	+|+	1|2	0|0	CRIPAK|CRIPAK	1378729|1378729	0.000000|0.000000	0.05858|0.05858	0.032000|0.032000	0.17829|0.17829	0.031000|0.031000	0.12232|0.12232	-2.156000|-2.156000	0.01283|0.01283	0.840000|0.840000	0.34995|0.34995	0.121000|0.121000	0.15741|0.15741	GGA|CGG	.		0.701	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
DCHS2	54798	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	155256161	155256161	+	Missense_Mutation	SNP	T	T	G			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr4:155256161T>G	ENST00000357232.4	-	8	1074	c.1075A>C	c.(1075-1077)Att>Ctt	p.I359L	DCHS2_ENST00000507542.1_5'UTR|DCHS2_ENST00000339452.1_Missense_Mutation_p.I858L	NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	359	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		TCGGCATTAATGACAGCTGTG	0.433																																					p.I858L		.											.	DCHS2-94	0			c.A2572C						.						110.0	109.0	109.0					4																	155256161		2203	4300	6503	SO:0001583	missense	54798	exon4			CATTAATGACAGC	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"""Cadherins / Cadherin-related"""	23111	protein-coding gene	gene with protein product	"""cadherin-related family member 7"""	612486	"""cadherin-like 27"", ""dachsous 2 (Drosophila)"""	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.1075A>C	4.37:g.155256161T>G	ENSP00000349768:p.Ile359Leu	Somatic	89	1		WXS	Illumina HiSeq	Phase_I	108	55	NM_001142552	0	0	0	0	0	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	.	.	.	.	.	.	.	.	.	.	T	2.461	-0.324065	0.05350	.	.	ENSG00000197410	ENST00000357232;ENST00000339452;ENST00000544161	T;T	0.52983	0.64;0.73	6.17	-3.98	0.04082	Cadherin (2);	1.778240	0.02970	N	0.144240	T	0.35128	0.0921	L	0.31926	0.97	0.09310	N	1	B;B	0.20887	0.049;0.024	B;B	0.20955	0.032;0.014	T	0.16660	-1.0395	10	0.23302	T	0.38	.	8.8965	0.35467	0.0:0.4543:0.2232:0.3226	.	858;359	E9PC11;Q6V1P9	.;PCD23_HUMAN	L	359;858;858	ENSP00000349768:I359L;ENSP00000345062:I858L	ENSP00000345062:I858L	I	-	1	0	DCHS2	155475611	0.000000	0.05858	0.000000	0.03702	0.354000	0.29330	-0.719000	0.04974	-0.924000	0.03780	-0.408000	0.06270	ATT	.		0.433	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
SLC27A6	28965	ucsc.edu	37	5	128302311	128302311	+	Splice_Site	SNP	G	G	A			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr5:128302311G>A	ENST00000262462.4	+	1	1491	c.481G>A	c.(481-483)Gat>Aat	p.D161N	SLC27A6_ENST00000506176.1_Splice_Site_p.D161N|SLC27A6_ENST00000395266.1_Splice_Site_p.D161N			Q9Y2P4	S27A6_HUMAN	solute carrier family 27 (fatty acid transporter), member 6	161					long-chain fatty acid metabolic process (GO:0001676)|long-chain fatty acid transport (GO:0015909)|transmembrane transport (GO:0055085)|very long-chain fatty acid metabolic process (GO:0000038)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	long-chain fatty acid-CoA ligase activity (GO:0004467)|nucleotide binding (GO:0000166)|very long-chain fatty acid-CoA ligase activity (GO:0031957)			NS(2)|endometrium(1)|kidney(3)|large_intestine(11)|liver(1)|lung(20)|prostate(1)|skin(4)|stomach(1)	44		all_cancers(142;0.0483)|Prostate(80;0.055)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Epithelial(69;0.171)|OV - Ovarian serous cystadenocarcinoma(64;0.186)		GGTGGGCGCAGGTAGAGTATG	0.517																																					p.D161N													.	SLC27A6-90	0			c.G481A						.						27.0	22.0	24.0					5																	128302311		2203	4300	6503	SO:0001630	splice_region_variant	28965	exon1			GGCGCAGGTAGAG	AF064254	CCDS4145.1	5q23.3	2013-05-22			ENSG00000113396	ENSG00000113396		"""Acyl-CoA synthetase family"", ""Solute carriers"""	11000	protein-coding gene	gene with protein product	"""fatty-acid-Coenzyme A ligase, very long-chain 2"""	604196				12556534, 10479480	Standard	XM_005271967		Approved	FATP6, VLCS-H1, FACVL2, ACSVL2	uc003kuy.3	Q9Y2P4	OTTHUMG00000128991	ENST00000262462.4:c.481+1G>A	5.37:g.128302311G>A		Somatic	37	0		WXS	Illumina HiSeq		21	4	NM_001017372	0	0	0	0	0	Q6IAM5|Q7Z6E6|Q86YF6	Missense_Mutation	SNP	ENST00000262462.4	37	CCDS4145.1	.	.	.	.	.	.	.	.	.	.	G	19.62	3.862321	0.71949	.	.	ENSG00000113396	ENST00000262462;ENST00000395266;ENST00000506176	T;T;T	0.50548	0.74;0.74;0.74	4.04	4.04	0.47022	AMP-dependent synthetase/ligase (1);	0.145674	0.64402	N	0.000010	T	0.53254	0.1785	M	0.79258	2.445	0.80722	D	1	B	0.18968	0.032	B	0.24848	0.056	T	0.58741	-0.7583	10	0.51188	T	0.08	-12.852	17.5013	0.87732	0.0:0.0:1.0:0.0	.	161	Q9Y2P4	S27A6_HUMAN	N	161	ENSP00000262462:D161N;ENSP00000378684:D161N;ENSP00000421024:D161N	ENSP00000262462:D161N	D	+	1	0	SLC27A6	128330210	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	8.984000	0.93482	2.536000	0.85505	0.561000	0.74099	GAT	.		0.517	SLC27A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250980.1	NM_014031	Missense_Mutation
PCDHB15	56121	hgsc.bcm.edu	37	5	140625665	140625665	+	Silent	SNP	T	T	C			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr5:140625665T>C	ENST00000231173.3	+	1	519	c.519T>C	c.(517-519)tcT>tcC	p.S173S		NM_018935.2	NP_061758.1	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15	173	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(8)|kidney(3)|large_intestine(14)|liver(1)|lung(18)|ovary(3)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	61			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ACAATATTTCTCCCAATTCTC	0.502																																					p.S173S		.											.	PCDHB15-156	0			c.T519C						.						44.0	47.0	46.0					5																	140625665		2203	4300	6503	SO:0001819	synonymous_variant	56121	exon1			TATTTCTCCCAAT	AF152494	CCDS4257.1	5q31	2011-06-07			ENSG00000113248	ENSG00000113248		"""Cadherins / Protocadherins : Clustered"""	8686	other	protocadherin		606341				10380929	Standard	NM_018935		Approved	PCDH-BETA15	uc003lje.3	Q9Y5E8	OTTHUMG00000129609	ENST00000231173.3:c.519T>C	5.37:g.140625665T>C		Somatic	61	0		WXS	Illumina HiSeq	Phase_I	27	2	NM_018935	0	0	36	36	0	Q8IUX5	Silent	SNP	ENST00000231173.3	37	CCDS4257.1																																																																																			.		0.502	PCDHB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251804.2	NM_018935	
PHYKPL	85007	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	177632984	177632984	+	IGR	SNP	G	G	A	rs201431713		TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr5:177632984G>A	ENST00000308158.5	-	0	2038				HNRNPAB_ENST00000515193.1_Silent_p.L117L|PHYKPL_ENST00000481811.1_5'Flank|HNRNPAB_ENST00000355836.5_Silent_p.L117L|HNRNPAB_ENST00000514633.1_Silent_p.L117L|HNRNPAB_ENST00000506259.1_Silent_p.L117L|HNRNPAB_ENST00000358344.3_Silent_p.L117L|HNRNPAB_ENST00000504898.1_Silent_p.L117L|HNRNPAB_ENST00000506339.1_Silent_p.L117L	NM_153373.2	NP_699204.1	Q8IUZ5	AT2L2_HUMAN	5-phosphohydroxy-L-lysine phospho-lyase							mitochondrion (GO:0005739)	lyase activity (GO:0016829)|pyridoxal phosphate binding (GO:0030170)|transaminase activity (GO:0008483)									L-Alanine(DB00160)	GGTTTATCCTGTTCAAAGATG	0.408																																					p.L117L		.											.	HNRNPAB-22	0			c.G351A						.						129.0	126.0	127.0					5																	177632984		2203	4300	6503	SO:0001628	intergenic_variant	3182	exon3			TATCCTGTTCAAA	BC037567	CCDS4434.1	5q35.3	2013-06-12	2013-06-12	2013-06-12	ENSG00000175309	ENSG00000175309	4.2.3.134		28249	protein-coding gene	gene with protein product	"""5-phosphonooxy-L-lysine phospho-lyase"""	614683	"""alanine-glyoxylate aminotransferase 2-like 2"""	AGXT2L2		22241472	Standard	NM_153373		Approved	MGC15875	uc003miz.3	Q8IUZ5	OTTHUMG00000130892		5.37:g.177632984G>A		Somatic	193	0		WXS	Illumina HiSeq	Phase_I	198	104	NM_031266	0	1	108	193	84	A8K7P6|B3KN36|D3DWP9|Q8WYS6|Q96HW8	Silent	SNP	ENST00000308158.5	37	CCDS4434.1																																																																																			G|0.999;C|0.001		0.408	PHYKPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253477.1	NM_032921	
MCUR1	63933	broad.mit.edu;ucsc.edu	37	6	13800602	13800602	+	Missense_Mutation	SNP	C	C	T	rs556879787		TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr6:13800602C>T	ENST00000379170.4	-	5	892	c.754G>A	c.(754-756)Gaa>Aaa	p.E252K		NM_001031713.3	NP_001026883.1	Q96AQ8	MCUR1_HUMAN	mitochondrial calcium uniporter regulator 1	252					calcium ion import (GO:0070509)|mitochondrial calcium ion transport (GO:0006851)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)	integral component of mitochondrial inner membrane (GO:0031305)											TGATGTAGTTCGAGTTTTATT	0.244													C|||	1	0.000199681	0.0	0.0	5008	,	,		16997	0.0		0.0	False		,,,				2504	0.001				p.E252K													.	CCDC90A-90	0			c.G754A						.						35.0	36.0	36.0					6																	13800602		2198	4287	6485	SO:0001583	missense	63933	exon5			GTAGTTCGAGTTT	BC016850	CCDS35495.1	6p23	2013-03-13	2013-03-13	2013-03-13	ENSG00000050393	ENSG00000050393			21097	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 79"", ""coiled-coil domain containing 90A"""	C6orf79, CCDC90A		23178883	Standard	NM_001031713		Approved	FLJ20958	uc003nbc.2	Q96AQ8	OTTHUMG00000014279	ENST00000379170.4:c.754G>A	6.37:g.13800602C>T	ENSP00000368468:p.Glu252Lys	Somatic	14	0		WXS	Illumina HiSeq	Phase_I	26	9	NM_001031713	0	0	0	0	0	Q96JS7|Q9H7F8	Missense_Mutation	SNP	ENST00000379170.4	37	CCDS35495.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.279411	0.80692	.	.	ENSG00000050393	ENST00000379170	T	0.45668	0.89	5.16	5.16	0.70880	.	0.050117	0.85682	D	0.000000	T	0.55955	0.1953	M	0.70595	2.14	0.80722	D	1	D	0.89917	1.0	D	0.68943	0.961	T	0.59064	-0.7524	10	0.62326	D	0.03	-18.5219	15.9312	0.79659	0.0:1.0:0.0:0.0	.	252	Q96AQ8	CC90A_HUMAN	K	252	ENSP00000368468:E252K	ENSP00000368468:E252K	E	-	1	0	CCDC90A	13908581	1.000000	0.71417	0.997000	0.53966	0.995000	0.86356	3.018000	0.49625	2.561000	0.86390	0.655000	0.94253	GAA	.		0.244	MCUR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039909.3	NM_022102	
MDFI	4188	broad.mit.edu;ucsc.edu	37	6	41614025	41614025	+	Intron	SNP	G	G	A	rs367874076		TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr6:41614025G>A	ENST00000373050.4	+	3	263							Q99750	MDFI_HUMAN	MyoD family inhibitor						activation of JUN kinase activity (GO:0007257)|cytoplasmic sequestering of transcription factor (GO:0042994)|dorsal/ventral axis specification (GO:0009950)|embryo development (GO:0009790)|embryonic skeletal system morphogenesis (GO:0048704)|negative regulation of DNA binding (GO:0043392)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of Wnt signaling pathway (GO:0030178)|trophoblast giant cell differentiation (GO:0060707)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|liver(2)|prostate(2)|skin(1)|urinary_tract(1)	8	Ovarian(28;0.0327)|Colorectal(47;0.121)		Colorectal(64;0.0123)|COAD - Colon adenocarcinoma(64;0.0264)|KIRC - Kidney renal clear cell carcinoma(1;0.138)			TGACCTCGACGTCCCCACAGA	0.627													G|||	1	0.000199681	0.0	0.0	5008	,	,		18391	0.001		0.0	False		,,,				2504	0.0				p.V80I													.	MDFI-90	0			c.G238A						.						36.0	34.0	35.0					6																	41614025		2203	4300	6503	SO:0001627	intron_variant	4188	exon3			CTCGACGTCCCCA	U78313	CCDS4857.1, CCDS75451.1	6p21	2008-08-29			ENSG00000112559	ENSG00000112559			6967	protein-coding gene	gene with protein product	"""inhibitor of MyoD family a"""	604971				9250874, 17289077	Standard	NM_005586		Approved	I-mfa	uc003oqq.4	Q99750	OTTHUMG00000014681	ENST00000373050.4:c.77-3332G>A	6.37:g.41614025G>A		Somatic	67	0		WXS	Illumina HiSeq	Phase_I	32	15	NM_005586	0	0	0	0	0		Missense_Mutation	SNP	ENST00000373050.4	37		.	.	.	.	.	.	.	.	.	.	G	11.01	1.512898	0.27123	.	.	ENSG00000112559	ENST00000432027;ENST00000419164;ENST00000373051;ENST00000441667;ENST00000230321;ENST00000543326;ENST00000446650	.	.	.	5.56	1.13	0.20643	.	0.618193	0.15698	N	0.249098	T	0.11153	0.0272	L	0.33485	1.01	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.29427	-1.0012	9	0.30078	T	0.28	-23.2738	6.7381	0.23421	0.2547:0.1343:0.611:0.0	.	80	Q99750	MDFI_HUMAN	I	80	.	ENSP00000230321:V80I	V	+	1	0	MDFI	41722003	0.117000	0.22190	0.791000	0.31998	0.989000	0.77384	1.430000	0.34914	0.280000	0.22209	0.655000	0.94253	GTC	.		0.627	MDFI-002	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000040519.2	NM_005586	
ICK	22858	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	52878690	52878690	+	Missense_Mutation	SNP	G	G	C			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr6:52878690G>C	ENST00000350082.5	-	9	1268	c.922C>G	c.(922-924)Ctg>Gtg	p.L308V	ICK_ENST00000356971.3_Missense_Mutation_p.L308V	NM_014920.3	NP_055735.1	Q9UPZ9	ICK_HUMAN	intestinal cell (MAK-like) kinase	308					intracellular signal transduction (GO:0035556)|multicellular organismal development (GO:0007275)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(3)|stomach(1)	31	Lung NSC(77;0.103)					GCCTTTTCCAGGATGCCTTTC	0.512																																					p.L308V		.											.	ICK-421	0			c.C922G						.						137.0	113.0	121.0					6																	52878690		2203	4300	6503	SO:0001583	missense	22858	exon10			TTTCCAGGATGCC	AB023153	CCDS4949.1	6p12.3-p11.2	2008-02-05			ENSG00000112144	ENSG00000112144			21219	protein-coding gene	gene with protein product		612325				12103360	Standard	NM_014920		Approved	MRK, LCK2, KIAA0936, MGC46090	uc003pbi.2	Q9UPZ9	OTTHUMG00000014870	ENST00000350082.5:c.922C>G	6.37:g.52878690G>C	ENSP00000263043:p.Leu308Val	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	48	23	NM_016513	0	0	6	10	4	A7MD41|O75985|Q5THL2|Q8IYH8|Q9BX17|Q9NYX3	Missense_Mutation	SNP	ENST00000350082.5	37	CCDS4949.1	.	.	.	.	.	.	.	.	.	.	G	3.787	-0.044509	0.07452	.	.	ENSG00000112144	ENST00000350082;ENST00000356971	T;T	0.72282	-0.64;-0.64	6.06	5.18	0.71444	Protein kinase-like domain (1);	1.200720	0.05905	N	0.630645	T	0.33498	0.0865	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.09377	0.004	T	0.26677	-1.0096	10	0.15499	T	0.54	5.3033	15.6578	0.77155	0.0661:0.0:0.9339:0.0	.	308	Q9UPZ9	ICK_HUMAN	V	308	ENSP00000263043:L308V;ENSP00000349458:L308V	ENSP00000263043:L308V	L	-	1	2	ICK	52986649	0.844000	0.29557	0.232000	0.24009	0.396000	0.30629	3.921000	0.56454	1.551000	0.49450	0.655000	0.94253	CTG	.		0.512	ICK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040952.1	NM_016513	
CCM2	83605	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	45112359	45112359	+	Silent	SNP	C	C	T			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr7:45112359C>T	ENST00000258781.6	+	7	929	c.780C>T	c.(778-780)acC>acT	p.T260T	CCM2_ENST00000475551.1_Silent_p.T254T|CCM2_ENST00000541586.1_Silent_p.T202T|CCM2_ENST00000381112.3_Silent_p.T281T|CCM2_ENST00000461377.1_3'UTR|CCM2_ENST00000474617.1_Silent_p.T163T|CCM2_ENST00000544363.1_Silent_p.T169T	NM_031443.3	NP_113631.1	Q9BSQ5	CCM2_HUMAN	cerebral cavernous malformation 2	260					blood vessel endothelial cell differentiation (GO:0060837)|cell-cell junction organization (GO:0045216)|endothelial cell development (GO:0001885)|endothelial tube morphogenesis (GO:0061154)|in utero embryonic development (GO:0001701)|inner ear development (GO:0048839)|integrin-mediated signaling pathway (GO:0007229)|multicellular organism growth (GO:0035264)|pericardium development (GO:0060039)|stress-activated MAPK cascade (GO:0051403)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)	cytoplasm (GO:0005737)|protein complex (GO:0043234)				NS(1)|endometrium(3)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19						TTAAGGAGACCTACGAGGTGG	0.507																																					p.T281T		.											.	CCM2-90	0			c.C843T						.						102.0	87.0	92.0					7																	45112359		2203	4300	6503	SO:0001819	synonymous_variant	83605	exon7			GGAGACCTACGAG	BC004903	CCDS5500.1, CCDS34630.1, CCDS55108.1, CCDS55109.1	7p13	2014-09-17	2004-02-13	2004-02-18	ENSG00000136280	ENSG00000136280			21708	protein-coding gene	gene with protein product	"""malcavernin"""	607929	"""chromosome 7 open reading frame 22"""	C7orf22		9811928	Standard	NM_001029835		Approved	MGC4607	uc003tms.3	Q9BSQ5	OTTHUMG00000129246	ENST00000258781.6:c.780C>T	7.37:g.45112359C>T		Somatic	93	0		WXS	Illumina HiSeq	Phase_I	174	41	NM_001029835	0	0	79	101	22	A4D2L4|B3KUV0|D3DVL4|E9PDJ3|F5H0E1|F5H551|Q71RE5|Q8TAT4	Silent	SNP	ENST00000258781.6	37	CCDS5500.1	.	.	.	.	.	.	.	.	.	.	C	7.888	0.731770	0.15507	.	.	ENSG00000136280	ENST00000480382	.	.	.	5.55	-2.66	0.06077	.	.	.	.	.	T	0.41328	0.1154	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.28235	-1.0050	4	.	.	.	-0.5904	2.9764	0.05939	0.3625:0.1562:0.3533:0.128	.	.	.	.	L	127	.	.	P	+	2	0	CCM2	45078884	0.004000	0.15560	0.000000	0.03702	0.904000	0.53231	-0.395000	0.07287	-0.809000	0.04381	-0.165000	0.13383	CCT	.		0.507	CCM2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251348.1	NM_031443	
ZKSCAN5	23660	broad.mit.edu	37	7	99123898	99123898	+	Missense_Mutation	SNP	G	G	T			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr7:99123898G>T	ENST00000394170.2	+	6	1486	c.1235G>T	c.(1234-1236)cGg>cTg	p.R412L	ZKSCAN5_ENST00000326775.5_Missense_Mutation_p.R412L|ZKSCAN5_ENST00000451158.1_Missense_Mutation_p.R412L	NM_014569.3	NP_055384.1	Q9Y2L8	ZKSC5_HUMAN	zinc finger with KRAB and SCAN domains 5	412					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|kidney(1)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	21	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)					AAGGCTTTCCGGGTGAGTTCC	0.582																																					p.R412L													.	ZKSCAN5-91	0			c.G1235T						.						144.0	141.0	142.0					7																	99123898		2203	4300	6503	SO:0001583	missense	23660	exon6			CTTTCCGGGTGAG	AF170025	CCDS5667.1	7q22	2013-01-09	2007-02-20	2007-02-20	ENSG00000196652	ENSG00000196652		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	12867	protein-coding gene	gene with protein product		611272	"""zinc finger protein homologous to Zfp95 in mouse"", ""zinc finger protein 95 homolog (mouse)"""	ZFP95		10585779	Standard	NM_014569		Approved	ZNF914, ZSCAN37	uc003uqv.3	Q9Y2L8	OTTHUMG00000156749	ENST00000394170.2:c.1235G>T	7.37:g.99123898G>T	ENSP00000377725:p.Arg412Leu	Somatic	244	0		WXS	Illumina HiSeq	Phase_I	299	7	NM_145102	0	0	16	16	0	A4D280|D6W5S9	Missense_Mutation	SNP	ENST00000394170.2	37	CCDS5667.1	.	.	.	.	.	.	.	.	.	.	G	16.35	3.099745	0.56183	.	.	ENSG00000196652	ENST00000537357;ENST00000326775;ENST00000451158;ENST00000394170	T;T;T	0.05925	3.37;3.37;3.37	4.63	4.63	0.57726	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.261790	0.27567	N	0.018793	T	0.06735	0.0172	N	0.16266	0.395	0.25005	N	0.991449	D;D	0.53619	0.961;0.961	P;P	0.51866	0.682;0.682	T	0.39603	-0.9606	10	0.15952	T	0.53	.	11.117	0.48266	0.0:0.1871:0.8129:0.0	.	412;412	Q8N718;Q9Y2L8	.;ZKSC5_HUMAN	L	412	ENSP00000322872:R412L;ENSP00000392104:R412L;ENSP00000377725:R412L	ENSP00000322872:R412L	R	+	2	0	ZKSCAN5	98961834	0.000000	0.05858	0.965000	0.40720	0.996000	0.88848	0.225000	0.17757	2.581000	0.87130	0.655000	0.94253	CGG	.		0.582	ZKSCAN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345597.1	NM_014569	
ZKSCAN1	7586	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	99621201	99621201	+	Silent	SNP	A	A	G			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr7:99621201A>G	ENST00000324306.6	+	2	306	c.72A>G	c.(70-72)gtA>gtG	p.V24V	ZKSCAN1_ENST00000426572.1_5'UTR|ZKSCAN1_ENST00000535170.1_Intron	NM_003439.1	NP_003430.1	P17029	ZKSC1_HUMAN	zinc finger with KRAB and SCAN domains 1	24					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(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(5)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	Lung NSC(181;0.0211)|all_lung(186;0.0323)|Esophageal squamous(72;0.0439)		STAD - Stomach adenocarcinoma(171;0.129)			ATGGTATCGTAATAGTGAAGG	0.542																																					p.V24V		.											.	ZKSCAN1-93	0			c.A72G						.						94.0	83.0	87.0					7																	99621201		2203	4300	6503	SO:0001819	synonymous_variant	7586	exon2			TATCGTAATAGTG	X52349	CCDS34698.1, CCDS69349.1, CCDS75640.1	7q22	2013-01-09	2004-11-16	2004-11-17	ENSG00000106261	ENSG00000106261		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13101	protein-coding gene	gene with protein product		601260	"""zinc finger protein 36 (KOX 18)"""	ZNF139, ZNF36			Standard	NM_001287055		Approved	KOX18, PHZ-37, ZSCAN33	uc003usk.1	P17029	OTTHUMG00000156534	ENST00000324306.6:c.72A>G	7.37:g.99621201A>G		Somatic	121	0		WXS	Illumina HiSeq	Phase_I	191	48	NM_003439	0	0	27	36	9	A4D294|P52745|Q2M1U1|Q8TBW5|Q8TEK7	Silent	SNP	ENST00000324306.6	37	CCDS34698.1																																																																																			.		0.542	ZKSCAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344550.2	NM_003439	
SLC4A2	6522	broad.mit.edu	37	7	150769158	150769158	+	Missense_Mutation	SNP	C	C	A			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr7:150769158C>A	ENST00000485713.1	+	16	3510	c.2470C>A	c.(2470-2472)Cag>Aag	p.Q824K	SLC4A2_ENST00000392826.2_Missense_Mutation_p.Q815K|RP11-148K1.12_ENST00000485974.1_RNA|SLC4A2_ENST00000461735.1_Missense_Mutation_p.Q810K|SLC4A2_ENST00000413384.2_Missense_Mutation_p.Q824K|SLC4A2_ENST00000310317.5_Missense_Mutation_p.Q742K	NM_001199692.1	NP_001186621.1	P04920	B3A2_HUMAN	solute carrier family 4 (anion exchanger), member 2	824	Membrane (anion exchange).			Q -> R (in Ref. 1; CAA44067 and 7; CAA27556). {ECO:0000305}.	anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|chloride transmembrane transporter activity (GO:0015108)|inorganic anion exchanger activity (GO:0005452)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(14)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	33			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CCGCTTCACCCAGGAGATCTT	0.617																																					p.Q824K													.	SLC4A2-90	0			c.C2470A						.						171.0	173.0	172.0					7																	150769158		2203	4300	6503	SO:0001583	missense	6522	exon16			TTCACCCAGGAGA		CCDS5917.1, CCDS56520.1, CCDS56521.1	7q36.1	2013-07-19	2013-07-19		ENSG00000164889	ENSG00000164889		"""Solute carriers"""	11028	protein-coding gene	gene with protein product	"""anion exchanger 2 type a"", ""anion exchanger 2 type b1"", ""anion exchanger 2 type b2"""	109280	"""erythrocyte membrane protein band 3-like 1"", ""solute carrier family 4, anion exchanger, member 2 (erythrocyte membrane protein band 3-like 1)"""	EPB3L1, AE2		8434259	Standard	NM_003040		Approved	HKB3, BND3L, NBND3	uc003wit.4	P04920	OTTHUMG00000158443	ENST00000485713.1:c.2470C>A	7.37:g.150769158C>A	ENSP00000419412:p.Gln824Lys	Somatic	266	0		WXS	Illumina HiSeq	Phase_I	376	12	NM_003040	0	0	266	266	0	B2R6T0|B4DIT0|D3DX05|F8W682|Q45EY5|Q969L3	Missense_Mutation	SNP	ENST00000485713.1	37	CCDS5917.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.442592	0.83993	.	.	ENSG00000164889	ENST00000485713;ENST00000413384;ENST00000310317;ENST00000392826;ENST00000461735	T;T;T;T;T	0.79845	-1.31;-1.31;-1.31;-1.31;-1.31	4.85	4.85	0.62838	Bicarbonate transporter, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.91593	0.7344	M	0.93106	3.38	0.80722	D	1	D;D;D	0.69078	0.982;0.997;0.997	D;D;D	0.74674	0.954;0.973;0.984	D	0.93451	0.6802	10	0.87932	D	0	.	15.534	0.75986	0.0:1.0:0.0:0.0	.	815;810;824	F8W682;P04920-2;P04920	.;.;B3A2_HUMAN	K	824;824;742;815;810	ENSP00000419412:Q824K;ENSP00000405600:Q824K;ENSP00000311402:Q742K;ENSP00000376571:Q815K;ENSP00000419164:Q810K	ENSP00000311402:Q742K	Q	+	1	0	SLC4A2	150400091	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.604000	0.82830	2.524000	0.85096	0.561000	0.74099	CAG	.		0.617	SLC4A2-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351039.1	NM_003040	
ASB10	136371	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	150878302	150878302	+	Silent	SNP	C	C	G			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr7:150878302C>G	ENST00000420175.2	-	3	852	c.828G>C	c.(826-828)ctG>ctC	p.L276L	ASB10_ENST00000422024.1_Silent_p.L321L|ASB10_ENST00000275838.1_Silent_p.L276L|ASB10_ENST00000377867.3_Silent_p.L261L|ASB10_ENST00000434669.1_Silent_p.L321L			Q8WXI3	ASB10_HUMAN	ankyrin repeat and SOCS box containing 10	276					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|endometrium(2)|lung(7)|skin(2)	12			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GCAAGCTGCACAGCTGCAGGC	0.682																																					p.L276L		.											.	ASB10-226	0			c.G828C						.						29.0	31.0	30.0					7																	150878302		2202	4297	6499	SO:0001819	synonymous_variant	136371	exon3			GCTGCACAGCTGC	AK055536	CCDS5921.2, CCDS47749.1, CCDS47750.1, CCDS47749.2, CCDS47750.2	7q35	2014-02-04	2011-01-25		ENSG00000146926	ENSG00000146926		"""Ankyrin repeat domain containing"""	17185	protein-coding gene	gene with protein product		615054	"""ankyrin repeat and SOCS box-containing 10"", ""glaucoma 1, open angle, F (adult-onset)"""	GLC1F		22156576	Standard	NM_080871		Approved		uc003wjm.1	Q8WXI3	OTTHUMG00000157013	ENST00000420175.2:c.828G>C	7.37:g.150878302C>G		Somatic	45	0		WXS	Illumina HiSeq	Phase_I	64	17	NM_001142459	0	0	0	0	0	A0AVH0|Q6ZUL6	Silent	SNP	ENST00000420175.2	37	CCDS47750.2																																																																																			.		0.682	ASB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347096.3	NM_080871	
WISP1	8840	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	8	134225321	134225321	+	Missense_Mutation	SNP	C	C	T			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr8:134225321C>T	ENST00000250160.6	+	2	390	c.284C>T	c.(283-285)cCc>cTc	p.P95L	WISP1_ENST00000519433.1_Intron|WISP1_ENST00000377863.2_Intron|WISP1_ENST00000220856.6_Missense_Mutation_p.P95L|WISP1_ENST00000517423.1_Missense_Mutation_p.P95L	NM_003882.3	NP_003873.1	O95388	WISP1_HUMAN	WNT1 inducible signaling pathway protein 1	95	IGFBP N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00653}.				cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|regulation of cell growth (GO:0001558)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	21	all_epithelial(106;5.39e-23)|Lung NSC(106;7.26e-07)|all_lung(105;2.77e-06)|Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0107)			ATCTGTGACCCCCACCGGGGC	0.612																																					p.P95L		.											.	WISP1-610	0			c.C284T						.						57.0	59.0	58.0					8																	134225321		2203	4300	6503	SO:0001583	missense	8840	exon2			GTGACCCCCACCG	AF100779	CCDS6371.1, CCDS6372.1, CCDS56555.1, CCDS56556.1	8q24.22	2007-05-14			ENSG00000104415	ENSG00000104415			12769	protein-coding gene	gene with protein product		603398				9843955	Standard	NM_003882		Approved	CCN4	uc003yub.3	O95388	OTTHUMG00000164440	ENST00000250160.6:c.284C>T	8.37:g.134225321C>T	ENSP00000250160:p.Pro95Leu	Somatic	141	0		WXS	Illumina HiSeq	Phase_I	82	41	NM_003882	0	0	0	0	0	A8KAG6|E7EMM5|Q5JBS6|Q5JBS7|Q5JBS8|Q9HCS3	Missense_Mutation	SNP	ENST00000250160.6	37	CCDS6371.1	.	.	.	.	.	.	.	.	.	.	C	15.65	2.895808	0.52121	.	.	ENSG00000104415	ENST00000250160;ENST00000517423;ENST00000220856	T;T;T	0.64618	-0.11;-0.11;-0.11	5.27	4.33	0.51752	Insulin-like growth factor-binding protein, IGFBP (3);	0.467062	0.24962	N	0.034202	T	0.57961	0.2089	M	0.63843	1.955	0.80722	D	1	P;P;B	0.45176	0.852;0.458;0.27	B;B;B	0.42462	0.388;0.137;0.089	T	0.62315	-0.6880	10	0.56958	D	0.05	-27.7812	7.9781	0.30166	0.0:0.7412:0.1659:0.0928	.	95;95;95	E7EMM5;O95388-2;O95388	.;.;WISP1_HUMAN	L	95	ENSP00000250160:P95L;ENSP00000427744:P95L;ENSP00000220856:P95L	ENSP00000220856:P95L	P	+	2	0	WISP1	134294503	0.959000	0.32827	1.000000	0.80357	0.965000	0.64279	1.247000	0.32815	2.460000	0.83146	0.542000	0.68232	CCC	.		0.612	WISP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378794.2	NM_003882	
COL27A1	85301	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	9	117047026	117047026	+	Missense_Mutation	SNP	C	C	G			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr9:117047026C>G	ENST00000356083.3	+	41	4347	c.3956C>G	c.(3955-3957)cCc>cGc	p.P1319R		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	1319	Collagen-like 12.|Pro-rich.|Triple-helical region.				extracellular matrix organization (GO:0030198)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|fibrillar collagen trimer (GO:0005583)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(30)|ovary(4)|prostate(6)|skin(3)|soft_tissue(1)|stomach(1)|urinary_tract(3)	80						ATTGTGGGACCCCTTGGACCT	0.557																																					p.P1319R		.											.	COL27A1-94	0			c.C3956G						.						142.0	119.0	127.0					9																	117047026		2203	4300	6503	SO:0001583	missense	85301	exon41			TGGGACCCCTTGG	AB058773	CCDS6802.1	9q33.1	2013-01-16			ENSG00000196739	ENSG00000196739		"""Collagens"""	22986	protein-coding gene	gene with protein product		608461				12766169	Standard	NM_032888		Approved	KIAA1870, MGC11337, FLJ11895	uc011lxl.2	Q8IZC6	OTTHUMG00000020537	ENST00000356083.3:c.3956C>G	9.37:g.117047026C>G	ENSP00000348385:p.Pro1319Arg	Somatic	138	0		WXS	Illumina HiSeq	Phase_I	98	35	NM_032888	0	1	13	36	22	Q66K43|Q96JF7	Missense_Mutation	SNP	ENST00000356083.3	37	CCDS6802.1	.	.	.	.	.	.	.	.	.	.	c	12.60	1.986411	0.35036	.	.	ENSG00000196739	ENST00000356083;ENST00000357257	D	0.93366	-3.21	4.71	3.82	0.43975	.	.	.	.	.	D	0.93779	0.8011	L	0.55017	1.72	0.38600	D	0.950644	P	0.52577	0.954	P	0.60012	0.867	D	0.91884	0.5518	9	0.22706	T	0.39	.	10.6899	0.45864	0.0:0.9065:0.0:0.0935	.	1319	Q8IZC6	CORA1_HUMAN	R	1319	ENSP00000348385:P1319R	ENSP00000348385:P1319R	P	+	2	0	COL27A1	116086847	1.000000	0.71417	1.000000	0.80357	0.672000	0.39443	5.396000	0.66297	1.205000	0.43262	-0.265000	0.10407	CCC	.		0.557	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888	
TMEM203	94107	broad.mit.edu;ucsc.edu	37	9	140099503	140099503	+	Missense_Mutation	SNP	A	A	T			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr9:140099503A>T	ENST00000343666.5	-	1	587	c.364T>A	c.(364-366)Ttc>Atc	p.F122I	NDOR1_ENST00000371521.4_5'Flank|NDOR1_ENST00000427047.2_5'Flank|TMEM203_ENST00000537254.1_Missense_Mutation_p.F122I|NDOR1_ENST00000458322.2_5'Flank|TPRN_ENST00000541945.1_5'Flank|NDOR1_ENST00000344894.5_5'Flank	NM_053045.1	NP_444273.1	Q969S6	TM203_HUMAN	transmembrane protein 203	122						integral component of membrane (GO:0016021)				central_nervous_system(1)|kidney(1)	2	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.00057)		AGGAGAATGAAGAGCGGGGAC	0.587																																					p.F122I													.	TMEM203-22	0			c.T364A						.						42.0	41.0	41.0					9																	140099503		2200	4294	6494	SO:0001583	missense	94107	exon1			GAATGAAGAGCGG	BC009283	CCDS35185.1	9q34.3	2007-12-18			ENSG00000187713	ENSG00000187713			28217	protein-coding gene	gene with protein product	"""HBeAg-binding protein 1"""					12477932	Standard	NM_053045		Approved	MGC14327, HBEBP1	uc004clv.3	Q969S6	OTTHUMG00000020985	ENST00000343666.5:c.364T>A	9.37:g.140099503A>T	ENSP00000375053:p.Phe122Ile	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	44	24	NM_053045	0	0	33	76	43	Q6NW08	Missense_Mutation	SNP	ENST00000343666.5	37	CCDS35185.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.394143	0.83011	.	.	ENSG00000187713	ENST00000343666;ENST00000537254	.	.	.	4.31	4.31	0.51392	.	0.158722	0.42053	U	0.000772	T	0.68860	0.3047	L	0.54323	1.7	0.80722	D	1	D	0.76494	0.999	D	0.68765	0.96	T	0.71334	-0.4624	9	0.59425	D	0.04	.	12.4385	0.55612	1.0:0.0:0.0:0.0	.	122	Q969S6	TM203_HUMAN	I	122	.	ENSP00000375053:F122I	F	-	1	0	TMEM203	139219324	1.000000	0.71417	0.992000	0.48379	0.369000	0.29798	8.717000	0.91425	1.799000	0.52666	0.533000	0.62120	TTC	.		0.587	TMEM203-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055325.2	NM_053045	
ARID4A	5926	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	14	58827698	58827698	+	Frame_Shift_Del	DEL	C	C	-			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr14:58827698delC	ENST00000355431.3	+	19	2391	c.2018delC	c.(2017-2019)tcafs	p.S673fs	ARID4A_ENST00000395168.3_Frame_Shift_Del_p.S673fs|ARID4A_ENST00000431317.2_Frame_Shift_Del_p.S673fs|ARID4A_ENST00000348476.3_Frame_Shift_Del_p.S673fs	NM_002892.3	NP_002883.3	P29374	ARI4A_HUMAN	AT rich interactive domain 4A (RBP1-like)	673					erythrocyte development (GO:0048821)|histone H3-K4 trimethylation (GO:0080182)|histone H3-K9 trimethylation (GO:0036124)|histone H4-K20 trimethylation (GO:0034773)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of gene expression by genetic imprinting (GO:0006349)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|central_nervous_system(1)|cervix(4)|endometrium(8)|kidney(2)|large_intestine(14)|lung(19)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	60						CCTTTAAAATCAACCCTCTCA	0.433																																					p.S673X		.											.	ARID4A-231	0			c.2018delC						.						169.0	155.0	159.0					14																	58827698		2203	4300	6503	SO:0001589	frameshift_variant	5926	exon19			.	S57153	CCDS9732.1, CCDS9733.1, CCDS45114.1	14q22.3	2013-02-07	2004-01-28	2004-01-28	ENSG00000032219	ENSG00000032219		"""-"""	9885	protein-coding gene	gene with protein product		180201	"""retinoblastoma-binding protein 1"""	RBBP1		1857421, 8455946	Standard	NM_023000		Approved	RBP1, RBP-1	uc001xdp.3	P29374	OTTHUMG00000140320	ENST00000355431.3:c.2018delC	14.37:g.58827698delC	ENSP00000347602:p.Ser673fs	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	132	59	NM_002892	0	0	0	0	0	Q15991|Q15992|Q15993	Nonsense_Mutation	DEL	ENST00000355431.3	37	CCDS9732.1																																																																																			.		0.433	ARID4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276927.2	NM_023001	
SLC6A4	6532	hgsc.bcm.edu	37	17	28525539	28525565	+	Splice_Site	DEL	TAATAATACGCTATTGGGAAGAAAATA	TAATAATACGCTATTGGGAAGAAAATA	-	rs202181933|rs201520429|rs200015551		TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	TAATAATACGCTATTGGGAAGAAAATA	TAATAATACGCTATTGGGAAGAAAATA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr17:28525539_28525565delTAATAATACGCTATTGGGAAGAAAATA	ENST00000401766.2	-	14	2331_2340	c.1819_1828delTATTTTCTTCCCAATAGCGTATTATTA	c.(1819-1830)tattttcttccc>cc	p.YFLP607del	SLC6A4_ENST00000261707.3_Splice_Site_p.YFLP607del			P31645	SC6A4_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 4	607					brain morphogenesis (GO:0048854)|cellular response to cGMP (GO:0071321)|cellular response to retinoic acid (GO:0071300)|circadian rhythm (GO:0007623)|memory (GO:0007613)|monoamine transport (GO:0015844)|negative regulation of cerebellar granule cell precursor proliferation (GO:0021941)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of organ growth (GO:0046621)|negative regulation of synaptic transmission, dopaminergic (GO:0032227)|positive regulation of cell cycle (GO:0045787)|positive regulation of gene expression (GO:0010628)|protein homooligomerization (GO:0051260)|protein oligomerization (GO:0051259)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|response to nutrient (GO:0007584)|response to toxic substance (GO:0009636)|serotonin transport (GO:0006837)|serotonin uptake (GO:0051610)|social behavior (GO:0035176)|sperm ejaculation (GO:0042713)|thalamus development (GO:0021794)|vasoconstriction (GO:0042310)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|cocaine binding (GO:0019811)|monoamine transmembrane transporter activity (GO:0008504)|Rab GTPase binding (GO:0017137)|serotonin transmembrane transporter activity (GO:0015222)|serotonin:sodium symporter activity (GO:0005335)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(4)	25					Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Atomoxetine(DB00289)|Chlorphenamine(DB01114)|Citalopram(DB00215)|Clomipramine(DB01242)|Cocaine(DB00907)|Desipramine(DB01151)|Desvenlafaxine(DB06700)|Dexfenfluramine(DB01191)|Dexmethylphenidate(DB06701)|Dextromethorphan(DB00514)|Dopamine(DB00988)|Doxepin(DB01142)|Duloxetine(DB00476)|Ephedra(DB01363)|Escitalopram(DB01175)|Fluoxetine(DB00472)|Fluvoxamine(DB00176)|Imipramine(DB00458)|Levomilnacipran(DB08918)|Loxapine(DB00408)|Mazindol(DB00579)|Methamphetamine(DB01577)|Methylphenidate(DB00422)|Mianserin(DB06148)|Milnacipran(DB04896)|Minaprine(DB00805)|Mirtazapine(DB00370)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Paroxetine(DB00715)|Pethidine(DB00454)|Phentermine(DB00191)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Sertraline(DB01104)|Sibutramine(DB01105)|Tapentadol(DB06204)|Tramadol(DB00193)|Trazodone(DB00656)|Trimipramine(DB00726)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vilazodone(DB06684)	GTAATACTTTTAATAATACGCTATTGGGAAGAAAATACAATGTTATA	0.335																																					p.607_610del		.											.	SLC6A4-94	0			c.1819_1828del						.																																			SO:0001630	splice_region_variant	6532	exon15			.	L05568	CCDS11256.1	17q11.2	2014-01-30	2013-07-19		ENSG00000108576	ENSG00000108576		"""Solute carriers"""	11050	protein-coding gene	gene with protein product	"""serotonin transporter 1"""	182138	"""solute carrier family 6 (neurotransmitter transporter, serotonin), member 4"", ""5-hydroxytryptamine (serotonin) transporter"", ""obsessive-compulsive disorder 1"""	HTT, OCD1		7681602, 19806148	Standard	NM_001045		Approved	5-HTT, SERT1	uc002hey.5	P31645	OTTHUMG00000132751	ENST00000401766.2:c.1819-1TATTTTCTTCCCAATAGCGTATTATTA>-	17.37:g.28525539_28525565delTAATAATACGCTATTGGGAAGAAAATA		Somatic	81	0		WXS	Illumina HiSeq	Phase_I	89	18	NM_001045	0	0	0	0	0	Q5EE02	Frame_Shift_Del	DEL	ENST00000401766.2	37	CCDS11256.1																																																																																			.		0.335	SLC6A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256115.3	NM_001045	In_Frame_Del
KIAA1211L	343990	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	2	99413866	99413867	+	Frame_Shift_Del	DEL	GT	GT	-	rs201196594		TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	GT	GT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr2:99413866_99413867delGT	ENST00000397899.2	-	8	2881_2882	c.2550_2551delAC	c.(2548-2553)gcacggfs	p.R851fs		NM_207362.2	NP_997245.2	Q6NV74	K121L_HUMAN	KIAA1211-like	851																	TTCAGGGTCCGTGCCCCAGGCT	0.619																																					p.850_851del		.											.	.	0			c.2550_2551del						.																																			SO:0001589	frameshift_variant	343990	exon8			.	BC068277	CCDS42720.1	2q11.2	2012-08-03	2012-08-03	2012-08-03	ENSG00000196872	ENSG00000196872			33454	protein-coding gene	gene with protein product			"""chromosome 2 open reading frame 55"""	C2orf55			Standard	NM_207362		Approved	MGC42367	uc002szf.1	Q6NV74	OTTHUMG00000153171	ENST00000397899.2:c.2550_2551delAC	2.37:g.99413866_99413867delGT	ENSP00000380996:p.Arg851fs	Somatic	181	0		WXS	Illumina HiSeq	Phase_I	102	42	NM_207362	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000397899.2	37	CCDS42720.1																																																																																			.		0.619	KIAA1211L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329933.1	NM_207362	
HIP1	3092	broad.mit.edu	37	7	75168684	75168684	+	Frame_Shift_Del	DEL	T	T	-			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr7:75168684delT	ENST00000336926.6	-	30	3046	c.3020delA	c.(3019-3021)aagfs	p.K1007fs	HIP1_ENST00000434438.2_Frame_Shift_Del_p.K956fs	NM_005338.5	NP_005329.3	O00291	HIP1_HUMAN	huntingtin interacting protein 1	1007	I/LWEQ. {ECO:0000255|PROSITE- ProRule:PRU00292}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell differentiation (GO:0030154)|clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|positive regulation of receptor-mediated endocytosis (GO:0048260)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	clathrin binding (GO:0030276)|phosphatidylinositol binding (GO:0035091)|structural constituent of cytoskeleton (GO:0005200)			breast(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						CTCGTAGTGCTTTTTCCGAAG	0.507			T	PDGFRB	CMML																																p.K1007fs				Dom	yes		7	7q11.23	3092	huntingtin interacting protein 1		L	.	HIP1-1085	0			c.3020delA						.						303.0	294.0	297.0					7																	75168684		2203	4300	6503	SO:0001589	frameshift_variant	3092	exon30			TAGTGCTTTTTCC	AF052288	CCDS34669.1, CCDS59060.1	7q11.23	2008-07-18			ENSG00000127946	ENSG00000127946			4913	protein-coding gene	gene with protein product		601767				9140394, 9147654	Standard	NM_005338		Approved	ILWEQ	uc003uds.2	O00291	OTTHUMG00000156050	ENST00000336926.6:c.3020delA	7.37:g.75168684delT	ENSP00000336747:p.Lys1007fs	Somatic	554	0		WXS	Illumina HiSeq	Phase_I	805	8	NM_005338	0	0	0	0	0	B4E3I7|E7ES17|O00328|Q2TB58|Q8TDL4	Frame_Shift_Del	DEL	ENST00000336926.6	37	CCDS34669.1																																																																																			.		0.507	HIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342863.2	NM_005338	
PDK4	5166	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	7	95221864	95221872	+	In_Frame_Del	DEL	CCAATGTGG	CCAATGTGG	-	rs138077797		TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	CCAATGTGG	CCAATGTGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr7:95221864_95221872delCCAATGTGG	ENST00000005178.5	-	5	764_772	c.567_575delCCACATTGG	c.(565-576)agccacattgga>aga	p.189_192SHIG>R		NM_002612.3	NP_002603.1	Q16654	PDK4_HUMAN	pyruvate dehydrogenase kinase, isozyme 4	189	Histidine kinase. {ECO:0000255|PROSITE- ProRule:PRU00107}.				cellular metabolic process (GO:0044237)|cellular response to fatty acid (GO:0071398)|cellular response to starvation (GO:0009267)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|insulin receptor signaling pathway (GO:0008286)|negative regulation of anoikis (GO:2000811)|protein phosphorylation (GO:0006468)|pyruvate metabolic process (GO:0006090)|reactive oxygen species metabolic process (GO:0072593)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of bone resorption (GO:0045124)|regulation of cellular ketone metabolic process (GO:0010565)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of fatty acid oxidation (GO:0046320)|regulation of glucose metabolic process (GO:0010906)|regulation of pH (GO:0006885)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|pyruvate dehydrogenase (acetyl-transferring) kinase activity (GO:0004740)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|liver(1)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	15	all_cancers(62;1.06e-10)|all_epithelial(64;1.04e-09)|Lung NSC(181;0.128)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0151)			ATCAATGCTTCCAATGTGGCTTGGGTTTC	0.321																																					p.189_192del		.											.	PDK4-358	0			c.567_575del						.																																			SO:0001651	inframe_deletion	5166	exon5			.	U54617	CCDS5643.1	7q21.3-q22.1	2008-07-18	2005-11-16		ENSG00000004799	ENSG00000004799			8812	protein-coding gene	gene with protein product		602527	"""pyruvate dehydrogenase kinase, isoenzyme 4"""			7499431	Standard	NM_002612		Approved		uc003uoa.3	Q16654	OTTHUMG00000153977	ENST00000005178.5:c.567_575delCCACATTGG	7.37:g.95221864_95221872delCCAATGTGG	ENSP00000005178:p.Ser189_Gly192delinsArg	Somatic	170	0		WXS	Illumina HiSeq	Phase_I	204	78	NM_002612	0	0	0	0	0		In_Frame_Del	DEL	ENST00000005178.5	37	CCDS5643.1																																																																																			.		0.321	PDK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333298.1	NM_002612	
KDM6A	7403	hgsc.bcm.edu;broad.mit.edu	37	X	44920581	44920581	+	Frame_Shift_Del	DEL	A	A	-			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chrX:44920581delA	ENST00000377967.4	+	14	1383	c.1342delA	c.(1342-1344)aatfs	p.N448fs	KDM6A_ENST00000536777.1_Frame_Shift_Del_p.N403fs|KDM6A_ENST00000382899.4_Frame_Shift_Del_p.N455fs|KDM6A_ENST00000543216.1_Frame_Shift_Del_p.N403fs	NM_021140.2	NP_066963.2	O15550	KDM6A_HUMAN	lysine (K)-specific demethylase 6A	448	Interaction with SUPT6H. {ECO:0000250}.				canonical Wnt signaling pathway (GO:0060070)|heart morphogenesis (GO:0003007)|histone H3-K4 methylation (GO:0051568)|in utero embryonic development (GO:0001701)|mesodermal cell differentiation (GO:0048333)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|notochord morphogenesis (GO:0048570)|regulation of gene expression (GO:0010468)|respiratory system process (GO:0003016)|somite rostral/caudal axis specification (GO:0032525)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)	p.0?(6)|p.0(2)		NS(1)|breast(7)|central_nervous_system(27)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(24)|kidney(24)|large_intestine(9)|liver(1)|lung(21)|oesophagus(11)|pancreas(2)|prostate(5)|skin(1)|soft_tissue(1)|urinary_tract(29)	170						TACTTCTGACAATTGGAGTGG	0.348			"""D, N, F, S"""		"""renal, oesophageal SCC, MM"""																																p.N448fs	Colon(129;1273 1667 15230 27352 52914)	.		Rec	yes		X	Xp11.2	7403	"""lysine (K)-specific demethylase 6A, UTX"""		"""E, L"""	.	KDM6A-2748	8	Whole gene deletion(6)|No detectable mRNA/protein(2)	haematopoietic_and_lymphoid_tissue(2)|oesophagus(2)|breast(2)|pancreas(2)	c.1342delA						.						58.0	47.0	51.0					X																	44920581		2203	4300	6503	SO:0001589	frameshift_variant	7403	exon14			.	AF000992	CCDS14265.1	Xp11.2	2014-09-17	2009-04-17	2009-04-17	ENSG00000147050	ENSG00000147050		"""Chromatin-modifying enzymes / K-demethylases"", ""Tetratricopeptide (TTC) repeat domain containing"""	12637	protein-coding gene	gene with protein product		300128	"""ubiquitously transcribed tetratricopeptide repeat, X chromosome"""	UTX		9499428, 9381176	Standard	XM_005272655		Approved		uc004dge.4	O15550	OTTHUMG00000021402	ENST00000377967.4:c.1342delA	X.37:g.44920581delA	ENSP00000367203:p.Asn448fs	Somatic	11	0		WXS	Illumina HiSeq	Phase_I	15	14	NM_021140	0	0	0	0	0	Q52LL9|Q5JVQ7	Frame_Shift_Del	DEL	ENST00000377967.4	37	CCDS14265.1																																																																																			.		0.348	KDM6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056324.1	NM_021140	
EMD	2010	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	X	153609241	153609241	+	Splice_Site	DEL	G	G	-			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chrX:153609241delG	ENST00000369842.4	+	6	737		c.e6-1		EMD_ENST00000369835.3_Splice_Site|EMD_ENST00000492448.1_Splice_Site	NM_000117.2	NP_000108.1	P50402	EMD_HUMAN	emerin						cellular response to growth factor stimulus (GO:0071363)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic nuclear envelope reassembly (GO:0007084)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of fibroblast proliferation (GO:0048147)|positive regulation of protein export from nucleus (GO:0046827)|regulation of canonical Wnt signaling pathway (GO:0060828)|skeletal muscle cell differentiation (GO:0035914)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|microtubule (GO:0005874)|nuclear envelope (GO:0005635)|nuclear inner membrane (GO:0005637)|nuclear membrane (GO:0031965)|nuclear outer membrane (GO:0005640)	actin binding (GO:0003779)|beta-tubulin binding (GO:0048487)			lung(5)	5	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					TTTTGCCTCAGGGAACGCCCC	0.622																																					.		.											.	EMD-130	0			c.450-1G>-						.						77.0	67.0	71.0					X																	153609241		2203	4300	6503	SO:0001630	splice_region_variant	2010	exon6			.	X82434	CCDS14745.1	Xq27.3-q28	2014-09-17	2008-07-29		ENSG00000102119	ENSG00000102119			3331	protein-coding gene	gene with protein product	"""LEM domain containing 5"""	300384	"""Emery-Dreifuss muscular dystrophy"""				Standard	NM_000117		Approved	STA, LEMD5	uc004fkl.3	P50402	OTTHUMG00000033186	ENST00000369842.4:c.450-1G>-	X.37:g.153609241delG		Somatic	70	0		WXS	Illumina HiSeq	Phase_I	45	40	NM_000117	0	0	0	0	0	Q6FI02	Splice_Site	DEL	ENST00000369842.4	37	CCDS14745.1																																																																																			.		0.622	EMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080921.1		Intron
SRSF7	6432	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	38978383	38978384	+	Missense_Mutation	DNP	GC	GC	AA			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr2:38978383_38978384GC>AA	ENST00000313117.6	-	1	252_253	c.15_16GC>TT	c.(13-18)ggGCgg>ggTTgg	p.R6W	SRSF7_ENST00000409276.1_Missense_Mutation_p.R6W|SRSF7_ENST00000446327.2_Missense_Mutation_p.R6W|GEMIN6_ENST00000409011.1_5'Flank	NM_001031684.2|NM_001195446.1	NP_001026854.1|NP_001182375.1	Q16629	SRSF7_HUMAN	serine/arginine-rich splicing factor 7	6					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12						CCTCCGTACCGCCCGTAACGCG	0.624																																					p.R6W		.											.	SRSF7	0			c.G15T						.																																			SO:0001583	missense	6432	exon1			GTACCGCCCGTAA	L41887	CCDS33183.1, CCDS56115.1	2p22.1	2013-02-12	2010-06-22	2010-06-22	ENSG00000115875	ENSG00000115875		"""Zinc fingers, CCHC domain containing"", ""Serine/arginine-rich splicing factors"", ""RNA binding motif (RRM) containing"""	10789	protein-coding gene	gene with protein product	"""SR splicing factor 7"""	600572	"""splicing factor, arginine/serine-rich 7 (35kD)"", ""splicing factor, arginine/serine-rich 7, 35kDa"""	SFRS7		8013463, 20516191	Standard	NM_001031684		Approved	9G8, ZCRB2, HSSG1, AAG3, RBM37, ZCCHC20	uc002rqz.3	Q16629	OTTHUMG00000102076	ENST00000313117.6:c.15_16delinsAA	2.37:g.38978383_38978384delinsAA	ENSP00000325905:p.Arg6Trp	Somatic	128.0	0.0		WXS	Illumina HiSeq	Phase_I	87.0	32.0		0	0	0	0	0	B4DLU6|G5E9M3|Q564D3	Missense_Mutation	DNP	ENST00000313117.6	37	CCDS33183.1																																																																																			.		0.624	SRSF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219889.2	NM_001031684	
